Locus 4309

Sequence ID 3R_DroMel_CAF1
Location 11,426,750 – 11,426,949
Length 199
Max. P 0.997510
window7024 window7025 window7026

overview

Window 4

Location 11,426,750 – 11,426,869
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.82
Mean single sequence MFE -27.22
Consensus MFE -26.92
Energy contribution -26.60
Covariance contribution -0.32
Combinations/Pair 1.06
Mean z-score -1.92
Structure conservation index 0.99
SVM decision value 2.87
SVM RNA-class probability 0.997510
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11426750 119 + 27905053
AGCAAAUAUUAAAUACAUUAAAACUGACAUGCGAGGUCGAGUCAAAUGAGUAAACAAAAUUCAAUUCGAGUUGUACUCAGAUUCA-AGCCACUUAAAUGGUCUUUGAUGUGGUAUUCCGC
.((...........((((((((...(((.......)))(((((...((((((.....(((((.....))))).))))))))))).-.((((......)))).))))))))((....)))) ( -24.70)
>DroSec_CAF1 174297 119 + 1
AGCAAAUAUUAAAUACAUUAAAACUGACAUGCGAGGUCGAGUCAAAUGAGUAAACAAAACUCUAUUCGAGUUGUACUCAGAUUCA-AGCCACUUAAAUGGACUUUGAUGUGGUAUUCCGC
.((.......................((((.((((((((((((...((((((.....(((((.....))))).))))))))))).-.....(......))))))))))))((....)))) ( -27.40)
>DroSim_CAF1 168515 119 + 1
AGCAAAUAUUAAAUACAUUAAAACUGACAUGCGAGGUCGAGUCAAAUGAGUAAACAAAACUCAAUUCGAGUUGUACUCAGAUUCA-AGCCACUUAAAUGGACUUUGAUGUGGUAUUCCGC
.((.......................((((.((((((((((((...((((((.....(((((.....))))).))))))))))).-.....(......))))))))))))((....)))) ( -27.50)
>DroEre_CAF1 163878 120 + 1
AGCAAAUAUUAAAUACAUUAAAACUGACAUGCGAGGUCGAGUCAAAUGAGUAAACAAAACUCAAUGCGAGUUGUACUCAGAUUCAAAGCCACUUAAAUGGACUUUGAUGUGGUAUUCCGC
.((.......................((((.((((((((((((...((((((.....(((((.....))))).))))))))))).......(......))))))))))))((....)))) ( -27.50)
>DroYak_CAF1 166612 119 + 1
AGCAAAUAUUAAAUACAUUAAAACUGACAUGCGAGGUCGAGUCAAAUGAGUAAACAAAACUCAAUGCGAGUUGUACUCAGAUUCA-AGCCACUUAAAUGGACUUUGAUGUGGCAUUCCGC
..............................(((..((.(((((...((((((.....(((((.....))))).))))))))))).-.((((((((((.....))))).)))))))..))) ( -29.00)
>consensus
AGCAAAUAUUAAAUACAUUAAAACUGACAUGCGAGGUCGAGUCAAAUGAGUAAACAAAACUCAAUUCGAGUUGUACUCAGAUUCA_AGCCACUUAAAUGGACUUUGAUGUGGUAUUCCGC
..............................(((..((.(((((...((((((.....(((((.....))))).)))))))))))...((((((((((.....))))).)))))))..))) (-26.92 = -26.60 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,426,790 – 11,426,909
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.15
Mean single sequence MFE -29.38
Consensus MFE -27.02
Energy contribution -27.06
Covariance contribution 0.04
Combinations/Pair 1.03
Mean z-score -1.47
Structure conservation index 0.92
SVM decision value 1.01
SVM RNA-class probability 0.899921
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11426790 119 + 27905053
GUCAAAUGAGUAAACAAAAUUCAAUUCGAGUUGUACUCAGAUUCA-AGCCACUUAAAUGGUCUUUGAUGUGGUAUUCCGCUAACUUUCAGUCUGAGGAUUACCUAAGGACCCCAGGCCAU
(((...((((((.....(((((.....))))).))))))......-............((((((((....((((.(((.(..((.....))..).))).))))))))))))...)))... ( -29.00)
>DroSec_CAF1 174337 119 + 1
GUCAAAUGAGUAAACAAAACUCUAUUCGAGUUGUACUCAGAUUCA-AGCCACUUAAAUGGACUUUGAUGUGGUAUUCCGCUAACUUUCAGUCUGAGGAUUACCUAAGGACCCCAGGCCAU
((((((((((((.....(((((.....))))).))))))......-..(((......)))..))))))..((((.(((.(..((.....))..).))).))))...((.((...)))).. ( -28.40)
>DroSim_CAF1 168555 119 + 1
GUCAAAUGAGUAAACAAAACUCAAUUCGAGUUGUACUCAGAUUCA-AGCCACUUAAAUGGACUUUGAUGUGGUAUUCCGCUAACUUUCAGUCUGAGGAUUACCUAAGGACCCCAGGCCAU
((((((((((((.....(((((.....))))).))))))......-..(((......)))..))))))..((((.(((.(..((.....))..).))).))))...((.((...)))).. ( -28.50)
>DroEre_CAF1 163918 120 + 1
GUCAAAUGAGUAAACAAAACUCAAUGCGAGUUGUACUCAGAUUCAAAGCCACUUAAAUGGACUUUGAUGUGGUAUUCCGCUAACUUUCAGUCUGAGGAUUACCUAAGGACCCCAGGCCAU
......((((((.....(((((.....))))).))))))...(((((((((......))).))))))...((((.(((.(..((.....))..).))).))))...((.((...)))).. ( -32.00)
>DroYak_CAF1 166652 119 + 1
GUCAAAUGAGUAAACAAAACUCAAUGCGAGUUGUACUCAGAUUCA-AGCCACUUAAAUGGACUUUGAUGUGGCAUUCCGCCAACUUUCAGUCUGAGGAUUACCCAAGGACCCCAGGCCAU
(((...((.((((.(..(((((.....)))))...(((((((..(-(((((......))).)))(((..((((.....))))....))))))))))).)))).))..))).......... ( -29.00)
>consensus
GUCAAAUGAGUAAACAAAACUCAAUUCGAGUUGUACUCAGAUUCA_AGCCACUUAAAUGGACUUUGAUGUGGUAUUCCGCUAACUUUCAGUCUGAGGAUUACCUAAGGACCCCAGGCCAU
......((((((.....(((((.....))))).))))))...(((.(((((......))).)).)))...((((.(((.(..((.....))..).))).))))...((.((...)))).. (-27.02 = -27.06 +   0.04)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,426,830 – 11,426,949
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.76
Mean single sequence MFE -29.26
Consensus MFE -27.46
Energy contribution -27.14
Covariance contribution -0.32
Combinations/Pair 1.11
Mean z-score -1.32
Structure conservation index 0.94
SVM decision value 0.98
SVM RNA-class probability 0.893239
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11426830 119 - 27905053
AUCAUUACACUACCCACCCAUUUUAAUUGUUAAGCUCCAGAUGGCCUGGGGUCCUUAGGUAAUCCUCAGACUGAAAGUUAGCGGAAUACCACAUCAAAGACCAUUUAAGUGGCU-UGAAU
.................((((((.(((.(((..(((((((.....))))))).....((((.(((.(.(((.....))).).))).))))........))).))).))))))..-..... ( -28.10)
>DroSec_CAF1 174377 111 - 1
--------ACUACCCACCCAUUUUAAUUGUUAAGCUACAGAUGGCCUGGGGUCCUUAGGUAAUCCUCAGACUGAAAGUUAGCGGAAUACCACAUCAAAGUCCAUUUAAGUGGCU-UGAAU
--------.....................(((((((((((((((.((..(((.....((((.(((.(.(((.....))).).))).))))..)))..)).))))))..))))))-))).. ( -29.10)
>DroSim_CAF1 168595 111 - 1
--------ACUACCCACCCAUUUUAAUUGUUAAGCUUCAGAUGGCCUGGGGUCCUUAGGUAAUCCUCAGACUGAAAGUUAGCGGAAUACCACAUCAAAGUCCAUUUAAGUGGCU-UGAAU
--------....((((.((((((.....(.....)...))))))..)))).......((((.(((.(.(((.....))).).))).))))...((((.(.((((....))))))-))).. ( -25.80)
>DroEre_CAF1 163958 112 - 1
--------GCUUCCCACCCGUUUUAAUUGUUAAGCCCCAGAUGGCCUGGGGUCCUUAGGUAAUCCUCAGACUGAAAGUUAGCGGAAUACCACAUCAAAGUCCAUUUAAGUGGCUUUGAAU
--------.........................(((((((.....))))))).....((((.(((.(.(((.....))).).))).))))...((((((.((((....)))))))))).. ( -34.00)
>DroYak_CAF1 166692 111 - 1
--------GCUUCCCACCCGUUUUAAUUGUUAAGCCCCAGAUGGCCUGGGGUCCUUGGGUAAUCCUCAGACUGAAAGUUGGCGGAAUGCCACAUCAAAGUCCAUUUAAGUGGCU-UGAAU
--------.........................(((((((.....)))))))...((((((.(((.(.(((.....))).).))).)))).))((((.(.((((....))))))-))).. ( -29.30)
>consensus
________ACUACCCACCCAUUUUAAUUGUUAAGCUCCAGAUGGCCUGGGGUCCUUAGGUAAUCCUCAGACUGAAAGUUAGCGGAAUACCACAUCAAAGUCCAUUUAAGUGGCU_UGAAU
.................................(((((((.....))))))).....((((.(((.(.(((.....))).).))).))))...(((.((.((((....)))))).))).. (-27.46 = -27.14 +  -0.32)

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 11:25:35 2006