dme-mir-4965

chrX:16500140-16500227 +

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

intron

Legend:

   mature strand at position 16500158-16500178
   star strand at position 16500195-16500215
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species Coordinate Alignment
dm3 chrX:16500125-16500242 + GTATTCGCAGTACAAGCA---CAAGGTGA-TCGATGGGAGATGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCAG-GTTTCATCCATACAAATGTGTTTG
droSim1 chrX_random:4339044-4339160 + GTATTCGCAATACAAGCA---CAAGGTGA-TCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCA--GTTTCATCCATGCAAATGTGTTTG
droSec1 super_17:323461-323577 + GTATTCGCAATACAAGCA---CAAGGTGA-TCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCA--GTTTCATCCATGCAAATGTGTTTG
droYak2 chrX:10606276-10606397 + GAATTTAGAATAAAAACA---AAAGGTGA-TCGATGGGAGCTGACCTTGAGCCTGAGCTGAGATGATGAAGTAGATCGATCACAC-ACTCACTCACTCACTCA--GTTTCATCCATGCAAATTTGTTTG
droEre2 scaffold_4690:6858715-6858812 + A--------ATAAAACCA---AAAGGTGA-TCGATGGGAGCTGA------GCCTGA--AGTGATGATGAAGTAAATCGATCACA-----C----ACTCACTCA--GATTCATCCATGCAAATTTGTTTG
droAna3 scaffold_13117:1712069-1712156 + A-----------------------GCTGAGTCGATTACAGAGCA----GAGCACGA--TGCGACGATCA-GT--ATCAGTATCAG-AATCAGT--ACCTCTCA--CTCTCATCCATGCAAAg----ttg
dp4 Unknown GCAATTGCATTGCGCAGACCACAATTTTG-ACACGAGAAATCGT------ACTT------------CAAAATATACTGACGGCAATAAGC----CTTTACCAG--AACTCATCAATTTGTACGTCTATA
droPer1 Unknown GCAATTGC-----------------------------------------------------------------------------------------------------CATCAATTTGTACGTCTATA
droWil1 Unknown ---------------------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_12932:390211-390213 + t------------------------------------------------------------------------------------------------------------------------------tG
droMoj3 scaffold_6473:1149601-1149676 - GTAAATGGTTTAAAGGAAACACAATC--------------------------TAGa--tg-------------------------tatatttatatatatctagatatctatataaatatatatTTTTG
droGri2 Unknown ---------------------------------------------------------------------------------------------------------------------------------

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

Species Coordinate Lastz Id Alignment
dm3 chrX:16500125-16500242 + NA GTATTCGCAGTACAA---GCA-C--AAGGTGATCGA----TGG--GAG----ATGAG-----CG------CCTGATG--TGATGATGAA---GTAGATCGATCACACCACACAC-----------------------T------------CACTCA-CCCAGG-TTTCATCCATACA--AATG--TGTTTG
droSim1 chrX_random:4339044-4339160 + 8 GTATTCGCAATACAA---GCA-C--AAGGTGATCGA----TGG--GAG----CTGAG-----CG------CCTGATG--TGATGATGAA---GTAGATCGATCACACCACACAC-----------------------T------------CACTCA-CCCA-G-TTTCATCCATGCA--AATG--TGTTTG
droSec1 super_17:323461-323577 + 6 GTATTCGCAATACAA---GCA-C--AAGGTGATCGA----TGG--GAG----CTGAG-----CG------CCTGATG--TGATGATGAA---GTAGATCGATCACACCACACAC-----------------------T------------CACTCA-CCCA-G-TTTCATCCATGCA--AATG--TGTTTG
droYak2 chrX:10606276-10606397 + 4 GAATTTAGAATAAAA---ACA-A--AAGGTGATCGA----TGG--GAG----CTGAC-----CTTGAGCCTGAGCTG--AGATGATGAA---GTAGATCGATCACAC-ACTCAC-----------------------T------------CACTCA-CTCA-G-TTTCATCCATGCA--AATT--TGTTTG
droEre2 scaffold_4690:6858711-6858812 + 1 CC-----CAATAAAA---CCA-A--AAGGTGATCGA----TGG--GAG----CTGAG-----CC--------TGAAG--TGATGATGAA---GTAAATCGATCACA-----CAC---------------------------------TCA-------CTCA-G-ATTCATCCATGCA--AATT--TGTTTG
droEug1 scf7180000409110:53770-53870 - 6 GAAATCC-AATTAAT-GCCCA-AAAGATATGATCGA----TGG--GAG----CAAAG-----CT------CCAACTGAATGATGATGAA---A------------------------------------------AAT------T--TCT-------CTCA-T-TTTCATCCATGCA--AATT--TGTTTG
droBia1 scf7180000302421:1779397-1779498 - 27 GTAAC-CCAGTGAAA---CCA-A--GAGATGATCGA----TGG--GAG----CAGAGCAGAGCT------CGCGATG--TGATGATATAAAC-------------------------------------------AAT------C--TCT-------CTCA-C-TTTCATCCATGCA--AATT--TGTTTG
droTak1 scf7180000415351:273301-273376 + 6 GTATT-GCAGTAAAA---CCA-A--GAGGTGATCGA----TGT--GTG----ATAAG----------------------------------C-------------------------------------------AA----------TCT-------CTCA-C-CTTCATCCATGCAGCAATT--TGTTTG
droEle1 scf7180000491023:1394532-1394635 - 32 CTATTAA-ACTATCAAA-CTATC--CCGATGATCGAAGGTGGG--GAG----CTAAGCTGAGCT--------CGATG--TGATGA---A--C-------------------------------------------AAT------CCCTCT-------CTCA-C-TTTCATCCATGCA--AATT--TGTGTG
droRho1 scf7180000779841:628688-628776 - 14 ACTATCCCTAAAAAT---CCA-A--GAGGTGATCGA----TGG--GAG----CAGAG-----CT--------CGATG--TGATGAA-----C-------------------------------------------AA----------TCT-------CTCA-C-TATCATCCATGCA--AATT--TGTTTG
droFic1 scf7180000454045:1297042-1297121 + 10 A------------------------GAGGTGATCGA----TGG--GAG----CCTAG-----CT------CCCGATG--TGATGATGAA--C-------------------------------------------AAT------CAGTCT-------CTCA-C-CTTCATCCATGCA--AATT--TGTTTG
droKik1 scf7180000302724:273010-273099 - 17 AATTC-CCAA------------A--GAGGTGATCGA----TAG--GAG----CAAAG-----CACG-----ACGATG--TGATGCAACG-------------------------------------------AAACAC---------CTT-------CATA-A-TTCCATCCATGCA--AATC--TGTTAA
droAna3 scaffold_13337:17013621-17013746 + 7 GAAATCTCAGCAGCAAGCTCA-G-----CGGATCGGGTGTTGG--AGG------------------------TGGTC--TGCCATTGAC---GAAGAGCAACAGCACCAATTCC-TTCC---------AGGAGCAT--------A--GCGCTCCCAA--GC-G-TCGTCCCAGTATG--GGTG--CCTTGG
droBip1 scf7180000396425:405817-405907 - 16 A------------------------------ATCGA----TGGAAGAG----CAGAG-----CA--------CGATGCGCGATGC---G--C-------GATCA-------------GTATCAGTATC------A-GTATCCGTA--CCT-------CTCA-CTTCTCATCCATGCA--AAGT--T----G
dp4 chrXL_group1a:8134511-8134553 - 21 ACTCC-------------------------------------------------------------------------------------------------------ACACAC-----------------------A------------CACA---CACA-C-AGACAGACATATA--AAGG--A-CATG
droPer1 super_5:779941-779973 + 8 ACACTCGCACTCC------CA-C--AAGAAGAGCAG----CAG--TAG-----------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_180698:6476640-6476654 + 6 ATT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG--AATG--TGTGTG
droVir3 scaffold_13042:4246856-4246902 - 46 CACACAC-AC----------------------------------------------------------------------------------------------------ACAC-----------------------A------------CACATGTACAG-C-TTTCACTCATGCA--TATT--TGTT--
droMoj3 scaffold_6500:26586811-26586907 + 40 GCATTTGCACTGC------TC-G--AAAATGAGCAA----TTG--CAAAGATCATTG-----CA--------C---------------A---ATACATTGC---------------------------AGAGAAAT--------A--CTG-------CACA-A-AATAATTTAGTTA--ATTTTAAGTTGA
droGri2 scaffold_15245:5234538-5234618 - 64 GCAAAATGAA----C---ACA-A--AAACTGTTG--------------------------------------------------------------------CATACCACACACTAACTGTAAATATC------ACAT---------------------TT-T-TATTATTCTTATA--ATTA--TTAATA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
GTATTCGCAGTACAAGCA---CAAGGTGA-TCGATGGGAGATGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCAG-GTTTCATCCATACAAATGTGTTTGSizeHit CountTotal Norm
droSim1
GTATTCGCAATACAAGCA---CAAGGTGA-TCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCA--GTTTCATCCATGCAAATGTGTTTGSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
...............GCA---CAAGGTGG-TCGATGC............................................................................................1811.000.000.001.000.00
droSec1
GTATTCGCAATACAAGCA---CAAGGTGA-TCGATGGGAGCTGA----GCGCCTGA--TGTGATGATGAAGTAGATCGATCACACCACACACTCACTCACCCA--GTTTCATCCATGCAAATGTGTTTGSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
................................GATGGGAGCTGA----GCGCCTGA--TGTG...................................................................2411.000.001.000.00
............CAAGxx---CAAGGTGA-TCGATGG............................................................................................1911.001.000.000.00
................................................................GATGAAGAAGATCGGTCAC..............................................1911.001.000.000.00
droYak2
GAATTTAGAATAAAAACA---AAAGGTGA-TCGATGGGAGCTGACCTTGAGCCTGAGCTGAGATGATGAAGTAGATCGATCACAC-ACTCACTCACTCACTCA--GTTTCATCCATGCAAATTTGTTTGSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
.............AAACA---AAAGGTGA-TCGATGGGA..........................................................................................2211.000.000.001.000.000.00
droEre2
A--------ATAAAACCA---AAAGGTGA-TCGATGGGAGCTGA------GCCTGA--AGTGATGATGAAGTAAATCGATCACA-----C----ACTCACTCA--GATTCATCCATGCAAATTTGTTTGSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
......................................................GA--AGTxATGATCAAGTAAA......................................................18119.000.000.000.0019.00
......................................................GA--AGTTATGATCAAGTAAA......................................................1914.000.000.000.004.00
.....................................................TGA--ACTGATGATGAAGTCA.......................................................1911.000.000.000.001.00
.......................................................A--ATTGATGATGAAGTAAG......................................................1811.001.000.000.000.00
......................................................GA--AGTAATGATCAAGTAA.......................................................1811.000.000.000.001.00
......................................................GA--AGTGATGATCAAGTAA.......................................................1811.000.000.000.001.00
droAna3
A-----------------------GCTGAGTCGATTACAGAGCA----GAGCACGA--TGCGACGATCA-GT--ATCAGTATCAG-AATCAGT--ACCTCTCA--CTCTCATCCATGCAAAg----ttgSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
....................................................................A-TT--ATCAGTATCAG-CATCA......................................1911.000.000.000.001.00
.................................................................ATCA-GA--ATCAGTATCAG-AAT........................................2011.001.000.000.000.00
...................................................................CA-GT--ATCAGTATCAG-AATCAGT--..................................2211.000.000.000.001.00
....................................AGAGxGCA----GAGCAAGA--TGC....................................................................1811.000.001.000.000.00
..........................................................................ATCAGAATCAG-AATCAGT--T.................................1911.000.001.000.000.00
.............................................................................ATCATCAG-AATCAGT--ACC...............................1811.000.000.000.001.00
dp4
GCAATTGCATTGCGCAGACCACAATTTTG-ACACGAGAAATCGT------ACTT------------CAAAATATACTGACGGCAATAAGC----CTTTACCAG--AACTCATCAATTTGTACGTCTATASizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
GCAATTGC-----------------------------------------------------------------------------------------------------CATCAATTTGTACGTCTATASizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
---------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
droVir3
t------------------------------------------------------------------------------------------------------------------------------tGSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
GTAAATGGTTTAAAGGAAACACAATC--------------------------TAGa--tg-------------------------tatatttatatatatctagatatctatataaatatatatTTTTGSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
---------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV109
Male body

12-way Secondary Structure

dm3 droSim1 droSec1 droYak2 droEre2 droAna3 dp4 droPer1 droWil1 droVir3 droMoj3 droGri2
RNAfold Image None None None
UNAFold Image None None None None

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 None

Generated: 04/20/2012 at 05:12:09 EDT