Locus 9868

Sequence ID dm3.chr3R
Location 9,508,892 – 9,509,004
Length 112
Max. P 0.993699
window13550 window13551

overview

Window 0

Location 9,508,892 – 9,509,004
Length 112
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 88.48
Shannon entropy 0.20685
G+C content 0.57344
Mean single sequence MFE -42.43
Consensus MFE -29.28
Energy contribution -30.00
Covariance contribution 0.72
Combinations/Pair 1.17
Mean z-score -2.33
Structure conservation index 0.69
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.74
SVM RNA-class probability 0.802654
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9508892 112 + 27905053
UGGCCAAGUGAGCAAAUGCAUCGCAGCAGCGGGUCGCUGCGUCUUUCACUCGGAAUACCAAAACGACGGGGCACAACUGCAGGCAUUUGGAAUCCGCCGCCACCUGGCCACA
((((((.(((.((((((((...(((((((((...))))))(((((....(((...........))).))))).....)))..))))))((......))))))).)))))).. ( -41.70, z-score =  -1.28, R)
>droEre2.scaffold_4770 5620060 112 - 17746568
UGACCAAGUGAGCAAAUGCAUCGCAGCAAUGGGUCGCCGCGUCUUCCACUCGGAAUACCACAGCGACGAGGGACAACGGCGCCCAUUUGGAGUCCAUCGCCACCUGGUCACA
((((((.(((.((...(((......)))(((((.(((((.....(((.((((..............)))))))...))))))))))............))))).)))))).. ( -42.24, z-score =  -2.11, R)
>droYak2.chr3R 13817311 110 + 28832112
UGGCCAAGUGAGCAAAUGCAUCGCAGCAAUGGGUCGCCGCGUCUUCCACUCGGAAUACCAAAACAAC--GGUACAACGGCACGCAUUUAGAGUCCGCCACCACCUGGCCACA
((((((.(((.((((((((..(.((....)).)..((((....((((....))))((((........--))))...))))..)))))).(....)))...))).)))))).. ( -34.20, z-score =  -1.15, R)
>droSec1.super_0 8622430 112 - 21120651
UGGCCAAGUGAGCAAAUGCAUCGCAGCAGAGGGUCGCCGAGUCUUCCACUCGGAAUACCAAAACGACUGGGGACAACUGCGUGCAUUUAGAAUCUGCCGUCACCUGGCCACA
((((((.(((((((((((((.(((((.....(((..((((((.....))))))...)))........((....)).))))))))))).......)))..)))).)))))).. ( -45.21, z-score =  -3.26, R)
>droSim1.chr3R 15590618 112 - 27517382
UGGCCAAGUGAGCAAAUGCAUCGCAGCAGAGGGUCGCCGAGUCUUCCACUCGGAAUACCAAAACGACUGGGGACAACUGCGUGCAUUUGGAAUCAGCCGCCACCUGGCCACA
((((((.(((.(((((((((.(((((.....(((..((((((.....))))))...)))........((....)).))))))))))))((......))))))).)))))).. ( -48.80, z-score =  -3.86, R)
>consensus
UGGCCAAGUGAGCAAAUGCAUCGCAGCAGAGGGUCGCCGCGUCUUCCACUCGGAAUACCAAAACGACGGGGGACAACUGCGCGCAUUUGGAAUCCGCCGCCACCUGGCCACA
((((((.(((.((((((((...((((......(((.((.((((((((....)))).........)))).)))))..))))..))))))((......))))))).)))))).. (-29.28 = -30.00 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 9,508,892 – 9,509,004
Length 112
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 88.48
Shannon entropy 0.20685
G+C content 0.57344
Mean single sequence MFE -49.76
Consensus MFE -39.36
Energy contribution -39.00
Covariance contribution -0.36
Combinations/Pair 1.23
Mean z-score -3.18
Structure conservation index 0.79
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.64
SVM RNA-class probability 0.993699
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9508892 112 - 27905053
UGUGGCCAGGUGGCGGCGGAUUCCAAAUGCCUGCAGUUGUGCCCCGUCGUUUUGGUAUUCCGAGUGAAAGACGCAGCGACCCGCUGCUGCGAUGCAUUUGCUCACUUGGCCA
..((((((((((((((......))((((((.((((((.(((....((((((((((....))))(((.....))))))))).))).))))))..)))))))).)))))))))) ( -47.30, z-score =  -2.00, R)
>droEre2.scaffold_4770 5620060 112 + 17746568
UGUGACCAGGUGGCGAUGGACUCCAAAUGGGCGCCGUUGUCCCUCGUCGCUGUGGUAUUCCGAGUGGAAGACGCGGCGACCCAUUGCUGCGAUGCAUUUGCUCACUUGGUCA
..(((((((((((((((((.........(((((....)))))...(((((((((...((((....))))..)))))))))))))))).((((.....)))).)))))))))) ( -53.30, z-score =  -3.68, R)
>droYak2.chr3R 13817311 110 - 28832112
UGUGGCCAGGUGGUGGCGGACUCUAAAUGCGUGCCGUUGUACC--GUUGUUUUGGUAUUCCGAGUGGAAGACGCGGCGACCCAUUGCUGCGAUGCAUUUGCUCACUUGGCCA
..((((((((((..((((.......(((((((((((..(((((--(......))))))..)).))......((((((((....))))))))))))))))))))))))))))) ( -46.81, z-score =  -2.52, R)
>droSec1.super_0 8622430 112 + 21120651
UGUGGCCAGGUGACGGCAGAUUCUAAAUGCACGCAGUUGUCCCCAGUCGUUUUGGUAUUCCGAGUGGAAGACUCGGCGACCCUCUGCUGCGAUGCAUUUGCUCACUUGGCCA
..(((((((((((..(((.......((((((((((((.(((((.((((..(((((....))))).....)))).)).))).....)))))).)))))))))))))))))))) ( -49.31, z-score =  -3.73, R)
>droSim1.chr3R 15590618 112 + 27517382
UGUGGCCAGGUGGCGGCUGAUUCCAAAUGCACGCAGUUGUCCCCAGUCGUUUUGGUAUUCCGAGUGGAAGACUCGGCGACCCUCUGCUGCGAUGCAUUUGCUCACUUGGCCA
..((((((((((((((......))(((((((((((((.(((((.((((..(((((....))))).....)))).)).))).....)))))).))))))))).)))))))))) ( -52.10, z-score =  -3.95, R)
>consensus
UGUGGCCAGGUGGCGGCGGAUUCCAAAUGCACGCAGUUGUCCCCAGUCGUUUUGGUAUUCCGAGUGGAAGACGCGGCGACCCACUGCUGCGAUGCAUUUGCUCACUUGGCCA
..(((((((((((.((.....))((((((((((((((........((((((.((...((((....))))..)).)))))).....)))))).)))))))).))))))))))) (-39.36 = -39.00 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:12:49 2011