AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_hpyl_reg_100.orf -o00230_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: HP1472 30 type IIS restriction enzyme M protein (mod) HP0617 34 aspartyl-tRNA synthetase (aspS) Input sequences: #1 HP0073 300 urease alpha subunit (ureA) (urea amidohydrolase) #2 HP0104 154 2',3'-cyclic-nucleotide 2'-phosphodiesterase (cpdB) #3 HP0194 214 triosephosphate isomerase (tpi) #4 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #5 HP0198 66 nucleoside diphosphate kinase (ndk) #6 HP0252 300 outer membrane protein (omp7) #7 HP0255 99 adenylosuccinate synthetase (purA) #8 HP0270 204 H. pylori predicted coding region HP0270 #9 HP0275 36 ATP-dependent nuclease (addB) #10 HP0277 56 ferredoxin #11 HP0322 141 poly E-rich protein #12 HP0364 205 ribonucleoside diphosphate reductase, beta subunit (nrdB) #13 HP0408 165 H. pylori predicted coding region HP0408 #14 HP0497 228 sodium- and chloride-dependent transporter #15 HP0500 57 DNA polymerase III beta-subunit (dnaN) #16 HP0572 57 adenine phosphoribosyltransferase (apt) #17 HP0573 51 H. pylori predicted coding region HP0573 #18 HP0577 73 methylene-tetrahydrofolate dehydrogenase (folD) #19 HP0584 81 flagellar switch protein (fliN) #20 HP0585 228 endonuclease III (nth) #21 HP0616 77 chemotaxis protein (cheV) #22 HP0680 171 ribonucleoside-diphosphate reductase 1 alpha subunit (nrdA) #23 HP0717 68 DNA polymerase III gamma and tau subunits (dnaX) #24 HP0718 207 conserved hypothetical integral membrane protein #25 HP0736_HP0737 146 HP0736: phosphoserine aminotransferase (serC), HP0737: conserved hypothetical integral membrane protein #26 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #27 HP0742 64 phosphoribosylpyrophosphate synthetase (prsA) #28 HP0777 107 uridine 5'-monophosphate (UMP) kinase (pyrH) #29 HP0830 58 amidase #30 HP0832 91 spermidine synthase (speE) #31 HP0833 76 H. pylori predicted coding region HP0833 #32 HP1112 109 adenylosuccinate lyase (purB) #33 HP1180 300 pyrimidine nucleoside transport protein (nupC) #34 HP1198 223 DNA-directed RNA polymerase, beta subunit (rpoB) #35 HP1215 35 H. pylori predicted coding region HP1215 #36 HP1217 48 H. pylori predicted coding region HP1217 #37 HP1218 119 glycinamide ribonucleotide synthetase (purD) #38 HP1295 22 ribosomal protein S11 (rps11) #39 HP1297 78 ribosomal protein L36 (rpl36) #40 HP1300 42 preprotein translocase subunit (secY) #41 HP1318 34 ribosomal protein L4 (rpl4) #42 HP1319 36 ribosomal protein L3 (rpl3) #43 HP1320 164 ribosomal protein S10 (rps10) #44 HP1386 70 D-ribulose-5-phosphate 3 epimerase (rpe) #45 HP1460 147 DNA polymerase III alpha-subunit (dnaE) #46 HP1470 67 DNA polymerase I (polA) #47 HP1471 65 type IIS restriction enzyme R protein (BCGIB) #48 HP1483 26 gerC2 protein (gerC2) #49 HP1490 103 hemolysin Motif number 1 TCACTCCAATTTTAATTCTCATTTTTTTGCGAGTT 1 65 1 TTTAATTTTT 0.800851 -236 TAGAAGTGCGTTTAATACCCCTTTAGAATTTATAA 1 108 0 TTTAATTTTA 0.846885 -193 CTAATAACGATTTTATAGCGCTTCAAAGATATAAC 1 140 1 TTTTATTTCA 0.773494 -161 TACGATGGTTTTTGATTGGAATTTAACGCTTATGG 2 71 0 TTTGATTTTA 0.698643 -84 TTCTACTACATTTGAAATAATTTTTCTTATAAACA 3 74 1 TTTGAATTTT 0.715542 -141 TTGAATTGAATTTTTTCTCAATTTAGGTTTTGTTT 3 104 0 TTTTTTTTTA 0.785722 -111 AAGGGTAATATTTTAAAAAATTTTTGTATAATCAA 5 22 1 TTTTAATTTT 0.917714 -45 ATAAAGAGGCTTTTTACTTTTTTTTTGGTATTCTA 7 27 1 TTTTTATTTT 0.799142 -73 AATTCTCGCCTTTAAACCCGCTTTTTCATTGGTTA 8 17 0 TTTAAATTTT 0.857171 -188 AAAATAGCGGTTTTTACAAGTTTTATGCAACAACC 8 120 0 TTTTTATTTA 0.845494 -85 TATTTTATTTCCTTTTTTGTATCACTG 9 20 0 TTTTATTTTT 0.881981 -17 ATTTTAAGCTAATTTAGAGTAAAAGT 10 2 1 TTTTAATTTA 0.938799 -55 AGCCTATCCATTTTATCGCTTTTTTTAAATCTTTT 11 80 0 TTTTATTTTT 0.881981 -62 GTATTTTAGCTTTTTAATCCTTTAAAAATACTGAA 12 63 1 TTTTTATTAA 0.562911 -143 AAACTCCAAATTTTAAAAAACTTCAATTTTTCAGT 12 92 0 TTTTAATTCA 0.835966 -114 AAATTTGGAGTTTTTTCTGGCTTTTAGGGGGTTTT 12 114 1 TTTTTTTTTT 0.727222 -92 TTTTAGGGGGTTTTAAATTCTTTTAAGGTATTCTA 12 135 1 TTTTAATTTA 0.938799 -71 ATTGAGATAGTTTTAAGGAAATTAAGGAACAAA 12 183 1 TTTTAATTAA 0.783084 -23 AATCAATGCGTTTAATTTCTGTTTTCAATATTGAC 13 124 1 TTTAATTTTT 0.800851 -42 TTTAGGTATTTTTAAAGTGGGTTTTTTCTTAAATC 14 102 1 TTTAAATTTT 0.857171 -127 GCTGTATTAGTTTTTAAAATCTTTAAAGATCTTAA 14 137 0 TTTTTATTTA 0.845494 -92 TTTGATTTCCTTTAATATAACGGAT 16 43 0 TTTGATTTAA 0.353004 -15 CAAACTAGGTTTTTATTCCATTAAACGCATGATT 18 10 1 TTTTTATTAA 0.562911 -64 GAGAAAGCGTTTTTTAAGGGCTTCATCGCAGTTAG 20 64 0 TTTTTATTCA 0.645145 -165 CCTAATTTAGTTTAAAAGGTTTTTACAAAC 21 6 0 TTTAAATTTA 0.891942 -72 GCATTTAATCTTTGATAGGGCTTTAGGGGAAAATA 21 52 1 TTTGATTTTA 0.698643 -26 TGAGAATAAGTTTTAAAGTTTTTTAATTTTTTTAT 22 42 0 TTTTAATTTA 0.938799 -130 AAACAAACGATTTAATTCAAATTTAAGGAAAAATT 22 147 1 TTTAATTTTA 0.846885 -25 TGTATCATCATTTAATTTTTATTTATAAAGGTCGT 24 88 1 TTTAATTTTA 0.846885 -120 GTGTTGGTAGTTTTTAGCTTATTTTGAGTGAAAGG 24 173 1 TTTTTATTTT 0.799142 -35 AATGCCATGATTTAAAAAGAATTTAAGGCAATGA 25 10 0 TTTAAATTTA 0.891942 -137 CATTTTAGCATTTTATTTGCATTAAAAAGCGATTT 25 41 1 TTTTATTTAA 0.707519 -106 TAAGGCTTAATTTTAAGCACGTTTTAGTATGATAA 25 86 1 TTTTAATTTT 0.917714 -61 TTTTAAGAAAATTCAAAAGCCTTTT 26 1 1 TTTTAATTCA 0.835966 -77 CTACAATTGATTTTAATTCATTTTAGGGAGTGTAA 27 37 1 TTTTAATTTA 0.938799 -28 CAATCACAAGTTTTATTAAAATTTTATTAATTAAT 28 72 1 TTTTATTTTT 0.881981 -36 TTACAAAAAATTTAATGGTAGTTTAACATGCTTAG 29 24 0 TTTAATTTTA 0.846885 -35 CTTTTTTATCGCTTCAATTTAATCAA 31 2 1 TTTTTTTTCA 0.549191 -75 TTTATGTTACTTTAAAGGGGTTTAAAGAATCAAGG 32 59 0 TTTAAATTAA 0.660165 -51 TTTAATGTAATTTTAATGGATTTTTAAGAAAGGTT 33 64 1 TTTTAATTTT 0.917714 -237 ATGATTTTGATTTAAACTTCATTTAATATCCGTTT 33 205 1 TTTAAATTTA 0.891942 -96 TTAATATCCGTTTAATCTTTTTTTTAGCAAAACTA 33 227 1 TTTAATTTTT 0.800851 -74 GGTTCTAAAGTTTAAAGATCCTTTTGCAATGCTTA 34 148 1 TTTAAATTTT 0.857171 -76 ATCAAACCCTTTATATTATATTCAATGTATGGTT 41 11 0 TTTATATTCA 0.494517 -24 TTTTTATATTTCCTTATAAAAAGGAAG 43 3 1 TTTATATTAT 0.335042 -162 TTTTTAGGGCTTTTTAGAGATTTTTACTTCCTTTT 43 29 0 TTTTTATTTT 0.799142 -136 TATTTTATTGTTTTATTCTGTTTTTTAGTAACGGA 43 114 1 TTTTATTTTT 0.881981 -51 TTTTTATTATTTTTAATGCTATTTTAGGAGTTCAT 45 12 0 TTTTAATTTT 0.917714 -136 ATAACCACCATTTTAAAATAATTCACCACTAAATA 45 57 1 TTTTAATTCA 0.835966 -91 AATTCTGAGATTTTATATATTTTATATTTATCGTT 49 60 1 TTTTATTTAT 0.63752 -44 ****** **** Masking position 12 Map Score: 61.6969 Number of sites scoring better than the average of aligned sites = 1899 Number in coding regions = 1403 Number in noncoding regions = 496 Number of orfs with sites within 600 bp upstream = 293 Fraction of orfs with sites within 600 bp upstream = 0.0470607 Motif number 2 AAAATGTAAATTTTAAACAATAGCCCCTTT 3 137 0 TTTTAAACAA 0.707517 -78 AATTTACATTTTTTAAACGCTATTAGATAT 3 155 1 TTTTAAACGC 0.774998 -60 AAAAATATTTTAAGGGTAATATTTTAA 5 8 1 TTTTAAGGGT 0.795473 -59 TACAAAAATTTTTTAAAATATTACCCTTAA 5 20 0 TTTTAAAATA 0.708619 -47 AATTGACATCTTTTAAGCAAAATGTTATAA 6 172 0 TTTTAAGCAA 0.848305 -129 AACTTTCTAATTTTAAGATAATCATTCTTA 6 233 0 TTTTAAGATA 0.84899 -68 GCTCTTTTTAGGGCTTATAAAGAG 7 5 1 TTTTTAGGGC 0.848429 -95 ATCTACTTTGTTTTAAGGATAATATTTT 7 82 1 TTTTAAGGAT 0.706223 -18 TCCTGAAAAATTTTAAGCTCAATTCTCGCC 8 42 0 TTTTAAGCTC 0.889085 -163 AAAAATATCGTTTTAAAGGTTGTCCCACGC 8 71 1 TTTTAAAGGT 0.62723 -134 AAACCGCTATTTTTTAGCTCAAAATTTAAA 8 142 1 TTTTTAGCTC 0.849301 -63 ATTTTAAGCTAATTTAGAGTA 10 2 1 TTTTAAGCTA 0.901081 -55 TTTATCGCTTTTTTTAAATCTTTTATTATA 11 74 0 TTTTTAAATC 0.600742 -68 TTTTCAGTATTTTTAAAGGATTAAAAAGCT 12 70 0 TTTTAAAGGA 0.796509 -136 AAACTCCAAATTTTAAAAAACTTCAATTTT 12 97 0 TTTTAAAAAA 0.595168 -109 TTTTAAATTCTTTTAAGGTATTCTAACAAG 12 145 1 TTTTAAGGTA 0.901081 -61 ATTGAGATAGTTTTAAGGAAATTAAGGAAC 12 183 1 TTTTAAGGAA 0.848305 -23 TATTGTATAATTTTAAGAAAATTTCATTAT 14 28 0 TTTTAAGAAA 0.775322 -201 TGCTCTGTATTTTTTAGGTATTTTTAAAGT 14 90 1 TTTTTAGGTA 0.864946 -139 TTTTTAGGTATTTTTAAAGTGGGTTTTTTC 14 100 1 TTTTTAAAGT 0.421991 -129 CTGTATTAGTTTTTAAAATCTTTAAAGATC 14 141 0 TTTTAAAATC 0.681561 -88 AAAAGCGTTCTTTTAYGCTATAATTAAGAC 15 11 1 TTTTAYGCTA 0.901081 -47 TAAAATATCCTTTTTAGCGAAACGATGTAA 17 27 0 TTTTTAGCGA 0.86415 -25 AGAAAGCGTTTTTTAAGGGCTTCATCGCAG 20 68 0 TTTTAAGGGC 0.888413 -161 TGTAAAAACCTTTTAAACTAAATTAGGGTA 21 14 1 TTTTAAACTA 0.797608 -64 TGAGAATAAGTTTTAAAGTTTTTTAATTTT 22 47 0 TTTTAAAGTT 0.628818 -125 AATCGTTTGTTTTTTAAATTTGGAATTGTA 22 129 0 TTTTTAAATT 0.423649 -43 CCTAAATGAGTTTTAAGGATTACAATCAAT 23 49 1 TTTTAAGGAT 0.706223 -20 AAAACCCCATTTTTTAGCGCTCTTAGTGGC 24 35 0 TTTTTAGCGC 0.848429 -173 AAAAATGGGGTTTTTAAATTTTCGCGCAAA 24 51 1 TTTTTAAATT 0.423649 -157 AACCCTAAAATTTTAAAATACCATTTTTGA 24 127 1 TTTTAAAATA 0.708619 -81 GTGTTGGTAGTTTTTAGCTTATTTTGAGTG 24 173 1 TTTTTAGCTT 0.733554 -35 CCTTAAATTCTTTTTAAATCATGGCATTTT 25 17 1 TTTTTAAATC 0.600742 -130 TAAGGCTTAATTTTAAGCACGTTTTAGTAT 25 86 1 TTTTAAGCAC 0.831109 -61 TTTTAAGAAAATTCAAAAGC 26 1 1 TTTTAAGAAA 0.775322 -77 CAAAAGCCTTTTTTTAGGTAAATATAGATA 26 24 1 TTTTTAGGTA 0.864946 -54 ATTGCAATCGTTTTTAGGGAGTTTGATC 26 60 1 TTTTTAGGGA 0.86415 -18 GAAAGGGTGTTTTTAAGCAAGATTAGGTTA 28 42 1 TTTTAAGCAA 0.848305 -66 TAATTTAGATTTTTTAGCTAGCATGTTAGC 30 24 1 TTTTTAGCTA 0.864946 -68 CTTAGCTTACTTTTTAACAATATCCATGCC 30 64 0 TTTTTAACAA 0.62583 -28 CCCATTTTGATTTTAAGGATTGTCG 32 95 1 TTTTAAGGAT 0.706223 -15 TTTAATGGATTTTTAAGAAAGGTTTTTGTA 33 75 1 TTTTAAGAAA 0.775322 -226 TTTAATCTTTTTTTTAGCAAAACTAAACTA 33 237 1 TTTTTAGCAA 0.797199 -64 GGCCTTTCTGTTTTTAAGTC 34 1 0 TTTTTAAGTC 0.709147 -223 TTTTTAAATCTGCCCCTAAG 37 1 1 TTTTTAAATC 0.600742 -119 TTTTTAGGGCTTTTTAGAGATTTTTACTTC 43 34 0 TTTTTAGAGA 0.796962 -131 ACTTTTGCTATTTTTAGGGCTTTTTAGAGA 43 44 0 TTTTTAGGGC 0.848429 -121 ATAACCACCATTTTAAAATAATTCACCACT 45 57 1 TTTTAAAATA 0.708619 -91 AATAAAGAGTTTTTTAAAGAGCGATAGGTA 45 96 1 TTTTTAAAGA 0.625491 -52 AAGGGGTTTTAAGCGCGCTAGCTTGT 46 7 1 TTTTAAGCGC 0.888413 -61 AAGGCTTGATTTTTAAAGTTAGGCTTAATC 49 19 1 TTTTAAAGTT 0.628818 -85 ********** Masking position 6 Map Score: 56.9937 Number of sites scoring better than the average of aligned sites = 2015 Number in coding regions = 1681 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 275 Fraction of orfs with sites within 600 bp upstream = 0.0441696 Motif number 3 TGTCTTCAAGGAAAAACACTTTAAGAATAGGAGA 1 272 1 GAAACCTTTA 0.716933 -29 GCTATTGTTTAAAATTTACATTTTTTAAACGCTA 3 143 1 AAAATCATTT 0.39826 -72 CTTAATCCATAAAAGAAACTTTCTAATTTTAAGA 6 245 0 AAAAACTTTT 0.852843 -56 AAAAAAAGTAAAAAGCCTCTTTATAAGCCCTAAA 7 17 0 AAAACCTTTT 0.985984 -83 TTCTCGCCTTTAAACCCGCTTTTTCATTGGTTAT 8 16 0 TAAACCTTTT 0.840811 -189 TAAAACTTGTAAAAACCGCTATTTTTTAGCTCAA 8 130 1 AAAACCTATT 0.810989 -75 AAATTTAAAAGAAAAACCCTTTATTGTAAGCTGT 8 163 1 GAAACCTTTT 0.954886 -42 ATTATAATCAAAAATCCACTTGGTTGGTTGTTTT 11 46 0 AAAACCTTGT 0.952416 -96 GATTTAAGAAAAAACCCACTTTAAAAATACCTAA 14 103 0 AAAACCTTTA 0.893883 -126 TCTGTTAAAATATCCTTTTTAGCGAAACGA 17 32 0 AAAATCTTTT 0.846847 -20 TGAAGCCCTTAAAAAACGCTTTCTCTCTTTTGGT 20 74 1 AAAACCTTTT 0.918262 -155 GCGAAAATTTAAAAACCCCATTTTTTAGCGCTCT 24 42 0 AAAACCATTT 0.88674 -166 TTTAGGGTTTAAAACGACCTTTATAAATAAAAAT 24 102 0 AAAAACTTTT 0.852778 -106 CTAAAATTTTAAAATACCATTTTTGAATGATTGG 24 131 1 AAAACATTTT 0.751189 -77 TATTGTTTAAGAAAATCGCTTTTTAATGCAAATA 25 54 0 GAAACCTTTT 0.911668 -93 AAGAAAATTCAAAAGCCTTTTTTTAGGTAAATAT 26 15 1 AAAACTTTTT 0.844877 -63 ATCTTGCTTAAAAACACCCTTTCTGAATTTTAAG 28 31 0 AAAACCTTTT 0.985984 -77 CAAGGCGCAAAAAAGCCCCTTGATTTAATTAAAG 32 13 0 AAAACCTTGT 0.952418 -97 AAAAACCCTTTTATGATTTGATTA 44 1 1 AAAACTTTTT 0.845597 -70 ATCGCTCTTTAAAAAACTCTTTATTAGATTATTT 45 87 0 AAAACCTTTT 0.979607 -61 CAATAAACTTAAAATTCGCTTGATTGAAGAGGGT 46 41 1 AAAACCTTGT 0.952343 -27 **** * **** * Masking position 4 Map Score: 30.3253 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 545 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 AGCGATTTTAGGTTAATTTTGAGTTTTTAG 3 22 0 GGTTAATTTT 0.943687 -193 TATAATGCTCGCTTAATTTTATTTGGGGTG 6 147 0 GCTTAATTTT 0.895124 -154 CTTTTTCATTGGTTATTTTTA 8 2 0 GGTTATTTTT 0.950125 -203 CCACTTGGTTGGTTGTTTTTATCATAGAGT 11 35 0 GGTTGTTTTT 0.961075 -107 ACTTGAATGCGGTTGATTTTAACCGAAAGC 20 161 0 GGTTGATTTT 0.955985 -68 GAATTAAATCGTTTGTTTTTTAAATTTGGA 22 135 0 GTTTGTTTTT 0.830956 -37 AAAGGGGCTAGTTTTAAGTCATTTT 23 6 1 GGCTAGTTTT 0.748698 -63 GTATGGTGTTGGTAGTTTTTAGCTTATTTT 24 168 1 GGTAGTTTTT 0.651393 -40 AAACAATAAGGCTTAATTTTAAGCACGTTT 25 80 1 GCTTAATTTT 0.895124 -67 AAAAATTAAAGGTTAATTTTA 25 136 1 GGTTAATTTT 0.943687 -11 AATTCAGAAAGGGTGTTTTTAAGCAAGATT 28 36 1 GGGTGTTTTT 0.770116 -72 ACACTCCTTAGCTTACTTTTTAACAATATC 30 70 0 GCTTACTTTT 0.693907 -22 GGCTATTGTAGTTTAGTTTTGCTAAAAAAA 33 245 0 GTTTAGTTTT 0.619885 -56 CAACGACTTTGGCTATTTTTCC 35 24 1 GGCTATTTTT 0.873878 -12 AGTTTGTCTTGTTTGTTTTTGA 36 37 1 GTTTGTTTTT 0.830956 -12 CCTGCAATGTGGTTGTTTTTAAACCCAGAT 37 94 0 GGTTGTTTTT 0.961075 -26 TTTTAGTAGTGCCTAATTTTTTCAAAGGAG 39 52 1 GCCTAATTTT 0.756355 -27 GTTTTTGAAGGCTTGATTTTTAAAGTTAGG 49 12 1 GCTTGATTTT 0.917097 -92 ********** Masking position 7 Map Score: 16.6448 Number of sites scoring better than the average of aligned sites = 368 Number in coding regions = 314 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 TATAGCGCTTCAAAGATATAACACTAATTCA 1 153 1 CAAAGATTAA 0.601941 -148 AACTGCTCCTAAAAACTCAAAATTAACCTAA 3 14 1 AAAAACTAAA 0.863937 -201 CTAAATTGAGAAAAAATTCAATTCAAAGGGG 3 113 1 AAAAAATCAA 0.882629 -102 AATAGCGTTTAAAAAATGTAAATTTTAAACA 3 148 0 AAAAAATTAA 0.824511 -67 ACAAGCTTTTAAATAATCCAATCTACTTTGT 7 62 1 AAATAATCAA 0.75014 -38 TGATTATAATAAAAGATTTAAAAAAAGCGAT 11 70 1 AAAAGATTAA 0.783875 -72 TAAAGGATTAAAAAGCTAAAATACTGCTTCT 12 56 0 AAAAGCTAAA 0.830555 -150 AATCCTTTAAAAATACTGAAAAATTGAAGTT 12 78 1 AAATACTAAA 0.717112 -128 CCAAATTTTAAAAAACTTCAATTTTTCAGTA 12 91 0 AAAAACTCAA 0.828119 -115 AAAAGCCAGAAAAAACTCCAAATTTTAAAAA 12 108 0 AAAAACTCAA 0.828119 -98 CCCCTTACTTAAATAATGAAATTTTCTTAAA 14 16 1 AAATAATAAA 0.798249 -213 AACTCCTTGTCAATGATTAAAATTAAAGAGC 14 196 0 CAATGATAAA 0.560141 -33 TAATTAAGACCAAAAATTCAAGGGGATTATT 15 31 1 CAAAAATCAA 0.75818 -27 AAAGCCCTATCAAAGATTAAATGCTATAATA 21 45 0 CAAAGATAAA 0.761322 -33 AGGGGGTATAAAAAAATTAAAAAACTTTAAA 22 35 1 AAAAAATAAA 0.908345 -137 AATGCAAATAAAATGCTAAAATGCCATGATT 25 33 0 AAATGCTAAA 0.661807 -114 TAAATTCTCTCAAAAATTAAAGGTTAATTTT 25 125 1 CAAAAATAAA 0.805144 -22 TTAGCCTTACAAAAAATTTAATGGTAGTTTA 29 34 0 AAAAAATTAA 0.824511 -25 CATGCTAGCTAAAAAATCTAAATTATTGTAA 30 18 0 AAAAAATTAA 0.824511 -74 TACCTTGACAAAAAAATAAAAGAATGAGATT 33 106 0 AAAAAATAAA 0.908345 -195 TTTGCTAAAAAAAAGATTAAACGGATATTAA 33 227 0 AAAAGATAAA 0.8844 -74 GCAAGAAATTAAAAGATGCAAGGCTATTGTA 33 265 0 AAAAGATCAA 0.853052 -36 ACAATAAAATAAAAACTGAAATACTACTCAA 43 94 0 AAAAACTAAA 0.863937 -71 ATAGCATTAAAAATAATAAAAACTTTCTTAT 45 25 1 AAATAATAAA 0.798249 -123 ATTCACCACTAAATAATCTAATAAAGAGTTT 45 77 1 AAATAATTAA 0.652265 -71 ******* *** Masking position 7 Map Score: 26.2617 Number of sites scoring better than the average of aligned sites = 797 Number in coding regions = 630 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 6 CGCTATTAGATATAATAAGGGATAGTTACCA 3 172 1 TATAATAGGG 0.809372 -43 TTACCACCTATAAAATAAGGATCGTTCA 3 197 1 TAAAATAGGA 0.911968 -18 GAATGATTATTTTAATAAGGACAATCA 4 48 1 TTTAATAGGA 0.662 -17 ACACCCCAAATAAAATTAAGCGAGCATTATA 6 146 1 TAAAATAAGC 0.696619 -155 ATGATTATCTTAAAATTAGAAAGTTTCTTTT 6 238 1 TAAAATAGAA 0.843018 -63 GAGTGTAATTTAAAATAAGGATCATTTG 11 8 0 TAAAATAGGA 0.911968 -134 AATCTTTTATTATAATCAAAAATCCACTTGG 11 57 0 TATAATAAAA 0.734624 -85 GCGTTTCTTATCAAATAAGGAGTCCCTAAA 11 122 1 TCAAATAGGA 0.552216 -20 TGTCAATGATTAAAATTAAAGAGCGATGTCC 14 189 0 TAAAATAAAG 0.770871 -40 TCTTTTAYGCTATAATTAAGACCAAAAATTC 15 19 1 TATAATAAGA 0.842276 -39 TTGTCCTTTATATAATTAAAATCCTATTATT 18 53 0 TATAATAAAA 0.734624 -21 AAATTTATAGTAAAATTAAGATTTTATAATC 19 28 1 TAAAATAAGA 0.901921 -54 ATTAAGATTTTATAATCAAAGTCAAATCATT 19 42 1 TATAATAAAG 0.661444 -40 AAAACGTGCTTAAAATTAAGCCTTATTGTTT 25 80 0 TAAAATAAGC 0.696619 -67 ATCGCTTCAATTTAATCAAAATTAGATTACA 31 18 1 TTTAATAAAA 0.474029 -59 TATTTAAAGCTTAAATAAGGGTCTAGCG 31 59 1 TTAAATAGGG 0.704172 -18 CCCTTTAATTAAATCAAGGGGCTTTTTTG 32 9 1 TTAAATAAGG 0.678764 -101 CGACAATCCTTAAAATCAAAATGGGATTTAT 32 89 0 TAAAATAAAA 0.826598 -21 TAAATGAAGTTTAAATCAAAATCATGGTGTC 33 199 0 TTAAATAAAA 0.608145 -102 ATTGAGATAATAAAATAAGGGTTAGAT 42 20 1 TAAAATAGGG 0.879683 -17 AATAAAACAATAAAATAAAAACTGAAATACT 43 100 0 TAAAATAAAA 0.826598 -65 AAATGGTGGTTATAATAAGAAAGTTTTTATT 45 39 0 TATAATAGAA 0.757194 -109 ****** **** Masking position 6 Map Score: 15.9986 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 276 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 7 TAAATTCTAAAGGGGTATTAAACGCACTTC 1 111 1 AGGGGTATTA 0.739889 -190 AAGGGGATAGGGGGGTAAAAATCATTCCCC 2 18 0 GGGGGTAAAA 0.62705 -137 ACAATTCACAAGGAGTTTAAA 5 56 1 AGGAGTTTAA 0.661181 -11 TAGCAAGAAAACGGGTTTGATCCATAAAGA 6 28 1 ACGGGTTTGA 0.89649 -273 GTGGAGTGTAGGGGGTTCGAACCCCTGACC 6 79 1 GGGGGTTCGA 0.951513 -222 CAATGAAAAAGCGGGTTTAAAGGCGAGAAT 8 21 1 GCGGGTTTAA 0.874919 -184 CTGGCTTTTAGGGGGTTTTAAATTCTTTTA 12 130 1 GGGGGTTTTA 0.944606 -76 GTATCCATGAAGGGGTTCAATGCATTCTTT 20 106 1 AGGGGTTCAA 0.904168 -123 ATTAAATGGAGGGGGTATAAAAAAATTAAA 22 26 1 GGGGGTATAA 0.862124 -146 ATCGTTTTTAGGGAGTTTGATC 26 66 1 GGGAGTTTGA 0.802328 -12 GTTACTTTAAAGGGGTTTAAAGAATCAAGG 32 59 0 AGGGGTTTAA 0.957109 -51 GCCGGAGGTCGGGGGTTCAAGTCCCCCTCT 33 168 1 GGGGGTTCAA 0.924405 -133 TTCTTGCATTAGGGATTTGACG 33 289 1 AGGGATTTGA 0.625838 -12 AGGCGGGTTTTAGCAACGACTT 35 3 1 GCGGGTTTTA 0.804846 -33 ATATAATATAAAGGGTTTGAT 41 24 1 AAGGGTTTGA 0.793556 -11 ATAATAAAATAAGGGTTAGAT 42 26 1 AAGGGTTAGA 0.508256 -11 AAATCCAAATAGGGGTTAGACA 45 136 1 AGGGGTTAGA 0.905919 -12 AAGGGGTTTTAAGCGCGCTAG 46 2 1 AGGGGTTTTA 0.929363 -66 ********** Masking position 6 Map Score: 19.9255 Number of sites scoring better than the average of aligned sites = 505 Number in coding regions = 433 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 ATCAAAACATTGCTACAATTACATCCAACCT 1 230 1 TGCTAAATTA 0.832729 -71 GAATGAAATAAGCTATAATAAGCCCATTTTG 4 12 1 AGCTAAATAA 0.832729 -53 CCCGTTTTCTTGCTAGTATTACCCATAATTA 6 12 0 TGCTATATTA 0.385775 -289 TTAAGCAAAATGTTATAATGCTCGCTTAATT 6 159 0 TGTTAAATGC 0.709218 -142 TTTAAAAGCTTGTTAGAATACCAAAAAAAAA 7 44 0 TGTTAAATAC 0.907131 -56 AGGATTAAAAAGCTAAAATACTGCTTCTTTA 12 53 0 AGCTAAATAC 0.825911 -153 GATATAGTCTTGTTAGAATACCTTAAAAGAA 12 152 0 TGTTAAATAC 0.907131 -54 CGTTCTTTTAYGCTATAATTAAGACCAAAAA 15 16 1 YGCTAAATTA 0.599905 -42 AGTTAAAATAATCCCCTTGAA 15 47 0 AGTTAAATAA 0.755331 -11 AAACGCTATAATAAATCAAAATTC 16 4 1 CGCTAAATAA 0.691609 -54 TCTGTTAAAATATCCTTTTTAGC 17 39 0 TGTTAAATAT 0.521708 -13 GCATGATTTTTGCTACAATAATAGGATTTTA 18 37 1 TGCTAAATAA 0.942951 -37 AAAGATTAAATGCTATAATACTACCCTAATT 21 34 0 TGCTAAATAC 0.940304 -44 GCAAATAAAATGCTAAAATGCCATGATTTAA 25 30 0 TGCTAAATGC 0.797288 -117 GCTTTTGTTACAATAATTTAGATTTT 30 6 1 TGTTAAATAA 0.911111 -86 AGTTTAGTTTTGCTAAAAAAAAGATTAAACG 33 235 0 TGCTAAAAAA 0.528598 -66 AATGAAAATATGTTAATATAAAAGTTTTTAG 39 27 1 TGTTATATAA 0.563916 -52 TTAAAATGGTGGTTATAATAAGAAAGTTTTT 45 42 0 GGTTAAATAA 0.581714 -106 CGCTAGCTTGTGTTACAATAAACTTAAAATT 46 26 1 TGTTAAATAA 0.911111 -42 TAATCTTTTATGTTAAAATTCTGAGATTTTA 49 44 1 TGTTAAATTC 0.746319 -60 ***** ***** Masking position 4 Map Score: 14.6758 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 85 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 9 AGCGGGTTTAAAGGCGAGAATTGAGCTTAA 8 30 1 AAGGCGAGAA 0.883965 -175 ATAAAATGGATAGGCTTAAAGAAGCGTTTC 11 99 1 TAGGCTTAAA 0.769324 -43 AGTATTTTTAAAGGATTAAAAAGCTAAAAT 12 65 0 AAGGATTAAA 0.725786 -141 TGACGCTTATAAGGATAAAAG 13 155 1 AAGGATAAAA 0.794872 -11 GATAGGGCTTTAGGGGAAAATAG 21 65 1 TAGGGGAAAA 0.704174 -13 GCTGAGAATGTAGGCTTAAAATTCAGAAAG 28 17 1 TAGGCTTAAA 0.769324 -91 AATTTTTTGTAAGGCTAAAAAC 29 47 1 AAGGCTAAAA 0.932127 -12 AAAATCGCACAAGGCGCAAAAAAGCCCCTT 32 26 0 AAGGCGCAAA 0.925635 -84 TTAAAGAATCAAGGGGAAAAATCGCACAAG 32 43 0 AAGGGGAAAA 0.870049 -67 AGATCAGAGAAAGGCGCAAAGGCCTTTCTG 34 21 0 AAGGCGCAAA 0.925635 -203 TTTTTGATCAAAGGCTTGAAAT 34 212 1 AAGGCTTGAA 0.764764 -12 AATTTTTTCAAAGGAGAAAAATC 39 66 1 AAGGAGAAAA 0.861152 -13 ********** Masking position 2 Map Score: 6.61393 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 223 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 10 ATCACTCCAATTTTAATTCTCATTTTTTTG 1 64 1 TTTTAATTCT 0.73169 -237 TTTTGATCTTTATAAATTCTAAAGGGGTAT 1 99 1 TATAAATTCT 0.73169 -202 GGGGCTATTGTTTAAAATTTACATTTTTTA 3 140 1 TTTAAAATTT 0.760598 -75 GGGTTTTTCTTTTAAATTTTGAGCTAAAAA 8 152 0 TTTAAATTTT 0.854085 -53 TTATCGCTTTTTTTAAATCTTTTATTATAA 11 73 0 TTTTAAATCT 0.596804 -69 ATTGAAGTTTTTTAAAATTTGGAGTTTTTT 12 100 1 TTTAAAATTT 0.760598 -106 TTTAGGGGGTTTTAAATTCTTTTAAGGTAT 12 136 1 TTTAAATTCT 0.924345 -70 AATCAATGCGTTTAATTTCTGTTTTCAATA 13 124 1 TTTAATTTCT 0.816641 -42 TGTATTAGTTTTTAAAATCTTTAAAGATCT 14 140 0 TTTAAAATCT 0.868967 -89 TTAATTTTACTATAAATTTTATAACAAATA 19 17 0 TATAAATTTT 0.566435 -65 TGACTTTGATTATAAAATCTTAATTTTACT 19 36 0 TATAAAATCT 0.596804 -46 TTTAAAGTTTTTTAATTTTTTTATACCCCC 22 36 0 TTTAATTTTT 0.680888 -136 AAATGGGGTTTTTAAATTTTCGCGCAAAGC 24 53 1 TTTAAATTTT 0.854085 -155 TGTATCATCATTTAATTTTTATTTATAAAG 24 88 1 TTTAATTTTT 0.680888 -120 AAAATGGTATTTTAAAATTTTAGGGTTTAA 24 124 0 TTTAAAATTT 0.760598 -84 TCATTGCCTTAAATTCTTTTTAAATCA 25 8 1 CTTAAATTCT 0.515337 -139 TATGATAACTTTTAAATTCTCTCAAAAATT 25 113 1 TTTAAATTCT 0.924345 -34 AAAATTAACCTTTAATTTTTGAGAGAATTT 25 126 0 TTTAATTTTT 0.680888 -21 AATCTCATTCTTTTATTTTTTTGTCAAGGT 33 106 1 TTTTATTTTT 0.322605 -195 CCTTGCATCTTTTAATTTCTTGCATTAGGG 33 273 1 TTTAATTTCT 0.816641 -28 TTTTTAAATCTGCCCCTAAGA 37 2 1 TTTTAAATCT 0.596804 -118 ATCTTTTATGTTAAAATTCTGAGATTTTAT 49 46 1 TTAAAATTCT 0.417728 -58 ATATAAAATATATAAAATCTCAGAATTTTA 49 57 0 TATAAAATCT 0.596804 -47 ********** Masking position 8 Map Score: 23.4963 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 415 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 11 ATAATTAGTTAATGAACGCTTCTGTTAATCTTA 1 193 1 AAAAGCTTCT 0.898433 -108 AACAGCTTACAATAAAGGGTTTTTCTTTTAAAT 8 165 0 AAAAGGTTTT 0.670908 -40 CTTATTTGATAAGAAACGCTTCTTTAAGCCTAT 11 108 0 AAAAGCTTCT 0.898429 -34 TAAAAAGCTAAAATACTGCTTCTTTATTTTCTA 12 46 0 AAACGCTTCT 0.688329 -160 TATAATACCCAATCAATGCGTTTAATTTCTGTT 13 114 1 AAAAGCGTTT 0.966068 -52 TTATAGCTAAAAGAACGCTTTT 15 1 0 AAAAGCTTTT 0.957613 -57 AATGTAGTATAATTACATCGTTTCGCTAAAAAG 17 15 1 AAACTCGTTT 0.606648 -37 ATTGTAGCAAAAATCATGCGTTTAATGGAATAA 18 23 0 AACAGCGTTT 0.876735 -51 ATACCAAAAGAGAGAAAGCGTTTTTTAAGGGCT 20 77 0 AGAAGCGTTT 0.783287 -152 GAAGGGGTTCAATGCATTCTTTTGCATTATTCC 20 114 1 AACATCTTTT 0.550361 -115 CTTAAATTTGAATTAAATCGTTTGTTTTTTAAA 22 141 0 AAAATCGTTT 0.860659 -31 TATTTACCTAAAAAAAGGCTTTTGAATTTTCTT 26 15 0 AAAAGCTTTT 0.956124 -63 AAACAAACGCTTTTAGTTTGGGTG 27 2 1 AAAAGCTTTT 0.957635 -63 ATGGATTTTTAAGAAAGGTTTTTGTATAATCTC 33 79 1 AAAAGTTTTT 0.578482 -222 GTTTAAGACAAACCAAAGAGTTTGTCTTGTTTG 36 19 1 AAAAGAGTTT 0.634354 -30 AACTCTCCTAAAAGAACTCGTTTTATCCGTTAC 43 141 0 AAAATCGTTT 0.860477 -24 ** ** ****** Masking position 11 Map Score: 10.2637 Number of sites scoring better than the average of aligned sites = 751 Number in coding regions = 659 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 12 GCAAAATGGGTAAAATAATGGGTAAGGGGATA 2 39 0 TAAATAAGGG 0.960575 -116 GCCAACAGCTTACAATAAAGGGTTTTTCTTTT 8 169 0 TACATAAGGG 0.903391 -36 ATTTCATTATTTAAGTAAGGGGAATTA 14 6 0 TTAATAAGGG 0.934919 -223 AACTATAGTATAATCTAAGGGCGTTGCTCTGT 14 66 1 TAATTAAGGC 0.79764 -163 TGATTTCCTTTAATATAACGGATTGGTTGTAG 16 34 0 TAATTAAGGA 0.824242 -24 AGGATTTTAATTATATAAAGGACAA 18 59 1 TTATTAAGGA 0.734397 -15 TATTTAAAGCTTAAATAAGGGTCTAGCG 31 59 1 TTAATAAGGT 0.766668 -18 GCCCCTTGATTTAATTAAAGGG 32 1 0 TTAATAAGGG 0.934919 -109 GGATTTATGTTACTTTAAAGGGGTTTAAAGAA 32 65 0 TACTTAAGGG 0.887218 -45 ACATTGAATATAATATAAAGGGTTTGAT 41 17 1 TAATTAAGGG 0.953496 -18 ATTGAGATAATAAAATAAGGGTTAGAT 42 20 1 TAAATAAGGT 0.847858 -17 **** *** *** Masking position 7 Map Score: 5.44768 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 37 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ATTTCAAATGTAGTAGAATTAAGGCAGTGT 3 62 0 TAGTAGAATT 0.781502 -153 TAAAAAATTTTTGTATAATCAACAATTCAC 5 35 1 TTGTATAATC 0.929898 -32 TTAAATCTTTTATTATAATCAAAAATCCAC 11 61 0 TATTATAATC 0.657404 -81 AAGTTACATATTGTATAATTTTAAGAAAAT 14 36 0 TTGTATAATT 0.908128 -193 AACTTAACTATAGTATAATCTAAGGGCGTT 14 61 1 TAGTATAATC 0.917735 -168 AACGGATTGGTTGTAGAATTTTGATTTATT 16 20 0 TTGTAGAATT 0.809535 -38 ACCTAATGTAGTATAATTACATCGTTTC 17 9 1 TAGTATAATT 0.892637 -43 TTGTCCTTTATATAATTAAAATCCTAT 18 57 0 TTATATAATT 0.492141 -17 ATAAAATTTATAGTAAAATTAAGATTTTAT 19 25 1 TAGTAAAATT 0.567343 -57 AAAATTAAGATTTTATAATCAAAGTCAAAT 19 39 1 TTTTATAATC 0.696304 -43 AGAAAGGTTTTTGTATAATCTCATTCTTTT 33 90 1 TTGTATAATC 0.929898 -211 ********** Masking position 5 Map Score: 3.6269 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 14 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 14 TTTTGCCCATAAGCGTTAAATTCCAATCAAAA 2 65 1 AAGCTTAATT 0.286511 -90 TTATATCTAATAGCGTTTAAAAAATGTAAATT 3 155 0 TAGCTTAAAA 0.786385 -60 AGAATGAAATAAGCTATAATAAGCCCATTTTG 4 11 1 AAGCATATAA 0.397124 -54 ATTTGCTATTAAGCGTTTCAAAAAAGCATCAA 6 201 0 AAGCTTCAAA 0.810911 -100 GATTTTACTTAATCCATAAAAGAAACTTTCTA 6 254 0 AATCATAAAG 0.247303 -47 GCCTCTTTATAAGCCCTAAAAAGAGC 7 5 0 AAGCCTAAAA 0.875214 -95 GTATTCTAACAAGCTTTTAAATAATCCAATCT 7 54 1 AAGCTTAAAT 0.835935 -46 TAAAAATAACCAATGAAAAAGCGGGTTTA 8 8 1 AACCATAAAA 0.449745 -197 ATTATAATAAAAGATTTAAAAAAAGCGATAAA 11 72 1 AAGATTAAAA 0.693838 -70 GATTTAAAAAAAGCGATAAAATGGATAGGCTT 11 84 1 AAGCATAAAT 0.769003 -58 TTAGCTTTTTAATCCTTTAAAAATACTGAAAA 12 68 1 AATCTTAAAA 0.773816 -138 AACCCCCTAAAAGCCAGAAAAAACTCCAAATT 12 115 0 AAGCAGAAAA 0.494003 -91 AATACCTTAAAAGAATTTAAAACCCCCTAAAA 12 135 0 AAGATTAAAA 0.693838 -71 AAGATCTTTAAAGATTTTAAAAACTAATACAG 14 139 1 AAGATTAAAA 0.693838 -90 ACGCTCAATGAAGCCATTAAAGACAAAGTTTA 20 15 1 AAGCATAAAG 0.691374 -214 AACTGCGATGAAGCCCTTAAAAAACGCTTTCT 20 66 1 AAGCCTAAAA 0.875214 -163 CATACAAACCAATCATTCAAAAATGGTATTTT 24 141 0 AATCTTAAAA 0.773816 -67 GTTTTTAGCCTTACAAAAAATTTAATG 29 42 0 TAGCTTCAAA 0.403627 -17 GATTAAATTGAAGCGATAAAAAAG 31 3 0 AAGCATAAAA 0.938427 -74 ACCCTTATTTAAGCTTTAAATAACTATAATAT 31 49 0 AAGCTTAATA 0.647691 -28 CGACAATCCTTAAAATCAAAATGGGA 32 94 0 AATCTTAAAT 0.427683 -16 CTTTCTTAAAAATCCATTAAAATTACATTAAA 33 64 0 AATCATAAAA 0.690913 -237 TCCCTAATGCAAGAAATTAAAAGATGCAAGGC 33 272 0 AAGAATAAAA 0.596891 -29 TAATTCAAGTAAGCATTGCAAAAGGATCTTTA 34 160 0 AAGCTTCAAA 0.810911 -64 AATCTCTAAAAAGCCCTAAAAATAGCAAAAGT 43 42 1 AAGCCTAAAA 0.875214 -123 AAACAGAATAAAACAATAAAATAAAAACTGAA 43 105 0 AAACATAAAT 0.233339 -60 TTTTACTTGAAAACATTGAAAATAGGGAAGTA 44 47 1 AAACTTAAAA 0.680777 -24 ACTCCTAAAATAGCATTAAAAATAATAAAAAC 45 16 1 TAGCTTAAAA 0.786385 -132 AGACAAGCCATGAAAAAAGAAAAGTC 48 5 1 AAGCATAAAA 0.938427 -22 TTTAAAAATCAAGCCTTCAAAAACC 49 4 0 AAGCTTAAAA 0.958892 -100 AGATTAAGCCTAACTTTAAAAATCAAGCCTTC 49 18 0 TAACTTAAAA 0.251812 -86 **** ** **** Masking position 2 Map Score: 28.0845 Number of sites scoring better than the average of aligned sites = 1787 Number in coding regions = 1579 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 15 GAGAGCGCAACGCTGGCAGCGTTGAGGTCAGGGGT 6 99 0 CGCTCCGTGA 0.993915 -202 GCCAGCGTTGCGCTCTCCCAGCTGAGCTAACACCC 6 117 1 CGCTCAGTGA 0.990618 -184 AAGACTTGAGCGCTAGCCAAGCTGAAGCGTGGGGT 13 61 1 CGCTCAGTGA 0.990618 -105 TCGTAGAAATCGCTAACTGCGATGAAGCCCTTAAA 20 52 1 CGCTCCGTGA 0.993915 -177 ACGCTTTCTTTGATGACAAGGTATTG 20 213 0 CGCTCTGTGA 0.983575 -16 **** * ** *** Masking position 4 Map Score: 2.89029 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 5 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185