dme-mir-4946

chr2L:18867045-18867161 -

Known_mirbase

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

intron


Legend:

   mature strand at position 18867114-18867134
   star strand at position 18867072-18867094
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species Coordinate Alignment
dm3 chr2L:18867030-18867176 - Ttttt------------tTtttttttTGCTCGATT---------------------------------------------------------GCTGCAACTAAGA---AACAAATATTTTCAGT---------------------------------------TGTTC----ATTGCAAA-TTAATTTATGTACATTGCTATGAAATCA------ATTGAAA-----A--------------------TATAAT---------------TGTA----------------------TCCTAGGCTTATCAGC--TGC--AATGCCTCTATGAAGGG
droSim1 chr2L:18557325-18557471 - Ttttt------------tTttCAAAACGCTCATTT---------------------------------------------------------GCTGCAAATAAGA---AACAAATATTTTCAGT---------------------------------------TGTTC----ATTGCAAG-TTAATTTATAAACATTGCTATGAAATCA------ATTGAAA-----A--------------------TATAAT---------------TGTA----------------------TCCCAGGCTTATCAGC--TGC--AATCCCCCCAAGAAGGG
droSec1 super_7:2494148-2494294 - Ttttt------------tTttCAAAACGTTCATTT---------------------------------------------------------GCTGATAATAAGA---AACAAATATCTTAAGA---------------------------------------TGTTC----ATTGCAAA-TTAATTTATGTACATTGCTATGAAATCA------ATTGAAA-----A--------------------TATAAT---------------TGTA----------------------TCCTAGGCTTATCAGC--TGC--AATCCCCCCAAGAAGGG
droYak2 chr2R:5382904-5383074 - Ttttt------------tTttCAAAGCATATTAGCAT-----------------------------------------------------ATGCTGCAAACAATA---AATAAATATTTTCAGC---------------------------------------TGTGC----ATTGCAAA-TTAATGTATTTACATAGCTATGAAAGCA------ATTGAAA-----C--------------------GACAAT---------------TGCAGGTCATTT--TTATTGCACACATCCTAGGCTTATCAGT--GGC--AATGCCCCTACGAAGAG
droEre2 scaffold_4845:5409251-5409398 + TACAA------------GTAACAAAGTGCTAATTC---------------------------------------------------------GCTGCAAATAGGA---AATAAATATTTTCATTA--------------------------------------------------------------TTATCACATTGCCA-GAAACCA------ATTGAAA-----A--------------------GATAAT---------------TGTAGGCCACTT--TTGTTGCACGCATCCTAGGCTTATCAGC--TGA--TATGCCCCCACGAAGGG
droAna3 Unknown TACAAGGAAAGAGCGCCATCTGGG--GAGATGAATCTTTCAGATAGCAAAGTA----------------------------------------------------------------TTTCATTCTTAAGAGAGGA------------------------------------------------------------------AAAAGTA------ACTAAAATAAATC--------------------CACAAGTACTAGGTAGTATAGGGCATCCCACAA--CCCATGTACCCCACTT------TCAG----GGCAA---CCCAC------AAG
dp4 Unknown GAGGA-AAAAGGTTACCAATTTTT--A----AAT--TCCCAAAAATCATAGAATTTATTCATTAAATCAATACT--------------------------------------------------TTTAATATATGATAAATCCATAAAATGAAGTCTTCTTTTTATGCAATGATTCCAAAGGAAATATATGTACGTTTTT-TTAAACCA------ATTACAA-----CTTCTTAAGATTAAACAGTATTTTGAT----AGTATGCCAATAGCTTTCCAATC--CCTTAACACCCTGCCA------AAAT----GGCCATACCCCACCAATAAGGG
droPer1 Unknown GTGGA-AAAAGGTTACCAA-------------------------ATCATAGAATTTATTTATTAAATCAATATTTCTTCAAAATAAACCCAAGG---------------------------T--TTTGATGTATAATAAATCTATAAAATGAATTCTTCTTTTTATGCAATGATTCCAGAGGAAATATA------CTTTT-TTAAACCA------ATTACAA-----CTTCTAATGATTAAACAGTATTTTGAT----ACTATGCCAATAGCTTTCCAATC--CCTTAACACCCTGCCA------AAAT----GGCCATACCCCACCAATAAGGG
droWil1 scaffold_180703:1741457-1741530 + GGCAA------------TTAGTTAAATTTTTTTGC---------------------------------------------------------GCACTAAACAACACTCATTGAATAATGCAAGC---------------------------------------TGTGC----AACACTGT-TTAAGT----------------------------------------------------------------------------------------------------------------------------------------------GttgtG
droVir3 Unknown -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6496:22830094-22830228 - GTGCC------------TTTTTGCATTAGATGAATCT-----------------------------------------------------ATGC---------------------------TCA---------------------------------------TGCAT----TTTATAGA-TCACTTTACGTA----------TTACTTATCTATATTTCAG-----A--------------------TATAAT---------------TCTC------TTAAGCGTTACACACTGCCT------AATAGATGTAT--GATACCTTTAGGAAGAG
droGri2 Unknown -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species Coordinate Lastz Id Alignment
dm3 chr2L:18867030-18867176 - NA TAAAAATAAAAAAATGCTCGA------------------------------TTG---------CTGCAACTAA-------------------------GAAACAA-----------------------------------------------ATATTTTCAGTTGTTCATTGCAAATTAA-------TT--------TATGTACATTGCTATGAAATCAATTGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------TTGT--------------------A---------------------------------TCCTAGGCTTATCA-----GCTGCAATGCCTCTATGAAGGG
droSim1 chr2L:18557325-18557471 - 45 TAAAAATAACAAAACGCTCAT------------------------------TTG---------CTGCAAATAA-------------------------GAAACAA-----------------------------------------------ATATTTTCAGTTGTTCATTGCAAGTTAA-------TT--------TATAAACATTGCTATGAAATCAATTGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------TTGT--------------------A---------------------------------TCCCAGGCTTATCA-----GCTGCAATCCCCCCAAGAAGGG
droSec1 super_7:2494148-2494294 - 110 TAAAAATAACAAAACGTTCAT------------------------------TTG---------CTGATAATAA-------------------------GAAACAA-----------------------------------------------ATATCTTAAGATGTTCATTGCAAATTAA-------TT--------TATGTACATTGCTATGAAATCAATTGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------TTGT--------------------A---------------------------------TCCTAGGCTTATCA-----GCTGCAATCCCCCCAAGAAGGG
droYak2 chr2R:5382904-5383074 - 400 TAAAAATAACAAAGCATAT--------------------------TAGCATATG---------CTGCAAACAA-------------------------TAAATAA-----------------------------------------------ATATTTTCAGCTGTGCATTGCAAATTAA-------TG--------TATTTACATAGCTATGAAAGCAATTGAAACG---------------------------------------ACAA------------------------------------------------------------------------------TTGCAGGTCATTTTTATTGCACACA---------------------------------TCCTAGGCTTATCA-----GTGGCAATGCCCCTACGAAGAG
droEre2 scaffold_4845:5409251-5409398 + 112 TACAAGTAACAAAGTGCTAAT------------------------------TCG---------CTGCAAATAG-------------------------GAAATAA-----------------------------------------------ATATTTTCAT---------------TA---------T--------TA-TCACATTGCCA-GAAACCAATTGAAAAG---------------------------------------ATAA------------------------------------------------------------------------------TTGTAGGCCACTTTTGTTGCACGCA---------------------------------TCCTAGGCTTATCA-----GCTGATATGCCCCCACGAAGGG
droEug1 scf7180000409478:17863-18010 + 131 TAGCAAAATTAATATTTTAAA------------------------------ATT---------GTGTAAAAAA-------------------------GTAACGG-----------------------------------------------GTATCTTA---TAGTCGTGGCA--CTCG-------AC--------TATAGCGTTTCCTCTTGTTTTGATTAGAAAT---------------------------------------GTGC------CTTGTATACCAAGGGGGCTTATCCG----------------------------------------------------------------------------------------------------------------------------CCATAGCCGGATACCGCAACGG
droBia1 scf7180000301754:1283245-1283392 - 59 TTACAATATTTAATTTAGT--------------------------------TTT---------TTATATTTAAAATTCAAACTGTTTGCCCACAGTAG-------------TATATTGAACAAAA---------------------------ATATT------------------------------------------TCTGTCTC-------AAAATACTGTTAAA-------------ATTAT---------------------TACT------------------------------------------------------------------------------TGAT--------------------A---------------------------------TTCATAGAGTATGT-----AAAAAAATATTTTTATGACTAC
droTak1 scf7180000415653:126845-126987 + 255 TTTTTATAAAAATGTTTTCAACTTAAGAGA--------------------G-CCTTTTTTATTTTTTATTTATCATTGAAACTGA-------------GAGGGGAACATATTTTTGA----------------------------------------------------GGTGAAATTCA-------GT-----------------------------AATTGA-----------------------------------------------------------------------------------------------------------------------------------------------------A---------------------------------TTTAGAGGC-CTAAATATAACTAAAATACCTCTAGAAAGGG
droEle1 scf7180000490094:78887-79034 - 306 TAAAATCGAACAAATTATAGC----------------------------TGCCA---------TAGTAACTAT-------------------------CGAATAA--------------------------------------------T--TAATCTTCAAATCATCATAGCT--TCAA-------TG--------TTTTTAAACATATACGCAAGTAAATCATAAT---------------------------------------ATTA------------------------------------------------------------------------------ATGT--------------------T--------------TTCAAGAA---TATTTAATT------------------TTTGCAATAG---CTGCAAGGG
droRho1 scf7180000767530:65055-65201 + 83 TAAGAAGCTGATTAAATTCTA------------------------------TTG---------AAGCACATAC-------------------------AGAGAAA-----------------------------------------------ATATTTCTTAAAATTCACTGTCCCTTAA-------TAATCAACAAAATTTAGATTGATATGGTTAGATTTGTATTT---------------------------------------ATAT------------------------------------------------------------------------------T-------------------------------------------------------------AAAATAACAT-----TCTTCAAGAGCACAATTAATGT
droFic1 scf7180000453829:52830-52979 - 190 TTAATATGAAAAA-TGAATGC-----------------------------------------------------------------------------------------------------------------------------------TGAATGGAACC------------------------------------------------------------------------------------------------------------------------------------TTAACAAAAAAAGCCCAATACCATAATAAAGTTAATAATAAAAATAAATTAAATACGT--------------------TATAAAATGTTTAATGCAAAGAA---CGCTTGTTCCTTGGATTTATTA-----A------TAAAACTATTAATGT
droKik1 scf7180000302469:216489-216636 - 177 TAAAATAATTAAAAAATTA--------------------------------TTA---------AAATAATTAA-------------------------AACATT------------------------------------------------ACTTATTATTTTATAAAATGTATTTAAA-------TT--------TTTTTTCATCTTCGTATA---------AATTGTATTATTTAAAT--------------------------AAAT------------------------------------------------------------------------------TTAA--------------------A---------------------------------TCTGATAAATGCCA-----ACCTAAATATATATTTAAATGA
droAna3 scaffold_13334:1096999-1097137 - 210 TAAATATTTTTAAGTAATTAA---------------------------TTG-GG---------CTACTGGCTT-------------------------TAAAAAA------------------TA---------------------------ATATTTTCAAATGTTATTGGTAATTTAA-------TT--------TTTTTATAATTTT-TAAAT---------------------------------------------------ACAT------------------------------------------------------------------------------TTTT--------------------T---------------TAAACTAAAATCCTTGTTTTCTG--------------------CTTCC--TTTTCAGCT
droBip1 scf7180000395356:37886-38031 - 77 AAAGGGTACATAGGATTAA--------------------------AAGCACTCG---------TTTAGACCAA-------------------------AGAATAA-------------ATGA------------------------------TAA---ATGGTGGTTTGTCTAAAA---------------------------CTTAATTAAGGAAAAGTATGAAAAA---------------------------------------TAAAATATACCT---------------------------------------------------------------------------------------------------------------TAGGTA---TACT-------TAGTATTCTCA-----CTTGTAACCTCTTTT----CGA
dp4 chrXR_group6:8932576-8932713 + 232 TTAAAATAAAAACATTTCATATTTAAATTA------------------CAA-GG---------TTTTATATTT-------------------------TAAATAA-----------------------------------------------ATATA------------TTT------------------------------CCC-------ACAAATTAAAGATAAT-------------ATATTTATTTTAAAGTAATTTATAATTAAA------------------------------------------------------------------------------TTGA--------------------A---------------------------------TATGGGCCC-----------------TACTACAAAGACTTT
droPer1 super_1:5889084-5889218 + 54 GATAGGTTTTTG----------------------------------------CA---------ACACAAAAAA-------------------------TAAACAA-----------------------------------------------AGATTAGTTTCCAGTTATTAAATATTAA-------TA--------TATATATTTGAAGCAGAAATATGTATATTTT---------------------------------------AGAA------------------------------------------------------------------------------TCGT--------------------T---------------------------------TCTGTGGGGTTTTC-----ATTGCAATACCT--TTTATGAA
droWil1 scaffold_180698:8557325-8557469 - 1564 ACCAAAGAGAAATATCTCAAACTCAAACTCACAAACAAGACACATCAGCG----------------------------------------------------------------------------------------------------------CGCAAGAGCAACAACGCAAAGAA--------CA--------ATTAAACAATTCTATTAAATTGATCGAAAAT---------------------------------------ATAA------------------------------------------------------------------------------ACAT--------------------T---------------------------------TCA-CAGCATAACA-----ACAACAA-----AAGAAAAGGA
droVir3 scaffold_12855:7203873-7204022 + 251 TGAAAATGAATAAATATAT--------------------------------ATG---------CTCCAATTAAAATTGAAACTACTATCCGATCGAAG-------------GTCTTT----------------------------------------------------GTTCAAATTCA-------TT----------TGAGGGGTTTTTCGCACTTTTTGGAAAAT---------------------------------------CCAT------------------------------------------------------------------------------CACT--------------------C---------------------------------CCCGATGGAAATGG-----GCTTCAATGACTTAGTGGGTGG
droMoj3 scaffold_6500:29247639-29247782 - 2815 GGCCAATTAACAAACGCAC--------------------------------GTG---------CAGCAGCTAC-------------------------AACAGCA-----------------------------------------------TCGTGTGCACACATACATTCAAACTTCTTCTGGAACA--------T-----TCTTTTAATCACATCAGCTGTTAGT------------T----------TGGTTTAGTT--T---TGGT------------------------------------------------------------------------------A--------------------------------------------------------------GATGGCGCT-----G------CAGCACTGAATCTAT
droGri2 scaffold_14853:9426729-9426870 + 576 TCCACAAAGATAT---------------------------------------------------------------------------------------------------------------CAAAATCTCAGATACTGCTTGAAAGTTGACATT--TCC---CTCATAGAATA-TCC-------TT--------TATGTACAGTAATATGAGT--GTTTGTATTT-----------------------GAA-------------GTCT------------------------------------------------------------------------------TCTT--------------------T---------------------------------TTCATCGTCATTTA-----TCTCCATCCTCTCTTTGACTGC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
Ttttt------------tTtttttttTGCTCGATT---------------------------------------------------------GCTGCAACTAAGA---AACAAATATTTTCAGT---------------------------------------TGTTC----ATTGCAAA-TTAATTTATGTACATTGCTATGAAATCA------ATTGAAA-----A--------------------TATAAT---------------TGTA----------------------TCCTAGGCTTATCAGC--TGC--AATGCCTCTATGAAGGGSizeHit CountTotal Norm
droSim1
Ttttt------------tTttCAAAACGCTCATTT---------------------------------------------------------GCTGCAAATAAGA---AACAAATATTTTCAGT---------------------------------------TGTTC----ATTGCAAG-TTAATTTATAAACATTGCTATGAAATCA------ATTGAAA-----A--------------------TATAAT---------------TGTA----------------------TCCCAGGCTTATCAGC--TGC--AATCCCCCCAAGAAGGGSizeHit CountTotal NormV044
Embryo
M023
Head
M024
Male body
M025
Embryo
droSec1
Ttttt------------tTttCAAAACGTTCATTT---------------------------------------------------------GCTGATAATAAGA---AACAAATATCTTAAGA---------------------------------------TGTTC----ATTGCAAA-TTAATTTATGTACATTGCTATGAAATCA------ATTGAAA-----A--------------------TATAAT---------------TGTA----------------------TCCTAGGCTTATCAGC--TGC--AATCCCCCCAAGAAGGGSizeHit CountTotal NormV113
Male body
V114
Embryo
V115
Head
..........................................................................................................................................................................................GTATGTAGATTGCTATGA...................................................................................................................................1811.000.001.000.00
droYak2
Ttttt------------tTttCAAAGCATATTAGCAT-----------------------------------------------------ATGCTGCAAACAATA---AATAAATATTTTCAGC---------------------------------------TGTGC----ATTGCAAA-TTAATGTATTTACATAGCTATGAAAGCA------ATTGAAA-----C--------------------GACAAT---------------TGCAGGTCATTT--TTATTGCACACATCCTAGGCTTATCAGT--GGC--AATGCCCCTACGAAGAGSizeHit CountTotal NormV046
Embryo
V052
Head
V120
Male body
V058
Head
M026
Head
............................................................................................................................................................................................................................AA-----C--------------------GACAAT---------------TGxATGTCAT........................................................1811.000.000.000.001.000.00
........................................................................................................................................................................................................ATGAAAGCA------ATCGAAT-----C--------------------GA.....................................................................................1911.000.000.001.000.000.00
droEre2
TACAA------------GTAACAAAGTGCTAATTC---------------------------------------------------------GCTGCAAATAGGA---AATAAATATTTTCATTA--------------------------------------------------------------TTATCACATTGCCA-GAAACCA------ATTGAAA-----A--------------------GATAAT---------------TGTAGGCCACTT--TTGTTGCACGCATCCTAGGCTTATCAGC--TGA--TATGCCCCCACGAAGGGSizeHit CountTotal NormV040
Embryo
V060
Head
V047
Embryo
V108
Head
..............................................................................................................TAGATATCTTCATTA--------------------------------------------------------------TTAT................................................................................................................................................1912.002.000.000.000.00
........................................................................................................................CCTTA--------------------------------------------------------------TTATCACxTTGCCA-.....................................................................................................................................1811.000.000.000.001.00
..............................................................................................TGCAAATAGGA---AATCAAC............................................................................................................................................................................................................................1811.000.000.000.001.00
...................AACAAAGTACxAATTC---------------------------------------------------------GCTG...............................................................................................................................................................................................................................................1911.000.000.000.001.00
...........................................................................................................................TA--------------------------------------------------------------TTATCAxATTGCCA-GCA..................................................................................................................................1811.000.000.001.000.00
droAna3
TACAAGGAAAGAGCGCCATCTGGG--GAGATGAATCTTTCAGATAGCAAAGTA----------------------------------------------------------------TTTCATTCTTAAGAGAGGA------------------------------------------------------------------AAAAGTA------ACTAAAATAAATC--------------------CACAAGTACTAGGTAGTATAGGGCATCCCACAA--CCCATGTACCCCACTT------TCAG----GGCAA---CCCAC------AAGSizeHit CountTotal NormV105
Male body
V106
Head
V055
Unknown
V039
Embryo
...................CTGGG--GAAATxAATCTTTC.......................................................................................................................................................................................................................................................................................................1811.000.000.000.001.00
...............................................................................................................................AAGAAAGGA------------------------------------------------------------------AAAAGGA------AC......................................................................................................................1811.000.000.001.000.00
......GAAAGAGCGxCAGCTGGG--G....................................................................................................................................................................................................................................................................................................................1811.000.000.001.000.00
dp4
GAGGA-AAAAGGTTACCAATTTTT--A----AAT--TCCCAAAAATCATAGAATTTATTCATTAAATCAATACT--------------------------------------------------TTTAATATATGATAAATCCATAAAATGAAGTCTTCTTTTTATGCAATGATTCCAAAGGAAATATATGTACGTTTTT-TTAAACCA------ATTACAA-----CTTCTTAAGATTAAACAGTATTTTGAT----AGTATGCCAATAGCTTTCCAATC--CCTTAACACCCTGCCA------AAAT----GGCCATACCCCACCAATAAGGGSizeHit CountTotal NormV112
Male body
V043
Embryo
V051
Head
M022
Male body
...................................................................................................................................................AATTATGTCTTCTTTTTAT.........................................................................................................................................................................1911.000.001.000.000.00
droPer1
GTGGA-AAAAGGTTACCAA-------------------------ATCATAGAATTTATTTATTAAATCAATATTTCTTCAAAATAAACCCAAGG---------------------------T--TTTGATGTATAATAAATCTATAAAATGAATTCTTCTTTTTATGCAATGATTCCAGAGGAAATATA------CTTTT-TTAAACCA------ATTACAA-----CTTCTAATGATTAAACAGTATTTTGAT----ACTATGCCAATAGCTTTCCAATC--CCTTAACACCCTGCCA------AAAT----GGCCATACCCCACCAATAAGGGSizeHit CountTotal NormV111
Male body
V042
Embryo
V050
Head
V057
Head
M021
Embryo
.............................................................................................................................................................................TTCCAGTGGAACTATA------CT..........................................................................................................................................1813.000.000.000.000.003.00
droWil1
GGCAA------------TTAGTTAAATTTTTTTGC---------------------------------------------------------GCACTAAACAACACTCATTGAATAATGCAAGC---------------------------------------TGTGC----AACACTGT-TTAAGT----------------------------------------------------------------------------------------------------------------------------------------------GttgtGSizeHit CountTotal NormV117
Male body
V118
Embryo
V119
Head
M020
Head
...AA------------TTATTTAAATTTTTGT..............................................................................................................................................................................................................................................................................................................1811.000.001.000.000.00
............................................................................................................ATTGAATAATGxAAGC---------------------------------------TGTT........................................................................................................................................................................1911.000.000.000.001.00
....................................................................................................................ATGGAAGA---------------------------------------TGTGC----AACACT.............................................................................................................................................................1911.000.000.001.000.00
droVir3
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV116
Male body
V053
Unknown
V047
Embryo
M027
Male body
M028
Head
droMoj3
GTGCC------------TTTTTGCATTAGATGAATCT-----------------------------------------------------ATGC---------------------------TCA---------------------------------------TGCAT----TTTATAGA-TCACTTTACGTA----------TTACTTATCTATATTTCAG-----A--------------------TATAAT---------------TCTC------TTAAGCGTTACACACTGCCT------AATAGATGTAT--GATACCTTTAGGAAGAGSizeHit 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
UNAFold Image 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
UNAFold Image

Generated: 04/20/2012 at 05:14:36 EDT