AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -iada_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 TP0141 171 methylated-DNA-protein-cysteine S-methyltransferase (dat) #2 TP0881 78 ABC transporter, ATP-binding protein (natA) #3 TP0884 29 conserved hypothetical integral membrane protein #4 TP0886 147 polyribonucleotide nucleotidyltransferase (pnp) #5 TP0891 175 translation initiation factor 2 (infB) #6 TP0892 49 N utilization substance protein A (nusA) #7 TP0893 174 conserved hypothetical protein #8 TP0895 21 T. pallidum predicted coding region TP0895 #9 TP0900 38 T. pallidum predicted coding region TP0900 #10 TP0901 40 conserved hypothetical integral membrane protein Motif number 1 CTGTATAGGGAGGGTGCACGAGCGAGCTCG 1 45 1 AGGGTGCACG 0.937792 -127 TGTCTCTCTCCCCCTCCACGAACACAGATA 1 148 0 CCCCTCCACG 0.968034 -24 CCTCGGCGGCACGCACTGCGAAACTTCCCC 4 22 0 ACGCACTGCG 0.907557 -126 CTATGCACAACCCCTCGGCGGCACGCACTG 4 34 0 CCCCTCGGCG 0.878829 -114 AGGGCTTGGTGCGGCCTGCGATACATTCTG 4 114 1 GCGGCCTGCG 0.967503 -34 GCTAGTGAGCAGGCTGTGCGTTCACCGGTG 5 60 1 AGGCTGTGCG 0.885415 -116 TCAACATCCGCCCGTGTACGAGAGGTAGTT 5 101 0 CCCGTGTACG 0.940479 -75 CCGCACCACGCCGGTGCACGTTACAGACTG 7 19 0 CCGGTGCACG 0.993096 -156 GGCGGCACCTCCGCACCACGCCGGTGCACG 7 29 0 CCGCACCACG 0.97607 -146 GGAGGTGCCGCCCGAGTGCGTTAGCACCCT 7 47 1 CCCGAGTGCG 0.937427 -128 CACAGTAACCGAGGCCCGCGTAGTGTGTAG 7 77 1 GAGGCCCGCG 0.921806 -98 ATGCTAGAGTGAGCCCCGCGAGGGGTGCGT 7 153 1 GAGCCCCGCG 0.90222 -22 AGCCCCGCGAGGGGTGCGTGC 7 164 1 GGGGTGCGTG 0.9033 -11 CCGCCTACCTCCGCTGCGTG 8 1 0 CCGCTGCGTG 0.972619 -21 CGGGTAAGGCACGGAGCATGGA 9 27 1 ACGGAGCATG 0.790161 -12 AAAAGGGAGTGCGGTGCACGG 10 30 1 GCGGTGCACG 0.990467 -11 ********** Masking position 10 Map Score: 22.533 Number of sites scoring better than the average of aligned sites = 3617 Number in coding regions = 3325 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 GCTCGCTCGTGCACCCTCCCTATACAGACA 1 42 0 GCACCCTCCC 0.990188 -130 CTGTCTCTCTCCCCCTCCACGAACACAGAT 1 149 0 CCCCCTCCAC 0.94896 -23 CACGCACTGCGAAACTTCCCCATGCAAAGC 4 13 0 GAAACTTCCC 0.722358 -135 ACCGTCCTATGCACAACCCCTCGGCGGCAC 4 40 0 GCACAACCCC 0.949296 -108 CCAAGCCCTGGCACAGCCACCTGCGAAGCT 4 93 0 GCACAGCCAC 0.883959 -55 TCCTTTACGTCAACATCCGCCCGTGTACGA 5 110 0 CAACATCCGC 0.934891 -66 CTTTTGGTCTGCACCTTCGCCCAAAATCGC 6 16 1 GCACCTTCGC 0.992543 -34 GCACCTTCGCCCAAAATCGCCTAAGGAGCC 6 26 1 CCAAAATCGC 0.685591 -24 CACTCGGGCGGCACCTCCGCACCACGCCGG 7 35 0 GCACCTCCGC 0.994735 -140 GAGTGCGTTAGCACCCTCACAGTAACCGAG 7 60 1 GCACCCTCAC 0.979944 -115 GCACGCACCCCTCGCGGGGCTCACT 7 160 0 CACCCCTCGC 0.907581 -15 CCCGCCTACCTCCGCTGCGTG 8 7 0 CTACCTCCGC 0.934644 -15 CCGTGCACCGCACTCCCTTTTGGGTAG 10 24 0 CCGCACTCCC 0.866702 -17 ********** Masking position 8 Map Score: 15.7286 Number of sites scoring better than the average of aligned sites = 1579 Number in coding regions = 1382 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 CACAACCCCTCGGCGGCACGCACTGCGAAA 4 29 0 CGGCGGCACG 0.98582 -119 AATGTATCGCAGGCCGCACCAAGCCCTGGC 4 111 0 AGGCCGCACC 0.992928 -37 TAGTTTGACCAGACGTCACCGGTGAACGCA 5 76 0 AGACGTCACC 0.962996 -100 AAGGGCTTTTGGTCTGCACCTTCGCCCAAA 6 11 1 GGTCTGCACC 0.957713 -39 AGGCGGCTCCTTAGGCGATT 6 40 0 AGGCGGCTCC 0.996285 -10 TAACGCACTCGGGCGGCACCTCCGCACCAC 7 40 0 GGGCGGCACC 0.99891 -135 AGTGTGTAGCGGGCGTATCCTCATTTTTGT 7 98 1 GGGCGTATCC 0.937203 -77 ********** Masking position 4 Map Score: 10.4083 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 97 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 4 GAACACGATAAGAACACATAGGTCGTAAAG 1 86 1 AGAACACATA 0.887363 -86 CCCCTCCACGAACACAGATATCCTCGTTTT 1 138 0 AACACAGATA 0.388632 -34 AGATTTTTATAGAAAACACATCC 2 4 0 AGAAAACACA 0.95319 -75 AATTCAAGACAGCAGACACACCACTGCAGT 2 42 0 AGCAGACACA 0.894984 -37 ATTCACCGTCAAAAAAGAATTCAAGACAGC 2 59 0 AAAAAAGAAT 0.57223 -20 AAAAAGCACTCTTCTCCACA 3 20 0 AAAAAGCACT 0.78595 -10 CAAAGAAAGCAGAACGGACAACCGTCCTAT 4 60 0 AGAACGGACA 0.941671 -88 ACGTTTCCTAAGAACAGAATGTATCGCAGG 4 128 0 AGAACAGAAT 0.890691 -20 ACAATACGCCTAAAGACACTTCCCGTGTTG 5 31 1 TAAAGACACT 0.639909 -145 ACGTCACCGGTGAACGCACAGCCTGCTCAC 5 64 0 TGAACGCACA 0.833643 -112 GACGTAAAGGAGAAAAGACTCGTAATAAAG 5 129 1 AGAAAAGACT 0.936301 -47 CTCGTAATAAAGAAGACAATCAAAGTGCGC 5 147 1 AGAAGACAAT 0.87403 -29 ********** Masking position 4 Map Score: 3.53462 Number of sites scoring better than the average of aligned sites = 595 Number in coding regions = 527 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 AAACTTCCCCATGCAAAGCCC 4 1 0 ATGCAAGCCC 0.956471 -147 ATCGCAGGCCGCACCAAGCCCTGGCACAGCC 4 105 0 GCACAAGCCC 0.980235 -43 GAAGGTGCAGACCAAAAGCCCTT 6 3 0 ACCAAAGCCC 0.979419 -47 CCCTCACAGTAACCGAGGCCCGCGTAGTGTG 7 73 1 AACCAGGCCC 0.979943 -102 TAAAACTCTCACACAAGGGCCCACAAAAATG 7 119 0 ACACAGGGCC 0.983376 -56 TCCGTGCCTTACCCGAAGGACGTAACACGTA 9 11 0 ACCCAAGGAC 0.961307 -28 **** ****** Masking position 6 Map Score: 1.17651 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 85 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 6 ********** No masking Map Score: 1.31694e-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 7 GTATATGCGTACGAGCTCGCTCGTGCACCCT 1 55 0 ACGGCTCGCT 0.965777 -117 GCAGTGGTGTGTCTGCTGTCTTGAATTCTTT 2 45 1 GTCGCTGTCT 0.862905 -34 CACTAGCAACACGGGAAGTGTCTTTAGGCGT 5 36 0 ACGGAAGTGT 0.890042 -140 CGTGTTGCTAGTGAGCAGGCTGTGCGTTCAC 5 54 1 GTGGCAGGCT 0.966316 -122 TTTCTTTGCGCGCACTTTGATTGTCTTC 5 158 0 GCGGCACTTT 0.910727 -18 CAGACGGGCAGTCTGTAACGTGCA 7 4 1 ACGGCAGTCT 0.992332 -171 TGTTACGTGATGTCTACCCAAAAGG 10 5 1 ACGGATGTCT 0.964428 -36 *** ******* Masking position 11 Map Score: 0.628846 Number of sites scoring better than the average of aligned sites = 608 Number in coding regions = 561 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 8 ********** No masking Map Score: 1.31694e-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 9 ********** No masking Map Score: 1.31694e-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: 1.31694e-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