# Primer: 338r 5'-GCTGCCTCCCGTAGGAGT-3' # Input fasta file: sample_bacteria_seqs_unaligned.fasta # Parameters # 3' length: 5 # non 3' mismatch penalty: 0.40 per mismatch # 3' mismatch penalty: 1.00 per mismatch # last base mismatch penalty: 3.00 # non 3' gap penalty: 1.00 per gap # 3' gap penalty: 3.00 per gap # Note - seq hit and primer hit are the best local pairwise alignment results for a given sequence and primer pair. A gap in seq hit represents a deletion in the sequence, whereas a gap in the primer hit signifies an insertion in the target sequence. # # seq ID, seq hit, primer hit, hit start position, non 3' mismatches, 3' mismatches (except last base), last base mismatch, non 3' gaps, 3' gaps, overall weighted score, hits sequence end 11544,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,307,0,0,False,0,0,0.0,False 57484,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,302,0,0,False,0,0,0.0,False 103547,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,330,0,0,False,0,0,0.0,False 120123,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,311,0,0,False,0,0,0.0,False 127471,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,329,0,0,False,0,0,0.0,False 199390,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,321,0,0,False,0,0,0.0,False 214073,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,306,0,0,False,0,0,0.0,False 235381,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,312,0,0,False,0,0,0.0,False 254376,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,331,0,0,False,0,0,0.0,False 256904,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,325,0,0,False,0,0,0.0,False 286896,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,330,0,0,False,0,0,0.0,False 300250,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,329,0,0,False,0,0,0.0,False 300253,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,331,0,0,False,0,0,0.0,False 300257,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,322,0,0,False,0,0,0.0,False 339039,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,312,0,0,False,0,0,0.0,False 359103,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,278,0,0,False,0,0,0.0,False 359108,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,322,0,0,False,0,0,0.0,False 370251,ACTCCTACGGGAGGCAGC,ACTCCTACGGGAGGCAGC,135,0,0,False,0,0,0.0,False