Locus 1420

Sequence ID X_DroMel_CAF1
Location 4,284,802 – 4,284,956
Length 154
Max. P 0.993438
window2262 window2263 window2264

overview

Window 2

Location 4,284,802 – 4,284,906
Length 104
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 95.89
Mean single sequence MFE -30.20
Consensus MFE -26.93
Energy contribution -26.71
Covariance contribution -0.22
Combinations/Pair 1.04
Mean z-score -2.48
Structure conservation index 0.89
SVM decision value 0.91
SVM RNA-class probability 0.880656
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4284802 104 + 22224390
AGGGGA--AAACAGAAAGUGGAACAAGUUAGGUGACAGGCAGAAACAACUUGGCCAGAUUCAAACUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUA
(((.((--.....(((..(((..((((((.(....).(.......))))))).)))..)))...(((..((((((....))))))..))).........)).))). ( -30.50)
>DroEre_CAF1 78372 104 + 1
AGGGGA--UAACAGAAAGUGGAACAAGUUAGGUGACAGGCAGAAACAACUUGGCCAGAUCCAAGCUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCAA
.((.((--(.........((((.(......(....).(((.((......)).))).).))))..(((..((((((....))))))..)))........))).)).. ( -29.90)
>DroYak_CAF1 72845 106 + 1
AGGGGAUAUAACAGAAAGUGGAACAAGUUAGGUGACAGGCAGAAACAACUUGGCCAGAUCCAAACUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCGA
.((.(((...........((((.(......(....).(((.((......)).))).).))))..(((..((((((....))))))..)))........))).)).. ( -30.20)
>consensus
AGGGGA__UAACAGAAAGUGGAACAAGUUAGGUGACAGGCAGAAACAACUUGGCCAGAUCCAAACUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCAA
.((.((............((((.(..(((((((..............)))))))..).))))..(((..((((((....))))))..))).........)).)).. (-26.93 = -26.71 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,284,837 – 4,284,937
Length 100
Sequences 5
Columns 100
Reading direction forward
Mean pairwise identity 96.30
Mean single sequence MFE -28.00
Consensus MFE -25.98
Energy contribution -26.02
Covariance contribution 0.04
Combinations/Pair 1.04
Mean z-score -1.83
Structure conservation index 0.93
SVM decision value 2.40
SVM RNA-class probability 0.993438
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4284837 100 + 22224390
GGCAGAAACAACUUGGCCAGAUUCAAACUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUAUGGAAUUCCAUUACUCGCCGCUCGUUAUUUG
..(((((((....((((.((........((..((((((....))))))..))(((((((.(((.....))))))))))....)).))))...))).)))) ( -27.20)
>DroSec_CAF1 71341 100 + 1
GGCAGAAACAACUUGGCCAGAUCCAAACUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUAUGGAAUUCCAUUUCUCGCCGCUCGUUAUUUG
((((((((....((((......))))..((..((((((....))))))..))(((((((.(((.....)))))))))).))))).)))............ ( -30.20)
>DroSim_CAF1 65616 100 + 1
GGCAGAAACAACUUGGCCAGAUCCAAACUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUAUGGAAUUCCAUUACUCGCCGCUCGUUAUUUG
(((((.......((((......))))..((..((((((....))))))..))(((((((.(((.....))))))))))....)).)))............ ( -27.30)
>DroEre_CAF1 78407 100 + 1
GGCAGAAACAACUUGGCCAGAUCCAAGCUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCAAUGAAAUUCCAUUACUCGCCGCUCGUUCUUCA
(((.(((....(((((......)))))(((..((((((....))))))..)))...)))........((((......))))....)))............ ( -25.60)
>DroYak_CAF1 72882 100 + 1
GGCAGAAACAACUUGGCCAGAUCCAAACUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCGAUGGAAUUCCAUUACUCGCCGCUCGUUAUUCG
....(((..(((.((((.((........((..((((((....))))))..))(((((((.((((...)))))))))))....)).))))...))).))). ( -29.70)
>consensus
GGCAGAAACAACUUGGCCAGAUCCAAACUGUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUAUGGAAUUCCAUUACUCGCCGCUCGUUAUUUG
(((.........((((......))))..((..((((((....))))))..))(((((((.(((.....)))))))))).......)))............ (-25.98 = -26.02 +   0.04)

alignment

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secondary structure

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dotplot

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Window 4

Location 4,284,866 – 4,284,956
Length 90
Sequences 5
Columns 90
Reading direction forward
Mean pairwise identity 94.33
Mean single sequence MFE -20.46
Consensus MFE -18.94
Energy contribution -19.14
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 0.93
SVM decision value 0.53
SVM RNA-class probability 0.772376
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4284866 90 + 22224390
GUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUAUGGAAUUCCAUUACUCGCCGCUCGUUAUUUGCUACUCGUUGUUAUUGUAC
(..((((((....))))))..).(((((((.(((.....))))))))))..(((..((.((..((........))..)).))....))). ( -20.60)
>DroSec_CAF1 71370 90 + 1
GUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUAUGGAAUUCCAUUUCUCGCCGCUCGUUAUUUGCUACUCGUUGUAAUUGUAC
(..((((((....))))))..).(((((((.(((.....))))))))))...................((((........))))...... ( -21.10)
>DroSim_CAF1 65645 90 + 1
GUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUAUGGAAUUCCAUUACUCGCCGCUCGUUAUUUGCUACUCGUUGUAAUUGUAC
(..((((((....))))))..).(((((((.(((.....))))))))))(((((.((..((.........))....))..)))))..... ( -22.60)
>DroEre_CAF1 78436 90 + 1
GUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCAAUGAAAUUCCAUUACUCGCCGCUCGUUCUUCACUACUCGUUCUAAUUGUAC
(..((((((....))))))..)((((.((((.........)))).))))......................................... ( -15.70)
>DroYak_CAF1 72911 90 + 1
GUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCGAUGGAAUUCCAUUACUCGCCGCUCGUUAUUCGCUACUCGUUUUCAUUUUAA
(..((((((....))))))..).(((((((.((((...)))))))))))......................................... ( -22.30)
>consensus
GUGAUUGACAACCGUCAAUUGCGGGAAUUCACAUCGCCUAUGGAAUUCCAUUACUCGCCGCUCGUUAUUUGCUACUCGUUGUAAUUGUAC
(..((((((....))))))..).(((((((.(((.....))))))))))......................................... (-18.94 = -19.14 +   0.20)

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 10:09:00 2006