Locus 2802

Sequence ID dm3.chr2L
Location 22,469,621 – 22,469,735
Length 114
Max. P 0.992934
window3863 window3864

overview

Window 3

Location 22,469,621 – 22,469,735
Length 114
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 84.03
Shannon entropy 0.26406
G+C content 0.53806
Mean single sequence MFE -35.75
Consensus MFE -29.36
Energy contribution -29.43
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.52
Structure conservation index 0.82
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.65
SVM RNA-class probability 0.773534
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22469621 114 + 23011544
UCCAGUCUGACAAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACACUACUACUGCC
(((((.((((..(((((....))))).((((((...))..(((((.(((((((................)))))))))))))))).)))).))))).................. ( -31.59, z-score =   0.22, R)
>droSim1.chr2h_random 2495535 104 - 3178526
GCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACAC----------
(((.(((((((((((((....))))))))).....((....(((.(((((..((......))..))))).))).))))))(((((....)))))))).......---------- ( -37.10, z-score =  -1.74, R)
>droSec1.super_0 20531174 97 - 21120651
UCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGG------UACUUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACA-----------
(((((.(((((((((((....)))))))(((....)))..(((((.((------((.(..(.......)..)))))))))).....)))).))))).......----------- ( -32.50, z-score =  -1.17, R)
>droEre2.scaffold_4929 21984527 107 + 26641161
-----UCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACUUGCUUACGCCGUGUUGCCAGACUGGGCUUUAGUCUGGGCGCCACAUCUACUCCC--
-----...(((((((((....))))))))).....(((.((((...(((((.(((....))).)))))(((.((((((((((.....)))))).)))).)))))))..))).-- ( -41.80, z-score =  -3.38, R)
>consensus
UCCAGUCUGACGAUAUCAGAAGAUAUCGUCCUCCAGGAAAGGUCUUGGCGUUAGUACCUGUUUUCGCCGUGAUGCCAGACCGGGCUUCAGUCUGGGCGCCACAC__________
........(((((((((....)))))))))..((((((....))))))....................(((.((((((((.(.....).)))).)))).)))............ (-29.36 = -29.43 +   0.06)

alignment

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secondary structure

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dotplot

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Window 4

Location 22,469,621 – 22,469,735
Length 114
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 84.03
Shannon entropy 0.26406
G+C content 0.53806
Mean single sequence MFE -39.31
Consensus MFE -34.62
Energy contribution -34.99
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -2.59
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.58
SVM RNA-class probability 0.992934
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 22469621 114 - 23011544
GGCAGUAGUAGUGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUUGUCAGACUGGA
(((..(((((.(((..(((((((((((.....))))))).......))))...)))..)))))..)))........(((.(...(((((((((....)))))))))...).))) ( -41.51, z-score =  -1.97, R)
>droSim1.chr2h_random 2495535 104 + 3178526
----------GUGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAGGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGC
----------..(((..(((.((((((.....)))))))))..)))((((..............))))..........(..(..(((((((((....)))))))))...)..). ( -38.44, z-score =  -2.32, R)
>droSec1.super_0 20531174 97 + 21120651
-----------UGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAAGUA------CCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGA
-----------.(((..(((.((((((.....)))))))))..)))..............------(((...((......))..(((((((((....)))))))))....))). ( -35.40, z-score =  -2.44, R)
>droEre2.scaffold_4929 21984527 107 - 26641161
--GGGAGUAGAUGUGGCGCCCAGACUAAAGCCCAGUCUGGCAACACGGCGUAAGCAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGA-----
--(((((.((..(((..(((.(((((.......))))))))..)))(((((.((......)).))))).....)))))))....(((((((((....)))))))))...----- ( -41.90, z-score =  -3.62, R)
>consensus
__________GUGUGGCGCCCAGACUGAAGCCCGGUCUGGCAUCACGGCGAAAACAAGUACUAACGCCAAGACCUUUCCUGGAGGACGAUAUCUUCUGAUAUCGUCAGACUGGA
............(((..(((.((((((.....)))))))))..)))((((..............))))....((......))..(((((((((....)))))))))........ (-34.62 = -34.99 +   0.37)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:58:19 2011