Locus 1996

Sequence ID 2R_DroMel_CAF1
Location 7,522,885 – 7,522,979
Length 94
Max. P 0.955738
window3294 window3295

overview

Window 4

Location 7,522,885 – 7,522,979
Length 94
Sequences 5
Columns 99
Reading direction forward
Mean pairwise identity 95.02
Mean single sequence MFE -21.85
Consensus MFE -19.21
Energy contribution -19.21
Covariance contribution 0.00
Combinations/Pair 1.09
Mean z-score -1.66
Structure conservation index 0.88
SVM decision value 1.46
SVM RNA-class probability 0.955738
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7522885 94 + 20766785
UAUGGCGCAAAAGAAAAGCGCAUAAAA-AAUGGGG----GGGAAAAAAACUGCAGUCCAAAAGAAGAAUGCGCUGCUCUCUAAACUCUCUGCCGUGGCA
....((((.........))))......-.((((.(----((((........(((((.((.........)).))))).........))))).)))).... ( -23.13)
>DroSec_CAF1 4774 95 + 1
UAUGGCGCAAAAGAAAAGCGCAUAAAAAAAUGGGG----GGAAAAAAAACUGCAGUCCAAAAGAAGAAUGCGCUGCUCUCUAAACUCUCUGCCGUGGCA
....((((.........))))........((((((----(((.........(((((.((.........)).))))).........))))).)))).... ( -20.27)
>DroSim_CAF1 4745 99 + 1
UAUGGCGCAAAAGAAAAGCGCAUAAAAAAAUGGGGGGGGGGGAAAAAAACUGCAGUCCAAAAGAAGAAUGCGCUGCUCUCUAAACUCUCUGCCGUGGCA
....((((.........))))........((((.((((((...........(((((.((.........)).)))))........)))))).)))).... ( -25.01)
>DroEre_CAF1 4823 94 + 1
UAUGGCGCAAAAGAAAAGCGCAUAAAA-AAUGGGG----GGAAAAAAAACUGCAGUCCAAAAGAAGAAUGCGCUGCUCUCUAAACUCUCAGCCAUAGCA
((((((((.........))........-..(((((----(...........(((((.((.........)).)))))........))))))))))))... ( -21.31)
>DroYak_CAF1 4823 92 + 1
UAUGGCGCAAAAGAAAAGCGCAUAAAA-AAUGGGG----G--AAAAAAACUGCAGUCCAAAAGAAGAAUGCGCUGCUCUCUAAACUCUCUGCCAUGGCA
(((((((....(((..(((((((....-..((.((----.--.......)).)).((.....))...)))))))..)))..........)))))))... ( -19.54)
>consensus
UAUGGCGCAAAAGAAAAGCGCAUAAAA_AAUGGGG____GGAAAAAAAACUGCAGUCCAAAAGAAGAAUGCGCUGCUCUCUAAACUCUCUGCCGUGGCA
(((((((....(((..(((((((.........(((....((........))....))).........)))))))..)))..........)))))))... (-19.21 = -19.21 +   0.00)

alignment

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secondary structure

Postscript

dotplot

Postscript

Window 5

Location 7,522,885 – 7,522,979
Length 94
Sequences 5
Columns 99
Reading direction reverse
Mean pairwise identity 95.02
Mean single sequence MFE -21.24
Consensus MFE -20.24
Energy contribution -20.24
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.25
Structure conservation index 0.95
SVM decision value 0.82
SVM RNA-class probability 0.858603
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7522885 94 - 20766785
UGCCACGGCAGAGAGUUUAGAGAGCAGCGCAUUCUUCUUUUGGACUGCAGUUUUUUUCCC----CCCCAUU-UUUUAUGCGCUUUUCUUUUGCGCCAUA
(((....)))....((..((((((.(((((((........(((.................----..)))..-....))))))).)))))).))...... ( -20.45)
>DroSec_CAF1 4774 95 - 1
UGCCACGGCAGAGAGUUUAGAGAGCAGCGCAUUCUUCUUUUGGACUGCAGUUUUUUUUCC----CCCCAUUUUUUUAUGCGCUUUUCUUUUGCGCCAUA
(((....)))....((..((((((.(((((((........(((.................----..))).......))))))).)))))).))...... ( -20.87)
>DroSim_CAF1 4745 99 - 1
UGCCACGGCAGAGAGUUUAGAGAGCAGCGCAUUCUUCUUUUGGACUGCAGUUUUUUUCCCCCCCCCCCAUUUUUUUAUGCGCUUUUCUUUUGCGCCAUA
(((....)))....((..((((((.(((((((........(((.......................))).......))))))).)))))).))...... ( -20.66)
>DroEre_CAF1 4823 94 - 1
UGCUAUGGCUGAGAGUUUAGAGAGCAGCGCAUUCUUCUUUUGGACUGCAGUUUUUUUUCC----CCCCAUU-UUUUAUGCGCUUUUCUUUUGCGCCAUA
...((((((.....((..((((((.(((((((........(((.................----..)))..-....))))))).)))))).)))))))) ( -22.25)
>DroYak_CAF1 4823 92 - 1
UGCCAUGGCAGAGAGUUUAGAGAGCAGCGCAUUCUUCUUUUGGACUGCAGUUUUUUU--C----CCCCAUU-UUUUAUGCGCUUUUCUUUUGCGCCAUA
....(((((.....((..((((((.(((((((........(((..............--.----..)))..-....))))))).)))))).))))))). ( -21.97)
>consensus
UGCCACGGCAGAGAGUUUAGAGAGCAGCGCAUUCUUCUUUUGGACUGCAGUUUUUUUCCC____CCCCAUU_UUUUAUGCGCUUUUCUUUUGCGCCAUA
......(((.....((..((((((.(((((((........(((.......................))).......))))))).)))))).)))))... (-20.24 = -20.24 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:18 2006