AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -imetR_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 TP0278 127 T. pallidum predicted coding region TP0278 #2 TP0279 45 ribosomal protein S1 (rpsA) #3 TP0283 177 lipopolysaccharide core biosynthesis protein (kdtB) #4 TP0284 104 T. pallidum predicted coding region TP0284 #5 TP0319 28 membrane lipoprotein (tmpC) #6 TP0321 75 ribose/galactose ABC transporter, ATP-binding protein (rbsA-2) #7 TP0324 103 T. pallidum predicted coding region TP0324 #8 TP0327 56 cationic outer membrane protein (ompH) #9 TP0328 55 DNA mismatch repair protein (mutS) #10 TP0329 117 serine hydroxymethyltransferase (glyA) Motif number 1 GCGCTCGTCTTCCTCGGAAGACT 1 2 1 CGCTCTCTCC 0.982137 -126 GAAGGGAGTGCGCTGGTGATCAGACAACAGAC 1 62 1 CGCTGTGTCA 0.965876 -66 AGACTGTTTGCGCTCCTCGTCTGTTGTCTGAT 1 80 0 CGCTCTCTCT 0.93901 -48 AGTCTCAGAACACTCATGGGCGGATGATGGA 1 107 1 CACTCTGGCG 0.767671 -21 CCGTTTTCTGCCCTGTACTTCCCTTCTTCGTT 2 14 1 CCCTGACTCC 0.943159 -32 ACAACGTGCGCACCGCACGGCGCGAACGCTTC 3 16 0 CACCGACGCG 0.67211 -162 AATCGGTGTTCACGCGAGCTCTCTACGCTTCC 3 55 0 CACGCAGTCT 0.83468 -123 CTCGCGTGAACACCGATTTTCCGCGAGGAGTT 3 69 1 CACCGTTTCC 0.940708 -109 TGTGTAGTTCGCCGCATGTTCCTGAACAACGT 3 141 1 GCCGCTGTCC 0.808528 -37 AAAAGCACAGCCCCGAAGATCACTCAACCGAG 4 48 0 CCCCGAGTCA 0.94942 -57 AAGAATCCTCCCCCCTTTATCGACAAAC 5 7 0 CCCCCTTTCG 0.946035 -22 TGTCTCGACCCGCCCGTGGTCAGTGGGTATGG 6 22 1 CGCCCTGTCA 0.984121 -54 AGCCCCTCCCTCAAGTTCATTACTGGACG 6 57 0 CCCTCAGTCA 0.953913 -19 CCACCCAACTCACCCTTCTTCCAAAAA 7 6 0 CACCCTCTCC 0.979802 -98 GAACCCCCTACCCGGGTGCTCATTGCAAAGAA 7 44 0 CCCGGTGTCA 0.946643 -60 GCACCGTGAGCACCGCGTCTCCTGCCTCCTAC 9 12 1 CACCGGTTCC 0.833679 -44 GTGGACGCTCCTGGGCCAACACGTAGG 9 39 0 CGCTCTGGCC 0.74148 -17 GAATATTGTTCGCTCTGTTTCTAGCGCAAAGA 10 73 0 CGCTCGTTCT 0.713927 -45 ***** ** *** Masking position 3 Map Score: 20.6135 Number of sites scoring better than the average of aligned sites = 1263 Number in coding regions = 1145 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 ATCACCAGCGCACTCCCTTCCCCACATGGAC 1 51 0 CACTCCCTCC 0.970998 -77 AGACTGTTTGCGCTCCTCGTCTGTTGTCTGA 1 81 0 CGCTCCTCTC 0.81224 -47 GCACGGCGCGAACGCTTCTCCTC 3 3 0 AACGCTTCCC 0.876875 -175 GAGAAGCGTTCGCGCCGTGCGGTGCGCACGT 3 14 1 CGCGCCGTCG 0.930755 -164 TGTTCACGCGAGCTCTCTACGCTTCCTAGCT 3 50 0 AGCTCTCTCG 0.797108 -128 CCACTCCGTCAACTCCTCGCGGAAAATCGGT 3 80 0 AACTCCTCCG 0.964917 -98 TTTATATTCGCACCCACTCCGTCAACTCCTC 3 93 0 CACCCACTCG 0.768526 -85 GCACGGCAACCCCTCACGTTGTTCAGGA 3 160 0 AACCCCTCCG 0.980498 -18 AAGAATCCTCCCCCCTTTATCGAC 5 15 0 AATCCTCCCC 0.69321 -14 GGTCGAGACACACGCCCCACT 6 1 0 CACGCCCCCT 0.906076 -75 GCGTGTGTCTCGACCCGCCCGTGGTCAGTGG 6 17 1 CGACCCGCCG 0.820937 -59 AGCCCCTCCCTCAAGTTCATT 6 65 0 AGCCCCTCCT 0.892276 -11 CCACCCAACTCACCCTTCTTCCAAAAA 7 7 0 CACCCTTCTC 0.671862 -97 CGGAATACAGAACCCCCTACCCGGGTGCTCA 7 54 0 AACCCCCTCC 0.971649 -50 CGTTCCGTGCCCGTTTTGAAA 8 1 1 CGTTCCGTCC 0.78131 -56 TGGTGGACGCAGCCCCGGACCGTTTCAAAAC 8 23 0 AGCCCCGGCC 0.864775 -34 ATCACTCCTTGCCTGGTGGACGC 8 44 0 CACTCCTTCC 0.964972 -13 GAATGGACAAAACGCCGCGCGCCGCATGCCC 10 44 0 AACGCCGCCG 0.9546 -74 GCGTTTTGTCCATTCTTTGCGCTAGAAACAG 10 60 1 CATTCTTTCG 0.447221 -58 ******** ** Masking position 5 Map Score: 21.4373 Number of sites scoring better than the average of aligned sites = 3133 Number in coding regions = 2736 Number in noncoding regions = 397 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 3 CGCTGGTGATCAGACAACAGACGAGGAGCGC 1 72 1 CAGACACAGA 0.962686 -56 CAAACAGTCTCAGAACACTCATGGGCGGATG 1 102 1 CAGAAACTCA 0.824555 -26 AAGTACAGGGCAGAAAACGGAAG 2 3 0 CAGAAACGGA 0.976791 -43 TCTACGCTTCCTAGCTACACAACGTGCGCAC 3 35 0 CTAGCACACA 0.808629 -143 GCGAACTACACAAAAAACAGGCAGCACTATT 3 122 0 CAAAAACAGG 0.963492 -56 ACGGGCGGGTCGAGACACACGCCCCACT 6 8 0 CGAGAACACG 0.92806 -68 CCCATACCCACTGACCACGGGCGGGTCGAGA 6 24 0 CTGACACGGG 0.966743 -52 AAAACGCGCCCGGAATACAGAACCCCCTACC 7 64 0 CGGAAACAGA 0.962781 -40 CTAAGTGTAGCAAAAAACGCGCCCGGAATAC 7 77 0 CAAAAACGCG 0.962356 -27 ACGTAGGAGGCAGGAGACGCGGTGCTCACGG 9 15 0 CAGGAACGCG 0.975603 -41 TCCCCTGTTACGCACGACGGGTATCGGGCAT 10 19 1 CGCACACGGG 0.897823 -99 ATTCTTTGCGCTAGAAACAGAGCGAACAATA 10 71 1 CTAGAACAGA 0.876781 -47 ***** ***** Masking position 7 Map Score: 11.9659 Number of sites scoring better than the average of aligned sites = 397 Number in coding regions = 359 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 GCGCTCGTCTTCCTCGGAAGACTGTGGC 1 9 1 CTTCCTCGGA 0.95324 -119 AGCGCACTCCCTTCCCCACATGGACTGCCG 1 46 0 CTTCCCCACA 0.904306 -82 TTTAAAAGCACAGCCCCGAAGATCACTCAA 4 53 0 CAGCCCCGAA 0.955424 -52 GCAGGAGAACCTTGCTCAAAACTTTTCTGA 4 85 0 CTTGCTCAAA 0.735795 -20 CATTACTGGACGTCCCCATACCCACTGACC 6 39 0 CGTCCCCATA 0.9314 -37 TAGCAAAAAACGCGCCCGGAATACAGAACC 7 71 0 CGCGCCCGGA 0.974242 -33 CGTTCCGTGCCCGTTTTGAAACGGT 8 6 1 CGTGCCCGTT 0.956118 -51 CTGGTGGACGCAGCCCCGGACCGTTTCAAA 8 25 0 CAGCCCCGGA 0.977909 -32 ATCACTCCTTGCCTGGTGGACGCAGCC 8 40 0 CTTGCCTGGT 0.823482 -17 CCGCGCGCCGCATGCCCGATACCCGTCGTG 10 31 0 CATGCCCGAT 0.952049 -87 ********** Masking position 5 Map Score: 7.31505 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 444 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 ACGTGCGCACCGCACGGCGCGAACGCTTCT 3 15 0 CGCACGGCGC 0.996485 -163 CCGTGCGGTGCGCACGTTGTGTAGCTAGGA 3 28 1 CGCACGTTGT 0.993786 -150 TGTAGTTCGCCGCATGTTCCTGAACAACGT 3 143 1 CGCATGTTCC 0.783574 -35 ACGGCAACCCCTCACGTTGTTCAGGAACAT 3 156 0 CTCACGTTGT 0.973749 -22 TGTCTCGACCCGCCCGTGGTCAGTGGGTAT 6 22 1 CGCCCGTGGT 0.952989 -54 AGACGCGGTGCTCACGGTGCA 9 2 0 CTCACGGTGC 0.981855 -54 TCCCCTGTTACGCACGACGGGTATCGGGCA 10 19 1 CGCACGACGG 0.963884 -99 GGGCATGCGGCGCGCGGCGTTTTGTCCATT 10 44 1 CGCGCGGCGT 0.98645 -74 ********** Masking position 6 Map Score: 10.24 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 503 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 CAACAGACGAGGAGCGCAAACAGTCTCAGA 1 86 1 GGAGCGCAAA 0.9266 -42 GGGAAGTACAGGGCAGAAAACGGAAG 2 7 0 GGGCAGAAAA 0.978107 -39 AGGGGTGAAAAACGAAGAAGG 2 35 0 GGGGTGAAAA 0.955332 -11 TGACGGAGTGGGTGCGAATATAAATAGTGC 3 100 1 GGTGCGAATA 0.951882 -78 CACTCAACCGAGTGAGAAAAAGAATCATCA 4 30 0 AGTGAGAAAA 0.94756 -75 TGCTTTTAAAGTTCAGAAAAGTTTTGAGCA 4 73 1 GTTCAGAAAA 0.735829 -32 CGCTAGAAACAGAGCGAACAATATTCTGCC 10 79 1 AGAGCGAACA 0.844951 -39 CTCCTCAGGTAGGCAGAATATTGTTCGCTC 10 90 0 AGGCAGAATA 0.842777 -28 GCCTACCTGAGGAGAGAAAAAC 10 106 1 GGAGAGAAAA 0.982185 -12 ********** Masking position 8 Map Score: 6.85432 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 245 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 ********** No masking Map Score: 1.12509e-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 8 ********** No masking Map Score: 1.12509e-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: 1.12509e-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