Locus 5711

Sequence ID 2R_DroMel_CAF1
Location 18,082,883 – 18,082,988
Length 105
Max. P 0.896222
window9147 window9148

overview

Window 7

Location 18,082,883 – 18,082,988
Length 105
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 78.71
Mean single sequence MFE -16.80
Consensus MFE -10.86
Energy contribution -10.75
Covariance contribution -0.11
Combinations/Pair 1.07
Mean z-score -1.69
Structure conservation index 0.65
SVM decision value 0.66
SVM RNA-class probability 0.813838
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18082883 105 + 20766785
CUGUAUUCGCACCCCCUGCCAUUCCUGCCUUCCAUUCAAAUGACUUUAGUCAUUGCAGUUAAUGAUGCCUGGCUUUAGGCUCCCAC-UCACUACGCAAACACCCAC
........((.........((((.((((..........((((((....))))))))))..))))..(((((....)))))......-.......)).......... ( -17.70)
>DroSec_CAF1 40427 105 + 1
CUGUAUUCCCACCCCCUGCCAUUCCUGCCUUCCAUUCAAAUGACUUUAGUCAUUGCAGUUAAUGAUGCCUGGCUUUAGGCUCCCUC-UCACUACGCAAACACCCAC
................(((((((.((((..........((((((....))))))))))..))))..(((((....)))))......-.......)))......... ( -17.30)
>DroSim_CAF1 41080 105 + 1
CUGUAUUCCCACCCCCUGCCAUUCCUGCCUUCCAUUCAAAUGACUUUAGUCAUUGCAGUUAAUGAUGCCUGGCUUUAGGCUCCCUC-UCACUACGCAAACACCCAC
................(((((((.((((..........((((((....))))))))))..))))..(((((....)))))......-.......)))......... ( -17.30)
>DroEre_CAF1 40880 104 + 1
CUGUAUUCCUGCCACCCGCCAUUC-UUCCUUCCAUUCAAAUGACUUUAGUCAUUGCAGUUAAUGAUGCCUGGCUUUAGGCUCACUC-CCACUACGCAAACACCCAC
..........(((....((((...-.............((((((....))))))(((........))).))))....)))......-................... ( -17.10)
>DroYak_CAF1 41902 82 + 1
CUGUAUUCCCGCC------------------------AAAUGACUUUAGUCAUUGCAGUUAAUGAUGCCUGGCUUUAGGCUCCCCCGUCACUACGCAAAUACCCAC
..(((((..((((------------------------(((((((....))))))(((........))).))))....(((......))).....)..))))).... ( -17.40)
>DroAna_CAF1 39758 82 + 1
CAGUG------------------UAUCCUUUCUAUUCAAAUGACUUUAGUCAUUGCAGUUAAUGAUGCCUGGCUUUAGGCCCCACC-AUACCUCCCA-----CCAC
.((.(------------------((((.((...(((..((((((....))))))..))).)).)))))))(((.....))).....-..........-----.... ( -14.00)
>consensus
CUGUAUUCCCACCCCCUGCCAUUCCUGCCUUCCAUUCAAAUGACUUUAGUCAUUGCAGUUAAUGAUGCCUGGCUUUAGGCUCCCUC_UCACUACGCAAACACCCAC
..(((.................................((((((....))))))............(((((....)))))...........)))............ (-10.86 = -10.75 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,082,883 – 18,082,988
Length 105
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 78.71
Mean single sequence MFE -26.92
Consensus MFE -17.49
Energy contribution -17.72
Covariance contribution 0.22
Combinations/Pair 1.20
Mean z-score -1.93
Structure conservation index 0.65
SVM decision value 0.99
SVM RNA-class probability 0.896222
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18082883 105 - 20766785
GUGGGUGUUUGCGUAGUGA-GUGGGAGCCUAAAGCCAGGCAUCAUUAACUGCAAUGACUAAAGUCAUUUGAAUGGAAGGCAGGAAUGGCAGGGGGUGCGAAUACAG
....(((((((((((((.(-((((..((((......)))).))))).)))))....(((...(((((((...((.....)).)))))))....))))))))))).. ( -32.90)
>DroSec_CAF1 40427 105 - 1
GUGGGUGUUUGCGUAGUGA-GAGGGAGCCUAAAGCCAGGCAUCAUUAACUGCAAUGACUAAAGUCAUUUGAAUGGAAGGCAGGAAUGGCAGGGGGUGGGAAUACAG
....((((((.((((((..-...(..((((......))))..)....)))))....(((...(((((((...((.....)).)))))))....)))).)))))).. ( -26.10)
>DroSim_CAF1 41080 105 - 1
GUGGGUGUUUGCGUAGUGA-GAGGGAGCCUAAAGCCAGGCAUCAUUAACUGCAAUGACUAAAGUCAUUUGAAUGGAAGGCAGGAAUGGCAGGGGGUGGGAAUACAG
....((((((.((((((..-...(..((((......))))..)....)))))....(((...(((((((...((.....)).)))))))....)))).)))))).. ( -26.10)
>DroEre_CAF1 40880 104 - 1
GUGGGUGUUUGCGUAGUGG-GAGUGAGCCUAAAGCCAGGCAUCAUUAACUGCAAUGACUAAAGUCAUUUGAAUGGAAGGAA-GAAUGGCGGGUGGCAGGAAUACAG
(((....((((((((((..-.(((((((((......)))).))))).)))))....(((...(((((((............-))))))).))).)))))..))).. ( -30.00)
>DroYak_CAF1 41902 82 - 1
GUGGGUAUUUGCGUAGUGACGGGGGAGCCUAAAGCCAGGCAUCAUUAACUGCAAUGACUAAAGUCAUUU------------------------GGCGGGAAUACAG
....((((((.(((.(((((...((.((((......)))).(((((......)))))))...)))))..------------------------.))).)))))).. ( -25.40)
>DroAna_CAF1 39758 82 - 1
GUGG-----UGGGAGGUAU-GGUGGGGCCUAAAGCCAGGCAUCAUUAACUGCAAUGACUAAAGUCAUUUGAAUAGAAAGGAUA------------------CACUG
..((-----(((.((..((-((((.(((.....)))...))))))...)).)((((((....))))))...............------------------)))). ( -21.00)
>consensus
GUGGGUGUUUGCGUAGUGA_GAGGGAGCCUAAAGCCAGGCAUCAUUAACUGCAAUGACUAAAGUCAUUUGAAUGGAAGGCAGGAAUGGCAGGGGGUGGGAAUACAG
(((....((((((((((.......((((((......)))).))....)))))((((((....))))))..........................)))))..))).. (-17.49 = -17.72 +   0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:27 2006