AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_mthe_reg_100.orf -o00680_mthe_100.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 Input sequences: #1 MTH310 178 conserved protein #2 MTH312 50 ATP-dependent helicase #3 MTH313 79 transcriptional regulator #4 MTH384 249 unknown #5 MTH387 24 conserved protein #6 MTH388 35 unknown #7 MTH393 41 NADH dehydrogenase (ubiquinone), subunit 1 related protein #8 MTH394 55 unknown #9 MTH397 40 formate hydrogenlyase, subunit 7 #10 MTH611 84 prolyl-tRNA synthetase #11 MTH612 50 unknown #12 MTH711 166 transcriptional regulator #13 MTH783 83 hydrogenase expression/formation protein HypA #14 MTH894 179 conserved protein #15 MTH895 51 conserved protein #16 MTH898 22 conserved protein #17 MTH1063 134 transcriptional regulator related protein #18 MTH1072 67 hydrogenase expression/formation protein HypD #19 MTH1141 300 conserved protein (FlpE) #20 MTH1193 146 transcriptional regulator #21 MTH1246 30 NADH dehydrogenase I, subunit N #22 MTH1251 147 conserved protein #23 MTH1287 177 transcriptional regulator HypF homolog #24 MTH1380 167 serine hydroxymethyltransferase #25 MTH1396 28 thiamine monphosphate kinase #26 MTH1398 269 conserved protein #27 MTH1522 116 nitrogenase alpha chain (NifD) related protein #28 MTH1547 118 nitrate assimilation protein, narQ #29 MTH1552 139 formate dehydrogenase, alpha subunit homolog #30 MTH1627 220 TATA-binding transcription initiation factor #31 MTH1634 151 transcriptional control factor (enhancer-binding protein) #32 MTH1649 110 hydrogenase expression/formation protein HypC #33 MTH1708 300 carbon monoxide dehydrogenase, alpha subunit #34 MTH1710 21 carbon monoxide dehydrogenase, alpha subunit #35 MTH1722 264 transcriptional regulator Icc related protein #36 MTH1740 86 pyruvate oxidoreductase, gamma subunit #37 MTH1795 72 transcriptional regulator Motif number 1 GAGGATTGATAGATAAATTTTTTTATAACCC 1 61 0 AGATAAATTT 0.847489 -118 TATTAAACACATTTAAAGATTTCTGAGGATT 1 85 0 ATTTAAAGTT 0.736127 -94 GGGAAAACATATATAAATGTTGTCATTGCAA 3 44 0 ATATAAATTT 0.94542 -36 ATATAAATCTTTTTAAAAAAG 4 239 0 ATATAAATTT 0.94542 -11 AGAGTTATCTATATAAAAATTGTTAATTACC 13 26 0 ATATAAAATT 0.858453 -58 TTAATTCTAATTATAAAATTTTGTCAGACTA 13 58 1 TTATAAAATT 0.744344 -26 AAATTTATGGATATAAAGGTAAATTGGGATT 14 148 0 ATATAAAGTA 0.736127 -32 ATTAACTACAAGTTAAATTTTAACCGAAAGT 17 36 0 AGTTAAATTT 0.451888 -99 AGTTAATGACATATAAATCTTCCGGTGCAAA 17 60 1 ATATAAATTT 0.94542 -75 TTCACATGCCTTTTAAATTTTAGGAACATTT 19 267 1 TTTTAAATTT 0.552323 -34 GTATTACATATATAAATGTTCCTAAAATTT 19 281 0 ATATAAATTT 0.94542 -20 GGATGTTCCCTTATAAATGTTTATCTGAAGA 20 38 0 TTATAAATTT 0.892654 -109 ATCCCCTATCTTATAAAAGTTGATGACTTCT 20 65 1 TTATAAAATT 0.744344 -82 GAAAGTTATATTATAAAGTTTTTTAAGTGAA 20 108 0 TTATAAAGTT 0.900267 -39 ATTTATGATAATATAAAGTTTTCTATATAAA 22 85 0 ATATAAAGTT 0.949503 -63 AGTATTACAGATATAAAAATATTACCTAAAT 26 32 1 ATATAAAATA 0.473627 -238 TAATAATACTTTATTAATATTTAGGTAATAT 26 50 0 TTATTAATTT 0.451778 -220 CATGATGCACAGATAAAGGTTATGAGTAGAG 29 26 0 AGATAAAGTT 0.857795 -114 CTGTGCATCATGATAAAGTTTCACCATAAAA 29 45 1 TGATAAAGTT 0.743315 -95 AAATGCACCTATATTAATATTGACGTAAAAA 30 160 0 ATATTAATTT 0.631891 -61 TTAAACCTACATATAAATTTAAATGCACCTA 30 180 0 ATATAAATTA 0.719883 -41 GATCCGTCACATATAAAGATTTGTGGGAAAC 32 31 0 ATATAAAGTT 0.949503 -80 CATTCATATAATATAAAGGTTGAAGTGATTA 33 29 1 ATATAAAGTT 0.949503 -272 TGGAATCTATATATAAACTTTGTGCATTGTC 33 220 0 ATATAAACTT 0.732052 -81 TTGTTAATCATTATAAATTTTTAATATATAT 36 47 0 TTATAAATTT 0.892654 -40 ******** ** Masking position 4 Map Score: 29.4725 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 26 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 ATCTTTAAATGTGTTTAATACCGGGAAGGGGGTTTTCAAAT 1 96 1 GTATGAGGGG 0.981597 -83 ACTCCATAGGAACCTCCAGGACATGATGGGGTGGGAAT 4 8 0 ATAGGAGGGG 0.980006 -242 TCACTTTCATAATCTCCATCTCTTGAAGGGGAACTGCTGGT 12 92 0 ATATGAGGGG 0.994587 -75 CTATATAAAAATTGTTAATTACCGGAAGGTGATTTTTC 13 8 0 ATATGAGGTG 0.965828 -76 ATTTATCACGATCATATATATATGGAGGAGGCCAAAGGATT 18 11 0 ATATGAGAGG 0.906658 -57 TTCCCTTATAAATGTTTATCTGAAGATGGGAAAATAAAAAA 20 23 0 ATATGAGGGA 0.975504 -124 AGGGGATCCGATGATTAAACACTTGAAGGGGAAGAGGCTGC 22 32 0 ATAAGAGGGG 0.947607 -116 AGTTAGAAAAAGGATAAAGGATTTGATGGGGTTAACCCAT 24 10 0 ATAGGAGGGG 0.980132 -158 TTTATCAAAAATAGTTGGATGGGAACAG 25 5 0 AAATGAGGGA 0.960587 -24 TAAAAAGGACACTGAAGATAACATGAAGGGGACTGTTAAAT 29 71 1 AAATGAGGGG 0.991187 -69 GGACTGTTAAATTTAGAATAGATGGAAGGGAACTTGAGGCT 29 100 1 AAATGAGGGA 0.960587 -40 ATAATTTAACATACTTAATGAATAGAGGGGGATGAA 30 6 0 ATATGAGGGG 0.994588 -215 ATTAAGTATGTTAAATTATTTAAGGATGGTGCTTAAAATAT 30 28 1 TAATGAGGTG 0.764489 -193 TAGACTCTCAGAAGATCATATGCTGAAGGGGGTACCATGTC 31 49 0 GAATGAGGGG 0.970278 -103 TCTGAGAGTCTATAAAGATCCGGAGAGGGTGAGAGAATCAG 31 78 1 TAATGAGGTG 0.764489 -74 TATTATATGAATGTTTGATATAGTGATTGGA 33 1 0 ATATGATGGA 0.677928 -300 * * ** ** **** Masking position 8 Map Score: 23.7002 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 111 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 3 TCCCCCCATCCAGTATCTGGCCGT 2 4 1 CCCCATCCAT 0.955884 -47 ATTCCCACCCCATCATGTCCTGGAGGTT 4 8 1 CCCCATCATT 0.871207 -242 TCCTATGGAGTCACATCCACTTACCGGTTTC 4 38 1 TCACATCCAT 0.850142 -212 CATTTTCATTCCACATCATGTCTT 8 4 0 CCACATCATT 0.66613 -52 TCTGATTAAATCCCTTCCATTTTCATTCCAC 8 21 0 TCCCTTCCAT 0.956264 -35 TAAATCCCCTCTTTTCTGATTAAAT 8 41 0 TCCCCTCTTT 0.785965 -15 TCAATCTCCCATCTCATATGATGTACC 11 34 0 TCCCATCTCT 0.818039 -17 ACCAGCAGTTCCCCTTCAAGAGATGGAGATT 12 92 1 CCCCTTCAAA 0.642495 -75 TTCACCTCAAATTCCAGGTTGA 15 40 0 TCACCTCAAT 0.897721 -12 GCAGCCTCTTCCCCTTCAAGTGTTTAATCAT 22 32 1 CCCCTTCAAT 0.959592 -116 TTTATAGCTCCCTTCTCTTTAGTACCAAT 22 129 0 TCCCTTCTCT 0.836353 -19 ATGGGTTAACCCCATCAAATCCTTTATCCT 24 10 1 CCCCATCAAT 0.954316 -158 CTGTTCCCATCCAACTATTTTTGAT 25 5 1 TCCCATCCAC 0.883667 -24 ATTACGTCACCTCAAATGTCTGTGGTT 27 100 0 TCACCTCAAT 0.897721 -17 ACACCCACCACCTCACATCTAAAAACAT 28 101 0 CCACCTCACT 0.862839 -18 CCTCTTCACCTCACTCTCTACTCATA 29 6 1 TCACCTCACC 0.688022 -134 ATTTAACAGTCCCCTTCATGTTATCTTCAGT 29 81 0 CCCCTTCATT 0.884922 -59 AGCCTCAAGTTCCCTTCCATCTATTCTAAAT 29 110 0 TCCCTTCCAC 0.896213 -30 TTCATCCCCCTCTATTCATTAAGTAT 30 6 1 CCCCCTCTAT 0.927405 -215 TTAGTAATAATCACTTCAACCTTTATATTAT 33 36 0 TCACTTCAAC 0.710609 -265 ATCTGGCACATCCCCACCATTTATTAAAAAG 33 166 1 TCCCCACCAT 0.654867 -135 AGGGTTCGAATCCCTTCCCCTGCACTAAGAA 35 118 1 TCCCTTCCCT 0.932933 -147 ********* * Masking position 7 Map Score: 20.8393 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 646 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 ATGTGTTTAATACCGGGAAGGGGGTTTTCA 1 104 1 TACCGGGAAG 0.759595 -75 GACTGGTTCCCACCGGGAAGCCAGGATTCT 1 148 1 CACCGGGAAG 0.949959 -31 GCCAGGCACGCACCGGGAGCATTCTC 2 35 1 CACCGGGAGC 0.972323 -16 TCACCATTAACACCGGAATGATTCTATTAT 7 18 0 CACCGGAATG 0.819195 -24 AATTGTTAATTACCGGAAGGTGATTTTTC 13 10 0 TACCGGAAGG 0.919668 -74 CAGCACCCTAAGGAGGTATGAT 16 4 1 CACCCTAAGG 0.962043 -19 AAACATTTTGCACCGGAAGATTTATATGTC 17 67 0 CACCGGAAGA 0.931951 -68 CTATTCCCTCCACTGTGAGATGGGCACGGT 23 85 0 CACTGTGAGA 0.656472 -93 TTCTCACGTATCCCGTGAGGCTGAGTTCCT 23 157 0 TCCCGTGAGG 0.872587 -21 AAATCACTGCCTCCCTGAGGGAATAATAAA 26 173 0 CTCCCTGAGG 0.87459 -97 GGTTTAACTTCACCGGGAGGTATCTAG 30 204 1 CACCGGGAGG 0.9939 -17 GGTAATATCGCACCCTGAGCGGAGGGATGA 33 89 1 CACCCTGAGC 0.928288 -212 TACCATTATACACCCTGAGACCCCCGGCAA 33 122 0 CACCCTGAGA 0.923022 -179 GGGATTCGAACCCTCGAAGGCCTGCGCCAG 35 102 0 CCCTCGAAGG 0.695531 -163 GGTTCGAATCCCCCCTAAGGCTTTTCTACT 35 228 1 CCCCCTAAGG 0.921 -37 ********** Masking position 8 Map Score: 14.726 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 949 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 TTATGAAAGTGAATCCCTCATTAACTAAAT 12 121 1 GAATCCCTCA 0.921817 -46 AAGATTGCCTGAATTCTTCCTTCAAGGGCG 14 58 1 GAATTCTTCC 0.680828 -122 TCTGAAAAATTAAGCCCGCCCTTGAAGGAA 14 74 0 TAAGCCCGCC 0.769941 -106 ATCATACCTCCTTAGGGTGCT 16 12 0 TCATACCTCC 0.70503 -11 AGAGTTAAGGGCAGCCTTCCAGTTAGGATC 19 24 0 GCAGCCTTCC 0.67772 -277 CGCCCTGGACTATTCCCTCCACTGTGAGAT 23 94 0 TATTCCCTCC 0.897013 -84 ATCGGATTCGGAATCCCCCCAGCTATCAAC 24 69 1 GAATCCCCCC 0.953627 -99 GGATCTTTATTATTCCCTCAGGGAGGCAGT 26 168 1 TATTCCCTCA 0.591761 -102 TCAGCGTTTATCATTCCTCAATTGAAAAAT 30 97 0 TCATTCCTCA 0.566862 -124 CCGGCAATGGTCATCCCTCCGCTCAGGGTG 33 99 0 TCATCCCTCC 0.968087 -202 TGAATTCCTCCATTATCCTGA 34 11 0 GAATTCCTCC 0.948362 -11 CAGAGGATCTTAAGTCCTCCCCCTTTGGCC 35 75 0 TAAGTCCTCC 0.846169 -190 TCGAGGGTTCGAATCCCTTCCCCTGCACTA 35 115 1 GAATCCCTTC 0.800325 -150 TCGGGGGTTCGAATCCCCCCTAAGGCTTTT 35 223 1 GAATCCCCCC 0.953627 -42 TTTAATCCATCCGAATATTTCA 37 3 1 TAATCCATCC 0.76774 -70 ********** Masking position 6 Map Score: 9.32748 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 676 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 6 TGAATACTTTAAGTACATGAAAAAACATTAAATTG 1 18 0 AAACAAAAAA 0.678164 -161 TCACATTCATAGGGTTATAAAAAAATTTATCTATC 1 50 1 AGTTAAAAAA 0.465395 -129 GGACCCTTCAGATATCAGTAAAAAAAAGTTTCTGT 4 134 1 GATCAAAAAA 0.922851 -116 GAAACCTCCAGATATTAGTAAAAAAGGCCATAATT 4 172 1 GATTAAAAAA 0.647866 -78 ACCTAAAAAAGACCTCTTAATAAAATTATGGCCTT 4 195 0 GATCTAAAAA 0.80578 -55 ATATAAATCTTTTTAAAAAAGGTGAGTTAG 4 230 0 AATTTAAAAA 0.370216 -20 AAATGGAAGGGATTTAATCAGAAAAGAGGGGATTT 8 30 1 GATAAAAAAA 0.705508 -26 CTGTGGTCTGATATTCAGAAAAAAAGATTTCGTGG 12 15 0 ATTCAAAAAA 0.732651 -152 CTGAATATCAGACCACAGAAAAAAACAAAACCCTT 12 32 1 GAACAAAAAA 0.695804 -135 TGTTTTTTCAAGCATCTTAAGAAAAAAAGGGTTTT 12 58 0 AGTCTAAAAA 0.662511 -109 AATTAATAGAGTTATCTATATAAAAATTGTTAATT 13 29 0 GTTCTAAAAA 0.507812 -55 AACTCTATTAATTCTAATTATAAAATTTTGTCAGA 13 51 1 ATTAAAAAAA 0.354354 -33 TAATTACATGAAAATCACAATAAAATCCAATTTTA 19 226 0 AATCAAAAAA 0.916803 -75 ATTTTATTACGATTTATATAGAAAACTTTATATTA 22 73 1 GATATAAAAA 0.453819 -75 TACCAGTTGCGATGTCAACATAAAAAACGCGTGTT 24 96 0 GATCAAAAAA 0.922851 -72 AAATAGTTGCAATGACAATATAAAATTGGTGTTAA 24 138 0 AAACAAAAAA 0.678164 -30 AATATATTATAGATTAAGGACAAAAGATCTGTTTA 28 44 1 AGTAAAAAAA 0.531296 -75 ATCATGATAAAGTTTCACCATAAAAAGGACACTGA 29 51 1 AGTCAAAAAA 0.849849 -89 TAAAATTAAAAACATCATTATAAATCATTAATAAT 33 251 1 AATCAAAAAT 0.42778 -50 AGAACACCTTAAAATCAGTAGAAAAGCCTTAGGGG 35 239 0 AATCAAAAAA 0.916803 -26 ** *** * **** Masking position 10 Map Score: 10.6479 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 108 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 AAATTTATCTATCAATCCTCAGAAATCTTTAAA 1 72 1 ATCAATCCGA 0.963454 -107 TTTTCTGAATATCAGACCACAGAAAAAAACAAA 12 28 1 ATCAGACCGA 0.846105 -139 CAGTGACTTCATCGAACCATGGAAAGTTATATA 14 108 1 ATCGAACCGA 0.976644 -72 GCTTCAATCCAGTGATCCTAACTGG 19 3 1 TTCAATCCGA 0.922704 -298 ATGAATATTAATCAATCCATGGATATGAATCAT 27 30 1 ATCAATCCGA 0.963454 -87 CATGATGCAAATCCATCCCATGATTCATATCCA 27 49 0 ATCCATCCGA 0.956248 -68 GGGGAAGGGATTCGAACCCTCGAAGGCCTGCGC 35 105 0 TTCGAACCGA 0.949835 -160 TTAGGGGGGATTCGAACCCCCGACCTATGCCTT 35 213 0 TTCGAACCGA 0.949835 -52 TTTAATCCATCCGAATATTTCACCAGA 37 5 1 ATCCATCCTA 0.656297 -68 TACTTTATAGATGGAACCGTAGATAATAATAAC 37 46 0 ATGGAACCGA 0.844107 -27 ******** ** Masking position 2 Map Score: 6.51594 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 26 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 ACTTAAAGTATTCACATTCATAGGGTTATAA 1 39 1 TTCAATTCAT 0.926277 -140 AACCAGTCTCTTCTGTTTTATTTGAAAACCC 1 125 0 TTCTTTTTAT 0.338964 -54 ATGAAAATCCTTAAAATTTATTACTAAATCT 4 94 1 TTAAATTTAT 0.712336 -156 GGCTTCCATGTTCTCATTCAGGATTATTTAC 6 11 1 TTCTATTCAG 0.706765 -25 TTAAATCCCTTCCATTTTCATTCCACATCAT 8 16 0 TCCATTTCAT 0.573854 -40 TAATGAGGGATTCACTTTCATAATCTCCATC 12 113 0 TTCATTTCAT 0.873425 -54 TTAATTTATTTTTCATTTATTTCAAT 14 6 1 TTATTTTCAT 0.687966 -174 TCAATATATTCAAATTTATGGATATAAAG 14 161 0 TTCAATTTAT 0.729123 -19 TGGCAGGAAATTATAATTCATAATAGATGAT 19 119 0 TTATATTCAT 0.800576 -182 AGATCCAGAGTTAATATTCTGGCAGGAAATT 19 138 0 TTAAATTCTG 0.4468 -163 CACATGCCTTTTAAATTTTAGGAACATTTAT 19 269 1 TTAATTTTAG 0.429322 -32 AAAATTGGTGTTAACTTCCATTACCAGTTGC 24 121 0 TTAATTCCAT 0.553678 -47 TCTGTAATACTTAATTTTCATTTGGTGATAT 26 12 0 TTAATTTCAT 0.864073 -258 TAATACTTTATTAATATTTAGGTAATATTTT 26 47 0 TTAAATTTAG 0.578344 -223 CTAAAATGGGTCCATATTCATTTTCTCCAGC 26 90 0 TCCAATTCAT 0.710305 -180 CATGGATTGATTAATATTCATTTAGAAGCTT 27 20 0 TTAAATTCAT 0.920475 -97 CATCCCATGATTCATATCCATGGATTGATTA 27 38 0 TTCAATCCAT 0.710305 -79 AATAACGCGGTTAATATTCAGCGTTTATCAT 30 113 0 TTAAATTCAG 0.864899 -108 ATTAACCGCGTTATTATTCATAATAACTAGT 30 129 1 TTATATTCAT 0.800576 -92 ATCAGAACCGTTAAAATTCTTAGTGCAGGGG 35 134 0 TTAAATTCTT 0.593539 -131 **** ****** Masking position 7 Map Score: 9.85198 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 284 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 9 TCTTCTGTAGAGGGACCCTTCAGATATCAGTAA 4 122 1 AGGACCCTAG 0.742398 -128 CATCTCTTGAAGGGGAACTGCTGGTGTTTTTTC 12 84 0 AGGGAACGTG 0.935695 -83 GTAATAAAATAGGGGATCCGATGATTAAACACT 22 50 0 AGGGATCGTG 0.955163 -98 TCACCATAAAAAGGACACTGAAGATAACATGAA 29 65 1 AAGACACGAG 0.728453 -75 GAATAGATGGAAGGGAACTTGAGGCTGAACCTG 29 115 1 AAGGAACTAG 0.582789 -25 GGAGAGGGTGAGAGAATCAGCAGGCTGAAATCA 31 99 1 AGGAATCGAG 0.949991 -53 TCATATATAAAGAGGCTCATAAGACTTGTTGAA 31 129 1 AGGGCTCTAG 0.946849 -23 CCACAATATAAGGGAAACCGAAGATTAGTAATA 33 58 0 AGGAAACGAG 0.928446 -243 GGCCTGCGCCAGAGGATCTTAAGTCCTCCCCCT 35 81 0 AGGGATCTAG 0.929945 -184 TGATTGCCTTAGTGGCTCAGGTGGTAGAGCGAT 35 172 1 AGGGCTCGTG 0.966203 -93 ATAATAACGCAGAGACTCTGGTGAAATATTCGG 37 21 0 AGGACTCGTG 0.93762 -52 ** ***** * ** Masking position 1 Map Score: 6.47115 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 222 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 10 AAATTTTTTTATAACCCTATGAATGTGAAT 1 48 0 ATAACCCTAT 0.904489 -131 GTTTTATTTGAAAACCCCCTTCCCGGTATT 1 112 0 AAAACCCCCT 0.814546 -67 GTTAACCCTCTAATGGAGTAT 10 2 1 TTAACCCTCT 0.87085 -83 TTTTATATAGATAACTCTATTAATTCTAAT 13 39 1 ATAACTCTAT 0.727676 -45 GGCTGCCGTAATAACCCCATGAGTCCT 22 8 0 ATAACCCCAT 0.956881 -140 ATGGGTTAACCCCATCAAATCCTTT 24 6 1 TTAACCCCAT 0.956881 -162 GTAACCTCCATACAGTAATCA 26 259 0 TAACCTCCAT 0.553429 -11 TCAATAACCCTCTCCAAATTAAT 32 98 0 ATAACCCTCT 0.870849 -13 TTCGTTACCCCCATTAATTTTAGT 36 5 1 TTACCCCCAT 0.940478 -82 AGTTTACCTCCATTTCTCATTGT 36 74 0 TTACCTCCAT 0.81679 -13 ********** Masking position 3 Map Score: 5.15045 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 127 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 11 TCGAACCATGGAAAGTTATATATACTGGCA 14 119 1 GAAAGTTATA 0.732749 -61 AAAATTAACTGACGGTTAAAGAG 17 4 0 GACGGTTAAA 0.956422 -131 AATTTTAACCGAAAGTTAAAAATTAACTGA 17 22 0 GAAAGTTAAA 0.896656 -113 GTGGATTTAAAACGGTTAAATGATTAAAAT 19 202 1 AACGGTTAAA 0.877946 -99 GTATGCCTATGAAAGTTATATTATAAAGTT 20 119 0 GAAAGTTATA 0.732749 -28 ATCTTTGATTAACAGTTAAACAGATCTTTT 28 65 0 AACAGTTAAA 0.896656 -54 ACATGAAGGGGACTGTTAAATTTAGAATAG 29 91 1 GACTGTTAAA 0.88946 -49 GCGACCGTTAAATTAATATACC 35 3 1 GACCGTTAAA 0.956422 -262 ACATGATCAGAACCGTTAAAATTCTTAGTG 35 140 0 AACCGTTAAA 0.877946 -125 ********** Masking position 6 Map Score: 3.93763 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 23 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 12 TTTTCTGGACTATGTTGCAGATGCAACAGTT 3 15 1 TATGTTGCAA 0.841061 -65 AAGACATGATGTGGAATGAAAATGG 8 5 1 CATGATGTGA 0.816842 -51 GTTAACATGACATGTTGTAGATTCT 15 5 0 CATGTTGTAA 0.917567 -47 AAATCCATCCCATGATTCATATCCATGGATT 27 43 0 CATGATTCAA 0.871884 -74 TGGCTGGAACCATGATGCAAATCCATCCCAT 27 61 0 CATGATGCAA 0.981522 -56 TGGTTCCAGCCATGTTGCATAACCACAGACA 27 80 1 CATGTTGCAA 0.976052 -37 GAAACTTTATCATGATGCACAGATAAAGGTT 29 36 0 CATGATGCAA 0.981522 -104 ********* * Masking position 2 Map Score: 2.8228 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 15 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 GCAATGACAACATTTATATATGTTTTCCCA 3 46 1 CATTTATATA 0.55235 -34 ATATGTTTTCCCACCAGATAGATCAGC 3 63 1 CCACCAGATA 0.862993 -17 GTAGAGGGACCCTTCAGATATCAGTAAAAA 4 128 1 CCTTCAGATA 0.863541 -122 TGTAGAGAAACCTCCAGATATTAGTAAAAA 4 166 1 CCTCCAGATA 0.951503 -84 CACCAGTAATCATCTATATATTC 5 4 0 CATCTATATA 0.79272 -21 CCTTTGGCCTCCTCCATATATATATGATCG 18 14 1 CCTCCATATA 0.974915 -54 ATTTTAGGAACATTTATATATGTAATAC 19 283 1 CATTTATATA 0.55235 -18 TTTATAAGTACATCAATATAATCTTAGCAT 23 18 1 CATCAATATA 0.727504 -160 GTAACCTCCATACAGTAATCACTT 26 256 0 CCTCCATACA 0.859745 -14 TGAAGTTAAACCTACATATAAATTTAAATG 30 186 0 CCTACATATA 0.792104 -35 CTATATCAAACATTCATATAATATAAAGGT 33 19 1 CATTCATATA 0.832812 -282 TGCGATATTACCACAATATAAGGGAAACCG 33 71 0 CCACAATATA 0.683241 -230 TGGCACATCCCCACCATTTATTAAAAAGGT 33 169 1 CCACCATTTA 0.570413 -132 ********** Masking position 6 Map Score: 5.0446 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 211 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 14 ATCAATCCTCAGAAATCTTTAAATGTGTTT 1 82 1 AGAAATCTTT 0.914669 -97 AATTTTATTAAGAGGTCTTTTTTAGGTCTA 4 203 1 AGAGGTCTTT 0.793541 -47 ATATAAATCTTTTTAAAAAAGG 4 238 0 ATAAATCTTT 0.745682 -12 AAAGCCACGAAATCTTTTTTTCTGAAT 12 8 1 CGAAATCTTT 0.805092 -159 ATCGTGATAAATAGATCTTTAAGTGTAATG 18 40 1 ATAGATCTTT 0.831451 -28 CGATTTATATAGAAAACTTTATATTATCAT 22 82 1 AGAAAACTTT 0.577619 -66 TGCGAGCAAGAGGGATCTTTATTATTCCCT 26 156 1 AGGGATCTTT 0.927127 -114 TAACAGTTAAACAGATCTTTTGTCCTTAAT 28 56 0 ACAGATCTTT 0.924362 -63 CTCACCCTCTCCGGATCTTTATAGACTCTC 31 81 0 CCGGATCTTT 0.79889 -71 ATTGTTTCCCACAAATCTTTATATGTGACG 32 28 1 ACAAATCTTT 0.89648 -83 TTTATATGTGACGGATCTTTATCTAAACAT 32 45 1 ACGGATCTTT 0.91139 -66 ********** Masking position 8 Map Score: 6.14672 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 ********** No masking Map Score: 1.49457e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0