Locus 4350

Sequence ID X_DroMel_CAF1
Location 11,451,237 – 11,451,517
Length 280
Max. P 0.995222
window7146 window7147 window7148

overview

Window 6

Location 11,451,237 – 11,451,357
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 94.44
Mean single sequence MFE -41.65
Consensus MFE -40.22
Energy contribution -39.98
Covariance contribution -0.25
Combinations/Pair 1.13
Mean z-score -2.83
Structure conservation index 0.97
SVM decision value 2.55
SVM RNA-class probability 0.995222
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11451237 120 + 22224390
UGCGAACAGGAAGUCGUAGCUACCGAUAAAACGGCCAUCAAUACAAUCUUGGAAGCUGAUGUGCGUCGCACAGAGAUGCUAAAGAAGGCCGAUGAACUGGAGAAACAGUUUGUCGCUGGC
(((((........)))))((((.((((....(((((.((...(((.((..(....).)))))(((((.......)))))....)).)))))..((((((......)))))))))).)))) ( -36.10)
>DroSec_CAF1 5168 120 + 1
UGCGAACAGGAAGUCGUAGCUACCGAUAAAACGGCCAUCAAUACAAUCCUGGAAGCGGAUGUGCGUCGCACAGAGAUGCUAAAGAAGGCCGAUGAACUGGAGAAACAGUUUGUCGGUGGC
(((((........)))))(((((((((....(((((.((...(((.(((.(....)))))))(((((.......)))))....)).)))))..((((((......))))))))))))))) ( -45.80)
>DroEre_CAF1 8527 120 + 1
UGCGAACAGGAAGUCGUAGCUACCGACAAAACGGCCAUCGAUACAAUCCUGGAAGCGGAUGUGCGACGCACACAGAUGCUAAAGAAGGCCGAUGAGUUGGAGAAACAGUUUGUCGGUGGC
(((((........)))))((((((((((((.(((((.(((.((((.(((.(....))))))))))).(((......))).......)))))....(((.....)))..)))))))))))) ( -44.10)
>DroYak_CAF1 8699 120 + 1
UGCGAACAGGAAGUCGUUGCUACCGACAAAACGGCCAUCGAUACAAUCCUGGAAGCGGAUGUGCGACGCACACAGAUGCUAAAGAAGGCUGAUGAACUGGAGAAACAGUUUGUUGGUGGC
.((((........)))).(((((((((....(((((.(((.((((.(((.(....))))))))))).(((......))).......)))))..((((((......))))))))))))))) ( -40.60)
>consensus
UGCGAACAGGAAGUCGUAGCUACCGACAAAACGGCCAUCAAUACAAUCCUGGAAGCGGAUGUGCGACGCACACAGAUGCUAAAGAAGGCCGAUGAACUGGAGAAACAGUUUGUCGGUGGC
(((((........)))))(((((((((....(((((.((....((....))..((((..(((((...)))))....))))...)).)))))..((((((......))))))))))))))) (-40.22 = -39.98 +  -0.25)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,451,317 – 11,451,437
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.14
Mean single sequence MFE -38.70
Consensus MFE -35.80
Energy contribution -35.67
Covariance contribution -0.12
Combinations/Pair 1.19
Mean z-score -1.55
Structure conservation index 0.93
SVM decision value 0.31
SVM RNA-class probability 0.680727
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11451317 120 + 22224390
AAAGAAGGCCGAUGAACUGGAGAAACAGUUUGUCGCUGGCGAUUUGACGGUGCAGGAGGAGCUAAACGAUACCUUCGCGGAACUGAAAGCCAUUGGAGCCUACUCGGCGGAAGCCAGGGC
.....(((((((..(((((......)))))..))).((((.......((((.(.(((((..(.....)...)))))...).))))...)))).....)))).((((((....))).))). ( -39.90)
>DroSec_CAF1 5248 120 + 1
AAAGAAGGCCGAUGAACUGGAGAAACAGUUUGUCGGUGGCGAUUUGACUGUGCAGGAGGAGCUAAACGAUACCUUCGCGGAACUGAAAGCCAUUGGAGCCUACUCGGCGGAAGCCAGGGC
.....(((((((..(((((......)))))..)))(((((..((((..(.(((.(((((..(.....)...)))))))).)..)))).)))))....)))).((((((....))).))). ( -42.70)
>DroEre_CAF1 8607 120 + 1
AAAGAAGGCCGAUGAGUUGGAGAAACAGUUUGUCGGUGGCGAUUUAACUGUGCAGGAGGAGCUAAACGAUACCUUCGCAGAACUGAAAGCAAUUGGAGCGUACUCGGCGGAAGCCAGAGC
.......(((((..(..((......))..)..))))).(((.(((((.(((.(((..((((.((.....)).))))......)))...))).))))).))).((((((....))).))). ( -34.90)
>DroYak_CAF1 8779 120 + 1
AAAGAAGGCUGAUGAACUGGAGAAACAGUUUGUUGGUGGCGAUUUGACUGUGCAGGAGGAGCUAAACGAUACCUUCGCGGAACUGAAAGCCAUUGGAGCGUACUCGGCGGAAGCCAGAGC
.......(((...((((((......)))))).(..(((((..((((..(.(((.(((((..(.....)...)))))))).)..)))).)))))..))))...((((((....))).))). ( -37.30)
>consensus
AAAGAAGGCCGAUGAACUGGAGAAACAGUUUGUCGGUGGCGAUUUGACUGUGCAGGAGGAGCUAAACGAUACCUUCGCGGAACUGAAAGCCAUUGGAGCCUACUCGGCGGAAGCCAGAGC
.....(((((((..(((((......)))))..)))(((((..((((..(.(((.(((((..(.....)...)))))))).)..)))).)))))....)))).((((((....))).))). (-35.80 = -35.67 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,451,397 – 11,451,517
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.19
Mean single sequence MFE -41.65
Consensus MFE -38.45
Energy contribution -38.83
Covariance contribution 0.37
Combinations/Pair 1.12
Mean z-score -1.45
Structure conservation index 0.92
SVM decision value 0.29
SVM RNA-class probability 0.668775
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11451397 120 + 22224390
AACUGAAAGCCAUUGGAGCCUACUCGGCGGAAGCCAGGGCACGAAGAAUCCUUGCCGGUUUGGGUUUCAGCAAAGAGAUGCAGGACAGGCCGACGAACAAAUUCUCCGGAGGCUGGCGCA
........(((..(((((((((..((((....)))..((((.(.......).)))).)..)))))))))(((......)))......((((..((...........))..)))))))... ( -40.40)
>DroSec_CAF1 5328 120 + 1
AACUGAAAGCCAUUGGAGCCUACUCGGCGGAAGCCAGGGCACGCAGAAUCCUUGCCGGUUUGGGUUUCAGCAAAGAGAUGCAGGACAGGCCGACGAACAAAUUCUCCGGAGGCUGGCGCA
........(((..(((((((((..((((....)))..((((...((....)))))).)..)))))))))(((......)))......((((..((...........))..)))))))... ( -39.70)
>DroEre_CAF1 8687 120 + 1
AACUGAAAGCAAUUGGAGCGUACUCGGCGGAAGCCAGAGCACGAAGAAUCCUUGCCGGUUUGGGUUUCAGCAAAGAAAUGCAGGAUAGGCCCACCAACAAAUUCUCUGGUGGCUGGCGCA
........((....(((.(((.((((((....))).))).))).....)))..(((((((((.(((((......))))).))))......((((((..........))))))))))))). ( -42.20)
>DroYak_CAF1 8859 120 + 1
AACUGAAAGCCAUUGGAGCGUACUCGGCGGAAGCCAGAGCACGACGAAUUCUUGCUGGUUUGGGUUUCAGCAAAGAGAUGCAGGAUAGGCCCACCAAUAAAUUCUCUGGUGGCUGGCGCA
....(..((((((..((((((.((((((....))).))).)))........(((.((((..(((((((.(((......)))..))..))))))))).)))...)))..))))))..)... ( -44.30)
>consensus
AACUGAAAGCCAUUGGAGCCUACUCGGCGGAAGCCAGAGCACGAAGAAUCCUUGCCGGUUUGGGUUUCAGCAAAGAGAUGCAGGACAGGCCCACCAACAAAUUCUCCGGAGGCUGGCGCA
....(..((((((((((((((.((((((....))).))).)))..........(((..((((.(((((......))))).))))...))).............)))))))))))..)... (-38.45 = -38.83 +   0.37)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:50 2006