sblock160004- 12- and 20-way alignments

sblock160004	chr3R:27223596-27223699 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	CDS

Legend:

   mature strand at position 27223657-27223677
   star strand at position 27223617-27223636
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:27223581-27223714 +	GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTAAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA
droSim1	chr3R:26858947-26859080 +	GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTGAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA
droSec1	super_4:6028735-6028868 +	GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTGAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA
droYak2	chr3R:28154940-28155073 +	AGAGTTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGCGACGTCCTAAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATTCCATTGCCCGCGAGGAGTCGCCAGTTGTACAAAA
droEre2	scaffold_4820:758228-758361 -	AGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTATGGTGACGTGCTAAAAGTGCGCAACATTTTGGACAACCGAGAGTACGCCATCAAGCGCATACCGTTGCCCGCGAGGAGTCGCCAGTTGTACAAAA
droAna3	scaffold_13340:5106925-5107058 +	GGAGTTTGAGGTCCTAATGTATCTGGGCAAGGGCGCCTATGGCGATGTGCTGAAAGTCCGCAACATTCTCGACAACCGGGAGTATGCAATCAAACGAATACCTCTGCCTGCTCGAAGTCGCCAGCTGTACAAGA
dp4	chr2:4422100-4422233 +	CGAGTTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTCGGGGACGTCCTGAAGGTGCGCAACATCCTGGACAACAGGGAGTATGCCATCAAGCGCATACCCCTGCCCGCCCGCAGTCGCCAGCTGTACAAGA
droPer1	super_19:124572-124705 +	CGAGTTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTCGGGGACGTCCTGAAGGTGCGCAACATCCTGGACAACAGGGAGTATGCCATCAAGCGCATACCCCTGCCCGCCCGCAGTCGCCAGCTGTACAAGA
droWil1	scaffold_181108:3264632-3264765 +	CGAATTCGAAGTGCTTATGTATCTGGGCAAGGGTGCCTTTGGGGATGTCCTCAAGGTGCGCAATATTCTGGACAATCGTGAGTATGCCATCAAGCGCATTCCCTTGCCGGCGCGCAGTCGTCAATTGTACAAGA
droVir3	scaffold_13047:12625472-12625605 +	CGAGTTCGAGGTTCTCATGTATTTGGGCAAAGGCGCATTTGGCGATGTGTTAAAAGTGCGCAACATACTGGATAACCGGGAATATGCAATCAAACGTATACCACTCCCGGCGCGCAGTCGCCAGCTATATAAGA
droMoj3	scaffold_6540:29210574-29210707 -	CGAGTTCGAGGTGCTCATGTATTTGGGCAAAGGCGCCTTTGGGGATGTGCTAAAGGTTCGCAATATACTGGACAATCGGGAGTATGCCATCAAACGTATACCACTGCCCGCCCGCAGTCGCCAGCTGTACAAGA
droGri2	scaffold_15074:2107771-2107904 -	CGAATTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTTGGCGATGTGCTCAAGGTGCGCAACATTCTCGATAATCGCGAGTATGCCATCAAGCGTATTCCGCTGCCGGGTCGCAGTCGCCAGCTATACAAGA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:27223581-27223714 +	NA	GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTAAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA
droSim1	chr3R:26858947-26859080 +	5	GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTGAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA
droSec1	super_4:6028735-6028868 +	3	GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTGAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA
droYak2	chr3R:28154940-28155073 +	2	AGAGTTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGCGACGTCCTAAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATTCCATTGCCCGCGAGGAGTCGCCAGTTGTACAAAA
droEre2	scaffold_4820:758228-758361 -	13	AGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTATGGTGACGTGCTAAAAGTGCGCAACATTTTGGACAACCGAGAGTACGCCATCAAGCGCATACCGTTGCCCGCGAGGAGTCGCCAGTTGTACAAAA
droEug1	scf7180000409243:23304-23437 +	2	CGAGTTTGAGGTGCTCATGTACTTGGGAAAAGGCGCGTTTGGGGACGTGTTGAAGGTACGCAACATTCTAGACAACCGAGAGTACGCCATCAAGCGTATACCACTTCCCGCGAGAAGTCGACAGCTGTACAAAA
droBia1	scf7180000302113:90831-90964 -	12	CGAGTTCGAGGTCCTTATGTACTTGGGAAAGGGCGCCTTTGGGGACGTGCTGAAGGTGCGCAATATTCTGGACAACCGAGAGTACGCCATCAAGCGGATACCACTGCCCGCGAGGAGTCGCCAGCTCTACAAGA
droTak1	scf7180000415286:363235-363368 +	3	CGAGTTCGAGGTGCTCATGTATTTGGGCAAGGGCGCCTTCGGGGATGTGCTGAAGGTGCGCAACATTCTGGACAACCGGGAGTACGCCATCAAGCGGATTCCACTGCCCGCGCGGAGTCGTCAGCTCTACAAGA
droEle1	scf7180000491194:1243055-1243188 +	6	CGAGTTTGAAGTACTCATGTACTTGGGCAAAGGGGCCTTCGGAGACGTTTTAAAGGTGCGCAACATTCTGGACAACCGGGAGTACGCCATTAAGCGGATACCACTGCCCGCGAGGAGTCGCCAGTTGTACAAGA
droRho1	scf7180000777206:96215-96348 -	16	CGAGTTCGAAGTGCTCATGTATTTGGGAAAGGGCGCCTTCGGGGACGTGCTGAAGGTGCGCAACATTCTGGACAACCGGGAGTACGCCATCAAGCGGATACCACTACCTGCGCGAAGTCGTCAGCTGTACAAGA
droFic1	scf7180000453782:90379-90512 -	11	AGAGTTCGAGGTGCTCATGTATTTGGGAAAGGGTGCGTTTGGGGACGTGCTGAAGGTGCGCAACATTCTGGACAACCGGGAGTACGCCATCAAACGGATTCCACTGCCCGCGAGGAGTCGCCAGTTGTACAAAA
droKik1	scf7180000302268:103445-103578 -	7	CGAGTTCGAGGTGCTTATGTATTTAGGAAAAGGAGCTTTTGGGGATGTCCTAAAAGTACGCAATATCCTGGACAACCGGGAGTATGCCATCAAGCGGATACCGCTACCCGCTCGCAGCCGGCAGCTATACAAGA
droAna3	scaffold_13340:5106925-5107058 +	10	GGAGTTTGAGGTCCTAATGTATCTGGGCAAGGGCGCCTATGGCGATGTGCTGAAAGTCCGCAACATTCTCGACAACCGGGAGTATGCAATCAAACGAATACCTCTGCCTGCTCGAAGTCGCCAGCTGTACAAGA
droBip1	scf7180000396359:88597-88730 -	11	GGAGTTTGAGGTCATCATGTATCTTGGCAAGGGTGCCTATGGGGATGTGTTGAAAGTTCGCAACAATCTCGACAACCGGGAGTATGCGATCAAACGAATACCTCTGCCTGCTCGAAGTCGCCAGCTATACAAGA
dp4	chr2:4422100-4422233 +	1	CGAGTTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTCGGGGACGTCCTGAAGGTGCGCAACATCCTGGACAACAGGGAGTATGCCATCAAGCGCATACCCCTGCCCGCCCGCAGTCGCCAGCTGTACAAGA
droPer1	super_19:124572-124705 +	13	CGAGTTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTCGGGGACGTCCTGAAGGTGCGCAACATCCTGGACAACAGGGAGTATGCCATCAAGCGCATACCCCTGCCCGCCCGCAGTCGCCAGCTGTACAAGA
droWil1	scaffold_181108:3264632-3264765 +	6	CGAATTCGAAGTGCTTATGTATCTGGGCAAGGGTGCCTTTGGGGATGTCCTCAAGGTGCGCAATATTCTGGACAATCGTGAGTATGCCATCAAGCGCATTCCCTTGCCGGCGCGCAGTCGTCAATTGTACAAGA
droVir3	scaffold_13047:12625472-12625605 +	1	CGAGTTCGAGGTTCTCATGTATTTGGGCAAAGGCGCATTTGGCGATGTGTTAAAAGTGCGCAACATACTGGATAACCGGGAATATGCAATCAAACGTATACCACTCCCGGCGCGCAGTCGCCAGCTATATAAGA
droMoj3	scaffold_6540:29210574-29210707 -	11	CGAGTTCGAGGTGCTCATGTATTTGGGCAAAGGCGCCTTTGGGGATGTGCTAAAGGTTCGCAATATACTGGACAATCGGGAGTATGCCATCAAACGTATACCACTGCCCGCCCGCAGTCGCCAGCTGTACAAGA
droGri2	scaffold_15074:2107771-2107904 -	13	CGAATTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTTGGCGATGTGCTCAAGGTGCGCAACATTCTCGATAATCGCGAGTATGCCATCAAGCGTATTCCGCTGCCGGGTCGCAGTCGCCAGCTATACAAGA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTAAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA

Size

Hit Count

Total Norm

droSim1

GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTGAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................TTGGTGACGTGCTGAAGGTGCGCAAC......................................................................	26	1	1.00	1.00	0.00	0.00	0.00
.............................................................................................GCGCATACCATCGCCGGC.......................	18	1	1.00	0.00	0.00	1.00	0.00
...................................................................TTAGACAATCGAGAGGAC.................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

GGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGTGACGTGCTGAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATACCATTGCCCGCGAGGAGTCGCCAGCTGTACAAAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.........................................................................AACCGAGAGTACGCCATCAAGCG......................................	23	1	1.00	1.00	0.00	0.00
.....................................................AGGCGTGCAACATTTTAGA..............................................................	19	1	1.00	0.00	1.00	0.00
.....................................................................................................CATTGCCCGCGAGGAGTCG..............	19	1	1.00	0.00	0.00	1.00
.....................................TTTGGTGACGTGCTGAAGGTGCGC.........................................................................	24	1	1.00	0.00	0.00	1.00
......................TTAGGAAAGGATGCCTTT..............................................................................................	18	1	1.00	0.00	1.00	0.00
.........................................................................TACCGAGAGTACGCCGTC...........................................	18	1	1.00	0.00	1.00	0.00

droYak2

AGAGTTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTTTGGCGACGTCCTAAAGGTGCGCAACATTTTAGACAACCGAGAGTACGCCATCAAGCGCATTCCATTGCCCGCGAGGAGTCGCCAGTTGTACAAAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................................ATTTTAGACAACCGAGAGTA..................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................TGTACTTGGGAAAGGGTGCCTTTGGC...........................................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
.......GAGGTGCTCATGTACTTGGGAAAG.......................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
..............................................................................................................CGAGAAGTCGCCGGTTGT......	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

AGAATTCGAGGTGCTCATGTACTTGGGAAAGGGTGCCTATGGTGACGTGCTAAAAGTGCGCAACATTTTGGACAACCGAGAGTACGCCATCAAGCGCATACCGTTGCCCGCGAGGAGTCGCCAGTTGTACAAAA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

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

dp4

CGAGTTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTCGGGGACGTCCTGAAGGTGCGCAACATCCTGGACAACAGGGAGTATGCCATCAAGCGCATACCCCTGCCCGCCCGCAGTCGCCAGCTGTACAAGA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.......................................................................................CATCAAGCGCATGCCCCTGC...........................	20	1	1.00	0.00	1.00	0.00	0.00

droPer1

CGAGTTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTCGGGGACGTCCTGAAGGTGCGCAACATCCTGGACAACAGGGAGTATGCCATCAAGCGCATACCCCTGCCCGCCCGCAGTCGCCAGCTGTACAAGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........................................GACGGCCTGGAGGTGCGCAA.......................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................................................................CGCAGTCGCCAxCTGTACT...	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................CATCAAGCGCATGCCCCTT............................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

CGAATTCGAAGTGCTTATGTATCTGGGCAAGGGTGCCTTTGGGGATGTCCTCAAGGTGCGCAATATTCTGGACAATCGTGAGTATGCCATCAAGCGCATTCCCTTGCCGGCGCGCAGTCGTCAATTGTACAAGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................CAAGGGTGCCTATGAGGA.........................................................................................	18	1	16.00	0.00	16.00	0.00	0.00
...............GATGxATCTGGGCAAGGGT....................................................................................................	18	1	4.00	3.00	1.00	0.00	0.00
...............GATGxATCTGGGCAAGGGTG...................................................................................................	19	1	4.00	0.00	4.00	0.00	0.00
....................................................GATGTGCGCAATATTCTG................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................................................................CCATCAAGCGCATGCCCCTGC...........................	21	1	1.00	0.00	1.00	0.00	0.00

droVir3

CGAGTTCGAGGTTCTCATGTATTTGGGCAAAGGCGCATTTGGCGATGTGTTAAAAGTGCGCAACATACTGGATAACCGGGAATATGCAATCAAACGTATACCACTCCCGGCGCGCAGTCGCCAGCTATATAAGA	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
..........................................................................................CAAACGTATACCACTCACTG........................	20	1	3.00	0.00	0.00	1.00	2.00	0.00
.....................................................................GGGTAACGGGGAATATG................................................	17	1	1.00	0.00	1.00	0.00	0.00	0.00
.........GGTTCTCATGTATTTGGGCAAAGGC....................................................................................................	25	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

CGAGTTCGAGGTGCTCATGTATTTGGGCAAAGGCGCCTTTGGGGATGTGCTAAAGGTTCGCAATATACTGGACAATCGGGAGTATGCCATCAAACGTATACCACTGCCCGCCCGCAGTCGCCAGCTGTACAAGA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CGAATTCGAGGTGCTCATGTATCTGGGCAAGGGCGCCTTTGGCGATGTGCTCAAGGTGCGCAACATTCTCGATAATCGCGAGTATGCCATCAAGCGTATTCCGCTGCCGGGTCGCAGTCGCCAGCTATACAAGA

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