Locus 5522

Sequence ID 2L_DroMel_CAF1
Location 15,789,069 – 15,789,204
Length 135
Max. P 0.932666
window8763 window8764

overview

Window 3

Location 15,789,069 – 15,789,164
Length 95
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.48
Mean single sequence MFE -29.55
Consensus MFE -18.58
Energy contribution -18.98
Covariance contribution 0.40
Combinations/Pair 1.22
Mean z-score -2.41
Structure conservation index 0.63
SVM decision value 1.07
SVM RNA-class probability 0.910343
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15789069 95 - 22407834
GCGCUGUCCAUUAGCGCAGGGCAUAAAUAAACAACC----------------AUUGUCCGGCAGCUGAAGCCAUUAACUGGCAUUGUUUAGUCGGGGAAAU---------AAUAAUAAUA
((((((.....)))))).(((((.............----------------..)))))(((.......))).((..(((((........)))))..))..---------.......... ( -25.06)
>DroSec_CAF1 12884 94 - 1
GCGCUGUCCAUUAGCGCCGGGCAUAAAUAAACAACC----------------AUUGUCCGGCAGCUGA-GCCAUUAACUGGCAUUGUUUAGUCGGGGAAAU---------AAUAAUAAUA
.(((((..(((((((((((((((.............----------------..)))))))).)))))-((((.....))))..))..))).)).......---------.......... ( -29.66)
>DroAna_CAF1 12070 120 - 1
GCGCUGUCCAUUAGCGGAUGGCGUAAAUAAACAACCAGAACCACUGGACCACAUUGUCCGACGGCUAAGGCCAUUAGCCAGUCCUAUUUAGUCGGGGCAGUAACAAUAGUAAUAAUCAUA
(((((((((......)))))))))..........((((.....))))...(((((((...((((((((.....)))))).(((((........))))).)).))))).)).......... ( -36.40)
>DroSim_CAF1 4054 95 - 1
GCGCUGUCCAUUAGCGCCGGGCAUAAAUAAACAACC----------------AUUGUCCGGCAGCUGAAGCCAUUAACUGGCAUUGUUUAGUCGGGGAAAU---------AAUAAUAAUA
.(((((..(((((((((((((((.............----------------..)))))))).))))).((((.....))))..))..))).)).......---------.......... ( -29.66)
>DroEre_CAF1 10871 95 - 1
GCGCUGUCCAUUAGCGCAGGGCAUAAAUAAACAACC----------------AUUGUCCGGCAGCUGAAGCCAUUAACUGGCUUUGUUUAGUCGGUGAAAU---------AAUAAUAAUA
((((((.....)))))).(((((.............----------------..)))))(((.......)))....(((((((......))))))).....---------.......... ( -26.96)
>consensus
GCGCUGUCCAUUAGCGCAGGGCAUAAAUAAACAACC________________AUUGUCCGGCAGCUGAAGCCAUUAACUGGCAUUGUUUAGUCGGGGAAAU_________AAUAAUAAUA
((((((.....))))))....................................((.((((((((.(((.((((.....)))).))).)).)))))).))..................... (-18.58 = -18.98 +   0.40)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,789,100 – 15,789,204
Length 104
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.95
Mean single sequence MFE -27.67
Consensus MFE -20.22
Energy contribution -20.42
Covariance contribution 0.20
Combinations/Pair 1.15
Mean z-score -2.54
Structure conservation index 0.73
SVM decision value 1.22
SVM RNA-class probability 0.932666
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15789100 104 - 22407834
AUAAAUAAUAUCCACCGAAGCAAACUCUUUCAGCGAUUCCGCGCUGUCCAUUAGCGCAGGGCAUAAAUAAACAACC----------------AUUGUCCGGCAGCUGAAGCCAUUAACUG
...........................(((((((....((((((((.....)))))).(((((.............----------------..)))))))..))))))).......... ( -25.66)
>DroSec_CAF1 12915 103 - 1
AUAAAUAAUAUCCACCGAAGCAAACUCUUUCAGCGAUUCCGCGCUGUCCAUUAGCGCCGGGCAUAAAUAAACAACC----------------AUUGUCCGGCAGCUGA-GCCAUUAACUG
...................((.........(((((......)))))....(((((((((((((.............----------------..)))))))).)))))-))......... ( -27.96)
>DroAna_CAF1 12110 120 - 1
AUAAAUAAUAUCAACCGAAGGAAACUCUUUUAGCAAUUCCGCGCUGUCCAUUAGCGGAUGGCGUAAAUAAACAACCAGAACCACUGGACCACAUUGUCCGACGGCUAAGGCCAUUAGCCA
...............((.((....))......(((((...(((((((((......)))))))))..........((((.....)))).....))))).))..((((((.....)))))). ( -31.10)
>DroSim_CAF1 4085 104 - 1
AUAAAUAAUAUCCACCGAAGCAAACUCUUUCAGCGAUUCCGCGCUGUCCAUUAGCGCCGGGCAUAAAUAAACAACC----------------AUUGUCCGGCAGCUGAAGCCAUUAACUG
...................((.........(((((......)))))....(((((((((((((.............----------------..)))))))).))))).))......... ( -27.96)
>DroEre_CAF1 10902 104 - 1
AUAAAUAAUAUCCACCAAAGCAAACUCUUUCAGCGAUUCCGCGCUGUCCAUUAGCGCAGGGCAUAAAUAAACAACC----------------AUUGUCCGGCAGCUGAAGCCAUUAACUG
...........................(((((((....((((((((.....)))))).(((((.............----------------..)))))))..))))))).......... ( -25.66)
>consensus
AUAAAUAAUAUCCACCGAAGCAAACUCUUUCAGCGAUUCCGCGCUGUCCAUUAGCGCAGGGCAUAAAUAAACAACC________________AUUGUCCGGCAGCUGAAGCCAUUAACUG
...........................(((((((....((((((((.....)))))).(((((...............................)))))))..))))))).......... (-20.22 = -20.42 +   0.20)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:46:15 2006