AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00750_ecoli_reg_300.orf -o00750_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 thrL 189 thr operon leader peptide #2 thrA 81 aspartokinase I, homoserine dehydrogenase I #3 ycaP 120 orf, hypothetical protein #4 serC 198 3-phosphoserine aminotransferase #5 rspA 205 starvation sensing protein #6 b1582 134 orf, hypothetical protein #7 pdxY 58 pyridoxal kinase 2 / pyridoxine kinase #8 tyrS 128 tyrosine tRNA synthetase #9 pdxH 58 pyridoxinephosphate oxidase #10 ydhA 178 orf, hypothetical protein #11 b1640 273 orf, hypothetical protein #12 gatD 47 galactitol-1-phosphate dehydrogenase #13 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #14 gatZ 28 putative tagatose 6-phosphate kinase 1 #15 gatY 197 tagatose-bisphosphate aldolase 1 #16 BIME96 27 BIME #17 b2097 184 orf, hypothetical protein #18 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #19 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #20 cvpA 165 membrane protein required for colicin V production #21 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #22 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #23 dedA 82 orf, hypothetical protein #24 usg 65 putative PTS system enzyme II A component #25 pdxB 98 erythronate-4-phosphate dehyrogenase #26 pdxK 104 pyridoxal/pyridoxine/pyridoxamine kinase #27 trxA 76 thioredoxin 1 #28 rhoL 140 rho operon leader peptide #29 rho 84 transcription termination factor Rho; polarity suppressor #30 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #31 metA 156 homoserine transsuccinylase #32 aceB 268 malate synthase A #33 aceA 29 isocitrate lyase #34 BIME206 22 BIME #35 aceK 27 isocitrate dehydrogenase kinase/phosphatase Motif number 1 CAGGAAACACAGAAAAAAGCCCGCACCTGACA 2 17 1 AAAAAAGCCC 0.949792 -65 CTTTGGTCGAAAAAAAAAGCCCGCACTGTCAG 2 43 0 AAAAAAGCCC 0.949792 -39 TCGGATTATTAGCAAAAAGCCGATGTTTTTAC 4 13 0 ACAAAAGCCG 0.919577 -186 GGAGTGATCACAAAAAAAGGCGTATATTTGCG 5 98 0 CAAAAAGGCG 0.935773 -108 GTATAAAGATCGAAAAAAGCCGGAGTGATCAC 5 119 0 CAAAAAGCCG 0.926163 -87 AGTGAAAGGCAAAAAAACGGCCTCCCGATAGG 15 76 0 AAAAAAGGCC 0.956471 -122 GATAACGATCACAAAAACGACAATATGAAAAT 15 117 0 AAAAAAGACA 0.77509 -81 CCGCGCATCAATAAAAATGGCGCTGAAAAAAT 20 59 0 AAAAAAGGCG 0.966512 -107 CGGTGAGAATAGCAAAAGGGCAGAGCCAGTGG 21 29 0 ACAAAAGGCA 0.934218 -41 TCTGTTGGGGGCAAAAATGGCATTATGCGTCC 22 86 1 GAAAAAGGCA 0.853194 -70 GTCCCCAAAGATAAAACTGGCATCGAACCAGG 22 114 1 AAAAACGGCA 0.818241 -42 TTGTCTTATGCCAAAAACGCCACGTGTTTACG 30 13 1 CAAAAAGCCA 0.930616 -227 CAGATATAAAAGCAAAACGCCACGTAAACACG 30 35 0 ACAAAAGCCA 0.924395 -205 CGTTTCGGAAATAAAAAAGGCACCCGAAGGTG 32 58 0 AAAAAAGGCA 0.968614 -211 * ***** **** Masking position 6 Map Score: 17.6295 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 239 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 2 TTCATTCTGACTGCAACGGGCAATATGTCTCT 1 16 1 CTGACGGGCA 0.985197 -174 ATGAGTAAAACCGTTGAGGGCAAAAATGTGGC 4 67 0 CCGTAGGGCA 0.971315 -132 GCTGGTACTCCTGATTCTGGCACTTTATTCTA 8 37 1 CTGTCTGGCA 0.9695 -92 TATGTCTCTTTCGCATCTGGCGAAAAGTCGTG 8 67 1 TCGACTGGCG 0.637979 -62 TATGTTTACACCGCATCCGGCATAAAAACACG 15 25 1 CCGACCGGCA 0.900437 -173 AATCCTGGTCGTTACGGGCGAGTTTTTCCA 17 165 0 TCGTCGGGCG 0.932052 -20 TATGCCTTTGCGGCATCGGGCAATGCGT 20 7 0 CGGACGGGCA 0.946458 -159 CCCTGTCATCCTGTTCGGGGCGCATTCTAACA 20 124 0 CTGTGGGGCG 0.969838 -42 TAACTGATAAGGGCAGGGCCACTGG 21 4 1 CTGTAGGGCA 0.973124 -66 CATTCATGGTCTGTTGGGGGCAAAAATGGCAT 22 77 1 CTGTGGGGCA 0.975054 -79 GAAACTTTACCTGATTCTGGCAGTCAAATCGG 26 40 0 CTGTCTGGCA 0.9695 -65 TTCTCTGCTCCTGATGAGGGCGCTAA 35 12 1 CTGTAGGGCG 0.967518 -16 *** * ****** Masking position 11 Map Score: 14.9198 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 797 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 TTGTCAACCATTCACAGCGCAAATATACGC 5 81 1 TTCACAGCGC 0.782471 -125 AACTGAATTTTTCTTACCGCGTCTGCCGTT 10 21 1 TTCTTACCGC 0.901178 -158 TTGCCGGTCCTTCTCTCCGGCTGTAGCGCC 10 138 1 TTCTCTCCGG 0.886938 -41 GAATGACCGATTTTTACCGTTGGTAGTAAA 11 187 0 TTTTTACCGT 0.779436 -87 TTTTTACCTGAGGGGGAGGT 12 1 1 TTTTTACCTG 0.457148 -47 GTTTTTTCCTTGTTAAATGGC 14 18 0 TTTTTTCCTT 0.513243 -11 GCCACGTATGTTTACACCGCATCCGGCATA 15 19 1 TTTACACCGC 0.86681 -179 TTTTTTGCCTTTCACTCCTCGAATAATTTT 15 92 1 TTCACTCCTC 0.75743 -106 CGCGGTCAAGTTTTCACCGCAAAGGTATTT 17 77 0 TTTTCACCGC 0.963194 -108 TTTGGATGTTTTTTCAGCGTTTTCTGTTGG 17 132 0 TTTTCAGCGT 0.848604 -53 GTTGAATATTTTTTCAGCGCCATTTTTATT 20 52 1 TTTTCAGCGC 0.899952 -114 CCTTTTGCTATTCTCACCGTAACGAATCAG 21 42 1 TTCTCACCGT 0.963266 -28 TTAATTTTTTCTCCTTGCCGATGATC 26 89 0 TTTTCTCCTT 0.829518 -16 TTTCTCTCCTTTTAGTCATTC 31 2 1 TTCTCTCCTT 0.886675 -155 CCTTGAAACTTTCTCACCTTCAACATGCAG 31 54 1 TTCTCACCTT 0.927452 -103 ATTCTCTGCTCCTGATGAGGG 35 2 1 TTCTCTGCTC 0.811883 -26 ********** Masking position 2 Map Score: 13.2392 Number of sites scoring better than the average of aligned sites = 1144 Number in coding regions = 1030 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 TCTGTCTGTGCGCTATGCCTATATTGGTTAAA 1 142 0 CGCTGCCTAT 0.939361 -48 GGTTGTTACCTCGTTACCTTTGGTCGAAAAA 2 61 0 CTCTACCTTT 0.626514 -21 CTATCACCGCCGCCATGCCGATGAACTGTTGA 3 60 1 CGCTGCCGAT 0.969692 -61 TATTATGTCGCCCTATAACTATACATGATGTC 6 99 1 CCCTAACTAT 0.815537 -36 AATAGCGTCACCCACTGACAATCCGTAAAGAA 9 33 1 CCCTGACAAT 0.940009 -26 GCAATACGCCCTCCCTAACGTTCCAAGTGTAA 10 49 0 CTCTAACGTT 0.749426 -130 GGAGGTTATCCCCCTTAACAATCAGGAGTTTT 12 25 1 CCCTAACAAT 0.893936 -23 ATCCCTCTGTAACAATAAAAAGGACT 13 5 1 CTCTAACAAT 0.895819 -26 ATGTAAGGTACGCGATGACAATACCACTTAAT 17 35 1 CGCTGACAAT 0.962254 -150 AAAACTTGACCGCGCTAACATTTTTTCTGATG 17 93 1 CGCTAACATT 0.814895 -92 AATAGCAAAGCTCCCTGCCAATGTTACAGCAG 24 28 0 CTCTGCCAAT 0.948766 -38 TTAATTTTTTCTCCTTGCCGATGATCCTCATC 26 83 0 CTCTGCCGAT 0.952522 -22 ATCTTAATGCCGCGCTGGCGATGTTAGGAAAA 30 69 1 CGCTGGCGAT 0.880036 -171 *** ******* Masking position 6 Map Score: 9.30361 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 588 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 CCCGTTGCAGTCAGAATGAAAAGCT 1 5 0 TCAGAAGAAA 0.683289 -185 GGCATAGCGCACAGACAGATAAAAATTACAG 1 155 1 ACAGACGATA 0.854561 -35 ATACAAGTATAAAGATCGAAAAAAGCCGGAG 5 126 0 AAAGATGAAA 0.733007 -80 TAAAGGCGCTACAGCCGGAGAGAAGGACCGG 10 141 0 ACAGCCGAGA 0.890642 -38 TGCGCAAACGTCAGATTGAAAAAGGATGAAC 11 252 1 TCAGATGAAA 0.876515 -22 AAAACATCCAAAAGATGGAAAAACTCGCCCG 17 150 1 AAAGATGAAA 0.733007 -35 TTAAAACATAACAGCCCGAAACTTTGGATAA 22 39 0 ACAGCCGAAA 0.975033 -117 CGAACCAGGTTCAGACAGAAAGGTCCCTA 22 137 1 TCAGACGAAA 0.943288 -19 TACGTTGGCTACAGCCTGAAATGTTCCGAGC 23 21 0 ACAGCCGAAA 0.975033 -62 CAACGTAGTTACAGCCTGAAAGATGACGAGT 23 45 1 ACAGCCGAAA 0.975033 -38 CATTAAGATTACAGATATAAAAGCAAAACGC 30 47 0 ACAGATTAAA 0.58405 -193 ****** **** Masking position 3 Map Score: 8.28512 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 311 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 AAAAAGCCCGCACCTGACAGTGCGGGCTTTTT 2 30 1 CACCTGAGTG 0.980592 -52 ATCGCTGGTACTCCTGATTCTGGCACTTTATT 8 34 1 CTCCTGACTG 0.947506 -95 GCGTATTGCCCTCCAGACCAGGAAAGTCTTCG 10 72 1 CTCCAGAAGG 0.83964 -107 TTTTTACCTGAGGGGGAGGTTATCCC 12 5 1 TACCTGAGGG 0.913015 -43 AAAAACTCCTGATTGTTAAGGGGGATA 12 31 0 CTCCTGAGTT 0.771189 -17 AAAAAACGGCCTCCCGATAGGGAAGCCGTAGC 15 65 0 CTCCCGAGGG 0.976116 -133 ACCGAAACTTTACCTGATTCTGGCAGTCAAAT 26 43 0 TACCTGACTG 0.76768 -62 AGCGACGGGGCACCCGAACATGAAATTCCC 28 9 0 CACCCGAATG 0.948465 -132 ATAAAAAAGGCACCCGAAGGTGCCTGAGGTAA 32 48 0 CACCCGAGTG 0.854152 -221 AAAATTTATTCACCTGCTGAGGTACGTTTCGG 32 82 0 CACCTGCAGG 0.866109 -187 ATTCTCTGCTCCTGATGAGGGCGCTAA 35 9 1 CTCCTGAAGG 0.966905 -19 ******* *** Masking position 4 Map Score: 7.70657 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 366 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 7 GTACTCTGTAATTTTTATCTGTCTGTGCGCTATGC 1 156 0 ATTTTCTGTG 0.77884 -34 GGCTTTTTTCTGTGTTTCCTGTACGCG 2 3 0 TTTTCCTGTG 0.964279 -79 ACAGGAATAATGTATTACCTGTGGTCGCAATCGAT 4 135 1 TTTTCCTGTT 0.806158 -64 AATTCATTCCCTGTATGAATGATTAAA 6 3 1 TCTTCCTGTG 0.984437 -132 CCCGAAGACTTTCCTGGTCTGGAGGGCAATACGCC 10 71 0 TCTGTCTGGG 0.796863 -108 TCGCGTACCTTACATTACCTGTCATGAAGGAATTA 17 15 0 TCTTCCTGTT 0.906936 -170 ATGTTTTTTCAGCGTTTTCTGTTGGCTCGATTCAT 17 122 0 ACTTTCTGTG 0.891916 -63 AAATAGTTGCCCTGTCAGACTTGCAGGC 18 77 0 TGTGCCTGTG 0.883945 -18 CGCAAACGTTTTCTTTTTCTGTTAGAATGCGCCCC 20 105 1 TCTTTCTGTG 0.97081 -61 ATGTGCAACATTCATGGTCTGTTGGGGGCAAAAAT 22 69 1 TCTGTCTGTG 0.954193 -87 GTTTGTGTTACCTGTATGAGACGAGAGT 25 81 0 TTTTCCTGTG 0.964279 -18 * * ** ***** * Masking position 10 Map Score: 7.04388 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 170 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 TAATTTACTCACGGCAGGTAACCAGTTCAG 1 83 0 ACGGCAGGTA 0.874715 -107 TTTAGTCGTACGGAAAGCGCGCAATAATA 3 10 1 ACGGAAAGCG 0.916049 -111 GTTAATAGCAACGCAACGTGGTGAGGGGAA 4 179 1 ACGCAACGTG 0.903323 -20 TTCATGCATCACGACAAGCGATGCAAGGAA 5 180 1 ACGACAAGCG 0.872038 -26 TCCACTGCGGACGCAAAACGTACCAGGAGG 6 53 1 ACGCAAAACG 0.643901 -82 TCCAAGTGTAACGGCAGACGCGGTAAGAAA 10 30 0 ACGGCAGACG 0.906613 -149 TCACCATGAAACGCCACGCAAGCATCCCTC 11 26 1 ACGCCACGCA 0.948444 -248 TCCTTGTTAAATGGCAGGTGCG 14 3 0 ATGGCAGGTG 0.694126 -26 TAAAAACTGGACGCCCGGCGTGAGTCATGC 28 40 1 ACGCCCGGCG 0.934666 -101 TTAAGATAAAACGGGAAGCGTTGGAAATTA 28 121 0 ACGGGAAGCG 0.864876 -20 TATGCCAAAAACGCCACGTGTTTACGTGGC 30 19 1 ACGCCACGTG 0.974174 -221 TAAAAGCAAAACGCCACGTAAACACGTGGC 30 31 0 ACGCCACGTA 0.892785 -209 ********** Masking position 1 Map Score: 6.16059 Number of sites scoring better than the average of aligned sites = 1771 Number in coding regions = 1689 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 9 CATCGGCATGGCGGCGGTGATAGCGCCTTTG 3 52 0 GCGGGGTGAT 0.962664 -69 ATCGAAAAAAGCCGGAGTGATCACAAAAAAA 5 112 0 GCCGAGTGAT 0.813212 -94 TAAGTGGAAAGGGGGAGTGAGAAATCACTCC 7 16 1 GGGGAGTGAG 0.951802 -43 ATAAAAACCAGGGGGAGTGATTTCTCACTCC 7 29 0 GGGGAGTGAT 0.986729 -30 TTTACCTGAGGGGGAGGTTATCCCCCTTAAC 12 13 1 GGGGGGTTAT 0.966086 -35 GGGGTGGTGTTGTTCGTATAA 16 17 0 GGGGGGTGTT 0.978461 -11 TGGTCGTTACGGGCGAGTTTTTCCATCTTTT 17 159 0 GGGCAGTTTT 0.749899 -26 CGTTCACAGTGGGGAAGTTTTCGGATCCATG 32 233 1 GGGGAGTTTT 0.947689 -36 **** ****** Masking position 8 Map Score: 3.93709 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 190 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 CGGTGATAGCGCCTTTGAGATAAAACCCGT 3 39 0 GCCTTTGAGA 0.747937 -82 AATGAGTAAAACCGTTGAGGGCAAAAATGT 4 70 0 ACCGTTGAGG 0.927259 -129 TAACGACTGCACCTTTGCCGGTACACGACT 8 92 0 ACCTTTGCCG 0.951743 -37 CCTTTTAAATACCTTTGCGGTGAAAACTTG 17 71 1 ACCTTTGCGG 0.985804 -114 TGCCTTCGCTGAGGGTGCCGG 18 2 1 GCCTTCGCTG 0.897108 -93 GACTTTTTATGCCTTTGCGGCATCGGGCAA 20 16 0 GCCTTTGCGG 0.988216 -150 GCAACAACAACCGTTGCTGACT 34 10 1 ACCGTTGCTG 0.940439 -13 ********** Masking position 5 Map Score: 2.85958 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 523 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 11 TGAAAAATCTCCTGTTCACCATGAAACG 11 9 1 CTCCTGTTCA 0.872819 -265 GCAAGCATCCCTCATGGTCAAAGTATATGG 11 43 1 CTCATGGTCA 0.921491 -231 GGGGGATAACCTCCCCCTCAGGTAAAAA 12 9 0 CTCCCCCTCA 0.917713 -39 TTTTGCTATTCTCACCGTAACGAATCAGCG 21 44 1 CTCACCGTAA 0.881484 -26 TCTCTTCTTCATGCTCTCTGC 24 2 1 CTCTTCTTCA 0.829997 -64 GCCGATGATCCTCATCGTAATCCAACCGAA 26 69 0 CTCATCGTAA 0.88356 -36 TTGAAACTTTCTCACCTTCAACATGCAGGC 31 56 1 CTCACCTTCA 0.940279 -101 CGTGCAGCTCCTCGTCATGGATCCGAA 32 252 0 CTCCTCGTCA 0.975647 -17 ********** Masking position 10 Map Score: 2.76057 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 169 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 GACATAGAATAAAGTGCCAGAATCAGGAGT 8 43 0 AAAGTGCCAG 0.786073 -86 GCCTTCGCTGAGGGTGCCGGTCTGGCACCC 18 12 1 AGGGTGCCGG 0.972682 -83 GTTGCAAGTCAGGGTGCCAGACCGGCACCC 18 23 0 AGGGTGCCAG 0.989835 -72 AATCCTGCAAAGTCTGCCTGCAAGTCTGAC 18 62 1 AGTCTGCCTG 0.941687 -33 TCTGCCTGCAAGTCTGACAGGGCAACTATT 18 74 1 AGTCTGACAG 0.8361 -21 CGCCCCGAACAGGATGACAGGGCGTAAAAT 20 134 1 AGGATGACAG 0.839512 -32 AATCTTCGCAAGTATGCCTGGCCGCGAGAT 25 30 1 AGTATGCCTG 0.912587 -69 TAACCGGACAAGTGTGCCATAATCTCGCGG 25 51 0 AGTGTGCCAT 0.857525 -48 AAGGCACCCGAAGGTGCCTGAGGTAAGGTG 32 44 0 AAGGTGCCTG 0.922774 -225 ********** Masking position 5 Map Score: 3.57166 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 402 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 13 CTGTTGACTATGCTTTTAGCGGATAAACCAC 3 85 1 TGCTTTAGCG 0.950997 -36 TTTTATGCTCTTAACGTGGTTTATCC 3 105 0 TGCTCTAACG 0.958788 -16 GCCACATTTTTGCCCTCAACGGTTTTACTCA 4 67 1 TGCCCTAACG 0.829115 -132 AGCTGACACTTCCTCTTATCTTATTGATAAA 5 25 0 TCCTCTATCT 0.705773 -181 GCAAAAATCTTGCTTTAATCGCTGGTACTCC 8 17 1 TGCTTTATCG 0.924507 -112 GTGCTCTGAGATGTGGCTTAAC 19 2 1 TGCTCTAGAT 0.892329 -35 CTCTTCTTCATGCTCTCTGCTGTAACATTGG 24 12 1 TGCTCTTGCT 0.890921 -54 CGTGGCGTTTTGCTTTTATATCTGTAATCTT 30 43 1 TGCTTTATAT 0.595927 -197 AATGCATGCTCTCAGAGAAAATTATTA 30 223 0 TGCTCTAGAG 0.951044 -17 AGGATCGTTGTGCTCTTTTCGTTCAGCACAA 32 201 0 TGCTCTTTCG 0.923469 -68 ****** **** Masking position 6 Map Score: 1.63618 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 284 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 AACATAAATCCATTTTATCAATAAGATAAG 5 12 1 CATTTTATCA 0.745045 -194 AAATAGAATACCTTTTGTCAGCTGACACTT 5 45 0 CCTTTTGTCA 0.967429 -161 TTCTATTTCATCTTTTGTCAACCATTCACA 5 67 1 TCTTTTGTCA 0.79393 -139 TGTAGAATCACCTTTAATCATTCATACAGG 6 20 0 CCTTTAATCA 0.960932 -115 GGCTGTAGCGCCTTTAATCAGCTGGTTGAG 10 156 1 CCTTTAATCA 0.960932 -23 ACCACGAAGACCTTTATTCAGAAGGGAAAG 30 182 0 CCTTTATTCA 0.906843 -58 TTTCTCTCCTTTTAGTCATTCTTATATT 31 9 1 CTTTTAGTCA 0.856801 -148 ********** Masking position 10 Map Score: 1.44781 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 116 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 15 AAAAAAAAAGCCCGCACTGTCAGGTGCGGG 2 36 0 CCCGCACTGT 0.883459 -46 AATATAAACACCCTCCTGGTACGTTTTGCG 6 64 0 CCCTCCTGGT 0.954091 -71 GAGAAATCACTCCCCCTGGTTTTTATACAG 7 34 1 TCCCCCTGGT 0.948922 -25 ACGCAAGCATCCCTCATGGTCAAAGTATAT 11 41 1 CCCTCATGGT 0.968636 -233 AATCGGTCATTCCGCATGGTATTCACGAAA 11 205 1 TCCGCATGGT 0.965038 -69 TTGCCGATGATCCTCATCGTAATCCAACCG 26 71 0 TCCTCATCGT 0.878988 -34 TCCGAAAACTTCCCCACTGTGAACGAAGGA 32 228 0 TCCCCACTGT 0.862592 -41 ********** Masking position 10 Map Score: 0.821456 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 139 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789