dme-mir-4942- 12- and 20-way alignments

dme-mir-4942	chr3L:23332327-23332437 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 23332387-23332408
   star strand at position 23332354-23332375
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3L:23332312-23332452 +	TATGACATCTGCCTGTTATGAAT------------------------------------ACATAT-ATTTTTATGTTTGAG-TC---------------------AACATCGAG-TTGCCG--ATGTT------------TGGAAAACA--TCGATGACATCG--------CTGTTGGCATCG----AAATATGTCCATATCTAATATATAGTTCCA-----------------TTC------TGTTTTATT
droSim1	chr3L:22456065-22456207 +	AATGACAGCTGCCTGTTATAAGT------------------------------------AATTGT-ATTTTTATGTTTGAGCTA---------------------AACATCGATTATGCCG--ATGTT------------TGGAAAACA--TCGATGACATCG--------CTCTTGCCATCA----AAGTATGTCCATATCTAATATATAGTTCCA-----------------TTC------TGTTATATT
droSec1	super_41:217199-217341 +	AATGACATCTGCCTGTTGTAAGT------------------------------------AATTGT-ATTTTTATGTTTGAGCTA---------------------AACATCGATTATGCCG--ATGTT------------TGGAAAACA--TCGATGACATCG--------CTGTTGCCATCA----AAGTATGTCCATATCTAATATATAGTTCCA-----------------TTC------TGTTATATT
droYak2	chr3L:23917805-23917956 +	TATGATATCTGAATATTTAGTT---------------------------TTTCTTTTGCATATTT-ATTTTTAATATTGAGCTT---------------------CACATATATATTGCCG--ATGTT------------TACAAAACA--TCGATGACATTG--------TTTTTGGCATCG----TCATATGCCCATCACTAATATATAGTCCCC-----------------TTC------TGTTTCATT
droEre2	scaffold_4784:22817455-22817606 -	AAAGGCATCTGTATAGGATGAAT------------------------------------AAATTA-ATTTTTAAGTTTGACCAC---------------------AACTTTCATTTTGCCG--ATGTT------------TAGAAAACA--TCGATGACACCGCATCAT---CGTTGTCATCGACTTACATATGTACATCTCTAATATATAGTATCA-----------------TTC------TGTTTTATT
droAna3	scaffold_13082:1965861-1965982 +	AAATACAACTTTTAATAGA---------------------------GTTACATTTT---------C-----------------------TAAAAT------A---------------------TTATT------------TAAAATTCT--ACGATA-CACTACGATATCACTA-TGACATTT----AAAAATGTTTCTGTCACT-TTAAAGACTAA-----------------ATT------TAGATACTT
dp4	Unknown	GAAGAAGTTTTAATGTCAACAA-----------------------------------------AA-ATTTCCA----------------CGACGT------GGAAG---------ACGCCGTTCTACG------------A---AAATA--CTGA-----------------------------------------------------AAAGATTTAATTTACATATAACTCTGGTCACACATATTTTATCC
droPer1	super_42:228005-228111 +	GAAGAAGTTTTAAtgatgtacat------------------------------------acatat-gtatgtatgtctgCTACAAAAGA--ATAAGTAC----------------GTGAGC--ACGTG------------CGGCAAACC-----------------------TCTT---GCTCATTTATATATTTACAC-ACTAACACATACATAC------------------------------------
droWil1	scaffold_181039:82894-83023 +	TGTGCTATTTTTGCGGTTAAACTCAATGTCTTTTCTTACCATTAGATTAAAATTTT---------G-----------------------TAAAAT------G---------------------GAAACTAAAAATATAAAG---TTC-------------------------------TATTA----A----AGTTTAAACTTTATAGAGAATTTTAAC---------------TTT------TACTCGGTT
droVir3	Unknown	------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6540:5163341-5163424 +	GCAACAACT-TTCTATGAGT--------------------------TGTCC---------------A----------------------AAAAATTGAAGCG---AATTT-----CTGAAATTTCGTT------------AA-----AAGTAAAAC----TTA--------CGAATTGtaatt----aaATATGTCCATGTCCATTAGTCAGTGCTG-----------------------------------
droGri2	Unknown	TCTGACACTGTAGATGCGC---------------------------CTTAC---------------AGTTTA-------------------ACACTGACATG---AACAT-----TCGCCGCTATGCT------------TA---CACA--CAAATAACAGAA--------CCA-----GTTC----AAGTAGTTC-------CGAAAATAATTCCA-----------------CT-------AGTTAATTG

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3L:23332312-23332452 +	NA	TATGACAT--CTGCCTGTTATGA--------ATACAT------------------------------------AT--------ATTTTTATGTTTGA-GTCAA---------------------------------------------CATCGA-GTTGCCGATGTT---TG---GAAAACATCGA------------------------TGACATCGCT----------GTTGGC----ATCGAA----ATATGTCCATATCTAAT----------ATATAGTTC--CATTCTGT----TTTATT
droSim1	chr3L:22456065-22456207 +	1629	AATGACAG--CTGCCTGTTATAA--------GTAATT------------------------------------GT--------ATTTTTATGTTTGAGCTAAA---------------------------------------------CATCGATTATGCCGATGTT---TG---GAAAACATCGA------------------------TGACATCGCT----------CTTGCC----ATCAAA----GTATGTCCATATCTAAT----------ATATAGTTC--CATTCTGT----TATATT
droSec1	super_41:217199-217341 +	1889	AATGACAT--CTGCCTGTTGTAA--------GTAATT------------------------------------GT--------ATTTTTATGTTTGAGCTAAA---------------------------------------------CATCGATTATGCCGATGTT---TG---GAAAACATCGA------------------------TGACATCGCT----------GTTGCC----ATCAAA----GTATGTCCATATCTAAT----------ATATAGTTC--CATTCTGT----TATATT
droYak2	chr3L:23917805-23917956 +	5972	TATGATAT--CTGAATATTTAGT--------TTTT----------------------------------CTTT-TGCATATTTATTTTTAATATTGAGCTTCA---------------------------------------------CATATATATTGCCGATGTT---TA---CAAAACATCGA------------------------TGACATTGTT----------TTTGGC----ATCGTC----ATATGCCCATCACTAAT----------ATATAGTCC--CCTTCTGT----TTCATT
droEre2	scaffold_4784:22817455-22817604 -	8386	GGCAT-----CTGTATAGGATGA--------ATAAAT------------------------------------TA--------ATTTTTAAGTTTGACCACAA---------------------------------------------CTTTCATTTTGCCGATGTT---TA---GAAAACATCGATGACACC-------------------GCATCATC----------GTTGTC----ATCGACTTACATATGTACATCTCTAAT----------ATATAGTAT--CATTCTGT----TTTATT
droEug1	scf7180000409208:8455-8591 +	2910	TGTGCCTT-----------AGAA--------AAGGA-------------------AAAACATCGATGTTCCTC-----------------------CGGTAAA---------------------------------------------CATCGATGTTGCCGATGTT---TC---GAAAACATCGA------------------------TGTCATCGAT----------GTTCGC----ATCGAT----GTTTCTCCACCTCTAAT----------GTAGCGTCT--ATTATAGT---CATTATT
droBia1	scf7180000301323:33962-34103 -	5959	TGCGCG-----------TTAGAG--------ATGGG-------------------AAAACATCGATGTTGCCT-----------------------GGTAAAA---------------------------------------------CATCGATGTTACCGATGTT---AC---GAAAACATCGA------------------------TGACATCGAT----------GTTGGC----ATCGAT----GTTTCTCCACCTCTACA----------AAGCACTTTATCATTTTGATAGGCTTGTT
droTak1	scf7180000415103:413904-414042 +	6201	TTGCAAAT--TT--ACGCCAAGC--------CTATATAAAT-GCCCATTTTTAGT---------CAAAACCAT-----------------------CG------------------------------------------------------AAAAACATCGATGTTTTTTGAC-AAAAACATCGA------------------------AAACATCGAT----------GTTCCCAAAAATCGAT----ATTTCTCCACCTCTATT----------GGATAG-------------------TGCC
droEle1	scf7180000491001:1165148-1165283 -	6492	ATGGACGG--ATAAACATTG--------------------------------------------ATAATCT-------------------------CTGTAAA---------------------------------------------AATCGATATAACCGATATT---TT---GGAAACATCGA------------------------TGACATCCAT----------GTTGGC----ATCGAT----GTTTCTCCACCTCTATACCACCTCTACACCCCTCTA--CTATCCGT----ACCATT
droRho1	scf7180000778134:11337-11464 +	7607	CATCGTTG--ATGCCT--------------------------------------------------------------------------------CACCAAA---------------------------------------------CATCGATATTACCGATGTT---TG---GAAAACATCGATATTACCGATGTTTAGAATATCGATGACCTCGAT----------GTTAGC----ATCGAT----GTTTGTCCGCCCCTAGC----------TAGT-------------AT----TTAATT
droFic1	scf7180000453143:456-611 +	242	TAATACCCTTTTGCTCTGCAAGG--------GTATA-------------------AAAACAACGATGTTGCCC-----------------------CGGTAAA---------------------------------------------CATCAATGTTGCCGATGTT---TC---AAAAACATCGA------------------------TGTCATCGAT----------GTTGGC----ATCGAC----GTTTCTCCACCTCTACGAAGTA-TTACAGATACTTA--TTTTCAAT----TTTTGT
droKik1	scf7180000302481:290430-290562 +	2103	TCTTATAT--CCGCCCCCTTCGG--------TTTTC-------------------ATTTAAATTATGTATCCC-----------------------TGGCAAA---------------------------------------------CATCGATTTTTGCGATGTT---TT---GAAAACATCGA------------------------TGACATCGAT----------G--GGT----ATCGCT----GTTTCTCCACCTCTAAT----------AAACAGTG----------------AAATT
droAna3	scaffold_12916:14167403-14167537 +	695	TGCTCG-----------TTAGAG--------ATG-A-------------------TAAACATCGATGTTGGCT-----------------------TGCCAAA---------------------------------------------CATCGATGTCAACGATGTT---TT---CAAAACATCGA------------------------TGACATCGAT----------GTTAAC----ATCGAT----GTTTCTCCACCTCTGAC----------CACTGGAGT--GAATTATT----TTTAGT
droBip1	scf7180000396634:6934-7072 +	3242	TACGATTT--ATTTATTCTATGT--------GTACAT------------------------------------AT--------GTATGTATATCTAAGATGA------CGTA-------------------------------------TTCCA-TTTTCTAAAGTA---GT---GATAATTTGAT------------------------AAAGATCTTT----------ATAGAC----TAC-GC----GTATTTCCATT--T--A----------ATATAGTTC--TATTAAAC----TTAACT
dp4	chrXL_group1e:10317112-10317245 +	471	TCAAACAT--ATTATTTTTATTG--------TAA-----ATATCCTAGTTATGGT-------------------------------------------GTAAA---------------------------------------------T-CTGAAAATATCGATGTT---TGAGAAAAAACATCGA------------------------TGACATCCAT----------GTTAAC----ATCGAT----GTTTGTCCAGCTTTAGC----------TTGCATCCC--TAG-----------CTTG
droPer1	super_69:203478-203603 -	5930	CATATT-------ATTATTGTAA--------ATA--------TCCTATTTATAGT-------------------------------------------GTAAA---------------------------------------------T-CTGAAAATATCGATGTT---TGAGAAAAAACATCGA------------------------TGACATCCAT----------GTTAAC----ATCGAT----GTTTGTCCAGCTTTAGC----------TTGCATCCC--TAG-----------CTTG
droWil1	scaffold_181155:90645-90784 -	12297	TATTGTTT--CCGCCTCTTCTGA--------TCAATC------------------------------------TA--------TTTCTAATTTATTTGCT-AA---CTTCTTCTCGACTACGTACATATCTACTACGTACAACTCTAGT--CAGATATATCCATATC---CTATAACGAA-------------------------------------------------------------------------------------------------ATCCAACTG--CATTCTTA----ATCGTG
droVir3	scaffold_13036:829247-829384 -	7674	TTTATCGT--TTATATTT-----------------G-------------------AAATTATTAATTAAA---TT--------ATTATTATTTTTAAGTAATA---------------------------------------------C----------------------A---AAATAAATTAA------------------------GGAAATAAAAGTGCAAATTTGTTGTT----TTCAAA----G-ATACATTTAATTAAT----------TTTTATTTT--TTTTTTAT----TTTATT
droMoj3	scaffold_6500:19787300-19787437 -	10909	TATTATGA--G---CTGAAATAA--------ATATAA------------------------------------AA--------ATATTTAA--TTAAATTCAACAAAATGAT-------------------------------------GTC-------TAGATATT---AA-----AAAAAAAAA------------------------AAAAAATAAA----------ATATAT----ATATAT----ATATATATATATATATA---------TATATATATA--TATTTTTT----TTTTTT
droGri2	scaffold_14853:4224791-4224937 -	652	TATATC-T--ATGCGTCTG-TAGATACTTGCATAAGT------------------------------------GT------AT-CATCTATGTACGGTTTACA---------------------------------------------TATAGTGT---ATGGTTTA---TA---AAAAATATTTC------------------------TCAATACGCC----------GTTAGT----ACAAAA----AAAAAGTAGTGTATAAA----------AAATGCTTG--CACTTTGT----TTTAGT

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TATGACATCTGCCTGTTATGAAT------------------------------------ACATAT-ATTTTTATGTTTGAG-TC---------------------AACATCGAG-TTGCCG--ATGTT------------TGGAAAACA--TCGATGACATCG--------CTGTTGGCATCG----AAATATGTCCATATCTAATATATAGTTCCA-----------------TTC------TGTTTTATT

Size

Hit Count

Total Norm

droSim1

AATGACAGCTGCCTGTTATAAGT------------------------------------AATTGT-ATTTTTATGTTTGAGCTA---------------------AACATCGATTATGCCG--ATGTT------------TGGAAAACA--TCGATGACATCG--------CTCTTGCCATCA----AAGTATGTCCATATCTAATATATAGTTCCA-----------------TTC------TGTTATATT	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
.........................................................................................................................................................GATGAAATCG--------CTCGTGCC.........................................................................	18	1	3.00	0.00	0.00	3.00	0.00
................................................................................................................................................................................................................ATAGTTCCA-----------------TTC------TGTTATAT.	20	1	1.00	1.00	0.00	0.00	0.00

droSec1

AATGACATCTGCCTGTTGTAAGT------------------------------------AATTGT-ATTTTTATGTTTGAGCTA---------------------AACATCGATTATGCCG--ATGTT------------TGGAAAACA--TCGATGACATCG--------CTGTTGCCATCA----AAGTATGTCCATATCTAATATATAGTTCCA-----------------TTC------TGTTATATT	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
............................................................................................................ATCGATTATGCCG--ATGTT------------TGGAAAA.........................................................................................................	25	1	1.00	0.00	1.00	0.00
.................................................................................................................................................AACA--TCGAGGACATCG--------AT...............................................................................	18	1	1.00	0.00	1.00	0.00
......ATTTGCCTGTTTTAAGT------------------------------------A................................................................................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

TATGATATCTGAATATTTAGTT---------------------------TTTCTTTTGCATATTT-ATTTTTAATATTGAGCTT---------------------CACATATATATTGCCG--ATGTT------------TACAAAACA--TCGATGACATTG--------TTTTTGGCATCG----TCATATGCCCATCACTAATATATAGTCCCC-----------------TTC------TGTTTCATT	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.....................................................TGTAGCATATTT-ATTTTT....................................................................................................................................................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................CATCG----TCATATGCCCATCACT.................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................................................................................................................................CATCG----TCATATGCCCATCACTAATA.............................................	25	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

AAAGGCATCTGTATAGGATGAAT------------------------------------AAATTA-ATTTTTAAGTTTGACCAC---------------------AACTTTCATTTTGCCG--ATGTT------------TAGAAAACA--TCGATGACACCGCATCAT---CGTTGTCATCGACTTACATATGTACATCTCTAATATATAGTATCA-----------------TTC------TGTTTTATT	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...................................................................................................................................................................CAGCAT---CGTGGTCATCGA....................................................................	18	1	2.00	0.00	0.00	0.00	2.00
.........................................................................................................................................................GATGACAxCGCAACAT---CGT.............................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.................................................................................................................................................................................................GTACATCTCTAATATATAGT.......................................	20	1	1.00	0.00	0.00	0.00	1.00
.................................................................................................................................................................................................GTACATCTCTAATATATAGTATC....................................	23	1	1.00	1.00	0.00	0.00	0.00
.................................................................................................................................................................CGCAACAT---CGTTxTCATCGAC...................................................................	20	1	1.00	0.00	0.00	1.00	0.00

droAna3

AAATACAACTTTTAATAGA---------------------------GTTACATTTT---------C-----------------------TAAAAT------A---------------------TTATT------------TAAAATTCT--ACGATA-CACTACGATATCACTA-TGACATTT----AAAAATGTTTCTGTCACT-TTAAAGACTAA-----------------ATT------TAGATACTT	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
.......................................................................................................................................................................................................................................................TTCTT	21	33	0.03	0.00	0.00	0.00	0.03
...................................................ATTTT---------C-----------------------CAAAAx------A---------------------TTATT------------T...............................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................A---------------------TTATC------------TAAAATTCA--ACGA.................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00

dp4

GAAGAAGTTTTAATGTCAACAA-----------------------------------------AA-ATTTCCA----------------CGACGT------GGAAG---------ACGCCGTTCTACG------------A---AAATA--CTGA-----------------------------------------------------AAAGATTTAATTTACATATAACTCTGGTCACACATATTTTATCC

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

GAAGAAGTTTTAAtgatgtacat------------------------------------acatat-gtatgtatgtctgCTACAAAAGA--ATAAGTAC----------------GTGAGC--ACGTG------------CGGCAAACC-----------------------TCTT---GCTCATTTATATATTTACAC-ACTAACACATACATAC------------------------------------	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
....................................................................................................................TAAGC--ACGGG------------CGGCAAAC........................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00
..................TACAT------------------------------------ACATAT-GTAGATATGT................................................................................................................................................................................	21	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................ATATAT-GTATGTATGTATG.............................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00	0.00
..................TACAT------------------------------------ACATAT-GTGTGTAC..................................................................................................................................................................................	19	2	0.50	0.00	0.00	0.50	0.00	0.00
.....................TT------------------------------------ACATAT-GGATGTATGT................................................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00	0.00

droWil1

TGTGCTATTTTTGCGGTTAAACTCAATGTCTTTTCTTACCATTAGATTAAAATTTT---------G-----------------------TAAAAT------G---------------------GAAACTAAAAATATAAAG---TTC-------------------------------TATTA----A----AGTTTAAACTTTATAGAGAATTTTAAC---------------TTT------TACTCGGTT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
..................................................................................................................................AAAATATAAAG---TTT-------------------------------TAGT......................................................................	18	1	2.00	0.00	2.00	0.00	0.00
..................................................................................................................................AAAATATAAAG---TTT-------------------------------TAGTA----.................................................................	19	1	1.00	0.00	1.00	0.00	0.00
............................................................................................................................AAAGTAAAAAAATAAAG---T...........................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.............................CTTATCTTACCATTACAT.............................................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
....................................................................................................................................AATATAAAG---TTT-------------------------------TAGTA----A----............................................................	18	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................AAG---TTC-------------------------------TATTA----A----AGTCTA......................................................	18	1	1.00	0.00	1.00	0.00	0.00
....................................................................................................................................AATATAAAG---TTT-------------------------------TAGTA----A----A...........................................................	19	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................TAAAAA------G---------------------GAAACAAAAAA......................................................................................................................	18	2	0.50	0.00	0.50	0.00	0.00
................................................AAAATCTT---------G-----------------------TAAAAT------G---------------------GAG..............................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
..........................................TAGAxTAAAGTTTT---------G-----------------------TAAA...............................................................................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

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

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

GCAACAACT-TTCTATGAGT--------------------------TGTCC---------------A----------------------AAAAATTGAAGCG---AATTT-----CTGAAATTTCGTT------------AA-----AAGTAAAAC----TTA--------CGAATTGtaatt----aaATATGTCCATGTCCATTAGTCAGTGCTG-----------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

droGri2

TCTGACACTGTAGATGCGC---------------------------CTTAC---------------AGTTTA-------------------ACACTGACATG---AACAT-----TCGCCGCTATGCT------------TA---CACA--CAAATAACAGAA--------CCA-----GTTC----AAGTAGTTC-------CGAAAATAATTCCA-----------------CT-------AGTTAATTG

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

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