AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_synecho_reg_100.orf -o00910_synecho_100.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/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 sll1027 278 gltD; NADH-glutamate synthase small subunit. [EC:1.4.1.14] #2 sll1502 221 gltB; ferredoxin-dependent glutamate synthase 1 (FD-gogat). #3 slr1756 218 glnA; glutamine synthetase (glutamate--ammonia ligase). [EC:6.3.1.2] #4 sll1454 300 narB; nitrate reductase. [EC:1.7.99.4] [SP:NARB_SYNY3] #5 slr1347 73 icfA; carbonic anhydrase. [EC:4.2.1.1] [SP:CYNT_SYNY3] #6 slr1348 300 cysE; serine acetyltransferase (SAT). [EC:2.3.1.30] [SP:CYSE_SYNY3] #7 sll0422 120 asparaginase. [EC:3.5.1.1] #8 slr0288 163 glnN; glutamate-ammonia ligase. [EC:6.3.1.2] #9 sll0171 168 gcvT; probable aminomethyltransferase (glycine cleavage system T #10 sll0069 26 hypothetical protein. #11 sll0068 157 hypothetical protein. #12 slr0898 223 nirA; ferredoxin-nitrite reductase. [EC:1.7.7.1] #13 slr0903 154 hypothetical 16.5 kD protein slr0903. [SP:Y903_SYNY3] #14 slr0710 70 gdhA; NADP-specific glutamate dehydrogenase (NADP-gdh). [EC:1.4.1.4] #15 slr0711 191 hypothetical protein. #16 sll1499 300 gltS; ferredoxin-dependent glutamate synthase 2 (FD-gogat). #17 slr0749 300 chlL, frxC; protochlorophyllide reductase iron-sulfur ATP-binding #18 sll0572 300 hypothetical protein. Motif number 1 TTTTGGAATATGGGGCATTCAGACGGTCAAAG 1 48 0 TGGGGCATCG 0.820691 -231 CCAATGGCAGAGGGGAAGTTTGTAACAAAAAG 1 140 1 AGGGGAATTG 0.965606 -139 CCTCTTGTGGTGGGGGCGATCGCCGTAAATAA 1 246 0 TGGGGGCATG 0.921725 -33 GACATTATTTAGGGGGAATTGTTCAACGCTGG 2 65 1 AGGGGGATTT 0.924736 -157 GGTCATTACGGGGGGGAGGTAGGTTTCCTTAA 2 178 0 GGGGGGAGTG 0.926498 -44 ATTTTTCTGGGGGGCGATTTTTCTTTTGGAAA 3 52 0 GGGGCGATTT 0.785345 -167 GGAGCAAAATGGGGCAAGTTTGGCGACAGTGT 6 174 1 GGGGCAATTG 0.893162 -127 CAAAAGCTTGAGGGGACTTTAAGCTGGTTTAC 8 95 1 AGGGGACTTA 0.752842 -69 ATTGGGGGCTAGGGGACTTTCAATACAGGTTT 9 23 0 AGGGGACTTA 0.752842 -146 CCCCCAATACTGGGGGAATCAGATTCGATAAT 9 47 1 TGGGGGATCG 0.949811 -122 TCCTTTAACCAGGGGGATTTTTTGTGCTTTTT 9 81 1 AGGGGGATTT 0.924736 -88 TAAACTATGATGGGGCCATGGGGTTAGGGTTT 11 33 0 TGGGGCCTGG 0.695715 -125 GATTGGTGGAAGTGCGAATTTGTCGGTAATTA 11 90 1 AGTGCGATTG 0.603984 -68 TGTAATACCCTGTGGGAGTTTTCCCGTGGGAA 12 144 0 TGTGGGATTT 0.671623 -80 CTGATAAATCTGGGGACATTAACGATGGGGAA 12 177 1 TGGGGACTTA 0.847238 -47 ATAATTATCCGGTGGGAATTGGTAATTTTAGT 13 65 0 GGTGGGATTG 0.872982 -90 CCTAAGTTTTGGGGGAAGTTAGCTCAAAGTTT 15 118 0 GGGGGAATTG 0.970169 -74 AGGGGGTAGCTGGGGACTTTTGAAACATGCTC 15 147 1 TGGGGACTTG 0.979164 -45 ACCATCAGGCTGGGCAATTTTGTTGGCCATGG 16 64 1 TGGGCAATTG 0.92928 -237 AACCGCTTCATGGGGGCGATCGCCAAATTTGG 16 187 0 TGGGGGCATG 0.921725 -114 CCCCTCAGCCTGGGGGCGGTGGTTAATTTTAC 16 251 0 TGGGGGCGTG 0.947956 -50 CCCCAGGCTGAGGGGCCCTTTGGGGTCTCCCA 16 268 1 AGGGGCCTTG 0.935187 -33 CCCCCAATACTGGGGGACTTAGAATTAGATTT 17 263 0 TGGGGGATTG 0.991608 -38 CCCCCAGTATTGGGGGATTTAGGGGGTTAGAC 17 279 1 TGGGGGATTG 0.991608 -22 TCCATCAAAATGGGCAATTTTTTGGCCGAACC 18 84 1 TGGGCAATTT 0.713287 -217 ******* ** * Masking position 4 Map Score: 36.7621 Number of sites scoring better than the average of aligned sites = 2185 Number in coding regions = 1855 Number in noncoding regions = 330 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 2 TTCGGGGCTTGGCCATGGCCCCACCAGGGA 1 91 1 GGCCATGGCC 0.499902 -188 TAACAAAAAGCAACATGGCCAGCAAATCTC 1 162 1 CAACATGGCC 0.646432 -117 CCTTATTTACGGCGATCGCCCCCACCACAA 1 244 1 GGCGATCGCC 0.49984 -35 AGCTGCTGGAGACCACCGCT 2 1 0 GACCACCGCT 0.764626 -221 TTATCCGTTTGGCGATCGCCGTTTAATTTA 3 83 1 GGCGATCGCC 0.49984 -136 CCCCGCCCTTGAGGACGGCCTTGCGTTCAC 6 25 1 GAGGACGGCC 0.739256 -276 GACAAAAAAAGGCGATCGCCAAGGCTTTTC 6 115 1 GGCGATCGCC 0.49984 -186 GGATGGGTAAAACCATCTCCCAATGCTGGG 8 127 0 AACCATCTCC 0.619567 -37 GAAACCCTAACCCCATGGCCCCATCATAGT 11 32 1 CCCCATGGCC 0.851939 -126 CCTATCCACGAACCATTGCCGCCCAGCAGA 12 98 1 AACCATTGCC 0.849815 -126 CATTTTTCTGCACCATGGCCAACAAAATTG 16 78 0 CACCATGGCC 0.955894 -223 CCCCAAATTTGGCGATCGCCCCCATGAAGC 16 185 1 GGCGATCGCC 0.49984 -116 AAGGCGAACGAACCACTGCCTAGGCTAACT 16 220 1 AACCACTGCC 0.77504 -81 TGGTAAAATTAACCACCGCCCCCAGGCTGA 16 249 1 AACCACCGCC 0.945251 -52 GAAAAAATATGACGATGGCAGAGAATATTT 17 129 0 GACGATGGCA 0.743013 -172 ********** Masking position 5 Map Score: 16.0971 Number of sites scoring better than the average of aligned sites = 8377 Number in coding regions = 7671 Number in noncoding regions = 706 Number of orfs with sites within 600 bp upstream = 457 Fraction of orfs with sites within 600 bp upstream = 0.0734019 Motif number 3 TCTGGGGGGCGATTTTTCTTTTGGAAAGAT 3 49 0 GATTTTTCTT 0.839561 -170 TATTGAAACAGATTTTTCCCAGGGCCACCG 3 171 1 GATTTTTCCC 0.979946 -48 AGGAAAAATCAGTTTTTCCTTATTCCAGGT 4 123 0 AGTTTTTCCT 0.667272 -178 AGGAAAAACTGATTTTTCCTGGCGAACAGT 4 133 1 GATTTTTCCT 0.963349 -168 TTGGCCGGATGTTTTTTCCTGTTTAATAAA 6 77 0 GTTTTTTCCT 0.824878 -224 CGATCGCCAAGGCTTTTCCCGCAACACCAA 6 127 1 GGCTTTTCCC 0.906694 -174 ATTGGGAGATGGTTTTACCCATCCCCCTGG 8 133 1 GGTTTTACCC 0.857591 -31 CTGCATAATAGATTTTTCCTAAAAAAAGCA 9 105 0 GATTTTTCCT 0.963349 -64 GGGTTTCTCCTTGTGATTAGT 12 2 1 GGTTTCTCCT 0.905832 -222 TACCCTGTGGGAGTTTTCCCGTGGGAATCC 12 141 0 GAGTTTTCCC 0.893477 -83 CTTAGAATTAGATTTCTCTCGCATATTTCT 17 248 0 GATTTCTCTC 0.754513 -53 ATATCCTAGCGGTTTTTCTCCATCAAAATG 18 66 1 GGTTTTTCTC 0.918497 -235 ACAGCAACGGGATTATTCCCAGAACCTTTG 18 153 0 GATTATTCCC 0.838708 -148 ********** Masking position 4 Map Score: 13.497 Number of sites scoring better than the average of aligned sites = 967 Number in coding regions = 834 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 CCCACCAGGGATTTTTGTTGGTAACTTGTAC 1 110 1 ATTTTGTTGG 0.578398 -169 TTTTAGACATTATTTAGGGGGAATTGTTCAA 2 60 1 TATTAGGGGG 0.686821 -162 CAAACGGATAATTTTTCTGGGGGGCGATTTT 3 63 0 ATTTTCTGGG 0.46085 -156 TTTCTAGACCAACTTAGTCGGGGCCATAATC 3 124 1 AATTAGTCGG 0.897762 -95 CCCCATTGCAACCTTTGTCGGATAAACGCAA 5 42 0 ACTTTGTCGG 0.844453 -32 GCTCCGAGGGAATTTTCTGGGGTTGGTGTTG 6 148 0 AATTTCTGGG 0.819985 -153 AAAATGGGGCAAGTTTGGCGACAGTGTGTGG 6 179 1 AATTTGGCGA 0.822247 -122 TTTTGGACAGAACTTTGGTGGTTAACCACAC 6 204 0 AATTTGGTGG 0.921606 -97 AAGCTTTTGGAAGTTTGGGGGGATTAATGAT 8 73 0 AATTTGGGGG 0.979364 -91 GTGGAAGTGCGAATTTGTCGGTAATTATTTG 11 95 1 GATTTGTCGG 0.833915 -63 TATTGCCGGAACTTTAGTGGGTCGATTTAGG 15 82 0 ACTTAGTGGG 0.800883 -110 CTTCCCCCAAAACTTAGGGGGTAGCTGGGGA 15 132 1 AATTAGGGGG 0.957049 -60 CAGGCTGGGCAATTTTGTTGGCCATGGTGCA 16 69 1 AATTTGTTGG 0.879676 -232 GGCGATCGCCAAATTTGGGGAGGGAGACGAA 16 174 0 AATTTGGGGA 0.879513 -127 TTAAAGCCTAAAATTTGGCGATTTCGTAATT 17 89 1 AATTTGGCGA 0.822247 -212 AGTATTGGGGGATTTAGGGGGTTAGAC 17 284 1 GATTAGGGGG 0.85677 -17 ** ******** Masking position 5 Map Score: 13.5715 Number of sites scoring better than the average of aligned sites = 1327 Number in coding regions = 1008 Number in noncoding regions = 319 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 5 CAGTTCCCAACCAATGGAGGGTAACTTTTA 1 194 0 CCAATGGAGG 0.877662 -85 GGGGAATTGTTCAACGCTGGAACTAACCAC 2 77 1 TCAACGCTGG 0.906289 -145 TGCTACTATCGCAATAGTGGCAATAAATTA 4 72 1 GCAATAGTGG 0.881192 -229 AAACCATCTCCCAATGCTGGGGTAAACCAG 8 118 0 CCAATGCTGG 0.963298 -46 TAGGGGACTTTCAATACAGGTTTTAAAACC 9 16 0 TCAATACAGG 0.833882 -153 CCCCTAGCCCCCAATACTGGGGGAATCAGA 9 40 1 CCAATACTGG 0.937437 -129 TAAAGTTCCGGCAATACTGGAAAACTTTGA 15 97 1 GCAATACTGG 0.959791 -95 GGCGAACTACCCAACGCTGACCGGTGGCA 16 10 0 CCAACGCTGA 0.775672 -291 CCTAAATCCCCCAATACTGGGGGACTTAGA 17 272 0 CCAATACTGG 0.937437 -29 ********** Masking position 4 Map Score: 8.98913 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 338 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 6 TGCTAAAAATACTTCGACCTTTGACCGTCTGAATGCC 1 30 1 ATCCTTTCCG 0.963478 -249 TTAATACGATTGGTCGATATTTGATCGCAGTGAAAAA 4 205 0 TTCTTTTTCG 0.857395 -96 GTATTAACTGTATTCATCTTTTGGTCAATTAGTGGTC 4 235 1 TTCCTTTTCA 0.953571 -66 AAAATTGGCATTGTTTGCGTTTATCCGACAAAGGTTG 5 28 1 TTTCTTTCCG 0.942463 -46 CCTTTTTTTGTCCTCAATTTTTGGCCGGATGTTTTTT 6 90 0 TTCTTTTCCG 0.942462 -211 TATATCTAAAAAATCAGCAATTTCCCGATCATTAATC 8 46 1 ATCCATTCCG 0.770219 -118 TCAGATTCGATAATCCTCCTTTAACCAGGGGGATTTT 9 65 1 TTCCTTTCCA 0.982426 -104 TTAGTGTTATTAATCTCCATTTAGCCAGATGGTTAGT 13 125 1 TTCCTTTCCA 0.982426 -30 AGGCAGTGGTTCGTTCGCCTTTAACCGCTTCATGGGG 16 204 0 TTTCTTTCCG 0.942463 -97 CTTTGATTATTAATCCACTTTTCCTCACTTACTCCCC 18 17 0 TTCCTTTTCA 0.953571 -284 CCCCGGTTGCTTTTCTACCTTTTATCATAAACAGCAA 18 176 0 TTCCTTTTCA 0.953571 -125 * ** * *** *** Masking position 11 Map Score: 9.31935 Number of sites scoring better than the average of aligned sites = 293 Number in coding regions = 256 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 TCATTACGGGGGGGAGGTAGGTTTCCTTAAT 2 177 0 GGGGAGGAGG 0.938964 -45 GCTAAAACTGGGTGAGATGGACTGGT 3 203 1 GGTGAGAGGA 0.836627 -16 GTTGCTAGGAGGTGAGAGGGAATGATCAAAG 4 14 0 GGTGAGAGGA 0.836627 -287 GGGATGTGGAGGGGCATAGGAGGTGACTATT 6 253 0 GGGGCATGGA 0.754453 -48 GAAGTCAGAAGGGAAGGCAGATCCAAACTTT 7 14 0 GGGAAGGAGA 0.919 -107 ACCCCAGCATTGGGAGATGGTTTTACCCATC 8 125 1 TGGGAGAGGT 0.54627 -39 CCCAATACTGGGGGAATCAGATTCGATAATC 9 49 1 GGGGAATAGA 0.920447 -120 AACGGTTCTAGGGTAGGTAGATTTGGTACAG 11 134 1 GGGTAGGAGA 0.817861 -24 TTATTTTTTCGGTGAGTAAGTTACCTACCTA 12 71 1 GGTGAGTAGT 0.83802 -153 CATTAACGATGGGGAAGCGGACTAGGACTAG 12 193 1 GGGGAAGGGA 0.947886 -31 TAAGTTTTGGGGGAAGTTAGCTCAAAGTTTT 15 117 0 GGGAAGTAGC 0.63135 -75 CGCCAAATTTGGGGAGGGAGACGAAATTAAC 16 168 0 GGGGAGGAGA 0.986625 -133 CCTCAGCCTGGGGGCGGTGGTTAATTTTACC 16 250 0 GGGGCGGGGT 0.929956 -51 AATTCTTCATGGGAAATAAGTTAAACGTAGC 17 213 1 GGGAAATAGT 0.546719 -88 CCCAATACTGGGGGACTTAGAATTAGATTTC 17 262 0 GGGGACTAGA 0.839026 -39 TGATTCGGGGAGTAAGTGAGGAAAAGT 18 7 1 GGGGAGTAGT 0.973109 -294 AACCAAGATTGGGGAGAAGGTTCCCAGGCAA 18 112 1 GGGGAGAGGT 0.960438 -189 ******* *** Masking position 2 Map Score: 17.5565 Number of sites scoring better than the average of aligned sites = 1453 Number in coding regions = 1298 Number in noncoding regions = 155 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 8 TTTTAGCAAAAAATCAGCAATCAAACC 1 8 0 AAATCAGCAA 0.920589 -271 CCATTGGTACAAGTTACCAACAAAAATCCC 1 117 0 AAGTTACCAA 0.868628 -162 CCCTCAGGACAAATTAACTATTAAAGTTTT 4 179 1 AAATTAACTA 0.757398 -122 TATATCTAAAAAATCAGCAATTTCCCGATC 8 46 1 AAATCAGCAA 0.920589 -118 AAAATCAAAGAAATCAGCAAGTCCTTTCTG 9 132 0 AAATCAGCAA 0.920589 -37 TTGACTATAAAAATAAACTATGATGGGGCC 11 48 0 AAATAAACTA 0.575956 -110 TTTATAGTCAAAATAAACTACATGATTGGT 11 67 1 AAATAAACTA 0.575956 -91 TTCGGTGAGTAAGTTACCTACCTATCCACG 12 78 1 AAGTTACCTA 0.774211 -146 AGGGTCACTAAAATTACCAATTCCCACCGG 13 59 1 AAATTACCAA 0.922041 -96 TGGACAATAAAAGTCAACAATGAAATTACC 17 37 1 AAGTCAACAA 0.842931 -264 GTCAACAATGAAATTACCAATAGGATGCTG 17 49 1 AAATTACCAA 0.922041 -252 AGGAATTACGAAATCGCCAAATTTTAGGCT 17 93 0 AAATCGCCAA 0.764031 -208 ********** Masking position 2 Map Score: 6.74072 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 305 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 GCCCTGGGAAAAATCTGTTTCAATAACCGG 3 166 0 AAATCTGTTT 0.850358 -53 CGATAGTAGCAAAGCTGATTATCACTGTCA 4 53 0 AAAGCTGATT 0.826887 -248 GGAATAAGGAAAAACTGATTTTTCCTGGCG 4 127 1 AAAACTGATT 0.76319 -174 TAATTGAAGCGAATTTGATTAGTTGACCAC 4 266 0 GAATTTGATT 0.893076 -35 ATTGGTCAATAGATTTGATTAAAACCC 8 8 0 AGATTTGATT 0.695987 -156 GAGGATTATCGAATCTGATTCCCCCAGTAT 9 53 0 GAATCTGATT 0.94078 -116 TTAATGGCACTAATTTGATTTAATAACGAT 13 95 0 TAATTTGATT 0.677654 -60 AGCTGGCTCAGAATCTGTTTGTAAAATCTG 15 43 1 GAATCTGTTT 0.780671 -149 TCTGTTTGTAAAATCTGATTTTTGACCCTA 15 56 1 AAATCTGATT 0.962069 -136 GGCAAATTTAAACTTTGATTATTAATCCAC 18 36 0 AACTTTGATT 0.695987 -265 CACCAGCTCGAAATATGATTAACCAGGGTA 18 237 0 AAATATGATT 0.766891 -64 TTAAGGTTGAAAATTTGATTGAACGGACGT 18 268 1 AAATTTGATT 0.930244 -33 ********** Masking position 6 Map Score: 7.90056 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 138 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 TTAGCTCCGGTGGCCCTGGGAAAAATCTGTTT 3 176 0 TGCCTGGGAA 0.886279 -43 AAAAACTGATTTTTCCTGGCGAACAGTTATTA 4 136 1 TTCCTGGCGA 0.910099 -165 TGCCCCATTTTGCTCCGAGGGAATTTTCTGGG 6 158 0 TGCCGAGGGA 0.787058 -143 TATTTGTTGGTTCACTTAGGAATTTTGGACAG 6 225 0 TTCTTAGGAA 0.525978 -76 GTTTTACCCATCCCCCTGGGGTGATATGCA 8 144 1 TCCCTGGGGT 0.853456 -20 AGTGACCAGATCAACCTGGGAAACCCTAACCC 11 13 1 TCCCTGGGAA 0.983706 -145 CCTAGAACCGTTGGCCGGGGCAAATAATTACC 11 114 0 TTCCGGGGCA 0.891519 -44 TGTGGGAGTTTTCCCGTGGGAATCCCATGGCT 12 134 0 TTCGTGGGAA 0.779838 -90 TTTACTTTAATTATCCTAGCGAAAAAGGGTCA 13 34 1 TTCCTAGCGA 0.764163 -121 TTTTGAAACATGCTCCTAGGAACTAGGATTAG 15 164 1 TGCCTAGGAA 0.922945 -28 AGTAGTACCATCAGGCTGGGCAATTTTGTTGG 16 58 1 TCGCTGGGCA 0.784874 -243 ATTTTACCAGTTAGCCTAGGCAGTGGTTCGTT 16 226 0 TTCCTAGGCA 0.923046 -75 AAAGGGCCCCTCAGCCTGGGGGCGGTGGTTAA 16 257 0 TCCCTGGGGG 0.911698 -44 CTATGGGAATTCTTCATGGGAAATAAGTTAAA 17 206 1 TCCATGGGAA 0.800401 -95 GTTACAATACTTTGCCTGGGAACCTTCTCCCC 18 122 0 TTCCTGGGAA 0.98123 -179 ** ******** Masking position 1 Map Score: 9.86795 Number of sites scoring better than the average of aligned sites = 2248 Number in coding regions = 2047 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 11 CCCCTCCACATCCCATCCCAGTTATGGCTACC 6 270 1 TCCCATCCGT 0.976451 -31 CCCGTGGGAATCCCATGGCTTTGAACTCTGCT 12 122 0 TCCCATGCTT 0.980564 -102 TGCTTCCTAATCCCGTCCATTTTTCACTGTTC 14 14 0 TCCCGTCATT 0.880769 -57 CTTTGGGGTCTCCCATTGCTGTCCAG 16 285 1 TCCCATGCGT 0.987552 -16 CATGAAGAATTCCCATAGAATTCGTGGAACTA 17 192 0 TCCCATGATT 0.944592 -109 CTGGGAATAATCCCGTTGCTGTTTATGATAAA 18 161 1 TCCCGTGCGT 0.985023 -140 ****** ** ** Masking position 6 Map Score: 1.75894 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 67 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 GGTCTCCAGCAGCTAGGGACTGACCTTCAG 2 17 1 AGCTAGGGAC 0.864694 -205 GCTCCGGTGGCCCTGGGAAAAATCTGTTTC 3 175 0 CCCTGGGAAA 0.76721 -44 CCCTCTCACCTCCTAGCAACTCGATCCATG 4 25 1 TCCTAGCAAC 0.830031 -276 AACTGATTTTTCCTGGCGAACAGTTATTAT 4 139 1 TCCTGGCGAA 0.92475 -162 CCCATTTTGCTCCGAGGGAATTTTCTGGGG 6 157 0 TCCGAGGGAA 0.628163 -144 GACCAGATCAACCTGGGAAACCCTAACCCC 11 16 1 ACCTGGGAAA 0.87975 -142 CAGCTGATAAATCTGGGGACATTAACGATG 12 174 1 ATCTGGGGAC 0.801893 -50 ACTTTAATTATCCTAGCGAAAAAGGGTCAC 13 37 1 TCCTAGCGAA 0.83003 -118 CTTAGGGGGTAGCTGGGGACTTTTGAAACA 15 144 1 AGCTGGGGAC 0.941459 -48 TGAAACATGCTCCTAGGAACTAGGATTAGT 15 167 1 TCCTAGGAAC 0.914609 -25 GGGCCCCTCAGCCTGGGGGCGGTGGTTAAT 16 256 0 GCCTGGGGGC 0.858319 -45 ACCAATAGGATGCTGGCGACGAAATTTAAA 17 64 1 TGCTGGCGAC 0.914783 -237 ACAATACTTTGCCTGGGAACCTTCTCCCCA 18 121 0 GCCTGGGAAC 0.938511 -180 ********** Masking position 3 Map Score: 7.37315 Number of sites scoring better than the average of aligned sites = 1394 Number in coding regions = 1240 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 13 AGCGTTGAACAATTCCCCCTAAATAATGTCT 2 64 0 ATTCCCCCTA 0.830392 -158 TCCAAAAGAAAAATCGCCCCCCAGAAAAATT 3 54 1 AATCGCCCCC 0.914082 -165 CTGCGATCAAATATCGACCAATCGTATTAAC 4 212 1 AATCGACCAA 0.913117 -89 TTCCCTTCTGACTTCGACCCATAATCACTAA 7 30 1 ATTCGACCCA 0.935568 -91 TCCCGATCATTAATCCCCCCAAACTTCCAAA 8 68 1 TATCCCCCCA 0.857521 -96 TGCATATCACCCCAGGGGGATGGG 8 150 0 AATCACCCCA 0.889364 -14 ACAAATTCGCACTTCCACCAATCATGTAGTT 11 82 0 ATTCCACCAA 0.864882 -76 TTTTGACCCTAAATCGACCCACTAAAGTTCC 15 75 1 AATCGACCCA 0.952356 -117 CTTTGAGCTAACTTCCCCCAAAACTTAGGGG 15 121 1 ATTCCCCCAA 0.952028 -71 AGCGTTGGGTAGTTCGCCCCATCTTCCTTCG 16 22 1 ATTCGCCCCA 0.978269 -279 AGGAATTACGAAATCGCCAAATTTTAGGCTT 17 92 0 AATCGCCAAA 0.700417 -209 CTAACCCCCTAAATCCCCCAATACTGGGGGA 17 278 0 AATCCCCCAA 0.964689 -23 * ********* Masking position 4 Map Score: 13.2039 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 491 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 14 ATGGCCAGCAAATCTCAATAAAAGTTACCCTC 1 176 1 AACTCAAAAA 0.94003 -103 CGCTGGAACTAACCACAACAAAATAGTTAAAT 2 91 1 AACACAAAAA 0.953294 -131 ACCATTGATTAGACTCAACAAATCTTTCCAAA 3 28 1 AGCTCAAAAA 0.949822 -191 TTGGTCTAGAAATAACAAAAAATTAAATTAAA 3 104 0 AAAACAAAAA 0.725836 -115 TTCCTAAAAAAAGCACAAAAAATCCCCCTGGT 9 88 0 AACACAAAAA 0.953294 -81 TTATTTTTATAGTCAAAATAAACTACATGATT 11 62 1 AGCAAAAAAA 0.761737 -96 AGTTAAACGTAGCCTCAAGAAATATGCGAGAG 17 231 1 AGCTCAAAAA 0.949822 -70 ** ***** *** Masking position 7 Map Score: 1.35896 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 55 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 15 CGCTACAATTCAAAAACCGGGGA 2 209 1 CAAAAACCGG 0.90829 -13 TTAGTCGGGGCCATAATCGGTGAACTAGGC 3 137 1 CCATAATCGG 0.891055 -82 AAATCTGTTTCAATAACCGGCCTAGTTCAC 3 156 0 CAATAACCGG 0.817712 -63 GCCACCGGAGCTAAAACTGGGTGAGATGGA 3 194 1 CTAAAACTGG 0.932099 -25 CAATTCCTACCTAAAATTGGCATTGTTTGC 5 16 1 CTAAAATTGG 0.838264 -58 CTCCCGGTAGCCATAACTGGGATGGGATGT 6 277 0 CCATAACTGG 0.961595 -24 CCCCTAGCCCCCAATACTGGGGGAATCAGA 9 40 1 CCAATACTGG 0.757601 -129 GTCTCCCTCCCCAAATTTGGCGATCGCCCC 16 177 1 CCAAATTTGG 0.476905 -124 CCTAAATCCCCCAATACTGGGGGACTTAGA 17 272 0 CCAATACTGG 0.757601 -29 TTTGGCCGAACCAAGATTGGGGAGAAGGTT 18 104 1 CCAAGATTGG 0.722918 -197 ********** Masking position 3 Map Score: 6.98125 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 379 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516