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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-312-as

chr2R:16471561-16471626 +

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

intergenic

Legend:

   mature strand at position 16471602-16471622
   star strand at position 16471565-16471586
   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 chr2R:16471546-16471641 + 1 GATTCGT-----------------------------------------TTTAAAGTAATCAGGCCGTC--------------TCAAGTGCAATACTAGTTAAAA----AATGCAGAATTGCCCTTGTGACGAACCAAATCGCTTCAAACTTAATT---------
droSim1 chr2R:15132834-15132929 + LASTZ 4 GATTCTT-----------------------------------------TTTAAAGTAATTCGGCCGTC--------------TCAAGTGCAATACAAGTTTAAA----AATGCAGAATTGCCCTTGTGACGAACCAAAACGCTTTAAACTTAATT---------
droSec1 super_1:14025748-14025843 + LASTZ 4 GATTCTT-----------------------------------------TTTAAAGTAATTCGGCCGTC--------------TCAAGTGCAATACAAGTTTAAA----AATGCAGAATTGCCCTTGTGACGAACCAAAACGCTTTAAACTTAATT---------
droYak2 chr2R:12724685-12724781 - LASTZ 5 GATTCGT-----------------------------------------TTAAAAGTAATCCGGCCGTC--------------TCAAGTGCAATACTAGCTTTAA---TAGTGCAGAATTGCTCCTGGGACGAACCGAAGCGCTTCAAACGCAATT---------
droEre2 scaffold_4845:10618147-10618242 + LASTZ 5 GTTTTGT-----------------------------------------TTAAAAGTAATCCGGCCGTC--------------TCAAGTGCAATACTAGCTTAAA----AATGCAGAATTGCTCCTGGTACGAACCGAAGCGCTTCAAACTTAATT---------
droEug1 scf7180000409474:1490038-1490133 - LASTZ 5 GTTTTGT----------------------------------------ATTTCAAGTCATCCGGCCGTC--------------TGAAGTGCAATTTTCTATT--G----ACTCTAAAATTGCACAAAAGGCGAACCGAAATACTAGAAATTTTATTT--------
droBia1 scf7180000302291:2816211-2816324 - LASTZ 5 AGTTTCT----------------ATGCACT----------TTCCTTGTTTTCAAGCACTCCGGCCGTC--------------TCAAGTGCAATTCTAGTCGGA-----AATACAGGATTGCTCCTGGGACGGACCGAAACGCCAAAAATATGCCTA--TAT---
droTak1 scf7180000415401:99973-100067 + LASTZ 5 GTTTCGT----------------------------------------ATTTAAAGTATTCCGGCCGTC--------------TCAAGTGCAATACTAGGTGAA-----AATTCAGAATTGCGCCTGAGACGGACCGGAACACCAGAAATAT-GTT---------
droEle1 scf7180000491201:736234-736328 + LASTZ 5 TTTTTAT-----------------------------------------TCCAAAGTGTTGCGGCCGTC--------------TCAAGTGCAATGCTAACCAGAA----AACGCAGAATTGCCCCATAGACGTACCGAAACACCAGAAAT-TAGTA---------
droRho1 scf7180000780104:82286-82422 + LASTZ 5 AATGCAAAAATAACTTTTT--CAATAAACTTGCTTAAATGTT-TTAAATCCAAAGTATTGCGGCCGTC--------------TCAAGTGCAATGCTAGCCAAGA--AAAACGAAGAATTGCTTTTGAGACGAGCCGAAACACCAGAAATTTGTTCG--------
droFic1 scf7180000454039:1776269-1776366 + LASTZ 5 ATA--AA-----------------------------------------TTTAAAGCATTTCGGCCGTC--------------TCAAGTGCAATGCTAGCCATAAAGTTAATTTAGTATTGCCACCCAAGACGACCGAAACACTCGAAATTGGTTT---------
droKik1 scf7180000302471:941817-941912 + LASTZ 5 GTTTTGG-----------------------------------------GCCGCCTTGATCTGGCCGTT--------------TCAAGTGCAATTCTGGCTATTA----ACCACAGATTTGCACCTCAAACAGCACAGACCTTTACGGCCGGAGCT---------
droAna3 scaffold_13266:4132676-4132765 - LASTZ 5 GCTTAGA-----------------------------------------TCCACTATATTTCGGCCGTC--------------TCAAGTGCAATACTTGTATAAA---AAACCAAGAGTTGCACTAGAGACGCACCGGAAAATTGTAGA----------------
droBip1 scf7180000396427:2575377-2575498 - LASTZ 5 CTTTCGGC---------TTG----------------TAGCTGCATAGATCCACAATATTCTGGCCGTC--------------TCGAGTGCAATTCTTGTTGGAA---AAACCAAGATTTGCACTGGAGATGACCCCGAAAATTGTAGACATAAATCCAAACACA
dp4 chr3:8679756-8679828 - LASTZ 0 TGTTGAAC---------CCA----------------GC---------AGTAGGCACTTTCAGGCCAGT--------------GGGTGTGCAATACTGGTGAAAT--ACAACACAGTATTGCCC-----------------------------------------
droPer1 super_4:2566585-2566655 - LASTZ 0 ATTCGTAT----------------------------------------TTGCAAGAACCACGGCCTACAAATCAAAGCAGCTCG--------------------------------------------ATGCACCCTTCCGCTTGTA-CACTAAT---------
droWil1 Unknown 0 --------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 scaffold_12875:13669092-13669193 + LASTZ 0 CTTGTGTT---------TTAA--ATGGA-------------------ATCTCAATTTTTCCGGCCGTG--------------AAAAGTGCAATACTTGTAAAAATAAAAAAAAAGAATTGACACTGACCACAGCCGAAAAACTAGC------------------
droMoj3 Unknown 0 --------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 scaffold_15245:17564268-17564358 - LASTZ 0 AGACCC---------------------------------------------TCATTTATCCGGCCGTG--------------AAGAGTGCAATGCTTGTCAAAT-----AAAAAGAATTGACACTAACCACAGCCGAAAAACTGAAGATTTGCTT---------

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 GATTCGT--------------------------------------TTTAAAGTAATCAGGCCGTCTCAAGTGCAATACTAGTTAAAA----AATGCAGAATTGCC-CTTGTGACGAACCAAATCGCTTCAAACTTAATT---------
droSim1 GATTCTT--------------------------------------TTTAAAGTAATTCGGCCGTCTCAAGTGCAATACAAGTTTAAA----AATGCAGAATTGCC-CTTGTGACGAACCAAAACGCTTTAAACTTAATT---------
droSec1 GATTCTT--------------------------------------TTTAAAGTAATTCGGCCGTCTCAAGTGCAATACAAGTTTAAA----AATGCAGAATTGCC-CTTGTGACGAACCAAAACGCTTTAAACTTAATT---------
droYak2 GATTCGT--------------------------------------TTAAAAGTAATCCGGCCGTCTCAAGTGCAATACTAGCTTTAA---TAGTGCAGAATTGCT-CCTGGGACGAACCGAAGCGCTTCAAACGCAATT---------
droEre2 GTTTTGT--------------------------------------TTAAAAGTAATCCGGCCGTCTCAAGTGCAATACTAGCTTAAA----AATGCAGAATTGCT-CCTGGTACGAACCGAAGCGCTTCAAACTTAATT---------
droEug1 GTTTTGT-------------------------------------ATTTCAAGTCATCCGGCCGTCTGAAGTGCAATTTTCTATT--G----ACTCTAAAATTGCA-CAAAAGGCGAACCGAAATACTAGAAATTTTATT--T------
droBia1 AGTTTCT--------------ATGCACTTTCCT---TG------TTTTCAAGCACTCCGGCCGTCTCAAGTGCAATTCTAGTCGG-A----AATACAGGATTGCT-CCTGGGACGGACCGAAACGCCAAAAATATGCCT--ATAT---
droTak1 GTTTCGT-------------------------------------ATTTAAAGTATTCCGGCCGTCTCAAGTGCAATACTAGGTGA-A----AATTCAGAATTGCG-CCTGAGACGGACCGGAACACCAGAAATAT-GTT---------
droEle1 TTTTTAT--------------------------------------TCCAAAGTGTTGCGGCCGTCTCAAGTGCAATGCTAACCAGAA----AACGCAGAATTGCC-CCATAGACGTACCGAAACACCAGAAAT-TAGTA---------
droRho1 AATGCAAAAATAACTTTTTCAATAAACTTGCTTAAATGTTTTAAATCCAAAGTATTGCGGCCGTCTCAAGTGCAATGCTAGCCAAGAA--AAACGAAGAATTGCT-TTTGAGACGAGCCGAAACACCAGAAATTTGTTC--G------
droFic1 AT--AAA--------------------------------------TTTAAAGCATTTCGGCCGTCTCAAGTGCAATGCTAGCCATAAAGTTAATTTAGTATTGCCACCCAAGACG-ACCGAAACACTCGAAATTGGTTT---------
droKik1 GTTTTGG--------------------------------------GCCGCCTTGATCTGGCCGTTTCAAGTGCAATTCTGGCTATTA----ACCACAGATTTGCA-CCTCAAACAGCACAGACCTTTACGGCCGGAGCT---------
droAna3 GCTTAGA--------------------------------------TCCACTATATTTCGGCCGTCTCAAGTGCAATACTTGTATAAA---AAACCAAGAGTTGCA-CTAGAGACGCACCGGAAAATTGTAGA----------------
droBip1 CTTTCGGC-------------TTGTAGCTGCAT---AG------ATCCACAATATTCTGGCCGTCTCGAGTGCAATTCTTGTTGGAA---AAACCAAGATTTGCA-CTGGAGATGACCCCGAAAATTGTAGACATAAATCCAAACACA

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 None None
UNAFold Image None None

Small RNA-seq read pileup

Species Alignment
droSim1
GATTCTT-----------------------------------------TTTAAAGTAATTCGGCCGTC--------------TCAAGTGCAATACAAGTTTAAA----AATGCAGAATTGCCCTTGTGACGAACCAAAACGCTTTAAACTTAATT---------SizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
...................................................................................................................AATTGCCCTTGTGACGAACTT............................2120.500.000.500.000.00
droSec1
GATTCTT-----------------------------------------TTTAAAGTAATTCGGCCGTC--------------TCAAGTGCAATACAAGTTTAAA----AATGCAGAATTGCCCTTGTGACGAACCAAAACGCTTTAAACTTAATT---------SizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
GATTCGT-----------------------------------------TTAAAAGTAATCCGGCCGTC--------------TCAAGTGCAATACTAGCTTTAA---TAGTGCAGAATTGCTCCTGGGACGAACCGAAGCGCTTCAAACGCAATT---------SizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
GTTTTGT-----------------------------------------TTAAAAGTAATCCGGCCGTC--------------TCAAGTGCAATACTAGCTTAAA----AATGCAGAATTGCTCCTGGTACGAACCGAAGCGCTTCAAACTTAATT---------SizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
GTTTTAT-----------------------------------------TAAAAAGTAAT.........................................................................................................1840.750.500.000.000.25
droEug1
GTTTTGT----------------------------------------ATTTCAAGTCATCCGGCCGTC--------------TGAAGTGCAATTTTCTATT--G----ACTCTAAAATTGCACAAAAGGCGAACCGAAATACTAGAAATTTTATTT--------SizeHit CountTotal Norm
droBia1
AGTTTCT----------------ATGCACT----------TTCCTTGTTTTCAAGCACTCCGGCCGTC--------------TCAAGTGCAATTCTAGTCGGA-----AATACAGGATTGCTCCTGGGACGGACCGAAACGCCAAAAATATGCCTA--TAT---SizeHit CountTotal Norm
droTak1
GTTTCGT----------------------------------------ATTTAAAGTATTCCGGCCGTC--------------TCAAGTGCAATACTAGGTGAA-----AATTCAGAATTGCGCCTGAGACGGACCGGAACACCAGAAATAT-GTT---------SizeHit CountTotal Norm
droEle1
TTTTTAT-----------------------------------------TCCAAAGTGTTGCGGCCGTC--------------TCAAGTGCAATGCTAACCAGAA----AACGCAGAATTGCCCCATAGACGTACCGAAACACCAGAAAT-TAGTA---------SizeHit CountTotal Norm
droRho1
AATGCAAAAATAACTTTTT--CAATAAACTTGCTTAAATGTT-TTAAATCCAAAGTATTGCGGCCGTC--------------TCAAGTGCAATGCTAGCCAAGA--AAAACGAAGAATTGCTTTTGAGACGAGCCGAAACACCAGAAATTTGTTCG--------SizeHit CountTotal Norm
droFic1
ATA--AA-----------------------------------------TTTAAAGCATTTCGGCCGTC--------------TCAAGTGCAATGCTAGCCATAAAGTTAATTTAGTATTGCCACCCAAGACGACCGAAACACTCGAAATTGGTTT---------SizeHit CountTotal Norm
droKik1
GTTTTGG-----------------------------------------GCCGCCTTGATCTGGCCGTT--------------TCAAGTGCAATTCTGGCTATTA----ACCACAGATTTGCACCTCAAACAGCACAGACCTTTACGGCCGGAGCT---------SizeHit CountTotal Norm
droAna3
GCTTAGA-----------------------------------------TCCACTATATTTCGGCCGTC--------------TCAAGTGCAATACTTGTATAAA---AAACCAAGAGTTGCACTAGAGACGCACCGGAAAATTGTAGA----------------SizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
...................................................................................................................AGTTGCACTAGAGACGCACCGGAAA........................2520.500.000.000.000.50
.................................................................ATA--------------TCAAGTGCAATACTTG..................................................................1920.500.000.000.000.50
droBip1
CTTTCGGC---------TTG----------------TAGCTGCATAGATCCACAATATTCTGGCCGTC--------------TCGAGTGCAATTCTTGTTGGAA---AAACCAAGATTTGCACTGGAGATGACCCCGAAAATTGTAGACATAAATCCAAACACASizeHit CountTotal Norm
dp4
TGTTGAAC---------CCA----------------GC---------AGTAGGCACTTTCAGGCCAGT--------------GGGTGTGCAATACTGGTGAAAT--ACAACACAGTATTGCCC-----------------------------------------SizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
.............................................................GGCCAGT--------------GGGTGCGCAATACTG...................................................................2230.330.000.000.330.00
droPer1
ATTCGTAT----------------------------------------TTGCAAGAACCACGGCCTACAAATCAAAGCAGCTCG--------------------------------------------ATGCACCCTTCCGCTTGTA-CACTAAT---------SizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
droVir3
CTTGTGTT---------TTAA--ATGGA-------------------ATCTCAATTTTTCCGGCCGTG--------------AAAAGTGCAATACTTGTAAAAATAAAAAAAAAGAATTGACACTGACCACAGCCGAAAAACTAGC------------------SizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
................................................................................................TGTAAACAAAAAAAAAAA..................................................18240.040.000.000.000.040.00
.............................................................................................ATTTGTAAAAAAAAAAAAAA...................................................2050.200.000.000.000.000.20
droMoj3
--------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
AGACCC---------------------------------------------TCATTTATCCGGCCGTG--------------AAGAGTGCAATGCTTGTCAAAT-----AAAAAGAATTGACACTAACCACAGCCGAAAAACTGAAGATTTGCTT---------SizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:20:59 EDT