# Primer: 27f 5'-AGAGTTTGATCMTGGCTCAG-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,TTGATCCTGGCTCAG,TTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 57484,AGGGTGCAAGCGTTACTCGG,AGAGTTTGATCMTGGCTCAG,478,8,1,False,0,0,4.2,False 103547,AGAGTTTGATTCTGGCTCAG,AGAGTTTGATCMTGGCTCAG,5,1,0,False,0,0,0.4,False 120123,AGTGAAAGCCCGGGGCTCAA,AGAGTTTGATCMTGGCTCAG,551,8,0,True,0,0,6.2,False 127471,AGAGTTTGATCCTGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 199390,AGAGTTTGATCCTGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 214073,AGAGTTTGATCATGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 235381,AGAGGATAAGCGAATCTCAG,AGAGTTTGATCMTGGCTCAG,1233,8,0,False,0,0,3.2,False 254376,AGAGTTTGATTATGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,1,0,False,0,0,0.4,True 256904,GAGTTTGATCCTGGCTCAG,GAGTTTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 286896,AGAGTCTTTTCCTGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,3,0,False,0,0,1.2,True 300250,AGAGTTTGATCCTGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 300253,AGAGTTTGATCCTGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 300257,AGAGTTTGATCCTGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 339039,AGAGTTTGATCATGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,0,0,False,0,0,0.0,True 359103,CGCTAGTAATCGCGGATCAG,AGAGTTTGATCMTGGCTCAG,1278,8,1,False,0,0,4.2,False 359108,AGGGTTTGATTATGGCTCAG,AGAGTTTGATCMTGGCTCAG,0,2,0,False,0,0,0.8,True 370251,ATCGAATGAGCCTGCGTCGG,AGAGTTTGATCMTGGCTCAG,20,6,2,False,0,0,4.4,False