dme-mir-4962- Best orthologs

dme-mir-4962	chrX:3671414-3671538 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 3671489-3671511
   star strand at position 3671441-3671464
   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	chrX:3671399-3671553 +		1	TGTGTTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTCTC----------------------CGTCTCTCTCTTTCCCT------CTCTCTGTTTACATTGAG-------CTGTTT--TGTCCGTGCACGTGCTA----------------------------------------------GAC-------GATGTA--GAGAGTGAGGGAGAG--AGC------GA---------------------ATA--GAATAA------CAGCTCATTG----------------------------TGCTGAGCGCC-CAGCCT
droSim1	chrX:2692027-2692181 +	LASTZ	1	TATGTTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTCTC----------------------CGTCTCTCTCTTTCCCT------CTCTCTGTTTACATTGAG-------CTGTTT--TGTCCGTGCACGTGCTA----------------------------------------------GAC-------GATGTA--GAGAGTGAGGGAGAG--AGC------GA---------------------ATA--CAATAA------CAGCTCATTG----------------------------TGCTGAGCGCC-CAGCCT
droSec1	super_13710:747-901 +	LASTZ	1	TATGTTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTTTC----------------------CGTCTCTCTCTTTCCCT------CTCTCTGTTTACATTGAG-------CTGTTT--TGTCCGTGCACGTGCTA----------------------------------------------GAC-------GATGTA--GAGAGTGAGGGAGAG--AGC------GA---------------------ATA--CAATAA------CAGCTCATTG----------------------------TGCTGAGCGTC-CAGCCT
droYak2	chrX:4740636-4740793 -	LASTZ	5	TGTGCTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTCTC----------------------CGCCTCTCTCTTTCCCT------CTCTCTGTTTACATTAAG-------CGGTTT--TGCCCGTGCACGTGCTA----------------------------------------------GAC-------GATATAGAAAGAGAGAGGGAGAG--AGC------GA---------------------ATAAC-AATAA------CAGCTCGTTT----------------------------TGCTGAGCGCC-CAGCCT
droEre2	scaffold_4690:1061104-1061256 +	LASTZ	5	TGTGTTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTCTC----------------------CGT--CTCTCATTCCCT------CTCTCTGTTTACATTAAG-------CGGTTT--TGCCTCTGCACGTGCTA----------------------------------------------GAC-------GGTATA--GAGAGAGAGGGAGAG--AGC------GA---------------------TTA--CAATAA------CAGCTCATTG----------------------------TGCTGAGCGCC-CAGCCT
droEug1	scf7180000408900:80143-80285 -	LASTZ	5	TGTGTTTTTTTATTTGTT------------------------------------TCTTCTCTCTT----------------------TAGCTCTC----TCTCT------CTCTCTGTTTACATTAAG-------CGGTGT--CGGTCGTGCACGTGCTA----------------------------------------------AGT-------G----A--GAGAG--GGAGAGAG--AAC------GA---------------------ATAAC-AATAA------CAGCGTTTTA----------------------------TACTGAGCGCC-CAGCCT
droBia1	scf7180000302126:1424433-1424605 -	LASTZ	5	TGTGTTTTGTTGTTTCTT-------------TTCTCTCCTTGTCCCTCTC-------------CCCACC---------CGAAG----CTCCTCTCTCTTTCGCTCTCTCCTTCTCTGTTTACATTAAG-------CGGTTT--TGTACGTGCACGTGCTA----------------------------------------------AGT-------G----AGAGAGCGAGAGGGTCAG--AGC------GA---------------------AT----AACAA------CAGCGCCTGC----------------------------TGCTGAGCGCC-CAGCCT
droTak1	scf7180000415078:324534-324728 +	LASTZ	5	TTTTGTTGTTTTATTTTTTTTCTTTGTTTTT---TCTCCTGGTCCGCC--------CCTT---CCCTCCATCAGTCTGTGTATCTCGACTCTCTCTCTTTCGCT------CTCTCTGTTTACATTAAG-------CGGTTT--TGTACGTGCACGTGCTA----------------------------------------------AGT-------G----GGAGAGCGAGAGGGAGAG--AGC------GA---------------------GTAGC-AATAA------CAGCGCTTTC----------------------------TGCTGAGCGCC-CAGCCT
droEle1	scf7180000490996:923512-923682 +	LASTZ	5	TGTTTGTTGTTTTTCTTC-------------TTT--------------------TTTTTTCTTTC----------------------TCTCCCTCTCTCTCTTT------TTCTCTGTTTACATTAAG-------CGGTTTCTCGCCCGTGCACGTGCTATTCGT-------GAGTG-----------AG------------------C-------GAGATATAAAG--AGA-GGTTAG--AGCGTACACAA---------------------GC---GAATAA------CAGCGCTTTG----------------------------TGCTGAGCGCC-CAGCCT
droRho1	scf7180000776529:17170-17316 -	LASTZ	5	TGTTTGTTGTTTCTATTT-------------ATT--------------------T-TTTT------------------------------------CTCTCGTT------CTCTCTGTTTACATTAAG-------CGGTTTCTCGCCCGTGCACGTGCTATTCAT-------GTGTG-----------AG----------------CGA-------GAGATC--AAA--AGAGAGAGAG--AGC------G----------------------------AATAA------CAGCGCTTTG----------------------------TGCTGAGCGCC-CAGCCT
droFic1	scf7180000453901:800509-800654 -	LASTZ	5	TTTATTTCTTTTCGTTTT-------------T-------------------------TTTTGTTT------------------------TCCCTCTC-TTCTCT------CTCTCTGTTTACATTAAG-------CAGTTT--TGCTCGTGCACGTGCTATT--------------------------------------------CAT-------GATTGA--GAGAACGAGAAAAAG--AGC------GC---------------------A-----AATAA------CAGAGCAATG----------------------------TGCTGAGCGCC-CAGCTT
droKik1	scf7180000302276:544719-544873 -	LASTZ	0	TGTTTTAGTGGCTCTCTC-------------CCT--------------------CCCATGCTCTC----------------------TTCCTCTCTCTCTCCCT------CTCTCTCTCTCTATCGGC-------G---TG--TGTGGGTGCGAGTCCCA----------------------------------------------AATAAAT---AGG-----CTACGAAAAATAATA--TGC------AA---------------------ACT--AATTAG--CA--CTTCCGTCAA----------------------------GCCCCAACGCC-AACGCA
droAna3	scaffold_13337:5571517-5571673 -	LASTZ	0	TGTGTTTTTGTTTTTGTT-------------GTC--------------------TCTGTTTTCTT----------------------CGCCTTTTTTTT-------------C-TCATTTTTGTGGAGCTTTGCATGCCCG--GCTGCAGGAGTGTTAGT------------GAGTGGTTTGACTTGT-------------TTTGCGGC-------AGCAGG--CAGCACACGCGCTGC--TGT---------------------------------------------------CGCCG----------------------------TCGCCGCTGTC-TAGC--
droBip1	scf7180000396423:461403-461557 +	LASTZ	0	TACGTTTGTTTTTTTTTTTTTTACTATTTTT---TCTAA-------------------------A----------------------AG--TTACCCTTTTTAT------TTTTTTTTTTATATTTGG-------CATTCC--AATTACTAT-TGTCCTA----------------------------------------------GAA-------GGCCTA--AACGC-------------------------------------------------------------------TTTCCCTTGATTGATTGAGACCTACCAGCTCATGTAAGCCACT-TGTTTT
dp4	Unknown_group_658:20580-20732 -	LASTZ	0	TACATTTTTCCACTTGCC-------------CACACTTTTCGCTGCGCTGCTCTCTCGCTC----------------------------TCTCTCTCTCTCATG------CTC-TCACTCTCAGAAAG-------CTGTGC--AAT--------GCACCA----------------------------------------------TGC----GACGACTGA--AAGCATGAGAGTGAGCCAGC------TT---------------------TCA--GTGTGG------CAGTTTTTTT----------------------------CGTTG-------------
droPer1	super_23:1560592-1560751 -	LASTZ	0	GTTTCTCTGCCTCTCCCT-------------CTC--------------------T-CCCTCTCTC----------------------TCTCTCTCGCTGTCTTC------CTCTTTCTCAACTATGTG-------TGGCCA--TGTGTGTGTGTGTGTGT------------GTGTGGGTTGTATCTG------------------TGT-------G----TGAGAGCGAAGCGCAGAC--A---------A---------------------TTAGT-TTTAT------TATGCTTTGT-----------------------------------TGCCGAGCTTC
droWil1	scaffold_181096:11652056-11652210 +	LASTZ	0	TCTGTTTGTGAGGGTCCC-------------TCT--------------------CTTTTACTCTC----------------------TGTCGCTCTCTCTCTCT------CTCGCGCTGCACAAAAAA-------ATTAGT--CA----TACCA----AA--AA-CAAAATA------------------------CAGATTGCAAAGC-------AATAGA--GAGAGAGAGGGAGAG--AGA------GA---------------GA----GT-------A---------AGTGAGTG----------------------------TG-AGAGCGCC-CA----
droVir3	scaffold_12855:8711965-8712121 +	LASTZ	0	TCTCTTTCTTTATTTCTC-------------TGCTTTT--CTCTG------------TCTCTCTTTATC------------------TGTATCTCTCTCTCTTT------CTCTCTATTTTCT-ATTGCT-----CTGTTA--TGTC-AAACATTTGCTG------------------------------------CATACTTTCAGGC-------GATATT--AAAAGCGTGCAAGAT--TTT------CA---------------------TTT--GTATAA------CTGCGTATT-----------------------------------------------
droMoj3	scaffold_6496:4311996-4312145 -	LASTZ	0	TGTCTCTCTATTTCTCTC---------------T--------------------CTCTCTCTCTC----------------------TCTCTCTCTCTCTCTCT------CTCTCTGCCTGCCTTCA----------CTTT--TATACAAAAA--T---A----------------------------ATGGCCAT----------CAA-------AATTAA--TAAAAACGTAATCAG--AGC------GAATGACTACAGAGGAAAACGA-AAA--GTATAA------AAG----------------------------------------------------C
droGri2	scaffold_15203:9842081-9842230 +	LASTZ	0	TCCCTTCTCTCTCTCTCT-------------C-------------------------------------------------------TCTCGCTCTCTCTCTCT------CTCTCTATTT-----------------GTCT--CTTCCGCATA-GCGCAA----------------------------------------------GTC-------GACGTC--GGGGCTGACGGGCAG--CGT-------------TTCACAGGAGAATCGGGTGAC-TATCACCCTGATTGC-TGTTG----------------------------TGCTG-CTGTT-CATCGT

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	TGTGTTTGGTTGTT-------TTTCCTTTCTTTTCTCTC-----------------------------------------------CGTCTCTCTCTTTCCCTCTCTCTGTTTACATTGAGCTGTTT--TGTCCGTGCACGTGCTA----------GACGATGTA----GAGAGTGAGGGAGAGAGCGAATA-G-----AATAACAGCTCATTGTGCTGAGCGCCCAGCCT
droSim1	TATGTTTGGTTGTT-------TTTCCTTTCTTTTCTCTC-----------------------------------------------CGTCTCTCTCTTTCCCTCTCTCTGTTTACATTGAGCTGTTT--TGTCCGTGCACGTGCTA----------GACGATGTA----GAGAGTGAGGGAGAGAGCGAATA-C-----AATAACAGCTCATTGTGCTGAGCGCCCAGCCT
droSec1	TATGTTTGGTTGTT-------TTTCCTTTCTTTTCTTTC-----------------------------------------------CGTCTCTCTCTTTCCCTCTCTCTGTTTACATTGAGCTGTTT--TGTCCGTGCACGTGCTA----------GACGATGTA----GAGAGTGAGGGAGAGAGCGAATA-C-----AATAACAGCTCATTGTGCTGAGCGTCCAGCCT
droYak2	TGTGCTTGGTTGTT-------TTTCCTTTCTTTTCTCTC-----------------------------------------------CGCCTCTCTCTTTCCCTCTCTCTGTTTACATTAAGCGGTTT--TGCCCGTGCACGTGCTA----------GACGATATA--GAAAGAGAGAGGGAGAGAGCGAATAAC-----AATAACAGCTCGTTTTGCTGAGCGCCCAGCCT
droEre2	TGTGTTTGGTTGTT-------TTTCCTTTCTTTTCTCTC-----------------------------------------------CGTCT--CTCATTCCCTCTCTCTGTTTACATTAAGCGGTTT--TGCCTCTGCACGTGCTA----------GACGGTATA----GAGAGAGAGGGAGAGAGCGATTA-C-----AATAACAGCTCATTGTGCTGAGCGCCCAGCCT
droEug1	TGTGTTTTTTTATT-------TG---TTTCTTCTCTCTT-----------------------------------------------TAGCTCTC----TCTCTCTCTCTGTTTACATTAAGCGGTGT--CGGTCGTGCACGTGCTA----------AGTGAG--A------GA--GGGAGAGAGAACGAATAAC-----AATAACAGCGTTTTATACTGAGCGCCCAGCCT
droBia1	TGTGTTTTGTTGTT-------T-------CTTTTCTCTCCTTGTCC-----CTCTCCCCACC-------------CGAAGCTCCTCTCTCTTTCGCTCTCTCCTTCTCTGTTTACATTAAGCGGTTT--TGTACGTGCACGTGCTA----------AGTGAG--A----GAGCGAGAGGGTCAGAGCGAATA--------ACAACAGCGCCTGCTGCTGAGCGCCCAGCCT
droTak1	TTTTGTTGTTT-TA---TTTTTTTTCTTTGTTTTTTCTCCTGGTCCGCCCCTTCCCTCCATCAGTCTGTGTATCTCGA---------CTCTCTCTCTTTCGCTCTCTCTGTTTACATTAAGCGGTTT--TGTACGTGCACGTGCTA----------AGTGGG--A----GAGCGAGAGGGAGAGAGCGAGTAGC-----AATAACAGCGCTTTCTGCTGAGCGCCCAGCCT
droEle1	TGTTTGTTGTTTTT-------CTTCTTTTTTTTTCTTTC-----------------------------------------------TCTCCCTCTCTCTCTTTTTCTCTGTTTACATTAAGCGGTTTCTCGCCCGTGCACGTGCTATTCGTGAGTGAGCGAGATA--TAAAGAG--A-GGTTAGAGCGTACA-CAAGCGAATAACAGCGCTTTGTGCTGAGCGCCCAGCCT
droRho1	TGTTT---GTTGTTTCT----ATTTATTT-TTTT-------------------------------------------------------------CTCTCGTTCTCTCTGTTTACATTAAGCGGTTTCTCGCCCGTGCACGTGCTATTCATGTGTGAGCGAG--AGATCA--AAAGAGAGAGAGAGCG-----------AATAACAGCGCTTTGTGCTGAGCGCCCAGCCT
droFic1	TTTATTTCTT------------TTCGTTTTTTTTTGTTT-------------------------------------------------TCCCTCTC-TTCTCTCTCTCTGTTTACATTAAGCAGTTT--TGCTCGTGCACGTGCTATTC--------ATGATTGA----GAGAACGAGAAAAAGAGCGCA---------AATAACAGAGCAATGTGCTGAGCGCCCAGCTT

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

TATGTTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTCTC----------------------CGTCTCTCTCTTTCCCT------CTCTCTGTTTACATTGAG-------CTGTTT--TGTCCGTGCACGTGCTA----------------------------------------------GAC-------GATGTA--GAGAGTGAGGGAGAG--AGC------GA---------------------ATA--CAATAA------CAGCTCATTG----------------------------TGCTGAGCGCC-CAGCCT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................................................................................................................................................AC-------GATGTA--GAGAGTGAGGGAG.............................................................................................................	21	3	1.33	0.00	0.67	0.67	0.00
................................................................................................................CTCTxTTAACATTGAG-------CTGT...............................................................................................................................................................................................................	19	3	1.33	0.00	0.00	1.33	0.00
............................................................................................................................................................................................................................GA--GAGAGAGAGGGAGAG--A........................................................................................................	18	41	0.02	0.02	0.00	0.00	0.00
..............................................................................................................................................................TA----------------------------------------------GAC-------GATGTA--GAGAGTGAGGGA..............................................................................................................	23	3	0.33	0.00	0.33	0.00	0.00
...............................................................TC----------------------AGTCTCTCTCTCTCCC...................................................................................................................................................................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00
...............................................................................................................................................................................................................AC-------GATGTA--GAGAGTGAGGGA..............................................................................................................	20	3	0.33	0.00	0.33	0.00	0.00
.................................................................................................................TCTxTTAACATTGAG-------CTGT...............................................................................................................................................................................................................	18	3	0.33	0.00	0.00	0.33	0.00
...............................................................TC----------------------GGTCTCTCTCTCTCCC...................................................................................................................................................................................................................................................	18	6	0.17	0.00	0.17	0.00	0.00
...............................................................................................................................................................A----------------------------------------------GAC-------GATGTA--GAGAGTCAGGGA..............................................................................................................	22	3	0.33	0.00	0.33	0.00	0.00
...............................................................................................................................................................................................................AC-------GATGTA--GAGAGTGAGGGAGA............................................................................................................	22	3	0.33	0.00	0.33	0.00	0.00
..............................................................................................................................................................................................................GAC-------GATGTA--GAGAGTGAGGGAGA............................................................................................................	23	3	0.33	0.00	0.00	0.00	0.33

droSec1

TATGTTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTTTC----------------------CGTCTCTCTCTTTCCCT------CTCTCTGTTTACATTGAG-------CTGTTT--TGTCCGTGCACGTGCTA----------------------------------------------GAC-------GATGTA--GAGAGTGAGGGAGAG--AGC------GA---------------------ATA--CAATAA------CAGCTCATTG----------------------------TGCTGAGCGTC-CAGCCT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................................................................................................GAC-------GATGTA--GAGAGTGAGGGAGA............................................................................................................	23	2	2.50	0.50	0.00	2.00
................................................................................................................CTCTxTTAACATTGAG-------CTGT...............................................................................................................................................................................................................	19	2	2.00	0.00	2.00	0.00
...............................................................................................................................................................................................................AC-------GATGTA--GAGAGTGAGGGAGA............................................................................................................	22	2	1.00	0.50	0.50	0.00
...............................................................................................................................................................................................................AC-------GATGTA--GAGAGTGAGGGAG.............................................................................................................	21	2	0.50	0.50	0.00	0.00
............................................................................................................................................................GCTA----------------------------------------------GAC-------GATGTA--GAGAGTGAGGGAGA............................................................................................................	27	2	0.50	0.50	0.00	0.00
...............................................................................................................................................................A----------------------------------------------GAC-------TATGTA--GAGAGTGAGGGA..............................................................................................................	22	2	0.50	0.00	0.00	0.50
...............................................................................................................................................................A----------------------------------------------GAC-------GATGTA--GAGAGTGAGGGA..............................................................................................................	22	2	0.50	0.50	0.00	0.00
.............................................................................................................................................................................................................................A--GAGAGAGAGGGAGAG--AGA------................................................................................................	19	35	0.03	0.03	0.00	0.00
............................................................................................................................................................................................................................CA--GAGAGTGAGCGAGAG--AGC------................................................................................................	20	3	0.33	0.00	0.00	0.33
.........................................................................................................................................................................................................................ATGTA--xAGAGTGAGGTAGA............................................................................................................	18	2	0.50	0.00	0.50	0.00
..............................................................................................................................................................TA----------------------------------------------GAC-------GATGTA--GAGAGTGAAG................................................................................................................	21	2	0.50	0.00	0.00	0.50
..............................................................................................................................................................TA----------------------------------------------GAT-------GATGTA--GAGAGTGAGGT...............................................................................................................	22	2	0.50	0.50	0.00	0.00

droYak2

TGTGCTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTCTC----------------------CGCCTCTCTCTTTCCCT------CTCTCTGTTTACATTAAG-------CGGTTT--TGCCCGTGCACGTGCTA----------------------------------------------GAC-------GATATAGAAAGAGAGAGGGAGAG--AGC------GA---------------------ATAAC-AATAA------CAGCTCGTTT----------------------------TGCTGAGCGCC-CAGCCT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.........................................................................................................................................................................................................................ATATAAAAAGAGAGAGAGAGAG--A........................................................................................................	23	3	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................................................................ATATAAAAAGAGAGAGAGAGA............................................................................................................	21	3	0.67	0.00	0.00	0.67	0.00	0.00
..........................................................................................................................................................................................................................TATAGAAAGAGAGAGGGAG.............................................................................................................	19	2	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................ATATAAAAAGAGAGAGAGA..............................................................................................................	19	3	0.33	0.00	0.00	0.33	0.00	0.00
.............................................................................................................................................................................................................................AGAACGAGAGAGGGAGGG--A........................................................................................................	19	3	0.33	0.00	0.00	0.33	0.00	0.00
....................................................................................................................................................................................................................................AAGAGGGAGAG--AGC------GG---------------------A........................................................................	17	5	0.20	0.00	0.00	0.00	0.20	0.00
.............................................................................................................................................................................................................................AGCAAGAGAGAGAGAGAG--AGC------................................................................................................	21	9	0.11	0.00	0.00	0.11	0.00	0.00
..............................................................................................................................................................................................................................GAAAAAGAGAGGGAGAG--A........................................................................................................	18	19	0.05	0.00	0.00	0.05	0.00	0.00
...................................................................................................................................................................................................................................AGCGAGGGATAG--AGC------GA---------------------ATA......................................................................	20	2	0.50	0.00	0.00	0.00	0.50	0.00
...........................................................................................................................................................................................................................ATAGAAAGAGAGAGAGAAAG--A........................................................................................................	21	12	0.08	0.00	0.00	0.08	0.00	0.00
..............................................................................................................................................................................................................................GAAAGAGAGAGTGAGAG--GG.......................................................................................................	19	13	0.08	0.00	0.00	0.08	0.00	0.00
........................................................................................................................................................................................................................GAGAAAGAAAGAGAGAGGGAGAG--.........................................................................................................	23	6	0.17	0.00	0.00	0.17	0.00	0.00
.................................................................................................................................................................................................................................................................................ATAAC-AATAA------CAGCTCGTC...............................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................................................................................................................GAAAGAGAGAGCGCGAG--A........................................................................................................	18	14	0.07	0.00	0.00	0.07	0.00	0.00
...........................................................................................................................................................................................................................ATAAAAAGAGAGAGAGAGA............................................................................................................	19	14	0.07	0.00	0.00	0.07	0.00	0.00
................................................................................................................................................................................................................................AATAGAGAGGGAGAG--AGA------G...............................................................................................	19	12	0.08	0.00	0.00	0.08	0.00	0.00
...............................................................................................TCTTTCTCT------CTCTCTGTGT..................................................................................................................................................................................................................................	19	7	0.14	0.00	0.00	0.00	0.14	0.00
...........................................................................................................................................................................................................................ATAAAAAGAGAGAGAGAGAG--A........................................................................................................	21	11	0.09	0.00	0.00	0.09	0.00	0.00
...........................................................................................................................................................................................................................ATAAAAAGAGAGAGAGAGAG--AGC------................................................................................................	23	3	0.33	0.00	0.00	0.33	0.00	0.00
.......................................................................................................................................................................................................................................................................................AATGA------CAGCTCATTT----------------------------TG................	17	2	0.50	0.00	0.00	0.00	0.50	0.00
.........................................................................................................................................................................................................................ATATACAAAGAGAGAGAGAGA............................................................................................................	21	2	0.50	0.00	0.00	0.50	0.00	0.00
................................................................................................................................................................................................................................AAGAGAGAGAGAGAG--AGC------................................................................................................	18	92	0.01	0.00	0.00	0.01	0.00	0.00

droEre2

TGTGTTTGGTTGTTTTTC-------------CTT--------------------TCTTTTCTCTC----------------------CGT--CTCTCATTCCCT------CTCTCTGTTTACATTAAG-------CGGTTT--TGCCTCTGCACGTGCTA----------------------------------------------GAC-------GGTATA--GAGAGAGAGGGAGAG--AGC------GA---------------------TTA--CAATAA------CAGCTCATTG----------------------------TGCTGAGCGCC-CAGCCT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................................................................................................................................................................................................TA--GAGAGAAAGGGAGAA--A........................................................................................................	18	4	0.25	0.25	0.00	0.00	0.00
................................................................................................................................................................................................................................GAAAGAGAGGGAGAG--AGA------GA---------------------.........................................................................	20	28	0.04	0.04	0.00	0.00	0.00
.................................................................................................................................................................................................................................................ATC------GA---------------------TTA--CAACAA------CAGC....................................................	18	4	0.25	0.00	0.00	0.00	0.25
........................................................................................................................................................................................................................GCTATA--GAGAGAGAGAGAG.............................................................................................................	19	11	0.09	0.00	0.00	0.00	0.09
............................................................................................................................................................................................................................GA--GAGAGAGAGGGAGAG--A........................................................................................................	18	31	0.03	0.00	0.00	0.00	0.03
...........................................................................................................................................................................................................................ATA--GAGAGAGAGAGAGAG--G........................................................................................................	19	48	0.02	0.02	0.00	0.00	0.00

droEug1

TGTGTTTTTTTATTTGTT------------------------------------TCTTCTCTCTT----------------------TAGCTCTC----TCTCT------CTCTCTGTTTACATTAAG-------CGGTGT--CGGTCGTGCACGTGCTA----------------------------------------------AGT-------G----A--GAGAG--GGAGAGAG--AAC------GA---------------------ATAAC-AATAA------CAGCGTTTTA----------------------------TACTGAGCGCC-CAGCCT

Size

Hit Count

Total Norm

droBia1

TGTGTTTTGTTGTTTCTT-------------TTCTCTCCTTGTCCCTCTC-------------CCCACC---------CGAAG----CTCCTCTCTCTTTCGCTCTCTCCTTCTCTGTTTACATTAAG-------CGGTTT--TGTACGTGCACGTGCTA----------------------------------------------AGT-------G----AGAGAGCGAGAGGGTCAG--AGC------GA---------------------AT----AACAA------CAGCGCCTGC----------------------------TGCTGAGCGCC-CAGCCT

Size

Hit Count

Total Norm

droTak1

TTTTGTTGTTTTATTTTTTTTCTTTGTTTTT---TCTCCTGGTCCGCC--------CCTT---CCCTCCATCAGTCTGTGTATCTCGACTCTCTCTCTTTCGCT------CTCTCTGTTTACATTAAG-------CGGTTT--TGTACGTGCACGTGCTA----------------------------------------------AGT-------G----GGAGAGCGAGAGGGAGAG--AGC------GA---------------------GTAGC-AATAA------CAGCGCTTTC----------------------------TGCTGAGCGCC-CAGCCT

Size

Hit Count

Total Norm

droEle1

TGTTTGTTGTTTTTCTTC-------------TTT--------------------TTTTTTCTTTC----------------------TCTCCCTCTCTCTCTTT------TTCTCTGTTTACATTAAG-------CGGTTTCTCGCCCGTGCACGTGCTATTCGT-------GAGTG-----------AG------------------C-------GAGATATAAAG--AGA-GGTTAG--AGCGTACACAA---------------------GC---GAATAA------CAGCGCTTTG----------------------------TGCTGAGCGCC-CAGCCT

Size

Hit Count

Total Norm

droRho1

TGTTTGTTGTTTCTATTT-------------ATT--------------------T-TTTT------------------------------------CTCTCGTT------CTCTCTGTTTACATTAAG-------CGGTTTCTCGCCCGTGCACGTGCTATTCAT-------GTGTG-----------AG----------------CGA-------GAGATC--AAA--AGAGAGAGAG--AGC------G----------------------------AATAA------CAGCGCTTTG----------------------------TGCTGAGCGCC-CAGCCT

Size

Hit Count

Total Norm

droFic1

TTTATTTCTTTTCGTTTT-------------T-------------------------TTTTGTTT------------------------TCCCTCTC-TTCTCT------CTCTCTGTTTACATTAAG-------CAGTTT--TGCTCGTGCACGTGCTATT--------------------------------------------CAT-------GATTGA--GAGAACGAGAAAAAG--AGC------GC---------------------A-----AATAA------CAGAGCAATG----------------------------TGCTGAGCGCC-CAGCTT

Size

Hit Count

Total Norm

droKik1

TGTTTTAGTGGCTCTCTC-------------CCT--------------------CCCATGCTCTC----------------------TTCCTCTCTCTCTCCCT------CTCTCTCTCTCTATCGGC-------G---TG--TGTGGGTGCGAGTCCCA----------------------------------------------AATAAAT---AGG-----CTACGAAAAATAATA--TGC------AA---------------------ACT--AATTAG--CA--CTTCCGTCAA----------------------------GCCCCAACGCC-AACGCA

Size

Hit Count

Total Norm

droAna3

TGTGTTTTTGTTTTTGTT-------------GTC--------------------TCTGTTTTCTT----------------------CGCCTTTTTTTT-------------C-TCATTTTTGTGGAGCTTTGCATGCCCG--GCTGCAGGAGTGTTAGT------------GAGTGGTTTGACTTGT-------------TTTGCGGC-------AGCAGG--CAGCACACGCGCTGC--TGT---------------------------------------------------CGCCG----------------------------TCGCCGCTGTC-TAGC--	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................................................................................................TTAAT------------GAGTGGTTAGACT.................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................................................................................CAGG--CAGCACACGCCCAG............................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................................................T-------------TGTGCGGC-------AGCCGG--CAG.......................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................................................................................................................................................................CGTCGC--TGT---------------------------------------------------CGCCG----------------------------TCGCC.............	19	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................................TTTTTTTTGGAGCTTTGC....................................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................GAGGGTTAGT------------GAGAGGTT......................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................CCTTTTTTAT-------------C-TGATTTTT................................................................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00

droBip1

TACGTTTGTTTTTTTTTTTTTTACTATTTTT---TCTAA-------------------------A----------------------AG--TTACCCTTTTTAT------TTTTTTTTTTATATTTGG-------CATTCC--AATTACTAT-TGTCCTA----------------------------------------------GAA-------GGCCTA--AACGC-------------------------------------------------------------------TTTCCCTTGATTGATTGAGACCTACCAGCTCATGTAAGCCACT-TGTTTT

Size

Hit Count

Total Norm

dp4

TACATTTTTCCACTTGCC-------------CACACTTTTCGCTGCGCTGCTCTCTCGCTC----------------------------TCTCTCTCTCTCATG------CTC-TCACTCTCAGAAAG-------CTGTGC--AAT--------GCACCA----------------------------------------------TGC----GACGACTGA--AAGCATGAGAGTGAGCCAGC------TT---------------------TCA--GTGTGG------CAGTTTTTTT----------------------------CGTTG-------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..........................................CTGCGTTGCGCTCTCGCTC----------------------------T................................................................................................................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
........................................................CTCTC----------------------------TCTCTxTCTCGCAT...................................................................................................................................................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

droPer1

GTTTCTCTGCCTCTCCCT-------------CTC--------------------T-CCCTCTCTC----------------------TCTCTCTCGCTGTCTTC------CTCTTTCTCAACTATGTG-------TGGCCA--TGTGTGTGTGTGTGTGT------------GTGTGGGTTGTATCTG------------------TGT-------G----TGAGAGCGAAGCGCAGAC--A---------A---------------------TTAGT-TTTAT------TATGCTTTGT-----------------------------------TGCCGAGCTTC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...............................................................................................................................................TGTTTGTTTGTGTGTGT------------GTGT..........................................................................................................................................................................	21	29	0.55	0.55	0.00	0.00	0.00	0.00
.........................................................................................................................................................TGTGTGT------------GTGxGGATTGTTTC................................................................................................................................................................	20	1	13.00	12.00	1.00	0.00	0.00	0.00
................................................................................................................................................GTGCGTGTGTGTGTGT------------GTGC..........................................................................................................................................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
..................................................................................................................................................GTGCGTGTGTGTGT------------GTGTGC........................................................................................................................................................................	20	50	0.24	0.06	0.18	0.00	0.00	0.00
.........................................................................................................................................................TGTGTGT------------GTGxGGATTGTTTCTG------------------............................................................................................................................................	22	1	11.00	10.00	1.00	0.00	0.00	0.00
.......................................................................................................................................................TGTGTGTGT------------GTGxGGATTGTTTC................................................................................................................................................................	22	1	10.00	9.00	1.00	0.00	0.00	0.00
................................................................................................................................................GTGCGTGTGTGTGTGT------------GTG...........................................................................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
................................................................................................................................................GTGCGTGTGTGTGTGT------------GT............................................................................................................................................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
..................................................................................................................................................GTGCGTGTGTGTGT------------GTGTG.........................................................................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
..................................................................................................................................................GTGCGTGTGTGTGT------------GTGT..........................................................................................................................................................................	18	47	0.17	0.02	0.15	0.00	0.00	0.00
...................................................................................................................................................TGTGTGTGTGTGT------------GTGTG.........................................................................................................................................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
.................................................................................................................................................TGTTTGTTTGTGTGT------------GTGTG.........................................................................................................................................................................	20	40	0.18	0.10	0.03	0.00	0.05	0.00
.................................................................................................................................................TGTGTGTGTGTGTGT------------GTG...........................................................................................................................................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
...............................................................................................................................................TGTGTGTGTGTGTGTGT------------G.............................................................................................................................................................................	18	41	0.17	0.07	0.00	0.07	0.02	0.00
...............................................................................................................................................TGTTTGTTTGTGTGTGT------------GTG...........................................................................................................................................................................	20	40	0.18	0.10	0.03	0.00	0.05	0.00
...........................................................................................................................................................TGTGT------------GTGxGGATTGTTTCTG------------------............................................................................................................................................	20	1	6.00	6.00	0.00	0.00	0.00	0.00
...............................................................................................................................................TGTGTGTGTGTGTGTGT------------GT............................................................................................................................................................................	19	32	0.16	0.16	0.00	0.00	0.00	0.00
....................................................................................................................................................GTGGGTGTGTGG------------GTGTGGGT......................................................................................................................................................................	20	5	1.00	0.80	0.00	0.00	0.20	0.00
...............................................................................................................................................TGTGTGTGTGTGTGTGT------------GTGTGTG.......................................................................................................................................................................	24	29	0.17	0.10	0.00	0.03	0.03	0.00
................................................................................................................................................GTGCGTGTGTGTGTGT------------GTGCG.........................................................................................................................................................................	21	41	0.12	0.10	0.02	0.00	0.00	0.00
.................................................................................................................................................TGTGTGTGTGTGTGT------------GTGT..........................................................................................................................................................................	19	32	0.16	0.16	0.00	0.00	0.00	0.00
..................................................................................................................................................GTGCGTGTGTGTGT------------GTGTGCG.......................................................................................................................................................................	21	41	0.12	0.10	0.02	0.00	0.00	0.00
...............................................................................................................................................TGTGTGTGTGTGTGTGT------------GTGTG.........................................................................................................................................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
.................................................................................................................................................TGTGTGTGTGTGTGT------------GTGTGTG.......................................................................................................................................................................	22	50	0.08	0.08	0.00	0.00	0.00	0.00
.....................................................................................................................................................TGTGTGTGTGT------------GTGxGGATTGTTTC................................................................................................................................................................	24	1	4.00	4.00	0.00	0.00	0.00	0.00
....................................................................................................................................................GTGTGTGTGTGT------------GGATGG........................................................................................................................................................................	18	10	0.40	0.40	0.00	0.00	0.00	0.00
...........................................................................................................................................................TGTGT------------GTGxGGATTGTTTCT...............................................................................................................................................................	19	1	4.00	3.00	1.00	0.00	0.00	0.00
........................................................................................................................................................GTGTGTGT------------GTGTGGATGG....................................................................................................................................................................	18	10	0.40	0.40	0.00	0.00	0.00	0.00
.........................................................................................................................................................TGTGTGT------------GTGxGGATTGTTTCT...............................................................................................................................................................	21	1	4.00	4.00	0.00	0.00	0.00	0.00
...............................................................................................................................................CGTGCGTGTGTGTGTGT------------GTG...........................................................................................................................................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
..................................................................................................................................................GTGTGTGTGTTTGT------------GTGTA.........................................................................................................................................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
................................................................................................................................................GTGTGTGTGTTTGTGT------------GTA...........................................................................................................................................................................	19	49	0.06	0.06	0.00	0.00	0.00	0.00
......................................................................................................................................................GTGTGTGTGT------------GTGTGCGCT.....................................................................................................................................................................	19	15	0.20	0.13	0.00	0.07	0.00	0.00
................................................................................................................................................GTGTTTGTGTGTGTGT------------TTGTG.........................................................................................................................................................................	21	32	0.09	0.09	0.00	0.00	0.00	0.00
.................................................................................................................................................CGTGCGTGTGTGTGT------------GTGTG.........................................................................................................................................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
...............................................................................................................................................GGTGTGTGTGTGTGTGT------------GT............................................................................................................................................................................	19	40	0.08	0.08	0.00	0.00	0.00	0.00
.......................................................................................................................................................TGTGTGTGT------------GTGxGGATTGTTTCTG------------------............................................................................................................................................	24	1	3.00	3.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................GTGTGT------------GTGxGGATTGTTTCTG------------------............................................................................................................................................	21	1	3.00	3.00	0.00	0.00	0.00	0.00
...........................................................................................................................................CG--TGCGTGTGTGTGTGTGT------------G.............................................................................................................................................................................	20	48	0.06	0.06	0.00	0.00	0.00	0.00
....................................................................................................................................................GTGTGCGTGTGT------------GTGTGGT.......................................................................................................................................................................	19	9	0.33	0.33	0.00	0.00	0.00	0.00
................................................................................................................................................GTTTGTTTGTGTGTGT------------GTGT..........................................................................................................................................................................	20	35	0.09	0.09	0.00	0.00	0.00	0.00
................................................................................................................................................GTGTGTGTGCGTGTGT------------GAGTG.........................................................................................................................................................................	21	30	0.10	0.10	0.00	0.00	0.00	0.00
.........................................................................................................................................................TGTGTGT------------GTGxGGATTGTTTCTG------------------T...........................................................................................................................................	23	1	3.00	3.00	0.00	0.00	0.00	0.00
.................................................................................................................................................GGTGTGTGTGTGTGT------------GTGT..........................................................................................................................................................................	19	40	0.08	0.08	0.00	0.00	0.00	0.00
....................................................................................................................................................GTGTGTGTGTGT------------TTGTGGT.......................................................................................................................................................................	19	6	0.50	0.50	0.00	0.00	0.00	0.00

droWil1

TCTGTTTGTGAGGGTCCC-------------TCT--------------------CTTTTACTCTC----------------------TGTCGCTCTCTCTCTCT------CTCGCGCTGCACAAAAAA-------ATTAGT--CA----TACCA----AA--AA-CAAAATA------------------------CAGATTGCAAAGC-------AATAGA--GAGAGAGAGGGAGAG--AGA------GA---------------GA----GT-------A---------AGTGAGTG----------------------------TG-AGAGCGCC-CA----	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..................................................................................................................................................................................................................................GAGGGAGGGAGAG--AGA------GA---------------...............................................................................	18	20	0.20	0.05	0.15	0.00	0.00
...........................................................................................................................................................................................................CAAAGC-------GACAGA--GAGAGA....................................................................................................................	18	13	0.23	0.15	0.08	0.00	0.00

droVir3

TCTCTTTCTTTATTTCTC-------------TGCTTTT--CTCTG------------TCTCTCTTTATC------------------TGTATCTCTCTCTCTTT------CTCTCTATTTTCT-ATTGCT-----CTGTTA--TGTC-AAACATTTGCTG------------------------------------CATACTTTCAGGC-------GATATT--AAAAGCGTGCAAGAT--TTT------CA---------------------TTT--GTATAA------CTGCGTATT-----------------------------------------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...............................................................................................................................................TGTC-AAACATCTGCTG------------------------------------CAG...................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
..............................................................................................................................TGCT-----CTGxAA--TGTC-AAA...................................................................................................................................................................................................	16	1	1.00	0.00	1.00	0.00	0.00	0.00
..TCTTTGTTTATCTCTC-------------TGCTTT.....................................................................................................................................................................................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

TGTCTCTCTATTTCTCTC---------------T--------------------CTCTCTCTCTC----------------------TCTCTCTCTCTCTCTCT------CTCTCTGCCTGCCTTCA----------CTTT--TATACAAAAA--T---A----------------------------ATGGCCAT----------CAA-------AATTAA--TAAAAACGTAATCAG--AGC------GAATGACTACAGAGGAAAACGA-AAA--GTATAA------AAG----------------------------------------------------C

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TCCCTTCTCTCTCTCTCT-------------C-------------------------------------------------------TCTCGCTCTCTCTCTCT------CTCTCTATTT-----------------GTCT--CTTCCGCATA-GCGCAA----------------------------------------------GTC-------GACGTC--GGGGCTGACGGGCAG--CGT-------------TTCACAGGAGAATCGGGTGAC-TATCACCCTGATTGC-TGTTG----------------------------TGCTG-CTGTT-CATCGT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:20:31 EDT

dme-mir-4962

chrX:3671414-3671538 +

Known_mirbase

intron

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