dme-mir-2492- 12- and 20-way alignments

dme-mir-2492	chrX:11441455-11441530 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 11441502-11441523
   star strand at position 11441463-11441484
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:11441440-11441545 +	ACAAAATTCACACTCGAATTTTTTTGGGATCTCTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTTCAAA---AAATT-------CAGAAGACAACAACGCA
droSim1	chrX_random:3203326-3203430 +	ACAAAATTCACACTCGAATTTTT-TGGGATCTCTTTATAAAGCGtttattattatttatttattatGTTTTGTCGAGAGCTTTCAAA---AAAGT-------CAGAAGACA---ACGCA
droSec1	super_36:155641-155745 +	ATAAAATTCACTCTCGAATTTTT-TGGGATCTCTTTATAAAGCatttattattatttatttattatGTTTTGTCGAGAGCTTTCAAA---AAAGC-------CAGAAGACA---ACGCA
droYak2	chrX:10720999-10721105 -	ACAAAATTCACACTCGAATTTTTTGGCAATCTGTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTTCaaaaatacaacaaaatagga------a---aaaaa
droEre2	scaffold_4690:3720651-3720750 -	ACAAAATTCACACTCGAATTT--TGGGTATCTCTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTAAAAA---AAAT------ATGAAAAGACA---A--CA
droAna3	scaffold_13047:188962-189050 +	ACAAAATTCACACTCGCTTT---TGGCCAAC--TCCATAAAGCGTTAATTA---TC---------TGGCATTCTGAGAGCCAAAAGC---TAAAT-------CAAATTCGA---TCGGA
dp4	chrXL_group1e:1762210-1762253 +	ACAAAATTCACACTCGAATT---TGGGGATCGCGTAGCGAGG------------------------------------------------------------------------GGGGG
droPer1	super_18:601670-601712 +	ACAAAATTCACACTCGAATT---TGGGGATCGCGTAGCAAGGGGGG-------------------------------------------------------------------------
droWil1	scaffold_180777:122952-122984 +	ATAAACTCAATACACGAATTTGGTACTGATTTC--------------------------------------------------------------------------------------
droVir3	Unknown	-----------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	-----------------------------------------------------------------------------------------------------------------------
droGri2	scaffold_15203:463820-463836 -	GTGAAATTCACACTCGA------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:11441440-11441545 +	NA	ACAAAATTCACACTCGAATT-TTTT-TGGGATCTC-------TTTATAAAGCGTTTATTA---TTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAAATT---------C--AGA------------AGACAACAACGCA
droSim1	chrX_random:3203326-3203430 +	5	ACAAAATTCACACTCGAATT-TTTT-G-GGATCTC-------TTTATAAAGCGTTTATTATTATTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAAAGT---------C--AGA------------AGA---CAACGCA
droSec1	super_36:155641-155745 +	3	ATAAAATTCACTCTCGAATT-TTTT-G-GGATCTC-------TTTATAAAGCATTTATTATTATTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAAAGC---------C--AGA------------AGA---CAACGCA
droYak2	chrX:10720999-10721105 -	3	ACAAAATTCACACTCGAATT-TTTT-GGCAATCTG-------TTTATAAAGCGTTTATTA---TTTATTTATTATGTTTT-GTCGAGAGCTTTCAAAAATACA--------A--CAA------------AATAGGAAAAAAA
droEre2	scaffold_4690:3720646-3720750 -	1	ACAAAATTCACACTCGAATT-T--TGG-GTATCTC-------TTTATAAAGCGTTTATTA---TTTATTTATTATGTTTT-GTCGAGAGCTTAAAAAAAAT----------ATGAAA------------AGACAACAACCAA
droEug1	scf7180000408176:611267-611357 +	1	ACAGAATTCACACTCGTTTT-T--T-G-GCATC---------TCTATAAAGCGTTTATTA---TTTATTTATTATGCTTGCTTTGAGAGCTTTCAAAGAGA----------C------------------------AAAAAT
droBia1	scf7180000301760:529098-529183 +	1	ACAAAATTCACACTCGAATT-TTTT-G-GCATC---------TCTATAAAGCGTTTATTA---TTTGTTTATTGTGTTGT-GTCGAGAGCTTTCAAAAGAGC----------------------------------------
droTak1	scf7180000415843:399035-399133 +	1	ACAAAATTCACACTCAAATT-T--T-G-GGACCTC-------TCTATAAAGCGTTTATTA---CTTATTTATTTTGTTAA-GTCGAGAGCTTTCAAAAGA-----------C--AAA------------AAAAACC--AAAA
droEle1	scf7180000491193:278928-279018 -	1	ACAAAATTCACACTCGATTT-TTTT-TTTTTTTTTTATTCTTGCTATAAAGACTTTATTA---TTTATTTATTATGTTTT-GTTGAGAGCTTTCAAA---------------------------------------------
droRho1	scf7180000779986:444043-444125 +	1	ACAAAATTCACACTCGAATTTT--T-G-GGATC---------TCTATAAAGCGTTTATTA---TTCATTTATTATGTTTT-GTCGAGAGCTTTCAAATGA------------------------------------------
droFic1	scf7180000453872:274536-274622 +	1	ACAAAATTCACACTCGAATT-T--C-G-GGAAC---------TCAATAAAGTGTTTATTA---TTTAATTATTATGTTTT-GTAAAGAGCTTTTAAAGAT-------------------------------------ACACA
droKik1	scf7180000302344:177104-177194 +	1	ACAAAATTCACACTCGAATT-T--G-G-AGATC---------TCTATAAAGCGTTTATTT---TTTGGTATTTGTATACCCTTCAAGAGGGTATTAAATAC----------T------------------------TTTAAG
droAna3	scaffold_13047:188962-189053 +	1	ACAAAATTCACACTCGCTTT-T--G-G-CCAAC---------TCCATAAAGCGTTAATTA---TCTGGC---------------------ATTCTGAGAGC----------C--AAAAGCTAAATCAAATTCGATCGGAGCG
droBip1	scf7180000396425:338388-338489 +	4	ACAAAATTCACACTCGCTTT-T--G-G-CCAACTC-------TCCATAAAGCGTTAATTA---TTTAAC---------------------ATTCTAAAAGCCGAAAAGCGGC----AAATGAATTCAAATTGAAGCAAAGCC
dp4	chrXL_group1e:1762210-1762257 +	2	ACAAAATTCACACTCGAATT-T--G-G-GGATC---------GCG----------------------------------T-AGCGAGGGGGGG---------------------------------------------GCAA
droPer1	super_18:601670-601716 +	1	ACAAAATTCACACTCGAATT-T--G-G-GGATC---------GCG----------------------------------T-AGCAAGGGGGGGCA----------------------------------------------A
droWil1	scaffold_180777:122952-122984 +	3	ATAAACTCAATACACGAATT-TGGT-ACTGATTTC-----------------------------------------------------------------------------------------------------------
droVir3	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:22511787-22511827 +	2	TCCGT------------------------------------------------------------------------------CAATCATCTCCTTAAAACT---------C--TAA------------AGCAAACCAAGCA
droGri2	scaffold_15203:463820-463836 -	7	GTGAAATTCACACTCGA-----------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ACAAAATTCACACTCGAATTTTTTTGGGATCTCTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTTCAAA---AAATT-------CAGAAGACAACAACGCA

Size

Hit Count

Total Norm

droSim1

ACAAAATTCACACTCGAATTTTT-TGGGATCTCTTTATAAAGCGtttattattatttatttattatGTTTTGTCGAGAGCTTTCAAA---AAAGT-------CAGAAGACA---ACGCA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................TTATGTTTTGTCGAGAGCTTTC...................................	22	1	1.00	0.00	0.00	0.00	1.00
...................................................................TTTTGTCGAGAGCTTTCAAA---.............................	20	1	1.00	0.00	1.00	0.00	0.00

droSec1

ATAAAATTCACTCTCGAATTTTT-TGGGATCTCTTTATAAAGCatttattattatttatttattatGTTTTGTCGAGAGCTTTCAAA---AAAGC-------CAGAAGACA---ACGCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................TGGGATCTCTTTATAAAGCAT..........................................................................	21	1	2.00	0.00	1.00	1.00
.................................................................TGTTTTGTCGAGAGCTTTCAA.................................	21	1	1.00	0.00	1.00	0.00
...................................................................TTTTCTCGAGAGCTTTCAAA---A............................	21	1	1.00	0.00	1.00	0.00
.....................................................................TTGTCGAGAGCTTTCAAA---.............................	18	1	1.00	0.00	1.00	0.00
.....................................................ATTTATTTATTATGTTTCGTCGAGA.........................................	25	1	1.00	0.00	1.00	0.00
........................TGGGATCTCTTTATAAAGCATT.........................................................................	22	1	1.00	1.00	0.00	0.00
.........................................................................TGAGAGCTCTCAAA---AAAG.........................	18	1	1.00	0.00	1.00	0.00
...................................................................TTTTGTCxxGAGCTTTCAAA---A............................	19	1	1.00	0.00	1.00	0.00
...................................................................TTTTGTCGAGAGCTTTCAAA---A............................	21	1	1.00	0.00	1.00	0.00

droYak2

ACAAAATTCACACTCGAATTTTTTGGCAATCTGTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTTCaaaaatacaacaaaatagga------a---aaaaa

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

ACAAAATTCACACTCGAATTT--TGGGTATCTCTTTATAAAGCGTTTATTA---TTTATTTATTATGTTTTGTCGAGAGCTTAAAAA---AAAT------ATGAAAAGACA---A--CA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
............................................TTTAGTT---TTTATTTATTA......................................................	18	1	3.00	0.00	0.00	0.00	3.00
....................................TTAAAGCxTTTATTA---TTTAT............................................................	19	1	2.00	0.00	0.00	2.00	0.00
........................................AGCTTTTCTTA---TTTATTT..........................................................	18	1	1.00	0.00	0.00	1.00	0.00
.............................................................ATTTTGxTTTGTCGAGAGC.......................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

ACAAAATTCACACTCGCTTT---TGGCCAAC--TCCATAAAGCGTTAATTA---TC---------TGGCATTCTGAGAGCCAAAAGC---TAAAT-------CAAATTCGA---TCGGA

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

ACAAAATTCACACTCGAATT---TGGGGATCGCGTAGCGAGG------------------------------------------------------------------------GGGGG

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

ACAAAATTCACACTCGAATT---TGGGGATCGCGTAGCAAGGGGGG-------------------------------------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
........................AGGGATCGGGTAGCAAGGG............................................................................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

ATAAACTCAATACACGAATTTGGTACTGATTTC--------------------------------------------------------------------------------------

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

GTGAAATTCACACTCGA------------------------------------------------------------------------------------------------------

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	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		None