dme-mir-4918

chr3R:4134153-4134207 -

Known_mirbase
[View on miRBase] [View on UCSC Genome Browser {Cornell Mirror}]

mirtron

Legend:

   mature strand at position 4134184-4134207
   star strand at position 4134153-4134173
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species Coordinate Alignment
dm3 chr3R:4134138-4134222 - TCGCACATGTCTAAGGTGAGCACGATGGCCAC--A-TTTAT--TGGGCAA----------CCAATGAATT---------CCCGCCT----------GC---CCACAGGTTCACTCGGTCTGC
droSim1 chr3R:17124439-17124521 + TCGCACATGTCCAAGGTGAGCACGATGGCCAC--A-TTTAT--TGGGCAA----------CCCATGAATC-----------CTCCT----------GC---CCACAGGTTCACTCGGTCTGC
droSec1 super_0:17695137-17695219 + TCGCACATGTCCAAGGTGAGCACGATGGCCAC--A-TTTAT--TGGGCAA----------CCCATGAATC-----------CTCCT----------GC---CCACAGGTTCACTCGGTCTGC
droYak2 chr3R:8209596-8209678 - GCGCACATGTCCAAGGTGAGCACGGCGGCCCCAA--------------AATCAAAGTTCTCTGACCAA------------AATCCC----------GC---CCACAGGTTCACTCCGTCTGC
droEre2 scaffold_4770:17439359-17439448 + GCGCACATGTCCAAGGTGAGCACGATGGCCCCGA--------------CATCGAAATTCT-----AAATCCCCAATCCAAAATCCC----------GC---CCACAGGTTCACTCAGTCTGC
droAna3 scaffold_13340:13231716-13231803 - GCCCATCTGAACAAGGTAATTTGAATTTGTGT--TTTTGGCCAGGAGCAA----------TTGATGTATT---------TGTTTAT----------GT---TCGAAGGTACACTCTGTTTGC
dp4 chr2:14657774-14657858 - GCCCACACGTCCAAGGTAAGAA-GCTAGTCGAAA--------------AATTGAGGCATTTTCACGAAAC-----------A-ATT----------GTCTGAGGCAGGTTCACTCCGTCTGC
droPer1 super_0:5758126-5758210 + GCCCACACGTCCAAGGTAAGAA-GCTGGTCGAAA--------------AATTGAGGCATTTTCACGAAAC-----------A-AAT----------GTCTGAGGCAGGTTCACTCCGTCTGC
droWil1 scaffold_181089:2794443-2794538 + GCACATATGTCCAAGGTAATCAAATTTAATGT--AATTTAC--CAGACAAGCGTTCCCTTTTTACAAATT-----------T-TCT----------TTCCCTGGCAGGTTCACTCGGTTTGC
droVir3 Unknown CCACACATGTCAAAGGTGGGTCTGTCGGTGGC--A-TTTAA--TTGG---------------------------------TTTTCT----------TT---TCGTAGGTGCATTCGGTGTGC
droMoj3 Unknown CCGCATATGTCAAAGGTGAGTATGC---CTCG--A-ATTGT--GTTGCAA----------TCTGC----------------TTCTTCTTCGCATTCG----CCTTAGGTGCATTCGGTTTGC
droGri2 Unknown CCACATACCGCAAAGGTAAAC--------------------------------------------------------------CTT----------CT---TTTTAGGTTCATTCGGTTTGC

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species Coordinate Lastz Id Alignment
dm3 chr3R:4134138-4134222 - NA TCGCACATGTCTAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCAATGAA----------TT---CC-CGCCTGCCCACAGGTTCACTCG--GTCTGC
droSim1 chr3R:17124439-17124521 + 2 TCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCCATGAA----------T-----C-CTCCTGCCCACAGGTTCACTCG--GTCTGC
droSec1 super_0:17695137-17695219 + 2 TCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCAC--ATTTA-TTG--GGCA-A-----------------------------CCCATGAA----------T-----C-CTCCTGCCCACAGGTTCACTCG--GTCTGC
droYak2 chr3R:8209596-8209678 - 6 GCGCACATGTCCAAGGTGAGCAC-GG-----CGGCCCCAA--------------AATCAAAGT----------TCT----------CTGACCAA-------------AA----TCCCGCCCACAGGTTCACTCC--GTCTGC
droEre2 scaffold_4770:17439359-17439448 + 1 GCGCACATGTCCAAGGTGAGCAC-GA-----TGGCCCCGA--------------CATCGAAATTCTAAATCCCC----------AATCCA---A-------------AA----TCCCGCCCACAGGTTCACTCA--GTCTGC
droEug1 scf7180000409490:587161-587244 + 3 GCTCACATGTCCAAGGTGAGCAT-TG-----TTTCCCGTTAATTCT------------GAA------------TT--T--------CTCTA--A-------------AATC-CGTCTGTCCACAGGTTCACTCT--GTTTGC
droBia1 scf7180000302402:6823672-6823766 - 5 GCGCACATGTCCAAGGTGAGCGC-GA-----TTTCCCGCCAATCCT------------GGGGA----------CTCCTCTCTGAAATCCA-GAG----------T-----C-CTCCTGCCCACAGGTGCACTCG--GTTTGC
droTak1 scf7180000415750:47169-47269 - 4 GCGCACATGTCCAAGGTAAACAC-GA-----TTTCCCGCCAAT-TA------------AGAAG----------CATCTCTCTGCAATCCAAGAATCCCCC---------TT-TCCACATCCACAGGTTCACTCG--GTTTGC
droEle1 scf7180000491212:1694399-1694504 + 3 GCGCACATGTCCAAGGTGAGCTT-GA-----TGTTCCCAGAGGTTC------------AAAGA----------TTTCTTACTAAAAATTGAGACTTGTCTTCATTGAAA----TC--CTTTCCAGGTTCACTCC--GTCTGC
droRho1 scf7180000779995:99582-99685 - 4 GCGCACATGTCCAAGGTGAGCTT-GA-----TTTCCGTTCCAC-TT------------AAAGA----------TTCCTCTCTAAAACTTGTAACTCCCAT---TTGAAA----TGCTGTCCACAGGTGCACTCC--GTTTGC
droFic1 scf7180000454073:3313771-3313857 + 2 GCGCACATGTCCAAGGTGAGCTT-GG-----CTTCCCTGCAATCCTTTGGTGC--------------------C----------GATCTGTAAA----------------C-CTCCCTTTTATAGGTTCACTCT--GTCTGC
droKik1 scf7180000302810:169514-169599 + 6 GCGCACATTTCCAAGGTAGGAGT-GA-----ATTCTGTGGGCTCTAGCG--GA--------------------CTT----------GCCACTGA----------T-----T-CTCCTGGTTGCAGGTCCATTCG--GTGTTC
droAna3 scaffold_13340:13231716-13231803 - 4 GCCCATCTGAACAAGGTAATTTG-AA-----TTTGTGT--TTTTGGCCAGGAGCA-A-----------------------------TTGATGTA----------TT---TG-TTTATGTTCGAAGGTACACTCT--GTTTGC
droBip1 scf7180000396691:2102175-2102262 - 5 GCGCATCTGAACAAGGTAATTGG-AA-----TTGATGT--TTTTAGCCTGTCAAA-A-----------------------------TGTATGCA----------TT---TT-TTTATATTTGAAGGTACACTCG--GTTTGC
dp4 chr2:14657774-14657858 - 13 GCCCACACGTCCAAGGTAAGAAG--C-----TAGTCGAAA--------------AATTGAGGC----------ATT----------TTCACGAA----------ACAA--T--TGTCTGAGGCAGGTTCACTCC--GTCTGC
droPer1 super_0:5758126-5758210 + 3 GCCCACACGTCCAAGGTAAGAAG--C-----TGGTCGAAA--------------AATTGAGGC----------ATT----------TTCACGAA----------ACAAA----TGTCTGAGGCAGGTTCACTCC--GTCTGC
droWil1 scaffold_181089:2794443-2794538 + 30 GCACATATGTCCAAGGTAATCAA-AT-----TTAATGT--AATTTACCA--GACAAGCGTTCC----------CTT----------TTTACAAA----------TT---TT-CTTTCCCTGGCAGGTTCACTCG--GTTTGC
droVir3 scaffold_12822:435887-435972 + 2 CCACACATGTCAAAGGTGGGTAT-AA-----AACCATT-TAGTCTGTCGGTGG--------------------CAT----------TTAATTGG----------------T-TTTCTTTTCGTAGGTGCATTCG--GTGTGC
droMoj3 scaffold_6540:27855886-27855971 - 132 CAGCAATAG-CAACAGCAACAGC-AA-----TAGCAAC--AGCAA-CAG-CAGCA-A-----------------------------CACCTGCA----------AG---CCGCGGCAGCCCAAAGTCTCGTTCG--CACCGC
droGri2 scaffold_15245:11304334-11304423 - 108 ATGCACAGCTCCTTAAGCAATATGAACAGCAGAGCCTGGG--------------TAGTGATGT------------------------ACCTGGA----------TC---CC-GGCCCATCTACACGTTCAGTGGACATCAGC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
TCGCACATGTCTAAGGTGAGCACGATGGCCAC--A-TTTAT--TGGGCAA----------CCAATGAATT---------CCCGCCT----------GC---CCACAGGTTCACTCGGTCTGCSizeHit CountTotal Norm
droSim1
TCGCACATGTCCAAGGTGAGCACGATGGCCAC--A-TTTAT--TGGGCAA----------CCCATGAATC-----------CTCCT----------GC---CCACAGGTTCACTCGGTCTGCSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
.........................TGTCCAG--A-TTTAT--TGGGC..........................................................................1811.000.001.000.000.00
droSec1
TCGCACATGTCCAAGGTGAGCACGATGGCCAC--A-TTTAT--TGGGCAA----------CCCATGAATC-----------CTCCT----------GC---CCACAGGTTCACTCGGTCTGCSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
GCGCACATGTCCAAGGTGAGCACGGCGGCCCCAA--------------AATCAAAGTTCTCTGACCAA------------AATCCC----------GC---CCACAGGTTCACTCCGTCTGCSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
........GTCCAAGGTGAACACGGTGG..............................................................................................2011.000.001.000.000.000.00
............ATGGTGAGCATGGCGGCC............................................................................................1811.000.000.000.001.000.00
droEre2
GCGCACATGTCCAAGGTGAGCACGATGGCCCCGA--------------CATCGAAATTCT-----AAATCCCCAATCCAAAATCCC----------GC---CCACAGGTTCACTCAGTCTGCSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droAna3
GCCCATCTGAACAAGGTAATTTGAATTTGTGT--TTTTGGCCAGGAGCAA----------TTGATGTATT---------TGTTTAT----------GT---TCGAAGGTACACTCTGTTTGCSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
.........................TTTGCGT--TTTCGGCCAGGAGC..........................................................................2111.000.001.000.000.00
.........................TTTGTGT--TTTTGGGCCGGAG...........................................................................2011.001.000.000.000.00
dp4
GCCCACACGTCCAAGGTAAGAA-GCTAGTCGAAA--------------AATTGAGGCATTTTCACGAAAC-----------A-ATT----------GTCTGAGGCAGGTTCACTCCGTCTGCSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
GCCCACACGTCCAAGGTAAGAA-GCTGGTCGAAA--------------AATTGAGGCATTTTCACGAAAC-----------A-AAT----------GTCTGAGGCAGGTTCACTCCGTCTGCSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
GCACATATGTCCAAGGTAATCAAATTTAATGT--AATTTAC--CAGACAAGCGTTCCCTTTTTACAAATT-----------T-TCT----------TTCCCTGGCAGGTTCACTCGGTTTGCSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
............................................AGACAAGAGTTCCCTTCT............................................................18111.000.0011.000.000.00
.................................................AGCGTTCATTTTTTACAAA......................................................1911.000.001.000.000.00
droVir3
CCACACATGTCAAAGGTGGGTCTGTCGGTGGC--A-TTTAA--TTGG---------------------------------TTTTCT----------TT---TCGTAGGTGCATTCGGTGTGCSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
CCGCATATGTCAAAGGTGAGTATGC---CTCG--A-ATTGT--GTTGCAA----------TCTGC----------------TTCTTCTTCGCATTCG----CCTTAGGTGCATTCGGTTTGCSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
CCACATACCGCAAAGGTAAAC--------------------------------------------------------------CTT----------CT---TTTTAGGTTCATTCGGTTTGCSizeHit CountTotal NormV109
Male body

12-way Secondary Structure

dm3 droSim1 droSec1 droYak2 droEre2 droAna3 dp4 droPer1 droWil1 droVir3 droMoj3 droGri2
RNAfold Image
UNAFold Image

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

Generated: 04/20/2012 at 05:28:56 EDT