dme-mir-4983- 12- and 20-way alignments

dme-mir-4983	chr2R:15524918-15525026 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intergenic

Legend:

   mature strand at position 15524986-15525007
   star strand at position 15524936-15524957
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2R:15524903-15525041 +	A--ACACATCTGCCCGCTGG-CTGGC--------TGT-------CTTGACCCACTTGCT---CGTTTGCA------TT-TCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----
droSim1	chr2R:14228631-14228769 +	A--ACACATCTGCCCGCTGG-CTGGC--------TGT-------CTTGACCCACTTGCT---CGTTTGCA------TT-TCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----
droSec1	super_1:13039564-13039702 +	A--ACACATCTGCCCGCTGG-CTGGC--------TGT-------CTTGACCCACTTGCT---TGTTTGCA------TT-TCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----
droYak2	chr2R:13649050-13649195 -	A--ACACATCTGCCCGCTGG-CTGGC--------TGT-------CTTGACCCACTTGCT---CGTTTGCATTTGTATTTTCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----
droEre2	scaffold_4845:9723500-9723642 +	A--ACACATCTGCCCGCTGG-CTGGC----TGGCTGT-------CTTGACCCACTTGCT---CGCTTGCA------TT-GCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCCTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----
droAna3	scaffold_13266:9754397-9754555 -	AAAACACAAACGCCCGCTGG-C------------TGT-------CTTGACCCACTTGCT---TGTTTGCA------TT-TCTCGCAAAAATATTCATATGCAAGACCAAAATCAGAATCAGAAATTCTTTTG-GGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTCTATATGTACATCTAGTAC----
dp4	chr3:12652733-12652881 +	A--ACACGTCTCTCCGTTTGTCAGTCTTTCAGTCTGTCAGCATGCTTGACCCACTTGATGTGCTTTTGAA------TT-TTAG--AAATATGT---------------AAATCAAATTCTGAAACATTTCGGGGACAAGTTTATGTGTCATTAAATTCCCCA----ATTTT-------AT-------------ACTAAA
droPer1	super_2:8929611-8929759 -	A--ACACTTCTCTCCGTTTGTCAGTCTTTCAGTCTGTCAGCATGCTTGACCCACTTGATGTGCTTTTGAA------TT-TTAG--AAATATGT---------------AAATCAAATTCTGAAACATTTCGGGGACAAGTTTATGTGTCATTAAATTCCCCA----ATTTT-------AT-------------ACTAAA
droWil1	Unknown	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	A--ACACTTTTGAGTGCCAG-CTTT-------------------CTCATATCAAACGCT---CG---ACATTTGTCTT-TTTG--AGGGGGGT--TCTCGCAC-----A------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:20896701-20896727 +	A--ACACTTTTGACTGCTGC-CAGCC--------TGC-------C----------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2R:15524903-15525041 +	NA	A--ACA-CATCTGCC---CGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-CG--TTTGCATTT-------CTG------AAAA---ATGTATACGCAA-AAA-CCAAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droSim1	chr2R:14228631-14228769 +	1	A--ACA-CATCTGCC---CGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-CG--TTTGCATTT-------CTG------AAAA---ATGTATACGCAA-AAA-CCAAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droSec1	super_1:13039564-13039702 +	1	A--ACA-CATCTGCC---CGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTT-------CTG------AAAA---ATGTATACGCAA-AAA-CCAAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droYak2	chr2R:13649050-13649195 -	1	A--ACA-CATCTGCC---CGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-CG--TTTGCATTTGTATTTTCTG------AAAA---ATGTATACGCAA-AAA-CCAAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droEre2	scaffold_4845:9723500-9723642 +	1	A--ACA-CATCTGCC---CGCTGG-CTGGCTG----------GCT----GT-------CTTGACCCACTTGCT-CG--CTTGCATTG-------CTG------AAAA---ATGTATACGCAA-AAA-CCAAAATCA------GAAATTCCTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droEug1	scf7180000409474:2425232-2425371 -	1	A--ACA-CATCTGCC--CCGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTT-------CTG------AAAA---ATGTATACGCAA-AAA-CCAAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droBia1	scf7180000302143:3024933-3025070 +	2	A--ACA-CATCTGCC---CGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTT-------CTG------AAAA---ATGTATACGCAAA--A-CCGAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droTak1	scf7180000415384:129223-129366 -	1	A--ACA-CATCTGCC---CGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTT-------CTGAATCTGAAAA---ATGTATACGCAAA--A-CCAAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droEle1	scf7180000491201:1980229-1980378 +	2	A--ACA-CATCTGCC---CGCTGG-CTGGCTGGCTGGTTG--GCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTT-------CTG------AAAT---ATGTATACGCAAA--A-CCAAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droRho1	scf7180000780066:106697-106838 -	1	A--ACA-CATCTGCC---CGCTGG-CTGGCTG----------GCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTT-------CTG------AAAT---ATGTATACGCAAA--A-CCAAAATCA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droFic1	scf7180000454039:817245-817390 +	2	A--ACA-CATCTGCC---CGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-CGCATTTGCATTT-------CTCAAAAAAAAAA---ATGTATACGCAAA--A-CCAAAATCC------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droKik1	scf7180000302679:61967-62124 +	3	A--ACAGCATCTGTGTGCTGCTGG-CTGG-----TGGCTGGCGCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTTCAAAAA--TG------AAAA---ATGTATACGCAA-AAACCCGAAAACA------GAAATTCTTTTGA-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATA---------------TAC
droAna3	scaffold_13266:9754397-9754555 -	2	AAAACA-CAAACGCC---CGCTG-------------------GCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTT-------CTCG-----CAAAAATATTCATATGCAAG--A-CCAAAATCAGAATCAGAAATTCTTTTGG-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCTCTATATGTA----CATCTAGTAC
droBip1	scf7180000396427:901727-901882 -	2	A--CCA-CAAACGCC---CGCTGG-CTG--------------GCT----GT-------CTTGACCCACTTGCT-TG--TTTGCATTT-------CTG------AAAAAATATTTATATGCAAG--A-CCAAAATCA------GAAATTCTTTTGG-GCAAGT----GTGTCATGAAATTGCC-ATTCGTTTCTGCTCT--ATATGTACATACATCTAGTAC
dp4	chr3:12652733-12652881 +	2	A--ACA-CGTCTCTC---CGTTTGTCAGTCTTTCAG------TCT----GTCAGCATGCTTGACCCACTTGATGTGCTTTTGAATTT-------TAG------AAAT---ATGTA---------AA-TCAAATTCT------GAAACATTTCGGGGACAAGTTTATGTGTCATTAAATTCCCCA----ATTTTATACT--AAA------------------
droPer1	super_2:8929657-8929759 -	3	A--ACA-CTTCTCTC---CGTTTGTCAGTCTTTCAG------TCT----GTCAGCATGCTTGACCCACTTGATGTGCTTTTGAATTT-------TAG------AAAT---ATGTA---------AA-TCAAATTCT------GAAACATTT----------------------------------------------------------------------
droWil1	Unknown	NA	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	scaffold_12875:4153222-4153295 -	2	A--ACA-CTTTTGAG---TGCCAG-CTT--------------TCTGAGCAT-------ATCAAA-CGCTCGA--CA--TTTGTCTTT-------TTG------AGGG---GGGTTCTCGCAC-A-------------------------------------------------------------------------------------------------
droMoj3	scaffold_6496:20896701-20896727 +	1	A--ACA-CTTTTGAC---TGCTGC-CAG--------------CCT----GC-------C------------------------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	NA	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

A--ACACATCTGCCCGCTGG-CTGGC--------TGT-------CTTGACCCACTTGCT---CGTTTGCA------TT-TCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----

Size

Hit Count

Total Norm

droSim1

A--ACACATCTGCCCGCTGG-CTGGC--------TGT-------CTTGACCCACTTGCT---CGTTTGCA------TT-TCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
....................................................................................................CAA-----AAACGAAAACCAGAA............................................................................	18	1	1.00	1.00	0.00	0.00	0.00

droSec1

A--ACACATCTGCCCGCTGG-CTGGC--------TGT-------CTTGACCCACTTGCT---TGTTTGCA------TT-TCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
........................................................................................................................GAAATTCTTTTG-AGCAAG----TGTG....................................................	22	1	2.00	1.00	0.00	1.00
.........................................................................................................................AAATTCTTTTG-AGCAAG----TGTG....................................................	21	1	1.00	0.00	0.00	1.00
........................................................................................................................GAAATTCTTTTG-AGCAAG----TGTGT...................................................	23	1	1.00	1.00	0.00	0.00
........................................................................................................................GAAATTCTTTTG-AGCAAG----TGT.....................................................	21	1	1.00	0.00	0.00	1.00
............................................................................................................AAACCAAAACCAGAAGTT.........................................................................	18	1	1.00	0.00	1.00	0.00
.........................................................................................................................AAATTCTTTTG-AGCAAG----TGT.....................................................	20	1	1.00	1.00	0.00	0.00
..........................................................................................................................AATTCTTTTG-AGCAAG----TGTGTCA.................................................	23	1	1.00	0.00	0.00	1.00
....................................................................................................................................................GATGAAATTGCC-ATTGGT................................	18	1	1.00	0.00	1.00	0.00
............................................................................................................................TTCTTTTG-AGCAAG----TGTGTCA.................................................	21	1	1.00	1.00	0.00	0.00
........................................................................................................................GAAATCCTTTTG-AGCAAG----TGT.....................................................	21	1	1.00	0.00	0.00	1.00
.........................................................................................................................AAATTCTTTTG-AGCAAC----TGTG....................................................	21	1	1.00	1.00	0.00	0.00

droYak2

A--ACACATCTGCCCGCTGG-CTGGC--------TGT-------CTTGACCCACTTGCT---CGTTTGCATTTGTATTTTCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCTTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
......................................................................................................................AAGAAATTCCTTTG-AGCA..............................................................	18	1	1.00	0.00	0.00	0.00	1.00	0.00

droEre2

A--ACACATCTGCCCGCTGG-CTGGC----TGGCTGT-------CTTGACCCACTTGCT---CGCTTGCA------TT-GCTG--AAAAATGT--ATACGCAA-----AAACCAAAATCAGAAATTCCTTTG-AGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTATAT-------------AC----	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
....................................................ACTTGCT---CGCTCGGA------TT-G.......................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00

droAna3

AAAACACAAACGCCCGCTGG-C------------TGT-------CTTGACCCACTTGCT---TGTTTGCA------TT-TCTCGCAAAAATATTCATATGCAAGACCAAAATCAGAATCAGAAATTCTTTTG-GGCAAG----TGTGTCATGAAATTGCC-ATTCGTTTCTGCTCTCTATATGTACATCTAGTAC----	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
...................................................................................ACAAAAATATTCTTAT....................................................................................................	16	1	1.00	0.00	0.00	1.00	0.00

dp4

A--ACACGTCTCTCCGTTTGTCAGTCTTTCAGTCTGTCAGCATGCTTGACCCACTTGATGTGCTTTTGAA------TT-TTAG--AAATATGT---------------AAATCAAATTCTGAAACATTTCGGGGACAAGTTTATGTGTCATTAAATTCCCCA----ATTTT-------AT-------------ACTAAA

Size

Hit Count

Total Norm

V112
Male body

V043
Embryo

V051
Head

M022
Male body

droPer1

A--ACACTTCTCTCCGTTTGTCAGTCTTTCAGTCTGTCAGCATGCTTGACCCACTTGATGTGCTTTTGAA------TT-TTAG--AAATATGT---------------AAATCAAATTCTGAAACATTTCGGGGACAAGTTTATGTGTCATTAAATTCCCCA----ATTTT-------AT-------------ACTAAA

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

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

Size

Hit Count

Total Norm

V117
Male body

V118
Embryo

V119
Head

M020
Head

droVir3

A--ACACTTTTGAGTGCCAG-CTTT-------------------CTCATATCAAACGCT---CG---ACATTTGTCTT-TTTG--AGGGGGGT--TCTCGCAC-----A------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

A--ACACTTTTGACTGCTGC-CAGCC--------TGC-------C----------------------------------------------------------------------------------------------------------------------------------------------------------

Size

Hit Count

Total Norm

V110
Male body

V056
Unknown

V049
Head

V041
Embryo

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
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			None
UNAFold Image																	None			None