AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_aful_reg_100.orf -o00970_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0260 30 glutamyl-tRNA synthetase (gltX) #2 AF0409 74 aspartate aminotransferase (aspB-4) #3 AF0410 56 signal-transducing histidine kinase, putative #4 AF0411 30 cysteinyl-tRNA synthetase (cysS) #5 AF0546 300 nitrate reductase, gamma subunit (narI) #6 AF0548 59 threonyl-tRNA synthetase (thrS) #7 AF0633 173 isoleucyl-tRNA synthetase (ileS) #8 AF0776 135 tyrosyl-tRNA synthetase (tyrS) #9 AF0894 300 arginyl-tRNA synthetase (argS) #10 AF0916 59 glycyl-tRNA synthetase (glyS) #11 AF0919 30 conserved hypothetical protein #12 AF0920 36 aspartyl-tRNA synthetase (aspS) #13 AF1216 101 lysyl-tRNA synthetase (lysS) #14 AF1424 112 phenylalanyl-tRNA synthetase, subunit beta (pheT) #15 AF1452 117 signal-transducing histidine kinase #16 AF1453 37 methionyl-tRNA synthetase (metS) #17 AF1609 59 prolyl-tRNA synthetase (proS) #18 AF1642 50 histidyl-tRNA synthetase (hisS) #19 AF1694 50 tryptophanyl-tRNA synthetase (trpS) #20 AF1955 68 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #21 AF2035 23 seryl-tRNA synthetase (serS) #22 AF2036 62 cytochrome C oxidase folding protein (coxD) #23 AF2037 54 translation initiation factor eIF-2B, subunit delta (eif2BD) #24 AF2224 38 valyl-tRNA synthetase (valS) #25 AF2225 64 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE-2) #26 AF2254 207 ATP-dependent RNA helicase, DEAD-family (deaD) #27 AF2255 53 alanyl-tRNA synthetase (alaS) #28 AF2421 58 leucyl-tRNA synthetase (leuS) #29 AF2425 85 methanol dehydrogenase regulatory protein (moxR) Motif number 1 GAAACCTGAACAGCCGGTGGATTAAAAAAG 7 154 0 ACCGACGGGG 0.990387 -20 GCCGAGGGGAGGCCTGTCAAGCGGGCGGCAGCGGTTCC 9 25 1 GCCGACGGGG 0.998325 -276 CAGAGTCCTCGTCCCGGAGGGCCGGCGGTTATGGCCGG 9 71 1 GCCGGCGGGG 0.999467 -230 CGGCGGTTATGGCCGGGCTGCCCGGAGGGGCTGTCCGC 9 93 1 GCCGGCGGGG 0.999541 -208 GGGGCTGTCCGCCATATTAGCCGGGGGGAACGGCCCAG 9 119 1 GCAAGCGGGG 0.984914 -182 GAACGGCCCAGGCCCGGAAGGGAGCAGGCTAACCCCGG 9 146 1 GCCGGGGCGG 0.986953 -155 AACCCCGGACGACCGGCGCTTCCGGGGGTGCGGGGAGG 9 176 1 GCCGTCGGGG 0.998237 -125 GCCTCGGGTCGACCTGCCTTACGGGCGGCTTGAAGCCC 9 223 0 GCCGTCGGGG 0.998325 -78 CGGTCAGAATTGGCTGGAGGATTTTTCAAT 9 281 0 GCAAGCGGGG 0.984914 -20 AAAGAATTTTAACCTGAAGCAGAGGTGGGAAC 23 5 0 ACCGCGGGGG 0.958602 -50 * ** * * * ** ** Masking position 3 Map Score: 24.365 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 16 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 2 AAAACTTGAGAAAATTTTAAATAATTCAAAA 5 26 0 AAAATTTTAA 0.690683 -275 AAAATTTTCTCAAGTTTTTAATAATTAAGAT 5 39 1 CAAGTTTTAA 0.816341 -262 AATAAAAATTAAATTTTTTATCTTAATTATT 5 58 0 AAATTTTTAT 0.593323 -243 AGGTCAAATCAAATGTTTGCAATTTCAATAT 5 122 1 AAATGTTTCA 0.891105 -179 AATAGACTTTAAATTATTAAATTTTCGTTTT 5 219 0 AAATTATTAA 0.607598 -82 TTATAAAGTTTTCCAAAGATAAGAT 5 286 0 AAAGTTTTCA 0.899058 -15 GAGGAGTAATAAATTTTTCTAAGCAATTAAA 6 23 0 AAATTTTTTA 0.861928 -37 AAAAGGTTGCAAAGGCTTGAAAATATATTTA 8 35 0 AAAGGCTTAA 0.887514 -101 AAAGTTGTTTAAATGTTTAAAAGCCCTCCAA 8 89 0 AAATGTTTAA 0.954394 -47 AAGTTGGGAAAAAGGTTTAAATAAAAAGCGT 13 30 0 AAAGGTTTAA 0.961127 -72 GTTGAGGTTAAAATTTTTTAGGTTGGGTGAT 14 77 0 AAATTTTTAG 0.799174 -36 ATAATCGGCCAAATGCTTTTATTTACAAAGA 15 84 1 AAATGCTTTA 0.683789 -34 GGCTGACACGAAAGTTTTTTATACAAAATGG 17 25 0 AAAGTTTTTA 0.880605 -35 AGGGTGTTTAAAAGGTTTTAGAGTTGAGCGA 18 15 0 AAAGGTTTAG 0.836165 -36 TGAGTAGTAGAAATGTTTTAAAGTGTTTCTT 20 44 0 AAATGTTTAA 0.954394 -25 CTTCAGGTTAAAATTCTTTAACCTTTGAAAA 23 24 1 AAATTCTTAA 0.860178 -31 GTGTTCAATTTTTTCAAAGGTTAAAG 23 39 0 CAATTTTTCA 0.595327 -16 GTAAGAAGGCAAAGGTTTTAAGAGTTATCTC 25 18 1 AAAGGTTTAA 0.961127 -47 TTTCATGGTGAAAGTTTTGTAAAGTTAAAAT 26 18 1 AAAGTTTTTA 0.880605 -190 GCCAAACGCCAAATTTTTTAATCCCATTTAT 28 26 1 AAATTTTTAA 0.950686 -33 ******** ** Masking position 7 Map Score: 20.9309 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 137 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 3 ACGCGGGGGCCGAAGCCGAGGGG 9 3 1 GCGGGGGCCA 0.803448 -298 GGGGGCCGAAGCCGAGGGGAGGCCTGTCAAG 9 15 1 GCCGAGGGGG 0.987596 -286 GGCCTGTCAAGCGGGCGGCAGCGGTTCCAGG 9 35 1 GCGGGCGGCG 0.964246 -266 AGTCCTCGTCCCGGAGGGCCGGCGGTTATGG 9 74 1 CCGGAGGGCG 0.986025 -227 GCCGGGCTGCCCGGAGGGGCTGTCCGCCATA 9 104 1 CCGGAGGGGT 0.972278 -197 CGCCATATTAGCCGGGGGGAACGGCCCAGGC 9 128 1 GCCGGGGGGA 0.928597 -173 CGGCCCAGGCCCGGAAGGGAGCAGGCTAACC 9 149 1 CCGGAAGGGG 0.952172 -152 CAGGCTAACCCCGGACGACCGGCGCTTCCGG 9 170 1 CCGGACGACG 0.654653 -131 ACCGGCGCTTCCGGGGGTGCGGGGAGGAGGT 9 187 1 CCGGGGGTGG 0.942308 -114 GGGAGGAGGTGCCTGGGGCTTCAAGCCGCCC 9 208 1 GCCTGGGGCT 0.539653 -93 GGTCGACCTGCCTTACGGGCGGCTTGAAGCC 9 224 0 CCTTACGGGG 0.619423 -77 GGCAGGTCGACCCGAGGCGTGCCCACCTTTT 9 243 1 CCCGAGGCGG 0.948015 -58 CGGTCAAGCTGAGGCGTTGCTGTTTTTA 13 84 0 GCTGAGGCGT 0.849188 -18 AAGCGTATTTGCTGGCGGCAGTTTTTTGGAA 15 39 1 GCTGGCGGCG 0.924284 -79 TTAACCTGAAGCAGAGGTGGGAAC 23 4 0 GCAGAGGTGG 0.829861 -51 AAGTTCTACGCCTGAGGTGATATC 25 51 1 CCTGAGGTGT 0.742142 -14 CCAACGCTTGGCTGAAGGGTATATAAGTCTT 26 153 0 GCTGAAGGGA 0.690611 -55 AACATCCAATGCAGAAGGCATCCG 27 40 1 GCAGAAGGCT 0.500237 -14 ********* * Masking position 7 Map Score: 15.2957 Number of sites scoring better than the average of aligned sites = 1358 Number in coding regions = 1277 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 4 AACGGTCATGGGTTTAAAAATT 4 1 0 GGTAAAAATT 0.584707 -30 ATAGCTAATAGTCTAAAAAGGTCAAATCAAAT 5 104 1 GTTAAAAGGT 0.918056 -197 TTTCAATATCGGTTTAAAAGGTATGAGATAGA 5 144 1 GGTAAAAGGT 0.976229 -157 AGCAATTAAAAAAGAAAAAAGT 6 1 0 AAGAAAAAGT 0.721023 -59 ACAGCCGGTGGATTAAAAAAGTTATCAGCTTT 7 143 0 GATAAAAAGT 0.927913 -31 ACCTGCTAATGATGAAAAAGGTTGCAAAGGCT 8 49 0 GAGAAAAGGT 0.973445 -87 TTTTCAATTTAACTGAAAAGGTGGGCACGCCT 9 257 0 AATAAAAGGT 0.898959 -44 TGCAGAATGCAACTTAAAAGGTTATCTTCTTA 10 34 0 AATAAAAGGT 0.898944 -26 ATTGCAAAGTTGGGAAAAAGGTTTAAATAAAA 13 35 0 TGGAAAAGGT 0.891845 -67 GGAGGGAAAAGGTTGCGAGGGGT 16 25 0 GAGAAAAGGT 0.973445 -13 TCGGCAAGGGTGTTTAAAAGGTTTTAGAGTTG 18 20 0 TGTAAAAGGT 0.900656 -31 TTTAGTTTGAGGGCAAAAAAGTTTTCGGAATT 22 33 0 GGCAAAAAGT 0.732295 -30 GTGTTCAATTTTTTCAAAGGTTAAAGAATTT 23 34 0 TTTCAAAGGT 0.399016 -21 TGTGGCGTAAGAAGGCAAAGGTTTTAAGAGTT 25 12 1 GAGCAAAGGT 0.907757 -53 TAATAAATGGGATTAAAAAATTTGGCGTTTGG 28 27 0 GATAAAAATT 0.58013 -32 ** * ******* Masking position 7 Map Score: 12.2136 Number of sites scoring better than the average of aligned sites = 380 Number in coding regions = 320 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 5 TTTTATTTAACTGAACAGCAAAGTTTATAT 3 12 1 CTGAACAGCA 0.932665 -45 TTAAGGCGAAAAAAACAGCAATTTAGGTTA 5 179 1 AAAAACAGCA 0.977634 -122 ATAATAATTTAAAAAAAGCATTAATAGACT 5 242 0 AAAAAAAGCA 0.858624 -59 GAAACCTGAACAGCCGGTGGATTAA 7 159 0 CTGAACAGCC 0.919321 -15 AAACAACTTTAAAAACAGCCTGGGTTTTCG 8 110 1 AAAAACAGCC 0.972944 -26 GCTAAACTTAAAAAACTGCCTGAAGGTGTA 12 12 1 AAAAACTGCC 0.889588 -25 AGGCAAGTTTAAAAACAGCAACGCCTCAGC 13 75 1 AAAAACAGCA 0.977634 -27 TCGGCCCAACCAGAACAACATCA 14 4 0 CAGAACAACA 0.736523 -109 ATCCATTCCAAAAAACTGCCGCCAGCAAAT 15 45 0 AAAAACTGCC 0.889588 -73 TATCTTTGTAAATAAAAGCATTTGGCCGAT 15 87 0 AATAAAAGCA 0.689764 -31 GAATTTATCGATTAACAGCAACCATCG 22 8 0 ATTAACAGCA 0.850507 -55 CAGAGAACAGAACAGCAACGTTCCACT 26 191 0 CAGAACAGCA 0.974974 -17 ********** Masking position 5 Map Score: 13.5058 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 260 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 6 GGCCCACCTGGGAAGTTGAGAAATATAAAG 1 11 0 GGAAGTTGAG 0.953807 -20 GTAAATATCAGAAGCTTGAGGTTCTTGC 2 9 0 GAAGCTTGAG 0.928177 -66 TTAAAAGGTATGAGATAGAGACTTAAGGCG 5 157 1 TGAGATAGAG 0.793979 -144 GGAGGGAGAGTGAGGGAAGG 7 1 1 GGAGGGAGAG 0.968536 -173 GCAAAAATTAGGAGGGATAGTAGGCTGAAA 7 64 0 GGAGGGATAG 0.884058 -110 GGATTTTGCTTGAAGTTGAGGTTAAAATTT 14 92 0 TGAAGTTGAG 0.760826 -21 CACCCTTGCCGAAGCTTGAGC 18 40 1 GAAGCTTGAG 0.928177 -11 ATAGAAAATTTAGTTTGAGGGCA 22 50 0 GAAAATTTAG 0.48887 -13 GGAGAGAGTCGAAGATTGAGGGATTCAAAC 26 122 1 GAAGATTGAG 0.939715 -86 CCAAGCGTTGGGAGATAGAGTGGAACGTTG 26 173 1 GGAGATAGAG 0.961561 -35 AAGAATGGTAGGAGGGTTAGAGCTATGGGA 29 43 0 GGAGGGTTAG 0.928225 -43 ********** Masking position 3 Map Score: 8.24863 Number of sites scoring better than the average of aligned sites = 1920 Number in coding regions = 1830 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 7 TTCTGGACGATGAATATAAACTTTGCTGTTCAGT 3 21 0 TAATTACTTT 0.876983 -36 GATAAAAAATTTAATTTTTATTTTTTATATACAT 5 67 1 TAATTTTTTT 0.955375 -234 TTTAAATTATTAAATTTTCGTTTTTTATAGCTCA 5 209 0 TAATTTTTTT 0.955375 -92 TTAAAGTCTATTAATGCTTTTTTTAAATTATTAT 5 238 1 TAATCTTTTT 0.801274 -63 ATGCTAAAGATGAATCTTATCTTTGGAAAACTTT 5 273 1 TAATTTCTTT 0.966367 -28 AAAAGCGTATTAAATCTTAGCGTTGAG 13 4 0 TAATTTCGTT 0.844017 -98 GTTGCTGTTTTTAAACTTGCCTTTATCGAGATTG 13 63 0 TAAATTCTTT 0.876986 -39 TTTTTAATTTTTGTTTTGGTTACCTGT 15 4 1 TAATTTTTTT 0.955378 -114 AAGCAGCAGGTTAATATTCTTTGTGCAGACTTAT 19 17 0 TAATTTTTGT 0.801273 -34 TTTTTTGCCCTCAAACTAAATTTTCTAT 22 45 1 TAAATATTTT 0.568189 -18 AATCCACTCCTTAATTTTAACTTTACAAAACTTT 26 28 0 TAATTTCTTT 0.966367 -180 * *** ** **** Masking position 4 Map Score: 7.56947 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 33 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 ATACCATCATGGTGGGGCAGCAAAAATTAG 7 83 0 GGTGGGGCAG 0.905772 -91 TCCTCGTCCCGGAGGGCCGGCGGTTATGGC 9 76 1 GGAGGGCCGG 0.927813 -225 GTTATGGCCGGGCTGCCCGGAGGGGCTGTC 9 98 1 GGCTGCCCGG 0.97532 -203 TCCCTTCCGGGCCTGGGCCGTTCCCCCCGG 9 139 0 GCCTGGGCCG 0.91439 -162 CTTCCGGGGGTGCGGGGAGGAGGTGCCTGG 9 194 1 TGCGGGGAGG 0.741502 -107 CCGTAAGGCAGGTCGACCCGAGGCGTGCCC 9 237 1 GGTCGACCCG 0.77191 -64 TAACTGAAAAGGTGGGCACGCCTCGGGTCG 9 250 0 GGTGGGCACG 0.950299 -51 ATTTTAGTGGCTGCGCGGCACCATAAGA 10 9 1 GGCTGCGCGG 0.979225 -51 ATGTTGTTCTGGTTGGGCCGATAAAAATTT 14 13 1 GGTTGGGCCG 0.982863 -100 GGAGGGAAAAGGTTGCGAGGGGTAAATAAC 16 18 0 GGTTGCGAGG 0.915673 -20 TAAAAAATTGGGCTGACACGAAAGTTTTTT 17 36 0 GGCTGACACG 0.865666 -24 ********** Masking position 5 Map Score: 8.36051 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 395 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 9 TAGACTATTAGCTATTGCATGTATATAAAA 5 89 0 GCTATTGCAT 0.94352 -212 GATGGTATATGCTTTTGCATGTCAAAATTC 7 105 1 GCTTTTGCAT 0.97462 -69 ATATTTTCAAGCCTTTGCAACCTTTTTCAT 8 40 1 GCCTTTGCAA 0.905903 -96 TGGATTTTGCTTGAAGTTGAGG 14 101 0 GATTTTGCTT 0.776594 -12 AGGCTATTGCCTATCTTTGTAA 15 106 0 GCTATTGCCT 0.947461 -12 AACTCTTAAAACCTTTGCCTTCTTACGCCA 25 14 0 ACCTTTGCCT 0.866546 -51 TATATCTCTTGCCTTTGCTTATTTCGATG 27 10 0 GCCTTTGCTT 0.970027 -44 ********** Masking position 5 Map Score: 3.35528 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 137 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 CCTGGGAAGTTGAGAAATATAAAG 1 2 0 TGAGATAAAA 0.921431 -29 GAGAAAATTTTAAATAATTCAAAAGAGAGAGAT 5 17 0 TAAAATTAAA 0.695676 -284 TGCATGTATATAAAAAATAAAAATTAAATTTTT 5 71 0 TAAAATAAAA 0.758861 -230 GATAGAGACTTAAGGCGAAAAAAACAGCAATTT 5 170 1 TAAGGAAAAA 0.656681 -131 ATTTAGGTTATGAGCTATAAAAAACGAAAATTT 5 199 1 TGAGATAAAA 0.921431 -102 TAAATTTTTCTAAGCAATTAAAAAAGAAAAAAG 6 12 0 TAAGATTAAA 0.911936 -48 GAAGTTAGTTTAAGAAGTATAAATATATTTTCA 8 16 1 TAAGGTAAAA 0.942902 -120 GGCTGTTTTTAAAGTTGTTTAAATGTTTAAAAG 8 97 0 AAAGGTTAAA 0.748515 -39 CAAAGTTGGGAAAAAGGTTTAAATAAAAAGCGT 13 30 0 AAAAGTTAAA 0.396515 -72 AAGCTGAGTAGTAGAAATGTTTTAAAG 20 52 0 TGAGGTAAAA 0.931438 -17 AGTCGAAGATTGAGGGATTCAAACAAAGACTTA 26 128 1 TGAGATTAAA 0.894947 -80 TAAGCAAAGGCAAGAGATATAAACATCCAATGC 27 19 1 CAAGATAAAA 0.748301 -35 **** *** *** Masking position 3 Map Score: 3.86419 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 59 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 AATAGTCTAAAAAGGTCAAATCAAATGTTTG 5 110 1 AAAGGCAAAT 0.855067 -191 GAAAAAGCGACAAATGGAGGAGTAA 6 45 0 AAGCGCAAAT 0.979693 -15 ACAGGCCTTTTAGCGGTAAATTTTTATCGGC 14 29 0 TAGCGTAAAT 0.829083 -84 AGGTTGGGTGATGCGCTAAATACTTCAAGAC 14 58 0 ATGCGTAAAT 0.82908 -55 GGTTGCTGTTAATCGATAAATTCCGAAAACT 22 15 1 AATCGTAAAT 0.854667 -48 CAATCAGGCCAAACGCCAAATTTTTTAATCC 28 19 1 AAACGCAAAT 0.968439 -40 GAGCTATGGGAAACGTCAAATAGCAGATTGC 29 23 0 AAACGCAAAT 0.968439 -63 ***** ***** Masking position 8 Map Score: 2.22684 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 35 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 CTTTATATTTCTCAACTTCCC 1 2 1 TTTATATTTC 0.930656 -29 TTTTTATTTAACTGAACAGC 3 1 1 TTTTTATTTA 0.787311 -56 AAAATTAAATTTTTTATCTTAATTATTAAA 5 55 0 TTTTTATCTT 0.776127 -246 AAAAATTTAATTTTTATTTTTTATATACAT 5 71 1 TTTTTATTTT 0.720933 -230 ATTTTCGTTTTTTATAGCTCATAACCTAAA 5 200 0 TTTATAGCTC 0.789752 -101 TGAAAATATATTTATACTTCTTAAACTAAC 8 19 0 TTTATACTTC 0.736777 -117 TTTAATACGCTTTTTATTTAAACCTTTTTC 13 24 1 TTTTTATTTA 0.787311 -78 TCAGCCCAATTTTTTATCTA 17 50 1 TTTTTATCTA 0.832429 -10 AATTAATTGTTTAATATCTCTGAAGAAACA 20 22 1 TTAATATCTC 0.695904 -47 GCAAAAAGTTATATTTCAAGTTTCTGT 24 8 1 GTTATATTTC 0.716511 -31 GCATTGGATGTTTATATCTCTTGCCTTTGC 27 22 0 TTTATATCTC 0.9474 -32 ********** Masking position 6 Map Score: 3.5333 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 57 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 13 TATTAAATCTTAGCGTTGAG 13 1 0 TAGCGTTGAG 0.988541 -101 TAAAAGGTTTTAGAGTTGAGCGAATTT 18 8 0 TAGAGTTGAG 0.955972 -43 GCCGAGACTCTAGCGTTCAGACATGTTTAG 26 74 1 TAGCGTTCAG 0.969862 -134 CCCTTCAGCCAAGCGTTGGGAGATAGAGTG 26 165 1 AAGCGTTGGG 0.952441 -43 ********** Masking position 6 Map Score: 0.0188399 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 34 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 ********** No masking Map Score: 2.12695e-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 Motif number 15 ACGAGGACTCTGCGGTGCCTGGAACCGCTGCC 9 51 0 TGGGTGCCTG 0.993921 -250 CGGCGCTTCCGGGGGTGCGGGGAGGAGGTGCC 9 189 1 GGGGTGCGGG 0.969718 -112 GGTGCGGGGAGGAGGTGCCTGGGGCTTCAAGC 9 202 1 GGGGTGCCTG 0.992676 -99 GTTATCTTCTTATGGTGCCGCGCAGCCACTAA 10 14 0 TAGGTGCCGG 0.978665 -46 AACAATTAATTGAGGTGGTTAG 20 1 0 TGGGTGGTTG 0.94263 -68 CAGGATAAGTTAGGGTGGCTTGT 21 2 0 TAGGTGGCTG 0.966637 -22 ** ******* * Masking position 6 Map Score: 2.25568 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 53 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185