AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_tpal_reg_100.orf -o00530_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -x5 -e 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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0029 107 UDP-N-acetylglucosamine 1-carboxyvinyltransferase (murA) #2 TP0085 80 PTS system, nitrogen regulatory IIA component (ptsN-1) #3 TP0090 181 UDP-N-acetylmuramate dehydrogenase (murB) #4 TP0251 153 DNA-binding protein II #5 TP0413 102 phosphoglucomutase #6 TP0417 26 apolipoprotein N-acyltransferase (cutE) #7 TP0505 300 hexokinase (hxk) #8 TP0755 199 PTS system, nitrogen regulatory IIA component (ptsN-2) #9 TP0861 236 glucosamine-fructose-6-phosphate aminotransferase (glmS) Motif number 1 CGCCTAAGTAAGTACACAGGATGGGGCCGTACTTTTGC 1 8 1 GGACAAGGGC 0.820676 -100 TGTTCTACAGGAATGTGTGCGCAAAGGGGTGAGAGC 1 82 1 GGGTGGGGGG 0.996984 -26 GATATCCTGGGAGCGGAAAGAGCGTGGGGAGCTTTTC 2 7 1 CGGCGAGCGG 0.966583 -74 GCTGGGCGTGGTCCGCACGTGTTCTGCGCCCGGTTGGGAGA 3 29 0 GGACGGGCGC 0.96143 -153 GGGCAAAGGCGTTTGCGCGACAATGGGGCTGGGCGTGGTCC 3 56 0 GGGCGCGGGG 0.99281 -126 TTCGAGGGAGGGTAGACTGAAGCGCAGGCGGGCAAAGGCGT 3 85 0 GGCTGAAGGG 0.887085 -97 CTTCACCCGAGGTGGTGCGCGTTTGAGGCGGCTGTTTGCCC 4 107 1 GGGCGGAGGG 0.996183 -47 GTGGTCGGGTGTAGGGGCGGGGGAGAGGTAGGA 5 3 0 GGGCGGAGGG 0.996183 -100 CGCGGGTGAAGGAAGTGCAAGGGAGGTGGTGGTCTTGACAG 5 57 0 GGGCAGGTGG 0.985033 -46 AGCGAAAAGAGGAGGTGCGTGGGACGCGACGATA 7 4 0 GGGCGGGCGG 0.999032 -297 GCCGAACACAACAGGGGCGTAGTAGGGGATTGACTGTGCAG 7 92 1 AGGCGAGGGT 0.91353 -209 GTAGGGGATTGACTGTGCAGTCACTGGGTCCGTCGGGTTCA 7 113 1 GGGCATGGGC 0.910036 -188 GGCCTATGCGGAACGAGTACGGCAAACGGAGTGTTCCTTGT 7 158 0 GGGTAGACGG 0.93143 -143 AAAAAGGGGTGCCGGCGTATGGGGCAGGGAGTTTATACCTA 7 206 0 GGGTAGAGGG 0.944192 -95 CTACCCTGGCAGCCGACCAGGGAGGGCGCGT 7 280 1 AGCCAGGCGT 0.614486 -21 AAGACACACTTGGGGTACGCATCATGCGTTGCGTAGAAATC 8 31 0 TGACGAGCGG 0.736149 -169 CGATAGAAGAGGTTGCGCGGTACCTGCGAATTTCTGAACGT 8 115 1 GGGCGTGCGT 0.97009 -85 TACCGTGTATGAGTGGGCGCAAAAGGGGAAGATTCCGTCAG 8 155 1 GGGCGAGGGG 0.99808 -45 ATGGGCATGGGATCGCCTGTGACCTGTGGGTTACCTTGCTC 9 33 1 GGCTGGGTGT 0.827409 -204 CTGTTGGTGCGCTGGACCGTAGCCTGCGAGGCGGCTCGTGG 9 113 1 GGCCGAGCGG 0.991959 -124 TGGTTCCTACGCGTGCGTGTGTTCTGTGGGTTTGAGTTTAA 9 170 1 GGGTGGGTGT 0.941992 -67 * * *** * *** * Masking position 5 Map Score: 37.404 Number of sites scoring better than the average of aligned sites = 1780 Number in coding regions = 1602 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 CTAAGTAAGTACACAGGATGGGGCCGTACTTT 1 14 1 ACAGGATGGG 0.760288 -94 GTTGGGAGAAACTTCGAAGGGGCGCAC 3 6 0 ACCGAAGGGG 0.959552 -176 TCCCAACCGGGCGCAGAACACGTGCGGACCAC 3 31 1 GCAGAACACG 0.646628 -151 AGGCGTTTGCGCGACAATGGGGCTGGGCGTGG 3 59 0 GCCAATGGGG 0.846077 -123 TGAAGCGCAGGCGGGCAAAGGCGTTTGCGCGA 3 77 0 GCGCAAAGGC 0.651822 -105 TCTTTGCGTTTCGAGGGAGGGTAGACTGAAGC 3 103 0 TCGGGAGGGT 0.783775 -79 CCCTCGAAACGCAAAGAAGGCCAAGACCGCGC 3 118 1 GCAGAAGGCC 0.927726 -64 ACGCGCTTATGCTACAATGGCGCGGTCTTGGC 3 137 0 GCCAATGGCG 0.75729 -45 TGACACCGCTGCCCGGAAAGGTGTTTTCGCTA 4 18 1 GCGGAAAGGT 0.906485 -136 AGGTGTTTTCGCTAGAAAGGCTGTGGCTCGCC 4 36 1 GCGAAAGGCT 0.876649 -118 GCAAACAGCCGCCTCAAACGCGCACCACCTCG 4 114 0 GCCAAACGCG 0.821889 -40 GGGTGTAGGGGCGGGGGAGAGGTAGGA 5 6 0 GCGGGAGAGG 0.970318 -97 TGAAGGAAGTGCAAGGGAGGTGGTGGTCTTGA 5 60 0 GCGGGAGGTG 0.931592 -43 GCGCGGAGGATAGGGCGCGGGTGA 5 89 0 GCAGGATAGG 0.69005 -14 TGCTTTTCTGGCAGGGGAAAGTT 6 14 1 GCGGGAAAGT 0.556174 -13 AAGAGGAGGTGCGTGGGACGCGACGATA 7 7 0 GCGGGACGCG 0.970357 -294 CACAACAGGGGCGTAGTAGGGGATTGACTGTG 7 98 1 GCAGTAGGGG 0.916897 -203 AACCGTTCCTGCAAAAAAGGGGTGCCGGCGTA 7 228 0 GCAAAAGGGG 0.97274 -73 TGCCAGGGTAGCACGGATAGCTCGTTTAGGAA 7 259 0 GCGGATAGCT 0.438621 -42 CTGGCAGCCGACCAGGGAGGGCGCGT 7 285 1 ACGGGAGGGC 0.890911 -16 GTGTCTTGTTACAGAGAAAGGGGAGGTTGGTT 8 65 1 ACAGAAAGGG 0.824111 -135 GTATGAGTGGGCGCAAAAGGGGAAGATTCCGT 8 161 1 GCAAAAGGGG 0.97274 -39 GTGCAGCAAGGCAACGGATGGGCATGGGATCG 9 16 1 GCCGGATGGG 0.953024 -221 ACTCACCACCTCCCCCAAGGGGAGACCCGACG 9 77 0 TCCCAAGGGG 0.670341 -160 CTGGACCGTAGCCTGCGAGGCGGCTCGTGGCT 9 124 1 GCGCGAGGCG 0.968467 -113 GTGCTTTTGCACTGAAAAGGCGTCT 9 222 1 ACAAAAGGCG 0.774531 -15 ** ******** Masking position 2 Map Score: 28.4667 Number of sites scoring better than the average of aligned sites = 1910 Number in coding regions = 1711 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 GTAAGTACACAGGATGGGGCCGTACTTTTGCGG 1 18 1 AGATGGGGGT 0.894894 -90 TCCTGGGAGCGGAAAGAGCGTGGGGAGCTTTTC 2 15 1 GGAAGAGCGG 0.977671 -66 CGCGACAATGGGGCTGGGCGTGGTCCGCACGTG 3 49 0 GGCTGGGCGG 0.972815 -133 ATGCTACAATGGCGCGGTCTTGGCCTTCTTTGC 3 128 0 GGGCGGTCGG 0.977309 -54 TGTAGGGGCGGGGGAGAGGTAGGA 5 2 0 GGGAGAGGGG 0.978596 -101 GATGAAATCAGGTGTGGTCGGGTGTAGGGGCGG 5 24 0 GGGTGGTCGT 0.919298 -79 AGGAAGTGCAAGGGAGGTGGTGGTCTTGACAGG 5 56 0 AGGAGGTGGG 0.936494 -47 GCGCGGAGGATAGGGCGCGGGTGAAGGAAG 5 83 0 GGTAGGGCGG 0.970793 -20 GGGCCTATGCGGAACGAGTACGGCAAACGGAGT 7 167 0 GGACGAGTGG 0.753462 -134 GGGGTGCCGGCGTATGGGGCAGGGAGTTTATAC 7 209 0 CGATGGGGGG 0.975407 -92 GCAGCCGACCAGGGAGGGCGCGT 7 288 1 AGGAGGGCGT 0.955409 -13 CTTGTTACAGAGAAAGGGGAGGTTGGTTTGTCC 8 69 1 AGAAGGGGGT 0.92139 -131 AGCAAGGCAACGGATGGGCATGGGATCGCCTGT 9 20 1 CGATGGGCGG 0.9813 -217 GGAGACCCGACGAACGAGCAAGGTAACCCACAG 9 56 0 CGACGAGCGG 0.923911 -181 TCTCCCCTTGGGGGAGGTGGTGAGTCTCCCTGT 9 84 1 GGGAGGTGGA 0.782723 -153 ** ****** ** Masking position 6 Map Score: 19.2604 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 620 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 GGATGGGGCCGTACTTTTGCGGTATTCGTG 1 29 1 GTACTTTTGC 0.682171 -79 GCTCTCACCCCTTTGCGCACACATTC 1 92 0 ACCCCTTTGC 0.974884 -16 AGAGCGTGGGGAGCTTTTCCAAAAAGCTTG 2 29 1 GAGCTTTTCC 0.82048 -52 ACCACGCCCAGCCCCATTGTCGCGCAAACG 3 58 1 GCCCCATTGT 0.791932 -124 TGTCGCGCAAACGCCTTTGCCCGCCTGCGC 3 75 1 ACGCCTTTGC 0.983936 -107 GGCCAAGACCGCGCCATTGTAGCATAAGCG 3 136 1 GCGCCATTGT 0.857269 -46 ACGATTTCACGCGCTTATGCTACAATGGCG 3 147 0 GCGCTTATGC 0.803517 -35 TCTAGCGAAAACACCTTTCCGGGCAGCGGT 4 22 0 ACACCTTTCC 0.919789 -132 TGGCGAGCCACAGCCTTTCTAGCGAAAACA 4 39 0 CAGCCTTTCT 0.647094 -115 AAATGCTTTTCTGGCAGGGGAA 6 3 1 ATGCTTTTCT 0.608292 -24 ATACGCCGGCACCCCTTTTTTGCAGGAACG 7 227 1 ACCCCTTTTT 0.71804 -74 CAAACCAACCTCCCCTTTCTCTGTAACAAG 8 69 0 TCCCCTTTCT 0.698021 -131 ACGGAATCTTCCCCTTTTGCGCCCACTCAT 8 163 0 CCCCTTTTGC 0.939789 -37 GGTGCCCACTTTTCCTGACGGAATC 8 185 0 CCACTTTTCC 0.821786 -15 GTTCTCCCGTGTGCTTTTGCACTGAAAAGG 9 212 1 GTGCTTTTGC 0.896533 -25 AGACGCCTTTTCAGTGCAAAAG 9 225 0 ACGCCTTTTC 0.913707 -12 ********** Masking position 8 Map Score: 11.3628 Number of sites scoring better than the average of aligned sites = 1067 Number in coding regions = 960 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 5 CCAACCGGGCGCAGAACACGTGCGGACCAC 3 33 1 GCAGAACACG 0.920735 -149 GGACAGAAAACATATACGATTT 3 170 0 ACAGAAAACA 0.970875 -12 CAGCCTTTCTAGCGAAAACACCTTTCCGGG 4 29 0 AGCGAAAACA 0.832298 -125 CCTCGGGTGAAGAGAACACACCGTTGTACA 4 89 0 AGAGAACACA 0.96873 -65 GACAAGAAACACACGCGGGCA 4 143 0 ACAAGAAACA 0.844097 -11 TATCCAAGTCGCCGAACACAACAGGGGCGT 7 82 1 GCCGAACACA 0.960477 -219 TTTCTCTGTAACAAGACACACTTGGGGTAC 8 54 0 ACAAGACACA 0.942922 -146 AAGGTAACCCACAGGTCACAGGCGATCCCA 9 40 0 ACAGGTCACA 0.929702 -197 ACTCAAACCCACAGAACACACGCACGCGTA 9 177 0 ACAGAACACA 0.990264 -60 ********** Masking position 8 Map Score: 9.15618 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 126 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 CCTTCGAAGTTTCTCCCAACCGGGCGCAGA 3 18 1 TTCTCCCAAC 0.924559 -164 CATATACGATTTCACGCGCTTATGCTACAA 3 152 0 TTCACGCGCT 0.923207 -30 CATTCGGGACTTCTGGCGAGCCACAGCCTT 4 52 0 TTCTGGCGAG 0.880812 -102 GTGTGTTCTCTTCACCCGAGGTGGTGCGCG 4 98 1 TTCACCCGAG 0.994384 -56 CCCCCGCCCCTACACCCGACCACACCTGAT 5 21 1 TACACCCGAC 0.955183 -82 TTGCACTTCCTTCACCCGCGCCCTATCCTC 5 78 1 TTCACCCGCG 0.990154 -25 GTCCGTCGGGTTCACCCTACAAGGAACACT 7 140 1 TTCACCCTAC 0.937883 -161 TCCGAAGAAATTCTCACGATAGAAGAGGTT 8 99 1 TTCTCACGAT 0.863348 -101 GAGTTTAACGTTCTCCCGTGTGCTTTTGCA 9 203 1 TTCTCCCGTG 0.967663 -34 ********** Masking position 1 Map Score: 7.18233 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 142 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 CGCACACATTCCTGTAGAACACCGATCAAC 1 73 0 CCTGTAGAAC 0.848028 -35 CAGTCTACCCTCCCTCGAAACGCAAAGAAG 3 107 1 TCCCTCGAAA 0.686312 -75 ATAGGGCGCGGGTGAAGGAAGTGCAAGGGA 5 74 0 GGTGAAGGAA 0.578122 -29 GTGCGTGGGACGCGACGATA 7 1 0 CGCGACGATA 0.741163 -300 TCAGTCCAAACCTCTAGGAAGATATCCAAG 7 60 1 CCTCTAGGAA 0.74017 -241 GTAGGGTGAACCCGACGGACCCAGTGACTG 7 130 0 CCCGACGGAC 0.970153 -171 CATCATGCGTTGCGTAGAAATCTCACGCCT 8 23 0 TGCGTAGAAA 0.799484 -177 GGTTGGTTTGTCCGAAGAAATTCTCACGAT 8 89 1 TCCGAAGAAA 0.89048 -111 GCCCACTTTTCCTGACGGAATCTTCCCCTT 8 177 0 CCTGACGGAA 0.950166 -23 CAAGGGGAGACCCGACGAACGAGCAAGGTA 9 64 0 CCCGACGAAC 0.96035 -173 AACACACGCACGCGTAGGAACCATTCTGAC 9 163 0 CGCGTAGGAA 0.94991 -74 ********** Masking position 7 Map Score: 4.68879 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 441 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 AGAGTTTTTAGCTTGGGGGA 2 71 1 GCTTGGGGGA 0.966718 -10 ACGCGCACCACCTCGGGTGAAGAGAACACA 4 99 0 CCTCGGGTGA 0.96437 -55 CCGAGGTGGTGCGCGTTTGAGGCGGCTGTT 4 113 1 GCGCGTTTGA 0.951207 -41 GGCTGTTTGCCCGCGTGTGTTTCTTGTC 4 136 1 CCGCGTGTGT 0.843505 -18 TCGGGTGTAGGGGCGGGGGAGAGGTAGGA 5 10 0 GGGCGGGGGA 0.96434 -93 GGAGGATAGGGCGCGGGTGAAGGAAGTGCA 5 79 0 GCGCGGGTGA 0.994596 -24 GCGCGGAGGATAGGGCGCGG 5 93 0 GCGCGGAGGA 0.98941 -10 AAAAGAGGAGGTGCGTGGGACGCGACGATA 7 11 0 GTGCGTGGGA 0.907529 -290 CTCACGCCTGGCGTGTATCAC 8 2 0 GCGTGTATCA 0.585235 -198 TCTGAACGTACCGTGTATGAGTGGGCGCAA 8 147 1 CCGTGTATGA 0.880876 -53 TCGGGTCTCCCCTTGGGGGAGGTGGTGAGT 9 79 1 CCTTGGGGGA 0.936948 -158 GCGGCTCGTGGCTTGGTTGAGTCAGAATGG 9 143 1 GCTTGGTTGA 0.805441 -94 GAACACACGCACGCGTAGGAACCATTCTGA 9 164 0 ACGCGTAGGA 0.831268 -73 ********** Masking position 5 Map Score: 17.7442 Number of sites scoring better than the average of aligned sites = 1039 Number in coding regions = 954 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 9 TGTGTGCGCAAAGGGGTGAGAGC 1 95 1 AAGGGGTGAG 0.924465 -13 AGAAACTTCGAAGGGGCGCAC 3 2 0 AAGGGGCGCA 0.940627 -180 GACTGAAGCGCAGGCGGGCAAAGGCGTTTG 3 82 0 CAGGCGGGCA 0.931761 -100 TTCGGGACTTCTGGCGAGCCACAGCCTTTC 4 50 0 CTGGCGAGCC 0.899431 -104 GGTGTAGGGGCGGGGGAGAGGTAGGA 5 7 0 CGGGGGAGAG 0.931611 -96 GCTTTTCTGGCAGGGGAAAGTT 6 15 1 CAGGGGAAAG 0.850738 -12 CCGAACACAACAGGGGCGTAGTAGGGGATT 7 93 1 CAGGGGCGTA 0.864334 -208 TCCTGCAAAAAAGGGGTGCCGGCGTATGGG 7 224 0 AAGGGGTGCC 0.95881 -77 GGTCGGCTGCCAGGGTAGCACGGATAGCTC 7 268 0 CAGGGTAGCA 0.861567 -33 TGATACACGCCAGGCGTGAGATTTCTACGC 8 12 1 CAGGCGTGAG 0.951008 -188 CCACAGGTCACAGGCGATCCCATGCCCATC 9 32 0 CAGGCGATCC 0.847235 -205 CACCTCCCCCAAGGGGAGACCCGACGAACG 9 73 0 AAGGGGAGAC 0.958901 -164 ********** Masking position 4 Map Score: 10.6024 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 531 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 10 ********** No masking Map Score: -2.77579e-12 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 11 ********** No masking Map Score: -2.77579e-12 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: -2.77579e-12 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