Table 1. Probe sets used in modeling.
| Set | Na | Probe Length | Description | Use |
| TileEb | 1380 | 22 | 22-nucleotide-long perfect match probes tiling the 16S rRNAgene of Escherichia coli. | Comparison to mismatches. |
| Length | 1045c | 18–26 | Probes with varied lengths (18, 20, 24, 26) targeting 209random sites on 16S rRNA. | Models M1–M3; fitting. |
| OneMb | 4140 | 22 | TileE set with all three types of mismatches inserted in the 11th position of each probe. | Models M4, M5; fitting. |
| PosM | 4092d | 22 | 62 probes from TileE set with all types of single mismatchesinserted in all positions. | Models M4, M5; verification and positional effects. |
| Gap | 248 | 22 | 62 probes from TileE set with a deletion at the 5th, 11th, 12th,or 18th position. | Models M6, M7; fitting. |
| Insertion | 248 | 23 | 62 probes from TileE set with all types of single insertion between 11th and 12th positions. | Models M6, M7; fitting. |
| TwoM | 1674 | 22 | 62 probes from TileE set with all types of mismatches inserted in positions 5 and 11, 11 and 18, or 5 and 18. | Models M4, M5; verification and double-mismatch effects. |
| Tandem | 558 | 22 | 62 probes from Tile set with all types of 2 mismatchesinserted in positions 11 and 12. | Models M8, M9; fitting. |
| TileRb | 1301 | 22 | 22-nucleotide-long perfect match probes tiling the 16SrRNA gene of Rhodobacter sphaeroides. | Target effects; evaluation of the extent of cross hybridization. |
| Nonsensee | 1 | 22 | Nonsense sequences not complementary to targets used. | Background fluorescence |
a
Number of probes in set. Not all probes are directly used in model development (see next footnote, text, and Table 2).
b
Probes targeting positions before the 50th and after the 1450th nucleotide (in E. coli positioning) were excluded from all analyses to avoid unamplified terminals of the targeted genes and other possible end effects.
c
209 probes shared with TileE set.
d
186 probes shared with OneM set.
e
Ten replicates of the probe 5′-AGAGAGAGAGAGAGAGAGAGAG-3′.