Locus 4892

Sequence ID X_DroMel_CAF1
Location 12,716,525 – 12,716,628
Length 103
Max. P 0.718834
window7983 window7984

overview

Window 3

Location 12,716,525 – 12,716,628
Length 103
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 79.06
Mean single sequence MFE -18.01
Consensus MFE -14.50
Energy contribution -14.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.81
SVM decision value 0.39
SVM RNA-class probability 0.718834
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12716525 103 + 22224390
AUAUA------------UAAAGGAAUAUAAUAACAAAACACAUCCGCAGAGAAAAGCACCCCAAACAUUGACAUGUAUUAAAAUACCUUUUUGCAUGUCCUGUGACAGGCAGCAA
.....------------....(((..................)))..........((.((....(((..((((((((..((......))..)))))))).)))....))..)).. ( -15.27)
>DroSec_CAF1 68864 115 + 1
AUAUACAUAUAUGUUAAUAAAGGAGUAUAAAAACAAAACCCACUCGCAGAGAAAAGCACCCCAAACAUUGACAUGUAUUAAAAUACCUUUUUGCAUGUCCUGUGACAGGCAGCAG
......((((((((((((....((((...............))))((........)).........)))))))))))).............(((.((.((((...))))))))). ( -21.16)
>DroSim_CAF1 53419 115 + 1
AUAUACAUAUAUGUUAAUAAAGGAGUAUGAAAACAAAACACAUUCGCAGAGAAAAGCACCCCAAACAUUGACAUGUAUUAAAAUACCUUUUUGCAUGUCCUGUGACAGGCAGCAA
......((((((((((((....((((.((.........)).))))((........)).........))))))))))))............((((.((.((((...)))))))))) ( -20.70)
>DroYak_CAF1 72587 78 + 1
-------------------------------------ACACACUCGCAGAGAAAAGCACCCCAAACAUUGACAUGUAUUAAAAUACCUUUUUGCAUGUCCUGUGACAGGCAGCAA
-------------------------------------.....(((...)))....((.((....(((..((((((((..((......))..)))))))).)))....))..)).. ( -14.90)
>consensus
AUAUA____________UAAAGGAGUAUAAAAACAAAACACACUCGCAGAGAAAAGCACCCCAAACAUUGACAUGUAUUAAAAUACCUUUUUGCAUGUCCUGUGACAGGCAGCAA
.......................................................((.((....(((..((((((((..((......))..)))))))).)))....))..)).. (-14.50 = -14.50 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 12,716,525 – 12,716,628
Length 103
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 79.06
Mean single sequence MFE -23.30
Consensus MFE -20.45
Energy contribution -20.57
Covariance contribution 0.12
Combinations/Pair 1.04
Mean z-score -1.26
Structure conservation index 0.88
SVM decision value 0.27
SVM RNA-class probability 0.659824
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12716525 103 - 22224390
UUGCUGCCUGUCACAGGACAUGCAAAAAGGUAUUUUAAUACAUGUCAAUGUUUGGGGUGCUUUUCUCUGCGGAUGUGUUUUGUUAUUAUAUUCCUUUA------------UAUAU
..(((((.((((....)))).))).(((((((((((((.((((....)))))))))))))))))....))(((((((.........))))))).....------------..... ( -23.10)
>DroSec_CAF1 68864 115 - 1
CUGCUGCCUGUCACAGGACAUGCAAAAAGGUAUUUUAAUACAUGUCAAUGUUUGGGGUGCUUUUCUCUGCGAGUGGGUUUUGUUUUUAUACUCCUUUAUUAACAUAUAUGUAUAU
.((((((.((((....)))).))).(((((((((((((.((((....)))))))))))))))))....))).(((.((..((((..((........))..))))...)).))).. ( -23.70)
>DroSim_CAF1 53419 115 - 1
UUGCUGCCUGUCACAGGACAUGCAAAAAGGUAUUUUAAUACAUGUCAAUGUUUGGGGUGCUUUUCUCUGCGAAUGUGUUUUGUUUUCAUACUCCUUUAUUAACAUAUAUGUAUAU
((((((((((...)))).)).))))(((((((((((((.((((....)))))))))))))))))...((((.(((((((.....................))))))).))))... ( -25.10)
>DroYak_CAF1 72587 78 - 1
UUGCUGCCUGUCACAGGACAUGCAAAAAGGUAUUUUAAUACAUGUCAAUGUUUGGGGUGCUUUUCUCUGCGAGUGUGU-------------------------------------
(((((((.((((....)))).))).(((((((((((((.((((....)))))))))))))))))....))))......------------------------------------- ( -21.30)
>consensus
UUGCUGCCUGUCACAGGACAUGCAAAAAGGUAUUUUAAUACAUGUCAAUGUUUGGGGUGCUUUUCUCUGCGAAUGUGUUUUGUUUUUAUACUCCUUUA____________UAUAU
(((((((.((((....)))).))).(((((((((((((.((((....)))))))))))))))))....))))........................................... (-20.45 = -20.57 +   0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:35:29 2006