dme-mir-3642- 12- and 20-way alignments

dme-mir-3642	chr3L:11622605-11622680 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	tailed_mirtron

Legend:

   mature strand at position 11622605-11622626
   star strand at position 11622648-11622669
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3L:11622590-11622695 +	ATGGATGACGTCAAGGTGAGTGGGTCG-----------------CACGGAGCGTCA-------------------TTTGGAAT-------------------TC------------CCATGGC-------TG------ACGAA-------------------ACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA
droSim1	chr3L:10995092-10995212 +	ATGGATGACGTCAAGGTGAGTGAG-CG-----------------CACGGG-GGCCA-------------------TTTGGAAT-------------------TC------------CCCTGGC-------TG------AGAAAACGCTA--AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA
droSec1	super_0:3809862-3809984 +	ATGGATGACGTCAAGGTGAGTGAGGCG-----------------CACGGAGCGTCA-------------------TTTGGAAT-------------------TC------------CCCTGGC-------TG------AGAAAACGCTA--AGAACTTCATTACGCTCACTCTGTTCTTCTCGATTACAGGACATCATCAGTAAA
droYak2	chr3L:11651195-11651318 +	ATGGATGACGTCAAGGTGAGTGCGGCG-----------------CACGAACCGCCA-------------------TTTGGAAT-------------------TC------------CCCTGGC-------TG------ACGAAACGCTAA-AGAACTTCATTACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEre2	scaffold_4784:11607138-11607238 +	ATGGATGACGTCAAGGTGAGTGAGGCG-----------------CACGGACCGCCA-------------------TTTCGAAT-------------------TC------------CCCTGTC-------TG------------------------------ACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droAna3	scaffold_13337:5894397-5894534 +	ATGGACGACGTCAAGGTGAGTAAGAAGTGGTGGAGGGGGTGTTGCAG---------------------CAAAGTGC-TGGAAC-------------------TT------------AATAAGC-------TA------ATGAAACGCTAA-AGAACTTCATTACCCTTTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
dp4	chrXR_group6:10064193-10064317 -	ATGGACGACGTGAAGGTGAGTGGGGCG--------------CTGCAC---------------------GTGCCCGCTTGAGAC-------------------TT------------GCTTGGC-------AA------TATCAACGCTAA-AGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA
droPer1	super_61:344655-344779 -	ATGGACGACGTGAAGGTGAGTGGGGCG--------------CTGCAC---------------------GTGTCCGCTTGAGAC-------------------TT------------GCTTGGC-------AA------TATCAACGCTAA-AGAACTTCATTACGCTCATTATGCTCTTCTCCGTTGCAGGACATAATCAGTAAA
droWil1	scaffold_180698:2114822-2114981 +	ATGGACGACGTAAAGGTGAGTGTAACA----------------GCACTAg-tgt--------------gtgtacgcctgtgc-gtgtgtgtgtgtgtgtgtgcgtATATTT-----TCATGTA-------ATTATCCAACG-ACCGCTAATAGAATTTCCTTACACTTACTTTGCTCTTCTCACTTGCAGGACATAATCAGTAAA
droVir3	scaffold_13049:23825799-23825928 +	ATGAATGATGTCAAGGTGAGTGCGCGG-----------------CGCGGCGGCTGC-----------------TTCTTAATAA-------------------TT--------GATG-------AATTGACAA------TCTTATCGTTAA-AGAATTTCCTTACTCTCTGTCTGCTCTTATCTCTTACAGGACATAATCAGTAAA
droMoj3	scaffold_6680:18448682-18448807 +	ATGAACGACGTGAAGGTGAGTGAGCGG-----------------AATG---------------------------C-T-GAAC-------------------TGAATTTATTGATG-------AATTGACAA------TCTTATCGTTAA-AGAATTTCATTACACTCTCCTTGCTCTTCTCTCTTGCAGGACATAATCAGTAAA
droGri2	scaffold_15110:13832957-13833097 -	ATGAGCGATGTAAAGGTGAGTTCGGAG------------------------CGTTATTCTAGTTGATTGTGTTTAATTTTTAT-------------------AT------------ATTTGGCAATTGTTAA------TCAATTCGTTAA-AGAATTTCCT--CACTCACTCTGCTCTTATCTCTTCCAGGACATAATCAGTAAA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3L:11622590-11622695 +	NA	ATGGATGACGTCAAGGTGAGTGGGTCG--------------CA------CGGAGCGT-------------CA--TTTG-------------------------GAATT-------------CCCATGGCTGACGAA---------------------ACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA
droSim1	chr3L:10995092-10995212 +	1	ATGGATGACGTCAAGGTGAGTGAG-CG--------------CA------CGG-GGGC-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGAGAAAACGCT--A--AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA
droSec1	super_0:3809862-3809984 +	1	ATGGATGACGTCAAGGTGAGTGAGGCG--------------CA------CGGAGCGT-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGAGAAAACGCT--A--AGAACTTCATTACGCTCACTCTGTTCTTCTCGATTACAGGACATCATCAGTAAA
droYak2	chr3L:11651195-11651318 +	1	ATGGATGACGTCAAGGTGAGTGCGGCG--------------CA------CGAACCGC-------------CA--TTTG-------------------------GAATT-------------CCCCTGGCTGACGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEre2	scaffold_4784:11607138-11607238 +	2	ATGGATGACGTCAAGGTGAGTGAGGCG--------------CA------CGGACCGC-------------CA--TTTC-------------------------GAATT-------------CCCCTGTC--------------------------TGACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droEug1	scf7180000409711:3494930-3495053 +	2	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CGGACCGC-------------CA--CTTG-------------------------GAATT-------------CCCATGGCTATCAAAACGCT--AA-AGAACTTCATAACGCTCACTCTGCTCTTTTCGATTACAGGACATAATCAGTAAA
droBia1	scf7180000302334:58069-58192 +	2	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGAGCGC-------------CA--TTCG-------------------------GAATT-------------CCCATGGCTATCGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTACAGGACATAATCAGTAAA
droTak1	scf7180000414445:587576-587697 -	2	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CGG--CGT-------------CA--CTCG-------------------------GAATT-------------CCCCTGGCTAGCGAAACGCT--AA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTGCAGGACATAATCAGTAAA
droEle1	scf7180000490993:2183328-2183453 -	1	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGGGCGT-------------CA--TTCG-------------------------GAATT-------------CCCGTGGCAATCGAAACGCTATAA-AGAACTTCATTACGCTCACTCTGCTCTTCTCGATTACAGGACATAATCAGTAAA
droRho1	scf7180000777142:12217-12340 +	2	ATGGATGACGTCAAGGTGAGTGGGGCG--------------CA------CTGAGCGT-------------CA--TTTG-------------------------GAACT-------------CCCCTGTCAAACGAAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCGATTACAGGACATAATCAGTAAA
droFic1	scf7180000454113:3086558-3086682 -	2	ATGGATGACGTCAAGGTGAGTGCGGCG--------------CT------TGGAGCGC------------CAT--TATC-------------------------GGATT-------------CCATTGGCAATCAAAGCGCT--AA-AGAACTTCATAACGCTCGCTCTGCTCTTTTCGATTTCAGGACATAATCAGTAAA
droKik1	scf7180000302391:1217462-1217584 -	2	ATGGATGACGTCAAGGTGAGTTCGGCT----------------------TGAACTGG-----A------AT---TCTA-------------------------GAATT-------------GACCTGACAATGGCAACGCT--AA-AGAACTTCATTACGCTCTGTCTGCTCTTTTCGATTACAGGACATAATCAGTAAA
droAna3	scaffold_13337:5894397-5894534 +	2	ATGGACGACGTCAAGGTGAGTAAGAAGTGGTGGAGGGGGTGTT------GCAGCAAA------------GT---GCTG-------------------------GAACT-------------TAATAAGCTAATGAAACGCT--AA-AGAACTTCATTACCCTTTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
droBip1	scf7180000396371:1230115-1230235 +	2	ATGGACGACGTCAAGGTGAGTTAGAAGAG------------GT------GCTGGTGCACCAAA------GC---TCTG-------------------------GAACT-------------TACTCA-----------GCT--AA-TGAACTTCATTACACTCTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA
dp4	chrXR_group6:10064193-10064317 -	1	ATGGACGACGTGAAGGTGAGTGGGGCG--------------CT------GCACGTGC------------CCG--CTTG-------------------------AGACT-------------TGCTTGGCAATATCAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA
droPer1	super_61:344655-344779 -	1	ATGGACGACGTGAAGGTGAGTGGGGCG--------------CT------GCACGTGT------------CCG--CTTG-------------------------AGACT-------------TGCTTGGCAATATCAACGCT--AA-AGAACTTCATTACGCTCATTATGCTCTTCTCCGTTGCAGGACATAATCAGTAAA
droWil1	scaffold_180698:2114822-2114981 +	2	ATGGACGACGTAAAGGTGAGTGTAACA----------------------GCAC--TA----GTGTGTGTACG--CCTGTGCGTGTGTGTGTGTGTGTGTGCGTATATTTTCATG-------TAATTATCCAACG-ACCGCT--AATAGAATTTCCTTACACTTACTTTGCTCTTCTCACTTGCAGGACATAATCAGTAAA
droVir3	scaffold_13049:23825799-23825928 +	3	ATGAATGATGTCAAGGTGAGTGCGCGG--------------CG------CGGCGGCT-------------GCTTCTTA-------------------------ATAAT-TGAT--------GAATTGACAATCTTATCGTT--AA-AGAATTTCCTTACTCTCTGTCTGCTCTTATCTCTTACAGGACATAATCAGTAAA
droMoj3	scaffold_6680:18448682-18448807 +	3	ATGAACGACGTGAAGGTGAGTGAGCGG------------AATG------CTGAACTG-------------AA--TTTA-------------------------TTGAT-------------GAATTGACAATCTTATCGTT--AA-AGAATTTCATTACACTCTCCTTGCTCTTCTCTCTTGCAGGACATAATCAGTAAA
droGri2	scaffold_15110:13832957-13833097 -	1	ATGAGCGATGTAAAGGTGAGTTCGGAGCGT---------TATTCTAGTTGATTGTGT------------TTA---------------------------------ATTTTTATATATTTGGCAATTGTTAATCAATTCGTT--AA-AGAATTTCCT--CACTCACTCTGCTCTTATCTCTTCCAGGACATAATCAGTAAA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ATGGATGACGTCAAGGTGAGTGGGTCG-----------------CACGGAGCGTCA-------------------TTTGGAAT-------------------TC------------CCATGGC-------TG------ACGAA-------------------ACGTTCACTCTGCTCTTCTCGATTACAGGACATCATCAGTAAA

Size

Hit Count

Total Norm

droSim1

ATGGATGACGTCAAGGTGAGTGAG-CG-----------------CACGGG-GGCCA-------------------TTTGGAAT-------------------TC------------CCCTGGC-------TG------AGAAAACGCTA--AGAACTTCATTACGCTCACTCTGTTATTCTCGATTACAGGACATCATCAGTAAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................................................................................................CTGGC-------TG------AGCAACCGCTA--......................................................	18	1	2.00	0.00	2.00	0.00	0.00
...............................................................................................................................................ACGCTA--AGAACTTCATTACG........................................	20	1	2.00	0.00	2.00	0.00	0.00

droSec1

ATGGATGACGTCAAGGTGAGTGAGGCG-----------------CACGGAGCGTCA-------------------TTTGGAAT-------------------TC------------CCCTGGC-------TG------AGAAAACGCTA--AGAACTTCATTACGCTCACTCTGTTCTTCTCGATTACAGGACATCATCAGTAAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......GACAGCAAGGTGAGTGAGGC...................................................................................................................................................................................	20	1	2.00	0.00	2.00	0.00
...............GTGAGTGAGGCG-----------------CACGGAGCGT.......................................................................................................................................................	22	1	1.00	1.00	0.00	0.00
.TGGATGACGTCAAGGACA..........................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00
.........AGCAAGGTGAGTGAGGCG-----------------.................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

ATGGATGACGTCAAGGTGAGTGCGGCG-----------------CACGAACCGCCA-------------------TTTGGAAT-------------------TC------------CCCTGGC-------TG------ACGAAACGCTAA-AGAACTTCATTACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
....ATGACGTAAAGGTGAATGC......................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

ATGGATGACGTCAAGGTGAGTGAGGCG-----------------CACGGACCGCCA-------------------TTTCGAAT-------------------TC------------CCCTGTC-------TG------------------------------ACGCTCACTCTGCTCTTTTCAATTACAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................................................................................................................AATCACAGGACATCATCA.....	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................CACGCTGCTCTTTCCAAT....................	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................................ATTACxGGAAATAATCAGT...	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

ATGGACGACGTCAAGGTGAGTAAGAAGTGGTGGAGGGGGTGTTGCAG---------------------CAAAGTGC-TGGAAC-------------------TT------------AATAAGC-------TA------ATGAAACGCTAA-AGAACTTCATTACCCTTTCTTTGCTCTTTTCAATTACAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.....................ATGAAGTGGAGGAGGGG.......................................................................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
..........................GCGGTGGxGGGGGTGTTGC................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......ACGTAAAGGTGAxTAAGAA...................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................GGGGTGGAGGGGGGGT...................................................................................................................................................................	16	1	1.00	0.00	0.00	1.00	0.00

dp4

ATGGACGACGTGAAGGTGAGTGGGGCG--------------CTGCAC---------------------GTGCCCGCTTGAGAC-------------------TT------------GCTTGGC-------AA------TATCAACGCTAA-AGAACTTCATTACGCTCATTATGCTCTTCTCCATTGCAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........GAAGGTGAGTTGGGTG--------------CT..................................................................................................................................................................	18	1	3.00	1.00	0.00	0.00	2.00
...........GAAGGTGAGTTGGGTG--------------CTG.................................................................................................................................................................	19	1	3.00	3.00	0.00	0.00	0.00
.............AGGTGAGTTGGGTG--------------CTGC................................................................................................................................................................	18	1	2.00	2.00	0.00	0.00	0.00
...........GAAGGTGAGTTGGGTG--------------CTGC................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
............AAGGTGAGTTGGGTG--------------CTGC................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................G--------------CTGCAC---------------------GTGCCCGCTTGAGAC-------------------T......................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
ATGGACGACGTGAAGGAC...........................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
............AAGGTGAGTTGGGTG--------------CTG.................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
...........GAGGGTGAGTTGGGCG--------------CT..................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droPer1

ATGGACGACGTGAAGGTGAGTGGGGCG--------------CTGCAC---------------------GTGTCCGCTTGAGAC-------------------TT------------GCTTGGC-------AA------TATCAACGCTAA-AGAACTTCATTACGCTCATTATGCTCTTCTCCGTTGCAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........GAAGGTGAGTTGGGTG--------------CT..................................................................................................................................................................	18	1	9.00	9.00	0.00	0.00	0.00	0.00
...........GAAGGTGAGTTGGGTG--------------CTGC................................................................................................................................................................	20	1	2.00	2.00	0.00	0.00	0.00	0.00
...........GAGGGTGAGTTGGGCG--------------CT..................................................................................................................................................................	18	1	2.00	2.00	0.00	0.00	0.00	0.00
...........GAAGGTGAGTTGGGTG--------------CTG.................................................................................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
....................................................................................................................................................GA-AGAACTTCAATACGCT......................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..........TGAAGGTGAGTTGGGTG--------------CTG.................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................................................................................................GA-AGAACTTCATTACGCT......................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...........GAAGGTGAGTTGGGCG--------------CTGC................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................................................................................................GA-AGAACTTCACTACGCT......................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
............AAGGGGAGTGGGGGG--------------CTG.................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

ATGGACGACGTAAAGGTGAGTGTAACA----------------GCACTAg-tgt--------------gtgtacgcctgtgc-gtgtgtgtgtgtgtgtgtgcgtATATTT-----TCATGTA-------ATTATCCAACG-ACCGCTAATAGAATTTCCTTACACTTACTTTGCTCTTCTCACTTGCAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
............................................................................GTGTGC-GTCTGTGTGTGTGT............................................................................................................	20	11	2.73	0.00	2.64	0.00	0.09
............................................................................GTGTGC-GTCTGTGTGTGTGTGT..........................................................................................................	22	8	3.25	0.13	3.13	0.00	0.00
....................................................................................TGTGTGCGTCTGTGTGTG.......................................................................................................	18	16	1.19	0.00	0.94	0.25	0.00
...............................................................................TGT-GTGTGTGTGTGTGTG...........................................................................................................	18	38	0.39	0.00	0.16	0.24	0.00
....................................................................................TGTGTGTGTGTGTGTGTG.......................................................................................................	18	38	0.39	0.00	0.16	0.24	0.00
.................................................................................T-GTGTGTGTGTGTGTGTG.........................................................................................................	18	38	0.39	0.00	0.16	0.24	0.00
.............................................................................TGTGT-GTGTGTGTGTGTG.............................................................................................................	18	38	0.39	0.00	0.16	0.24	0.00
..............................................................................GTGT-GTGTGTGTGTGTGTGTGTG.......................................................................................................	23	16	0.94	0.00	0.19	0.75	0.00
......................................................................................TGTGTGTGTGTGTGTGTG.....................................................................................................	18	38	0.39	0.00	0.16	0.24	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTGTG.........................................................................................................	22	20	0.65	0.00	0.10	0.55	0.00
...............................................................................TGT-GTGTGTGTGTGTGTGTGTG.......................................................................................................	22	20	0.65	0.00	0.10	0.55	0.00
...................................................................................GTGTGCGTCTGTGTGTGTG.......................................................................................................	19	12	1.00	0.00	1.00	0.00	0.00
............................................................................GTGTGC-GTCTGTGTGTGTG.............................................................................................................	19	12	1.00	0.00	1.00	0.00	0.00
...............................................................................TGT-GTGTGTGTGTGTGTGTG.........................................................................................................	20	30	0.37	0.00	0.07	0.30	0.00
.................................................................................T-GTGTGTGTGTGTGTGTGTG.......................................................................................................	20	30	0.37	0.00	0.07	0.30	0.00
...............................................................................TGT-GTGTGTGTGTGTGTGTGT........................................................................................................	21	26	0.42	0.00	0.23	0.19	0.00
.............................................................................TGTGC-GTATATGTGTGTGTGT..........................................................................................................	21	1	11.00	2.00	9.00	0.00	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTGT..........................................................................................................	21	26	0.42	0.00	0.23	0.19	0.00
....................................................................................TGTGTGTGTGTGTGTGTGTG.....................................................................................................	20	30	0.37	0.00	0.07	0.30	0.00
....................................................................................TGTGTGTGTGTGTGTGTGTGT....................................................................................................	21	26	0.42	0.00	0.23	0.19	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTG...........................................................................................................	20	30	0.37	0.00	0.07	0.30	0.00
.........................................................................................GTGTTTGTGTGTGCGTGT..................................................................................................	18	21	0.48	0.10	0.33	0.05	0.00
...............................................................................TGT-GTATGTGTGTGTGTGTGTG.......................................................................................................	22	24	0.42	0.00	0.00	0.42	0.00
............................................................................GTGTGC-GTCTGTGTGTGTGTG...........................................................................................................	21	8	1.25	0.00	1.25	0.00	0.00
.............................................................................TGTGT-ATGTGTGTGTGTGTGTG.........................................................................................................	22	24	0.42	0.00	0.00	0.42	0.00
...................................................................................GTGTTTGTGTGTGCGTGT........................................................................................................	18	21	0.48	0.10	0.33	0.05	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTGTGTG.......................................................................................................	24	12	0.83	0.00	0.00	0.83	0.00
.....................................................................................GTGTGTGTGTGTGTGTGT......................................................................................................	18	41	0.22	0.07	0.07	0.07	0.00
............................................................................GTGTGC-GTGTGTGTGTGT..............................................................................................................	18	43	0.21	0.00	0.19	0.02	0.00
..............................................................................GTGT-GCGTGTGTGTGTGT............................................................................................................	18	43	0.21	0.00	0.19	0.02	0.00
................................................................................GT-GTGTGTGTGTGTGTGT..........................................................................................................	18	41	0.22	0.07	0.07	0.07	0.00
...................................................................................GTGTGCGTGTGTGTGTGT........................................................................................................	18	43	0.21	0.00	0.19	0.02	0.00
.......................................................................................GTGTGTGTGTGTGTGTGT....................................................................................................	18	41	0.22	0.07	0.07	0.07	0.00
................................................................................GT-GTGCGTGTGTGTGTGT..........................................................................................................	18	43	0.21	0.00	0.19	0.02	0.00
.......................................................................................GTGTGCGTGTGTGTGTGT....................................................................................................	18	43	0.21	0.00	0.19	0.02	0.00
....................................................................................TATGTGTGTGTGTGTGTGTG.....................................................................................................	20	38	0.24	0.00	0.00	0.24	0.00
.....................................................................................GTGTGCGTGTGTGTGTGT......................................................................................................	18	43	0.21	0.00	0.19	0.02	0.00
...............................................................................TAT-GTGTGTGTGTGTGTGTG.........................................................................................................	20	38	0.24	0.00	0.00	0.24	0.00
.............................................................................TATGT-GTGTGTGTGTGTGTG...........................................................................................................	20	38	0.24	0.00	0.00	0.24	0.00
.................................................................................T-ATGTGTGTGTGTGTGTGTG.......................................................................................................	20	38	0.24	0.00	0.00	0.24	0.00
..............................................................................GTGT-GTGTGTGTGTGTGT............................................................................................................	18	41	0.22	0.07	0.07	0.07	0.00
...................................................................................GTGTGTGTGTGTGTGTGT........................................................................................................	18	41	0.22	0.07	0.07	0.07	0.00
.................................................................................T-GTGTATGTGTGTGTGTGTG.......................................................................................................	20	33	0.24	0.00	0.03	0.21	0.00
............................................................................GTGTGC-GTCTGTGTGTGT..............................................................................................................	18	15	0.53	0.00	0.53	0.00	0.00
.............................................................................TGTGT-ATGTGTGTGTGTGTG...........................................................................................................	20	33	0.24	0.00	0.03	0.21	0.00
...............................................................................TGT-GTATGTGTGTGTGTGTG.........................................................................................................	20	33	0.24	0.00	0.03	0.21	0.00
...................................................................................GTGTGCGTCTGTGTGTGT........................................................................................................	18	15	0.53	0.00	0.53	0.00	0.00
....................................................................................TGTCTGTGTGTGTGTGTGC......................................................................................................	19	18	0.44	0.00	0.39	0.06	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTGTGTGC......................................................................................................	25	13	0.62	0.00	0.00	0.62	0.00
....................................................................................TGTGTATGTGTGTGTGTGTG.....................................................................................................	20	33	0.24	0.00	0.03	0.21	0.00
..............................................................................GTGT-GTGTGTGTGTGTGTGTGTGC......................................................................................................	24	16	0.44	0.00	0.06	0.38	0.00
.............................................................................TGTGC-GTATATGTGTGTGTG...........................................................................................................	20	1	7.00	0.00	7.00	0.00	0.00
................................................................................GT-GTGTGTGTGTGTGTGTGTG.......................................................................................................	21	25	0.28	0.00	0.04	0.24	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTGTGTGCG.....................................................................................................	26	9	0.78	0.00	0.00	0.78	0.00
...................................................................................GTGTGTGTGTGTGTGTGTGTG.....................................................................................................	21	25	0.28	0.00	0.04	0.24	0.00
..............................................................................GTGT-GTGTGTGTGTGTGTGTG.........................................................................................................	21	25	0.28	0.00	0.04	0.24	0.00
..............................................................................GTGC-GTGTGTGTGTGTGT............................................................................................................	18	15	0.40	0.07	0.33	0.00	0.00
....................................................................................TGTGTATGTGTGTGTGTGTGT....................................................................................................	21	29	0.21	0.00	0.07	0.14	0.00
.............................................................................TGTGC-GTATATGTGTGTGTGTG.........................................................................................................	22	1	6.00	0.00	6.00	0.00	0.00
...................................................................................GTGCGTGTGTGTGTGTGT........................................................................................................	18	15	0.40	0.07	0.33	0.00	0.00
.............................................................................TGTGT-ATGTGTGTGTGTGTGT..........................................................................................................	21	29	0.21	0.00	0.07	0.14	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTGTGTGCA.....................................................................................................	26	7	0.86	0.00	0.00	0.86	0.00
...............................................................................TGT-GTATGTGTGTGTGTGTGT........................................................................................................	21	29	0.21	0.00	0.07	0.14	0.00
...................................................................................ATATGTGTGTGTGTGTGTG.......................................................................................................	19	22	0.23	0.14	0.00	0.09	0.00
................................................................................AT-GTGTGTGTGTGTGTGTGTGC......................................................................................................	22	14	0.36	0.00	0.07	0.29	0.00
...............................................................................TAT-GTGTGTGTGTGTGTG...........................................................................................................	18	49	0.10	0.00	0.02	0.08	0.00
.................................................................................T-ATGTGTGTGTGTGTGTG.........................................................................................................	18	49	0.10	0.00	0.02	0.08	0.00
...............................................................................TGT-GTGTGTGTGTGTGTGT..........................................................................................................	19	35	0.14	0.03	0.06	0.06	0.00
........................................................................................................................................CATCG-ACCGCTAATGGAA..................................................	18	1	5.00	0.00	5.00	0.00	0.00
.................................................................................T-GTGTGTGTGTGTGTGTGT........................................................................................................	19	35	0.14	0.03	0.06	0.06	0.00
......................................................................................TGTGTGTGTGTGTGTGTGT....................................................................................................	19	35	0.14	0.03	0.06	0.06	0.00
....................................................................................TGTGTGTGTGTGTGTGTGT......................................................................................................	19	35	0.14	0.03	0.06	0.06	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGT............................................................................................................	19	35	0.14	0.03	0.06	0.06	0.00
.............................................................................TATGT-GTGTGTGTGTGTG.............................................................................................................	18	49	0.10	0.00	0.02	0.08	0.00
......................................................................................TATGTGTGTGTGTGTGTG.....................................................................................................	18	49	0.10	0.00	0.02	0.08	0.00
....................................................................................TATGTGTGTGTGTGTGTG.......................................................................................................	18	49	0.10	0.00	0.02	0.08	0.00
...................................................................................ATGTGTGTGTGTGTGTGTG.......................................................................................................	19	15	0.33	0.00	0.13	0.20	0.00
...............................................................................TAT-GTGTGTGTGTGTGTGTGTG.......................................................................................................	22	26	0.19	0.00	0.04	0.15	0.00
...................................................................................ATGTGTGTGTGTGTGTGT........................................................................................................	18	18	0.28	0.17	0.11	0.00	0.00
.............................................................................TATGT-GTGTGTGTGTGTGTGTG.........................................................................................................	22	26	0.19	0.00	0.04	0.15	0.00
...............................................................................TGC-GTATATGTGTGTGTGTG.........................................................................................................	20	2	2.50	0.00	2.50	0.00	0.00
...............................................................................TGC-GTCTGTGTGTGTGTGT..........................................................................................................	19	17	0.29	0.00	0.29	0.00	0.00
.............................................................................TGTGT-ATGTGTGTGTGTG.............................................................................................................	18	41	0.10	0.00	0.00	0.10	0.00
...............................................................................TGT-ATGTGTGTGTGTGTGTG.........................................................................................................	20	35	0.11	0.00	0.09	0.03	0.00
.................................................................................T-GTATGTGTGTGTGTGTGTG.......................................................................................................	20	35	0.11	0.00	0.09	0.03	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTGC..........................................................................................................	21	31	0.13	0.00	0.03	0.10	0.00
............................................................................TTGTGT-GTGTGTGTGTGTGTGTGTGC......................................................................................................	26	6	0.67	0.00	0.00	0.67	0.00
...............................................................................TGT-GTATGTGTGTGTGTG...........................................................................................................	18	41	0.10	0.00	0.00	0.10	0.00
.....................................................................................GTGTGTGTGTGTGTGTGTGT....................................................................................................	20	30	0.13	0.10	0.03	0.00	0.00
................................................................................GT-GTGTGTGTGTGTGTGTGT........................................................................................................	20	30	0.13	0.10	0.03	0.00	0.00
......................................................................................TGTGTATGTGTGTGTGTG.....................................................................................................	18	41	0.10	0.00	0.00	0.10	0.00
.................................................................................T-GTGTGTGTGTGTGTGTGTGAG.....................................................................................................	22	23	0.17	0.00	0.04	0.13	0.00
...................................................................................GTGTGTGTGTGTGTGTGTGTGT....................................................................................................	22	21	0.19	0.05	0.05	0.10	0.00
..............................................................................GTGT-GTGTGTGTGTGTGTGTGT........................................................................................................	22	21	0.19	0.05	0.05	0.10	0.00
......................................................................................TGTATGTGTGTGTGTGTG.....................................................................................................	18	44	0.09	0.00	0.00	0.09	0.00
.............................................................................TGTAT-GTGTGTGTGTGTG.............................................................................................................	18	44	0.09	0.00	0.00	0.09	0.00
.................................................................................T-GTATGTGTGTGTGTGTG.........................................................................................................	18	44	0.09	0.00	0.00	0.09	0.00
.............................................................................TGTAT-GTGTGTGTGTGTGTG...........................................................................................................	20	35	0.11	0.00	0.09	0.03	0.00
...............................................................................TGT-ATGTGTGTGTGTGTG...........................................................................................................	18	44	0.09	0.00	0.00	0.09	0.00
....................................................................................TGTGTATGTGTGTGTGTG.......................................................................................................	18	41	0.10	0.00	0.00	0.10	0.00
.............................................................................TGTGT-GTGTGTGTGTGTGTGAG.........................................................................................................	22	23	0.17	0.00	0.04	0.13	0.00

droVir3

ATGAATGATGTCAAGGTGAGTGCGCGG-----------------CGCGGCGGCTGC-----------------TTCTTAATAA-------------------TT--------GATG-------AATTGACAA------TCTTATCGTTAA-AGAATTTCCTTACTCTCTGTCTGCTCTTATCTCTTACAGGACATAATCAGTAAA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..................................................................................A-------------------TT--------GATG-------AATTGACAA------ACTG...............................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

ATGAACGACGTGAAGGTGAGTGAGCGG-----------------AATG---------------------------C-T-GAAC-------------------TGAATTTATTGATG-------AATTGACAA------TCTTATCGTTAA-AGAATTTCATTACACTCTCCTTGCTCTTCTCTCTTGCAGGACATAATCAGTAAA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

ATGAGCGATGTAAAGGTGAGTTCGGAG------------------------CGTTATTCTAGTTGATTGTGTTTAATTTTTAT-------------------AT------------ATTTGGCAATTGTTAA------TCAATTCGTTAA-AGAATTTCCT--CACTCACTCTGCTCTTATCTCTTCCAGGACATAATCAGTAAA

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