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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-3641

chrX:2065119-2065187 +

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

tailed_mirtron

Legend:

   mature strand at position 2065119-2065138
   star strand at position 2065161-2065182
   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 chrX:2065104-2065202 + 1 GGCGAACTTTTTAATGTGAGTGTCCT-------G--------------------------------------------------------------------TTTACAGCTGGTATATTTTTCGAAAAGCCCTCTA-----AACTGGT-CACTTCCACTCTACAGATCTATAACTACATA
droSim1 chrX:1441441-1441539 + LASTZ 5 GGCGAACTGTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------CTTACAGCTGGTATATTTCTCGAACAGTCCTCTA-----AACTGGT-CTCTTCCGCTCCGCAGATCTACAACTACATA
droSec1 super_10:1848730-1848828 + LASTZ 5 GGCGAACTGTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------CTTACAGCTGGTATATTTCGCGAACAGTCCTCTA-----AACTGGT-CCCTTCCGCTCCGCAGATCTACAACTACATA
droYak2 chrX:6259202-6259289 - LASTZ 5 GGCGAACTCTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------TGTTTCGCATGTACATA-----------TATCTA-----AATTGGT-TCCTTCTCCTCTGCAGATCTACAACTACATA
droEre2 scaffold_4644:2028284-2028382 + LASTZ 5 GGCGAACTGTTCAATGTGAGTATCCT-------G--------------------------------------------------------------------TGATCCGCTTGTACTTATCTCGAGCAGTTCTCTA-----AACTGGT-CCCTGATCCTCTGCAGATCTACAACTACATA
droEug1 scf7180000409093:49412-49503 - LASTZ 5 GGGGAGCTGTTCAATGTGAGTTATTTGA------G---------------------------------------------------------------------TTATATTCCTG-------CTTATAACCCTCTA-----AATTGGA-CTTGTTGGTCTTGCAGATCTACAACTATATA
droBia1 scf7180000301760:2041662-2041749 + LASTZ 5 GGCGAGCTGTTCAACGTGAGTTCCCT-------T--------------------------------------------------------------------GCCCTCGCCGGCCTCTCCCTCAAGTAATCATCC-----------------ACCCTGCCCGCAGATCTACAACTACATA
droTak1 scf7180000415191:145537-145623 + LASTZ 5 GGCGAGCTGTTCAATGTGAGTTTCTTGG------G-----------------------------------------------------------------T-TTTCCAGGTGACCTAGTGACT------------G-----AGTGGG----CTACTATCTTACAGATCTACAACTACATA
droEle1 scf7180000491001:1609052-1609151 + LASTZ 5 GGCGAGCTGTTCAATGTGAGTAGCGC-----------------TCGGTTGCCCCCTAATCCTGCATTCCTTATCCTAATCCTTAT--------------------------------------------------------------C-CTCCCACCCCCCGCAGATCTACAACTACATC
droRho1 scf7180000779506:128106-128197 + LASTZ 5 GGCGAGCTGTTCAATGTGAGTGGTTT-------------------------------------------------------------------------------ACAGTC----CTTGTCCCTAGTGGCCCTCTA-ATCC--CTTGT--GTGTTCCTCCTGCAGATCTACAACTACATC
droFic1 scf7180000454072:3187079-3187168 + LASTZ 5 GGCGAGCTGTTCAACGTGAGTTCCTCCG------G-------------------------------------------------------CATCCCTTCTTC--------------------TTCCTGCTCCTCTA-----ATCCGGC-CA---CTTGCTTGCAGATCTACAACTACATC
droKik1 scf7180000302696:632884-632975 + LASTZ 5 GGCGAGCTGTTCAATGTGAGTTTTGGGA------C---------------------------------------------------------------------CTTCCCCCCCC-------TTTCCGATGATCCC-----AACTGAC-ACAATATTCTTGGCAGATCTACAACTACATC
droAna3 scaffold_13117:1070684-1070773 - LASTZ 5 GGCGAGCTCTTCAACGTAAGTTTCCCCG------C--------------------------------------------------------------------TTAAACGCCTAA----------GATTTTCCCTA-----AACCGTT-GCTGTTCTGTCTCTAGATCTACAACTATATC
droBip1 scf7180000396425:1044645-1044733 + LASTZ 5 GGTGAGCTCTTCAATGTAAGTTTTCT-------T--------------------------------------------------------------------ACAACGCGTCATA----------GAATTTCCGTA-----AACCATT-GATGTTCTGTTTTCAGATCTACAACTATATC
dp4 chrXL_group1e:3790116-3790235 - LASTZ 5 GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCA-GCCTCGAATTCGGCAGTCACTTGA------------------------TACTCTCCCACCTCCCTCTC--------------------CCTC-------------TG--CCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droPer1 super_17:723995-724114 - LASTZ 5 GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCA-GCCTCGAATTCGGCAGTCACTTAA------------------------TACTCTCCCACCTCCCTCTC--------------------CCTC-------------TG--CCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droWil1 scaffold_181096:7421152-7421244 - LASTZ 5 GGCGAGCTTTTCAACGTGAGTTACTCAG------T------------------------CCAAAGAAACTGGTTTTAGTTATGAT-----------------------------------------TAA--------------CTCA--CTTTTTTTTGTTATAGATTTACAACTATATA
droVir3 scaffold_12928:7113520-7113613 + LASTZ 5 GGCGAGTTGTTCAACGTAAGTCGATG-------A--------------------------------------------------------------------CCTCGCGTATGTGGG-----CGTACTTTCACTGA-----CGCCTGC-CTCTTTGTCTATTCAGATTTACAACTACATT
droMoj3 scaffold_6328:2787435-2787524 + LASTZ 5 GGGGAGTTGTTCAACGTAAATTCTAT-----------------------------------------------------------------------------TCTCACTTAACACAAGAATC----AAA--TCTC-----ATCTAAT--TTTTCGCTCGTTTAGATTTACAACTACATT
droGri2 scaffold_14853:3491672-3491772 - LASTZ 5 GGAGAGTTGTTTAATGTAAGCTAAA---------C-------TTCGCCCATCCT-------------------------------------------------CTCCAGCTGTTTGG-----TTAA-----CTTTCAACTG--TTTGT--CCTCCATCTCCTCAGATTTACAACTACATT

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 GGCGAACTTTTTAATGTGAGTGTCCT-------G--------------------------------------------------------------------TTTACAGCTGGTATATTTTTCGAAAAGCCCTCTA-----AACTGGT-CACTTCCACTCTACAGATCTATAACTACATA
droSim1 GGCGAACTGTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------CTTACAGCTGGTATATTTCTCGAACAGTCCTCTA-----AACTGGT-CTCTTCCGCTCCGCAGATCTACAACTACATA
droSec1 GGCGAACTGTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------CTTACAGCTGGTATATTTCGCGAACAGTCCTCTA-----AACTGGT-CCCTTCCGCTCCGCAGATCTACAACTACATA
droYak2 GGCGAACTCTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------TGTTTCGCATGTACATA-----------TATCTA-----AATTGGT-TCCTTCTCCTCTGCAGATCTACAACTACATA
droEre2 GGCGAACTGTTCAATGTGAGTATCCT-------G--------------------------------------------------------------------TGATCCGCTTGTACTTATCTCGAGCAGTTCTCTA-----AACTGGT-CCCTGATCCTCTGCAGATCTACAACTACATA
droEug1 GGGGAGCTGTTCAATGTGAGTTATTTGA------G---------------------------------------------------------------------TTATATTCCTG-------CTTATAACCCTCTA-----AATTGGA-CTTGTTGGTCTTGCAGATCTACAACTATATA
droBia1 GGCGAGCTGTTCAACGTGAGTTCCCT-------T--------------------------------------------------------------------GCCCTCGCCGGCCTCTCCCTCAAGTAATCATCC-----------------ACCCTGCCCGCAGATCTACAACTACATA
droTak1 GGCGAGCTGTTCAATGTGAGTTTCTTGG------G-----------------------------------------------------------------T-TTTCCAGGTGACCTAGTGACT------------G-----AGTGGG----CTACTATCTTACAGATCTACAACTACATA
droEle1 GGCGAGCTGTTCAATGTGAGTAGCGC-----------------TCGGTTGCCCCCTAATCCTGCATTCCTTATCCTAATCCTTAT--------------------------------------------------------------C-CTCCCACCCCCCGCAGATCTACAACTACATC
droRho1 GGCGAGCTGTTCAATGTGAGTGGTTT-------------------------------------------------------------------------------ACAGTC----CTTGTCCCTAGTGGCCCTCTA-ATCC--CTTGT--GTGTTCCTCCTGCAGATCTACAACTACATC
droFic1 GGCGAGCTGTTCAACGTGAGTTCCTCCG------G-------------------------------------------------------CATCCCTTCTTC--------------------TTCCTGCTCCTCTA-----ATCCGGC-CA---CTTGCTTGCAGATCTACAACTACATC
droKik1 GGCGAGCTGTTCAATGTGAGTTTTGGGA------C---------------------------------------------------------------------CTTCCCCCCCC-------TTTCCGATGATCCC-----AACTGAC-ACAATATTCTTGGCAGATCTACAACTACATC
droAna3 GGCGAGCTCTTCAACGTAAGTTTCCCCG------C--------------------------------------------------------------------TTAAACGCCTAA----------GATTTTCCCTA-----AACCGTT-GCTGTTCTGTCTCTAGATCTACAACTATATC
droBip1 GGTGAGCTCTTCAATGTAAGTTTTCT-------T--------------------------------------------------------------------ACAACGCGTCATA----------GAATTTCCGTA-----AACCATT-GATGTTCTGTTTTCAGATCTACAACTATATC
dp4 GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCA-GCCTCGAATTCGGCAGTCACTTGA------------------------TACTCTCCCACCTCCCTCTC--------------------CCTC-------------TG--CCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droPer1 GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCA-GCCTCGAATTCGGCAGTCACTTAA------------------------TACTCTCCCACCTCCCTCTC--------------------CCTC-------------TG--CCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droWil1 GGCGAGCTTTTCAACGTGAGTTACTCAG------T------------------------CCAAAGAAACTGGTTTTAGTTATGAT-----------------------------------------TAA--------------CTCA--CTTTTTTTTGTTATAGATTTACAACTATATA
droVir3 GGCGAGTTGTTCAACGTAAGTCGATG-------A--------------------------------------------------------------------CCTCGCGTATGTGGG-----CGTACTTTCACTGA-----CGCCTGC-CTCTTTGTCTATTCAGATTTACAACTACATT
droMoj3 GGGGAGTTGTTCAACGTAAATTCTAT-----------------------------------------------------------------------------TCTCACTTAACACAAGAATC----AAA--TCTC-----ATCTAAT--TTTTCGCTCGTTTAGATTTACAACTACATT
droGri2 GGAGAGTTGTTTAATGTAAGCTAAA---------C-------TTCGCCCATCCT-------------------------------------------------CTCCAGCTGTTTGG-----TTAA-----CTTTCAACTG--TTTGT--CCTCCATCTCCTCAGATTTACAACTACATT

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
GGCGAACTGTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------CTTACAGCTGGTATATTTCTCGAACAGTCCTCTA-----AACTGGT-CTCTTCCGCTCCGCAGATCTACAACTACATASizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
droSec1
GGCGAACTGTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------CTTACAGCTGGTATATTTCGCGAACAGTCCTCTA-----AACTGGT-CCCTTCCGCTCCGCAGATCTACAACTACATASizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
..................................................................................................................................................GT-CGCTTxCGCTCCGCAGA..............1811.000.001.000.00
droYak2
GGCGAACTCTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------TGTTTCGCATGTACATA-----------TATCTA-----AATTGGT-TCCTTCTCCTCTGCAGATCTACAACTACATASizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
GGCGAACTGTTCAATGTGAGTATCCT-------G--------------------------------------------------------------------TGATCCGCTTGTACTTATCTCGAGCAGTTCTCTA-----AACTGGT-CCCTGATCCTCTGCAGATCTACAACTACATASizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droEug1
GGGGAGCTGTTCAATGTGAGTTATTTGA------G---------------------------------------------------------------------TTATATTCCTG-------CTTATAACCCTCTA-----AATTGGA-CTTGTTGGTCTTGCAGATCTACAACTATATASizeHit CountTotal Norm
droBia1
GGCGAGCTGTTCAACGTGAGTTCCCT-------T--------------------------------------------------------------------GCCCTCGCCGGCCTCTCCCTCAAGTAATCATCC-----------------ACCCTGCCCGCAGATCTACAACTACATASizeHit CountTotal Norm
droTak1
GGCGAGCTGTTCAATGTGAGTTTCTTGG------G-----------------------------------------------------------------T-TTTCCAGGTGACCTAGTGACT------------G-----AGTGGG----CTACTATCTTACAGATCTACAACTACATASizeHit CountTotal Norm
droEle1
GGCGAGCTGTTCAATGTGAGTAGCGC-----------------TCGGTTGCCCCCTAATCCTGCATTCCTTATCCTAATCCTTAT--------------------------------------------------------------C-CTCCCACCCCCCGCAGATCTACAACTACATCSizeHit CountTotal Norm
droRho1
GGCGAGCTGTTCAATGTGAGTGGTTT-------------------------------------------------------------------------------ACAGTC----CTTGTCCCTAGTGGCCCTCTA-ATCC--CTTGT--GTGTTCCTCCTGCAGATCTACAACTACATCSizeHit CountTotal Norm
droFic1
GGCGAGCTGTTCAACGTGAGTTCCTCCG------G-------------------------------------------------------CATCCCTTCTTC--------------------TTCCTGCTCCTCTA-----ATCCGGC-CA---CTTGCTTGCAGATCTACAACTACATCSizeHit CountTotal Norm
droKik1
GGCGAGCTGTTCAATGTGAGTTTTGGGA------C---------------------------------------------------------------------CTTCCCCCCCC-------TTTCCGATGATCCC-----AACTGAC-ACAATATTCTTGGCAGATCTACAACTACATCSizeHit CountTotal Norm
droAna3
GGCGAGCTCTTCAACGTAAGTTTCCCCG------C--------------------------------------------------------------------TTAAACGCCTAA----------GATTTTCCCTA-----AACCGTT-GCTGTTCTGTCTCTAGATCTACAACTATATCSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
.......................................................................................................................................A-----AACCGTT-GCTAGTCTGTCT...................2011.000.000.001.000.00
droBip1
GGTGAGCTCTTCAATGTAAGTTTTCT-------T--------------------------------------------------------------------ACAACGCGTCATA----------GAATTTCCGTA-----AACCATT-GATGTTCTGTTTTCAGATCTACAACTATATCSizeHit CountTotal Norm
dp4
GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCA-GCCTCGAATTCGGCAGTCACTTGA------------------------TACTCTCCCACCTCCCTCTC--------------------CCTC-------------TG--CCTCTCCATCATCCTCTTCCAGATCTACAACTACATCSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCA-GCCTCGAATTCGGCAGTCACTTAA------------------------TACTCTCCCACCTCCCTCTC--------------------CCTC-------------TG--CCTCTCCATCATCCTCTTCCAGATCTACAACTACATCSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
..............................................................................................................................................................CTTCCAGATCAACGACTAC...19129.000.000.000.000.0029.00
..............................................................................................................................................................CTTCCAGATCAACGACTA....18125.000.000.000.000.0025.00
.............................................................................................................................................................TCTTCCAGATCAACGACT.....18113.000.000.000.000.0013.00
...............................................................................................................................................................TTCCAGATCAACGACTAC...1819.000.000.000.000.009.00
.............................................................................................................................................................TCTTCCAGATCAACGACTAC...2014.000.000.000.000.004.00
.............................................................................................................................................................TCTTCCAGATCGACAAGT.....1811.000.000.000.000.001.00
.............................................................................................CTGCCTCTG--------------------CCTC-------------TG--CCT..................................18180.060.000.000.000.000.06
............................................................................................................................................................CTCTACCAGATCTACAAC......1811.000.000.000.000.001.00
droWil1
GGCGAGCTTTTCAACGTGAGTTACTCAG------T------------------------CCAAAGAAACTGGTTTTAGTTATGAT-----------------------------------------TAA--------------CTCA--CTTTTTTTTGTTATAGATTTACAACTATATASizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
.......................................................................................................................................................TTTTTTTGTTATTTATTTA..........19180.060.000.060.000.00
droVir3
GGCGAGTTGTTCAACGTAAGTCGATG-------A--------------------------------------------------------------------CCTCGCGTATGTGGG-----CGTACTTTCACTGA-----CGCCTGC-CTCTTTGTCTATTCAGATTTACAACTACATTSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
GGGGAGTTGTTCAACGTAAATTCTAT-----------------------------------------------------------------------------TCTCACTTAACACAAGAATC----AAA--TCTC-----ATCTAAT--TTTTCGCTCGTTTAGATTTACAACTACATTSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
.......................TAT-----------------------------------------------------------------------------TATCACTTCACACAA..............................................................1811.000.000.001.000.00
droGri2
GGAGAGTTGTTTAATGTAAGCTAAA---------C-------TTCGCCCATCCT-------------------------------------------------CTCCAGCTGTTTGG-----TTAA-----CTTTCAACTG--TTTGT--CCTCCATCTCCTCAGATTTACAACTACATTSizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:17:15 EDT