AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_mjan_reg_300.orf -o00710_mjan_300.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 Purged sequences: MJ0679 39 transketolase'' MJ0680 23 pentose-5-phosphate-3-epimerase MJ1425 25 malate dehydrogenase Input sequences: #1 MJ0002 300 M. jannaschii predicted coding region MJ0002 #2 MJ0107 167 dihydropteroate synthase #3 MJ0641 166 phosphoglycerate kinase (pgk) #4 MJ0681 156 transketolase' #5 MJ0682 26 conserved hypothetical protein #6 MJ0683 29 conserved hypothetical protein #7 MJ0684 68 aspartate aminotransferase (aspB2) #8 MJ1235 284 ribulose bisphosphate carboxylase, large subunit (rbcL) #9 MJ1236 239 putative mRNA 3'-end processing factor 2 #10 MJ1237 120 proteasome, subunit beta (psmB) #11 MJ1238 90 prolyl-tRNA synthetase (proS) #12 MJ1424 202 tRNA intron endonuclease (endA) #13 MJ1479 259 putative aminotransferase #14 MJ1603 300 ribose 5-phosphate isomerase Motif number 1 TTTATATAATTTTTTATAATTGGTATTTTGA 1 203 0 TTTTTATAAT 0.813428 -98 CTTATGTAATTTTTTATATAATTTTTTATAA 1 215 0 TTTTTATATA 0.889554 -86 CAATTAGAATTTCTAATAATTTTGGAGATAT 1 265 1 TTCTAATAAT 0.572706 -36 GCTATTGGATTTTTAATATCTCCAAAATTAT 1 280 0 TTTTAATATT 0.953068 -21 ATAAATTATGTTTTAATTTAATTACATTTAT 2 23 1 TTTTAATTTA 0.82463 -145 TTTAATTACATTTATAGTTTTCATTTTAAGA 2 39 1 TTTATAGTTT 0.505268 -129 TCTAAATGCCTTTTAATATATAATACTGCGA 2 73 0 TTTTAATATT 0.953066 -95 AAATAAATTTTTTAAAGAAAATTTATGCTTA 2 110 0 TTTAAAGAAA 0.48618 -58 ATTAAGTTAATTTTAATAACTGAT 3 4 0 TTTTAATAAT 0.87378 -163 TTAAGATTTCTTTATATTTATTCTTTCTGCA 3 41 1 TTTATATTTT 0.555277 -126 ATTTTAAAGTTTTTAAGGTTTTTGCAGAAAG 3 63 0 TTTTAAGGTT 0.8475 -104 GTAGAAACTTTTCTTAGATATTTCCTAATTA 3 96 0 TTCTTAGATT 0.66946 -71 TTTTTAGAAGTTTTAATAGATTATCGTCATT 3 128 0 TTTTAATAGT 0.794627 -39 CCCTCTAAGATTTTTATGTTTTTAGAAGTTT 3 146 0 TTTTTATGTT 0.810565 -21 CTATCTATTATTTTTAGGTGTAAGTTTTAAA 4 25 1 TTTTTAGGTT 0.777775 -132 AGGTGTAAGTTTTAAATATGACTAACAATTA 4 40 1 TTTAAATATA 0.772437 -117 GTTTTTGCTTTTTTTATTAATTCATTGAGTA 4 100 1 TTTTTATTAT 0.615934 -57 AGTTTCACCTTTTTAAGATTTAAAAAATAAT 4 136 0 TTTTAAGATT 0.943216 -21 ATTGATTTGATTTTAATATTTTGAAAAAATT 8 54 0 TTTTAATATT 0.953068 -231 CATTCATCCTTTTTTATATTTGGTTAAAATA 8 118 1 TTTTTATATT 0.92748 -167 CAATAATTAATTTAAATATATAAACTAAAGG 8 173 1 TTTAAATATT 0.8435 -112 GTATGGTCGTTTCTAATATAAATAGTGTTAG 8 213 0 TTCTAATATA 0.712202 -72 AGATTAAAAATTTTAAGAAAAATATAGATAA 9 67 1 TTTTAAGAAA 0.780657 -173 ATTAAGAGATTTTATAGATTTTTATCTATAT 9 88 0 TTTATAGATT 0.735203 -152 TATGCTATATTTTTAATTTTAACATTTTTTC 9 139 1 TTTTAATTTA 0.824696 -101 TCTTTTCTTATTTTTAGGTTAAGATTTATGA 10 12 1 TTTTTAGGTA 0.687909 -109 CAAAATAAAATTTTTATTTATTGAAATATTA 10 44 1 TTTTTATTTT 0.824696 -77 TTTAATAGCTTTCTAATAATATTTCAATAAA 10 60 0 TTCTAATAAA 0.457663 -61 TATTTCTCACTTTTAATAGCTTTCTAATAAT 10 71 0 TTTTAATAGT 0.794669 -50 CAGTTGGTTATTTAAAGTTTTTCATGGTGGG 11 14 0 TTTAAAGTTT 0.618563 -77 TAAATATTAATTTTTATTTAAAATGACAGTT 11 40 0 TTTTTATTTA 0.747648 -51 CTAAATACCTTTTTAATATAAAAACTGCGAA 12 81 1 TTTTAATATA 0.9272 -122 CCACAATAAATTTTAAGATTTTATAAATAAT 12 178 1 TTTTAAGATT 0.943216 -25 TAACTGCAATTTTTAAGGTAAGAATATAAAA 13 49 1 TTTTAAGGTA 0.777775 -211 GAGTTCTATTTTTTTATATGTTTGAAGTGTT 13 148 0 TTTTTATATT 0.92748 -112 TAGAACTCTATTTTAAGAGTAAAGTTTATAT 13 171 1 TTTTAAGAGA 0.665962 -89 ATTGGTCTGATTTTAATTATAGGGATTATGG 14 44 0 TTTTAATTAA 0.615891 -257 AATTTATAGATTTAAATATATAAATATAATG 14 115 0 TTTAAATATT 0.8435 -186 TTACAAAAACTTTTTATAACATTCTTAATAC 14 144 1 TTTTTATAAA 0.733029 -157 ********* * Masking position 6 Map Score: 43.2186 Number of sites scoring better than the average of aligned sites = 3130 Number in coding regions = 2269 Number in noncoding regions = 861 Number of orfs with sites within 600 bp upstream = 554 Fraction of orfs with sites within 600 bp upstream = 0.0889817 Motif number 2 AAATAAACCTTTAATTAACTAAACGCTAAA 1 113 1 TTAATTAACT 0.537648 -188 ACCAATTATAAAAAATTATATAAAAAATTA 1 210 1 AAAAATTATA 0.817632 -91 AAATTATATAAAAAATTACATAAGTCCTAT 1 222 1 AAAAATTACA 0.711834 -79 AAATTAAAACATAATTTATACTTAGCTAAA 2 12 0 ATAATTTATA 0.745671 -156 TTTTTTAAAGAAAATTTATGCTTAAGGGCA 2 104 0 AAAATTTATG 0.681906 -64 TTTTCTTTAAAAAATTTATTTCTACGAAAG 2 120 1 AAAATTTATT 0.763758 -48 ATCAGTTATTAAAATTAACTTAATAATTAT 3 11 1 AAAATTAACT 0.813077 -156 TAAAGAAATCTTAAATAATTATTAAGTTAA 3 25 0 TTAAATAATT 0.678702 -142 ACTTACACCTAAAAATAATAGATAGTAAAT 4 20 0 AAAAATAATA 0.916437 -137 GATGTTATGCTAAAATAATTGTTAGTCATA 4 56 0 TAAAATAATT 0.763756 -101 TTAAGATTTAAAAAATAATATCATTACTCA 4 125 0 AAAAATAATA 0.916437 -32 GGAATTATTATTAATTAATAATACTTTTCG 7 23 0 TTAATTAATA 0.745671 -46 ATTCGGAATGAAAATTTATTAATTCATTAA 8 83 1 AAAATTTATT 0.763758 -202 GGATGAATGTAAAATTAATGAATTAATAAA 8 97 0 AAAATTAATG 0.839727 -188 TATTGAACAGTAAAATAATGCTAAAGGCTT 8 148 0 TAAAATAATG 0.681906 -137 TTACTGTTCAATAATTAATTTAAATATATA 8 165 1 ATAATTAATT 0.837734 -120 GACCATACAAAAAATTAATAATACTTAATA 8 236 1 AAAATTAATA 0.916438 -49 TCTTTCACCTTAAATAATTACCTATTTCC 10 102 0 TTAAATAATT 0.678702 -19 ATTTTAAATAAAAATTAATATTTATTAATT 11 47 1 AAAATTAATA 0.916438 -44 GTTATTTAACAAAATTAATGAATGAATTAA 12 120 0 AAAATTAATG 0.839727 -83 ATTAATTTTGTTAAATAACATAAACCATAT 12 131 1 TTAAATAACA 0.617446 -72 GGATAATAAAATAAATAACATATGGTTTAT 12 150 0 ATAAATAACA 0.797764 -53 ATAAAATCTTAAAATTTATTGTGGATAATA 12 172 0 AAAATTTATT 0.763758 -31 TTAAGATTTTATAAATAATAACT 12 190 1 ATAAATAATA 0.877537 -13 CGTGCTTTTCAAAATTAACTGCAATTTTTA 13 34 1 AAAATTAACT 0.813077 -226 GATAAAACACAAAAATAATATTATTTTCTT 14 79 1 AAAAATAATA 0.916437 -222 ATTTAAATCTATAAATTACAAAAACTTTTT 14 129 1 ATAAATTACA 0.617446 -172 TCTTTTTACATTAAATAATATCTTATCCTC 14 225 1 TTAAATAATA 0.745671 -76 ********** Masking position 6 Map Score: 29.4306 Number of sites scoring better than the average of aligned sites = 1414 Number in coding regions = 967 Number in noncoding regions = 447 Number of orfs with sites within 600 bp upstream = 379 Fraction of orfs with sites within 600 bp upstream = 0.0608738 Motif number 3 TTATGGAGAATATTTAGCGTTTAGTTAATTAAAGGT 1 119 0 TTTAGTTTGT 0.891298 -182 TAATTTTTTATAATTGGTATTTTGATGCTCTATTAA 1 192 0 TTTGGTTTGT 0.895775 -109 TAGTATTTTATAATAGGACTTATGTAATTTTTTATA 1 228 0 TTAGGTTAGA 0.783086 -73 CAATTAGAATTTCTAATAATTTTGGAGATATTAAAA 1 265 1 TTAATTTTGA 0.51321 -36 ATAGTTTTCATTTTAAGACTTTCGCAGTATTATATA 2 52 1 TTAAGTTTGA 0.956853 -116 TATTATATATTAAAAGGCATTTAGATGCCCTTAAGC 2 79 1 TAAGGTTTGT 0.795355 -89 TCAATATAAGATTTAGGACTTTCGTAGAAATAAATT 2 132 0 ATAGGTTTGA 0.907538 -36 ATTTTAAAGTTTTTAAGGTTTTTGCAGAAAGAATAA 3 58 0 TTAAGTTTGA 0.956701 -109 CCTCTAAGATTTTTATGTTTTTAGAAGTTTTAATAG 3 140 0 TTATGTTTGA 0.670029 -27 TATTAGCCCCTTATAAAGTTTTTGCTTAT 6 4 0 TTAAATTTGT 0.784348 -26 AATTGATTTGATTTTAATATTTTGAAAAAATTTAAC 8 50 0 ATTAATTTGA 0.611091 -235 TATTTGGTTAAAATAAGCCTTTAGCATTATTTTACT 8 134 1 ATAAGTTTGA 0.903206 -151 GTATTAAGTATTATTAATTTTTTGTATGGTCGTTTC 8 231 0 TTTAATTTGA 0.787092 -54 CCCCACGAATTCTTTGGTATTAAGTATTATTAATTT 8 247 0 TTTGGTTAGA 0.687043 -38 TATATTAAACTTATTAGCCTTTAGCTTAATTCTAAC 9 31 0 TTTAGTTTGT 0.891298 -209 ATTGAAAATTTTGATAATATTTTGTAATTGTTTATG 9 169 0 TATAATTTGA 0.505494 -71 CGGCAGAGATTTTTAAAAGTTAAGGAGGAGGATTAT 9 213 1 TTAAATTAGA 0.474952 -27 CACCTCAATATTATAGAACTTTCGCAGGAATAAATG 12 16 1 TTAGATTTGA 0.865437 -187 TTTTTATATTAAAAAGGTATTTAGATGCCTAAAGGC 12 69 0 AAAGGTTTGT 0.621397 -134 AGGTAAGAATATAAAAGTCTTTGGTTTTATAAGTGC 13 64 1 AAAAGTTTGT 0.610348 -196 GCCTTTTCTATAGTAAGTTTTTTGTAACGCACTATA 13 98 1 TTAAGTTTGA 0.956701 -162 ATAGGGATTATGGTTGGAGTTTCGATGATTATATTA 14 21 0 TTTGGTTTGT 0.895776 -280 TAAGAATGTTATAAAAAGTTTTTGTAATTTATAGAT 14 135 0 AAAAATTTGA 0.412908 -166 CTATATATTGAGTTTGGAATTTTGATGCCAAAGGCA 14 189 1 ATTGGTTTGT 0.783995 -112 * **** *** * * Masking position 10 Map Score: 24.363 Number of sites scoring better than the average of aligned sites = 722 Number in coding regions = 574 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 4 AATTATAAAAAATTATATAAAAAATTACATA 1 213 1 AATATATAAA 0.6868 -88 TATAAAATACTACCAATTAGAATTTCTAATA 1 252 1 TACAATTAGA 0.15719 -49 TAAAACTTCTAAAAACATAAAAATCTTAGAG 3 144 1 AAAACATAAA 0.63803 -23 AAATAATAGATAGTAAATAGAGGAAGT 4 7 0 TATAAATAGA 0.725522 -150 CTTACACCTAAAAATAATAGATAGTAAATAG 4 18 0 AAATAATAGA 0.571021 -139 TGAAAAAATTTAACAAATAGAATTAAACAGT 8 33 0 TACAAATAGA 0.653021 -252 GGCTTATTTTAACCAAATATAAAAAAGGATG 8 122 0 AACAAATATA 0.217505 -163 TAATTAATTTAAATATATAAACTAAAGGTAA 8 176 1 AATATATAAA 0.6868 -109 AATAAATTAGATATGGAATTG 9 1 1 AAAAATTAGA 0.571019 -239 AAATTTTAAGAAAAATATAGATAAAAATCTA 9 74 1 AAAATATAGA 0.897319 -166 AAAAATATAGCATAAAATAGAGATATTTAGT 9 122 0 CAAAAATAGA 0.857098 -118 AAGATTTATGAACAAAATAAAATTTTTATTT 10 32 1 AAAAAATAAA 0.875918 -89 AATAATATTTCAATAAATAAAAATTTTATTT 10 46 0 CATAAATAAA 0.600803 -75 ATTAATTTGCTATAAAATAAAAGGTGATATC 11 70 1 TAAAAATAAA 0.744051 -21 GATTCACCTCAATATTATAGAACTTTCGCAG 12 12 1 AAATTATAGA 0.464096 -191 TAATGAATGAATTAATATAGAACTTCGCAGT 12 104 0 ATAATATAGA 0.464097 -99 AATTTTGTTAAATAACATAAACCATATGTTA 12 134 1 AAAACATAAA 0.63803 -69 TATTGTGGATAATAAAATAAATAACATATGG 12 155 0 AAAAAATAAA 0.875916 -48 TTTTTAAGGTAAGAATATAAAAGTCTTTGGT 13 58 1 AAAATATAAA 0.821195 -202 TCAAACATATAAAAAAATAGAACTCTATTTT 13 154 1 AAAAAATAGA 0.93071 -106 AAACTTTACTCTTAAAATAGAGTTCTATTTT 13 167 0 CTAAAATAGA 0.372795 -93 ATTATCCCAGTAGTATATAAACTTTACTCTT 13 185 0 TATATATAAA 0.474729 -75 AAAAGTGTCATACAAAATAGAGTTCCATTTT 13 228 1 TAAAAATAGA 0.847002 -32 TTATAGATTTAAATATATAAATATAATGAAG 14 112 0 AATATATAAA 0.6868 -189 ATTCCAAACTCAATATATAGACTGTGAAAGT 14 178 0 CATATATAGA 0.650733 -123 ** ******** Masking position 8 Map Score: 16.7552 Number of sites scoring better than the average of aligned sites = 1322 Number in coding regions = 961 Number in noncoding regions = 361 Number of orfs with sites within 600 bp upstream = 286 Fraction of orfs with sites within 600 bp upstream = 0.0459364 Motif number 5 GCTATTGGATTTTTAATATCTCCAA 1 286 0 ATGGATTTTA 0.682989 -15 TAAATTTTTTAAAGAAAATTTATGCTTAAGGG 2 106 0 AAGAAAATTA 0.705074 -62 GAATAAATATAAAGAAATCTTAAATAATTATT 3 32 0 AAGAAATTTA 0.911657 -135 GTTTTTGCAGAAAGAATAAATATAAAGAAATC 3 45 0 AAGAATAATA 0.705047 -122 TTCTAAAAACATAAAAATCTTAGAGGG 3 150 1 ATAAAATTTA 0.52988 -17 TGTTATGCTAAAATAATTGTTAGTCATATTTA 4 52 0 AATAATTTTA 0.593189 -105 ATCATTACTCAATGAATTAATAAAAAAAGCAA 4 104 0 AAGAATTATA 0.911599 -53 GCCACCACGAAAAGTATTATTAATTAATAATA 7 16 1 AAGTATTTTA 0.67208 -53 TAAACACTAAAAGGAATTATTATTAATTAATA 7 33 0 AAGAATTTTA 0.959926 -36 ATGTAAAATTAATGAATTAATAAATTTTCATT 8 89 0 AAGAATTATA 0.911599 -196 ACGACCATACAAAAAATTAATAATACTTAATA 8 234 1 AAAAATTATA 0.613566 -51 TAAATTAGATATGGAATTGTTAGAATTAAGCT 9 13 1 ATGAATTTTA 0.944409 -227 TATGAACAAAATAAAATTTTTATTTATTGAAA 10 38 1 ATAAATTTTA 0.723204 -83 ATTTTTATTTATTGAAATATTATTAGAAAGCT 10 53 1 ATGAAATTTA 0.879926 -68 AAAATTAATGAATGAATTAATATAGAACTTCG 12 108 0 AAGAATTATA 0.911599 -95 AGTGTTATATATCGAATACTTATAGTGCGTTA 13 122 0 ATGAATATTA 0.797143 -138 TGTGGTTGTTATTGAAATATTACAGGACTTTC 14 258 0 ATGAAATTTA 0.879926 -43 ** ***** *** Masking position 6 Map Score: 16.3938 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 368 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 6 CTGCGAAAGTCTTAAAATGAAAACTATAAATG 2 47 0 CTTAAATGAA 0.727996 -121 CTAAATGCCTTTTAATATATAATACTGCGAAA 2 71 0 TTTAAATATA 0.555214 -97 CCTTAAAAACTTTAAAATGATAATTAGGAAAT 3 76 1 TTTAAATGAA 0.95711 -91 TAACAATTATTTTAGCATAACATCATTATGGA 4 62 1 TTTAGATAAA 0.889453 -95 GGCTAATAAGTTTAATATAAGATTAAAAATTT 9 48 1 TTTAAATAAA 0.939151 -192 AAATTAAAAATATAGCATAAAATAGAGATATT 9 126 0 TATAGATAAA 0.548084 -114 TCTGCCGTGTTTTAAATTGAAAATTTTGATAA 9 188 0 TTTAATTGAA 0.819431 -52 TTTTCTTATTTTTAGGTTAAGATTTATGAACA 10 14 1 TTTAGTTAAA 0.621711 -107 TAGAAAGCTATTAAAAGTGAGAAATAGGAAAT 10 76 1 TTAAAGTGAA 0.521911 -45 TAGGTAATTATTTAAGGTGAAAGA 10 107 1 TTTAAGTGAA 0.931198 -14 TTAATTTTTATTTAAAATGACAGTTGGTTATT 11 33 0 TTTAAATGAA 0.95738 -58 ATTAATTTGCTATAAAATAAAAGGTGATATC 11 70 1 TATAAATAAA 0.696448 -21 TAAATACCTTTTTAATATAAAAACTGCGAAGT 12 82 1 TTTAAATAAA 0.901581 -121 AACTGCAATTTTTAAGGTAAGAATATAAAAGT 13 50 1 TTTAAGTAAA 0.904463 -210 TGGAACTCTATTTTGTATGACACTTTTGTGTA 13 223 0 TTTTGATGAA 0.496981 -37 AGAGTTCCATTTTGAGATGAAAAC 13 246 1 TTTGAATGAA 0.740156 -14 TAAGATATTATTTAATGTAAAAAGATGCCTTT 14 218 0 TTTAAGTAAA 0.867582 -83 ***** **** * Masking position 8 Map Score: 14.5298 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 99 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 TTTTAATTTAATTACATTTATAGTTTTCAT 2 33 1 ATTACATTTA 0.716811 -135 AGTTTCACCTTTTTAAGATTTAA 4 144 0 TTCACCTTTT 0.877797 -13 TATGCATCACCATTAATGTGTTTTT 5 12 0 ATCACCATTA 0.915508 -15 GACATCACCATTTATAAACACTA 7 56 0 ATCACCATTT 0.915508 -13 GTTAGAAAGCTTTACCTTTAGTTTATATAT 8 188 0 TTTACCTTTA 0.86894 -97 ACCTTAAATAATTACCTATTTCCTATTTCT 10 95 0 ATTACCTATT 0.673231 -26 GATATCACCTTTTATTTTATAGC 11 78 0 ATCACCTTTT 0.9407 -13 TAGGCATCTAAATACCTTTTTAATATAAAA 12 74 1 AATACCTTTT 0.67323 -129 TTTTGTGTAATTTACCATTATCCCAGTAGT 13 202 0 TTTACCATTA 0.819123 -58 CGATGATTATATTACAATTATTTC 14 5 0 ATTACAATTA 0.633555 -296 ********** Masking position 4 Map Score: 3.80533 Number of sites scoring better than the average of aligned sites = 243 Number in coding regions = 189 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 8 TGGATATATTATATTTAGTGCTACTGGAAA 1 60 0 ATATTTAGTG 0.932495 -241 ATTATGGAGAATATTTAGCGTTTAGTTAAT 1 126 0 ATATTTAGCG 0.919692 -175 AACATAATTTATACTTAGCTAAAT 2 5 0 ATACTTAGCT 0.770344 -163 ACTATCTATTATTTTTAGGTGTAAGTTTTA 4 24 1 ATTTTTAGGT 0.895335 -133 ATCCTTTTTTATATTTGGTTAAAATAAGCC 8 123 1 ATATTTGGTT 0.801826 -162 TAAAATAGAGATATTTAGTTAAATTAAGAG 9 111 0 ATATTTAGTT 0.950983 -129 ATCTTTTCTTATTTTTAGGTTAAGATTTAT 10 11 1 ATTTTTAGGT 0.895335 -110 AAGTTCTATAATATTGAGGTGAATCT 12 7 0 ATATTGAGGT 0.929735 -196 ATATTTAGGGAATTATCGTT 13 1 1 ATATTTAGGG 0.956352 -259 CACAGTCTATATATTGAGTTTGGAATTTTG 14 183 1 ATATTGAGTT 0.892958 -118 ********** Masking position 5 Map Score: 7.28935 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 100 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 ATGCGTCAACAAACAATCCAAATAAACCTTTA 1 94 1 AAACAATCAA 0.51563 -207 CAATTATAAAAAATTATATAAAAAATTACATA 1 212 1 AAATTATTAA 0.316217 -89 TCCTATTATAAAATACTACCAATTAGAATTTC 1 246 1 AAATACTCAA 0.813205 -55 TTGGATTTTTAATATCTCCAAAATTATTAGAA 1 275 0 AATATCTCAA 0.325941 -26 GTCTTAAAATGAAAACTATAAATGTAATTAAA 2 39 0 GAAAACTTAA 0.627704 -129 TTTTAATATATAATACTGCGAAAGTCTTAAAA 2 62 0 TAATACTCAA 0.689816 -106 CAAAAACCTTAAAAACTTTAAAATGATAATTA 3 70 1 AAAAACTTAA 0.925521 -97 GATAATCTATTAAAACTTCTAAAAACATAAAA 3 134 1 TAAAACTCAA 0.893793 -33 AAGCAAAAACAAAAAATCCATAATGATGTTAT 4 78 0 AAAAAATCTA 0.454426 -79 TATTATTTTTTAAATCTTAAAAAGGTGAAACT 4 135 1 TAAATCTAAA 0.382351 -22 ATAAGCAAAAACTTTATAAGGGGCTAAT 6 7 1 AAAAACTTTA 0.680517 -23 TTGAACAGTAAAATAATGCTAAAGGCTTATTT 8 144 0 AAATAATCAA 0.562184 -141 ATAATTAATTTAAATATATAAACTAAAGGTAA 8 175 1 TAAATATTAA 0.471947 -110 AATATAAGATTAAAAATTTTAAGAAAAATATA 9 61 1 TAAAAATTAA 0.648975 -179 AAAAATCTATAAAATCTCTTAATTTAACTAAA 9 96 1 AAAATCTTAA 0.855768 -144 ATTGTTTATGAAAAAATGTTAAAATTAAAAAT 9 147 0 AAAAAATTAA 0.785648 -93 CCCCACCATGAAAAACTTTAAATAACCAACTG 11 13 1 AAAAACTTAA 0.925521 -78 TTTTTAATATAAAAACTGCGAAGTTCTATATT 12 90 1 AAAAACTCAA 0.942774 -113 TATTATTTATAAAATCTTAAAATTTATTGTGG 12 178 0 AAAATCTAAA 0.547886 -25 ATTCGATATATAACACTTCAAACATATAAAAA 13 137 1 TAACACTCAA 0.648344 -123 TTTATATATTTAAATCTATAAATTACAAAAAC 14 122 1 TAAATCTTAA 0.751915 -179 TATAAATTACAAAAACTTTTTATAACATTCTT 14 138 1 AAAAACTTTA 0.680478 -163 ******* * ** Masking position 7 Map Score: 15.0545 Number of sites scoring better than the average of aligned sites = 1348 Number in coding regions = 1124 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 10 AAGGGCATCTAAATGCCTTTTAATATATAA 2 81 0 AAATGCCTTT 0.940484 -87 AAAGGCATTTAGATGCCCTTAAGCATAAAT 2 91 1 AGATGCCCTT 0.940084 -77 TTAATTTTATGTGCCTTTCAAAACTGTT 8 9 1 ATGTGCCTTT 0.937326 -276 TTTGGTTAAAATAAGCCTTTAGCATTATTT 8 136 1 ATAAGCCTTT 0.825273 -149 TATTGAATAATGATGCCTTTAGGCATCTAA 12 55 1 TGATGCCTTT 0.914683 -148 TTAGGCATCTAAATACCTTTTTAATATAAA 12 73 1 AAATACCTTT 0.808865 -130 TTGGTTTTATAAGTGCCTTTTCTATAGTAA 13 84 1 AAGTGCCTTT 0.946352 -176 TAATGTAAAAAGATGCCTTTGGCATCAAAA 14 208 0 AGATGCCTTT 0.982199 -93 ********** Masking position 9 Map Score: 7.78232 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 77 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 ATTGGACAACCACCCATTAATAGAGCATCA 1 176 1 CACCCATTAA 0.826341 -125 TATGCATCACCATTAATGTGTTTTTA 5 11 0 TCACCATTAA 0.705934 -16 TTTATGCCACCACGAAAAGTATTATT 7 7 1 CCACCACGAA 0.979371 -62 GTATATCCCTCCCCCACGAATTCTTTGGTA 8 264 0 CCCCCACGAA 0.964138 -21 TGCCCCACCATGAAAAACTTTAAA 11 5 1 CCACCATGAA 0.979772 -86 ATTTTATTATCCACAATAAATTTTAAGATT 12 168 1 CCACAATAAA 0.774766 -35 ATCGAAACTCCAACCATAATCCCTATAATT 14 31 1 CAACCATAAT 0.683322 -270 ATTTCAATAACAACCACAAAGCCAGAAAAG 14 272 1 CAACCACAAA 0.921888 -29 ********** Masking position 6 Map Score: 1.91328 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 104 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 TAATTGGTATTTTGATGCTCTATTAATGGG 1 188 0 TTTGATGCTC 0.847168 -113 TAAAAGGCATTTAGATGCCCTTAAGCATAA 2 89 1 TTAGATGCCC 0.972849 -79 TTTATTGAATAATGATGCCTTTAGGCATCT 12 53 1 AATGATGCCT 0.905074 -150 AAAAAGGTATTTAGATGCCTAAAGGCATCA 12 65 0 TTAGATGCCT 0.970753 -138 AGTTTGGAATTTTGATGCCAAAGGCATCTT 14 199 1 TTTGATGCCA 0.929261 -102 TTTAATGTAAAAAGATGCCTTTGGCATCAA 14 210 0 AAAGATGCCT 0.905074 -91 ********** Masking position 5 Map Score: 0.653693 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 89 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 13 ATATATAATACTGCGAAAGTCTTAAAATGA 2 59 0 CTGCGAAAGT 0.994702 -109 AAATTTATTTCTACGAAAGTCCTAAATCTT 2 131 1 CTACGAAAGT 0.984483 -37 CTTATATTGACTATGAAAGT 2 158 1 CTATGAAAGT 0.975815 -10 TCATTTATTCCTGCGAAAGTTCTATAATAT 12 23 0 CTGCGAAAGT 0.994702 -180 AATATATAGACTGTGAAAGTCCTGTATTAA 14 168 0 CTGTGAAAGT 0.991695 -133 ATCTTATCCTCTGTGAAAGTCCTGTAATAT 14 244 1 CTGTGAAAGT 0.991695 -57 ********** Masking position 6 Map Score: 13.9009 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 11 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 14 ********** No masking Map Score: 5.27466e-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: 5.27466e-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