dme-mir-13b-2-as- 12- and 20-way alignments

dme-mir-13b-2-as	chrX:8985263-8985332 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 8985267-8985285
   star strand at position 8985312-8985331
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:8985248-8985347 -	AGGC------TG-GCTGTC-CAACAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGCTCACAGTCATTTTGACGCGTTAATAGAC---------AGCAGAGG---TAGA
droSim1	chrX_random:2632466-2632565 -	AGGC------TG-GCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGCTCACAGTCATTTTGACGCGTTGATAGAC---------AGCAGAGG---CAGA
droSec1	super_34:345603-345702 -	AGGC------TG-GCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGCTCACAGTCATTTTGACGCGTTGATAGAC---------AGCAGAGG---CAGG
droYak2	chrX:12330556-12330651 +	AG-----------ACTGGC-CAGCAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGCTCACAGTCATTTTGACGCGTTACTAGAC---------AGCAGGGG---TAAG
droEre2	scaffold_4690:6132295-6132393 +	GG-----------GCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGTTCACAGTCACTTTGACGCGCTAATAGAC---------AGCAGGGGGTTTAAA
droAna3	scaffold_13047:797463-797571 -	ACTT------TC-ACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGACA-TCAAAT----ACGCATAAGTCACAGTCATTTCGACGCGCTGGGAAACAGGTAATGAAGCAGAAG---CGGG
dp4	chrXL_group1e:7000785-7000885 +	GAGT------GGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAGA-TCAAAA----ACACATAGCTCACAGTCATTTTGACGCGTAAATGTGC---------AGCAGCAG---TAGC
droPer1	super_13:1553253-1553353 -	GAGT------GGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAGA-TCAAAA----ACACATAGCTCACAGTCATTTTGACGCGTAAATGTGC---------AGCAGCAG---TAGC
droWil1	scaffold_180777:2053070-2053171 -	TCGT----------ATGCC-CATCGAACTCGTCAAAATGGCTGTGATATGAATTTCTGACCGGTTAACATAGCTCACAGTCATTTTGACGCGACCATGGAC---------ATCAGTTG---TAAG
droVir3	scaffold_12970:9304321-9304422 -	TG-----------GCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATGGCAAATGCAACAACATAGCTCACAGTCATTTTGACGCGCCAATATGG---------AGCATTGG---CAGC
droMoj3	scaffold_6473:13342543-13342650 +	TTGCAGTTGGTG-GCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGATAATCTCAT----AAACATAGCTCACAGTCAATTTGACGCGCAAATATGG---------AGCATTAG---AGGA
droGri2	scaffold_15203:307003-307104 -	TG-----------GCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATTACAACTGCAACAACATAGCTCACAGTCAATTTGACGCGCCAATATGG---------AGCACTGA---TAGC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:8985248-8985347 -	NA	AGGCT-GGCTGTC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-A--GG-----------TAGA
droSim1	chrX_random:2632466-2632565 -	15	AGGCT-GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAG-A--GG-----------CAGA
droSec1	super_34:345603-345702 -	15	AGGCT-GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAG-A--GG-----------CAGG
droYak2	chrX:12330556-12330651 +	11	A-----GACTGGC-CAGCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-ACTAGACAGCAG-G--GG-----------TAAG
droEre2	scaffold_4690:6132295-6132393 +	4	G-----GGCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGTTCACAGTCACTTTGACGCGCT-AATAGACAGCAG-G--GG------GT--TTAAA
droEug1	scf7180000409631:397666-397764 -	11	ATG-T-GCCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCAACATAGCTCACAGTCATTTTAACGCGTT-AATAGACAGCAA-A--GG-----------TAAG
droBia1	scf7180000301760:4584589-4584685 -	14	ATGC--GCATGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAG-G-TTAA----ATGCACATAGCTCACAGTCATTTTGACGCGCT-GATAGACAGCAG-A--AG-----------TA--
droTak1	scf7180000415169:933669-933769 +	6	AATGC-GACTGGC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-G--GT----------ATAAA
droEle1	scf7180000491006:2500509-2500618 -	9	ATG-T-GCCTGCC-CACCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGTTCACAGTCATTTTGACGCGTT-AATAGACAGCAG-T--AGCAGAGGCATAAGAGA
droRho1	scf7180000779841:510723-510819 -	13	T-----GCCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATTTTGACGCGTT-AATAGACAGCAA-A--GC-----------TGAA
droFic1	scf7180000453829:954200-954296 -	9	A-----GGCTGTC-CGCCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAA----ATCCACATAGCTCACAGTCATCTTGACGCTTT-GAAAGACAGCAG-A--TG----------ATGGA
droKik1	scf7180000301542:45346-45455 -	15	ATG-A-GTCTGTC-CATCAAACTCGTCAAAATGGCTGTGATATGAA-G-TCAAAT---TCAACATAGCTCACAGTCATTTTGACGCGTT-GATAGACAGCAA-A--GC-ACAGGTGGAGGAGA
droAna3	scaffold_13047:797460-797571 -	12	ACTTT-CACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGAC-A-TCAA----ATACGCATAAGTCACAGTCATTTCGACGCGCT-GGGAAACAGGTAATGAAGCAGAAGCG--GGACA
droBip1	scf7180000396431:582372-582471 -	6	GTTAT-GACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGGC-A-TCAA----ATACGCATAAGTCACAGTCATTTCGACGCGTT-GGGAAACAGCAA-G--AT-----------TAGC
dp4	chrXL_group1e:7000785-7000885 +	4	GAGTGGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAG-A-TCAA----AAACACATAGCTCACAGTCATTTTGACGCGTA-AATGTGCAGCAG-C--AG-----------TAGC
droPer1	super_13:1553253-1553353 -	11	GAGTGGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAG-A-TCAA----AAACACATAGCTCACAGTCATTTTGACGCGTA-AATGTGCAGCAG-C--AG-----------TAGC
droWil1	scaffold_181089:4662175-4662263 +	3	CTGCC-TTCAGCT----CCAATTC-----AA-----TGTTGAGCAA-G-GCAA----TCTTGCACTTCTCATAGGCTTTGGGGGCCATCTCAAAGCCAGCAT-A--GG-----------AAAA
droVir3	scaffold_12970:9304312-9304422 -	13	T-----GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATG-GCAAATGCAACAACATAGCTCACAGTCATTTTGACGCGCC-AATATGGAGCAT-T--GGCAGCAGCG--AGAGA
droMoj3	scaffold_6473:13342549-13342650 +	2	TTGGT-GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAT-AATCTC----ATAAACATAGCTCACAGTCAATTTGACGCGCA-AATATGGAGCAT-T--AG-----------AGGA
droGri2	scaffold_15203:306998-307104 -	11	T-----GGCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATT-ACAACTGCAACAACATAGCTCACAGTCAATTTGACGCGCC-AATATGGAGCAC-T--GATAGC------AACGA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AGGC------TG-GCTGTC-CAACAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGCTCACAGTCATTTTGACGCGTTAATAGAC---------AGCAGAGG---TAGA

Size

Hit Count

Total Norm

droSim1

AGGC------TG-GCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGCTCACAGTCATTTTGACGCGTTGATAGAC---------AGCAGAGG---CAGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................CAAACTCGTCAAATCGGC....................................................................................	18	3	4.67	0.00	0.00	1.00	3.67
...........................................................................ACAGACATTTTGACGAGT................................	18	7	1.14	1.14	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGACGCGT................................	18	7	0.86	0.86	0.00	0.00	0.00
.......................................................................TATCACAGTCATTTTGACG...................................	19	7	0.57	0.00	0.57	0.00	0.00
.......................................................................GATCACAGCCATTTTGACGCGT................................	22	5	0.60	0.60	0.00	0.00	0.00
.......................................................................TCTCACAGCCATTTTGACGCGT................................	22	5	0.60	0.60	0.00	0.00	0.00
.......................................................................TATCACAGTCATTTTGACGCGTT...............................	23	5	0.40	0.40	0.00	0.00	0.00
.....................AACAAACTCGTCAAAAAG......................................................................................	18	2	1.00	0.00	0.00	0.00	1.00
.....................AACAAACTCGTCAAAATGGCTGG.................................................................................	23	2	0.50	0.00	0.00	0.50	0.00
.......................................................................GATCACAGCCATTTTGACGCG.................................	21	5	0.20	0.20	0.00	0.00	0.00
......................AAAAACTCGTCCAAATGG.....................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
...........................................................................ACAGCCATTTTGACGCGTT...............................	19	7	0.14	0.14	0.00	0.00	0.00
........................................................................ATCACAGTCATTTTGACGAGT................................	21	7	0.14	0.14	0.00	0.00	0.00
...........................................................................ACAGACATTTTGACGAGTT...............................	19	7	0.14	0.14	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGACGTGT................................	18	7	0.14	0.14	0.00	0.00	0.00
.......................................................................TATCACAGTCATTTTGACGCGT................................	22	5	0.20	0.20	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGACGGGT................................	18	7	0.14	0.14	0.00	0.00	0.00
..............................................................................GTCATTTTGxCGCGTGGATA...........................	19	2	0.50	0.00	0.00	0.50	0.00
.......................................................................TCTCACAGCCATTTTGACGCGTT...............................	23	5	0.20	0.20	0.00	0.00	0.00
.......................................................................GATCACAGTCATTTTGACGAGTT...............................	23	5	0.20	0.20	0.00	0.00	0.00
.......................................................................TCTCACAGACATTTTGACGCGT................................	22	2	0.50	0.50	0.00	0.00	0.00
.......................................................................GGTCACAGTCATTTTGACGAGT................................	22	2	0.50	0.50	0.00	0.00	0.00
.................CG-CAACAAACTCGTCAAAAAG......................................................................................	21	2	0.50	0.00	0.50	0.00	0.00
.......................................................................GATCACAGTCATTTTGACGAGT................................	22	5	0.20	0.20	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGATGCGTT...............................	19	7	0.14	0.14	0.00	0.00	0.00

droSec1

AGGC------TG-GCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGCTCACAGTCATTTTGACGCGTTGATAGAC---------AGCAGAGG---CAGG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................CAAACTCGTCAAATCGGC....................................................................................	18	3	1.00	0.00	1.00	0.00
...........................................................................ACAGCCATTTTGACGGGT................................	18	7	0.43	0.00	0.00	0.43
...........................................................................ACAGTCATTTTGACGAGT................................	18	7	0.29	0.00	0.14	0.14
........................................................................CTCACAGCCATTTTGACGAGT................................	21	7	0.29	0.00	0.29	0.00
.......................................................................TCTCACAGCCATTTTGACGCGT................................	22	5	0.20	0.00	0.00	0.20
...........................................................................ACAGCCATTTTGACGGGTT...............................	19	7	0.14	0.00	0.14	0.00
...........................................................................ACAGCCATTTTGACGTGTT...............................	19	7	0.14	0.00	0.00	0.14
...........................................................................ACAGTCATTTTGACGAGTT...............................	19	7	0.14	0.00	0.14	0.00
.........................................................................TCACAGCCATTTTGACGTGT................................	20	7	0.14	0.00	0.00	0.14
...........................................................................ACAGCCATTTTGACGCGTT...............................	19	7	0.14	0.00	0.14	0.00
.......................................................................GCTCACAGCCATTTTGACGAGTT...............................	23	5	0.20	0.00	0.00	0.20
...........................................................................ACAGCCATTTTGACGAGTTG..............................	20	7	0.14	0.00	0.14	0.00
...........................................................................ACAGACATTTTGACGAGT................................	18	7	0.14	0.00	0.00	0.14
...........................................................................ACAGCCATTTTGACGCGT................................	18	7	0.14	0.00	0.00	0.14

droYak2

AG-----------ACTGGC-CAGCAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGCTCACAGTCATTTTGACGCGTTACTAGAC---------AGCAGGGG---TAAG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................ACAGCCATTTTGACGCGTT...............................	19	7	1.43	0.29	0.00	0.00	1.14	0.00
...........................................................................ACAGCCATTTTGACGCGT................................	18	7	1.29	0.00	0.00	0.00	1.29	0.00
...........................................................................ACAGCCATTTTGACGAGTTA..............................	20	7	1.00	0.71	0.14	0.00	0.14	0.00
.......................................................................TCTCACAGCCATTTTGACGCGT................................	22	5	1.20	0.60	0.20	0.00	0.40	0.00
.......................................................................TATCACAGTCATTTTGACGCGT................................	22	5	1.20	0.40	0.00	0.00	0.80	0.00
.......................................................................TCTCACAGCCATTTTGACGCGTT...............................	23	5	1.20	0.20	0.00	0.00	1.00	0.00
.......................................................................TATCACAGTCATTTTGACGCGTT...............................	23	5	0.80	0.40	0.00	0.00	0.40	0.00
...........................................................................ACAGACATTTTGACGAGTT...............................	19	7	0.43	0.14	0.00	0.00	0.29	0.00
.......................................................................TCTCACAGTCATTTTGACGAGT................................	22	5	0.40	0.00	0.00	0.00	0.40	0.00
............................................................................CAGCCATTTTGACGAGTTA..............................	19	7	0.29	0.29	0.00	0.00	0.00	0.00
.......................................................................GCTCACAGCCATTTTGACGAGT................................	22	5	0.40	0.40	0.00	0.00	0.00	0.00
...........................................................................ACAGACATTTTGACGAGT................................	18	7	0.29	0.29	0.00	0.00	0.00	0.00
.........................................................................TCACAGCCATTTTGACGAGTTA..............................	22	7	0.29	0.29	0.00	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGATGCGTT...............................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
...........................................................................ACAGGCATTTTGACGAGT................................	18	7	0.14	0.14	0.00	0.00	0.00	0.00
.......................................................................GCTCACAGCCATTTTGACGAGTT...............................	23	5	0.20	0.00	0.20	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGACGTGT................................	18	7	0.14	0.00	0.00	0.00	0.14	0.00
.......................................................................AATCACAGTCATTTTGACGCGT................................	22	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................ACAGACATTTTGACGCGT................................	18	5	0.20	0.00	0.00	0.00	0.20	0.00
.......................................................................GATCACAGCCATTTTGACGCGT................................	22	5	0.20	0.20	0.00	0.00	0.00	0.00
.......................................................................GATCACAGCCATTTTGACGCGTT...............................	23	5	0.20	0.00	0.00	0.00	0.20	0.00
.......................................................................GATCACAGTCATTTTGACGTGT................................	22	2	0.50	0.50	0.00	0.00	0.00	0.00
.........................................................................TCACAGCCCTTTTGACGCGT................................	20	5	0.20	0.00	0.00	0.00	0.20	0.00
..........................................................................CACAGCCATTTTGACGCGT................................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
...........................................................................ACAGCCATTTTGACGCAT................................	18	5	0.20	0.00	0.00	0.00	0.20	0.00
...........................................................................ACAGCCATTTTGCCGCGT................................	18	5	0.20	0.00	0.00	0.00	0.20	0.00
...........................................................................ACAGTCATTTTGATGAGTT...............................	19	7	0.14	0.14	0.00	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGACGGGTT...............................	19	7	0.14	0.14	0.00	0.00	0.00	0.00
...........................................................................ACAGTCATTTTGACGCGC................................	18	2	0.50	0.50	0.00	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGACGCCT................................	18	5	0.20	0.00	0.00	0.00	0.20	0.00
...........................................................................ACAGCCATTTTGACGGG.................................	17	7	0.14	0.00	0.00	0.00	0.14	0.00
........................................................................ATCACAGCCATTTTGACGCGTT...............................	22	7	0.14	0.00	0.00	0.00	0.14	0.00
.......................................................................TCTCACAGTAATTTTGACGCGT................................	22	2	0.50	0.50	0.00	0.00	0.00	0.00
...........................................................................ACAGTCATTTTGACGAGTT...............................	19	7	0.14	0.14	0.00	0.00	0.00	0.00
.............................................................................AGCCATTTTGACGAGTTA..............................	18	7	0.14	0.14	0.00	0.00	0.00	0.00
.......................................................................TATCACAGTCATTTTGACG...................................	19	7	0.14	0.00	0.14	0.00	0.00	0.00
...............................................................................................CTAGAC---------AGCGGGGG---AA..	16	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

GG-----------GCTGCC-CAACAAACTCGTCAAAATGGCTGTGATATGAAG-TCAAAT----CCACATAGTTCACAGTCACTTTGACGCGCTAATAGAC---------AGCAGGGGGTTTAAA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

ACTT------TC-ACTGTC-CACCAAACTCGTCAAAATGGCTGTGATATGACA-TCAAAT----ACGCATAAGTCACAGTCATTTCGACGCGCTGGGAAACAGGTAATGAAGCAGAAG---CGGG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................ACAGCCATTTCGACGAGC................................	18	5	0.40	0.00	0.00	0.00	0.40
....................................ATGGxTGTGACATGACA-T......................................................................	17	2	0.50	0.00	0.00	0.50	0.00

dp4

GAGT------GGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAGA-TCAAAA----ACACATAGCTCACAGTCATTTTGACGCGTAAATGTGC---------AGCAGCAG---TAGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........................................................................ACAGACATTTTGACGAGT................................	18	7	1.29	0.00	1.00	0.29	0.00
.......................................................................TCTCACAGCCATTTTGACGCGT................................	22	5	1.00	0.00	0.80	0.20	0.00
...........................................................................ACAGCCATTTTGACGCGT................................	18	7	0.57	0.00	0.43	0.14	0.00
...........................................................................ACAGCCATTTTGACGCGTT...............................	19	7	0.57	0.14	0.29	0.14	0.00
.......................................................................TATCACAGTCATTTTGACGCGT................................	22	5	0.80	0.00	0.40	0.40	0.00
.......................................................................GATCACAGCCATTTTGACGCGT................................	22	5	0.60	0.00	0.00	0.60	0.00
...........................................................................ACAGTCATTTTGACGAGT................................	18	7	0.29	0.00	0.29	0.00	0.00
...........................................................................ACAGCCATTTTGACGTGT................................	18	7	0.29	0.00	0.14	0.14	0.00
.......................................................................GGTCACAGTCATTTTGACGGGT................................	22	2	0.50	0.00	0.50	0.00	0.00
...........................................................................ACAGGCATTTTGACGTGT................................	18	5	0.20	0.00	0.20	0.00	0.00
...........................................................................ACAGCCATTTTGCCGCGT................................	18	5	0.20	0.00	0.20	0.00	0.00
...........................................................................ACAGCCATTTTGACGGGT................................	18	7	0.14	0.00	0.00	0.14	0.00
.........................................................................TCACAGCCATTTTGACGCGTT...............................	21	7	0.14	0.00	0.14	0.00	0.00
...........................................................................ACAGTCATTTTGATGGGT................................	18	4	0.25	0.00	0.25	0.00	0.00
...........................................................................ACAGCCATTTTGACCCGT................................	18	5	0.20	0.00	0.00	0.20	0.00
...........................................................................ACAGCCATTTTGACGAGTAA..............................	20	5	0.20	0.00	0.20	0.00	0.00
..........................................................................CACAGCCATTTTGACGCGTT...............................	20	7	0.14	0.00	0.14	0.00	0.00
...........................................................................ACAGGCATTTTGACGAGT................................	18	7	0.14	0.00	0.14	0.00	0.00
...........................................................................ACAGCCATTTTGTCGCGT................................	18	5	0.20	0.00	0.20	0.00	0.00
...........................................................................ACAGTTATTTTGACGAGT................................	18	5	0.20	0.00	0.20	0.00	0.00
...........................................................................ACAGACATTTTGAAGCGT................................	18	2	0.50	0.00	0.00	0.50	0.00
...........................................................................ACAGTCATTTTGACGAGG................................	18	5	0.20	0.00	0.20	0.00	0.00

droPer1

GAGT------GGGACTGCA-CATCAAACTCGTCAAAATGGCTGTGATATGAGA-TCAAAA----ACACATAGCTCACAGTCATTTTGACGCGTAAATGTGC---------AGCAGCAG---TAGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................................TATCACAGTCATTTTGACGCGT................................	22	5	1.40	0.00	0.20	0.00	1.20	0.00
...........................................................................ACAGCCATTTTGACGCGT................................	18	7	0.86	0.00	0.14	0.14	0.57	0.00
.......................................................................TCTCACAGCCATTTTGACGCGT................................	22	5	1.00	0.00	0.00	0.00	1.00	0.00
...........................................................................ACAGACATTTTGACGAGT................................	18	7	0.43	0.00	0.14	0.29	0.00	0.00
...........................................................................ACAGCCATTTTGACGTGT................................	18	7	0.43	0.00	0.00	0.00	0.43	0.00
...........................................................................ACAGCCATTTTGACGCGTT...............................	19	7	0.43	0.00	0.00	0.00	0.43	0.00
...........................................................................ACAGCCATTTTGACGGGT................................	18	7	0.14	0.00	0.14	0.00	0.00	0.00
.....................................................................TAGCTCACAGTCATTTTGACGCG.................................	23	2	0.50	0.00	0.00	0.00	0.50	0.00
..........................................................AA----ACACAGAGCTCACAGTA............................................	19	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................ACAGGCATTTTGACGCGTT...............................	19	5	0.20	0.00	0.00	0.00	0.20	0.00
........................................................................ATCACAGCCATTTTGACGCGT................................	21	7	0.14	0.00	0.00	0.00	0.14	0.00
..........................................................................CACAGCCATTTTGACGCGTT...............................	20	7	0.14	0.00	0.00	0.00	0.14	0.00
.......................................................................GCTCACCGTCATTTTGACGAGT................................	22	2	0.50	0.00	0.50	0.00	0.00	0.00
.......................................................................TATCACAGTCATTTTGACGCG.................................	21	5	0.20	0.00	0.00	0.00	0.20	0.00
...........................................................................CCAGTCATTTTGACGCCT................................	18	2	0.50	0.00	0.00	0.50	0.00	0.00
.......................................................................GATCACAGCCATTTTGACGCGT................................	22	5	0.20	0.00	0.00	0.00	0.20	0.00
...........................................................................ACAGCCATTTTGACGAGTA...............................	19	7	0.14	0.00	0.00	0.00	0.14	0.00

droWil1

TCGT----------ATGCC-CATCGAACTCGTCAAAATGGCTGTGATATGAATTTCTGACCGGTTAACATAGCTCACAGTCATTTTGACGCGACCATGGAC---------ATCAGTTG---TAAG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................................................................ACAGTCATTTTGACGAGT................................	18	7	0.43	0.00	0.14	0.14	0.14
.......................................................................TCTCACAGCCATTTTGACG...................................	19	7	0.29	0.00	0.00	0.29	0.00
.......................................................................GATCACAGCCATTTTGACG...................................	19	7	0.29	0.00	0.00	0.29	0.00
..........................................................................CACAGCCATTTTGACGAGA................................	19	7	0.29	0.00	0.00	0.29	0.00
.......................CGxAGTCGTCAAAATGGCT...................................................................................	18	2	0.50	0.00	0.00	0.50	0.00
..........................................................................CACAGCCATTTTGACGCG.................................	18	7	0.14	0.00	0.00	0.14	0.00
.......................................................................TATCACAGTCATTTTGACG...................................	19	7	0.14	0.00	0.00	0.14	0.00
..........................................................................................CGACCATGGAC---------ATCAGTTG---T...	20	2	0.50	0.00	0.00	0.50	0.00

droVir3

TG-----------GCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATGGCAAATGCAACAACATAGCTCACAGTCATTTTGACGCGCCAATATGG---------AGCATTGG---CAGC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...........................................................................ACAGCCATTTTGACGAGC................................	18	7	1.57	0.14	1.29	0.14	0.00	0.00
...........................................................................ACAGCCATTTTGACGCGT................................	18	7	0.43	0.00	0.43	0.00	0.00	0.00
.......................................................................GCTCACAGCCATTTTGACGAGCC...............................	23	2	0.50	0.00	0.00	0.50	0.00	0.00
...........................................................................ACAGTCATTTTGACGAGT................................	18	7	0.14	0.00	0.14	0.00	0.00	0.00
.......................................................................TATCACAGTCATTTTGACG...................................	19	7	0.14	0.00	0.14	0.00	0.00	0.00
...........................................................................ACAGACATTTTGACGAGC................................	18	5	0.20	0.00	0.20	0.00	0.00	0.00

droMoj3

TTGCAGTTGGTG-GCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGATAATCTCAT----AAACATAGCTCACAGTCAATTTGACGCGCAAATATGG---------AGCATTAG---AGGA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.................................AAGATGTCTGTGATATGAT.........................................................................	19	3	26.00	24.67	0.67	0.67	0.00
.................................AAGATGTCTGTGATATGATA........................................................................	20	3	8.33	7.67	0.33	0.33	0.00
..................................AGATGTCTGTGATATGATA........................................................................	19	3	0.67	0.67	0.00	0.00	0.00
...........................................................................ACAGCCATTTTGACGCGC................................	18	5	0.20	0.00	0.00	0.20	0.00
................................CAAGATGTCTGTGATATGATA........................................................................	21	3	0.33	0.33	0.00	0.00	0.00
...................................GATGTCTGTGATATGATA........................................................................	18	3	0.33	0.33	0.00	0.00	0.00

droGri2

TG-----------GCTGCCACATCAAACTCGTCAAAATGGCTGTGATATGAATTACAACTGCAACAACATAGCTCACAGTCAATTTGACGCGCCAATATGG---------AGCACTGA---TAGC

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