dme-mir-4954- 12- and 20-way alignments

dme-mir-4954	chrX:1923036-1923127 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	intron

Legend:

   mature strand at position 1923090-1923111
   star strand at position 1923057-1923077
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chrX:1923021-1923142 -	ATATAAGTGTTC-----------GATTTGGCGCTTGGAATCGATACCCGAGCCATGATAGATTGAAGTCAACCC-AATCGAT--CGC-GGT-TCGAGTGCTCGAGTCTTGTGCGCCGGCATGCT-TGAGATG-------TCCACTA
droSim1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	super_10:1708076-1708197 -	ATATAAGTGTTC-----------GATTTGGCGCTTGGAATCGACACCCGTGCCCTGATAGATTGAAGTCAACCC-AATCGAT--CGC-GGT-TCGGGTGCTCGAGTCTTGTGCGCCGGCATGCT-TGAGATG-------TCCACTA
droYak2	chrX:6403257-6403382 +	ACATAAAAGTTC-----------AATTTGGCGCTTGGAATCGTAACTCGAGCCCTCAAAGATTGAAGTCAAATGCAATCGAT--CCGGGGTGTCGAGTGCTCGATTCTGGTGCGCCGGCATGCTTTGAGATG-------TCCACTA
droEre2	scaffold_4644:1895276-1895400 -	ATATAAGTGTTC-----------GATTTGGCGCTTGGAATCGAACCTCGAGCCCTGACAGATTGAAGTCAACCCAAAACGAT--CCCGGGG-TCGAGTGTTCGAGTCCGGTGCGCCGGCATGCTTTGAGTTG-------TCCACTA
droAna3	scaffold_12929:1917024-1917094 -	CCTTGACT---TCATAA------------------------G------GAACAAT------------------------GAT--CAT----------------GTTAAGGTTCTCAGGCATGTCTCGAGATTATATCGAATCACTA
dp4	Unknown	tTtTtttT---tgtTtCTGCATAGTGTAGCAGAATGGACTCGGAACTCGATCCATGgtTGggtgtTGggtgtT--GggtgtTAGCGT-GGC-TCGAGTGCCAGAGTCCGGCGAG---GCATG-----A---G-------ACTACTT
droPer1	super_28:1034314-1034357 -	AG----------------------------------------------------------------------------------CGT-GGC-TCGAGTGCCAGAGTCCGGCGAG---GCATG-----A---G-------ACTACTT
droWil1	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------
droGri2	Unknown	--------------------------------------------------------------------------------------------------------------------------------------------------

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

Species	Coordinate	Lastz Id	Alignment
dm3	chrX:1923021-1923142 -	NA	ATATAAGTGTTCGATTT---------------------GGCGCTTGGAATCGATACCCGAGCCATG---------------ATAGATTGAAGTCAAC-CC-AATC-------G-------ATCGCG--GTTCGAGTG-CTCGAGTCTTG-----TGCGCCGGCATGC--TTGAGAT---GTCCACTA
droSim1	Unknown	NA	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droSec1	super_10:1708076-1708197 -	1	ATATAAGTGTTCGATTT---------------------GGCGCTTGGAATCGACACCCGTGCCCTG---------------ATAGATTGAAGTCAAC-CC-AATC-------G-------ATCGCG--GTTCGGGTG-CTCGAGTCTTG-----TGCGCCGGCATGC--TTGAGAT---GTCCACTA
droYak2	chrX:6403257-6403382 +	1	ACATAAAAGTTCAATTT---------------------GGCGCTTGGAATCGTAACTCGAGCCCTC---------------AAAGATTGAAGTCAAATGC-AATC-------G-------ATCCGGGGTGTCGAGTG-CTCGATTCTGG-----TGCGCCGGCATGC-TTTGAGAT---GTCCACTA
droEre2	scaffold_4644:1895276-1895400 -	3	ATATAAGTGTTCGATTT---------------------GGCGCTTGGAATCGAACCTCGAGCCCTG---------------ACAGATTGAAGTCAAC-CCAAAAC-------G-------ATCCCGG-GGTCGAGTG-TTCGAGTCCGG-----TGCGCCGGCATGC-TTTGAGTT---GTCCACTA
droEug1	scf7180000409182:466737-466875 -	1	ATATAAGTGTTGAATTT---------------------GGCGCTTGGAACCGAAACTCGATACGTGATCTATGATCCCTCAATAGGTTCAAGTTAAC-CA-AGGG-------G-------ATCTTT--GAAGCAGTG---CGAGTTCTG-----GGCGCCGGCATGT-TTTCAAATTATGTCCACTA
droBia1	scf7180000301760:4528531-4528646 -	3	-TATAAGTGTTTAACTG---------------------GGCGCTTGAACCCGAAACTCGACCCCTG---------------AGA--ACGACCTCAAG-TC-AAGG-----------------------GATCAAGGG-ATCGAGTTTTG-----GGCGCCGGCATGT-TTTGAGATT-TGTACACTA
droTak1	scf7180000415211:15932-16040 +	1	-TATAAGTGTTTAATTT---------------------GGCGCCTGCAACCGAAACTCGATCCCTG---------------ATATATT---------------------------------TCCCAGAAAATAAGTT-ATCGAGTTTTG-----AGCGCCGGCATGT-TTTGAGATGA--TTAACTA
droEle1	scf7180000491001:1438856-1438974 -	2	-TATAGGTGTTTAATAA---------------------GGCGCTCGGAACCAAAACTCGATCCCTG---------------ATAGGATAAA--AAAC-CA-AAAA-------C-------ATTTTA--GATCCAGTG-TTCGAGTTTTG-----TGCGCCGAAAT------GAGATTGTGTCCACTA
droRho1	scf7180000777830:9566-9691 -	2	-TATAAGTGTTTAATAT---------------------GGCGCTCGGAACCAAAACTCGATCCCTG---------------ATAGGATGAAGTAAAC-CG-AAAC-------C-------ATCTTG--TATCCAGTG-TTCGAGTTCTG-----TGCGCCGGCATGT-CTTGAGATTATGTCTACTA
droFic1	scf7180000454072:3036564-3036665 -	4	-TACAGGTGTTTAAT-T---------------------GGCGCTTCGAAGCAAGACTCGAACTCGA---------------ACCCA--------------------------G-------ATCCTGG----ACAGGA-TTCGAGTTTTG-----TGCGCCGGCATGC-TC-CAGTA---TTCCAATA
droKik1	scf7180000302610:194767-194895 -	3	ACATAACAATAATAATAACAATA----ACAATAGTGAGGATGCAGAGCTCTTAAGCCCGATCTATG---------------ATTGCCCTGTT-----------AA-------G-------ATCGTA--C---------ATCGAGTTTACTTACTAACCCCAAAATATGATTGTGAT---TGATACTA
droAna3	scaffold_12929:1917028-1917098 -	1	ATATCCTTGACTTC------ATAAGGAACAAT--------------------------------------------------------------------------------G-------ATCATG------------T-----TAAGG-----TTCTCAGGCATGT-CTCGAGATTATATCGAATC
droBip1	scf7180000396543:377182-377261 -	3	ATGTATGTATTTTAGGATCTATACCGAACAAA------------------------------------------------------------------------------------------------GATCAAGTTGTATGAGTT----------CTCAGGCATGT-CTCGAGTTTATATCGAGTA
dp4	chrXL_group1a:2597066-2597203 -	2	ATATAAATACATACTGC---A----------TAGTGTAGCAGAATGGACTCGGAACTCGATCCATG---------------CATGCCACATGCCACATGC-CACATGTCGCAGAGGGGGCAGCGTG--GCTCGAGTG-CCAGAGTCC-------------GGCGAGG-CATGAGACTA---CTTACC
droPer1	super_28:1034311-1034357 -	8	A-G-----------------------------------------------------------------------------------------------------------------------CGTG--GCTCGAGTG-CCAGAGTCC-------------GGCGAGG-CATGAGACTA---CTTACC
droWil1	Unknown	NA	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droVir3	Unknown	NA	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
droMoj3	scaffold_6473:2911987-2912050 +	2	ATATATGTGTGTGTGTT---------------------TGTGTATTGTATTTAGATTTGAGCTATA---------------AAATGTTTAATAAAAC-TC-A-------------------------------------------------------------------------------------
droGri2	Unknown	NA	-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

ATATAAGTGTTC-----------GATTTGGCGCTTGGAATCGATACCCGAGCCATGATAGATTGAAGTCAACCC-AATCGAT--CGC-GGT-TCGAGTGCTCGAGTCTTGTGCGCCGGCATGCT-TGAGATG-------TCCACTA

Size

Hit Count

Total Norm

droSim1

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

Size

Hit Count

Total Norm

V044
Embryo

M023
Head

M024
Male body

M025
Embryo

droSec1

ATATAAGTGTTC-----------GATTTGGCGCTTGGAATCGACACCCGTGCCCTGATAGATTGAAGTCAACCC-AATCGAT--CGC-GGT-TCGGGTGCTCGAGTCTTGTGCGCCGGCATGCT-TGAGATG-------TCCACTA	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...............................................................................GAT--CGA-GGA-TCGGGTGCT.............................................	18	1	1.00	0.00	0.00	1.00
...........................................GACCCGTGCCCTGATGGA.....................................................................................	18	1	1.00	0.00	1.00	0.00
.................................................................................T--CGC-GAT-TCGGGxGCTCGA..........................................	18	1	1.00	0.00	1.00	0.00
............................................................................ATCGAT--CGC-GGT-TCGGGTGCTC............................................	22	1	1.00	1.00	0.00	0.00
............................................................................ATCGAT--CGC-GGT-TCGGGTGCT.............................................	21	1	1.00	1.00	0.00	0.00

droYak2

ACATAAAAGTTC-----------AATTTGGCGCTTGGAATCGTAACTCGAGCCCTCAAAGATTGAAGTCAAATGCAATCGAT--CCGGGGTGTCGAGTGCTCGATTCTGGTGCGCCGGCATGCTTTGAGATG-------TCCACTA	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
...........................................................................AATCGAT--CCGGGGTGTCGAGTGCTCGAT.........................................	28	1	1.00	0.00	0.00	1.00	0.00	0.00
.........................................................................GCAATCGAT--CCGGGGTGTCGA..................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00

droEre2

ATATAAGTGTTC-----------GATTTGGCGCTTGGAATCGAACCTCGAGCCCTGACAGATTGAAGTCAACCCAAAACGAT--CCCGGGG-TCGAGTGTTCGAGTCCGGTGCGCCGGCATGCTTTGAGTTG-------TCCACTA	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
.........................................................................................GG-TCGTGGGTTCGAGTCC......................................	18	1	4.00	0.00	0.00	0.00	4.00
.........................................................................................GG-TCGAGGGTTCGAGTCCC.....................................	19	1	3.00	0.00	0.00	0.00	3.00
......................................................................................CAGGG-TCGTGTGTTCGAG.........................................	18	1	2.00	0.00	0.00	0.00	2.00
........................................................................................TGG-TCGAGGGTTCGAGTC.......................................	18	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................ATGG-TCGAGTGTTCGAGTCC......................................	20	1	1.00	0.00	0.00	0.00	1.00
........................................................................................GGG-TCCAGTGTTCAAGTC.......................................	18	1	1.00	0.00	0.00	0.00	1.00
........................................................................................GGG-TCGTGGGTTCGAGTCC......................................	19	1	1.00	0.00	0.00	0.00	1.00
.........................................................................................GG-TCGATGGTTCGAGTCC......................................	18	1	1.00	0.00	0.00	1.00	0.00
.........................................................................................GG-TCGAGGGTTCGACTCC......................................	18	1	1.00	0.00	0.00	0.00	1.00
........................................................................................GGG-TCGTGTGTTCGAGCCC......................................	19	1	1.00	0.00	0.00	0.00	1.00
........................................................................................GGG-TCGTGTGTTCGAATCC......................................	19	1	1.00	0.00	0.00	0.00	1.00

droAna3

CCTTGACT---TCATAA------------------------G------GAACAAT------------------------GAT--CAT----------------GTTAAGGTTCTCAGGCATGTCTCGAGATTATATCGAATCACTA

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

tTtTtttT---tgtTtCTGCATAGTGTAGCAGAATGGACTCGGAACTCGATCCATGgtTGggtgtTGggtgtT--GggtgtTAGCGT-GGC-TCGAGTGCCAGAGTCCGGCGAG---GCATG-----A---G-------ACTACTT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
..........................................................TGGGTGGTGGGTGGT--GGGT...................................................................	19	1	3.00	2.00	1.00	0.00	0.00
..........................................................TGGGTGGTGGGTGGT--GGGTG..................................................................	20	1	1.00	1.00	0.00	0.00	0.00
.....................................................................TGTT--GAGTGTTTGCGT-GGC-......................................................	19	1	1.00	1.00	0.00	0.00	0.00
..........................................................TGGGTGTTGGGGGGT--GGG....................................................................	18	2	0.50	0.50	0.00	0.00	0.00

droPer1

AG----------------------------------------------------------------------------------CGT-GGC-TCGAGTGCCAGAGTCCGGCGAG---GCATG-----A---G-------ACTACTT

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

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

Size

Hit Count

Total Norm

V116
Male body

V053
Unknown

V047
Embryo

M027
Male body

M028
Head

droMoj3

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

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