Locus 5341

Sequence ID 3L_DroMel_CAF1
Location 14,746,382 – 14,746,535
Length 153
Max. P 0.952713
window8441 window8442 window8443

overview

Window 1

Location 14,746,382 – 14,746,496
Length 114
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 82.78
Mean single sequence MFE -27.47
Consensus MFE -21.69
Energy contribution -22.13
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.46
Structure conservation index 0.79
SVM decision value 1.42
SVM RNA-class probability 0.952713
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14746382 114 + 23771897
AUAAACCAGUUUCUGGAGAAAGAGAGGAGGGGG------AGGGAAAAGGGGGAGUGGCAGUUGUUGCUUUCCACGGCAAAAGAAAAGGCAACAAACUCUCAACGAGAGGGAGAGAGAGAA
.....((..(((((........)))))..))..------.........((..((..((....))..))..))..............(....)...(((((..(....)...))))).... ( -28.40)
>DroSec_CAF1 11493 120 + 1
AUAAACCAGUUUCUGGAGAAAGAGAGGAGGGGGAGGAGGAGGAAAAAGGGGGAGUGGCAGUUGUUGCUUUCCACGGUAAAAGAAAAGGCAACAAACUCUCAACGAAGGCGAGAGAGAGAA
....(((..(((((......))))).......................((..((..((....))..))..))..))).........(....)...(((((..(....).)))))...... ( -27.50)
>DroEre_CAF1 11781 111 + 1
AUAAACCAGUUUCUGGGC-------CGAGCGGCGGGGGGAGAGAAAAGGGGGAGUGGCAGUUGUUGCUUUUCAUGGCAAAAGAAAAGGCAACGGAC--UCAACGAGAGGGAGAGAGAGAA
.....((..((((...((-------(....)))..(..(((.......(..(((..((....))..)))..)..............(....)...)--))..))))).)).......... ( -26.50)
>consensus
AUAAACCAGUUUCUGGAGAAAGAGAGGAGGGGG_GG_GGAGGGAAAAGGGGGAGUGGCAGUUGUUGCUUUCCACGGCAAAAGAAAAGGCAACAAACUCUCAACGAGAGGGAGAGAGAGAA
.....((((...))))................................((((((..((....))..))))))..............(....)...(((((..(....)...))))).... (-21.69 = -22.13 +   0.45)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,746,382 – 14,746,496
Length 114
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 82.78
Mean single sequence MFE -18.37
Consensus MFE -14.09
Energy contribution -14.53
Covariance contribution 0.45
Combinations/Pair 1.05
Mean z-score -2.24
Structure conservation index 0.77
SVM decision value 1.02
SVM RNA-class probability 0.901762
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14746382 114 - 23771897
UUCUCUCUCUCCCUCUCGUUGAGAGUUUGUUGCCUUUUCUUUUGCCGUGGAAAGCAACAACUGCCACUCCCCCUUUUCCCU------CCCCCUCCUCUCUUUCUCCAGAAACUGGUUUAU
....(((((...........))))).(((((((.(((((.........)))))))))))).....................------.................((((...))))..... ( -17.90)
>DroSec_CAF1 11493 120 - 1
UUCUCUCUCUCGCCUUCGUUGAGAGUUUGUUGCCUUUUCUUUUACCGUGGAAAGCAACAACUGCCACUCCCCCUUUUUCCUCCUCCUCCCCCUCCUCUCUUUCUCCAGAAACUGGUUUAU
..(((((...((....))..))))).(((((((.(((((.........))))))))))))............................................((((...))))..... ( -18.90)
>DroEre_CAF1 11781 111 - 1
UUCUCUCUCUCCCUCUCGUUGA--GUCCGUUGCCUUUUCUUUUGCCAUGAAAAGCAACAACUGCCACUCCCCCUUUUCUCUCCCCCCGCCGCUCG-------GCCCAGAAACUGGUUUAU
............(((.....))--)...(((((.(((((.........)))))))))).............................(((....)-------))((((...))))..... ( -18.30)
>consensus
UUCUCUCUCUCCCUCUCGUUGAGAGUUUGUUGCCUUUUCUUUUGCCGUGGAAAGCAACAACUGCCACUCCCCCUUUUCCCUCC_CC_CCCCCUCCUCUCUUUCUCCAGAAACUGGUUUAU
....(((((...........)))))...(((((.(((((.........))))))))))..............................................((((...))))..... (-14.09 = -14.53 +   0.45)

alignment

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secondary structure

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dotplot

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Window 3

Location 14,746,416 – 14,746,535
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 92.16
Mean single sequence MFE -38.97
Consensus MFE -34.45
Energy contribution -34.57
Covariance contribution 0.12
Combinations/Pair 1.13
Mean z-score -1.81
Structure conservation index 0.88
SVM decision value 0.17
SVM RNA-class probability 0.616331
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14746416 119 + 23771897
GGGAAAAGGGGGAGUGGCAGUUGUUGCUUUCCACGGCAAAAGAAAAGGCAACAAACUCUCAACGAGAGGGAGAGAGAGAAACGCGACACGCACACACCCCCAUUUCCGCGGCCUGACCC
.(((((.(((((.(((((.((.(((((((((...............(....)...(((((..(....)...))))).)))).))))))))).))).))))).)))))............ ( -43.60)
>DroSec_CAF1 11533 119 + 1
GGAAAAAGGGGGAGUGGCAGUUGUUGCUUUCCACGGUAAAAGAAAAGGCAACAAACUCUCAACGAAGGCGAGAGAGAGAAACGCGACACGCACACACCCCCAUUUCCGCGGCCUGACCC
(((((..(((((.(((((.((.((((((((((..............(....)...(((((..(....).))))).).)))).))))))))).))).))))).)))))............ ( -40.70)
>DroEre_CAF1 11814 116 + 1
GAGAAAAGGGGGAGUGGCAGUUGUUGCUUUUCAUGGCAAAAGAAAAGGCAACGGAC--UCAACGAGAGGGAGAGAGAGAAACGCG-CACGCACACACCCUCAUUUCCGCGGCCUGACCC
(.((((.(((((.(((((..(((((((((((..(......)..))))))))))).(--((..(....)...)))...........-...)).))).))))).)))))............ ( -32.60)
>consensus
GGGAAAAGGGGGAGUGGCAGUUGUUGCUUUCCACGGCAAAAGAAAAGGCAACAAACUCUCAACGAGAGGGAGAGAGAGAAACGCGACACGCACACACCCCCAUUUCCGCGGCCUGACCC
(((((..(((((.(((((..((((((((((..............)))))))))).(((((..(....)...))))).............)).))).))))).)))))............ (-34.45 = -34.57 +   0.12)

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 11:47:45 2006