Locus 8513

Sequence ID 3R_DroMel_CAF1
Location 22,721,022 – 22,721,113
Length 91
Max. P 0.619788
window13688 window13689

overview

Window 8

Location 22,721,022 – 22,721,113
Length 91
Sequences 5
Columns 93
Reading direction forward
Mean pairwise identity 90.92
Mean single sequence MFE -28.42
Consensus MFE -23.28
Energy contribution -24.48
Covariance contribution 1.20
Combinations/Pair 1.08
Mean z-score -1.39
Structure conservation index 0.82
SVM decision value 0.17
SVM RNA-class probability 0.614793
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22721022 91 + 27905053
AAAAUCGUUUGGGAAUGUUGGCCGAAAACGUUGCGCUGU-GCUCACUC-UGGUACUGGCUAGUACGCCAAUCUUGGCCAGCAGUUCGUUUUUC
...........(((.((((((((((............((-(((.....-.)))))((((......))))...)))))))))).)))....... ( -27.40)
>DroSec_CAF1 11309 93 + 1
AAAAUCGUUUGGGAAUGUUGGCCAAAAACGUUGCGCUGUUGCGCUCUCUUGGUACUGGCUAGUUCGCCAAUCUUGGCCAGCAGUUCGUUUUCC
...........(((.((((((((((.......((((....))))...........((((......))))...)))))))))).)))....... ( -30.90)
>DroSim_CAF1 11231 93 + 1
AAAAUCGUUUGGGAAUGUUGGCCAAAAACGUUGCGCUGUUGCGCUCUCUUGGUACUGGCUAGUACGCCAAUCUUGGCCAGCAGUUCGUUUUCC
...........(((.((((((((((.......((((....))))...........((((......))))...)))))))))).)))....... ( -30.90)
>DroEre_CAF1 12699 90 + 1
AAAAUUGUUUGGGAAUGUUGGCCAAAAACGGUGCGGUGU---GCUUUCUUGGUACCGGCUAGUACGCCAAUCUUGGCUAGCAGAUCGUUUUCC
...........((..((((((((((....(((..(((((---(((...(((....)))..)))))))).)))))))))))))..))....... ( -28.30)
>DroYak_CAF1 11795 90 + 1
AAAAUCGUUUGGGAAUGUUGGCCAAAAACGGUGCGGUGC---GCUUUCUUGGUACUGGCUAGUACGCCAAUCUUGGCUAGCAGAUCGUUUUCC
...........((..((((((((((....((((((((((---.(......))))))).......))))....))))))))))..))....... ( -24.61)
>consensus
AAAAUCGUUUGGGAAUGUUGGCCAAAAACGUUGCGCUGU_GCGCUCUCUUGGUACUGGCUAGUACGCCAAUCUUGGCCAGCAGUUCGUUUUCC
...........(((.((((((((((.......((((....))))......(((..((((......))))))))))))))))).)))....... (-23.28 = -24.48 +   1.20)

alignment

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secondary structure

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dotplot

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Window 9

Location 22,721,022 – 22,721,113
Length 91
Sequences 5
Columns 93
Reading direction reverse
Mean pairwise identity 90.92
Mean single sequence MFE -24.20
Consensus MFE -19.52
Energy contribution -21.36
Covariance contribution 1.84
Combinations/Pair 1.04
Mean z-score -1.43
Structure conservation index 0.81
SVM decision value 0.18
SVM RNA-class probability 0.619788
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22721022 91 - 27905053
GAAAAACGAACUGCUGGCCAAGAUUGGCGUACUAGCCAGUACCA-GAGUGAGC-ACAGCGCAACGUUUUCGGCCAACAUUCCCAAACGAUUUU
.......(((.((.(((((...((((((......))))))....-..((..((-.....)).))......))))).)))))............ ( -22.00)
>DroSec_CAF1 11309 93 - 1
GGAAAACGAACUGCUGGCCAAGAUUGGCGAACUAGCCAGUACCAAGAGAGCGCAACAGCGCAACGUUUUUGGCCAACAUUCCCAAACGAUUUU
((((.......((.((((((((((((((......)))))).........((((....))))......)))))))).))))))........... ( -29.61)
>DroSim_CAF1 11231 93 - 1
GGAAAACGAACUGCUGGCCAAGAUUGGCGUACUAGCCAGUACCAAGAGAGCGCAACAGCGCAACGUUUUUGGCCAACAUUCCCAAACGAUUUU
((((.......((.((((((((((((((......)))))).........((((....))))......)))))))).))))))........... ( -29.61)
>DroEre_CAF1 12699 90 - 1
GGAAAACGAUCUGCUAGCCAAGAUUGGCGUACUAGCCGGUACCAAGAAAGC---ACACCGCACCGUUUUUGGCCAACAUUCCCAAACAAUUUU
((((...(((((........)))))((((((((....)))))((((((.((---.....))....)))))))))....))))........... ( -19.50)
>DroYak_CAF1 11795 90 - 1
GGAAAACGAUCUGCUAGCCAAGAUUGGCGUACUAGCCAGUACCAAGAAAGC---GCACCGCACCGUUUUUGGCCAACAUUCCCAAACGAUUUU
((((...(((((........)))))((((((((....)))))((((((.((---(...)))....)))))))))....))))........... ( -20.30)
>consensus
GGAAAACGAACUGCUGGCCAAGAUUGGCGUACUAGCCAGUACCAAGAGAGCGC_ACAGCGCAACGUUUUUGGCCAACAUUCCCAAACGAUUUU
.......(((.((.((((((((((((((......)))))).........((((....))))......)))))))).)))))............ (-19.52 = -21.36 +   1.84)

alignment

Postscript

secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:04 2006