dme-mir-4963- Best orthologs

dme-mir-4963	chrX:5684785-5684894 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	three_prime_UTR

Legend:

   mature strand at position 5684851-5684872
   star strand at position 5684813-5684833
   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:5684770-5684909 +		1	CACCCACTGCGAATTGCTGTAGGAAAT--------------------------TTTTTGGGGTACTTCTGG-TTTCATAACGCAGAGAATCAT----CAGCGTGAAG--GAATGATTC--TCTGCGGGCTGGAACCAGAAGTCCTGCAAATGTTCTTTTACGGAT------------------------------------------TTTAA---CCAG---------------G
droSim1	chrX:4425250-4425396 +	LASTZ	3	CACCCACTGCGAATTGCTATAGGAAATG--------------ATG----GAG-TTTTTGGGGTACTTCTGG-TTTCATACTGCAGAGAATCTT----CAGCGTGCAG--TAATGATAT--CCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGAT------------------------------------------TTTAA---CCAG---------------G
droSec1	super_4:1079282-1079434 -	LASTZ	3	CACCCACTGCGAATTGCTATAGGAAATG--------------ATG----GAG-TTTTTGGGGTACTTCTGG-TTTCATAACTCAGAGAATCTTCATGATTTCTTAATCATAATGATTT--CCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGAT------------------------------------------TTTAA---CCAG---------------G
droYak2	chrX:2788911-2789034 -	LASTZ	3	CACCCACTGCGAAATGCTATAGGACATG--------------ATG----GAGCTTCTGGAGGTACTTCTGG-TTTTATAATGCAGAGAATCGT----AATCGTGAAG--GAATGATTC--TATGCGTACTGAAATCGGGAGTCCTGCAGAT------------------------------------------------------------------------------------
droEre2	scaffold_4690:3033374-3033523 +	LASTZ	4	CACCCACTGCGAAATGCTATAGGAAACG--------------ATG----GGG-TTTCTGGGGTACTTCTGG-TTTTATAACGCACGGAATCTG----AATCGTGAAT--GAATGATTC--CTTGCGGACTGGAACCAGAAGTCCTGCAGAGGCTTCTTGAATGAT------------------------------------------TTGAAGTTTCGG---------------A
droEug1	scf7180000409061:10542-10726 -	LASTZ	4	AACCCACTGTGATATGCTATAGGAAAGC--------------ATG----GAG-TTTTTAAAGTACTTCTGA-TTTTACTCAGTAGAGAATCTC----ATCTGTTAAT--GGTTGATTC--TCTGCTGGGTAAAACCAGAAGTCCTTCATATGCTCCTTGAATGATTGTGGCATGTGGTGGCCAAAGAATCAATATGGAATCAGAGG----AA---TTCG---------------T
droBia1	scf7180000298389:804043-804185 +	LASTZ	4	CACCCACTGCGATATGGTGTAGGATAAG-----------C--ATA----GGG-TTTTTGGGGAACTTCTTG-TTTAACCCACTAGAGAACTTT----ATCTTATAAT--AGATGATAA--TCTGTGGGGTAAAACCAGAAGTTCTCCAAAGGTTCTTTTAATGAT------------------------------------------AT--------AG---------------G
droTak1	scf7180000415769:818285-818415 -	LASTZ	4	CACCCACTGCGATTTGCTATAGGAAAGG-----------GATACA----GGT-TTTTTGGGGTACTTTTGG-TCTTAACCTGCAGAGTAT-TC----ATCTGATTTT--GGATGATTC--TCTGCGGGTTGAAACCAGAAGTTCCGCCAAAGCTCCT------------------------------------------------------------------------------
droEle1	scf7180000491356:73896-74031 -	LASTZ	5	AGT---------------------------------------------------TTTTGGTGTACTTTTGGGTCCCATCCAGCAGAGAAATTT----ATCTGATATT--GGAAGTGAT--TTAGCTGTATGAAATCAGAAGTTCCTCAGCTGCTCCTTGATTGTT------------------AAGTATTGATTTAAGACTAAAAA----GC---TCGG---------------A
droRho1	scf7180000779467:553932-554101 +	LASTZ	4	AACCCACTGCGATATGCTTTAGGAGATC--------------AAG----GGG-TTTTTGGGGTGCTTCTGG-ACTTATCCAGCTGAGATTTTC----ATCTGATATT--GGATGTTTT--TCTGCTGACTAAAATCAGAAGCCCTTCAAATGCTCCTTGAAGGTA------------------AAGTATTGATAAA-AACCTGAGATTTTGC---TTCC---------------G
droFic1	scf7180000453927:1329186-1329343 +	LASTZ	5	CACCCACTGCGACGTGGTCTACTAGTCCGTTGGCCTGTGCAGGCG----GGC-TCTGTGGAGCACTTCTGG-TGCTGCCACGCGGAGGACCCG----AGTCCTT------------AT--TCCGCGGGGTGGGACCACAAGTGCCACAAGTGCTGCTGTC--------------------------------------------------GC---CTTCGAATGGATTCTCCAAA
droKik1	scf7180000302481:398483-398533 -	LASTZ	0	CACCGAATGCGGGCTGCTCTAGGCGGTT--------------AGTCAGTGGG-TT-----------TTAAA-TTTT----------------------------------------------------------------------------------------------------------------------------------------------G---------------T
droAna3	scaffold_13117:1117754-1117783 +	LASTZ	0	CACCCACTGCGACGTACTTTAGAGAGTT--------------GT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396425:998854-998938 -	LASTZ	0	CACCCACTGCGACGTGCTCTAGGTGGTTGCAAGCCTG-----GTC----ACAC------------------------TATTGTAGGTAGATTT----AAGTG-------TCACGATTTCATCTGCGAGC----------------------------------------------------------------------------------------------------------
dp4	chr3:13862643-13862665 +	LASTZ	0	CACCAGCTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	super_4:1457976-1457998 -	LASTZ	0	CACCAACTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:7345062-7345085 -	LASTZ	0	AACCCACTGTGATGTCCTGTAAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_13324:2924689-2924720 +	LASTZ	0	CACGGCCTGTGGTGTGCTATAAATTT------------------------------------------------------------------T----ATGT-------------------------------------------------------------------------------------------------------------------------------------G
droMoj3	scaffold_6496:13805954-13805976 -	LASTZ	0	CACCGACTGCGGCGTCCTCTGAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15112:3786307-3786359 +	LASTZ	0	CACCAGCTGCGGCGTGCTATAAATTC---------------------------TTTTCGTTGTATTTCTGG-GTGTTCAAC----------------------------------------------------------------------------------------------------------------------------------------------------------

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	CACCCACTGCGAATTGCTGTAGGAAAT---------------------TTTTTGG-GGTACTTCTG-GTTTCATAACGCAGAGAATCAT----CAGCGTGAAG--GAATGATTCTCTGCGGGCTGGAACCAGAAGTCCTGCAAATGTTCTTTTACGGAT------------------------------------------TTTAACC---------------AGG
droSim1	CACCCACTGCGAATTGCTATAGGAAATG--------------ATGGAGTTTTTGG-GGTACTTCTG-GTTTCATACTGCAGAGAATCTT----CAGCGTGCAG--TAATGATATCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGAT------------------------------------------TTTAACC---------------AGG
droSec1	CACCCACTGCGAATTGCTATAGGAAATG--------------ATGGAGTTTTTGG-GGTACTTCTG-GTTTCATAACTCAGAGAATCTTCATGATTTCTTAATCATAATGATTTCCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGAT------------------------------------------TTTAACC---------------AGG
droYak2	CACCCACTGCGAAATGCTATAGGACATG--------------ATGGAGCTTCTGGAGGTACTTCTG-GTTTTATAATGCAGAGAATCGT----AATCGTGAAG--GAATGATTCTATGCGTACTGAAATCGGGAGTCCTGCAGAT---------------------------------------------------------------------------------
droEre2	CACCCACTGCGAAATGCTATAGGAAACG--------------ATGGGGTTTCTGG-GGTACTTCTG-GTTTTATAACGCACGGAATCTG----AATCGTGAAT--GAATGATTCCTTGCGGACTGGAACCAGAAGTCCTGCAGAGGCTTCTTGAATGAT------------------------------------------TTGAAG------------TTTCGGA
droEug1	AACCCACTGTGATATGCTATAGGAAAGC--------------ATGGAGTTTTTAA-AGTACTTCTG-ATTTTACTCAGTAGAGAATCTC----ATCTGTTAAT--GGTTGATTCTCTGCTGGGTAAAACCAGAAGTCCTTCATATGCTCCTTGAATGATTGTGGCATGTGGTGGCCAAAGAATCAATATGGAATCAGAGG----AATT---------------CGT
droBia1	CACCCACTGCGATATGGTGTAGGATAAG-----------C--ATAGGGTTTTTGG-GGAACTTCTT-GTTTAACCCACTAGAGAACTTT----ATCTTATAAT--AGATGATAATCTGTGGGGTAAAACCAGAAGTTCTCCAAAGGTTCTTTTAATGAT------------------------------------------AT--------------------AGG
droTak1	CACCCACTGCGATTTGCTATAGGAAAGG-----------GATACAGGTTTTTTGG-GGTACTTTTG-GTCTTAACCTGCAGAGTAT-TC----ATCTGATTTT--GGATGATTCTCTGCGGGTTGAAACCAGAAGTTCCGCCAAAGCTCCT---------------------------------------------------------------------------
droEle1	A----------------------------------------------GTTTTTGG-TGTACTTTTGGGTCCCATCCAGCAGAGAAATTT----ATCTGATATT--GGAAGTGATTTAGCTGTATGAAATCAGAAGTTCCTCAGCTGCTCCTTGATTGTT------------------AAGTATTGATTTAAGACTAAAAA----GCTC---------------GGA
droRho1	AACCCACTGCGATATGCTTTAGGAGATC--------------AAGGGGTTTTTGG-GGTGCTTCTG-GACTTATCCAGCTGAGATTTTC----ATCTGATATT--GGATGTTTTTCTGCTGACTAAAATCAGAAGCCCTTCAAATGCTCCTTGAAGGTA------------------AAGTATTGATAAAA-ACCTGAGATTTTGCTT---------------CCG
droFic1	CACCCACTGCGACGTGGTCTACTAGTCCGTTGGCCTGTGCAGGCGGGCTCTGTGG-AGCACTTCTG-GTGCTGCCACGCGGAGGACCCG----AGTCCTT------------ATTCCGCGGGGTGGGACCACAAGTGCCACAAGTGCTGCTGTC--------------------------------------------------GCCTTCGAATGGATTCTCCAAA

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																	None

Small RNA-seq read pileup

Species

Alignment

droSim1

CACCCACTGCGAATTGCTATAGGAAATG--------------ATG----GAG-TTTTTGGGGTACTTCTGG-TTTCATACTGCAGAGAATCTT----CAGCGTGCAG--TAATGATAT--CCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGAT------------------------------------------TTTAA---CCAG---------------G	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................................................................GATGATATTTTACGGAT------------------------------------------T...........................	18	1	3.00	0.00	0.00	3.00	0.00
.................................................................................................................GATAT--CCTGCGGCCTGCC......................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................GATAT--CCTGCGGCCTGCT......................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................TGCGGGCTGCAACCAGAAGTC............................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................TGCGGGCTGCAACCAGAAGTCC...........................................................................................	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

CACCCACTGCGAATTGCTATAGGAAATG--------------ATG----GAG-TTTTTGGGGTACTTCTGG-TTTCATAACTCAGAGAATCTTCATGATTTCTTAATCATAATGATTT--CCTGCGGGCTGCAACCAGAAGTCCTGCAGATGCTCTTTTACGGAT------------------------------------------TTTAA---CCAG---------------G	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.....................................................TGTTTGGGCTACTTCTGG-T..................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00
.......................AAATG--------------ATG----GxG-TTGTTGGG..............................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00
.......................AAATG--------------ATG----GGG-TTTCTGG...............................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

CACCCACTGCGAAATGCTATAGGACATG--------------ATG----GAGCTTCTGGAGGTACTTCTGG-TTTTATAATGCAGAGAATCGT----AATCGTGAAG--GAATGATTC--TATGCGTACTGAAATCGGGAGTCCTGCAGAT------------------------------------------------------------------------------------	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................CATG--------------GTG----GAGCTTCTGTAG..............................................................................................................................................................................	19	1	178.00	6.00	0.00	170.00	2.00	0.00
........................CATG--------------GTG----GAGCTTCTGTA...............................................................................................................................................................................	18	1	14.00	1.00	1.00	4.00	4.00	4.00
.........................ATG--------------GTG----GAGCTTCTGTAG..............................................................................................................................................................................	18	1	6.00	0.00	0.00	6.00	0.00	0.00
.............................................................................................................................GTACTGAAATCGGGAGTCCTGCA.......................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................................................................ATTC--TATGCGTACTGAAATCG..................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00
..................................................................................................................ATTC--TATGCGTACTGAAATCGG.................................................................................................	22	1	1.00	0.00	0.00	0.00	0.00	1.00
........................CATG--------------GTG----GAGCTTCTGAAG..............................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
........................CATG--------------TTG----GAGCTTCTGTAG..............................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
........................CATG--------------GTG----GAGCTTCTGTAGG.............................................................................................................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
........................CATG--------------GTG----GAGCTTCTGT................................................................................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CACCCACTGCGAAATGCTATAGGAAACG--------------ATG----GGG-TTTCTGGGGTACTTCTGG-TTTTATAACGCACGGAATCTG----AATCGTGAAT--GAATGATTC--CTTGCGGACTGGAACCAGAAGTCCTGCAGAGGCTTCTTGAATGAT------------------------------------------TTGAAGTTTCGG---------------A	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............................................................................................................................................................AATGGT------------------------------------------TTGCAGTTTCGG---------------.	18	1	1.00	1.00	0.00	0.00	0.00

droEug1

AACCCACTGTGATATGCTATAGGAAAGC--------------ATG----GAG-TTTTTAAAGTACTTCTGA-TTTTACTCAGTAGAGAATCTC----ATCTGTTAAT--GGTTGATTC--TCTGCTGGGTAAAACCAGAAGTCCTTCATATGCTCCTTGAATGATTGTGGCATGTGGTGGCCAAAGAATCAATATGGAATCAGAGG----AA---TTCG---------------T

Size

Hit Count

Total Norm

droBia1

CACCCACTGCGATATGGTGTAGGATAAG-----------C--ATA----GGG-TTTTTGGGGAACTTCTTG-TTTAACCCACTAGAGAACTTT----ATCTTATAAT--AGATGATAA--TCTGTGGGGTAAAACCAGAAGTTCTCCAAAGGTTCTTTTAATGAT------------------------------------------AT--------AG---------------G

Size

Hit Count

Total Norm

droTak1

CACCCACTGCGATTTGCTATAGGAAAGG-----------GATACA----GGT-TTTTTGGGGTACTTTTGG-TCTTAACCTGCAGAGTAT-TC----ATCTGATTTT--GGATGATTC--TCTGCGGGTTGAAACCAGAAGTTCCGCCAAAGCTCCT------------------------------------------------------------------------------

Size

Hit Count

Total Norm

droEle1

AGT---------------------------------------------------TTTTGGTGTACTTTTGGGTCCCATCCAGCAGAGAAATTT----ATCTGATATT--GGAAGTGAT--TTAGCTGTATGAAATCAGAAGTTCCTCAGCTGCTCCTTGATTGTT------------------AAGTATTGATTTAAGACTAAAAA----GC---TCGG---------------A

Size

Hit Count

Total Norm

droRho1

AACCCACTGCGATATGCTTTAGGAGATC--------------AAG----GGG-TTTTTGGGGTGCTTCTGG-ACTTATCCAGCTGAGATTTTC----ATCTGATATT--GGATGTTTT--TCTGCTGACTAAAATCAGAAGCCCTTCAAATGCTCCTTGAAGGTA------------------AAGTATTGATAAA-AACCTGAGATTTTGC---TTCC---------------G

Size

Hit Count

Total Norm

droFic1

CACCCACTGCGACGTGGTCTACTAGTCCGTTGGCCTGTGCAGGCG----GGC-TCTGTGGAGCACTTCTGG-TGCTGCCACGCGGAGGACCCG----AGTCCTT------------AT--TCCGCGGGGTGGGACCACAAGTGCCACAAGTGCTGCTGTC--------------------------------------------------GC---CTTCGAATGGATTCTCCAAA

Size

Hit Count

Total Norm

droKik1

CACCGAATGCGGGCTGCTCTAGGCGGTT--------------AGTCAGTGGG-TT-----------TTAAA-TTTT----------------------------------------------------------------------------------------------------------------------------------------------G---------------T

Size

Hit Count

Total Norm

droAna3

CACCCACTGCGACGTACTTTAGAGAGTT--------------GT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

droBip1

CACCCACTGCGACGTGCTCTAGGTGGTTGCAAGCCTG-----GTC----ACAC------------------------TATTGTAGGTAGATTT----AAGTG-------TCACGATTTCATCTGCGAGC----------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

dp4

CACCAGCTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CACCAACTGTGGGCTGCTTTAGG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

AACCCACTGTGATGTCCTGTAAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CACGGCCTGTGGTGTGCTATAAATTT------------------------------------------------------------------T----ATGT-------------------------------------------------------------------------------------------------------------------------------------G

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CACCGACTGCGGCGTCCTCTGAG--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CACCAGCTGCGGCGTGCTATAAATTC---------------------------TTTTCGTTGTATTTCTGG-GTGTTCAAC----------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V109
Male body

Generated: 04/20/2012 at 05:19:43 EDT

dme-mir-4963

chrX:5684785-5684894 +

Known_mirbase

three_prime_UTR

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