sblock53978- 12- and 20-way alignments

sblock53978	chr2R:1252139-1252239 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1252194-1252217
   star strand at position 1252162-1252183
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:1252124-1252254 +	TTGAACTTACTGTTTAATAATGTTAAATACAGA-------------------TATATAA---T-TAAAGTTGCCTTGGCTACGACTTGCTGGCTCGTCGGTATGGCTGCGATTGAGCTATGATCTGCA-T------------TTAATTATGGTCCCCGCCATATTCC
droSim1	chr2R:202584-202646 +	TTGAACTTACTGTTTATTAATTTCAAACACAGT-------------------TTGAACACAGTT-------------------------------------------------------------------------------------TGGTCCCCGCCATATTCG
droSec1	super_59:159253-159315 +	TTGAACTTACTGTTTATTAATTTCAAACACAGT-------------------TTGAACACAGTT-------------------------------------------------------------------------------------TGGACCCCGCCATATTCG
droYak2	chrU:3064916-3065032 +	CTTAACTAATT-----TTAGTTAAAGGTAAAAA-------------------TGTATAA---TTTTATGTTGCCTTAGTTGCAACTGAAAAACTTATTAGTACGGCTACCATTAAGCTATGCTTTGCAAT------------TTATTTATGCTCCCCGCCATATTTT
droEre2	Unknown	GTTAGCTTAT-----GTTAATTTATGGCATAAA-------------------TTAATCA---ATTTCAGTTGCCTTAGTTGCAACTG-CAAAGTTGTCAGTAAAGCAACTATTGCGTTGTACTTTTTA-T------------GTCAGACTAATCCTCTCTCCGCTCC
droAna3	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181154:1315791-1315797 -	ATGAACT----------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:12787943-12788046 +	TTT-----ACCGTCTGCGAATGTTAACAACAAATATTTGATGAAAATGAAATCTAA---CAATT-----------------------GAATGC---------------CCGTCGGGCTGAGCATTTAA-TAATTTACTGCGCATAACAATG----------------
droGri2	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:1252124-1252254 +	NA	TTG--AACTTACTGTTTAATAA---TGTT-------AAAT----------ACAGATATA------------TAA-TTAA----------------------------------------------------------AG------------------------------------------------------------TTGCCTTGGCTACGACTTGCTGGCTCGTCGGTATGGCTGCGATT-------GAGCTATGATCTGCATTTAATTATGG---------TCCC--------------------------------------------------CGCCATATTCC
droSim1	chr3R:1415632-1415763 +	599	TTG--AACTCACTGTTTATAAT---TTTC-------AAAC----------AGAGATATA------------TAATTTCA----------------------------------------------------------AA------------------------------------------------------------TTGCCTTGGCTGTGTTCTGCTGGCTCGTCGGTATGGCTGCGATT-------GAGCTACGAATTCCATTTAATCATGG---------TCCC--------------------------------------------------TGCCATATTCC
droSec1	super_6:1494904-1495035 +	149	TTG--AACTCACTGTTTATAAT---TTTC-------AAAC----------AGAGATATA------------TAATTTCA----------------------------------------------------------AA------------------------------------------------------------TTGCCTTGGCTGTGTCCTGCTGGCTCGTCGGTATGGCTGCGATT-------GAGCTACGAATTCCATTTAATCATGG---------TCCC--------------------------------------------------TGCCATATTCC
droYak2	chr2h_random:1463679-1463807 +	184	TTA--AACTCACTGTTTATTAA---TTTC-------ACAC----------ACAGATAGA------------AAAATTAA----------------------------------------------------------AG------------------------------------------------------------TTGCCCGAGCTGCAACTTAATGGCTCATTAGTAGGGCTGCGATT-------GAGCTATGATTTGCATTTCATG---C---------TGCC--------------------------------------------------CGCTATATTCC
droEre2	scaffold_4929:26255623-26255753 +	1738	TTA--A-CTCACTGTTTCTTAA---TTTC-------CCAC----------ACAGATATA------------AAAATTTA----------------------------------------------------------AG------------------------------------------------------------GTGCCCTAGCTGCAACTTGATAGCTCGACGGTATGGCTACGATT-------GAGCTATGATTTCCATTTTACCATGC---------TCCC--------------------------------------------------CGCCATATTCC
droEug1	scf7180000407524:9378-9509 -	2377	TTC--T---CAGTGATTAATGC---AATC-------ACTT----------TGTGAAATT------------TGTTT------------------------------------------------------------------------------------------------------------------------------CGCGAGCT---------------------------------------------CGGTTTCACTTTGATCATCCG---------AATCCGCAATATGACAGCTACTGATTAGTAGTTTGGCCTACATATCGTAGGCCTCGCCATT-TTC
droBia1	scf7180000301469:14871-15004 -	4191	TAC--CACTCACTTTTATTTTA---TTTT-------TGGC----------ACAAAATTT------------A-A-CTTA----------------------------------------------------------GG------------------------------------------------------------C--TTCTAGCTGCATCTGTCTGGTTCGGCAATATGGCTGCGACG-------ATACCCATATCTGCTGATCATT---TTTATTTCTGCCCC--------------------------------------------------CGCCATATTAC
droTak1	scf7180000410435:1249-1378 +	74	TAA--CACTCACTTCTTTCTGT---TTTT-------TTGC----------ACAAACACT------------TA--TTTA----------------------------------------------------------AG------------------------------------------------------------TAACTCCCGCTGCGTCCAGCTTCTGGGTCAATATGGCTGCGACT-------ATTCTA--ATCTGCCTATCATCATGACG-------ATAT--------------------------------------------------CGCCATATTCC
droEle1	scf7180000490995:30198-30325 -	4335	TTC--AAATGGCTTTGTACGTT---TTTT-------TGTA----------------ATT------------TA--TTAA------------------------------AATCGCCCACTGACGA----------------------------------------------------------------------------------GGTTTGATTTTCTCCCTAGGCTCTATTACTGTGTTT-------ATGCTATGAATTTCATGAATTATTGA----------A-T-------------------------------------------------AC-ATGAAATCA
droRho1	scf7180000780189:8752-8880 -	13464	TCTACCACTCACTTTTTTTTGA---TTTC--------GGC----------ACAAACAGT------------A-A-TTTA----------------------------------------------------------A-------------------------------------------------------------AAACTCCCGCTCCGTCTAGCTTCCTGGACAATATGGCTGCGACC-------ATCCCATTATCTGCCTATCATT---GCC-------ATAT--------------------------------------------------CGCCATATTCC
droFic1	scf7180000453278:52662-52792 +	335	TCT--AACTCACTTTTTACAAA---ATTT-------ACAC----------AAAATTAAT-------------AC--TCG----------------------GTTAA---AATTGTCCGTCTACCACTTTTGCCTTTT--------------------------------------------------------------------CGGGTACAACTGAACGGT-------GATCCGTATGATC-------ACGC-----------------CATGT---------TCCC-----------------------------------------------TA--ACATCTTTTC
droKik1	scf7180000302639:2558577-2558706 +	2608	TCC--AGCTTATGTA-A-TTAG---CTCG-------ACTC----------CAGACTATA------------TAATCACG----------------------------------------------------------CT----T-------------------------------------------------------TTGCCTTAGATTCAATTAGCTAGTGAGGCGTTAAGCTTGTTCAG-------GTTCCAATTGCTGCATTTACTTTCG----------GCAT--------------------------------------------------CGCATTACCGT
droAna3	scaffold_13337:22759501-22759624 +	2775	TTA--ACTT-ATTTGCTCCGTTTATTTCCCGCAGATTCAC----------CTACGCATG------------ACA-TTAA--------------------------A---GATGGTCTTTTT---------------A---------CGT------------------------------------------------------CAACACTAGAATT------------GGATTGGTTATTATC-------ACGTGAAGATCTG-------------------------------------------------------------------------GCTCAAGATA-TAG
droBip1	scf7180000395368:41128-41264 +	1841	TTG--AATTTTCTGTATC--------------------------------AAAAATTTA------------AAA-TTAA----------------------------------------------AATAT-------GTTTTTCTTATTATTAATT-----------TTTACTAAATTATCTTATTCTTATCATTTCAT--------------------------AGCCATTTTTCTGTTTTC-------ATTTTATTTGTTGCATATGCGATAG----------AC-----------------------------------------------------------ATCT
dp4	Unknown_group_9:35228-35362 -	1819	TCA--AGCCCAGCC--TGATAA---TCGT-------TATTC---------TAGA-TTTC------------TAA---------------------------------------------------AAAAT-------AATTTCCTTATTTATGAGTTAAGTTTCCTACCCGCTATTTTATACGGTTCTTAGTGGTTTTC--------------------------AATCT-------------------------------CCTATTTACTACTAT---------TT-------------------------------------------------------TCCGCCCT
droPer1	super_3:1090211-1090335 -	4147	TTT--ACCATATAGCTTGCATA---TGCT-------ACAT----------ACATATATG------------TAGTTTCG----------AA------------GAA-------------------------------AT------------------------------------------------------------TTAC---AATTTTAAAAAGCTGAT-------GAATGCTGTCCTT-------GGGCTCTAAATATCCTTAAATATCCG---------TATC--------------------------------------------------C--TTTATATT
droWil1	scaffold_180935:22520-22643 +	1683	ATA--TACCCTTGCA-G------------------------------------------------------------------------------TCCTTGGTAATAATAATTTTACATGTACAAAATTT-------GT------------------------------------------------------------------TTTCTGCAACTC---AATTCATCAGAATACAAACAATT-------TTACTCTATTTTACAATTTGTT---C---------TTCT--------------------------------------------------TCCCTCATTCC
droVir3	scaffold_12963:2382868-2383002 +	1915	TGT--ACTGGGG-GATGCTGAA---C-TT-------GAACTTGGGCGGGCATAAATACAGATTGATGTATAAGCTTTAA----------------------------------------------------------TA------------------------------------------------------------ATACCTCCACTGGAACCTGCCG----CACAGCTTGGCCGTAAAG-------TGAGTGTATTTAACATTTTATTT------------------------------------------------------------------------TGTTC
droMoj3	scaffold_6680:16275074-16275209 -	7391	ACT--TGTCTG---TAA-ATGA---TGTT-------AAAT----------CAGAACACA------------AAA-TTAAAATTGAATTGTTGCATTTTGTGGCAGC----------------------------------------------------------------------------------------------------------------------AATCATATTGACTGCGAGTTGATTTGAAGCTGAAATTTCCATTTTACTTTAA---------AT------------------------------------------------GCTTTACTGTATCAA
droGri2	scaffold_14853:628777-628885 -	1128	TAC--AATTTCAAGT-TGTAAA---GTAT-------ATAT----------ATATATATA------------TAGTGTTG----------TTG------------------------------------------------------GCTTGGACGTG-------------------------------------------------------GAAGCGCTTACGCGTGTGTATATATAATATA-------TAG----------CATATAATA----------------------------------------------------------------------TACATATA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTGAACTTACTGTTTAATAATGTTAAATACAGA-------------------TATATAA---T-TAAAGTTGCCTTGGCTACGACTTGCTGGCTCGTCGGTATGGCTGCGATTGAGCTATGATCTGCA-T------------TTAATTATGGTCCCCGCCATATTCC

Size

Hit Count

Total Norm

droSim1

TTGAACTTACTGTTTATTAATTTCAAACACAGT-------------------TTGAACACAGTT-------------------------------------------------------------------------------------TGGTCCCCGCCATATTCG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.....................................................TGAACACAGCT-------------------------------------------------------------------------------------TGGTACC...........	18	1	1.00	0.00	1.00	0.00	0.00
.....................................................TGAACACAGCT-------------------------------------------------------------------------------------TGGTACCC..........	19	1	1.00	0.00	1.00	0.00	0.00

droSec1

TTGAACTTACTGTTTATTAATTTCAAACACAGT-------------------TTGAACACAGTT-------------------------------------------------------------------------------------TGGACCCCGCCATATTCG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................ACACAGTT-------------------------------------------------------------------------------------TGGACCCCGCCAT.....	21	1	1.00	0.00	1.00	0.00

droYak2

CTTAACTAATT-----TTAGTTAAAGGTAAAAA-------------------TGTATAA---TTTTATGTTGCCTTAGTTGCAACTGAAAAACTTATTAGTACGGCTACCATTAAGCTATGCTTTGCAAT------------TTATTTATGCTCCCCGCCATATTTT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GTTAGCTTAT-----GTTAATTTATGGCATAAA-------------------TTAATCA---ATTTCAGTTGCCTTAGTTGCAACTG-CAAAGTTGTCAGTAAAGCAACTATTGCGTTGTACTTTTTA-T------------GTCAGACTAATCCTCTCTCCGCTCC

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

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

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

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

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

ATGAACT----------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

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

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TTT-----ACCGTCTGCGAATGTTAACAACAAATATTTGATGAAAATGAAATCTAA---CAATT-----------------------GAATGC---------------CCGTCGGGCTGAGCATTTAA-TAATTTACTGCGCATAACAATG----------------

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	None	None		None
UNAFold Image						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