Locus 4992

Sequence ID 3L_DroMel_CAF1
Location 13,750,784 – 13,750,935
Length 151
Max. P 0.999720
window7885 window7886 window7887

overview

Window 5

Location 13,750,784 – 13,750,895
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.00
Mean single sequence MFE -34.64
Consensus MFE -30.39
Energy contribution -30.87
Covariance contribution 0.48
Combinations/Pair 1.04
Mean z-score -2.19
Structure conservation index 0.88
SVM decision value 2.74
SVM RNA-class probability 0.996742
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13750784 111 - 23771897
AUCCCAACCCAGCAGCCCUUCA-------UCUCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA--GCUCCAGACCCGGCGGACGCAUAAUUCCGGUUGCUCACCCGCGUUUAAAUGUAC
...........((((((((...-------..((((((....)))))).....))))))))....--.....((((.(((..((.(((..........)))))..))).))))........ ( -37.50)
>DroSec_CAF1 157526 111 - 1
AUCCCAACCCACCAGCCCUUCA-------UCUCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA--GCUCCAGACCCGGCGGACGCAUAAUUCCGGUUGCUCACCCGCGUUUAAAUGUAC
............(((((((...-------..((((((....)))))).....))))))).....--.....((((.(((..((.(((..........)))))..))).))))........ ( -32.90)
>DroSim_CAF1 169768 111 - 1
AUCCCAACCCAGCAGCCCUUCA-------UCUCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA--GCUCCAGACCCGGCGGACGCAUAAUUCCGGUUGCUCACCCGCGUUUAAAUGUAC
...........((((((((...-------..((((((....)))))).....))))))))....--.....((((.(((..((.(((..........)))))..))).))))........ ( -37.50)
>DroEre_CAF1 164382 117 - 1
AUCCCAACCCUGCAGCCCCACAUCGCAGG-ACCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA--GCUUCAGACCCGGCGGACGCAUAAUUCCGGUUGCUCACCCGCGUUUAAAUGUAC
..........((((((((......((((.-...)))).......((....)).))))))))...--.....((((.(((..((.(((..........)))))..))).))))........ ( -34.50)
>DroYak_CAF1 168711 120 - 1
AUCCCAACCCAGCAGCUCCUCCUCCUUCAUCUCCUGCCGUCGCAGGACUCCCAGAGCUGCACCAGAGCUCCAGACCCGGCGGACGCAUAAUUCCGGUUGCUCACCCGCGUUUAAAUGUAC
...........(((((((.............((((((....))))))......)))))))....((((.((.((....((....)).....)).))..))))....((((....)))).. ( -30.81)
>consensus
AUCCCAACCCAGCAGCCCUUCA_______UCUCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA__GCUCCAGACCCGGCGGACGCAUAAUUCCGGUUGCUCACCCGCGUUUAAAUGUAC
...........((((((((............((((((....)))))).....))))))))...........((((.(((..((.(((..........)))))..))).))))........ (-30.39 = -30.87 +   0.48)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,750,824 – 13,750,935
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.00
Mean single sequence MFE -45.67
Consensus MFE -37.89
Energy contribution -37.57
Covariance contribution -0.32
Combinations/Pair 1.09
Mean z-score -2.24
Structure conservation index 0.83
SVM decision value 2.13
SVM RNA-class probability 0.988697
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13750824 111 + 23771897
GCCGGGUCUGGAGC--UGGUGCAGCCCUGGGAGUCCUGCGAUGGCAGGAGA-------UGAAGGGCUGCUGGGUUGGGAUUUUCGAACAGUUUGCUAAAUUGGCAUGGCCAGACUGAAGG
.((.(((((((.((--..((((((((((.....((((((....))))))..-------...))))))))...(((.((....)).)))..........))..))....)))))))...)) ( -46.80)
>DroSec_CAF1 157566 111 + 1
GCCGGGUCUGGAGC--UGGUGCAGCCCUGGGAGUCCUGCGAUGGCAGGAGA-------UGAAGGGCUGGUGGGUUGGGAUUUUCGAACAGUUUGCUAAAUUGGCAUGGCCAGACUGAAGG
.((.(((((((.((--..((.(((((((.....((((((....))))))..-------...)))))))(..(..((...........))..)..)...))..))....)))))))...)) ( -44.80)
>DroSim_CAF1 169808 111 + 1
GCCGGGUCUGGAGC--UGGUGCAGCCCUGGGAGUCCUGCGAUGGCAGGAGA-------UGAAGGGCUGCUGGGUUGGGAUUUUCGAACAGUUUGCUAAAUUGGCAUGGCCAGACUGAAGG
.((.(((((((.((--..((((((((((.....((((((....))))))..-------...))))))))...(((.((....)).)))..........))..))....)))))))...)) ( -46.80)
>DroEre_CAF1 164422 117 + 1
GCCGGGUCUGAAGC--UGGUGCAGCCCUGGGAGUCCUGCGAUGGCAGGGU-CCUGCGAUGUGGGGCUGCAGGGUUGGGAUUUUCGAACAGUUUGCUAAAUUGGCAUGGCCAGACUGAAGG
.((.((((((((((--((.(.((((((((.(.((((..(.((.((((...-.)))).)))..))))).)))))))).).........))))))(((.....))).....))))))...)) ( -49.10)
>DroYak_CAF1 168751 120 + 1
GCCGGGUCUGGAGCUCUGGUGCAGCUCUGGGAGUCCUGCGACGGCAGGAGAUGAAGGAGGAGGAGCUGCUGGGUUGGGAUUUUCGAACAGUUUGCUAAAUUGGCAUGGCCAGACUGAAGG
.((.((((((((((((....((((((((.....((((((....))))))............)))))))).))))).................((((.....))))...)))))))...)) ( -40.83)
>consensus
GCCGGGUCUGGAGC__UGGUGCAGCCCUGGGAGUCCUGCGAUGGCAGGAGA_______UGAAGGGCUGCUGGGUUGGGAUUUUCGAACAGUUUGCUAAAUUGGCAUGGCCAGACUGAAGG
.((.(((((((.........((((((((.....((((((....))))))............))))))))...(((.((....)).)))....((((.....))))...)))))))...)) (-37.89 = -37.57 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,750,824 – 13,750,935
Length 111
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.00
Mean single sequence MFE -33.44
Consensus MFE -29.13
Energy contribution -29.45
Covariance contribution 0.32
Combinations/Pair 1.09
Mean z-score -2.93
Structure conservation index 0.87
SVM decision value 3.94
SVM RNA-class probability 0.999720
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13750824 111 - 23771897
CCUUCAGUCUGGCCAUGCCAAUUUAGCAAACUGUUCGAAAAUCCCAACCCAGCAGCCCUUCA-------UCUCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA--GCUCCAGACCCGGC
......((((((...(((.......))).......................((((((((...-------..((((((....)))))).....))))))))....--...))))))..... ( -36.50)
>DroSec_CAF1 157566 111 - 1
CCUUCAGUCUGGCCAUGCCAAUUUAGCAAACUGUUCGAAAAUCCCAACCCACCAGCCCUUCA-------UCUCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA--GCUCCAGACCCGGC
......((((((...(((.......)))........................(((((((...-------..((((((....)))))).....))))))).....--...))))))..... ( -31.90)
>DroSim_CAF1 169808 111 - 1
CCUUCAGUCUGGCCAUGCCAAUUUAGCAAACUGUUCGAAAAUCCCAACCCAGCAGCCCUUCA-------UCUCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA--GCUCCAGACCCGGC
......((((((...(((.......))).......................((((((((...-------..((((((....)))))).....))))))))....--...))))))..... ( -36.50)
>DroEre_CAF1 164422 117 - 1
CCUUCAGUCUGGCCAUGCCAAUUUAGCAAACUGUUCGAAAAUCCCAACCCUGCAGCCCCACAUCGCAGG-ACCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA--GCUUCAGACCCGGC
......((((((...(((.......)))......................((((((((......((((.-...)))).......((....)).))))))))...--...))))))..... ( -31.40)
>DroYak_CAF1 168751 120 - 1
CCUUCAGUCUGGCCAUGCCAAUUUAGCAAACUGUUCGAAAAUCCCAACCCAGCAGCUCCUCCUCCUUCAUCUCCUGCCGUCGCAGGACUCCCAGAGCUGCACCAGAGCUCCAGACCCGGC
......((((((...(((.......)))....(((((.....)........(((((((.............((((((....))))))......)))))))....)))).))))))..... ( -30.91)
>consensus
CCUUCAGUCUGGCCAUGCCAAUUUAGCAAACUGUUCGAAAAUCCCAACCCAGCAGCCCUUCA_______UCUCCUGCCAUCGCAGGACUCCCAGGGCUGCACCA__GCUCCAGACCCGGC
......((((((...(((.......))).......................((((((((............((((((....)))))).....)))))))).........))))))..... (-29.13 = -29.45 +   0.32)

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 11:38:55 2006