AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -intrC_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 TP0082 300 formate hydrogenlyase transcriptional activator (fhlA) #2 TP0227 66 cobalt ABC transporter, ATP-binding protein #3 TP0519 300 response regulatory protein (atoC) #4 TP0965 24 membrane fusion protein, putative #5 TP0966 46 T. pallidum predicted coding region TP0966 #6 TP0970 21 T. pallidum predicted coding region TP0970 #7 TP0971 155 membrane antigen, pathogen-specific (tpd) #8 TP0972 87 conserved hypothetical integral membrane protein Motif number 1 GCTCACCCACGTGCGCGAAAGTCCTTAAGTCGCG 1 155 1 GTCGCGAGTC 0.98147 -146 AAAGTCCTTAAGTCGCGCGAGGTCATGACACCTC 1 172 1 AGCGCGAGGC 0.984022 -129 AAGATTATTGCTGCGGGAGAGAACTGGTTCTTGC 1 215 0 CTCGGGAGAC 0.910892 -86 TGCCATAGTATTCGCGTGTCGCGGGTGTGTACG 2 10 1 ATCGCGTCGG 0.862921 -57 TCGCGGGTGTGTACGCGCCACAGGGCACGGTGAA 2 29 1 GTCGCGACAG 0.971067 -38 AAAACTGAAGGTACGGGGTTAGGGTTAACCTTAA 3 110 1 GTCGGGTAGG 0.911307 -191 CTCTACTGTTGGACGGGGTACGTGTTTTACTCTC 3 187 1 GGCGGGACGG 0.993915 -114 GGCCCCAGTAGGACGCGACACAGCCGTCCCAAGC 7 11 0 GGCGCGACAC 0.993148 -145 GTCCTACTGGGGCCGGGTGTGTGCTGCGCCGTGG 7 31 1 GGCGGGTGTC 0.967703 -125 AAGAAGCGCTGGACGGGAGAAGGCGTTTTGAAAA 7 99 1 GGCGGGAAGC 0.99205 -57 TGAAAAGGAGGGGCGCGTGACGCCCCAGGGGAGT 7 127 1 GGCGCGACGC 0.997743 -29 TACATCTAAACGGCGCGAAAATACGTT 8 4 0 CGCGCGAATC 0.938087 -84 ** **** *** * Masking position 4 Map Score: 17.4775 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 304 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 GTAACCAAAACCGCTCCGTTATCCGGATGT 1 40 1 CCGCTCCGTT 0.949527 -261 GCATCAATTCCCTCTCCTGTATCCGAAATA 3 40 0 CCTCTCCTGT 0.986831 -261 ATCAGTGTGTCCTCTACTGTTGGACGGGGT 3 176 1 CCTCTACTGT 0.880182 -125 TACGTGTTTTACTCTCCTTTTACCCATAGA 3 205 1 ACTCTCCTTT 0.978834 -96 AAGATACCAGACTCCCCATGT 5 2 0 ACTCCCCATG 0.906003 -45 CTTACCCCCCGTTGGATTGCAGC 5 34 0 ACCCCCCGTT 0.945272 -13 CGCTTCTTTTCCTCACCATTATAGAAAAAC 7 77 0 CCTCACCATT 0.906987 -79 GCGTCACGCGCCCCTCCTTTTCAAAACGCC 7 120 0 CCCCTCCTTT 0.980934 -36 TCTTCACTCCCCTGGGGCGTCACGC 7 141 0 ACTCCCCTGG 0.94812 -15 ********** Masking position 4 Map Score: 9.20261 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 189 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 CCGCTACCAATGACGCAGTGTTTCTCAGCA 1 11 0 TGACGCAGTG 0.729382 -290 TTTCAATGGCTGCGGCTGAGACACAAAAAC 1 81 1 TGCGGCTGAG 0.969833 -220 CTTTCGCGCACGTGGGTGAGCAACTACCAA 1 146 0 CGTGGGTGAG 0.863776 -155 AGATTATTGCTGCGGGAGAGAACTGGTTCT 1 218 0 TGCGGGAGAG 0.977789 -83 CTAACCGAAACGCCAGAGAGCAGTACGTCT 1 250 1 CGCCAGAGAG 0.979036 -51 ATTCGCGTGTCGCGGGTGTGTACGCGCCAC 2 20 1 CGCGGGTGTG 0.973266 -47 GGTGTGTACGCGCCACAGGGCACGGTGAAT 2 34 1 CGCCACAGGG 0.965529 -33 CCCAGTAGGACGCGACACAGCCGTCCCAAG 7 12 0 CGCGACACAG 0.830237 -144 GTGTGTGCTGCGCCGTGGAGATTTCCATTT 7 47 1 CGCCGTGGAG 0.950917 -109 GGGCGCGTGACGCCCCAGGGGAGTGAAGA 7 137 1 CGCCCCAGGG 0.942468 -19 CGTATTTTCGCGCCGTTTAGATGTAGGCTG 8 13 1 CGCCGTTTAG 0.809623 -75 AGGGTACATCTGCCGTAGTGTGGAGAAATA 8 67 1 TGCCGTAGTG 0.930412 -21 ********** Masking position 2 Map Score: 12.0229 Number of sites scoring better than the average of aligned sites = 900 Number in coding regions = 826 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 4 TGAGCAACTACCAAAGAAGGTAGTGAAGAA 1 130 0 CCAAAGAAGG 0.962498 -171 GCGTCCACAGAAGATTCACCGTGC 2 53 0 CCACAGAAGA 0.987007 -14 GTACCCCGTCCAACAGTAGAGGACACACTG 3 178 0 CAACAGTAGA 0.867243 -123 AAATATCCACCCACCTAAGACATACGAGTA 3 264 1 CCACCTAAGA 0.827612 -37 AGAATACCCCAAGAAGGAAGTTGT 4 8 1 CCCAAGAAGG 0.97383 -17 CTTACCCCCCGTTGGATTGCAGCAT 5 32 0 CCCCCGTTGG 0.570039 -15 ACACACCCGGCCCCAGTAGGACGCGACACA 7 23 0 CCCCAGTAGG 0.976531 -133 GCGCGTGACGCCCCAGGGGAGTGAAGA 7 139 1 CCCCAGGGGA 0.909614 -17 ********** Masking position 9 Map Score: 6.33765 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 219 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 TGCTGAGAAACACTGCGTCATTGGTA 1 7 1 GAAACACTGC 0.973443 -294 TTACGCTCAAGACGTACTGCTCTCTGGCGT 1 259 0 GACGTACTGC 0.949439 -42 ACACACCCGCGACACGCGAATACTATGGCA 2 11 0 GACACGCGAA 0.826248 -56 TCCTGTATCCGAAATACTGATACTGATGTG 3 26 0 GAAATACTGA 0.937055 -275 TTTTAGTAGTGAAGTACGGCTCAAAAATAT 3 84 0 GAAGTACGGC 0.920663 -217 AACAGTAGAGGACACACTGATGTCACCGCC 3 167 0 GACACACTGA 0.973993 -134 ACCCACCTAAGACATACGAGTAAAGAATAA 3 272 1 GACATACGAG 0.851081 -29 GTGAGGAAAAGAAGCGCTGGACGGGAGAAG 7 91 1 GAAGCGCTGG 0.933488 -65 ********** Masking position 2 Map Score: 4.29678 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 279 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 TGGTAGCGGTAACCAAAACCGCTCCGTTAT 1 32 1 AACCAAAACC 0.936652 -269 GCGGCTGAGACACAAAAACCTTTTCCCGAT 1 92 1 CACAAAAACC 0.87398 -209 CACGTGGGTGAGCAACTACCAAAGAAGGTA 1 138 0 AGCAACTACC 0.913558 -163 TCGAGACGTAAGCAAGAACCAGTTCTCTCC 1 204 1 AGCAAGAACC 0.978122 -97 TCTCTCCCGCAGCAATAATCTTGCTAACCG 1 227 1 AGCAATAATC 0.763462 -74 CGTTAAGGTTAACCCTAACCCCGTACCTTC 3 116 0 AACCCTAACC 0.910026 -185 AGGAGAGTAAAACACGTACCCCGTCCAACA 3 193 0 AACACGTACC 0.923188 -108 TCCACGGCGCAGCACACACCCGGCCCCAGT 7 36 0 AGCACACACC 0.936882 -120 ********** Masking position 8 Map Score: 2.04916 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 161 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 CCGCTCCGTTATCCGGATGTACCTCAAGAT 1 50 1 ATCCGGATGT 0.9758 -251 CGAAATACTGATACTGATGTGGTCAGTTTG 3 17 0 ATACTGATGT 0.977954 -284 AGTAGAGGACACACTGATGTCACCGCCATG 3 164 0 ACACTGATGT 0.984726 -137 CGGCAGATGTACCCTGATGCAGAACGAAAA 8 52 0 ACCCTGATGC 0.984217 -36 ********** Masking position 7 Map Score: 1.59666 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 13 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 8 AGGTTTTTGTGTCTCAGCCGCAGCCATTGA 1 83 0 GTCTCAGCCG 0.985218 -218 CTTTGGTAGTTGCTCACCCACGTGCGCGAA 1 144 1 TGCTCACCCA 0.837763 -157 CAAGAACCAGTTCTCTCCCGCAGCAATAAT 1 216 1 TTCTCTCCCG 0.870124 -85 CTGTGGCGCGTACACACCCGCGACACGCGA 2 22 0 TACACACCCG 0.985382 -45 ACACACTGATGTCACCGCCATGTTCTTTAA 3 156 0 GTCACCGCCA 0.899749 -145 AGTAGGACGCGACACAGCCGTCCCAAGC 7 9 0 GACACAGCCG 0.992869 -147 CACGGCGCAGCACACACCCGGCCCCAGTAG 7 34 0 CACACACCCG 0.975334 -122 GAAAAATTGAGAAACAGCCTACATCTAAAC 8 27 0 GAAACAGCCT 0.70633 -61 ********** Masking position 5 Map Score: 4.35195 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 271 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 9 TTGATGCCCGAAATATTCACAATATTTTTG 3 63 1 AAATATTCAC 0.936295 -238 TTACAAGAAAAAATATCCACCCACCTAAGA 3 254 1 AAATATCCAC 0.983163 -47 AAACAAATGGAAATCTCCACGGCGCAGCAC 7 51 0 AAATCTCCAC 0.98905 -105 CTATTTCTCCACACTACGGCAG 8 76 0 ATTTCTCCAC 0.933985 -12 ********** Masking position 6 Map Score: 1.31778 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 9 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 TATCCGGATGTACCTCAAGATCTTTCAATG 1 59 1 TACCTCAAGA 0.986614 -242 GAGGTCATGACACCTCGAGACGTAAGCAAG 1 190 1 CACCTCGAGA 0.973219 -111 ACTCTCCTTTTACCCATAGATAAATTGGGA 3 215 1 TACCCATAGA 0.942109 -86 AGAATACCCCAAGAAGGAAGTTGT 4 5 1 TACCCCAAGA 0.991305 -20 ********** Masking position 8 Map Score: 0.59165 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 13 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 ********** No masking Map Score: -1.97998e-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: -1.97998e-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: -1.97998e-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