Locus 4881

Sequence ID 2R_DroMel_CAF1
Location 15,957,867 – 15,957,990
Length 123
Max. P 0.999584
window7829 window7830 window7831

overview

Window 9

Location 15,957,867 – 15,957,964
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 93.81
Mean single sequence MFE -34.39
Consensus MFE -30.36
Energy contribution -31.64
Covariance contribution 1.28
Combinations/Pair 1.07
Mean z-score -2.63
Structure conservation index 0.88
SVM decision value 3.75
SVM RNA-class probability 0.999584
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15957867 97 + 20766785
AUUGCUGGCAUAAUUAGCCGAGUUGGAGCUGGAGGCGCCUGGCCAAAAGUCAGAGGCAUACAGCAACGAAAAGCCUCUAGACUGUGGUCGACUGAAU
.....((((.......))))((((((.((.....)).)).(((((..((((((((((...............)))))).)))).))))))))).... ( -31.16)
>DroSec_CAF1 13720 91 + 1
AUUGCUGGCAUAAUUAGCCGAGUUGGAGCUGGAGGCG-----CCAAAAGUCAGAGGCAUACAGCAACGAAAAGCCUCCAGACU-CGGUCGGCUGAAU
.............((((((((..(.((((((((((((-----((..........)))...(......)....)))))))).))-).))))))))).. ( -35.20)
>DroSim_CAF1 13717 97 + 1
AUUGCUGGCAUAAUUAGCCGAGUUGGAGCUGGAGGCGCCUGGCCAAAAGUCAGAGGCAUACAGCAACGAAAAGCCUCCAGACUGUGGUCGGCUGAAU
.............((((((((.(((.((((((((((..(((((.....)))))..((.....))........)))))))).)).))))))))))).. ( -38.40)
>DroEre_CAF1 20393 97 + 1
AUUGCUGGCAUAAUUAGCCGAGUUGGAGCAGGAGGCGCCUGGCCAAAAGUCAGAGGAAUACGGCAACAAAAAGCCUCCAGACUGUGGUCGGCUGAAU
.............((((((((.(((.(((.((((((..(((((.....)))))........(....).....)))))).).)).))))))))))).. ( -33.40)
>DroYak_CAF1 21028 97 + 1
AUUGCUGGCAUAAUUAGCCGAGUUGGAGCUGGAGGCGCCUGGCCAAAAGUCAGAGGCAUACGGCAACAAAAAGCCUACAGACUGUGGUCGGCUGAAU
.............((((((((.(((.(((((.(((((((((((.....)))..))))....(....).....)))).))).)).))))))))))).. ( -33.80)
>consensus
AUUGCUGGCAUAAUUAGCCGAGUUGGAGCUGGAGGCGCCUGGCCAAAAGUCAGAGGCAUACAGCAACGAAAAGCCUCCAGACUGUGGUCGGCUGAAU
.............((((((((.(((.((((((((((..(((((.....)))))..((.....))........)))))))).)).))))))))))).. (-30.36 = -31.64 +   1.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,957,867 – 15,957,964
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 93.81
Mean single sequence MFE -28.19
Consensus MFE -24.62
Energy contribution -24.46
Covariance contribution -0.16
Combinations/Pair 1.20
Mean z-score -1.69
Structure conservation index 0.87
SVM decision value 1.53
SVM RNA-class probability 0.961565
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15957867 97 - 20766785
AUUCAGUCGACCACAGUCUAGAGGCUUUUCGUUGCUGUAUGCCUCUGACUUUUGGCCAGGCGCCUCCAGCUCCAACUCGGCUAAUUAUGCCAGCAAU
....(((((((((.((((.((((((...............))))))))))..)))...((.((.....)).))...))))))............... ( -26.86)
>DroSec_CAF1 13720 91 - 1
AUUCAGCCGACCG-AGUCUGGAGGCUUUUCGUUGCUGUAUGCCUCUGACUUUUGG-----CGCCUCCAGCUCCAACUCGGCUAAUUAUGCCAGCAAU
....((((((..(-((.((((((((.....((......))(((..........))-----))))))))))))....))))))............... ( -31.30)
>DroSim_CAF1 13717 97 - 1
AUUCAGCCGACCACAGUCUGGAGGCUUUUCGUUGCUGUAUGCCUCUGACUUUUGGCCAGGCGCCUCCAGCUCCAACUCGGCUAAUUAUGCCAGCAAU
....((((((....((.((((((((........(((....(((..........)))..))))))))))))).....))))))............... ( -30.60)
>DroEre_CAF1 20393 97 - 1
AUUCAGCCGACCACAGUCUGGAGGCUUUUUGUUGCCGUAUUCCUCUGACUUUUGGCCAGGCGCCUCCUGCUCCAACUCGGCUAAUUAUGCCAGCAAU
....((((((....(((..((((((..((((..((((...((....))....)))))))).)))))).))).....))))))............... ( -26.50)
>DroYak_CAF1 21028 97 - 1
AUUCAGCCGACCACAGUCUGUAGGCUUUUUGUUGCCGUAUGCCUCUGACUUUUGGCCAGGCGCCUCCAGCUCCAACUCGGCUAAUUAUGCCAGCAAU
....((((((....((.(((.((((........(((....(((..........)))..))))))).))))).....))))))............... ( -25.70)
>consensus
AUUCAGCCGACCACAGUCUGGAGGCUUUUCGUUGCUGUAUGCCUCUGACUUUUGGCCAGGCGCCUCCAGCUCCAACUCGGCUAAUUAUGCCAGCAAU
....(((((((((.((((.((((((....((....))...))))))))))..)))...((.((.....)).))...))))))............... (-24.62 = -24.46 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,957,895 – 15,957,990
Length 95
Sequences 5
Columns 95
Reading direction forward
Mean pairwise identity 92.84
Mean single sequence MFE -31.98
Consensus MFE -26.12
Energy contribution -27.60
Covariance contribution 1.48
Combinations/Pair 1.08
Mean z-score -1.55
Structure conservation index 0.82
SVM decision value 0.51
SVM RNA-class probability 0.763058
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15957895 95 + 20766785
CUGGAGGCGCCUGGCCAAAAGUCAGAGGCAUACAGCAACGAAAAGCCUCUAGACUGUGGUCGACUGAAUGGAUUUUCGACCAGAGGUUGCUGUCC
((((((((..(((((.....)))))..((.....))........)))))))).((.(((((((............))))))).)).......... ( -33.40)
>DroSec_CAF1 13748 89 + 1
CUGGAGGCG-----CCAAAAGUCAGAGGCAUACAGCAACGAAAAGCCUCCAGACU-CGGUCGGCUGAAUGGAAUUUCGACCAGAGGUUGCUGUCC
(((((((((-----((..........)))...(......)....)))))))).((-(((((((............)))))).))).......... ( -28.70)
>DroSim_CAF1 13745 95 + 1
CUGGAGGCGCCUGGCCAAAAGUCAGAGGCAUACAGCAACGAAAAGCCUCCAGACUGUGGUCGGCUGAAUGGAAUUUCGACCAGAGGUUGCUGUCC
((((((((..(((((.....)))))..((.....))........)))))))).((.(((((((............))))))).)).......... ( -34.80)
>DroEre_CAF1 20421 95 + 1
CAGGAGGCGCCUGGCCAAAAGUCAGAGGAAUACGGCAACAAAAAGCCUCCAGACUGUGGUCGGCUGAAUGGAAUUUCGACGAGAGGUUGCUGUCC
..(((((((((.(((((..((((.((((.....(....)......))))..)))).)))))))).......((((((.....))))))))).))) ( -31.00)
>DroYak_CAF1 21056 95 + 1
CUGGAGGCGCCUGGCCAAAAGUCAGAGGCAUACGGCAACAAAAAGCCUACAGACUGUGGUCGGCUGAAUGGAAUUUCGACCAGAGGUUGCUGUCC
..(((((((((((((((..((((..((((....(....).....))))...)))).)))))((.((((......)))).))..))).)))).))) ( -32.00)
>consensus
CUGGAGGCGCCUGGCCAAAAGUCAGAGGCAUACAGCAACGAAAAGCCUCCAGACUGUGGUCGGCUGAAUGGAAUUUCGACCAGAGGUUGCUGUCC
((((((((..(((((.....)))))..((.....))........)))))))).((.(((((((............))))))).)).......... (-26.12 = -27.60 +   1.48)

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 11:31:24 2006