sblock192886- 12- and 20-way alignments

sblock192886	chrX:453811-453911 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 453872-453892
   star strand at position 453830-453851
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:453796-453926 +	CATCTCAAAGGAAAAGACTAGGTCTGAGAA----ACGTTCATTGTTGTCTGTTCATAATTAGAGAGGGAAAATCTCTCGCGTTGAGTGCAATTAGCGTGGGCATTGTCTGCAAACTCGCTGCAGGACACCACT-----------------------TA
droSim1	chrX:339791-339921 +	TATCTCAAAGGAAAAGCCCAGGTCTGAGAA----AAGTTCATTGTTGTCTGTTTATAATTAGAGAGTGAAAATCTCTCTCGTTGAGTGCAATCGGCGTCGGCATTGTCGGCAAACTCGCTGCAGGACACCATT-----------------------TA
droSec1	super_10:302522-302652 +	TATCTCAGAGGAAAAGCCCAGGTCTGAGAA----ACGTTCATTGTTGTCTGTTCATAATTAGAGAGTGAAAATCTCTCTCGTTGAGTGCAATCGGCGTCGGCATTGTCTGCAAACTCGCTGCAGGACACCATT-----------------------TA
droYak2	chrX:374570-374700 +	CATCTCAAAGGAAAAGTCCAGATCTAAGAA----ACTTCCATTGTTGCCTGCTCGTAATTAGAGAGGGAAAATCTCTCGCGTTGAGTGCAATCAGCGCAGGCATTGTCTGCAAACTCGCTGCAGGACCCCATT-----------------------CA
droEre2	scaffold_4644:400337-400446 +	CATCT--------------------GGGAA----ACTTTCATTGT-GCCTGTTCATAATTAGAGAGTGAAAATCCGTTGCGCTGAGTGCAATCAGCAGCGGCATTGTCTGCCAACTCGCTGCAGGACCCCATT-----------------------CA
droAna3	scaffold_12929:346324-346432 +	TGGCTAGAATGGAAAAAAA---TGGCAAAAAAAGGACTCCCTTTTTATCTCATCCTGG----------CAAACAACTCGCTTTGATTGCC--------CATCATTGTCTT-----TCGATTCGGGAGGCAATT-----------------------CA
dp4	chrXL_group1e:183558-183701 +	CAAATTAAAAGCAAAGCGCAGATCGCAAAAT---ACGTTTATTGTTC-CCGGTCATAATTGAGAGCTGGAAAG------CTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTCTC-CCAGGC-CGTATTACCCTTACCCTGGCTGGCTGCGCCA
droPer1	super_60:145499-145640 -	T----TAAAAGCAAAGCGCAGATCGCAAAAT---ACGTTTATTGTTC-CCGGTCATAATTGAGAGCTGGAAAG------CTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTCTC-CCAGGC-CGTATTACCCTTACCCTGGCTGGCTGCGCCA
droWil1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:453796-453926 +	NA	CATCTC------------------------------------------------AA---------------AGGAAAAGACTAGGTCTG------------AGAA-ACGTTCATTGTTGTCTGTTCATAATTAGAGA----------GGGA-AAATCTC-----------------------TCGCGTTGAGTGCAATTAGCGTGGGCATTGTCTGCAAACTC-GCTG---CAGGACACCACTTA
droSim1	chrX:339791-339921 +	43	TATCTC------------------------------------------------AA---------------AGGAAAAGCCCAGGTCTG------------AGAA-AAGTTCATTGTTGTCTGTTTATAATTAGAGA----------GTGA-AAATCTC-----------------------TCTCGTTGAGTGCAATCGGCGTCGGCATTGTCGGCAAACTC-GCTG---CAGGACACCATTTA
droSec1	super_10:302522-302652 +	7	TATCTC------------------------------------------------AG---------------AGGAAAAGCCCAGGTCTG------------AGAA-ACGTTCATTGTTGTCTGTTCATAATTAGAGA----------GTGA-AAATCTC-----------------------TCTCGTTGAGTGCAATCGGCGTCGGCATTGTCTGCAAACTC-GCTG---CAGGACACCATTTA
droYak2	chrX:374570-374700 +	24	CATCTC------------------------------------------------AA---------------AGGAAAAGTCCAGATCTA------------AGAA-ACTTCCATTGTTGCCTGCTCGTAATTAGAGA----------GGGA-AAATCTC-----------------------TCGCGTTGAGTGCAATCAGCGCAGGCATTGTCTGCAAACTC-GCTG---CAGGACCCCATTCA
droEre2	scaffold_4644:400337-400446 +	4	CATCT-----------------------------------------------------------------------------------G------------GGAA-ACTTTCATTGTGC-CTGTTCATAATTAGAGA----------GTGA-AAATCCG-----------------------TTGCGCTGAGTGCAATCAGCAGCGGCATTGTCTGCCAACTC-GCTG---CAGGACCCCATTCA
droEug1	scf7180000409277:837087-837231 +	2	TAGCCG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CCGGTCATAATTGGAGA----------GTGG-AAATCTC-GGG-------CCGGCATGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTCCCAATTC-TGCT---CCGAATCCCGCTCC
droBia1	scf7180000301760:1504308-1504434 +	2	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------AAAA-ACTACCATTGTTG-CCGGTCATAATTGGAGA----------GTGA-AAAGCTG-GGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTCAAAACTC----------------------
droTak1	scf7180000415281:267243-267386 -	2	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTCGGGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCACCGGCATTGTCTCGCAATTCTGCTC---GAA-AT--CTCCAC
droEle1	scf7180000491023:732380-732525 +	2	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGGA-GCACCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTA-GGG-------CCGGCGAGCAACTCGCTTTGATTGCAATCAGCGCCGGCATTGTCTTCCAATTCTGCCC---CAAAATCCCTCGCC
droRho1	scf7180000779514:227802-227944 +	2	TAGCTG------------------------------------------------AA---------------AGGAAAAGCACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------GTGG-AAATCTC-GGG-------CTGGCGAGCAACTCGCTTTGATTGCAATCAGTGTCGGCATTGTCTTTCAATTC-TCCC---CGAAACCCCCCT--
droFic1	scf7180000453927:933548-933674 +	2	TAGCTG------------------------------------------------AA---------------AGGAAAAGGACAGATCAG------------GGAA-ACTCCCATTGTTG-CTGGTCATAATTGGAGA----------ATGG-AAATCTC-GGG-------CCGCCGAGCAACTCGCTTTGATTGCAATCAGCGCCGCCATTGTTTCACAATTC----------------------
droKik1	scf7180000302469:1872056-1872218 -	4	CAGGAG-----------------------------A------------------AAATGAAAGA-------AAGTAAAGCGCGGATCGGCCGGTAAGGCTGGAGA-TTTGCCATTGTTG-CTGGCCATAATTGGAGAGAAGAGAGAGTGGGAAAATCTC-TG---------CAGC-AGCAACTCGCTTTGATTGCAATCAGAGGTGGCATTGTCTCTCAATTCAGCTG---CA------------
droAna3	scaffold_12929:346312-346432 +	1	GATTGA-----------------------------A-------AGAGATGGCTAGAATGGAAAAAAATGGCAAA-------------AA------------AAGG-ACTCCCTTTTT-ATCTCATC--------------------------------------------CTGGCAAACAACTCGCTTTGATTGC--------CCATCATTGTCTTTCGATTC---------GGGAGGCAATTCA
droBip1	scf7180000395176:43762-43879 -	2	CGAATC------------------------------------------------GC---------------AAAAAGAACTC--------------------------GGCCATTGTTG-CAGCTCATAATTGGTAA----------ATCA-GAGCATG-AGAGTGAGGGCT--AGAGGGAGTCCTTTTTTT-----------------TTGTCT--TATCGC-ATCC---TGGCAAACAACTAA
dp4	chrXL_group1e:183509-183683 +	2	CAAATAGAACAGAGCGGGAGGTGGCACGGAGGTGGAAATTGAAGCTGTGAATT-AA---------------AAGCAAAGCGCAGATCGC------------AAAATACGTTTATTGTTC-CCGGTCATAATTGAGAG----------CTGG-AAA-----------------------------GCTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTC-TCCCAGGCCGTATTACCCTTA
droPer1	super_60:145517-145640 -	2	TT----------------------------------------------------AA---------------AAGCAAAGCGCAGATCGC------------AAAATACGTTTATTGTTC-CCGGTCATAATTGAGAG----------CTGG-AAA-----------------------------GCTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTC-TCCCAGGCCGTATTACCCTTA
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

CATCTCAAAGGAAAAGACTAGGTCTGAGAA----ACGTTCATTGTTGTCTGTTCATAATTAGAGAGGGAAAATCTCTCGCGTTGAGTGCAATTAGCGTGGGCATTGTCTGCAAACTCGCTGCAGGACACCACT-----------------------TA

Size

Hit Count

Total Norm

droSim1

TATCTCAAAGGAAAAGCCCAGGTCTGAGAA----AAGTTCATTGTTGTCTGTTTATAATTAGAGAGTGAAAATCTCTCTCGTTGAGTGCAATCGGCGTCGGCATTGTCGGCAAACTCGCTGCAGGACACCATT-----------------------TA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
............................................................................................................GGCxAACTCGGTGCAGGAC...............................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

TATCTCAGAGGAAAAGCCCAGGTCTGAGAA----ACGTTCATTGTTGTCTGTTCATAATTAGAGAGTGAAAATCTCTCTCGTTGAGTGCAATCGGCGTCGGCATTGTCTGCAAACTCGCTGCAGGACACCATT-----------------------TA

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CATCTCAAAGGAAAAGTCCAGATCTAAGAA----ACTTCCATTGTTGCCTGCTCGTAATTAGAGAGGGAAAATCTCTCGCGTTGAGTGCAATCAGCGCAGGCATTGTCTGCAAACTCGCTGCAGGACCCCATT-----------------------CA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..................................................................................................................CTCGCTGCAxGACCTCATT-----------------------C.	19	1	1.00	0.00	0.00	0.00	0.00	1.00

droEre2

CATCT--------------------GGGAA----ACTTTCATTGT-GCCTGTTCATAATTAGAGAGTGAAAATCCGTTGCGCTGAGTGCAATCAGCAGCGGCATTGTCTGCCAACTCGCTGCAGGACCCCATT-----------------------CA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................................................AGTGCAATCTGCAGCAGC........................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................................ATAATTAGCGAGxGAAAAT.....................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droAna3

TGGCTAGAATGGAAAAAAA---TGGCAAAAAAAGGACTCCCTTTTTATCTCATCCTGG----------CAAACAACTCGCTTTGATTGCC--------CATCATTGTCTT-----TCGATTCGGGAGGCAATT-----------------------CA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........GAAAAAAA---CGCCAAAAAAA.............................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
........ATGGAAAAAAA---GGGTAAAAA...............................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............ATAAA---TGGAAAAAAAAGGA..........................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..............AAAAA---TGTCGAAAAAAGGA..........................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
............AAAAAAA---CAGCAAAAAAA.............................................................................................................................	18	9	0.11	0.00	0.00	0.00	0.11
...............AAAA---GGACAAAAAAAGGA..........................................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
............AAAAAAA---AGGxAAAAAAAGGA..........................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............AAAAA---CGGxAAAAAAAGGA..........................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
............AAAAAAA---AGGCAGAAAAA.............................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........AGAAAAAAA---CGGCAAAAAA..............................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

dp4

CAAATTAAAAGCAAAGCGCAGATCGCAAAAT---ACGTTTATTGTTC-CCGGTCATAATTGAGAGCTGGAAAG------CTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTCTC-CCAGGC-CGTATTACCCTTACCCTGGCTGGCTGCGCCA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

T----TAAAAGCAAAGCGCAGATCGCAAAAT---ACGTTTATTGTTC-CCGGTCATAATTGAGAGCTGGAAAG------CTTTGATTGCAATCAGCGTTGGCATTGTCTCCGATCTCTC-CCAGGC-CGTATTACCCTTACCCTGGCTGGCTGCGCCA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................................................................G------TTTTGATTGCAGTCAGC..............................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................TTAATTGAAAGCTGGAAA......................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

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

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

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

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

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

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

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
UNAFold Image									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	None
UNAFold Image																	None	None	None	None