TABLE 4.

Mismatches between primers and bacterial gene sequences

Bacterial division or parameterNo. of mismatches in sequence alignment with primera:
ITSFITSReubS-D-Bact-1522-b-S-20L-D-Bact-132-a-A-181406F23Sr
Actinomycetales 0/1,0050/27716/8800/2230/10010/225
Chlamydiae 0/1080/760/930/750/1530/70
Cyanobacteria 0/5220/1198/3070/933/8780/68
Firmicutes 0/1,0000/5710/1,0820/2470/1,0141/255
Proteobacteria 0/1,0080/6971/1,0082/6630/1,0064/687
Spirochaetales 0/2730/54/1840/132/6370/15
Aquificales 0/120/10/10/10/430/1
Thermotogales 0/320/10/100/10/600/1
Green nonsulfur bacteria0/1NSbNMcNS29/29NS
Green sulfur bacteria2/180/31/30/30/180/3
Thermus 0/910/30/560/31/1210/3
Deinococcus 0/240/70/70/70/240/7
CFB group2/5140/32/750/30/9900/3
Planctomycetes 0/870/20/190/10/1240/1
Synergistes 0/1NSNMNS0/1NS
Holophaga 0/31NS0/21NS0/39NS
Thermodesulfobacterium group0/1NSNMNS0/7NS
Verrucomicrobia 1/93/7NMNM1/52NM
Total no. of alignments4,7371,6643,7461,3336,1971,339
Total no. (%) of 3′-end mismatches5 (0.10)3 (0.18)122 (3.26)2 (0.15)7 (0.11)5 (0.37)
No. of phylogenetic groups showing 3′-end mismatches316152
No. of phylogenetic groups with no matches004101
  • a For each bacterial division, results are expressed as number of sequences containing a mismatch with the 3′-end position of the primers/total number of sequences showing a significant alignment, determined by using the BLAST program. BLAST parameters used were 1,000 matches as the maximum expected value, while the word size required was 7.

  • b NS, no 23S rRNA gene sequence available in the NCBI database.

  • c NM, no match with the available sequences.