sblock181387- 12- and 20-way alignments

sblock181387	chrX:9538471-9538556 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 9538521-9538543
   star strand at position 9538500-9538519
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:9538456-9538571 -	TTTTCAGATCTCCAAGATATTTGCAAAGAT-----ACTGAATTTATGCGATAAACTTGCACTGTCATAGTAGTA-----GTTCTTTCCATAAATTCGTAATGTAATGGAAACGAAT-------TAAAAATCTG
droSim1	chrX:7590585-7590703 -	TTTTCAGATCTCCAAGATATTTGCGAAGAT-----ACTGAATTTATGCGATAAACTTGCACTGTCATAGTAGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGGAATCGAAT-------TAAAAATCGG
droSec1	super_15:302161-302279 -	TTTTCAGATCTCCAAGATATTTGCAAAGAT-----ACTGAATTTATGCGATAAGCTTGCACTGTCATAGTAGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGGAATCGAAT-------TAAAAATCGG
droYak2	chrX:18128933-18129060 -	TTTTCAGATCTCCAAGATATTGACAAAGAT-----ACTGGATTCATGCGATAAACTCGTACCGTCGGAACTGTAGTGTACTTGTCCTCATAAATTCGCAATGTAATGGAATTGAATCACTCTTTAAAGATCTT
droEre2	scaffold_4690:5579674-5579798 +	TCTTCAGATCTCCAAGATATTTGCTAAGATACGATACTGGAATTATGCGATAAACTTGTATTGTCAGGG--------TACTTGTTCTCATAAATTCGTAATGTCATGGAATTGAATCACTCTTTAAGAGTCTT
droAna3	Unknown	-------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	-------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	-------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181096:3465786-3465830 +	tttTTgtTTTtTtttTTTttTtGtTT----------------------------------------------------------------------------------------tTTtttTtGTATATAGCGT
droVir3	Unknown	-------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6473:12829321-12829420 -	TTCATTGATAACT--GATACTAGCCAAGCC-----CTCGATAGCACGTGAGCAA--AGTCTTGTCAGAA----------ATGCATTTCATAAATTTGTAGTGTAGAATATATGAAT-------GAA-------
droGri2	Unknown	-------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:9538456-9538571 -	NA	TTTTC--AGATCTCCAAGA-----------------------------------TATTTGCAAAGA-----TACTGAATTTATGCGATAAACTTGCAC-TGTCATAGTAGT-----AGTTCTTTCCATAAATTCGTAATGTAATGG----AAA-----------------------------------------------------------------------------------------------------------CGA-----------------AT-------TA--------------------AAAATC--TG
droSim1	chrX:7590407-7590546 -	3	TGATTTCCATTCTGGAAACTATTAATTCATTTTTTCGTGGAACATATGCAAAAATATTTATAGTAT-----TCCTAGCTTTTCTCAGAAAACTTATTT-ATTAGAGGT-------------------------CGTAA-------------------------------------------------------------------------------------------TTACTACGCAAC-------------------CTA-----------------ATCAATTCACT---------------------AGAAG--TG
droSec1	super_15:302161-302279 -	8	TTTTC--AGATCTCCAAGA-----------------------------------TATTTGCAAAGA-----TACTGAATTTATGCGATAAGCTTGCAC-TGTCATAGTAGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGG----AAT-----------------------------------------------------------------------------------------------------------CGA-----------------AT-------TA--------------------AAAATC--GG
droYak2	chrX:18128934-18129060 -	15	TTTTC--AGATCTCCAAGA-----------------------------------TATTGACAAAGA-----TACTGGATTCATGCGATAAACTCGTAC-CGTCGGAACTGTAGTGTACTTGTCCTCATAAATTCGCAATGTAATGG----AAT-----------------------------------------------------------------------------------------------------------TGA-----------------ATCACTCTTTA--------------------AAGAT---CT
droEre2	scaffold_4690:5579674-5579800 +	1	TCTTC--AGATCTCCAAGA-----------------------------------TATTTGCTAAGATACGATACTGGAATTATGCGATAAACTTGTAT-TGTCAGGGT--------ACTTGTTCTCATAAATTCGTAATGTCATGG----AAT-----------------------------------------------------------------------------------------------------------TGA-----------------ATCACTCTTTA--------------------AGAGTCTTGG
droEug1	scf7180000409032:387239-387428 +	1	TTTTC--AGATCTCCAAGA-----------------------------------TATTTGTTAAGA-----TACTGGACTTAAGCGGTTAACTTGTAC-TGTCAGATA--------AATATTTCCCATAAATTCAAAGTGTTATGGCTGAAATTGATTTTCTAAAAGCAATCTAATCG--AAGA----------------------------------------------------------------------------TTATATATCCCATAAATTGGATTAATATCTATGAAATGGAAGGGCTGAAAAGGGGGC--TT
droBia1	scf7180000301760:5525605-5525707 -	5	TTTCA--GGATCTCCGAGG-----------------------------------TACT-GCACAGA-----CACTTGACGCAAGCGCTAAACCTGTGC-TGTCCCAGT--------GCTATTTCACATAAACTCGTAATGTAATGG----AAT-----------------------------------------------------------------------------------------------------------CGA-----------------TT--------------------------------------T
droTak1	scf7180000415872:166233-166330 -	7	TTTCA--AGATCTCGAAGA-----------------------------------TATTTGTACAGAT---ATACTGGATTTAAGCGATAAACTTGTACTTGTCACAGT--------ACTATTTCCCATAAAATCGCAAAATAATCG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000491013:359530-359622 -	16	TTTTA--AGATCTCGAACA-----------------------------------TATTGCAAGAGA-----TACTGAACTTAAGCGATTAACTTCGAC-TGTCAGAAT--------CATATTTTTCATTAGCTCGTAAAGCAAT---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droRho1	scf7180000780080:558549-558656 +	2	TTTTA--AGATCTCGAAGA-----------------------------------TATT----AAAA-----CAACGCACTCTTGCGATAAAATTGAAC-TGTCAGAGT--------ACTATTTTCTATAAA-TCGTATTGTAATGG----TTT-----------------------------------------------------------------------------------------------------------TAA-----------------AA-------TG--------------------GAATCC--AG
droFic1	scf7180000454076:123635-123714 -	19	TGATGCGTAAATTATACATTTTTGCTTTAGTAGTTCTTGAAAGATTTCGCA-AAGAAGTGTACCGAT---T---------T-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AA-------GA--------------------TTTTCT--AG
droKik1	scf7180000302395:626782-626857 -	7	CATAT--CTTTC-----------------------------------------------GCAATGA-----GACTTGTCTTCTGAGAGAAAA-------------------------------------------------------------------------------CTTACCAAATAG-TTTGGAATATATGAAAT-----------------------------------------------------------CTT-----------------TT----------------------------------G--AA
droAna3	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396571:278436-278548 +	2	TGCA----GACCTCTAAAA-----------------------------------AATTTCAAAATA-----AAATGACTTTAAA--ATT------ATC-TGCCAACATAATA-TA-TCCTTTTGTTACTAAT-TGAAG-TTAAAAA----ATA-----------------------------------------------------------------------------------------------------------TTA-----------------ATTATTACTTT---------------------AAATT--TA
dp4	chr4_group1:5095426-5095542 -	6	CTTCG--AAAACAAAT-----------------------------------------------------------------------------------------------------------------------------------------------------------CTTCCCTTTTTT-TTTCAAGGGTATCAAACACTCGACTCCCCTTGCCAGGGTGCTTTTTTGTTGCCTTCTTCTTTTATTTTGACTTGAGCCA-----------------AG-------TC--------------------AAGTTG--TG
droPer1	super_7:3845924-3845978 -	6	ATTTG--AAGTATTGGAGG-----------------------------------AGC-----------------------------------------------------------GCATAGTTCAATGAACCGGAAATCTAATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------AATT--AA
droWil1	scaffold_181096:3465786-3465827 +	2	AAATT--CATTTATAAATT----------------------------------------------------TAATA--------------------------------------------------------------------G-----------------------------------ATTA----------------------------------------------------------------------------TTA-----------------AA-------TA--------------------GTATAT--AG
droVir3	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6473:12829321-12829420 -	12	TTCAT--TGATAACT--GA-----------------------------------TACTAGCCAAGC-----CCTCGATAGCACGTGAGCAA--AGTCT-TGTCAGA----------AATGCATTTCATAAATTTGTAGTGTAGAAT----ATA-----------------------------------------------------------------------------------------------------------TGA-----------------AT----------------------------------G--AA
droGri2	scaffold_14853:2001546-2001618 -	11	GCGGG--AAAAATA---------------------------------------------------------TACTACAATAAAACA-------TGTAT-TTTTTATAT--------GC---------------CATTC-------------------------------------------------------------------------------------------TTTTTGTGTTCT---------------------C-----------------GT-------TG--------------------TAAATT--TG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTTTCAGATCTCCAAGATATTTGCAAAGAT-----ACTGAATTTATGCGATAAACTTGCACTGTCATAGTAGTA-----GTTCTTTCCATAAATTCGTAATGTAATGGAAACGAAT-------TAAAAATCTG

Size

Hit Count

Total Norm

droSim1

TTTTCAGATCTCCAAGATATTTGCGAAGAT-----ACTGAATTTATGCGATAAACTTGCACTGTCATAGTAGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGGAATCGAAT-------TAAAAATCGG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.......................................................................................................AATGGACTCGAAT-------GAAAA.....	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

TTTTCAGATCTCCAAGATATTTGCAAAGAT-----ACTGAATTTATGCGATAAGCTTGCACTGTCATAGTAGTAG--TAGTTATTTCCATAAATTCGTAATGTAATGGAATCGAAT-------TAAAAATCGG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................ATTTAAGCGATAAGCGTGC..........................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

TTTTCAGATCTCCAAGATATTGACAAAGAT-----ACTGGATTCATGCGATAAACTCGTACCGTCGGAACTGTAGTGTACTTGTCCTCATAAATTCGCAATGTAATGGAATTGAATCACTCTTTAAAGATCTT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TCTTCAGATCTCCAAGATATTTGCTAAGATACGATACTGGAATTATGCGATAAACTTGTATTGTCAGGG--------TACTTGTTCTCATAAATTCGTAATGTCATGGAATTGAATCACTCTTTAAGAGTCTT

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

tttTTgtTTTtTtttTTTttTtGtTT----------------------------------------------------------------------------------------tTTtttTtGTATATAGCGT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.........TTTTTTTTTTTTTTTTT----------------------------------------------------------------------------------------TTTTTT.............	23	51	0.06	0.00	0.06	0.00	0.00
..........TTTTTTTTTTTTTTTT----------------------------------------------------------------------------------------TTTTTTT............	23	51	0.06	0.00	0.06	0.00	0.00
...........TTTTTTTTTTTTTTT----------------------------------------------------------------------------------------TTTTTTTT...........	23	51	0.06	0.00	0.06	0.00	0.00
.......TTTTTTTTTTTTTTTTTTT----------------------------------------------------------------------------------------TTTT...............	23	51	0.06	0.00	0.06	0.00	0.00
......TTTTTTTTTTTTTTTTTTTT----------------------------------------------------------------------------------------TTT................	23	51	0.06	0.00	0.06	0.00	0.00
........TTTTTTTTTTTTTTTTTT----------------------------------------------------------------------------------------TTTTT..............	23	51	0.06	0.00	0.06	0.00	0.00

droVir3

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

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TTCATTGATAACT--GATACTAGCCAAGCC-----CTCGATAGCACGTGAGCAA--AGTCTTGTCAGAA----------ATGCATTTCATAAATTTGTAGTGTAGAATATATGAAT-------GAA-------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...............................................................TCAGTA----------AAGCATTTCATA..........................................	18	1	6.00	0.00	3.00	3.00	0.00
............................................................................................ATTTGTAxTGTAGAATATACG....................	20	1	1.00	1.00	0.00	0.00	0.00

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
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													None		None			None
UNAFold Image													None		None			None