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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-2501

chr3L:8104207-8104277 +

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

tailed_mirtron

Legend:

   mature strand at position 8104207-8104229
   star strand at position 8104252-8104273
   mutations
   read mismatches

Notes: "droFic1, droEle1, and droRho1 all have long introns > 300nt"


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

Visually pleasing best hits from LASTZ and MAF


Species Coordinate Source Confidence Alignment
dm3 chr3L:8104192-8104292 + 1 GGTGGTAAAAGTGGAGTAAGTTTGGAGTGCCT-GGGCT------AAGAA---CT-T-------C--------------------------------------------------------------CA-----------TTCTGAAACTTAA----------------------------------------CTCTTGC-AATCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACCAAGCGTGGCAG
droSim1 chr3L:7572156-7572239 + LASTZ 5 GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCT-GGGCT------AAGAA---CT-T-------C----------------------------------------------------------------------------------------------------------------------------------CATTC-AATCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACCAAGCGTGGCAG
droSec1 super_0:391632-391715 + LASTZ 5 GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCT-GGGCT------AAGAA---CT-T-------C----------------------------------------------------------------------------------------------------------------------------------CATTG-AAGCA---------------------------------------------------A--------ACTT----------TCTTTTAGAACCAAGCGTGGTAG
droYak2 chr3L:8691884-8691979 + LASTZ 5 CGTTGTAAAAGTGGAGTAAGTTTGCGA-------------------------CTT----------------------------------------------------------------------ACGTTCCTTTTATATACCGACA-T----------A----------------------------CC--GTCTTAC-AACCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACTAAGCGCGGCAG
droEre2 scaffold_4784:3260723-3260819 - LASTZ 5 GGTGGTAAAAGTGGAGTAAGCTTGCAA-------------------------CTTGAGTTATATCTTT----------------------------------------------------------TA-----------TCCCGCTA-T----------A----------------------------CT--TACTTAC-AATCA---------------------------------------------------A--------ACTT----------TCTCGCAGAACCAAGCGCGGCAG
droEug1 scf7180000409524:537792-537938 - LASTZ 5 AGTGGTTAAAGTAGAGTAAGTACGCCT----------T------GAA-----------AGATCTTATTAACGCCAGAAAATAAATTTAAAATAAATTGCTTATATCGAATA--------------ATGCATTCTGCATATATTAA-------------TAAT---------------------------------TTGC-TATTT--AA-----------------------------------------------C--------TTTC----------TCTTCTAGAACGAAGCGGGGAAG
droBia1 scf7180000302428:1148690-1148776 - LASTZ 5 GGTGGTCAAAGTGGAGTGAGTTACGGG--CCGCGAAG----------A----------------------------------------------------------------------TGGCTTGGTTCT----------C-----------------------------------------------------TTTCT-AATCC---------------------------------------------------A--------AATT----------ATTTGTAGAACTAAACGTGGCCG
droTak1 scf7180000415862:172750-172835 + LASTZ 5 GGTGGTCAAAGTGGAGTGAGTTTGGGC----------T------TAA-------------------------------------------------------------------------------AGAT----------TC--CAA-A--------------------------------------TTGAT--TGAGT-AACTG--AA-----------------------------------------------A--------TCCT----------CTTTTCAGAACCAAGCGCGGCCG
droEle1 scf7180000490993:1776117-1776147 - LASTZ 5 TT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---------------------------------------------------A--------AACT----------AATTTCAGAACCAAGCGCGGCAG
droRho1 scf7180000757809:23187-23275 - LASTZ 5 ATTGACTTTAATGTATTTTA---------------CCT------AAGAA---AT-TCAATCT------------------------------------------------------------------------------C---CAACT----------------------------------------AATCTCAAAC-CATTA--AT-----------------------------------------------G-------TACTC----------TATTTAAGAACAAAGCGGGGCAG
droFic1 scf7180000454065:425620-425678 + LASTZ 5 TTA-------------------------ACCC-TTGCT------AAGTT---T---------------------------------------------------------------------------------------------------------------------------------------------CAAAG-TAAAGC-T------------------------------------------------G-------TCCCT----------TTTTTTAGAACCAAGCGCGGCAG
droKik1 scf7180000302274:453761-453897 + LASTZ 5 GGTGGTAAAAGTGGAGTAAGTTCCAGGC-------AATA---------------------------------ATC----------TT-----------------------------ATCAAATCT-TA-----------TCTCATATGACTATTCCCCTGATGAAATTCCCCTGGGAAATACTTAAGCTGAT--ATAAA-AACTA-------------------------------------------------------------TAA----------TTTTCTAGGACAAAGCGCGGTCG
droAna3 scaffold_13337:13543116-13543232 - LASTZ 5 AGTGGTTAAAGTGGAGTAAGTGGCGTT--TAAGGGAGTGATGGATAGATGGACCT----------------------------------------------------------------------GAGTCTTTTTTA---GTTGTTCTC----------T----------------------------TT--CTCTAAC-ATTCA---------------------------------------------------T--------AATC----------CGTTTCAGAAACAAACGTGGCCG
droBip1 scf7180000396589:509214-509318 + LASTZ 5 AGTGGTTAAAGTAGAGTAAGTGACGTT--CCAAGAAGCG---------------------------------ATA----------CT-----------------------------AATAGATATAGA-----------TTC--CAA-G----------A----------------------------CT--TTTATAC-AAGTA---------------------------------------------------A-------TACTC----------TGTTTCAGAACCAAACGCGGCCG
dp4 chrXR_group3a:1131777-1131868 + LASTZ 5 GGTGGTCAAAGTAGAGTAAGTGATCCC--CACCGAACT----------------------------------------------------------------------------ATTGTGACTTTACGCT--------------C-------------TAAT------------------------------------TG-G---GTAC-----------------------------------------------A--------TTTT----------TTGTGCAGAACCAAGCGTGGCCG
droPer1 super_23:1158678-1158769 + LASTZ 5 GGTGGTCAAAGTAGAGTAAGTGATCCC--CACCGAACT----------------------------------------------------------------------------ATTGTGGCTTTACGCT--------------C-------------TAAT------------------------------------TG-G---GTAC-----------------------------------------------A--------TTTT----------TTGTGCAGAACCAAGCGTGGCCG
droWil1 scaffold_180727:72451-72556 + LASTZ 5 AGTGGTCAAAGTACAGTAAGTACATGG--------AAT------GAC-----------CAATCCAATTAACTATA----------TA-----------------------------TGTACATATATGTT--------------A-------------AATC------------------------------------CA-A---CCAT-----------------------------------------------C--------TCTT----------TTATCCAGAAATAGACGTGGCCG
droVir3 scaffold_13049:9356761-9356852 - LASTZ 5 GGTTGTCAAAGTTGAGTAAGTTTCTAT--CAACAAT--------------------------------------------------------------------------AACTA----AGCTTGGTTAT----------GGTAA-------------TAAT------------------------------------TT-G-AC---------------------------------------------------A--------CTTT----------TCTGTTAGAAATAAGCGCGGTCG
droMoj3 scaffold_6680:11400964-11401055 + LASTZ 5 CGTTGTCAAGGTTGAGTAAGTTTGTAGGCTCT-TAACT----------------------------------------------------------------------------GGCGAAACCAGATGAT--------------C-------------TAAT------------------------------------TA-CACA---------------------------------------------------A--------TTTT----------CCCATTAGAAACAAACGTGGTCG
droGri2 scaffold_15110:6804388-6804550 + LASTZ 5 CGTTGTCAAAGTCGAGTGAGTAATTTG--GCAAAAACT----------------------------------------------------------------------------G-----GCTTT----------------TAATGAGATTACTCCTCTTAT------------------------------------CA-GACA---GTTCTCCAAACTCCTCATTTATCTTAGAGCAAATATCAGATTTAAAAATAAAATTATTTTTTCTTCTTTTGATCTTCAGAAATAAGCGCGGTCG

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 GGTGGTAAAAGTGGAGTAAGTTTGGAGTGCCT-GGGCT------AAGAA---CT-T-------C--------------------------------------------------------------CA-----------TTCTGAAACTTAA----------------------------------------CTCTTGC-AATCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACCAAGCGTGGCAG
droSim1 GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCT-GGGCT------AAGAA---CT-T-------C----------------------------------------------------------------------------------------------------------------------------------CATTC-AATCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACCAAGCGTGGCAG
droSec1 GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCT-GGGCT------AAGAA---CT-T-------C----------------------------------------------------------------------------------------------------------------------------------CATTG-AAGCA---------------------------------------------------A--------ACTT----------TCTTTTAGAACCAAGCGTGGTAG
droYak2 CGTTGTAAAAGTGGAGTAAGTTTGCGA-------------------------CTT----------------------------------------------------------------------ACGTTCCTTTTATATACCGACA-T----------A----------------------------CC--GTCTTAC-AACCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACTAAGCGCGGCAG
droEre2 GGTGGTAAAAGTGGAGTAAGCTTGCAA-------------------------CTTGAGTTATATCTTT----------------------------------------------------------TA-----------TCCCGCTA-T----------A----------------------------CT--TACTTAC-AATCA---------------------------------------------------A--------ACTT----------TCTCGCAGAACCAAGCGCGGCAG
droEug1 AGTGGTTAAAGTAGAGTAAGTACGCCT----------T------GAA-----------AGATCTTATTAACGCCAGAAAATAAATTTAAAATAAATTGCTTATATCGAATA--------------ATGCATTCTGCATATATTAA-------------TAAT---------------------------------TTGC-TATTT--AA-----------------------------------------------C--------TTTC----------TCTTCTAGAACGAAGCGGGGAAG
droBia1 GGTGGTCAAAGTGGAGTGAGTTACGGG--CCGCGAAG----------A----------------------------------------------------------------------TGGCTTGGTTCT----------C-----------------------------------------------------TTTCT-AATCC---------------------------------------------------A--------AATT----------ATTTGTAGAACTAAACGTGGCCG
droTak1 GGTGGTCAAAGTGGAGTGAGTTTGGGC----------T------TAA-------------------------------------------------------------------------------AGAT----------TC--CAA-A--------------------------------------TTGAT--TGAGT-AACTG--AA-----------------------------------------------A--------TCCT----------CTTTTCAGAACCAAGCGCGGCCG
droEle1 TT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---------------------------------------------------A--------AACT----------AATTTCAGAACCAAGCGCGGCAG
droRho1 ATTGACTTTAATGTATTTTA---------------CCT------AAGAA---AT-TCAATCT------------------------------------------------------------------------------C---CAACT----------------------------------------AATCTCAAAC-CATTA--AT-----------------------------------------------G-------TACTC----------TATTTAAGAACAAAGCGGGGCAG
droFic1 TTA-------------------------ACCC-TTGCT------AAGTT---T---------------------------------------------------------------------------------------------------------------------------------------------CAAAG-TAAAGC-T------------------------------------------------G-------TCCCT----------TTTTTTAGAACCAAGCGCGGCAG
droKik1 GGTGGTAAAAGTGGAGTAAGTTCCAGGC-------AATA---------------------------------ATC----------TT-----------------------------ATCAAATCT-TA-----------TCTCATATGACTATTCCCCTGATGAAATTCCCCTGGGAAATACTTAAGCTGAT--ATAAA-AACTA-------------------------------------------------------------TAA----------TTTTCTAGGACAAAGCGCGGTCG
droAna3 AGTGGTTAAAGTGGAGTAAGTGGCGTT--TAAGGGAGTGATGGATAGATGGACCT----------------------------------------------------------------------GAGTCTTTTTTA---GTTGTTCTC----------T----------------------------TT--CTCTAAC-ATTCA---------------------------------------------------T--------AATC----------CGTTTCAGAAACAAACGTGGCCG
droBip1 AGTGGTTAAAGTAGAGTAAGTGACGTT--CCAAGAAGCG---------------------------------ATA----------CT-----------------------------AATAGATATAGA-----------TTC--CAA-G----------A----------------------------CT--TTTATAC-AAGTA---------------------------------------------------A-------TACTC----------TGTTTCAGAACCAAACGCGGCCG
dp4 GGTGGTCAAAGTAGAGTAAGTGATCCC--CACCGAACT----------------------------------------------------------------------------ATTGTGACTTTACGCT--------------C-------------TAAT------------------------------------TG-G---GTAC-----------------------------------------------A--------TTTT----------TTGTGCAGAACCAAGCGTGGCCG
droPer1 GGTGGTCAAAGTAGAGTAAGTGATCCC--CACCGAACT----------------------------------------------------------------------------ATTGTGGCTTTACGCT--------------C-------------TAAT------------------------------------TG-G---GTAC-----------------------------------------------A--------TTTT----------TTGTGCAGAACCAAGCGTGGCCG
droWil1 AGTGGTCAAAGTACAGTAAGTACATGG--------AAT------GAC-----------CAATCCAATTAACTATA----------TA-----------------------------TGTACATATATGTT--------------A-------------AATC------------------------------------CA-A---CCAT-----------------------------------------------C--------TCTT----------TTATCCAGAAATAGACGTGGCCG
droVir3 GGTTGTCAAAGTTGAGTAAGTTTCTAT--CAACAAT--------------------------------------------------------------------------AACTA----AGCTTGGTTAT----------GGTAA-------------TAAT------------------------------------TT-G-AC---------------------------------------------------A--------CTTT----------TCTGTTAGAAATAAGCGCGGTCG
droMoj3 CGTTGTCAAGGTTGAGTAAGTTTGTAGGCTCT-TAACT----------------------------------------------------------------------------GGCGAAACCAGATGAT--------------C-------------TAAT------------------------------------TA-CACA---------------------------------------------------A--------TTTT----------CCCATTAGAAACAAACGTGGTCG
droGri2 CGTTGTCAAAGTCGAGTGAGTAATTTG--GCAAAAACT----------------------------------------------------------------------------G-----GCTTT----------------TAATGAGATTACTCCTCTTAT------------------------------------CA-GACA---GTTCTCCAAACTCCTCATTTATCTTAGAGCAAATATCAGATTTAAAAATAAAATTATTTTTTCTTCTTTTGATCTTCAGAAATAAGCGCGGTCG

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
GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCT-GGGCT------AAGAA---CT-T-------C----------------------------------------------------------------------------------------------------------------------------------CATTC-AATCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACCAAGCGTGGCAGSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
droSec1
GGTGGTAAAAGTGGAGTAAGTTTGGAGTCCCT-GGGCT------AAGAA---CT-T-------C----------------------------------------------------------------------------------------------------------------------------------CATTG-AAGCA---------------------------------------------------A--------ACTT----------TCTTTTAGAACCAAGCGTGGTAGSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
..........GTGGTGGAAGTTTGGAGT..................................................................................................................................................................................................................................................................................18111.002.009.000.00
.........AGTGGTGGAAGTTTGGAGT..................................................................................................................................................................................................................................................................................1911.000.001.000.00
..........GTGGTGGAAGTTTGGAGTCC................................................................................................................................................................................................................................................................................2011.001.000.000.00
droYak2
CGTTGTAAAAGTGGAGTAAGTTTGCGA-------------------------CTT----------------------------------------------------------------------ACGTTCCTTTTATATACCGACA-T----------A----------------------------CC--GTCTTAC-AACCA---------------------------------------------------A--------ACTT----------TCTTTCAGAACTAAGCGCGGCAGSizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
GGTGGTAAAAGTGGAGTAAGCTTGCAA-------------------------CTTGAGTTATATCTTT----------------------------------------------------------TA-----------TCCCGCTA-T----------A----------------------------CT--TACTTAC-AATCA---------------------------------------------------A--------ACTT----------TCTCGCAGAACCAAGCGCGGCAGSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droEug1
AGTGGTTAAAGTAGAGTAAGTACGCCT----------T------GAA-----------AGATCTTATTAACGCCAGAAAATAAATTTAAAATAAATTGCTTATATCGAATA--------------ATGCATTCTGCATATATTAA-------------TAAT---------------------------------TTGC-TATTT--AA-----------------------------------------------C--------TTTC----------TCTTCTAGAACGAAGCGGGGAAGSizeHit CountTotal Norm
droBia1
GGTGGTCAAAGTGGAGTGAGTTACGGG--CCGCGAAG----------A----------------------------------------------------------------------TGGCTTGGTTCT----------C-----------------------------------------------------TTTCT-AATCC---------------------------------------------------A--------AATT----------ATTTGTAGAACTAAACGTGGCCGSizeHit CountTotal Norm
droTak1
GGTGGTCAAAGTGGAGTGAGTTTGGGC----------T------TAA-------------------------------------------------------------------------------AGAT----------TC--CAA-A--------------------------------------TTGAT--TGAGT-AACTG--AA-----------------------------------------------A--------TCCT----------CTTTTCAGAACCAAGCGCGGCCGSizeHit CountTotal Norm
droEle1
TT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---------------------------------------------------A--------AACT----------AATTTCAGAACCAAGCGCGGCAGSizeHit CountTotal Norm
droRho1
ATTGACTTTAATGTATTTTA---------------CCT------AAGAA---AT-TCAATCT------------------------------------------------------------------------------C---CAACT----------------------------------------AATCTCAAAC-CATTA--AT-----------------------------------------------G-------TACTC----------TATTTAAGAACAAAGCGGGGCAGSizeHit CountTotal Norm
droFic1
TTA-------------------------ACCC-TTGCT------AAGTT---T---------------------------------------------------------------------------------------------------------------------------------------------CAAAG-TAAAGC-T------------------------------------------------G-------TCCCT----------TTTTTTAGAACCAAGCGCGGCAGSizeHit CountTotal Norm
droKik1
GGTGGTAAAAGTGGAGTAAGTTCCAGGC-------AATA---------------------------------ATC----------TT-----------------------------ATCAAATCT-TA-----------TCTCATATGACTATTCCCCTGATGAAATTCCCCTGGGAAATACTTAAGCTGAT--ATAAA-AACTA-------------------------------------------------------------TAA----------TTTTCTAGGACAAAGCGCGGTCGSizeHit CountTotal Norm
droAna3
AGTGGTTAAAGTGGAGTAAGTGGCGTT--TAAGGGAGTGATGGATAGATGGACCT----------------------------------------------------------------------GAGTCTTTTTTA---GTTGTTCTC----------T----------------------------TT--CTCTAAC-ATTCA---------------------------------------------------T--------AATC----------CGTTTCAGAAACAAACGTGGCCGSizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
...................................AGTGATGGAAAGATGAA..........................................................................................................................................................................................................................................................1711.000.000.001.000.00
...............................AGGCAGTGxTGGATAGATGG...........................................................................................................................................................................................................................................................1911.000.000.001.000.00
droBip1
AGTGGTTAAAGTAGAGTAAGTGACGTT--CCAAGAAGCG---------------------------------ATA----------CT-----------------------------AATAGATATAGA-----------TTC--CAA-G----------A----------------------------CT--TTTATAC-AAGTA---------------------------------------------------A-------TACTC----------TGTTTCAGAACCAAACGCGGCCGSizeHit CountTotal Norm
dp4
GGTGGTCAAAGTAGAGTAAGTGATCCC--CACCGAACT----------------------------------------------------------------------------ATTGTGACTTTACGCT--------------C-------------TAAT------------------------------------TG-G---GTAC-----------------------------------------------A--------TTTT----------TTGTGCAGAACCAAGCGTGGCCGSizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
GGTGGTCAAAGTAGAGTAAGTGATCCC--CACCGAACT----------------------------------------------------------------------------ATTGTGGCTTTACGCT--------------C-------------TAAT------------------------------------TG-G---GTAC-----------------------------------------------A--------TTTT----------TTGTGCAGAACCAAGCGTGGCCGSizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
droWil1
AGTGGTCAAAGTACAGTAAGTACATGG--------AAT------GAC-----------CAATCCAATTAACTATA----------TA-----------------------------TGTACATATATGTT--------------A-------------AATC------------------------------------CA-A---CCAT-----------------------------------------------C--------TCTT----------TTATCCAGAAATAGACGTGGCCGSizeHit CountTotal NormV117
Male body		V118
Embryo		V119
Head		M020
Head
AGTGGTCAAGGTATAGTA............................................................................................................................................................................................................................................................................................1811.000.001.000.000.00
droVir3
GGTTGTCAAAGTTGAGTAAGTTTCTAT--CAACAAT--------------------------------------------------------------------------AACTA----AGCTTGGTTAT----------GGTAA-------------TAAT------------------------------------TT-G-AC---------------------------------------------------A--------CTTT----------TCTGTTAGAAATAAGCGCGGTCGSizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
...............................................................................................................................................................AAT------------------------------------TG-G-AC---------------------------------------------------A--------CTTT----------TCAGT..................1811.001.000.000.000.000.00
droMoj3
CGTTGTCAAGGTTGAGTAAGTTTGTAGGCTCT-TAACT----------------------------------------------------------------------------GGCGAAACCAGATGAT--------------C-------------TAAT------------------------------------TA-CACA---------------------------------------------------A--------TTTT----------CCCATTAGAAACAAACGTGGTCGSizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
CGTTGTCAAAGTCGAGTGAGTAATTTG--GCAAAAACT----------------------------------------------------------------------------G-----GCTTT----------------TAATGAGATTACTCCTCTTAT------------------------------------CA-GACA---GTTCTCCAAACTCCTCATTTATCTTAGAGCAAATATCAGATTTAAAAATAAAATTATTTTTTCTTCTTTTGATCTTCAGAAATAAGCGCGGTCGSizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:18:18 EDT