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

View all possible LASTZ hits (20-flies)

sblock97631

chr3L:4091108-4091180 +

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

three_prime_UTR

Legend:

   mature strand at position 4091154-4091176
   star strand at position 4091122-4091142
   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 chr3L:4091093-4091195 + 1 CAG--AATCACGC-AGGGCTTCCAGTGCGTCGCCTC--------GGAGGATGAGGATGCCC----TCCCAAAAGG------------------CATCCGAAATCCCCGG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droSim1 chr3L:3630503-3630604 + LASTZ 4 CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TCCCAAA-GG------------------GATTCGTAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droSec1 super_2:4083741-4083842 + LASTZ 1 CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TACCAAA-GG------------------GATTCGTAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droYak2 chr3L:4661209-4661310 + LASTZ 1 CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----AACCAAA-GG------------------AATCCAAAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGATGA-----T
droEre2 scaffold_4784:6799989-6800090 + LASTZ 1 CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TCCCAAG-GG------------------AGTCCAAAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droEug1 scf7180000409466:1855824-1855927 + LASTZ 4 CAA--GATCACAA-AGGGCTTCCAGTGGGCCGTCTA--------GGAGGATTAGGGTCTTTA---TACCAAATGG------------------GATCCGAATTCACCAG-GGCG------GACACAACCCCTAATT--------------AGGTGA-----T
droBia1 scf7180000302428:785187-785288 + LASTZ 4 CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATTAGGATCTTT-----CCTAAT-GC-----------------AGATCCGAATTCC-CCG-GGCG------CGCACAACCCGTATTTA-------------AGGTGA-----T
droTak1 scf7180000415778:104468-104585 - LASTZ 4 CAA--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCTTT----TCCCAAATGG------------------GATCCTATATCCACCG-GACG------GACACAACCCGTATTG----ATTAGTAGTTAAGTGAGCTTCT
droEle1 scf7180000491249:4938292-4938395 + LASTZ 4 CAG--AATCACAC-AGGGCTTCCAGTGCGCCAACTC--------GGAGGACGAGGATCCCT----AGCCAAAGGG------------------GATCCAAAGTCCTCCGTGGAG------GACACAACCCAATTTT--------------AAGTGA-----T
droRho1 scf7180000779198:68875-68978 - LASTZ 4 CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----AGCCAAAGGG------------------GATCCGAACTCATCCGTGGGG------GTCACAACCCATATTT--------------AAGTGA-----T
droFic1 scf7180000454113:1306944-1307044 + LASTZ 4 CAG--AATCACAA-AGGGCTTCCAGTGCGCCGTTCC--------GGAGGATGTGGATCCTG----TC-GAAAGGG------------------GATCCTGCTACCTCCG-GACG------GACACAACCCGTAATT--------------AGGTGA------
droKik1 scf7180000302388:258053-258145 - LASTZ 4 CAG--AATCACCC-AGGGCTTCCAGTGCTCC-CTTG--------GGGGGACGAGGATCTTC-------------G------------------GATCCTTCAATTCCCA-AGAG------GACACAACCCGTAATT--------------AAGTGA-----T
droAna3 scaffold_13337:7133496-7133604 + LASTZ 1 CAA--GATCACAA-AGGGCTTCCAGTGTTCCGCTTC--------GGAGGACGAGGCTTCCT------CCAAA-GGAATTTGA--AG-------GATCCTCAACTTCT-GTTGTG------GGCACAACCCATAATT--------------AAGTGA-----T
droBip1 scf7180000396418:140234-140343 + LASTZ 4 CAA-AGATCACAA-AGGGCTTCCAGTGTTCCGCTTC--------GGAGGACGAGA-TATCC----T-TTAAA-GAAATTTGA--CG-------GATCCTCAACTTCC-GTTGTG------GGCACAACCCATAATT--------------AAGTGA-----T
dp4 chrXR_group6:6380845-6380933 - LASTZ 1 CAG--AATCACGC-AGGGCTTCCAGTGTCCCCACGC--------TGGATAGAAGGATCACTC---ATCCCTTGGG------------------CATCCGG-------CG-TGGG------GGCACAACCCACAGT---------------------------
droPer1 super_82:217037-217125 + LASTZ 1 CAG--AATCACGC-AGGGCTTCCAGTGTCCCCTCGC--------TGGATAGAAGGATCACTC---ATCCCTTGGG------------------CATCCGG-------CG-TGGG------GGCACAACCCACAGT---------------------------
droWil1 scaffold_180949:5996173-5996259 - LASTZ 1 CAA--AATCACTTAAGGGCTTCCAGTGCATTTTTCT---C----TGA-GCCGAGTC------------------AA-TT-----CTCGGT---TCGCAAG-------AA-TTTTGCCACAAA--CC-CCCC----T--------------A----A-----A
droVir3 scaffold_13049:15328257-15328357 - LASTZ 3 CAA-AAATCACAAAAGGGCTTCCAGTGCGGCATTGGCATC--------CATG-GGATACTG----TT-------AA-TT-----CG--GT---TAGC--CAGATGCA-GATGTCAGCACAAATAAAACC------T--------------AAG-GA-----T
droMoj3 scaffold_6680:21529581-21529704 + LASTZ 4 CAACAAATCACAAAAGGGCTTCCAGTGCGGCGCG-GTATCTATATCTGTATCAGGGTCTATA---T--------AACTCCGATATA--G-C--TCTT--CAGATGCC-GATGCCTGCACAAATACAAACC-----TAAGGATT-------AG-TTG-----T
droGri2 scaffold_15110:19733397-19733505 - LASTZ 4 CAA--AATCACAAAAGGGCTTCCAGTGCGGCATTGGTATC----TGA----AGGACATGGTGATATATCAAATAG---------------CCATATCCAGA--TCCA-GTTGTTGGCACAAATACAAACC-----T--------------AAG-GA-----T

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 CAG--AATCACGC-AGGGCTTCCAGTGCGTCGCCTC--------GGAGGATGAGGATGCCC----TCCCAAAAGG------------------CATCCGAAATCCCCGG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droSim1 CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TCCCAAA-GG------------------GATTCGTAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droSec1 CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TACCAAA-GG------------------GATTCGTAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droYak2 CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----AACCAAA-GG------------------AATCCAAAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGATGA-----T
droEre2 CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TCCCAAG-GG------------------AGTCCAAAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----T
droEug1 CAA--GATCACAA-AGGGCTTCCAGTGGGCCGTCTA--------GGAGGATTAGGGTCTTTA---TACCAAATGG------------------GATCCGAATTCACCAG-GGCG------GACACAACCCCTAATT--------------AGGTGA-----T
droBia1 CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATTAGGATCTTT-----CCTAAT-GC-----------------AGATCCGAATTCC-CCG-GGCG------CGCACAACCCGTATTTA-------------AGGTGA-----T
droTak1 CAA--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCTTT----TCCCAAATGG------------------GATCCTATATCCACCG-GACG------GACACAACCCGTATTG----ATTAGTAGTTAAGTGAGCTTCT
droEle1 CAG--AATCACAC-AGGGCTTCCAGTGCGCCAACTC--------GGAGGACGAGGATCCCT----AGCCAAAGGG------------------GATCCAAAGTCCTCCGTGGAG------GACACAACCCAATTTT--------------AAGTGA-----T
droRho1 CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----AGCCAAAGGG------------------GATCCGAACTCATCCGTGGGG------GTCACAACCCATATTT--------------AAGTGA-----T
droFic1 CAG--AATCACAA-AGGGCTTCCAGTGCGCCGTTCC--------GGAGGATGTGGATCCTG----TC-GAAAGGG------------------GATCCTGCTACCTCCG-GACG------GACACAACCCGTAATT--------------AGGTGA------
droKik1 CAG--AATCACCC-AGGGCTTCCAGTGCTCC-CTTG--------GGGGGACGAGGATCTTC-------------G------------------GATCCTTCAATTCCCA-AGAG------GACACAACCCGTAATT--------------AAGTGA-----T
droAna3 CAA--GATCACAA-AGGGCTTCCAGTGTTCCGCTTC--------GGAGGACGAGGCTTCCT------CCAAA-GGAATTTGA--AG-------GATCCTCAACTTCT-GTTGTG------GGCACAACCCATAATT--------------AAGTGA-----T
droBip1 CAA-AGATCACAA-AGGGCTTCCAGTGTTCCGCTTC--------GGAGGACGAGA-TATCC----T-TTAAA-GAAATTTGA--CG-------GATCCTCAACTTCC-GTTGTG------GGCACAACCCATAATT--------------AAGTGA-----T
dp4 CAG--AATCACGC-AGGGCTTCCAGTGTCCCCACGC--------TGGATAGAAGGATCACTC---ATCCCTTGGG------------------CATCCGG-------CG-TGGG------GGCACAACCCACAGT---------------------------
droPer1 CAG--AATCACGC-AGGGCTTCCAGTGTCCCCTCGC--------TGGATAGAAGGATCACTC---ATCCCTTGGG------------------CATCCGG-------CG-TGGG------GGCACAACCCACAGT---------------------------
droWil1 CAA--AATCACTTAAGGGCTTCCAGTGCATTTTTCT---C----TGA-GCCGAGTC------------------AA-TT-----CTCGGT---TCGCAAG-------AA-TTTTGCCACAAA--CC-CCCC----T--------------A----A-----A
droVir3 CAA-AAATCACAAAAGGGCTTCCAGTGCGGCATTGGCATC--------CATG-GGATACTG----TT-------AA-TT-----CG--GT---TAGC--CAGATGCA-GATGTCAGCACAAATAAAACC------T--------------AAG-GA-----T
droMoj3 CAACAAATCACAAAAGGGCTTCCAGTGCGGCGCG-GTATCTATATCTGTATCAGGGTCTATA---T--------AACTCCGATATA--G-C--TCTT--CAGATGCC-GATGCCTGCACAAATACAAACC-----TAAGGATT-------AG-TTG-----T
droGri2 CAA--AATCACAAAAGGGCTTCCAGTGCGGCATTGGTATC----TGA----AGGACATGGTGATATATCAAATAG---------------CCATATCCAGA--TCCA-GTTGTTGGCACAAATACAAACC-----T--------------AAG-GA-----T

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
CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TCCCAAA-GG------------------GATTCGTAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----TSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
.............................................................................................GATTCGTAGCCCTCCG-GACG------GAC.......................................2312.000.000.000.002.00
..................CTTCCAGGACGCCGCCTC--------......................................................................................................................1811.000.000.000.001.00
...................................C--------GGAGGATGAGGATTCCC----.................................................................................................1811.000.000.001.000.00
.................................................................................................CGTAGCCCTCCG-GACG------GACACAAC..................................2411.000.000.000.001.00
.....................................................................AAA-GG------------------GATTCGTAGCCCTCCG-GACG------GAC.......................................2811.000.000.000.001.00
droSec1
CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TACCAAA-GG------------------GATTCGTAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----TSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
...........................CGCCGCCTC--------GGAGGATGAGGAT.........................................................................................................2211.000.001.000.00
droYak2
CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----AACCAAA-GG------------------AATCCAAAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGATGA-----TSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
....................TCCAGTGCGCCGCCTC--------GGAGGATGAGG...........................................................................................................2711.000.000.001.000.000.00
.......................AGTGCGCCGxATC--------GGAGGAT...............................................................................................................1911.000.000.001.000.000.00
.....................CCAGTGCGCCGCCTC--------GGAGGATGAGG...........................................................................................................2611.000.000.001.000.000.00
......................CAGTGCGCCGCCTC--------GGAGGATGAGG...........................................................................................................2511.000.000.001.000.000.00
droEre2
CAG--AATCACGC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----TCCCAAG-GG------------------AGTCCAAAGCCCTCCG-GACG------GACACAACCCGTATTT--------------AGGTGA-----TSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
..............................CGCCTx--------GCAGGATGAGGAT.........................................................................................................1815.000.000.000.005.00
..........................GCGCCGCCTC--------GGAGGATGCGG...........................................................................................................2111.000.001.000.000.00
droEug1
CAA--GATCACAA-AGGGCTTCCAGTGGGCCGTCTA--------GGAGGATTAGGGTCTTTA---TACCAAATGG------------------GATCCGAATTCACCAG-GGCG------GACACAACCCCTAATT--------------AGGTGA-----TSizeHit CountTotal Norm
droBia1
CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATTAGGATCTTT-----CCTAAT-GC-----------------AGATCCGAATTCC-CCG-GGCG------CGCACAACCCGTATTTA-------------AGGTGA-----TSizeHit CountTotal Norm
droTak1
CAA--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCTTT----TCCCAAATGG------------------GATCCTATATCCACCG-GACG------GACACAACCCGTATTG----ATTAGTAGTTAAGTGAGCTTCTSizeHit CountTotal Norm
droEle1
CAG--AATCACAC-AGGGCTTCCAGTGCGCCAACTC--------GGAGGACGAGGATCCCT----AGCCAAAGGG------------------GATCCAAAGTCCTCCGTGGAG------GACACAACCCAATTTT--------------AAGTGA-----TSizeHit CountTotal Norm
droRho1
CAG--AATCACAC-AGGGCTTCCAGTGCGCCGCCTC--------GGAGGATGAGGATCCCC----AGCCAAAGGG------------------GATCCGAACTCATCCGTGGGG------GTCACAACCCATATTT--------------AAGTGA-----TSizeHit CountTotal Norm
droFic1
CAG--AATCACAA-AGGGCTTCCAGTGCGCCGTTCC--------GGAGGATGTGGATCCTG----TC-GAAAGGG------------------GATCCTGCTACCTCCG-GACG------GACACAACCCGTAATT--------------AGGTGA------SizeHit CountTotal Norm
droKik1
CAG--AATCACCC-AGGGCTTCCAGTGCTCC-CTTG--------GGGGGACGAGGATCTTC-------------G------------------GATCCTTCAATTCCCA-AGAG------GACACAACCCGTAATT--------------AAGTGA-----TSizeHit CountTotal Norm
droAna3
CAA--GATCACAA-AGGGCTTCCAGTGTTCCGCTTC--------GGAGGACGAGGCTTCCT------CCAAA-GGAATTTGA--AG-------GATCCTCAACTTCT-GTTGTG------GGCACAACCCATAATT--------------AAGTGA-----TSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
.......................AGTCTTCCGCTTC--------AGAGG.................................................................................................................1811.000.001.000.000.00
................GGCTTCCAGTGTTCCGCTTC--------GGAGGACGA.............................................................................................................2911.001.000.000.000.00
droBip1
CAA-AGATCACAA-AGGGCTTCCAGTGTTCCGCTTC--------GGAGGACGAGA-TATCC----T-TTAAA-GAAATTTGA--CG-------GATCCTCAACTTCC-GTTGTG------GGCACAACCCATAATT--------------AAGTGA-----TSizeHit CountTotal Norm
dp4
CAG--AATCACGC-AGGGCTTCCAGTGTCCCCACGC--------TGGATAGAAGGATCACTC---ATCCCTTGGG------------------CATCCGG-------CG-TGGG------GGCACAACCCACAGT---------------------------SizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
.............................................................C---ATCCCTTGGG------------------CATCCGG-------CG-T...................................................2111.001.000.000.000.00
.........................TGTCCCCACGC--------TGGATGGAAGGAT.........................................................................................................2411.001.000.000.000.00
droPer1
CAG--AATCACGC-AGGGCTTCCAGTGTCCCCTCGC--------TGGATAGAAGGATCACTC---ATCCCTTGGG------------------CATCCGG-------CG-TGGG------GGCACAACCCACAGT---------------------------SizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
CAG--AATCACGC-AGGGCTTCCA..........................................................................................................................................2112.000.000.000.000.002.00
..................................GC--------TGGATAGAAGGATCACTC---.................................................................................................2011.001.000.000.000.000.00
..............................................................................................ATCCTG-------CG-TGAG------GGCACAA...................................1911.000.000.000.001.000.00
...................TTCCAGTGGCCCCTGGC--------TG....................................................................................................................1911.000.000.000.000.001.00
droWil1
CAA--AATCACTTAAGGGCTTCCAGTGCATTTTTCT---C----TGA-GCCGAGTC------------------AA-TT-----CTCGGT---TCGCAAG-------AA-TTTTGCCACAAA--CC-CCCC----T--------------A----A-----ASizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
.......................AGTGCATTTTTCT---C----TGA-GC................................................................................................................1911.000.001.000.000.00
.........................TGAATTTTTCT---A----TGA-GCC...............................................................................................................1811.000.001.000.000.00
.........ACTTAAGCGTTTCCAGTGC......................................................................................................................................1911.000.001.000.000.00
............................ATTTTTCT---A----TGA-GCCTAG............................................................................................................1811.000.001.000.000.00
.......................ACTGAATTTTTCT---C----TGA-GCC...............................................................................................................2011.000.001.000.000.00
..............................................................................T-----CTCGGT---TCGCAAG-------AA-TTTTGCCACA..........................................2611.000.001.000.000.00
.......................................C----TGA-GCCGAGTC------------------AA-TT-----CTC...........................................................................1911.000.001.000.000.00
.......................ACTGCATTTTTCT---A----TGA-GCC...............................................................................................................2011.000.001.000.000.00
..............................TTTTCT---C----TGA-GCCGAGTC------------------AA-TT-----CTC...........................................................................2511.000.000.000.001.00
.......................ACTGCATTTTTCT---A----TGA-GC................................................................................................................1911.000.001.000.000.00
droVir3
CAA-AAATCACAAAAGGGCTTCCAGTGCGGCATTGGCATC--------CATG-GGATACTG----TT-------AA-TT-----CG--GT---TAGC--CAGATGCA-GATGTCAGCACAAATAAAACC------T--------------AAG-GA-----TSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
...................TTCCAGTGCGGCATTGGC.............................................................................................................................1811.000.000.001.000.000.00
droMoj3
CAACAAATCACAAAAGGGCTTCCAGTGCGGCGCG-GTATCTATATCTGTATCAGGGTCTATA---T--------AACTCCGATATA--G-C--TCTT--CAGATGCC-GATGCCTGCACAAATACAAACC-----TAAGGATT-------AG-TTG-----TSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
CAA--AATCACAAAAGGGCTTCCAGTGCGGCATTGGTATC----TGA----AGGACATGGTGATATATCAAATAG---------------CCATATCCAGA--TCCA-GTTGTTGGCACAAATACAAACC-----T--------------AAG-GA-----TSizeHit CountTotal NormV109
Male body
......................AAGTxCGGCATTGGTATC----TG....................................................................................................................1912.002.00

Generated: 04/20/2012 at 05:17:57 EDT