dme-mir-965- 12- and 20-way alignments

dme-mir-965	chr2L:243035-243141 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 243055-243076
   star strand at position 243096-243118
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:243020-243156 -	TAATTGTACAATC--TGG---ACAATAT--TG--CTCAACA-TTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCTG-TGATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTATTGCAACGA------AAA---GTGTTTTTC
droSim1	chr2L:248245-248381 -	TACTTGTACAATC--TGG---ACAAAAT--TG--CTCAACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTG-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA------AAA---GTGGTTTTC
droSec1	super_14:240987-241123 -	TACTTGTACAATC--TGG---ACAAAAT--TG--CTCAACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTG-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA------AAA---GTGGTTTTC
droYak2	chr2L:236040-236180 -	TAATTGTACAATCACCATCTGACAAAAT--TG--CTCAACA-TTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTT-T-GTAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAACAGCAACAA------ATA---GTGTATTTC
droEre2	scaffold_4929:289337-289472 -	TACTTGTAGAACC--TG----ACAAAAT--TG--CTCAACA-TTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCTG-TAAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGCAACAGCAACAA------AAA---GTGAATCTT
droAna3	scaffold_12943:4147953-4148086 +	GGGTTT-TCTG------G---A--------AG--CTCAACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCTT-AGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGTCAACAAATCTCAACTAAAGTG--TTTT
dp4	chr4_group1:4362150-4362279 +	A--TTTCCCCATC-----------------TG--CTCAAAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATT-CGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAA-TCGCAACA---ACAATTCTA
droPer1	super_5:848161-848290 -	A--TTTCCCCATC-----------------TG--CTCAAAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATT-CGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAA-TCGCAACA---ACAATTCTA
droWil1	scaffold_180764:130089-130225 -	AAATTAAAGAATC--A--------ATTC--TA--CACAACA--TTTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGTTAAATCAACAA-TGTAAACA---ATTATTTTG
droVir3	scaffold_12963:8856390-8856513 +	TAG-TGTAGAAAA--AGA---AAAA-AACACACACACAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAATG-A-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGTGACGACAACA----------------------
droMoj3	scaffold_6500:2474485-2474605 -	AATGTGAACAA---------------AA--CA--CTCAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGTAAACA-A-TGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGGAATCAACA-------------GCAA-TTTA
droGri2	Unknown	G----------------G---AAAATAA--CA--CTCAAAT-GTTTAGGGGGTCAAACTGTACGTTATATGTGTAAATG-A-AGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGATAGCAACAA------AAA---GTC-----T

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:243020-243156 -	NA	TAATTGTACA------ATCTG------------------------------------GACA------ATATTGCTCAAC-ATTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCT-GTGATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTATTGCAACGA---------AAA----------GTGT--------------TTTT---------C
droSim1	chr2L:248245-248381 -	1	TACTTGTACA------ATCTG------------------------------------GACA------AAATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCT-GTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA---------AAA----------GTGG--------------TTTT---------C
droSec1	super_14:240987-241123 -	1	TACTTGTACA------ATCTG------------------------------------GACA------AAATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCT-GTGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA---------AAA----------GTGG--------------TTTT---------C
droYak2	chr2L:236040-236180 -	1	TAATTGTACAATCACCATC-------------------------------------TGACA------AAATTGCTCAAC-ATTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTTT-GT-AAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAACAGCAACAA---------ATA----------GTGT--------------ATTT---------C
droEre2	scaffold_4929:289337-289472 -	1	TACTTGTAGA------ACC-------------------------------------TGACA------AAATTGCTCAAC-ATTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCT-GTAAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGCAACAGCAACAA---------AAA----------GTGA--------------ATCT---------T
droEug1	scf7180000409461:574432-574571 +	2	TAATTTTTTT--GAGAACC-------------------------------------TGACA------ATATTGCTCAAC-ATTTTAGGGGGTTAAACTGTACGTTATATGTGCTATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAAAGCAACAGCAGCAA---------AAA----------GTGT--------------TTTT---------A
droBia1	scf7180000301547:14040-14201 +	1	CACTTGTGCC------ATC---------------------------------------ACG------ATATTGCCCGAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAGAAGTTGGTGCAACAGCAACGACCGT-GTGA---TAAATTGTAG----GAGTA------TATGTTCTTTTATGATC
droTak1	scf7180000413017:293129-293264 +	1	TACTTTTACA------ATC-------------------------------------TGACA------ATATTGCTTAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAAAAGCAACAG---------AAA----------GTAT--------------GATT---------A
droEle1	scf7180000490454:128315-128470 +	2	TAGTTTTACA------ACC-------------------------------------TGACA------ATATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTATATGTGCCATTCT-ATAAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAACAGCAACAA---------AAATAAATTGTAA----GAGTAAAACAATGCGTTC---------T
droRho1	scf7180000779252:273002-273136 -	3	TCCTTTTACA------ACC-------------------------------------TGAGA------ATATTGCTCAAC-ATTTTGGGGGGTGAAACTGTACGTTGTATGTGTCATTCT-TTAAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAATGCAACAGCAACAA---------AAA----------GGA---------------TGAT---------A
droFic1	scf7180000453904:509771-509921 -	2	ACGGTGTAAA------AGC-------------------------------------CAAAG-ATT--TTATTGCTCAAC-ATTTTGAGGGGTGAAACTGTACGTTGTATGTGCCCTATT-ATAAAAACCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGCAACACCAACAA---------AAA----------GTGACCGATAAATAAT--CTCT---------A
droKik1	scf7180000302401:552944-553112 -	1	TAGTC---CA------AAT-TGCAGCTAATGTGTTATGATATATAAATAGAATGAATAATA------TTATTGCTCATC-ATTTTGGGGGGTCAAACTGTACGTTATATGTGCCAATCT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGCAACAACAACGA---------AAA--------A-GTGT--------------A-AT---------A
droAna3	scaffold_12943:4147952-4148086 +	1	TGGGTTTTCT----------G------------------------------------GA------------AGCTCAACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCT-TAGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGTCAACAAATCTCAACTAAA----------GTGT----------------TT---------T
droBip1	scf7180000395973:371238-371378 +	1	ATACTATATA------GTCTA-------------------------GTAGTATTAATGACA------ATATTGCTCAAC-CATTTGGGGGGTCAAACTGTACGTTGTATGTGCCAAACT-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGCCAGCAA----------------------------------------TTGT---------C
dp4	chr4_group1:4362148-4362281 +	3	TCATTTCCCC------ATC----------------------------------------------------TGCTCAAA-AATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATAT-TCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGC-AACA---ACAATTCTA----------------------G---------C
droPer1	super_5:848159-848292 -	3	TCATTTCCCC------ATC----------------------------------------------------TGCTCAAA-AATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATAT-TCGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAATCGC-AACA---ACAATTCTA----------------------G---------C
droWil1	scaffold_180764:130106-130233 -	3	TATGT--AATA--AA-TT----------------------------------------AAAGAATCAATTCTACACAAC-AT-TTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGTTAAATCAACAA------------------------------------------------------
droVir3	scaffold_12963:8856389-8856513 +	8	TTAGTGTAGA------AAA-------------------------------------AGAAAAAAAC--ACACACACAAA-TGTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAAT-G-ATGAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGTGACGACAAC--------------------------------------------------------
droMoj3	scaffold_6500:2474475-2474605 -	3	AATGTGAACA------A----------------------------------------------------AACACTCAAA-TGTTTAGGGGGTCAAACTGTACGTTGTATGTGTAA-ACA-ATGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGGAATCAACAG---------CAA----TTTAA-GCAT--------------AGCT---------A
droGri2	scaffold_15252:12933990-12934109 -	5	G--------------------------------------------------------GAAA------ATAACACTCAAA-TGTTTAGGGGGTCAAACTGTACGTTATATGTGTAAAT-G-AAGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGATAGCAACCT---------AAA----------AAG----------------TCT---------T

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TAATTGTACAATC--TGG---ACAATAT--TG--CTCAACA-TTTTGGGGGGTAAAACTGTACGTTATATGTGCCCTTCTG-TGATATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTATTGCAACGA------AAA---GTGTTTTTC

Size

Hit Count

Total Norm

droSim1

TACTTGTACAATC--TGG---ACAAAAT--TG--CTCAACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTG-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA------AAA---GTGGTTTTC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................GGGGTGAAACTGTACGTTATATG......................................................................................	23	1	929.00	364.00	253.00	46.00	266.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	355.00	263.00	11.00	74.00	7.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	262.00	25.00	181.00	32.00	24.00
................................................GGGGTGAAACTGTACGTTATA........................................................................................	21	1	38.00	15.00	10.00	2.00	11.00
................................................GGGGTGAAACTGTACGTTATAT.......................................................................................	22	1	34.00	18.00	6.00	3.00	7.00
...........................................................................................TAATCGTATAGCTTTTCCCCT.............................................	21	1	25.00	0.00	19.00	1.00	5.00
...........................................................................................TAAGCGTATAGCTTTTCCCCC.............................................	21	1	24.00	0.00	22.00	2.00	0.00
...........................................................................................TAACCGTATAGCTTTTCCCCT.............................................	21	1	21.00	0.00	19.00	0.00	2.00
.....................................................GAAACTGTACGTTATATG......................................................................................	18	1	16.00	0.00	4.00	2.00	10.00
.......................................................................TGCCCTTCTG-TGAAATTC...................................................................	18	1	14.00	0.00	9.00	0.00	5.00
.......................................................................TGCCCTTCTG-TGAAATTCA..................................................................	19	1	12.00	2.00	4.00	0.00	6.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	11.00	0.00	6.00	5.00	0.00
................................................GGGGTGAAACTGTACGTTATATT......................................................................................	23	1	9.00	8.00	0.00	0.00	1.00
...........................................................................................TAATCGTATAGCTTTTCCCCTT............................................	22	1	9.00	0.00	6.00	0.00	3.00
...............................................GGGGGTGAAACTGTACGTTATATG......................................................................................	24	1	7.00	2.00	1.00	0.00	4.00
................................................GGGGAGAAACTGTACGTTATATG......................................................................................	23	1	7.00	6.00	0.00	0.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	6.00	6.00	0.00	0.00	0.00
....................................................TGAAACTGTACGTTATATG......................................................................................	19	1	6.00	0.00	2.00	1.00	3.00
.................................................GGGTGAAACTGTACGTTATATG......................................................................................	22	1	6.00	0.00	0.00	0.00	6.00
................................................GGGGGGAAACTGTACGTTATATG......................................................................................	23	1	5.00	3.00	0.00	0.00	2.00
...........................................................................................TAAGCGTATAGCTTTTCCCCG.............................................	21	1	5.00	0.00	4.00	1.00	0.00
................................................GGGGTGAAACTGTACGTTATATGA.....................................................................................	24	1	5.00	3.00	1.00	0.00	1.00
................................................GGGGTGAAACTGTACGCTATATG......................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
................................................GGGGTGAAACTGTACGTTCTATG......................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
................................................GGGGTGAAACTGTACGTTATCTG......................................................................................	23	1	4.00	4.00	0.00	0.00	0.00
...........................................................................................TAAGCGGATAGCTTTTCCCCTT............................................	22	1	4.00	3.00	0.00	1.00	0.00
...........................................................................................TAATCGTATAGCTTTTCCCCC.............................................	21	1	3.00	0.00	3.00	0.00	0.00
................................................GGGGTGAAACTGTACGTTTTATG......................................................................................	23	1	3.00	3.00	0.00	0.00	0.00
...........................................................................................................TCCCTTAAAAGTTGGAGC................................	18	1	3.00	0.00	0.00	3.00	0.00
................................................GGTGTGAAACTGTACGTTATATG......................................................................................	23	1	3.00	0.00	2.00	0.00	1.00
................................................GGGGTGAAACTGTACGTTA..........................................................................................	19	1	3.00	2.00	0.00	0.00	1.00
...........................................................................................TAAGTGTATAGCTTTTCCCCT.............................................	21	1	3.00	0.00	3.00	0.00	0.00
...........................................................................................TAAGAGTATAGCTTTTCCCCTT............................................	22	1	3.00	3.00	0.00	0.00	0.00

droSec1

TACTTGTACAATC--TGG---ACAAAAT--TG--CTCAACA-TTTTGGGGGGTGAAACTGTACGTTATATGTGCCCTTCTG-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTAGAGCTACTGCAACGA------AAA---GTGGTTTTC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................GGGGTGAAACTGTACGTTATATG......................................................................................	23	1	892.00	99.00	485.00	308.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	855.00	138.00	385.00	332.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	213.00	25.00	49.00	139.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	47.00	7.00	16.00	24.00
...........................................................................................TAAGCGTATAGCTTTTCCCTTT............................................	22	1	28.00	0.00	27.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	21.00	0.00	7.00	14.00
................................................GGGGTGAAACTGTACGTTATAT.......................................................................................	22	1	18.00	2.00	11.00	5.00
............................................................................................AAGCGTATAGCTTTTCCCCTT............................................	21	1	9.00	0.00	2.00	7.00
...........................................................................................TAAGCGTATAGTTTTTCCCCTT............................................	22	1	6.00	0.00	6.00	0.00
...............................................GGGGGTGAAACTGTACGTTATATG......................................................................................	24	1	5.00	0.00	3.00	2.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	5.00	1.00	3.00	1.00
................................................GGGGTGAAGCTGTACGTTATATG......................................................................................	23	1	4.00	0.00	3.00	1.00
................................................GGGGTTAAACTGTACGTTGTATG......................................................................................	23	1	4.00	0.00	0.00	4.00
.............................................................................................AGCGTATAGCTTTTCCCCTT............................................	20	1	4.00	0.00	3.00	1.00
................................................GGGGTGAAACTxTACGTTATATG......................................................................................	22	1	4.00	0.00	3.00	1.00
................................................GGGGTGAAATTGTACGTTATATG......................................................................................	23	1	4.00	0.00	4.00	0.00
...........................................................................................TAAGCCTATAGCTTTTCCCCTT............................................	22	1	4.00	0.00	2.00	2.00
................................................GGGGTGAAACTGTACGTTATA........................................................................................	21	1	4.00	1.00	3.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTC............................................	22	1	4.00	0.00	4.00	0.00
................................................GGGGCGAAACTGTACGTTATATG......................................................................................	23	1	3.00	0.00	2.00	1.00
................................................GGGGTAAAACTGTACGTTATATG......................................................................................	23	1	3.00	1.00	1.00	1.00
...........................................................................................TAAGCGTATAGCTCTTCCCCTT............................................	22	1	3.00	0.00	3.00	0.00
................................................GGGGTGAAACTGTACGTTATATGA.....................................................................................	24	1	3.00	1.00	2.00	0.00
.................................................GGGTGAAACTGTACGTTATATG......................................................................................	22	1	3.00	0.00	2.00	1.00
...........................................................................................TAAGTGTATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	3.00	0.00

droYak2

TAATTGTACAATCACCATCTGACAAAAT--TG--CTCAACA-TTTTAGGGGGTTAAACTGTACGTTATATGTGCCCTTT-T-GTAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAACAGCAACAA------ATA---GTGTATTTC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	1047.00	211.00	262.00	45.00	525.00	4.00
................................................GGGGTTAAACTGTACGTTATATG......................................................................................	23	1	174.00	100.00	5.00	12.00	14.00	43.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	169.00	16.00	42.00	13.00	84.00	14.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	32.00	8.00	7.00	2.00	15.00	0.00
................................................GGGGTTAAACTGTACGTTATA........................................................................................	21	1	20.00	11.00	0.00	0.00	0.00	9.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	18.00	1.00	4.00	0.00	12.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	12.00	5.00	3.00	0.00	4.00	0.00
...........................................................................................TAAGCGTATAACTTTTCCCCTT............................................	22	1	6.00	1.00	2.00	0.00	3.00	0.00
...........................................................................................TAAGAGTATAGCTTTTCCCCTT............................................	22	1	6.00	2.00	0.00	0.00	4.00	0.00
................................................GGGGTTAAACTGTACGTTATATT......................................................................................	23	1	5.00	4.00	1.00	0.00	0.00	0.00
...........................................................................................TAAGCGTGTAGCTTTTCCCCTT............................................	22	1	4.00	1.00	1.00	0.00	2.00	0.00
...........................................................................................TAAGCGTATACCTTTTCCCCTT............................................	22	1	4.00	0.00	0.00	0.00	4.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCCT............................................	22	1	4.00	1.00	0.00	0.00	3.00	0.00
...........................................................................................TAGGCGTATAGCTTTTCCCCTT............................................	22	1	4.00	1.00	2.00	0.00	1.00	0.00
...........................................................................................TAAGCGTATCGCTTTTCCCCTT............................................	22	1	4.00	1.00	1.00	0.00	2.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAA..........................................	24	1	4.00	3.00	0.00	0.00	1.00	0.00
...........................................................................................TAATCGTATAGCTTTTCCCCT.............................................	21	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................................................TCAGCGTATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	0.00	0.00	3.00	0.00
...........................................................................................TAAGCGTGTAGCTTTTCCCCT.............................................	21	1	3.00	0.00	0.00	0.00	3.00	0.00
................................................GGGGTTAAACTGTACGTTATATGTGCC..................................................................................	27	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGCGGATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	0.00	0.00	3.00	0.00
................................................GGGGTTAAACTGTACGTTATATGT.....................................................................................	24	1	3.00	1.00	0.00	1.00	0.00	1.00
...........................................................................................TAAGCGTATAGCTTTTACCCTT............................................	22	1	3.00	0.00	0.00	0.00	3.00	0.00
...........................................................................................TAACAGTATAGCTTTTCCCCTT............................................	22	1	3.00	1.00	0.00	0.00	2.00	0.00
...............................................GGGGGTTAAACTGTACGTTATATG......................................................................................	24	1	3.00	2.00	0.00	0.00	0.00	1.00
...........................................................................................TAAGCGTATTGCTTTTCCCCTT............................................	22	1	3.00	0.00	1.00	0.00	2.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTTT..........................................	24	1	3.00	1.00	0.00	0.00	2.00	0.00

droEre2

TACTTGTAGAACC--TG----ACAAAAT--TG--CTCAACA-TTTTAGGGGGTGAAACTGTACGTTATATGTGTCCTTCTG-TAAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTACAGCAACAGCAACAA------AAA---GTGAATCTT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
................................................GGGGTGAAACTGTACGTTATATG......................................................................................	23	1	1327.00	172.00	20.00	0.00	1135.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	774.00	213.00	139.00	72.00	350.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	181.00	19.00	13.00	12.00	137.00
................................................GGGGTCAAACTGTACGTTGTATG......................................................................................	23	1	116.00	1.00	1.00	114.00	0.00
................................................GGGGTGAAACTGTACGTTATATT......................................................................................	23	1	43.00	28.00	0.00	0.00	15.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	42.00	5.00	14.00	8.00	15.00
................................................GGGGTGAAACTGTACGTTATAT.......................................................................................	22	1	28.00	12.00	0.00	0.00	16.00
................................................TGGGTGAAACTGTACGTTATATG......................................................................................	23	1	25.00	1.00	0.00	0.00	24.00
................................................GTGGTGAAACTGTACGTTATATG......................................................................................	23	1	21.00	0.00	0.00	0.00	21.00
................................................GGGGTGAAACTGTACGTTATATA......................................................................................	23	1	16.00	1.00	0.00	0.00	15.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	16.00	0.00	1.00	4.00	11.00
................................................GGTGTGAAACTGTACGTTATATG......................................................................................	23	1	15.00	0.00	0.00	0.00	15.00
................................................GGGGTGAAACTGTACGTTATA........................................................................................	21	1	11.00	5.00	0.00	0.00	6.00
...........................................................................................TAAGCGTATAGCTTTTCCCATT............................................	22	1	11.00	0.00	0.00	0.00	11.00
................................................GGGGTTAAACTGTACGTTATATG......................................................................................	23	1	10.00	1.00	0.00	0.00	9.00
................................................GGGGTGAAACTGTACGTTATATC......................................................................................	23	1	10.00	0.00	0.00	0.00	10.00
................................................GGGGTGAAACTTTACGTTATATG......................................................................................	23	1	9.00	0.00	0.00	0.00	9.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTG...........................................	23	1	8.00	0.00	1.00	1.00	6.00
................................................GGGGCGAAACTGTACGTTATATG......................................................................................	23	1	7.00	2.00	0.00	0.00	5.00
................................................GGGGTGAAAATGTACGTTATATG......................................................................................	23	1	7.00	0.00	0.00	0.00	7.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	6.00	1.00	1.00	0.00	4.00
................................................GGGTTGAAACTGTACGTTATATG......................................................................................	23	1	6.00	0.00	0.00	0.00	6.00
................................................GGGGTGAAACTGTACTTTATATG......................................................................................	23	1	6.00	0.00	0.00	0.00	6.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAA..........................................	24	1	6.00	4.00	0.00	2.00	0.00
................................................GGGGTGAAACTGTACGTTATCTG......................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
...........................................................................................TAAGCGTATAGCTTTTCCC...............................................	19	1	5.00	0.00	1.00	0.00	4.00
...........................................................................................TAAGCGTATAGATTTTCCCCTT............................................	22	1	4.00	0.00	0.00	0.00	4.00
...........................................................................................TAAGCGTATAGCTTTTCCACT.............................................	21	1	4.00	0.00	0.00	0.00	4.00
................................................GGGGTGAAACTGTATGTTATATG......................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAT..........................................	24	1	4.00	0.00	0.00	4.00	0.00
................................................GGGGAGAAACTGTACGTTATATG......................................................................................	23	1	4.00	1.00	0.00	0.00	3.00
................................................GGGGTCAAACTGTACGTTGTAT.......................................................................................	22	1	4.00	0.00	0.00	4.00	0.00
................................................GGGGTCAAACTGTACGTTGTA........................................................................................	21	1	3.00	0.00	0.00	3.00	0.00
.................................................GGGTCAAACTGTACGTTGTATG......................................................................................	22	1	3.00	0.00	0.00	3.00	0.00
............................................................................................AAGCGTATAGCTTTTCCCCTT............................................	21	1	3.00	1.00	1.00	0.00	1.00
...........................................................................................TAAGCGTATACCTTTTCCCCTT............................................	22	1	3.00	2.00	0.00	1.00	0.00
................................................GGGGTGAGACTGTACGTTATATG......................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGCGTATAGCTCTTCCCCTT............................................	22	1	3.00	0.00	1.00	1.00	1.00
................................................GGGGTGAAACTGTACGCTATATG......................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
...............................................GGGGGTGAAACTGTACGTTATATG......................................................................................	24	1	3.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGCGGATAGCTTTTCCCCTT............................................	22	1	3.00	3.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTACCCTT............................................	22	1	3.00	0.00	0.00	0.00	3.00
................................................GGGGTGAAACTGTAAGTTATATG......................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGCGTATAGCTTTTCCCAT.............................................	21	1	3.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGCGTATAGCTTTTCCACTT............................................	22	1	3.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGCGTATAGCCTTTCCCCTT............................................	22	1	3.00	0.00	0.00	1.00	2.00
.................................................GGGTGAAACTGTACGTTATATG......................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
................................................AGGGTGAAACTGTACGTTATATG......................................................................................	23	1	3.00	0.00	0.00	0.00	3.00
.......................................................................TGTCCTTCTG-TAAAATTCA..................................................................	19	1	3.00	0.00	1.00	0.00	2.00
...........................................................................................TAAGTGTATAGCTTTTCCCCTT............................................	22	1	3.00	1.00	0.00	1.00	1.00
................................................GGGGTCAAACTGTACGTTTTATG......................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
...............................................CGGGGTGAAACTGTACGTTATATG......................................................................................	24	1	3.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGAGTATAGCTTTTCCCCTT............................................	22	1	3.00	1.00	0.00	0.00	2.00
................................................GGGGTGAAACTGTACGTTA..........................................................................................	19	1	3.00	2.00	0.00	0.00	1.00

droAna3

GGGTTT-TCTG------G---A--------AG--CTCAACCCTTTTGGGGGGTCAAACTGTACGTTCTATGTGGCAATCTT-AGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGCAAAGTCAACAAATCTCAACTAAAGTG--TTTT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	785.00	76.00	161.00	351.00	197.00
................................................GGGGTCAAACTGTACGTTCTATG......................................................................................	23	1	662.00	3.00	632.00	11.00	16.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	296.00	30.00	122.00	81.00	63.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	81.00	15.00	16.00	39.00	11.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	35.00	0.00	17.00	13.00	5.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	18.00	0.00	2.00	6.00	10.00
................................................GGTGTCAAACTGTACGTTCTATG......................................................................................	23	1	15.00	0.00	15.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTG...........................................	23	1	12.00	1.00	6.00	4.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTTT..........................................	24	1	11.00	2.00	1.00	8.00	0.00
................................................GGGGTCAAACTGTACGTTCTATT......................................................................................	23	1	9.00	0.00	6.00	0.00	3.00
................................................GGGGTCAAACTGTACGTTCTATGT.....................................................................................	24	1	8.00	0.00	7.00	0.00	1.00
...........................................................................................TAAGCGGATAGCTTTTCCCCTT............................................	22	1	6.00	0.00	0.00	2.00	4.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAA..........................................	24	1	6.00	0.00	0.00	0.00	6.00
.......................................................................TGGCAATCTT-AGAAATTCA..................................................................	19	1	6.00	0.00	3.00	0.00	3.00
...........................................................................................TAATCGTATAGCTTTTCCCCTT............................................	22	1	6.00	1.00	3.00	0.00	2.00
...........................................................................................TAAGAGTATAGCTTTTCCCCTT............................................	22	1	6.00	0.00	0.00	5.00	1.00
................................................GGGGTCAAACTGTACGTTCTAT.......................................................................................	22	1	5.00	0.00	5.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTA............................................	22	1	5.00	0.00	0.00	0.00	5.00
...........................................................................................TAAGCGTATAGCTTTTCCCCA.............................................	21	1	4.00	0.00	4.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCAT............................................	22	1	4.00	2.00	2.00	0.00	0.00
................................................GGGGTCAAACTGCACGTTCTATG......................................................................................	23	1	4.00	0.00	3.00	1.00	0.00
................................................GGGGTCAAGCTGTACGTTCTATG......................................................................................	23	1	4.00	0.00	3.00	1.00	0.00
................................................GGGGTCAAACTGTACGTTATATG......................................................................................	23	1	4.00	0.00	4.00	0.00	0.00
............................................................................................AAGCGTATAGCTTTTCCCCTT............................................	21	1	4.00	2.00	1.00	1.00	0.00
................................................GGGGTCAAACTGTACGTTCTATGTG....................................................................................	25	1	3.00	0.00	2.00	0.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCC...............................................	19	1	3.00	2.00	0.00	1.00	0.00
................................................GGGGTCAAACTGTACGTTCTGTG......................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
................................................GTGGTCAAACTGTACGTTCTATG......................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
...........................................................................................TAAGCGGATAGCTTTTCCCCT.............................................	21	1	3.00	0.00	0.00	3.00	0.00
............................................................................................AAGCGTATAGCTTTTCCCCTTT...........................................	22	1	3.00	0.00	1.00	2.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAAA.........................................	25	1	3.00	1.00	0.00	0.00	2.00
...........................................................................................TAAGCGTATAGCTTTTTCCCTT............................................	22	1	3.00	0.00	0.00	1.00	2.00
...........................................................................................TAAGCGTATAGCTTTTCCCTTT............................................	22	1	3.00	1.00	0.00	1.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCACT.............................................	21	1	3.00	0.00	3.00	0.00	0.00
...........................................................................................TAAGCGTATACCTTTTCCCCTT............................................	22	1	3.00	0.00	0.00	2.00	1.00
...........................................................................................GAAGCGTATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	0.00	2.00	1.00
................................................GGGGTGAAACTGTACGTTATATG......................................................................................	23	1	3.00	0.00	1.00	0.00	2.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTG............................................	22	1	3.00	0.00	0.00	2.00	1.00
...........................................................................................TAAGCGTATATCTTTTCCCCTT............................................	22	1	3.00	0.00	1.00	1.00	1.00
...........................................................................................TAAGCGTACAGCTTTTCCCCTT............................................	22	1	3.00	1.00	1.00	0.00	1.00
...........................................................................................TAAGCGTATAGATTTTCCCCT.............................................	21	1	3.00	1.00	2.00	0.00	0.00
...........................................................................................TAAGCGTAGAGCTTTTCCCCTT............................................	22	1	3.00	1.00	0.00	2.00	0.00

dp4

A--TTTCCCCATC-----------------TG--CTCAAAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATT-CGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAA-TCGCAACA---ACAATTCTA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	642.00	62.00	379.00	201.00	0.00
................................................GGGGTCAAACTGTACGTTCTATG......................................................................................	23	1	104.00	13.00	87.00	4.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	103.00	20.00	61.00	22.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	42.00	7.00	27.00	8.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	16.00	0.00	15.00	1.00	0.00
................................................GGGGTCAAACTGTACGTTGTATG......................................................................................	23	1	8.00	0.00	8.00	0.00	0.00
...........................................................................................TAAGCGGATAGCTTTTCCCCTT............................................	22	1	7.00	0.00	6.00	1.00	0.00
.......................................................................TGACAATATT-CGAAATTCA..................................................................	19	1	6.00	0.00	5.00	1.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	6.00	0.00	2.00	4.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAA..........................................	24	1	5.00	0.00	5.00	0.00	0.00
............................................................................................AAGCGTATAGCTTTTCCCCTT............................................	21	1	5.00	1.00	1.00	3.00	0.00
...........................................................................................TAAGAGTATAGCTTTTCCCCTT............................................	22	1	4.00	0.00	4.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCCT............................................	22	1	4.00	0.00	3.00	1.00	0.00
................................................GGGGTGAAACTGTACGTTATATG......................................................................................	23	1	4.00	0.00	4.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTTT..........................................	24	1	3.00	0.00	2.00	1.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCTTT............................................	22	1	3.00	0.00	1.00	2.00	0.00
...........................................................................................TAAGCGTGTAGCTTTTCCCCTT............................................	22	1	3.00	0.00	1.00	2.00	0.00
................................................GGGGTCAAACTGTACGTTCTAT.......................................................................................	22	1	3.00	1.00	2.00	0.00	0.00

droPer1

A--TTTCCCCATC-----------------TG--CTCAAAA-ATTTGAGGGGTCAAACTGTACGTTCTATGTGACAATATT-CGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAACTTGATGCAACAGCAACAA-TCGCAACA---ACAATTCTA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	740.00	28.00	192.00	123.00	397.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	114.00	10.00	31.00	8.00	60.00	5.00
................................................GGGGTCAAACTGTACGTTCTATG......................................................................................	23	1	105.00	8.00	34.00	6.00	6.00	51.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	52.00	2.00	9.00	15.00	26.00	0.00
...........................................................................................TAAGCGGATAGCTTTTCCCCTT............................................	22	1	16.00	0.00	1.00	0.00	15.00	0.00
................................................GGGGTCAAACTGTACGTTCTA........................................................................................	21	1	12.00	0.00	0.00	0.00	0.00	12.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	6.00	0.00	4.00	0.00	2.00	0.00
...........................................................................................TAAGCGTGTAGCTTTTCCCCTT............................................	22	1	5.00	0.00	1.00	1.00	3.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	5.00	0.00	0.00	2.00	3.00	0.00
...........................................................................................TAAGCGTATAGCCTTTCCCCTT............................................	22	1	5.00	0.00	0.00	0.00	5.00	0.00
...........................................................................................TAAACGTATAGCTTTTCCCCTT............................................	22	1	5.00	0.00	3.00	1.00	1.00	0.00
................................................GGGGTCAAACTGTACGTTC..........................................................................................	19	1	4.00	0.00	0.00	0.00	0.00	4.00
.......................................................................TGACAATATT-CGAAATTCA..................................................................	19	1	4.00	0.00	3.00	0.00	1.00	0.00
...........................................................................................TAAGAGTATAGCTTTTCCCCTT............................................	22	1	4.00	0.00	0.00	1.00	3.00	0.00
................................................GGGGTCAAACTGTACGTTCT.........................................................................................	20	1	4.00	0.00	0.00	0.00	0.00	4.00
..................................................................................................................................CAACAT-TCGGAACA---ACAA.....	18	1	3.00	0.00	0.00	0.00	0.00	3.00
................................................GGGGTCAAACTGTACGTTCTATGA.....................................................................................	24	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGCGTATAGCTTTTCCCCCT............................................	22	1	3.00	0.00	0.00	1.00	2.00	0.00
...........................................................................................TAAGTGTATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	1.00	0.00	2.00	0.00

droWil1

AAATTAAAGAATC--A--------ATTC--TA--CACAACA--TTTATGGGGTTAAACTGTACGTTGTATGTGCAAATCTTAAGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGATGTTAAATCAACAA-TGTAAACA---ATTATTTTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................GGGGTTAAACTGTACGTTGTATG......................................................................................	23	1	1768.00	19.00	784.00	484.00	481.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	948.00	76.00	618.00	249.00	5.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	410.00	15.00	211.00	139.00	45.00
................................................GGGGTTAAACTGTACGTTGTAT.......................................................................................	22	1	149.00	2.00	104.00	33.00	10.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	78.00	2.00	39.00	36.00	1.00
................................................GGGGTTAAACTGTACGTTGTA........................................................................................	21	1	62.00	1.00	37.00	15.00	9.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	31.00	5.00	17.00	9.00	0.00
................................................GGGGTTAAACTGTACGTTGTATGT.....................................................................................	24	1	29.00	0.00	9.00	7.00	13.00
................................................GGGGTTAAACTGTACGTTGTATGA.....................................................................................	24	1	19.00	0.00	15.00	2.00	2.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	18.00	1.00	17.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAA..........................................	24	1	17.00	0.00	17.00	0.00	0.00
.......................................................................TGCAAATCTTAAGAAATCCA..................................................................	20	1	14.00	1.00	10.00	3.00	0.00
................................................GGGGTTAAACTGTACGTTGCATG......................................................................................	23	1	9.00	0.00	5.00	2.00	2.00
................................................GGGGTTAAACTGTACGTTGT.........................................................................................	20	1	9.00	1.00	7.00	1.00	0.00
...........................................................................................TAATCGTATAGCTTTTCCCCT.............................................	21	1	8.00	0.00	0.00	1.00	7.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTA............................................	22	1	6.00	0.00	5.00	1.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAAA.........................................	25	1	6.00	0.00	6.00	0.00	0.00
................................................GGGGTGAAACTGTACGTTATATG......................................................................................	23	1	6.00	0.00	1.00	5.00	0.00
................................................GGGGTTAAACTGTACGTTGGATG......................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
................................................TGGGTTAAACTGTACGTTGTATG......................................................................................	23	1	5.00	0.00	1.00	3.00	1.00
................................................GGGGTTAAACTGTACGTTGTATA......................................................................................	23	1	4.00	0.00	1.00	3.00	0.00
.................................................GGGTTAAACTGTACGTTGTATG......................................................................................	22	1	4.00	0.00	3.00	1.00	0.00
...........................................................................................TACGCGTATAGCTTTTCCCCTT............................................	22	1	4.00	1.00	2.00	1.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCATT............................................	22	1	4.00	0.00	4.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTG...........................................	23	1	4.00	1.00	1.00	2.00	0.00
...........................................................................................TAATCGTATAGCTTTTCCCCTT............................................	22	1	4.00	0.00	2.00	1.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCACTT............................................	22	1	3.00	0.00	3.00	0.00	0.00
................................................GGGGTTAAACTGTAAGTTGTATG......................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
................................................GCGGTTAAACTGTACGTTGTATG......................................................................................	23	1	3.00	0.00	1.00	2.00	0.00
................................................GGAGTTAAACTGTACGTTGTATG......................................................................................	23	1	3.00	0.00	3.00	0.00	0.00
...........................................................................................TAAGCGTATAACTTTTCCCCT.............................................	21	1	3.00	0.00	0.00	0.00	3.00
................................................GGGGTTAAACTGTACGTTATATG......................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
................................................GGTGTTAAACTGTACGTTGTATG......................................................................................	23	1	3.00	0.00	1.00	0.00	2.00
................................................GGGGTTAAACTGTACGTTTTATG......................................................................................	23	1	3.00	0.00	0.00	3.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCC...............................................	19	1	3.00	0.00	3.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCC.............................................	21	1	3.00	0.00	0.00	0.00	3.00
................................................GGGGTTAAACTGTACGTTGTATGG.....................................................................................	24	1	3.00	0.00	0.00	1.00	2.00
................................................GGGGTTAAAATGTACGTTGTATG......................................................................................	23	1	3.00	0.00	1.00	2.00	0.00
...........................................................................................TAAGCGTATAGCTTTCCCCTT.............................................	21	1	3.00	0.00	3.00	0.00	0.00

droVir3

TAG-TGTAGAAAA--AGA---AAAA-AACACACACACAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGCAAATG-A-TGAAATTCATAAGCGTATAGCTTTTCCCCTTAAACGTTGATGTGACGACAACA----------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	1173.00	143.00	956.00	72.00	0.00	2.00
................................................GGGGTCAAACTGTACGTTGTATG......................................................................................	23	1	312.00	54.00	60.00	114.00	40.00	44.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	248.00	44.00	174.00	12.00	1.00	17.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	114.00	20.00	86.00	8.00	0.00	0.00
...........................................................................................TAAGCGAATAGCTTTTCCCCTT............................................	22	1	18.00	0.00	18.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTC...........................................	23	1	13.00	1.00	11.00	1.00	0.00	0.00
................................................GGGGTCAAACTGTACGTTGTATT......................................................................................	23	1	12.00	0.00	1.00	11.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	10.00	3.00	7.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	7.00	0.00	3.00	4.00	0.00	0.00
................................................GGGGTCAAACTGTACGTTGTAT.......................................................................................	22	1	7.00	1.00	1.00	4.00	1.00	0.00
...........................................................................................TAAGCGGATAGCTTTTCCCCTT............................................	22	1	7.00	0.00	7.00	0.00	0.00	0.00
...........................................................................................TAAGAGTATAGCTTTTCCCCTT............................................	22	1	7.00	0.00	7.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAA..........................................	24	1	6.00	0.00	4.00	2.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCCT............................................	22	1	6.00	1.00	4.00	1.00	0.00	0.00
.................................................GGGTCAAACTGTACGTTGTATG......................................................................................	22	1	6.00	0.00	0.00	3.00	1.00	2.00
...........................................................................................TAAGCGGATAGCTTTTCCCCT.............................................	21	1	5.00	0.00	4.00	0.00	0.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTTT..........................................	24	1	5.00	0.00	5.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTTA..........................................	24	1	5.00	0.00	5.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCG.............................................	21	1	4.00	0.00	0.00	0.00	0.00	4.00
...........................................................................................TAAGCGTATAGCTTTTCTCCTT............................................	22	1	4.00	0.00	4.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAT..........................................	24	1	4.00	0.00	0.00	4.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTC............................................	22	1	4.00	1.00	3.00	0.00	0.00	0.00
................................................GGGGTCAAACTGTACGTTTTATG......................................................................................	23	1	4.00	0.00	1.00	3.00	0.00	0.00
...........................................................................................TAAGCGAATAGCTTTTCCCCT.............................................	21	1	4.00	0.00	4.00	0.00	0.00	0.00
................................................GGGGTCAAACTGTACGTTGTA........................................................................................	21	1	4.00	0.00	0.00	3.00	0.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCCTT.............................................	21	1	3.00	0.00	3.00	0.00	0.00	0.00
...........................................................................................CAAGCGTATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
...........................................................................................TAACCGTATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
................................................GGGGTCAAACTGTACGTTGTATGT.....................................................................................	24	1	3.00	0.00	0.00	0.00	0.00	3.00
................................................GGGGTCAAATTGTACGTTGTATG......................................................................................	23	1	3.00	1.00	1.00	1.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTTC..........................................	24	1	3.00	0.00	3.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTCCCCCTT............................................	22	1	3.00	1.00	2.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAACTTTTCCCCTT............................................	22	1	3.00	0.00	2.00	1.00	0.00	0.00
...........................................................................................TAAGCCAATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTCTTCCCCTT............................................	22	1	3.00	0.00	2.00	1.00	0.00	0.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTG...........................................	23	1	3.00	0.00	2.00	1.00	0.00	0.00
.....................................................CAAACTGTACGTTGTATG......................................................................................	18	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................................................TAAGCGCATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
...........................................................................................TAAGCGTATGGCTTTTCCCCTT............................................	22	1	3.00	0.00	3.00	0.00	0.00	0.00
............................................................................................AAGCGTATAGCTTTTCCCCTT............................................	21	1	3.00	0.00	3.00	0.00	0.00	0.00

droMoj3

AATGTGAACAA---------------AA--CA--CTCAAAT-GTTTAGGGGGTCAAACTGTACGTTGTATGTGTAAACA-A-TGAAATCCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGGAATCAACA-------------GCAA-TTTA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	1023.00	112.00	153.00	115.00	643.00
................................................GGGGTCAAACTGTACGTTGTATG......................................................................................	23	1	772.00	86.00	27.00	20.00	639.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	205.00	46.00	49.00	48.00	62.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	86.00	10.00	6.00	8.00	62.00
................................................GGGGTCAAACTGTACGTTGTAT.......................................................................................	22	1	44.00	4.00	0.00	0.00	40.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAA..........................................	24	1	31.00	0.00	0.00	0.00	31.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTA...........................................	23	1	23.00	1.00	3.00	2.00	17.00
...........................................................................................TAAGCGTATAGCTTTTCCCC..............................................	20	1	16.00	1.00	5.00	3.00	7.00
................................................GGGGTCAAACTGTACGTTGTATT......................................................................................	23	1	13.00	0.00	0.00	1.00	12.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTC...........................................	23	1	12.00	4.00	2.00	1.00	5.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTG...........................................	23	1	8.00	0.00	5.00	1.00	2.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAT..........................................	24	1	7.00	1.00	0.00	0.00	6.00
...........................................................................................TAAGCGGATAGCTTTTCCCCTT............................................	22	1	7.00	0.00	2.00	1.00	4.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTAAA.........................................	25	1	6.00	1.00	1.00	0.00	4.00
................................................GGGGTCAAACTGTACGTTGT.........................................................................................	20	1	6.00	0.00	2.00	0.00	4.00
................................................GGGGTCAAACTGTACGTTGTATGA.....................................................................................	24	1	6.00	0.00	0.00	0.00	6.00
...........................................................................................TAAGCGTATAGCCTTTCCCCTT............................................	22	1	5.00	3.00	1.00	0.00	1.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTC............................................	22	1	5.00	1.00	2.00	0.00	2.00
................................................GGGGTCAAACTGTACGTTGTCTG......................................................................................	23	1	5.00	0.00	0.00	0.00	5.00
...........................................................................................TAAGAGTATAGCTTTTCCCCTT............................................	22	1	5.00	0.00	0.00	0.00	5.00
................................................GGGGTCAAACTGTACGCTGTATG......................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTA............................................	22	1	4.00	1.00	0.00	0.00	3.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTTT..........................................	24	1	4.00	0.00	2.00	0.00	2.00
...........................................................................................TAAGCGTATAGCTTTTACCCTT............................................	22	1	4.00	0.00	0.00	1.00	3.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTTAT.........................................	25	1	4.00	1.00	0.00	0.00	3.00
...........................................................................................TAAGCGCATAGCTTTTCCCCTT............................................	22	1	3.00	1.00	0.00	0.00	2.00
...........................................................................................TAAGTGTATAGCTTTTCCCCTT............................................	22	1	3.00	0.00	1.00	0.00	2.00
................................................GGGGTCAAACTGTACGGTGTATG......................................................................................	23	1	3.00	0.00	0.00	1.00	2.00

droGri2

G----------------G---AAAATAA--CA--CTCAAAT-GTTTAGGGGGTCAAACTGTACGTTATATGTGTAAATG-A-AGAAATTCATAAGCGTATAGCTTTTCCCCTTAAAAGTTGAAGTGATAGCAACAA------AAA---GTC-----T	Size	Hit Count	Total Norm	V109 Male body
...........................................................................................TAAGCGTATAGCTTTTCCCCTT............................................	22	1	33.00	33.00
................................................GGGGTCAAACTGTACGTTATATG......................................................................................	23	1	6.00	6.00
...........................................................................................TAAGCGTATAGCTTTTCCCCT.............................................	21	1	6.00	6.00
...........................................................................................TAAGCGTATAGCTTTTCCCCTTT...........................................	23	1	4.00	4.00
....................................................................ATGTCAAAATG-A-AGAAATT....................................................................	19	1	3.00	3.00
....................................................................ATGTCAAAATG-A-AGAAATTCA..................................................................	21	1	2.00	2.00
....................................................................ATGTCTAAGTG-A-AGAAATT....................................................................	19	1	1.00	1.00
...........................................................................................TAAGCGxxTAGCTTTTCCCCTT............................................	20	1	1.00	1.00
..........................................................................AAGTG-A-AGAAATTCATAAGCGC...........................................................	22	1	1.00	1.00
.............................................................................................AGCGTATAGCTTTTCCCCTTT...........................................	21	1	1.00	1.00
...........................................................................................TAAGCGTATAGGTTTTCCCCTT............................................	22	1	1.00	1.00
...........................................................................................TAAGCGTCTAGCTTTTCCCCT.............................................	21	1	1.00	1.00

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