dme-mir-994- 12- and 20-way alignments

dme-mir-994	chr3R:6233859-6233949 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 6233870-6233891
   star strand at position 6233916-6233938
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:6233844-6233964 +	C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAGAA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAACAG-----CCTAGATCC
droSim1	chr3R:15159284-15159404 -	C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATGCA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATCC
droSec1	super_0:15709450-15709570 -	C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATGAT--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATCC
droYak2	chr3R:10262359-10262479 +	C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAGAA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTCC
droEre2	scaffold_4770:15384035-15384155 -	C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATGAA--TTGTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTCC
droAna3	scaffold_13340:867356-867472 -	G-------------------CAAGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCTCGAA-GTCATTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATTT
dp4	chr2:7233487-7233613 -	TG-TC--GC-----GTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATACAAA--TCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATCG
droPer1	super_0:1094175-1094302 -	TG-TC--GC-----GTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATAACAA-ATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATCG
droWil1	scaffold_181108:487-611 +	CA-TCT-TC-----GCCGACATGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAATTATTCAAATCTTTGACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTA-----
droVir3	scaffold_13047:1194149-1194278 +	AAGTCT-ACGTTCCAGCGATTTTGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTAGAA--GCTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAA----
droMoj3	scaffold_6540:5225156-5225286 +	AGGTCTAACGTTGAAGCGATATCAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTTCAA--CCTATTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAA----
droGri2	scaffold_14906:5077444-5077577 -	GA-TG--AC-----AATGATTTACATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTTGAAACTCTCTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAACAAACCCTAACTCC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:6233844-6233964 +	NA	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA-GAA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAACAG-----CCTAGATC---C
droSim1	chr3R:15159284-15159404 -	2	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT-GCA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droSec1	super_0:15709450-15709570 -	2	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT-GAT--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droYak2	chr3R:10262359-10262479 +	1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA-GAA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTC---C
droEre2	scaffold_4770:15384035-15384155 -	1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT-GAA--TTGTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTC---C
droEug1	scf7180000409692:710064-710184 +	2	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CTTA-GAA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTTGATC---C
droBia1	scf7180000302402:8322793-8322912 +	1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAT-GCA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC----
droTak1	scf7180000415380:1406182-1406305 -	2	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA-GAA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CTTAGATCATCC
droEle1	scf7180000490995:508571-508691 -	4	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA-GAA--TATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---C
droRho1	scf7180000777158:16475-16595 -	2	C--------------GC------GCTCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA-GAA--TATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CTTAGATT---C
droFic1	scf7180000453800:2313511-2313631 +	1	C--------------GC------GTCCTGTATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAA-GAT--TATTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---C
droKik1	scf7180000302475:1425726-1425847 +	1	C--------------GC------GTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCTCAGAA--TCTTTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---T
droAna3	scaffold_13340:867356-867469 -	3	-----------------------------GATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCTC-GAA-GTCATTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---T
droBip1	scf7180000394085:131779-131890 +	2	------------------------------ATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--CCAG-AAG--TCTTTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATT---C
dp4	chr2:7233487-7233613 -	2	T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAAC--ATAC-AAA--TCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---G
droPer1	super_0:1094175-1094302 -	2	T--------------GTCGCGTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAAC--ATAA-CAA-ATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATC---G
droWil1	scaffold_181089:74381-74499 -	10	C--------------G--------ACATGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAATTATTC-AAA--TCTTTGACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAAA------
droVir3	scaffold_13047:1194160-1194276 +	2	C------------CAGC------GATTTTGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTA-GAA--GCTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCT---------
droMoj3	scaffold_6540:5225156-5225284 +	2	AGGTCTAACGTTGAAGC------GATATCAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTT-CAA--CCTATTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCT---------
droGri2	scaffold_14906:5077444-5077577 -	1	G--------------ATGACAATGATTTACATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAC--ATTT-GAAACTCTCTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAACAAACCCTAACTC---C

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAGAA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAACAG-----CCTAGATCC

Size

Hit Count

Total Norm

droSim1

C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATGCA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATCC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................................................TATCACAGTGGCTGTTTTTTT....................................	21	4	4.75	0.00	0.00	0.00	4.75
.....................................................................................TATCACAGTGGCTGTTTTTTTT...................................	22	4	3.25	0.00	0.00	0.00	3.25
.....................................................................................TATCACAGTGGCTGTTTTTT.....................................	20	4	2.00	0.00	0.00	0.00	2.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	1.25	0.25	0.00	0.00	1.00
.....................................................................................TATCACAGTTGCTGTTCTTTT....................................	21	4	0.75	0.25	0.00	0.00	0.50
.....................................................................................TATCACAGTGGCTGGTTCTTTT...................................	22	1	2.00	0.00	0.00	0.00	2.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	2.00	0.00	0.00	0.00	2.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	2.00	0.00	0.00	0.00	2.00
.....................................................................................TATCACAGTTGCTGTTCGT......................................	19	4	0.25	0.25	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGG.................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
........................................CTAACGAAATAGTAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................TATCACAGTGGCTGTTCCTTTT...................................	22	4	0.25	0.00	0.00	0.00	0.25
.....................................................................................TATCACAGTAGCTGTTTTTTTT...................................	22	4	0.25	0.00	0.00	0.00	0.25
........................................CTAAGGAAATAGTAGCCGTGATT...............................................................................	23	1	1.00	0.00	1.00	0.00	0.00
......................................................................................ATCACAGTGGCTGTTTTTTT....................................	20	4	0.25	0.00	0.00	0.00	0.25
.....................................................................................TATCACAGTTGCxATTTCTT.....................................	19	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTTCTTTTT..................................	23	2	0.50	0.00	0.00	0.00	0.50
.....................................................................................TATCACAGTGGCTGTTTGTTT....................................	21	4	0.25	0.25	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATGAT--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATCC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	530.00	187.00	0.00	343.00
.....................................................................................TATCACAGTGGCTGTTCCTTTT...................................	22	4	77.75	0.00	76.75	1.00
.....................................................................................TATCACAGTGGCTGTTTTTTTT...................................	22	4	57.00	0.00	55.50	1.50
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	211.00	80.00	1.00	130.00
........................................................................................CACAGTTGCTGTTTCTTTTAGAT...............................	23	1	167.00	28.00	0.00	139.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	137.00	63.00	0.00	74.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	23.00	0.00	22.75	0.25
.....................................................................................TATCACAGTGGCTGTTCCTTT....................................	21	4	17.75	0.00	17.75	0.00
.....................................................................................TATCACAGTGGCTGTTTTTTT....................................	21	4	16.25	0.00	16.00	0.25
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	61.00	25.00	0.00	36.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	48.00	21.00	0.00	27.00
.......................................TCTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	31.00	8.00	0.00	23.00
.....................................................................................TATCACAGTTGCTGTTTCTTTT...................................	22	1	21.00	3.00	0.00	18.00
.....................................................................................TATCACAGTGGCTGTTTTT......................................	19	4	5.00	0.00	5.00	0.00
.....................................................................................TATCACAGTGGCTGTTTTTT.....................................	20	4	4.75	0.00	4.75	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTT....................................	21	4	4.25	0.00	4.25	0.00
.......................................................................................TCACAGTTGCTGTTTCTTTTAG.................................	22	1	13.00	1.00	0.00	12.00
......................................................................................ATCACAGTTGCTGTTTCTTTTAG.................................	23	1	10.00	1.00	0.00	9.00
........................................CTAAGGAAATAGTAGCCGTG..................................................................................	20	1	9.00	0.00	0.00	9.00
........................................CTAAGGAAATAGTAGCCGTGATT...............................................................................	23	1	9.00	4.00	0.00	5.00
........................................................................................CACAGTTGCTGTTTCTTTTAG.................................	21	1	8.00	1.00	0.00	7.00
.......................................................................................TCACAGTTGCTGTTTCTTTTAGA................................	23	1	7.00	0.00	0.00	7.00
.....................................................................................TATCACAGTGGCTGTTCCTT.....................................	20	4	1.75	0.00	1.75	0.00
.........................................................................................ACAGTTGCTGTTTCTTTTAGATT..............................	23	1	5.00	2.00	0.00	3.00
.....................................................................................TATCACAGTTGCTGTTCTTT.....................................	20	4	1.25	0.00	1.25	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTT....................................	21	1	4.00	1.00	0.00	3.00
........................................CTAAGGAAATAGTAGCCGTGATA...............................................................................	23	1	4.00	2.00	0.00	2.00
.....................................................................................TATCACAGTGGCTGTTTT.......................................	18	4	1.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCTTGATT...............................................................................	22	1	3.00	0.00	0.00	3.00
.........................................................................................ACAGTGGCTGTTCCTTTT...................................	18	4	0.75	0.00	0.75	0.00
........................................................................................CACAGTTGCTGTTTCTTTTAGA................................	22	1	3.00	0.00	0.00	3.00
........................................................................................CACAGTTGCTGTTTCTTTTAGATT..............................	24	1	3.00	0.00	0.00	3.00
........................................CTAAGGAAATAGTAGCCGAGAT................................................................................	22	1	3.00	1.00	0.00	2.00

droYak2

C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCAAGAA--TTTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTCC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	168.00	0.00	16.00	83.00	55.00	14.00
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	120.00	0.00	15.00	63.00	30.00	12.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	76.00	0.00	4.00	50.00	16.00	6.00
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	20.00	0.00	2.00	9.00	7.00	2.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	20.00	0.00	0.00	15.00	4.00	1.00
........................................................................................CACAGTTGCTGTTTCTTTTAGAT...............................	23	1	12.00	0.00	0.00	10.00	2.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	11.00	0.00	1.00	6.00	4.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATT...............................................................................	23	1	6.00	0.00	0.00	4.00	2.00	0.00
........................................CTAAGGAAATAGTAGCCGTGCT................................................................................	22	1	3.00	0.00	0.00	0.00	2.00	1.00
.....................................................................................TATCACAGTTGCTGTTTCTTTT...................................	22	1	3.00	0.00	0.00	2.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATA...............................................................................	23	1	3.00	0.00	1.00	2.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGTT................................................................................	22	1	2.00	0.00	0.00	0.00	2.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTG..................................................................................	21	1	2.00	0.00	1.00	0.00	0.00	1.00
.........................................TAAGGAAATGGTAGCCGTGATT...............................................................................	22	1	2.00	0.00	0.00	0.00	2.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	0.50	0.50	0.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGG.................................................................................	20	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................CTAAGGAAATAGTAGCCGTGGT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATATTAGCCGTGATT...............................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................TAAGGAAATAGTAGCAGTGAT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGCTT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATTTA.............................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................ATCACAGTTGCTGTTTCTTTTAG.................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATGGTAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGCAATAGTAGCCGGGAT................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................TAAGGAGATAGTAGCCGTGAT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGGAGCCGTGTTT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGxAATAGTAGCCGTGATT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................ACAGTTGCTGTTTCTTTTAGATT..............................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTTTTT.....................................	20	4	0.25	0.25	0.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGAC................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................TATCACAGTTGCTGTTTTTTTT...................................	22	4	0.25	0.25	0.00	0.00	0.00	0.00
.........................................TAATGAAATAGTAGCCGTGA.................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................ATAAGGAAATACTAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGGGT...............................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................CTAAGGAACTAGCAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATTT..............................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTT....................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGGAGCCGTGATT...............................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................TAGCACAGATGCTGTTTCT......................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................TAAGGAAATATTAGCCGTGA.................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGAG................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................TAAGGAAATAGTAGCCGTGATA...............................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCG....................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................ACAGTTGCTGTTTCTTTTTGAT...............................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTAGCTGTTTTTTT....................................	21	4	0.25	0.25	0.00	0.00	0.00	0.00
........................................CTAAGGAAATAGCAGCCGCGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTGAT................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGTTT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTTAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGGAGCCGTGAT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTTTA..................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCCTGGT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGCAATAGTAGCCGAGATT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTTGTTGTTTCTTTT...................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................................................................................TATCACAGTGGCGGTTTCTTTT...................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTATCCGTGATT...............................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCCTGAT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGCT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATAA..............................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................................................AGTTGCTGTTTxTTTTACA................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGATATAGTAGCCGCGAT................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAACCGTGAT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGATATAGTAGCCGTGAG................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGGAATAGTAGCCGTGAT................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................CTAATGAAATAGTAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................TACGGAAATAGTAGCCGTGATT...............................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................TAAGGAAATAATAGCCGTGATT...............................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................CTAAGGGAATAGTAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGCAAATAGTAGCCGTTA.................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATAGAAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAACTAGTAGCCGTGA.................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATC...............................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................CTAAGGAAATAGTAGCCTTGAC................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................................CACAGTTGCTGTTTCTTTTA..................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGAGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................TAAGGAATTAGTAGCCGTGATT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAACTAGTAGCCTTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCCTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGG.................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................TAAGGAAATAGCAGCCGTGAT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAAGAGTAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATCGTAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

C--------------GCGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCATGAA--TTGTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGTTCC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................................................TATCACAGTGGCTGTTTTTTTT...................................	22	4	1.25	1.00	0.00	0.25	0.00
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	3.00	0.00	3.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	0.50	0.25	0.00	0.25	0.00
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	2.00	0.00	0.00	1.00	1.00
.....................................................................................TATCACAGTGGCTGTTTTTTT....................................	21	4	0.25	0.25	0.00	0.00	0.00
.......................................................................................TCACAGTTGCTGTTTCTTTTAG.................................	22	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTT....................................	21	1	1.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................TATCACAGTGGCTGGTTCTTT....................................	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTCCTTTT...................................	22	4	0.25	0.25	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
............................................................ATTTTACCTATGAT--TTGTT.............................................................	19	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................TATCACAGTTTCTGTTGCTTTT...................................	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGAGGCTGTTTCT......................................	19	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTGGCTGTTTCTTT....................................	21	4	0.25	0.25	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	1.00	0.00	0.00	1.00	0.00

droAna3

G-------------------CAAGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACCCTCGAA-GTCATTCCCATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATTT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	5.00	5.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	5.00	4.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	4.00	3.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTG..................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	2.00	2.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	2.00	2.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATT...............................................................................	23	1	2.00	2.00	0.00	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTTTTTTT...................................	22	4	0.50	0.00	0.00	0.00	0.50
........................................CTAAGGAAATAGTAGCCGTGT.................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.............................................GATATGGTAGCCGTGAT................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	0.25	0.00	0.25	0.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTAA.................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................................................................CACAGTTGCTGTTTCTTTTAGAT...............................	23	1	1.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATTTT.............................................................................	25	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGTT................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	1.00	0.00	0.00	1.00	0.00

dp4

TG-TC--GC-----GTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATACAAA--TCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATCG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	9.00	9.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	8.00	5.00	0.00	0.00	3.00
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	5.00	5.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	5.00	4.00	0.00	0.00	1.00
.......................................TCTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTT....................................	21	4	0.50	0.00	0.50	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	0.50	0.00	0.50	0.00	0.00
.....................................................................................TATCACAGATGCTGGTTCT......................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................................................................CACAGTTGCTGTTTCTTTTAGAT...............................	23	1	1.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGT.................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTTTTTT....................................	21	4	0.25	0.00	0.25	0.00	0.00
.........................................TAAGGAAATAGTAGCCGAGA.................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.......................................TCTAAGGAAATGGTAGCCGTG..................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTAGCTGTTTTTT.....................................	20	4	0.25	0.00	0.25	0.00	0.00
.....................................................................................TATCACAGTGGCTGTGTCTTTT...................................	22	1	1.00	0.00	1.00	0.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTG..................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
........................................................................................CACAGTTGCTGGTTCTTTTAGAT...............................	23	1	1.00	0.00	1.00	0.00	0.00

droPer1

TG-TC--GC-----GTTGTCCTGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTAACATAACAA-ATCCTTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAGATCG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	10.00	7.00	0.00	2.00	0.00	1.00
.....................................................................................TATCACAGTGGCTGTTTTTTTT...................................	22	4	1.25	0.50	0.00	0.00	0.00	0.75
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	3.00	2.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	2.00	1.00	0.00	1.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	2.00	1.00	0.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	2.00	1.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGT.................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATT...............................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................................TCTAAGGAAATACTAGCCGTG..................................................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGAC................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................TCTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTG..................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGTT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	0.25	0.00	0.25	0.00	0.00	0.00
.......................................TCTAAGGGAATAGTAGCCGTGA.................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................AGTTATCTAAGGAAATGGG.........................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

CA-TCT-TC-----GCCGACATGAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTAATTATTCAAATCTTTGACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTA-----	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................................................................TATCACAGTGGCTGTTTTTTTT...................................	22	4	53.75	0.00	53.50	0.25	0.00
.....................................................................................TATCACAGTGGCTGTTCCTTTT...................................	22	4	53.25	0.00	53.25	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	204.00	85.00	11.00	2.00	106.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	48.50	0.00	48.50	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	118.00	47.00	2.00	0.00	69.00
.....................................................................................TATCACAGTGGCTGTTCCTTT....................................	21	4	16.25	0.00	16.00	0.25	0.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	60.00	21.00	0.00	0.00	39.00
.....................................................................................TATCACAGTTGCTGTTCTTTT....................................	21	4	13.50	0.00	13.50	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGAC................................................................................	22	1	39.00	7.00	0.00	0.00	32.00
.....................................................................................TATCACAGTGGCTGTTTTTTT....................................	21	4	6.00	0.00	6.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	17.00	15.00	0.00	0.00	2.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	12.00	10.00	2.00	0.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	12.00	7.00	0.00	0.00	5.00
.....................................................................................TATCACAGTGGCTGTTTTT......................................	19	4	2.75	0.00	2.75	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTT.....................................	20	4	2.25	0.00	2.25	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTTTTT.....................................	20	4	2.25	0.00	2.25	0.00	0.00
........................................................................................CACAGTTGCTGTTTCTTTTAGAC...............................	23	1	8.00	0.00	0.00	0.00	8.00
........................................................................................CACAGTTGCTGTTTCTTTTAGAT...............................	23	1	7.00	2.00	3.00	2.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTTA..................................	23	4	1.50	0.00	1.50	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATT...............................................................................	23	1	5.00	2.00	1.00	0.00	2.00
.....................................................................................TATCACAGTGGCTGTTTTTTTTA..................................	23	4	1.25	0.00	1.25	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTCCTTTTA..................................	23	4	1.25	0.00	1.25	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGAC................................................................................	21	1	4.00	0.00	0.00	0.00	4.00
........................................CTAAGGAAATAGTAGCCGTGACT...............................................................................	23	1	4.00	0.00	0.00	0.00	4.00
........................................CTAAGGAAATAGTAGCCGTG..................................................................................	20	1	3.00	2.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGG.................................................................................	21	1	3.00	0.00	0.00	0.00	3.00
.......................................TCTAAGGAAATAGTAGCCGTGG.................................................................................	22	1	3.00	0.00	0.00	0.00	3.00
.....................................................................................TATCACAGTGGCTGTTCCTT.....................................	20	4	0.75	0.00	0.75	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTCT.......................................	18	4	0.50	0.00	0.50	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTTCTTT....................................	21	4	0.50	0.00	0.50	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTCCT......................................	19	4	0.50	0.00	0.50	0.00	0.00
........................................CTAATGAAATAGTAGCCGTGAC................................................................................	22	1	2.00	0.00	0.00	0.00	2.00
.........................................TAAGGAAATAGTAGCCGTGATC...............................................................................	22	1	2.00	0.00	0.00	0.00	2.00
.........................................TAAGGAAATAGTAGCCGTGG.................................................................................	20	1	2.00	0.00	0.00	0.00	2.00
.....................................................................................TATCACAGTGGCTGTTTT.......................................	18	4	0.50	0.00	0.50	0.00	0.00
.........................................................................................ACAGTGGCTGTTTTTTTT...................................	18	4	0.50	0.00	0.50	0.00	0.00
........................................CTAAGGAAATAGTAGCCTTGAT................................................................................	22	1	2.00	1.00	0.00	0.00	1.00
........................................CTAAGGAAATAGTAGCCGTGACC...............................................................................	23	1	2.00	0.00	0.00	0.00	2.00
........................................CTAAGGAAATAGTAGCCCTGAC................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
......................................................................................ATCACAGTTGCTGTTTCTTTT...................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................TAGGGAAATAGTAGCCGTGAT................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................TATCACAGTTGCTGTTCCTTT....................................	21	4	0.25	0.00	0.25	0.00	0.00
.........................................TAAGGAAATAGGAGCCGTGAT................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGxTTCTTTTAA.................................	23	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTT....................................	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTCC.......................................	18	4	0.25	0.00	0.25	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGAG................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
........................................CTAAGGAAATATTAGCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTGAT................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
........................................CTAAGGAAATAGTAGCCGTGATC...............................................................................	23	1	1.00	0.00	0.00	0.00	1.00
........................................CTAAGGAAATATTAGCCGTGAC................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................TATCACAGTTGCTGTTTCTTTT...................................	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTTTA..................................	23	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGGT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................TTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.......................................TCTAAGGACATAGTAGCCGTGA.................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCG....................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.........................................TAAGGAAATAGTAGCCTTGATT...............................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGGGAT................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.........................................TAAGGAAATAGTAGCCGTG..................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................TCACAGTTGCTGTTTCTTTTAG.................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATTTTAAT..........................................................................	27	1	1.00	1.00	0.00	0.00	0.00
........................................................................................CACAGATGCTGTTTCTTTTAGAT...............................	23	1	1.00	0.00	0.00	1.00	0.00
.......................................TCTAAGGAAATAGCAGCCGTGA.................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCTGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAATAGCCGTGATT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00
..........................................AAGGAAATAGTAGCCGTGATTT..............................................................................	22	1	1.00	1.00	0.00	0.00	0.00
......................................................................................ATCACAGTGGCTGTTTTTTTT...................................	21	4	0.25	0.00	0.25	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATTG..............................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTGGCTGGTTCTTT....................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................TAACGAAATAGTAGCCGTGATT...............................................................................	22	1	1.00	0.00	0.00	0.00	1.00

droVir3

AAGTCT-ACGTTCCAGCGATTTTGATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTAGAA--GCTTTCACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAA----	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	40.00	3.00	21.00	1.00	1.00	14.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	13.00	0.00	6.00	0.00	1.00	6.00
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	11.00	0.00	7.00	0.00	0.00	4.00
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	10.00	0.00	7.00	1.00	0.00	2.00
.......................................TCTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	3.00	0.00	2.00	0.00	0.00	1.00
.....................................................................................TATCACAGTTGCTGTTTCTTTT...................................	22	1	2.00	0.00	2.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	2.00	0.00	2.00	0.00	0.00	0.00
........................................CTAAGGAAATAGGAGCCGTGAT................................................................................	22	1	2.00	0.00	2.00	0.00	0.00	0.00
.....................................................................................TATCACAGAGGCTGTTTCT......................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................................................................................TCACAGTTGCTGTTTCTTTTAG.................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................TAAGGAAATAGTAGCGGTGCTT...............................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGACC...............................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTT....................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGG.................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................CTAAGGAAATAGTAGCCGTGATAA..............................................................................	24	1	1.00	0.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTGGCTGTTTTTTTT...................................	22	4	0.25	0.00	0.00	0.25	0.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTG..................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGAAT...............................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	0.25	0.00	0.00	0.25	0.00	0.00
........................................................................................CACAGTTGCTGTTTCTTTTAG.................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTG..................................................................................	20	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCG....................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droMoj3

AGGTCTAACGTTGAAGCGATATCAATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTTCAA--CCTATTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAG-----CCTAA----	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	331.00	324.00	2.00	3.00	2.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	128.00	123.00	4.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGAT................................................................................	21	1	90.00	88.00	1.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGA.................................................................................	21	1	61.00	59.00	2.00	0.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	60.00	58.00	2.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGA.................................................................................	20	1	46.00	44.00	1.00	0.00	1.00
........................................CTAAGGAAATAGTAGCCGTGATT...............................................................................	23	1	19.00	19.00	0.00	0.00	0.00
........................................................................................CACAGTTGCTGTTTCTTTTAGAT...............................	23	1	13.00	11.00	0.00	0.00	2.00
.......................................TCTAAGGAAATAGTAGCCGTG..................................................................................	21	1	4.00	4.00	0.00	0.00	0.00
.......................................................................................TCACAGTTGCTGTTTCTTTTAG.................................	22	1	4.00	4.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTTT...................................	22	1	3.00	3.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATTT..............................................................................	24	1	3.00	3.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTTT....................................	21	1	3.00	3.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTTCTT.....................................	20	1	2.00	2.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATC...............................................................................	23	1	2.00	2.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATTT..............................................................................	23	1	2.00	2.00	0.00	0.00	0.00
......................................................................................ATCACAGTTGCTGTTTCTTTTAG.................................	23	1	2.00	1.00	0.00	0.00	1.00
........................................CTAAGGAAATAGTAGCCGTGAC................................................................................	22	1	2.00	2.00	0.00	0.00	0.00
........................................................................................CACAGTTGCTGTTTCTTTTAG.................................	21	1	2.00	1.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTG..................................................................................	19	1	2.00	1.00	0.00	1.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATC...............................................................................	22	1	2.00	1.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATTC..............................................................................	24	1	2.00	2.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTG..................................................................................	20	1	2.00	2.00	0.00	0.00	0.00
.........................................CAAGGAAATAGTAGCCGTGATT...............................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAATAGCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGxAATAGTAGCCGTGAT................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.......................................TCTAAGGAAATAGTAGCCGT...................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.........................................TGAGGAAATAGTAGCCGTGATT...............................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.......................................TCTAAGGAAATAGTAGCCGTGAA................................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................TCACAGTTGCTGTTTCTTTTAGA................................	23	1	1.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAATAGTAGCCGTGACT...............................................................................	23	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTATCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.......................................TCTAAGGAAGTAGTAGCCGTG..................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGAAGCCGTGA.................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................ACAGTTGCTGTTTCTTTTAGATT..............................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATA...............................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGCAGCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGCTTTTTT....................................	21	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................TCACAGTTGCTGTTTCTTTT...................................	20	1	1.00	0.00	0.00	1.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTTA..................................	23	4	0.25	0.00	0.00	0.00	0.25
.........................................TAAGGACATAGTAGCCGTGAT................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................AAAGGAAATAGTAGCCGTGAT................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
........................................................................................CACAGTTGCTGTATCTTTTAGATT..............................	24	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTCCTTCT...................................	22	1	1.00	0.00	0.00	0.00	1.00
.........................................TAAGGAAATAGTAGCCGCGAT................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTAAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTTGCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATATTAGCCGTGAT................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAACCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAGTAGTAGCCGTGATA...............................................................................	23	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGCAAATAGTAGCCATGAT................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................TAAGAAAATAGTAGCCGTGATT...............................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGCT................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGGGAT................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................TATCACTGTTGCTGTCTCTTTT...................................	22	1	1.00	0.00	0.00	0.00	1.00
.GTTCGAACGTTGAAGCGA...........................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
........................................CTAAGGAAGTAGTAGCCGTGA.................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCTTGAT................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATGGTAGCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TATCACAGTTGCTGTTCTTTTT...................................	22	4	0.25	0.00	0.00	0.00	0.25
.....................................................................................TATCACAGTTGCTGxCTCTTTTA..................................	22	1	1.00	0.00	0.00	0.00	1.00
........................................CTAAGGAAATAGTAGCCGTGT.................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
.......................................TTTAAGGAAATAGTAGCCGTGA.................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTACCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCGTGATG...............................................................................	23	1	1.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCCTGA.................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
........................................CAAAGGAAATAGTAGCCGTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
........................................CTAAGGAAATAGTAGCCTTGAT................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................TCACAGTTGCTGTTTCTTTTCG.................................	22	1	1.00	0.00	0.00	1.00	0.00
.........................................TAATGAAATAGTAGCCGTGATT...............................................................................	22	1	1.00	1.00	0.00	0.00	0.00
......................................................................................ATCACAGTTGCTGTTTCTTTT...................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................TAAGGAAATAGTAGCCGTGATTTC.............................................................................	24	1	1.00	1.00	0.00	0.00	0.00
.GTTCGAACGTTGAAGCGAT..........................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
......................................................................................ATCACAGTTGCTGTTTCTTTTA..................................	22	1	1.00	0.00	0.00	0.00	1.00
.........................................TAAGGAAGTAGTAGCCGTGATT...............................................................................	22	1	1.00	1.00	0.00	0.00	0.00

droGri2

GA-TG--AC-----AATGATTTACATTTATATCGAGTTATCTAAGGAAATAGTAGCCGTGATTTTACATTTGAAACTCTCTTACATATCACAGTTGCTGTTTCTTTTAGATAGCTCTTTTGTAAGCAACAAACCCTAACTCC	Size	Hit Count	Total Norm	V109 Male body
........................................CTAAGGAAATAGTAGCCGTGAT................................................................................	22	1	1.00	1.00
.........................................TAAGGAAATAGTAGCCGTGATT...............................................................................	22	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