Locus 6188

Sequence ID 2L_DroMel_CAF1
Location 17,255,886 – 17,256,068
Length 182
Max. P 0.694754
window9888 window9889

overview

Window 8

Location 17,255,886 – 17,255,978
Length 92
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 83.61
Mean single sequence MFE -19.33
Consensus MFE -11.69
Energy contribution -12.25
Covariance contribution 0.56
Combinations/Pair 1.11
Mean z-score -3.02
Structure conservation index 0.60
SVM decision value 0.34
SVM RNA-class probability 0.694754
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17255886 92 + 22407834
CCAUUUUCCGCCGCACCCA----------AAAGGC-AAAGCAAAACUGGAUGAACGCAUAAACAAAUAUGCCAAAAACAUAGUA-AAAAAAUUGUGUGCAAAAU
.........(((.......----------...)))-...((..............(((((......))))).....(((((((.-.....)))))))))..... ( -15.00)
>DroSec_CAF1 98632 92 + 1
CCAUUUUGCAACGCACCCA----------A-AGGC-AAAGCCAAACUGGAUGAACGCAUAAACAAAUAUGCCAAAAACAUAGUAGAAAAAACUGUGUGCAAAAU
..(((((((....((.(((----------.-.(((-...)))....))).))...(((((......))))).....(((((((.......)))))))))))))) ( -20.80)
>DroSim_CAF1 103687 92 + 1
CCAUUUUGCAACGCACCCA----------A-AGGC-AAAGCAAAACUGGAUGAACGCAUAAACAAAUAUGCCAAAAACAUAGUAGAAAAAACUGUGUGCAAAAU
(((((((((...((.....----------.-..))-...)))))).)))......(((((......))))).....(((((((.......)))))))....... ( -19.20)
>DroEre_CAF1 97707 92 + 1
CCAUUUUCCAGCGCGGCGA----------C-AGGC-AAAGCAAAACUGGCUGAACGCAUAAACAAAUAUGCCAAAAACAUAGUAGAAAAAACUGUGUGGAAAAU
..(((((((.(..((((..----------(-((..-.........)))))))..)(((((......))))).....(((((((.......)))))))))))))) ( -22.10)
>DroYak_CAF1 99490 92 + 1
CCAUUUUCCACUGCGCCCA----------C-AGGC-GAAGCAAAACUGGCUGAACGCAUAAACAAAUAUGCCAAAAACAUAGUAGAAAAAACUGUGUGGAAAAU
..(((((((....((((..----------.-.)))-).(((.......)))....(((((......))))).....(((((((.......)))))))))))))) ( -22.90)
>DroAna_CAF1 168746 100 + 1
CCAUUUUCGCCCCAGCCCAGUCGGAUUUAA-AUCCGAGACCAAAACUUGC-CAACGCAUAAACAAAUAUGCCAAAAAA--AAUACAAAAAAAUGUGUGGAAAAU
...(((((((..........((((((....-)))))).............-....(((((......))))).......--...............))))))).. ( -16.00)
>consensus
CCAUUUUCCACCGCACCCA__________A_AGGC_AAAGCAAAACUGGAUGAACGCAUAAACAAAUAUGCCAAAAACAUAGUAGAAAAAACUGUGUGCAAAAU
..(((((((..............................................(((((......))))).....(((((((.......)))))))))))))) (-11.69 = -12.25 +   0.56)

alignment

Postscript

secondary structure

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dotplot

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Window 9

Location 17,255,978 – 17,256,068
Length 90
Sequences 4
Columns 91
Reading direction forward
Mean pairwise identity 91.53
Mean single sequence MFE -19.49
Consensus MFE -13.85
Energy contribution -14.97
Covariance contribution 1.12
Combinations/Pair 1.06
Mean z-score -2.46
Structure conservation index 0.71
SVM decision value 0.25
SVM RNA-class probability 0.653099
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17255978 90 + 22407834
CUCGCGCGCUUUCGGAAAAAUAAACAAAGCUAAAGGAAAACCCACAAAAAAUGAUUUGGAUCCAUUUGCUGACCC-AAAAAAAGGAGCGCA
...(((((((((.(..........))))))....((.....))...........(((((.((........)).))-))).......)))). ( -16.50)
>DroSec_CAF1 98724 91 + 1
CUCGCGCUCUUACGGAAAAAUAAACAAAGCAAAAGGAAAUCCCACAAGAAAUGAUUCGGAUCCAUUUGCUGACCCCAAAAAAAGGAGCGCA
...((((((((..(..........)..((((((.(((..(((....(....).....)))))).))))))............)))))))). ( -23.60)
>DroSim_CAF1 103779 89 + 1
CUCGCGCGCUUACGGAAAAAUAAACAAAGCAAAAGGAAAUCCCACAAAAAAUGAUUCGGAUCCAUUUGCUGACCC--AAAAAAGGAGCGCA
.....(((((.................((((((.(((..(((...............)))))).))))))...((--......))))))). ( -19.86)
>DroYak_CAF1 99582 90 + 1
CUCGCGCGCUUACGGCCAAACAAACAAAGCAAAGGCAAAACCCACAAAAAAUGAUUCGGAUCCAUUUGCUGAUCC-AAAAAAAGGAGUGCA
.....((((((...(((................))).....................(((((........)))))-........)))))). ( -17.99)
>consensus
CUCGCGCGCUUACGGAAAAAUAAACAAAGCAAAAGGAAAACCCACAAAAAAUGAUUCGGAUCCAUUUGCUGACCC_AAAAAAAGGAGCGCA
.....((((((................((((((.(((..(((...............)))))).))))))..............)))))). (-13.85 = -14.97 +   1.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:04:44 2006