dme-mir-1016- Best orthologs

dme-mir-1016	chr2R:10120635-10120692 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 10120635-10120655
   star strand at position 10120668-10120692
   mutations
   read mismatches

Notes: Surprisingly no reads in simulans but reads in other related species. The miRNA looks present from dm3 -droEug1 given that the mature region is conserved well. droBia1 - droGri2 have large bulges in the hairpin or poor structures.

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

Visually pleasing best hits from LASTZ and MAF

Species	Coordinate	Source	Confidence	Alignment
dm3	chr2R:10120620-10120707 -		1	CTCCAAGCTTTTCCAGTAAGTATAGAG---AG----GATGTGA-TT---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droSim1	chr2R:8883298-8883385 -	LASTZ	4	CTCCAAGCTTTTCCAGTAAGTACAGAG---AT----GATGTAA-TG---CGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droSec1	super_1:7628246-7628333 -	LASTZ	1	CTCCAAGCTTTTCCAGTAAGTATAGAG---AG----GATGTAA-TG---CGTA-----------------TA-T---------------TCCAATGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droYak2	chr2R:10057668-10057755 -	LASTZ	1	CTCCAAGCTGTTCCAGTAAGTATAGAG---GG----GATGTGA-TG---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droEre2	scaffold_4845:15723071-15723158 +	LASTZ	1	CTCCAAGCTGTTTCAGTAAGTATAGAG---AG----GATGTGA-TG---GGCA-----------------AA-A---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droEug1	scf7180000409462:2724067-2724155 +	LASTZ	4	CTCAAAGCTTTTCCAGTGAGTATAGAG---AG----GATGTGA-TGG--TGTA-----------------AT-T---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGTGGCGTTAT
droBia1	scf7180000301506:3144548-3144634 +	LASTZ	5	CTCAAAGCTCTTCCAGTGAGTATAAAG---AG----GACGTGA-TG----CCA-----------------AG-T---------------GCCAAAGTTTACCTGTCTCCA--TA-CTTAGTCGGCGCGGAGTTAT
droTak1	scf7180000414111:24446-24536 -	LASTZ	5	CTCCAAGCTTTTCCAGTGAGTATAGAG---AG----CATGTGA-TGCAAGGTA-----------------AT-G---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGGCGCGGAGTTAT
droEle1	scf7180000491349:753074-753164 +	LASTZ	5	CTCCAAGCTTTTTCAGTGAGTATCGAA---GG----CATATGC-AA---GATA-----------------T--------GA--T-GTATACTAAGATTAACCTCT--TTA--AA-CTTAGTCGTCGCGGAGTTAT
droRho1	scf7180000777200:436780-436870 -	LASTZ	5	CTCCAAGCTTTTCCAGTTAGTATCAAATTTAT----GATATGA-TT---GGTA-----------------AA-T---------------ACTTAAATTGACCTCTCTCCA--TT-CTTAGTCGTCGCGGAGTTAT
droFic1	scf7180000453948:312447-312534 +	LASTZ	5	TTCCAAGCTTTTCCAGTAAGTATAGAG---CA----GATGTGA-TG---GGTC-----------------AG-A---------------ACCAAACTTCACCTGCCTCTG--TA-CTTAGTCGTCGCGGAGTGAT
droKik1	scf7180000302366:807245-807331 -	LASTZ	5	CTCGAAGCTGTTCCAGTGAGTAACGAG---AA----AGGGGAG-TT---GGAA-----------------GC-C---------------ACATAAACTAACATGCATCC---TT-CGTAGTCGCCGAGGTGTGAT
droAna3	scaffold_13266:5804278-5804360 +	LASTZ	5	CTCTAAACTTTTTCAGTGAGTACTTGT---AA------TATAAATC---CATA-----------------A------------------ATCAAAACTCACTTT-TTCCA---A-CTTAGTCGCCGTGGTGTGAT
droBip1	scf7180000396372:418170-418256 +	LASTZ	5	CTCCAAACTGTTTCAGTGAGTACATGC---AA--TGGATATATGTA---CATA-----------------A--A---------------TCCA-GACTTACTT-TCTCC---TA-CTTAGTCGCCGTGGTGTGAT
dp4	chr3:17369366-17369470 -	LASTZ	5	CTCAAAGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATCGTCTGAAAC----TAATT----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGTCGCGGCGTCAT
droPer1	super_31:422912-423016 +	LASTZ	5	TTCAAAGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATTGTCTGAAAC----TAATG----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGGCGCGGCGTCAT
droWil1	scaffold_180700:1839743-1839828 +	LASTZ	5	TTCCAAATTGTTCCAGTAAGTTAAAAT---GA------T---C-TA---AAAT-----------------CATTTC------AA-----ATT--GATTCAATAATCTCTT--CC-ATTAGTCGACGCGGTGTCAT
droVir3	scaffold_12875:17586457-17586541 +	LASTZ	5	TTCCAAACTATTTCAGTAAGTAGCAGG---T----------GC-TG---AGTG-----------------CA-TGATTGTC--------TCTATATCTTGATTATC------T-TTGCAGTCGACGCGGGGTTAT
droMoj3	scaffold_6496:11208550-11208642 +	LASTZ	5	TTCCAAGCTGTTTCAGTAAGTAGAGCA---CG----CATTTCC-AG---TACCCAACTAT----------------TCGTT--------ACTATATCTGTACAATT------T-TTGTAGTCGACGCGGGGTTAT
droGri2	scaffold_15245:14096515-14096602 -	LASTZ	5	TTCCAAACTGTTTCAGTAAGTGGTAAC---ACAACTACTATGT-TT-------------------------G-TGC-----AACA----TTTAATG-------GACAGTATCT-TTGCAGTCGACGGGGAGTTAT

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	CTCCAAGCTTTTCCAGTAAGTATAGAG---AG----GATGTGA-TT---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droSim1	CTCCAAGCTTTTCCAGTAAGTACAGAG---AT----GATGTAA-TG---CGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droSec1	CTCCAAGCTTTTCCAGTAAGTATAGAG---AG----GATGTAA-TG---CGTA-----------------TA-T---------------TCCAATGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droYak2	CTCCAAGCTGTTCCAGTAAGTATAGAG---GG----GATGTGA-TG---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droEre2	CTCCAAGCTGTTTCAGTAAGTATAGAG---AG----GATGTGA-TG---GGCA-----------------AA-A---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT
droEug1	CTCAAAGCTTTTCCAGTGAGTATAGAG---AG----GATGTGA-TGG--TGTA-----------------AT-T---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGTGGCGTTAT
droBia1	CTCAAAGCTCTTCCAGTGAGTATAAAG---AG----GACGTGA-TG----CCA-----------------AG-T---------------GCCAAAGTTTACCTGTCTCCA--TA-CTTAGTCGGCGCGGAGTTAT
droTak1	CTCCAAGCTTTTCCAGTGAGTATAGAG---AG----CATGTGA-TGCAAGGTA-----------------AT-G---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGGCGCGGAGTTAT
droEle1	CTCCAAGCTTTTTCAGTGAGTATCGAA---GG----CATATGC-AA---GATA-----------------T--------GA--T-GTATACTAAGATTAACCTCT--TTA--AA-CTTAGTCGTCGCGGAGTTAT
droRho1	CTCCAAGCTTTTCCAGTTAGTATCAAATTTAT----GATATGA-TT---GGTA-----------------AA-T---------------ACTTAAATTGACCTCTCTCCA--TT-CTTAGTCGTCGCGGAGTTAT
droFic1	TTCCAAGCTTTTCCAGTAAGTATAGAG---CA----GATGTGA-TG---GGTC-----------------AG-A---------------ACCAAACTTCACCTGCCTCTG--TA-CTTAGTCGTCGCGGAGTGAT
droKik1	CTCGAAGCTGTTCCAGTGAGTAACGAG---AA----AGGGGAG-TT---GGAA-----------------GC-C---------------ACATAAACTAACATGCATCC---TT-CGTAGTCGCCGAGGTGTGAT
droAna3	CTCTAAACTTTTTCAGTGAGTACTTGT---AA------TATAAATC---CATA-----------------A------------------ATCAAAACTCACTTT-TTCCA---A-CTTAGTCGCCGTGGTGTGAT
droBip1	CTCCAAACTGTTTCAGTGAGTACATGC---AA--TGGATATATGTA---CATA-----------------A--A---------------TCCA-GACTTACTT-TCTCC---TA-CTTAGTCGCCGTGGTGTGAT
dp4	CTCAAAGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATCGTCTGAAAC----TAATT----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGTCGCGGCGTCAT
droPer1	TTCAAAGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATTGTCTGAAAC----TAATG----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGGCGCGGCGTCAT
droWil1	TTCCAAATTGTTCCAGTAAGTTAAAAT---GA------T---C-TA---AAAT-----------------CATTTC------AA-----ATT--GATTCAATAATCTCTT--CC-ATTAGTCGACGCGGTGTCAT
droVir3	TTCCAAACTATTTCAGTAAGTAGCAGG---T----------GC-TG---AGTG-----------------CA-TGATTGTC--------TCTATATCTTGATTATC------T-TTGCAGTCGACGCGGGGTTAT
droMoj3	TTCCAAGCTGTTTCAGTAAGTAGAGCA---CG----CATTTCC-AG---TACCCAACTAT----------------TCGTT--------ACTATATCTGTACAATT------T-TTGTAGTCGACGCGGGGTTAT
droGri2	TTCCAAACTGTTTCAGTAAGTGGTAAC---ACAACTACTATGT-TT-------------------------G-TGC-----AACA----TTTAATG-------GACAGTATCT-TTGCAGTCGACGGGGAGTTAT

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

CTCCAAGCTTTTCCAGTAAGTACAGAG---AT----GATGTAA-TG---CGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................................................................TCCA--TA-CTTAGTCGTCGAGGG.....	21	1	2.00	0.00	0.00	0.00	2.00

droSec1

CTCCAAGCTTTTCCAGTAAGTATAGAG---AG----GATGTAA-TG---CGTA-----------------TA-T---------------TCCAATGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................................................................TTCACCTCTCTCCA--TA-CTTAGT..............	22	1	8.00	2.00	3.00	3.00
...............GTAAGTATAGAG---AG----GATGTAA-TG---C.....................................................................................	24	1	3.00	2.00	0.00	1.00
...............GTAAGTATAGAG---AG----GATGTAA-TG---......................................................................................	23	1	2.00	1.00	1.00	0.00
...............GTAAGTATAGAG---AG----GATG...............................................................................................	18	1	2.00	0.00	0.00	2.00
................TAAGTATAGAG---AG----GATGTAA-T..........................................................................................	21	1	1.00	1.00	0.00	0.00
...............GTAAGTATAGAG---AG----GATGT..............................................................................................	19	1	1.00	1.00	0.00	0.00
...............GTAAGTATCGAG---AG----GATGTAA-TG---C.....................................................................................	24	1	1.00	1.00	0.00	0.00
...............GTAAGTATAGAG---AG----GATGTAA-TG---CGT...................................................................................	26	1	1.00	1.00	0.00	0.00
................TAAGTATAGAG---AG----GATGTAA-TG---......................................................................................	22	1	1.00	0.00	1.00	0.00
...............GTAAGTATAGAG---AG----GATGTAA-TG---CG....................................................................................	25	1	1.00	1.00	0.00	0.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGTT.............	22	1	1.00	0.00	1.00	0.00
...............GTAAGTATAGAG---AG----GATGTAA-A..........................................................................................	22	1	1.00	0.00	1.00	0.00

droYak2

CTCCAAGCTGTTCCAGTAAGTATAGAG---GG----GATGTGA-TG---GGTA-----------------AA-T---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................................................TTCACCTCTCTCCA--TA-CTTAGT..............	22	1	168.00	41.00	52.00	11.00	60.00	4.00
...............GTAAGTATAGAG---GG----GATGTGA-TG---......................................................................................	23	1	11.00	1.00	2.00	8.00	0.00	0.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGTT.............	22	1	7.00	7.00	0.00	0.00	0.00	0.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAG...............	21	1	6.00	1.00	0.00	0.00	4.00	1.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGT..............	21	1	3.00	1.00	0.00	0.00	2.00	0.00
................................................................................................TTCACCTCTCTCCA--TA-CTTATT..............	22	1	3.00	0.00	1.00	0.00	2.00	0.00
................................................................................................TTCACCTCTCTCCC--TA-CTTAGT..............	22	1	3.00	0.00	1.00	0.00	2.00	0.00
...............GTAAGTATAGAG---GG----GATGTGA-TG---G.....................................................................................	24	1	3.00	0.00	0.00	3.00	0.00	0.00
................................................................................................TTCACCTCTCTCCA--TC-CTTAGT..............	22	1	2.00	0.00	1.00	0.00	1.00	0.00
................................................................................................TTCACCTCTCTCCA--TA-CTTA................	20	1	2.00	0.00	2.00	0.00	0.00	0.00
...................................................................................................ACCTCTCTCCA--TA-CTTAGT..............	19	1	2.00	1.00	0.00	0.00	1.00	0.00
................................................................................................TTCACCTCTCTCAA--TA-CTTTGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTAAGTATAGAG---GG----GATGTGA-...........................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAGA..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
................................................................................................TGCACCTCTCTCCA--TA-CTGAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCACCTCTCTCCT--TG-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCACCTCTCTCCA--TA-TTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAT...............	21	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCAACTCTCTCCA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCAACTCTCTCCC--TA-CTTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................TTCACCTATCTCCC--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCACCTCTCTCCA--TA-CTT.................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCACTTATCTCCA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCACCTCTCTTCA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCACCTCTCTCCG--TA-CTTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00
...................................................................................................ACCTCTCTCCC--TA-CTTAGT..............	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...............GTAAGTATAGAG---GG----GATGTG.............................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...............GTAAGTATAGAG---GG----GATGGGC-T..........................................................................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCATCTCTCTCCA--TA-CTTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................................................TCACCTCTCTCCA--TC-CTTAGTT.............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCAACTCTCTCCA--TT-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTAAGTATAGAG---GG----GATG...............................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................................TCACCCCTCTCCA--TA-CTTAGTT.............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................TTCACCGCTCTCCG--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................TTCATCTCTCTCCA--TC-CTTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................CTCACCTCTCTCCA--TA-CTTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

CTCCAAGCTGTTTCAGTAAGTATAGAG---AG----GATGTGA-TG---GGCA-----------------AA-A---------------TCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGAGGGGTTAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
................................................................................................TTCACCTCTCTCCA--TA-CTTAGT..............	22	1	866.00	21.00	58.00	0.00	787.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGT..............	21	1	58.00	1.00	5.00	0.00	52.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGTT.............	22	1	36.00	3.00	4.00	0.00	29.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAG...............	21	1	22.00	0.00	1.00	0.00	21.00
...............GTAAGTATAGAG---AG----GATGTGA-TG---G.....................................................................................	24	1	12.00	0.00	0.00	0.00	12.00
...............GTAAGTATAGAG---AG----GATGTGA-...........................................................................................	21	1	11.00	0.00	1.00	0.00	10.00
................................................................................................TTCACCTCTCTCAA--TA-CTTAGT..............	22	1	9.00	0.00	0.00	0.00	9.00
...............GTAAGTATAGAG---AG----GATGTGA-TG---GGC...................................................................................	26	1	8.00	0.00	0.00	0.00	8.00
...............GTAAGTATAGAG---AG----GATGTGA-TG---......................................................................................	23	1	7.00	0.00	1.00	0.00	6.00
................................................................................................TTCACATCTCTCCA--TA-CTTAGT..............	22	1	7.00	0.00	0.00	0.00	7.00
................................................................................................TTCACCTCTATCCA--TA-CTTAGT..............	22	1	6.00	0.00	0.00	0.00	6.00
................................................................................................TTCACCTATCTCCA--TA-CTTAGT..............	22	1	6.00	0.00	0.00	0.00	6.00
................................................................................................TTCACCTCTCTCCA--TA-CTTA................	20	1	5.00	0.00	1.00	0.00	4.00
................................................................................................TTAACCTCTCTCCA--TA-CTTAGT..............	22	1	4.00	0.00	0.00	0.00	4.00
...............GTAAGTATAGAG---AG----GATGTGA-TG---GG....................................................................................	25	1	4.00	1.00	0.00	0.00	3.00
................................................................................................TTCACCTCTCTCCA--TA-CTT.................	19	1	4.00	0.00	0.00	0.00	4.00
................................................................................................TTCACCTCTCTACA--TA-CTTAGT..............	22	1	3.00	0.00	0.00	0.00	3.00
................................................................................................TTCACCTCTCTCCA--TA-ATTAGT..............	22	1	3.00	0.00	0.00	0.00	3.00
................................................................................................TTCACCTCTCTCCA--TA-CCTAGT..............	22	1	3.00	0.00	0.00	0.00	3.00
...................................................................................................ACCTCTCTCCA--TA-CTTAGT..............	19	1	3.00	1.00	1.00	0.00	1.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAGA..............	22	1	3.00	0.00	1.00	0.00	2.00
................................................................................................TTCACCTCTCTCCA--TA-CTTATT..............	22	1	2.00	0.00	0.00	0.00	2.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGTA.............	22	1	2.00	0.00	0.00	0.00	2.00
................................................................................................TTCACCTCTTTCCA--TA-CTTAGT..............	22	1	2.00	0.00	1.00	0.00	1.00
................................................................................................TTCAACTCTCTCCA--TA-CTTAGT..............	22	1	2.00	0.00	0.00	0.00	2.00
................................................................................................TTCACCTCTCTCCA--TA-CTTGGT..............	22	1	2.00	1.00	0.00	0.00	1.00
................................................................................................TTCACCCCTCTCCA--TA-CTTAGT..............	22	1	2.00	0.00	0.00	0.00	2.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAGTT.............	23	1	2.00	0.00	0.00	0.00	2.00
................................................................................................TTCACCTCTCTCCA--TC-CTTAGT..............	22	1	2.00	0.00	0.00	0.00	2.00
...............................................................................................CTTCACCTCTCTCCA--TA-CTTAGT..............	23	1	2.00	0.00	1.00	0.00	1.00
................................................................................................TTCGCCTCTCTCCA--TA-CTTAGT..............	22	1	2.00	0.00	1.00	0.00	1.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAGC..............	22	1	2.00	0.00	0.00	0.00	2.00
...............GTAAGTATAGAG---AG----GATGTGA-TC---GGC...................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
...............TTAAGTATAGAG---AG----GATGTG.............................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCTCTA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCTCCC--TA-CTTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00
................TAAGTATAGAG---AG----GATGTGA-TG---......................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGTAA............	23	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAG---AG----GATGT..............................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
............................................................................................AAAGTTCACCTCTCTCCA--TA-CT..................	22	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................TCACCTCTCTCCC--TA-CTTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCTCCA--TC-CTTCGT..............	22	1	1.00	0.00	1.00	0.00	0.00
...............GTAAGTATAGAG---AT----GATGT..............................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAGCA.............	23	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAG---AG----GATGTG.............................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAG---AG----GATGTGA-T..........................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................GTTCACCTCTCTCCA--TA-CTTAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCAACTCTCTCAA--TA-CTT.................	19	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCTACA--TA-ATTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACACCTCTCCA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................CTCACCTCTCTCCA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
.................AAGTATAGAG---AG----GATGTGA-TG---GGC...................................................................................	24	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................CACCTCTCTCCA--TA-CTTAGT..............	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................TCACCTCTCTCCA--TA-ATTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................TAACCTCTCTCCA--TA-CTTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGTGT............	23	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCTCCA--TA-CTTAGG..............	22	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAG...............	20	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTGACCTCTCTCCA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAG---AG----GATTTGA-TG---GGC...................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
...............TTAAGTATAGAG---AG----GATGCGA-...........................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCAGCTCTCTCCA--TA-CTTAGT..............	22	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................TCACATCTCTCCA--TA-CTTAGTT.............	22	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAG---AG----GATGTGA-TC---......................................................................................	23	1	1.00	0.00	0.00	0.00	1.00
...............GTAAGTATAGAG---AG----GATGTCA-T..........................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................TCACCTATCTCCA--TA-CTTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................CCTCTCTCCA--TA-CTTAGT..............	18	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................TCACCTCTCTCCA--TA-CTTAGAT.............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCTGCA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCxCCA--TA-CTTAGT..............	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTCTCTCCA--CA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................GTCAACTCTCTCCA--TA-CTTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................................TTCACATCTCTACA--TA-CTTAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TTCACCTGTCTCCA--TG-CTTAGT..............	22	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................TCACCTCTCTCCA--TA-CTTATT..............	21	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................TCACCTTTCTCCA--TA-CTTAGTT.............	22	1	1.00	0.00	0.00	0.00	1.00
...............................................................................................CTTCACCTCTCTCCA--TA-CTTAG...............	22	1	1.00	0.00	0.00	0.00	1.00

droEug1

CTCAAAGCTTTTCCAGTGAGTATAGAG---AG----GATGTGA-TGG--TGTA-----------------AT-T---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGTCGTGGCGTTAT

Size

Hit Count

Total Norm

droBia1

CTCAAAGCTCTTCCAGTGAGTATAAAG---AG----GACGTGA-TG----CCA-----------------AG-T---------------GCCAAAGTTTACCTGTCTCCA--TA-CTTAGTCGGCGCGGAGTTAT

Size

Hit Count

Total Norm

droTak1

CTCCAAGCTTTTCCAGTGAGTATAGAG---AG----CATGTGA-TGCAAGGTA-----------------AT-G---------------GCCAAAGTTCACCTCTCTCCA--TA-CTTAGTCGGCGCGGAGTTAT

Size

Hit Count

Total Norm

droEle1

CTCCAAGCTTTTTCAGTGAGTATCGAA---GG----CATATGC-AA---GATA-----------------T--------GA--T-GTATACTAAGATTAACCTCT--TTA--AA-CTTAGTCGTCGCGGAGTTAT

Size

Hit Count

Total Norm

droRho1

CTCCAAGCTTTTCCAGTTAGTATCAAATTTAT----GATATGA-TT---GGTA-----------------AA-T---------------ACTTAAATTGACCTCTCTCCA--TT-CTTAGTCGTCGCGGAGTTAT

Size

Hit Count

Total Norm

droFic1

TTCCAAGCTTTTCCAGTAAGTATAGAG---CA----GATGTGA-TG---GGTC-----------------AG-A---------------ACCAAACTTCACCTGCCTCTG--TA-CTTAGTCGTCGCGGAGTGAT

Size

Hit Count

Total Norm

droKik1

CTCGAAGCTGTTCCAGTGAGTAACGAG---AA----AGGGGAG-TT---GGAA-----------------GC-C---------------ACATAAACTAACATGCATCC---TT-CGTAGTCGCCGAGGTGTGAT

Size

Hit Count

Total Norm

droAna3

CTCTAAACTTTTTCAGTGAGTACTTGT---AA------TATAAATC---CATA-----------------A------------------ATCAAAACTCACTTT-TTCCA---A-CTTAGTCGCCGTGGTGTGAT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

CTCCAAACTGTTTCAGTGAGTACATGC---AA--TGGATATATGTA---CATA-----------------A--A---------------TCCA-GACTTACTT-TCTCC---TA-CTTAGTCGCCGTGGTGTGAT

Size

Hit Count

Total Norm

dp4

CTCAAAGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATCGTCTGAAAC----TAATT----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGTCGCGGCGTCAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...................................................................................................................TGCAGTGGTCGGGGCGTC..	18	1	1.00	0.00	0.00	1.00	0.00

droPer1

TTCAAAGCTCTTCCAGTGAGTACACAA---TT----CAATTCC-TC---GGCAAGGCTATTGTCTGAAAC----TAATG----------TC---CCTTCACTTATCCCTG--CCCTGCAGTCGGCGCGGCGTCAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..........................................C-TA---GGCAAGGCTGTTGTCTGAA...................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

TTCCAAATTGTTCCAGTAAGTTAAAAT---GA------T---C-TA---AAAT-----------------CATTTC------AA-----ATT--GATTCAATAATCTCTT--CC-ATTAGTCGACGCGGTGTCAT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

TTCCAAACTATTTCAGTAAGTAGCAGG---T----------GC-TG---AGTG-----------------CA-TGATTGTC--------TCTATATCTTGATTATC------T-TTGCAGTCGACGCGGGGTTAT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....AAACGATTTCxGTAAGTAGC...............................................................................................................	19	1	9.00	9.00	0.00	0.00	0.00	0.00
.....AACGATTTCxGTAAGTAGC...............................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droMoj3

TTCCAAGCTGTTTCAGTAAGTAGAGCA---CG----CATTTCC-AG---TACCCAACTAT----------------TCGTT--------ACTATATCTGTACAATT------T-TTGTAGTCGACGCGGGGTTAT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TTCCAAACTGTTTCAGTAAGTGGTAAC---ACAACTACTATGT-TT-------------------------G-TGC-----AACA----TTTAATG-------GACAGTATCT-TTGCAGTCGACGGGGAGTTAT	Size	Hit Count	Total Norm	V109 Male body
...........................................................................................TAATG-------GACAGTATCT-TTGCAG...............	21	1	1.00	1.00

Generated: 04/20/2012 at 05:18:43 EDT

dme-mir-1016

chr2R:10120635-10120692 -

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