AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -irpoN_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 CGCGACTTAAGGACTTTCGCGCACGTGGGTGAGC 1 155 0 GACTCGCGAC 0.979447 -146 GAGGTGTCATGACCTCGCGCGACTTAAGGACTTT 1 172 0 GCCTCGCGCT 0.98228 -129 GCAAGAACCAGTTCTCTCCCGCAGCAATAATCTT 1 215 1 GTCTCCCGAG 0.901936 -86 CGTACACACCCGCGACACGCGAATACTATGGCA 2 10 0 CCGACGCGAT 0.849934 -57 TTCACCGTGCCCTGTGGCGCGTACACACCCGCGA 2 29 0 CTGTCGCGAC 0.967946 -38 TTAAGGTTAACCCTAACCCCGTACCTTCAGTTTT 3 110 0 CCTACCCGAC 0.902385 -191 GAGAGTAAAACACGTACCCCGTCCAACAGTAGAG 3 187 0 CCGTCCCGCC 0.993241 -114 GCTTGGGACGGCTGTGTCGCGTCCTACTGGGGCC 7 11 1 GTGTCGCGCC 0.992391 -145 CCACGGCGCAGCACACACCCGGCCCCAGTAGGAC 7 31 0 GACACCCGCC 0.964247 -125 TTTTCAAAACGCCTTCTCCCGTCCAGCGCTTCTT 7 99 0 GCTTCCCGCC 0.991172 -57 ACTCCCCTGGGGCGTCACGCGCCCCTCCTTTTCA 7 127 0 GCGTCGCGCC 0.997492 -29 AACGTATTTTCGCGCCGTTTAGATGTA 8 4 1 GATTCGCGCG 0.931657 -84 * *** **** ** Masking position 8 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 TTCTTCACTACCTTCTTTGGTAGTTGCTCA 1 130 1 CCTTCTTTGG 0.960316 -171 AGGACTTTCGCGCACGTGGGTGAGCAACTA 1 150 0 CGCACGTGGG 0.742509 -151 CAAGACGTACTGCTCTCTGGCGTTTCGGTT 1 252 0 TGCTCTCTGG 0.817693 -49 AGATTCACCGTGCCCTGTGGCGCGTACACA 2 36 0 TGCCCTGTGG 0.965716 -31 GCACGGTGAATCTTCTGTGGACGC 2 53 1 TCTTCTGTGG 0.967567 -14 CAGTGTGTCCTCTACTGTTGGACGGGGTAC 3 178 1 TCTACTGTTG 0.701551 -123 ACAACTTCCTTCTTGGGGTATTCT 4 8 0 CCTTCTTGGG 0.957031 -17 CTTACCCCCCGTTGGATTGCAGCAT 5 32 0 CCCCCGTTGG 0.631871 -15 TGTGTCGCGTCCTACTGGGGCCGGGTGTGT 7 23 1 CCTACTGGGG 0.970089 -133 TCTTCACTCCCCTGGGGCGTCACGCGC 7 139 0 TCCCCTGGGG 0.96835 -17 GTACATCTGCCGTAGTGTGGAGAAATAG 8 70 1 CGTAGTGTGG 0.794304 -18 ********** Masking position 10 Map Score: 9.58624 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 487 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 GTAACCAAAACCGCTCCGTTATCCGGATGT 1 40 1 CCGCTCCGTT 0.952417 -261 GCATCAATTCCCTCTCCTGTATCCGAAATA 3 40 0 CCTCTCCTGT 0.987613 -261 ATCAGTGTGTCCTCTACTGTTGGACGGGGT 3 176 1 CCTCTACTGT 0.886568 -125 TACGTGTTTTACTCTCCTTTTACCCATAGA 3 205 1 ACTCTCCTTT 0.980081 -96 AAGATACCAGACTCCCCATGT 5 2 0 ACTCCCCATG 0.911153 -45 CTTACCCCCCGTTGGATTGCAGC 5 34 0 ACCCCCCGTT 0.948393 -13 CGCTTCTTTTCCTCACCATTATAGAAAAAC 7 77 0 CCTCACCATT 0.912088 -79 GCGTCACGCGCCCCTCCTTTTCAAAACGCC 7 120 0 CCCCTCCTTT 0.98206 -36 TCTTCACTCCCCTGGGGCGTCACGC 7 141 0 ACTCCCCTGG 0.951087 -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 4 TCCCGATCGACTATCTTCTTCACTACCTTC 1 115 1 CTATCTTCTT 0.94697 -186 ATCTTCTTCACTACCTTCTTTGGTAGTTGC 1 127 1 CTACCTTCTT 0.978579 -174 AGGGATTGTACCGTATTACTCCTTACG 1 284 0 GTACCGTATT 0.818687 -17 AGGGCACGGTGAATCTTCTGTGGACGC 2 50 1 GAATCTTCTG 0.905366 -17 CCCTAACCCCGTACCTTCAGTTTTAGTAGT 3 104 0 GTACCTTCAG 0.954806 -197 ACAACTTCCTTCTTGGGGTATTCT 4 11 0 CTTCCTTCTT 0.891148 -14 GGGGAGTCTGGTATCTTATGCTGCAATCCA 5 15 1 GTATCTTATG 0.913346 -32 CCTCGGACCTTCTGAACGTCC 6 8 0 GGACCTTCTG 0.973172 -14 ********** Masking position 7 Map Score: 4.93205 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 165 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 5 TACCAATGACGCAGTGTTTCTCAGCA 1 7 0 GCAGTGTTTC 0.984763 -294 ACGCCAGAGAGCAGTACGTCTTGAGCGTAA 1 259 1 GCAGTACGTC 0.947842 -42 CACATCAGTATCAGTATTTCGGATACAGGA 3 26 1 TCAGTATTTC 0.951775 -275 ATATTTTTGAGCCGTACTTCACTACTAAAA 3 84 1 GCCGTACTTC 0.890904 -217 GGCGGTGACATCAGTGTGTCCTCTACTGTT 3 167 1 TCAGTGTGTC 0.962648 -134 CTTCTCCCGTCCAGCGCTTCTTTTCCTCAC 7 91 0 CCAGCGCTTC 0.935868 -65 ********** Masking position 9 Map Score: 3.63214 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 6 ATCTTGAGGTACATCCGGATAACGGAGCGG 1 50 0 ACATCCGGAT 0.976004 -251 CAAACTGACCACATCAGTATCAGTATTTCG 3 17 1 ACATCAGTAT 0.97814 -284 CATGGCGGTGACATCAGTGTGTCCTCTACT 3 164 1 ACATCAGTGT 0.98484 -137 TTTTCGTTCTGCATCAGGGTACATCTGCCG 8 52 1 GCATCAGGGT 0.984352 -36 ********** Masking position 4 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 7 GAGGTACATCCGGATAACGGAGCGGTTTTGG 1 44 0 CGGTAACGGA 0.98049 -257 GATAGTCGATCGGGAAAAGGTTTTTGTGTCT 1 99 0 CGGAAAAGGT 0.93651 -202 TGACCTCGCGCGACTTAAGGACTTTCGCGCA 1 166 0 CGATTAAGGA 0.942585 -135 ATCAGTATTTCGGATACAGGAGAGGGAATTG 3 35 1 CGGTACAGGA 0.98049 -266 ACGTTTAAGGTGATTAAAGAACATGGCGGTG 3 143 1 TGATAAAGAA 0.769434 -158 ATTTATCTATGGGTAAAAGGAGAGTAAAACA 3 209 0 GGGAAAAGGA 0.942166 -92 CTAAGACATACGAGTAAAGAATAAGGAAATG 3 278 1 CGATAAAGAA 0.955697 -23 *** ******* Masking position 9 Map Score: 1.31122 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 80 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 TGCTGAGAAACACTGCGTCATTGGTAGCG 1 10 1 ACACTGCGTC 0.811494 -291 GTAGCGGTAACCAAAACCGCTCCGTTATCC 1 34 1 CCAAAACCGC 0.801368 -267 GGTTTTTGTGTCTCAGCCGCAGCCATTGAA 1 82 0 TCTCAGCCGC 0.97641 -219 ACTATCTTCTTCACTACCTTCTTTGGTAGT 1 124 1 TCACTACCTT 0.565753 -177 AAGAACCAGTTCTCTCCCGCAGCAATAATC 1 217 1 TCTCTCCCGC 0.965837 -84 TGTGGCGCGTACACACCCGCGACACGCGAA 2 21 0 ACACACCCGC 0.985955 -46 GTAGGACGCGACACAGCCGTCCCAAGC 7 8 0 ACACAGCCGT 0.92387 -148 ACGGCGCAGCACACACCCGGCCCCAGTAGG 7 33 0 ACACACCCGG 0.910714 -123 CAAATGGAAATCTCCACGGCGCAGCACACA 7 48 0 TCTCCACGGC 0.88334 -108 ACAGCCTACATCTAAACGGCGCGAAAATAC 8 14 0 TCTAAACGGC 0.79128 -74 CTATTTCTCCACACTACGGCAGATGTACCC 8 68 0 ACACTACGGC 0.966111 -20 ********** Masking position 7 Map Score: 7.49101 Number of sites scoring better than the average of aligned sites = 985 Number in coding regions = 903 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 9 ********** 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 10 ********** 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 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