dme-mir-2489- 12- and 20-way alignments

dme-mir-2489	chr2L:13609988-13610055 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 13610035-13610055
   star strand at position 13609988-13610015
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:13609973-13610070 +	AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACGT-------AAGTTCTAATG-----TATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA
droSim1	chr2L:13379253-13379350 +	AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACAT-------ACGTTCTAATG-----CATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA
droSec1	super_16:1746050-1746147 +	AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACAT-------ACGTTCTAATG-----CATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA
droYak2	chr2L:10029706-10029801 +	AGCAATAAGTTAGATGTGAGTATG------GCTATTTAAAT---------CAACC-GAAC--GT-ATGT-------ATGTTATATAG-----T-----TTG---CATT-----TTGTATTTGCAGTTTTATGATAGCAAA
droEre2	scaffold_4929:11847836-11847927 -	AGCAATAAGTTAGACGTGAGTATG------GCTATCTAAAT---------CAGCC--------GAACGT-------GTATTCTAATG-----TTTG--------CACT-----TTGTATTTGCAGTTTTATGATAGCAAA
droAna3	scaffold_12943:1669999-1670103 +	AGCGATAAGTTAGACGTGAGTATT-----GTCTCTGTCAAG---------TGTAT-------GGTACTAATATTTA----ACTAATT-----CTTGTATTAACTTGTT-----TTTAATTTCCAGTTTTATGATAGCAAT
dp4	chr4_group1:1879331-1879430 -	AGCGATAAGTTAGACGTGAGTATA------TCTTTGCCATC---------TCTTT-----TTAAAACAA-------TCATTTTCATA-----TACATATAT---ATTT-----TTGTGTGTTTAGTTTTATGATAGCAAC
droPer1	super_5:3326174-3326277 +	AGCGATAAGTTAGACGTGAGTATA------TCTTTGCCATC---------TCttt-----ttaaaatat----tttatatttttatatattacatatattt------------tttGGTGTTTAGTTTTATGATAGCAAC
droWil1	scaffold_180772:852551-852648 -	AGCGATAAGTTAGATGTGAGTATA------T-TATATCTTTTGTCCCATT----------TTGGAATAT-------GTTTTTGAATA-----CCTT--------TTCT-----TTGGGATTTCAGTTTTATGATAGCAAC
droVir3	scaffold_12723:5236355-5236448 -	AGTGATAAGTTAGACGTGAGTATT------ATCAACATATATGAATTATT----------T-TAAAATA-------ATAATC-------------GAAT-T---TAAT-----TTGTTATCCCAGTTTTATGATAGCAAC
droMoj3	scaffold_6500:16444108-16444197 +	AGTGATAAGTTAGACGTGAGTATTACAGAGGCCCTATCAA------------------------AAT-A-------TC------ATT-----CGTGTATCT---AATATAATAT----TTTTCAGTTTTATGATAACAAC
droGri2	scaffold_15126:8263493-8263587 -	AGTGATAAGTTAGACGTGAGTATTT-----ATTAAC--------------TTCATTCAAC--GTAATAT-------ACATACTAAAA-----TATGAA--------TACATCAT----TTTGCAGTCTTATGATAGCAAC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:13609973-13610070 +	NA	AGCAATAAGTTAGACGTGAGTATGGC--------TATACAAATCA---TCT-----------GGAAC----GTAAGTTCTA------AT-------GT---ATGTAT---T-GTATGTTG-TATTTGCAGTTTTATGATAGCAAA
droSim1	chr2L:13379253-13379350 +	1	AGCAATAAGTTAGACGTGAGTATGGC--------TATACAAATCA---TCT-----------GGAAC----ATACGTTCTA------AT-------GC---ATGTAT---T-GTATGTTG-TATTTGCAGTTTTATGATAGCAAA
droSec1	super_16:1746050-1746147 +	1	AGCAATAAGTTAGACGTGAGTATGGC--------TATACAAATCA---TCT-----------GGAAC----ATACGTTCTA------AT-------GC---ATGTAT---T-GTATGTTG-TATTTGCAGTTTTATGATAGCAAA
droYak2	chr2L:10029706-10029801 +	1	AGCAATAAGTTAGATGTGAGTATGGC--------TATTTAAATCA---ACC-GAACG------T-AT----GTATGTTATA------TA-------GT---TTGCA-----T----TTTG-TATTTGCAGTTTTATGATAGCAAA
droEre2	scaffold_4929:11847836-11847927 -	2	AGCAATAAGTTAGACGTGAGTATGGC--------TATCTAAATCA---GCC------------GAAC----GTGTATTCTA------AT-------GT---TTGCA-----C----TTTG-TATTTGCAGTTTTATGATAGCAAA
droEug1	scf7180000409452:191304-191394 +	1	AGCAATAAGTTAGACGTGAGTATAGTACTTAA---ATTAT---AA----TTT-----------TAAA----TCACATTATA------AT-------G-------TA-----C----TTTGTACTTTTCAGTTTTATGATAGCAAA
droBia1	scf7180000302408:2742692-2742786 -	3	AGCAATAAGTTAGAGGTGAGTACTCCTAAAA--T---------AT----ACTAAAAA------TAAG----A-AAAC----ATTCTAAC-------AA---CCAAT-----A----TTTG-CCCTTGCAGATTTATGATAGCAAA
droTak1	scf7180000415285:144401-144496 +	2	AGCAATAAGTTAGACGTGAGTATATA--------AATATATATTA---ATT-----------AAAAT----TTAAATCTTA------AA-------TC-----GTAA---C-ATTTGTTG-TACTTTCAGTTTTATGATAGCAAA
droEle1	scf7180000491338:1217909-1218003 +	4	AGCAATAAGTTAGACGTGAGTATTGTC--------ATTAAGATAG---AAC--A---------ACAT----AAACATGTTA------AA----CATAT---TTGTA---------TTTT--TTTTTTCAGTTTTATGATAGCAAA
droRho1	scf7180000780107:475244-475335 -	7	AGCAATAAGTTAGACGTGAGTATTTTTTAAA--T---------AA---TTT-AAA--------AAAC----TTACAACTTA------AT-------GT---GTACA-----C----CTTG-TATTTTCAGTTTTATGATAGCAAA
droFic1	scf7180000453925:389428-389520 -	4	AGCAATAAGTTAGACGTGAGTATTGCTCTCAAG--ATTAAAATCA-------------------AAA----ACCCTTACTA------AG-------AC---ATA-------C----TTTTTTATTTTTAGTTTTATGATAGCAAA
droKik1	scf7180000302656:77455-77548 +	3	AGCAATAAGTTAGACGTGAGTATTACATACG--C---------AATTATAT-----------TAATT----TTAAG---TA------AT-------GC---TCGTATTTC-C----TTTA-CTTTTCCAGTTTTATGATAGCAAG
droAna3	scaffold_12943:1669999-1670103 +	1	AGCGATAAGTTAGACGTGAGTATTGTC-------TCTGTCAAGTG---TAT-----------GGTACTAATATTTA-ACTA------AT-------TC---TTGTATTAA-CTTGTTTTT-AATTTCCAGTTTTATGATAGCAAT
droBip1	scf7180000396728:1558161-1558257 -	6	AGCGATAAGTTAGACGTGAGTATTAATATAATC--CTTAAAATAT-----------------AAAATCAATAATTAATC------------------------AAAACCT-C----TTTCTGATCCATAGTTTTATGATAGCAAT
dp4	chr4_group1:1874149-1874246 -	6	AGCGATAAGTTAGACGTGAGTATTTTCCATA--C---------CT----TTTTAAAA------C-------AATCATTTTG------ATATA-C--AT---ATATAT---T-TTTTGTTG---TGTTTAGTTTTATGATAGCAAC
droPer1	super_5:3326174-3326277 +	2	AGCGATAAGTTAGACGTGAGTATATC--------TTTGCCATCTC---TTTTTAAAA------TATT----TTATATTTTT------ATATATT--AC---ATATAT---T-TTTT-----GGTGTTTAGTTTTATGATAGCAAC
droWil1	scaffold_180772:852551-852648 -	20	AGCGATAAGTTAGATGTGAGTATATTATATC--T---------TT-TGTCC--C---ATTTTGGAAT----ATGTTTTTGA------AT-------AC---CTTTT-----C----TTTG-GGATTTCAGTTTTATGATAGCAAC
droVir3	scaffold_12723:5236355-5236448 -	16	AGTGATAAGTTAGACGTGAGTATTATCAACA--T---------ATATGAAT--T---ATTT-TAAAA----TAATAATC------------------------GAATTTA-A----TTTG-TTATCCCAGTTTTATGATAGCAAC
droMoj3	scaffold_6500:16444108-16444197 +	2	AGTGATAAGTTAGACGTGAGTATTACAGAGG--C---------CC----TATCAAAA------TA--------------TCATTCGTGT-------ATCTAATATA-----------AT--ATTTTTCAGTTTTATGATAACAAC
droGri2	scaffold_15126:8263493-8263587 -	19	AGTGATAAGTTAGACGTGAGTATTTATTAAC--T---------TC----ATTCAACG------TAAT----ATACATACTA------AAATA-----T-GAATACA-----------TC--ATTTTGCAGTCTTATGATAGCAAC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACGT-------AAGTTCTAATG-----TATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA

Size

Hit Count

Total Norm

droSim1

AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACAT-------ACGTTCTAATG-----CATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
................................................................................................TATTG---TATG-----TTGTATTTGCAGT..............	22	1	49.00	11.00	18.00	0.00	20.00
................................................................................................TATTG---TATG-----TTGTATTTGCAG...............	21	1	45.00	5.00	37.00	0.00	3.00
................................................................................................TATTG---TATG-----TTGTATTTGC.................	19	1	37.00	0.00	36.00	1.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTGCA................	20	1	29.00	1.00	28.00	0.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTGCAGA..............	22	1	10.00	1.00	4.00	0.00	5.00
................................................................................................TATTG---TATG-----TTGTATTTGCAGC..............	22	1	5.00	0.00	4.00	0.00	1.00
................................................................................................TATTG---TATG-----TTGTATTTTCAGT..............	22	1	2.00	2.00	0.00	0.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTGCAGG..............	22	1	2.00	0.00	0.00	0.00	2.00
...........................................................................................................G-----TTTTATTTGCAGTTTTATC........	20	1	1.00	1.00	0.00	0.00	0.00
................................................................................................TATTG---TATG-----CTGTATTTGCAGT..............	22	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................ATTG---TATG-----TTGTATTTGCAGA..............	21	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TATTG---TATG-----TTGTATTTGCT................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................................TATTG---TATG-----TTGTCTTTGCAGT..............	22	1	1.00	1.00	0.00	0.00	0.00
................................................................................................TATTG---TATG-----TTCTATTTGC.................	19	1	1.00	0.00	1.00	0.00	0.00
................................................................................................TATTG---TATG-----GTGTATTTGCA................	20	1	1.00	0.00	1.00	0.00	0.00
................................................................................................TATTG---TATG-----TTGTGTTTGCAGT..............	22	1	1.00	0.00	1.00	0.00	0.00

droSec1

AGCAATAAGTTAGACGTGAGTATG------GCTATACAAAT---------CATCT-------GGAACAT-------ACGTTCTAATG-----CATGTATTG---TATG-----TTGTATTTGCAGTTTTATGATAGCAAA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
................................................................................................TATTG---TATG-----TTGTATTTGCAGT..............	22	1	131.00	13.00	100.00	18.00
................................................................................................TATTG---TATG-----TTGTATTTGCAG...............	21	1	100.00	9.00	19.00	72.00
................................................................................................TATTG---TATG-----TTGTATTTGCA................	20	1	52.00	4.00	1.00	47.00
................................................................................................TATTG---TATG-----TTGTATTTGCAGA..............	22	1	35.00	6.00	22.00	7.00
................................................................................................TATTG---TATG-----TTGTATTTGC.................	19	1	10.00	0.00	0.00	10.00
................................................................................................TATTG---TATG-----TTGTATTTGCAGC..............	22	1	5.00	0.00	3.00	2.00
................................................................................................TATTG---TATG-----TTGTATTTCCAGT..............	22	1	2.00	0.00	2.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTGCTGT..............	22	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTCCAGA..............	22	1	1.00	1.00	0.00	0.00
.............................................................................................ATATATTG---TATx-----TTGTATT....................	18	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TATG-----TCGTATTTGC.................	19	1	1.00	0.00	0.00	1.00
................................................................................................TATTG---TCTG-----TTGTATCTGCAGT..............	22	1	1.00	0.00	1.00	0.00
................................................................................................TTTTG---TATG-----TTGTATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---AATG-----TTGTATTTGCA................	20	1	1.00	0.00	0.00	1.00
................................................................................................TATAT---TATG-----TTGTATTTGCAG...............	21	1	1.00	0.00	0.00	1.00
.....................................AAAT---------CATCT-------GGAACAT-------ACGTT...........................................................	21	1	1.00	1.00	0.00	0.00
................................................................................................GATTG---TATG-----TTGTATTTGC.................	19	1	1.00	0.00	0.00	1.00
.................................................................................................ATTG---TATG-----TTGTATTTGC.................	18	1	1.00	0.00	0.00	1.00
...............................................................................................CTATTG---TATG-----TTGTATTTGCAGC..............	23	1	1.00	0.00	1.00	0.00
................................................................................................TATTC---TATG-----TTGTATTTGCAG...............	21	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTGCAT...............	21	1	1.00	0.00	0.00	1.00
................................................................................................CATTG---TATG-----TTGTATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
.................................................................................................ATTG---TATG-----TTGTATTTGCAG...............	20	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TATT-----TTGTATTTGCAG...............	21	1	1.00	0.00	0.00	1.00
................................................................................................TATTG---TATG-----TTCTATTTGCA................	20	1	1.00	0.00	0.00	1.00
..................................................................................................TTG---TATG-----TTGTATTTGCA................	18	1	1.00	0.00	0.00	1.00
................................................................................................TATTG---TATG-----TTGTATTTGCCG...............	21	1	1.00	1.00	0.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTGCAGTA.............	23	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TATT-----TTGTATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TACG-----TTGTATTTGCAGA..............	22	1	1.00	0.00	0.00	1.00
................................................................................................TATTG---TATG-----TTGTATTTGCCGA..............	22	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTGCAGAT.............	23	1	1.00	1.00	0.00	0.00
................................................................................................GATTG---TATG-----TTGTATTTGCA................	20	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TATG-----TTGTATTTGCAGG..............	22	1	1.00	0.00	1.00	0.00
................................................................................................TATTG---TACG-----TTGTATTTGCAGT..............	22	1	1.00	0.00	1.00	0.00

droYak2

AGCAATAAGTTAGATGTGAGTATG------GCTATTTAAAT---------CAACC-GAAC--GT-ATGT-------ATGTTATATAG-----T-----TTG---CATT-----TTGTATTTGCAGTTTTATGATAGCAAA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..................................................................................................................TGTATTTGCTGTTTTAAGA.......	19	1	3.00	1.00	0.00	2.00	0.00	0.00
...................................................................................................................GTATTTGCTGTTTTAAGA.......	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...................................................................................ATAG-----x-----TTG---CATT-----TTGTAGTT...................	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

AGCAATAAGTTAGACGTGAGTATG------GCTATCTAAAT---------CAGCC--------GAACGT-------GTATTCTAATG-----TTTG--------CACT-----TTGTATTTGCAGTTTTATGATAGCAAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................................................................................GTATTTGCTGTTTTAAGA.......	18	1	24.00	1.00	0.00	7.00	16.00
..................................................................................................................TGTATTTGCTGTTTTAAGA.......	19	1	18.00	3.00	0.00	2.00	13.00
..................................................................................................................TGTATTTGCTGTTTTAAG........	18	1	11.00	0.00	0.00	2.00	9.00
......................................................................................................................TTTGCAGTTTTAxGATAGT...	18	1	1.00	0.00	0.00	0.00	1.00
..............................................................................ATTCTAATG-----TTTG--------CAGC-----T..........................	18	1	1.00	0.00	0.00	1.00	0.00

droAna3

AGCGATAAGTTAGACGTGAGTATT-----GTCTCTGTCAAG---------TGTAT-------GGTACTAATATTTA----ACTAATT-----CTTGTATTAACTTGTT-----TTTAATTTCCAGTTTTATGATAGCAAT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
............................................................................................CTTGTATTxATTTGTT-----TTTA.......................	19	1	1.00	0.00	1.00	0.00	0.00

dp4

AGCGATAAGTTAGACGTGAGTATA------TCTTTGCCATC---------TCTTT-----TTAAAACAA-------TCATTTTCATA-----TACATATAT---ATTT-----TTGTGTGTTTAGTTTTATGATAGCAAC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
................................................................................................TAAAT---ATTT-----ATGTGTGTTTA................	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

AGCGATAAGTTAGACGTGAGTATA------TCTTTGCCATC---------TCttt-----ttaaaatat----tttatatttttatatattacatatattt------------tttGGTGTTTAGTTTTATGATAGCAAC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
............................................................................ATxTTTATATATATTATATATA..........................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
................................................................AATAT----TTTAGATTTTTTT......................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
.......................................................................................................................GTTTAGTTTTATGTTAGCA..	19	1	1.00	0.00	0.00	0.00	1.00	0.00
....................................................................T----TGTATTTTTTTATATATT.................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................TGTATTTTTTTATATATT.................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.................................................................................................ATTT------------TTTGGCGTTTGGTTTT...........	20	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

AGCGATAAGTTAGATGTGAGTATA------T-TATATCTTTTGTCCCATT----------TTGGAATAT-------GTTTTTGAATA-----CCTT--------TTCT-----TTGGGATTTCAGTTTTATGATAGCAAC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.................................................T----------TTGGAAGAT-------GTTATTGA........................................................	18	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................CT-----TTGTGATTTCATTTTT...........	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................T--------TTAT-----TTGGGxTTTCAGTT.............	18	1	1.00	0.00	1.00	0.00	0.00
...........................................................................................................T-----TTGGGxTTTCAGTTTGAT.........	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

AGTGATAAGTTAGACGTGAGTATT------ATCAACATATATGAATTATT----------T-TAAAATA-------ATAATC-------------GAAT-T---TAAT-----TTGTTATCCCAGTTTTATGATAGCAAC

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

AGTGATAAGTTAGACGTGAGTATTACAGAGGCCCTATCAA------------------------AAT-A-------TC------ATT-----CGTGTATCT---AATATAATAT----TTTTCAGTTTTATGATAACAAC

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

AGTGATAAGTTAGACGTGAGTATTT-----ATTAAC--------------TTCATTCAAC--GTAATAT-------ACATACTAAAA-----TATGAA--------TACATCAT----TTTGCAGTCTTATGATAGCAAC

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