CG15160_in3

chr2L:18592119-18592176 +

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

mirtron

Legend:

   mature strand at position 18592119-18592139
   star strand at position 18592155-18592175
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species Coordinate Alignment
dm3 chr2L:18592104-18592191 + AAAGTGGTAGCCAGTGTAAGTT--AAATCTATTAAG-------------CTATCAAGATT--ACGAAGTCTAAATA-AT--TTAATCTTACAGGCCTATAAGAGCTTT
droSim1 chr2L:18282956-18283043 + AAAGTGGTAGCCAGTGTAAGTT--GAATCTATTAAG-------------CTATCAAGATT--ACGAAGTCTAAATA-AT--TAAATCTTACAGGCCTATAAGAGCTTT
droSec1 super_7:2217339-2217426 + AAAGTGGTAGCCAGTGTAAGTT--GAATCTATTAAG-------------CTATCAATATT--ACAAAGTCTAACTA-AT--TAAATCTTACAGGCCTATAAGAGCTTT
droYak2 chr2R:5109327-5109417 + AAAGTGGTTGCCAGTGTAAGTT--AATTCTATTTAG-------------CCATTCTAATT--ACAAAGCATTAACAAATGGTTTATCTTACAGGCCTATAAGAGCTTT
droEre2 scaffold_4845:5679928-5680018 - AAAGTGGTCGCCAGCGTAAGTC--GTTTCTATTCAG-------------TCATTCAAATT--ACAAAGCATTTACAAATGGTTTATCTTACAGGCCTATAAGAGCTTT
droAna3 scaffold_12916:2495263-2495349 + AAAGTGGTGGCAAGTGTAAGTTTTTCAAAAA-----TAATTCGG-----CTT----C--TTCCTG--GACTAATTG-GT--TATCTCCATCAGGCCTATAAGAGCTTC
dp4 chr4_group3:3803651-3803745 + AAAGTGGTGGCCAGTGTAAGTC--CCTATAA-----TAATGCTGATCGATCTCTCT----CTCTGTAGCATTTTTCTGTCACTC--ATCTTAGGCCTATAAAAGTTTC
droPer1 super_1:5283458-5283552 + AAAGTGGTGGCCAGTGTAAGTC--CCTATAA-----TAATGCTGATCGATCTCTCT----CTCTGTAGCATTTTTCTGTCACTC--ATCTTAGGCCTATAAAAGTTTC
droWil1 Unknown AAAGTGGTGGCGAGTGTAAGTG--AACTATATCGTT-------------ATATCTAAACT--TCAAATT--------T--CTCTTTATCAAAGGCCTACAAAAGTTTT
droVir3 Unknown AAAGTTGTCGCAAGTGTAAGTC--CAACACATGCAT-------------TTATTTTCATT--TTATTTT--------A--TGTGCATTTTTAGGCCTACAAAAGCTTT
droMoj3 Unknown AAAGTTGTGGCAAGCGTAAGTT--AAAGataataaacaatttag-----tta----ataa--ttatatt--------t--atattCATTTCAGGCTTATAAAAGTTTT
droGri2 Unknown AAAGTGGTTGCCAGTGTGAGTA--GAAAAAA-----TAGAT-AGATTG--------ATTT--TAACATT--------C--GCTTTTGTTGTAGGCCTATAAAAGTTTT

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

Species Coordinate Lastz Id Alignment
dm3 chr2L:18592104-18592191 + NA AAAGTGGTAGCCAGTGTAAGTTAAATCTAT----TAA-----GCTAT---CA--AGATT-ACGA------A-GT-----------CTAAATAA-----TTT--AATCTTACAGGCCTATAAGAGCTTT
droSim1 chr2L:18282956-18283043 + 1 AAAGTGGTAGCCAGTGTAAGTTGAATCTAT----TAA-----GCTAT---CA--AGATT-ACGA------A-GT-----------CTAAATAA-----TTA--AATCTTACAGGCCTATAAGAGCTTT
droSec1 super_7:2217339-2217426 + 1 AAAGTGGTAGCCAGTGTAAGTTGAATCTAT----TAA-----GCTAT---CA--ATATT-ACAA------A-GT-----------CTAACTAA-----TTA--AATCTTACAGGCCTATAAGAGCTTT
droYak2 chr2R:5109327-5109417 + 1 AAAGTGGTTGCCAGTGTAAGTTAATTCTAT----TTA-----GCCAT---TC--TAATT-ACAA------A-GC-----------ATTAACAAA-TGG-TT--TATCTTACAGGCCTATAAGAGCTTT
droEre2 scaffold_4845:5679928-5680018 - 3 AAAGTGGTCGCCAGCGTAAGTCGTTTCTAT----TCA-----GTCAT---TC--AAATT-ACAA------A-GC-----------ATTTACAAA-TGG-TT--TATCTTACAGGCCTATAAGAGCTTT
droEug1 scf7180000409447:540216-540308 + 2 AAGGTGGTTGCCAGTGTAAGTAGATAAAGT----TAA-----ATAAT---AA--ATATG-CAGA------A-GT-----------GTAAGAAAAATTATAT--ATTTTTATAGGCCTATAAAAGTTTT
droBia1 scf7180000302422:5087976-5088062 - 1 AAGGTGGTGGCCAGCGTAAGTTTATAAAAT----GTA-----GAAGC-GAG-----TAT-ATGA------A-GA-----------TTATAATT-----ATC--ACTATTCCAGGCCTATAAAAGTTTC
droTak1 scf7180000415867:892356-892443 + 2 AAGGTGGTGGCCAGTGTAAGTGTATTATTT----TTA-----GTAAT---AA--ATACA-AAAA------G-GT-----------CTAAAAGA-----AAT--ATTTTTACAGGCCTATAAAAGTTTT
droEle1 scf7180000491338:2569757-2569847 + 3 AAAGTGGTGGCCAGTGTAGGTTGAACTAAT----GGA-----GTTGT---AT--AATGT-ACAA------A-GT-----------CTAAGCTCG-TTT-CA--TATTTTACAGGCCTATAAAAGCTTT
droRho1 scf7180000778026:24955-25047 + 2 AAAGTGGTGGCCAGTGTAAGTTGATCTAAT----TGA-----ATAAA---ACACATATT-TAAA------A-GT-----------CTTAACCAA-CTT-AA--TAATTTACAGGCCTATAAAAGCTTT
droFic1 scf7180000454059:343979-344067 - 4 AAAGTGGTGGCCAGTGTAAGTTGATGATAAAGTA-CC-------------T-----TTAT-AC-CTAACA--TTCTAGAG------------AA-CAA-TG--CTTTTTATAGGCCTATAAAAGTTTT
droKik1 scf7180000302221:23696-23781 - 2 AAGGTGGTGGCCAGTGTAAGATAAATACAA------------ATT--TGAG-----TTTT-A--------------GCTGG----ATTTATTTA-C---TTTTGATTTAACAGGCCTACAAGAGCTTC
droAna3 scaffold_12916:2495263-2495349 + 1 AAAGTGGTGGCAAGTGTAAGTTTTTCAAAA----ATA-----ATTCG--GC-----TTCTTCCT------G-GA-----------CTAATTGG-----TTA--TCTCCATCAGGCCTATAAGAGCTTC
droBip1 scf7180000396430:434558-434644 + 1 AAGGTGGTGGCAAGTGTAAGTCTTTCAATC----TTC-----ATACT--GC-----TTTTCACG------G-GA-----------CTAATGTG-----TAT--TCTCCCCCAGGCCTACAAAAGTTTC
dp4 chr4_group3:3803651-3803745 + 1 AAAGTGGTGGCCAGTGTAAGTCCCTATAATAATG-CTGATCGATC--TCTC-----TCTC-T--------------GTAGC----ATTTTTCTG-T---CA--CTCATCTTAGGCCTATAAAAGTTTC
droPer1 super_1:5283458-5283552 + 1 AAAGTGGTGGCCAGTGTAAGTCCCTATAATAATG-CTGATCGATC--TCTC-----TCTC-T--------------GTAGC----ATTTTTCTG-T---CA--CTCATCTTAGGCCTATAAAAGTTTC
droWil1 scaffold_180772:3053226-3053306 - 1 AG--TCCTTAAATG------CCATATCTAA----TTC-----TATAT---CG--TTATA-TCTA------A-AC----------TTCAAATTT-----CTC--TTTATCAAAGGCCTACAAAAGTTTT
droVir3 scaffold_12963:18639372-18639466 + 2 AAAGTTGTCGCAAGTGTAAGTCCAGCCGGT----ACT-----TTTCT---AC--ACATG-CATT------TATT----------TTCATTTTATTTTATGT--GCATTTTTAGGCCTACAAAAGCTTT
droMoj3 scaffold_6500:6015082-6015180 - 2 AAAGTTGTGGCAAGCGTAAGTTAATACAATAA-G-TTGATAGATA--ATAA-----AC------------A-ATTTAGTTAATAATTATATTT-----ATA--TTCATTTCAGGCTTATAAAAGTTTT
droGri2 scaffold_15252:6570131-6570224 + 2 AAAGTGGTTGCCAGTGTGAGTAGTAGAGAA-A-TTCA-----TGAAA---AAATAGATA-GATT------GATT----------TTAACATTCG-----CT--TTTGTTGTAGGCCTATAAAAGTTTT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
AAAGTGGTAGCCAGTGTAAGTT--AAATCTATTAAG-------------CTATCAAGATT--ACGAAGTCTAAATA-AT--TTAATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal Norm
droSim1
AAAGTGGTAGCCAGTGTAAGTT--GAATCTATTAAG-------------CTATCAAGATT--ACGAAGTCTAAATA-AT--TAAATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
droSec1
AAAGTGGTAGCCAGTGTAAGTT--GAATCTATTAAG-------------CTATCAATATT--ACAAAGTCTAACTA-AT--TAAATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
AAAGTGGTTGCCAGTGTAAGTT--AATTCTATTTAG-------------CCATTCTAATT--ACAAAGCATTAACAAATGGTTTATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
AAAGTGGTCGCCAGCGTAAGTC--GTTTCTATTCAG-------------TCATTCAAATT--ACAAAGCATTTACAAATGGTTTATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droAna3
AAAGTGGTGGCAAGTGTAAGTTTTTCAAAAA-----TAATTCGG-----CTT----C--TTCCTG--GACTAATTG-GT--TATCTCCATCAGGCCTATAAGAGCTTCSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
..AGTGGxGGCAAGTGGAAGT.......................................................................................1811.000.000.001.000.00
dp4
AAAGTGGTGGCCAGTGTAAGTC--CCTATAA-----TAATGCTGATCGATCTCTCT----CTCTGTAGCATTTTTCTGTCACTC--ATCTTAGGCCTATAAAAGTTTCSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
AAAGTGGTGGCCAGTGTAAGTC--CCTATAA-----TAATGCTGATCGATCTCTCT----CTCTGTAGCATTTTTCTGTCACTC--ATCTTAGGCCTATAAAAGTTTCSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
AAAGTGGTGGCGAGTGTAAGTG--AACTATATCGTT-------------ATATCTAAACT--TCAAATT--------T--CTCTTTATCAAAGGCCTACAAAAGTTTTSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
......GTGTCGAGTGTAAGTG--CA..................................................................................1811.000.001.000.000.00
droVir3
AAAGTTGTCGCAAGTGTAAGTC--CAACACATGCAT-------------TTATTTTCATT--TTATTTT--------A--TGTGCATTTTTAGGCCTACAAAAGCTTTSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
..................................................................TTT--------A--TGTGCAxTCTTAGGC.............1812.000.000.000.000.002.00
droMoj3
AAAGTTGTGGCAAGCGTAAGTT--AAAGataataaacaatttag-----tta----ataa--ttatatt--------t--atattCATTTCAGGCTTATAAAAGTTTTSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
..AGTTxTGGCAAGCGTAAG........................................................................................1711.000.001.000.000.00
droGri2
AAAGTGGTTGCCAGTGTGAGTA--GAAAAAA-----TAGAT-AGATTG--------ATTT--TAACATT--------C--GCTTTTGTTGTAGGCCTATAAAAGTTTTSizeHit 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 05:20:51 EDT