sblock179483- 12- and 20-way alignments

sblock179483	chrX:7824544-7824616 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 7824585-7824604
   star strand at position 7824555-7824576
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chrX:7824529-7824631 -	TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------CGGTGGTGGCTAGTGGGTGGGTTA----AAGAACTGC---CCCGCTCTTCACCATT-CGAAACTAAGTCCCCCACTTCGTCCGA--CC
droSim1	chrX:6274364-6274467 -	TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------CGGTGGTGGCTATTGGGTGGGTGA----AAGAACTGC--CCCCGCTCTTCACCATT-CGAAACTAAGTCCCACACTTCGTCCGA--CC
droSec1	super_50:111506-111609 -	TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------CGGTGGTGGCTATTGGGTGGGTGA----AAGAACTGC--CCCCGCTCTTCACCATT-CGAAACTAAGTTCCACACTTCGTCTGA--CC
droYak2	chrX:13488072-13488175 +	TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------CGGTGGTGGCTAGTGGGTGGGTGA----TGGAACCGCACTCCCCCTTTTCATCATTCCGTAACTAAGTCCCACCCCTCGGC-----CC
droEre2	scaffold_4690:16736829-16736927 -	TTG--------GCGATGCTGTATTGATTTTT---------------------------------------CGGTGGTGGCTAGTGGGTGGGTGA----TGGAACCGC--CCCCGCTCTTCACCATT-CGAAACTGAGTCCCACCCTTCGTC-----CC
droAna3	scaffold_13117:2045785-2045865 -	CCG----T---GCGATGCTGTATTGATTTTTT--------------------------------------CGGTGGTG-------GGTGGGTGTCCTCCGACTCTGTTA---CGGTCTCCACC-------------------CGGTTTC---GATACT
dp4	chrXL_group1a:2469603-2469682 +	TTTGCCGT--AGCGATGCTGTATTGATTTTTTCT------------------------------------CCGTGGTG-------GGTGGGTTC----GGGA-----TG---CGGTC------------AACCTGAGCCACACGCTTTC---------
droPer1	super_28:903927-904006 +	TTTGCCGT--AGCGATGCTGTATTGATTTTTTCT------------------------------------CCGTGGTG-------GGTGGGTTC----GGGA-----TG---CGGTC------------AACCTGAGCCACACGCTTTC---------
droWil1	scaffold_180777:545832-545921 -	TTTGCTGTTTTGCGATGCTCTATTGATTTTTT-TTtTTTTtTTTTTTTTTTTTTTATATATGTATATATTTGGTGGTG-------GGAGGAA------GAGA-----AG-------------------------------------------------
droVir3	scaffold_12970:10151308-10151337 +	CTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------TTGCG-----------------------------------------------------------------------------------
droMoj3	scaffold_6473:11301064-11301096 -	TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------TATTTGCG--------------------------------------------------------------------------------
droGri2	scaffold_14853:6560969-6560993 +	CTG--------GCGATGCTGTATTGATTTTTT-T----------------------------------------------------------------------------------------------------------------------------

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:7824529-7824631 -	NA	TTG--------GCGATGCTGTATTGATTTTTT-TCG----------------GTGGTGGCTAG-------TGGGTGGGTTA---AAGAACTGCC---CCGCTCTTC--AC--------------CATTC-GAAACTA-AGTCCCC------CAC---------TTCGTCC---GACC
droSim1	chrX:6274364-6274467 -	4	TTG--------GCGATGCTGTATTGATTTTTT-TCG----------------GTGGTGGCTAT-------TGGGTGGGTGA---AAGAACTGCCC--CCGCTCTTC--AC--------------CATTC-GAAACTA-AGTCCCA------CAC---------TTCGTCC---GACC
droSec1	super_50:111506-111609 -	3	TTG--------GCGATGCTGTATTGATTTTTT-TCG----------------GTGGTGGCTAT-------TGGGTGGGTGA---AAGAACTGCCC--CCGCTCTTC--AC--------------CATTC-GAAACTA-AGTTCCA------CAC---------TTCGTCT---GACC
droYak2	chrX:13488072-13488176 +	1	TTG--------GCGATGCTGTATTGATTTTTT-TCG----------------GTGGTGGCTAG-------TGGGTGGGTGA---TGGAACCGCACTCCCCCTTTTC--AT--------------CATTCCGTAACTA-AGTCCCA------CCC---------CTCGGCC-----CC
droEre2	scaffold_4690:16736830-16736927 -	4	TTG--------GCGATGCTGTATTGATTTTT---CG----------------GTGGTGGCTAG-------TGGGTGGGTGA---TGGAACCGCCC--CCGCTCTTC--AC--------------CATTC-GAAACTG-AGTCCCA------CCC---------TTCG-------TCC
droEug1	scf7180000409830:75845-75947 -	4	TTG--------GCGATGCTGTATTGATTTTT---CG----------------GTGGTGGTTAG-------TGGGTGGGTGG---TAAAACCGATC--CC-CGC-------CCTATGCCTGTCAA-ACTC-AAAAATAAAAAAAAA------CAC---------C----------TCT
droBia1	scf7180000302198:25129-25216 -	3	T-G--------GCGATGCTGTATTGATTTTT--TCG----------------GTGGTGGCTAG-------TGGGTGGGTGG---TGGAACCGTTA--CCGCCCTC-----CCTTTGCCT--------------------------------------AT----CCAGTCC---AGCC
droTak1	scf7180000415262:139383-139482 -	3	TTG--------GCGATGCTGTATTGATTTTT--TCG----------------GTGGTGGCTAG-------TGGGTGGGTGG---TGGAACCGCCC---CTCTCT---------CGGCCTATCCCCCTTC-TAAATTA-ACTCCCC------CTC-----------CG----------
droEle1	scf7180000491044:620034-620139 +	3	TTG--------GCGATGCTGTATTGATTTTT--CCG----------------GTGGTGGAAAGTTGTGGGTGGGTGGGTGG---TGGAACCGCCCGGCC-GTCTTC--AT--------------TCTGC-CAAAGCA-ACCCCCC------T----------GAT----C---TATC
droRho1	scf7180000776942:301298-301369 +	1	TTG--------GCGATGCTGTATTGATTTTT--CCG----------------GTGGTGGAAAG-------TGGGTGGGTGG---TGGAACCGCCC--CCGCTCTT----------------------------------------------------------------C---GGCC
droFic1	scf7180000454077:2195920-2195996 +	6	TTG--------GCGATGCTGTATTGATTTTT--TCG----------------GTGGTGGATAG-------TGGGTGGGCAA---TGGAACCGCCC--CC-CTC-------TCTCTGCT---------------------------------------------------C---ATCC
droKik1	scf7180000302696:1693213-1693329 -	3	TCGCTGCCGCTGCGATGCTGTATTGATTTTT--TCG----------------GTGGTGGGTGG-------CGGATAGGTGG---TTGGCC-------CTGCTTCTCCTGT--------C-----ATCCC-GAGCCCC-AGTTCAAGTCTCCCTGTCGAGCACGTT----------TC
droAna3	scaffold_13117:2045785-2045865 -	5	CCG-------TGCGATGCTGTATTGATTTTT--TCG----------------GTGGTGG---G-------TGGGTGTCCTCCGA----------------CTC-----------------------TGT-TACG-----------GTCTCC------ACCCGGTT----TCGATACT
droBip1	scf7180000396425:26892-26973 +	1	CCG-------TGCGATGCTGTATTGATTTTT--TCG----------------GTGGTGG---G-------TGGGTGTCCTCCGA----------------CTCT----------------------TGT-TACG-----------GTCTCC------ACCCGGTT----TCGATACT
dp4	chrXL_group1a:2469610-2469680 +	4	--A--------GCGATGCTGTATTGATTTTTTCTCC----------------GTGGTGG---G-------TGGGTTCGGGA---TGCGGTC----------------------------------------AACCTG-AGCCACA------CGC---------TT------------
droPer1	super_28:903934-904004 +	2	--A--------GCGATGCTGTATTGATTTTTTCTCC----------------GTGGTGG---G-------TGGGTTCGGGA---TGCGGTC----------------------------------------AACCTG-AGCCACA------CGC---------TT------------
droWil1	scaffold_180777:545798-545893 -	1	TTT--------TTTATTTTATTTTTTTTTTTT-TTATATATGTATATATTTGGTGGTGG---G-------AGGAAGAGAAGAGTATG---A----------------------------------------GATAAA-AGTGATG------CGT---------TTTCTAT---TACT
droVir3	scaffold_12970:10151308-10151337 +	2	CTG--------GCGATGCTGTATTGATTTTTT-TTT----------------GCG--------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6473:11301064-11301096 -	2	TTG--------GCGATGCTGTATTGATTTTTT-TTA----------------TTTGCG-----------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_14853:6560969-6560993 +	2	CTG--------GCGATGCTGTATTGATTTTTT-T-----------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------CGGTGGTGGCTAGTGGGTGGGTTA----AAGAACTGC---CCCGCTCTTCACCATT-CGAAACTAAGTCCCCCACTTCGTCCGA--CC

Size

Hit Count

Total Norm

droSim1

TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------CGGTGGTGGCTATTGGGTGGGTGA----AAGAACTGC--CCCCGCTCTTCACCATT-CGAAACTAAGTCCCACACTTCGTCCGA--CC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................ATTGATTTTCT-T------------------------------------CGGTGC..................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................TTGAxTTTTT-T------------------------------------GGGTGGTGGC..............................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------CGGTGGTGGCTATTGGGTGGGTGA----AAGAACTGC--CCCCGCTCTTCACCATT-CGAAACTAAGTTCCACACTTCGTCTGA--CC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................GTGGTGGCxAGTGGGTGGG...................................................................	18	1	1.00	0.00	0.00	1.00
.........................................................................TGGTGGCGAxTGGGTGGGT..................................................................	18	1	1.00	0.00	1.00	0.00
.......................TGTTTTTTT-T------------------------------------CGGGGGTG................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------CGGTGGTGGCTAGTGGGTGGGTGA----TGGAACCGCACTCCCCCTTTTCATCATTCCGTAACTAAGTCCCACCCCTCGGC-----CC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................................................GTGGTGGCTAGTGGGTGGGT..................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................AGTGGGTGGGCGA----TGGAG.......................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................T------------------------------------GGGTGGTGGCTGGTGGGTGG....................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

TTG--------GCGATGCTGTATTGATTTTT---------------------------------------CGGTGGTGGCTAGTGGGTGGGTGA----TGGAACCGC--CCCCGCTCTTCACCATT-CGAAACTGAGTCCCACCCTTCGTC-----CC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........................................................................GTGGGTGGTGGGTGGGTGA----............................................................	19	1	13.00	0.00	0.00	0.00	13.00
...........................................................................GTGGGTGGTGGGTGGGTG.................................................................	18	2	3.00	0.00	0.00	0.00	3.00
...........................................................................GTGGAAAGTGGGTGGGTG.................................................................	18	1	4.00	0.00	0.00	0.00	4.00
............................................................................TGGGTGGTGGGTGGGTGA----............................................................	18	1	2.00	0.00	0.00	0.00	2.00
...........................................................................GTGGGTCGTGGGTGGGTG.................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................GTCGGTAGTGGGTGGGTG.................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................GGTGGTGGGTGGTGGGTG.....................................................................	18	3	0.33	0.00	0.00	0.00	0.33
..........................................................................GGTGGCTAGTGGGTGGGTGA----TGGAA.......................................................	25	1	1.00	0.00	0.00	0.00	1.00
TTA--------GCGATTCTGTATTGAT...................................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...........................................................................GTGGCTAGTGGGTGGGTGA----TGGAA.......................................................	24	1	1.00	0.00	0.00	0.00	1.00
........................................................................GTGGTGTGTAGTGGGTGGGT..................................................................	20	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................TACACCxTT-CGAAACTGAGT....................	19	1	1.00	0.00	0.00	0.00	1.00
........................GATTTTG---------------------------------------CGGTGGTGGCA.............................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droAna3

CCG----T---GCGATGCTGTATTGATTTTTT--------------------------------------CGGTGGTG-------GGTGGGTGTCCTCCGACTCTGTTA---CGGTCTCCACC-------------------CGGTTTC---GATACT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................GTTGGTG-------GGTGGGTGGCC..............................................................	18	1	130.00	0.00	130.00	0.00	0.00
.......................................................................GTGGGTG-------GGTGGGTGTCC..............................................................	18	3	23.00	0.33	22.67	0.00	0.00
........................GATTTTTT--------------------------------------GGGTGGTG-------GT.......................................................................	18	1	15.00	12.00	2.00	0.00	1.00
..............................TC--------------------------------------GGGTGGTG-------GGTGGGTG.................................................................	18	1	8.00	0.00	8.00	0.00	0.00
.......................................................................GGGGGTG-------GGTGGGTGGCC..............................................................	18	2	2.50	0.00	2.00	0.50	0.00
..............................TC--------------------------------------GGGTGGTG-------GGTGGGT..................................................................	17	1	3.00	0.00	0.00	3.00	0.00
.......................................................................GTTGGTG-------GGTGGGTGTCC..............................................................	18	1	3.00	0.00	3.00	0.00	0.00
.......................TGATTTTTT--------------------------------------GGGTGGTG-------GT.......................................................................	19	1	3.00	2.00	1.00	0.00	0.00
......................TTGATTTTGT--------------------------------------GGGTGGTG-------GG.......................................................................	20	1	2.00	2.00	0.00	0.00	0.00
......................TTGATTTTTT--------------------------------------GGGTGGTG-------GT.......................................................................	20	1	2.00	0.00	2.00	0.00	0.00
..............................TT--------------------------------------CGGTGGTG-------GGTGGGTGTCCT.............................................................	22	1	2.00	0.00	2.00	0.00	0.00
...............................T--------------------------------------CGGTGGTG-------GGTGGGTGTC...............................................................	19	1	2.00	0.00	2.00	0.00	0.00
..............................GT--------------------------------------GGGTGGTG-------GGTGGGTG.................................................................	18	1	2.00	0.00	2.00	0.00	0.00
.......................................................................GGTGGTG-------GGCGGGTGGCC..............................................................	18	1	1.00	0.00	0.00	1.00	0.00
.............................TTT--------------------------------------CGGTGGTG-------GGxGGGTGC................................................................	19	1	1.00	0.00	0.00	1.00	0.00
......................TTGATTTTGT--------------------------------------CGGTGGTG-------GT.......................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...............................T--------------------------------------CGGTGGTG-------GGTGGGTGTCAA.............................................................	21	1	1.00	0.00	1.00	0.00	0.00
..............................TT--------------------------------------CGGGGGTG-------GGTxGGTGTC...............................................................	19	1	1.00	0.00	0.00	1.00	0.00
........................GATTTTGT--------------------------------------GGGTGGTG-------GGT......................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................GTGGGTG-------GGTGGGTGTCCT.............................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................................ACC-------------------CGGGTTC---GATACC	16	1	1.00	0.00	0.00	1.00	0.00
.......................................................................GGTTGTG-------GGTGCGTGTCC..............................................................	18	1	1.00	0.00	0.00	0.00	1.00
........................GATTTTGT--------------------------------------CGGTGGTG-------GT.......................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....................CTTGATTTTTT--------------------------------------GGGTGGTG-------.........................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................T--------------------------------------GGGTGGTG-------GGTGGGTGG................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................................GTTGGTG-------GGTGGGTGTCG..............................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................GTGGGT-------GGTGGGTGTCC..............................................................	17	1	1.00	0.00	0.00	1.00	0.00
...............................T--------------------------------------CGGTGGTG-------GGTGGGTGTCA..............................................................	20	1	1.00	0.00	1.00	0.00	0.00
..............................GT--------------------------------------GGGTGGTG-------GGTGGGT..................................................................	17	1	1.00	0.00	0.00	1.00	0.00
..............................TT--------------------------------------CGGTGGTG-------GGTGGGTGTCC..............................................................	21	1	1.00	0.00	1.00	0.00	0.00
...............................T--------------------------------------CGGTGGTG-------GGTGGGTGTA...............................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................................GTTGGTG-------TGTGGGTGTCC..............................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................TTG--------------------------------------CGGTxGTG-------GGTGGGTG.................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.......................................................................GCTGGTG-------GGTGGGTGGCC..............................................................	18	1	1.00	0.00	1.00	0.00	0.00

dp4

TTTGCCGT--AGCGATGCTGTATTGATTTTTTCT------------------------------------CCGTGGTG-------GGTGGGTTC----GGGA-----TG---CGGTC------------AACCTGAGCCACACGCTTTC---------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................................................GTGGTG-------GGTGGGTTC----GGG.........................................................	18	1	5.00	5.00	0.00	0.00	0.00
.......................................................................CGTGGTG-------GGTGGGTTC----GGG.........................................................	19	1	2.00	1.00	0.00	1.00	0.00
......................................................................CCGTGGTG-------GGTGGGTTC----GGG.........................................................	20	1	1.00	0.00	0.00	1.00	0.00
...........................................................................GTG-------GGTGGGTGG----GGGA-----TG---..............................................	18	1	1.00	1.00	0.00	0.00	0.00
.......................................................................CGTGGTG-------GGTGGGTTC----GGGA-----TG---CA............................................	24	1	1.00	0.00	0.00	1.00	0.00

droPer1

TTTGCCGT--AGCGATGCTGTATTGATTTTTTCT------------------------------------CCGTGGTG-------GGTGGGTTC----GGGA-----TG---CGGTC------------AACCTGAGCCACACGCTTTC---------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................................................GTGGTG-------GGTGGGTTC----GGG.........................................................	18	1	6.00	6.00	0.00	0.00	0.00	0.00
..........................................................................GCTG-------GATGGGTTC----GGGA-----T..................................................	18	1	4.00	4.00	0.00	0.00	0.00	0.00
.......................................................................CGTGGTG-------GGTGGGTTC----GGG.........................................................	19	1	3.00	3.00	0.00	0.00	0.00	0.00
...........................................................................GTG-------GGTGGGTTC----GGGA-----TG---CGGTC------------.............................	23	1	2.00	2.00	0.00	0.00	0.00	0.00
........................................................................GTGGTG-------GGTGGGTTC----GGGA-----T..................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................GTG-------GGTGGGTTC----GGGA-----TG---CGGTA------------.............................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.......................................................................CGTGGTG-------GGTGGGTTC----GGGA-----T..................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................GGTG-------GGTGGGATC----GGGA-----T..................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................................................GTGGTG-------GGAGGGTTC----GGG.........................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

TTTGCTGTTTTGCGATGCTCTATTGATTTTTT-TTtTTTTtTTTTTTTTTTTTTTATATATGTATATATTTGGTGGTG-------GGAGGAA------GAGA-----AG-------------------------------------------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
............................TTTT-TTTTTTTTTTTTTTT..............................................................................................................	19	89	0.08	0.00	0.08	0.00	0.00
.................................ATTTTTTTTTTTTTTTTTTTTT.......................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
............................ATTT-TTTTTTTTTTTTTTTTTT...........................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
..........................ATTTTT-TTTTTTTTTTTTTTTT.............................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
.............................ATT-TTTTTTTTTTTTTTTTTTT..........................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
...............................A-TTTTTTTTTTTTTTTTTTTTT........................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
..............................AT-TTTTTTTTTTTTTTTTTTTT.........................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
...........................ATTTT-TTTTTTTTTTTTTTTTT............................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
.........................ATTTTTT-TTTTTTTTTTTTTTT..............................................................................................................	22	16	0.31	0.00	0.31	0.00	0.00
..................................TTTTTTTTTTTTTTTTTTT.........................................................................................................	19	89	0.04	0.00	0.00	0.04	0.00
...........................TTTTT-TTTTTTTTTTTTTTTTT............................................................................................................	22	58	0.07	0.00	0.00	0.07	0.00
..........................ATTTTT-TTTTTTTTTTTTTTT..............................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
...............................T-TTTTTTTTTTTTTTTTTTTTTT.......................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
.........................TTTTTTT-TTTTTTTTTTTTTTTT.............................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
.............................TTT-TTTTTTTTTTTTTTTTTTTT.........................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
............................ATTT-TTTTTTTTTTTTTTTTTTTTT........................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
.............................TTT-TTTTTTTTTTTTTTTTTT...........................................................................................................	21	68	0.04	0.00	0.00	0.00	0.04
..............................TT-TTTTTTTTTTTTTTTTTTTTT........................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
.........................ATTTTTT-TTTTTTTTTTTTTTTTTT...........................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
..................................ATTTTTTTTTTTTTTTTTTTT.......................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
.................................TTTTTTTTTTTTTTTTTTTTTTT......................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
...........................ATTTT-TTTTTTTTTTTTTTTT.............................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
...............................A-TTTTTTTTTTTTTTTTTTTT.........................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
.............................ATT-TTTTTTTTTTTTTTTTTTTTTT.......................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
...........................ATTTT-TTTTTTTTTTTTTTTTTTTT.........................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
..............................AT-TTTTTTTTTTTTTTTTTTT..........................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
.............................ATT-TTTTTTTTTTTTTTTTTT...........................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
.........................ATTTTTT-TTTTTTTTTTTTTT...............................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
.................................ATTTTTTTTTTTTTTTTTTTT........................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
..........................ATTTTT-TTTTTTTTTTTTTTTTTTT..........................................................................................................	25	10	0.30	0.00	0.30	0.00	0.00
...........................TTTTT-TTTTTTTTTTTTTTTTTT...........................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
............................ATTT-TTTTTTTTTTTTTTTTT............................................................................................................	21	19	0.16	0.00	0.16	0.00	0.00
............................TTTT-TTTTTTTTTTTTTTTTTTT..........................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
..........................TTTTTT-TTTTTTTTTTTTTTTTT............................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00
..................................TTTTTTTTTTTTTTTTTTTTTTT.....................................................................................................	23	51	0.06	0.00	0.06	0.00	0.00

droVir3

CTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------TTGCG-----------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.............AGTGCTGTATTGATTTTT...............................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

TTG--------GCGATGCTGTATTGATTTTTT-T------------------------------------TATTTGCG--------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CTG--------GCGATGCTGTATTGATTTTTT-T----------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

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