Locus 5236

Sequence ID X_DroMel_CAF1
Location 13,662,007 – 13,662,164
Length 157
Max. P 0.628978
window8483 window8484

overview

Window 3

Location 13,662,007 – 13,662,111
Length 104
Sequences 4
Columns 104
Reading direction reverse
Mean pairwise identity 96.31
Mean single sequence MFE -29.23
Consensus MFE -25.34
Energy contribution -25.65
Covariance contribution 0.31
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.87
SVM decision value 0.09
SVM RNA-class probability 0.577220
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13662007 104 - 22224390
GUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGGGGCGACAAACUUUGGUCAAACGGUUGCCGCUAACCGGUUUAAUUUUAAGUCCUUUACCUGAACCGAU
..........((((........(((((((((((((..((((((....(((....)))..)))))))))))))))))))..((((.((.....)).)))).)))) ( -28.80)
>DroSec_CAF1 4987 102 - 1
GUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGGGGCGACAAACUUUGGUCAAACGGUU--UGGUAACCGGUUUAAUUUUAAGUCCUUUACCUGAACCGAU
...........((((.(((((.......)))))))))...(((........)))...(((((--((((((..(..(((....)))..)..))))).)))))).. ( -25.40)
>DroEre_CAF1 5112 104 - 1
GUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGGGGCGACAAACUUUGGUCAAACGGUUGCCGCUAACCGGUUUAUUUUCCAGUCCUUUACCUGAACCGAU
..........((((.......((((((((((((((..((((((....(((....)))..))))))))))))))))))))....(((........)))...)))) ( -31.30)
>DroYak_CAF1 4882 104 - 1
GUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGGGGCGACAAACUUUGGUCAAACGGUUGCCGCUAACCGGUUUAUUUUCAAGUCCUUUACCUGAACCGAU
..........((((.......((((((((((((((..((((((....(((....)))..)))))))))))))))))))).((((.((.....)).)))).)))) ( -31.40)
>consensus
GUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGGGGCGACAAACUUUGGUCAAACGGUUGCCGCUAACCGGUUUAAUUUCAAGUCCUUUACCUGAACCGAU
..........((((........(((((((((((((((((((((........))).....))).)))))))))))))))..((((.((.....)).)))).)))) (-25.34 = -25.65 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 13,662,074 – 13,662,164
Length 90
Sequences 4
Columns 102
Reading direction reverse
Mean pairwise identity 91.80
Mean single sequence MFE -33.33
Consensus MFE -26.12
Energy contribution -25.88
Covariance contribution -0.25
Combinations/Pair 1.04
Mean z-score -1.72
Structure conservation index 0.78
SVM decision value 0.20
SVM RNA-class probability 0.628978
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13662074 90 - 22224390
AGAGGUAUGACG-----GGCUGAGCUUGGUUUCUCCAAAGGGGUUGGGUUC-------CGUUCGUGUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGG
.(((..((((((-----(((.(((((..(..(((....)))..)..)))))-------.))))..)))))..)))..(((.(((((.......)))))))). ( -32.70)
>DroSec_CAF1 5052 89 - 1
AGAGGUAUGACG-----GGCUGAGCUUGGUUUCUCCA-AGGGGUUGGGUUC-------CGUUCGUGUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGG
.(((..((((((-----(((.(((((..(..((....-.))..)..)))))-------.))))..)))))..)))..(((.(((((.......)))))))). ( -32.10)
>DroEre_CAF1 5179 89 - 1
AGAGGUAUGAUG-----GGUUGAGCUUGGUUUCUCCA-AGGGGUUGGGUUC-------CGUUCGUGUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGG
.(((..((((((-----..(.(((((..(..((....-.))..)..)))))-------.)..)..)))))..)))..(((.(((((.......)))))))). ( -28.70)
>DroYak_CAF1 4949 101 - 1
AGAGGUAUGAUGGGACGGGUUGAGCUUGGUUUCUCCA-AGGGGUUGGGUUCCACCAACCGUUCGUGUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGG
.(((...((((((.(((..(....(((((.....)))-)).((((((......)))))))..))).)))))))))..(((.(((((.......)))))))). ( -39.80)
>consensus
AGAGGUAUGACG_____GGCUGAGCUUGGUUUCUCCA_AGGGGUUGGGUUC_______CGUUCGUGUCAUCACUCAUCGCUCAAUCAUAAACCGGUUGGCGG
.(((..((((((.........(((((..(..(((....)))..)..))))).............))))))..)))..(((.(((((.......)))))))). (-26.12 = -25.88 +  -0.25)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:42:57 2006