sblock222077

chr3RHet:576709-576818 +

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

intergenic

Legend:

   mature strand at position 576781-576802
   star strand at position 576728-576746
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species Coordinate Alignment
dm3 chr3RHet:576694-576833 + ATTTGTTTTCGGTTGTTTTCTTATTTTCGTATATAAAATTATAAATGG-----GTTACATAATGTTATATAATGCTACATAAATGTATAATATGTAACCCATTTA---TAATTTTATATACGAAAATACTTATCCTCTGAGGGAGTGA
droSim1 chrU:3635252-3635359 + TGTTTTTCATTTCTTTTTTAATATT---ATGAATAAAATCATTATTTAATCCAATAAT-----ATACCATATGCTTA--TAAAAAATTTATAAACAACTTAATTAGCATAGTCTTACA------------------------------
droSec1 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------
droYak2 chr2R:1225697-1225811 + ATTTATTTTGTATTTTTTTATTCGT---GTCTTTAAAAGAATTTTAAAAACAAACTAC-----ATT---TAGTGCTCCTTAAAATATTAATATTAAAACCGTTTA---C-ATTTTACGTCTGAATGTACTCGTCGTCGGAGATGACGA
droEre2 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------
droAna3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------
dp4 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------
droPer1 super_81:115497-115545 - ACTTGTGTTTGGTTGTAGTATCTTTTG-----------------ATGG-----GCTACAGATCTTTGTTTA-----------------------------------------------------------------------------
droWil1 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------
droVir3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------
droGri2 Unknown ----------------------------------------------------------------------------------------------------------------------------------------------------

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species Coordinate Lastz Id Alignment
dm3 chr3RHet:576694-576833 + NA ATTTGTTTTCGGTTGTT-TT------CTTATTTTCGTATATAAAATTATAAATGGGTT-------------------------------------------------------ACAT--------AAT--GTTA-------------------------------------------------TATAATGC-----------TAC---------ATAAATGTATAAT-----------------------------ATGTAA----CCCATTTATAATTTTAT------ATACGAAA--ATACTTAT--C-CTCTGAGG-GAGTGA
droSim1 chrU:9556601-9556718 - 238 ATTTGTTTTCGGTTGTT-TT------CTTATTTTCCTATATAAAATTATAAATGGATT-------------------------------------------------------TTGGGTTA-CATATT--TTGATAATCCGTATAGTATAATAAGTACA-------ATAATAATAAGTGTTGC-------------GATGATA---------------------------------------------------------------------------------------------------------------------------
droSec1 super_7722:503-638 - 662 ATTTGTTTTCGATTGTT-TT------CTTATTTTCCTATATAAAATTATAAATGGATT-------------------------------------------------------TTGGGTTA-CATATT--TTGATAATCCGTATAGTATAATAAGTACA-------ATAATAATAAGTGTTAC-------------TATAATATAAAAT-----ATGG------------------------TATTATTT----------------------------------------------------------------------------
droYak2 chr3R:6981890-6982030 - 287 ATTATTTTTTGCTTGTT-TT------CTGAATTTTTTATATAAAACAGTTAGTGGATT-------------------------------------------------------TAGTGTAA-AAATTT--TTGATAGGACAAGAAAAATTATAAGAACA-------ATAACTAAAATTATTAT-------------AGTTGCATAAAAT-----GTGG------------------------TATTATTT-----------------------------------------------------------TC---T---------GA
droEre2 scaffold_4684:13326-13445 + 137 ATTTGTTTTCGGTTGTT-TT------CTTTTTTTCGTATATAAAATTATAAATGGGTT-------------------------------------------------------ACAT--------ATT--TTGATAATCCGTATAGTATAATAAG----------------------TTTTAT-------------GATAATATAAAAT-----ATGA------------------------TATTATTT-----------------------------------------------------------T-----------TTTGA
droEug1 scf7180000409434:14602-14733 + 26 ATTATTTTTTGATTGTT-TT------CTAAATTTTGTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAGTATAA-ACAATT--TT-A--------------TAATATGATCATTTTATGATAACTACTAATATTAT-------TAT---TATATTTTAAAAT-----GTC--------------------------ATTATGT-----------------------------------------------------------TC---T-----------
droBia1 scf7180000300680:23-161 - 178 ATTATTTTTTTCTTGTT-TT------CTAAATTTTGTATATAAAATGATAAGTGGATT-------------------------------------------------------AAGTGAGAAACAATT--TTGATAGGGCAAGAAAAATAATAAGAACA-------ATAACTACAATTA---T-------------AATCACTTAA-GT-----GTAGA-----------------------TTTTATTT-----------------------------------------------------------TC---T---------GA
droTak1 scf7180000415873:9535-9670 + 111 TTCTGTACTCTTTTGTG-TATCTTCCTTTGGTTTTACATATTTTACAATAAGTTTTCT-------------------------------------------------------TGGTATGC-TCTT-AAATTTAT---------------------ACA-------ATAACAAAGGTTGTTAA-------AGT---GATTATTTGGAATACATTATAA------------------------TATTTTGT----------------------------------------------------------------------GTGTGA
droEle1 scf7180000491055:5756-5897 + 155 ATTATTTTTTGCTTGTC-TT------CTTAATTTTGTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAGTGATA-AAATTG--TTGATAGGACAAGAAAAATAATAAGAACA-------ATAATTATAATTATTAT-------------AATTACGTAAAGA-----GTGG------------------------TATTATCA-----------------------------------------------------------G-----------ATGAA
droRho1 scf7180000762627:316-437 - 292 ATTATTTTTTGCTTGTT-TT------TTAAATTTTGTATATGAAAAGGTAAGTGGGTT-------------------------------------------------------TAGTGTAC-ACATTT--TTGATAGGACAAGAAAAATAATAAGAACA-------ATAATTACAATTATTAT-------------AATTACAAAA-----------------------------------------------------------------------------------------------------------------------A
droFic1 scf7180000454094:3746-3886 - 187 ATTATTTTTTTCTTGTT-TT------CTAAATTTTGTATATAAAATGGTGAGTGGATT-------------------------------------------------------TAGTGTAA-AAAATT--TTGATAGGGCAAGAAAAATAATAAGAACA-------ATAACTACAATTATTAT-------------AATTACGTAAAGT-----GTAG------------------------TGTTATTT-----------------------------------------------------------TC---T---------GA
droKik1 scf7180000301889:2472-2603 - 217 ATAATGTTTTGATTGTT-TT------CTGAATTTTGTATATAAAAGAGTAAGTGGCTT-------------------------------------------------------TTTTTTTA-TTTATTTATTTAT------------TTATTAAGAA---------------------------------T-----------AGC---------AAATATCTGCCAT-----------------------------TTTAAATCCATATCCT-----------------------------------TTC-CTCAGACC-GGATAA
droAna3 scaffold_13079:304244-304384 - 324 ATTGTCTTTTACTTGTT-TT------CTTAGTTTTTTATATAAAAAGGTAAGTGGATT-------------------------------------------------------TAAAGTAA-AGAATT--TTGAAAGGACAAATAAAATAATAATAACA-------ATAACTAAAATTATTAT-------------AATTATATAATTT-----GTGG------------------------AATTATTT-----------------------------------------------------------TC---T---------GA
droBip1 scf7180000394965:14885-15019 + 31 GTTAGATTTTTATTTTATTT------TATTTTTTTATATTTTTTTTTGTATATTTTTT-------------------------------------------------------ATAT--------AAA--TATA-------------------------------------------------TATAATTT-----------TAT---------ATATATATAT-------ATATATGTATT------------------------------TTTTTTATTGTGTACATGTATGTATCTATATTTAT--TC---T---------TT
dp4 Unknown_singleton_1998:3876-4037 - 207 ACTTGTGTTTTGTTGTC-GC------ATTAATGGGTTACAGATCTCTGTTTACA---CCCGTGTAGTCATAAATTGTCTACTTTATGTGATTTCTTTAGAGAATATATAGATCAAATATG----------------------------------------------------------------------T-----------AAC---------AAATATGTAACAC-----------------------------ATGTAA----CACATCCATACATATAT------AGACGT--------------------------AAATA
droPer1 super_28:207610-207724 - 220 TATTTTC------AGTT-TT------CGGATTAAAGCTAATGAAAGTGTATGAAAATT-------------------------------------------------------AAATTATT----------AAA---------------------------------------------------------TTGATT---AAAAT---------AAATATACATAAT-----------------------------ATGTAA----TATATTTA------ATT------AAATAAAT--AAAT-----------------ATTAAT
droWil1 scaffold_181089:9808790-9808940 + 112 TTTTGTTTTTATTTTTA-TA------TATATTTATATATATATATATATATATTGTAT-------------------------------------------------------ATAT--------AAT--TTGT----------------------TCT-------GTTTTTTTTTTTT---T-------------ATTTACTTTT-GT-----TTAAATT-----------------------CATTTCCCTATTAAGTTA----CACACACATATGTATAT------GTATATAT--ATAC-----------------ATATAC
droVir3 scaffold_12723:5508367-5508489 + 70 TGTGCTTGTATTTAAAG-AT------TTAAAATTTTTA-------------TTATAAT-------------------------------------------------------ATAT--------ATT--GTTATTAAGAGCTAAATAT-----------------------------------------------------------------AAAAATATATAAGATAA-----------A-GATACCGTTATA----AATATAGAAACA-----------------------------------CTA-ACGAAGAT-ATATAT
droMoj3 scaffold_6541:2286599-2286731 - 462 ATTTTTGTATAGTAGTT-TTAG---TCTAGATTTGGT---GACAATTGAAGACGGTTT---------------------A-------------------------------TTAAATATAA--------------------------------------------------------------AATCAAGCTTTATG--------------------AATATAAAACCAAA-----------C-AACACTGTTATT----ATTTCACTATAA-----------------------------------TTA-ATCAACCTTGGAGGG
droGri2 scaffold_6998:1526-1648 - 67 ATTTGTGTGTGTGTGTG-TG------TATATATACATACATACACACAGATATATGTT-------------------------------------------------------ATGT--------ATA--TGTA-------------------------------------------------TATATTTT-----------TAT---------AAATATGTAT-------ATATATATATG------------------------------TATATATATAT------ATATACAT--ATAT-----------------ATATAT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species Alignment
dm3
ATTTGTTTTCGGTTGTTTTCTTATTTTCGTATATAAAATTATAAATGG-----GTTACATAATGTTATATAATGCTACATAAATGTATAATATGTAACCCATTTA---TAATTTTATATACGAAAATACTTATCCTCTGAGGGAGTGASizeHit CountTotal Norm
droSim1
TGTTTTTCATTTCTTTTTTAATATT---ATGAATAAAATCATTATTTAATCCAATAAT-----ATACCATATGCTTA--TAAAAAATTTATAAACAACTTAATTAGCATAGTCTTACA------------------------------SizeHit CountTotal NormV044
Embryo		M023
Head		M024
Male body		M025
Embryo
.......................................CATTATTTAATACAATGA...........................................................................................1816.000.000.001.005.00
..................................AAAAGCATTATTTAATACAAT.............................................................................................2111.001.000.000.000.00
.......................................CATTATTTAATACAATGAT-----.....................................................................................1911.000.001.000.000.00
....................................AAGCATTATTTAATACAAT.............................................................................................1911.001.000.000.000.00
.................................TAAAAGCATTATTTAATA.................................................................................................1811.001.000.000.000.00
...............................TATAAAAGCATTATTTAAT..................................................................................................1911.001.000.000.000.00
.....................................AGCATTATTTAATACAAT.............................................................................................1811.000.000.001.000.00
..................................AAAAGCATTATTTAATACA...............................................................................................1911.001.000.000.000.00
droSec1
----------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV113
Male body		V114
Embryo		V115
Head
droYak2
ATTTATTTTGTATTTTTTTATTCGT---GTCTTTAAAAGAATTTTAAAAACAAACTAC-----ATT---TAGTGCTCCTTAAAATATTAATATTAAAACCGTTTA---C-ATTTTACGTCTGAATGTACTCGTCGTCGGAGATGACGASizeHit CountTotal NormV046
Embryo		V052
Head		V120
Male body		V058
Head		M026
Head
................................................AACATACTAC-----ATT---TAGTG..........................................................................1811.000.000.000.001.000.00
...............................................AAACAAGCTAC-----xTT---TAGTG..........................................................................1811.000.000.000.001.000.00
ATTTATTTTGxATTTTTTTGT...............................................................................................................................2011.000.001.000.000.000.00
droEre2
----------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV040
Embryo		V060
Head		V047
Embryo		V108
Head
droAna3
----------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV105
Male body		V106
Head		V055
Unknown		V039
Embryo
dp4
----------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV112
Male body		V043
Embryo		V051
Head		M022
Male body
droPer1
ACTTGTGTTTGGTTGTAGTATCTTTTG-----------------ATGG-----GCTACAGATCTTTGTTTA-----------------------------------------------------------------------------SizeHit CountTotal NormV111
Male body		V042
Embryo		V050
Head		V057
Head		M021
Embryo
.....CGTTTGGTGGTAGTATCT.............................................................................................................................1811.000.001.000.000.000.00
............................................ATGG-----GCxACAGATCTTGGT................................................................................1811.000.000.000.001.000.00
.....................................................................Tx-----------------------------------------------------------------------------1820.500.500.000.000.000.00
..............................................GG-----GTTGCAGATCTTTGTT...............................................................................1811.000.001.000.000.000.00
.............TGTAGTATCTTTTA-----------------ATGG-----GCT............................................................................................2111.000.000.000.000.001.00
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
----------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV110
Male body		V056
Unknown		V049
Head		V041
Embryo
droGri2
----------------------------------------------------------------------------------------------------------------------------------------------------SizeHit CountTotal NormV109
Male body

12-way Secondary Structure

dm3 droSim1 droSec1 droYak2 droEre2 droAna3 dp4 droPer1 droWil1 droVir3 droMoj3 droGri2
RNAfold Image None None None None None None None None
UNAFold Image None None None None None None None None

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

Generated: 04/20/2012 at 05:19:31 EDT