dme-mir-287- 12- and 20-way alignments

dme-mir-287	chr2L:17574610-17574702 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 17574674-17574694
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:17574595-17574717 +	AAGCCCACT-------CAC---------------------AGAGGACGCCGGGGATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA---AACAC----GTCGGA
droSim1	chr2L:17277816-17277938 +	AAGCTCACT-------CAC---------------------AGAGGACGCCGTGGATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA---AACAC----GTCGGA
droSec1	super_7:1215433-1215555 +	AAGCTCACT-------CAC---------------------AGAGGACGCCGTGGATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA---AACAC----GTCGGA
droYak2	chr2R:3525115-3525236 -	ACATATATAC-----ACAC---------------------AGAGCAAGCCGTGGATGTATGGGTGT---GGGTCTGAAATTTTGCACACATTTACAGTAATTGTAAATGTGTTGAAAATCGTTTGCATG-ACTGTGAGCAA---AACAC----TTCGGA
droEre2	scaffold_4845:6676077-6676186 -	GTGTGGACGC-----------------------------------------TGGATGTATGGGTGTGTGGGCTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGCGAGCAA---AACAC----GTCGGA
droAna3	scaffold_12916:3302442-3302544 -	AGGGC--------------------------------------------TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA---AGCAC----GTCGGA
dp4	chr4_group3:10858860-10858990 -	ACACACACAC-----A--TA--AAT-------ATATTCACGGAGACAGTCT--TATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA---AACAC----GTCGGA
droPer1	super_8:2069946-2070076 -	ACACACACAC-----A--TA--AAT-------ATATTCACGGAGACCTGCT--TATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA---AACAC----GTCGGA
droWil1	scaffold_180764:928810-928952 -	ATACTCCCAC-----A--TA--CATTGGAAAGAGCTTCTCCGTAATATGTA--TATGTATTGCT--GTAAAGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACAAACTGTGAGCAA---AATCCTGTAGCTGGG
droVir3	scaffold_12963:16502537-16502656 +	ACTCCCACGCTTTCG-CACACACAC---------------A------------------AACGTGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAACCGAACAG----ACAtgt
droMoj3	scaffold_6500:21428983-21429092 +	ACTCCCACGC-------ACA-----------------------------------CACACACGCGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAACC-AACA-----GCAtgt
droGri2	scaffold_15252:13917097-13917209 +	ACTCCCACAC-------ACT---------------------------------CACACACACATGCATAATGCTTGAAATTTTGCACACATTTACAATATTTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAAGC-AACAC----ACAtgt

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:17574595-17574717 +	NA	AA-GCC--------CAC---------TCAC-----------------AGAGGACGCCGGG--GATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droSim1	chr2L:17277816-17277938 +	1	AA-GCT--------CAC---------TCAC-----------------AGAGGACGCCGTG--GATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droSec1	super_7:1215433-1215555 +	1	AA-GCT--------CAC---------TCAC-----------------AGAGGACGCCGTG--GATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA--AACAC---G-TCGGA
droYak2	chr2R:3525115-3525236 -	1	AC-A--------T----ATATACAC---AC-----------------AGAGCAAGCCGTG--GATGTATGGGTGT---GGGTCTGAAATTTTGCACACATTTACAGTAATTGTAAATGTGTTGAAAATCGTTTGCATG-ACTGTGAGCAA--AACAC---T-TCGGA
droEre2	scaffold_4845:6676077-6676186 -	2	GT-GTG-------------------------------------------GA--CGC--TG--GATGTATGGGTGTGTGGGCTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGCGAGCAA--AACAC---G-TCGGA
droEug1	scf7180000409016:198057-198168 +	1	AATA--------------------------------A----------AGTG--CTC--TA--GATGTATGGGTGTATAGGGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGT
droBia1	scf7180000302422:6132274-6132381 -	1	CG----------------------------------------------GGG--CGC--TG--GTTGTGTGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droTak1	scf7180000415617:9738-9849 -	2	CA-C----------------------T--------------------GGGG--CGC--TG--GTTGTATGGGTGTGTGGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droEle1	scf7180000491046:278921-279029 +	1	GC-A--------C----------------------------------GGGG--CAC--TG--GGTGTATGGGT--GTAAGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droRho1	scf7180000777709:31207-31296 +	1	G---------------------------------------------------------------------GTT--GTAAGGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGCTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droFic1	scf7180000453855:358907-359016 +	2	AC-A--------C----------------------------------TGGG--CGC--TG--GGTGTATGGGT--GTAAGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCCGA
droKik1	scf7180000302246:110146-110268 -	3	AG-GAC--------GAC---------GACA-ACG--A----------AGGC--CAG--TGCGTTTGTGTGGGT--GTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--GACAT---G-TCGGA
droAna3	scaffold_12916:3302442-3302546 -	3	AT-A--------------------------------------------GG----GC--TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA
droBip1	scf7180000396737:1470812-1470916 +	3	AT-A--------------------------------------------GG----GC--TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AGCAC---G-TCGGA
dp4	chr4_group3:10858860-10858990 -	3	AC-A--------C----ACACACATA----------AATATATTCACGGAGACAGTC--T--TATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droPer1	super_8:2069946-2070076 -	3	AC-A--------C----ACACACATA----------AATATATTCACGGAG--ACC--TGCTTATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--AACAC---G-TCGGA
droWil1	scaffold_180764:928810-928950 -	5	AC-T--------CCCAC---------ATACATTGGAAAGAGCTTCTCCGTAATATG--TA--TATGTATTGCT--GTAAAGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACAAACTGTGAGCAA--AATCCTGTAGCTGGG
droVir3	scaffold_12963:16502531-16502646 +	3	AG-ATT--------GAC---------TCCC-----------------ACGCTTTCGCACA--CACACAAACGTGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA-------------CCGA
droMoj3	scaffold_6500:21428983-21429089 +	2	AC-T--------CCCAC---------GCAC---------------------------------ACACACACGCGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA--CCAAC---A---GCA
droGri2	scaffold_15252:13917089-13917209 +	15	CA-GTTTTCACTCCCAC---------ACA-----------------------------CT--CACACACACATGCATAATGCTTGAAATTTTGCACACATTTACAATATTTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAAGCAACAC---A-CATGT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AAGCCCACT-------CAC---------------------AGAGGACGCCGGGGATGTATGGGTGTGTAGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA---AACAC----GTCGGA

Size

Hit Count

Total Norm

droSim1

AAGCTCACT-------CAC---------------------AGAGGACGCCGTGGATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA---AACAC----GTCGGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................................................................TTTGAAAATGGTTTGCAC...............................	18	1	1.00	0.00	0.00	1.00	0.00
.......................................................TGTATGTGTGTGTAGGTTC.....................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
................................................................................................................TGAAAATGGTTTGCACG-C............................	18	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................CAAAAATTGTACATGTGT...............................................	18	1	1.00	1.00	0.00	0.00	0.00

droSec1

AAGCTCACT-------CAC---------------------AGAGGACGCCGTGGATGTATGGGTGTGTAGGGTCGGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGTGAGCAA---AACAC----GTCGGA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................CAAAAATTGTACATGTGT...............................................	18	1	2.00	0.00	2.00	0.00
..................................................GTGTATGTGTGGGTGTGT...........................................................................................	18	1	1.00	0.00	1.00	0.00
................................................................................................................TGAAAATGGTTTGCACG-C............................	18	1	1.00	0.00	1.00	0.00

droYak2

ACATATATAC-----ACAC---------------------AGAGCAAGCCGTGGATGTATGGGTGT---GGGTCTGAAATTTTGCACACATTTACAGTAATTGTAAATGTGTTGAAAATCGTTTGCATG-ACTGTGAGCAA---AACAC----TTCGGA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...................................................TGGGTGGATGGGTGT---GGG.......................................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................GTGGGTGTGTGGGTGT---GGGT......................................................................................	20	2	0.50	0.00	0.00	0.50	0.00	0.00

droEre2

GTGTGGACGC-----------------------------------------TGGATGTATGGGTGTGTGGGCTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACG-ACTGCGAGCAA---AACAC----GTCGGA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
........................................................................................TATTTACAACAATTGTAA.....................................................	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................................AAAATTGTACATGTGTTGA............................................	19	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................GCAGATCGTTTGCACG-AC...........................	18	1	1.00	0.00	0.00	1.00	0.00
.....GACGC-----------------------------------------xGGATGGATGGGTG..............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
..............................................................................................CAAAAATTGTACATGTGT...............................................	18	1	1.00	1.00	0.00	0.00	0.00

droAna3

AGGGC--------------------------------------------TG--TGTGTATTGGT--AGTGGGTCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA---AGCAC----GTCGGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................................................................AAGTGTAAATxTGTTGAAAA.........................................	19	1	1.00	0.00	1.00	0.00	0.00
.....................................................................................................TGAAAATGCGTTGAAAAT........................................	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................................................................GTTGAAAATAGTATGCACA-.............................	19	1	1.00	1.00	0.00	0.00	0.00

dp4

ACACACACAC-----A--TA--AAT-------ATATTCACGGAGACAGTCT--TATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA---AACAC----GTCGGA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

ACACACACAC-----A--TA--AAT-------ATATTCACGGAGACCTGCT--TATGTGTGAGT--GTGGGGCCTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAA---AACAC----GTCGGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..............................................CTGCT--TGTGTGTGTGT--GTG..........................................................................................	19	5	0.40	0.00	0.00	0.00	0.00	0.40
..............................................CTGTG--TATGTGTGAGT--GT...........................................................................................	18	2	0.50	0.50	0.00	0.00	0.00	0.00
.CACACACAC-----A--TA--CAT-------ATGT...........................................................................................................................	19	2	0.50	0.00	0.50	0.00	0.00	0.00
....................................................................................................GTGTAAATxTGTTGAAAAT........................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

ATACTCCCAC-----A--TA--CATTGGAAAGAGCTTCTCCGTAATATGTA--TATGTATTGCT--GTAAAGTCTGAAATTTTGCACACATTTACAATTATTGTAAATGTGTTGAAAATCGTTTGCACAAACTGTGAGCAA---AATCCTGTAGCTGGG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................................................................................TTACAATTxTTGGAAATGTG................................................	19	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................GATTGTAAATGTGTGGAA...........................................	18	2	0.50	0.00	0.50	0.00	0.00
...................................................................................................ATTGTAAATGTATTGAAT..........................................	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................TCTGATATTTTGCACACC.....................................................................	18	1	1.00	0.00	0.00	0.00	1.00
............................................ATATGTA--TATGTATGTCT--.............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................AATAATCGTTTGCACAAA............................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................ATAATCGTTTGCACAAAA...........................	18	1	1.00	0.00	1.00	0.00	0.00
.......................................................................................................AAAATGTGTTGATAATCGT.....................................	19	1	1.00	1.00	0.00	0.00	0.00

droVir3

ACTCCCACGCTTTCG-CACACACAC---------------A------------------AACGTGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAACCGAACAG----ACAtgt	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
................CACACACAC---------------A------------------ACCGGGCA............................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droMoj3

ACTCCCACGC-------ACA-----------------------------------CACACACGCGCATAATGTTTGAAATTTTGCACACATTTACAATAATTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAACC-AACA-----GCAtgt	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......ATAC-------ACA-----------------------------------CACACACGCGC.............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.....CACAC-------ACA-----------------------------------CACACACACGCATA..........................................................................................	22	2	0.50	0.00	0.50	0.00	0.00
......ACAC-------ACA-----------------------------------CACACACGCGCA............................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
............................................................................................................GTGTTGAAAATxGGTTGCAC...............................	19	1	1.00	0.00	1.00	0.00	0.00

droGri2

ACTCCCACAC-------ACT---------------------------------CACACACACATGCATAATGCTTGAAATTTTGCACACATTTACAATATTTGTAAATGTGTTGAAAATCGTTTGCACA-ACTGTGAGCAAGC-AACAC----ACAtgt

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
UNAFold Image

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
UNAFold Image