AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00472_tpal_reg_300.orf -o00472_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: TP0244 21 ribosomal protein S7 Input sequences: #1 TP0231 100 conserved hypothetical protein #2 TP0232 99 T. pallidum predicted coding region TP0232 #3 TP0233 30 anti-sigma F factor antagonist, putative #4 TP0234 234 ribosomal protein L33 (rpmG) #5 TP0235 149 preprotein translocase subunit (secE) #6 TP0237 106 ribosomal protein L11 (rplK) #7 TP0240 108 ribosomal protein L7/L12 (rplL) #8 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #9 TP0243 102 ribosomal protein S12 (rpsL) #10 TP0245 23 T. pallidum predicted coding region TP0245 #11 TP0246 145 T. pallidum predicted coding region TP0246 #12 TP0247 50 N-acetylmuramoyl-L-alanine amidase (amiA) #13 TP0248 66 T. pallidum predicted coding region TP0248 #14 TP0249 78 flagellar filament outer layer protein (flaA-1) #15 TP0250 50 T. pallidum predicted coding region TP0250 #16 TP0251 153 DNA-binding protein II #17 TP0417 26 apolipoprotein N-acyltransferase (cutE) #18 TP0844 92 glyceraldehyde 3-phosphate dehydrogenase (gap) Motif number 1 CTCTCTCCTTTCCGTCCCGCACCTATACCAGGC 1 75 0 TCCTCCGCCC 0.866846 -26 AACTCAAAACCACACACCGCCTACCAGAATGCC 2 24 0 CACCCCGCTA 0.979302 -76 ATTGTATAACGCCTCACCTCACACATCAAGCAC 4 69 0 GCCCCCTCCA 0.866341 -166 TTACCATGGTTGCGCTCTGCCAACTGAGCTACA 4 149 0 TGCCCTGCAA 0.675539 -86 ACCACCCCTCCTCACATCCACAGA 4 221 0 CCACCTCCCA 0.842079 -14 CGCATTGCAACACTCTCCACCCTGGAAGAAGAA 6 13 0 CACCCCACCT 0.861857 -94 TGCGCATGATTGCCTGCCGCTTACGCGTTGGTT 6 42 1 TGCTCCGCTA 0.850925 -65 GACCGCCTAACACATACCCCGTAACTAAGTTAC 7 20 0 CACTCCCCTA 0.919734 -89 AATAGAAGCCCACGCTCTACTCAAAAGCGCGAC 8 80 0 CACCCTACCA 0.975478 -183 CGGGTTGGGTCGCGTTCTCCTCACTTGAGTGGA 8 146 1 CGCTCTCCCA 0.973505 -117 GGAGACGCCGTCCCCTCCACTCAAGTGAGGAGA 8 161 0 TCCCCCACCA 0.978957 -102 TCTACCGTAATACTCCCCACACAGGGGAGACGC 8 186 0 TACCCCACCA 0.962192 -77 GCACTCCCCCCTCAAGCTGCACCG 8 249 0 CACCCCCCCA 0.994891 -14 TAAACCTTGCCGCACACAGCACACGCGGCTAGG 9 42 0 CGCCCAGCCA 0.974122 -61 TCTTTTCGCTCACTTCCCCAAAAAAATCC 9 84 0 CGCCCTTCCC 0.9381 -19 AATTCTCTTGCGCACGCTTCGCATCACAT 11 7 0 CGCCCTTCCA 0.977172 -139 AACGAAAATGCGCATCCCCCGCAAAGGTGGCGA 11 73 0 CGCTCCCCCA 0.988363 -73 AGCACATACGTCCACGCACCACA 12 1 0 TCCCCACCCA 0.913606 -50 ACCTGTCCCCTCTCCCTACTCACAATAA 12 33 0 TCCCCTCCTA 0.921841 -18 CAACACACCGCCCTCACTACACCGTACAATGCT 13 24 0 CCCCCTACCC 0.962613 -43 TTCGAGTATACGCTCACCGCCTATTTTGTCAAC 14 21 0 CGCCCCGCTA 0.989801 -58 AACCCCACCGCCCCCTCTCCCTAGGAAGACTAC 15 15 0 CCCCCTCCTA 0.977075 -36 CCGCCTCAAACGCGCACCACCTCGGGTGAAGAG 16 105 0 CGCCCCACTC 0.948667 -49 AAAAAGAGCACACATCCCGCGCAACGCTATCTG 18 54 0 CACTCCGCCA 0.973227 -39 *** * **** ** Masking position 7 Map Score: 40.7064 Number of sites scoring better than the average of aligned sites = 1588 Number in coding regions = 1375 Number in noncoding regions = 213 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 GGTCAACCAAACACGCAAACAGCAGGATAACAC 1 29 0 ACCGCAACAC 0.910591 -72 ACTCAAAACCACACACCGCCTACCAGAATGCCC 2 23 0 ACCACCGCTC 0.724019 -77 TCTTTCTGTTACCGGCAGAACTCAAAACCACAC 2 42 0 ACGGCAGACC 0.952914 -58 ACCTCCCTAAACAGGCAGCCAACCAGCCTGCCC 4 31 0 ACGGCAGCAC 0.955529 -204 GTTATACAATGCGGGCCGGCCTCCGGGCGGCTC 4 92 1 GCGGCCGCCC 0.988774 -143 CAGAAGCAACACAGACAGGACTCCCCGAGCCGC 4 118 0 ACGACAGACC 0.925973 -117 GGATTGAACCGCTGACCTCAACCTTACCATGGT 4 172 0 GCGACCTAAC 0.5468 -63 CCCACAAATCCCCGGAAAACACCAGAAAACCCC 5 35 0 CCGGAAACAC 0.615156 -115 AGCACTCAGGCCAGGAAGGACTCGAACCTTCAA 5 111 0 CCGGAAGACC 0.795865 -39 ACAACAAAACACCCGAAACCAACGCGTAAGCGG 6 58 0 ACCGAAACAC 0.804188 -49 CTATAAACGGACAGGAAGACAGCACCCCAGAAG 7 56 0 ACGGAAGCAC 0.896532 -53 GCACACAACGACGCGCCGGACGCATGCAAAAAA 8 20 0 ACCGCCGACC 0.974069 -243 AAAGGGTGTCAGAGGCACACAACGACGCGCCGG 8 34 0 AGGGCACCAC 0.448189 -229 CTACTCAAAAGCGCGACGCCCTCCCACACGAAA 8 64 0 GCCGACGCCC 0.977785 -199 AGTGAGGAGAACGCGACCCAACCCGCATGCCAA 8 138 0 ACCGACCAAC 0.768137 -125 CACACAGGGGAGACGCCGTCCCCTCCACTCAAG 8 169 0 AGCGCCGCCC 0.873313 -94 CTCAAGCTGCACCGAACCGACACGGTGCTCCCT 8 230 0 ACGAACCACC 0.781647 -33 GCACTCCCCCCTCAAGCTGCACC 8 250 0 GCCTCCCCCC 0.74356 -13 AAACCTTGCCGCACACAGCACACGCGGCTAGGA 9 41 0 GCCACAGACC 0.95143 -62 TCGCTCACTTCCCCAAAAAAATCCTCAACACCG 9 75 0 CCCAAAAAAC 0.34737 -28 CCGTGCTTCAGCGGAAAAAAAACGCGCAAAATT 11 36 0 GCGAAAAAAC 0.536626 -110 CAACGAAAATGCGCATCCCCCGCAAAGGTGGCG 11 74 0 GCCATCCCCC 0.596643 -72 CCCCTCCTGCGGAACAAACACAAACCGATCA 11 125 0 GCGAACAACC 0.789826 -21 CCCTCTCCCTACTCACAATAAGCACATACGTCC 12 21 0 ACCACAAAAC 0.734247 -30 AGAGAGTCCAACACACCGCCCTCACTACACCGT 13 32 0 ACCACCGCCC 0.981447 -35 GCGCCTAGAACCCCACCGCCCCCTCTCCCTAGG 15 23 0 CCCACCGCCC 0.961936 -28 AGAAACACACGCGGGCAAACAGCCGCCTCAAAC 16 127 0 GCGGCAACAC 0.910832 -27 TCTAAAAAGAGCACACATCCCGCGCAACGCTAT 18 57 0 GCCACATCCC 0.827091 -36 TTGCCCAACCTCCTCTAAAAAGAGC 18 78 0 GCCAACCCCC 0.927392 -15 ** ***** ** * Masking position 13 Map Score: 33.0843 Number of sites scoring better than the average of aligned sites = 3030 Number in coding regions = 2733 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 3 ACCAGCCTGCCCCAGAAAGAAAGGCGCGTC 4 13 0 CCCAGAAAGA 0.958279 -222 TCCCCGAGCCGCCCGGAGGCCGGCCCGCAT 4 100 0 GCCCGGAGGC 0.901271 -135 GTTCAATCCCGCTCGGAAGCTTCCGTCTGT 4 196 1 GCTCGGAAGC 0.917999 -39 ACCCACAAATCCCCGGAAAACACCAGAAAA 5 39 0 CCCCGGAAAA 0.971745 -111 AAGCACTCAGGCCAGGAAGGACTCGAACCT 5 115 0 GCCAGGAAGG 0.989016 -35 ACACTCTCCACCCTGGAAGAAGAAAA 6 7 0 CCCTGGAAGA 0.933175 -100 GAAGACAGCACCCCAGAAGCCTGACCGCCT 7 45 0 CCCCAGAAGC 0.891653 -64 CCTATAAACGGACAGGAAGACAGCACCCCA 7 60 0 GACAGGAAGA 0.814857 -49 CGCTCACTTCCCCAAAAAAATCCTCAACAC 9 77 0 CCCAAAAAAA 0.440539 -26 ACGCCCCAGGAAGAGACGCGTAT 10 10 0 CCCAGGAAGA 0.988839 -14 AATGCGCATCCCCCGCAAAGGTGGCGATAT 11 70 0 CCCCGCAAAG 0.823078 -76 GCCCCCTCTCCCTAGGAAGACTACTGCA 15 9 0 CCTAGGAAGA 0.936488 -42 TGACACCGCTGCCCGGAAAGGTGTTTTCGC 16 18 1 GCCCGGAAAG 0.972203 -136 AGGTGTTTTCGCTAGAAAGGCTGTGGCTCG 16 36 1 GCTAGAAAGG 0.795348 -118 ACTTTCCCCTGCCAGAAAAGCATTT 17 6 0 GCCAGAAAAG 0.881801 -21 ********** Masking position 7 Map Score: 18.7364 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 292 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 AACTCAAAACCACACACCGCCTACCAGAATG 2 26 0 CACACCCGCC 0.9363 -74 AAATTCACACGACACTCTTTCTGTTACCGGC 2 59 0 GACACCTTTC 0.962856 -41 GTGACGCGCCTTTCTTTCTGGGG 4 3 1 GACGCCCTTT 0.950605 -232 CATCAAGCACGAAACACCTCCCTAAACAGGC 4 48 0 GAAACCCTCC 0.950903 -187 ACCACCCCTCCTCACATCCAC 4 224 0 ACCACCCTCC 0.83004 -11 TTTGGAGACCGACGCTCTGCCATTAGAGCTA 5 72 0 GACGCCTGCC 0.963434 -78 GAAACACCTTTTCGAAAGCAC 5 139 0 GAAACCCTTT 0.812518 -11 GGCACACAACGACGCGCCGGACGCATGCAAA 8 23 0 GACGCCCGGA 0.786087 -240 GTGTGCCTCTGACACCCTTTCGTGTGGGAGG 8 47 1 GACACCTTTC 0.962856 -216 TCAAAAGCGCGACGCCCTCCCACACGAAAGG 8 62 0 GACGCCTCCC 0.822835 -201 CCACACAGGGGAGACGCCGTCCCCTCCACTC 8 172 0 GAGACCCGTC 0.889446 -91 GCACCGAACCGACACGGTGCTCCCTATACCA 8 224 0 GACACGTGCT 0.627878 -39 AAGAGAGTCCAACACACCGCCCTCACTACAC 13 35 0 AACACCCGCC 0.979366 -32 CGGTGTGTTGGACTCTCTTGCTAATAATTG 13 47 1 GACTCCTTGC 0.709411 -20 CTATTTTGTCAACACCCCTGCAT 14 3 0 AACACCCTGC 0.963974 -76 TCAAACGCTCCTTTCGCACAATAA 14 65 0 AACGCCCTTT 0.867176 -14 AGCGACTTGACACCGCTGCCCGGAAAGGT 16 9 1 GACACGCTGC 0.884542 -145 CTTTCTAGCGAAAACACCTTTCCGGGCAGCG 16 24 0 AAAACCCTTT 0.580085 -130 GGGTGAAGAGAACACACCGTTGTACAGTCTA 16 84 0 AACACCCGTT 0.9125 -70 ***** ***** Masking position 5 Map Score: 18.3432 Number of sites scoring better than the average of aligned sites = 1065 Number in coding regions = 952 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 5 TCCCCACTAGCGGTTTCGCACACT 3 3 0 CGTTCGCACA 0.97642 -28 AACCTTACCATGGTTGCGCTCTGCCAACTGAG 4 154 0 TGTTCGCTCT 0.844235 -81 GTCGTCATATCTGTTACGCACGGGGTTTTCTG 5 14 1 CTTTCGCACG 0.978619 -136 TTTATAGGGGTTATTTCGCATACAAGGAGAAG 7 82 1 TTTTCGCATA 0.834561 -27 ACACCGTAAACCTTGCCGCACACAGCACACGC 9 49 0 CCTGCGCACA 0.88634 -54 TCTTTTCGCTCACTTCCCCAAA 9 91 0 TCTTCGCTCA 0.963109 -12 GCGCAAAATTCTCTTGCGCACGCTTCGCATCA 11 14 0 CTTTCGCACG 0.978619 -132 TTGCGCGTTTTTTTTCCGCTGAAGCACGGAAT 11 40 1 TTTTCGCTGA 0.890262 -106 CGGTTTGTGTTTGTTCCGCAGGAGGGG 11 129 1 TTTTCGCAGG 0.937135 -17 TCAAACGCTCCTTTCGCACAATAAGATAAC 14 59 0 TCTTCGCACA 0.977914 -20 CCCGGAAAGGTGTTTTCGCTAGAAAGGCTGTG 16 29 1 TGTTCGCTAG 0.759527 -125 ** ** ****** Masking position 4 Map Score: 8.00118 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 196 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 CCTTTCCGTCCCGCACCTATACCAGGCACC 1 72 0 CCGCACCTAT 0.658468 -29 CAAAACCACACACCGCCTACCAGAATGCCC 2 23 0 CACCGCCTAC 0.699354 -77 TTGTATAACGCCTCACCTCACACATCAAGC 4 71 0 CCTCACCTCA 0.823873 -164 TACAATGCGGGCCGGCCTCCGGGCGGCTCG 4 96 1 GCCGGCCTCC 0.852096 -139 ACAGGACTCCCCGAGCCGCCCGGAGGCCGG 4 107 0 CCGAGCCGCC 0.981156 -128 ACCACCCCTCCTCACATCCACAGACGGAA 4 216 0 CCTCACATCC 0.891716 -19 ACCCCAGAAGCCTGACCGCCTAACACATAC 7 36 0 CCTGACCGCC 0.963283 -73 TCAAGCTGCACCGAACCGACACGGTGCTCC 8 232 0 CCGAACCGAC 0.899544 -31 TTCTGAGTATCCTAGCCGCGTGTGCTGTGT 9 32 1 CCTAGCCGCG 0.939238 -71 TCGAGTATACGCTCACCGCCTATTTTGTCA 14 23 0 GCTCACCGCC 0.921042 -56 GCGCCTAGAACCCCACCGCCCCCTCTCCCT 15 26 0 CCCCACCGCC 0.991772 -25 GCCCCGCGCCTAGAACCCCACCG 15 38 0 CCGCGCCTAG 0.940132 -13 AAACACCTTTCCGGGCAGCGGTGTCAAGTC 16 14 0 CCGGGCAGCG 0.84523 -140 CTCAAACGCGCACCACCTCGGGTGAAGAGA 16 104 0 CACCACCTCG 0.827914 -50 AGCACACATCCCGCGCAACGCTATCTGAAA 18 51 0 CCGCGCAACG 0.637289 -42 TTGCCCAACCTCCTCTAAAAAGA 18 80 0 CCCAACCTCC 0.96085 -13 ********** Masking position 6 Map Score: 15.7809 Number of sites scoring better than the average of aligned sites = 1319 Number in coding regions = 1154 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 7 ACCGGTCAACCAAACACGCAAACAGCAGGA 1 35 0 CAAACACGCA 0.954361 -66 GCCCCAGAAAGAAAGGCGCGTCAC 4 5 0 GAAAGGCGCG 0.861745 -230 ACAGAAGCAACACAGACAGGACTCCCCGAG 4 122 0 CACAGACAGG 0.734867 -113 TCCTCACATCCACAGACGGAAGCTTCCGAG 4 207 0 CACAGACGGA 0.953074 -28 CAGAGGCACACAACGACGCGCCGGACGCAT 8 28 0 CAACGACGCG 0.851293 -235 ACGCTCTACTCAAAAGCGCGACGCCCTCCC 8 72 0 CAAAAGCGCG 0.891973 -191 TAATACTCCCCACACAGGGGAGACGCCGTC 8 182 0 CACACAGGGG 0.908265 -81 CCGCACACAGCACACGCGGCTAGGATACTC 9 36 0 CACACGCGGC 0.934104 -67 CAGCGGAAAAAAAACGCGCAAAATTCTCTT 11 31 0 AAAACGCGCA 0.725058 -115 ACAGCCGCCTCAAACGCGCACCACCTCGGG 16 112 0 CAAACGCGCA 0.970988 -42 GACAAGAAACACACGCGGGCAAACAGCCG 16 135 0 CACACGCGGG 0.986592 -19 AGCCCTACAGCAAAGAGGGATTGACGTGCC 18 14 1 CAAAGAGGGA 0.790272 -79 ********** Masking position 2 Map Score: 8.7708 Number of sites scoring better than the average of aligned sites = 960 Number in coding regions = 866 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 8 AGTATGCGGTGCCTGGTATAGGTGCGGGACG 1 65 1 GCCTGGTTAG 0.900704 -36 TACCAGAATGCCCTGCTACAGGCAA 2 5 0 CCCTGCTCAG 0.972374 -95 GGTAGGCGGTGTGTGGTTTTGAGTTCTGCCG 2 32 1 GTGTGGTTTG 0.727305 -68 CAGCCAACCAGCCTGCCCCAGAAAGAAAGGC 4 18 0 GCCTGCCCAG 0.963675 -217 GCTCTGCCAACTGAGCTACAGAAGCAACACA 4 138 0 CTGAGCTCAG 0.749257 -97 GCGCGTCGTTGTGTGCCTCTGACACCCTTTC 8 37 1 GTGTGCCCTG 0.883069 -226 ACGGTAGAGCGTGTGGTATAGGGAGCACCGT 8 211 1 GTGTGGTTAG 0.914687 -52 TGGCGATATTCCGTGCTTCAGCGGAAAAAAA 11 48 0 CCGTGCTCAG 0.985338 -98 GGGACTTCTGGCGAGCCACAGCCTTTCTAGC 16 46 0 GCGAGCCCAG 0.928872 -108 AGAGAACACACCGTTGTACAGTCTACACATT 16 78 0 CCGTTGTCAG 0.785392 -76 GTCAATCCCTCTTTGCTGTAGGGCTCCC 18 8 0 CTTTGCTTAG 0.633301 -85 ******* *** Masking position 11 Map Score: 5.63687 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 559 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 TTGAGGTCAGCGGTTCAATCCCGCTCGGAAGC 4 184 1 CGTCAATCCC 0.975749 -51 GAGCTACTGACCCACAAATCCCCGGAAAACAC 5 46 0 CCCAAATCCC 0.975752 -104 AGGGGAGACGCCGTCCCCTCCACTCAAGTGAG 8 165 0 CGCCCCTCCA 0.919948 -98 ATAGCCAAACCAGGTCAATCCA 9 1 0 CGTCAATCCA 0.901999 -102 TCTTTTCGCTCACTTCCCCAAAAAAATC 9 85 0 CCCACTTCCC 0.929829 -18 CCGTACAATGCTGCCCCATCCCCTA 13 4 0 CGCCCATCCC 0.993913 -63 AAAAGATCGGCACGTCAATCCCTCTTTGCTGT 18 20 0 CCTCAATCCC 0.975752 -73 CTCTAAAAAGAGCACACATCCCGCGCAACGCT 18 59 0 ACCACATCCC 0.876961 -34 * * ******** Masking position 9 Map Score: 4.4191 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 168 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 ********** No masking Map Score: 6.87338e-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: 6.87338e-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: 6.87338e-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