Locus 6601

Sequence ID X_DroMel_CAF1
Location 16,469,589 – 16,469,749
Length 160
Max. P 0.979030
window10782 window10783 window10784

overview

Window 2

Location 16,469,589 – 16,469,709
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 95.00
Mean single sequence MFE -39.47
Consensus MFE -36.77
Energy contribution -37.10
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.86
Structure conservation index 0.93
SVM decision value 0.47
SVM RNA-class probability 0.748461
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16469589 120 + 22224390
UUUGGCCCAAAACGAUGCAAACGAUGCAGCCGAUGCAACGCGACGCCUGCAACUGACAAACGGCGGCAUCAGCCACUGUGCGUUCGUUUUAGUUCGCUUUUCGUUUUCGUUUUGGUUUUU
......(((((((((...((((((((((.....))))..((((...(((.(((.(((..((((.(((....))).))))..))).))).))).))))...)))))))))))))))..... ( -40.60)
>DroSec_CAF1 7611 113 + 1
UUUGGCCCAAAACGAUGCAAACGAUGCAGCCGAUGCAACGCGACGCCUGCAACUGACAAACGGCGGCAUCAGCCACUGUGCGUUCGUUUCAGUUCGCUUUUCGUUUUGGUUUU-------
......(((((((((.((.(((..(((((.((.(((...))).)).)))))((.(((..((((.(((....))).))))..))).))....))).))...)))))))))....------- ( -38.90)
>DroSim_CAF1 4898 120 + 1
UUUGGCCCAAAACGAUGCAAACGAUGCAGCCGAUGCAACGCGACGCCUGCAACUGACAAACGGCGGCAUCAGCCACUGUGCGUUCGUUUCAGUUCGCUUUUCGUUUUGGUUUUGGUUUUU
......(((((((((.((.(((..(((((.((.(((...))).)).)))))((.(((..((((.(((....))).))))..))).))....))).))...)))))))))........... ( -38.90)
>consensus
UUUGGCCCAAAACGAUGCAAACGAUGCAGCCGAUGCAACGCGACGCCUGCAACUGACAAACGGCGGCAUCAGCCACUGUGCGUUCGUUUCAGUUCGCUUUUCGUUUUGGUUUUGGUUUUU
......(((((((((.((.(((..(((((.((.(((...))).)).)))))((.(((..((((.(((....))).))))..))).))....))).))...)))))))))........... (-36.77 = -37.10 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,469,589 – 16,469,709
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -47.63
Consensus MFE -44.37
Energy contribution -45.03
Covariance contribution 0.67
Combinations/Pair 1.00
Mean z-score -4.27
Structure conservation index 0.93
SVM decision value 1.83
SVM RNA-class probability 0.979030
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16469589 120 - 22224390
AAAAACCAAAACGAAAACGAAAAGCGAACUAAAACGAACGCACAGUGGCUGAUGCCGCCGUUUGUCAGUUGCAGGCGUCGCGUUGCAUCGGCUGCAUCGUUUGCAUCGUUUUGGGCCAAA
.....(((((((((((((((...(((..(......)..)))...(..((((((((((((((((((.....)))))))..)))..))))))))..).))))))...)))))))))...... ( -47.10)
>DroSec_CAF1 7611 113 - 1
-------AAAACCAAAACGAAAAGCGAACUGAAACGAACGCACAGUGGCUGAUGCCGCCGUUUGUCAGUUGCAGGCGUCGCGUUGCAUCGGCUGCAUCGUUUGCAUCGUUUUGGGCCAAA
-------....(((((((((.(((((((((((..((((((....(((((....))))))))))))))))(((((.((..((...))..)).)))))))))))...)))))))))...... ( -47.90)
>DroSim_CAF1 4898 120 - 1
AAAAACCAAAACCAAAACGAAAAGCGAACUGAAACGAACGCACAGUGGCUGAUGCCGCCGUUUGUCAGUUGCAGGCGUCGCGUUGCAUCGGCUGCAUCGUUUGCAUCGUUUUGGGCCAAA
...........(((((((((.(((((((((((..((((((....(((((....))))))))))))))))(((((.((..((...))..)).)))))))))))...)))))))))...... ( -47.90)
>consensus
AAAAACCAAAACCAAAACGAAAAGCGAACUGAAACGAACGCACAGUGGCUGAUGCCGCCGUUUGUCAGUUGCAGGCGUCGCGUUGCAUCGGCUGCAUCGUUUGCAUCGUUUUGGGCCAAA
...........(((((((((.((((((((((..(((((((....(((((....))))))))))))))))(((((.((..((...))..)).)))))))))))...)))))))))...... (-44.37 = -45.03 +   0.67)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,469,629 – 16,469,749
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 89.83
Mean single sequence MFE -24.19
Consensus MFE -23.40
Energy contribution -23.73
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.22
Structure conservation index 0.97
SVM decision value 0.19
SVM RNA-class probability 0.628271
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16469629 120 - 22224390
CCAUUUUCGCAUUAAAAUUUGUAACCAAACCAAAAAGAAAAAAAACCAAAACGAAAACGAAAAGCGAACUAAAACGAACGCACAGUGGCUGAUGCCGCCGUUUGUCAGUUGCAGGCGUCG
.....(((((.......((((....))))......................((....))....)))))......(((.(((...(..(((((((........)))))))..)..)))))) ( -22.70)
>DroSec_CAF1 7651 104 - 1
CCAUUUUCGCAUUAAAAUUUGUAACCAAACC----------------AAAACCAAAACGAAAAGCGAACUGAAACGAACGCACAGUGGCUGAUGCCGCCGUUUGUCAGUUGCAGGCGUCG
((.((((((........((((.........)----------------))).......))))))((.((((((..((((((....(((((....))))))))))))))))))).))..... ( -25.06)
>DroSim_CAF1 4938 114 - 1
CCAUUUUCGCAUUAAAAUUUGUAACCAAACCAAA------AAAAACCAAAACCAAAACGAAAAGCGAACUGAAACGAACGCACAGUGGCUGAUGCCGCCGUUUGUCAGUUGCAGGCGUCG
.......(((.......((((....)))).....------.......................((.((((((..((((((....(((((....)))))))))))))))))))..)))... ( -24.80)
>consensus
CCAUUUUCGCAUUAAAAUUUGUAACCAAACCAAA______AAAAACCAAAACCAAAACGAAAAGCGAACUGAAACGAACGCACAGUGGCUGAUGCCGCCGUUUGUCAGUUGCAGGCGUCG
.......(((.......((((....))))..................................((.(((((..(((((((....(((((....)))))))))))))))))))..)))... (-23.40 = -23.73 +   0.33)

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 12:18:00 2006