SeqFindR Antibiotic_markers.fa assemblies/ -o run1 -l 
SeqFindR Antibiotic_markers.fa assemblies/ -m consensus/ -o run2 -l
SeqFindR Antibiotic_markers.fa assemblies/ -m consensus/ -o run3 -l -r
SeqFindR Antibiotic_markers.fa assemblies/ -m consensus/ -o run4 -l -r --index_file dummy.order

SeqFindR Antibiotic_markers.fa assemblies/ -o run1 -l 
SeqFindR Antibiotic_markers.fa assemblies/ -m consensus/ -o run2 -l
SeqFindR Antibiotic_markers.fa assemblies/ -m consensus/ -o run3 -l -r
SeqFindR Antibiotic_markers.fa assemblies/ -m consensus/ -o run4 -l -r --index_file dummy.order
SeqFindR Antibiotic_markers.fa assemblies/ -o run5 -l --careful 0.1

Add example for running with careful
Add example for running with careful
