Locus 5306

Sequence ID dm3.chr2R
Location 19,369,189 – 19,369,301
Length 112
Max. P 0.697937
window7269 window7270

overview

Window 9

Location 19,369,189 – 19,369,301
Length 112
Sequences 3
Columns 112
Reading direction forward
Mean pairwise identity 97.02
Shannon entropy 0.04100
G+C content 0.36905
Mean single sequence MFE -25.87
Consensus MFE -24.29
Energy contribution -24.19
Covariance contribution -0.11
Combinations/Pair 1.06
Mean z-score -1.45
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.44
SVM RNA-class probability 0.697937
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19369189 112 + 21146708
AUACUCUUAAGCACUUCAUAAGAAAUUUUCAAACACAAUUUGAAUUUUGGUGCGUGGGCUUAAUGGAGCCACCGUAGAAGUGAAAUCUCAUAUUGAUGAGACAACAGAAUAU
....(((....((((((......((..((((((.....))))))..))..((((..(((((....)))))..))))))))))...((((((....))))))....))).... ( -27.70, z-score =  -2.56, R)
>droSim1.chr2R 17950587 112 + 19596830
GUACUCUUAAGCACUUCGUAAGAAAUUUUCCAACACAAUUUGAAUUUUGGUGCGUGGGCUUAAUGGAGCCACCGUGGAAGUGAAAUCUCAUAUUGAUGAGACAACAGAAUAU
(((.(((....((((((....)))...((((.((.(((........)))))(((..(((((....)))))..))))))))))...((((((....))))))....))).))) ( -25.50, z-score =  -0.96, R)
>droSec1.super_9 2657928 112 + 3197100
GUACUCUUAAGCUCUUCGUAAGAAAUUUUCCAACACAAUUUGAAUUUUGGUGCGUGGGCUUAAUGGAGCCACCGUAGAAGUGAAAUCUCAUAUUGAUGAGACAACAGAAUAU
...(((((((((((..((((.(((((((.............)))))))..)))).)))))))..)))).(((.......)))...((((((....))))))........... ( -24.42, z-score =  -0.84, R)
>consensus
GUACUCUUAAGCACUUCGUAAGAAAUUUUCCAACACAAUUUGAAUUUUGGUGCGUGGGCUUAAUGGAGCCACCGUAGAAGUGAAAUCUCAUAUUGAUGAGACAACAGAAUAU
(((.(((....((((((....(((((((.............)))))))..((((..(((((....)))))..))))))))))...((((((....))))))....))).))) (-24.29 = -24.19 +  -0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 19,369,189 – 19,369,301
Length 112
Sequences 3
Columns 112
Reading direction reverse
Mean pairwise identity 97.02
Shannon entropy 0.04100
G+C content 0.36905
Mean single sequence MFE -25.33
Consensus MFE -21.70
Energy contribution -22.37
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.86
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.41
SVM RNA-class probability 0.684003
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 19369189 112 - 21146708
AUAUUCUGUUGUCUCAUCAAUAUGAGAUUUCACUUCUACGGUGGCUCCAUUAAGCCCACGCACCAAAAUUCAAAUUGUGUUUGAAAAUUUCUUAUGAAGUGCUUAAGAGUAU
(((((((...(((((((....)))))))..((((((...(((((((......)))).....)))....(((((((...)))))))..........))))))....))))))) ( -26.40, z-score =  -2.62, R)
>droSim1.chr2R 17950587 112 - 19596830
AUAUUCUGUUGUCUCAUCAAUAUGAGAUUUCACUUCCACGGUGGCUCCAUUAAGCCCACGCACCAAAAUUCAAAUUGUGUUGGAAAAUUUCUUACGAAGUGCUUAAGAGUAC
.((((((...(((((((....)))))))..((((((..((..((((......))))..))..((((.((.......)).))))............))))))....)))))). ( -25.40, z-score =  -1.83, R)
>droSec1.super_9 2657928 112 - 3197100
AUAUUCUGUUGUCUCAUCAAUAUGAGAUUUCACUUCUACGGUGGCUCCAUUAAGCCCACGCACCAAAAUUCAAAUUGUGUUGGAAAAUUUCUUACGAAGAGCUUAAGAGUAC
.(((((((..(((((((....)))))))..).((((..((..((((......))))..))..((((.((.......)).))))............))))......)))))). ( -24.20, z-score =  -1.46, R)
>consensus
AUAUUCUGUUGUCUCAUCAAUAUGAGAUUUCACUUCUACGGUGGCUCCAUUAAGCCCACGCACCAAAAUUCAAAUUGUGUUGGAAAAUUUCUUACGAAGUGCUUAAGAGUAC
.((((((...(((((((....)))))))..((((((..((..((((......))))..))..((((.((.......)).))))............))))))....)))))). (-21.70 = -22.37 +   0.67)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:45:40 2011