dme-mir-2490- 12- and 20-way alignments

dme-mir-2490	chr2LHet:27336-27410 +	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_intron

Legend:

   mature strand at position 27344-27366
   star strand at position 27382-27402
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr2LHet:27321-27425 +	ACAATCGTACGTTCTGAGCGAGTTGAAGC-------GATAAAGCAGGTTGCAAACTGCTCTCTCGCT----TTGCTCTTACTTTATCGCTTAAACT-------------------------------------------------------------------------------------CGCAA--CTCGCTTCGCTCTCA
droSim1	Unknown	ACAATCGTACGCTCTGAGCGAGTTGAAGC-------GATAAAGTTGGTTCAAACTGCCTCTCTCGCT----TTGTTCTTGCTTTATCGTTTGAGCT-------------------------------------------------------------------------------------CGCAA--CTCCCTTTGCTTTCA
droSec1	super_894:1929-1994 +	ACAATCGTACGCTCTGAGCGAGTTGCAGC-------GATAAAGCAGGTTGGAAAAGGCGATTTCGATAA--TTTATATCGCTTTATCGCTTGAGCT-------------------------------------------------------------------------------------CGCAA--CTAGCTTCACTCTCA
droYak2	chr2L_random:2701901-2701994 +	ACAATCGTACGCTCTGAGCGAGTTGAAGC-------GATAAAGCAGGTTGCAAACTGCTCTCTAGC---------------TTTATCGCTTGAGCT-------------------------------------------------------------------------------------CGCTA--CTCGCCTCGCTCTCA
droEre2	scaffold_4784:23773188-23773264 -	CC-----------------GAGTTGATGC-------GATAAACCAGGCTGCAAGCTGATCTCTCGC---------------TTTATCGCTTGAGCT-------------------------------------------------------------------------------------CGCAA--CTCGATTCGCTCTCA
droAna3	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
dp4	Unknown	AAAAGCATGAGCGT-CCACGAGATCAAGC-------GATAAGACATTTGCAAAGCTACTCTCTTGCT----TC--------------GCTTGCACTCGTTGCTGTCTTCGCTATAACTTGTTTCCCGCTCTTCACTGTAAATCGTTTTGCACTCTTCGCTCAAACT----------AGCCGCGCTG--CTCTCTTTGCTCTCA
droPer1	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	Unknown	ACACACGTATAACAACAGTTGGATGAAGC-------GATAAAGCGAGATCAGAATCGCTTTCTCGCA-A--CTCGCTTCAACTTGTCGCTTTGGCT-------------------------------------------------------------------------------------CTCTT--CTCGCTTCGCTTGCA
droVir3	Unknown	-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6500:29678071-29678204 +	TCAAGCG-AAGCGAGAAGAGAGCCAAAGCGTGTTGCGAAAAAGCTTGATA-AAGCTGTTCT---GATACGTGTGTTTTTTTTTTGC----------------------------------------------------------------GTTCTGAGCTTAAATAACCGTTGGTTAGTCGGGGAAGTATATTCCTTTTCGCA
droGri2	scaffold_15110:6573670-6573765 -	TCAAGTGCAACATCAGCGCGAGTGTTAGA-------TACAAAGAC------AAGTAGTTGTCACAC---------------T--------------------------------------------------CATTGC------------AAGTAG------AGCT----------GAAAGAGATG-AATTTCTTCGCTCTCA

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr2LHet:27321-27425 +	NA	ACAATCGTACGTTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGC--TTTGCT----------------CTTACTTTATCGCTTAAACTCGCAACTCGCTT--------------------------------------------------------------------------CGCT-----CTCA
droSim1	chr4:281112-281214 +	69	AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGC--TTTGCT----------------CTCGCTATATCGCTTGAGCTCGCAACTCGCTT--------------------------------------------------------------------------CGCT-------CA
droSec1	super_30:85009-85111 +	41	AAAATCGTACGCTCTGAGCGAGTTGAAGCAATAAAGCAGGTTGCAAACTGCTCTTTCGC--TTTGCT----------------CTCGCTATATCGCTTGAGCTCGCAACTCGCTT--------------------------------------------------------------------------CGCT-------CA
droYak2	chrU:9061077-9061181 +	96	ACAATCGTACGCTCTGAGCGAGTTGAAGCGATAAAGCAGGTTGCAAACTGCTCTCTCGC--TTTGCT----------------CTCGCTTTATCGCTTGAGCTCGCTACTCGCCT--------------------------------------------------------------------------CGCT-----CTCA
droEre2	scaffold_4784:23192819-23192904 -	56	ACTATCAGACGCTCTGAGCGAGTTGCAGCGATAATGCAGGTTGCAAACTGTTCTCT-------------------------------------CGCTTGAGCTCGCAACTCGTTT--------------------------------------------------------------------------CGCT-----CTCA
droEug1	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBia1	scf7180000301391:7073-7197 -	13	ACTTTTGTAGCTTCTGCAGGCATTTGG----CTGTGTAGATTGTATGGTCTCCGAT-------------------------------------AAGTAGTAGTCGAAAGTCCCT--------------CACGATGACAACGTTTGTAACG--------TACCAGGGGAGCTCGAATGCTCGCCG-----A--G-------CT
droTak1	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droEle1	scf7180000490727:38228-38321 -	15	AGAA-CTTACGTTTTGATTAAGTTCAAGCGATAAAGCAAGTTCAAAACTGATCTCTTTC--TTTGCC----------------CTCAATTTTTCGCTTCGTT----------TTT--------------------------------------------------------------------------CGCA-----GCCA
droRho1	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droFic1	scf7180000453955:804345-804445 -	31	AAAATTTTTCGATCGG-----G--------------CTCCCCCCAAAATTTTTTCTGCG--TCCGC-----------------------------------------CCCTGACTG------------------------GCTTGTGACC--------TACCAGGGAAGCCCGGATGCCCGTCG-----A--GCAGCACGTG
droKik1	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droAna3	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droBip1	scf7180000396710:138523-138625 +	61	ACAATCGAACGCTCTGAGCGAGTTGAAGCGATGAAGCTGGTTGCAAACTGCTCTCTC----TTTCCT----------------CCCGCTTTATCGCTTGAACTCGCAACTCGCTT--------------------------------------------------------------------------CGGT-----TTTA
dp4	chr4_group4:3101286-3101457 +	2	AGCAT-GAGCG---TCCACGAGATCAAGCGATAAGACATTTGCAAAGCTACTCTCTTGC--TTCGCTTGCACTCGTTGCTGTCTTCGCTATAA-------------------CTTGTTTCCCGCTCTTCACTGTAAATCGTTTTGCACTCTTCGCTCAAACTAGCCGCGCTGCTCTCTTCGCTTATCTTTGCT-----CTCA
droPer1	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droWil1	scaffold_181143:687820-687924 +	3	ACACACGTATAACAGCAGCTGGATGAAGCGATAAAGCGA-TTCAGAATCGCTTTCTCGCAACTCGCT-----------------TCAACTTGTCGCTTTGGCTCTCTTCTCGCTT--------------------------------------------------------------------------CGCT-----TGCA
droVir3	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6498:432956-433055 +	4	AACAC---ACTTTAT-CATGCGATTAAGCGAGAAAGCGA-TTCAGGAATGCTTTCTCGC--AACTCG----------------CTTAACTTCTCGCTTTGGGTCTCTTCTCGCTT--------------------------------------------------------------------------CGCT-----TGCA
droGri2	Unknown	NA	----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ACAATCGTACGTTCTGAGCGAGTTGAAGC-------GATAAAGCAGGTTGCAAACTGCTCTCTCGCT----TTGCTCTTACTTTATCGCTTAAACT-------------------------------------------------------------------------------------CGCAA--CTCGCTTCGCTCTCA

Size

Hit Count

Total Norm

droSim1

ACAATCGTACGCTCTGAGCGAGTTGAAGC-------GATAAAGTTGGTTCAAACTGCCTCTCTCGCT----TTGTTCTTGCTTTATCGTTTGAGCT-------------------------------------------------------------------------------------CGCAA--CTCCCTTTGCTTTCA	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..AATCGTACGCTCTGAGCGA......................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...................................................................................TATCGCTTGAGCT-------------------------------------------------------------------------------------CGCAA--CTC............	21	1	1.00	0.00	1.00	0.00	0.00
..AATCGTACGCTCTGAGCGG......................................................................................................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
...ATCGTACGCTCTGAGCGG......................................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..AATCGTACGCTCTGAGCGAGTTAAAGC-------.......................................................................................................................................................................	27	1	1.00	0.00	0.00	1.00	0.00

droSec1

ACAATCGTACGCTCTGAGCGAGTTGCAGC-------GATAAAGCAGGTTGGAAAAGGCGATTTCGATAA--TTTATATCGCTTTATCGCTTGAGCT-------------------------------------------------------------------------------------CGCAA--CTAGCTTCACTCTCA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
......................TTGAAGC-------AATAAAGCAGGTTG.........................................................................................................................................................	21	1	2.00	0.00	0.00	2.00
...............................................................................................T-------------------------------------------------------------------------------------CGCAA--CTCGCTTCGCTCTCA	21	1	1.00	1.00	0.00	0.00
.......................................TGAGCAGGTTGGAAAAGG..................................................................................................................................................	18	1	1.00	0.00	0.00	1.00

droYak2

ACAATCGTACGCTCTGAGCGAGTTGAAGC-------GATAAAGCAGGTTGCAAACTGCTCTCTAGC---------------TTTATCGCTTGAGCT-------------------------------------------------------------------------------------CGCTA--CTCGCCTCGCTCTCA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
.....................GTTGAAGC-------GATAAAGCAGGTTGCA.......................................................................................................................................................	24	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................TGAAGC-------GATAAAGCAGGTTGCA.......................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.......................TGAAGC-------GATAAAGTAGGTTGCAAACAGC.................................................................................................................................................	28	1	1.00	0.00	0.00	1.00	0.00	0.00
.....................GTTGAAGC-------GATAAAGCAGGTTGC........................................................................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
.......................TGAAGC-------GATAAAGCAGGTTGCC.......................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00

droEre2

CC-----------------GAGTTGATGC-------GATAAACCAGGCTGCAAGCTGATCTCTCGC---------------TTTATCGCTTGAGCT-------------------------------------------------------------------------------------CGCAA--CTCGATTCGCTCTCA

Size

Hit Count

Total Norm

V040
Embryo

V060
Head

V047
Embryo

V108
Head

droAna3

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

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

AAAAGCATGAGCGT-CCACGAGATCAAGC-------GATAAGACATTTGCAAAGCTACTCTCTTGCT----TC--------------GCTTGCACTCGTTGCTGTCTTCGCTATAACTTGTTTCCCGCTCTTCACTGTAAATCGTTTTGCACTCTTCGCTCAAACT----------AGCCGCGCTG--CTCTCTTTGCTCTCA	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
........................................................................................CTTGCACTCGTTTCGGTC.................................................................................................	18	1	3.00	0.00	0.00	0.00	3.00
........................................................................................CTTGCACTCGTTTCGGTCT................................................................................................	19	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................TTGCACTCGTTTCGGTCT................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................GCACTCGTTGCTGTTGTCGC............................................................................................	20	1	1.00	0.00	1.00	0.00	0.00

droPer1

Size

Hit Count

Total Norm

V111
Male body

V042
Embryo

V050
Head

V057
Head

M021
Embryo

droWil1

ACACACGTATAACAACAGTTGGATGAAGC-------GATAAAGCGAGATCAGAATCGCTTTCTCGCA-A--CTCGCTTCAACTTGTCGCTTTGGCT-------------------------------------------------------------------------------------CTCTT--CTCGCTTCGCTTGCA	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...............................................TTCAGAATCGCTTTCTCGCA-A--CTCGCT..............................................................................................................................	27	1	4.00	0.00	4.00	0.00	0.00
...................................................................................TGTCGCTTTGGCT-------------------------------------------------------------------------------------CTCTT--CTCGCTT........	25	1	2.00	0.00	2.00	0.00	0.00
...............................................TTCAGAATCGCTTTCTCGCA-A--CTCGCTT.............................................................................................................................	28	1	2.00	0.00	2.00	0.00	0.00
........ATAACAAAAGTTGTATGA.................................................................................................................................................................................	18	1	2.00	0.00	2.00	0.00	0.00
.CACACGTATAACAATAGTTGGATG..................................................................................................................................................................................	24	1	2.00	0.00	0.00	0.00	2.00
.........................................................................CGCTTCAACTTGTCGCTTTGGCT-------------------------------------------------------------------------------------......................	23	1	1.00	0.00	1.00	0.00	0.00
................................................TCAGAATCGCTTTCTCGCA-A--CTCGCT..............................................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00
.......................................................CGCTTTCTCGCA-A--CTCGCTTCAAC.........................................................................................................................	24	1	1.00	0.00	1.00	0.00	0.00
................................................TCAGAATCGCTTTCTCGCA-A--CTCACT..............................................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00
.............................................................................TCAACTTGTCGCTTTGGCT-------------------------------------------------------------------------------------CTCTT--CT.............	26	1	1.00	0.00	1.00	0.00	0.00
.......................................................CGCTTTCTCGCA-A--CTCACTTCAACT........................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
.......TATAACAACAGTTGGATGAAG...............................................................................................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00
...................................................................................TGTCGCTTTGGCT-------------------------------------------------------------------------------------CTCTT--CTCGCT.........	24	1	1.00	0.00	1.00	0.00	0.00
...................................................................................TGTCGCTTTGGCT-------------------------------------------------------------------------------------CTCTT--CTC............	21	1	1.00	0.00	1.00	0.00	0.00
...........................GC-------GATAAAGCGAxTTCAGAATCG..................................................................................................................................................	22	1	1.00	0.00	1.00	0.00	0.00
........ATAACAAAAGTTGTATGAA................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
......................................................................................CGCTTTGGCT-------------------------------------------------------------------------------------CTCTT--CTCGCTTCGC.....	25	1	1.00	0.00	1.00	0.00	0.00
............................................................TCTCGCA-A--CTCGCTTCAACTTGTCG...................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
............CAACAGTTGGATGAAGC-------GATA...................................................................................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00
..................TTGGATGAAGC-------GATAAAGCGAG............................................................................................................................................................	22	1	1.00	1.00	0.00	0.00	0.00
.............AACAGTTGGATGAAGC-------GATAAAG................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
......................................................TCGCTTTCTCGCA-A--CTCGCTTCAAC.........................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
......................................................................................CGCTTTGTCT-------------------------------------------------------------------------------------CTCTT--CTCGCTTCGCT....	26	1	1.00	0.00	1.00	0.00	0.00
.................................................CAGAATCGCTTTCTCGCA-A--CTCGCTT.............................................................................................................................	26	1	1.00	0.00	1.00	0.00	0.00
.CACACGTATAACAACAGTTGGATGAAG...............................................................................................................................................................................	27	1	1.00	0.00	1.00	0.00	0.00
.............AACAGTTGGATGAAGC-------GA.....................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................A-A--CTCGCTTCAACTTGTCGCTTTTGCT-------------------------------------------------------------------------------------C.....................	28	1	1.00	0.00	1.00	0.00	0.00
.........................................................................CGCTTCAACTTGTCGCTTTGGCT-------------------------------------------------------------------------------------CT....................	25	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

TCAAGCG-AAGCGAGAAGAGAGCCAAAGCGTGTTGCGAAAAAGCTTGATA-AAGCTGTTCT---GATACGTGTGTTTTTTTTTTGC----------------------------------------------------------------GTTCTGAGCTTAAATAACCGTTGGTTAGTCGGGGAAGTATATTCCTTTTCGCA	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
......................................................................CGTGTTTTTTTGTTGC----------------------------------------------------------------GTTCT................................................	21	1	1.00	1.00	0.00	0.00	0.00

droGri2

TCAAGTGCAACATCAGCGCGAGTGTTAGA-------TACAAAGAC------AAGTAGTTGTCACAC---------------T--------------------------------------------------CATTGC------------AAGTAG------AGCT----------GAAAGAGATG-AATTTCTTCGCTCTCA

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
UNAFold Image						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		None		None		None	None			None		None		None
UNAFold Image						None		None		None		None	None			None		None		None