Table 4.
Highest Scoring Patterns for the ClusterC(5,2,4)(0000022)
| Pattern | N+ | Total+ | Score | TRANSFAC (exact matches) |
| A. Highest score in experiment allowing patterns to have at most 3 wild cards and no group characters | ||||
| CCCCT..T | 22 | 27 | 7.09 | Y$DDR2_01, Y$DDR2_02, Y$TPI_02 |
| A..AGGGG | 22 | 27 | 7.09 | – |
| GGGGC | 20 | 27 | 4.09 | Y$GAL2_02, Y$SUC2_02, Y$RRNA_01 Y$ERG11_01 |
| GCCCC | 20 | 27 | 4.09 | Y$CYB2_02 |
| G..GGGG | 19 | 28 | 3.73 | Y$CYC1_04, Y$CYC1_05, Y$CYC1_06 |
| CCCC..C | 19 | 28 | 3.73 | Y$GAL3_01, Y$MAL2R_01 |
| CCCC...T | 25 | 42 | 3.65 | Y$SUC2_01, Y$DDR2_01, Y$DDR2_02 Y$TPI_02, Y$GAL3_01, Y$GAL4_01 Y$MAL2R_01, Y$MAL63_01, Y$PDC1_02 Y$HAP4_01 |
| A...GGGG | 25 | 42 | 3.65 | Y$SUC2_02, Y$RRNA_01, Y$ERG11_01 Y$MEL1_02, Y$FPS1_01 |
| CCCCT | 25 | 38 | 3.03 | Y$DDR2_01, Y$DDR2_02, Y$TPI_02 |
| AGGGG | 25 | 38 | 3.03 | Y$CAR1_02 |
| CCCT..TT | 19 | 22 | 2.95 | Y$DDR2_01 |
| AA..AGGG | 19 | 22 | 2.95 | – |
| GGG.TG | 20 | 21 | 2.93 | – |
| CA.CCC | 20 | 21 | 2.93 | Y$GAL1_04, Y$CYC1_12, Y$GAL1_14 Y$DDR2_02, Y$TPI_02 |
| B. Highest score in experiment allowing patterns having at most one group character with two alternative letters (all pairs allowed) | ||||
| CCCCT[GT] | 20 | 28 | 3.86 | Y$DDR2_01, Y$DDR2_02, Y$TPI_02 |
| CCCCT[AT] | 20 | 24 | 3.58 | Y$DDR2_02, Y$TPI_02 |
| [CG]CCCC | 24 | 47 | 3.27 | Y$CYB2_02, Y$GAL2_02, Y$SUC2_02, Y$RRNA_01, Y$ERG11_01 |
| CCCC[CT] | 29 | 58 | 2.94 | Y$DDR2_01, Y$DDR2_02, Y$TPI_02, Y$SUC2_02, Y$CAR1_02, Y$ERG11_01 |
| [AG]CCCC | 29 | 48 | 2.90 | Y$CYB2_02, Y$DDR2_02, Y$TPI_02, Y$CYC1_04, Y$CYC1_05, Y$CYC1_06, Y$GAL2_02, Y$SUC2_02, Y$RRNA_01, Y$CAR1_02, Y$ERG11_01, Y$GAL1_15 |
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Trivial pattern variants were removed, e.g., patterns ending with a wild-card character.
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↵No. of upstream regions matching the pattern.
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↵Total number of matches in the upstream regions.
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↵Normalized version of pattern score.
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TRANSFAC entries matching the pattern.
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↵Best patterns from experiment 2 not also found in experiment 1.
