dme-mir-4960- 12- and 20-way alignments

dme-mir-4960	chrX:463935-464036 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 463999-464019
   star strand at position 463961-463982
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:463920-464051 +	TGGAGTGACCAGCACAACACAAGGCCTGCCGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGAAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGG-G------ACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT
droSim1	chrX_random:776904-777034 +	CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGGAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGGGG------CCT-T-GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droSec1	super_10:310837-310968 +	CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGGAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGGG-------GCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droYak2	chrX:383437-383616 +	TGCAATGCCCACCACAACACAAGGCCTGATGCCCGAGAAT-CGGTTTATTTCCTCCTCT------------------T-------------------------------------------------------------------------------CCGCAGGCCCAGGAGTCCGGCAGTC----------------GAGCAGTCGAGCTGTTCACCCGGTCAGTCCTT-GGTCCTTGGTCCTTGGGCCTTGGGCTTTCGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droEre2	scaffold_4644:409107-409303 +	TGCAATGACCCTCACCACACAAGGCCCGATGCCCGGGAAT-CGGTTTATTTCCTCTTCT------------------T-------------------------------------------------------------------------------CCGCAGGCCCAGGagtccggcagtccgacagtccagcagtccggcagtcGAGTTGTCGAGTAGTCCAGTCATGAGGGGCTGGGGCCTTGGGCCTTGGGCTTACGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droAna3	scaffold_12929:357992-358198 +	TGGAATGACC---ACAGCAGAAGGCCTTCTGCCAA-GACTTGGGTGTAGATATGAGTGTGTGTGGGTGTGGGTGTGTTTT--GGCCAGAATATGGTGGGTGATTGTGCAGGGAGGCGTGGCAGATGGGGG-GGCG-------GAGGATGAAGAAGAAGCAGTAGCAGAGGAG--------------------------------------------------------------------G------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
dp4	chrXL_group1e:196231-196421 +	TGGAATGACC---ACGGCACAAGGCCT--TG-CCAAGACT-TGTTTTATTTTTTGCTGA------------------TTTGGGGGCAGGAACT-GTAGGTGCCT--GCCGCGCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAG---GACGCAGGAGGCTT-------------CGCAGGA----------------GAG--------------------------------------AA------CTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCAT
droPer1	Unknown	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180777:2769923-2769983 +	CAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGATTGACG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droVir3	scaffold_12970:10710181-10710231 +	G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droMoj3	scaffold_6473:10704148-10704209 -	GGGG--------------------------------GGCTTGGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droGri2	scaffold_14853:6069294-6069344 -	G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:463920-464051 +	NA	TGGAGTGACCAGC----------------------------AC--AACACAAGGCCTGCCGCCCAA-GAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAAGCCCAGAAGTCC--------GGCAGTCGAG---------AA--------------------------------------------TCACGAGGGAC--TG------------------------------------GGACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT
droSim1	chrX_random:776904-777034 +	4	CGGAGTGACCAGC----------------------------AC--ATCACAAGGCCTGGTGCCCAA-GAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAAGCCCAGGAGTCC--------GGCAGTCGAG---------AA--------------------------------------------TCACGAGGGAC--TG-----------------------------------GGGCCTT--GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droSec1	super_10:310837-310968 +	1	CGGAGTGACCAGC----------------------------AC--ATCACAAGGCCTGGTGCCCAA-GAAA--------------------------------------------------------------------------------------------------------------------------------------------------------------------CGCAAGCCCAGGAGTCC--------GGCAGTCGAG---------AA--------------------------------------------TCACGAGGGAC--TG------------------------------------GGGCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT
droYak2	chrX:383437-383616 +	3	TGCAATGCCCACC----------------------------AC--AACACAAGGCCTGATGCCCGA-GAATCG-GTTTA----------------------------TTTCCTCCTCTTCCGC-------------------------------------------------------------------------------------------------------------------AGGCCCAGGAGTCC--------GGCAGTCGAGCAGTCGAGCTGTTCA--------------------CCCGGTCAG-----------TCCTT-GGTCC--TTGGTCCTT-----------------------------GGGCCTTGGGCTTTCGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droEre2	scaffold_4644:409107-409303 +	2	TGCAATGACCCTC----------------------------AC--CACACAAGGCCCGATGCCCGG-GAATCG-GTTTA----------------------------TTTCCTCTTCTTCCGC-------------------------------------------------------------------------------------------------------------------AGGCCCAGGAGTCC--------GGCAGTCCGACAGTCCAGCAGTCCG----GCAGTCGAGTTGTCGAGTAGTCCAG-----------TCATGAGGGGC--TGGGGCCTT-----------------------------GGGCCTTGGGCTTACGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT
droEug1	scf7180000409277:848596-848784 +	1	TGGAATGACC-------------------------------AC--AGCACAAGGTCTTATGGCCAG-GACTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------GA--------AGTCC--------GGCAGTCGAGCAGTCGAGCAGTCCAGCCAGCAGTC-------CGGGCAGTCCGGTGGAGAA----TC--GAGGGGTTC-C-GGG-----------------------------GAGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droBia1	scf7180000301760:1515569-1515727 +	2	TGGAATGACCAGGACAGCACA-GCACAGCAGAGCACATAGCACATAGCACAAGGCCTTATGCCCAA-GTCTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------GA--------AGTCC--------GGCAGTCG----------------------------------------------------------------------------------------------------------AGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droTak1	scf7180000415281:255352-255504 -	2	TGGAATGACCGGCACAGCACAAGCACA----AGCACA-AGCAC--ATCACAAGGCCTTATGCCCAA-GACTTG-GTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------AA--------AGTCC--------GGCAGTCG----------------------------------------------------------------------------------------------------------AGGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droEle1	scf7180000491023:745050-745100 +	2	G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGCCTTTGGGGTTTCGGTTTTCAGTTTGTCTTGACATGCATCAGCATCAT
droRho1	scf7180000779514:240474-240645 +	2	TGGAATGACC-------------------------------AC--AGCACAAGGCCTTTCGCCCGA-GACTTG-CTTTA----------------------------TTTTCTGTTTGTCCGG------------------------------------------------------------------------------------------------------------------AA--------AGTCC--------GGCAGTTCAG---TTCAGTAGG----------------------AG-GATAAAATGGGGGGGAAGGGAGGAGGGGG--TG---------------------------------GAGGTCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droFic1	scf7180000453927:944869-945084 +	2	TGGAATGACC-------------------------------AC--AGCACAAGGCCTTCTGCCCAAAGACTGGGGTTTA----------------------------TTTTCTGTTTGTCGGG-----------------------------------------------------------------------------------------------------------------GAAA--------GTCCGGCAGTCCGGCAGTCGGG---------AGTCCAGTCG---ATC-------CGAG-AATCCAGTGGGAGG----TT--CGGGGGTTC-G-GGGCTTCGGGTTGGCAGAGAGTGTATGAAGTAGAGGGCCTTTGGGGTTTTGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droKik1	scf7180000302469:1859429-1859538 -	2	TGAAATGACC-------------------------------AC--AGCA----------------G-GTCCTG-CTTTT----------------------------CTTACTAGGGGG-CGA------------------------------------------------------------------------------------------------------------------AA--------TGGAA--------TGGAGGCG----------------------------------------------------------------------------------------------------------GTATCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droAna3	scaffold_12929:357992-358198 +	2	TGGAATGACC-------------------------------AC--AGCAGAAGGCCTTCTGCC-AA-GACTTGGGTGTAGATATGAGTGTGTGTGGGTGTGGGTGTGTTTT------G------GCCAGAATATGGT------GGGTGATTGTGCAGGGAGGCGTGGCAGATGGGGGGGCGG--------------------------AGGATGAAGAAGAAG------------CAGTAGCAGAGGA--------------------------------------------------------------------------------------------------------------------------------GGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droBip1	scf7180000395176:32639-32844 -	2	TGGAATGACC-------------------------------AC--AGCAGAAGGCCTTCTGCC-AA-GACTTTGGTGTCAAT----------GTATGTGTGTGTGTGTTT------TG------GCCAGAATATGATAGAGTAGGGGGATTGTGCATGGAGGCGTGGCAG------GGGCGG--------------------------AGGAAGAAGAAGAGGCAGAAGCAGAAACAGAAGCGG-----------------------------------------------------------------------------------------------------------------------------------AGGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
dp4	chrXL_group1e:196231-196421 +	1	TGGAATGACC-------------------------------AC--GGCACAAGGCCTT--G-CCAA-GACTTG-TTTTA----------------------------TTTTTTGCTGATTTGGGGGCAGGAACT-GT------AGGTGCC--------------TGCCGC------GCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAG---GACGCAG-----------------GA--------GGCTT--------CGCAGGAG----------------------------------------------------------------------------------------------------------AGAACTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCAT
droPer1	Unknown	NA	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_180777:2769923-2769983 +	3	CAG----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGAT--TG-----------------------------------ACGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droVir3	scaffold_12970:10710181-10710231 +	2	G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droMoj3	scaffold_6473:10704148-10704209 -	3	GGGG---------------------------------------------------------------GGCTTG-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGTGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT
droGri2	scaffold_14853:6069294-6069344 -	2	G---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGCCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TGGAGTGACCAGCACAACACAAGGCCTGCCGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGAAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGG-G------ACCTTGGGCTTACGGTTCTCAGTTTGGCTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

droSim1

CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGGAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGGGG------CCT-T-GGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...................................................................................................................................................................................................................................................................CGGTTTTCGATTTGGCTTGAC...............	21	2	0.50	0.00	0.00	0.00	0.50
......................................................................................................................................................................................................GAGAA----------------------GCACGAGGGTCTG.........................................................	18	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................................................................................................................................TCCCGTGGGACTGGGG------CC..............................................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

CGGAGTGACCAGCACATCACAAGGCCTGGTGCCCAAGAA----------------------------------------------------------------------------------------------------------------------ACGCAAGCCCAGGAGTCCGGCAGTC----------------GAGAA----------------------TCACGAGGGACTGGG-------GCCTTGGGCTTACGGTTTTCATTTTGGCTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
....................................................................................................................................................................................................................................................................GGTTTTCGATTTGGCTTGAC...............	20	2	0.50	0.50	0.00	0.00

droYak2

TGCAATGCCCACCACAACACAAGGCCTGATGCCCGAGAAT-CGGTTTATTTCCTCCTCT------------------T-------------------------------------------------------------------------------CCGCAGGCCCAGGAGTCCGGCAGTC----------------GAGCAGTCGAGCTGTTCACCCGGTCAGTCCTT-GGTCCTTGGTCCTTGGGCCTTGGGCTTTCGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................................................................................................................................................................................................................................CGGTTTTCGATTTGGCTTGAC...............	21	2	0.50	0.00	0.00	0.00	0.00	0.50
..................................................................................................................................................................................................................................................................TCGGTTTTCGGTTTGGTTTGA................	21	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

TGCAATGACCCTCACCACACAAGGCCCGATGCCCGGGAAT-CGGTTTATTTCCTCTTCT------------------T-------------------------------------------------------------------------------CCGCAGGCCCAGGagtccggcagtccgacagtccagcagtccggcagtcGAGTTGTCGAGTAGTCCAGTCATGAGGGGCTGGGGCCTTGGGCCTTGGGCTTACGGTTTTCAGTTTGGCTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................................................................................................................................................................AAAGTCCAGCAGTCCGGT.............................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

TGGAATGACC---ACAGCAGAAGGCCTTCTGCCAA-GACTTGGGTGTAGATATGAGTGTGTGTGGGTGTGGGTGTGTTTT--GGCCAGAATATGGTGGGTGATTGTGCAGGGAGGCGTGGCAGATGGGGG-GGCG-------GAGGATGAAGAAGAAGCAGTAGCAGAGGAG--------------------------------------------------------------------G------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.....................................................GTGGGTGTGTGGGTGTGGGTGT............................................................................................................................................................................................................................	22	1	11.00	3.00	8.00	0.00	0.00
......................................................AGTGTGTGTGTGTGTGTG...............................................................................................................................................................................................................................	18	16	0.69	0.06	0.63	0.00	0.00
......................................................AGTGTGTGTGTGTGTGTGT..............................................................................................................................................................................................................................	19	14	0.57	0.00	0.57	0.00	0.00
.......................................................GTGGGTGTGGGTGTGGGT..............................................................................................................................................................................................................................	18	5	1.40	0.00	1.40	0.00	0.00
.............................................................GTGGGTGTGGGTGTGGGT........................................................................................................................................................................................................................	18	5	1.40	0.00	1.40	0.00	0.00
.......................................................GTGGGAGTGGGTGTGGGT..............................................................................................................................................................................................................................	18	3	1.67	0.00	1.67	0.00	0.00
.....................................................GTGGGTGTGTGGGTGTGGGTGTG...........................................................................................................................................................................................................................	23	1	4.00	1.00	3.00	0.00	0.00
.......................................................GTGGGTGTGGGTGTGGGTG.............................................................................................................................................................................................................................	19	4	1.00	0.00	1.00	0.00	0.00
.......................................................GTGGGTGTGGGTGTGGGA..............................................................................................................................................................................................................................	18	4	1.00	0.00	1.00	0.00	0.00
.................................................................GTGTGTGTGTGTTGT--GGC..................................................................................................................................................................................................................	18	1	4.00	1.00	3.00	0.00	0.00
..............................................................................................GTGGGTGGTTGTGCATGG.......................................................................................................................................................................................	18	1	3.00	2.00	1.00	0.00	0.00
........................................................TGTGTGTGTGTGTGGGTG.............................................................................................................................................................................................................................	18	18	0.17	0.00	0.17	0.00	0.00
.....................................................GTGGGTGTGTGGGTGTGGGT..............................................................................................................................................................................................................................	20	2	1.50	0.00	1.50	0.00	0.00
..................................................TGTGTGTGTGTGTGGGTG...................................................................................................................................................................................................................................	18	18	0.17	0.00	0.17	0.00	0.00
...........................................................GTGGGTGTGTGGGTGTGT..........................................................................................................................................................................................................................	18	8	0.38	0.13	0.25	0.00	0.00

dp4

TGGAATGACC---ACGGCACAAGGCCT--TG-CCAAGACT-TGTTTTATTTTTTGCTGA------------------TTTGGGGGCAGGAACT-GTAGGTGCCT--GCCGCGCGGGGAAGTAGAAGGGAAAGGCGTGGCTGCGAG---GACGCAGGAGGCTT-------------CGCAGGA----------------GAG--------------------------------------AA------CTTTTGGGGTTTCGGTTTTGAGTTTGACTTGACATGCATCAGCATCAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
...........................................................................................................................................GGAGxG---GACGCAGGAGGCT......................................................................................................................................	18	1	9.00	7.00	0.00	2.00	0.00
............................................................................................................................................GAGxG---GACGCAGGAGGCTA-------------........................................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00
.........................................................................................................................................GATGxGAG---GACGCAGGAGGC.......................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................................................................GAG---GACGCAGGAGGCTA-------------T.......................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droPer1

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

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

CAG------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GGGATTGACG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

G----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GGGG--------------------------------GGCTTGGG---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TG------CCTTTGGGGTTTCGGTTTTCAGTTTGACTTGACATGCATCAGCATCAT

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