Additional file 4 Original position weight matrices (PWM) in two different formats. For Rap1_MR2 and IFHL the rows correspond to the sequence positions and each row contains weights for the four bases in alphabetic order (A,C,G,T). For the other factors each column correspond to one sequence position and each row contains the base weights in the order given in the first column (A,C,T,G). Rap1_MR2 33 12 4 50 74 6 12 8 26 69 4 2 94 5 1 1 0 50 1 50 2 98 0 0 3 87 1 9 51 1 41 7 13 8 9 70 90 1 6 3 5 94 0 2 89 9 0 2 3 19 3 74 22 26 2 50 IFHL 1 41 8 0 0 19 0 31 39 0 7 4 0 0 50 0 5 1 44 0 0 50 0 0 11 6 28 5 1 0 49 0 27 5 18 0 23 6 21 0 Abf1 A -0.999 -7.562 -7.562 -7.562 0.304 -0.540 0.860 0.323 1.260 0.640 -7.562 -7.562 1.684 -7.562 C 0.454 2.390 -7.562 -7.562 -0.401 0.363 -1.682 -1.559 -1.149 -7.562 -0.250 -7.562 -7.562 0.394 T 0.913 -7.562 -7.562 1.684 -0.371 0.490 -0.731 0.473 -7.562 -7.562 1.434 -7.562 -7.562 1.270 G -7.562 -7.562 2.390 -7.562 0.299 -0.831 0.011 -0.694 -0.158 1.436 -7.562 2.390 -7.562 -7.562 Reb1 A -1.099 -2.176 -1.468 -6.524 -6.524 -6.524 -6.524 1.679 1.679 -6.524 C -6.524 1.784 2.216 -6.524 -6.524 -6.524 -6.524 -6.524 -6.524 1.370 T 0.699 -2.425 -6.524 -6.524 -6.524 -6.524 1.679 -6.524 -6.524 0.499 G 0.881 0.208 -6.524 2.383 2.383 2.383 -6.524 -6.524 -6.524 -1.498 Fhl1 A 1.360 -6.858 -6.858 -6.858 1.195 -6.858 -6.858 -6.858 0.672 -6.858 -6.858 C -6.858 -6.858 -6.858 -0.277 -2.086 1.298 -6.858 -6.858 -6.858 -6.858 -6.858 T -6.858 1.681 -6.858 1.436 -0.755 0.770 -6.858 -6.858 -6.858 1.681 -0.068 G 0.073 -6.858 2.386 -6.858 -1.616 -6.858 2.386 2.386 1.401 -6.858 1.881 Sfp1 A 0.929 -4.079 -11.731 -3.053 1.412 -2.460 -1.593 -3.457 0.596 -11.731 -5.072 C -3.502 -4.084 -11.720 -0.914 -5.077 1.589 -4.084 -11.720 -4.084 -11.720 -5.077 T -1.888 1.428 -11.731 1.362 -3.053 0.346 -4.079 -11.731 -2.738 1.626 -0.800 G 0.671 -0.836 2.506 -2.346 -0.914 -11.725 2.294 2.463 1.359 -11.720 2.183 Rpn4 A 0.821 1.630 1.630 0.260 0.657 -4.087 -0.290 0.821 -4.087 0.472 1.630 -1.190 1.224 -1.190 0.260 0.472 0.821 0.657 0.472 0.260 0.260 0.011 -4.087 -4.087 C -0.561 -4.087 -4.087 -0.561 -4.087 -4.087 -0.018 -0.018 2.325 -0.018 -4.087 0.375 -4.087 -4.087 0.684 -0.018 -0.018 -0.561 -0.561 -1.441 0.375 -1.441 -4.087 -4.087 T -4.087 -4.087 -4.087 0.011 -0.290 -4.087 0.260 -4.087 -4.087 -0.671 -4.087 0.657 -0.290 1.441 -2.008 -0.290 -1.190 0.011 -0.290 0.472 0.260 0.472 1.224 1.630 G 0.684 -4.087 -4.087 -0.018 0.375 2.325 -0.018 0.375 -4.087 -0.018 -4.087 -0.561 -4.087 -4.087 0.375 -0.561 -0.561 -1.441 -0.018 -0.561 -4.087 -0.018 0.375 -4.087 Cbf1 A -4.087 1.630 -4.087 -4.087 -2.008 -4.087 1.630 -4.087 C 2.325 -4.087 2.325 -4.087 -4.087 -4.087 -4.087 1.916 T -4.087 -4.087 -4.087 -4.087 1.539 -4.087 -4.087 -1.190 G -4.087 -4.087 -4.087 2.325 -4.087 2.325 -4.087 -0.561 Yap1 A 1.333 -4.700 -4.700 1.651 -4.700 -4.700 1.017 1.651 -4.700 0.355 C 0.071 -4.700 -4.700 -4.700 -4.700 -4.700 0.896 -4.700 -4.700 1.621 T -4.700 1.651 1.651 -4.700 -4.700 1.651 -4.700 -4.700 0.611 -4.700 G -4.700 -4.700 -4.700 -4.700 2.350 -4.700 -4.700 -4.700 1.417 -4.700 Met31 A -3.700 -3.700 1.611 0.398 -3.700 -3.700 -0.284 -0.803 -0.803 -3.700 -1.621 1.611 C 1.541 2.303 -3.700 1.325 -3.700 -1.054 -1.054 1.071 -3.700 -3.700 -3.700 -3.700 T 0.398 -3.700 -3.700 -1.621 1.611 -0.803 0.097 -0.284 -3.700 -3.700 0.647 -3.700 G -3.700 -3.700 -3.700 -3.700 -3.700 1.896 0.762 -0.174 2.045 2.303 1.071 -3.700 Gcn4 A 0.714 0.141 -5.170 -5.170 1.662 -5.170 -5.170 -5.170 1.662 -5.170 C -0.398 0.072 -5.170 -5.170 -5.170 -5.170 -5.170 2.363 -5.170 1.053 T -5.170 -0.823 1.662 -5.170 -5.170 -5.170 1.662 -5.170 -5.170 0.547 G 0.834 0.575 -5.170 2.363 -5.170 2.363 -5.170 -5.170 -5.170 -0.398 Leu3 A 1.641 0.167 -0.045 1.234 -0.294 1.641 -4.392 -0.595 -4.392 0.352 -0.976 -4.392 -4.392 -4.392 -4.392 C -4.392 -0.865 -0.865 0.379 -0.865 -4.392 -4.392 -0.865 0.379 -1.745 0.071 -4.392 -4.392 -4.392 -4.392 T -4.392 -0.045 -4.392 -4.392 0.167 -4.392 1.411 0.516 1.234 -0.045 0.919 1.641 1.641 -4.392 1.641 G -4.392 0.379 1.611 -4.392 0.634 -4.392 -0.323 0.379 -4.392 0.379 -1.745 -4.392 -4.392 2.339 -4.392