sblock177188- Best orthologs

sblock177188	chrX:4976268-4976379 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 4976272-4976295
   star strand at position 4976354-4976373
   mutations
   read mismatches

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chrX:4976253-4976394 -		1	G-------GCGCGCAC-------------------TGGTG--TGTGT----G--TGTGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGCAGCAAAA-----A-----------CGTGT--ATAATTTACCTGAT----T-TTTC----TA-CATCTCACTTACAGTTAGTAATC--AAATTGCA---CAA
droSim1	chrX_random:1727169-1727312 -	LASTZ	1	G-------GCGCGCAC-------------------TGGTG--TGTGT--GTG--TGTGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGCAGCAAAA-----A-----------CGTGT--ATAATTTACCTGAC----T-TTTC----TA-CATCTCACTTACAGTTAGTAATC--AAATTGCA---CAA
droSec1	super_4:1770865-1771007 +	LASTZ	4	G-------GCGCGCAC-------------------TGGTG--TGTGT--GTG--TGTGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGCAGCA-AA-----A-----------CGTGT--ATAATTTACCTGAC----T-TTTT----TA-CATCTCACTTACAGTTAATAATC--AAATTGCA---CAA
droYak2	chrX:3486274-3486412 +	LASTZ	1	G-------GCGCGCTT-------------------GTGTG--TGT------G--TGTGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGC---A-AAACTAAG-----------CGCGT--ATAATTTACTTGAT----T-TTTC----TA-CAT--CACTTACAGTTAGTAATC--AAATTGCA---CAA
droEre2	scaffold_4690:2335787-2335926 -	LASTZ	4	G-------GCGCGCGC-------------------TTGTG--TGTGT----G--TGCGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGCAGCAAAA-----A-----------CGTGT--ATAATTTACCTGAT----T-TTTC----TA-CAT--CCCTTACAGTTAGTAATC--AAATTGCA---CAA
droEug1	scf7180000409548:787929-788067 -	LASTZ	5	G-------GCGCGCGC-------------------GTACT--TGTGT--GTG--TGCGTGTGTGGGT---------------------------------GGAAAATACGATTTCGTAAAACGCATTTCATT----------------------------------G--------------------------------TT--AACA-------AA-----A-----------CGTGTG-TTAATTTACCTAAA---CT-TTTC----TT-TAC--CTTTTACAGTTAGTAATCAAAAATTGCA---CAA
droBia1	scf7180000301760:317175-317313 -	LASTZ	5	G-------GCGCGCGC-------------------CTGTG--TGTGT--GTG--TGTGTGGGTGGGT---------------------------------GGAAAATCCGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TA--AGCAACAACAAAA-----A-----------CGTGT--GTAATTTACCTGCT----TCTTTC----CA-TAT--CGTTTACAGTTAGTA------AATTGCA---CAA
droTak1	scf7180000415352:1030839-1030982 +	LASTZ	4	G-------GCGCGCGC-------------------CCATG--TGTGC--GTG------TGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAACAACAAGA-----A-----------CGTGT--GTAATTTACCTGAT----T-TTTTTTTCTC-AATTTCCCTTACAGTTAGTAATC--AAATTGCA---CAA
droEle1	scf7180000491272:492430-492559 +	LASTZ	4	G-------GCGCGCGT-------------------ATGTG--TGT--------------GTGTGGGT---------------------------------GGAAAATCCGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AATAAC---A-AA-----A-----------CGTGGGTGTAATTTACATGAT----T-TTTC----TA-CAT--TATTCACAGTTAGTAAGC--AAACTGCA---CAA
droRho1	scf7180000776532:19535-19662 +	LASTZ	5	G-------GCGCGTGT-------------------TTGTG--T----------------GTGTGGAT---------------------------------GAAAAATTCGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAAC---A-AA-----A-----------CGTGTATGTAATTTACCTGAT----T-TTTC----TA-CAT--TATTTACAGTTAGTAAGC--AAGCTGCA---CAA
droFic1	scf7180000454045:81404-81534 -	LASTZ	4	G-------GCGCGCGC-------------------GTATG--TGT--------------GTGTGGGT---------------------------------GGAAAATCCGATTTCGTAGAACGCATTTAATT----------------------------------G--------------------------------TT--AACAACAACA-AA-----T-----------CGTGT--CTAATTTACCTGAC----T-TTTC----TA-TAT--CATTTTCAGTTAGTAATT--AAATTGCA---CAA
droKik1	scf7180000302469:619020-619157 -	LASTZ	4	ACTAGTTCGTGTGAGT-------------------GTATG--TGT--------------GTGTGAGA------TCTCCTGAATAGGTTTCTGTGTGTG-TG-------TGATTTCGTAAAACGCATTTAAAT---------T-----------------------TG--------------------------------TT--AATAAA---AAAA-----A-----------CGTGT--GTA-TTTAT-----------------------------CTTACAGTTAG--AAC--CAATTGCA---CAA
droAna3	scaffold_13417:338832-338967 -	LASTZ	3	G-------AGACGTAT-------------------GTGTG--TGTGT--GTGAGTGTGAGTGTGGGA------G------------------------GAGGAAAAGCGGATTTCGTAAAACGCATTTACTA-----ATT-T-----------------------TCTTAAAAATAA-------------------------CAAAAACAACA-AA-----A-----------CGTGT------------------------------------TTCCATTACAGTTAG--AAC--CAATTGCA---CAA
droBip1	scf7180000396573:132829-133007 +	LASTZ	5	C-------TCGCGCGCGTGTTAGTGCTAAGTGTGTGTGTGTGTGTGT--GTG--TGTGTGTGTGTGT--GGAAA------------------------ACGGAAAAATGGATTTCGTAAAACGCATTTACTA-----ATTTT-----------------------TCTTAAAAATAATAATAA-------AATCAACAACTACAACAACAACAACA-----T-----------TGTGT------------------------------------TTCCATTACAGTTAG--AAC--CAATTGCA---CAA
dp4	chrXL_group1e:6745504-6745680 -	LASTZ	3	C-------GCGTGCGT-------------------ATGTG--TGTGT--GTA--TGTGCATGCGAGG--GGGGATATGCATATTTGTTA------ATG-TGCTAGGAACGATTCTGTAAAACGAATTTATTA----------------------------------T-----------ATTAT-------ATCTA----TT--AATTAC---C-AA-----TTTATTAAATAATGTGT-----------TTGTG----T-TTTCTTT-TGTATCCAAAATTGCAGT-AG--AAT--CAATTGCA---CAA
droPer1	super_20:728747-728881 +	LASTZ	3	GT------GTGCGTGT---------------------GT----GTGT--GCG--TGTGTGTGTAAAA---------------------------------AGAAAAAAGGATTTCGTAAAAACAAATCAAAC----------------------------------A-------T---AACATTATGTTGG--------CC--C---ACGGCA-AA-----GCG---AA----CT--A--ATAAATTTCCAAGC----A-AATC----CA-CA---------------AAAATC--A-AATG-----CAA
droWil1	scaffold_180777:148015-148154 +	LASTZ	0	T-------GCGTGTGT-------------------GTGTG--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---TGTGTGTGTGTAGCACTTCCGTTC-----CAT-T-----------------------TACAACAAACAC-------------------------AAAGAAGAACA-A----------------------T--ATCAGCTCCCTTTT----T-TTTT----TT-TGT--TATTTTCATTTTTT--------TCTATG---CAG
droVir3	scaffold_12963:15848081-15848201 -	LASTZ	0	G--------TGTGCAT-------------------GTGTG--TGCGT----G--TGTGTGTGTGTGTGCAAAAATATGCAAATCGGTTT-------TG-CACTGCTGACG------------------ACTT----------------------------------C--------------------------------TT--CACAGCAGCTGAA-----A-----------TGTGC--TTAAAATTC--GCAAAATT-GT------------------------------------AGTTCA---TTT
droMoj3	scaffold_6496:18207583-18207733 -	LASTZ	0	G-------ACACAGTC-------------------TGTCG--TGTGTGTGTG--TGTGTGTCTGTGT---------------------------------GTA-TTTCCTTTCTTGTTAAGCTGCTTTGGCTTTTCAATT-TTATTCCTGTATTTGCGTGTCCAATG--------------------------------TT--CAAATTAGCA-AA-----A-----------TGTAC--A--A-------------------------------------GCAGTAAATATCT--ACATTACATGGCCA
droGri2	scaffold_15252:15271605-15271725 -	LASTZ	0	T-------GTGTATGT-------------------GTGTG--TGTGT--CTA--TGTTATCGTTTGC--TG-------------------------------------TGA-CTTGCAAATAAAATTTGACT----------------------------------A--------------------------------CT--GCTAAC------------A-----------GT------TATCTCTCTCTCT----C-TCTC----TC-TGTCGCACACACATTTA-----C--ACAGTGCA---AGT

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	G-------GCGCGCACTGGTG---------TG------------TGT--GTGTGA--GTG---------------------T------GGG---TGGAA----------------------AATCGGATTTCGTAAAACGCATTTAATT------G-----------------------TT----------AACAGCAGCAAAA-----ACG-----------TGT--ATAATTTACCTG-ATT-TTT----CTACAT-CT-CACTTACAGTTAGTAATCA--AATTGCACAA
droSim1	G-------GCGCGCACTGGTG---------TGTG----------TGT--GTGTGA--GTG---------------------T------GGG---TGGAA----------------------AATCGGATTTCGTAAAACGCATTTAATT------G-----------------------TT----------AACAGCAGCAAAA-----ACG-----------TGT--ATAATTTACCTG-ACT-TTT----CTACAT-CT-CACTTACAGTTAGTAATCA--AATTGCACAA
droSec1	G-------GCGCGCACTGGTG---------TGTG----------TGT--GTGTGA--GTG---------------------T------GGG---TGGAA----------------------AATCGGATTTCGTAAAACGCATTTAATT------G-----------------------TT----------AACAGCAGCA-AA-----ACG-----------TGT--ATAATTTACCTG-ACT-TTT----TTACAT-CT-CACTTACAGTTAATAATCA--AATTGCACAA
droYak2	G-------GCGCGCTTGTGTG-----------------------TGT--GTGTGA--GTG---------------------T------GGG---TGGAA----------------------AATCGGATTTCGTAAAACGCATTTAATT------G-----------------------TT----------AACAGC---A-AAACTAAGCG-----------CGT--ATAATTTACTTG-ATT-TTT----CTACATC----ACTTACAGTTAGTAATCA--AATTGCACAA
droEre2	G-------GCGCGCGCTTGTG---------TG------------TGT--GTGCGA--GTG---------------------T------GGG---TGGAA----------------------AATCGGATTTCGTAAAACGCATTTAATT------G-----------------------TT----------AACAGCAGCAAAA-----ACG-----------TGT--ATAATTTACCTG-ATT-TTT----CTACATC----CCTTACAGTTAGTAATCA--AATTGCACAA
droEug1	G-------GCGCGCGCGTACT---------TGTG----------TGT--GTGCGT--GTG---------------------T------GGG---TGGAA----------------------AATACGATTTCGTAAAACGCATTTCATT------G-----------------------TT----------AACA-------AA-----ACG-----------TGTG-TTAATTTACCTAAACT-TTT----CTTTACC----TTTTACAGTTAGTAATCAAAAATTGCACAA
droBia1	G-------GCGCGCGCCTGTG---------TGTG----------TGT--GTGTGT--GGG---------------------T------GGG---TGGAA----------------------AATCCGATTTCGTAAAACGCATTTAATT------G-----------------------TA----------AGCAACAACAAAA-----ACG-----------TGT--GTAATTTACCTG-CTTCTTT----CCATATC----GTTTACAGTTAGTA------AATTGCACAA
droTak1	G-------GCGCGCGCCCATG---------TGTG----------------CGTGT--GTG---------------------T------GGG---TGGAA----------------------AATCGGATTTCGTAAAACGCATTTAATT------G-----------------------TT----------AACAACAACAAGA-----ACG-----------TGT--GTAATTTACCTG-ATT-TTTTTTTCTCAAT-TT-CCCTTACAGTTAGTAATCA--AATTGCACAA
droEle1	G-------GCGCGCGTATGTG-----------------------TGT----------GTG---------------------T------GGG---TGGAA----------------------AATCCGATTTCGTAAAACGCATTTAATT------G-----------------------TT----------AATAAC---A-AA-----ACG-----------TGGGTGTAATTTACATG-ATT-TTT----CTACATT----ATTCACAGTTAGTAAGCA--AACTGCACAA
droRho1	G-------GCGCGTGTTTGTG---------T--------------------------GTG---------------------T------GGA---TGAAA----------------------AATTCGATTTCGTAAAACGCATTTAATT------G-----------------------TT----------AACAAC---A-AA-----ACG-----------TGTATGTAATTTACCTG-ATT-TTT----CTACATT----ATTTACAGTTAGTAAGCA--AGCTGCACAA
droFic1	G-------GCGCGCGCGTATG-----------------------TGT----------GTG---------------------T------GGG---TGGAA----------------------AATCCGATTTCGTAGAACGCATTTAATT------G-----------------------TT----------AACAACAACA-AA-----TCG-----------TGT--CTAATTTACCTG-ACT-TTT----CTATATC----ATTTTCAGTTAGTAATTA--AATTGCACAA
droKik1	ACTAGTTCGTGTGAGTGTATG-----------------------TGT--GTGTGA--GA-TCTCCTGAATAGGTTTCTGTGT------GTG---TG-----------------------------TGATTTCGTAAAACGCATTTAAAT----TTG-----------------------TT----------AATAAA---AAAA-----ACG-----------TGT--GTA-TTTAT---------------------------CTTACAGTTAGAA--CC--AATTGCACAA
droAna3	G-------AGACGTATGTGTG-----------------------TGT--GTGTGA--GTG---------------------TGAGTGTGGGAGGAGGAA----------------------AAGCGGATTTCGTAAAACGCATTTACTAATT-TTCTTAAAAATA--------------AC----------AAAAACAACA-AA-----ACG-----------TGT---------------------------------TT-CCATTACAGTTAGAA--CC--AATTGCACAA
droBip1	C-------TCGCGCGCGTGTTAGTGCTAAGTGTGTGTGTGTGTGTGTGTGTGTGT--GTG---------------------T--GTGTGGAAAACGGAA----------------------AAATGGATTTCGTAAAACGCATTTACTAATTTTTCTTAAAAATAATAATAA----AAT--CAACAACTACAACAACAACAACA-----TTG-----------TGT---------------------------------TT-CCATTACAGTTAGAA--CC--AATTGCACAA
dp4	C-------GCGTGCGTATGTG---------TGTG----------TGT--ATGTGCATGCG---------------------A------GGG---GGGATATGCATATTTGTTAATGTGCTAGGAACGATTCTGTAAAACGAATTTATTA------T-----------ATTAT----ATC--TATT------AATTAC---C-AA-----TTTATTAAATAATGTG-----------TTTG-TGT-TTTCTT-TTGTATC-CAAAATTGCAGT-AG-AA-TC--AATTGCACAA
droPer1	GT------GTGCGTGTG-------------TGTG----------TGC--GTGTGT--GTG---------------------T------AAA---AAGAA----------------------AAAAGGATTTCGTAAAAACAAATCAAAC------A-------T---AACATTATG---TTG---------GCCCACGGCA-AA-----GCG---AA------CTA--ATAAATTTCCAA-GCA-AAT----CCACA-----------------AAAATCA---AATG--CAA

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

Small RNA-seq read pileup

Species

Alignment

droSim1

G-------GCGCGCAC-------------------TGGTG--TGTGT--GTG--TGTGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGCAGCAAAA-----A-----------CGTGT--ATAATTTACCTGAC----T-TTTC----TA-CATCTCACTTACAGTTAGTAATC--AAATTGCA---CAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................ATG--TGTCT--GTG--TGTGAGT.........................................................................................................................................................................................................................................................	18	3	0.67	0.00	0.00	0.67	0.00
......................................TG--TTTGT--GTG--TGTGGGTG........................................................................................................................................................................................................................................................	18	5	0.40	0.00	0.40	0.00	0.00
..............................................T--GTT--TGTGTGTGTGGGT---------------------------------G.................................................................................................................................................................................................................	18	5	0.40	0.00	0.40	0.00	0.00
......................................GC--TGTGT--GTG--TGTGAGTG........................................................................................................................................................................................................................................................	18	4	0.50	0.00	0.00	0.00	0.50
...................................................G--AGTxxGTTTGGGT---------------------------------GGAAAA............................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................TGTGT--GTG--TGCGAGAGTG......................................................................................................................................................................................................................................................	18	7	0.14	0.00	0.14	0.00	0.00
..........................................TGTGT--GTG--TGTGTGTGTGCGT---------------------------------..................................................................................................................................................................................................................	21	3	0.33	0.33	0.00	0.00	0.00
...................................TGGTx--TGTGT--GTG--TGTTAGT.........................................................................................................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00
..............................................T--GTG--TGTGTGTGTGGTT---------------------------------G.................................................................................................................................................................................................................	18	5	0.20	0.00	0.00	0.20	0.00
..........................................TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	18	40	0.03	0.03	0.00	0.00	0.00
......................................TG--TGTGT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	18	40	0.03	0.03	0.00	0.00	0.00
..............................................T--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	18	40	0.03	0.03	0.00	0.00	0.00
....................................................................................................................................................................................................................................................................TTTC----TA-CATCTCACTTACAGTT.......................	22	1	1.00	1.00	0.00	0.00	0.00
......................................TG--TCTGT--GTG--TGTGTGTGT.......................................................................................................................................................................................................................................................	19	14	0.07	0.07	0.00	0.00	0.00
..............................................T--GTG--TGTGTGTGTGTGT---------------------------------GG................................................................................................................................................................................................................	19	19	0.05	0.05	0.00	0.00	0.00
......................................TG--TGTGT--GTG--TGTGGTTG........................................................................................................................................................................................................................................................	18	5	0.20	0.00	0.00	0.20	0.00
............................................TGT--GTG--TGTGAGTGTATGT---------------------------------..................................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
......................................TG--TGTGT--GTG--TGTGAGTG........................................................................................................................................................................................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
......................................TG--TGTGT--GTG--TGTGTGTGTGCG....................................................................................................................................................................................................................................................	22	2	0.50	0.50	0.00	0.00	0.00
..........................................TGTGT--GTG--TGTTAGTGTT......................................................................................................................................................................................................................................................	18	5	0.20	0.20	0.00	0.00	0.00
......................................TG--TGTGT--GTG--TGTGTGTGG.......................................................................................................................................................................................................................................................	19	19	0.05	0.05	0.00	0.00	0.00
............................................TGT--GTG--TGTGTGTGTGGTT---------------------------------..................................................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
......................................TG--TGTGT--GTG--TGTGTGTGT.......................................................................................................................................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
..................................................................................................................................................................................................................................................................T-TTTC----TA-CATCTCACTTACAGT........................	22	1	1.00	1.00	0.00	0.00	0.00
......................................TG--TGTGT--GCG--TGTGAGCG........................................................................................................................................................................................................................................................	18	8	0.13	0.13	0.00	0.00	0.00
..................................................................................................................................................................................................................................................................T-TTTC----TA-CATCTCACTTACAG.........................	21	1	1.00	0.00	1.00	0.00	0.00
..........................................TGTGT--GTG--TGTGTGTGTGG.....................................................................................................................................................................................................................................................	19	19	0.05	0.05	0.00	0.00	0.00
..........................................TGTGT--GTG--TGTGTGTGTGT.....................................................................................................................................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
.............CGC-------------------TGGTG--TGTGT--GTG--GG..............................................................................................................................................................................................................................................................	18	2	0.50	0.50	0.00	0.00	0.00
......................................TG--TGTGT--GTG--CGAGAGTG........................................................................................................................................................................................................................................................	18	7	0.14	0.00	0.14	0.00	0.00
............................................TGT--GTG--TGTGTGTGTGGT....................................................................................................................................................................................................................................................	18	10	0.10	0.10	0.00	0.00	0.00
....................................TGTG--TGTGT--GTG--TGTGGGTGT.......................................................................................................................................................................................................................................................	21	4	0.25	0.25	0.00	0.00	0.00
....................................TGTG--TGTGT--GTG--TGTGTGT.........................................................................................................................................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
.............................................GT--GTG--TGGGCGTGTGGGT---------------------------------..................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
......................................TA--TGTGT--GTG--TGTGAGTGC.......................................................................................................................................................................................................................................................	19	10	0.10	0.00	0.00	0.10	0.00
......................................AG--TGTGT--GTG--AGTGAGTG........................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
....................................TGTG--TGTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	18	40	0.03	0.03	0.00	0.00	0.00
.......................................G--TGCGT--GTG--TGTGAGTGG.......................................................................................................................................................................................................................................................	18	3	0.33	0.33	0.00	0.00	0.00
...................................TGTTG--TGTGT--GTG--TGTGTGT.........................................................................................................................................................................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
..................................................TG--TGGGTGxGTGGGT---------------------------------GGAA..............................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
............................................TGT--GTG--TGTGTGTGTGGGT---------------------------------GT................................................................................................................................................................................................................	21	4	0.25	0.25	0.00	0.00	0.00
............................................TGT--GTG--TGTGTGTGTGTGT---------------------------------..................................................................................................................................................................................................................	19	34	0.03	0.03	0.00	0.00	0.00
............................................TGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	18	40	0.03	0.03	0.00	0.00	0.00

droSec1

G-------GCGCGCAC-------------------TGGTG--TGTGT--GTG--TGTGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGCAGCA-AA-----A-----------CGTGT--ATAATTTACCTGAC----T-TTTT----TA-CATCTCACTTACAGTTAATAATC--AAATTGCA---CAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	18	27	0.30	0.00	0.00	0.30
..............................................T--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	18	27	0.30	0.00	0.00	0.30
....................................TGTG--TGTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	18	27	0.30	0.00	0.00	0.30
......................................TG--TGTGT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	18	27	0.30	0.00	0.00	0.30
............................................TGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	18	27	0.30	0.00	0.00	0.30
.............................................GT--GTG--TGTGTGTGTGTGT---------------------------------..................................................................................................................................................................................................................	18	26	0.27	0.12	0.00	0.15
.......................................G--TGTGT--GTG--TGTGTGTGT.......................................................................................................................................................................................................................................................	18	26	0.27	0.12	0.00	0.15
...........................................GTGT--GTG--TGTGTGTGTGT.....................................................................................................................................................................................................................................................	18	26	0.27	0.12	0.00	0.15
.....................................GTG--TGTGT--GTG--TGTGTGT.........................................................................................................................................................................................................................................................	18	26	0.27	0.12	0.00	0.15
.......................................G--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	23	9	0.67	0.22	0.00	0.44
....................................TGTG--TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	22	10	0.60	0.30	0.10	0.20
......................................TG--TGTGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	22	10	0.60	0.30	0.10	0.20
......................................TG--TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	20	17	0.35	0.06	0.00	0.29
............................................TGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	20	17	0.35	0.06	0.00	0.29
.....................................GTG--TGTGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	23	9	0.67	0.22	0.00	0.44
......................................TG--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	24	4	1.50	0.75	0.00	0.75
..........................................TGTGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	22	10	0.60	0.30	0.10	0.20
....................................AGTG--TGTGT--GTG--TGTGAGTGTGTG....................................................................................................................................................................................................................................................	24	2	3.00	0.00	0.00	3.00
..........................................TGTGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	20	17	0.35	0.06	0.00	0.29
....................................TGTG--TGTGT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	20	17	0.35	0.06	0.00	0.29
....................................AGTG--TGTGT--GTG--TGTGTGTGT.......................................................................................................................................................................................................................................................	21	4	1.25	0.25	0.25	0.75
.......................................G--TGTGT--GTG--TGCGTGTGT.......................................................................................................................................................................................................................................................	18	10	0.40	0.00	0.40	0.00
......................................TG--TGTGT--GTG--TGTGTGTGTGT.....................................................................................................................................................................................................................................................	21	11	0.36	0.09	0.00	0.27
...........................................GTGT--GTG--TGTGCGTGTGT.....................................................................................................................................................................................................................................................	18	10	0.40	0.00	0.40	0.00
..................................................TG--TGGGTGxGTGGGT---------------------------------GGAA..............................................................................................................................................................................................................	18	1	4.00	0.00	1.00	3.00
......................................TG--TGTGT--GTG--TGTGTGTGT.......................................................................................................................................................................................................................................................	19	19	0.21	0.11	0.00	0.11
.....................................GTG--TGTGT--GTG--CGTGTGT.........................................................................................................................................................................................................................................................	18	10	0.40	0.00	0.40	0.00
............................................TGT--GTG--TGTGTGTGTGTGT---------------------------------..................................................................................................................................................................................................................	19	19	0.21	0.11	0.00	0.11
....................................TGTG--TGTGT--GTG--TGTGTGT.........................................................................................................................................................................................................................................................	19	19	0.21	0.11	0.00	0.11
..........................................TGTGT--GTG--TGTGTGTGTGTGT---------------------------------..................................................................................................................................................................................................................	21	11	0.36	0.09	0.00	0.27
....................................TGTG--TGTGT--GTG--TGTGTGTGT.......................................................................................................................................................................................................................................................	21	11	0.36	0.09	0.00	0.27
..........................................TGTGT--GTG--TGTGTGTGTGT.....................................................................................................................................................................................................................................................	19	19	0.21	0.11	0.00	0.11
.............................................GT--GGG--TGTGAGTGTGGGT---------------------------------GGTA..............................................................................................................................................................................................................	22	1	3.00	0.00	0.00	3.00
...........................................GTGT--GGG--TGTGxGTGTGGGT---------------------------------..................................................................................................................................................................................................................	19	1	3.00	3.00	0.00	0.00
......................................CG--TGCGT--GTG--TGTGAGTG........................................................................................................................................................................................................................................................	18	2	1.50	0.00	0.00	1.50
.............................................GT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	19	21	0.14	0.00	0.10	0.05
.....................................GTG--TGTGT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	19	21	0.14	0.00	0.10	0.05
...........................................GTGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	19	21	0.14	0.00	0.10	0.05
.......................................G--TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	19	21	0.14	0.00	0.10	0.05
.....................................GTG--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	25	4	0.75	0.25	0.00	0.50
.....................................GTG--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------..................................................................................................................................................................................................................	24	5	0.60	0.40	0.20	0.00

droYak2

G-------GCGCGCTT-------------------GTGTG--TGT------G--TGTGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGC---A-AAACTAAG-----------CGCGT--ATAATTTACTTGAT----T-TTTC----TA-CAT--CACTTACAGTTAGTAATC--AAATTGCA---CAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................................................................................................................................................................................................................................................AT----T-TTTC----TA-CAT--CACTTACAGT........................	22	2	1.50	1.00	0.50	0.00	0.00	0.00
.............................................................................................................................................................................................................................................................T----T-TTTC----TA-CAT--CACTTACAGT........................	21	2	1.00	0.00	0.00	0.50	0.50	0.00
....................................TGTG--TGT------G--TGTGTGTGTGA.....................................................................................................................................................................................................................................................	19	31	0.06	0.06	0.00	0.00	0.00	0.00
...............T-------------------GTGTG--TGT------G--TGTGTGTGA.......................................................................................................................................................................................................................................................	19	31	0.06	0.06	0.00	0.00	0.00	0.00
...............T-------------------GTGTG--TGT------G--TTTGATTG........................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25	0.00
...................................................................................................................................................................................................................................................ATTTGCTTGAT----T-TTTC----GA-.......................................	18	2	0.50	0.00	0.00	0.00	0.50	0.00
.....................................CTG--TGT------G--CGTGAGTGTGG.....................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
...................................GTGTG--TGT------G--CGTGTGTGT.......................................................................................................................................................................................................................................................	18	32	0.03	0.00	0.00	0.00	0.03	0.00
...................................GTGAG--TGA------G--TGTGAGTGT.......................................................................................................................................................................................................................................................	18	3	0.33	0.33	0.00	0.00	0.00	0.00
.............CTT-------------------GCGTG--GGT------G--TGTGA...........................................................................................................................................................................................................................................................	17	2	0.50	0.00	0.00	0.00	0.50	0.00
............................................................................................................................................................................................................................................................AT----T-TTTA----TA-CAT--CACTTAGAG.........................	21	2	0.50	0.50	0.00	0.00	0.00	0.00
....................................TGTG--TGT------G--TGTGTGTGTT......................................................................................................................................................................................................................................................	18	41	0.02	0.02	0.00	0.00	0.00	0.00
.......................................G--TGT------G--TGTGCGTGTGTGT---------------------------------..................................................................................................................................................................................................................	18	32	0.03	0.00	0.00	0.00	0.03	0.00
........................................................................................................AATCGGATTTCGTAAAACGCATTTA.....................................................................................................................................................................................	25	2	0.50	0.00	0.00	0.00	0.00	0.50
...................................GTGTG--TGT------G--TGTGTGTGTGTGT---------------------------------..................................................................................................................................................................................................................	22	41	0.02	0.00	0.00	0.00	0.02	0.00
..............TT-------------------GTGTG--TGT------G--CGTGCGTGT.......................................................................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00
...............T-------------------GTGTG--TGT------G--CGTGTGTGT.......................................................................................................................................................................................................................................................	19	29	0.03	0.00	0.00	0.03	0.00	0.00
...................................GTGTG--CGT------G--TGTGTGTGT.......................................................................................................................................................................................................................................................	18	33	0.03	0.00	0.00	0.03	0.00	0.00
..........TTGCTT-------------------GTGTG--TGT------G--TGT.............................................................................................................................................................................................................................................................	18	7	0.14	0.00	0.00	0.14	0.00	0.00
...................................GTGTG--TGT------G--TGTGCGTGTGT.....................................................................................................................................................................................................................................................	20	22	0.05	0.00	0.00	0.05	0.00	0.00
.......................................G--TGA------G--TGTGAGTGTGAGT---------------------------------..................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
......................................TG--TGT------G--TGTGCGTGTGTGT---------------------------------..................................................................................................................................................................................................................	19	29	0.03	0.00	0.00	0.03	0.00	0.00
.....................................GTG--GGT------G--TGTGGGTGTGGGT---------------------------------G.................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
...............T-------------------GTGTG--TGT------G--TGTGTGTGTG......................................................................................................................................................................................................................................................	20	21	0.05	0.05	0.00	0.00	0.00	0.00
...............T-------------------GTGTG--TGT------G--TGTGTGTT........................................................................................................................................................................................................................................................	18	41	0.02	0.02	0.00	0.00	0.00	0.00
...............T-------------------GTGTG--TGT------G--TGTGTGTG........................................................................................................................................................................................................................................................	18	31	0.03	0.00	0.00	0.03	0.00	0.00
..............GT-------------------GTGAG--TGT------G--TGTGAGT.........................................................................................................................................................................................................................................................	18	10	0.10	0.00	0.00	0.10	0.00	0.00
.....................................GTG--GGT------G--TGTGGGTGTGGGT---------------------------------..................................................................................................................................................................................................................	20	3	0.33	0.00	0.00	0.33	0.00	0.00
...................................GTGTG--TGT------G--TGTGCGTGT.......................................................................................................................................................................................................................................................	18	31	0.03	0.00	0.00	0.03	0.00	0.00
....................................TGTG--TGT------G--TGTGTGTGTG......................................................................................................................................................................................................................................................	18	31	0.03	0.00	0.00	0.03	0.00	0.00
...................................GTGTG--TGT------G--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	23	36	0.03	0.00	0.00	0.03	0.00	0.00
..............GT-------------------GTGTG--TGT------G--TGTGCGTGT.......................................................................................................................................................................................................................................................	20	22	0.05	0.00	0.00	0.05	0.00	0.00
.....................................GTG--TGT------G--TGTGAGTGTGGGA---------------------------------GC................................................................................................................................................................................................................	22	2	0.50	0.00	0.00	0.50	0.00	0.00
...............T-------------------GTGTG--TGC------G--TGTGAGTGA.......................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
...............T-------------------CTGTG--TGC------G--TGTGAGTGT.......................................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
...............T-------------------GCGTG--TGT------G--CGTGAGTGT.......................................................................................................................................................................................................................................................	19	3	0.33	0.00	0.00	0.33	0.00	0.00

droEre2

G-------GCGCGCGC-------------------TTGTG--TGTGT----G--TGCGAGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAGCAGCAAAA-----A-----------CGTGT--ATAATTTACCTGAT----T-TTTC----TA-CAT--CCCTTACAGTTAGTAATC--AAATTGCA---CAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................GTG--TGTGT----G--TGCGTGTGTC......................................................................................................................................................................................................................................................	19	9	0.33	0.11	0.00	0.00	0.22
..........GTGCGC-------------------TTGTG--TGTGT----G--TTC.............................................................................................................................................................................................................................................................	20	3	0.33	0.33	0.00	0.00	0.00
..........................................TGTGT----G--TGCGAGTGTGTG....................................................................................................................................................................................................................................................	18	14	0.07	0.00	0.00	0.00	0.07
................................................................................................................................AATT----------------------------------G--------------------------------TG--AACAGCAGCAG................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
....................................TGTG--TGTGT----G--TGCGTGTGTTGG....................................................................................................................................................................................................................................................	22	3	0.33	0.00	0.00	0.00	0.33
....................................CGTG--TGTGT----G--TGCGTGTGT.......................................................................................................................................................................................................................................................	19	7	0.14	0.00	0.00	0.00	0.14
.....................................GTG--TGTGT----G--TGCGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	23	13	0.08	0.00	0.00	0.00	0.08
......................................TG--CGTGT----G--TGCGTGTGTG......................................................................................................................................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14
.......................................G--TGTGA----G--TGCGAGTGCGGGT---------------------------------G.................................................................................................................................................................................................................	21	3	0.33	0.00	0.00	0.00	0.33
..............GC-------------------TCGTG--TGTGT----G--TGTGA...........................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
........GCGCGCGT-------------------GTGTG--TGTGT----...................................................................................................................................................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
............................................AGT----G--TGCGAGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25
..........................................TCTGT----G--TGCGAGTGTGAG....................................................................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.00	0.33
.....................................GTG--TGTGT----G--CGCGAGTGT.......................................................................................................................................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.14
.....................................GTG--TGTGT----G--TGCGTGTGT.......................................................................................................................................................................................................................................................	18	7	0.14	0.14	0.00	0.00	0.00
..........GCGCGC-------------------CTGTG--TGTGT----G--A...............................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25
....................................TGTG--TGTGT----G--TGCGAGTGT.......................................................................................................................................................................................................................................................	19	5	0.20	0.00	0.00	0.00	0.20
..........GCGCGC-------------------GTGTG--TGTGT----G--T...............................................................................................................................................................................................................................................................	18	6	0.17	0.00	0.00	0.00	0.17
.....................................GTG--TGTGT----G--TGCGTATGT.......................................................................................................................................................................................................................................................	18	14	0.07	0.07	0.00	0.00	0.00
......................................TG--TGTGT----G--TGCGAGTGAGAGT---------------------------------..................................................................................................................................................................................................................	21	3	0.33	0.00	0.00	0.00	0.33
....................................TGTG--TGTGT----G--TGTGAGTGAG......................................................................................................................................................................................................................................................	20	4	0.25	0.00	0.00	0.00	0.25
...................................................G--TGCGAGTCTCGGT---------------------------------GGAA..............................................................................................................................................................................................................	18	3	0.33	0.33	0.00	0.00	0.00
.....................................GTG--TGTAT----G--TGCGGGTGT.......................................................................................................................................................................................................................................................	18	7	0.14	0.14	0.00	0.00	0.00
....................................TGTG--TGTGT----G--TGTGAGTGC.......................................................................................................................................................................................................................................................	19	8	0.13	0.00	0.00	0.00	0.13
....................................TGTG--TGTGT----G--TGCGAGTGAGAGT---------------------------------..................................................................................................................................................................................................................	23	3	0.33	0.33	0.00	0.00	0.00
..........................................TGTGT----G--TGCGTGTGTGTG....................................................................................................................................................................................................................................................	18	50	0.02	0.00	0.00	0.00	0.02
............................................TGT----G--TGAGAGTGTGTGT---------------------------------GG................................................................................................................................................................................................................	19	3	0.33	0.00	0.33	0.00	0.00

droEug1

G-------GCGCGCGC-------------------GTACT--TGTGT--GTG--TGCGTGTGTGGGT---------------------------------GGAAAATACGATTTCGTAAAACGCATTTCATT----------------------------------G--------------------------------TT--AACA-------AA-----A-----------CGTGTG-TTAATTTACCTAAA---CT-TTTC----TT-TAC--CTTTTACAGTTAGTAATCAAAAATTGCA---CAA

Size

Hit Count

Total Norm

droBia1

G-------GCGCGCGC-------------------CTGTG--TGTGT--GTG--TGTGTGGGTGGGT---------------------------------GGAAAATCCGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TA--AGCAACAACAAAA-----A-----------CGTGT--GTAATTTACCTGCT----TCTTTC----CA-TAT--CGTTTACAGTTAGTA------AATTGCA---CAA

Size

Hit Count

Total Norm

droTak1

G-------GCGCGCGC-------------------CCATG--TGTGC--GTG------TGTGTGGGT---------------------------------GGAAAATCGGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAACAACAAGA-----A-----------CGTGT--GTAATTTACCTGAT----T-TTTTTTTCTC-AATTTCCCTTACAGTTAGTAATC--AAATTGCA---CAA

Size

Hit Count

Total Norm

droEle1

G-------GCGCGCGT-------------------ATGTG--TGT--------------GTGTGGGT---------------------------------GGAAAATCCGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AATAAC---A-AA-----A-----------CGTGGGTGTAATTTACATGAT----T-TTTC----TA-CAT--TATTCACAGTTAGTAAGC--AAACTGCA---CAA

Size

Hit Count

Total Norm

droRho1

G-------GCGCGTGT-------------------TTGTG--T----------------GTGTGGAT---------------------------------GAAAAATTCGATTTCGTAAAACGCATTTAATT----------------------------------G--------------------------------TT--AACAAC---A-AA-----A-----------CGTGTATGTAATTTACCTGAT----T-TTTC----TA-CAT--TATTTACAGTTAGTAAGC--AAGCTGCA---CAA

Size

Hit Count

Total Norm

droFic1

G-------GCGCGCGC-------------------GTATG--TGT--------------GTGTGGGT---------------------------------GGAAAATCCGATTTCGTAGAACGCATTTAATT----------------------------------G--------------------------------TT--AACAACAACA-AA-----T-----------CGTGT--CTAATTTACCTGAC----T-TTTC----TA-TAT--CATTTTCAGTTAGTAATT--AAATTGCA---CAA

Size

Hit Count

Total Norm

droKik1

ACTAGTTCGTGTGAGT-------------------GTATG--TGT--------------GTGTGAGA------TCTCCTGAATAGGTTTCTGTGTGTG-TG-------TGATTTCGTAAAACGCATTTAAAT---------T-----------------------TG--------------------------------TT--AATAAA---AAAA-----A-----------CGTGT--GTA-TTTAT-----------------------------CTTACAGTTAG--AAC--CAATTGCA---CAA

Size

Hit Count

Total Norm

droAna3

G-------AGACGTAT-------------------GTGTG--TGTGT--GTGAGTGTGAGTGTGGGA------G------------------------GAGGAAAAGCGGATTTCGTAAAACGCATTTACTA-----ATT-T-----------------------TCTTAAAAATAA-------------------------CAAAAACAACA-AA-----A-----------CGTGT------------------------------------TTCCATTACAGTTAG--AAC--CAATTGCA---CAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............T-------------------GTGTG--TGTCT--GTGTGTGTGA...........................................................................................................................................................................................................................................................	21	5	2.80	0.00	2.80	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................A	18	27	0.41	0.04	0.37	0.00	0.00
...............A-------------------GTGTG--TGTGT--GTGTGTG..............................................................................................................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
...........AGTGT-------------------GTGTG--TGTGT--GTG..................................................................................................................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
....................................AGTG--TGTGT--GTGTGTGTG............................................................................................................................................................................................................................................................	18	27	0.41	0.04	0.37	0.00	0.00
....................................TGTG--TGTGA--ATxxGTGTGAG..........................................................................................................................................................................................................................................................	18	2	5.00	1.00	2.00	2.00	0.00
...................................GTGTG--TGTGT--GTGTGTGT.............................................................................................................................................................................................................................................................	18	20	0.50	0.00	0.50	0.00	0.00
....................................TGTG--TGTGA--ATxxGTGTGAGT.........................................................................................................................................................................................................................................................	19	2	4.50	3.50	1.00	0.00	0.00
...............A-------------------GTGTG--TGTGT--GTGTGTGT.............................................................................................................................................................................................................................................................	19	22	0.36	0.00	0.36	0.00	0.00
.....................................................................................................................................................................................................................................................................................................................A	19	22	0.36	0.00	0.36	0.00	0.00
....................................TGTG--TGTGT--GTGTGTGTG............................................................................................................................................................................................................................................................	18	23	0.30	0.00	0.30	0.00	0.00
...............T-------------------GTGTG--TGTGT--GTGTGTG..............................................................................................................................................................................................................................................................	18	23	0.30	0.00	0.30	0.00	0.00
.......................................G--TGTGT--GTGAATGTGTGT.........................................................................................................................................................................................................................................................	18	9	0.78	0.22	0.33	0.22	0.00
...............T-------------------GTGTG--TGTGT--GTGAGTGTGTGTGC.......................................................................................................................................................................................................................................................	25	4	1.50	0.00	1.50	0.00	0.00
...............T-------------------GTGTG--TGTGT--GTGTGTGT.............................................................................................................................................................................................................................................................	19	19	0.32	0.00	0.32	0.00	0.00
...............T-------------------GTGTG--TGTGT--GTGTGTGTG............................................................................................................................................................................................................................................................	20	15	0.33	0.00	0.33	0.00	0.00
.................................................GTGGGTGTGGGTGTGGGA------.............................................................................................................................................................................................................................................	18	2	2.00	0.00	2.00	0.00	0.00
...............T-------------------GTGTG--TGTGT--GTGAGTGTGTGTG........................................................................................................................................................................................................................................................	24	5	0.60	0.00	0.60	0.00	0.00
....................................TGTG--TGTGT--GTGTGTGTGAGTGTGTG....................................................................................................................................................................................................................................................	26	4	0.75	0.00	0.75	0.00	0.00
...............G-------------------GTGTG--TGTGT--GTGTGTGT.............................................................................................................................................................................................................................................................	19	21	0.14	0.05	0.10	0.00	0.00
...................................GTGTG--TGTGT--GTGAGTGTGTGTGCG......................................................................................................................................................................................................................................................	25	4	0.75	0.00	0.75	0.00	0.00
....................................TGTG--TGTGT--GTGTGGGTG............................................................................................................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00
...............T-------------------GTGTG--TGTGT--GTGGGTG..............................................................................................................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00
....................................TGTG--TGTGT--GTGAGTGTGTGTGCG......................................................................................................................................................................................................................................................	24	5	0.60	0.00	0.60	0.00	0.00
..........................................TGTGT--GTGTGTGTGGGTG........................................................................................................................................................................................................................................................	18	32	0.09	0.00	0.09	0.00	0.00
..............AT-------------------GTGTG--TGTGT--CTGTGTGTG............................................................................................................................................................................................................................................................	21	10	0.30	0.00	0.30	0.00	0.00
...............T-------------------GTGTG--TGTGT--GTGAGTGTGTGTGCG......................................................................................................................................................................................................................................................	26	4	0.75	0.00	0.75	0.00	0.00

droBip1

C-------TCGCGCGCGTGTTAGTGCTAAGTGTGTGTGTGTGTGTGT--GTG--TGTGTGTGTGTGT--GGAAA------------------------ACGGAAAAATGGATTTCGTAAAACGCATTTACTA-----ATTTT-----------------------TCTTAAAAATAATAATAA-------AATCAACAACTACAACAACAACAACA-----T-----------TGTGT------------------------------------TTCCATTACAGTTAG--AAC--CAATTGCA---CAA

Size

Hit Count

Total Norm

dp4

C-------GCGTGCGT-------------------ATGTG--TGTGT--GTA--TGTGCATGCGAGG--GGGGATATGCATATTTGTTA------ATG-TGCTAGGAACGATTCTGTAAAACGAATTTATTA----------------------------------T-----------ATTAT-------ATCTA----TT--AATTAC---C-AA-----TTTATTAAATAATGTGT-----------TTGTG----T-TTTCTTT-TGTATCCAAAATTGCAGT-AG--AAT--CAATTGCA---CAA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............GT-------------------ACGTG--TGTGT--GTG--TGTGC...........................................................................................................................................................................................................................................................	20	6	1.33	0.00	1.33	0.00	0.00
..............GT-------------------ACGTG--TGTGT--GTG--TGTG............................................................................................................................................................................................................................................................	19	46	0.11	0.04	0.04	0.02	0.00
.............CGT-------------------ACGTG--TGTGT--GTG--TGTG............................................................................................................................................................................................................................................................	20	6	0.33	0.00	0.17	0.17	0.00
....................................TGTG--TGTGT--GTG--TGTGCA..........................................................................................................................................................................................................................................................	18	8	0.25	0.00	0.00	0.25	0.00
..............GT-------------------TTGTG--TGTGT--GTT--TGTG............................................................................................................................................................................................................................................................	19	41	0.05	0.02	0.00	0.02	0.00
.......................................................................................................................................................................................................................A-----ATTATTAAAAAATGTGT-----------T............................................................	19	1	2.00	0.00	2.00	0.00	0.00
.............CGT-------------------ACGTG--TGTGT--GTG--TGTGC...........................................................................................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
..............GT-------------------GTGTG--TGTAT--GTA--TGTG............................................................................................................................................................................................................................................................	19	42	0.02	0.02	0.00	0.00	0.00
..........................................................................................................................................................................................................................................................TGTG----T-TTTATTT-TGTATACA..................................	20	1	1.00	0.00	0.00	1.00	0.00
........................................................................................................................ACGAGTTTGTTA----------------------------------T-----------ATTAT-------........................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............TGT-------------------ATGTG--TGTGT--GTA--TGTA............................................................................................................................................................................................................................................................	20	7	0.14	0.14	0.00	0.00	0.00
...................................ATGTG--TGTTT--GTA--TGTGCAA.........................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
..........GTGTGC-------------------ATGTG--TGTGT--GT...................................................................................................................................................................................................................................................................	18	45	0.02	0.02	0.00	0.00	0.00
........................................................................................................................................................................................................................................ATGTGT-----------GTGTG----T-TTTTTTT-T.........................................	20	1	1.00	1.00	0.00	0.00	0.00
..............GT-------------------GTGTG--TGTGG--GTA--TGTG............................................................................................................................................................................................................................................................	19	38	0.03	0.03	0.00	0.00	0.00
........................................................................................................................ACGAATTTGTTA----------------------------------T-----------ATAAT-------........................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..............GT-------------------ATGTG--CGTGT--GTG--TGT.............................................................................................................................................................................................................................................................	18	49	0.02	0.00	0.02	0.00	0.00
...........TGTGT-------------------ATGTG--TGTGT--GTC--TG..............................................................................................................................................................................................................................................................	20	58	0.02	0.02	0.00	0.00	0.00
...............T-------------------GTGTG--TGTGA--GTA--TGTGCA..........................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
............................................TGT--GTA--TGTGCATGCGTGT--G................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.................................................................GA--GGGGATAAGCATATTT.................................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................................GGGAGATGCATATTTTTT..............................................................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................TG--TGTGT--GTT--GGTGCATG........................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..............GT-------------------ATGTA--TGTGT--GTA--TGTA............................................................................................................................................................................................................................................................	19	6	0.17	0.00	0.17	0.00	0.00

droPer1

GT------GTGCGTGT---------------------GT----GTGT--GCG--TGTGTGTGTAAAA---------------------------------AGAAAAAAGGATTTCGTAAAAACAAATCAAAC----------------------------------A-------T---AACATTATGTTGG--------CC--C---ACGGCA-AA-----GCG---AA----CT--A--ATAAATTTCCAAGC----A-AATC----CA-CA---------------AAAATC--A-AATG-----CAA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........GTGCGTGT---------------------GT----GTGT--GTG--TGC.............................................................................................................................................................................................................................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
........GTGCGTGT---------------------GT----GTGT--GTG--T...............................................................................................................................................................................................................................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
........GTGCGTGT---------------------GT----GTGT--GTG--TG..............................................................................................................................................................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
........GTGCGTGT---------------------GT----GTGT--GTG--TGCG............................................................................................................................................................................................................................................................	21	41	0.12	0.10	0.02	0.00	0.00	0.00
..............GT---------------------GT----GTGT--GCG--TGTGTGAGTG......................................................................................................................................................................................................................................................	21	30	0.10	0.10	0.00	0.00	0.00	0.00
...........CGTGC---------------------GT----GTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
.....................................GT----GTGT--GTG--TTTGTGTGTA......................................................................................................................................................................................................................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
GT------GTGCGTGT---------------------GT----GTGT--GGT--................................................................................................................................................................................................................................................................	19	9	0.33	0.33	0.00	0.00	0.00	0.00
.C------GTGCGTGT---------------------GT----GTGT--GTG--TG..............................................................................................................................................................................................................................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00

droWil1

T-------GCGTGTGT-------------------GTGTG--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---TGTGTGTGTGTAGCACTTCCGTTC-----CAT-T-----------------------TACAACAAACAC-------------------------AAAGAAGAACA-A----------------------T--ATCAGCTCCCTTTT----T-TTTT----TT-TGT--TATTTTCATTTTTT--------TCTATG---CAG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
......................................................TGTGTGCGTCTGT---------------------------------GTGTG---TGTG......................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
...........TGTGT-------------------GCGTC--TGTGT--GTG--TGTG............................................................................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
..................................................TG--TGTGCGTCTGTGT---------------------------------GTGTG---TG........................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
....................................TGTG--TGCGT--CTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
......................................TG--TGTGC--GTC--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
........................................................TGTGTGCGTCT---------------------------------GTGTG---TGTGTG....................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
...............T-------------------GTGTG--CGTCT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
............................................TGT--GTG--CGTCTGTGTGTGT---------------------------------GTG...............................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
..........................................................TGTGTGCGT---------------------------------CTGTG---TGTGTGTG..................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
..............................................T--GTG--TGCGTCTGTGTGT---------------------------------GTGTG---..........................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
.............TGT-------------------GTGCG--TCTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
..........................................TGTGT--GCG--TCTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
............................................................TGTGTGC---------------------------------GTCTG---TGTGTGTGTG................................................................................................................................................................................................	22	47	0.68	0.00	0.66	0.02	0.00
...........................................GTGT--GCG--TCTGTGTGTGTGT---------------------------------GT................................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
...........................................................GTGTGCGT---------------------------------CTGTG---TGTGTGTGT.................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
.........................................................GTGTGCGTCT---------------------------------GTGTG---TGTGTGT...................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
..........GTGTGC-------------------GTCTG--TGTGT--GTG--TGT.............................................................................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
..............GT-------------------GTGCG--TCTGT--GTG--TGTGTGT.........................................................................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
.....................................GTG--TGCGT--CTG--TGTGTGTGTGT.....................................................................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
.......................................................GTGTGCGTCTGT---------------------------------GTGTG---TGTGT.....................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
...................................................G--TGTGCGTCTGTGT---------------------------------GTGTG---TGT.......................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
.............................................................GTGTGC---------------------------------GTCTG---TGTGTGTGTGT...............................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
............GTGT-------------------GCGTC--TGTGT--GTG--TGTGT...........................................................................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
.......................................G--TGTGC--GTC--TGTGTGTGTGTGT---------------------------------..................................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
...................................GTGTG--CGTCT--GTG--TGTGTGTGT.......................................................................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
.................................................GTG--TGCGTCTGTGTGT---------------------------------GTGTG---T.........................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
.............................................GT--GTG--CGTCTGTGTGTGT---------------------------------GTGT..............................................................................................................................................................................................................	22	47	0.55	0.02	0.53	0.00	0.00
...................................................G--TGTGTGTGTGTGT---------------------------------GTGTG---TGTG......................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
..........GTGTGT-------------------GTGTG--TGTGT--GTG--TGTG............................................................................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
.............................................GT--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---..........................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
..............GT-------------------GTGTG--TGTGT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
.......................................................GTGTGTGTGTGT---------------------------------GTGTG---TGTGTG....................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
...........................................GTGT--GTG--TGTGTGTGTGTGT---------------------------------GTG...............................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
.....................................GTG--TGTGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
...........................................................GTGTGTGT---------------------------------GTGTG---TGTGTGTGTG................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
............GTGT-------------------GTGTG--TGTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
.................................................GTG--TGTGTGTGTGTGT---------------------------------GTGTG---TG........................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
.........................................................GTGTGTGTGT---------------------------------GTGTG---TGTGTGTG..................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
.......................................G--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
...................................GTGTG--TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	23	31	0.48	0.00	0.10	0.39	0.00
...........................................................GTGTGTGT---------------------------------GTGTG---TGTGTGTGTGTG..............................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
..........GTGTGT-------------------GTGTG--TGTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
.............TGT-------------------GTGTG--TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
....................................TGTG--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
..............................................T--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---TGTG......................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
.............................................GT--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---TG........................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
..............GT-------------------GTGTG--TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
T-------GTGTGTGT-------------------GTGTG--TGTGT--GTG--TGTG............................................................................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
........................................................TGTGTGTGTGT---------------------------------GTGTG---TGTGTGTGTG................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
......................................TG--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------GTG...............................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
............................................TGT--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---TG........................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
.................................................GTG--TGTGTGTGTGTGT---------------------------------GTGTG---TGTG......................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
.........................................................GTGTGTGTGT---------------------------------GTGTG---TGTGTGTGTG................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
...........TGTGT-------------------GTGTG--TGTGT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
...................................GTGTG--TGTGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
..................................................TG--TGTGTGTGTGTGT---------------------------------GTGTG---TGTGTG....................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
...................................................G--TGTGTGTGTGTGT---------------------------------GTGTG---TGTGTG....................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
..........................................................TGTGTGTGT---------------------------------GTGTG---TGTGTGTGTGTG..............................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
...........................................GTGT--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---..........................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
........GTGTGTGT-------------------GTGTG--TGTGT--GTG--TGTG............................................................................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
............GTGT-------------------GTGTG--TGTGT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
..........................................TGTGT--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---..........................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
.........TGTGTGT-------------------GTGTG--TGTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
.....................................GTG--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
.......................................................GTGTGTGTGTGT---------------------------------GTGTG---TGTGTGTG..................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
.......................................G--TGTGT--GTG--TGTGTGTGTGTGT---------------------------------GTG...............................................................................................................................................................................................................	25	51	0.27	0.00	0.02	0.25	0.00
......................................................TGTGTGTGTGTGT---------------------------------GTGTG---TGTGTGTG..................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
...............T-------------------GTGTG--TGTGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	26	44	0.32	0.00	0.02	0.30	0.00
......................................TG--TGTGT--GTG--TGTGTGTGTGTG....................................................................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
...............T-------------------GTGTG--TGTGT--GTG--TGTGTGTG........................................................................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
......................................................TGTGTGTGTGTGT---------------------------------GTGTG---TGTG......................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
........................................................TGTGTGTGTGT---------------------------------GTGTG---TGTGTG....................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
....................................TGTG--TGTGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
..............................................T--GTG--TGTGTGTGTGTGT---------------------------------GTGTG---..........................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
..........................................TGTGT--GTG--TGTGTGTGTGTGT---------------------------------G.................................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
...........TGTGT-------------------GTGTG--TGTGT--GTG--TGTG............................................................................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
..................................................TG--TGTGTGTGTGTGT---------------------------------GTGTG---TG........................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
............................................................TGTGTGT---------------------------------GTGTG---TGTGTGTGTG................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
............................................TGT--GTG--TGTGTGTGTGTGT---------------------------------GTG...............................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
..........................................................TGTGTGTGT---------------------------------GTGTG---TGTGTGTG..................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
.............TGT-------------------GTGTG--TGTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	22	40	0.33	0.00	0.05	0.28	0.00
................................................................TGT---------------------------------GTGTG---TGTGTTTGTGCAGCA...........................................................................................................................................................................................	23	1	12.00	0.00	0.00	12.00	0.00
..............................................T--GTG--TGTGTGTGTGTGT---------------------------------GTGT..............................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
......................................................TGTGTGTGTGTGT---------------------------------GTGTG---TGT.......................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
......................................TG--TGTGT--GTG--TGTGTGTGTGT.....................................................................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
............................................................TGTGTGT---------------------------------GTGTG---TGTGTGTGT.................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
..............................................................TGTGT---------------------------------GTGTG---TGTGTGTGTGT...............................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
............................................TGT--GTG--TGTGTGTGTGTGT---------------------------------GT................................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
..................................................TG--TGTGTGTGTGTGT---------------------------------GTGTG---T.........................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
........................................................TGTGTGTGTGT---------------------------------GTGTG---TGTGT.....................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
.............TGT-------------------GTGTG--TGTGT--GTG--TGTGT...........................................................................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
..........................................................TGTGTGTGT---------------------------------GTGTG---TGTGTGT...................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
...........TGTGT-------------------GTGTG--TGTGT--GTG--TGT.............................................................................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
...............T-------------------GTGTG--TGTGT--GTG--TGTGTGT.........................................................................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
..........................................TGTGT--GTG--TGTGTGTGTGTGT---------------------------------..................................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
....................................TGTG--TGTGT--GTG--TGTGTGTGT.......................................................................................................................................................................................................................................................	21	56	0.20	0.00	0.11	0.09	0.00
....................................TGTG--TATGT--GTG--TGTGTGTGTG......................................................................................................................................................................................................................................................	22	53	0.19	0.00	0.00	0.19	0.00
............................................................TGTGTAT---------------------------------GTGTG---TGTGTGTGTG................................................................................................................................................................................................	22	53	0.19	0.00	0.00	0.19	0.00
............................................TGT--GTA--TGTGTGTGTGTGT---------------------------------GTG...............................................................................................................................................................................................................	22	53	0.19	0.00	0.00	0.19	0.00
..................................................TG--TGTATGTGTGTGT---------------------------------GTGTG---TG........................................................................................................................................................................................................	22	53	0.19	0.00	0.00	0.19	0.00
.............TGT-------------------GTATG--TGTGT--GTG--TGTGTG..........................................................................................................................................................................................................................................................	22	53	0.19	0.00	0.00	0.19	0.00

droVir3

G--------TGTGCAT-------------------GTGTG--TGCGT----G--TGTGTGTGTGTGTGCAAAAATATGCAAATCGGTTT-------TG-CACTGCTGACG------------------ACTT----------------------------------C--------------------------------TT--CACAGCAGCTGAA-----A-----------TGTGC--TTAAAATTC--GCAAAATT-GT------------------------------------AGTTCA---TTT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....................................TGTA--TGCGT----G--CGTGTGTGTGT.....................................................................................................................................................................................................................................................	21	11	0.27	0.09	0.18	0.00	0.00	0.00

droMoj3

G-------ACACAGTC-------------------TGTCG--TGTGTGTGTG--TGTGTGTCTGTGT---------------------------------GTA-TTTCCTTTCTTGTTAAGCTGCTTTGGCTTTTCAATT-TTATTCCTGTATTTGCGTGTCCAATG--------------------------------TT--CAAATTAGCA-AA-----A-----------TGTAC--A--A-------------------------------------GCAGTAAATATCT--ACATTACATGGCCA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......................................................................................................................................................................................................................A-----A-----------TGTCC--A--A-------------------------------------GCAGTAAGT....................	18	1	3.00	1.00	1.00	1.00	0.00
..............................................TGTGxG--TGTATGTCTGTGT---------------------------------GT................................................................................................................................................................................................................	20	21	0.10	0.00	0.10	0.00	0.00
...............................................GAGTG--TGxGTGTCTGTGT---------------------------------GT................................................................................................................................................................................................................	19	14	0.14	0.00	0.14	0.00	0.00
......................................CG--TGTGTGTGTG--TGTATGCCT.......................................................................................................................................................................................................................................................	21	11	0.18	0.18	0.00	0.00	0.00
..........................................TGTGTGTGTG--TGTATGCCTG......................................................................................................................................................................................................................................................	20	28	0.07	0.04	0.04	0.00	0.00
..........................................TGTGTGTGTA--TGTGTGTCTG......................................................................................................................................................................................................................................................	20	8	0.25	0.00	0.25	0.00	0.00
..........................................TGTGTGTGTG--TGTATGCCTGTG....................................................................................................................................................................................................................................................	22	12	0.17	0.00	0.08	0.08	0.00
......................................................TGAGTGTGTGTGT---------------------------------GTA-TTTC..........................................................................................................................................................................................................	20	6	0.17	0.17	0.00	0.00	0.00
......................................CC--TGTGTGTGCG--TGTGTG..........................................................................................................................................................................................................................................................	18	41	0.02	0.00	0.00	0.02	0.00
..................................................TG--TGAGTGTGTGTGT---------------------------------GTA-TT............................................................................................................................................................................................................	20	34	0.03	0.03	0.00	0.00	0.00
..........................................TGTGTGTGTx--CGGGTGTCTGTG....................................................................................................................................................................................................................................................	21	5	0.20	0.20	0.00	0.00	0.00
.............................................GTGTGAG--TGCGTGTCTGTG....................................................................................................................................................................................................................................................	19	5	0.20	0.20	0.00	0.00	0.00
.......................................G--TGTGTGTGTA--TGTGTGTCTGTC....................................................................................................................................................................................................................................................	23	6	0.17	0.00	0.00	0.17	0.00
.............................................GTGTGTG--TATGTGTCTGTA....................................................................................................................................................................................................................................................	19	36	0.03	0.03	0.00	0.00	0.00
......................................CG--AGTGTGTGTG--TGTGTG..........................................................................................................................................................................................................................................................	18	13	0.08	0.08	0.00	0.00	0.00
................................................TGTG--TGTGTGTATGTGT---------------------------------GTC-TT............................................................................................................................................................................................................	22	18	0.06	0.06	0.00	0.00	0.00
...............A-------------------TGTCG--TGTGTGTGTG--TGTG............................................................................................................................................................................................................................................................	20	6	0.17	0.00	0.00	0.17	0.00
..........................................TGTGTGTGTA--TGTGTGTCTGTG....................................................................................................................................................................................................................................................	22	129	0.01	0.01	0.00	0.00	0.00
...........................................CTGTGTGTG--TGTGTGTCAG......................................................................................................................................................................................................................................................	19	30	0.03	0.03	0.00	0.00	0.00
......................................CG--TGCGTGTGTG--TGTATGTC........................................................................................................................................................................................................................................................	20	6	0.17	0.17	0.00	0.00	0.00
..........................................TGTGTGTGTG--TGAGTTTC........................................................................................................................................................................................................................................................	18	36	0.03	0.03	0.00	0.00	0.00
.................................................ATG--CGTGTGTCTGTGT---------------------------------GT................................................................................................................................................................................................................	18	48	0.02	0.00	0.02	0.00	0.00
..........................................TGTGTGTGxG--TGTATGTCTGTGT---------------------------------..................................................................................................................................................................................................................	22	6	0.17	0.17	0.00	0.00	0.00
..............................................TGGGTG--TGTGTGTCTGTGT---------------------------------AT................................................................................................................................................................................................................	21	19	0.05	0.00	0.05	0.00	0.00
.......................................G--TATGTGTGTG--TGTATGTC........................................................................................................................................................................................................................................................	19	42	0.02	0.02	0.00	0.00	0.00
...................................TAGCG--TGTGTGTGTG--TGTGTG..........................................................................................................................................................................................................................................................	21	19	0.05	0.00	0.00	0.00	0.05
..........................................TATGTGTGTG--TGTGTGTCTGT.....................................................................................................................................................................................................................................................	21	26	0.04	0.04	0.00	0.00	0.00
.......................................G--TGTGTGTGTG--TGTGTGTCT.......................................................................................................................................................................................................................................................	20	155	0.01	0.01	0.00	0.00	0.00
..............................................TGTGTG--TGTGTGTCTGTAT---------------------------------GC................................................................................................................................................................................................................	21	32	0.03	0.00	0.03	0.00	0.00
.............................................GTGTGTx--CGGGTGTCTGTG....................................................................................................................................................................................................................................................	18	11	0.09	0.09	0.00	0.00	0.00
................................................TGTG--TGTGTGTCTGTGA---------------------------------GA................................................................................................................................................................................................................	19	15	0.07	0.00	0.07	0.00	0.00
.......................................T--TGTGTGTGTG--TGTGTTTCTG......................................................................................................................................................................................................................................................	21	8	0.13	0.00	0.00	0.13	0.00
..........................................TGTGTGTTTG--TGTGTGTCTG......................................................................................................................................................................................................................................................	20	175	0.01	0.00	0.00	0.01	0.00
............................................TGTGTGTG--CGTGTGTCTATGT---------------------------------G.................................................................................................................................................................................................................	22	11	0.09	0.00	0.00	0.00	0.09
.....................................GCA--TGTGTGTGTG--TGTGTGTCTG......................................................................................................................................................................................................................................................	23	11	0.09	0.00	0.00	0.00	0.09
................................................TGTG--TATGTGTGTGTGT---------------------------------GTA-TT............................................................................................................................................................................................................	22	28	0.04	0.04	0.00	0.00	0.00
......................................CG--TGTGCGTGTG--TGTTTGTC........................................................................................................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
...............A-------------------TGTCA--TGTGTGTGTG--TGTGT...........................................................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50
..........................................TGTGTGAGTG--TGTGTGTCTGTG....................................................................................................................................................................................................................................................	22	111	0.01	0.00	0.00	0.00	0.01
......................................CG--TGTGTGTGTA--TGTGTGTC........................................................................................................................................................................................................................................................	20	19	0.05	0.05	0.00	0.00	0.00
.....................................TCG--AGTGTGTGTG--TGTGT...........................................................................................................................................................................................................................................................	18	28	0.04	0.00	0.00	0.04	0.00
...................................TGCCG--TGTGTGTGTG--TGTGTG..........................................................................................................................................................................................................................................................	21	9	0.11	0.00	0.00	0.00	0.11
.............................................GTTTGTG--TGCGTGTCTGT.....................................................................................................................................................................................................................................................	18	8	0.13	0.00	0.00	0.00	0.13
....................................CTCG--TGTGTGTGTG--TGTGTGTGTGT.....................................................................................................................................................................................................................................................	25	14	0.07	0.00	0.07	0.00	0.00
..............................................TATGTG--TGTGTGTCTGAGT---------------------------------GT................................................................................................................................................................................................................	21	24	0.04	0.04	0.00	0.00	0.00
....................................GTGG--TGTTTGTGTG--TGTGT...........................................................................................................................................................................................................................................................	19	8	0.13	0.00	0.00	0.13	0.00
................................................TGTG--TGTGTGTCTGTTT---------------------------------C.................................................................................................................................................................................................................	18	43	0.02	0.00	0.02	0.00	0.00
.................................................GTG--TGTGTGGCTGTGT---------------------------------GG................................................................................................................................................................................................................	18	18	0.06	0.06	0.00	0.00	0.00
..........................................TGTGTGTGTG--TCTGTTTC........................................................................................................................................................................................................................................................	18	43	0.02	0.00	0.02	0.00	0.00
...............................................GTGGG--TGGGTGTCTGTG....................................................................................................................................................................................................................................................	17	15	0.07	0.00	0.07	0.00	0.00
..................................................TG--TGAGTGTGTGTGT---------------------------------GTA-TTT...........................................................................................................................................................................................................	21	22	0.05	0.00	0.05	0.00	0.00
............................................TGTGTGTG--TTTGTGCCTGTGT---------------------------------..................................................................................................................................................................................................................	21	2	0.50	0.00	0.00	0.00	0.50
.......................................................GTGTGTTTGTGT---------------------------------GTA-TTTGC.........................................................................................................................................................................................................	20	7	0.14	0.14	0.00	0.00	0.00
.............................................GTGTGTA--TGTGTGTCTGT.....................................................................................................................................................................................................................................................	18	14	0.07	0.00	0.00	0.00	0.07
...........................................GTGTGTATG--TGTGTATCTG......................................................................................................................................................................................................................................................	19	22	0.05	0.00	0.00	0.00	0.05
................................................TCTG--TATGTGTCTGTGT---------------------------------GT................................................................................................................................................................................................................	19	49	0.02	0.02	0.00	0.00	0.00

droGri2

T-------GTGTATGT-------------------GTGTG--TGTGT--CTA--TGTTATCGTTTGC--TG-------------------------------------TGA-CTTGCAAATAAAATTTGACT----------------------------------A--------------------------------CT--GCTAAC------------A-----------GT------TATCTCTCTCTCT----C-TCTC----TC-TGTCGCACACACATTTA-----C--ACAGTGCA---AGT	Size	Hit Count	Total Norm	V109 Male body
T-------GTGTTTGT-------------------TTGTG--TGTGT--C....................................................................................................................................................................................................................................................................	20	27	0.04	0.04
.........TGCATGT-------------------GTGTG--TGTGT--GTA--TG..............................................................................................................................................................................................................................................................	22	40	0.03	0.03
...........TGTGT-------------------GTGTG--AGTGT--CTA--TGT.............................................................................................................................................................................................................................................................	21	22	0.05	0.05
A-------GTGTATGT-------------------GTGTG--TGTGT--.....................................................................................................................................................................................................................................................................	19	23	0.04	0.04

Generated: 04/20/2012 at 05:17:08 EDT

sblock177188

chrX:4976268-4976379 -

Candidate

intron

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup