Locus 4003

Sequence ID 3R_DroMel_CAF1
Location 10,910,843 – 10,910,937
Length 94
Max. P 0.829173
window6417

overview

Window 7

Location 10,910,843 – 10,910,937
Length 94
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 79.66
Mean single sequence MFE -23.82
Consensus MFE -11.64
Energy contribution -13.67
Covariance contribution 2.03
Combinations/Pair 1.04
Mean z-score -2.54
Structure conservation index 0.49
SVM decision value 0.71
SVM RNA-class probability 0.829173
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10910843 94 + 27905053
------GCGGCACAACAACAUAUGUGCAAGUGUGCGCCAGCGAAUUGAACAAUGC------AAAUUACGCAUUAAUU-UUGCAUUUAAUUCGGUGCGAAAGCAAAAG------
------(((.((((...((....)).....)))))))...((((((((...((((------(((............)-)))))))))))))).(((....)))....------ ( -26.30)
>DroPse_CAF1 225614 95 + 1
AAAAGCGCAGCAGAGCAA-----ACGCAAAA-------CGUAAAUUGAACAAUGA------AAAUUACGCAUUUAUUUUUGGCUGCAAUUAAGCGAGAAAGGAAAAAUAGUGG
.....(((.((...((..-----..))....-------.((((.((.........------)).)))))).(((.(((((.(((.......))).))))).))).....))). ( -14.00)
>DroSec_CAF1 181488 92 + 1
------GCGGCACAACAACAAAUGUGCAAGU--GCGCCAGCGAAUUGAACAAUGC------AAAUUACGCAUUAAUU-UUGCAUUUAAUUCGGUGCGAAAGCAAAAG------
------((.(((((........)))))...(--(((((...(((((((...((((------(((............)-)))))))))))))))))))...)).....------ ( -26.20)
>DroSim_CAF1 184227 92 + 1
------GCGGCACAACAACAAAUGUGCAAGU--GCGCCAGCGAAUUGAACAAUGC------AAAUUACGCAUUAAUU-UUGCAUUUAAUUCGGUGCGAAAGCAAAAG------
------((.(((((........)))))...(--(((((...(((((((...((((------(((............)-)))))))))))))))))))...)).....------ ( -26.20)
>DroEre_CAF1 180912 87 + 1
------GCGGCACAACAA-----GUGCAAGU--GCGCCAGCGAAUUGAACAAUGC------AAAUUACGCAUUAAUU-UCGCAUUUAAUUCGGUGCGAAAGCAAAAG------
------((.((((.....-----))))...(--(((((...(((((((...((((------((((((.....)))))-).)))))))))))))))))...)).....------ ( -25.00)
>DroYak_CAF1 188190 93 + 1
------GCGGCACAACAA-----GUGCAAGU--GCGCCUGCAAAUUGAACAAUGCGAAUACAAAUUACGCAUUAAUU-UUGCAUUUAAUUCGGUGCGAAAGCAAAAG------
------((.((((.....-----))))...(--(((((((((((......(((((((((....))).))))))...)-)))))........))))))...)).....------ ( -25.20)
>consensus
______GCGGCACAACAA_____GUGCAAGU__GCGCCAGCGAAUUGAACAAUGC______AAAUUACGCAUUAAUU_UUGCAUUUAAUUCGGUGCGAAAGCAAAAG______
......((.((((..........))))......(((((...((((((((.(((..........)))..(((........))).)))))))))))))....))........... (-11.64 = -13.67 +   2.03)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:38 2006