Locus 87

Sequence ID	dm3.chr2L
Location	630,016 – 630,160
Length	144
Max. P	0.974208

overview

Window 6

Location	630,016 – 630,123
Length	107
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	83.08
Shannon entropy	0.32173
G+C content	0.53244
Mean single sequence MFE	-39.32
Consensus MFE	-30.73
Energy contribution	-30.77
Covariance contribution	0.04
Combinations/Pair	1.32
Mean z-score	-1.42
Structure conservation index	0.78
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.60
SVM RNA-class probability	0.758560
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 630016 107 + 23011544
CUGCAGGUGGC----AGUUUGGAGCCUUCAAUUCAAGUUGGCAACAUGCAAGUUGGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCAAGCGGCAAUUUAG
((((...((((----..((((((........))))))((((((((.(((......)))))))))))(((((.(((((.....))))).))))).)))).))))........ ( -40.30, z-score =  -1.93, R)
>droSim1.chr2L 636500 107 + 22036055
CUGCAGGUGGC----AGUUUGGAGCCUUCAAUUCAAGUUGGCAACAUGCAAGUUGGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCGAGCGGCAAUUUAG
((((...((((----..((((((........))))))((((((((.(((......)))))))))))(((((.(((((.....))))).))))).)))).))))........ ( -39.60, z-score =  -1.57, R)
>droSec1.super_14 612202 107 + 2068291
CUGCAGGUGGC----AGUUUGGUGCCUUCAACUCAAUUUGGCAACAUGCAAGUUUGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCGAGCGGCAAUUUAG
.....((((((----(((...((((((.....((((((.((((((.((((....)))))))))))))))).....))))))))).))))))...(((....)))....... ( -43.50, z-score =  -2.69, R)
>droYak2.chr2L 620002 107 + 22324452
CUGCAGGUGGC----AGCUUGGAGCCUUCAAUUCAAGUUGGCAACAUACAAGUUGGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCAAGCGGCAAUUUAG
((((...((((----((((((((........))))))))((((((...(.....)...))))))..(((((.(((((.....))))).))))).)))).))))........ ( -39.00, z-score =  -1.80, R)
>droEre2.scaffold_4929 688004 107 + 26641161
CUGCAGGUGGC----AGUUUGGAGCCUUCAAUUCAAGUAAGCAACAUACAAGUUGGCAGUUGCCAAUUGCCAAUCGGGCACACUGGUCGGCAAAGCCAAGGGGCAAUUUAG
.(((...((((----.((.((..(((((......)))...))..)).)).(((((((....)))))))(((.(((((.....))))).)))...))))....)))...... ( -32.20, z-score =  -0.57, R)
>droAna3.scaffold_12916 1624501 109 + 16180835
CUGCAGGUGGCCCGCAGUGGCAGGUUCCGAGCUGCUAGCUGCUAGUUGCGAGCUGCCACUUGCCAAUUGGAAGUCUCGC-UUCUGGCC-CAAAAGCCAGCCAGCAAUUUAG
..(((((((((..((((((((((.(....).)))))).)))).(((.....))))))))))))..............((-(.(((((.-.....)))))..)))....... ( -41.30, z-score =   0.01, R)
>consensus
CUGCAGGUGGC____AGUUUGGAGCCUUCAAUUCAAGUUGGCAACAUGCAAGUUGGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCAAGCGGCAAUUUAG
.(((...((((......((((((........))))))((((((((.(((......)))))))))))(((((.(((((.....))))).))))).))))....)))...... (-30.73 = -30.77 +   0.04)

alignment

secondary structure

dotplot

Window 7

Location	630,045 – 630,160
Length	115
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	86.03
Shannon entropy	0.27387
G+C content	0.48766
Mean single sequence MFE	-42.37
Consensus MFE	-30.97
Energy contribution	-34.33
Covariance contribution	3.36
Combinations/Pair	1.10
Mean z-score	-2.56
Structure conservation index	0.73
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	1.90
SVM RNA-class probability	0.974208
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 630045 115 + 23011544
CAAGUUGGCAACAUGCAAGUUGGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCAAGCGGCAAUUUAGCAAUUUUAUUUAGCAAGUGAGCAUGUUGCUGGCUCAU
..(((..(((((((((.(((((((....)))))))(((.(((((.....))))).)))...(((....)))...........................)))))))))..)))... ( -45.60, z-score =  -3.14, R)
>droSim1.chr2L 636529 115 + 22036055
CAAGUUGGCAACAUGCAAGUUGGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCGAGCGGCAAUUUAGCAAUUAAAUUUAGCAAGUGAGCAUGUUGCUGGCUCAU
..(((..(((((((((.(((((((....)))))))(((.(((((.....))))).)))...(((....)))...........................)))))))))..)))... ( -46.10, z-score =  -3.24, R)
>droSec1.super_14 612231 115 + 2068291
CAAUUUGGCAACAUGCAAGUUUGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCGAGCGGCAAUUUAGCAAUUGAAUUUAGCAAGUGAGCAUGUUGCUGGCUCAU
....((((((((.((((....))))))))))))(((((.(((((.....))))).)))))((((.(((((((((((((...))))))...((......)).)))))))))))... ( -43.20, z-score =  -2.29, R)
>droYak2.chr2L 620031 115 + 22324452
CAAGUUGGCAACAUACAAGUUGGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCAAGCGGCAAUUUAGCAAUUGAAUUUAGCAAGUGAGCAUGUUGCUGGCUCAU
..(((..(((((((.........(((((((...(((((.(((((.....))))).))))).(((....)))......)))))))......((......)))))))))..)))... ( -42.20, z-score =  -2.43, R)
>droEre2.scaffold_4929 688033 115 + 26641161
CAAGUAAGCAACAUACAAGUUGGCAGUUGCCAAUUGCCAAUCGGGCACACUGGUCGGCAAAGCCAAGGGGCAAUUUAGCAAUUGAAUUUAGCAAGUGAGCAUGUUGCUGGCUCAU
..(((.((((((((.........(((((((...(((((.(((((.....))))).))))).(((....)))......)))))))......((......)))))))))).)))... ( -39.00, z-score =  -2.10, R)
>droAna3.scaffold_12916 1624541 101 + 16180835
-------GCUAGUUGCGAGCUGCCACUUGCCAAUUGGAAGUCUCGC-UUCUGGCC-CAAAAGCCAGCCAGCAAUUUAGCAAUCG-----AGCGAGUGAACAUGUCGCUGGCUCAU
-------(((((((((((((.(..((((.((....))))))..)))-))(((((.-.....)))))...)))).)))))....(-----(((.(((((.....))))).)))).. ( -38.10, z-score =  -2.17, R)
>consensus
CAAGUUGGCAACAUGCAAGUUGGCAGUUGCCAAUUGGCAAUCGGGCACACUGGUCGCCAAAGCCAAGCGGCAAUUUAGCAAUUGAAUUUAGCAAGUGAGCAUGUUGCUGGCUCAU
..((((((((((((((..((((((((((((...(((((.(((((.....))))).))))).(((....)))......)))))))...)))))......))))))))))))))... (-30.97 = -34.33 +   3.36)

alignment

secondary structure

dotplot

Window 8

Location	630,045 – 630,160
Length	115
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	86.03
Shannon entropy	0.27387
G+C content	0.48766
Mean single sequence MFE	-35.45
Consensus MFE	-26.47
Energy contribution	-26.37
Covariance contribution	-0.10
Combinations/Pair	1.20
Mean z-score	-1.74
Structure conservation index	0.75
Background model	dinucleotide
Decision model	sequence based alignment quality
SVM decision value	0.62
SVM RNA-class probability	0.763976
Prediction	RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 630045 115 - 23011544
AUGAGCCAGCAACAUGCUCACUUGCUAAAUAAAAUUGCUAAAUUGCCGCUUGGCUUUGGCGACCAGUGUGCCCGAUUGCCAAUUGGCAACUGCCAACUUGCAUGUUGCCAACUUG
..(((...(((((((((......((...........))....((((((.(((((...((((.......)))).....))))).))))))..........)))))))))...))). ( -35.00, z-score =  -1.63, R)
>droSim1.chr2L 636529 115 - 22036055
AUGAGCCAGCAACAUGCUCACUUGCUAAAUUUAAUUGCUAAAUUGCCGCUCGGCUUUGGCGACCAGUGUGCCCGAUUGCCAAUUGGCAACUGCCAACUUGCAUGUUGCCAACUUG
..(((...(((((((((.................((((((((..(((....)))))))))))..(((..((....(((((....)))))..))..))).)))))))))...))). ( -34.60, z-score =  -1.51, R)
>droSec1.super_14 612231 115 - 2068291
AUGAGCCAGCAACAUGCUCACUUGCUAAAUUCAAUUGCUAAAUUGCCGCUCGGCUUUGGCGACCAGUGUGCCCGAUUGCCAAUUGGCAACUGCAAACUUGCAUGUUGCCAAAUUG
........(((((((((....((((.........((((((((..(((....))))))))))).............(((((....)))))..))))....)))))))))....... ( -36.30, z-score =  -1.77, R)
>droYak2.chr2L 620031 115 - 22324452
AUGAGCCAGCAACAUGCUCACUUGCUAAAUUCAAUUGCUAAAUUGCCGCUUGGCUUUGGCGACCAGUGUGCCCGAUUGCCAAUUGGCAACUGCCAACUUGUAUGUUGCCAACUUG
..(((...(((((((((......((...........))....((((((.(((((...((((.......)))).....))))).))))))..........)))))))))...))). ( -33.00, z-score =  -1.11, R)
>droEre2.scaffold_4929 688033 115 - 26641161
AUGAGCCAGCAACAUGCUCACUUGCUAAAUUCAAUUGCUAAAUUGCCCCUUGGCUUUGCCGACCAGUGUGCCCGAUUGGCAAUUGGCAACUGCCAACUUGUAUGUUGCUUACUUG
..(((..((((((((((..............(((((....)))))....(((((.(((((((......((((.....)))).)))))))..)))))...))))))))))..))). ( -36.30, z-score =  -3.00, R)
>droAna3.scaffold_12916 1624541 101 - 16180835
AUGAGCCAGCGACAUGUUCACUCGCU-----CGAUUGCUAAAUUGCUGGCUGGCUUUUG-GGCCAGAA-GCGAGACUUCCAAUUGGCAAGUGGCAGCUCGCAACUAGC-------
........((((..(((.((((.((.-----((((((.....(((((..((((((....-)))))).)-))))......)))))))).)))))))..)))).......------- ( -37.50, z-score =  -1.40, R)
>consensus
AUGAGCCAGCAACAUGCUCACUUGCUAAAUUCAAUUGCUAAAUUGCCGCUUGGCUUUGGCGACCAGUGUGCCCGAUUGCCAAUUGGCAACUGCCAACUUGCAUGUUGCCAACUUG
..((((((((((.........)))))..........((......)).....)))))((((((.(.........).)))))).(((((((((((......))).)))))))).... (-26.47 = -26.37 +  -0.10)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:06:25 2011