Locus 14564

Sequence ID dm3.chrX
Location 14,140,237 – 14,140,372
Length 135
Max. P 0.944879
window20053 window20054

overview

Window 3

Location 14,140,237 – 14,140,336
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 66.50
Shannon entropy 0.55306
G+C content 0.67649
Mean single sequence MFE -42.30
Consensus MFE -24.74
Energy contribution -28.05
Covariance contribution 3.31
Combinations/Pair 1.28
Mean z-score -1.43
Structure conservation index 0.58
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.50
SVM RNA-class probability 0.944879
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14140237 99 - 22422827
GCCGGGAUUGAGCUUGGCCGCAGCACUGGCCUGGCCACCUGGACUGGCGACCGUACUGCGACCUGAUCUCGUACCCGGACCAGAUGCGCCAGCUGAAUC
.(((((..((.(((.(((((......))))).)))))))))).((((((..((.....))..(((.((.((....)))).)))...))))))....... ( -35.80, z-score =  -0.62, R)
>droAna3.scaffold_13248 2998160 81 + 4840945
GCCGGGAUCG-GUGGGACUGACUGUAUGGGUUGGUCGGAUGGGCUUG-----GAGGUGUGUCCGGAUACUAUGCCGGGACUACUGUC------------
.((((.((.(-(((.(((..(((.....)))..)))(((((.(((..-----..))).)))))...)))))).))))(((....)))------------ ( -29.70, z-score =  -1.45, R)
>droSec1.super_20 743695 99 - 1148123
GCCGGGACGGGGCUUGGCUGCAGCGGUCGGCUGGCCACCUGGACUGGCGACCGUACUGCGACCUGGUCUCGUACCCGGACCCGAACCGCCAGCGGAGUC
.(((((((((((((.((.(((((((((((.(..(((....)).)..)))))))..))))).)).)))))))).))))).......(((....))).... ( -53.50, z-score =  -2.32, R)
>droSim1.chrX 10859334 99 - 17042790
GCCGGGAUGGGGCUUGGCUGCAGCGGUCGGCUGGCCACCUGGAGUGGCGACCGUACUGCGACCUGGUCUCGUACCCGGACCCGAACCGCCAGCGGAGUC
.(((((((((((((.((.(((((((((((.(...((....))...).))))))..))))).)).)))))))).))))).......(((....))).... ( -50.20, z-score =  -1.35, R)
>consensus
GCCGGGAUGGGGCUUGGCUGCAGCGGUCGGCUGGCCACCUGGACUGGCGACCGUACUGCGACCUGAUCUCGUACCCGGACCAGAACCGCCAGCGGAGUC
.(((((((((((((.((.(((((((((((.((((((....)).))))))))))..))))).)).)))))))).)))))..................... (-24.74 = -28.05 +   3.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,140,259 – 14,140,372
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 65.04
Shannon entropy 0.64808
G+C content 0.66164
Mean single sequence MFE -41.10
Consensus MFE -19.13
Energy contribution -19.98
Covariance contribution 0.85
Combinations/Pair 1.42
Mean z-score -1.27
Structure conservation index 0.47
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.16
SVM RNA-class probability 0.902567
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chrX 14140259 113 + 22422827
CGGGUACGAGAUCAGGUCGCAGUACGGUCGCCAGUCCAGGUGGCCAGGCCAGUGCUGCGGCCAAGCUCAAUCCCGGCGAGAAACGACAGCGACUACAGCGCCUGGACACGUUG
((((...(((....(((((((((((((((((((.......))))..)))).)))))))))))...)))...))))......((((.(((((.(....))).)))....)))). ( -46.80, z-score =  -1.44, R)
>droAna3.scaffold_13248 2998170 101 - 4840945
-----CCGGCAUAGUAUCCGGACACACCUCCAAGCCCAUCCGACCAACCCAUACAGUCAGUCCCAC-CGAUCCCGGCGAGAAGCGAUCCCAGCGACUAGUCAUGGAG------
-----((((........))))...........................((((((((((..((.(.(-((....))).).)).((.......)))))).)).))))..------ ( -21.20, z-score =  -0.45, R)
>droYak2.chrX 8393632 86 + 21770863
CGGGUUCGAAACCAGGUCGCAGUACGGCUG---------GUGGC------------------AAGCCCCAUCCCGGCGAGAAACGCCAGCGGCUACAGCGCCUGGACACAUUG
...........(((((.(((.((((.((((---------(((.(------------------..(((.......)))..)...))))))).).))).))))))))........ ( -35.70, z-score =  -1.57, R)
>droSec1.super_20 743717 113 + 1148123
CGGGUACGAGACCAGGUCGCAGUACGGUCGCCAGUCCAGGUGGCCAGCCGACCGCUGCAGCCAAGCCCCGUCCCGGCGAGAAACGCCAGCGGCUGCAGCGCCUGGACACGUUG
(((((.........(((((..((..(((((((......))))))).)))))))(((((((((..(........)((((.....))))...))))))))))))))......... ( -50.90, z-score =  -1.28, R)
>droSim1.chrX 10859356 113 + 17042790
CGGGUACGAGACCAGGUCGCAGUACGGUCGCCACUCCAGGUGGCCAGCCGACCGCUGCAGCCAAGCCCCAUCCCGGCGAGAAACGCCAGCGGCUGCAGCGCCUGGACACGUUG
(((((.........(((((..((..(((((((......))))))).)))))))(((((((((..(........)((((.....))))...))))))))))))))......... ( -50.90, z-score =  -1.63, R)
>consensus
CGGGUACGAGACCAGGUCGCAGUACGGUCGCCAGUCCAGGUGGCCAGCCCACCGCUGCAGCCAAGCCCCAUCCCGGCGAGAAACGCCAGCGGCUACAGCGCCUGGACACGUUG
...........(((((.(((.....(((((((......))))))).............................((((.....))))..........))))))))........ (-19.13 = -19.98 +   0.85)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 01:42:32 2011