AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -iarcA_rpxx_opreg_300.orf -g0.290 -x5 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 = 0.29 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 RP039 300 30S RIBOSOMAL PROTEIN S6 (rpsF) #2 RP040 24 30S RIBOSOMAL PROTEIN S18 (rpsR) #3 RP042 158 CELL CYCLE PROTEIN MESJ (mesJ) #4 RP043 50 CELL DIVISION PROTEIN FTSH (ftsH) #5 RP044 244 SUCCINATE DEHYDROGENASE IRON-SULFUR PROTEIN (sdhB) #6 RP122 98 HFLK PROTEIN (hflK) #7 RP123 143 HFLC PROTEIN (hflC) #8 RP124 30 PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA) #9 RP125 104 unknown #10 RP126 137 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT (sdhC) #11 RP127 158 SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN (sdhD) #12 RP128 133 SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT (sdhA) #13 RP215 297 unknown #14 RP216 172 CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT I (cydA) #15 RP217 93 CYTOCHROME D UBIQUINOL OXIDASE SUBUNIT II (cydB) #16 RP264 300 unknown #17 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #18 RP459 300 unknown #19 RP460 146 DIHYDROLIPOAMIDE DEHYDROGENASE PRECURSOR (pdhD) #20 RP805 249 DIHYDROLIPOAMIDE DEHYDROGENASE (pdhD) #21 RP806 300 unknown #22 RP844 300 CITRATE SYNTHASE (gltA) Motif number 1 AGCCTTTGTCTTTGTTTATTTAATTTTTTATGTCATTT 1 94 1 TTTTTATTTT 0.913328 -207 AATAAGATTTTTAATTTTTGAAGATAATACTTGAATTT 1 209 1 TTATTTTATT 0.609932 -92 TATAAATACCTTTATTTTAAAGTTTGTTTATTGGAGAT 1 262 1 TTTTTTATTT 0.920334 -39 AGCATTATTATTGTTTAATTGAATTGATATATATCAGA 3 41 1 TTGTAATTTT 0.68792 -118 TACCGATAAAATTTTTATTAGGTTTTATATCG 4 29 1 ATTTATTTTT 0.71035 -22 CTTGTATACTTTGTTATTAGCTATTTTTGTATGAGTAT 5 13 1 TTGTTTATTT 0.86381 -232 ATTTTTCGCAATTTTAATAATTATTAATTATTTTAACT 5 62 0 ATTTATATTT 0.651679 -183 ATACATAAAAATGATAATTGTAATTATTTTTCACTACA 5 107 0 ATGTATTTTT 0.57383 -138 TTCAACAGTATTTGTTTATGATTTTCTTATGTCCCGTA 5 160 0 TTTTTATTTT 0.913328 -85 TTGCTTTTTTATATTATTTTAAGATTAA 6 81 0 TTGTTTTTTT 0.892629 -18 AATATTCCTTATTATTTTATAATATCATACTAAAAAAG 7 114 0 ATTTTTAATT 0.455797 -30 TCAGAAAATTATTATATTTGTATTTCTTGGTTATGAAG 10 32 0 ATTTTTTTTT 0.865535 -106 AAACTAAGAGTTTTTTATAGTTGATACTATGGTCAAGA 10 69 1 TTTTATAATT 0.59911 -69 TCAAGACACTATAGTATTAAATTTTATTATTTTTATAT 10 101 1 ATATTTATTT 0.599091 -37 AAATTTTATTATTTTTATATTGAATAGTT 10 119 1 ATTTATAATT 0.38849 -19 AAATAGTATGTTTATATTTGCGATTGTTCTGAAATGAA 11 62 1 TTTTTTTTTT 0.93805 -97 ATTATTGACTTTATTAAATGATTTTTATTTCATTTCAG 11 90 0 TTATAATTTT 0.549886 -69 TAATTTTCTCTAAACATATTTTAAGTTGTAAT 11 137 0 TTTTTAAATT 0.731888 -22 ATACACAATAATGCTATTAATTGTTTTTCAATATTCCA 12 33 0 ATGTTTATTT 0.72946 -101 TAATAGCATTATTGTGTATTGAATTACTTAATAATGTG 12 52 1 ATTTTATTTT 0.817507 -82 TGTAATTTGTATTTTATTTGGTATTATTCCAGCA 13 7 0 ATTTTTTTTT 0.865536 -291 TAAAGTAATCTTAATTTTATCAAATTTTAAAAAATAAA 13 50 1 TTATTTAATT 0.544117 -248 TAAATATTAATTTGTGTTAATTGTTAGTTTATTAAAAT 13 153 1 TTTTTTATTT 0.920334 -145 TTGTTTATTATTTTTCAATAGATTTAATATTTTGAGGT 13 208 0 TTTTAATTTT 0.800593 -90 TGTCTTGATGTTATTGTATGTAATTTTTCTGTGGCGTC 14 24 1 TTATTATTTT 0.762272 -149 AAAAGCAAATTTTTTATATATTTTTGCTTCCTGACGCC 14 56 0 TTTTTATTTT 0.913328 -117 TATAAAAAATTTGCTTTTTATATATTTTCCGGACATAT 14 76 1 TTGTTTTATT 0.738408 -97 TTATTATATATTGTTAATTATTTGCACA 16 1 1 TTATTATTTT 0.762272 -300 TATAGACAAATTACTTAATGTTATTTATCTTAGATTAA 16 132 1 TTATAATTTT 0.549886 -169 AGCATTTTTAATTATTTTTTGGATTGCTAAGTCACTGC 16 196 0 ATTTTTTTTT 0.865536 -105 CTAAGCAATCTTTTTAAAAAGCATTTTTAATTATTTTT 16 215 0 TTTTAAATTT 0.753883 -86 ATGAATGGGTTTGCTATATTAATATGATGACGTTTGCT 18 74 0 TTGTTATATT 0.662668 -227 TATTTTAGTTATAATATATCTCTTTTTTTGATAATCTG 18 133 0 ATATTATTTT 0.576825 -168 ACTCTCTCACTTGTTTTAATTAAATCTTTTATTTTAGT 18 162 0 TTGTTAAATT 0.5998 -139 GTATCTAATCTTTATAATAATCTTTTTTAAAATATCGT 19 52 0 TTTTATATTT 0.814864 -95 TTATCAACACTTGATTTTAACCTTTACTGAAAAAATAT 20 125 0 TTGTTTATTT 0.86381 -125 AATCAAATGTTTTGTATTAGATAATTTTCTTAGTATTA 21 73 1 TTTTTTAATT 0.79685 -228 TTTAGCTATAATTATATTATTAATTAATAGTTAATTTA 21 131 1 ATTTTTATTT 0.824197 -170 TAATAGTTAATTTATATATCATTTTGCTATTCCTTTGT 21 155 1 TTTTTATTTT 0.913328 -146 TTGCTATTCCTTTGTATTTAAAAATTTTTAATTAAATA 21 178 1 TTTTTTTATT 0.837167 -123 ATTATATAATTTTCTATTATATATTAATTATTTAATTA 21 206 0 TTTTTTATTT 0.920334 -95 AAGGAGTTATTTTTTGTTACTGTTTGTTATTGTTAATA 22 71 1 TTTTTTATTT 0.920334 -230 TCAGATTACATTTTTATATTAGCTTTATTAACAATAAC 22 96 0 TTTTTATTTT 0.913328 -205 TGAATTACGATTTATAAATTTTTTTGATATCTTGCTCA 22 221 0 TTTTAATTTT 0.800593 -80 *** * *** ** * Masking position 5 Map Score: 41.6747 Number of sites scoring better than the average of aligned sites = 2110 Number in coding regions = 1378 Number in noncoding regions = 732 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 2 GCAGCCTTTTAATATATTAAATCCTTCTATT 1 52 1 AATATATTAA 0.73594 -249 AATGACATAAAAAATTAAATAAACAAAGACA 1 100 0 AAAATTAAAA 0.825896 -201 TAATCAACAGATTATTTAAAAGTGTTTGATA 1 139 0 ATTATTTAAA 0.739669 -162 ATTATCTTCAAAAATTAAAAATCTTATTAAT 1 206 0 AAAATTAAAA 0.825896 -95 AATATATAAGAATCTCCAATA 1 290 0 AATATATAAA 0.806011 -11 AGTATTCACGAATATTTTACAATACTAACAT 3 126 1 AATATTTTAA 0.865062 -33 TATCGGTACTATAATTTAATACCGGG 4 6 0 ATAATTTAAA 0.632174 -45 CGAAAGTTAAAATAATTAATAATTATTAAAA 5 58 1 AATAATTAAA 0.852507 -187 ATTTTTATGTATAAATTTATAGATTTTTACG 5 133 1 ATAAATTTAA 0.410899 -112 ATCTTAAAATAATATAAAAAAGCAA 6 84 1 AATATAAAAA 0.773241 -15 AATATTCCTTATTATTTTATAATATCATACT 7 121 0 ATTATTTTAA 0.655861 -23 ACAATTTTAAATTAAATTAAAGTT 9 91 1 ATTAAATTAA 0.333931 -14 TAAAAATAATAAAATTTAATACTATAGTGTC 10 105 0 AAAATTTAAA 0.852507 -33 CTATTTTTAAAAAATTAAAAATTCGTTTTAT 11 37 0 AAAATTAAAA 0.825896 -122 AATAATACCAAATAAAATACAAATTACAGTT 13 17 1 AATAAAATAA 0.580517 -281 TCAAATTTTAAAAAATAAATACCTAAGCTAA 13 69 1 AAAAATAAAA 0.741566 -229 AACACAAATTAATATTTAAGAATTGAGGTAC 13 140 0 AATATTTAAA 0.905261 -158 AATATACCTCAAAATATTAAATCTATTGAAA 13 203 1 AAAATATTAA 0.62773 -95 TCTATTGAAAAATAATAAACAAGCCTTGCTT 13 224 1 AATAATAAAA 0.825896 -74 AGGAAGCAAAAATATATAAAAAATTTGCTTT 14 62 1 AATATATAAA 0.80601 -111 ATGTCCGGAAAATATATAAAAAGCAAATTTT 14 81 0 AATATATAAA 0.80601 -92 TATTTTGAGTAATATTTTATACTGCAAGCAA 15 29 0 AATATTTTAA 0.864992 -65 ATGCTGTGCAAATAATTAACAATATATAATA 16 12 0 AATAATTAAA 0.852507 -289 TAATTTGTCTATAATTAAAAACTGCACCTTT 16 114 0 ATAATTAAAA 0.585154 -187 CAATCCAAAAAATAATTAAAAATGCTTTTTA 16 208 1 AATAATTAAA 0.852507 -93 AGACTATGCAAAAAATAAACAATGGTAATTT 17 47 1 AAAAATAAAA 0.741566 -56 TATTATAACTAAAATAAAAGATTTAATTAAA 18 155 1 AAAATAAAAA 0.67349 -146 ACAATACTACAATATTATAAACA 19 3 0 AATATTATAA 0.840258 -144 TTTAAAAAAGATTATTATAAAGATTAGATAC 19 59 1 ATTATTATAA 0.610033 -88 AAAACTAAAAAATATAAAACAACGATACAAA 20 20 0 AATATAAAAA 0.773242 -230 GCAGTTAAGAAATATAAAACATTTAGCTCTT 20 69 1 AATATAAAAA 0.773242 -181 CCTTTACTGAAAAAATATATAGAATTTAGTA 20 112 0 AAAAATATAA 0.658139 -138 CCTTTTTTGGAATAATTTATACCTTAAAATA 20 207 1 AATAATTTAA 0.794915 -43 AAATAGAACCAATAAAATAAAAATAAA 20 233 1 AATAAAATAA 0.580454 -17 TTTCCGTCATATTATTTTATATATGGTAATT 21 36 1 ATTATTTTAA 0.655861 -265 TAATTATATTATTAATTAATAGTTAATTTAT 21 139 1 ATTAATTAAA 0.632174 -162 TTTTTAATTAAATAATTAATATATAATAGAA 21 202 1 AATAATTAAA 0.852507 -99 TATATAATAGAAAATTATATAATTTAATATC 21 221 1 AAAATTATAA 0.760915 -80 AAGGTTCATGAAAATTAAAAACGCATACTCT 22 184 0 AAAATTAAAA 0.825896 -117 AAGATATCAAAAAAATTTATAAATCGTAATT 22 226 1 AAAAATTTAA 0.701112 -75 ********* * Masking position 4 Map Score: 44.3622 Number of sites scoring better than the average of aligned sites = 1622 Number in coding regions = 993 Number in noncoding regions = 629 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 3 AATCTGTTGATTAATATTGTTTACAGTAAACCT 1 157 1 TTAAATTTTA 0.674285 -144 TCTTCAAAAATTAAAAATCTTATTAATTTGTTG 1 200 0 TTAAAATTAT 0.634776 -101 CAATTAAACAATAATAATGCTATATTTTGACAA 3 29 0 ATAAAATTAT 0.803116 -130 ATAAAACCTAATAAAAATTTTATCGGTACTATA 4 24 0 ATAAAATTAT 0.52395 -27 TAACTTTCGTATAAAAATACTCATACAAAAATA 5 34 0 ATAAAATTCA 0.678695 -211 GTTAAAATAATTAATAATTATTAAAATTGCGAA 5 63 1 TTAAAATTTA 0.853321 -182 AAATTTATACATAAAAATGATAATTGTAATTAT 5 118 0 ATAAAATTAA 0.623145 -127 AAATACTCTCTTAAAATTGATTTTATACATTTT 5 220 0 TTAAATTTTT 0.853251 -25 TTAATATTCCTTATTATTTTATA 7 131 0 TTAAATTTTA 0.69897 -13 AAATACAAATATAATAATTTTCTGAAACTAAGA 10 45 1 ATAAAATTCT 0.823301 -93 ACTATTCAATATAAAAATAATAAAATTTAATAC 10 114 0 ATAAAATTAA 0.623145 -24 TTTTAAAAAATTAAAAATTCGTTTTATCTCACT 11 31 0 TTAAAATGTT 0.691035 -128 TTTTAATTTTTTAAAAATAGTATGTTTATATTT 11 48 1 TTAAAATTAT 0.881264 -111 CTGAAATGAAATAAAAATCATTTAATAAAGTCA 11 90 1 ATAAAATTTT 0.89256 -69 ATTGAATTACTTAATAATGTGCTTAAGTTAAGT 12 69 1 TTAAAATGCT 0.587216 -65 TTTGATAAAATTAAGATTACTTTATTAACTGTA 13 41 0 TTAAATTTTT 0.853251 -257 TGTTAGTTTATTAAAATTTTTTTTGTAAAAATA 13 174 1 TTAAATTTTT 0.835279 -124 GTAATATGATTTAATAATTATATGTCCGGAAAA 14 100 0 TTAAAATTAT 0.881264 -73 CAAAAAATAATTAAAAATGCTTTTTAAAAAGAT 16 213 1 TTAAAATTTT 0.935758 -88 CAATGGTAATTTAACATTGGTTTACGAAAAGAT 17 66 1 TTAAATTTTT 0.853251 -37 TGCTGACACTTTAAAAATATTCTCAGTATCAAT 18 45 0 TTAAAATTCT 0.894838 -256 TCTAATCTTTATAATAATCTTTTTTAAAATATC 19 54 0 ATAAAATTTT 0.873739 -93 TCCTTTGTATTTAAAAATTTTTAATTAAATAAT 21 185 1 TTAAAATTTA 0.840571 -116 TTTTGAGTTTATAACATTTCTTTAGATACTTCA 21 255 0 ATAAATTTTT 0.768266 -46 AATCTGAACTTTAACAATAATCTTTATCAAAGC 22 127 1 TTAAAATTCT 0.902652 -174 **** *** *** Masking position 8 Map Score: 29.8846 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 369 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 TAAACCTTGTATAACATCAACAAATTAATAAG 1 183 1 ATAACTCAAA 0.958132 -118 AATTCAAGTATTATCTTCAAAAATTAAAAATC 1 214 0 TTATCTCAAA 0.710084 -87 ACTAAAACTATTAAATTCAAGTATTATCTTCA 1 227 0 TTAAATCAAT 0.724998 -74 GACAAAATGTATAAAATCAATTTTAAGAGAGT 5 217 1 ATAAATCAAT 0.822136 -28 ATAATAGTATATAACGTCAAGTTACCAGCTTA 6 37 0 ATAACTCAAT 0.928837 -62 TGTAAGAAGATCAACTTCAAAAAGAGCAAAGA 7 79 0 TCAACTCAAA 0.655644 -65 AAATCATTTAATAAAGTCAATAATGTTAATGG 11 104 1 ATAAATCAAA 0.890161 -55 AATTCAGAAAATAACTTCAAAATCATAAGAA 13 277 1 ATAACTCAAA 0.958132 -21 ATTACATACAATAACATCAAGACAGTATTTGA 14 16 0 ATAACTCAAA 0.958132 -157 TTTATATTTCTTAACTGCAATACATACTAGTA 20 55 0 TTAACGCAAA 0.655644 -195 TCAGTAAAGGTTAAAATCAAGTGTTGATAAAG 20 133 1 TTAAATCAAT 0.724998 -117 GTAAAATGAGATAACCTCAGCATTTAAAGAAC 20 164 0 ATAACTCAGA 0.769491 -86 AAGAAATGTTATAAACTCAAAAAGTTCATAAG 21 266 1 ATAAATCAAA 0.890161 -35 ATATCCTCAAATTCTTATGAAC 21 289 0 ATATCTCAAT 0.710084 -12 ***** **** * Masking position 9 Map Score: 11.7243 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 89 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 TTTTGACAATAGTAACAATAAAGAAAC 3 8 0 AGTAACAATA 0.883554 -151 AGTTAAAATAATTAATAATTATTAAAATTG 5 62 1 ATTAATAATT 0.515368 -183 AATAATTACAATTATCATTTTTATGTATAA 5 117 1 ATTATCATTT 0.373962 -128 TAAGCTAAGCAGTAACAATTTTAAATTAAA 9 77 1 AGTAACAATT 0.861991 -28 TTTTTAAAAAATTAAAAATTCGTTTTATCT 11 35 0 ATTAAAAATT 0.515369 -124 TTGTAATACCATTAACATTATTGACTTTAT 11 114 0 ATTAACATTA 0.676615 -45 ATTTTAATAAACTAACAATTAACACAAATT 13 161 0 ACTAACAATT 0.826245 -137 TGTGCAAATAATTAACAATATATAATAA 16 9 0 ATTAACAATA 0.9366 -292 AAGTTAGAAGATTAACACTATGTTATATGA 16 55 1 ATTAACACTA 0.76395 -246 AAATATTCTCAGTATCAATAAGAAACTGCA 18 34 0 AGTATCAATA 0.724642 -267 CTGATACTTAATTATCAATACGCCATGAAT 18 106 0 ATTATCAATA 0.8367 -195 TAAGTATCAGATTATCAAAAAAAGAGATAT 18 126 1 ATTATCAAAA 0.392617 -175 TTAACTATTAATTAATAATATAATTATAGC 21 135 0 ATTAATAATA 0.563676 -166 TGATATATAAATTAACTATTAATTAATAAT 21 146 0 ATTAACTATT 0.452045 -155 TAATTATTTAATTAAAAATTTTTAAATACA 21 190 0 ATTAAAAATT 0.515369 -111 AATATACCATACTATCAATTTTTCTTT 22 8 0 ACTATCAATT 0.622537 -293 GAAATATTGCACTAACACTTCAATATACCA 22 29 0 ACTAACACTT 0.510227 -272 AATAACAAACAGTAACAAAAAATAACTCCT 22 72 0 AGTAACAAAA 0.489082 -229 TATTAGCTTTATTAACAATAACAAACAGTA 22 88 0 ATTAACAATA 0.9366 -213 TAATCTGAACTTTAACAATAATCTTTATCA 22 126 1 TTTAACAATA 0.500548 -175 ********** Masking position 3 Map Score: 8.22504 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 297 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 TGACATAAAAAATTAAATAAACAAAGACAAAG 1 97 0 AATTAATAAC 0.65227 -204 TATTAAAAGAAATGACATAAAAAATTAAATAA 1 109 0 AATGAATAAA 0.963894 -192 CTATGTGTTTAATGACATACTATGTTTGATCA 3 93 1 AATGAATACA 0.941645 -66 TTAATCTTAAAATAATATAAAAAAGCAA 6 81 1 AATAAATAAA 0.828765 -18 GCAAAGATCCAATGAGATAAAATCTTATCCTA 7 54 0 AATGAATAAA 0.963894 -90 TTCAGTGTAAAGTGAGATAAAACGAATTTTTA 11 21 1 AGTGAATAAA 0.771979 -138 ATTGTTCTGAAATGAAATAAAAATCATTTAAT 11 84 1 AATGAATAAA 0.963894 -75 AATAATACCAAATAAAATACAAATTACAGTTA 13 17 1 AATAAATACA 0.745255 -281 GCCACAGAAAAATTACATACAATAACATCAAG 14 27 0 AATTAATACA 0.671232 -146 CAGGATCAGGAATGATAGAATCAT 14 159 1 AATGAAGAAC 0.652796 -14 GCATGCAGCTAATGATATAATAAGTCGGTTAG 18 277 1 AATGAATAAA 0.963864 -24 TCTATGGTAAAATGAGATAACCTCAGCATTTA 20 170 0 AATGAATAAC 0.936811 -80 AAATAGAACCAATAAAATAAAAATAAA 20 233 1 AATAAATAAA 0.828765 -17 GGAATAGCAAAATGATATATAAATTAACTATT 21 156 0 AATGAATATA 0.755629 -145 TATCTAAAGAAATGTTATAAACTCAAAAAGTT 21 260 1 AATGTATAAC 0.559191 -41 GGAAATTAGAAATGAATTACGATTTATAAATT 22 239 0 AATGATTACA 0.579959 -62 ***** **** * Masking position 9 Map Score: 14.1198 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 67 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 TAAGCATAAATAGAAGGATTTAATATATTAAAAG 1 57 0 TAAATTTAAT 0.936779 -244 TTATAGCAACTAAAACTATTAAATTCAAGTATTA 1 233 0 TAAATTAAAT 0.465258 -68 AATATAGCATTATTATTGTTTAATTGAATTGATA 3 36 1 TAAGTTTAAT 0.574473 -123 ATTTTATCGGTACTATAATTTAATACCGGG 4 7 0 TAAATTTAAT 0.936779 -44 TATACGAAAGTTAAAATAATTAATAATTATTAAA 5 54 1 TTAAATTAAT 0.534485 -191 CTATTATATATATAATCACTTAATCTTAAAATAA 6 62 1 TAAACTTAAT 0.941459 -37 TTAAATTTCATACTATGACTTACTTGTGGTCTCT 9 11 1 TAAACTTACT 0.583299 -94 AATATAAAAATAATAAAATTTAATACTATAGTGT 10 106 0 TAAATTTAAT 0.936779 -32 GAAATGAAATAAAAATCATTTAATAAAGTCAATA 11 92 1 AAAATTTAAT 0.465254 -67 ATGTTAATGGTATTACAACTTAAAATATGTTTAG 11 126 1 TAAACTTAAA 0.635512 -33 TTATTGTGTATTGAATTACTTAATAATGTGCTTA 12 60 1 TTAACTTAAT 0.823378 -74 TTGATAAAATTAAGATTACTTTATTAACTGTAAT 13 39 0 TAAACTTTAT 0.635512 -259 AACTAACAATTAACACAAATTAATATTTAAGAAT 13 148 0 TAAAATTAAT 0.799368 -150 CTGAATTTTGTAGCATTATTTAATGTAAGAAGCA 13 250 0 TAAATTTAAT 0.936779 -48 AAAATAACTGTAATATGATTTAATAATTATATGT 14 108 0 TAAATTTAAT 0.936779 -65 TGCAAATAATTAACAATATATAATAA 16 3 0 TAAATATAAT 0.476683 -298 CTGCAATACATACTAGTACTTAAAAACTAAAAAA 20 39 0 TAAACTTAAA 0.635508 -211 ACCTCAGCATTTAAAGAACTTTATCAACACTTGA 20 149 0 TTAACTTTAT 0.335767 -101 TTCTATTCTTTTTTAGTACTTAATTTCCGTCATA 21 13 1 TTAACTTAAT 0.822036 -288 GCTATAATTATATTATTAATTAATAGTTAATTTA 21 135 1 TAAAATTAAT 0.799364 -166 CCTTTGTATTTAAAAATTTTTAATTAAATAATTA 21 186 1 TAATTTTAAT 0.476664 -115 TAATAGAAAATTATATAATTTAATATCGCTTGAA 21 225 1 TTAATTTAAT 0.811218 -76 ATAAAGCTAATATAAAAATGTAATCTGAACTTTA 22 106 1 TAAATGTAAT 0.574477 -195 ** * ******* Masking position 5 Map Score: 19.7138 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 195 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 TTTAGTTGCTATAAATACCTTTATTTTAAA 1 253 1 ATAAATACCT 0.925412 -48 ATACTCATACAAAAATAGCTAATAACAAAG 5 21 0 AAAAATAGCT 0.74781 -224 AGTATCAACTATAAAAAACTCTTAGTTTCA 10 67 0 ATAAAAAACT 0.59268 -71 ATTTTAAAAAATAAATACCTAAGCTAAATG 13 73 1 ATAAATACCT 0.925412 -225 TTTTTTGTAAAAATATACCTCAAAATATTA 13 192 1 AAATATACCT 0.806148 -106 ACAAAATTCAGAAAATAACTTCAAAATCAT 13 273 1 GAAAATAACT 0.787171 -25 TAATATCCATAAAAATAACTGTAATATGAT 14 123 0 AAAAATAACT 0.905987 -50 TTAATCTAAGATAAATAACATTAAGTAATT 16 140 0 ATAAATAACA 0.59268 -161 AGCCTATTAAATATATAACTCTCTCACTTG 18 187 0 ATATATAACT 0.820185 -114 AACAGTAACAAAAAATAACTCCTTATTTTG 22 65 0 AAAAATAACT 0.905987 -236 AATGTATATACCTCATTCAGTCA 22 288 0 GTATATACCT 0.654777 -13 ********** Masking position 5 Map Score: 4.11512 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 76 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 9 ATTTAATATATTAAAAGGCTGCAACTCTAGTCAG 1 40 0 TTAAAGCTAA 0.949421 -261 AGACAAAGGCTTAATAAGCATAAATAGAAGGATT 1 71 0 TTATAGCAAA 0.733387 -230 CACGAATATTTTACAATACTAACATCCTTCAATA 3 132 1 TTAAAACTCA 0.865939 -27 AGTTACCAGCTTAAAGAGCTTTAAAAAGGAAATT 6 16 0 TTAAGGCTAA 0.759323 -83 AAAAAAAATTTTAATAAACTAACAATTAACACAA 13 164 0 TTATAACTCA 0.792073 -134 CTTTGATCCTTATAGAGCTTAAACAGTGTATGT 16 278 0 TTAAGGCTAA 0.87376 -23 ATTAAAATACTCTCATCTTTTCGTA 17 88 0 TTAAAACTCA 0.864903 -15 AGTTATATATTTAATAGGCTAAAATTACAAGATC 18 197 1 TTATAGCTAA 0.917246 -104 AATAGCTTATTTATAAAGCATGCAGCTAATGATA 18 260 1 TTAAAGCACA 0.813547 -41 ACAACAGGCATTACAATACTACAATATTATAAAC 19 12 0 TTAAAACTAA 0.87248 -135 TATAGCTAAATTAATATGCTTCAAATAGGATAAT 21 107 0 TTATAGCTAA 0.916985 -194 *** ** *** ** Masking position 3 Map Score: 5.00656 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 41 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 TTTTTAATTTTTGAAGATAATACTTGAATTTAA 1 216 1 TTGAAAATAC 0.712396 -85 ATGCTATATTTTGACAATAGTAACAATAAAGAA 3 13 0 TTGAAAGTAA 0.593058 -146 CATACTATGTTTGATCACAGTATTCACGAATAT 3 108 1 TTGAAAGTAT 0.926374 -51 TAAAATCAATTTTAAGAGAGTATTTAA 5 228 1 TTTAAAGTAT 0.83333 -17 ATCGTAGTACTTTAGCATGATATATCTAATT 7 9 0 TTTAAGATAT 0.83333 -135 ACAAGGCTTTTTTAGTATGATATTATAAAATAA 7 108 1 TTTAAGATAT 0.83333 -36 CTATAGTGTCTTGACCATAGTATCAACTATAAA 10 82 0 TTGAAAGTAT 0.926374 -56 TTTTAATTTTTTAAAAATAGTATGTTTATATTT 11 48 1 TTAAAAGTAT 0.55227 -111 ATTTTTTACTTTTGATACGGTATATCTCTGTTA 12 104 0 TTTGAGGTAT 0.699611 -30 AGCATGGTATTTGATCACGATACGGTACCTCAA 13 116 1 TTGAAGATAC 0.798998 -182 TAAAATTTTTTTTGTAAAAATATACCTCAAAAT 13 185 1 TTTGAAATAT 0.474884 -113 TGCCTGTTGTGTGACTACGATATTTTAAAAAAG 19 36 1 GTGAAGATAT 0.647317 -111 ATACCGTATATTGACTACGGTATCTAATCTTTA 19 76 0 TTGAAGGTAT 0.952812 -71 ACCTTACACGTTGAGCAAGATATCAAAAAAATT 22 210 1 TTGAAGATAT 0.926374 -91 **** * ***** Masking position 7 Map Score: 3.60609 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 110 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 11 TAATATCATCATGTAACTTATCTTCATAAC 10 10 1 CATTAACTTA 0.960525 -128 TCTCTGTTAACACTTAACTTAAGCACATTAT 12 82 0 CACTAACTTA 0.899027 -52 TCTAAATCTACATTTAGCTTAGGTATTTATT 13 82 0 CATTAGCTTA 0.882251 -216 TAGTGTTAATCTTCTAACTTAACATAAATTG 16 44 0 CTTTAACTTA 0.913742 -257 ATCAGCACCTCATATAACATAGTGTTAATCT 16 63 0 CATTAACATA 0.91373 -238 TGCAATAATGCAGGTAACATACACTGTTTAA 16 262 1 CAGTAACATA 0.794748 -39 TTTATCAAAGCTTTTAACTTATAGATGAAAG 22 149 1 CTTTAACTTA 0.913742 -152 *** ******* Masking position 6 Map Score: 0.975197 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 21 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 TGCGTGGATCTGATATATATCAATTCAATTAA 3 55 0 TGATATATCA 0.411421 -104 AACTATTCAATATAAAAATAATAAAAT 10 121 0 TTCAATATAA 0.693806 -17 TTAATTGTTTTTCAATATTCCAGAACTGCTGG 12 23 0 TTCAATATCA 0.86596 -111 GGATGCAAATTGCATTATGACAATGTAGGCAG 15 69 1 TGCATTATCA 0.923243 -25 GTATGTTACCTGCATTATTGCAAGCAATATAC 16 252 0 TGCATTATCA 0.603652 -49 GATCATAAGGTTAAATATGCCAAGAATTTGAT 19 122 1 TTAAATATCA 0.824775 -25 GCACTAACACTTCAATATACCATACTATCAAT 22 19 0 TTCAATATCA 0.935987 -282 GAAGTGTTAGTGCAATATTTCATGGATCAAAA 22 38 1 TGCAATATCA 0.52151 -263 ******** ** Masking position 7 Map Score: 1.16455 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 32 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 ********** No masking Map Score: 1.15701e-11 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 14 ********** No masking Map Score: 1.15701e-11 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 1.15701e-11 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0