AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i180_molybdopterin_biosyntesis_ecoli_reg_300.orf -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 talB 278 transaldolase B #2 mog 114 required for the efficient incorporation of molybdate into molybdoproteins #3 moaA 300 molybdopterin biosynthesis, protein A #4 moaB 21 molybdopterin biosynthesis, protein B #5 moeA 203 molybdopterin biosynthesis Motif number 1 CAGGAAAGTCATCGCGACCGGCAATAAGAG 1 19 0 ATCGCGACCG 0.986664 -260 CTGCGTTGATATCGCCCGCCATTTTTATAC 1 128 0 ATCGCCCGCC 0.86651 -151 CAAGACGGTTATCGCCAGGCGAGACTGTTT 1 171 0 ATCGCCAGGC 0.982765 -108 ATCACGACGCAACGTCAGCGCAACCGCCGA 1 201 0 AACGTCAGCG 0.928917 -78 CCCTGATGATATCACGACGCAACGTCAGCG 1 211 0 ATCACGACGC 0.94916 -68 GCGTCGTGATATCATCAGGGCAGACCGGTT 1 221 1 ATCATCAGGG 0.949291 -58 TCATTCTTAGCGTGACCGGGAAGTCGGT 2 9 1 AGCGTGACCG 0.971047 -106 CAGAAGAGGTAGCGTGACCGACTTCCCGGT 2 25 0 AGCGTGACCG 0.971047 -90 TTTGATATACATCATCAGGGAGGCATAGCG 3 33 0 ATCATCAGGG 0.949291 -268 AAATAGCACGATCATGACGCTATATACATG 3 95 1 ATCATGACGC 0.931097 -206 CTTTACGAGCATTGTCACGGCCAAAGCACC 3 224 0 ATTGTCACGG 0.871287 -77 GGCAGGACCCAGCGCTACGCCCGAGGTGGC 5 118 1 AGCGCTACGC 0.862887 -86 ATGTCAGAAAAACGCCACAGACTGTATGCC 5 145 0 AACGCCACAG 0.815076 -59 ********** Masking position 1 Map Score: 15.1022 Number of sites scoring better than the average of aligned sites = 5001 Number in coding regions = 4828 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 2 GCATATCCCTCTTATTGCCGGTCGCGATGACTTTCC 1 11 1 CTTTCGTGCG 0.994552 -268 CAGAAGTTATCAAGTACCTCGTAGCGTATATACTTC 1 72 0 CATATGTGCG 0.934574 -207 CGATAACCGTCTTGTCGGCGGTTGCGCTGACGTTGC 1 187 1 CTTCCGTGCG 0.988447 -92 GTAGCGTGACCGACTTCCCGGTCACGCTAAGAATGA 2 11 0 CATTCGTACG 0.956905 -104 AAGATTTTTCCGTTTAAACAGTCTCGTTAAACAGAA 2 88 0 CTTACGTTCG 0.968396 -27 CCGCCATTTTCCCTTATTCTGTAGCGAAATAGCACG 3 69 1 CCTACGTGCG 0.996527 -232 GTACACCTTTCCAGATACGGGAGGCGAAG 3 282 0 CCTTCGAACG 0.886719 -19 GACTGTATGCCACCTCGGGCGTAGCGCTGGGTCCTG 5 120 0 CCTCGGTGCG 0.948577 -84 CCCGAGGTGGCATACAGTCTGTGGCGTTTTTCTGAC 5 137 1 CTCACGTGCG 0.982386 -67 * * ** * ** *** Masking position 15 Map Score: 10.0399 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 353 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 TCTTATTGCCGGTCGCGATGACTTTCCTGT 1 20 1 GGTCGCGATG 0.921029 -259 ACATCATCAGGGAGGCATAGCGTGCATCGT 3 25 0 GGAGGCATAG 0.975133 -276 CCTTCGCCCTGGTGGCAATCTTTACGAGCA 3 243 0 GGTGGCAATC 0.980403 -58 TCCAGATACGGGAGGCGAAGTCATTTCTTC 3 272 0 GGAGGCGAAG 0.990865 -29 TTATAGCAAAAGTGGCGAACCACCCTTAAT 5 22 0 AGTGGCGAAC 0.948281 -182 CTACGCCCGAGGTGGCATACAGTCTGTGGC 5 132 1 GGTGGCATAC 0.980494 -72 ACACTCCTGCGGAGGCAAAATCGAATTTGC 5 180 0 GGAGGCAAAA 0.957786 -24 ********** Masking position 5 Map Score: 8.1479 Number of sites scoring better than the average of aligned sites = 999 Number in coding regions = 953 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 TACTTGATAACTTCTGCGTAGCATACATGAG 1 92 1 CTTCTGCGAG 0.900012 -187 CGGATTTCTGACACTGCGTTGATATCGCCCG 1 140 0 ACACTGCGTG 0.913106 -139 ACAGAATGATACACTGCGAAGGGAGTGACAG 2 63 0 ACACTGCGAG 0.980584 -52 TATCAGTTGACCCAGGTGCAGAGGCTAGAGT 3 192 0 CCCAGGTGAG 0.897504 -109 AAGATTGCCACCAGGGCGAAGGAAGAAATGA 3 251 1 CCAGGGCGAG 0.990078 -50 TGTATGCCACCTCGGGCGTAGCGCTGGGTCC 5 122 0 CTCGGGCGAG 0.923891 -82 GAAAACACTCCTGCGGAGGCAAAATCGA 5 186 0 CTCCTGCGAG 0.885429 -18 ******** ** Masking position 6 Map Score: 5.02097 Number of sites scoring better than the average of aligned sites = 886 Number in coding regions = 840 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TCGCCAGGCGAGACTGTTTCGGATTTCTGA 1 160 0 AGACTGTTTC 0.985653 -119 TCATCAGGGCAGACCGGTTACATCCCCCTA 1 232 1 AGACCGGTTA 0.944659 -47 TCCCCCTAACAAGCTGTTTAAAGAGAAATA 1 254 1 AAGCTGTTTA 0.878543 -25 CTGTTTAACGAGACTGTTTAAACGGAAAAA 2 90 1 AGACTGTTTA 0.988077 -25 TGCAGAGGCTAGAGTGTTTAGTGGTTATGC 3 177 0 AGAGTGTTTA 0.972199 -124 TCGTCCATTAAGGGTGGTTCGCCACTTTTG 5 16 1 AGGGTGGTTC 0.929215 -188 AAAACGCCACAGACTGTATGCCACCTCGGG 5 137 0 AGACTGTATG 0.885721 -67 ********** Masking position 1 Map Score: 4.41143 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 132 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 GATGACTTTCCTGTGTAAACGTTACCAATTG 1 36 1 CTTGTAAACG 0.981003 -243 AGCGTATATACTTCTTAAACAATTGGTAACG 1 55 0 CTCTTAAACA 0.971316 -224 GATAGTATTTCTCTTTAAACAGCTTGTTAGG 1 258 0 CTTTTAAACA 0.986866 -21 TTTAAACAGTCTCGTTAAACAGAATGATACA 2 81 0 CTGTTAAACA 0.971322 -34 TTTAACGAGACTGTTTAAACGGAAAAATCTT 2 93 1 CTTTTAAACG 0.983945 -22 CACACTTTCGCTATGTAATCATGTATATAGC 3 113 0 CTTGTAATCA 0.938941 -188 ** ******** Masking position 6 Map Score: 6.06026 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 32 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 7 CATCGCGACCGGCAATAAGAGGGATATGC 1 5 0 GAAGAGGGAT 0.990978 -274 CTTCTGCGTAGCATACATGAGGTTTTGTATAAAAA 1 102 1 GAAGAGGTTT 0.985765 -177 CAGCGCAACCGCCGACAAGACGGTTATCGCCAGGC 1 181 0 GAAGACGGTT 0.990751 -98 TACAGAATAAGGGAAAATGGCGGTTTTACTTTGAT 3 57 0 GAAGGCGGTT 0.975104 -244 CGATACTAGCGTGTAAATGAGATTTTTACCATCCA 3 142 0 GAAGAGATTT 0.959016 -159 AACGTCAAAAGGAGAGATCAG 4 4 1 GAAGAGAGAT 0.973764 -18 * * * ******* Masking position 7 Map Score: 2.10199 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 44 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 AAGTCATCGCGACCGGCAATAAGAGGGATA 1 14 0 GACCGGCAAT 0.957005 -265 CATCAGGGCAGACCGGTTACATCCCCCTAA 1 233 1 GACCGGTTAC 0.982527 -46 GAGGTAGCGTGACCGACTTCCCGGTCACGC 2 20 0 GACCGACTTC 0.982521 -95 GGGAGTGACAGACAGGCTTCAGAAGAGGTA 2 44 0 GACAGGCTTC 0.982492 -71 ********** Masking position 2 Map Score: 0.211001 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 249 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 GCATATCCCTCTTATTGCCGGT 1 3 1 ATATCCCTCT 0.988597 -276 CTCGTAGCGTATATACTTCTTAAACAATTG 1 61 0 ATATACTTCT 0.914848 -218 TCGCCTGGCGATAACCGTCTTGTCGGCGGT 1 179 1 ATAACCGTCT 0.920823 -100 CAGACCGGTTACATCCCCCTAACAAGCTGT 1 241 1 ACATCCCCCT 0.920632 -38 TTTTACTTTGATATACATCATCAGGGAGGC 3 39 0 ATATACATCA 0.823805 -262 TTTACATGCCATATCCATCTTTCTATATTC 5 88 0 ATATCCATCT 0.982346 -116 ********** Masking position 3 Map Score: 1.68543 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 107 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 ********** No masking Map Score: -7.08111e-13 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 11 ********** No masking Map Score: -7.08111e-13 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: -7.08111e-13 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