Locus 4768

Sequence ID dm3.chr2R
Location 15,564,837 – 15,564,931
Length 94
Max. P 0.993985
window6549 window6550

overview

Window 9

Location 15,564,837 – 15,564,931
Length 94
Sequences 4
Columns 97
Reading direction forward
Mean pairwise identity 91.16
Shannon entropy 0.14034
G+C content 0.36065
Mean single sequence MFE -21.22
Consensus MFE -21.56
Energy contribution -21.12
Covariance contribution -0.44
Combinations/Pair 1.11
Mean z-score -2.27
Structure conservation index 1.02
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 2.66
SVM RNA-class probability 0.993985
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15564837 94 + 21146708
GGAAAGUUUUUUAACUGGCGCUGACUUUAAGUGCAAUUCAGUGCCGAGGACAAGAAAACCUCAAAAACUCAAAAAAAAGA--AGA-AAAAAAGGACG
.....(((((((....((((((((.............))))))))((((.........))))..................--...-...))))))). ( -21.02, z-score =  -1.93, R)
>droEre2.scaffold_4845 9764881 97 + 22589142
GGAAAGUUUUUUAACUGGCGCUGACUUUAAGUGCAAUUCAGUGCCGAGGACAAGAAAACCUCAAAACUCAAAAAAAAAAAAAAAACAAAAAGGAACG
.....(((((((....((((((((.............))))))))((((.........)))).................)))))))........... ( -21.32, z-score =  -2.58, R)
>droSec1.super_1 13079307 96 + 14215200
GGAAAGUUUUUUAGCUGGCGCUGACUUUAAGUGCAAUUCAGUGCCGAGGACAAGAAAACCUCAAAAACUAAAAAAAAAAAGAAGA-AAAAAAGAACG
......((((((((..((((((((.............))))))))((((.........)))).....))))))))..........-........... ( -21.52, z-score =  -2.41, R)
>droSim1.chr2R 14270095 93 + 19596830
-GAAAGUUUUUUAACUGGCGCUGACUUUAAGUGCAAUUCAGUGCCGAGGACAAGAAAACCUCAAAAACUCAAAAAAAAAG--AAG-AAAAAAGGACG
-....(((((((....((((((((.............))))))))((((.........))))..................--...-...))))))). ( -21.02, z-score =  -2.16, R)
>consensus
GGAAAGUUUUUUAACUGGCGCUGACUUUAAGUGCAAUUCAGUGCCGAGGACAAGAAAACCUCAAAAACUAAAAAAAAAAA__AAA_AAAAAAGAACG
.....(((((((....((((((((.............))))))))((((.........))))...........................))))))). (-21.56 = -21.12 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,564,837 – 15,564,931
Length 94
Sequences 4
Columns 97
Reading direction reverse
Mean pairwise identity 91.16
Shannon entropy 0.14034
G+C content 0.36065
Mean single sequence MFE -20.07
Consensus MFE -17.09
Energy contribution -17.40
Covariance contribution 0.31
Combinations/Pair 1.05
Mean z-score -2.10
Structure conservation index 0.85
Background model dinucleotide
Decision model sequence based alignment quality
SVM decision value 1.12
SVM RNA-class probability 0.894741
Prediction RNA

Download alignment: ClustalW | MAF

>dm3.chr2R 15564837 94 - 21146708
CGUCCUUUUUU-UCU--UCUUUUUUUUGAGUUUUUGAGGUUUUCUUGUCCUCGGCACUGAAUUGCACUUAAAGUCAGCGCCAGUUAAAAAACUUUCC
...........-...--..........((((((((((((.........))))(((.((((.((.......)).)))).))).....))))))))... ( -19.90, z-score =  -1.90, R)
>droEre2.scaffold_4845 9764881 97 - 22589142
CGUUCCUUUUUGUUUUUUUUUUUUUUUUGAGUUUUGAGGUUUUCUUGUCCUCGGCACUGAAUUGCACUUAAAGUCAGCGCCAGUUAAAAAACUUUCC
............................(((((((((((.........))))(((.((((.((.......)).)))).)))......)))))))... ( -19.00, z-score =  -1.51, R)
>droSec1.super_1 13079307 96 - 14215200
CGUUCUUUUUU-UCUUCUUUUUUUUUUUAGUUUUUGAGGUUUUCUUGUCCUCGGCACUGAAUUGCACUUAAAGUCAGCGCCAGCUAAAAAACUUUCC
...........-..........((((((((((...((((.........))))(((.((((.((.......)).)))).)))))))))))))...... ( -21.50, z-score =  -3.10, R)
>droSim1.chr2R 14270095 93 - 19596830
CGUCCUUUUUU-CUU--CUUUUUUUUUGAGUUUUUGAGGUUUUCUUGUCCUCGGCACUGAAUUGCACUUAAAGUCAGCGCCAGUUAAAAAACUUUC-
...........-...--..........((((((((((((.........))))(((.((((.((.......)).)))).))).....))))))))..- ( -19.90, z-score =  -1.91, R)
>consensus
CGUCCUUUUUU_UCU__UUUUUUUUUUGAGUUUUUGAGGUUUUCUUGUCCUCGGCACUGAAUUGCACUUAAAGUCAGCGCCAGUUAAAAAACUUUCC
............................(((((((((((.........))))(((.((((.((.......)).)))).))).....))))))).... (-17.09 = -17.40 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Tue Apr 19 22:35:38 2011