Locus 3074

Sequence ID dm3.chr2R
Location 2,044,809 – 2,044,863
Length 54
Max. P 0.874640
window4215 window4216

overview

Window 5

Location 2,044,809 – 2,044,863
Length 54
Sequences 5
Columns 54
Reading direction forward
Mean pairwise identity 95.19
Shannon entropy 0.08483
G+C content 0.56296
Mean single sequence MFE -14.54
Consensus MFE -12.60
Energy contribution -12.60
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.01
Structure conservation index 0.87
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.84
SVM RNA-class probability 0.831763
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2044809 54 + 21146708
CGGCCAGAGCAACAACAACUCGUUGCAGUAGCCACAGCGGCAGCAUUCAGGUAC
..(((...(((((........))))).((.(((.....))).)).....))).. ( -16.00, z-score =  -2.46, R)
>droEre2.scaffold_4929 6353440 54 - 26641161
CGACCAGAGCAACAACAACUCGUUGCAGUAGCCACAGCGGCAGCAUUCACGUAC
......(((((((........))))).((.(((.....))).))..))...... ( -12.50, z-score =  -1.65, R)
>droYak2.chr2L 1890395 54 - 22324452
CGGUUAGAGCAACGAUAACUCGUUGCAGUAGCCACAGCGGCAGCAUUCAGGUAC
.(((((..(((((((....)))))))..)))))...((....)).......... ( -18.40, z-score =  -3.66, R)
>droSec1.super_26 687853 54 + 826190
CGGCCAGAGCAACAACAACUCGUUGCAGUAGCCACAGCGGCAGCAUUCACGUAC
..(((...(((((........)))))....((....)))))............. ( -12.90, z-score =  -1.14, R)
>droSim1.chr2R 940561 54 + 19596830
CGGCCAGAGCAACAACAACUCGUUGCAGUAGCCACAGCGGCAGCAUUCACGUAC
..(((...(((((........)))))....((....)))))............. ( -12.90, z-score =  -1.14, R)
>consensus
CGGCCAGAGCAACAACAACUCGUUGCAGUAGCCACAGCGGCAGCAUUCACGUAC
......(((((((........))))).((.(((.....))).))..))...... (-12.60 = -12.60 +  -0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 2,044,809 – 2,044,863
Length 54
Sequences 5
Columns 54
Reading direction reverse
Mean pairwise identity 95.19
Shannon entropy 0.08483
G+C content 0.56296
Mean single sequence MFE -16.38
Consensus MFE -16.20
Energy contribution -15.92
Covariance contribution -0.28
Combinations/Pair 1.21
Mean z-score -1.33
Structure conservation index 0.99
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.02
SVM RNA-class probability 0.874640
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 2044809 54 - 21146708
GUACCUGAAUGCUGCCGCUGUGGCUACUGCAACGAGUUGUUGUUGCUCUGGCCG
..........((....))...(((((..(((((((....)))))))..))))). ( -16.90, z-score =  -1.61, R)
>droEre2.scaffold_4929 6353440 54 + 26641161
GUACGUGAAUGCUGCCGCUGUGGCUACUGCAACGAGUUGUUGUUGCUCUGGUCG
....(((........)))...(((((..(((((((....)))))))..))))). ( -15.10, z-score =  -0.48, R)
>droYak2.chr2L 1890395 54 + 22324452
GUACCUGAAUGCUGCCGCUGUGGCUACUGCAACGAGUUAUCGUUGCUCUAACCG
..........((..(....)..))....(((((((....)))))))........ ( -14.30, z-score =  -1.77, R)
>droSec1.super_26 687853 54 - 826190
GUACGUGAAUGCUGCCGCUGUGGCUACUGCAACGAGUUGUUGUUGCUCUGGCCG
....(((........)))...(((((..(((((((....)))))))..))))). ( -17.80, z-score =  -1.39, R)
>droSim1.chr2R 940561 54 - 19596830
GUACGUGAAUGCUGCCGCUGUGGCUACUGCAACGAGUUGUUGUUGCUCUGGCCG
....(((........)))...(((((..(((((((....)))))))..))))). ( -17.80, z-score =  -1.39, R)
>consensus
GUACGUGAAUGCUGCCGCUGUGGCUACUGCAACGAGUUGUUGUUGCUCUGGCCG
..........((....))...(((((..(((((((....)))))))..))))). (-16.20 = -15.92 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:03:07 2011