dme-mir-979- 12- and 20-way alignments

dme-mir-979	chrX:19455870-19455964 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_3pUTR

Legend:

   mature strand at position 19455928-19455950
   star strand at position 19455892-19455914
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:19455855-19455979 +	TTAATCACTGGA--------------------------------------------------------------ACA------TACATGTGAGGATGTCACAAAT------------------------------------------------------------------------------------------------ACACTGAATTTGGGGGGAATTCTTATGTATATACAAATTCTTCCCGAACTCAG-GCTAATTTTGTGGCATCCGTATACACAAAAGTATA
droSim1	chrX_random:5079602-5079664 +	TTAATATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATTCTTCACGAATTCAG-GCTAATTTTGTAGGAGCCGTATATACAAAAGTATA
droSec1	super_8:1738459-1738521 +	TTAATATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAATCTTCACGAATTCAG-GCTACTTTTGTAGGAACCGTATATACAAAAGTATA
droYak2	chrX:11883257-11883281 -	TTAATGGCTGGG--------------------------------------------------------------AAA------TACGTAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG
droEre2	scaffold_4690:9691773-9691847 +	TTAATCGTTGGC--------------------------------------------------------------AAA------TACGTATGGG-GTGCCAC------------------ACAAATCGAT-------------TA---------------------------------------------------------GCTC----------------------------------------TGAATTCGG-GCG-------GA----------ATTCTGAAGCACG
droAna3	Unknown	TTAATCACCGtt--------------------------------------------------------------tca------t----------------------------------------------ttaaaaagttatta-----agtaatcaattataaattgtataaatataattCAGGTAACGTCTAAAAAATG-----------------------------------------TTTCAAGTCTGG-GTTTTATTTGTTAGA----------CCAAAACTCA
dp4	chrXL_group1e:12509670-12509797 -	TTAAGCATTTTAATTTTTGTATTTTTCAAGATCGAAAATATTTATGCGCGTAAATTTAAGAGTAAGTCCTTAGTAAG------TAAGGAAGAA-CT----------------------------------------------------------------------------------------------------------------------------------------------------------ACGC-TCTGGATTTGATATACTCGTGAAGTTAAAACAATA
droPer1	super_14:1990605-1990740 -	TTAAGCATTTTAATTTTTATATTTTTCAAGATCGAAAATATTTAAACGCGTTAAATTAAGAGTAAGTCCTTAGTAAG------TAAGGAAGAA-CT-------------------------------------------------------------------------------------------------------------------------------------------------TCTACGAATTTAT-ATAGATTTTATATTC-TCTTGAAGCTAAAACAATA
droWil1	scaffold_181096:7961894-7962010 +	TTAGATTATGAT--------------------------------------------------------TAGA--ATAAGcacacacaacacacgcacacacacacacacacaTCTATATATAAATCAACCAAGAAAACACAATA-----TCGA--------------------------------------------------------------------------------------------AGAAATTAG-AAA-------Gt----------atatatatatata
droVir3	scaffold_13042:902095-902094 -	--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6328:2896306-2896380 -	ATGAGAAAGGGC--------------------------------------------------------TATAGAAAT------TGATGACGAT-------------------------------------------------------------------------------------------------------------------------------------------------ATAATCCAAAACTAAG-ATTACAATAATAATAATa-------ataaacaaaa
droGri2	scaffold_15081:2040291-2040415 -	TAATTTAAGA-T--------------------------------------------------------G-----AAG------A----------------------------------------------TGAAGACAATAATAATAATAGTGATAGGAGTTGAAGAGCTTAAATGTAAACTGATAATTGTATATACAAAG-----------------------------------------TTGAAAATGTCATTCTCTGGTTATTGGA----------TTAAAATGAG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:19455855-19455979 +	NA	TTAATCACTGGAACA-----------------TACATGTG-----AGGA--------------------------------------------TGTCA---------------CAAA--T------ACACTGAA--------------------------------------------------------------TTTGGGGGGAATTCT--------TATG----------------T-----------------------------------------------------------------------------------------------------------------------------------------------ATATACAAATTCTTCC---------C-------------GAACTCAGGCTAATTTTGTGGCATCCGT--------------------------------------------------------AT----------A-CA------------------------CAAAAGTATA-------
droSim1	chr2L:11773332-11773488 -	6	TCTTCCAAAAGTATA-----------------TACATCC-----CTAGCT-------------------------ATTAAAA----------------------------------T--C------ACAT--------------------------------------------------------------------------------------------------------------TT-------------------------------------TATTTAGATTTTGATATATTTTACAGAAATTCAACATTTAAAAA-----------------------------------------------------------------------------------------------------------------------------------------------TCCAGGAAAATAGTTTCTAAGAAGATATAATACTTT-------TAGGATCC-------ATATCTG---CTTATTAA---ACTACATTTTA-------
droSec1	super_16:165683-165811 -	4	TATCTTCCAAAAGTA---------------TATACATCC-----CTAGAT-------------------------TTTAAAA----------------------------------T--C------ACAT--------------------------------------------------------------------------------------------------------------TT-------------------------------------TATTTAGATTTTGACATATTTTACAGAAATTCAACATTTAAA-----------------------------------AAT---------------------------------------------------------------------------------------CAAACAAATCAACAAAAAAATCCAGGAAA-----------------------------------------------------------------------ATAGTTTCTA-------
droYak2	chrX:11883259-11883281 -	1	TTAATGGCTGGGAAA-----------------TACGTAAA-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEre2	scaffold_4690:9691773-9691867 +	1	TTAATCGTTGGCAAA-----------------TACGTATG------GGG--------------------------------------------TGCCA---------------CACAAATCGATTAGCTCTGAA--------------------------------------------------------------TTCGGGCGGAATTCTGAAGCACGCATC----------------C-----------------------------------------------------------------------------------------------------------------------------------------------AC--------------------------------------------------TTT------------------------------------------------------------------------------------------------------------TGTAGCATCC-------
droEug1	scf7180000409230:876782-876877 -	2	TTAATCATCGTAAAT-----------------TAAATAAA---TTAAAATATTTATAGCA------------------------------------------------------------------AT----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATT---------TTTCGTAGATATTCTACTTAACTTAACTTAA-----ATCAAT-------------------------------------------------------------------CAAT-------------------------ACAAAATATA-------
droBia1	scf7180000302069:1147456-1147673 -	2	TTAATCATTGGAACA-----------------GCGTCAAT-----AAA-T-------------------------AGTAAAAGCAATAGTTAGAACCGGAGTTAAGCCAACCAACA---------------------------------------------------------------------------------------------------------------------------------------TAAAAA------TGAGGAAAAT------------------------------------TGTACAATTAAAAGAAACAAACGATAGTGCAAAGGAATGTGATCAAAAACCTTGGAATCTATCAAATATAACGTATATAATGCA---TCGCTCCCAACCC-------------TACTAAAATGAATTCAG-------------------------------------------------------------------GAA-----TACTACT-------------------------CTAAGTTCTA-------
droTak1	scf7180000415169:841429-841556 -	3	CTAATCAGTGGAGCAGTTTTA-AT--------TTGATATG-----AG------------------------------------TAATAATAAGAAGCGGTCCTAAAGTAG---CCAA--T------A----------------------------------------------------------------------------------------------------------------------------CAGAAA------AAATAA----GAACCAAA------------------------------------------------------TTTCAAAAAACTTTGACTAAAAAC---------------------------------------------------------------------------------------CATT---------------------------------------------------------T----------A-A------------------------GCTAAGAAATG-------
droEle1	scf7180000491006:819941-820067 -	6	CTACACTGATAAAAA---------AAAGTG------CAAAAGTAC----A----AATAAATATATG-----------------------------------------------------G------TTA----------------------------------------------------------------------------------------TATGGT----------------T-----------------------------------------------------------------------------------------------------------------------------------------------AAATATAAAATCATAT---------C-------------AAGCATGTCTTAATATTAAA-----------------------------A------------------------------------------TATTTTAGTTTACTTTA---AATGC---CAT-ATTCAAATTA-------
droRho1	scf7180000761121:186691-186818 -	3	TTAATCATTGGGATA-----------------CATTAAAA-----AAA------------------------------------------------------------------------------------------------------------------------------ATGTATAAGTAATTGTAGTCAATATTGTATAAATAAT--------AATG----------------T-----------------------------------------------------------------------------------------------------------------------------------------------AAAAA-----AATTCATATTCATTGC-------------TAATATAAATAAATTACGATAAATATTT--------------------------------------------------------A---------------------------------------TATGGTAAGG-------
droFic1	scf7180000454073:1736548-1736631 +	3	TTAACCATTGAAGAA-----------------ATTTTAAT-----GAA------------------------------------------------------------------------------------------------------------------------------ATGCGTAATGCATTGTAAAAACTATTGTA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AACATTGAA--------------------------AAG-----TATTTTA-------------------------ATATGTTATA-------
droKik1	scf7180000302621:248346-248471 -	6	GAAAGCATTCCGTTT-----------------ACCAATTT-----CGGA--------------------------------------------TGCCC---------------TAAC--C------ACCCAGAAGGGTGGTCCTTTAAGGGAAAAGGTTTTGGTTCTACAGAAAATGTATGAA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ATTTTATATACAAAATTATA-TA------------------------CAAAATTATA-------
droAna3	scaffold_13417:2459297-2459411 -	5	TAAGTTACTTATAAT-----------------TAAATTTA-----AATA--------------------------------------------TTTCG---------------AAAT--A------AAACTATA-------------AA-------------------------ATA----------------------------------------------------------------------------------------------AT------------------------------------TGTCTTATT---------------------------------------------------------------------------------------------------------------------------------------------------------------------TCAGAAAATATGTACATAT-------TTATACCA-------ATCTTTA---CATATT--TCAATAAAAATATA-------
droBip1	scf7180000395874:31563-31685 -	1	TTATTCAACAAAAGA-----------------CATACATA---CGTATGTATGTACACCA-----------------------------------------------------ATA----------------------------------------------------------------------------------------------------------------------------TT-----------AAAA------AAAATATGAA--TGTCTA----------------------------------TTT--------------------CTA--------------------------------------------A-----ATACTTCA---------TATTTG-------------TAGAGTAAAGTAATAATATGGAA--------------------------------------------------------AT-----------GT-------------------------ACATGGATTA-------
dp4	chrXL_group1e:12509670-12509797 -	4	TTAAGCATTTTAATT-----------------TTTGTATT---TTTCAAGATCGAAAATATTTATGCGCGTAAATTTAA-------------GAGTAA---------------GTC----------------------------------------------------------------------------------------------------------------------------CTTAGTAAGTAAGGAAG------AACTA-----------CGCTCTG---------------------------------------------------------------------------------------------------G-----ATTTGATA---------TACTCG-----------------------------------T--------------------------------------------------------GA----------A-GT------------------------TAAAACAATA-------
droPer1	super_14:1989251-1989367 -	5	CTAAGTCATCGTGCG-----------------CATCTGTT-----GGGG--------------------------------------------AGTAA---------------AAAC--T------AAA----------------------------------------------------------------------------------------------------------------------------ATTA------GAGTGG----AAACTCTATTTTG---------------------------------------------------------------------------------------------------A-----GTTGAATT---------TTTCCATGAAAATCTGCT-------------------------------------------------------------------------------------------------ACATTTTG---GGTTT---TAAATTTGTATTTT-------
droWil1	scaffold_181096:7961895-7962008 +	2	TAGATTATGATTAG--------AATAAGCACACACAACA-----CACGCA-------------------------CACACAC----------------------------------A--C------ACA----------------------------------------------------------------------------------------CACATC----------------T-----------------------------------------------------------------------------------------------------------------------------------------------ATATATAAAT-----------------------------------------------------CAACCAAGAAAACAC-AATATCGAAGAAATTAGA--------------------------AAG-----------TA------------------------TATATATATA-------
droVir3	scaffold_13042:902091-902097 -	2	TCAATCA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:27198225-27198308 -	2	GCAAGGAATTCCACA-----------------TAGTTATG-----GAA------------------------------------------------------------------------------AGTCTGAA--------------------------------------------------------------TTTGAG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GG--------------------------ATTTCAAATGTAGCATAC----------TTTCCGGCGCTCTG-----GAGTAAAGCA-------
droGri2	scaffold_15081:2040284-2040418 -	2	TTGTAATTTAAGATGA-----AGATGAAGA------CAATAATAA----T----AATAGTGATAGG---------------------------------------------------AGTTGAAGAGC----------------------------------------------------------------------------------------------TTAAATGTAAACTGATA-AT-----------TGTATATACAAAGTTGAAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TGTCA-------TTCTCTG---GTTATTGG---ATTAAAATGAGGACACTT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TTAATCACTGGA--------------------------------------------------------------ACA------TACATGTGAGGATGTCACAAAT------------------------------------------------------------------------------------------------ACACTGAATTTGGGGGGAATTCTTATGTATATACAAATTCTTCCCGAACTCAG-GCTAATTTTGTGGCATCCGTATACACAAAAGTATA

Size

Hit Count

Total Norm

droSim1

TTAATATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAATTCTTCACGAATTCAG-GCTAATTTTGTAGGAGCCGTATATACAAAAGTATA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..................................................................................................................................................................................................................................................................AATTTTGTAGGAGCTGCA..............	18	2	1.50	0.50	0.00	1.00	0.00
........................................................................................................................................................................................................................................................................GTAGGAGCCGTAGATACC........	18	2	0.50	0.00	0.00	0.50	0.00

droSec1

TTAATATAC----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AAAATCTTCACGAATTCAG-GCTACTTTTGTAGGAACCGTATATACAAAAGTATA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..............................................................................................................................................................................................................................................................................ACCGTATATACAAAGATA..	18	2	0.50	0.00	0.50	0.00

droYak2

TTAATGGCTGGG--------------------------------------------------------------AAA------TACGTAAA-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------AG

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TTAATCGTTGGC--------------------------------------------------------------AAA------TACGTATGGG-GTGCCAC------------------ACAAATCGAT-------------TA---------------------------------------------------------GCTC----------------------------------------TGAATTCGG-GCG-------GA----------ATTCTGAAGCACG	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..................................................................................................CAC------------------ACAGATCGAx-------------TA---------------------------------------------------------GCTC----------------------------------------T............................................	19	2	0.50	0.00	0.00	0.50	0.00

droAna3

TTAATCACCGtt--------------------------------------------------------------tca------t----------------------------------------------ttaaaaagttatta-----agtaatcaattataaattgtataaatataattCAGGTAACGTCTAAAAAATG-----------------------------------------TTTCAAGTCTGG-GTTTTATTTGTTAGA----------CCAAAACTCA	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...............................................................................................................................................................................ATAATGCAGGTAACGGC..................................................................................................	17	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................................................................................................................GGTAACGTCTxAAACATG-----------------------------------------................................................	17	2	0.50	0.00	0.00	0.50	0.00

dp4

TTAAGCATTTTAATTTTTGTATTTTTCAAGATCGAAAATATTTATGCGCGTAAATTTAAGAGTAAGTCCTTAGTAAG------TAAGGAAGAA-CT----------------------------------------------------------------------------------------------------------------------------------------------------------ACGC-TCTGGATTTGATATACTCGTGAAGTTAAAACAATA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
....................................................AATTTATGAGTAAATCCT............................................................................................................................................................................................................................	18	2	0.50	0.00	0.00	0.50	0.00

droPer1

TTAAGCATTTTAATTTTTATATTTTTCAAGATCGAAAATATTTAAACGCGTTAAATTAAGAGTAAGTCCTTAGTAAG------TAAGGAAGAA-CT-------------------------------------------------------------------------------------------------------------------------------------------------TCTACGAATTTAT-ATAGATTTTATATTC-TCTTGAAGCTAAAACAATA	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
..........................................TAAACGTGTTAAATCAAGA.....................................................................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.00	0.50	0.00

droWil1

TTAGATTATGAT--------------------------------------------------------TAGA--ATAAGcacacacaacacacgcacacacacacacacacaTCTATATATAAATCAACCAAGAAAACACAATA-----TCGA--------------------------------------------------------------------------------------------AGAAATTAG-AAA-------Gt----------atatatatatata	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..........AT--------------------------------------------------------TAGA--ATAAGCACAxACAAC.........................................................................................................................................................................................................	20	2	1.50	0.00	1.50	0.00	0.00

droVir3

--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

ATGAGAAAGGGC--------------------------------------------------------TATAGAAAT------TGATGACGAT-------------------------------------------------------------------------------------------------------------------------------------------------ATAATCCAAAACTAAG-ATTACAATAATAATAATa-------ataaacaaaa

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TAATTTAAGA-T--------------------------------------------------------G-----AAG------A----------------------------------------------TGAAGACAATAATAATAATAGTGATAGGAGTTGAAGAGCTTAAATGTAAACTGATAATTGTATATACAAAG-----------------------------------------TTGAAAATGTCATTCTCTGGTTATTGGA----------TTAAAATGAG

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										None
UNAFold Image				None						None

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																		None
UNAFold Image				None														None