Locus 2485

Sequence ID 3R_DroMel_CAF1
Location 6,815,660 – 6,815,809
Length 149
Max. P 0.992013
window4067 window4068 window4069

overview

Window 7

Location 6,815,660 – 6,815,769
Length 109
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 96.86
Mean single sequence MFE -36.55
Consensus MFE -31.95
Energy contribution -32.20
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.56
Structure conservation index 0.87
SVM decision value 0.96
SVM RNA-class probability 0.889252
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6815660 109 + 27905053
UCUCGAUGGGGAAAGCGGAGUG-----AAGCGAAAUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCU
((((....)))).(((((.(((-----(((.(.(((......((((((((((((.....))).))))))))).....))).)))))))((((((((.....))))))))))))) ( -36.90)
>DroSec_CAF1 74811 109 + 1
UCUCGAUGGGGAAAGCGGAGUG-----AAGCGAAAUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCU
((((....)))).(((((.(((-----(((.(.(((......((((((((((((.....))).))))))))).....))).)))))))((((((((.....))))))))))))) ( -36.90)
>DroSim_CAF1 79921 109 + 1
UCUCGAUGGGGAAAGCGGAGUG-----AAGCGAAAUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCU
((((....)))).(((((.(((-----(((.(.(((......((((((((((((.....))).))))))))).....))).)))))))((((((((.....))))))))))))) ( -36.90)
>DroEre_CAF1 59716 114 + 1
UCUCGAUGGGAAAAGCGGAGUGAAGUGAAGCGAAAUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCA
(((.....)))...((((......((((((.(.(((......((((((((((((.....))).))))))))).....))).)))))))((((((((.....)))))))))))). ( -35.50)
>consensus
UCUCGAUGGGGAAAGCGGAGUG_____AAGCGAAAUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCU
((((....))))..(((((((........((.(((((.....))))).)).((((((........)))))).))).............((((((((.....)))))))))))). (-31.95 = -32.20 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,815,689 – 6,815,809
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.33
Mean single sequence MFE -33.22
Consensus MFE -32.16
Energy contribution -31.60
Covariance contribution -0.56
Combinations/Pair 1.09
Mean z-score -1.62
Structure conservation index 0.97
SVM decision value 2.30
SVM RNA-class probability 0.992013
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6815689 120 + 27905053
AUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCUGGCUUGAGUUUUUCUCCGCUCGGGUUUUUCCGCUUCUCGU
..((((((((((((((((((.....))).)))))))).................((((((((.....))))))))(((..(((..(((.....))).))))))))))))).......... ( -34.90)
>DroSec_CAF1 74840 120 + 1
AUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCUCGCUUGAGUUUUCCUCUGCUCGGGGUUUUCCGCUUCUCUU
..(.(((((.(..(((((...(.(((((...((((((((.((((.....)))).((((((((.....))))))))....))))))))))))).).)))))..).))))).)......... ( -34.70)
>DroSim_CAF1 79950 120 + 1
AUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCUCGCUUGAGUUUUCCUCUGCUCGGGUUUUUCCGCUUCUCGU
..(((((((.(..(((((...(.(((((...((((((((.((((.....)))).((((((((.....))))))))....))))))))))))).).)))))..)))))))).......... ( -35.50)
>DroEre_CAF1 59750 120 + 1
AUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCACGCUUAAGUUUUCCUCUGCUUGGGUUUUUCCGCUUCUCUU
..(((((.((((((((((((.....))).)))))))))................((((((((.....))))))))......((((((((........))))))))))))).......... ( -31.60)
>DroYak_CAF1 72886 120 + 1
AUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGUCCGUUCACUUAAGUUUUCCUCUGCUUGGGUUUUUCCGCUACUCCU
..(((((.((((((((((((.....))).)))))))))................((((((((.....))))))))......((((((((........))))))))))))).......... ( -29.40)
>consensus
AUGAAAAACGUUUGGCAGUUUGAAAAGCAUGUCAAGCGACUAAAUUACCUUUAUGCUGGGUGCCACUCACUCAGCCCGCUCGCUUGAGUUUUCCUCUGCUCGGGUUUUUCCGCUUCUCGU
..(((((.((((((((((((.....))).)))))))))................((((((((.....))))))))......((((((((........))))))))))))).......... (-32.16 = -31.60 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,815,689 – 6,815,809
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.33
Mean single sequence MFE -33.40
Consensus MFE -30.62
Energy contribution -30.70
Covariance contribution 0.08
Combinations/Pair 1.10
Mean z-score -1.47
Structure conservation index 0.92
SVM decision value 1.27
SVM RNA-class probability 0.938342
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6815689 120 - 27905053
ACGAGAAGCGGAAAAACCCGAGCGGAGAAAAACUCAAGCCAGCGGGCUGAGUGAGUGGCACCCAGCAUAAAGGUAAUUUAGUCGCUUGACAUGCUUUUCAAACUGCCAAACGUUUUUCAU
..(((((((((......))(.((((......(((((.(((....))))))))(((.((((.((........)).......(((....))).)))).)))...)))))....))))))).. ( -33.00)
>DroSec_CAF1 74840 120 - 1
AAGAGAAGCGGAAAACCCCGAGCAGAGGAAAACUCAAGCGAGCGGGCUGAGUGAGUGGCACCCAGCAUAAAGGUAAUUUAGUCGCUUGACAUGCUUUUCAAACUGCCAAACGUUUUUCAU
..(((((((((......))(.((((..((((((((((((((....((((.(((.....))).)))).((((.....)))).))))))))...).)))))...)))))....))))))).. ( -36.50)
>DroSim_CAF1 79950 120 - 1
ACGAGAAGCGGAAAAACCCGAGCAGAGGAAAACUCAAGCGAGCGGGCUGAGUGAGUGGCACCCAGCAUAAAGGUAAUUUAGUCGCUUGACAUGCUUUUCAAACUGCCAAACGUUUUUCAU
..(((((((((......))(.((((..((((((((((((((....((((.(((.....))).)))).((((.....)))).))))))))...).)))))...)))))....))))))).. ( -36.60)
>DroEre_CAF1 59750 120 - 1
AAGAGAAGCGGAAAAACCCAAGCAGAGGAAAACUUAAGCGUGCGGGCUGAGUGAGUGGCACCCAGCAUAAAGGUAAUUUAGUCGCUUGACAUGCUUUUCAAACUGCCAAACGUUUUUCAU
..(((((((((......))..((((..((((.....(((((((((((.((.(((((...(((.........))).))))).))))))).))))))))))...)))).....))))))).. ( -35.80)
>DroYak_CAF1 72886 120 - 1
AGGAGUAGCGGAAAAACCCAAGCAGAGGAAAACUUAAGUGAACGGACUGAGUGAGUGGCACCCAGCAUAAAGGUAAUUUAGUCGCUUGACAUGCUUUUCAAACUGCCAAACGUUUUUCAU
..........(((((((....((((..((((((((((((((...(.(((.(((.....))).)))).((((.....)))).))))))))...).)))))...)))).....))))))).. ( -25.10)
>consensus
AAGAGAAGCGGAAAAACCCGAGCAGAGGAAAACUCAAGCGAGCGGGCUGAGUGAGUGGCACCCAGCAUAAAGGUAAUUUAGUCGCUUGACAUGCUUUUCAAACUGCCAAACGUUUUUCAU
..(((((((((......))..((((..(((((((((((((.((..((((.(((.....))).)))).((((.....)))))))))))))...).)))))...)))).....))))))).. (-30.62 = -30.70 +   0.08)

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 10:37:32 2006