AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_pyro_reg_300.orf -o02010_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 PH0024 36 284aa long hypothetical sugar transport membrane protein #2 PH0025 169 426aa long hypothetical protein #3 PH0151 107 340aa long hypothetical protein #4 PH0154 55 248aa long hypothetical transport system protein #5 PH0206 132 544aa long hypothetical protein #6 PH0207 206 428aa long hypothetical protein #7 PH0209 300 131aa long hypothetical protein #8 PH0502 151 641aa long hypothetical protein #9 PH0503 35 330aa long hypothetical oligopeptide transport system permease protein AppB #10 PH0507 300 321aa long hypothetical oligopeptide transport ATP-binding protein AppF #11 PH0806 85 148aa long hypothetical protein #12 PH0807 174 597aa long hypothetical oligopeptide binding protein APPA #13 PH0808 41 323aa long hypothetical oligopeptide transport permease protein APPB #14 PH1037 129 142aa long hypothetical protein #15 PH1214 267 441aa long hypothetical cytoplasmic protein #16 PH1238 73 231aa long hypothetical protein #17 PH1239 59 237aa long hypothetical protein #18 PH1241 48 167aa long hypothetical protein #19 PH1349 131 347aa long hypothetical thiamin-binding periplasmic protein precursor #20 PH1353 66 679aa long hypothetical formate dehydrogenase #21 PH1354 28 196aa long hypothetical protein #22 PH1408 233 226aa long hypothetical protein #23 PH1409 250 721aa long hypothetical protein #24 PH1410 117 332aa long hypothetical dipeptide transport system permease protein dppB #25 PH1713 45 498aa long hypothetical sugar transport ATP-binding protein #26 PH1714 300 405aa long hypothetical protein #27 PH1961 198 349aa long hypothetical oligopeptide transport system permease protein appB #28 PH1962 300 841aa long hypothetical protein Motif number 1 TTTTAATTGGTAAATTTAAGCCCTTT 2 3 0 TAAATTAGCT 0.877998 -167 TGTATCTTCCTAAAATTCAAATCTATTATGTTAG 2 38 1 TAAAATAAAT 0.935778 -132 TTCTTTTTCCCAAAAGTTAAAATTATTCTTATGT 3 12 1 CAAAATAAAT 0.80552 -96 GAAAGTACACTAAAATTGAAAAGTCCAATGTAAG 5 81 0 TAAAATAAAT 0.935778 -52 AATGATGCCTCAAATGTAAAATATCTAGAAAAGA 6 103 0 CAAATTAAAT 0.80552 -104 TTTCGTCAATTAAATATAAATGTTTCGGCATTTC 6 176 0 TAAATTAATT 0.847391 -31 CATGTTACTGTAAATTTGAATGTTTTTATAACTT 8 27 1 TAAATTAATT 0.847391 -125 AGTGATATGTTAAAATTTAACCCTATATTTTTGA 12 41 0 TAAAATAACT 0.916033 -134 TTCCGATCCATAAAAATTAAATATACGCTTCGAC 12 112 1 TAAAATAAAT 0.935778 -63 CCCCCAATTTTAAATCTTAAAACTATGTACGTCG 12 142 0 TAAATTAAAT 0.935778 -33 ACCTAAAGTTGAAAACTAAAACTTTTA 16 4 1 TAAAGTAAAT 0.732907 -70 ATTTAAAAATCAAGTGTTAATCCTTAA 18 4 1 TAAAATAAGT 0.7144 -45 TATGGTAAAATAAATCTTAAAAATTGCCAATTTT 19 35 0 TAAATTAAAT 0.935778 -97 TATTCGATGCTAAAACTAAGTATTTTGCATAGAA 19 69 0 TAAAATAGTT 0.785543 -63 ATAAATGTTAAAAATAAAAATATTA 20 52 0 TAAATTAAAT 0.935778 -15 TGAAGATGCTTAAAAATCAGTGGTGTATCATTTT 23 27 1 TAAAATAGTT 0.785543 -224 ATTTCAACACTAAAACTCAACGCTAGAATACTTA 26 119 1 TAAAATAACT 0.916033 -182 GAAGGGTTTCTAAAATTTAAAAATCAAGGAGAAA 27 29 0 TAAAATAAAT 0.935778 -170 TAATTGTTAATAAATTTGAGCTATAGCCTGTCTA 28 128 1 TAAATTAGCT 0.877998 -173 GACTATTCCGCAAATTTAAGCTATAAATGGGTAT 28 173 0 CAAATTAGCT 0.671666 -128 TCGCAATCCTTAAATATCAGAGTTTGTGTATAAA 28 205 1 TAAATTAGAT 0.905767 -96 ***** * *** * Masking position 7 Map Score: 23.4316 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 55 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 2 CCCCCCTTAGAGGACGAATTAAGAAAGTACACT 5 104 0 AGGCGATAAG 0.846882 -29 TCGTCCTCTAAGGGGGGTGAAAG 5 120 1 AGGGGGGAAG 0.992621 -13 GCACCGCCGAAGGCGGAGTCAATGAACTTGGGC 6 53 1 AGGGGATAAT 0.959345 -154 TCTAGAAAAGATGCGGGGGTAATAACCCGCCCA 6 81 0 ATGGGGGAAT 0.940687 -126 ATTGACATCAAGGAGGGCGAAGGAAAGGTTCTA 7 186 1 AGGGGGGAGG 0.94806 -115 CAGTAACATGATGAGGGGGAGATTGA 8 4 0 ATGGGGGGAT 0.8098 -148 GAGGATTAAAAGGGGGGATTAATTCAGATTTAA 8 64 0 AGGGGGTAAT 0.977343 -88 TACAACCCTCAGGAGGATTCAAGAGACTAATCG 10 173 0 AGGGGATAAG 0.970855 -128 AACCTATTTAAGGGCGAACAAAGCTATTAAACA 11 25 0 AGGCGACAAG 0.844267 -61 TCATCGGTTCAGGAGGGATGAATCATGTCATCG 15 68 1 AGGGGGTAAT 0.977343 -200 TGGTGGAACTAAGCTTGAGATTC 22 1 1 TGGGGACAAG 0.850002 -233 AGAATGTACAAGGAGGGGCAAAT 24 105 1 AGGGGGCAAT 0.976895 -13 ATGCTCCTGGAGGGGGATGAAATTTGAGGAGGT 26 233 1 AGGGGAGAAT 0.981179 -68 GGGATGAAATTTGAGGAGGTAATCGTTAAATAT 26 246 1 TTGGGAGAAT 0.600918 -55 TGGAATGTTCAGGAGGGTGTGAG 27 186 1 AGGGGGGGAG 0.973057 -13 *** *** * *** Masking position 6 Map Score: 17.3337 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 209 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 CAGATAAAAAAGAAATAGAGAAA 1 2 0 AGAAAAGAAA 0.848529 -35 AATTTACATTAAAAACAGATAACAAAGCTAAC 2 67 0 AAAAAAGAAA 0.862512 -103 TTTCAAAGGCAAAAACAGAAAAATAAATAAAG 2 114 1 AAAAAAGAAA 0.862512 -56 AGAGTTAAGTAAAAACAGTTAACATAAGAATA 3 35 0 AAAAAAGTAA 0.796356 -73 AATTTCTCTCAGAATAGGTAAAATAATGAAAA 5 11 0 AGAATGGTAA 0.578816 -122 AGTAAACATGAAAATCAGGAAATGCCGAAACA 6 158 1 AAAATAGGAA 0.85155 -49 CCTCCAACAAAGAAAAGGGGAATAAAAATAAA 13 13 0 AGAAAGGGAA 0.950556 -29 TAAAACTTTTAAAAATTGTTAAAAGCTGTAAC 16 27 1 AAAAATGTAA 0.609012 -47 ACGATCTTTGAAAAATAGAAAAGGGCTTTTAG 17 37 0 AAAAAAGAAA 0.862512 -23 TGTTCATGTTAAAAATTGGCAATTTTTAAGAT 19 24 1 AAAAATGGAA 0.875869 -108 TATTTTGCATAGAATATGGTAAAATAAATCTT 19 51 0 AGAATTGGAA 0.671085 -81 AAATATGACCAAAAATGGGGAAC 20 2 0 AAAAAGGGAA 0.955613 -65 AAAAACCTCCAAAAAGAGGAAAGAAA 21 5 0 AAAAAAGGAA 0.946566 -24 GGAGGCATATAGAAAGGGGAAGAGGATATATT 22 155 1 AGAAAGGGAG 0.695917 -79 AACATCTCAAAAAATAAGGGAATTAGAGAGAT 23 82 0 AAAATAGGAA 0.85155 -169 TTTGGTGTTTAAATAAGGGCAATAAAGAAAAG 24 26 0 AAATAGGGAA 0.633593 -92 CCTTAAAGGTAGAAAAGGAAAAAGGAATAAAA 25 14 0 AGAAAGGAAA 0.87193 -32 ***** *** ** Masking position 3 Map Score: 14.2603 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 222 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 TAATCCTCAAGATTGTTAACT 4 45 0 TAATCCTCAG 0.957434 -11 TCCCCCCTTTTAATCCTCAAGCTAATTATAA 8 79 1 TAATCCTCAG 0.957434 -73 AGGAGGTTCTAGAATCTCCAGCTCACCCGTA 10 62 1 AGAATCTCAG 0.938579 -239 CCATAAGCTTAAATTCTCTAGAGATAACCTA 11 59 1 AAATTCTCAG 0.968895 -27 TGAAGATCATAGATTCTCAAGATTGCATTAG 12 73 0 AGATTCTCAG 0.971221 -102 GGAAAAACCTCCAAAAAGAGGAAA 21 15 0 AAAACCTCAA 0.79543 -14 GAGGATTTTAAGAATCTCAAGCTTAGTTCCA 22 14 0 AGAATCTCAG 0.938579 -220 GAGATTCTTAAAATCCTCGAGGAAAGAGAGA 22 27 1 AAATCCTCAG 0.980266 -207 TGCGATAATATAATTCTCAAACGATGTTATA 24 69 1 TAATTCTCAA 0.709155 -49 CCTCCTACTGAGATCCTCAAGAAAAACGTTT 26 76 0 AGATCCTCAG 0.981758 -225 ******** ** Masking position 7 Map Score: 9.90181 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 91 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 5 TTCAAATCTATTATGTTAGCTTTGTTATCTGTTTT 2 53 1 TTTTACTTTT 0.95483 -117 AAAATTATTCTTATGTTAACTGTTTTTACTTAACT 3 30 1 TTTTACTGTT 0.783963 -78 ATTTATATTTCCTTTCTTGAAATAATT 6 3 1 TTTTTCTTTT 0.95483 -204 GAAGTTCACATTATATAAACTTTTTGATTATAATT 8 102 0 TTTAACTTTT 0.710011 -50 TTCACCCCCTGTTTAATAGCTTTGTTCGCCCTTAA 11 16 1 GTTTACTTTT 0.890266 -70 ACGTCGAAGCGTATATTTAATTTTTATGGATCGGA 12 113 0 GTTTTATTTT 0.529902 -62 GGCCTAACTCTTGTAATTCCTTTATATGCTGATGA 22 113 0 TTTTTCTTTT 0.95483 -121 AATCTTTCTTCTCTCTTTTCTTTATTGCCCTTATT 24 12 1 CTTTTCTTTT 0.815102 -106 AGTTTTTATTCCTTTTTCCTTTTCTAC 25 3 1 TTTTTCTTTT 0.95483 -43 CCCTTTAGTTTTCTCCTTGATTTTTAAATTTTAGA 27 20 1 TTTTTATTTT 0.746 -179 CTTAAGAACCTTTTAATAACTTTCTAA 28 3 0 TTTTACTTTT 0.95483 -298 GTTCTTAAGTTTTTTCTACCTTTCTTTTTTGGTTC 28 29 1 TTTTACTTTT 0.95483 -272 ** * ** **** * Masking position 11 Map Score: 7.52884 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 70 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 TCCCTTATGCCCTAAATCTTTATTTATTTT 2 133 0 CCTAAATCTT 0.929696 -37 ACTGTTTTTACTTAACTCTTTCGAGAAGTT 3 48 1 CTTAACTCTT 0.929696 -60 TTCACCATTCCCTAACTATGAACTAGTAAA 7 68 0 CCTAACTATG 0.883609 -233 TATAACTTCCCTTAAATCTGAATTAATCCC 8 53 1 CTTAAATCTG 0.813302 -99 CTTTATGAGGCCTAACTCTTGTAATTCCTT 22 126 0 CCTAACTCTT 0.979788 -108 ATCTATGAGTCCTAACTCTTTAAGTATTCT 26 143 0 CCTAACTCTT 0.979788 -158 CAGGCTTTGGCCTATCTCTGGTACCATAAT 26 171 0 CCTATCTCTG 0.923967 -130 ********** Masking position 4 Map Score: 4.51025 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 36 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 TAACTCTTTCGAGAAGTTTATAAAATTTAGTTAC 3 60 1 GAGAAGTTTA 0.968502 -48 CGGATAAGTGAAGTTACTTAACAGAATGTTT 4 8 1 GTGAAGTATA 0.752405 -48 AAAGATGTACGGGAAGCTGATATATAACACCAGG 7 119 1 GGGAAGTGTA 0.948913 -182 AAGTACATTGGAAAAGTTGATGAAATTGTAATTG 7 156 1 GAAAAGTGTA 0.707906 -145 ATAGGGTGATGATTATGTACGCTGGGAAG 10 6 1 GTGATGTTTA 0.680062 -295 TATGTACGCTGGGAAGGTTGTTGAGATTGGAAGC 10 24 1 GGGAAGTTTA 0.961971 -277 TGGAAGCATGGAGGAGGTTCTAGAATCTCCAGCT 10 51 1 GAGGAGTTTA 0.891946 -250 ATGTAAATCCTAGAAGAGATTCTAACAAAAACTT 15 197 1 TAGAAGGATA 0.431005 -71 AAAGGGCTTTTAGGAGTTTTTAAAATAAAAGGTT 17 16 0 TAGGAGTTTA 0.660862 -44 ATATAGAAAGGGGAAGAGGATATATTACAAGCTG 22 161 1 GGGAAGGGTA 0.887048 -73 TTGTTTCACCTTGAAGATGCTTAAAAATCAGTGG 23 16 1 TTGAAGTGTA 0.679798 -235 GGGAATTAGAGAGATGTTTTTGAATGTTTTATGA 23 63 0 GAGATGTTTA 0.842184 -188 TACATCACCAGGGAAGGTTATCCAAAGAGATATA 23 225 0 GGGAAGTTTA 0.96197 -26 GAGAGCTTAAGAGAAGGGTTTCTAAAATTTAAAA 27 41 0 GAGAAGGTTA 0.928573 -158 AGAAAGTTATTAAAAGGTTCTTAAGTTTTTTCTA 28 13 1 TAAAAGTTTA 0.437933 -288 ****** ** * * Masking position 14 Map Score: 5.3364 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 412 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 8 TAACTCTTTCGAGAAGTTTATAAAATTTAGT 3 60 1 GAGAAGTTTT 0.785663 -48 GGAGGGCGAAGGAAAGGTTCTAATACTTGCA 7 197 1 GGAAAGGTTT 0.953767 -104 TATGTACGCTGGGAAGGTTGTTGAGATTGGA 10 24 1 GGGAAGGTTT 0.975147 -277 TGGAAGCATGGAGGAGGTTCTAGAATCTCCA 10 51 1 GAGGAGGTTT 0.941529 -250 TTGAAAAATAGAAAAGGGCTTTTAGGAGTTT 17 31 0 GAAAAGGGCT 0.784498 -29 AACCAAGATCGAAAAGCTTATTAGCGAGGTG 23 188 1 GAAAAGCTTT 0.740691 -63 TACATCACCAGGGAAGGTTATCCAAAGAGAT 23 228 0 GGGAAGGTTT 0.975147 -23 AACTGAAGAGGGAAAGGTCATTCTCATGCTC 26 208 1 GGAAAGGTCT 0.898687 -93 GATGAAATTTGAGGAGGTAATCGTTAAATAT 26 248 1 GAGGAGGTAT 0.717389 -53 GAGAGCTTAAGAGAAGGGTTTCTAAAATTTA 27 44 0 GAGAAGGGTT 0.941529 -155 AGAAAGTTATTAAAAGGTTCTTAAGTTTTTT 28 13 1 TAAAAGGTTT 0.634784 -288 ********* * Masking position 5 Map Score: 4.44326 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 242 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 TTTTGCCTTTGAAAACAAAACTAATGCCTA 2 98 0 GAAAACAAAA 0.43229 -72 GGCAAAAACAGAAAAATAAATAAAGATTTA 2 121 1 GAAAAATAAA 0.932255 -49 TTCAAGAAAGGAAATATAAAT 6 2 0 GAAATATAAA 0.704867 -205 TTTCGTCAATTAAATATAAATGTTTCGGCA 6 180 0 TAAATATAAA 0.628495 -27 TTCCGATCCATAAAAATTAAATATACGCTT 12 112 1 TAAAAATTAA 0.530306 -63 AAAAGGGGAATAAAAATAAAAA 13 3 0 TAAAAATAAA 0.90696 -39 ACCTAAAGTTGAAAACTAAAACTTTTAAAA 16 11 1 GAAAACTAAA 0.89268 -63 TTAGGAGTTTTTAAAATAAAAGGTTAAAAA 17 11 0 TTAAAATAAA 0.628493 -49 GACGATCTTTGAAAAATAGAAAAGGGCTTT 17 40 0 GAAAAATAGA 0.651218 -20 ATTTAAAAATCAAGTGTTAATCC 18 4 1 TAAAAATCAA 0.817717 -45 ATAGAATATGGTAAAATAAATCTTAAAAAT 19 45 0 GTAAAATAAA 0.704867 -87 ATAAATGTTAAAAATAAAAATATTATTC 20 49 0 TAAAAATAAA 0.90696 -18 ATTTCAACACTAAAACTCAACGCTAGAATA 26 119 1 TAAAACTCAA 0.73057 -182 AAATCAAGGAGAAAACTAAAGGGGAGGAGA 27 13 0 GAAAACTAAA 0.89268 -186 TTCTAAAATTTAAAAATCAAGGAGAAAACT 27 26 0 TAAAAATCAA 0.817717 -173 ********** Masking position 4 Map Score: 9.90974 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 58 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 ACACTTTTTAAATACCCCGAATAACTTACAT 5 57 1 AAACCCCGAA 0.852005 -76 CGGGGGTAATAACCCGCCCAAGTTCATTGAC 6 70 0 AACCGCCCAA 0.888316 -137 AATATTCCCCCCAACAAAATAATA 9 22 0 ATCCCCCCAA 0.96183 -14 TAGTCTCTTGAATCCTCCTGAGGGTTGTAGG 10 177 1 AACCTCCTGA 0.824874 -124 CTAAGATTACCCCCAATTTTAAATCT 12 159 0 ATACCCCCAA 0.956049 -16 TAGGAACTAGATACCTCCTAATTTTCATCCC 14 12 0 ATCCTCCTAA 0.908024 -118 CGATGCCATCAATACTCCCATGAACGGGATT 14 77 0 AAACTCCCAT 0.721032 -53 GACATGATTCATCCCTCCTGAACCGATGATG 15 66 0 ATCCTCCTGA 0.773832 -202 ATGTCTCCTCATAACTCCCAAAACTTTGACA 15 160 1 ATACTCCCAA 0.941892 -108 TTTTATTTTAAAAACTCCTAAAAGCCCTTTT 17 20 1 AAACTCCTAA 0.92146 -40 GGAAAAACCTCCAAAAAGAGGAAA 21 15 0 AAACCTCCAA 0.682406 -14 AAGCACTAGGAAAACCCCTAAAGTATCAAGC 22 79 1 AAACCCCTAA 0.940279 -155 ** ******** Masking position 1 Map Score: 6.12693 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 174 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 AAAAATGTATCTTCCTAAAATTCAAATCTATTATGTTAGCT 2 33 1 CTTAATTAAT 0.668813 -137 TTTACCTATTCTGAGAGAAATTAATATCTAACCGAAACACT 5 21 1 CTGAATTAAA 0.855534 -112 TAACCTACAACTTTACAAAAGTAAACATGAAAATCAGGAAA 6 139 1 CTTAAGTAAA 0.855534 -68 TGGTATGTTTCGTCAATTAAATATAAATGTTTCGGCA 6 180 0 GTTAATTAAA 0.720352 -27 AGGAGCCTTGCTTATAAAAATTTGCTACTAATACTTTTAAA 7 27 1 CTTAATTGAA 0.947693 -274 ATGTGAACTTCTTATAAAAATTGAGTCTTAATTATA 8 126 1 CTTAATTAAA 0.956634 -26 CCTGGGGAAACTTCAACTAATTCAGGCTCAACCTCACGACA 10 241 0 CTTAATTAAA 0.956626 -60 TGGACTTTCAATTCGACAAATTTATTCAAAAATATAGGGTT 12 16 1 ATTAATTAAA 0.753849 -159 ACTCCCAAAACTTTGACAAATTTAATGTAAATCCTAGAAGA 15 173 1 CTTAATTAAA 0.95659 -95 CTGTAACACTTTTTCTGAAATTGGTGTGAAAA 16 52 1 TTTAATTGAA 0.715665 -22 GAAGATCCAAATTATAACAATTAGTAATAAAATTATGAAGT 23 131 0 ATTAATTGAA 0.715618 -120 GCTTTTCGATCTTGGTTCACTTTGTGGAAAATAGAAGATCC 23 164 0 CTTACTTGAA 0.710821 -87 ACTCCATATTTTTCCCAAAAGTAACGTAGAACCAAAAAAGA 28 51 0 TTTAAGTAAA 0.451398 -250 AACAATTACGCTTAGTTCAATTTAACGTTAAAACCAACAGT 28 95 0 CTTAATTAAA 0.956606 -206 TTAGGCATCTCTGTTTCAAATTTGGATCTAAAGTGTGTAGG 28 261 1 CTGAATTGAA 0.829466 -40 *** **** * ** Masking position 9 Map Score: 7.61499 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 28 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 AGATAAAAAAGAAATAGAGAAA 1 3 0 GAAATAGAGA 0.950975 -34 ACAAAATAATAAAAGAGAGAGC 9 3 0 AAAAGAGAGA 0.942077 -33 AATCCTCGAGGAAAGAGAGATGTACGCCTA 22 38 1 GAAAGAGAGA 0.986132 -196 ATTACAAGCTGACTGAGAGAGGTAGAAGGC 22 184 1 GACTGAGAGA 0.873644 -50 AAAAATAAGGGAATTAGAGAGATGTTTTTG 23 75 0 GAATTAGAGA 0.876563 -176 GGCAATAAAGAAAAGAGAGAAGAAAGATTA 24 11 0 AAAAGAGAGA 0.942077 -107 GAACTAACGAGAAAGAGAGCTTAAGAGAAG 27 59 0 GAAAGAGAGC 0.949715 -140 ATCCAAATTTGAAACAGAGATGCCTAAGGT 28 258 0 GAAACAGAGA 0.94221 -43 ********** Masking position 6 Map Score: 6.90818 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 74 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 TTATCTGTTTTTAATGTAAATTAGGCATTAG 2 77 1 TTATGTAAAT 0.940013 -93 CCCCGGGACTTTGATGTAACTAAATTTTATA 3 78 0 TTGTGTAACT 0.882461 -30 TTCGCCCTCCTTGATGTCAATTACAATTTCA 7 176 0 TTGTGTCAAT 0.782072 -125 ATATCTCCAACTGCTGTAACTTTTTCGTAAG 7 253 0 CTGTGTAACT 0.785861 -48 CCTCATCATGTTACTGTAAATTTGAATGTTT 8 21 1 TTATGTAAAT 0.940013 -131 TTTGACAAATTTAATGTAAATCCTAGAAGAG 15 184 1 TTATGTAAAT 0.940013 -84 TTTGGTCATATTTATGTAAATTACTTGCGAA 20 21 1 TTTTGTAAAT 0.794489 -46 GGTAGAAGGCTTATTGAAAATCTTGAGTAGA 22 204 1 TTATGAAAAT 0.711838 -30 GATGTTTAACCTAGTGTAAATGAACTTCATA 23 108 1 CTATGTAAAT 0.884522 -143 *** ******* Masking position 5 Map Score: 2.61502 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 14 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 14 TATTTAAGGAGCCTTGCTTATAAAAATTTGC 7 21 1 GCCTGCTTAT 0.957451 -280 TAACTTAATTGCCTGGTCAATTGGAATAGCC 14 41 1 GCCTGTCAAT 0.86453 -89 AATTGGAATAGCCTGGCTAATCCCGTTCATG 14 59 1 GCCTGCTAAT 0.983992 -71 TCCCCCAGGAGCCCGCTTAATTTATAATTCC 15 29 0 GCCCCTTAAT 0.851657 -239 TCATGTCATCGCCCAGCTAATTCTAGATACA 15 90 1 GCCCGCTAAT 0.972073 -178 CTTTCTATATGCCTCCTTTATGAGGCCTAAC 22 140 0 GCCTCTTTAT 0.787757 -94 ATAACCAGGCACCTCGCTAATAAGCTTTTCG 23 197 0 ACCTGCTAAT 0.872839 -54 TTGAGCTATAGCCTGTCTAATCTTGGCCGAA 28 143 1 GCCTTCTAAT 0.904845 -158 **** ****** Masking position 10 Map Score: 2.20655 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 48 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 15 ATATATAACACCAGGGGCAAGTACATTGGAA 7 138 1 CCAGGGGCAG 0.987402 -163 ACTTGCACTACCAGGAGAAAGGGTTGGAGTT 7 221 1 CCAGGAGAAG 0.962422 -80 AAGCGGTCCCCCAGGAGCCCGCTTAATTTAT 15 35 0 CCAGGAGCCG 0.993008 -233 AGCTTATTAGCGAGGTGCCTGGTTATATCTC 23 202 1 CGAGGTGCCG 0.941879 -49 TCATCCCCCTCCAGGAGCATGAGAATGACCT 26 222 0 CCAGGAGCAG 0.992556 -79 ********* * Masking position 3 Map Score: 1.77493 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 20 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084