Locus 3143

Sequence ID 3R_DroMel_CAF1
Location 8,328,088 – 8,328,322
Length 234
Max. P 0.995942
window5093 window5094

overview

Window 3

Location 8,328,088 – 8,328,206
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.81
Mean single sequence MFE -39.60
Consensus MFE -18.87
Energy contribution -21.83
Covariance contribution 2.96
Combinations/Pair 1.22
Mean z-score -1.93
Structure conservation index 0.48
SVM decision value 0.67
SVM RNA-class probability 0.816398
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8328088 118 - 27905053
UAUUUAUACUCCG-GCGCUCUUUUCGCGAACAUUCGAGGCGCGCUCUCUCGAACCAACGAGAGCAGUAUGUCGUUUACUGUGUGACAGAGUGAGAGAGCAUUAGUG-CAGAGAGGGAGAG
........((((.-.(((.......)))....(((...(((((((((((((......((...((((((.......)))))).))......)))))))))....)))-)...))))))).. ( -37.50)
>DroSec_CAF1 6443 118 - 1
UAUUUAUACUCCG-GCGCUCUUUUCGCGAACAUUCGAGGCGCGCUCUCUCGAAGCAACGAGAACAGUCUUUCGUUUACUGUGUGACAGAGUGAGGGAGCUUUAGUG-CAGAGAGGGAGAG
........((((.-.(((.......)))....(((...(((((((((((((....(((((((......)))))))..(((.....)))..)))))))))....)))-)...))))))).. ( -36.80)
>DroSim_CAF1 6524 119 - 1
UAUUUAUACUCCGGGCGCUCUUUUCGCGAACAUUCGAGGCGCGCUCUCUCGAAGCAACGAGAACAGUAUGCCGUUUACUGUGUGUCAGAGUGAGAGAGCAUUAGUG-CAGAGAGGGAGAG
........(((((..(((.......)))..).(((...(((((((((((((.....(((...((((((.......)))))).))).....)))))))))....)))-)...))))))).. ( -41.50)
>DroEre_CAF1 6868 120 - 1
UAUUUAUACACCCGGCGCUCCUUUCGAGAACAUUCGAAGCGUGCUCUCUCGAAGCAACGAGAACAGUAUGCUGUUUAGUAUGUGCCAGAAUGAGAUAGCAAUAAUGUCUGGGAAGGUGAG
...((((...((((((((.....(((((....)))))((((((((.(((((......)))))..)))))))).........)))))......(((((.......))))))))...)))). ( -36.40)
>DroAna_CAF1 3986 107 - 1
UAUUUAUACUCGG-CUGCUCGGGCGGGGAAAAUUCGAGAUUUCCCUUCUCGAAGUCUC---------ACGACGUUUCCUAUGAGAGCGAGUGAGACAGCAGCGGAG-AAAAAUGGAAA--
........(((.(-(((((((((.(((((((........))))))).))))).(((((---------((..(((((.......))))).))))))).))))).)))-...........-- ( -45.80)
>consensus
UAUUUAUACUCCG_GCGCUCUUUUCGCGAACAUUCGAGGCGCGCUCUCUCGAAGCAACGAGAACAGUAUGCCGUUUACUGUGUGACAGAGUGAGAGAGCAUUAGUG_CAGAGAGGGAGAG
........((((..(((((....(((........))))))))(((((((((...........((((((.......)))))).........)))))))))...............)))).. (-18.87 = -21.83 +   2.96)

alignment

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secondary structure

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dotplot

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Window 4

Location 8,328,206 – 8,328,322
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 70.44
Mean single sequence MFE -25.74
Consensus MFE -12.55
Energy contribution -14.14
Covariance contribution 1.59
Combinations/Pair 1.19
Mean z-score -2.43
Structure conservation index 0.49
SVM decision value 2.63
SVM RNA-class probability 0.995942
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8328206 116 + 27905053
GAGGCGCUUCGUCUACGGAGCGACAAUUCAAUUCAAACAAGCAAAGUGAACACGUCGCUAAGCGAAAGCUAAGCAAAUAAACAAGCGCAGCUGAACAAGCUAAA----CAAUCUGCAGUA
(((.(((((((....)))))))....)))...........(((...((........(((.(((....))).)))..............((((.....))))...----))...))).... ( -31.30)
>DroSec_CAF1 6561 120 + 1
GAGCCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAAAACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAACAAACAAUCUGCAUUA
((((......)))).((((((((......................((....))...(((.(((....))).)))..........))))((((.....))))..........))))..... ( -26.80)
>DroSim_CAF1 6643 104 + 1
GAGCCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAA----------------
..((.(((((((((...)))))..................((..(((((.....))))).(((....)))..))........))))))((((.....))))...---------------- ( -24.20)
>DroEre_CAF1 6988 116 + 1
GCGCUGCUUGUUUCUUUUAGCGUCAUUUCAAUUCAAAGAAGCAAAGUGAACACAUCGCUCAGCGAAAGUUAAGCAACCAAAUAAGCGCAGCUGAACAAGCUAAA----CAAACUGCAGUG
.((((((((((((......(((((((((...(((...)))...)))))).......(((.(((....))).)))...........)))((((.....)))))))----)))...)))))) ( -29.70)
>DroAna_CAF1 4093 93 + 1
GCGGCGGAAAUUUCCCAG----CCAGCACAUUUGA-------AAAGUGAAAAG-----CAAGUGAAAAGUUUG-----AAAGAAAGACAGCUGAAAAAGCUAAA------AUCUGAAAGG
((((((((....)))..)----)).)).((((((.-------...........-----))))))....((((.-----......))))((((.....))))...------.......... ( -16.70)
>consensus
GAGCCGCUUCGUUCCCAGAGCGUCAAUUCAAUUCAAACAAGCAAAGUGAACACAUCGCUAAGCGAAAGCUAAGCAAACAAACAAGCGCAGCUGAACAAGCUAAA____CAAUCUGCAGUA
..(.(((((........))))).)................................(((.(((....))).)))..............((((.....))))................... (-12.55 = -14.14 +   1.59)

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 10:54:07 2006