Correlation of Clusters With Their Cognate CRM Sequences
| Motif | BCD | CAD | KR | HG | ABDB | KNI | GT | PRD | EN | TLL | TTK | FTZF1 | FTZ | DFD |
| Site PWM cutoff | 4.2 | 4.8 | 4 | 6.5 | 5.4 | 3.6 | 7 | 7.5 | 4 | 4.3 | 3.6 | 4.5 | 4.3 | 2.6 |
| Cluster Ecutoff | 4 * 10−4 | 1.2 * 10−3 | 2.3 * 10−3 | 4.4 * 10−3 | 2.3 * 10−3 | 1.1 * 10−2 | 1.1 * 10−2 | 4.1 * 10−2 | 3 * 10−4 | 1.4 * 10−2 | 4.4 * 10−3 | 4.1 * 10−2 | 6 * 10−4 | 7 * 10−4 |
| Locus name | ||||||||||||||
| abda | −0.05 | 0.275 | ||||||||||||
| btd | 0.918 | −0.07 | −0.09 | |||||||||||
| dll | ||||||||||||||
| ems | 0.771 | 0 | ||||||||||||
| en | 0 | 0.623 | ||||||||||||
| eve | 0.547 | 0.459 | 0.246 | 0.413 | 0.544 | 0.656 | ||||||||
| ftz | 0 | 0.493 | 0.406 | 0 | ||||||||||
| gsb | 0.665 | |||||||||||||
| gt | 0.93 | 0.754 | 0.438 | |||||||||||
| hairy | 0.779 | 0.376 | 0.476 | −0.1 | ||||||||||
| hb | 0.417 | 0.758 | 0.684 | |||||||||||
| kni | 0.620 | 0.404 | 0.933 | 0.4 | ||||||||||
| kr | 0.702 | −0.06 | 0.615 | 0.325 | ||||||||||
| otd | −0.06 | |||||||||||||
| prd | 0 | 0 | ||||||||||||
| runt | 0.351 | 0.424 | 0.088 | −0.06 | −0.08 | |||||||||
| sal | 0.769 | −0.05 | 0.854 | −0.03 | ||||||||||
| tll | −0.04 | 0.958 | ||||||||||||
| ubx | 0.276 | 0.398 | 0.04 |
[i] Correlation coefficients (CC) are shown for some of the tested motif/locus combinations. High CC reflects the presence of a binding motif cluster in its cognate CRM region. A moderate CC value indicates the presence of additional clusters of the motif in the locus or shift of binding site clusters relative to the regulatory regions. Motifs tested and the optimal parameter settings are shown in the top rows; gene names are given in the first column. In all tests, the size of the resolution window was set to 575 bp, according to the results of the global optimization procedure (see Table 1). All combinations tested correspond to known regulatory interactions.