AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_aful_reg_100.orf -o00300_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: AF1510 24 long-chain-fatty-acid--CoA ligase (fadD-6) Input sequences: #1 AF0051 132 succinyl-diaminopimelate desuccinylase (dapE-1) #2 AF0700 41 aspartate kinase (lysC) #3 AF0703 38 A. fulgidus predicted coding region AF0703 #4 AF0747 47 diaminopimelate epimerase (dapF) #5 AF0800 31 diaminopimelate decarboxylase (lysA) #6 AF0899 300 conserved hypothetical protein #7 AF0909 31 dihydrodipicolinate reductase (dapB) #8 AF0911 24 SSU ribosomal protein S17E (rps17E) #9 AF0912 51 A. fulgidus predicted coding region AF0912 #10 AF0913 144 A. fulgidus predicted coding region AF0913 #11 AF0932 41 conserved hypothetical protein #12 AF0933 22 branched-chain amino acid aminotransferase (ilvE) #13 AF1216 101 lysyl-tRNA synthetase (lysS) #14 AF1506 30 aspartate-semialdehyde dehydrogenase (asd) #15 AF1507 62 A. fulgidus predicted coding region AF1507 #16 AF1508 61 A. fulgidus predicted coding region AF1508 #17 AF1512 71 conserved hypothetical protein #18 AF1513 257 A. fulgidus predicted coding region AF1513 Motif number 1 AACTTTGATTTAATAAATCTTTCGCATAAAATC 1 26 1 TATAAACTTC 0.961656 -107 TAAGCAAGAAATATAAATCTTGCTGAG 2 5 0 AATAAACTTC 0.946758 -37 AGATAAAGTTGCCGGGAACTTTT 4 1 1 AATAAATTGC 0.793542 -47 CGGGCGAGATTTTTAAAAGTTCCCGGCAACTTT 4 15 0 TTTAAAGTTC 0.87006 -33 GAAATTAAAAGTGTGGAGGGATTAA 5 17 0 ATTAAAGTGG 0.621559 -15 AAATAAAATTGAGCTGGAGTATA 7 19 0 AATAAATTGG 0.721362 -13 CGCAAATTAATCTTAAAATTTTCTTTCAAAAAA 9 18 0 TTTAAATTTC 0.922024 -34 ATATGCAAAATTTTAAATTTTCGGTTACATCAT 10 44 1 TTTAAATTTG 0.888449 -101 ATACGAGGGGTTAAAAACCTTTGACGTCATCAA 10 112 0 TAAAAACTTG 0.575699 -33 ATAAAAAGCGTATTAAATCTTAGCGTTGAG 13 8 0 TTTAAACTTG 0.949814 -94 TACGCTTTTTATTTAAACCTTTTTCCCAACTTT 13 29 1 ATTAAACTTT 0.754251 -73 GCGTTGCTGTTTTTAAACTTGCCTTTATCGAGA 13 66 0 TTTAAATTGC 0.858624 -36 GCGAGGCTAAAGATAAATCTTCTGGTTGTTTGT 15 25 0 AATAAACTTT 0.732584 -38 GAAGAAGTAATGATAAATCTTTCCATTTATTAA 16 27 0 TATAAACTTC 0.961656 -35 TGGTTGAGAATAATAAAGCTTTGATTTTGGTGC 17 39 0 TATAAACTTG 0.944112 -33 GTATCTTGGCTGTTGAATCTTACCGGAAAATTA 18 124 1 TTTGAACTTC 0.769843 -134 AATAATTACTATTTAAAGTTTTCCTTTCTTTTT 18 222 0 ATTAAATTTC 0.893434 -36 * ***** *** * Masking position 7 Map Score: 16.4503 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 164 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 2 ACCTGAAGCTCCGCCTTGCCAACATGCA 6 9 0 CCGCCTTGCC 0.98935 -292 GTTGAGATTGCAGCCTTCCCCATCTCTCCC 6 123 1 CAGCCTTCCC 0.981158 -178 CAGCCTTCCCCATCTCTCCCATGATTTGAT 6 133 1 CATCTCTCCC 0.793291 -168 CTTCCCGCTTAACCTCCTTTTTAA 10 5 1 CCGCTTAACC 0.939247 -140 TCGGTTACATCATCATTCCCTGCTTTGCAT 10 64 1 CATCATTCCC 0.933917 -81 CAAAGCTAAACCGCATTGCCTATGCAAAGC 10 85 0 CCGCATTGCC 0.983355 -60 TTTATTTAAACCTTTTTCCCAACTTTGCAA 13 36 1 CCTTTTTCCC 0.79024 -66 AGCAACGCCTCAGCTTGACCG 13 91 1 CAGCTTGACC 0.84722 -11 CGGCCTAACGCCTCATAGCCGGGGCTGAAT 18 11 0 CCTCATAGCC 0.888484 -247 CTCCAGGCGTGCGCCTTACCGCTCGGCAAC 18 43 0 GCGCCTTACC 0.884394 -215 ********** Masking position 9 Map Score: 7.79152 Number of sites scoring better than the average of aligned sites = 870 Number in coding regions = 822 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 AGTTTTTGGAATCAAAAGGGATAAAGGGCA 1 82 1 ATCAAAAGGG 0.916106 -51 ATCGGCGGAGATAAAAACGGTTGCG 3 24 1 ATAAAAACGG 0.823324 -15 TGTGGAGGGATTAAAAACAG 5 1 0 TTAAAAACAG 0.918891 -31 TGCAACTGAGATCAAAAACGCTCTGATCAA 6 38 0 ATCAAAAACG 0.917632 -263 CAATCTCAACTACAAAAGAGTCTTGACGGC 6 103 0 TACAAAAGAG 0.788825 -198 AAAATTTTCTTTCAAAAAAGAAATTA 9 7 0 TTCAAAAAAG 0.964392 -45 AAAGGTTTAAATAAAAAGCGTATTAAATCT 13 21 0 ATAAAAAGCG 0.823324 -81 AAAGGCAAGTTTAAAAACAGCAACGCCTCA 13 73 1 TTAAAAACAG 0.918891 -29 CAGGGGGCAATTTAAAAAAG 14 1 0 TTTAAAAAAG 0.77842 -30 CTGTGGAATTTCCAAAAAAGCAAGCATAAA 18 160 1 TCCAAAAAAG 0.849585 -98 ATAATAATCAATCAAAAAAGAAAGGAAAAC 18 208 1 ATCAAAAAAG 0.957969 -50 ********** Masking position 5 Map Score: 7.81544 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 256 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 CTATAACAATGCCTACCCACTCAACTC 1 116 1 GCTACCCCAC 0.986858 -17 GACACCCTGAGGACGAAGACACATCTTGCAACTGA 6 59 0 GGCGAGCCAC 0.930443 -242 TTCGTCCTCAGGGTGTCGACCCAGCTGCCGTCAAG 6 77 1 GGTGCGCCAC 0.978123 -224 AGATGGGGAAGGCTGCAATCTCAACTACAAAAGAG 6 113 0 GGTGAACCAC 0.975234 -188 ATATTGTATGGTTGGCATCACGCC 8 10 1 GGTGCACCGC 0.951293 -15 TTAAAATTTTGCATATACCCACTTCTTAAAAAGGA 10 25 0 GCTAACCCTC 0.947424 -120 CTTTAGCCTCGCTTACAATCACATCAG 15 46 1 GCTAAACCAC 0.980527 -17 GGCAACCCCGGCCTAACGCCTCATAGCCGGGGCTG 18 14 0 GCTACGCCAA 0.81834 -244 CCAGGCGTGCGCCTTACCGCTCGGCAACCCCGGCC 18 36 0 GCTTCCCCGC 0.870032 -222 GCGGGCGAACGCCCACACGCTCTCCAGGCGTGCGC 18 59 0 GCCAACCCTC 0.861868 -199 CGCCCGCGTGGGTTCGAATCCCACCCCCGGCGCTG 18 87 1 GGTCAACCAC 0.916937 -171 AAAAAAGCAAGCATAAAAACTCATGTTTTATTCGT 18 173 1 GCTAAACCAG 0.854656 -85 ** ** ** * ** * Masking position 10 Map Score: 7.96838 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 386 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 ACGCTCTGATCAACCTGAAGCTCCGCCTTG 6 21 0 CAACCTGAAG 0.991332 -280 GCTGGGTCGACACCCTGAGGACGAAGACAC 6 72 0 CACCCTGAGG 0.978354 -229 CAACCAGAAATGAAGGGTGA 12 13 0 CAACCAGAAA 0.956447 -10 CGGTCAAGCTGAGGCGTTGCTGTT 13 88 0 CAAGCTGAGG 0.965947 -14 TATGCACAAACAACCAGAAGATTTATCTTT 15 20 1 CAACCAGAAG 0.991332 -43 TTATTATTCTCAACCAGATTGTTTCT 17 56 1 CAACCAGATT 0.896806 -16 ********** Masking position 8 Map Score: 4.97255 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 78 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GTTATAGCTGTTGCCCTTTATCCCTTTTGATT 1 91 0 TTGCCTTTAC 0.973527 -42 CCTAATCTTGCTTTCCTTTAATTTTTCATAAT 6 199 1 CTTCCTTTAT 0.94453 -102 TAATTTTCTTATTACCTTTACCGATTCCTAAC 6 227 1 ATTCCTTTAC 0.961767 -74 TTACCGATTCCTAACCTTTACCAAACCCAATC 6 244 1 CTACCTTTAC 0.97555 -57 TGTTTTTAAACTTGCCTTTATCGAGATTGCAA 13 60 0 CTTCCTTTAC 0.99244 -42 AAATTGCCCCCTGTCCTTCAACC 14 18 1 CTGCCTTCAC 0.971004 -13 AACCAGAAGATTTATCTTTAGCCTCGCTTACA 15 31 1 TTTTCTTTAC 0.851933 -32 *** ****** * Masking position 10 Map Score: 4.61641 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 122 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 TTACATGATTTTATGCGAAAGATTTATTAAAT 1 33 0 TATCGAAAGA 0.860115 -100 TTATCCCTTTTGATTCCAAAAACTATCATAAT 1 74 0 TATCCAAAAA 0.946842 -59 CTTAAAATTTTCTTTCAAAAAAGAAATTA 9 8 0 TTTCAAAAAA 0.750463 -44 TATTAAAAATTAATACGAAAAA 16 1 0 TATCGAAAAA 0.979497 -61 GTTTAGAAAATAATTCGAAAAAAG 17 3 0 TATCGAAAAA 0.876081 -69 TGATTGATTATTATACGAATAAAACATGAGTT 18 190 0 TATCGAATAA 0.684789 -68 CGTATAATAATCAATCAAAAAAGAAAGGAAAA 18 205 1 TAACAAAAAA 0.824749 -53 * ** ******* Masking position 8 Map Score: 3.83402 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 15 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ATGAAAAATTAAAGGAAAGCAAGATTAGGAA 6 197 0 AAAGGAAAGA 0.950213 -104 AGGAATCGGTAAAGGTAATAAGAAAATTATG 6 225 0 AAAGGTAATA 0.925165 -76 TGGGTTTGGTAAAGGTTAGGAATCGGTAAAG 6 242 0 AAAGGTTAGA 0.749226 -59 TTTCTTTCAAAAAAGAAATTA 9 1 0 AAAAGAAATA 0.882039 -51 CAATCTCGATAAAGGCAAGTTTAAAAACAGC 13 63 1 AAAGGCAAGT 0.863058 -39 ATTTTTAATAAATGGAAAGATTTATCATTAC 16 23 1 AATGGAAAGT 0.653525 -39 AACTGTAGGAAGAAGTAATGATAAATCTTTC 16 37 0 AGAAGTAATA 0.779525 -25 GAAATTCCACAGAAGTAATTTTCCGGTAAGA 18 141 0 AGAAGTAATT 0.584769 -117 GAATTTCCAAAAAAGCAAGCATAAAAACTCA 18 165 1 AAAAGCAAGA 0.921817 -93 AATCAATCAAAAAAGAAAGGAAAACTTTAAA 18 213 1 AAAAGAAAGA 0.934305 -45 GAAAACTTTAAATAGTAATTATTTATCGGGA 18 232 1 AATAGTAATA 0.695656 -26 ********* * Masking position 8 Map Score: 5.04536 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 233 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 TGATCAACCTGAAGCTCCGCCTTGCCAACA 6 15 0 GAAGCTCCGC 0.858137 -286 TTAATTTGCGGAACTCCCAGT 9 41 1 GAACTCCCAG 0.880823 -11 ATTCAGCCCCGGCTATGAGGCG 18 3 1 TCAGCCCCGG 0.947692 -255 TTACCGCTCGGCAACCCCGGCCTAACGCCT 18 28 0 GCAACCCCGG 0.980843 -230 GCGGTAAGGCGCACGCCTGGAGAGCGTGTG 18 51 1 GCACGCCTGG 0.921256 -207 CCACGCGGGCGAACGCCCACACGCTCTCCA 18 68 0 GAACGCCCAC 0.925317 -190 GGTGGGATTCGAACCCACGCGGGCGAACGC 18 82 0 GAACCCACGC 0.934796 -176 GGTTCGAATCCCACCCCCGGCGCTGTTGTA 18 97 1 CCACCCCCGG 0.98451 -161 ********** Masking position 3 Map Score: 2.11675 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 248 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 CGTTTTTATCTCCGCCGATTTAAAGTTCAGGT 3 11 0 TCGCGATTTA 0.968902 -28 TTAAAAGTTCCCGGCAACTTTATCT 4 4 0 CCGCACTTTA 0.885757 -44 TTTCCTCGTGACTGCTGGTTAAAAATTTCCTG 6 275 0 ACGCGGTTAA 0.928921 -26 ACTGGGAGTTCCGCAAATTAATCTTAAAATT 9 31 0 TCGCAATTAA 0.924496 -21 TGATGATGTAACCGAAAATTTAAAATTTTGCA 10 47 0 ACGAAATTTA 0.817943 -98 ACGTTTTAAATCAGCTGATTAACTCGCCGAGT 11 20 1 TCGCGATTAA 0.951031 -22 AATCTCGATAAAGGCAAGTTTAAAAACAGCAA 13 64 1 AAGCAGTTTA 0.596127 -38 GCACAAACAACCAGAAGATTTATCTTTAGCCT 15 23 1 CCGAGATTTA 0.884962 -40 ** ** ****** No masking Map Score: -1.00199 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 150 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 ACCTGAACTTTAAATCGGCGGAGATAAAAACG 3 11 1 TAAATCGCGA 0.969943 -28 AGATAAAGTTGCCGGGAACTTTTAA 4 4 1 TAAAGTGCGG 0.889265 -44 CAGGAAATTTTTAACCAGCAGTCACGAGGAAA 6 275 1 TTAACCGCGT 0.931206 -26 AATTTTAAGATTAATTTGCGGAACTCCCAGT 9 31 1 TTAATTGCGA 0.926912 -21 TGCAAAATTTTAAATTTTCGGTTACATCATCA 10 47 1 TAAATTTCGT 0.823117 -98 ACTCGGCGAGTTAATCAGCTGATTTAAAACGT 11 20 0 TTAATCGCGA 0.952642 -22 TTGCTGTTTTTAAACTTGCCTTTATCGAGATT 13 64 0 TAAACTGCTT 0.604557 -38 AGGCTAAAGATAAATCTTCTGGTTGTTTGTGC 15 23 0 TAAATCTCGG 0.888491 -40 ****** ** ** No masking Map Score: -1.00199 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 150 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 CGTTTTTATCTCCGCCGATTTAAAGTTCAGGT 3 11 0 TCGCGATTTA 0.972854 -28 TTAAAAGTTCCCGGCAACTTTATCT 4 4 0 CCGCACTTTA 0.899177 -44 TTTCCTCGTGACTGCTGGTTAAAAATTTCCTG 6 275 0 ACGCGGTTAA 0.937627 -26 ACTGGGAGTTCCGCAAATTAATCTTAAAATT 9 31 0 TCGCAATTAA 0.933706 -21 TGATGATGTAACCGAAAATTTAAAATTTTGCA 10 47 0 ACGAAATTTA 0.83787 -98 ACGTTTTAAATCAGCTGATTAACTCGCCGAGT 11 20 1 TCGCGATTAA 0.957154 -22 AATCTCGATAAAGGCAAGTTTAAAAACAGCAA 13 64 1 AAGCAGTTTA 0.62933 -38 GCACAAACAACCAGAAGATTTATCTTTAGCCT 15 23 1 CCGAGATTTA 0.898464 -40 ** ** ****** No masking Map Score: -1.00199 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 150 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789