Locus 3493

Sequence ID dm3.chr2R
Location 5,788,988 – 5,789,133
Length 145
Max. P 0.939156
window4791 window4792 window4793

overview

Window 1

Location 5,788,988 – 5,789,101
Length 113
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 92.36
Shannon entropy 0.13577
G+C content 0.55565
Mean single sequence MFE -41.47
Consensus MFE -36.61
Energy contribution -39.01
Covariance contribution 2.40
Combinations/Pair 1.00
Mean z-score -1.92
Structure conservation index 0.88
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.06
SVM RNA-class probability 0.884220
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5788988 113 + 21146708
AAAGUGGUCGUAGCCACAUGUGAGUACGAGUAUGAGGCAACCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGCUGGACAGUGGCCACA
...(((((((..(((.((((..........)))).)))..(((.((((((((((((((..((................))..)).)))))))))))).)))....))))))). ( -45.29, z-score =  -2.81, R)
>droEre2.scaffold_4929 18061502 97 - 26641161
AAAGUGGUCGUAGCC------------GAGUAUGAGGCAACCAACCAGUUAGCCGUCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGACUGACUGGC----CAGUGGCCACA
...((((((((((..------------........((((((......))).)))((((...))))..))))......(((((.(((.....)))))))----)...)))))). ( -32.30, z-score =  -1.35, R)
>droYak2.chr2L 18414575 109 + 22324452
AAAGUGGUCGUAGCCACAUGUGAGUACGAGUAUGAGGCAACCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGC----CAGUGGCCACA
...((((((((.(((.((((..........)))).))).))...((((((((((((((..((................))..)).)))))))))))).----....)))))). ( -40.59, z-score =  -1.92, R)
>droSec1.super_1 3399792 113 + 14215200
AAAGUGGUCGUAGCCACAUGUGAGUGCGAGUAUGAGGCAACCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGCUGGCCAGUGGCCACA
...(((((((..(((.((((..........)))).)))..(((.((((((((((((((..((................))..)).)))))))))))).)))....))))))). ( -44.59, z-score =  -1.77, R)
>droSim1.chr2R 4419854 113 + 19596830
AAAGUGGUCGUAGCCACAUGUGAGUGCGAGUAUGAGGCAACCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGCUGGCCAGUGGCCACA
...(((((((..(((.((((..........)))).)))..(((.((((((((((((((..((................))..)).)))))))))))).)))....))))))). ( -44.59, z-score =  -1.77, R)
>consensus
AAAGUGGUCGUAGCCACAUGUGAGUACGAGUAUGAGGCAACCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGCUGG_CAGUGGCCACA
...(((((((..(((.((((..........)))).)))..(((.((((((((((((((..((................))..)).)))))))))))).)))....))))))). (-36.61 = -39.01 +   2.40)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,788,988 – 5,789,101
Length 113
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 92.36
Shannon entropy 0.13577
G+C content 0.55565
Mean single sequence MFE -40.14
Consensus MFE -32.12
Energy contribution -34.00
Covariance contribution 1.88
Combinations/Pair 1.06
Mean z-score -2.56
Structure conservation index 0.80
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.43
SVM RNA-class probability 0.939156
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5788988 113 - 21146708
UGUGGCCACUGUCCAGCCAGUCAGCCAAACGUGGCCUAAUCUGCAAUUGUCGCUCCGCCGGCUAACUGGUUGGUUGCCUCAUACUCGUACUCACAUGUGGCUACGACCACUUU
.((((((((((((((((((((.((((...((..((.((((.....))))..))..))..)))).))))))))).(((.........)))...))).))))))))......... ( -40.10, z-score =  -2.57, R)
>droEre2.scaffold_4929 18061502 97 + 26641161
UGUGGCCACUG----GCCAGUCAGUCAAACGUGGCCUAAUCUGCAAUUGUCGCUCCGACGGCUAACUGGUUGGUUGCCUCAUACUC------------GGCUACGACCACUUU
((.(((.((..----((((((.((((....(..(......)..)....((((...)))))))).))))))..)).))).))...((------------(....)))....... ( -34.00, z-score =  -2.13, R)
>droYak2.chr2L 18414575 109 - 22324452
UGUGGCCACUG----GCCAGUCAGCCAAACGUGGCCUAAUCUGCAAUUGUCGCUCCGCCGGCUAACUGGUUGGUUGCCUCAUACUCGUACUCACAUGUGGCUACGACCACUUU
((.(((.((..----((((((.((((...((..((.((((.....))))..))..))..)))).))))))..)).))).))...(((((..((....))..)))))....... ( -39.40, z-score =  -2.38, R)
>droSec1.super_1 3399792 113 - 14215200
UGUGGCCACUGGCCAGCCAGUCAGCCAAACGUGGCCUAAUCUGCAAUUGUCGCUCCGCCGGCUAACUGGUUGGUUGCCUCAUACUCGCACUCACAUGUGGCUACGACCACUUU
.((((((((((((((((((((.((((...((..((.((((.....))))..))..))..)))).))))))))))(((.........)))....)).))))))))......... ( -43.60, z-score =  -2.87, R)
>droSim1.chr2R 4419854 113 - 19596830
UGUGGCCACUGGCCAGCCAGUCAGCCAAACGUGGCCUAAUCUGCAAUUGUCGCUCCGCCGGCUAACUGGUUGGUUGCCUCAUACUCGCACUCACAUGUGGCUACGACCACUUU
.((((((((((((((((((((.((((...((..((.((((.....))))..))..))..)))).))))))))))(((.........)))....)).))))))))......... ( -43.60, z-score =  -2.87, R)
>consensus
UGUGGCCACUG_CCAGCCAGUCAGCCAAACGUGGCCUAAUCUGCAAUUGUCGCUCCGCCGGCUAACUGGUUGGUUGCCUCAUACUCGCACUCACAUGUGGCUACGACCACUUU
.((((((((...(((((((((.((((...((..((.((((.....))))..))..))..)))).))))))))).(((.........))).......))))))))......... (-32.12 = -34.00 +   1.88)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,789,028 – 5,789,133
Length 105
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 96.75
Shannon entropy 0.05599
G+C content 0.57241
Mean single sequence MFE -41.46
Consensus MFE -37.08
Energy contribution -37.88
Covariance contribution 0.80
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.89
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.62
SVM RNA-class probability 0.763395
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 5789028 105 + 21146708
CCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGCUGGACAGUGGCCACAUAACUGGCUGGCUGGGUUUCUGAGUGUCAACG
....((((((((((((....((((...))))......(((((((((..(((....)))..))).))))))......))))))))))))................. ( -46.10, z-score =  -3.17, R)
>droEre2.scaffold_4929 18061530 101 - 26641161
CCAACCAGUUAGCCGUCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGACUGACUGGC----CAGUGGCCACAUAACUGGCUGGCUGGGUUUCUGAGUGUCAACG
....(((((((((((((((.((((...))))...((((((...)))))))))))((((----(...))))).......))))))))))................. ( -34.60, z-score =  -0.83, R)
>droYak2.chr2L 18414615 101 + 22324452
CCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGC----CAGUGGCCACAUAACUGGCUGGCUGGGUUUCUGAGUGUCAACG
....((((((((((((....((((...))))......((((((...(((((....)))----))))))))......))))))))))))................. ( -42.20, z-score =  -2.34, R)
>droSec1.super_1 3399832 105 + 14215200
CCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGCUGGCCAGUGGCCACAUAACUGGCUGGCUGGGUUUCUGAGUGUCAACG
....((((((((((((....((((...))))......((((((...(((((........)))))))))))......))))))))))))................. ( -42.20, z-score =  -1.46, R)
>droSim1.chr2R 4419894 105 + 19596830
CCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGCUGGCCAGUGGCCACAUAACUGGCUGGCUGGGUUUCUGAGUGUCAACG
....((((((((((((....((((...))))......((((((...(((((........)))))))))))......))))))))))))................. ( -42.20, z-score =  -1.46, R)
>consensus
CCAACCAGUUAGCCGGCGGAGCGACAAUUGCAGAUUAGGCCACGUUUGGCUGACUGGCUGG_CAGUGGCCACAUAACUGGCUGGCUGGGUUUCUGAGUGUCAACG
....((((((((((((....((((...))))......((((((..(..(((....)))..)...))))))......))))))))))))................. (-37.08 = -37.88 +   0.80)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:11:12 2011