Locus 4669

Sequence ID 3L_DroMel_CAF1
Location 13,213,443 – 13,213,553
Length 110
Max. P 0.948569
window7346 window7347

overview

Window 6

Location 13,213,443 – 13,213,553
Length 110
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 93.33
Mean single sequence MFE -27.31
Consensus MFE -25.64
Energy contribution -25.89
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.95
Structure conservation index 0.94
SVM decision value 1.38
SVM RNA-class probability 0.948569
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13213443 110 + 23771897
GGUCUCCCAAGUCAUGCACAUGCACACAUGGGUCCAUCCAUGUUCCUGUCUGCAUUUUCGCCAUCC--UCCAGUUUUCCAGCACCGCUUUGCGUGCCAGGAAAAUUGUCUUC
(((......((.(((((....))).(((((((....)))))))...)).))........)))....--..(((((((((.((((.((...))))))..)))))))))..... ( -28.04)
>DroSec_CAF1 6786 108 + 1
GGUCUCCCAAGUCAUGCAC----ACACAUGGGUCCAUCCAUGUUCCUGUCUGCAUUUUCGCCAUCCUCUCCAGUUUUCCCGCACCGCUUUGCGUGCCAGGAAAAUUGUCUUC
(((.....((((((.(((.----..(((((((....)))))))...))).)).))))..)))........(((((((((.((((.((...))))))..)))))))))..... ( -27.70)
>DroSim_CAF1 11859 108 + 1
GGUCUCCCAAGUCAUGCAC----ACACAUGGGUCCAUCCAUGUUCCUGUCUGCAUUUUCGCCAUCCUCUCCAGUUUUCCCGCACCGCUUUGCGUGCCAGGAAAAUUGUCUUC
(((.....((((((.(((.----..(((((((....)))))))...))).)).))))..)))........(((((((((.((((.((...))))))..)))))))))..... ( -27.70)
>DroYak_CAF1 6688 108 + 1
GGUCUCCCAAGUCAUGCAC----ACACAUGGGUCCAUCCAUGUACCCGUCUGCAUUUUCGCCCAACCCCCCAGUUUUCCCGCCCCGCUUUGCGUGCCAGGAAAAUUGUCUUC
(((..........(((((.----(((((((((....)))))))....)).))))).........)))...(((((((((.((..(((...))).))..)))))))))..... ( -25.81)
>consensus
GGUCUCCCAAGUCAUGCAC____ACACAUGGGUCCAUCCAUGUUCCUGUCUGCAUUUUCGCCAUCCUCUCCAGUUUUCCCGCACCGCUUUGCGUGCCAGGAAAAUUGUCUUC
((....)).....(((((.......(((((((....))))))).......)))))...............(((((((((.((((.((...))))))..)))))))))..... (-25.64 = -25.89 +   0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,213,443 – 13,213,553
Length 110
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 93.33
Mean single sequence MFE -33.85
Consensus MFE -28.54
Energy contribution -28.79
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.60
Structure conservation index 0.84
SVM decision value 0.18
SVM RNA-class probability 0.623336
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13213443 110 - 23771897
GAAGACAAUUUUCCUGGCACGCAAAGCGGUGCUGGAAAACUGGA--GGAUGGCGAAAAUGCAGACAGGAACAUGGAUGGACCCAUGUGUGCAUGUGCAUGACUUGGGAGACC
.....((.((((((.(((((((...)).))))))))))).))((--(....(((...(((((.(((((..((....))..))..))).))))).)))....)))((....)) ( -34.90)
>DroSec_CAF1 6786 108 - 1
GAAGACAAUUUUCCUGGCACGCAAAGCGGUGCGGGAAAACUGGAGAGGAUGGCGAAAAUGCAGACAGGAACAUGGAUGGACCCAUGUGU----GUGCAUGACUUGGGAGACC
.(((.((.((((((((.(((((...)).))))))))))).))...............(((((.((....((((((......))))))))----.)))))..)))((....)) ( -32.60)
>DroSim_CAF1 11859 108 - 1
GAAGACAAUUUUCCUGGCACGCAAAGCGGUGCGGGAAAACUGGAGAGGAUGGCGAAAAUGCAGACAGGAACAUGGAUGGACCCAUGUGU----GUGCAUGACUUGGGAGACC
.(((.((.((((((((.(((((...)).))))))))))).))...............(((((.((....((((((......))))))))----.)))))..)))((....)) ( -32.60)
>DroYak_CAF1 6688 108 - 1
GAAGACAAUUUUCCUGGCACGCAAAGCGGGGCGGGAAAACUGGGGGGUUGGGCGAAAAUGCAGACGGGUACAUGGAUGGACCCAUGUGU----GUGCAUGACUUGGGAGACC
.....((.((((((((.(.(((...))).).)))))))).))...((((...(((..(((((.((....((((((......))))))))----.)))))...)))...)))) ( -35.30)
>consensus
GAAGACAAUUUUCCUGGCACGCAAAGCGGUGCGGGAAAACUGGAGAGGAUGGCGAAAAUGCAGACAGGAACAUGGAUGGACCCAUGUGU____GUGCAUGACUUGGGAGACC
.(((.((.((((((((...(((...)))...)))))))).))...............(((((.......((((((......)))))).......)))))..)))((....)) (-28.54 = -28.79 +   0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:11 2006