AlignACE version 2.2 July 7, 1998 AlignACE -jMSH.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 YCR092C 300 bp YCR092C MSH3 1-3144 mutS homolog, forms a complex with Msh2p to repair insertion-deletion mispairs\; redundant with Pms3\/Msh6p in repair of insertion-deletion mispairs #2 YDL154W 300 bp YDL154W MSH5 1-2706 MutS homolog involved in chromosome exchange #3 YDR097C 340 bp YDR097C MSH6 1-3729 Homolog of the human GTBP protein, forms a complex with Msh2p to repair both single-base and insertion-deletion mispairs, redundant with Msh3p in repair of insertion-deletion mispairs #4 YFL003C 328 bp YFL003C MSH4 1-2637 meiosis specific protein, E.coli MutS protein, localizes to discrete sites on meiotic chromosomes #5 YHR120W 300 bp YHR120W msh1 1-2880 mutS homolog involved in mitochondrial DNA repair #6 YOL090W 300 bp YOL090W msh2 1-2895 MutS homolog encoding major mismatch repair activity in mitosis and meiosis, functions with Pms1p and Pms2\/Mlh1p in a complex which interacts with either Pms3\/Msh6p to repair single-base and insertion-deletion mispairs, or Msh3p to repair only insertion-deletion mispairs Motif number 1 CAGCATCTAATTTAGAAACATCAAAGGAAAAACAGGCCGCT 1 30 0 TTAAATAAAA 0.979215 -271 TGGCAACCAAAGTCAAACCATCGAATTCGAATAAGATAAAC 1 181 0 ATACATAAAA 0.912997 -120 ACAGAGTAGAAAGATCTAACTAAAAAGCCTCAGCT 2 5 1 ATAAATAAAA 0.938481 -296 GTAATAAACATATGTAACTTTTTAACCTTAAAACATACTAA 2 115 1 TTACTTAAAA 0.830209 -186 GGCGGTTAATTATTAAAAAATTGAAGCTAAAATCAAGGTTA 2 214 1 TTAAATAAAA 0.979215 -87 ATAAATAGATGTATTTAGTGTAAATTGAAACAGAAAAGTC 3 10 1 TTTATGAAAA 0.651655 -331 GGGCAATGGTTGTTCAAAAAGCCAAACTTAACCAGAAGCCA 3 103 0 TTAAAGAAAA 0.981686 -238 CTCTTATTAGTTTCAACAGATGTAATTTCAAATATTTTCTC 3 222 0 TTAAATAAAA 0.979215 -119 AACTAGTTAATTTTGACAAAGCCAATTTGAACTCCAAA 3 313 1 TTAAAGAAAA 0.981686 -28 TGGAAAAAGATATGATACAATAAAATCTAAATCTTAGAAAC 4 29 0 TTTCATAAAA 0.882296 -300 ATTTTACTTAAAGTGAAACATATAAAAATAACTAGTTATAG 4 260 1 AGAAATAAAA 0.803743 -69 TAACATATCGTTGCTTTCCAGCAAAAGGTAAAGATAAATAC 5 58 1 TGTCAGAAAA 0.69602 -243 GCAAACTGACCAAAAATCCAATCAGAACTCCAGCACT 6 7 1 TAAAATAAAA 0.891023 -294 CAGCACTCCGTATAAACAAAGCCAAAGACAAGTTCCGCACT 6 41 1 TTAAAGAAAA 0.981686 -260 CAAGTTCCGCACTCCATCAAGTGAACCTCAACAGCTACACA 6 69 1 ATACAGAAAA 0.922722 -232 TTTTTTCATATATGTATATATAGAATATTAAGGATTATAAA 6 114 0 TTAAATAAAA 0.979214 -187 TATACATATATGAAAAAATAGAAAACGCGAAAACTTGTCAT 6 137 1 TAAAAGAAAA 0.902943 -164 * * * * ** ** ** Masking position 14 Map Score: 14.4953 Number of sites scoring better than the average of aligned sites = 1250 Number in coding regions = 645 Number in noncoding regions = 605 Number of orfs with sites within 600 bp upstream = 446 Fraction of orfs with sites within 600 bp upstream = 0.0716351 Motif number 2 TGACGTTTCTCAATTGCTTATCTTTTACCAATAG 1 121 1 CTTTTATCTT 0.876589 -180 CTCACCTTTGCCCCTGTTTATCTTATTCGAATTC 1 166 1 CCTTTATCTT 0.947839 -135 TACACGAAAATTTTTCTTTTTTTTCGGTGGCAAC 1 215 0 TTTTTTTTTT 0.807627 -86 CATACTAATCTCCGTACTTTTTTTAAAGCATCCA 2 148 1 TGTTTTTTTT 0.944285 -153 TTATTTTGAATGAGTTGTTTTGTTAACCTTGATT 2 244 0 TGTTTTTGTT 0.895354 -57 TAATGAATGGCTTCTGGTTAAGTTTGGCTTTTTG 3 96 1 CCTTTAAGTT 0.745763 -245 AGCTACTGCTCACGCGTTTATTTTCTCCGGGCAA 3 138 0 CGCTTATTTT 0.934138 -203 TTAATTGGAGCAACTAGTTAATTTTGACAAAGCC 3 302 1 CCTTTAATTT 0.853168 -39 TGCTATGAACCAGTTTATTATTTTTTTTTAATTC 4 142 1 CTTTTATTTT 0.933643 -187 TTCAATGCTATAACTAGTTATTTTTATATGTTTC 4 274 0 TCTTTATTTT 0.946087 -55 TGTATACAGTTTAGTATTTATCTTTACCTTTTGC 5 78 0 TGTTTATCTT 0.933243 -223 ATAAGTAATCTCGGCCATTATTTTAACGATTAGT 5 115 1 TGCTTATTTT 0.873653 -186 ATTTTAACGATTAGTACTTTTGTTCGTGTCATTT 5 134 1 TGTTTTTGTT 0.895354 -167 TACTTTTGTTCGTGTCATTTTTTTGGAAAATTTT 5 148 1 CGTTTTTTTT 0.972039 -153 AACGCGAAAACTTGTCATTTTTTTTTTAGGCGTT 6 160 1 CGTTTTTTTT 0.972039 -141 ATTTAAAGAGCCTCTTTTTATTTTCAGTATATTA 6 198 0 CCTTTATTTT 0.97297 -103 * ** ******* Masking position 8 Map Score: 10.7657 Number of sites scoring better than the average of aligned sites = 2874 Number in coding regions = 1267 Number in noncoding regions = 1607 Number of orfs with sites within 600 bp upstream = 1128 Fraction of orfs with sites within 600 bp upstream = 0.181176 Motif number 3 TTTTCGTGTATTTATCACTCCTGACGGAATATTG 1 239 1 TTTTCTCTGA 0.928315 -62 GTTACATATGTTTATTACTGATGATTAAAGTTTT 2 99 0 TTTTCTGTGA 0.9901 -202 TCAAATATTTTCTCTATATGGCGATGACCTATAC 3 202 0 TCTTATGCGA 0.957734 -139 AGCATTGAAATCTGTAGCTGATCAACGCAAACTA 4 299 1 TCTTCTGTCA 0.975272 -30 TTCTTGAACTGACGATGATACATTG 5 2 1 TCTGCTGCGA 0.96471 -299 AATTTTGCGATCTCTCACTGTTGAAGAATAAAGA 5 176 1 TCTTCTGTGA 0.996733 -125 TATAAAAGAATGTGTAGCTGTTGAGGTTCACTTG 6 86 0 TGTTCTGTGA 0.983209 -215 AAAAAGAGGCTCTTTAAATGTTGACACTCTACTC 6 213 1 TCTTATGTGA 0.98139 -88 GATAAAGAGATTTTTTACAGTTGATATTGGAGTA 6 242 0 TTTTCAGTGA 0.933652 -59 GTAAAAAATCTCTTTATCTGCTGACCTAACATCA 6 258 1 TCTTCTGTGA 0.996693 -43 *** * *** *** Masking position 3 Map Score: 10.7866 Number of sites scoring better than the average of aligned sites = 1005 Number in coding regions = 849 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 4 AAAAAAGAAAAATTTTCGTGTATTTATCACT 1 227 1 ATTTTCGTGT 0.970826 -74 TTTATCATTGAAAATTCACGTGATCGCAATA 1 268 0 AAATTCACGT 0.865967 -33 TGATGATTAAAGTTTTTGTGTGCAAAAGACG 2 84 0 ATTTTTGTGT 0.905349 -217 ACCGCCGAGCTAATTTCGCGTCATATCCATA 2 189 0 TATTTCGCGT 0.970742 -112 CACTTTTTCATAAATTCATGTATAGGTCATC 3 183 1 TAATTCATGT 0.616687 -158 AATCGATTAAAGTTTTTATGTGTTGCATCTG 4 76 1 ATTTTTATGT 0.655685 -253 TTATTTTTTTTTAATTCGCGTCTTCATTTCC 4 159 1 TAATTCGCGT 0.937592 -170 TGCATATAGTTTGCGTTGATCAGCTA 4 313 0 AAGTTTGCGT 0.936176 -16 GATTAGTACTTTTGTTCGTGTCATTTTTTTG 5 142 1 TTGTTCGTGT 0.916448 -159 TTTTTTTGGAAAATTTTGCGATCTCTCACTG 5 165 1 AATTTTGCGA 0.807974 -136 TGAAGAATAAAGATTTCGCGATGACTTTTGC 5 197 1 AATTTCGCGA 0.936054 -104 TATATTATTGAATGTTCGTGTTTTCAGGCAT 5 238 0 ATGTTCGTGT 0.959503 -63 AAAAATGACAAGTTTTCGCGTTTTCTATTTT 6 151 0 ATTTTCGCGT 0.984093 -150 * ********* Masking position 6 Map Score: 7.49577 Number of sites scoring better than the average of aligned sites = 1207 Number in coding regions = 711 Number in noncoding regions = 496 Number of orfs with sites within 600 bp upstream = 438 Fraction of orfs with sites within 600 bp upstream = 0.0703501 Motif number 5 AAACGTCACTCAGGGACAATTGATTACATGCTATCGG 1 92 0 CAGAATTATC 0.962521 -209 TTCATAAATTCATGTATAGGTCATCGCCATATAGAGA 3 189 1 CAGAAGTATC 0.994975 -152 TGCTGGAAAGCAACGATATGTTAAATCAGGAAGCTCC 5 44 0 CACAAGTAAC 0.991436 -257 CGTTGCTTTCCAGCAAAAGGTAAAGATAAATACTAAA 5 66 1 CACAAGTAAT 0.937562 -235 AAACTGTATACATCTATAAGTAATCTCGGCCATTATT 5 100 1 CACAAGTATC 0.99341 -201 CATTTCTCTGCAAGCAAAAGTCATCGCGAAATCTTTA 5 204 0 CAGAAGTATC 0.994975 -97 AACATATGCGCAAGAAAACGTAAAGGCCACGG 5 279 1 CAGAAGTAAC 0.993466 -22 ** * * * ** ** * Masking position 8 Map Score: 4.86272 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 70 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 GAGCGGCCTGTTTTTCCTTTGATGTTTCTA 1 29 1 TTTTTCCTTT 0.818409 -272 TACACGAAAATTTTTCTTTTTTTTCGGTGG 1 219 0 TTTTTCTTTT 0.815595 -82 TAATGAATCCTTTTTCCTTTGTTGATGCCA 2 53 0 TTTTTCCTTT 0.818409 -248 ATCTCCGTACTTTTTTTAAAGCATCCACAA 2 155 1 TTTTTTTAAA 0.716325 -146 TTAGCTTCAATTTTTTAATAATTAACCGCC 2 214 0 TTTTTTAATA 0.884602 -87 ACGCGTCTCACTTTTTCATAAATTCATGTA 3 175 1 CTTTTTCATA 0.792265 -166 ACAGATAAGATTTTTTAATTGGAGCAACTA 3 288 1 TTTTTTAATT 0.79795 -53 TTTTTTTATTCAAAATCAGT 4 1 1 TTTTTTTATT 0.934241 -328 GTATCATATCTTTTTCCATACTGAAATCGA 4 52 1 TTTTTCCATA 0.94441 -277 CAGTTTATTATTTTTTTTTAATTCGCGTCT 4 152 1 TTTTTTTTTA 0.934241 -177 TATAACTAGTTATTTTTATATGTTTCACTT 4 270 0 TATTTTTATA 0.716325 -59 TGTCTTTGGCTTTGTTTATACGGAGTGCTG 6 41 0 TTTGTTTATA 0.789148 -260 CAGCTACACATTCTTTTATAATCCTTAATA 6 100 1 TTCTTTTATA 0.78915 -201 GCGTTTTCTATTTTTTCATATATGTATATA 6 135 0 TTTTTTCATA 0.965642 -166 AACTTGTCATTTTTTTTTTAGGCGTTTTTA 6 168 1 TTTTTTTTTA 0.934241 -133 ********** Masking position 5 Map Score: 7.17245 Number of sites scoring better than the average of aligned sites = 4742 Number in coding regions = 1708 Number in noncoding regions = 3034 Number of orfs with sites within 600 bp upstream = 1597 Fraction of orfs with sites within 600 bp upstream = 0.256505 Motif number 7 TTTGTGCAATGACGATTTGAGCGGCCTG 1 6 1 GCAATGAGAT 0.954457 -295 TAAAAGATAAGCAATTGAGAAACGTCACTCAGG 1 115 0 GCAATTGGAC 0.958933 -186 ATAAACAGGGGCAAAGGTGAGTCGGGGAAACAC 1 154 0 GCAAAGGGAC 0.994142 -147 CCATTAGTTGGAAATGGAGACTTTTCTGTTTCA 3 36 0 GAAATGGGAT 0.954457 -305 TTTTCTCCGGGCAATGGTTGTTCAAAAAGCCAA 3 119 0 GCAATGGTGC 0.909246 -222 ATGAATTTATGAAAAAGTGAGACGCGTATCAGC 3 169 0 GAAAAAGGAC 0.906074 -172 TTATCTGTTAGCAAAGAAGGCTCCAAGGAAAAG 3 263 0 GCAAAGAGGC 0.976865 -78 GTTCATAGCAGAAAAGAGGAGACTAAATAAGAT 4 119 0 GAAAAGAGAC 0.977762 -210 ATTTGAAAAGGAAATGAAGACGCGAATTAAAAA 4 166 0 GAAATGAGAC 0.981874 -163 ******* ** * Masking position 4 Map Score: 3.38358 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 744 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 8 TTGGTGGCAGTATATGAATGAGTAAGTTAT 2 274 0 TATATGAATG 0.944184 -27 ATAAATAGATGTATTTAGTGTAAAT 3 6 1 TAGATGTATT 0.934671 -335 CAAGCATTTTTATATGTGTGACATAATGAA 3 73 1 TATATGTGTG 0.961561 -268 GTTGATGCCTTATATGTATGAAAGCTGTAC 4 206 0 TATATGTATG 0.983437 -123 AGATTACTTATAGATGTATACAGTTTAGTA 5 96 0 TAGATGTATA 0.959379 -205 TATTTTTTCATATATGTATATATAGAATAT 6 127 0 TATATGTATA 0.92753 -174 ********** Masking position 5 Map Score: 2.27921 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 78 Number in noncoding regions = 421 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 9 ATGCTATCGGCCACATACCGTGATTTGAACA 1 71 0 CCACAACCGT 0.98571 -230 CACGTGATCGCAATATTCCGTCAGGAGTGAT 1 252 0 CAATATCCGT 0.950745 -49 TTTAAAGCATCCACAATCCATATGGATATGA 2 169 1 CCACATCCAT 0.990169 -132 ATCAGAACTCCAGCACTCCGTATAAACAAAG 6 31 1 CAGCATCCGT 0.990837 -270 AAGACAAGTTCCGCACTCCATCAAGTGAACC 6 65 1 CCGCATCCAT 0.990837 -236 ***** ***** Masking position 5 Map Score: 0.213647 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 155 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 ********** No masking Map Score: -2.27841e-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: -2.27841e-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: -2.27841e-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