AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00660_aful_reg_300.orf -o00660_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 AF1540 143 succinyl-CoA synthetase, beta subunit (sucC-1) #2 AF1542 135 conserved hypothetical protein #3 AF1665 147 ornithine cyclodeaminase (arcB) #4 AF1667 158 sulfate adenylyltransferase (sat) #5 AF1669 48 adenylylsulfate reductase, subunit B (aprB) #6 AF1671 64 coenzyme F390 synthetase (ftsA-2) #7 AF1720 182 acetolactate synthase, large subunit (ilvB-1) #8 AF1778 105 stage V sporulation protein (spoVG) #9 AF1779 57 2-hydroxyacid dehydrogenase, putative #10 AF2009 101 heme biosynthesis protein (nirJ-2) #11 AF2010 46 A. fulgidus predicted coding region AF2010 #12 AF2011 175 conserved hypothetical protein #13 AF2013 275 coenzyme F390 synthetase (ftsA-3) #14 AF2014 63 sugar transporter, putative #15 AF2100 106 acetolactate synthase, large subunit (ilvB-4) #16 AF2186 65 succinyl-CoA synthetase, beta subunit (sucC-2) #17 AF2187 174 A. fulgidus predicted coding region AF2187 Motif number 1 AGAAATTCCGAAAATTTTTTATATTGAAAA 1 35 1 AAAATTTTTT 0.926982 -109 AAGGGCAGGCAAAATTGTTTTATCTTTCTT 3 25 0 AAAATTGTTT 0.829752 -123 ATTGAATAGAAAAATTTTTCTTACAGCATC 3 78 1 AAAATTTTTC 0.928687 -70 CATTAACTTTAATACTTTTCAAGAAGACAG 3 122 1 AATACTTTTC 0.769305 -26 GTAGAAAATTTTTTGAACTCCTTT 4 5 1 AAAATTTTTT 0.926982 -154 GCGCAATTTTCAAACTCTTCGAAAATAAAA 4 38 0 CAAACTCTTC 0.729284 -121 TGAAAATTCGAAAACCTTTAATCATTAAAA 4 83 1 AAAACCTTTA 0.904669 -76 TAATCATTAAAATATTTTTCGAAACCTTTA 4 101 1 AATATTTTTC 0.609529 -58 AGCTCTAAAATTTTTCTTTTTTCTAA 6 7 1 AAAATTTTTC 0.928687 -58 CAATGCAATAAAAACTTTTAGATTTAGAAA 6 30 0 AAAACTTTTA 0.959965 -35 TGGGCGAACCAAAACTTTTTAAAGCGCATG 7 70 1 AAAACTTTTT 0.96026 -113 TCTTTTCCAGAGAACTTTTTCATCACTCCC 7 108 0 AGAACTTTTT 0.745454 -75 TCCTGCAATCAAAATTCTTATATACCACTT 8 49 1 AAAATTCTTA 0.792941 -57 AAGCAAAAGCCAAACTCTTAA 9 2 0 CAAACTCTTA 0.699297 -56 CTTTTGCTTCAAAACCTTTTTATCTTTTCT 9 23 1 AAAACCTTTT 0.915926 -35 CCTAAATAGTAAAATTTTTATTTTTGTTAG 11 13 1 AAAATTTTTA 0.918334 -34 TGAAGGTTATAAAACTTATTATTAAGCTTA 12 138 0 AAAACTTATT 0.663401 -38 AACTGGCGGGAAAACCGTTTTTTAATACTG 13 60 0 AAAACCGTTT 0.804397 -216 TTATTTGCATAAAATTTTTAGCTTTTTAAT 14 31 1 AAAATTTTTA 0.918334 -33 TCAACCTTAGCAAACTTTTTAAAATTATAA 15 74 1 CAAACTTTTT 0.896782 -33 GCTGCTTAGAAAAACCGTTACAAGACTCAA 17 43 1 AAAACCGTTA 0.763648 -132 ********** Masking position 9 Map Score: 24.4674 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 168 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 2 TCGAACTTAAAAGGTGGTTGGATGTGCAGGCAGAAT 1 80 1 AGGGGGATGG 0.962339 -64 ATCAGCCTTAGCGGCGGTTGAAGGTGGACGCCATCA 2 38 1 GGGGGGAGGG 0.996714 -98 CTCTTCGAAAATAAAAGGCAAAGGAGTTCAAAAAAT 4 18 0 AAAAGAAGGG 0.740342 -141 AAAAATGTATGAAAAGGTTGGAGGTGAGTTGA 5 27 1 GAAGGGAGGG 0.98589 -22 TTTAAAGCGCATGCTGGTGGTGGGAGTGATGAAAAA 7 87 1 AGCGGGGGGG 0.933347 -96 CTTCTTTTCTAAAGGAGTTAGAGGTGGTTTTAA 7 160 1 AAGAGAAGGG 0.819718 -23 GAACATCGAGGAGACGGATGAAGGTTATGTAGCTCA 12 37 1 GGAGGGAGGT 0.98589 -139 ACTTGAAGTAAAGAAGGATAAAGGAGCAGGCAGTCT 12 97 1 AGAGGAAGGG 0.980535 -79 TAATCATTACAGAGGGGCCGTAGGGTAGCCTGGTGA 13 147 0 AAGGGGAGGT 0.977666 -129 TCTTTCTGTCATGAGGGAGGCAGGATTTAAATACTT 13 239 0 AGAGGGAGGT 0.986793 -37 TTAAGTTGTAGAGGGGGCAGAAGGTTCTGCCTATTG 17 81 0 GGGGGGAGGT 0.991105 -94 * ** ** * *** * Masking position 7 Map Score: 11.229 Number of sites scoring better than the average of aligned sites = 855 Number in coding regions = 819 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 TTTATTTTCGAAGAGTTTGAAAATTGCGCGGTT 4 39 1 AAGATTGAAA 0.753842 -120 ACCTTTATATAAGGCTGTGAAAAAAAATACATC 4 124 1 AAGGTTGAAA 0.915638 -35 GCTGCAAGCTAAGTTTTAAAAACTACTTACCTT 7 20 0 AAGTTAAAAC 0.842346 -163 AAAAGATAAAAAGGTTTTGAAGCAAAAGCCAAA 9 18 0 AAGGTTGAAC 0.984322 -40 TTAGTTCCAAAAGGTTAAATATCTGGATGCACA 10 22 0 AAGGTAATAC 0.858746 -80 GAGACGGATGAAGGTTATGTAGCTCAGGCACTG 12 47 1 AAGGTTGTAC 0.933631 -129 TTTCGATGTGAAGGTTATAAAACTTATTATTAA 12 143 0 AAGGTTAAAC 0.987067 -33 TTTGCAGCAAAAGGCTTTAAAAGCCACTGCCTT 13 183 0 AAGGTTAAAG 0.953288 -93 CAGGATGGTGAAGTATTTAAATCCTGCCTCCCT 13 229 1 AAGTTTAAAC 0.93761 -47 GGAAATTTAAAGAATTAAAAAGCTAAAAATTT 14 42 0 AAGATAAAAG 0.671831 -22 GTCAGGCTGCAAGAGTTTAAAACCCATCGAATA 15 37 0 AAGATTAAAC 0.955623 -70 TTTAGGTTTTAAGGTTCTAAATCGATCTGCCTT 16 14 0 AAGGTTAAAC 0.987067 -52 **** * **** * Masking position 11 Map Score: 12.8146 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 164 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 TTCGGAATTTCTTTTCCAAAAAATTTAAATAGT 1 14 0 CTTCCAAAAA 0.848296 -130 TCGAGAGCATCTATTGAAGGAAAAATTGAATAG 3 54 1 CTTGAAGAAA 0.981508 -94 TTTCTTACAGCATCTCAAGAAAACTTGACATTA 3 94 1 CCTCAAGAAA 0.893398 -54 AACTTTAATACTTTTCAAGAAGACAGGACATC 3 126 1 CTTCAAGAGA 0.893398 -22 AAACTACTTACCTTTGTAGGAAA 7 1 0 CTTGTAGAAA 0.929049 -182 ACAATGAACTCTTTTCCAGAGAACTTTTTCATC 7 114 0 CTTCCAGGAA 0.930385 -69 ATAAGAATTTTGATTGCAGGAAACGTTAGATTA 8 37 0 TTTGCAGAAA 0.88088 -69 AGATAAAAAGGTTTTGAAGCAAAAGCCAAACTC 9 15 0 GTTGAAGAAA 0.872981 -43 TCAATTTTTACACTTGAAGTAAAGAAGGATAAA 12 86 1 CTTGAAGAAA 0.981508 -90 GTCTGAGCTGCAGTTCCAGAAAAGCTGACAGGT 13 18 0 CTTCCAGAAA 0.986105 -258 AAAACGAATGCGTTTGCAGCAAAAGGCTTTAAA 13 195 0 CTTGCAGAAA 0.988323 -81 * ****** *** Masking position 8 Map Score: 11.8005 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 68 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 GTTACTATTTAAATTTTTTGGAAAAGAA 1 9 1 TTAAATTTTT 0.74672 -135 ATTTAACATTCTCAATTTTTCAATATAAAA 1 51 0 CTCAATTTTT 0.733795 -93 AATTTTTCTATTCAATTTTTCCTTCAATAG 3 64 0 TTCAATTTTT 0.897173 -84 TGACATTAACTTTAATACTTTTCAAGAAGA 3 119 1 TTTAATACTT 0.856471 -29 TTTAATTTTTTTTTAGAAAA 5 1 1 TTTAATTTTT 0.903191 -48 TAGTACAGCTTTTACTTCTTTTCTAAAGGA 7 146 1 TTTACTTCTT 0.802849 -37 CTTTTCTGGGTTCAATTCTGTC 9 46 1 TTCAATTCTG 0.79203 -12 AAATAAAAATTTTACTATTTAGGCC 11 6 0 TTTACTATTT 0.577083 -41 ATAGTAAAATTTTTATTTTTGTTAGCATGT 11 18 1 TTTTATTTTT 0.498203 -29 CACTGGGGCACTCAATTTTTACACTTGAAG 12 75 1 CTCAATTTTT 0.733795 -101 AAAACCGTTTTTTAATACTGCCAGATACTG 13 50 0 TTTAATACTG 0.653407 -226 GAGGCAGGATTTAAATACTTCACCATCCTG 13 229 0 TTAAATACTT 0.653462 -47 TTTTTAGCTTTTTAATTCTTTAAATTTCC 14 45 1 TTTAATTCTT 0.928005 -19 ********** Masking position 6 Map Score: 7.04107 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 155 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 6 GTGGTTGGATGTGCAGGCAGAATGGCGGAA 1 93 1 GTGCAGGCAG 0.984706 -51 TTCAACCGCCGCTAAGGCTGATGACGCCTG 2 30 0 GCTAAGGCTG 0.908717 -106 TGCTCTCGAAGGGCAGGCAAAATTGTTTTA 3 33 0 GGGCAGGCAA 0.957839 -115 GATGCAGAGTTAAGGCAATGCAATAAAA 6 47 0 GTTAAGGCAA 0.770599 -18 GTTTTGGTTCGCCCAGGCAAGGTAATTGCA 7 55 0 GCCCAGGCAA 0.965718 -128 ACTTTTTAAAGCGCATGCTGGTGGTGGGAG 7 83 1 GCGCATGCTG 0.886463 -100 AGGTTATGTAGCTCAGGCACTGGGGCACTC 12 58 1 GCTCAGGCAC 0.973418 -118 AAGGATAAAGGAGCAGGCAGTCTTGTCGTA 12 110 1 GAGCAGGCAG 0.974829 -66 TGGAACTGCAGCTCAGACAGTATCTGGCAG 13 33 1 GCTCAGACAG 0.940061 -243 ********** Masking position 5 Map Score: 6.79743 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 296 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 CTTCGAAAATAAAAGGCAAAGGAGTTCAAAA 4 21 0 AAAAGGCAAG 0.56156 -138 TTTTAATGATTAAAGGTTTTCGAATTTTCAA 4 82 0 TAAAGGTTTC 0.763795 -77 CAGCCTTATATAAAGGTTTCGAAAAATATTT 4 110 0 TAAAGGTTCG 0.784801 -49 AAACCTTTATATAAGGCTGTGAAAAAAAATA 4 122 1 ATAAGGCTTG 0.903264 -37 AAAATGTATGAAAAGGTTGGAGGTGAGTTGA 5 28 1 AAAAGGTTGA 0.666014 -21 GATGCAGAGTTAAGGCAATGCAATAAAAAC 6 45 0 TTAAGGCATG 0.65845 -20 CATGCGCTTTAAAAAGTTTTGGTTCGCCCAG 7 69 0 AAAAAGTTTG 0.72325 -114 AGAAAAGAAGTAAAAGCTGTACTACAATGAA 7 139 0 TAAAAGCTTA 0.562739 -44 AGAAAAGATAAAAAGGTTTTGAAGCAAAAGC 9 22 0 AAAAGGTTTG 0.965543 -36 ATTTAGTTCCAAAAGGTTAAATATCTGGATG 10 26 0 AAAAGGTTAA 0.703485 -76 AGGAGACGGATGAAGGTTATGTAGCTCAGGC 12 45 1 TGAAGGTTTG 0.920113 -131 AATTTCGATGTGAAGGTTATAAAACTTATTA 12 147 0 TGAAGGTTTA 0.848802 -29 CTGTAATGATTAAAGGCAGTGGCTTTTAAAG 13 171 1 TAAAGGCATG 0.868198 -105 CGTTTGCAGCAAAAGGCTTTAAAAGCCACTG 13 187 0 AAAAGGCTTA 0.93356 -89 AGTTTAGGTTTTAAGGTTCTAAATCGATCTG 16 18 0 TTAAGGTTTA 0.781197 -48 TAGAGGGGGCAGAAGGTTCTGCCTATTGATT 17 78 0 AGAAGGTTTG 0.928078 -97 ATTCGACGAGAAAAGGCTATATCAGCCAGAT 17 121 1 AAAAGGCTTA 0.939484 -54 ******** ** Masking position 4 Map Score: 14.1704 Number of sites scoring better than the average of aligned sites = 756 Number in coding regions = 677 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 8 ATTTCTTTTCCAAAAAATTTAAATAGTAAC 1 11 0 CAAAAAATTT 0.749565 -133 AAAGAAATTCCGAAAATTTTTTATATTGAA 1 33 1 CGAAAATTTT 0.940242 -111 AAATTGAATAGAAAAATTTTTCTTACAGCA 3 76 1 GAAAAATTTT 0.888117 -72 GTAGAAAATTTTTTGAACTCCT 4 3 1 AGAAAATTTT 0.859312 -156 TTTAATCATTAAAATATTTTTCGAAACCTT 4 99 1 AAAATATTTT 0.380372 -60 AGCTCTAAAATTTTTCTTTTTTCT 6 5 1 CTAAAATTTT 0.949942 -60 TTTTCTAAATCTAAAAGTTTTTATTGCATT 6 29 1 CTAAAAGTTT 0.816062 -36 CTGGGCGAACCAAAACTTTTTAAAGCGCAT 7 69 1 CAAAACTTTT 0.798193 -114 GGCCTAAATAGTAAAATTTTTATTTTTGTT 11 11 1 GTAAAATTTT 0.889017 -36 ATTTATTTGCATAAAATTTTTAGCTTTTTA 14 29 1 ATAAAATTTT 0.880351 -35 ********** Masking position 4 Map Score: 4.09032 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 103 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 9 ATTTAAATTTTTTGGAAAAGAAATTCCGAA 1 17 1 TTTGGAAAAG 0.925046 -127 TATATAAAGGTTTCGAAAAATATTTTAATG 4 105 0 TTTCGAAAAA 0.93694 -54 TTAATTTTTTTTTAGAAAAATGTATGAAAA 5 12 1 TTTAGAAAAA 0.970481 -37 AACTTTTAGATTTAGAAAAAAGAAAAATTT 6 18 0 TTTAGAAAAA 0.970481 -47 CTCTAACTCCTTTAGAAAAGAAGTAAAAGC 7 153 0 TTTAGAAAAG 0.964751 -30 CGTAACGCTGCTTAGAAAAACCGTTACAAG 17 37 1 CTTAGAAAAA 0.923491 -138 ********** Masking position 6 Map Score: 4.96663 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 9 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 TGAGAACAGGCGTCATCAGCCTTAGCGGCGGTTG 2 24 1 CGACACCTTA 0.970341 -112 TGAAGGTGGACGCCATCACCCATACCGATTCAAT 2 56 1 CGACACCATA 0.953258 -80 TCAACTCACCTCCAACCTTTTCATACATTT 5 29 0 CATCACCTTT 0.702626 -20 CTATCATTCCTTGTGCATCCAGATATTTAACCT 10 10 1 CTTCACCAGA 0.96051 -92 GATTTAAATACTTCACCATCCTGAAAAACGAATG 13 218 0 CTACACCTGA 0.984276 -58 GGGTTTTAAACTCTTGCAGCCTGACAAAATCAAC 15 45 1 CTTCACCTGA 0.975012 -62 TGCAGCCTGACAAAATCAACCTTAGCAAACTTTT 15 59 1 CAACACCTTA 0.954856 -48 CGAGAAAAGGCTATATCAGCCAGATATAGCAGCA 17 127 1 CTACACCAGA 0.975012 -48 ** * ** ***** Masking position 8 Map Score: 5.06931 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 150 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 TTTAACATTCTCAATTTTTCAATATAAAAAA 1 49 0 TCAATTTTTA 0.764842 -95 CCTTTTAAGTTCGATTTAACATTCTCAATTT 1 63 0 TCGATTTAAA 0.898512 -81 ATATCGGTTCTCGATTTATAAGGATTCCGTT 2 104 0 TCGATTTATA 0.966808 -32 ATCGATTTTCGATATCGGTTCT 2 124 0 TCGATTTTCA 0.953753 -12 TTAAAGGTTTTCGAATTTTCAAAGACATTCA 4 73 0 TCGAATTTTA 0.83883 -86 ATCCGTCTCCTCGATGTTCAAATCTATCGGG 12 25 0 TCGATGTTCA 0.864983 -151 ACTCGATTTATGATTATAATTTT 15 94 0 TCGATTTATA 0.966781 -13 GAAAGGCAGATCGATTTAGAACCTTAAAACC 16 12 1 TCGATTTAGA 0.929188 -54 ********* * Masking position 4 Map Score: 4.15996 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 37 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 AAAATTTTCGGAATTTCTTTTCCAAAAAAT 1 23 0 GAATTTCTTT 0.894324 -121 CAGAATGGCGGAAGTCCTTTTGGTTTCGTT 1 110 1 GAAGTCCTTT 0.943131 -34 AAAATTTTTTGAACTCCTTTGCCTTTTATT 4 15 1 GAACTCCTTT 0.978045 -144 GCGCGGTTTTGAATGTCTTTGAAAATTCGA 4 64 1 GAATGTCTTT 0.827332 -95 GTACTACAATGAACTCTTTTCCAGAGAACT 7 122 0 GAACTCTTTT 0.924169 -61 AAACCACCTCTAACTCCTTTAGAAAAGAAG 7 160 0 TAACTCCTTT 0.832989 -23 CCTGAAAAACGAATGCGTTTGCAGCAAAAG 13 203 0 GAATGCGTTT 0.826953 -73 TTTTCTCGTCGAATTCTATTAAGTTGTAGA 17 105 0 GAATTCTATT 0.64398 -70 ********** Masking position 3 Map Score: 1.87388 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 271 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 13 ********** No masking Map Score: -6.29298e-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: -6.29298e-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: -6.29298e-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