dme-mir-4970- 12- and 20-way alignments

dme-mir-4970	chr2L:10741884-10741987 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 10741905-10741926
   star strand at position 10741949-10741970
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:10741869-10742002 +	CATGTTTAGATCGGACCCAAAGGTGGGCGACAAG---GGCTGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGCTG------CTCTTCCGTGGGTTGctc-------------------------ttgctcctgacc---------ctcctcttcctccgcttcatcctcct-ccgcat
droSim1	chr2L:10541288-10541421 +	CATGTTTAGATCTGACCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTT------CTTTTTCGTGGGCAGCTC-------------------------TCGCTCCTGACC---------CTCCTCTTCCTCCGCTTCGTCTTCCC-CCGCAT
droSec1	super_3:6159513-6159646 +	CATGTTTAGATCGGACCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTG------CTTTTTCGTGGGCAGCTC-------------------------TCGCTCCTGACC---------CTCCTCTTCCTCCGCTTCGTCTTCCC-CCGCAT
droYak2	chr2L:7146365-7146495 +	CATGTTCAAATCGGAGCCAAAGGTGGGCGAGAGG---GGCTGTGAGCAGCCGTTGCTGGCGGTGTTCTGTCTCTG------CTCCTCCGCCGGCTGCTG-------------------------TTGCTCCTGACC---------CTCCTCGTCCTCCGCGTCTTCCTCGCC----GT
droEre2	scaffold_4929:14689286-14689416 -	CATGTTCAAATCGGACCCAAAGGTAGGTGAGAGG---GGCTGGGAGCAGCCGTTGCTGGCGGTATTCTGCCTCTG------CTCCTCCACCGGCTGCTG-------------------------TTGTTCCTGAAC---------CACCTCGTCCTCTGGTTCGTCATCGCC----TT
droAna3	scaffold_12916:14589365-14589483 +	CATGTTCAGATCGGAGCCAAAAGTGGGTGAAAGC---TGCTGGGAGCAGTTATCGCCCTCAGCTTGTTCCTTTTCCTC-AGTATCCTCGTCT------------------------------------------GCCT---------CCTCTGTTTCCCCATCTTCGTTCTC----GT
dp4	chr3:14693225-14693346 -	CATGTTCAGATCCGATCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATGTGCTGCTCCTCCCGCTCTCCCGTTGGCAG----------------------------------------TTCCTCATCCT---------CCTCGTCCGGGTCTAG----TT
droPer1	super_4:2921871-2921992 +	CATGTTCAGATCCGATCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATGTGCTGCTCCTCCCGCTCTCCCGTTGGCAG----------------------------------------TTCCTCATCCT---------CCTCGTCCGGGTCTAG----TT
droWil1	scaffold_180708:9012148-9012236 -	CATGTTTAAATCTGAACCAAATGTGGCCGACAAT---GGTTGAGAGCAGCCATTTGTTA------------------------------------G----------------------------------------TTGTTCATCCT---------CTTCA-CAGGCTCCAGCAGCTT
droVir3	scaffold_12963:15905415-15905563 -	CATGTTTAAATCGGAGCCATAGGTAGCCGACAATGCCGGCTGCGAGCAGCCATTGCTTAGGGTTATCTGCGGCTTCTGTGG------TGCCT----GTTCCGTTGCGTTAATCGGCTGGGAGTAGAGCTCACCGGC---------------GGCCTCCAGATCGCTGTCGCC----TC
droMoj3	scaffold_6500:18910664-18910815 -	CATGTTCAGGTCGGAGCCGTAGGTTGCCGAAAGA---GGCTGCGAGCAGCAGTCGCCCAAGGTTTGCAGTTGCTTCTGTGG------CGCTG----GCTCGGCCGCTTTGATTGGCTGCGAGTAGAGCTCGTCAGC---------TGCCTCGGCGTCCAGATCGCTGTCGCC----CT
droGri2	scaffold_15252:8305987-8306138 -	CATGTTCAAATCGGAGCCATAGGTGGCCGACATG---GGTTGTGACCACTCATTGGCCGATGCTTGCGGTTCCTTCTCGGG------TTCCG----GTTCCGCTTCGGTCGCTGGCTGGGAATAGGGTTCCTCAGC---------TGCATTCGCTTCCTGATCGCTGTCCTC----CT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:10741869-10742002 +	NA	CATGTTTAGATCGGA-----CCCAAAGGTGGGCGACAAG---GGCTGGGAGCAGCAGTTGCTGGCGGTATTC---TGAAGCTGCTCTTCCGTGGGTTGCTCTT---------------------------GCTCCTG----------------------------ACCCTCCTCT---TCCTCCGCTTC------ATCCTCC--------------TCCGCAT
droSim1	chr2L:10541288-10541421 +	1	CATGTTTAGATCTGA-----CCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTC---TGAAGTTTCTTTTTCGTGGGCAGCTCTC---------------------------GCTCCTG----------------------------ACCCTCCTCT---TCCTCCGCTTC------GTCTTCC--------------CCCGCAT
droSec1	super_3:6159513-6159646 +	1	CATGTTTAGATCGGA-----CCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTC---TGAAGTTGCTTTTTCGTGGGCAGCTCTC---------------------------GCTCCTG----------------------------ACCCTCCTCT---TCCTCCGCTTC------GTCTTCC--------------CCCGCAT
droYak2	chr2L:7146365-7146495 +	1	CATGTTCAAATCGGA-----GCCAAAGGTGGGCGAGAGG---GGCTGTGAGCAGCCGTTGCTGGCGGTGTTC---TGTCTCTGCTCCTCCGCCGGCTGCTGTT---------------------------GCTCCTG----------------------------ACCCTCCTCG---TCCTC---CGC------GTCTTCC--------------TCGCCGT
droEre2	scaffold_4929:14689286-14689416 -	10	CATGTTCAAATCGGA-----CCCAAAGGTAGGTGAGAGG---GGCTGGGAGCAGCCGTTGCTGGCGGTATTC---TGCCTCTGCTCCTCCACCGGCTGCTGTT---------------------------GTTCCTG----------------------------AACCACCTCG---TCCT---CTGG------TTCGTCA--------------TCGCCTT
droEug1	scf7180000409554:3760859-3760992 +	1	CATGTTTAAATCGGA-----ACCAAATGTTGGTGAAAGA---GGCTGGGAGCAGCCGTTGCTTGCGTTATTC---TGCTGCTGCTCCTCCACTGGCTGCTGTT---------------------------TCTCCTG----------------------------ACCTTCCTCC---TCATCATCTTG------GTCTTCA--------------TCAACAT
droBia1	scf7180000302422:2382746-2382879 -	21	CATGTTTAGGTCGGA-----TCCATAGGTGGGAGAAAGG---GGCTGGGAACAGTTGTTGCTGGCGAAGTTT---TGCGGCTGCTCTTCCACCGGCTGCTGTT---------------------------GCTCTTG----------------------------ACCTTCTTCC---TCATCCTCCAG------GCCCTCG--------------GGGCCTT
droTak1	scf7180000415385:189147-189283 +	5	CATGTTCAAATCGGA-----GCCAAAGGTGGGCGAAAGC---GGCTGGGAACAGCCGTTGCTGGCGGAATCC---TTGCCCTGCTCCTCCGCCGGCTGCTGTTCCG------------------------CCTCCTG----------------------------ACCCTCCTCC---TCCTCCTCGAG------GTCCTCG--------------CCGCCGT
droEle1	scf7180000490971:131834-131988 -	12	CATGTTTAGATCTGA-----GCCAAAGGTGGGTGAAAGT---GGCTGGGAGCAGCCGTTGTTGGCGGAATTC---GGCTGCTCCTCCTCCGCCGGCGGCTGTG---------------------------GCTCCTGCCCTTCCTCCT-C---------CTCCAAA------------TCCTCCTCTTCCGGCTCCT-----CTTCAT-C--CTCCTCCTCGC
droRho1	scf7180000780267:27189-27328 +	3	CATGTTAAGGTCCGA-----GCCAAAAGTGGGTGAAAGT---GGCTGCGAGCAGCCGTTGTTGGCCGAATTCGGCTGCTGCTCCTCCTCCGCCGGCTGCTGTG---------------------------GCTCCTG----------------------------GCCTTCTTCCTCATCATTAGGCTC------CCCCTCC--------------TCTTCGT
droFic1	scf7180000454111:160465-160601 +	13	CATGTTGAGATCCGA-----ACCGAAGGTGGGCGAAAGC---GGCTGGGAGCATCCGTTGCTGGGGGAGTTC---TGCTGCTCCTTCTCCGTCGGCTGCTGTG---------------------------GCTCCTG----------------------------GCCTTCCTCCTCCTCGTCCTCCGC------CTCCTCC--------------TCTTCAT
droKik1	scf7180000302472:2579939-2580081 -	8	CATGTTTAGATCGGA-----ACCAAAGGTGGGCGACAGG---TTCTGCCCGCAGTCGGAGGCC---------------TCTTTCTCCTCCTCTGGCTTCTCAG---------------------AGTCTTCCTCCTG------ATTAT-------------------CCTCCACC---TCATCACCCTCTGCCTCAG-----GATCTT-C--CACTTCATCCT
droAna3	scaffold_13117:2651271-2651404 -	3	CAGCATTAGGGCGATCCTCCGCCAGTGGTTGATCGAA-G---GCATGGGATCCACCC----CAGCGTCTATC---TGAAAACGATGTTTATCCACCTGCTCCT---------------------------GCTCCTG----------------------------CTCCTCATCC---TCCTTCCCTTC------GTCTTCG--------------TCATCAT
droBip1	scf7180000396572:2390673-2390782 -	7	CATGTTCAGGTCGGA-----GCCAAAAGTGGGTGAAAGC---TGTTGCGAGCAATTATCTCCCTCTAC---------------------------TACATCCT---------------------------TCTCCTC----------------------------AGTATCCTCA---TCGTCCTCCAC------ATCTTCA--------------TTCTCTT
dp4	chr3:14693225-14693346 -	5	CATGTTCAGATCCGA-----TCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATG---TGCTGCTCCTCCCGC---------TCT----------------------------------------------CCCGTTGGCAGTTCCTCA---------------TCCTCCTC------GTCCGGG--------------TCTAGTT
droPer1	super_4:2921871-2921992 +	2	CATGTTCAGATCCGA-----TCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATG---TGCTGCTCCTCCCGC---------TCT----------------------------------------------CCCGTTGGCAGTTCCTCA---------------TCCTCCTC------GTCCGGG--------------TCTAGTT
droWil1	scaffold_180708:9012130-9012236 -	1	CATGTTTAAATCTGA-----ACCAAATGTGGCCGACAAT---GGTTGAGAGCAGCCATTTGTTAG------------------------------TTGTTCAT---------------------------CCTCTTC----------------------------ACAGGCTCCA---GCAGCTTGCTC------ACCCCCC--------------TCAGCGT
droVir3	scaffold_12963:15905405-15905563 -	4	CATGTTTAAATCGGA-----GCCATAGGTAGCCGACAATGCCGGCTGCGAGCAGCCATTGCTTAGGGTTATC---TGCGGCTTCTGTGGT------GCCTGTTCCGTTGCGTTAATCGGCTGGGAGT---AGAGCTC----------------------------ACCGGCGGCC---------TCCAG------ATCGCTG----TCGCCTCCTGTCGCGAT
droMoj3	scaffold_6500:3051871-3052002 +	7	CGTGCGTAGCT---G-----CTCGTGGCTGGGTGGCGTG---GCATTGTAGAGT-CTCAGC--------TGCTGCTGCTGCTGCTGCTCAGACTCCTGCTCTT---------------------------GCTCATG----------------------------CCCCTCCAGC---TCCTCCTCTTCAGCCTCGCTGTC-------------GCTCAGCGG
droGri2	scaffold_15252:8305990-8306138 -	4	CATGTTCAAATCGGA-----GCCATAGGTGGCCGACATG---GGTTGTGACCACTCATTGGCCGATGCTTGC---GGT---TCCTTCT---CGGGTTCCGGTTCCGCTTCGGTCGCTGGCTGGG------AATAGGG----------------------------TTCCTCAGCT---GCATTCGCTTC------CTGATCG--------------CTGTCCT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CATGTTTAGATCGGACCCAAAGGTGGGCGACAAG---GGCTGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGCTG------CTCTTCCGTGGGTTGctc-------------------------ttgctcctgacc---------ctcctcttcctccgcttcatcctcct-ccgcat

Size

Hit Count

Total Norm

droSim1

CATGTTTAGATCTGACCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTT------CTTTTTCGTGGGCAGCTC-------------------------TCGCTCCTGACC---------CTCCTCTTCCTCCGCTTCGTCTTCCC-CCGCAT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................................................................CAGCTC-------------------------TAGATCCTGACC---------.................................	18	1	1.00	0.00	0.00	1.00	0.00

droSec1

CATGTTTAGATCGGACCCAAAGGTGGGCGACAAG---GGATGGGAGCAGCAGTTGCTGGCGGTATTCTGAAGTTG------CTTTTTCGTGGGCAGCTC-------------------------TCGCTCCTGACC---------CTCCTCTTCCTCCGCTTCGTCTTCCC-CCGCAT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................................GATGGGAGCAGCAGTTGCTGG.......................................................................................................................	21	1	1.00	0.00	1.00	0.00
...............................................AGCAxTTGCTGGCGGTATG................................................................................................................	18	1	1.00	0.00	1.00	0.00

droYak2

CATGTTCAAATCGGAGCCAAAGGTGGGCGAGAGG---GGCTGTGAGCAGCCGTTGCTGGCGGTGTTCTGTCTCTG------CTCCTCCGCCGGCTGCTG-------------------------TTGCTCCTGACC---------CTCCTCGTCCTCCGCGTCTTCCTCGCC----GT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........................................TGTGAGCAGCCGTTGCTGGCG.....................................................................................................................	21	1	18.00	3.00	8.00	0.00	7.00	0.00
........................................TGTGAGCAGCCGTTGCTGGCGG....................................................................................................................	22	1	11.00	7.00	1.00	0.00	3.00	0.00
........................................TGTGAGCAGCCGTTGCTGGCGGT...................................................................................................................	23	1	3.00	1.00	1.00	0.00	1.00	0.00
........................................TGTGAGCAGCCGTTGCTGGCGGC...................................................................................................................	23	1	2.00	0.00	1.00	0.00	1.00	0.00
.........................................GTGAxCAACCGTTGCTGGC......................................................................................................................	18	1	2.00	0.00	1.00	0.00	0.00	1.00
........................................TGTGAGCAGCCGTTGCTGGCGGTT..................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................................................CTC------CTTCTCCGCCGGCTG..................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.......................................CTGTGAGCAGCCGTTGCTGGCG.....................................................................................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
........................................TGGGAGCAGCCGTTGCTGGTGGT...................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................TGTGAGCAGCCGTTGCTGGCGGG...................................................................................................................	23	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................TGTGAGCAGCCGTTGATGGCGGG...................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
.........................................................................................CCGGCTGCTG-------------------------TTTCTCCTGACC---------C................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
....................AGGTGGGCTGGAGG---GGCT.........................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
........................................TGTGAxCAACCGTTGCTGGC......................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..................AAGGGTGGGCGAGAGG---GGC..........................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

CATGTTCAAATCGGACCCAAAGGTAGGTGAGAGG---GGCTGGGAGCAGCCGTTGCTGGCGGTATTCTGCCTCTG------CTCCTCCACCGGCTGCTG-------------------------TTGTTCCTGAAC---------CACCTCGTCCTCTGGTTCGTCATCGCC----TT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................ATGTTGGCGGTATTCTGC............................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

CATGTTCAGATCGGAGCCAAAAGTGGGTGAAAGC---TGCTGGGAGCAGTTATCGCCCTCAGCTTGTTCCTTTTCCTC-AGTATCCTCGTCT------------------------------------------GCCT---------CCTCTGTTTCCCCATCTTCGTTCTC----GT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................AGC---xCCTGGGAGCAGTTATC............................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

dp4

CATGTTCAGATCCGATCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATGTGCTGCTCCTCCCGCTCTCCCGTTGGCAG----------------------------------------TTCCTCATCCT---------CCTCGTCCGGGTCTAG----TT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................................................................................................................CTCGTCATCCT---------CCTCGTCCG.............	20	1	1.00	1.00	0.00	0.00	0.00

droPer1

CATGTTCAGATCCGATCCAAATGTGGGGGACAAG---GGCTGGGAACAGCCATTGCTCTGAGTGATGTGCTGCTCCTCCCGCTCTCCCGTTGGCAG----------------------------------------TTCCTCATCCT---------CCTCGTCCGGGTCTAG----TT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...............................................................................................G----------------------------------------TTCCTGATCCT---------CTTCGTC...............	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droWil1

CATGTTTAAATCTGAACCAAATGTGGCCGACAAT---GGTTGAGAGCAGCCATTTGTTA------------------------------------G----------------------------------------TTGTTCATCCT---------CTTCA-CAGGCTCCAGCAGCTT

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

CATGTTTAAATCGGAGCCATAGGTAGCCGACAATGCCGGCTGCGAGCAGCCATTGCTTAGGGTTATCTGCGGCTTCTGTGG------TGCCT----GTTCCGTTGCGTTAATCGGCTGGGAGTAGAGCTCACCGGC---------------GGCCTCCAGATCGCTGTCGCC----TC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
.........................................................................................................CGTTAAACGGCxGGGAGTA......................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
................................................................................................................CGGCTGAGAGGAGAGCTC................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00
........................................................................................................GCGTTAAACGGCxGGGAGT.......................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
.......................TAGGCGACAATGCCGGCTTC.......................................................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................................................................CTCGCCGGx---------------GGCCTCCA...................	16	1	1.00	0.00	1.00	0.00	0.00	0.00

droMoj3

CATGTTCAGGTCGGAGCCGTAGGTTGCCGAAAGA---GGCTGCGAGCAGCAGTCGCCCAAGGTTTGCAGTTGCTTCTGTGG------CGCTG----GCTCGGCCGCTTTGATTGGCTGCGAGTAGAGCTCGTCAGC---------TGCCTCGGCGTCCAGATCGCTGTCGCC----CT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......................................GCAGCGAGCAGCAGTGGC..........................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.............................................GCAGCAGTCGACCAAAGTT..................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00

droGri2

CATGTTCAAATCGGAGCCATAGGTGGCCGACATG---GGTTGTGACCACTCATTGGCCGATGCTTGCGGTTCCTTCTCGGG------TTCCG----GTTCCGCTTCGGTCGCTGGCTGGGAATAGGGTTCCTCAGC---------TGCATTCGCTTCCTGATCGCTGTCCTC----CT	Size	Hit Count	Total Norm	V109 Male body
...............................................................................................................CTGGxxGTAAATAGGGTTCCT..............................................	19	1	21.00	21.00
...............................................................................................................CTGGxxGTGAATAGGGTTCCT..............................................	19	1	2.00	2.00
...............................................................................................................CTGGxxGTCAATAGGGTTCCT..............................................	19	1	1.00	1.00
...............................................................................................................CTGGxxGTAAATAGGGTTCC...............................................	18	1	1.00	1.00

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