AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_aful_reg_100.orf -o00190_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 AF0190 135 cytochrome C oxidase, subunit II, putative #3 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #4 AF1158 163 ATP synthase, subunit E, putative #5 AF1160 27 H+-transporting ATP synthase, subunit K (atpK-1) #6 AF1168 25 H+-transporting ATP synthase, subunit D (atpD) #7 AF1462 136 A. fulgidus predicted coding region AF1462 #8 AF2046 26 cytochrome oxidase, subunit I, putative #9 AF2297 126 cytochrome oxidase, subunit I (cydA-2) #10 AF2351 219 conserved hypothetical protein Motif number 1 TACAGGCTGCATGTTTTTTGGGTAAAAAGATGCCAGGATG 1 52 1 ATGGAAAAAA 0.986227 -72 AGAAGAAAAGGGCTTAAGGATTCATTTATA 1 104 0 AAGGTTAAGA 0.73813 -20 CAACGATATTAAGGAAACTTAGAATAAAAAGTTTGGAATC 2 77 0 ATTGATAAAA 0.820707 -59 CCTTAATATCGTTGGAACCGAGTAAAAAAATTTTTAAAAT 2 103 1 GCGGAAAAAA 0.924458 -33 TGTATTGATTAGTACGCACGAGAAAAAAGATTTTATATAA 3 30 0 ACGGAAAAAA 0.987276 -116 AAAACGGAAAATAATCGATGAGATAAAAAACGGT 4 5 0 ATGGTAAAAA 0.970721 -159 TTAATTACAAATTCTACCTGTGTAAAAATAACAAAGCTTA 4 82 1 ATGGAAAAAA 0.986229 -82 TTTATGAAAGAGCTTTTGAAAAAATACGGTTTCCTC 7 7 1 ATTGAAAAAA 0.93446 -130 AAGCGAGTAAATTGTTACCGCAAAAAAAAAAAAAAACGAA 7 62 0 ACGAAAAAAA 0.835969 -75 CGGTTTTCCAAGGCGGACTGCGTTAAAGGAGGCTATCTCC 7 104 1 ATGGTAAAGA 0.943621 -33 TGTTAGTAGAACCATGGAAGAGAAAAAGAAAAAGGAGTAC 9 27 0 AAGGAAAAGA 0.949912 -100 TGGTTCTACTAACAATAAATCGTTTAAAAAATTTGCTTTC 9 53 1 AATGTTAAAA 0.526427 -74 CAAAGCTGCTAAATTCTACGGGGAAAAATACTACCTCTAC 10 30 1 ACGGAAAAAA 0.987275 -190 * ** * ***** * Masking position 16 Map Score: 12.3528 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 188 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 TTTTAAATTTTCGCTCCTTTG 1 2 1 TTTAAATTTT 0.821646 -122 AACCACTCGATCTAAGCATTAGTCTAGCAA 2 42 1 TCTAAGCATT 0.908328 -94 AACAAAAGATTCCAAACTTTTTATTCTAAG 2 70 1 TCCAAACTTT 0.884243 -66 AACTTTTTATTCTAAGTTTCCTTAATATCG 2 84 1 TCTAAGTTTC 0.754177 -52 TAAAAAAATTTTTAAAATTTT 2 125 1 TTTAAAATTT 0.86844 -11 ATATAACAAACCTAAACTTCAAGCG 3 6 0 CCTAAACTTC 0.810262 -140 GTTGCCTCTCTTTAAAATTCACTTCGTATG 3 73 0 TTTAAAATTC 0.786796 -73 AATCCCTCTATATAAACATTATACTAACTG 3 102 0 TATAAACATT 0.672348 -44 ACAAATCGTATTTAAGCTTTGTTATTTTTA 4 104 0 TTTAAGCTTT 0.936114 -60 CTGATCAAACTCTAAACTTTAAAGACATTC 4 143 0 TCTAAACTTT 0.97802 -21 CCCTGTCACCTCTAAAAATTGTTT 6 5 0 TCTAAAAATT 0.816975 -21 CTACATAAAATTTAATCTTTTCGTTCGATT 9 96 0 TTTAATCTTT 0.786691 -31 ********** Masking position 5 Map Score: 7.28874 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 151 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 3 ATCGCCCATTGAATTTACAGGCTGCATGTTTTTTGGGTAA 1 37 1 GATTGCTGTT 0.993293 -87 AGGTTGTGGTATAGAGAGCTGAACTTTTCAAAACCAC 2 8 1 GGATGCTGCT 0.910008 -128 CTTTAAAATTCACTTCGTATGCTTTGTATTGATTAGTACG 3 54 0 CATTGCTTTT 0.970617 -92 GCTTAAATACGATTTGTAAGGCTTTCGAATGTCTTTAAAG 4 117 1 GATTGCTTGT 0.971542 -47 TTTGCGGTAACAATTTACTCGCTTGACGGTTTTCCAAGGC 7 78 1 CATTGCTTCT 0.956949 -59 TTTCCCCGTAGAATTTAGCAGCTTTGTACTCGTTCTCTGT 10 16 0 GATTGCTTTT 0.989403 -204 TCGTAAAGAGGGTTTTTGAGGCTGGTTGCTCGGAAATAGA 10 71 1 GGTTGCTGTT 0.988216 -149 TTTCAAAGGGGAGTTTGTTTGCTGGATCTTGAATTATCTC 10 109 0 GATTGCTGTT 0.993293 -111 ** ** **** * * Masking position 13 Map Score: 5.5119 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 46 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 AATTTTTTTACTCGGTTCCAACGATATTAAGGA 2 102 0 CTCGTTCCAG 0.990992 -34 ACGAACAGGAGGCTCTTCCAGAGGAAACCGTAT 7 34 0 GGCTTTCCAG 0.97903 -103 ACTCGCTTGACGGTTTTCCAAGGCGGACTGCGT 7 94 1 CGGTTTCCAG 0.975099 -43 CGCTTTTCCCAAGATTTACATTG 8 14 0 CGCTTTCCCG 0.992751 -13 CTTTTTCTTTTTCTCTTCCATGGTTCTACTAAC 9 33 1 TTCTTTCCAG 0.963093 -94 CTTGAATTATCTCTATTTCCGAGCAACCAGCCT 10 89 0 CTCTTTTCCG 0.968524 -131 AAGGCCTCCACTCGATTTCAAAGGGGAGTTTGT 10 131 0 CTCGTTTCAG 0.968709 -89 **** ***** * Masking position 7 Map Score: 4.94221 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 112 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 GCTGAACTTTTCAAAACCACTCGATCTAAGC 2 28 1 TCAAAACACT 0.970987 -108 TCTCACCTCCTCAAACACACC 5 1 0 TCAAACCACC 0.977593 -27 CCGTATTTTTTCAAAAGCTCTTTCATAAA 7 9 0 TCAAAACTCT 0.970987 -128 GCAACCAGCCTCAAAAACCCTCTTTACGATG 10 69 0 TCAAAACCCT 0.981049 -151 GATCCAGCAAACAAACTCCCCTTTGAAATCG 10 121 1 ACAAACCCCC 0.943339 -99 CTCAACACCTCCAGCAAAATTA 10 208 0 TCAACACTCC 0.950598 -12 ****** **** Masking position 4 Map Score: 3.3848 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 194 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 ATTCATTTATACCTTTCGTTTACCATCCTG 1 85 0 ACCTTTCGTT 0.920599 -39 ACTTTTCAAAACCACTCGATCTAAGCATTA 2 33 1 ACCACTCGAT 0.933339 -103 TTAAAAAATTTGCTTTCGATAATCGAACGA 9 76 1 TGCTTTCGAT 0.936078 -51 TAAAATTTAATCTTTTCGTTCGATTATCGA 9 91 0 TCTTTTCGTT 0.92808 -36 TTAGCAGCTTTGTACTCGTTCTCTGTTAAA 10 12 0 TGTACTCGTT 0.83471 -208 TCAAAAACCCTCTTTACGATGTAGAGGTAG 10 60 0 TCTTTACGAT 0.777205 -160 TAGTAAGGCCTCCACTCGATTTCAAAGGGG 10 138 0 TCCACTCGAT 0.969866 -82 ********** Masking position 10 Map Score: 1.93264 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 226 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 TACACCACCTTGTTTAACTCTA 3 134 0 ACACCCCTTG 0.965615 -12 TCTGGAAGAGCCTCCTGTTCGTTTTTTTTTT 7 45 1 CCTCCGTTCG 0.966244 -92 CCTTTAACGCAGTCCGCCTTGGAAAACCGTC 7 102 0 AGTCCCCTTG 0.963099 -35 CCTCCTCCCCCTCGTAGTACTCCT 9 4 1 CCTCCCCTCG 0.996459 -123 AAAAATACTACCTCTACATCGTAAAGAGGGT 10 53 1 CCTCTCATCG 0.91638 -167 CAGCAAACAAACTCCCCTTTGAAATCGAGTG 10 125 1 ACTCCCTTTG 0.98059 -95 ***** ***** Masking position 9 Map Score: 1.80371 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 486 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 8 ATGGTAAACGAAAGGTATAAATGAATCCTTAA 1 89 1 AAGGTATAAT 0.946269 -35 ATGTTTATATAGAGGGATTAATAGAGTTAAAC 3 113 1 AAGGGATTAT 0.979323 -33 GTAATTAAAAACGAGGATTAATTATATATCCG 4 58 0 AGAGGATTAT 0.799015 -106 TTATTTTTACACAGGTAGAATTTGTAATTAAA 4 81 0 AAGGTAGAAT 0.955091 -83 GAGAAAAAGAAAAAGGAGTACTACGAGGGGGA 9 16 0 AAAGGAGTAT 0.939767 -111 TTTACGATGTAGAGGTAGTATTTTTCCCCGTA 10 46 0 AAGGTAGTAT 0.965146 -174 TTGCTCGGAAATAGAGATAATTCAAGATCCAG 10 96 1 AAGAGATAAT 0.825115 -124 * ******** * Masking position 7 Map Score: 1.15542 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 109 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 AATTTTAAAGAGAGGCAACAGTTAGTATAAT 3 84 1 AGAGGAACAG 0.992695 -62 AACAATTTTTAGAGGTGACAGGGA 6 12 1 AGAGGGACAG 0.995265 -14 AGGCTCTTCCAGAGGAAACCGTATTTTTTCA 7 27 0 AGAGGAACCG 0.98761 -110 AAAGGAGATAGCCTCCTTTAA 7 126 0 AAAGGGATAG 0.930151 -11 ***** ***** Masking position 8 Map Score: 0.827018 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 13 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 AGGTTGTGGTATAGAGAGCTGAACTTTTC 2 10 1 TATAGAGAGC 0.934794 -126 AAGTGAATTTTAAAGAGAGGCAACAGTTAG 3 79 1 TAAAGAGAGG 0.98009 -67 GTATAATGTTTATATAGAGGGATTAATAGA 3 108 1 TATATAGAGG 0.943751 -38 TATAGAGGGATTAATAGAGTTAAACAAGGT 3 120 1 TTAATAGAGT 0.877366 -26 CTCTACATCGTAAAGAGGGTTTTTGAGGCT 10 64 1 TAAAGAGGGT 0.943418 -156 CTTCATATTTTAAATATAGTTTCCGTAACG 10 175 0 TAAATATAGT 0.817727 -45 ********** Masking position 6 Map Score: 0.179262 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 102 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 ********** No masking Map Score: 2.42538e-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: 2.42538e-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 13 ********** No masking Map Score: 2.42538e-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