Locus 5342

Sequence ID 2L_DroMel_CAF1
Location 15,128,210 – 15,128,343
Length 133
Max. P 0.987588
window8485 window8486 window8487

overview

Window 5

Location 15,128,210 – 15,128,314
Length 104
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 75.07
Mean single sequence MFE -41.57
Consensus MFE -31.97
Energy contribution -32.30
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.49
Structure conservation index 0.77
SVM decision value 1.22
SVM RNA-class probability 0.932433
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15128210 104 - 22407834
GGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAGUCCCACACCUGGCAU-------------UCGAGGUUAAUAAUUUAUUCGUC---
.(((((((...((((.....))(((((............((((((....))))))(((((.......)))))..)))))..-------------.)).)))))))............--- ( -37.70)
>DroSec_CAF1 72779 114 - 1
GGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAAAGAGAGCGUGGGUUGGAAUACCACACCUGGCAGAAGCGCACACCUGGCAAGGUUC---AAUUAUGCGUU---
((((((((..((........))(((((......((((((((((((....))))))..(((((((....))).))))..))).)))......)))))..)).))---)))).......--- ( -41.00)
>DroYak_CAF1 88261 112 - 1
GGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCCCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCAAGG-----UAGGUGGGUGGUUCC---CCUUAUCCCUUUAG
....((((....)))).((((.(((((............((((((....))))))(((((.......)))))..)))))..((-----((((.(((.....))---)))))))))))... ( -46.00)
>consensus
GGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAAUCCCACACCUGGCAA________A__UGGCAAGGUUC___AAUUAUCCGUU___
....((((....))))......(((((............((((((....))))))(((((.......)))))..)))))......................................... (-31.97 = -32.30 +   0.33)

alignment

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secondary structure

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dotplot

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Window 6

Location 15,128,234 – 15,128,343
Length 109
Sequences 3
Columns 109
Reading direction forward
Mean pairwise identity 87.77
Mean single sequence MFE -33.87
Consensus MFE -31.09
Energy contribution -31.20
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -2.18
Structure conservation index 0.92
SVM decision value 1.29
SVM RNA-class probability 0.938466
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15128234 109 + 22407834
UGCCAGGUGUGGGACUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUGUGAAAUAUCUAACUUUAAAAUUA
.((((((((((((.......)))))(((((.((....))...)))))....)))))))...(((((...(.(((((.....))))).).....)))))........... ( -35.70)
>DroSec_CAF1 72813 109 + 1
UGCCAGGUGUGGUAUUCCAACCCACGCUCUCUUUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUAUGAAAAAUCUCACUUUCAAAUUA
.(((((((((((.........))))((((((....)))).(((((.......))))).))....(.((....)).).)))))))..(((((........)))))..... ( -30.50)
>DroYak_CAF1 88293 109 + 1
UGCCAGGUGUGGGGUUCGAACCCACGCUCUCUCACGAGAACCAGGGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUACAAAGAAAGAAACUUUCACAGUU
.((((((((((((.......))))).........((((....((((((.......))).))).......))))....)))))))......(((((...)))))...... ( -35.40)
>consensus
UGCCAGGUGUGGGAUUCGAACCCACGCUCUCUCUCGAGAACCAGAGCUUAAAUCUGGCGCCUUAGACCGCUCGGCCAACCUGGCUAUGAAAAAUCUAACUUUCAAAUUA
.((((((((((((.......)))))((((((....)))).(((((.......))))).))....(.((....)).).)))))))......................... (-31.09 = -31.20 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,128,234 – 15,128,343
Length 109
Sequences 3
Columns 109
Reading direction reverse
Mean pairwise identity 87.77
Mean single sequence MFE -42.53
Consensus MFE -39.03
Energy contribution -39.70
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -3.05
Structure conservation index 0.92
SVM decision value 2.09
SVM RNA-class probability 0.987588
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15128234 109 - 22407834
UAAUUUUAAAGUUAGAUAUUUCACAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAGUCCCACACCUGGCA
.........................(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......)))))))))))). ( -41.70)
>DroSec_CAF1 72813 109 - 1
UAAUUUGAAAGUGAGAUUUUUCAUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAAAGAGAGCGUGGGUUGGAAUACCACACCUGGCA
.....((((((......))))))..(((((((.((((....))))....((((((((.......))))))((((....))))))((((.........))))))))))). ( -42.70)
>DroYak_CAF1 88293 109 - 1
AACUGUGAAAGUUUCUUUCUUUGUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCCCUGGUUCUCGUGAGAGAGCGUGGGUUCGAACCCCACACCUGGCA
.((...(((((...)))))...)).(((((((.((((....))))....(((((((.........)))))((((....))))))(((((.......)))))))))))). ( -43.20)
>consensus
UAAUUUGAAAGUUAGAUUUUUCAUAGCCAGGUUGGCCGAGCGGUCUAAGGCGCCAGAUUUAAGCUCUGGUUCUCGAGAGAGAGCGUGGGUUCGAAUCCCACACCUGGCA
.........................(((((((.((((....))))....((((((((.......))))))((((....))))))(((((.......)))))))))))). (-39.03 = -39.70 +   0.67)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:51 2006