Table 5. Summary of elements and data from the analysis.
| Element name | Sequence region (bp) | Candidate genes from search type | Selectivity ratios | |||
| |
|
Pattern |
PROSPECT |
Matrix + PROSPECT |
PROSPECT |
Matrix + PROSPECT |
| (A) Site data derived from SCPD | ||||||
| MCM1 | 200 | 440 (7) | 268 (6) | 65 (2) | 1.4 | 1.9 |
| 600 | 1631 (22) | 114 (5) | 379 (1) | 3.3 | NA | |
| 1000 | 2498 (25) | 128 (5) | 366 (1) | 3.9 | NA | |
| RAP1 | 200 | 338 (3) | 186 (0) | 85 (3) | ND | 4.0 |
| 600 | 1231 (13) | 176 (6) | 622 (8) | 3.2 | 1.2 | |
| 1000 | 2035 (15) | 205 (7) | 715 (7) | 4.6 | NA | |
| MCB | 200 | 507 (4) | 319 (4) | 116 (3) | 1.6 | 3.3 |
| 600 | 1218 (6) | 200 (3) | 246 (5) | 3.0 | 4.1 | |
| 1000 | 1677 (6) | 214 (3) | 326 (6) | 3.9 | 5.1 | |
| ABF1 | 200 | 837 (8) | 208 (6) | 210 (7) | 3.0 | 3.5 |
| 600 | 2144 (15) | 458 (7) | 425 (8) | 2.2 | 2.7 | |
| 1000 | 2974 (19) | 607 (8) | 333 (4) | 2.1 | 1.9 | |
| REB1 | 200 | 494 (2) | 363 (0) | 217 (2) | ND | 2.5 |
| 600 | 1097 (10) | 314 (4) | 360 (2) | 1.4 | 0.6 | |
| 1000 | 1440 (12) | 340 (4) | 418 (5) | 1.4 | 1.4 | |
| MIG1 | 200 | 143 (3) | 117 (3) | 83 (3) | 1.2 | 1.7 |
| 600 | 414 (7) | 247 (6) | 225 (6) | 1.4 | 1.6 | |
| 1000 | 652 (8) | 34 (0) | 315 (6) | ND | 1.6 | |
| GAL4 | 200 | 51 (2) | 35 (2) | 5 (2) | 1.5 | 10.2 |
| 600 | 214 (6) | 149 (6) | 21 (6) | 1.4 | 10.2 | |
| 1000 | 349 (6) | 230 (5) | 27 (6) | 1.3 | 12.9 | |
| PDR3 | 200 | 24 (1) | 17 (1) | 40 (1) | 2.0 | 0.8 |
| 600 | 118 (7) | 97 (7) | 144 (7) | 1.2 | 0.8 | |
| 1000 | 182 (7) | 142 97) | 206 (7) | 1.3 | 0.9 | |
| Repressor of CAR3 | 200 | 90 (3) | 75 (3) | 51 (1) | 1.2 | 0.6 |
| 600 | 292 (11) | 212 (5) | 119 (3) | 0.6 | 0.7 | |
| 1000 | 471 (13) | 292 (7) | 33 (0) | 0.9 | ND | |
| MATα2 | 200 | 554 (1) | 313 (1) | 143 (0) | 1.8 | 0.0 |
| 600 | 1476 (7) | 99 (0) | 199 (0) | ND | ND | |
| 1000 | 2178 (7) | 103 (0) | 364 (0) | ND | ND | |
| TATA | 200 | 2497 (15) | 128 (0) | 141 (0) | ND | ND |
| 600 | 4275 (16) | 66 (0) | 49 (0) | ND | ND | |
| 1000 | 4944 (16) | 327 (0) | 30 (0) | ND | NA | |
| HSE, HSTF | 200 | 1641 (3) | 95 (0) | NM | ND | NM |
| 600 | 4042 (6) | 39 (0) | ND | |||
| 1000 | 5225 (6) | 27 (0) | NA | |||
| GCR1 | 200 | 2778 (4) | 75 (0) | 119 (0) | ND | ND |
| 600 | 5409 (6) | 209 (0) | 167 (0) | NA | ND | |
| 1000 | 6016 (6) | 906 (0) | 227 (0) | NA | NA | |
| GCN4 | 200 | 5177 (8) | 672 (0) | 38 (0) | NA | ND |
| 600 | 6162 (9) | 717 (0) | 216 (1) | NA | 3.2 | |
| 1000 | 6193 (9) | 881 (0) | 193 (0) | NA | NA | |
| (B) Site data derived from SCPD and YPD | ||||||
| MCM1 | 200 | 440 (8) | 268 (7) | 65 (2) | 1.4 | 1.7 |
| 600 | 1631 (24) | 114 (6) | 379 (1) | 3.6 | NA | |
| 1000 | 2498 (28) | 128 (6) | 366 (1) | 4.2 | NA | |
| RAP1 | 200 | 338 (3) | 186 (0) | 85 (3) | ND | 4.0 |
| 600 | 1231 (14) | 176 (7) | 622 (10) | 3.5 | 1.4 | |
| 1000 | 2035 (18) | 205 (9) | 715 (9) | 5.0 | NA | |
| MCB | 200 | 507 (23) | 319 (20) | 116 (17) | 1.4 | 3.2 |
| 600 | 1218 (33) | 200 (16) | 246 (23) | 3.0 | 3.5 | |
| 1000 | 1677 (33) | 214 (16) | 326 (24) | 3.8 | 3.7 | |
| ABF1 | 200 | 837 (11) | 208 (7) | 210 (7) | 2.6 | 2.5 |
| 600 | 2144 (19) | 458 (8) | 425 (9) | 2.0 | 2.4 | |
| 1000 | 2974 (23) | 607 (9) | 333 (5) | 1.9 | 1.9 | |
| REB1 | 200 | 494 (20 | 363 (0) | 217 (2) | ND | 2.5 |
| 600 | 1097 (10) | 314 (4) | 360 (2) | 1.4 | 0.6 | |
| 1000 | 1440 (13) | 340 (4) | 418 (8) | 1.3 | 2.1 | |
| MIG1 | 200 | 143 (6) | 117 (6) | 83 (6) | 1.2 | 1.7 |
| 600 | 414 (15) | 247 (12) | 225 (14) | 1.3 | 1.7 | |
| 1000 | 652 (18) | 34 (1) | 315 (14) | ND | 1.6 | |
| GAL4 | 200 | 51 (3) | 35 (2) | 5 (2) | 1.0 | 6.8 |
| 600 | 214 (7) | 149 (6) | 21 (6) | 1.2 | 8.7 | |
| 1000 | 349 (7) | 230 (5) | 27 (6) | 1.1 | 11.1 | |
| PDR3 | 200 | 24 (1) | 17 (1) | 40 (1) | 2.0 | 0.8 |
| 600 | 118 (7) | 97 (7) | 144 (7) | 1.2 | 0.8 | |
| 1000 | 182 (7) | 142 (7) | 206 (7) | 1.2 | 0.9 | |
| Repressor of CAR3 | 200 | 90 (9) | 75 (9) | 51 (1) | 1.2 | 0.2 |
| 600 | 292 (21) | 212 (15) | 119 (3) | 1.0 | 0.4 | |
| 1000 | 471 (24) | 292 (17) | 33 (0) | 1.1 | ND | |
| MATα2 | 200 | 554 (1) | 313 (1) | 143 (0) | 1.8 | ND |
| 600 | 1476 (7) | 99 (0) | 199 (0) | ND | ND | |
| 1000 | 2178 (7) | 103 (0) | 364 (0) | ND | ND | |
| TATA | 200 | 2497 (15) | 128 (0) | 141 (0) | ND | ND |
| 600 | 4275 (16) | 66 (0) | 49 (0) | ND | ND | |
| 1000 | 4944 (16) | 327 (0) | 30 (0) | ND | NA | |
| HSE, HSTF | 200 | 1641 (8) | 95 (1) | NM | 2.2 | NM |
| 600 | 4042 (12) | 39 (0) | ND | |||
| 1000 | 5225 (14) | 27 (0) | NA | |||
| GCR1 | 200 | 2778 (9) | 75 (0) | 119 (0) | ND | ND |
| 600 | 5409 (15) | 209 (0) | 167 (0) | NA | ND | |
| 1000 | 6016 (15) | 906 (3) | 227 (0) | 1.3 | NA | |
| GCN4 | 200 | 5177 (44) | 672 (5) | 38 (2) | NA | 6.2 |
| 600 | 6162 (50) | 717 (6) | 216 (3) | NA | 1.7 | |
| 1000 | 6193 (50) | 881 (8) | 193 (3) | NA | NA |
Numbers under the Candidate genes from search type columns show the number of candidates predicted with each method in each set of upstream sequences. Numbers in parentheses are the annotated elements (10; see also Materials and Methods) that were correctly predicted. The PEA value was ≤0.1 for all searches.
ND, no data obtained at this threshold; NA, not applicable for the analysis due to the large number of candidates detected in the pattern search; NM, no matrix available for this element.