Locus 3031

Sequence ID X_DroMel_CAF1
Location 8,103,432 – 8,103,546
Length 114
Max. P 0.998149
window4963 window4964

overview

Window 3

Location 8,103,432 – 8,103,546
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.67
Mean single sequence MFE -32.22
Consensus MFE -25.52
Energy contribution -25.56
Covariance contribution 0.04
Combinations/Pair 1.14
Mean z-score -3.24
Structure conservation index 0.79
SVM decision value 2.85
SVM RNA-class probability 0.997404
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8103432 114 + 22224390
-----CAACAAUAUGAAACAAA-AUGUUGUUGCCAUUUGGCCAAAUGCCACAGCAUAGCAACAACUUGGGGGAUUGGCAACAAAGUAAGCUGACUUAACUCUCUGAAAGUCAGCUACUCC
-----.............(((.-.((((((((((....)))...((((....)))))))))))..)))((((.(((....)))....(((((((((..........))))))))).)))) ( -33.20)
>DroSec_CAF1 8727 120 + 1
AGCAGCAACAAUAUGAAAAAAAAAAUUUGUUGCCAUUUGGCCAAAUGCCACAACACAGCAACAACUUGGGGGAUUGGCAACAAAGUAAGCUGACUUAACCCUCUGAAAGUCAGCUACUAC
..........................(((((((((..((((.....))))(..((.((......))))..)...)))))))))((((.((((((((..........)))))))))))).. ( -31.40)
>DroSim_CAF1 14002 119 + 1
AGCAGCAACAAUAUGAAACAAA-AUGUUGUUGCCAUUUGGCCAAAUGCCACAACACAGCAACAACUUGGGGGAUUGGCAACAAAGUAAGCUGACUUAACCCUCUGAAAGUCAGCUACUAC
....((((((((((........-))))))))))......(((((.(.((.(((............))))).).))))).....((((.((((((((..........)))))))))))).. ( -35.50)
>DroEre_CAF1 8257 117 + 1
GGCAGCAGCAAUAUGAAAUAAA-AUGCUGUUGCCAUUUGGCCAAAUGCCACAACACAGCAACAAGUUGG--GAUUGGCAACAAAGUAAGUUGACUUAACCCUCUGAGAGUCCACUGCUCU
((((((((((............-.)))))))))).....(((((...((.((((..........)))))--).))))).....((((.((.(((((..........))))).)))))).. ( -35.82)
>DroYak_CAF1 11730 117 + 1
AGCAGCAACAAUAUGAAAUAAA-AUGUUGUUGCCAUUUGGCCAAAUGCCACAGCACAGCAACAACUUAG--GAUUGGCAGCAAAGUAAGUUUAGUUAACCCACUGAAAGUCAACUACUCC
.((.((((((((((........-))))))))))....((((.....))))..))..............(--(((((((.....(((..(((.....)))..)))....)))))....))) ( -25.20)
>consensus
AGCAGCAACAAUAUGAAACAAA_AUGUUGUUGCCAUUUGGCCAAAUGCCACAACACAGCAACAACUUGGGGGAUUGGCAACAAAGUAAGCUGACUUAACCCUCUGAAAGUCAGCUACUCC
..........................(((((((((..((((.....))))........(((....)))......)))))))))((((.((((((((..........)))))))))))).. (-25.52 = -25.56 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,103,432 – 8,103,546
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.67
Mean single sequence MFE -37.52
Consensus MFE -30.48
Energy contribution -31.08
Covariance contribution 0.60
Combinations/Pair 1.10
Mean z-score -3.09
Structure conservation index 0.81
SVM decision value 3.02
SVM RNA-class probability 0.998149
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8103432 114 - 22224390
GGAGUAGCUGACUUUCAGAGAGUUAAGUCAGCUUACUUUGUUGCCAAUCCCCCAAGUUGUUGCUAUGCUGUGGCAUUUGGCCAAAUGGCAACAACAU-UUUGUUUCAUAUUGUUG-----
.(((((((((((((..........)))))))).)))))((((((((.....((((((.((..(......)..)))))))).....))))))))....-.................----- ( -37.70)
>DroSec_CAF1 8727 120 - 1
GUAGUAGCUGACUUUCAGAGGGUUAAGUCAGCUUACUUUGUUGCCAAUCCCCCAAGUUGUUGCUGUGUUGUGGCAUUUGGCCAAAUGGCAACAAAUUUUUUUUUUCAUAUUGUUGCUGCU
((((((((((((((..........))))))))....((((((((((.....((((((.((..(......)..)))))))).....))))))))))..................)))))). ( -41.60)
>DroSim_CAF1 14002 119 - 1
GUAGUAGCUGACUUUCAGAGGGUUAAGUCAGCUUACUUUGUUGCCAAUCCCCCAAGUUGUUGCUGUGUUGUGGCAUUUGGCCAAAUGGCAACAACAU-UUUGUUUCAUAUUGUUGCUGCU
((((((((((((((..........)))))))).....(((((((((.....((((((.((..(......)..)))))))).....)))))))))...-...............)))))). ( -40.70)
>DroEre_CAF1 8257 117 - 1
AGAGCAGUGGACUCUCAGAGGGUUAAGUCAACUUACUUUGUUGCCAAUC--CCAACUUGUUGCUGUGUUGUGGCAUUUGGCCAAAUGGCAACAGCAU-UUUAUUUCAUAUUGCUGCUGCC
..(((((..(.........(((....(.((((.......)))))....)--))...((((((((((....((((.....)))).))))))))))...-...........)..)))))... ( -34.70)
>DroYak_CAF1 11730 117 - 1
GGAGUAGUUGACUUUCAGUGGGUUAACUAAACUUACUUUGCUGCCAAUC--CUAAGUUGUUGCUGUGCUGUGGCAUUUGGCCAAAUGGCAACAACAU-UUUAUUUCAUAUUGUUGCUGCU
..((((((.(((....((((((((.....))))))))............--....(((((((((((....((((.....)))).)))))))))))..-.............))))))))) ( -32.90)
>consensus
GGAGUAGCUGACUUUCAGAGGGUUAAGUCAGCUUACUUUGUUGCCAAUCCCCCAAGUUGUUGCUGUGUUGUGGCAUUUGGCCAAAUGGCAACAACAU_UUUAUUUCAUAUUGUUGCUGCU
..((((((((((((..........)))))))).))))(((((((((.....((((((.((..(......)..)))))))).....))))))))).......................... (-30.48 = -31.08 +   0.60)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:23 2006