dme-mir-2279-as- 12- and 20-way alignments

dme-mir-2279-as	chr2RHet:1322833-1322945 +	Novel
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 1322860-1322881
   star strand at position 1322896-1322917
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2RHet:1322818-1322960 +	ATGTATGTTGGCACCCCGGTTATTAT--A---------------GGGACAAATGTAAAAATAAATATCTTCGCGTGAAATTAATCTTTTAAAT----------------------------------------------------AATTTCACACACAGATATTTAATTTCAAATTGTC--------------TTT---------CATAATCCTCTC--CCGCC-------ATGGGTCATCGGA
droSim1	chr3R:467591-467699 +	CGCC-T------------------CGGGGCAGATG---------GGGAC-----------TCCGTAGT--------------------------------GTAGTGGACAAGCAAGTTTCCAAAAAATATAGGTGAAT-TTTAATAATTTCACACGCAGATATTTAATTTAAAATTGCC--------------TTT---------CCAAATCCTCTC--CCGGC-------TTGGGCCATTGGA
droSec1	super_60:6933-7052 -	TATA-TGTTGGTTCGCCGATTATTCT--T---------------GGGACAAATGTAAAAATAAATATCTTTGCGGGAAAATAAAGTTTTAA----------------------------------------ACTCACT----------------------------------------------GCATTTGCATTTCATGATCCCCGCC--GTATTC--CCGCC-------TTGG---------
droYak2	Unknown	TTATGTATAACT----------------------T---------GGAAT-----------------------------ATCACTCCGATTAACCAAAGTTGTAACAATCAAGt--------------------------------aatttttattgaaaata-ataaccttataaaaat--------------att---------tACTATATACAAACCT----------AATATTTACCGAA
droEre2	Unknown	TTAT-G-TTGGGACCCCGGTTACTCT--G------TTTATCCCCGCGACAAATGTAGAAATAAATAACTGCTGACGACACTAAATTATCTA----------------------------------------ACTCACTGTTTTTTAATTTCCCGCACAGATATATAA-----AGTTATG--------------TAT---------TTTAATTTGCTC--CCCGCATATTCCTTGCGTCATTGAA
droAna3	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droPer1	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181143:1203866-1203907 -	tttt-t------------------cttgt---------------ggaatgtttgaattgataaatatc------------------------------------------------------------------------------------------------------------------------------------------------------------------------tcgtttga
droVir3	Unknown	TTAT-T------------------AT--G---------------AGGATAAATGAAGGGATAAACTGGCTGGGATGATACCTATACATTTAAT----------------------------------------------------CACATTTAGGATTAACATGTGCTCTGATTTAGATTCTCAGCAGTTGCA------------------GTTTCC--CCGTC-------ATGGGCCAATGAC
droMoj3	scaffold_6474:62415-62475 -	AATT-T----------------------------------------------------------------------------ATTTGTTGAAT----------------------------------------------------AATTTCTTTTGTAGACATACGATCTTAATGAAAC--------------TTT---------CAAAACGT-------------------------------
droGri2	Unknown	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2RHet:1322818-1322960 +	NA	ATGTATG-TTGG---CACC-------------------------------------------------------CC-------------------------------GGTTATT--ATAGGGACAAATGTAAA-------------------------AATAAATATCTTCGCGTGAAATTAAT----------------------------------------------------CTTTTAA-ATAAT------TTCAC-A----------------------------------------------------C-------------------------------------------------------ACAGATATTTAATTTCAAATTGTCT-TTCATAATCCTCTCCCGCCATGGGT-CATCGGA
droSim1	chr2R:265657-265783 -	1498	TTTA-TGT-CGG---CATA-------------------------------------------------------CT-------------------------------GGTTATT--CTAGGGAA-AATTTA----------------------AACAAAATAAATATCTTTACGTGAAACTAAACCTTTGA----A---------------------------CTCATT-------GTTTTTA-ATAAT------TCCAC-A----------------------------------------------------C-------------------------------------------------------ACAGATATTTAATTGAAAAT--------------TGC--------------------CT
droSec1	super_55:122657-122780 -	2351	TTTA-TG-TTGG---CCCC-------------------------------------------------------CC-------------------------------GGTTATT--CTATGGACAAATGTAAA-------------------------AATAAATACTTTCGCGTGAAACTAAACTTTCGA----A---------------------------CTTACC-------GTTTA---TTAAT------TTCAC-A----------------------------------------------------C-------------------------------------------------------ACATATTTATAATTT-------------TAAGTTTAC--------------------TT
droYak2	chr2h_random:1837226-1837349 +	420	TTTA-TG-TTGG---GACC-------------------------------------------------------TC-------------------------------GGTTATT--CTAGGGACAAATGCAGA-------------------------AATAAATAACTTTACACGAAACTAAATTTTCGA----A---------------------------CTCACT-------GTTTC---TTAAT------TTCCC-A----------------------------------------------------C-------------------------------------------------------ACAGATATAAAAATTTAAG-------------TTGTC--------------------TT
droEre2	scaffold_4845:21278391-21278511 -	3798	TACA-AAAA--------------------------------------------------------------------------------------------------------------------AATGTA----------------------AAAAAAATAAATTTTTAAAT--------------TTGA----A---------------------------TGCAGT-------TTTTTAG-ATAAT------TGCACCACAAACATTTAGAGGTATGC----------------------------------------------------CACTTCAAAATCCGATTAAGAT-------------------------------AAG-------TTG-------------------AGT-TATGGAG
droEug1	scf7180000409142:16534-16652 +	1009	TTTT-TATAG-G-------------------------------------------------------------------------------------------------------------AAATAACGCAAA-------------------------TTTAAATATATTAATTTATTATTGAT--------------------------------------------T-------TTTTTTAATATATCTGGCAATTCATAAAAAGGTTTACATGAAT------------------------------------------TTA-----------------------------------------------------------TGAAAAT-TTTC-TTTCTTCTTTT--------------------TC
droBia1	scf7180000302069:1281651-1281776 +	539	ATGT-CTTTATG---AAAC-TGGGC---------------------ACTATAAGAT--GCACC---------------CC--------------------------------------------------AGAAACTACTGCATAGAAGTTTGAA---AAAAAA------------------------------------------------------------------------AACTTAA-ATAAT------ATCGT-A----------------------------------------------------C-------------------------------------------------------ATAGATATGTTTTGCATATTTGCACTTCAATTTCTTC--------------------CC
droTak1	scf7180000414441:15526-15661 +	1141	AAGCATG-TAAG---AATT-------------------------------------------------------GT-------------------------------ACTCGTT--ATAGGGTT-----------------------------------------------------------------------------------------------------------------TCCTTAAATTAC------ACTTATAGAAATATTTACAGGGATCGCAAGTAAGAGTTACTTTTTTAAAAAAATTGACAA-------------------------------------------------------ATAAGTCTTATTTTTCAAT-------TTGTATTATAA--------------------AA
droEle1	scf7180000486807:9902-10004 -	200	TGTC-AGAAG----------------------------------------------AAATATC---------------TT-TT-----------------------GATGAATTTAAT----------------------------------------------------AAT--------------ATTG----ATTGGATTTCCATAAAATT----------------------------------------------------------------TTC----------------------------------------------------CGCTTTCAAGTCAGTTTCTTAT-------------------------------AAA-------T----------TTACCGATATGGAT------CA
droRho1	scf7180000767875:903-1047 -	2845	TGAG-AGACATG---ACTG---CTAAAATA--------------------------------------------CCTCTTATTACAAAGAACTTATGATATCTCTTA---------------------AGA---------------------------AATTCAGAACTCTC------------------C----AAACACTTAA---------------------------------------------------------------TTTAAAAGTGTAC----------------------------------------------------CCTTTCTTAATACAAAAC-------------------AAGA-GAGAACGCTAT-AG-------TCG-------------------GGT-GCTCCGA
droFic1	Unknown	NA	---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droKik1	scf7180000298698:14727-14830 +	14	TTAT-TATAG-C---GCCC-------------------------------------------------------AA-------------------------------A-----------------CGTGTT----------------------GGCCAAATCAAAGTTTTGTT--------------TTGA----A---------------------------TTTAAT-------GTTTAAA-ATGAT------GTCAC-A----------------------------------------------------CACATGTTTTTTTTAGTTTTGCT-----------------------------------------------------------TC----GTTTT--------------------TC
droAna3	scaffold_13334:5190-5293 -	1128	TCTT-AAAAAGA---CT-AATATTTAACTACCAATTGCCATATAAA----------AAATATC---------------TT-TT-----------------------A---------------------------------------------------------------------------------------------------------------------------------------A-AAAAT------CCCAC-C----------------------------------------------------A------------------------------------------TATTT-------------TTTTTTATTTATTATTTTTT-TTACTAATTTT--------------------TT
droBip1	scf7180000395238:27783-27922 -	117	ATTG-TAGG----------------------------------------------------------------------------------------------------------------GGCACATGTAAA-------------------------AGCTCCACGATTTGCGTGAAGTCTAAAA-CTGTAATAATTGAATGTAAAAAA--TTTTATATATTT--TTT-------TTATCGA-AAAGT------TGTATTATACATA--------------------------------------------------------------------------------------------------------------------------------CC----ATCGTCTGCCGTTATATGGCCATGACG
dp4	Unknown_group_37:8363-8450 -	142	AAAA-TA-TACA---ACCC---------------------------GCAGTAAAAT--GTATC---------------CT-TTGCGTAGGTCTAAC-----------GATA--------------ATT-------------------------------------------------------------------ATAGAATAC----AAAATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCCCTC-CTACCTCATTG--------------------CC
droPer1	super_5473:1216-1318 -	1446	ATGT-TAAAGCT---TAAA----------------------------------------CC-------------TC--AG-CT-----------------------TAGGAATGCAATA------GGTACA----------------------GGCGAATCGACTTTCTTCATGTGAAATCATT----------------------------------------------------CCCCTGC-ATAGT------TCCAC-T----------------------------------------------------T-------------------------------------------------------ACAC----------------------------ACGTA--------------------TA
droWil1	scaffold_180772:5217896-5218034 -	2179	GGTC-GAAATCTAGACA-AATATTAAA----------------AAA----------AAATTCATTGCAACAAGTCC----------------------------------------------------------------------------------------TCTTTCAAT--------------TTTA----ATTGAATTTTCAGGA--A----------CATACT-------ATCCA---GCTAA------CTCTG-A----------------------------------------------------C----------------------------------------AAGAATATGTGCACT--T-TGGCGCCGCC------------AC-------------------TGGT-CAACGGC
droVir3	scaffold_291:1622-1745 +	3	ATATATA-TAAA---TATT-------------------------------------------------------TA-------------------------------ATATATT--ATATAATTAACAATTTA-------------------------AATAAAAAATTTCGCAATCCAAA-----------------------------------------------------------------------------------AATCATTACAAATATGGTAAA-----------------------------A------------------------------------------AAAAA-------------TCTATATTTTAAAGATTTAT-CTAATGATTCT--------------------TT
droMoj3	scaffold_6473:7010400-7010528 -	602	ATGT-ATGTGCA---TACA-------------------------------------------------------TA-------------------------------TATATAT--TTATGTACATATGTAAA-------------------------TATAGAAATCTACGTATGATTTGTTGGCATTGC----A---------------------------CTCTTTACACACTTTTGTTTGTTTAT------TTTTT------------------------------------------------------------------------------------------------------------------TTATTTTATT------------TTTTTTTGTCT--------------------TT
droGri2	scaffold_14906:12727535-12727642 -	35	ATAC-AAATATA---AATT-TATTCAAATTCAAATT------------------------ATC---------------TT-----------------------------------------------------------------------------------------------------------TCAA----A-TAAAAGGACAAGA--T-------------AAG-------ATAAA---TTAAA------TAATA-T----------------------------------------------------A--------A--------------------------C----AAAATTG-----------------TATTCT-------------CGTTTTCCCTTCTCGG-------------CA

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ATGTATGTTGGCACCCCGGTTATTAT--A---------------GGGACAAATGTAAAAATAAATATCTTCGCGTGAAATTAATCTTTTAAAT----------------------------------------------------AATTTCACACACAGATATTTAATTTCAAATTGTC--------------TTT---------CATAATCCTCTC--CCGCC-------ATGGGTCATCGGA

Size

Hit Count

Total Norm

droSim1

CGCC-T------------------CGGGGCAGATG---------GGGAC-----------TCCGTAGT--------------------------------GTAGTGGACAAGCAAGTTTCCAAAAAATATAGGTGAAT-TTTAATAATTTCACACGCAGATATTTAATTTAAAATTGCC--------------TTT---------CCAAATCCTCTC--CCGGC-------TTGGGCCATTGGA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.............................................................................................................................................................ATATAxTTAATTTAAAACTG...................................................................	19	2	0.50	0.00	0.50	0.00	0.00
..................................................................................................................................................................................................................TCCTCTC--CCGTC-------xTGGGCC......	18	2	0.50	0.00	0.00	0.00	0.50

droSec1

TATA-TGTTGGTTCGCCGATTATTCT--T---------------GGGACAAATGTAAAAATAAATATCTTTGCGGGAAAATAAAGTTTTAA----------------------------------------ACTCACT----------------------------------------------GCATTTGCATTTCATGATCCCCGCC--GTATTC--CCGCC-------TTGG---------	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
..................................................AATGxAAAAAGAAATATCT...............................................................................................................................................................................	18	2	3.00	0.00	3.00	0.00
..................................................AATGxAAAAAGAAATATCTT..............................................................................................................................................................................	19	2	1.50	0.00	1.50	0.00
..................................................AATGxAAAAAGAAATATCTTT.............................................................................................................................................................................	20	2	0.50	0.00	0.50	0.00

droYak2

TTATGTATAACT----------------------T---------GGAAT-----------------------------ATCACTCCGATTAACCAAAGTTGTAACAATCAAGt--------------------------------aatttttattgaaaata-ataaccttataaaaat--------------att---------tACTATATACAAACCT----------AATATTTACCGAA

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

TTAT-G-TTGGGACCCCGGTTACTCT--G------TTTATCCCCGCGACAAATGTAGAAATAAATAACTGCTGACGACACTAAATTATCTA----------------------------------------ACTCACTGTTTTTTAATTTCCCGCACAGATATATAA-----AGTTATG--------------TAT---------TTTAATTTGCTC--CCCGCATATTCCTTGCGTCATTGAA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
......................................................................................................................................................................A-----AGTTxTA--------------TAT---------TTTAATTT...............................	18	2	0.50	0.00	0.00	0.00	0.50
............................................................................................................................................................................ATTTATG--------------TAT---------TTTGATTTG..............................	19	2	0.50	0.00	0.00	0.00	0.50
......................................................................................................................................................................A-----ATTTATG--------------TAT---------TTTGATT................................	18	2	0.50	0.00	0.00	0.00	0.50

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

tttt-t------------------cttgt---------------ggaatgtttgaattgataaatatc------------------------------------------------------------------------------------------------------------------------------------------------------------------------tcgtttga	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...T-T------------------CTTGA---------------GGAATGTTTGAAATGATAAA....................................................................................................................................................................................	27	1	7.00	1.00	5.00	1.00	0.00
..........................TGA---------------GGAATGTTTGAAATGATAAATATC------------------------------------------------------------------------------------------------------------------------------------------------------------------------........	27	1	3.00	0.00	3.00	0.00	0.00
................................................TGTTTGAAATGATAAATATC------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGTT...	25	1	3.00	0.00	3.00	0.00	0.00
................................................TGTTTGAAATGATAAATATT------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGTT...	25	1	2.00	0.00	2.00	0.00	0.00
.....T------------------CTTGA---------------GGAATGTTTGAAATGATAA.....................................................................................................................................................................................	25	1	2.00	0.00	2.00	0.00	0.00
.....T------------------CTTGA---------------GGAATGTTTGAAATGATAAA....................................................................................................................................................................................	26	1	2.00	0.00	2.00	0.00	0.00
.................................................GTTTGAAATGATAAATATC------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGTTT..	25	1	1.00	0.00	1.00	0.00	0.00
........................CTTGC---------------GGAATGTTTGAAAT..........................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
...............................................ATGTTTGAAATGATAAATATC------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGTT...	26	1	1.00	0.00	1.00	0.00	0.00
....................................................TGAAATGATAAATATC------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGTT...	21	1	1.00	0.00	1.00	0.00	0.00
................................................TGTTTGAAATGATAAATATC------------------------------------------------------------------------------------------------------------------------------------------------------------------------TCGTTT..	26	1	1.00	0.00	0.00	1.00	0.00
..........................TGT---------------GTAATGTTTGAAGTGA........................................................................................................................................................................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................TTGT---------------GGAATGTTTACATT..........................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................TTGT---------------GGAATGTTTGAATTGATAAATA..................................................................................................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00
TATT-T------------------CTTGA---------------GGAATGTTTGA.............................................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...T-T------------------CTTGA---------------GGAATGTTTGAAATGAT.......................................................................................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
.........................TTGA---------------GGAATGTTTGAAATGATAAATA..................................................................................................................................................................................	26	1	1.00	0.00	0.00	0.00	1.00
........................CTTGA---------------GGAATGTTTGAAATGA........................................................................................................................................................................................	21	1	1.00	1.00	0.00	0.00	0.00

droVir3

TTAT-T------------------AT--G---------------AGGATAAATGAAGGGATAAACTGGCTGGGATGATACCTATACATTTAAT----------------------------------------------------CACATTTAGGATTAACATGTGCTCTGATTTAGATTCTCAGCAGTTGCA------------------GTTTCC--CCGTC-------ATGGGCCAATGAC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...............................................ATAAATGATGGGATAATCT..................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
...........................................................ATAAACTGGATGGGATGCT......................................................................................................................................................................	19	2	0.50	0.50	0.00	0.00	0.00	0.00

droMoj3

AATT-T----------------------------------------------------------------------------ATTTGTTGAAT----------------------------------------------------AATTTCTTTTGTAGACATACGATCTTAATGAAAC--------------TTT---------CAAAACGT-------------------------------	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
...............................................................................................................................................................ACGTACGATCTTCATGAAAC--------------T..................................................	21	2	0.50	0.00	0.50	0.00	0.00
....................................................................................................................................................TTTTTTTGTGGACATACGATC...........................................................................	21	2	0.50	0.00	0.50	0.00	0.00
..........................................................................................................................................................TGTGGACATACGATCTTCATG.....................................................................	21	2	0.50	0.00	0.00	0.00	0.50
.....................................................................................................................................................TCTTTTGTAGACATACGATCCTAATGAA...................................................................	28	2	0.50	0.00	0.00	0.00	0.50
.ATT-T----------------------------------------------------------------------------ATTTGTCGAAT----------------------------------------------------AATTTC.............................................................................................	21	2	0.50	0.00	0.00	0.50	0.00
..............................................................................................................................................................GACGTACGATCTTCATGAAAC--------------T..................................................	22	2	0.50	0.00	0.00	0.00	0.50
...........................................................................................AT----------------------------------------------------AATTTCTTTTGTAGACGT.................................................................................	20	2	0.50	0.50	0.00	0.00	0.00
............................................................................................................................................................................ATGAAAC--------------TTT---------CAGAATGT-------------------------------	18	2	0.50	0.50	0.00	0.00	0.00
.................................................................................................................................................................ATACGATCTTCATGAAAC--------------A..................................................	19	2	0.50	0.00	0.00	0.00	0.50
.....................................................................................................................................................TCTTTTGTAAACATATGATCTTAATG.....................................................................	26	2	0.50	0.50	0.00	0.00	0.00

droGri2

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	None	None				None
UNAFold Image						None	None	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