Oatp58Dc_in3- 12- and 20-way alignments

Oatp58Dc_in3	chr2R:18113752-18113821 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 18113753-18113774
   star strand at position 18113776-18113796
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:18113737-18113836 -	GATGGATTGGTTTTGGTAAGTTATATAGAA--------------------GGATATA----TATAAT-AATCGG------------AGGT------------TAAC-------G-TATAATTATCCTTTTATTACT--GCGCAGGTCTTCTTACCATCG
droSim1	chr2R:16713489-16713586 -	GATGGATTGGTTTCGGTAACTTATATTAAA--------------------AGATACA----TACGAG-ACTCGG------------AAGT------------GA---------GAT-AAATGGTCGCTTTATTACT--CTGCAGGTCTCCTTACCATCG
droSec1	super_9:1424074-1424171 -	GATGGATTGGTTTTGGTAAGATATATGAAA--------------------AGATACA----AACGAG-ACTCGG------------AAGT------------GA---------GCT-AAATGGTCCCTTTATTACT--GTGCAGGTCTTCTTACCATCG
droYak2	chr2R:17860970-17861071 -	GATGGATTGGTTTTGGTAAGATCTATAGAA--------------------AGATATATTT--ATGTT-ACTCAG------------AAGT------------TAAG-------G-TATAATTGCCATTTTGTAAAT--GTTCAGGTCTTCTTACCATCG
droEre2	scaffold_4845:12253086-12253177 -	GATGGATTGGTTTTGGTAAGATATAT------------------------------------ATGTT-ACTCGG------CTTAATAATC------------AG---------GTT-TAATTTTACTTTTATAACT--GTGCAGGTCTTCTCACCATCG
droAna3	scaffold_13266:2121470-2121555 -	GATGGATTGGCTTTGGTACGTAGTCACCAA-------------------AGAA---------------------CATTTATTTTCA-AGT------------TATT-------A-TGAAATA----------TC--CCTTTTAGGCTTGTTGACCATTG
dp4	chr3:15029496-15029588 +	GCTGGATAGGATTCGGTAAGAGCAG----------------CATTCCGATGGA----TTTTTA--T---------------------------CGATTCCATTACAGCTTATCG-GCT--------------AC--TCCCCCAGGTCTCCTCACCATTG
droPer1	super_4:4021493-4021585 -	GCTGGATAGGATTCGGTAAGAGCAG----------------CATTCCGATGGA----TTTCTA--T---------------------------CGATTCCATTACAGCTTATCG-GCT--------------AC--TCCCCCAGGTCTCCTCACCATTG
droWil1	scaffold_180697:335215-335309 +	GTTGGATTGGCTTTGGTATGATTAA-AG----------------ACTCATTAA----TATATA--TTGACTTGA-------------AA------------TGGTT----------------GCAAATTTGTGATTTCTGACAGGTCTTCTAACAATTG
droVir3	scaffold_10324:576498-576590 -	GCTGGATAGGATTTGGTGAGTGA-ATGAGCGG---------AAATCTAAA---------------GTAGCTTCT--C----------------TTAT-----------------------TCATCTTTTTCTTTCTGCCAACAGGCCTACTAACTATTG
droMoj3	scaffold_6496:2407447-2407535 -	GTTGGATAGGATTTGGTAAGATCTACAAATGATGCCAGCAACAT------------------------------CTTCTATCTCAT-TGC-------------------------------------TGACATT--TCCCCCAGGTCTATTGACTATCG
droGri2	scaffold_15245:8299183-8299271 -	GGTGGATTGGCTTTGGTAAGCTGTGAAATA--------------------AACT--------------------CTTTAATTTGAT-AACTAAGGGTTCAAAT---------------------------AACGAT--TTACAGGTTTATTAACCATTG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:18113737-18113836 -	NA	GATGGATTGGTTTTGGTAAGTT------ATATAGAAG-------------GATATA--TATAATA-ATCGGAGGT-------------------------------------TAACGTATAATTATCC-----------TTTTAT--T---ACTGCGCAGGTCTTCTTACCATCG
droSim1	chr2R:16713489-16713586 -	7	GATGGATTGGTTTCGGTAACTT------ATATTAAAA-------------GATACA--TACGAGA-CTCGGAAGT-------------------------------GAGATA--------AATGGTCG-----------CTTTAT--T---ACTCTGCAGGTCTCCTTACCATCG
droSec1	super_9:1424074-1424171 -	7	GATGGATTGGTTTTGGTAAGAT------ATATGAAAA-------------GATACA--AACGAGA-CTCGGAAGT-------------------------------GAGCTA--------AATGGTCC-----------CTTTAT--T---ACTGTGCAGGTCTTCTTACCATCG
droYak2	chr2R:17860970-17861071 -	7	GATGGATTGGTTTTGGTAAGAT------CTATAGAAA-------------GATATATTTATGTTA-CTCAGAAGT-------------------------------------TAAGGTATAATTGCCA-----------TTTTGT--A---AATGTTCAGGTCTTCTTACCATCG
droEre2	scaffold_4845:12253086-12253177 -	9	GATGGATTGGTTTTGGTAAGAT------ATATA---------------------------TGTTA-CTCGGC---TTAATAATC----------------------AGGTTT--------AATTTTAC-----------TTTTAT--A---ACTGTGCAGGTCTTCTCACCATCG
droEug1	scf7180000409672:6008742-6008837 -	11	GATGGATTGGGTTCGGTAAGAT------GTTTACAGG-------------AAGA-----TATGTT-CTCAAACAA--------------A----AATACTATAGTT-----------------CGACC--------------ATA--T---ACCCCTCAGGTCTTCTTACCATAG
droBia1	scf7180000302143:2603202-2603295 +	1	GGTGGATTGGGTTTGGTAAGAC------ATATACAAG-------------AATA-----AAGTGT-CCCAGAAAG-----------------------------------------------------TAAAAAAATATTTTCCTATG---TTTGATAAGGTCTTCTCACCATTG
droTak1	scf7180000415243:306616-306705 -	11	GATGGATTGGGTTTGGTAAGAT------ATGGACAAG-------------AATT-----AAGTTT-GTCAGAAAA---------------------------------------ATGTA---GAGCCC-----------TTTTCT-------TTATTTAGGTCTCCTAACCATCG
droEle1	scf7180000491282:187924-188020 +	5	GATGGATTGGTTTTGGTAAGAC------TTGTACA-------TTTACTGGAAAA-------------------GT-----TTTCCCCGTT----TCT---GGGACT----------------------TATAAAACTG-----------T-TTGCCTTAGGTCTTCTCACCATCG
droRho1	scf7180000779898:29354-29438 -	8	GATGGATTGGATTTGGTAAGAT------ATTTACTGG-------------TAAA-----GGGTTT-CTCAGATCA-----------------------------------------------------TGTAACACTG-----------C-CTGCTTCAGGTCTTCTCACCATCG
droFic1	scf7180000454066:2005007-2005107 -	8	GGTGGATTGGGTTTGGTAAGAT------ATACCATATTG--------CATTACATA--TAAGTAC-ATCAGAAGA-------------------------------------TATAATAT----TTTA-----------AATCAT--A---ATTTAATAGGTCTCCTTACCATTG
droKik1	scf7180000302471:1382481-1382572 +	1	GGTGGATTGGCTTTGGTAAGCT------CTTAAGTAA-------------AATATA--T---ACTCTTCAA-GGATTGA----------A-------------------------------------------AATGCTTTTCCT--A---TATAAATAGGCCTGCTCACCATTG
droAna3	scaffold_13266:2121470-2121555 -	11	GATGGATTGGCTTTGGTACGTA------GTCACCAAAGAACATT--------------TAT---T-TTCAA--GT-------------------------------------TATTA-------------T-GAAATA-----------T-CCCTTTTAGGCTTGTTGACCATTG
droBip1	scf7180000396384:456386-456471 +	1	GATGGATTGGCTTTGGTAAGTA------TTCCCCAAAGGACATT--------------TAATTG------AATCT---------------------TATTATA------------------------------AACTA-----------T-CTTTTTTAGGTCTGTTAACCATTG
dp4	chr3:15036317-15036415 +	4	GCTGGATGGGAATAGGTAAGCC------TTAACTTTGGG--------CAC-----CTTTACGTAG-CTC--------------------------CTTCTCTCGGT------TAT-----------CT--C-TGA-----ATATC--T---TCTGGATAGGGTTGCTAACAATTG
droPer1	super_4:4021493-4021585 -	11	GCTGGATAGGATTCGGTAAGAG------CAGCATTCCGA--------TGG-----ATTTCTATC-----------------------GAT----TCCATTACAGCT------TAT-----------CG--------------GCT--A---CTCCCCCAGGTCTCCTCACCATTG
droWil1	scaffold_180697:335215-335309 +	1	GTTGGATTGGCTTTGGTATGATTAAAGACTCATTAATATATATTGACTTGAAAT-------------------GG-----------------------------------------------TTGCAA-----------ATTTGT--GAT-TTCTGACAGGTCTTCTAACAATTG
droVir3	scaffold_10324:576498-576590 -	11	GCTGGATAGGATTTGGTGAGTG--AATGAGCGGAAATCT-------------------AAAGTA------------------------------GCTTCTCTTAT-----------------TCATCT-----------TTTTCT--T-TCTGCCAACAGGCCTACTAACTATTG
droMoj3	scaffold_6496:2396237-2396342 -	8	GTTGGATGGGTTTGGGTAAAT-------ATATATAAA--------------ATATA--TATAA---TAAAAAAAT-----TATGT----AAAGAACTTCTCAAATTAAAGTA--------AAT--------------C-----------C-CACTTCCAGGTCTGTTTACAATCG
droGri2	scaffold_15245:8292349-8292444 -	15	GCTGGATTGGATTTGGTAAATA------AAATAAACCGG--------CGA-----CT-TAAGTGT---T------------------AAT----CTCACAATA-------------------------AAAAACAT----AATTT--A---CCTTGCCAGGATATTTTACGGTTA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GATGGATTGGTTTTGGTAAGTTATATAGAA--------------------GGATATA----TATAAT-AATCGG------------AGGT------------TAAC-------G-TATAATTATCCTTTTATTACT--GCGCAGGTCTTCTTACCATCG

Size

Hit Count

Total Norm

droSim1

GATGGATTGGTTTCGGTAACTTATATTAAA--------------------AGATACA----TACGAG-ACTCGG------------AAGT------------GA---------GAT-AAATGGTCGCTTTATTACT--CTGCAGGTCTCCTTACCATCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................................................................A---------CAT-AAATGGTCGTTTTA............................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

GATGGATTGGTTTTGGTAAGATATATGAAA--------------------AGATACA----AACGAG-ACTCGG------------AAGT------------GA---------GCT-AAATGGTCCCTTTATTACT--GTGCAGGTCTTCTTACCATCG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...................GATATATGAAA--------------------AGAGATA----..................................................................................................	18	1	15.00	0.00	15.00	0.00
..................AGATATATGAAA--------------------AGAGATA----..................................................................................................	19	1	4.00	0.00	4.00	0.00
...............GAGAGATATATGAAA--------------------AGA..........................................................................................................	18	1	4.00	0.00	4.00	0.00
.................GAGATATATGAAA--------------------AGAGA........................................................................................................	18	1	2.00	0.00	2.00	0.00
...................GATATATGAAA--------------------AGAGATA----A.................................................................................................	19	1	1.00	0.00	1.00	0.00
......TTGGTTTTGGTAAGATATATG....................................................................................................................................	21	1	1.00	1.00	0.00	0.00
...........................ACA--------------------AGATACA----AACGAG-AA.........................................................................................	18	1	1.00	0.00	1.00	0.00
...............ATAAGATATAxGAAA--------------------AGAT.........................................................................................................	18	1	1.00	0.00	0.00	1.00
..............GGAGAGATATATGAAA--------------------AG...........................................................................................................	18	1	1.00	0.00	0.00	1.00
...................GATATATGAAA--------------------AGAGATA----AA................................................................................................	20	1	1.00	0.00	1.00	0.00
...................GATATATGAAA--------------------AGACATA----..................................................................................................	18	1	1.00	0.00	1.00	0.00
GATxxTTTGGTTTTGGTAAG...........................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

GATGGATTGGTTTTGGTAAGATCTATAGAA--------------------AGATATATTT--ATGTT-ACTCAG------------AAGT------------TAAG-------G-TATAATTGCCATTTTGTAAAT--GTTCAGGTCTTCTTACCATCG	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.ATGGGCTGGTTTTGGTAAG...........................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...GGATTGCTTTAGGTAAGAT.........................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

GATGGATTGGTTTTGGTAAGATATAT------------------------------------ATGTT-ACTCGG------CTTAATAATC------------AG---------GTT-TAATTTTACTTTTATAACT--GTGCAGGTCTTCTCACCATCG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..........................................................................................................................TTACTTTTATAACT--GTGTT................	19	1	1.00	1.00	0.00	0.00	0.00
..........................................................................................................................TTACTTGTATAACT--GTGG.................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................TACTTTTATAACT--GTGCT................	18	1	1.00	1.00	0.00	0.00	0.00

droAna3

GATGGATTGGCTTTGGTACGTAGTCACCAA-------------------AGAA---------------------CATTTATTTTCA-AGT------------TATT-------A-TGAAATA----------TC--CCTTTTAGGCTTGTTGACCATTG

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

GCTGGATAGGATTCGGTAAGAGCAG----------------CATTCCGATGGA----TTTTTA--T---------------------------CGATTCCATTACAGCTTATCG-GCT--------------AC--TCCCCCAGGTCTCCTCACCATTG	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...GGATxGGATTCAGTAAGAGC........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droPer1

GCTGGATAGGATTCGGTAAGAGCAG----------------CATTCCGATGGA----TTTCTA--T---------------------------CGATTCCATTACAGCTTATCG-GCT--------------AC--TCCCCCAGGTCTCCTCACCATTG	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..................AGAGCAx----------------CATTCCGCTGGA----T.....................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

GTTGGATTGGCTTTGGTATGATTAA-AG----------------ACTCATTAA----TATATA--TTGACTTGA-------------AA------------TGGTT----------------GCAAATTTGTGATTTCTGACAGGTCTTCTAACAATTG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........................................................................................................................................TAACAGGTCTTCTAGCAA...	18	1	2.00	0.00	0.00	2.00	0.00

droVir3

GCTGGATAGGATTTGGTGAGTGA-ATGAGCGG---------AAATCTAAA---------------GTAGCTTCT--C----------------TTAT-----------------------TCATCTTTTTCTTTCTGCCAACAGGCCTACTAACTATTG

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GTTGGATAGGATTTGGTAAGATCTACAAATGATGCCAGCAACAT------------------------------CTTCTATCTCAT-TGC-------------------------------------TGACATT--TCCCCCAGGTCTATTGACTATCG

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

GGTGGATTGGCTTTGGTAAGCTGTGAAATA--------------------AACT--------------------CTTTAATTTGAT-AACTAAGGGTTCAAAT---------------------------AACGAT--TTACAGGTTTATTAACCATTG

Size

Hit Count

Total Norm

V109
Male body

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

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