Locus 8642

Sequence ID 3L_DroMel_CAF1
Location 22,440,906 – 22,441,013
Length 107
Max. P 0.801001
window14161 window14162

overview

Window 1

Location 22,440,906 – 22,441,013
Length 107
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 91.48
Mean single sequence MFE -26.72
Consensus MFE -21.60
Energy contribution -22.10
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -1.90
Structure conservation index 0.81
SVM decision value 0.62
SVM RNA-class probability 0.801001
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22440906 107 + 23771897
UCAAAUGCCACCAAAAUCAAACGGAAAGCGCCACUUACGACUAAUGGCAUCA--------CGGCAUCGGUGGCAAGAUGCCACAUCCUGACACA-----GCUGCCUACCACCAGCAAACA
(((.(((((.((..........)).....((((.(((....)))))))....--------.)))))..(((((.....)))))....)))....-----((((........))))..... ( -25.80)
>DroSec_CAF1 12592 107 + 1
UCAAAGGCCACCAAAAUCAAAAGGAAAGCGCCACUUACGACUAAUGGCAUCA--------CGGCAUCGGUGGCAAGAUGCCACAUCCUGACACA-----ACUGCCUGCCACCAGCAAACA
.....(((.............((((....((((.(((....)))))))....--------.((((((........))))))...))))......-----.......)))........... ( -25.07)
>DroSim_CAF1 17139 107 + 1
UCAAAUGCCACCAAAAUCAAAAGGAAAGCGCCACUUACGACUAAUGGCAUCA--------CGGCAUCGGUGGCAAGAUGCCACAUCCUGACACA-----ACUGCCUGCCACCAGCAAACA
....(((((.((..........)).....((((.(((....)))))))....--------.))))).(((((((.((((...))))....((..-----..))..)))))))........ ( -24.70)
>DroEre_CAF1 19205 120 + 1
UCAAAUGCCACCAAAAUCAGAAGGAGAGCGCCACUUACGACUAAUGGCAUCACGGCAUCACGGCAUCGGUGGCAAGAUGCCACAUCCUGACACAUGUAUGCUGCCUGCCACCAGCAAACA
(((.(((((.((..........)).((..((((.(((....))))))).))..)))))...((((((........))))))......)))....(((.(((((........))))).))) ( -31.30)
>consensus
UCAAAUGCCACCAAAAUCAAAAGGAAAGCGCCACUUACGACUAAUGGCAUCA________CGGCAUCGGUGGCAAGAUGCCACAUCCUGACACA_____ACUGCCUGCCACCAGCAAACA
....(((((.((..........)).....((((.(((....))))))).............))))).(((((((.((((...))))......((.......))..)))))))........ (-21.60 = -22.10 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 22,440,906 – 22,441,013
Length 107
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 91.48
Mean single sequence MFE -38.13
Consensus MFE -33.01
Energy contribution -33.33
Covariance contribution 0.31
Combinations/Pair 1.03
Mean z-score -1.64
Structure conservation index 0.87
SVM decision value 0.52
SVM RNA-class probability 0.768428
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22440906 107 - 23771897
UGUUUGCUGGUGGUAGGCAGC-----UGUGUCAGGAUGUGGCAUCUUGCCACCGAUGCCG--------UGAUGCCAUUAGUCGUAAGUGGCGCUUUCCGUUUGAUUUUGGUGGCAUUUGA
.....((((((((((((((.(-----.(((.(((((((...))))))).))).).)))).--------...))))))))))..((((((.((((.((.....))....)))).)))))). ( -36.90)
>DroSec_CAF1 12592 107 - 1
UGUUUGCUGGUGGCAGGCAGU-----UGUGUCAGGAUGUGGCAUCUUGCCACCGAUGCCG--------UGAUGCCAUUAGUCGUAAGUGGCGCUUUCCUUUUGAUUUUGGUGGCCUUUGA
.....((((((((((((((..-----.(((.(((((((...))))))).)))...)))).--------...))))))))))..((((.(((.(...((..........)).)))))))). ( -34.90)
>DroSim_CAF1 17139 107 - 1
UGUUUGCUGGUGGCAGGCAGU-----UGUGUCAGGAUGUGGCAUCUUGCCACCGAUGCCG--------UGAUGCCAUUAGUCGUAAGUGGCGCUUUCCUUUUGAUUUUGGUGGCAUUUGA
.....((((((((((((((..-----.(((.(((((((...))))))).)))...)))).--------...))))))))))..((((((.((((.((.....))....)))).)))))). ( -38.80)
>DroEre_CAF1 19205 120 - 1
UGUUUGCUGGUGGCAGGCAGCAUACAUGUGUCAGGAUGUGGCAUCUUGCCACCGAUGCCGUGAUGCCGUGAUGCCAUUAGUCGUAAGUGGCGCUCUCCUUCUGAUUUUGGUGGCAUUUGA
.....((((((((((.((.((((.((((.(.((....(((((.....)))))...))))))))))).))..))))))))))..((((((.((((..............)))).)))))). ( -41.94)
>consensus
UGUUUGCUGGUGGCAGGCAGC_____UGUGUCAGGAUGUGGCAUCUUGCCACCGAUGCCG________UGAUGCCAUUAGUCGUAAGUGGCGCUUUCCUUUUGAUUUUGGUGGCAUUUGA
.....((((((((((((..........((((((.....))))))))))))))))..))...........(((((((((((...((((.((......)).))))...)))))))))))... (-33.01 = -33.33 +   0.31)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:21:09 2006