dme-mir-4957- Best orthologs

dme-mir-4957	chrX:15213986-15214070 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 15214004-15214024
   star strand at position 15214034-15214054
   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:15213971-15214085 -		1	CTTTTTT-TTCT----CTG----CTCG--------------------------TTGTATTTTACGCACTCTGCTGGCAGCGCTGTCG------GCGTCGCTGCCAGCTGCCAGCAGC------------------------------------GAGCG--------------GT--ACACTTGCAACTA---------TCCTGTGCACCCT---ACAATT
droSim1	chrX:11736931-11737042 -	LASTZ	4	CTTTTTT-TTTTTTCTCTG----CTCG--------------------------TTGCATTTTACGCACTCTGCTGGCAGCGACGCCG------ACAGCGCTGCCAGCA-------GC------------------------------------GAGCG--------------GT--ACACTTGCAACTA---------TCCTGCGCACCCT---ACAATT
droSec1	super_56:101687-101796 -	LASTZ	4	CTTTTTT-TTTT--CTCTG----CTCG--------------------------TTGCATTTTACGCACTCTGCTGGCAGCGACGCCG------ACAGCGGTGCCAGCA-------GC------------------------------------GAGCG--------------GT--ACACTTGCAACTA---------TCCTGCACACCCT---ACAATT
droYak2	chrX:9414156-9414285 -	LASTZ	5	TTTTTTT-------CTCTG----CTCGTTTT---TCTCTCTTTTTCTTCTCGCCTGCATTTTACGCACTCTGCTAGCAGCGACGCCG------ACTGCGCTGCCAACA-------GC------------------------------------AAGCG--------------GT--ACACTTGCAACTA---------TTCTATGCACCCT---ACAATT
droEre2	scaffold_4690:11807313-11807440 +	LASTZ	5	TTTTTTC-T-------CCG----CTCGTTTT---TCTCTCCTTTTCTGCTCGCCTGCATTTTACGCACTCTGCTGGCAGCGACGCCG------ACTGCGCTGCAAACA-------GC------------------------------------GAGCG--------------GT--ACACTTGCAACTA---------TTCTGTGCACCCT---ACAATT
droEug1	scf7180000409533:350907-351023 -	LASTZ	5	TTTTTTC-TCT-----CTG----CTAGTTTTTTTT----------------GCTTGCATTTTACGCACTCTGCTGGCAGCGACGTCG------ACTGCGCTGCCAAGT-------GC------------------------------------AAGCG--------------GT--ACACTTGCAACTA---------TTCGTTGTACTCC----GAATT
droBia1	scf7180000299226:181007-181106 +	LASTZ	5	CTTCCCC-TCCC----CCG----CCCG------------------CCCCGCGGCAGCGTTTTACGCACTCTGCCGGCAGCGACGTCG------ACCGC-----------------------------------------------------------G--------------GT--ACACTTGCCACAA---------TTCCTTGTACCCC---CGAGAG
droTak1	scf7180000415381:822078-822183 -	LASTZ	5	TTTTTTT-------CTCAG----CC---------------------------CCTGCATTTTACGCACTCCGCTGGCAGCGACGTCG------ACTGCGCTGCCGACG-------TC------------------------------------AGGC-----------GGCGGT--ACACTTGCCACTA---------TTCTTTGTACCC------CCGT
droEle1	scf7180000491023:1386855-1386967 +	LASTZ	5	TTTTTTT-TTTT----TTGGGG-----TTTTTTTT----------------GCCTGCATTTTACGCACTCTGCTGGCAGCGACGTCG------ACTGCGACGCCGACT-------GC------------------------------------A-GCC--------------GT--ACACTTGCAACTA---------TTCGTTGTACCC------AATT
droRho1	scf7180000777097:282566-282669 +	LASTZ	5	TTTTTTT-TGCT---------TTTTC--------------------------GCTGCATTTTACGCACTCTGCTGGCAGCGACGTCG------ACTGCGACGGCGACT-------GC------------------------------------AGGCG--------------GT--ACACTTGCAACTA---------TTCTGTGTACCC------AATT
droFic1	scf7180000454038:448768-448871 -	LASTZ	5	TTTTTTG-TTGC----T----TTT----------T----------------GCCTGCATTTTACGCACACTGCTGGCAGCGACGTCG------ACTGCGACGCCGACC-------GC------------------------------------GAGT---------------GT--ACACTTTCAACTA---------TTTCATGTACCCC---ACA---
droKik1	scf7180000302816:65604-65724 -	LASTZ	0	CTTTTGC-TTTG--CTATG----CCTGTGG-CTCTGC-----CCGCAATTTGTCCGTGCCGTACGCAC--TGCGGGCAGAGACGCCG------ACTGCGTAGCA------------------------------------------------------------------------CCACTTGCAACTGGGTTATTTCTT--TTGTATT-G---TCTTTT
droAna3	scaffold_13117:1427273-1427395 -	LASTZ	0	ATTTTTC-TTCC----C-A---TG----------CAACCTGTGTCCAT----TGTACGTTTTACGCACTCTCC--CCAGCAACACCG------CCGCCGATAGCGACT-------GC------------------------------------GACGAGTACGTTGGCAGCGG----CACTTGACTCT--------------TTTT--GCG---GCAATT
droBip1	scf7180000396425:686944-687063 +	LASTZ	0	GCATTCA-ACCT----GTG----TCCA--------------------T----TTTACGTTTTACGCACTCAGCC--CAGCAACAACGCCGTCGAGTGC------GACT-------GC------------------------------------GACGAGTACGCTGGCAGCGG----CACTTGACTCTT-------TTTGC--GGCAATTT---TCGACA
dp4	chrXL_group1e:12152468-12152588 -	LASTZ	0	CTTTAGC-TTTT-----TGCGT-----TTGCGTTTGCCCCGATTTCAATGCA-ATGTGTTGTACGCACACGGGTT---TTTATCTCA------GCTGTGGGATGAACG-------GC--------------------------------------CCG--------------AG--ACACTTGC--CGA---------TGCGGCGACCCC------AGGC
droPer1	super_14:1456573-1456693 +	LASTZ	0	CTTTAGC-TTTT-----TGCGT-----TTGCGTTTGCCCCGATTTCAATGCA-ATGTGTTGTACGCACACGGGTT---TTTATCTCA------GCTGTGGGATGAACG-------GC--------------------------------------CCG--------------AG--ACACTTGC--CGA---------TGCGGCGACCCC------AGGC
droWil1	Unknown		0	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12928:4095173-4095244 -	LASTZ	0	CTCTTTA-TTGC----A----ATG----------C----------------GAC-------TACGCATG-------------------------------------AT-------TT------------------------------------A-GGCGCAGGTTGGT----CG--ACACTTGCATTGG---------TTGCAAGT----------ACTT
droMoj3	scaffold_6680:3750941-3751063 -	LASTZ	0	TTTGTTT-TTGT----TTT----CTTT--T----------------TGTAGCCTAGGAATTTACC---TCTTGTGGCATATCAGCTG---TTGGCTTTGGTTGCAAAC-------AC------------------------------------ACGTT-------GACT---TTTCACACACAGAATTC---------TGT--TGAAATGTTTAACACTT
droGri2	scaffold_14853:566008-566117 +	LASTZ	0	CTCTTTTATTGC----A----ATG----------A----------GACTGCG-ACGCAT----------------------------------------------GAT-------TTGGGCGCAGGTCTATCACCACTTGCACTGACGACTGCTTTTG--------------CT--TTTGCTACTACTT---------TTACTTGCCAGCG---GAACTT

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	CTTTTTT----TTCTCTGCTCG----------------------------TTGTATTTTACGCACTCTGCTGGCAGCGCTGTCGGCGTCGCTGCCAGCTGCCAGCAGCGA---GCGGTACACTTGCAACTATCCTGTGCACCCTACAATT
droSim1	CTTTTTTTTTTTTCTCTGCTCG----------------------------TTGCATTTTACGCACTCTGCTGGCAGCGACGCCGACAGCGCTGCCAGCAG-------CGA---GCGGTACACTTGCAACTATCCTGCGCACCCTACAATT
droSec1	CTTTTTT--TTTTCTCTGCTCG----------------------------TTGCATTTTACGCACTCTGCTGGCAGCGACGCCGACAGCGGTGCCAGCAG-------CGA---GCGGTACACTTGCAACTATCCTGCACACCCTACAATT
droYak2	TTTTTT------TCTCTGCTCGTTTTTCTCTCTTTTTCTTCTC-----GCCTGCATTTTACGCACTCTGCTAGCAGCGACGCCGACTGCGCTGCCAACAG-------CAA---GCGGTACACTTGCAACTATTCTATGCACCCTACAATT
droEre2	TTTTT-------TCTCCGCTCGTTTTTCTCTCCTTTTCTGCTC-----GCCTGCATTTTACGCACTCTGCTGGCAGCGACGCCGACTGCGCTGCAAACAG-------CGA---GCGGTACACTTGCAACTATTCTGTGCACCCTACAATT
droEug1	TTTTTTC-----TCTCTGCTAGTTT------------------TTTTTGCTTGCATTTTACGCACTCTGCTGGCAGCGACGTCGACTGCGCTGCCAAGTG-------CAA---GCGGTACACTTGCAACTATTCGTTGTACTCC-GAATT
droBia1	CTTCCCC----TCCCCCGCCCG--C------------------CCCGCGGCAGCGTTTTACGCACTCTGCCGGCAGCGACGTCGACCGC--------------------------GGTACACTTGCCACAATTCCTTGTACCCCCGAGAG
droTak1	TTTTTT------TCTCAGCC-----------------------------CCTGCATTTTACGCACTCCGCTGGCAGCGACGTCGACTGCGCTGCCGACGT-------CAGGCGGCGGTACACTTGCCACTATTCTTTGTACCCC---CGT
droEle1	TTTTTTT----TTTTTTG-GGGTTT------------------TTTTTGCCTGCATTTTACGCACTCTGCTGGCAGCGACGTCGACTGCGACGCCGACTG-------C-A---GCCGTACACTTGCAACTATTCGTTGTACCC---AATT
droRho1	TTTTTTT----TGC-----------------------------TTTTTCGCTGCATTTTACGCACTCTGCTGGCAGCGACGTCGACTGCGACGGCGACTG-------CAG---GCGGTACACTTGCAACTATTCTGTGTACCC---AATT
droFic1	TTTTTTG----TTG----------C------------------TTTTTGCCTGCATTTTACGCACACTGCTGGCAGCGACGTCGACTGCGACGCCGACCG-------CGA---GT-GTACACTTTCAACTATTTCATGTACCCCACA---

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																	None
UNAFold Image																	None

Small RNA-seq read pileup

Species

Alignment

droSim1

CTTTTTT-TTTTTTCTCTG----CTCG--------------------------TTGCATTTTACGCACTCTGCTGGCAGCGACGCCG------ACAGCGCTGCCAGCA-------GC------------------------------------GAGCG--------------GT--ACACTTGCAACTA---------TCCTGCGCACCCT---ACAATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..........................................................TTTTACGCACTCTGCTGGCAGCG...........................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................CGCTGCCAGCA-------GC------------------------------------GAGCG--------------GT--AC..........................................	22	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................A-------GC------------------------------------GAGCG--------------GT--ACACGGGC....................................	18	1	1.00	0.00	1.00	0.00	0.00
...............TCTG----CGCG--------------------------TTGCATTTTACGCA.........................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
...........................................................................................................................................................................................................................C	18	3	0.33	0.00	0.33	0.00	0.00
............................................................TTACGCACTCTGCTGGCA..............................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................................................TACGCACTCTGCTGGCAGCG...........................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
...........................................................TTTAAGCACTCTGATGGC...............................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.............................................................TACGCACTCTGCTGGCAGCGA..........................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................................................CG--------------GT--ACACTTGCAACTA---------TCCT..................	21	1	1.00	0.00	0.00	1.00	0.00
.TTTTTT-TTTTTTCTGTG----ATC..................................................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
............................................................TTACGCACTCTGCTGGCAGCG...........................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
..........................................................................GGCAGCGACGTCG------ACTGC..........................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.............................................................TACGCACTCTGCTGGCAGCGACG........................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00

droSec1

CTTTTTT-TTTT--CTCTG----CTCG--------------------------TTGCATTTTACGCACTCTGCTGGCAGCGACGCCG------ACAGCGGTGCCAGCA-------GC------------------------------------GAGCG--------------GT--ACACTTGCAACTA---------TCCTGCACACCCT---ACAATT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...................................................................................................GTGCCAGCA-------GC------------------------------------xCGCG--------------GT--A...........................................	18	1	4.00	1.00	2.00	1.00
...........................................................................GCAGCGACGCCG------ACAGCGGTG......................................................................................................................	21	1	2.00	0.00	0.00	2.00
.............................................................TACGCACTCTGCTGGCAGCGAC.........................................................................................................................................	22	1	1.00	0.00	1.00	0.00
..........................................................................GGCAGCGACGCCG------ACAGCGGT.......................................................................................................................	21	1	1.00	0.00	0.00	1.00
......................................................................................................CCAGGA-------GC------------------------------------GAGGG--------------GT--ACA.........................................	18	1	1.00	0.00	1.00	0.00
...........................................................................GCAGCGACGTCG------ACAGCGGTGCCG...................................................................................................................	24	1	1.00	1.00	0.00	0.00
.........................................................................TGGCAGCGACGCCG------ACAGCGT........................................................................................................................	21	1	1.00	1.00	0.00	0.00
.............................................................TACGCACTCTGCTGGCAGAGACGCCG------ACA............................................................................................................................	29	1	1.00	1.00	0.00	0.00
.........................................................................TGGCAGCGACGCCG------ACAGCGG........................................................................................................................	21	1	1.00	0.00	0.00	1.00
.............................................................TACGCACTCTGCTGGCAGCGA..........................................................................................................................................	21	1	1.00	1.00	0.00	0.00
.............................................................................................ACAGCAGTGCGAGCA-------GC------------------------------------G..................................................................	18	3	0.33	0.00	0.00	0.33

droYak2

TTTTTTT-------CTCTG----CTCGTTTT---TCTCTCTTTTTCTTCTCGCCTGCATTTTACGCACTCTGCTAGCAGCGACGCCG------ACTGCGCTGCCAACA-------GC------------------------------------AAGCG--------------GT--ACACTTGCAACTA---------TTCTATGCACCCT---ACAATT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TTTTTTC-T-------CCG----CTCGTTTT---TCTCTCCTTTTCTGCTCGCCTGCATTTTACGCACTCTGCTGGCAGCGACGCCG------ACTGCGCTGCAAACA-------GC------------------------------------GAGCG--------------GT--ACACTTGCAACTA---------TTCTGTGCACCCT---ACAATT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.......................................................................................................AAACA-------GC------------------------------------GAGCG--------------GT--ACACTTG.....................................	21	1	1.00	0.00	1.00	0.00	0.00
........T-------CCG----TTTGTTTT---TCTCTCCTTT................................................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
............................................................................CTGCGACGCCG------GCTGCGCT.......................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................A-------GC------------------------------------GAGCG--------------GT--ACACGGGC....................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

TTTTTTC-TCT-----CTG----CTAGTTTTTTTT----------------GCTTGCATTTTACGCACTCTGCTGGCAGCGACGTCG------ACTGCGCTGCCAAGT-------GC------------------------------------AAGCG--------------GT--ACACTTGCAACTA---------TTCGTTGTACTCC----GAATT

Size

Hit Count

Total Norm

droBia1

CTTCCCC-TCCC----CCG----CCCG------------------CCCCGCGGCAGCGTTTTACGCACTCTGCCGGCAGCGACGTCG------ACCGC-----------------------------------------------------------G--------------GT--ACACTTGCCACAA---------TTCCTTGTACCCC---CGAGAG

Size

Hit Count

Total Norm

droTak1

TTTTTTT-------CTCAG----CC---------------------------CCTGCATTTTACGCACTCCGCTGGCAGCGACGTCG------ACTGCGCTGCCGACG-------TC------------------------------------AGGC-----------GGCGGT--ACACTTGCCACTA---------TTCTTTGTACCC------CCGT

Size

Hit Count

Total Norm

droEle1

TTTTTTT-TTTT----TTGGGG-----TTTTTTTT----------------GCCTGCATTTTACGCACTCTGCTGGCAGCGACGTCG------ACTGCGACGCCGACT-------GC------------------------------------A-GCC--------------GT--ACACTTGCAACTA---------TTCGTTGTACCC------AATT

Size

Hit Count

Total Norm

droRho1

TTTTTTT-TGCT---------TTTTC--------------------------GCTGCATTTTACGCACTCTGCTGGCAGCGACGTCG------ACTGCGACGGCGACT-------GC------------------------------------AGGCG--------------GT--ACACTTGCAACTA---------TTCTGTGTACCC------AATT

Size

Hit Count

Total Norm

droFic1

TTTTTTG-TTGC----T----TTT----------T----------------GCCTGCATTTTACGCACACTGCTGGCAGCGACGTCG------ACTGCGACGCCGACC-------GC------------------------------------GAGT---------------GT--ACACTTTCAACTA---------TTTCATGTACCCC---ACA---

Size

Hit Count

Total Norm

droKik1

CTTTTGC-TTTG--CTATG----CCTGTGG-CTCTGC-----CCGCAATTTGTCCGTGCCGTACGCAC--TGCGGGCAGAGACGCCG------ACTGCGTAGCA------------------------------------------------------------------------CCACTTGCAACTGGGTTATTTCTT--TTGTATT-G---TCTTTT

Size

Hit Count

Total Norm

droAna3

ATTTTTC-TTCC----C-A---TG----------CAACCTGTGTCCAT----TGTACGTTTTACGCACTCTCC--CCAGCAACACCG------CCGCCGATAGCGACT-------GC------------------------------------GACGAGTACGTTGGCAGCGG----CACTTGACTCT--------------TTTT--GCG---GCAATT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
......................................................................................................GCGGCG-------GC------------------------------------GACGAGTACG.........................................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................................GACT-------GC------------------------------------GACGCGTAGGTT.......................................................	18	1	1.00	0.00	0.00	1.00	0.00

droBip1

GCATTCA-ACCT----GTG----TCCA--------------------T----TTTACGTTTTACGCACTCAGCC--CAGCAACAACGCCGTCGAGTGC------GACT-------GC------------------------------------GACGAGTACGCTGGCAGCGG----CACTTGACTCTT-------TTTGC--GGCAATTT---TCGACA

Size

Hit Count

Total Norm

dp4

CTTTAGC-TTTT-----TGCGT-----TTGCGTTTGCCCCGATTTCAATGCA-ATGTGTTGTACGCACACGGGTT---TTTATCTCA------GCTGTGGGATGAACG-------GC--------------------------------------CCG--------------AG--ACACTTGC--CGA---------TGCGGCGACCCC------AGGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...............................................................................TTATCTCA------GCTGTGGGATGA...................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
......................................CCGATTTCAATGCA-ATGTGTT................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
............................TGCGTTTGCCCCGATTTCAAT...........................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00
......C-TTTT-----TGCGT-----TTGCGTTTGCC......................................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
......................................................................................A------GCTGTGGGATGAACC-------GA--------------------------------------.................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................TGTCx------GCTGTGGGATGAAC.................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droPer1

CTTTAGC-TTTT-----TGCGT-----TTGCGTTTGCCCCGATTTCAATGCA-ATGTGTTGTACGCACACGGGTT---TTTATCTCA------GCTGTGGGATGAACG-------GC--------------------------------------CCG--------------AG--ACACTTGC--CGA---------TGCGGCGACCCC------AGGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................................................................................TGTCx------GCTGTGGGATGAAC.................................................................................................................	18	1	3.00	2.00	0.00	0.00	0.00	1.00
....................................................................................TCA------GCTGTGGGATGAACG-------G........................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................TCTCx------GCTGTGGGATGAACC-------.........................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................A------GCTGTGGGATGAACG-------GC--------------------------------------C................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CTCTTTA-TTGC----A----ATG----------C----------------GAC-------TACGCATG-------------------------------------AT-------TT------------------------------------A-GGCGCAGGTTGGT----CG--ACACTTGCATTGG---------TTGCAAGT----------ACTT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...........................................................................................................T-------TT------------------------------------A-GGCGCAGGTTGGT----CG--AC..........................................	21	1	2.00	0.00	0.00	0.00	2.00	0.00
....................................................................................................................T------------------------------------G-GGCGCAGGTTGGT----CG--ACACT.......................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00

droMoj3

TTTGTTT-TTGT----TTT----CTTT--T----------------TGTAGCCTAGGAATTTACC---TCTTGTGGCATATCAGCTG---TTGGCTTTGGTTGCAAAC-------AC------------------------------------ACGTT-------GACT---TTTCACACACAGAATTC---------TGT--TGAAATGTTTAACACTT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CTCTTTTATTGC----A----ATG----------A----------GACTGCG-ACGCAT----------------------------------------------GAT-------TTGGGCGCAGGTCTATCACCACTTGCACTGACGACTGCTTTTG--------------CT--TTTGCTACTACTT---------TTACTTGCCAGCG---GAACTT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:17:17 EDT

dme-mir-4957

chrX:15213986-15214070 -

Known_mirbase

intergenic

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

Visually pleasing best hits from LASTZ and MAF

Legend

Re-alignment after removal of non-confident orthologs

20-way Secondary Structure

Small RNA-seq read pileup