Locus 454

Sequence ID 3R_DroMel_CAF1
Location 1,726,161 – 1,726,270
Length 109
Max. P 0.768367
window735 window736

overview

Window 5

Location 1,726,161 – 1,726,270
Length 109
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 90.80
Mean single sequence MFE -39.97
Consensus MFE -34.17
Energy contribution -33.95
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.18
Structure conservation index 0.85
SVM decision value 0.52
SVM RNA-class probability 0.768367
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1726161 109 + 27905053
GAUGCCUGGCAUCCAGCAGACAG-------CAUCCAGCAGCCGGGCGCCCAGGUGAGCUUUAAAAAUCAAUUAACCUUGAUUUUGCCACGGGCUUUAAGUCCACUGUGGGUUAAAU
...(((((((.((.....))..(-------(.....)).)))))))(((((((((..(((..((((((((......))))))))(((...)))...)))..)))).)))))..... ( -36.50)
>DroSec_CAF1 35290 116 + 1
GAUGCCCGGCAUCCAGGAGGCAGUAUCCAGCAUCCAGCAGCCGGGCGCCCAGGUGAGCUUUAAAAAUCAAUUAACCUUGAUUGUGCCACGGGCUUUAAGUCCACUGUGGGUUAAAU
...(((((((.....(((.......))).((.....)).)))))))(((((.(((.((......((((((......))))))..)))))((((.....))))....)))))..... ( -42.50)
>DroSim_CAF1 36411 112 + 1
GAUGCCCGGCAUCCAGCAGCCAGCAUCCAGCAUCCAGCAGCCGGGCGCCCAGGUGAGCUUUAAAAAUCAAUUAACCUUGAUUGUGCCACGGGCUUUAAGUCCACUGUGGGUU----
...(((((((.....((.....)).....((.....)).)))))))(((((.(((.((......((((((......))))))..)))))((((.....))))....))))).---- ( -40.90)
>consensus
GAUGCCCGGCAUCCAGCAGACAG_AUCCAGCAUCCAGCAGCCGGGCGCCCAGGUGAGCUUUAAAAAUCAAUUAACCUUGAUUGUGCCACGGGCUUUAAGUCCACUGUGGGUUAAAU
...(((((((.............................)))))))(((((.(((.((......((((((......))))))..)))))((((.....))))....)))))..... (-34.17 = -33.95 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 1,726,161 – 1,726,270
Length 109
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 90.80
Mean single sequence MFE -40.17
Consensus MFE -33.16
Energy contribution -33.50
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 0.83
SVM decision value -0.05
SVM RNA-class probability 0.509991
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 1726161 109 - 27905053
AUUUAACCCACAGUGGACUUAAAGCCCGUGGCAAAAUCAAGGUUAAUUGAUUUUUAAAGCUCACCUGGGCGCCCGGCUGCUGGAUG-------CUGUCUGCUGGAUGCCAGGCAUC
..........(((..(((....((((.(.(((((((((((......))))))))....((((....))))))))))))((.....)-------).)))..)))(((((...))))) ( -37.30)
>DroSec_CAF1 35290 116 - 1
AUUUAACCCACAGUGGACUUAAAGCCCGUGGCACAAUCAAGGUUAAUUGAUUUUUAAAGCUCACCUGGGCGCCCGGCUGCUGGAUGCUGGAUACUGCCUCCUGGAUGCCGGGCAUC
......((((..(((..(((...(((...)))..((((((......))))))....)))..))).)))).((((((((.(.(((.((........)).))).).).)))))))... ( -41.60)
>DroSim_CAF1 36411 112 - 1
----AACCCACAGUGGACUUAAAGCCCGUGGCACAAUCAAGGUUAAUUGAUUUUUAAAGCUCACCUGGGCGCCCGGCUGCUGGAUGCUGGAUGCUGGCUGCUGGAUGCCGGGCAUC
----..((((..(((..(((...(((...)))..((((((......))))))....)))..))).)))).(((((((..(..(..((..(...)..))..)..)..)))))))... ( -41.60)
>consensus
AUUUAACCCACAGUGGACUUAAAGCCCGUGGCACAAUCAAGGUUAAUUGAUUUUUAAAGCUCACCUGGGCGCCCGGCUGCUGGAUGCUGGAU_CUGCCUGCUGGAUGCCGGGCAUC
......((((..(((..(((...(((...)))..((((((......))))))....)))..))).)))).(((((((..(..(.................)..)..)))))))... (-33.16 = -33.50 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:43:35 2006