dme-mir-1005- 12- and 20-way alignments

dme-mir-1005	chr2L:4343696-4343756 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 4343736-4343756
   star strand at position 4343696-4343718
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:4343681-4343771 +	CCACCATTCTGACCTGTGAGTTGAT-CGAT----TTCGAGGTTTTG-------------------------------GCACAC-------GAA-TATA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT
droSim1	chr2L:4265544-4265633 +	CTACCATTCTGACCTGTGAGTTGAT-CGAT----TTCGAGTTTTTG-------------------------------GC-CAC-------AAA-TATA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT
droSec1	super_5:2441095-2441185 +	CCACCATTCTGACCTGTGAGTTGAT-CGAT----TTCGAGGTTTTG-------------------------------GCACAC-------AAA-TGTA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT
droYak2	chr2L:4375638-4375728 +	CCACCATTCTGACCTGTGAGTTGAT-CGAT----TTCGAGGTTTTG-------------------------------GCAGCC-------AAA-AATA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT
droEre2	scaffold_4929:4420541-4420630 +	CCACCATTCTGACCTGTGAGTTCAT-CGAT----TTCGAGGTTT-G-------------------------------CCAGCC-------AAA-AATA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT
droAna3	scaffold_12916:13781299-13781395 -	TAACGGTTTTGACTTGTAAGAACCA-AAACTACTTTCTGTATC----------------------------------AAAGCC-------AGAAACTAATCGTAA-TT-GAA-AT-TATCTTAACCAGTCCCCATTGAGCTGT
dp4	chr4_group2:339129-339252 +	CCACCATTTTGACATGTAAGTGTCC-ATATC---CTCGAGGCTCctgcaatgcactgcaatgcactgcaatgaccgc------aatgcTGACG-TATT------ATTTATGT-TC-TCCGATCCCCAGTTCCCACTGAAATGT
droPer1	super_8:3550415-3550538 -	CCACCATTTTGACATGTAAGTGTCC-ATATC---CTCGAGGCTCctgcaatgcactgcaatgcactgcaatgaccgc------aatgcTGACG-TATT------ATTTATGT-TC-TCCGATCCCCAGTTCCCACTGAAATGT
droWil1	scaffold_180772:1844874-1844969 -	TTACAATTCTATCATGTAAGTTAAAACGAT----TAAGTAATTTC--------------------------------ACACTT-------ACA-TATAT--TT-ATTTAACTTTCTCTTGTCTCCTAGTCCCACTTGAAATGC
droVir3	Unknown	CAGTGGTATTGACCTGTAAGTATGT-T----------------------------------------------------------------------------------GAA-TT-TTCTTACTGCAGTTCCGCTGGAGATCG
droMoj3	scaffold_6500:22625692-22625724 +	CCTCCATATTGCTCTGCGTGCAAGA-TGCG----CCCG---------------------------------------------------------------------------------------------------------
droGri2	Unknown	CCACCATTCTGACATGTAACC--AC-TGAT----CCTGATCCTT-G-------------------------------ATTGC-ACTGCCCATT-TTGA------ATGTTTTC-TT-TCTGCTTTGCAGTTCCCACGGAAATGG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:4343681-4343771 +	NA	CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGG--T----T-----TTGGCAC-AC------GAATATAATCTGGAATCTT--TAATTCGCAGTTCCCACCGAAATGT
droSim1	chr2L:4265544-4265633 +	6	CTACCATTCTGACCTGTGAGTTGATCGATTTCGAGT--T----T-----TTGGCC--AC------AAATATAATCTGGAATCTT--TAATTCGCAGTTCCCACCGAAATGT
droSec1	super_5:2441095-2441185 +	5	CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGG--T----T-----TTGGCAC-AC------AAATGTAATCTGGAATCTT--TAATTCGCAGTTCCCACCGAAATGT
droYak2	chr2L:4375638-4375728 +	5	CCACCATTCTGACCTGTGAGTTGATCGATTTCGAGG--T----T-----TTGGCAG-CC------AAAAATAATCTGGAATCTT--TAATTCGCAGTTCCCACCGAAATGT
droEre2	scaffold_4929:4420541-4420630 +	9	CCACCATTCTGACCTGTGAGTTCATCGATTTCGAGG--T----T------TGCCAG-CC------AAAAATAATCTGGAATCTT--TAATTCGCAGTTCCCACCGAAATGT
droEug1	scf7180000409554:1722173-1722263 -	14	CCACCATCCTGACCTGTGAGTTGATCGATTTCGAGG--T----T-----TTGGCTC-TT------AGAAACAATCTGGAATCTT--TAATTCGCAGTTCCCACCGAAATGT
droBia1	scf7180000302261:2802460-2802551 +	15	CCACCATCCTGACCTGTGAGTTGATCGATTTCGGGG--T----TT----TTGGCTG-CC------TTCAATAATCTGGAATCTT--TAATTCGCAGTTCCCACCGAAATGT
droTak1	scf7180000414050:34777-34868 -	19	CCACCATTCTGACCTGTGAGTTGTGAGATTTCATGG--T----TC----CTTTCGG-TC------ATTTTTAATCTGGAATCTT--TAATTCGCAGTCCCCACCGAAATGT
droEle1	scf7180000490458:268801-268894 +	4	CTACCATTCTGACCTGTGAGTTTATGGATTTCCAAG--T----T-----TTTTTG-AC-ATTT--TACAATAATCTGGAATCTT--TAATTCGCAGTTCCCACTGAAATGT
droRho1	scf7180000778291:9908-9998 -	15	CCACCATCCTCACCTGTGAGTTGATCGATTTCGAGG--T----T-----GTGGCAT-CT------AACATTAATCTGGAATCTT--TAATTCGCAGTTCCCACTGAAATGT
droFic1	scf7180000453904:1262363-1262454 -	8	CCACCATCCTGACCTGTGGGTTGATCGATTTCGAGG--T----TGCGGGTTG-----GC------GCTTCTAATCTGGAATCTT--TAATTCGCAGTTCCCACTGAGATGT
droKik1	scf7180000302570:979763-979851 -	16	CAGTGTTGCTGTACTGTGAGTTGAAAATCCTTGAGG--A----T-----CTTGATA-CC------TTAATCTAGCAGAATTCTC----TTTCTTAGTTCCCTCGGAAATCA
droAna3	scaffold_12916:1534568-1534658 +	1	CCACCATCCTGACCTGTAAGTACATTGT------GGA-T--ATT-----G--TTT-ATA-CTACAGCCTCTAATCTTATACTAT--ATTTTTGCAGTTCCAACCGAAATGT
droBip1	scf7180000396728:196247-196338 +	7	CTACCATCCTTACTTGTGAGTACATCTGTT--GATA-TA-AT-TT----TTTTATA-CT------GCCTCTAATTT-GATCTTA--TATATTGCAGTTCCCACTGAAATGT
dp4	chrXR_group6:10049476-10049560 -	17	CC---ATCCTTAGCTGTGAGTCGCC----TCAGAGG----GCCC-----TTGTCG-AG-CGTA--CCCACTGACCT----TCCT--CCATTCGTAGATCCCGCCGAGGTTA
droPer1	super_61:329872-329956 -	17	CC---ATCCTTAGCTGTGAGTCGCCTCATA--GG------GCCC-----TTGTCG-AG-CGTA--CCCACTGACCT----TCCT--CCATTCGTAGATCCCGCCGAGGTTA
droWil1	scaffold_180772:2076013-2076099 +	7	CAACCATTCTGACATGTAAGTGTGC----T-CTATG--T-CTTC-----TCAATA-AG-CAG-------TCACTCATTACTTAT--CCATTTGTAGTTCCAACCGAGATGT
droVir3	scaffold_13246:412893-412984 +	18	CCACCATTTTAACATGTAAGGG-CTGAATTTTAAAA--TTGAAT-----TTAACA-AG-TATAC-AACAATATTAT------AA--TCCCACACAGTTCCCACAGAGATGT
droMoj3	scaffold_6500:244430-244523 -	11	TAACCATCTTGTCATGTAAGTCTATAATCT-CTATG--T----A-----TTGTCAA-CA-CA---AAATACAAATCACAATGTTTCATATCAACAGTCCCTCTTGAAATGC
droGri2	scaffold_15252:17037648-17037738 +	14	TTACGATTTTGTCATGTAAGTCGATCTGTTTGATAG--A-AATT-----GTATTC-AT-ATAA--CACAATAATAT------AA--ATATTTTTAGTCCCACTTGAAATGC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CCACCATTCTGACCTGTGAGTTGAT-CGAT----TTCGAGGTTTTG-------------------------------GCACAC-------GAA-TATA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT

Size

Hit Count

Total Norm

droSim1

CTACCATTCTGACCTGTGAGTTGAT-CGAT----TTCGAGTTTTTG-------------------------------GC-CAC-------AAA-TATA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAG...............	21	1	196.00	5.00	115.00	15.00	61.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGC.................	19	1	37.00	0.00	37.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGT..............	22	1	13.00	0.00	9.00	0.00	4.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCA................	20	1	10.00	0.00	9.00	0.00	1.00
...............GTGAGTTGAT-CGAT----TTCGAGTT.....................................................................................................	22	1	7.00	1.00	0.00	0.00	6.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCT................	20	1	3.00	0.00	3.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGG..............	22	1	3.00	0.00	0.00	0.00	3.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAC...............	21	1	3.00	0.00	2.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGA..............	22	1	2.00	1.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTA.............	23	1	2.00	0.00	1.00	0.00	1.00
.........................................................................................................TCTGGAA-TT-TTTAATTCGCAG...............	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAA...............	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGTAA-TC-TTTAATTCGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGGA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCCCA................	20	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCGG...............	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTT.............	23	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTCGAA-TC-TTTAATTCGCAG...............	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTAGCAG...............	21	1	1.00	0.00	1.00	0.00	0.00
..................AGTTGAT-CGAT----TTCGAGTTTTTG-------------------------------GC-...............................................................	25	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TA-TTTAATTCGCAG...............	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGA.................	19	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCG..................	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGC..............	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

CCACCATTCTGACCTGTGAGTTGAT-CGAT----TTCGAGGTTTTG-------------------------------GCACAC-------AAA-TGTA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAG...............	21	1	309.00	25.00	161.00	123.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGT..............	22	1	45.00	8.00	26.00	11.00
...............GTGAGTTGAT-CGAT----TTCGAGGTT....................................................................................................	23	1	43.00	1.00	38.00	4.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCA................	20	1	28.00	2.00	13.00	13.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGA..............	22	1	19.00	1.00	7.00	11.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGC.................	19	1	12.00	0.00	0.00	12.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTT.............	23	1	9.00	5.00	1.00	3.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTA.............	23	1	6.00	1.00	1.00	4.00
...............GTGAGTTGAT-CGAT----TTCGAGGT.....................................................................................................	22	1	4.00	0.00	4.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCG..................	18	1	3.00	0.00	0.00	3.00
.........................................................................................................TCTAGAA-TC-TTTAATTCGCAG...............	21	1	2.00	0.00	2.00	0.00
.........................................................................................................TTTGGAA-TC-TTTAATTCGCAGT..............	22	1	2.00	0.00	2.00	0.00
.........................................................................................................CCTGGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTTGCAG...............	21	1	1.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCCCA................	20	1	1.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTGATTCGC.................	19	1	1.00	0.00	0.00	1.00
.................GAGTTGAT-CGAT----TTCGAGGT.....................................................................................................	20	1	1.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATCCGCAG...............	21	1	1.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCCCAG...............	21	1	1.00	0.00	0.00	1.00
..........................................................................................................CTGGAA-TC-TTTAATTCGCAGT..............	21	1	1.00	0.00	1.00	0.00
.........................................................................................................TCTGCAA-TC-TTTAATTCGCAGT..............	22	1	1.00	1.00	0.00	0.00
........................................................................................................CTCTGGAA-TC-TTTAATTCGCAGT..............	23	1	1.00	0.00	0.00	1.00
...............GTGAGTTGAT-CGAT----TTCGAGG......................................................................................................	21	1	1.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGC..............	22	1	1.00	0.00	1.00	0.00
...............GTGAGTTGAT-CGAT----TTCGAGATT....................................................................................................	23	1	1.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TATAATTCGCAG...............	21	1	1.00	0.00	1.00	0.00
.........................................................................................................TCCGGAA-TC-TTTAATTCGCAG...............	21	1	1.00	1.00	0.00	0.00
.........................................................................................................TCTGCAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCTCAGA..............	22	1	1.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TCTAATTCGCAG...............	21	1	1.00	1.00	0.00	0.00
...............GTGAGTTGAT-TGAT----TTCGAGGTT....................................................................................................	23	1	1.00	0.00	1.00	0.00
...............GTGAGTTGAC-CGAT----TTCGAGGTTT...................................................................................................	24	1	1.00	0.00	1.00	0.00
.........................................................................................................TCTTGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00
.........................................................................................................TCTGTAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00
...............GTGAGTTGAT-CGAT----TTCGAG.......................................................................................................	20	1	1.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTACTTCGCAG...............	21	1	1.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-CTTAATTCGCAG...............	21	1	1.00	0.00	0.00	1.00

droYak2

CCACCATTCTGACCTGTGAGTTGAT-CGAT----TTCGAGGTTTTG-------------------------------GCAGCC-------AAA-AATA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAG...............	21	1	579.00	18.00	79.00	9.00	234.00	239.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGT..............	22	1	135.00	7.00	25.00	24.00	55.00	24.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGC.................	19	1	73.00	0.00	12.00	0.00	25.00	36.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCA................	20	1	73.00	0.00	4.00	8.00	41.00	20.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTT.............	23	1	42.00	5.00	5.00	7.00	19.00	6.00
...............GTGAGTTGAT-CGAT----TTCGAGGTT....................................................................................................	23	1	13.00	5.00	0.00	1.00	1.00	6.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCCG...............	21	1	12.00	1.00	1.00	0.00	7.00	3.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGA..............	22	1	11.00	0.00	1.00	2.00	6.00	2.00
.........................................................................................................TCTGGGA-TC-TTTAATTCGCAG...............	21	1	6.00	1.00	2.00	0.00	3.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCG..................	18	1	5.00	0.00	0.00	0.00	0.00	5.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAC...............	21	1	5.00	0.00	0.00	0.00	0.00	5.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGC..............	22	1	3.00	0.00	0.00	0.00	1.00	2.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTA.............	23	1	3.00	1.00	1.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAT...............	21	1	3.00	0.00	2.00	0.00	1.00	0.00
.........................................................................................................CCTGGAA-TC-TTTAATTCGCAG...............	21	1	2.00	0.00	0.00	0.00	2.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCTCAG...............	21	1	2.00	0.00	0.00	0.00	2.00	0.00
...............GTGAGTTGAT-CGAT----TTCGAGG......................................................................................................	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................................................................................TCTGGAA-TC-TTTAATTCACAG...............	21	1	2.00	1.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAA...............	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................................................................................TCTGGTA-TA-TTTAATTCGCAG...............	21	1	2.00	0.00	0.00	0.00	2.00	0.00
.........................................................................................................TCTGGAG-TC-TTTAATTCGCAG...............	21	1	2.00	0.00	0.00	0.00	2.00	0.00
.........................................................................................................TCCGGAA-TC-TTTAATTCGCAG...............	21	1	2.00	1.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCGG...............	21	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................................................................................TCTGGAA-TT-TTTAATTCGCAG...............	21	1	2.00	0.00	0.00	0.00	1.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGG..............	22	1	2.00	0.00	0.00	0.00	0.00	2.00
.........................................................................................................TCTGGCA-TC-TTTAATTCGCAG...............	21	1	2.00	0.00	1.00	0.00	1.00	0.00
.........................................................................................................TATGGAA-TC-TGTAATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTTGAT-CGAT----TTCGAGGTTT...................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTCACTTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTGATTCGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATCCGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTGGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTGAATTCGAAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGGA-TC-TTTAATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................................................CTGGAC-TC-TTTAATTCGCGGT..............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................................................CTGGAA-TC-TTTAATTCGCA................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCGGGGA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTGAATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TATGGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGTAG...............	21	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGCA-TC-TTGAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...............GTGAGTTGAT-CGAT----TTCGAGGT.....................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCTCAGTT.............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................GCTGGAA-TC-TTTAATGCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-CC-TTTAATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TCTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTCGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTCATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTGATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TTTGGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCGGGAA-TC-TTTAATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAC-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCC................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTCATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTCATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCT................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTTGAT-CGAT----TTCGAGGC.....................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TATGGAA-TC-TGTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCATGT.............	23	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCG................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTCAATTCGCAT...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TGTGGGA-TC-TTTAATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTTGAC-CGAT----TTCGAGAT.....................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
..........................................................................................................CTGGAA-TC-TTTAATTCGCAGT..............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCTC.................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-GC-TTTAAGTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TA-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCGGGAA-TC-TTGAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCGGGCA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGCA-TC-TTTAATTCGCCG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TATTGAA-TC-TTTAATTCGCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTTCAT-CCAT----TTCGAGGTT....................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGCA-TC-TTTATTTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGAAA-TC-TTTAATTCTCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTCAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTC.............	23	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................ACTGGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGGA-TC-TTTAATTCGCTGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATACGCAG...............	21	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAACTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TGTAATTCGCT................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TTTGTAA-TC-TTTAATTCGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTAGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCTCA................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTG.............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TGTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGACG...............	21	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATGCGTAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TA-TTTAATTCGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCCTTT.............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCTCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................TCGGGAA-TC-TGTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CCACCATTCTGACCTGTGAGTTCAT-CGAT----TTCGAGGTTT-G-------------------------------CCAGCC-------AAA-AATA------ATCTGGAA-TC-TTTAATTCGCAGTTCCCACCGAAATGT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAG...............	21	1	132.00	4.00	19.00	0.00	109.00
...............GTGAGTTCAT-CGAT----TTCGAGGTT....................................................................................................	23	1	14.00	6.00	0.00	0.00	8.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGT..............	22	1	13.00	0.00	3.00	0.00	10.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGA..............	22	1	10.00	0.00	2.00	0.00	8.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCA................	20	1	7.00	0.00	4.00	0.00	3.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAGTT.............	23	1	2.00	0.00	0.00	0.00	2.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGC.................	19	1	2.00	0.00	0.00	0.00	2.00
.........................................................................................................TCTGGCA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCCGGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAGTTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTTAAT-CGAT----TTCGAGGTT....................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGCAT...............	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TATGGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TA-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTTCAT-CGAT----TTCGA........................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGCAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCTCAG...............	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAATTCGAAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-TTTAATTCACAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTGGAA-TC-CTTAATTCGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCTTGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TCCTGAA-TC-TTTAATTCGCAG...............	21	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................................TTTGGGA-TC-TTTAATTCGCAG...............	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................TCTGGAA-TC-TTTAAxTCGC.................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

TAACGGTTTTGACTTGTAAGAACCA-AAACTACTTTCTGTATC----------------------------------AAAGCC-------AGAAACTAATCGTAA-TT-GAA-AT-TATCTTAACCAGTCCCCATTGAGCTGT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

CCACCATTTTGACATGTAAGTGTCC-ATATC---CTCGAGGCTCctgcaatgcactgcaatgcactgcaatgaccgc------aatgcTGACG-TATT------ATTTATGT-TC-TCCGATCCCCAGTTCCCACTGAAATGT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CCACCATTTTGACATGTAAGTGTCC-ATATC---CTCGAGGCTCctgcaatgcactgcaatgcactgcaatgaccgc------aatgcTGACG-TATT------ATTTATGT-TC-TCCGATCCCCAGTTCCCACTGAAATGT

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TTACAATTCTATCATGTAAGTTAAAACGAT----TAAGTAATTTC--------------------------------ACACTT-------ACA-TATAT--TT-ATTTAACTTTCTCTTGTCTCCTAGTCCCACTTGAAATGC

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CAGTGGTATTGACCTGTAAGTATGT-T----------------------------------------------------------------------------------GAA-TT-TTCTTACTGCAGTTCCGCTGGAGATCG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CCTCCATATTGCTCTGCGTGCAAGA-TGCG----CCCG---------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CCACCATTCTGACATGTAACC--AC-TGAT----CCTGATCCTT-G-------------------------------ATTGC-ACTGCCCATT-TTGA------ATGTTTTC-TT-TCTGCTTTGCAGTTCCCACGGAAATGG

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

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

20-way Secondary Structure

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