AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_pyro_reg_300.orf -o00260_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 PH0134 300 300aa long hypothetical protein #2 PH0318 300 433aa long hypothetical phosphoribosylglycinamide formyl transferase #3 PH0697 300 641aa long hypothetical protein #4 PH0698 216 160aa long hypothetical nucleoside-diphosphate kinase #5 PH0699 34 625aa long hypothetical threonyl-tRNA synthetase #6 PH0710 32 460aa long hypothetical seryl-tRNA synthetase #7 PH0857 300 394aa long hypothetical threonine synthase #8 PH0858 201 359aa long hypothetical protein #9 PH0859 138 590aa long hypothetical transport protein #10 PH1075 83 319aa long hypothetical homoserine dehydrogenase #11 PH1086 199 346aa long hypothetical aspartokinase #12 PH1087 62 271aa long hypothetical homoserine kinase #13 PH1361 274 537aa long hypothetical proline permease #14 PH1363 211 493aa long hypothetical protein #15 PH1406 300 440aa long hypothetical threonine synthase #16 PH1614 61 570aa long hypothetical glycyl-tRNA synthetase #17 PH1654 185 427aa long hypothetical serine hydroxymethyltransferase #18 PH1886 206 272aa long hypothetical L-isoaspartyl protein carboxyl methyltransferase #19 PH1995 61 449aa long hypothetical glycine dehydrogenase subunit 1 #20 PH1996 150 225aa long hypothetical protein Motif number 1 AAAAAATAGAAAGATTTATTATAGCGAAAGG 8 153 1 AAATTTATTA 0.722169 -49 GGAAAGTTACAAAATTTTTTAATTTTGTTTA 9 34 0 AAATTTTTTA 0.520756 -105 AAGAACTTAGAAACTTTATTAACCTCAAACC 10 24 0 AACTTTATTA 0.960342 -60 GTTCTTTCATAAGCTTTTTAAACCTTTCTCC 10 49 1 AACTTTTTAA 0.794143 -35 AAAAGTGGATAAGCTTTATTTATATTTTCGC 11 28 0 AACTTTATTT 0.942571 -172 TTTTTGAGAAATTCTTTATTTCAATTTTATG 11 89 1 ATCTTTATTT 0.600398 -111 ATACCCCCTAAATCTTTATATACTATAAGTC 13 52 1 AACTTTATAT 0.862155 -223 TTGCCCTTGCAACCTTTATTTTCTCACTCTT 14 60 0 AACTTTATTT 0.942571 -152 GGCCTTCTTTAACCTTTTTTTGCTAACCTAA 14 132 1 AACTTTTTTT 0.872792 -80 CTTCCATATTAACCTTTATTACTTCAGTTCT 15 73 0 AACTTTATTA 0.960342 -228 TCAGTTACATAACCTTTTTAAGGAAGTATTA 17 36 0 AACTTTTTAA 0.794143 -150 ATTTTGGCGAAAACTTTATAAATCTAATCCA 18 35 1 AACTTTATAA 0.90223 -172 AGCTTTGTTAAATCTTTATTTTCAGAAAAGT 18 168 0 AACTTTATTT 0.942571 -39 TTGCTTGAAGAAGCTTTGTTAAATCTTTATT 18 179 0 AACTTTGTTA 0.820154 -28 TTATCACCGAAACCTTTATTACGCTTTCAAT 20 12 1 AACTTTATTA 0.960342 -139 ** ******** Masking position 1 Map Score: 19.1315 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 68 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 TCAGCACGGTTTTACCTTCTTGATACCAAAA 1 78 1 TTTCCTTCTT 0.923777 -223 CTATGTCATACTTTCCTTCTTTAAAAGCAAC 3 136 1 CTTCCTTCTT 0.972273 -165 CTTTATCAGAACTACCTCCTTTATAGGTGGC 4 75 1 ACTCCTCCTT 0.699736 -142 AAGTAAGTTCCTAACCTTCCATAATAAGAAT 4 170 0 CTACCTTCCA 0.742761 -47 CCTACCACCTTCCTTAACCTAAAAC 5 20 0 CCACTTCCTT 0.629568 -15 CTCAGCGTATCTATCCTTTTTATAGTGAGGG 7 19 1 CTACCTTTTT 0.66082 -282 AGGAATTTTTCTTTCCTTCTAGAGCGAACCT 7 59 0 CTTCCTTCTA 0.883467 -242 GGAAACTCATCGTTCCTCCTTATTCAGGAGA 7 90 1 CGTCCTCCTT 0.861952 -211 TAGCAACCTACTATCCTCCTTTAAAGTGCTA 7 135 0 CTACCTCCTT 0.976047 -166 TAGTCCTAAATCACCCTTCTTCCTACTTCAT 7 183 0 TCACCTTCTT 0.923807 -118 CCCCCTGGAGTTAACCTCCTTTCGCTATAAT 8 170 0 TTACCTCCTT 0.933701 -32 AATTTTGTAACTTTCCTTATTCCCAAAGCCC 9 49 1 CTTCCTTATT 0.634906 -90 GCTCTACCCTCCTTGGTAAGCTCT 13 261 0 CTACCTCCTT 0.976047 -14 GCAATTGCTTCCGGCCTTCTTTAACCTTTTT 14 120 1 CCGCCTTCTT 0.879751 -92 CCGCTCTGAACTTGCCTTCCAAGGGTTC 15 8 0 CTTCCTTCCA 0.720459 -293 TTACTTCAGTTCTCCCTTCCTCACCAACCAT 15 55 0 TCTCCTTCCT 0.786283 -246 TTTTTAGGTCTTAACCTTCTTCAGTAAGGGG 16 35 1 TTACCTTCTT 0.931402 -27 AAGTTCAGCCTCCTTCTTCTCTCGA 18 5 1 TCACCTCCTT 0.92634 -202 *** ******* Masking position 7 Map Score: 16.6572 Number of sites scoring better than the average of aligned sites = 867 Number in coding regions = 795 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 ATAATATTAAAGCCGGGGTCAGAAATACCT 2 25 1 AGCCGGGGTC 0.938618 -276 CCTTTGTTCTTGCCGGGATCTTTACTGGAG 4 136 1 TGCCGGGATC 0.889923 -81 ATTGGCTATTGTCGCGGGTGCTCTGACTTT 12 16 0 GTCGCGGGTG 0.879738 -47 ACGATAGAGTGGCCGGGGTGGTGTAGCCTG 18 73 1 GGCCGGGGTG 0.992978 -134 TGGATCCCCTGGCCCGGGTTCAAATCCCGG 18 120 1 GGCCCGGGTT 0.982751 -87 CTGGGGCCGGGGCCGGGATTTGAACCCGGG 18 132 0 GGCCGGGATT 0.990788 -75 TAAATTTTTAGTCGGGGATTTGCA 19 48 1 GTCGGGGATT 0.914824 -14 GGAGCCGAAGGTCCCGGGTTCAAATCCCGG 20 96 1 GTCCCGGGTT 0.964751 -55 TTGGCGGGCCGGCCGGGATTTGAACCCGGG 20 108 0 GGCCGGGATT 0.990788 -43 ********** Masking position 9 Map Score: 10.8554 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 56 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 AGTCTATTAGTTTTTCATTTAGCGAGGGTACCCTTGCT 1 40 0 TTTTCATTGG 0.922618 -261 CAAACCAAGGTTTTTAATCTAAACTAGCGAAAAGTTCT 1 136 0 TTTTAACTGC 0.855821 -165 GAGGGAAAAGTTTTTAATTTGAAAAAGTCGTTCCCAAA 1 213 1 TTTTAATTGT 0.744024 -88 ACGATGCTTGTTTTAGGTTAAGGAAGGTGGTAGG 5 10 1 GTTTAGTTGG 0.703082 -25 TCTTTGGGAGTTTTGAAGTTGGGACGGGTAATTGACCA 7 249 1 TTTTAATTGG 0.979487 -52 GTTACAAAATTTTTTAATTTTGTTTAGGTAATTACCCT 9 22 0 TTTTAATTGG 0.979487 -117 TTCATAAGCTTTTTAAACCTTTCTCCGCTTACCTTTCG 10 54 1 TTTTAACTGC 0.855821 -30 CACTTTTAAATTTTCAATTTGATCTCAGAATATACAAT 11 52 1 TTTTAATTAG 0.826515 -148 ATATTTACATTTTGAAATTTATTGGAGGTGACTTAGAT 13 85 1 TTTGAATTGG 0.922618 -190 AGATGTTGTTAAACTGCATAAGGAGCTCTTTAA 14 6 1 TTGTAACTGG 0.829078 -206 ACGTCTTTGATTTTGCAATTGCTTCCGGCCTTCTTTAA 14 106 1 TTTTCATTGG 0.922618 -106 TGTTGAATTTGTTTCAATTTTTGGAGGG 14 194 1 GTTTAATTGG 0.949166 -18 TTTTAGACGTTTTGAAAACTCACAGAGGATAAAACTCC 17 94 0 TTTGAACTGG 0.899262 -92 AATGCACAAGGTTTAAATTTAAGTTAAGCAAATATTAG 17 144 1 GTTTAATTAG 0.650715 -42 GGCGAAAACTTTATAAATCTAATCCAGGAGCACACGAT 18 40 1 TTATAACTGG 0.765959 -167 TTGTGGAAGTTTTAAAGTTATTGTTGGCGGGCCGGCC 20 124 0 TTTTAATTGG 0.979487 -27 **** ** ** ** Masking position 10 Map Score: 11.0136 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 140 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 ATTCCTTCCCCTTTCCCACTTTTAGAA 1 284 0 CCCCTTTCCC 0.938132 -17 TAGGGGTAATCCCCTGTGCCACCTATAAAG 4 93 0 CCCCTGTGCC 0.948322 -124 CAGGGGATTACCCCTACCCTCAAAGACTCC 4 107 1 CCCCTACCCT 0.953262 -110 CCCCGAACCTAACTAGTGCG 11 1 1 CCCCGAACCT 0.881888 -199 CTACATAGTACTCCTTCCCCGTAATTTTGT 13 206 0 CTCCTTCCCC 0.772165 -69 GGCTACACCACCCCGGCCACTCTATCGTGT 18 71 0 CCCCGGCCAC 0.954193 -136 GATCCACAGTCCCCTGTGCTAACCAGGCTA 18 96 0 CCCCTGTGCT 0.906087 -111 GACTGTGGATCCCCTGGCCCGGGTTCAAAT 18 115 1 CCCCTGGCCC 0.978341 -92 CAAATCCCGGCCCCGGCCCCAGAAACAGAC 18 140 1 CCCCGGCCCC 0.996232 -67 CAGGCTAGGCCACCGGCCCTCAGAAAAGGC 20 48 0 CACCGGCCCT 0.923919 -103 GGGATTTGAACCCGGGACCTTCGGCTCCGA 20 94 0 CCCGGGACCT 0.815774 -57 ********** Masking position 3 Map Score: 9.58652 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 151 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 6 CAAAGGCTTCAGCTTTATCTAAAGGCCCTT 3 89 0 AGCTTTATCT 0.76794 -212 AGAACTTAGAAACTTTATTAACCTCAAACC 10 24 0 AACTTTATTA 0.793022 -60 TTCTTTCATAAGCTTTTTAAACCTTTCTCC 10 50 1 AGCTTTTTAA 0.677492 -34 AAAGTGGATAAGCTTTATTTATATTTTCGC 11 28 0 AGCTTTATTT 0.896075 -172 TACCCCCTAAATCTTTATATACTATAAGTC 13 53 1 ATCTTTATAT 0.52128 -222 TTTCTATCGGAACTTTTTTAAAGAGCTCCT 14 31 0 AACTTTTTTA 0.639475 -181 TGCCCTTGCAACCTTTATTTTCTCACTCTT 14 60 0 ACCTTTATTT 0.896075 -152 GCCTTCTTTAACCTTTTTTTGCTAACCTAA 14 133 1 ACCTTTTTTT 0.799666 -79 TTCCATATTAACCTTTATTACTTCAGTTCT 15 73 0 ACCTTTATTA 0.907423 -228 AGACCTAAAAAGCTTTGTCTCTACATCTGG 16 16 0 AGCTTTGTCT 0.559486 -46 CAGTTACATAACCTTTTTAAGGAAGTATTA 17 36 0 ACCTTTTTAA 0.677492 -150 TTTTGGCGAAAACTTTATAAATCTAATCCA 18 36 1 AACTTTATAA 0.639475 -171 GCTTTGTTAAATCTTTATTTTCAGAAAAGT 18 168 0 ATCTTTATTT 0.701682 -39 TGCTTGAAGAAGCTTTGTTAAATCTTTATT 18 179 0 AGCTTTGTTA 0.790001 -28 TATCACCGAAACCTTTATTACGCTTTCAAT 20 13 1 ACCTTTATTA 0.907423 -138 ********** Masking position 1 Map Score: 8.01839 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 217 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 7 CTTTTCGCTAGTTTAGATTAAAAACCTTGG 1 140 1 GTTTAGATTA 0.635276 -161 TCCTCAAGAATTGGAGATGAGGGAAAAGTT 1 195 1 TTGGAGATGA 0.909976 -106 TGGGAAGGTATTTGAGATGAAAGATAGAA 3 10 0 TTTGAGATGA 0.941653 -291 ACGATGCTTGTTTTAGGTTAAGGAAGGTGG 5 11 1 TTTTAGGTTA 0.841002 -24 CGCAAACAATTTTTAGATGAATGCTCAAGT 6 13 1 TTTTAGATGA 0.894575 -20 TCAACTATACTTGTAGGTGATATATTGAAT 8 73 0 TTGTAGGTGA 0.909976 -129 TTTTAATTTTGTTTAGGTAATTACCCTAAG 9 19 0 GTTTAGGTAA 0.698067 -120 AAACTTAAGGTTTGAGGTTAATAAAGTTTC 10 16 1 TTTGAGGTTA 0.909586 -68 AATAAAACAATTTGAGATAATTTTTAATAA 11 120 0 TTTGAGATAA 0.786843 -80 TTGAAATTTATTGGAGGTGACTTAGATGGG 13 96 1 TTGGAGGTGA 0.950557 -179 ACACCATAAGGTTGAGGTGACAGC 15 287 1 GTTGAGGTGA 0.950557 -14 ********** Masking position 5 Map Score: 8.25772 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 107 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GAAGTCTATTAGTTTTTCATTTAGCGAGGGT 1 49 0 ATTTTTCATT 0.91601 -252 ATGAGGGAAAAGTTTTTAATTTGAAAAAGTC 1 211 1 ATTTTTAATT 0.903979 -90 TGCTGGGGATATTTTTCCATCCCTATTCACT 2 161 1 ATTTTCCATC 0.678775 -140 TGTCAAGAAAATTTCTCAATTTTCTTCTTTT 2 194 0 ATTCTCAATT 0.77728 -107 GAGAATTTCAACTTCTTCATAGTGCATTATC 3 203 1 ATTCTTCATA 0.665222 -98 TTCTCTCGGAGTTTTTAATTAAATTCCAAG 3 281 0 ATTTTTAATT 0.903979 -20 AGTTTCCAGGAATTTTTCTTTCCTTCTAGAG 7 66 0 ATTTTTCTTT 0.537168 -235 TTTAATTGATATTTCTTCATTAGATTCTTGA 8 117 0 ATTCTTCATT 0.888993 -85 AAGTTACAAAATTTTTTAATTTTGTTTAGGT 9 31 0 ATTTTTAATT 0.903979 -108 TCCACTTTTAAATTTTCAATTTGATCTCAGA 11 50 1 ATTTTCAATT 0.825993 -150 ATTTTTGAGAAATTCTTTATTTCAATTTTAT 11 88 1 ATTCTTTATT 0.553353 -112 AATTTGAGATAATTTTTAATAACATAAAATT 11 111 0 ATTTTTAATA 0.700239 -89 TCCTAATAGGAATTTTTAATCCTAAAAAATA 11 149 1 ATTTTTAATC 0.783237 -51 * ********* Masking position 1 Map Score: 6.12501 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 77 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TGATAATATTAAAGCCGGGGTCAGAAATAC 2 23 1 AAAGCCGGGG 0.773953 -278 TTGTCAGATAAAATGCTGGGGATATTTTTC 2 148 1 AAATGCTGGG 0.854624 -153 CCGGGATCTTTACTGGAGGGGTATTCTTAT 4 148 1 TACTGGAGGG 0.582345 -69 CAAGAAAAGTTAATGGAGGGTGCAAA 7 285 1 TAATGGAGGG 0.815274 -16 AAAGGAGGTTAACTCCAGGGGGAATGAACA 8 179 1 AACTCCAGGG 0.928009 -23 TAATCTATTTAAAACGAGGGAAAGCTCAGT 9 102 1 AAAACGAGGG 0.845906 -37 AAGCTCAGTGAAATGGGGGGAAAGTT 9 123 1 AAATGGGGGG 0.913513 -16 AAATATATAAAAATCGTGAGCTT 11 187 1 AAATCGTGAG 0.65457 -13 CAAAAACGTCAAATCCAGGGCCAAAATTGG 12 41 0 AAATCCAGGG 0.976078 -22 GCTAGTTGCTAAATCGAGGCACTTTTGTGG 15 211 0 AAATCGAGGC 0.936856 -90 GTTTTCGCCAAAATCGAGAGAAGAAGGAGG 18 19 0 AAATCGAGAG 0.857072 -188 GCCCGGGTTCAAATCCCGGCCCCGGCCCCA 18 131 1 AAATCCCGGC 0.861949 -76 TCCCGGGTTCAAATCCCGGCCGGCCCGCCA 20 107 1 AAATCCCGGC 0.861949 -44 ********** Masking position 2 Map Score: 6.76326 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 202 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 TACTCAATATGAGTATTGGGAAGGTATTTG 3 26 0 GAGTATTGGG 0.793967 -275 TCATGAAAGACGTCTTTGGGAGTTTTGAAG 7 237 1 CGTCTTTGGG 0.960588 -64 TGGGCAACCTGGGCTTTGGGAATAAGGAAA 9 60 0 GGGCTTTGGG 0.97457 -79 CTGGATTTGACGTTTTTGGG 12 53 1 CGTTTTTGGG 0.967104 -10 GATAGTTTATGGGTTTTGGGACAAAATTAC 13 186 1 GGGTTTTGGG 0.978826 -89 AAACCTTGTGCATTTTTGGGCAATCCTTTT 17 128 0 CATTTTTGGG 0.908541 -58 ********** Masking position 6 Map Score: 2.22657 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 30 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 TAGCAATTTCCAGAGCTTCCTGCAGGTATT 2 48 0 CAGAGCTTCC 0.931343 -253 TTTCATCTCAAATACCTTCCCAATACTCAT 3 18 1 AATACCTTCC 0.893383 -283 ATTGCTATGTCATACTTTCCTTCTTTAAAA 3 132 1 CATACTTTCC 0.836084 -169 AAGTAAGTTCCTAACCTTCCATAATAAGAA 4 171 0 CTAACCTTCC 0.786507 -46 AGGAGGAACGATGAGTTTCCAGGAATTTTT 7 80 0 ATGAGTTTCC 0.648043 -221 GACGTCTTTCATGACCTTTCTCCAAGACAA 7 221 0 ATGACCTTTC 0.875799 -80 ATAGATTATTCATACATTCCTGGGCAACCT 9 80 0 CATACATTCC 0.607894 -59 CCCCATTTCACTGAGCTTTCCCTCGTTTTA 9 111 0 CTGAGCTTTC 0.859946 -28 CCTTTCTCCGCTTACCTTTCGTC 10 71 1 CTTACCTTTC 0.889285 -13 GCATATGATGAAGAGCTTACCAAGGAGGGT 13 250 1 AAGAGCTTAC 0.557784 -25 TTTATAAATTATGACTTTACATAGGTAATG 14 166 1 ATGACTTTAC 0.468582 -46 CCGCTCTGAACTTGCCTTCCAAGGGTTC 15 9 0 CTTGCCTTCC 0.721334 -292 GCCCCAGAAACAGACTTTTCTGAAAATAAA 18 155 1 CAGACTTTTC 0.811048 -52 GATTATAATAAATACCTTTCCTAAGGTTGA 19 14 0 AATACCTTTC 0.791358 -48 ********** Masking position 7 Map Score: 3.59862 Number of sites scoring better than the average of aligned sites = 482 Number in coding regions = 445 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 AGTTTTTCATTTAGCGAGGGTACCCTTGCTA 1 39 0 TTAGCGGGGT 0.931342 -262 CGTTCCCAAATTAGCGAGGGATTAAGTCGAT 1 241 1 TTAGCGGGGA 0.989734 -60 TTTCAAGTGAATAGGGATGGAAAAATATCCC 2 166 0 ATAGGGTGGA 0.801829 -135 CGGTAGGTTTTTAGCCTTGGAATTTAATTAA 3 266 1 TTAGCCTGGA 0.948061 -35 TGCAATAATCTTAGCGTTAGAGGTGGTCTTT 4 20 1 TTAGCGTAGA 0.801322 -197 TATCCTTTTTATAGTGAGGGAGTATACTAAG 7 30 1 ATAGTGGGGA 0.859737 -271 ATAGCCAATTTTGGCCCTGGATTTGACGTTT 12 37 1 TTGGCCTGGA 0.886987 -26 ATATCATAAATTAGGGGGTGAAAACTAT 13 8 0 TTAGGGGTGA 0.769782 -267 CAACCAAATTTTGGCGAGGGAT 17 2 0 TTGGCGGGGA 0.976444 -184 TACTAAATTTTTAGTCGGGGATTTGCA 19 45 1 TTAGTCGGGA 0.907262 -17 ****** **** Masking position 2 Map Score: 4.88328 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 109 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 13 TTTTTCATTTAGCGAGGGTACCCTTGCTAT 1 38 0 AGCGAGGGTA 0.917389 -263 AAGAATTGGAGATGAGGGAAAAGTTTTTAA 1 200 1 GATGAGGGAA 0.895087 -101 TTCCCAAATTAGCGAGGGATTAAGTCGATG 1 243 1 AGCGAGGGAT 0.973911 -58 TCCTTTTTATAGTGAGGGAGTATACTAAGG 7 32 1 AGTGAGGGAG 0.965467 -269 ATCTATTTAAAACGAGGGAAAGCTCAGTGA 9 104 1 AACGAGGGAA 0.935864 -35 TCCAATGGTTGGTGAGGAAGGGAGAACTGA 15 51 1 GGTGAGGAAG 0.814099 -250 ACCAAATTTTGGCGAGGGAT 17 1 0 GGCGAGGGAT 0.978298 -185 ********** Masking position 5 Map Score: 1.88934 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 108 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 TTGGAAATCAGGAACTAGCAACCTACTATC 7 151 0 GGAACTAGCA 0.987844 -150 AAGAATCGTTGGAACTAGCAGCGTGGCCCA 13 142 0 GGAACTAGCA 0.987844 -133 CCTCGATTTAGCAACTAGCATACACAGAAA 15 222 1 GCAACTAGCA 0.977856 -79 ********** Masking position 4 Map Score: 0.17815 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 7 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 15 GCTCTGGAAATTGCTATAGATTATAATATCTCCATT 2 62 1 TTGTGTTAAA 0.747514 -239 AATACTCATATTGAGTAAGTCTTCAATCTTAGATCA 3 39 1 TTGAGCTTAA 0.791927 -262 CACTGACAATTTGGAAAAGCTTAGAAAAAGGACAAA 8 19 0 TTGAGTTAAA 0.922658 -183 TTCACTGAGCTTTCCCTCGTTTTAAATAGATTATTC 9 99 0 TTTTGTTTAA 0.788695 -40 TTCTAAGTTCTTTCATAAGCTTTTTAAACCTTTCTC 10 43 1 TTTAGTTTTA 0.657083 -41 TTTTGACATATTTTTTAGGATTAAAAATTCCTATTA 11 152 0 TTTAGTTAAA 0.898876 -48 TGGGCAATCCTTTTAGACGTTTTGAAAACTCACAGA 17 106 0 TTTAGTTTAA 0.871874 -80 TTGCCCAAAAATGCACAAGGTTTAAATTTAAGTTAA 17 135 1 ATGAGTTTAA 0.720001 -51 CGACTAAAAATTTAGTAAGATTATAATAAATACCTT 19 26 0 TTTAGTTAAA 0.898902 -36 CACCGAAACCTTTATTACGCTTTCAATTTAAAGCCT 20 16 1 TTTAGTTTAA 0.937293 -135 TTGTGGAAGTTTTAAAGTTATTGTTG 20 135 0 TTGAGTTTAA 0.952173 -16 *** * * *** ** Masking position 16 Map Score: 3.46836 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 67 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159