Locus 5967

Sequence ID 3L_DroMel_CAF1
Location 15,979,523 – 15,979,653
Length 130
Max. P 0.623453
window9529 window9530

overview

Window 9

Location 15,979,523 – 15,979,631
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.86
Mean single sequence MFE -35.46
Consensus MFE -26.91
Energy contribution -27.91
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -1.63
Structure conservation index 0.76
SVM decision value 0.18
SVM RNA-class probability 0.623453
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15979523 108 - 23771897
CCACGGCACGUGGUAAACGCGCUGCAUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAAGCUGGCUUCAAUCUGGCGGCAUC------------CAACAUCCAGCAAGAUUGAAGAUC
...((((..(((((....(((((........)))))..))))).....((......))...)))).(((((((((.((((.((.------------....)))).)).)))))))))... ( -33.80)
>DroSec_CAF1 8736 108 - 1
CCACGGCACGUGGUAAACGCGCUGCAUCAAAGGCGCCGGCCACAUCCCACCUCAAUGUAAAGCUGGCUUCAAUCUGGCGGCAUC------------CAACAUCCAGCAAGAUUGAAGAUC
...((((..(((((....(((((........)))))..))))).....((......))...)))).(((((((((.((((.((.------------....)))).)).)))))))))... ( -33.80)
>DroSim_CAF1 9411 108 - 1
CCACGGCACGUGGUAGACGCGCUGCAUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAAGCUGGCUUCAAUCUGGCGGCAUC------------CAACAUGCAGCAAGAUUGAAGAUC
...((((..(((((....(((((........)))))..))))).....((......))...)))).(((((((((.((.((((.------------....)))).)).)))))))))... ( -38.40)
>DroEre_CAF1 8936 120 - 1
CCACGGCACGUGGUAAACGCGCCGCUUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAAGCUGGCUUCAGACUGGCGGCAUCGGAAACUCCAGCCAACGUACACAAAGAUCGAAGAUC
....(((..(((.....)))((((((.....((.((((((.((((.........))))...)))))).)).....))))))...((.....)).)))............((((...)))) ( -34.40)
>DroYak_CAF1 8849 117 - 1
CCACGGCACGUGGUAAACGCGCUGCUUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAGGCUGGCUUCAGUCUGGCGGCAUCGGAGACUCCGACCAACCUCCACCAAGAUCCAAG---
....((....((((......((((((....(((((((((((((((.........))))..)))))))....)))))))))).((((.....)))).........))))....))...--- ( -36.90)
>consensus
CCACGGCACGUGGUAAACGCGCUGCAUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAAGCUGGCUUCAAUCUGGCGGCAUC____________CAACAUCCAGCAAGAUUGAAGAUC
...((((..(((((....(((((........)))))..))))).....((......))...)))).(((((((((.((...........................)).)))))))))... (-26.91 = -27.91 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 15,979,551 – 15,979,653
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 76.83
Mean single sequence MFE -37.52
Consensus MFE -26.76
Energy contribution -26.60
Covariance contribution -0.16
Combinations/Pair 1.04
Mean z-score -1.33
Structure conservation index 0.71
SVM decision value 0.15
SVM RNA-class probability 0.605390
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15979551 102 - 23771897
AUGG---------------C---GGAGUGGCUCCAACUUGCCACGGCACGUGGUAAACGCGCUGCAUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAAGCUGGCUUCAAUCUGGCGG
..((---------------.---(((((((((.....((((((((...))))))))..(((((........))))).)))))).)))..))..........((..(.......)..)).. ( -35.50)
>DroSec_CAF1 8764 83 - 1
AU-------------------------------------GCCACGGCACGUGGUAAACGCGCUGCAUCAAAGGCGCCGGCCACAUCCCACCUCAAUGUAAAGCUGGCUUCAAUCUGGCGG
.(-------------------------------------((((((...)))))))..((((((........)))((((((.((((.........))))...)))))).........))). ( -26.70)
>DroSim_CAF1 9439 83 - 1
AU-------------------------------------GCCACGGCACGUGGUAGACGCGCUGCAUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAAGCUGGCUUCAAUCUGGCGG
.(-------------------------------------((((((...)))))))..((((((........)))((((((.((((.........))))...)))))).........))). ( -26.70)
>DroEre_CAF1 8976 117 - 1
AUGGUG---GAGGCGGAGGCGGAGGAGUGGCUUGAACUUGCCACGGCACGUGGUAAACGCGCCGCUUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAAGCUGGCUUCAGACUGGCGG
..((((---(..(.((.((((..((((((((.((...((((((((...)))))))).)).)))))))).....))))..)).)...)))))..........((..((....).)..)).. ( -45.90)
>DroYak_CAF1 8886 117 - 1
AAGGGAUGGGAUGGGAAGGC---GGAGUGGUUUGAACUUGCCACGGCACGUGGUAAACGCGCUGCUUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAGGCUGGCUUCAGUCUGGCGG
..(((.(((((((((..(((---(..(((((........)))))((((((((.....)))).)))).......))))..)).))))))))))...(((.((((((....)))))).))). ( -52.80)
>consensus
AUGG_______________C___GGAGUGG_U__AACUUGCCACGGCACGUGGUAAACGCGCUGCAUCAAAGGCGCCGGCCACAUCCCACCUAAAUGUAAAGCUGGCUUCAAUCUGGCGG
.......................................((((((((.(((.....))).)))).......((.((((((.((((.........))))...)))))).))....)))).. (-26.76 = -26.60 +  -0.16)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:22 2006