Locus 1508

Sequence ID X_DroMel_CAF1
Location 4,430,007 – 4,430,127
Length 120
Max. P 0.707105
window2437 window2438

overview

Window 7

Location 4,430,007 – 4,430,127
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.83
Mean single sequence MFE -28.06
Consensus MFE -23.72
Energy contribution -24.24
Covariance contribution 0.52
Combinations/Pair 1.06
Mean z-score -1.42
Structure conservation index 0.85
SVM decision value 0.37
SVM RNA-class probability 0.707105
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4430007 120 + 22224390
CAGCUGCCAAACAGCAGCAACAGGUUCAUCAACUUACCUCGACUGACGAUAAGAGCUAAAAACAUAUAGCAUAUAAGGUUGUGGAAGAACGGUAAUUUUCUUGCCACGCUAAUUUAAUGC
..(((((......))))).....((((.((.((..((((((.....))).....((((........))))......))).)).)).))))(((((.....)))))............... ( -26.70)
>DroSec_CAF1 32371 120 + 1
CAGCUGCCAAACAGCAGCAGCAGGUUCAUCAACUUGCCUCGACUGACGAUAAGAAUUUAAAACAUAUAGCAUAUAAGGCUGUGGAAGAACGGUAAUUUCCUUGCCACGCUAAUUUAAUGC
..(((((......)))))(((..((((.((..((((..(((.....)))))))...........((((((.......)))))))).))))(((((.....)))))..))).......... ( -29.00)
>DroSim_CAF1 33697 120 + 1
CAGCUGCCAAACAGCAGCAGCAGGUUCAUCAACUUGCCUCGACUGACGAUAAGAAUUUAAAACAUAUAGCAUAUAAGGCUGUGGAAGAACGGUAAUUUCCUUGCCACGCUAAUUUAAUGC
..(((((......)))))(((..((((.((..((((..(((.....)))))))...........((((((.......)))))))).))))(((((.....)))))..))).......... ( -29.00)
>DroEre_CAF1 33419 120 + 1
CAGCUGCCAAACGGCAGCAGCAGGUUCAUCAACUUACCUCGCCUGACGAUAAGAACUAAAAACAUAUAGCAUAUAAGGUUGUGGAAAAACGGUAAUUUCCUUGCCACGCUAAUUUAAUGC
..((((((....))))))(((...((((.((((((...(((.....)))......(((........)))......)))))))))).....(((((.....)))))..))).......... ( -27.00)
>DroYak_CAF1 32757 120 + 1
CAGCUGCCAAACGGCAGCAGCAGGUUCAUCAACUUACCUCCACUGACGAUAAGAGCUAAAAACAUAUAGCAUAUAAGGUUGUGGAAAAACUGUAAUUUCCUUGCCACGCUAAUUUAAUGC
..((((((....))))))(((((((..........))))...............((((........))))......(((...(((((........)))))..)))..))).......... ( -28.60)
>consensus
CAGCUGCCAAACAGCAGCAGCAGGUUCAUCAACUUACCUCGACUGACGAUAAGAACUAAAAACAUAUAGCAUAUAAGGUUGUGGAAGAACGGUAAUUUCCUUGCCACGCUAAUUUAAUGC
..(((((......)))))(((..((((.((..((((..(((.....)))))))...........((((((.......)))))))).))))(((((.....)))))..))).......... (-23.72 = -24.24 +   0.52)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,430,007 – 4,430,127
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.83
Mean single sequence MFE -31.57
Consensus MFE -31.60
Energy contribution -30.32
Covariance contribution -1.28
Combinations/Pair 1.14
Mean z-score -1.03
Structure conservation index 1.00
SVM decision value 0.21
SVM RNA-class probability 0.634522
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4430007 120 - 22224390
GCAUUAAAUUAGCGUGGCAAGAAAAUUACCGUUCUUCCACAACCUUAUAUGCUAUAUGUUUUUAGCUCUUAUCGUCAGUCGAGGUAAGUUGAUGAACCUGUUGCUGCUGUUUGGCAGCUG
(((....((((((((((.(((((........))))))))).(((......((((........)))).....(((.....))))))..)))))).....))).((((((....)))))).. ( -31.00)
>DroSec_CAF1 32371 120 - 1
GCAUUAAAUUAGCGUGGCAAGGAAAUUACCGUUCUUCCACAGCCUUAUAUGCUAUAUGUUUUAAAUUCUUAUCGUCAGUCGAGGCAAGUUGAUGAACCUGCUGCUGCUGUUUGGCAGCUG
(((....((((((((((.(((((........))))))))).(((((...(((.(((.............))).).))...)))))..)))))).....))).((((((....)))))).. ( -32.42)
>DroSim_CAF1 33697 120 - 1
GCAUUAAAUUAGCGUGGCAAGGAAAUUACCGUUCUUCCACAGCCUUAUAUGCUAUAUGUUUUAAAUUCUUAUCGUCAGUCGAGGCAAGUUGAUGAACCUGCUGCUGCUGUUUGGCAGCUG
(((....((((((((((.(((((........))))))))).(((((...(((.(((.............))).).))...)))))..)))))).....))).((((((....)))))).. ( -32.42)
>DroEre_CAF1 33419 120 - 1
GCAUUAAAUUAGCGUGGCAAGGAAAUUACCGUUUUUCCACAACCUUAUAUGCUAUAUGUUUUUAGUUCUUAUCGUCAGGCGAGGUAAGUUGAUGAACCUGCUGCUGCCGUUUGGCAGCUG
((.........((.((((..(((((........)))))............((((........)))).......)))).)).((((..........)))))).((((((....)))))).. ( -30.80)
>DroYak_CAF1 32757 120 - 1
GCAUUAAAUUAGCGUGGCAAGGAAAUUACAGUUUUUCCACAACCUUAUAUGCUAUAUGUUUUUAGCUCUUAUCGUCAGUGGAGGUAAGUUGAUGAACCUGCUGCUGCCGUUUGGCAGCUG
(((....((((((((((.(((((........))))))))).(((((...(((.(((.((.....))...))).).))...)))))..)))))).....))).((((((....)))))).. ( -31.20)
>consensus
GCAUUAAAUUAGCGUGGCAAGGAAAUUACCGUUCUUCCACAACCUUAUAUGCUAUAUGUUUUUAGUUCUUAUCGUCAGUCGAGGUAAGUUGAUGAACCUGCUGCUGCUGUUUGGCAGCUG
(((....((((((((((.(((((........))))))))).(((((...(((.(((.............))).).))...)))))..)))))).....))).((((((....)))))).. (-31.60 = -30.32 +  -1.28)

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 10:11:36 2006