Locus 1145

Sequence ID 3L_DroMel_CAF1
Location 3,325,135 – 3,325,300
Length 165
Max. P 0.860784
window1778 window1779 window1780 window1781

overview

Window 8

Location 3,325,135 – 3,325,226
Length 91
Sequences 5
Columns 92
Reading direction forward
Mean pairwise identity 92.58
Mean single sequence MFE -27.26
Consensus MFE -24.86
Energy contribution -25.30
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.34
Structure conservation index 0.91
SVM decision value 0.83
SVM RNA-class probability 0.860784
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3325135 91 + 23771897
AAACCUGCUCUUGCCUUCCUUUCUGCCAGGUGAAAUUUCGCGGCA-AAGAGGUGGCUCUCUUUCACUCGGCUGGCAGCUGAAAAGGCCCCGA
......((.((((((..(((((.((((..((((....))))))))-.))))).)))..........(((((.....))))).)))))..... ( -27.70)
>DroSec_CAF1 13146 91 + 1
AAACCUGCUCUUGCCUUCCUUUCUGCCAGGUGAAAUUUCGCGGCC-AAGAGGUGGCUCUCUUUCACUCGGCUGGCAGCAGAAAAGGCCCCGA
............(((((..((((((((((((((((....((.(((-....))).))....))))))....))))))).))).)))))..... ( -30.90)
>DroSim_CAF1 5488 91 + 1
AAACCUGCUCUUGCCUUCCUUUCUGCCAGGUGAAAUUUCGCGGCC-AAGAGGUGGCUCUCUUUCACUCGGCUGGCAGCAGAAAAGGCCCCGA
............(((((..((((((((((((((((....((.(((-....))).))....))))))....))))))).))).)))))..... ( -30.90)
>DroEre_CAF1 13326 91 + 1
AAACCUGCUCUUGCCUUCCUUUCUGCCGGGUGAAAU-UCGCGGCCAAAGAGGUGGCUCUCUUUCACUCCACUGCCAGUAAAAAAGACCCCAA
............(((..(((((..((((.(......-.).))))...))))).)))(((.(((.(((........))).))).)))...... ( -19.20)
>DroYak_CAF1 8282 92 + 1
AAACCUGCUCUUGCCUUCUUUUCUGCCAGGUGAAAUUUCGCGGCCAAAGAGGUGGCUCUCUUUCACUCCACUGCCAGCAAAAGAGGCCCCAA
............((((.((((((((.(((((((((....((.(((.....))).))....))))))....))).))).)))))))))..... ( -27.60)
>consensus
AAACCUGCUCUUGCCUUCCUUUCUGCCAGGUGAAAUUUCGCGGCC_AAGAGGUGGCUCUCUUUCACUCGGCUGGCAGCAGAAAAGGCCCCGA
............(((((..((.(((((((((((((....((.(((.....))).))....))))))....))))))).))..)))))..... (-24.86 = -25.30 +   0.44) 

alignment

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secondary structure

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Window 9

Location 3,325,135 – 3,325,226
Length 91
Sequences 5
Columns 92
Reading direction reverse
Mean pairwise identity 92.58
Mean single sequence MFE -31.88
Consensus MFE -26.14
Energy contribution -26.58
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.60
Structure conservation index 0.82
SVM decision value 0.68
SVM RNA-class probability 0.819432
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3325135 91 - 23771897
UCGGGGCCUUUUCAGCUGCCAGCCGAGUGAAAGAGAGCCACCUCUU-UGCCGCGAAAUUUCACCUGGCAGAAAGGAAGGCAAGAGCAGGUUU
((...(((((((...(((((((....(((..((((((....)))))-)..)))((....))..)))))))...)))))))..))........ ( -31.40)
>DroSec_CAF1 13146 91 - 1
UCGGGGCCUUUUCUGCUGCCAGCCGAGUGAAAGAGAGCCACCUCUU-GGCCGCGAAAUUUCACCUGGCAGAAAGGAAGGCAAGAGCAGGUUU
((...((((((..(.(((((((....((((((....((..((....-))..))....))))))))))))).)..))))))..))........ ( -33.70)
>DroSim_CAF1 5488 91 - 1
UCGGGGCCUUUUCUGCUGCCAGCCGAGUGAAAGAGAGCCACCUCUU-GGCCGCGAAAUUUCACCUGGCAGAAAGGAAGGCAAGAGCAGGUUU
((...((((((..(.(((((((....((((((....((..((....-))..))....))))))))))))).)..))))))..))........ ( -33.70)
>DroEre_CAF1 13326 91 - 1
UUGGGGUCUUUUUUACUGGCAGUGGAGUGAAAGAGAGCCACCUCUUUGGCCGCGA-AUUUCACCCGGCAGAAAGGAAGGCAAGAGCAGGUUU
...((.(((((((((((........))))))))))).))((((((((.(((....-.((((........))))....))).)))).)))).. ( -30.30)
>DroYak_CAF1 8282 92 - 1
UUGGGGCCUCUUUUGCUGGCAGUGGAGUGAAAGAGAGCCACCUCUUUGGCCGCGAAAUUUCACCUGGCAGAAAAGAAGGCAAGAGCAGGUUU
.....(((((((((.(((.(((((((((....(.(.((((......))))).)...)))))).))).)))))))).))))............ ( -30.30)
>consensus
UCGGGGCCUUUUCUGCUGCCAGCCGAGUGAAAGAGAGCCACCUCUU_GGCCGCGAAAUUUCACCUGGCAGAAAGGAAGGCAAGAGCAGGUUU
((...(((((((...(((((((....((((((....((..((.....))..))....)))))))))))))...)))))))..))........ (-26.14 = -26.58 +   0.44) 

alignment

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secondary structure

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Window 0

Location 3,325,164 – 3,325,266
Length 102
Sequences 5
Columns 103
Reading direction reverse
Mean pairwise identity 92.99
Mean single sequence MFE -31.52
Consensus MFE -23.36
Energy contribution -23.48
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -2.20
Structure conservation index 0.74
SVM decision value 0.45
SVM RNA-class probability 0.739633
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3325164 102 - 23771897
CCGCAAACUCGAAAGCCAGGCCAAAACAAAGACCAAAUCUUCGGGGCCUUUUCAGCUGCCAGCCGAGUGAAAGAGAGCCACCUCUU-UGCCGCGAAAUUUCAC
.(((..((((((((...(((((....(.((((.....)))).).))))))))).((.....)).)))).((((((......)))))-)...)))......... ( -26.60)
>DroSec_CAF1 13175 102 - 1
CCGCAAACUCGAAAGCCUGGCCAAAACAAAGACCAAAUCUUCGGGGCCUUUUCUGCUGCCAGCCGAGUGAAAGAGAGCCACCUCUU-GGCCGCGAAAUUUCAC
.(((.....(....)...((((((....((((.....)))).((((((((((..(((........)))..))))).))).))..))-)))))))......... ( -29.30)
>DroSim_CAF1 5517 102 - 1
CCGCAAACUCGAAAGCCUGGCCAAAACAAAGACCAAAUCUUCGGGGCCUUUUCUGCUGCCAGCCGAGUGAAAGAGAGCCACCUCUU-GGCCGCGAAAUUUCAC
.(((.....(....)...((((((....((((.....)))).((((((((((..(((........)))..))))).))).))..))-)))))))......... ( -29.30)
>DroEre_CAF1 13355 102 - 1
CCGAAAACUCGAAAGCCAGGCCAAAACAAAGACCAAAUCUUUGGGGUCUUUUUUACUGGCAGUGGAGUGAAAGAGAGCCACCUCUUUGGCCGCGA-AUUUCAC
..........((((..(.(((((((.((((((.....))))))((.(((((((((((........))))))))))).)).....)))))))..).-.)))).. ( -35.30)
>DroYak_CAF1 8311 103 - 1
CCGAAAACUCGAAAGCCAGGCCAAAACAAAGACCAAAUCUUUGGGGCCUCUUUUGCUGGCAGUGGAGUGAAAGAGAGCCACCUCUUUGGCCGCGAAAUUUCAC
..((((..(((.......(((((((.((((((.....)))))).(((((((((..((........))..)))))).))).....))))))).)))..)))).. ( -37.10)
>consensus
CCGCAAACUCGAAAGCCAGGCCAAAACAAAGACCAAAUCUUCGGGGCCUUUUCUGCUGCCAGCCGAGUGAAAGAGAGCCACCUCUU_GGCCGCGAAAUUUCAC
.(((.....(....)...((((......((((.....)))).((((((((((..(((........)))..))))).))).)).....)))))))......... (-23.36 = -23.48 +   0.12) 

alignment

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secondary structure

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dotplot

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Window 1

Location 3,325,194 – 3,325,300
Length 106
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 92.75
Mean single sequence MFE -35.62
Consensus MFE -26.86
Energy contribution -27.02
Covariance contribution 0.16
Combinations/Pair 1.12
Mean z-score -1.80
Structure conservation index 0.75
SVM decision value 0.17
SVM RNA-class probability 0.616450
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 3325194 106 + 23771897
UUUCACUCGGCUGGCAGCUGAAAAGGCCCCGAAGAUUUGGUCUUUGUUUUGGCCUGGCUUUCGAGUUUGCGGACCUGGGCCAUAAACAAUUGCC----AGCAGGUUGUUC
...((..(.((((((((....(((((((..........)))))))(((((((((..(..((((......)))).)..))))).))))..)))))----))).)..))... ( -38.20)
>DroSec_CAF1 13205 106 + 1
UUUCACUCGGCUGGCAGCAGAAAAGGCCCCGAAGAUUUGGUCUUUGUUUUGGCCAGGCUUUCGAGUUUGCGGACCUGGGCCAUAAACAAUUGUC----AGCAGGUUGUUC
...((..(.((((((((....(((((((..........)))))))((((((((((((..((((......))))))).))))).))))..)))))----))).)..))... ( -34.70)
>DroSim_CAF1 5547 106 + 1
UUUCACUCGGCUGGCAGCAGAAAAGGCCCCGAAGAUUUGGUCUUUGUUUUGGCCAGGCUUUCGAGUUUGCGGACCUGGGCCAUAAACAAUUGCC----AGCAGGUUGUUC
...((..(.((((((((....(((((((..........)))))))((((((((((((..((((......))))))).))))).))))..)))))----))).)..))... ( -37.40)
>DroEre_CAF1 13385 106 + 1
UUUCACUCCACUGCCAGUAAAAAAGACCCCAAAGAUUUGGUCUUUGUUUUGGCCUGGCUUUCGAGUUUUCGGACCUGGGCCAUAAACAAUUGCC----AGCAGGUUGUUC
..........((((..((((.(((((((..........)))))))(((((((((..(..((((......)))).)..))))).))))..)))).----.))))....... ( -33.30)
>DroYak_CAF1 8342 110 + 1
UUUCACUCCACUGCCAGCAAAAGAGGCCCCAAAGAUUUGGUCUUUGUUUUGGCCUGGCUUUCGAGUUUUCGGACCUGGGCCAUAAACAAUUGCCAGCCAGCAGGUUGUUC
..........((((..((......(....).......((((..(((((((((((..(..((((......)))).)..))))).))))))..))))))..))))....... ( -34.50)
>consensus
UUUCACUCGGCUGGCAGCAGAAAAGGCCCCGAAGAUUUGGUCUUUGUUUUGGCCUGGCUUUCGAGUUUGCGGACCUGGGCCAUAAACAAUUGCC____AGCAGGUUGUUC
............((((((...(((((((..........)))))))((((((((((((..((((......)))).)))))))).))))..((((......)))))))))). (-26.86 = -27.02 +   0.16) 

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 10:00:16 2006