dme-mir-289- 12- and 20-way alignments

dme-mir-289	chr3L:13613922-13614020 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3L:13613907-13614035 +	TA------------------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TTCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSim1	chr3L:12997848-12997976 +	TA------------------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TCCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSec1	super_0:5775586-5775714 +	TA------------------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TCCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droYak2	chr3L:13706954-13707082 +	TA------------------------------------CGGTTCTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TCCAGTCCCTCTGACTGACTGGGGTAAGTCTCTCGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEre2	scaffold_4784:13614855-13614983 +	AA------------------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TCCAGTCCCTCTGACGGACTGGGGTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droAna3	scaffold_13337:21827571-21827720 -	CAGCT---------------------------------CGGGTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGACTctg----ctactgccactgccactgccactgccactgccGCTC------------------------GGGGAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
dp4	chrXR_group8:6818889-6819054 -	CAGTTCAGTTCAGTTGGGAACCAGTACGTATATCCGTCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGG---------------------------------------------GACTCCAGCTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droPer1	super_36:488110-488275 +	CAGTTCAGTTCAGTTGGGAACCAGTACGTATATCCGTCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGG---------------------------------------------GACTCCAGCTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droWil1	scaffold_180698:607141-607313 -	TT------------------------------------TTTTTTTTAGGTTGAAGTTTACAGTAAAATAAATATTTAAGTGGAGTC---GACTGTGTCGACTACAGCCCGGACTACCCGGACTGCTAGAACGACTCGGTTCCGACTCTTTTTCTGTCGGGGTAAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droVir3	scaffold_13049:19817984-19818084 -	GT-------------------------------------GTTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-GCCT-----------------------------------------------------------------------G-GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droMoj3	scaffold_6680:7513468-7513567 -	G--------------------------------------GCTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGGGCCC-------------------------------------------------------------------------GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droGri2	scaffold_15110:17555344-17555443 +	CA--------------------------------------GTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-GCCT-----------------------------------------------------------------------G-GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3L:13613907-13614035 +	NA	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TT----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSim1	chr3L:12997848-12997976 +	1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droSec1	super_0:5775586-5775714 +	1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droYak2	chr3L:13706954-13707082 +	1	TA------------------------CGGTTCTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACTGACTG-----------------------------GGGTAAGTCTCTCGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEre2	scaffold_4784:13614855-13614983 +	3	AA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC----------------------------------------------CAGTCCCTCTGACGGACTG-----------------------------GGGTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEug1	scf7180000409121:150423-150560 +	1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------GCTTTCTCTCTCTCTCTCTCTTTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droBia1	scf7180000302428:6302592-6302720 -	1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGTGAC-----------------------------------------------------CG----------------------------------------------CGACGACTCCCCTCCACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droTak1	scf7180000415161:62315-62434 +	1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------CTTGCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droEle1	scf7180000491255:2056112-2056232 +	1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTGAGTGGAGCCTGCGAC-----------------------------------------------------TC------------------------------------------------------CTTGCCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droRho1	scf7180000779509:202440-202560 +	1	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTGAGTGGAGCCTGCGAC-----------------------------------------------------TC------------------------------------------------------CTTGCCGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droFic1	scf7180000454048:90357-90510 -	3	TA------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT------------------TCGCTA---A-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droKik1	scf7180000302808:404338-404457 -	3	TA------------------------GGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------TGGCTGACTG-----------------------------GGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droAna3	scaffold_13337:21827571-21827739 -	5	TT-CCGGCACTCCGGCATTCCAGCT-CGGGTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC-------------------------------------------------------TG--CTACTGCCACTGCCACTGCCACTGCCACTGCCGCTCGGGGAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droBip1	scf7180000396730:303852-303987 -	1	CA----GTACTCTGGCATTCCGGCT-CGGGTTCTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC-----------------------------------------------------TC---------------------------------------------------------TGCCACTG-----------------------------GGG-GAGTCACTTGAGCGTTTGCTGGCACGTAAAAGACATCATAATTAGCATT
dp4	chrXR_group8:6818889-6819024 -	8	TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTCTCCGACTG-----------------------------GGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droPer1	super_36:488140-488275 +	8	TATCCG------------------TCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGGG---AC--------------------------------------------TC----------------------------------------------CAG-----CTCTCCGACTG-----------------------------GGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droWil1	scaffold_180698:607141-607313 -	3	TT------------------------TTTTTTTTAGGTTGAAGTTTACAGTAAAATAAATATTTAAGTGGAGTC---GACTGTGTCGACTACAGCCCGGACTACCCGGACTGCTAGAACGACTCGGTTCCGACTC-----------------------------------------------------TTTTTCTGTCGG-----------------------------GGTAAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT
droVir3	scaffold_13049:19817984-19818083 -	1	---------------------------GTTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-G----------------------------------------------------------------------------------------------------------------------------CCTG------------------------------GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droMoj3	scaffold_6680:7513468-7513568 -	2	G--------------------------GCTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGGGCCC-----------------------------------------------------------------------------------------------------------------------------------------------------------GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT
droGri2	scaffold_15110:17555344-17555443 +	1	---------------------------AGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-G----------------------------------------------------------------------------------------------------------------------------CCTG------------------------------GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TA------------------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TTCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

droSim1

TA------------------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TCCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................................TCAGTGGAGCCTGCGGC----------------------------------------------T.........................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...................................................................TAATTATTTAAGTGGGGCC..............................................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.......................................................................TATGTAAGTGGAGCCTGG...........................................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

TA------------------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TCCAGTCCCTCTGACTGACTGGGGTAAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................................................................................................................AGTTGAGCGTTTGGTGGCA.........................	19	1	2.00	1.00	1.00	0.00
.............................................................................AGTGGAGCCTGCGAT----------------------------------------------CCC.......................................................................	18	1	1.00	0.00	1.00	0.00
................................................................AAATAAATATCTAAGTGT..................................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

TA------------------------------------CGGTTCTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TCCAGTCCCTCTGACTGACTGGGGTAAGTCTCTCGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
............................................................................GAGTGGAGCCTGCGGC----------------------------------------------..........................................................................	16	1	4.00	0.00	0.00	0.00	4.00	0.00
.................................................................AATAAATATGTAATTGGA.................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
............................................................................GAGTGGAGCCTGCGGC----------------------------------------------T.........................................................................	17	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

AA------------------------------------CGGTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGAC----------------------------------------------TCCAGTCCCTCTGACGGACTGGGGTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

CAGCT---------------------------------CGGGTTTTAGGTTGA-GTTTACAGTAAAATAAATATTTAAGTGGAGCCTGCGACTctg----ctactgccactgccactgccactgccactgccGCTC------------------------GGGGAGTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
..................................................................................................................................CCGCTC------------------------GGGGAGGCAGT.........................................	17	1	1.00	0.00	0.00	1.00	0.00
...........................................................................................................CACTGCCACTGCCACTGCCTCC...................................................................................	22	2	0.50	0.00	0.50	0.00	0.00
.............................................................................AGTGGAGCCTGCGGCTT......................................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
............................................................................GAGTGGAGCCTGCGGCT.......................................................................................................................	17	2	0.50	0.00	0.00	0.50	0.00
.................................................................................................................CCCTGCCACTGCCTCTGC.................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
..................................................................................................................................CAGCTC------------------------GGGGAGGCACT.........................................	17	1	1.00	0.00	0.00	1.00	0.00
.................................................................................................................CACTGCCACTGCCACTGCCTCC.............................................................................	22	2	0.50	0.00	0.50	0.00	0.00
...........................................................................................................CCCTGCCACTGCCTCTGC.......................................................................................	18	2	0.50	0.00	0.00	0.00	0.50
.......................................................................TATGTAAGTGGAGCCGGC...........................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................................CTGTCTCTGCCACTGCCGCT.............................................................................	20	1	1.00	0.00	1.00	0.00	0.00

dp4

CAGTTCAGTTCAGTTGGGAACCAGTACGTATATCCGTCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGG---------------------------------------------GACTCCAGCTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CAGTTCAGTTCAGTTGGGAACCAGTACGTATATCCGTCGGGTTTTTAGGTTGA-GTTTACAGTGAAATAAATATTTAAGTGGAGCCTGCGACTGG---------------------------------------------GACTCCAGCTCTCCGACTGGGCTAACTCACTTGAGCGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
............................................................................AAGTGGATCCGGCGACTGG---------------------------------------------........................................................................	19	1	3.00	0.00	0.00	0.00	0.00	3.00
.......................................................................................GCGACTGG---------------------------------------------AACTCCTGCTC.............................................................	19	1	2.00	0.00	0.00	0.00	0.00	2.00
..................................................................................AGACTGAGACTGG---------------------------------------------GACTCC..................................................................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
..................................................................................AGACTGCGACxGG---------------------------------------------GACTCCAGCTC.............................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

TT------------------------------------TTTTTTTTAGGTTGAAGTTTACAGTAAAATAAATATTTAAGTGGAGTC---GACTGTGTCGACTACAGCCCGGACTACCCGGACTGCTAGAACGACTCGGTTCCGACTCTTTTTCTGTCGGGGTAAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCATT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
................................................................AAATAAACATTTAAGTGT..................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................AATATxAATATTGAAGTGGA.................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................GTCGACTACACCCGGGAC...................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................TTTTATATTGAAGTTTACA.......................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
........................................TTTTTTAGGTTGxAGTTCAC........................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................TTTATAGGTTGAAGTCTA.........................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...............................................................AAGATAAATxTTTAAGTGG..................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

GT-------------------------------------GTTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-GCCT-----------------------------------------------------------------------G-GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.................................................................AATAATTATTGAAGAGG-G................................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................TTTGTTGGCACGGAACAG.................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

G--------------------------------------GCTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGGGCCC-------------------------------------------------------------------------GGGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CA--------------------------------------GTTTTTAGGTTGA-GTTTACAGTAAAATAAATATTGAAGTGG-GCCT-----------------------------------------------------------------------G-GGGAAGTCACTTGAACGTTTGTTGGCACGTAAAAGACATCATAATTAGCCGT

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