Locus 413

Sequence ID 2L_DroMel_CAF1
Location 1,234,969 – 1,235,168
Length 199
Max. P 0.930256
window667 window668

overview

Window 7

Location 1,234,969 – 1,235,088
Length 119
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 94.98
Mean single sequence MFE -30.55
Consensus MFE -27.05
Energy contribution -28.05
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.24
Structure conservation index 0.89
SVM decision value 1.20
SVM RNA-class probability 0.930256
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1234969 119 - 22407834
GAGGAAAAACAUCUGAUCCUGAAGGAA-AAAAUCCGGGAUUUGGGUGAAAUGUUAAAUGGGCGACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGCUGACAAACAAAUUACAC
.((((...........))))...(((.-....))).(((((((((((((((((((((((.....)))))).)))))..))))))))))))......((((((........)))))).... ( -32.10)
>DroSec_CAF1 12288 119 - 1
GAAUAAAAACCUCUGAUCAUGAAGGAA-AAAAUCCGGGAUUUGGGUGAAAUGUUAAAUGGGCGACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGCUGACAAACAAAUUACAC
..........(((..........(((.-....))).(((((((((((((((((((((((.....)))))).)))))..)))))))))))))))...((((((........)))))).... ( -32.10)
>DroSim_CAF1 8105 119 - 1
GAAGAAAAACCUCUGAUCCUGAAGGAA-AAAAUCCGGGAUUUGGGGGAAAUGUUAAAUGGGCGACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGCUGACAAACAAAUUACAC
..........(((...(((....))).-........(((((((((..((((((((((((.....)))))).)))))..)..))))))))))))...((((((........)))))).... ( -28.60)
>DroYak_CAF1 8339 120 - 1
AAAGAAAAACCUCUGAUCCUGAGGCAAAAAAAUCCGGGAUUUUGGUGAAAUGUUAAAUGGGCAACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGUUGACAAACAAAUUACAC
.........((((.......))))............((((((.((((((((((((((((.....)))))).)))))..))))).))))))......((((((((....)))))))).... ( -29.40)
>consensus
GAAGAAAAACCUCUGAUCCUGAAGGAA_AAAAUCCGGGAUUUGGGUGAAAUGUUAAAUGGGCGACAUUUACACAUUCGUUACCCAGGUCCGAGCCCAAUUUGCUGACAAACAAAUUACAC
..........(((..........(((......))).(((((((((((((((((((((((.....)))))).)))))..)))))))))))))))...((((((........)))))).... (-27.05 = -28.05 +   1.00) 

alignment

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secondary structure

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dotplot

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Window 8

Location 1,235,049 – 1,235,168
Length 119
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 92.05
Mean single sequence MFE -36.01
Consensus MFE -28.35
Energy contribution -28.73
Covariance contribution 0.37
Combinations/Pair 1.09
Mean z-score -1.85
Structure conservation index 0.79
SVM decision value 0.36
SVM RNA-class probability 0.702838
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1235049 119 + 22407834
AUCCCGGAUUUU-UUCCUUCAGGAUCAGAUGUUUUUCCUCUCUUUGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGCGGGUAGGUGGGUCCGUUCGGACUCCAUCAUGGGAACCAUU
.(((((......-..(((.((..((((((((((............))))))(((((((......)))))))))))..)).)))..(((((((((....)))).))))).)))))...... ( -37.20)
>DroSec_CAF1 12368 119 + 1
AUCCCGGAUUUU-UUCCUUCAUGAUCAGAGGUUUUUAUUCUCUGUGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGAGGGUAGGUGGGUCCGUUUGGAUUCCAUCAUCGGAAACAUU
...((((.....-..(((((((.(((((.....(((((((.....(((...)))....))))))).....))))).)))))))..(((((((((....))).)))))).))))....... ( -38.40)
>DroSim_CAF1 8185 119 + 1
AUCCCGGAUUUU-UUCCUUCAGGAUCAGAGGUUUUUCUUCUCUGCGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGCGGGUAGGUGGGUCCGUUCGGAUUCCAUCAUGGGAAACAUU
.((((((((...-.(((....((((((((((.....)))))(((((.(((((((((((......))))))).)))).))))).......)))))....)))....))).)))))...... ( -38.60)
>DroYak_CAF1 8419 120 + 1
AUCCCGGAUUUUUUUGCCUCAGGAUCAGAGGUUUUUCUUUUCUUUGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGCGGGUAGGUGGCUCCAUUCAGAUUCCAUCAUCGGAACCAUU
.(((.(((.......(((((.......))))).......))).........(((((((......))))))).(((((((.((((.((((....))))...))))))))))))))...... ( -29.84)
>consensus
AUCCCGGAUUUU_UUCCUUCAGGAUCAGAGGUUUUUCUUCUCUGUGACAUUGUCUAAUGAGUAAAUUAGGCUGGUGAUGCGGGUAGGUGGGUCCGUUCGGAUUCCAUCAUCGGAAACAUU
..((((((......)))....(.((((((((.......)))))...((...(((((((......)))))))..))))).))))..(((((((((....)))).)))))...(....)... (-28.35 = -28.73 +   0.37) 

alignment

Postscript

secondary structure

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dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:35:33 2006