Locus 5265

Sequence ID 2R_DroMel_CAF1
Location 17,128,652 – 17,128,852
Length 200
Max. P 0.991123
window8411 window8412 window8413

overview

Window 1

Location 17,128,652 – 17,128,772
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.50
Mean single sequence MFE -40.92
Consensus MFE -36.02
Energy contribution -36.46
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.98
Structure conservation index 0.88
SVM decision value 2.25
SVM RNA-class probability 0.991123
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17128652 120 - 20766785
CCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGAGGCAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCCUGCAGCAGUACUUCCAGAAGAUUGUCAUGCUCACAAACUU
(((...((((((.((((.....)).)).))))))..))).(..((((...((((((.((..((((.(((((......))))))))).(......).)).))))))..))))..)...... ( -39.00)
>DroSec_CAF1 64545 120 - 1
CCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGGGGCAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCCUGCAGCAGUACUUCCAGAAGAUUGUCAUGCUCACAAACUU
(((...((((((.((((.....)).)).))))))..)))(((((......((((((.((..((((.(((((......))))))))).(......).)).))))))..)))))........ ( -39.60)
>DroSim_CAF1 55390 120 - 1
CCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGGGGCAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCCUGCAGCAGUACUUCCAGAAGAUUGUCAUGCUCACAAACUU
(((...((((((.((((.....)).)).))))))..)))(((((......((((((.((..((((.(((((......))))))))).(......).)).))))))..)))))........ ( -39.60)
>DroEre_CAF1 70073 120 - 1
CCAGAACACGCAGCGUUACAUUCGACGCUGCGUUGAUGGUGGAAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCCUGCAGCAGUACUUCCAGAAGAUUGUCAUGCUCACCAACUU
.......((((((((((......))))))))))...(((((..((((...((((((.((..((((.(((((......))))))))).(......).)).))))))..))))))))).... ( -43.60)
>DroYak_CAF1 71967 120 - 1
CCAAAACACGCAGCGCUACAUACGUCGCUGCGUGGAUGGAGGAAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCCUGCAGCAGUACUUUCAGAAGAUUGUCAUGCUCACAAACUU
(((...((((((((((.......).)))))))))..))).(..((((...((((((.((..((((.(((((......))))))))).(......).)).))))))..))))..)...... ( -42.80)
>consensus
CCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGAGGCAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCCUGCAGCAGUACUUCCAGAAGAUUGUCAUGCUCACAAACUU
(((...((((((.((((.....)).)).))))))..))).(..((((...((((((.((..((((.(((((......))))))))).(......).)).))))))..))))..)...... (-36.02 = -36.46 +   0.44)

alignment

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secondary structure

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dotplot

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Window 2

Location 17,128,692 – 17,128,812
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.75
Mean single sequence MFE -40.76
Consensus MFE -31.80
Energy contribution -32.24
Covariance contribution 0.44
Combinations/Pair 1.09
Mean z-score -1.63
Structure conservation index 0.78
SVM decision value 0.13
SVM RNA-class probability 0.600137
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17128692 120 - 20766785
CACUGCCCAAUACAAUCUUCGAGUUCUGGCUUAUGAUAUACCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGAGGCAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCC
...(((((..............(((((((...........)))))))..(((.((((.....)).)).)))((.(((((((((.((....)).).)))).)))).))..)).)))..... ( -36.10)
>DroSec_CAF1 64585 120 - 1
CGUUGCCCAAUACAAUCUUCGAGUUCUGGCUUAUGAUCUACCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGGGGCAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCC
..((((((....((((.(((..(((((((...........)))))))(((((.((((.....)).)).))))))))(((((((.((....)).))))))).))))....)).)))).... ( -39.80)
>DroSim_CAF1 55430 120 - 1
CGUUGCCCAAUACAAUCUUCGAGUUCUGGCUCAUGAUCUACCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGGGGCAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCC
.(((((((............((((....))))........(((...((((((.((((.....)).)).))))))..))))))))))....((..((((..........))))))...... ( -40.40)
>DroEre_CAF1 70113 120 - 1
CGUUGCCCAAUACUAUCUUCGAGUUCUGGCUAAUGAUCUACCAGAACACGCAGCGUUACAUUCGACGCUGCGUUGAUGGUGGAAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCC
.(((((....(((((((.....(((((((.((......)))))))))((((((((((......)))))))))).)))))))...))))).((..((((..........))))))...... ( -44.20)
>DroYak_CAF1 72007 120 - 1
CGCUGCCCAAUACGAUCUUCGAGUUCUGGCUAAUGAUCUACCAAAACACGCAGCGCUACAUACGUCGCUGCGUGGAUGGAGGAAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCC
.(((.(((.....((((....(((....)))...))))........((((((((((.......).)))))))))(((((((((.((....))..))))).))))....))))))...... ( -43.30)
>consensus
CGUUGCCCAAUACAAUCUUCGAGUUCUGGCUAAUGAUCUACCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGAGGCAGCAGCAGCAGUCCUCACGUUGACAGGGAGCAAAUCC
.(((.(((..............(((((((...........)))))))..(((.((((.....)).)).)))((.((((((((..((....))...)))).)))).)).))))))...... (-31.80 = -32.24 +   0.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 17,128,732 – 17,128,852
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.25
Mean single sequence MFE -43.32
Consensus MFE -37.78
Energy contribution -38.22
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.67
Structure conservation index 0.87
SVM decision value 1.46
SVM RNA-class probability 0.955671
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17128732 120 - 20766785
CCCGACUACGUGUCGAAGUGCUAUGUGGCCACGCAGGGUCCACUGCCCAAUACAAUCUUCGAGUUCUGGCUUAUGAUAUACCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGA
.(((.(((((..(((...(..((((((((...((.((((.....))))..............(((((((...........)))))))..))...)))))))).).)))..))))).))). ( -42.50)
>DroSec_CAF1 64625 120 - 1
CCCGACUACGUGUCGAAGUGCUAUGUGGCCACGCAGGGUCCGUUGCCCAAUACAAUCUUCGAGUUCUGGCUUAUGAUCUACCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGG
((((.(((((..(((...(..((((((((...((.((((.....))))..............(((((((...........)))))))..))...)))))))).).)))..))))).)))) ( -44.40)
>DroSim_CAF1 55470 120 - 1
CCCGACUACGUGUCGAAGUGCUAUGUGGCCACGCAGGGUCCGUUGCCCAAUACAAUCUUCGAGUUCUGGCUCAUGAUCUACCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGG
((((.(((((..(((...(..((((((((...((.((((.....))))..............(((((((...........)))))))..))...)))))))).).)))..))))).)))) ( -44.40)
>DroEre_CAF1 70153 120 - 1
CCCGACUACGUGUCGAAGUGCUAUGUGGCCACGCAGGGUCCGUUGCCCAAUACUAUCUUCGAGUUCUGGCUAAUGAUCUACCAGAACACGCAGCGUUACAUUCGACGCUGCGUUGAUGGU
..((((.....))))..(.((.(((.((((......))))))).)).)...((((((.....(((((((.((......)))))))))((((((((((......)))))))))).)))))) ( -45.20)
>DroYak_CAF1 72047 120 - 1
CCCGACUACGUGUCGAAGUGCUAUGUGGCCACGCAGGGUCCGCUGCCCAAUACGAUCUUCGAGUUCUGGCUAAUGAUCUACCAAAACACGCAGCGCUACAUACGUCGCUGCGUGGAUGGA
..((((.....))))..(.((...((((((......)).)))).)).).....((((....(((....)))...))))..(((...((((((((((.......).)))))))))..))). ( -40.10)
>consensus
CCCGACUACGUGUCGAAGUGCUAUGUGGCCACGCAGGGUCCGUUGCCCAAUACAAUCUUCGAGUUCUGGCUAAUGAUCUACCAGAACACGCAGCGCUACAUAAGACGGUGCGUGGAUGGA
.(((.((((((..((......((((((((...((.((((.....))))..............(((((((...........)))))))..))...))))))))...))..)))))).))). (-37.78 = -38.22 +   0.44)

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 11:40:36 2006