sblock36967- 12- and 20-way alignments

sblock36967	chr2R:2948548-2948660 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 2948554-2948576
   star strand at position 2948634-2948655
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:2948533-2948675 -	GATTGCACAACTTCCCCTGGGGCCCAAATG---GGTTGCAAAAT--------------GCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTTTAGCTTCGAT----------------------------------------TGCCGAGGCACTTTGCATTCGATTTGGGTCT-------TGGGTCTCTGTTTGTTTTGACAT
droSim1	chr2R:1748656-1748798 -	GATTGCACAACTTCCCCTGGGGCCCAAATG---GGTTGCAAAAT--------------GCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTTTGGCTTCGAT----------------------------------------TGCCGAGGCACTTTGCATTCGATTTGGGTCT-------TGGGTCTGTGTTTGTTTTGCCAT
droSec1	super_1:616417-616559 -	GATTGCACAACTTCCCCTGGGGCCCAAATG---GGTTGCAAAAT--------------GCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTTTGGCTTCGAT----------------------------------------TGCCGAGGCACTTTGCATTCGATTTGGGTCT-------TGGGTCTGTGTTTGTTTTGCCAT
droYak2	chr2L:15661832-15661981 -	GATTGCACAACTTCCCCTGGGGCCCAAATG---GGTTGCAAAAT--------------GCAAGTGTTCCATTCGAGTGGCTCGCCTCCGCGT--TTTTTAGCTTCGAT----------------------------------------TGCCGCGGCACTTTGCATTTGATTTGGGTCTTGTGTCTTGGGTTTCTGTTTGTTTTGCCAT
droEre2	scaffold_4929:19619112-19619253 +	TATTGCACAACTTCCCCTGGGGCCCAAATA---GGTTGCAAAAT--------------GCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTGT-GCTTCGAT----------------------------------------TGCCGAGGCACTTTGCATTTGATTTGGGTCT-------TGAGTCTCTGTTTGTTTTGCCAT
droAna3	Unknown	AATTGCACAACTTCCGCGGAGGTGC----T---TGTTGCAAC-------CGTCCGT--CCAAGAGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTTTG----CTAG----------------------------------------TGCC-AAGTGTTTTGCATTTTATTTGGGTCT-CTGTT-TTGGTTTTCGTTTGTTTTGCCAT
dp4	chr3:1224831-1224985 -	CATTGCATAATTTCCTTTGGAGCCCACGTCTGG----CCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTT--T---------------------------CGGTTTTCGGTGTTTTGGTGTTCGGTCTTCAAACCACTTTGCATTTCTT---------------------CTTGTTTGTTTTGCCAT
droPer1	super_2:1392971-1393125 -	CATTGCATAATTTCCTTTGGAGCCCACGTCTGG----CCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTT--T---------------------------CGGTTTTCGGTGTTTTGGTGTTCGGTCTTCAAACCACTTTGCATTTCTT---------------------CTTGTTTGTTTTGCCAT
droWil1	Unknown	C------------------------------------------------------------------------------CTGGCCTCGGCTT--T---------------------------TGATTTTGA------------------TTTAAACCACTTTGCtTTTttTTTt---TT-------TTTTTTTGTTTTTtTTTGGGCAT
droVir3	scaffold_10324:1098530-1098634 -	CTT----------------------GAGTG---GGCCGCTGGCT--------------G-----------GACGGGTATCTCTCATCTCCAG---------------------CCTTGCTTTCGATTTT--------------------G-CTGGCTACTTTGCATTTTTTTACGG------------CATTTCTACTTGTTTTGgTGg
droMoj3	scaffold_6496:4946449-4946559 +	G----------------------------------TTGCAAGTG--------------GCTGTTGTTACACTCGAGTGGGTTGACTCGACTTCATCTTCATCTCCATTTCCAGCCTTGCTTTCGATTTT-------TTTCCG----------TAGCTATTTTGCAT-------------------------TTCCACTTGT--------
droGri2	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:2948533-2948675 -	NA	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTAGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TCT-------------------------------GTTTGTTTTGAC---AT-
droSim1	chr2R:1748656-1748798 -	7	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTGGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TGT-------------------------------GTTTGTTTTGCC---AT-
droSec1	super_1:616417-616559 -	6	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTTGGCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTCGATTTGGGTCTTGGGTC-----------TGT-------------------------------GTTTGTTTTGCC---AT-
droYak2	chr2L:15661832-15661981 -	9	GATTGCACAAC--------TTCCC-CTGGGGCCCAAATG------GGTTGCAAAA-------TGCAAGTGTTCCATTCGAGTGGCTCGCCTCCGCGTT--TTTTAGCT-----------------------T------CGATT----------GC--CGCGGCACTTTGCATTTGATTTGGGTCTTGTGTCT----TGGGTTTCT-------------------------------GTTTGTTTTGCC---AT-
droEre2	scaffold_4929:19619112-19619253 +	6	TATTGCACAAC--------TTCCC-CTGGGGCCCAAATA------GGTTGCAAAA-------TGCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTGT-GCT-----------------------T------CGATT----------GC--CGAGGCACTTTGCATTTGATTTGGGTCTTGAGTC-----------TCT-------------------------------GTTTGTTTTGCC---AT-
droEug1	scf7180000409672:4966061-4966186 -	12	GATTGCACAAC--------TTCCCTTTGGGGCCCC----------AGTTGCAAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGCCTCCGCGT----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droBia1	scf7180000302292:3194465-3194584 +	5	GATTGCCCAAC--------TTCCCTTCGGGGCCCC----------GGTTGCAAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGC------------------T-----------------------T------CGATT----------GCGCGGAGGCACTTTGCATTCGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTGGCC---AT-
droTak1	scf7180000415382:187919-188034 -	9	GATTGCACAAC--------TTCCC-CGC------A----------GGTTGCCAAA-------TGCAAGTGTTCCACTCGAGTGCCTCGT------------------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCTCGTCTCT------------T-------------------------------GTTTGTTTGGCC---CT-
droEle1	scf7180000491265:55250-55375 -	14	GATTGCACAAC--------TTCCCTTTGGGGCTCG----------AATTGCAAAA-------TGCAAGAGTTCCACTCGAGTGCCTCGCCTCCGCGA----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droRho1	scf7180000780072:208014-208139 +	5	GATTGCACAAT--------TTCCCTTTGGCGCTCG----------AATTGCAAAA-------TGCAAGAGTTCCACTCGAGTGCCTCGCCTCCGCGA----------T-----------------------T------CGATT----------GC--GGAGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droFic1	scf7180000453955:317044-317167 +	5	GATTGCCCAAC--------TTCCT-TGGGGGCTCG----------AGTTGCAAAA-------TGCAAGAGTTCCACTCGAGCGAACCGCCTCCGCGT----------T-----------------------T------CGATT----------GC---GGGGCACTTTGCATTTGATTTGGGTCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droKik1	scf7180000302640:45649-45757 -	10	AGTTGCCCAACGAAGGCTGTGCCT-TCGGGGCGCG----------TGTTGCAATC-------TGCAAGAGTTCCACTCGAGTGCCTC---------------------------------------------------------------------------CACTCCGCATTGGATGTGGGGCT-----CT------------T-------------------------------GTTTGTTTTGCC---AT-
droAna3	scaffold_13266:3185126-3185263 -	10	AATTGCACAAC--------TTCCG-CGGAGGTGCT----------TGTTGCAACCGTCCG--TCCAAGAGTTCCAGTCGAGTGCCTCGCCTCCGCGTT--TTTT---------------------------G------CTAGT----------GC--C-AAGTGTTTTGCATTTTATTTGGGTCT-----CTGTTTTGGTT-TTC-------------------------------GTTTGTTT----------
droBip1	scf7180000396427:1655567-1655694 -	6	AGTTGCACAAC--------TTCCG-CGGAGGTGCT----------TGTTGCAACCG------TTTTGGAGTTCCAGTCGAGTGCCTCGCCTCCGCATT--TTT-----------------------------------TGCTT----------GC--C-AAGTGTTTTGCATTTTATTTGGATTT-----CT-----------GT-------------------------------TTTTGTTTTCGC---TT-
dp4	chr3:1224831-1224985 -	6	CATTGCATAAT--------TTCCT-TTGGAGCCCACGTCTGGCCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTTT-----CGGTT-----------------------TTCGGTGTTTTGGTGTTCGGTCTT--CAAACCACTTTGCATTTCTT-------------CT------------T-------------------------------GTTTGTTTTGCC---AT-
droPer1	super_2:1392971-1393125 -	11	CATTGCATAAT--------TTCCT-TTGGAGCCCACGTCTGGCCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTTT-----CGGTT-----------------------TTCGGTGTTTTGGTGTTCGGTCTT--CAAACCACTTTGCATTTCTT-------------CT------------T-------------------------------GTTTGTTTTGCC---AT-
droWil1	scaffold_180700:2520193-2520301 -	7	C-----------------------------------------------------------------------------------CTGGCCTCGGCTTT-----TGATT-----------------------T------TGATT--------------TAAACCACTTTGCATTTAATTTATTTTT-----TTT---------TGTTTTTATTTTATGCGTTTGGGCATTTCTTCTTATTTGTTTACCTCGTATA
droVir3	scaffold_10324:1098530-1098634 -	6	CTT-------------------------------GAGTG------GGCCGCTGGC-------TGGA-----------CGGGTATCTCTCATCTCCAG---------------------CCTTGCTT-----T------CGATT----------TTG-CTGGCTACTTTGCATTTTTTTACGGCAT-----T-----------TCT-------------------------------ACTTGTTTTGCT---GC-
droMoj3	scaffold_6496:4946449-4946566 +	3	G----------------------------------------------TTGCAAGT-------GGCTGTTGTTACACTCGAGTGGGTTGACTCGACTTCATCTTCATCTCCATTTCCAGCCTTGCTTTCGATT------TTTTT----------CC--GTAGCTATTTTGCATT-----------------------------TCC-------------------------------ACTTGTATTGTT---A--
droGri2	Unknown	NA	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GATTGCACAACTTCCCCTGGGGCCCAAATG---GGTTGCAAAAT--------------GCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTTTAGCTTCGAT----------------------------------------TGCCGAGGCACTTTGCATTCGATTTGGGTCT-------TGGGTCTCTGTTTGTTTTGACAT

Size

Hit Count

Total Norm

droSim1

GATTGCACAACTTCCCCTGGGGCCCAAATG---GGTTGCAAAAT--------------GCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTTTGGCTTCGAT----------------------------------------TGCCGAGGCACTTTGCATTCGATTTGGGTCT-------TGGGTCTGTGTTTGTTTTGCCAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................................................................................................................CTTTGCATTCGATTTGGGTCT-------T......................	22	1	2.00	0.00	1.00	1.00	0.00
....................................................................................CTCCGCGT--TTTTTCGCTG.........................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

GATTGCACAACTTCCCCTGGGGCCCAAATG---GGTTGCAAAAT--------------GCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTTTGGCTTCGAT----------------------------------------TGCCGAGGCACTTTGCATTCGATTTGGGTCT-------TGGGTCTGTGTTTGTTTTGCCAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................................................CTTTGCATTCGATTTGGGTCT-------TG.....................	23	1	3.00	3.00	0.00	0.00
..............................................................................................................................................................CTTTGCATTCGATTTGGGTCT-------.......................	21	1	1.00	0.00	0.00	1.00
..............................................................................................................................................................CTTTGCATTCGATTTGGGTCT-------T......................	22	1	1.00	1.00	0.00	0.00
.............................................................................................................................................................ACTTTGCATTCGATTTGGGT................................	20	1	1.00	0.00	1.00	0.00

droYak2

GATTGCACAACTTCCCCTGGGGCCCAAATG---GGTTGCAAAAT--------------GCAAGTGTTCCATTCGAGTGGCTCGCCTCCGCGT--TTTTTAGCTTCGAT----------------------------------------TGCCGCGGCACTTTGCATTTGATTTGGGTCTTGTGTCTTGGGTTTCTGTTTGTTTTGCCAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................................................................................................TGTGTCTTGGGTTTCGGAT...........	19	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................................................................................................................................GTGTCTTGGGTTTCGGAT...........	18	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................GT--TTTTTGGCTTCGAT----------------------------------------TGA..........................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

TATTGCACAACTTCCCCTGGGGCCCAAATA---GGTTGCAAAAT--------------GCAAGTGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTGT-GCTTCGAT----------------------------------------TGCCGAGGCACTTTGCATTTGATTTGGGTCT-------TGAGTCTCTGTTTGTTTTGCCAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.................................................................................................................................................................TGCATTTGATTTGGGTCT-------TGAG...................	22	1	1.00	0.00	0.00	0.00	1.00
.............................................................................................................................................................................................GTCCCTGTTTGTTTTTCC..	18	1	1.00	0.00	0.00	1.00	0.00

droAna3

AATTGCACAACTTCCGCGGAGGTGC----T---TGTTGCAAC-------CGTCCGT--CCAAGAGTTCCAGTCGAGTGCCTCGCCTCCGCGT--TTTTTG----CTAG----------------------------------------TGCC-AAGTGTTTTGCATTTTATTTGGGTCT-CTGTT-TTGGTTTTCGTTTGTTTTGCCAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......CAACTTGCGCGGAGTTGC----....................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

dp4

CATTGCATAATTTCCTTTGGAGCCCACGTCTGG----CCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTT--T---------------------------CGGTTTTCGGTGTTTTGGTGTTCGGTCTTCAAACCACTTTGCATTTCTT---------------------CTTGTTTGTTTTGCCAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.........................................................................................TTT--T---------------------------CGGTTTTCGGTGTCTT.......................................................................	20	1	1.00	1.00	0.00	0.00	0.00
..............................TGG----CCATGTTGCGGGTGACTG..........................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00

droPer1

CATTGCATAATTTCCTTTGGAGCCCACGTCTGG----CCATGTTGCAAGTGACTGGCTGTTGTTGTTCCACTCGAGCGGGTCGCCTCGACTT--T---------------------------CGGTTTTCGGTGTTTTGGTGTTCGGTCTTCAAACCACTTTGCATTTCTT---------------------CTTGTTTGTTTTGCCAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...............................GG----CCATGTTGCAAGTGACTG..........................................................................................................................................................	20	1	3.00	0.00	0.00	0.00	0.00	3.00
.................................................................................CGCCTCGACTT--T---------------------------CGGTTTTCG..............................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................G----CCATGTTGTAAGGGACT...........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................C--T---------------------------AGGTTTTCGGTGTTTT.......................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................CAAGxGACTGGATGTTGTTGT...............................................................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

C------------------------------------------------------------------------------CTGGCCTCGGCTT--T---------------------------TGATTTTGA------------------TTTAAACCACTTTGCtTTTttTTTt---TT-------TTTTTTTGTTTTTtTTTGGGCAT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
....................................................................................................................................................................TTTTTTTTTT---TT-------TTTTTTTTTTT............	23	51	0.06	0.00	0.06	0.00	0.00
.........................................................................................................................................................................TTTTT---TT-------TTTTTTTTTTTTTTTT.......	23	51	0.06	0.00	0.06	0.00	0.00
..........................................................................................................................................................................TTTT---TT-------TTTTTTTTTTTTTTTTT......	23	51	0.06	0.00	0.06	0.00	0.00
.....................................................................................................................................................................TTTTTTTTT---TT-------TTTTTTTTTTTT...........	23	51	0.06	0.00	0.06	0.00	0.00
......................................................................................................................................................................TTTTTTTT---TT-------TTTTTTTTTTTTT..........	23	51	0.06	0.00	0.06	0.00	0.00
...........................................................................................T--T---------------------------TGAATTTGA------------------TTTAAAA.....................................................	18	1	3.00	0.00	0.00	0.00	3.00
.......................................................................................................................................................................TTTTTTT---TT-------TTTTTTTTTTTTTT.........	23	51	0.06	0.00	0.06	0.00	0.00
........................................................................................................................................................................TTTTTT---TT-------TTTTTTTTTTTTTTT........	23	51	0.06	0.00	0.06	0.00	0.00

droVir3

CTT----------------------GAGTG---GGCCGCTGGCT--------------G-----------GACGGGTATCTCTCATCTCCAG---------------------CCTTGCTTTCGATTTT--------------------G-CTGGCTACTTTGCATTTTTTTACGG------------CATTTCTACTTGTTTTGgTGg	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...............................................................................................................................................................TTTGTATTTTTTTATGG------------CA...................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

G----------------------------------TTGCAAGTG--------------GCTGTTGTTACACTCGAGTGGGTTGACTCGACTTCATCTTCATCTCCATTTCCAGCCTTGCTTTCGATTTT-------TTTCCG----------TAGCTATTTTGCAT-------------------------TTCCACTTGT--------

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
UNAFold Image												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
UNAFold Image																				None