AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00030_tpal_reg_300.orf -o00030_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 TP0261 114 catabolite gene activator, putative #2 TP0278 127 T. pallidum predicted coding region TP0278 #3 TP0279 45 ribosomal protein S1 (rpsA) #4 TP0283 177 lipopolysaccharide core biosynthesis protein (kdtB) #5 TP0284 104 T. pallidum predicted coding region TP0284 #6 TP0289 22 T. pallidum predicted coding region TP0289 #7 TP0290 54 conserved hypothetical protein #8 TP0291 36 T. pallidum predicted coding region TP0291 #9 TP0413 102 phosphoglucomutase #10 TP0475 63 glucose-6-phosphate isomerase (gpi) #11 TP0476 66 acetate kinase (ack) #12 TP0477 60 glucose-6-phosphate 1-dehydrogenase, putative #13 TP0478 72 glucose-6-phosphate 1-dehydrogenase (zwf) #14 TP0479 111 T. pallidum predicted coding region TP0479 #15 TP0560 110 transketolase A (tktA) #16 TP0561 170 conserved hypothetical protein #17 TP0609 300 asparaginyl-tRNA synthetase (asnS) #18 TP0611 141 ABC transporter, ATP-binding protein #19 TP0612 80 conserved hypothetical protein #20 TP0613 26 conserved hypothetical protein #21 TP0615 50 nitrogen fixation protein (nifU) #22 TP0662 266 fructose-bisphosphate aldolase (cbbA) #23 TP0945 151 ribulose-phosphate 3-epimerase (cfxE) Motif number 1 AGAGATCGTTCGCACGCCTTTTCCAGGAAAG 1 15 0 CGCACCCTTT 0.833169 -100 CGCTCCTGCGCGCACACCTGCAGAGATCGTT 1 36 0 CGCACCCTGC 0.974048 -79 ATTCACGTCACGCGCTCCTGCGCGCACACCT 1 48 0 CGCGCCCTGC 0.979293 -67 GCGCTCGTCTTCCTCGGAAGAC 2 2 1 CGCTCTCTTC 0.963391 -126 TGATCACCAGCGCACTCCCTTCCCCACATGG 2 53 0 CGCACCCCTT 0.955338 -75 AGACTGTTTGCGCTCCTCGTCTGTTGTCTGA 2 81 0 CGCTCTCGTC 0.973232 -47 TCCATCATCCGCCCATGAGTGT 2 116 0 CCATCTCCGC 0.942159 -12 ACGGCGCGAACGCTTCTCCTC 4 1 0 CGCTTTCCTC 0.879972 -177 GCGTGAACACCGATTTTCCGCGAGGAGTTGA 4 72 1 CGATTTCCGC 0.749995 -106 TATATTCGCACCCACTCCGTCAACTCCTCGC 4 91 0 CCCACCCGTC 0.923383 -87 GCGATCTTCCTTTTCCCTAAAA 8 25 0 CGATCTCCTT 0.859885 -12 TCCTACCTCTCCCCCGCCCCTACACCC 9 7 1 CTCTCCCCGC 0.955784 -96 GTCAAGACCACCACCTCCCTTGCACTTCCTT 9 59 1 CCACCCCCTT 0.599004 -44 CCTTGCACTTCCTTCACCCGCGCCCTATCCT 9 76 1 CCTTCCCCGC 0.915817 -27 CACCCGCGCCCTATCCTCCGCGC 9 90 1 CTATCTCCGC 0.801383 -13 TGCGCGTTCTCCTTTTATCGTTCTA 10 49 0 CGTTCCCTTT 0.488999 -15 GAACATCCTCCTCTCTCCCGCTACGTTCTAG 12 36 0 CTCTCCCCGC 0.955784 -25 GGGCGAACATCCTCCTCTCTCCCG 12 47 0 CGAACTCCTC 0.9518 -14 AGGCGTTTAGCGCGCGCCGTCAAGTTTTTCT 14 49 1 CGCGCCCGTC 0.977272 -63 GCCCTCCCCCCTTCCTTGCGAAGAGGA 14 95 0 CCCCCTCCTT 0.793608 -17 GCCGTTCATCCTCGGCACCCGCA 16 158 0 CGTTCTCCTC 0.933561 -13 GCGCGGTAATCGTTCACCCGCGCGTCCTTTC 17 23 1 CGTTCCCCGC 0.968557 -278 CACAGAAGACCGCGCCTCGGCCGCTCCTCAT 17 118 1 CGCGCTCGGC 0.978397 -183 GCGCCTCGGCCGCTCCTCATCTAGAGAGTAA 17 129 1 CGCTCTCATC 0.892657 -172 GACGCCACGGCGCACGCCCTGCGCGGCATCT 17 229 0 CGCACCCCTG 0.833272 -72 TGCCGGTCCACGCCCTTCCACAAAGAGGGTA 17 269 1 CGCCCTCCAC 0.916163 -32 GTGGGGGCAGCGCGCCTCCACAAAAGGATAA 19 21 0 CGCGCTCCAC 0.949373 -60 GCGCGCTGCCCCCACGCCAGCAGACCGCATA 19 37 1 CCCACCCAGC 0.807275 -44 GCCAGCAGACCGCATATCCACCGCTTAGAGG 19 52 1 CGCATTCCAC 0.491867 -29 ACGCGCTTCCTCTAAGCGGTGG 19 69 0 CGCGCTCCTC 0.989294 -12 TGCTGCCGTTCCAACGCCTGCGTGTGGACTC 22 124 1 CCAACCCTGC 0.781154 -143 CTCAAGCCTTCGCGCTTCGGTTGACTAGAGC 22 152 1 CGCGCTCGGT 0.90155 -115 GAGAAGCGTGCCACCCTCGGCAAGAGGGGCA 22 201 0 CCACCTCGGC 0.715105 -66 GCAAACAAATCGAGCACCTGTAAATATGGAT 23 119 0 CGAGCCCTGT 0.720275 -33 ***** ***** Masking position 8 Map Score: 53.8102 Number of sites scoring better than the average of aligned sites = 1988 Number in coding regions = 1760 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 CTGCAGAGATCGTTCGCACGCCTTTTCCAGG 1 19 0 CGTTCGCACC 0.614946 -96 CACGCGCTCCTGCGCGCACACCTGCAGAGAT 1 40 0 TGCGCGCACC 0.975425 -75 CGCACCGCACGGCGCGAACGCTTCTCCTC 4 9 0 GGCGCGAACC 0.848138 -169 CGCGCCGTGCGGTGCGCACGTTGTGTAGCTA 4 24 1 GGTGCGCACT 0.896617 -154 TCGGTGTTCACGCGAGCTCTCTACGCTTCCT 4 54 0 CGCGAGCTCC 0.939391 -124 ACCGATTTTCCGCGAGGAGTTGACGGAGTGG 4 80 1 CGCGAGGAGT 0.742842 -98 TTGTTTTTTGGGTGTGCACTTGTTCAAGTTC 7 21 1 GGTGTGCACT 0.669405 -34 GATGAAATCAGGTGTGGTCGGGTGTAGGGGC 9 26 0 GGTGTGGTCG 0.688526 -77 TGCGCGTTCTCCTTTTATCGT 10 53 0 TGCGCGTTCC 0.858975 -11 TGTCGTTCAAGGCTCGGCATTACCG 12 5 0 GGCTCGGCAT 0.549887 -56 TTCTAAAGGCTGCGAGGCAATTATTAGGCGT 14 24 1 TGCGAGGCAT 0.479869 -88 AGGCGTTTAGCGCGCGCCGTCAAGTTTTTCT 14 49 1 CGCGCGCCGC 0.984793 -63 ATCTATAGTGTGCTCGGTGACGCACGGGAAA 15 71 1 TGCTCGGTGC 0.79984 -40 GAGTCTTATAGGCGCGGTAATCGTTCACCCG 17 12 1 GGCGCGGTAT 0.917779 -289 ATCGTTCACCCGCGCGTCCTTTCTGCGGGAG 17 31 1 CGCGCGTCCT 0.802464 -270 TATGTCGTACGGCGTGGTCCCGGTCACAGAA 17 94 1 GGCGTGGTCC 0.972425 -207 GAGCGGCCGAGGCGCGGTCTTCTGTGACCGG 17 113 0 GGCGCGGTCT 0.98231 -188 TTTTTCGCACGGTTCGCTCTCCCCAGTCCTG 17 183 1 GGTTCGCTCC 0.76619 -118 TCCCCAGTCCTGCGCGGCGTTCCATGCAGAT 17 202 1 TGCGCGGCGT 0.944545 -99 GCGCACGCCCTGCGCGGCATCTGCATGGAAC 17 220 0 TGCGCGGCAC 0.936693 -81 CCGCGCAGGGCGTGCGCCGTGGCGTCACAGC 17 234 1 CGTGCGCCGG 0.802431 -67 TTTGTGGAAGGGCGTGGACCGGCAAGCAGCT 17 262 0 GGCGTGGACG 0.857388 -39 GGTTTAATACCGTGCGCAGTGTATGTCCTAC 18 20 0 CGTGCGCAGG 0.716059 -122 CTGTGCAGGATGCGTGGTCTCTTTCCCTTGC 18 63 1 TGCGTGGTCC 0.938488 -79 CTTTTGTGGAGGCGCGCTGCCCCCACGCCAG 19 26 1 GGCGCGCTGC 0.987986 -55 ACTGCTGTGCGCCCTCAGGAAGGGAG 20 11 0 TGTGCGCCCC 0.942655 -16 ATGCCAGGAAGGCGCACTGGC 21 1 0 GGCGCACTGC 0.687071 -50 AGCTGGCGCCTGCGAGGCGTTAGGGGTGGTG 22 26 0 TGCGAGGCGT 0.742842 -241 GCTAGAATGCGGCGAGCTGGCGCCTGCGAGG 22 40 0 GGCGAGCTGC 0.933339 -227 TCAAACCTCCCGCGTGGTACCTGTCCAAATC 22 89 1 CGCGTGGTAC 0.831624 -178 CCAACGCCTGCGTGTGGACTCAAGCCTTCGC 22 134 1 CGTGTGGACC 0.815491 -133 ********* * Masking position 2 Map Score: 35.689 Number of sites scoring better than the average of aligned sites = 4452 Number in coding regions = 4088 Number in noncoding regions = 364 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 3 AAGCGGCAGTCCATGTGGGGAAGGGAGTGCGCT 2 43 1 CATGTGGGAG 0.807941 -85 GGGTGAAAAACGAAGAAGGGAAGTACAGGGCAG 3 21 0 CAAGAAGGAG 0.974908 -25 CGTTGTGTAGCTAGGAAGCGTAGAGAGCTCGCG 4 42 1 CAGGAAGGAG 0.850021 -136 GAAAGTGGCGCATTTTGCGTGTA 11 1 1 GAAGTGGGAT 0.953546 -66 GAGAAATTACCAAAACGGTGGAGGTGTATT 11 47 1 CAAACGGGAG 0.893219 -20 AACGTAGCGGGAGAGAGGAGGATGTTCGCCC 12 40 1 GGAGAGGGAT 0.857469 -21 TCGCACCGTTGAAAGAAGGGGCGGTTT 13 56 1 GAAGAAGGCG 0.901545 -17 GCAGCCTTTAGAAAAAGGAGGAGCTC 14 4 0 GAAAAGGGAG 0.950333 -108 CCCTTCCTTGCGAAGAGGAGTATGCCAAACGGT 14 81 0 CAAGAGGGAT 0.980585 -31 AGTCTCTCTTGGAAGAGGTGTATCTATAGTGTG 15 50 1 GAAGAGGGAT 0.977944 -61 AAAACCAGATGCAAGTAGAGTATCAGAAACACT 17 60 0 GAAGTAGGAT 0.896247 -241 GCGAACCGTGCGAAAAAGCGTCGTTTCATTTCC 17 167 0 CAAAAAGGCG 0.711175 -134 CGCGCTTCCTCTAAGCGGTGGATATGCGGTCTG 19 57 0 CAAGCGGGAT 0.950943 -24 GCCACCCTCGGCAAGAGGGGCATGGTAGGGCGA 22 190 0 GAAGAGGGAT 0.977944 -77 AGAAGAGTCACGAAATAGAGAAGCGTGCCACCC 22 216 0 CAAATAGGAG 0.809384 -51 * ****** * ** Masking position 8 Map Score: 17.4087 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 240 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TGCAGGTGTGCGCGCAGGAGCGCGTGACGTGA 1 45 1 CGCGCAGGAG 0.95186 -70 AGCGGCAGTCCATGTGGGGAAGGGAGTGCGCT 2 44 1 CATGTGGGGG 0.70407 -84 ACCGATTTTCCGCGAGGAGTTGACGGAGTGGG 4 80 1 CGCGAGGAGG 0.79948 -98 TCCTGAACAACGTGAGGGGTTGCCGTGC 4 160 1 CGTGAGGGGG 0.98514 -18 GGTTGAGTGATCTTCGGGGCTGTGCTTTTAAA 5 51 1 TCTTCGGGGG 0.937098 -54 GTAGGTAAACCCTACGGGGTAGAACGATAAAA 10 30 1 CCTACGGGGG 0.975013 -34 TGCCTTAGGGAGCGGAGAGTCTGC 13 3 1 CCTTAGGGAG 0.945408 -70 ATCCTCGGCACCCGCAGGGCCGACACGACGGT 16 142 0 CCCGCAGGGG 0.972897 -29 GCGCGTCCTTTCTGCGGGAGTGTTTCTGATAC 17 42 1 TCTGCGGGAG 0.945901 -259 TTTTCTATGTCGTACGGCGTGGTCCCGGTCAC 17 89 1 CGTACGGCGG 0.753508 -212 CATGGAACGCCGCGCAGGACTGGGGAGAGCGA 17 196 0 CGCGCAGGAG 0.95214 -105 GAATGTATGTTGCAAGGGAAAGAGACCACGCA 18 73 0 TGCAAGGGAG 0.674677 -69 CTGCTGTGCGCCCTCAGGAAGGGAG 20 4 0 CCCTCAGGAG 0.897588 -23 AGGGAGATCTCCTTAGAGAAAGGCAGCGAATG 21 29 0 CCTTAGAGAG 0.462478 -22 GCCTGCGAGGCGTTAGGGGTGGTGAAAAGGAG 22 18 0 CGTTAGGGGG 0.969044 -249 GGTCAGCCTACCCGCGGGAAGGATATTTTTCT 23 16 1 CCCGCGGGAG 0.989776 -136 CTGTCTTGAATGTTTGGGGTTGTTCACGCCAG 23 86 1 TGTTTGGGGG 0.696523 -66 ********* * Masking position 12 Map Score: 18.3869 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 822 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 TTGTGTAGTTCGCCGCATGTTCCTGAACAACGTGA 4 140 1 CCGCATCCTG 0.868752 -38 GTGCGACCTACACCGGATGTGCCGCAGGCAGACTC 13 27 0 CCGGAGCCGC 0.991358 -46 CTCGGTGACGCACGGGAAAAGCATAAGGAGTGAGA 15 83 1 CCGGAGCATA 0.826061 -28 CGCACACTATCTTAGCACCTGCCTCTTACCCATAC 16 82 0 CTGCAGCCTC 0.977861 -89 GCCGTTCATCCTCGGCACCCGCAGGGCCGACACGA 16 146 0 CCGCAGCAGG 0.991962 -25 GCACGCCCTGCGCGGCATCTGCATGGAACGCCGCG 17 214 0 CCGCAGCATG 0.981371 -87 TCAGTTTACTCCTTGCAGGAGCCGCTC 18 125 1 CTGCAGCCGC 0.99043 -17 AGTGCGCCTTCCTGGCATTCGCTGCCTTTCTCTAA 21 14 1 CTGCAGCTGC 0.941203 -37 ACCCCTAACGCCTCGCAGGCGCCAGCTCGCCGCAT 22 30 1 CTGCAGCCAG 0.930674 -237 CACACGCAGGCGTTGGAACGGCAGCAAGACGATTT 22 115 0 CTGGAGCAGC 0.974241 -152 GCGCAAATAAAACAGGATAAGCAGGACACTGTCTT 23 58 1 ACGGAGCAGG 0.85003 -94 * * *** ***** Masking position 7 Map Score: 10.7808 Number of sites scoring better than the average of aligned sites = 385 Number in coding regions = 353 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 CACCGATTTTCCGCGAGGAGTTGACGGAGT 4 79 1 CCGCGAGGAG 0.916995 -99 ACCGGATGTGCCGCAGGCAGACTCTCCGCT 13 21 0 CCGCAGGCAG 0.992725 -52 CCCATACAAACCACGGCAAGGATTGCCTAC 16 59 0 CCACGGCAAG 0.955552 -112 AGAAACACTCCCGCAGAAAGGACGCGCGGG 17 39 0 CCGCAGAAAG 0.956209 -262 GGGCGTGGACCGGCAAGCAGCTGTGACGCC 17 254 0 CGGCAAGCAG 0.879573 -47 TGCTGTGCGCCCTCAGGAAGGGAG 20 5 0 CCTCAGGAAG 0.974652 -22 GGCGTTGGAACGGCAGCAAGACGATTTGGA 22 112 0 CGGCAGCAAG 0.958675 -155 AGGCTTGAGTCCACACGCAGGCGTTGGAAC 22 131 0 CCACACGCAG 0.840028 -136 AGCGTGCCACCCTCGGCAAGAGGGGCATGG 22 198 0 CCTCGGCAAG 0.955548 -69 GTCAGCCTACCCGCGGGAAGGATATTTTTC 23 17 1 CCGCGGGAAG 0.994368 -135 ********** Masking position 9 Map Score: 11.6338 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 176 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 7 GCAAATAAGCGGCAGTCCATGTGGGGAAGGG 2 37 1 GGCGTCCATG 0.970952 -91 GGAAGTACAGGGCAGAAAACGGAAG 3 5 0 GGCGAAAACG 0.702172 -41 TCAACGGTGCGACCTACACCGGATGTGCCGC 13 37 0 GACTACACCG 0.860574 -36 TCACGCGTTTGGCGTACAATGCCCC 16 5 0 GGCTACAATG 0.958316 -166 AGTCCTGCGCGGCGTTCCATGCAGATGCCGC 17 207 1 GGCTTCCATG 0.968605 -94 ACAGCTGCTTGCCGGTCCACGCCCTTCCACA 17 260 1 GCCGTCCACG 0.927601 -41 GCCAAGGTAGGACATACACTGCGCACGGTAT 18 14 1 GACTACACTG 0.850681 -128 GCGCCTTCCTGGCATTCGCTGCCTTTCTCTA 21 17 1 GGCTTCGCTG 0.884582 -34 CGTCCCGATCGCCCTACCATGCCCCTCTTGC 22 182 1 GCCTACCATG 0.94111 -85 CCCGCGGGTAGGCTGACCCCGTC 23 3 0 GGCGACCCCG 0.982883 -149 *** ******* Masking position 3 Map Score: 5.83241 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 161 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 AAGCGTTCGCGCCGTGCGGTGCGCACGTTG 4 17 1 GCCGTGCGGT 0.946134 -161 AGTTGCCGTGTTGTTTTTTGGGTG 7 5 1 GCCGTGTTGT 0.925554 -50 CGGTAATGCCGAGCCTTGAACGACACT 12 8 1 GCCGAGCCTT 0.771346 -53 AGAAAAAGAAACCGTGCTGTGCTAGGAGCA 15 12 0 ACCGTGCTGT 0.924386 -99 GGCAATCCTTGCCGTGGTTTGTATGGGTAA 16 62 1 GCCGTGGTTT 0.94491 -109 TTTTTGCAGTACCGTCGTGTCGGCCCTGCG 16 132 1 ACCGTCGTGT 0.914825 -39 ATGAGGAGCGGCCGAGGCGCGGTCTTCTGT 17 119 0 GCCGAGGCGC 0.949852 -182 CAGGGCGTGCGCCGTGGCGTCACAGCTGCT 17 239 1 GCCGTGGCGT 0.994399 -62 TGTATGTCCTACCTTGGCGTT 18 2 0 ACCTTGGCGT 0.915923 -140 CCGTTCCAACGCCTGCGTGTGGACTCAAGC 22 129 1 GCCTGCGTGT 0.715075 -138 GTGGACTCAAGCCTTCGCGCTTCGGTTGAC 22 147 1 GCCTTCGCGC 0.867976 -120 ********** Masking position 3 Map Score: 9.04959 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 272 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 CTGATCACCAGCGCACTCCCTTCCCCACAT 2 55 0 GCGCACTCCC 0.990913 -73 CTATTTATATTCGCACCCACTCCGTCAACT 4 97 0 TCGCACCCAC 0.759608 -81 AACTTTAAAAGCACAGCCCCGAAGATCACT 5 56 0 GCACAGCCCC 0.804697 -49 GCGATCTTCCTTTTCCCTAA 8 27 0 GCGATCTTCC 0.777545 -10 TCCTACCTCTCCCCCGCCCCTAC 9 4 1 TACCTCTCCC 0.776287 -99 ATCCTGTCAAGACCACCACCTCCCTTGCAC 9 54 1 GACCACCACC 0.723678 -49 GAGCTCCTCCTTTTTCTAAA 14 1 1 GAGCTCCTCC 0.939072 -111 GCCCTCCCCCCTTCCTTGCG 14 102 0 GCCCTCCCCC 0.989786 -10 TTCGCACGGTTCGCTCTCCCCAGTCCTGCG 17 186 1 TCGCTCTCCC 0.961769 -115 TGACGCCACGGCGCACGCCCTGCGCGGCAT 17 231 0 GCGCACGCCC 0.975528 -70 TTGTGGAGGCGCGCTGCCCCCACGCCAGCA 19 29 1 GCGCTGCCCC 0.982025 -52 TTTCTCTAAGGAGATCTCCCT 21 40 1 GAGATCTCCC 0.909058 -11 GAGAACCCCCTTTGTTAGGA 22 257 0 GAGAACCCCC 0.950159 -10 ********** Masking position 10 Map Score: 15.8103 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 688 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 10 TCCTGGAAAAGGCGTGCGAACGATCTCTGC 1 18 1 GGCGTGCGAA 0.907348 -97 CAACAGACGAGGAGCGCAAACAGTCTCAGA 2 86 1 GGAGCGCAAA 0.963692 -42 AGGGGTGAAAAACGAAGAAGG 3 35 0 GGGGTGAAAA 0.846288 -11 TGACGGAGTGGGTGCGAATATAAATAGTGC 4 100 1 GGTGCGAATA 0.676881 -78 ATCACTCAACCGAGTGAGAAAAAGAATCAT 5 32 0 CGAGTGAGAA 0.89023 -73 GAACGTAGCGGGAGAGAGGAGGATGTTCGC 12 39 1 GGAGAGAGGA 0.844976 -22 TATGCCAAACGGTGAGAAAAACTTGACGGC 14 64 0 GGTGAGAAAA 0.878172 -48 AAAAGCATAAGGAGTGAGAACA 15 99 1 GGAGTGAGAA 0.971455 -12 GAGAGCGAACCGTGCGAAAAAGCGTCGTTT 17 174 0 CGTGCGAAAA 0.780113 -127 GCAGGACTGGGGAGAGCGAACCGTGCGAAA 17 185 0 GGAGAGCGAA 0.960696 -116 CTAGTCAACCGAAGCGCGAAGGCTTGAGTC 22 150 0 GAAGCGCGAA 0.799102 -117 ********** Masking position 10 Map Score: 6.14553 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 220 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 CTTCCGAGGAAGACGAGCGC 2 1 0 AGACGAGCGC 0.917338 -127 TTGTCTGATCACCAGCGCACTCCCTTCCCC 2 59 0 ACCAGCGCAC 0.96862 -69 ACACAACGTGCGCACCGCACGGCGCGAACG 4 20 0 CGCACCGCAC 0.712083 -158 GAACTTTAAAAGCACAGCCCCGAAGATCAC 5 57 0 AGCACAGCCC 0.883874 -48 CTGAACTTGAACAAGTGCACACCCAAAAAA 7 24 0 ACAAGTGCAC 0.819519 -31 TCCCTAAAAAAGCACTGCCCTCT 8 4 0 AGCACTGCCC 0.817774 -33 CCGCCCCTACACCCGACCACACCTGATTTC 9 24 1 ACCCGACCAC 0.861292 -79 CATCCTGTCAAGACCACCACCTCCCTTGCA 9 53 1 AGACCACCAC 0.611009 -50 CACTTCCTTCACCCGCGCCCTATCCTCCGC 9 81 1 ACCCGCGCCC 0.940608 -22 AATACACCTCCACCGTTTTGGTA 11 54 0 ACACCTCCAC 0.42672 -13 CTGCTCCTAGCACAGCACGGTTTCTTTT 15 9 1 AGCACAGCAC 0.923969 -102 TAGATGTCTGACAAGCGCACACTATCTTAG 16 102 0 ACAAGCGCAC 0.925144 -69 GTAATCGTTCACCCGCGCGTCCTTTCTGCG 17 28 1 ACCCGCGCGT 0.625248 -273 TCCCGGTCACAGAAGACCGCGCCTCGGCCG 17 111 1 AGAAGACCGC 0.841835 -190 CTGGCGTGGGGGCAGCGCGCCTCCACAAAA 19 27 0 GGCAGCGCGC 0.926749 -54 CCCCCACGCCAGCAGACCGCATATCCACCG 19 45 1 AGCAGACCGC 0.930038 -36 GCCAGTGCGCCTTCCTGGCA 21 1 1 GCCAGTGCGC 0.788872 -50 CACGAAATAGAGAAGCGTGCCACCCTCGGC 22 211 0 AGAAGCGTGC 0.50343 -56 ********** Masking position 8 Map Score: 14.6576 Number of sites scoring better than the average of aligned sites = 2237 Number in coding regions = 2079 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 12 GTGCGCTGGTGATCAGACAACAGACGAGGA 2 69 1 GATCAGACAA 0.845844 -59 CCCTCACGTTGTTCAGGAACATGCGGCGAA 4 148 0 GTTCAGGAAC 0.867241 -30 CACATACTCAGCTCATGCAAT 5 2 0 GCTCATGCAA 0.779297 -103 TGCTTTTAAAGTTCAGAAAAGTTTTGAGCA 5 73 1 GTTCAGAAAA 0.932793 -32 GAGACTGCCCGTACAGAAAAAGAAACCGTG 15 26 0 GTACAGAAAA 0.896424 -85 GCTCGGTGACGCACGGGAAAAGCATAAGGA 15 82 1 GCACGGGAAA 0.902413 -29 ATTGCCTACCGATCAGGAAAGCTATACACC 16 38 0 GATCAGGAAA 0.961186 -133 CACGCATCCTGCACAGGAAACACATACAGG 18 49 0 GCACAGGAAA 0.972077 -93 ********** Masking position 9 Map Score: 1.69875 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 192 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 ********** No masking Map Score: 2.16959e-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: 2.16959e-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 15 ********** No masking Map Score: 2.16959e-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