Locus 1962

Sequence ID 3L_DroMel_CAF1
Location 5,440,748 – 5,440,868
Length 120
Max. P 0.594074
window3071

overview

Window 1

Location 5,440,748 – 5,440,868
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.50
Mean single sequence MFE -30.09
Consensus MFE -21.21
Energy contribution -21.09
Covariance contribution -0.12
Combinations/Pair 1.14
Mean z-score -1.60
Structure conservation index 0.71
SVM decision value 0.12
SVM RNA-class probability 0.594074
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5440748 120 + 23771897
GGCGAAGGGGAUGAGUCGAGGAAAUCUUCGCAUAUUGCAAGAAUGAGCCUCAUGAAAACUCCAAAGAAAUGAGGUAAAGUACCGGCUGCAAGUUUCCACAUGCGUAAAAUGCAAGAGCAU
.((...((..((.(((((......((((.((.....))))))....(((((((...............))))))).......)))))....))..))...(((((...)))))...)).. ( -29.26)
>DroSec_CAF1 2369 120 + 1
GGCGAAGGGGAUGAGUUGAGGAAAUCUUCGCAUAUUGCAAGAAUGAGCCUCAUGAAAACUCCAAAGAAAUGAGGUAAAGUGCAGGCUGCAAGUUCCCACAUGCGUAAAAUGCAAGAGAAU
......((((((.....((((....))))(((..(((((....(..(((((((...............)))))))..).)))))..)))..))))))...(((((...)))))....... ( -31.86)
>DroSim_CAF1 2443 120 + 1
GGCGAAGGGGAUGAGUCGAGGAAAUCUUCACAUAUUGCAAGAAUGAGCCUCAUGAAAACUCCAAAGAAAUGAGGUAAAGUGCAGGCUGCAAGUUCCCACAAGCGUAAAAUGAAAUAGAAU
.((...((((((.((((((((....))))......((((....(..(((((((...............)))))))..).))))))))....))))))....))................. ( -29.56)
>DroEre_CAF1 2290 114 + 1
---GAUGUGGAUAAGUCGUGGAAAUCUUCGCAUAUUCUAGGAAUGAGCCUCAUGAAAACUCCAAUGAAAUGAGGCAGACUGCAGGCUGCAAGUUUCCACAUACAUAAAGUGCAAGGG---
---.(((((((..(((((((((....)))))...............(((((((...............))))))).))))((.....)).....)))))))................--- ( -29.66)
>consensus
GGCGAAGGGGAUGAGUCGAGGAAAUCUUCGCAUAUUGCAAGAAUGAGCCUCAUGAAAACUCCAAAGAAAUGAGGUAAAGUGCAGGCUGCAAGUUCCCACAUGCGUAAAAUGCAAGAGAAU
......((((((.((((((((....)))).................(((((((...............)))))))........))))....))))))....................... (-21.21 = -21.09 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:11 2006