AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_tpal_reg_300.orf -o00260_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 TP0647 49 seryl-tRNA synthetase (serS) #8 TP0651 175 conserved hypothetical integral membrane protein #9 TP0672 134 glycyl-tRNA synthetase (glyS) #10 TP0673 177 glutamyl-tRNA synthetase (gltX) #11 TP0837 147 threonyl-tRNA synthetase (thrS) Motif number 1 TGTCGATAAAGGGGGGAGGATTCTT 1 14 1 GGGGGGAGGA 0.961531 -15 ACTGACCACGGGCGGGTCGAGACACACGCC 2 16 0 GGCGGGTCGA 0.924546 -60 AGTGGGTATGGGGACGTCCAGTAATGAACT 2 43 1 GGGACGTCCA 0.886963 -33 ATGAACTTGAGGGAGGGGCT 2 66 1 GGGAGGGGCT 0.98014 -10 TGAGCACCCGGGTAGGGGGTTCTGTATTCC 3 54 1 GGTAGGGGGT 0.843769 -50 TTCTGTATTCCGGGCGCGTTTTTTGCTACA 3 73 1 CGGGCGCGTT 0.94896 -31 CGTTTCAAAACGGGCACGGAACG 4 4 0 CGGGCACGGA 0.886047 -53 GAAACGGTCCGGGGCTGCGTCCACCAGGCA 4 28 1 GGGGCTGCGT 0.811596 -29 TAGGAGGCAGGAGACGCGGTGCTCACGGTG 5 13 0 GAGACGCGGT 0.874061 -43 GGGCATGCGGCGCGCGGCGTTTTGTCCATT 6 44 1 CGCGCGGCGT 0.95854 -74 CTTCTCATTGCGGAGGCCGATGGTGCGGTA 8 13 1 CGGAGGCCGA 0.987975 -163 GTTCTGTCAAGGCTCGCGGTTGGGGTACGC 8 52 1 GGCTCGCGGT 0.910497 -124 CAAGGACACACGGACGCCTTGCGTACCCCA 8 72 0 CGGACGCCTT 0.908293 -104 GCGTAAGACGGGGTGGTCCTTTCTTCCTCA 8 153 0 GGGTGGTCCT 0.793368 -23 TGTTCAAAGGCGGGCGCGATCTCTGTGAGG 9 59 1 CGGGCGCGAT 0.913509 -76 GTGAGGTCGCCGCGGGTGCTGACAGTATGC 9 83 1 CGCGGGTGCT 0.881957 -52 TGCTAGACAGGGGGGAAGGTGAGCGGCGCG 9 110 1 GGGGGAAGGT 0.736418 -25 GGGGAAGACAGGGAGGCGGTCACGGTGCAT 10 73 1 GGGAGGCGGT 0.996081 -105 AAGCATCCCTGTGAGGCCCTGAAAATTACA 10 109 0 GTGAGGCCCT 0.726292 -69 GCTTGCGCCCCGGAGGGGGATGTGCGATAA 10 135 1 CGGAGGGGGA 0.981451 -43 TCGCCCTCCCCGGGGGCCGATTATCGCACA 10 155 0 CGGGGGCCGA 0.991855 -23 TCGGCCCCCGGGGAGGGCGAGCG 10 165 1 GGGAGGGCGA 0.983081 -13 TCTGTAGGAAGGGACGTGGTATGTAGGGTA 11 46 0 GGGACGTGGT 0.981649 -102 GCAGTGACGGCGCAGGCGCACTGGCTCAGT 11 78 1 CGCAGGCGCA 0.915003 -70 GGTTTGTCAATGGGCGCCGTTTTGGAGGAA 11 110 0 TGGGCGCCGT 0.924743 -38 ********** Masking position 2 Map Score: 37.6722 Number of sites scoring better than the average of aligned sites = 1905 Number in coding regions = 1643 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 2 AGTGGGGCGTGTGTCTCGACCCG 2 2 1 GGGGGGTGTG 0.927451 -74 CGACCCGCCCGTGGTCAGTGGGTATGGGGACG 2 27 1 GGGTCGTGGG 0.993317 -49 TTTGGAAGAAGGGTGAGTTGGGTGGCACCTAT 3 13 1 GGTGATTGGG 0.799271 -91 GGCAGGAGACGCGGTGCTCACGGTGCA 5 6 0 GGGTGTCACG 0.902912 -50 GGGCCAACACGTAGGAGGCAGGAGACGCGGTG 5 22 0 GAGGAGCAGG 0.947221 -34 CGGGTATCGGGCATGCGGCGCGCGGCGTTTTG 6 36 1 GATGCGCGCG 0.791812 -82 GGCCGATGGTGCGGTATTTGGGTATGTTCTGT 8 27 1 GGGTATTGGG 0.964839 -149 GCTCGCGGTTGGGGTACGCAAGGCGTCCGTGT 8 63 1 GGGTAGCAAG 0.861103 -113 GCTCGCTGGCGCGAGAAGTGCGCATGAGGAAG 8 129 1 GGAGAGTGCG 0.962105 -47 CTCAGTTAACGCGGGCTATAGGGAAAAGAGGT 9 15 1 GGGGCATAGG 0.856922 -120 ATAGGGAAAAGAGGTATGCAGGGGATGTGTTC 9 32 1 GGGTAGCAGG 0.986103 -103 CGATCTCTGTGAGGTCGCCGCGGGTGCTGACA 9 75 1 GGGTCCCGCG 0.931497 -60 AGGGGGGAAGGTGAGCGGCGCGTCACC 9 118 1 GGAGCGCGCG 0.969077 -17 GGCATCCTGCGTGGTAGGAAGGGGAAGACAGG 10 53 1 GGGTAGAAGG 0.933213 -125 GGGCCTCACAGGGATGCTTGCGCCCCGGAGGG 10 120 1 GGATGTTGCG 0.719676 -58 GCGCCCCGGAGGGGGATGTGCGATAATCGGCC 10 139 1 GGGGAGTGCG 0.9944 -39 CGGCCCCCGGGGAGGGCGAGCG 10 166 1 GAGGGGAGCG 0.835552 -12 AGGAAGGGACGTGGTATGTAGGGTATAGTAGA 11 39 0 GGGTAGTAGG 0.984218 -109 CGCCGTCACTGCAGTCTGTAGGAAGGGACGTG 11 58 0 GAGTCGTAGG 0.921662 -90 * **** ***** Masking position 1 Map Score: 26.8709 Number of sites scoring better than the average of aligned sites = 1896 Number in coding regions = 1681 Number in noncoding regions = 215 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 TTTTTGGAAGAAGGGTGAGTTGGGT 3 6 1 GGAAGAAGGG 0.879973 -98 AAACGCGCCCGGAATACAGAACCCCCTACC 3 64 0 GGAATACAGA 0.845592 -40 GCCAACACGTAGGAGGCAGGAGACGCGGTG 5 22 0 AGGAGGCAGG 0.958321 -34 TCTCTCCTCAGGTAGGCAGAATATTGTTCG 6 93 0 GGTAGGCAGA 0.965369 -25 AATAAGTAAGGGGAGAAAGGCGC 7 37 1 GGGAGAAAGG 0.982497 -13 GTGCGCATGAGGAAGAAAGGACCACCCCGT 8 146 1 GGAAGAAAGG 0.97894 -30 CAGTTAACGCGGGCTATAGGGAAAAGAGGT 9 17 1 GGGCTATAGG 0.844043 -118 AGGGAAAAGAGGTATGCAGGGGATGTGTTC 9 34 1 GGTATGCAGG 0.988707 -101 CTGACAGTATGCTAGACAGGGGGGAAGGTG 9 101 1 GCTAGACAGG 0.939639 -34 CATCCTGCGTGGTAGGAAGGGGAAGACAGG 10 55 1 GGTAGGAAGG 0.989476 -123 GGTAGGAAGGGGAAGACAGGGAGGCGGTCA 10 65 1 GGAAGACAGG 0.990903 -113 GAAGGGACGTGGTATGTAGGGTATAGTAGA 11 39 0 GGTATGTAGG 0.966322 -109 CCGTCACTGCAGTCTGTAGGAAGGGACGTG 11 58 0 AGTCTGTAGG 0.534223 -90 ********** Masking position 9 Map Score: 19.3314 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 296 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 4 TATTCTTTGCAATGAGCACCCGGGTAGGGG 3 42 1 AATGAGCACC 0.762553 -62 TGCACCGTGAGCACCGCGTCTCCTG 5 6 1 CGTGAGCACC 0.981233 -50 CGATACCCGTCGTGCGTAACAGGGGAACAT 6 15 0 CGTGCGTAAC 0.966107 -103 ACACGGACGCCTTGCGTACCCCAACCGCGA 8 65 0 CTTGCGTACC 0.979977 -111 GCAAGGCGTCCGTGTGTCCTTGCTGGACAG 8 80 1 CGTGTGTCCT 0.758661 -96 CTCGCGCCAGCGAGCGTAACACGCCAGCGG 8 114 0 CGAGCGTAAC 0.842235 -62 CTTTCTTCCTCATGCGCACTTCTCGCGCCA 8 135 0 CATGCGCACT 0.957149 -41 CACAGGGATGCTTGCGCCCCGGAGGGGGAT 10 126 1 CTTGCGCCCC 0.969429 -52 AGTGACGGCGCAGGCGCACTGGCTCAGTGC 11 80 1 CAGGCGCACT 0.915652 -68 ********** Masking position 6 Map Score: 7.44237 Number of sites scoring better than the average of aligned sites = 1020 Number in coding regions = 934 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 TCGATAAAGGGGGGAGGATTCTT 1 16 1 GGGGAGGATT 0.776708 -13 AGTGGGGCGTGTGTCTCGACCCG 2 4 1 GGGGCGTGTG 0.976958 -72 CCACTGACCACGGGCGGGTCGAGACACACG 2 18 0 CGGGCGGGTC 0.918251 -58 TGAGTTGGGTGGCACCTATTCTTTGCAATG 3 26 1 GGCACCTATT 0.525251 -78 CTGTATTCCGGGCGCGTTTTTTGCTACACT 3 75 1 GGCGCGTTTT 0.961729 -29 GACGCAGCCCCGGACCGTTTCAAAACGGGC 4 19 0 CGGACCGTTT 0.757039 -38 CATGCGGCGCGCGGCGTTTTGTCCATTCTT 6 47 1 GCGGCGTTTT 0.925984 -71 TCTCATTGCGGAGGCCGATGGTGCGGTATT 8 15 1 GAGGCCGATG 0.928868 -161 TCTGTCAAGGCTCGCGGTTGGGGTACGCAA 8 54 1 CTCGCGGTTG 0.907539 -122 CAGATTACCGCTGGCGTGTTACGCTCGCTG 8 107 1 CTGGCGTGTT 0.75929 -69 AGAGATCGCGCCCGCCTTTGAACACATCCC 9 53 0 CCCGCCTTTG 0.836031 -82 CTGTGAGGTCGCCGCGGGTGCTGACAGTAT 9 81 1 GCCGCGGGTG 0.971457 -54 GATGCCGCTTCACGCGGTTGATTGCACAGA 10 29 0 CACGCGGTTG 0.933538 -149 TTGCGCCCCGGAGGGGGATGTGCGATAATC 10 137 1 GAGGGGGATG 0.64321 -41 GCCCTCCCCGGGGGCCGATTATCGCACATC 10 153 0 GGGGCCGATT 0.97392 -25 TTTGTCAATGGGCGCCGTTTTGGAGGAAGC 11 108 0 GGCGCCGTTT 0.975741 -40 ********** Masking position 9 Map Score: 14.4282 Number of sites scoring better than the average of aligned sites = 1826 Number in coding regions = 1642 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 6 TCCTTGCCTGGTGGACGCAGCCCCGGACCGT 4 31 0 GTGGACGCGC 0.992042 -26 GTAGGAGGCAGGAGACGCGGTGCTCACGGTG 5 13 0 GGAGACGCGT 0.809813 -43 GTGGACGCTCCTGGGCCAACA 5 45 0 GTGGACGCCC 0.993736 -11 CGACCTCACAGAGATCGCGCCCGCCTTTGAA 9 61 0 GAGATCGCCC 0.943473 -74 CGATCTCTGTGAGGTCGCCGCGGGTGCTGAC 9 75 1 GAGGTCGCGC 0.984786 -60 GGTGACGCGCCGCTCACCTTC 9 124 0 GGTGACGCCC 0.971071 -11 TACCACGCAGGATGCCGCTTCACGCGGTTGA 10 38 0 GATGCCGCTC 0.808248 -140 CTCATGCACCGTGACCGCCTCCCTGTCTTCC 10 75 0 GTGACCGCTC 0.883699 -103 GGGTATAGTAGAGGATGCTTTCTGTTTTGGA 11 20 0 GAGGATGCTT 0.779174 -128 CGCCGTTTTGGAGGAAGCACTGAGCCAGTGC 11 95 0 GAGGAAGCCT 0.879181 -53 ******** ** Masking position 8 Map Score: 9.00064 Number of sites scoring better than the average of aligned sites = 423 Number in coding regions = 387 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 GACGCGGTGCTCACGGTGCA 5 1 0 TCACGGTGCA 0.99511 -55 ATAAAAAACCTGTCTGTGCAATCAACCGCG 10 17 1 TGTCTGTGCA 0.952982 -161 AGGGAGGCGGTCACGGTGCATGAGGAGTGT 10 82 1 TCACGGTGCA 0.99511 -96 CAGACTGCAGTGACGGCGCAGGCGCACTGG 11 72 1 TGACGGCGCA 0.991683 -76 ********** Masking position 1 Map Score: 3.90194 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 23 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 CGGGTATCGGGCATGCGGCGCGCGGCGTTT 6 36 1 GCATGCGGCG 0.989019 -82 TATTCTGCCTACCTGAGGAGAGAAAAAC 6 100 1 ACCTGAGGAG 0.974777 -18 CGAGAAGTGCGCATGAGGAAGAAAGGACCA 8 140 1 GCATGAGGAA 0.985049 -36 CGGTCACGGTGCATGAGGAGTGTAATTTTC 10 89 1 GCATGAGGAG 0.996194 -89 ********** Masking position 4 Map Score: 2.14376 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 38 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ********** No masking Map Score: 2.38275e-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: 2.38275e-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: 2.38275e-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