Locus 8129

Sequence ID 3L_DroMel_CAF1
Location 21,414,090 – 21,414,196
Length 106
Max. P 0.801814
window13282 window13283

overview

Window 2

Location 21,414,090 – 21,414,196
Length 106
Sequences 4
Columns 107
Reading direction forward
Mean pairwise identity 83.08
Mean single sequence MFE -41.00
Consensus MFE -23.73
Energy contribution -26.23
Covariance contribution 2.50
Combinations/Pair 1.03
Mean z-score -2.47
Structure conservation index 0.58
SVM decision value 0.62
SVM RNA-class probability 0.801814
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21414090 106 + 23771897
GCGGAAAUUCAGCAGACGGCGCUAAGUCUGGACUCUGGACUCCGGAAUCUGGAGUCGAGUAUUCGGAGUCCGGGUCCG-GGUCCGGGUCCGGAUCCGGAUUCCUACC
..(((.((((..(((((........))))).......((((((((...)))))))))))).)))((((((((((((((-((......)))))))))))))))).... ( -55.10)
>DroSec_CAF1 5488 94 + 1
GCGGAAAUUCAGCAGACGGCGCUAAGUCUGGACUCUGGACCCCGGAAUCUGGAGUCGAGUAUUCCGAGUCCGAGUCCG-GGU------------CCGGAUUCCUACC
..((((......(((((........)))))...(((((((((.(((.((.(((.(((.......))).))))).))))-)))------------))))))))).... ( -41.70)
>DroSim_CAF1 5692 94 + 1
GCGGAAAUUCAGCAGACGGCGCUAAGUCUGGACUCUGGACCCCGGAAUCUGGAGUCGAGUAUUCCGAGUCCGAGUCCG-GGU------------CCGGAUUCCUACC
..((((......(((((........)))))...(((((((((.(((.((.(((.(((.......))).))))).))))-)))------------))))))))).... ( -41.70)
>DroYak_CAF1 5548 88 + 1
GCGGAAAUUCAGCAGACGGCGCUAAGUCUGGACU-------CCGGAAUCUGGAGCCGCGUAUUCCGAAGCUGGAUCCUGAAU------------CCUGAAUCCUACC
.(((((.....((((((........))))((.((-------((((...))))))))))...))))).....((((.(.....------------...).)))).... ( -25.50)
>consensus
GCGGAAAUUCAGCAGACGGCGCUAAGUCUGGACUCUGGACCCCGGAAUCUGGAGUCGAGUAUUCCGAGUCCGAGUCCG_GGU____________CCGGAUUCCUACC
.(((((((((..(((((........)))))(((((((((........))))))))))))).))))).....(((((((.................)))))))..... (-23.73 = -26.23 +   2.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 21,414,090 – 21,414,196
Length 106
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 83.08
Mean single sequence MFE -36.38
Consensus MFE -23.81
Energy contribution -26.12
Covariance contribution 2.31
Combinations/Pair 1.03
Mean z-score -1.68
Structure conservation index 0.65
SVM decision value 0.10
SVM RNA-class probability 0.583999
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21414090 106 - 23771897
GGUAGGAAUCCGGAUCCGGACCCGGACC-CGGACCCGGACUCCGAAUACUCGACUCCAGAUUCCGGAGUCCAGAGUCCAGACUUAGCGCCGUCUGCUGAAUUUCCGC
....(((((((((.((((....)))).)-))))...((((((.((....))((((((.......))))))..))))))....((((((.....))))))..)))).. ( -43.20)
>DroSec_CAF1 5488 94 - 1
GGUAGGAAUCCGG------------ACC-CGGACUCGGACUCGGAAUACUCGACUCCAGAUUCCGGGGUCCAGAGUCCAGACUUAGCGCCGUCUGCUGAAUUUCCGC
((..(((.((.((------------(((-((((.(((((.((((.....)))).))).)).))).)))))).)).)))....((((((.....))))))....)).. ( -36.50)
>DroSim_CAF1 5692 94 - 1
GGUAGGAAUCCGG------------ACC-CGGACUCGGACUCGGAAUACUCGACUCCAGAUUCCGGGGUCCAGAGUCCAGACUUAGCGCCGUCUGCUGAAUUUCCGC
((..(((.((.((------------(((-((((.(((((.((((.....)))).))).)).))).)))))).)).)))....((((((.....))))))....)).. ( -36.50)
>DroYak_CAF1 5548 88 - 1
GGUAGGAUUCAGG------------AUUCAGGAUCCAGCUUCGGAAUACGCGGCUCCAGAUUCCGG-------AGUCCAGACUUAGCGCCGUCUGCUGAAUUUCCGC
((...((((((((------------((((.(((((.((((.((.....)).))))...)).))).)-------))))(((((........)))))))))))).)).. ( -29.30)
>consensus
GGUAGGAAUCCGG____________ACC_CGGACCCGGACUCGGAAUACUCGACUCCAGAUUCCGGGGUCCAGAGUCCAGACUUAGCGCCGUCUGCUGAAUUUCCGC
....((((......................(((((((((((((((((.((.......))))))))).)))).))))))....((((((.....))))))..)))).. (-23.81 = -26.12 +   2.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:07:01 2006