Locus 2606

Sequence ID 2R_DroMel_CAF1
Location 9,185,624 – 9,185,744
Length 120
Max. P 0.973663
window4293 window4294

overview

Window 3

Location 9,185,624 – 9,185,744
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.36
Mean single sequence MFE -26.68
Consensus MFE -23.73
Energy contribution -24.04
Covariance contribution 0.31
Combinations/Pair 1.17
Mean z-score -2.23
Structure conservation index 0.89
SVM decision value 1.72
SVM RNA-class probability 0.973663
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9185624 120 + 20766785
CGGUCUCUGAAGAACCAAUGUAUUAAACACGGUCUAAGCCAAAGCAUUGCAGAAGAAUUCUACAAAGCUAUGGCUAAGCUAGAAAAGAUGAGUGCAAAUGAAAAACUUAAGACUGAAUCU
.(((.((....))))).............((((((.(((((.(((.(((.(((.....))).))).))).))))).............(((((...........)))))))))))..... ( -28.00)
>DroSec_CAF1 69939 120 + 1
CGGUCUCUGAAGAACCAAUGCAUUAAACACGGUCUUAGCCAAAGUAUUGUAGAAGAAUUCUGCAAAGCUAAGGCUAAGCUAGAAAAUAUGAGUGCAAAUGAAAAGCUUAAGACAGAAUCU
..((((...(((...((.((((((......((.(((((((..(((.(((((((.....))))))).)))..)))))))))..........))))))..)).....))).))))....... ( -30.09)
>DroSim_CAF1 62285 120 + 1
CGGUCUCUGAAGAACCAAUGCAUUAAACACGGUCUUAGCCAAAGUAUUGUAGAAGAACUCUGCAAAGCUAAGGCUAAGCUAGAAAAUAUGAGUGCAAAUGAAAAGCUUAAGACAGAAUCU
..((((...(((...((.((((((......((.(((((((..(((.(((((((.....))))))).)))..)))))))))..........))))))..)).....))).))))....... ( -30.29)
>DroYak_CAF1 61393 120 + 1
GGGUCUGUAAAGAACCAAUGCAUUAAAGAAGGCCUUAACCAAAGUAUUGAAGAGGAAUUCUACAAAACGAAGGCUAAGCUAGAAAAAAUAAAUGCGAACGAAAAUCUUGAGCCAAAUUCU
((.(((....))).))..........((((..((((...(((....)))..))))..))))..........((((..((..............))...(((.....)))))))....... ( -18.34)
>consensus
CGGUCUCUGAAGAACCAAUGCAUUAAACACGGUCUUAGCCAAAGUAUUGUAGAAGAAUUCUACAAAGCUAAGGCUAAGCUAGAAAAUAUGAGUGCAAAUGAAAAGCUUAAGACAGAAUCU
.(((((....)).)))..((((((......((.(((((((..(((.(((((((.....))))))).)))..)))))))))..........))))))........................ (-23.73 = -24.04 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,185,624 – 9,185,744
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.36
Mean single sequence MFE -25.27
Consensus MFE -18.46
Energy contribution -19.77
Covariance contribution 1.31
Combinations/Pair 1.14
Mean z-score -1.64
Structure conservation index 0.73
SVM decision value 0.24
SVM RNA-class probability 0.650535
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9185624 120 - 20766785
AGAUUCAGUCUUAAGUUUUUCAUUUGCACUCAUCUUUUCUAGCUUAGCCAUAGCUUUGUAGAAUUCUUCUGCAAUGCUUUGGCUUAGACCGUGUUUAAUACAUUGGUUCUUCAGAGACCG
.......(((((..............................((.(((((.(((.(((((((.....))))))).))).))))).))(((((((.....))).))))......))))).. ( -30.00)
>DroSec_CAF1 69939 120 - 1
AGAUUCUGUCUUAAGCUUUUCAUUUGCACUCAUAUUUUCUAGCUUAGCCUUAGCUUUGCAGAAUUCUUCUACAAUACUUUGGCUAAGACCGUGUUUAAUGCAUUGGUUCUUCAGAGACCG
.......(((((..((.........))...............(((((((..((..(((.(((.....))).)))..))..)))))))(((((((.....))).))))......))))).. ( -26.00)
>DroSim_CAF1 62285 120 - 1
AGAUUCUGUCUUAAGCUUUUCAUUUGCACUCAUAUUUUCUAGCUUAGCCUUAGCUUUGCAGAGUUCUUCUACAAUACUUUGGCUAAGACCGUGUUUAAUGCAUUGGUUCUUCAGAGACCG
.......(((((..((.........))...............(((((((..((..(((.((((...)))).)))..))..)))))))(((((((.....))).))))......))))).. ( -25.70)
>DroYak_CAF1 61393 120 - 1
AGAAUUUGGCUCAAGAUUUUCGUUCGCAUUUAUUUUUUCUAGCUUAGCCUUCGUUUUGUAGAAUUCCUCUUCAAUACUUUGGUUAAGGCCUUCUUUAAUGCAUUGGUUCUUUACAGACCC
(((((((......))))))).....(((((............(((((((...((.(((.(((.....))).))).))...))))))).........)))))...((((.......)))). ( -19.40)
>consensus
AGAUUCUGUCUUAAGCUUUUCAUUUGCACUCAUAUUUUCUAGCUUAGCCUUAGCUUUGCAGAAUUCUUCUACAAUACUUUGGCUAAGACCGUGUUUAAUGCAUUGGUUCUUCAGAGACCG
.......(((((..............................(((((((..(((.(((.(((.....))).))).)))..)))))))(((((((.....))).))))......))))).. (-18.46 = -19.77 +   1.31)

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 10:34:18 2006