AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ipurR_mthe_opreg_300.orf -g0.495 -x5 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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH130 171 cobalamin biosynthesis protein M #2 MTH132 86 cobalt transport protein Q #3 MTH133 167 cobalt transport ATP-binding protein O #4 MTH137 57 unknown #5 MTH139 269 heterodisulfide reductase HdrD related protein #6 MTH140 52 conserved protein #7 MTH141 102 conserved protein #8 MTH147 23 phenylacrylic acid decarboxylase #9 MTH148 47 conserved protein #10 MTH150 75 conserved protein #11 MTH170 141 phosphoribosylaminoimidazolesuccinocarboxamide synthase #12 MTH615 173 adenylosuccinate synthetase #13 MTH616 238 conserved protein #14 MTH648 65 ribosomal protein L37 #15 MTH649 300 conserved protein #16 MTH661 119 ammonium transporter #17 MTH662 61 nitrogen regulatory protein P-II #18 MTH663 205 ammonium transporter #19 MTH709 300 GMP synthetase, subunit A #20 MTH710 102 GMP synthetase, subunit B #21 MTH784 83 ribose-phosphate pyrophosphokinase #22 MTH997 31 carbamoyl-phosphate synthase, large subunit #23 MTH1201 95 conserved protein #24 MTH1202 236 proteasome, beta subunit #25 MTH1203 69 cleavage and polyadenylation specificity factor #26 MTH1204 46 phosphoribosylformylglycinamidine cyclo-ligase #27 MTH1375 22 isoleucyl-tRNA synthetase #28 MTH1376 65 conserved protein #29 MTH1380 167 serine hydroxymethyltransferase #30 MTH1381 151 heterodisulfide reductase, subunit A #31 MTH1383 52 DNA repair protein RadA #32 MTH1385 300 replication factor A related protein #33 MTH1393 141 phosphoribosylaminoimidazole carboxylase #34 MTH1445 64 glycinamide ribonucleotide synthetase #35 MTH1537 300 adenylosuccinate lyase #36 MTH1862 300 conserved protein #37 MTH1864 109 phosphoribosylformylglycinamidine synthase II related protein #38 MTH1865 37 conserved protein Motif number 1 ATAGCCCACCATCTGGAGGTATCAGAAATC 3 49 0 ATCTGGAGGT 0.968448 -119 AGAAGGTTTAAACAGGAGATCAGCT 4 43 1 AACAGGAGAT 0.715801 -15 ATCGGAACTTATCAGGAGGAGAAACG 6 37 1 ATCAGGAGGA 0.867164 -16 CATGATTTTTACCAGGAGGTTATAGA 7 87 1 ACCAGGAGGT 0.989491 -16 GTTAATCTGTTCCAGGAGGTTTCTGTCCTG 9 18 0 TCCAGGAGGT 0.912324 -30 GACGAGTGCAACCAGAATGTAAATTATATC 19 215 1 ACCAGAATGT 0.831036 -86 ACTGGGACCTGAAGGTACCCACCCTA 20 7 1 ACCTGAAGGT 0.937134 -96 ATTGTTAATTACCGGAAGGTGATTTTTC 21 66 1 ACCGGAAGGT 0.900466 -18 ACCAATATATAACAGGAGGTCCTTATTAAA 24 96 0 AACAGGAGGT 0.97451 -141 ATTTCTCCTGAACTGGATGTATATACTTAT 28 12 1 AACTGGATGT 0.715046 -54 ATATGGGGACATCAGAAGGTTAAAGAGGCT 32 90 0 ATCAGAAGGT 0.96057 -211 GTTACAGAGTATCAGAAGGTGTACTG 33 7 0 ATCAGAAGGT 0.96057 -135 TCTCTCAGTAATCTGGAGGTCCTTCAGTTT 35 30 1 ATCTGGAGGT 0.968448 -271 ********** Masking position 7 Map Score: 16.3061 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 301 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 ATTATTCTGATGATTCACCCCTGCCCCTGTAG 2 42 0 TGATTCCCCT 0.942355 -45 TCTGTGGCCCTGGATATCCCGTGCAGTCTCTC 5 124 0 TGGATACCCT 0.925264 -146 AATCATGGAATGAATATCCCAAGAAACATGAT 7 62 0 TGAATACCCA 0.866831 -41 TCCTGAGGTGTGAAAAACCCCTTGAAAACTTG 12 71 1 TGAAAACCCT 0.616249 -103 AAACTTTTATTGGATACCCCTTAATATATGAG 12 126 1 TGGATACCCT 0.925264 -48 GGTGATTCTCCCTAAAATTTCTGC 12 160 0 TGATTCCCCA 0.912633 -14 TCTGTAAAGTTGATCCACCCTTCCCCTTACAA 14 17 0 TGATCCCCCT 0.943369 -49 GTCCGCCCTGGGATCCCCCCATCCATGAGAGA 15 138 0 GGATCCCCCT 0.952931 -163 ATCCATTCCAGGGTCCGCCCTGGGATCCCCCC 15 150 0 GGGTCCCCCG 0.851827 -151 TATGTCCATGGGGACAGCCCTTTGCAGGGTTA 24 136 1 GGGACACCCT 0.938772 -101 GGATTTGATGGGGTTAACCCAT 29 1 0 GGGTTACCCT 0.937681 -167 AATCGGATTCGGAATCCCCCCAGCTATCAACA 29 68 1 GGAATCCCCA 0.926983 -100 TAACACTCCTTGATCATCCCGAAAATCTGAGT 35 277 0 TGATCACCCA 0.868989 -24 TCAGCTTTGAGGGATCACCCTAATAAATGTAC 36 265 0 GGGATCCCCA 0.939133 -36 ****** *** * Masking position 8 Map Score: 11.6743 Number of sites scoring better than the average of aligned sites = 237 Number in coding regions = 206 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 3 TTTTCTATAAATTCTGATCTAAATTAAAGTTTCCTTGAT 1 88 0 ATGATTAAAG 0.868008 -84 AAACTTTAAAATTGAGGTATATAATGTTTTCTATAAATT 1 114 0 AAGGTTATAT 0.819995 -58 AAAGAAAGGTATAAAAAGGTGCTGTGCTAGA 7 3 1 AAGGTTAAAG 0.85433 -100 TCCAATACTTATATAGGTGTAAATTCTATTATGAGTTAT 11 69 0 AAGGTTAAAT 0.898424 -73 TCAGCTCGTTAGTTAGATTTAAATATAATCCGGCTAAAT 15 257 1 AAGATTAAAT 0.936031 -44 ACACAGATTTAAACATGGTTCACAGAAGT 17 1 1 AAGATTAAAT 0.935928 -61 GAGTAAGATGATGCTGATATATAAATCTTTCGGATATAG 18 99 0 ATGATTATAT 0.836279 -107 CCTATTTCCGACTATGATATAAATTGTTGGAGAGAAAAA 18 158 1 ATGATTAAAG 0.868008 -48 GCAGATGCGCAACCTGATTTAAACTCATTTCATAAAAAG 19 28 0 ATGATTAAAT 0.908257 -273 CCTTCCCCGCAGGAAGATGTATATGATGTATGCAATTAT 19 119 1 AAGATTATAT 0.882856 -182 AAAAACTTTAAGTAAGGTTTATATACTATTACACTTTCC 30 71 0 AAGGTTATAT 0.819995 -81 CCGGGTGAAAATATAGATGTAAAATTCAGACGAGTTTTT 32 154 0 AAGATTAAAG 0.906566 -147 ATACTTTGATAATAAGATTTAAATATATAGTAATAACTT 32 201 1 AAGATTAAAA 0.650262 -100 AATCACCATAAGTTTGATGTATAAAGCTTATTATATCTC 35 94 0 ATGATTATAT 0.836279 -207 TGGCTCCCAGATGCTGATTTAAATAACCTAACGAAAACT 36 14 0 ATGATTAAAT 0.908405 -287 * **** **** * Masking position 11 Map Score: 11.2115 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 16 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 ACCGTGATCCCTTAAACGTTATGA 3 154 0 TGATCCCTTA 0.81749 -14 ATATCAGTTATGTTCCCTGACTATTAATAG 5 60 0 TGTTCCCTGA 0.906469 -210 AGGAGTGCTGTGGACCATGCAGTACCGCGC 13 55 0 TGGACCATGC 0.858907 -184 ACTTAAGTTTTGGTCCCTGATGGTCAGCAG 13 165 0 TGGTCCCTGA 0.980087 -74 GATCCCAGGGCGGACCCTGGAATGGATTTG 15 155 1 CGGACCCTGG 0.866905 -146 TTTACCGACGATCCATGCTTAATGAATA 31 9 1 CGATCCATGC 0.709209 -44 GGAACCTTTATGAACCCTTCAATTATTCTG 32 25 0 TGAACCCTTC 0.73564 -276 TTCCAGCAAGTGGTCCATGGGGCAGTCTGT 32 51 1 TGGTCCATGG 0.847297 -250 TTTGGTCCCTCACTTGATTAAT 32 289 0 TGGTCCCTCA 0.929382 -12 GACCTGTAAATGGTCCCTGCGGGAGGTGCC 33 74 1 TGGTCCCTGC 0.985086 -68 GTGTGAGTTTCGGTCCCTTCGTCTCCTCTT 35 198 0 CGGTCCCTTC 0.892 -103 CCCTAATAAATGTACCCTGAGATGATGAAG 36 250 0 TGTACCCTGA 0.81774 -51 TTTATTAGGGTGATCCCTCAAAGCTGAAGA 36 270 1 TGATCCCTCA 0.828623 -31 ********** Masking position 8 Map Score: 10.0079 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 672 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TTCTTTTTCTCAGGGCTGCTGACAACTATTAA 5 35 1 CAGGCGCTGA 0.993252 -235 ACGGGATATCCAGGGCCACAGAGAAGATACTC 5 134 1 CAGGCACAGA 0.954514 -136 AGAAGATACTCAGAGCCGCAGGACTGGAATAC 5 155 1 CAGGCGCAGG 0.989002 -115 TCCGGGGAACCTTTGCAGCTGATACCTTCGTA 13 84 1 CTTGCGCTGA 0.857812 -155 TTTATGTTGACATCGCAACTGGTAATGGAAGT 29 107 1 CATGCACTGG 0.883004 -61 CACTTCCACCCAGCGGTGCAGGTCTTGTAAGG 35 159 1 CAGGGGCAGG 0.937043 -142 TTAAAGTCTTCAGAGCTGCTGAATGGTAACCG 36 148 0 CAGGCGCTGA 0.993252 -153 TTTCCTGGGGCAGTGCAGCTGATTGCATTTTT 36 215 1 CAGGCGCTGA 0.993252 -86 *** ** ***** Masking position 5 Map Score: 8.25648 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 77 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 TGTAAGGACATAAAGTTCAGTAGAGTCGATTTC 1 16 0 TAATTCAGAG 0.977942 -156 ATCGATCCGATAGGATTAAGCAGACTTAAATAT 3 105 1 TAGTTAAGAG 0.814331 -63 TGACTATTAATAGTTGTCAGCAGCCCTGAGAAA 5 40 0 TAGGTCAGAG 0.916249 -230 TCATGTGGGTAACATTCAGAAGA 8 2 0 TAATTCAGAG 0.977942 -22 TTAACGCAGTTAATTTTCAGCAGTCACCTCCGC 13 126 1 TAATTCAGAG 0.977942 -113 TTTTGGTCCCTGATGGTCAGCAGGTGCCGGCGG 13 155 0 TGAGTCAGAG 0.855014 -84 ACAGATTAACTGATTTTAAGGAGGATTAGAAC 14 44 1 TGATTAAGAG 0.702751 -22 AGTATATACATCCAGTTCAGGAGAAATT 28 6 0 TCCTTCAGAG 0.818824 -60 AATATAGATGTAAAATTCAGACGAGTTTTTCAG 32 151 0 TAATTCAGCG 0.88387 -150 AATAACTTATTAGTTTTCAGGAGCTCACCAAGT 32 232 1 TAGTTCAGAG 0.969294 -69 CCATATAATATAAGTTTCACTAGCTGAAACTGA 35 53 0 TAATTCACAG 0.825017 -248 TCAGCCCGGTTACCATTCAGCAGCTCTGAAGAC 36 142 1 TACTTCAGAG 0.955891 -159 *** ***** ** Masking position 9 Map Score: 9.0846 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 57 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 AACCACAGCATGACTCTTCATCAAGGACTCT 5 187 0 TACTCTTCAT 0.764013 -83 TCTGAATCTCTGCCTCTTCAAGGAACCCTGT 5 232 0 TCCTCTTCAA 0.966658 -38 TAAAAGTTTTTCCCACCTCATCATTAACCCT 12 104 0 TCCACCTCAT 0.910982 -70 TGCACTGCAGTACCTCTTCAAATCCATTCCA 15 172 0 TCCTCTTCAA 0.966658 -129 TACTCCCACCTCATTCCTTTTAAT 24 4 1 TCCACCTCAT 0.910982 -233 GTCCCTTCGTCTCCTCTTCAAAGTACCTTAC 35 185 0 CCCTCTTCAA 0.942586 -116 GATTGCATTTTTCCTCTTCATCATCTCAGGG 36 235 1 TCCTCTTCAT 0.966658 -66 TTTCCAAGTCCTCCACTTCAATTGTG 37 6 0 CCCACTTCAA 0.910982 -104 * ********* Masking position 10 Map Score: 5.07948 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 157 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 GTTGCGGGGGCCTCTGAAAGGATAATATATG 1 56 0 CCTCTGAAGG 0.876567 -116 CTGCTGATATCCTCACATCGGTTTTTTGATT 3 22 1 CCTCACATGG 0.881708 -146 TCAGGATCAGCCTCAGAAGTATCC 4 4 0 CCTCAGAATA 0.911536 -54 TGCAAGACATCCTCTGAAGTAGATAACCATA 5 90 0 CCTCTGAATA 0.875593 -180 GGAACCCTGTCCTCAGAAGGACCGAACCACA 5 211 0 CCTCAGAAGA 0.965572 -59 GTTTTTCACACCTCAGGATGAACGCCCTTTT 12 58 0 CCTCAGGAGA 0.853991 -116 AAAATTTCTGCCTCTCATATATTAAGGGGTA 12 140 0 CCTCTCATTA 0.829754 -34 TCAACCACTCCTCACATAGAAGTCTGTCTT 13 219 0 CCTCACATGA 0.951029 -20 TATCCCCATTCCTCTCATCTAATATTCCC 22 9 0 CCTCTCATTA 0.829756 -23 GTGTTTCTCCCTCAGCTGGATA 27 3 0 CCTCAGCTGA 0.87422 -20 TTAAATATGACCTCCGATAGATTCTCTATAT 33 109 1 CCTCCGATGA 0.911136 -33 ******** ** Masking position 3 Map Score: 5.53876 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 362 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 CTGATCTAAATTAAAGTTTCCTTGATGGTTG 1 83 0 TTAAAGTTTC 0.941351 -89 TACCTCAATTTTAAAGTTTACTTTAGAAGGA 1 134 1 TTAAAGTTTC 0.937346 -38 GTATTCTATATTTAAGTCTGCTTAATCCTAT 3 114 0 TTTAAGTCTC 0.742753 -54 GGGTATCCAATAAAAGTTTTTCCCACCTCAT 12 114 0 TAAAAGTTTT 0.506242 -60 ATTGACTCATTTAAACTCTTCTGCAAGTATA 15 65 1 TTAAACTCTC 0.850679 -236 TCTACTAATATATAAGTTTTCTTGCACTGCA 15 194 0 TATAAGTTTC 0.623773 -107 GAGGTCCTTATTAAACTTTGCGATTTTTTTA 24 80 0 TTAAACTTTC 0.910478 -157 TTAGATAACCTTAAACTATTCTTTAGTGGTG 26 21 1 TTAAACTATC 0.589194 -26 TTATATACTATTACACTTTCCTCAGTTTTTT 30 61 0 TTACACTTTC 0.616544 -91 TAAACCTTACTTAAAGTTTTTGATAGAAATA 30 89 1 TTAAAGTTTT 0.76098 -63 CTTTAACTTTATATATAGAGAA 33 130 0 TTTAACTTTT 0.394458 -12 GTTTCCATCCTTAAAGTCTTCAGAGCTGCTG 36 159 0 TTAAAGTCTC 0.899902 -142 AGATCCTTTTTAAAAGTTTCCAAGTCCTCCA 37 22 0 TAAAAGTTTC 0.837675 -88 ********* * Masking position 5 Map Score: 5.13188 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 49 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 10 GATATGATAATTTTTTTAATTTATCTAGCA 7 35 0 TTTTTTTAAT 0.741968 -68 TTATTTATATTAAAAGTCCCT 13 2 1 TATTTATATT 0.845713 -237 CTCTCTACTTTTTTTATTCTCATGATAT 16 9 1 TTTTTTTATT 0.779864 -111 ATTCTCATGATATTTATAATGTTGGTAGAT 16 26 1 TATTTATAAT 0.816489 -94 ATTAAACAATTATTTTTATTTAACATATTT 18 14 1 TATTTTTATT 0.871026 -192 TCTGAAAAGCTATTTATATTTTACCGAATA 19 267 0 TATTTATATT 0.845713 -34 CTTTGCGATTTTTTTATAATAGATGGGGCT 24 66 0 TTTTTATAAT 0.700055 -171 GGTTTTTTATTATTTTTATTAGAGGTGTAT 24 215 1 TATTTTTATT 0.871026 -22 TTTTTCTCCTATTTTTAATTGCAGTAAAC 25 10 1 TATTTTTAAT 0.845719 -60 ********** Masking position 5 Map Score: 4.04574 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 17 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 AAGGATAATATATGTAAGATATGTAAGGACATAA 1 36 0 TATTAAATGT 0.810074 -136 AATTTACACCTATATAAGTATTGGAGAGTTGATC 11 83 1 TATTAATTGG 0.668001 -59 CCATCCTTAACATTAAATAGATGTCCTGCAAGAT 20 56 1 CATAAAATGT 0.927161 -47 TAGAGTTATCTATATAAAAATTGTTAATTACCGG 21 47 1 TATTAAATGT 0.810074 -37 CCGTAAAAGCCATTAAATACTTGGAGGAAAAAAG 23 51 0 CATAAAATGG 0.928422 -45 TCCCCATGGACATAAAAGTTCTGTACCAATATAT 24 116 0 CATAAATTGT 0.854921 -121 CAGGGAATATCAGTAAACAGGTGTTTACTGCAAT 25 28 0 CAGAAAATGT 0.667515 -42 GCGATGTCAACATAAAAAACGCGTGTTGATAGCT 29 89 0 CATAAAACGT 0.667515 -79 GCAATGACAATATAAAATTGGTGTTAACTTCCAT 29 131 0 TATAAATTGT 0.810074 -37 TTTTCAGGTATATTAAATAAATGTTTATTCTGTG 30 30 0 TATAAAATGT 0.902088 -122 ACGCCCCGTCTATAAAAGACTTGGTGAGCTCCTG 32 249 0 TATAAAATGG 0.903738 -52 TCGGAGGTCATATTTAATAGATGGCACCTCCCGC 33 92 0 TATTAAATGG 0.812953 -50 AAGCTTTATACATCAAACTTATGGTGATTTTTCA 35 104 1 CATAAATTGG 0.85724 -197 *** *** * *** Masking position 7 Map Score: 4.08718 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 38 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 TCCTGCTTATCTGAATCTCTGCCTCTTCAA 5 242 0 CTGAATCTCT 0.827212 -28 AACTAACGAGCTGAAAATCTTCCAATCAGA 15 241 0 CTGAAAATCT 0.959331 -60 TAACCTACTTCCGAAAATCTACCAACATTA 16 42 0 CCGAAAATCT 0.951117 -78 ATACATTTATCTGAAACTATATCCGAAAGA 18 83 1 CTGAAACTAT 0.748568 -123 TCTTCTGATTCTGAAAAGCTATTTATATTT 19 276 0 CTGAAAAGCT 0.86236 -25 CGCCTTCATACTGAAAAACTCGTCTGAATT 32 141 1 CTGAAAAACT 0.808695 -160 AGTACACCTTCTGATACTCTGTAACTCTCT 33 12 1 CTGATACTCT 0.827212 -130 GACGAAGGGACCGAAACTCACACCGGAACA 35 205 1 CCGAAACTCA 0.797933 -96 CTTGATCATCCCGAAAATCTGAGTACAAGG 35 271 0 CCGAAAATCT 0.951117 -30 ********** Masking position 4 Map Score: 3.4504 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 GCCCCCGCAACCATCAAGGAAACTTTAATT 1 76 1 CCATCAAGGA 0.913273 -96 ATGAATTTATCCATTCATGATCTGTTTCAT 3 77 1 CCATTCATGA 0.884443 -91 CAGCCGAATTCCATCCAGGTTCTGTGATGA 12 17 0 CCATCCAGGT 0.835131 -157 CACCTGCTGACCATCAGGGACCAAAACTTA 13 162 1 CCATCAGGGA 0.793843 -77 AGACTGCAGACCATTCATAAAATGAACAGG 15 12 0 CCATTCATAA 0.715428 -289 ATCTGCTTTACCATCATTGACTCATTTAAA 15 50 1 CCATCATTGA 0.888371 -251 TGGGATCCCCCCATCCATGAGAGATGCATG 15 132 0 CCATCCATGA 0.974949 -169 AGAACACCGTCCATCCTTAACATTAAATAG 20 46 1 CCATCCTTAA 0.888376 -57 ATGTCTGTTTCCATCCTTAAAGTCTTCAGA 36 166 0 CCATCCTTAA 0.888376 -135 ********** Masking position 4 Map Score: 3.02922 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 305 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 TCTTCATCAAGGACTCTGTATTCCAGTCCTGC 5 172 0 GGATCTGTAT 0.873765 -98 CCTCTTCAAGGAACCCTGTCCTCAGAAGGACC 5 219 0 GAACCTGTCT 0.905168 -51 TGTTCCAGGAGGTTTCTGTCCTGATTTTTT 9 9 0 GGTTCTGTCT 0.97371 -39 TCCTCACATAGAAGTCTGTCTTTTGGATAATA 13 209 0 GAATCTGTCT 0.972927 -30 ATGTTCACTGGATAACTGTCTTTCGCCTTCAT 32 118 1 GATACTGTCT 0.771597 -183 CTTGAACGGAATCTGTCATTATTATTAAT 34 8 1 GGATCTGTCT 0.986034 -57 TATTTTATAGGAAATATGTCATTAATAATAAT 34 28 0 GAATATGTCT 0.778909 -37 CATTTTTGCAGGAATCTTTCCTGGGGCAGTGC 36 199 1 GGATCTTTCT 0.873765 -102 GGGGGTCTCTGTCTTCAGCTTTGAG 36 286 0 GGTTCTGTCT 0.97371 -15 *** ****** * Masking position 7 Map Score: 5.39032 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 53 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 ACTCAGAGCCGCAGGACTGGAATACAGAGT 5 162 1 GCAGGACTGG 0.983606 -108 TCGGTCCTTCTGAGGACAGGGTTCCTTGAA 5 217 1 TGAGGACAGG 0.809806 -53 ATTCAGATAAGCAGGACAGGAAGC 5 256 1 GCAGGACAGG 0.984697 -14 TTATTATCTTGCAGGACATCTATTTAATGT 20 65 0 GCAGGACATC 0.858554 -38 ACAATGGGATCCAGGACTGGTTTTTTATTA 24 197 1 CCAGGACTGG 0.928295 -40 ACCCAGCGGTGCAGGTCTTGTAAGGTACTT 35 166 1 GCAGGTCTTG 0.894987 -135 CAATTGAAGTGGAGGACTTGGAAACTTTTA 37 13 1 GGAGGACTTG 0.945502 -97 ********** Masking position 3 Map Score: 2.74876 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 101 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084