AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -irpoN_tpal_opreg_100.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) Motif number 1 ATCTTTCAATGGCTGCGGCTGAGACACAAAAAC 1 78 1 GGGCGGCGAG 0.995862 -223 GCAAGATTATTGCTGCGGGAGAGAACTGGTTCT 1 218 0 TGGCGGGGAG 0.993349 -83 TCTTGCTAACCGAAACGCCAGAGAGCAGTACGT 1 245 1 CGACGCCGAG 0.958929 -56 AGTATTCGCGTGTCGCGGGTGTGTACGCGCCAC 2 17 1 TGGCGGGGTG 0.989649 -50 TCAGTATTTCGGATACAGGAGAGGGAATTGATG 3 36 1 GGACAGGGAG 0.992489 -265 TAAAACTGAAGGTACGGGGTTAGGGTTAACCTT 3 109 1 GGCGGGGTAG 0.881684 -192 AGAACATGGCGGTGACATCAGTGTGTCCTCTAC 3 160 1 GGACATCGTG 0.770819 -141 TTTATCTATGGGTAAAAGGAGAGTAAAACACGT 3 206 0 GGAAAGGGAG 0.920285 -95 GCTTGGGACGGCTGTGTCGCGTCCTA 7 4 1 TGACGGCGTG 0.964708 -152 GCGTCCTACTGGGGCCGGGTGTGTGCTGCGCCG 7 29 1 GGCCGGGGTG 0.995221 -127 GGAAAAGAAGCGCTGGACGGGAGAAGGCGTTTT 7 95 1 CGGGACGGAG 0.918376 -61 GTTTTGAAAAGGAGGGGCGCGTGACGCCCCAGG 7 123 1 GGGGGCGGTG 0.976092 -33 GGGCGCGTGACGCCCCAGGGGAGTGAAGA 7 137 1 CGCCAGGGAG 0.98113 -19 ** ***** *** Masking position 2 Map Score: 19.6804 Number of sites scoring better than the average of aligned sites = 955 Number in coding regions = 840 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 TCAATGGCTGCGGCTGAGACACAAAAACCTT 1 83 1 CGGCGAGACA 0.803403 -218 CTTTCGCGCACGTGGGTGAGCAACTACCAAA 1 145 0 CGTGGTGAGC 0.864041 -156 CACCCACGTGCGCGAAAGTCCTTAAGTCGCG 1 158 1 CGCGAAGTCC 0.844378 -143 GTCCTTAAGTCGCGCGAGGTCATGACACCTC 1 175 1 CGCGGAGGTC 0.9771 -126 ATTATTGCTGCGGGAGAGAACTGGTTCTTGC 1 215 0 CGGGGAGAAC 0.988246 -86 CTAACCGAAACGCCAGAGAGCAGTACGTCTT 1 250 1 CGCCGAGAGC 0.983575 -51 ACACCCGCGACACGCGAATACTATGGCA 2 8 0 CACGGAATAC 0.650078 -59 TCGCGTGTCGCGGGTGTGTACGCGCCACAGG 2 22 1 CGGGGTGTAC 0.954357 -45 GGTGTGTACGCGCCACAGGGCACGGTGAATC 2 34 1 CGCCCAGGGC 0.949751 -33 ATTTCGGATACAGGAGAGGGAATTGATGCCC 3 41 1 CAGGGAGGGA 0.942939 -260 CCCCGTCCAACAGTAGAGGACACACTGATGT 3 174 0 CAGTGAGGAC 0.695355 -127 CCCAGTAGGACGCGACACAGCCGTCCCAAGC 7 11 0 CGCGCACAGC 0.872223 -145 CTACTGGGGCCGGGTGTGTGCTGCGCCGTGG 7 34 1 CGGGGTGTGC 0.984808 -122 AAGCGCTGGACGGGAGAAGGCGTTTTGAAAA 7 102 1 CGGGGAAGGC 0.98293 -54 AAAGGAGGGGCGCGTGACGCCCCAGGGGAGT 7 130 1 CGCGGACGCC 0.967385 -26 CGTGACGCCCCAGGGGAGTGAAGA 7 142 1 CAGGGAGTGA 0.896783 -14 **** ****** Masking position 1 Map Score: 18.5349 Number of sites scoring better than the average of aligned sites = 1532 Number in coding regions = 1403 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 3 TACCAAAGAAGGTAGTGAAGAAGATAGTCG 1 122 0 GGTAGTGAAG 0.931071 -179 TTATTGCTGCGGGAGAGAACTGGTTCTTGC 1 215 0 GGGAGAGAAC 0.985 -86 AGGGATTGTACCGTATTACTC 1 290 0 GGGATTGTAC 0.888779 -11 CGCGTGTCGCGGGTGTGTACGCGCCACAGG 2 23 1 GGGTGTGTAC 0.961469 -44 TTTCGGATACAGGAGAGGGAATTGATGCCC 3 42 1 AGGAGAGGGA 0.827958 -259 CTTCAGTTTTAGTAGTGAAGTACGGCTCAA 3 90 0 AGTAGTGAAG 0.813321 -211 CCCGTCCAACAGTAGAGGACACACTGATGT 3 174 0 AGTAGAGGAC 0.849534 -127 TATGGGTAAAAGGAGAGTAAAACACGTACC 3 203 0 AGGAGAGTAA 0.856492 -98 ACATGGGGAGTCTGGTATCTTATGC 5 6 1 GGGAGTCTGG 0.878678 -41 TACTGGGGCCGGGTGTGTGCTGCGCCGTGG 7 35 1 GGGTGTGTGC 0.953549 -121 AGCGCTGGACGGGAGAAGGCGTTTTGAAAA 7 103 1 GGGAGAAGGC 0.837134 -53 GACGCCCCAGGGGAGTGAAGA 7 145 1 GGGAGTGAAG 0.98392 -11 ********** Masking position 2 Map Score: 10.3889 Number of sites scoring better than the average of aligned sites = 984 Number in coding regions = 851 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 TACCAATGACGCAGTGTTTCTCAGCA 1 7 0 GCAGTGTTTC 0.988229 -294 ACGCCAGAGAGCAGTACGTCTTGAGCGTAA 1 259 1 GCAGTACGTC 0.939827 -42 CACATCAGTATCAGTATTTCGGATACAGGA 3 26 1 TCAGTATTTC 0.964838 -275 ATATTTTTGAGCCGTACTTCACTACTAAAA 3 84 1 GCCGTACTTC 0.877595 -217 GGCGGTGACATCAGTGTGTCCTCTACTGTT 3 167 1 TCAGTGTGTC 0.972891 -134 CTTCTCCCGTCCAGCGCTTCTTTTCCTCAC 7 91 0 CCAGCGCTTC 0.951942 -65 ********** Masking position 9 Map Score: 4.16473 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 114 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 AACGGAGCGGTTTTGGTTACCGCTACCAATG 1 29 0 TTTGGTTACC 0.886767 -272 CGATCGACTATCTTCTTCACTACCTTCTTTG 1 118 1 TTTCTTCACT 0.852439 -183 CTTCTTTGGTAGTTGCTCACCCACGTGCGCG 1 141 1 ATTGCTCACC 0.928978 -160 GAGAACTGGTTCTTGCTTACGTCTCGAGGTG 1 200 0 TTTGCTTACG 0.952304 -101 GCAGCAATAATCTTGCTAACCGAAACGCCAG 1 235 1 TTTGCTAACC 0.934988 -66 GCTCAAGACGTACTGCTCTCTGGCGTTTCGG 1 254 0 TCTGCTCTCT 0.812854 -47 TGTACCGTATTACTCCTTACGCTCAAGACGT 1 274 0 TCTCCTTACG 0.873912 -27 GGGGTACGTGTTTTACTCTCCTTTTACCCAT 3 201 1 TTTACTCTCC 0.799913 -100 CGCATTTCCTTATTCTTTACTCGTATGTCTT 3 280 0 TTTCTTTACT 0.746213 -21 CCAGCGCTTCTTTTCCTCACCATTATAGAAA 7 80 0 TTTCCTCACC 0.986851 -76 * ********* Masking position 7 Map Score: 4.08661 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 240 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 6 AAACACTGCGTCATTGGTAGCGGTAACCAAAAC 1 18 1 TCATGGTAGG 0.98851 -283 TTCACTACCTTCTTTGGTAGTTGCTCACCCACG 1 133 1 TCTTGGTAGG 0.995421 -168 GCACGGTGAATCTTCTGTGGACGC 2 53 1 TCTTTGTGGG 0.988322 -14 TACTCGTATGTCTTAGGTGGGTGGATATTTTTT 3 261 0 TCTTGGTGGG 0.997035 -40 **** ***** * Masking position 8 Map Score: 1.60075 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 7 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 7 GCGTCCACAGAAGATTCACCGTGCCCTGT 2 48 0 GAAGATTCAC 0.935512 -19 TTGATGCCCGAAATATTCACAATATTTTTG 3 63 1 AAATATTCAC 0.976852 -238 TTACAAGAAAAAATATCCACCCACCTAAGA 3 254 1 AAATATCCAC 0.98491 -47 AAACAAATGGAAATCTCCACGGCGCAGCAC 7 51 0 AAATCTCCAC 0.974548 -105 ********** Masking position 6 Map Score: 0.843086 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 15 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 GAAGATTCACCGTGCCCTGTGGCGCGTACA 2 38 0 CGTGCCCTGT 0.964793 -29 AAGGTTAACCCTAACCCCGTACCTTCAGTT 3 112 0 CTAACCCCGT 0.985641 -189 GAGTAAAACACGTACCCCGTCCAACAGTAG 3 189 0 CGTACCCCGT 0.995915 -112 CTTACCCCCCGTTGGATTGC 5 37 0 CTTACCCCCC 0.966549 -10 TTCAAAACGCCTTCTCCCGTCCAGCGCTTC 7 101 0 CTTCTCCCGT 0.9621 -55 ********** Masking position 6 Map Score: 1.34424 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 82 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 ********** No masking Map Score: 4.64285e-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 10 ********** No masking Map Score: 4.64285e-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: 4.64285e-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