AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_hpyl_reg_300.orf -o00230_hpyl_300.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: HP0106 24 cystathionine gamma-synthase (metB) HP0406 25 H. pylori predicted coding region HP0406 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 HP0105 37 conserved hypothetical protein #4 HP0107 38 cysteine synthetase (cysK) #5 HP0194 214 triosephosphate isomerase (tpi) #6 HP0197 64 S-adenosylmethionine synthetase 2 (metX) #7 HP0198 66 nucleoside diphosphate kinase (ndk) #8 HP0252 300 outer membrane protein (omp7) #9 HP0255 99 adenylosuccinate synthetase (purA) #10 HP0262 157 H. pylori predicted coding region HP0262 #11 HP0263 111 adenine specific DNA methyltransferase (hpaim) #12 HP0264 72 ATP-dependent protease binding subunit (clpB) #13 HP0265 53 cytochrome c biogenesis protein (ccdA) #14 HP0268 60 H. pylori predicted coding region HP0268 #15 HP0270 204 H. pylori predicted coding region HP0270 #16 HP0275 36 ATP-dependent nuclease (addB) #17 HP0277 56 ferredoxin #18 HP0322 141 poly E-rich protein #19 HP0364 205 ribonucleoside diphosphate reductase, beta subunit (nrdB) #20 HP0404 80 protein kinase C inhibitor (SP:P16436) #21 HP0407 103 biotin sulfoxide reductase (bisC) #22 HP0408 165 H. pylori predicted coding region HP0408 #23 HP0497 228 sodium- and chloride-dependent transporter #24 HP0500 57 DNA polymerase III beta-subunit (dnaN) #25 HP0572 57 adenine phosphoribosyltransferase (apt) #26 HP0573 51 H. pylori predicted coding region HP0573 #27 HP0577 73 methylene-tetrahydrofolate dehydrogenase (folD) #28 HP0584 81 flagellar switch protein (fliN) #29 HP0585 228 endonuclease III (nth) #30 HP0616 77 chemotaxis protein (cheV) #31 HP0680 171 ribonucleoside-diphosphate reductase 1 alpha subunit (nrdA) #32 HP0681 39 H. pylori predicted coding region HP0681 #33 HP0682 153 H. pylori predicted coding region HP0682 #34 HP0683 300 UDP-N-acetylglucosamine pyrophosphorylase (glmU) #35 HP0717 68 DNA polymerase III gamma and tau subunits (dnaX) #36 HP0718 207 conserved hypothetical integral membrane protein #37 HP0736_HP0737 146 HP0736: phosphoserine aminotransferase (serC), HP0737: conserved hypothetical integral membrane protein #38 HP0738 77 D-alanine:D-alanine ligase A (ddlA) #39 HP0742 64 phosphoribosylpyrophosphate synthetase (prsA) #40 HP0777 107 uridine 5'-monophosphate (UMP) kinase (pyrH) #41 HP0778 127 H. pylori predicted coding region HP0778 #42 HP0830 58 amidase #43 HP0832 91 spermidine synthase (speE) #44 HP0833 76 H. pylori predicted coding region HP0833 #45 HP1108 259 pyruvate ferredoxin oxidoreductase, gamma subunit #46 HP1112 109 adenylosuccinate lyase (purB) #47 HP1180 300 pyrimidine nucleoside transport protein (nupC) #48 HP1198 223 DNA-directed RNA polymerase, beta subunit (rpoB) #49 HP1199 45 ribosomal protein L7/L12 (rpl7/l12) #50 HP1200 108 ribosomal protein L10 (rpl10) #51 HP1201 44 ribosomal protein L1 (rpl1) #52 HP1203 300 transcription termination factor NusG (nusG) #53 HP1215 35 H. pylori predicted coding region HP1215 #54 HP1217 48 H. pylori predicted coding region HP1217 #55 HP1218 119 glycinamide ribonucleotide synthetase (purD) #56 HP1295 22 ribosomal protein S11 (rps11) #57 HP1297 78 ribosomal protein L36 (rpl36) #58 HP1300 42 preprotein translocase subunit (secY) #59 HP1318 34 ribosomal protein L4 (rpl4) #60 HP1319 36 ribosomal protein L3 (rpl3) #61 HP1320 164 ribosomal protein S10 (rps10) #62 HP1386 70 D-ribulose-5-phosphate 3 epimerase (rpe) #63 HP1460 147 DNA polymerase III alpha-subunit (dnaE) #64 HP1470 67 DNA polymerase I (polA) #65 HP1471 65 type IIS restriction enzyme R protein (BCGIB) #66 HP1483 26 gerC2 protein (gerC2) #67 HP1490 103 hemolysin #68 HP1491 138 phosphate permease Motif number 1 ATATAACACTAATTCATTTTAAATAATAATTAGTTAAT 1 168 1 AATTTAAATA 0.820271 -133 GTCTTCAAGGAAAAACACTTTAAGAATAGGAGAATAAG 1 273 1 AACTTTAATA 0.896601 -28 AATCGCAAAATTGAATTTTATTGTTTGTTATAGGA 4 8 1 AAATTTTATT 0.640714 -31 CATTTGAAATAATTTTTCTTATAAACAAAACCTAAATT 5 82 1 AACTTATAAA 0.654146 -133 GCGTTTAAAAAATGTAAATTTTAAACAATAGCCCCTTT 5 137 0 AAATTTTAAA 0.625879 -78 AAAAATATTTTAAGGGTAATATTTTAAA 7 1 1 AATTTTAATA 0.906824 -66 TTGATTATACAAAAATTTTTTAAAATATTACCCTTAAA 7 19 0 AATTTTAAAT 0.854416 -48 TTAAAATTAGAAAGTTTCTTTTATGGATTAAGTAAAAT 8 247 1 AACTTTTAAT 0.763801 -54 AGGGCTTATAAAGAGGCTTTTTACTTTTTTTTTGGTAT 9 20 1 AATTTTTATT 0.828341 -80 TTGGTATTCTAACAAGCTTTTAAATAATCCAATCTACT 9 51 1 AATTTTAAAT 0.854416 -49 CTAAAATTTAAATTTCATTTTTATTATAAGCTTGTTTC 10 92 1 AATTTTTATA 0.857522 -66 AAAAGCCTTTTTAAATCTTCTAATAAATT 11 93 0 AATTTTAATT 0.886402 -19 TAAAGGCGAGAATTGAGCTTAAAATTTTTCAGGAAAAA 15 38 1 AACTTAAATT 0.765271 -167 TTTCAGGAAAAATATCGTTTTAAAGGTTGTCCCACGCT 15 64 1 AATTTTAATT 0.886402 -141 AAAAAGTTTGAATACGACTTTTACTCTAAATTAGCTTA 17 15 0 AACTTTTATA 0.842828 -42 GACTAACTCCTTTTAAAAAGTTTGAATACGAC 17 35 0 AATTTAAATT 0.785369 -22 TTTGATAAGAAACGCTTCTTTAAGCCTATCCATTTTAT 18 99 0 AACTTTAATA 0.896601 -43 GAAAATAAAGAAGCAGTATTTTAGCTTTTTAATCCTTT 19 48 1 AAATTTTATT 0.640714 -158 TAACGATCCTTATATTTTATTTTTAAAAA 20 2 1 AACTTATATA 0.715481 -79 AAAAAGCTATAATACAACTTTAATAAAAGAAAAACCTT 20 35 1 AACTTTAAAA 0.867056 -46 CAATATTGAAAACAGAAATTAAACGCATTGATTGGGTA 22 119 0 AAATTAAAAT 0.504237 -47 TTAAATAATGAAATTTTCTTAAAATTATACAATATGTA 23 24 1 AACTTAAAAT 0.710323 -205 ATTTAAGAAAAAACCCACTTTAAAAATACCTAAAAAAT 23 98 0 AACTTTAATA 0.896601 -131 AAAAGCGTTCTTTTAYGCTATAATTAAGAC 24 3 1 AACTTTTATA 0.842828 -55 TCTGTTAAAATATCCTTTTTAGCGAAACGATGTAAT 26 26 0 AATTTTTAAA 0.819065 -26 TTGCTACAATAATAGGATTTTAATTATATAAAGGACAA 27 46 1 AATTTTAATA 0.906824 -28 TTGATTATAAAATCTTAATTTTACTATAAATTTTATAA 28 23 0 AAATTTTATA 0.68985 -59 GTTTGTAAAAACCTTTTAAACTAAATTAGGGTAG 30 7 1 AATTTTAAAA 0.879808 -71 TAAAAAAATTAAAAAACTTTAAAACTTATTCTCATTAA 31 43 1 AATTTAAATA 0.820271 -129 CAAACGATTTAATTCAAATTTAAGGAAAAATT 31 150 1 AAATTTAAAA 0.730108 -22 TTAAAGGGCAAATGAGGATTAAAAAAATGAAAAAACGC 34 184 1 AAATTAAAAT 0.504237 -117 TGATGAAACGAAGTCAAATTATAAGATAAGGCATGTTA 34 243 1 AAATTATATA 0.510535 -58 CAATACTCCTAAATGAGTTTTAAGGATTACAATCAAT 35 42 1 AATTTTAATT 0.886402 -27 AGCGCTAAAAAATGGGGTTTTTAAATTTTCGCGCAAAG 36 44 1 AATTTTTATT 0.828341 -164 TAGGGTTTAAAACGACCTTTATAAATAAAAATTAAATG 36 96 0 AATTTATAAA 0.679778 -112 ATCATTCAAAAATGGTATTTTAAAATTTTAGGGTTTAA 36 124 0 AATTTTAATT 0.886384 -84 TCATTGCCTTAAATTCTTTTTAAATCATGGCATTTTAG 37 11 1 AATTTTAAAT 0.854416 -136 TGTTTAAGAAAATCGCTTTTTAATGCAAATAAAATGCT 37 47 0 AATTTTAAAA 0.879808 -100 TATCATACTAAAACGTGCTTAAAATTAAGCCTTATTGT 37 82 0 AACTTAAAAA 0.7536 -65 TAAAATTAACCTTTAATTTTTGAGAGAATTT 37 126 0 AACTTTAATT 0.874249 -21 GAAAATTCAAAAGCCTTTTTTTAGGTAAATATAGATAG 38 17 1 AATTTTTAAA 0.819065 -61 TACACTCCCTAAAATGAATTAAAATCAATTGTAGCGCA 39 33 0 AAATTAAAAA 0.559196 -32 AAAATTCAGAAAGGGTGTTTTTAAGCAAGATTAGGTTA 40 34 1 AATTTTTAAA 0.819065 -74 CTCATTAATTAATAAAATTTTAATAAAACTTGTGATTG 40 72 0 AATTTTAAAA 0.879808 -36 CCATGATAACAAAACTCTTTTTACTTTTAGTTAAGTTG 41 58 1 AATTTTTATT 0.82834 -70 AAGCATGTTAAACTACCATTAAATTTTTTGTAAGGCTA 42 26 1 AAATTAAATT 0.574879 -33 ATTGTAATCTAATTTTGATTAAATTGAAGCGATAAAAA 44 13 0 AAATTAAAAA 0.559196 -64 CTTAAATAATAACAAAGTTTAAAATAAATATTAGTGGT 45 44 1 AATTTAAAAA 0.774403 -216 AAAAACTATTAATGTGTCTTATAACAATATCTTTTTAG 45 172 0 AACTTATAAT 0.602613 -88 GGCTGAATTCAATTTATTTTATACGATATTAAGGAGAC 45 224 1 AATTTATATA 0.738385 -36 ATAAAAGTTTAATGTAATTTTAATGGATTTTTAAGAAA 47 57 1 AATTTTAAAT 0.854416 -244 ACGGATATTAAATGAAGTTTAAATCAAAATCATGGTGT 47 200 0 AATTTAAAAA 0.774403 -101 ATATCCGTTTAATCTTTTTTTTAGCAAAACTAAACTAC 47 230 1 AATTTTTAAA 0.819065 -71 AAGCATTGCAAAAGGATCTTTAAACTTTAGAACCATCC 48 144 0 AACTTTAATT 0.874249 -80 TCTTTTTAAAAAAGAAATTTTAAGCTTTTTAGCTCTTA 50 44 0 AATTTTAATT 0.886402 -65 TTGGAATTGAAAGAAATTTTTAAGGATTAGAATC 51 21 1 AATTTTAATT 0.886402 -24 AATTCTATCCAAAATAGCTTAAACTAAAATTAAAAAAT 52 12 0 AACTTAAAAA 0.7536 -289 TTATACATTAAAAGAATTTTTAATTCTATCCAAAATAG 52 33 0 AATTTTAATA 0.906824 -268 AAAAACCCTTTTATGATTTGATTAAAGA 62 1 1 AACTTTTATT 0.811299 -70 TGGTTATAATAAGAAAGTTTTTATTATTTTTAATGCTA 63 26 0 AATTTTTATT 0.828341 -122 TTCTTATTATAACCACCATTTTAAAATAATTCACCACT 63 49 1 AAATTTTATA 0.68985 -99 CTCTTCAATCAAGCGAATTTTAAGTTTATTGTAACACA 64 34 0 AATTTTAATA 0.906824 -34 TTTTTAAAACTCTCTTTAAAATTTTACTTTAAGA 68 7 1 AACTTTAATT 0.874249 -132 ** ****** ** Masking position 9 Map Score: 72.2606 Number of sites scoring better than the average of aligned sites = 1455 Number in coding regions = 1064 Number in noncoding regions = 391 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 2 AATTTTGAGTTTTTAGGAGCAGTTTTT 5 3 0 TTTTAGGATT 0.840661 -212 CGTCAAGCGATTTTAGGTTAATTTTGAGTTTTTAG 5 22 0 TTTTAGGATT 0.840661 -193 AAAAATATTTTAAGGGTAATATTTTAAAAAAT 7 8 1 TTTTAAGATT 0.857684 -59 AATTGACATCTTTTAAGCAAAATGTTATAATGCTC 8 167 0 TTTTAAGATT 0.857684 -134 AACTTTCTAATTTTAAGATAATCATTCTTAATTTG 8 228 0 TTTTAAGACT 0.750501 -73 GCTCTTTTTAGGGCTTATAAAGAGGCTTTT 9 6 1 TTTTAGGTTA 0.920733 -94 TTTTACTTTTTTTTTGGTATTCTAACAAGCTTTTA 9 38 1 TTTTTGGTTA 0.836287 -62 ATCTACTTTGTTTTAAGGATAATATTTT 9 82 1 TTTTAAGATT 0.857684 -18 TTAGCAATACTTTTAAGCAGAATATCTAAAATTTA 10 67 1 TTTTAAGATT 0.857684 -91 ATCAAAATGGTTTTTGGCTAAATAAAGGCCATCTC 11 31 0 TTTTTGGATA 0.802278 -81 TTTCTTGTCTTTTTTAGGATAACAAAACC 13 5 0 TTTTTAGACA 0.698195 -49 ATTTTAAGCTAATTTAGAGTAAAAGT 17 2 1 TTTTAAGATA 0.914231 -55 TTTTTCTGGCTTTTAGGGGGTTTTAAATTCTTTTA 19 125 1 TTTTAGGTTA 0.921555 -81 TTTTAAATTCTTTTAAGGTATTCTAACAAGACTAT 19 145 1 TTTTAAGTCA 0.870094 -61 ATTGAGATAGTTTTAAGGAAATTAAGGAACAAA 19 183 1 TTTTAAGATA 0.914231 -23 TTTTGCTCCCTTTTAAGGTTTTTCTTTTATTAAAG 20 52 0 TTTTAAGTTT 0.883546 -29 TTAGCGGTAATTTTAGGTGAATCTATGTTAGAATT 21 41 1 TTTTAGGACA 0.823246 -63 GCTCTGTATTTTTTAGGTATTTTTAAAGTGGGTTT 23 91 1 TTTTAGGTTA 0.921555 -138 TAAAATATCCTTTTTAGCGAAACGATGTAATTATA 26 22 0 TTTTTAGACA 0.698196 -30 AGAAAGCGTTTTTTAAGGGCTTCATCGCAGTTAGC 29 63 0 TTTTAAGTCT 0.791097 -166 ATGATTAATATTTTAGGATTTTTCATTATTCAAAC 33 14 0 TTTTAGGTTA 0.921555 -140 CTTAAACTCATTTTAGGGAATTTTAACATGCCTTA 34 269 0 TTTTAGGTTA 0.921555 -32 AAGGGGCTAGTTTTAAGTCATTTTGCATTACAATA 35 12 1 TTTTAAGTTG 0.783765 -57 CCTAAATGAGTTTTAAGGATTACAATCAAT 35 49 1 TTTTAAGTCA 0.870091 -20 AAAACCCCATTTTTTAGCGCTCTTAGTGGCGTTTA 36 30 0 TTTTTAGTTA 0.853696 -178 GTGTTGGTAGTTTTTAGCTTATTTTGAGTGAAAGG 36 173 1 TTTTTAGATT 0.723799 -35 AACCTTTAATTTTTGAGAGAATTTAAAAGTTATCA 37 115 0 TTTTGAGATA 0.662126 -32 TTTTAAGAAAATTCAAAAGCCTTTT 38 1 1 TTTTAAGATA 0.914231 -77 CAAAAGCCTTTTTTTAGGTAAATATAGATAGACTT 38 24 1 TTTTTAGATT 0.723799 -54 TTGCAATCGTTTTTAGGGAGTTTGATC 38 61 1 TTTTAGGTTA 0.921555 -17 TTTTAATTCATTTTAGGGAGTGTAAGCG 39 47 1 TTTTAGGTTA 0.921555 -18 GTTTTTAGCCTTACAAAAAATTTAAT 42 43 0 TTTTTAGTCA 0.743876 -16 AACAATATCTTTTTAGGAATTTTTATAGGAAAATG 45 153 0 TTTTAGGTTA 0.921555 -107 CCCATTTTGATTTTAAGGATTGTCG 46 95 1 TTTTAAGTTG 0.783765 -15 TTTAATCTTTTTTTTAGCAAAACTAAACTACAATA 47 237 1 TTTTTAGACA 0.698196 -64 TGCAGGTGGGTTTTTGGTATTTTTATCATGGATGG 48 115 1 TTTTTGGTTA 0.836287 -109 TGATCAAAAATTTTGAGTTATTTAATGCATTAATT 48 187 0 TTTTGAGTTA 0.711575 -37 AAAAAAGAAATTTTAAGCTTTTTAGCTCTTACGAT 50 40 0 TTTTAAGTTG 0.783765 -69 TATCACGCTGTTTTTAGCTTTGTTGGATTTTTCTC 52 221 1 TTTTTAGTTG 0.611813 -80 AATATAAAAGTTTTTAGTAGTGCCTAATTTTTTCA 57 41 1 TTTTTAGTCT 0.622165 -38 CTTTTGCTATTTTTAGGGCTTTTTAGAGATTTTTA 61 38 0 TTTTAGGTTA 0.921555 -127 AAATGGCGCATTTTGAGTAGTATTTCAGTTTTTAT 61 82 1 TTTTGAGTTT 0.582442 -83 ATCAAGCGAATTTTAAGTTTATTGTAACACAAGCT 64 30 0 TTTTAAGATT 0.857684 -38 ******* * * * Masking position 4 Map Score: 61.1256 Number of sites scoring better than the average of aligned sites = 753 Number in coding regions = 597 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 ATATCTAATAGCGTTTAAAAAATGTAAATTT 5 154 0 GGTTTAAAAA 0.911616 -61 TTGCTATTAAGCGTTTCAAAAAAGCATCAAA 8 200 0 GGTTTCAAAA 0.660141 -101 GCGTTTTAAAAACCTTTGAGG 12 1 1 GGTTTTAAAA 0.953093 -72 AATCCTTTTTGAGTTTTAAAATCTTTACTAT 12 48 0 GGTTTTAAAA 0.953093 -25 ATGAAAAAGCGGGTTTAAAGGCGAGAATTGA 15 23 1 GGTTTAAAGG 0.815362 -182 AAAAATTGAAGTTTTTTAAAATTTGGAGTTT 19 96 1 GTTTTTAAAA 0.888747 -110 GGCTTTTAGGGGGTTTTAAATTCTTTTAAGG 19 132 1 GGTTTTAAAT 0.768056 -74 TTGTATTATAGCTTTTTAAAAATAAAATATA 20 21 0 GTTTTTAAAA 0.888747 -60 AGAATTTGGGGTGTTTTAACAGAATGCAAGC 21 70 1 GGTTTTAACA 0.789906 -34 TAGCATGAGGGTGTTTTAGAAAGACTTAAGC 22 26 1 GGTTTTAGAA 0.890203 -140 GATCTTTAAAGATTTTAAAAACTAATACAGC 23 141 1 GTTTTAAAAA 0.802185 -88 GAGAGAAAGCGTTTTTTAAGGGCTTCATCGC 29 70 0 GTTTTTAAGG 0.773768 -159 TAAATCGTTTGTTTTTTAAATTTGGAATTGT 31 130 0 GTTTTTAAAT 0.565581 -42 ATCATTAGGAGCGTTTAAAGAGAGATTGACG 34 116 1 GGTTTAAAGA 0.898791 -185 TCCCTAAAATGAGTTTAAGGATTTTA 34 285 1 GGTTTAAGGA 0.779912 -16 ACTCCTAAATGAGTTTTAAGGATTACAATCA 35 46 1 GGTTTTAAGG 0.896899 -23 GCTCTTAGTGGCGTTTAAGAATAAGTTAAGA 36 16 0 GGTTTAAGAA 0.804525 -192 TAAAAAATGGGGTTTTTAAATTTTCGCGCAA 36 49 1 GTTTTTAAAT 0.565581 -159 TAAAATTTTAGGGTTTAAAACGACCTTTATA 36 111 0 GGTTTAAAAC 0.644701 -97 AGTCAATAATGCGATTTAAAAAGGAGAA 41 8 0 GGATTTAAAA 0.467567 -120 TACTTTAAAGGGGTTTAAAGAATCAAGGGGA 46 56 0 GGTTTAAAGA 0.898791 -54 ATCCCATTTTGATTTTAAGGATTGTCG 46 93 1 GTTTTAAGGA 0.582155 -17 AATTTTAATGGATTTTTAAGAAAGGTTTTTG 47 72 1 GTTTTTAAGA 0.873066 -229 AGGCGGGTTTTAGCAACGACTTTGG 53 5 1 GGTTTTAGCA 0.600043 -31 GCGGTCATCTGGGTTTAAAAACAACCACATT 55 88 1 GGTTTAAAAA 0.911617 -32 TATTTTTAGGGCTTTTTAGAGATTTTTACTT 61 35 0 GTTTTTAGAG 0.613171 -130 CTAATAAAGAGTTTTTTAAAGAGCGATAGGT 63 94 1 GTTTTTAAAG 0.798891 -54 AAGGGGTTTTAAGCGCGCTAGCTT 64 4 1 GGTTTTAAGC 0.754767 -64 TTGAAGGCTTGATTTTTAAAGTTAGGCTTAA 67 16 1 GTTTTTAAAG 0.798891 -88 ATTTTAAAGAGAGTTTTAAAAA 68 2 0 GGTTTTAAAA 0.953093 -137 ATCAAACAACGCTTTTTAAGAGTGGCTCAAG 68 67 1 GTTTTTAAGA 0.873065 -72 * ********* Masking position 6 Map Score: 32.6591 Number of sites scoring better than the average of aligned sites = 1122 Number in coding regions = 954 Number in noncoding regions = 168 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 AATGTTATGAATCTCTTGTATTAAAAGGACTTCA 2 131 1 ACTTTTTAAA 0.863892 -24 TATTAAAATAATCATTCGTATTCAAAATGGGCTTA 6 30 0 ACTCTTTCAA 0.865944 -35 TGTTTCAAACACCAGCCATTATCAAAATTTTGTAT 10 124 1 ACCCTATCAA 0.851956 -34 TTTAGCCAAAAACCATTTTGATCAAAGCTCTAAAA 11 44 1 ACTTTATCAA 0.921489 -68 AAGCCTTTTTAAATCTTCTAATAAATTTTCTATGC 11 85 0 AATTTATAAA 0.817526 -27 TTTTCAGGAAAAATATCGTTTTAAAGGTTGTCCCA 15 63 1 AATCTTTAAA 0.711459 -142 AATTTAGAGTAAAAGTCGTATTCAAACTTTTTAAA 17 21 1 AATCTTTCAA 0.754027 -36 ATTTTAAATTACACTCTATGATAAAAACAACCAAC 18 23 1 AACTTATAAA 0.728515 -119 TATCCATTTTATCGCTTTTTTTAAATCTTTTATTA 18 76 0 ACTTTTTAAA 0.863892 -66 GGCTTAAAGAAGCGTTTCTTATCAAATAAGGAGTC 18 111 1 ACTTTATCAA 0.921489 -31 AAACGCTATAATAAATCAAAATTCT 25 1 1 AACTTATAAA 0.728515 -57 TCTACAACCAATCCGTTATATTAAAGGAAATCAAA 25 33 1 ACTTTTTAAA 0.863892 -25 AGTAAAATTAAGATTTTATAATCAAAGTCAAATCA 28 36 1 AATTTATCAA 0.847793 -46 ATGAAGCACAATACCTTGTCATCAAAGAAAGCGT 29 205 1 AATTTATCAA 0.847793 -24 GTTGTGGTATAAATATTCTTATCAAG 33 138 1 AATTTATCAA 0.847793 -16 TAGGGTTTAAAACGACCTTTATAAATAAAAATTAA 36 99 0 ACCCTATAAA 0.822343 -109 TGCATTAAAAAGCGATTTTCTTAAACAATAAGGCT 37 58 1 ACTTTTTAAA 0.863892 -89 GGTTACAATCACAAGTTTTATTAAAATTTTATTAA 40 67 1 AATTTTTAAA 0.750754 -41 TAAAAAGACAAGCGTTCTTAATAAAAACCACTAAT 45 73 0 ACTCTATAAA 0.885429 -187 GAAAATGCCCAACTTTTGTCATCAATTTGAGGAAG 47 11 1 ACTTTATCAA 0.921489 -290 AATTACATTAAACTTTTATTATCAATCCTACTTCC 47 41 0 ACTTTATCAA 0.921489 -260 AGATTATACAAAAACCTTTCTTAAAAATCCATTAA 47 76 0 AACTTTTAAA 0.64338 -225 AAACTTTAGAACCATCCATGATAAAAATACCAAAA 48 126 0 ACCCTATAAA 0.822343 -98 TAAATAACTCAAAATTTTTGATCAAAGGCTTGAAA 48 198 1 AATTTATCAA 0.847793 -26 TTCTAAAGTGATATTTCCTATTAAAGAGCAGATAC 52 149 1 AATCTTTAAA 0.711459 -152 TTTTTATATTTCCTTATAAAAAGGAAGTAA 61 6 1 AATCTATAAA 0.785754 -159 GTAAAATATTAGCATCTTTAATCAAATCATAAAAG 62 18 0 ACCTTATCAA 0.875467 -53 TTCTTATTATAACCACCATTTTAAAATAATTCACC 63 49 1 ACCCTTTAAA 0.75681 -99 GTTAGGCTTAATCTTTTATGTTAAAATTCTGAGAT 67 36 1 ACTTTTTAAA 0.863892 -68 CCATATAATGAGCCATTTTTATCAAACAACGCTTT 68 47 1 ACTTTATCAA 0.921489 -92 * * ** * ***** Masking position 9 Map Score: 36.2798 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 271 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 ATCCCCTTACCCATTATTTTACCCATTTTGC 2 40 1 CCATTATTTA 0.797468 -115 GTTTTTAACTCCTTTATTCATAAATTGTAA 3 18 0 TCCTTTATTA 0.840545 -20 TGGTAACTATCCCTTATTATATCTAATAGCG 5 172 0 CCCTTATTAA 0.88103 -43 TGAACGATCCTTATTTTATAGGTGGTAA 5 197 0 TCCTTATTTA 0.971805 -18 TGATTGTCCTTATTAAAATAATCATTC 6 48 0 TCCTTATTAA 0.946432 -17 TCAATCCTTTTTCAAAAATAACCAT 13 39 0 TCCTTTTTCA 0.815212 -15 TGACTCTTTCCTTAATTGATTTAGATTTC 14 42 0 TCCTTAATTA 0.922799 -19 CAAATGATCCTTATTTTAAATTACACTC 18 8 1 TCCTTATTTA 0.971805 -134 TTTAGGGACTCCTTATTTGATAAGAAACGC 18 122 0 TCCTTATTTA 0.971805 -20 TAAGAAAATTTCATTATTTAAGTAAGGGGAA 23 14 0 TCATTATTTA 0.903791 -215 TTGTCCTTTATATAATTAAAATCC 27 60 0 TCCTTTATAA 0.72988 -14 AAACTTATTCTCATTAATAGAACAAATCCAA 31 64 1 TCATTAATAA 0.625472 -108 TTAGGATTTTTCATTATTCAAACAAA 33 6 0 TCATTATTCA 0.73167 -148 TTGCGTTTTTTCATTTTTTTAATCCTCATTT 34 193 0 TCATTTTTTA 0.805535 -108 GATCCCTTCTCATTAATTAATAAAATTTTA 40 88 0 TCATTAATTA 0.765154 -20 TTCTCCTTTTTAAATCGCATTATT 41 4 1 TCCTTTTTAA 0.886243 -124 CGCTAGACCCTTATTTAAGCTTTAAATA 44 59 0 CCCTTATTTA 0.935263 -18 TATTCTCCTTATTTAAAGCCACCAAC 52 285 0 TCCTTATTTA 0.971805 -16 ATCTAACCCTTATTTTATTATCTCAAT 60 20 0 CCCTTATTTA 0.935263 -17 GATTTTTACTTCCTTTTTATAAGGAAATATA 61 15 0 TCCTTTTTAA 0.886243 -150 ********* * Masking position 5 Map Score: 19.6163 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 109 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 AAAGAGGCTTTTTACTTTTTTTTTGGTATT 9 29 1 TTTACTTTTT 0.866257 -71 AAAATTTAAATTTCATTTTTATTATAAGCT 10 94 1 TTTCATTTTT 0.759701 -64 TTTTAAAATCTTTACTATTTTACACTATTT 12 36 0 TTTACTATTT 0.665203 -37 AATAAAGGGTTTTTCTTTTAAATTTTGAGC 15 158 0 TTTTCTTTTA 0.76194 -47 TATTTTATTTCCTTTTTTGTATCACTG 16 20 0 TTTCCTTTTT 0.732515 -17 GATCCTTATATTTTATTTTTAAAAAGCTAT 20 15 1 TTTTATTTTT 0.872935 -66 CTTTTAAGGTTTTTCTTTTATTAAAGTTGT 20 48 0 TTTTCTTTTA 0.76194 -33 TGCTAGTATGTTTACTCTTT 22 1 0 TTTACTCTTT 0.718944 -165 AATTCTCAATTTTTATATTATAATACCCAA 22 96 1 TTTTATATTA 0.531277 -70 GACATCGCTCTTTAATTTTAATCATTGACA 23 190 1 TTTAATTTTA 0.800861 -39 TATTATAGCATTTAATCTTTGATAGGGCTT 30 45 1 TTTAATCTTT 0.747032 -33 TTTAAAGTTTTTTAATTTTTTTATACCCCC 31 36 0 TTTAATTTTT 0.882039 -136 CAACTTGAACTTTTCTTTTTCTTAAGTTTT 31 92 1 TTTTCTTTTT 0.856133 -80 TTTTGCGTTTTTTCATTTTTTTAATCCTCA 34 196 0 TTTCATTTTT 0.759701 -105 TGTATCATCATTTAATTTTTATTTATAAAG 36 88 1 TTTAATTTTT 0.882039 -120 AAAATTAACCTTTAATTTTTGAGAGAATTT 37 126 0 TTTAATTTTT 0.882039 -21 CAAAACTCTTTTTACTTTTAGTTAAGTTGT 41 67 1 TTTACTTTTA 0.776965 -61 AATCTCATTCTTTTATTTTTTTGTCAAGGT 47 106 1 TTTTATTTTT 0.872935 -195 TTAATATCCGTTTAATCTTTTTTTTAGCAA 47 227 1 TTTAATCTTT 0.747032 -74 GTTAGGAGTTTTTAATCTTAGGCTGAAGAT 50 12 1 TTTAATCTTA 0.613643 -97 AATTTTTTAATTTTAGTTTAAGCTA 52 6 1 TTTAATTTTA 0.800861 -295 TACTAAAAACTTTTATATTAACATATTTTC 57 30 0 TTTTATATTA 0.531277 -49 TTTTTATATTTCCTTATAAAA 61 2 1 TTTTATATTT 0.67819 -163 GTATTTCAGTTTTTATTTTATTGTTTTATT 61 101 1 TTTTATTTTA 0.787004 -64 GACTTTTCTTTTTTCATGGCTTG 66 14 0 TTTTCTTTTT 0.856133 -13 ATTTTATATATTTTATATTTATCGTTAGGT 67 69 1 TTTTATATTT 0.67819 -35 ********** Masking position 6 Map Score: 22.7347 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 478 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 7 CTAAAAACTCAAAATTAACCTAAAATCGCT 5 22 1 AAAATTAACC 0.942138 -193 CACCCCAAATAAAATTAAGCGAGCATTATA 8 147 1 AAAATTAAGC 0.911647 -154 ATCCTTTTTCAAAAATAACCATTTCTTGTC 13 31 0 AAAAATAACC 0.922044 -23 TAAAAATAACCAATGAAAAAG 15 2 1 AAAAATAACC 0.922044 -203 ACTCTATGATAAAAACAACCAACCAAGTGG 18 35 1 AAAAACAACC 0.896748 -107 GCTTTCGGTTAAAATCAACCGCATTCAAGT 29 161 1 AAAATCAACC 0.922817 -68 AAACGTGCTTAAAATTAAGCCTTATTGTTT 37 80 0 AAAATTAAGC 0.911647 -67 TAAAATTAACCTTTAATTTTT 37 136 0 AAAATTAACC 0.942138 -11 GATATTGTTAAAAAGTAAGCTAAGGAGTGT 43 70 1 AAAAGTAAGC 0.732663 -22 GGAAAAATAGCCAAAGTCGTTG 53 24 0 AAAAATAGCC 0.788884 -12 ATCTGGGTTTAAAAACAACCACATTGCAGG 55 94 1 AAAAACAACC 0.896748 -26 CTCCTTTGAAAAAATTAGGCACTACTAAAA 57 52 0 AAAATTAGGC 0.76525 -27 CCTAACTTTAAAAATCAAGCCTTCAAAAAC 67 12 0 AAAATCAAGC 0.883405 -92 ********** Masking position 4 Map Score: 13.883 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 105 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TGAAGCGCTATAAAATCGTTATTAGAAGTGCGTTTAA 1 128 0 TAAACTTTAA 0.943777 -173 TCTTAGTAAATCAAAACATTGCTACAATTACATCCAA 1 221 1 TAAACTTTAA 0.943776 -80 ATGGATTAAGTAAAATCACTTATCAAAGCAAAAAGGA 8 269 1 TAAACCTTAA 0.849626 -32 ATTGGATTATTTAAAAGCTTGTTAGAATACCAAAAAA 9 47 0 TAAAGTTTAA 0.645492 -53 GCTCTTGATTTTAGAGCTTTGATCAAAATGGTTTTTG 11 50 0 TAGACTTTAA 0.583019 -62 TTTTGAGTTTTAAAATCTTTACTATTTTACACTATTT 12 36 0 TAAACTTTTT 0.434528 -37 ATCGCTTTTTTTAAATCTTTTATTATAATCAAAAATC 18 64 0 TAAACTTTTA 0.876372 -78 ATAATCAAAGTCAAATCATTCTTGAAAGAGTAGAGTT 28 53 1 TAAACTTTAA 0.943777 -29 CTAATTTAGTTTAAAAGGTTTTTACAAAC 30 3 0 TAAAGTTTAA 0.645492 -75 TAAATTTGAATTAAATCGTTTGTTTTTTAAATTTGGA 31 135 0 TAAACTTTTT 0.434527 -37 ACAACCCTATTAAAAGCGTTGTTATAGATCAGCAAAA 33 106 0 TAAACTTTAG 0.604653 -48 AATTCTAGCCTTAAATCTTTGATGAAACGAAGTCAAA 34 224 1 TAAACTTTAA 0.943777 -77 TTAAAATCCTTTTTTGTATCGCATGGTA 41 110 0 TAAACTTTTA 0.876373 -18 TGAGATTATACAAAAACCTTTCTTAAAAATCCATTAA 47 76 0 CAAACTTTAA 0.583021 -225 CGTCAAATCCCTAATGCAAGAAATTAAAA 47 282 0 TAAACCTTAA 0.84963 -19 TTTGAGTTATTTAATGCATTAATTCAAGTAAGCATTG 48 174 0 TAATCTTTAA 0.496389 -50 ATTTCAAGCCTTTGATCAAAAATTTTGAGT 48 204 0 TAAGCTTTAA 0.59364 -20 CTAAAAAGCTTAAAATTTCTTTTTTAAAAAGATAATC 50 50 1 TAAATCTTAA 0.183461 -59 ATTCTAATCCTTAAAAATTTCTTTCAATTCCAACAAA 51 17 0 TAAAATTTAA 0.400316 -28 TAGGCACTACTAAAAACTTTTATATTAACATATTTTC 57 30 0 TAAACTTTTA 0.876373 -49 ATCAAACCCTTTATATTATATTCAATGT 59 17 0 TAAACTTTTA 0.876373 -18 TTAAAAATAATAAAAACTTTCTTATTATAACCACCAT 63 31 1 TAAACTTTTA 0.876372 -117 TTTTTAAAACTCTCTTTAAAATTTTACTTT 68 4 1 TAAACCTTAA 0.849626 -135 ATCGTCATAAAAACCTTGTTCTAATAGTGGTCTT 68 115 0 TAAACTTTAA 0.943669 -24 * *** * ** * ** Masking position 10 Map Score: 24.1917 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 247 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 AAACAATAGCCCCTTTGAATTGAATTTTTT 5 123 0 CCCTTTGAAT 0.858612 -92 TAAAATATTACCCTTAAAATATTTTT 7 7 0 CCCTTAAAAT 0.554092 -60 GTCTAGCCCTTTGATTAAATTCTTTC 10 7 1 CCCTTTGATT 0.928236 -151 AATTTAAAACCCCCTAAAAGCCAGAAAAAA 19 124 0 CCCCTAAAAG 0.587481 -82 TAATTCCCCTTACTTAAATAATGAA 23 6 1 CCCCTTACTT 0.629723 -223 CAGAGCAACGCCCTTAGATTATACTATAGT 23 67 0 CCCTTAGATT 0.762844 -162 TTAAAATAATCCCCTTGAATTTTTGGTCTT 24 36 0 CCCCTTGAAT 0.884419 -22 ATGCATTGAACCCCTTCATGGATACCAAAA 29 101 0 CCCCTTCATG 0.74025 -128 CTTTAATATGCCCTTTAATGAGCGCTGATA 34 160 0 CCCTTTAATG 0.906368 -141 TCCTCATTTGCCCTTTAATATGCCCTTTAA 34 172 0 CCCTTTAATA 0.725327 -129 CCCTTTAATTAAATCAAGGG 46 1 1 CCCTTTAATT 0.91411 -109 CGCAAAAAAGCCCCTTGATTTAATTAAAGG 46 12 0 CCCCTTGATT 0.942191 -98 TGCGATTTTTCCCCTTGATTCTTTAAACCC 46 47 1 CCCCTTGATT 0.942191 -63 TTCTTTAAACCCCTTTAAAGTAACATAAAT 46 65 1 CCCTTTAAAG 0.81965 -45 AAAAACCCTTTTATGATTTGATTAA 62 6 1 CCCTTTTATG 0.604115 -65 GCCCCCTTAATAGCCAACTCAA 65 3 1 CCCCTTAATA 0.768914 -63 ********** Masking position 5 Map Score: 11.8831 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 222 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 ATATCTTTGAAGCGCTATAAAATCGTTATT 1 142 0 AGCGCTATAA 0.87323 -159 ACATTTTTTAAACGCTATTAGATATAATAA 5 160 1 AACGCTATTA 0.942524 -55 AATACAGAGCAACGCCCTTAGATTATACTA 23 71 0 AACGCCCTTA 0.758507 -158 AAACGCTATAATAAATCAAAA 25 2 1 AACGCTATAA 0.827562 -56 TTTCCCCTAAAGCCCTATCAAAGATTAAAT 30 54 0 AGCCCTATCA 0.708875 -24 TTTATACCACAACCCTATTAAAAGCGTTGT 33 121 0 AACCCTATTA 0.78662 -33 TCTCTCTTTAAACGCTCCTAATGATCCTAA 34 111 0 AACGCTCCTA 0.733742 -190 CGCTAGGCAAAGCGCTATCAGCGCTCATTA 34 145 1 AGCGCTATCA 0.915479 -156 CCCATTTTTTAGCGCTCTTAGTGGCGTTTA 36 30 0 AGCGCTCTTA 0.970783 -178 AAACAAACGCTTTTAGTTTGGGTGC 39 6 1 AACGCTTTTA 0.820093 -59 TAAAAAGACAAGCGTTCTTAATAAAAACCA 45 78 0 AGCGTTCTTA 0.622325 -182 TTATGAGACCAGCGCTCTAAACCAGCTGAG 47 138 0 AGCGCTCTAA 0.906752 -163 GCAGATACGCAACGCACTTATTTCTGTTTT 52 176 1 AACGCACTTA 0.679405 -125 GGTGGTGGTGAGCGCTATCACGCTGTTTTT 52 206 1 AGCGCTATCA 0.915479 -95 AAAAACCCTTTTATGATTTGATT 62 4 1 AACCCTTTTA 0.506115 -67 AACACAAGCTAGCGCGCTTAAAACCCCTT 64 10 0 AGCGCGCTTA 0.81845 -58 TAGCCAACTCAACGCTATTAAGTGGGGCGA 65 21 1 AACGCTATTA 0.942524 -45 ********** Masking position 1 Map Score: 11.1284 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 495 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 TATATCTTTGAAGCGCTATAAAATCGTTAT 1 143 0 AAGCGCTATA 0.384342 -158 TTTTGCCCATAAGCGTTAAATTCCAATCAA 2 65 1 AAGCGTTAAA 0.79704 -90 AGAATGAAATAAGCTATAATAAGCCCATTT 6 11 1 AAGCTATAAT 0.799744 -54 GCCTCTTTATAAGCCCTAAAAAGAGC 9 7 0 AAGCCCTAAA 0.737042 -93 ATTTTGATCAAAGCTCTAAAATCAAGAGCA 11 58 1 AAGCTCTAAA 0.898702 -54 TAAAGACAGAATGCGTTAAAATGAGAAATC 14 18 1 ATGCGTTAAA 0.343859 -43 GATTTAAAAAAAGCGATAAAATGGATAGGC 18 84 1 AAGCGATAAA 0.90379 -58 AAGGATTAAAAAGCTAAAATACTGCTTCTT 19 55 0 AAGCTAAAAT 0.51346 -151 TATTTTTAAAAAGCTATAATACAACTTTAA 20 28 1 AAGCTATAAT 0.799744 -53 AGAAAGACTTAAGCGCTAAAGACTTGAGCG 22 43 1 AAGCGCTAAA 0.901982 -123 GCGTTCTTTTAYGCTATAATTAAGACCAAA 24 15 1 AYGCTATAAT 0.799744 -43 AAACGCTATAATAAATCAAAAT 25 3 1 ACGCTATAAT 0.309365 -55 CAAAGATTAAATGCTATAATACTACCCTAA 30 36 0 ATGCTATAAT 0.34766 -42 ACGCCACTAAGAGCGCTAAAAAATGGGGTT 36 33 1 GAGCGCTAAA 0.480589 -175 CACTCAAAATAAGCTAAAAACTACCAACAC 36 173 0 AAGCTAAAAA 0.705302 -35 GATTAAATTGAAGCGATAAAAAAG 44 5 0 AAGCGATAAA 0.90379 -72 ACCCTTATTTAAGCTTTAAATAACTATAAT 44 51 0 AAGCTTTAAA 0.791062 -26 AAGAGCTAAAAAGCTTAAAATTTCTTTTTT 50 45 1 AAGCTTAAAA 0.500125 -64 AAATCCAACAAAGCTAAAAACAGCGTGATA 52 221 0 AAGCTAAAAA 0.705302 -80 AATCTCTAAAAAGCCCTAAAAATAGCAAAA 61 42 1 AAGCCCTAAA 0.737042 -123 ********** Masking position 8 Map Score: 11.4087 Number of sites scoring better than the average of aligned sites = 629 Number in coding regions = 539 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 12 AATCGCAAAATTGAATTTTATTGTTTGTTAT 4 11 1 TTGATTTTAT 0.305389 -28 CCCCTTTGAATTGAATTTTTTCTCAATTTAG 5 113 0 TTGATTTTTT 0.75587 -102 ACAAAGTAGATTGGATTATTTAAAAGCTTGT 9 62 0 TTGGTTATTT 0.703438 -38 CGCTTTTTCATTGGTTATTTTTA 15 3 0 TTGGTATTTT 0.507844 -202 ATCCACTTGGTTGGTTGTTTTTATCATAGAG 18 36 0 TTGGTGTTTT 0.699244 -106 AACCAACCAAGTGGATTTTTGATTATAATAA 18 51 1 GTGGTTTTTG 0.765703 -91 TTTTAAAATTTGGAGTTTTTTCTGGCTTTTA 19 109 1 TGGATTTTTT 0.737628 -97 TGTTAGAATTTGGGGTGTTTTAACAGAATGC 21 66 1 TGGGTGTTTT 0.67857 -38 TATTTTTAAAGTGGGTTTTTTCTTAAATCTT 23 108 1 GTGGTTTTTT 0.936047 -121 AATAATCCCCTTGAATTTTTGGTCTTAATTA 24 31 0 TTGATTTTTG 0.408747 -27 AAAAATTCAAGGGGATTATTTTAACT 24 42 1 GGGGTTATTT 0.751706 -16 AACCGAAAGCGTGGCTTTTTTCATGGAATAA 29 140 0 GTGGTTTTTT 0.936047 -89 AAAGTTCAAGTTGGATTTGTTCTATTAATGA 31 74 0 TTGGTTTGTT 0.745428 -98 AAAACACTTATTGAGTTTTTTGTGATCTTTT 33 79 1 TTGATTTTTT 0.75587 -75 CGCTAAAAAATGGGGTTTTTAAATTTTCGCG 36 46 1 TGGGTTTTTA 0.346982 -162 ATCGTTTTTAGGGAGTTTGATC 38 66 1 GGGATTTGAT 0.136296 -12 ATAAATATTAGTGGTTTTTATTAAGAACGCT 45 67 1 GTGGTTTTAT 0.675152 -193 ATTAAATCAAGGGGCTTTTTTGCGCCTTGTG 46 18 1 GGGGTTTTTT 0.930022 -92 AAATCAAAATGGGATTTATGTTACTTTAAAG 46 77 0 GGGATTATGT 0.12126 -33 AGTATTGCAGGTGGGTTTTTGGTATTTTTAT 48 110 1 GTGGTTTTTG 0.765703 -114 ATCAAAAATTTTGAGTTATTTAATGCATTAA 48 189 0 TTGATTATTT 0.413595 -35 TTGGGTTTTGTTGGAATTGAAA 51 2 1 TGGGTTTGTT 0.726688 -43 TTTAGCTTTGTTGGATTTTTCTCTAGGGGCT 52 233 1 TTGGTTTTTC 0.464469 -68 TTTTTCTCTAGGGGCTTTTGTCTCTAGTGTT 52 248 1 GGGGTTTTGT 0.670753 -53 AGCAACGACTTTGGCTATTTTTCC 53 22 1 TTGGTATTTT 0.507844 -14 TTCCTGCAATGTGGTTGTTTTTAAACCCAGA 55 95 0 GTGGTGTTTT 0.765703 -25 TTATTTAGTGGTGAATTATTTTAAAATGGTG 63 62 0 GTGATTATTT 0.497844 -86 GTTCAGATTGGGGGATTTGTTTGAA 65 51 1 GGGGTTTGTT 0.788913 -15 **** ****** Masking position 6 Map Score: 9.00017 Number of sites scoring better than the average of aligned sites = 1990 Number in coding regions = 1781 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 13 CCCATAAGCGTTAAATTCCAATCAAAAACCAT 2 70 1 TTATTCCAAT 0.582903 -85 AGTTTCATTACAATTTATGAATAA 3 3 1 TTATTACAAT 0.921506 -35 TATCAAAATTTTGTATTATAATTTG 10 143 1 TTATTATAAT 0.806107 -15 GATCCTTATTTTAAATTACACTCTATGATAAA 18 16 1 TTATTACACT 0.732614 -126 CAAGTGGATTTTTGATTATAATAAAAGATTTA 18 58 1 TTATTATAAT 0.806107 -84 TTCTCAATTTTTATATTATAATACCCAATCAA 22 98 1 TTATTATAAT 0.806107 -68 AGCAACGCCCTTAGATTATACTATAGTTAAGT 23 62 0 TTATTATACT 0.492463 -167 AAGCGTTCTTTTAYGCTATAATTAAGACCAAA 24 13 1 TTGCTATAAT 0.524724 -45 AACGCATGATTTTTGCTACAATAATAGGATTT 27 34 1 TTGCTACAAT 0.757137 -40 AAGCCACGCTTTCGGTTAAAATCAACCGCATT 29 154 1 TTGTTAAAAT 0.746757 -75 TTAAGTCATTTTGCATTACAATACTCCTAAAT 35 24 1 TTATTACAAT 0.921506 -45 TTAAGCAAGATTAGGTTACAATCACAAGTTTT 40 54 1 TTGTTACAAT 0.930352 -54 CAATCACAAGTTTTATTAAAATTTTATTAATT 40 72 1 TTATTAAAAT 0.72157 -36 GCTTTTGTTACAATAATTTAGATT 43 3 1 TTGTTACAAT 0.930352 -89 TTAATCAAAATTAGATTACAATATTATAGTTA 44 29 1 TTATTACAAT 0.921506 -48 GCGCGCTAGCTTGTGTTACAATAAACTTAAAA 64 23 1 TTGTTACAAT 0.930352 -45 GCTTAATCTTTTATGTTAAAATTCTGAGATTT 67 41 1 TTGTTAAAAT 0.746757 -63 ** ******** Masking position 7 Map Score: 13.3522 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 5 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 TAATCTTAGTAAATCAAAACATTGCTACAA 1 218 1 AAATCAAAAC 0.911057 -83 TGCTCCTAAAAACTCAAAATTAACCTAAAA 5 17 1 AACTCAAAAT 0.815057 -198 TTAAAATGAGAAATCTAAATCAATTAAGGA 14 33 1 AAATCTAAAT 0.832201 -28 ACGCTATAATAAATCAAAATTCTACAACCA 25 13 1 AAATCAAAAT 0.933108 -45 AATTTGTGTAAAAACAAAACACTTATTGAG 33 64 1 AAAACAAAAC 0.676595 -90 GCTAGCTAAAAAATCTAAATTATTGTAACA 43 16 0 AAATCTAAAT 0.832201 -76 CGCTTCAATTTAATCAAAATTAGATTACAA 44 20 1 TAATCAAAAT 0.5975 -57 ATACAGACTAAAATCAAATCACACCTTAAA 45 20 1 AAATCAAATC 0.521542 -240 ACAATCCTTAAAATCAAAATGGGATTTATG 46 88 0 AAATCAAAAT 0.933108 -22 AATGAAGTTTAAATCAAAATCATGGTGTCA 47 198 0 AAATCAAAAT 0.933108 -103 TTTTTTTAGCAAAACTAAACTACAATAGCC 47 245 1 AAAACTAAAC 0.426542 -56 TGCATTAAATAACTCAAAATTTTTGATCAA 48 193 1 AACTCAAAAT 0.815057 -31 TAATGGCATTAAATCCAAATAGGGGTTAGA 63 126 1 AAATCCAAAT 0.744189 -22 ********** Masking position 7 Map Score: 6.25795 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 123 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 GTTTTTAACTCCTTTATTCATAAA 3 24 0 TTTACTCCTT 0.75424 -14 TATTTTAGCTTTTTAATCCTTTAAAAATACT 19 64 1 TTTTATCCTT 0.853997 -142 GCTTTTTTGCTCCCTTTTAAGGTTT 20 66 0 TTTTCTCCCT 0.910469 -15 CTTTTATCCTTATAAGCGTCA 22 155 0 CTTTATCCTT 0.765806 -11 GTTTTTAGCCTTACAAAAAATT 42 47 0 TTTTAGCCTT 0.845444 -12 CAAGGGGCTTTTTTGCGCCTTGTGCGATTTT 46 25 1 TTTTCGCCTT 0.96121 -85 CCTTGTGCGATTTTTCCCCTTGATTCTTTAA 46 42 1 TTTTCCCCTT 0.875585 -68 ACAGAAAGGCCTTTGCGCCTTTCTCTGATCT 48 20 1 CTTTCGCCTT 0.932673 -204 CGGCAGATGATTTTGCTCCATGATTTTGTTT 48 55 1 TTTTCTCCAT 0.788508 -169 CTTTTCCTCCTTTCTAGACTAG 50 97 0 TTTTCTCCTT 0.963632 -12 TCCATAGTTCCTTTTCGCCCTCACTTAAACT 52 79 0 CTTTCGCCCT 0.841691 -222 GATTTTTCTCCTTTGAAAAAATT 57 66 0 TTTTCTCCTT 0.963632 -13 **** ****** Masking position 3 Map Score: 8.82886 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 105 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234