You can use the * symbol at the end of the line to pull out the representative sequence. I think that this script I wrote, will pull out the representative sequence: https://github.com/josephhughes/TCRclust/blob/master/sort_cdhit.pl
sort-cdhit.pl -i INFILE.fa -o OUTFILE_rep.fa -clstr INFILE.clstr -rep
You will need to make sure you use the option
-d 0 when you run cd-hit to be sure to get the complete identifier in the .clstr output file.