sblock103084- 12- and 20-way alignments

sblock103084	chr3L:11689515-11689577 +	Candidate
	[View on UCSC Genome Browser {Cornell Mirror}]	antisense_to_5pUTR

Legend:

   mature strand at position 11689556-11689575
   star strand at position 11689521-11689541
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

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

Species	Coordinate	Alignment
dm3	chr3L:11689500-11689592 +	CGGAT---------------------------------------CGTTCGATACCTTTATCAGTTGGACGTTAGACGCCGTCT---GA---GTTTCAGGGGTTGCGTTTGC-------------CGTTTG--GCTGCTGCACA--AA-TTTTGGTC
droSim1	chr3L:11059386-11059485 +	CGGAT---------------------------------------CGTGCGATACCTTTATCAGTTGGACGTTAGACGCCGTCT---GA---ATTTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA--GA-AATTGGTC
droSec1	super_0:3875908-3876007 +	AGGAT---------------------------------------CGTTCGATACCTTTATCAGTTGGACGTTAGATGCCGTCT---GA---GTTTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA--GA-AATTGGTC
droYak2	chr3L:11719778-11719883 +	CGGAA---------------------------------------CGCTCGATACCTTTATCAGTTGGCCGTTGGACGCCGTCT---GA---GTTTCAGGGGTTGCGTTTGCTGTTTGCCGTTGGCGTTTG--GCTGCTGCACA--GA-AATTGGTC
droEre2	scaffold_4784:11672204-11672298 +	CGGAC---------------------------------------AGTTCAATAC-TTTATCAGTTGGCCGTTAGACGCCGTCT---GAGGAGTTTCAGGGGTTGCGTTTGG-------------CGTTTG--GCTGCTGCACA--GA-AATTGGTC
droAna3	scaffold_13337:5952676-5952761 +	CGGAT---------------------------------------CGTTCGACACCTTTATCAGTTGGACGTTAGACGCCTTCT---GA---C-TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA--GA-AATTGGTC
dp4	chrXR_group6:10003251-10003350 -	CAAACGA----GTGCCAACTTCTAGC-------TTC-------------------TATGCCGCGTGAACGTTAAGTGCTGTCT---GG---G-TTCGGGGGTTGCGCCTGC-------------TGCT----GCTGCTGCACA--GAAAATTGGTC
droPer1	super_61:283689-283791 -	CAAACGA----GTGCCAACTTCTAGC-------TTC-------------------TATGCCGCGTGAACGTTAAGTGCTGTCT---GG---G-TTCGGGGGTTGCGCCTGC-------------TGCT-GCTGCTGCTGCACA--GAAAATTGGTC
droWil1	scaffold_180949:2659355-2659454 -	CAGACTC----CGGTTTATTTCTAAT-------TTC-------------------GACTCGACGTTATCAGGTTGAACTGTCTGCTTG---C-TTCAGGGGTTGCACT-AC-------------AA-TTG--GT-TTTGTTTC--G--ATTTGGTC
droVir3	scaffold_13049:23903492-23903584 -	CGAAATA----ATATTTGCAATTAATGACTGTCTA-------------C------GAAAACAGTTCAAATTTAAATGCTGCTT---G----C-CTCAGGGGTTG-----------------------------CTGTTGCACG--AA-AATTGGTC
droMoj3	scaffold_6680:18531558-18531651 -	TCTAAGA----TTATTTGCAATTAGTTGCTGCC--------------------TCGCTAACAGTTCAAATTTAAATGCGG-CT---AT---G-CTCAGGGGTTGCAGT-----------------------------TGCACTACGG-AATTGGTC
droGri2	scaffold_15110:9775676-9775767 +	TGTGTTTGCGTG---TGATTTTCAAT-------TAAAACATATTCGTTCGA--------------AAATGTTGAATACTGCTT---G----G-TTCGAGGGTTG-----------------------------CCGTTGCACT--AA-AATTGGTC

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

Species	Coordinate	Lastz Id	Alignment
dm3	chr3L:11689500-11689592 +	NA	CGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGC-------------CGTTTG--GCTGCTGCACA-----------AA-TTTTGGTC
droSim1	chr3L:11059386-11059485 +	1	CGG---------------------------------------------------ATCGTGCGATACCTTTATCAGTTGGACGTTAG------ACGCCGTCTG---AA---T------TTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droSec1	super_0:3875908-3876007 +	1	AGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ATGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droYak2	chr3L:11719778-11719883 +	1	CGG---------------------------------------------------AACGCTCGATACCTTTATCAGTTGGCCGTTGG------ACGCCGTCTG---AG---T------TTCAGGGGTTGCGTTTGCTGTTTGCCGTTGGCGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEre2	scaffold_4784:11672204-11672298 +	1	CGG---------------------------------------------------ACAGTTCAATA-CTTTATCAGTTGGCCGTTAG------ACGCCGTCTG---AGGAGT------TTCAGGGGTTGCGTTTGG-------------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEug1	scf7180000409711:3565307-3565407 +	1	CGG---------------------------------------------------A-CGTTCGATACCTTTATCAGTTGGACGTTAG------ACACTGTCTG---AATGGTTTCAACTTCAGGGGTTGCGTTTTG-------------TGTTTG--GCTGCTGCACA-----------AA-AATTGGTC
droBia1	scf7180000302334:131835-131925 +	1	CGG---------------------------------------------------ACGGTTCGATACCTTTGTCAGTTGGACGTTAG------ACGCAGTCTG---AC----------TTCAGGGGTTGCGATTCG-------------CGTTTG--GCTGCTGCA-A-----------GA-AATTGGTC
droTak1	scf7180000414445:514999-515100 -	1	GTGCG--------------------------GATTG----GG------------ATCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCTGTCTG---AA---T------TTCAGGGGTTGCGTTTCG-------------CGTTTG--GCTGCTGCACA-----------GA-AATTGGTC
droEle1	scf7180000490993:2107331-2107434 -	2	GGA---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGGACGTCAG------ACGCTGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------CGTTTG--GCTGCTGCACAGAAACAACATAGA-AATTGGTC
droRho1	scf7180000767448:131229-131349 -	2	ACACAAACTGCGA------------------GATTG----GA------------TTCGTTCGATACCTTTATCAGTTGGACGTTAG------ACGCGGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------TGTTTG--GCTGCTGCACAGAAACAACACAGA-AATTGGTC
droFic1	scf7180000454113:3011634-3011728 -	1	CGG---------------------------------------------------ATCGTTCGATACCTTTATCAGTTGAACGTTAG------ACGCGGTCTG---AA---T------TTCAGGGGTTGCGTTTTG-------------CCTTTG--GCTGCTGCACG---------CAGA-AATTGGTC
droKik1	scf7180000302391:1149742-1149835 -	1	TTG---------------------------------------------------ATCGTTCAACTTCTTTATCAGTTAAACGTTAG------ACGCCGTCTG---AT---T-CCGA-GTCTAGGGGTGTGTTTT--------------CGTTTG--GCTGCTGCA-------------GA-AATTGGTC
droAna3	scaffold_13337:5952676-5952761 +	1	CGG---------------------------------------------------ATCGTTCGACACCTTTATCAGTTGGACGTTAG------ACGCCTTCTG---AC----------TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA-----------GA-AATTGGTC
droBip1	scf7180000396518:16786-16877 +	1	TGTTT-----------------------------TG----GC------------ATCGTTCGACACCTTTATCAGTTGGACGTTAG------ACGCCTACTG---AC----------TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA-----------GA-AATTGGTC
dp4	chrXR_group6:10003251-10003350 -	1	CAAAC--------------------------GAGTG----CC------------AACTTCTAGCTTCTATGCCGCGTGAACGTTAA------GTGCTGTCTG---GG----------TTCGGGGGTTGCGCCTGC-------------TGCT----GCTGCTGCACA-----------GAAAATTGGTC
droPer1	super_61:283689-283791 -	1	CAAAC--------------------------GAGTG----CC------------AACTTCTAGCTTCTATGCCGCGTGAACGTTAA------GTGCTGTCTG---GG----------TTCGGGGGTTGCGCCTGC-------------TGCT-GCTGCTGCTGCACA-----------GAAAATTGGTC
droWil1	scaffold_180949:2659355-2659454 -	2	CAGAC--------------------------TCCG----------------------GTTTATTTCTAATTTCGACTCGACGTTATCAGGTTGAACTGTCTGCTTG----C------TTCAGGGGTTGCACT-A--------------CAATTG--GTT-TTGTTTC------------G-ATTTGGTC
droVir3	scaffold_13049:23903492-23903589 -	2	CTGCT-----CGAAAT---AATATTTGCAATTAATGACTGTC----------------TAC------GAAAACAGTTCAAATTTAA------ATGCTGCTTG---C-----------CTCAGGGGTTG-----------------------------CTGTTGCACG-----------AA-AATTGGTC
droMoj3	scaffold_6680:18531558-18531638 -	2	GCAAT--------------------------TAGTT----G-------------------CTGCCTCGCTAACAGTTCAAATTTAA------ATGCGG-CTA---TG----------CTCAGGGGTTGCAGT-----------------------------TGCACT---------ACGG-AATTGGTC
droGri2	scaffold_15110:9775660-9775767 +	2	CGTTTATCTG---GCTGTGTGTGTTTGCG---TGTGATTTTCAATTAAAACATATTCGTTCGA--------------AAATGTTGA------ATACTGCTTG---G-----------TTCGAGGGTTG-----------------------------CCGTTGCACT-----------AA-AATTGGTC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

CGGAT---------------------------------------CGTTCGATACCTTTATCAGTTGGACGTTAGACGCCGTCT---GA---GTTTCAGGGGTTGCGTTTGC-------------CGTTTG--GCTGCTGCACA--AA-TTTTGGTC

Size

Hit Count

Total Norm

droSim1

CGGAT---------------------------------------CGTGCGATACCTTTATCAGTTGGACGTTAGACGCCGTCT---GA---ATTTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA--GA-AATTGGTC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
..............................................................................................................GCGTTTGC------CGTTTG--GCTG....................	18	1	1.00	0.00	1.00	0.00	0.00

droSec1

AGGAT---------------------------------------CGTTCGATACCTTTATCAGTTGGACGTTAGATGCCGTCT---GA---GTTTCAGGGGTTGCGTTTGGCGTTTGC------CGTTTG--GCTGCTGCACA--GA-AATTGGTC

Size

Hit Count

Total Norm

V113
Male body

V114
Embryo

V115
Head

droYak2

CGGAA---------------------------------------CGCTCGATACCTTTATCAGTTGGCCGTTGGACGCCGTCT---GA---GTTTCAGGGGTTGCGTTTGCTGTTTGCCGTTGGCGTTTG--GCTGCTGCACA--GA-AATTGGTC

Size

Hit Count

Total Norm

V046
Embryo

V052
Head

V120
Male body

V058
Head

M026
Head

droEre2

CGGAC---------------------------------------AGTTCAATAC-TTTATCAGTTGGCCGTTAGACGCCGTCT---GAGGAGTTTCAGGGGTTGCGTTTGG-------------CGTTTG--GCTGCTGCACA--GA-AATTGGTC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
..........................................................................................AGTATCAGGGGGTGCGTT................................................	18	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................................TTGCGTTTGG-------------CGTTTG--TT......................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................................T---GAGGAGxTTCAGGGGTTC....................................................	18	1	1.00	0.00	0.00	0.00	1.00
...................................................................................................GTTTGCGTTTxG-------------CGTTTG--GCTG....................	21	1	1.00	0.00	0.00	0.00	1.00

droAna3

CGGAT---------------------------------------CGTTCGACACCTTTATCAGTTGGACGTTAGACGCCTTCT---GA---C-TTCGGGGGTTGCGAT-------------------TTG--GCTGCTGCACA--GA-AATTGGTC

Size

Hit Count

Total Norm

V105
Male body

V106
Head

V055
Unknown

V039
Embryo

dp4

CAAACGA----GTGCCAACTTCTAGC-------TTC-------------------TATGCCGCGTGAACGTTAAGTGCTGTCT---GG---G-TTCGGGGGTTGCGCCTGC-------------TGCT----GCTGCTGCACA--GAAAATTGGTC	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
....................................................................................................GTTGCGTCxGC-------------TGCT----GCTGCT..................	20	1	1.00	1.00	0.00	0.00	0.00
....................................................................................................GTTGCGTCxGC-------------TGCT----GCTGC...................	19	1	1.00	1.00	0.00	0.00	0.00

droPer1

CAAACGA----GTGCCAACTTCTAGC-------TTC-------------------TATGCCGCGTGAACGTTAAGTGCTGTCT---GG---G-TTCGGGGGTTGCGCCTGC-------------TGCT-GCTGCTGCTGCACA--GAAAATTGGTC	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
...........................................................................................................CTCC-------------TGCT-GCTGCGGCTG.................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................CTGC-------------TGCT-GCTGGTGCTG.................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
........................................................................................................CTCCTTC-------------TGCT-GCTGCTG....................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................CTCC-------------TTCT-GCTGCTGCTG.................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................C-------------TGCT-GCAGCTGCTGAAC..............	18	1	2.00	0.00	0.00	0.00	0.00	2.00
........................................................................................................CTCCTGC-------------TGCT-GCGGCTG....................	18	2	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................CTAC-------------TACT-GCTGCTGCTG.................	18	1	2.00	0.00	0.00	0.00	0.00	2.00
............................................................................................................TGC-------------TGCT-GCTGCTGCTGCC...............	19	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................................................................CTTC-------------TGCT-GCTGCTGGTG.................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
.....................................................................................................TTGCGTCTGC-------------TGTT-GCTGC......................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
......................................................................................................TGCGCCGGA-------------TGCT-GCTGCTG....................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
..........................................................................GTGCTGxCT---GG---G-ATCGGGG........................................................	18	1	1.00	1.00	0.00	0.00	0.00	0.00
............................................................................................................TGT-------------TGCT-GCTGCTGCTGCT...............	19	1	1.00	0.00	1.00	0.00	0.00	0.00
...........................................................................................................CTGC-------------TGCT-GCTGGAGCTGC................	19	1	1.00	0.00	0.00	0.00	0.00	1.00
...........................................................................................................CTGC-------------TGCT-GCTGTTGCTG.................	18	1	1.00	0.00	0.00	0.00	0.00	1.00
........................................................................................................CTCCTGC-------------TGCT-GTTGCTG....................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
...........................................................................................................CTCC-------------TGCT-GCTGTTGCTG.................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
...........................................................................................................CCGC-------------TGCC-GCTGCTGCTG.................	18	2	0.50	0.00	0.00	0.00	0.00	0.50
...........................................................................................................CTGC-------------TGCT-GCTGCTGTTGCT...............	20	1	1.00	0.00	0.00	0.00	0.00	1.00

droWil1

CAGACTC----CGGTTTATTTCTAAT-------TTC-------------------GACTCGACGTTATCAGGTTGAACTGTCTGCTTG---C-TTCAGGGGTTGCACT-AC-------------AA-TTG--GT-TTTGTTTC--G--ATTTGGTC	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
.................ATTTCGAAT-------TTC-------------------GGCTCG...............................................................................................	18	1	1.00	1.00	0.00	0.00	0.00
.................ATTTCTAAT-------TTC-------------------GAGTTGA..............................................................................................	19	1	1.00	0.00	1.00	0.00	0.00
.............................................................ACTTTATCAGGTTGAAGT.............................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

CGAAATA----ATATTTGCAATTAATGACTGTCTA-------------C------GAAAACAGTTCAAATTTAAATGCTGCTT---G----C-CTCAGGGGTTG-----------------------------CTGTTGCACG--AA-AATTGGTC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
...................................................................................................GGTTG-----------------------------CGGTTGCAAG--AA-AA......	19	1	1.00	0.00	0.00	1.00	0.00	0.00

droMoj3

TCTAAGA----TTATTTGCAATTAGTTGCTGCC--------------------TCGCTAACAGTTCAAATTTAAATGCGG-CT---AT---G-CTCAGGGGTTGCAGT-----------------------------TGCACTACGG-AATTGGTC	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
.....GA----TTTATTGCAATTAGTT.................................................................................................................................	18	1	10.00	1.00	6.00	3.00	0.00
....AGA----TTTATTGCAATTAGTT.................................................................................................................................	19	1	2.00	0.00	1.00	1.00	0.00
...............TTGCAATTAGTTTCTACC--------------------T......................................................................................................	19	1	2.00	0.00	1.00	1.00	0.00
................TGCAATTAGTTTCGGCC--------------------T......................................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
.........................................................TAACAGTTTAAAGTTAAA.................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
...............TTGCAATTAGTTTCTTCC--------------------T......................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
................TGCAATTAGTTTCTACC--------------------T......................................................................................................	18	1	1.00	0.00	0.00	1.00	0.00

droGri2

TGTGTTTGCGTG---TGATTTTCAAT-------TAAAACATATTCGTTCGA--------------AAATGTTGAATACTGCTT---G----G-TTCGAGGGTTG-----------------------------CCGTTGCACT--AA-AATTGGTC

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
UNAFold Image

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