block665662- 12- and 20-way alignments

block665662	chr2R:1365763-1365863 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1365784-1365805
   star strand at position 1365844-1365861
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:1365748-1365878 -	GCCTAGTTCTCTCTCGCTGGCTTGAGTTAAGTAA-AAATAAACTCAGAAACTA-AA-AATAATTTCTGAGTTTCTTTTT-AGTTTCTGAG-----------------------------------------------------------------------------------------TT--------------------TCTTTTTACTTAACTTA-AGTAAAAGTAAAAAAAACAAGTAACT
droSim1	chr2h_random:1957079-1957156 +	CACTAG------tttTTTg-Gg--------------GTTgGgtTTgGg-----------------------------------tgTtTgTttGTttgGGGTgGGGGttgTggttT---------tTtGgtTTgTgTgTTGgTTTAAAATAAATTTTACGTTTTCTT-------------TT--------ATATGTCTAAAATGTTTTTCCTTATTTTA-TGCCAACTTTGGA----GACACAATT
droSec1	super_49:69261-69260 +	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droYak2	chrU:5296924-5297045 -	CGCCCA------CGCGGTGTCCGCTGATTGGTGC-AATTAAACTCAGATAACAGA-GTACAA-A-----------------------------------GCTAGAGCTTACCTCA------------------------------------------CGCTCGCTC-------------TT--------------------ATTGCTGGCTTGAGTTA-AGTAA---TAAGAACAATAACCAAAA
droEre2	scaffold_4784:24699890-24700005 +	CGCCCA------CGCGGTGTCCGATATTTAGTGATAAGCAAACTCAGACAACAGA-GAAAAACTTGCATATTACTT----------CTCTTCCCTTAGGGCAAGAGTTTATCTCT--------------------------------------------------------------------------CGT--------------------------------------GATTAATGAATGATG
droAna3	scaffold_13337:22362177-22362239 -	AAACAA------AATTTTTGAG------------------------------------------------GAACTTTTTAAG-TTTTTAA-----------------------------------------------------------------------------------------GTTCTTTTGTTAA--------------------------------------CATTTATTAATTGTT
dp4	Unknown_group_197:8680-8790 -	TAGGCA---------------------------A-AAAAAAACTTTAAAGATA-AG-ATTTATTA-----------------------------------ACAAAGTTTTTTTTA------------GGC--------------GGAA-----TAAGGAATAATTATAATGCGGTTTGAGCCTTACTGAAAA--------------------------------------AATGAATTAATAGCG
droPer1	super_42:425670-425715 -	TTCTGA------TCCTAAATT---------------------------------------------------------------------------------------------------------------------------------TACTTT---------------------------------ATATATGC-------------------------------AAAAAAAAGGAATAACT
droWil1	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12855:1272249-1272352 -	AATTCA------CTTGCAGTGCGA--------------GTAACTCAAACACTT-TT-AAGAATTTCATCGTCAC--TTA-AGTTTATGAG----------------CTT--TTAA--------------------------------C--TGCTGC---------------------------------AAATACTT-------------------------------CAAGCTTAAGTGCAAAA
droMoj3	scaffold_6473:9948517-9948664 -	AGTCAA------AATTCAATAT------------------------------------------------AAACTCAA-----------TTTA------GTAAAAACTGAAATCCATTTTTCTTATAGACTTAAGTCTCAATTTAAAT-----TTAGCAACAACTCAAATGTAGTTTCTCTC--AGT-------------GTATTACTCAT--TTTTGCACTTGGAATCAAAATCTTAAATAACT
droGri2	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:1365748-1365878 -	NA	GCCTAGTTCTCTCT-CGCTGGCTT--GAGTTAAGTAAAAATAAACTC-------------------------------------------AGAAACT---AA---------------------------------------------------------------------------------------AAATAATTTCT----------------------------G-AGTT------------------------------------------------------TCTTTT------TAGTTTCTGA-------------------------------------------------------------------------------GT-----------------------------TTCTTTT-------TA-------------CTTAA-CTTAAGT--------------------------------AAAAGT-A-AAAAAAACA----AGTAACT
droSim1	chr3R:3312089-3312223 +	580	GTGAAATAAAC----------------------------ATGGAAAA---------------------------AT-----------------AAAC---TA--------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATTATTTTCCGAAATATTTT-------T---------ATTAAATTAAACTTTCGGTTTG--------------------------------ATAA-----G-----------------------------------------------------------------------ATTTTTCTTTTTTAAGCT-AGTTAACTTG------------AAGACACAATAAT---TAA--A------ACAATAAA-GTTGC
droSec1	super_0:5232275-5232400 -	1395	TCTGTTTAGATA--------ATAT--AAA---------------------------------------------AT-----------------ACTT---AA---------------------------------------------------------------------------------------AAACT-ACCTAAATACCTTTA--------------------AAACTATTTTAAAAC-------------------------------------------TCATTA------AATTTTCTGA-------------------------------------------------------------------------------GCATCCTTTAATTTTGTTGTAA------------------------------ATTTCCGGTTTAA-AATAA--------------------------------------------------AT----A-TAACT
droYak2	chrU:7699741-7699868 -	7880	GCCGAGAATCCTTC-CACTGGATT-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CTTGTTTAGTTCTGAAAAGATACAACAGTTTATTTATTTTTTGTGGGTTTCAGTT---------------TTTTAAGTACA-----------------------------TTTA-------GA-------------TTTAT-GTAGAGT--------------------------------TAAAGTTT-AAGA--AAA----A-CAATT
droEre2	scaffold_4690:10662768-10662889 +	217	TTCCCCGATTTCTTCCAATAGAG------TT----------------TTGCAAAGAAAGATTGTAATTTGAAA---------------------AAT----------------------------------------------------------------------------------------------CCA-ATTTA------------------------------TATA------------------------------------------------------TA---------------------------------------------------------------------------------------------C-----ATACA-----------------------------ATAAG--------CTTAAATTTACTATTTAA-----AGT--------------------------------AAAAGT-A-AAAAATATA----A-GTAGC
droEug1	scf7180000409589:17030-17151 -	4158	TAAAAATA----------------------------------AGGTC-------------------------------------------GAAATTT---AA---------------------------------------------------------------------------------------AAATA-ATTTA----------------------------A-GCTT-----------TTTGCTTCGAAAAATAAGATTATTTTGTTTTC-----------------------------------------------------------------------------TCTAGATTTT--TT---------------G-----TTTGA-----------------------------GCAAG-ATCCAT------------------A----------------------------------GGT---AATGGT-A-AAAAATAAA----G---TTA
droBia1	scf7180000302412:53148-53274 -	5382	GCCTAATATTATAT-TGATGACTT--CAAACAT-TCATAGAGGC---TCGTTA------------------ATAAAATTAAGG----TTTGTAAAAT---AA--------TAAATATTT------------------------------------------------------------------------------TTT----------------------------A-TTTC------------------------------------------------------TA-------------------A-------------------------------------------------------------------------------AT-----------------------------TAATTTT-------A---------TCCTTTTTAA-AGTAA-A-----------------------------------AAA--A------ATAA-------AAA
droTak1	scf7180000414114:18056-18179 -	8384	TTACTCGTTGTG----ATCGGGTT-----------------------GC----------------------AATTAATGTAGG----TA-----------------------------------------------------------------------------------CAACC-------------------------------------------------------------------------CGTGAAAATTAAAAAAAGTTTAATTTC-----------------------------------------------------------------------------TGGCGTTTTT--TT---------------G-----TTATA-----------------------------GCTAG--------TTTTCATTT---ACTTAA-AAA-AAT-----------------------------------ACA--A------GTAA-------AAA
droEle1	scf7180000490214:566191-566317 -	3296	TATTTTTCACCC----AATAATTT--TATTTAAAAAAA---------------------------------AAAATATATAAG----TTCGGAGACT---AA--------AAACTATTTTTAATTTAAATTTTAAGTTTTTTCTTCCGATTATC-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TT------------------------TTTGA-TTTATA------------------------------GAT---CAC----------AA----A-TCACT
droRho1	scf7180000779438:6612-6740 -	12035	CCCATCCCTTTTTC--AATAACAT--AAGTTAACGTAACATAG---------------------------------ATTAAGA----TT------------------------------------------------------------------------------------------------------------TG-----------------------------AAAACTTATTTTTAGTC---------------------------------------T---CTTAAG------TAATA-GAGA-------------------------------------------------------------------------------AGA----------------------------TTCAATA-------AATAAGAATAA--------A--GTTAAA--------------------------------AAAAA----AAAA--AAA----A-AAGTA
droFic1	scf7180000454069:4434-4563 -	1681	TATTTTGCTGAC----------CA--TAGCTACTGT-----------------------------------AAAATATGCAAGCTTTTTCGCAAACTGTTAAAAATAAATAGACGATTTTG--------CTTTAGGGTTTTTATTCG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GA-----------------------------TTTA-------TA-------------TTTAA-TGTAAAC--------------------------------AAAAAC-A-AA----AAA----A-AAAGG
droKik1	scf7180000302385:653912-654032 -	4041	TTTTAAGTCTTTGT-AGATGAGCT-----------------------TCA--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTAAAAAACTAACTCGTTT-------G---------AATAA-------------------------------------------------------------------------------ATATAACCCTGTTTCATTATATATTCCTAATTTTTCTTA------AC-------------CCTAA-CTTACC---------------------------AATAAT---TAT--C------CAAA-------AAA
droAna3	scaffold_13340:15609788-15609911 -	6100	CTCTTCCTCCGGCT-TCATGATTT--TTTGAAACTAAAATGAAA-TG------------------------------------------CAGAAATG---TA---------------------------------------------------------------------------------------ACAGGGTTTTT---------GAAATAATATTATGTTTTTGATATTTGCCT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAA-------G------AT-----TCTTAA-GTTAAGA-----------------------------------ATA--A------ACAA-------AAA
droBip1	scf7180000395052:42630-42754 +	1581	TAGATCAGTCTT----ACTGTTTTTTTTGTT----AAA-ATAATATA-------------------------------------------TAAAACA---AT---------------------------------------------------------------------------------------AAATAATATAT----------------------------A-AATT------------------------------------------------------TACTTTTA---------------------------------------------------------------CTTA-----G-----------------------------------------------------------------------ACTTTTCTAATTCA-----A-A----------ATAGTATTGGTCAATTAATTAT---TGT--A------AAAA-------AAA
dp4	Unknown_group_314:10340-10462 -	2042	GACCAGGTTTCCCA-TGCAAGAACTAGATTTATAA--AGTTCATTTT------------------------AAAACTTGCATATAACTCCGC-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTTCC----------------------------------------------------------------------------GTTGTATTTTG----------------------------------------ACTAG-G----AACAAAATTATTCTTATTAA-ATTAAAT-------------------------------------T----------AA----A-TTAAA
droPer1	super_56:319063-319192 -	4745	CCCGAATACTTTGT-AGCTAAAGC------------------------------------TTATGGTCTAGAAAATATTCAGC----TT------------------------------------------------------------------------------------------------------------------------------------------------------------T-CAATTTGAAAATTAAAAATAT-----TTTTGGTGGTATTTTTA-------------------A-------------------------------------------------------------------------A-----CTAAA-----------------------------GTTTGACTTTAA------AA-----CCTCTA-GAA--AA-----------------------------------GCT--T------GAAA-------TAA
droWil1	scaffold_180764:2005052-2005182 -	5944	TTTGGTTGGTTGTT-TTTAAGTAT-----------AAAATAAAT-TA-------------------------------------------AGAAATT---AT---------------------------------------------------------------------------------------AAAATATGTTA----------------------------G-AGTG------------------------------------------------------TTTGTT---------------------------------------------------------------TGGTTTCGGTG---------------TTGAAATGA-T-----------------------------ATATGATA---ATGTAAGAT--------ATA----------------------------------GGT---AAATGT-G-ATATATAGA----A-AGATT
droVir3	scaffold_13049:25084925-25085038 +	2522	AAGTAAAAAT-----------------------------ATGATATC--------------------------------------------TCAATA---AA---------------------------------------------------------------------------------------AAATTACTTTC----------------------------A-AGTT------------------------------------------------------TCTTTTTC---------------------------------------------------------------ATCT-----TTTTTTTTTATTTTA----------------------------------------ATTAA------A---------------------T--------------------ATTTACCAAATAACT--GAAGAT-A-ACAACAATA---TT-TTACT
droMoj3	scaffold_6500:769823-769955 -	5287	GTAAAGTGATAA----------------------------------A-------------------------------------------GAAAATA---AA---------------------------------------------------------------------------------------ATGAA-A-------------------------------------------------T-AAATGTACAAATAAAATA-TAATTTTTTT------------TTATTTTTATTTTATTTTATTA-------------------------------------------------------------------------------TTATT-----------------------------ATTAT--------TTTTT-------TTTTAA-CTTAAGTTAAATTGAAAAAAG-------------------------------CAATA---GC-TGACT
droGri2	scaffold_15110:11942882-11943003 +	343	GCTGAGAATTCTCT-ACTGGGAGT-------------------------------------------------------------------------------------------------------------------------------ATCTCTTGGTTTAATTTAGTATAAGCGGCTGGAACTATAAGACAATCTG----------------------------C-AACT------------------------------------------------------ATTTTT---------------------------------------------------------------TTT-----------------------------------------------------------------TT-------TG-------------TATAA-CTAAAAA--------------------------------AAAGAT-A-AAAGATACA----A---GTA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GCCTAGTTCTCTCTCGCTGGCTTGAGTTAAGTAA-AAATAAACTCAGAAACTA-AA-AATAATTTCTGAGTTTCTTTTT-AGTTTCTGAG-----------------------------------------------------------------------------------------TT--------------------TCTTTTTACTTAACTTA-AGTAAAAGTAAAAAAAACAAGTAACT

Size

Hit Count

Total Norm

droSim1

CACTAG------tttTTTg-Gg--------------GTTgGgtTTgGg-----------------------------------tgTtTgTttGTttgGGGTgGGGGttgTggttT---------tTtGgtTTgTgTgTTGgTTTAAAATAAATTTTACGTTTTCTT-------------TT--------ATATGTCTAAAATGTTTTTCCTTATTTTA-TGCCAACTTTGGA----GACACAATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
........................................................................................................................................................................................................................TA-TGCCAAGTTTAGA----GAC......	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CGCCCA------CGCGGTGTCCGCTGATTGGTGC-AATTAAACTCAGATAACAGA-GTACAA-A-----------------------------------GCTAGAGCTTACCTCA------------------------------------------CGCTCGCTC-------------TT--------------------ATTGCTGGCTTGAGTTA-AGTAA---TAAGAACAATAACCAAAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................TTGGTAC-AATTAAACACA.......................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CGCCCA------CGCGGTGTCCGATATTTAGTGATAAGCAAACTCAGACAACAGA-GAAAAACTTGCATATTACTT----------CTCTTCCCTTAGGGCAAGAGTTTATCTCT--------------------------------------------------------------------------CGT--------------------------------------GATTAATGAATGATG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................................................................GCAAGAGTTTATxTAT--------------------------------------------------------------------------CGT--------------------------------------G..............	19	1	1.00	0.00	0.00	0.00	1.00

droAna3

AAACAA------AATTTTTGAG------------------------------------------------GAACTTTTTAAG-TTTTTAA-----------------------------------------------------------------------------------------GTTCTTTTGTTAA--------------------------------------CATTTATTAATTGTT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

TAGGCA---------------------------A-AAAAAAACTTTAAAGATA-AG-ATTTATTA-----------------------------------ACAAAGTTTTTTTTA------------GGC--------------GGAA-----TAAGGAATAATTATAATGCGGTTTGAGCCTTACTGAAAA--------------------------------------AATGAATTAATAGCG

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TTCTGA------TCCTAAATT---------------------------------------------------------------------------------------------------------------------------------TACTTT---------------------------------ATATATGC-------------------------------AAAAAAAAGGAATAACT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.................AATT---------------------------------------------------------------------------------------------------------------------------------TACTTT---------------------------------ATTTATGA-------------------------------.................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.................AATT---------------------------------------------------------------------------------------------------------------------------------TACTTT---------------------------------ATTTATGG-------------------------------.................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

AATTCA------CTTGCAGTGCGA--------------GTAACTCAAACACTT-TT-AAGAATTTCATCGTCAC--TTA-AGTTTATGAG----------------CTT--TTAA--------------------------------C--TGCTGC---------------------------------AAATACTT-------------------------------CAAGCTTAAGTGCAAAA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.................AGTACTA--------------GTAACTCAAAC....................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droMoj3

AGTCAA------AATTCAATAT------------------------------------------------AAACTCAA-----------TTTA------GTAAAAACTGAAATCCATTTTTCTTATAGACTTAAGTCTCAATTTAAAT-----TTAGCAACAACTCAAATGTAGTTTCTCTC--AGT-------------GTATTACTCAT--TTTTGCACTTGGAATCAAAATCTTAAATAACT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

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			None						None			None
UNAFold Image			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