what happens to paired reads that do not overlap?

Commands in mothur
1

Hi, I understand that in the make.contigs step, paired reads that overlap will be reconstructed to make longer contigs. I am wondering what happen to those reads that do not overlap because the fragments are too long? Are they included in output fasta file or throw away?
Thanks.

2

See my response to a similar question that was recently asked:

http://mothur.ltcmp.net/t/make-contigs-no-scrap/2777/1