AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00940_synecho_reg_300.orf -o00940_synecho_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #2 sll1191 233 hypothetical protein. #3 ssr2153 300 hypothetical protein. #4 slr1706 232 dfrA; putative dihydroflavonol-4-reductase (DFR) (dihydrokaempferol #5 ssr2857 125 hypothetical protein. #6 slr1708 214 lysostaphin. #7 sll1572 55 dnaE; DNA polymerase III alpha subunit. [EC:2.7.7.7] #8 sll1571 100 hypothetical protein. #9 sll1570 41 hypothetical protein. #10 slr1710 148 mrcB; penicillin-binding protein 1B. #11 sll1568 91 fibrillin. #12 sll1927 77 oppF; oligopeptide transport ATP-binding protein OppF. #13 sll1926 91 hypothetical protein. #14 slr2005 178 hypothetical protein. #15 sll1925 214 hypothetical protein. #16 slr2007 111 ndhD; NADH dehydrogenase subunit 4. [EC:1.6.5.3] #17 slr2008 49 hypothetical protein. #18 slr2012 247 hypothetical protein. #19 slr2013 142 hypothetical protein. #20 sll1924 300 hypothetical protein. #21 slr1254 60 pds, crtD; phytoene dehydrogenase (phytoene desaturase). #22 slr1255 176 crtB, pys; phytoene synthase. [EC:2.5.1.-] [SP:CRTB_SYNY3] #23 sll1147 157 hypothetical protein. #24 slr1256 155 ureA; urease gamma subunit (ureA amidohydrolase). [EC:3.5.1.5] #25 tRNA-Glu 219 tRNA-Glu. #26 slr1257 196 hypothetical protein. #27 slr1258 130 hypothetical protein. #28 slr1259 55 hypothetical protein. #29 slr1260 63 hypothetical protein. #30 slr1262 195 hypothetical protein. #31 slr1263 27 hypothetical protein. #32 sll1961 80 hypothetical protein. #33 sll1960 34 hypothetical protein. #34 sll1958 138 hisC; histidinol phosphate aminotransferase. [EC:2.6.1.9] #35 sll1957 300 arsA; arsenical resistance operon repressor. #36 sll1869 149 cbaB; 3-chlorobenzoate-3,4-dioxygenase. [EC:1.14.-.-] #37 slr1984 300 rps1b; 30S ribosomal protein S1 homolog B. [SP:RS1B_SYNY3] #38 sll1538 116 bgl; beta-glucosidase. [EC:3.2.1.21] #39 slr1627 118 hypothetical 22.0 kD protein slr1627. [SP:YG27_SYNY3] #40 sll1536 135 moeB; molybdopterin biosynthesis MoeB protein. #41 slr1629 124 hypothetical protein. #42 sll1535 99 rfbP; galactosyl-1-phosphate transferase. #43 sll1533 300 pilT; twitching mobility protein. Motif number 1 TGAAAATAGTTGGGGGACAAAGGCTTTAGT 1 188 0 TGGGGGACAA 0.767996 -113 TCCGGCAAGGTTGGGGGATTTGGACTTACA 1 225 1 TTGGGGGATT 0.950525 -76 GTCCCATCTTTGGGGGGATGAACATGGAAA 2 105 1 TGGGGGGATG 0.958137 -129 TTTGGGGGCCAGGGGGGCTTTTAAAACAGG 4 130 0 AGGGGGGCTT 0.976403 -103 CCCCAAAATTTGGGGGGAAACTGAGTGAAA 4 153 1 TGGGGGGAAA 0.849067 -80 CCCCCAATACTGGGGGACTTTCACTCAGTT 4 171 0 TGGGGGACTT 0.976735 -62 TCCCCCAGTATTGGGGGATTTGGGGGGCAG 4 184 1 TTGGGGGATT 0.950525 -49 TTGGGGGATTTGGGGGGCAGAATAAAACTT 4 194 1 TGGGGGGCAG 0.926581 -39 CGACTTAGGTAGGGGAAATTGACATTGATT 6 73 1 AGGGGAAATT 0.825678 -142 TTGGGGGGCTAGGGGGGCTTTTAAAACACG 10 13 0 AGGGGGGCTT 0.976403 -136 CCCCCAACTCTGGGGGGAACAGTGTTCAAA 10 36 1 TGGGGGGAAC 0.858611 -113 CTGGCAAGTTTGGGGGAATTTGAACACTGT 10 54 0 TGGGGGAATT 0.974779 -95 GATGGAGGTAAGGGGAAATTGACGCTACCG 12 26 1 AGGGGAAATT 0.825678 -52 TCCGGCAATATGGGGGACTTTCACTCAGTT 14 60 1 TGGGGGACTT 0.976735 -119 CCCCAAATTTTGGGGGAAACTGAGTGAAAG 14 77 0 TGGGGGAAAC 0.766887 -102 TTGGGGGGTCAGGGGGGCTTTTAAAACAGG 14 101 1 AGGGGGGCTT 0.976403 -78 TTTGATAACCTGGGGAGATTAATCAAACTG 16 24 0 TGGGGAGATT 0.942448 -88 AAGGGGGGCTAGGGGGGATTAAACGGCCAA 18 81 0 AGGGGGGATT 0.97442 -167 CACTTTCCAGTGGGGAAATTTGCGGTTAGC 18 203 1 TGGGGAAATT 0.898695 -45 TTTTCGACCCATGGGGAATTAACCAAAA 19 9 0 ATGGGGAATT 0.84749 -134 AAGGAAGGTTAGGGGAGATTAACCAGTCGT 19 91 0 AGGGGAGATT 0.897365 -52 GAGAGGGTCTAGGGGAGAATTTAGTTATTG 20 266 1 AGGGGAGAAT 0.816122 -35 CCTACAACGGTTGGGGGCTTTTTTTCAGCG 22 111 1 TTGGGGGCTT 0.954273 -66 GAAGAAGAAGCGGGGAGCTTGTCGAGGGAA 25 94 0 CGGGGAGCTT 0.641387 -126 TTTAAACTTCTTGGGGAATTGTTTGGGTGA 25 147 1 TTGGGGAATT 0.912341 -73 ACTACAATCAATGGGGAAATCGACACTTTT 30 68 0 ATGGGGAAAT 0.73828 -128 ATTTTACTTTTTGGGGGCAAGAATTTGGCT 35 80 1 TTGGGGGCAA 0.621996 -221 GGTTAGATGCTGGGGAAATGTAGCCAAATT 35 101 0 TGGGGAAATG 0.739984 -200 AAATTGGGGACAGAAATAACCAA 37 4 1 TTGGGGACAG 0.648019 -297 AATGGGGACATTGGGGACATTATTTAATAG 43 169 0 TTGGGGACAT 0.851608 -132 ********** Masking position 5 Map Score: 50.0884 Number of sites scoring better than the average of aligned sites = 2255 Number in coding regions = 1835 Number in noncoding regions = 420 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 2 CAGATTCTTACCCTCCACCCAACTGTAA 1 7 0 CCCTACCCAA 0.600677 -294 GTCCAAATCCCCCAACCTTGCCGGAGCTTTAG 1 218 0 CCCACTTGCC 0.823499 -83 AGGAGATTTTCCCTCGCCTGCCCTTAGTAATA 3 186 1 CCCTCCTGCC 0.982581 -115 TTAAAAGCCCCCCTGGCCCCCAAAATTTGGGG 4 136 1 CCCTCCCCCA 0.974979 -97 ATTCTGCCCCCCAAATCCCCCAATACTGGGGG 4 185 0 CCAACCCCCA 0.536149 -48 TTAAAAGCCCCCCTAGCCCCCCAACTCTGGGG 10 19 1 CCCTCCCCCC 0.995108 -130 TTCAAATTCCCCCAAACTTGCCAGAGCCGGAG 10 60 1 CCCACTTGCC 0.823499 -89 ATGGTCCGCCCCCTAAATCGACCCACTAAAGC 10 91 0 CCCTATCGAC 0.596721 -58 CGTCAATTTCCCCTTACCTCCATCGACATACC 12 18 0 CCCTCCTCCA 0.950088 -60 TTATTCCGCCCCCTAAATCGACCCACTAAAGC 14 28 1 CCCTATCGAC 0.596721 -151 TTAAAAGCCCCCCTGACCCCCCAAATTTTGGG 14 93 0 CCCTCCCCCC 0.995108 -86 TCCTAATTATCCCAGGCCTCCCCCTCCATCAG 15 180 0 CCCACCTCCC 0.961183 -35 GTTTAATCCCCCCTAGCCCCCCTTGGGAAGGG 18 87 1 CCCTCCCCCC 0.995108 -161 TGGTAACATTTCCTCCCTTCCCAAGGGGGGCT 18 101 0 TCCTCTTCCC 0.742649 -147 GGTTAATCTCCCCTAACCTTCCTTGATTCCGA 19 97 1 CCCTCCTTCC 0.831315 -46 CCTACAATCCCCCTCCCCCCCATCTATTCCCT 20 15 0 CCCTCCCCCA 0.974979 -286 CGTTTTTAGGCCCATACTTCACCTTCCTACAA 20 40 0 CCCACTTCAC 0.623567 -261 CTAAATTCTCCCCTAGACCCTCTCAAACCCCA 20 258 0 CCCTACCCTC 0.619818 -43 GTTGATCTGATCCTGACTTCCCGCTGAAAAAA 22 130 0 TCCTCTTCCC 0.742649 -47 AAACAGTCCGCCCTGACCGGCCAGCTCATTA 24 135 1 CCCTCCGGCC 0.906398 -21 AGAACTACGCCCCTATACTGCCATAGATGGAG 25 36 1 CCCTACTGCC 0.91529 -184 CCGTCATCACCCCCCAGAACGAACC 33 20 0 TCATCCCCCC 0.679334 -15 TACAGACCATACCCCGACACCGTTGCCG 34 121 0 CCATCCCGAC 0.734769 -18 TGAATTGATCCCATTCACCCCCCATCTAGCTA 35 190 0 CCATACCCCC 0.822654 -111 GAGAAACTCTCCCTGACTCCACCAAATGTTGT 37 140 0 CCCTCTCCAC 0.931547 -161 GTCTATTTATCCCTTCCTTGCATCCATAGCAA 41 100 1 CCCTCTTGCA 0.781977 -25 **** ****** Masking position 2 Map Score: 41.8854 Number of sites scoring better than the average of aligned sites = 2347 Number in coding regions = 2046 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 251 Fraction of orfs with sites within 600 bp upstream = 0.0403148 Motif number 3 GGACTTAGAGCCTGTTTTAAAAGCCCCCCTGGC 4 120 1 CGTTTAAAAG 0.985882 -113 TTCTAAGAACGTGTTTGGAAAGTTTTATTCTG 4 211 0 CGTTTGAAAG 0.975025 -22 AACGTGTTTTAAAAGCCCCCCTAGC 10 3 1 CGTTTAAAAG 0.985879 -146 GATCAAAAAGCTTGTTTAAAAAGTCATGGTCCG 10 115 0 CGTTTAAAAG 0.985203 -34 AACGTGTTTGGAAAGTTTTATTCCG 14 3 1 CGTTTGAAAG 0.975025 -176 TTTCTAAGAGCCTGTTTTAAAAGCCCCCCTGAC 14 108 0 CGTTTAAAAG 0.985882 -71 GGAAAAAATGGGTTTAAAAGCCTGATGTTA 17 8 1 AGGTTAAAAG 0.842339 -42 ATTGTTAGAGCGTGTTTCAAAAGTCGAGTTTTG 18 51 1 CGTTTAAAAG 0.985879 -197 CACTAAGGCTCCGGTTTAAAAAGGGAGACTTTG 18 131 0 CGTTTAAAAG 0.985882 -117 CCCACTGGAAAGTGTTTGAAAAGTGCAAGGCTA 18 184 0 AGTTTAAAAG 0.939084 -64 AGACGGCCAGATGGGTTAAAAAGTGTCGATTTC 30 50 1 AGGTTAAAAG 0.842339 -146 AACCCACTCCCTAGTTTTGAACGGAATCTTTGC 35 127 1 CGTTTGAACG 0.870164 -174 * **** ***** Masking position 10 Map Score: 21.1715 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 10 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 GTCGCCGTGGCTGACGGCCAACTATTTTAA 2 193 1 CTGACGGCCA 0.831866 -41 CTTAAGCCCGCCGATGGGCAGGACCGCGGG 3 54 1 CCGATGGGCA 0.773316 -247 GGATTCTACCCCGATCGCCTAAAAAGTCTG 8 49 0 CCGATCGCCT 0.939957 -52 TCTGGGAATCCCGATCGCCAGTCCCGGCCA 11 22 1 CCGATCGCCA 0.987121 -70 AGTCCATGCGGCGATCGCCAAAGGTTTGTC 13 54 0 GCGATCGCCA 0.9918 -38 GGATTTTATGGCGATCGCCATTGCTATTGG 15 149 0 GCGATCGCCA 0.9918 -66 AAACATCGGGGCGATCGCCTTTGTTCGCTA 22 43 1 GCGATCGCCT 0.961095 -134 AATGGAACCCGAGACGGCCAGATGGGTTAA 30 39 1 GAGACGGCCA 0.815758 -157 ATGGAGATATGCCATGGCCAAACTGCCAA 34 10 0 GCCATGGCCA 0.945246 -129 CAGGAAAATGGCGATCGCCAATATGATCAA 39 42 0 GCGATCGCCA 0.9918 -77 ATACAAAAAAGTGACCGCCATCTCCACTAC 39 72 0 GTGACCGCCA 0.944826 -47 CCATGGTAGTGCCGCCGCCAAAAAGACTAA 40 60 1 GCCGCCGCCA 0.858868 -76 ACTGAGGACTCCCACCGCCA 42 1 0 CCCACCGCCA 0.960708 -99 ********** Masking position 9 Map Score: 19.64 Number of sites scoring better than the average of aligned sites = 7024 Number in coding regions = 6411 Number in noncoding regions = 613 Number of orfs with sites within 600 bp upstream = 403 Fraction of orfs with sites within 600 bp upstream = 0.0647286 Motif number 5 ACCGAGCGATCACTAAAGCCTTTGTCCCCCAACT 1 177 1 CCTAAACCTG 0.917203 -124 CAACTATTTTCACTAAAGCTCCGGCAAGGTTGGG 1 206 1 CCTAAACTGG 0.985528 -95 TTAAAACAGGCTCTAAGTCCCTTGTCGTTGCACT 4 106 0 CCTAAGCCTG 0.734471 -127 CTCAGTTTCCCCCCAAATTTTGGGGGCCAGGGGG 4 144 0 CCCAAATTGG 0.594412 -89 CCCCCAAATCCCCCAATACTGGGGGACTTTCACT 4 176 0 CCCAATCTGG 0.846292 -57 CCCCCCTAGCCCCCCAACTCTGGGGGGAACAGTG 10 26 1 CCCCAATCGG 0.72951 -123 TAAATCGACCCACTAAAGCTCCGGCTCTGGCAAG 10 76 0 CCTAAACTGG 0.985528 -73 CAAACAGAGCCGCAAAAACCACGGTAGCGTCAAT 12 43 0 CCAAAACCGG 0.907793 -35 TAAATCGACCCACTAAAGCTCCGGCAATATGGGG 14 41 1 CCTAAACTGG 0.985528 -138 CCCCCTGACCCCCCAAATTTTGGGGGAAACTGAG 14 83 0 CCCAAATTGG 0.594412 -96 TAAATCTCCTCACTAAGGCTCCGGTTTAAAAAGG 18 140 0 CCTAAGCTGG 0.944456 -108 CAGAGATGTTCTCTAAAACTTCGTTTTTAGGCCC 20 59 0 CCTAAACTGT 0.771541 -242 TTAGCCAGCTCACCAAAACCTGTGACAATAAACA 20 185 1 CCCAAACCTG 0.915586 -116 CTATAATTTTCCCTGAAACTGGGGTTTGAGAGGG 20 239 1 CCTGAACTGG 0.886866 -62 TGTTTTTTACCGTTAAACCCCAGGCCTGTTGACC 24 106 0 CTTAAACCGG 0.878375 -50 TTTTAGTCATCGTTCAAACTGGGGAGAGTCCTTT 37 267 1 CTTCAACTGG 0.613129 -34 ACAATCTTCACACCAAAACCATGGTAGTGCCGCC 40 42 1 CCCAAACCGG 0.986993 -94 * ***** ** ** Masking position 6 Map Score: 17.5406 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 615 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 6 TCCCCCAACCTTGCCGGAGCTTTAGTGAAA 1 213 0 TTGCCGGAGC 0.933331 -88 TTGACAATTTTTGCCAGTGTGGAGGCAAAA 3 141 0 TTGCCAGTGT 0.626076 -160 ATTGTTTCAATTCCCTGAGTGCATCCAACT 6 156 0 TTCCCTGAGT 0.570475 -59 TCCCCCAAACTTGCCAGAGCCGGAGCTTTA 10 67 1 TTGCCAGAGC 0.944582 -82 GCGATCGGGATTCCCAGAGCATAAAGAAC 11 10 0 TTCCCAGAGC 0.869092 -82 GTCCCCCATATTGCCGGAGCTTTAGTGGGT 14 48 0 TTGCCGGAGC 0.933331 -131 CTTTGAAGGTTTACCAAAGCTCC 14 166 1 TTACCAAAGC 0.747363 -13 ATTTCCTCCCTTCCCAAGGGGGGCTAGGGG 18 96 0 TTCCCAAGGG 0.53652 -152 GGAGGAAATGTTACCAAAGTCTCCCTTTTT 18 117 1 TTACCAAAGT 0.648306 -131 AGCGGTCAAGTTGCCGAGGCCAAACCTCAG 19 48 1 TTGCCGAGGC 0.889061 -95 GTCAGGAAGATTACCAGGGAGTCCAGGCGG 21 40 1 TTACCAGGGA 0.76814 -21 ATTATAAGTTTTACCAGGGT 26 187 1 TTACCAGGGT 0.912921 -10 TCTGAAAATTTTACCAAGGCTGTTACTCTG 27 108 0 TTACCAAGGC 0.842215 -23 CCCGGCAATTTTGCCAAAGTAACCGAAGAA 30 97 0 TTGCCAAAGT 0.771151 -99 TTTGGCAAAATTGCCGGGGACAGTTAGCTA 30 109 1 TTGCCGGGGA 0.832602 -87 GGGACGGCCCTTACCTGGGTAGGATCAGTT 36 94 1 TTACCTGGGT 0.770948 -56 TTTTACTGAGTTGCCTGGGTACCCTGTTTT 37 241 1 TTGCCTGGGT 0.860192 -60 CATCAAAGGTTTACCGGGGGTTAGCTGTGC 43 251 1 TTACCGGGGG 0.808022 -50 ********** Masking position 2 Map Score: 16.6689 Number of sites scoring better than the average of aligned sites = 1249 Number in coding regions = 1101 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 7 CGGCGGCTGTGGGCAAAGTTTGGCATTGCC 1 98 0 GGGCAAAGTT 0.669448 -203 CCATCCCATTGGGCAAAGAACGATGGCATT 16 52 0 GGGCAAAGAA 0.98341 -60 TACCGAAAACGGGGAAAAAATTTGATTACA 18 16 1 GGGGAAAAAA 0.935112 -232 CTTCACCTAAGGGGAAACATCGGGGCGATC 22 29 1 GGGGAAACAT 0.8774 -148 CGGTCATGGTGAAAGAAAGTATATTTT 23 141 0 GGTGAAAGAA 0.928556 -17 AGAGCCTCAAGGACAAAGAACTACGCCCCT 25 20 1 GGACAAAGAA 0.823655 -200 TGATGAAGCAGGGCAAAGAACGGGCAATGG 30 14 1 GGGCAAAGAA 0.98341 -182 GGAAAAAACAGGGGAAAGAATGCCCTTTGT 34 73 0 GGGGAAAGAA 0.989423 -66 TTACTTTTTGGGGGCAAGAATTTGGCTACA 35 83 1 GGGGCAAGAA 0.936524 -218 CAGGCTGATTGGGCAAAGATTCCGTTCAAA 35 142 0 GGGCAAAGAT 0.950078 -159 AAATTGGGGACAGAAATAACCAAAC 37 6 1 GGGGACAGAA 0.936524 -295 GGACAAACGTGGGGAAACAAATGCGTCGTT 43 99 1 GGGGAAACAA 0.957066 -202 TGCAAAATCCGGTGAAAAAATCCC 43 287 1 GGTGAAAAAA 0.666922 -14 ********** Masking position 7 Map Score: 15.2549 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 437 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 8 ACAAACCGCTTGACAACCGCTTATCAATTA 1 43 1 TGACAACCGC 0.831834 -258 TATTTGACTATGGCAACAGCCTAGACAATT 6 115 0 TGGCAACAGC 0.962018 -100 GGCAAATTAGGGCAAAAGCAGTCCAATTT 9 10 1 GGGCAAAAGC 0.791914 -32 TGGCCGGGACTGGCGATCGGGATTCCCAGA 11 22 0 TGGCGATCGG 0.817022 -70 GACAAACCTTTGGCGATCGCCGCATGGACT 13 54 1 TGGCGATCGC 0.976737 -38 CCAATAGCAATGGCGATCGCCATAAAATCC 15 149 1 TGGCGATCGC 0.976737 -66 AGTCGTACAAGGGCAACTGCTGAGGTTTGG 19 67 0 GGGCAACTGC 0.899171 -76 GGAAACATCGGGGCGATCGCCTTTGTTCGC 22 41 1 GGGCGATCGC 0.979854 -136 AGCTTGTCGAGGGAAACAGCGCAGAAATGG 25 79 0 GGGAAACAGC 0.803016 -141 TTGGCAACAGCTTAGCCACTA 29 53 0 TGGCAACAGC 0.962018 -11 TGCGCGAGTTGGGAAACCGCCACTGAGATT 37 97 1 GGGAAACCGC 0.917325 -204 TTGATCATATTGGCGATCGCCATTTTCCTG 39 42 1 TGGCGATCGC 0.976737 -77 ********** Masking position 6 Map Score: 13.6768 Number of sites scoring better than the average of aligned sites = 3117 Number in coding regions = 2816 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 261 Fraction of orfs with sites within 600 bp upstream = 0.041921 Motif number 9 GACTTACCCTCAGAGCCTAAGTAAATCCG 1 282 1 CAGAGCCTAA 0.971429 -19 TGTTCAGAGCCTCACACACACATA 5 5 1 CAGAGCCTCA 0.987115 -121 CCAAACTTGCCAGAGCCGGAGCTTTAGTGG 10 71 1 CAGAGCCGGA 0.980971 -78 TCGGGATTCCCAGAGCATAAAGAAC 11 6 0 CAGAGCATAA 0.791531 -86 CTCTAGCAAACAGAGCCGCAAAAACCACGG 12 53 0 CAGAGCCGCA 0.980971 -25 GGCTAAACCCCAGAGTCTGAGTTGTAGTAG 16 80 1 CAGAGTCTGA 0.895342 -32 TTGCCAGACAGAGCCTCAAGGACAAAGA 25 9 1 CAGAGCCTCA 0.987115 -211 AGTAGGGTTGCAGAGCCAGAACGGTATTAT 26 162 1 CAGAGCCAGA 0.949748 -35 ********** Masking position 4 Map Score: 9.92039 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 73 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 TCTACAGATTCTTACCCTCCACCCAACTGT 1 13 0 CTTACCCTCC 0.788752 -288 AAAAGCCCCCCTGGCCCCCAAAATTTGGGG 4 138 1 CTGGCCCCCA 0.966262 -95 AAGTTTTATTCTGCCCCCCAAATCCCCCAA 4 194 0 CTGCCCCCCA 0.956149 -39 AAAAGCCCCCCTAGCCCCCCAACTCTGGGG 10 21 1 CTAGCCCCCC 0.980227 -128 AAAAGCCCCCCTGACCCCCCAAATTTTGGG 14 93 0 CTGACCCCCC 0.983753 -86 TATCCCAGGCCTCCCCCTCCATCAGGGGAT 15 175 0 CTCCCCCTCC 0.915475 -40 TTAATCCCCCCTAGCCCCCCTTGGGAAGGG 18 89 1 CTAGCCCCCC 0.980227 -159 TACAATCCCCCTCCCCCCCATCTATTCCCT 20 15 0 CTCCCCCCCA 0.966262 -286 CCGTCATCACCCCCCAGAACGAACC 33 20 0 ATCACCCCCC 0.86238 -15 TAGCCAAATTCTTGCCCCCAAAAAGTAAAA 35 81 0 CTTGCCCCCA 0.927067 -220 ATTGATCCCATTCACCCCCCATCTAGCTAC 35 189 0 TTCACCCCCC 0.86238 -112 TGTGGCACAGCTAACCCCCGGTAAACCTTT 43 255 0 CTAACCCCCG 0.864372 -46 ********** Masking position 2 Map Score: 15.2425 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 342 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 11 TCCTAACACACCGAGACCAAATTAGAGCTT 2 31 1 CCGAGACCAA 0.902286 -203 ATGGCAACAGCCTAGACAATTCCAACAAAA 6 106 0 CCTAGACAAT 0.762525 -109 GATCGGGATTCCCAGAGCATAAAGAAC 11 8 0 CCCAGAGCAT 0.790912 -84 CCAGCACAAACCCAGACCAATCAGGCCCGA 15 41 1 CCCAGACCAA 0.974842 -174 GTTAGCTAACCCCAGACCAACGCATCTCAA 18 227 1 CCCAGACCAA 0.974842 -21 GGTCAAGTTGCCGAGGCCAAACCTCAGCAG 19 51 1 CCGAGGCCAA 0.852581 -92 CACTGTCAACCCTAGACAATGAATTTTTTC 24 73 1 CCTAGACAAT 0.762525 -83 TTGTTGCTCACCCAAACAATTCCCCAAGAA 25 154 0 CCCAAACAAT 0.85696 -66 TGTTTGCGCTCCCAGTCCAAAAAATACTTT 26 112 1 CCCAGTCCAA 0.915047 -85 TCCATGTCGTCCCAATCCATCCCTAAAAAA 34 35 1 CCCAATCCAT 0.755868 -104 TAAAAAATAGCCCAAACAAAGGGCATTCTT 34 58 1 CCCAAACAAA 0.85696 -81 TCACGAAAGTCCCAAGCAATCCTGCTAGAA 36 47 0 CCCAAGCAAT 0.789577 -103 AAACAGGGTACCCAGGCAACTCAGTAAAAC 37 240 0 CCCAGGCAAC 0.800667 -61 ********** Masking position 4 Map Score: 8.86466 Number of sites scoring better than the average of aligned sites = 731 Number in coding regions = 644 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 12 GGGGGATTTGGACTTACACTTCCCTCATAA 1 237 1 GACTTACACT 0.916279 -64 TCATCAGAAGGACTTACCCTCAGAGCCTAA 1 272 1 GACTTACCCT 0.954162 -29 AGATGGGACTGACATGCCCTGAAGAGAGCC 2 84 0 GACATGCCCT 0.845266 -150 AACACCAGTGGACTTGCCCTATTCCACTTT 2 135 0 GACTTGCCCT 0.977269 -99 AATACTGGGGGACTTTCACTCAGTTTCCCC 4 166 0 GACTTTCACT 0.884232 -67 TGCATTTATAGCCTAACCCTCTACAATCGA 5 54 0 GCCTAACCCT 0.797188 -72 CCTGTATTTTGCCTTCCCCT 8 91 1 GCCTTCCCCT 0.967903 -10 CAATATGGGGGACTTTCACTCAGTTTCCCC 14 65 1 GACTTTCACT 0.884232 -114 ATTATCCCAGGCCTCCCCCTCCATCAGGGG 15 177 0 GCCTCCCCCT 0.862805 -38 GAAATACCTAGCCTTGCACTTTTCAAACAC 18 176 1 GCCTTGCACT 0.968086 -72 ATTGATGTTAGCCTTGGACTAGCTGTGTTC 26 73 0 GCCTTGGACT 0.779856 -124 ********** Masking position 10 Map Score: 7.92046 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 156 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 TCTAAGTCCCTTGTCGTTGCACTGGAACGG 4 99 0 TTGTCGTTGC 0.905678 -134 CAGTGACGATTTTTCGTTCCGGCTGTTCTG 5 87 0 TTTTCGTTCC 0.93211 -39 CTTGAGGGATTTTTTGATGCTGATTAATTA 7 13 0 TTTTTGATGC 0.864376 -43 TTAAACAAGCTTTTTGATCAACCCAGTTAA 10 129 1 TTTTTGATCA 0.569409 -20 CGGGGCTTCTTTTTTGTTGCTCACCCAAAC 25 167 0 TTTTTGTTGC 0.932282 -53 TCTTTGTTGGTTTTCGTTCCACGATGTAAA 27 31 0 TTTTCGTTCC 0.93211 -100 GCTTAGCGGTTTTTCGTTGAGT 31 3 0 TTTTCGTTGA 0.845377 -25 GTGGTGGATATTTTTGATCCAAAC 35 5 0 TTTTTGATCC 0.821445 -296 AAAAGTAAAATTTTCGTTGATTTTGTACAA 35 61 0 TTTTCGTTGA 0.845377 -240 CAAACTTTATTTTTTGTTACAAAAATCGTG 37 31 1 TTTTTGTTAC 0.605889 -270 CCACCAAATGTTGTTGTTGCTTGAGGAAAT 37 124 0 TTGTTGTTGC 0.874213 -177 TTCCTAATAGTTGTTGATCACGTTGATCAT 39 20 1 TTGTTGATCA 0.400327 -99 CGACCGGTTATATTCGTTGCTGCAGGCTGT 43 204 1 TATTCGTTGC 0.669324 -97 ********** Masking position 4 Map Score: 6.55041 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 245 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 14 AGGGACTTAGAGCCTGTTTTAAAAGCCCCCC 4 118 1 AGCCTGTTTA 0.947694 -115 TTCTAAGAACGTGTTTGGAAAGTTTTAT 4 215 0 AACGTGTTTG 0.912848 -18 AACGTGTTTTAAAAGCCCCCC 10 1 1 AACGTGTTTA 0.943578 -148 TTGATCAAAAAGCTTGTTTAAAAAGTCATGG 10 119 0 AGCTTGTTTA 0.737046 -30 AACGTGTTTGGAAAGTTTTAT 14 1 1 AACGTGTTTG 0.912848 -178 ACTTTCTAAGAGCCTGTTTTAAAAGCCCCCC 14 112 0 AGCCTGTTTA 0.947694 -67 CCATTGTTAGAGCGTGTTTCAAAAGTCGAGT 18 49 1 AGCGTGTTTA 0.947694 -199 TCCCCACTGGAAAGTGTTTGAAAAGTGCAAG 18 188 0 AAAGTGTTTA 0.805542 -60 AGAAACAAGTAAACTGTTTTGGTGTTTATTG 20 210 0 AAACTGTTTG 0.7218 -91 AGCGTACTTAAAACTGTTTTACTGAGTTGCC 37 225 1 AAACTGTTTA 0.805542 -76 TTGCCTGGGTACCCTGTTTTAGTCATCGTTC 37 251 1 ACCCTGTTTA 0.837287 -50 ********* * Masking position 1 Map Score: 6.1128 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 67 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 15 GCGAGAACTTTCCCGACAAAATCGTCTCCACT 3 11 0 TCCGAAAAAT 0.965182 -290 GCCTAGACAATTCCAACAAAATGTAATCAATG 6 95 0 TCCAAAAAAT 0.945601 -120 TGGTGTAACTACCCAATAAAATTTTTAACGGA 11 64 1 ACCAAAAAAT 0.688345 -28 CCGCATGGACTCCCAGCATAATAACAACA 13 73 1 TCCAGATAAT 0.673794 -19 AAACCCCAGTTTCAGGGAAAATTATAGAAACA 20 234 0 TCAGGAAAAT 0.671339 -67 TAGCTGCCATTACCGAGAAAATAAACCCCAGG 26 42 1 TCCGAAAAAT 0.965182 -155 AAGATCCATTTCCCGGAAAAATCCGTTCACAA 28 13 0 TCCGGAAAAT 0.962859 -43 TTGCCGATATTGCCGACAAAATTTTCCAACAC 32 56 0 TCCGAAAAAT 0.965182 -25 TCCCAATCCATCCCTAAAAAATAGCCCAAACA 34 44 1 TCCTAAAAAT 0.810907 -95 TTTCATTGATTGCCAAAAAAAACTGATTTTAG 38 17 0 TCCAAAAAAA 0.688345 -100 CCATCTCCACTACCAGGAAAATGGCGATCGCC 39 53 0 TCCAGAAAAT 0.94205 -66 * **** ***** Masking position 8 Map Score: 5.4463 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 126 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665