Locus 5046

Sequence ID 2L_DroMel_CAF1
Location 14,478,049 – 14,478,325
Length 276
Max. P 0.594907
window8022 window8023 window8024

overview

Window 2

Location 14,478,049 – 14,478,165
Length 116
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.51
Mean single sequence MFE -33.10
Consensus MFE -25.80
Energy contribution -27.30
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.78
SVM decision value 0.12
SVM RNA-class probability 0.594907
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14478049 116 + 22407834
AAAGG-GGUUGCAAUCUA-CCUCCUCGACUGCUGACACUUGAAAAAGUGUGCAUAACAAAUUCGAUAAUGAACUAUGAAAUUUUUGCCAGAUUGUAACCCUUUUUGGCAUUGUCGG--AA
..(((-(((((((((((.-...............((((((....))))))(((....(((((..(((......)))..))))).))).))))))))))))))((((((...)))))--). ( -31.60)
>DroSec_CAF1 2652 116 + 1
AAAGG-GGUUGCAAUCUA-CCUCCUCGACUGCUGACACUUGAAAAAGUGUGCAUAACAAAUUCGAUAAUGAACUAUGAAAUUUUUGCCAGAUUGUAACCCUUUUUGGCAUUGUCGG--AA
..(((-(((((((((((.-...............((((((....))))))(((....(((((..(((......)))..))))).))).))))))))))))))((((((...)))))--). ( -31.60)
>DroEre_CAF1 1054 120 + 1
AAAGGGGGUUGCAAUCUCUCCGCUUCGACUGCUGACACUUGAAAAAGUGUGCAUAACAAAUUCGAUAAUGUACUAUGAAAUUUUUGCCAGAUUGUAACCCUUUUUGGCAUUGUCGGCCAA
(((((((((((((((((....((.......))..((((((....))))))(((....(((((..(((......)))..))))).))).)))))))))))))))))(((.......))).. ( -36.10)
>consensus
AAAGG_GGUUGCAAUCUA_CCUCCUCGACUGCUGACACUUGAAAAAGUGUGCAUAACAAAUUCGAUAAUGAACUAUGAAAUUUUUGCCAGAUUGUAACCCUUUUUGGCAUUGUCGG__AA
(((((.(((((((((((.................((((((....))))))(((....(((((..(((......)))..))))).))).))))))))))))))))((((...))))..... (-25.80 = -27.30 +   1.50)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,478,165 – 14,478,285
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.78
Mean single sequence MFE -27.07
Consensus MFE -26.67
Energy contribution -26.67
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.99
SVM decision value 0.04
SVM RNA-class probability 0.551911
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14478165 120 - 22407834
UAUUAUGCAAAUGGAAACCCAUUUCAAGGAUUCCCUUUGCCGGCUAUAAAUGGCAAUAAUUGUUAUUUCAAAAUUUAUGACAGCAAAAUAAAUUUCAACUGUGACAUGUGGGGCAGGGAU
.....((.((((((....)))))))).....(((((..(((.((((....))))......((((((....((((((((.........)))))))).....)))))).....)))))))). ( -27.10)
>DroSec_CAF1 2768 120 - 1
UAUUAUGCAAAUGGAAACCCAUUUCAAGGAUUCCCUUUGCCGGCUAUAAAUGGCAAUAAUUGUUAUUUCAAAAUUUAUGACAGCAAAAUAAAUUUCAACUGUGACAUGUGGGGCAGGGAU
.....((.((((((....)))))))).....(((((..(((.((((....))))......((((((....((((((((.........)))))))).....)))))).....)))))))). ( -27.10)
>DroEre_CAF1 1174 120 - 1
UAUUAUGCAAAUGGCAACCCAUUUCAAGGAUUCCCUUUGCCAGCUAUAAAUGGCAAUAAUUGUUAUUUCAAAAUUUAUGACAGCAAAAUAAAUUUCAGCCGUGACAUGUGGGGCAGGGAU
.....((.((((((....)))))))).....(((((..(((.((.....(((((.....(((......)))(((((((.........)))))))...))))).....))..)))))))). ( -27.00)
>consensus
UAUUAUGCAAAUGGAAACCCAUUUCAAGGAUUCCCUUUGCCGGCUAUAAAUGGCAAUAAUUGUUAUUUCAAAAUUUAUGACAGCAAAAUAAAUUUCAACUGUGACAUGUGGGGCAGGGAU
.....((.((((((....)))))))).....(((((..(((.((((....))))......((((((....((((((((.........)))))))).....)))))).....)))))))). (-26.67 = -26.67 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 14,478,205 – 14,478,325
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -27.63
Consensus MFE -26.49
Energy contribution -26.60
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -1.49
Structure conservation index 0.96
SVM decision value -0.00
SVM RNA-class probability 0.532167
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14478205 120 + 22407834
UCAUAAAUUUUGAAAUAACAAUUAUUGCCAUUUAUAGCCGGCAAAGGGAAUCCUUGAAAUGGGUUUCCAUUUGCAUAAUAAACGCUUGUCCCAGAGGAAGACGUAUUUCAUCCUUGGCAU
.........................((((...........(((((((((((((.......)))))))).)))))...................(((((.((......)).))))))))). ( -28.50)
>DroSec_CAF1 2808 120 + 1
UCAUAAAUUUUGAAAUAACAAUUAUUGCCAUUUAUAGCCGGCAAAGGGAAUCCUUGAAAUGGGUUUCCAUUUGCAUAAUAAACGCUUGUCCCAGAGGAAGACGUAUUUCAUCCUUGGCAU
.........................((((...........(((((((((((((.......)))))))).)))))...................(((((.((......)).))))))))). ( -28.50)
>DroEre_CAF1 1214 120 + 1
UCAUAAAUUUUGAAAUAACAAUUAUUGCCAUUUAUAGCUGGCAAAGGGAAUCCUUGAAAUGGGUUGCCAUUUGCAUAAUAAACGCUUGUCCCAGAGGAAGACGUAUUUCAUUCUUGGCAU
.........................(((((..........(((((((.(((((.......))))).)).))))).......(((.((.(((....))).)))))..........))))). ( -25.90)
>consensus
UCAUAAAUUUUGAAAUAACAAUUAUUGCCAUUUAUAGCCGGCAAAGGGAAUCCUUGAAAUGGGUUUCCAUUUGCAUAAUAAACGCUUGUCCCAGAGGAAGACGUAUUUCAUCCUUGGCAU
.........................((((...........(((((((((((((.......)))))))).)))))...................(((((.((......)).))))))))). (-26.49 = -26.60 +   0.11)

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 11:34:29 2006