Locus 7470

Sequence ID 3L_DroMel_CAF1
Location 20,033,707 – 20,033,806
Length 99
Max. P 0.992846
window12144 window12145

overview

Window 4

Location 20,033,707 – 20,033,806
Length 99
Sequences 4
Columns 99
Reading direction forward
Mean pairwise identity 96.46
Mean single sequence MFE -33.58
Consensus MFE -33.40
Energy contribution -33.02
Covariance contribution -0.38
Combinations/Pair 1.07
Mean z-score -3.10
Structure conservation index 0.99
SVM decision value 2.36
SVM RNA-class probability 0.992846
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20033707 99 + 23771897
ACCACCCGACCACCCAAGCCAUUCAAAACCACCCACACACUUGUGCCAUCGACUGGCGCAGCCUUUAAAGGUCAAGAGUGCAGCCAGGGUGGUUUGCUU
.......((((((((..(((((((.................(((((((.....)))))))((((....))))...)))))..))..))))))))..... ( -33.30)
>DroSec_CAF1 848 99 + 1
ACCACCCGGCCACCCAAGCCAUUCAAAACCACCCACACACUUGUGCCAUCGACUGGCGCAGCCUUUAAAGGUCAAGAGUGCAGCCAGGGUGGUUCGCUU
((((((((((.......))).................(((((((((((.....)))))).((((....))))...)))))......)))))))...... ( -33.20)
>DroSim_CAF1 844 99 + 1
ACCACCCGACCACCCAAGCCAUUCAAAACCACCCACACACUUGUGCCAUCGACUGGCGCAGCCUUUAAAGGUCAAGAGUGCAGCCAGGGUGGUUCGCUU
......(((((((((..(((((((.................(((((((.....)))))))((((....))))...)))))..))..)))))).)))... ( -33.80)
>DroEre_CAF1 5021 97 + 1
ACCCGCCGACCACCCAAGCCAUUCAA-ACCACCCACACACUUGUGCCAUCGACUGGCGCAGCCUUUAAAGGUCAAGAGUGCAGCCAGGGUGGCUCG-UU
......(((((((((..(((((((..-..............(((((((.....)))))))((((....))))...)))))..))..)))))).)))-.. ( -34.00)
>consensus
ACCACCCGACCACCCAAGCCAUUCAAAACCACCCACACACUUGUGCCAUCGACUGGCGCAGCCUUUAAAGGUCAAGAGUGCAGCCAGGGUGGUUCGCUU
......(((((((((..(((((((.................(((((((.....)))))))((((....))))...)))))..))..)))))).)))... (-33.40 = -33.02 +  -0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 20,033,707 – 20,033,806
Length 99
Sequences 4
Columns 99
Reading direction reverse
Mean pairwise identity 96.46
Mean single sequence MFE -38.30
Consensus MFE -36.00
Energy contribution -36.38
Covariance contribution 0.38
Combinations/Pair 1.06
Mean z-score -1.52
Structure conservation index 0.94
SVM decision value 0.09
SVM RNA-class probability 0.578375
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20033707 99 - 23771897
AAGCAAACCACCCUGGCUGCACUCUUGACCUUUAAAGGCUGCGCCAGUCGAUGGCACAAGUGUGUGGGUGGUUUUGAAUGGCUUGGGUGGUCGGGUGGU
......(((((((.(((..(((((..(.((....(((((..(((((.....))))(((....)))..)..)))))....)))..))))))))))))))) ( -37.80)
>DroSec_CAF1 848 99 - 1
AAGCGAACCACCCUGGCUGCACUCUUGACCUUUAAAGGCUGCGCCAGUCGAUGGCACAAGUGUGUGGGUGGUUUUGAAUGGCUUGGGUGGCCGGGUGGU
......(((((((.(((..(((((..(.((....(((((..(((((.....))))(((....)))..)..)))))....)))..))))))))))))))) ( -40.50)
>DroSim_CAF1 844 99 - 1
AAGCGAACCACCCUGGCUGCACUCUUGACCUUUAAAGGCUGCGCCAGUCGAUGGCACAAGUGUGUGGGUGGUUUUGAAUGGCUUGGGUGGUCGGGUGGU
......(((((((.(((..(((((..(.((....(((((..(((((.....))))(((....)))..)..)))))....)))..))))))))))))))) ( -37.80)
>DroEre_CAF1 5021 97 - 1
AA-CGAGCCACCCUGGCUGCACUCUUGACCUUUAAAGGCUGCGCCAGUCGAUGGCACAAGUGUGUGGGUGGU-UUGAAUGGCUUGGGUGGUCGGCGGGU
..-((((((((((((((.(((..(((........)))..))))))).......((((....)))))))))))-)))..(((((.....)))))...... ( -37.10)
>consensus
AAGCGAACCACCCUGGCUGCACUCUUGACCUUUAAAGGCUGCGCCAGUCGAUGGCACAAGUGUGUGGGUGGUUUUGAAUGGCUUGGGUGGUCGGGUGGU
......(((((((.(((..(((((..(.((....(((((..(((((.....))))(((....)))..)..)))))....)))..))))))))))))))) (-36.00 = -36.38 +   0.38)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:00 2006