Locus 9860

Sequence ID dm3.chr3R
Location 9,447,743 – 9,447,835
Length 92
Max. P 0.893550
window13538 window13539

overview

Window 8

Location 9,447,743 – 9,447,835
Length 92
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 91.69
Shannon entropy 0.14021
G+C content 0.46000
Mean single sequence MFE -26.98
Consensus MFE -25.46
Energy contribution -24.98
Covariance contribution -0.48
Combinations/Pair 1.08
Mean z-score -1.59
Structure conservation index 0.94
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.11
SVM RNA-class probability 0.893550
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9447743 92 + 27905053
UUCUGGUUGCCGAAUCUGCAGGACGUUUGGCACAUUUGCUGAUUACGCUCGUCCUGCUUGGUCUACAUAGGAAAAAAAUGUAGUUACUAAGC
...((((.(((((....((((((((.(..(((....)))..).......)))))))))))))((((((.........))))))..))))... ( -25.60, z-score =  -1.48, R)
>droSim1.chr3R 15528582 92 - 27517382
UUCUGGUUGCCGAAGCUGCAGGACGUUUGGCACAUUUGCUGAUUACGCUCGUCCUGCUUGGUCUACAUGGGAAAAAAAUGUAGUUGCUAAGA
....((((.....))))((((((((.(..(((....)))..).......))))))))(((((((((((.........))))))..))))).. ( -26.90, z-score =  -0.98, R)
>droSec1.super_0 8561240 92 - 21120651
UUCUGGUUGCCGAAGCUGCAGGACGUUUGGCACAUUUGCUGAUUACGCUCGUCCUGCUUGGUCUACAUGGGAAAAAAAUGUAGUUGCUAAGA
....((((.....))))((((((((.(..(((....)))..).......))))))))(((((((((((.........))))))..))))).. ( -26.90, z-score =  -0.98, R)
>droYak2.chr3R 13756919 87 + 28832112
UUCUGGUUGCCGAAGCUGCAGGACGUUUGGCACAUUUGCUGAUUACGCUCGUCCUGCUCGGUCUACAUAGGAAACAA-UUUAGUUGAU----
(((((((.(((((....((((((((.(..(((....)))..).......)))))))))))))..)).))))).....-..........---- ( -27.30, z-score =  -1.92, R)
>droEre2.scaffold_4770 5558980 87 - 17746568
UUCUGGUUGCCGAAGCUGCAGGACGUUUGGCACAUUUGCUGAUUACGCUCGUCCUGCUCGGUAUACAUAGGAAAAAA-UUUUGUUGAU----
(((((((((((((....((((((((.(..(((....)))..).......)))))))))))))).)).))))).....-..........---- ( -28.20, z-score =  -2.57, R)
>consensus
UUCUGGUUGCCGAAGCUGCAGGACGUUUGGCACAUUUGCUGAUUACGCUCGUCCUGCUUGGUCUACAUAGGAAAAAAAUGUAGUUGCUAAG_
(((((((.(((((....((((((((.(..(((....)))..).......)))))))))))))..)).))))).................... (-25.46 = -24.98 +  -0.48)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,447,743 – 9,447,835
Length 92
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 91.69
Shannon entropy 0.14021
G+C content 0.46000
Mean single sequence MFE -23.12
Consensus MFE -18.76
Energy contribution -18.96
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.81
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.57
SVM RNA-class probability 0.745245
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr3R 9447743 92 - 27905053
GCUUAGUAACUACAUUUUUUUCCUAUGUAGACCAAGCAGGACGAGCGUAAUCAGCAAAUGUGCCAAACGUCCUGCAGAUUCGGCAACCAGAA
(((.(((..((((((.........)))))).....(((((((((......)).(((....))).....)))))))..))).)))........ ( -24.40, z-score =  -2.35, R)
>droSim1.chr3R 15528582 92 + 27517382
UCUUAGCAACUACAUUUUUUUCCCAUGUAGACCAAGCAGGACGAGCGUAAUCAGCAAAUGUGCCAAACGUCCUGCAGCUUCGGCAACCAGAA
.........((((((.........)))))).....(((((((((......)).(((....))).....))))))).((....))........ ( -24.70, z-score =  -2.46, R)
>droSec1.super_0 8561240 92 + 21120651
UCUUAGCAACUACAUUUUUUUCCCAUGUAGACCAAGCAGGACGAGCGUAAUCAGCAAAUGUGCCAAACGUCCUGCAGCUUCGGCAACCAGAA
.........((((((.........)))))).....(((((((((......)).(((....))).....))))))).((....))........ ( -24.70, z-score =  -2.46, R)
>droYak2.chr3R 13756919 87 - 28832112
----AUCAACUAAA-UUGUUUCCUAUGUAGACCGAGCAGGACGAGCGUAAUCAGCAAAUGUGCCAAACGUCCUGCAGCUUCGGCAACCAGAA
----.((.......-....................(((((((((......)).(((....))).....))))))).((....)).....)). ( -20.90, z-score =  -0.95, R)
>droEre2.scaffold_4770 5558980 87 + 17746568
----AUCAACAAAA-UUUUUUCCUAUGUAUACCGAGCAGGACGAGCGUAAUCAGCAAAUGUGCCAAACGUCCUGCAGCUUCGGCAACCAGAA
----.((.......-....................(((((((((......)).(((....))).....))))))).((....)).....)). ( -20.90, z-score =  -1.69, R)
>consensus
_CUUAGCAACUACAUUUUUUUCCUAUGUAGACCAAGCAGGACGAGCGUAAUCAGCAAAUGUGCCAAACGUCCUGCAGCUUCGGCAACCAGAA
...................................(((((((((......)).(((....))).....))))))).((....))........ (-18.76 = -18.96 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Wed Apr 20 00:12:39 2011