AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00670_tpal_reg_300.orf -o00670_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -x5 -e 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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0319 28 membrane lipoprotein (tmpC) #2 TP0321 75 ribose/galactose ABC transporter, ATP-binding protein (rbsA-2) #3 TP0324 103 T. pallidum predicted coding region TP0324 #4 TP0327 56 cationic outer membrane protein (ompH) #5 TP0328 55 DNA mismatch repair protein (mutS) #6 TP0329 117 serine hydroxymethyltransferase (glyA) #7 TP0732 95 methylenetetrahydrofolate dehydrogenase (folD) #8 TP0757 40 polypeptide deformylase (def) #9 TP0758 118 ribosomal protein S21 (rpsU) Motif number 1 TGACCACGGGCGGGTCGAGACACACGCCCC 2 14 0 CGGGTCGAGA 0.909919 -62 CCGTGGTCAGTGGGTATGGGGACGTCCAGT 2 35 1 TGGGTATGGG 0.833305 -41 AATGAGCACCCGGGTAGGGGGTTCTGTATT 3 52 1 CGGGTAGGGG 0.99726 -52 TAGCAAAAAACGCGCCCGGAATACAGAACC 3 71 0 CGCGCCCGGA 0.987029 -33 CGTTTCAAAACGGGCACGGAACG 4 4 0 CGGGCACGGA 0.994139 -53 CGTTTTGAAACGGTCCGGGGCTGCGTCCAC 4 22 1 CGGTCCGGGG 0.977011 -35 CTGCGTCCACCAGGCAAGGAGTGAT 4 42 1 CAGGCAAGGA 0.91168 -15 CCTGGGCCAACACGTAGGAGGCAGGAGACG 5 27 0 CACGTAGGAG 0.899199 -29 GTGGACGCTCCTGGGCCAACACGTA 5 41 0 CGCTCCTGGG 0.896045 -15 CCCTGTTACGCACGACGGGTATCGGGCATG 6 21 1 CACGACGGGT 0.720834 -97 CGACGGGTATCGGGCATGCGGCGCGCGGCG 6 33 1 CGGGCATGCG 0.981426 -85 TTTCTCTCCTCAGGTAGGCAGAATATTGTT 6 95 0 CAGGTAGGCA 0.933014 -23 AAAGACCGAACACGCACGGACACTAGACGG 7 43 0 CACGCACGGA 0.974337 -53 AGTATAGACACGCGCACGCAACAGCGCAAA 7 70 0 CGCGCACGCA 0.938006 -26 GCGGGTATGAGTTTCTCTTGG 8 2 1 CGGGTATGAG 0.919881 -39 TGGGTAAGAGCGGGAAGAGGCG 8 29 1 CGGGAAGAGG 0.911436 -12 GACACGTAGGGTGTGCGTGCAG 9 3 1 CACGTAGGGT 0.92776 -116 GTAGGGTGTGCGTGCAGGGGAGGCAGGAGT 9 16 1 CGTGCAGGGG 0.983646 -103 ********** Masking position 1 Map Score: 31.1233 Number of sites scoring better than the average of aligned sites = 1900 Number in coding regions = 1727 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 CGTGGTCAGTGGGTATGGGGACGTCCAGTA 2 36 1 GGGTATGGGG 0.95997 -40 AATGAACTTGAGGGAGGGGCT 2 65 1 AGGGAGGGGC 0.947669 -11 ATGAGCACCCGGGTAGGGGGTTCTGTATTC 3 53 1 GGGTAGGGGG 0.993617 -51 GTTTCAAAACGGGCACGGAACG 4 3 0 GGGCACGGAA 0.935162 -54 TCCTTGCCTGGTGGACGCAGCCCCGGACCG 4 32 0 GTGGACGCAG 0.900772 -25 TGCGTCCACCAGGCAAGGAGTGAT 4 43 1 AGGCAAGGAG 0.815436 -14 GAGACGCGGTGCTCACGGTGCA 5 3 0 GCTCACGGTG 0.660152 -53 GTAGGAGGCAGGAGACGCGGTGCTCACGGT 5 14 0 GGAGACGCGG 0.913522 -42 CTGGGCCAACACGTAGGAGGCAGGAGACGC 5 26 0 ACGTAGGAGG 0.734488 -30 GTGGACGCTCCTGGGCCAAC 5 46 0 GTGGACGCTC 0.781267 -10 GACGGGTATCGGGCATGCGGCGCGCGGCGT 6 34 1 GGGCATGCGG 0.957654 -84 TTCTCTCCTCAGGTAGGCAGAATATTGTTC 6 94 0 AGGTAGGCAG 0.959746 -24 ACGACGCCGAGCATACGGTGTTTCTTGGGC 7 11 1 GCATACGGTG 0.759474 -85 AAGACCGAACACGCACGGACACTAGACGGA 7 42 0 ACGCACGGAC 0.825153 -54 GTATAGACACGCGCACGCAACAGCGCAAAG 7 69 0 GCGCACGCAA 0.858543 -27 AGTTTCTCTTGGGTAAGAGCGGGAAGAGGC 8 20 1 GGGTAAGAGC 0.5673 -21 GACACGTAGGGTGTGCGTGCAGG 9 4 1 ACGTAGGGTG 0.925409 -115 TGTGCGTGCAGGGGAGGCAGGAGTGCTTTC 9 22 1 GGGGAGGCAG 0.989572 -97 AGCCTACCAGGGGTAGGCTAGCGCAAAAGA 9 76 0 GGGTAGGCTA 0.930819 -43 AGCCTACCCCTGGTAGGCTGTGTTTTTTTC 9 87 1 TGGTAGGCTG 0.831927 -32 GTTTTTTTCAGGGGAGGGTCG 9 108 1 GGGGAGGGTC 0.976417 -11 ********** Masking position 5 Map Score: 27.8988 Number of sites scoring better than the average of aligned sites = 3177 Number in coding regions = 2800 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 3 AGCAAAAAACGCGCCCGGAATACAGAACCCC 3 69 0 GCGCCCGGAT 0.990831 -35 GTTTCAAAACGGGCACGGAACG 4 2 0 GGGCACGGAC 0.960404 -55 GAGACGCGGTGCTCACGGTGCA 5 2 0 GCTCACGGGC 0.858563 -54 CCTGTTACGCACGACGGGTATCGGGCATGCG 6 22 1 ACGACGGGAT 0.585377 -96 CGGGCATGCGGCGCGCGGCGTTTTGTCCATT 6 43 1 GCGCGCGGGT 0.859965 -75 TCTGTTTCTAGCGCAAAGAATGGACAAAACG 6 61 0 GCGCAAAGAT 0.973592 -57 TAGAAACAGAGCGAACAATATTCTGCCTACC 6 82 1 GCGAACAAAT 0.729372 -36 ACGACGCCGAGCATACGGTGTTTC 7 4 1 ACGCCGAGAT 0.872397 -92 AAGACCGAACACGCACGGACACTAGACGGAA 7 41 0 ACGCACGGCA 0.859572 -55 GCACGCAACAGCGCAAAGACCGAACACGCAC 7 56 0 GCGCAAAGCC 0.954541 -40 GTATAGACACGCGCACGCAACAGCGCAAAGA 7 68 0 GCGCACGCAC 0.983242 -28 GCGCCCAGTATAGACACGCGC 7 85 0 GCGCCCAGAT 0.991867 -11 CCTCCCCTGCACGCACACCCTACGTGTC 9 8 0 ACGCACACCT 0.838752 -111 GGGTAGGCTAGCGCAAAAGACGTCCCCTGTC 9 65 0 GCGCAAAAAC 0.839224 -54 ******** ** Masking position 3 Map Score: 15.4623 Number of sites scoring better than the average of aligned sites = 2849 Number in coding regions = 2631 Number in noncoding regions = 218 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 4 ACCACGGGCGGGTCGAGACACACGCCCCAC 2 12 0 GGTCGAGACA 0.861084 -64 TTTTTGGAAGAAGGGTGAGTTGGGT 3 6 1 GGAAGAAGGG 0.836081 -98 GCTAAGTGTAGCAAAAAACGCGCCCGGAAT 3 79 0 GCAAAAAACG 0.980596 -25 TTCAAAACGGGCACGGAACG 4 1 0 GCACGGAACG 0.970678 -56 CACGTAGGAGGCAGGAGACGCGGTGCTCAC 5 17 0 GCAGGAGACG 0.951767 -39 CGCAAAGAATGGACAAAACGCCGCGCGCCG 6 51 0 GGACAAAACG 0.969648 -67 CATTCTTTGCGCTAGAAACAGAGCGAACAA 6 70 1 GCTAGAAACA 0.936667 -48 AGACGGAAGCCCAAGAAACACCGTATGCTC 7 19 0 CCAAGAAACA 0.820119 -77 ATAGACACGCGCACGCAACAGCGCAAAGAC 7 67 0 GCACGCAACA 0.864319 -29 GTTTCTCTTGGGTAAGAGCGGGAAGAGGCG 8 21 1 GGTAAGAGCG 0.649265 -20 GGTAAGAGCGGGAAGAGGCG 8 31 1 GGAAGAGGCG 0.974017 -10 GAGTGCTTTCGGAAGAAACGATTGACAGGG 9 42 1 GGAAGAAACG 0.991926 -77 GTAGGCTAGCGCAAAAGACGTCCCCTGTCA 9 64 0 GCAAAAGACG 0.971022 -55 ACCCTCCCCTGAAAAAAACACAGCCTACCA 9 97 0 GAAAAAAACA 0.666495 -22 ********** Masking position 9 Map Score: 18.5393 Number of sites scoring better than the average of aligned sites = 1030 Number in coding regions = 962 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 AGAACCCCCTACCCGGGTGCTCATTGCAAA 3 47 0 ACCCGGGTGC 0.930846 -57 GGTGGACGCAGCCCCGGACCGTTTCAAAAC 4 23 0 GCCCCGGACC 0.984538 -34 CTACGTGTTGGCCCAGGAGCGTCCAC 5 40 1 GCCCAGGAGC 0.989041 -16 CGCGCCGCATGCCCGATACCCGTCGTGCGT 6 28 0 GCCCGATACC 0.955869 -90 CTAGACGGAAGCCCAAGAAACACCGTATGC 7 21 0 GCCCAAGAAA 0.944446 -75 GCGCCCAGTATAGACACGCGCA 7 84 0 GCCCAGTATA 0.905469 -12 TCCCGCTCTTACCCAAGAGAAACTCATACC 8 14 0 ACCCAAGAGA 0.948521 -27 ********** Masking position 4 Map Score: 5.43724 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 142 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 GTTTGTCGATAAAGGGGGGAGGATTCT 1 8 1 GATAAAGGGG 0.92671 -21 TAATGAACTTGAGGGAGGGGCT 2 64 1 GAGGGAGGGG 0.989225 -12 TTTTTGGAAGAAGGGTGAGTTGGGTG 3 7 1 GAAGAAGGGT 0.76577 -97 CAACACGTAGGAGGCAGGAGACGCGGTGCT 5 20 0 GAGGCAGGAG 0.978195 -36 CCCGTCGTGCGTAACAGGGGAACATACCA 6 10 0 GTAACAGGGG 0.990398 -108 TTTCTCTTGGGTAAGAGCGGGAAGAGGCG 8 22 1 GTAAGAGCGG 0.825339 -19 GCGTGCAGGGGAGGCAGGAGTGCTTTCGGA 9 25 1 GAGGCAGGAG 0.978195 -94 GAAGAAACGATTGACAGGGGACGTCTTTTG 9 53 1 TTGACAGGGG 0.969894 -66 AAAACACAGCCTACCAGGGGTAGGCTAGCG 9 83 0 CTACCAGGGG 0.88493 -36 GGCTGTGTTTTTTTCAGGGGAGGGTCG 9 102 1 TTTTCAGGGG 0.76791 -17 ********** Masking position 6 Map Score: 9.49591 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 585 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 7 ********** No masking Map Score: -7.36532e-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 8 ********** No masking Map Score: -7.36532e-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 9 ********** No masking Map Score: -7.36532e-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