AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_mjan_reg_100.orf -o00970_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 MJ0237 300 arginyl-tRNA synthetase (argS) #2 MJ0389 90 tyrosyl-tRNA synthetase (trS) #3 MJ0487 282 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #4 MJ0539 267 tRNA synthetase, putative #5 MJ0564 300 alanyl-tRNA synthetase (alaS) #6 MJ0633 137 leucyl-tRNA synthetase (leuS) #7 MJ0948 25 M. jannaschii predicted coding region MJ0948 #8 MJ0949 43 conserved hypothetical protein #9 MJ0950 184 conserved hypothetical protein #10 MJ1000 202 histidyl-tRNA synthetase (hisS) #11 MJ1007 101 valyl-tRNA synthetase (valS) #12 MJ1077 89 seryl-tRNA synthetase (serS) #13 MJ1078 273 M. jannaschii predicted coding region MJ1078 #14 MJ1108 300 phenylalanyl-tRNA synthetase, subunit beta (pheT) #15 MJ1197 85 threonyl-tRNA synthetase (thrS) #16 MJ1238 90 prolyl-tRNA synthetase (proS) #17 MJ1263 130 methionyl-tRNA synthetase (metS) #18 MJ1377 184 glutamyl-tRNA synthetase (gltX) #19 MJ1415 66 tryptophanyl-tRNA synthetase (trpS) #20 MJ1555 150 aspartyl-tRNA synthetase (aspS) Motif number 1 TTACTATGGAAAATATAAAAACCCAATGGG 1 124 0 AAATATAAAA 0.91334 -177 TAATTTATTAATTTAAATAAATGATAGAAA 1 216 0 ATTTAAATAA 0.486925 -85 TTAAATTAATAAATTAAAAAGAAGGTATTT 1 230 1 AAATTAAAAA 0.936434 -71 TTTTTTATTTAATTTAAAAATTGGGGATTT 1 265 0 AATTTAAAAA 0.782125 -36 TTTTTAAATTAAATAAAAAATGAGAGAGGG 1 275 1 AAATAAAAAA 0.931754 -26 AGTATCACCAAAATAATAAAGTAAATTTAT 2 11 1 AAATAATAAA 0.82215 -80 ATAATAAAGTAAATTTATAAATTACCATAG 2 23 1 AAATTTATAA 0.900439 -68 ACCATAGCTTATATAATAAAGTTTTGCATG 2 46 1 ATATAATAAA 0.623859 -45 TAATAATCTCAATTAATAAAAATTTATTTT 3 28 0 AATTAATAAA 0.529734 -255 TTATTAATTGAGATTATTAAAGTTCATTAT 3 39 1 AGATTATTAA 0.538682 -244 AAAGTTTTACAAATAGAAAAAGAAGGACGA 3 126 1 AAATAGAAAA 0.839765 -157 AGAAGGACGAAAATTTTTAAAATAAGAATA 3 146 1 AAATTTTTAA 0.753832 -137 TTTCTTTAATAAATAGATAACTATGTTTAT 3 215 0 AAATAGATAA 0.806502 -68 CAATCATCAAAAATAGATAACATTTTCTAA 4 12 1 AAATAGATAA 0.806502 -256 TTTTATAGTTATATAATAAACTTATAGAAG 4 69 0 ATATAATAAA 0.623859 -199 TACCAAAATGATATAAATAACTTAGTTTTA 4 135 0 ATATAAATAA 0.795649 -133 ATATTATTTAAAATATAAAAATCAAAAAAT 4 208 0 AAATATAAAA 0.91334 -60 ATAAGTTTAGAATTTGAAAATAAGAGCATT 5 30 0 AATTTGAAAA 0.579477 -271 AAGTAGCTATAATTTTATAAGTTATATTTA 5 175 0 AATTTTATAA 0.687876 -126 TGTATCTCACAAATTAATAAAATTTATTTA 5 213 1 AAATTAATAA 0.921358 -88 CAAAAGGGTTAAATTAATAAATGGAGTTTT 6 34 1 AAATTAATAA 0.921358 -104 TAATTAAGGTATATTAATAAGGCGTTTAAA 6 61 0 ATATTAATAA 0.807705 -77 TACATTATTAAAATAATTAAGGTATATTAA 6 74 0 AAATAATTAA 0.786161 -64 GAAAATTTAAAATTAATATTAA 8 3 1 AAATTTAAAA 0.919173 -41 TTTAAAATTAATATTAAAAAACACGTTTAG 8 16 1 ATATTAAAAA 0.840875 -28 CAAAGCATTAAGATTTATAAGCAACTATAT 9 91 0 AGATTTATAA 0.726942 -94 CAATAACTGTAAATATATAAATACTTATAT 10 103 1 AAATATATAA 0.89341 -100 GATGAAACAAAGATTTATAAGATAGCTTTG 10 149 1 AGATTTATAA 0.726942 -54 ACATATTTGTAAATTTATAAATC 11 4 0 AAATTTATAA 0.900439 -98 GTTGAGGTTTAAATAAATAACTCTCTAATA 11 33 0 AAATAAATAA 0.915668 -69 TATTTTTATTAAATTAAAAACTCTTCAAAA 11 63 1 AAATTAAAAA 0.936434 -39 TTAGAGGGACAGATTTTAAATAAAAGAACA 13 18 1 AGATTTTAAA 0.531272 -256 AATTAGTGTTAATTTTAAAAAAACAAACAT 13 112 1 AATTTTAAAA 0.734828 -162 CTACTGCAAAAAATAATAAAAAATGTTTGT 13 134 0 AAATAATAAA 0.82215 -140 ATTAGGATTGAGATATAAAACATTACTACT 13 159 0 AGATATAAAA 0.756237 -115 CAATGTTGGTATTTTTAAAAAGATTTTCCA 13 202 0 ATTTTTAAAA 0.498537 -72 TATTAAAAATATATTAAAAATGCATCTTTT 13 242 0 ATATTAAAAA 0.840875 -32 GAAAGATAATATATTAAAAATATATTAAAA 13 253 0 ATATTAAAAA 0.840875 -21 CTTAGAAATTAAATTTAAAACCTCTAAATA 14 15 1 AAATTTAAAA 0.919173 -286 TAAAACCTCTAAATAAATAAATAATTCCTA 14 30 1 AAATAAATAA 0.915668 -271 TCAATTAACAAAATTGAAAATCCTAAAACC 14 110 1 AAATTGAAAA 0.849737 -191 TAACGATAGAATATTATTAAACAAACTATA 14 160 1 ATATTATTAA 0.587337 -141 ATTACAACTAAGATAAAAAATACTGCTGGT 14 275 1 AGATAAAAAA 0.800751 -26 AACAAAGCAAAAATATTTAATATATCTTTT 15 35 1 AAATATTTAA 0.739448 -51 AGATAAAGATAATTATAAAAGAAAAAGATA 15 57 0 AATTATAAAA 0.719746 -29 ATTTTATAGCAAATTAATAAATATTAATTT 16 58 0 AAATTAATAA 0.921358 -33 AAATATATAAATATTGTAAAATATTATTGT 18 22 0 ATATTGTAAA 0.407224 -163 AATAATAGTTAAATATATAAATATTGTAAA 18 32 0 AAATATATAA 0.89341 -153 ATAGTTATGCAATTTTAAAAGCTCATCCTC 18 82 0 AATTTTAAAA 0.734828 -103 AATAAAAAATAATTAAAAAATTAAAT 20 7 0 AATTAAAAAA 0.768887 -144 AAATTGTCAAAAATAAAAAATAATTAAAAA 20 18 0 AAATAAAAAA 0.931754 -133 TTGTGTATCTATATATTTAATTTTATAGGT 20 50 0 ATATATTTAA 0.504519 -101 ********** Masking position 4 Map Score: 63.8057 Number of sites scoring better than the average of aligned sites = 2832 Number in coding regions = 1949 Number in noncoding regions = 883 Number of orfs with sites within 600 bp upstream = 578 Fraction of orfs with sites within 600 bp upstream = 0.0928365 Motif number 2 TTTAGGTATGTAATTAAATTTATTTAAAAACCC 1 94 1 TATTAATTAT 0.915818 -207 TTTTCCATAGTAAATAAGTTTATTTGATGATTG 1 141 1 TAATAATTAT 0.921647 -160 AAATAAATGATAGAAAAGTTTATATATGAAGAT 1 199 0 TAAAAATTAT 0.937039 -102 TTTTTGTTCATGCAAAACTTTATTATATAAGCT 2 51 0 TGAAAATTAT 0.886156 -40 CATACAGAACTGCTAAATTTTATTCTTTTTATA 3 252 0 TGTAAATTAT 0.878036 -31 CCAATAACCTTAGAAAATGTTATCTATTTTTGA 4 18 0 TAAAAATTAT 0.937039 -250 ATTATATAACTATAAAAACTTTTGATGATTGAC 4 82 1 TAAAAATTTT 0.877222 -186 ATCATTTTGGTAGTTAATATTTTAACAAATTAT 4 153 1 TATTAATTTT 0.839297 -115 TCTCACAAATTAATAAAATTTATTTATGAACCA 5 217 1 TATAAATTAT 0.932271 -84 TATAAGCAACTATATATCGTTATTTACCTATTT 9 73 0 TAATATTTAT 0.824441 -112 ACTGTAAATATATAAATACTTATATCTTACAAA 10 108 1 TAAAATTTAT 0.855944 -95 GATAATTAGGTATTTATGTTTTTTATTGTGTTT 12 29 0 TATTATTTTT 0.675858 -61 TTTGATAATATGTATAAAATTATGCCCAACGAT 13 65 0 TGATAATTAT 0.860181 -209 AAGTTATCGTTGGAAAATCTTTTTAAAAATACC 13 192 1 TGAAAATTTT 0.788889 -82 AAACAAACTATAATTAAAATTATCTACAGACTC 14 178 1 TATTAATTAT 0.915818 -123 GAAAAAGATATATTAAATATTTTTGCTTTGTTT 15 34 0 TATAAATTTT 0.868559 -52 TTTTCTTTTATAATTATCTTTATCTAAAATTTA 15 62 1 TATTATTTAT 0.812848 -24 GACAGTTGGTTATTTAAAGTTTTTCATGGTGGG 16 14 0 TATTAATTTT 0.839297 -77 AATTAATAAATATTAATTTTTATTTAAAATGAC 16 44 0 TATAATTTAT 0.846043 -47 TCAAAAAAGGTATTAAAGTTTATTAAGGAAATT 17 17 1 TATAAATTAT 0.932271 -114 TAATAGTTATTACAAAATATTTTGAAAGACACT 17 86 1 TAAAAATTTT 0.877218 -45 ATATAAATATTGTAAAATATTATTGTGGTGGAT 18 15 0 TGAAAATTAT 0.886156 -170 TTAAGTAACATAAATATAGTTATGCAATTTTAA 18 94 0 TAATATTTAT 0.824441 -91 TGTATCTATATATTTAATTTTATAGGTTAAAAT 20 44 0 TATTAATTAT 0.915818 -107 TTAATAATTGTGTAAATGGTTTTTATAGTTTCC 20 87 0 TGAAATTTTT 0.598696 -64 ** **** **** Masking position 10 Map Score: 33.7125 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 371 Number in noncoding regions = 207 Number of orfs with sites within 600 bp upstream = 215 Fraction of orfs with sites within 600 bp upstream = 0.0345326 Motif number 3 ATACCTAAACTTTGATGATTGATTGTTTTGT 1 72 0 TTTGTGATTG 0.976532 -229 AATAAGTTTATTTGATGATTGATTGTAGCAG 1 153 1 TTTGTGATTG 0.976532 -148 TTCTTTTTAATTTATTAATTTAAATAAATGA 1 222 0 TTTATAATTT 0.84365 -79 AAAATAAATTTTTATTAATTGAGATTATTAA 3 28 1 TTTATAATTG 0.930924 -255 GTTATCTATTTTTGATGATTGA 4 2 0 TTTGTGATTG 0.976532 -266 TATAAAAACTTTTGATGATTGACTATAATTC 4 92 1 TTTGTGATTG 0.976532 -176 GAAATTTGGATTTTTTGATTTTTATATTTTA 4 199 1 TTTTTGATTT 0.792129 -69 TGTTGTTTGGTTTATGGATTGTCTTGTTGGA 5 59 0 TTTAGGATTG 0.935237 -242 AATTTCTGATTTTGTTGTTTGGTTTATGGAT 5 71 0 TTTGTGTTTG 0.758982 -230 ATAAATAAATTTTATTAATTTGTGAGATACA 5 213 0 TTTATAATTT 0.84365 -88 CCCATCACCTTTAATGATTGCAGTTTTTAG 5 281 0 TTTATGATTG 0.977 -20 TAAAACTCCATTTATTAATTTAACCCTTTTG 6 34 0 TTTATAATTT 0.84365 -104 AAAAAACACGTTTAGGGATAGTT 8 31 1 TTTAGGATAG 0.522186 -13 TGTTAATTGATTTATTGATTGTCTTGTTGTA 14 89 0 TTTATGATTG 0.977 -212 GATTTTCAATTTTGTTAATTGATTTATTGAT 14 101 0 TTTGTAATTG 0.929585 -200 ATTATTAGGGTTTTAGGATTTTCAATTTTGT 14 117 0 TTTTGGATTT 0.564358 -184 AAAATTAATATTTATTAATTTGCTATAAAAT 16 57 1 TTTATAATTT 0.84365 -34 TTAAAAAGTTTTTAGTGATTTGGGAAACACA 20 122 1 TTTATGATTT 0.944468 -29 **** ****** Masking position 3 Map Score: 28.5148 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 177 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 4 TTTTAATGGCAATCTTTGAATAGGACTTCGCAGTTTG 3 78 0 ATTTTGTAAT 0.869969 -205 AAGGACGAAAATTTTTAAAATAAGAATATGGACGAAA 3 148 1 ATTTAATAAT 0.575746 -135 GCTAAATTTTATTCTTTTTATAGTATTATTTTCTTTA 3 237 0 ATTTTTTAAT 0.861219 -46 TGAAAATAAGAGCATTTAGGAATTATTTCTTTATT 5 9 0 ACTTTAAAAT 0.788959 -292 AGAAGACAAAAATGTTTGTATATGAATTTGCCTATAA 5 118 0 ATTTTGTAAT 0.869969 -183 TATGAAAATTAATATTTAAATATAACTTATAAAATTA 5 159 1 ATTTTATAAT 0.968151 -142 TTCAATACTTAGTTTTTACAAAACATTACATTATTAA 6 93 0 ATTTTAAAAT 0.575746 -45 AGAAAGCGAAACTTTTTAGATATAAATTTCAATAGAA 9 150 1 ATTTTATAAT 0.968151 -35 ACAAAACCGAAAGGTTTATATAGAATTTCATTAACAT 10 48 0 AGTTTATAAT 0.807408 -155 TTCCAACGATAACTTTTAATTAGGATTGAGATATAAA 13 170 0 ACTTTATAAT 0.955975 -104 TTAAAAATGCATCTTTTAATTCTAAATCAATGTTGGT 13 222 0 ACTTTATCAT 0.793271 -52 TAGAAATGAGAGTATTTAGGAATTATTTATTTATTTA 14 39 0 ATTTTAAAAT 0.848828 -262 ATAATATTCTATCGTTATTCTATCATTACATTATTAG 14 140 0 ACTTATTAAT 0.416786 -161 ATTATCACAAAATGTTTATATACGAGTCTGTAGATAA 14 197 0 ATTTTATAAT 0.968151 -104 CTTTTATAATTATCTTTATCTAAAATTTAA 15 66 1 TTTTTATAAT 0.787655 -20 AATAAATATTAATTTTTATTTAAAATGACAGTTGGTT 16 36 0 ATTTTATAAG 0.74002 -55 TTTTGTAATAACTATTAATGTATTAATGAACGCCTTC 17 66 0 ATTTAATAAT 0.848828 -65 ACAATATTTATATATTTAACTATTATTATTCAGATTA 18 35 1 TTTTTATAAT 0.789913 -150 AACTTTAAGTATCCTTTTCCTAATAATCAGTTAAGGT 18 125 1 ACTTTTTAAT 0.804267 -60 ATTATCACCATTTACCTACCATTAACTTTAAAA 18 162 0 ACTTTATAAT 0.956124 -23 GATGTATTTAAATCTTTATATCAAAATGAAGG 19 45 1 ATTTTATCAT 0.851119 -22 ATTTAATTTTTTAATTATTTTTTATTTTTGAC 20 6 1 ATTTTATATT 0.670065 -145 * * **** ** * * Masking position 6 Map Score: 21.1295 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 178 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 5 CCCAATGGGTTTTTAAATAAATTTAATTACATA 1 100 0 TTTAATAAAT 0.585208 -201 TAAACTTATTTACTATGGAAAATATAAAAACCC 1 130 0 TCTATGAAAT 0.720482 -171 AAAAGAAGGTATTTAAAGAAAATCCCCAATTTT 1 246 1 ATTAAGAAAT 0.958574 -55 TAATAATCTCAATTAATAAAAATTTATTTTAGT 3 25 0 ATTAAAAAAT 0.822322 -258 GTTATCTATTTATTAAAGAAAATAATACTATAA 3 224 1 TTTAAGAAAT 0.958644 -59 GGTAGTTAATATTTTAACAAATTATTATGTAAC 4 161 1 ATTTACAAAT 0.436455 -107 TTATTATGTAACCTAAAGAAATTTGGATTTTTT 4 182 1 ACTAAGAAAT 0.953338 -86 TTTGTCTTCTTTCTTATGAAAATTAATATTTAA 5 145 1 TCTTAGAAAT 0.805686 -156 GTATCTCACAAATTAATAAAATTTATTTATGAA 5 214 1 ATTAAAAAAT 0.822322 -87 CTAATACTAATGAAAATTAACCAAT 7 9 0 TCTAAGAAAT 0.953339 -17 TAATGCATCGTTTTGATGAAACTTTC 9 4 0 TTTGAGAAAT 0.734007 -181 TTCGCTTTCTATTAAATGAAAATTATAGGATTT 9 127 0 ATAAAGAAAT 0.745191 -58 AATTTAGTTTCTATTGAAATTTATATCTAAA 9 164 0 TCTATGAAAT 0.720482 -21 GGTATGTATATGTTAATGAAATTCTATATAAAC 10 39 1 TTTAAGAAAT 0.958644 -164 AGAGTTTTTAATTTAATAAAAATAGTTGAGGTT 11 54 0 ATTAAAAAAT 0.822322 -48 CCAACGATATAACAAAAGAAACTATTGTTCTTT 13 40 0 ACAAAGAAAT 0.720482 -234 TCAATAAATCAATTAACAAAATTGAAAATCCTA 14 102 1 ATTAAAAAAT 0.822322 -199 GATAGAATATTATTAAACAAACTATAATTAAAA 14 164 1 TTTAACAAAT 0.793764 -137 TATTAAAGTTTATTAAGGAAATTTGAATGCCTT 17 27 1 TTTAAGAAAT 0.958644 -104 GATACACAAAAGCTTAGGAAACTATAAAAACCA 20 71 1 ACTTAGAAAT 0.805627 -80 * **** **** * Masking position 13 Map Score: 17.2664 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 226 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 6 ATACCTTCTTTTTAATTTATTAATTTAAAT 1 228 0 TTTAATTTAT 0.598288 -73 TCTCTCATTTTTTATTTAATTTAAAAATTG 1 272 0 TTTATTTAAT 0.745624 -29 ATAGTATTATTTTCTTTAATAAATAGATAA 3 225 0 TTTCTTTAAT 0.847912 -58 ATTTGGATTTTTTGATTTTTATATTTTAAA 4 202 1 TTTGATTTTT 0.76692 -66 CCTCAAAATTTTTGTTTCTTCTATTTTATT 4 242 0 TTTGTTTCTT 0.759928 -26 TTAGGAATTATTTCTTTATT 5 1 0 TTTCTTTATT 0.847912 -300 ATCCTTTCATTTTTAATGTTCAAT 6 124 0 TTTCATTTTT 0.73909 -14 ATTGGTTAATTTTCATTAGTATTAG 7 11 1 TTTCATTAGT 0.488848 -15 CTTATAAATCTTTGTTTCATCAGCATAATT 10 140 0 TTTGTTTCAT 0.759928 -63 TTAAATACGTTTTGTTTTTTGTAAATAAAT 10 181 0 TTTGTTTTTT 0.891864 -22 AGAACAATAGTTTCTTTTGTTATATCGTTG 13 42 1 TTTCTTTTGT 0.753275 -232 ATAAAAAATGTTTGTTTTTTTAAAATTAAC 13 119 0 TTTGTTTTTT 0.891864 -155 TTAGGAATTATTTATTTATTTAGAGGTTTT 14 31 0 TTTATTTATT 0.745628 -270 TTAATTATAGTTTGTTTAATAATATTCTAT 14 165 0 TTTGTTTAAT 0.866235 -136 ATATTTTTGCTTTGTTTAATCAATTTATAA 15 21 0 TTTGTTTAAT 0.866235 -65 AATATATCTTTTTCTTTTATAATTATCTTT 15 53 1 TTTCTTTTAT 0.876551 -33 GATATCACCTTTTATTTTATAGCAAATTAA 16 71 0 TTTATTTTAT 0.788728 -20 ATTTAATTTTTTAATTATTTT 20 2 1 TTTAATTTTT 0.598291 -149 ********** Masking position 6 Map Score: 14.5569 Number of sites scoring better than the average of aligned sites = 1206 Number in coding regions = 913 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 7 GTTTAGGTATGTAATTAAATTTATTTAAAA 1 93 1 GTAATTAAAT 0.421853 -208 AACCCAATGGGTTTTTAAATAAATTTAATT 1 105 0 GTTTTTAAAT 0.883109 -196 AACCCATTGGGTTTTTATATTTTCCATAGT 1 122 1 GTTTTTATAT 0.898881 -179 TGATAGAAAAGTTTATATATGAAGATGATA 1 195 0 GTTTATATAT 0.601954 -106 TTTCTATCATTTATTTAAATTAATAAATTA 1 216 1 TTATTTAAAT 0.567776 -85 TAAAAAGAAGGTATTTAAAGAAAATCCCCA 1 244 1 GTATTTAAAG 0.924068 -57 ATCATCAAAAGTTTTTATAGTTATATAATA 4 81 0 GTTTTTATAG 0.897003 -187 TAAAACTAAGTTATTTATATCATTTTGGTA 4 135 1 TTATTTATAT 0.607199 -133 TTTATAAGTTATATTTAAATATTAATTTTC 5 162 0 ATATTTAAAT 0.477618 -139 AACTTTGTAGTTATAGTCCTTTGCAA 6 7 1 GTAGTTATAG 0.554851 -131 ATGTCTCTTAGTATATAAATAGGTAAATAA 9 57 1 GTATATAAAT 0.678979 -128 ACCTTATTCGGTATGTATATGTTAATGAAA 10 30 1 GTATGTATAT 0.595181 -173 AAACCGAAAGGTTTATATAGAATTTCATTA 10 52 0 GTTTATATAG 0.598608 -151 TAAGATATAAGTATTTATATATTTACAGTT 10 107 0 GTATTTATAT 0.935951 -96 AAAACAAAACGTATTTAAGG 10 193 1 GTATTTAAGG 0.681643 -10 CTTTTGAAGAGTTTTTAATTTAATAAAAAT 11 64 0 GTTTTTAATT 0.462211 -38 TGATAATTAGGTATTTATGTTTTTTATTGT 12 33 0 GTATTTATGT 0.720109 -57 CACTCTTATTGTTTTTATTGAATTGATAAT 12 56 0 GTTTTTATTG 0.497635 -34 TGACAGTTGGTTATTTAAAGTTTTTCATGG 16 18 0 TTATTTAAAG 0.562668 -73 ATATTTTACAATATTTATATATTTAACTAT 18 28 1 ATATTTATAT 0.517769 -157 ATCAGTTAAGGTTTTTAAAGTTAATGGTAG 18 150 1 GTTTTTAAAG 0.88096 -35 TACAACTGATGTATTTAAATCTTTATATCA 19 38 1 GTATTTAAAT 0.925494 -29 AAGCTTTTGTGTATCTATATATTTAATTTT 20 56 0 GTATCTATAT 0.595181 -95 TGTGTAAATGGTTTTTATAGTTTCCTAAGC 20 82 0 GTTTTTATAG 0.897003 -69 ********** Masking position 6 Map Score: 17.3017 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 395 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 8 AGTATCACCAAAATAATAAAGT 2 3 1 TATCACCAAA 0.835075 -88 GATATATCACCACAACATTTTTGT 2 77 0 TATCACCACA 0.722273 -14 AATATCAAAGTTTTACAAATAGAAAAAGAA 3 120 1 TTTTACAAAT 0.651023 -163 CTACCATGTATCTCACAAATTAATAAAATT 5 207 1 TCTCACAAAT 0.766542 -94 AATACTTAGTTTTTACAAAACATTACATTA 6 97 0 TTTTACAAAA 0.60038 -41 TTAAAATTAATATTAAAAAACACGTTTAGG 8 17 1 TATTAAAAAA 0.634222 -27 AATACTTATATCTTACAAAATTATGCTGAT 10 122 1 TCTTACAAAA 0.699323 -81 TTTATCACCAATAACACTCTTA 12 78 0 TATCACCAAT 0.862675 -12 TGCCCAACGATATAACAAAAGAAACTATTG 13 46 0 TATAACAAAA 0.542032 -228 TTATACATATTATCAAAAATTGATTTAGAT 13 81 1 TATCAAAAAT 0.709971 -193 ATTAAAAATATATTAAAAATGCATCTTTTA 13 241 0 TATTAAAAAT 0.682681 -33 AAAGATAATATATTAAAAATATATTAAAAA 13 252 0 TATTAAAAAT 0.682681 -22 AAAGCTTTATTATCACAAAATGTTTATATA 14 212 0 TATCACAAAA 0.913783 -89 ATTATCCTATTATTACAACTAATTATTACA 14 251 1 TATTACAACT 0.85582 -50 TACAACTAATTATTACAACTAAGATAAAAA 14 264 1 TATTACAACT 0.85582 -37 CATTAATAGTTATTACAAAATATTTTGAAA 17 83 1 TATTACAAAA 0.903022 -48 ATTATCACCATTTACCTACCAT 18 173 0 TATCACCATT 0.382062 -12 ATAATAAATATATTACAACTGATGTATTTA 19 25 1 TATTACAACT 0.85582 -42 ********** Masking position 3 Map Score: 12.8553 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 266 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 9 CCTAAACTTTGATGATTGATTGTTTTGTGGG 1 69 0 GATGATTGAT 0.981012 -232 AAGTTTATTTGATGATTGATTGTAGCAGTGT 1 156 1 GATGATTGAT 0.981012 -145 AAAAACTTTTGATGATTGACTATAATTCAGC 4 95 1 GATGATTGAT 0.981025 -173 TTTCAATTTTGTTAATTGATTTATTGATTGT 14 98 0 GTTAATTGAT 0.87459 -203 GTAATAATAGGATAATTGACTTAATAAAGCT 14 236 0 GATAATTGAT 0.95824 -65 ********* * Masking position 6 Map Score: 3.01218 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 10 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 TTAAATCTACAATTCATCAGTTTCGTCCATATT 3 172 0 ATTCTAGTTT 0.46671 -111 AATAGATAACATTTTCTAAGGTTATTGGTATAG 4 23 1 ATTTTAGGTT 0.955947 -245 AAAAATCCAAATTTCTTTAGGTTACATAATAAT 4 181 0 ATTCTAGGTT 0.86299 -87 GAAGAAACAAAAATTTTGAGGGAAATT 4 251 1 AATTTAGGGA 0.738401 -17 AGTAGCTATAATTTTATAAGTTATATTTAAATA 5 171 0 ATTTTAGTTA 0.632303 -130 AAATTTTATTAATTTGTGAGATACATGGTAGGT 5 205 0 ATTTTAGATA 0.632297 -96 CATCAGCATAATTTTGTAAGATATAAGTATTTA 10 120 0 ATTTTAGATA 0.632303 -83 TTTTAAATTTAATTTCTAAGGGTT 14 2 0 ATTTTAGGGT 0.963457 -299 TTCTATCATTACATTATTAGGGTTTTAGGATTT 14 127 0 AATTTAGGGT 0.831892 -174 TTGTTTAATCAATTTATAAGGGTGTAGTT 15 7 0 ATTTTAGGGT 0.963457 -79 GGTTATTTAAAGTTTTTCATGGTGGGGCA 16 7 0 ATTTTATGGT 0.634646 -84 AAGGTATTAAAGTTTATTAAGGAAATTTGAATG 17 23 1 ATTTTAAGGA 0.497676 -108 CTATATATTTAATTTTATAGGTTAAAATTGTCA 20 39 0 ATTTAAGGTT 0.681025 -112 ATCACTAAAAACTTTTTAAGGTTAATAATTGTG 20 108 0 ATTTTAGGTT 0.955935 -43 * *** * ***** Masking position 9 Map Score: 6.28548 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 174 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 11 ATAAATTAAAAAGAAGGTATTTAAAGAAAAT 1 238 1 AAAAGGTATT 0.945366 -63 AAGGTATATTAATAAGGCGTTTAAAACTCCA 6 55 0 AAAAGGCGTT 0.871605 -83 TAATTATTTTAATAATGTAATGTTTTGTAAA 6 85 1 AAAATGTAAT 0.71692 -53 ATAAATTTACAAATATGTATTAGAGAGTTAT 11 16 1 AATATGTATT 0.716924 -86 TTGAATTGATAATTAGGTATTTATGTTTTTT 12 38 0 AATAGGTATT 0.873304 -52 CTAAAACCCTAATAATGTAATGATAGAATAA 14 132 1 AAAATGTAAT 0.71692 -169 TGCTATAAAATAAAAGGTGATATC 16 77 1 TAAAGGTGAT 0.632314 -14 TGTCTTTCAAAAAAGGTATTAAAGTTTATT 17 10 1 AAAAGGTATT 0.945366 -121 CGCCTTCTTATAGAAGGCATTCAAATTTCCT 17 42 0 TAAAGGCATT 0.81194 -89 TGCCTTCTATAAGAAGGCGTTCATTAATACA 17 54 1 AAAAGGCGTT 0.871612 -77 GTAATATATTTATTATGTATTCTCTTTAAG 19 10 0 TATATGTATT 0.502186 -57 ** ******** Masking position 5 Map Score: 2.78455 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 339 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 12 CTACCAGCCCACAAAACAATCAATCATCAAA 1 62 1 ACAAACAATC 0.980107 -239 AATAATATAGACAATAAAATAGAAGAAACAA 4 230 1 ACAAAAAATA 0.866803 -38 AACTTATCCAACAAGACAATCCATAAACCAA 5 53 1 ACAAACAATC 0.980107 -248 CATAAACCAAACAACAAAATCAGAAATTCCA 5 74 1 ACAAAAAATC 0.930751 -227 CTTAGTTTTTACAAAACATTACATTATTAAA 6 92 0 ACAAACATTA 0.832005 -46 TGTATTTCTAAAAACACAATAAAAAACATAA 12 18 1 AAAAACAATA 0.755757 -72 AACTTATACAACAAGACAATCAATAAATCAA 14 83 1 ACAAACAATC 0.980107 -218 **** ****** Masking position 6 Map Score: 4.15621 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 22 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 TTATATAAGCTATGGTAATTTATAAATTTACTTT 2 28 0 TATGTATATA 0.781156 -63 AAAAATTTATTTTAGTAGTTAATATTTAAT 3 7 0 TTTGTGTATA 0.954829 -276 TTTATATCATTTTGGTAGTTAATATTTTAACAAA 4 148 1 TTTGTGTATA 0.954829 -120 TTAAAACATTTTAAGTGGTTCATAAATAAATTTT 5 231 0 TTAGTGTATA 0.814425 -70 AATAACGATATATAGTTGCTTATAAATCTTAATG 9 82 1 TATGTGTATA 0.964719 -103 TCTTTTGTTATATCGTTGGGCATAATTTTATACA 13 54 1 TATGTGGATA 0.948555 -220 TGTAAAATATTATTGTGGTGGATATTG 18 4 0 TATGTGGATA 0.948724 -181 *** ** * * *** Masking position 12 Map Score: 0.334388 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 53 Number in noncoding regions = 14 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: -3.99082e-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: -3.99082e-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