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View alignment of MAF (12-files) vs LASTZ top hits (20-flies)

View all possible LASTZ hits (20-flies)

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

20-way Fast Statistical Aligner (FSA) re-alignment

Visually pleasing best hits from LASTZ and MAF


Species Coordinate Source Confidence Alignment
dm3 chr2L:18592104-18592191 + 1 AAAGTGGTAGCCAGTGTAAGTTAAATCTAT----TAA-----GCTAT---CA--AGATT-ACGA------A-GT-----------CTAAATAA-----TTT--AATCTTACAGGCCTATAAGAGCTTT
droSim1 chr2L:18282956-18283043 + LASTZ 4 AAAGTGGTAGCCAGTGTAAGTTGAATCTAT----TAA-----GCTAT---CA--AGATT-ACGA------A-GT-----------CTAAATAA-----TTA--AATCTTACAGGCCTATAAGAGCTTT
droSec1 super_7:2217339-2217426 + LASTZ 5 AAAGTGGTAGCCAGTGTAAGTTGAATCTAT----TAA-----GCTAT---CA--ATATT-ACAA------A-GT-----------CTAACTAA-----TTA--AATCTTACAGGCCTATAAGAGCTTT
droYak2 chr2R:5109327-5109417 + LASTZ 5 AAAGTGGTTGCCAGTGTAAGTTAATTCTAT----TTA-----GCCAT---TC--TAATT-ACAA------A-GC-----------ATTAACAAA-TGG-TT--TATCTTACAGGCCTATAAGAGCTTT
droEre2 scaffold_4845:5679928-5680018 - LASTZ 5 AAAGTGGTCGCCAGCGTAAGTCGTTTCTAT----TCA-----GTCAT---TC--AAATT-ACAA------A-GC-----------ATTTACAAA-TGG-TT--TATCTTACAGGCCTATAAGAGCTTT
droEug1 scf7180000409447:540216-540308 + LASTZ 5 AAGGTGGTTGCCAGTGTAAGTAGATAAAGT----TAA-----ATAAT---AA--ATATG-CAGA------A-GT-----------GTAAGAAAAATTATAT--ATTTTTATAGGCCTATAAAAGTTTT
droBia1 scf7180000302422:5087976-5088062 - LASTZ 5 AAGGTGGTGGCCAGCGTAAGTTTATAAAAT----GTA-----GAAGC-GAG-----TAT-ATGA------A-GA-----------TTATAATT-----ATC--ACTATTCCAGGCCTATAAAAGTTTC
droTak1 scf7180000415867:892356-892443 + LASTZ 4 AAGGTGGTGGCCAGTGTAAGTGTATTATTT----TTA-----GTAAT---AA--ATACA-AAAA------G-GT-----------CTAAAAGA-----AAT--ATTTTTACAGGCCTATAAAAGTTTT
droEle1 scf7180000491338:2569757-2569847 + LASTZ 4 AAAGTGGTGGCCAGTGTAGGTTGAACTAAT----GGA-----GTTGT---AT--AATGT-ACAA------A-GT-----------CTAAGCTCG-TTT-CA--TATTTTACAGGCCTATAAAAGCTTT
droRho1 scf7180000778026:24955-25047 + LASTZ 5 AAAGTGGTGGCCAGTGTAAGTTGATCTAAT----TGA-----ATAAA---ACACATATT-TAAA------A-GT-----------CTTAACCAA-CTT-AA--TAATTTACAGGCCTATAAAAGCTTT
droFic1 scf7180000454059:343979-344067 - LASTZ 5 AAAGTGGTGGCCAGTGTAAGTTGATGATAAAGTA-CC-------------T-----TTAT-AC-CTAACA--TTCTAGAG------------AA-CAA-TG--CTTTTTATAGGCCTATAAAAGTTTT
droKik1 scf7180000302221:23696-23781 - LASTZ 4 AAGGTGGTGGCCAGTGTAAGATAAATACAA------------ATT--TGAG-----TTTT-A--------------GCTGG----ATTTATTTA-C---TTTTGATTTAACAGGCCTACAAGAGCTTC
droAna3 scaffold_12916:2495263-2495349 + LASTZ 5 AAAGTGGTGGCAAGTGTAAGTTTTTCAAAA----ATA-----ATTCG--GC-----TTCTTCCT------G-GA-----------CTAATTGG-----TTA--TCTCCATCAGGCCTATAAGAGCTTC
droBip1 scf7180000396430:434558-434644 + LASTZ 5 AAGGTGGTGGCAAGTGTAAGTCTTTCAATC----TTC-----ATACT--GC-----TTTTCACG------G-GA-----------CTAATGTG-----TAT--TCTCCCCCAGGCCTACAAAAGTTTC
dp4 chr4_group3:3803651-3803745 + LASTZ 5 AAAGTGGTGGCCAGTGTAAGTCCCTATAATAATG-CTGATCGATC--TCTC-----TCTC-T--------------GTAGC----ATTTTTCTG-T---CA--CTCATCTTAGGCCTATAAAAGTTTC
droPer1 super_1:5283458-5283552 + LASTZ 5 AAAGTGGTGGCCAGTGTAAGTCCCTATAATAATG-CTGATCGATC--TCTC-----TCTC-T--------------GTAGC----ATTTTTCTG-T---CA--CTCATCTTAGGCCTATAAAAGTTTC
droWil1 scaffold_180772:3053226-3053306 - LASTZ 5 AG--TCCTTAAATG------CCATATCTAA----TTC-----TATAT---CG--TTATA-TCTA------A-AC----------TTCAAATTT-----CTC--TTTATCAAAGGCCTACAAAAGTTTT
droVir3 scaffold_12963:18639372-18639466 + LASTZ 5 AAAGTTGTCGCAAGTGTAAGTCCAGCCGGT----ACT-----TTTCT---AC--ACATG-CATT------TATT----------TTCATTTTATTTTATGT--GCATTTTTAGGCCTACAAAAGCTTT
droMoj3 scaffold_6500:6015082-6015180 - LASTZ 5 AAAGTTGTGGCAAGCGTAAGTTAATACAATAA-G-TTGATAGATA--ATAA-----AC------------A-ATTTAGTTAATAATTATATTT-----ATA--TTCATTTCAGGCTTATAAAAGTTTT
droGri2 scaffold_15252:6570131-6570224 + LASTZ 4 AAAGTGGTTGCCAGTGTGAGTAGTAGAGAA-A-TTCA-----TGAAA---AAATAGATA-GATT------GATT----------TTAACATTCG-----CT--TTTGTTGTAGGCCTATAAAAGTTTT

Legend

0- The ortholog is absent. A better synthenic sequence candidate could not be found.
1- Reads w/ good pileup on mature and star strand & folds into hairpin structure.
2- Reads w/ good pileup on mature and star strand BUT does not fold into hairpin structure.
3- Sporadic reads & folds into a hairpin structure.
4- No reads but folds into a hairpin structure.
5- Ortholog is confident but miRNA appears absent (no reads and does not fold into a hairpin)

Re-alignment after removal of non-confident orthologs

Species Alignment
dm3 AAAGTGGTAGCCAGTGTAAGTTAAATCTAT----TAA-----GCTAT---CA--AGATT-ACGA------A-GT-----------CTAAATAA-----TTT--AATCTTACAGGCCTATAAGAGCTTT
droSim1 AAAGTGGTAGCCAGTGTAAGTTGAATCTAT----TAA-----GCTAT---CA--AGATT-ACGA------A-GT-----------CTAAATAA-----TTA--AATCTTACAGGCCTATAAGAGCTTT
droSec1 AAAGTGGTAGCCAGTGTAAGTTGAATCTAT----TAA-----GCTAT---CA--ATATT-ACAA------A-GT-----------CTAACTAA-----TTA--AATCTTACAGGCCTATAAGAGCTTT
droYak2 AAAGTGGTTGCCAGTGTAAGTTAATTCTAT----TTA-----GCCAT---TC--TAATT-ACAA------A-GC-----------ATTAACAAA-TGG-TT--TATCTTACAGGCCTATAAGAGCTTT
droEre2 AAAGTGGTCGCCAGCGTAAGTCGTTTCTAT----TCA-----GTCAT---TC--AAATT-ACAA------A-GC-----------ATTTACAAA-TGG-TT--TATCTTACAGGCCTATAAGAGCTTT
droEug1 AAGGTGGTTGCCAGTGTAAGTAGATAAAGT----TAA-----ATAAT---AA--ATATG-CAGA------A-GT-----------GTAAGAAAAATTATAT--ATTTTTATAGGCCTATAAAAGTTTT
droBia1 AAGGTGGTGGCCAGCGTAAGTTTATAAAAT----GTA-----GAAGC-GAG-----TAT-ATGA------A-GA-----------TTATAATT-----ATC--ACTATTCCAGGCCTATAAAAGTTTC
droTak1 AAGGTGGTGGCCAGTGTAAGTGTATTATTT----TTA-----GTAAT---AA--ATACA-AAAA------G-GT-----------CTAAAAGA-----AAT--ATTTTTACAGGCCTATAAAAGTTTT
droEle1 AAAGTGGTGGCCAGTGTAGGTTGAACTAAT----GGA-----GTTGT---AT--AATGT-ACAA------A-GT-----------CTAAGCTCG-TTT-CA--TATTTTACAGGCCTATAAAAGCTTT
droRho1 AAAGTGGTGGCCAGTGTAAGTTGATCTAAT----TGA-----ATAAA---ACACATATT-TAAA------A-GT-----------CTTAACCAA-CTT-AA--TAATTTACAGGCCTATAAAAGCTTT
droFic1 AAAGTGGTGGCCAGTGTAAGTTGATGATAAAGTA-CC-------------T-----TTAT-AC-CTAACA--TTCTAGAG------------AA-CAA-TG--CTTTTTATAGGCCTATAAAAGTTTT
droKik1 AAGGTGGTGGCCAGTGTAAGATAAATACAA------------ATT--TGAG-----TTTT-A--------------GCTGG----ATTTATTTA-C---TTTTGATTTAACAGGCCTACAAGAGCTTC
droAna3 AAAGTGGTGGCAAGTGTAAGTTTTTCAAAA----ATA-----ATTCG--GC-----TTCTTCCT------G-GA-----------CTAATTGG-----TTA--TCTCCATCAGGCCTATAAGAGCTTC
droBip1 AAGGTGGTGGCAAGTGTAAGTCTTTCAATC----TTC-----ATACT--GC-----TTTTCACG------G-GA-----------CTAATGTG-----TAT--TCTCCCCCAGGCCTACAAAAGTTTC
dp4 AAAGTGGTGGCCAGTGTAAGTCCCTATAATAATG-CTGATCGATC--TCTC-----TCTC-T--------------GTAGC----ATTTTTCTG-T---CA--CTCATCTTAGGCCTATAAAAGTTTC
droPer1 AAAGTGGTGGCCAGTGTAAGTCCCTATAATAATG-CTGATCGATC--TCTC-----TCTC-T--------------GTAGC----ATTTTTCTG-T---CA--CTCATCTTAGGCCTATAAAAGTTTC
droWil1 AG--TCCTTAAATG------CCATATCTAA----TTC-----TATAT---CG--TTATA-TCTA------A-AC----------TTCAAATTT-----CTC--TTTATCAAAGGCCTACAAAAGTTTT
droVir3 AAAGTTGTCGCAAGTGTAAGTCCAGCCGGT----ACT-----TTTCT---AC--ACATG-CATT------TATT----------TTCATTTTATTTTATGT--GCATTTTTAGGCCTACAAAAGCTTT
droMoj3 AAAGTTGTGGCAAGCGTAAGTTAATACAATAA-G-TTGATAGATA--ATAA-----AC------------A-ATTTAGTTAATAATTATATTT-----ATA--TTCATTTCAGGCTTATAAAAGTTTT
droGri2 AAAGTGGTTGCCAGTGTGAGTAGTAGAGAA-A-TTCA-----TGAAA---AAATAGATA-GATT------GATT----------TTAACATTCG-----CT--TTTGTTGTAGGCCTATAAAAGTTTT

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

Small RNA-seq read pileup

Species Alignment
droSim1
AAAGTGGTAGCCAGTGTAAGTTGAATCTAT----TAA-----GCTAT---CA--AGATT-ACGA------A-GT-----------CTAAATAA-----TTA--AATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
droSec1
AAAGTGGTAGCCAGTGTAAGTTGAATCTAT----TAA-----GCTAT---CA--ATATT-ACAA------A-GT-----------CTAACTAA-----TTA--AATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
AAAGTGGTTGCCAGTGTAAGTTAATTCTAT----TTA-----GCCAT---TC--TAATT-ACAA------A-GC-----------ATTAACAAA-TGG-TT--TATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
AAAGTGGTCGCCAGCGTAAGTCGTTTCTAT----TCA-----GTCAT---TC--AAATT-ACAA------A-GC-----------ATTTACAAA-TGG-TT--TATCTTACAGGCCTATAAGAGCTTTSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droEug1
AAGGTGGTTGCCAGTGTAAGTAGATAAAGT----TAA-----ATAAT---AA--ATATG-CAGA------A-GT-----------GTAAGAAAAATTATAT--ATTTTTATAGGCCTATAAAAGTTTTSizeHit CountTotal Norm
droBia1
AAGGTGGTGGCCAGCGTAAGTTTATAAAAT----GTA-----GAAGC-GAG-----TAT-ATGA------A-GA-----------TTATAATT-----ATC--ACTATTCCAGGCCTATAAAAGTTTCSizeHit CountTotal Norm
droTak1
AAGGTGGTGGCCAGTGTAAGTGTATTATTT----TTA-----GTAAT---AA--ATACA-AAAA------G-GT-----------CTAAAAGA-----AAT--ATTTTTACAGGCCTATAAAAGTTTTSizeHit CountTotal Norm
droEle1
AAAGTGGTGGCCAGTGTAGGTTGAACTAAT----GGA-----GTTGT---AT--AATGT-ACAA------A-GT-----------CTAAGCTCG-TTT-CA--TATTTTACAGGCCTATAAAAGCTTTSizeHit CountTotal Norm
droRho1
AAAGTGGTGGCCAGTGTAAGTTGATCTAAT----TGA-----ATAAA---ACACATATT-TAAA------A-GT-----------CTTAACCAA-CTT-AA--TAATTTACAGGCCTATAAAAGCTTTSizeHit CountTotal Norm
droFic1
AAAGTGGTGGCCAGTGTAAGTTGATGATAAAGTA-CC-------------T-----TTAT-AC-CTAACA--TTCTAGAG------------AA-CAA-TG--CTTTTTATAGGCCTATAAAAGTTTTSizeHit CountTotal Norm
droKik1
AAGGTGGTGGCCAGTGTAAGATAAATACAA------------ATT--TGAG-----TTTT-A--------------GCTGG----ATTTATTTA-C---TTTTGATTTAACAGGCCTACAAGAGCTTCSizeHit CountTotal Norm
droAna3
AAAGTGGTGGCAAGTGTAAGTTTTTCAAAA----ATA-----ATTCG--GC-----TTCTTCCT------G-GA-----------CTAATTGG-----TTA--TCTCCATCAGGCCTATAAGAGCTTCSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
..AGTGGxGGCAAGTGGAAGT...........................................................................................................1811.000.000.001.000.00
droBip1
AAGGTGGTGGCAAGTGTAAGTCTTTCAATC----TTC-----ATACT--GC-----TTTTCACG------G-GA-----------CTAATGTG-----TAT--TCTCCCCCAGGCCTACAAAAGTTTCSizeHit CountTotal Norm
dp4
AAAGTGGTGGCCAGTGTAAGTCCCTATAATAATG-CTGATCGATC--TCTC-----TCTC-T--------------GTAGC----ATTTTTCTG-T---CA--CTCATCTTAGGCCTATAAAAGTTTCSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
AAAGTGGTGGCCAGTGTAAGTCCCTATAATAATG-CTGATCGATC--TCTC-----TCTC-T--------------GTAGC----ATTTTTCTG-T---CA--CTCATCTTAGGCCTATAAAAGTTTCSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
AG--TCCTTAAATG------CCATATCTAA----TTC-----TATAT---CG--TTATA-TCTA------A-AC----------TTCAAATTT-----CTC--TTTATCAAAGGCCTACAAAAGTTTTSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
droVir3
AAAGTTGTCGCAAGTGTAAGTCCAGCCGGT----ACT-----TTTCT---AC--ACATG-CATT------TATT----------TTCATTTTATTTTATGT--GCATTTTTAGGCCTACAAAAGCTTTSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
..............................................................................................TTTATGT--GCAxTCTTAGGC.............1812.000.000.000.000.002.00
droMoj3
AAAGTTGTGGCAAGCGTAAGTTAATACAATAA-G-TTGATAGATA--ATAA-----AC------------A-ATTTAGTTAATAATTATATTT-----ATA--TTCATTTCAGGCTTATAAAAGTTTTSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
..AGTTxTGGCAAGCGTAAG............................................................................................................1711.000.001.000.000.00
droGri2
AAAGTGGTTGCCAGTGTGAGTAGTAGAGAA-A-TTCA-----TGAAA---AAATAGATA-GATT------GATT----------TTAACATTCG-----CT--TTTGTTGTAGGCCTATAAAAGTTTTSizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:26:32 EDT