Locus 3823

Sequence ID 3R_DroMel_CAF1
Location 10,419,363 – 10,419,494
Length 131
Max. P 0.944796
window6122 window6123

overview

Window 2

Location 10,419,363 – 10,419,460
Length 97
Sequences 3
Columns 102
Reading direction reverse
Mean pairwise identity 91.18
Mean single sequence MFE -29.53
Consensus MFE -26.77
Energy contribution -27.10
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.91
SVM decision value 0.28
SVM RNA-class probability 0.666613
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10419363 97 - 27905053
UGGGCAGCCACUGGAGGAGUC-----AACAGGGGGGAAAACCCCAGAAGGGAGGACUUUUGGGGCAUGAAAAUGGAGUAGCAGGCAAAGGGGAGUGAACGCC
..(((.(((.(((........-----..))).........(((((((((......)))))))))(((....)))........)))........(....)))) ( -28.00)
>DroSec_CAF1 82773 102 - 1
UGGGCAGCCGCUGGAGGAGUCGGGGGAGCAAGGGGAAAACCCCCAGAAGGGAGGACUUUUGGGGCAUGGAAAUGGAGGAGCAGGCAAAGGGGAGUGAACGCC
..(((.(((.((.((....)).))...((...........(((((((((......)))))))))(((....))).....)).)))........(....)))) ( -30.50)
>DroSim_CAF1 70481 102 - 1
UGGGCAGCCGCUGGAGGAGUCGGGGGAGCAAGGGGAAAAUCCCCAGAAGGGAGGACUUUUGGGGCAUGGAAAUGGAGGAGCGGGCAAAGGGGAGUGAACGCC
..(((.(((.((.((....)).))...((...........(((((((((......)))))))))(((....))).....)).)))........(....)))) ( -30.10)
>consensus
UGGGCAGCCGCUGGAGGAGUCGGGGGAGCAAGGGGAAAAACCCCAGAAGGGAGGACUUUUGGGGCAUGGAAAUGGAGGAGCAGGCAAAGGGGAGUGAACGCC
..(((.((((((............................(((((((((......)))))))))(((....)))....))).)))........(....)))) (-26.77 = -27.10 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,419,388 – 10,419,494
Length 106
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 83.88
Mean single sequence MFE -31.70
Consensus MFE -26.60
Energy contribution -27.10
Covariance contribution 0.50
Combinations/Pair 1.04
Mean z-score -2.13
Structure conservation index 0.84
SVM decision value 1.35
SVM RNA-class probability 0.944796
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10419388 106 - 27905053
CAAACGUGAUGCAAAGCUGCGAGGUAAAGGUUGUUGGGCAGCCACUGGAGGAGUC-----AACAGGGGGGAAAACCCCAGAAGGGAGGACUUUUGGGGCAUGAAAAUGGAG---
....(.((.((....(((.(..(((...(((((.....))))))))...).))))-----).)).)........(((((((((......)))))))))(((....)))...--- ( -29.10)
>DroSec_CAF1 82798 111 - 1
CAAACGUGAUGCAAAGCUUCGAGGUAAAGGUUGUUGGGCAGCCGCUGGAGGAGUCGGGGGAGCAAGGGGAAAACCCCCAGAAGGGAGGACUUUUGGGGCAUGGAAAUGGAG---
....((((.......(((((........(((((.....))))).((.((....)).)))))))...........(((((((((......))))))))))))).........--- ( -33.90)
>DroSim_CAF1 70506 111 - 1
CAAACGUGAUGCAAAGCUUCGAGGUAAAGGUUGUUGGGCAGCCGCUGGAGGAGUCGGGGGAGCAAGGGGAAAAUCCCCAGAAGGGAGGACUUUUGGGGCAUGGAAAUGGAG---
....((((.......(((((........(((((.....))))).((.((....)).)))))))...........(((((((((......))))))))))))).........--- ( -33.70)
>DroYak_CAF1 81026 97 - 1
CAAACGUGAUGCAAAGCUUCGAGGUAAAGG-----------CCGCUGGAGGAGUU------AGUUGGGGGAAAGCCCCAGAAGGGUGGACUUUUGGGGCAGGGAAAUGGAGUGG
((..(((..(.(....((((.((.(((...-----------((......))..))------).)).))))...((((((((((......)))))))))).).)..)))...)). ( -30.10)
>consensus
CAAACGUGAUGCAAAGCUUCGAGGUAAAGGUUGUUGGGCAGCCGCUGGAGGAGUC_____AACAAGGGGAAAAACCCCAGAAGGGAGGACUUUUGGGGCAUGGAAAUGGAG___
....((((.......(((((..(((...(((((.....))))))))...)))))....................(((((((((......)))))))))))))............ (-26.60 = -27.10 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:10:54 2006