AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -irpoH_mjan_opreg_300.orf -g0.314 -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 = 0.314 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MJ0150 65 M. jannaschii predicted coding region MJ0150 #2 MJ0152 256 carbon monoxide dehydrogenase, subunit alpha #3 MJ0153 239 acetyl-CoA decarbonylase/synthase, subunit alpha (cdhA) #4 MJ0154 43 acetyl-CoA decarbonylase/synthase, subunit epsilon (cdhB) #5 MJ0156 22 acetyl-CoA decarbonylase/synthase, subunit beta (cdhC) #6 MJ0623 300 conserved hypothetical protein #7 MJ0625 49 M. jannaschii predicted coding region MJ0625 #8 MJ0626 92 conserved hypothetical protein #9 MJ0627 30 M. jannaschii predicted coding region MJ0627 #10 MJ0999 202 thermosome (ths) #11 MJ1146 66 glyceraldehyde 3-phosphate dehydrogenase #12 MJ1156 119 cell division control protein 48 (cdc48), AAA family #13 MJ1176 121 proteasome regulatory AAA-ATPase #14 MJ1206 300 conserved hypothetical protein #15 MJ1237 120 proteasome, subunit beta (psmB) #16 MJ1238 90 prolyl-tRNA synthetase (proS) #17 MJ1376 86 cell division protein FtsJ #18 MJ1417 132 ATP-dependent protease LA, putative (lon) Motif number 1 GGATTATTCATTAATAAAGCTTGTTTATTCTG 1 16 0 TTAATAAATT 0.590795 -50 CTACATTTGTTATATAAATCTTTGACTGT 1 47 1 TATATAAATT 0.904167 -19 AAATAGGGCTTTTTTAAATGTTTCTATTTGAT 2 59 0 TTTTTAAATT 0.88744 -198 AAAAAAGCCCTATTTTTTATTTTGCAAGTCAT 2 76 1 TATTTTTTTT 0.787888 -181 ACCTAAGCATTAATTAAAAATTTCTATGACTT 2 101 0 TAATTAAATT 0.825409 -156 TTACCATGGATATTAAAATCTTTAATAAGTTA 2 144 1 TATTAAAATT 0.896209 -113 AAGTTATTTGTATTAAATTTTTCGCAATGCGT 2 170 1 TATTAAATTT 0.839117 -87 TACAGTAGTCTAATTTTAAGTTTATGCATTAC 2 217 0 TAATTTTATT 0.650944 -40 CACTAATTTATTTTTTTAAATTAATAGATACT 3 44 1 TTTTTTTATT 0.756423 -196 TTACGCATTTTAAAAATTGTTTTGTAGGGATT 3 86 0 TAAAAATTTT 0.427047 -154 AAAACTTTAATATATAAAGTTTGTTATGACTA 3 170 0 TATATAAATT 0.904168 -70 TTAAGGTTAGTTTTTAAAACTTTAATATATAA 3 185 0 TTTTTAAATT 0.88744 -55 TTAATCATTATAATTTAAGGTTAGTTTTTAAA 3 199 0 TAATTTAATT 0.705013 -41 TAGGACTTTTTATATATAGTTTGTGGTGGTGC 6 16 0 TATATATATT 0.880412 -285 TAAAAAGTCCTATTATATTATTAATTGGTGTG 6 36 1 TATTATATTT 0.724708 -265 CCAAAAAAGATATATAATGTTTGTTTAAAATC 7 21 0 TATATAATTT 0.850737 -29 CATTACATAATAAAAAATCTTTTAGGTTTAGC 8 26 0 TAAAAAATTT 0.488544 -67 GTTTTGAGTATTTTAAAACCTTAATGGTTTCA 8 56 0 TTTTAAAATT 0.813392 -37 AATAGCATTTATATTGTTTTGAGTATTTT 8 74 0 TTTATATTTT 0.691837 -19 TAATTTTTTATAATACTTTTTGGTGAAA 9 7 1 TTTATAATTT 0.742078 -24 CAAAGCTATCTTATAAATCTTTGTTTCATCAG 10 45 1 TTATAAATTT 0.443887 -158 AAGATATAAGTATTTATATATTTACAGTTATT 10 88 1 TATTTATATT 0.923888 -115 AATGAAATTCTATATAAACCTTTCGGTTTTGT 10 139 0 TATATAAATT 0.904169 -64 GTAGGATTAATAATAATTACTTTGGCAATATA 11 23 0 TAATAATTTT 0.552337 -44 GTTGAAGTTCTATATAAACCTTTCGGTTTTGT 12 38 0 TATATAAATT 0.904169 -82 TTTATCTTTTTATAATAATTTTCTCACTGGAG 12 80 0 TATAATAATT 0.724729 -40 TCCCTCCGTTTATTTTATCTTTTTATAATAAT 12 93 0 TATTTTATTT 0.826472 -27 AAAATTCTTATATTTAAATTTTATGT 13 5 0 TATTTAAATT 0.939783 -117 TATAAGAATTTTTATTATAATTCCATATGGTA 13 25 1 TTTATTATTT 0.592231 -97 ATTATAATCATTTTATTTTATTATGGATTATC 13 64 0 TTTTATTTTT 0.509123 -58 ATATCACCGGTAAATTTAAGTTAAGTGAAGGG 13 99 0 TAAATTTATT 0.529756 -23 TCAGAACTACTATAAATACTTTTCGGTTTTAT 14 135 1 TATAAATATT 0.802769 -166 GGTTTTATTGTATTAAATATTTTAATTAATGT 14 159 1 TATTAAATTT 0.839109 -142 TATAAAAAATTATTTTTATTTTGACGCCTATT 14 204 0 TATTTTTATT 0.860078 -97 TAAAAATAATTTTTTATACTTTGATTTGTTTT 14 218 1 TTTTTATATT 0.860179 -83 CTTTGATTTGTTTTATTAGATTATGTTAGATA 14 236 1 TTTTATTATT 0.631936 -65 ATCTTTTCTTATTTTTAGGTTAAGATTTATG 15 10 1 TATTTTTATT 0.860179 -111 TAAATAAAAATTTTATTTTGTTCATAAATCTT 15 32 0 TTTTATTTTT 0.509124 -89 CAAAATAAAATTTTTATTTATTGAAATATTAT 15 44 1 TTTTTATTTT 0.787972 -77 TATTTCTCACTTTTAATAGCTTTCTAATAATA 15 70 0 TTTTAATATT 0.772789 -51 GACAGTTGGTTATTTAAAGTTTTTCATGGTGG 16 15 0 TATTTAAATT 0.939825 -76 ACTGTCATTTTAAATAAAAATTAATATTTATT 16 41 1 TAAATAAATT 0.740751 -50 TAAAAATTAATATTTATTAATTTGCTATAAAA 16 55 1 TATTTATTTT 0.880169 -36 TAATAGGTAATAAAATAAACTTAGGAAAAGCT 17 18 0 TAAAATAATT 0.443887 -69 TTTTATTACCTATTATTTCTTTAAAAATTACA 17 35 1 TATTATTTTT 0.672628 -52 ACATTTAATATTTTTAAAATTTGTGGTGAAAC 17 64 1 TTTTTAAATT 0.88744 -23 CATAATCTTATATTTATAATTTTTAGTTATGG 18 15 0 TATTTATATT 0.924028 -118 TATATTGACATATATAAATCTTTTAAATTTTT 18 83 0 TATATAAATT 0.904167 -50 ******** ** Masking position 11 Map Score: 55.4449 Number of sites scoring better than the average of aligned sites = 3967 Number in coding regions = 2548 Number in noncoding regions = 1419 Number of orfs with sites within 600 bp upstream = 747 Fraction of orfs with sites within 600 bp upstream = 0.119981 Motif number 2 CAAAGATTTATATAACAAATGTAGGATTAT 1 41 0 TATAACAAAT 0.61652 -25 TATTATTTAGTAATAAAATT 2 1 0 TAATAAAATT 0.638367 -256 TGACTTGCAAAATAAAAAATAGGGCTTTTT 2 77 0 AATAAAAAAT 0.644138 -180 CCTAAGCATTAATTAAAAATTTCTATGACT 2 102 0 AATTAAAAAT 0.840039 -155 GCGAAAAATTTAATACAAATAACTTATTAA 2 165 0 TAATACAAAT 0.884681 -92 ATCTATTAATTTAAAAAAATAAATTAGTGT 3 43 0 TTAAAAAAAT 0.846512 -197 AGATACTCATTTTTAAAAATCCCTACAAAA 3 69 1 TTTTAAAAAT 0.906794 -171 AAATTACGCATTTTAAAAATTGTTTTGTAG 3 91 0 TTTTAAAAAT 0.906794 -149 TTTCATTACATAATAAAAAATCTTTTAGGT 8 31 0 TAATAAAAAA 0.638366 -62 CAAAAAGTATTATAAAAAATTA 9 3 0 TATAAAAAAT 0.868117 -28 ATTATAAAAATATATATTGCC 11 2 1 TTATAAAAAT 0.941185 -65 TTTGTAGGATTAATAATAATTACTTTGGCA 11 28 0 TAATAATAAT 0.764831 -39 TTTTATCTTTTTATAATAATTTTCTCACTG 12 83 0 TTATAATAAT 0.62364 -37 TATGGAATTATAATAAAAATTCTTATATTT 13 22 0 TAATAAAAAT 0.969145 -100 GGTTTTATTGTATTAAATATTTTAATTAAT 14 159 1 TATTAAATAT 0.747907 -142 ATAGGCGTCAAAATAAAAATAATTTTTTAT 14 205 1 AAATAAAAAT 0.896234 -96 CAAATCAAAGTATAAAAAATTATTTTTATT 14 216 0 TATAAAAAAT 0.868117 -85 CATAATCTAATAAAACAAATCAAAGTATAA 14 231 0 TAAAACAAAT 0.725562 -70 ATATTTCAATAAATAAAAATTTTATTTTGT 15 43 0 AAATAAAAAT 0.896234 -78 CTGTCATTTTAAATAAAAATTAATATTTAT 16 42 1 AAATAAAAAT 0.896234 -49 TATAGCAAATTAATAAATATTAATTTTTAT 16 54 0 TAATAAATAT 0.829898 -37 TCACCACAAATTTTAAAAATATTAAATGTA 17 63 0 TTTTAAAAAT 0.906794 -24 TAACTAAAAATTATAAATATAAGATTATGA 18 18 1 TTATAAATAT 0.713116 -115 ATTAACACCTTATAAAAATCTCTGTAAAT 18 114 0 TTATAAAAAT 0.941185 -19 ********** Masking position 5 Map Score: 27.5539 Number of sites scoring better than the average of aligned sites = 1298 Number in coding regions = 838 Number in noncoding regions = 460 Number of orfs with sites within 600 bp upstream = 360 Fraction of orfs with sites within 600 bp upstream = 0.057822 Motif number 3 ATATAGTTTGTGGTGGTGCGTAGA 6 4 0 TGGGGTGCGT 0.820105 -297 TTGGTGTGCATGGCTAGGCCGGGGGGTTGGG 6 60 1 TGGTAGGCCG 0.858562 -241 CTAGGCCGGGGGGTTGGGCGTCCCCTGTAAC 6 73 1 GGGTGGGCGT 0.95121 -228 ATCGCCCTTATGCGGGGGCCGAAAACTTGGG 6 109 1 TGCGGGGCCG 0.912726 -192 CCGAAAACTTGGGGGCGGCATGTCCTCCAGT 6 127 1 GGGGCGGCAT 0.984127 -174 TCGTCCCGTGGGGCTCGGCGGTGGGGGAGCA 6 187 1 GGGTCGGCGG 0.965478 -114 GGCTCGGCGGTGGGGGAGCATCTCCTGTAGG 6 198 1 TGGGGAGCAT 0.869398 -103 GGGCCTGGCGGGGTTCGGCAGGTAAAGGGGG 6 239 0 GGGTCGGCAG 0.958618 -62 TTGAAGCCAGTGGTGCGGCCTCCGGGATTTG 14 24 1 TGGGCGGCCT 0.990579 -277 CCCGGGGTCCGGGCGTGGCAGGCCCGTGTGT 14 57 1 GGGGTGGCAG 0.951438 -244 GGAGCGGCCTTGGTGTAGCCTGGTAACACAC 14 82 0 TGGGTAGCCT 0.815474 -219 TTGCTTGCAATGGAGCGGCCTTGGTGTAGCC 14 93 0 TGGGCGGCCT 0.990579 -208 *** ******* Masking position 9 Map Score: 13.8344 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 52 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 GCATTGCGAAAAATTTAATACAAATAACTT 2 170 0 AAATTTAATA 0.329426 -87 TAATGCATAAACTTAAAATTAGACTACTGT 2 218 1 ACTTAAAATT 0.267313 -39 CCTATCATAAACTTTATATTTTATGCCAAC 3 15 1 ACTTTATATT 0.844288 -225 GTCATAACAAACTTTATATATTAAAGTTTT 3 172 1 ACTTTATATA 0.919145 -68 TTAAAAACTAACCTTAAATTATAATGATTA 3 200 1 ACCTTAAATT 0.720507 -40 TAATTCTTTTACTTTAAATTTCTGAAGTTG 4 15 1 ACTTTAAATT 0.856659 -29 ATATAATAGGACTTTTTATATATAGTTTGT 6 24 0 ACTTTTTATA 0.899918 -277 TTTTAAACAAACATTATATATCTTTTTTGG 7 23 1 ACATTATATA 0.672852 -27 TAATTTTTTATAATACTTTTTG 9 3 1 ATTTTTTATA 0.529801 -28 AACATCAATAACTGTAAATATATAAATACT 10 96 0 ACTGTAAATA 0.545238 -107 GTTTATTTTATCTTTTTATAATAATTTTCT 12 88 0 TCTTTTTATA 0.345546 -32 ACATAAAATTTAAATATAAGAATTTT 13 7 1 AATTTAAATA 0.713258 -115 TAAATATAAGAATTTTTATTATAATTCCAT 13 21 1 AATTTTTATT 0.505177 -101 TATGGATTATCATTTATATACCATATGGAA 13 45 0 CATTTATATA 0.303208 -77 CCCTTCACTTAACTTAAATTTACCGGTGAT 13 99 1 AACTTAAATT 0.374138 -23 ACTCAGAACTACTATAAATACTTTTCGGTT 14 133 1 ACTATAAATA 0.446787 -168 AATAAAAATAATTTTTTATACTTTGATTTG 14 216 1 ATTTTTTATA 0.529801 -85 AACAAAATAAAATTTTTATTTATTGAAATA 15 42 1 AATTTTTATT 0.505177 -79 CCTATTTCTCACTTTTAATAGCTTTCTAAT 15 74 0 ACTTTTAATA 0.919148 -47 TCTTTCACCTTAAATAATTACCTATT 15 105 0 ACCTTAAATA 0.843116 -16 ACCATGAAAAACTTTAAATAACCAACTGTC 16 17 1 ACTTTAAATA 0.933937 -74 ACCAACTGTCATTTTAAATAAAAATTAATA 16 37 1 ATTTTAAATA 0.642579 -54 GATATCACCTTTTATTTTATAGCAAA 16 75 0 ACCTTTTATT 0.617115 -16 TTTAAAAATTACATTTAATATTTTTAAAAT 17 54 1 ACATTTAATA 0.672852 -33 AAGGCATCTTCCTTTTAATAGTAACTAAAA 18 57 1 CCTTTTAATA 0.645662 -76 ********** Masking position 9 Map Score: 15.8309 Number of sites scoring better than the average of aligned sites = 828 Number in coding regions = 622 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 5 GCTTTCTCACCTTTAAGTGTTT 5 7 0 TCTCACCTAA 0.982785 -16 AATATCACCAAAAAAGATATATAA 7 36 0 TATCACCAAA 0.963666 -14 AATTTCACCAAAAAGTATTATAAA 9 17 0 TTTCACCAAA 0.963662 -14 CTTCTCACCTCAGATTGTTACCTT 10 189 0 TCTCACCAGA 0.979404 -14 ATAATAATTTTCTCACTGGAGATAATATACCG 12 69 0 TCTCACTAGA 0.9224 -51 AATATCACCGGTAAATTTAAGTTA 13 108 0 TATCACCTAA 0.957116 -14 GTGAGATTACTCTCACTCATGAGACTGGTAGA 14 270 1 TCTCACTTGA 0.909669 -31 ATTTCCTATTTCTCACTTTTAATAGCTTTCTA 15 76 0 TCTCACTTAA 0.933964 -45 TCTTTCACCTTAAATAATTACCTA 15 107 0 TTTCACCAAA 0.963496 -14 GATATCACCTTTTATTTTATAGCA 16 77 0 TATCACCTTA 0.799992 -14 AGTTTCACCACAAATTTTAAAAAT 17 73 0 TTTCACCAAA 0.963662 -14 ******* *** Masking position 5 Map Score: 15.6449 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 70 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 6 ATGGCTAGGCCGGGGGGTTGGGCGTCCCCTGT 6 69 1 CGGGGGTGGG 0.992454 -232 GAGACCTCATCGAGGAGTCTGGGAAGGAAGGA 6 157 0 CGGGAGTTGG 0.977078 -144 GGTCTCGTCCCGTGGGGCTCGGCGGTGGGGGA 6 183 1 CGGGGGCCGG 0.996798 -118 TTCCGGGCCTGGCGGGGTTCGGCAGGTAAAGG 6 242 0 GGGGGGTCGG 0.99491 -59 CTAATTGAAGCCAGTGGTGCGGCCTCCGGGAT 14 20 1 CCGTGGTCGG 0.981589 -281 GGGATTTGAACCCGGGGTCCGGGCGTGGCAGG 14 47 1 CCGGGGTCGG 0.993598 -254 GAGCGGCCTTGGTGTAGCCTGGTAACACACGG 14 80 0 GGGTAGCTGG 0.767858 -221 ** ***** *** Masking position 7 Map Score: 6.45531 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 1 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 TTTTATTACTAAATAATAAACAAAAAAATCA 2 13 1 AAATATAAAC 0.684761 -244 TCAGATATTACTAAAAAAATCAAATAGAAAC 2 41 1 CTAAAAAATC 0.722038 -216 TTTACCATGGATATTAAAATCTTTAATAAGT 2 143 1 ATATAAAATC 0.832367 -114 ATGCCCTATCATAAACTTTATATTTT 3 6 1 CTATATAAAC 0.852065 -234 ACACCAATTAATAATATAATAGGACTTTTTA 6 36 0 ATAAATAATA 0.777466 -265 TTATAAAAAGATAAAATAAACGGAGGGATTT 12 97 1 ATAAATAAAC 0.934332 -23 TATGGTATATAAATGATAATCCATAATAAAA 13 50 1 AAATATAATC 0.762184 -72 ATAATCCATAATAAAATAAAATGATTATAAT 13 65 1 ATAAATAAAA 0.70308 -57 AGTGAAGGGAATATTATAATCATTTTATTTT 13 77 0 ATATATAATC 0.94863 -45 GCAAGCAACAATAACATACTCAGAACTACTA 14 116 1 ATAAATACTC 0.740144 -185 CTCACAATATCTAACATAATCTAATAAAACA 14 244 0 CTAAATAATC 0.906197 -57 TTAATTTGCTATAAAATAAAAGGTGATATC 16 71 1 ATAAATAAAA 0.70308 -20 ATAATAGGTAATAAAATAAACTTAGGAAAAG 17 20 0 ATAAATAAAC 0.934332 -67 CCTTATCATAATATCATAATCTTATATTTAT 18 30 0 ATATATAATC 0.94863 -103 ATTAACACCTTATAAAAATCTCTGTAAATA 18 113 0 TTATAAAATC 0.36513 -20 **** ****** Masking position 6 Map Score: 10.2038 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 353 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 8 CTACATTTGTTATATAAATCTTTGACTGT 1 47 1 TATATAAATC 0.972803 -19 TAACTGTAAATATATAAATACTTATATCTT 10 88 0 TATATAAATA 0.84059 -115 AATGAAATTCTATATAAACCTTTCGGTTTT 10 141 0 TATATAAACC 0.960697 -62 GTTGAAGTTCTATATAAACCTTTCGGTTTT 12 40 0 TATATAAACC 0.960697 -80 TTCCATATGGTATATAAATGATAATCCATA 13 45 1 TATATAAATG 0.892466 -77 TATATTGACATATATAAATCTTTTAAATTT 18 85 0 TATATAAATC 0.972803 -48 ATTAACACCTTATAAAAATCTCTGTAAATA 18 113 0 TATAAAAATC 0.882952 -20 ********** Masking position 6 Map Score: 7.95085 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 29 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 9 ATTAAAGTTTTAAAAACTAACCTTAAATTA 3 191 1 TAAAAACTAA 0.654921 -49 GATTTTAAGGCTAAACCTAAAAGATTTTTT 8 17 1 CTAAACCTAA 0.929311 -76 TTGAGTATTTTAAAACCTTAATGGTTTCAT 8 55 0 TAAAACCTTA 0.75233 -38 CAACTTTACACAAAACCGAAAGGTTTATAT 10 130 1 CAAAACCGAA 0.973329 -73 CAAATATGAACAAAACCGAAAGGTTTATAT 12 29 1 CAAAACCGAA 0.973329 -91 TTTAATACAATAAAACCGAAAAGTATTTAT 14 146 0 TAAAACCGAA 0.946436 -155 GTTCATAAATCTTAACCTAAAAATAAGAAA 15 15 0 CTTAACCTAA 0.731854 -106 ********** Masking position 5 Map Score: 2.571 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 87 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 AAATAAAAAATAGGGCTTTTTTAAATGTTT 2 68 0 TAGGGCTTTT 0.92962 -189 TTGCAAGTCATAGAAATTTTTAATTAATGC 2 97 1 TAGAAATTTT 0.87002 -160 AATAACTTATTAAAGATTTTAATATCCATG 2 148 0 TAAAGATTTT 0.819615 -109 AATTGTTTTGTAGGGATTTTTAAAAATGAG 3 74 0 TAGGGATTTT 0.948854 -166 AATAATATAATAGGACTTTTTATATATAGT 6 28 0 TAGGACTTTT 0.924197 -273 TAATTTTTTATAATACTTTTTGGTGAAATT 9 11 1 TAATACTTTT 0.675913 -20 TATCTTTTTATAATAATTTTCTCACTGGAG 12 80 0 TAATAATTTT 0.745498 -40 AAAATAAACGGAGGGATTTTT 12 109 1 GAGGGATTTT 0.794619 -11 AATTTAAATATAAGAATTTTTATTATAATT 13 17 1 TAAGAATTTT 0.914806 -105 TTTCAATAAATAAAAATTTTATTTTGTTCA 15 40 0 TAAAAATTTT 0.807586 -81 ********** Masking position 7 Map Score: 6.24416 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 213 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 TTTAGTAATATCTGATTTTTTTGTTTATTATT 2 24 0 TCTGTTTTTT 0.78485 -233 AATGTTTCTATTTGATTTTTTTAGTAATATCT 2 43 0 TTTGTTTTTT 0.926295 -214 TGCTTAGGTTTGTGCTATTTTTACCATGGATA 2 124 1 TGTGTATTTT 0.745198 -133 TTAAATACGTTTTGTTTTTTGTAAATAAATAG 10 13 1 TTTGTTTTTT 0.926295 -190 ATAAGATAGCTTTGCTATTTATTTACAAAAAA 10 27 0 TTTGTATTTT 0.94883 -176 TATATAAACCTTTCGGTTTTGTGTAAAGTTGA 10 129 0 TTTCGTTTTT 0.741336 -74 AGATTCACCATTTGAAATTTTTGTAGGATTAA 11 45 0 TTTGAATTTT 0.791111 -22 TTTCGGTTTTGTTCATATTTGTGAAATAATTA 12 18 0 GTTCTATTTT 0.644891 -102 TATAAATACTTTTCGGTTTTATTGTATTAAAT 14 145 1 TTTCGTTTTT 0.741336 -156 TTTTTTATACTTTGATTTGTTTTATTAGATTA 14 227 1 TTTGTTTGTT 0.630337 -74 ATCTTTTCTTATTTTTAGGTTAAGAT 15 5 1 TTTCTATTTT 0.930482 -116 TAATTACCTATTTCCTATTTCTCACTTTTAAT 15 85 0 TTTCTATTTT 0.930482 -36 AAAAATTACATTTAATATTTTTAAAATTTGTG 17 57 1 TTTATATTTT 0.674336 -30 AATATCATAATCTTATATTTATAATTTTTAGT 18 20 0 TCTTTATTTT 0.514526 -113 TATATAAATCTTTTAAATTTTTAGTTACTATT 18 73 0 TTTTAATTTT 0.427182 -60 **** ***** * Masking position 8 Map Score: 8.0338 Number of sites scoring better than the average of aligned sites = 741 Number in coding regions = 556 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 12 ********** No masking Map Score: 4.34385e-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: 4.34385e-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: 4.34385e-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