dme-mir-4979- 12- and 20-way alignments

dme-mir-4979	chr2R:19621555-19621664 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 19621580-19621601
   star strand at position 19621618-19621639
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:19621540-19621679 -	GGATGGGAAA----TTATACATAGGTG-----TTAT-------ATC-TAGGCCAAATATATATACTTGTTCTATGTATT---AGTTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droSim1	chr2R:18187644-18187778 -	GGATGGGAAA----CT----ATAGGTA-----TTAT-------ATC-TAGGCCAAATATATATACTTG-TCTATGTATT---AGTTATTTGCAAAGGAATACATGTG-CGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droSec1	super_9:2901906-2902041 -	GGATGGGAAA----CT----ATAGGTA-----TTAT-------ATC-TAGGCCAAATATATATACTTGTTCTATGTATT---AGTTATTTGCAAAGGAATACATGTG-CGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droYak2	chr2R:19599592-19599718 -	TAAGGGGAAA----------------------TTAT-------ACC-TAGGCCAAATATATATACTTGTTCTGTGTATC---AATTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droEre2	scaffold_4845:20984379-20984505 -	GAAGGAAAA-G---------------------TTAC-------ACC-TAGGCCAAATATATATACTTGTTCTATGTATT---AATTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT
droAna3	scaffold_13266:8260384-8260512 -	TATT-AG-AGC---------------------TAAC-------AACTAATGCCAAATATATATACTCAATCGATGTACT--TGGTTATTTGCAAAGGAATACACTGCGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCAAAGCTTGTTAGT
dp4	chr3:9376521-9376668 +	ACG--AGAAA----TGCCATATAGGCA-----ATA-AACTATTAGC-TATCGCAAATATATATACTCATTTCATGTACT--TGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTAATCACATCTTTGAATCTTT-CCATAGCTCGTTAGA
droPer1	super_4:4699742-4699885 +	GAGA----------TGCCATATAGGCA-----ATA-AGCTATTAGC-TATCGCAAATATATATACTCATTTCATGTACT--TGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTGATCACATCTTTGAATCTCT-CCATAGCTCGTTAGA
droWil1	scaffold_181141:2403444-2403586 +	GTAGGTATAAGTGTTGCCT-TTTTGTG-----TTAT-------TTC-TAGTTCAAtTtTtTtTtgGgtTTTTgTGTtTt--TGtgTtTtTGgtttGGTtTtgtTTTt---TGTtTtTtTtTTTGGTAAAATCACATCTTTGAAT--AATCCATAGCTCGTCAGA
droVir3	scaffold_12823:519085-519222 +	TTGC-AA-AAGTAT-T------ATCTA----CATAT-------ATC-TATGTCAAATATATATATCCCCATTTTGTATAACTATTTATATGCAAGGGTATACGTTTA---CGTATATATATTTGTTAAAATCACATCTTTGAAT--GCTATATAGCTCGTTAGC
droMoj3	scaffold_6496:318095-318227 +	TTGC-AG-AAGTATTC----ATATGTA-----CAAA-------ATCTTATATCAAATATATATATATGTCCCA----------TTTGTATGCAAGGGTATGCGTTTC-TCTATATATATATTTGTTAAAATCACATCTTTGAAT--GGTATTTAGCTCGTTAGC
droGri2	scaffold_15245:6158007-6158151 -	TTGCCAGGA-GT-----CTTACAACTAACTACTTAT-------AAC-TATATCAAATATATATACTCACTTTGTGTATAGCTACGTATAAGCAAAGGTATACGCTTG---CGTATATATATTTGTTAAAATCACATCTTTGAAT--GGTATATAGCTCGTCAGC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:19621540-19621679 -	NA	GGATGGGAAATTA--------------T--ACATA--GGTG-----TTATA------------------------------TCTAG-GCCAAATATATATAC-TT--GTTCTATGTA-TTAGTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droSim1	chr2R:18187644-18187778 -	1	GGATGGGAAACTA--------------T------A--GGTA-----TTATA------------------------------TCTAG-GCCAAATATATATAC-TT--G-TCTATGTA-TTAGTTATTTGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droSec1	super_9:2901906-2902041 -	1	GGATGGGAAACTA--------------T------A--GGTA-----TTATA------------------------------TCTAG-GCCAAATATATATAC-TT--GTTCTATGTA-TTAGTTATTTGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droYak2	chr2R:19599592-19599718 -	1	TAAGGGGAAA------------------------------------TTATA------------------------------CCTAG-GCCAAATATATATAC-TT--GTTCTGTGTA-TCAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droEre2	scaffold_4845:20984379-20984510 -	1	CTGTAGAA--GGA-AAAG----------------------------TTACA------------------------------CCTAG-GCCAAATATATATAC-TT--GTTCTATGTA-TTAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droEug1	scf7180000409474:21612-21738 +	1	CG---GGAAA-------G----------------------------TTATG------------------------------CCTAA-GCCAAATATATATAC-TC--GTTCTATGTACTTAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATC-----ACATCTTTGAAG--TG-CCACAGCTCGCTAGT-
droBia1	scf7180000302143:1773637-1773756 +	1	AG--------------------------------------------TTACG------------------------------CCTAA-GCCAAATATATATAC-TC--GTTCTATGTATTTAATTATTTGCAAAGGAATACAC-ATATTTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACTGCTCGCTAGT-
droTak1	scf7180000415400:558002-558129 -	2	AGTTGGGAGA------TA----------------------------T--TG------------------------------CCTAA-GCCAAATATATATAC-TC--GTTTTATGTACTTAATTATTTGCAAAGGAATACAA-GTATATGTATATATATTTGGTAAAATC-----ACATCTTTGAAT--TG-CCGGAGCTCGCTAGT-
droEle1	scf7180000491201:1147757-1147882 +	1	GGA-----AA------TA----------------------------TTATG------------------------------CCTAA-GCCAAATATATATAC-TC--GTTCTATGTACTTAATTATTTGCAAAGGAATACAC-TTGCCTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACAGCTCGTTAGT-
droRho1	scf7180000778122:26363-26489 +	1	CA----GAAA------TA----------------------------TTATG------------------------------CCTAA-GCCAAATATATATAC-TC--GTTCTATGTACTTATTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droFic1	scf7180000453809:586655-586785 +	1	AGTTGGAAAAA-----AA----------------------------TTATG------------------------------CCTAG-GCCAAATATATATAC-TC--GTTCTATGTACTTATTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droKik1	scf7180000302470:2102706-2102852 +	1	AAAAT-GAAATTCC------------------AGTAAAGCAGTAT-GTATG------------------------------TCTAGCGCCAAATATATATACGTT--GTTCTATGTACTTGGTTATATGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--CG-CCACAGCTCGTTAGTT
droAna3	scaffold_13266:8260384-8260523 -	1	GGTTCAATGAT-----TA---------T-------------------TAGAGCTAA-----------------------CAACTAATGCCAAATATATATAC-TC--AATCGATGTACTTGGTTATTTGCAAAGGAATACACTGCGTATGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--TG-CCAAAGCTTGTTAGT-
droBip1	scf7180000396759:556673-556805 +	1	GTTTTGCAAAT-----CG----------------------------TTATA------------------------------GCTAATGCCAAATATATATAC-TC--GATCGATGTACTTGGTTATTTGCAAAGGAATACACTGTGTATGTATATATATTCGGTAAAATC-----ACATCTTTGAAT--CG-CCATAGCTTGTTAGT-
dp4	chr3:9376521-9376668 +	2	ACG--AGAAATGCC------------------ATATAGGCAATAAACTAT-----------------------------TAGCTAT-CGCAAATATATATAC-TC--ATTTCATGTACTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTAATC-----ACATCTTTGAATCTTT-CCATAGCTCGTTAGA-
droPer1	super_4:4699742-4699885 +	2	GAGATG------CC------------------ATATAGGCAATAAGCTAT-----------------------------TAGCTAT-CGCAAATATATATAC-TC--ATTTCATGTACTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTGATC-----ACATCTTTGAATCTCT-CCATAGCTCGTTAGA-
droWil1	scaffold_181141:2403442-2403586 +	3	GTGTAGGTATA-----AGTGTTGCCTTT------T--TGTG-----TTATT------------------------------TCTAG-TTCAAATATATATAC-GC--ATTTTCTGTATATGACTATATGCAAAGGTATACAT-TTA--TGTATATATATTTGGTAAAATC-----ACATCTTTGAAT--AATCCATAGCTCGTCAGA-
droVir3	scaffold_12823:519093-519222 +	3	GTATTAT---CTA--------------C------------------ATATA------------------------------TCTAT-GTCAAATATATATAT-CCCCATTTTGTATAACTATTTATATGCAAGGGTATACGT-TTA--CGTATATATATTTGTTAAAATC-----ACATCTTTGAATG-CT-ATATAGCTCGTTAGC-
droMoj3	scaffold_6496:318093-318227 +	2	AGTTGCAGAAG-----TA---------T--TCATA--TGTA-----CAAAA-----T------------------------CTTAT-ATCAAATATATATAT-AT--GTCCCAT--------TTGTATGCAAGGGTATGCGT-TTCTCTATATATATATTTGTTAAAATC-----ACATCTTTGAAT--GGTATTTAGCTCGTTAGC-
droGri2	scaffold_15245:6157822-6157948 -	1	TACATT-AAATTA--------------TGTTCGTT--TTTA-----GGAAA-----CCTGTTCAAAAGATTCGTCTTGTTTATCA---------------------------------TTACACACTTACATAATAACCT------------AATCTAATTGATAAAATCTACAGACAATTTTTGGT--TA-CCTTAG------AAA-

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GGATGGGAAA----TTATACATAGGTG-----TTAT-------ATC-TAGGCCAAATATATATACTTGTTCTATGTATT---AGTTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT

Size

Hit Count

Total Norm

droSim1

GGATGGGAAA----CT----ATAGGTA-----TTAT-------ATC-TAGGCCAAATATATATACTTG-TCTATGTATT---AGTTATTTGCAAAGGAATACATGTG-CGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................ATATATATACTTG-CCTATG.........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.......................................................ATATATATACTTG-TCTATG.........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

GGATGGGAAA----CT----ATAGGTA-----TTAT-------ATC-TAGGCCAAATATATATACTTGTTCTATGTATT---AGTTATTTGCAAAGGAATACATGTG-CGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................ATATATACTTGTTCTATGT........................................................................................	19	1	1.00	0.00	0.00	1.00
...................................................................................................TACATGTG-CGTGTATATATATT..........................................	22	1	1.00	0.00	0.00	1.00
...................................................................................................TACATGTG-CGTGTATATATAT...........................................	21	1	1.00	1.00	0.00	0.00
..................................................................................................................TATATATTCGGTAAAATCACA.............................	21	1	1.00	1.00	0.00	0.00
..................................................................................................ATACATGTG-CGTGTATATATA............................................	21	1	1.00	1.00	0.00	0.00

droYak2

TAAGGGGAAA----------------------TTAT-------ACC-TAGGCCAAATATATATACTTGTTCTGTGTATC---AATTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GAAGGAAAA-G---------------------TTAC-------ACC-TAGGCCAAATATATATACTTGTTCTATGTATT---AATTATTTGCAAAGGAATACATGTG-CCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................ATTTGCCAAGGAATAGAT............................................................	18	1	2.00	0.00	0.00	0.00	2.00
........................................................................ATGTATT---TTTTATTTGCAAA.....................................................................	20	1	1.00	1.00	0.00	0.00	0.00

droAna3

TATT-AG-AGC---------------------TAAC-------AACTAATGCCAAATATATATACTCAATCGATGTACT--TGGTTATTTGCAAAGGAATACACTGCGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCAAAGCTTGTTAGT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................................................................................................................................AATCACATCTTTGTAA--TG-CC.............	20	1	1.00	0.00	0.00	1.00	0.00
......................................................................CGAGGTAGT--TGGTTATTT..........................................................................	18	1	1.00	0.00	0.00	1.00	0.00

dp4

ACG--AGAAA----TGCCATATAGGCA-----ATA-AACTATTAGC-TATCGCAAATATATATACTCATTTCATGTACT--TGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTAATCACATCTTTGAATCTTT-CCATAGCTCGTTAGA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GAGA----------TGCCATATAGGCA-----ATA-AGCTATTAGC-TATCGCAAATATATATACTCATTTCATGTACT--TGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTGATCACATCTTTGAATCTCT-CCATAGCTCGTTAGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................................................................................................................ATATATATTTTCTATGAT.................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00

droWil1

GTAGGTATAAGTGTTGCCT-TTTTGTG-----TTAT-------TTC-TAGTTCAAtTtTtTtTtgGgtTTTTgTGTtTt--TGtgTtTtTGgtttGGTtTtgtTTTt---TGTtTtTtTtTTTGGTAAAATCACATCTTTGAAT--AATCCATAGCTCGTCAGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.............................................................................................................................................AAT--AATCGCTAGCTCGTC...	18	1	14.00	0.00	0.00	0.00	14.00
..................................................................................................TTTGTGTTT---TGTTGTTTTTTT..........................................	21	2	2.50	0.50	2.00	0.00	0.00
..........................................................TTTTTTGTGTTTTTxTGTTTT--TGTG...............................................................................	24	1	5.00	0.00	5.00	0.00	0.00
...................................................................................................TTGTGTTT---TGTTGTTTTTTTT.........................................	21	2	2.00	0.00	2.00	0.00	0.00
.............................................................................................................................................AAT--AATCGCTAGCTCGTCA..	19	1	2.00	0.00	0.00	1.00	1.00
.........................................................................................................TT---TGTTTTTTTTGTTGGTC.....................................	19	1	2.00	0.00	0.00	0.00	2.00
.....................................................................................TTTTTGTTTTGTTTTTGTT............................................................	19	16	0.06	0.06	0.00	0.00	0.00
..........................................................TTTTTTGTGTTTTTxTGTTTT--TGTGT..............................................................................	25	1	1.00	0.00	1.00	0.00	0.00
........................................................TTTTTTTTGTGTTTGTGTGTT.......................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................TTGTTTTT---TGTTTTTTTATT..........................................	20	6	0.17	0.00	0.17	0.00	0.00
............................................TG-TAGTTCTATTTTTTTT.....................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................TTTGTTGGGTTTTGTTTTT---TGTTT.................................................	24	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................TGTTTTTTTTTTTGGACA....................................	18	3	0.33	0.00	0.00	0.00	0.33
.....................................................................................................TGTTTT---TGTTTTTTTTTTTG........................................	20	12	0.08	0.00	0.00	0.00	0.08
....................................................................................GTTTTTGTTATGGTTTTGTT............................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................GTTTGGTTTTGCTTTT---TGC...................................................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................TTTGATTTTTTGGTAAAA..................................	18	1	1.00	0.00	1.00	0.00	0.00
......................................................ATTTTTTTTTTGGTTTTGGT..........................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................TTTGTTTTT---TGTTTTTGGT............................................	19	7	0.14	0.00	0.14	0.00	0.00
............................................................................................TTTGGTTTTTTTTTT---TTTTTTTTTTTT..........................................	27	8	0.13	0.00	0.13	0.00	0.00
.....................................................................TTTGTGTTTT--TTTTTTTTTGGT.......................................................................	22	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................TTTT---TGTTTTTCTTTTTGGT......................................	20	4	0.25	0.00	0.25	0.00	0.00
......................................................................................TTTTGTTTTGTTTTTGTTTTT---T.....................................................	22	8	0.13	0.00	0.13	0.00	0.00
........................................................ATTTTTTTGGGTTTTTGC..........................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................ATTTTTTTTGGTTTTTTG...........................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................TTTTCGTTTT---TGTTTTTTTTT...........................................	21	9	0.11	0.11	0.00	0.00	0.00
.............................................................................................TTTTTTTTGTTTTT---TGTTTTTT..............................................	22	27	0.04	0.00	0.04	0.00	0.00
.........................................................................................................TT---TGTTTGTATTTTTGGT......................................	18	2	0.50	0.00	0.50	0.00	0.00
...................................................................................................TTGTTTTT---TGTTGTTGTTTTT.........................................	21	6	0.17	0.17	0.00	0.00	0.00
............................................................................................TTTTTTTTTGTTTTT---TGTTTTTTTTT...........................................	26	15	0.07	0.00	0.07	0.00	0.00
........................................................................................................TTT---TGTTTATGTTTTTGGT......................................	19	2	0.50	0.00	0.50	0.00	0.00
.........................................................TTTTTTTGTGTTTTTxTGTTTT--TGT................................................................................	24	2	0.50	0.00	0.50	0.00	0.00
..................................................................GTGTTTTTGTTTT--TGTGTT.............................................................................	19	3	0.33	0.00	0.00	0.33	0.00
.......................................................TTTTTTTTTGGGTTTTTGTTTAT......................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...........................................................TTTTTGTGTTTTGGTGTT.......................................................................................	18	3	0.33	0.00	0.33	0.00	0.00
..............................................................TTGCGTTTTTGTGTGTT--TGTG...............................................................................	21	1	1.00	1.00	0.00	0.00	0.00
...................................................................................................ATGTTTTT---TGTTTTTTTCTT..........................................	20	3	0.33	0.00	0.33	0.00	0.00
........................................................................................................TTT---TGTTTTTTCTTTTGGT......................................	19	5	0.20	0.00	0.20	0.00	0.00
...............................................................TGCGTTTTTGTGTGTT--TGTGTT.............................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...................................................................TTTTTGTGTTTT--GGTGTT.............................................................................	18	3	0.33	0.00	0.33	0.00	0.00
.........................................................TATTTTTGGGTTTTTGTT.........................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................GAT---TGTTTTTTTTTTTGGT......................................	19	1	1.00	0.00	1.00	0.00	0.00
......................................................................................TGTTGGTTTGGTTTTGCT............................................................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................................................AAACACATCTTTGAAG--AA................	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................GTTTTGTTTTT---GGTTGTT...............................................	18	2	0.50	0.00	0.50	0.00	0.00
..........................................................TTTTTTTGGTTTTTGTGT........................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
...............................................................TGCGTTTTTGTGTGTT--TGTGT..............................................................................	21	2	0.50	0.50	0.00	0.00	0.00
...........................................................TTTTTTGGTGTTTGTGTT.......................................................................................	18	4	0.25	0.00	0.00	0.25	0.00
.....................................................................................TTTTTGTTATGGTTTTGT.............................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................TTTTTTTTT---TGTGTTTTTTTTT.........................................	22	28	0.04	0.00	0.04	0.00	0.00
......................................................................TTGTGTTTG--TGTGTTTTG..........................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................TTCTTTTTTT---TGTTTTTTTT............................................	20	31	0.03	0.00	0.03	0.00	0.00
.................................................................................................TTTTTTTTTT---TGCTTTTTT.............................................	19	42	0.02	0.00	0.02	0.00	0.00
............................................................................................TTTGTTTTTGTTTTT---TGTTTT................................................	21	14	0.07	0.00	0.07	0.00	0.00
..................................................................................................TTTGTATTT---TGTTTTTTATTT..........................................	21	3	0.33	0.00	0.33	0.00	0.00
................................................................................................ATTTTGTTTTT---TGTTTTTTC.............................................	20	5	0.20	0.00	0.20	0.00	0.00
......................................................................................ATTTGGTTTGGTTTTGGTT...........................................................	19	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................TTTTTGGTTTGGTTTTTGTT...........................................................	20	3	0.33	0.33	0.00	0.00	0.00
...........................................................................TTTT--TGTTTTTTCGGTTTGGT..................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.........................................................TTTTTTTGTGTTTTTxTGTTTT--TGTG...............................................................................	25	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................TTTGTTTTT---TTTGTTTTT.............................................	18	51	0.02	0.00	0.02	0.00	0.00
............................................................TTTTGTGTTTTTxTGTTTT--TGTGT..............................................................................	23	1	1.00	0.00	1.00	0.00	0.00
................................................................................................GTTTTTTTTTT---TGTTTCTT..............................................	19	10	0.10	0.00	0.10	0.00	0.00
.....................................................................................................GTTTTT---TGTTTTTTTTTGTT........................................	20	12	0.08	0.00	0.08	0.00	0.00
.....................................................................................TATTTGGTTTGATTTTGT.............................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................TTTTTTTTT---TGTTGTTTT.............................................	18	50	0.02	0.00	0.02	0.00	0.00
........................................................................................TTGGTTTTGTTTTGTTGTT---T.....................................................	20	3	0.33	0.00	0.33	0.00	0.00
......................................................................................TTTAGTTTTGGTTTTGTTT...........................................................	19	1	1.00	0.00	1.00	0.00	0.00
.........................................................................TGTTTT--TGTTTTCTTGGTTTGGT..................................................................	23	1	1.00	0.00	1.00	0.00	0.00
...................................................................................................TTGTTTTT---TGTTTTTGTTTT..........................................	20	15	0.07	0.00	0.07	0.00	0.00
.............................................................TTTGCGTTTTTGTGTGTT--TGTG...............................................................................	22	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................TTTTTTTTTT---TGTTTTTGTTTTTG........................................	24	7	0.14	0.00	0.14	0.00	0.00
........................................................TTTTTTTTAGGTTTGTGTG.........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

TTGC-AA-AAGTAT-T------ATCTA----CATAT-------ATC-TATGTCAAATATATATATCCCCATTTTGTATAACTATTTATATGCAAGGGTATACGTTTA---CGTATATATATTTGTTAAAATCACATCTTTGAAT--GCTATATAGCTCGTTAGC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TTGC-AG-AAGTATTC----ATATGTA-----CAAA-------ATCTTATATCAAATATATATATATGTCCCA----------TTTGTATGCAAGGGTATGCGTTTC-TCTATATATATATTTGTTAAAATCACATCTTTGAAT--GGTATTTAGCTCGTTAGC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TTGCCAGGA-GT-----CTTACAACTAACTACTTAT-------AAC-TATATCAAATATATATACTCACTTTGTGTATAGCTACGTATAAGCAAAGGTATACGCTTG---CGTATATATATTTGTTAAAATCACATCTTTGAAT--GGTATATAGCTCGTCAGC

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