dme-mir-4979- Best orthologs

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

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:19621540-19621679 -		1	GG-ATGGGAAA---------TTATACATAG---GT-----G-TTA-TATCTAG-GCCAAATATATATAC-TTGTTCTATGTA---TTAGTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droSim1	chr2R:18187644-18187778 -	LASTZ	1	GG-ATGGGAAA---------CTA----TAG---GT-----A-TTA-TATCTAG-GCCAAATATATATAC-TTG-TCTATGTA---TTAGTTATTTGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droSec1	super_9:2901906-2902041 -	LASTZ	1	GG-ATGGGAAA---------CTA----TAG---GT-----A-TTA-TATCTAG-GCCAAATATATATAC-TTGTTCTATGTA---TTAGTTATTTGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droYak2	chr2R:19599592-19599718 -	LASTZ	5	TA-AGGGGAAA-------------------------------TTA-TACCTAG-GCCAAATATATATAC-TTGTTCTGTGTA---TCAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droEre2	scaffold_4845:20984379-20984510 -	LASTZ	5	CT-GTAGAA------------------------GGAA-AAG-TTA-CACCTAG-GCCAAATATATATAC-TTGTTCTATGTA---TTAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droEug1	scf7180000409474:21612-21738 +	LASTZ	5	CG----GGAA-----------------------------AG-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAG--TG-CCACAGCTCGCTAGT-
droBia1	scf7180000302143:1773637-1773756 +	LASTZ	5	AG----------------------------------------TTA-CGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--TTTAATTATTTGCAAAGGAATACAC-ATATTTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACTGCTCGCTAGT-
droTak1	scf7180000415400:558002-558129 -	LASTZ	5	AG-TTGGGAGA----------------------------TA-T---TGCCTAA-GCCAAATATATATAC-TCGTTTTATGTA--CTTAATTATTTGCAAAGGAATACAA-GTATATGTATATATATTTGGTAAAATCACATCTTTGAAT--TG-CCGGAGCTCGCTAGT-
droEle1	scf7180000491201:1147757-1147882 +	LASTZ	5	GG------AAA----------------------------TA-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTAATTATTTGCAAAGGAATACAC-TTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGTTAGT-
droRho1	scf7180000778122:26363-26489 +	LASTZ	5	CA-----GAAA----------------------------TA-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTATTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droFic1	scf7180000453809:586655-586785 +	LASTZ	5	AG-TTGGAAAA---------A------------------AA-TTA-TGCCTAG-GCCAAATATATATAC-TCGTTCTATGTA--CTTATTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droKik1	scf7180000302470:2102706-2102852 +	LASTZ	5	AA-AAT-GAAA---------TTC--CAGT-AAAGCAGT--ATGTA-TGTCTAGCGCCAAATATATATACGTTGTTCTATGTA--CTTGGTTATATGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--CG-CCACAGCTCGTTAGTT
droAna3	scaffold_13266:8260384-8260523 -	LASTZ	5	GG-TTCAATGA---------TTA----TTA---G-----AGCTAA-CAACTAATGCCAAATATATATAC-TCAATCGATGTA--CTTGGTTATTTGCAAAGGAATACACTGCGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCAAAGCTTGTTAGT-
droBip1	scf7180000396759:556673-556805 +	LASTZ	5	GT-TTTGCAAA---------T------------------CG-TTA-TAGCTAATGCCAAATATATATAC-TCGATCGATGTA--CTTGGTTATTTGCAAAGGAATACACTGTGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--CG-CCATAGCTTGTTAGT-
dp4	chr3:9376521-9376668 +	LASTZ	5	AC-G--AGAAA---------TGC--CATA-TAGGCAATAAA-CTATTAGCTAT-CGCAAATATATATAC-TCATTTCATGTA--CTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTAATCACATCTTTGAATCTTT-CCATAGCTCGTTAGA-
droPer1	super_4:4699742-4699885 +	LASTZ	5	GAGATGCCA------------------TA-TAGGCAATAAG-CTATTAGCTAT-CGCAAATATATATAC-TCATTTCATGTA--CTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTGATCACATCTTTGAATCTCT-CCATAGCTCGTTAGA-
droWil1	scaffold_181141:2403442-2403586 +	LASTZ	5	GT-GTAGGTATAAGTGTTGCCTT----TTT---GT-----G-TTA-TTTCTAG-TTCAAATATATATAC-GCATTTTCTGTA--TATGACTATATGCAAAGGTATACAT-TTA--TGTATATATATTTGGTAAAATCACATCTTTGAAT--AATCCATAGCTCGTCAGA-
droVir3	scaffold_12823:519093-519222 +	LASTZ	5	GT-ATTAT------------CTA----C--------------ATA-TATCTAT-GTCAAATATATATAT-CCCCATTTTGTATAACTATTTATATGCAAGGGTATACGT-TTA--CGTATATATATTTGTTAAAATCACATCTTTGAAT--GCTATATAGCTCGTTAGC-
droMoj3	scaffold_6496:318093-318227 +	LASTZ	5	AG-TTGCAGAA---------GTATTCATAT---GT-----A-CAA-AATCTTATATCAAATATATATAT-ATGTCCCAT----------TTGTATGCAAGGGTATGCGT-TTCTCTATATATATATTTGTTAAAATCACATCTTTGAAT--GGTATTTAGCTCGTTAGC-
droGri2	scaffold_15245:6158007-6158151 -	MAF	5	TT-GCCAGGAG----------TC---TTA-CAACTAACT-ACTTA-TAACTAT-ATCAAATATATATAC-TCACTTTGTGTATAGCTACGTATAAGCAAAGGTATACGC-TTG--CGTATATATATTTGTTAAAATCACATCTTTGAAT--GGTATATAGCTCGTCAGC-

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species	Alignment
dm3	GG-ATGGGAAA---------TTATACATAG---GT-----G-TTA-TATCTAG-GCCAAATATATATAC-TTGTTCTATGTA---TTAGTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droSim1	GG-ATGGGAAA---------CTA----TAG---GT-----A-TTA-TATCTAG-GCCAAATATATATAC-TTG-TCTATGTA---TTAGTTATTTGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droSec1	GG-ATGGGAAA---------CTA----TAG---GT-----A-TTA-TATCTAG-GCCAAATATATATAC-TTGTTCTATGTA---TTAGTTATTTGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droYak2	TA-AGGGGAAA-------------------------------TTA-TACCTAG-GCCAAATATATATAC-TTGTTCTGTGTA---TCAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droEre2	CT-GTAGAA------------------------GGAA-AAG-TTA-CACCTAG-GCCAAATATATATAC-TTGTTCTATGTA---TTAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droEug1	CG----GGAA-----------------------------AG-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAG--TG-CCACAGCTCGCTAGT-
droBia1	AG----------------------------------------TTA-CGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--TTTAATTATTTGCAAAGGAATACAC-ATATTTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACTGCTCGCTAGT-
droTak1	AG-TTGGGAGA----------------------------TA-T---TGCCTAA-GCCAAATATATATAC-TCGTTTTATGTA--CTTAATTATTTGCAAAGGAATACAA-GTATATGTATATATATTTGGTAAAATCACATCTTTGAAT--TG-CCGGAGCTCGCTAGT-
droEle1	GG------AAA----------------------------TA-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTAATTATTTGCAAAGGAATACAC-TTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGTTAGT-
droRho1	CA-----GAAA----------------------------TA-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTATTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droFic1	AG-TTGGAAAA---------A------------------AA-TTA-TGCCTAG-GCCAAATATATATAC-TCGTTCTATGTA--CTTATTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-
droKik1	AA-AAT-GAAA---------TTC--CAGT-AAAGCAGT--ATGTA-TGTCTAGCGCCAAATATATATACGTTGTTCTATGTA--CTTGGTTATATGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--CG-CCACAGCTCGTTAGTT
droAna3	GG-TTCAATGA---------TTA----TTA---G-----AGCTAA-CAACTAATGCCAAATATATATAC-TCAATCGATGTA--CTTGGTTATTTGCAAAGGAATACACTGCGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCAAAGCTTGTTAGT-
droBip1	GT-TTTGCAAA---------T------------------CG-TTA-TAGCTAATGCCAAATATATATAC-TCGATCGATGTA--CTTGGTTATTTGCAAAGGAATACACTGTGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--CG-CCATAGCTTGTTAGT-
dp4	AC-G--AGAAA---------TGC--CATA-TAGGCAATAAA-CTATTAGCTAT-CGCAAATATATATAC-TCATTTCATGTA--CTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTAATCACATCTTTGAATCTTT-CCATAGCTCGTTAGA-
droPer1	GAGATGCCA------------------TA-TAGGCAATAAG-CTATTAGCTAT-CGCAAATATATATAC-TCATTTCATGTA--CTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTGATCACATCTTTGAATCTCT-CCATAGCTCGTTAGA-
droWil1	GT-GTAGGTATAAGTGTTGCCTT----TTT---GT-----G-TTA-TTTCTAG-TTCAAATATATATAC-GCATTTTCTGTA--TATGACTATATGCAAAGGTATACAT-TTA--TGTATATATATTTGGTAAAATCACATCTTTGAAT--AATCCATAGCTCGTCAGA-
droVir3	GT-ATTAT------------CTA----C--------------ATA-TATCTAT-GTCAAATATATATAT-CCCCATTTTGTATAACTATTTATATGCAAGGGTATACGT-TTA--CGTATATATATTTGTTAAAATCACATCTTTGAAT--GCTATATAGCTCGTTAGC-
droMoj3	AG-TTGCAGAA---------GTATTCATAT---GT-----A-CAA-AATCTTATATCAAATATATATAT-ATGTCCCAT----------TTGTATGCAAGGGTATGCGT-TTCTCTATATATATATTTGTTAAAATCACATCTTTGAAT--GGTATTTAGCTCGTTAGC-
droGri2	TT-GCCAGGAG----------TC---TTA-CAACTAACT-ACTTA-TAACTAT-ATCAAATATATATAC-TCACTTTGTGTATAGCTACGTATAAGCAAAGGTATACGC-TTG--CGTATATATATTTGTTAAAATCACATCTTTGAAT--GGTATATAGCTCGTCAGC-

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

Small RNA-seq read pileup

Species

Alignment

droSim1

GG-ATGGGAAA---------CTA----TAG---GT-----A-TTA-TATCTAG-GCCAAATATATATAC-TTG-TCTATGTA---TTAGTTATTTGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................ATATATATAC-TTG-CCTATG..........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................ATATATATAC-TTG-TCTATG..........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

GG-ATGGGAAA---------CTA----TAG---GT-----A-TTA-TATCTAG-GCCAAATATATATAC-TTGTTCTATGTA---TTAGTTATTTGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.............................................................ATATATAC-TTGTTCTATGT.........................................................................................	19	1	1.00	0.00	0.00	1.00
........................................................................................................TACAT-GTGCGTGTATATATATT...........................................	22	1	1.00	0.00	0.00	1.00
........................................................................................................TACAT-GTGCGTGTATATATAT............................................	21	1	1.00	1.00	0.00	0.00
.......................................................................................................................TATATATTCGGTAAAATCACA..............................	21	1	1.00	1.00	0.00	0.00
.......................................................................................................ATACAT-GTGCGTGTATATATA.............................................	21	1	1.00	1.00	0.00	0.00

droYak2

TA-AGGGGAAA-------------------------------TTA-TACCTAG-GCCAAATATATATAC-TTGTTCTGTGTA---TCAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

CT-GTAGAA------------------------GGAA-AAG-TTA-CACCTAG-GCCAAATATATATAC-TTGTTCTATGTA---TTAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--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
.............................................................................ATGTA---TTTTTTATTTGCAAA......................................................................	20	1	1.00	1.00	0.00	0.00	0.00
...GTAGAA------------------------GGAA-AAG-TTA-CACCT.......................................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00

droEug1

CG----GGAA-----------------------------AG-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTAATTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAG--TG-CCACAGCTCGCTAGT-

Size

Hit Count

Total Norm

droBia1

AG----------------------------------------TTA-CGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--TTTAATTATTTGCAAAGGAATACAC-ATATTTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACTGCTCGCTAGT-

Size

Hit Count

Total Norm

droTak1

AG-TTGGGAGA----------------------------TA-T---TGCCTAA-GCCAAATATATATAC-TCGTTTTATGTA--CTTAATTATTTGCAAAGGAATACAA-GTATATGTATATATATTTGGTAAAATCACATCTTTGAAT--TG-CCGGAGCTCGCTAGT-

Size

Hit Count

Total Norm

droEle1

GG------AAA----------------------------TA-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTAATTATTTGCAAAGGAATACAC-TTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGTTAGT-

Size

Hit Count

Total Norm

droRho1

CA-----GAAA----------------------------TA-TTA-TGCCTAA-GCCAAATATATATAC-TCGTTCTATGTA--CTTATTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-

Size

Hit Count

Total Norm

droFic1

AG-TTGGAAAA---------A------------------AA-TTA-TGCCTAG-GCCAAATATATATAC-TCGTTCTATGTA--CTTATTTATTTGCAAAGGAATACAT-GTGCCTGTATATATATTCGGTAAAATCACATCTTTGAAT--TG-CCACAGCTCGCTAGT-

Size

Hit Count

Total Norm

droKik1

AA-AAT-GAAA---------TTC--CAGT-AAAGCAGT--ATGTA-TGTCTAGCGCCAAATATATATACGTTGTTCTATGTA--CTTGGTTATATGCAAAGGAATACAT-GTGCGTGTATATATATTCGGTAAAATCACATCTTTGAAT--CG-CCACAGCTCGTTAGTT

Size

Hit Count

Total Norm

droAna3

GG-TTCAATGA---------TTA----TTA---G-----AGCTAA-CAACTAATGCCAAATATATATAC-TCAATCGATGTA--CTTGGTTATTTGCAAAGGAATACACTGCGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--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
...........................................................................CGAGGTA--GTTGGTTATTT...........................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droBip1

GT-TTTGCAAA---------T------------------CG-TTA-TAGCTAATGCCAAATATATATAC-TCGATCGATGTA--CTTGGTTATTTGCAAAGGAATACACTGTGTATGTATATATATTCGGTAAAATCACATCTTTGAAT--CG-CCATAGCTTGTTAGT-

Size

Hit Count

Total Norm

dp4

AC-G--AGAAA---------TGC--CATA-TAGGCAATAAA-CTATTAGCTAT-CGCAAATATATATAC-TCATTTCATGTA--CTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTAATCACATCTTTGAATCTTT-CCATAGCTCGTTAGA-

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GAGATGCCA------------------TA-TAGGCAATAAG-CTATTAGCTAT-CGCAAATATATATAC-TCATTTCATGTA--CTTGTTTATGTGCAAAGGAATACATTTTTGTTCTATATATATTTGCTTTGATCACATCTTTGAATCTCT-CCATAGCTCGTTAGA-	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................................................................................................................................................................GA-	19	14	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................................................................................................AGA-	20	7	1.14	1.14	0.00	0.00	0.00	0.00
.....................................................................................................................................................................TAGA-	19	4	1.25	1.25	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GA-	18	14	0.36	0.36	0.00	0.00	0.00	0.00
.....................................................................................................................................................................TAGA-	20	4	0.75	0.75	0.00	0.00	0.00	0.00
.....................................................................................................................................................................TAGA-	21	4	0.75	0.75	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GA-	20	3	0.67	0.00	0.00	0.00	0.00	0.67
.......................................................................................................................................................................GA-	19	35	0.06	0.00	0.00	0.00	0.00	0.06
......................................................................................................................................................................GAA-	23	12	0.17	0.00	0.00	0.00	0.00	0.17
......................................................................................................................ATATATATTTTCTATGAT..................................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................................................................................................................................A-	18	36	0.03	0.03	0.00	0.00	0.00	0.00
........................................................................................................................................................................A-	20	6	0.17	0.00	0.17	0.00	0.00	0.00
......................................................................................................................................................................AGG-	20	4	0.25	0.00	0.00	0.00	0.25	0.00
........................................................................................................................................................................A-	18	11	0.09	0.00	0.09	0.00	0.00	0.00
........................................................................................................................................................................A-	26	24	0.04	0.04	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GA-	19	14	0.07	0.00	0.07	0.00	0.00	0.00
........................................................................................................................................................................G-	21	16	0.06	0.06	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GA-	19	7	0.14	0.00	0.14	0.00	0.00	0.00
......................................................................................................................................................................AGA-	20	8	0.13	0.13	0.00	0.00	0.00	0.00
......................................................................................................................................................................ATA-	24	5	0.20	0.00	0.20	0.00	0.00	0.00
......................................................................................................................................................................AGA-	20	8	0.13	0.00	0.13	0.00	0.00	0.00
........................................................................................................................................................................A-	19	10	0.10	0.10	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GA-	19	8	0.13	0.00	0.00	0.00	0.00	0.13
.....................................................................................................................................................................TAGC-	18	3	0.33	0.33	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GA-	22	3	0.33	0.00	0.00	0.00	0.00	0.33

droWil1

GT-GTAGGTATAAGTGTTGCCTT----TTT---GT-----G-TTA-TTTCTAG-TTCAAATATATATAC-GCATTTTCTGTA--TATGACTATATGCAAAGGTATACAT-TTA--TGTATATATATTTGGTAAAATCACATCTTTGAAT--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
..................................................................................................................................................AAT--AATCGCTAGCTCGTCA...	19	1	2.00	0.00	0.00	1.00	1.00
..........................................................................................................CAT-TTA--TGxATATTTATTTG.........................................	19	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
.............................................................................................ATGGAAAAGTATACAT-TT..........................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................................TA--TATATTTATATTTGGT.......................................	18	9	0.11	0.00	0.11	0.00	0.00
.....................................................................................................................TATATATTTCTGGTAAAAT..................................	19	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................AT-TTA--TGTATATATATTAGCT.......................................	21	2	0.50	0.00	0.50	0.00	0.00

droVir3

GT-ATTAT------------CTA----C--------------ATA-TATCTAT-GTCAAATATATATAT-CCCCATTTTGTATAACTATTTATATGCAAGGGTATACGT-TTA--CGTATATATATTTGTTAAAATCACATCTTTGAAT--GCTATATAGCTCGTTAGC-	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.......................................................................................................................................................................GA-	19	41	0.05	0.02	0.00	0.02	0.00	0.00
.......................................................................................................................................................................GC-	21	26	0.04	0.04	0.00	0.00	0.00	0.00
........................................................................................................................................................................C-	18	24	0.04	0.00	0.00	0.04	0.00	0.00
.....................................................................................................................................................................TAGC-	18	47	0.02	0.02	0.00	0.00	0.00	0.00
......................................................................................................................................................................AGC-	26	18	0.06	0.06	0.00	0.00	0.00	0.00
........................................................................................................................................................................C-	19	14	0.07	0.07	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GA-	23	25	0.04	0.04	0.00	0.00	0.00	0.00
......................................................................................................................................................................TTC-	18	32	0.03	0.03	0.00	0.00	0.00	0.00
.......................................................................................................................................................................GT-	18	24	0.04	0.00	0.00	0.04	0.00	0.00
.......................................................................................................................................................................GC-	20	41	0.02	0.02	0.00	0.00	0.00	0.00
....................................................................................................................................................................ATAGC-	18	16	0.06	0.06	0.00	0.00	0.00	0.00

droMoj3

AG-TTGCAGAA---------GTATTCATAT---GT-----A-CAA-AATCTTATATCAAATATATATAT-ATGTCCCAT----------TTGTATGCAAGGGTATGCGT-TTCTCTATATATATATTTGTTAAAATCACATCTTTGAAT--GGTATTTAGCTCGTTAGC-

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TT-GCCAGGAG----------TC---TTA-CAACTAACT-ACTTA-TAACTAT-ATCAAATATATATAC-TCACTTTGTGTATAGCTACGTATAAGCAAAGGTATACGC-TTG--CGTATATATATTTGTTAAAATCACATCTTTGAAT--GGTATATAGCTCGTCAGC-

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:18:45 EDT

dme-mir-4979

chr2R:19621555-19621664 -

Known_mirbase

intergenic

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup