dme-mir-4942- Best orthologs

dme-mir-4942	chr3L:23332327-23332437 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 23332387-23332408
   star strand at position 23332354-23332375
   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	chr3L:23332312-23332452 +		1	TATGACAT--CTGCCTGTTATGA--------ATACAT------------------------------------AT--------ATTTTTATGTTTGA-GTCAA---------------------------------------------CATCGA-GTTGCCGATGTT---TG---GAAAACATCGA------------------------TGACATCGCT----------GTTGGC----ATCGAA----ATATGTCCATATCTAAT----------ATATAGTTC--CATTCTGT----TTTATT
droSim1	chr3L:22456065-22456207 +	LASTZ	5	AATGACAG--CTGCCTGTTATAA--------GTAATT------------------------------------GT--------ATTTTTATGTTTGAGCTAAA---------------------------------------------CATCGATTATGCCGATGTT---TG---GAAAACATCGA------------------------TGACATCGCT----------CTTGCC----ATCAAA----GTATGTCCATATCTAAT----------ATATAGTTC--CATTCTGT----TATATT
droSec1	super_41:217199-217341 +	LASTZ	5	AATGACAT--CTGCCTGTTGTAA--------GTAATT------------------------------------GT--------ATTTTTATGTTTGAGCTAAA---------------------------------------------CATCGATTATGCCGATGTT---TG---GAAAACATCGA------------------------TGACATCGCT----------GTTGCC----ATCAAA----GTATGTCCATATCTAAT----------ATATAGTTC--CATTCTGT----TATATT
droYak2	chr3L:23917805-23917956 +	LASTZ	0	TATGATAT--CTGAATATTTAGT--------TTTT----------------------------------CTTT-TGCATATTTATTTTTAATATTGAGCTTCA---------------------------------------------CATATATATTGCCGATGTT---TA---CAAAACATCGA------------------------TGACATTGTT----------TTTGGC----ATCGTC----ATATGCCCATCACTAAT----------ATATAGTCC--CCTTCTGT----TTCATT
droEre2	scaffold_4784:22817455-22817604 -	LASTZ	0	GGCAT-----CTGTATAGGATGA--------ATAAAT------------------------------------TA--------ATTTTTAAGTTTGACCACAA---------------------------------------------CTTTCATTTTGCCGATGTT---TA---GAAAACATCGATGACACC-------------------GCATCATC----------GTTGTC----ATCGACTTACATATGTACATCTCTAAT----------ATATAGTAT--CATTCTGT----TTTATT
droEug1	scf7180000409208:8455-8591 +	LASTZ	0	TGTGCCTT-----------AGAA--------AAGGA-------------------AAAACATCGATGTTCCTC-----------------------CGGTAAA---------------------------------------------CATCGATGTTGCCGATGTT---TC---GAAAACATCGA------------------------TGTCATCGAT----------GTTCGC----ATCGAT----GTTTCTCCACCTCTAAT----------GTAGCGTCT--ATTATAGT---CATTATT
droBia1	scf7180000301323:33962-34103 -	LASTZ	0	TGCGCG-----------TTAGAG--------ATGGG-------------------AAAACATCGATGTTGCCT-----------------------GGTAAAA---------------------------------------------CATCGATGTTACCGATGTT---AC---GAAAACATCGA------------------------TGACATCGAT----------GTTGGC----ATCGAT----GTTTCTCCACCTCTACA----------AAGCACTTTATCATTTTGATAGGCTTGTT
droTak1	scf7180000415103:413904-414042 +	LASTZ	0	TTGCAAAT--TT--ACGCCAAGC--------CTATATAAAT-GCCCATTTTTAGT---------CAAAACCAT-----------------------CG------------------------------------------------------AAAAACATCGATGTTTTTTGAC-AAAAACATCGA------------------------AAACATCGAT----------GTTCCCAAAAATCGAT----ATTTCTCCACCTCTATT----------GGATAG-------------------TGCC
droEle1	scf7180000491001:1165148-1165283 -	LASTZ	0	ATGGACGG--ATAAACATTG--------------------------------------------ATAATCT-------------------------CTGTAAA---------------------------------------------AATCGATATAACCGATATT---TT---GGAAACATCGA------------------------TGACATCCAT----------GTTGGC----ATCGAT----GTTTCTCCACCTCTATACCACCTCTACACCCCTCTA--CTATCCGT----ACCATT
droRho1	scf7180000778134:11337-11464 +	LASTZ	0	CATCGTTG--ATGCCT--------------------------------------------------------------------------------CACCAAA---------------------------------------------CATCGATATTACCGATGTT---TG---GAAAACATCGATATTACCGATGTTTAGAATATCGATGACCTCGAT----------GTTAGC----ATCGAT----GTTTGTCCGCCCCTAGC----------TAGT-------------AT----TTAATT
droFic1	scf7180000453143:456-611 +	LASTZ	0	TAATACCCTTTTGCTCTGCAAGG--------GTATA-------------------AAAACAACGATGTTGCCC-----------------------CGGTAAA---------------------------------------------CATCAATGTTGCCGATGTT---TC---AAAAACATCGA------------------------TGTCATCGAT----------GTTGGC----ATCGAC----GTTTCTCCACCTCTACGAAGTA-TTACAGATACTTA--TTTTCAAT----TTTTGT
droKik1	scf7180000302481:290430-290562 +	LASTZ	0	TCTTATAT--CCGCCCCCTTCGG--------TTTTC-------------------ATTTAAATTATGTATCCC-----------------------TGGCAAA---------------------------------------------CATCGATTTTTGCGATGTT---TT---GAAAACATCGA------------------------TGACATCGAT----------G--GGT----ATCGCT----GTTTCTCCACCTCTAAT----------AAACAGTG----------------AAATT
droAna3	scaffold_12916:14167403-14167537 +	LASTZ	0	TGCTCG-----------TTAGAG--------ATG-A-------------------TAAACATCGATGTTGGCT-----------------------TGCCAAA---------------------------------------------CATCGATGTCAACGATGTT---TT---CAAAACATCGA------------------------TGACATCGAT----------GTTAAC----ATCGAT----GTTTCTCCACCTCTGAC----------CACTGGAGT--GAATTATT----TTTAGT
droBip1	scf7180000396634:6934-7072 +	LASTZ	0	TACGATTT--ATTTATTCTATGT--------GTACAT------------------------------------AT--------GTATGTATATCTAAGATGA------CGTA-------------------------------------TTCCA-TTTTCTAAAGTA---GT---GATAATTTGAT------------------------AAAGATCTTT----------ATAGAC----TAC-GC----GTATTTCCATT--T--A----------ATATAGTTC--TATTAAAC----TTAACT
dp4	chrXL_group1e:10317112-10317245 +	LASTZ	0	TCAAACAT--ATTATTTTTATTG--------TAA-----ATATCCTAGTTATGGT-------------------------------------------GTAAA---------------------------------------------T-CTGAAAATATCGATGTT---TGAGAAAAAACATCGA------------------------TGACATCCAT----------GTTAAC----ATCGAT----GTTTGTCCAGCTTTAGC----------TTGCATCCC--TAG-----------CTTG
droPer1	super_69:203478-203603 -	LASTZ	0	CATATT-------ATTATTGTAA--------ATA--------TCCTATTTATAGT-------------------------------------------GTAAA---------------------------------------------T-CTGAAAATATCGATGTT---TGAGAAAAAACATCGA------------------------TGACATCCAT----------GTTAAC----ATCGAT----GTTTGTCCAGCTTTAGC----------TTGCATCCC--TAG-----------CTTG
droWil1	scaffold_181155:90645-90784 -	LASTZ	0	TATTGTTT--CCGCCTCTTCTGA--------TCAATC------------------------------------TA--------TTTCTAATTTATTTGCT-AA---CTTCTTCTCGACTACGTACATATCTACTACGTACAACTCTAGT--CAGATATATCCATATC---CTATAACGAA-------------------------------------------------------------------------------------------------ATCCAACTG--CATTCTTA----ATCGTG
droVir3	scaffold_13036:829247-829384 -	LASTZ	0	TTTATCGT--TTATATTT-----------------G-------------------AAATTATTAATTAAA---TT--------ATTATTATTTTTAAGTAATA---------------------------------------------C----------------------A---AAATAAATTAA------------------------GGAAATAAAAGTGCAAATTTGTTGTT----TTCAAA----G-ATACATTTAATTAAT----------TTTTATTTT--TTTTTTAT----TTTATT
droMoj3	scaffold_6500:19787300-19787437 -	LASTZ	0	TATTATGA--G---CTGAAATAA--------ATATAA------------------------------------AA--------ATATTTAA--TTAAATTCAACAAAATGAT-------------------------------------GTC-------TAGATATT---AA-----AAAAAAAAA------------------------AAAAAATAAA----------ATATAT----ATATAT----ATATATATATATATATA---------TATATATATA--TATTTTTT----TTTTTT
droGri2	scaffold_14853:4224791-4224937 -	LASTZ	0	TATATC-T--ATGCGTCTG-TAGATACTTGCATAAGT------------------------------------GT------AT-CATCTATGTACGGTTTACA---------------------------------------------TATAGTGT---ATGGTTTA---TA---AAAAATATTTC------------------------TCAATACGCC----------GTTAGT----ACAAAA----AAAAAGTAGTGTATAAA----------AAATGCTTG--CACTTTGT----TTTAGT

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	TATGACATCTGCCTGTTATGAATACATATATTTTTATGTTTGAG-TCAACATCGAGT-TGCCGATGTTTGGAAAACATCGATGACATCGCTGTTGGCATCGAAATATGTCCATATCTAATATATAGTTCCATTCTGTTTTATT
droSim1	AATGACAGCTGCCTGTTATAAGTAATTGTATTTTTATGTTTGAGCTAAACATCGATTATGCCGATGTTTGGAAAACATCGATGACATCGCTCTTGCCATCAAAGTATGTCCATATCTAATATATAGTTCCATTCTGTTATATT
droSec1	AATGACATCTGCCTGTTGTAAGTAATTGTATTTTTATGTTTGAGCTAAACATCGATTATGCCGATGTTTGGAAAACATCGATGACATCGCTGTTGCCATCAAAGTATGTCCATATCTAATATATAGTTCCATTCTGTTATATT

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

AATGACAG--CTGCCTGTTATAA--------GTAATT------------------------------------GT--------ATTTTTATGTTTGAGCTAAA---------------------------------------------CATCGATTATGCCGATGTT---TG---GAAAACATCGA------------------------TGACATCGCT----------CTTGCC----ATCAAA----GTATGTCCATATCTAAT----------ATATAGTTC--CATTCTGT----TATATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................................................................................................................GA------------------------TGAAATCGCT----------CGTGCC----..................................................................	18	1	3.00	0.00	0.00	3.00	0.00
.......................................................................................................................................................................................................................................................................................ATAGTTC--CATTCTGT----TATAT.	20	1	1.00	1.00	0.00	0.00	0.00

droSec1

AATGACAT--CTGCCTGTTGTAA--------GTAATT------------------------------------GT--------ATTTTTATGTTTGAGCTAAA---------------------------------------------CATCGATTATGCCGATGTT---TG---GAAAACATCGA------------------------TGACATCGCT----------GTTGCC----ATCAAA----GTATGTCCATATCTAAT----------ATATAGTTC--CATTCTGT----TATATT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....................................................................................................................................................ATCGATTATGCCGATGTT---TG---GAAAA..............................................................................................................................	25	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................................AACATCGA------------------------GGACATCGAT----------............................................................................	18	4	0.25	0.00	0.25	0.00
......AT--TTGCCTGTTTTAA--------GTA................................................................................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

TATGATAT--CTGAATATTTAGT--------TTTT----------------------------------CTTT-TGCATATTTATTTTTAATATTGAGCTTCA---------------------------------------------CATATATATTGCCGATGTT---TA---CAAAACATCGA------------------------TGACATTGTT----------TTTGGC----ATCGTC----ATATGCCCATCACTAAT----------ATATAGTCC--CCTTCTGT----TTCATT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................TGT-AGCATATTTATTTTT.........................................................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................C----ATCGTC----ATATGCCCATCACT..........................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................................C----ATCGTC----ATATGCCCATCACTAAT----------A............................	25	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

GGCAT-----CTGTATAGGATGA--------ATAAAT------------------------------------TA--------ATTTTTAAGTTTGACCACAA---------------------------------------------CTTTCATTTTGCCGATGTT---TA---GAAAACATCGATGACACC-------------------GCATCATC----------GTTGTC----ATCGACTTACATATGTACATCTCTAAT----------ATATAGTAT--CATTCTGT----TTTATT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....................................................................................................................................................................................................................CAGCATC----------GTGGTC----ATCGA.............................................................	18	1	2.00	0.00	0.00	0.00	2.00
........................................................................................................................................................................................GATGACAxC-------------------GCAACATC----------GT..........................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..............................................................................................................................................................................................................................................................GTACATCTCTAAT----------ATATAGTAT--C.................	23	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................................................................................................................................GTACATCTCTAAT----------ATATAGT......................	20	1	1.00	0.00	0.00	0.00	1.00

droEug1

TGTGCCTT-----------AGAA--------AAGGA-------------------AAAACATCGATGTTCCTC-----------------------CGGTAAA---------------------------------------------CATCGATGTTGCCGATGTT---TC---GAAAACATCGA------------------------TGTCATCGAT----------GTTCGC----ATCGAT----GTTTCTCCACCTCTAAT----------GTAGCGTCT--ATTATAGT---CATTATT

Size

Hit Count

Total Norm

droBia1

TGCGCG-----------TTAGAG--------ATGGG-------------------AAAACATCGATGTTGCCT-----------------------GGTAAAA---------------------------------------------CATCGATGTTACCGATGTT---AC---GAAAACATCGA------------------------TGACATCGAT----------GTTGGC----ATCGAT----GTTTCTCCACCTCTACA----------AAGCACTTTATCATTTTGATAGGCTTGTT

Size

Hit Count

Total Norm

droTak1

TTGCAAAT--TT--ACGCCAAGC--------CTATATAAAT-GCCCATTTTTAGT---------CAAAACCAT-----------------------CG------------------------------------------------------AAAAACATCGATGTTTTTTGAC-AAAAACATCGA------------------------AAACATCGAT----------GTTCCCAAAAATCGAT----ATTTCTCCACCTCTATT----------GGATAG-------------------TGCC

Size

Hit Count

Total Norm

droEle1

ATGGACGG--ATAAACATTG--------------------------------------------ATAATCT-------------------------CTGTAAA---------------------------------------------AATCGATATAACCGATATT---TT---GGAAACATCGA------------------------TGACATCCAT----------GTTGGC----ATCGAT----GTTTCTCCACCTCTATACCACCTCTACACCCCTCTA--CTATCCGT----ACCATT

Size

Hit Count

Total Norm

droRho1

CATCGTTG--ATGCCT--------------------------------------------------------------------------------CACCAAA---------------------------------------------CATCGATATTACCGATGTT---TG---GAAAACATCGATATTACCGATGTTTAGAATATCGATGACCTCGAT----------GTTAGC----ATCGAT----GTTTGTCCGCCCCTAGC----------TAGT-------------AT----TTAATT

Size

Hit Count

Total Norm

droFic1

TAATACCCTTTTGCTCTGCAAGG--------GTATA-------------------AAAACAACGATGTTGCCC-----------------------CGGTAAA---------------------------------------------CATCAATGTTGCCGATGTT---TC---AAAAACATCGA------------------------TGTCATCGAT----------GTTGGC----ATCGAC----GTTTCTCCACCTCTACGAAGTA-TTACAGATACTTA--TTTTCAAT----TTTTGT

Size

Hit Count

Total Norm

droKik1

TCTTATAT--CCGCCCCCTTCGG--------TTTTC-------------------ATTTAAATTATGTATCCC-----------------------TGGCAAA---------------------------------------------CATCGATTTTTGCGATGTT---TT---GAAAACATCGA------------------------TGACATCGAT----------G--GGT----ATCGCT----GTTTCTCCACCTCTAAT----------AAACAGTG----------------AAATT

Size

Hit Count

Total Norm

droAna3

TGCTCG-----------TTAGAG--------ATG-A-------------------TAAACATCGATGTTGGCT-----------------------TGCCAAA---------------------------------------------CATCGATGTCAACGATGTT---TT---CAAAACATCGA------------------------TGACATCGAT----------GTTAAC----ATCGAT----GTTTCTCCACCTCTGAC----------CACTGGAGT--GAATTATT----TTTAGT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................................................................................................................................ATGCCAAAGATGTT---TT---CA.................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
...................................................................TTGGCT-----------------------TGCCAAA---------------------------------------------CATCGATGTCAACG................................................................................................................................................	27	4	0.25	0.00	0.00	0.00	0.25
.........................................................................................................................................................................................A------------------------TGACATCGAT----------GTTAAC----ATCC..............................................................	21	5	0.20	0.00	0.00	0.00	0.20
.......................................................TAAACATCGATGTTGGCT-----------------------TGC...............................................................................................................................................................................................................	21	4	0.25	0.00	0.00	0.00	0.25
.........................................................AACATCGATGTTGGCT-----------------------TGCCAAA---------------------------------------------CAT...........................................................................................................................................................	26	4	0.25	0.00	0.00	0.00	0.25
...................................................................TTGGCT-----------------------TGCCAAA---------------------------------------------CATCGCTGTCAACG................................................................................................................................................	27	4	0.25	0.00	0.00	0.00	0.25
....................................................................................................................................................CAAGGATGTCAACGATGTT---........................................................................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
...................................................................TTGGCT-----------------------TGCCAAA---------------------------------------------CATCGATGTCAACGA...............................................................................................................................................	28	4	0.25	0.00	0.00	0.00	0.25
..................TAGAG--------ATG-A-------------------TAAACATCGATGTTTGC..........................................................................................................................................................................................................................................	26	4	0.25	0.00	0.00	0.00	0.25

droBip1

TACGATTT--ATTTATTCTATGT--------GTACAT------------------------------------AT--------GTATGTATATCTAAGATGA------CGTA-------------------------------------TTCCA-TTTTCTAAAGTA---GT---GATAATTTGAT------------------------AAAGATCTTT----------ATAGAC----TAC-GC----GTATTTCCATT--T--A----------ATATAGTTC--TATTAAAC----TTAACT

Size

Hit Count

Total Norm

dp4

TCAAACAT--ATTATTTTTATTG--------TAA-----ATATCCTAGTTATGGT-------------------------------------------GTAAA---------------------------------------------T-CTGAAAATATCGATGTT---TGAGAAAAAACATCGA------------------------TGACATCCAT----------GTTAAC----ATCGAT----GTTTGTCCAGCTTTAGC----------TTGCATCCC--TAG-----------CTTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..............................................CGTTATGGx-------------------------------------------GTAAA---------------------------------------------T-CTGA........................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CATATT-------ATTATTGTAA--------ATA--------TCCTATTTATAGT-------------------------------------------GTAAA---------------------------------------------T-CTGAAAATATCGATGTT---TGAGAAAAAACATCGA------------------------TGACATCCAT----------GTTAAC----ATCGAT----GTTTGTCCAGCTTTAGC----------TTGCATCCC--TAG-----------CTTG

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TATTGTTT--CCGCCTCTTCTGA--------TCAATC------------------------------------TA--------TTTCTAATTTATTTGCT-AA---CTTCTTCTCGACTACGTACATATCTACTACGTACAACTCTAGT--CAGATATATCCATATC---CTATAACGAA-------------------------------------------------------------------------------------------------ATCCAACTG--CATTCTTA----ATCGTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
............................................................................................TATTTGCT-AA---CTTCTTCTCGACTACG........................................................................................................................................................................................	26	1	21.00	0.00	21.00	0.00	0.00
.........................................................................................................................................TACAACTCTAGT--CAGATATATCCATA.............................................................................................................................................	26	1	16.00	0.00	15.00	1.00	0.00
...........................................................................................................................................................................TATAACGAA-------------------------------------------------------------------------------------------------ATCCAACTG--TATTCT............	24	1	5.00	0.00	5.00	0.00	0.00
...............TCTTCTGA--------TCAATC------------------------------------TA--------TTTCTAATT......................................................................................................................................................................................................................	25	1	5.00	0.00	5.00	0.00	0.00
.........................................................................TA--------TTTCTAATTTATTTGCT-AA---CTTCT...................................................................................................................................................................................................	26	1	5.00	0.00	5.00	0.00	0.00
...........................................................................................................................................................................TATAACGAA-------------------------------------------------------------------------------------------------ATCCAACTG--CATTCTTA----......	26	1	4.00	0.00	4.00	0.00	0.00
...........................................................................................................................................................................TATAACGAA-------------------------------------------------------------------------------------------------ATCCAACTG--CATTCT............	24	1	4.00	0.00	4.00	0.00	0.00
.........................................................................................................................................TACAACTCTAGT--CAGATATATCCA...............................................................................................................................................	24	1	3.00	0.00	3.00	0.00	0.00
...............................................................................................................TCTCGACTACGTACATATCTACTAAG.........................................................................................................................................................................	26	1	3.00	0.00	3.00	0.00	0.00
............................................................................................TATTTGCT-AA---CTTCTTCTCGACTA..........................................................................................................................................................................................	24	1	3.00	0.00	3.00	0.00	0.00
...........................................................................................................TTCTTCTCGACTACGTACATATCTAC.............................................................................................................................................................................	26	1	3.00	0.00	3.00	0.00	0.00
............................................................................................TATTTGCC-AA---CTTCTTCTCGACTACG........................................................................................................................................................................................	26	1	3.00	0.00	3.00	0.00	0.00
..........................................................................................................................................................................CTATAACGAA-------------------------------------------------------------------------------------------------ATCCAACTG--CATTCT............	25	1	3.00	0.00	0.00	0.00	3.00
..............................................................................................................................TATCCACTAAGTACAACTCTAGT--CAGA.......................................................................................................................................................	27	1	3.00	0.00	0.00	0.00	3.00
................................................................................................TGCT-AA---CTTCTTCTCGACTACGTACA....................................................................................................................................................................................	26	1	3.00	0.00	3.00	0.00	0.00
...........................................................................................TTATTTGCT-AA---CTTCTTCTCGACTA..........................................................................................................................................................................................	25	1	3.00	0.00	3.00	0.00	0.00

droVir3

TTTATCGT--TTATATTT-----------------G-------------------AAATTATTAATTAAA---TT--------ATTATTATTTTTAAGTAATA---------------------------------------------C----------------------A---AAATAAATTAA------------------------GGAAATAAAAGTGCAAATTTGTTGTT----TTCAAA----G-ATACATTTAATTAAT----------TTTTATTTT--TTTTTTAT----TTTATT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGTGCAAATTTGTC.........................................................................	27	3	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGTGCAAATTTGTTG........................................................................	28	3	0.67	0.67	0.00	0.00	0.00	0.00
..................................................................................................................................................................................TAAATTAA------------------------GGAAATAAAAGTGCAAATTC............................................................................	28	3	0.67	0.67	0.00	0.00	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGTGCAAATTTGTTC........................................................................	28	3	0.67	0.67	0.00	0.00	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGTGCAAATTTGTCC........................................................................	28	3	0.67	0.33	0.33	0.00	0.00	0.00
.......................................................................................................................................................................................................................TAAAAGTGCAAATTTGTTGTT----..................................................................	21	3	0.33	0.33	0.00	0.00	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGTTCAAATTTGTC.........................................................................	27	3	0.33	0.33	0.00	0.00	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGCGCAAATTTG...........................................................................	25	3	0.33	0.00	0.00	0.33	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGTGCAAATC.............................................................................	23	3	0.33	0.33	0.00	0.00	0.00	0.00
............................................................ATTxATTAAA---TT--------ATTAATA........................................................................................................................................................................................................................	18	7	0.14	0.00	0.00	0.00	0.00	0.14
.......................................................................................................................................................................................................................TGAAAGAGCAAATTTGTTGTT----..................................................................	21	3	0.33	0.33	0.00	0.00	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGTGTAAATT.............................................................................	23	3	0.33	0.00	0.00	0.33	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAATGTGCAAATTTG...........................................................................	25	3	0.33	0.00	0.33	0.00	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAAAGTGCAAAT..............................................................................	22	3	0.33	0.33	0.00	0.00	0.00	0.00
......................................................................................................................................................................................TTAA------------------------GGAAATAAATGTGCAAATTTGTC.........................................................................	27	3	0.33	0.33	0.00	0.00	0.00	0.00

droMoj3

TATTATGA--G---CTGAAATAA--------ATATAA------------------------------------AA--------ATATTTAA--TTAAATTCAACAAAATGAT-------------------------------------GTC-------TAGATATT---AA-----AAAAAAAAA------------------------AAAAAATAAA----------ATATAT----ATATAT----ATATATATATATATATA---------TATATATATA--TATTTTTT----TTTTTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..........................................................................................................................................................................AG-----AAAAAAAAA------------------------GAAAAATAA.......................................................................................	20	27	0.04	0.00	0.00	0.00	0.04
.................................................................................................................................................................................................................................................................................................ATTTTTT----TTTTTT	19	15	0.07	0.00	0.00	0.00	0.07

droGri2

TATATC-T--ATGCGTCTG-TAGATACTTGCATAAGT------------------------------------GT------AT-CATCTATGTACGGTTTACA---------------------------------------------TATAGTGT---ATGGTTTA---TA---AAAAATATTTC------------------------TCAATACGCC----------GTTAGT----ACAAAA----AAAAAGTAGTGTATAAA----------AAATGCTTG--CACTTTGT----TTTAGT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:21:38 EDT

dme-mir-4942

chr3L:23332327-23332437 +

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