sblock147283- 12- and 20-way alignments

sblock147283	chr3R:11757153-11757237 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 11757203-11757225
   star strand at position 11757170-11757191
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:11757138-11757252 +	CGCCAGCTTTGCGGCCAGAGCTGCAATGGCGCTTGTCCGGAAGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGCCTTCAGCTCCTCACGCGCCGCTGCC
droSim1	chr3R:9721216-9721330 -	CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC
droSec1	super_0:10201448-10201562 -	CGCCAGCTGTGCGGCCAAAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTTATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC
droYak2	chr3R:14680051-14680165 -	CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCAGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTGCAGCTCCTCACGCGCCGCTGCC
droEre2	scaffold_4770:11278284-11278398 +	CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTACAGCTCCTCACGCGCCGCTGCC
droAna3	scaffold_13340:16358935-16359049 +	CGGCAATTGTGCGGCCAGAGCTGCAACGGCGCATGCCCAGAGGTGGAAAGAGTTATGCTGGCCGATGGGTGCCGAATCTCTGATAAAGGCCTGCAATTGCTGACCCGCCGATGCC
dp4	chr2:20443804-20443918 +	CGGCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC
droPer1	super_3:3191078-3191192 +	CGTCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC
droWil1	scaffold_181089:5116759-5116873 -	CGGCAATTATGCGGTCAAAGTTGTAACGGTTCTTGCCCGGAGGTAGAACGGGTGATGCTCGCTGACGGTTGTCGCATCTCGGACAAGGGCTTGCAAATGTTAGCCCGGCGTTGTC
droVir3	scaffold_13047:2419453-2419567 +	CGCCAGCTGTGCGGACAGAGCTGCAATGGCGCCTGCCCGGAGGTGGAACGCGTTATGCTCGCCGATGGCTGTCGCATTTCAGACAAAGGTCTGCAGTTGCTCACGCGTCGCTGTC
droMoj3	scaffold_6540:15231982-15232096 -	CGCCAGCTGTGCGGACAGAGCTGCAACGGCGCCTGCCCAGAGGTTGAGCGCGTCATGCTTGCCGATGGCTGTCGCATCTCAGACAAGGGTCTGCAGCTGCTGACGCGTCGCTGTC
droGri2	scaffold_15074:5996241-5996355 +	CGGCAGTTGTGCGGCCAGAGTTGCAATGGTGCCTGCCCCGAGGTGGAACGCGTGATGCTCGCCGATGGCTGTCGCATCTCGGACAAGGGTCTGCAGTTGCTCACCCGTCGGTGTC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:11757138-11757252 +	NA	CGCCAGCTTTGCGGCCAGAGCTGCAATGGCGCTTGTCCGGAAGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGCCTTCAGCTCCTCACGCGCCGCTGCC
droSim1	chr3R:9721216-9721330 -	1	CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC
droSec1	super_0:10201448-10201562 -	1	CGCCAGCTGTGCGGCCAAAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTTATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC
droYak2	chr3R:14680051-14680165 -	2	CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCAGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTGCAGCTCCTCACGCGCCGCTGCC
droEre2	scaffold_4770:11278284-11278398 +	1	CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTACAGCTCCTCACGCGCCGCTGCC
droEug1	scf7180000409797:1781742-1781856 -	1	CGGCAGCTGTGCGGCCAGAGTTGTAATGGCGCCTGTCCAGAAGTGGAGCGTGTGATGCTCGCCGATGGCTGCCGCATCTCGGACAAAGGACTCCAGCTTCTAACTCGCCGTTGTC
droBia1	scf7180000302136:1362905-1363019 +	1	CGGCAGCTGTGCGGGCAAAGTTGCAACGGAGCCTGTCCGGAAGTGGAGCGCGTAATGCTGGCCGATGGCTGCCGCATCTCGGATAAGGGTCTCCAGCTCCTCACCCGTCGCTGCC
droTak1	scf7180000415242:370457-370571 -	2	CGGCAGCTGTGCGGCCAGAGTTGCAATGGCGCCTGTCCGGAAGTAGAGCGCGTCATGCTTTCTGATGGCTGTCGCATCTCGGACAAGGGCCTCCAGCTGCTCACCCGCCGATGTC
droEle1	scf7180000491080:1541800-1541914 +	2	CGTCAGCTGTGCGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTGGAGCGCGTGATGCTCGCCGATGGCTGCCGCCTTTCGGACAAGGGCCTCCAGCTGCTGACGCGTCGCTGCC
droRho1	scf7180000758667:164702-164816 +	2	CGGCAGCTTTGTGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTCGAGCGCGTAATGCTCGCCGATGGCTGCCGCATCTCGGATAAGGGTCTGCAGCTGCTCACGCGTCGCTGCC
droFic1	scf7180000452523:1135130-1135244 +	2	CGGCAGTTGTGTGGCCAGAGTTGCAATGGCGCCTGTCCGGAAGTGGAGCGCGTGATGCTCGCCGATGGCTGCCGCATCTCAGACAAGGGCCTCCAGTTGCTCACCCGTCGCTGCC
droKik1	scf7180000302639:921690-921804 -	4	CGGCAGCTGTGCGGCCAGAGCTGCAACGGCGCCTGTCCGGAGGTGGAGCGTGTCATGCTTGGCGACGGCTGCCGCATCACGGACAAGGGACTCCAGCTGCTCACGCGTCGCTGCC
droAna3	scaffold_13340:16358935-16359049 +	3	CGGCAATTGTGCGGCCAGAGCTGCAACGGCGCATGCCCAGAGGTGGAAAGAGTTATGCTGGCCGATGGGTGCCGAATCTCTGATAAAGGCCTGCAATTGCTGACCCGCCGATGCC
droBip1	scf7180000396708:3686195-3686309 -	3	CGGCAATTGTGCGGCCAGAGCTGCAATGGAGCCTGTCCGGAGGTGGAACGGGTGATGCTGGCCGATGGCTGCCGCATCTCAGACAAAGGCCTCCAATTGCTGACCCGCCGATGCC
dp4	chr2:20443804-20443918 +	1	CGGCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC
droPer1	super_3:3191078-3191192 +	1	CGTCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC
droWil1	scaffold_181089:5116759-5116873 -	2	CGGCAATTATGCGGTCAAAGTTGTAACGGTTCTTGCCCGGAGGTAGAACGGGTGATGCTCGCTGACGGTTGTCGCATCTCGGACAAGGGCTTGCAAATGTTAGCCCGGCGTTGTC
droVir3	scaffold_13047:2419453-2419567 +	2	CGCCAGCTGTGCGGACAGAGCTGCAATGGCGCCTGCCCGGAGGTGGAACGCGTTATGCTCGCCGATGGCTGTCGCATTTCAGACAAAGGTCTGCAGTTGCTCACGCGTCGCTGTC
droMoj3	scaffold_6540:15231982-15232096 -	3	CGCCAGCTGTGCGGACAGAGCTGCAACGGCGCCTGCCCAGAGGTTGAGCGCGTCATGCTTGCCGATGGCTGTCGCATCTCAGACAAGGGTCTGCAGCTGCTGACGCGTCGCTGTC
droGri2	scaffold_15074:5996241-5996355 +	6	CGGCAGTTGTGCGGCCAGAGTTGCAATGGTGCCTGCCCCGAGGTGGAACGCGTGATGCTCGCCGATGGCTGTCGCATCTCGGACAAGGGTCTGCAGTTGCTCACCCGTCGGTGTC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CGCCAGCTTTGCGGCCAGAGCTGCAATGGCGCTTGTCCGGAAGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGCCTTCAGCTCCTCACGCGCCGCTGCC

Size

Hit Count

Total Norm

droSim1

CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...............................................................................CGGACAAGGGTCGTCAGCT.................	19	1	1.00	0.00	0.00	0.00	1.00
.................................................................................GACAATGGACTTCAGCTC................	18	1	1.00	0.00	0.00	0.00	1.00
AGCCAGCTGTGCGGACAG.................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droSec1

CGCCAGCTGTGCGGCCAAAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTTATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTTCAGCTCCTCACGCGCCGCTGCC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................................CGCCGCTxGCTGCCGCATC.....................................	18	1	1.00	0.00	1.00	0.00
.....................................................TATGGTCGTCGATGGCTGCC..........................................	20	1	1.00	0.00	1.00	0.00
..................AGCTGCAATGGCGCCTGTC..............................................................................	19	1	1.00	0.00	0.00	1.00
.....................AGCAATGCCGCCTGTCCGG...........................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCAGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTGCAGCTCCTCACGCGCCGCTGCC

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

CGCCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGCGTCATGCTCGCCGATGGCTGCCGCATCTCGGACAAGGGTCTACAGCTCCTCACGCGCCGCTGCC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..............................CCCTATCCGGAGGTGGAG...................................................................	18	1	3.00	0.00	0.00	0.00	3.00
..............................CCCTATCCGGAGGTGGAGC..................................................................	19	1	2.00	0.00	0.00	0.00	2.00

droAna3

CGGCAATTGTGCGGCCAGAGCTGCAACGGCGCATGCCCAGAGGTGGAAAGAGTTATGCTGGCCGATGGGTGCCGAATCTCTGATAAAGGCCTGCAATTGCTGACCCGCCGATGCC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........CGGCCTGAGCTGCAACGCC.....................................................................................	19	1	1.00	0.00	0.00	1.00	0.00

dp4

CGGCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................................GACAAGGGCTTCCAGCTG................	18	1	1.00	0.00	1.00	0.00	0.00
....AGCTGTGCGGCGAGTGCT.............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droPer1

CGTCAGCTGTGCGGCCAGAGCTGCAATGGCGCCTGTCCGGAGGTGGAGCGAGTGATGCTCGCCGATGGCTGCCGCATCTCCGACAAGGGCCTCCAGCTGCTGACACGACGCTGCC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........CGGCCTGAGCTGCAATGCC.....................................................................................	19	1	10.00	0.00	0.00	0.00	0.00	10.00
................................CTATCCGGAGGTGGAGCT.................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................TGGAGCGAGTGATGGTGGC.....................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droWil1

CGGCAATTATGCGGTCAAAGTTGTAACGGTTCTTGCCCGGAGGTAGAACGGGTGATGCTCGCTGACGGTTGTCGCATCTCGGACAAGGGCTTGCAAATGTTAGCCCGGCGTTGTC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................GAGGGCGAACGGGTGATG..........................................................	18	1	1.00	1.00	0.00	0.00	0.00
......................................................................GTCGCATCTCGGACAAGGGC.........................	20	1	1.00	0.00	0.00	1.00	0.00

droVir3

CGCCAGCTGTGCGGACAGAGCTGCAATGGCGCCTGCCCGGAGGTGGAACGCGTTATGCTCGCCGATGGCTGTCGCATTTCAGACAAAGGTCTGCAGTTGCTCACGCGTCGCTGTC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CGCCAGCTGTGCGGACAGAGCTGCAACGGCGCCTGCCCAGAGGTTGAGCGCGTCATGCTTGCCGATGGCTGTCGCATCTCAGACAAGGGTCTGCAGCTGCTGACGCGTCGCTGTC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.............GACAGAGCGGGAACGGCG....................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
...........................GGCGCCTGCCCAGAGGTTGAGC..................................................................	22	1	1.00	1.00	0.00	0.00	0.00
..........................................GTTGAGCGCGTCATGCTTGCCGATGGC..............................................	27	1	1.00	1.00	0.00	0.00	0.00
............................................................................................GCAGCCGCAGACGCGTCGCT...	20	1	1.00	1.00	0.00	0.00	0.00

droGri2

CGGCAGTTGTGCGGCCAGAGTTGCAATGGTGCCTGCCCCGAGGTGGAACGCGTGATGCTCGCCGATGGCTGTCGCATCTCGGACAAGGGTCTGCAGTTGCTCACCCGTCGGTGTC

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