Locus 5599

Sequence ID 2R_DroMel_CAF1
Location 17,868,577 – 17,868,680
Length 103
Max. P 0.993373
window8966 window8967

overview

Window 6

Location 17,868,577 – 17,868,680
Length 103
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 81.22
Mean single sequence MFE -32.67
Consensus MFE -23.44
Energy contribution -25.24
Covariance contribution 1.80
Combinations/Pair 1.00
Mean z-score -2.77
Structure conservation index 0.72
SVM decision value 2.27
SVM RNA-class probability 0.991566
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17868577 103 + 20766785
UGCUCCCCCAACAUC---U-------------C-CUGCUGCAGGACCCAGCAUCCAGGAUCCUGUUUUGUGCAGCGUUUUAAUUGGCUUUUCUGCCAUAUUAGAUUUCAGAGCCUCACUU
.((((..........---.-------------.-..((((((.((..(((.(((...))).)))..)).))))))..((((((((((......)))).)))))).....))))....... ( -29.90)
>DroSec_CAF1 33442 106 + 1
UGCUCCUCCAGCUCCUCCU-------------C-CAGCUGCAGGACCCAGGAUCCAGGAUCCUGUUUUGUGCAGCGUUUUAAUUGGGUUUUCUGCCAUAUUAGAUUUCAGAGCCUCACUU
..........((((.....-------------.-..((((((.((..(((((((...)))))))..)).))))))..((((((..(((.....)))..)))))).....))))....... ( -33.60)
>DroSim_CAF1 33797 103 + 1
UGCUCCUCCAGCUCC---U-------------C-CAGCUGCAGGACCCAGGAUCCAGGAUCCUGUUUUGUGCAGCGUUUUAAUUGGGUUUUCUGCCAUAUUAGAUUUCAGAGCCUCACUU
..........((((.---.-------------.-..((((((.((..(((((((...)))))))..)).))))))..((((((..(((.....)))..)))))).....))))....... ( -33.60)
>DroEre_CAF1 35882 120 + 1
UGCUCCACUACCCACUACCCAGUACCCAUUACCCACGAGCCAGGAUCCAGGAUCCAGGAUCCUGUCUUGUGCAGCGUUUUAAUUGGGUUUUCUGCCAUAUUACAUUUCAGAGCCUCAGUU
.((((..............(((.(((((..(((((((((.((((((((.(....).)))))))).))))))..).))......)))))...)))...............))))....... ( -33.85)
>DroYak_CAF1 32286 113 + 1
UGCUCCAGGACCCAAGACCCAGGAU-------CUAGGAUCCAGGAUCCAGCAACCAGGAUCCUGUUUUGUGCAGCGUUUUAAUUGGGUUUUCUGCCAUAUUAGAUUUCAGAGCCUCAGUU
.((((..((....((((((((((((-------(...)))))(((((((........)))))))....................))))))))...))......(....).))))....... ( -32.40)
>consensus
UGCUCCACCACCCAC__CU_____________C_CAGCUGCAGGACCCAGGAUCCAGGAUCCUGUUUUGUGCAGCGUUUUAAUUGGGUUUUCUGCCAUAUUAGAUUUCAGAGCCUCACUU
.((((...............................((((((.((..(((((((...)))))))..)).))))))..(((((((((........))).)))))).....))))....... (-23.44 = -25.24 +   1.80)

alignment

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secondary structure

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dotplot

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Window 7

Location 17,868,577 – 17,868,680
Length 103
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.22
Mean single sequence MFE -36.02
Consensus MFE -27.92
Energy contribution -27.08
Covariance contribution -0.84
Combinations/Pair 1.25
Mean z-score -2.74
Structure conservation index 0.78
SVM decision value 2.39
SVM RNA-class probability 0.993373
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17868577 103 - 20766785
AAGUGAGGCUCUGAAAUCUAAUAUGGCAGAAAAGCCAAUUAAAACGCUGCACAAAACAGGAUCCUGGAUGCUGGGUCCUGCAGCAG-G-------------A---GAUGUUGGGGGAGCA
.......(((((....(((((((((((......))).........((((((.......((((((........))))))))))))..-.-------------.---.))))))))))))). ( -34.91)
>DroSec_CAF1 33442 106 - 1
AAGUGAGGCUCUGAAAUCUAAUAUGGCAGAAAACCCAAUUAAAACGCUGCACAAAACAGGAUCCUGGAUCCUGGGUCCUGCAGCUG-G-------------AGGAGGAGCUGGAGGAGCA
..((..((((((....((((...(((........)))........((((((..(..(((((((...)))))))..)..))))))))-)-------------)...))))))......)). ( -34.90)
>DroSim_CAF1 33797 103 - 1
AAGUGAGGCUCUGAAAUCUAAUAUGGCAGAAAACCCAAUUAAAACGCUGCACAAAACAGGAUCCUGGAUCCUGGGUCCUGCAGCUG-G-------------A---GGAGCUGGAGGAGCA
..(((.(((((((..((.....))..))))...............))).)))....(((((((...)))))))(.((((.(((((.-.-------------.---..))))).)))).). ( -32.96)
>DroEre_CAF1 35882 120 - 1
AACUGAGGCUCUGAAAUGUAAUAUGGCAGAAAACCCAAUUAAAACGCUGCACAAGACAGGAUCCUGGAUCCUGGAUCCUGGCUCGUGGGUAAUGGGUACUGGGUAGUGGGUAGUGGAGCA
.......(((((...........(((........)))((((...((((((...((.((((((((.(....).))))))))((((((.....)))))).))..))))))..))))))))). ( -40.10)
>DroYak_CAF1 32286 113 - 1
AACUGAGGCUCUGAAAUCUAAUAUGGCAGAAAACCCAAUUAAAACGCUGCACAAAACAGGAUCCUGGUUGCUGGAUCCUGGAUCCUAG-------AUCCUGGGUCUUGGGUCCUGGAGCA
.......((((............((((((.................)))).))...((((((((........((((((.(((((...)-------)))).)))))).)))))))))))). ( -37.23)
>consensus
AAGUGAGGCUCUGAAAUCUAAUAUGGCAGAAAACCCAAUUAAAACGCUGCACAAAACAGGAUCCUGGAUCCUGGGUCCUGCAGCUG_G_____________AG__GGAGCUGGAGGAGCA
.......(((((...........((((((.................)))).))...((((((((........))))))))(((((......................)))))..))))). (-27.92 = -27.08 +  -0.84)

alignment

Postscript

secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:33 2006