dme-mir-2501

chr3L:8104207-8104277 +

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

tailed_mirtron

Legend:

   mature strand at position 8104207-8104229
   star strand at position 8104252-8104273
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species Coordinate Alignment
dm3 chr3L:8104192-8104292 + GGTGGTAAAAGTGGAGTAAGTTTGGAGTG----CCTGGGCTAAGAACTTCCATT---------------------------------------------------------CTGAAACTTAACTCTTGCAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAG
droSim1 chr3L:7572156-7572239 + GGTGGTAAAAGTGGAGTAAGTTTGGAGTC----CCTGGGCTAAGAACTTCCATT--------------------------------------------------------------------------CAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAG
droSec1 super_0:391632-391715 + GGTGGTAAAAGTGGAGTAAGTTTGGAGTC----CCTGGGCTAAGAACTTCCATT--------------------------------------------------------------------------GAAGCAAACTTTC------------------------------------------------------------------TTTTAGAACCAAGCGTGGTAG
droYak2 chr3L:8691884-8691979 + CGTTGTAAAAGTGGAGTAAGTTTGCGA----------------------------------------------------------------CTTACGTTC-CTTTTATATACCG-ACATACCGTCTTACAACCAAACTTTC------------------------------------------------------------------TTTCAGAACTAAGCGCGGCAG
droEre2 scaffold_4784:3260723-3260819 - GGTGGTAAAAGTGGAGTAAGCTTGCAA----------------------------------------------------------------CTTGAGTTATATCTTTTATCCCG-CTATACTTACTTACAATCAAACTTTC------------------------------------------------------------------TCGCAGAACCAAGCGCGGCAG
droAna3 scaffold_13337:13543116-13543232 - AGTGGTTAAAGTGGAGTAAGTGGCGT----------------------TTAAGGG------AGTGATG----------G---ATAGATGGACCTGAGTCT-TTTTTAGT---TGTTCTCTTTCTCTAACATTCATAATCCG------------------------------------------------------------------TTTCAGAAACAAACGTGGCCG
dp4 chrXR_group3a:1131777-1131868 + GGTGGTCAAAGTAGAGTAAGTGATCC----------------------CCACCGA------ACTATTGTGACTTTACGC------T-------------C-TAATTGGG----------------------TACATTTTTT------------------------------------------------------------------GTGCAGAACCAAGCGTGGCCG
droPer1 super_23:1158678-1158769 + GGTGGTCAAAGTAGAGTAAGTGATCC----------------------CCACCGA------ACTATTGTGGCTTTACGC------T-------------C-TAATTGGG----------------------TACATTTTTT------------------------------------------------------------------GTGCAGAACCAAGCGTGGCCG
droWil1 scaffold_180727:72451-72556 + AGTGGTCAAAGTACAGTAAGTACATGG-----------AATGACCAATCCAATTAACTATA--TA-TGTACATATATGT------T-------------A-AATCCAAC----------------------CATCTCTTTT------------------------------------------------------------------ATCCAGAAATAGACGTGGCCG
droVir3 scaffold_13049:9356761-9356852 - GGTTGTCAAAGTTGAGTAAGTTTCTA----------------------TCAAC----AATAACTA-AGCTTGGTTATGG------TA------------A-TAATTTG------------------------ACACTTTTC------------------------------------------------------------------TGTTAGAAATAAGCGCGGTCG
droMoj3 scaffold_6680:11400964-11401055 + CGTTGTCAAGGTTGAGTAAGTTTGTAGGC----TCTTAACT-----------------------GGCGAAACCAGATGA------T-------------C-TAATTAC-----------------------ACAATTTTCC------------------------------------------------------------------CATTAGAAACAAACGTGGTCG
droGri2 scaffold_15110:6804388-6804550 + CGTTGTCAAAGTCGAGTGAGTAATTTGGCAAAAACTGGCTT-------TTAATG-------------------AGATTACTCC--T-------------C-TTATCAG-----------------------ACAGTTCTCCAAACTCCTCATTTATCTTAGAGCAAATATCAGatttaaaaataaaattattttttCTTCTTTTGATCTTCAGAAATAAGCGCGGTCG

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

Species Coordinate Lastz Id Alignment
dm3 chr3L:8104192-8104292 + NA GGTGGTAAAAGTGGAGTAAGTTTGGAGTGCCT-GGGCT------AAGAA---CT-T-------C--------------------------------------------------------------CA-----------TTCTGAAACTTAA----------------------------------------CTCTTGC-AATCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACCAAGCGTGGCAG
droSim1 chr3L:7572156-7572239 + 1 GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCT-GGGCT------AAGAA---CT-T-------C----------------------------------------------------------------------------------------------------------------------------------CATTC-AATCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACCAAGCGTGGCAG
droSec1 super_0:391632-391715 + 1 GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCT-GGGCT------AAGAA---CT-T-------C----------------------------------------------------------------------------------------------------------------------------------CATTG-AAGCA---------------------------------------------------A--------ACTT----------TCTTTTAGAACCAAGCGTGGTAG
droYak2 chr3L:8691884-8691979 + 1 CGTTGTAAAAGTGGAGTAAGTTTGCGA-------------------------CTT----------------------------------------------------------------------ACGTTCCTTTTATATACCGACA-T----------A----------------------------CC--GTCTTAC-AACCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACTAAGCGCGGCAG
droEre2 scaffold_4784:3260723-3260819 - 1 GGTGGTAAAAGTGGAGTAAGCTTGCAA-------------------------CTTGAGTTATATCTTT----------------------------------------------------------TA-----------TCCCGCTA-T----------A----------------------------CT--TACTTAC-AATCA---------------------------------------------------A--------ACTT----------TCTCGCAGAACCAAGCGCGGCAG
droEug1 scf7180000409524:537792-537938 - 1 AGTGGTTAAAGTAGAGTAAGTACGCCT----------T------GAA-----------AGATCTTATTAACGCCAGAAAATAAATTTAAAATAAATTGCTTATATCGAATA--------------ATGCATTCTGCATATATTAA-------------TAAT---------------------------------TTGC-TATTT--AA-----------------------------------------------C--------TTTC----------TCTTCTAGAACGAAGCGGGGAAG
droBia1 scf7180000302428:1148690-1148776 - 1 GGTGGTCAAAGTGGAGTGAGTTACGGG--CCGCGAAG----------A----------------------------------------------------------------------TGGCTTGGTTCT----------C-----------------------------------------------------TTTCT-AATCC---------------------------------------------------A--------AATT----------ATTTGTAGAACTAAACGTGGCCG
droTak1 scf7180000415862:172750-172835 + 2 GGTGGTCAAAGTGGAGTGAGTTTGGGC----------T------TAA-------------------------------------------------------------------------------AGAT----------TC--CAA-A--------------------------------------TTGAT--TGAGT-AACTG--AA-----------------------------------------------A--------TCCT----------CTTTTCAGAACCAAGCGCGGCCG
droEle1 scf7180000490993:1776117-1776147 - 1 TT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---------------------------------------------------A--------AACT----------AATTTCAGAACCAAGCGCGGCAG
droRho1 scf7180000757809:23187-23275 - 1 ATTGACTTTAATGTATTTTA---------------CCT------AAGAA---AT-TCAATCT------------------------------------------------------------------------------C---CAACT----------------------------------------AATCTCAAAC-CATTA--AT-----------------------------------------------G-------TACTC----------TATTTAAGAACAAAGCGGGGCAG
droFic1 scf7180000454065:425620-425678 + 2 TTA-------------------------ACCC-TTGCT------AAGTT---T---------------------------------------------------------------------------------------------------------------------------------------------CAAAG-TAAAGC-T------------------------------------------------G-------TCCCT----------TTTTTTAGAACCAAGCGCGGCAG
droKik1 scf7180000302274:453761-453897 + 1 GGTGGTAAAAGTGGAGTAAGTTCCAGGC-------AATA---------------------------------ATC----------TT-----------------------------ATCAAATCT-TA-----------TCTCATATGACTATTCCCCTGATGAAATTCCCCTGGGAAATACTTAAGCTGAT--ATAAA-AACTA-------------------------------------------------------------TAA----------TTTTCTAGGACAAAGCGCGGTCG
droAna3 scaffold_13337:13543116-13543232 - 1 AGTGGTTAAAGTGGAGTAAGTGGCGTT--TAAGGGAGTGATGGATAGATGGACCT----------------------------------------------------------------------GAGTCTTTTTTA---GTTGTTCTC----------T----------------------------TT--CTCTAAC-ATTCA---------------------------------------------------T--------AATC----------CGTTTCAGAAACAAACGTGGCCG
droBip1 scf7180000396589:509214-509318 + 1 AGTGGTTAAAGTAGAGTAAGTGACGTT--CCAAGAAGCG---------------------------------ATA----------CT-----------------------------AATAGATATAGA-----------TTC--CAA-G----------A----------------------------CT--TTTATAC-AAGTA---------------------------------------------------A-------TACTC----------TGTTTCAGAACCAAACGCGGCCG
dp4 chrXR_group3a:1131777-1131868 + 1 GGTGGTCAAAGTAGAGTAAGTGATCCC--CACCGAACT----------------------------------------------------------------------------ATTGTGACTTTACGCT--------------C-------------TAAT------------------------------------TG-G---GTAC-----------------------------------------------A--------TTTT----------TTGTGCAGAACCAAGCGTGGCCG
droPer1 super_23:1158678-1158769 + 1 GGTGGTCAAAGTAGAGTAAGTGATCCC--CACCGAACT----------------------------------------------------------------------------ATTGTGGCTTTACGCT--------------C-------------TAAT------------------------------------TG-G---GTAC-----------------------------------------------A--------TTTT----------TTGTGCAGAACCAAGCGTGGCCG
droWil1 scaffold_180727:72451-72556 + 1 AGTGGTCAAAGTACAGTAAGTACATGG--------AAT------GAC-----------CAATCCAATTAACTATA----------TA-----------------------------TGTACATATATGTT--------------A-------------AATC------------------------------------CA-A---CCAT-----------------------------------------------C--------TCTT----------TTATCCAGAAATAGACGTGGCCG
droVir3 scaffold_13049:9356761-9356852 - 1 GGTTGTCAAAGTTGAGTAAGTTTCTAT--CAACAAT--------------------------------------------------------------------------AACTA----AGCTTGGTTAT----------GGTAA-------------TAAT------------------------------------TT-G-AC---------------------------------------------------A--------CTTT----------TCTGTTAGAAATAAGCGCGGTCG
droMoj3 scaffold_6680:11400964-11401055 + 1 CGTTGTCAAGGTTGAGTAAGTTTGTAGGCTCT-TAACT----------------------------------------------------------------------------GGCGAAACCAGATGAT--------------C-------------TAAT------------------------------------TA-CACA---------------------------------------------------A--------TTTT----------CCCATTAGAAACAAACGTGGTCG
droGri2 scaffold_15110:6804388-6804550 + 1 CGTTGTCAAAGTCGAGTGAGTAATTTG--GCAAAAACT----------------------------------------------------------------------------G-----GCTTT----------------TAATGAGATTACTCCTCTTAT------------------------------------CA-GACA---GTTCTCCAAACTCCTCATTTATCTTAGAGCAAATATCAGATTTAAAAATAAAATTATTTTTTCTTCTTTTGATCTTCAGAAATAAGCGCGGTCG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
GGTGGTAAAAGTGGAGTAAGTTTGGAGTG----CCTGGGCTAAGAACTTCCATT---------------------------------------------------------CTGAAACTTAACTCTTGCAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAGSizeHit CountTotal Norm
droSim1
GGTGGTAAAAGTGGAGTAAGTTTGGAGTC----CCTGGGCTAAGAACTTCCATT--------------------------------------------------------------------------CAATCAAACTTTC------------------------------------------------------------------TTTCAGAACCAAGCGTGGCAGSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
droSec1
GGTGGTAAAAGTGGAGTAAGTTTGGAGTC----CCTGGGCTAAGAACTTCCATT--------------------------------------------------------------------------GAAGCAAACTTTC------------------------------------------------------------------TTTTAGAACCAAGCGTGGTAGSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
..........GTGGTGGAAGTTTGGAGT........................................................................................................................................................................................................18111.002.009.000.00
.........AGTGGTGGAAGTTTGGAGT........................................................................................................................................................................................................1911.000.001.000.00
..........GTGGTGGAAGTTTGGAGTC----C..................................................................................................................................................................................................2011.001.000.000.00
droYak2
CGTTGTAAAAGTGGAGTAAGTTTGCGA----------------------------------------------------------------CTTACGTTC-CTTTTATATACCG-ACATACCGTCTTACAACCAAACTTTC------------------------------------------------------------------TTTCAGAACTAAGCGCGGCAGSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
GGTGGTAAAAGTGGAGTAAGCTTGCAA----------------------------------------------------------------CTTGAGTTATATCTTTTATCCCG-CTATACTTACTTACAATCAAACTTTC------------------------------------------------------------------TCGCAGAACCAAGCGCGGCAGSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droAna3
AGTGGTTAAAGTGGAGTAAGTGGCGT----------------------TTAAGGG------AGTGATG----------G---ATAGATGGACCTGAGTCT-TTTTTAGT---TGTTCTCTTTCTCTAACATTCATAATCCG------------------------------------------------------------------TTTCAGAAACAAACGTGGCCGSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
.............................................................AGTGATG----------G---AAAGATGAA.........................................................................................................................................1711.000.000.001.000.00
...................................................AGGC------AGTGxTG----------G---ATAGATGG..........................................................................................................................................1911.000.000.001.000.00
dp4
GGTGGTCAAAGTAGAGTAAGTGATCC----------------------CCACCGA------ACTATTGTGACTTTACGC------T-------------C-TAATTGGG----------------------TACATTTTTT------------------------------------------------------------------GTGCAGAACCAAGCGTGGCCGSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
GGTGGTCAAAGTAGAGTAAGTGATCC----------------------CCACCGA------ACTATTGTGGCTTTACGC------T-------------C-TAATTGGG----------------------TACATTTTTT------------------------------------------------------------------GTGCAGAACCAAGCGTGGCCGSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
AGTGGTCAAAGTACAGTAAGTACATGG-----------AATGACCAATCCAATTAACTATA--TA-TGTACATATATGT------T-------------A-AATCCAAC----------------------CATCTCTTTT------------------------------------------------------------------ATCCAGAAATAGACGTGGCCGSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
AGTGGTCAAGGTATAGTA..................................................................................................................................................................................................................1811.000.001.000.000.00
droVir3
GGTTGTCAAAGTTGAGTAAGTTTCTA----------------------TCAAC----AATAACTA-AGCTTGGTTATGG------TA------------A-TAATTTG------------------------ACACTTTTC------------------------------------------------------------------TGTTAGAAATAAGCGCGGTCGSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
......................................................................................................AATTGG------------------------ACACTTTTC------------------------------------------------------------------AGT..................1811.001.000.000.000.000.00
droMoj3
CGTTGTCAAGGTTGAGTAAGTTTGTAGGC----TCTTAACT-----------------------GGCGAAACCAGATGA------T-------------C-TAATTAC-----------------------ACAATTTTCC------------------------------------------------------------------CATTAGAAACAAACGTGGTCGSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
CGTTGTCAAAGTCGAGTGAGTAATTTGGCAAAAACTGGCTT-------TTAATG-------------------AGATTACTCC--T-------------C-TTATCAG-----------------------ACAGTTCTCCAAACTCCTCATTTATCTTAGAGCAAATATCAGatttaaaaataaaattattttttCTTCTTTTGATCTTCAGAAATAAGCGCGGTCGSizeHit 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 05:11:28 EDT