Locus 567

Sequence ID 3R_DroMel_CAF1
Location 2,121,247 – 2,121,339
Length 92
Max. P 0.531694
window901 window902

overview

Window 1

Location 2,121,247 – 2,121,339
Length 92
Sequences 4
Columns 92
Reading direction forward
Mean pairwise identity 86.59
Mean single sequence MFE -16.86
Consensus MFE -11.69
Energy contribution -12.88
Covariance contribution 1.19
Combinations/Pair 1.11
Mean z-score -1.47
Structure conservation index 0.69
SVM decision value -0.01
SVM RNA-class probability 0.527080
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2121247 92 + 27905053
CCAAGGGUAAGCUAUACCAGCAUUUUAAAUCACUAGGAGUAGAAAUCAAUAAAAGACUUGCCAAGCCACGUUAUAGAAACAAUUACCCCUGA
.((.((((((.((((.((((............)).)).))))............(((.((......)).)))..........)))))).)). ( -12.80)
>DroSec_CAF1 264299 92 + 1
CCAAGGGUAAGCUGUACCAGCAUUUUAAAUCGCUAGGAGUAGAAAUCAAUAAAAGACUUGCCAAGGCACGUUAUAUACACCAUUACCCCUGA
.((.((((((((((...))))..............((.((((....).......(((.(((....))).)))...))).)).)))))).)). ( -21.60)
>DroSim_CAF1 282812 92 + 1
CCAAGGGUAAGCUGUACCAGCAUUUUAAAUCGCUAGGAGUAGAAAUCAAUAAAAGACUUGCCAAGGCACGUUAUAUACACCAUUACCCCUGA
.((.((((((((((...))))..............((.((((....).......(((.(((....))).)))...))).)).)))))).)). ( -21.60)
>DroEre_CAF1 267252 91 + 1
CCAAGAGUAAGCUGUCCCAGCUUAUUAAAUCAAUAAGCGUAAACAUCAAUCAACAACUUGUCAAGGCAAUUUAUAAAAACAAUUAAC-CUGA
.....(((((((((...)))))))))..........((.(..(((.............)))..).))....................-.... ( -11.42)
>consensus
CCAAGGGUAAGCUGUACCAGCAUUUUAAAUCACUAGGAGUAGAAAUCAAUAAAAGACUUGCCAAGGCACGUUAUAUAAACAAUUACCCCUGA
.((.((((((((((...)))).................................(((.(((....))).)))..........)))))).)). (-11.69 = -12.88 +   1.19)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 2,121,247 – 2,121,339
Length 92
Sequences 4
Columns 92
Reading direction reverse
Mean pairwise identity 86.59
Mean single sequence MFE -23.45
Consensus MFE -15.02
Energy contribution -15.40
Covariance contribution 0.38
Combinations/Pair 1.25
Mean z-score -1.74
Structure conservation index 0.64
SVM decision value -0.00
SVM RNA-class probability 0.531694
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2121247 92 - 27905053
UCAGGGGUAAUUGUUUCUAUAACGUGGCUUGGCAAGUCUUUUAUUGAUUUCUACUCCUAGUGAUUUAAAAUGCUGGUAUAGCUUACCCUUGG
.((((((((...(((.....)))..((((..((.(((.(((((..((((.(((....))).))))))))).))).))..)))))))))))). ( -22.00)
>DroSec_CAF1 264299 92 - 1
UCAGGGGUAAUGGUGUAUAUAACGUGCCUUGGCAAGUCUUUUAUUGAUUUCUACUCCUAGCGAUUUAAAAUGCUGGUACAGCUUACCCUUGG
.(((((((((.(.(((((......(((....)))(((.(((((..((((.(((....))).))))))))).))).))))).)))))))))). ( -27.00)
>DroSim_CAF1 282812 92 - 1
UCAGGGGUAAUGGUGUAUAUAACGUGCCUUGGCAAGUCUUUUAUUGAUUUCUACUCCUAGCGAUUUAAAAUGCUGGUACAGCUUACCCUUGG
.(((((((((.(.(((((......(((....)))(((.(((((..((((.(((....))).))))))))).))).))))).)))))))))). ( -27.00)
>DroEre_CAF1 267252 91 - 1
UCAG-GUUAAUUGUUUUUAUAAAUUGCCUUGACAAGUUGUUGAUUGAUGUUUACGCUUAUUGAUUUAAUAAGCUGGGACAGCUUACUCUUGG
((((-(.(((((.........))))).)))))((((..((.......(((((..((((((((...))))))))..)))))....)).)))). ( -17.80)
>consensus
UCAGGGGUAAUGGUGUAUAUAACGUGCCUUGGCAAGUCUUUUAUUGAUUUCUACUCCUAGCGAUUUAAAAUGCUGGUACAGCUUACCCUUGG
.((((((((((((((..............(((.(((((.......))))))))...((((((........))))))))))).))))))))). (-15.02 = -15.40 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:15 2006