AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_bsub_reg_300.orf -o00240_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: rpsM 22 ribosomal protein S13 cheW 21 cheW flhA 32 flagella-associated protein yncF 29 similar to deoxyuridine 5'-triphosphate pyrophosphatase yxeM 24 similar to amino acid ABC transporter (binding protein) Input sequences: #1 dnaA 300 alternate gene name: dnaH, dnaJ, dnaK #2 dnaN 188 DNA polymerase III (beta subunit) #3 dnaX 300 DNA polymerase III (gamma and tau subunits) #4 csfB 300 alternate gene name: yaaM; sigma-F transcribed gene #5 xpaC 119 xpaC #6 yaaO 81 similar to lysine decarboxylase #7 yaaQ 73 similar to hypothetical proteins #8 cysE 300 serine acetyltransferase #9 sigH 62 RNA polymerase sigma-30 factor (sigma-H) #10 rpmG 92 ribosomal protein L33 #11 secE 33 preprotein translocase subunit #12 nusG 178 transcription antitermination factor #13 rplK 167 ribosomal protein L11 (BL11) #14 rplA 93 ribosomal protein L1 (BL1) #15 rplJ 251 ribosomal protein L10 (BL5) #16 rplL 46 ribosomal protein L12 (BL9) #17 ybxB 89 alternate gene name: ybaA; similar to hypothetical proteins #18 rpoB 245 RNA polymerase (beta subunit) #19 rpoC 61 RNA polymerase (beta' subunit) #20 infA 300 initiation factor IF-I #21 rpmJ 33 ribosomal protein L36 (ribosomal protein B) #22 rpoA 176 RNA polymerase (alpha subunit) #23 rplQ 77 ribosomal protein L17 (BL15) #24 ybxA 127 alternate gene name: ybaD; similar to ABC transporter (ATP-binding protein) #25 yfkN 242 similar to 2',3'-cyclic-nucleotide 2'-phosphodiesterase #26 ileS 300 isoleucyl-tRNA synthetase #27 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #28 lsp 102 signal peptidase II #29 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #30 pyrP 171 uracil permease #31 pyrB 145 aspartate carbamoyltransferase #32 flgB 300 flagellar basal-body rod protein #33 fliF 45 flagellar basal-body M-ring protein #34 fliH 117 flagellar assembly protein #35 fliK 160 fliK #36 flgE 21 flagellar hook protein #37 fliL 251 flagellar protein #38 fliM 33 flagellar motor switch protein #39 cheY 25 two-component response regulator #40 sigD 22 RNA polymerase sigma-28 factor (sigma-D) #41 ylxL 28 ylxL #42 rpsB 143 ribosomal protein S2 #43 tsf 101 elongation factor Ts #44 smbA 145 uridylate kinase #45 yluA 130 similar to hypothetical proteins #46 yluB 61 similar to hypothetical proteins #47 proS 32 prolyl-tRNA synthetase #48 polC 108 DNA polymerase III (alpha subunit) #49 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #50 nusA 34 nusA #51 truB 81 tRNA pseudouridine 55 synthase #52 rpsO 156 ribosomal protein S15 (BS18) #53 pnpA 172 polynucleotide phosphorylase (PNPase) #54 miaA 98 tRNA isopentenylpyrophosphate transferase #55 ymaH 39 similar to host factor-1 protein #56 ymzC 195 ymzC #57 ymzA 81 ymzA #58 ymaA 242 similar to ribonucleoprotein #59 yncE 300 yncE #60 thyA 300 thymidylate synthase A #61 deoD 300 purine nucleoside phosphorylase #62 yosS 45 similar to deoxyuridine 5'-triphosphate nucleotidohydrolase #63 yosR 300 similar to thioredoxin #64 yosP 300 similar to ribonucleoside-diphosphate reductase (beta subunit) #65 thyB 83 thymidylate synthase B #66 ypjP 259 ypjP #67 ypiP 296 ypiP #68 yphP 106 similar to hypothetical proteins from B. subtilis #69 ilvD 288 dihydroxy-acid dehydratase #70 ypgR 59 similar to hypothetical proteins #71 bsaA 300 glutathione peroxidase #72 ndk 115 nucleoside diphosphate kinase #73 gerCA 162 heptaprenyl diphosphate synthase component I #74 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #75 mtrA 187 GTP cyclohydrolase I #76 hbs 300 non-specific DNA-binding protein HBsu #77 cmk 78 cytidylate kinase #78 ypfB 44 alternate gene name: jofB #79 ypfA 92 alternate gene name: jofA #80 ypeB 34 alternate gene name: joeB, yzuA; similar to hypothetical proteins #81 sleB 138 spore cortex-lytic enzyme #82 ypdC 119 similar to hypothetical proteins #83 ypdA 108 similar to thioredoxin reductase #84 ypcA 155 similar to glutamate dehydrogenase #85 ypbH 158 similar to negative regulation of competence MecA homolog #86 ypbG 85 similar to hypothetical proteins #87 ypbF 62 ypbF #88 ypbD 59 ypbD #89 ypbB 265 ypbB #90 drm 160 phosphodeoxyribomutase #91 ripX 300 integrase/recombinase #92 cdd 118 cytidine/deoxycytidine deaminase #93 yqfF 78 yqfF #94 yqfC 56 yqfC #95 yqfB 24 yqfB #96 yqfA 21 yqfA #97 yqeZ 130 yqeZ #98 rpsU 163 ribosomal protein S21 #99 comEB 66 alternate gene name: comD #100 comEA 83 integral membrane protein #101 yrrM 151 similar to caffeoyl-CoA O-methyltransferase #102 yrrL 130 similar to folate metabolism #103 yrrK 300 similar to hypothetical proteins #104 polA 243 DNA polymerase I #105 phoP 211 two-component response regulator #106 citH 43 malate dehydrogenase #107 citC 163 isocitrate dehydrogenase #108 citZ 300 citrate synthase II #109 dnaE 300 DNA polymerase III (alpha subunit) #110 trxB 205 thioredoxin reductase #111 yvcE 300 alternate gene name: yzkA; similar to cell wall-binding protein #112 upp 134 uracil phosphoribosyltransferase #113 glyA 206 serine hydroxymethyltransferase #114 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #115 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #116 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #117 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #118 ywlB 66 alternate gene name: ipc-28d #119 spoIIR 140 alternate gene name: ipc-27d, csfX #120 tdk 88 thymidine kinase #121 rpmE 118 ribosomal protein L31 #122 rho 300 transcriptional terminator Rho #123 ctrA 241 CTP synthetase #124 rpoE 182 RNA polymerase (delta subunit) #125 ywjF 154 similar to hypothetical proteins #126 pdp 29 pyrimidine-nucleoside phosphorylase #127 nupC 115 pyrimidine-nucleoside transport protein #128 dra 105 deoxyribose-phosphate aldolase #129 deoR 90 transcriptional regulator #130 yxxB 72 yxxB #131 yxeR 69 similar to ethanolamine transporter #132 yxeN 22 similar to amino acid ABC transporter (permease) #133 yxeK 185 similar to monooxygenase #134 yxeI 154 similar to penicillin amidase #135 yxeH 39 similar to hypothetical proteins #136 yxeF 87 yxeF Motif number 1 AGCGCCATTTGCTCTTTTTTTGTGTTCTATA 1 233 1 GCCTTTTTTT 0.959679 -68 GGCTGTGTTTCCTGTCTTTTTCACAACTTAT 2 85 1 CCGTCTTTTT 0.70916 -104 ACCTGAAAAGGTCTTTTTTTGTACTCTTAA 5 10 1 GGCTTTTTTT 0.895167 -110 AACCCGTTCAGCGGGTTTTTTATTGTGGCTT 12 56 1 GCGGTTTTTT 0.762643 -123 TATTAGAACCTCCTTTTTTCATGGCTTAA 17 71 0 CCCCTTTTTT 0.897928 -19 GGGGCCTACCTCCCTTTTTATCTTCGGAT 19 43 0 CCCCCTTTTT 0.745069 -19 CTGGATCTATGCCCTTTTTTTAGATACTGCA 24 55 1 GCCTTTTTTT 0.959679 -73 TGGGATGAGAGGGCTTTTTTTATTTTCTGAA 26 258 1 GGCTTTTTTT 0.895167 -43 CGTAAAAGCCGGGCTTTTTTTGTGCCAAGAG 27 26 1 GGCTTTTTTT 0.895167 -52 ATCTTAGACCGGGGTTTTTTTTCAGCCTTAA 31 102 1 GGGTTTTTTT 0.853526 -44 ATGTTTACAGGGGGTTTTTTTGTTAATACTG 45 53 1 GGGTTTTTTT 0.853526 -78 ATACGCCTATCCTCTCTTTTT 51 1 0 CCCTCTTTTT 0.781329 -81 CGGGAGGATTCCCGCTTTTTTATCGTATTAA 53 21 1 CCGCTTTTTT 0.857208 -152 TATCCATTTTGCCCTTTTTTTGCATCGGTAA 54 19 0 GCCTTTTTTT 0.959679 -80 GCCAAGGCACGGTCTTTTTTTATGAGAACAA 56 119 1 GGCTTTTTTT 0.895167 -77 GCAGTTTTTTTTCATGTTATG 58 1 1 GCGTTTTTTT 0.942002 -242 TTCTCGTTCTGCTCTCTTTTTTGGGCCCTAA 58 77 1 GCCTCTTTTT 0.887733 -166 AAGCTGCTTTGCAGTTTTTATGGTGTGTTCA 67 78 0 GCGTTTTTAT 0.79732 -219 ATACTAGAGGGGGCTTTTTTT 68 96 1 GGCTTTTTTT 0.895167 -11 TGCATGATCTGCACCTTTTTTATCT 69 5 0 GCCCTTTTTT 0.951144 -284 TGCAGATCATGCACCTTTTTTATGTGAATTC 69 23 1 GCCCTTTTTT 0.951144 -266 TTTGTTCTTTCGTGTTTTTATATTTATATAG 69 155 0 CGGTTTTTAT 0.389404 -134 AATTCATATGGCTCGTTTTTTATCTTATCAT 71 160 0 GCCGTTTTTT 0.824819 -141 TTATCACACCTCTTTTTATGCTTTCTCAT 80 16 0 CCCTTTTTAT 0.722597 -19 CAGCAACCGTGCGGCTTTTTTGTGTGCAGTT 81 19 1 GCGCTTTTTT 0.929998 -120 TTTTTTGTGTGCAGTTTTTATGTTCTGAGGG 81 34 1 GCGTTTTTAT 0.79732 -105 GCTGATTTCAGCAGTTTTTTTTCGTTAAAAA 84 28 1 GCGTTTTTTT 0.942002 -128 CAAGCACAATGCAGTTTTTATTGCCATACGG 85 29 0 GCGTTTTTAT 0.79732 -130 ACGATAGAAACGTCTTTTTTTATTGTCCGTC 86 29 1 CGCTTTTTTT 0.794175 -57 TCGTTGATTTGCTCTTTTTATTTTAACAGAT 89 215 0 GCCTTTTTAT 0.852173 -51 GCAGGTGGCTGCGGCTTTTTTGTTTAGAGCG 90 13 1 GCGCTTTTTT 0.929998 -148 CTTGAAAGCCTCCTTTTTTTCTATACGTC 90 142 0 CCCCTTTTTT 0.897928 -19 ACATAATCGCGCGCTTTTTTTCACGCCCATT 92 48 0 GCCTTTTTTT 0.959679 -71 CTATACTGCTCCGGCTTTTTTCTGCTTTATG 102 37 1 CCGCTTTTTT 0.857208 -94 GCTTTATGCAGGCCTCTTTTTGTAATAAATT 102 60 1 GGCTCTTTTT 0.739374 -71 TTTGTGTTCCCGTCCTTTTTTGTGTCTTCTC 104 116 1 CGCCTTTTTT 0.75939 -128 CTTATGCCCGGCGGGTTTTTTGACGATGTTC 112 31 1 GCGGTTTTTT 0.762643 -104 CTGTGTTTCAGCTCCTTTTTTATTGTCCCAT 112 113 0 GCCCTTTTTT 0.951144 -22 TTGGACACGCCCCGCTTTTTTAGCCTATGCG 116 43 0 CCGCTTTTTT 0.857208 -36 AAAATTCGCAGCACTCTTTATTTTTACCT 122 9 0 GCCTCTTTAT 0.65697 -292 GTAGGGGATCGCGGTCTTTATCAGTAAAAAG 125 123 1 GCGTCTTTAT 0.566528 -32 TCTTTCCTCCTTTTTTGGGCGAATGC 136 72 0 CCCCTTTTTT 0.897928 -16 ** ******** Masking position 7 Map Score: 52.946 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 544 Number in noncoding regions = 244 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 2 GGATAAGTTGTGAAAAAGACAGGAAACACA 2 88 0 TGAAAAAGAC 0.540178 -101 TTTTGTTATGTAAAAAGAGCTTTTGGAATC 3 228 1 TAAAAAGAGC 0.51901 -73 CTCTTAATAATAAAAAGAAGATGAAACTTG 5 34 1 TAAAAAGAAG 0.693998 -86 CTTTAAGCCATGAAAAAAGGAGGTTCTAAT 17 69 1 TGAAAAAAGG 0.823233 -21 TTGCAGTATCTAAAAAAAGGGCATAGATCC 24 57 0 TAAAAAAAGG 0.653569 -71 ATGATTATTGTAAAAGGGAGAAAAATGAGT 25 143 0 TAAAAGGGAG 0.817344 -100 CAAATTTCGTTGAAAGGTGGAGAACTG 25 226 1 TGAAAGGTGG 0.571254 -17 AAAAAACGGTTGAAAGGGACAGTCATGTTT 26 33 1 TGAAAGGGAC 0.772285 -268 ATATTGAGGGTGAAAAAAACTGAAATGGAG 32 271 1 TGAAAAAAAC 0.479891 -30 GCTAAAAACATGAAAAGTAGCCAGGAGTTT 35 52 1 TGAAAAGTAG 0.356838 -109 ACATTTTTCTTGAAAAAAGGTGATAAAAGG 43 39 0 TGAAAAAAGG 0.823233 -63 CTATACTGCCTGAAAAGAGCCGACTTAGCC 44 28 0 TGAAAAGAGC 0.727052 -118 GGGAGATTTATAAAAGAGAGTGATACATA 54 80 1 TAAAAGAGAG 0.706055 -19 AATACAGGTGTAAAAGAGGGGGATTAACTC 60 153 1 TAAAAGAGGG 0.788239 -148 CAACTGAAAATGAAAGAAGGATATGAATAG 60 279 1 TGAAAGAAGG 0.878302 -22 AAACTTGAATTAAAAGGAGCTAATACATA 62 27 1 TAAAAGGAGC 0.625772 -19 TCCCTTTAGTTGAAAAGAAGTCATGGGATT 63 208 0 TGAAAAGAAG 0.848453 -93 CAATATTTCATGAAAGGAGGCTTTCCGCAT 66 104 0 TGAAAGGAGG 0.930772 -156 CGCCTTAAAATAAAAGAAAGTGTCCCCAGC 68 14 0 TAAAAGAAAG 0.653569 -93 CATTATAGCATAAAAAAAAGAATTGGCTGT 73 61 0 TAAAAAAAAG 0.549022 -102 GGATGAAAAAAGGAAAAAAAGGA 76 4 1 TGAAAAAAGG 0.823233 -297 ACGAACTTTATGAAAAAGGGTGAAAAATTG 77 19 0 TGAAAAAGGG 0.85569 -60 AAGCACGTAATGAAAAAAAGGAAAAGACAT 79 31 0 TGAAAAAAAG 0.750328 -62 TGAGAAAGCATAAAAAGAGGTGTGATAA 80 17 1 TAAAAAGAGG 0.778495 -18 TACTATTCTCTGAAAGGGAGCATGTGAGAA 84 109 1 TGAAAGGGAG 0.916987 -47 TCTGTTAAAATAAAAAGAGCAAATCAACGA 89 216 1 TAAAAAGAGC 0.51901 -50 TGGATCAGGATGAAAAAGGCGGATGGTTCG 91 239 1 TGAAAAAGGC 0.645451 -62 GAAATGGGCGTGAAAAAAAGCGCGCGATTA 92 46 1 TGAAAAAAAG 0.750328 -73 GTGTATGATTTGAAAGGAGGTTCTAACACT 94 11 0 TGAAAGGAGG 0.930772 -46 ACACATGAGATGAAAGGGGGTTCTTTTTGT 94 37 1 TGAAAGGGGG 0.944807 -20 GCACTTATTATAAAAGGAAGGAGGGATACA 97 105 1 TAAAAGGAAG 0.778495 -26 GTCTATATAATGAAAGAAAGGGGTTG 98 7 0 TGAAAGAAAG 0.823233 -157 CCTCCCGTTCTAAAAAGGAGTGCCCCAGTC 101 123 0 TAAAAAGGAG 0.74277 -29 TTCGCAAACTTGAAAGAGACGAATTAATCG 103 230 1 TGAAAGAGAC 0.645451 -71 GGAAATTTATTGAAAAGGAGATGTTATAT 108 282 1 TGAAAAGGAG 0.876971 -19 AGGTTCACAGTAAAAGGGAGGATATAAAAA 111 281 1 TAAAAGGGAG 0.817344 -20 TATACCAATAAAAGAAACGAAGTCGCCG 115 9 1 TAAAAGAAAC 0.366775 -67 TCCTAGTGCTTAAAAGAAGGTATTACGCAG 122 41 0 TAAAAGAAGG 0.74513 -260 TTCAATTTCTTGAAAGGGAGCATAACGTAC 123 102 0 TGAAAGGGAG 0.916987 -140 TTCAAGAAATTGAAAGGGAGCTTTCTTATT 123 118 1 TGAAAGGGAG 0.916987 -124 TCTTTATCAGTAAAAAGGGGGAATTGGA 125 137 1 TAAAAAGGGG 0.817344 -18 AAGATTTCTGTGAAAGAGGGTTGGACAC 130 55 1 TGAAAGAGGG 0.901853 -18 TAATCTGAATTGAAAAGGGGACTGATCAA 134 136 1 TGAAAAGGGG 0.916987 -19 ********** Masking position 5 Map Score: 37.7344 Number of sites scoring better than the average of aligned sites = 1026 Number in coding regions = 720 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 325 Fraction of orfs with sites within 600 bp upstream = 0.0522004 Motif number 3 GGCTCATGGATCTCTCTCAGCCAATGAAGAT 8 63 0 TCTCTCTCGC 0.54963 -238 GTCCAGTCCTTCCCTCCCCGCATTTGGTTTT 12 145 0 TCCCTCCCGC 0.854829 -34 AGCGGTTAGGCCCCTACTGTCTACGGTATAA 15 69 0 CCCCTACTTC 0.561626 -183 TAAAAAAAGCCCTCTCATCCCATAAGGGACG 26 249 0 CCTCTCATCC 0.676842 -52 GAAGAAAAAACCCCTCCTGCCAGAGCATAGA 29 228 0 CCCCTCCTCC 0.986268 -46 CTTTGTTGTGCACCTCTTTGCAACCTCTCTG 30 33 0 CACCTCTTGC 0.684724 -139 GTTCTTTCCCCTCTCTTTTCAACTTAAGGC 31 126 0 CCTCTCTTTC 0.798956 -20 TTACTCGCCTCCCCTCCCTCC 37 1 0 CCCCTCCCCC 0.976692 -251 TAAAAGGCAGTCCCTCTTATCACCTTTTGAA 43 15 0 TCCCTCTTTC 0.696562 -87 CCATGTCCCACCCCTCCTTCCTGCGGTTAGG 61 106 1 CCCCTCCTCC 0.986268 -195 GCCTTTCACCTCCTCCCAAAAGGATAC 76 284 0 CACCTCCTCC 0.908143 -17 AATTCCTCTCCTTGCTCTTTTCTCC 77 64 0 CCTCTCCTGC 0.945864 -15 AACGTTCCCTCCTGCCTCTACTTGCA 85 143 0 TCCCTCCTCC 0.952096 -16 GTGTACATTCCTCTCTTACCTATAATGGTA 92 99 0 CCTCTCTTCC 0.937048 -20 GGGCGGTGTATCCCTCCTTCCTTTTATAATA 97 110 0 TCCCTCCTCC 0.952096 -21 TCTCTTTCCCTCCCTCCGAATACACCA 98 147 0 TCCCTCCCCC 0.92061 -17 CACCGTTTTGCACCTCTTTCCCAAATTCG 103 9 0 CACCTCTTCC 0.810498 -292 GTCTCTCTTCTCCTTTATGGCT 106 32 0 TCTCTCTTTC 0.523754 -12 CAGCGAGATCCTCTCCTATCCGTATCCTGT 113 187 0 CCTCTCCTTC 0.901828 -20 GCTTCGCTCCCCTCTCTCTGCCAGCTGTGTT 120 66 0 CCTCTCTCGC 0.815157 -23 TGTATCCATCTCCTTCCGCCCTGAATC 121 102 0 CATCTCCTCC 0.825674 -17 TTCGTTTGCTCCTCTCTTCGCTCTTAGCTAC 123 221 0 CCTCTCTTGC 0.883157 -21 AGACCGCGATCCCCTACCCCCGAATCTGTAT 125 109 0 CCCCTACCCC 0.736826 -46 ******** ** Masking position 5 Map Score: 21.8186 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 135 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 ACTTTGTGGATAAAGAGGAAAGGTAGGATTA 1 76 0 TAAGAGGAAA 0.733116 -225 ACATTATCCGTTAGGAGGATAAAA 2 175 1 TAGGAGGATA 0.776629 -14 TCCTACTCTCACAGGGGGAAACCCCCGACTA 4 91 0 AAGGGGGAAA 0.941612 -210 AATAATAAAAAGAAGATGAAACTTGTTTAAG 5 39 1 AAAGATGAAA 0.41397 -81 TATAACCACATAAGGAGGAAATTTTAAA 14 76 1 TAGGAGGAAA 0.953309 -18 GTTACGATGCTCAAGAGGAAAAAGTGTATGC 26 177 1 TAAGAGGAAA 0.733116 -124 CCATCCACGAACAGGAGAATATGTCGAATTT 29 11 1 AAGGAGAATA 0.280621 -263 AAGTCAACAATCAGGGGGAAATCATC 30 156 1 TAGGGGGAAA 0.937786 -16 TGCCGAAAAGAAAGGAGAAAAAACAGAAATT 32 70 1 AAGGAGAAAA 0.696118 -231 ACAAGGATATTGAGGGTGAAAAAAACTGAAA 32 265 1 TAGGGTGAAA 0.783693 -36 TTAAGGTATTAGGGGGATAACA 40 9 1 TAGGGGGATA 0.71964 -14 AAATGACCTAAGCGGAGGAAAAAAACCATTA 42 106 1 ACGGAGGAAA 0.599702 -38 AACCATTATATTAGGAGGAAATAAC 42 129 1 TAGGAGGAAA 0.953309 -15 TTTAAACATATAAGGAGGAATACAA 43 87 1 TAGGAGGAAT 0.633296 -15 CAGATCAAACAGAGGGTGAAAAC 57 69 1 AAGGGTGAAA 0.794924 -13 ATTTAGATTTACAGGAGGATATGAG 61 286 1 AAGGAGGATA 0.788127 -15 GACTACTTTTAAAGGATGAAAAAA 65 70 1 AAGGATGAAA 0.840012 -14 CTATACGTGTTGAGGGGGAAACAACAGAAAA 71 40 1 TAGGGGGAAA 0.937786 -261 ACTTTATGAAAAAGGGTGAAAAATTGATGAA 77 14 0 AAGGGTGAAA 0.794924 -65 TACAATCCTTAGAGGAGAAAAGAGCAAGGAG 77 51 1 AAGGAGAAAA 0.696118 -28 AAACAGGAGGAAAGGACTAAATG 79 3 1 AAGGAGGAAA 0.956225 -90 AAACCGGTAAACAGGATGAAAACTTTCAATG 91 108 0 AAGGATGAAA 0.840012 -193 TTGAAATGGATCAGGATGAAAAAGGCGGATG 91 233 1 TAGGATGAAA 0.830724 -68 CTGAGGCTTCTTAGGAGGAAATTGA 104 229 1 TAGGAGGAAA 0.953309 -15 ACAACACTCTTAAAGGGGAAATTTATTGAAA 108 266 1 TAAGGGGAAA 0.669747 -35 AAGATCGTTTTGAAGATGAAATCTGATA 123 8 0 TAAGATGAAA 0.397684 -234 TTATCAGTAAAAAGGGGGAATTGGA 125 140 1 AAGGGGGAAT 0.577003 -15 TACGTTTGAAAAAGGAGAAAACC 131 57 1 AAGGAGAAAA 0.696118 -13 TTCGCCCAAAAAAGGAGGAAAGA 136 75 1 AAGGAGGAAA 0.956225 -13 * ********* Masking position 9 Map Score: 29.3346 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 183 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 5 TGTAAAAGGGAGAAAAATGAGTATTATGTA 25 135 0 AGAAAAATGA 0.907126 -108 AAGTTCGTGTAAAAAAATGTCCTCACAATT 32 180 0 AAAAAAATGT 0.74461 -121 TTCTGCCGCTAAAAACATGAAAAGTAGCCA 35 45 1 AAAAACATGA 0.889382 -116 GCAGTTCTGTACAAAAATGACCTAAGCGGA 42 92 1 ACAAAAATGA 0.775565 -52 CCTTTTTTCAAGAAAAATGTGTAATATACA 43 49 1 AGAAAAATGT 0.759778 -53 CGATTTATCAAAAAACATGTTAAAATAGAA 48 20 1 AAAAACATGT 0.722493 -89 ACCGAGGATTACAAAAATGATTATTTGTTT 59 61 1 ACAAAAATGA 0.775565 -240 CTACCCTTAGAAAAAAATGTCCCAAAACAA 59 85 0 AAAAAAATGT 0.74461 -216 CTAAAATAAGAGAAACATGACAATAAAATA 66 223 1 AGAAACATGA 0.897139 -37 CCTGTCTCAGAAAAAAATGAGAGCAAGTAA 76 206 0 AAAAAAATGA 0.900038 -95 ACATTTCAACAGAAAAATGATTGAGAATGC 89 115 1 AGAAAAATGA 0.907126 -151 TTTTATACATAAAAAAATGAAACCTTTGAT 97 51 1 AAAAAAATGA 0.900038 -80 AGAGTGTTGTAAAAACATGAGGCTTACTTA 108 246 0 AAAAACATGA 0.889382 -55 TACACGCTTAAGAAAAATGACAAATGATGT 111 14 1 AGAAAAATGA 0.907126 -287 AAGCGAGGACAAAAACATGAGAAGATCAAT 122 107 0 AAAAACATGA 0.889382 -194 ATGATTTATAAGAAAAATGAGGGGTGAAAA 123 146 0 AGAAAAATGA 0.907126 -96 TATTCAGCCTAAAAACATGATAAAAGGAGT 133 160 1 AAAAACATGA 0.889382 -26 ********** Masking position 5 Map Score: 14.3944 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 201 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 6 AGAGGGCTTTTTTTATTTTCTGAAAAAATGCAGTGGAGGA 26 265 1 TTTTTTTAAG 0.662514 -36 AAAAAACCTCTTTGCTTTTTTACGCAAAGAGGCATACAAA 30 87 0 TTTTTTTAAA 0.859537 -85 GATTGTTGACTTTCATTTTAGGATGACTCAATGACTGTAT 30 128 0 TTTTTTTATA 0.666625 -44 AGTTTTCTTTTTTCCTTTTGTGGAGAAATAGATGATTCTT 34 22 0 TTTTTTTAAA 0.859537 -96 GGATTCAGATTTCATTTTTACCGAGAAAGGATGTATTCA 63 272 1 TTCTTTTAAG 0.643458 -29 TTAAATTCACTGCATTTTTTTCGGAAAAAAATATTTCAAT 64 254 1 TGCTTTTAAA 0.567551 -47 CTCCGGGCATTTTCTTTTTGGGAGTACAGAAGATGATAAC 67 20 1 TTTTTTTAAA 0.859537 -277 TTTATGTGAATTCACTTTTTATAAAAATTATTTCGAATAT 69 41 1 TTCTTTTATA 0.647677 -248 ATGCTCTTTTTGTTTTTTTAAGTGCAGACAGATGTAAAAT 82 37 1 TGTTTTTAAA 0.588067 -83 ATAGGAGATTTTTTATTTTTATGCAAATCATCAAC 83 6 0 TTTTTTTATA 0.666625 -103 GGTATTATTTTTATTTTACGTTCATATATTGTAGCAAT 87 9 1 TTTTTTTAAA 0.859537 -54 TATCAAAGGTTTCATTTTTTTATGTATAAAAAAAGACATC 97 42 0 TTCTTTTAAA 0.849071 -89 TTTCGTCATATTTTATTTTCATAACACATATGGTTTAGAG 100 38 0 TTTTTTTAAA 0.859537 -46 AATACAGCCTTTCTCTTTTTACTATAAATGAAAGCGCTAT 105 34 1 TTCTTTTAAG 0.643458 -178 TTAGAAAACATTTTATTTTTCTTATATAGAAAATAAAATG 107 104 0 TTTTTTTAAA 0.859537 -60 ACTAAAACCCTTTGCTTTTGAAAGAACATAACAAATTTTT 108 141 0 TTTTTTTAAA 0.859526 -160 AATGTAAGCATTTTCTTTTTGGGGGAGAGAAATACTTGCA 108 196 1 TTTTTTTAAA 0.859537 -105 TGAAACTCAATGTCTTTTTTTGTAGAATCAATAGAAGTGT 112 63 1 TGTTTTTATA 0.318102 -72 ATAGCCAGTCTTTTCTTTTATTTTAAGATAGTGAAATAAA 113 20 1 TTTTTTTAAA 0.859537 -187 GTTATTAATATTCGTTTTTACCAATAAAAATTTAGATTTT 113 84 1 TTCTTTTAAA 0.849058 -123 AAGTCGCCGTTTCTTTTTTCTTCATATATAATAGAGAAAA 115 30 1 TTCTTTTAAA 0.849071 -46 CCAAAGCACATTCTTTTTTTAACATAAAGGAACTTCTATC 122 200 0 TTCTTTTAAG 0.643458 -101 GCATATTCTGTTTTATTTTGTTTATAATGAGAGGTATGGT 124 74 1 TTTTTTTATA 0.666625 -109 GCAGACTGCTTTCCGTTTTCTGAGGAAACAGTAATTGTAA 127 59 1 TTCTTTTAAA 0.849071 -57 AATATAGGAGTTTATTTTTCGCATTATTCAGCCTAAAAAC 133 136 1 TTTTTTTATA 0.666625 -50 *** **** * * * Masking position 9 Map Score: 17.4882 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 173 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 7 AATGAAACCTTGAGTGGGAGGGTTTACCCTATTAC 13 114 1 TAGGGAGGTT 0.91096 -54 AGCCTCCATGAGACATGGAGGCTGTATATACAAGC 15 148 0 AATGGAGGTT 0.921483 -104 TTAAGCCATGAAAAAAGGAGGTTCTAATA 17 71 1 AAAGGAGGTT 0.891192 -19 GTAGACATATAAAGCGGGAGGTTATGAATC 25 6 0 AAGGGAGGTT 0.983319 -237 GGCAATGTTTACACTTGGAGGTTATC 44 130 1 AATGGAGGTT 0.921483 -16 TCGTAAAAAGCGGGAGGATTCCCGCTTTTTT 53 7 1 AAGGGAGGTC 0.972701 -166 GCACTTGCAGATAAAGTGAGGATCTTATTCCACTC 60 200 0 AAGTGAGGTT 0.769345 -101 AACAATATTAATAGTTGGAGGGTTCAAATCGAAAG 69 116 1 AATGGAGGTC 0.87645 -173 ATGCTCGCAAACAGCGGGAGGATACAGCCAATTCT 73 38 1 AAGGGAGGTC 0.972701 -125 CACCAAGAACAATCTGGGAGGTTTTATTC 89 5 0 ATGGGAGGTT 0.843664 -261 GACGTATAGAAAAAAAGGAGGCTTTCAAG 90 142 1 AAAGGAGGTT 0.891192 -19 ACTCCTTTTTAGAACGGGAGGCTGTTTGTA 101 132 1 AAGGGAGGTT 0.983319 -20 TATGAATTACATACTGGGAGGTTTTTATT 107 145 1 AAGGGAGGTT 0.983319 -19 AGGTTCACAGTAAAAGGGAGGATATAAAAA 111 281 1 TAGGGAGGTT 0.91096 -20 TATAAGTAATAGAAAGGGAGTGTCCGACC 124 164 1 AAGGGAGTTC 0.66845 -19 * * ****** * * Masking position 9 Map Score: 16.0338 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 27 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 TCCGGCACGTCCCTCCTTTTCTTAGAAAATGGC 1 276 0 CCTCCTTTTT 0.933774 -25 TAACAAAAAACTCACCTAATATTAGGTGAGTCT 3 203 0 CCACCTATTT 0.527664 -98 GTCATTACACCTTTTTCTAAATAGACAT 10 75 0 TCACCTTTCT 0.784087 -18 TGTATAGGCGCGCACCTTGTCCTAAAACCCCTC 29 197 1 CCACCTTTCT 0.944288 -77 ATTGATCATTCTCACCTTTTGCAGGCTGAAGAG 34 81 1 CCACCTTTCA 0.902996 -37 AATCTATCTCTCTCCTTGTGTTTCG 39 4 0 CCTCCTTTTT 0.933774 -22 GTTCTTCCTCCTTGTGCTGTCGATCTCA 49 283 0 TCTCCTTTCT 0.766315 -18 TTGCCTTTCACTCCTTCTTTTGAGTTTTTTT 51 61 0 CCTCCTTTTT 0.933774 -21 GTGCATGATCTGCACCTTTTTTATCT 69 4 0 TCACCTTTTA 0.647558 -285 GTGCAGATCATGCACCTTTTTTATGTGAATTCA 69 22 1 TCACCTTTTA 0.647558 -267 ACAGGCCGCCCTCACCTTGTTTTGTTCTTTCGT 69 173 0 CCACCTTTTT 0.939811 -116 AATTCCTCTCCTTGCTCTTTTCTCCTCT 77 61 0 CCTCCTTCCT 0.749175 -18 TTATCACACCTCTTTTTATGCTTTCTC 80 18 0 CCACCTCTTT 0.623456 -17 ACGCTTCACACCTTGTCCATTTTCATTGC 87 44 0 CCACCTTTCA 0.902996 -19 GGCGGTGTATCCCTCCTTCCTTTTATAATAAGT 97 107 0 CCTCCTTCTT 0.733444 -24 GAGCAAAAAGCTCTCCTTTTGTTCGCTTTCCGC 101 16 1 CCTCCTTTTT 0.933774 -136 TCTTTATCACCTCACCTTTTATATCATATTGAG 109 171 1 CCACCTTTTA 0.895567 -130 GTCAGTCACCCCTTATTTTTCTCTATTAT 115 57 0 CCCCCTTTTT 0.746224 -19 TTATCCCAGGCTCTCCTTGTCCATAATAGGGCT 119 84 1 CCTCCTTTCA 0.893684 -57 GGTTTTCTCCTTTTTCAAACGTATGAT 131 53 0 TCTCCTTTCA 0.642986 -17 * ****** * ** Masking position 7 Map Score: 12.4874 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 146 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 9 TCAGATAGAGAAACGGGGGGAAGCAT 8 285 1 AACGGGGGAA 0.891933 -16 GCATTCCAATAAAGGAGGGGACATCAC 23 61 1 AAGGGGGGAC 0.962761 -17 AATTTCGTTGAAAGGTGGAGAACTG 25 228 1 AAGGGGAGAA 0.947382 -15 CTCATCCCATAAGGGACGAGAAAGCTTATCTC 26 235 0 AAGGCGAGAA 0.70892 -66 TTAAGTTGAAAAGAGAGGGGAAAGAAC 31 129 1 AAAGGGGGAA 0.872362 -17 TTAATCATAAAACAGCGGAGAAGCGATTACTC 37 26 0 AAAGGGAGAA 0.809537 -226 TACCGAGGCAAAGAGTGGGGAAACCCGCTCTT 49 150 1 AAAGGGGGAA 0.872362 -151 CAAATGTTTTAAGGGGGGAGACCGTTAA 50 17 1 AAGGGGAGAC 0.941444 -18 TGAATGCTATAATGGGGGAGATTTATAAAAGA 54 65 1 AAGGGGAGAT 0.675897 -34 AACGCTTCTTACAGGGGGAGAAAGAACCT 67 278 1 ACGGGGAGAA 0.681866 -19 ATTTGCTTTTAACAGCGGGGACAGCCAGC 73 8 0 AAAGGGGGAC 0.859217 -155 ATAGAAACGAGGAGAAGTTAT 96 5 1 AACGGGAGAA 0.83694 -17 ATAATAGCTCAAAGGAGGGGAAACCA 100 5 0 AAGGGGGGAA 0.966613 -79 ATAAGAGCTGATGGGAGGAGACCTA 102 116 1 ATGGGGAGAC 0.563575 -15 AAGACACAAAAAAGGACGGGAACACAAATAGG 104 112 0 AAGGCGGGAA 0.796595 -132 AAGAACGCAAAAACGGGGTGAACGG 118 52 1 AACGGGTGAA 0.587933 -15 CACGGAGAGGAACGGTGGGGACCG 119 127 1 AAGGGGGGAC 0.962761 -14 GAAACGGCGGTGACTCACCAGA 132 3 1 AAGGGGTGAC 0.81716 -20 ** ** ****** Masking position 11 Map Score: 16.9583 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 75 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 10 AGAAAATGGCGTCTTTCTCTGTTATAGAAC 1 256 0 GTCTTTCTCT 0.8905 -45 TGAAATGTACGCTTTTCTCCGTCTGCTGTT 20 127 0 GCTTTTCTCC 0.815122 -174 CTAATGCTCTGCTTTTCTCTCTATTAAAAG 24 87 0 GCTTTTCTCT 0.897264 -41 GTTTTTCACTCGCTAACCAT 41 19 0 GTTTTTCACT 0.689214 -10 TTGCCTTTCACTCCTTCTTTTG 51 70 0 GCCTTTCACT 0.928963 -12 TTTTACACCTGTATTTCTCCATAACATAGT 60 138 0 GTATTTCTCC 0.573655 -163 CCGTTTAATTGTCTTTCTCTTACTTGCTCT 76 187 1 GTCTTTCTCT 0.8905 -114 GCCTTTCACCTCCTCCCAAA 76 291 0 GCCTTTCACC 0.868449 -10 CCTGCGATTGGCATTTCACTTCATATTTTC 83 78 0 GCATTTCACT 0.810817 -31 TATTAAGCAAGCCTTTCTCTCTTTTTA 105 8 0 GCCTTTCTCT 0.953413 -204 GCTTAATACAGCCTTTCTCTTTTTACTATA 105 30 1 GCCTTTCTCT 0.953413 -182 CACGATGCAAGTATTTCTCTCCCCCAAAAA 108 211 0 GTATTTCTCT 0.727173 -90 CATATGATGTGCTTTTCACTATATTCTACT 114 59 0 GCTTTTCACT 0.848041 -98 ********** Masking position 5 Map Score: 7.91362 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 148 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 11 GGGAATGATGAATAACGGAGGAGGGCAAACC 3 279 1 AATAAGGAGG 0.883527 -22 TTAAGCCATGAAAAAAGGAGGTTCTAATA 17 71 1 AAAAAGGAGG 0.883527 -19 ATCCGAAGATAAAAAGGGAGGTAGGCCCC 19 43 1 AAAAAGGAGG 0.883527 -19 TACTGATTTGAAGAAGGGAGAACACTTGA 20 282 1 AAGAAGGAGA 0.901193 -19 ACAGCATTCCAATAAAGGAGGGGACATCAC 23 58 1 AATAAGGAGG 0.883527 -20 TGTGTATCTAAAGAAGGGCGGGACAGTTTCT 24 22 1 AAGAAGGCGG 0.758543 -106 AAATGCCGAAAAGAAAGGAGAAAAAACAGAA 32 67 1 AAGAAGGAGA 0.901193 -234 TGATATAGAGAATCAAGGAGGACGAAAC 55 22 1 AATCAGGAGG 0.654471 -18 ACAATATTTCATGAAAGGAGGCTTTCCGCAT 66 104 0 ATGAAGGAGG 0.679447 -156 AAGTTCTAAAAAGAATGGAGAGTTTTTT 86 68 1 AAGAAGGAGA 0.901193 -18 TTTTGTCAGGAAGAATGTAGGTGGATAGG 89 247 1 AAGAAGTAGG 0.566865 -19 GACGTATAGAAAAAAAGGAGGCTTTCAAG 90 142 1 AAAAAGGAGG 0.883527 -19 TCTCTCTAAGAAGGGAGAACGCTG 95 8 1 AAGAAGGAGA 0.901193 -17 CTTATTATAAAAGGAAGGAGGGATACACCGC 97 108 1 AAGGAGGAGG 0.781688 -23 GCTAGAAACAAAGCACGGAGAGGAACGGTGG 119 114 1 AAGCAGGAGA 0.694882 -27 AGCGAATACAAATAAAGGAGAAACACAT 127 98 1 AATAAGGAGA 0.723887 -18 GCATTCGCCCAAAAAAGGAGGAAAGA 136 72 1 AAAAAGGAGG 0.883527 -16 ***** ***** Masking position 5 Map Score: 16.963 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 84 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 12 AGACACATTCAAAGGATTGTTTTC 6 68 1 AAAGATTGTT 0.882659 -14 TAAATGATTGTTGACAGGGAAG 8 2 1 AAAGATTGTT 0.882659 -299 ATAAAGGGTTAAATGATTGATATTCTTTTTC 20 166 0 AAAGATTGAT 0.58533 -135 AGGATTACAAAAATGATTATTTGTTTTGGGA 59 65 1 AAAGATTATT 0.672348 -236 CCCCTTACTTAAACGATTTTTGTGAATACGA 59 275 0 AAAGATTTTT 0.866552 -26 CTGAACCCAGAAATGATTTTTTTATAG 65 7 0 AAAGATTTTT 0.866552 -77 CTGGGTTCAGAAATGATTTTTTATTGTGTTA 65 28 1 AAAGATTTTT 0.866552 -56 TTTCACAGTAAAATGATTTTCAAAGATGTAA 71 105 1 AAAGATTTTC 0.653363 -196 ATAGAAAATAAAATGATTTTTCCTAACATTC 107 88 0 AAAGATTTTT 0.866552 -76 AGGCCGATGTAAAAGATTATTTTTAAAAAAT 113 119 0 AAAGATTATT 0.672347 -88 CACAACAATAAAACGATTGTTTTACGCGTGT 117 116 0 AAAGATTGTT 0.882659 -41 GCTTTTGTTAAAAGGATTGTCTTAATGAGTT 122 144 0 AAAGATTGTC 0.685873 -157 TTAGCCTTTTAAATGATTTATAAGAAAAATG 123 157 0 AAAGATTTAT 0.549253 -85 TTAAAAGGCTAAATGATTTTTTATAAAATAG 123 176 1 AAAGATTTTT 0.866552 -66 *** ******* Masking position 6 Map Score: 8.15327 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 109 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 13 AACTTGTGGACAACCTTCTACACAAGCTGTGTG 1 130 0 CCCTTTACAC 0.763173 -171 TACAGTTAGCCTCCCCTTAAAACGGATATTGTA 4 264 0 CCCCTAAAAC 0.955853 -37 GCTTTATACTCTTCCCTGTCAACAATCATTTA 8 10 0 CCCCTTCAAC 0.848549 -291 CTGATTCACCCCTCAAATCATGCGTATTA 18 227 0 CCCCTAAATC 0.649446 -19 CCCAAGCTTTCTGCCCTATCAAGCTTGAAAAAC 20 27 0 CCCCTTCAAG 0.658214 -274 TACTTAAAACCCTCCTTCAAAACGTCGAAACCT 22 154 0 CCCTTAAAAC 0.930867 -23 CCAAGAGTGACATCCTTTAGAACGAAAGGAAAA 27 50 1 CCCTTAGAAC 0.679869 -28 TTTGAACGGGCAGCCCTTTACACTGAATGCGCT 37 67 1 CCCCTTACAC 0.838236 -185 AGACAGTATCCCTCCCTAAAAACATCATAAGTG 48 84 0 CCCCTAAAAC 0.955853 -25 TTAACGGTCTCCCCCCTTAAAACATTTGTATTC 50 12 0 CCCCTAAAAC 0.955853 -23 AAGGAATCGACTGCCTTTTCAACCGATTATCTT 59 206 0 CCCTTTCAAC 0.776999 -95 TTTTTTCATCCTTTAAAAGTAGTCTTCTA 65 65 0 CCCTTAAAAG 0.822323 -19 TCTTTTACATCGGCCTTAAAAACCATGTACAAT 113 134 1 CCCTTAAAAC 0.930867 -73 TTTGTCCTCGCTTCCTTCAAAACTCATTAAGAC 122 124 1 CCCTTAAAAC 0.930867 -177 ACAGAATATGCTACCCTTAACAGCGTTAATTTA 124 52 0 CCCCTAACAG 0.744259 -131 TAAAAAATCCAGCCTTCTAAAGGCTGGATCTT 134 10 1 CCCTTTAAAG 0.739079 -145 * **** ***** Masking position 7 Map Score: 8.07397 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 52 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 TTGAAAAACATCTGTCTTCGGAATT 20 5 0 TCTGTTTCGG 0.658836 -296 CAAGAAGCAAGATGAATTCGGTCTTGCCAAT 20 65 0 GATGATTCGG 0.801756 -236 CCTAACCTACTGTGAGTTCAGCAAGGAAACT 26 135 0 TGTGATTCAG 0.647985 -166 AGCAACCGTCGGTGACTTCGGATTGCCAAGC 52 97 0 GGTGATTCGG 0.93681 -60 CAGTTTTTATGGTGTGTTCAGACGGTCTATA 67 67 0 GGTGTTTCAG 0.926246 -230 ATCACGTTCAGCTGATTTCAGCAGGTGCTCA 67 156 0 GCTGATTCAG 0.94551 -141 TCTGAACATCGCTGTATTCGGATGAAAAAAG 67 243 0 GCTGTTTCGG 0.938511 -54 ACGGAAAACTGCTGATTTCAGCAGTTTTTTT 84 18 1 GCTGATTCAG 0.94551 -138 TGCATCGACAGCTGTTTTCAGGAATCTTCCC 91 79 0 GCTGTTTCAG 0.937416 -222 GTAGTCGATTGGTGTATTCGGAGGGAGGGAA 98 138 1 GGTGTTTCGG 0.927522 -26 GATGTATCATGATGTATTCAGAGAGTGTCCT 101 84 1 GATGTTTCAG 0.774059 -68 TAAATGAGGTGCTGATTACAGTGTATGACGC 103 98 1 GCTGATACAG 0.648701 -203 AACTCTATTCGGTGATTTCAGATGATATGAT 131 15 1 GGTGATTCAG 0.935687 -55 ***** ***** Masking position 7 Map Score: 8.01701 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 120 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 TTCATAACCTCCCGCTTTATATGTCTACAT 25 13 1 CCCGCTTTAT 0.758802 -230 GTTCTTTCCCCTCTCTTTTCAACTTAAG 31 128 0 CCCTCTCTTT 0.907066 -18 CCCCGGTCATTCCACTCTTTCTCTAAATCG 33 20 0 TCCACTCTTT 0.476366 -26 TAATCGCTTCTCCGCTGTTTTATGATTAAA 37 29 1 TCCGCTGTTT 0.745734 -223 AGCGGGTTTCCCCACTCTTTGCCTCGGTAA 49 149 0 CCCACTCTTT 0.80938 -152 AGTGGGGAAACCCGCTCTTTTGTATTGAAC 49 163 1 CCCGCTCTTT 0.973375 -138 CTTTTTAGCCCCTGCTCTTTTGAAGCAGGG 49 226 1 CCTGCTCTTT 0.592472 -75 TATACGCCTATCCTCTCTTTTT 51 3 0 TCCTCTCTTT 0.676501 -79 CGGGAATCCTCCCGCTTTTTACGA 53 5 0 CCCGCTTTTT 0.926659 -168 CGGGAGGATTCCCGCTTTTTTATCGTATTA 53 21 1 CCCGCTTTTT 0.926659 -152 GTTTTCACCCTCTGTTTGATCTGTGTC 57 65 0 CCCTCTGTTT 0.785163 -17 AGGAGTTAATCCCCCTCTTTTACACCTGTA 60 155 0 CCCCCTCTTT 0.867862 -146 GACTGCTTATTCCTCTCTATTTTATTGTCA 66 240 0 TCCTCTCTAT 0.342402 -20 TACAGCTCAAACCGCTCTTTGCCGACCACA 67 192 0 ACCGCTCTTT 0.658978 -105 TGAAATCCGGCCCTCTCTATAGTATCCTTT 68 52 1 CCCTCTCTAT 0.708474 -55 GCTGGCTGTCCCCGCTGTTAAAAGCAAATG 73 11 1 CCCGCTGTTA 0.468914 -152 GCTGTATCCTCCCGCTGTTTGCGAGCATTT 73 36 0 CCCGCTGTTT 0.931921 -127 GCGCAGCCTGTCCGCTCTTTGATTCACACC 114 88 0 TCCGCTCTTT 0.886784 -69 ATGCGGCCCGCCCGCTTTATTGACCGCGCA 114 113 0 CCCGCTTTAT 0.758802 -44 TTGGACACGCCCCGCTTTTTTAGCCTATGC 116 44 0 CCCGCTTTTT 0.926659 -35 TCCAATTCCCCCTTTTTACTGATAAAG 125 138 0 CCCCCTTTTT 0.694184 -17 ********** Masking position 6 Map Score: 20.504 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 256 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392