AlignACE version 2.2 July 7, 1998 AlignACE -jALG.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 YBR110W 509 bp YBR110W alg1 1-1350 beta-1,4-mannosyltransferase #2 YBR243C 600 bp YBR243C alg7 1-1347 UDP-N-acetyl-glucosamine-1-P transferase (GPT) #3 YGL065C 300 bp YGL065C ALG2 1-1512 glycosyltransferase #4 YNL219C 574 bp YNL219C ALG9 1-1668 mannosyltransferase #5 YNL048W 300 bp YNL048W ALG11 1-1647 Required for aspargine-linked glycosylation #6 YOR002W 383 bp YOR002W ALG6 1-1635 Required for glucosylation in the N-linked glycosylation pathway #7 YOR067C 405 bp YOR067C alg8 1-1734 glycosyl transferase #8 YPL227C 599 bp YPL227C ALG5 1-1005 UDP-glucose:dolichyl-phosphate glucosyltransferase Motif number 1 TATGTTTGCTTTGTCGATTTTTGCATGCTTTG 1 281 1 TTGCATTTTT 0.915649 -229 TACACAAATCTTGACTATTTTTGATAGATGCA 2 239 0 TTGCATTTTT 0.915649 -362 ACGTCCGTATTTTCCTTTTTTTAGCGGATGAT 2 297 1 TTTCTTTTTT 0.883493 -304 TCTCCTGTATATGGCCCTTTCCTTTTATATTG 2 445 1 ATGCCTTTCC 0.86708 -156 GCTTGTCTAATCGACTCTTTTTTATCTGTCTT 3 275 0 TCGCCTTTTT 0.915828 -26 GTATATCCAGTTGTCCCTTTTTCAAGCTTGTA 4 419 0 TTGCCTTTTT 0.988479 -156 CTGTATCGAATTGGCTCTTTTTTCACCCTGAA 4 534 1 TTGCCTTTTT 0.988479 -41 TTTATTGAACTTTTCACTTTTTGTTTAGCTTA 5 196 0 TTTCCTTTTT 0.97665 -105 ATGCACACCATTTTCTCTTTTTTTGTTTCTGT 6 118 1 TTTCCTTTTT 0.97665 -266 GAAAAATGAAATTTCACTTTTCGGAAGTTGTC 7 271 0 ATTCCTTTTC 0.851337 -135 ACCTTGAAACTTTTCTTTTTCCATTGAAAAAT 8 165 1 TTTCTTTTCC 0.622182 -435 GAAGCAGTGTATGCCATTTTTTTCATGAGAAA 8 361 1 ATGCTTTTTT 0.844864 -239 AATACGCCAAATTTCGCTTTCTCATGAAAAAA 8 378 0 ATTCCTTTCT 0.890505 -222 TTTCTTCTTGTTTACACTTTTTTTCGAATACG 8 404 0 TTTCCTTTTT 0.97665 -196 GCCTTGAAAATTGGCACGTTTTCTTCTTGTTT 8 423 0 TTGCCGTTTT 0.915828 -177 CTCTCTGTTTTTGTCCCTTTCTTACGTTATCA 8 547 0 TTGCCTTTCT 0.979444 -53 *** * ****** Masking position 9 Map Score: 16.3251 Number of sites scoring better than the average of aligned sites = 1669 Number in coding regions = 914 Number in noncoding regions = 755 Number of orfs with sites within 600 bp upstream = 682 Fraction of orfs with sites within 600 bp upstream = 0.109541 Motif number 2 TGTACTTTTTTATTTGTATTAACTAAGCTCTTT 1 8 1 TTTTTGTTAC 0.977857 -502 CAAGATGTATTTATATTTTCGTGTACTGTGATATGA 1 169 0 TTTTTTTGAC 0.932723 -341 CAGGTTCTACTTATGTTTGCTTTGTCGATTTTTGCA 1 270 1 TTTTTGTTTC 0.943911 -240 CTTTGTCGATTTTTGCATGCTTTGACTGTGACTTTC 1 289 1 TTTATGTTAC 0.801692 -221 AACGTCCGTATTTTCCTTTTTTTAGCGGATGATGAG 2 296 1 TTTTTTTTGC 0.825007 -305 TGCGTATAGCTTCTTTTTTTATAAACAAGTGCCTGG 3 140 1 TTTTTTTAAC 0.898134 -161 TGAATACATCATTTATTTTGTTGTTCGCGCGTTCAT 3 180 0 ATTTTTTGTC 0.46029 -121 ATCGACTCTTTTTTATCTGTCTTTACTACTGTATCT 3 262 0 TTTCTGTTAC 0.856973 -39 TTTTGCTTGTCTAATCGACTCTTTTT 3 285 0 TTTTTGTATC 0.843818 -16 CATCTGTTTTTTGTTTTTTAATTGACATTCAATCAT 4 147 0 TTTTTTTTAC 0.964866 -428 CGTAACGGACTTATTGTTGCATTTTCAAGTAAATAA 4 334 0 TTTTTGTTTC 0.943911 -241 AACTTTTCACTTTTTGTTTAGCTTACCCGAAGGACA 5 185 0 TTTTTTCTAC 0.776923 -116 CCTCTCAATCTTATTATTTATTGAACTTTTCACTTT 5 208 0 TTTTTTTGAC 0.932723 -93 ATTAAGAGATATATGGTTTCGTTCACTACGTAGTTA 7 159 1 ATTTTTTTAC 0.815946 -247 TTAGCACTGATTGTCGTTGTATTTACAGTTTACAAG 8 22 1 TTTTTGTTAC 0.977857 -578 TTGGCACGTTTTCTTCTTGTTTACACTTTTTTTCGA 8 409 0 TTTTTGTAAC 0.934114 -191 ** * *** ** ** Masking position 8 Map Score: 7.98158 Number of sites scoring better than the average of aligned sites = 1280 Number in coding regions = 680 Number in noncoding regions = 600 Number of orfs with sites within 600 bp upstream = 477 Fraction of orfs with sites within 600 bp upstream = 0.0766142 Motif number 3 TTAACAAGAGATCTTGTTAACTCACAAGGG 1 98 0 ATCTTGTTAA 0.847298 -412 TTAACAAGATCTCTTGTTAAACACCTTCTT 1 108 1 CTCTTGTTAA 0.911628 -402 ATATAAATACATCTTGAAAATGTCTCAAAT 1 189 1 ATCTTGAAAA 0.932819 -321 TAGATGCAGTCTCTTGAAATGACCAACGAC 2 217 0 CTCTTGAAAT 0.733126 -384 TCTTCCAAAGATCATCAAAAAGCACCAGAG 3 20 1 ATCATCAAAA 0.834318 -281 ATATACATTTATCATGATAATCTCTGGTGC 3 41 0 ATCATGATAA 0.932819 -260 CAGAACGGTTCTCATCAAAATTCAATATTG 4 370 0 CTCATCAAAA 0.903493 -205 TGAATAATGTCTCATCATAAGAAGAGGGTG 5 26 0 CTCATCATAA 0.889883 -275 CATCTCCTTTATTATGAAAAGTACAAGTTT 6 159 1 ATTATGAAAA 0.670535 -225 AAGGGATTTGCTCATGTTAAAGCAATGGCA 6 309 1 CTCATGTTAA 0.922783 -75 CATAATTTATATCTTGTAAACTGTAAATAC 8 40 0 ATCTTGTAAA 0.865375 -560 ATTTCGCTTTCTCATGAAAAAAATGGCATA 8 370 0 CTCATGAAAA 0.967643 -230 AGATTAGGTGCTTTTGATAACGTAAGAAAG 8 533 1 CTTTTGATAA 0.738174 -67 ********** Masking position 9 Map Score: 5.20298 Number of sites scoring better than the average of aligned sites = 1406 Number in coding regions = 1074 Number in noncoding regions = 332 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 4 ATTGGTCATATATCTTTCAATCAGCAATTA 1 431 1 TATCTTTCAA 0.898083 -79 TGCACATTTTTTAAAGCAGGCTGG 2 5 1 CATTTTTTAA 0.907436 -596 CAAGAGACTGCATCTATCAAAAATAGTCAA 2 231 1 CATCTATCAA 0.804704 -370 TTTAGTAAAGCATTTTTCGAGATTGAGGCA 2 475 0 CATTTTTCGA 0.956623 -126 TCCAGTTGTCCCTTTTTCAAGCTTGTATTG 4 416 0 CCTTTTTCAA 0.916135 -159 TTGCTTAACCCATTTTTCAAAGCATTTTTA 7 208 1 CATTTTTCAA 0.984528 -198 TTTTTCAAAGCATTTTTAAAATTTACTGTT 7 220 1 CATTTTTAAA 0.847548 -186 AGTGAAATTTCATTTTTCAAAACGACAATA 7 285 1 CATTTTTCAA 0.984528 -121 AATATATTATTATTTTTTAACATTTATTGC 8 111 1 TATTTTTTAA 0.708313 -489 CACCACATCTAATTTTTCAATGGAAAAAGA 8 178 0 AATTTTTCAA 0.861845 -422 GGCTCTGTTGTATCTTTCGAAGCAGTGTAT 8 343 1 TATCTTTCGA 0.753327 -257 GAAAACGTGCCAATTTTCAAGGCTTTATCG 8 432 1 CAATTTTCAA 0.880532 -168 ********** Masking position 10 Map Score: 6.02724 Number of sites scoring better than the average of aligned sites = 2160 Number in coding regions = 1599 Number in noncoding regions = 561 Number of orfs with sites within 600 bp upstream = 462 Fraction of orfs with sites within 600 bp upstream = 0.0742049 Motif number 5 ATAAATCCACAAGAAATTTTTTACTCATCATCC 2 322 0 AAAATTTTTA 0.771006 -279 GCTGTTTAGTAAAGCATTTTTCGAGATTGAGGC 2 476 0 AACATTTTCG 0.94579 -125 ACATGTTAACAATTTAATTTTCGCGCTGTTTAG 2 500 0 AATATTTTCG 0.89415 -101 TTCTGCTAATAAGCTATTTTTTACCTGTCGATG 4 53 1 AATATTTTTA 0.67736 -522 GACCTACCTTAAAACACGTTTCGTTTAAGACAA 4 85 1 AACAGTTTCG 0.858087 -490 CTTATTATTTATTGAACTTTTCACTTTTTGTTT 5 202 0 ATAATTTTCA 0.92632 -99 TTTATAAATTATGGTAATTTTCATTTAAGACCT 6 37 1 ATTATTTTCA 0.886839 -347 ACCTTTGCTTAACCCATTTTTCAAAGCATTTTT 7 204 1 AACATTTTCA 0.968952 -202 GAAAAGTGAAATTTCATTTTTCAAAACGACAAT 7 281 1 ATCATTTTCA 0.941813 -125 TCAAGGTGGAAAAAAAATTTTCAGCAGCATCGC 8 139 0 AAAATTTTCA 0.96028 -461 TCAATGGAAAAAGAAAAGTTTCAAGGTGGAAAA 8 159 0 AAAAGTTTCA 0.893628 -441 CAAACACCACATCTAATTTTTCAATGGAAAAAG 8 179 0 ATAATTTTCA 0.92632 -421 ** ** ****** Masking position 6 Map Score: 2.62887 Number of sites scoring better than the average of aligned sites = 1298 Number in coding regions = 899 Number in noncoding regions = 399 Number of orfs with sites within 600 bp upstream = 355 Fraction of orfs with sites within 600 bp upstream = 0.057019 Motif number 6 ACTATCGAACTACAAAGAAAGAGCTTAGTTAATACAAAT 1 22 0 TAAAAAGGTT 0.974859 -488 ATGTTACGAATACAAACACAGAGGTTGATGCATGAATTT 2 355 1 TAAAAAGGTT 0.974842 -246 AAGGGACAACTGGATATACAGGGGTGTTTTTGACACAAT 4 432 1 TGATAAGGTT 0.967223 -143 CCAAGCACACTGCAAATGAAGGGTTAGATGAAGAGTTCG 5 94 1 TGAAAAGGTT 0.993014 -207 TTATGTAAAACAAGCGTATTTTTTTATTTATA 6 4 1 TGAAAAGGAT 0.967223 -380 AAATCCCTGCTGCAAATTAAGAGATATATGGTTTCGTTC 7 144 1 TGAAAAGGTT 0.993014 -262 ATAGTCACTGTGGAAAGGTAGTGGTATCTAATTGGATGC 8 485 1 TGAAAAGGTT 0.993014 -115 ** *** ** * * * Masking position 10 Map Score: 2.25179 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 34 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 GACCACTTATCACTTGGATATGTTGTCAAA 4 239 1 CACTTGGATA 0.985281 -336 GAAAAAGGGACAACTGGATATACAGGGGTG 4 428 1 CAACTGGATA 0.967238 -147 AAAAAAGAGCCAATTCGATACAGCTAAAGT 4 527 0 CAATTCGATA 0.958216 -48 ATGTTGGTCACACTTGGATACTAACATCTA 5 259 0 CACTTGGATA 0.985281 -42 CATTTGACGTCTATTGGATAGCCTACG 7 389 1 CTATTGGATA 0.9522 -17 TTACAGCATCCAATTAGATACCACTACCTT 8 499 0 CAATTAGATA 0.939293 -101 ********** Masking position 5 Map Score: 1.74567 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 72 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 GAGACATTTTCAAGATGTATTTATATTTTCGTGTACT 1 178 0 CAGTATTATT 0.986374 -332 TTGATGTTCTCAGGTTCTACTTATGTTTGCTTTGTCG 1 260 1 CAGTACTATT 0.986102 -250 GATTTGTGTACATGTTCGTCGTACATTTAGTAAGTAA 2 261 1 CAGTTCTATT 0.926315 -340 CAGAGATTATCATGATAAATGTATATTCTTGTAAATA 3 45 1 CAGTATTATT 0.986374 -256 TGCTCTTGCGCATGTTATACCTACTTTTTACTATCTA 4 276 1 CAGTACTATT 0.986094 -299 TTGCAGTGTGCTTGGTTGATGAACCTTCTTCCATTAA 5 72 0 CTGTATAATT 0.826059 -229 ATGAAAAGTACAAGTTTTATATAATTTCAACGTCGGA 6 172 1 CAGTATTATT 0.986374 -212 CTTGTTATTGCAGGATGTATGAAAGTTTATAAAATCC 7 113 1 CAGTATAATT 0.963638 -293 ** * * ** ** ** Masking position 13 Map Score: 2.28329 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 55 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TGTACTTTTTTATTTGTATT 1 1 1 TGTACTTTTT 0.743668 -509 TGCACATTTTTTAAAGCAGG 2 1 1 TGCACATTTT 0.945969 -600 TCAAGATTTGTGTACATGTTCGTCGTACAT 2 257 1 TGTACATGTT 0.932967 -344 CACAGTTATATACACATGTTAACAATTTAA 2 516 0 TACACATGTT 0.945958 -85 CATCTAGCCAGGCACTTGTTTATAAAAAAA 3 153 0 GGCACTTGTT 0.91804 -148 GTTTTGCTCTTGCGCATGTTATACCTACTT 4 272 1 TGCGCATGTT 0.968144 -303 TGCAATCACCTGAACATGTTGGTCACACTT 5 274 0 TGAACATGTT 0.88755 -27 AATAAAAAAATACGCTTGTTTTACATAA 6 9 0 TACGCTTGTT 0.863669 -375 AAAAGGGATTTGCTCATGTTAAAGCAATGG 6 307 1 TGCTCATGTT 0.917643 -77 CACTTGACTTTGGACTTGTTAGTTGTGACT 8 246 0 TGGACTTGTT 0.907786 -354 TCTTCTTGTTTACACTTTTTTTCGAATACG 8 404 0 TACACTTTTT 0.784924 -196 ********** Masking position 7 Map Score: 4.05558 Number of sites scoring better than the average of aligned sites = 1179 Number in coding regions = 874 Number in noncoding regions = 305 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 10 TAATAGTACAGGTTTCCTTCATCTCCTGTATAT 2 424 1 GTTCCTTCTC 0.971538 -177 TCTACTTTTTGTTACCGTTCTCCGCCTTGCTCT 2 574 0 GTACGTTCCC 0.99155 -27 GGCTAAAGCTCTTCCAAAGATCAT 3 2 1 GTAAGCTCTC 0.910619 -299 AACATCAAAAGATTACGTTCGCCATTTAAGAAG 3 220 1 GTTCGTTCCC 0.993117 -81 AGATCTTACCGCTAGCGTTCTTCTGCTAATAAG 4 33 1 GTACGTTCTC 0.989147 -542 GTGTCATGGAGTTATGGCTCCCCCATGCACACC 6 94 1 GTAGGCTCCC 0.91685 -290 TTGTTTCTGTGTTTCCCTTCATCTCCTTTATTA 6 140 1 GTTCCTTCTC 0.97159 -244 TCTCCCTCATGATTTAGTTCGTCCAAACAGGTG 7 53 1 GTTAGTTCTC 0.962513 -353 AGAGATATATGGTTTCGTTCACTACGTAGTTAT 7 163 1 GTTCGTTCCT 0.93409 -243 * ** ***** ** Masking position 9 Map Score: 3.42808 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 171 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 11 CAAACATAAGTAGAACCTGAGAACATCAAC 1 259 0 TAGAACCTGA 0.871639 -251 CAATTGACTATAGCCCCTAAAATGCCGTTA 1 484 0 TAGCCCCTAA 0.944619 -26 TATTAGTGCAAAGCCCCTAAGCCAGCCTGC 2 26 0 AAGCCCCTAA 0.975129 -575 GATCATCAAAAAGCACCAGAGATTATCATG 3 29 1 AAGCACCAGA 0.961514 -272 TTTCGCCTGCAATCACCTGAACATGTTGGT 5 281 0 AATCACCTGA 0.939793 -20 GATAATCTAGAAGCACCTGTTTGGACGAAC 7 69 0 AAGCACCTGT 0.961514 -337 ACGTTATCAAAAGCACCTAATCTATCCTTA 8 526 0 AAGCACCTAA 0.983127 -74 ********** Masking position 2 Map Score: 1.08525 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 316 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 12 ATTAGTTCCATTGTCTCCGTATTAGTGCAA 2 45 0 TTGTCTCCGT 0.970818 -556 AGTCTACTTTTTGTTACCGTTCTCCGCCTT 2 579 0 TTGTTACCGT 0.892482 -22 GTATCTGTGATTGTGACCCTTTCGTATATA 3 90 0 TTGTGACCCT 0.967468 -211 ATTGGCTCTTTTTTCACCCTGAAGCACAAT 4 543 1 TTTTCACCCT 0.973107 -32 GCTCTGAGTTTTATCTCCCTCATGATTTAG 7 40 1 TTATCTCCCT 0.916653 -366 AGTTATCCTATTTTCACCGTTATCACTTCA 8 281 1 TTTTCACCGT 0.964972 -319 GCCTCTCTGTTTTTGTCCCTTTCTTACGTT 8 551 0 TTTTGTCCCT 0.935586 -49 ********** Masking position 4 Map Score: 0.999064 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 268 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 13 TTTGTAGTTCGATAGTTTCCGGTCAAGAATAAG 1 45 1 GAATTCCGGT 0.971508 -465 ACATATGGTTGATGTTCTCAGGTTCTACTTATG 1 252 1 GAGTTCAGGT 0.986335 -258 CATTTATCATGATAATCTCTGGTGCTTTTTGAT 3 33 0 GAATTCTGGT 0.867265 -268 TATAAAAAAAGAAGCTATACGCAAGGCTCTCGA 3 130 0 GAGTTACGCA 0.923451 -171 TTCAACGTCGGAGGTTATCCGGAAATCTATAGT 6 197 1 GAGTTCCGGA 0.993337 -187 ACTCCGAATGGACGGTGTCAGGAATTCTTTTCT 6 338 1 GAGTTCAGGA 0.986335 -46 TCACTTTTCGGAAGTTGTCCGCTAAGAACAACT 7 257 0 GAGTTCCGCT 0.981393 -149 TATCTAATTGGATGCTGTAAGGATAGATTAGGT 8 509 1 GAGTTAAGGA 0.942887 -91 ** * * ****** Masking position 2 Map Score: 1.74651 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 152 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 ACTATTTTTGATAGATGCAGTCTCTTGAAAT 2 227 0 ATAGATGAGT 0.978053 -374 AAGTCACGAAATAGATACAGTAGTAAAGACA 3 250 1 ATAGATAAGT 0.937751 -51 CCAATTCGATACAGCTAAAGTTTTGAAATCT 4 517 0 ACAGCTAAGT 0.951535 -58 TTAATGATCGACAGCTGCAGTGAATAATGTC 5 45 0 ACAGCTGAGT 0.976403 -256 CCCGAAGGACATAGATGTAGCGATGACAACG 5 165 0 ATAGATGAGC 0.942202 -136 TACGTTAAAAATAGCTGAAGTTCATTACAGT 7 339 1 ATAGCTGAGT 0.98593 -67 ******* *** Masking position 6 Map Score: 0.282111 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 77 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 15 TCTTTTTTCACCCTGAAGCACAATTATAAGGG 4 549 1 CCTAAGCACA 0.985238 -26 AGAGGGTGTACCCTCAAGCTCAG 5 2 0 CCTAAGCTCA 0.932689 -299 GAAGGTTCATCAACCAAGCACACTGCAAATGA 5 81 1 CACAAGCACA 0.969452 -220 TGTTTAGCTTACCCGAAGGACATAGATGTAGC 5 175 0 ACCAAGGACA 0.938663 -126 AGTTATGGCTCCCCCATGCACACCATTTTCTC 6 103 1 CCCATGCACA 0.980693 -281 CGGAAGTTGTCCGCTAAGAACAACTAAGTGAT 7 250 0 CCCAAGAACA 0.97426 -156 GCCAAAAATTACACAAAGCACAACAAAA 8 582 1 ACCAAGCACA 0.985238 -18 ** * ******* Masking position 6 Map Score: 0.850418 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 225 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401