Locus 665

Sequence ID 3R_DroMel_CAF1
Location 2,435,093 – 2,435,213
Length 120
Max. P 0.944924
window1053 window1054

overview

Window 3

Location 2,435,093 – 2,435,213
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.33
Mean single sequence MFE -31.50
Consensus MFE -31.22
Energy contribution -31.06
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.60
Structure conservation index 0.99
SVM decision value 1.35
SVM RNA-class probability 0.944924
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2435093 120 + 27905053
AGUCCUGCUGGCUAACCGGAAAUGCAUCAGUGUCAGUUUCGCUGGCUGCGCAAUUUCGUUAAGAAGUGCGCAAAGUUGUUAAAUUUUACGAUUUAAUUGCGAAACUAUUAAAAAUUACGU
.((....((((....))))....)).........((((((((....((((((.((((.....))))))))))(((((((........)))))))....)))))))).............. ( -31.60)
>DroSec_CAF1 1040 120 + 1
AGUCCUGCUGGCUAACCGGAAAUGCAUCAGUGUCAGUUUCGCUGGCUGCGCAAUUUUGUUAAGAAGUGCGCAAAGUUGUUAAAUUUUACGAUUUAAUUGCGAAACUAUUAAAAAUUACGU
.((....((((....))))....)).........((((((((....((((((.((((....)))).))))))(((((((........)))))))....)))))))).............. ( -30.40)
>DroSim_CAF1 1083 120 + 1
AGUCCUGCUGGCUAACCGGAAAUGCAUCAGUGUCAGUUUCGCUGGCUGCGCAAUUUCGUUAAGAAGUGCGCAAAGUUGUUAAAUUUUACGAUUUAAUUGCGAAACUAUUAAAAAUUACGU
.((....((((....))))....)).........((((((((....((((((.((((.....))))))))))(((((((........)))))))....)))))))).............. ( -31.60)
>DroEre_CAF1 1104 120 + 1
GGUCCUGCUGGCUAACCGGAAAUGCAUCAGUGUCAGUUUCGCUGGCUGCGCAAUUUCGUUAAGAAGUGCGCAAAGUUGUUAAAUUUUACGAUUUAAUUGCGAAACUAUUAAAAAUUACGU
((..(((((((....))))........)))..))((((((((....((((((.((((.....))))))))))(((((((........)))))))....)))))))).............. ( -32.30)
>DroYak_CAF1 1106 120 + 1
AGUCCUGCUGGCUAACCGGAAAUGCAUCAGUGUCAGUUUCGCUGGCUGCGCAAUUUCGUUAAGAAGUGCGCAAAGUUGUUAAAUUUUACGAUUUAAUUGCGAAACUAUUAAAAAUUACGU
.((....((((....))))....)).........((((((((....((((((.((((.....))))))))))(((((((........)))))))....)))))))).............. ( -31.60)
>consensus
AGUCCUGCUGGCUAACCGGAAAUGCAUCAGUGUCAGUUUCGCUGGCUGCGCAAUUUCGUUAAGAAGUGCGCAAAGUUGUUAAAUUUUACGAUUUAAUUGCGAAACUAUUAAAAAUUACGU
.((....((((....))))....)).........((((((((....((((((.((((.....))))))))))(((((((........)))))))....)))))))).............. (-31.22 = -31.06 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,435,093 – 2,435,213
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.33
Mean single sequence MFE -26.28
Consensus MFE -25.64
Energy contribution -25.84
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.98
SVM decision value 0.58
SVM RNA-class probability 0.789348
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2435093 120 - 27905053
ACGUAAUUUUUAAUAGUUUCGCAAUUAAAUCGUAAAAUUUAACAACUUUGCGCACUUCUUAACGAAAUUGCGCAGCCAGCGAAACUGACACUGAUGCAUUUCCGGUUAGCCAGCAGGACU
..(((.((.....(((((((((..((((((......)))))).....(((((((.(((.....)))..)))))))...))))))))).....)))))...(((.(((....))).))).. ( -26.60)
>DroSec_CAF1 1040 120 - 1
ACGUAAUUUUUAAUAGUUUCGCAAUUAAAUCGUAAAAUUUAACAACUUUGCGCACUUCUUAACAAAAUUGCGCAGCCAGCGAAACUGACACUGAUGCAUUUCCGGUUAGCCAGCAGGACU
..(((.((.....(((((((((..((((((......)))))).....(((((((.((........)).)))))))...))))))))).....)))))...(((.(((....))).))).. ( -25.00)
>DroSim_CAF1 1083 120 - 1
ACGUAAUUUUUAAUAGUUUCGCAAUUAAAUCGUAAAAUUUAACAACUUUGCGCACUUCUUAACGAAAUUGCGCAGCCAGCGAAACUGACACUGAUGCAUUUCCGGUUAGCCAGCAGGACU
..(((.((.....(((((((((..((((((......)))))).....(((((((.(((.....)))..)))))))...))))))))).....)))))...(((.(((....))).))).. ( -26.60)
>DroEre_CAF1 1104 120 - 1
ACGUAAUUUUUAAUAGUUUCGCAAUUAAAUCGUAAAAUUUAACAACUUUGCGCACUUCUUAACGAAAUUGCGCAGCCAGCGAAACUGACACUGAUGCAUUUCCGGUUAGCCAGCAGGACC
..(((.((.....(((((((((..((((((......)))))).....(((((((.(((.....)))..)))))))...))))))))).....)))))...(((.(((....))).))).. ( -26.60)
>DroYak_CAF1 1106 120 - 1
ACGUAAUUUUUAAUAGUUUCGCAAUUAAAUCGUAAAAUUUAACAACUUUGCGCACUUCUUAACGAAAUUGCGCAGCCAGCGAAACUGACACUGAUGCAUUUCCGGUUAGCCAGCAGGACU
..(((.((.....(((((((((..((((((......)))))).....(((((((.(((.....)))..)))))))...))))))))).....)))))...(((.(((....))).))).. ( -26.60)
>consensus
ACGUAAUUUUUAAUAGUUUCGCAAUUAAAUCGUAAAAUUUAACAACUUUGCGCACUUCUUAACGAAAUUGCGCAGCCAGCGAAACUGACACUGAUGCAUUUCCGGUUAGCCAGCAGGACU
..(((.((.....(((((((((..((((((......)))))).....(((((((.(((.....)))..)))))))...))))))))).....)))))...(((.(((....))).))).. (-25.64 = -25.84 +   0.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:46 2006