AlignACE version 2.2 July 7, 1998 AlignACE -jAPC.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 YDL008W 300 bp YDL008W APC11 1-498 subunit of the anaphase promoting complex (APC) #2 YDR118W 300 bp YDR118W APC4 1-1959 subunit of the anaphase promoting complex (APC) #3 YLR102C 300 bp YLR102C APC9 1-798 subunit of the anaphase promoting complex (APC) #4 YLR127C 300 bp YLR127C APC2 1-2562 subunit of the anaphase promoting complex (APC) #5 YNL172W 578 bp YNL172W APC1 1-5247 Component of the anaphase-promoting complex #6 YOR249C 300 bp YOR249C APC5 1-2058 subunit of the anaphase promoting complex Motif number 1 GCATTAAGCGTTTTATGTTTTCACAACCCTTT 1 25 0 TTTTTTTTTC 0.942274 -276 CCGAGATAACTTTTGTATCTTCCGTGTCTGCA 1 194 1 TTTTTTCTTC 0.912165 -107 AATGCATTATTTTTTTATCTGCAGACACGGAA 1 213 0 TTTTTTCTGC 0.779272 -88 TTAGGTTTACATTTTTGTTTTCCGTAGCTAGC 2 168 1 ATTTTTTTTC 0.952946 -133 TAGGTTTTTTTTTTTGTTTTGTCAAGAGCCGC 3 199 0 TTTTGTTTGT 0.7971 -102 ATTTCCTTTTATTTAGGTTTTTTTTTTTGTTT 3 212 0 ATTTGTTTTT 0.934799 -89 TGTCACAGCTATTTCTTTCCTTCCTGAATTTG 3 272 0 ATTTTTCCTT 0.85579 -29 TATGTTTTTAATTTCGTTTCTTTAGTTCTCAG 4 65 0 ATTTGTTCTT 0.872601 -236 CTCTTCAAAAATTTCTTTTTTTATTGGGTACT 4 120 1 ATTTTTTTTT 0.951279 -181 GTTTTCGATATTTTGGCTCTTTTGTCTATTAC 4 215 0 TTTTGTCTTT 0.880268 -86 GTATTACCTAATTTTCTTTCTCTTGATGGTAT 5 61 0 ATTTCTTCTC 0.897958 -518 ATCGGCCACCTTTTATTTTTTTAAACCACAAG 5 134 1 TTTTTTTTTT 0.940254 -445 TTGACTACTTTTTTTCATTTTTATCGCTTCTT 5 327 1 TTTTCTTTTT 0.9347 -252 TTCATTTAGTATTTACATTTGCACAAAAGTAG 5 398 1 ATTTCTTTGC 0.862298 -181 TTTAATCTGTTTTTCCTTTCTTTAGTTTCTAG 5 546 1 TTTTCTTCTT 0.87242 -33 TGTTTGGGTGATTTTTATTTTTAATTTTTCCA 6 140 1 ATTTTTTTTT 0.951279 -161 AATATTGCCAATTTGTGTCTTTGACATTATTT 6 188 1 ATTTTTCTTT 0.925495 -113 ATCAGTTTTGATTTGCCTTTTCCTTTTAACTC 6 272 0 ATTTCTTTTC 0.948507 -29 **** * ***** Masking position 8 Map Score: 15.9075 Number of sites scoring better than the average of aligned sites = 13670 Number in coding regions = 3529 Number in noncoding regions = 10141 Number of orfs with sites within 600 bp upstream = 2670 Fraction of orfs with sites within 600 bp upstream = 0.428847 Motif number 2 CGAAACCATAAACTTATATATGTATATATGAAGGCATTAAG 1 49 0 ACTTAATATA 0.881464 -252 AAATAATGCATTCTTCAAAAACTTTGTACAATATCGGGAGA 1 233 1 TCTTAGTACA 0.98754 -68 GTGAGGCTCCTTCTTAAACATAGCTGTACTAATCCTGCGCT 2 52 1 TCTTAGTACA 0.987541 -249 TTTTAAGTCCAACTTTTCTATAATAATACCATATTTTGTGC 3 158 1 ACTTAATACA 0.986988 -143 GCAACTAATGAACTTACGCAGTAACATGCAAGTACCCAATA 4 141 0 ACTTAATGCA 0.984269 -160 TATCTTATAATGCTTAGAAAGTTAAATACCATCAAGAGAAA 5 36 1 TCTTAATACA 0.984016 -543 TGGATGTAAAACCTTAACCATGTCAATGCAAGGGCTCCCGC 5 181 1 ACTTAATGCA 0.984269 -398 ACTATTACGTATCTTCTCTACTTTTGTGCAAATGTAAATAC 5 406 0 ACTTAGTGCA 0.987738 -173 ACCCAAACAATACTTCGACAGTACAGTACGATATTTGTATG 6 108 0 TCTTAGTACA 0.9875 -193 * *** * **** * Masking position 10 Map Score: 6.28297 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 203 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 3 AATGTAAACCTAAAAAACCGTGAAATAACACAT 2 148 0 TAAAAACGTA 0.950791 -153 GAAACGAAATTAAAAACATACCATGTCCTGAAT 4 77 1 TAAAAAAACA 0.915224 -224 CTATATTACATAAAAATCGGCCACCTTTTATTT 5 119 1 TAAAAACGCA 0.994254 -460 CCGCACAAAGTAAAAAGAAGCGATAAAAATGAA 5 340 0 TAAAAAAGCA 0.975354 -239 AAAAACAGATTAAAACGCTGCTATAACACACTG 5 527 0 TAAAACCGCA 0.978702 -52 AAATTAAAAATAAAAATCACCCAAACAATACTT 6 134 0 TAAAAACCCA 0.975413 -167 TTGCGCTAGCTAAAAAACTGCTGCAGTTTCATC 6 218 1 TAAAAACGCG 0.978703 -83 TCGAGGAATATAAAAAACGACGAGAGTTAAAAG 6 249 1 TAAAAACACA 0.979253 -52 ****** * ** * Masking position 5 Map Score: 4.83943 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 233 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 AGTTATGCAACGCACTTTTGTCTACGCCTGC 1 141 1 CGCCTTTTGT 0.982321 -160 GTTAAACTCTCCCGATATTGTACAAAGTTTT 1 250 0 CCCATATTGT 0.914319 -51 GCATTCTGTGCTCCATTTTGTTATGCTTGGT 2 211 0 CTCATTTTGT 0.897551 -90 GCTTTTAAGTCCAACTTTTCTATAATAATAC 3 156 1 CCACTTTTCT 0.870601 -145 TATAATAATACCATATTTTGTGCGCGGCTCT 3 176 1 CCAATTTTGT 0.9658 -125 TTCTTTCCTTCCTGAATTTGTCCTTCCAAAC 3 261 0 CCTAATTTGT 0.915122 -40 TCGATATTTTGGCTCTTTTGTCTATTACTGT 4 212 0 GGCCTTTTGT 0.855262 -89 CTCTGTATTACCTAATTTTCTTTCTCTTGAT 5 66 0 CCTATTTTCT 0.878176 -513 TAAAAATCGGCCACCTTTTATTTTTTTAAAC 5 129 1 CCACTTTTAT 0.711592 -450 ATCATTCTCCCCCTCTCTTGTGGTTTAAAAA 5 151 0 CCCCTCTTGT 0.950549 -428 TAAATGAAAGCCCTATTTTGTGTAGGGTTTA 5 375 0 CCCATTTTGT 0.990125 -204 ACGTATCTTCTCTACTTTTGTGCAAATGTAA 5 410 0 TCTCTTTTGT 0.849965 -169 ACTTTGTCACCGTGAATTTGTCAGCAAGCAC 5 470 0 CGTAATTTGT 0.830964 -109 TTAACAATATTGCCAATTTGTGTCTTTGACA 6 183 1 TGCAATTTGT 0.628657 -118 *** ******* Masking position 8 Map Score: 5.50538 Number of sites scoring better than the average of aligned sites = 2344 Number in coding regions = 1657 Number in noncoding regions = 687 Number of orfs with sites within 600 bp upstream = 543 Fraction of orfs with sites within 600 bp upstream = 0.0872149 Motif number 5 TGAAAACATAAAACGCTTAATGCCTTCATA 1 34 1 AAACGCTTAA 0.947363 -267 AGCCTCACATAAAAGCTTTAAGTAATTTGA 2 30 0 AAAAGCTTTA 0.92004 -271 GTAAACCTAAAAAACCGTGAAATAACACAT 2 148 0 AAAACCGTGA 0.924076 -153 AAAAGCTTGAAAAAGCTTAGATTTTATATT 3 132 0 AAAAGCTTAG 0.946675 -169 AGTTGGACTTAAAAGCTTGAAAAAGCTTAG 3 142 0 AAAAGCTTGA 0.977677 -159 AACAAAAAAAAAAACCTAAATAAAAGGAAA 3 213 1 AAAACCTAAA 0.924268 -88 GATGGAAAAACCTTAACTATAAGCCA 4 285 0 AAAACCTTAA 0.985506 -16 TGATGGATGTAAAACCTTAACCATGTCAAT 5 178 1 AAAACCTTAA 0.985506 -401 ********** Masking position 3 Map Score: 5.09399 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 181 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 CTATGTTTAAGAAGGAGCCTCACATAAAAGCTTT 2 41 0 GAAGGGCCAA 0.983779 -260 GTTTTCCGTAGCTAGCGCCTAAGTTTAACCAAGC 2 184 1 GCTAGGCCAT 0.946396 -117 TGAAAGTTCCATAATTGAAATACGT 3 2 1 GAAAGTCCAT 0.87703 -299 TTTTGTTTTGTCAAGAGCCGCGCACAAAATATGG 3 186 0 TCAAGGCCGA 0.949849 -115 GTTAGTACTTTGAAGAGCCTGAGAACTAAAGAAA 4 47 1 TGAAGGCCAA 0.954175 -254 GCAGTAACATGCAAGTACCCAATAAAAAAAGAAA 4 131 0 GCAAGACCAA 0.982004 -170 AGTAATAGACAAAAGAGCCAAAATATCGAAAACT 4 214 1 AAAAGGCCAT 0.892291 -87 GCAGCGAAGCGAAGGGGCCCGATAGGAACTTTTG 5 224 0 GAAGGGCCAA 0.983442 -355 GAATTTGTCAGCAAGCACCAAAAATGTCGATGCT 5 454 0 GCAAGACCAA 0.982004 -125 AATTATCTGTTCAAGAGCCTTATATCAAATCCAT 6 77 1 TCAAGGCCAA 0.989035 -224 ***** *** * * Masking position 8 Map Score: 3.3557 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 443 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 7 AAGCAAAGTGGCAATACAGATTATAAAAAT 1 281 1 GCAATACAGA 0.901025 -20 GAAGAATTCCGAAAGAAAGAA 2 2 0 GAAAGAAAGA 0.977605 -299 TAAATAAAAGGAAATTAAGAACAGGGAACT 3 229 1 GAAATTAAGA 0.811858 -72 ACAAATTCAGGAAGGAAAGAAATAGCTGTG 3 271 1 GAAGGAAAGA 0.949417 -30 AAGAGCCTGAGAACTAAAGAAACGAAATTA 4 59 1 GAACTAAAGA 0.864784 -242 ACCATGTCCTGAATGCAAGAACGTCTCTTC 4 96 1 GAATGCAAGA 0.811674 -205 CCAAAATATCGAAAACTAGACGAAAGCCAG 4 231 1 GAAAACTAGA 0.764405 -70 AAAACTAGACGAAAGCCAGACTTAGCGGGA 4 242 1 GAAAGCCAGA 0.977578 -59 AGAAAATTAGGTAATACAGAGGACAGAAGG 5 76 1 GTAATACAGA 0.915476 -503 ACAGAGGACAGAAGGACAGAAGTCGTTTCT 5 91 1 GAAGGACAGA 0.967671 -488 CGATTTTTATGTAATATAGAAACGACTTCT 5 108 0 GTAATATAGA 0.747132 -471 CTAAAGAAAGGAAAAACAGATTAAAACGCT 5 541 0 GAAAAACAGA 0.949975 -38 ********** Masking position 3 Map Score: 5.10638 Number of sites scoring better than the average of aligned sites = 1986 Number in coding regions = 1225 Number in noncoding regions = 761 Number of orfs with sites within 600 bp upstream = 626 Fraction of orfs with sites within 600 bp upstream = 0.100546 Motif number 8 ACTTATATATGTATATATGAAGGCATTAAGCGT 1 46 0 GTATATATAG 0.95019 -255 AGACTCATGTGTTAATTTTGACGCATATGTGTT 2 122 1 GTTAATTTAG 0.952936 -179 TCATATGCTGGTATATATGTACGACTAAATAAT 3 100 0 GTATATATAG 0.95019 -201 AATAAAAAAAGAAATTTTTGAAGAGACGTTCTT 4 112 0 GAAATTTTAG 0.783948 -189 CCAAAGGTTTGAAAATTTAGATGCAACTAATGA 4 171 0 GAAAATTTAG 0.952936 -130 TAGCGGGACTGTAAATATTTATGGCTTATAGTT 4 264 1 GTAAATATAG 0.98117 -37 AGCATTATAAGATAATATTAAAGGGAAAGTGTT 5 17 0 GATAATATAG 0.952931 -562 TGGCAATATTGTTAATATATAAGCGTTGGAAAA 6 165 0 GTTAATATAG 0.97013 -136 ******** * * Masking position 11 Map Score: 1.71168 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 410 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 9 AGAGCCGCGCACAAAATATGGTATTATTAT 3 177 0 ACAAAATATG 0.902043 -124 GTTTGGAAGGACAAATTCAGGAAGGAAAGA 3 261 1 ACAAATTCAG 0.885582 -40 AATAGCTGTGACAAAGTAAG 3 291 1 ACAAAGTAAG 0.991029 -10 ATACATACTATCAAAGTAAGGGCATTGGTG 5 296 0 TCAAAGTAAG 0.958217 -283 TTTACACCGCACAAAGTAAAAAGAAGCGAT 5 349 0 ACAAAGTAAA 0.934762 -230 TAAACCCTACACAAAATAGGGCTTTCATTT 5 375 1 ACAAAATAGG 0.931731 -204 ATTCACGGTGACAAAGTGAGCTAGAATATT 5 484 1 ACAAAGTGAG 0.97584 -95 ********** Masking position 5 Map Score: 0.977096 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 307 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 10 ********** No masking Map Score: -7.23089e-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 11 ********** No masking Map Score: -7.23089e-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 12 ********** No masking Map Score: -7.23089e-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