AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_aful_reg_300.orf -o00130_aful_300.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 AF2350 300 ATP-dependent RNA helicase HepA, putative #18 AF2351 219 conserved hypothetical protein Motif number 1 AGAAAAGGGCTTAAGGATTCATTTATACCTT 1 100 0 TTAAGGATCA 0.480616 -24 TCCAGATTTCTTGAGCTTGTGTCAGATTGAC 2 17 1 TTGAGCTGTG 0.732116 -81 TAGCGCTTCATGAAGGACGTAACGTTGAGGA 7 138 1 TGAAGGAGTA 0.928063 -163 GGACGTAACGTTGAGGACGTGTTGAATAACA 7 152 1 TTGAGGAGTG 0.957734 -149 AAGAAAAAAGTGAAGGAGGTGTATT 7 286 1 TGAAGGAGTG 0.94795 -15 CAGTAAAGCCTGAAGGAGGCATTCCGGGATT 11 141 1 TGAAGGAGCA 0.933308 -160 CCGAGAGCCGTTAAGGCTGCACCGACCTCAA 11 171 0 TTAAGGCGCA 0.797982 -130 ATTTTTAAGGTAGAGGTGGTGAT 14 3 0 TAGAGGTGTG 0.87746 -178 TCTGGAGGCAGCAGTTCTCTGCG 16 3 1 TGGAGGCGCA 0.968914 -298 AGGGAGATAATGGAGGATGCAATGAACATTG 16 97 1 TGGAGGAGCA 0.97767 -204 GCAATGAACATTGAGGATGCGATGGAGTTTC 16 115 1 TTGAGGAGCG 0.960909 -186 GGCAGAGAGATGGAGCTTGTGATTGTAAGAA 16 157 1 TGGAGCTGTG 0.873056 -144 CTTTACGATGTAGAGGTAGTATTTTTCCCCG 18 48 0 TAGAGGTGTA 0.835321 -172 TGAAATCGAGTGGAGGCCTTACTACGTATGG 18 144 1 TGGAGGCTTA 0.827109 -76 TTAATTTTGCTGGAGGTGTTGAG 18 207 1 TGGAGGTTTG 0.873315 -13 ******* *** Masking position 4 Map Score: 15.9744 Number of sites scoring better than the average of aligned sites = 1405 Number in coding regions = 1334 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 2 TAATGAGAAATCTCCCTGTTGGCT 6 52 1 TCTCCCGTGG 0.988818 -14 AAAGTTCTGGACTTCCGGAAGGCACTGGCCCC 7 42 1 ACTTCCGAGG 0.848901 -259 ATCTGCGTTATCACCCTGTAGGGGCCAGTGCC 7 62 0 TCACCCGAGG 0.993236 -239 TTTGAAATTATCATCCCGGAGGAAGTCGAGTA 7 188 1 TCATCCGAGG 0.973829 -113 CCTCGCTTCTTCATCCAGCTGAGGTGTGAACC 11 69 0 TCATCCGTGA 0.828505 -232 TCCTCCATTATCTCCCTGTAGGTCTCCTTAAG 16 82 0 TCTCCCGAGG 0.995042 -219 TACGTCCTGCTCTCCCAGCAGGTACATGTTGA 16 212 0 TCTCCCGAGG 0.995042 -89 AGGTAGTATTTTTCCCCGTAGAATTTAGCAGC 18 34 0 TTTCCCGAGA 0.920907 -186 GAAGATTTAATTTTGCTGGAGGTGTTGAG 18 201 1 TTTTGCGAGG 0.815658 -19 ****** * *** Masking position 6 Map Score: 13.0711 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 0.876568 -123 ATTGACTTTATTTAAATTTTTTGGATTTTCAG 2 42 1 TTTAATTTTT 0.913686 -56 TTAACATATATATTACTATTTTGCTGTAATTT 4 16 0 TATTAATTTT 0.584148 -35 TTTTAATTTTTATTTTTTCCAACAGATAG 6 8 1 TTTTATTTTC 0.876568 -58 CGCTTTTTATTTAAACCTTTTTCCCAACTTTG 8 60 0 TTAAATTTTT 0.857863 -42 GTGTTGAACTTATAACATTTTCGAGATTTTTT 9 29 0 TATAATTTTC 0.876524 -37 GCGAAGTGTATTTAAGCTTTTTGCTATAGTAT 11 252 0 TTTAATTTTT 0.913686 -49 CAAAGTGGTATATAAGAATTTTGATTGCAGGA 12 49 0 TATAAATTTT 0.770652 -57 TTCAAAACCTTTTTATCTTTTCTGGGTTCAAT 13 30 1 TTTTATTTTC 0.876568 -28 ATGCTGACAATTTAACCTTTTCTAAAAAGATT 14 35 1 TTTAATTTTC 0.944406 -146 TAACCTTTTCTAAAAAGATTTTGCGGTAGTTT 14 47 1 TAAAAATTTT 0.657091 -134 ATCTTTAATTTTAAAAAATTTCCTAAACTACC 14 71 0 TTAAAATTTC 0.880341 -110 TTGTCAACATTTAAACAATTTTAACATTACCA 14 115 1 TTAAAATTTT 0.820932 -66 GCCAAATCCCTTAAAAAATTTCCCGATTAAAG 14 148 0 TTAAAATTTC 0.880341 -33 ***** ***** Masking position 5 Map Score: 10.431 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 TTTCAAAAGAGCTGTTATTCAACACGTCCTCAACG 7 160 0 GTGTTTACAC 0.919564 -141 CTGAGGCGTTGCTGTTTTTAAACTTGCCTTTATCG 8 19 1 GTGTTTACTT 0.913383 -83 CAGGTTCTTTCATGGTGTTGAACTTATAACATTTT 9 40 0 CTGTTTACTT 0.804202 -26 GCTTTACTGTGCTGGCCTTAACCTCAATCATGAGA 11 115 0 GTGCTTACTC 0.991442 -186 AGAAAGTTTAGGTGACTTTTACCTCTTTTTTGCCA 11 218 1 GTGCTTACTC 0.991444 -83 TTGTTTAAATGTTGACAATGAACTTTCAATATCTT 14 98 0 GTGCATACTT 0.843971 -83 TCTCCCTGTAGGTCTCCTTAAGCACGGGGAAGTCG 16 69 0 GTCCTTACAC 0.947283 -232 ATCCCTCTCCCTTCGCCTTCAACATGTACCTGCTG 16 194 1 CTCCTTACAT 0.720084 -107 CGCCCATTACCTTCTCGTGAAGCTCCTTCAGAATC 16 267 0 CTCCTGACTC 0.768004 -34 TAATAACTCCGATGGCGTTTATCTCTCCAGTTTTG 17 30 0 GTGCTTACTC 0.991444 -271 ATGCATCTATGATGACGTTGAAATCGTGAGGTTCG 17 237 0 GTGCTTAATC 0.901262 -64 * ** * ** * *** Masking position 11 Map Score: 7.08039 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 390 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AATCCTTAAGCCCTTTTCTTCT 1 112 1 CCCTTTCTTC 0.909526 -12 CCTGTAGGGGCCAGTGCCTTCCGGAAGTCCA 7 49 0 CCAGTCCTTC 0.869755 -252 GCTAAGAGCTTCATTCTCTTCGTTTGCTCAT 7 111 0 TCATTTCTTC 0.879012 -190 ATTGCATCCTCCATTATCTCCCTGTAGGTCT 16 89 0 CCATTTCTCC 0.962533 -212 TCCTCAATGTTCATTGCATCCTCCATTATCT 16 101 0 TCATTCATCC 0.781153 -200 GCCAGAAACTCCATCGCATCCTCAATGTTCA 16 119 0 CCATCCATCC 0.866745 -182 TATCCCTCTCCCTTCGCCTTCAACATGTACC 16 193 1 CCTTCCCTTC 0.821773 -108 AAGCACTACGTCCTGCTCTCCCAGCAGGTAC 16 219 0 TCCTGTCTCC 0.857295 -82 AGAATCTTCCTCCTGTCCTCCATAAGCACTA 16 242 0 TCCTGCCTCC 0.929932 -59 TGAATCACGCCCATTACCTTCTCGTGAAGCT 16 278 0 CCATTCCTTC 0.972573 -23 CATTTTTCAGCCATGATCTTCTCCAGAGAAC 17 145 1 CCATGTCTTC 0.929772 -156 CTCAACACCTCCAGCAAAATTA 18 208 0 TCAACCCTCC 0.729177 -12 ***** ***** Masking position 9 Map Score: 6.9866 Number of sites scoring better than the average of aligned sites = 1554 Number in coding regions = 1485 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 AGTTAAATAAATCTTACTGAAAATCCAAAAAATTTA 2 54 0 ACACGAAACC 0.979475 -44 ACAACTCCCGGATACCTCGACGGTAGCA 7 3 1 ACCCGATATC 0.936094 -298 GAGATTTTTTATCACTCTCAAAATCCAC 9 3 0 ACTCCAAACC 0.964366 -63 TTAAGGCTGCACCGACCTCAAATCCCGGAATGCCTC 11 156 0 ACCCCAAACC 0.994316 -145 AAATTTCCTAAACTACCGCAAAATCTTTTTAGAAAA 14 52 0 ACCCCAAACT 0.951303 -129 CAATACCGTAACCGTCCAGATAATCCTGTATCCTGA 17 194 0 ACCCGATACC 0.984625 -107 GTTATCACCTCACCGAAATCTCACCAAATTTC 17 279 0 ACACGAAATC 0.916074 -22 TTTCCGAGCAACCAGCCTCAAAAACCCTCTTTACGA 18 71 0 ACCCCAAACC 0.994316 -149 * * ** **** ** Masking position 10 Map Score: 6.08743 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 104 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 TTATTCAACACGTCCTCAACGTTACGTCCT 7 151 0 CGTCCTCAAC 0.868796 -150 TCGGTGTACTCGACTTCCTCCGGGATGATA 7 196 0 CGACTTCCTC 0.978695 -105 TTAAGTGTGTCGATTTCCTCTCTTGTTGGT 7 229 0 CGATTTCCTC 0.818294 -72 TGAACCAAAGCTTCTTCATCAGGTCTTCGG 11 45 0 CTTCTTCATC 0.935931 -256 TTCCTCCTCGCTTCTTCATCCAGCTGAGGT 11 76 0 CTTCTTCATC 0.935931 -225 GATTTTCTATCTTCCTCCTCGCTTCTTCAT 11 87 0 CTTCCTCCTC 0.982872 -214 GCTACTACCCCGACTTCCCCGTGCTTAAGG 16 59 1 CGACTTCCCC 0.924249 -242 ATAAGCACTACGTCCTGCTCTCCCAGCAGG 16 222 0 CGTCCTGCTC 0.942467 -79 CCTTCAGAATCTTCCTCCTGTCCTCCATAA 16 248 0 CTTCCTCCTG 0.892909 -53 ********** Masking position 6 Map Score: 6.70023 Number of sites scoring better than the average of aligned sites = 927 Number in coding regions = 882 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 TACCTCGACGGTAGCAGAGAAAGTTCTGGACT 7 23 1 GTCAGAGAAA 0.855461 -278 TAAGAGATGATCCACCGAGAGCCGTTAAGGCT 11 184 0 TCCCGAGAGC 0.944395 -117 AACAGATGTCTCCGCAGATAAAAATATATCTT 15 11 1 TCCAGATAAA 0.837476 -41 TAGTATTGAGTCCGCAGAGAACTGCTGCCTCC 16 14 0 TCCAGAGAAC 0.987959 -287 CTGGCAAAGGTTGGCAGAGAGATGGAGCTTGT 16 145 1 TTCAGAGAGA 0.928281 -156 GCCATGATCTTCTCCAGAGAACCAGTAGTTAA 17 154 1 TCCAGAGAAC 0.987923 -147 CTTTAACAGAGAACGAGTACAAAG 18 3 1 TTCAGAGAAC 0.975446 -217 ** ******** Masking position 8 Map Score: 2.18819 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 120 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 TTAAATTTTTTGGATTTTCAGTAAGATTTAT 2 53 1 TGGATTTCAG 0.755399 -45 GAGAAAGTTCTGGACTTCCGGAAGGCACTGG 7 39 1 TGGACTTCGG 0.929803 -262 GGTCAAGCTGAGGCGTTGCTGTTTTTAAACT 8 12 1 AGGCGTTCTG 0.979443 -90 TGCCTCCTTCAGGCTTTACTGTGCTGGCCTT 11 131 0 AGGCTTTCTG 0.968052 -170 AGCCTGAAGGAGGCATTCCGGGATTTGAGGT 11 147 1 AGGCATTCGG 0.921596 -154 GAGGATGCGATGGAGTTTCTGGCAAAGGTTG 16 127 1 TGGAGTTCTG 0.951653 -174 ATCAGGATACAGGATTATCTGGACGGTTACG 17 193 1 AGGATTACTG 0.708561 -108 AATCGAGTGGAGGCCTTACTACGTATGGCGT 18 147 1 AGGCCTTCTA 0.762285 -73 TTACTACGTATGGCGTTACGGAAACTATATT 18 162 1 TGGCGTTCGG 0.974297 -58 ******* *** Masking position 6 Map Score: 4.58333 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 357 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 10 CAAATCCAGTCGTCCAAAGGAGTATA 5 5 0 CGTCAAAGGG 0.941214 -23 CGGGATGATAATTTCAAAAGAGCTGTTATTCA 7 174 0 ATTCAAAAGG 0.95474 -127 CTTTATCGAGATTGCAAAGTTGGGAAAAAGGT 8 46 1 ATTCAAAGTG 0.93678 -56 GAGTAACGAAATTTGAAAGGAGGGTTAGAA 12 86 1 ATTGAAAGGG 0.936972 -20 AGTATTTCAAATTGCAAAACTGGAGAGATAAA 17 16 1 ATTCAAAACG 0.916844 -285 ACAGAGAACGAGTACAAAGCTGCTAAATTCTA 18 16 1 AGTCAAAGCG 0.964535 -204 CCTCCACTCGATTTCAAAGGGGAGTTTGTTTG 18 128 0 ATTCAAAGGG 0.987233 -92 *** ****** * Masking position 6 Map Score: 1.99091 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 74 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 11 ATTGGTGTTTACGGTTTTGATGAGCAAACGA 7 92 1 ACGTTTTGAT 0.804796 -209 AAGATTTAATACGCTTTTTATTTAAACCTTT 8 72 0 ACGTTTTTAT 0.762038 -30 GATTGGGTCAAAGTTTTTTAAAA 10 16 1 AAGTTTTTAA 0.953985 -13 AAAAGATAAAAAGGTTTTGAAGCAAAAGCCA 13 20 0 AAGTTTTGAA 0.963887 -38 GTAGTTTAGGAAATTTTTTAAAATTAAAGAT 14 72 1 AAATTTTTAA 0.803242 -109 TTTAAAATTAAAGATATTGAAAGTTCATTGT 14 88 1 AAGTATTGAA 0.807974 -93 TTTAATCGGGAAATTTTTTAAGGGATTTGGC 14 149 1 AAATTTTTAA 0.803242 -32 ACTCAATACTAAGCTTTTTAAGGCGCTACTA 16 35 1 AAGTTTTTAA 0.953985 -266 GGACAGGAGGAAGATTCTGAAGGAGCTTCAC 16 255 1 AAGTTCTGAA 0.861806 -46 *** ******* Masking position 5 Map Score: 3.83164 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 66 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 12 AATTTAAATAAAGTCAATCTGACACAAGCTCAA 2 27 0 AATAATCTAC 0.976112 -71 AAACTCAGTTAAATAAATCTTACTGAAAATCCA 2 63 0 AATAATCTAC 0.976112 -35 AGAGCGTGGTAATTTAATCTAACGTTTCCTGCA 12 23 1 AATAATCTAC 0.976112 -83 TCTACCTTAAAAATTATGCTGACAATTTAACCT 14 20 1 AATATGCTAC 0.845431 -161 CCGCAGATAAAAATATATCTTACCGAAACCAAC 15 22 1 AATTATCTAC 0.894549 -30 GCTATGACTGAATTCATTCTCCCAAACAGGAGT 17 88 0 AATATTCTCC 0.922849 -213 CCTCCAGCAAAATTAAATCTTCATATTTTAAAT 18 190 0 AATAATCTCA 0.781015 -30 ** * ***** ** Masking position 2 Map Score: 1.36162 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 ********** No masking Map Score: 5.58019e-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 14 ********** No masking Map Score: 5.58019e-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 15 ********** No masking Map Score: 5.58019e-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