Locus 582

Sequence ID dm3.chr2L
Location 4,128,556 – 4,128,650
Length 94
Max. P 0.998718
window773 window774

overview

Window 3

Location 4,128,556 – 4,128,650
Length 94
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 92.21
Shannon entropy 0.13272
G+C content 0.59283
Mean single sequence MFE -24.00
Consensus MFE -18.65
Energy contribution -20.05
Covariance contribution 1.40
Combinations/Pair 1.00
Mean z-score -2.26
Structure conservation index 0.78
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.75
SVM RNA-class probability 0.806908
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4128556 94 + 23011544
CUCCAGCAACUGUGCUCCUCUUCAGAACCAGCUCCUGAUUCUGCAGGAUGCUGCCAGCUCC---GUUUCCCAUUCUCCUGCAACAUUCCCACUCCCC
.....(((.(((..........)))...(((((((((......))))).))))........---..............)))................ ( -16.40, z-score =  -0.45, R)
>droSim1.chr2L 4084016 94 + 22036055
CUCCAGCAACUGUGCUCCUCUCCAGAACCAGCUCCUGGUUCUGCAGGAUGCUGCCAGCUCC---GUUUCCCAUUCUCCGGCAGCAUUCCCACUCCCC
....((((....))))......(((((((((...)))))))))..((((((((((......---..............))))))))))......... ( -29.95, z-score =  -3.43, R)
>droSec1.super_5 2227213 94 + 5866729
CUCCAGCAACUGUGCUCCUCUCCAGAACCAGCUCCUGGUUCUGCAGGAUGCUGCCAGCUCC---GUUUCCCAUUCUCCUGCAGCAUUCCCACUCCCC
....((((....))))......(((((((((...)))))))))..(((((((((.((....---.............)))))))))))......... ( -26.43, z-score =  -2.66, R)
>droYak2.chr2L 4150295 95 + 22324452
CUCCAGCAACUGUGCUCCUC--CAGAACCUCCUCCUGGUUCAGCAGGAUGCUGCCAGCUUCCCAGUUACCCAACCUCCUGCAACAUUCCCACUCCCC
....((((....))))....--..(((((.......))))).((((((.(.((..((((....))))...)).).))))))................ ( -20.80, z-score =  -1.91, R)
>droEre2.scaffold_4929 4188832 92 + 26641161
CUCCAGCAACUGUGCUCCUC--CAGAACCUGCUCCUGGUUCUGCAGGAUGCUGCCAGCUCC---GUUUCCCAACCUCCUGCAGCAUUCCCACUCCCC
.....(((....)))((((.--(((((((.......))))))).))))((((((.((....---(((....)))...))))))))............ ( -26.40, z-score =  -2.85, R)
>consensus
CUCCAGCAACUGUGCUCCUCU_CAGAACCAGCUCCUGGUUCUGCAGGAUGCUGCCAGCUCC___GUUUCCCAUUCUCCUGCAGCAUUCCCACUCCCC
....((((....))))......(((((((((...)))))))))..(((((((((.........................)))))))))......... (-18.65 = -20.05 +   1.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,128,556 – 4,128,650
Length 94
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 92.21
Shannon entropy 0.13272
G+C content 0.59283
Mean single sequence MFE -39.06
Consensus MFE -36.12
Energy contribution -36.32
Covariance contribution 0.20
Combinations/Pair 1.07
Mean z-score -4.03
Structure conservation index 0.92
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 3.46
SVM RNA-class probability 0.998718
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 4128556 94 - 23011544
GGGGAGUGGGAAUGUUGCAGGAGAAUGGGAAAC---GGAGCUGGCAGCAUCCUGCAGAAUCAGGAGCUGGUUCUGAAGAGGAGCACAGUUGCUGGAG
.....(..(((.((((((...((..(.(....)---.)..)).)))))))))..)....((((.((((((((((.....))))).))))).)))).. ( -36.80, z-score =  -4.39, R)
>droSim1.chr2L 4084016 94 - 22036055
GGGGAGUGGGAAUGCUGCCGGAGAAUGGGAAAC---GGAGCUGGCAGCAUCCUGCAGAACCAGGAGCUGGUUCUGGAGAGGAGCACAGUUGCUGGAG
.....(..(((.(((((((((....(.(....)---.)..))))))))))))..)....((((.((((((((((.....))))).))))).)))).. ( -47.10, z-score =  -6.00, R)
>droSec1.super_5 2227213 94 - 5866729
GGGGAGUGGGAAUGCUGCAGGAGAAUGGGAAAC---GGAGCUGGCAGCAUCCUGCAGAACCAGGAGCUGGUUCUGGAGAGGAGCACAGUUGCUGGAG
.....(..(((.((((((...((..(.(....)---.)..)).)))))))))..)....((((.((((((((((.....))))).))))).)))).. ( -42.00, z-score =  -4.95, R)
>droYak2.chr2L 4150295 95 - 22324452
GGGGAGUGGGAAUGUUGCAGGAGGUUGGGUAACUGGGAAGCUGGCAGCAUCCUGCUGAACCAGGAGGAGGUUCUG--GAGGAGCACAGUUGCUGGAG
....((..(((.((((((.((...(..(....)..)....)).)))))))))..))...((((.((..(((((..--...)))).)..)).)))).. ( -30.40, z-score =  -1.00, R)
>droEre2.scaffold_4929 4188832 92 - 26641161
GGGGAGUGGGAAUGCUGCAGGAGGUUGGGAAAC---GGAGCUGGCAGCAUCCUGCAGAACCAGGAGCAGGUUCUG--GAGGAGCACAGUUGCUGGAG
.....(..(((.((((((...((.((.(....)---.)).)).)))))))))..)....((((.(((..((((..--...))))...))).)))).. ( -39.00, z-score =  -3.82, R)
>consensus
GGGGAGUGGGAAUGCUGCAGGAGAAUGGGAAAC___GGAGCUGGCAGCAUCCUGCAGAACCAGGAGCUGGUUCUG_AGAGGAGCACAGUUGCUGGAG
.....(..(((.((((((.((......(....).......)).)))))))))..)....((((.((((((((((.....))))).))))).)))).. (-36.12 = -36.32 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:15:26 2011