sblock2216- 12- and 20-way alignments

sblock2216	chr2L:2765182-2765267 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 2765229-2765251
   star strand at position 2765199-2765220
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:2765167-2765282 -	TTTGTGTA-------ACCATTATCTCACACTCGCAAAATATGTAGG-TACAGTGGATAA---TCTCTAAGGCGAA----------------------TATTGTCTGTATCTT-CTTAGGTGTCTGGGAGCGAGCCACAA---G---TGCTGAGTAT
droSim1	Unknown	TTTGTGTA---------------------------------------TACAGTGGAAAA---TCTCTAAGGCGAA----------------------TATTGTCTGTATCTT-CCTAGGTGTCTGGGAGCGAGCCACAA---G---TGCGGAGTAT
droSec1	Unknown	TTTGTGTA---------------------------------------TACAGTGGAAAA---TCTATAAGGCGAA----------------------TATTGTCTGTATCTT-CGTAGGTGTCTGGGAACGAGACACAA---G---TGCGGAATAT
droYak2	Unknown	TTTGTATA---------------------------------------TACAGTGGAAAC---TCTCTAAGCTGAA----------------------CATTTTCTATATCTT--CCAGGTGTCTGGGAGCGACCCACTA---C---TGCGGAGTAT
droEre2	scaffold_4929:2817993-2818096 -	TAAATACATGGAAAAACGATCATC----------------AGTAGGTCACAGTGGAAAC---TCTCTAAGACGAA----------------------TGTGGTCTATATCTT-CCTAGGTGTCTGGGAGCGACCCGCTA---G---TGCTGAATAC
droAna3	Unknown	TTTGTTTA---------------------------------------TACAGTGGGAACGAGTCTTAAAAATGAA----------------------AAA--------TATT-TTCAGGCATCTGGGAGCGACCAGCACAGACGGCCACTTCTTAT
dp4	Unknown	TTTGAC-----------------------------------------GGCAGTGGGTCCG-GTCTGACAAATGAA------------------------------GT-TTT-CCGCAGGTTTCTGGGAGCGCCCCACAT---CGTCCACCACGTAT
droPer1	Unknown	TTTGAC-----------------------------------------GGCAGTGGGTCCG-GTCTGACAAATGAA------------------------------GT-TTT-CCGCAGGTTTCTGGGAGCGCCCCACAT---CGTCCACCACGTAT
droWil1	scaffold_180772:1542185-1542212 -	CT-----------------------------------------------------------------------------------------------------------------------TCTGGGAACGACCA---------GCCACAAAATAT
droVir3	scaffold_12963:11387645-11387742 -	TGCGTATGCTAG----ATACC--------------------------AGAAGCAGATCAA-GTTTG--------------------CTCACTTT--ACATTTTATGT-CCG-CAACAGCTTTCTGGGAGAGTTTTAATC---CAGTTAAAAGATTT
droMoj3	Unknown	TGAGCTAATT-------------------------------------------------G-GAATCCAAAGTGCAGTTTTTTtTtTTtTtTtTtgtTtgtTtTtTGT--tTtTTTAAGCGTTCTGGGAGAGCTACAATT---CAGCTAAAAAGTTT
droGri2	Unknown	TGCGTACC---------------------------------------------------------------CAAA----------------------TATTTTCAAT-TCC-CAATAGCTTGCTGGAAGAAGAGCTTTC---C---ACATAGGTTT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:2765167-2765282 -	NA	TTTGTGTAACCATTATCTCACAC--------------TCGCAAAATATGTAGGTA-------CAG-----------------------------------------------------------------------------------------TGGATAATCTCTAAGGCGAATAT-TGTCTGT-ATC---------------------TTCTTAGGTGTCTGGGAGCGAGCCACA---AGTGCTGA---GTAT
droSim1	chr2L:2727612-2727727 -	2	TTTGTGTAACCATTACCTCACAC--------------TCGCCAAATATGAAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAAATCTCTAAGGCGAATAT-TGTCTGT-ATC---------------------TTCCTAGGTGTCTGGGAGCGAGCCACA---AGTGCGGA---GTAT
droSec1	super_5:931138-931253 -	1	TTTGTGTAACCATTTTCTCACAC--------------TCGCCAAATATGAAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAAATCTATAAGGCGAATAT-TGTCTGT-ATC---------------------TTCGTAGGTGTCTGGGAACGAGACACA---AGTGCGGA---ATAT
droYak2	chr2L:2760749-2760863 -	1	TTTGTATAATCATTATCTTACAT--------------TCAAATAATATGTAGGTA-------CAG-----------------------------------------------------------------------------------------TGGAAACTCTCTAAGCTGAACAT-TTTCTA-TA-T---------------------CTTCCAGGTGTCTGGGAGCGACCCACT---ACTGCGGA---GTAT
droEre2	scaffold_4929:2817993-2818131 -	1	TAAAACC----ATAATCTCACAT--------------TTGCATAATATGTAGGTA-------CA-----------------------------------------TGGA------------AAAACGATCATCA---------GTAGGTCACAGTGGAAACTCTCTAAGACGAATGT-GGTCTAT-ATC---------------------TTCCTAGGTGTCTGGGAGCGACCCGCT---AGTGCTGA---ATAC
droEug1	scf7180000409554:3346024-3346246 +	1	TTTGTATAATCATAATTTCCCATGACTATATTTCAATGCCCCTATTGTGGGGCTT-------CAG----TACA-CATCTTCA---AGAATCATTTAATATTCACATTGGGATGCAGATTATCATATAATCATCACCTTAGTGTGTAAAGGACAATGAAAGCTT-CCAAAAAAAATTT---TTTA-TT-T--------AAGTTTTTCCATCTTTTTAGGTGTCTGGGAGCGGCCAACAATGAGTTCCGA---GTAC
droBia1	scf7180000302188:1767970-1768092 -	1	TTTGTATAAG-GTCTA-----------------------------------AGGACATTGGCCGTTAT-TAA--C--CATAT---AAA--------------------------------------------------------------ACTATAAAAATTACATAACTTAAATAT-ACTTATT-TCC---------------------TGTTTAGGTTTCTGGGAGCGACCCACAACCAGTGCCGA---GTAC
droTak1	scf7180000415705:514059-514162 -	1	ATTCATTGAAT------------------------------------------CCATTCATGCAGTGCTCTA--A--TATGTATAG--------------------------------------------------------------------CAAATAAT-----------ATATATTTTTG-TA-C---------------------CTTTTAGGTTTCTGGGAGCGACCAACGTCTAGCGCCGA---GTAC
droEle1	scf7180000491273:412313-412354 +	2	TTTG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TAGGTGTCTGGGAGCGACCCACGTCTAATGCCGA---CTTC
droRho1	scf7180000766156:59158-59229 +	2	CTAAAGCAACATTTATTA----T---------------------------------------------------------------------------------------------------------------------------------------------------------T-TGTTTCAAA-A---------------------CTTGTAGATGTCTGGGCGCGACCCACAACAAATGCCGA---GTAC
droFic1	scf7180000453924:716599-716727 -	1	TATGTACATATGGA-------------------------------------T-----GAGTATA----------C--TTTTT---AAAATTAAAAAATATATAAATTGG------------TTTA-----------------------------TGAATATCATCTCA-ATAAATAC-TTTTTG-AA-C---------------------TTTTTAGGTGTCTGGGAGCGACCCACAACGAATTCCGA---GTAT
droKik1	scf7180000302271:228107-228177 -	1	TTTCTAAAACC---------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACAA-ATTATG-T--A---------------------TTTATAGGAGTCTGGGAGCGACCCTCATCGAGTACCGAAACCTTT
droAna3	scaffold_12984:244381-244458 -	2	TAC------------------------------------------------------------AGTGGGAACG--------------------------------------------------------------------------------------AGTCTTAAAAATGAAAAA-T---------A---------------------TTTTCAGGCATCTGGGAGCGACCAGCACAGACGGCCACTTCTTAT
droBip1	scf7180000396574:369645-369692 -	2	AT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------A---------------------CTTTCAGGTATCTGGGAGCGACCAGCACAGACGGCCGCTTCTTAT
dp4	chr4_group4:2108184-2108280 -	1	TTTGACGCTA-ATTGG-----------------------------------TGCACACTAAGCAGTGGGTCCGG-------TCTGA------------------------------------------------------------------------------------CAAA-----TGAAG-TT-T---------------------TCCGCAGGTTTCTGGGAGCGCCCCACATCGTCCACCAC---GTAT
droPer1	super_10:1114845-1114941 -	1	TTTGACGCTA-ATTGG-----------------------------------TGCACACTAAGCAGTGGGTCCGG-------TCTGA------------------------------------------------------------------------------------CAAA-----TGAAG-TT-T---------------------TCCGCAGGTTTCTGGGAGCGCCCCACATCGTCCACCAC---GTAT
droWil1	scaffold_180772:1542185-1542212 -	1	CT--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCTGGGAACGACCAGC------CACAAA---ATAT
droVir3	scaffold_12963:11387645-11387742 -	1	TGCGTATGCTAGATA------------------------------------------CC-AGAAGCAGATCAAG-------TTTG-------------------------------------------------------------------------------CTCA-CTTTACAT-TTTATG-TC-C---------------------GCAACAGCTTTCTGGGAGAGTTTTAATCCAGTTAAAAG---ATTT
droMoj3	scaffold_6500:20137581-20137687 -	1	TGAGCTA----ATTGG-----------------------------------AATCCAAAGTGCAGTTTTTTA--T--ATTATATAT--------------------------------------------------------------------ACAT---------A-CAT-ATATATATATG-TA-T---------------------ATTTAAGCGTTCTGGGAGAGCTACAATTCAGCTAAAAA---GTTT
droGri2	scaffold_15126:5047932-5047984 -	1	AATATTT-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAA-TT-CCCAATAGC-------------TTGCTGGA---AGAAGAGCTTTCCACA--------TAG---GTTT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTTGTGTA-------ACCATTATCTCACACTCGCAAAATATGTAGG-TACAGTGGATAA---TCTCTAAGGCGAA----------------------TATTGTCTGTATCTT-CTTAGGTGTCTGGGAGCGAGCCACAA---G---TGCTGAGTAT

Size

Hit Count

Total Norm

droSim1

TTTGTGTA---------------------------------------TACAGTGGAAAA---TCTCTAAGGCGAA----------------------TATTGTCTGTATCTT-CCTAGGTGTCTGGGAGCGAGCCACAA---G---TGCGGAGTAT

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

TTTGTGTA---------------------------------------TACAGTGGAAAA---TCTATAAGGCGAA----------------------TATTGTCTGTATCTT-CGTAGGTGTCTGGGAACGAGACACAA---G---TGCGGAATAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......TA---------------------------------------TAAAGTGAAAAA---TCTATA........................................................................................	20	1	1.00	0.00	1.00	0.00
..................................................................................................................AAAGGTGTCTGGGAACGAGA......................	20	1	1.00	1.00	0.00	0.00
.........................................................................................................................TCTGGGAACGAGACACAA---G---TGC.......	22	1	1.00	1.00	0.00	0.00
..........................................................................................................................CTGGGAACGAGACACAA---G---TGC.......	21	1	1.00	0.00	0.00	1.00
....................................................................................................................AGGTGTCTGGGAACGAGA......................	18	1	1.00	0.00	1.00	0.00
......TA---------------------------------------TAAAGTGAAAAA---TCTAT.........................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

TTTGTATA---------------------------------------TACAGTGGAAAC---TCTCTAAGCTGAA----------------------CATTTTCTATATCTT--CCAGGTGTCTGGGAGCGACCCACTA---C---TGCGGAGTAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.......................................................................................................................TGTCTGGGxGCGGCCCA....................	16	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

TAAATACATGGAAAAACGATCATC----------------AGTAGGTCACAGTGGAAAC---TCTCTAAGACGAA----------------------TGTGGTCTATATCTT-CCTAGGTGTCTGGGAGCGACCCGCTA---G---TGCTGAATAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................GAAGC---TCTCGAAGACGAA----------------------...........................................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

TTTGTTTA---------------------------------------TACAGTGGGAACGAGTCTTAAAAATGAA----------------------AAA--------TATT-TTCAGGCATCTGGGAGCGACCAGCACAGACGGCCACTTCTTAT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

TTTGAC-----------------------------------------GGCAGTGGGTCCG-GTCTGACAAATGAA------------------------------GT-TTT-CCGCAGGTTTCTGGGAGCGCCCCACAT---CGTCCACCACGTAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...................................................................................................................AAGGTTTCTGGGAGCGCC.......................	18	1	1.00	0.00	0.00	1.00	0.00

droPer1

TTTGAC-----------------------------------------GGCAGTGGGTCCG-GTCTGACAAATGAA------------------------------GT-TTT-CCGCAGGTTTCTGGGAGCGCCCCACAT---CGTCCACCACGTAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....AC-----------------------------------------CGCAGTGGGTCCG-GGC............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................GCAGTGGGTCCG-GGCAGA.........................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

CT-----------------------------------------------------------------------------------------------------------------------TCTGGGAACGACCA---------GCCACAAAATAT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

TGCGTATGCTAG----ATACC--------------------------AGAAGCAGATCAA-GTTTG--------------------CTCACTTT--ACATTTTATGT-CCG-CAACAGCTTTCTGGGAGAGTTTTAATC---CAGTTAAAAGATTT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TGAGCTAATT-------------------------------------------------G-GAATCCAAAGTGCAGTTTTTTtTtTTtTtTtTtgtTtgtTtTtTGT--tTtTTTAAGCGTTCTGGGAGAGCTACAATT---CAGCTAAAAAGTTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.............................................................................TTTTTTTTTTTTTTTTTGTTG..........................................................	21	14	0.07	0.00	0.00	0.00	0.07
.....................................................................................TTGTTTTTTGTTTGTTGTT....................................................	19	3	0.33	0.33	0.00	0.00	0.00
...............................................................................TTTTTTTTTTTTTTCTTTTG.........................................................	20	12	0.08	0.00	0.00	0.08	0.00
.........................................................................CCGTTTTTTTTTTTGTTTTT...............................................................	20	2	0.50	0.00	0.00	0.50	0.00
.......................................................................................TTTTTTTGTTTTTTGTTTGT--T..............................................	21	12	0.08	0.08	0.00	0.00	0.00
.........................................................................................TTTTTGTTTGTGTTTTGT--CT.............................................	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................TTTTTTTGTTTTTTGTTTGTT.......................................................	21	12	0.08	0.08	0.00	0.00	0.00
...........................................................................................TTTTTTTGTTTTTTGT--TTGTT..........................................	21	12	0.08	0.08	0.00	0.00	0.00
.....................................................................ATAGCAGTTTTTTTTTTTTTT..................................................................	21	1	1.00	0.00	0.00	0.00	1.00
............................................................................TTTTTTTTTTTTTTTTTTTTTT..........................................................	22	51	0.02	0.02	0.00	0.00	0.00
..............................................................................TTTTTTTTTTTTTTTTTGTTG.........................................................	21	14	0.07	0.00	0.00	0.00	0.07
................................................................................TTTTTTTTTCTGTTGTTTGT........................................................	20	1	1.00	1.00	0.00	0.00	0.00
.................................................................................TTTTTTTTTTTTTTTTTGTTG......................................................	21	14	0.07	0.00	0.00	0.00	0.07
...........................................................................TTTTTTTTTTTTTTCTTTTG.............................................................	20	12	0.08	0.00	0.00	0.08	0.00
............................................................................TTTTTTTGTTTTTTGTTTGTT...........................................................	21	12	0.08	0.08	0.00	0.00	0.00
......................................................................TTGCAGTGTTTTTTTTTTTTTTT...............................................................	23	1	1.00	0.00	0.00	0.00	1.00

droGri2

TGCGTACC---------------------------------------------------------------CAAA----------------------TATTTTCAAT-TCC-CAATAGCTTGCTGGAAGAAGAGCTTTC---C---ACATAGGTTT

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