AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_mgen_reg_300.orf -o00230_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MG001 300 DNA polymerase III, subunit beta (dnaN) #2 MG014 239 ABC transporter, ATP-binding protein #3 MG015 46 ABC transporter, ATP-binding protein #4 MG017 65 ATP-dependent RNA helicase, putative #5 MG018 188 ATP-dependent RNA helicase, putative #6 MG019 41 heat shock protein (dnaJ) #7 MG022 29 DNA-directed RNA polymerase, subunit delta (rpoE) #8 MG031 264 DNA polymerase III, subunit alpha (polC-1) #9 MG058 85 ribose-phosphate pyrophosphokinase (prs) #10 MG140 300 conserved hypothetical protein #11 MG142 258 translation initiation factor 2 (infB) #12 MG144 24 conserved hypothetical protein #13 MG148 38 conserved hypothetical protein #14 MG149 75 lipoprotein, putative #15 MG149.1 90 conserved hypothetical protein #16 MG150 89 ribosomal protein S10 (rpS10) #17 MG210.1 200 conserved hypothetical protein #18 MG211 189 conserved hypothetical protein #19 MG227 300 thymidylate synthase (thyA) #20 MG261 300 DNA polymerase III, subunit alpha (polC-2) #21 MG277_MG278 42 MG277: conserved hypothetical protein, MG278: guanosine-3',5'-bis(diphosphate) 3'- pyrophosphohydrolase (spoT) #22 MG341 89 DNA-directed RNA polymerase, subunit beta (rpoB) #23 MG342 78 conserved hypothetical protein #24 MG345 43 isoleucyl-tRNA synthetase (ileS) #25 MG422 37 conserved hypothetical protein #26 MG424 188 ribosomal protein S15 (rps15) #27 MG459 172 conserved hypothetical protein Motif number 1 CATATGTACATAGTACATATGTAAAATATCATTAATTT 1 25 1 TAAAATAAAA 0.776988 -276 TACTATTATATATAACAGAAATTAATGATATTTTACAT 1 43 0 TAAAAATAAA 0.868512 -258 GAGTATTAATTATTACTATAATTAAGCATTTATGCTTA 1 92 1 TAATTATAAA 0.702495 -209 CTTTAATATCTATTATTTATTATAAGAACTAAAATGTC 1 159 0 TAATATTAAA 0.824909 -142 ATAATAGATATTAAAGAAAATAAAAAAATAGAAATAAA 1 181 1 TTAAAAAAAA 0.870454 -120 TTATAACAATTTTAATTTAACCAAAATACCCCTCGAAT 2 178 1 TTATAAAAAA 0.886624 -62 CCTCGAATTTTAACAGTTTTTATAATCAAAACAGCTAA 2 208 1 TAATTTTAAA 0.591769 -32 TCTTGAAAGATTTTAAAGAGATTAATTACTTCA 3 24 1 TTAAAGTAAA 0.545195 -23 TGGGAATGTTTTCAAATCTTCTTAAATAATCTATTTGA 5 90 0 TTATTTTAAA 0.63184 -99 TTGAAAACATTCCCATTAAAGATAAGAATCAAATTGCG 5 113 1 TCATAATAAA 0.763156 -76 ATCAATGGTTTTGTAATCATCAAAAACAGTTTTAAAAA 5 152 0 TTATATAAAA 0.827606 -37 TAAAGGTTAATTAGATACAGAATAAACAACTATTTGAA 8 22 1 TTAAAGTAAA 0.545196 -243 GTGTAACATTTAAAACTGTTAGTAAGAACTAACCAAAA 8 88 1 TAATTTTAAA 0.591769 -177 CACTTTTTCGTAAAAAAAAAAAAAAAAAAAGCAGTTTT 8 172 0 TAAAAAAAAA 0.850195 -93 AAAAAGTGGCTAAAACTAAAAATAATTATTGATAAATT 8 202 1 TAATAATAAA 0.884892 -63 AAGCGTTTATTAAAAAAATCAAAATAAAAGATCGAAA 8 238 0 TTAAATAAAA 0.804875 -27 AGTGTTTTGCTTTTAGATAAACTAAAAATAACGTGCTT 9 15 0 TTAAAATAAA 0.886624 -71 AAGTAACTGTTTCTATAAAAATAAATCAGGTTTTTAAC 10 169 0 TTAAAAAAAA 0.870453 -132 GAAGATTCACTACTAATAATTTAAATTAAGCACTCATA 10 208 1 TAATATAAAA 0.801973 -93 TTTTGAATTTTTCTAAATAAGCTAACAAATTAAACC 14 9 0 TTAAAATAAA 0.886623 -67 TTTAGAAAAATTCAAAATAAGCAAATTATAATTAGGTG 14 30 1 TTAAAAAAAA 0.870454 -46 ATTAGTTAATTCTAAATTAAGTTAATAACTATCTTTTT 15 14 0 TCATAATAAA 0.763156 -77 CCCAATATTTTCTCAATTAAATAAAAAAACAGTGTAAG 15 63 0 TCATAAAAAA 0.734648 -28 AAAAGTTAGTTTAAAAACTAGTAAAAAAGTGTTAATAC 17 65 0 TTAATAAAAA 0.673617 -136 TACAAGTAGCTATTAGTAAAGAAAACTACCAGAAATTA 17 121 0 TAATAAAAAA 0.868511 -80 TGCCTAAGATTGAAGTTAAAAATGATGATTTA 18 5 1 TAATAATAAA 0.884892 -185 GAGCTAGCTTTAAAAAAGTTTAAAAGGATATCACTGGA 18 43 1 TAAATTAAAA 0.516949 -147 GGGATGCGGTTAAGAGAAAAACAAAAGATAGCACAGAA 18 124 1 TAAAAAAAAA 0.850196 -66 GAGCAGGGTATCGCAAACAAGGTAACAATAATGGCATC 19 52 1 TCAAAATAAA 0.734649 -249 TTAAAATGTTTATTAAAAAAACAAAATAAAAAGCGGTT 19 238 1 TAAAAAAAAA 0.850195 -63 ATGAAATCGTTTAAATTCTAATAAAGAATTAGATTGTT 20 20 0 TTATTAAAAA 0.706059 -281 AACTTAAATTTTATATAAATATTAAGTA 21 1 0 TTAAATTAAA 0.827431 -42 TTATATAAAATTTAAGTTATTAAAAATAGTTA 21 21 1 TTATATAAAA 0.827611 -22 TACGCTTCTATTAAATTGTTTTTAAATACTTTTTATTT 23 32 1 TTATTTTAAA 0.63184 -47 AAATTAACACTTAAATTTTAAATAAAAAGTATTTAAAA 23 51 0 TTATTATAAA 0.736537 -28 CAGATGTAAGTTAGATAAATATTAATAAAATTACTCTG 24 11 1 TTAAATTAAA 0.827609 -33 CGAGAGAATTTATTAATAAAAATAAAAACTATATTTAT 26 67 1 TAATAATAAA 0.884798 -122 CCTACTTACTTATTACTTATAATAAATATAGTTTTTAT 26 88 0 TAATATTAAA 0.825152 -101 GCAAAATTTATTAAAGTGAACCAAAATAAAATTGAAGT 27 31 0 TTATAAAAAA 0.886624 -142 ** * * ** *** * Masking position 5 Map Score: 44.8302 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 435 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 2 TATTAAAGAAAATAAAAAAATAGAAATAAA 1 189 1 AATAAAAAAA 0.785935 -112 TGAAAATATTAATTAATAAAAGTGAATTGA 1 263 1 AATTAATAAA 0.734551 -38 TTGTTATAATAATTAGTTAAATACCCTTAG 2 157 0 AATTAGTTAA 0.691926 -83 CTCAAAAAACTAATACATCAAAC 5 4 1 AAAAAACTAA 0.853036 -185 CTTGTTCATAAAAAAGTAAACGGTTGAAGT 5 32 0 AAAAAGTAAA 0.775391 -157 TTTTAGTCTAAAATAGCAAAAACTGCTTTT 8 154 1 AAATAGCAAA 0.836286 -111 TTCGTAAAAAAAAAAAAAAAAAAAGCAGTT 8 174 0 AAAAAAAAAA 0.739851 -91 AAATATCTGCAAAAAACTAAATATTTCAGA 9 59 1 AAAAAACTAA 0.853036 -27 TTTTCTTGTTAATAAACAAAGTCTTGTTAT 11 19 0 AATAAACAAA 0.906312 -240 GCAACTAATTAATTAGTTAACTAATA 13 23 1 AATTAGTTAA 0.691926 -16 AATTTTTCTAAATAAGCTAACAAATTAAAC 14 12 0 AATAAGCTAA 0.887026 -64 AAAAATTCAAAATAAGCAAATTATAATTAG 14 35 1 AATAAGCAAA 0.910203 -41 CTTAATTTAGAATTAACTAATGACAGTGTA 15 31 1 AATTAACTAA 0.829791 -60 TTCTCAATTAAATAAAAAAACAGTGTAAGT 15 62 0 AATAAAAAAA 0.785935 -29 AAAATTCACTAATTAACTAACAAAAATTAT 17 29 1 AATTAACTAA 0.829791 -172 AGCTACTTGTAAAAAATTAAAAGTTAGAAT 17 148 1 AAAAAATTAA 0.718473 -53 ATGTTTATTAAAAAAACAAAATAAAAAGCG 19 243 1 AAAAAACAAA 0.882261 -58 GCAAAAGATAAAAAAAATAAGGTTGATGGA 20 80 1 AAAAAAATAA 0.687787 -221 TGATGATATTAAAAAGATAACAGAGCTTAG 20 181 1 AAAAAGATAA 0.697727 -120 CATCTAAACAAATTAACAAAGCCATTTAAC 26 13 0 AATTAACAAA 0.862895 -176 ATTATAACAAAATTAGAAAACGGCTCATTG 26 150 0 AATTAGAAAA 0.714519 -39 TAATTAATAAACACGTTGAAT 26 178 0 AATTAATAAA 0.734551 -11 TGTAATCCAAAAAAAGTAAATTCAGGCAAC 27 104 0 AAAAAGTAAA 0.775391 -69 ********** Masking position 5 Map Score: 20.5005 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 330 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 ATAAATGCTTAATTATAGTAATAATTAATACTCTC 1 90 0 AATAGATAAT 0.572566 -211 TCTTATAATAAATAATAGATATTAAAGAAAATAAA 1 170 1 AATAGTTTAA 0.685451 -131 AAGAAAATAAAAAAATAGAAATAAATATCATAACC 1 194 1 AAAAGATAAA 0.928342 -107 TGTAAAACCAAGTTCTTGAAAGATTTTAA 3 5 1 AAAAGTTTGA 0.723954 -42 TGTAATCATCAAAAACAGTTTTAAAAAGCGCAATT 5 144 0 AAAAGTTAAA 0.96216 -45 GAAAAGTAGTATTAGAATTTTATTGA 7 2 1 AAAAGATAGA 0.759855 -28 AGAACTAACCAAAAGAAGGTTTAAATTTTGGTATA 8 112 1 AAAAGTTAAA 0.96216 -153 TTTTCACTGGATAAGCAGTTTTAATGGTTCCACTA 10 77 0 ATAAGTTAAT 0.733252 -224 TTTGATTATAAAGGGAAGTTTTAAAGAGTTAAGCA 10 269 0 AAGAGTTAAA 0.929584 -32 TTTTTGGTTTAAAGCTAGATAAAAAACACCTCAAA 11 149 1 AAAAGTAAAA 0.797958 -110 AAAACACCTTAAGGTTAGTTGTAATGATGCAAAGC 11 195 1 AAGAGTTAAT 0.870568 -64 CTAAAAAAGATAGTTATTAACTTAATTTAG 15 6 1 AAAAGTTTAA 0.914805 -85 CTACTTGTATATTCAGTTAAAATTCACTAATTA 17 9 1 ATAAGTAAAT 0.29924 -192 TACACTTAAAAAAGTTAGTTTAAAAACTAGTAAAA 17 77 0 AAAAGTAAAA 0.797958 -124 TAAAAAATTAAAAGTTAGAATTAATGGCACTATTT 17 157 1 AAAAGATAAT 0.868433 -44 AAACTTTTTTAAAGCTAGCTCTAAATCATCATTTT 18 29 0 AAAAGTTAAA 0.96216 -161 TGTCAGGTGAAAAGTTAGGTATAAACACCCAC 19 8 0 AAAAGTTAAA 0.96216 -293 TGACCAGGTGAAACCTAGTAGTAGTAGCAACACGT 19 94 1 AAAAGATAGT 0.617173 -207 ATTTATATAAAATTTAAGTTATTAAAAATAGTTA 21 19 1 AATAGTTTAA 0.685451 -24 TAAATTTTAAATAAAAAGTATTTAAAAACAATTTA 23 43 0 ATAAGATTAA 0.537187 -36 GTACCTTAAAGATTAGCAATTAAAATTTGAAAG 25 9 1 AAGAGATTAA 0.739612 -29 ATTTGTTTAGATGTATAGATTTAAATATCGAAAAT 26 30 1 ATGAGTTAAA 0.736943 -159 TACTTATAATAAATATAGTTTTTATTTTTATTAAT 26 78 0 AAAAGTTTAT 0.845454 -111 GCTCATTGCCAAGGTTAGAAGTAATAAATTCTCCT 26 123 0 AAGAGATAAT 0.774112 -66 *** ** * **** Masking position 7 Map Score: 17.8255 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 415 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 TTAATTATAGTAATAATTAATACTCTCTAA 1 87 0 TAATAATTAA 0.608894 -214 TTAATTATTACTATAATTAAGCATTTATGC 1 97 1 CTATAATTAA 0.684954 -204 CATAAAAAGCTTATAATTAAGCATAAATGC 1 117 0 TTATAATTAA 0.950939 -184 ATTTTAGTTCTTATAATAAATAATAGATAT 1 162 1 TTATAATAAA 0.95094 -139 ATTAAAATTGTTATAATAATTAGTTAAATA 2 164 0 TTATAATAAT 0.745197 -76 TTAACAGTTTTTATAATCAAAACAGCTAAT 2 217 1 TTATAATCAA 0.892871 -23 AGCAAGAATTATAATTAACACTCTAAGG 6 9 1 TTATAATTAA 0.950939 -33 ATTTTGATTTTTTTAATAAACGCTT 8 250 1 TTTTAATAAA 0.745197 -15 AAACTTCCCTTTATAATCAAATATCGCC 10 283 1 TTATAATCAA 0.892871 -18 AATAAGCAAATTATAATTAGGTGTCTTTCT 14 45 1 TTATAATTAG 0.710828 -31 TTAACTTAATTTAGAATTAACTAATGACAG 15 27 1 TTAGAATTAA 0.809386 -64 AAATTAAAAGTTAGAATTAATGGCACTATT 17 161 1 TTAGAATTAA 0.809386 -40 CCAATTCTTCTGATAATAAAGTCACTCAAG 19 135 1 TGATAATAAA 0.697651 -166 TATTTTGTTTTTTTAATAAACATTTTAACA 19 236 0 TTTTAATAAA 0.745197 -65 ATCGTTTAAATTCTAATAAAGAATTAGATT 20 23 0 TTCTAATAAA 0.710828 -278 TACTTATTACTTATAATAAATATAGTTTTT 26 90 0 TTATAATAAA 0.95094 -99 ACACGTTGAATTATAACAAAATTAGAAAAC 26 159 0 TTATAACAAA 0.684952 -30 ATGAGCGATATTATAATTATTTGTAACA 27 155 1 TTATAATTAT 0.745197 -18 ********** Masking position 5 Map Score: 13.2978 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 3 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 AAATTAATACTTAATCAAAAATGAAAATATT 1 242 1 TAATCAAAAA 0.880377 -59 CAATTTTAATTTAACCAAAATACCCCTCGAA 2 184 1 TAACCAAAAT 0.941835 -56 AAAGTGGTTATATACCAAAATTTAAACCTTC 8 126 0 TTACCAAAAT 0.882301 -139 AAGCGTTTATTAAAAAAATCAAAATA 8 249 0 TTATTAAAAA 0.546727 -16 TGCTTTTAGATAAACTAAAAATAACGTGCTT 9 15 0 TAACTAAAAA 0.909536 -71 GAAATTGATCTTAATCAAAATCTCAAGGGCA 11 100 1 TAATCAAAAT 0.807607 -159 TATCTAGCTTTAAACCAAAAACACTCAAATA 11 139 0 TAACCAAAAA 0.965975 -120 GGTGTCTTTCTTTACTAAAAAT 14 64 1 TTACTAAAAA 0.823146 -12 TTTTGGTGTATCAACTAAAAACTAAAGCGTT 16 28 0 TAACTAAAAA 0.909536 -62 TTTTAGTTGATACACCAAAATCCGTAGTCAA 16 39 1 TCACCAAAAT 0.771529 -51 TGTTAAAATGTTTATTAAAAAAACAAAATAA 19 236 1 TTATTAAAAA 0.546727 -65 AACATACTTTTGAACCACAAACAAGAATGCA 20 222 1 TAACCACAAA 0.805501 -79 TTTATTAAAGTGAACCAAAATAAAATTGAAG 27 32 0 TAACCAAAAT 0.941835 -141 TGTTGTTTTGTAATCCAAAAAAAGTAAATTC 27 111 0 TATCCAAAAA 0.736443 -62 * ********* Masking position 7 Map Score: 10.2036 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 125 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GGTGGAAGTAAATGGACTTGAACCATCGACCTC 2 71 1 ATGGATTAAC 0.873709 -169 CAAAATACCCCTCGAATTTTAACAGTTTTTATA 2 199 1 CCGAATTAAC 0.911847 -41 AAACTAATACATCAAACTTCAACCGTTTACTTT 5 17 1 ACAAATTAAC 0.659492 -172 TGGTTATATACCAAAATTTAAACCTTCTTTTGG 8 120 0 CAAAATTAAC 0.658612 -145 AAAATAAAAGATCGAAATTTATCAATAATTATT 8 222 0 ACGAATTATC 0.885168 -43 TAGCGTTGATCAAGGAATTGATCGCTACTTGGG 10 124 0 CAGGATTATC 0.750119 -177 AGACAACCAACTTGAAATTGATCTTAATCAAAA 11 87 1 CTGAATTATC 0.898841 -172 CAGCTTGAAGTAAAATTAATCCTA 12 9 1 ATAAATTATC 0.624823 -16 TTAGTTAATTAGTGAATTTTAACTGAATATACA 17 16 0 ATGAATTAAC 0.946474 -185 AAGAAAACTACCAGAAATTAAACTAGGATTACA 17 108 0 CAGAATTAAC 0.926162 -93 TAATTCTTTATTAGAATTTAAACGATTTCATCT 20 27 1 TAGAATTAAC 0.659915 -274 ACAAGTTTTAAATGAAGTTGAACTTGATGATAT 20 157 1 ATGAATTAAC 0.946449 -144 AGAGCTTAGAAAAGAACTTGAACATACTTTTGA 20 202 1 AAGAATTAAC 0.938543 -99 GCGTGAAATTAAAGAAATAGAACGCAAAATGAA 20 259 1 AAGAATAAAC 0.711421 -42 AACGCATGCTAATGGACTTAATCACAGTTCGCT 22 14 0 ATGGATTATC 0.808947 -76 CCAAAATAAAATTGAAGTATATCTCTAGATAAA 27 16 0 ATGAATAATC 0.636074 -157 * **** ** *** Masking position 6 Map Score: 9.50847 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 94 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 CTATTTTAGAGAGTATTAATTATTACTATA 1 82 1 GAGTATTAAT 0.728474 -219 TACTATAATTAAGCATTTATGCTTAATTAT 1 105 1 AAGCATTTAT 0.631586 -196 ATTTTTGATTAAGTATTAATTTCTGGGTTA 1 234 0 AAGTATTAAT 0.894649 -67 TCAAAAATGAAAATATTAATTAATAAAAGT 1 256 1 AAATATTAAT 0.628345 -45 TGCATCCTTAGAGTGTTAATTATAATTCTT 6 14 0 GAGTGTTAAT 0.870993 -28 AAGTTTTTCAAAGTGTGAATTTAAAAACTT 8 58 0 AAGTGTGAAT 0.771198 -207 TTTAGACTAAAAGTGGTTATATACCAAAAT 8 136 0 AAGTGGTTAT 0.68292 -129 AAGCGTTTATTAAAAAAATC 8 255 0 AAGCGTTTAT 0.811822 -10 ACTAGTAAAAAAGTGTTAATACTCCTTAAT 17 57 0 AAGTGTTAAT 0.955298 -144 GTGACTGTTAAAATGTTTATTAAAAAAACA 19 231 1 AAATGTTTAT 0.731083 -70 TTTAAAATTTAAGTGTTAATTT 23 67 1 AAGTGTTAAT 0.955298 -12 TAAGTTAGATAAATATTAATAAAATTACTC 24 17 1 AAATATTAAT 0.628345 -27 TTATAATTCAACGTGTTTATTAATTA 26 173 1 ACGTGTTTAT 0.68292 -16 ********** Masking position 9 Map Score: 6.46322 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 117 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 AAAATTAGCTGTTTTGATTATAAAA 2 225 0 AAAGCGTTTT 0.980424 -15 TTGTAATCATCAAAAACAGTTTTAAAAAGCGCA 5 147 0 CAAACGTTTT 0.902495 -42 TTCTGCTAAATCAATGGTTTTGTAATCATCA 5 168 0 AAAATGTTTT 0.779086 -21 GGTTAGTTCTTACTAACAGTTTTAAATGTTACA 8 89 0 TAAACGTTTT 0.861976 -176 AAAAAAAAAAAAAAAGCAGTTTTTGCTATTTTA 8 162 0 AAAGCGTTTT 0.980378 -103 TTTTTCACTGGATAAGCAGTTTTAATGGTTCCA 10 80 0 GAAGCGTTTT 0.90414 -221 TGAATCTTCAAAGTAACTGTTTCTATAAAAATA 10 184 0 AAAACGTTTC 0.885743 -117 GTTCTCTTTTAACAAAATGTTTTCTTGTTAATA 11 35 0 AAAAAGTTTT 0.778423 -224 CTAGTTTTTAAACTAACTTTTTTAAGTGTAATC 17 82 1 AAAACTTTTT 0.763849 -119 AAAACAAAATAAAAAGCGGTTTTATACAATGTA 19 255 1 AAAGCGTTTT 0.980378 -46 TAACCTTGGCAATGAGCCGTTTTCTAATTTTGT 26 141 1 AAAGCGTTTT 0.980424 -48 AAGTAAATTCAGGCAACAGTTTTTTGACTTCAA 27 88 0 AGAACGTTTT 0.885743 -85 GCTCATCTTTAAATAACAGTGTTGTTTTGTAAT 27 128 0 AAAACGTGTT 0.885742 -45 ** *** ***** Masking position 5 Map Score: 11.2916 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 102 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 9 TAGATACAGAATAAACAACTATTTGAAGTT 8 33 1 ATAAACAACT 0.834658 -232 GCTTTAAACCAAAAACACTCAAATAATAAC 11 134 0 AAAAACACTC 0.859076 -125 AAGCTAGATAAAAAACACCTCAAAGCTGTA 11 160 1 AAAAACACCT 0.963132 -99 GCTGTAGTTGAAAAACACCTTAAGGTTAGT 11 184 1 AAAAACACCT 0.963132 -75 TTTAGTAAAGAAAGACACCTAATTATAATT 14 53 0 AAAGACACCT 0.918252 -23 AAAGTTAGGTATAAACACCCAC 19 3 0 ATAAACACCC 0.893868 -298 CCCCAGCCAAAAAAACAACCACCTATCCTG 19 174 1 AAAAACAACC 0.888115 -127 AACCTGTCTAAAAGACAATTTC 19 289 1 AAAGACAATT 0.611056 -12 AAAAGTATTTAAAAACAATTTAATAGAAGC 23 35 0 AAAAACAATT 0.785121 -44 TAATTAATAAACACGTTGAATTATAA 26 173 0 ATAAACACGT 0.694569 -16 ********** Masking position 5 Map Score: 5.92935 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 121 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 AGATATTAAAGAAAATAAAAAAATAGAAAT 1 186 1 GAAAATAAAA 0.615904 -115 ATACTTAATCAAAAATGAAAATATTAATTA 1 248 1 AAAAATGAAA 0.618427 -53 TTTTGATCAGCTAAATAAAACAAAGCAA 4 48 1 CTAAATAAAA 0.498653 -18 TAAAAAAAAAAAAAAAAAAAGCAGTTTTTG 8 170 0 AAAAAAAAAA 0.626617 -95 TTAAAAAAATCAAAATAAAAGATCGAAATT 8 236 0 CAAAATAAAA 0.925281 -29 TAGTTTATCTAAAAGCAAAACACTGGTTGA 9 29 1 AAAAGCAAAA 0.727421 -57 AATATCTGCAAAAAACTAAATATTTCAGAG 9 60 1 AAAAACTAAA 0.560132 -26 TAAGGAACAACAAAGGAAAAGGTTTGACTA 10 20 0 CAAAGGAAAA 0.512751 -281 TGTATCAACTAAAAACTAAAGCGTTATGAT 16 23 0 AAAAACTAAA 0.560132 -67 CGGTTAAGAGAAAAACAAAAGATAGCACAG 18 130 1 AAAAACAAAA 0.880057 -60 GCTCCCCAGCCAAAAAAACAACCACCTATC 19 171 1 CAAAAAAACA 0.445491 -130 ATTAAAAAAACAAAATAAAAAGCGGTTTTA 19 249 1 CAAAATAAAA 0.925281 -52 AAATAGAACGCAAAATGAAACGTTCTAGTC 20 273 1 CAAAATGAAA 0.768755 -28 ATTTATTAATAAAAATAAAAACTATATTTA 26 74 1 AAAAATAAAA 0.857898 -115 TAAAGTGAACCAAAATAAAATTGAAGTATA 27 28 0 CAAAATAAAA 0.925281 -145 CTTATTTAGACAAAGCAAAATTTATTAAAG 27 53 0 CAAAGCAAAA 0.845534 -120 TTTTGGATTACAAAACAACACTGTTATTTA 27 122 1 CAAAACAACA 0.778394 -51 ********** Masking position 4 Map Score: 9.15046 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 270 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 TTTAAAGAGATTAATTACTTCA 3 35 1 TTAATTACTT 0.362793 -12 AAGTGTGAATTTAAAAACTTCAAATAGTTG 8 48 0 TTAAAAACTT 0.560885 -217 GTTTTTGCTATTTTAGACTAAAAGTGGTTA 8 147 0 TTTTAGACTA 0.5201 -118 ATAAATCAGGTTTTTAACTATTCAATGGCG 10 157 0 TTTTTAACTA 0.878581 -144 TGCTTAACTCTTTAAAACTTCCCTTTATAA 10 269 1 TTTAAAACTT 0.762 -32 TTTGAGGTGTTTTTTATCTAGCTTTAAACC 11 154 0 TTTTTATCTA 0.506132 -105 CTTAAGGTGTTTTTCAACTACAGCTTTGAG 11 178 0 TTTTCAACTA 0.554007 -81 AAAAAGATAGTTATTAACTTAATTTAGAAT 15 14 1 TTATTAACTT 0.817064 -77 CGTAGTCAATTTATTAACTAACTAGTGAAC 16 61 1 TTATTAACTA 0.742717 -29 GTATTAACACTTTTTTACTAGTTTTTAAAC 17 65 1 TTTTTTACTA 0.64279 -136 TTTTACTAGTTTTTAAACTAACTTTTTTAA 17 77 1 TTTTAAACTA 0.80147 -124 TAAATCATCATTTTTAACTTCAATCTTAGG 18 13 0 TTTTTAACTT 0.918002 -177 AGTGATATCCTTTTAAACTTTTTTAAAGCT 18 48 0 TTTTAAACTT 0.861994 -142 AACCTTATTTTTTTTATCTTTTGCCATATG 20 74 0 TTTTTATCTT 0.613245 -227 TTCAACTTCATTTAAAACTTGTGTATCTTC 20 149 0 TTTAAAACTT 0.762 -152 TAACTATTTTTAATAACTTAAATTTTATA 21 24 0 TTAATAACTT 0.695997 -19 AGTAGGAGAATTTATTACTTCTAACCTTGG 26 120 1 TTTATTACTT 0.58799 -69 AGGCAACAGTTTTTTGACTTCAAATATCCT 27 81 0 TTTTTGACTT 0.750343 -92 ********** Masking position 2 Map Score: 10.42 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 290 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 TTCTTCATAAAACCTTTGTAGTGCTTGTTC 5 55 0 AACCTTTGTA 0.779366 -134 CACTTTGAAAAACTTGTGTAACATTTAAAA 8 73 1 AACTTGTGTA 0.948294 -192 AGATATTTTCAACCAGTGTTTTGCTTTTAG 9 37 0 AACCAGTGTT 0.821728 -49 CAAATACGGGAACTAGTGGAACCATTAAAA 10 64 1 AACTAGTGGA 0.798137 -237 TTAAATAAAAAAACAGTGTAAGTGTACACT 15 55 0 AAACAGTGTA 0.741417 -36 TTTATTAACTAACTAGTGAACTAGATTTTG 16 70 1 AACTAGTGAA 0.72735 -20 GCGTTGTGCTAACCTGCGTACTTCCAGTGA 18 73 0 AACCTGCGTA 0.89383 -117 TACAATGTATAACCTGTCTAAAAGACAATT 19 279 1 AACCTGTCTA 0.839629 -22 CTTCATTTAAAACTTGTGTATCTTCAAGTT 20 144 0 AACTTGTGTA 0.948294 -157 ********** Masking position 2 Map Score: 0.922698 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 22 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 TGTACATATGTAATTATTACTGCT 1 4 0 TAATTATTCT 0.923903 -297 TAGAGAGTATTAATTATTACTATAATTAAGC 1 88 1 TAATTATTCT 0.923903 -213 AGGGTTATGATATTTATTTCTATTTTTTTAT 1 200 0 TATTTATTCT 0.584418 -101 ACCCAGAAATTAATACTTAATCAAAAATGAA 1 236 1 TAATACTTAT 0.54441 -65 CAAACATTATTAATTTTTGATCAGCTAAATA 4 34 1 TAATTTTTAT 0.575514 -32 CTATTTGAAATAATTCTTCATAAAACCTTTG 5 67 0 TAATTCTTAT 0.923903 -122 GTGTTAATTATAATTCTTGCT 6 1 0 TAATTCTTCT 0.957576 -41 TTCTTTTGGTTAGTTCTTACTAACAGTTTTA 8 98 0 TAGTTCTTCT 0.794867 -167 AAACTAAAAATAATTATTGATAAATTTCGAT 8 214 1 TAATTATTAT 0.867208 -51 TGTCATTAGTTAATTCTAAATTAAGTTAATA 15 25 0 TAATTCTAAT 0.694965 -66 ATAGTGCCATTAATTCTAACTTTTAATTTTT 17 159 0 TAATTCTACT 0.809002 -42 AAGAACAATCTAATTCTTTATTAGAATTTAA 20 17 1 TAATTCTTAT 0.923903 -284 TTCTCCTACTTACTTATTACTTATAATAAAT 26 99 0 TACTTATTCT 0.675773 -90 AGCGATATTATAATTATTTGTAACA 27 158 1 TAATTATTGT 0.667713 -15 ******** ** Masking position 2 Map Score: 8.18757 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 52 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 ATATAATAGTATCTATTTTAGAGAGTATTA 1 70 1 ATCTATTTTA 0.887529 -231 TAATTATTATAACAATTTTAATTTAACCAA 2 172 1 AACAATTTTA 0.596904 -68 TTCTTAAATAATCTATTTGAAATAATTCTT 5 80 0 ATCTATTTGA 0.889394 -109 CAGAATAAACAACTATTTGAAGTTTTTAAA 8 39 1 AACTATTTGA 0.889394 -226 GGGAAGCTTCATCTTTTTTCACTGGATAAG 10 97 0 ATCTTTTTTC 0.713718 -204 TCTAAACTTTTTGCAACTAATTAA 13 5 1 AACTTTTTGC 0.717548 -34 GTTAATAACTATCTTTTTTAG 15 2 0 ATCTTTTTTA 0.887529 -89 TTTTTAAACTAACTTTTTTAAGTGTAATCC 17 86 1 AACTTTTTTA 0.887529 -115 GCTCTAAATCATCATTTTTAACTTCAATCT 18 17 0 ATCATTTTTA 0.596905 -173 TATCCTTTTAAACTTTTTTAAAGCTAGCTC 18 43 0 AACTTTTTTA 0.887529 -147 ATGTGATTTGAACTATTAGATGAAATCGTT 20 47 0 AACTATTAGA 0.441786 -254 CAATCAGTTGATCTATTTGAACGTACAAAA 20 116 1 ATCTATTTGA 0.889394 -185 AAGCTCTGTTATCTTTTTAATATCATCAAG 20 179 0 ATCTTTTTAA 0.554363 -122 TAACTATTTTTAATAACTTAA 21 32 0 AACTATTTTT 0.477537 -11 ********** Masking position 1 Map Score: 7.75923 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 118 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 GTCTATAATTTTGTTCATAAAAAGCTTATAA 1 131 0 TTTTCATAAA 0.945635 -170 AATATTTTCATTTTTGATTAAGTATTAATTT 1 242 0 TTTTGATTAA 0.59984 -59 TTTGTAGTGCTTGTTCATAAAAAAGTAAACG 5 40 0 TTTTCATAAA 0.945635 -149 TTTGAAATAATTCTTCATAAAACCTTTGTAG 5 64 0 TTTTCATAAA 0.945635 -125 TTTTAGCCACTTTTTCGTAAAAAAAAAAAAA 8 186 0 TTTTCGTAAA 0.85804 -79 CTAAAAATAATTATTGATAAATTTCGATCTT 8 217 1 TTTTGATAAA 0.928877 -48 TATTTTGATTTTTTTAATAAACGCTT 8 249 1 TTTTAATAAA 0.930891 -16 AGTGTTTTGCTTTTAGATAAACTAAAAATAA 9 22 0 TTTAGATAAA 0.606164 -64 AAATGTTTTCTTGTTAATAAACAAAGTCTTG 11 23 0 TTTTAATAAA 0.931345 -236 ATTTTTAGTAAAGAAAGACACC 14 64 0 TTTTAGTAAA 0.824625 -12 TTATTTTGTTTTTTTAATAAACATTTTAACA 19 236 0 TTTTAATAAA 0.930891 -65 TCGAGAGAATTTATTAATAAAAATAAAAACT 26 66 1 TTTTAATAAA 0.931304 -123 ** ******** Masking position 10 Map Score: 15.1819 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 97 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911