Locus 1328

Sequence ID 3R_DroMel_CAF1
Location 3,903,076 – 3,903,166
Length 90
Max. P 0.873471
window2173

overview

Window 3

Location 3,903,076 – 3,903,166
Length 90
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 78.29
Mean single sequence MFE -32.28
Consensus MFE -18.75
Energy contribution -18.48
Covariance contribution -0.28
Combinations/Pair 1.23
Mean z-score -2.04
Structure conservation index 0.58
SVM decision value 0.88
SVM RNA-class probability 0.873471
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3903076 90 + 27905053
-----------------GUGUAUGU-----UU-CAUGCCACAAAAGACAACGCUAAGUGGCCUG-GGGCGCAAUUUUAGC-CAUUGGCGCUCGUUAAAUUUGCAUGUGCAUGCCU
-----------------((((((((-----..-((.(((((...((......))..))))).))-..))((((.((((((-...........)))))).))))..)))))).... ( -26.80)
>DroVir_CAF1 40115 95 + 1
U----------------GCUUGUUUGAUGAUG-UUUGCCACAA-AGACAACGCCACGUGGCCUAUGGGCGCAAUUUU-GC-CAUUGGCGCUCGUUAAAUUUGCAUGCGGAAGCGC
(----------------((..(((((((((((-(((.......-))))).(((((.((((((....)))(((....)-))-)))))))).)))))))))..))).((....)).. ( -33.90)
>DroSec_CAF1 26298 90 + 1
-----------------AUGUAUGU-----UC-CAUGCCACAAAAGACAACGCUAAGUGGCCUG-GGGCGCAAUUUUAGC-CAUUGGCGCUCGUUAAAUUUGCAUGUGCAUGCCC
-----------------((((((((-----((-((.(((((...((......))..))))).))-))))((((.((((((-...........)))))).))))..)))))).... ( -28.30)
>DroEre_CAF1 26180 91 + 1
U----------------GUGUGUGC-----UU-CAUGCCACAAAAGACAACGCUAAGUGGCCUG-GGGCGCAAUUUUAGC-CAUUGGCGCUCGUUAAAUUUGCAUGUGCAUGCCU
.----------------((((((((-----((-((.(((((...((......))..))))).))-))))((((.((((((-...........)))))).))))....)))))).. ( -28.70)
>DroMoj_CAF1 40771 96 + 1
U----------------GUUUGUAUGAUGAUG-UUUGCCACAA-AGGCAACGUCACGUGGCCUGUGGGCGCAAUUUC-GCCCAUUGGCGCUCGUUAAAUUUGCAUGCGGAAGCGC
.----------------.((((((((..((((-((.(((....-.)))))))))(((.((((.(((((((......)-)))))).))).).)))........))))))))..... ( -38.90)
>DroAna_CAF1 27569 108 + 1
UACAUAUGUAUGUGCGAGUGUAUGU-----GCUGCUGCCACAAAAGACAACGCUAAGUGGCCUG-GGGCGCAAUUUUUGC-CAUUGGCGCUCGUUAAAUUUGCAUGUGCAUGCUG
....(((((((((((((((...(((-----(((.(.(((((...((......))..)))))..)-.))))))......((-(...))).........)))))))))))))))... ( -37.10)
>consensus
U________________GUGUAUGU_____UC_CAUGCCACAAAAGACAACGCUAAGUGGCCUG_GGGCGCAAUUUUAGC_CAUUGGCGCUCGUUAAAUUUGCAUGUGCAUGCCC
.................((((((((...........(((((...............)))))....(((((((((........))).))))))...........)))))))).... (-18.75 = -18.48 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:06:53 2006