AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_mjan_reg_100.orf -o00350_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MJ0002 300 M. jannaschii predicted coding region MJ0002 #2 MJ0102 300 Phenylacrylic acid decarboxylase #3 MJ0684 68 aspartate aminotransferase (aspB2) #4 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #5 MJ0955 48 histidinol-phosphate aminotransferase (hisC) #6 MJ1027 125 formate hydrogenlyase, subunit 5 #7 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #8 MJ1029 47 dimethyladenosine transferase (ksgA) #9 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #10 MJ1530 178 ribosomal protein S18 alanine acetyltransferase #11 MJ1575 300 GMP synthase (guaA) #12 MJ1576 80 LemA protein #13 MJ1577 29 M. jannaschii predicted coding region MJ1577 #14 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) #15 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 GGGATTGGTGAAAACCATTATCAACAAACCATGG 1 13 1 AAAAATTTAA 0.953936 -288 GTCCAATTAGAGAAACATTGAGAACTGATTATGG 1 149 0 AGAAATTAAA 0.795273 -152 AGAGCATCAAAATACCAATTATAAAAAATTATAT 1 197 1 AATAAATAAA 0.880638 -104 CCAATTATAAAAAATTATATAAAAAATTACATAA 1 211 1 AAAAATAAAA 0.930917 -90 AAACTTTTAGAAAAAGTTAAACAAAATCTTTCAG 2 138 0 AAAATTAAAA 0.815888 -163 AACAACCTAAAATAAAATAATAAAATGGTGCCGA 2 188 0 AATAATATAA 0.886113 -113 ATAAATCTAAAAAAATAAATATAACAACCTAAAA 2 210 0 AAAAAAAAAA 0.902413 -91 TTAAAAAATAAATACTATTTAAAAATAGTTAATC 2 245 0 AATAATTAAA 0.914902 -56 TGCCACCACGAAAAGTATTATTAATTAATAATAA 3 15 1 AAAAATTTAA 0.953933 -54 ATTTTATAAAATTACAATTAAAAACTTTTTTAGA 4 59 0 ATTAATTAAA 0.772506 -30 ATTTTTAACCAAAAATATTTTAAATAAGATTTCT 5 24 0 AAAAATTTAA 0.953934 -25 CTCGATAACTTTATTAAAACAAAACTAT 6 5 1 ATAATTATAA 0.596073 -121 TTATTAAAACAAAACTATATAAAAGGTTAAGCTA 6 21 1 AAAAATAAAA 0.930917 -105 GGTTAAGCTAATTATCATTATTAATTATGATAAA 6 45 1 ATTAATTTAA 0.781712 -81 TAATGAATAGATAATTTATCATAATTAATAATGA 6 59 0 ATAATATAAA 0.583277 -67 AGTTTAAAAATAGTTTAGTTAATTTCTATTTT 7 9 1 AATATTATAA 0.719004 -52 TAAATATCAGTAAAATAAATAATGTAACAAAA 7 39 0 AGTAATAAAA 0.593416 -22 TAAAAAAGAGAAAAGAAAATAAAAAT 8 3 0 AAAAAAAAAA 0.902413 -45 TCTCTTTTTTAGAATAAATAAAAAGTGAAACA 8 26 1 AGAAAATAAA 0.727203 -22 TAAATTTTGAATTAAAAATTTAAAAATTGAAA 9 9 0 ATTAAATTAA 0.710721 -138 AAGAATATAAAATAAGAATATAAAAATATAAGTT 9 42 0 AATAAATTAA 0.886115 -105 TTTAAATATCAATAAAATTAAAAAGATAAGGTAA 9 88 0 AATAATTAAA 0.914902 -59 ATTTATTACTATTATGTTTTTAAATATCAATAAA 9 106 0 ATTATTTTAA 0.540801 -41 CATAATAGTAATAAATTATTTGAATGTGAAACT 9 124 1 ATAATATTAA 0.596142 -23 TTAGTATTTCAAAATGTTTTAAAAGACTCTATAA 10 52 1 AAAATTTAAA 0.865909 -127 AGACTCTATAAAAAGAATTTAAAATAATACTAAA 10 75 1 AAAAATTAAA 0.951542 -104 AATTTAAAATAATACTAAAATTAAAATAGAATTT 10 90 1 AATAAAATAA 0.842258 -89 AATAGAATTTAATAAATTACACAACATTCATTGA 10 114 1 AATATTAAAA 0.708138 -65 AAGCCTTTGAATAATTTTAATCAATGAATGTTGT 10 134 0 ATAATTATAA 0.596141 -45 TAATCATAATAAAAGAAATTTTAAAATATAGTGT 11 36 1 AAAAAATTAA 0.934258 -265 CAAAGTTGTTAAAATTAATATTAATAATGGATAT 11 74 1 AAAAAATTAA 0.934258 -227 AGTATCTTTCAAAAACATTTTGAAAGAACCTTTT 11 256 0 AAAAATTTAA 0.953936 -45 TTTCACCACAAAAAAGAATTTGAATTATTTGGAT 12 55 0 AAAAAATTAA 0.934259 -26 AAATCCCCTAAAAATTAAAATTAATAA 13 4 0 AAAAAAATAA 0.906996 -26 GACCTACTATAAAAACAAAAACAAGAGGAGAAAT 14 42 1 AAAAAAAAAA 0.902413 -25 AAAAGTGTCTAAAATAATACACAAATAAAAGTCC 15 38 0 AAAAATAAAA 0.930917 -263 ATTCCTCCTCAAAATCAATATTAAGAGATAGTTC 15 108 0 AAAAAATTAA 0.934259 -193 **** *** * ** Masking position 4 Map Score: 49.9147 Number of sites scoring better than the average of aligned sites = 2848 Number in coding regions = 2001 Number in noncoding regions = 847 Number of orfs with sites within 600 bp upstream = 517 Fraction of orfs with sites within 600 bp upstream = 0.0830389 Motif number 2 TTTATATAATTTTTTATAATTGGTATTTTGA 1 203 0 TTTTATAATT 0.731469 -98 GACTTATGTAATTTTTTATATAATTTTTTAT 1 217 0 ATTTTTATAT 0.858278 -84 ACATAAGTCCTATTATAAAATACTACCAATT 1 239 1 TTTATAAAAT 0.775701 -62 GCTATTGGATTTTTAATATCTCCAAAATT 1 282 0 ATTTTAATAT 0.762577 -19 CTCGGCACCATTTTATTATTTTATTTTAGGT 2 187 1 TTTATTATTT 0.795739 -114 ATGGATTAACTATTTTTAAATAGTATTTATT 2 242 1 TTTTTTAAAT 0.934988 -59 AATAGTATTTATTTTTTAAATCTTAACTTAA 2 260 1 ATTTTTAAAT 0.684402 -41 CCACGAAAAGTATTATTAATTAATAATAATT 3 20 1 TTTATTAATT 0.868325 -49 TTCCTTTTAGTGTTTATAAATGGTGATGTC 3 49 1 TTTTATAAAT 0.754626 -20 TATCTAAAAAAGTTTTTAATTGTAATTTTAT 4 57 1 ATTTTTAATT 0.910232 -32 CTTACGATTTTATAAAATTACAATTAAA 4 71 0 TTTATAAAAT 0.775701 -18 CCTATTATCATGTTTATAATTGTTGG 6 110 1 TTTTATAATT 0.754626 -16 AGTTTAAAAATAGTTTAGTTA 7 1 1 ATTTAAAAAT 0.493261 -60 TGTTTCACTTTTTATTTATTCTAAAAA 8 31 0 ATTTTTATTT 0.86373 -17 TTTCAATTTTTAAATTTTTAATTCA 9 5 1 ATTTTTAAAT 0.684402 -142 ATTTAACTTATATTTTTATATTCTTATTTTA 9 38 1 TTTTTTATAT 0.895652 -109 CTTTACCTTATCTTTTTAATTTTATTGATAT 9 86 1 TTTTTTAATT 0.940931 -61 ATTACTATTATGTTTTTAAATATCAATAAAA 9 105 0 TTTTTTAAAT 0.940931 -42 ATTTTAGTATTATTTTAAATTCTTTTTATAG 10 80 0 TTTTTAAATT 0.883167 -99 TATTAAATTCTATTTTAATTTTAGTATTATT 10 97 0 TTTTTAATTT 0.82192 -82 ATGTTGTGTAATTTATTAAATTCTATTTTAA 10 110 0 ATTATTAAAT 0.575425 -69 TAATAAAAGAAATTTTAAAATATAGTGTCTT 11 42 1 ATTTTAAAAT 0.573326 -259 TTATTAATTTTAATTTTTAGGGGATT 13 6 1 ATTTTAATTT 0.762577 -24 CATAAGTAAATTTTATTAATTTTGAAAGACC 14 15 1 TTTATTAATT 0.868325 -52 TGAATCATTAACTTATTATTTAAGAGATTGT 15 196 1 ATTATTATTT 0.742051 -105 TAAGAGATTGTTTTATAATTTTAGAGGACTA 15 216 1 TTTATAATTT 0.676865 -85 * ********* Masking position 4 Map Score: 33.4519 Number of sites scoring better than the average of aligned sites = 2342 Number in coding regions = 1596 Number in noncoding regions = 746 Number of orfs with sites within 600 bp upstream = 504 Fraction of orfs with sites within 600 bp upstream = 0.0809509 Motif number 3 GTTGTCCAATTAGAGAAACATTGAGAACTGATTATG 1 150 0 TAGCATTAGA 0.776202 -151 AGCCCGAAGCTAACGCTTCGGTTAAATGAAAACTAA 2 95 0 TAGCGGTAAA 0.859554 -206 GAAAAAGTTAAACAAAATCTTTCAGATTTTGTAGCC 2 127 0 AAACTTTAGA 0.784516 -174 GGAGGGATACAAACGAAACTTTTAGAAAAAGTTAAA 2 151 0 AAGCTTTAGA 0.939107 -150 ACACCCCCTTTATGAAAGCGTTCAAAATTCA 10 6 0 TAACGTTAAA 0.782142 -173 AAATTCTTTTTATAGAGTCTTTTAAAACATTTTGAA 10 59 0 TAGCTTTAAA 0.980213 -120 TAATCATAATAAAAGAAATTTTAAAATATAGTGTCT 11 36 1 AAGTTTTAAA 0.59078 -265 AATTTTAAAATATAGTGTCTTTCAAAGTTGTTAAAA 11 52 1 TAGCTTTAAA 0.980213 -249 CACCTCCCTATAGGAGAGCGTTCAAATATCCATTAT 11 97 0 TAACGTTAAA 0.84327 -204 ACCTTTTACTAAAAGGTTCTTTCAAAATGTTTTTGA 11 246 1 AAGCTTTAAA 0.962285 -55 CTTATATTTTATTAGTATCTTTCAAAAACATTTTGA 11 267 0 ATGCTTTAAA 0.872782 -34 TTTGTTTTTATAGTAGGTCTTTCAAAATTAATAAAA 14 25 0 TAACTTTAAA 0.921227 -42 TGTGTATTATTTTAGACACTTTTAGAGATGAGGCTA 15 49 1 TTGCTTTAGA 0.889384 -252 GAGGAGGAATTAATGGAGCTGTTAAAAAAGAGATTT 15 132 1 TAGCTGTAAA 0.930065 -169 AACCTCTGTTTTTGGGAACTTTAAAATCTCTTTTTT 15 155 0 TTGCTTTAAA 0.930092 -146 ** * **** *** Masking position 14 Map Score: 14.4524 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 273 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 TTCCCATGGTTTGTTGATAATGGTTTTCAC 1 20 0 TTGTTGATAA 0.500741 -281 TATAATTGGTATTTTGATGCTCTATTAATG 1 190 0 ATTTTGATGC 0.822175 -111 ATTTCTAATAATTTTGGAGATATTAAAAAT 1 273 1 ATTTTGGAGA 0.672022 -28 AATGCATCCTATTTTGATGAAATGGAAAGC 2 39 1 ATTTTGATGA 0.951947 -262 TGACAATAAATTTTTGGTGAC 4 2 0 TTTTTGGTGA 0.961464 -87 TTAAAAACTTTTTTAGATAACTTACTATAT 4 46 0 TTTTAGATAA 0.668613 -43 ATTTAAAATATTTTTGGTTAAAAATT 5 33 1 TTTTTGGTTA 0.60298 -16 ACTTCAATAAATTTGGAGGATAATCATAAT 11 16 1 ATTTGGAGGA 0.718011 -285 AGGTGTTAGATTTTTGATGAACCTTTTACT 11 226 1 TTTTTGATGA 0.965446 -75 CAAATTCTTTTTTGTGGTGAAATT 12 67 1 TTTGTGGTGA 0.748118 -14 TAATTTTAATTTTTAGGGGATTTTT 13 15 1 TTTTAGGGGA 0.89765 -15 CTTAATATTGATTTTGAGGAGGAATTAATG 15 117 1 ATTTTGAGGA 0.936838 -184 TCAACCTCTGTTTTTGGGAACTTTAAAATC 15 163 0 TTTTTGGGAA 0.741813 -138 TGTTTTATAATTTTAGAGGACTATGTTGAT 15 224 1 TTTTAGAGGA 0.907592 -77 TTAGAGGACTATGTTGATGATTATTTAGAT 15 236 1 ATGTTGATGA 0.822175 -65 GTTGATGATTATTTAGATGAGGGTGATGAA 15 248 1 ATTTAGATGA 0.902921 -53 AGTAGGGGAGTTTTAGATGCATTTAGGGAG 15 281 1 TTTTAGATGC 0.75379 -20 ********** Masking position 2 Map Score: 15.1012 Number of sites scoring better than the average of aligned sites = 919 Number in coding regions = 765 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 5 TTGGTGAAAACCATTATCAACAAACCATGG 1 17 1 CCATTATCAA 0.920653 -284 CTAAAAGGAATTATTATTAATTAATAATAC 3 29 0 TTATTATTAA 0.640188 -40 AAGCTAATTATCATTATTAATTATGATAAA 6 49 1 TCATTATTAA 0.946804 -77 ATTATGTTTTTAAATATCAATAAAATTAAA 9 100 0 TAAATATCAA 0.681441 -47 GTTCAAATATCCATTATTAATATTAATTTT 11 84 0 CCATTATTAA 0.90007 -217 AGTAGGTCTTTCAAAATTAATAAAATTTAC 14 20 0 TCAAAATTAA 0.701016 -47 AGATAGTTCTTCAATATCAAAACCAAAGCT 15 87 0 TCAATATCAA 0.948905 -214 CTCCTCAAAATCAATATTAAGAGATAGTTC 15 108 0 TCAATATTAA 0.890584 -193 AGTTAATGATTCATTATCAACCTCTGTTTT 15 179 0 TCATTATCAA 0.959517 -122 ********** Masking position 6 Map Score: 7.34203 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 156 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 AAACAATCCAAATAAACCTTTAATTAACTAAAC 1 104 1 AAAACCTTAA 0.95437 -197 CTAATTGGACAACCACCCATTAATAGAGCATCA 1 173 1 AAACCCTTAA 0.921214 -128 TTCCAGCTATGAAAACTCTTTTAGTTTTCATTT 2 75 1 GAACTCTTTA 0.487207 -226 GAGGGATACAAACGAAACTTTTAGAAAAAGTTA 2 153 0 AAAAACTTTA 0.656258 -148 AAATTCACCATTAAAAACTGTTAA 2 287 0 AACACCTTAA 0.938868 -14 GACATCACCATTTATAAACACTAA 3 55 0 ACCACCTTTA 0.9289 -14 ATGATAATTAGCTTAACCTTTTATATAGTTTTG 6 30 0 GCAACCTTTA 0.899818 -96 AGGACCAATAAACACCCCCTTTATGAAAGCGTT 10 20 0 AACCCCTTTA 0.908647 -159 GTTCTCACTTAACCTTTAGTAAAGCCTTT 10 160 0 ACAACCTTAG 0.707802 -19 TTAGATTTTTGATGAACCTTTTACTAAAAGGTT 11 231 1 GAAACCTTTA 0.924425 -70 AAACATTTTGAAAGAACCTTTTAGTAAAAGGTT 11 245 0 AAAACCTTTA 0.960365 -56 CTCTTTTTTAACAGCTCCATTAATTCCTCCTCA 15 131 0 ACCTCCTTAA 0.613427 -170 AGAGGTTGATAATGAATCATTAACTTATTATTT 15 184 1 AAAATCTTAA 0.743983 -117 ** **** **** Masking position 10 Map Score: 5.8077 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 146 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 AAACCTTTAATTAACTAAACGCTAAATATT 1 117 1 TTAACTAAAC 0.964476 -184 TTTTTAAATCTTAACTTAACAGTTTTTAAT 2 272 1 TTAACTTAAC 0.964476 -29 CTATATAAATTTAGCTAAATTGACAATAAA 4 22 0 TTAGCTAAAT 0.883798 -67 ATAATGATAATTAGCTTAACCTTTTATATA 6 36 0 TTAGCTTAAC 0.957462 -90 AAAATAGAAATTAACTAAACTATTTTTAAA 7 13 0 TTAACTAAAC 0.964476 -48 TAATGAATCATTAACTTATTATTTAAGAGA 15 193 1 TTAACTTATT 0.69356 -108 ********** Masking position 6 Map Score: 2.96099 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 39 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 AATTAAAGGTTTATTTGGATTGTTTGTTGA 1 99 0 TTATTTGGAT 0.956334 -202 TTTATAATTGGTATTTTGATGCTCTATTAA 1 192 0 GTATTTTGAT 0.815164 -109 GCAATGCATCCTATTTTGATGAAATGGAAA 2 37 1 CTATTTTGAT 0.815164 -264 TTATCATTATTAATTATGATAAATTATCTA 6 56 1 TAATTATGAT 0.768325 -70 TTTTATATTCTTATTCTGATATCTTTACCT 9 64 1 TTATTCTGAT 0.845479 -83 TAGTAATAAATTATTTGAATGTGAAACT 9 129 1 TTATTTGAAT 0.844359 -18 AGCCTTTGAATAATTTTAATCAATGAATGT 10 137 0 TAATTTTAAT 0.67346 -42 AAAATTTCTTTTATTATGATTATCCTCCAA 11 28 0 TTATTATGAT 0.903176 -273 ACCTTATATTTTATTAGTATCTTTCAAAAA 11 275 0 TTATTAGTAT 0.460976 -26 AGAATTTGAATTATTTGGATAGTTTAGTAT 12 45 0 TTATTTGGAT 0.956334 -36 TTATTAATTTTAATTTTTAGGGGA 13 5 1 TAATTTTAAT 0.67346 -25 ATGTTGATGATTATTTAGATGAGGGTGATG 15 246 1 TTATTTAGAT 0.807573 -55 ********** Masking position 3 Map Score: 6.46383 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 259 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 TTAGTGCTACTGGAAATATTTCAGCGTTCC 1 46 0 TGGAAATATT 0.832019 -255 ACGCATTGATTGGATATATTATATTTAGTG 1 70 0 TGGATATATT 0.952554 -231 AAGGTTTATTTGGATTGTTTGTTGACGCAT 1 94 0 TGGATTGTTT 0.88443 -207 CTAATAATTTTGGAGATATTAAAAATCCAA 1 277 1 TGGAGATATT 0.880111 -24 ATAAGATTTCTGGATTTTTTATTA 5 5 0 TGGATTTTTT 0.919177 -44 ATATTAATAATGGATATTTGAACGCTCTCC 11 91 1 TGGATATTTG 0.889429 -210 TTGAATTATTTGGATAGTTTAGTATGTTTG 12 40 0 TGGATAGTTT 0.946212 -41 ********** Masking position 4 Map Score: 2.69256 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 211 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 TGATAATGGTTTTCACCAATCCCAG 1 6 0 TTTCACCAAT 0.919437 -295 TAGCTTTCCATTTCATCAAAATAGGATGCA 2 41 0 TTTCATCAAA 0.923462 -260 TTAGTTTTCATTTAACCGAAGCGTTAGCTT 2 95 1 TTTAACCGAA 0.839266 -206 TTTAGAAAAAGTTAAACAAAATCTTTCAGA 2 137 0 GTTAAACAAA 0.680845 -164 AATTTTTAACCAAAAATATTTTAA 5 35 0 TTTAACCAAA 0.951037 -14 TTTGAATAATTTTAATCAATGAATGTTGTG 10 133 0 TTTAATCAAT 0.776429 -46 TTAGTAAAAGGTTCATCAAAAATCTAACAC 11 228 0 GTTCATCAAA 0.894595 -73 AATTTCACCACAAAAAAGAATT 12 69 0 TTTCACCACA 0.892259 -12 ********** Masking position 5 Map Score: 1.42194 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 189 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 11 ACCAATTATAAAAAATTATATAAAAAATTAC 1 210 1 AAAATTATAT 0.448633 -91 TCAATTTAGCTAAATTTATATAGTAAGTTAT 4 29 1 TAATTTATAT 0.858616 -60 ATAATTAGCTTAACCTTTTATATAGTTTTGT 6 29 0 TACCTTTTAT 0.729194 -97 AATAGTTTAGTTAATTTCTATTTTGTTACAT 7 19 1 TAATTTCTAT 0.816828 -42 TTCTATTTTGTTACATTATTTATTTTACTGA 7 34 1 TACATTATTT 0.702968 -27 TGTTTCACTTTTTATTTATTCTAAA 8 33 0 TACTTTTTAT 0.578153 -15 AATTCAAAATTTAACTTATATTTTTATATTC 9 30 1 TAACTTATAT 0.922669 -117 TTTTATATTCTTATTTTATATTCTTATTCTG 9 51 1 TATTTTATAT 0.460775 -96 TCTGATATCTTTACCTTATCTTTTTAATTTT 9 78 1 TACCTTATCT 0.650718 -69 TAGTATTATTTTAAATTCTTTTTATAGAGTC 10 76 0 TAAATTCTTT 0.656431 -103 GTGTAATTTATTAAATTCTATTTTAATTTTA 10 105 0 TAAATTCTAT 0.867164 -74 TTTATCACCTTATATTTTATTAGTA 11 286 0 TACCTTATAT 0.915629 -15 ATGTTTGATATCAACTTATATAAATTTTATT 12 16 0 TAACTTATAT 0.92267 -65 TCCAAATAATTCAAATTCTTTTTTGTGGTGA 12 56 1 TAAATTCTTT 0.656438 -25 CATAGTCCTCTAAAATTATAAAACAATCTCT 15 218 0 TAAATTATAA 0.448633 -83 * ********* Masking position 3 Map Score: 4.69635 Number of sites scoring better than the average of aligned sites = 447 Number in coding regions = 319 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 12 ********** No masking Map Score: -1.97288e-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 13 ********** No masking Map Score: -1.97288e-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 14 ********** No masking Map Score: -1.97288e-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