dme-mir-305-as- 12- and 20-way alignments

dme-mir-305-as	chr2L:7425972-7426044 -	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 7425979-7426001
   star strand at position 7426016-7426036
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:7425957-7426059 -	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGAG-ACACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAGTT----------------------------------G--------ATAC
droSim1	chr2L:7217527-7217627 -	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAGCATGTGCCGGGTTACGAG-ACACACCAGAGCA-CTGATGAAGTACAATAGACATGGG--AGACAG-T----------------------------------G--------ATAC
droSec1	super_3:2941418-2941520 -	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGAG-ACACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAGTT----------------------------------G--------ATAC
droYak2	chr2L:5473614-5473716 +	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGGG-CCACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAGTT----------------------------------G--------ATAC
droEre2	scaffold_4929:16344683-16344785 -	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGGA-CCACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAGTT----------------------------------G--------ATAC
droAna3	scaffold_12916:15334141-15334251 -	GT----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGGT-GGACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACATAT----------------------------------TTCTCAAAAATAC
dp4	chr4_group1:4175870-4175974 -	GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAGG-ACACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACACAT----------------------------------GG------AATAT
droPer1	super_5:1086315-1086419 +	GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAGG-ACACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACACAT----------------------------------GG------AATAT
droWil1	scaffold_180772:5257378-5257513 +	------------------ATGAAGATCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAAACGGACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAACAACAATAAATTAAAAATGCCAATAAAAAAAAAAGAG--------AATC
droVir3	scaffold_12963:15419813-15419927 +	TTAACCCAAA--CAGCAAATGCAAATCAACGCATATTGAGTGTACTTCAACATGTGCCGGGTTACAAG-TCACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACA--T----------------------------------G--------AAAC
droMoj3	scaffold_6500:18399235-18399351 +	CGGGCCGAAA--CAGCAACTGCAAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTTCCAC-TGACACCAGAGCACCTGATGAAGTACAATAGACATGGGGGAGACA--C----------------------------------A--------AGTA
droGri2	scaffold_15126:5008532-5008648 -	TTAATTAAAACGCAGCAAATGCCAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTACGAG-TGACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACA--T----------------------------------G--------AAAT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:7425957-7426059 -	NA	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droSim1	chr2L:7217527-7217627 -	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAGCATGTGCCGGGTTACGA-GACACACCAGAGCA-CTGATGAAGTACAATAGACATGGGAGACAGT-G--------ATAC------------------------------------------
droSec1	super_3:2941418-2941520 -	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droYak2	chr2L:5473614-5473716 +	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEre2	scaffold_4929:16344683-16344785 -	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-ACCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEug1	scf7180000409463:614863-614965 -	1	GT----------------ATGCAAATCACCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droBia1	scf7180000302422:9125681-9125783 -	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTCG--------ATAC------------------------------------------
droTak1	scf7180000415604:142269-142370 +	2	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACG--GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droEle1	scf7180000491028:1624701-1624808 +	2	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACTT-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATACACAAC-------------------------------------
droRho1	scf7180000766421:7519-7621 +	1	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACTT-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droFic1	scf7180000454115:155833-155935 -	2	GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTGCGG-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAGTTG--------ATAC------------------------------------------
droKik1	scf7180000302384:54674-54769 +	1	AT----------------TTGGAAATCACCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GCCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAG---------------ATAC------------------------------------------
droAna3	scaffold_12916:15334141-15334251 -	1	GT----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGG-TGGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACATATTTCTCAAAAATAC------------------------------------------
droBip1	scf7180000396572:1689256-1689352 +	1	GA----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-TAGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACATT--------------------------------------------------------
dp4	chr4_group1:4175881-4175974 -	1	GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGAC-----------------------------------------------------------
droPer1	super_5:1086315-1086408 +	1	GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAG-GACACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGAC-----------------------------------------------------------
droWil1	scaffold_180772:5257378-5257513 +	2	------------------ATGAAGATCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAAACGGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACAA--------------C--AACAATAAATTAAAAATGCCAATAAAAAAAAAAGAGAATC
droVir3	scaffold_12963:15419827-15419927 +	1	AA----------------ATGCAAATCAACGCATATTGAGTGTACTTCAACATGTGCCGGGTTACAA-GTCACACCAGAGCACCTGATGAAGTACAATAGACATGGGAGACA--TG--------AAAC------------------------------------------
droMoj3	scaffold_6500:18399247-18399346 +	2	GC--------------AACTGCAAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTTCCA-CTGACACCAGAGCACCTGATGAAGTACAATAGACATGGGGGA-----G--------ACAC------------------------------------------
droGri2	scaffold_15126:5008541-5008648 -	3	TTAATTAAAACGCAGCAAATGCCAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTACGA-GTGACACCAGAGCACCTGATGAAGTACAATAGACATGGGAG-------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGAG-ACACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAGTT----------------------------------G--------ATAC

Size

Hit Count

Total Norm

droSim1

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAGCATGTGCCGGGTTACGAG-ACACACCAGAGCA-CTGATGAAGTACAATAGACATGGG--AGACAG-T----------------------------------G--------ATAC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................ATTGTACTTCATCATGTGC...........................................................................................................	19	2	1.50	0.00	1.50	0.00	0.00
......................................................................................ATGAAGxACAATAGGCATG...........................................................	18	2	0.50	0.00	0.50	0.00	0.00
......................................ATTGTACTTCATCATGTGCC..........................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00

droSec1

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGAG-ACACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAGTT----------------------------------G--------ATAC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................................................CAGAGCACCTGATGAAGTACAAT..................................................................	23	2	10.00	6.00	0.00	4.00
...........................................................................CAGAGCACCTGATGAAGTACA....................................................................	21	2	3.00	2.00	0.00	1.00
...........................................................................CAGAGCACCTGATGAAGTACAA...................................................................	22	2	1.50	1.00	0.50	0.00
............................................................................AGAGCACCTGATGAAGTACAAT..................................................................	22	2	1.00	0.00	0.50	0.50
............................................................................AGAGCACCTGTTGAAGTACAAT..................................................................	22	2	0.50	0.00	0.00	0.50
...........................................................................CAGAGCACCTGATGAAGTTCAAT..................................................................	23	2	0.50	0.50	0.00	0.00
...........................................................................CAGAGCACCTGATGAAGTACAAA..................................................................	23	2	0.50	0.00	0.00	0.50
...........................................................................CAGAGCACCTGATGAAGTA......................................................................	19	2	0.50	0.00	0.00	0.50

droYak2

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGGG-CCACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAGTT----------------------------------G--------ATAC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................CAGAGCACCTGATGAAGTACA....................................................................	21	2	3.00	0.00	0.00	1.50	1.00	0.50
...........................................................................CAGAGCACCTGATGAAGTACAAT..................................................................	23	2	2.00	0.00	0.00	1.50	0.50	0.00
...........................................................................CAGAGCACCTGATGAAGTACAA...................................................................	22	2	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................................CAGAGCACCTGATGAAGTAC.....................................................................	20	2	0.50	0.00	0.00	0.00	0.50	0.00

droEre2

GT----------------ATGCAAATCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGGA-CCACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAGTT----------------------------------G--------ATAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........................................................................CAGAGCACCTGATGAAGTACAAT..................................................................	23	2	2.00	0.00	0.00	0.00	2.00
...........................................................................CAGAGCACCTGATGAAGTACA....................................................................	21	2	1.00	0.00	0.00	0.00	1.00
......................................ATTGTACTTCATCATGTGC...........................................................................................................	19	4	0.25	0.00	0.00	0.00	0.25
...........................................................................CATAGCACCTGATGAAGTAC.....................................................................	20	2	0.50	0.00	0.00	0.00	0.50
...........................................................................CAGAGCACCTGATGAAGTAC.....................................................................	20	2	0.50	0.00	0.00	0.00	0.50
...........................................................................CAGAGCACCTGATGAGGTA......................................................................	19	2	0.50	0.00	0.00	0.00	0.50
......................................ATTGTACTTCATCATGTG............................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25

droAna3

GT----------------TTGACATTCGCCTCATATTGAGTGTACTTCAACATGTGCCGGGTTACGGT-GGACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACATAT----------------------------------TTCTCAAAAATAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................CAGAGCACCTGATGAAGTACA....................................................................	21	2	0.50	0.00	0.50	0.00	0.00

dp4

GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAGG-ACACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACACAT----------------------------------GG------AATAT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.......................................GTGTACTTCAACCTGGGC...........................................................................................................	18	2	0.50	0.00	0.00	0.00	0.50

droPer1

GC----------------ACGAACTTCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAGG-ACACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACACAT----------------------------------GG------AATAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........................................................................CAGAGCACCTGATGAAGTACA....................................................................	21	2	0.50	0.50	0.00	0.00	0.00	0.00
...........................................................................CAGAGCACCTGATGAAGTACAAT..................................................................	23	2	0.50	0.50	0.00	0.00	0.00	0.00

droWil1

------------------ATGAAGATCGCCACATATTGAGTGTACTTCAACATGTGCCGGGTTACAAACGGACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACAACAACAATAAATTAAAAATGCCAATAAAAAAAAAAGAG--------AATC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...........................................................................CAGAGCACCTGATGAAGTACAAT..................................................................	23	2	1.00	0.00	0.00	1.00	0.00
........................................................................................................................................AAACAAAAAAAAAGAG--------AA..	18	6	0.17	0.00	0.17	0.00	0.00
........................................................................................................................................TAAAAAAAAAAAAGAG--------AA..	18	4	0.25	0.00	0.25	0.00	0.00
....................GAAGATCxCGACATATTGAGT...........................................................................................................................	20	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................................CAAAAAAAAAAAAAGAG--------A...	18	8	0.13	0.00	0.13	0.00	0.00
........................................................................................................................................AAAAAAAAAAAAAGAG--------AA..	18	43	0.02	0.02	0.00	0.00	0.00
..................................................................................................................................AATGTTAATAAAAAAAAA................	18	2	0.50	0.00	0.50	0.00	0.00
................................................................................................................................AAAATGACATTAAAAAAAA.................	19	2	0.50	0.00	0.50	0.00	0.00
........................................................................................................................................AACAAAAAAAAAAGAA--------AA..	18	46	0.02	0.00	0.02	0.00	0.00
.......................................................................................................................................AAAAAAAAAAAAAAGAG--------AA..	19	36	0.03	0.00	0.03	0.00	0.00
......................................................................................................................................TCAATAAAAGAAAAAGAG--------A...	19	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................................AAAAAAAAAAAAAAGAG--------A...	18	47	0.02	0.00	0.02	0.00	0.00
.......................................................................................................................................AAACAAAAAAAAAAGAG--------A...	18	8	0.13	0.00	0.13	0.00	0.00

droVir3

TTAACCCAAA--CAGCAAATGCAAATCAACGCATATTGAGTGTACTTCAACATGTGCCGGGTTACAAG-TCACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACA--T----------------------------------G--------AAAC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
......................................AGTGTACTTCATCAGGTG............................................................................................................	18	4	0.25	0.00	0.25	0.00	0.00	0.00
........................................TGTACTTCAACATGTGCCGGGT......................................................................................................	22	2	0.50	0.00	0.00	0.00	0.50	0.00
.................................................................AAG-TCACACCAGAGCACCTGA.............................................................................	21	2	0.50	0.50	0.00	0.00	0.00	0.00

droMoj3

CGGGCCGAAA--CAGCAACTGCAAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTTCCAC-TGACACCAGAGCACCTGATGAAGTACAATAGACATGGGGGAGACA--C----------------------------------A--------AGTA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........................................................................CAGAGCACCTGATGAAGTACA....................................................................	21	2	0.50	0.50	0.00	0.00	0.00

droGri2

TTAATTAAAACGCAGCAAATGCCAATCACCGCATATTGAGTGTACTTCAACATGTGCCGGGTTACGAG-TGACACCAGAGCACCTGATGAAGTACAATAGACATGGG--AGACA--T----------------------------------G--------AAAT	Size	Hit Count	Total Norm	V109 Male body
............................................................................AGAGCACCTGATGAAGTACAAT..................................................................	22	2	0.50	0.50

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