AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_tpal_reg_300.orf -o00190_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 TP0382 83 T. pallidum predicted coding region TP0382 #2 TP0383 27 conserved hypothetical protein #3 TP0390 45 cell division protein (ftsZ) #4 TP0394 32 DNA topoisomerase I (topA) #5 TP0396 147 flagellar basal-body rod protein (flgB) #6 TP0397 84 flagellar basal-body rod protein (flgC) #7 TP0398 55 flagellar hook-basal body complex protein (fliE) #8 TP0399 116 flagellar basal-body M ring protein (fliF) #9 TP0401 47 flagellar assembly protein (fliH) #10 TP0402 27 flagellum-specific ATP synthase (fliI) #11 TP0418 26 galactokinase #12 TP0421 133 conserved hypothetical protein #13 TP0423 24 conserved hypothetical protein #14 TP0424 202 V-type ATPase, subunit E, putative #15 TP0426 141 V-type ATPase, subunit A (atpA-1) #16 TP0430 36 V-type ATPase, subunit K (atpK-1) #17 TP0527 94 V-type ATPase, subunit D (atpD-2) #18 TP0531 300 V-type ATPase, subunit F, putative #19 TP0535 140 T. pallidum predicted coding region TP0535 #20 TP0536 149 T. pallidum predicted coding region TP0536 #21 TP0537 150 triosephosphate isomerase (tpi) Motif number 1 ACGTCCACCCCCCCCCCCCCGACGAGA 1 5 1 CCCCCCCCCC 0.998754 -79 AAAAGAACATTGTCACCCATACCGTTGCCGGTT 1 38 1 TGCACCCACC 0.648862 -46 GATTTCCTACCTTCCCCTATATTTTT 2 12 0 TTCTACCCCC 0.743536 -16 TCCCCTCCCATTCCCCTACACCGC 3 32 0 CCCTCCCTCC 0.981386 -14 GTTTTCCGCCCCCTATGCTTACCGAAAC 4 15 0 CCCCCCCTGC 0.987055 -18 GTTTGGACGCTCCGTTCCTACCCC 5 2 0 TCGTTCCCCC 0.808486 -146 ACATTCTCTGCAGCTCGCTTCCCCGCATCGTTT 5 31 0 CACTCGCCCC 0.802736 -117 CCGACTACCCCCGACCCATTGTCGACC 5 131 0 CTCCCCCCCC 0.996293 -17 ACCCATCACGCTTCTCCATACGC 6 1 0 CTCTCCACGC 0.937351 -84 CCAAGCGCTGCGCGCTCATACCCGTCGCGGCAA 6 53 0 CGGCTCACCC 0.749072 -32 ATCGGCCCGCCAAGCGCTGCGCGCT 6 70 0 CGCCCGCAGC 0.918263 -15 TGTATCCTCCCCTCACACAGCACAGACATCT 7 35 0 CCCTCACAGC 0.871127 -21 GCGCACTAAGCGCGTCCCACCCTCTTTTCACCT 8 59 0 CGGTCCCCCT 0.834362 -58 CACTATAGAACGAGCCAATGCGCACTAAGCGCG 8 78 0 CGGCCAACGC 0.66022 -39 GCGTGTCCCCTCCCCTCACTATAG 8 103 0 CGGTCCCCCC 0.991069 -14 ACACGCACACCCACGCCTCTTTCTCT 10 12 0 CGACACCCGC 0.604934 -16 CAGACGCACACCACGCCCTATCC 12 1 0 CCCGCCCTCC 0.877353 -133 TTCGACCATCCGGCTCCACACGCTACGGGACAA 14 38 0 CGCTCCACGC 0.964281 -165 ACTATACGTTCTCCTCGCAGCCCTCCGAGTATA 14 105 0 CTCTCGCCCC 0.962706 -98 GTAAGCAACATCAGCTGCAGCCCGTACAAAAAC 15 41 0 TCGCTGCCCC 0.548765 -101 AGAAATCACCCTTCTCCAAGAGCCTTATAGGAC 17 20 0 CTCTCCAAGC 0.713894 -75 CTCTGTATCCTCTCCCTGCGTGGCCAAGACA 17 74 0 CCCTCCCCGT 0.946076 -21 CCAACGCAAGCGAGCCCCACCGCGAGTCCTGCG 18 123 0 CGGCCCCCGC 0.993808 -178 TACTGCAAGGCCTCCCCCAACGCAAGCGAGCCC 18 139 0 CCCCCCCCGC 0.998508 -162 TCCTCACTCATTGCCCCCATCGCTGCAGCCCCG 18 180 0 TTCCCCCCGC 0.974617 -121 GCACATCGACCTACTCCCGTACC 19 1 0 CTCTCCCACC 0.9628 -140 GCGGCCGCATCCTCCACCTCCGCTAGGCGGACC 19 82 0 CCCCACCCGC 0.986505 -59 CCGTGCGCCTGCTCCTGCGCCTTCTCCACG 19 121 0 CCGCTCCCGC 0.972745 -20 TTACGCAATACCGCACACCACCCAGAATCCTTT 20 19 0 CCCACACCCC 0.918214 -131 CTTCAACCTTTCACTCCCTGTCCCGAGAACAGA 20 90 0 TCCTCCCTCC 0.900193 -60 GCCAGGAGATCTCGCCCCAACCCAAGGGAAAAT 21 30 0 CTGCCCCCCC 0.990699 -121 TTCGTTCACACCACAAACACCCCGCCGATAGCT 21 107 0 CCCAAACCCC 0.550767 -44 ATCCCCTCCTTAGCACATCCTTTC 21 137 0 TCCCTCCAGC 0.71984 -14 ** ***** *** Masking position 13 Map Score: 55.3865 Number of sites scoring better than the average of aligned sites = 2346 Number in coding regions = 2026 Number in noncoding regions = 320 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 2 CTCGTCGGGGGGGGGGGGGTGGACGT 1 4 0 GGGGGGGGGA 0.994162 -80 ACCGCGCACAGCATGCGGCACGCGGTGTAGGGG 3 11 1 GCGCGGCCGC 0.878484 -35 CGGTGTAGGGGAATGGGAGGGGA 3 33 1 GAGGGAGGGA 0.959912 -13 TTTCGGTAAGCATAGGGGGCGGAAAAC 4 16 1 CAGGGGGGGA 0.97696 -17 AACGATGCGGGGAAGCGAGCTGCAGAGAATGTA 5 32 1 GGGCGAGTGC 0.748915 -116 GTCGACAATGGGTCGGGGGTAGTCGG 5 132 1 GGGGGGGAGT 0.904579 -16 GGTGAAAAGAGGGTGGGACGCGCTTAGTGCGCA 8 60 1 GGGGGACCGC 0.9688 -57 TATAGTGAGGGGAGGGGACACGC 8 104 1 GGGGGACCGC 0.968802 -13 TATGGGGTTCGAAAGGAAGCAGACAGT 9 31 1 GAGGAAGAGA 0.384539 -17 TAGTTTGTCCCGTAGCGTGTGGAGCCGGATGGT 14 34 1 CGGCGTGGGA 0.750225 -169 AAAAAGTCCCCACCGGGACAAGCATAACACACT 14 70 0 CAGGGACAGC 0.8771 -133 ATACTCGGAGGGCTGCGAGGAGAACGTATAGTG 14 106 1 GGGCGAGAGA 0.890948 -97 GTTGCCTCTTCCGAGGAGCAGGCGTCTCGT 14 183 1 CCGGAGCGGC 0.840324 -20 AAGACACACAGCAAGGGAGCGCCGCAAAGAAAT 17 47 0 GCGGGAGGCC 0.817984 -48 GTCTTGGCCACGCAGGGAGAGGATACAGAG 17 75 1 CGGGGAGGGA 0.983554 -20 ATCTACATGAGAGGGCGGCTGACTCTCCGCGTT 18 70 0 GAGCGGCGAC 0.802238 -231 GCAGGACTCGCGGTGGGGCTCGCTTGCGTTGGG 18 124 1 CGGGGGCCGC 0.982138 -177 GGCTCGCTTGCGTTGGGGGAGGCCTTGCAGTAG 18 140 1 CGGGGGGGGC 0.995783 -161 GGGGCTGCAGCGATGGGGGCAATGAGTGAGGAT 18 181 1 CGGGGGGAAT 0.507165 -120 TATTACCAACCCACGCGGCCGACACTCAGCGAG 19 33 0 CCGCGGCGAC 0.749501 -108 GTCCGCCTAGCGGAGGTGGAGGATGCGGCCGCT 19 83 1 CGGGTGGGGA 0.835758 -58 TCTCCACGAGGACAGCGGCCGCATCCTCCACCT 19 96 0 GAGCGGCGCA 0.656608 -45 GTGGAGAAGGCGCAGGAGCAGGCGCACGG 19 122 1 CGGGAGCGGC 0.94687 -19 CTGTTCTCGGGACAGGGAGTGAAAGGTTGAAGT 20 91 1 GAGGGAGGAA 0.767233 -59 TTTTCCCTTGGGTTGGGGCGAGATCTCCTGGCG 21 31 1 GGGGGGCAGA 0.973404 -120 ** ***** *** Masking position 5 Map Score: 32.2071 Number of sites scoring better than the average of aligned sites = 1851 Number in coding regions = 1616 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 CCCCCCCCCCGACGAGAAAAAGAACATTGTC 1 21 1 GAGAGAAAAA 0.691308 -63 ACCCATTGTCGACCAAAAAAAAGCGAGCTTA 5 114 0 GACAAAAAAA 0.639937 -34 CTTTCCCCTGCCAGAAAAGCATTT 11 13 1 CCGAAAAGCA 0.795152 -14 AGACTACCTCGAACAGACGCACACCACGCCC 12 16 0 GACAGACGCA 0.908063 -118 GAGCACGCAGGCCAAGACAAAGAGACTACCT 12 38 0 GCAAGACAAA 0.658661 -96 CAAACAAAAAGCAGAGAGAAAAAAGGAGCAC 12 63 0 GCGAGAGAAA 0.928396 -71 CACAAAAGGTGCACAAACAAAAAGCAGAGAG 12 76 0 GCCAAACAAA 0.886066 -58 AAGAGACTGCGCTGAAAGGCA 12 123 1 GCGAAAGGCA 0.919534 -11 AGAGCGATGACAGGAGAGGCAGTAGTTTGTC 14 12 1 CAGAGAGGCA 0.827172 -191 GACCCGTTTTCCTCAGAGGCAGTGTTTTTGT 15 18 1 CCCAGAGGCA 0.962546 -124 CAAGGGAGCGCCGCAAAGAAATCACCCTTCT 17 38 0 CCCAAAGAAA 0.864667 -57 TCCCTGCGTGGCCAAGACACACAGCAAGGGA 17 62 0 GCAAGACACA 0.804775 -33 ACGCACAAGCCAGCAAACACACCCGTAAACC 18 32 0 CACAAACACA 0.765103 -269 GCTTCTTAACGCGGAGAGTCAGCCGCCCTCT 18 63 1 GCGAGAGTCA 0.731626 -238 CCTGAAATTTCAGGAAAGGCACTTCCCTTTA 18 214 1 CAGAAAGGCA 0.691393 -87 CCAAAAAACCCCACAGACAAATGCCTTCTGC 18 253 0 CCCAGACAAA 0.91163 -48 CGTGGAGAAGGCGCAGGAGCAGGCGCACGG 19 121 1 GCCAGGAGCA 0.683996 -20 CATGTGAACGGCACAAAAAAAGAAACCTGCT 20 51 0 GCCAAAAAAA 0.849148 -99 CCTGTCCCGAGAACAGAAAAACGACCATGTG 20 76 0 GACAGAAAAA 0.791529 -74 ACCAAAGCGTGCGCAAAAACAAGGACTTCAA 20 117 0 GCCAAAAACA 0.923226 -33 TATAGAGCCACCGCAGAGACATACCCTCGCC 21 60 0 CCCAGAGACA 0.966842 -91 ** ******** Masking position 5 Map Score: 19.9526 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 935 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 TTCTGAGACTTTTTTGAAGAAGACTTTCTTA 5 85 1 TTTTGAAGAA 0.642199 -63 GCGTATGGAGAAGCGTGATGGG 6 2 1 CGTTGGAGAA 0.84476 -83 GTCGGTACTCTTTTTGCAGAACAGCCCGGCC 8 20 0 TTTTGCAGAA 0.877393 -97 TTTTGTGAGCTTTCTGGAGAAAGAAGAGACT 12 100 1 TTTTGGAGAA 0.941625 -34 CTGTCATGGGGAAAGCGAATTTA 13 3 1 GTCTGGGGAA 0.954408 -22 TATTATACAATTCTTGGAGCATATAC 15 126 1 TTCTGGAGCA 0.965111 -16 TCCTATAAGGCTCTTGGAGAAGGGTGATTTC 17 21 1 CTCTGGAGAA 0.989862 -74 CAGCCGCCCTCTCATGTAGATGGCGGCTTAA 18 82 1 CTCTGTAGAT 0.710889 -219 CCCACCGCGAGTCCTGCGGCAATGTATTTTA 18 110 0 GTCTGCGGCA 0.838512 -191 CCCTTTATCGGTCTTGCAGAAGGCATTTGTC 18 238 1 GTCTGCAGAA 0.963965 -63 GGCCGCTGTCCTCGTGGAGAAGGCGCAGGAG 19 109 1 CTCTGGAGAA 0.989925 -32 AGAACAGTTTCTCGTGGAGCTATCGGCGGGG 21 90 1 CTCTGGAGCT 0.924868 -61 *** ******* Masking position 5 Map Score: 10.3557 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 146 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 AATGTACACCAGTGCGAAGTGCTTTTTTCTGAG 5 59 1 AGGCGAGGCT 0.985289 -89 CGTATGGAGAAGCGTGATGGGTTTGTTTAGTGG 6 12 1 AGGTGAGGTT 0.954418 -73 GACGGGTATGAGCGCGCAGCGCTTGGCGGGCCG 6 60 1 AGGCGCGGCT 0.724953 -25 ATGTCTGTGCTGTGTGAGGGGAGGATACA 7 37 1 TGGTGAGGAG 0.920313 -19 AGGTGAAAAGAGGGTGGGACGCGCTTAGTGCGC 8 59 1 AGGTGGAGCG 0.770747 -58 GGCTCGTTCTATAGTGAGGGGAGGGGACACGC 8 95 1 ATGTGAGGAG 0.570406 -22 GGATAGGGCGTGGTGTGCGTCTGTTCG 12 5 1 AGGCGTGGTG 0.957671 -129 GAGAGCGATGACAGGAGAGGCAGT 14 2 1 AGGCGAGCAG 0.872586 -201 TTTGTCCCGTAGCGTGTGGAGCCGGATGGTCGA 14 37 1 AGGTGTGGCC 0.878925 -166 TGGAGCCGGATGGTCGAAGTGTGTTATGCTTGT 14 53 1 TGTCGAGGTG 0.808501 -150 GACCGAATTAAGCGCGAAGCGTTGCCTCTTCCG 14 163 1 AGGCGAGGTT 0.955874 -40 AGGTAGAAAAAGAGTGGAGGGCTCGTT 16 20 1 AGGTGGGGCT 0.970635 -17 GTACGGGAGTAGGTCGATGTGCTCGCTGAGTGT 19 12 1 AGTCGAGGCT 0.929876 -129 ATGTGCTCGCTGAGTGTCGGCCGCGTGGGTTGG 19 28 1 TGGTGTGCCG 0.844834 -113 TAAAGGATTCTGGGTGGTGTGCGGTATTGCGTA 20 18 1 TGGTGGGGCG 0.96694 -132 AGGGAGTGAAAGGTTGAAGTCCTTGTTTTTGCG 20 104 1 AGTTGAGCCT 0.726896 -46 ATCGGCGGGGTGTTTGTGGTGTGAACGAAAGGA 21 111 1 TGTTGTGGTG 0.632051 -40 ** **** * *** Masking position 6 Map Score: 17.4648 Number of sites scoring better than the average of aligned sites = 1223 Number in coding regions = 1099 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 ACACCGCGTGCCGCATGCTGTGCGCGGT 3 9 0 CCGCATGCTG 0.892456 -37 CCGCCAAGCGCTGCGCGCTCATACCCGTCG 6 59 0 CTGCGCGCTC 0.931975 -26 GCGTGTCCCCTCCCCTCACTAT 8 105 0 GTGTCCCCTC 0.738751 -12 ACTGTCTGCTTCCTTTCGAAC 9 37 0 CTGTCTGCTT 0.866633 -11 GGCGTGGTGTGCGTCTGTTCGAGGTAGTCT 12 17 1 GCGTCTGTTC 0.713269 -117 TTGTCTTGGCCTGCGTGCTCCTTTTTTCTC 12 49 1 CTGCGTGCTC 0.958267 -85 ACGAGACGCCTGCTCCTCGGAAGAG 14 188 0 ACGCCTGCTC 0.947376 -15 GCTTTGGACCCCGCCTGCATTGTGAAACGC 15 83 0 CCGCCTGCAT 0.834222 -59 ATAAAGAGCTGCGTATGCTTTGGACCCCGC 15 99 0 GCGTATGCTT 0.856549 -43 CTCTGTATCCTCTCCCTGCGTG 17 83 0 CTGTATCCTC 0.69741 -12 TTGCTGGCTTGTGCGTGCTTCTTAACGCGG 18 47 1 GTGCGTGCTT 0.878707 -254 GGAGAGTCAGCCGCCCTCTCATGTAGATGG 18 75 1 CCGCCCTCTC 0.928321 -226 AGGACAGCGGCCGCATCCTCCACCTCCGCT 19 91 0 CCGCATCCTC 0.954251 -50 GCCTGCTCCTGCGCCTTCTCCACGAGGACA 19 115 0 GCGCCTTCTC 0.953421 -26 CCGTGCGCCTGCTCCTGCGCCTTC 19 127 0 GCGCCTGCTC 0.993251 -14 CCTTGTTTTTGCGCACGCTTTGGTGTAGCA 20 124 1 GCGCACGCTT 0.916958 -26 ********** Masking position 3 Map Score: 17.9805 Number of sites scoring better than the average of aligned sites = 1467 Number in coding regions = 1363 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 7 CGGGGGGGGGGGGGTGGACGT 1 2 0 GGGGTGGACG 0.974845 -82 TGCGGCACGCGGTGTAGGGGAATGGGAGGG 3 24 1 GGTGTAGGGG 0.736926 -22 GGGGTAGGAACGGAGCGTCCAA 5 3 1 GGTAGGAACG 0.644829 -145 CCAAACGATGCGGGGAAGCGAGCTGCAGAG 5 29 1 CGGGGAAGCG 0.700054 -119 CAATGGGTCGGGGGTAGTCGG 5 137 1 GGGGTAGTCG 0.895341 -11 TGCCGCGACGGGTATGAGCGCGCAGCGCTT 6 54 1 GGTATGAGCG 0.757014 -31 GGTGAAAAGAGGGTGGGACGCGCTTAGTGC 8 60 1 GGGTGGGACG 0.688097 -57 GTTCTATAGTGAGGGGAGGGGACACGC 8 100 1 GAGGGGAGGG 0.846718 -17 CTGTCATGGGGAAAGCGAATTTAT 13 8 1 GGGGAAAGCG 0.967006 -17 GGAGGGCTGCGAGGAGAACGTATAGTGGAG 14 112 1 GAGGAGAACG 0.909104 -91 CACTGCCTCTGAGGAAAACGGGTCAAGCGG 15 12 0 GAGGAAAACG 0.829815 -130 CCTTGCAGTAGGTAAAATCGGGGCTGCAGC 18 162 1 GGTAAAATCG 0.270036 -139 TATGGATAAAGGGGTGATGGTCCGCCTAGC 19 64 1 GGGGTGATGG 0.861924 -77 CCGCCTAGCGGAGGTGGAGGATGCGGCCGC 19 85 1 GAGGTGGAGG 0.76672 -56 CCTTCTCCACGAGGACAGCGGCCGCATCCT 19 102 0 GAGGACAGCG 0.67515 -39 CTGTCCTCGTGGAGAAGGCGCAGGAGCAGG 19 114 1 GGAGAAGGCG 0.652521 -27 GGGTGTTTGTGGTGTGAACGAAAGGATGTG 21 118 1 GGTGTGAACG 0.926589 -33 ********** Masking position 10 Map Score: 10.8593 Number of sites scoring better than the average of aligned sites = 1741 Number in coding regions = 1550 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 8 GATTTCCTACCTTCCCCTATAT 2 16 0 TTTCCTACCT 0.867085 -12 GTTTTCCGCCCCCTATGCTTAC 4 21 0 TTTCCGCCCC 0.974743 -12 TGGACGCTCCGTTCCTACCCC 5 2 0 GTTCCTACCC 0.939568 -146 TGTATCCTCCCCTCACACAGCA 7 44 0 TATCCTCCCC 0.964378 -12 GTCTGCTTCCTTTCGAACCCCATATCGCTT 9 25 0 TTTCGAACCC 0.952982 -23 CTGCGTATGCTTTGGACCCCGCCTGCATTG 15 91 0 TTTGGACCCC 0.791299 -51 CTCTGTATCCTCTCCCTGCGTGGCC 17 80 0 TATCCTCTCC 0.726332 -15 ACCATGCTCTTTTCCAACCCATAC 18 5 0 TTTCCAACCC 0.985195 -296 TTTATCCATATTACCAACCCACGCGGCCGA 19 44 0 TTACCAACCC 0.912969 -97 ********** Masking position 9 Map Score: 6.69867 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 117 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TTAGTGGTATCAATATTGCCGCGACGGGTATG 6 38 1 CATATTGCCC 0.800606 -47 CTACGGGACAAACTACTGCCTCTCCTGTCATC 14 17 0 AATACTGCCC 0.954029 -186 GACAAGCATAACACACTTCGACCATCCGGCTC 14 55 0 ACCACTTCGC 0.778447 -148 ATTAAGCGCGAAGCGTTGCCTCTTCCGAGGAG 14 169 1 AACGTTGCCC 0.953251 -34 GCCCGTACAAAAACACTGCCTCTGAGGAAAAC 15 23 0 AACACTGCCC 0.990601 -119 GCGGCTTAAAATACATTGCCGCAGGACTCGCG 18 104 1 ATCATTGCCC 0.955616 -197 CAGGATCCTCACTCATTGCCCCCATCGCTGCA 18 186 0 ACCATTGCCC 0.988445 -115 GCAAGATGATAAGCAATGCGACCAAAAAACCC 18 273 0 AACAATGCGC 0.934414 -28 AAACCTGCTTACGCAATACCGCACACCACCCA 20 28 0 ACCAATACCC 0.836595 -122 ** ******* * Masking position 7 Map Score: 3.12544 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 209 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ATGGGTGACAATGTTCTTTTTCTCGTCGGG 1 28 0 ATGTTCTTTT 0.708348 -56 CCAGTGCGAAGTGCTTTTTTCTGAGACTTT 5 67 1 GTGCTTTTTT 0.949302 -81 TATACCGTCGGTACTCTTTTTGCAGAACAG 8 27 0 GTACTCTTTT 0.899022 -90 CTTGGCCTGCGTGCTCCTTTTTTCTCTCTG 12 53 1 GTGCTCCTTT 0.988079 -81 CTTTTTGTTTGTGCACCTTTTGTGAGCTTT 12 83 1 GTGCACCTTT 0.94508 -51 CCCGTAAACCATGCTCTTTTCCAACCCATA 18 12 0 ATGCTCTTTT 0.949302 -289 TGGCTTGTGCGTGCTTCTTAACGCGGAGAG 18 51 1 GTGCTTCTTA 0.824387 -250 ********** Masking position 8 Map Score: 2.9658 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 225 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 AAAATTTACTGGACAACCGGCAACGGTATG 1 55 0 GGACAACCGG 0.88087 -29 TGCGGCACGCGGTGTAGGGGAATGGGAGGG 3 24 1 GGTGTAGGGG 0.875339 -22 CAAACGATGCGGGGAAGCGAGCTGCAGAGA 5 30 1 GGGGAAGCGA 0.58639 -118 GCGTATGGAGAAGCGTGATGGGTTTG 6 7 1 GGAGAAGCGT 0.957203 -78 AGCGATGACAGGAGAGGCAGTAGTTTGTCC 14 14 1 GGAGAGGCAG 0.964464 -189 GTCCCCACCGGGACAAGCATAACACACTTC 14 68 0 GGACAAGCAT 0.924445 -135 CGCTTAATTCGGTCAATCAGATCTTGCAGT 14 147 0 GGTCAATCAG 0.757669 -56 GAGGAAAACGGGTCAAGCGGC 15 2 0 GGTCAAGCGG 0.977376 -140 TAAGGCTCTTGGAGAAGGGTGATTTCTTTG 17 26 1 GGAGAAGGGT 0.893332 -69 TTCTTAACGCGGAGAGTCAGCCGCCCTCTC 18 65 1 GGAGAGTCAG 0.759167 -236 CATTGCCGCAGGACTCGCGGTGGGGCTCGC 18 117 1 GGACTCGCGG 0.844617 -184 TCCCTTTATCGGTCTTGCAGAAGGCATTTG 18 237 1 GGTCTTGCAG 0.565871 -64 CTGTCCTCGTGGAGAAGGCGCAGGAGCAGG 19 114 1 GGAGAAGGCG 0.842443 -27 TCTGTTCTCGGGACAGGGAGTGAAAGGTTG 20 90 1 GGACAGGGAG 0.899211 -60 CGCACGCTTTGGTGTAGCATGAGGC 20 135 1 GGTGTAGCAT 0.751815 -15 ********** Masking position 2 Map Score: 10.8874 Number of sites scoring better than the average of aligned sites = 669 Number in coding regions = 608 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 12 GGTGACAATGTTCTTTTTCTCGTCGGGGGG 1 25 0 TTCTTTTTCT 0.904935 -59 TGCGCATTGGCTCGTTCTATAGTGAGGGGA 8 87 1 CTCGTTCTAT 0.844315 -30 ACACCCACGCCTCTTTCTCTA 10 2 0 CTCTTTCTCT 0.988922 -26 TCGAGGTAGTCTCTTTGTCTTGGCCTGCGT 12 35 1 CTCTTTGTCT 0.95342 -99 TGCGTGCTCCTTTTTTCTCTCTGCTTTTTG 12 60 1 TTTTTTCTCT 0.79578 -74 GCGCAGTCTCTTCTTTCTCCAGAAAGCTCA 12 105 0 TTCTTTCTCC 0.902613 -29 CTTTTTCTACCTCTTTCTATG 16 2 0 CTCTTTCTAT 0.953311 -35 GAGCCCTCCACTCTTTTTCTACCTCTTTCT 16 14 0 CTCTTTTTCT 0.960556 -23 ********** Masking position 5 Map Score: 6.69263 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 114 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 ********** No masking Map Score: 4.08095e-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: 4.08095e-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: 4.08095e-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