Locus 4304

Sequence ID X_DroMel_CAF1
Location 11,353,083 – 11,353,216
Length 133
Max. P 0.984652
window7074 window7075 window7076

overview

Window 4

Location 11,353,083 – 11,353,176
Length 93
Sequences 4
Columns 93
Reading direction reverse
Mean pairwise identity 86.16
Mean single sequence MFE -16.60
Consensus MFE -15.16
Energy contribution -15.73
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -1.96
Structure conservation index 0.91
SVM decision value 1.34
SVM RNA-class probability 0.944195
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11353083 93 - 22224390
AAAUAGUAAAAAUGCCCCAUCAUAUGUACAUACAUACAUAUAUGGGAUGUGAGAAGUUCUCGCUGCUCCAAACAAUAAAAAUUUUAAUUUAUG
....((((.......(((((.(((((((......))))))))))))..(((((.....))))))))).......................... ( -19.80)
>DroSec_CAF1 14049 93 - 1
AUAUAGUAAAAAUGCCCCAUCAUAUGUACAUUCAUGCAUAUAUGGGAUGUGAGAAGUUCUCGCUGCUCCAAACAAUAAAAAUUUUAAUUUAUG
....((((.......(((((.(((((((......))))))))))))..(((((.....))))))))).......................... ( -19.80)
>DroEre_CAF1 17644 77 - 1
AAAUAGUAAAAAUGCCCCAUCAU----------------AUAUGGGAUGUGAGAAGUUCUCGCUGCUUCAAACAAUAAAAAUUUUAAUUUAUG
.....(((((.....(((((...----------------..))))).(((..(((((.......)))))..))).............))))). ( -13.30)
>DroYak_CAF1 18122 77 - 1
AAAUAGUAAAAAUGGCCCAUCAU----------------AUAUGGGAUGUGAGAAGUUCUCGCUGCUCCAAACAAUAAAAAUUUUAAUUUAUG
............((((((((...----------------..)))))..(((((.....)))))....)))....................... ( -13.50)
>consensus
AAAUAGUAAAAAUGCCCCAUCAU________________AUAUGGGAUGUGAGAAGUUCUCGCUGCUCCAAACAAUAAAAAUUUUAAUUUAUG
....((((.......(((((.(((((((......))))))))))))..(((((.....))))))))).......................... (-15.16 = -15.73 +   0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 11,353,098 – 11,353,216
Length 118
Sequences 4
Columns 118
Reading direction forward
Mean pairwise identity 86.27
Mean single sequence MFE -25.20
Consensus MFE -21.33
Energy contribution -21.95
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -2.48
Structure conservation index 0.85
SVM decision value 1.88
SVM RNA-class probability 0.981103
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11353098 118 + 22224390
UUAUUGUUUGGAGCAGCGAGAACUUCUCACAUCCCAUAUAUGUAUGUAUGUACAUAUGAUGGGGCAUUUUUACUAUUUAAAUAUUAUUGUUAUUGCUUCUUCAUCUUUUGGUGAUUUC
.........(((((((((((.....)))....(((((((((((((....)))))))).)))))))..............((((....))))..)))))).(((((....))))).... ( -30.60)
>DroSec_CAF1 14064 118 + 1
UUAUUGUUUGGAGCAGCGAGAACUUCUCACAUCCCAUAUAUGCAUGAAUGUACAUAUGAUGGGGCAUUUUUACUAUAUAAAUAUUAUUGUUGUUGCUUCUUCAUCUUUCGGUGGAUUC
.........(((((((((((.....)))...(((((((((((.((....)).))))).))))))...........................))))))))((((((....))))))... ( -28.70)
>DroEre_CAF1 17659 102 + 1
UUAUUGUUUGAAGCAGCGAGAACUUCUCACAUCCCAUAU----------------AUGAUGGGGCAUUUUUACUAUUUAAAUAUUAUUGUUAUUGCUUCUCCAUCUUUUGGUGAUUUC
.........(((((((((((.....)))....(((((..----------------...)))))))..............((((....))))..))))))..((((....))))..... ( -21.70)
>DroYak_CAF1 18137 102 + 1
UUAUUGUUUGGAGCAGCGAGAACUUCUCACAUCCCAUAU----------------AUGAUGGGCCAUUUUUACUAUUUAAAUAUUAUUGUUAUUGCUUCUACAUCUUUUGAUGAUUUC
.........(((((((.(((.....)))....(((((..----------------...))))).............................)))))))..((((....))))..... ( -19.80)
>consensus
UUAUUGUUUGGAGCAGCGAGAACUUCUCACAUCCCAUAU________________AUGAUGGGGCAUUUUUACUAUUUAAAUAUUAUUGUUAUUGCUUCUUCAUCUUUUGGUGAUUUC
.........(((((((.(((.....)))....(((((((((((((....)))))))).))))).............................)))))))..((((....))))..... (-21.33 = -21.95 +   0.62)

alignment

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secondary structure

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dotplot

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Window 6

Location 11,353,098 – 11,353,216
Length 118
Sequences 4
Columns 118
Reading direction reverse
Mean pairwise identity 86.27
Mean single sequence MFE -21.90
Consensus MFE -18.16
Energy contribution -18.73
Covariance contribution 0.56
Combinations/Pair 1.05
Mean z-score -2.62
Structure conservation index 0.83
SVM decision value 1.98
SVM RNA-class probability 0.984652
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11353098 118 - 22224390
GAAAUCACCAAAAGAUGAAGAAGCAAUAACAAUAAUAUUUAAAUAGUAAAAAUGCCCCAUCAUAUGUACAUACAUACAUAUAUGGGAUGUGAGAAGUUCUCGCUGCUCCAAACAAUAA
...................(.((((..............................(((((.(((((((......))))))))))))..(((((.....))))))))).)......... ( -22.80)
>DroSec_CAF1 14064 118 - 1
GAAUCCACCGAAAGAUGAAGAAGCAACAACAAUAAUAUUUAUAUAGUAAAAAUGCCCCAUCAUAUGUACAUUCAUGCAUAUAUGGGAUGUGAGAAGUUCUCGCUGCUCCAAACAAUAA
.....((.(....).))..(.((((..............................(((((.(((((((......))))))))))))..(((((.....))))))))).)......... ( -24.80)
>DroEre_CAF1 17659 102 - 1
GAAAUCACCAAAAGAUGGAGAAGCAAUAACAAUAAUAUUUAAAUAGUAAAAAUGCCCCAUCAU----------------AUAUGGGAUGUGAGAAGUUCUCGCUGCUUCAAACAAUAA
.......(((.....))).((((((..............................(((((...----------------..)))))..(((((.....)))))))))))......... ( -22.00)
>DroYak_CAF1 18137 102 - 1
GAAAUCAUCAAAAGAUGUAGAAGCAAUAACAAUAAUAUUUAAAUAGUAAAAAUGGCCCAUCAU----------------AUAUGGGAUGUGAGAAGUUCUCGCUGCUCCAAACAAUAA
.....((((....))))..(.((((..............................(((((...----------------..)))))..(((((.....))))))))).)......... ( -18.00)
>consensus
GAAAUCACCAAAAGAUGAAGAAGCAAUAACAAUAAUAUUUAAAUAGUAAAAAUGCCCCAUCAU________________AUAUGGGAUGUGAGAAGUUCUCGCUGCUCCAAACAAUAA
...................(.((((..............................(((((.(((((((......))))))))))))..(((((.....))))))))).)......... (-18.16 = -18.73 +   0.56)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:42 2006