consensus<-function(list, threshold){
if(missing(threshold)==T){
	threshold=0
	}
seqs<-list
sizeseq<-length(strsplit(seqs[[1]],"")[[1]])
motif<-matrix(0, nrow=4, ncol=sizeseq)
for(i in 1:length(seqs)){site<-strsplit(seqs[[i]],"")[[1]]; for(k in 1:length(site)){if (site[k]=="A") {motif[1,k]=motif[1,k]+1}; if (site[k]=="C") {motif[2,k]=motif[2,k]+1}; if (site[k]=="G") {motif[3,k]=motif[3,k]+1}; if (site[k]=="T") {motif[4,k]=motif[4,k]+1}}}
motif<-motif/length(seqs)
motif<-as.data.frame(motif)
row.names(motif)=c("A","C","G","T");
columns<-0;for(i in 1:sizeseq){columns[i]<-paste("P",i,sep="")};
colnames(motif)<-columns
consensus<-""
for(i in 1:length(motif)){if(max(motif[,i])>=threshold) {residue<-rownames(motif)[which(motif[,i]==max(motif[,i]))]} else{residue<-paste("[",paste(rownames(motif)[which(motif[,i]>=1-threshold)], collapse=""), "]",collapse="", sep="")}; consensus<-paste(consensus,residue,sep="")}
return(consensus)
}