Locus 4900

Sequence ID 3L_DroMel_CAF1
Location 13,639,812 – 13,639,965
Length 153
Max. P 0.978917
window7732 window7733 window7734

overview

Window 2

Location 13,639,812 – 13,639,926
Length 114
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 97.72
Mean single sequence MFE -30.92
Consensus MFE -30.08
Energy contribution -30.00
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -1.61
Structure conservation index 0.97
SVM decision value 1.82
SVM RNA-class probability 0.978917
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13639812 114 + 23771897
CAAUGUGAGAAACGUUUUCGGUGCUCCGCACUGCUUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCG
..(..((((((.((((((((((((...))))).......((((((((..(...(((...........)))...)..))))))))........)))))))))))))..)...... ( -32.30)
>DroSec_CAF1 47328 114 + 1
CAAUGUGAGAAACGUUUUCGAUGCUCCGCACUGCUUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCG
..(..((((((.((((((((((.....(((......)))((((((((..(...(((...........)))...)..)))))))).....))))))))))))))))..)...... ( -32.10)
>DroSim_CAF1 57299 114 + 1
CAAUGUGAGAAACGUUUUCGGUGCUCCGCACUGCUUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCG
..(..((((((.((((((((((((...))))).......((((((((..(...(((...........)))...)..))))))))........)))))))))))))..)...... ( -32.30)
>DroEre_CAF1 49719 114 + 1
CAAUGUGAGAAACGCUUUCGGUGCUACGCGCUGCUUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCG
..(..((((((..((...((((((...))))))....))((((((((..(...(((...........)))...)..))))))))...............))))))..)...... ( -28.20)
>DroYak_CAF1 54460 114 + 1
CAAUGUGAGAAACGCUUUUGGUGCUCCGCAGUGCUUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCG
......(((...(((.....))))))(((((..(.....((((((((..(...(((...........)))...)..))))))))........((((....))))..)..))))) ( -29.70)
>consensus
CAAUGUGAGAAACGUUUUCGGUGCUCCGCACUGCUUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCG
..(..((((((.((((((((((.....(((......)))((((((((..(...(((...........)))...)..)))))))).....))))))))))))))))..)...... (-30.08 = -30.00 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 3

Location 13,639,846 – 13,639,965
Length 119
Sequences 5
Columns 119
Reading direction forward
Mean pairwise identity 99.16
Mean single sequence MFE -29.22
Consensus MFE -29.18
Energy contribution -29.02
Covariance contribution -0.16
Combinations/Pair 1.03
Mean z-score -1.71
Structure conservation index 1.00
SVM decision value 1.82
SVM RNA-class probability 0.978558
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13639846 119 + 23771897
UUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCGAGCGUGAAACAAUUUUCGUUCGUUUGUUUAUCUGGGCAA
.....((((((((..(...(((...........)))...)..)))))))).............(((((..(((.((.(((((((.(((....))).)))))))..)).)))..))))). ( -29.20)
>DroSec_CAF1 47362 119 + 1
UUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCGAGCGUGAAACAAUUUUCGUUCGUUUGUUUAUCUGGGCAA
.....((((((((..(...(((...........)))...)..)))))))).............(((((..(((.((.(((((((.(((....))).)))))))..)).)))..))))). ( -29.20)
>DroSim_CAF1 57333 119 + 1
UUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCGAGCGUGAAACAAUUUUCGUUCGUUUGUUUAUCUGGGCAA
.....((((((((..(...(((...........)))...)..)))))))).............(((((..(((.((.(((((((.(((....))).)))))))..)).)))..))))). ( -29.20)
>DroEre_CAF1 49753 119 + 1
UUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCGAGCGUGAAACAAUUUUCGUUCGUCUGUUUAUCUGGGCAA
.....((((((((..(...(((...........)))...)..)))))))).............(((((..(((.((.(((((((.(((....))).)))))))..)).)))..))))). ( -29.10)
>DroYak_CAF1 54494 119 + 1
UUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCGAGCGUGAAACAAUUUUCGUUCGUCUGUUUAUCUGGGCGA
.....((((((((..(...(((...........)))...)..))))))))........((((((..((((((((.......))))))))..))))))..((((((........)))))) ( -29.40)
>consensus
UUUGCUUUUGGCUUGGUUUGCUUUAGUUUGGUUGGCUUUUUGGGCCAAAAUUUUAAUUGAAAAUGUUUUCGUGUGCUGCGAGCGUGAAACAAUUUUCGUUCGUUUGUUUAUCUGGGCAA
.....((((((((..(...(((...........)))...)..)))))))).............(((((..(((.((.(((((((.(((....))).)))))))..)).)))..))))). (-29.18 = -29.02 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,639,846 – 13,639,965
Length 119
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 99.16
Mean single sequence MFE -16.10
Consensus MFE -15.56
Energy contribution -15.76
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.97
SVM decision value 1.55
SVM RNA-class probability 0.962879
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13639846 119 - 23771897
UUGCCCAGAUAAACAAACGAACGAAAAUUGUUUCACGCUCGCAGCACACGAAAACAUUUUCAAUUAAAAUUUUGGCCCAAAAAGCCAACCAAACUAAAGCAAACCAAGCCAAAAGCAAA
((((..................((((((..((((..((.....))....))))..))))))........(((((((.......((.............)).......))))))))))). ( -16.36)
>DroSec_CAF1 47362 119 - 1
UUGCCCAGAUAAACAAACGAACGAAAAUUGUUUCACGCUCGCAGCACACGAAAACAUUUUCAAUUAAAAUUUUGGCCCAAAAAGCCAACCAAACUAAAGCAAACCAAGCCAAAAGCAAA
((((..................((((((..((((..((.....))....))))..))))))........(((((((.......((.............)).......))))))))))). ( -16.36)
>DroSim_CAF1 57333 119 - 1
UUGCCCAGAUAAACAAACGAACGAAAAUUGUUUCACGCUCGCAGCACACGAAAACAUUUUCAAUUAAAAUUUUGGCCCAAAAAGCCAACCAAACUAAAGCAAACCAAGCCAAAAGCAAA
((((..................((((((..((((..((.....))....))))..))))))........(((((((.......((.............)).......))))))))))). ( -16.36)
>DroEre_CAF1 49753 119 - 1
UUGCCCAGAUAAACAGACGAACGAAAAUUGUUUCACGCUCGCAGCACACGAAAACAUUUUCAAUUAAAAUUUUGGCCCAAAAAGCCAACCAAACUAAAGCAAACCAAGCCAAAAGCAAA
((((..................((((((..((((..((.....))....))))..))))))........(((((((.......((.............)).......))))))))))). ( -16.36)
>DroYak_CAF1 54494 119 - 1
UCGCCCAGAUAAACAGACGAACGAAAAUUGUUUCACGCUCGCAGCACACGAAAACAUUUUCAAUUAAAAUUUUGGCCCAAAAAGCCAACCAAACUAAAGCAAACCAAGCCAAAAGCAAA
..((..................((((((..((((..((.....))....))))..))))))........(((((((.......((.............)).......)))))))))... ( -15.06)
>consensus
UUGCCCAGAUAAACAAACGAACGAAAAUUGUUUCACGCUCGCAGCACACGAAAACAUUUUCAAUUAAAAUUUUGGCCCAAAAAGCCAACCAAACUAAAGCAAACCAAGCCAAAAGCAAA
((((..................((((((..((((..((.....))....))))..))))))........(((((((.......((.............)).......))))))))))). (-15.56 = -15.76 +   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 11:36:28 2006