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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-4915

chrX:29772-29889 +

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

mirtron

Legend:

   mature strand at position 29772-29796
   star strand at position 29868-29889
   mutations
   read mismatches

Notes: "droPer1's intron may be too long, however lastz only reported one piece vs. two for the other long introns."


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

Visually pleasing best hits from LASTZ and MAF


Species Coordinate Source Confidence Alignment
dm3 chrX:29757-29904 + 1 GAAAATGCCACCCAGGTGAGAAA-AAGTA-------------GTAAATTAAGCAT---ATCACGCAAG-----GACAAACATTAAGTTAAGG----------CCTAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TC--AA----TCCTACTTATGCCTC-TTATT---CTT---CT-TTTCTCAGACCTCCGCCAAAGAA
droSim1 chrX:14351-14498 + LASTZ 5 GAAAATGCCACCCAGGTGAGAAA-AAGTA-------------GAAAATTAAGCAT---ATCGCGCAAG-----GACAAGTATTAAGTAAAGT----------TATAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TG--CAT----TCTACTTATGCCTC-TTATT---CTT---TT-TTTCCCAGACCTCCGCCAAAGAA
droSec1 super_108:19641-19788 + LASTZ 5 GAAAATGCCACCCAGGTGAGAAA-AAGTA-------------GAAAATTAAGCAT---ATCACGCAAG-----GACAAGTATTAAGTAAAGT----------TATAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TG--CAT----TCTCCTTATGCCTC-TTATT---CTT---TT-TTTCCCAGACCTCCGCCAAAGAA
droYak2 chrX:20604-20735 + LASTZ 5 GAAAATGCCACCCAGGTGAGAGA-ACTAA-------------GTAAAATAAAAAT---ATCCTGCCAA-----G-----TTAAAAGTGAAATCTTATAATTGCAT------------------------------------------------------------------------------------------------------AG--TTTTCCTACTAATGTCCCTTTCTT---CTT---CT-TTTCCCAGACCTCCGCCGAAGAA
droEre2 scaffold_4644:14892-15014 + LASTZ 5 GAAAATGCCGCCCAGGTGAGAAA-ATTTA-------------GTCAAATAAGCATCTTATCCTGCAAA-----GAA-------AAGTTAACT----------TAT-----------------------------------------------------------------------------------------------------AAG--TTTCCCTACTAATGCCCC-TTTTT---CTT---CT-TTTCCCAGACCTCCGCCAAAGAA
droEug1 scf7180000409277:365472-365581 + LASTZ 5 GAAAATGCCACCCAGGTGAGTGA-ACTATGAGCTATGAACTA----T-------------------------------------GTCTAGGT----------AGT-----------------------------------------------------------------------------------------------------AGT--TACCCTTACTAATATCTC-TCCTT---TTTGCATT-CATTGCAGACCTCCACCAAAGAA
droBia1 scf7180000301760:995900-995994 + LASTZ 5 GAAAATGCCACCCAGGTGAGCCA-GTT------------------------------------------------------TTAAGTGATTC----------TAC-----------------------------------------------------------------------------------------------------CGA--TTTCCCTACCAATAACCCCGCCTC---TTC---GC-CCCCACAGACCTCCGCCAAAGAA
droTak1 scf7180000415151:113068-113158 - LASTZ 5 GAAAATGCCACCCAGGTGAATAA-CCCATTTAAT-TATATAA----CCTATAA-------------------------------------------------------------TTTACTA-------------------------AGAA-------------------------------------------------------------------------AA-------ACC---CTC---TC-TTTCACAGACCTCCGCCAAAGAA
droEle1 scf7180000491011:1024807-1024905 + LASTZ 5 GAAAATGCCACCCAGGTGAGTGA-ACCAT-------------GTGGGTTAATCCT---GTAGAGGAAGCTTGGGCCAGGCCTCAAGAGACAT----------TAGGTTT-----------------------------C----GATT------------------------------------TAATA---------------G------------------------------C------------------------------TGGTA
droRho1 scf7180000779506:817615-817802 + LASTZ 5 CA------------GTTGAGAAATGAATA-------------GAAGATTAAACAC---CACCTACAAA-----TTCGATTATTTAGTGATTT----------TCC---------------CACTTTTACATTAGCTTAGAACCTAATTCCTTACTCACGATATATCTAAAAATGTTCCATTTGTGATTTCCCAATTTTATACAT----G------TACATGTACG-------CTT---GTT---CC-ATCTGCAGACCTCCGCCAAAGAA
droFic1 scf7180000453927:476227-476337 + LASTZ 5 GAAAATGCCACCAAGGTGAGCAA-TACCT-------------TCCTGACAATCCT---CTCTAG----------------------------------------------------------------------------------------------------------TTTGGTTTTTTTGTGAATA--------------T----GT----TCTTACATATG-------TTT---TAT---AC-CCTCGCAGACCTCCGCCAAAGAA
droKik1 scf7180000302610:258637-258672 + LASTZ 5 CT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C-TTCCC---CCT---CT-TCCTACAGACCTCCGCCCAAGAA
droAna3 scaffold_12929:1781922-1782010 - LASTZ 5 AGAAATGCCACCCAGGTGAGTCT-GTCTAGAGTT-T-G----ATGGGATTGGA-----------------------------------------------------GTT-----------------------------G----AAAT------------------------------------TAATG---------------G------------------------------A---TTG---TG-ATTTTCAGACCTCCGCCAAAGAA
droBip1 scf7180000396543:239472-239562 - LASTZ 5 GAAAATGCCACCCAGGTGAGTCT-ATCGCGAGTC-TGGATGG----GATTGGG-----------------------------------------------------ATT-----------------------------G----GAAT-------------------------------------------------------------------------TAATG-------ATT---CAT---TA-TGTTGCAGACCTCCGCCAAAGAA
dp4 chrXL_group1a:594378-594471 + LASTZ 5 GAAAATGCCACCCAGGTGAGTGT-CCGAGGTGCC-T-------------------------------------------------------T----------CAA-----------------------------------------------------------------------------------------------------TGG--ACTACTGACCAATATCGTCTT--TGATCCT---TT-CCCGGCAGACCTCCTCCAAAGAA
droPer1 super_157:12433-12452 + LASTZ 0 GAAAAAGCCACCCAGGTGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 scaffold_181150:2495748-2495847 + LASTZ 5 GAAAATGCCACCAAGGTGAGTGA-GATAA-------------GTTAT------------------------------------------------------------TTCCTTTTTTTCTC------------------------------A----------------------C-----------------------------AG--TTA----A---CTAATTACCGTTTCCA---CTT---CTTATTTTCAGGCCACCGCCTAAGGC
droVir3 scaffold_12928:440188-440230 + LASTZ 5 GAAAATGCCACCCAGGTAAATGC-GCGTA------------------------------------------------------TGTTGATTA--------------------------------------------------------------------------------------------------------------------------------------------------------------ACCA--------------GA
droMoj3 scaffold_6328:1398758-1398785 + LASTZ 5 CA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---CC-CATTGCAGACCGCCGCCAAAGAA
droGri2 scaffold_15203:6869198-6869248 + LASTZ 5 TATTTTTG--------------------------------------------------------------------------------------------------TTT-----------------------------T----TTTT------------------------------------TGATT---------------T------------------------------G---TTG---TT-ATCTGCAGACCGCCGCCAAAGAA

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 GAAAATGCCACCCAGGTGAGAAA-AAGTA-------------GTAAATTAAGCAT---ATCACGCAAG-----GACAAACATTAAGTTAAGG----------CCTAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TC--AA----TCCTACTTATGCCTC-TTATT---CTT---CT-TTTCTCAGACCTCCGCCAAAGAA
droSim1 GAAAATGCCACCCAGGTGAGAAA-AAGTA-------------GAAAATTAAGCAT---ATCGCGCAAG-----GACAAGTATTAAGTAAAGT----------TATAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TG--CAT----TCTACTTATGCCTC-TTATT---CTT---TT-TTTCCCAGACCTCCGCCAAAGAA
droSec1 GAAAATGCCACCCAGGTGAGAAA-AAGTA-------------GAAAATTAAGCAT---ATCACGCAAG-----GACAAGTATTAAGTAAAGT----------TATAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TG--CAT----TCTCCTTATGCCTC-TTATT---CTT---TT-TTTCCCAGACCTCCGCCAAAGAA
droYak2 GAAAATGCCACCCAGGTGAGAGA-ACTAA-------------GTAAAATAAAAAT---ATCCTGCCAA-----G-----TTAAAAGTGAAATCTTATAATTGCAT------------------------------------------------------------------------------------------------------AG--TTTTCCTACTAATGTCCCTTTCTT---CTT---CT-TTTCCCAGACCTCCGCCGAAGAA
droEre2 GAAAATGCCGCCCAGGTGAGAAA-ATTTA-------------GTCAAATAAGCATCTTATCCTGCAAA-----GAA-------AAGTTAACT----------TAT-----------------------------------------------------------------------------------------------------AAG--TTTCCCTACTAATGCCCC-TTTTT---CTT---CT-TTTCCCAGACCTCCGCCAAAGAA
droEug1 GAAAATGCCACCCAGGTGAGTGA-ACTATGAGCTATGAACTA----T-------------------------------------GTCTAGGT----------AGT-----------------------------------------------------------------------------------------------------AGT--TACCCTTACTAATATCTC-TCCTT---TTTGCATT-CATTGCAGACCTCCACCAAAGAA
droBia1 GAAAATGCCACCCAGGTGAGCCA-GTT------------------------------------------------------TTAAGTGATTC----------TAC-----------------------------------------------------------------------------------------------------CGA--TTTCCCTACCAATAACCCCGCCTC---TTC---GC-CCCCACAGACCTCCGCCAAAGAA
droTak1 GAAAATGCCACCCAGGTGAATAA-CCCATTTAAT-TATATAA----CCTATAA-------------------------------------------------------------TTTACTA-------------------------AGAA-------------------------------------------------------------------------AA-------ACC---CTC---TC-TTTCACAGACCTCCGCCAAAGAA
droEle1 GAAAATGCCACCCAGGTGAGTGA-ACCAT-------------GTGGGTTAATCCT---GTAGAGGAAGCTTGGGCCAGGCCTCAAGAGACAT----------TAGGTTT-----------------------------C----GATT------------------------------------TAATA---------------G------------------------------C------------------------------TGGTA
droRho1 CA------------GTTGAGAAATGAATA-------------GAAGATTAAACAC---CACCTACAAA-----TTCGATTATTTAGTGATTT----------TCC---------------CACTTTTACATTAGCTTAGAACCTAATTCCTTACTCACGATATATCTAAAAATGTTCCATTTGTGATTTCCCAATTTTATACAT----G------TACATGTACG-------CTT---GTT---CC-ATCTGCAGACCTCCGCCAAAGAA
droFic1 GAAAATGCCACCAAGGTGAGCAA-TACCT-------------TCCTGACAATCCT---CTCTAG----------------------------------------------------------------------------------------------------------TTTGGTTTTTTTGTGAATA--------------T----GT----TCTTACATATG-------TTT---TAT---AC-CCTCGCAGACCTCCGCCAAAGAA
droKik1 CT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C-TTCCC---CCT---CT-TCCTACAGACCTCCGCCCAAGAA
droAna3 AGAAATGCCACCCAGGTGAGTCT-GTCTAGAGTT-T-G----ATGGGATTGGA-----------------------------------------------------GTT-----------------------------G----AAAT------------------------------------TAATG---------------G------------------------------A---TTG---TG-ATTTTCAGACCTCCGCCAAAGAA
droBip1 GAAAATGCCACCCAGGTGAGTCT-ATCGCGAGTC-TGGATGG----GATTGGG-----------------------------------------------------ATT-----------------------------G----GAAT-------------------------------------------------------------------------TAATG-------ATT---CAT---TA-TGTTGCAGACCTCCGCCAAAGAA
dp4 GAAAATGCCACCCAGGTGAGTGT-CCGAGGTGCC-T-------------------------------------------------------T----------CAA-----------------------------------------------------------------------------------------------------TGG--ACTACTGACCAATATCGTCTT--TGATCCT---TT-CCCGGCAGACCTCCTCCAAAGAA
droWil1 GAAAATGCCACCAAGGTGAGTGA-GATAA-------------GTTAT------------------------------------------------------------TTCCTTTTTTTCTC------------------------------A----------------------C-----------------------------AG--TTA----A---CTAATTACCGTTTCCA---CTT---CTTATTTTCAGGCCACCGCCTAAGGC
droVir3 GAAAATGCCACCCAGGTAAATGC-GCGTA------------------------------------------------------TGTTGATTA--------------------------------------------------------------------------------------------------------------------------------------------------------------ACCA--------------GA
droMoj3 CA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---CC-CATTGCAGACCGCCGCCAAAGAA
droGri2 TATTTTTG--------------------------------------------------------------------------------------------------TTT-----------------------------T----TTTT------------------------------------TGATT---------------T------------------------------G---TTG---TT-ATCTGCAGACCGCCGCCAAAGAA

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 None None

Small RNA-seq read pileup

Species Alignment
droSim1
GAAAATGCCACCCAGGTGAGAAA-AAGTA-------------GAAAATTAAGCAT---ATCGCGCAAG-----GACAAGTATTAAGTAAAGT----------TATAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TG--CAT----TCTACTTATGCCTC-TTATT---CTT---TT-TTTCCCAGACCTCCGCCAAAGAASizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
droSec1
GAAAATGCCACCCAGGTGAGAAA-AAGTA-------------GAAAATTAAGCAT---ATCACGCAAG-----GACAAGTATTAAGTAAAGT----------TATAGTTCCTATTATACTA-------------------------GGAATA----------------------C-----------------------------TG--CAT----TCTCCTTATGCCTC-TTATT---CTT---TT-TTTCCCAGACCTCCGCCAAAGAASizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
............................................................................AAGTxTTAAGTGAAGT----------TAT.....................................................................................................................................................................1811.000.000.001.00
.................TAGAAA-AAGTA-------------GAAAAGT.............................................................................................................................................................................................................................1811.000.000.001.00
........................................................................................................................................................................................................................................................CACCCAGACCTCCGCCAAAG..2011.000.001.000.00
droYak2
GAAAATGCCACCCAGGTGAGAGA-ACTAA-------------GTAAAATAAAAAT---ATCCTGCCAA-----G-----TTAAAAGTGAAATCTTATAATTGCAT------------------------------------------------------------------------------------------------------AG--TTTTCCTACTAATGTCCCTTTCTT---CTT---CT-TTTCCCAGACCTCCGCCGAAGAASizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
..................AGTGA-ACTAA-------------GTGAAATAAA..........................................................................................................................................................................................................................2011.000.000.001.000.000.00
...................GTGA-ACTAA-------------GTGAAATAAA..........................................................................................................................................................................................................................1911.001.000.000.000.000.00
...................................................................................AAGTGAAATTTTATATTT.........................................................................................................................................................................1811.001.000.000.000.000.00
droEre2
GAAAATGCCGCCCAGGTGAGAAA-ATTTA-------------GTCAAATAAGCATCTTATCCTGCAAA-----GAA-------AAGTTAACT----------TAT-----------------------------------------------------------------------------------------------------AAG--TTTCCCTACTAATGCCCC-TTTTT---CTT---CT-TTTCCCAGACCTCCGCCAAAGAASizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
.................................................................AAA-----GAA-------AATTTAATT----------TAT-----------------------------------------------------------------------------------------------------................................................................1830.330.000.000.000.33
...........................................................................................................................................................................................................................................................CCAGACCTTCGCCAAGGA.1811.000.000.000.001.00
droEug1
GAAAATGCCACCCAGGTGAGTGA-ACTATGAGCTATGAACTA----T-------------------------------------GTCTAGGT----------AGT-----------------------------------------------------------------------------------------------------AGT--TACCCTTACTAATATCTC-TCCTT---TTTGCATT-CATTGCAGACCTCCACCAAAGAASizeHit CountTotal Norm
droBia1
GAAAATGCCACCCAGGTGAGCCA-GTT------------------------------------------------------TTAAGTGATTC----------TAC-----------------------------------------------------------------------------------------------------CGA--TTTCCCTACCAATAACCCCGCCTC---TTC---GC-CCCCACAGACCTCCGCCAAAGAASizeHit CountTotal Norm
droTak1
GAAAATGCCACCCAGGTGAATAA-CCCATTTAAT-TATATAA----CCTATAA-------------------------------------------------------------TTTACTA-------------------------AGAA-------------------------------------------------------------------------AA-------ACC---CTC---TC-TTTCACAGACCTCCGCCAAAGAASizeHit CountTotal Norm
droEle1
GAAAATGCCACCCAGGTGAGTGA-ACCAT-------------GTGGGTTAATCCT---GTAGAGGAAGCTTGGGCCAGGCCTCAAGAGACAT----------TAGGTTT-----------------------------C----GATT------------------------------------TAATA---------------G------------------------------C------------------------------TGGTASizeHit CountTotal Norm
droRho1
CA------------GTTGAGAAATGAATA-------------GAAGATTAAACAC---CACCTACAAA-----TTCGATTATTTAGTGATTT----------TCC---------------CACTTTTACATTAGCTTAGAACCTAATTCCTTACTCACGATATATCTAAAAATGTTCCATTTGTGATTTCCCAATTTTATACAT----G------TACATGTACG-------CTT---GTT---CC-ATCTGCAGACCTCCGCCAAAGAASizeHit CountTotal Norm
droFic1
GAAAATGCCACCAAGGTGAGCAA-TACCT-------------TCCTGACAATCCT---CTCTAG----------------------------------------------------------------------------------------------------------TTTGGTTTTTTTGTGAATA--------------T----GT----TCTTACATATG-------TTT---TAT---AC-CCTCGCAGACCTCCGCCAAAGAASizeHit CountTotal Norm
droKik1
CT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C-TTCCC---CCT---CT-TCCTACAGACCTCCGCCCAAGAASizeHit CountTotal Norm
droAna3
AGAAATGCCACCCAGGTGAGTCT-GTCTAGAGTT-T-G----ATGGGATTGGA-----------------------------------------------------GTT-----------------------------G----AAAT------------------------------------TAATG---------------G------------------------------A---TTG---TG-ATTTTCAGACCTCCGCCAAAGAASizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
.................GAGTCA-GTCTAGAGTT-T-A----....................................................................................................................................................................................................................................1811.000.001.000.000.00
...................................................GA-----------------------------------------------------GGT-----------------------------G----AAAT------------------------------------TATTG---------------G------------------------------A---T...............................1811.000.000.001.000.00
...............................................................................................................................................AAAT------------------------------------TAATG---------------G------------------------------A---TTG---TG-ATTTTCA................2311.000.000.001.000.00
..........................................ATGGGATTGGA-----------------------------------------------------GTT-----------------------------G----GAGT------------------------------------T......................................................................................2011.000.000.001.000.00
.............................GTGTT-T-G----ATGGGATTGT..........................................................................................................................................................................................................................1711.000.000.001.000.00
droBip1
GAAAATGCCACCCAGGTGAGTCT-ATCGCGAGTC-TGGATGG----GATTGGG-----------------------------------------------------ATT-----------------------------G----GAAT-------------------------------------------------------------------------TAATG-------ATT---CAT---TA-TGTTGCAGACCTCCGCCAAAGAASizeHit CountTotal Norm
dp4
GAAAATGCCACCCAGGTGAGTGT-CCGAGGTGCC-T-------------------------------------------------------T----------CAA-----------------------------------------------------------------------------------------------------TGG--ACTACTGACCAATATCGTCTT--TGATCCT---TT-CCCGGCAGACCTCCTCCAAAGAASizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
GAAAAAGCCACCCAGGTGAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
GAAAATGCCACCAAGGTGAGTGA-GATAA-------------GTTAT------------------------------------------------------------TTCCTTTTTTTCTC------------------------------A----------------------C-----------------------------AG--TTA----A---CTAATTACCGTTTCCA---CTT---CTTATTTTCAGGCCACCGCCTAAGGCSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
droVir3
GAAAATGCCACCCAGGTAAATGC-GCGTA------------------------------------------------------TGTTGATTA--------------------------------------------------------------------------------------------------------------------------------------------------------------ACCA--------------GASizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
CA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T---CC-CATTGCAGACCGCCGCCAAAGAASizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
TATTTTTG--------------------------------------------------------------------------------------------------TTT-----------------------------T----TTTT------------------------------------TGATT---------------T------------------------------G---TTG---TT-ATCTGCAGACCGCCGCCAAAGAASizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:20:13 EDT