AlignACE version 2.2 July 7, 1998 AlignACE -jPMT.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 YAL023C 325 bp YAL023C PMT2 1-2277 dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase #2 YDL095W 363 bp YDL095W PMT1 1-2454 dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase #3 YDL093W 396 bp YDL093W PMT5 1-2232 dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase #4 YGR199W 355 bp YGR199W PMT6 1-2280 dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase #5 YJR143C 300 bp YJR143C PMT4 1-2289 dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase #6 YOR321W 600 bp YOR321W PMT3 1-2262 dolichyl phosphate-D-mannose:protein O-D-mannosyltransferase Motif number 1 TCTTTTCTTATGTTTTTTTTTTTCAGGGCG 1 122 0 TGTTTTTTTT 0.943561 -204 TTTTTTTTCGTATTCTTTTCTTATGTTTTT 1 135 0 TATTCTTTTC 0.757973 -191 TAAGTTCTTTCGTTCTTTTTTTTCGTATTC 1 150 0 CGTTCTTTTT 0.982156 -176 AATAGTGTTGCATTCTTTTTGAGGGTAAAA 1 210 1 CATTCTTTTT 0.96141 -116 CGAGAAATGACCTTTTTTTTACCCTCAAAA 1 226 0 CCTTTTTTTT 0.972158 -100 TCGCTACTGTCATTCTGTTTCGAACCGTGG 1 296 1 CATTCTGTTT 0.747843 -30 TGATGATATACCTTTTTTTTTTTTTTCGCT 2 186 1 CCTTTTTTTT 0.972158 -178 TTTTTCGCTGCGTTTTTTTTCTCGACACGT 2 207 1 CGTTTTTTTT 0.979746 -157 TTATTCATGATGTTTTTTTTGTCTATTTTC 3 78 0 TGTTTTTTTT 0.943561 -319 AGCTTCAAGACATTTTTTTTATTCATGATG 3 96 0 CATTTTTTTT 0.956324 -301 CATTTCGCACCGTTTTTTTTCCAAGAACTC 3 211 1 CGTTTTTTTT 0.979746 -186 ACTACGCTTCTGTTCCTTTTCTATTGTTCT 3 279 0 TGTTCCTTTT 0.907154 -118 TGCATAGACCCGTTTCTTTTCTTCTTTTTC 3 317 1 CGTTTCTTTT 0.961309 -80 TCCTACTTGTCCTTTCTTTCCTTTTTTAGT 5 57 1 CCTTTCTTTC 0.867074 -244 TTAGTCTCTACCGTCTTTTTAAATAGTTTC 5 82 1 CCGTCTTTTT 0.825467 -219 TTTCATTTTTTATTTTTTTTGTCAAGAAAT 5 153 0 TATTTTTTTT 0.88328 -148 GCATTCCAACTCTTCCTTTCGACATAAGAG 6 531 1 TCTTCCTTTC 0.719508 -70 ********** Masking position 4 Map Score: 21.2564 Number of sites scoring better than the average of aligned sites = 3460 Number in coding regions = 1526 Number in noncoding regions = 1934 Number of orfs with sites within 600 bp upstream = 1341 Fraction of orfs with sites within 600 bp upstream = 0.215387 Motif number 2 AAAAAAAAAAACATAAGAAAAGAATACGAAAA 1 129 1 AATAAGAAAG 0.906573 -197 ATACGAAAAAAAAGAACGAAAGAACTTACGGA 1 152 1 AAGAACAAAG 0.917429 -174 AAACAGAATGACAGTAGCGATGTGGACTAAGC 1 284 0 AAGTAGGATG 0.851554 -42 AGGCCAACTAACAGAAGCGCTGAAAGAGGACA 2 42 0 AAGAAGGCTG 0.939144 -322 AGAAAGCGTAATTGAAGCAAAGATCCGTTAAA 2 76 0 ATGAAGAAAG 0.958523 -288 GCATTCGAGAACAATAGAAAAGGAACAGAAGC 3 272 1 AAATAGAAAG 0.821457 -125 TAGAAAAGGAACAGAAGCGTAGTACATATTAT 3 286 1 AAGAAGGTAG 0.950044 -111 TATTTTCGAAAAAGAAGAAAAGAAACGGGTCT 3 322 0 AAGAAGAAAG 0.991945 -75 CAAAACCGTTATTGAAGAGAAGATGTTCCATT 4 155 0 ATGAAGGAAG 0.965619 -201 GGTAGAGACTAAAAAAGGAAAGAAAGGACAAG 5 62 0 AAAAAGAAAG 0.960812 -239 TACAGTTAATATAGAAGTAAGGATTCGAGTGA 5 218 0 AAGAAGAAGG 0.954836 -83 CTGACAGTCCACAGAAGTACAG 5 289 1 AAGAAGACAG 0.98417 -12 ACATACTTACAGAAAAGGGAAGTATTCTCTTA 6 230 0 AAAAAGGAAG 0.96753 -371 GAAAATCTCTAAAGAAGGGCATTCCAACTCTT 6 513 1 AAGAAGGCAT 0.821408 -88 * ***** **** Masking position 6 Map Score: 11.2646 Number of sites scoring better than the average of aligned sites = 2272 Number in coding regions = 1496 Number in noncoding regions = 776 Number of orfs with sites within 600 bp upstream = 636 Fraction of orfs with sites within 600 bp upstream = 0.102152 Motif number 3 AATAATATGTATGTTTGTCGCTATGTACGA 1 84 0 ATGTTTGTCG 0.850431 -242 TCTTATGTTTTTTTTTTTCAGGGCGACGTG 1 117 0 TTTTTTTTCA 0.916866 -209 TCTTTCGTTCTTTTTTTTCGTATTCTTTTC 1 145 0 TTTTTTTTCG 0.965771 -181 CTTGGTAATGTTGTTAGTCTCGAGAAATGA 1 246 0 TTGTTAGTCT 0.887707 -80 TACCTTTTTTTTTTTTTTCGCTGCGTTTTT 2 194 1 TTTTTTTTCG 0.965771 -170 TTTCGCTGCGTTTTTTTTCTCGACACGTGT 2 209 1 TTTTTTTTCT 0.954596 -155 AACAATGCACCTGTTTGTCTTGTTTTGCTG 2 285 0 CTGTTTGTCT 0.867616 -79 TCATGATGTTTTTTTTGTCTATTTTCGTTT 3 74 0 TTTTTTGTCT 0.957996 -323 CAAGACATTTTTTTTATTCATGATGTTTTT 3 91 0 TTTTTATTCA 0.807797 -306 TTTCGCACCGTTTTTTTTCCAAGAACTCGT 3 213 1 TTTTTTTTCC 0.866118 -184 GTTTCTTTTCTTCTTTTTCGAAAATATTCT 3 328 1 TTCTTTTTCG 0.854737 -69 TCCTAACATACTGTTTTTCTTATTATTTAC 4 334 1 CTGTTTTTCT 0.857984 -22 TTTCTTTCCTTTTTTAGTCTCTACCGTCTT 5 69 1 TTTTTAGTCT 0.896816 -232 AAATTTCGTGATGTTATTCGTGTATTTCTT 5 130 1 ATGTTATTCG 0.666377 -171 ATTTTTTATTTTTTTTGTCAAGAAATACAC 5 149 0 TTTTTTGTCA 0.922863 -152 ********** Masking position 5 Map Score: 12.3057 Number of sites scoring better than the average of aligned sites = 3851 Number in coding regions = 1310 Number in noncoding regions = 2541 Number of orfs with sites within 600 bp upstream = 1804 Fraction of orfs with sites within 600 bp upstream = 0.289753 Motif number 4 AAGAACTTACGGAAAGATCCGTTTCGTGTACTGTTTATT 1 171 1 GAAATCCGTT 0.96176 -155 CGTAATTGAAGCAAAGATCCGTTAAATAAGGCCAACTAA 2 63 0 GAAATCCGAA 0.947251 -301 CTTCTTTTTCGAAAATATTCTTATTGATTTAACAATTAA 3 337 1 GAAATTCTTT 0.971961 -60 ATATTCTGGTGTAAAGATACTCATAGAAAGCATAAAGAT 4 61 1 GAAATACTTA 0.882669 -295 GTTTCGCGTTGAAACAATTCTTTAAATTATCTTCTCTTG 4 271 1 GAAATTCTAA 0.961166 -85 TAATATAGAAGTAAGGATTCGAGTGAGTAGTTTTGATAA 5 205 0 GAAATTCGTA 0.982232 -96 TGGAATAAATGTAATAATTCTGGTACGGTTGCCGGATGT 6 65 1 GAAATTCTTT 0.971961 -536 TACTAAAAAAGTAAGTAATCTGTTTACTTGAACTTCCTC 6 104 1 GAAAATCTTT 0.814972 -497 TACAGAAAAGGGAAGTATTCTCTTAACAAGGCAGAAATT 6 216 0 GAAATTCTTA 0.979475 -385 TTTCTTTATAGTAATCATCCTAGAGGCATTACAGCTAAA 6 266 1 GAAATCCTAT 0.918439 -335 TTTCGTTAACGCAAACATTCGTCAAGTCATCTGGAATAC 6 324 0 GAAATTCGAA 0.966298 -277 TTACCACCCTGTAAGAACTCGTTTAAGAACAAAGCTCAG 6 387 1 GAAACTCGTA 0.912361 -214 * ** ***** * * Masking position 7 Map Score: 6.86042 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 368 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 5 AATACGAAAAAAAAGAACGAAAGAACTTACGGAAAGA 1 151 1 AAAACGAAAT 0.903213 -175 TTTACCCTCAAAAAGAATGCAACACTATTAATAAACA 1 202 0 AAAATGAAAA 0.892765 -124 AAAAAAAACATCATGAATAAAAAAAATGTCTTGAAGC 3 88 1 TAAATAAAAT 0.809354 -309 AAATTAATATAAATCAATGAATAATATAATACAACTA 4 111 0 AAAATGATAT 0.923471 -245 ATTAATTTGATGAACAATGGAACATCTTCTCTTCAAT 4 140 1 TAAATGAAAT 0.98338 -216 TTACCCGTTTTTATAAATGTAATAAGTTCAATAATTT 4 210 1 TAAATGAAAT 0.98338 -146 ATTTATCGACAGAATAATGGAAGAAACTATTTAAAAA 5 97 0 AAAATGAAAC 0.970655 -204 ACAAAAAAAATAAAAAATGAAAAATATGCATAATGAA 5 161 1 TAAATGAAAT 0.983379 -140 TTACCAATGAATACCAATGCAATAAACTTTTGAAAAT 6 23 1 AAAATGAAAC 0.970655 -578 AATGCTTCTGGAATAAATGTAATAATTCTGGTACGGT 6 57 1 GAAATGAAAT 0.947932 -544 TTACTGCGGCTTAAAAATTCAACAGGTTTACTCTCCT 6 164 1 TAAATTAAAT 0.809354 -437 TGATTACTATAAAGAAATGTAACATACTTACAGAAAA 6 246 0 AAAATGAAAC 0.970655 -355 AATGGATATGTAAAGAATGAATGAGTTACCACCCTGT 6 362 1 TAAATGATAT 0.923573 -239 * * **** ** * * Masking position 7 Map Score: 9.1716 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 556 Number in noncoding regions = 333 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 6 AAAAAGGTCATTTCTCGAGACTAACAACATT 1 239 1 TTTTCGAGAC 0.978735 -87 CTGCGTTTTTTTTCTCGACACGTGTCGAAGA 2 214 1 TTTTCGACAC 0.995043 -150 CGCCAAACTCTTCTTCGACACGTGTCGAGAA 2 225 0 TTCTCGACAC 0.984067 -139 TCCATCTGCGTTTAGAGACACGTATTCTATT 3 136 1 TTTGAGACAC 0.946005 -261 TCGATAGACTTTTCGCGGCACGTAAACGAGT 3 237 0 TTTGCGGCAC 0.976505 -160 CATCACGAAATTTATCGACAGAATAATGGAA 5 112 0 TTTTCGACAG 0.974741 -189 TACTAAGAAGTTTGTCGATACATATTTTACC 5 248 1 TTTTCGATAC 0.968802 -53 *** ******* Masking position 10 Map Score: 3.47049 Number of sites scoring better than the average of aligned sites = 253 Number in coding regions = 185 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AACCAGAAGAGAATATACATCATTCGGGGT 2 129 1 GAATATACAT 0.951106 -235 TAATACCACTGAAACTACTTGCAGATCATA 3 180 0 GAAACTACTT 0.873422 -217 AAAGTCTATCGAATAGGCATTCGAGAACAA 3 256 1 GAATAGGCAT 0.899316 -141 CTTTACACCAGAATATACTTGCGCCCATAT 4 47 0 GAATATACTT 0.959549 -309 CTCTAACCTTGAAAATGCTTTTCATCGTAC 5 19 1 GAAAATGCTT 0.983057 -282 AAAAAATGAAAAATATGCATAATGAAACGC 5 172 1 AAATATGCAT 0.789353 -129 ATAAACTTTTGAAAATGCTTCTGGAATAAA 6 44 1 GAAAATGCTT 0.983057 -557 GCCTTGTTAAGAGAATACTTCCCTTTTCTG 6 223 1 GAGAATACTT 0.872282 -378 TTGCGTTAACGAAAATGGATATGTAAAGAA 6 349 1 GAAAATGGAT 0.872506 -252 ********** Masking position 2 Map Score: 1.64943 Number of sites scoring better than the average of aligned sites = 1259 Number in coding regions = 894 Number in noncoding regions = 365 Number of orfs with sites within 600 bp upstream = 259 Fraction of orfs with sites within 600 bp upstream = 0.0415997 Motif number 8 TAGATACTGTACATACCGAAACGCCATCATT 1 12 1 ACAACCGAAA 0.942609 -314 GAACGAAAGAACTTACGGAAAGATCCGTTTC 1 165 1 ACTACGGAAA 0.949769 -161 TTGCTGGACCACGGTTCGAAACAGAATGACA 1 303 0 ACGTTCGAAA 0.903269 -23 AATAAGGCCAACTAACAGAAGCGCTGAAAGA 2 47 0 ACTACAGAAG 0.907465 -317 GAGAAAAAAAACGCAGCGAAAAAAAAAAAAA 2 199 0 ACGAGCGAAA 0.964956 -165 TGGAAAAAAAACGGTGCGAAATGATAATACC 3 203 0 ACGTGCGAAA 0.935251 -194 GTGTAAAGATACTCATAGAAAGCATAAAGAT 4 69 1 ACTATAGAAA 0.919679 -287 ACTTCTGTGGACTGTCAGAAAATATCTTGGT 5 276 0 ACTTCAGAAA 0.956555 -25 AATGTAACATACTTACAGAAAAGGGAAGTAT 6 237 0 ACTACAGAAA 0.97673 -364 *** ******* Masking position 9 Map Score: 2.13764 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 293 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 9 ********** No masking Map Score: 1.66429e-14 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 10 TAAAAAAAAGGTCATTTCTCGAGACTAACAA 1 235 1 GTCTTTCTCG 0.966854 -91 GAAGTTCCTCGTTTATAGATT 2 1 1 GAATTCCTCG 0.988614 -363 CTATTCGATAGACTTTTCGCGGCACGTAAAC 3 241 0 GACTTTCGCG 0.987587 -156 TAGCTATAGTCACGTTTCGCGTTGAAACAAT 4 258 1 CACTTTCGCG 0.929418 -98 ATAACATCACGAAATTTATCGACAGAATAAT 5 116 0 GAATTTATCG 0.919935 -185 ACTGTACTAAGAAGTTTGTCGATACATATTT 5 244 1 GAATTTGTCG 0.944535 -57 CTGTTTACTTGAACTTCCTCATAACTAAGGA 6 123 1 GAATTCCTCA 0.906504 -478 TATTATATTTGCCTTTCCTCGCGTCGCGATT 6 459 0 GCCTTCCTCG 0.976945 -142 *** ******* Masking position 6 Map Score: 0.311754 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 329 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 11 ********** No masking Map Score: 1.66429e-14 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: 1.66429e-14 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: 1.66429e-14 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