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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-984

chrX:4262679-4262768 -

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

antisense_to_intron

Legend:

   mature strand at position 4262731-4262753
   star strand at position 4262694-4262714
   mutations
   read mismatches

Notes: No other otholog substitution patterns look real.


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

Visually pleasing best hits from LASTZ and MAF


Species Coordinate Source Confidence Alignment
dm3 chrX:4262664-4262783 - 1 TGGC-TTCTATT-GCGTAGA-----AACAAATTTCATTGAG-----------------------------------------------------------GTAAATACGGTTGGAATTTTGT--CTTTTAACTATAA---ATCCAACCGAATTTGGCTCGGCGAAATTTTTCAGTTTACTGG-----CGTCGAAAA
droSim1 chrX:3277428-3277474 - LASTZ 0 TGGC-TTCTACT-CTCT-------------ACTTCATTGCT-----------------------------------------------------------TTGCATATGAT------------------------------------------------------A---------------------TCTTGCAGT
droSec1 super_4:2462188-2462234 + LASTZ 0 TGGC-TTCTACT-ATCT-------------ACTTCATTGCT-----------------------------------------------------------TTGCATATGAT------------------------------------------------------A---------------------TGTTGCAGT
droYak2 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2 scaffold_4690:1633226-1633277 - LASTZ 0 CTTG-TAAATGT-A----CA-----AACAAATCTCAGTGTA-----------------------------------------------------------TAGCTTAAATC------------------------------------------------------C---------------------ACCGGAATT
droEug1 scf7180000409076:263221-263311 - LASTZ 0 TTCATTTATTTTTTCTATGATTTTGAC-AGTTA--ATT-------------------------------------------------------------------------TGAGGTTTTGT--TTTCAAATTATAA---AGCTGA---AAATTGACTTGTCGAAA---------------------TCTTTAAAA
droBia1 scf7180000301703:494692-494801 + LASTZ 0 TGAT-TTATTTT-GCCATATTTGTTAACATATTCTAAAAAGATCAATTTTTTTACAATATTAAACCATATTTCTTGTAAACGTTCCATTGATTTTATGATTGG------------------------------------------------------------------------------------TGCTGTACA
droTak1 scf7180000415394:1159636-1159737 + LASTZ 0 TTAG-TACTTAT-A----TA----------------------------------------------------------AATGTTACAATGTTTTAGTGACTGGTTCAGT--ATCAA--CTATGTTT-CTAA----TTCAGT---------------------TGTACTTTTCCAGTTCCTAGATCAATGTCACGAA
droEle1 scf7180000491011:2112563-2112618 + LASTZ 0 AACT-GA-------------------------------------------------------------------------------------------------------------------ATTC-TTGAATATTTCAGT---------------------AATGTTTTTCAACTCACTAAAACA--ATGGTAAC
droRho1 scf7180000779334:414414-414509 + LASTZ 0 TATC-ATACATT-GCAGAGATTTTAGA-AGTCG--AGA-------------------------------------------------------------------------ATGGTTACTGTATTT-TTAAATATAACAGTGACCA---GACCCGAAC-----------------TCT-CCAATCTTTGTCAAAAA
droFic1 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 scaffold_6359:3791288-3791288 - LASTZ 0 T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown 0 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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 TGGCTTCTATTGCGTAGAAACAAATTTCATTGAGGTAAATACGGTTGGAATTTTGTCTTTTAACTATAAATCCAACCGAATTTGGCTCGGCGAAATTTTTCAGTTTACTGGCGTCGAAAA

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 None None None None None None None None None
UNAFold Image None None None None None None None None None None None

Small RNA-seq read pileup

Species Alignment
droSim1
TGGC-TTCTACT-CTCT-------------ACTTCATTGCT-----------------------------------------------------------TTGCATATGAT------------------------------------------------------A---------------------TCTTGCAGTSizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
...........T-CTCT-------------ACTTCATTGGT-----------------------------------------------------------TG..............................................................................................1812.000.002.000.000.00
droSec1
TGGC-TTCTACT-ATCT-------------ACTTCATTGCT-----------------------------------------------------------TTGCATATGAT------------------------------------------------------A---------------------TGTTGCAGTSizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
droEre2
CTTG-TAAATGT-A----CA-----AACAAATCTCAGTGTA-----------------------------------------------------------TAGCTTAAATC------------------------------------------------------C---------------------ACCGGAATTSizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droEug1
TTCATTTATTTTTTCTATGATTTTGAC-AGTTA--ATT-------------------------------------------------------------------------TGAGGTTTTGT--TTTCAAATTATAA---AGCTGA---AAATTGACTTGTCGAAA---------------------TCTTTAAAASizeHit CountTotal Norm
droBia1
TGAT-TTATTTT-GCCATATTTGTTAACATATTCTAAAAAGATCAATTTTTTTACAATATTAAACCATATTTCTTGTAAACGTTCCATTGATTTTATGATTGG------------------------------------------------------------------------------------TGCTGTACASizeHit CountTotal Norm
droTak1
TTAG-TACTTAT-A----TA----------------------------------------------------------AATGTTACAATGTTTTAGTGACTGGTTCAGT--ATCAA--CTATGTTT-CTAA----TTCAGT---------------------TGTACTTTTCCAGTTCCTAGATCAATGTCACGAASizeHit CountTotal Norm
droEle1
AACT-GA-------------------------------------------------------------------------------------------------------------------ATTC-TTGAATATTTCAGT---------------------AATGTTTTTCAACTCACTAAAACA--ATGGTAACSizeHit CountTotal Norm
droRho1
TATC-ATACATT-GCAGAGATTTTAGA-AGTCG--AGA-------------------------------------------------------------------------ATGGTTACTGTATTT-TTAAATATAACAGTGACCA---GACCCGAAC-----------------TCT-CCAATCTTTGTCAAAAASizeHit CountTotal Norm
droFic1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal Norm
droKik1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal Norm
droAna3
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
droBip1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal Norm
dp4
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------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
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV116
Male body		V053
Unknown		V047
Embryo		M027
Male body		M028
Head
droMoj3
T---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV109
Male body

Generated: 04/20/2012 at 05:27:15 EDT