AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -inagC_tpal_opreg_300.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0861 236 glucosamine-fructose-6-phosphate aminotransferase (glmS) #2 TP0862 134 peptidyl-prolyl cis-trans isomerase, FKBP-type, 22 kDa (fklB) Motif number 1 CCTGTGACCTGTGGGTTACCTTGCTCGTTCGTCGGGT 1 48 1 GTGTCCTGCG 0.994906 -189 CTCGTTCGTCGGGTCTCCCCTTGGGGGAGGTGGTGAG 1 71 1 GGCTCCTGGG 0.998326 -166 GGGGGAGGTGGTGAGTCTCCCTGTTGGTGCGCTGGAC 1 93 1 GTGTCCTGTG 0.968 -144 TTGGTGCGCTGGACCGTAGCCTGCGAGGCGGCTCGTG 1 116 1 GGCGGCTGCG 0.999345 -121 CCTGCGAGGCGGCTCGTGGCTTGGTTGAGTCAGAATG 1 135 1 GGCGGCTGGG 0.998943 -102 AGTCAGAATGGTTCCTACGCGTGCGTGTGTTCTGTGG 1 162 1 GTCTGCTGCG 0.996743 -75 GGTGCGTACGATGCCTGAAAAGTGGGT 2 1 1 GGCGCGTGCG 0.996404 -134 GATAGCTAATGCCCCGATCCTTCCTTGAGCCACACCC 2 34 0 GCCGCCTCCG 0.992548 -101 GGATGGGGTAGGCTGGTCGCCTCGGGGCGGCGCGGAT 2 90 1 GGGGGCTCGG 0.993313 -45 ** ** ** *** * Masking position 12 Map Score: 18.7598 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 264 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 GCGATGTGCAGCAAGGCAACGGATGG 1 3 1 GATGGCACAG 0.967147 -234 CAAGGCAACGGATGGGCATGGGATCGCCTGTGAC 1 22 1 GATGGCAGGT 0.906361 -215 CCTCCCCCAAGGGGAGACCCGACGAACGAGCAAG 1 67 0 GGGGGACCGG 0.985119 -170 TCTCCCCTTGGGGGAGGTGGTGAGTCTCCCTGTT 1 84 1 GGGGGGTGTG 0.968636 -153 TCTCCCTGTTGGTGCGCTGGACCGTAGCCTGCGA 1 108 1 GGTGGCTGAG 0.987991 -129 CGTAGCCTGCGAGGCGGCTCGTGGCTTGGTTGAG 1 130 1 GAGGGGCCGG 0.994557 -107 TCGTGGCTTGGTTGAGTCAGAATGGTTCCTACGC 1 148 1 GTTGGTCGAG 0.923763 -89 GGTGCGTACGATGCCTGAAAAGTG 2 1 1 GGTGGTAGAC 0.841407 -134 CTGAAAAGTGGGTGTGGCTCAAGGAAGGATCGGG 2 25 1 GGTGGGCCAG 0.996529 -110 GTGAAGTACGGATGGGGTAGGCTGGTCGCCTCGG 2 81 1 GATGGGTGGG 0.989141 -54 TGGTCGCCTCGGGGCGGCGCGGATGAGCGCGCAA 2 103 1 GGGGGGCCGT 0.986671 -32 **** *** ** * Masking position 6 Map Score: 13.8205 Number of sites scoring better than the average of aligned sites = 923 Number in coding regions = 803 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 GCGATCCCATGCCCATCCGTTGCCTTGCTGC 1 18 0 GCCCTCCGTT 0.947676 -219 ATGGGCATGGGATCGCCTGTGACCTGTGGGT 1 33 1 GATCCCTGTG 0.875462 -204 GGGTTACCTTGCTCGTTCGTCGGGTCTCCCC 1 60 1 GCTCTTCGTC 0.937116 -177 AGACTCACCACCTCCCCCAAGGGGAGACCCG 1 80 0 CCTCCCCAAG 0.783631 -157 AGTCAGAATGGTTCCTACGCGTGCGTGTGTT 1 162 1 GTTCTACGCG 0.966411 -75 TGAGTTTAACGTTCTCCCGTGTGCTTTTGCA 1 202 1 GTTCCCCGTG 0.991401 -35 ACTTTTCAGGCATCGTACGCACC 2 3 0 CATCTACGCA 0.787582 -132 CCCATCCGTACTTCACACGTCAAGGAGATAG 2 66 0 CTTCCACGTC 0.91521 -69 GACCAGCCTACCCCATCCGTACTTCACACGT 2 77 0 CCCCTCCGTA 0.955788 -58 CCTTTTGCGCGCTCATCCGCGCCGCCCCGAG 2 110 0 GCTCTCCGCG 0.995567 -25 **** ****** Masking position 4 Map Score: 6.67153 Number of sites scoring better than the average of aligned sites = 1239 Number in coding regions = 1131 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 GCATGGGATCGCCTGTGACCTGTGGGTTACCT 1 37 1 GCCTTGCCTG 0.995139 -200 CGCCTCGCAGGCTACGGTCCAGCGCACCAACA 1 114 0 GCTAGGCCAG 0.969698 -123 CTGCGAGGCGGCTCGTGGCTTGGTTGAGTCAG 1 136 1 GCTCTGCTTG 0.909763 -101 ACACACGCACGCGTAGGAACCATTCTGACTCA 1 160 0 GCGTGGACCA 0.862573 -77 TCCTACGCGTGCGTGTGTTCTGTGGGTTTGAG 1 174 1 GCGTTGTCTG 0.97514 -63 TCTCCCGTGTGCTTTTGCACTGAAAAGGCGTC 1 214 1 GCTTTGACTG 0.988156 -23 CAAGGAGATAGCTAATGCCCCGATCCTTCCTT 2 45 0 GCTATGCCCG 0.988895 -90 TAGGCTGGTCGCCTCGGGGCGGCGCGGATGAG 2 98 1 GCCTGGGCGG 0.962506 -37 **** ** **** Masking position 7 Map Score: 4.95703 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 368 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 5 GATGTGCAGCAAGGCAACGGATGGGCATGG 1 13 1 AAGGCAACGG 0.983612 -224 ACGAGCAAGGTAACCCACAGGTCACAGGCG 1 46 0 TAACCCACAG 0.963819 -191 AGCCGCCTCGCAGGCTACGGTCCAGCGCAC 1 119 0 CAGGCTACGG 0.984786 -118 CTGACTCAACCAAGCCACGAGCCGCCTCGC 1 138 0 CAAGCCACGA 0.970817 -99 CGTTAAACTCAAACCCACAGAACACACGCA 1 183 0 AAACCCACAG 0.985361 -54 TTCAGTGCAAAAGCACACGGGAGAACGTTA 1 208 0 AAGCACACGG 0.97978 -29 ********** Masking position 7 Map Score: 5.69398 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 170 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 AGACGCCTTTTCAGTGCAAAAGCA 1 223 0 CCCTTTTCAG 0.996936 -14 TGAGCCACACCCACTTTTCAGGCATCGTACG 2 15 0 CACTTTTCAG 0.991847 -120 CGCTCCTTTTGCGCGCTCATCCG 2 122 0 CCCTTTTGCG 0.992626 -13 * ********* Masking position 6 Map Score: 0.443161 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 11 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 ********** No masking Map Score: -1.25466e-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: -1.25466e-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 9 ********** No masking Map Score: -1.25466e-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