dme-mir-4912- 12- and 20-way alignments

dme-mir-4912	chr2L:4829980-4830039 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	mirtron

Legend:

   mature strand at position 4830017-4830039
   star strand at position 4829980-4830001
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2L:4829965-4830054 -	CATTCGCAGCTTTAAGTGAGTAGTC---G--------------------TATGTTTATTA---------------------AGATT-TACT----TTCTATA--AATTAATGTCCA-----------------------CTACTTTTAGTCTCTATGACGATGA
droSim1	chr2L:4699797-4699886 -	CATTCGCAGCTTTAAGTGAGTAATC---G--------------------TATGTTTATTA---------------------AGATT-CACT----TTCTATA--AACTAATTTGCA-----------------------CTACTTGTAGTCTCTATGACGACGA
droSec1	super_5:2925673-2925762 -	CATTCGCAGCTTTAAGTGAGTAATC---G--------------------TATGTTTATTA---------------------AGATT-CACT----TTCTATA--AACTAATTTGCA-----------------------CTACTTGTAGTCTCTATGACGACGA
droYak2	chr2L:4839794-4839887 -	CATTCGCAGCTTTAAGTGAGTAAAA---C--------------------TATGTCTATTA----------GGTG-------AAATT-AACT----TTCTATA--AATTACTTTTCT-----------------------TTATTTTTAGTCTATATGACGACGA
droEre2	scaffold_4929:4910720-4910828 -	CATTCGCAGTTTTAAGTGAGTAAAA---T--------------------TAGGTTTAATTTGGTTTATTAGGAGAATTTTAAAAT--TAC-----TTTTTTA--AATTGCTTTTCA-----------------------TTATTTGCAGTCTCTATGACGACGA
droAna3	scaffold_12916:9399289-9399374 -	CATTCGAAGCTTCAAGTATGTTAAGA---------AATCCACGATT-----------------------------------TTT--T-TATATTTTCATACA--AAAT-----TC------------------------ATTTTTTCAGCTTGTACGACGACGA
dp4	chr4_group3:3587822-3587933 -	CATACGCACATTTAAGTGAGTAGGAA---------AAATCGTTGTTTAAGCTGTTTACTG---------------------CGATTGTA--------------------CTTTACTGTATTTACTGTATTTGGTA--CATGCCTTGCAGCCTCTATGATTCCGA
droPer1	super_1:5067398-5067508 -	CATACGCACATTTAAGTGAGTAGGA----------AAATCGCTGTTTAAGCTGTTTACTG---------------------CGATTGTA--------------------CTTTACTGTATTTACTGTATTTGGTA--CATGCCTTGCAGCCTCTATGATTCCGA
droWil1	scaffold_180772:1562219-1562313 -	CATTAAAACGTTTAAGTGAGTAGTAAATCTTGGTTAAC----------------CCAATA---------------------CGATTT-CATTGGCGTTTATA--AATT-----CC------------------------TCCACCTTAGCCTTTACGACGACGA
droVir3	scaffold_12963:8507047-8507138 +	CATACGCACATTCAAGTATGTCA---------------------------------ACTA---------------------TGAT----------------A--AAATGCTTTGCAGTACTCTTTAAATATTGTATTCTCATTCGATAGCCTCTATGACGACGA
droMoj3	scaffold_6500:1118880-1118971 +	CATACGTACATTCAAGTAAGCCCAA---T-TCGCC-------GACG-----------------------------------TTA--T-GGTATTCATATACAAATGCTAATCATTT-----------------------ATCCCTTTAGCCTCTATGACGACGA
droGri2	scaffold_15252:11699277-11699378 +	CATACGCACCTTCAAGTATGTGCAA---T-GGGTAAACCATATGTGAGAGATTTAAACCT---------------------TAATTTTA--------------------CTTTCCTATATCT-----------------GCCCAAACAGTCTGTACGATGACGA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2L:4829965-4830054 -	NA	CATTCGCAGCTTTAAGTGAGTAGTCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TTACTTTCTATAAAT----------------------------------------------------T-AATGT--CC-----ACTACTTTTAGTCTCTATGACGATGA
droSim1	chr2L:4699797-4699886 -	1	CATTCGCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGACGACGA
droSec1	super_5:2925673-2925762 -	1	CATTCGCAGCTTTAAGTGAGTAATCGT---ATGTTTATTAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT-TCACTTTCTATAAAC----------------------------------------------------T-AATTT--GC-----ACTACTTGTAGTCTCTATGACGACGA
droYak2	chr2L:4839794-4839887 -	1	CATTCGCAGCTTTAAGTGAGTAAAACT---ATGTCTATTA--------------------------------------------GGT---------------------------------------------------------------------------------------------------------------------GA----AAT-TAACTTTCTATAAAT----------------------------------------------------T-ACTTT--TC-----TTTATTTTTAGTCTATATGACGACGA
droEre2	scaffold_4929:4910720-4910828 -	1	CATTCGCAGTTTTAAGTGAGTAAAATT---AGGTTTAATTT--------------------------------GG-TTTATTA-GGAGAA--------------------------------------------T-TTTAA------------------------------------------------------------AATT----------A-C-TTTTTTAAAT----------------------------------------------------T-GCTTT--TC-----ATTATTTGCAGTCTCTATGACGACGA
droEug1	scf7180000409005:708020-708177 -	1	AATTCGCAGCTTCAAGTAAGTATATGT---ATATATGTATATATTATTC-------------------------------------------------------AAATCGA------------------------------TGA--------------------------------------------TTAAATATAGATTAG----GTCAATTC--------------C-------TATTTGAATCCATTTATTCATAAAGGTTCCTTTTTATTCAAAA-TA--TTCCTAT-----TTTATTTTCAGACTCTACGACGACGA
droBia1	scf7180000302188:1402569-1402698 -	1	CATACGCAGTTTCAAGTGAGTGGGGAT---TT----------------------TGGGGAG-------------------------------------------------------------------------TCATTAAAGC-CTTTAAAGATGTCGAACTTTATGGTA-----------------TTAAG--------C------------AAGCAT--------------------------TTAATGGA-------------------------TT-T-ATG----AACGTATATACTTCCAGACTCTACGACGACGA
droTak1	scf7180000415705:123599-123784 -	1	CATAAAAAGCTTCAAGTGAGTGGGGATAGCAAGTTTATA---------------------------GCACATAGGTTCTATTA---------------------CAA---------------------------CAGATCTACATATCTAAAGTCATTGAAATTT--GGCCTAAAATTGCTTTTATATTAGTTATTTTATTA----------------------------------------------------ACATAAATGATAAAGCTTTAATAAAT-TC--TCCCCAT-----TGTAATTCCAGACTCTACGACGACGA
droEle1	scf7180000491046:2483308-2483395 -	1	GATTTACAT--TCAATCAAGTTTTTGT---TC------------------------------------------------------------------------------------------------------------AAGT--------------------------------------------TTAAGTACTTATTGA----CTCAATTT--------------CACT-----------------------------------------------------TT--TT-----TAAATTTATAGACTCTATGACGACGA
droRho1	scf7180000768274:29807-29997 +	1	CATTCGTACCTTCAAGTGAGTGGGGAT---TTGGGAA-----------------------TTCATTCCAAATAGATTTTATAAAGGG-GACATTTATAATGTTCAAATTCAAGACCCCCAGACAATTTTGTTCCTTTTTAAAGTTATTTATTTC------------------------------AAGTTCGTTAATTTACTAA----TTTAATTT--------------TGCC-------------------------------------------------TTACT----A----ATGTTTTTCCAGGCTCTTCGACGATGA
droFic1	scf7180000453842:1425509-1425600 +	1	TATTCGCACCTTCAAGTAAGTGGTTGT---ACATT----------ATAC-------------------------------------------------------A--------------------------------------------------------------------------------------AATATCGA--AATGAGTTCAATAC--------------------------------------------------------------------CATTC--CT-----ATTATCTCCAGGCTTTATGACGACGA
droKik1	scf7180000302472:3508957-3509047 -	1	CATACGCACCTTCAAGTGAGTCTAATTATTA-------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------C------------------------TCTTTTTTTGTAT----GTTTTA-------------------------AATT-CAGTCT--CT-----GATCCTTGCAGCCTCTATGATGATGA
droAna3	scaffold_12916:9399289-9399374 -	1	CATTCGAAGCTTCAAGTATGTTAAGAA---AT----------------------CCA-----------------------------------------------------------------------------C------------------------------------------------------------------GATTT----TTTTA------------------------TAT----T------TTCATACA---------------AA---------------ATTCA-TTTTTTCAGCTTGTACGACGACGA
droBip1	scf7180000396535:1966691-1966779 -	1	CATTAGGAGTTTCAAGTGGGTTAAGAA---AT------------------------------------------------------------------------------------------------------------------------------------------------------------------ACCCATAGCTTT----ACTTA------------------------TAT----T------TTCATTAA-----------------------GA-------ATTCG-TTATTTCAGCCTGTACGATGACGA
dp4	chr4_group3:3587822-3587933 -	1	CATACGCACATTTAAGTGAGTAGGAAA---AA----------------------TCG-----------------------------------------------------------------------------TTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGATTCCGA
droPer1	super_1:5067398-5067508 -	1	CATACGCACATTTAAGTGAGTAGGAAA---AT-----------------------CG-----------------------------------------------------------------------------CTGTTTAAGCTGTTTACTGC--------------------------------------------------------GATTG--------------TACTTTACTGTAT----TTACTGTA-------------------------TT-TGGTA----C-----ATGCCTTGCAGCCTCTATGATTCCGA
droWil1	scaffold_180772:1562219-1562313 -	2	CATTAAAACGTTTAAGTGAGTAGTAAA---TC-------------TTGGTTAACCCA-----------------------------------------------------------------------------A------------------------------------------------------------------TAC------GATT--------------------------------TCATTGGCGTTT--------------------------ATA----AATTCCT-CCACCTTAGCCTTTACGACGACGA
droVir3	scaffold_12963:8507047-8507138 +	1	CATACGCACATTCAAGTATGTCAACTA---T-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GAT------------AAAATGCTTTGCAGTAC----TCTTTAAA-------------------------TA-TTGTAT--TC-----TCATTCGATAGCCTCTATGACGACGA
droMoj3	scaffold_6500:1118880-1118971 +	1	CATACGTACATTCAAGTAAGCCCAATTCGCCG------------------------------------------------------------------------------------------------------------AC--------------------------------------------------------------GT----TAT------------------------GGTAT----T------CATATACA---------------AATGCT-AATCA--TT-----TATCCCTTTAGCCTCTATGACGACGA
droGri2	scaffold_15252:11699277-11699378 +	2	CATACGCACCTTCAAGTATGTGCAATGGGTAA--------------------ACCAT-----------------------------------------------------------------------------ATGTGAGAGATTTAAACCTT--------------------------------------------------------AATTT--------------TACTTTCCTATAT-----------------------------------------------------CTG-CCCAAACAGTCTGTACGATGACGA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CATTCGCAGCTTTAAGTGAGTAGTC---G--------------------TATGTTTATTA---------------------AGATT-TACT----TTCTATA--AATTAATGTCCA-----------------------CTACTTTTAGTCTCTATGACGATGA

Size

Hit Count

Total Norm

droSim1

CATTCGCAGCTTTAAGTGAGTAATC---G--------------------TATGTTTATTA---------------------AGATT-CACT----TTCTATA--AACTAATTTGCA-----------------------CTACTTGTAGTCTCTATGACGACGA

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

CATTCGCAGCTTTAAGTGAGTAATC---G--------------------TATGTTTATTA---------------------AGATT-CACT----TTCTATA--AACTAATTTGCA-----------------------CTACTTGTAGTCTCTATGACGACGA

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CATTCGCAGCTTTAAGTGAGTAAAA---C--------------------TATGTCTATTA----------GGTG-------AAATT-AACT----TTCTATA--AATTACTTTTCT-----------------------TTATTTTTAGTCTATATGACGACGA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
........GCTTTAAGTGACTAAAA---G--------------------...................................................................................................................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
...............GTGAGTAAAA---C--------------------TATGACTAAT.........................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00	0.00
...............................................................................................TTCTAGA--CATTACTTTTCT-----------------------.........................	19	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

CATTCGCAGTTTTAAGTGAGTAAAA---T--------------------TAGGTTTAATTTGGTTTATTAGGAGAATTTTAAAAT--TAC-----TTTTTTA--AATTGCTTTTCA-----------------------TTATTTGCAGTCTCTATGACGACGA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........TTTTGAATGAGTAAAA---T--------------------T..................................................................................................................	18	1	4.00	0.00	0.00	0.00	4.00
.......ATTTTTAAGxGAGTAAAA---T--------------------T..................................................................................................................	19	1	3.00	0.00	0.00	0.00	3.00
..................AGTTAAA---T--------------------TxGGTTTAATT........................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00
.....................AAAG---C--------------------TAGGTTTAATTTGGT....................................................................................................	20	1	1.00	0.00	0.00	0.00	1.00
....................TAAAG---C--------------------TAGGTTTAATTTGGT....................................................................................................	21	1	1.00	0.00	0.00	0.00	1.00
...................GTAAGA---T--------------------TAGCTTTAATT........................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

CATTCGAAGCTTCAAGTATGTTAAGA---------AATCCACGATT-----------------------------------TTT--T-TATATTTTCATACA--AAAT-----TC------------------------ATTTTTTCAGCTTGTACGACGACGA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
............................................TT-----------------------------------TTT--T-TATATATTCTTA................................................................	18	2	0.50	0.00	0.00	0.50	0.00
......................................CCACGAAT-----------------------------------TTG--T-TATATT......................................................................	18	1	1.00	0.00	0.00	0.00	1.00
......................................TCACGATT-----------------------------------TTG--T-TATATT......................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................TATATTCATACA--AAAT-----CC------------------------A........................	19	1	1.00	0.00	0.00	0.00	1.00
......................................CCACGATT-----------------------------------TTG--T-TATATA......................................................................	18	1	1.00	0.00	0.00	0.00	1.00

dp4

CATACGCACATTTAAGTGAGTAGGAA---------AAATCGTTGTTTAAGCTGTTTACTG---------------------CGATTGTA--------------------CTTTACTGTATTTACTGTATTTGGTA--CATGCCTTGCAGCCTCTATGATTCCGA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

CATACGCACATTTAAGTGAGTAGGA----------AAATCGCTGTTTAAGCTGTTTACTG---------------------CGATTGTA--------------------CTTTACTGTATTTACTGTATTTGGTA--CATGCCTTGCAGCCTCTATGATTCCGA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................................................................................................................GTATTTACTGTATTAAGTA--...........................	19	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

CATTAAAACGTTTAAGTGAGTAGTAAATCTTGGTTAAC----------------CCAATA---------------------CGATTT-CATTGGCGTTTATA--AATT-----CC------------------------TCCACCTTAGCCTTTACGACGACGA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................................................................TA-CATTGGCGTTTATA--TATT-----...................................................	20	1	1.00	0.00	1.00	0.00	0.00

droVir3

CATACGCACATTCAAGTATGTCA---------------------------------ACTA---------------------TGAT----------------A--AAATGCTTTGCAGTACTCTTTAAATATTGTATTCTCATTCGATAGCCTCTATGACGACGA

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

CATACGTACATTCAAGTAAGCCCAA---T-TCGCC-------GACG-----------------------------------TTA--T-GGTATTCATATACAAATGCTAATCATTT-----------------------ATCCCTTTAGCCTCTATGACGACGA

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

CATACGCACCTTCAAGTATGTGCAA---T-GGGTAAACCATATGTGAGAGATTTAAACCT---------------------TAATTTTA--------------------CTTTCCTATATCT-----------------GCCCAAACAGTCTGTACGATGACGA

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