dme-mir-4948- Best orthologs

dme-mir-4948	chr3R:26876819-26876925 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 26876845-26876866
   star strand at position 26876884-26876902
   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	chr3R:26876804-26876940 -		1	GCACTCCCAGTCCCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGCGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT----------------
droSim1	chr3R:26523820-26523956 -	LASTZ	4	GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGTT----------------
droSec1	super_4:5701489-5701625 -	LASTZ	4	GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGTGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT----------------
droYak2	chr3R:27815996-27816132 -	LASTZ	5	GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTGGTGGTGACCACTCCAGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTACCTTGCT----------------
droEre2	scaffold_4820:1105506-1105642 +	LASTZ	5	GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTTGTGGTGACCACTCCAGTACGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTGCCCTGCT----------------
droEug1	scf7180000409166:158947-159083 +	LASTZ	5	GCACTCCCAATCTCTGTCGTAGATGTGGGCGTAGGTGGCGGCAGGCGTTGCATGGGTGATCCTGGTGGTGGTGACAATACCAGTGCGCTTGCCCTCCTTTTGGGCCCACTCCATCACGCTTTGAACCCTGCCCTGTT----------------
droBia1	scf7180000302113:442836-442972 +	LASTZ	5	GCACTCCCAATCCCTGTCGTAAATATGGGCGTAGGTGGCCGCAGGCGTGGCGTGGGTGATCCTGGTGGTGGTGACGATTCCCGTGCGCTTGCCCGCCTTCTGGGCCCACTCCATTACGTTCTGGATCCTGCCTTGCT----------------
droTak1	scf7180000415236:217947-218083 -	LASTZ	5	GCACTCCCAATCGCGGTCGTAGATGTGGGCGTAGGTGGCAGCGGGCGTGGCATGAGTGATCCTGGTGGTGGTGACAATTCCAGTGCGCTTGCCCTCCTTTTGTGCCCATTCCATGACGCTTTGGACCCTGCCCTGCT----------------
droEle1	scf7180000491212:972484-972620 -	LASTZ	5	GCATTCCCAATTCCTGTCGTAAATATGGGCGTAAGTGGCGGCGGGCGTGGCATGGGTGATCCTAGTGGTGGTGACTATTCCCGTGCGTTTGCCCAGCTTTTGGGCCCACTCCATGACGCTTTGAACGCGACCTTGCT----------------
droRho1	scf7180000761687:129-265 +	LASTZ	5	GCACTCCCAATCTCTGTCGTAAATGTGGGCGTAGGTGGCGGAGGGCGTGGCATGTGTGATCCTGGTGGTGGTGACTATTCCCGTGCGCTTGCCCTCTTTTTGGGCCCACTCCATGACGCTTTGAACCTGACCTTGCT----------------
droFic1	scf7180000453782:423025-423161 +	LASTZ	5	GCACTCCCAATCCCTGTCGTAGATGTGGGCGTAAGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTGGTGGTGACAATTCCGGTGCGCTTGCCCGCCTTCTGAGCCCACTCCATGATGCTTTCGACGCGACCTTGCT----------------
droKik1	scf7180000302238:91277-91413 -	LASTZ	5	GCACTCCCAGTCCCGGTTGTATATATGGGCATATGTGGCAGCGGGTGTGGCATGCGTGATCCTGGTCGTGGTGACTACTCCAGTGCGTTTTCCCTCCTTTTGGGCCCAATCCATAATGCTCTGGACGCGACCCGATT----------------
droAna3	scaffold_12911:4046748-4046884 +	LASTZ	5	GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCGTGGGTAATCCGAGTGGTGGTCACTATTCCAGTTCGCTTCTTCTCCTTTTGGGCCCACTCCATGACGCTCTGAACGCGTCCTTGCT----------------
droBip1	scf7180000396640:894541-894677 +	LASTZ	5	GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCATGGGTAATCCGAGTGGTGGTAACTATTCCAGTTCGCTTTTTCTCCTTTTGGGCCCACTCCATGACGCTCGCGACACGTCCTTGCT----------------
dp4	chr2:271882-272018 +	LASTZ	5	GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT----------------
droPer1	super_7:3056347-3056483 +	LASTZ	5	GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT----------------
droWil1	scaffold_181108:531799-531935 -	LASTZ	5	GCATTCCCAGTCCCGATCATATATATGCGCATAGGTTGAGGCAGGCGTGGCATGTGTAATTCTGGTAGTGGTAACAATTCCCGTTCGTTTACCCGCACGCTGGGCCCAATCCATAATGGATTCCACCCGACCCTGTT----------------
droVir3	scaffold_12855:1470098-1470234 +	LASTZ	5	GCACTCCCAGTCCCGATGATAGACACGCGCAAAGGTGGCTGCGGGCGTGGCGTGCGTAATGCGTGTGGTGGTCACCACGCCAGTGCGTTTGCCTTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC----------------
droMoj3	scaffold_6540:27213622-27213758 +	LASTZ	5	GCACTCCCAGTCCCGATGATAGATCCTTGCATAGGTGGCCGCAGGTGTGGCGTGTGTTATACGCGTGGTAGTCACGACGCCGGTCCGCTTGCCCTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC----------------
droGri2	scaffold_15203:6653367-6653519 -	LASTZ	5	GCACTCCCACCGCCGATCGGCGACATGGGCGTAGAGGGCAGCGGGTGTGGCATGGGTTACCCGCGTTGTGGTCACAAATCCAGTGCGCATGCCATCCACCTGCGCCCAGTTGAATATGTTCTGGACGTGATGTTCCTCCTTGAGAGAGGCACT

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	GCACTCCCAGTCCCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGCGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT----------------
droSim1	GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGTT----------------
droSec1	GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGTGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT----------------
droYak2	GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTGGTGGTGACCACTCCAGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTACCTTGCT----------------
droEre2	GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTTGTGGTGACCACTCCAGTACGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTGCCCTGCT----------------
droEug1	GCACTCCCAATCTCTGTCGTAGATGTGGGCGTAGGTGGCGGCAGGCGTTGCATGGGTGATCCTGGTGGTGGTGACAATACCAGTGCGCTTGCCCTCCTTTTGGGCCCACTCCATCACGCTTTGAACCCTGCCCTGTT----------------
droBia1	GCACTCCCAATCCCTGTCGTAAATATGGGCGTAGGTGGCCGCAGGCGTGGCGTGGGTGATCCTGGTGGTGGTGACGATTCCCGTGCGCTTGCCCGCCTTCTGGGCCCACTCCATTACGTTCTGGATCCTGCCTTGCT----------------
droTak1	GCACTCCCAATCGCGGTCGTAGATGTGGGCGTAGGTGGCAGCGGGCGTGGCATGAGTGATCCTGGTGGTGGTGACAATTCCAGTGCGCTTGCCCTCCTTTTGTGCCCATTCCATGACGCTTTGGACCCTGCCCTGCT----------------
droEle1	GCATTCCCAATTCCTGTCGTAAATATGGGCGTAAGTGGCGGCGGGCGTGGCATGGGTGATCCTAGTGGTGGTGACTATTCCCGTGCGTTTGCCCAGCTTTTGGGCCCACTCCATGACGCTTTGAACGCGACCTTGCT----------------
droRho1	GCACTCCCAATCTCTGTCGTAAATGTGGGCGTAGGTGGCGGAGGGCGTGGCATGTGTGATCCTGGTGGTGGTGACTATTCCCGTGCGCTTGCCCTCTTTTTGGGCCCACTCCATGACGCTTTGAACCTGACCTTGCT----------------
droFic1	GCACTCCCAATCCCTGTCGTAGATGTGGGCGTAAGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTGGTGGTGACAATTCCGGTGCGCTTGCCCGCCTTCTGAGCCCACTCCATGATGCTTTCGACGCGACCTTGCT----------------
droKik1	GCACTCCCAGTCCCGGTTGTATATATGGGCATATGTGGCAGCGGGTGTGGCATGCGTGATCCTGGTCGTGGTGACTACTCCAGTGCGTTTTCCCTCCTTTTGGGCCCAATCCATAATGCTCTGGACGCGACCCGATT----------------
droAna3	GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCGTGGGTAATCCGAGTGGTGGTCACTATTCCAGTTCGCTTCTTCTCCTTTTGGGCCCACTCCATGACGCTCTGAACGCGTCCTTGCT----------------
droBip1	GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCATGGGTAATCCGAGTGGTGGTAACTATTCCAGTTCGCTTTTTCTCCTTTTGGGCCCACTCCATGACGCTCGCGACACGTCCTTGCT----------------
dp4	GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT----------------
droPer1	GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT----------------
droWil1	GCATTCCCAGTCCCGATCATATATATGCGCATAGGTTGAGGCAGGCGTGGCATGTGTAATTCTGGTAGTGGTAACAATTCCCGTTCGTTTACCCGCACGCTGGGCCCAATCCATAATGGATTCCACCCGACCCTGTT----------------
droVir3	GCACTCCCAGTCCCGATGATAGACACGCGCAAAGGTGGCTGCGGGCGTGGCGTGCGTAATGCGTGTGGTGGTCACCACGCCAGTGCGTTTGCCTTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC----------------
droMoj3	GCACTCCCAGTCCCGATGATAGATCCTTGCATAGGTGGCCGCAGGTGTGGCGTGTGTTATACGCGTGGTAGTCACGACGCCGGTCCGCTTGCCCTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC----------------
droGri2	GCACTCCCACCGCCGATCGGCGACATGGGCGTAGAGGGCAGCGGGTGTGGCATGGGTTACCCGCGTTGTGGTCACAAATCCAGTGCGCATGCCATCCACCTGCGCCCAGTTGAATATGTTCTGGACGTGATGTTCCTCCTTGAGAGAGGCACT

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

GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTTGTGGTGACCACGCCCGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGTT----------------	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................CGTCGCGTGGGTGGTCCTG.........................................................................................	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

GCACTCCCAGTCGCGGTCGTAGATGTGGGCGTAGGTGGCGGCGGGCGTGGCGTGTGTGATCCTGGTTGTGGTGACCACGCCGGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTCTGGACCCTGCCTTGCT----------------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......TTGTCGCGGTCGTAGATG................................................................................................................................	18	1	1.00	1.00	0.00	0.00
...............................TAGGCGGCGGGGGGCGTGGCG.....................................................................................................	21	1	1.00	0.00	1.00	0.00
..........................................................................CCACGCCGGTGCGCTTGCCCTC.........................................................	22	1	1.00	0.00	1.00	0.00
.................................................................TTCTAGTGACCACGCCGG......................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTGGTGGTGACCACTCCAGTGCGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTACCTTGCT----------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................ATGGGGGCGTCCGTGGC..................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................GTGGCGGCAGGTGGGGC......................................................................................................	17	2	0.50	0.00	0.00	0.00	0.50	0.00
..............................................GTGGCATGGGCGTTCCTGGT.......................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................GCATGGATxATCCTGGTGGT....................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GCACTCCCAATCCCGGTCGTAGATGTGGGCGTACGTGGCGGCAGGCGTGGCATGGGTGATCCTGGTTGTGGTGACCACTCCAGTACGCTTGCCCTCCTTCTGGGCCCACTCCATGACGCTTTGGACCCTGCCCTGCT----------------	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................GCAGGCGTGGCATGGGCT...............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droEug1

GCACTCCCAATCTCTGTCGTAGATGTGGGCGTAGGTGGCGGCAGGCGTTGCATGGGTGATCCTGGTGGTGGTGACAATACCAGTGCGCTTGCCCTCCTTTTGGGCCCACTCCATCACGCTTTGAACCCTGCCCTGTT----------------

Size

Hit Count

Total Norm

droBia1

GCACTCCCAATCCCTGTCGTAAATATGGGCGTAGGTGGCCGCAGGCGTGGCGTGGGTGATCCTGGTGGTGGTGACGATTCCCGTGCGCTTGCCCGCCTTCTGGGCCCACTCCATTACGTTCTGGATCCTGCCTTGCT----------------

Size

Hit Count

Total Norm

droTak1

GCACTCCCAATCGCGGTCGTAGATGTGGGCGTAGGTGGCAGCGGGCGTGGCATGAGTGATCCTGGTGGTGGTGACAATTCCAGTGCGCTTGCCCTCCTTTTGTGCCCATTCCATGACGCTTTGGACCCTGCCCTGCT----------------

Size

Hit Count

Total Norm

droEle1

GCATTCCCAATTCCTGTCGTAAATATGGGCGTAAGTGGCGGCGGGCGTGGCATGGGTGATCCTAGTGGTGGTGACTATTCCCGTGCGTTTGCCCAGCTTTTGGGCCCACTCCATGACGCTTTGAACGCGACCTTGCT----------------

Size

Hit Count

Total Norm

droRho1

GCACTCCCAATCTCTGTCGTAAATGTGGGCGTAGGTGGCGGAGGGCGTGGCATGTGTGATCCTGGTGGTGGTGACTATTCCCGTGCGCTTGCCCTCTTTTTGGGCCCACTCCATGACGCTTTGAACCTGACCTTGCT----------------

Size

Hit Count

Total Norm

droFic1

GCACTCCCAATCCCTGTCGTAGATGTGGGCGTAAGTGGCGGCGGGCGTGGCGTGGGTGATCCTGGTGGTGGTGACAATTCCGGTGCGCTTGCCCGCCTTCTGAGCCCACTCCATGATGCTTTCGACGCGACCTTGCT----------------

Size

Hit Count

Total Norm

droKik1

GCACTCCCAGTCCCGGTTGTATATATGGGCATATGTGGCAGCGGGTGTGGCATGCGTGATCCTGGTCGTGGTGACTACTCCAGTGCGTTTTCCCTCCTTTTGGGCCCAATCCATAATGCTCTGGACGCGACCCGATT----------------

Size

Hit Count

Total Norm

droAna3

GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCGTGGGTAATCCGAGTGGTGGTCACTATTCCAGTTCGCTTCTTCTCCTTTTGGGCCCACTCCATGACGCTCTGAACGCGTCCTTGCT----------------	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
................................................GGCGTGGGGAATCCGACTGG.....................................................................................	20	1	1.00	0.00	0.00	1.00	0.00
.............................................................................................................TCCATGAGGCTCTTAACG..........................	18	1	1.00	0.00	0.00	1.00	0.00
.......................TGTGGTCGTAGGTTGGA.................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
............................................................................ATTCCAGTTCGCTTGTGCT..........................................................	19	1	1.00	0.00	0.00	0.00	1.00

droBip1

GCACTCCCAATCCCGATCGTAGATGTGGGCGTAGGTTGCAGCTGGCGTGGCATGGGTAATCCGAGTGGTGGTAACTATTCCAGTTCGCTTTTTCTCCTTTTGGGCCCACTCCATGACGCTCGCGACACGTCCTTGCT----------------

Size

Hit Count

Total Norm

dp4

GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT----------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...................TAAATGTGGGCGTGGGTGGCC.................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00

droPer1

GCACTCCCAGTCGCGATCGTAGATGTGGGCGTAGGTGGCCGCAGGCGTGGCATGCGTAATCCTCGTTGTGGTCACGATTCCCGTGCGCTTGCCTTCCTTCTGGGCCCACTCCATGATAGTCTCAATCCGGCCCAGCT----------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.......................TGTGGGCGAAGGTGGACGC...............................................................................................................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
..................GTAGATGTCGGCGTAGGC.....................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...................TGGCTGTGGGCGTAGGTGG...................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00
.......................TGTGGGCGAAGGTGGACG................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

GCATTCCCAGTCCCGATCATATATATGCGCATAGGTTGAGGCAGGCGTGGCATGTGTAATTCTGGTAGTGGTAACAATTCCCGTTCGTTTACCCGCACGCTGGGCCCAATCCATAATGGATTCCACCCGACCCTGTT----------------	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................AAGTTGAGGCAGACGTGG.......................................................................................................	18	1	16.00	11.00	0.00	5.00	0.00
....................................................TGTGTAATTATGGTAGTGGTAAT..............................................................................	23	1	1.00	0.00	1.00	0.00	0.00

droVir3

GCACTCCCAGTCCCGATGATAGACACGCGCAAAGGTGGCTGCGGGCGTGGCGTGCGTAATGCGTGTGGTGGTCACCACGCCAGTGCGTTTGCCTTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC----------------	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................................CGTAATGCGTGTxGTGGCCA...............................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
......................................................................................GTTTGCCGTxACGCTGTGCC...............................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

GCACTCCCAGTCCCGATGATAGATCCTTGCATAGGTGGCCGCAGGTGTGGCGTGTGTTATACGCGTGGTAGTCACGACGCCGGTCCGCTTGCCCTCACGCTGTGCCCAGTCCATGATGGAGTCGAGTCGACCCTGGC----------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GCACTCCCACCGCCGATCGGCGACATGGGCGTAGAGGGCAGCGGGTGTGGCATGGGTTACCCGCGTTGTGGTCACAAATCCAGTGCGCATGCCATCCACCTGCGCCCAGTTGAATATGTTCTGGACGTGATGTTCCTCCTTGAGAGAGGCACT

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:38:39 EDT

dme-mir-4948

chr3R:26876819-26876925 -

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