AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoN_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 glnP 138 glutamine high-affinity transport system; membrane component #2 glnH 300 periplasmic glutamine-binding protein; permease #3 pspF 151 psp operon transcriptional activator #4 hycB 124 probable small subunit of hydrogenase-3, iron-sulfur protein (part of formate hydrogenlyase (FHL) complex) #5 hycA_hypA 211 hycA: transcriptional repression of hyc and hyp operons, hypA: pleiotrophic effects on 3 hydrogenase isozymes #6 hypE 38 plays structural role in maturation of all 3 hydrogenases #7 glnL 285 histidine protein kinase sensor for GlnG regulator (nitrogen regulator II, NRII) #8 glnA 300 glutamine synthetase #9 fdhF 197 selenopolypeptide subunit of formate dehydrogenase H #10 yjcQ 140 putative enzyme #11 yjcR 300 putative membrane protein #12 HI0536 102 urease accessory protein (ureG) #13 HI0537 107 urease accessory protein (ureF) #14 HI0538 127 urease accessory protein (ureE) #15 HI0540 75 urease, beta subunit (ureB) #16 HI0541 162 urease, gamma subunit (ureA) #17 HI0865 230 glutamine synthetase (glnA) #18 HI1079 67 amino acid ABC transporter, permease protein #19 HI1080 300 amino acid ABC transporter, periplasmic-binding protein Motif number 1 ATCTGGTGCGCTAAAATTGTGCACTCAACACAG 2 115 0 CAATTGTGCA 0.865822 -186 TTTTAGCGCACCAGATTGGTGCCCCAGAATGGT 2 132 1 CAATGGTGCC 0.918838 -169 GATTGGTGCCCCAGAATGGTGCATCTTCAGGGT 2 145 1 CAATGGTGCA 0.983638 -156 CAAGGAGTTGCAAAACTGGCACGATTTTTTCAT 2 225 1 CAATGGCACG 0.959482 -76 CAAAAAGATAAAAAATTGGCACGCAAATTGTAT 3 61 0 AAATGGCACG 0.89346 -91 CAGGGATAATCAACACTGGCACAATTATTGCTT 5 40 0 CAATGGCACA 0.972762 -172 ACAATAAATTAAAAGTTGGCACAAAAAATGCTT 5 154 1 AAGTGGCACA 0.89346 -58 CTATAATGCACTAAAATGGTGCAACCTGTTCAG 7 252 1 CAATGGTGCA 0.983638 -34 ACATTAAGCACCATGTTGGTGCAATGACCTTTG 8 80 0 CAGTGGTGCA 0.975527 -221 CATTGAAGCACTATATTGGTGCAACATTCACAT 8 116 1 CAATGGTGCA 0.983638 -185 TGCAACATTCACATCGTGGTGCAGCCCTTTTGC 8 135 1 AACTGGTGCA 0.800366 -166 CAGCCCTTTTGCACGATGGTGCGCATGATAACG 8 156 1 GAGTGGTGCG 0.773884 -145 GGGGCAATTTAAAAGTTGGCACAGATTTCGCTT 8 196 1 AAGTGGCACA 0.89346 -105 GGCAGCCTACCCAGAGTTGCACGGTCTGCGGCA 10 98 0 CAATTGCACG 0.717662 -43 ATTGTTACATAAAAAATGGCGCAATGAATTGCA 17 51 1 AAATGGCGCA 0.967797 -180 * * * ******* Masking position 3 Map Score: 19.2928 Number of sites scoring better than the average of aligned sites = 761 Number in coding regions = 672 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 GAAGAATCAACAGCAACATGCCAGGATGAGT 3 112 1 CAGCAACAGC 0.89032 -40 TTTCGACACTCATCGACACGCCCATCCCCAA 4 48 0 CATCGACAGC 0.97824 -77 AATGACATTTCATCGGCATGTTTTCGTCAAA 4 78 1 CATCGGCAGT 0.804751 -47 TAACTATTGCCAGCTACAAGCAATAATTGTG 5 23 1 CAGCTACAGC 0.89032 -189 CGAAATGACACGTCGACACGGCGACGAAATT 5 95 1 CGTCGACAGG 0.97355 -117 CCCACGGTAGCGGCGGCCAGGCG 6 26 1 CGGCGGCCGG 0.964748 -13 CCAGGCCTGCCAGAGACAGGCGAAAAGTTTC 7 28 0 CAGAGACAGC 0.940187 -258 GGCCTGGGATCGGTGGCAAGCACATCACGCC 7 52 1 CGGTGGCAGC 0.930271 -234 ATCTTTTTTACGGCGACACGGCCAAAATAAT 8 230 1 CGGCGACAGG 0.989317 -71 GTTAAGCGAGCGGCGACCAGGTCGCGTGCCG 10 72 1 CGGCGACCGG 0.96696 -69 GTTGCACGGTCTGCGGCACGCGACCTGGTCG 10 85 0 CTGCGGCAGC 0.956455 -56 TTTTGAGTTGCATCGCCATGCGAGAGAGAAC 11 26 0 CATCGCCAGC 0.956474 -275 CACATTATAACGTAGCCATGCTATTTTTTCA 17 172 0 CGTAGCCAGC 0.830128 -59 ******** ** Masking position 7 Map Score: 14.046 Number of sites scoring better than the average of aligned sites = 1542 Number in coding regions = 1475 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 3 CACCAGATTGGTGCCCCAGAATGGTGCATCT 2 140 1 GTGCCCCAGA 0.938308 -161 CTTCAGGGTATTGCCCTATAAATCGTGCATC 2 169 1 TTGCCCTATA 0.824548 -132 CCAAAGGTCATTGCACCAACATGGTGCTTAA 8 79 1 TTGCACCAAA 0.957693 -222 GATGTGAATGTTGCACCAATATAGTGCTTCA 8 119 0 TTGCACCAAA 0.957693 -182 AACTTTTAAATTGCCCCTAAAAGGCGTTATC 8 182 0 TTGCCCCTAA 0.992989 -119 CAAATGTGATTTGCCCCTACAAGTAAAATCT 12 30 0 TTGCCCCTAA 0.992989 -73 CAAATCACATTTGCCCTTGAACATTCGTTGA 12 48 1 TTGCCCTTGA 0.94045 -55 CAAGTTACATTTGCCCCTATATATCAACGAA 12 71 0 TTGCCCCTAA 0.992989 -32 CAAATGTAACTTGCCCCTACACCC 12 89 1 TTGCCCCTAA 0.992989 -14 ********* * Masking position 2 Map Score: 13.1914 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 73 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 AGGGAACTGCCAGTGCGTTTTACAGGTGTAGCG 1 14 0 CAGTGTTTTC 0.877283 -125 ATTGTTTTTTCATCAGGTTTTACGCTAAATAAT 2 80 1 CATCGTTTTC 0.932629 -221 ATAAATCGTGCATCACGTTTTTGCCGCATCTCG 2 186 1 CATCGTTTTG 0.909028 -115 GACATTTCATCGGCATGTTTTCGTCAAAAATGA 4 81 1 CGGCGTTTTG 0.937494 -44 AAACTGACGACAGCCTGTTTTTCGTCAGAGTTT 9 61 1 CAGCGTTTTC 0.990063 -137 CTTATTATCCCAGCTGGTTTTTCTGCGCCATTG 11 129 1 CAGCGTTTTC 0.990063 -172 GCGCCATTGCCAGCCTTATTTTGACGCTCATCA 11 153 1 CAGCTATTTG 0.673567 -148 ATTATTTATACCGCCCTTTTTGCTCTCTACGCC 11 233 1 CCGCTTTTTC 0.904507 -68 ATACGAAAGTCAGCGAATTTTACGTAAAAAATC 16 119 0 CAGCATTTTC 0.907128 -44 ATTACATACTCAGCTCGTTCTGCACTCATAAAT 18 29 0 CAGCGTTCTC 0.971855 -39 AGTATGTAATCAGCTCGTTTTGGCCT 18 52 1 CAGCGTTTTG 0.986286 -16 AAATAATCTACCGCACTTTCTTGTAGAAAAATA 19 144 0 CCGCTTTCTG 0.703228 -157 **** ***** * Masking position 9 Map Score: 13.2112 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 768 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 GAGGATTAGGGTGAGGGGCGCAAACCCGCT 1 61 1 GTGAGGGGCG 0.989066 -78 CGCCTGTTTGGGGATGGGCGTGTCGATGAG 4 41 1 GGGATGGGCG 0.994284 -84 ACTCGCCCACGGTAGCGGCGGCCAGGCG 6 21 1 GGTAGCGGCG 0.933628 -18 TGGCAGGCCTGGGATCGGTGGCAAGCACAT 7 47 1 GGGATCGGTG 0.971635 -239 TGTCTGCCGCGTGATGGCTGTCACGCGGTA 9 13 1 GTGATGGCTG 0.868037 -185 GAAGAGTTAAGCGAGCGGCGACCAGGTCGC 10 67 1 GCGAGCGGCG 0.976049 -74 GCCGATCACCGGGATTGCCGGAGATAATGA 11 98 0 GGGATTGCCG 0.91034 -203 GGCAATCCCGGTGATCGGCGCTTATTATCC 11 109 1 GTGATCGGCG 0.990964 -192 AACTCGCCTCGTGATGAGCGTCAAAATAAG 11 167 0 GTGATGAGCG 0.914905 -134 ********** Masking position 4 Map Score: 9.65991 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 558 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 ATGTTGTTCCTGTTACCGTGGTGT 1 125 0 TTGTTCCTTT 0.762165 -14 AGCATTTCCTTTTTTCTATCCACG 2 287 0 ATTTCCTTTT 0.804473 -14 GTGCCAATTTTTTATCTTTTTGATTTATAAA 3 72 1 TTTATCTTTT 0.882096 -80 CAGATTTCGCTTTATCTTTTTTACGGCGACA 8 217 1 TTTATCTTTT 0.882096 -84 GATTAATTTCCTTCTTAATAATTTGT 16 6 1 ATTTCCTTTT 0.804473 -157 ATAAGGAGGATTTTTTTTCTTTCAAGGGGCT 16 52 1 TTTTTTTTTT 0.705526 -111 TGACAAAATATTTTTCCTATTTTAGATTTTT 16 95 1 TTTTTCCTTT 0.949154 -68 ACATGTATAATTTTTCCTTTTCGACAAATGT 17 96 0 TTTTTCCTTT 0.949154 -135 TATACATGTATTTTTCTTTTTCTGCTATGAC 17 118 1 TTTTTCTTTT 0.970923 -113 ATGAAATTTATTTTTCTTATTCTAGTCATAG 17 142 0 TTTTTCTTTT 0.970923 -89 GCGGTAGATTATTTTCTTATTTTGATAGTAA 19 163 1 ATTTTCTTTT 0.92231 -138 TTTTTCTTCCTTGTGTTGTGT 19 290 0 TTTTTCTTCT 0.851461 -11 ******** ** Masking position 8 Map Score: 9.86846 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 95 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 CTATCCACGGGACGATCCCCTGCGTGACATTCA 2 263 0 GAGATCCCGC 0.952654 -38 GATCTGATTGAAGAATCAACAGCAACATGCCAG 3 103 1 AAAATCACGC 0.904946 -49 CGTCAAAAATGACAATCACCTGAGGAATGCCTG 4 102 1 GAAATCCCGA 0.908345 -23 GCCTCCCATTAACTATTGCCAGCTACAAGCAAT 5 14 1 AATATTCCGC 0.821625 -198 ACATCATCGACATTATTCACCGCAGGGATAATC 5 62 0 CATATTACGC 0.672083 -150 CGAAGCATCAGAGAATTGACGGAGAAAAAAGCC 7 199 0 GAAATTACGA 0.68052 -87 ACTCTTCATGAAAGAACGCCAGCAGCCTGACCA 10 41 0 AAGAACCCGC 0.81688 -100 CGAGATCAGAATCACCAGCAGGCAGCCTA 10 122 0 CAAATCCCGC 0.972576 -19 AAACAGCCTGGATAATTCCCGTCTTCATGGTTT 11 57 1 GAAATTCCTC 0.681314 -244 TCGGGATGCTCATTATCTCCGGCAATCCCGGTG 11 89 1 CATATCCCGC 0.905086 -212 GGCAATGGCGCAGAAAAACCAGCTGGGATAATA 11 131 0 CAAAAACCGC 0.65983 -170 ATGCCAGATTGATATTTGCCCGCTGAATAACTC 11 192 0 GAATTTCCGC 0.775909 -109 AAATAATTCCGACAAATGCCAGATTGATATTTG 11 207 0 GAAAATCCGA 0.7747 -94 AAATAGATTAGAAAAATGCCAGCCAGAACAGCA 11 267 0 GAAAATCCGC 0.960082 -34 AAATCTCAATAAAAAATAACCGCAC 12 3 0 AAAAATACGC 0.767612 -100 CTCTTCGAAAGAAAAACTACAGCTACAATGATT 14 80 0 GAAAACACGC 0.930394 -48 AAAATAAGAAAATAATCTACCGCACTTTCTTGT 19 153 0 AAAATCACGC 0.904946 -148 ** **** ** ** Masking position 2 Map Score: 10.9907 Number of sites scoring better than the average of aligned sites = 2373 Number in coding regions = 2214 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 8 CTGTGTTGAGTGCACAATTTTAGCGCACCA 2 115 1 TGCACAATTT 0.912033 -186 ACCATTCTGGGGCACCAATCTGGTGCGCTA 2 135 0 GGCACCAATC 0.856244 -166 ACCCTGAAGATGCACCATTCTGGGGCACCA 2 148 0 TGCACCATTC 0.962503 -153 AAAAACGTGATGCACGATTTATAGGGCAAT 2 178 0 TGCACGATTT 0.941306 -123 TTGCAAAACTGGCACGATTTTTTCATATAT 2 232 1 GGCACGATTT 0.937493 -69 AATCAACACTGGCACAATTATTGCTTGTAG 5 36 0 GGCACAATTA 0.780201 -176 CTGAACAGGTTGCACCATTTTAGTGCATTA 7 255 0 TGCACCATTT 0.978415 -31 ATGTGAATGTTGCACCAATATAGTGCTTCA 8 119 0 TGCACCAATA 0.804589 -182 TGATATTACGGGCACTATTTATTCAAAACT 9 89 0 GGCACTATTT 0.846122 -109 CTGGTTTTTCTGCGCCATTGCCAGCCTTAT 11 142 1 TGCGCCATTG 0.842597 -159 TGCAATTCATTGCGCCATTTTTTATGTAAC 17 54 0 TGCGCCATTT 0.945644 -177 ********** Masking position 7 Map Score: 10.0064 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 227 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 TGCACAATTTTAGCGCACCAGATTGGTGCC 2 125 1 TAGCGCACCA 0.788573 -176 CACCGATCCCAGGCCTGCCAGAGACAGGCG 7 37 0 AGGCCTGCCA 0.846827 -249 GCGTCTTATCCGGCCTACACGGTGATGATG 7 98 1 CGGCCTACAC 0.880088 -188 TCACCTGCTCCGGCCTACCACATCATCACC 7 118 0 CGGCCTACCA 0.963792 -168 AGAACGCCAGCAGCCTGACCACCGGTAATG 10 32 0 CAGCCTGACC 0.691364 -109 CACCAGCAGGCAGCCTACCCAGAGTTGCAC 10 109 0 CAGCCTACCC 0.983506 -32 TTGTGGGCTAAAGCCCACCCTACGG 15 6 0 AAGCCCACCC 0.978742 -70 GGGTGGGCTTTAGCCCACAAAATAAAAATA 15 16 1 TAGCCCACAA 0.833082 -60 GGGTGGGCTTTAGCCCACCATTGATATTTT 15 40 0 TAGCCCACCA 0.966506 -36 TGGTGGGCTAAAGCCCACCCTACAAGGAAC 15 50 1 AAGCCCACCC 0.978742 -26 ********** Masking position 4 Map Score: 6.68061 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 480 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 GGAGTTGCAAAACTGGCACGATTTTTTCAT 2 228 1 AACTGGCACG 0.952012 -73 AAAGATAAAAAATTGGCACGCAAATTGTAT 3 61 0 AATTGGCACG 0.848429 -91 ACGCCTGCAAAACGGGCAAAGCCTCAGC 4 9 0 AACGGGCAAA 0.904271 -116 TATTGCTTGTAGCTGGCAATAGTTAATGGG 5 18 0 AGCTGGCAAT 0.949611 -194 GGATAATCAACACTGGCACAATTATTGCTT 5 40 0 CACTGGCACA 0.891132 -172 ATAAATTAAAAGTTGGCACAAAAAATGCTT 5 157 1 AGTTGGCACA 0.958614 -55 GGCTACAGATAGCTGACAAACTTCACGTTG 7 157 0 AGCTGACAAA 0.8181 -129 GCAATTTAAAAGTTGGCACAGATTTCGCTT 8 199 1 AGTTGGCACA 0.958614 -102 GTCAAAATAAGGCTGGCAATGGCGCAGAAA 11 148 0 GGCTGGCAAT 0.814923 -153 CGAGTTATTCAGCGGGCAAATATCAATCTG 11 191 1 AGCGGGCAAA 0.956775 -110 ********** Masking position 8 Map Score: 4.95291 Number of sites scoring better than the average of aligned sites = 1153 Number in coding regions = 1097 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 CGTTACATAAAGATTGTTTTTTCATCAGGTTTT 2 68 1 AATTTTTTTC 0.927651 -233 TGCAAAACTGGCACGATTTTTTCATATATGTGA 2 233 1 GAGTTTTTTC 0.718292 -68 CCATCTCTGCATGGGCTTTTTTCTCCGTCAATT 7 186 1 AGGTTTTTTC 0.924351 -100 GGAATTATCCAGGCTGTTTTTTTGAGTTGCATC 11 43 0 AGTTTTTTTT 0.77284 -258 CTATATAAGGAGGATTTTTTTTCTTTCAAGGGG 16 48 1 AGTTTTTTTC 0.913406 -115 GAAAAATTATACATGTATTTTTCTTTTTCTGCT 17 111 1 AAGATTTTTC 0.915176 -120 TTTTTTCATGAAATTTATTTTTCTTATTCTAGT 17 147 0 AATATTTTTC 0.903043 -84 TAACGTAGCCATGCTATTTTTTCATGAAATTTA 17 163 0 AGTTTTTTTC 0.913406 -68 CTTTCTTTAGAAAGGCATTTTTTTACTGAAATT 19 76 1 AAGATTTTTT 0.776781 -225 CATTGTTTAGAAACGTATTTTTCTACAAGAAAG 19 129 1 AAGATTTTTC 0.915176 -172 GTAATCACTTATATTAATTTTTTATAACTAAAA 19 190 1 AATATTTTTT 0.750254 -111 CCATAAATAAATAATCTTTTTTTTTCATAAGTT 19 231 1 AATTTTTTTT 0.805279 -70 * * * ******* Masking position 8 Map Score: 7.1459 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 157 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 12 AAAGGTCATTGCACCAACATGGTGCTTAAT 8 81 1 GCACCAACAT 0.792372 -220 CTTTTAAATTGCCCCTAAAAGGCGTTATCA 8 181 0 GCCCCTAAAA 0.932034 -120 ATCAGGGAATGACCCCACATAAAATGTGGC 9 115 1 GACCCCACAT 0.849765 -83 AATGTGATTTGCCCCTACAAGTAAAATCTC 12 29 0 GCCCCTACAA 0.985844 -74 AGTTACATTTGCCCCTATATATCAACGAAT 12 70 0 GCCCCTATAT 0.905492 -33 AATGTAACTTGCCCCTACACCC 12 91 1 GCCCCTACAC 0.969109 -12 GTGCAACAACGCACCTAAATCCGTTAAAGA 13 16 0 GCACCTAAAT 0.826601 -92 GGCTAAAGCCCACCCTACAAGGAACAAAGA 15 55 1 CACCCTACAA 0.840111 -21 TATAGAAACCGCACTTACAAATTATTAAGA 16 23 0 GCACTTACAA 0.631912 -140 CAATGAATTGCACCCTACATTTCTACATTT 17 72 1 CACCCTACAT 0.866193 -159 ********** Masking position 7 Map Score: 4.60042 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 180 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 TTACTTAATCAGCTGGAGATAGCAGATGG 2 9 0 AGCTGGGATA 0.784526 -292 GATTGTGTGATGATGTGGATACAAAAAATTT 2 38 0 TGATGTGATA 0.867577 -263 CAGGGGATCGTCCCGTGGATAGAAAAAAGGA 2 274 1 TCCCGTGATA 0.831241 -27 CCTGGCATGTTGCTGTTGATTCTTCAATCAG 3 106 0 TGCTGTGATT 0.913307 -46 GACGAAAACATGCCGATGAAATGTCATTTTC 4 75 0 TGCCGAGAAA 0.837737 -50 ATAATGTCGATGATGTCGAAATGACACGTCG 5 79 1 TGATGTGAAA 0.794357 -133 GTGTTTTAGTTGCCGTGGAAACTTTTCGCCT 7 11 1 TGCCGTGAAA 0.961343 -275 ATCAGAGAATTGACGGAGAAAAAAGCCCATG 7 195 0 TGACGGGAAA 0.869687 -91 GTAGGCTGCCTGCTGGTGATTCTGATCTCG 10 121 1 TGCTGGGATT 0.919444 -20 TCACCGGGATTGCCGGAGATAATGAGCATCC 11 92 0 TGCCGGGATA 0.978585 -209 TACAAGAAAGTGCGGTAGATTATTTTCTTAT 19 152 1 TGCGGTGATT 0.793902 -149 ****** **** Masking position 9 Map Score: 4.99691 Number of sites scoring better than the average of aligned sites = 1120 Number in coding regions = 1051 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 14 AGACGCATTTGCGTCGCATCCGGCGTGATGT 7 73 0 GCTCGCATCC 0.954706 -213 CGACGCAAATGCGTCTTATCCGGCCTACACG 7 88 1 GCTCTTATCC 0.990454 -198 GATGCTTCGCGCTTTTTATCCGTAAAAAGCT 7 223 1 GCTTTTATCC 0.963149 -63 GGTGATCGGCGCTTATTATCCCAGCTGGTTT 11 118 1 GCTATTATCC 0.963017 -183 AATAAAAATTGCATCTTATCCAATTAAAGCA 17 18 0 GCTCTTATCC 0.990285 -213 ** ******** Masking position 4 Map Score: 2.32037 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 23 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 GTGAGGGGCGCAAACCCGCTCCGGGGCCATTAAT 1 71 1 CACCGCTCCG 0.994762 -68 ATAATATCCAACTCGCCCACGGTAGCGGCGG 6 8 1 CACCGCCCAG 0.982991 -31 TGGAGAGCGACTCACCTGCTCCGGCCTACCACAT 7 125 0 CACTGCTCCG 0.981096 -161 TCAAATCACGCATACGCGCTCTCGACTACAGTAT 9 156 0 CACCGCTCTG 0.991666 -42 CGGTCTCGCTCCAGTTAATCAAAT 9 184 0 CTCCGCTCCG 0.975292 -14 AGGGGCAAATCACATTTGCCCTTGAACATTCGTT 12 43 1 CATTGCCCTG 0.83792 -60 AGAGGCGTATCGTACACGCCCTTTTACACTAATT 14 30 0 CACCGCCCTT 0.949878 -98 * ** ****** * Masking position 8 Map Score: 3.02043 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 150 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925