AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i071_ecoli_bsub_300.orf -o071_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 trpE 91 anthranilate synthase component I #2 trpL 137 trp operon leader peptide #3 pabB 73 p-aminobenzoate synthetase, component I #4 pabA 31 p-aminobenzoate synthetase, component II #5 yhfG 104 orf, hypothetical protein #6 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #7 spoIIE 300 serine phosphatase #8 yabS 84 similar to hypothetical proteins #9 yabT 88 yabT #10 yacA 103 similar to cell-cycle protein #11 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #12 yacB 194 similar to hypothetical proteins #13 yacC 85 similar to hypothetical proteins #14 yacD 46 similar to protein secretion PrsA homolog #15 cysK 75 cysteine synthetase A #16 pabB 166 para-aminobenzoate synthase (subunit A) #17 trpE 215 anthranilate synthase #18 aroB 61 3-dehydroquinate synthase #19 aroF 69 chorismate synthase #20 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #21 ndk 115 nucleoside diphosphate kinase #22 gerCA 162 heptaprenyl diphosphate synthase component I #23 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #24 mtrA 187 GTP cyclohydrolase I #25 hbs 300 non-specific DNA-binding protein HBsu Motif number 1 TTTTGTTCAAAAAAAAGCCCGCTCATTAGGCGG 1 56 0 AAAAGCCGCT 0.986748 -36 GGCTCCGGTACAAAAGAACCGCGCTATT 4 6 0 CAAAACCGCG 0.969216 -26 AAGCGCGGGCAAGATTGCCCGCGCGAGAAATCA 5 11 0 AAGAGCCGCG 0.941903 -94 AAAATCACCTAAAATCGCCCGCTCGCGGCATAT 6 48 0 AAAAGCCGCT 0.986748 -223 TCTAAAAATGAAAAAAATCGGCTTCTGCAAGAG 7 129 0 AAAAACGGCT 0.945183 -172 TCTTTCTAAAAAAACTGCCGGCTGACGCTGGCA 12 18 1 AAAAGCGGCT 0.977473 -177 TTTACATAAAAAAACTGCCAGCGTCAGCCGGCA 12 33 0 AAAAGCAGCG 0.977729 -162 GGATGATTGTAAAAGCCGCAGCTGAGCCAATCA 12 66 0 AAAACCAGCT 0.879736 -129 GATTTGTTTACAAATGAGCCGCTGATCGTGTAT 12 111 1 CAAAACCGCT 0.951502 -84 ATTGATTTATGAAAGAAACCGCGTAGGAAGTGT 13 48 1 GAAAACCGCG 0.899417 -38 GAAATATAAAAAAACTCCCGGCGAACCGGGAGT 16 22 0 AAAACCGGCG 0.949032 -145 ATCAAATTGACCGCATTAGAGAAAA 18 3 1 CAAAGCCGCA 0.898454 -59 AAACAGAACAAAAACCGGCGGCGTTATATGTTG 20 39 0 AAAAGCGGCG 0.985842 -198 TTGTTTCAATAAAAAAATCAGCTTTTCAGCTGA 20 151 0 AAAAACAGCT 0.915759 -86 TATACTAGGACAAAAAGACAGCGAGACTGGGAG 20 207 1 CAAAGCAGCG 0.966788 -30 **** * ***** Masking position 4 Map Score: 23.5571 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 418 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 AGAACCGTTATGATGTCGGCGCAAAAAACATTA 2 30 0 TGATTCGCCA 0.861594 -108 TCCTCTCATCTCCCACCTGTTAT 7 288 0 TCCTTCTCCC 0.951739 -13 ATTCATATATTCCCATCTTCGCCAGAAGAAATT 8 28 0 TCCCTCTCCC 0.964597 -57 TTAAAGATATTCATATCCTAACACTTTCAACCC 10 53 0 TCATTCTACA 0.657219 -51 AATGTCCTCCTCACAATGAGCAGGT 10 89 0 TGTCTCTCCA 0.908809 -15 TCCTTACCTCCTCCCACAGTAAGCAC 11 82 0 TTACTCTCCA 0.929483 -16 ACCTGCTTTCAGCCCCTTTTCTCAAA 14 31 0 TGCTTCGCCC 0.808331 -16 TTATATAGTATTTTATCCTCTCATGCCATCTTC 17 163 1 TTTTTCTCCA 0.777412 -53 TATCCTCTCATGCCATCTTCTCATTCTCCTTGC 17 176 1 TGCCTCTCCA 0.973353 -40 GACTTCTTCTCCCTTCATCGCATTAACGCTTT 19 48 0 TCCCTCTCCA 0.981809 -22 TACATACACTTTATTTCTTCACAGAAAAGCCCC 24 42 1 TTATTCTCCA 0.905127 -146 TCGTTTATTATCATTTCTTCACAGTTCAGTCTG 25 244 0 TCATTCTCCA 0.966788 -57 GCCTTTCACCTCCTCCCAAAAGGATACA 25 283 0 TCACTCTCCA 0.975739 -18 **** ** ** ** Masking position 6 Map Score: 13.9576 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 162 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 CGCGGCATATCCCGCTATGCCATTTTATTTTTGAAC 6 22 0 CCCGTGTTTT 0.77088 -249 ATATATGTAACCTGACGATCACTTTTTATTCCGTGA 6 144 0 CCTGCTTTTT 0.536767 -127 ACAAGGCCATCCCTTTACCTAATTTTACGTATCTGA 6 181 0 CCCTTCTTTT 0.940644 -90 TATTTAGAATCTCTTCACTTGCTTTTTTTCTGCTCT 6 227 1 CTCTCTTTTT 0.878008 -44 AAATGATTGGCTCAGCTGCGGCTTTTACAATCATCC 12 63 1 CTCACCTTTT 0.848163 -132 TGAATAGTTTCTCTACTTTACTTTTTACAAACATTC 12 153 0 CTCTCTTTTT 0.878008 -42 CCTCTATCACCACTTTTGAATAGTTTC 12 178 0 CTCTTCTTTT 0.975919 -17 GCTCTTTAGCGGGTTTTTAATTTGAGA 14 2 1 CTCTTCTTTT 0.975919 -45 TCTCGACACCTCAATTTCCGACTATTT 15 59 0 CTCGCCATTT 0.786548 -17 CCTCTATTTTCTTTTTTACTTGTTTTTAATTGTAAA 16 131 0 CTTTTCTTTT 0.938954 -36 ATGTTGCCGGCTCTGTTGCTTATTTTCACAATGA 20 9 0 CTCTTCTTTT 0.975919 -228 AAAAAATCAGCTTTTCAGCTGATTTTAGATCGTTGG 20 137 0 CTTTCCTTTT 0.937761 -100 CTCTCCCAGTCTCGCTGTCTTTTTGTCCTAGTATAG 20 206 0 CTCGTCTTGT 0.847916 -31 ACGAATATTCCTTTTTTTCCTTTTTTCATCC 25 6 0 CTTTTCTTTT 0.938954 -295 CTTTAAAATGCTTGATATGGCTTTTTATATGTGTTA 25 84 1 CTTGTGTTTT 0.765561 -217 CTTTCTCTTACTTGCTCTCATTTTTTTCTGAGACAG 25 199 1 CTTGTCTTTT 0.943456 -102 **** * * **** Masking position 14 Map Score: 13.0599 Number of sites scoring better than the average of aligned sites = 285 Number in coding regions = 213 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 GCGCACTCCCGTTCTGGATAATGTTTTTTGC 2 12 1 GTCTGGATAA 0.587009 -126 CATCATAACGGTTCTGGCAAATATTCTGAAA 2 48 1 GTCTGGCAAA 0.90221 -90 AGTCCTGACTCTACTGGCTATGTGCCGGGTA 3 52 0 CTCTGGCTAT 0.750604 -22 CGCTTCTGCTCTCCCGGCGTAACCCGGATTT 5 39 1 CTCCGGCGTA 0.962544 -66 GCCGCTTATACTTGTGGCAAATGGACACGTT 5 70 1 CTGTGGCAAA 0.902208 -35 AAATCGCCCGCTCGCGGCATATCCCGCTATG 6 39 0 CTGCGGCATA 0.79643 -232 AACAAATATGGTAGCGGCGGAGGGGATC 7 8 0 GTGCGGCGGA 0.857758 -293 AATCAAATTTCTTCTGGCGAAGATGGGAATA 8 23 1 CTCTGGCGAA 0.983766 -62 ATTCATTCCTCCTGGAGAATACGAGGATT 8 66 0 CTCTGGAGAA 0.903247 -19 TCTAAAAAAACTGCCGGCTGACGCTGGCAGT 12 22 1 CTCCGGCTGA 0.939532 -173 TATAAAAAAACTCCCGGCGAACCGGGAGTTT 16 20 0 CTCCGGCGAA 0.987845 -147 ** ******** Masking position 2 Map Score: 6.74194 Number of sites scoring better than the average of aligned sites = 1047 Number in coding regions = 999 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 5 TTTGAACAAAATTAGAGAATAACA 1 78 1 ATTAGAGAAT 0.801413 -14 ATCGGCTTCTGCAAGAGAAACCGATTTGTT 7 116 0 GCAAGAGAAA 0.708535 -185 GAATATATGAATCTGAGAATCCTCGTATTC 8 49 1 ATCTGAGAAT 0.505333 -36 TAAAAAGTAAAGTAGAGAAACTATTCAAAA 12 162 1 AGTAGAGAAA 0.904969 -33 CGGGTTTTTAATTTGAGAAAAGGGGCTGAA 14 20 1 ATTTGAGAAA 0.735854 -27 TGTTATTCTTGGAAGAGAAATTCACTTTTT 16 85 1 GGAAGAGAAA 0.926713 -82 AAGCAATGTTGTTAGTGAAAAAAGTGAATT 16 103 0 GTTAGTGAAA 0.713127 -64 AATGAGTTGAGTTAGAGAATAGGGTAGCAG 17 61 1 GTTAGAGAAT 0.880626 -155 AGAATAGGGTAGCAGAGAATGAGTTTAGTT 17 76 1 AGCAGAGAAT 0.777386 -140 AATTGACCGCATTAGAGAAAATGTGGAGAA 18 15 1 ATTAGAGAAA 0.886821 -47 AATGTGGAGAATATGAGAAAACTGTCGAGG 18 34 1 ATATGAGAAA 0.669269 -28 ATCAATCCGGGGCGGAGAAATTTCTTAATA 21 21 0 GGCGGAGAAA 0.873881 -95 ATAATGATGGGGTGGAGAAT 21 106 1 GGTGGAGAAT 0.833671 -10 ATGAGAGCAAGTAAGAGAAAGACAATTAAA 25 190 0 GTAAGAGAAA 0.912315 -111 CCTTTTGGGAGGAGGTGAAAGGC 25 288 1 GGAGGTGAAA 0.550941 -13 ********** Masking position 8 Map Score: 7.59971 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 492 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 TAATTGTCAACAGCTCATTTCAGAATATTT 2 66 0 CAGCTCATTT 0.928581 -72 TCTGCAAGAGAAACCGATTTGTTAGGATGA 7 109 0 AAACCGATTT 0.719332 -192 TCTCTTGCAGAAGCCGATTTTTTTCATTTT 7 128 1 AAGCCGATTT 0.953205 -173 CCCCTTTACCAAGCTGTTTACGCAATGTAT 9 58 0 AAGCTGTTTA 0.719251 -31 ACACGATCAGCGGCTCATTTGTAAACAAAT 12 112 0 CGGCTCATTT 0.672207 -83 AAATCAATTCCAGCCCTTTTAGGGTTAAGA 13 26 0 CAGCCCTTTT 0.957171 -60 ACCTGCTTTCAGCCCCTTTTCTCAAATTA 14 28 0 CAGCCCCTTT 0.964271 -19 CACTGCCATTCAACCCTTTATTCACTTTAA 20 86 0 CAACCCTTTA 0.566919 -151 ATCAGCTTTTCAGCTGATTTTAGATCGTTG 20 138 0 CAGCTGATTT 0.917989 -99 ATCAGCTGAAAAGCTGATTTTTTTATTGAA 20 150 1 AAGCTGATTT 0.890132 -87 CTTCACAGAAAAGCCCCTTTCTAAGGGGCT 24 58 1 AAGCCCCTTT 0.951299 -130 GAAATATGAAAAGCCCCTTAGAAAGGGGCT 24 69 0 AAGCCCCTTA 0.900429 -119 TTTTCTTAAAAAGCCGTTTAATTGTCTTTC 25 174 1 AAGCCGTTTA 0.865717 -127 ********** Masking position 8 Map Score: 9.49186 Number of sites scoring better than the average of aligned sites = 676 Number in coding regions = 627 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 TACGTAAAATTAGGTAAAGGGATGGCCTTG 6 186 1 TAGGTAAAGG 0.933207 -85 TTCTGCTCTGTTTGTTAAGGAAATCTC 6 254 1 TTTGTTAAGG 0.835805 -17 CGTAAACAGCTTGGTAAAGGGGCCAATGGA 9 66 1 TTGGTAAAGG 0.963813 -23 ATGGTTATTGTTTGTATTGGAATGATTTTC 11 30 1 TTTGTATTGG 0.842586 -68 GCAGTTTTTTTATGTAAATGATTGGCTCAG 12 48 1 TATGTAAATG 0.624138 -147 TTTCCGACTATTTGTATTGGTATTATGTAT 15 42 0 TTTGTATTGG 0.842586 -34 TTTGTTCTGTTTTGTAAAGGTTTACATTAA 20 60 1 TTTGTAAAGG 0.969961 -177 TTTTAGATCGTTGGGAAAGGCAGAGGTCTG 20 121 0 TTGGGAAAGG 0.861553 -116 CATCATTATGTATGTATAGGCTTTCACACT 21 85 0 TATGTATAGG 0.89884 -31 ********** Masking position 1 Map Score: 5.11561 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 72 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 CGGGCAATCTTGCCCGCGCTTCTGCTCTCCCGG 5 23 1 TGCCCGCTTT 0.908926 -82 TTAGAATCTCTTCACTTGCTTTTTTTCTGCTCT 6 230 1 TTCATGCTTT 0.623532 -41 CCATTCCACTTGCCTTTGATTGTCGTACCCGGC 9 17 0 TGCCTGATTT 0.893743 -72 CAAACTGCAGAGCCTATGCTTCTTCTTTGCTTG 10 17 1 AGCCTGCTTT 0.987868 -87 TTTACAAATGAGCCGCTGATCGTGTATGGTATT 12 117 1 AGCCTGATCT 0.929705 -78 GCTGTTTGCGAGCATTTGCTTTTAACAGCGGGG 22 20 0 AGCATGCTTT 0.941296 -143 GGGAGGATACAGCCAATTCTTTTTTTTATGCTA 22 53 1 AGCCTTCTTT 0.888678 -110 CCTGTCAGGAAGCCCATGCTCTTGAAATATGAA 24 89 0 AGCCTGCTCT 0.98533 -99 TAAAGCGTCAATCCCTTGCTCGTCAAGGATTTA 25 56 0 ATCCTGCTCT 0.929706 -245 **** ***** * Masking position 10 Map Score: 3.93079 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 336 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 9 GCGTAACCCGGATTTGCCGCTTATACTTGT 5 55 1 GATTTGCCGC 0.944512 -50 TGAACGTGTCCATTTGCCACAAGTATAAGC 5 73 0 CATTTGCCAC 0.765357 -32 GGCATAGCGGGATATGCCGCGAGCGGGCGA 6 37 1 GATATGCCGC 0.964673 -234 AATTCCATTGGCCCCTTTACCAAGC 9 74 0 CATTGGCCCC 0.884634 -15 TGGATGATTGTAAAAGCCGCAGCTGAGCCA 12 70 0 TAAAAGCCGC 0.714693 -125 TTTCTTCACAGAAAAGCCCCTTTCTAAGGG 24 55 1 GAAAAGCCCC 0.944966 -133 CTTGAAATATGAAAAGCCCCTTAGAAAGGG 24 72 0 GAAAAGCCCC 0.944966 -116 GATTCTAGCACATATGCCCCGCTAAAAGCA 24 132 0 CATATGCCCC 0.964673 -56 ********** Masking position 2 Map Score: 2.75997 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 232 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 ATTGCTTTACGCATGGTGAATACACTGCCCGT 1 12 0 GCATGGAATA 0.81876 -80 ACAATCAAAGGCAAGTGGAATGGAAACACTTA 9 27 1 GCAATGAATG 0.970117 -62 TGTGTATAAAGCAATTAGAATGAGTTGAGTTA 17 43 1 GCAATGAATG 0.970117 -173 ACTCCTTATGGCAAGGAGAATGAGAAGATGGC 17 187 0 GCAAGGAATG 0.989699 -29 ATTTCGGTGTGCAGTGTGAAAGCCTATACATA 21 73 1 GCAGGGAAAG 0.914365 -43 CCCGCTAAAAGCAAAGTGAATGCCCTGTCAGG 24 113 0 GCAAGGAATG 0.989699 -75 **** * ***** Masking position 9 Map Score: 2.52314 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 60 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 TGGGTATCTGATTGCTTTACGCATGGTGAA 1 24 0 ATTGCTTTAC 0.940188 -68 AAGGGCTGGAATTGATTTATGAAAGAAACC 13 38 1 ATTGATTTAT 0.714907 -48 CACTAACAACATTGCTTTACAATTAAAAAC 16 116 1 ATTGCTTTAC 0.940188 -51 ACTCATTCTAATTGCTTTATACACACTCTT 17 38 0 ATTGCTTTAT 0.935519 -178 GGGCGGAGAAATTTCTTAATATCTACAAAA 21 12 0 ATTTCTTAAT 0.850056 -104 TCCGCCCCGGATTGATTAATTATCAGAAAG 21 35 1 ATTGATTAAT 0.608744 -81 ATTCACATTTATTTCTTAATCTATGTATGA 22 122 0 ATTTCTTAAT 0.850056 -41 CATACACTTTATTTCTTCACAGAAAAGCCC 24 44 1 ATTTCTTCAC 0.868987 -144 AAAGTGAAGAATTTCTGTATGTAGAGTAAC 25 116 0 ATTTCTGTAT 0.65486 -185 GTTTATTATCATTTCTTCACAGTTCAGTCT 25 245 0 ATTTCTTCAC 0.868987 -56 ********** Masking position 6 Map Score: 4.83925 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 193 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 GTTCAAAAAAAAGCCCGCTCATTAGGCGGG 1 55 0 AAGCCCGCTC 0.950304 -37 AACCGTTATGATGTCGGCGCAAAAAACATT 2 31 0 ATGTCGGCGC 0.891298 -107 GCGGGCAAGATTGCCCGCGCGAGAAATCA 5 10 0 TTGCCCGCGC 0.994572 -95 GCGGGCAATCTTGCCCGCGCTTCTGCTCTC 5 22 1 TTGCCCGCGC 0.994572 -83 TCACCTAAAATCGCCCGCTCGCGGCATATC 6 47 0 TCGCCCGCTC 0.97992 -224 GCGTTATATGTTGCCGGCTCTGTTGCTTAT 20 22 0 TTGCCGGCTC 0.980507 -215 ********** Masking position 5 Map Score: 6.29293 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 246 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 13 TACGTATCTGAAATATATGTAACCTGACGATCAC 6 158 0 AATATGTAAC 0.965014 -113 CGCCAGAAGAAATTTGATTTATACGGAAGCG 8 8 0 AATATTTATC 0.823529 -77 CCCTTTATTCACTTTAATGTAAACCTTTACAAAA 20 69 0 ACTATGTAAC 0.89475 -168 TAAAAAAAAGAATTGGCTGTATCCTCCCGCTGTT 22 47 0 AATCTGTATC 0.917153 -116 TGAAGAAATAAAGTGTATGTAAGCTAGATGCATA 24 29 0 AATATGTAAC 0.965071 -159 CTAGAATCGAAATTAAATGTATTCATTGGTGGAG 24 154 1 AATATGTATC 0.969081 -34 ATAATAAACGAACTGAATGTATCCTTTTGGGAGG 25 266 1 AATATGTATC 0.972956 -35 ** * ****** * Masking position 11 Map Score: 1.46404 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 8 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 ACGGTTCTGGCAAATATTCTGAAATGAGCT 2 55 1 CAAATATTCT 0.883833 -83 CGTCAGGTTACATATATTTCAGATACGTAA 6 163 1 CATATATTTC 0.619085 -108 TTCTCAGATTCATATATTCCCATCTTCGCC 8 38 0 CATATATTCC 0.935697 -47 TTACTTTTTACAAACATTCTACAATACCAT 12 142 0 CAAACATTCT 0.812525 -53 TTTCGTGCATCAAATATGCCATGTCTGCGA 16 51 1 CAAATATGCC 0.949633 -116 TCGATTCTAGCACATATGCCCCGCTAAAAG 24 134 0 CACATATGCC 0.873761 -54 ATTTACCGAACGAATATTCCTTTTTTTCCT 25 21 0 CGAATATTCC 0.893264 -280 CTTTGTTGGACAAACATTCCTCAGAGTGCA 25 142 1 CAAACATTCC 0.949853 -159 ********** Masking position 6 Map Score: 2.38198 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 140 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 CATGGTGAATACACTGCCCGTT 1 2 0 ACACGCCCGT 0.981947 -90 GCAATCAGATACCCAGCCCGCCTAATGAGCG 1 39 1 ACCCGCCCGC 0.983178 -53 TTTGTTCAAAAAAAAGCCCGCTCATTAGGCG 1 57 0 AAAAGCCCGC 0.921628 -35 ATTTCATGCTACCCGGCACATAGCCAGTAGA 3 43 1 ACCCGCACAT 0.487652 -31 AAATCACCTAAAATCGCCCGCTCGCGGCATA 6 49 0 AAATGCCCGC 0.869603 -222 GCCTTCAAGAACAAGGCCATCCCTTTACCTA 6 196 0 ACAAGCCATC 0.733071 -75 AGCGGTTAAGACACCGCCCTTTCACGGCGGT 7 53 1 ACACGCCCTT 0.958698 -248 CTTTCTAAAAAAACTGCCGGCTGACGCTGGC 12 19 1 AAACGCCGGC 0.917293 -176 TTACATAAAAAAACTGCCAGCGTCAGCCGGC 12 34 0 AAACGCCAGC 0.949768 -161 GGTCTGATGCACACTGCCATTCAACCCTTTA 20 96 0 ACACGCCATT 0.851846 -141 ATAGGCTTTCACACTGCACACCGAAATCGTA 21 69 0 ACACGCACAC 0.894899 -47 TTTTTAAGAAAAACTGCACTCTGAGGAATGT 25 155 0 AAACGCACTC 0.877915 -146 **** ****** Masking position 1 Map Score: 8.35332 Number of sites scoring better than the average of aligned sites = 1165 Number in coding regions = 1075 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706