AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_mthe_reg_300.orf -o00720_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MTH1735 22 fumarate hydratase, class I 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 MTH184 125 isocitrate dehydrogenase #7 MTH216 96 acetyl-CoA synthetase #8 MTH217 134 acetyl-CoA synthetase #9 MTH218 140 chaperonin #10 MTH219 51 unknown #11 MTH220 227 flavoprotein A homolog (II) #12 MTH221 97 unknown #13 MTH222 51 unknown #14 MTH223 163 unknown #15 MTH224 300 conserved protein #16 MTH460 300 phosphoenolpyruvate synthase homolog #17 MTH563 140 succinyl-CoA synthetase, alpha subunit #18 MTH564 52 conserved protein #19 MTH700 110 conserved protein #20 MTH702 27 acetyl-CoA synthetase related protein #21 MTH964 103 unknown #22 MTH966 21 conserved protein #23 MTH1026 222 phosphatidylserine decarboxylase #24 MTH1027 39 CDP-diacylglycerol-serine O-phosphatidyltransferase #25 MTH1029 41 unknown #26 MTH1030 30 unknown #27 MTH1031 59 conserved protein #28 MTH1032 229 ferredoxin (putative 2-oxoglutarate oxidoreductase, delat subunit) #29 MTH1115 21 fumarate hydratase, class I #30 MTH1116 146 glutamate decarboxylase #31 MTH1117 43 phosphoenolpyruvate synthase #32 MTH1119 132 ribosomal protein L10 #33 MTH1201 95 conserved protein #34 MTH1202 236 proteasome, beta subunit #35 MTH1203 69 cleavage and polyadenylation specificity factor #36 MTH1204 46 phosphoribosylformylglycinamidine cyclo-ligase #37 MTH1502 189 succinate dehydrogenase, flavoprotein subunit #38 MTH1603 63 acetyl-CoA synthetase #39 MTH1740 86 pyruvate oxidoreductase, gamma subunit #40 MTH1850_MTH1851 105 MTH1850: fumarate reductase, MTH1851: unknown #41 MTH1910 209 fumarate hydratase, class I related protein Motif number 1 CATGTTCAGGATCAGCCTCAGAAGTATCC 4 9 0 ATCAGCTCAG 0.976068 -49 GCACGGGATATCCAGGGCCACAGAGAAGATA 5 132 1 TCCAGGCCAC 0.7547 -138 CCACACGCCACCATCTCCAGTCAATTATTT 9 10 1 ACCATCCCAG 0.930351 -131 AGCCTGAAAAATCAGCACCACAAATTGTATA 11 130 1 ATCAGCCCAC 0.979614 -98 AAATTGTATAATCACCCCCCCCAAAATCAGC 11 151 1 ATCACCCCCC 0.855347 -77 CCCCCCCAAAATCAGCACCACCTCACCCCAT 11 166 1 ATCAGCCCAC 0.979614 -62 GGTTACCAGCCTCAGTCTCCTTATA 15 286 0 ACCAGCTCAG 0.976505 -15 ATTACACCTCATCAGCGTCAGGAAAAATTAA 19 89 0 ATCAGCTCAG 0.976069 -22 GTCGATCAGTTCCAGCATCACCGGGCAGATC 21 42 0 TCCAGCTCAC 0.894245 -62 TTTTTCACCTCCAGTTTAACTTTA 21 90 0 TTCACCCCAG 0.904601 -14 TAAGCCTTCAATCAGGATCAGTCGCCTGATT 37 40 0 ATCAGGTCAG 0.888672 -150 AAATCCATACATCACCCTCAGATTAGAACGT 37 70 1 ATCACCTCAG 0.940781 -120 CAGGTGATGAACCATCACCCGGTCCTCTACG 37 102 0 ACCATCCCCG 0.808432 -88 ****** **** Masking position 4 Map Score: 11.8119 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 314 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 ATTATCCTTTCAGAGGCCCCCGCAACCATCA 1 61 1 CAGAGGCCCC 0.879235 -111 AAGGGTCATAAACTGAACGCCGCCCTCATCG 7 38 1 AACTGAACCC 0.858218 -59 TATTTCCAGGAAGAGGAATCCATCTGCAACT 9 40 1 AAGAGGAACC 0.766525 -101 GTCTGCAGAAACCAGAAACCCACAGGATCTT 9 81 1 ACCAGAAACC 0.703624 -60 ATTCAGTGAACCCCCAGAGTAGAG 13 4 1 CAGTGAACCC 0.979721 -48 AGAGTAGAGGCAGAGAACGCCCGGAATGGTG 13 26 1 CAGAGAACCC 0.979721 -26 CTGAAAAAATCAGAGGAAACCCTTTGCCATG 16 188 1 CAGAGGAACC 0.930099 -113 TTTTTTCAGTGACCTCCACCGATGTGG 17 7 1 CAGTGACCCC 0.913674 -134 TACTACCACACAGGGGACACCGCCTGG 20 11 1 CAGGGGACCC 0.968827 -17 GAACTGATCGACCGGAAATCCCGCAAGCGTA 21 61 1 ACCGGAAACC 0.689465 -43 GTTCATATCGCTGTGAACTCCATGTGAAATG 23 114 1 CTGTGAACCC 0.915429 -109 GTTCATGTCACCGTGAACTCCATGTGAGAAG 23 144 1 CCGTGAACCC 0.979307 -79 TTACATAGGCCCCGGAAAACCTGAAAACCGG 28 46 1 CCCGGAAACC 0.899983 -184 ACCTCTGGTGAAGGGAACACCCTGATAATTT 28 123 1 AAGGGAACCC 0.917682 -107 CCTCACCCAGTACACCCTCGCCATAG 31 6 1 CCCAGTACCC 0.718891 -38 TTTTTGTCTTCCGTAAAAGCCATTAAATACT 33 64 0 CCGTAAAACC 0.623637 -32 TCTTCAACCCCTCAGGAAGCCCCATCTATTA 34 49 1 CTCAGGAACC 0.602205 -188 TTTTTAATTGCAGTAAACACCTGTTTACTGA 35 22 1 CAGTAAACCC 0.808605 -48 ******** ** Masking position 10 Map Score: 12.5225 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 927 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TTCTGATCTAAATTAAAGTTTCCTTGATGGT 1 85 0 AATTAAAGTT 0.536613 -87 TATACCTCAATTTTAAAGTTTACTTTAGAAG 1 132 1 TTTTAAAGTT 0.483449 -40 GTTCCCTGACTATTAATAGTTGTCAGCAGCC 5 48 0 TATTAATATT 0.604134 -222 CGAGGTTATTAATAAAAAATTTATAATAAAT 8 27 1 AATAAAAATT 0.719879 -108 TCTTCCTGGAAATAAATAATTGACTGGAGAT 9 23 0 AATAAATATT 0.81153 -118 TTTAAGGTTCTATAAATAATTTGTGTAGAAG 9 109 0 TATAAATATT 0.719879 -32 ACACCGGATCATTTAATAATTTGAAGAATTC 15 78 1 ATTTAATATT 0.777156 -223 AAAGCATATAAATAAATGTTTATATTACTGG 15 108 0 AATAAATGTT 0.766571 -193 TAAACTTATTATTTAAAAATTTTGGTCCATT 15 246 0 ATTTAAAATT 0.675012 -55 CATGAGCATAATTAAATATTTCAGACCACAA 17 112 1 ATTAAATATT 0.854869 -29 GAGCTGCCTGAATAAATAGTTTAGAGGGGAC 18 19 0 AATAAATATT 0.812296 -34 TTAATTTCTTATTTAATATTTTAT 25 28 1 ATTTAATATT 0.777662 -14 TCATTCCATTAAAAGCTTTTCTCCAGGG 27 42 0 ATTAAAAGTT 0.726336 -18 GCCTTCAGAATTTAAATAATTAATCAAGAAT 28 181 0 TTTAAATATT 0.77767 -49 AGACAATATTTATTAATGGTTACCGAGATAC 32 70 1 TATTAATGTT 0.536613 -63 CGTAAAAGCCATTAAATACTTGGAGGAAAAA 33 53 0 ATTAAATATT 0.854869 -43 TAATTCATGATTTAAATAGTTGGCAGAATAT 38 21 0 TTTAAATATT 0.777671 -43 ATGTATATATATTAAAAATTTATAATGATTA 39 43 1 ATTAAAAATT 0.777671 -44 GTCTGTATTGTTTAAAAGATTATCAGTTAAA 40 13 1 TTTAAAAGTT 0.611814 -93 ******** ** Masking position 3 Map Score: 10.4236 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 15 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 AATAACCTCGAAAAAAATGAGGTGGG 8 2 0 AAAATAGGGG 0.933646 -133 ACTGCTGACTAACTGGAACTGGCGGTTCTTGCTGG 14 27 0 AAGAATGGGG 0.949508 -137 GATTGGTGCTATTAAAAATAGGCGGCAAGTACTGA 14 105 0 ATAAAAGGGG 0.966657 -59 TAACAGAGTTATTTATAACAGGTGT 14 149 1 ATAAAAGGGT 0.638304 -15 TTAATATAAAAATTGCAAATGGTAGTCATATCCAT 15 174 0 AAGAATGGAG 0.65233 -127 TCATTCCTTAATTTGGATTAGGGGGCATCTAATGG 15 216 1 ATGATAGGGG 0.922987 -85 CGCAAGCGTAAAGTTAAACTGGAGGTGAAAAA 21 82 1 AATAATGGGG 0.709237 -22 TATTACCGGTAATGGGAACAGGTGAGTTATTTGTT 23 190 1 AAGAAAGGGA 0.811299 -33 ACCAGATTATAAGTAAAACAGGTGGCGG 24 22 1 AAAAAAGGGG 0.973631 -18 CCGGTCATTAAAAGGAATGAGGTGGGAGTA 34 6 0 AAGATAGGGG 0.938514 -231 TTCTGTACCAATATATAACAGGAGGTCCTTATTAA 34 97 0 ATAAAAGGGG 0.966657 -140 GTTTACTGCAATTAAAAATAGGAGAAAAA 35 5 0 ATAAAAGGGA 0.756803 -65 TTTATTCGATAATGATCACTGGGGGTTCTGT 37 7 0 AAACATGGGG 0.687345 -183 TTAAAAAAATATTAACAGAAGGGGG 38 49 1 ATAAGAGGGG 0.832689 -15 AATGATTAACAATGAGAAATGGAGGTAAACT 39 66 1 AAAAATGGGG 0.94546 -21 TGCCAGAGAGATCAGTATGAGGTAGAAC 41 4 0 ATGATAGGAG 0.544581 -206 ** * ** *** ** Masking position 1 Map Score: 10.7392 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 168 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 GTTGCGGGGGCCTCTGAAAGGATAATATAT 1 57 0 CCTCTGAAAG 0.942431 -115 CATAGCCCACCATCTGGAGGTATCAGAAAT 3 50 0 CATCTGGAGG 0.798528 -118 TCAGGATCAGCCTCAGAAGTATCC 4 5 0 CCTCAGAAGT 0.949 -53 TGCAAGACATCCTCTGAAGTAGATAACCAT 5 91 0 CCTCTGAAGT 0.931115 -179 GGAACCCTGTCCTCAGAAGGACCGAACCAC 5 212 0 CCTCAGAAGG 0.98276 -58 AATTAATAAACATCTGAATGCACATCACAT 11 23 1 CATCTGAATG 0.8575 -205 GGGATTTCTGCAGCAGAAGGGAGACAACAT 16 89 1 CAGCAGAAGG 0.736467 -212 ATATGATGAACCTCAGAATGTGATATGCCG 23 81 0 CCTCAGAATG 0.967012 -142 TTAGCTTTGCCTTCAGAATTTAAATAATTA 28 190 0 CTTCAGAATT 0.650971 -40 GTCCCTCCTCTGAAATTCGGCGAGAA 30 131 0 CCTCTGAAAT 0.840862 -16 TTCTTCAACCCCTCAGGAAGCCCCATCTAT 34 48 1 CCTCAGGAAG 0.884275 -189 ATATGAAAAACTTCAGAATGAACTGAATTT 40 78 0 CTTCAGAATG 0.852542 -28 ********** Masking position 8 Map Score: 9.85617 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 483 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 TTATCATAACGTTTAAGGGATCACGGT 3 151 1 GTTTAAGGGA 0.962917 -17 AGGAAACATAGTTTAAAGGATGCAGTGATT 10 30 1 GTTTAAAGGA 0.879903 -22 CCTTTTAAGAATTTAGGGGGCACACCGGAT 15 57 1 ATTTAGGGGG 0.791012 -244 ATCAACCAATGTTTAAGTGAAAGCATATAA 15 128 0 GTTTAAGTGA 0.879903 -173 CCTTAATTTGGATTAGGGGGCATCTAATGG 15 221 1 GATTAGGGGG 0.859073 -80 TGAATAAATAGTTTAGAGGGGACCTCATCT 18 12 0 GTTTAGAGGG 0.924379 -41 AAAGAGTGAAGTTTAAGTGATTGACAGTAC 27 13 1 GTTTAAGTGA 0.879903 -47 CCCAAAAATAGTTTAGAGGAGTTCCTGTGC 30 55 0 GTTTAGAGGA 0.944959 -92 TGTTTAGGGGAGTGTTTAAAA 33 2 1 GTTTAGGGGA 0.983831 -94 GCAGTCAATAGTTAAGGTGATGAACCATAA 37 152 0 GTTAAGGTGA 0.707235 -38 ********** Masking position 5 Map Score: 7.7548 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 77 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 TTTACTATTATTAATCATGATAGATAATAT 8 56 0 TTAATCATGA 0.938895 -79 ATTGTATAATTTAATAATGAAGTTCAACAT 11 200 1 TTAATAATGA 0.949167 -28 CATATTATCCTTAATTGTGAAGGGCTCTTC 17 41 1 TTAATTGTGA 0.601125 -100 GGAGAAGTGTTTAATTATGATAGAGTTCTG 17 70 0 TTAATTATGA 0.838501 -71 TTAATAATGATTATTAATGATAAATGTCTC 19 63 0 TTATTAATGA 0.647306 -48 TCAGGAAAAATTAATAATGATTATTAATGA 19 73 0 TTAATAATGA 0.949167 -38 ATTTAAATAATTAATCAAGAATAATATTAT 28 173 0 TTAATCAAGA 0.640252 -57 ATCGCAAAGTTTAATAAGGACCTCCTGTTA 34 87 1 TTAATAAGGA 0.85509 -150 GCCAAACCTTATAATAATGA 37 180 1 ATAATAATGA 0.647676 -10 GCCAACTATTTAAATCATGAATTAAAAAAA 38 28 1 TAAATCATGA 0.601958 -36 ATATTAAAAATTTATAATGATTAACAATGA 39 51 1 TTTATAATGA 0.647675 -36 TTTATAATGATTAACAATGAGAAATGGAGG 39 61 1 TTAACAATGA 0.731513 -26 TCGAATAAATTTAATAGGGATCAGATTTTT 41 71 0 TTAATAGGGA 0.631377 -139 TTTTTGGCACTTAATCATGAGTTCGTGCCA 41 101 0 TTAATCATGA 0.938895 -109 ********** Masking position 10 Map Score: 7.97725 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 15 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 TTAAAATTGAGGTATATAATGTTTTCTATAAATTCTG 1 111 0 GGTTTTTTCT 0.942295 -61 TCCCCCCATGGGTGTATTCGTGGTTCTTTTTCTCAGG 5 12 1 GGTTTGTTCT 0.974531 -258 GGAAGCTGGGGGTTTTTATGATGTCTTCATATTCCCT 6 16 0 GGTTTGTCTT 0.918084 -110 TCATGGCGAAGGTGTCTTTTCAGTTCTTCGATGAGGG 7 60 0 GGTTTGTTCT 0.974531 -37 GGTCTTTTTGGGTCTGTGTTTTGTTTTT 16 2 0 GGTTTGTTTT 0.981732 -299 GGTTTTTTGGTGTGTTTGTGTTGTTTTTCTGGTCTTT 16 32 0 TGTTTGTTTT 0.824415 -269 CATGGCAAAGGGTTTCCTCTGATTTTTTCAGAGTGGA 16 182 0 GGTTCTTTTT 0.827077 -119 AGTATGGTGAGGTTTCTTCTACTTTTTTGTTCACGTG 16 235 0 GGTTTTTTTT 0.958219 -66 GTGTTTTTATGGTATATAAAGGGTTTTCATTTAACCC 34 162 0 GGTTTGTTTT 0.981732 -75 ATCCAGGACTGGTTTTTTATTATTTTTATTAGAGGTG 34 205 1 GGTTTTTTTT 0.958219 -32 *** * * ***** Masking position 5 Map Score: 7.07616 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 25 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 GAACCTTAAACCCATGGATAA 9 130 1 CCCATGGATA 0.943864 -11 ATAGTGAAAACACATGGACACTATATCCAT 12 32 1 CACATGGACA 0.974911 -66 TGGAATTCATCCCATGGATATGACTACCAT 15 161 1 CCCATGGATA 0.943864 -140 CAACAGAGCACACGTGGTCATACCTCATTC 16 125 1 CACGTGGTCA 0.872214 -176 TGTCAGCGCTCACGTGAACAAAAAAGTAGA 16 225 1 CACGTGAACA 0.809642 -76 AAAGGGTCTACCCGAGGAAAAAGTACTTGA 30 99 1 CCCGAGGAAA 0.77383 -48 AAGGGCTGTCCCCATGGACATAAAAGTTCT 34 128 0 CCCATGGACA 0.984034 -109 GTGCACCATGCACAAGGACACCGAATCACG 41 166 0 CACAAGGACA 0.93432 -44 ********** Masking position 10 Map Score: 4.45369 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 133 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 TAACCTCGAAAAAAATGAGGTGGG 8 2 0 AAAAAAGGGG 0.936169 -133 ACCAACCAAGAAAAAGATGGCGGTATGAAAA 8 114 1 AAAAATGGGG 0.965845 -21 TATAAGTAATAAATATGTGGCTGGCACCACTGC 14 57 0 AAATATGGTG 0.91115 -107 TTGGTGCTATTAAAAATAGGCGGCAAGTACTGA 14 105 0 TAAAAAGGGG 0.766686 -59 ATTATAAGTAAAACAGGTGGCGG 24 27 1 AAACATGGGG 0.959089 -13 CCCTGAAAATAAAAAAATGGTTGGTGGA 26 6 0 AAAAATGGTG 0.875072 -25 AAAAGCCATTAAATACTTGGAGGAAAAAAGAAC 33 48 0 AAATATGGGG 0.976415 -48 CTGTACCAATATATAACAGGAGGTCCTTATTAA 34 97 0 ATATAAGGGG 0.82791 -140 AGTTGGCAGAATATAGATGGGTGC 38 2 0 ATATATGGTG 0.696756 -62 TTCATGATTTAAATAGTTGGCAGAATATAGATG 38 16 0 AAATATGGAG 0.802318 -48 AAAAAAATATTAACAGAAGGGGG 38 51 1 TAACAAGGGG 0.731491 -13 TGGTCAACTAAAATTAATGGGGGTAACGAA 39 8 0 AAATTTGGGG 0.827444 -79 ***** *** ** Masking position 3 Map Score: 6.04768 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 41 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 11 ATCCCGTGCAGTCTCTCCCTTGCAAGACATCC 5 109 0 GCTCTCCTTG 0.903223 -161 GCGGCTCTGAGTATCTTCTCTGTGGCCCTGGA 5 142 0 GATCTCTCTG 0.974245 -128 GGCGTTCTCTGCCTCTACTCTGGGGGTTCACT 13 15 0 GCTCTCTCTG 0.99141 -37 CATGTATGTTGTCTCCCTTCTGCTGCAGAAAT 16 92 0 GCTCCTTCTG 0.846879 -209 ATCAATCCAGGAATCCACTCTGAAAAAATCAG 16 169 1 GATCCCTCTG 0.948692 -132 AATGATAAATGTCTCTTCCCTTAATAAAGTTT 19 46 0 GCTCTCCCTT 0.903223 -65 TGTGATGGTGGGATCTGCCCGGTGATGCTGGA 21 31 1 GATCTCCCGG 0.938466 -73 TTGAGGAGGAGTCTCTGCTCGGCCCTTGCAAC 30 19 0 GCTCTCTCGG 0.982583 -128 GTCCCTCCTCTGAAATTCGGCG 30 135 0 GCCCTCTCTG 0.964243 -12 * **** ***** Masking position 5 Map Score: 4.93174 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 176 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 AGAGGCCCCCGCAACCATCAAGGAAACTTT 1 72 1 GCAACCATCA 0.96396 -100 AAATTCATAGCCCACCATCTGGAGGTATCA 3 55 0 CCCACCATCT 0.976775 -113 CCACACGCCACCATCTCCAGTCAATT 9 7 1 GCCACCATCT 0.976775 -134 GGGATGAATTCCAACCATCAACCAATGTTT 15 144 0 CCAACCATCA 0.96396 -157 CCGGGCAGATCCCACCATCACATCACAATT 21 23 0 CCCACCATCA 0.963258 -81 TCCACCAACCATTTTTTTATTTTC 26 5 1 CCAACCATTT 0.827335 -26 CTCGGCCCTTGCAACCGTCTTCC 30 4 0 GCAACCGTCT 0.919333 -143 GCACCCATCTATATTCTGCC 38 1 1 GCACCCATCT 0.919333 -63 ********** Masking position 8 Map Score: 7.57292 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 69 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 CTTTGAGGTACGATGGCATCAG 2 75 1 CGATGGCACA 0.917224 -12 ATCAAAAAACCGATGTGAGGATATCAGCAGA 3 21 0 CGATGTGAGA 0.953085 -147 TTCATCGATCCGATAGGATTAAGCAGACTTA 3 102 1 CGATAGGATA 0.639848 -66 ACGAATACACCCATGGGGGGAA 5 2 0 CCATGGGGGA 0.94679 -268 GTAGTCATATCCATGGGATGAATTCCAACCA 15 157 0 CCATGGGAGA 0.978881 -144 GATATGAACACCATATGATGAACCTCAGAAT 23 92 0 CCATATGAGA 0.808401 -131 GAGTTCACAGCGATATGAACACCATATGATG 23 103 0 CGATATGACA 0.721707 -120 ACCGTGAACTCCATGTGAGAAGAAACCTATC 23 153 1 CCATGTGAAA 0.688414 -70 ACTTTTATGTCCATGGGGACAGCCCTTTGCA 34 131 1 CCATGGGGCA 0.90167 -106 TAAATTTATTCGATGGCACGAACTCATGATT 41 88 1 CGATGGCAGA 0.955626 -122 TTGTAATATTCGATGGCACGAACTCGTGATT 41 142 1 CGATGGCAGA 0.955626 -68 ******** ** Masking position 3 Map Score: 5.3755 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 145 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 CTTCGGCTACTACAGGGGCAGGGGTGAATCAT 2 33 1 TACGGGCAGG 0.815823 -54 GAATACAGAGTCCTTGATGAAGAGTCATGCTG 5 181 1 TCCTGAGAAG 0.824433 -89 AGGACAGGGTTCCTTGAAGAGGCAGAGATTCA 5 229 1 TCCTGAGAGG 0.983498 -41 TCTTTTCAGTTCTTCGATGAGGGCGGCGTTCA 7 51 0 TCTCGAGAGG 0.843697 -46 ATTATTTATTTCCAGGAAGAGGAATCCATCTG 9 34 1 TCCGGAGAGG 0.989588 -107 TCTGCAGACTTACTGGAAGAGTTGCAGATGGA 9 58 0 TACGGAGAGT 0.761663 -83 TATACAATTTTATGGGGTGAGGTGGTGCTGAT 11 176 0 TATGGGGAGG 0.903805 -52 GATTGATTACTGCCTGATGAGGAATGAGGTAT 16 144 0 TGCTGAGAGG 0.919725 -157 TTCCTGTGCGGCCTTGAGGAGGAGTCTCTGCT 30 32 0 GCCTGAGAGG 0.918189 -115 GGCGAGGGTGTACTGGGTGAGG 31 1 0 TACGGGGAGG 0.974313 -43 ATTGTACCTGTCTATGGCGAGGGTGTACTGGG 31 16 0 TCTTGGGAGG 0.932459 -28 *** *** **** Masking position 10 Map Score: 5.08776 Number of sites scoring better than the average of aligned sites = 733 Number in coding regions = 706 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 CTCAGAGCCGCAGGACTGGAATACAGAGTC 5 163 1 CAGGACTGGA 0.82264 -107 CGGTCCTTCTGAGGACAGGGTTCCTTGAAG 5 218 1 GAGGACAGGG 0.960295 -52 TTCAGATAAGCAGGACAGGAAGC 5 257 1 CAGGACAGGA 0.936215 -13 AATTTAGGGGGCACACCGGATCATTTAATA 15 66 1 GCACACCGGA 0.703017 -235 TACTACCACACAGGGGACACCGCCT 20 6 1 CCACACAGGG 0.745687 -22 TCAGTTCCAGCATCACCGGGCAGATCCCAC 21 38 0 CATCACCGGG 0.895662 -66 TTACCCCGGGACTGACAGGGCATTTTGCTG 28 90 1 ACTGACAGGG 0.681095 -140 CTCCTCAAGGCCGCACAGGAACTCCTCTAA 30 43 1 CCGCACAGGA 0.902713 -104 ATTCTCACAGGATCACAGGAGGATTATTT 32 114 1 GATCACAGGA 0.887942 -19 CATTCCTTTTAATGACCGGATAACCGTTCT 34 22 1 AATGACCGGA 0.663161 -215 ATTCGATAATGATCACTGGGGGTTCTGT 37 9 0 GATCACTGGG 0.775761 -181 AACGTCCGTAGAGGACCGGGTGATGGTTCA 37 96 1 GAGGACCGGG 0.957661 -94 CTTATCTACTGAGGGCAGGAG 41 199 1 GAGGGCAGGA 0.734119 -11 ********** Masking position 6 Map Score: 3.94677 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 476 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974