dme-mir-2489- Best orthologs

dme-mir-2489	chr2L:13609988-13610055 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 13610035-13610055
   star strand at position 13609988-13610015
   mutations
   read mismatches

Notes: miRNA only appears present form dm3 - droSec1.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2L:13609973-13610070 +		1	AGCAATAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACGTAAG--T------TCTAATGTATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATAGCAAA
droSim1	chr2L:13379253-13379350 +	LASTZ	1	AGCAATAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACATACG--T------TCTAATGCATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATAGCAAA
droSec1	super_16:1746050-1746147 +	LASTZ	1	AGCAATAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACATACG--T------TCTAATGCATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATAGCAAA
droYak2	chr2L:10029706-10029801 +	LASTZ	5	AGCAATAAGTTAGATGTGAGTATGGC-------TATT-T----AAATCAACC-----G--A---------ACGTATG--T----ATGTTAT---ATAGT----TTGCA-TTT-TGTATTTGCAGTTTTATGATAGCAAA
droEre2	scaffold_4929:11847836-11847927 -	LASTZ	5	AGCAATAAGTTAGACGTGAGTATGGC-------TATC-T----AAATCAGCC-----G--A---------ACGTGTA--T------TCTAATGTTT---------GCA-CTT-TGTATTTGCAGTTTTATGATAGCAAA
droEug1	scf7180000409452:191304-191394 +	LASTZ	5	AGCAATAAGTTAGACGTGAGTATAGTA------CTTA-A----ATTATAAT----TTT-AA----------ATCACA--T------TATAAT-------------GTA-CTTTGTACTTTTCAGTTTTATGATAGCAAA
droBia1	scf7180000302408:2742692-2742786 -	LASTZ	5	AGCAATAAGTTAGAGGTGAGTACTCCTAAAATA--TA-C----T-------------AAAAATAA-----GAAAACA--T------TCTAACAACC---------AAT-ATT-TGCCCTTGCAGATTTATGATAGCAAA
droTak1	scf7180000415285:144401-144496 +	LASTZ	5	AGCAATAAGTTAGACGTGAGTATATA-------AATA-T----ATATTAATT-----A-AA---------ATTTAAA--T------CTTAAAT--CGTA----ACATT-TGT-TGTACTTTCAGTTTTATGATAGCAAA
droEle1	scf7180000491338:1217909-1218003 +	LASTZ	5	AGCAATAAGTTAGACGTGAGTATTGT-------CATTAAGATAGAACAA-----------C---------ATAAACA--T------GTTAA-A--CATA---TTTGTA--TT-TTTTTTTTCAGTTTTATGATAGCAAA
droRho1	scf7180000780107:475244-475335 -	LASTZ	5	AGCAATAAGTTAGACGTGAGTATTTTTTAAATA---------------ATTT-----A-AA-AA------ACTTACA--A------CTTAATGTGT---------ACA-CCT-TGTATTTTCAGTTTTATGATAGCAAA
droFic1	scf7180000453925:389428-389520 -	LASTZ	5	AGCAATAAGTTAGACGTGAGTATTGCTCTCAAG-ATT-A----AAATCA-----------A---------AAACCCT--T------ACTAAGACAT----------AC-TTT-TTTATTTTTAGTTTTATGATAGCAAA
droKik1	scf7180000302656:77455-77548 +	LASTZ	5	AGCAATAAGTTAGACGTGAGTATTACATACGCA------------ATTATATTAATTTTAA---------------G-----------TAATGCTCGTA----TT-TC-CTT-TACTTTTCCAGTTTTATGATAGCAAG
droAna3	scaffold_12943:1669999-1670103 +	LASTZ	5	AGCGATAAGTTAGACGTGAGTATTGTC------TCTG-T----CAAGTGTAT-----G-GT--ACTAATATTTA------------ACTAATTCTTGTATTA-ACTTG-TTT-TTAATTTCCAGTTTTATGATAGCAAT
droBip1	scf7180000396728:1558161-1558257 -	LASTZ	5	AGCGATAAGTTAGACGTGAGTATTAATATAATC-CTTAA------A--ATAT--------A---------AAATCAA--T------AATTAAT--CAAA----ACCTC-TTT-CTGATCCATAGTTTTATGATAGCAAT
dp4	chr4_group1:1879331-1879430 -	LASTZ	5	AGCGATAAGTTAGACGTGAGTATATC-------TTTG-C----CATCTCTT----TTTAAA---------ACAATCA--T------TTTCATATACATA----TATAT-TTT-TGTGTGTTTAGTTTTATGATAGCAAC
droPer1	super_5:3326174-3326277 +	LASTZ	5	AGCGATAAGTTAGACGTGAGTATATC-------TTTG-C----CATCTCTT----TTTAAAATA------TTTTATATTTTTATATA---TTACATATA----TT-----TT-TTGGTGTTTAGTTTTATGATAGCAAC
droWil1	scaffold_180772:852551-852648 -	LASTZ	5	AGCGATAAGTTAGATGTGAGTATATTATATCTT--TT-------GTCCCAT----TTTGGA---------ATATGTT--T------TTGAATACCT---------TTT-CTT-TGGGATTTCAGTTTTATGATAGCAAC
droVir3	scaffold_12723:5236355-5236448 -	LASTZ	5	AGTGATAAGTTAGACGTGAGTATTATCAACATA--TA-T----GAATTATT-----TTAAA---------AT-AATA--A------------T--CGAA----T-TTA-ATT-TGTTATCCCAGTTTTATGATAGCAAC
droMoj3	scaffold_6500:16444108-16444197 +	LASTZ	5	AGTGATAAGTTAGACGTGAGTATTACAGAGGCC-CTA-------------------TCAAA---------AT---------------ATCATTCGTGTA----TCTAATATA-ATATTTTTCAGTTTTATGATAACAAC
droGri2	scaffold_15126:8263493-8263587 -	LASTZ	5	AGTGATAAGTTAGACGTGAGTATTTATTAACTT--CA------------------TTCAACGTA------ATATACA--T------ACTAAAATATGAA-------TA--CA-TCATTTTGCAGTCTTATGATAGCAAC

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	AGCAATAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACGTAAG--T------TCTAATGTATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATAGCAAA
droSim1	AGCAATAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACATACG--T------TCTAATGCATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATAGCAAA
droSec1	AGCAATAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACATACG--T------TCTAATGCATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATAGCAAA
droYak2	AGCAATAAGTTAGATGTGAGTATGGC-------TATT-T----AAATCAACC-----G--A---------ACGTATG--T----ATGTTAT---ATAGT----TTGCA-TTT-TGTATTTGCAGTTTTATGATAGCAAA
droEre2	AGCAATAAGTTAGACGTGAGTATGGC-------TATC-T----AAATCAGCC-----G--A---------ACGTGTA--T------TCTAATGTTT---------GCA-CTT-TGTATTTGCAGTTTTATGATAGCAAA
droEug1	AGCAATAAGTTAGACGTGAGTATAGTA------CTTA-A----ATTATAAT----TTT-AA----------ATCACA--T------TATAAT-------------GTA-CTTTGTACTTTTCAGTTTTATGATAGCAAA
droBia1	AGCAATAAGTTAGAGGTGAGTACTCCTAAAATA--TA-C----T-------------AAAAATAA-----GAAAACA--T------TCTAACAACC---------AAT-ATT-TGCCCTTGCAGATTTATGATAGCAAA
droTak1	AGCAATAAGTTAGACGTGAGTATATA-------AATA-T----ATATTAATT-----A-AA---------ATTTAAA--T------CTTAAAT--CGTA----ACATT-TGT-TGTACTTTCAGTTTTATGATAGCAAA
droEle1	AGCAATAAGTTAGACGTGAGTATTGT-------CATTAAGATAGAACAA-----------C---------ATAAACA--T------GTTAA-A--CATA---TTTGTA--TT-TTTTTTTTCAGTTTTATGATAGCAAA
droRho1	AGCAATAAGTTAGACGTGAGTATTTTTTAAATA---------------ATTT-----A-AA-AA------ACTTACA--A------CTTAATGTGT---------ACA-CCT-TGTATTTTCAGTTTTATGATAGCAAA
droFic1	AGCAATAAGTTAGACGTGAGTATTGCTCTCAAG-ATT-A----AAATCA-----------A---------AAACCCT--T------ACTAAGACAT----------AC-TTT-TTTATTTTTAGTTTTATGATAGCAAA
droKik1	AGCAATAAGTTAGACGTGAGTATTACATACGCA------------ATTATATTAATTTTAA---------------G-----------TAATGCTCGTA----TT-TC-CTT-TACTTTTCCAGTTTTATGATAGCAAG
droAna3	AGCGATAAGTTAGACGTGAGTATTGTC------TCTG-T----CAAGTGTAT-----G-GT--ACTAATATTTA------------ACTAATTCTTGTATTA-ACTTG-TTT-TTAATTTCCAGTTTTATGATAGCAAT
droBip1	AGCGATAAGTTAGACGTGAGTATTAATATAATC-CTTAA------A--ATAT--------A---------AAATCAA--T------AATTAAT--CAAA----ACCTC-TTT-CTGATCCATAGTTTTATGATAGCAAT
dp4	AGCGATAAGTTAGACGTGAGTATATC-------TTTG-C----CATCTCTT----TTTAAA---------ACAATCA--T------TTTCATATACATA----TATAT-TTT-TGTGTGTTTAGTTTTATGATAGCAAC
droPer1	AGCGATAAGTTAGACGTGAGTATATC-------TTTG-C----CATCTCTT----TTTAAAATA------TTTTATATTTTTATATA---TTACATATA----TT-----TT-TTGGTGTTTAGTTTTATGATAGCAAC
droWil1	AGCGATAAGTTAGATGTGAGTATATTATATCTT--TT-------GTCCCAT----TTTGGA---------ATATGTT--T------TTGAATACCT---------TTT-CTT-TGGGATTTCAGTTTTATGATAGCAAC
droVir3	AGTGATAAGTTAGACGTGAGTATTATCAACATA--TA-T----GAATTATT-----TTAAA---------AT-AATA--A------------T--CGAA----T-TTA-ATT-TGTTATCCCAGTTTTATGATAGCAAC
droMoj3	AGTGATAAGTTAGACGTGAGTATTACAGAGGCC-CTA-------------------TCAAA---------AT---------------ATCATTCGTGTA----TCTAATATA-ATATTTTTCAGTTTTATGATAACAAC
droGri2	AGTGATAAGTTAGACGTGAGTATTTATTAACTT--CA------------------TTCAACGTA------ATATACA--T------ACTAAAATATGAA-------TA--CA-TCATTTTGCAGTCTTATGATAGCAAC

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

AGCAATAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACATACG--T------TCTAATGCATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATAGCAAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGT..............	22	1	49.00	11.00	18.00	0.00	20.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAG...............	21	1	45.00	5.00	37.00	0.00	3.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGC.................	19	1	37.00	0.00	36.00	1.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCA................	20	1	29.00	1.00	28.00	0.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGA..............	22	1	10.00	1.00	4.00	0.00	5.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGC..............	22	1	5.00	0.00	4.00	0.00	1.00
.................................................................................................TA----TTGTA-TGT-TGTATTTTCAGT..............	22	1	2.00	2.00	0.00	0.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGG..............	22	1	2.00	0.00	0.00	0.00	2.00
..............................................................................................................GT-TTTATTTGCAGTTTTATC........	20	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................TA----TTGTA-TGC-TGTATTTGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................A----TTGTA-TGT-TGTATTTGCAGA..............	21	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCT................	20	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTCTTTGCAGT..............	22	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................TA----TTGTA-TGT-TCTATTTGC.................	19	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................TA----TTGTA-TGG-TGTATTTGCA................	20	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTGTTTGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

AGCAATAAGTTAGACGTGAGTATGGC-------TATA-C----AAATCATCT-----G-GA---------ACATACG--T------TCTAATGCATGTA----TTGTA-TGT-TGTATTTGCAGTTTTATGATAGCAAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGT..............	22	1	131.00	13.00	100.00	18.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAG...............	21	1	100.00	9.00	19.00	72.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCA................	20	1	52.00	4.00	1.00	47.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGA..............	22	1	35.00	6.00	22.00	7.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGC.................	19	1	10.00	0.00	0.00	10.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGC..............	22	1	5.00	0.00	3.00	2.00
.................................................................................................TA----TTGTA-TGT-TGTATTTCCAGT..............	22	1	2.00	0.00	2.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCTGT..............	22	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTCCAGA..............	22	1	1.00	1.00	0.00	0.00
.................................................................................................TA----TTGTA-TGT-CGTATTTGC.................	19	1	1.00	0.00	0.00	1.00
.................................................................................................TA----TTGTC-TGT-TGTATCTGCAGT..............	22	1	1.00	0.00	1.00	0.00
.................................................................................................TT----TTGTA-TGT-TGTATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGAA-TGT-TGTATTTGCA................	20	1	1.00	0.00	0.00	1.00
.................................................................................................TA----TATTA-TGT-TGTATTTGCAG...............	21	1	1.00	0.00	0.00	1.00
...........................................AAATCATCT-----G-GA---------ACATACG--T------T....................................................	21	1	1.00	1.00	0.00	0.00
.................................................................................................GA----TTGTA-TGT-TGTATTTGC.................	19	1	1.00	0.00	0.00	1.00
..................................................................................................A----TTGTA-TGT-TGTATTTGC.................	18	1	1.00	0.00	0.00	1.00
................................................................................................CTA----TTGTA-TGT-TGTATTTGCAGC..............	23	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTCTA-TGT-TGTATTTGCAG...............	21	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAT...............	21	1	1.00	0.00	0.00	1.00
.................................................................................................CA----TTGTA-TGT-TGTATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
..................................................................................................A----TTGTA-TGT-TGTATTTGCAG...............	20	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGTA-TTT-TGTATTTGCAG...............	21	1	1.00	0.00	0.00	1.00
.................................................................................................TA----TTGTA-TGT-TCTATTTGCA................	20	1	1.00	0.00	0.00	1.00
.......................................................................................................TTGTA-TGT-TGTATTTGCA................	18	1	1.00	0.00	0.00	1.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCCG...............	21	1	1.00	1.00	0.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGTA.............	23	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGTA-TTT-TGTATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGTA-CGT-TGTATTTGCAGA..............	22	1	1.00	0.00	0.00	1.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCCGA..............	22	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGAT.............	23	1	1.00	1.00	0.00	0.00
.................................................................................................GA----TTGTA-TGT-TGTATTTGCA................	20	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGTA-TGT-TGTATTTGCAGG..............	22	1	1.00	0.00	1.00	0.00
.................................................................................................TA----TTGTA-CGT-TGTATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00

droYak2

AGCAATAAGTTAGATGTGAGTATGGC-------TATT-T----AAATCAACC-----G--A---------ACGTATG--T----ATGTTAT---ATAGT----TTGCA-TTT-TGTATTTGCAGTTTTATGATAGCAAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.................................................................................................................TGTATTTGCTGTTTTAAGA.......	19	1	3.00	1.00	0.00	2.00	0.00	0.00
..................................................................................................................GTATTTGCTGTTTTAAGA.......	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..............................................................................................ATAGx----TTGCA-TTT-TGTAGTT...................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AGCAATAAGTTAGACGTGAGTATGGC-------TATC-T----AAATCAGCC-----G--A---------ACGTGTA--T------TCTAATGTTT---------GCA-CTT-TGTATTTGCAGTTTTATGATAGCAAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................................................................................................GTATTTGCTGTTTTAAGA.......	18	1	17.00	1.00	0.00	0.00	16.00
.................................................................................................................TGTATTTGCTGTTTTAAGA.......	19	1	16.00	3.00	0.00	0.00	13.00
.................................................................................................................TGTATTTGCTGTTTTAAG........	18	1	9.00	0.00	0.00	0.00	9.00
.....................................................................................................................TTTGCAGTTTTAxGATAGT...	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

AGCAATAAGTTAGACGTGAGTATAGTA------CTTA-A----ATTATAAT----TTT-AA----------ATCACA--T------TATAAT-------------GTA-CTTTGTACTTTTCAGTTTTATGATAGCAAA

Size

Hit Count

Total Norm

droBia1

AGCAATAAGTTAGAGGTGAGTACTCCTAAAATA--TA-C----T-------------AAAAATAA-----GAAAACA--T------TCTAACAACC---------AAT-ATT-TGCCCTTGCAGATTTATGATAGCAAA

Size

Hit Count

Total Norm

droTak1

AGCAATAAGTTAGACGTGAGTATATA-------AATA-T----ATATTAATT-----A-AA---------ATTTAAA--T------CTTAAAT--CGTA----ACATT-TGT-TGTACTTTCAGTTTTATGATAGCAAA

Size

Hit Count

Total Norm

droEle1

AGCAATAAGTTAGACGTGAGTATTGT-------CATTAAGATAGAACAA-----------C---------ATAAACA--T------GTTAA-A--CATA---TTTGTA--TT-TTTTTTTTCAGTTTTATGATAGCAAA

Size

Hit Count

Total Norm

droRho1

AGCAATAAGTTAGACGTGAGTATTTTTTAAATA---------------ATTT-----A-AA-AA------ACTTACA--A------CTTAATGTGT---------ACA-CCT-TGTATTTTCAGTTTTATGATAGCAAA

Size

Hit Count

Total Norm

droFic1

AGCAATAAGTTAGACGTGAGTATTGCTCTCAAG-ATT-A----AAATCA-----------A---------AAACCCT--T------ACTAAGACAT----------AC-TTT-TTTATTTTTAGTTTTATGATAGCAAA

Size

Hit Count

Total Norm

droKik1

AGCAATAAGTTAGACGTGAGTATTACATACGCA------------ATTATATTAATTTTAA---------------G-----------TAATGCTCGTA----TT-TC-CTT-TACTTTTCCAGTTTTATGATAGCAAG

Size

Hit Count

Total Norm

droAna3

AGCGATAAGTTAGACGTGAGTATTGTC------TCTG-T----CAAGTGTAT-----G-GT--ACTAATATTTA------------ACTAATTCTTGTATTA-ACTTG-TTT-TTAATTTCCAGTTTTATGATAGCAAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.............................................................................................CTTGTATTx-ATTTG-TTT-TTA.......................	19	1	1.00	0.00	1.00	0.00	0.00

droBip1

AGCGATAAGTTAGACGTGAGTATTAATATAATC-CTTAA------A--ATAT--------A---------AAATCAA--T------AATTAAT--CAAA----ACCTC-TTT-CTGATCCATAGTTTTATGATAGCAAT

Size

Hit Count

Total Norm

dp4

AGCGATAAGTTAGACGTGAGTATATC-------TTTG-C----CATCTCTT----TTTAAA---------ACAATCA--T------TTTCATATACATA----TATAT-TTT-TGTGTGTTTAGTTTTATGATAGCAAC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................................................TA----AATAT-TTA-TGTGTGTTTA................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

AGCGATAAGTTAGACGTGAGTATATC-------TTTG-C----CATCTCTT----TTTAAAATA------TTTTATATTTTTATATA---TTACATATA----TT-----TT-TTGGTGTTTAGTTTTATGATAGCAAC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
............................................................AATA------TTTTAGATTTTTTT.......................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
......................................................................................................................GTTTAGTTTTATGTTAGCA..	19	1	1.00	0.00	0.00	0.00	1.00	0.00
......................................................................TTGTATTTTTTTATATA---TT...............................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.......................................................................TGTATTTTTTTATATA---TT...............................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................................A----TT-----TT-TTGGCGTTTGGTTTT...........	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

AGCGATAAGTTAGATGTGAGTATATTATATCTT--TT-------GTCCCAT----TTTGGA---------ATATGTT--T------TTGAATACCT---------TTT-CTT-TGGGATTTCAGTTTTATGATAGCAAC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................TTTGGA---------AGATGTT--A------TTGA.................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................................................................CTT-TGTGATTTCATTTTT...........	18	2	0.50	0.00	0.50	0.00	0.00
..............................................................................................................TT-TGGGxTTTCAGTTTGAT.........	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

AGTGATAAGTTAGACGTGAGTATTATCAACATA--TA-T----GAATTATT-----TTAAA---------AT-AATA--A------------T--CGAA----T-TTA-ATT-TGTTATCCCAGTTTTATGATAGCAAC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AGTGATAAGTTAGACGTGAGTATTACAGAGGCC-CTA-------------------TCAAA---------AT---------------ATCATTCGTGTA----TCTAATATA-ATATTTTTCAGTTTTATGATAACAAC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

AGTGATAAGTTAGACGTGAGTATTTATTAACTT--CA------------------TTCAACGTA------ATATACA--T------ACTAAAATATGAA-------TA--CA-TCATTTTGCAGTCTTATGATAGCAAC

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:20 EDT

dme-mir-2489

chr2L:13609988-13610055 +

Known_mirbase

mirtron

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