Locus 8265

Sequence ID 3R_DroMel_CAF1
Location 22,123,142 – 22,123,266
Length 124
Max. P 0.936876
window13327 window13328 window13329

overview

Window 7

Location 22,123,142 – 22,123,234
Length 92
Sequences 3
Columns 92
Reading direction reverse
Mean pairwise identity 99.28
Mean single sequence MFE -16.47
Consensus MFE -16.47
Energy contribution -16.47
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 1.00
SVM decision value 0.30
SVM RNA-class probability 0.677452
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22123142 92 - 27905053
ACAUCCACAUCCGCAUCCGCAUCCUUCUGCCCCAGCUUCUCCUUCGCCUCAUCCUGCACAUCCACUCAGCUCGGCGGUUGCCUUUAAUGCGA
...........(((((..(((.....(((((..((((........((........))..........)))).))))).))).....))))). ( -16.47)
>DroSec_CAF1 53259 92 - 1
ACAUCCACAUCCGCAUCCGCAUCCUUCUGCCCCAGCUCCUCCUUCGCCUCAUCCUGCACAUCCACUCAGCUCGGCGGUUGCCUUUAAUGCGA
...........(((((..(((.....(((((..((((........((........))..........)))).))))).))).....))))). ( -16.47)
>DroSim_CAF1 45851 92 - 1
ACAUCCACAUCCGCAUCCGCAUCCUUCUGCCCCAGCUCCUCCUUCGCCUCAUCCUGCACAUCCACUCAGCUCGGCGGUUGCCUUUAAUGCGA
...........(((((..(((.....(((((..((((........((........))..........)))).))))).))).....))))). ( -16.47)
>consensus
ACAUCCACAUCCGCAUCCGCAUCCUUCUGCCCCAGCUCCUCCUUCGCCUCAUCCUGCACAUCCACUCAGCUCGGCGGUUGCCUUUAAUGCGA
...........(((((..(((.....(((((..((((........((........))..........)))).))))).))).....))))). (-16.47 = -16.47 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,123,174 – 22,123,266
Length 92
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 87.75
Mean single sequence MFE -34.12
Consensus MFE -24.81
Energy contribution -24.88
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -1.62
Structure conservation index 0.73
SVM decision value 0.19
SVM RNA-class probability 0.627503
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22123174 92 + 27905053
----UGUG------------CAGGAUGAGGCGAAGG---AGAAGCUGG-GGCAGAAGGAUGCGGAUGCGGAUGUGGAUGUCCUAGGACGGCAACUUGUCCUGUGGCUCCUGC
----...(------------(((((...(.((.(((---(.((.((((-((((...(.((.((....)).)).)...))))))))...(....))).)))).)).))))))) ( -32.70)
>DroSec_CAF1 53291 92 + 1
----UGUG------------CAGGAUGAGGCGAAGG---AGGAGCUGG-GGCAGAAGGAUGCGGAUGCGGAUGUGGAUGUCCUAGGACGGCAACUUGUCCUGUGGCUCCUGC
----...(------------(((((...(.((.(((---(.((.((((-((((...(.((.((....)).)).)...))))))))...(....))).)))).)).))))))) ( -33.10)
>DroSim_CAF1 45883 92 + 1
----UGUG------------CAGGAUGAGGCGAAGG---AGGAGCUGG-GGCAGAAGGAUGCGGAUGCGGAUGUGGAUGUCCUAGGACGGCAACUUGUCCUGUGGCUCCUGC
----...(------------(((((...(.((.(((---(.((.((((-((((...(.((.((....)).)).)...))))))))...(....))).)))).)).))))))) ( -33.10)
>DroYak_CAF1 46028 112 + 1
UGGAUGUGGAAGUGGAAAUGCAGGAUGAGGCUAAGGAGGAGGAGCUGGAGGCAGAAGGAUGCGAGUGCGGAUGCGGAUGUCCUAGGACGGCAACUUGUCCUGUGGCUCCUGC
...................((((((....((((((((.(((..((((.(((((...(.((.((....)).)).)...)).)))....))))..))).)))).)))))))))) ( -37.60)
>consensus
____UGUG____________CAGGAUGAGGCGAAGG___AGGAGCUGG_GGCAGAAGGAUGCGGAUGCGGAUGUGGAUGUCCUAGGACGGCAACUUGUCCUGUGGCUCCUGC
.......................................(((((((((.((((...(.((.((....)).)).)...))))))(((((((....)))))))..))))))).. (-24.81 = -24.88 +   0.06)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,123,174 – 22,123,266
Length 92
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 87.75
Mean single sequence MFE -26.18
Consensus MFE -18.80
Energy contribution -18.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.80
Structure conservation index 0.72
SVM decision value 1.26
SVM RNA-class probability 0.936876
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22123174 92 - 27905053
GCAGGAGCCACAGGACAAGUUGCCGUCCUAGGACAUCCACAUCCGCAUCCGCAUCCUUCUGCC-CCAGCUUCU---CCUUCGCCUCAUCCUG------------CACA----
((((((((...((((.((((((..(((....)))................(((......))).-.)))))).)---)))..))....)))))------------)...---- ( -27.10)
>DroSec_CAF1 53291 92 - 1
GCAGGAGCCACAGGACAAGUUGCCGUCCUAGGACAUCCACAUCCGCAUCCGCAUCCUUCUGCC-CCAGCUCCU---CCUUCGCCUCAUCCUG------------CACA----
((((((((...((((..(((((..(((....)))................(((......))).-.)))))..)---)))..))....)))))------------)...---- ( -25.90)
>DroSim_CAF1 45883 92 - 1
GCAGGAGCCACAGGACAAGUUGCCGUCCUAGGACAUCCACAUCCGCAUCCGCAUCCUUCUGCC-CCAGCUCCU---CCUUCGCCUCAUCCUG------------CACA----
((((((((...((((..(((((..(((....)))................(((......))).-.)))))..)---)))..))....)))))------------)...---- ( -25.90)
>DroYak_CAF1 46028 112 - 1
GCAGGAGCCACAGGACAAGUUGCCGUCCUAGGACAUCCGCAUCCGCACUCGCAUCCUUCUGCCUCCAGCUCCUCCUCCUUAGCCUCAUCCUGCAUUUCCACUUCCACAUCCA
((((((((...((((..(((((..(((....)))....((....))....(((......)))...)))))..)))).....))....))))))................... ( -25.80)
>consensus
GCAGGAGCCACAGGACAAGUUGCCGUCCUAGGACAUCCACAUCCGCAUCCGCAUCCUUCUGCC_CCAGCUCCU___CCUUCGCCUCAUCCUG____________CACA____
(((((((....(((((........))))).(((........)))((....))...))))))).................................................. (-18.80 = -18.80 +   0.00)

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 13:07:16 2006