AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iphoB_ecoli_opreg_300.orf -g0.5 -x5 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 = 0 Input sequences: #1 phoE 287 outer membrane pore protein E (E,Ic,NmpAB) #2 yaiB 300 orf, hypothetical protein #3 phoA 31 alkaline phosphatase #4 psiF 100 induced by phosphate starvation #5 phoB 189 positive response regulator for pho regulon, sensor is PhoR (or CreC) #6 phoR 57 positive and negative sensor protein for pho regulon #7 phoH 300 PhoB-dependent, ATP-binding pho regulon component; may be helicase; induced by P starvation #8 ugpA 97 sn-glycerol 3-phosphate transport system, integral membrane protein #9 ugpB 300 sn-glycerol 3-phosphate transport system; periplasmic binding protein #10 pstB 182 ATP-binding component of high-affinity phosphate-specific transport system #11 pstC 86 high-affinity phosphate-specific transport system, cytoplasmic membrane component #12 pstS 300 high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein #13 phnQ 125 orf, hypothetical protein #14 phnL 110 ATP-binding component of phosphonate transport #15 phnE 54 membrane channel protein component of Pn transporter #16 phnD 24 periplasmic binding protein component of Pn transporter #17 phnC 132 ATP-binding component of phosphonate transport #18 phnB 300 orf, hypothetical protein Motif number 1 ACGCTTGCGCGTCTTATCATGCCTACAATCAG 7 10 1 CGCATCATGC 0.963271 -291 GCGGCGTGAACGCCTTATCCAGCCTACCAAACC 7 47 0 CGCATCCAGC 0.989981 -254 AAGGCGTTCACGCCGCATCCGGCGATCGTGCAC 7 64 1 CGCATCCGGC 0.999678 -237 CAGATAAGCGAAACGCATCCGACATTACACTGA 8 11 0 AACATCCGAC 0.681858 -87 CGGATAAGCGAAGCGCATCCGGCACAGTTCAGG 8 64 1 AACATCCGGC 0.935951 -34 GCGGCGTAAACGCCTTATCAGGCCTACAAGATC 9 33 0 CGCATCAGGC 0.998786 -268 AAGGCGTTTACGCCGCATCCGGCATGAAACGAT 9 50 1 CGCATCCGGC 0.999678 -251 CAGGCGTTCACGCCGCATCCGGCAAAGTGTTAA 10 99 0 CGCATCCGGC 0.999678 -84 GCGGCGTGAACGCCTGATCCGGCCTACGGTAAG 10 116 1 CGCATCCGGC 0.999678 -67 CGGCGTAAAACACCGTACCCGGCCTGGAGTTTT 11 12 0 CACACCCGGC 0.950463 -75 CGGTGTTTTACGCCGCATCCGGCATTACAAAAT 11 30 1 CGCATCCGGC 0.999678 -57 AAGGCGTTTACGCCGCATCCGGCACCGGC 14 7 0 CGCATCCGGC 0.999678 -104 GCGGCGTAAACGCCTTATCCGGCCTACAAATGC 14 24 1 CGCATCCGGC 0.999678 -87 GACGCTGACGCGTCTTATCCGACCTACGGGGAG 14 58 0 CGCATCCGAC 0.997806 -53 GACGCGTCAGCGTCGCATCCGACACCCGAACCA 14 77 1 CGCATCCGAC 0.997806 -34 GACGCCGGGGCGTCTTATCCGACCTACGAT 15 8 0 CGCATCCGAC 0.997806 -47 GACGCCCCGGCGTCGCATCCGACAATGTGCAGG 15 27 1 CGCATCCGAC 0.997806 -28 GACGCGCAAGCGTCGCATCAGGCAGTC 18 5 0 CGCATCAGGC 0.998786 -296 GACGCTTGCGCGTCTTATCAGGCCTACAAATTC 18 24 1 CGCATCAGGC 0.998786 -277 GCGGCGTAAACGCCTTATCCGGCCTACGGAGGG 18 62 0 CGCATCCGGC 0.999678 -239 AAGGCGTTTACGCCGCATCCGGCAATGGTGCCG 18 79 1 CGCATCCGGC 0.999678 -222 GACGCGCAAGCGTCGCATCAGGCAGTCGGCACC 18 105 0 CGCATCAGGC 0.998786 -196 GACGCTTGCGCGTCTTATCAGGCCTACAAATTC 18 124 1 CGCATCAGGC 0.998786 -177 GCGGCGTAAACGCCTTATCCGGCCTACGGAGGG 18 162 0 CGCATCCGGC 0.999678 -139 AAGGCGTTTACGCCGCATCCGGCAACAGTGCCG 18 179 1 CGCATCCGGC 0.999678 -122 GACGCGCGAGCGTCGCATCAGGCAGTCGGCACT 18 205 0 CGCATCAGGC 0.998786 -96 GACGCTCGCGCGTCTTATCAGGCCGCCTCTCAT 18 224 1 CGCATCAGGC 0.998786 -77 ** * ******* Masking position 7 Map Score: 155.454 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 74 Number in noncoding regions = 536 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 2 GCGCGTCTTATCATGCCTACAATCAGTGCG 7 17 1 TCATGCCTAC 0.957999 -284 GAACGCCTTATCCAGCCTACCAAACCCGCA 7 43 0 TCCAGCCTAC 0.954302 -258 TCACGCCGCATCCGGCGATCGTGCACTGAT 7 71 1 TCCGGCGATC 0.838873 -230 GCTTCGCTTATCCGGCCTACACGCGATGCC 8 48 0 TCCGGCCTAC 0.997988 -50 AAACGCCTTATCAGGCCTACAAGATCGTGC 9 29 0 TCAGGCCTAC 0.996746 -272 AGAGTTTGATTCAGACCTTCTATATTTTCC 9 94 1 TCAGACCTTC 0.943495 -207 GTAGGCCGGATCAGGCGTTCACGCCGCATC 10 113 0 TCAGGCGTTC 0.957933 -70 GAACGCCTGATCCGGCCTACGGTAAGCCTG 10 123 1 TCCGGCCTAC 0.997988 -60 ACTTCGCTAATCAGGCTTACCGTAGGCCGG 10 134 0 TCAGGCTTAC 0.942339 -49 TTACGCCGCATCCGGCATTACAAAATGACT 11 37 1 TCCGGCATTA 0.626833 -50 TAATCAAACATCCTGCCAACTCCATGTGAC 12 47 1 TCCTGCCAAC 0.839111 -254 AAACGCCTTATCCGGCCTACAAATGCGCTC 14 31 1 TCCGGCCTAC 0.997988 -80 ACGCGTCTTATCCGACCTACGGGGAGCGCA 14 54 0 TCCGACCTAC 0.981401 -57 GGGCGTCTTATCCGACCTACGAT 15 4 0 TCCGACCTAC 0.981401 -51 AAGCGTCGCATCAGGCAGTC 18 1 0 TCAGGCAGTC 0.92008 -300 GCGCGTCTTATCAGGCCTACAAATTCCCGC 18 31 1 TCAGGCCTAC 0.996746 -270 AAACGCCTTATCCGGCCTACGGAGGGTGCG 18 58 0 TCCGGCCTAC 0.997988 -243 AAGCGTCGCATCAGGCAGTCGGCACCATTG 18 101 0 TCAGGCAGTC 0.92008 -200 GCGCGTCTTATCAGGCCTACAAATTCCCGC 18 131 1 TCAGGCCTAC 0.996746 -170 AAACGCCTTATCCGGCCTACGGAGGGTGCG 18 158 0 TCCGGCCTAC 0.997988 -143 GAGCGTCGCATCAGGCAGTCGGCACTGTTG 18 201 0 TCAGGCAGTC 0.92008 -100 GCGCGTCTTATCAGGCCGCCTCTCATCTGT 18 231 1 TCAGGCCGCC 0.946144 -70 ********** Masking position 1 Map Score: 63.7455 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 278 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 TGGCAGATCACGGGCGCATACGCTCATGGTTAA 4 75 1 CGGGCGACGC 0.989126 -26 AACGGTTCCCTGGCGAAAAAGCATGGGCGCGA 5 10 1 CTGGCGAAGC 0.735354 -180 AAAAAGCATGGGCGCGATTATACCCAAACAGAT 5 26 1 GGCGCGATAC 0.474962 -164 ATCGCCGGATGCGGCGTGAACGCCTTATCCAGC 7 57 0 GCGGCGACGC 0.998414 -244 CACGCCGCATCCGGCGATCGTGCACTGATGCCT 7 72 1 CCGGCGGTGC 0.984758 -229 CTTCGCTTATCCGGCCTACACGCGATGCCAGGT 8 44 0 CCGGCCACGC 0.975752 -54 TTCCTGAACTGTGCCGGATGCGCTTCGCTTATC 8 66 0 GTGCCGGCGC 0.907032 -32 CATGCCGGATGCGGCGTAAACGCCTTATCAGGC 9 43 0 GCGGCGACGC 0.998589 -258 TGGGAGATGGGGCACGGATAAGCGGGAAAATAT 9 115 0 GGCACGAAGC 0.674248 -186 TCTCCCCAGAGGGGCGAGGGGACCGACCGAGCG 10 45 1 GGGGCGGGAC 0.890578 -138 TTTGCCGGATGCGGCGTGAACGCCTGATCCGGC 10 106 1 GCGGCGACGC 0.998414 -77 GAAGAAAAATGCCCCGCTTACGCA 12 2 0 GCCCCGACGC 0.955612 -299 TTAGGGTGAGGGGGCCAGCGCGCACATTCCCTC 13 14 0 GGGGCCGCGC 0.980676 -112 TCTCCCCAGAGGGGCGAGGGGACCGATTGTGCT 13 50 1 GGGGCGGGAC 0.890578 -76 GGTGCCGGATGCGGCGTAAACGCCTTATCCGGC 14 14 1 GCGGCGACGC 0.998589 -97 GGTGTCGGATGCGACGCTGACGCGTCTTATCCG 14 70 0 GCGACGACGC 0.983552 -41 ATTGTCGGATGCGACGCCGGGGCGTCTTATCCG 15 20 0 GCGACGGGGC 0.744911 -35 CCCGCCGGGAGGCCCGCCCTCCC 17 1 1 CCCGCCAGGC 0.731074 -132 ACAATAATCCGCCACGATGGAGCCACTTTTTTA 17 97 1 GCCACGGAGC 0.893931 -36 ACTGCCTGATGCGACGCTTGCGCGTCTTATCAG 18 12 1 GCGACGGCGC 0.995197 -289 ATTGCCGGATGCGGCGTAAACGCCTTATCCGGC 18 72 0 GCGGCGACGC 0.998589 -229 TACGCCGCATCCGGCAATGGTGCCGACTGCCTG 18 87 1 CCGGCAGTGC 0.811907 -214 ACTGCCTGATGCGACGCTTGCGCGTCTTATCAG 18 112 1 GCGACGGCGC 0.995197 -189 GTTGCCGGATGCGGCGTAAACGCCTTATCCGGC 18 172 0 GCGGCGACGC 0.998589 -129 TACGCCGCATCCGGCAACAGTGCCGACTGCCTG 18 187 1 CCGGCAGTGC 0.811913 -114 ACTGCCTGATGCGACGCTCGCGCGTCTTATCAG 18 212 1 GCGACGGCGC 0.995197 -89 ****** **** Masking position 5 Map Score: 70.7995 Number of sites scoring better than the average of aligned sites = 2621 Number in coding regions = 2245 Number in noncoding regions = 376 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 4 AACCGCGCCCGGCAGTGAATTTTCGCTGC 4 9 1 CCGGCAGTGA 0.691238 -92 AAAAAACCACCCGGCAGCGAAAATTCACTGC 4 22 0 CCGGCAGCGA 0.927899 -79 GCCTACCAAACCCGCACTGATTGTAGGCATG 7 28 0 CCCGCACTGT 0.926593 -273 GCGGAAGTTCCCGGCAGTGATAGTCAGTCAC 7 266 1 CCGGCAGTGT 0.560802 -35 CGAAGCGCATCCGGCACAGTTCAGGAATTAA 8 72 1 CCGGCACAGT 0.676518 -26 CTCCCATTTTCCCTCACCCACGCCGTCACCG 9 142 1 CCCTCACCCC 0.992972 -159 CTCACCCACGCCGTCACCGCCTTGTCATCTT 9 154 1 CCGTCACCGC 0.981041 -147 CACGGTTTTCCCCTCACCCTAACCCTCTCCC 10 20 1 CCCTCACCCA 0.99238 -163 CTCACCCTAACCCTCTCCCCAGAGGGGCGAG 10 32 1 CCCTCTCCCA 0.965704 -151 TCGGTCGGTCCCCTCGCCCCTCTGGGGAGAG 10 44 0 CCCTCGCCCT 0.945465 -139 CGCGCTGGCCCCCTCACCCTAACCCTCTCCC 13 25 1 CCCTCACCCA 0.99238 -101 CTCACCCTAACCCTCTCCCCAGAGGGGCGAG 13 37 1 CCCTCTCCCA 0.965704 -89 ACAATCGGTCCCCTCGCCCCTCTGGGGAGAG 13 49 0 CCCTCGCCCT 0.945465 -77 CTCGTTTTCTCCCTCTCCCCATTGGGGTGAG 13 100 1 CCCTCTCCCA 0.965704 -26 CGCCCCTCACCCCAATGGGGAGAG 13 112 0 CCCTCACCCA 0.99238 -14 TACGCCGCATCCGGCACCGGC 14 1 0 CCGGCACCGC 0.986864 -110 AGCGTCGCATCCGACACCCGAACCACGAGGC 14 85 1 CCGACACCCA 0.900206 -26 GGCCCGCCCTCCCGCACTGTCATCGAATTCC 17 21 1 CCCGCACTGC 0.960013 -112 CCTACAAATTCCCGCACCCTCCGTAGGCCGG 18 46 1 CCCGCACCCC 0.995157 -255 CCTACAAATTCCCGCACCCTCCGTAGGCCGG 18 146 1 CCCGCACCCC 0.995157 -155 ********* * Masking position 5 Map Score: 46.5985 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 669 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 CAACCGACGACAGTCCTGCTAAAACGTTCGT 1 49 0 CAGTCCTGCA 0.766891 -239 GCGGGATCAGCAAGCCTAGCGGCAGTTGTTT 1 116 1 CAAGCCTAGG 0.769775 -172 CGCGTCTTATCATGCCTACAATCAGTGCGGG 7 18 1 CATGCCTACA 0.918868 -283 AACGCCTTATCCAGCCTACCAAACCCGCACT 7 41 0 CCAGCCTACA 0.97617 -260 CTTCGCTTATCCGGCCTACACGCGATGCCAG 8 46 0 CCGGCCTACC 0.987591 -52 AACGCCTTATCAGGCCTACAAGATCGTGCAA 9 27 0 CAGGCCTACA 0.994654 -274 GAGTTTGATTCAGACCTTCTATATTTTCCCG 9 95 1 CAGACCTTCA 0.752937 -206 AACGCCTGATCCGGCCTACGGTAAGCCTGAT 10 124 1 CCGGCCTACG 0.997589 -59 AACACCGTACCCGGCCTGGAGTTTTA 11 6 0 CCGGCCTGGG 0.944912 -81 AACGCCTTATCCGGCCTACAAATGCGCTCCC 14 32 1 CCGGCCTACA 0.997387 -79 CGCGTCTTATCCGACCTACGGGGAGCGCATT 14 52 0 CCGACCTACG 0.985687 -59 GGCGTCTTATCCGACCTACGAT 15 2 0 CCGACCTACA 0.984499 -53 CGCGTCTTATCAGGCCTACAAATTCCCGCAC 18 32 1 CAGGCCTACA 0.994654 -269 AACGCCTTATCCGGCCTACGGAGGGTGCGGG 18 56 0 CCGGCCTACG 0.997589 -245 CGCGTCTTATCAGGCCTACAAATTCCCGCAC 18 132 1 CAGGCCTACA 0.994654 -169 AACGCCTTATCCGGCCTACGGAGGGTGCGGG 18 156 0 CCGGCCTACG 0.997589 -145 ********* * Masking position 7 Map Score: 44.7505 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 134 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 6 GATTTTAATTAACGCGCGAATATTCAGCGG 1 258 0 AACGCGCGAA 0.901365 -30 TAGGCATGATAAGACGCGCAAGCGT 7 6 0 AAGACGCGCA 0.967479 -295 TAGGCTGGATAAGGCGTTCACGCCGCATCC 7 54 1 AAGGCGTTCA 0.973972 -247 TAGGCCTGATAAGGCGTTTACGCCGCATCC 9 40 1 AAGGCGTTTA 0.940288 -261 GCGAGCATAAAACGCGTGAATTCGCGCATT 9 258 1 AACGCGTGAA 0.820537 -43 TGTTGTACCGAATGCGCGAATTCACGCGTT 9 268 0 AATGCGCGAA 0.755586 -33 CAGAGTCAAAAAGGCGCTCGGTCGGTCCCC 10 62 0 AAGGCGCTCG 0.949222 -121 TAGGCCGGATCAGGCGTTCACGCCGCATCC 10 112 0 CAGGCGTTCA 0.807589 -71 TCTTCAGTTAAACGCGTTTACAAAGTCATT 11 60 0 AACGCGTTTA 0.843997 -27 AGAGGGAGAAAACGAGCGCAATATTCAATA 13 86 0 AACGAGCGCA 0.659374 -40 TAGGCCGGATAAGGCGTTTACGCCGCATCC 14 20 0 AAGGCGTTTA 0.940288 -91 CCGGCCTACAAATGCGCTCCCCGTAGGTCG 14 42 1 AATGCGCTCC 0.68466 -69 TAGGTCGGATAAGACGCGTCAGCGTCGCAT 14 65 1 AAGACGCGTC 0.757594 -46 TAGGCCTGATAAGACGCGCAAGCGTCGCAT 18 20 0 AAGACGCGCA 0.967479 -281 TAGGCCGGATAAGGCGTTTACGCCGCATCC 18 69 1 AAGGCGTTTA 0.940288 -232 TAGGCCTGATAAGACGCGCAAGCGTCGCAT 18 120 0 AAGACGCGCA 0.967479 -181 TAGGCCGGATAAGGCGTTTACGCCGCATCC 18 169 1 AAGGCGTTTA 0.940288 -132 GCGGCCTGATAAGACGCGCGAGCGTCGCAT 18 220 0 AAGACGCGCG 0.881351 -81 ********** Masking position 2 Map Score: 25.1239 Number of sites scoring better than the average of aligned sites = 1349 Number in coding regions = 1066 Number in noncoding regions = 283 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 7 ATTTATTAAATCTGTAATAAAAGCGTAAAC 1 143 0 TCTGTAATAA 0.776126 -145 ATATTATTAATCTGTAATATATCTTTAACA 1 188 1 TCTGTAATAT 0.800647 -100 AAGTATTTCCTTTGTCATAAAAATAATACT 2 214 1 TTTGTCATAA 0.776126 -87 CTTTTCAACAGCTGTCATAAAG 3 20 1 GCTGTCATAA 0.858803 -12 TTTTCATAAATCTGTCATAAATCTGACGCA 5 119 1 TCTGTCATAA 0.969968 -71 TTTTTTCATCACTGTCATCACTCTGTCATC 7 133 1 ACTGTCATCA 0.936089 -168 CTGTCATCACTCTGTCATCTTTCCAGTAGA 7 144 1 TCTGTCATCT 0.975955 -157 TTGTCATCTTTCTGACACCTTACTATCTTA 9 175 1 TCTGACACCT 0.691923 -126 AAGATGACGGTTTGTCACATGGAGTTGGCA 12 60 0 TTTGTCACAT 0.708251 -241 CTACTTTTTCTCTGTCACAGAATGAAAATT 12 93 1 TCTGTCACAG 0.917046 -208 TGAAAATTTTTCTGTCATCTCTTCGTTATT 12 115 1 TCTGTCATCT 0.975955 -186 ACTTTATCTCTCTGTCATAAAACTGTCATA 12 194 1 TCTGTCATAA 0.969968 -107 CTGTCATAAAACTGTCATATTCCTTACATA 12 205 1 ACTGTCATAT 0.939909 -96 CTTACATATAACTGTCACCTGTTTGTCCTA 12 227 1 ACTGTCACCT 0.91116 -74 GCCCTCCCGCACTGTCATCGAATTCCCGTT 17 26 1 ACTGTCATCG 0.892403 -107 ********** Masking position 7 Map Score: 18.5296 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 193 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 ACGCTTGCGCGTCTTATCATGCC 7 3 1 GCTGCGCGTC 0.998879 -298 GGGTGAGGGGGCCAGCGCGCACATTCCCTCT 13 13 0 GCCGCGCGCA 0.959901 -113 CGGATGCGACGCTGACGCGTCTTATCCGACC 14 67 0 GCTACGCGTC 0.991422 -44 CGGATGCGACGCCGGGGCGTCTTATCCGACC 15 17 0 GCCGGGCGTC 0.990777 -38 CTGATGCGACGCTTGCGCGTCTTATCAGGCC 18 17 1 GCTGCGCGTC 0.998879 -284 CTGATGCGACGCTTGCGCGTCTTATCAGGCC 18 117 1 GCTGCGCGTC 0.998879 -184 CTGATGCGACGCTCGCGCGTCTTATCAGGCC 18 217 1 GCTGCGCGTC 0.998879 -84 *** ******* Masking position 7 Map Score: 19.0827 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 107 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TTCATTCCTGATTTTAATTAACGCGCGAATA 1 266 0 ATTTTATTAA 0.599229 -22 GAGTTTTTTTCTCTTAATTATAAGTTAACGA 2 58 1 CTCTTATTAT 0.949087 -243 GAAATATATTCTCTTCGTTAACTTATAATTA 2 72 0 CTCTTCTTAA 0.921476 -229 TATTTCATAACTTTTATTTATAATAAAGGTT 2 97 1 CTTTTATTAT 0.921195 -204 AAAATATAGGCTTTTAATTATCAACCTTTAT 2 119 0 CTTTTATTAT 0.921195 -182 CGAAACGTTTCTCTTATTTAAATAATTACCC 2 154 0 CTCTTATTAA 0.964654 -147 AATATATTTACTTATATTTAACTATAAAACA 7 194 0 CTTATATTAA 0.70658 -107 TTTCTGTCATCTCTTCGTTATTAATGTTTGT 12 123 1 CTCTTCTTAT 0.88908 -178 TGAATATCAACGCTTATTTAAATCAGACTGA 12 161 1 CGCTTATTAA 0.850559 -140 CTGTTAGTCACTTTTAATTAACCAAATCGTC 17 66 1 CTTTTATTAA 0.944794 -67 ****** **** Masking position 5 Map Score: 6.83863 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 41 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 GCTTTTATTACAGATTTAATAAATTACCACATTTT 1 149 1 CAGAAAAATT 0.959985 -139 AGATATATTACAGATTAATAATATTCTTAAAATGT 1 177 0 CAGAATAATT 0.933971 -111 TTAACAATCTCAGGTTAAAAACTTTCCTGTTTTCA 1 212 1 CAGGAAATTT 0.856019 -76 CGCTGGTAATCAAACAAAAAATATTTGCGCAAAGT 2 183 1 CAAAAAAATT 0.855961 -118 ATTTTTATGACAAAGGAAATACTTTGCGCAAATAT 2 203 0 CAAAAAATTT 0.875957 -98 GGAAAGATGACAGAGTGATGACAGTGATGAAAAAA 7 133 0 CAGAATAAGT 0.727057 -168 AACACCATTTCAGTGACATTAGTTTCTACTGGAAA 7 163 0 CAGTATATTT 0.702835 -138 CAAGATCGTGCAAATTCAACATATTGCCA 9 5 0 CAAAAAAATT 0.855961 -296 GCTCGAATTACAGAAAAATAACTTTTTTGTTACAT 9 208 0 CAGAATATTT 0.943848 -93 TTCTCTGTCACAGAATGAAAATTTTTCTGTCATCT 12 100 1 CAGAAAATTT 0.966111 -201 TTATTTAAATCAGACTGAAGACTTTATCTCTCTGT 12 174 1 CAGAAAATTT 0.966111 -127 **** ** * *** Masking position 8 Map Score: 6.71552 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 86 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 AATAAGAGAAACGTTTCGCTGGTAATCAAA 2 167 1 ACGTTTCGCT 0.905828 -134 AACGGTTCCCTGGCGAAAAAG 5 2 1 ACGGTTCCCT 0.95587 -188 AATGTCGGATGCGTTTCGCTTATCTGACCT 8 18 1 GCGTTTCGCT 0.966063 -80 TGTGCCGGATGCGCTTCGCTTATCCGGCCT 8 60 0 GCGCTTCGCT 0.984648 -38 AGGCGCTCGGTCGGTCCCCTCGCCCCTCTG 10 51 0 TCGGTCCCCT 0.955041 -132 CGTGCCTGATGCACTTCGCTAATCAGGCTT 10 146 0 GCACTTCGCT 0.877487 -37 TCGAGCACAATCGGTCCCCTCGCCCCTCTG 13 56 0 TCGGTCCCCT 0.955041 -70 GCCTACAAATGCGCTCCCCGTAGGTCGGAT 14 45 1 GCGCTCCCCG 0.943496 -66 ********** Masking position 5 Map Score: 5.26046 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 402 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 12 ACCGAATGCGCGAATTCACGCGTTTTATGC 9 262 0 CGAATTCACG 0.947167 -39 GCACTGTCATCGAATTCCCGTTAACTCTTC 17 34 1 CGAATTCCCG 0.991443 -99 ATCAGGCCTACAAATTCCCGCACCCTCCGT 18 40 1 CAAATTCCCG 0.975099 -261 GCAATGGTGCCGACTGCCTGATGCGACGCT 18 100 1 CGACTGCCTG 0.964175 -201 ATCAGGCCTACAAATTCCCGCACCCTCCGT 18 140 1 CAAATTCCCG 0.975099 -161 GCAACAGTGCCGACTGCCTGATGCGACGCT 18 200 1 CGACTGCCTG 0.964175 -101 ********** Masking position 5 Map Score: 5.07693 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 96 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 ACGGGACTCTCCCGCTGAATATTCGCGCGTT 1 247 1 CCCCTGAATA 0.727027 -41 TACTTCCAGACACTATGAAGTTGTGAAACAT 2 240 1 CACATGAAGT 0.74602 -61 GATAGTCAGTCACTATGGAGATCGCGG 7 284 1 CACATGGAGA 0.969882 -17 GTCCCCTCGCCCCTCTGGGGAGAGGGTTAGG 10 37 0 CCCCTGGGGA 0.984652 -146 GTGCATCAGGCACGATGAGGAAAAGATTGCA 10 162 1 CACATGAGGA 0.954755 -21 TTATTTAAATCAGACTGAAGACTTTATCTCT 12 174 1 CAGCTGAAGA 0.754065 -127 GTCCCCTCGCCCCTCTGGGGAGAGGGTTAGG 13 42 0 CCCCTGGGGA 0.984652 -84 CGCCCCTCACCCCAATGGGGAGAGGGAGAAA 13 105 0 CCCATGGGGA 0.981608 -21 AATAATCCGCCACGATGGAGCCACTTTTTTA 17 99 1 CACATGGAGC 0.895324 -34 *** ******* Masking position 6 Map Score: 5.6714 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 341 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 14 ACCAGACTTAATGGCAGATCACGGGCGCAT 4 64 1 ATGGCAGATC 0.842145 -37 AAAAAAGCAAATGGCACATCTGTTTGGGTA 5 46 0 ATGGCACATC 0.694319 -144 GCGATCATTAATGCGACGTCATTATGCGTC 5 143 0 ATGCGACGTC 0.793588 -47 CGATCGCCGGATGCGGCGTGAACGCCTTAT 7 62 0 ATGCGGCGTG 0.835952 -239 TCGTGCACTGATGCCTGATGCAAATCCTGC 7 89 1 ATGCCTGATG 0.966702 -212 GTTGCAATAAATGCGAGATCTGTTGTACTT 7 225 1 ATGCGAGATC 0.929216 -76 CCTACACGCGATGCCAGGTCAGATAAGCGA 8 33 0 ATGCCAGGTC 0.942278 -65 TCATCGTTTCATGCCGGATGCGGCGTAAAC 9 55 0 ATGCCGGATG 0.969187 -246 GTGAGGGAAAATGGGAGATGGGGCACGGAT 9 129 0 ATGGGAGATG 0.807042 -172 ACTTTGCCGGATGCGGCGTGAACGCCTGAT 10 104 1 ATGCGGCGTG 0.835952 -79 TGCGGCGTGAACGCCTGATCCGGCCTACGG 10 115 1 ACGCCTGATC 0.70918 -68 TTTCCTCATCGTGCCTGATGCACTTCGCTA 10 155 0 GTGCCTGATG 0.808978 -28 TCATTTTGTAATGCCGGATGCGGCGTAAAA 11 35 0 ATGCCGGATG 0.969187 -52 ACATTGTCGGATGCGACGCCGGGGCGTCTT 15 25 0 ATGCGACGCC 0.313978 -30 GACTGCCTGATGCGACGCTTGC 18 3 1 CTGCCTGATG 0.919046 -298 ATGGTGCCGACTGCCTGATGCGACGCTTGC 18 103 1 CTGCCTGATG 0.919046 -198 ACAGTGCCGACTGCCTGATGCGACGCTCGC 18 203 1 CTGCCTGATG 0.919046 -98 ********** Masking position 3 Map Score: 18.9423 Number of sites scoring better than the average of aligned sites = 1954 Number in coding regions = 1328 Number in noncoding regions = 626 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 15 ACCGCATGGCCATTTAAGCCAGGAATAAATT 2 27 0 CATTTAAGCA 0.754724 -274 TAAGATACTCCAGTTAAGAAATCATAAGCCC 6 36 0 CAGTTAAGAA 0.941196 -22 TATAAAACACCATTTCAGTGACATTAGTTTC 7 172 0 CATTTCAGGA 0.883712 -129 GATGCCAGGTCAGATAAGCGAAACGCATCCG 8 23 0 CAGATAAGGA 0.955515 -75 GCGTGTAGGCCGGATAAGCGAAGCGCATCCG 8 54 1 CGGATAAGGA 0.850859 -44 GCATCCGGCACAGTTCAGGAATTAACCGTA 8 78 1 CAGTTCAGAA 0.900632 -20 TAAGAGAAGCCAGTTAAGTGTAGTTCGAAAT 18 265 0 CAGTTAAGGT 0.913154 -36 ATGGTGACCTCAGTTAAGAGAAGCCAGTTAA 18 279 0 CAGTTAAGGA 0.983242 -22 ******** ** Masking position 7 Map Score: 2.80292 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 141 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