Locus 2970

Sequence ID 3R_DroMel_CAF1
Location 7,930,398 – 7,930,597
Length 199
Max. P 0.984653
window4776 window4777 window4778 window4779

overview

Window 6

Location 7,930,398 – 7,930,518
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.67
Mean single sequence MFE -23.78
Consensus MFE -22.50
Energy contribution -22.22
Covariance contribution -0.28
Combinations/Pair 1.10
Mean z-score -1.73
Structure conservation index 0.95
SVM decision value 1.98
SVM RNA-class probability 0.984653
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7930398 120 + 27905053
CCCCCUUACAAGGACUUACAAAUACCCAAUGCACCACAAAAAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGG
..((((((.(((((....................(((((((............)))))))((((......)))).))))))))))).........((((((((.........)))))))) ( -24.30)
>DroSec_CAF1 61979 120 + 1
CCCCCUUACAAGGACUUACAAAUACCCAAUGCACCACAAAAAUAAAUUCUCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGG
..((((((.(((((....................(((((((............)))))))((((......)))).))))))))))).........((((((((.........)))))))) ( -24.30)
>DroSim_CAF1 63815 120 + 1
CCCCCUUACAAGGACUUACAAAUACCCAAUGCACCACAAAAAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGG
..((((((.(((((....................(((((((............)))))))((((......)))).))))))))))).........((((((((.........)))))))) ( -24.30)
>DroEre_CAF1 62889 120 + 1
CCUUCUUACAAGGACUUACCAAUACCCAAUGCACCACAAAAAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGG
((((.....)))).................................(((((((......(((((......)))))......))))))).......((((((((.........)))))))) ( -22.70)
>DroYak_CAF1 64266 120 + 1
CUCCUCUACAAGGACUUACAAAUACCCAAUGCACCACAAAAAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGG
.((((.....))))................................(((((((......(((((......)))))......))))))).......((((((((.........)))))))) ( -23.30)
>consensus
CCCCCUUACAAGGACUUACAAAUACCCAAUGCACCACAAAAAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGG
..((((((.(((((....................(((((((............)))))))((((......)))).))))))))))).........((((((((.........)))))))) (-22.50 = -22.22 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 7,930,438 – 7,930,558
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 99.00
Mean single sequence MFE -28.30
Consensus MFE -28.02
Energy contribution -27.86
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.65
Structure conservation index 0.99
SVM decision value 1.63
SVM RNA-class probability 0.968683
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7930438 120 + 27905053
AAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGGUUUUAAUUGAAAAUGCAAACUCUGCCUUGAGCAAGCAGUG
......(((((((......(((((......)))))......)))))))...((((((((((((.........)))))))))))).........(((...(((......)))...)))... ( -30.90)
>DroSec_CAF1 62019 120 + 1
AAUAAAUUCUCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGGUUUUAAUUGAAAAUGCAAACUCUGCCUUGAGCAACCCGUG
......(((((((......(((((......)))))......)))))))...((((((((((((.........))))))))))))..(((..((.(((.....))).))...)))...... ( -25.40)
>DroSim_CAF1 63855 120 + 1
AAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGGUUUUAAUUGAAAAUGCAAACUCUGCCUUGAGCAACCCGUG
......(((((((......(((((......)))))......)))))))...((((((((((((.........))))))))))))..(((..((.(((.....))).))...)))...... ( -28.40)
>DroEre_CAF1 62929 120 + 1
AAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGGUUUUAAUUGAAAAUGCAAACUCUGCCUUGAGCAACCCGUG
......(((((((......(((((......)))))......)))))))...((((((((((((.........))))))))))))..(((..((.(((.....))).))...)))...... ( -28.40)
>DroYak_CAF1 64306 120 + 1
AAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGGUUUUAAUUGAAAAUGCAAACUCUGCCUUGAGCAACCCGUG
......(((((((......(((((......)))))......)))))))...((((((((((((.........))))))))))))..(((..((.(((.....))).))...)))...... ( -28.40)
>consensus
AAUAAAUUCCCUCUUUUGUGUUUGACUAAGCAAAUUCCUUUGAGGGAAAUCAAAACCGAUUUGAUUGCAGGCUAAAUCGGUUUUAAUUGAAAAUGCAAACUCUGCCUUGAGCAACCCGUG
......(((((((......(((((......)))))......)))))))...((((((((((((.........))))))))))))..(((..((.(((.....))).))...)))...... (-28.02 = -27.86 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 8

Location 7,930,438 – 7,930,558
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 99.00
Mean single sequence MFE -28.42
Consensus MFE -25.64
Energy contribution -26.04
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.90
SVM decision value 0.93
SVM RNA-class probability 0.884923
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7930438 120 - 27905053
CACUGCUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCAAAGGAAUUUGCUUAGUCAAACACAAAAGAGGGAAUUUAUU
...(((..((((......))))..))).....(((((((((((((((...........)))))))))))))))((((((....(..((((......))))..)....))))))....... ( -32.20)
>DroSec_CAF1 62019 120 - 1
CACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCAAAGGAAUUUGCUUAGUCAAACACAAAAGAGAGAAUUUAUU
...(((((.(((.(((((((............(((((((((((((((...........)))))))))))))))(((......))).))))))).((.....))......))))))))... ( -25.00)
>DroSim_CAF1 63855 120 - 1
CACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCAAAGGAAUUUGCUUAGUCAAACACAAAAGAGGGAAUUUAUU
.....((.((((......))))..))......(((((((((((((((...........)))))))))))))))((((((....(..((((......))))..)....))))))....... ( -28.30)
>DroEre_CAF1 62929 120 - 1
CACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCAAAGGAAUUUGCUUAGUCAAACACAAAAGAGGGAAUUUAUU
.....((.((((......))))..))......(((((((((((((((...........)))))))))))))))((((((....(..((((......))))..)....))))))....... ( -28.30)
>DroYak_CAF1 64306 120 - 1
CACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCAAAGGAAUUUGCUUAGUCAAACACAAAAGAGGGAAUUUAUU
.....((.((((......))))..))......(((((((((((((((...........)))))))))))))))((((((....(..((((......))))..)....))))))....... ( -28.30)
>consensus
CACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCAAAGGAAUUUGCUUAGUCAAACACAAAAGAGGGAAUUUAUU
.....((.((((......))))..))......(((((((((((((((...........)))))))))))))))((((((....(..((((......))))..)....))))))....... (-25.64 = -26.04 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 7,930,478 – 7,930,597
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.49
Mean single sequence MFE -31.42
Consensus MFE -27.80
Energy contribution -28.04
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.71
Structure conservation index 0.88
SVM decision value 1.21
SVM RNA-class probability 0.930765
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7930478 119 - 27905053
AUGGAAUAUCCCAAAGGGUUUGGAAA-AAAGUAAAGCCGGCACUGCUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCA
.(((......))).((((........-........((..((.((((((.....)))))).))..))......(((((((((((((((...........))))))))))))))).)))).. ( -33.80)
>DroSec_CAF1 62059 119 - 1
AUGGAAUAUCCCAAAGGGUUUGGAAA-AAAGUAAAGCCGGCACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCA
.(((......))).((((....((((-(..((((((((((((.....))))...)))....))))).)))))(((((((((((((((...........))))))))))))))).)))).. ( -30.60)
>DroSim_CAF1 63895 120 - 1
AUGGAAUAUCCCAAAGGGUUUGGAAAAAAAGUAAAGCCGGCACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCA
.(((......))).((((....(((((...((((((((((((.....))))...)))....))))).)))))(((((((((((((((...........))))))))))))))).)))).. ( -30.40)
>DroEre_CAF1 62969 120 - 1
AUGGAAUAUCCGAAAGGGCUCGGAAAAAAAGUAAAACCGGCACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCA
..((((..(((((......))))).......(((((((((....((((((...((((.(((((.(..(((......))).).))))).))))))))))...)))))))))..)))).... ( -31.70)
>DroYak_CAF1 64346 119 - 1
AUGGAAUAUCCCAAAGGGUUUGGAAA-AAAGUAAAGCCGGCACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCA
.(((......))).((((....((((-(..((((((((((((.....))))...)))....))))).)))))(((((((((((((((...........))))))))))))))).)))).. ( -30.60)
>consensus
AUGGAAUAUCCCAAAGGGUUUGGAAA_AAAGUAAAGCCGGCACGGGUUGCUCAAGGCAGAGUUUGCAUUUUCAAUUAAAACCGAUUUAGCCUGCAAUCAAAUCGGUUUUGAUUUCCCUCA
.(((......)))..(((...(((((.....(((((((((....((((((...((((.(((((.(..(((......))).).))))).))))))))))...))))))))).)))))))). (-27.80 = -28.04 +   0.24)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:03 2006