AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -inarP_mthe_opreg_300.orf -g0.495 -x5 Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH170 141 phosphoribosylaminoimidazolesuccinocarboxamide synthase #2 MTH420 300 conserved protein #3 MTH1354 124 NADH oxidase Motif number 1 AGTGTGTCCCCTCTGATACGGGGATTGCCGGTGCT 2 47 0 CCTGTCGGAT 0.99832 -254 TTATCTGTCAGTCTGCAGCCCGGAGTGTGTCCCCT 2 70 0 GCTGACGGAG 0.989593 -231 ATTTCGGTGTCCCTGTATCATGGATTTATCTGTCA 2 95 0 CCTGACGGAT 0.998715 -206 GCTCACAGAACACTGCAGCACTGATATGAGTAAAG 2 155 1 CCTGACTGAT 0.991711 -146 TACCATAGATCTCTGGTCCCGGGTTAATATGCTTT 2 195 0 CCTGTCGGTT 0.991988 -106 TCCTTACCTTCCCTTTACCATAGATCTCTGGTCCC 2 210 0 CCTTACAGAT 0.970407 -91 CTATCCCCTTCTCCTAGGAGTTATCGGTTA 3 105 0 CCTTTCGGAG 0.99087 -20 * *** * * **** Masking position 4 Map Score: 10.3745 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 153 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 TTCACCCTAAGAAGCATGAATCTGATTTCGCA 1 14 1 GAAGCAGATC 0.905785 -128 TATAAGTATTGGAGAGTTGATCAGGATTTCAT 1 95 1 GGAGAGTATC 0.971425 -47 TGCTGCACCCGGAGAAATCAACCACAAAAACT 2 19 0 GGAGAATAAC 0.956105 -282 TCCGGGTGCAGCACCGGCAATCCCCGTATCAG 2 38 1 GCACCGCATC 0.984854 -263 ACCGAAATATGCAGCATTTAACCAAAAATCTA 2 122 1 GCAGCATAAC 0.984208 -179 ACAGAACACTGCAGCACTGATATGAGTAAAGG 2 159 1 GCAGCATATA 0.923228 -142 TATTAACCCGGGACCAGAGATCTATGGTAAAG 2 201 1 GGACCAAATC 0.966069 -100 TGATACTGAAGGACAGATAATCACATCCTTAC 2 238 0 GGACAGTATC 0.958652 -63 CCTTCTGTCTGCGCCAGCAATCCATTCCCTGA 2 267 0 GCGCCACATC 0.950114 -34 TAGTTATAAGGGAGCATCAAAC 3 1 0 GGAGCACAAC 0.986957 -124 ****** * *** Masking position 10 Map Score: 9.34057 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 317 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 TCGCAAGATTATATAACTGAATCGCAATAT 1 41 1 ATATAACTGA 0.95439 -101 CTGAATCGCAATATAACTCATAATAGAATT 1 57 1 ATATAACTCA 0.940939 -85 TGTATCATGGATTTATCTGTCAGTCTGCAG 2 87 0 ATTTATCTGT 0.928446 -214 TCCCTTTACCATAGATCTCTGGTCCCGGGT 2 206 0 ATAGATCTCT 0.872386 -95 GGATACATCAATAGATCTGTGTGGTAGTTA 3 27 0 ATAGATCTGT 0.875903 -98 AAATTTATAAATATATCTGAATTATTTATA 3 57 1 ATATATCTGA 0.979477 -68 GTTATCGGTTATAGGTCTCTTCTTCATTTT 3 86 0 ATAGGTCTCT 0.938684 -39 ********** Masking position 1 Map Score: 9.01649 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 31 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 TGGTTGATTTCTCCGGGTGCAGCACCGGCA 2 27 1 CTCCGGGTGC 0.969424 -274 GGGGACACACTCCGGGCTGCAGACTGACAG 2 71 1 TCCGGGCTGC 0.960779 -230 TCATGGATTTATCTGTCAGTCTGCAGCCCG 2 83 0 ATCTGTCAGT 0.767749 -218 TGCTGCATATTTCGGTGTCCCTGTATCATG 2 108 0 TTCGGTGTCC 0.962128 -193 TGCTGCAGTGTTCTGTGAGCATAGATTTTT 2 145 0 TTCTGTGAGC 0.981815 -156 AAGCATATTAACCCGGGACCAGAGATCTAT 2 196 1 ACCCGGGACC 0.870973 -105 AAAACAGCCCTTCTGTCTGCGCCAGCAATC 2 277 0 TTCTGTCTGC 0.981562 -24 ACATCAATAGATCTGTGTGGTAGTTATAAG 3 23 0 ATCTGTGTGG 0.927471 -102 ********** Masking position 5 Map Score: 2.13421 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 648 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 GAATCGCAATATAACTCATAATAGAATTTA 1 59 1 ATAACTCATA 0.961117 -83 TCAACTCTCCAATACTTATATAGGTGTAAA 1 85 0 AATACTTATA 0.939545 -57 ATCAGGATTTCATACTCAAATTCTTTAAAA 1 114 1 CATACTCAAA 0.858933 -28 ATCAACCACAAAAACTTAAATAGA 2 5 0 AAAACTTAAA 0.85085 -296 CTTTATTGCCTTTACTCATATCAGTGCTGC 2 169 0 TTTACTCATA 0.859064 -132 TTGATGTATCCAAATTTATAAATATATCTG 3 46 1 CAAATTTATA 0.705747 -79 ATATATCTGAATTATTTATAAAATGAAGAA 3 67 1 ATTATTTATA 0.780864 -58 CCTATAACCGATAACTCCTAGGAGAAGGGG 3 101 1 ATAACTCCTA 0.867817 -24 ********** Masking position 4 Map Score: 1.9248 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 241 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 ********** No masking Map Score: 1.72962e-13 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 7 ********** No masking Map Score: 1.72962e-13 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 8 ********** No masking Map Score: 1.72962e-13 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