Locus 8023

Sequence ID 3L_DroMel_CAF1
Location 21,141,549 – 21,141,749
Length 200
Max. P 0.999711
window13106 window13107 window13108

overview

Window 6

Location 21,141,549 – 21,141,644
Length 95
Sequences 3
Columns 95
Reading direction reverse
Mean pairwise identity 87.19
Mean single sequence MFE -22.70
Consensus MFE -16.46
Energy contribution -16.80
Covariance contribution 0.34
Combinations/Pair 1.11
Mean z-score -3.04
Structure conservation index 0.73
SVM decision value 0.97
SVM RNA-class probability 0.891265
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21141549 95 - 23771897
AGAAAUAUGUUUUAAGUGCAACAUGGAGAUAUGUAACUAGCUUUAGUUCAGCACCAGUGCAAUCUAAUCUAACUGUUGCAAAUAUCAAUAUUUCU
((((((((....((..(((((((...((((.((.(((((....)))))))(((....)))......))))...)))))))..))...)))))))) ( -24.10)
>DroSec_CAF1 12733 90 - 1
A-AAAUAUGUUUUAAGUGCAACAAGGAGAUAUGUAACUAGCUUUAGUUCAGCACCAGUGCA----AAUCUAAUUGUUGCAAAUAUCAAUAUUUCU
.-((((((....((..((((((((..((((.((.(((((....)))))))(((....))).----.))))..))))))))..))...)))))).. ( -22.70)
>DroEre_CAF1 8955 91 - 1
AGGAAUAUGCGUUAAGUGCAACAAGGAGAUAUGUAACAAGCUUUAAAUAGGCACCAGUGCA----AGUCGAACUUUUGCAAAUAUCAAUAUUUCU
((((((((....((..(((((.(((..(((.((((....((((.....)))).....))))----.)))...))))))))..))...)))))))) ( -21.30)
>consensus
AGAAAUAUGUUUUAAGUGCAACAAGGAGAUAUGUAACUAGCUUUAGUUCAGCACCAGUGCA____AAUCUAACUGUUGCAAAUAUCAAUAUUUCU
((((((((....((..(((((((...((((.((((....(((.......))).....)))).....))))...)))))))..))...)))))))) (-16.46 = -16.80 +   0.34)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,141,644 – 21,141,749
Length 105
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 75.94
Mean single sequence MFE -32.53
Consensus MFE -18.99
Energy contribution -18.45
Covariance contribution -0.54
Combinations/Pair 1.20
Mean z-score -4.52
Structure conservation index 0.58
SVM decision value 3.93
SVM RNA-class probability 0.999711
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21141644 105 + 23771897
AGUCUCCUAAGAGUCUGUCGUUGCUCCUAUUAUUUAGUUUUUAACUACGCA----------AGCUUU----CUUAUUAACUAAAAACAUGAGCUUCGG-CAUUCUUUUAGGGAAUUAGCA
(((..((((((((..(((((..((((......(((((((..(((...(...----------.)....----.)))..))))))).....))))..)))-))..))))))))..))).... ( -31.40)
>DroSec_CAF1 12823 106 + 1
AGUUUCCUAAAAGUCUGUCGUUGCUCCUAUUAUUUAGUUUUUAACUACGCA----------AGCUUU----CUUAUUAACUAAAAAUAUGAGCUUCGGACAUUCUUUUAGGGAAUUAGUA
(((((((((((((..(((((..((((.((((.(((((((..(((...(...----------.)....----.)))..))))))))))).))))..).))))..))))))))))))).... ( -33.80)
>DroEre_CAF1 9046 114 + 1
AGU-UCCCAAAAGAUCGUCGUUGCUC---UUUUUUAGUU-AUAACUACGCAGGAUUAGGUGAGCUUUCAAUCUGAAAGGCUAAAAAUCUGAGUUUCGA-CACUCUUUUGUUGAAUUAGUA
(((-((.(((((((..((((..((((---.((((((((.-.......(((........)))..(((((.....)))))))))))))...))))..)))-)..)))))))..))))).... ( -32.40)
>consensus
AGU_UCCUAAAAGUCUGUCGUUGCUCCUAUUAUUUAGUUUUUAACUACGCA__________AGCUUU____CUUAUUAACUAAAAAUAUGAGCUUCGG_CAUUCUUUUAGGGAAUUAGUA
(((.(((((((((..(((((..((((......(((((((.........((............)).............))))))).....))))..))).))..))))))))).))).... (-18.99 = -18.45 +  -0.54)

alignment

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secondary structure

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dotplot

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Window 8

Location 21,141,644 – 21,141,749
Length 105
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.94
Mean single sequence MFE -24.43
Consensus MFE -12.34
Energy contribution -13.23
Covariance contribution 0.89
Combinations/Pair 1.05
Mean z-score -2.47
Structure conservation index 0.51
SVM decision value 0.44
SVM RNA-class probability 0.738090
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21141644 105 - 23771897
UGCUAAUUCCCUAAAAGAAUG-CCGAAGCUCAUGUUUUUAGUUAAUAAG----AAAGCU----------UGCGUAGUUAAAAACUAAAUAAUAGGAGCAACGACAGACUCUUAGGAGACU
.......(((((((.((..((-.((..((((.(((((((((((..(((.----...(..----------..)....)))..))))))).)))).))))..)).))..)).))))).)).. ( -22.60)
>DroSec_CAF1 12823 106 - 1
UACUAAUUCCCUAAAAGAAUGUCCGAAGCUCAUAUUUUUAGUUAAUAAG----AAAGCU----------UGCGUAGUUAAAAACUAAAUAAUAGGAGCAACGACAGACUUUUAGGAAACU
.........((((((((..((((.(..((((.(((((((((((..(((.----...(..----------..)....)))..))))))).)))).))))..)))))..))))))))..... ( -26.60)
>DroEre_CAF1 9046 114 - 1
UACUAAUUCAACAAAAGAGUG-UCGAAACUCAGAUUUUUAGCCUUUCAGAUUGAAAGCUCACCUAAUCCUGCGUAGUUAU-AACUAAAAAA---GAGCAACGACGAUCUUUUGGGA-ACU
......(((..(((((((.((-(((...(((.((((...(((.((((.....))))))).....)))).....((((...-.)))).....---)))...))))).))))))).))-).. ( -24.10)
>consensus
UACUAAUUCCCUAAAAGAAUG_CCGAAGCUCAUAUUUUUAGUUAAUAAG____AAAGCU__________UGCGUAGUUAAAAACUAAAUAAUAGGAGCAACGACAGACUUUUAGGA_ACU
.........((((((((......((..((((.........................((............)).((((.....))))........))))..)).....))))))))..... (-12.34 = -13.23 +   0.89)

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 13:04:09 2006