dme-mir-1015- 12- and 20-way alignments

dme-mir-1015	chr3R:20164954-20165017 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 20164996-20165017
   star strand at position 20164954-20164975
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:20164939-20165032 +	TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGGCTGAGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAG
droSim1	chr3R:19998542-19998635 +	TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGGCTGAGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droSec1	super_0:20503496-20503589 +	TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGTCTGAGTG-------AGACTTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droYak2	chr3R:26340571-26340664 -	TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGATAGCTTGACTGGGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAC
droEre2	scaffold_4820:7895693-7895786 -	TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGATAGCTTGGCTGAGTG-------AGGACTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAAATCCTAAAAC
droAna3	scaffold_13088:204245-204339 +	TCATGGGCTACGACAGTGAGTG-----ATGCTCCAGATAGGTTGGCTTAGGAAGTC------ATTAA------------AGCCCTGGGAT-----GTCTCTCTTGCAGTTAAGATCCTGAAAC
dp4	chr2:18646206-18646298 -	TGATGGGCTACGATGGTAAGAG--C---TAGC---------C-----ACACAAATTATTAGTATT----------TCTATTTCTCAAAATATTT-CTTTCTTTTGCAGTCAAGATACTAAAGC
droPer1	super_3:1376406-1376498 -	TGATGGGCTACGATGGTAAGAG--C---TAGC---------C-----ACACAAATTATTAGTATT----------TCTATTTCTCAAAATATTC-CTTTCTTTTGCAGTCAAGATCCTAAAGC
droWil1	scaffold_181108:4541725-4541808 -	TAATGGGTTATGACAGTAAGTTAGC---TGGTAAAGTTGATTTCT------------------TTTA------------ACTAATGT-GT-----ATATTTACTGTAGTAAGAATTTTAAAGC
droVir3	scaffold_13047:3497490-3497590 +	TTGTGGGCTACGAAAGTAAGTA------TTTACTTGATAACTCG------TT-------AAACCTAAAG--TCTGTTAACCACTCTTATAACTATG-CATCTAAACAGTTAAGGTACTAAAGA
droMoj3	scaffold_6540:20508341-20508431 +	TAATGGGCTACGATGGTAAATG--CTGATGTTCATGAATATTTATCCAAGTA-------ATTT------------------CTTTACGTT-----GTCTTCTTAACAGTTAAGGTTTTGAAAA
droGri2	scaffold_14906:156637-156731 +	TGGTGGGCTATGATAGTGAGTT--G--ATTCTATT---------------GTAATAATCA------AATCGTTTTTGTTATTTTATAAACA---TGCCATTTTAACAGTCAAGATACTCAAGA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:20164939-20165032 +	NA	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAG
droSim1	chr3R:19998542-19998635 +	1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGGCTGAGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droSec1	super_0:20503496-20503589 +	1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGTTAGCTTGTCTGAGTGAG-A--------C----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG
droYak2	chr3R:26340571-26340664 -	3	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGACTGGGTGAG-G--------A----TT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAC
droEre2	scaffold_4820:7895693-7895786 -	2	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTGAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAAATCCTAAAAC
droEug1	scf7180000409798:215829-215922 -	11	TAATGGGCTACAATGGTGAGTG----ATGCTCCAGATAGCTTCGCAAAGTAAG-G--------A----TA------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAGAC
droBia1	scf7180000302136:526695-526788 +	1	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGATGGCTGGGCTAAGTGAG-G--------A----CT------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAGC
droTak1	scf7180000415769:2262017-2262110 -	4	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGCTGGCTTGGCAAAGCGTG-G--------A----TC------TAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTCAAGC
droEle1	scf7180000491008:477705-477804 +	3	TCATGGGCTACGACGGTGAGTG----ATGCTCCAGAAAGCTTGGCCAAGTGAC-C--------A----CCCATACTTAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCTGAAGC
droRho1	scf7180000779477:268222-268317 +	5	TCATGGGATACGACGGTGAGTG----ATGCTCCAGATAGCTTGGCTAAGTGAG-G--------A----TTAA----TAAGCCCTGGGAC-----ATCTCTCTTGCAGTGAAGGTCCTGAAGC
droFic1	scf7180000453912:1339925-1340020 +	6	TCATGGGCTACCAAGGTGAGTG----ATGCTCCAGATAACTTGGAAAAGTGGG-A--------ATACGGA------TAAGTCC--GGAC-----TTCTCTCTTGCAGTCAAGATTCTGAAAT
droKik1	scf7180000302387:55058-55154 +	3	TGATGGGCTATGACGGTGAGTG----ATGCTCCAGATAGCTTAGTTTAAAAAAAG--------A----TTCA----AAAGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAGC
droAna3	scaffold_13088:204245-204339 +	1	TCATGGGCTACGACAGTGAGTG----ATGCTCCAGATAGGTTGGCTTAGGAAGTC--------A----TT------AAAGCCCTGGGAT-----GTCTCTCTTGCAGTTAAGATCCTGAAAC
droBip1	scf7180000396413:258464-258558 +	1	TCATGGGCTACGATAGTGAGTG----ATGCTCTAGATAGGTTAGCTGATGAAG-T--------C---TTT------CAAGCCCTAGGTC-----ATCTCTCTTGCAGTTAAAATCCTGAAAC
dp4	chr2:18646206-18646298 -	1	TGATGGGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTT-CTTTCTTTTGCAGTCAAGATACTAAAGC
droPer1	super_3:1376406-1376498 -	1	TGATGGGCTACGATGGTAAGAG----CTAGCCA-CACAAATTA------TTAG-T--------A----TTTC----TATTTCTCAAAATATTC-CTTTCTTTTGCAGTCAAGATCCTAAAGC
droWil1	scaffold_181108:4541725-4541808 -	1	TAATGGGTTATGACAGTAAGTTA--GCTGGTAAAGTTGATTTCT------------------------TT------TAACTAATGT-GT-----ATATTTACTGTAGTAAGAATTTTAAAGC
droVir3	scaffold_13047:3497490-3497590 +	1	TTGTGGGCTACGAAAGTAAGTA----T-TTACTTGATAACTCGTT------AA-ACCTAAAGTC----TGTT----AACCACTCTTATAACTATG-CATCTAAACAGTTAAGGTACTAAAGA
droMoj3	scaffold_6540:20508341-20508431 +	2	TAATGGGCTACGATGGTAAATG-CTGATGTTCATGAATATTTATCCAAGTAAT-T--------T----------------CTTTACGTT-----GTCTTCTTAACAGTTAAGGTTTTGAAAA
droGri2	scaffold_14906:156637-156731 +	2	TGGTGGGCTATGATAGTGAGTTG---ATTCTATTGT--AATAATC-AAATC-G-T--------T----TTTG----TTATTTTATAAAC---ATGCCATTTTAACAGTCAAGATACTCAAGA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGGCTGAGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAG

Size

Hit Count

Total Norm

droSim1

TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGGCTGAGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGT..............	23	1	34.00	1.00	0.00	33.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAG...............	22	1	28.00	1.00	0.00	25.00	2.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGTT.............	24	1	5.00	0.00	0.00	5.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGC.................	20	1	4.00	0.00	0.00	4.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCA................	21	1	2.00	0.00	0.00	1.00	1.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGG..............	23	1	2.00	0.00	0.00	1.00	1.00
...............GTGAGTG-----ATGCTCCAGTTAGCT.................................................................................	22	1	2.00	1.00	0.00	1.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGTTT............	25	1	1.00	0.00	0.00	1.00	0.00
...................................................................................CTGGGAC-----ATCTCTCTTGCAGTT.............	22	1	1.00	0.00	0.00	1.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAA...............	22	1	1.00	0.00	0.00	1.00	0.00
..........................................TGGCTGAGTG-------AGGATTTA------------AG..........................................	20	1	1.00	0.00	0.00	1.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAC...............	22	1	1.00	0.00	0.00	1.00	0.00
.................................................................................TCCTTGGAC-----ATCTCTCTTGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGC..............	23	1	1.00	0.00	0.00	1.00	0.00
...............GTGAGTG-----ATGCTCCCGTTAGCTTG...............................................................................	24	1	1.00	1.00	0.00	0.00	0.00
...............................................................................AGTCCTGGGAC-----ATCTCTCTTGC.................	22	1	1.00	1.00	0.00	0.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGAAA...............	22	1	1.00	0.00	0.00	1.00	0.00

droSec1

TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGTTAGCTTGTCTGAGTG-------AGACTTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTAAAAG	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGT..............	23	1	18.00	18.00	0.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAG...............	22	1	11.00	10.00	1.00	0.00
...............GTGAGTG-----ATGCTCCAGTTAGCT.................................................................................	22	1	11.00	5.00	6.00	0.00
...............GTGAGTG-----ATGCTCCAGTTAGCTTG...............................................................................	24	1	8.00	7.00	1.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGA..............	23	1	6.00	6.00	0.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCA................	21	1	3.00	1.00	1.00	1.00
...............GTGAGTG-----ATGCTCCAGTTAGCTT................................................................................	23	1	3.00	3.00	0.00	0.00
...............................................................................AGTCCTGGGAC-----ATCTCTCTTGC.................	22	1	2.00	0.00	2.00	0.00
...............GTGAGTG-----ATGCTCCAGTTAGC..................................................................................	21	1	2.00	2.00	0.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTACAGA..............	23	1	1.00	1.00	0.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTACAGT..............	23	1	1.00	1.00	0.00	0.00
.................................................................TA------------AGTxCTGGGAC-----AACTCTCT....................	20	1	1.00	0.00	0.00	1.00

droYak2

TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGATAGCTTGACTGGGTG-------AGGATTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAGATCCTGAAAC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...............GTGAGTG-----ATGCTCCAGATAGCTTG...............................................................................	24	1	7.00	0.00	1.00	6.00	0.00	0.00
...............GTGAGTG-----ATGCTCCAGATAGCTT................................................................................	23	1	6.00	0.00	1.00	5.00	0.00	0.00
...............GTGAGTG-----ATGCTCCAGATAGCT.................................................................................	22	1	4.00	0.00	1.00	3.00	0.00	0.00
...............GTGAGTG-----ATGCTCCAGATAGCTTGT..............................................................................	25	1	3.00	1.00	0.00	2.00	0.00	0.00
...............GTGAGTG-----ATGCTCCAGATAG...................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGT..............	23	1	1.00	0.00	0.00	0.00	1.00	0.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCATT..............	23	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................GACTGGGTG-------AGGATTTG------------C...........................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
...............GTGAGTG-----ATGCTCCAGATAGCTTGTT.............................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

TCATGGGCTACGACGGTGAGTG-----ATGCTCCAGATAGCTTGGCTGAGTG-------AGGACTTA------------AGTCCTGGGAC-----ATCTCTCTTGCAGTCAAAATCCTAAAAC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...............GTGAGTG-----ATGCTCCAGATAGCT.................................................................................	22	1	7.00	0.00	0.00	0.00	7.00
...............GTGAGTG-----ATGCTCCAGATAGCTT................................................................................	23	1	4.00	0.00	0.00	0.00	4.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGT..............	23	1	3.00	0.00	0.00	0.00	3.00
...............GTGAGTG-----ATGCTCCAGATAGCTTG...............................................................................	24	1	2.00	0.00	0.00	0.00	2.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00
.................................................................................TCCTGGGAC-----ATCTCTCTTG..................	19	1	1.00	0.00	0.00	0.00	1.00
.................................................................................TCCTGGGAC-----ATCCCTCTTGCAGT..............	23	1	1.00	0.00	0.00	0.00	1.00
..........................................TGGCTGAGTG-------AGGACTTA------------AG..........................................	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................TCCTTGGAC-----ATCTCTCTTGCAG...............	22	1	1.00	0.00	0.00	0.00	1.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGCAGC..............	23	1	1.00	0.00	0.00	0.00	1.00
...............................................................................AGTCCTGGGAC-----ATCTCTCTTGC.................	22	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTG-----ATGCCCCAGATAGCT.................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
...............GTGAGTG-----ATGCTCCAGATATCT.................................................................................	22	1	1.00	0.00	0.00	0.00	1.00
.................................................................................TCCTGGGAC-----ATCTCTCTTGC.................	20	1	1.00	0.00	0.00	0.00	1.00

droAna3

TCATGGGCTACGACAGTGAGTG-----ATGCTCCAGATAGGTTGGCTTAGGAAGTC------ATTAA------------AGCCCTGGGAT-----GTCTCTCTTGCAGTTAAGATCCTGAAAC	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............GTGAGTG-----ATGCTCCAGATAGGT.................................................................................	22	1	2.00	1.00	1.00	0.00	0.00
...............GTGAGTG-----ATGCTCCAGATAGGTTGGCT............................................................................	27	1	1.00	1.00	0.00	0.00	0.00
...............GTGAGTG-----ATGCTCCAGATAGGTTGGC.............................................................................	26	1	1.00	1.00	0.00	0.00	0.00
.................................................................................CCCTGGGAT-----GTCTCTCTTGCA................	21	1	1.00	0.00	1.00	0.00	0.00

dp4

TGATGGGCTACGATGGTAAGAG--C---TAGC---------C-----ACACAAATTATTAGTATT----------TCTATTTCTCAAAATATTT-CTTTCTTTTGCAGTCAAGATACTAAAGC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

TGATGGGCTACGATGGTAAGAG--C---TAGC---------C-----ACACAAATTATTAGTATT----------TCTATTTCTCAAAATATTC-CTTTCTTTTGCAGTCAAGATCCTAAAGC

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

TAATGGGTTATGACAGTAAGTTAGC---TGGTAAAGTTGATTTCT------------------TTTA------------ACTAATGT-GT-----ATATTTACTGTAGTAAGAATTTTAAAGC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...............................................................................................ATATTTACTGTAGGAATA..........	18	1	157.00	1.00	66.00	3.00	87.00
.........................................................................................T-----ATATTTACTGTAGGAATA..........	19	1	149.00	7.00	39.00	1.00	102.00
.........................................................................................T-----ATATTTACTGTAGGAAT...........	18	1	39.00	0.00	5.00	0.00	34.00
........................................................................................AT-----ATATTTACTGTAGGAA............	18	1	6.00	0.00	2.00	0.00	4.00
.................................................................................................ATTTACTGTAGTAGGACT........	18	1	3.00	0.00	0.00	0.00	3.00
...............................................................................................ATATTTACTGTAGGAACA..........	18	1	2.00	0.00	1.00	0.00	1.00
.........................................................................................T-----ATATTTACTGTAGGAAAAA.........	20	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................ATATTTACTGTAGAAATA..........	18	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TATTTACTGTAGTAGGACT........	19	1	1.00	0.00	0.00	0.00	1.00
................................................................................................TATTTACTGTAGGAAAAA.........	18	1	1.00	0.00	1.00	0.00	0.00
...............................................................................................ATATTTACTGTAGTAATA..........	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................TATTTACTGTAGGAGGAA.........	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................T-----ATATTTACTGTAGTAATA..........	19	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................T-----ATATTTACTGTAGGAAA...........	18	1	1.00	0.00	1.00	0.00	0.00
........................................................................................GA-----ATATTTACTGTAGGAA............	18	1	1.00	0.00	1.00	0.00	0.00
................................................................................................TATTTACTGTAGTAGGAAT........	19	1	1.00	0.00	0.00	0.00	1.00

droVir3

TTGTGGGCTACGAAAGTAAGTA------TTTACTTGATAACTCG------TT-------AAACCTAAAG--TCTGTTAACCACTCTTATAACTATG-CATCTAAACAGTTAAGGTACTAAAGA

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

TAATGGGCTACGATGGTAAATG--CTGATGTTCATGAATATTTATCCAAGTA-------ATTT------------------CTTTACGTT-----GTCTTCTTAACAGTTAAGGTTTTGAAAA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...........GATGGxAAATG--CTGATGAT...........................................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droGri2

TGGTGGGCTATGATAGTGAGTT--G--ATTCTATT---------------GTAATAATCA------AATCGTTTTTGTTATTTTATAAACA---TGCCATTTTAACAGTCAAGATACTCAAGA

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