Locus 493

Sequence ID dm3.chr2L
Location 3,441,223 – 3,441,313
Length 90
Max. P 0.906659
window664 window665

overview

Window 4

Location 3,441,223 – 3,441,313
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 86.22
Shannon entropy 0.25317
G+C content 0.42286
Mean single sequence MFE -19.01
Consensus MFE -12.53
Energy contribution -14.48
Covariance contribution 1.95
Combinations/Pair 1.00
Mean z-score -2.48
Structure conservation index 0.66
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.19
SVM RNA-class probability 0.906659
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3441223 90 + 23011544
UAUCCUUUUAAUGCUGUAAUUUCAGCAUGCAUUUAUCCUUAAUGGAUUGUGCAUGUCUGCUGCCGCAGUCUUGCCACUCUUAUACCCGCC
........(((.(((((.....((((((((((..((((.....)))).))))))).))).....))))).)))................. ( -22.90, z-score =  -3.11, R)
>droSim1.chr2L 3379423 90 + 22036055
UAUCCUUUUAAUGCUGUAAUUUCAGCAUGCAUUUAUCCUUAAUGGAUUGUGCAUGUCUGCUGCCGCAGUCUUGCCACUCUUAUACCCGCC
........(((.(((((.....((((((((((..((((.....)))).))))))).))).....))))).)))................. ( -22.90, z-score =  -3.11, R)
>droSec1.super_129 3344 90 + 51580
UAUCCUUUUAAUGCUGUAAUUUCAGCAUGCAUUUAUCCUUAAUGGAUUGUGCAUGUCUGCUGCCGCCGUCUUCCCACUCUUAUACCCGCC
............((.(((....((((((((((..((((.....)))).))))))).))).))).))........................ ( -19.80, z-score =  -3.22, R)
>droEre2.scaffold_4929 3470989 90 + 26641161
UAUCCUUUUAAUGCUGUAAUUUCAGCAUGCAUUUAUCCUUAAUGGAUUGUGCAUGUCUGCUGCCGCUGUCUUGCCACUCUUAUACCCGCC
............((.(((....((((((((((..((((.....)))).))))))).))).))).))........................ ( -20.20, z-score =  -2.51, R)
>droAna3.scaffold_12916 2905061 73 - 16180835
UAUCCUUUCAAGGCUAUAGUUCU----UGCUUUUAUCCUUAAUGGACUGUGCAU-------------GUCUUACCACUCUUAUACUCGUU
.........(((((((((((((.----................))))))))...-------------))))).................. (  -9.23, z-score =  -0.45, R)
>consensus
UAUCCUUUUAAUGCUGUAAUUUCAGCAUGCAUUUAUCCUUAAUGGAUUGUGCAUGUCUGCUGCCGCAGUCUUGCCACUCUUAUACCCGCC
............((.(((....((((((((((..((((.....)))).))))))).))).))).))........................ (-12.53 = -14.48 +   1.95)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,441,223 – 3,441,313
Length 90
Sequences 5
Columns 90
Reading direction reverse
Mean pairwise identity 86.22
Shannon entropy 0.25317
G+C content 0.42286
Mean single sequence MFE -20.70
Consensus MFE -14.21
Energy contribution -15.84
Covariance contribution 1.63
Combinations/Pair 1.09
Mean z-score -2.15
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.79
SVM RNA-class probability 0.817822
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 3441223 90 - 23011544
GGCGGGUAUAAGAGUGGCAAGACUGCGGCAGCAGACAUGCACAAUCCAUUAAGGAUAAAUGCAUGCUGAAAUUACAGCAUUAAAAGGAUA
.((..(((.....((.(((....))).))..(((.((((((..((((.....))))...)))))))))....))).))............ ( -24.60, z-score =  -2.68, R)
>droSim1.chr2L 3379423 90 - 22036055
GGCGGGUAUAAGAGUGGCAAGACUGCGGCAGCAGACAUGCACAAUCCAUUAAGGAUAAAUGCAUGCUGAAAUUACAGCAUUAAAAGGAUA
.((..(((.....((.(((....))).))..(((.((((((..((((.....))))...)))))))))....))).))............ ( -24.60, z-score =  -2.68, R)
>droSec1.super_129 3344 90 - 51580
GGCGGGUAUAAGAGUGGGAAGACGGCGGCAGCAGACAUGCACAAUCCAUUAAGGAUAAAUGCAUGCUGAAAUUACAGCAUUAAAAGGAUA
.((..(((.....((.(.....).)).....(((.((((((..((((.....))))...)))))))))....))).))............ ( -21.00, z-score =  -2.24, R)
>droEre2.scaffold_4929 3470989 90 - 26641161
GGCGGGUAUAAGAGUGGCAAGACAGCGGCAGCAGACAUGCACAAUCCAUUAAGGAUAAAUGCAUGCUGAAAUUACAGCAUUAAAAGGAUA
.((..(((.....((.((......)).))..(((.((((((..((((.....))))...)))))))))....))).))............ ( -23.70, z-score =  -2.98, R)
>droAna3.scaffold_12916 2905061 73 + 16180835
AACGAGUAUAAGAGUGGUAAGAC-------------AUGCACAGUCCAUUAAGGAUAAAAGCA----AGAACUAUAGCCUUGAAAGGAUA
...........(.(((......)-------------)).)...((((.((((((.....((..----....))....))))))..)))). (  -9.60, z-score =  -0.19, R)
>consensus
GGCGGGUAUAAGAGUGGCAAGACUGCGGCAGCAGACAUGCACAAUCCAUUAAGGAUAAAUGCAUGCUGAAAUUACAGCAUUAAAAGGAUA
.((..(((.....((.((......)).))..(((.((((((..((((.....))))...)))))))))....))).))............ (-14.21 = -15.84 +   1.63)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:13:53 2011