AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i250_bsub_mtub_300.orf -o250_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ddlA 174 D-alanyl-D-alanine ligase A #2 murF 71 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6- diaminopimelate-D-alanyl-D-alanyl ligase #3 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #4 yllA 70 yllA #5 yllB 125 similar to hypothetical proteins #6 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #7 ftsL 39 cell-division protein #8 spoVD 116 penicillin-binding protein #9 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #10 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #11 spoVE 60 spoVE #12 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #13 murB 26 UDP-N-acetylenolpyruvoylglucosamine reductase #14 divIB 130 cell-division initiation protein #15 ylxX 22 similar to hypothetical proteins #16 ftsA 173 cell-division protein #17 ftsZ 35 cell-division initiation protein #18 murC 249 UDP-N-acetyl muramate-alanine ligase #19 ytpS 159 ytpS #20 ytpP 234 similar to thioredoxin H1 #21 murB 26 murB #22 ftsZ 172 ftsZ #23 murE 22 murE #24 hypothetical 267 hypothetical protein Rv2160c #25 Rv2161c 102 hypothetical protein Rv2161c #26 PE_PGRS 209 PE_PGRS #27 Rv2166c 300 hypothetical protein Rv2166c #28 ddlA 77 ddlA #29 gpdA2 118 gpdA2 Motif number 1 ATATAAAATACGCCGCTAAGGGAGGCTTTTC 18 156 1 CGCCGCTAGG 0.843426 -94 GCTTTTCAGCCGCCGCGGTCGCAAATTGAAA 18 180 1 CGCCGCGGCG 0.994233 -70 TTAATCTTTTCTGGGCCGACCAGCAGTGGTA 19 93 1 CTGGGCCGCC 0.757003 -67 CGCGCCGATACGCGGCGGGCATTTTTTCGG 22 10 0 CGCGGCGGCA 0.877214 -163 CGCCGCGTATCGGCGCGCCTGCACGGTTAGC 22 24 1 CGGCGCGCTG 0.977251 -149 CCTACCGACAGGGCGCGCACAC 23 2 0 GGGCGCGCCA 0.642533 -21 CGCCGACGTCGGCCGCCAAAC 24 1 1 CGCCGACGCG 0.810499 -267 CGCGCAGGATCTGCGCCCGGGTTTGGCGGCC 24 21 0 CTGCGCCCGG 0.874196 -247 ATATCCATCGCGGCGCGCAGGATCTGCGCCC 24 34 0 CGGCGCGCGG 0.992565 -234 AAGGGGCTCTCGGGGCTGTCCATCGGCGAGC 24 75 1 CGGGGCTGCC 0.900822 -193 GGCTGTCCATCGGCGAGCTTGCCGGGCGGCT 24 88 1 CGGCGAGCTG 0.852801 -180 TCCGGCATTTCGGCGCCAAGGAGCAGCTGCA 24 142 1 CGGCGCCAGG 0.980645 -126 TGGCGACCGTCGAGGCCGCCGTGAGCGTGTT 24 175 1 CGAGGCCGCG 0.559986 -93 GCGTGTTCGAAGCCGAGGTCGTGGCTCCCGC 24 199 1 AGCCGAGGCG 0.654662 -69 GCGATGGCAGCGCCGCCCGGGGTGGACCGGG 24 228 1 CGCCGCCCGG 0.984074 -40 GCATGCATGAGGGCGCGCACCCGGTCCACCC 24 247 0 GGGCGCGCCC 0.91226 -21 ACCGCTCGCTCGGGGCCCGGG 25 1 0 CGGGGCCCGG 0.976992 -102 GCTTAATGAAAGCCGCCGCCG 25 92 1 AGCCGCCGCG 0.90885 -11 GCGCCGTTACCGGCGCCGCCGCC 26 3 0 CGGCGCCGCG 0.573565 -207 GCGCCGGTAACGGCGCGCGCCGGTTCGTTTC 26 18 1 CGGCGCGCCC 0.991232 -192 CCCAGACCTGCGACACCGTCGGCAGGGCTTT 26 152 0 CGACACCGCG 0.685806 -58 CCGGACTCACCGGGGCGGTTCACCCAGCCGG 27 31 1 CGGGGCGGTC 0.90191 -270 GACTCAATATCGCCGACAGCCGGTGACGACC 27 61 0 CGCCGACACC 0.807225 -240 CCCATTTGCCCGGCGACATGCGGTTTTCTGA 27 134 1 CGGCGACAGC 0.744217 -167 CACTGAAGCGCGCGGCTAGCCCGGCTACGAC 27 166 0 CGCGGCTACC 0.650902 -135 TCGCACGGGCCGGCACGACCGAAAACTGCAG 28 14 1 CGGCACGACG 0.891731 -64 ACGGCATTGCCGCCACGGTCGTGGCCGGGGC 29 51 1 CGCCACGGCG 0.950765 -68 CGGTCGTGGCCGGGGCCCAGGCACGGTCCCG 29 66 1 CGGGGCCCGG 0.980921 -53 CACTAATCTGCGCCGCGGTTGCCGTCGGGAC 29 91 0 CGCCGCGGTG 0.974688 -28 ******** ** Masking position 2 Map Score: 48.2781 Number of sites scoring better than the average of aligned sites = 2010 Number in coding regions = 1886 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 2 GAGTTAAGGAGAGAAAGTGGGGCAAGAGATC 5 105 1 GGAGTGGGGC 0.956573 -21 TTCGGCTTCCTCCCTGGTGGGGCTCGGTTCTTC 22 148 0 TCCGTGGGGC 0.921542 -25 CGCCGACGTCGGCCGCCAAACCCG 24 2 1 GCGGTCGGCC 0.855147 -266 GACGTCGGCCGCCAAACCCGGGCGCAGATCCTG 24 15 1 GCACCCGGGC 0.80619 -253 CTCGGTGAAGGGGCTCTCGGGGCTGTCCATCGG 24 68 1 GGCTCGGGGC 0.904123 -200 GTCCATCGGCGAGCTTGCCGGGCGGCTGGGCAT 24 92 1 GGCGCCGGGC 0.994612 -176 GGCTGGGCATGAGCAAGTCGGGCCTGTTCCGGC 24 115 1 GGCGTCGGGC 0.99025 -153 GGGCGGCGCTGCCATCGCGGGAGCCACGACCTC 24 213 0 GCAGCGGGAG 0.774783 -55 CGCGCACCCGGTCCACCCCGGGCGGCGCTGCCA 24 232 0 GCCCCCGGGC 0.978539 -36 TTTAACGATGGTCCGCCTGGGGCGTGCTGTCAA 25 46 0 GCCCTGGGGC 0.681083 -57 AAGTTGTGCTGAGCTGGTCGGAGGTGCGGG 26 190 1 GGCGTCGGAG 0.76797 -20 AGAGTCTCCGGACTCACCGGGGCGGTTCACCCA 27 24 1 GCTCCGGGGC 0.753135 -277 TGGCAAGTGGGGCCAAGTGGGGCACAACTGGGG 27 101 0 GCCGTGGGGC 0.903331 -200 GTTTTCTGAGGTCGTAGCCGGGCTAGCCGCGCG 27 156 1 GCGGCCGGGC 0.991523 -145 CCAGTTATGGGGCAAAGTGGGGGATTGTGGGGT 27 229 1 GCAGTGGGGG 0.956521 -72 GGTCGTGCCGGCCCGTGCGAGGC 28 1 0 GCCGCGAGGC 0.836856 -77 CTGCAGAGGCTACCGGGTCAGGCAGACGGGCTC 28 52 0 TCCGTCAGGC 0.669692 -26 TGCCGCCACGGTCGTGGCCGGGGCCCAGGCACG 29 58 1 GCGGCCGGGG 0.981341 -61 TTGCCGTCGGGACCGTGCCTGGGCCCCGGCCAC 29 71 0 GCCGCCTGGG 0.901542 -48 * ** ******* Masking position 11 Map Score: 32.651 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 342 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 TGCCCTTTTACCGGCAGTGTCCTTCTTCA 2 10 0 CCGGCAGTGT 0.878839 -62 CTGCTGTAAAGCGGCATAGCTGTTAAATGC 18 55 0 GCGGCATAGC 0.810297 -195 CCGCTTTACAGCAGCTGTGCATAGACAAAT 18 71 1 GCAGCTGTGC 0.827469 -179 CAAGGGCTTAGCGGCTTTTCACATGATTCG 19 36 0 GCGGCTTTTC 0.880875 -124 CCCTTGTTTAGCGGCTTGGTTTCTGCTGAT 19 60 1 GCGGCTTGGT 0.91189 -100 CCTACCGACAGGGCGCGCACAC 23 9 0 CCGACAGGGC 0.59917 -14 AGCTTGCCGGGCGGCTGGGCATGAGCAAGT 24 103 1 GCGGCTGGGC 0.98682 -165 CGGGCCTGTTCCGGCATTTCGGCGCCAAGG 24 133 1 CCGGCATTTC 0.779101 -135 GTCGCCAGCTGCAGCTGCTCCTTGGCGCCG 24 152 0 GCAGCTGCTC 0.511562 -116 AGCCACGACCTCGGCTTCGAACACGCTCAC 24 195 0 TCGGCTTCGA 0.42906 -73 TCCACCCCGGGCGGCGCTGCCATCGCGGGA 24 224 0 GCGGCGCTGC 0.657085 -44 CCGGGGTGGACCGGGTGCGCGCCCTCATGC 24 244 1 CCGGGTGCGC 0.821213 -24 GTCACGCAATCCGGCATTGACAGCACGCCC 25 30 1 CCGGCATTGA 0.638594 -73 CGGCGGCGGCTTTCATTAAGCA 25 91 0 GCGGCGGCTT 0.709107 -12 GGCGGCGGCGCCGGTAACGGC 26 2 1 GCGGCGGCGC 0.931664 -208 GCGCTGACGATCGGGTTGGCGGAAGCTCTT 26 78 1 TCGGGTTGGC 0.501348 -132 TGCGACACCGTCGGCAGGGCTTTCGATCCT 26 145 0 TCGGCAGGGC 0.921317 -65 CGGTGACGACCCGGCTGGGTGAACCGCCCC 27 42 0 CCGGCTGGGT 0.918216 -259 GGGTATCAAAGCGGCGTTTTGCCGTCTCTG 27 200 0 GCGGCGTTTT 0.5726 -101 GCACACTTCGACGGCATTGCCGCCACGGTC 29 41 1 ACGGCATTGC 0.681013 -78 ********** Masking position 2 Map Score: 11.9394 Number of sites scoring better than the average of aligned sites = 2619 Number in coding regions = 2458 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 4 TTTTAATTTTGCGTTCGCGTTTCG 7 5 0 GCGTTCGCGT 0.749922 -35 TGCTAACCGTGCAGGCGCGCCGATACGCGG 22 26 0 GCAGGCGCGC 0.832494 -147 GTGTGCGCGCCCTGTCGGTA 23 1 1 GTGTGCGCGC 0.922502 -22 CGGGCGCAGATCCTGCGCGCCGCGATGGAT 24 33 1 TCCTGCGCGC 0.95507 -235 GGGGTGGACCGGGTGCGCGCCCTCATGCAT 24 246 1 GGGTGCGCGC 0.940384 -22 CCCCGAGCGAGCGGTCACGCAATCCGGCAT 25 17 1 GCGGTCACGC 0.787845 -86 ATGGTCCGCCTGGGGCGTGCTGTCAATGCC 25 42 0 TGGGGCGTGC 0.880283 -61 TTAAACACGAACGTTCGTGCTTAATGAAAG 25 74 1 ACGTTCGTGC 0.838095 -29 GCCGAAACGAACCGGCGCGCGCCGTTACCG 26 22 0 ACCGGCGCGC 0.973335 -188 TTTGCGCAACATGTGCGCGCTGACGATCGG 26 62 1 ATGTGCGCGC 0.931559 -148 TAGCCGGGCTAGCCGCGCGCTTCAGTGGTA 27 170 1 AGCCGCGCGC 0.794025 -131 GCTGCAGTTTTCGGTCGTGCCGGCCCGTGC 28 16 0 TCGGTCGTGC 0.842413 -62 ********** Masking position 6 Map Score: 9.15505 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 399 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 5 TGCAATAAAAGAATAGGCAGCCCGAA 9 4 0 GAAGGCACCC 0.912425 -172 CTGTTTCTTTCAAACGACATACGTAGTTATCAT 10 75 0 CACGACAACG 0.914766 -38 GTCTTGAAGTAAATCGGCAGCCCTAATGACTTT 11 17 1 AACGGCACCC 0.898892 -44 AGCAATCGACACCCCAAGCTTAAAG 11 46 0 CACGACACCC 0.977181 -15 GGAAACAATTGATGCGATAACCCTGTCCAACAA 12 49 1 GACGATACCC 0.721908 -74 TGAAGCTGTTCATATGACATACTGTAAGCAAAC 14 24 1 CATGACAACT 0.611712 -107 AGCAAACGAACAAACGGCATCATAGTATGCCGT 14 50 1 CACGGCACAT 0.895337 -81 TATTCCAAAACAAACGGCATACTATGATGCCGT 14 63 0 CACGGCAACT 0.981194 -68 GTTTGTTTTGGAATAGACAGACTTTTAACAGCT 14 81 1 GAAGACAACT 0.692123 -50 ATAGATAGTCATTCGGCAGATTAGGAGGATTT 17 10 1 CACGGCAATT 0.774595 -26 GAGAGTTTGCCAGCAGACACACCGAAGAACCGA 22 125 1 CAAGACAACC 0.846145 -48 CAGTGGTACAGAGACGGCAAAACGCCGCTTTGA 27 192 1 GACGGCAAAC 0.825422 -109 CCGTCTGCCTGACCCGGTAGCCTCTGCAGGTT 28 56 1 GACGGTACCT 0.817012 -22 AGCGTCGATCCACGCGGCACACTTCGACGGCAT 29 25 1 CACGGCAACT 0.981194 -94 AGGCACGGTCCCGACGGCAACCGCGGCGCAGAT 29 84 1 CCCGGCACCG 0.83007 -35 ** ***** *** Masking position 9 Map Score: 8.09725 Number of sites scoring better than the average of aligned sites = 1063 Number in coding regions = 986 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 GGTTAGCAACCGTCGTAGCCATACGGTTCT 22 48 1 CGTCGTAGCC 0.97654 -125 AGCTGGCGACCGTCGAGGCCGCCGTGAGCG 24 172 1 CGTCGAGGCC 0.952769 -96 TCGAAGCCGAGGTCGTGGCTCCCGCGATGG 24 205 1 GGTCGTGGCT 0.961544 -63 GGTCCACCCCGGGCGGCGCTGCCATCGCGG 24 226 0 GGGCGGCGCT 0.91018 -42 GTGACCGCTCGCTCGGGGCCCGGG 25 5 0 GCTCGGGGCC 0.958144 -98 GGCGGCGGCGCCGGTAACGGCG 26 3 1 CGGCGGCGCC 0.970704 -207 GTGCTGAGCTGGTCGGAGGTGCGGG 26 195 1 GGTCGGAGGT 0.720269 -15 CACCCAGCCGGGTCGTCACCGGCTGTCGGC 27 51 1 GGTCGTCACC 0.904953 -250 GGTTTTCTGAGGTCGTAGCCGGGCTAGCCG 27 155 1 GGTCGTAGCC 0.982948 -146 AACTGCAGCTCGTGGGAGCCCGTCTGCCTG 28 37 1 CGTGGGAGCC 0.893838 -41 TTGCCGCCACGGTCGTGGCCGGGGCCCAGG 29 57 1 GGTCGTGGCC 0.990824 -62 CCGCGGTTGCCGTCGGGACCGTGCCTGGGC 29 80 0 CGTCGGGACC 0.955493 -39 ********** Masking position 5 Map Score: 15.2072 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 241 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 TTAATATAAAATAAAAAGGAATTACATACA 1 38 1 ATAAAAAGGA 0.862109 -137 CTGTTTACCCATAAAAAGAAACCCTGAACT 5 36 0 ATAAAAAGAA 0.917921 -90 GGTAAACAGTGTAAAATGAAGTTGTGGAGC 5 57 1 GTAAAATGAA 0.634762 -69 CGAACGCAAAATTAAAAGGAGGTCATCAGC 7 18 1 ATTAAAAGGA 0.764299 -22 CTGAAGGCATAAAAAAAGAAAGCCTGCATA 8 26 0 AAAAAAAGAA 0.890395 -91 AAATTCAGGCATAAAATGAAACAAGCCTAA 8 78 1 ATAAAATGAA 0.756617 -39 TTTTTTCTGCAATAAAAGAATAGGCAGCCC 9 14 0 AATAAAAGAA 0.808185 -162 TTTTAGCGTAAATAAAAGGATACATCCAGC 9 65 0 AATAAAAGGA 0.70198 -111 GACTTCAATGATAAAAAGAACGAATTAGAA 9 137 1 ATAAAAAGAA 0.917921 -39 TAGACTGGGGGAAAAAAGAA 12 113 1 GAAAAAAGAA 0.819544 -10 AATCCGCCAAAAAAAACGAATCATGTGAAA 19 20 1 AAAAAACGAA 0.777434 -140 TGTACACGATGTTAAACGAAACGAGCTTGA 20 58 1 GTTAAACGAA 0.582339 -177 ********** Masking position 5 Map Score: 7.40355 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 460 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 8 TATATACAAAAGAAAGAGAGGGACCTTAC 2 53 1 AAAAGAGGGA 0.881722 -19 TGTAGAAACAACAAAGGGGGAGATTTGT 3 6 0 AAAAGGGGGA 0.982898 -154 CGTAAATGCTAAATTGGGTGTGACATC 3 143 1 AATTGGGGGA 0.911499 -17 AATAGTGGTGAGTTAAGGAGAGAAAGTGGGGCA 5 96 1 ATTAAGGGGA 0.866547 -30 ATTCATCCTGATAAAAGGTGGGACCAACACAAT 6 47 1 AAAAAGGGGA 0.973143 -23 AAACAAGCCTAAATAAGGAGTGAACGGTCTC 8 96 1 AATAAGGGGA 0.973143 -21 CTGAAAAAGCGGGTGAAATAGA 15 4 1 AAAAGCGGGA 0.917004 -19 AGATGGATATACATAAGGAGGGATTTTTATT 20 9 0 AATAAGGGGA 0.973143 -226 * ****** * ** Masking position 1 Map Score: 4.88251 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 68 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 AATGAAGTTGTGGAGCGAAGTGGTGAATAGTGG 5 71 1 TGGAGCAAGG 0.954364 -55 GGGCTTGTCTTGAAGTAAATCGGCAGCCCTAAT 11 11 1 TGAAGTAAGG 0.761825 -50 TTCATTTGAATGAGGTGAACAGGCA 14 116 1 TGAGGTAAGG 0.942008 -15 TCTTGATATCTGGGTTTAATCGGAAAGAAATAA 18 100 1 TGGGTTAAGG 0.889952 -150 ATGGTCCGCCTGGGGCGTGCTGTCAATGCCGGA 25 39 0 TGGGGCTGGT 0.730735 -64 GGGTGGCAAGTGGGGCCAAGTGGGGCACAACTG 27 104 0 TGGGGCAAGG 0.990672 -197 ACCCCAGTTATGGGGCAAAGTGGGGGATTGTGG 27 226 1 TGGGGCAAGG 0.990672 -75 TGGGGGATTGTGGGGTATGGTGGCTGAGGTGTT 27 246 1 TGGGGTTGGG 0.955559 -55 GCTGAGGTGTTTGGGTGAGATGGATTTGGCAGG 27 268 1 TTGGGTAGGG 0.86963 -33 ****** ** ** Masking position 1 Map Score: 4.34446 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 95 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 ATGTCACATCTCCTTTTCAATGCCATTTTA 1 11 1 TCCTTTTCAA 0.877348 -164 TACTATCTTATCATTTTCACCGGAAAATGA 1 105 0 TCATTTTCAC 0.877348 -70 ATATGAAAAATCTTTTTCAAGCTCCATTAT 10 28 0 TCTTTTTCAA 0.584814 -85 TGTCCTTTTCTCCTCCTGTTTC 10 101 0 TCCTTTTCTC 0.821928 -12 TGCCTGTTCACCTCATTCAAA 14 120 0 GCCTGTTCAC 0.949264 -11 TATTTCACCCGCTTTTTCAG 15 1 0 GCTTTTTCAG 0.745151 -22 TATTTTTATGTGCTTTTCACATTTTATGTT 16 49 0 TGCTTTTCAC 0.954893 -125 TATGGGTTCATTTTCACACCAAACATG 18 8 1 TCATTTTCAC 0.877348 -242 CGCTAAGGGAGGCTTTTCAGCCGCCGCGGT 18 169 1 GGCTTTTCAG 0.896406 -81 AGGGCTTAGCGGCTTTTCACATGATTCGTT 19 34 0 GGCTTTTCAC 0.965997 -126 GACTCACCGGGGCGGTTCACCCAGCCGGGT 27 34 1 GGCGGTTCAC 0.672487 -267 ********** Masking position 6 Map Score: 4.01568 Number of sites scoring better than the average of aligned sites = 821 Number in coding regions = 665 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 11 AAGCTTGGAAACAATTGATGCGATAACCCTGTC 12 43 1 ACATTGGCGA 0.813005 -80 TTTTTAGTATACCACTGCTGGTCGGCCCAGAAA 19 100 0 ACACTGGGTC 0.945436 -60 AAGAACATAAACAACTGGAGGGATATGAA 20 216 1 ACACTGGGGA 0.930103 -19 CCGTATGGCTACGACGGTTGCTAACCGTGCAGG 22 41 0 ACACGGGCTA 0.849413 -132 TTCGGCTCCAACAACTTTTGCGCAACATGTGCG 26 46 1 ACACTTGCGC 0.929902 -164 CAAGTGGGGCACAACTGGGGCTCAAACCGGACT 27 88 0 ACACTGGCTC 0.984802 -213 CCGTCTCTGTACCACTGAAGCGCGCGGCTAGCC 27 176 0 ACACTGGCGC 0.993457 -125 GGCACGACCGAAAACTGCAGCTCGTGGGAGCCC 28 25 1 AAACTGGCTC 0.849878 -53 GGCCCCGGCCACGACCGTGGCGGCAATGCCGTC 29 50 0 ACACCGGCGG 0.934505 -69 GGTCCCGACGGCAACCGCGGCGCAGATTAGTGT 29 90 1 GCACCGGCGC 0.939312 -29 ** **** **** Masking position 4 Map Score: 5.98208 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 100 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 12 AGGACACTGCCGGTAAAAGGGCAGTGTTTTT 2 17 1 CGGTAAAGGG 0.666244 -55 TGAAGTTGTGGAGCGAAGTGGTGAATAGTGG 5 73 1 GAGCAAGTGG 0.911005 -53 GAATAGTGGTGAGTTAAGGAGAGAAAGTGGG 5 95 1 GAGTAAGGAG 0.623266 -31 CTGAAAAAGCGGGTGAAATAGA 15 11 1 GGGTAAATAG 0.65027 -12 CGCTAAACAAGGGCTTAGCGGCTTTTCACAT 19 42 0 GGGCTAGCGG 0.947058 -118 ATCTGCGCCCGGGTTTGGCGGCCGACGTCGG 24 13 0 GGGTTGGCGG 0.930539 -255 GATATCGCCTCGGTGAAGGGGCTCTCGGGGC 24 60 1 CGGTAAGGGG 0.900425 -208 GGCTGGGCATGAGCAAGTCGGGCCTGTTCCG 24 115 1 GAGCAGTCGG 0.608462 -153 GTGGCAAGTGGGGCCAAGTGGGGCACAACTG 27 104 0 GGGCAAGTGG 0.982597 -197 GCATGTCGCCGGGCAAATGGGTGGCAAGTGG 27 124 0 GGGCAATGGG 0.904069 -177 CCCAGTTATGGGGCAAAGTGGGGGATTGTGG 27 228 1 GGGCAAGTGG 0.982597 -73 GGGGATTGTGGGGTATGGTGGCTGAGGTGTT 27 248 1 GGGTTGGTGG 0.925188 -53 TGAGGTGTTTGGGTGAGATGGATTTGGCAGG 27 270 1 GGGTAGATGG 0.903177 -31 AGAGGCTACCGGGTCAGGCAGACGGGCTCCC 28 50 0 GGGTAGGCAG 0.89247 -28 **** ****** Masking position 3 Map Score: 10.3394 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 444 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 13 TAAGCAAACGAACAAACGGCATCATAGTAT 14 48 1 AACAAACGGC 0.988744 -83 TCTATTCCAAAACAAACGGCATACTATGAT 14 68 0 AACAAACGGC 0.988744 -63 TTGTACCTCCAACAAACGTCTATCTGTTCC 18 228 0 AACAAACGTC 0.956727 -22 TTTGGATCATACCAAACTGCTTGAGGCAAA 20 160 0 ACCAAACTGC 0.928414 -75 ********** Masking position 5 Map Score: 0.803508 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 28 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 AATAAAAATCCCTCCTTATGTATAT 20 6 1 AAATCCCTCC 0.95405 -229 CTCCTTATGTATATCCATCTGTAAATTTCA 20 22 1 ATATCCATCT 0.946779 -213 TTCATATCCCTCCAGTTGTTTAT 20 222 0 ATATCCCTCC 0.96748 -13 CACCGAGGCGATATCCATCGCGGCGCGCAG 24 45 0 ATATCCATCG 0.9374 -223 CCTCCCTGCCAAATCCATCTCACCCAAACA 27 275 0 AAATCCATCT 0.925488 -26 ********** Masking position 4 Map Score: 0.0208315 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 36 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 TGATTCTTCGTGTATAACACTCTAAAAAC 6 9 1 CGTGTTAACA 0.971463 -61 AAAAAGAAAGCCTGCATAACGACGGCTTTCT 8 13 0 CCTGCTAACG 0.954674 -104 TTCCAAGCCTCCTGTCTAACATGAAGCTTGG 12 20 1 CCTGTTAACA 0.962855 -103 ATGCGATAACCCTGTCCAACAAAACAGGGTT 12 60 1 CCTGTCAACA 0.888592 -63 TGGCTTTACAAGTGTGTAACAAAAAATAACA 16 85 0 AGTGTTAACA 0.815372 -89 CACGAACGTTCGTGTTTAACGATGGTCCGCC 25 62 0 CGTGTTAACG 0.976127 -41 CACGAACGTTCGTGCTTAATGAAAGCCGCCG 25 79 1 CGTGCTAATG 0.782069 -24 ***** ***** Masking position 8 Map Score: 0.814354 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 42 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701