AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -inarL_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 RP122 98 HFLK PROTEIN (hflK) #2 RP123 143 HFLC PROTEIN (hflC) #3 RP124 30 PROBABLE PERIPLASMIC SERINE PROTEASE DO-LIKE PRECURSOR (htrA) #4 RP125 104 unknown #5 RP126 137 SUCCINATE DEHYDROGENASE CYTOCHROME B560 SUBUNIT (sdhC) #6 RP127 158 SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR PROTEIN (sdhD) #7 RP128 133 SUCCINATE DEHYDROGENASE FLAVOPROTEIN SUBUNIT (sdhA) #8 RP264 300 unknown #9 RP265 102 ISOCITRATE DEHYDROGENASE (icd) #10 RP266 90 unknown #11 RP267 83 unknown #12 RP396 140 unknown #13 RP397 187 THIOL:DISULFIDE INTERCHANGE PROTEIN TLPA (tlpA) #14 RP585 300 unknown #15 RP587 147 SCO2 PROTEIN PRECURSOR (sco2) #16 RP588 101 CYTOCHROME C-TYPE BIOGENESIS PROTEIN CCME (ccmE) #17 RP702 300 unknown #18 RP794 300 HEME EXPORTER PROTEIN A (ccmA) #19 RP830 144 HEME EXPORTER PROTEIN C (ccmC) #20 RP831 25 unknown #21 RP832 121 PROTEIN P34 (p34) Motif number 1 TTGCTTTTTTATATTATTTTAAGATTA 1 82 0 TTTATATTAT 0.427939 -17 ATCATTTAGGATAAGATTTTATCTCATTGG 2 48 1 ATAAGATTTT 0.553644 -96 AATATTCCTTATTATTTTATAATATCATAC 2 122 0 ATTATTTTAT 0.816914 -22 GTTTCAGAAAATTATTATATTTGTATTTCT 5 43 0 ATTATTATAT 0.855512 -95 AGTATTAAATTTTATTATTTTTATATTGAA 5 113 1 TTTATTATTT 0.920117 -25 AAACGAATTTTTAATTTTTTAAAAATAGTA 6 40 1 TTAATTTTTT 0.814701 -119 TTATTAAATGATTTTTATTTCATTTCAGAA 6 88 0 ATTTTTATTT 0.667166 -71 TCAATTAATTTTTTACTTTTGATA 7 120 0 TTAATTTTTT 0.814701 -14 TTATATATTGTTAATTATTTGCACAGCATT 8 14 1 TTAATTATTT 0.853643 -287 AGCATTTTTAATTATTTTTTGGATTGCTAA 8 204 0 ATTATTTTTT 0.938294 -97 ATTACCATTGTTTATTTTTTGCATAGTCTA 9 46 0 TTTATTTTTT 0.896723 -57 TAATTCAGATATTATTCTTT 12 1 0 ATTATTCTTT 0.658517 -140 ATTTTTTCATATTAGTATTTATATTTAGTT 13 136 0 ATTAGTATTT 0.917186 -52 AAGGCATTTTATTATTTTTTCATATTAGTA 13 149 0 ATTATTTTTT 0.938294 -39 ATAATAATTTATAGTAATGA 13 178 0 ATAATAATTT 0.749477 -10 CTTGAAGAGTATAATATTTTACCCTTGCAT 14 90 1 ATAATATTTT 0.6894 -211 TTAGGTAGCTATTTTTATTTTATTAGACTT 14 128 1 ATTTTTATTT 0.667166 -173 GATAATGATTTTTATTATATTATTGTGTAC 15 20 1 TTTATTATAT 0.771744 -128 AATTCATTTCATTATTATTTTGTGGCTTGA 15 121 0 ATTATTATTT 0.952768 -27 TATTAGTATCATATTTATTTACCTTTTTAA 16 16 1 ATATTTATTT 0.503726 -86 TTTTTAATATTTTATAATTTAAAAAATTTA 16 67 0 TTTATAATTT 0.771744 -35 TAAAGTTTTGTTTATTTTTTAATATTTTAT 16 82 0 TTTATTTTTT 0.896723 -20 TGCAATACATATTAGTATATTTTAAAAAAA 17 218 1 ATTAGTATAT 0.764761 -83 AATTATTAATATAATTATTTATAGTTAATT 17 265 1 ATAATTATTT 0.910826 -36 CATATTGTACTTTAGTATTTTTGTATTCTT 18 15 0 TTTAGTATTT 0.863462 -286 TACATTTCCTATTATTAGTTGTTTAACTTT 18 49 0 ATTATTAGTT 0.525887 -252 GTAACTGCTAATAATTTTATGAGATATCTT 18 262 1 ATAATTTTAT 0.688146 -39 AAATACTAATATTAGTATTTTCAAGTTATT 19 25 0 ATTAGTATTT 0.917186 -120 AAATACTAATATTAGTATTTTTAGCTGTAT 19 35 1 ATTAGTATTT 0.917186 -110 AATTATTAAAATAAGTTTTT 20 1 0 ATAAGTTTTT 0.808705 -25 ACTTATTTTAATAATTTTTTC 20 15 1 ATAATTTTTT 0.885001 -11 ATCCTCTCTAATTATTATTTAAATAAGTAT 21 14 1 ATTATTATTT 0.952768 -108 TATTATTTAAATAAGTATATGGTTTTTAGA 21 26 1 ATAAGTATAT 0.622086 -96 GTATATGGTTTTTAGAATTTTGTAAAGTAT 21 40 1 TTTAGAATTT 0.649899 -82 CTCATTGAATTTTATATTTTCTTTGTTAAA 21 74 1 TTTATATTTT 0.718205 -48 ATCTTCTAAATTTATATTATAAGTTTAACA 21 97 0 TTTATATTAT 0.427939 -25 ********** Masking position 2 Map Score: 37.6546 Number of sites scoring better than the average of aligned sites = 1530 Number in coding regions = 949 Number in noncoding regions = 581 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 2 TTATATATATAATAGTATATAACGTCAAGTTA 1 45 0 AATTATATAA 0.490743 -54 ATAATCACTTAATCTTAAAATAATATAAAAAA 1 73 1 AATTAAAATA 0.93601 -26 TTTAGTATGATATTATAAAATAATAAGGAATA 2 118 1 TATTAAAATA 0.438566 -26 AAGCAGTAACAATTTTAAATTAAATTAAAGTT 4 83 1 AATTAAATTA 0.738053 -22 AACTATTCAATATAAAAATAATAAAATTTA 5 118 0 AATAAAAATA 0.887525 -20 TAAACATACTATTTTTAAAAAATTAAAAATTC 6 44 0 ATTTAAAAAA 0.804264 -115 ATTGTTCTGAAATGAAATAAAAATCATTTAAT 6 84 1 AATAATAAAA 0.728469 -75 ATACCGTATCAAAAGTAAAAAATTAATTGA 7 114 1 AAATAAAAAA 0.468447 -20 TTCGTAAACCAATGTTAAATTACCATTGTTTA 9 62 0 AATTAAATTA 0.739189 -41 CATTAATAACATTATAAAAAAA 10 79 1 ATTAAAAAAA 0.693615 -12 TTGACATGAGAATCATATAAAACATCTTAAGA 11 23 0 AATTATAAAA 0.832964 -61 TAAATACTAATATGAAAAAATAATAAAATGCC 13 145 1 TATAAAAATA 0.428471 -43 CAAGAAGTCTAATAAAATAAAAATAGCTACCT 14 130 0 AATAATAAAA 0.728469 -171 ATAATGGTAAATTTGTAAAAAACCCAGCACAT 14 175 1 ATTTAAAAAA 0.807964 -126 TACGGTACACAATAATATAATAAAAATCATTA 15 22 0 AATTATAATA 0.887435 -126 GTGATGCAGCATTCTTATAATAACCTACGGTA 15 47 0 ATTTATAATA 0.781629 -101 AAATTTTTTAAATTATAAAATATTAAAAAATA 16 68 1 AATTAAAATA 0.928068 -34 TTTCTATACGATTTTTAAAATAACAAGAAATT 17 129 1 ATTTAAAATA 0.8606 -172 TGCAATACGTAATCCTATAAAAGCTGTGGTAC 17 190 0 AATTATAAAA 0.833002 -111 ATATTAGTATATTTTAAAAAAACATTAGGAAA 17 226 1 ATTAAAAAAA 0.693577 -75 AAAAAAGAATACAAAAATACTAAAGTACA 18 8 1 AATAAAAATA 0.887527 -293 ATTTGGTATTAATAATAAAATAGATAATACAA 18 132 1 AATTAAAATA 0.936094 -169 TAAAATAGATAATACAAAATTAACTAGTGTTA 18 147 1 AATAAAATTA 0.603874 -154 GAAAAAATTATTAAAATAAGTTTTT 20 8 0 ATTTAAAATA 0.869325 -18 CCATATACTTATTTAAATAATAATTAGAGAGG 21 16 0 ATTAATAATA 0.658216 -106 TTTCTTTGTTAAACTTATAATATAAATTTAGA 21 91 1 AAATATAATA 0.428499 -31 *** ******* Masking position 7 Map Score: 26.1055 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 717 Number in noncoding regions = 419 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 GGTTATGAAGATAAGTTACATGATGATATTA 5 8 0 ATAATCTGAT 0.862243 -130 TACCATTAACATTATTGACTTTATTAAATGATTT 6 104 0 ATTATCTTAT 0.968027 -55 TTGAAAAACAATTAATAGCATTATTGTGTATTGA 7 40 1 ATTATCTTAT 0.968027 -94 TGCTGTGCAAATAATTAACAATATATAATAA 8 8 0 ATAATCATAT 0.671017 -293 TTAATCTAAGATAAATAACATTAAGTAATTTGTC 8 136 0 ATAATCTTAA 0.667807 -165 TAACTGTTACATTAATAACATTATAAAAAAA 10 70 1 ATTATCTTAT 0.968027 -21 TCATTTGATTATTAATGAATTGATTGTTATAGTA 12 41 0 ATTATATGAT 0.607168 -100 AATTATTTTTATTAATCAAATTATTTTTATTCTC 12 73 0 ATTATATTAT 0.683386 -68 TTTTTATAACTATCTTTATAGAGTTCTAA 12 122 0 ATAATCTTAT 0.897786 -19 ATTATTAGTGACATTATTCACTTTCAT 14 4 1 ATTATCTTAT 0.968027 -297 ATTCACTTTCATTATTCACTTTATATCTAATTAA 14 26 1 ATTATCTTAT 0.968027 -275 CAATAATATAATAAAAATCATTATCGACAACTTC 15 11 0 ATAAACTTAT 0.667414 -137 GAGATAACTTATTAATATCGTAATTTCAATGAGC 15 89 0 ATTATCTAAT 0.784588 -59 AAGATATAATTCATTTCATTATTATTTTGTGG 15 126 0 ATTCTCTTAT 0.83215 -22 ATCTATAATTATTAATATAATTATTTATAGTTAA 17 259 1 ATTATATTAT 0.683386 -42 CACAATAAGTTTAATTTTCATTATGTTCATCTAA 18 181 0 TTAATCTTAT 0.667807 -120 **** * * **** Masking position 2 Map Score: 17.3397 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 93 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 GCTTTTTTATATTATTTTAAGATTAAGTGA 1 77 0 ATTATTTTAA 0.802536 -22 ATTAAATTTTATTATTTTTATATTGAATAG 5 116 1 ATTATTTTTA 0.93522 -22 TTTTAAAAATAGTATGTTTATATTTGCGAT 6 56 1 AGTATGTTTA 0.670454 -103 ACTTTATTAAATGATTTTTATTTCATTTCA 6 91 0 ATGATTTTTA 0.698086 -68 TATATTGTTAATTATTTGCACAGCATTCAA 8 17 1 ATTATTTGCA 0.489162 -284 AGCATTTTTAATTATTTTTTGGATTGCTAA 8 204 0 ATTATTTTTT 0.599168 -97 CTTTTTAAAAAGCATTTTTAATTATTTTTT 8 214 0 AGCATTTTTA 0.535973 -87 AAAAGATGAGAGTATTTTAAT 9 92 1 AGTATTTTAA 0.788866 -11 GTAGATTATTATCAAAGCGTGACT 10 5 1 ATTATTATCA 0.668983 -86 ATTATTTTAAAACGTCATTG 11 74 0 ATTATTTTAA 0.802536 -10 TATTAATCAAATTATTTTTATTCTCATTTG 12 68 0 ATTATTTTTA 0.93522 -73 ATTTAAATCAATTATTTTTATTAATCAAAT 12 86 0 ATTATTTTTA 0.93522 -55 AGCAAGAGATAGTATTGTCATCATATGGAA 13 76 0 AGTATTGTCA 0.455627 -112 TTTTCATATTAGTATTTATATTTAGTTGTG 13 133 0 AGTATTTATA 0.784932 -55 AAGGCATTTTATTATTTTTTCATATTAGTA 13 149 0 ATTATTTTTT 0.599168 -39 GTTGTCGATAATGATTTTTATTATATTATT 15 14 1 ATGATTTTTA 0.698086 -134 TCATTAGTACAGTATTATCAGATAAATGAT 17 50 1 AGTATTATCA 0.650099 -251 AAAATCTATAATTATTAATATAATTATTTA 17 256 1 ATTATTAATA 0.45725 -45 TATTAATATAATTATTTATAGTTAATTTAT 17 268 1 ATTATTTATA 0.798791 -33 ATTGTACTTTAGTATTTTTGTATTCTTTTT 18 12 0 AGTATTTTTG 0.535973 -289 TATCTATTTTATTATTAATACCAAATCCTA 18 128 0 ATTATTAATA 0.45725 -173 TTTAATTTTCATTATGTTCATCTAATGTAA 18 176 0 ATTATGTTCA 0.593471 -125 TACTAATATTAGTATTTTCAAGTTATTCTG 19 22 0 AGTATTTTCA 0.897491 -123 TACTAATATTAGTATTTTTAGCTGTATCAC 19 38 1 AGTATTTTTA 0.929934 -107 CTCTCTAATTATTATTTAAATAAGTATATG 21 17 1 ATTATTTAAA 0.527768 -105 ********** Masking position 5 Map Score: 21.1189 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 532 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 5 GTATATTCAGTGTAAAGTGAGATAAAACGAATTT 6 16 1 TGTTGAGATA 0.982902 -143 TTAAGTTAAGTGTTAACAGAGATATACCGTATCA 7 91 1 TGTAGAGATA 0.900622 -43 ATTCAATTTATGTTAAGTTAGAAGATTAACACTA 8 41 1 TGTTTAGAAG 0.791873 -260 ATTAACACTATGTTATATGAGGTGCTGATGTCTC 8 65 1 TGTTGAGGTG 0.917213 -236 CAATTTCTCTTGTAGTTTGAGATAACTGTTACAT 10 48 1 TGTTGAGATA 0.982903 -43 TATTACAGAATGTATCCTTAGATACCGTGATCAA 13 24 0 TGTTTAGATA 0.966921 -164 AATATTTAAATGTTTAATTAGATATAAAGTGAAT 14 39 0 TGTTTAGATA 0.966503 -262 ATTATTATTTTGTGGCTTGAGATAACTTATTAAT 15 107 0 TGTTGAGATA 0.982898 -41 AATTAACTAGTGTTACATTAGATGAACATAATGA 18 164 1 TGTTTAGATG 0.960215 -137 *** ******* Masking position 10 Map Score: 8.70111 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 8 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 6 TTATTTTAAGATTAAGTGATTATATATATAAT 1 64 0 ATAAGGATTA 0.623028 -35 AGGCTTTTTTAGTATGATATTATAAAATAATA 2 111 1 AGATGTATTA 0.743439 -33 GATAAGTTACATGATGATATTA 5 1 0 ATATGTATTA 0.955271 -137 GTCAATAATGTTAATGGTATTACAACTTAAAA 6 119 1 TTATGTATTA 0.949461 -40 TCAATACACAATAATGCTATTAATTGTTTTTC 7 42 0 ATATGTATTA 0.955271 -92 GACAAATTACTTAATGTTATTTATCTTAGATT 8 136 1 TTATGTATTT 0.649005 -165 TTTTTTTATAATGTTATTAATGTAACAGT 10 72 0 ATATGTATTA 0.955271 -19 CTTTGTTATAATTCAGATATTATTCTTT 12 7 0 ATCAGTATTA 0.623028 -134 TATTATACTCTTCAAGATATTATTTAGCATAT 14 74 0 TTAAGTATTA 0.914641 -227 TACCCTTGCATTAAAGCTATTAGGTAGCTATT 14 109 1 TTAAGTATTA 0.914639 -192 GGTAGCTATTTTTATTTTATTAGACTTCTTGC 14 131 1 TTATTTATTA 0.757669 -170 GATAATGATTTTTATTATATTATTGTGTACCG 15 20 1 TTATTTATTA 0.757669 -128 GCTCATTGAAATTACGATATTAATAAGTTATC 15 89 1 ATACGTATTA 0.816646 -59 TTAACTATAAATAATTATATTAATAATTATAG 17 261 0 ATATTTATTA 0.780427 -40 TATTAGTATTTTCAAGTTATTCTGTGATAAAA 19 14 0 TTAAGTATTC 0.609842 -131 ** *** ***** Masking position 9 Map Score: 10.5087 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 151 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 ATTAAATTTCCTTTTTAAAGCTCTTTAAGCT 1 12 1 CTTTTTAAGC 0.630895 -87 ACTAAAAAAGCCTTGTAAGAAGATCAACTTC 2 93 0 CCTTGTAAAA 0.8235 -51 ATTTGTATTTCTTGGTTATGAAGATAAGTTA 5 24 0 CTTGGTTAGA 0.77713 -114 TAAGAGATGTCATTGTAAGGAGGACCGCAGT 8 170 1 CATTGTAAGA 0.637665 -131 ACTAAGCAATCTTTTTAAAAAGCATTTTTAA 8 223 0 CTTTTTAAAA 0.845356 -78 ATACAATCAACTTGGTAACAAATGGCACACT 9 12 0 CTTGGTAAAA 0.895686 -91 TTATAGTAAACTTTGTTATAATTCAGATATT 12 18 0 CTTTGTTAAA 0.94736 -123 CTTCTAAAGGCTTTTTTATACCACAACTAAA 13 112 1 CTTTTTTAAC 0.689539 -76 ATAATGGTAAATTTGTAAAAAACCCAGCACA 14 175 1 ATTTGTAAAA 0.639986 -126 TCTTTGTTAGAATATAAATTAA 17 289 0 CTTTGTTAAA 0.94736 -12 CATGCGAGAGCTTTGTAAAAATGTCTTCAAA 19 110 1 CTTTGTAAAA 0.9612 -35 TTTATATTTTCTTTGTTAAACTTATAATATA 21 84 1 CTTTGTTAAC 0.909593 -38 ******** ** Masking position 8 Map Score: 5.43542 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 79 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 AACATTAAGTAATTTGTCTATAATTAAAAACTG 8 121 0 AATTTTCATA 0.814246 -180 AATTATAACAAAGTTTACTATAACAATCAATTC 12 26 1 AAGTTACATA 0.950448 -115 GGTTTTTTACAAATTTACCATTATTAGCTATCT 14 166 0 AAATTACATA 0.966086 -135 GAAGTTGTCGATAATGATTTTTAT 15 2 1 AAGTTTCATA 0.922816 -146 ATAATTTAAAAAATTTACTATTAACAATATCGC 16 51 0 AAATTACATA 0.966086 -51 GACTCATCTAAAATTATCATTTATCTGATAATA 17 62 0 AAATTTCTTA 0.760979 -239 AAATAACAAGAAATTCACAATGACCAGAGTATA 17 146 1 AAATTACATA 0.966086 -155 GTTAGAATATAAATTAACTATAAATAATTATAT 17 273 0 AAATTACATA 0.966106 -28 ***** ** ** * Masking position 2 Map Score: 4.30591 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 47 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 TTAAAATTGTTACTGCTTAGCTTAAGCACGTAGTC 4 66 0 TACTGTCTAA 0.949935 -39 CCATTAACATTATTGACTTTATTAAATGATTTTTA 6 101 0 TATTGTATAA 0.935327 -58 CATTATTGTGTATTGAATTACTTAATAATGTGCTT 7 58 1 TATTGTCTAA 0.97784 -76 TTGCTTAGTATATTGCTTGCAATAATGCAGGTAAC 8 245 1 TATTGTATAA 0.935327 -56 TTTATTATATTATTGTGTACCGTAGGTTATTATAA 15 30 1 TATTGTCTAG 0.901988 -118 ATTATAAGAATGCTGCATCACCTAACCTATAGCTC 15 58 1 TGCTGTCTAA 0.798267 -90 ACCTTAGCGATATTGTTAATAGTAAATTTTTTAAA 16 45 1 TATTGAATAA 0.800807 -57 AATAAGAGTATATTGACTCATCTAAAATTATCATT 17 74 0 TATTGTTTAA 0.851275 -227 TACTAATATGTATTGCAATACGTAATCCTATAAAA 17 200 0 TATTGACTAA 0.924621 -101 CAATGATATCTATTGGTTTTCACAATAAGTTTAAT 18 200 0 TATTGTCCAA 0.901974 -101 ***** * * *** Masking position 4 Map Score: 2.26119 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 36 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ATTGCTTGCAATAATGCAGGTAACATACAC 8 256 1 ATAATGCAGG 0.96446 -45 ACCGTGATCAATTATGCAAGTATA 13 5 0 ATTATGCAAG 0.970355 -183 TATAAAGTGAATAATGAAAGTGAATAATGT 14 21 0 ATAATGAAAG 0.83509 -280 CCTAATAGCTTTAATGCAAGGGTAAAATAT 14 103 0 TTAATGCAAG 0.908669 -198 TATTAGCTATCTTATGCAAGAAGTCTAATA 14 148 0 CTTATGCAAG 0.936454 -153 TTAAAGTTTGATTATGCAGGACTTATCAAA 18 79 0 ATTATGCAGG 0.96446 -222 ********** Masking position 5 Map Score: 1.84285 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 17 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 AGAGCAAAGATCCAATGAGATAAAATCTTATCC 2 56 0 TCAATGAGTA 0.900102 -88 ATTGACTTTATTAAATGATTTTTATTTCATTTC 6 92 0 TAAATGATTT 0.713686 -67 CGGTCCTCCTTACAATGACATCTCTTATTAATC 8 164 0 TCAATGACTT 0.967528 -137 TGTTTCTTATCGCAATGACGTTTTAAAATAAT 11 62 1 CCAATGACTT 0.901653 -22 ATATCGTAATTTCAATGAGCTATAGGTTAGGTG 15 76 0 TCAATGAGTT 0.977478 -72 TGTATTACAATACAATGATATCTATTGGTTTTC 18 214 0 TCAATGATTT 0.950647 -87 AAATATAAAATTCAATGAGTTTTATACTTTACA 21 60 0 TCAATGAGTT 0.977477 -62 * ******* * * Masking position 8 Map Score: 1.0751 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 13 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 ATTATATATATAATAGTATATAACGTCAAG 1 48 0 TAATAGTATA 0.767019 -51 TCATGTGCAGTAATGGTAAAGGTGCAGTTT 8 97 1 TAATGGTAAA 0.91078 -204 GAATTGATTGTTATAGTAAACTTTGTTATA 12 29 0 TTATAGTAAA 0.916353 -112 ATAATAATTTATAGTAATGAAGGCATTT 13 170 0 TTATAGTAAT 0.633293 -18 AGATAGCTAATAATGGTAAATTTGTAAAAA 14 166 1 TAATGGTAAA 0.91078 -135 GCGATATTGTTAATAGTAAATTTTTTAAAT 16 51 1 TAATAGTAAA 0.954305 -51 ATATAATTATTTATAGTTAATTTATATTCT 17 273 1 TTATAGTTAA 0.633291 -28 AAACAACTAATAATAGGAAATGTATTTGAT 18 55 1 TAATAGGAAA 0.829916 -246 GATTTGGTATTAATAATAAAATAGATAATA 18 131 1 TAATAATAAA 0.671848 -170 ********** Masking position 4 Map Score: 3.26202 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 66 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 AAATAAAGACGACAGTAAATATA 3 3 0 GAAGTAAATA 0.686687 -28 TTATTATTTTTATATTGAATAGTT 5 124 1 TAATTGAATA 0.909673 -14 TATCTCACTTTACACTGAATATACGTACT 6 9 0 TAACTGAATA 0.939716 -150 AATCATTTAATAAAGTCAATAATGTTAATGG 6 105 1 TAAGTCAATA 0.851544 -54 TAACTTAACATAAATTGAATGCTGTGCAAAT 8 30 0 TAATTGAATG 0.728114 -271 AGTGAATAATGAAAGTGAATAATGTCACTAA 14 15 0 GAAGTGAATA 0.944124 -286 TAATTAGATATAAAGTGAATAATGAAAGTGA 14 28 0 TAAGTGAATA 0.967568 -273 GACCAGAGTATATACTGAATAAAGTACCACA 17 167 1 TAACTGAATA 0.938985 -134 ** ******** Masking position 4 Map Score: 1.29901 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 15 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 ********** No masking Map Score: 3.69725e-12 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: 3.69725e-12 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