AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iargR_ecoli_hinf_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 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 argF 300 ornithine carbamoyltransferase 2, chain F #3 argA 141 N-acetylglutamate synthase; amino acid acetyltransferase #4 argG 300 argininosuccinate synthetase #5 argR 300 repressor of arg regulon; cer-mediated site specific recombination #6 argD 85 acetylornithine delta-aminotransferase #7 pabA 31 p-aminobenzoate synthetase, component II #8 yhfG 104 orf, hypothetical protein #9 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #10 argE_argC 153 argE: acetylornithine deacetylase, argC: N-acetyl-gamma-glutamylphosphate reductase #11 argH 60 argininosuccinate lyase #12 argI 161 ornithine carbamoyltransferase 1 #13 HI0596 300 ornithine carbamoyltransferase (arcB) #14 HI0811 134 argininosuccinate lyase (argH) #15 HI0812 21 glucosephosphate uridylyltransferase (galU) #16 HI0813 77 carbon storage regulator (csrA) #17 HI0814 187 alanyl-tRNA synthetase (alaS) #18 HI0815 101 universal stress protein A (uspA) #19 HI0817 170 conserved hypothetical protein #20 HI0819 37 galactokinase (galK) #21 HI0820 207 galactose-1-phosphate uridylyltransferase (galT) #22 HI1209 206 arginine repressor (argR) #23 HI1723 135 conserved hypothetical protein #24 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) #25 HI1727 155 argininosuccinate synthetase (argG) Motif number 1 TCATCATTGTGAATTAATATGCAAATAAAGTGA 1 255 1 GAATAAATCA 0.960562 -46 ACCCTCCAGAGAATATTCACTCACTTTATTTGC 1 275 0 GAATTTACCA 0.929051 -26 GGTTGCAAATGAATAATTACACATATAAAGTGA 2 238 1 GAATATACCA 0.915104 -63 CATATAAAGTGAATTTTAATTCAATAAGTGGCG 2 259 1 GAATTTATCA 0.985316 -42 CGAAAAAACAGAATAAAAATACACTAATTTCGA 3 96 1 GAATAAATCA 0.960562 -46 CACTAATTTCGAATAATCATGCAAAGAGGTGTG 3 117 1 GAATATATCA 0.982218 -25 CTAATCATGTGAATGAATATCCAGTTCACTTTC 4 95 1 GAATAAATCA 0.960562 -206 CGCTCTCACTGAATTTTTATGCAAAATAAATGA 4 234 0 GAATTTATCA 0.985316 -67 GCATACAGATGAATTTTTATGCAAACAGTCAGC 5 241 0 GAATTTATCA 0.985316 -60 GCCATTTAGTGATTTTTTATGCATATTTTGTGG 6 20 1 GATTTTATCA 0.927699 -66 CAGTATTTATGAATAAAAATACACTAACGTTGA 10 91 0 GAATAAATCA 0.960562 -63 AATACTGCATGAATATTGATACTATCATGACCA 10 117 1 GAATTTATCT 0.81989 -37 ACTTGCAAATGAATAATCATCCATATAAATTGA 12 101 1 GAATATATCA 0.982218 -61 CATATAAATTGAATTTTAATTCATTGAGGCGTT 12 122 1 GAATTTATCA 0.985316 -40 ATACATTGGGGAATAAACATACATCATTCGAGA 13 255 0 GAATAAATCA 0.960562 -46 ATTGCTTTATGAATAAATATGCACAATAATAGA 14 83 1 GAATAAATCA 0.960562 -52 TGATGAAAGTGAATTTTTATGCAATTCTTATGC 22 159 1 GAATTTATCA 0.985316 -48 AAATTAGGATTTTTTATGCACAAAGCTAAA 25 8 1 GATTTTATCA 0.927699 -148 ATACTCTATAGAATTTTTATTCACAAAAATCGA 25 96 1 GAATTTATCA 0.985316 -60 CACAAAAATCGATTATTTATTCAATTCTAATTA 25 117 1 GATTTTATCA 0.927699 -39 **** ** ** ** Masking position 4 Map Score: 50.6131 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 15 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 ATTTCACAATTCTTTCTTACAAAGGTGGAGGCA 2 203 0 TCTTTTAAAA 0.63683 -98 TAAAGTGAATTTTAATTCAATAAGTGGCGTTCG 2 263 1 TTTATCATAA 0.507768 -38 GAGAGCGACTTTTTTATCAGTAATGCCGTGAAT 3 38 0 TTTTTCATAA 0.853331 -104 AAAACTCATTTATTTTGCATAAAAATTCAGTGA 4 229 1 TATTGCAAAA 0.852384 -72 ATTAATTTACTTTTAAGCAGAATTTGCATGCCG 5 131 1 TTTTGCAAAT 0.526624 -170 GACGCAGGCATGTTTCTCAATAACGAAATTTGA 5 165 1 TGTTTCATAA 0.545667 -136 ACAGATGAATTTTTATGCAAACAGTCAGCCCTG 5 237 0 TTTTGCAACA 0.759015 -64 GATACAACATTATTGTGCATACAGATGAATTTT 5 257 0 TATTGCAACA 0.439541 -44 ATGATCACCCTGTTACGCATAAACAAATGTGAA 6 60 0 TGTTGCAAAA 0.82721 -26 GTTAGTGTATTTTTATTCATAAATACTGCATGA 10 96 1 TTTTTCAAAA 0.962317 -58 AAAGCATAAATCTTTGTCACAAAGGTGGAGGCA 12 66 0 TCTTTCAAAA 0.925837 -96 CATTTGCAAGTCTAAAGCATAAATCTTTGTCAC 12 79 0 TCTAGCAAAA 0.667936 -83 GACACATTCCTCTTCATCAAAAATAAACTAAAA 13 29 1 TCTTTCAAAA 0.92589 -272 TATTGTGCATATTTATTCATAAAGCAATATTCT 14 78 0 ATTTTCAAAA 0.579191 -57 AGTTATTTCAGATTATTCAAAAAACAATTTCTT 17 16 0 GATTTCAAAA 0.576556 -172 TTATTTTGGAGTTTTGGCAAAAAGCCTTTTTAT 17 93 1 GTTTGCAAAA 0.828326 -95 AATGCTAACATTTTGAGCAATAAAAAACTGTGT 18 37 0 TTTTGCATAA 0.840839 -65 TGTAATGACATTTTTATTATAAATAATGGC 19 8 0 TTTTTTAAAA 0.773665 -163 GCGATGGCTTTTTTATTTACAAAGGTTTACACT 19 120 1 TTTTTTAAAA 0.781876 -51 AAATCTTATATTTTGATCATAAATAATTTACGA 21 35 1 TTTTTCAAAA 0.96221 -173 TAAACCGTGATCTTTGTCACAAAATAAGAAAAT 21 124 0 TCTTTCAAAA 0.925837 -84 GAAGAAAATATTTATCTCAGAAATGTGAACTAG 22 101 0 TTTATCAAAA 0.819078 -106 ATCTCGTAAAGTTTTTTCAAAAAAGTGAGATAA 23 13 0 GTTTTCAAAA 0.84537 -123 AAACGTTTGCTATTTTTTAAAAAGAAATAAAAA 24 84 0 TATTTTAAAA 0.471583 -41 AATTAGGATTTTTTATGCACAAAGCTAAATAAA 25 12 1 TTTTGCAAAA 0.958664 -144 GATTTTTGCTTTTAATGCACAAAACACTAGACA 25 45 1 TTTAGCAAAA 0.804376 -111 TCTATAGAATTTTTATTCACAAAAATCGATTAT 25 100 1 TTTTTCAAAA 0.962323 -56 ATATTTTCCTTACTAATAATTAGAAT 25 140 0 TTTTTTATAA 0.449509 -16 **** *** *** Masking position 9 Map Score: 27.5122 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 277 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 AAAAGTGGACCAAATGGTCAAAATTTACA 1 7 0 CAAATCAAAA 0.757218 -294 GCATGAAATAAAAACGAGCAGAAAAAAGTGGAC 1 30 0 AAAACCAGAA 0.603348 -271 CATGAGCCACAAAATAATATAAAAAATCCCGCC 1 137 1 AAAATATAAA 0.595105 -164 AAACAGAATAAAAATACACTAATTTCGAATAAT 3 101 1 AAAATCTAAT 0.717955 -41 TATTTTACAAAAAACACACTAAACTCTTCCTGT 4 173 1 AAAACCTAAA 0.858992 -128 TTATAACCACAAAATATGCATAAAAAATCACTA 6 26 0 AAAATCATAA 0.817807 -60 AACAGATCACAAAATCACCTAAAATCGCCCGCT 9 58 0 AAAATCTAAA 0.965286 -213 TCAGATACGTAAAATTAGGTAAAGGGATGGCCT 9 181 1 AAAATGTAAA 0.800358 -90 TTTATGAATAAAAATACACTAACGTTGAGCGTA 10 86 0 AAAATCTAAC 0.91002 -68 ATTGAATTTCAAAATAAGGAAACAGAGTT 11 42 1 AAAATGAAAC 0.593184 -19 CTCTTCATCAAAAATAAACTAAAACATATTTTC 13 38 1 AAAATCTAAA 0.965286 -263 AGAATTTAATAAAATAATCTAACTCTTTATTGT 13 107 0 AAAATCTAAC 0.91002 -194 TAATACAAATAAAATGGACAAAATGAAAGATTT 14 18 1 AAAATCAAAA 0.965286 -117 TAATAAAACAAAAATGGACAAAATCTTTCATTT 14 38 0 AAAATCAAAA 0.965286 -97 ATAAATTTCAAAAATATGCAAAAATAGGGCGAC 17 124 1 AAAATCAAAA 0.965286 -64 ACAAAATAAGAAAATAAGCAAAATTTTTTATGA 21 106 0 AAAATCAAAA 0.965286 -102 TTCAATAGTCAAAATTTGCATAAGAATTGCATA 22 176 0 AAAATCATAA 0.817807 -31 AAAAGAAATAAAAATCCTCTGAAATGTTAGGGG 24 65 0 AAAATCTGAA 0.874106 -60 ***** ***** Masking position 4 Map Score: 17.2488 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 103 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 ATAATATAAAAAATCCCGCCATTAAGTTGACT 1 150 1 AAATCCGCAT 0.98823 -151 GTAAGGCAGCAAGCCTCGCCATGTTCTCCGCC 2 25 1 AAGCCCGCAT 0.959905 -276 AAATTTGATAAAATCCCGCTCTTTCATAACAT 5 190 1 AAATCCGCCT 0.979142 -111 AAGTCACCCGATATGGTGGTTG 5 289 0 AAGTCCCCAT 0.972484 -12 CGGTACAAAAGAACCGCGCTATT 7 2 0 GAACCCGCAT 0.858541 -30 CGCTCGCGGCATATCCCGCTATGCCATTTTAT 9 30 0 ATATCCGCAT 0.906702 -241 AAATCACCTAAAATCGCCCGCTCGCGGCATAT 9 48 0 AAATCCCCCT 0.960028 -223 ATAATACTAAAAATCTCGCAATAAAATTCTAC 13 141 1 AAATCCGCAT 0.988232 -160 AATAAAAACTAAGTCGCCCTATTTTTGCATAT 17 137 0 AAGTCCCCAT 0.972482 -51 TATAGTCAGTCTCCCTCTTTAGCTTTAG 20 7 1 CAGTCCCCCT 0.883492 -31 TTTTTCCTAGAAATCGTGCTATAATCTCGTAA 23 37 0 AAATCTGCAT 0.857527 -99 CCTAAAATTTCAATCCCGCCATTATCTAATAA 23 98 0 CAATCCGCAT 0.969906 -38 ***** *** ** Masking position 12 Map Score: 13.6413 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 151 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 GACCATTTGGTCCACTTTTTTCTGCTCGTTT 1 21 1 TCCATTTTTT 0.834327 -280 CACTTTTTTCTGCTCGTTTTTATTTCATGCA 1 33 1 TGCTGTTTTT 0.702992 -268 TGTATTTTTATTCTGTTTTTTCGCAGGGTGC 3 88 0 TTCTTTTTTT 0.837159 -54 TCTCTTCACTTGCTTTTTTTCTGCTCTGTTT 9 236 1 TGCTTTTTTC 0.789586 -35 TTTTTTTCTGCTCTGTTTGTTAAGGAAATCT 9 249 1 CTCTTTTGTT 0.476828 -22 TTCGAGATACTGCTTGTTGTTCGAACAGTTG 13 231 0 TGCTGTTGTT 0.742042 -70 GACAAAATCTTTCATTTTGTCCATTTTATTT 14 24 0 TTCATTTGTC 0.545862 -111 AAAGATTTTGTCCATTTTTGTTTTATTATTA 14 43 1 TCCATTTTGT 0.423503 -92 AATTTTTCCTTTTTGTTTTAATTAATT 14 118 0 TCCTTTTGTT 0.936064 -17 TTTGACTCCTGTTTTTTATCAATGTAA 21 191 0 TCCTTTTTTT 0.923352 -17 AAATATTTTCTTCTCTTTGTTCTTATTCATA 22 121 1 TTCTTTTGTT 0.862031 -86 TCAAGTGCAATCCAGTTTTTTCCTAGAAATC 23 54 0 TCCATTTTTT 0.834327 -82 AGCAAACGTTTGCTATTTTTTAAAAAGAAAT 24 89 0 TGCTTTTTTT 0.890762 -36 ACCGCACTTTTCCTCTTTGTCTAGTGTTTTG 25 64 0 TCCTTTTGTC 0.870759 -92 **** ****** Masking position 7 Map Score: 6.04019 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 242 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 ATATCTCCAGAATGCCGCCGTTTGCCAGAAATT 1 192 1 AAGCCGCGTT 0.950079 -109 AATCATAAAGAAGGCCAATCATTCTCATTTCTG 2 79 1 AAGCCATCTT 0.890448 -222 TCGCATGGCGAACGCCACTTATTGAATTAAAAT 2 271 0 AAGCCATTTT 0.67173 -30 TAAATGTTTTATTGCAATCGGTTGCTAAATTGC 9 91 1 ATGCAACGTT 0.845676 -180 CTTCAAGAACAAGGCCATCCCTTTACCTAATTT 9 192 0 AAGCCACCTT 0.978828 -79 TGGTTGGTGGAATGCCAACCGTTCCTTGATTGA 16 18 1 AAGCCACCTT 0.979154 -60 TGTAAATAAAAAAGCCATCGCTTGACCAATTAA 19 108 0 AAGCCACGTT 0.989154 -63 CATACTTATGAAAGTAACCGCTTTCAATTTATC 21 66 0 AAGTAACGTT 0.870674 -142 AGTATAAATTAATGTAATCGTTTACATTGATAA 21 170 1 AAGTAACGTT 0.870668 -38 TAAATCAAATAAAGCAAACGTTTGCTATTTTTT 24 99 0 AAGCAACGTT 0.974965 -26 ** **** ** ** Masking position 12 Map Score: 6.84488 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 479 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 7 ATTTTATGCGAGAGCGACTTTTTTATCAGTAATGCC 3 44 0 AGGCGACTTT 0.970092 -98 AATAGCGCGGTTCTTTTGTACCGGAGCCG 7 4 1 AGGCGGTTTT 0.991437 -28 CTATTTGAGAAGTGCGGTTAAAATTTAAGTTATTTC 17 40 0 AGGCGGTTTT 0.991437 -148 AGCGTCGTGAAGTGCGGTTTTATTTTGGAGTTTTGG 17 74 1 AGGCGGTTTT 0.991437 -114 ATGCAAAAATAGGGCGACTTAGTTTTTATTTTTATT 17 139 1 AGGCGACTTT 0.970092 -49 AAAGAGGAAAAGTGCGGTTATACTCTATAGAATTTT 25 77 1 AGGCGGTTTT 0.991437 -79 ** ****** * * Masking position 9 Map Score: 5.1396 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 26 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 Motif number 8 TTTGTCGCTTAATGCCTGTAAAACATGCAT 1 110 1 AATGCCTGTA 0.83932 -191 TAATATAAAAAATCCCGCCATTAAGTTGAC 1 151 1 AATCCCGCCA 0.983633 -150 ATATCTCCAGAATGCCGCCGTTTGCCAGAA 1 192 1 AATGCCGCCG 0.918815 -109 CGGTACACCAAATCCCAGCAG 4 2 0 AATCCCAGCA 0.934286 -299 GGATCACTATAATGCCTGCAGATTTTACGT 4 39 0 AATGCCTGCA 0.934286 -262 AATTTGATAAAATCCCGCTCTTTCATAACA 5 191 1 AATCCCGCTC 0.80613 -110 GCTCGCGGCATATCCCGCTATGCCATTTTA 9 31 0 TATCCCGCTA 0.718899 -240 GAGCGTAATAAAACCCACCAGCCGTAAGGT 10 63 0 AAACCCACCA 0.695249 -91 TTTGAAATTCAATGCCGGAAAGCTGCGCCT 11 25 0 AATGCCGGAA 0.828893 -36 CACCACTGACATTGCCTCCACCTTTGTGAC 12 54 1 ATTGCCTCCA 0.695249 -108 TTCAACTGGTAATGCCAGTATGTAGAATTT 13 164 0 AATGCCAGTA 0.83932 -137 CTAAAATTTCAATCCCGCCATTATCTAATA 23 99 0 AATCCCGCCA 0.983633 -37 ********** Masking position 5 Map Score: 4.7554 Number of sites scoring better than the average of aligned sites = 1525 Number in coding regions = 1424 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 9 ATTCACTCACTTTATTTGCATATTAATTCA 1 264 0 TTTATTTGCA 0.808133 -37 TGTGTAATTATTCATTTGCAACCCCATTTC 2 231 0 TTCATTTGCA 0.969963 -70 GCATAAAATTTACACTTGCACCCTGCGAAA 3 71 1 TACACTTGCA 0.932837 -71 GAATATCCAGTTCACTTTCATTTGTTGAAT 4 109 1 TTCACTTTCA 0.948171 -192 TTAGAATCTCTTCACTTGCTTTTTTTCTGC 9 230 1 TTCACTTGCT 0.932987 -41 TGGATGATTATTCATTTGCAAGTCTAAAGC 12 94 0 TTCATTTGCA 0.969963 -68 TGCATAAAAATTCACTTTCATCAACTGAAA 22 152 0 TTCACTTTCA 0.948171 -55 ********** Masking position 4 Map Score: 4.52487 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 19 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 TGAAATGGGGTTGCAAATGAATAATTACACATATA 2 230 1 TTAAATAAAT 0.66596 -71 ATAAAGTGAATTTTAATTCAATAAGTGGCGTTCGC 2 262 1 TTAATTAAAG 0.576238 -39 CAAATTCTGCTTAAAAGTAAATTAATTGTTATCAA 5 122 0 TTAAGTAAAA 0.669636 -179 CGGCATTGAATTTCAAAATAAGGAAACAGAGTT 11 38 1 TTAAAAAAAA 0.641178 -23 TGCTTTAGACTTGCAAATGAATAATCATCCATATA 12 93 1 TTAAATAAAT 0.66596 -69 CCTCAATGAATTAAAATTCAATTTATATGGATGAT 12 116 0 TTAATTAATA 0.453877 -46 TTCCTCTTCATCAAAAATAAACTAAAACATATTTT 13 35 1 TCAAATAAAA 0.588167 -266 TCATCTACTATTAGAAATCAAACAAATAACAATAA 13 79 1 TTAAATAAAA 0.937262 -222 TTTAGTATTATTAGAATTTAATAAAATAATCTAAC 13 117 0 TTAATTAAAA 0.8682 -184 ATATTCTATATTAATAATAAAACAAAAATGGACAA 14 50 0 TTTAATAAAA 0.490635 -85 AGAAGTGCGGTTAAAATTTAAGTTATTTCAGATTA 17 34 0 TTAATTAATA 0.453877 -154 TTTGCATATTTTTGAAATTTATAAAAAGGCTTTTT 17 111 0 TTAAATTAAA 0.797538 -77 GTGTAAACCTTTGTAAATAAAAAAGCCATCGCTTG 19 117 0 TTAAATAAAG 0.755132 -54 TTTACACTAATTTCAAATTTACTCAGGAAATCTAT 19 145 1 TTAAATTACA 0.29509 -26 AATCAGTCTGTTTTAAATTAACTAACACATAAGGA 22 17 0 TTAAATAAAA 0.937257 -190 CATCTTACAATTACAAATAGAGAAATATCATTCTA 22 62 1 TTAAATGAAA 0.640082 -145 AATGGCGGGATTGAAATTTTAGGAAAGTAGGAAAT 23 107 1 TTAATTTAAA 0.634861 -29 ATGTTTATTATTGGAAATTTAGTAAATCCTACGGC 24 15 0 TTAAATTAAA 0.797538 -110 TTTGCTATTTTTTAAAAAGAAATAAAAATCCTCTG 24 77 0 TTAAAAAAAA 0.641212 -48 TTTTAAATCAAATAAAGCAAACGTT 24 110 0 TTAAATAAAA 0.937262 -15 TTACTAATAATTAGAATTGAATAAATAATCGATTT 25 122 0 TTAATTAAAA 0.868205 -34 ** **** ** ** Masking position 1 Map Score: 12.0755 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 46 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 11 GGTCCACTTTTTTCTGCTCGTTTTTATTTC 1 29 1 TTTCTGCTCG 0.927982 -272 CTTTTGCCTTCTCCTGCTCTCCCTTAAGCG 4 140 1 CTCCTGCTCT 0.958952 -161 TGAGCCTGGATTTCCGCTCTCACTGAATTT 4 251 0 TTTCCGCTCT 0.965729 -50 ATTTGATAAAATCCCGCTCTTTCATAACAT 5 192 1 ATCCCGCTCT 0.852146 -109 CTTGCCCGCGCTTCTGCTCTCCCGGCGTAA 8 31 1 CTTCTGCTCT 0.972002 -74 ACTTGCTTTTTTTCTGCTCTGTTTGTTAAG 9 243 1 TTTCTGCTCT 0.976677 -28 AGATAAATATTTTCTTCTCTTTGTTCTTAT 22 117 1 TTTCTTCTCT 0.844523 -90 ********** Masking position 8 Map Score: 4.63269 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 86 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 TCTGCTCGTTTTTATTTCATGCAATCTTCTTGC 1 41 1 TTTATCATCA 0.843592 -260 TTTGCATTGATTTACGTCATCATTGTGAATTAA 1 239 1 TTTAGCATAT 0.59105 -62 TTCACTTTCATTTGTTGAATACTTTTGCCTTCT 4 119 1 TTTGTAATCT 0.78914 -182 GTTAGATTATTTTATTAAATTCTAATAATACTA 13 117 1 TTTATAATCT 0.9472 -184 TCCTTTTTGTTTTAATTAATTATTCTATTATTG 14 106 0 TTTATAATAT 0.756233 -29 TTTTTTATGATTTAGTTCATACTTATGAAAGTA 21 83 0 TTTATCATCT 0.951077 -125 AAAGTGAATTTTTATGCAATTCTTATGCAAATT 22 164 1 TTTAGAATCT 0.88526 -43 CTAATAACCCTTTACTCCATTCAAGTGCAATCC 23 72 0 TTTATCATCA 0.843866 -64 TTATTGGAAATTTAGTAAATCCTACGGCTTAA 24 10 0 TTTATAATCT 0.947222 -115 AAATCGATTATTTATTCAATTCTAATTATTAGT 25 122 1 TTTATAATCT 0.9472 -34 **** * *** ** Masking position 9 Map Score: 3.5791 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 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 13 ATAATGTTATGAAAGAGCGGGATTTTATCA 5 195 0 GAAAGAGCGG 0.88912 -106 AATAGCGCGGTTCTTTTGTA 7 1 1 AATAGCGCGG 0.922947 -31 CCGGGAGAGCAGAAGCGCGGGCAAGATTGC 8 26 0 AGAAGCGCGG 0.987071 -79 ACGCTATTTGAGAAGTGCGGTTAAAATTTA 17 49 0 AGAAGTGCGG 0.986057 -139 AATAGCGTCGTGAAGTGCGGTTTTATTTTG 17 71 1 TGAAGTGCGG 0.955547 -117 GACAAAGAGGAAAAGTGCGGTTATACTCTA 25 74 1 AAAAGTGCGG 0.97825 -82 ********** Masking position 4 Map Score: 3.62313 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 100 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 CTAATAAACGGTAAACATTCTTTTTATATTCACGG 3 5 1 TAAATAATCT 0.766887 -137 AAAAGATGATTAAATGAAAACTCATTTATTTTGCATAAAAA 4 213 1 TAAAAAATTT 0.950671 -88 AAATTCTGCTTAAAAGTAAATTAATTGTTATCAAATTGATG 5 115 0 TAAAAAATTT 0.950677 -186 GTTGCCAGGTTAAACGTAAAACATTCACCTTACGGCTGGTG 10 37 1 TAAAAAATCT 0.946037 -117 TAGATGAATTTAAACGAAAATATGTTTTAGTTTATTTTTGA 13 45 0 TAAAAAATTT 0.950677 -256 TAAATTCTAATAATACTAAAAATCTCGCAATAAAATTCTAC 13 132 1 TAATAAATCT 0.766887 -169 ATAAGAGAGGTAAAATGAAATTTGTTGTCGTTTTTCAACTG 13 186 0 TAAAAAATTT 0.950677 -115 CATTGGGGAATAAACATACATCATTCGAGATACTGCTTGTT 13 244 0 TAAAACATCT 0.718891 -57 ATATTAATAATAAAACAAAAATGGACAAAATCTTTCATTTT 14 37 0 TAAAAAAACT 0.766887 -98 GTTTTTTGAATAATCTGAAATAACTTAAATTTTAACCGCAC 17 24 1 TAATAAATTT 0.783405 -164 TAAACCTTTGTAAATAAAAAAGCCATCGCTTGACCAATTAA 19 108 0 TAAAAAAATT 0.783405 -63 TAATTTACGATAAATTGAAAGCGGTTACTTTCATAAGTATG 21 58 1 TAAAAAATTT 0.950677 -150 AAGTATGAACTAAATCATAAAAAATTTTGCTTATTTTCTTA 21 92 1 TAAATAATTT 0.783405 -116 TTTTGTGCATTAAAAGCAAAAATCTTTATTTAGCTTTGTGC 25 28 0 TAAAAAATTT 0.950677 -128 **** *** ** * Masking position 10 Map Score: 11.0449 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 32 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 GGCACACCTCTTTGCATGATTA 3 130 0 CACACCTCTT 0.976643 -12 TGTTGACACACCTCTGGTCATGATAG 10 138 0 CACACCTCTG 0.978202 -16 GGCTCATTCCTCTTAATGTCCTGC 12 5 1 CATTCCTCTT 0.928336 -157 CTTATTGTCACACACCACTGACATTGCCTC 12 42 1 CACACCACTG 0.931991 -120 TAGATAGACACATTCCTCTTCATCAAAAAT 13 23 1 CATTCCTCTT 0.928336 -278 ********** Masking position 2 Map Score: 0.903578 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 7 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701