Locus 866

Sequence ID X_DroMel_CAF1
Location 2,445,008 – 2,445,286
Length 278
Max. P 0.972866
window1401 window1402 window1403 window1404

overview

Window 1

Location 2,445,008 – 2,445,126
Length 118
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.43
Mean single sequence MFE -32.90
Consensus MFE -31.47
Energy contribution -30.92
Covariance contribution -0.55
Combinations/Pair 1.09
Mean z-score -2.06
Structure conservation index 0.96
SVM decision value 1.02
SVM RNA-class probability 0.902342
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2445008 118 - 22224390
CACGCCGCUCUCUCGGCGUACUUUGCACAGGAAAAAAAAACGAAGGAAUUGCAGCAGAGGCGCUUGGAAAAGCUCAAGCUAACAGCGAUUUGUUUAAAAGGAAAAUCGAUUUUCCCAC--
.((((((......))))))......................(((.(((((((.((....))((((((......)))))).....))))))).)))....((((((....))))))...-- ( -30.90)
>DroSec_CAF1 5841 119 - 1
CACGCCGCUCUUUCGGCGUACUUUGCACAG-AAAAAAAAGCAAAGGAAUUGCAGUAGAGGCGCUUGGAAAAGCCCAAACUAGCAGCGAUUUGUUUAAAAGGAAAAUCGAUUUUCCCACGA
.((((((......)))))).((((((....-........))))))(((((((.((((.((.((((....))))))...)).)).)))))))........((((((....))))))..... ( -33.90)
>DroSim_CAF1 8026 119 - 1
CACGCCGCUCUUUCGGCGUACUUUGCACAG-AAAAAAAAGCAAAGGAAUUGCAGUAGAGGCGCUUGGAAAAGCCCAAACUAGCAGCGAUUUGUUUAAAAGGAAAAUCGAUUUUCCCACGA
.((((((......)))))).((((((....-........))))))(((((((.((((.((.((((....))))))...)).)).)))))))........((((((....))))))..... ( -33.90)
>consensus
CACGCCGCUCUUUCGGCGUACUUUGCACAG_AAAAAAAAGCAAAGGAAUUGCAGUAGAGGCGCUUGGAAAAGCCCAAACUAGCAGCGAUUUGUUUAAAAGGAAAAUCGAUUUUCCCACGA
.((((((......)))))).((((((.............))))))((((((((((...((.((((....))))))..)))....)))))))........((((((....))))))..... (-31.47 = -30.92 +  -0.55)

alignment

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secondary structure

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dotplot

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Window 2

Location 2,445,046 – 2,445,166
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 91.55
Mean single sequence MFE -47.40
Consensus MFE -41.12
Energy contribution -40.69
Covariance contribution -0.43
Combinations/Pair 1.13
Mean z-score -3.55
Structure conservation index 0.87
SVM decision value 1.61
SVM RNA-class probability 0.967660
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2445046 120 + 22224390
AGCUUGAGCUUUUCCAAGCGCCUCUGCUGCAAUUCCUUCGUUUUUUUUUCCUGUGCAAAGUACGCCGAGAGAGCGGCGUGAACCGGUGCAGAGAGAGAGAGAUUAAGUGAGAAGGGGUGA
.(((((........)))))((((((.((.((....(((.((((((((((((((..(....(((((((......))))))).....)..))).))))))))))).))))))).)))))).. ( -46.40)
>DroSec_CAF1 5881 115 + 1
AGUUUGGGCUUUUCCAAGCGCCUCUACUGCAAUUCCUUUGCUUUUUUUU-CUGUGCAAAGUACGCCGAAAGAGCGGCGUGAACCGGUGCAGAGAGAGAGCG----AGCGUGAAGAGGUGA
.(((((((....)))))))((((((.((((.......(((((((((((.-(((..(....(((((((......))))))).....)..)))))))))))))----)))).).)))))).. ( -48.01)
>DroSim_CAF1 8066 115 + 1
AGUUUGGGCUUUUCCAAGCGCCUCUACUGCAAUUCCUUUGCUUUUUUUU-CUGUGCAAAGUACGCCGAAAGAGCGGCGUGAACCGGUGCAGAGAGAGAGCG----AGUGUGAAGAGGUGA
.(((((((....)))))))((((((.(.(((.....((((((((((((.-(((..(....(((((((......))))))).....)..)))))))))))))----)))))).)))))).. ( -47.80)
>consensus
AGUUUGGGCUUUUCCAAGCGCCUCUACUGCAAUUCCUUUGCUUUUUUUU_CUGUGCAAAGUACGCCGAAAGAGCGGCGUGAACCGGUGCAGAGAGAGAGCG____AGUGUGAAGAGGUGA
.(((((((....)))))))((((((.((((........((((((((((..(((..(....(((((((......))))))).....)..))))))))))))).....))).).)))))).. (-41.12 = -40.69 +  -0.43)

alignment

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secondary structure

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dotplot

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Window 3

Location 2,445,046 – 2,445,166
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 91.55
Mean single sequence MFE -35.62
Consensus MFE -32.89
Energy contribution -32.79
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -2.72
Structure conservation index 0.92
SVM decision value 1.70
SVM RNA-class probability 0.972866
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2445046 120 - 22224390
UCACCCCUUCUCACUUAAUCUCUCUCUCUCUGCACCGGUUCACGCCGCUCUCUCGGCGUACUUUGCACAGGAAAAAAAAACGAAGGAAUUGCAGCAGAGGCGCUUGGAAAAGCUCAAGCU
..........................(((((((..((((((((((((......)))))).(((((...............)))))))))))..))))))).((((((......)))))). ( -33.26)
>DroSec_CAF1 5881 115 - 1
UCACCUCUUCACGCU----CGCUCUCUCUCUGCACCGGUUCACGCCGCUCUUUCGGCGUACUUUGCACAG-AAAAAAAAGCAAAGGAAUUGCAGUAGAGGCGCUUGGAAAAGCCCAAACU
...............----.((.((((..(((((...((((((((((......)))))).((((((....-........))))))))))))))).))))))((((....))))....... ( -36.80)
>DroSim_CAF1 8066 115 - 1
UCACCUCUUCACACU----CGCUCUCUCUCUGCACCGGUUCACGCCGCUCUUUCGGCGUACUUUGCACAG-AAAAAAAAGCAAAGGAAUUGCAGUAGAGGCGCUUGGAAAAGCCCAAACU
....((.(((.((..----(((.((((..(((((...((((((((((......)))))).((((((....-........))))))))))))))).)))))))..))))).))........ ( -36.80)
>consensus
UCACCUCUUCACACU____CGCUCUCUCUCUGCACCGGUUCACGCCGCUCUUUCGGCGUACUUUGCACAG_AAAAAAAAGCAAAGGAAUUGCAGUAGAGGCGCUUGGAAAAGCCCAAACU
..........................(((((((..((((((((((((......)))))).((((((.............))))))))))))..))))))).((((....))))....... (-32.89 = -32.79 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 2,445,166 – 2,445,286
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.08
Mean single sequence MFE -23.65
Consensus MFE -20.90
Energy contribution -21.23
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.80
Structure conservation index 0.88
SVM decision value -0.02
SVM RNA-class probability 0.522550
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2445166 120 + 22224390
GAGAGUGGAAGAAGGUGUUCAUUGGCAGAAAAUUAGCAAGGCGACAAACGUUUAUAAAUAUAAACACAUAUAUUCCAAUAUAAAAAUCGCAAAUAUUAAUGACGAGACAAGAGCGCCUGC
............((((((((.(((.......(((((....((((.....((((((....))))))...(((((....)))))....)))).....))))).......))))))))))).. ( -23.94)
>DroSec_CAF1 5996 117 + 1
GAGAGAG---GAAGGUGUUCAUCGGCGGAAAAUUAGCAAGGCAACAAACGUUUAUAAAUAUAAACACAUAUAUUCCAAUAUAAAAAUCGCAAAUAUUAAUGACGAGACAAGAGCGCCUGC
.......---..((((((((......((((.........(....)....((((((....)))))).......))))..........(((((........)).))).....)))))))).. ( -23.50)
>DroSim_CAF1 8181 117 + 1
GAGAGAG---GAAGGUGUUCAUCGGCGGAAAAUUAGCAAGGCAACAAACGUUUAUAAAUAUAAACACAUAUAUUCCAAUAUAAAAAUCGCAAAUAUUAAUGACGAGACAAGAGCGCCUGC
.......---..((((((((......((((.........(....)....((((((....)))))).......))))..........(((((........)).))).....)))))))).. ( -23.50)
>consensus
GAGAGAG___GAAGGUGUUCAUCGGCGGAAAAUUAGCAAGGCAACAAACGUUUAUAAAUAUAAACACAUAUAUUCCAAUAUAAAAAUCGCAAAUAUUAAUGACGAGACAAGAGCGCCUGC
............((((((((......((((.........(....)....((((((....)))))).......))))..........(((((........)).))).....)))))))).. (-20.90 = -21.23 +   0.33)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:55:45 2006