dme-mir-3641- 12- and 20-way alignments

dme-mir-3641	chrX:2065119-2065187 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	tailed_mirtron

Legend:

   mature strand at position 2065119-2065138
   star strand at position 2065161-2065182
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:2065104-2065202 +	GGCGAACTTTTTAATGTGAGTGTCCTGTTTA-------------------------------CAGCTGGTATATTTTTCGAAAAGCCCTCTAAAC---------TGGTCA----------------CTTCCAC-TCTACAGATCTATAACTACATA
droSim1	chrX:1441441-1441539 +	GGCGAACTGTTCAATGTGAGTTTCCTACTTA-------------------------------CAGCTGGTATATTTCTCGAACAGTCCTCTAAAC---------TGGTCT----------------CTTCCGC-TCCGCAGATCTACAACTACATA
droSec1	super_10:1848730-1848828 +	GGCGAACTGTTCAATGTGAGTTTCCTACTTA-------------------------------CAGCTGGTATATTTCGCGAACAGTCCTCTAAAC---------TGGTCC----------------CTTCCGC-TCCGCAGATCTACAACTACATA
droYak2	chrX:6259202-6259289 -	GGCGAACTCTTCAATGTGAGTTTCCTATGTT-------------------------------TCGCATGTACATAT-----------ATCTAAAT---------TGGTTC----------------CTTCTCC-TCTGCAGATCTACAACTACATA
droEre2	scaffold_4644:2028284-2028382 +	GGCGAACTGTTCAATGTGAGTATCCTGTGAT-------------------------------CCGCTTGTACTTATCTCGAGCAGTTCTCTAAAC---------TGGTCC----------------CTGATCC-TCTGCAGATCTACAACTACATA
droAna3	scaffold_13117:1070684-1070773 -	GGCGAGCTCTTCAACGTAAGTTTCCCCGCTTA------------------------------AACGCCTAAGATT----------TTCCCTAAAC---------CGTTGC----------------TGTTCTG-TCTCTAGATCTACAACTATATC
dp4	chrXL_group1e:3790116-3790235 -	GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCAGCCTCGAATTCGGC---AGTCACTTGATA--------------------------------ctctcccacctcc-ctctccctctgcctctccatcatcctcttccAGATCTACAACTACATC
droPer1	super_17:723995-724114 -	GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCAGCCTCGAATTCGGC---AGTCACTTAATA--------------------------------ctctcccacctcc-ctctccctctgcctctccatcatcctcttccAGATCTACAACTACATC
droWil1	scaffold_181096:7421152-7421244 -	GGCGAGCTTTTCAACGTGAGTTACTCAGTCCA----AAGAAACTGGTTTTAGTTA--TGA----------------------------------TTAACTC-----A-CT----------------TTTTTTT-GTTATAGATTTACAACTATATA
droVir3	scaffold_12928:7113520-7113613 +	GGCGAGTTGTTCAACGTAAGTCGATGACCTC-----GCGTATGTGGG-------------------------------CGTACTTTCA------CTGACGC---CTGCCT----------------CTTTGTC-TATTCAGATTTACAACTACATT
droMoj3	scaffold_6328:2787435-2787524 +	GGGGAGTTGTTCAACGTAAATTCT--ATTCT-------------------------------CACTTAACACAAGAATCAAA------TCTCATC---------TAAT-T----------------TTTCGCT-CGTTTAGATTTACAACTACATT
droGri2	scaffold_14853:3491672-3491772 -	GGAGAGTTGTTTAATGTAAGCTAA--ACTTC-----GCCCATCC-TCTCCAGCTGTTTGG------------------TTAA-----CTTTCAAC---------TGTTTG-------------TC-CTCCATC-TCCTCAGATTTACAACTACATT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:2065104-2065202 +	NA	GGCGAACTTTTTAATGTGAGTGTCCT-------G--------------------------------------------------------------------TTTACAGCTGGTATATTTTTCGAAAAGCCCTCTA-----AACTGGT-CACTTCCACTCTACAGATCTATAACTACATA
droSim1	chrX:1441441-1441539 +	1	GGCGAACTGTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------CTTACAGCTGGTATATTTCTCGAACAGTCCTCTA-----AACTGGT-CTCTTCCGCTCCGCAGATCTACAACTACATA
droSec1	super_10:1848730-1848828 +	1	GGCGAACTGTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------CTTACAGCTGGTATATTTCGCGAACAGTCCTCTA-----AACTGGT-CCCTTCCGCTCCGCAGATCTACAACTACATA
droYak2	chrX:6259202-6259289 -	11	GGCGAACTCTTCAATGTGAGTTTCCT-------A--------------------------------------------------------------------TGTTTCGCATGTACATA-----------TATCTA-----AATTGGT-TCCTTCTCCTCTGCAGATCTACAACTACATA
droEre2	scaffold_4644:2028284-2028382 +	1	GGCGAACTGTTCAATGTGAGTATCCT-------G--------------------------------------------------------------------TGATCCGCTTGTACTTATCTCGAGCAGTTCTCTA-----AACTGGT-CCCTGATCCTCTGCAGATCTACAACTACATA
droEug1	scf7180000409093:49412-49503 -	3	GGGGAGCTGTTCAATGTGAGTTATTTGA------G---------------------------------------------------------------------TTATATTCCTG-------CTTATAACCCTCTA-----AATTGGA-CTTGTTGGTCTTGCAGATCTACAACTATATA
droBia1	scf7180000301760:2041662-2041749 +	1	GGCGAGCTGTTCAACGTGAGTTCCCT-------T--------------------------------------------------------------------GCCCTCGCCGGCCTCTCCCTCAAGTAATCATCC-----------------ACCCTGCCCGCAGATCTACAACTACATA
droTak1	scf7180000415191:145537-145623 +	1	GGCGAGCTGTTCAATGTGAGTTTCTTGG------G-----------------------------------------------------------------T-TTTCCAGGTGACCTAGTGACT------------G-----AGTGGG----CTACTATCTTACAGATCTACAACTACATA
droEle1	scf7180000491001:1609052-1609151 +	3	GGCGAGCTGTTCAATGTGAGTAGCGC-----------------TCGGTTGCCCCCTAATCCTGCATTCCTTATCCTAATCCTTAT--------------------------------------------------------------C-CTCCCACCCCCCGCAGATCTACAACTACATC
droRho1	scf7180000779506:128106-128197 +	5	GGCGAGCTGTTCAATGTGAGTGGTTT-------------------------------------------------------------------------------ACAGTC----CTTGTCCCTAGTGGCCCTCTA-ATCC--CTTGT--GTGTTCCTCCTGCAGATCTACAACTACATC
droFic1	scf7180000454072:3187079-3187168 +	5	GGCGAGCTGTTCAACGTGAGTTCCTCCG------G-------------------------------------------------------CATCCCTTCTTC--------------------TTCCTGCTCCTCTA-----ATCCGGC-CA---CTTGCTTGCAGATCTACAACTACATC
droKik1	scf7180000302696:632884-632975 +	3	GGCGAGCTGTTCAATGTGAGTTTTGGGA------C---------------------------------------------------------------------CTTCCCCCCCC-------TTTCCGATGATCCC-----AACTGAC-ACAATATTCTTGGCAGATCTACAACTACATC
droAna3	scaffold_13117:1070684-1070773 -	17	GGCGAGCTCTTCAACGTAAGTTTCCCCG------C--------------------------------------------------------------------TTAAACGCCTAA----------GATTTTCCCTA-----AACCGTT-GCTGTTCTGTCTCTAGATCTACAACTATATC
droBip1	scf7180000396425:1044645-1044733 +	3	GGTGAGCTCTTCAATGTAAGTTTTCT-------T--------------------------------------------------------------------ACAACGCGTCATA----------GAATTTCCGTA-----AACCATT-GATGTTCTGTTTTCAGATCTACAACTATATC
dp4	chrXL_group1e:3790116-3790235 -	8	GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCA-GCCTCGAATTCGGCAGTCACTTGA------------------------TACTCTCCCACCTCCCTCTC--------------------CCTC-------------TG--CCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droPer1	super_17:723995-724114 -	7	GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCA-GCCTCGAATTCGGCAGTCACTTAA------------------------TACTCTCCCACCTCCCTCTC--------------------CCTC-------------TG--CCTCTCCATCATCCTCTTCCAGATCTACAACTACATC
droWil1	scaffold_181096:7421152-7421244 -	4	GGCGAGCTTTTCAACGTGAGTTACTCAG------T------------------------CCAAAGAAACTGGTTTTAGTTATGAT-----------------------------------------TAA--------------CTCA--CTTTTTTTTGTTATAGATTTACAACTATATA
droVir3	scaffold_12928:7113520-7113613 +	4	GGCGAGTTGTTCAACGTAAGTCGATG-------A--------------------------------------------------------------------CCTCGCGTATGTGGG-----CGTACTTTCACTGA-----CGCCTGC-CTCTTTGTCTATTCAGATTTACAACTACATT
droMoj3	scaffold_6328:2787435-2787524 +	5	GGGGAGTTGTTCAACGTAAATTCTAT-----------------------------------------------------------------------------TCTCACTTAACACAAGAATC----AAA--TCTC-----ATCTAAT--TTTTCGCTCGTTTAGATTTACAACTACATT
droGri2	scaffold_14853:3491672-3491772 -	150	GGAGAGTTGTTTAATGTAAGCTAAA---------C-------TTCGCCCATCCT-------------------------------------------------CTCCAGCTGTTTGG-----TTAA-----CTTTCAACTG--TTTGT--CCTCCATCTCCTCAGATTTACAACTACATT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

GGCGAACTTTTTAATGTGAGTGTCCTGTTTA-------------------------------CAGCTGGTATATTTTTCGAAAAGCCCTCTAAAC---------TGGTCA----------------CTTCCAC-TCTACAGATCTATAACTACATA

Size

Hit Count

Total Norm

droSim1

GGCGAACTGTTCAATGTGAGTTTCCTACTTA-------------------------------CAGCTGGTATATTTCTCGAACAGTCCTCTAAAC---------TGGTCT----------------CTTCCGC-TCCGCAGATCTACAACTACATA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

GGCGAACTGTTCAATGTGAGTTTCCTACTTA-------------------------------CAGCTGGTATATTTCGCGAACAGTCCTCTAAAC---------TGGTCC----------------CTTCCGC-TCCGCAGATCTACAACTACATA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..........................................................................................................GTCG----------------CTTxCGC-TCCGCAGA..............	18	1	1.00	0.00	1.00	0.00

droYak2

GGCGAACTCTTCAATGTGAGTTTCCTATGTT-------------------------------TCGCATGTACATAT-----------ATCTAAAT---------TGGTTC----------------CTTCTCC-TCTGCAGATCTACAACTACATA

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

GGCGAACTGTTCAATGTGAGTATCCTGTGAT-------------------------------CCGCTTGTACTTATCTCGAGCAGTTCTCTAAAC---------TGGTCC----------------CTGATCC-TCTGCAGATCTACAACTACATA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

GGCGAGCTCTTCAACGTAAGTTTCCCCGCTTA------------------------------AACGCCTAAGATT----------TTCCCTAAAC---------CGTTGC----------------TGTTCTG-TCTCTAGATCTACAACTATATC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...........................................................................................AAAC---------CGTTGC----------------TAGTCTG-TCT...................	20	1	1.00	0.00	0.00	1.00	0.00

dp4

GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCAGCCTCGAATTCGGC---AGTCACTTGATA--------------------------------ctctcccacctcc-ctctccctctgcctctccatcatcctcttccAGATCTACAACTACATC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GGCGAGTTGTTCAACGTAAGTTCCAGCATTTCAGCCTCGAATTCGGC---AGTCACTTAATA--------------------------------ctctcccacctcc-ctctccctctgcctctccatcatcctcttccAGATCTACAACTACATC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................................................................................................CTTCCAGATCAACGACTAC...	19	1	29.00	0.00	0.00	0.00	0.00	29.00
......................................................................................................................................CTTCCAGATCAACGACTA....	18	1	25.00	0.00	0.00	0.00	0.00	25.00
.....................................................................................................................................TCTTCCAGATCAACGACT.....	18	1	13.00	0.00	0.00	0.00	0.00	13.00
.......................................................................................................................................TTCCAGATCAACGACTAC...	18	1	9.00	0.00	0.00	0.00	0.00	9.00
.....................................................................................................................................TCTTCCAGATCAACGACTAC...	20	1	4.00	0.00	0.00	0.00	0.00	4.00
.....................................................................................................................................TCTTCCAGATCGACAAGT.....	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................................................................................CTGC-CTCTGCCTCTGCCT..................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
....................................................................................................................................CTCTACCAGATCTACAAC......	18	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

GGCGAGCTTTTCAACGTGAGTTACTCAGTCCA----AAGAAACTGGTTTTAGTTA--TGA----------------------------------TTAACTC-----A-CT----------------TTTTTTT-GTTATAGATTTACAACTATATA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..............................................................................................................................TTTTTTT-GTTATTTATTTA..........	19	1	1.00	0.00	1.00	0.00	0.00

droVir3

GGCGAGTTGTTCAACGTAAGTCGATGACCTC-----GCGTATGTGGG-------------------------------CGTACTTTCA------CTGACGC---CTGCCT----------------CTTTGTC-TATTCAGATTTACAACTACATT

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GGGGAGTTGTTCAACGTAAATTCT--ATTCT-------------------------------CACTTAACACAAGAATCAAA------TCTCATC---------TAAT-T----------------TTTCGCT-CGTTTAGATTTACAACTACATT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.......................T--ATTAT-------------------------------CACTTCACACAA..................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droGri2

GGAGAGTTGTTTAATGTAAGCTAA--ACTTC-----GCCCATCC-TCTCCAGCTGTTTGG------------------TTAA-----CTTTCAAC---------TGTTTG-------------TC-CTCCATC-TCCTCAGATTTACAACTACATT

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