Locus 1737

Sequence ID dm3.chr2L
Location 13,417,343 – 13,417,441
Length 98
Max. P 0.922133
window2381 window2382

overview

Window 1

Location 13,417,343 – 13,417,441
Length 98
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 94.94
Shannon entropy 0.08262
G+C content 0.43769
Mean single sequence MFE -22.05
Consensus MFE -20.49
Energy contribution -20.93
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.49
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 0.59
SVM RNA-class probability 0.754971
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13417343 98 + 23011544
UUGCUGUUGCCAUUUGUUGGUGGUUUCUACCGCCG-GUUGUUGUUCCUCCUGUUUUGGCCCUGCAGCUUGACUUGUAAUGAAUAUAAAACUGCCUUUUA
..(((((.((((......((((((....))))))(-(........))........))))...)))))................................ ( -23.40, z-score =  -1.91, R)
>droSim1.chr2L 13207120 99 + 22036055
UUGCUGUUGCCAUUUGUUGGUGGUUUCUCCCACCGGCUUGUUGUUCCUGUUGUUUUGGCCCUGCAGCUUGACUUGUAAUGAAUAUAAAACUGCCUUUUA
..(((((.((((...((((((((......))))))))..................))))...)))))................................ ( -22.70, z-score =  -1.44, R)
>droSec1.super_16 1571326 99 + 1878335
UUGCUGUUGCCAUUUGUUGGUGGUUUCUCCCACCGGCUUGUUGUUCCUGUUGUUUUGGCCCUGCAGCUUGACUUGUAAUGAAUAUAAAACUGCCUUUUA
..(((((.((((...((((((((......))))))))..................))))...)))))................................ ( -22.70, z-score =  -1.44, R)
>droEre2.scaffold_4929 14616903 97 - 26641161
UUGCUGUUGCCAUUUGUUGGUGGUCCC-CCCACCG-UUUGUUGUUCCUGUUGUUUUGGCCCUGCAGCUUGACUUGUAAUGAAUAUAAAACUGCCUUUUA
..((.(((...(((..(((((((....-.)))))(-((.(((((.((.........))....)))))..)))....))..)))....))).))...... ( -19.40, z-score =  -1.19, R)
>consensus
UUGCUGUUGCCAUUUGUUGGUGGUUUCUCCCACCG_CUUGUUGUUCCUGUUGUUUUGGCCCUGCAGCUUGACUUGUAAUGAAUAUAAAACUGCCUUUUA
..(((((.((((...((((((((......))))))))..................))))...)))))................................ (-20.49 = -20.93 +   0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 13,417,343 – 13,417,441
Length 98
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 94.94
Shannon entropy 0.08262
G+C content 0.43769
Mean single sequence MFE -22.25
Consensus MFE -20.75
Energy contribution -21.00
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.93
Structure conservation index 0.93
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.29
SVM RNA-class probability 0.922133
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2L 13417343 98 - 23011544
UAAAAGGCAGUUUUAUAUUCAUUACAAGUCAAGCUGCAGGGCCAAAACAGGAGGAACAACAAC-CGGCGGUAGAAACCACCAACAAAUGGCAACAGCAA
......(((((((.((...........)).)))))))...((((........((........)-)((.(((....))).))......))))........ ( -20.20, z-score =  -1.37, R)
>droSim1.chr2L 13207120 99 - 22036055
UAAAAGGCAGUUUUAUAUUCAUUACAAGUCAAGCUGCAGGGCCAAAACAACAGGAACAACAAGCCGGUGGGAGAAACCACCAACAAAUGGCAACAGCAA
......(((((((.((...........)).)))))))...((((........((.........))(((((......)))))......))))........ ( -23.40, z-score =  -2.17, R)
>droSec1.super_16 1571326 99 - 1878335
UAAAAGGCAGUUUUAUAUUCAUUACAAGUCAAGCUGCAGGGCCAAAACAACAGGAACAACAAGCCGGUGGGAGAAACCACCAACAAAUGGCAACAGCAA
......(((((((.((...........)).)))))))...((((........((.........))(((((......)))))......))))........ ( -23.40, z-score =  -2.17, R)
>droEre2.scaffold_4929 14616903 97 + 26641161
UAAAAGGCAGUUUUAUAUUCAUUACAAGUCAAGCUGCAGGGCCAAAACAACAGGAACAACAAA-CGGUGGG-GGGACCACCAACAAAUGGCAACAGCAA
......(((((((.((...........)).)))))))...((((........(......)...-.(((((.-....)))))......))))........ ( -22.00, z-score =  -1.99, R)
>consensus
UAAAAGGCAGUUUUAUAUUCAUUACAAGUCAAGCUGCAGGGCCAAAACAACAGGAACAACAAG_CGGUGGGAGAAACCACCAACAAAUGGCAACAGCAA
......(((((((.((...........)).)))))))...((((........(......).....(((((......)))))......))))........ (-20.75 = -21.00 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 21:37:46 2011