Locus 857

Sequence ID 2L_DroMel_CAF1
Location 2,444,770 – 2,444,867
Length 97
Max. P 0.989043
window1392 window1393

overview

Window 2

Location 2,444,770 – 2,444,867
Length 97
Sequences 5
Columns 97
Reading direction forward
Mean pairwise identity 86.55
Mean single sequence MFE -22.69
Consensus MFE -14.81
Energy contribution -14.53
Covariance contribution -0.28
Combinations/Pair 1.12
Mean z-score -2.55
Structure conservation index 0.65
SVM decision value 0.59
SVM RNA-class probability 0.792809
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2444770 97 + 22407834
GCGGUGCAAAAACCGCGCGAACAAACAAACAAAACUGCAUUUGCAUUUGCAAAUUCGCUCAAAUUGAAUUUCGUUUUGCGGCUGCACUUAUGCAUUU
(((((......)))))...................(((((.((((.(((((((..((.((.....))....)).))))))).))))...)))))... ( -24.60)
>DroSec_CAF1 24016 97 + 1
GCGGUGCAAAAACCGCGCGAACAAACAAACAAAACUCCAUUUGCAUUUGCAAAUUCGCUCAAAUUGAAUUUCGUUUUUUGGCUGCACUUAUGCAUUU
(((((......)))))(((..((((.((((.(((.((.(((((.....((......)).))))).)).))).))))))))..)))............ ( -22.30)
>DroSim_CAF1 24413 91 + 1
GCGGUGCAAAAACCGCGCGAACAAACAAACAAAACU------GCAUUUGCAAAUUCGCUCAAAUUGAAUUUCGUUUUGUGGCUGCACUUAUGCAUUU
(((((......)))))............(((((((.------((....))(((((((.......))))))).)))))))...((((....))))... ( -21.00)
>DroEre_CAF1 25849 86 + 1
GCAGUGCAAAAACCGCGCGAACAAACAAACAAAACUGCAUUUGCA-------GUUCGCUCAAAUUGAAUUUCAUUUUGCGGUUGCACUUA----UUU
..((((((...(((((((((.............(((((....)))-------))))))..(((.((.....)).))))))))))))))..----... ( -25.21)
>DroYak_CAF1 24440 86 + 1
GCAGUGCAAAAACCGCGCGAACAAACAAACAAAACUGCAUUUGCA-------AUUCGCUCAAAUUGAAUUUCAUUCUGCGGUUGCACUUA----UUU
..((((((...((((((((((..............(((....)))-------.))))).......((((...)))).)))))))))))..----... ( -20.36)
>consensus
GCGGUGCAAAAACCGCGCGAACAAACAAACAAAACUGCAUUUGCAUUUGCAAAUUCGCUCAAAUUGAAUUUCGUUUUGCGGCUGCACUUAUGCAUUU
..((((((....(((((((((................................)))))((.....))..........)))).))))))......... (-14.81 = -14.53 +  -0.28) 

alignment

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secondary structure

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dotplot

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Window 3

Location 2,444,770 – 2,444,867
Length 97
Sequences 5
Columns 97
Reading direction reverse
Mean pairwise identity 86.55
Mean single sequence MFE -28.22
Consensus MFE -21.08
Energy contribution -21.64
Covariance contribution 0.56
Combinations/Pair 1.12
Mean z-score -3.05
Structure conservation index 0.75
SVM decision value 2.15
SVM RNA-class probability 0.989043
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2444770 97 - 22407834
AAAUGCAUAAGUGCAGCCGCAAAACGAAAUUCAAUUUGAGCGAAUUUGCAAAUGCAAAUGCAGUUUUGUUUGUUUGUUCGCGCGGUUUUUGCACCGC
..........((((((((((....((((......)))).((((((..((((..(((((......)))))))))..)))))))))))...)))))... ( -30.80)
>DroSec_CAF1 24016 97 - 1
AAAUGCAUAAGUGCAGCCAAAAAACGAAAUUCAAUUUGAGCGAAUUUGCAAAUGCAAAUGGAGUUUUGUUUGUUUGUUCGCGCGGUUUUUGCACCGC
...((((....))))(((((((((((((((((.(((((.(((....))).....))))).))))))))))).))))...))(((((......))))) ( -26.00)
>DroSim_CAF1 24413 91 - 1
AAAUGCAUAAGUGCAGCCACAAAACGAAAUUCAAUUUGAGCGAAUUUGCAAAUGC------AGUUUUGUUUGUUUGUUCGCGCGGUUUUUGCACCGC
..........((((((((.(....((((......)))).((((((..((((((..------......))))))..))))))).)))...)))))... ( -24.50)
>DroEre_CAF1 25849 86 - 1
AAA----UAAGUGCAACCGCAAAAUGAAAUUCAAUUUGAGCGAAC-------UGCAAAUGCAGUUUUGUUUGUUUGUUCGCGCGGUUUUUGCACUGC
...----..(((((((((((....((.....))......((((((-------.((((((........))))))..)))))))))))...)))))).. ( -30.20)
>DroYak_CAF1 24440 86 - 1
AAA----UAAGUGCAACCGCAGAAUGAAAUUCAAUUUGAGCGAAU-------UGCAAAUGCAGUUUUGUUUGUUUGUUCGCGCGGUUUUUGCACUGC
...----..(((((((((((.((((...)))).......((((((-------.((((((........))))))..)))))))))))...)))))).. ( -29.60)
>consensus
AAAUGCAUAAGUGCAGCCGCAAAACGAAAUUCAAUUUGAGCGAAUUUGCAAAUGCAAAUGCAGUUUUGUUUGUUUGUUCGCGCGGUUUUUGCACCGC
..........((((((((((....((((......)))).((((((........(((((......)))))......)))))))))))...)))))... (-21.08 = -21.64 +   0.56) 

alignment

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secondary structure

Postscript

dotplot

Postscript


Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:19 2006