Locus 1037

Sequence ID 3R_DroMel_CAF1
Location 3,231,051 – 3,231,249
Length 198
Max. P 0.999857
window1678 window1679 window1680

overview

Window 8

Location 3,231,051 – 3,231,147
Length 96
Sequences 5
Columns 96
Reading direction forward
Mean pairwise identity 98.12
Mean single sequence MFE -25.62
Consensus MFE -25.04
Energy contribution -25.28
Covariance contribution 0.24
Combinations/Pair 1.03
Mean z-score -1.56
Structure conservation index 0.98
SVM decision value 1.57
SVM RNA-class probability 0.964786
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3231051 96 + 27905053
UUCCUGCCGCUGUUUCAGUUUUCUGCUGCUCAUUUGCAUGUGGCCUUGUACAAAAUGUUUUUUGUCAUUACCGUUGAAAGUCAGCUAAGCAGGGCA
.((((((.((((((((((......(((((......))).))((...((.((((((....))))))))...)).))))))..))))...)))))).. ( -26.30)
>DroSec_CAF1 55618 96 + 1
UUCCUGCCGCUGUUUCAGUUUUCUGCUGCUCAUUUGCAUGUGGCCUUGCACAAAAUGUUUUUUGUCAUUACCGUUGAAAGUCAGCUAAGCAGGGCA
.((((((.((((((((((......(((((......))).))((...((.((((((....))))))))...)).))))))..))))...)))))).. ( -26.30)
>DroSim_CAF1 57057 96 + 1
UUCCUGCCGCUGUUUCAGUUUUCUGCUGCUCAUUUGCAUGUGGCCUUGCACAAAAUGUUUUUUGUCAUUACCGUUGAAAGUCAGCUAAGCAGGGCA
.((((((.((((((((((......(((((......))).))((...((.((((((....))))))))...)).))))))..))))...)))))).. ( -26.30)
>DroEre_CAF1 50500 94 + 1
UUCCUGCCGCUGUUUCAGUUUUCUGCUGCUCAUUUGCAUGUGGCCUUGCGCAAAAUGUU-UUUGUCAUUACCGUUGAAAGUCAGCUAAGCAGGG-A
(((((((.((((((((((......(((((......))).))((...((.(((((.....-)))))))...)).))))))..))))...))))))-) ( -24.60)
>DroYak_CAF1 41638 95 + 1
UUCCUGCCGCUGUUUCAGUUUUCUGCUGCUCAUUUGCAUGUGGCCUUGCACAAAAUGUU-UUUGUCAUUACCGUUGAAAGUCAGCUAAGCAGGGCA
.((((((.((((((((((......(((((......))).))((...((.(((((.....-)))))))...)).))))))..))))...)))))).. ( -24.60)
>consensus
UUCCUGCCGCUGUUUCAGUUUUCUGCUGCUCAUUUGCAUGUGGCCUUGCACAAAAUGUUUUUUGUCAUUACCGUUGAAAGUCAGCUAAGCAGGGCA
.((((((.((((((((((......(((((......))).))((...((.((((((....))))))))...)).))))))..))))...)))))).. (-25.04 = -25.28 +   0.24) 

alignment

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secondary structure

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dotplot

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Window 9

Location 3,231,051 – 3,231,147
Length 96
Sequences 5
Columns 96
Reading direction reverse
Mean pairwise identity 98.12
Mean single sequence MFE -27.36
Consensus MFE -26.26
Energy contribution -26.46
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -2.91
Structure conservation index 0.96
SVM decision value 4.27
SVM RNA-class probability 0.999857
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3231051 96 - 27905053
UGCCCUGCUUAGCUGACUUUCAACGGUAAUGACAAAAAACAUUUUGUACAAGGCCACAUGCAAAUGAGCAGCAGAAAACUGAAACAGCGGCAGGAA
...((((((..((((..(((((..(((..((((((((....)))))).))..)))...(((......))).........))))))))))))))).. ( -28.20)
>DroSec_CAF1 55618 96 - 1
UGCCCUGCUUAGCUGACUUUCAACGGUAAUGACAAAAAACAUUUUGUGCAAGGCCACAUGCAAAUGAGCAGCAGAAAACUGAAACAGCGGCAGGAA
...((((((..((((..(((((..(((..((((((((....)))))).))..)))...(((......))).........))))))))))))))).. ( -28.20)
>DroSim_CAF1 57057 96 - 1
UGCCCUGCUUAGCUGACUUUCAACGGUAAUGACAAAAAACAUUUUGUGCAAGGCCACAUGCAAAUGAGCAGCAGAAAACUGAAACAGCGGCAGGAA
...((((((..((((..(((((..(((..((((((((....)))))).))..)))...(((......))).........))))))))))))))).. ( -28.20)
>DroEre_CAF1 50500 94 - 1
U-CCCUGCUUAGCUGACUUUCAACGGUAAUGACAAA-AACAUUUUGCGCAAGGCCACAUGCAAAUGAGCAGCAGAAAACUGAAACAGCGGCAGGAA
.-.((((((..((((..(((((..(((..((.((((-.....))))..))..)))...(((......))).........))))))))))))))).. ( -24.90)
>DroYak_CAF1 41638 95 - 1
UGCCCUGCUUAGCUGACUUUCAACGGUAAUGACAAA-AACAUUUUGUGCAAGGCCACAUGCAAAUGAGCAGCAGAAAACUGAAACAGCGGCAGGAA
...((((((..((((..(((((..(((..(((((((-.....))))).))..)))...(((......))).........))))))))))))))).. ( -27.30)
>consensus
UGCCCUGCUUAGCUGACUUUCAACGGUAAUGACAAAAAACAUUUUGUGCAAGGCCACAUGCAAAUGAGCAGCAGAAAACUGAAACAGCGGCAGGAA
...((((((..((((..(((((..(((..(((((((......))))).))..)))...(((......))).........))))))))))))))).. (-26.26 = -26.46 +   0.20) 

alignment

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secondary structure

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dotplot

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Window 0

Location 3,231,147 – 3,231,249
Length 102
Sequences 4
Columns 113
Reading direction forward
Mean pairwise identity 87.52
Mean single sequence MFE -32.23
Consensus MFE -24.20
Energy contribution -24.33
Covariance contribution 0.12
Combinations/Pair 1.00
Mean z-score -1.96
Structure conservation index 0.75
SVM decision value 0.67
SVM RNA-class probability 0.819223
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3231147 102 + 27905053
GCACAAAAGGAUGCCAAAGACAAAAGGGGAAGCUGAACUCGCAUCCGUAUCCGC-AUCCGCAACCGGGGAUGCAUCC----------GGGAGCAUCCGCAAAAAUGUCAACAA
........(((((((...((.......(((.((.......)).)))......((-((((.(....).)))))).)).----------..).))))))................ ( -28.00)
>DroSim_CAF1 57153 102 + 1
GCACAAAAGGAUGCCAAAGACAAAGGGGGAAGCUGCACUCGCAUCCGUAUCCGC-AUCCGCACCCGGGGAUGCAUCC----------GCGAGCAUCCGCAAAAAUGUCAACAA
(((........)))....((((..((((((.(((((....)))...)).)))((-....)).)))(.((((((....----------....)))))).).....))))..... ( -30.20)
>DroEre_CAF1 50594 113 + 1
GCACAAAAGGAUGCCAAAGACAAAAGGGGAAGCUGCACUCGCAUCCGUAUCCGCGAGUCGCAUUCGGGGAUGCAUCCGCGAGCAUCCGCGAGCAUCCGCAAAAAUGUCAACAA
(((........)))....((((...(.(((.(((((((((((..........)))))).))).(((.((((((........)))))).))))).))).).....))))..... ( -38.60)
>DroYak_CAF1 41733 106 + 1
GCACAAAAGGAUGCCAAAGACAAAAGGGGAAGCUGCACUCGCAUCCGUAUCCG-------CACCCGGGGAUGCAUCCGCAAGCAUCCGCGAGCAUCCGCAAAAAUGUCAACAA
........((((((...........(.(((.(((((....)))...)).))).-------)...((.((((((........)))))).)).))))))................ ( -32.10)
>consensus
GCACAAAAGGAUGCCAAAGACAAAAGGGGAAGCUGCACUCGCAUCCGUAUCCGC_AUCCGCACCCGGGGAUGCAUCC__________GCGAGCAUCCGCAAAAAUGUCAACAA
(.(((...((((((......(....).(((.((.......)).))))))))).............(.((((((.((((........)).)))))))).).....))))..... (-24.20 = -24.33 +   0.12) 

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 09:58:58 2006