Locus 2708

Sequence ID 2R_DroMel_CAF1
Location 9,515,009 – 9,515,166
Length 157
Max. P 0.997420
window4476 window4477

overview

Window 6

Location 9,515,009 – 9,515,126
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.68
Mean single sequence MFE -29.28
Consensus MFE -28.22
Energy contribution -27.82
Covariance contribution -0.40
Combinations/Pair 1.14
Mean z-score -1.78
Structure conservation index 0.96
SVM decision value 2.86
SVM RNA-class probability 0.997420
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9515009 117 + 20766785
CGAAAA--UCAAAUUGCCUGGAAAAAGGGUGAAAAAGGUGGGGAAUAUGUUGAAUAUGAAAUU-UCUAGACGGAAAGAGCCCUAUCUCUGUUUGACUUGUUUUUGUUUGGUAUUCUUUAC
.(((.(--((((((......(((((..(((.(((.((((((((.((((.....))))....((-(((....)))))...))))))))...))).)))..)))))))))))).)))..... ( -25.70)
>DroSec_CAF1 12018 117 + 1
CGAAAA--UGAAAUUGCCUGGAAAAAGGGUGAAAAAGGUGGGGAAUAUGUUGAAUAUGAAAUU-GUUAGACGGAAAGAGCCCUAUCUCUGUUUGACUUGUUUUUGUUUGGUAUUCUUCAC
......--.....(..(((.......)))..).....((((((((((..(..((((.(((...-((((((((((..((......))))))))))))...))).))))..))))))))))) ( -30.20)
>DroSim_CAF1 12059 119 + 1
CGAAAAAUUCAAAUUGCCUGGAAAAAGGGUGAAAAAGGUGGGGAAUAUGUUGAAUAUGAAAUU-GUUAGACGGAAAGAGCCCUAUCUCUGUUUGACUUGUUUUUGUUUGGUAUUCUUUAC
.............(..(((.......)))..).....((((((((((..(..((((.(((...-((((((((((..((......))))))))))))...))).))))..))))))))))) ( -28.10)
>DroEre_CAF1 12294 118 + 1
CGAAAA--UCAAAUUGCCUGGAAAAAGGGUGAAAAAGGUGGAGAAUAUGUUGAAUAUGAAAUUUGCUAGACUGAAAGAGCCCUAUCUCUGUUUGGCUUGUUUUUGUUUGGUAUUCUUUAC
......--.....(..(((.......)))..).....((((((((((..(..((((.(((((..(((((((....((((......)))))))))))..)))))))))..))))))))))) ( -29.20)
>DroYak_CAF1 12153 118 + 1
CAAAAA--UCAAAUUGCCUGGAAAAAGGGUGAAAAAGGUGGAGAAUAUGUUGAAUAUGAAAUUUGCUAGGCAGAAGGAGCCCUAUCUCUGUUUGGCUUGUUUUUGUUUGGUAUUCUUUAC
......--.....(..(((.......)))..).....((((((((((..(..((((.(((((..(((((((((((((...)))...))))))))))..)))))))))..))))))))))) ( -33.20)
>consensus
CGAAAA__UCAAAUUGCCUGGAAAAAGGGUGAAAAAGGUGGGGAAUAUGUUGAAUAUGAAAUU_GCUAGACGGAAAGAGCCCUAUCUCUGUUUGACUUGUUUUUGUUUGGUAUUCUUUAC
.............(..(((.......)))..).....((((((((((..(..((((.(((((..((((((((((..((......))))))))))))..)))))))))..))))))))))) (-28.22 = -27.82 +  -0.40)

alignment

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secondary structure

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dotplot

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Window 7

Location 9,515,047 – 9,515,166
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.57
Mean single sequence MFE -28.91
Consensus MFE -25.35
Energy contribution -25.31
Covariance contribution -0.04
Combinations/Pair 1.11
Mean z-score -1.37
Structure conservation index 0.88
SVM decision value 0.63
SVM RNA-class probability 0.804599
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9515047 119 + 20766785
GGGAAUAUGUUGAAUAUGAAAUU-UCUAGACGGAAAGAGCCCUAUCUCUGUUUGACUUGUUUUUGUUUGGUAUUCUUUACUUGAUUUCAUACCCGUCACACGAACAUUACGUAGGGUAUA
.(((((..((.((((((.((((.-.(.((.((((.((((......)))).)))).)).).....)))).))))))...))...)))))((((((.....(((.......))).)))))). ( -24.50)
>DroSec_CAF1 12056 119 + 1
GGGAAUAUGUUGAAUAUGAAAUU-GUUAGACGGAAAGAGCCCUAUCUCUGUUUGACUUGUUUUUGUUUGGUAUUCUUCACUUGAUUUUAUACCCGUCACACGAACAUUACGUAGGGUAUA
.(((..(((..(((((.(((...-((((((((((..((......))))))))))))...))).)))))..)))..))).........(((((((.....(((.......))).))))))) ( -27.90)
>DroSim_CAF1 12099 119 + 1
GGGAAUAUGUUGAAUAUGAAAUU-GUUAGACGGAAAGAGCCCUAUCUCUGUUUGACUUGUUUUUGUUUGGUAUUCUUUACUUGAUUUUAUACCCGUCACACGAACAUUACGUAGGGUAUA
(((((((..(..((((.(((...-((((((((((..((......))))))))))))...))).))))..))))))))..........(((((((.....(((.......))).))))))) ( -27.60)
>DroEre_CAF1 12332 120 + 1
GAGAAUAUGUUGAAUAUGAAAUUUGCUAGACUGAAAGAGCCCUAUCUCUGUUUGGCUUGUUUUUGUUUGGUAUUCUUUACUUGAUUUUAUACCCGGCACACGAACAUUACGAAGGGUAUA
(((((((..(..((((.(((((..(((((((....((((......)))))))))))..)))))))))..))))))))..........(((((((..(.............)..))))))) ( -27.72)
>DroYak_CAF1 12191 120 + 1
GAGAAUAUGUUGAAUAUGAAAUUUGCUAGGCAGAAGGAGCCCUAUCUCUGUUUGGCUUGUUUUUGUUUGGUAUUCUUUACUUGAUUUUAUACCCUGCACACCGAGAUUACGUAGGGUAUA
(((((((..(..((((.(((((..(((((((((((((...)))...))))))))))..)))))))))..))))))))..........((((((((((.............)))))))))) ( -36.82)
>consensus
GGGAAUAUGUUGAAUAUGAAAUU_GCUAGACGGAAAGAGCCCUAUCUCUGUUUGACUUGUUUUUGUUUGGUAUUCUUUACUUGAUUUUAUACCCGUCACACGAACAUUACGUAGGGUAUA
(((((((..(..((((.(((((..((((((((((..((......))))))))))))..)))))))))..))))))))..........(((((((...................))))))) (-25.35 = -25.31 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:37:16 2006