Locus 1238

Sequence ID 2R_DroMel_CAF1
Location 4,852,943 – 4,853,040
Length 97
Max. P 0.824909
window2152 window2153

overview

Window 2

Location 4,852,943 – 4,853,040
Length 97
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 94.50
Mean single sequence MFE -41.83
Consensus MFE -40.44
Energy contribution -40.00
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.97
SVM decision value 0.69
SVM RNA-class probability 0.824909
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4852943 97 + 20766785
GGUGGAGUUCCAGCGGGCUUUGAGUGGGAGGCUCCACGGGAGGCCAGCUGGGAGGCGUCACCGUGGCUCGAACUCAGCUCAACUGAAGCGUUUUAAU
((((..((((((((.((((((..(((((....)))))..)))))).))))))..))..))))...(((.....((((.....)))))))........ ( -39.90)
>DroSim_CAF1 14224 97 + 1
GGUGGAGUUCCAGCGGGCUUUGAGUGGGAGGCUCCACGGGAGGCCGGCUGGUGGGCGUCACCGUGGCUCGAACUCAGCGCAACUGAAGCGUUUUAAU
....((((((.((((((((((......)))))))(((((((.(((.(....).))).)).)))))))).))))))(((((.......)))))..... ( -42.70)
>DroYak_CAF1 13778 97 + 1
GGUGGAGUUCCAGCGGGCUUUGUGUGGGAGGUUCCACGGAAGGCCGGCUGGGAGGCGUCGCCGUGGCUCGAACUCAGCUCAACUGAAGCGUUUUAAU
((((..((((((((.((((((.((((((....)))))).)))))).))))))..))..))))...(((.....((((.....)))))))........ ( -42.90)
>consensus
GGUGGAGUUCCAGCGGGCUUUGAGUGGGAGGCUCCACGGGAGGCCGGCUGGGAGGCGUCACCGUGGCUCGAACUCAGCUCAACUGAAGCGUUUUAAU
((((..((((((((.((((((..(((((....)))))..)))))).)))))..)))..))))...(((.....((((.....)))))))........ (-40.44 = -40.00 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,852,943 – 4,853,040
Length 97
Sequences 3
Columns 97
Reading direction reverse
Mean pairwise identity 94.50
Mean single sequence MFE -32.60
Consensus MFE -30.35
Energy contribution -30.47
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.96
Structure conservation index 0.93
SVM decision value 0.64
SVM RNA-class probability 0.809034
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4852943 97 - 20766785
AUUAAAACGCUUCAGUUGAGCUGAGUUCGAGCCACGGUGACGCCUCCCAGCUGGCCUCCCGUGGAGCCUCCCACUCAAAGCCCGCUGGAACUCCACC
..........((((((.(.(((((((..(((((((((.((.(((........))).))))))))...)))..))))..)))).))))))........ ( -33.50)
>DroSim_CAF1 14224 97 - 1
AUUAAAACGCUUCAGUUGCGCUGAGUUCGAGCCACGGUGACGCCCACCAGCCGGCCUCCCGUGGAGCCUCCCACUCAAAGCCCGCUGGAACUCCACC
..........((((((.((..(((((..(((((((((.((.(((........))).))))))))...)))..)))))..))..))))))........ ( -33.40)
>DroYak_CAF1 13778 97 - 1
AUUAAAACGCUUCAGUUGAGCUGAGUUCGAGCCACGGCGACGCCUCCCAGCCGGCCUUCCGUGGAACCUCCCACACAAAGCCCGCUGGAACUCCACC
........((((.....)))).(((((((((...((....)).))).((((.(((.....((((......)))).....))).)))))))))).... ( -30.90)
>consensus
AUUAAAACGCUUCAGUUGAGCUGAGUUCGAGCCACGGUGACGCCUCCCAGCCGGCCUCCCGUGGAGCCUCCCACUCAAAGCCCGCUGGAACUCCACC
..........((((((.(.(((((((..(((((((((.((.(((........))).))))))))...)))..))))..)))).))))))........ (-30.35 = -30.47 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:59:49 2006