Locus 3389

Sequence ID 2R_DroMel_CAF1
Location 11,449,567 – 11,449,661
Length 94
Max. P 0.775985
window5539 window5540

overview

Window 9

Location 11,449,567 – 11,449,661
Length 94
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 82.22
Mean single sequence MFE -21.84
Consensus MFE -15.10
Energy contribution -15.34
Covariance contribution 0.24
Combinations/Pair 1.06
Mean z-score -1.90
Structure conservation index 0.69
SVM decision value 0.54
SVM RNA-class probability 0.775985
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11449567 94 + 20766785
AGCAUCGAUGUUUUUCGAUACAUCGUCAAUGUUUCAUCGAUGAAAUACCAACUUAAUGGGCACUGCUUACAAAAACAAGGUCAAGCAGUUUACC
.((..((((((........))))))....(((((((....)))))))(((......)))))(((((((((.........)).)))))))..... ( -21.30)
>DroSec_CAF1 1972 94 + 1
AGCAUCGAUGAUUUUCGAUACAUCGUCAAUGUUUCAUCGAUAAAAUACCAACCUAAUGGGCACUGCUUACAAAAACCAAGGCAAGCAGUUUACG
.((((((((((..(.(((....))).....)..))))))))......(((......)))))(((((((.(..........).)))))))..... ( -21.00)
>DroSim_CAF1 1970 94 + 1
AGCAUCGAUGAUUUUCGAUACAUCGUCAAUGUUUCAUCGAUGAAAUACCAACCUAAUGGGCACUGCUUACAAAAACAAAGGCAAGCAGUUUACG
..(((((((((..(.(((....))).....)..))))))))).....(((......)))..(((((((.(..........).)))))))..... ( -21.50)
>DroEre_CAF1 2007 92 + 1
UACAUCGAUGUUUUUCGAUACA-CCUUAAUGUCUCAUCGAUGACACACCGUCUUAAUUUAAACUGCUUAGCGAAAGCAGUGCAAGCAGUU-AGC
..((((((((......((((..-......)))).))))))))..................((((((((.((....)).....))))))))-... ( -23.00)
>DroYak_CAF1 1981 93 + 1
UGCAUCGAUGUUUUUCGAUAAA-CGUCAAUGUUUCAUCGAUGACAUACCGUCCUAAUGAAAACUGCUUGGCGAAAUUAGGGGAAGCAGUUCAGC
.((((.(((((((......)))-)))).))))(((((.((((......))))...)))))((((((((..(........)..)))))))).... ( -22.40)
>consensus
AGCAUCGAUGUUUUUCGAUACAUCGUCAAUGUUUCAUCGAUGAAAUACCAACCUAAUGGGCACUGCUUACAAAAACAAGGGCAAGCAGUUUACC
..((((((((......(((.....))).......))))))))...................(((((((..............)))))))..... (-15.10 = -15.34 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 11,449,567 – 11,449,661
Length 94
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 82.22
Mean single sequence MFE -24.32
Consensus MFE -16.62
Energy contribution -16.86
Covariance contribution 0.24
Combinations/Pair 1.05
Mean z-score -1.82
Structure conservation index 0.68
SVM decision value 0.37
SVM RNA-class probability 0.709593
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11449567 94 - 20766785
GGUAAACUGCUUGACCUUGUUUUUGUAAGCAGUGCCCAUUAAGUUGGUAUUUCAUCGAUGAAACAUUGACGAUGUAUCGAAAAACAUCGAUGCU
((...((((((((............))))))))..)).....((..((.(((((....))))).))..))...(((((((......))))))). ( -26.10)
>DroSec_CAF1 1972 94 - 1
CGUAAACUGCUUGCCUUGGUUUUUGUAAGCAGUGCCCAUUAGGUUGGUAUUUUAUCGAUGAAACAUUGACGAUGUAUCGAAAAUCAUCGAUGCU
.....(((((((((..........))))))))).........((..((.(((((....))))).))..))...(((((((......))))))). ( -24.30)
>DroSim_CAF1 1970 94 - 1
CGUAAACUGCUUGCCUUUGUUUUUGUAAGCAGUGCCCAUUAGGUUGGUAUUUCAUCGAUGAAACAUUGACGAUGUAUCGAAAAUCAUCGAUGCU
.....(((((((((..........))))))))).........((..((.(((((....))))).))..))...(((((((......))))))). ( -26.50)
>DroEre_CAF1 2007 92 - 1
GCU-AACUGCUUGCACUGCUUUCGCUAAGCAGUUUAAAUUAAGACGGUGUGUCAUCGAUGAGACAUUAAGG-UGUAUCGAAAAACAUCGAUGUA
...-((((((((((.........)).))))))))..........((((((....((((((..((......)-).))))))...))))))..... ( -23.70)
>DroYak_CAF1 1981 93 - 1
GCUGAACUGCUUCCCCUAAUUUCGCCAAGCAGUUUUCAUUAGGACGGUAUGUCAUCGAUGAAACAUUGACG-UUUAUCGAAAAACAUCGAUGCA
...(((((((((..(........)..)))))))))(((((..(((.....)))...)))))..((((((.(-(((......)))).)))))).. ( -21.00)
>consensus
GGUAAACUGCUUGCCCUGGUUUUUGUAAGCAGUGCCCAUUAGGUUGGUAUUUCAUCGAUGAAACAUUGACGAUGUAUCGAAAAACAUCGAUGCU
.....((((((((............))))))))...................((((((((.....((((.......))))....)))))))).. (-16.62 = -16.86 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:22 2006