dme-mir-966- 12- and 20-way alignments

dme-mir-966	chr2L:6045627-6045713 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 6045678-6045698
   star strand at position 6045642-6045663
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:6045612-6045728 -	ATTTCG---------CTCGGCTGTAACCTGATCCG-----------------CTGCTGTGGGTTGTGGGCTGTGT-------GGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AG-----CGTGGGCAC-----------GGACCCACTGGTCGTCAACCGC
droSim1	chr2L:5834370-5834493 -	ATTTCG---------TTCGGCTGTAACCTGATCCG-----------------CTGgTGTGGGgTGTGGGgTGTGGGgTGTttGGgTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AG-----CGTGGGCAC-----------GGCCCCACTGGTCGTCAACCGC
droSec1	super_5:4116543-4116659 -	ATTTCG---------TTCGGCTGTAACCTGATCCG-----------------CTGCTGCGGGTTGTGGGCTGTGA-------GGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AG-----CGTGGGCAC-----------GGCCCCACTGGTCGTCAACCGC
droYak2	chr2L:13146709-13146824 +	ATTCCG---------CTCGGCTGTAACCTGATCCG-----------------CTGCTGTGGGATGTGGGATGTG--------GGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AG-----CGTGGGCAC-----------GGCCCCACTGGTCGTCAACCGC
droEre2	scaffold_4929:11075516-11075624 +	ATTCCA------TCATTCGGCTGTAACCTGATCCC-----------------CTGCTGTGG----------------------GCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AGCACAGCGTGGGCAC-----------GGC-CCACTGGTCGTCAACCGC
droAna3	scaffold_12916:8156171-8156273 +	CATCCGATCTGA----TTGGCAGTAACCTGATCCG-----------------CGGTTGTG-----------------------GTTGTGG-----TGGAGGTG---CTACTTGATAACCCAC-------------------TG-----CGTGGGCAC-----------TGGCCTTTCGGTTGTCAACGGC
dp4	chr4_group1:223199-223319 +	GATCCAATCGGATCGGGTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTGCGGTGGA--------------------------GT-----TGGAGGTGTCGGCTGTTGATAACCCCC-------------------AG-----CGTAGGCAC-----------TGG---TATGGTTGTGAACGGC
droPer1	super_1:219428-219548 +	GATCCAATCGGATCGGGTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTGCTGTGGA--------------------------GT-----TGGAGGTGTCGGCTGTTGATAACCCCC-------------------AG-----CGTAGGCAC-----------TGG---TATGGTTGTCAACGGC
droWil1	scaffold_180708:7887456-7887585 +	ATTGCAATTGGTT--GTGGGCTGTAACCTGATCTGGA----------------AGCTATAG-----------------------ATGTGATGATGCGGAGGTGTCGTCAGATGATAACCCCCCAGGGTAGACAGCTTAGACAT-----CGTAGGCAT-----------TGGC---CTGGTTGTCAACGGC
droVir3	scaffold_12963:3941701-3941790 -	GG--C----------GTCTGCTGTAACTTGAAGCG-----------------CTGAT-----------------------------------------------CTGTGGTTGATAACCCCC-------------------TG-----CCAAGGTGCTCGTAGGCAGCTACCGCTCCGGTTGTCAACGGC
droMoj3	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15252:1454932-1454939 +	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTAG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:6045612-6045728 -	NA	A-TT----TC-GC---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGTTGTGGGCTGTG-------TGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGACCCACTGGTCGTCAACCGC
droSim1	chr2L:5834370-5834493 -	1	A-TT----TC-GT---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGCTGTGGGCTGTGGGCTGTAAGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droSec1	super_5:4116543-4116659 -	1	A-TT----TC-GT---TCGGCTGTAACCTGATCC-----------------GCTG--CTGCGGGTTGTGGGCTGTG-------AGGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droYak2	chr2L:13146709-13146824 +	1	A-TT----CC-GC---TCGGCTGTAACCTGATCC-----------------GCTG--CTGTGGGATGTGGGATGTG--------GGCTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-A----------------------GCGTGGGCA-CGGCCCCACTGGTCGTCAACCGC
droEre2	scaffold_4929:11075516-11075624 +	2	A-TT-CCATC-AT---TCGGCTGTAACCTGATCC-----------------CCTG--CTGTGGG----------------------CTGT------GG-----TATAGGTGCCGCCAGTTGATAACCCCC-AGCA-----------------CAGCGTGGGCA-CGG-CCCACTGGTCGTCAACCGC
droEug1	scf7180000409676:526352-526439 +	1	T-------TT-GA---TCGGCTGTAACCTGATCT-----------------ACAT--CTG-----------------------------C------GG-----TAAAGGTG---CCAATTGATAACC--C-A----------------------GCGTGGGCA-CTG-CTAACTGGTCGTCAACGGC
droBia1	scf7180000302055:11613-11705 +	4	T-------TC-GA---TCGTCTGTAACCTGATCC-----------------AAGG--CTG-----------------------------C------GT-----TATAGGTGTCGCCGGTTGATAACCCCC-A----------------------GCGTGGGCA-CGG-CTCACTAGTCGTCAACAGC
droTak1	scf7180000415447:53169-53260 -	1	--------TC-GA---TCGGCTGTAACCTGATCC-----------------GCGG--CTG-----------------------------C------GG-----TATAGGTGTCGCCAGTTGATAACCCTC-A----------------------GCGTGGGCA-CGG-CCCACTAGTCGTCAACGGC
droEle1	scf7180000490399:107074-107177 -	2	--------TC-GA---TCTGCTGTAACCTAATCCGA--TCG----------GCTG--CTGTGGTATATGTA--------------------------------CATAGGTGCCGCCAGTTGATAACCC-C-A----------------------GTGTAGGCA-CGG-CCCACTGGCTGTCAACGGC
droRho1	scf7180000779105:24952-25021 -	1	--------TC-GA---TCTGCTGTAACCTGATCT-----------------GCTG--CTG-----------------------------T------GG-----TATAGGTGCCGCAAGTTGATAACCCCA--------------------------GTGGGCA-CGG--------------------
droFic1	scf7180000452562:15607-15693 +	1	A-------TC---------GATGTAACCTGATCG-----------------GCGG--CTG-----------------------------T------GG-----TCTAGGTGGATTCAGTTGATAACCCTC-A----------------------GCGTGGGCT-CAG-CCTACTGGTTGTCAACGGC
droKik1	scf7180000302468:107704-107788 -	1	G-ATTGGATCGGA---TTGGCTGTAACCTGAACC-----------------GCGG--CTGTG-------------------------------------------------------GTTGATAACCCCC-A----------------------ACGTGGGCT-GCGGCCCACTGGTTGTCAACGGC
droAna3	scaffold_12916:8156171-8156273 +	1	C-ATCCGATCTGA---TTGGCAGTAACCTGATCC-----------------GCGG--TTGTGG-----------------------TTGT------GG-----TGGAGGT---GCTACTTGATAACCCAC-T----------------------GCGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC
droBip1	scf7180000396554:766763-766860 +	2	G-AT----CT-GA---TTGGCAGTAACCTGATCC-----------------GCGG--TTGTGG-----------------------TTGT------GC-----TGGAGGT---GCTACTTGATAACCCAC-T----------------------GCGTGGGCA-CTGGCCTTTCGGTTGTCAACGGC
dp4	chr4_group1:223208-223319 +	1	G-GA----TC-GG---GTGGCTGTAACCTGATCTGGGAGCGGTGCAGC---AGGG--CTG-----------------------------CGGTGGAGT-----TGGAGGTGTCGGCTGTTGATAACCCCC-A----------------------GCGTAGGCA-CTGG---TATGGTTGTGAACGGC
droPer1	super_1:219437-219548 +	1	G-GA----TC-GG---GTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTG--CTGTGGA--------------------------------GT-----TGGAGGTGTCGGCTGTTGATAACCCCC-A----------------------GCGTAGGCA-CTGG---TATGGTTGTCAACGGC
droWil1	scaffold_180708:7887454-7887585 +	1	GGATTGCAATTGGTTGTGGGCTGTAACCTGATCTGG----------------AAG--CTATAG-----------------------ATGT------GATGATGCGGAGGTGTCGTCAGATGATAACCCCCCAG----GGTAGACAGCTTAGACATCGTAGGCA-TTGGC---CTGGTTGTCAACGGC
droVir3	scaffold_12963:3941701-3941794 -	2	A-TT-------GGGCGTCTGCTGTAACTTGAAGC-----------------GCTGATCTG-------------------------------------------------------TGGTTGATAACCCCC-TGCCAAGGTG------------CTCGTAGGCAGCTACCGCTCCGGTTGTCAACGGC
droMoj3	Unknown	NA	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15252:1454932-1454939 +	1	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTAG

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ATTTCG---------CTCGGCTGTAACCTGATCCG-----------------CTGCTGTGGGTTGTGGGCTGTGT-------GGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AG-----CGTGGGCAC-----------GGACCCACTGGTCGTCAACCGC

Size

Hit Count

Total Norm

droSim1

ATTTCG---------TTCGGCTGTAACCTGATCCG-----------------CTGgTGTGGGgTGTGGGgTGTGGGgTGTttGGgTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AG-----CGTGGGCAC-----------GGCCCCACTGGTCGTCAACCGC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................GTGAGGGGTGTGGGGAGTT.............................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00

droSec1

ATTTCG---------TTCGGCTGTAACCTGATCCG-----------------CTGCTGCGGGTTGTGGGCTGTGA-------GGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AG-----CGTGGGCAC-----------GGCCCCACTGGTCGTCAACCGC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................TGCGGGTTGTGGGCTGTGA-------GG..........................................................................................................	21	1	5.00	1.00	2.00	2.00
........................................................TGCGGGTTGTGGGCTGTGA-------GGCT........................................................................................................	23	1	5.00	2.00	1.00	2.00
........................................................TGCGGGTTGTGGGCTGTGA-------GGC.........................................................................................................	22	1	3.00	1.00	1.00	1.00
........................................................TTCGGGTTGTGGGCTGTGA-------GG..........................................................................................................	21	1	1.00	0.00	0.00	1.00
.......................................................................................................CCGCCAGTTGATAACCCCC-------------------AG-----C.........................................	22	1	1.00	0.00	1.00	0.00
........................................................TGCGGGTTGTGGGCTGTG....................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

ATTCCG---------CTCGGCTGTAACCTGATCCG-----------------CTGCTGTGGGATGTGGGATGTG--------GGCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AG-----CGTGGGCAC-----------GGCCCCACTGGTCGTCAACCGC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.......................................................CTGxGCGATGTGGGATG......................................................................................................................	16	1	2.00	0.00	0.00	0.00	2.00	0.00
........................................................TGTGGGATGGGGGATCT.....................................................................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00
.........................................................GTGGGAGGTGGGAGGTG--------GG..........................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................TGGGAGGTGGGAGGTG--------GG..........................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
................................................................GTGGGATGTG--------GGxGGTGG-----T..............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

ATTCCA------TCATTCGGCTGTAACCTGATCCC-----------------CTGCTGTGG----------------------GCTGTGG-----TATAGGTGCCGCCAGTTGATAACCCCC-------------------AGCACAGCGTGGGCAC-----------GGC-CCACTGGTCGTCAACCGC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................C-----------------CTGCxGTGG----------------------GCTGTAG-----TA.............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
ATTCCA------TCATCAGGCTGT......................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

CATCCGATCTGA----TTGGCAGTAACCTGATCCG-----------------CGGTTGTG-----------------------GTTGTGG-----TGGAGGTG---CTACTTGATAACCCAC-------------------TG-----CGTGGGCAC-----------TGGCCTTTCGGTTGTCAACGGC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.........................................................GTG-----------------------GTGGTGG-----TGGAGGCG---....................................................................................	18	3	1.00	0.00	1.00	0.00	0.00
......................................................GTGGTG-----------------------GTGGTGG-----TGGAGGTG---....................................................................................	21	2	1.00	0.00	1.00	0.00	0.00
....................................................CGGGTGTG-----------------------GTTGTGG-----TGGTGG.........................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
........................................................AGTG-----------------------GTGGTGG-----TGGAG..........................................................................................	16	3	0.33	0.00	0.00	0.33	0.00
.....................................................GGTGGTG-----------------------GTTGTGG-----TGGT...........................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
......................................................GTGGTG-----------------------GTGGTGG-----TGGAG..........................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.....................................................................................GGTGG-----TGGAGCTG---CTACT...............................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....................................................GGTGGTG-----------------------GTGGTGG-----TGGA...........................................................................................	18	5	0.20	0.00	0.20	0.00	0.00
.....................................................GGTGGTG-----------------------GTGGTGG-----TGGAGG.........................................................................................	20	3	0.33	0.00	0.33	0.00	0.00
......................................................GTTGTG-----------------------GTGGTGG-----TGGTGGT........................................................................................	20	3	0.33	0.00	0.33	0.00	0.00
.......................................................TGGTG-----------------------GTGGTGG-----TGGAGGT........................................................................................	19	4	0.25	0.00	0.25	0.00	0.00
..................................G-----------------CGGGTGTG-----------------------GTTGTGG-----TGGTG..........................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
.......................................................TTGGG-----------------------GTTGTGG-----GGGAG..........................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
......................................................GTTGTG-----------------------GTGGTGG-----TGGAA..........................................................................................	18	2	0.50	0.00	0.50	0.00	0.00

dp4

GATCCAATCGGATCGGGTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTGCGGTGGA--------------------------GT-----TGGAGGTGTCGGCTGTTGATAACCCCC-------------------AG-----CGTAGGCAC-----------TGG---TATGGTTGTGAACGGC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..................................................ATCTGCGGTGGA--------------------------GT-----TGGAG..........................................................................................	19	1	8.00	8.00	0.00	0.00	0.00
.....................................................TGCGGTGGA--------------------------GT-----TGGAGTTT.......................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
....................................................CTGCGGTGGA--------------------------GT-----TGGAGTTT.......................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.................................TGGGAGTGGTGCGGCAGGG..........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.....GAGCGGATCGGGTGGCTGT......................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.....................................................TGCGGTGGA--------------------------GT-----TGGAGCG........................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droPer1

GATCCAATCGGATCGGGTGGCTGTAACCTGATCTGGGAGCGGTGCAGCAGGGCTGCTGTGGA--------------------------GT-----TGGAGGTGTCGGCTGTTGATAACCCCC-------------------AG-----CGTAGGCAC-----------TGG---TATGGTTGTCAACGGC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................GCTGTGGA--------------------------GT-----TxGCGGTGTC.....................................................................................	19	1	2.00	2.00	0.00	0.00	0.00	0.00
.................................TGGGAGTGGTGCGGCAGGG..........................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................CAC-----------TGG---TATGGTTGTCAACGG.	21	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................GGCTGCTGTGGA--------------------------TC-----TGGA...........................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...................................AGTGCxGTGCAGCAGGGCTGC......................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00	0.00

droWil1

ATTGCAATTGGTT--GTGGGCTGTAACCTGATCTGGA----------------AGCTATAG-----------------------ATGTGATGATGCGGAGGTGTCGTCAGATGATAACCCCCCAGGGTAGACAGCTTAGACAT-----CGTAGGCAT-----------TGGC---CTGGTTGTCAACGGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
........................................................TATAG-----------------------ATGAGATGATGTGG............................................................................................	19	1	7.00	0.00	7.00	0.00	0.00
.....ATATGGTT--GTGGGCTGTA.....................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.TTGCTATTGGTT--GGGGGCTG.......................................................................................................................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.TTGCTATTGGTT--GGGGGCT........................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................TTC---CTGGTTGTCAACGGC	18	1	1.00	0.00	0.00	0.00	1.00
........................................................TATAG-----------------------ATGAGATGATGTG.............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.....AATTGGTT--GAGGGTTGTA.....................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................ATAG-----------------------ATGAGATGATGTGG............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

GG--C----------GTCTGCTGTAACTTGAAGCG-----------------CTGAT-----------------------------------------------CTGTGGTTGATAACCCCC-------------------TG-----CCAAGGTGCTCGTAGGCAGCTACCGCTCCGGTTGTCAACGGC

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

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAACTAG

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

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
UNAFold Image																			None	None