AlignACE version 2.2 July 7, 1998 AlignACE -jSRB.orf -y -e Parameter values: expect = 10 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 YBR253W 300 bp YBR253W SRB6 1-366 transcription factor, part of Srb\/Mediator complex #2 YCR081W 300 bp YCR081W SRB8 1-4284 activation mediator subcomplex of RNA polymerase I holoenzyme #3 YDR308C 598 bp YDR308C SRB7 1-423 RNA polymerase II holoenzyme component #4 YER022W 300 bp YER022W SRB4 1-2064 subunit of RNA polymerase II holoenzyme\/mediator complex #5 YGR104C 300 bp YGR104C SRB5 1-924 subunit of RNA polymerase II holoenzyme\/mediator complex #6 YHR041C 600 bp YHR041C srb2 1-14, 116-734 RNA polymerase II holoenzyme\/mediator subunit Motif number 1 AAAAGGAAGAAAAAAAATACAAAAGATGATTA 2 144 0 AAAAAATAAA 0.931249 -157 ATGCGCTATAAAGAATATAAAAAGTAATATAT 2 192 0 AAGAAATAAA 0.959978 -109 TGCTAATCGAAAGATTAAAAAAAGGTCTATAG 2 261 1 AAGATAAAAA 0.891393 -40 CAGAAAATGAAAAAAAAAAAAAAAAAAAATTC 3 19 1 AAAAAAAAAA 0.968472 -580 AAAAAAAAAAAAAAAAATTCAAAGAATCAGCT 3 31 1 AAAAAATTAA 0.71003 -568 AATGAGATTAACGAGTAAAAAACGAATGAATG 3 95 0 ACGAGAAAAA 0.818003 -504 ATAAAGAACAAAGAAAAAAGAATGAGGAAACG 3 131 0 AAGAAAAAAA 0.981948 -468 GTAACTAAAGCAGAAGAAATAATATTGTTAGC 3 196 0 CAGAAAAAAA 0.972888 -403 TGTGTTTTAAAAGAAGATATAATAAACGAATG 3 266 0 AAGAAATAAA 0.959978 -333 AGAAAGTTAGAAAAAAAATCAATTCTGAAAGA 3 494 1 AAAAAAATAA 0.8474 -105 TGTTAAAGAGCATATAATGTATTGAAC 3 582 0 AAGAGATAAA 0.914607 -17 AGGGCGCATAAAAAATAAATAACTACCATTCA 4 18 1 AAAAAAAAAA 0.968472 -283 TGCAGTGCACAAGAGAAAACAACTTTTCCTCA 4 167 0 AAGAGAAAAA 0.960458 -134 AGTAGAACTGCAGAAAAAATAACTGAACGTAA 4 211 1 CAGAAAAAAA 0.972888 -90 TTTGCCTTTGAAAAGTAAATAATGCTTTACGT 4 237 0 AAAAGAAAAA 0.932049 -64 ACCAAGACTTCAAAAGAATCAAATAATGGCTG 5 74 0 CAAAAAATAA 0.785554 -227 TTATTTTTTTCAAATAAAAGAAAGGCAAAAGA 5 175 0 CAAATAAAAA 0.753538 -126 CTTTTATTTGAAAAAAATAAAATAACCTAGAA 5 187 1 AAAAAATAAA 0.931249 -114 GACAAACAACCAAAATAAAAAAAAAGGTAGAA 5 236 1 CAAAAAAAAA 0.952971 -65 GAAAAGCAGCCCGAAAAAAAAATGCAAAACGA 6 89 1 CCGAAAAAAA 0.86911 -512 ACTAACGCATAAGAAAACACAAGAAGAGAAAC 6 487 0 AAGAAACAAA 0.880676 -114 ***** *** ** Masking position 7 Map Score: 26.7509 Number of sites scoring better than the average of aligned sites = 9912 Number in coding regions = 2191 Number in noncoding regions = 7721 Number of orfs with sites within 600 bp upstream = 2190 Fraction of orfs with sites within 600 bp upstream = 0.351751 Motif number 2 ATAGGCATCCTGTACTCCTTTTTTTTACAAGAAA 1 277 1 TTTCTTTTTT 0.973976 -24 AGATTGTGCATTCATTAGTTTGGTTTCTCTTTGGGG 2 58 0 TCTGTTGTTT 0.895793 -243 TTAGTTTAATTTTGTTTCGTTAGATTGTGCATTCAT 2 79 0 TTTCTTGATT 0.884717 -222 TTTGTATTTTTTTTCTTCCTTTTATTAGTATGTATA 2 153 1 TTTCTTTATT 0.866585 -148 TTTTTTTTTTTTTTTTTCATTTTCTGTCCTTAGC 3 9 0 TTTCTTTCTG 0.716301 -590 TATAAGCTGATTCTTTGAATTTTTTTTTTTTTTTTT 3 31 0 TCTATTTTTT 0.787381 -568 CCATCTGAAGTATCATTCATTCGTTTTTTACTCGTT 3 82 1 TTTCTTGTTT 0.977885 -517 TACTCGTTAATCTCATTCATTCGTTTCCTCATTCTT 3 110 1 TTTCTTGTTT 0.977885 -489 CAATATTATTTCTTCTGCTTTAGTTACAAAACAAGG 3 201 1 TTTCTTGTTA 0.759825 -398 CTTGGCGTTATCCCATACATTCGTTTATTATATCTT 3 249 1 TCTCTTGTTT 0.948808 -350 ACAGTTAAACTTTTCTGATTTATTATATATTACTTA 3 307 1 TTTATTTTAT 0.628176 -292 GAAAACAACTTTTCCTCACTTTTCTTCCCCGTCTAT 4 149 0 TTTATTTCTT 0.848965 -152 AATAATGCTTTACGTTCAGTTATTTTTTCTGCAGTT 4 216 0 TCTATTTTTT 0.787381 -85 TAGTGAGAGCTCTTTTGCCTTTCTTTTATTTGAAAA 5 165 1 TTTCTTCTTT 0.865318 -136 TATTTGATAATTTTCTAGGTTATTTTATTTTTTTCA 5 195 0 TTTGTTTTTT 0.945529 -106 TTTTTTTTATTTTGGTTGTTTGTCTTCGATATTTGA 5 224 0 TTTGTTTCTT 0.916968 -77 GAAAATTCAATTTTCTACCTTTTTTTTTATTTTGGT 5 244 0 TTTCTTTTTT 0.973976 -57 TCCAGCCAGCTTTTATCGTTTTGCATTTTTTTTTCG 6 100 0 TTTGTTGCAT 0.713876 -501 CGCGTGATTTTATCGTTGTTTCTCTTCTTGTGTTTT 6 470 1 TTTGTTTCTT 0.916968 -131 TCTTGTGTTTTCTTATGCGTTAGTATGCCAGTTTCG 6 495 1 TTTCTTGTAT 0.89424 -106 * * * * ** **** Masking position 10 Map Score: 14.9481 Number of sites scoring better than the average of aligned sites = 4139 Number in coding regions = 1935 Number in noncoding regions = 2204 Number of orfs with sites within 600 bp upstream = 1430 Fraction of orfs with sites within 600 bp upstream = 0.229682 Motif number 3 ATTTATCCTGATTTTATTATACATTATACAAGTG 1 117 0 ATTATATAAT 0.90094 -184 AAAAAGTAATATATATGTATACATACTAATAAAA 2 172 0 ATATTATAAT 0.926047 -129 ATACATATATATTACTTTTTATATTCTTTATAGC 2 186 1 ATTTTTTAAT 0.775374 -115 CTTCACGCATATAAGCATATAAATGTTAGTTATA 3 353 0 ATACTATAAT 0.94728 -246 ACAGAAATTCATTCGTATATACATAAAGTTCTCA 4 52 1 ATTTTATAAT 0.959468 -249 TCATAAACGTATATATATATATATATATATACTT 4 83 1 ATATTATAAT 0.499644 -218 ATATATATATATATACTTATTGATATCAAAGTGT 4 99 1 ATACTATTAT 0.850078 -202 AGTAAACAGCATAAGTTTATTAATCACCGCACGA 5 30 1 ATATTATTAT 0.904562 -271 TGTTCACCATATTATACTATATATATAACCTCGC 6 20 1 ATTATATAAT 0.899986 -581 TATAGAATACATAGCTATATAGATGGGTAGTGCG 6 383 1 ATATTATAAT 0.971354 -218 *** * **** ** Masking position 8 Map Score: 3.40264 Number of sites scoring better than the average of aligned sites = 3719 Number in coding regions = 357 Number in noncoding regions = 3362 Number of orfs with sites within 600 bp upstream = 646 Fraction of orfs with sites within 600 bp upstream = 0.103758 Motif number 4 AGTGCTACCAAAGCCACCGGCCCCTCTTGCACTTTCTTCCA 1 46 0 AACCCGTGCA 0.813619 -255 TACATTATACAAGTGTGCCAAAGTATATACACTAAGTTAGT 1 91 0 AATGCCAACA 0.969808 -210 CCCAAAGAGAAACCAAACTAATGAATGCACAATCTAACGAA 2 59 1 AACACTAACA 0.834428 -242 AATAGTGAAAAAATAGCCGAAATAAAGAACAAAGAAAAAAG 3 143 0 AATCCGAACA 0.961714 -456 ACATTCATTTAACTTGGCGTTATCCCATACATTCGTTTATT 3 237 1 AATGCGCACA 0.969373 -362 TTTAAAGGCCAACCGTACGTGCTTAATTACAAGCTTTGTTC 3 445 1 AACACGAACA 0.980919 -154 CTATATATATAACCTCGCGCTGAGCTTTACAGGTGCGTTTG 6 36 1 AACGCGCACA 0.985901 -565 TGTATTCTATATCCACGCCTGCAAACGCACACTGTTCGTCC 6 353 0 ATCGCCAACA 0.891535 -248 GGGAAAGTGCAATTGAGCGAAGGAAGGGGCAGGTGGACTGT 6 420 1 AATGCGAGCA 0.97877 -181 ACAACGATAAAATCACGCGGCGACATCTACAGTCCACCTGC 6 448 0 AACGCGAACA 0.994541 -153 TCACTTTGGGAATCACACCGCGAAACTGGCATACTAACGCA 6 510 0 AACACCAGCA 0.917992 -91 CAAATCTTGTAAGTCGGCGCTCGAAAGCACAGTAGCAATCC 6 567 1 AATGCGAACA 0.98802 -34 ** * *** * *** Masking position 1 Map Score: 5.66637 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 304 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 5 GCTACCAAAGCCACCGGCCCCTCTTGCACT 1 54 0 CCACCGGCCC 0.99704 -247 TCCAATTGGGCAACTGGCCCAATGTTGACA 2 21 1 CAACTGGCCC 0.992925 -280 AATGTTGACAGAACTGGCCCCAAAGAGAAA 2 41 1 GAACTGGCCC 0.989666 -260 TCGCTCAATTGCACTTTCCCATGCGCACTA 6 410 0 GCACTTTCCC 0.948633 -191 CATCTACAGTCCACCTGCCCCTTCCTTCGC 6 436 0 CCACCTGCCC 0.993441 -165 ********** Masking position 3 Map Score: 3.14706 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 53 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 ACTCCTTTTTTTTACAAGAAA 1 290 1 TTTACAAGAA 0.839942 -11 GAAATTGTGTTTTAAAAGAAGATATAATAA 3 273 0 TTTAAAAGAA 0.91479 -326 AAAGTTTAACTGTAAAAGAAATTGTGTTTT 3 290 0 TGTAAAAGAA 0.954737 -309 TAAACCATTGGTTAAAAGAGGGACATAACA 3 544 1 GTTAAAAGAG 0.945647 -55 TGTTAAAGAGCATATAATGT 3 589 0 TGTTAAAGAG 0.86725 -10 AGGGCTGCAGTGCACAAGAGAAAACAACTT 4 174 0 TGCACAAGAG 0.963072 -127 ACTTTTCAAAGGCAAAAGAGATAGAGCCAA 4 253 1 GGCAAAAGAG 0.977782 -48 TAACCAAGACTTCAAAAGAATCAAATAATG 5 78 0 TTCAAAAGAA 0.932437 -223 ATAAAAGAAAGGCAAAAGAGCTCTCACTAT 5 164 0 GGCAAAAGAG 0.977782 -137 ********** Masking position 6 Map Score: 5.12348 Number of sites scoring better than the average of aligned sites = 1022 Number in coding regions = 714 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 7 CTCTTGTGCACTGCAGCCCTTTGAAAAAGT 4 184 1 CTGCAGCCCT 0.993964 -117 ATGCTGTTTACTGCAGCGATGGTGGTACTG 5 12 0 CTGCAGCGAT 0.978507 -289 CGAGGAACATCTACAGCCATTATTTGATTC 5 61 1 CTACAGCCAT 0.974414 -240 GAAGAACGAAAAGCAGCCCGAAAAAAAAAT 6 82 1 AAGCAGCCCG 0.919278 -519 CGCTATTGTTCTCCAGCCAGCTTTTATCGT 6 117 0 CTCCAGCCAG 0.979027 -484 CGCTGGTACCATGCAGCCATCACTACATAC 6 212 0 ATGCAGCCAT 0.985235 -389 ********** Masking position 5 Map Score: 1.89088 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 285 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 8 TACCTATCACTTAGTAGCATGCATAAGCCATGG 1 221 1 TTATACTGCA 0.975598 -80 AGGACCATCTGAAGTATCATTCATTCGTTTTTT 3 78 1 GAATACTTCA 0.945593 -521 TTTTTACTCGTTAATCTCATTCATTCGTTTCCT 3 106 1 TTATCCTTCA 0.926098 -493 ATTGTTCATATAACTAACATTTATATGCTTATA 3 345 1 TAATACTTTA 0.879349 -254 ATTTTTTTTCTAACTTTCTTGCAATGCGAACAA 3 480 0 TAATTCTGCA 0.930146 -119 GTTTGAATTATAATTATCTTTCAGAATTGATTT 3 509 0 TAATACTTCA 0.984947 -90 AAAAAATAAATAACTACCATTCATAACAGAAAT 4 27 1 TAATACTTCA 0.98493 -274 TCACTATATATTACTAACCTGCAAGCTAAAATG 5 138 0 TTATACTGCA 0.975598 -163 *** ** * **** Masking position 3 Map Score: 1.84265 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 89 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 AGCCCATGGCTTATGCATGCTACTAAGTGAT 1 226 0 TTATCATGCT 0.876286 -75 AATGCTGAGATTTTTGATGCTAATCGAAAGA 2 244 1 TTTTGATGCT 0.890882 -57 TAGTTATTTATTTTTTATGCGCCCTTATAAG 4 12 0 TTTTTATGCG 0.941537 -289 GCTGTAGATGTTCCTCGTGCGGTGATTAATA 5 47 0 TTCCCGTGCG 0.967855 -254 GCGCTGAGCTTTACAGGTGCGTTTGTCCTCG 6 52 1 TTACGGTGCG 0.937949 -549 TTTGCATTTTTTTTTCGGGCTGCTTTTCGTT 6 86 0 TTTTCGGGCT 0.853374 -515 ATCTTTTGAGTTTTGCGTGCGTTATCTACTG 6 287 1 TTTTCGTGCG 0.987014 -314 TCAATTGCACTTTCCCATGCGCACTACCCAT 6 405 0 TTTCCATGCG 0.987014 -196 CTTCTTGTGTTTTCTTATGCGTTAGTATGCC 6 493 1 TTTCTATGCG 0.953989 -108 **** ****** Masking position 2 Map Score: 1.5487 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 377 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 217 Fraction of orfs with sites within 600 bp upstream = 0.0348538 Motif number 10 TTTCAGTAATTCAGTCCGGGTCACACTGGA 1 150 0 TCAGTCCGGG 0.926586 -151 AGGACTTGTTTCACCCAGGGGGGTGTTTAG 2 111 0 TCACCCAGGG 0.966516 -190 GCTGTTTACTGCAGCGATGGTGGTACTGC 5 10 0 GCAGCGATGG 0.801295 -291 AGTTTATTAATCACCGCACGAGGAACATCT 5 43 1 TCACCGCACG 0.951612 -258 CCTGTAAAGCTCAGCGCGAGGTTATATATA 6 39 0 TCAGCGCGAG 0.962705 -562 CTACCGAACGTCACCGCTGGTACCATGCAG 6 226 0 TCACCGCTGG 0.986911 -375 TCAAAAGATGGCACACCGGGGGAACAAAGG 6 266 0 GCACACCGGG 0.933941 -335 ACTGTAGATGTCGCCGCGTGATTTTATCGT 6 456 1 TCGCCGCGTG 0.942558 -145 ACTTTGGGAATCACACCGCGAAACTGGCAT 6 519 0 TCACACCGCG 0.952851 -82 ATCTTGTAAGTCGGCGCTCGAAAGCACAGT 6 570 1 TCGGCGCTCG 0.935268 -31 ********** Masking position 2 Map Score: 1.46813 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 370 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 11 TAGCCGAAATAAAGAACAAAGAAAAAAGAAT 3 140 0 AAGAACAAAG 0.881259 -459 TTTCTTGCAATGCGAACAAAGCTTGTAATTA 3 468 0 TGGAACAAAG 0.949967 -131 ATTCATAGACGGGGAAGAAAAGTGAGGAAAA 4 145 1 GGGAAGAAAA 0.904489 -156 AGTATAATATGGTGAACAATGTAGCTT 6 7 0 GGGAACAATG 0.989159 -594 GTTTGTCCTCGAAGAACGAAAAGCAGCCCGA 6 72 1 GAGAACGAAA 0.855918 -529 AAAGCTGGCTGGAGAACAATAGCGGGTTGAC 6 123 1 GGGAACAATA 0.972727 -478 TGGCACACCGGGGGAACAAAGGAGAGTAGAG 6 257 0 GGGAACAAAG 0.993215 -344 AGAGGCTGAGGACGAACAGTGTGCGTTTGCA 6 344 1 GAGAACAGTG 0.904519 -257 ** ******** Masking position 6 Map Score: 0.852576 Number of sites scoring better than the average of aligned sites = 787 Number in coding regions = 611 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 12 ********** No masking Map Score: 4.48596e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 ********** No masking Map Score: 4.48596e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 4.48596e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0