AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icpxR9_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 TP0363 300 chemotaxis histidine kinase (cheA) #2 TP0438 29 conserved hypothetical protein #3 TP0439 86 purine-binding chemotaxis protein (cheW-2) #4 TP0726 57 flagellar protein (flbD) #5 TP0727 70 flagellar hook protein (flgE) #6 TP0728 75 flagellar hook assembly scaffolding protein (flgD) #7 TP0773 300 periplasmic serine protease DO (htrA-1) #8 TP0841 300 periplasmic serine protease DO (htrA-2) #9 TP0949 275 membrane protein #10 TP0951 119 ribosomal protein L34 (rpmH) #11 TP0952 81 lipase, putative #12 TP0953 86 pheromone shutdown protein (traB) #13 TP0954 71 conserved hypothetical protein #14 TP0955 95 T. pallidum predicted coding region TP0955 #15 TP1016 72 basic membrane protein (tpn39b) #16 TP1017 171 alanyl-tRNA synthetase (alaS) Motif number 1 TATCGATTGGCGGACACGCCAGCC 1 3 0 CGGCACGCCG 0.954891 -298 GCTTTCTACCCACGCGCGGTCGTCTTGGGTAT 1 32 0 CACCGCGGTG 0.859981 -269 AAACCAGACCCTCTCGCAGCTTTCTACCCACG 1 50 0 CTCCGCAGCT 0.928272 -251 AGTAGGACCAGTCCCGCGGCATACAAGGAGTA 1 127 1 GTCCGCGGCT 0.884049 -174 CAAACGTACCTGCGCGCGGGCCATGGCGGAGT 1 186 1 TGCCGCGGGC 0.559185 -115 AAGACCCCGCCACCCGCTGCATCCCTTGACAC 1 237 0 CACCGCTGCT 0.975449 -64 ACTCCGTTCGCTCACGCACCTTGCAGAGCA 3 9 0 CTCCGCACCT 0.916104 -78 CGGAGTGCAGGACACGCGCTTGACTGCAGCTG 3 35 1 GACCGCGCTG 0.900868 -52 ATAGGCGCGCCGGTTTTGCCTAC 6 2 1 TAGCGCGCCG 0.90759 -74 GACTTGAACTCCCACGCCGGTGAAGGCACT 7 9 1 CTCCACGCCG 0.969976 -292 CCGGTGAAGGCACTAGCACCTGAAGCTAGCGT 7 27 1 CACAGCACCG 0.875205 -274 GTGGAATTGGCAGACACGCTAGCTTCAGGTGC 7 42 0 CAGCACGCTG 0.887228 -259 CCAATTCCAATACACGCTGCCCGCGGCGCTGC 7 182 1 TACCGCTGCC 0.839669 -119 CCCACGGCGCCACGCGCAGCGCCGCGGGCAGC 7 197 0 CACCGCAGCC 0.979695 -104 TCGAACCATCGACCCACGCCTTAAAAGGGCGT 7 252 0 GACCACGCCT 0.925301 -49 GCCTACCGTGCACAAACTGCTCCCTGCATGTA 8 34 0 CACAACTGCC 0.652861 -267 CACGTACACTTACACGCTGCCTACCGTGCACA 8 52 0 TACCGCTGCT 0.828333 -249 GTGTACGTGGCGGGCACAGGTGAAGAGGGGAT 8 75 1 CGGCACAGGG 0.516518 -226 AGTTTTTTTACAGCAGCGGCGTTGCTCGTTTT 8 245 1 CAGAGCGGCT 0.861275 -56 GATCACACAACACGCACAGCAGCCGCTGATAC 9 52 0 CACCACAGCG 0.974749 -224 ATTCAGAGAACAGACGCGCGCGATCACACAAC 9 73 0 CAGCGCGCGG 0.599289 -203 AAGCGACGCACACTCACGGCCTATTCCTGCCT 9 116 0 CACCACGGCT 0.986769 -160 CCATGTACTCGCACGCTCTCATAGGCATA 9 257 0 CTCCACGCTT 0.723438 -19 AGGTGCTGACGCGGCTCCTCCCGAGGA 10 6 1 CTGCGCGGCC 0.782283 -114 CATCACTTTACACGTGCTGCAGCACGTCCTTA 11 18 0 CACTGCTGCG 0.648094 -64 GCCGCTTACACGCCCGCTCCGTTTGCCCGTGA 11 56 0 CGCCGCTCCT 0.945713 -26 CTGTCCCTCCCACACACGGTGGCGCCCAAGAC 12 14 0 CACCACGGTG 0.958438 -73 CGCCATCAACCAGTCGCACCTTGCCGACTGTC 12 41 0 CAGCGCACCT 0.942022 -46 CTTTACCCGAGACTCACGCCATCAACCAGTCG 12 57 0 GACCACGCCT 0.925776 -30 ACGCTGCCGACACCCGCGCGTCGCTGAATTCT 13 32 0 CACCGCGCGC 0.509742 -40 CCCCCTGTACCGCACGCTGCCGACACCCGCGC 13 45 0 CGCCGCTGCG 0.967809 -27 TCCACTCGCACAGAAACTGCTCGTACGCGGCT 14 54 1 CAGAACTGCC 0.432061 -42 CAGTCACCAGCACACACGCCGGAGAAACTATA 15 25 0 CACCACGCCG 0.992153 -48 GCTGGTGACTGAGTCGCGGTTGTTACGGGGAG 15 46 1 GAGCGCGGTG 0.805497 -27 TGACAGAATTCGCACACACCTCTAGCCTCTCG 16 53 0 CGCCACACCC 0.887087 -119 *** ****** * Masking position 7 Map Score: 56.8494 Number of sites scoring better than the average of aligned sites = 3820 Number in coding regions = 3516 Number in noncoding regions = 304 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 2 CTCCTCTACCGAGCGGTGGGGGTCTACGTT 1 99 0 GAGCGGTGGG 0.98753 -202 TACTCCTTGTATGCCGCGGGACTGGTCCTA 1 129 0 ATGCCGCGGG 0.605169 -172 CAAGGAGTAACCACCGAGGGCGAGAAACCG 1 150 1 CCACCGAGGG 0.712894 -151 GCCATGGCCCGCGCGCAGGTACGTTTGTCA 1 183 0 GCGCGCAGGT 0.851384 -118 GGGATGCAGCGGGTGGCGGGGTCTTTTGGA 1 244 1 GGGTGGCGGG 0.871156 -57 GTGCGTGAGCGAACGGAGTGCAGGACACGC 3 22 1 GAACGGAGTG 0.515252 -65 GACTGCAGCTGAGAGGAGGGATTGTACGAA 3 56 1 GAGAGGAGGG 0.924769 -31 AATGTATCTTAAGCGGCAGGTGGCGTGATG 4 28 1 AAGCGGCAGG 0.818032 -30 GCGGCAGGTGGCGTGATGGGGATGAGGG 4 40 1 GCGTGATGGG 0.715576 -18 ATAGGCGCGCCGGTTTTGCCTACC 6 5 1 GCGCGCCGGT 0.902076 -71 CCGGTGAAAAAAGAGGAGGGCCGGGGC 6 59 1 AAGAGGAGGG 0.841717 -17 GAAAACCCTTCCATGGTGGGAAATATAGTT 7 85 1 CCATGGTGGG 0.781721 -216 GCCACGCGCAGCGCCGCGGGCAGCGTGTAT 7 191 0 GCGCCGCGGG 0.9853 -110 GCTGCGCGTGGCGCCGTGGGCTATTAGCTC 7 209 1 GCGCCGTGGG 0.979035 -92 CATCATGGCTCAGAGGTGGGATTG 7 287 1 CAGAGGTGGG 0.769086 -14 AAGTGTGCGCGGTGTGCTGATAGTAC 8 7 1 GCGCGGTGTG 0.935146 -294 TGCTGATAGTACATGCAGGGAGCAGTTTGT 8 25 1 ACATGCAGGG 0.607323 -276 AGCAGTTTGTGCACGGTAGGCAGCGTGTAA 8 45 1 GCACGGTAGG 0.841731 -256 GTGTAAGTGTACGTGGCGGGCACAGGTGAA 8 69 1 ACGTGGCGGG 0.973915 -232 GGGTTTGGGTACGCGCAGGGACGTGGAGGG 8 160 1 ACGCGCAGGG 0.961035 -141 ACGCGCAGGGACGTGGAGGGACTCATGAAC 8 170 1 ACGTGGAGGG 0.958705 -131 ATTTACCGCTGAAAGGCAGGAATAGGCCGT 9 103 1 GAAAGGCAGG 0.308011 -173 AGGGGAAAGAGCGCGCTGGTAAAAACGGAT 9 185 0 GCGCGCTGGT 0.865195 -91 GCGGGCGTGTAAGCGGCGGCG 11 71 1 AAGCGGCGGC 0.842112 -11 TCCCTCCCACACACGGTGGCGCCCAAGACG 12 13 0 ACACGGTGGC 0.731883 -74 ********** Masking position 9 Map Score: 30.2438 Number of sites scoring better than the average of aligned sites = 1869 Number in coding regions = 1667 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 3 ACCCCCACCGCTCGGTAGAGGAGTAGGACCAGTCCCG 1 106 1 CTCGTGGGGG 0.997441 -195 ATTCTCGGCTGATGGAAGTGTCAAGGGATGCAGCGGG 1 220 1 GATGAGGTGG 0.863914 -81 CGGCAGGTGGCGTGATGGGGATGAGGG 4 41 1 CGTGTGGAGG 0.928553 -17 GTTTTCTTGCCTCGATGGTGGAATTGGCAGACACGCT 7 54 0 CTCGTGGGGG 0.997442 -247 CGGTAGGCAGCGTGTAAGTGTACGTGGCGGGCACAGG 8 58 1 CGTGAGGTGG 0.961848 -243 CCCGGGCTGTGTCGGTAGGGGTTTGGGTACGCGCAGG 8 142 1 GTCGTGGGGG 0.993458 -159 TATTGTTTACCTCGTTTGTGTGTGGGGTACATGCGGT 8 201 1 CTCGTGGTGG 0.994026 -100 GTGAGTGTGCGTCGCTTGTGTGCATGGGTATTTAGTG 9 131 1 GTCGTGGTGG 0.984804 -145 AAGATCCCCTCTTGTAGGGGGAACCGGCTCCTCGGGA 10 29 0 CTTGAGGGGG 0.991794 -91 TTCTTTTCCATGCTCAGGGGCGAGGCAGTGCTCAG 14 9 1 CATGTAGGGG 0.83617 -87 ACAGAAACTGCTCGTACGCGGCTATGGTAGCGTCCAG 14 63 1 CTCGAGGGGG 0.995669 -33 **** * * ** ** Masking position 10 Map Score: 18.2783 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 91 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 CTGACAAACGTACCTGCGCGCGGGCCATGG 1 182 1 TACCTGCGCG 0.562548 -119 CAATCCCTCCTCTCAGCTGCAGTCAAGCGC 3 50 0 TCTCAGCTGC 0.958692 -37 CAATACACGCTGCCCGCGGCGCTGCGCGTG 7 189 1 TGCCCGCGGC 0.836165 -112 TGGGCTATTAGCTCAGCTGGTAGAGCAACG 7 225 1 GCTCAGCTGG 0.884885 -76 AAGTGTGCGCGGTGTGCTGATAGTACATGC 8 11 1 GGTGTGCTGA 0.497569 -290 ACCATATCGCTGTGTGCTGCTTTTAACCCG 8 116 1 TGTGTGCTGC 0.958423 -185 TCCCTCCACGTCCCTGCGCGTACCCAAACC 8 161 0 TCCCTGCGCG 0.799476 -140 TTACCTCGTTTGTGTGTGGGGTACATGCGG 8 207 1 TGTGTGTGGG 0.439879 -94 TGCTCGTTTTTATCTGCTGCTCTGGTCATC 8 267 1 TATCTGCTGC 0.926503 -34 GCTTGCGGCGTATCAGCGGCTGCTGTGCGT 9 43 1 TATCAGCGGC 0.868382 -233 GCCGTTATTATCCGAGTTGCTCGCAGTATG 9 231 1 TCCGAGTTGC 0.517935 -45 TGACGGTAAGGACGTGCTGCAGCACGTGTA 11 12 1 GACGTGCTGC 0.833334 -70 CGTTTGCCCGTGACTGCTCCATCACTTTAC 11 39 0 TGACTGCTCC 0.518395 -43 GGAGCGGGCGTGTAAGCGGCGGCG 11 68 1 TGTAAGCGGC 0.573982 -14 TCTTTTCCATGCTCAGGGGCGAGGCAGTGC 14 12 1 GCTCAGGGGC 0.499819 -84 GCGAGGCAGTGCTCAGCTGGCGTCTCCACT 14 30 1 GCTCAGCTGG 0.884885 -66 CTTGCCCTGCTGCGTATAGTTTC 15 4 1 GCCCTGCTGC 0.963201 -69 TTCTCCGGCGTGTGTGCTGGTGACTGAGTC 15 31 1 TGTGTGCTGG 0.915386 -42 GTGTGTGCTCCTTATATTTTT 16 2 1 TGTGTGCTCC 0.856445 -170 TATCGCCTTTTCCCTGCTGCGGTCAACATC 16 143 0 TCCCTGCTGC 0.973844 -29 ********** Masking position 6 Map Score: 13.6307 Number of sites scoring better than the average of aligned sites = 1715 Number in coding regions = 1583 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 5 AAGACGACCGCGCGTGGGTAGAAAGCTGCG 1 38 1 CGCGTGGGTA 0.898847 -263 TAGAAAGCTGCGAGAGGGTCTGGTTTTGAT 1 56 1 CGAGAGGGTC 0.965447 -245 AACGTACCTGCGCGCGGGCCATGGCGGAGT 1 188 1 CGCGCGGGCC 0.892309 -113 TGAGTCACATGAGGAGGACACAGAGCAT 5 53 1 GAGGAGGACA 0.71766 -18 GGTGAAAAAAGAGGAGGGCCGGGGC 6 61 1 GAGGAGGGCC 0.920264 -15 CGCGGCGCTGCGCGTGGCGCCGTGGGCTAT 7 203 1 CGCGTGGCGC 0.882665 -98 GCCCTTTTAAGGCGTGGGTCGATGGTTCGA 7 254 1 GGCGTGGGTC 0.896689 -47 GGGCACAGGTGAAGAGGGGATAAACTCGTA 8 86 1 GAAGAGGGGA 0.919149 -215 CAACGGAAACCAAGAGGACCAAA 9 4 0 CAAGAGGACC 0.861314 -272 GAAGGCAAAAGATGAGGGGAAAGAGCGCGC 9 199 0 GATGAGGGGA 0.702394 -77 ACCGGCTCCTCGGGAGGAGCCGCGTCAGCA 10 14 0 CGGGAGGAGC 0.959487 -106 GTTCCCCCTACAAGAGGGGATCTTGACGCC 10 42 1 CAAGAGGGGA 0.949276 -78 CTGCTAAGAACACGAGGGTCCACTCTGTAC 10 85 0 CACGAGGGTC 0.948133 -35 TTCTTAGCAGGGGGAGGAGAAATCG 10 105 1 GGGGAGGAGA 0.899465 -15 AGTTTCTGTGCGAGTGGAGACGCCAGCTGA 14 42 0 CGAGTGGAGA 0.838201 -54 AACTGTCTTGCGAGAGGCTAGAGGTGTGTG 16 43 1 CGAGAGGCTA 0.805474 -129 ********** Masking position 6 Map Score: 15.3834 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 515 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 CCCACCGCTCGGTAGAGGAGTAGGACCAGTCC 1 109 1 GGTAGAGGGA 0.876247 -192 GGATGCAGCGGGTGGCGGGGTCTTTTGGACGT 1 245 1 GGTGGCGGGC 0.958165 -56 GCTCCTTGCAGGTAACTGCGCCGTGAAAA 2 11 1 GGTAACTGGC 0.955035 -19 AGAGAGATTAGGAAAATGAGTCACATGAGGAG 5 37 1 GGAAAATGGC 0.909551 -34 CTCCCACGCCGGTGAAGGCACTAGCACCTGAA 7 19 1 GGTGAAGGAT 0.47119 -282 GTACGTGGCGGGCACAGGTGAAGAGGGGATAA 8 77 1 GGCACAGGGA 0.776797 -224 TTGTGTGTGGGGTACATGCGGTATGCCGCAGT 8 216 1 GGTACATGGT 0.89018 -85 TCTTGTAGGGGGAACCGGCTCCTCGGGAGGAG 10 25 0 GGAACCGGTC 0.518348 -95 CTGTACCAAAGGTACCGGAGGCGTCAAGATCC 10 59 0 GGTACCGGGC 0.990953 -61 GTGAGTCTCGGGTAAAGGTTACCCT 12 72 1 GGTAAAGGTC 0.913642 -15 GGCAGCGTGCGGTACAGGGGGTCGGT 13 56 1 GGTACAGGGT 0.969038 -16 CGTGTGTGCTGGTGACTGAGTCGCGGTTGTTA 15 39 1 GGTGACTGGC 0.923943 -34 AACGGGAAAAAGAAACGGGGACTCTCTGAGCA 16 103 0 AGAAACGGGC 0.741589 -69 ACCGCAGCAGGGAAAAGGCGATAATACCCTCC 16 150 1 GGAAAAGGGT 0.925988 -22 ******** * * Masking position 8 Map Score: 10.3915 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 471 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 GCTCCTTGCAGGTAACTGCGCCG 2 4 1 CCTTGCAGGT 0.626124 -26 CGCTCACGCACCTTGCAGAGCA 3 3 0 CCTTGCAGAG 0.826158 -84 GTTTTGCCTACCCTGTAGGGGGGTCAGCGT 6 23 1 CCCTGTAGGG 0.557014 -53 GATTAGAGCAGCTTTCAGGGCACGGGATGC 7 128 1 GCTTTCAGGG 0.886993 -173 AGAGCAACGCCCTTTTAAGGCGTGGGTCGA 7 246 1 CCTTTTAAGG 0.615249 -55 TGCTGATAGTACATGCAGGGAGCAGTTTGT 8 25 1 ACATGCAGGG 0.659181 -276 CCTATTCCTGCCTTTCAGCGGTAAATTCAG 9 99 0 CCTTTCAGCG 0.957337 -177 CAAGATCCCCTCTTGTAGGGGGAACCGGCT 10 37 0 TCTTGTAGGG 0.842837 -83 CTTGCCCTGCTGCGTATAGTTTCT 15 5 1 CCCTGCTGCG 0.884073 -68 TTTCTTTTTCCCGTTTAGGGTCAGATGTTG 16 120 1 CCGTTTAGGG 0.863111 -52 ATCGCCTTTTCCCTGCTGCGGTCAACATCT 16 142 0 CCCTGCTGCG 0.884073 -30 ********** Masking position 4 Map Score: 6.99931 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 383 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 TAACCACCGAGGGCGAGAAACCGACCTGAC 1 157 1 GGGCGAGAAA 0.819113 -144 CGCGGGCCATGGCGGAGTCTATTCTCGGCT 1 200 1 GGCGGAGTCT 0.715695 -101 CACTTCCATCAGCCGAGAATAGACTCCGCC 1 210 0 AGCCGAGAAT 0.935569 -91 CTTGACCAAAGGCTGAGAATGCGGGAAGAT 1 280 1 GGCTGAGAAT 0.86748 -21 CAGGTAACTGCGCCGTGAAAA 2 19 1 CGCCGTGAAA 0.879164 -11 AGCGTACACAACCGGTGAAAAAAGAGGAGG 6 48 1 ACCGGTGAAA 0.755081 -28 GAACTCCCACGCCGGTGAAGGCACTAGCAC 7 16 1 GCCGGTGAAG 0.819848 -285 GGCAGGAATAGGCCGTGAGTGTGCGTCGCT 9 117 1 GGCCGTGAGT 0.886513 -159 CTTAGCAGGGGGAGGAGAAATCG 10 107 1 GGAGGAGAAA 0.688028 -13 CGCTCCGTTTGCCCGTGACTGCTCCATCAC 11 44 0 GCCCGTGACT 0.929923 -38 GGTAACCTTTACCCGAGACTCACGCCATCA 12 65 0 ACCCGAGACT 0.837242 -22 AAAAGAAAGACGCCGAGAATTCAGCGACGC 13 17 1 CGCCGAGAAT 0.940029 -55 CAGCACACACGCCGGAGAAACTATACGCAG 15 20 0 GCCGGAGAAA 0.951167 -53 ********** Masking position 5 Map Score: 6.3078 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 160 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 ACTCCGTTCGCTCACGCACCTTGCAGAGCA 3 11 0 CTCACGCACC 0.832426 -76 GGGGGGTCAGCGTACACAACCGGTGAAAAA 6 40 1 CGTACACAAC 0.911361 -36 GACTTGAACTCCCACGCCGGTGAAGGCA 7 9 1 CTCCCACGCC 0.757683 -292 ATCAGCACACCGCGCACACTT 8 2 0 CGCGCACACT 0.867445 -299 CGCTGCCTACCGTGCACAAACTGCTCCCTG 8 40 0 CGTGCACAAA 0.840255 -261 CGTCCCTGCGCGTACCCAAACCCCTACCGA 8 153 0 CGTACCCAAA 0.450696 -148 CCGCATGTACCCCACACACAAACGAGGTAA 8 207 0 CCCACACACA 0.820146 -94 ACGCGCAGAACTTGGATGACC 8 290 0 CGCGCAGAAC 0.859694 -11 CGCAAGCTGTCTTCCACAACGGAAACCAAG 9 20 0 CTTCCACAAC 0.755357 -256 ACACAAGCGACGCACACTCACGGCCTATTC 9 122 0 CGCACACTCA 0.871415 -154 ACTAAATACCCATGCACACAAGCGACGCAC 9 137 0 CATGCACACA 0.521998 -139 GCCGCTTACACGCCCGCTCCGTTTGCCCGT 11 58 0 CGCCCGCTCC 0.793917 -24 CCGACTGTCCCTCCCACACACGGTGGCGCC 12 20 0 CTCCCACACA 0.921421 -67 CGTCTCCACTCGCACAGAAACTGCTCGTAC 14 50 1 CGCACAGAAA 0.781859 -46 GCTATGGTAGCGTCCAGACCGAT 14 83 1 CGTCCAGACC 0.883576 -13 TGACAGAATTCGCACACACCTCTAGCCTCT 16 55 0 CGCACACACC 0.986184 -117 ********** Masking position 5 Map Score: 11.7882 Number of sites scoring better than the average of aligned sites = 1674 Number in coding regions = 1533 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 10 GGACCAGTCCCGCGGCATACAAGGAGTAAC 1 131 1 CGCGGCATAC 0.677648 -170 CTGTAGGGGGGTCAGCGTACACAACCGGTG 6 35 1 GTCAGCGTAC 0.606038 -41 GGGATGCAAAGGCGGCGTACTTGACAAAAT 7 151 1 GGCGGCGTAC 0.990105 -150 CAGCGCCGCGGGCAGCGTGTATTGGAATTG 7 183 0 GGCAGCGTGT 0.870708 -118 ACACGCTGCCCGCGGCGCTGCGCGTGGCGC 7 193 1 CGCGGCGCTG 0.756709 -108 GCCTTAAAAGGGCGTTGCTCTACCAGCTGA 7 237 0 GGCGTTGCTC 0.878544 -64 GCCCTTTTAAGGCGTGGGTCGATGGTTCGA 7 254 1 GGCGTGGGTC 0.449247 -47 GTGCACGGTAGGCAGCGTGTAAGTGTACGT 8 53 1 GGCAGCGTGT 0.870708 -248 GTAAAAAAACTGCGGCATACCGCATGTACC 8 226 0 TGCGGCATAC 0.660715 -75 TTACAGCAGCGGCGTTGCTCGTTTTTATCT 8 252 1 GGCGTTGCTC 0.878544 -49 GAAGACAGCTTGCGGCGTATCAGCGGCTGC 9 36 1 TGCGGCGTAT 0.810707 -240 GCCGTGAGTGTGCGTCGCTTGTGTGCATGG 9 128 1 TGCGTCGCTT 0.650373 -148 TCCCACACACGGTGGCGCCCAAGACGGC 12 9 0 GGTGGCGCCC 0.677213 -78 CTGAATTCTCGGCGTCTTTCTTTTACCTTT 13 11 0 GGCGTCTTTC 0.709211 -61 CGCGGGTGTCGGCAGCGTGCGGTACAGGGG 13 46 1 GGCAGCGTGC 0.966132 -26 TCAGGGGCGAGGCAGTGCTCAGCTGGCGTC 14 24 1 GGCAGTGCTC 0.878544 -72 ********** Masking position 3 Map Score: 5.36283 Number of sites scoring better than the average of aligned sites = 1606 Number in coding regions = 1480 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 11 TGGACGTTGCCTTGACCAAAGGCTGAGAAT 1 270 1 CTTGACCAAA 0.964773 -31 AGGACACGCGCTTGACTGCAGCTGAGAGGA 3 43 1 CTTGACTGCA 0.967864 -44 GCTCTAATCCCTTGACTAGAAAAACTATAT 7 107 0 CTTGACTAGA 0.912341 -194 AGGCGGCGTACTTGACAAAATGCCAATTCC 7 160 1 CTTGACAAAA 0.946645 -141 CGACAAGATCCTTGACAGAATTCGCACACA 16 67 0 CTTGACAGAA 0.965398 -105 AGGGTCAGATGTTGACCGCAGCAGGGAAAA 16 136 1 GTTGACCGCA 0.914397 -36 ********** Masking position 5 Map Score: 1.42408 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 21 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 ********** No masking Map Score: 4.90518e-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 13 ********** No masking Map Score: 4.90518e-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 14 ********** No masking Map Score: 4.90518e-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