Locus 11409

Sequence ID dm3.chr3R
Location 20,915,810 – 20,915,918
Length 108
Max. P 0.997701
window15686 window15687

overview

Window 6

Location 20,915,810 – 20,915,918
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 92.86
Shannon entropy 0.12947
G+C content 0.48158
Mean single sequence MFE -37.10
Consensus MFE -34.30
Energy contribution -35.13
Covariance contribution 0.83
Combinations/Pair 1.00
Mean z-score -3.50
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.16
SVM RNA-class probability 0.997701
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20915810 108 + 27905053
GGCGGCGCAGCG--GCUAAGUAGCUUCAACACCGAAAACUAGUUUC--ACACACAGACUAGUUUGCACUCGAGCU--------CGGCUCGGGUGUUGAUGCUGAUUAACCAUAUUUAUAC
.((......))(--(.(((.((((.(((((((((.((((((((((.--......)))))))))).)...(((((.--------..))))))))))))).)))).))).)).......... ( -39.00, z-score =  -3.95, R)
>droYak2.chr3R 3251328 118 - 28832112
GGCAUCGCAGCGAAGCUAAGUAGCUUCAACACCGAAAACUAGUUUC--ACACACAGACUAGUUUGCACUCGAGCUUGGGUGCUCGGCUCGGGUGUUGAUGCUGAUUAACCAUAUUUAUAC
((((((.....((((((....))))))(((((((.((((((((((.--......)))))))))).)..((((((......))))))....)))))))))))).................. ( -41.70, z-score =  -3.76, R)
>droEre2.scaffold_4820 3335382 108 - 10470090
GGCAUCGCAGCG--GCUAAGUAGCUUCAACACCGAAAACUAGUUUC--ACACACAGACUAGUUUGCACUCGAGCU--------CGGCUCGGGUGUUGAUGCUGAUUAACCAUAUUUAUAC
.((......))(--(.(((.((((.(((((((((.((((((((((.--......)))))))))).)...(((((.--------..))))))))))))).)))).))).)).......... ( -38.30, z-score =  -4.42, R)
>droSec1.super_33 176946 108 + 478481
GGCGGCGCAGCG--GCUAAGUAGCUUCAACACCGAAAACUAGUUUC--ACACACAGACUAGCUUGCACUCGAGCU--------CGGCUCGGGUGUUGAUGCUGAUUAACCAUAUUUAUAC
.((......))(--(.(((.((((.((((((((.....(((((((.--......)))))))........(((((.--------..))))))))))))).)))).))).)).......... ( -35.00, z-score =  -2.53, R)
>droSim1.chr3R 20745957 108 + 27517382
GGCGGCGCAGCG--GCUAAGUAGCUUCAACACCGAAAACUAGUUUC--ACACACAGACUAGCUUGCACUCGAGCU--------CGGCUCGGGUGUUGAUGCUGAUUAACCAUAUUUAUAC
.((......))(--(.(((.((((.((((((((.....(((((((.--......)))))))........(((((.--------..))))))))))))).)))).))).)).......... ( -35.00, z-score =  -2.53, R)
>droAna3.scaffold_13340 6778131 104 + 23697760
------GCAUCA--GCUAAGUAGCUUCAACACCGAAAACUAGUUUCGCACACACAGACUAGUUUGCACUCGAGCU--------CGGCUCGGGUGUUGAUGCUGAUUAACCAUAUUUAUAC
------((....--))(((.((((.(((((((((.((((((((((.(......))))))))))).)...(((((.--------..))))))))))))).)))).)))............. ( -33.60, z-score =  -3.84, R)
>consensus
GGCGGCGCAGCG__GCUAAGUAGCUUCAACACCGAAAACUAGUUUC__ACACACAGACUAGUUUGCACUCGAGCU________CGGCUCGGGUGUUGAUGCUGAUUAACCAUAUUUAUAC
((.....((((...(((....))).(((((((((.((((((((((.........)))))))))).)...((((((.........)))))))))))))).)))).....)).......... (-34.30 = -35.13 +   0.83)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,915,810 – 20,915,918
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 92.86
Shannon entropy 0.12947
G+C content 0.48158
Mean single sequence MFE -36.77
Consensus MFE -31.14
Energy contribution -30.92
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.94
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.26
SVM RNA-class probability 0.987106
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 20915810 108 - 27905053
GUAUAAAUAUGGUUAAUCAGCAUCAACACCCGAGCCG--------AGCUCGAGUGCAAACUAGUCUGUGUGU--GAAACUAGUUUUCGGUGUUGAAGCUACUUAGC--CGCUGCGCCGCC
..........((((((..(((.(((((((((((((..--------.)))))...(.((((((((........--...)))))))).))))))))).)))..)))))--)((......)). ( -36.30, z-score =  -2.91, R)
>droYak2.chr3R 3251328 118 + 28832112
GUAUAAAUAUGGUUAAUCAGCAUCAACACCCGAGCCGAGCACCCAAGCUCGAGUGCAAACUAGUCUGUGUGU--GAAACUAGUUUUCGGUGUUGAAGCUACUUAGCUUCGCUGCGAUGCC
..........(((....((((...((((((...(((((((......))))).))(.((((((((........--...)))))))).)))))))((((((....))))))))))....))) ( -38.50, z-score =  -2.95, R)
>droEre2.scaffold_4820 3335382 108 + 10470090
GUAUAAAUAUGGUUAAUCAGCAUCAACACCCGAGCCG--------AGCUCGAGUGCAAACUAGUCUGUGUGU--GAAACUAGUUUUCGGUGUUGAAGCUACUUAGC--CGCUGCGAUGCC
((((.....(((((((..(((.(((((((((((((..--------.)))))...(.((((((((........--...)))))))).))))))))).)))..)))))--)).....)))). ( -38.10, z-score =  -3.73, R)
>droSec1.super_33 176946 108 - 478481
GUAUAAAUAUGGUUAAUCAGCAUCAACACCCGAGCCG--------AGCUCGAGUGCAAGCUAGUCUGUGUGU--GAAACUAGUUUUCGGUGUUGAAGCUACUUAGC--CGCUGCGCCGCC
..........((((((..(((.(((((((((((((..--------.)))))...(.((((((((........--...)))))))).))))))))).)))..)))))--)((......)). ( -36.30, z-score =  -2.48, R)
>droSim1.chr3R 20745957 108 - 27517382
GUAUAAAUAUGGUUAAUCAGCAUCAACACCCGAGCCG--------AGCUCGAGUGCAAGCUAGUCUGUGUGU--GAAACUAGUUUUCGGUGUUGAAGCUACUUAGC--CGCUGCGCCGCC
..........((((((..(((.(((((((((((((..--------.)))))...(.((((((((........--...)))))))).))))))))).)))..)))))--)((......)). ( -36.30, z-score =  -2.48, R)
>droAna3.scaffold_13340 6778131 104 - 23697760
GUAUAAAUAUGGUUAAUCAGCAUCAACACCCGAGCCG--------AGCUCGAGUGCAAACUAGUCUGUGUGUGCGAAACUAGUUUUCGGUGUUGAAGCUACUUAGC--UGAUGC------
..........((((((..(((.(((((((((((((..--------.)))))...(.((((((((...((....))..)))))))).))))))))).)))..)))))--).....------ ( -35.10, z-score =  -3.12, R)
>consensus
GUAUAAAUAUGGUUAAUCAGCAUCAACACCCGAGCCG________AGCUCGAGUGCAAACUAGUCUGUGUGU__GAAACUAGUUUUCGGUGUUGAAGCUACUUAGC__CGCUGCGCCGCC
...........(((((..(((.(((((((((((((...........)))))...(.((((((((.............)))))))).))))))))).)))..))))).............. (-31.14 = -30.92 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:42:28 2011