dme-mir-282-as- 12- and 20-way alignments

dme-mir-282-as	chr3L:3251022-3251118 -	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 3251036-3251057
   star strand at position 3251079-3251100
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3L:3251007-3251133 -	TCCGTTTTC----------GCTGATTGTT--------CGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAGAAGGAAACTATAG------------------T-T------AAAGAACGG
droSim1	chr3L:2784381-2784507 -	TCCGTTTTC----------GCTGATTGTT--------CGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAACTTTAG------------------T-T------TAAGAACGG
droSec1	super_2:3244745-3244871 -	TCCGTTTTC----------GCTGATTGTT--------CACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAACTTTAT------------------T-T------TAAGAACGG
droYak2	chr3L:3795918-3796050 -	TCCGTTTTC----------GCTGATTTTT--------CACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTCGTA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAACTGATA------------------T-AACGGATATAGAACGA
droEre2	scaffold_4784:5933708-5933834 -	TCCGTTTTC----------GCTGCTTGTT--------CGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTTGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAACTGTGG------------------T-G------ATAGAACGA
droAna3	scaffold_13337:7556585-7556720 -	TCCGTTTTTGT--------GATGTCTTGT--------CGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGACT-TTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAATTTTC--------GA--------TTTT-CGAA-TTAGAACGG
dp4	chrXR_group8:3299974-3300083 +	TCCGCTTTT----------GATGCATTTC--------TTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA-------------------------------------------
droPer1	super_65:103931-104040 +	TCCGCTTTT----------GATGCATTTC--------TTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA-------------------------------------------
droWil1	Unknown	T------------------GTTGTATTTT--------CTCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGAA------TCCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGATATTAATA------------------T-T------ACATAAAGG
droVir3	scaffold_12758:910696-910830 +	--CGCCCTC----------GCTGCTTGT---------CCCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGACCGTAT-ATCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAATTTGTCGGACGCCGC--------CCCT------TGAAAAAAA
droMoj3	scaffold_6680:1963284-1963406 +	TCTC----T----------GCTGTTTGA---------CCCCTTGCTACACCTAACCTCTCATAGGCTATGTCTGATCTTAT-ATCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAAT---G--------CACCGCtttttt-t------ttT------
droGri2	scaffold_15110:607062-607202 -	TCATTTTTAGTCCCCGACAGCAGCCTTGTTGCTTTGATCCATTTGTACACCTAACCTCTCATAGGCTATGTCTGATTGAAT-TGAAAAAGTGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAATT---C--------CA--------TTTG--------A----GA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3L:3251007-3251133 -	NA	TCCGTTTT------------------CGCTGATTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAGAAGGAAA-CTATA--------G-TTAAAGAAC-----------GG-------------
droSim1	chr3L:2784381-2784507 -	8	TCCGTTTT------------------CGCTGATTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-CTTTA--------G-TTTAAGAAC-----------GG-------------
droSec1	super_2:3244745-3244871 -	8	TCCGTTTT------------------CGCTGATTGTTCACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-CTTTA--------T-TTTAAGAAC-----------GG-------------
droYak2	chr3L:3795918-3796050 -	14	TCCGTTTT------------------CGCTGATTTTTCACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGTA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-CTGAT--A-TAACGGATATAGAAC-----------GA-------------
droEre2	scaffold_4784:5933708-5933834 -	1	TCCGTTTT------------------CGCTGCTTGTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTTGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-CTGTG--------G-TGATAGAAC-----------GA-------------
droEug1	scf7180000409466:975797-975923 -	1	TCCGTTTT------------------TGCTGACTTTTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTAGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTC--------G-GTGTATAAC-----------GG-------------
droBia1	scf7180000302428:2604017-2604144 -	1	TCCGATTC------------------CGATGATTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG--TTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAA-TCTGC----------ACTTAGAAG-----------GGTAC----------
droTak1	scf7180000415378:123710-123845 +	1	TCCGTTTTC-----------------TGATGATTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGA-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGTAGATTG-CAGATTCTCG-ATTTAGAAT-----------GG-------------
droEle1	scf7180000491249:2016913-2017039 +	1	GCCGTTTT------------------TGATGCTTTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTT--------G-AGTTAGAAC-----------AG-------------
droRho1	scf7180000757706:21549-21675 +	1	TCCGTTTT------------------TGCTGATTTTTCGCCTTTGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-TTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTATT--------G-GATTAGAAC-----------GG-------------
droFic1	scf7180000454105:1571232-1571357 -	1	GCCCTCTT------------------CGCTGCTCTTTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAGA-TTCTC--------G-G-CCAGAAC-----------GG-------------
droKik1	scf7180000302391:353031-353159 -	1	TCCGCCTTT-----------------CGCTGCACATTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGG-ATTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTCTC--------GGATTCAGAAC-----------GG-------------
droAna3	scaffold_13337:7556582-7556720 -	2	TCCGTTTTTG----------------TGATGTCTTGTCGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGA-CTTTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAA-TTTTC-GATTTTCG-AATTAGAAC-----------GGCCA----------
droBip1	scf7180000395543:216902-217046 -	2	TCCGTTTTAA----------------TGATGACT-TTTGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATC--------GAA--AACACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAA-TTTTC--------G-ATTTAGAACGTAGAGCATATTGCCACGCCCACACG
dp4	chrXR_group8:3299974-3300083 +	1	TCCGCTTT------------------TGATGCATTTCTTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA----------------------------------------------------
droPer1	super_65:103931-104040 +	1	TCCGCTTT------------------TGATGCATTTCTTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA----------------------------------------------------
droWil1	scaffold_181136:1999668-1999787 -	1	T--------------------------GTTGTATTTTCTCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGAA------TCCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGATA-TATTA-ATATT------ACATAAA-----GGAA--AA-------------
droVir3	scaffold_12758:910696-910814 +	1	--CGCCCT------------------CGCTGCTT-GTCCCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGACCGT-ATATCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TTT--------------GTCGGAC-----------GC-------------
droMoj3	scaffold_6680:1963284-1963406 +	1	TCT----C------------------TGCTGTT-TGACCCCTTGCTACACCTAACCTCTCATAGGCTATGTCTGATCTT-ATATCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAA-TGCAC--------CGCAAAAAAAA-----------AT-------------
droGri2	scaffold_15110:607074-607202 -	1	TCATTTTTAGTCCCCGACAGCAGCCTTGTTGCTTTGATCCATTTGTACACCTAACCTCTCATAGGCTATGTCTGATTGA-ATTGAAAAAGTGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAA----------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TCCGTTTTC----------GCTGATTGTT--------CGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAGAAGGAAACTATAG------------------T-T------AAAGAACGG

Size

Hit Count

Total Norm

droSim1

TCCGTTTTC----------GCTGATTGTT--------CGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAACTTTAG------------------T-T------TAAGAACGG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
......................................................CCTCTTCTAGGCTTTGTCT....................................................................................................	19	4	0.25	0.00	0.00	0.25	0.00

droSec1

TCCGTTTTC----------GCTGATTGTT--------CACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTAAAAGGAAACTTTAT------------------T-T------TAAGAACGG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.......................................................................................A--TACAAAGACAAAGCCTA..................................................................	18	2	0.50	0.00	0.50	0.00

droYak2

TCCGTTTTC----------GCTGATTTTT--------CACCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTCGTA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAACTGATA------------------T-AACGGATATAGAACGA

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TCCGTTTTC----------GCTGCTTGTT--------CGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGCT-TTTGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAACTGTGG------------------T-G------ATAGAACGA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

TCCGTTTTTGT--------GATGTCTTGT--------CGCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGACT-TTCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATCTATAAGGAAATTTTC--------GA--------TTTT-CGAA-TTAGAACGG	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...................................................TAGCCTCTTATAGGCTTTGTCT....................................................................................................	22	4	0.25	0.00	0.00	0.25	0.00
.........................................................................................................................TATAAAGAAAxTTTC--------GA--------TT.................	18	2	0.50	0.00	0.50	0.00	0.00

dp4

TCCGCTTTT----------GATGCATTTC--------TTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA-------------------------------------------	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
......................................................................................AA--TGCAATGACAAAGCCTA..................................................................	19	2	0.50	0.00	0.50	0.00	0.00
...................................................TAGCCTCTTATAGGCTTTGTCT....................................................................................................	22	4	0.25	0.00	0.25	0.00	0.00
......................................................................................AA--TACAAAGACAAAGCCTAG.................................................................	20	2	0.50	0.00	0.50	0.00	0.00

droPer1

TCCGCTTTT----------GATGCATTTC--------TTCCTTGGTACACCTAACCTCTTATAGGCTATGTCTGATCGGGTTTTCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGCA-------------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
............................................................................................CAATGACAAAGCCTAGTAG..............................................................	19	2	0.50	0.00	0.50	0.00	0.00	0.00

droWil1

T------------------GTTGTATTTT--------CTCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGAA------TCCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGATATTAATA------------------T-T------ACATAAAGG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.......................................................................................................................TTTATAAGAATAGTAATA------------------T-T------.........	20	2	41.00	4.50	36.50	0.00	0.00
........................................................................................................................TTATAAGAATAGTAATA------------------T-T------.........	19	2	14.50	0.00	14.00	0.50	0.00
.......................................................................................................................TTTATAAGAATAGTAATA------------------T-................	19	2	11.00	0.50	10.50	0.00	0.00
.........................................................................................................................TATAAGAATAGTAATA------------------T-T------.........	18	2	8.00	0.00	8.00	0.00	0.00
........................................................................................................................TTATAAGAATAGTAATA------------------T-................	18	2	5.00	0.00	4.50	0.00	0.50
.......................................................................................................................TTTATAAGAATAGTAATA------------------..................	18	2	3.00	0.00	3.00	0.00	0.00
.........................................................................................................................TATAAGAATAGTAATA------------------T-T------A........	19	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................TTTATAAGCATAGTAATA------------------T-................	19	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................A--TACAAAGACAAAGCCTA..................................................................	18	2	0.50	0.00	0.50	0.00	0.00
.......................................................................................................................TTTATAAGAATATTAATA------------------T-T------C........	21	2	0.50	0.00	0.00	0.50	0.00
........................................................................................................................TTATAAGCATAGTAATA------------------T-T------.........	19	2	0.50	0.00	0.50	0.00	0.00

droVir3

--CGCCCTC----------GCTGCTTGT---------CCCCTTGGTACACCTAACCTCTCATAGGCTATGTCTGACCGTAT-ATCGAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAATTTGTCGGACGCCGC--------CCCT------TGAAAAAAA

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TCTC----T----------GCTGTTTGA---------CCCCTTGCTACACCTAACCTCTCATAGGCTATGTCTGATCTTAT-ATCAAA--TGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAAAT---G--------CACCGCtttttt-t------ttT------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....................................................ACCTCTCATAGGCTATGTCTGA..................................................................................................	22	2	1.50	0.00	0.50	0.50	0.50
.....................................................ACCTCTCATAGGCTATGTCTG...................................................................................................	21	2	1.00	0.50	0.00	0.00	0.50
.....................................................ACCTCTCATAGGCTATGTCT....................................................................................................	20	2	0.50	0.00	0.00	0.00	0.50
.....................................................ACCTCTCATAGGCTATGTCTGT..................................................................................................	22	2	0.50	0.00	0.00	0.00	0.50
...........................................................................................................................TAAGGAAAT---G--------CAGCGCGTT....................	19	1	1.00	1.00	0.00	0.00	0.00
.......................................................CTCTAATAGGCTTTGTCT....................................................................................................	18	4	0.25	0.00	0.00	0.00	0.25

droGri2

TCATTTTTAGTCCCCGACAGCAGCCTTGTTGCTTTGATCCATTTGTACACCTAACCTCTCATAGGCTATGTCTGATTGAAT-TGAAAAAGTGCACAGACAAAGCCTAGTAGAGGCTAGATTTATAAGGAATT---C--------CA--------TTTG--------A----GA

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