AlignACE version 2.2 July 7, 1998 AlignACE -jPOL.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 YBL035C 300 bp YBL035C POL12 1-2118 B subunit of DNA polymerase alpha-primase complex #2 YBR088C 423 bp YBR088C pol30 1-777 profilerating cell nuclear antigen (PCNA)\; accessory factor for DNA polymerase delta, mRNA increases in G1, peaks in S in mitosis, and increases prior to DNA synthesis in meiosis #3 YCR014C 300 bp YCR014C POL4 1-1749 DNA polymerase IV #4 YEL055C 600 bp YEL055C POL5 1-3069 DNA polymerase V that has motifs typical of DNA polymerase family #5 YJR043C 300 bp YJR043C POL32 1-1053 third (55 kDa) subunit of DNA polymerase delta #6 YNL262W 371 bp YNL262W pol2 1-6669 DNA polymerase II #7 YNL102W 333 bp YNL102W pol1 1-4407 DNA polymerase I alpha subunit, p180 Motif number 1 TCACGGTAAAAAAAAATTACGCGTCTACCACGCT 1 79 0 AAATACGCGT 0.98919 -222 ATCCAAAAAAAAAAAGTTACGCGTTTCGCGTTTT 2 229 0 AAATACGCGT 0.98919 -195 AAAGGAAGGCTAAAGCAAAAGTGTTTCTTATATA 2 310 0 TAAAAAGTGT 0.80014 -114 AAAGGCCGGGTAAAATGATAGCGTCCGTTGATTT 4 410 0 TAAATAGCGT 0.912941 -191 CCATCGCAATAAAATTTTTCGTGTTATTCACGCT 4 446 0 AAATTCGTGT 0.877467 -155 TTCGCGTGTTTAACTCATACGCGTTTACTACTTC 5 159 0 TAATACGCGT 0.992591 -142 TTTTCAAAATTAAGAGTTTCGCGTGTTTAACTCA 5 176 0 TAATTCGCGT 0.983782 -125 TCAGGTAGGGTAACCAGAACGCGTAAGTTTCTTG 6 249 1 TAAAACGCGT 0.992591 -123 GCTAACAAAAAAATTTTAACGCGTTTGAATAGAT 7 126 0 AAAAACGCGT 0.989189 -208 TGTTAGCCTATAAGTAAAACGCGTCGCGTGTATC 7 153 1 TAAAACGCGT 0.992591 -181 *** ******* Masking position 3 Map Score: 11.1109 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 98 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 CGCCTCAAACGAATAGAGAATAGCGTGGTAGA 1 58 1 GAAAGAGATA 0.941559 -243 TACAGTTTTAGAAAAGAGAAAGAACTAAGAAA 1 128 0 GAAAGAGAAG 0.972264 -173 TACATAAAAGAAAAGAAGGATATATAAGTAAA 2 117 0 AAAGAAGATA 0.759791 -307 GTGCAAGTGGAAAGAAAGGAAGGCTAAAGCAA 2 326 0 AAAAAAGAAG 0.849908 -98 CGGCGAAAGTGAAAGGTGCAAGTGGAAAGAAA 2 341 0 GAAGGTGAAG 0.960472 -83 TACGCAGTCAAAAGAGAGAAAAA 2 411 1 AAAAGAGAAA 0.960025 -13 AAAAAGAAAAAACAGGAGGAAAATTAGCGGTA 3 95 0 AACGGAGAAA 0.8098 -206 GGAGATAGAAGAATAGTGCAAGCGAAATACTA 3 142 0 GAAAGTGAAG 0.952366 -159 TAACTGATTCGAAAAGTGGAAACTTACAGTTC 4 134 1 GAAAGTGAAA 0.956487 -467 TTGCAATAATGAAAGGAGGAAAACAAAACCTT 4 240 1 GAAGGAGAAA 0.979097 -361 TTAAAATGGTAAAAGATGCAAGAAACTTACGC 6 269 0 AAAGATGAAG 0.796961 -103 AGGACCTATCAAAAAGAGCATATGATGATGAA 6 308 1 AAAAGAGATA 0.909416 -64 GATGTGTGATGAATGAAGAATAGAGATTGCAG 7 97 0 GAAGAAGATA 0.835419 -237 GGCATAAAATAAACAGTGGAAA 7 322 1 AAAAGTGAAA 0.931961 -12 *** **** *** Masking position 10 Map Score: 9.1953 Number of sites scoring better than the average of aligned sites = 2726 Number in coding regions = 1660 Number in noncoding regions = 1066 Number of orfs with sites within 600 bp upstream = 879 Fraction of orfs with sites within 600 bp upstream = 0.141182 Motif number 3 TAAAAAAAAATTACGCGTCTACCACGCTAT 1 77 0 TTACGCGTCT 0.91483 -224 TTTTTTACCGTGACGCGTCTCACCAGAGTT 1 100 1 TGACGCGTCT 0.656102 -201 AAAAAAAAAGTTACGCGTTTCGCGTTTTGG 2 227 0 TTACGCGTTT 0.96274 -197 TGTTTAACTCATACGCGTTTACTACTTCCG 5 157 0 ATACGCGTTT 0.696944 -144 TGCAAGAAACTTACGCGTTCTGGTTACCCT 6 255 0 TTACGCGTTC 0.971751 -117 AAAAAAATTTTAACGCGTTTGAATAGATGT 7 124 0 TAACGCGTTT 0.720565 -210 TGGATACACGCGACGCGTTTTACTTATAGG 7 159 0 CGACGCGTTT 0.768288 -175 ********** Masking position 3 Map Score: 9.10603 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 17 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 TGCCTAAGAATGTCTTTAAAATGATCATGTTCATCGCC 1 24 1 TGAAAAATAT 0.750216 -277 ATAATATATTTGCATATAAAAATATCAAGATAATTGAT 1 207 1 TGAAAAATAA 0.891354 -94 CAGGAGCAAGTGACTGAAAAAAAAAAAA 1 283 1 TGAAAAAAAA 0.881073 -18 AAGAAGGATATATAAGTAAAATAATGATAATAGTAATA 2 99 0 TAAAAAATAT 0.725247 -325 CAGCATAAGTTGTGCGAAAAAGGAAGAGAATACATAAA 2 141 0 TGAAAAAAAG 0.955428 -283 ATGGAGAAGAAAAATGCTAAATAATTAGATATTGAAGA 2 181 0 AATAAAATAG 0.792671 -243 CTATCAGTTGAAATCCAAAAAAAAAAAGTTACGCGTTT 2 237 0 AAAAAAAAAG 0.944481 -187 AGAGGAAGCAAAGTACGAAAACTATCAGTTGAAATCCA 2 258 0 AAAAAAATAG 0.949594 -166 ATTTTATCTTTACTTAAAAAAGAAAAAACAGGAGGAAA 3 105 0 TAAAAAAAAA 0.866863 -196 GTTCTTTGCAAGCCCTTAAAATTATTAGCCCCATGTAT 3 213 0 AGAAAAATAG 0.955428 -88 GTCACAGTGGTAATAAGTAAAGGATAAACATGCGACCT 3 257 1 TATAAAATAA 0.594041 -44 TGGCTGCCTCTGCGGTAAAAACTATCAAAATATTATTT 4 315 1 TGAAAAATAA 0.891354 -286 GGACATAAAATATCCGCAAAAGTAATAGTCTTCAAAAT 4 376 1 TAAAAAAAAG 0.949594 -225 TCATAAGGTGAAACGATAAAAATATAAAAATTAAGCTT 5 11 0 AAAAAAATAA 0.866863 -290 ACTTCTGCGTACTTTTCAAAATTAAGAGTTTCGCGTGT 5 184 0 ACAAAAAAAG 0.854985 -117 CTTACAATCGAAAAGTCAAAAAGATGAGTTGTAGTATA 6 65 1 AAAAAAATAG 0.949594 -307 AAAGATGAGTTGTAGTATAAAACAACAGCTCTGGTGTG 6 84 1 TGTAAAAAAG 0.813092 -288 CTGTTTTAGCACTGAGAAAAAGTAATAGTAACACTGTC 6 155 1 ACAAAAAAAG 0.854985 -217 AAATAGTATCAAGGCATAAAATAAACAGTGGAAA 7 310 1 AAAAAAAAAG 0.944481 -24 ** **** ** ** Masking position 9 Map Score: 11.8557 Number of sites scoring better than the average of aligned sites = 3022 Number in coding regions = 1362 Number in noncoding regions = 1660 Number of orfs with sites within 600 bp upstream = 1164 Fraction of orfs with sites within 600 bp upstream = 0.186958 Motif number 5 AGACACATATAACATTTTGTTTCATATACATA 1 178 1 AACTTTGTTT 0.762925 -123 CCTCCCATACAACGTACTTTTGAAACTTCAGA 2 33 1 AACTCTTTTG 0.909785 -391 CAACCTACTCAACTTCTTTCTGAAGTTTCAAA 2 51 0 AACTTTTCTG 0.981158 -373 CTAATTATTTAGCATTTTTCTTCTCCATCCGA 2 191 1 AGCTTTTCTT 0.968654 -233 CGAAACGCGTAACTTTTTTTTTTTGGATTTCA 2 235 1 AACTTTTTTT 0.923006 -189 GGCTAAAGCAAAAGTGTTTCTTATATATAATT 2 305 0 AAATTTTCTT 0.753555 -119 TAGTGCTTGCTGCTTGTTGCTGTGAGTGAAAA 2 377 0 TGCTTTGCTG 0.803058 -47 TAAATATCTGAACTTACTTCTGCTAATGGTTG 4 94 1 AACTCTTCTG 0.959942 -507 TTTCCACAAGTGCATCTTTTTGTCCACAAAAA 4 577 1 TGCTTTTTTG 0.86472 -24 AAGCTTAATTTTTATATTTTTAT 5 2 1 AGCTATTTTT 0.601002 -299 ATTGCGATGTAACGAACTTCTGCGTACTTTTC 5 205 0 AACACTTCTG 0.686887 -96 AGTTAACTAAAGCCTATTTCTGGTTGTTAGTT 5 266 0 AGCTTTTCTG 0.982605 -35 TATATATACGTGCATTTTTCTTAAAGAAATAT 7 46 1 TGCTTTTCTT 0.89258 -288 AAAGAAATATAACTTTTTTCTTGTACTGCCTG 7 68 1 AACTTTTCTT 0.966086 -266 CAAACGCGTTAAAATTTTTTTGTTAGCCTATA 7 133 1 AAATTTTTTG 0.701687 -201 *** * ****** Masking position 8 Map Score: 7.09118 Number of sites scoring better than the average of aligned sites = 2580 Number in coding regions = 1820 Number in noncoding regions = 760 Number of orfs with sites within 600 bp upstream = 574 Fraction of orfs with sites within 600 bp upstream = 0.092194 Motif number 6 AGGTAAATTTAGGCAGGAGCAAGTGACTGAAAAAA 1 270 1 AGAAGCAAGG 0.952594 -31 TCTCCATCCGACGCACCAAAACGCGAAACGCGTAA 2 212 1 AGAAAAACGG 0.967166 -212 AGCACTAAGTACGCAGTCAAAAGAGAGAAAAA 2 402 1 AGACAAAAGG 0.955352 -22 TTACTTAAAAAAGAAAAAACAGGAGGAAAATTAGC 3 99 0 AGAAACAGGG 0.969181 -202 GTAATAAGTAAAGGATAAACATGCGACCTGTTAGA 3 266 1 AGAAACATGG 0.954991 -35 CCTCAACTATAACGATTAACAAGTGTTTACGAACT 4 48 0 ACAAACAAGG 0.985801 -553 TGAATCGGGTATCCATTAACAAGGGTGATTCTTTC 4 546 1 ACAAACAAGG 0.985802 -55 CTGGAAGAGGACCTATCAAAAAGAGCATATGATGA 6 301 1 ACAAAAAAGG 0.972482 -71 TTCATCACACATCTATTCAAACGCGTTAAAATTTT 7 116 1 ACACAAACGG 0.920786 -218 * * * ****** * Masking position 5 Map Score: 2.10582 Number of sites scoring better than the average of aligned sites = 363 Number in coding regions = 204 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 7 TGTTCATCGCCTCAAACGAATAGAGAATAGCGTGG 1 51 1 CAGAATAGAG 0.946768 -250 GAAGAGAATACATAAAAGAAAAGAAGGATATATAA 2 122 0 CAGAAAAGAA 0.9818 -302 AAAAGGACGGCGAAAGTGAAAGGTGCAAGTGGAAA 2 345 0 CAGAAAGGTG 0.961565 -79 CGACCAATAACTGATTCGAAAAGTGGAAACTTACA 4 127 1 CAGAAAAGTG 0.972314 -474 CGCCCATCAGCGCATCTGAAAGTAGCCTTGAAGGA 4 164 0 CAGAAAGTAG 0.967206 -437 ACGTTAATTGCAATAATGAAAGGAGGAAAACAAAA 4 233 1 CTGAAAGGAG 0.926786 -368 AAAGTTACACCGTAGTGGAAAATAGACCTATTCGT 5 118 0 CAGAAAATAG 0.976431 -183 TTCTGGTTACCCTACCTGAAAATAAACCATTCTGA 6 233 0 CAGAAAATAA 0.946466 -139 TATATATCATCCAATGAGTAAAGAATTTAATTCAG 7 195 0 CAGTAAAGAA 0.883591 -139 CCAATTCAGACTCACGAGAAAAAAAACTGTCTTCA 7 258 1 CAGAAAAAAA 0.874954 -76 * * ******** Masking position 10 Map Score: 2.00952 Number of sites scoring better than the average of aligned sites = 1031 Number in coding regions = 690 Number in noncoding regions = 341 Number of orfs with sites within 600 bp upstream = 301 Fraction of orfs with sites within 600 bp upstream = 0.0483456 Motif number 8 CATATAAAAATATCAAGATAATTGATTGTC 1 219 1 TATCAAGATA 0.648859 -82 GATTCTTCAATATCTAATTATTTAGCATTT 2 178 1 TATCTAATTA 0.820523 -246 AGGGAGGGTATATCTAAATATCTGAACTTA 4 80 1 TATCTAAATA 0.665493 -521 CCCATCAGCTTTTCAAGTTATGTATACGTT 4 208 1 TTTCAAGTTA 0.839681 -393 CGGTAAAAACTATCAAAATATTATTTTGCA 4 327 1 TATCAAAATA 0.939888 -274 CGAGACTCTGTATCAAGATCCATATTGCAC 6 119 0 TATCAAGATC 0.907778 -253 GAGCACATTCTATCAAGATAACACTCTCAG 6 341 1 TATCAAGATA 0.648859 -31 ********** Masking position 6 Map Score: 1.99576 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 223 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 9 TTTTTTTTGGATTTCAACTGATAGTTTTCGTAC 2 251 1 ATTTAACTGA 0.962057 -173 TTCGCCGTCCTTTTTCACTCACAGCAACAAGCA 2 366 1 TTTTCACTCA 0.855002 -58 TTCCATTATTATTAGCACTGCAACGTCCTGGTT 3 62 0 ATTACACTGA 0.984325 -239 TCCTTTACTTATTACCACTGTGACATATAAGTT 3 248 0 ATTACACTGA 0.984325 -53 CAAAATATTATTTTGCATTGGTAAATATGATAG 4 340 1 TTTTCATTGA 0.888781 -261 GATATGCTGTTTTAGCACTGAGAAAAAGTAATA 6 149 1 TTTACACTGA 0.970536 -223 AAAAAGTAATAGTAACACTGTCAGTGTTCGTCA 6 171 1 AGTACACTGA 0.936191 -201 GTTTATTGTCATTTGAATTGTCAGAATGGTTTA 6 213 1 ATTTAATTGA 0.833134 -159 ATCTTTTACCATTTTAACTGGAAGAGGACCTAT 6 284 1 ATTTAACTGA 0.962057 -88 **** ***** * Masking position 7 Map Score: 1.37412 Number of sites scoring better than the average of aligned sites = 563 Number in coding regions = 407 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 10 GTGCAAGCGAAATACTATTTTATCTTTACT 3 129 0 AATACTATTT 0.847087 -172 GTCTCGGTCTAAAATTACTTTGAGATGTTC 3 181 1 AAAATTACTT 0.885302 -120 AAACTATCAAAATATTATTTTGCATTGGTA 4 333 1 AATATTATTT 0.947373 -268 GATTTTGAAGACTATTACTTTTGCGGATAT 4 385 0 ACTATTACTT 0.96157 -216 GTTAATGTGAAATATTATTTCGAGCTGATC 5 239 0 AATATTATTT 0.947373 -62 TGACAGTGTTACTATTACTTTTTCTCAGTG 6 164 0 ACTATTACTT 0.96157 -208 TTCTTAAAGAAATATAACTTTTTTCTTGTA 7 63 1 AATATAACTT 0.885289 -271 ********** Masking position 4 Map Score: 1.10816 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 184 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 11 CTACCTCCCATACAACGTACTTTTGAAACT 2 30 1 TACAACGTAC 0.951177 -394 TAACACATAATGCAACCTACTCAACTTCTT 2 65 0 TGCAACCTAC 0.966527 -359 TACCAGAGGAAGCAAAGTACGAAAACTATC 2 270 0 AGCAAAGTAC 0.93788 -154 TTATTAGCACTGCAACGTCCTGGTTATATA 3 57 0 TGCAACGTCC 0.978821 -244 TTTAAGGGCTTGCAAAGAACTTATATGTCA 3 231 1 TGCAAAGAAC 0.969359 -70 CTCTTAATTTTGAAAAGTACGCAGAAGTTC 5 194 1 TGAAAAGTAC 0.91837 -107 CTGATTGCGATGTAACGAACTTCTGCGTAC 5 210 0 TGTAACGAAC 0.909977 -91 ********** Masking position 5 Map Score: 0.692122 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 291 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 12 AGAATAGCGTGGTAGACGCGTAATTTTTTT 1 74 1 GGTAGACGCG 0.989296 -227 AGAAACTCTGGTGAGACGCGTCACGGTAAA 1 103 0 GTGAGACGCG 0.986107 -198 GCACCAAAACGCGAAACGCGTAACTTTTTT 2 224 1 GCGAAACGCG 0.980477 -200 CGACGGAAGTAGTAAACGCGTATGAGTTAA 5 154 1 AGTAAACGCG 0.935319 -147 ACGCGTATGAGTTAAACACGCGAAACTCTT 5 169 1 GTTAAACACG 0.930534 -132 TAGCCTATAAGTAAAACGCGTCGCGTGTAT 7 156 1 GTAAAACGCG 0.969126 -178 AGTAAAATTGGATACACGCGACGCGTTTTA 7 167 0 GATACACGCG 0.948486 -167 ********** Masking position 6 Map Score: 2.03498 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 75 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 13 ATTCTCTATTCGTTTGAGGCGATGAACATG 1 49 0 CGTTTGAGGC 0.963524 -252 ACTTACAGTTCCTTCAAGGCTACTTTCAGA 4 155 1 CCTTCAAGGC 0.974944 -446 ATAGTTTTTACCGCAGAGGCAGCCAGTAAG 4 310 0 CCGCAGAGGC 0.96942 -291 GTTATTCACGCTTTAAAGGCCGGGTAAAAT 4 428 0 CTTTAAAGGC 0.943629 -173 GTTAAATTGCCCTCTAAGGCAATTCTGGCC 4 478 0 CCTCTAAGGC 0.98648 -123 TGTCAGTGTTCGTCAAAGGCCCAAGTTTAT 6 189 1 CGTCAAAGGC 0.986263 -183 ********** Masking position 7 Map Score: 0.0981762 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 159 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 14 ********** No masking Map Score: -6.5843e-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 15 ********** No masking Map Score: -6.5843e-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