Locus 4658

Sequence ID 3L_DroMel_CAF1
Location 13,191,759 – 13,191,905
Length 146
Max. P 0.987329
window7322 window7323

overview

Window 2

Location 13,191,759 – 13,191,867
Length 108
Sequences 3
Columns 108
Reading direction reverse
Mean pairwise identity 96.28
Mean single sequence MFE -36.03
Consensus MFE -33.30
Energy contribution -33.63
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.64
Structure conservation index 0.92
SVM decision value 0.02
SVM RNA-class probability 0.542375
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13191759 108 - 23771897
CCUUUGAGGUGGGGCAUUGUCCUUAGCCACACCGCAGGCUGAAAAGCGGAGCGUGCACAACAACAAUCGCCAGCGAGACGCCGCAACAAGGCGAAAAAGAGAGGGUAA
(((((..((((.(((..........))).))))(((.(((.........))).)))..........(((((.(((......))).....))))).....))))).... ( -33.30)
>DroSec_CAF1 43051 107 - 1
CCU-UGUGGUGGGGCAUUGUCCUUAGCCUCACCGCAGGCUGAAAAGCAAAGCGUGCGCAACAACAAUCGCCAGCGAGACGCCGCAACAAGGCGAAAAAGAGAGGGUAA
(((-(((((((((((..........))))))))))..(((....)))...((....))........(((((.(((......))).....)))))......)))).... ( -37.80)
>DroSim_CAF1 41460 107 - 1
CCU-UGUGGUGGGGCAUUGUCCUUAGCCUCACCGCAGGCUGAAAAGCGGAGCGUGCACAACAACAAUCGCCAGCGAGACGCCGCAACAAGGCGAAAAAGAGAGGGUAA
(((-(((((((((((..........))))))))))..((((....((((...((........))..))))))))....((((.......)))).......)))).... ( -37.00)
>consensus
CCU_UGUGGUGGGGCAUUGUCCUUAGCCUCACCGCAGGCUGAAAAGCGGAGCGUGCACAACAACAAUCGCCAGCGAGACGCCGCAACAAGGCGAAAAAGAGAGGGUAA
(((....((((((((..........))))))))(((.(((.........))).)))..........(((((.(((......))).....))))).......))).... (-33.30 = -33.63 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 13,191,799 – 13,191,905
Length 106
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 80.09
Mean single sequence MFE -38.33
Consensus MFE -29.81
Energy contribution -29.88
Covariance contribution 0.06
Combinations/Pair 1.11
Mean z-score -2.38
Structure conservation index 0.78
SVM decision value 2.08
SVM RNA-class probability 0.987329
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13191799 106 - 23771897
GGUUGCAGCUCUCCCCCCCCCCCCCCACUGCCUCCGCC---CCUU-----------UGAGGUGGGGCAUUGUCCUUAGCCACACCGCAGGCUGAAAAGCGGAGCGUGCACAACAACAAUC
.((((..((.((((...........((.((((.(((((---....-----------...))))))))).))...((((((........)))))).....)))).))...))))....... ( -34.40)
>DroSec_CAF1 43091 94 - 1
AGUUGCAGCUCC-C----------CUCCUGCCUCCGCC---CCU------------UGUGGUGGGGCAUUGUCCUUAGCCUCACCGCAGGCUGAAAAGCAAAGCGUGCGCAACAACAAUC
.(((((.((...-.----------((..(((.((.(((---...------------(((((((((((..........)))))))))))))).))...))).))...)))))))....... ( -35.40)
>DroSim_CAF1 41500 95 - 1
AGUUGGAGCUCCCC----------CUCCUGCCCCCGCC---CCU------------UGUGGUGGGGCAUUGUCCUUAGCCUCACCGCAGGCUGAAAAGCGGAGCGUGCACAACAACAAUC
.(((((.(((((..----------..............---..(------------(((((((((((..........))))))))))))(((....))))))))...).))))....... ( -38.20)
>DroYak_CAF1 42702 113 - 1
AGUGGCAGCUCCCCC----CC---CCCCUGCCCCCUCCUUCCCAUGAAGAAAGAGGUGAGGAGGGGCAUUGUCCUUAGCCUCACCGCAGGCUGAAAAGCGGAGCGUGCACAACAACAAUC
.((.((((((((...----..---...((((......((((....)))).....(((((((.(((((...)))))...)))))))))))(((....)))))))).)))...))....... ( -45.30)
>consensus
AGUUGCAGCUCCCC__________CCCCUGCCCCCGCC___CCU____________UGAGGUGGGGCAUUGUCCUUAGCCUCACCGCAGGCUGAAAAGCGGAGCGUGCACAACAACAAUC
.((.((((((((................((((.(((((.....................)))))))))..((..((((((........))))))...))))))).))))).......... (-29.81 = -29.88 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:49 2006