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

View all possible LASTZ hits (20-flies)

dme-mir-3644

chr3R:11018019-11018079 -

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

tailed_mirtron

Legend:

   mature strand at position 11018058-11018079
   star strand at position 11018025-11018047
   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 chr3R:11018004-11018094 - 1 TTATTGCTGCAGGAGGTGAGTGATTAT----GGTTTA--A--G--T----AATA---CGAATTACATAAACTAT----ATTT---AACCA--------CTA-TTCTTAGATACAAAACACTGCT
droSim1 chr3R:10448012-10448102 + LASTZ 4 TTACTGCTGCAGGAGGTGAGTGTTTAT----GGTTTA--A--A--T----TATA---CGATTTACATAAACTAT----ATTT---AACCA--------CTA-CTCTTAGATCCAAAACACCGCT
droSec1 super_0:10933739-10933828 + LASTZ 5 TTACTGCTGCAGGAGGTGAGGTTTTAT----GGTT-A--A--G--T----TATA---CGATTTGCATAAACTAT----ATTT---AACCA--------CTA-CTCTTAGATCCAAAACACCGCT
droYak2 chr3R:15416636-15416724 + LASTZ 5 TTACTGCTTCAGGAGGTAAGTTTTTGG------TTCA--G--G--T----TTCA---TGAATTACATAAACTAT----ATTT---AACCA--------CAT-TCCTTAGATCCAAAATACCGCT
droEre2 scaffold_4770:10539530-10539618 - LASTZ 5 TTACTGCTTCAGGAGGTCAGTTTTTGG------TTCG--A--T--T----TCAA---CGATTTACATAAACTGT----ATTT---AACCA--------TAT-TTCGTAGATCCAAAACACCGCT
droEug1 scf7180000409100:50607-50694 + LASTZ 5 TTACTGCTGCAGGAGGTAAGTTTGTGG------ATAG--C--G--A----TTTA---AGATGTACATAAACTAT----ATTA---AATC---------TTT-GTTTCAGATCCAAAACACAGCT
droBia1 scf7180000302402:3994917-3995007 - LASTZ 5 TTGCTACTGCAGGAGGTTAGTATGTGA------GCTA--A--A--G----TGTG---CCATCCACATAAACAAA----ATTT---ATTGG------TTTTA-TTGCCAGATCCAAAACACTGCT
droTak1 scf7180000415310:927278-927369 + LASTZ 5 TTGCTTCTTCAGGAGGTGAGTTTTTTG-----AAGTG--T--G--T----CTTG---CGATAAATATAAACCTA----ATTT---TCCTG------TTTAT-TTTCCAGATCCAAAACACCGCT
droEle1 scf7180000486474:959724-959811 + LASTZ 5 TTGCTGCTGCAAGAGGTGAGTTTTG-T----GATTTA--A-CA--T----TTTT---TAATTAACAGAAA----------TT---AAC---T--CGTTTTT-CTGTCAGATCCAAAACACCGCT
droRho1 scf7180000766350:39148-39233 - LASTZ 5 TTACTGCTGCAAGAGGTGCGTTAATGG------TTTA--A--G--T----TT-----TGAACAAAAAGAA---------TTT---CACTA---A-ATAATT-TTTTTAGATCCAAAACACCGCT
droFic1 scf7180000454104:344170-344253 + LASTZ 5 TTGCTGCTGCAGGAGGTGAGTTAATCA------TTTT--T--G--T---TTCTT----CAACCA---AAAATAT----AT-----TCCTG--------TGT-TTTTCAGATACAAAACACAGCT
droKik1 scf7180000301612:29528-29617 - LASTZ 5 TTGCTGCTTCAAGAGGTACTTTTATTT------ACCA--G--A--C----TTAC---CAAGCTAAAGG----TA----ATTC---AACCG---ATTT-TATTTTCGCAGATCCAGAACACCGCT
droAna3 scaffold_13340:6107797-6107878 - LASTZ 5 TTGTTGCTGCAGGAGGTGGGTAGTG--------------A--A--C----TTTT---CAAATTACTATAC---------CTT------CATGAA-TGTTCT-TTTGTAGATTCAAAATACTGCG
droBip1 scf7180000396708:2731560-2731641 + LASTZ 5 TTACTGCTGCAGGAGGTAGGTTGTG--------------T--A--C----TCTC---CGAACTACTATGT---------CTT------TATAAA-AGTTAC-TTTTTAGATCCAAAACACTGCA
dp4 chr2:21002920-21003004 - LASTZ 5 CTGTTGCTGCAGGAGGTAGGCTACAGA-------G----AACA--T----TTA------------GTAAATAAT----AGTC---GCTCATT--CTTTTCC-CTAATAGATCCAAAACACTGCC
droPer1 super_3:3754054-3754138 - LASTZ 5 CTGTTGCTGCAGGAGGTAGGCTACAGA----G-------AAC------------------TTTAAGTAAATAAT----AGTC---GCTCATT--CTCTTCC-CTAATAGATCCAAAACACTGCC
droWil1 scaffold_181130:7245340-7245433 + LASTZ 5 TTGCTATTGCAAGAGGTCAGTTAGAAT----AGCA----A--AAGACACTCTTGGGATGGTTAATA------AT----ATT-------CATA--TTTGGTT-TTTGCAGATTCAAAATACTGCC
droVir3 scaffold_13047:7744104-7744193 - LASTZ 5 CTGCTGCTTCAAGAGGTGAGCAACTGCTTTTGGCTTA--T--G---------TT---CGATTTTCAATGA---------TCTCTCGAATA--------CTT-TTTATAGATACAAAACACAGCG
droMoj3 scaffold_6540:3682572-3682661 - LASTZ 5 TTGCTGCTGCAAGAGGTAAAATGTTGA----G-CTCATAA--AAGTTTCCTTTT-------------CAATTAC----ATT-------CACA--TTCATTC-GTTTTAGATACAAAATACGGCC
droGri2 scaffold_14830:3558248-3558343 - LASTZ 5 CTGCTGCTGCAGGAGGTGAGTTGCACCAACTGACACA--------------------GTGTTTCCATAATTTACATTTTCTC------TTTATA-TCTTTG-TTCTCAGATACAAAACACGGCT

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 TTATTGCTGCAGGAGGTGAGTGATTAT----GGTTTA--A--G--T----AATA---CGAATTACATAAACTAT----ATTT---AACCA--------CTA-TTCTTAGATACAAAACACTGCT
droSim1 TTACTGCTGCAGGAGGTGAGTGTTTAT----GGTTTA--A--A--T----TATA---CGATTTACATAAACTAT----ATTT---AACCA--------CTA-CTCTTAGATCCAAAACACCGCT
droSec1 TTACTGCTGCAGGAGGTGAGGTTTTAT----GGTT-A--A--G--T----TATA---CGATTTGCATAAACTAT----ATTT---AACCA--------CTA-CTCTTAGATCCAAAACACCGCT
droYak2 TTACTGCTTCAGGAGGTAAGTTTTTGG------TTCA--G--G--T----TTCA---TGAATTACATAAACTAT----ATTT---AACCA--------CAT-TCCTTAGATCCAAAATACCGCT
droEre2 TTACTGCTTCAGGAGGTCAGTTTTTGG------TTCG--A--T--T----TCAA---CGATTTACATAAACTGT----ATTT---AACCA--------TAT-TTCGTAGATCCAAAACACCGCT
droEug1 TTACTGCTGCAGGAGGTAAGTTTGTGG------ATAG--C--G--A----TTTA---AGATGTACATAAACTAT----ATTA---AATC---------TTT-GTTTCAGATCCAAAACACAGCT
droBia1 TTGCTACTGCAGGAGGTTAGTATGTGA------GCTA--A--A--G----TGTG---CCATCCACATAAACAAA----ATTT---ATTGG------TTTTA-TTGCCAGATCCAAAACACTGCT
droTak1 TTGCTTCTTCAGGAGGTGAGTTTTTTG-----AAGTG--T--G--T----CTTG---CGATAAATATAAACCTA----ATTT---TCCTG------TTTAT-TTTCCAGATCCAAAACACCGCT
droEle1 TTGCTGCTGCAAGAGGTGAGTTTTG-T----GATTTA--A-CA--T----TTTT---TAATTAACAGAAA----------TT---AAC---T--CGTTTTT-CTGTCAGATCCAAAACACCGCT
droRho1 TTACTGCTGCAAGAGGTGCGTTAATGG------TTTA--A--G--T----TT-----TGAACAAAAAGAA---------TTT---CACTA---A-ATAATT-TTTTTAGATCCAAAACACCGCT
droFic1 TTGCTGCTGCAGGAGGTGAGTTAATCA------TTTT--T--G--T---TTCTT----CAACCA---AAAATAT----AT-----TCCTG--------TGT-TTTTCAGATACAAAACACAGCT
droKik1 TTGCTGCTTCAAGAGGTACTTTTATTT------ACCA--G--A--C----TTAC---CAAGCTAAAGG----TA----ATTC---AACCG---ATTT-TATTTTCGCAGATCCAGAACACCGCT
droAna3 TTGTTGCTGCAGGAGGTGGGTAGTG--------------A--A--C----TTTT---CAAATTACTATAC---------CTT------CATGAA-TGTTCT-TTTGTAGATTCAAAATACTGCG
droBip1 TTACTGCTGCAGGAGGTAGGTTGTG--------------T--A--C----TCTC---CGAACTACTATGT---------CTT------TATAAA-AGTTAC-TTTTTAGATCCAAAACACTGCA
dp4 CTGTTGCTGCAGGAGGTAGGCTACAGA-------G----AACA--T----TTA------------GTAAATAAT----AGTC---GCTCATT--CTTTTCC-CTAATAGATCCAAAACACTGCC
droPer1 CTGTTGCTGCAGGAGGTAGGCTACAGA----G-------AAC------------------TTTAAGTAAATAAT----AGTC---GCTCATT--CTCTTCC-CTAATAGATCCAAAACACTGCC
droWil1 TTGCTATTGCAAGAGGTCAGTTAGAAT----AGCA----A--AAGACACTCTTGGGATGGTTAATA------AT----ATT-------CATA--TTTGGTT-TTTGCAGATTCAAAATACTGCC
droVir3 CTGCTGCTTCAAGAGGTGAGCAACTGCTTTTGGCTTA--T--G---------TT---CGATTTTCAATGA---------TCTCTCGAATA--------CTT-TTTATAGATACAAAACACAGCG
droMoj3 TTGCTGCTGCAAGAGGTAAAATGTTGA----G-CTCATAA--AAGTTTCCTTTT-------------CAATTAC----ATT-------CACA--TTCATTC-GTTTTAGATACAAAATACGGCC
droGri2 CTGCTGCTGCAGGAGGTGAGTTGCACCAACTGACACA--------------------GTGTTTCCATAATTTACATTTTCTC------TTTATA-TCTTTG-TTCTCAGATACAAAACACGGCT

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
TTACTGCTGCAGGAGGTGAGTGTTTAT----GGTTTA--A--A--T----TATA---CGATTTACATAAACTAT----ATTT---AACCA--------CTA-CTCTTAGATCCAAAACACCGCTSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
droSec1
TTACTGCTGCAGGAGGTGAGGTTTTAT----GGTT-A--A--G--T----TATA---CGATTTGCATAAACTAT----ATTT---AACCA--------CTA-CTCTTAGATCCAAAACACCGCTSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
TTACTGCTTCAGGAGGTAAGTTTTTGG------TTCA--G--G--T----TTCA---TGAATTACATAAACTAT----ATTT---AACCA--------CAT-TCCTTAGATCCAAAATACCGCTSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
........TCAGGAGGGGAGTTTT....................................................................................................1620.500.000.000.000.500.00
droEre2
TTACTGCTTCAGGAGGTCAGTTTTTGG------TTCG--A--T--T----TCAA---CGATTTACATAAACTGT----ATTT---AACCA--------TAT-TTCGTAGATCCAAAACACCGCTSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droEug1
TTACTGCTGCAGGAGGTAAGTTTGTGG------ATAG--C--G--A----TTTA---AGATGTACATAAACTAT----ATTA---AATC---------TTT-GTTTCAGATCCAAAACACAGCTSizeHit CountTotal Norm
droBia1
TTGCTACTGCAGGAGGTTAGTATGTGA------GCTA--A--A--G----TGTG---CCATCCACATAAACAAA----ATTT---ATTGG------TTTTA-TTGCCAGATCCAAAACACTGCTSizeHit CountTotal Norm
droTak1
TTGCTTCTTCAGGAGGTGAGTTTTTTG-----AAGTG--T--G--T----CTTG---CGATAAATATAAACCTA----ATTT---TCCTG------TTTAT-TTTCCAGATCCAAAACACCGCTSizeHit CountTotal Norm
droEle1
TTGCTGCTGCAAGAGGTGAGTTTTG-T----GATTTA--A-CA--T----TTTT---TAATTAACAGAAA----------TT---AAC---T--CGTTTTT-CTGTCAGATCCAAAACACCGCTSizeHit CountTotal Norm
droRho1
TTACTGCTGCAAGAGGTGCGTTAATGG------TTTA--A--G--T----TT-----TGAACAAAAAGAA---------TTT---CACTA---A-ATAATT-TTTTTAGATCCAAAACACCGCTSizeHit CountTotal Norm
droFic1
TTGCTGCTGCAGGAGGTGAGTTAATCA------TTTT--T--G--T---TTCTT----CAACCA---AAAATAT----AT-----TCCTG--------TGT-TTTTCAGATACAAAACACAGCTSizeHit CountTotal Norm
droKik1
TTGCTGCTTCAAGAGGTACTTTTATTT------ACCA--G--A--C----TTAC---CAAGCTAAAGG----TA----ATTC---AACCG---ATTT-TATTTTCGCAGATCCAGAACACCGCTSizeHit CountTotal Norm
droAna3
TTGTTGCTGCAGGAGGTGGGTAGTG--------------A--A--C----TTTT---CAAATTACTATAC---------CTT------CATGAA-TGTTCT-TTTGTAGATTCAAAATACTGCGSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
...............................................................ACTATAC---------CTT------TATGTA-TGT..........................19215.500.502.006.506.50
..............................................................TACTATAC---------CTT------TATGTA-TGT..........................2022.500.000.501.001.00
TTGTTGCTGGAGGAGGTGGT........................................................................................................2030.670.330.330.000.00
.............................................................GTACTATAC---------CTT------CATGTA-TG...........................2020.500.000.000.000.50
.....GCTGCAGGAACTGGGTAG.....................................................................................................1820.500.500.000.000.00
................................................................CGATAC---------CTT------TATGAA-TGT..........................1830.330.000.000.330.00
....................................................TT---CAAATTACTATCC---------TTT------CA..................................2020.500.000.000.000.50
droBip1
TTACTGCTGCAGGAGGTAGGTTGTG--------------T--A--C----TCTC---CGAACTACTATGT---------CTT------TATAAA-AGTTAC-TTTTTAGATCCAAAACACTGCASizeHit CountTotal Norm
dp4
CTGTTGCTGCAGGAGGTAGGCTACAGA-------G----AACA--T----TTA------------GTAAATAAT----AGTC---GCTCATT--CTTTTCC-CTAATAGATCCAAAACACTGCCSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
CTGTTGCTGCAGGAGGTAGGCTACAGA----G-------AAC------------------TTTAAGTAAATAAT----AGTC---GCTCATT--CTCTTCC-CTAATAGATCCAAAACACTGCCSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
TTGCTATTGCAAGAGGTCAGTTAGAAT----AGCA----A--AAGACACTCTTGGGATGGTTAATA------AT----ATT-------CATA--TTTGGTT-TTTGCAGATTCAAAATACTGCCSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
.................................................TCTTGGGATGGTTAATA------TT----..............................................1920.500.500.000.000.00
droVir3
CTGCTGCTTCAAGAGGTGAGCAACTGCTTTTGGCTTA--T--G---------TT---CGATTTTCAATGA---------TCTCTCGAATA--------CTT-TTTATAGATACAAAACACAGCGSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
TTGCTGCTGCAAGAGGTAAAATGTTGA----G-CTCATAA--AAGTTTCCTTTT-------------CAATTAC----ATT-------CACA--TTCATTC-GTTTTAGATACAAAATACGGCCSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
CTGCTGCTGCAGGAGGTGAGTTGCACCAACTGACACA--------------------GTGTTTCCATAATTTACATTTTCTC------TTTATA-TCTTTG-TTCTCAGATACAAAACACGGCTSizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:17:36 EDT