AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_aful_reg_100.orf -o00130_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 Input sequences: #1 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #2 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #3 AF1191 32 dihydroxynaphthoic acid synthase (menB) #4 AF1192 50 conserved hypothetical protein #5 AF1195 27 activator 1, replication factor C, 53 KD subunit #6 AF1196 65 N5,N10-methylenetetrahydromethanopterin reductase (mer-2) #7 AF1197 300 3-ketoacyl-CoA thiolase (fadA-2) #8 AF1215 101 cell division protein, putative #9 AF1551 65 octaprenyl-diphosphate synthase (ispB) #10 AF1552 28 conserved hypothetical protein #11 AF1604 300 anthranilate synthase component II (trpD) #12 AF1778 105 stage V sporulation protein (spoVG) #13 AF1779 57 2-hydroxyacid dehydrogenase, putative #14 AF1855 180 2,3-dihydrosybenzoate-AMP ligase (entE) #15 AF2151 51 isochorismatase (entB) #16 AF2176 300 4-hydroxybenzoate octaprenyltransferase (ubiA) #17 AF2351 219 conserved hypothetical protein Motif number 1 AAGAAAAGGGCTTAAGGATTCATTTATACCTT 1 100 0 CTTAAGGTCA 0.435137 -24 CTCCAGATTTCTTGAGCTTGTGTCAGATTGAC 2 16 1 CTTGAGCGTG 0.739266 -82 TTAGCGCTTCATGAAGGACGTAACGTTGAGGA 7 137 1 ATGAAGGGTA 0.89345 -164 AGGACGTAACGTTGAGGACGTGTTGAATAACA 7 151 1 GTTGAGGGTG 0.964595 -150 TAAGAAAAAAGTGAAGGAGGTGTATT 7 285 1 GTGAAGGGTG 0.963753 -16 ACAGTAAAGCCTGAAGGAGGCATTCCGGGATT 11 140 1 CTGAAGGGCA 0.938329 -161 ACCGAGAGCCGTTAAGGCTGCACCGACCTCAA 11 171 0 GTTAAGGGCA 0.881861 -130 TTAATCCCACATGGTGGGAGCAG 11 288 1 ATGGTGGGCA 0.806398 -13 AATTTTTAAGGTAGAGGTGGTGAT 14 3 0 GTAGAGGGTG 0.944392 -178 TCTGGAGGCAGCAGTTCTCTGCG 16 2 1 CTGGAGGGCA 0.977789 -299 CAGGGAGATAATGGAGGATGCAATGAACATTG 16 96 1 ATGGAGGGCA 0.965042 -205 TGCAATGAACATTGAGGATGCGATGGAGTTTC 16 114 1 ATTGAGGGCG 0.933475 -187 TGGCAGAGAGATGGAGCTTGTGATTGTAAGAA 16 156 1 ATGGAGCGTG 0.833903 -145 TCACGAGAAGGTAATGGGCGTGATTCAGA 16 282 1 GTAATGGGTG 0.469667 -19 TCTTTACGATGTAGAGGTAGTATTTTTCCCCG 17 48 0 GTAGAGGGTA 0.922072 -172 TTGAAATCGAGTGGAGGCCTTACTACGTATGG 17 143 1 GTGGAGGTTA 0.884568 -77 TTTAATTTTGCTGGAGGTGTTGAG 17 206 1 CTGGAGGTTG 0.888135 -14 ******* *** Masking position 2 Map Score: 20.3459 Number of sites scoring better than the average of aligned sites = 1782 Number in coding regions = 1704 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 TAATGAGAAATCTCCCTGTTGGCT 6 52 1 TCTCCCGTGG 0.990441 -14 AAAGTTCTGGACTTCCGGAAGGCACTGGCCCC 7 42 1 ACTTCCGAGG 0.837142 -259 ATCTGCGTTATCACCCTGTAGGGGCCAGTGCC 7 62 0 TCACCCGAGG 0.994221 -239 TTTGAAATTATCATCCCGGAGGAAGTCGAGTA 7 188 1 TCATCCGAGG 0.973016 -113 CCTCGCTTCTTCATCCAGCTGAGGTGTGAACC 11 69 0 TCATCCGTGA 0.852203 -232 TCCTCCATTATCTCCCTGTAGGTCTCCTTAAG 16 82 0 TCTCCCGAGG 0.99526 -219 TACGTCCTGCTCTCCCAGCAGGTACATGTTGA 16 212 0 TCTCCCGAGG 0.99526 -89 AGGTAGTATTTTTCCCCGTAGAATTTAGCAGC 17 34 0 TTTCCCGAGA 0.933684 -186 GAAGATTTAATTTTGCTGGAGGTGTTGAG 17 201 1 TTTTGCGAGG 0.843238 -19 ****** * *** Masking position 6 Map Score: 14.3429 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 164 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 TTTTAAATTTTCGCTCCTTTGC 1 1 1 TTTTATTTTC 0.872148 -123 ATTGACTTTATTTAAATTTTTTGGATTTTCAG 2 42 1 TTTAATTTTT 0.910459 -56 TTAACATATATATTACTATTTTGCTGTAATTT 4 16 0 TATTAATTTT 0.574343 -35 TTTTAATTTTTATTTTTTCCAACAGATAG 6 8 1 TTTTATTTTC 0.872148 -58 CGCTTTTTATTTAAACCTTTTTCCCAACTTTG 8 60 0 TTAAATTTTT 0.852889 -42 GTGTTGAACTTATAACATTTTCGAGATTTTTT 9 29 0 TATAATTTTC 0.872106 -37 GCGAAGTGTATTTAAGCTTTTTGCTATAGTAT 11 252 0 TTTAATTTTT 0.910459 -49 CAAAGTGGTATATAAGAATTTTGATTGCAGGA 12 49 0 TATAAATTTT 0.763464 -57 TTCAAAACCTTTTTATCTTTTCTGGGTTCAAT 13 30 1 TTTTATTTTC 0.872148 -28 ATGCTGACAATTTAACCTTTTCTAAAAAGATT 14 35 1 TTTAATTTTC 0.942255 -146 TAACCTTTTCTAAAAAGATTTTGCGGTAGTTT 14 47 1 TAAAAATTTT 0.647971 -134 ATCTTTAATTTTAAAAAATTTCCTAAACTACC 14 71 0 TTAAAATTTC 0.876038 -110 TTGTCAACATTTAAACAATTTTAACATTACCA 14 115 1 TTAAAATTTT 0.814941 -66 GCCAAATCCCTTAAAAAATTTCCCGATTAAAG 14 148 0 TTAAAATTTC 0.876038 -33 ***** ***** Masking position 5 Map Score: 12.4099 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 116 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 4 CTTCCGGAAGTCCAGAACTTTCTCTGCTACCGTC 7 29 0 TCAACTTCTC 0.949784 -272 AGAGCTGTTATTCAACACGTCCTCAACGTTACGT 7 154 0 TCAACTCCTC 0.992708 -147 TGGTTCGGTGTACTCGACTTCCTCCGGGATGATA 7 196 0 TCTACTCCTC 0.94036 -105 CAAGTTTAAAAACAGCAACGCCTCAGCTTGACCG 8 11 0 ACAAAGCCTC 0.759306 -91 TGCCGGGTTTTCAAGCACCTCCTC 11 1 0 TAAACTCCTC 0.967795 -300 TGAGGTGTGAACCAAAGCTTCTTCATCAGGTCTT 11 48 0 ACAGCTCTTC 0.871166 -253 GAGTCCGCAGAGAACTGCTGCCTCCAGA 16 5 0 AAAGCGCCTC 0.888696 -296 ATCCTCAATGTTCATTGCATCCTCCATTATCTCC 16 99 0 TCAGCTCCTC 0.991149 -202 TGCCAGAAACTCCATCGCATCCTCAATGTTCATT 16 117 0 TCAGCTCCTC 0.991149 -184 GTCCTCCATAAGCACTACGTCCTGCTCTCCCAGC 16 225 0 ACAACTCCTG 0.924141 -76 CTGAATCACGCCCATTACCTTCTCGTGAAGCTCC 16 276 0 CCAACTTCTC 0.853367 -25 TTCTACGGGGAAAAATACTACCTCTACATCGTAA 17 43 1 AAAACACCTC 0.780619 -177 * ** ** ***** Masking position 13 Map Score: 10.0555 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 956 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TTGGGTAAAAAGATGCCAGGATGGTAAACGA 1 69 1 AGAGCCAGGA 0.941314 -55 ATACTCCTTTGGACGACTGGATTTGA 5 12 1 GGAGACTGGA 0.922921 -16 GTAACGTTGAGGACGTGTTGAATAACAGCTC 7 156 1 GGAGTGTTGA 0.945512 -145 AGCTGGATGAAGAAGCGAGGAGGAAGATAGA 11 81 1 AGAGCGAGGA 0.95208 -220 TTTTTAAGGTAGAGGTGGTGAT 14 2 0 AGAGTGGTGA 0.840903 -179 TTAAGCACGGGGAAGTCGGGGTAGTAGCGCC 16 56 0 GGAGTCGGGG 0.912048 -245 AGATAATGGAGGATGCAATGAACATTGAGGA 16 101 1 GGAGCAATGA 0.8723 -200 TGAACATTGAGGATGCGATGGAGTTTCTGGC 16 119 1 GGAGCGATGG 0.949965 -182 TAGTGCTTATGGAGGACAGGAGGAAGATTCT 16 242 1 GGAGACAGGA 0.950516 -59 TAATTTTGCTGGAGGTGTTGAG 17 208 1 GGAGTGTTGA 0.945512 -12 *** ******* Masking position 3 Map Score: 5.69334 Number of sites scoring better than the average of aligned sites = 689 Number in coding regions = 664 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 6 GTCAATCTGACACAAGCTCAAGAAATCTGG 2 18 0 CACAAGCTCA 0.835553 -80 ATAAATCTTACTGAAAATCCAAAAAATTTA 2 54 0 CTGAAAATCC 0.909983 -44 TTTTATCACTCTCAAAATCCAC 9 3 0 CTCAAAATCC 0.957957 -63 CTGCCGGGTTTTCAAGCACCTCCTC 11 6 0 TTCAAGCACC 0.844078 -295 CAACCTTTGCCAGAAACTCCATCGCATCCT 16 128 0 CAGAAACTCC 0.941793 -173 TTCTTACAATCACAAGCTCCATCTCTCTGC 16 158 0 CACAAGCTCC 0.983096 -143 TTACCTTCTCGTGAAGCTCCTTCAGAATCT 16 266 0 GTGAAGCTCC 0.878967 -35 AGCAACCAGCCTCAAAAACCCTCTTTACGA 17 71 0 CTCAAAAACC 0.863644 -149 ATAGAGATAATTCAAGATCCAGCAAACAAA 17 106 1 TTCAAGATCC 0.892598 -114 AGATCCAGCAAACAAACTCCCCTTTGAAAT 17 120 1 AACAAACTCC 0.82549 -100 ********** Masking position 5 Map Score: 6.2371 Number of sites scoring better than the average of aligned sites = 1098 Number in coding regions = 1049 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 AGAAGAAAAGGGCTTAAGGATTC 1 111 0 AGAAGAAAGC 0.948262 -13 CACCAACAAGAGAGGAAATCGACACACTTAAAG 7 228 1 AGAGGAATGC 0.978444 -73 TCGACACACTTAAAGAATTGGACCCGGATGGTA 7 246 1 TAAAGATTGC 0.718911 -55 ATCTCATGATTGAGGTTAAGGCCAGCACAGTAA 11 114 1 TGAGGTAAGC 0.898123 -187 ATGGCAAAAAAGAGGTAAAAGTCACCTAAACTT 11 221 0 AGAGGAAAGC 0.982432 -80 AAAAAGGTTTTGAAGCAAAAGCCAAACTCTTAA 13 11 0 TGAAGAAAGC 0.948262 -47 GGAAATTTTTTAAGGGATTTGGCAATTATAGAT 14 157 1 TAAGGATTGC 0.886412 -24 AGGCGAAGGGAGAGGGATAGGGCGTTCTTACAA 16 179 0 AGAGGATAGC 0.967035 -122 AGCTTCACGAGAAGGTAATGGGCGTGATTCAGA 16 278 1 GAAGGAATGC 0.870158 -23 ***** *** * * Masking position 3 Map Score: 4.45561 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 330 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 TAGGGGCCAGTGCCTTCCGGAAGTCCAGAA 7 46 0 TGCCTTCCGG 0.846255 -255 GTCAAGCTGAGGCGTTGCTGTTTTTAAACT 8 13 1 GGCGTTGCTG 0.972893 -89 GCCTCCTTCAGGCTTTACTGTGCTGGCCTT 11 131 0 GGCTTTACTG 0.938527 -170 GCCTGAAGGAGGCATTCCGGGATTTGAGGT 11 148 1 GGCATTCCGG 0.947565 -153 AGCTTTTTAAGGCGCTACTACCCCGACTTC 16 46 1 GGCGCTACTA 0.892146 -255 AGAGGGATAGGGCGTTCTTACAATCACAAG 16 172 0 GGCGTTCTTA 0.807682 -129 ATCGAGTGGAGGCCTTACTACGTATGGCGT 17 148 1 GGCCTTACTA 0.942122 -72 TACTACGTATGGCGTTACGGAAACTATATT 17 163 1 GGCGTTACGG 0.987357 -57 ********** Masking position 6 Map Score: 3.07169 Number of sites scoring better than the average of aligned sites = 321 Number in coding regions = 296 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 GTATTTTCCAGTACATTTTTCCC 3 3 1 ATTTTCCGTA 0.965051 -30 ATATATTACTATTTTGCTGTAATTTTTAAT 4 10 0 ATTTTGCGTA 0.978226 -41 TAATTTTTATTTTTTCCAACAGATAGTTAAA 6 14 1 TTTTTCCACA 0.768558 -52 TTTTACCTCTTTTTTGCCATACTATAGCAAA 11 234 1 TTTTTGCATA 0.946122 -67 GTATTTAAGCTTTTTGCTATAGTATGGCAAA 11 246 0 TTTTTGCATA 0.946122 -55 TTCTAAAAAGATTTTGCGGTAGTTTAGGAAA 14 54 1 ATTTTGCGTA 0.978226 -127 GAGGTAGTATTTTTCCCCGTAGAATTTAGCA 17 36 0 TTTTCCCGTA 0.880012 -184 TGAAGATTTAATTTTGCTGGAGGTGTTGAG 17 200 1 ATTTTGCGGA 0.932539 -20 ******* *** Masking position 11 Map Score: 4.38884 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 100 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 TATACTCCTTTGGACGACTGGATTT 5 5 1 CTCCTTGGAC 0.898069 -23 TGAATAACAGCTCTTTTGAAATTATCATCCC 7 174 1 CTCTTTGAAA 0.741984 -127 TTCTAACCCTCCTTTCAAATTTCGTTACT 12 87 0 CTCCTTCAAA 0.916268 -19 GGGGTAGTAGCGCCTTAAAAAGCTTAGTATT 16 39 0 CGCCTTAAAA 0.944279 -262 CCCTGTAGGTCTCCTTAAGCACGGGGAAGTC 16 70 0 CTCCTTAGCA 0.969442 -231 CCTCTCCCTTCGCCTTCAACATGTACCTGCT 16 197 1 CGCCTTAACA 0.933238 -104 TCCTCCTGTCCTCCATAAGCACTACGTCCTG 16 235 0 CTCCATAGCA 0.833565 -66 TCTCGTGAAGCTCCTTCAGAATCTTCCTCCT 16 259 0 CTCCTTAGAA 0.974699 -42 CAAACAAACTCCCCTTTGAAATCGAGTGGAG 17 128 1 CCCCTTGAAA 0.90026 -92 ****** **** Masking position 6 Map Score: 3.33416 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 289 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 11 GATTTTCAGTAAGATTTATTTAACTGAGTT 2 65 1 AAGATTTATT 0.953349 -33 CTCAACGCTAAGATTTAATACGCTTTTTA 8 83 0 AAGATTTAAT 0.955098 -19 TGGTTTCGGTAAGATATATTTTTATCTGCG 15 23 0 AAGATATATT 0.870855 -29 TTAAAATATGAAGATTTAATTTTGCTGGAG 17 192 1 AAGATTTAAT 0.955098 -28 ********** Masking position 5 Map Score: 0.560885 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 6 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 TGCATGTTTTTTGGGTAAAAAGATGCCAGG 1 59 1 TTGGGTAAAA 0.960912 -65 CTCCGGGCAGGGAAAAATGTACTGGAA 3 16 0 CAGGGAAAAA 0.920384 -17 TAACTATCTGTTGGAAAAAATAAAAATTAA 6 13 0 TTGGAAAAAA 0.876489 -53 GATTGCAAAGTTGGGAAAAAGGTTTAAATA 8 55 1 TTGGGAAAAA 0.978666 -47 AGATAGATTGGGTCAAAGTTTTTTAAA 10 8 1 TTGGGTCAAA 0.899654 -21 CTAAATTCTACGGGGAAAAATACTACCTCT 17 38 1 CGGGGAAAAA 0.944854 -182 ********** Masking position 8 Map Score: 1.87217 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 40 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 AGAGAAAGTTCTGGACTTCCGGAAGGCACT 7 38 1 CTGGACTTCC 0.973487 -263 GTTCGGTGTACTCGACTTCCTCCGGGATGA 7 198 0 CTCGACTTCC 0.993794 -103 CTTTAAGTGTGTCGATTTCCTCTCTTGTTG 7 231 0 GTCGATTTCC 0.958934 -70 GCGCTACTACCCCGACTTCCCCGTGCTTAA 16 57 1 CCCGACTTCC 0.983208 -244 CTTGAATTATCTCTATTTCCGAGCAACCAG 17 92 0 CTCTATTTCC 0.940317 -128 AAGGCCTCCACTCGATTTCAAAGGGGAGTT 17 134 0 CTCGATTTCA 0.940317 -86 ********** Masking position 5 Map Score: 5.95146 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 121 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 14 TCACCCTGTAGGGGCCAGTGCCTTCCGGAAGT 7 52 0 GGGCCAGTCC 0.9715 -249 AATACCATCCGGGTCCAATTCTTTAAGTGTGT 7 249 0 GGGCCAATCT 0.981295 -52 CCCACCATGTGGGATTAATCCCGCGAAGTGTA 11 274 0 GGGTTAATCC 0.495005 -27 TATCTTTTCTGGGTTCAATTCTGTC 13 43 1 GGGTCAATCT 0.97988 -15 TCTGGAGGCAGCAGTTCTCTGCGGACTC 16 7 1 GGCGCAGTCT 0.947563 -294 AGTTCTCTGCGGACTCAATACTAAGCTTTTTA 16 23 1 GGATCAATCT 0.943086 -278 TGGGAGAGCAGGACGTAGTGCTTATGGAGGAC 16 227 1 GGAGTAGTCT 0.85477 -74 *** ***** ** Masking position 7 Map Score: 0.372289 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 45 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 15 ********** No masking Map Score: -4.33898e-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