AlignACE version 2.2 July 7, 1998 AlignACE -jAAD.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 YCR107W 433 bp YCR107W aad3 1-1092 Hypothetical aryl-alcohol dehydrogenase (AAD) #2 YDL243C 392 bp YDL243C aad4 1-990 Hypothetical aryl-alcohol dehydrogenase #3 YFL056C 600 bp YFL056C aad6 1-639 Hypothetical aryl-alcohol dehydrogenase (AAD) #4 YJR155W 580 bp YJR155W aad10 1-867 Hypothetical aryl-alcohol dehydrogenase (AAD) #5 YNL331C 600 bp YNL331C aad14 1-1131 Hypothetical aryl-alcohol dehydrogenase #6 YOL165C 600 bp YOL165C aad15 1-432 Hypothetical aryl-alcohol dehydrogenase (AAD) Motif number 1 TGGAACGAGGTCTGCTTACTAATTTTATGTTGAC 2 35 0 TCGCTACATT 0.989455 -358 GGTTCAAAAATCTGCCCCCAATTTGTTCGAGGAT 2 93 0 TCGCCCCATT 0.97659 -300 CTTTCATCGGCCAGCTGACGAATTGACTGAGCGG 2 177 1 CCGCTACATT 0.987211 -216 TCTACCTGAACCACCTACCGAGTTGGGACGTCTC 2 285 1 CCCCTCCATT 0.950538 -108 AATGTGAAAATTGGCTTACGAATTAGCCACTGCA 3 331 0 TTGCTACATT 0.976997 -270 ATTTTCACATTTCGCTTACTAATTTTGCTCTCAA 3 354 1 TTGCTACATT 0.976997 -247 TCGATACGGATTTGCTTACTAATTGAGAGCAAAA 3 376 0 TTGCTACATT 0.976997 -225 TGCACCTGAACCACCTACCGAGTTAGGACGTCTT 4 347 1 CCCCTCCATT 0.950538 -234 TCGTACGAGATCTGCTTACTGGTTTTGTACAGCG 5 383 0 TCGCTACGTT 0.970167 -218 GGTTGGAAATTTTGCCCCCCGGTTTCCTTGAATA 5 442 0 TTGCCCCGTT 0.86745 -159 TCTTCATTAACTAGCTAACCAATTAGCTGAACGG 5 525 1 CTGCTACATT 0.972176 -76 TGGCAGCATTTCAGCAGCCAATTTCTTGTACATG 6 14 0 TCGCACCATT 0.938629 -587 ** *** ** * ** Masking position 13 Map Score: 12.169 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 323 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 2 TTTTTTTAATCTATTTTATGCATGTAGGAC 1 258 0 CTATTTTATG 0.885555 -176 GGATATGCTTCTTCTAGATGATCGAAAGAG 1 402 0 CTTCTAGATG 0.942546 -32 ATTGTCATGACTTTTATATGGTTCAAAAAT 2 116 0 CTTTTATATG 0.981406 -277 GGTATTGCTCCTTTTATATGTCTGAAGATT 3 467 0 CTTTTATATG 0.981406 -134 CTGAATATCTCTTCTATATCATTTTCAATA 3 569 1 CTTCTATATC 0.881551 -32 TGCCACTATCCTTTTATATGTTTTAAAATC 4 189 0 CTTTTATATG 0.981406 -392 AGCTTTTGAGCTACTTGATGCTTTTTACCA 4 488 1 CTACTTGATG 0.856476 -93 GTTACTACGACTTTTATATGTCATTCAATA 5 269 1 CTTTTATATG 0.981406 -332 TCCTAGTATACTTCTTGATGTGTCTTCACA 6 471 0 CTTCTTGATG 0.95444 -130 TAAAAATGGCCTTTTCTATGAATGACAATG 6 502 0 CTTTTCTATG 0.942287 -99 ********** Masking position 5 Map Score: 10.1532 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 210 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 3 CCTATTACATTCCGCCTGCCTAACCATGCT 1 173 0 TCCGCCTGCC 0.958472 -261 TGGAACGAGGTCTGCTTACTAATTTTATGT 2 39 0 TCTGCTTACT 0.985358 -354 CTATATTGCATCTGCTTGCCTTGCTGGTTT 3 94 1 TCTGCTTGCC 0.971959 -507 ATTTTCACATTTCGCTTACTAATTTTGCTC 3 354 1 TTCGCTTACT 0.958546 -247 TCGATACGGATTTGCTTACTAATTGAGAGC 3 380 0 TTTGCTTACT 0.961128 -221 CAATGAAATTTCCGCCTGCTTGGTAAAAAG 4 508 0 TCCGCCTGCT 0.983643 -73 GATCCAAGTCTCTGACTGCTCATACTAATA 4 552 0 TCTGACTGCT 0.835164 -29 ACTTCTTGTTTTCGCATACTTCGATGATTT 5 212 0 TTCGCATACT 0.805593 -389 TCGTACGAGATCTGCTTACTGGTTTTGTAC 5 387 0 TCTGCTTACT 0.985358 -214 TAAACTGCGGCCTGCTTGCTCGCGATGCCA 6 89 1 CCTGCTTGCT 0.949583 -512 TGAACTCGAAATTGCTTACTATGTTCTATC 6 536 0 ATTGCTTACT 0.77674 -65 ********** Masking position 7 Map Score: 8.56132 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 425 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 4 AAACACTGCGAAATGTGAGGAATCTTTCCGTCTTGTCGAGTCT 1 99 0 AAGGAATTCT 0.90049 -335 CATGACTTTTATATGGTTCAAAAATCTGCCCCCAATTTGTTCG 2 98 0 ATGAAATTCC 0.957273 -295 TCCTCCCAGAATTAGCGGTGAAACTCTTATGCCGGCAGTTTTA 2 330 0 ATGGAATTCC 0.996116 -63 TAGTAAGCAAATCCGTATCGAAGGTATACAACCACGTTCACCG 3 389 1 ATGGAATTCC 0.996116 -212 ATTTAGGTTGAACAGAGAGGAAATTGTTTCTCATTGCGACGGT 3 494 0 AAGGAATTCA 0.941028 -107 AGTTGTTCGATTTCGGTACGAAGTTTTCTTACCGGTTCCGTGC 4 110 0 TTGGAATTCC 0.986166 -471 ACCTCCCAGGATTAGTGGAGAAACTCTTATACCAGCTGTTTTA 4 392 0 ATGGAATTCC 0.996116 -189 TCATACTTAAATATGGTTGGAAATTTTGCCCCCCGGTTTCCTT 5 447 0 ATGGAATTCC 0.996116 -154 ACCTTCAGGCACTTGTAAGGAATATCTAAGCCCAGTCCTTTCA 6 239 0 ACGGAATTCC 0.985531 -362 CAATTTCGAGTTCAGCCTGGAACGTGTTGAACAGAGATTTTGA 6 552 1 TTGGAATTCA 0.933497 -49 ** * *** * * ** Masking position 12 Map Score: 8.89843 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 110 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 GATGATCGAAAGAGTAATTGAATTTTTTCAAGT 1 383 0 AGAGTTGAAT 0.914015 -51 GACGGTTGAAAGCGGATTTTAAAACGT 2 5 0 AGCGTTTAAA 0.957028 -388 GAATTGACTGAGCGGCTTTGTATTTCACTAGAA 2 196 1 AGCGTTGTAT 0.986904 -197 GAAAACGGTGAACGTGGTTGTATACCTTCGATA 3 404 0 AACGTTGTAT 0.905075 -197 CATTTTCAATAGCGATTTTTAAT 3 588 1 AGCGTTTAAT 0.972109 -13 AATTTAAGGGAGCGGGATTTTAAAACATATAAA 4 174 1 AGCGTTTTAA 0.972109 -407 TTTACATACTAGAGATATTTTAATATTGAAACA 5 70 1 AGAGTTTTAA 0.884977 -531 CAGCGCTGAAAGCGAATTTGAAAATATATGCAA 5 355 0 AGCGTTGAAA 0.968523 -246 CAATTAGCTGAACGGCTTTGTATTTTACTTAAC 5 544 1 AACGTTGTAT 0.905075 -57 GCTGAATAGTGGTTTTTTATGCAATAGACA 5 581 0 AGTGTTTTAT 0.826551 -20 TGAGCTTATGAGAGGAATTGAATCCATCAGAGT 6 184 0 AGAGTTGAAT 0.914015 -417 CCATATCGACAGCGTAGTATTAACGACACCTTC 6 276 0 AGCGTATTAA 0.876826 -325 AGAGATTTTGAGCGTGATATTATTCCA 6 584 1 AGCGTATTAT 0.91763 -17 **** ****** Masking position 12 Map Score: 9.11485 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 439 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 6 TCGGTAGGTGGTTCAGGTAGAGGTTTAAATAATTCACTA 2 267 0 GTCAGGGTAA 0.987685 -126 ATTGAAGCTCCTCCCAGAATTAGCGGTGAAACTCTTATG 2 342 0 CTCCAGGCGA 0.9199 -51 TAAAATGTGCGTACAGGAAGCCGTAAAGATCTATATTGC 3 64 1 GTCAGGGTGA 0.99593 -537 CACAACAAAACTGCAAGAACCTGTGTTGATTCGGAACGG 3 278 0 CTCAAGGTGA 0.990154 -323 CCTTAAATTTGTACAAGTGCAAGTAATGAAAGTTGTTCG 4 144 0 GTCAAGGTGA 0.992036 -437 TCGGTAGGTGGTTCAGGTGCAGGTCCAAAAGCCTCAGAC 4 329 0 GTCAGGGTAA 0.987686 -252 ATAGACATACCTCCCAGGATTAGTGGAGAAACTCTTATA 4 404 0 CTCCAGGTGA 0.980061 -177 GTCCTTTCAAGTACAGGTTGCTGTTCGAAATTGAGCTTA 6 209 0 GTCAGGGTAA 0.987685 -392 TTAACGACACCTTCAGGCACTTGTAAGGAATATCTAAGC 6 251 0 CTCAGGGTGA 0.994964 -350 ** **** ** ** Masking position 2 Map Score: 7.63254 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 93 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 TACTTATTTATACGCACCGCACCTATTACA 1 194 0 TACGCACCGC 0.991019 -240 ACTTTCTGGTTTGCCACCGCTCCTATAGAA 3 164 1 TTGCCACCGC 0.995982 -437 GCTTACGAATTAGCCACTGCATGTTCTACG 3 322 0 TAGCCACTGC 0.961081 -279 ATAGCTTCATAACCCACCGCCCCAAAATGT 4 287 1 AACCCACCGC 0.972795 -294 TAAACGTCTCGTCCCACCGCTGTTGATAAA 5 129 1 GTCCCACCGC 0.985716 -472 ATAAATTATATTGGCACCGCTTTATCAACA 5 149 0 TTGGCACCGC 0.994726 -452 ATGAATTTTGTTGGCATCGCGAGCAAGCAG 6 100 0 TTGGCATCGC 0.960754 -501 ********** Masking position 6 Map Score: 6.17028 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 117 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 TTCTTGTTTTTGGCTTGTTTTTTTTTTTTT 1 34 0 TGGCTTGTTT 0.8913 -400 GATAACAGTGTTTCTTGTTTTTGGCTTGTT 1 45 0 TTTCTTGTTT 0.956758 -389 TCGTAATCTTTTGCTGGTTTCGATGATGAC 1 355 1 TTGCTGGTTT 0.990748 -79 TCTGCTTGCCTTGCTGGTTTTAAAAAGCAA 3 104 1 TTGCTGGTTT 0.990748 -497 ATATTTAGACTTTCTGGTTTGCCACCGCTC 3 156 1 TTTCTGGTTT 0.985404 -445 TAGTACTTCCCTGCTGTTTTCGCACGGAAC 4 89 1 CTGCTGTTTT 0.836902 -492 TGAATAAAGACTTCTTGTTTTCGCATACTT 5 221 0 CTTCTTGTTT 0.915363 -380 CGAGATCTGCTTACTGGTTTTGTACAGCGC 5 382 0 TTACTGGTTT 0.95353 -219 ATTAGTCACATTTCTGGATTATCCTTTTGC 6 338 1 TTTCTGGATT 0.914107 -263 ********** Masking position 5 Map Score: 7.26028 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 511 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 9 ACGTTTTAAAATCCGCTTTCAACCGTC 2 7 1 TAAAACCGCT 0.955699 -386 CTAGTGAAATACAAAGCCGCTCAGTCAATTC 2 196 0 ACAAACCGCT 0.988367 -197 ATTAAAAATCGCTATTGAAAATG 3 588 0 TAAAATCGCT 0.920659 -13 ACATATCACCACAAGTTCGCTGTAAATGTGC 4 27 1 ACAAGTCGCT 0.905036 -554 TATATGTTTTAAAATCCCGCTCCCTTAAATT 4 174 0 AAAATCCGCT 0.923095 -407 TTTCAATATTAAAATATCTCTAGTATGTAAA 5 70 0 AAAATTCTCT 0.615277 -531 ATAATAAAAAACAAATTCGGTTACTACGACT 5 250 1 ACAAATCGGT 0.907574 -351 GCATATATTTTCAAATTCGCTTTCAGCGCTG 5 357 1 TCAAATCGCT 0.966889 -244 TCAGCGCTGTACAAAACCAGTAAGCAGATCT 5 379 1 ACAAACCAGT 0.759409 -222 TAAGTAAAATACAAAGCCGTTCAGCTAATTG 5 544 0 ACAAACCGTT 0.870031 -57 TCTATTGCATAAAAAACCACTATTCAGC 5 583 1 AAAAACCACT 0.853721 -18 TCTGATGGATTCAATTCCTCTCATAAGCTCA 6 186 1 TCAATCCTCT 0.82702 -415 AATATCACGCTCAAAATCTCTGTTCAACACG 6 574 0 TCAAATCTCT 0.878541 -27 ***** ***** Masking position 4 Map Score: 4.78847 Number of sites scoring better than the average of aligned sites = 1151 Number in coding regions = 915 Number in noncoding regions = 236 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 10 ATTATCCTTCTATTTACCGCAAAGTGTGTTG 1 323 0 TATTACCGCA 0.799719 -111 CTACCTGAACCACCTACCGAGTTGGGACGTC 2 286 1 CACCACCGAG 0.965432 -107 CCAGTCTGCACATTTACAGCGAACTTGTGGT 4 34 0 CATTACAGCG 0.976036 -547 GCACCTGAACCACCTACCGAGTTAGGACGTC 4 348 1 CACCACCGAG 0.965432 -233 CCATTCACCGATCCAAGTCTCT 4 569 0 CATTACCGAT 0.799719 -12 TCCGTTCATACATCAACCGCGTCCCATACGT 5 12 1 CATCACCGCG 0.993473 -589 GGCACCGCTTTATCAACAGCGGTGGGACGAG 5 136 0 TATCACAGCG 0.96518 -465 AATTAAAAGTCATTTACCCAGGCGTGATTAT 5 177 0 CATTACCCAG 0.915905 -424 TCTCTCTTCATATTCACACCGTAATGAATTT 6 122 0 TATTACACCG 0.822943 -479 CGGCGTTCCATATCGACAGCGTAGTATTAAC 6 285 0 TATCACAGCG 0.96518 -316 **** ****** Masking position 6 Map Score: 3.63224 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 449 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 11 ATTCCGCCTGCCTAACCATGCTCATTTTTTC 1 164 0 CCTAACCAGC 0.978258 -270 GACAATATTTCCAGATCAAGGACAGTTGCAG 2 140 1 CCAGATCAGG 0.957463 -253 AAAGCCTGACCATGCATCGCCGATT 2 378 0 CCTGACCAGC 0.996572 -15 AGCTCCTTCTCCTGTTCACGCCCTCTACGAA 3 20 0 CCTGTTCAGC 0.960391 -581 TCCCATGAATCCAGACCAGGCGTCACCAATA 4 440 0 CCAGACCAGC 0.996574 -141 TCATGTTGCGCCAGACTATGCGCAGCAAAAG 6 361 0 CCAGACTAGC 0.978234 -240 ******** ** Masking position 8 Map Score: 2.80554 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 102 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 CGGAACGGTACTATCTCTTCGTAATATCAA 3 256 0 CTATCTCTTC 0.979068 -345 AAACAATTTCCTCTCTGTTCAACCTAAATC 3 508 1 CTCTCTGTTC 0.986367 -93 TACTAACTGAATATCTCTTCTATATCATTT 3 563 1 ATATCTCTTC 0.954042 -38 TCATCTGATTCACTCTCTTCTAATTGCATA 5 332 1 CACTCTCTTC 0.97155 -269 GATAAATCTGTTCTCTCTTCATATTCACAC 6 134 0 TTCTCTCTTC 0.972098 -467 CACGCTCAAAATCTCTGTTCAACACGTTCC 6 570 0 ATCTCTGTTC 0.969798 -31 ********** Masking position 6 Map Score: 2.53783 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 201 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 13 AGAAACACTGCGAAATGTGAGGAATCTTTC 1 114 0 CGAAATGTGA 0.934801 -320 TTCTATTTACCGCAAAGTGTGTTGTTGTTA 1 317 0 CGCAAAGTGT 0.959692 -117 AAAATCTGCCCCCAATTTGTTCGAGGATAT 2 91 0 CCCAATTTGT 0.790397 -302 GATGGAGTAACGCAAAATGAACTTTGATAT 3 233 1 CGCAAAATGA 0.966234 -368 AATTAGTAAGCGAAATGTGAAAATTGGCTT 3 348 0 CGAAATGTGA 0.934801 -253 GCAATACCGTCGCAATGAGAAACAATTTCC 3 489 1 CGCAATGAGA 0.919861 -112 AGGTGTATTACCCAATATGATTCTCACCTT 4 231 1 CCCAATATGA 0.959442 -350 AACCCACCGCCCCAAAATGTGCTCTTCGAA 4 297 1 CCCAAAATGT 0.885527 -284 CATAGTCTGGCGCAACATGACCACTATATC 6 372 1 CGCAACATGA 0.943773 -229 ********** Masking position 5 Map Score: 2.56315 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 330 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 14 GATTAAAAAAAGGGATCACGATACTCAAATATGCA 1 277 1 AATACGATAT 0.978333 -157 GAAACCAGCAAAAGATTACGATATTATCCTTCTAT 1 341 0 AATACGATAT 0.978333 -93 ACCATATAAAAGTCATGACAATATTTCCAGATCAA 2 124 1 AATACAATAT 0.985102 -269 CAACGCACGGATTGATAACAATATTTAGACTTTCT 3 136 1 AATACAATAT 0.98531 -465 ACGTTTAGATAGTAATTACAATAGAAATACAACTG 5 101 0 AATACAATAA 0.933018 -500 AACCATATTTAAGTATGACAATATTTCCAAGTCAA 5 472 1 AATACAATAT 0.985305 -129 GGCCTTTTCTATGAATGACAATGGTCCTAGTATAC 6 490 0 AATACAATGT 0.953564 -111 * ** ****** * Masking position 8 Map Score: 2.01593 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 182 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 15 CTTTTAACCTGCTCGTCAATTTGAAAAAATGAG 1 142 1 GCTGTCAATG 0.961431 -292 ATATTTTGTAGCTATAGGAAGTGTATTCTAGTG 2 221 0 GCTTAGGATG 0.938159 -172 GAAGGAGCTGGCTTGTCGAGTTTAAAATGTGCG 3 42 1 GCTGTCGATT 0.977065 -559 ATTAAAAATCGCTATTGAAAATGATATAGAAGA 3 578 0 GCTTTGAATG 0.950872 -23 CCCAAAATGTGCTCTTCGAAATGTCTGAGGCTT 4 307 1 GCTTTCGATG 0.991086 -274 AATGTCTGAGGCTTTTGGACCTGCACCTGAACC 4 326 1 GCTTTGGATG 0.988325 -255 AGTACAGGTTGCTGTTCGAAATTGAGCTTATGA 6 206 0 GCTTTCGATT 0.977509 -395 ACGGCATGGCGCTTGTTGACTTTAGCAATTATG 6 424 1 GCTGTTGATT 0.89087 -177 *** ***** ** Masking position 9 Map Score: 2.39552 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 170 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459