block806263- 12- and 20-way alignments

block806263	chr2R:11750900-11750969 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 11750906-11750926
   star strand at position 11750933-11750959
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:11750885-11750984 -	TACAATATAATATTATGTTCCAACGTGGGCGGA-------GCGCTCTACACGCCACGGATGCGTGTTA-GGTGCTCCGTC------GGTGCTCCAAC---A---AAGAC---------GTTGGATAC---------------TT
droSim1	chr2R:10492788-10492882 -	T-----ATAATATTATATTCCAGCGTGGGCGGA-------GCGCTCTGCACGCCGCGGATGCGTGTTA-GGTGCTCCGTC------GGTGCTCCCAC---A---AAGAC---------GTTGGATAC---------------TT
droSec1	super_1:9245417-9245511 -	T-----ATAATATTATATTCCAGCGTGGGCGGA-------GCGCTCTGCACGCCGCGGATGCGTGTTA-GGTGCTCCGTC------GGTGCTCCCAC---A---AAGAC---------GTTGGATAC---------------TT
droYak2	chr2R:17232130-17232223 +	A-----ATACTATTATATTCCAGCGTGGGCGGA-------GCGCTCTGCACGCCGATGGTGCGTGTTA-GGTGCTC----------TGTGCTCCGG---CGGACAAGAC---------GTTGGATAC---------------TT
droEre2	scaffold_4845:14107458-14107544 +	A-----ATAATATTGTATTCCAGCGTGGGCGGA-------GCGTTCTGCACGCCGCGGATGCGTGCTA-GGTGCTGCGG--------------------CGGACAAGAC---------GTTGGATAC---------------TT
droAna3	scaffold_13266:12444035-12444112 +	C---------------ATTCCGGCGTGGGCGGA-------GCACTCTGCACGCCGCAGTTGCGTGCTT-CTACCACAGC--------------------CGGACAATCC---------CTTGGATACA--------------CT
dp4	chr3:19435500-19435615 +	T-----------------TTCCGTGTGGGTGGT-------GCG--CTGCACGCAACAGCTGCGTGTTATCGTCCCGTGTCCGTATCTGTGCCGCCGCGCCGGACAAGCTCTACGGAGAGTCGGATATA-TACTACTCA-CACTT
droPer1	super_37:437405-437520 +	T-----------------TTCCGTGTGGGTGGT-------GCG--CTGCACGCAACAGCTGCGTGTTATCGTCCCGTGTCCGTATCTGTGCCGCCGCGCCGGACAAGCTCTACGGAGAGTCGGATATA-TACTACTCG-CACTT
droWil1	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12875:16868532-16868550 +	A-----------------------------------------------------------------------------------------------C---G---AAGAA---------ACGATACGT---------------TT
droMoj3	scaffold_6496:11133484-11133578 -	G------------------------TGGGTGGAGGAGTGGGCGTGCGACACGCAACAGATGCGTGAAT-CGTGGCCGGCA------GAATATG------------------GCGAAAAGCTGTAAACCGGCCTAAACACCATTT
droGri2	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:11750885-11750984 -	NA	TACAATATAATATTATGTTCCAACGTGGGCGGA------------G--------CG-CTCTACACGCCACGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCAACAAAGAC---------GTTGGAT-------------AC-TT
droSim1	chr2R:10492788-10492882 -	1	T-----ATAATATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGCGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCCACAAAGAC---------GTTGGAT-------------AC-TT
droSec1	super_1:9245417-9245511 -	1	T-----ATAATATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGCGGATGCGTGTTAGGTG----------------------CTCCG-TCGGTGCTCCCACAAAGAC---------GTTGGAT-------------AC-TT
droYak2	chr2R:17232130-17232223 +	1	A-----ATACTATTATATTCCAGCGTGGGCGGA------------G--------CG-CTCTGCACGCCGATGGTGCGTGTTAGGTGC------------TCTGT---GCTCCG-GCGGA--------CAAGAC---------GTTGGAT-------------AC-TT
droEre2	scaffold_4845:14107458-14107544 +	1	A-----ATAATATTGTATTCCAGCGTGGGCGGA------------G--------CG-TTCTGCACGCCGCGGATGCGTGCTAGGTG----------------------CTGCG-GCGGA--------CAAGAC---------GTTGGAT-------------AC-TT
droEug1	scf7180000409672:658894-658978 -	1	A-----CT-----AATATTCCAGCGTGGGCGTA----------GAG--------CGCCTCTGCACGATGCTGGTGCGTGTTAAACG----------------------TTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droBia1	scf7180000302292:3898618-3898709 +	2	C------------AAGATTCCAGCGTGGGCGGTGGTGGAGGTGGAG--------CA-CTCTGCACGCTGTGGGTGCGTGCTAAGCG----------------------CTCCG-CCGGG--------CGATCC---------GTTGGAT-------------AC-TT
droTak1	scf7180000415795:825736-825817 +	2	C------------AAGATTCCAGCGTGGGCGGA-------GCAGAG--------CG-GTCTGCACGAAGTGGGTGCGTGTTAAACG----------------------CTCCG-CCGGA--------CA---C---------TTTGGAT-------------AC-TT
droEle1	scf7180000491107:745400-745492 -	1	T---------TATAATATTCCGGCGTGGGTGGA------------G--------CA-TTCGGCACGCAGTGGGTGCGTGGTAGGCGTTTCG---------CTTC---GTTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droRho1	scf7180000779911:353759-353845 +	2	T------------AATAACTCAGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGCGGGTGCGTGTTGAGCGT------------AGTAC---GTTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droFic1	scf7180000453809:251717-251796 -	1	T------------GGTACTCCAGCGTGGGCGGA------------G--------CG-CTCTCCACGCAGTGGGAGCGTGCAAGGTG----------------------TTCCG-CCGGA--------CAATCC---------GTTGGAT-------------AC-TT
droKik1	scf7180000302682:1952965-1953055 -	2	--------------ATATTCCAGCGTGGGCGGA------------GTCTCTCTCCG-CTCTGCACGCTGCTGCTGCGTGTTGAGTG-------TCCG------C----GTCCG-CCGGA--------CAATTC----------TTGGAT-------------AC-TT
droAna3	scaffold_13266:12444035-12444112 +	1	C---------------ATTCCGGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGCAGTTGCGTGCTTCTAC----------------------CACAG-CCGGA--------CAATCC---------CTTGGAT-------------ACACT
droBip1	scf7180000396547:44441-44521 -	1	C---------------ATTCCGGCGTGGGCGGA------------G--------CA-CTCTGCACGCCGTAGTTGCGTGCTTCTAC--------------------CGCCGCCGCCGGA--------CAATCC---------CTTGGAT-------------ACACT
dp4	chr3:19435499-19435615 +	1	T-----------------TTCCGTGTGGGTGGT------------G--------CG---CTGCACGCAACAGCTGCGTGTTAT-CGTCCCGTGTCCGTATCTGTGCCGCCGCG-CCGGA--------CAAGCTCTACGGAGAGTCGGATATATACTACTCACAC-TT
droPer1	super_37:437404-437520 +	1	T-----------------TTCCGTGTGGGTGGT------------G--------CG---CTGCACGCAACAGCTGCGTGTTAT-CGTCCCGTGTCCGTATCTGTGCCGCCGCG-CCGGA--------CAAGCTCTACGGAGAGTCGGATATATACTACTCGCAC-TT
droWil1	Unknown	NA	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	NA	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	NA	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	NA	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TACAATATAATATTATGTTCCAACGTGGGCGGA-------GCGCTCTACACGCCACGGATGCGTGTTA-GGTGCTCCGTC------GGTGCTCCAAC---A---AAGAC---------GTTGGATAC---------------TT

Size

Hit Count

Total Norm

droSim1

T-----ATAATATTATATTCCAGCGTGGGCGGA-------GCGCTCTGCACGCCGCGGATGCGTGTTA-GGTGCTCCGTC------GGTGCTCCCAC---A---AAGAC---------GTTGGATAC---------------TT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.................................................................TTA-GGTGCTCCGTC------GGTGCTC...................................................	21	1	7.00	0.00	4.00	1.00	2.00
.................................................................TTA-GGTGCTCCGTC------GGTGCTCC..................................................	22	1	7.00	0.00	5.00	2.00	0.00
..................................................................TA-GGTGCTCCGTC------GGTGCTCC..................................................	21	1	3.00	0.00	3.00	0.00	0.00
.................................................................TTA-GGTGCTCCGTC------GGTGCT....................................................	20	1	2.00	0.00	2.00	0.00	0.00
.................................................................TTA-GGTGCTCCGTC------GGTGCC....................................................	20	1	2.00	0.00	1.00	1.00	0.00
.................................................................TTA-GGTGCTCCGTC------GGTGC.....................................................	19	1	2.00	0.00	1.00	1.00	0.00
.................................................................TTA-GGTGCTCCxTC------GGTGCTCCC.................................................	22	1	1.00	0.00	1.00	0.00	0.00
.................................................................TTA-GGTGCTCCGTC------GGTGA.....................................................	19	1	1.00	0.00	1.00	0.00	0.00
.................................................................TTA-GGTGCTCCGTC------GGTGCTCCC.................................................	23	1	1.00	0.00	0.00	1.00	0.00
....................CAGCGTGGGCGGA-------GCGCTCTGC...............................................................................................	22	1	1.00	0.00	0.00	1.00	0.00
.................................................................TTA-GGTGCTCCGTC------GGTGCTT...................................................	21	1	1.00	0.00	1.00	0.00	0.00
.................................................................TTA-TGTGCTCCGTC------GGTGCTCCC.................................................	23	1	1.00	0.00	0.00	1.00	0.00

droSec1

T-----ATAATATTATATTCCAGCGTGGGCGGA-------GCGCTCTGCACGCCGCGGATGCGTGTTA-GGTGCTCCGTC------GGTGCTCCCAC---A---AAGAC---------GTTGGATAC---------------TT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................TTA-GGTGCTCCGTC------GGTGCTC...................................................	21	1	4.00	2.00	0.00	2.00
.................................................................TTA-GGTGCTCCGTC------GGTGCT....................................................	20	1	3.00	1.00	0.00	2.00
...................................................................A-GGTGCTCCGTC------GGTGCT....................................................	18	1	1.00	1.00	0.00	0.00

droYak2

A-----ATACTATTATATTCCAGCGTGGGCGGA-------GCGCTCTGCACGCCGATGGTGCGTGTTA-GGTGCTC----------TGTGCTCCGG---CGGACAAGAC---------GTTGGATAC---------------TT

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

A-----ATAATATTGTATTCCAGCGTGGGCGGA-------GCGTTCTGCACGCCGCGGATGCGTGCTA-GGTGCTGCGG--------------------CGGACAAGAC---------GTTGGATAC---------------TT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

C---------------ATTCCGGCGTGGGCGGA-------GCACTCTGCACGCCGCAGTTGCGTGCTT-CTACCACAGC--------------------CGGACAATCC---------CTTGGATACA--------------CT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................CGAGGGCGGA-------GCACTGTGC...............................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
................ATTCCGGCGTGGGCGGA-------GCACT...................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
...............................................................TGCTT-CTACCACAGC--------------------CGGACA.......................................	21	1	1.00	0.00	0.00	1.00	0.00

dp4

T-----------------TTCCGTGTGGGTGGT-------GCG--CTGCACGCAACAGCTGCGTGTTATCGTCCCGTGTCCGTATCTGTGCCGCCGCGCCGGACAAGCTCTACGGAGAGTCGGATATA-TACTACTCA-CACTT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........................GGTGGA-------GCG--CGGCACGCA..........................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droPer1

T-----------------TTCCGTGTGGGTGGT-------GCG--CTGCACGCAACAGCTGCGTGTTATCGTCCCGTGTCCGTATCTGTGCCGCCGCGCCGGACAAGCTCTACGGAGAGTCGGATATA-TACTACTCG-CACTT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...............................................GCACGCATCAGxTGCGTGT..............................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................CTGCGTGTTATCGTCCCG....................................................................	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

A-----------------------------------------------------------------------------------------------C---G---AAGAA---------ACGATACGT---------------TT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

G------------------------TGGGTGGAGGAGTGGGCGTGCGACACGCAACAGATGCGTGAAT-CGTGGCCGGCA------GAATATG------------------GCGAAAAGCTGTAAACCGGCCTAAACACCATTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.........................TGGGTGGATGGGTGGGCGT....................................................................................................	19	1	12.00	1.00	5.00	6.00	0.00
............................GTGGAGGGGTGGGCGGGCG.................................................................................................	19	1	6.00	5.00	0.00	1.00	0.00
.........................TGGGTGGTGGAGTGGGTGT....................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...........................GGTGGAxGAGTGGGCGGGCG.................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................TGGGTGGAGGxGCGGGCGT....................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
G------------------------TGGGTGGTGGAxTGGGCG.....................................................................................................	18	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
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																	None	None	None	None
UNAFold Image																	None	None	None	None