Table 3.
FISH probes designed in this study.
| Probe | E. coli pos. | Target group | Coverage∗ | Sequence (5′-3′) | [FA]%∗∗ |
|---|---|---|---|---|---|
| CFX-A6-1278 | 1278–1298 | A6 clade | 81% | GAG GCC TGC TTT CAG GAT TG | 45 |
| CFX-A6-1278_C1 | 1278–1298 | Competitor probe for CFX-A6-1278 | N/A | GAG GCC GGC TTT CAG GAT TG | – |
| CFX-A6-1278_C2∗∗∗ | 1278–1298 | Competitor probe for CFX-A6-1278 | N/A | GAG GCC TGC TTT DAG GAT TG | – |
| CFX-A6-1278_H1 | 1262–1277 | Helper probe for CFX-A6-1278 | N/A | GCT CCG CCT YGC GRC T | – |
| CFX-A6-1278_H2∗∗∗∗ | 1299–1322 | Helper probe for CFX-A6-1278 | N/A | GRG TTG CAG ACT GCA ATC TGA ACT | – |
| CFX-A6-450 | 450–492 | A6 clade | 86% | GGG AGT ACA GTC CTT CCT C | 40 |
| CFX-A6-450_C | 450–492 | Competitor probe for CFX-A6-450 | N/A | GGG AGT ACY GTC CTT CCT C | – |
| CFX-A6-450_H∗∗∗∗ | 494–519 | Helper probe for CFX-A6-450 | N/A | GGC ACG TAG TTA GCC GAG ACT TAT TC | – |
| CFX-A6-mix | N/A | A6 clade | 96% | CFX-A6-1278 + CFX-A6-450 | 45 |
∗Coverage based on the MiDAS taxonomy version 2.1 (McIlroy et al., 2017). There were no non-target hits for either probe. ∗∗Optimal hybridisation formamide concentration % [v/v]. ∗∗∗The CFX-A6-1278 probe did not give a positive signal when applied to Pelolinea submarina MO-CFX1T (at the recommended formamide concentration), which represents the non-target single base mismatched sequences covered by this competitor probe – the CFX-A6-1278_C2 probe is therefore not required. ∗∗∗∗Addition of these helper probes did not improve fluorescence when applied with their respective probes and are therefore not required.