AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -ifruR_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 TP0108 101 pyrophosphate--fructose 6-phosphate 1-phosphotransferase (pfk) #2 TP0109 300 rRNA methylase, putative #3 TP0568 121 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase (eda) #4 TP0569 24 aminopeptidase P #5 TP0570 26 T. pallidum predicted coding region TP0570 #6 TP0747 88 T. pallidum predicted coding region TP0747 #7 TP0844 92 glyceraldehyde 3-phosphate dehydrogenase (gap) Motif number 1 ATGGTAGCACCGCAGATTCTGGTTCTG 2 6 0 CGCAGATTTG 0.644898 -295 GTGTTCGTTATCTGCTTGACAGAAAATACGTG 2 73 0 TCTGCTTGCG 0.8136 -228 ACCCGGTACCTCCACTTGACCGACGCAGACTG 2 124 1 TCCACTTGCG 0.976809 -177 GCTGTGGGGCTGCTGATGGCAGCTGCCAGTCT 2 150 0 TGCTGATGCG 0.964424 -151 CCACAGCACACGCGCATTCCGGCAAAGACACA 2 175 1 CGCGCATTCG 0.978356 -126 GACACACAACTGCACATTGCCGATACAATTGT 2 201 1 TGCACATTCG 0.954733 -100 ATTGTGCAGTCGCTCCTTCCAGTCAGTAGCGC 2 228 1 CGCTCCTTCG 0.981601 -73 TATTGCAAAGCGCGCCTGGCTGCGATACAAGG 2 260 1 CGCGCCTGCG 0.986037 -41 CGTTTTCCTGTTGATTGGTGTTATACG 3 6 1 TCCTGTTGTG 0.852958 -116 AATTCCCTCCTCTTGCCCGCGGACATCTT 3 103 0 TCCTCTTGCG 0.989361 -19 CGCTCTTGGCGCGGCAACGCAC 5 15 0 CGCTCTTGCC 0.951944 -12 GCACGTCAATCCCTCTTTGCTGTAGGGCTCCC 7 11 0 CCCTCTTTCG 0.985748 -82 GCGGGATGTGTGCTCTTTTTAGAGGAGGTTGG 7 67 1 TGCTCTTTTG 0.940221 -26 ******** * * Masking position 7 Map Score: 17.6753 Number of sites scoring better than the average of aligned sites = 791 Number in coding regions = 718 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 AAAGATGCGAAGATGCCCTGGGTGTTT 1 6 0 AGTGCCTGGG 0.917936 -96 TTAGCCTGAGGGAGTCTCTACGCACGCGGTAC 1 68 1 GGGTCCTACG 0.782672 -34 GGGGTCCTCCGCGTACCGCGTGC 1 89 0 GGTCCCCGCG 0.978528 -13 GTTGTGTAATGGTAGCACCGCAGATTCTGGTT 2 14 0 GGAGCCCGCA 0.991034 -287 CAACCAGGGAGGGAGGCCCAGGCTAGTACGAC 2 42 1 GGAGGCCAGG 0.871664 -259 TCGGTCAAGTGGAGGTACCGGGTAAGTTTTTG 2 115 0 GGGGTCCGGG 0.94648 -186 AGCTGCCATCAGCAGCCCCACAGCACACGCGC 2 158 1 AGAGCCCACA 0.880709 -143 CTGACTGGAAGGAGCGACTGCACAATTGTATC 2 222 0 GGGCGCTGCA 0.847341 -79 AAGCGCGCCTGGCTGCGATACAAGGAGGAGAA 2 267 1 GGTGCATACA 0.843698 -34 TAGCTTAGGCGGGTGCACTGCATGTGGTGTCT 3 68 1 GGTGCCTGCA 0.993176 -54 AATTGAATCGGTGTTCTGCGTAGT 4 9 1 CGTGTCTGCG 0.861796 -16 CGCTCTTGGCGCGGCAACGCACACAC 5 6 0 CGGGCACGCA 0.866731 -21 AAAAGTTCCAGGGAGCTTCGGATCACGACAAA 6 28 0 GGAGCTCGGA 0.868446 -61 GGGAGCCCTACAGCAAAGAGGG 7 1 1 GGAGCCTACA 0.974831 -92 TTTCAGATAGCGTTGCGCGGGATGTGTGCTCT 7 51 1 CGTGCCGGGA 0.860527 -42 ** *** ***** Masking position 2 Map Score: 15.235 Number of sites scoring better than the average of aligned sites = 1902 Number in coding regions = 1773 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 3 ATGCGAAGATGCCCTGGGTGTTT 1 4 0 GCCCTGGGTG 0.878069 -98 TCCGCGTACCGCGTGCGTAGAGACTCCCTC 1 75 0 GCGTGCGTAG 0.978787 -27 TACGCACGCGGTACGCGGAGGACCCC 1 86 1 GTACGCGGAG 0.918168 -16 CAGAACCAGAATCTGCGGTGCTACCATTAC 2 11 1 ATCTGCGGTG 0.893794 -290 GCAGCTGCCAGTCTGCGTCGGTCAAGTGGA 2 134 0 GTCTGCGTCG 0.954647 -167 CGGAATGCGCGTGTGCTGTGGGGCTGCTGA 2 166 0 GTGTGCTGTG 0.974527 -135 TCGCAGCCAGGCGCGCTTTGCAATAGCGCT 2 255 0 GCGCGCTTTG 0.963045 -46 CGGGTGCACTGCATGTGGTGTCTGAAAAGA 3 77 1 GCATGTGGTG 0.847162 -45 CCCTCCTCTTGCCCGCGGACATCTTTTCAG 3 98 0 GCCCGCGGAC 0.667929 -24 AATTGAATCGGTGTTCTGCGTAGT 4 11 1 GTGTTCTGCG 0.722084 -14 GTGTGTGCGTTGCCGCGCCAAG 5 3 1 GTGTGCGTTG 0.984536 -24 AGATAGCGTTGCGCGGGATGTGTGCTCTTT 7 55 1 GCGCGGGATG 0.895294 -38 ********** Masking position 1 Map Score: 10.2896 Number of sites scoring better than the average of aligned sites = 3243 Number in coding regions = 2982 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 4 TGCATCTTTCACCCCATTGCGTTAGCCTGAG 1 47 1 ACCCATTGCG 0.973335 -55 GATGGCAGCTGCCAGTCTGCGTCGGTCAAGT 2 137 0 GCCATCTGCG 0.916798 -164 GCCATCAGCAGCCCCACAGCACACGCGCATT 2 162 1 GCCCACAGCA 0.991482 -139 GTGTGTCTTTGCCGGAATGCGCGTGTGCTGT 2 177 0 GCCGAATGCG 0.933793 -124 CGGCAAAGACACACAACTGCACATTGCCGAT 2 194 1 ACACACTGCA 0.943151 -107 AGGAGCGACTGCACAATTGTATCGGCAATGT 2 214 0 GCACATTGTA 0.763515 -87 CCAGTCAGTAGCGCTATTGCAAAGCGCGCCT 2 246 1 GCGCATTGCA 0.965133 -55 TGCAAAGCGCGCCTGGCTGCGATACAAGGAG 2 263 1 GCCTGCTGCG 0.942324 -38 GGGAGCCCTACAGCAAAGAGGGATT 7 5 1 GCCCACAGCA 0.991482 -88 **** ****** Masking position 2 Map Score: 6.22874 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 416 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TGCGAAGATGCCCTGGGTGTTT 1 1 0 CCCGGTGTTT 0.984744 -101 TTGCGTTAGCCTGAGGGAGTCTCTACGCACGC 1 63 1 CTGGGAGTCT 0.95354 -39 GGGCCTCCCTCCCTGGTTGTGTAATGGTAGCA 2 29 0 CCCGGTGTGT 0.992555 -272 AGTTTTTGATCTGAGTGAGTGTTCGTTATCTG 2 91 0 CTGGTAGTGT 0.965809 -210 AGTGGAGGTACCGGGTAAGTTTTTGATCTGAG 2 108 0 CCGGTAGTTT 0.97589 -193 ACGGAGTAAGTGTTCTCCTCCTT 2 288 0 CGGGTAGTGT 0.977626 -13 ATCCGAAGCTCCCTGGAACTTTTCTGTTTCGG 6 37 1 CCCGGACTTT 0.944867 -52 GATAGCGTTGCGCGGGATGTGTGCTCTTTTTA 7 56 1 CGCGGTGTGT 0.985852 -37 *** ** ***** Masking position 10 Map Score: 9.24931 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 105 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 CCGCGTACCGCGTGCGTAGAGACTCCCTCA 1 74 0 CGTGCGTAGA 0.934284 -28 AGAACCAGAATCTGCGGTGCTACCATTACA 2 12 1 TCTGCGGTGC 0.985318 -289 CAGCTGCCAGTCTGCGTCGGTCAAGTGGAG 2 133 0 TCTGCGTCGG 0.982138 -168 GGAATGCGCGTGTGCTGTGGGGCTGCTGAT 2 165 0 TGTGCTGTGG 0.870525 -136 AAAATCAAGATCTGCGTATAACACCAATCA 3 22 0 TCTGCGTATA 0.89051 -100 GAATCGGTGTTCTGCGTAGT 4 15 1 TCTGCGTAGT 0.96897 -10 GTGTGTGCGTTGCCGCGCCAAGA 5 4 1 TGTGCGTTGC 0.987178 -23 ********** Masking position 3 Map Score: 4.3861 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 300 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 CCCATTGCGTTAGCCTGAGGGAGTCTCTAC 1 59 1 TAGCCTGAGG 0.933276 -43 CGTGTCGTACTAGCCTGGGCCTCCCTCCCT 2 47 0 TAGCCTGGGC 0.994914 -254 TAAAGGACATTAGCTTAGGCGGGTGCACTG 3 58 1 TAGCTTAGGC 0.978551 -64 AAGTTCCAGGGAGCTTCGGATCACGACAAA 6 28 0 GAGCTTCGGA 0.948378 -61 CTTTTTAGAGGAGGTTGGGCAA 7 81 1 GAGGTTGGGC 0.982322 -12 ********** Masking position 6 Map Score: 0.764212 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 59 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GGGGTCCTCCGCGTACCGCGTGCGT 1 87 0 CCTCCGCGTA 0.985561 -15 CCTGGGCCTCCCTCCCTGGTTGTGTAATGG 2 34 0 CCTCCCTGGT 0.936012 -267 TTACCCGGTACCTCCACTTGACCGACGCAG 2 122 1 CCTCCACTTG 0.923742 -179 TAAGTGTTCTCCTCCTTGTATCGCAGCCAG 2 275 0 CCTCCTTGTA 0.978487 -26 AATTCCCTCCTCTTGCCCGCGGACA 3 107 0 CCTCCTCTTG 0.968361 -15 GTGATCCGAAGCTCCCTGGAACTTTTCTGT 6 34 1 GCTCCCTGGA 0.9545 -55 TGATTAAAAAGCTCCCCGAAACAGAAAAGT 6 54 0 GCTCCCCGAA 0.971985 -35 TTGCCCAACCTCCTCTAAAAAGAGCACA 7 75 0 CCTCCTCTAA 0.960596 -18 ********** Masking position 3 Map Score: 8.11923 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 178 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 ********** No masking Map Score: -1.51102e-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: -1.51102e-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 11 ********** No masking Map Score: -1.51102e-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