Return to list

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

View all possible LASTZ hits (20-flies)

Eaat2_in6

chr2L:738436-738507 -

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

mirtron

Legend:

   mature strand at position 738487-738507
   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:738421-738522 - 1 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTAATTTG-----------TAATGGCAGT-----TC-CACT-GCGAA--AAAGCTTTATCGAA-G--------------ATCCAT---CTCCTTGCAGGGATCGGATTCGCAC
droSim1 chr2L:739962-740062 - LASTZ 3 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAATGGCAGT-----TC-CACT-GCGCC--AAAGCTTTATCGAA----------------GATTCT---TCTCTTGCAGGGATCGGATTCGCAC
droSec1 super_14:710120-710220 - LASTZ 4 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAATGGCAGT-----TC-CACT-GCACA--AAAGCTTTATCGAA----------------GATTCT---TCTCTTGCAGGGATCGGATTCGCAC
droYak2 chr2L:721660-721764 - LASTZ 5 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTAG-----------GATTCC-AATGTAATTC-TACT-GCGAA--ACAGCTTCATCGAA----------------GGTTCT---TCTCTTGCAGGGATCGGATTCGCAC
droEre2 scaffold_4929:793076-793176 - LASTZ 5 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CCGATTCA-----------GAATGCTGAT-----TC-CACT-GCGAA--GAAGCTTCATCGAA----------------GGGGCT---TCTCTTGCAGGGATCGGATTCGCAC
droEug1 scf7180000409554:1463548-1463649 - LASTZ 4 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GACTAATTAC-----TC-CCCC-GAAGA--AGTCGCTTAACAAA-G--------------GACTCT---GTTCTTGCAGGGATCGCATTCGCAC
droBia1 scf7180000302261:3089215-3089316 + LASTZ 4 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTC-----------GAGTGGTTAT-----CG-CACG-GGGAA--AGCCACTAATGCAA-G--------------GGATCT---TGTGTTGCAGGGATCGGATTCGGAC
droTak1 scf7180000415856:360180-360285 - LASTZ 4 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAGTGGCTAT-----CCTCATT-AGGTA--GATGACTAACCCAA-G--------------GAATCTTGTCTTGTCGCAGGGATCGGATTCGCAC
droEle1 scf7180000491026:48627-48723 + LASTZ 4 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GTTTGTTTTT-----CT-CAAC-CGAAT--G----GTAACCTAC----------------AATTTA---ACATTTCTAGGGATCGGATTCGCAC
droRho1 scf7180000767553:111843-111943 + LASTZ 4 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAACATCTTT-----CT-GGGG-GCAAT--CATAATTTATACAA----------------TATTTG---GGATTTCCAGGGACCGGATTCGCAC
droFic1 scf7180000453904:1013475-1013577 - LASTZ 4 CGTGGACTGGTTTGTGTGAGTACGG-----AT------CTGGCTTT-----------GGTTGC-GGT-T---AA-CCCT-GGGGAGTAGTGAGTAATGTGG----------------GCCTTC---CACTTTTCAGGGACAGGATTCGGAC
droKik1 scf7180000301725:290060-290161 + LASTZ 5 CGTGGACTGGTTTGTGTGAGTATGA-----AGGGGGT---TTTCTG-------------------GT-----AT-CCTTGAGGGG--GATATTTGACCTAA-AGGGAT----------TATGT---TTTCCTAAAGGGATCGAATTCGCAC
droAna3 scaffold_12916:1707814-1707900 - LASTZ 3 CGTGGACTGGTTTGTGTGAGTATGA-----GA------TGGATGGAGGGCTCAGTCCGTGTAG-------------------------TAACC-------------------------ACATC---CCCTTTCCAGAGACCGCATCCGCAC
droBip1 scf7180000396728:369103-369188 - LASTZ 4 CGTCGACTGGTTTGTGTGAGTATGG-----GA------CCCAGTCC-----------GTGTGT--------------------------------------AAACCACTGTT--ATAATCCAC---TTCCCTCCAGAGATCGCATCCGCAC
dp4 chr4_group3:8989807-8989896 + LASTZ 5 CGTCGACTGGTTTGTGTAAGTCCTG-----A-----------TCCC-----------GACTC-----------------------TC----CTCC----TTAGAGCTTCGCTTCATTGTGTCC---TTTGCTGCAGCGACCGCATTCGGAC
droPer1 super_8:173764-173853 + LASTZ 5 CGTCGACTGGTTTGTGTAAGTCCTG-----A-----------TCCC-----------GACTC-----------------------TC----CTCC----TTAGAGCTTCGCTTCATTGTGTCC---TTTGCTGCAGCGACCGCATCCGGAC
droWil1 scaffold_180708:429041-429131 + LASTZ 5 CGTGGATTGGTTGCTGTAAGCAATATAT--AT------CTCTTTTG-----------CATAAT-TGT---------ATA-ATGCC---------AACTGCT------------------AATT---TATTTTCCAGGGATCGGTTCCGCAC
droVir3 scaffold_12723:5465392-5465486 - LASTZ 5 TGTCGACTGGCTGCTGTATGTAAAT-----GC------TAGAACTT-----------TATGT-----------------------TT----GGTC----CTGGATATACATTTTCTGTTCGAT---TAATTTTTAGTGATCGTTTCCGCAC
droMoj3 scaffold_6500:11048776-11048863 - LASTZ 5 TGTCGATTGGCTACTGTATGTAGATGTC--AA---AATTTGTACTT-----------GACTGT-----------------------T----ATTTATTGAA-----------------ATTTG---ATTGTCTTAGGGATCGTTTCCGTAC
droGri2 scaffold_15252:7120755-7120854 - LASTZ 5 TGTCGATTGGTTTGTGTAAGTACTGGG-GGAGGGGAT-----TATG-----------GATTA-----------------------TC----CCAA----ATATAGTTTTGAATTTATAAATTC---TGATTTAAAGTGATCGCATTCGCAC

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 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTAATTTG-----------TAATGGCAGT-----TC-CACT-GCGAA--AAAGCTTTATCGAA-G--------------ATCCAT---CTCCTTGCAGGGATCGGATTCGCAC
droSim1 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAATGGCAGT-----TC-CACT-GCGCC--AAAGCTTTATCGAA----------------GATTCT---TCTCTTGCAGGGATCGGATTCGCAC
droSec1 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAATGGCAGT-----TC-CACT-GCACA--AAAGCTTTATCGAA----------------GATTCT---TCTCTTGCAGGGATCGGATTCGCAC
droYak2 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTAG-----------GATTCC-AATGTAATTC-TACT-GCGAA--ACAGCTTCATCGAA----------------GGTTCT---TCTCTTGCAGGGATCGGATTCGCAC
droEre2 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CCGATTCA-----------GAATGCTGAT-----TC-CACT-GCGAA--GAAGCTTCATCGAA----------------GGGGCT---TCTCTTGCAGGGATCGGATTCGCAC
droEug1 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GACTAATTAC-----TC-CCCC-GAAGA--AGTCGCTTAACAAA-G--------------GACTCT---GTTCTTGCAGGGATCGCATTCGCAC
droBia1 CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTC-----------GAGTGGTTAT-----CG-CACG-GGGAA--AGCCACTAATGCAA-G--------------GGATCT---TGTGTTGCAGGGATCGGATTCGGAC
droTak1 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAGTGGCTAT-----CCTCATT-AGGTA--GATGACTAACCCAA-G--------------GAATCTTGTCTTGTCGCAGGGATCGGATTCGCAC
droEle1 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GTTTGTTTTT-----CT-CAAC-CGAAT--G----GTAACCTAC----------------AATTTA---ACATTTCTAGGGATCGGATTCGCAC
droRho1 CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAACATCTTT-----CT-GGGG-GCAAT--CATAATTTATACAA----------------TATTTG---GGATTTCCAGGGACCGGATTCGCAC
droFic1 CGTGGACTGGTTTGTGTGAGTACGG-----AT------CTGGCTTT-----------GGTTGC-GGT-T---AA-CCCT-GGGGAGTAGTGAGTAATGTGG----------------GCCTTC---CACTTTTCAGGGACAGGATTCGGAC
droKik1 CGTGGACTGGTTTGTGTGAGTATGA-----AGGGGGT---TTTCTG-------------------GT-----AT-CCTTGAGGGG--GATATTTGACCTAA-AGGGAT----------TATGT---TTTCCTAAAGGGATCGAATTCGCAC
droAna3 CGTGGACTGGTTTGTGTGAGTATGA-----GA------TGGATGGAGGGCTCAGTCCGTGTAG-------------------------TAACC-------------------------ACATC---CCCTTTCCAGAGACCGCATCCGCAC
droBip1 CGTCGACTGGTTTGTGTGAGTATGG-----GA------CCCAGTCC-----------GTGTGT--------------------------------------AAACCACTGTT--ATAATCCAC---TTCCCTCCAGAGATCGCATCCGCAC
dp4 CGTCGACTGGTTTGTGTAAGTCCTG-----A-----------TCCC-----------GACTC-----------------------TC----CTCC----TTAGAGCTTCGCTTCATTGTGTCC---TTTGCTGCAGCGACCGCATTCGGAC
droPer1 CGTCGACTGGTTTGTGTAAGTCCTG-----A-----------TCCC-----------GACTC-----------------------TC----CTCC----TTAGAGCTTCGCTTCATTGTGTCC---TTTGCTGCAGCGACCGCATCCGGAC
droWil1 CGTGGATTGGTTGCTGTAAGCAATATAT--AT------CTCTTTTG-----------CATAAT-TGT---------ATA-ATGCC---------AACTGCT------------------AATT---TATTTTCCAGGGATCGGTTCCGCAC
droVir3 TGTCGACTGGCTGCTGTATGTAAAT-----GC------TAGAACTT-----------TATGT-----------------------TT----GGTC----CTGGATATACATTTTCTGTTCGAT---TAATTTTTAGTGATCGTTTCCGCAC
droMoj3 TGTCGATTGGCTACTGTATGTAGATGTC--AA---AATTTGTACTT-----------GACTGT-----------------------T----ATTTATTGAA-----------------ATTTG---ATTGTCTTAGGGATCGTTTCCGTAC
droGri2 TGTCGATTGGTTTGTGTAAGTACTGGG-GGAGGGGAT-----TATG-----------GATTA-----------------------TC----CCAA----ATATAGTTTTGAATTTATAAATTC---TGATTTAAAGTGATCGCATTCGCAC

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
CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAATGGCAGT-----TC-CACT-GCGCC--AAAGCTTTATCGAA----------------GATTCT---TCTCTTGCAGGGATCGGATTCGCACSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
.........................................ATTTG-----------GACTGGCACT-----TC-C...........................................................................1812.000.000.000.002.00
.........GTTTGTGTGTGTATGG-----GT------.................................................................................................................1820.500.500.000.000.00
....................................................................................C--AAAACTTTATCGAA----------------GGT...............................1811.000.000.001.000.00
droSec1
CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAATGGCAGT-----TC-CACT-GCACA--AAAGCTTTATCGAA----------------GATTCT---TCTCTTGCAGGGATCGGATTCGCACSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTAG-----------GATTCC-AATGTAATTC-TACT-GCGAA--ACAGCTTCATCGAA----------------GGTTCT---TCTCTTGCAGGGATCGGATTCGCACSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
CGTGGACTGGTTTGTGTGAGTATGG-----AT------CCGATTCA-----------GAATGCTGAT-----TC-CACT-GCGAA--GAAGCTTCATCGAA----------------GGGGCT---TCTCTTGCAGGGATCGGATTCGCACSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droEug1
CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GACTAATTAC-----TC-CCCC-GAAGA--AGTCGCTTAACAAA-G--------------GACTCT---GTTCTTGCAGGGATCGCATTCGCACSizeHit CountTotal Norm
droBia1
CGTGGACTGGTTTGTGTGAGTATGG-----AT------CTGATTTC-----------GAGTGGTTAT-----CG-CACG-GGGAA--AGCCACTAATGCAA-G--------------GGATCT---TGTGTTGCAGGGATCGGATTCGGACSizeHit CountTotal Norm
droTak1
CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAGTGGCTAT-----CCTCATT-AGGTA--GATGACTAACCCAA-G--------------GAATCTTGTCTTGTCGCAGGGATCGGATTCGCACSizeHit CountTotal Norm
droEle1
CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GTTTGTTTTT-----CT-CAAC-CGAAT--G----GTAACCTAC----------------AATTTA---ACATTTCTAGGGATCGGATTCGCACSizeHit CountTotal Norm
droRho1
CGTGGATTGGTTTGTGTGAGTATGG-----AT------CTGATTTG-----------GAACATCTTT-----CT-GGGG-GCAAT--CATAATTTATACAA----------------TATTTG---GGATTTCCAGGGACCGGATTCGCACSizeHit CountTotal Norm
droFic1
CGTGGACTGGTTTGTGTGAGTACGG-----AT------CTGGCTTT-----------GGTTGC-GGT-T---AA-CCCT-GGGGAGTAGTGAGTAATGTGG----------------GCCTTC---CACTTTTCAGGGACAGGATTCGGACSizeHit CountTotal Norm
droKik1
CGTGGACTGGTTTGTGTGAGTATGA-----AGGGGGT---TTTCTG-------------------GT-----AT-CCTTGAGGGG--GATATTTGACCTAA-AGGGAT----------TATGT---TTTCCTAAAGGGATCGAATTCGCACSizeHit CountTotal Norm
droAna3
CGTGGACTGGTTTGTGTGAGTATGA-----GA------TGGATGGAGGGCTCAGTCCGTGTAG-------------------------TAACC-------------------------ACATC---CCCTTTCCAGAGACCGCATCCGCACSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
.......................GA-----GA------xGGATGGAGGGGT....................................................................................................1612.000.000.002.000.00
...............GTGAGTATGA-----GA------TGGATGG..........................................................................................................1911.000.001.000.000.00
....................GATGA-----GA------xGGATGGAGGGC.....................................................................................................1811.000.001.000.000.00
.......................................CGATGGTGGGCTCAGTCCG.............................................................................................1911.000.001.000.000.00
droBip1
CGTCGACTGGTTTGTGTGAGTATGG-----GA------CCCAGTCC-----------GTGTGT--------------------------------------AAACCACTGTT--ATAATCCAC---TTCCCTCCAGAGATCGCATCCGCACSizeHit CountTotal Norm
dp4
CGTCGACTGGTTTGTGTAAGTCCTG-----A-----------TCCC-----------GACTC-----------------------TC----CTCC----TTAGAGCTTCGCTTCATTGTGTCC---TTTGCTGCAGCGACCGCATTCGGACSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
CGTCGACTGGTTTGTGTAAGTCCTG-----A-----------TCCC-----------GACTC-----------------------TC----CTCC----TTAGAGCTTCGCTTCATTGTGTCC---TTTGCTGCAGCGACCGCATCCGGACSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
CGTGGATTGGTTGCTGTAAGCAATATAT--AT------CTCTTTTG-----------CATAAT-TGT---------ATA-ATGCC---------AACTGCT------------------AATT---TATTTTCCAGGGATCGGTTCCGCACSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
CGTGGATTGGTTGCTGGA.....................................................................................................................................1811.000.000.000.001.00
droVir3
TGTCGACTGGCTGCTGTATGTAAAT-----GC------TAGAACTT-----------TATGT-----------------------TT----GGTC----CTGGATATACATTTTCTGTTCGAT---TAATTTTTAGTGATCGTTTCCGCACSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
TGTCGATTGGCTACTGTATGTAGATGTC--AA---AATTTGTACTT-----------GACTGT-----------------------T----ATTTATTGAA-----------------ATTTG---ATTGTCTTAGGGATCGTTTCCGTACSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
..........CTACTGTGTGTAGATCTC--AA---A...................................................................................................................2111.001.000.000.000.00
droGri2
TGTCGATTGGTTTGTGTAAGTACTGGG-GGAGGGGAT-----TATG-----------GATTA-----------------------TC----CCAA----ATATAGTTTTGAATTTATAAATTC---TGATTTAAAGTGATCGCATTCGCACSizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:31:10 EDT