AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icoldbox_tpal_opreg_300.orf -g0.528 -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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0766 300 T. pallidum predicted coding region TP0766 #2 TP0767 210 translation elongation factor G (fusA-2) #3 TP0768 138 membrane protein (tmpA) #4 TP0770 44 ATP-dependent RNA helicase Motif number 1 AAGTTCTCCCCCCGCCCTCAAAAAGGCCCT 1 23 0 CCCGCCCTCA 0.957542 -278 CTGACTGTTTGTAGCGCGTATTCATCTCAG 1 82 1 GTAGCGCGTA 0.899846 -219 GGCCGGCGTGCCCGCGCGCACTGCAAAAGG 1 121 0 CCCGCGCGCA 0.941244 -180 TGCGCGCGGGCACGCCGGCCCATGATACAC 1 131 1 CACGCCGGCC 0.923221 -170 TTTTTTTGCAGCACCGTGCATACCGCCCCA 1 225 0 GCACCGTGCA 0.796029 -76 GTAAGCAATAGCCGCGCGCGTGTGTTTTTT 1 249 0 GCCGCGCGCG 0.517133 -52 TGCTTACCCTCATGCGCGCGTTCACCGAAA 1 272 1 CATGCGCGCG 0.869636 -29 ACTAGCGGTTCTAGCCCGGAGGGGTGAAGC 2 28 1 CTAGCCCGGA 0.809614 -183 CCGGAGGGGTGAAGCGCGCCGTGTGCATCG 2 43 1 GAAGCGCGCC 0.574202 -168 TGCATCGGCACGACCCCGCCAGAGAAGGCG 2 66 1 CGACCCCGCC 0.977718 -145 GGGGAAGACGGGCGCCCGCCTTCTCTGGCG 2 82 0 GGCGCCCGCC 0.637903 -129 GGGCGCCCGTCTTCCCCGCGGTGGCGGGCT 2 95 1 CTTCCCCGCG 0.896681 -116 GTAGCAGGGCGCAGCCCGCCACCGCGGGGA 2 107 0 GCAGCCCGCC 0.985967 -104 CTGCGCCCTGCTACCCCGTCTGCTGTGGAG 2 123 1 CTACCCCGTC 0.937001 -88 AAAAGACAAGGCCCCGCTCCACAGCAGACG 2 139 0 GCCCCGCTCC 0.64597 -72 CGCAGCGTAACAAGCCCTCAGGAAAAAGAC 2 162 0 CAAGCCCTCA 0.838635 -49 GGCTTGTTACGCTGCGCGCCAGTCCCCGAG 2 176 1 GCTGCGCGCC 0.900625 -35 AACGTGCTAGGCGGCGCGTCCTTCTCGACG 3 15 1 GCGGCGCGTC 0.839699 -124 CAAGACTTCGCCACCGCGTCGAGAAGGACG 3 31 0 CCACCGCGTC 0.933126 -108 CTGGTGTACCCTCCCGGGCCGAACGGTACT 3 75 1 CTCCCGGGCC 0.91448 -64 ********** Masking position 5 Map Score: 40.5378 Number of sites scoring better than the average of aligned sites = 3460 Number in coding regions = 3196 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 AGGCTCCCTTTTGCAGTGCGCGCGGGCACGC 1 115 1 TGCAGTGCGC 0.974313 -186 CAGTGCGCGCGGGCACGCCGGCCCATGATAC 1 128 1 GGCACGCCGG 0.918528 -173 TCGCTAAGCTGCGCCGTACGGCTCTCACACA 1 187 0 GGCCGTACGG 0.952001 -114 GCGCAGCTTAGCGACGTCCGCTGGGGCGGTA 1 204 1 GGACGTCCGC 0.946678 -97 TTGCAGCACCGTGCATACCGCCCCAGCGGAC 1 219 0 GGCATACCGC 0.917968 -82 GGGTAAGCAATAGCCGCGCGCGTGTGTTTTT 1 250 0 TGCCGCGCGC 0.983592 -51 GGGGTGAAGCGCGCCGTGTGCATCGGCACGA 2 48 1 GGCCGTGTGC 0.649058 -163 CACCGCGGGGAAGACGGGCGCCCGCCTTCTC 2 87 0 AGACGGGCGC 0.971657 -124 GCAGACGGGGTAGCAGGGCGCAGCCCGCCAC 2 115 0 TGCAGGGCGC 0.969289 -96 TTCTTCCTCGGGGACTGGCGCGCAGCGTAAC 2 181 0 GGACTGGCGC 0.971836 -30 CCACCGCGTCGAGAAGGACGCGCCGCCTAGC 3 20 0 GGAAGGACGC 0.981225 -119 GTACCCTCCCGGGCCGAACGGTACTCTCCTC 3 80 1 GGCCGAACGG 0.972551 -59 * ********* Masking position 3 Map Score: 20.791 Number of sites scoring better than the average of aligned sites = 1185 Number in coding regions = 1061 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 GCAGTGCGCGCGGGCACGCCGGCCCATGATAC 1 127 1 CGGGCCCCGG 0.917892 -174 ACCGTGCATACCGCCCCAGCGGACGTCGCTAA 1 211 0 CCGCCCGCGG 0.563321 -90 TGAAGCGCGCCGTGTGCATCGGCACGACCCCG 2 52 1 CGTGTCTCGG 0.969852 -159 GGGCGCCCGCCTTCTCTGGCGGGGTCGTGCCG 2 71 0 CTTCTTGCGG 0.94851 -140 AGGGCGCAGCCCGCCACCGCGGGGAAGACGGG 2 100 0 CCGCCCGCGG 0.642824 -111 CCTGCTACCCCGTCTGCTGTGGAGCGGGGCCT 2 129 1 CGTCTCGTGG 0.982458 -82 TTCCTGAGGGCTTGTTACGCTGCGCGCCAGTC 2 168 1 CTTGTAGCTG 0.566883 -43 AGCAATTCCTTCTTCCTCGGGGACTGGCGC 2 191 0 CTTCTCTCGG 0.953891 -20 GCGTAACGTGCTAGGCGGCGCGTCCTTC 3 7 1 CGTGCAGCGG 0.985204 -132 CTAGGCGGCGCGTCCTTCTCGACGCGGTGGCG 3 21 1 CGTCCTTCGA 0.836153 -118 GATACCTCCTCGGCTCATGTGAGGAGAGTACC 3 99 0 CGGCTAGTGA 0.813482 -40 GATGTTAACCTCCCACGTGATACCTCCTCG 3 119 0 CCTCCAGTGA 0.813883 -20 ***** * **** Masking position 1 Map Score: 12.6282 Number of sites scoring better than the average of aligned sites = 1268 Number in coding regions = 1149 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 4 GTATCATGGGCCGGCGTGCCCGCGCGCACTG 1 128 0 CCGGGTGCCC 0.955831 -173 TTAGCGACGTCCGCTGGGGCGGTATGCACGG 1 211 1 CCGCGGGGCG 0.998516 -90 TAAGCAATAGCCGCGCGCGTGTGTTTTTTTG 1 247 0 CCGCCGCGTG 0.937542 -54 CGGTTCTAGCCCGGAGGGGTGAAGCGCGCCG 2 33 1 CCGGGGGGTG 0.996546 -178 CCCGCCTTCTCTGGCGGGGTCGTGCCGATGC 2 67 0 CTGGGGGGTC 0.963089 -144 CCCGTCTTCCCCGCGGTGGCGGGCTGCGCCC 2 100 1 CCGCGTGGCG 0.995438 -111 GCTACCCCGTCTGCTGTGGAGCGGGGCCTTG 2 132 1 CTGCGTGGAG 0.979718 -79 TCCTCGGGGACTGGCGCGCAGCGTAACAAGC 2 177 0 CTGGGCGCAG 0.562988 -34 GTCCTTCTCGACGCGGTGGCGAAGTCTTGAA 3 32 1 ACGCGTGGCG 0.975819 -107 GAGTACCGTTCGGCCCGGGAGGGTACACCAG 3 75 0 CGGCCGGGAG 0.605209 -64 **** ****** Masking position 3 Map Score: 15.8828 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 516 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 ACTGTTTGTAGCGCGTATTCATCTCAGTTA 1 85 1 GCGCGTATTC 0.844779 -216 CTGCAAAAGGGAGCCTTAACTGAGATGAAT 1 101 0 GAGCCTTAAC 0.832225 -200 TGCAGTGCGCGCGGGCACGCCGGCCCATGA 1 126 1 GCGGGCACGC 0.913506 -175 ACAGTCTGTCGACGTTTCACCTTCTTTTCG 1 160 0 GACGTTTCAC 0.795651 -141 ACGCGCGCATGAGGGTAAGCAATAGCCGCG 1 263 0 GAGGGTAAGC 0.957067 -38 ACCCTCATGCGCGCGTTCACCGAAACTTCA 1 277 1 GCGCGTTCAC 0.987275 -24 TTCGGCCCGGGAGGGTACACCAGAAAGCCC 3 68 0 GAGGGTACAC 0.993094 -71 ATGAGCCGAGGAGGTATCACGTGGGAGGTT 3 113 1 GAGGTATCAC 0.827545 -26 GGATAGACAAGAGCGTATACGCTTTTTCCC 4 12 1 GAGCGTATAC 0.969501 -33 ********** Masking position 10 Map Score: 5.24794 Number of sites scoring better than the average of aligned sites = 805 Number in coding regions = 747 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 TTAAAAAACCCGAATGGATCTGAAGAATCAT 1 51 1 CGAATGGTCT 0.972671 -250 TAAGCTGCGCCGTACGGCTCTCACACAGTCT 1 183 0 CGTACGGTCT 0.988975 -118 ACCGCCCCAGCGGACGTCGCTAAGCTGCGCC 1 203 0 CGGACGTGCT 0.945397 -98 TGGGGCGGTATGCACGGTGCTGCAAAAAAAC 1 225 1 TGCACGGGCT 0.961523 -76 AAAACACACGCGCGCGGCTATTGCTTACCCT 1 251 1 CGCGCGGTAT 0.962127 -50 TTACGCAAAACTAGCGGTTCTAGCCCGGAGG 2 19 1 CTAGCGGTCT 0.958771 -192 CCTCCCGGGCCGAACGGTACTCTCCTCACAT 3 84 1 CGAACGGACT 0.984493 -55 ******* *** Masking position 11 Map Score: 4.35553 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 185 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 CCCCCGCCCTCAAAAAGGCCCTTCGTCGTCA 1 14 0 CAAAAAGCCC 0.993367 -287 GGGGAGAACTTAAAAAACCCGAATGGATCTG 1 42 1 TAAAAAACCG 0.803615 -259 ATACGCGCTACAAACAGTCAGATGATTCTTC 1 72 0 CAAACAGCAG 0.956275 -229 CAGCACCGTGCATACCGCCCCAGCGGACGTC 1 216 0 CATACCGCCC 0.932428 -85 CACGGTGCTGCAAAAAAACACACGCGCGCGG 1 237 1 CAAAAAACAC 0.944752 -64 GAGGGTACACCAGAAAGCCCCCTTATTCAAG 3 57 0 CAGAAAGCCC 0.985394 -82 ******* *** Masking position 4 Map Score: 0.259379 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 133 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 ********** No masking Map Score: -1.36181e-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 9 ********** No masking Map Score: -1.36181e-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 10 ********** No masking Map Score: -1.36181e-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