dme-mir-4950- 12- and 20-way alignments

dme-mir-4950	chr3R:3277173-3277265 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 3277226-3277247
   star strand at position 3277187-3277208
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3R:3277158-3277280 +	TTTATACATTTGT-TTATAATGCAC---ATAATAAA----------------TGCCAACCATTCATCATGAAATTATAAATAGTATCATTTCA----------------------------------------------AGATGCATGGTAAGGC---------------------------TTTATTTTGTTTTGCAATCAAAGACATCTTTCTT
droSim1	chr3R:3321450-3321569 +	tttatatatattatttattatGCTC---AGCATAAA----------------TGCCAAGCATTCGTCGTGaaattataaattatatattatat----------------------------------------------aaattCATGGTAAGGC---------------------------TTCATTTTTTAACGCAGTCTAAGACATC----TT
droSec1	super_6:3368064-3368189 +	tttatatatattatttattatGCTC---AGCATAAA----------------TGCCAAGCATTCGTCGTGaaattataaattatatattat-------------------------------------------ttCT-AGATTCATGGTAAAGT---------------------------TTCATTTTGTAACGCAGTCTAAGACATCTTTCTC
droYak2	chr3R_random:971773-971840 +	aattataattttaattaGCATGTTTAATTT----------------TTA-------------------TGTAA-----------------------------------------------------------------------------------------------------------------TTTTGTAACATTGTCAAAGATTTCTTTCTT
droEre2	scaffold_4770:3542423-3542469 +	aataataattttaatttGCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCACTGTCACTGTCACTGGCTTC---CTT
droAna3	scaffold_13340:3059605-3059688 +	TTTAAACATTTTT-TT------TTT---AATATAACTACTTAACTTTTTTGT------------AACCCAACATCATATGAAAAATAATTTACAAATTTGCAATATGATTTAATGAACCTGGTTTTATGAT----------------------------------------------------------------------------------CAT
dp4	Unknown	CTCCCATTTACAT-T---------CAGTTT----------------TTA-------------------TAACAT----------------------------------TTTAATGAGGATCGTTTTACGATCACTCTGG--------CGTGT---GTGCTGGTAT----------TTATAAA-------------------------CATTTTAAA
droPer1	Unknown	CTCCCATTTACAT-T---------CAGTTT----------------TTA-------------------TAACAT----------------------------------TTTAATGAGCCTCGTTTTACGATCACTCTGG--------CGTGT---GTGCTGGTAT----------TTATAAA-------------------------CATTTTGAT
droWil1	Unknown	TCTTCACATATTT-T---------TGTTAATTATGATACCAAATCCAATTCTTGCCAGAAATTTGAAGTAA--------------------------------------------------------------TATTGA--------AGTAA---AACTTAATATTAAGCATTATTAATGCT-------------------------TTTTTTGAG
droVir3	Unknown	ttaattaatatat-t---------ctgtat----------------cag-------------------tatcat-----attttagtatgtat------------------------------------atataaatta---------------------------------------------cgatttattttaattt-atatacatatattaa
droMoj3	Unknown	ctaattgattaat-t---------taattt----------------tat-------------------tttttt-----attatatCACATTT------------------------------------ATTT---------------------T---------------------------TATTTTTTCTTTCGCAATCGATTAGTT----CTT
droGri2	Unknown	ttaattattattattttttt---------t----------------tta-------------------tttcaA-----ATTTTAGCTTATAG------------------------------------ATATTTATTG--------CT---------------------------------TCTGTTTTTTTTTGTTGTT-AAAACATTTTTTAT

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:3277158-3277280 +	NA	TTTATACATT-T-GTT--------------TATAATGCA----CA------------------TAATAAATGCCAACCATTCATCATGAAATTATAAATAG-------------------T------------ATCA--------------TTTC---------------------------------------------------------------------------------------AAGAT--------GCATGGTAAGGCTTTAT-------TTTGTTTTGCAATCAAAGACATCTTTCTT
droSim1	chr3R:3321450-3321569 +	363	TTTATATATA-TTATT--------------TATTATGCT----------------------CAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTA-------------------T----------ATATT----------------ATA---------------------------------------------------------------------------------------TAAAT--------TCATGGTAAGGCTTCAT-------TTTTTAACGCAGTCTAAGACA----TCTT
droSec1	super_6:3368064-3368189 +	101	TTTATATATA-TTATT--------------TATTATGCT----------------------CAGCATAAATGCCAAGCATTCGTCGTGAAATTATAAATTA-------------------T----------ATATTA--------------TTTC---------------------------------------------------------------------------------------TAGAT--------TCATGGTAAAGTTTCAT-------TTTGTAACGCAGTCTAAGACATCTTTCTC
droYak2	chr2L_random:3663454-3663574 -	7020	TTTAGCCAAG-T-TAA--------------TTTGGT-------------------------AAAAACAAAAACCAGAAACCGGCTACACGATGAAACGCTA-------------------A----------ATGCCA--------------TTTT---------------------------------------------------------------------------------------AGCAG--------TC-AGGTAATTATATAT-------TTATTTTTAAATTTAAACCCATTTTTTAT
droEre2	scaffold_4784:2237866-2237984 -	2014	TTTCCAAATT-T-GAA--------------TGCAGATTT----TTAGA-----------------CAATTGCTCCAGAAACATTT-----------AGAGG-------------------T----------ATGCCA--------------CTTC----------A-------------AAAT-------------ACGATA-------------------------------------------AT--------TGAAGGTTGAATTAT----------GGACTTTAGA-ACTTCAGCCTTCTTTTT
droEug1	scf7180000405460:7334-7455 +	36	TTTAACAAATGT---TTAT-----------TTAAATAAGACTATAAGA----------------------TACCCGTGACTGT------------------------------------------------------------------------TCTATACAATTAT---AAAATATTCATTTAATATAATAGTA---------------------------------------CCACTATAAGAT--------A---------------------------CGCTGGTATCT-AAAGATTGTACAT
droBia1	scf7180000302178:13133-13249 +	1028	TTTATACAAT-T-TGT--------------TATATAGGA----AACA-TAAGTT-----------------------------------------------------------------------------TTACCACTTTT-------------------------------------AAAA-------------AAAATAGATAGTTTG------------------------GCGAGA-AAAAT--------GCTGAGAATAGCTTAAT-------TTTG--TA-CACATGAAAAAAATTTTGTT
droTak1	scf7180000413709:12828-12948 -	4691	TTTATACTAA-T-AATAAAACAGATTAGTATAATTTTCT----------------------TTATAAGGAAATTAAACTTTTGTTAG----------------------------------------------------------------------------------------------------------------------------------------------------TGGAGTGAAAAT--------GCTTGATTTAATTTTGT-------TATCTTTTGCAATTTATTACATTTTTGTT
droEle1	scf7180000491080:2841398-2841515 -	524	AAAT-ATATC-GAATT--------------TAAAAAGAA----AAAG-TGAGTGCTAATAC---------------ATTTTTTTTATACAATTGGAAATAA-------------------A------------AACA--------------TTT-----------------------------------------------------------------------------------------AAAA--------AAAGAGCAGGGCTCAAC-------CGGGA-TTTGA-----ACCCGGGACCTCT
droRho1	scf7180000776225:2196-2314 +	1770	TATATTAAGT-T-GTT--------------GAG---GCA----AA------------------TATTAAG-------------------------------TACGT-TGAA-AAGTACAAGAACTTGCAATTTATCATTATT----------------------------------------------------------------------------------------------------AAAAC--------AAAAGTTAACATTTTGT-------TTAATATAACAAGCAAGGAAAGCTAACTT
droFic1	scf7180000454048:281166-281287 -	52	TCCAGAGGTT-T--TC--------------TGTACTAGATACTTTAAT-----------------A-----AAAAAG----------------------------------------------------------------------------------------------------------------------------------TTTTTTAATATAAGTTATAAGTTCATCTT------AATGTACATTTT-G---AGGAAATATATAT-------TATTTATTAACAATAAAAAAGTTCTGGTT
droKik1	scf7180000302517:216660-216785 -	58	TTTATATTAT-A-AAT--------------TATAATGCC----------------------GAAAACAGACACTAAACAGATAACATAACATTTTACCTAT-------------------A------------CTTA---TTACCATAT---GTT-----------------------------------------------TACAGTTTGACAGTTATA---------------------------------------------GTTAT-----------ACATTCACAGCT----TTACATTTTCT
droAna3	scaffold_13340:2198726-2198841 +	44	TTAATAATTT-T-ATT--------------TATCGAACT----AA------------------TT---------AGGCTTTTCATA---------------CAGATTTAAG-CTTAATATTAAATT--------------------------A----------------------------------------------------------------------------------TAGAG------CACTGGCT-G---CGGTGGTATAT----------ATATTTTTCA-ATAAACACATTTTTATG
droBip1	scf7180000395023:6052-6160 -	352	TATATATATA-T-ATA--------------TATAATATA----TATA-TATATATAATATA---------------------------ATATATAATATAT-------------------A------------TATT---ATATTATAATATTTC---------------------------------------------------------------------------------------AGCAT--------ACATTTTAAA--TTTAT-------TTAGAAATGAG-------------ATTAA
dp4	chrXR_group6:912830-912970 -	72	TTTATACCAC-G-CAC--------------TAGATTGGGTTCTCCAGA-----------------T-----AACGAATGTTGT------------------------------------------------------------------------CCAGTAAAATCCC---AATCCATTCAAATGGATTATGTGAC---------------------------------------CAGTGTTAAGAT--------GCGTCGAGGGCAGTCAG-------CTTGTGTTGCTATCTCGCTCCCCTCCGCC
droPer1	super_3:249021-249147 +	5	TTTTAAATCTGT--TC-CC-----------TAAAATATACTTTT-----------------TGAACGAGAGAGTATATATGTATG----------------TATGC-CGAGCAACTTCTAGTACCCCC----------------------------------------------------------------------------------------------------------------------T-----AC---TCAATATGTTTTTTT-------TTGGCTTAGTAAAATAATACATCTATATC
droWil1	scaffold_180708:152570-152690 -	2812	TTTATATATA-T-ATA--------------TATGATGTA----GATA-TATATTTTTTATA-------------------------------------------------------------------------------------------------------TTTA---AATTTTTTTAAA-------------GTGATTTTTGTCAAG------------------------GC---------------------TAGAAAAGCTTTATTTTTTGTTTTGT--TTTAGTTTATGCGATATTTCTT
droVir3	scaffold_135:841-956 -	576	TATATATATG-T-GAA--------------CATAACTTA----TATAATA-------------------------------------------------CA-------------------T----------ATGACA--------------TACTGCCAGACAAATAAACGTAACTATTTATGTTTGAAATCAAGA---------------------------------------T----------CACCAAAATAAATGA--TGATTTTAT-------TT----------------------TACAA
droMoj3	scaffold_6308:1934837-1934961 -	1172	TTTATATATT-A-TAA--------------AAAAAATTA----CT----------------TAAATTAAAGCTTAGGAAATATTTGTA--TCCATAAAAAA-------------------T----------ATGATA--------------TATT---------------------------------------------------------------------------------------TTTAT--------GCATGGTAAATTTAATT-------TTTAATTTCTAATAAAAAAAATTATATAT
droGri2	scaffold_14906:7885716-7885837 +	8	ATTATTATTT-T-TTT--------------TTTATTTCA------------------------AGTTAATTTACAATTATCGAA-----------------CCGGT-TAAA-CTAAATTTTAGCTT--------------------------A----------------------------------------------------------------------------------TAGATATTTATT--------G---CTTAATTAACTGT-------TTTTTTTTGTT-GTTAAAACATTTTTTTT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTTATACATTTGT-TTATAATGCAC---ATAATAAA----------------TGCCAACCATTCATCATGAAATTATAAATAGTATCATTTCA----------------------------------------------AGATGCATGGTAAGGC---------------------------TTTATTTTGTTTTGCAATCAAAGACATCTTTCTT

Size

Hit Count

Total Norm

droSim1

tttatatatattatttattatGCTC---AGCATAAA----------------TGCCAAGCATTCGTCGTGaaattataaattatatattatat----------------------------------------------aaattCATGGTAAGGC---------------------------TTCATTTTTTAACGCAGTCTAAGACATC----TT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................TGCCAAGCATTCGTCGTGAAATTATAAA........................................................................................................................................	28	1	1.00	0.00	0.00	0.00	1.00

droSec1

tttatatatattatttattatGCTC---AGCATAAA----------------TGCCAAGCATTCGTCGTGaaattataaattatatattat-------------------------------------------ttCT-AGATTCATGGTAAAGT---------------------------TTCATTTTGTAACGCAGTCTAAGACATCTTTCTC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
.ATATATATAxTATTTATTAT...................................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00

droYak2

aattataattttaattaGCATGTTTAATTT----------------TTA-------------------TGTAA-----------------------------------------------------------------------------------------------------------------TTTTGTAACATTGTCAAAGATTTCTTTCTT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
................................................A-------------------TGTAA-----------------------------------------------------------------------------------------------------------------xTTTGTAACATAGT................	19	1	4.00	0.00	0.00	1.00	3.00	0.00
....................................................................TGTAA-----------------------------------------------------------------------------------------------------------------xTTTGTAACATAGT................	18	1	2.00	0.00	1.00	0.00	1.00	0.00
....................................................................TGTAA-----------------------------------------------------------------------------------------------------------------xTTTGTAACATAGTCA..............	20	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

aataataattttaatttGCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCACTGTCACTGTCACTGGCTTC---CTT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.....AAATTTTAATTTGCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------TTCA..........................	19	1	1.00	1.00	0.00	0.00	0.00
.ATAATAATTTTATTTCGCT----------------------------------------------------------------------------------------------------------------------------------------------------------------------..............................	19	1	1.00	0.00	0.00	0.00	1.00

droAna3

TTTAAACATTTTT-TT------TTT---AATATAACTACTTAACTTTTTTGT------------AACCCAACATCATATGAAAAATAATTTACAAATTTGCAATATGATTTAATGAACCTGGTTTTATGAT----------------------------------------------------------------------------------CAT

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

CTCCCATTTACAT-T---------CAGTTT----------------TTA-------------------TAACAT----------------------------------TTTAATGAGGATCGTTTTACGATCACTCTGG--------CGTGT---GTGCTGGTAT----------TTATAAA-------------------------CATTTTAAA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.......TCACAT-C---------CAGTTT----------------TTA-------------------TAAC................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droPer1

CTCCCATTTACAT-T---------CAGTTT----------------TTA-------------------TAACAT----------------------------------TTTAATGAGCCTCGTTTTACGATCACTCTGG--------CGTGT---GTGCTGGTAT----------TTATAAA-------------------------CATTTTGAT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
.............................................................................................................................................................TCTGGTAT----------TTxTAAA-------------------------CATTTT...	20	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

TCTTCACATATTT-T---------TGTTAATTATGATACCAAATCCAATTCTTGCCAGAAATTTGAAGTAA--------------------------------------------------------------TATTGA--------AGTAA---AACTTAATATTAAGCATTATTAATGCT-------------------------TTTTTTGAG	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.....................................................................................................................................................TAA---AACATAATATTAAGT..............................................	18	1	1.00	0.00	1.00	0.00	0.00
.....................................................................AA--------------------------------------------------------------TATTGA--------AGxAA---AACTTTATA....................................................	21	1	1.00	0.00	1.00	0.00	0.00
...................................................TTGCCAGGACTTTGAAGT...................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.....ATAxAGTT-T---------TGTTAATTAT......................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

ttaattaatatat-t---------ctgtat----------------cag-------------------tatcat-----attttagtatgtat------------------------------------atataaatta---------------------------------------------cgatttattttaattt-atatacatatattaa

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

ctaattgattaat-t---------taattt----------------tat-------------------tttttt-----attatatCACATTT------------------------------------ATTT---------------------T---------------------------TATTTTTTCTTTCGCAATCGATTAGTT----CTT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...................................................................................TATCACAGTT------------------------------------ATTT---------------------T---------------------------TCTTTTTT..........................	23	1	2.00	0.00	0.00	0.00	2.00
..................................................................................................................................................................................................GGCAACCGATTAGTT----CTT	18	1	1.00	0.00	0.00	0.00	1.00
...................................................................................TATCACATTA------------------------------------ATTT---------------------T---------------------------GATTT.............................	20	1	1.00	0.00	1.00	0.00	0.00

droGri2

ttaattattattattttttt---------t----------------tta-------------------tttcaA-----ATTTTAGCTTATAG------------------------------------ATATTTATTG--------CT---------------------------------TCTGTTTTTTTTTGTTGTT-AAAACATTTTTTAT

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