AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -iargR_mjan_opreg_100.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 MJ0069 145 acetylglutamate kinase (argB) #2 MJ0429 167 argininosuccinate synthetase (argG) #3 MJ0721 194 acetylornithine aminotransferase (argD) #4 MJ0791 300 argininosuccinate lyase (argH) #5 MJ0881 300 ornithine carbamoyltransferase (argF) #6 MJ1019 132 carbamoyl-phosphate synthase, small (or glutamine) subunit (carA) #7 MJ1096 221 N-acetyl-gamma-glutamyl-phosphate reductase (argC) #8 MJ1378 184 carbamoyl-phosphate synthase, medium subunit (carB1) #9 MJ1381 124 carbamoyl-phosphate synthase, large subunit (carB2) #10 MJ1495 151 conserved hypothetical protein Motif number 1 ATCTTAATTTTTATTAATTACCTTAGTTACG 1 50 1 TATTAATTAC 0.468048 -96 AGTTATTGTTTGATAAATTTTAAATAATTCC 1 96 1 TATAAATTTT 0.775265 -50 TCCTTAAACTTTTTGTATTTTATTGCTTATA 2 101 0 TTTGTATTTT 0.799458 -67 AGTTTAAGGATTTATAATTTTATGTAAGATA 2 122 1 TTATAATTTT 0.82242 -46 AAAAGTTTTATTTTTAATTTTAAAATCATTT 3 164 1 TTTTAATTTT 0.968174 -31 CGCCAACTATTCTTTAATTTTTTGTATGGTG 4 36 1 TTTTAATTTT 0.968174 -265 TATATAGAGGTTTTGTATTATTACATTTGTG 4 90 0 TTTGTATTAT 0.707279 -211 TATAATTTACTATTTAACTTTAAATCATAAT 4 122 0 TTTTAACTTT 0.963049 -179 TATGTTAAAATTTTTAACTTATTAGAATTTT 4 153 1 TTTTAACTTA 0.546695 -148 AAGTTATAATTGTTTTATTATTAAAAATTCT 4 176 0 TTTTTATTAT 0.935108 -125 TAGTTAAAAATAATTTACTTTTTTAAAGTTA 4 201 0 TATTTACTTT 0.840944 -100 AAGTAAATTATTTTTAACTATTTTATAATTT 4 212 1 TTTTAACTAT 0.940465 -89 TTTTAACTATTTTATAATTTTATATCAAAAA 4 223 1 TTATAATTTT 0.82242 -78 ATATTGATTATGTTATATTTCATTTTTTGAT 4 246 0 TTTATATTTC 0.656312 -55 CTTAAACAGTTAATTTATTATAAAAAATACA 5 13 1 TATTTATTAT 0.789039 -288 TTTTAAGAACTGTTTTATTATTGTATTTTTT 5 34 0 TTTTTATTAT 0.935108 -267 ATTAACTTTGTGTTATATTTTTCAGTGCTAT 5 70 0 TTTATATTTT 0.91218 -231 TTCTTTTTATTTATTAACTTTGTGTTATATT 5 82 0 TATTAACTTT 0.871217 -219 TGCCCTTATTTATTTAATTTCATTCAATAAC 5 165 1 TTTTAATTTC 0.848319 -136 TTAAAAACTATTTTATATTATCATGAGCCAT 5 261 0 TTTATATTAT 0.862931 -40 TTTATCACCTTTTATACTATTAAAAACTAT 5 281 0 TTTATACTAT 0.843597 -20 TCCAATCTTTAATTTTTTATCTATTC 7 6 1 TTTTAATTTT 0.968174 -216 TTTTATCTATTCTTTTATTTTTTAAACTGAA 7 25 1 TTTTTATTTT 0.959637 -197 AGATGCTCTTTATAATATTTTCAGTTTAAAA 7 44 0 TTAATATTTT 0.612604 -178 TATTAGTTTTTAATAAACTTTTTGTAAAAAA 7 109 0 TATAAACTTT 0.747189 -113 TTATAAAAAATCTTAAATTATACA 7 208 1 TTTAAATTAT 0.889568 -14 ATATTTATGTTACTTAACTTTAAGTATCCTT 8 65 0 TCTTAACTTT 0.792996 -120 AATATTTATATATTTAACTATTATTATTCAG 8 138 0 TTTTAACTAT 0.940465 -47 AGGAACGTCTTCTTTAACTATCTTCCAAAGA 9 42 0 TTTTAACTAT 0.940465 -83 CTCAACTTCTTTCTTTATTTTAGGAACGTCT 9 63 0 TCTTTATTTT 0.777507 -62 TTCAATATCTTTTAAAACTATCTCAACTTCT 9 84 0 TTAAAACTAT 0.51236 -41 TAATCACCTATTTTTTATTTTCAATATCTTT 9 103 0 TTTTTATTTT 0.959637 -22 * ********* Masking position 7 Map Score: 38.4887 Number of sites scoring better than the average of aligned sites = 1937 Number in coding regions = 1368 Number in noncoding regions = 569 Number of orfs with sites within 600 bp upstream = 424 Fraction of orfs with sites within 600 bp upstream = 0.0681015 Motif number 2 ATCAATCTAAATAGAAATTTTTGGGGATAAA 2 10 0 ATAAAATTTT 0.929797 -158 CTCACCTATTATATATAAACTGCTAATAATAA 2 51 0 ATAATAAATG 0.854391 -117 AAGCAATAAAATACAAAAAGTTTAAGGATTTA 2 104 1 ATAAAAAATT 0.942256 -64 TATGTAAGATATAAAAATATTTTGTGAGGGAT 2 142 1 ATAAAATATT 0.980417 -26 AGCAATATTAATAAAAATACTTTCACATAAAA 3 36 1 ATAAAATATT 0.980438 -159 ATACTTTCACATAAAAATGTTTTGTTGGTGAC 3 52 1 ATAAAATGTT 0.916511 -143 ACAACACAAAATATAAATACTTATAATGCATT 3 123 1 ATAAAATATT 0.980438 -72 TAGGGGCACCATACAAAAAATTAAAGAATAGT 4 41 0 ATAAAAAATT 0.942256 -260 CAAAACCTCTATATATATTATGATTTAAAGTT 4 106 1 ATAATATTTG 0.826468 -195 AAAAATTTTAACATATATAATTTACTATTTAA 4 136 0 ACAATATATT 0.726109 -165 TATAAAATAGTTAAAAATAATTTACTTTTTTA 4 207 0 TTAAAATATT 0.754969 -94 AAGTTAATAAATAAAAAGAATTACAAAAACAT 5 93 1 ATAAAAGATT 0.856457 -208 AACTACAACAATATAAATAATGGCTCATGATA 5 242 1 ATAAAATATG 0.968785 -59 ACTATCACATATATATATGATTGGGATAATCA 6 88 0 ATAATATGTT 0.864363 -45 CAAAGGTTTTATAAAAAATCTTAAATTATACA 7 200 1 ATAAAAATTT 0.811749 -22 GTTAAGTAACATAAATATAGTTATGCAATTTT 8 78 1 ATAATATATT 0.966763 -107 GATAATCTGAATAATAATAGTTAAATATATAA 8 132 1 ATATAATATT 0.754969 -53 ATAGTTAAATATATAAATATTGTAAAATATTA 8 148 1 ATAAAATATG 0.968784 -37 TTCATAAATATTTTGGGATTGATTA 9 4 1 ATAATATTTG 0.826451 -121 CTCCAAATTTATACATAAACTGCGAAAGTCCT 10 41 0 ATAATAAATG 0.854391 -111 TCAATATTCAATAAAAATATTTTTCCTGCGAA 10 92 1 ATAAAATATT 0.980417 -60 TTCATGAATATAAATATAGTTGCCTTATTAA 10 131 0 ATAATATATT 0.966763 -21 *** ***** ** Masking position 11 Map Score: 35.8995 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 298 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 3 CTTATCTCACCAACTACCAAAAA 1 3 1 TATTCACCAA 0.985615 -143 TTTATCCCCAAAAATTTCTAT 2 1 1 TTTTCCCCAA 0.944235 -167 GGAGTATATATAACTCACCTATTATATATAA 2 65 0 TAATCACCTA 0.933654 -103 ACTTATCACCAAAAAGATTAAT 3 2 1 CTTTCACCAA 0.976304 -193 TGATATGGTTTAAGTCACCAACAAAACATTT 3 66 0 TAATCACCAA 0.977414 -129 TTAATCACCAAAATGATTTTA 3 184 0 TTATCACCAA 0.985619 -11 ATTTTCCACATTTTTCACAAATGTAATAATA 4 75 1 TTTTCACAAA 0.874821 -226 TATTTCACCAATGCATTTTAA 4 290 0 TATTCACCAA 0.985615 -11 TTTATCACCTTTTATACTATT 5 290 0 TTTTCACCTT 0.917111 -11 GTCTATTCACCATTTCATCAATT 6 3 1 CTATCACCAT 0.89421 -130 ATATTTCACCAAAATACCTATA 6 121 0 TATTCACCAA 0.985615 -12 ATTATCACCATTTACCTACCA 8 1 1 ATTTCACCAT 0.895305 -184 ATAATCACCTATTTTTTATTT 9 114 0 ATATCACCTA 0.845309 -11 *** ******* Masking position 5 Map Score: 18.1236 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 131 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 CTAAAATCTTAATTTTTATTAATTACCTTA 1 45 1 AATTTTTATT 0.597007 -101 CAAAAATTTCTATTTAGATTGATTATTGAC 2 19 1 TATTTAGATT 0.778855 -149 CCTCACAAAATATTTTTATATCTTACATAA 2 141 0 TATTTTTATA 0.804441 -27 TATGTGAAAGTATTTTTATTAATATTGCTA 3 35 0 TATTTTTATT 0.958219 -160 GCATTATAAGTATTTATATTTTGTGTTGTT 3 122 0 TATTTATATT 0.972823 -73 TTAAAAGTTTTATTTTTAATTTTAAAATCA 3 162 1 TATTTTTAAT 0.733539 -33 ACAAAACCTCTATATATATTATGATTTAAA 4 105 1 TATATATATT 0.777531 -196 AATAGTAAATTATATATGTTAAAATTTTTA 4 139 1 TATATATGTT 0.4621 -162 AACTATTTTATAATTTTATATCAAAAAATG 4 227 1 TAATTTTATA 0.429171 -74 TTTTTGTAATTCTTTTTATTTATTAACTTT 5 92 0 TCTTTTTATT 0.922764 -209 AATTAACTATTAATAATATTTGATGTTTTT 5 117 0 TAATAATATT 0.546372 -184 CATGAGCCATTATTTATATTGTTGTAGTTT 5 241 0 TATTTATATT 0.972823 -60 TAATAGATGCTCTTTATAATATTTTCAGTT 7 49 0 TCTTTATAAT 0.695979 -173 TAGAAGCCATTCATTATATTCCTCTTACTA 7 159 1 TCATTATATT 0.775755 -63 TGCATAACTATATTTATGTTACTTAACTTT 8 75 0 TATTTATGTT 0.877932 -110 ATTCAGATTATCTTAATATTGAGGATGAGC 8 114 0 TCTTAATATT 0.775749 -71 TATATTTAACTATTATTATTCAGATTATCT 8 131 0 TATTATTATT 0.806134 -54 TATTTTACAATATTTATATATTTAACTATT 8 147 0 TATTTATATA 0.859197 -38 TCAACTTCTTTCTTTATTTTAGGAACGTCT 9 63 0 TCTTTATTTT 0.577904 -62 GCAGGAAAAATATTTTTATTGAATATTGAC 10 91 0 TATTTTTATT 0.958219 -61 AAGGCAACTATATTTATATTCATGAA 10 136 1 TATTTATATT 0.972823 -16 ********** Masking position 1 Map Score: 20.774 Number of sites scoring better than the average of aligned sites = 1050 Number in coding regions = 680 Number in noncoding regions = 370 Number of orfs with sites within 600 bp upstream = 343 Fraction of orfs with sites within 600 bp upstream = 0.0550916 Motif number 5 AAAATCTTAATTTTTATTAATTACCTTAGTTA 1 47 1 TTTTTAAATT 0.764981 -99 GCTTCTATTATTTAAAGTTATTGTTTGATAAA 1 81 1 TTTAAATATT 0.874346 -65 AAAGGAATTATTTAAAATTTATCAAACAATAA 1 98 0 TTTAAATTAT 0.786922 -48 AAAACCTTTTAAGTTTATGAGTGGATAA 1 128 0 TTTTAATTAT 0.662173 -18 TTATTAGCAGTTTATATATAATAGGTGAGTTA 2 54 1 TTTATATAAT 0.851946 -114 AGTTTAAGGATTTATAATTTTATGTAAGATAT 2 122 1 TTTATATTTA 0.765101 -46 TGTGAAAGTATTTTTATTAATATTGCTATAAT 3 31 0 TTTTTAAATA 0.680659 -164 TTGTTGAGTATTTTAATCATTTTTGATATGGT 3 88 0 TTTTAAATTT 0.574661 -107 CCAAAATGATTTTAAAATTAAAAATAAAACTT 3 166 0 TTTAAATAAA 0.792913 -29 TATATTATGATTTAAAGTTAAATAGTAAATTA 4 119 1 TTTAAATAAA 0.792913 -182 AAGTTAAAAATTTTAACATATATAATTTACTA 4 141 0 TTTTAATATA 0.717684 -160 ATGTTAAAATTTTTAACTTATTAGAATTTTTA 4 154 1 TTTTAATATT 0.786923 -147 CTTATTAGAATTTTTAATAATAAAACAATTAT 4 170 1 TTTTTAAATA 0.691734 -131 AATTTACTTTTTTAAAGTTATAATTGTTTTAT 4 189 0 TTTAAATATA 0.827115 -112 AAGTAAATTATTTTTAACTATTTTATAATTTT 4 212 1 TTTTTATATT 0.825343 -89 ATTTTATAATTTTATATCAAAAAATGAAATAT 4 231 1 TTTATAAAAA 0.769097 -70 TTTAATCGTGTTTAAATAATATTGATTATGTT 4 263 0 TTTAAAATAT 0.717748 -38 TATTGTATTTTTTATAATAAATTAACTGTTTA 5 15 0 TTTATAAAAT 0.859687 -286 TTTGTAATTCTTTTTATTTATTAACTTTGTGT 5 88 0 TTTTTATATT 0.825092 -213 TTTATCACCTTTTATACTATTAAAAACTATTT 5 279 0 TTTATAATTA 0.691844 -22 CATTATGCATTTTATAATTTATGGTTGTTAAT 6 34 0 TTTATATTAT 0.82534 -99 TATGTGATAGTTTATAGGTATTTTGGTGAAAT 6 109 1 TTTATATATT 0.899028 -24 AATCTTTAATTTTTTATCTATTCTTTTATTTT 7 14 1 TTTTTATATT 0.825338 -208 ATATTTTCAGTTTAAAAAATAAAAGAATAGAT 7 29 0 TTTAAAATAA 0.636788 -193 ATAGATGCTCTTTATAATATTTTCAGTTTAAA 7 45 0 TTTATAATTT 0.765104 -177 ATGGATTCCTTTTAAATCTAATAGATGCTCTT 7 65 0 TTTAAATAAT 0.87348 -157 AAATCCTGTTTTTTTACAAAAAGTTTATTAAA 7 100 1 TTTTTAAAAA 0.677689 -122 GTTCAAAGGTTTTATAAAAAATCTTAAATTAT 7 197 1 TTTATAAAAT 0.85963 -25 AGTTAAGGTTTTTAAAGTTAATGGTAGGTAAA 8 21 0 TTTAAATAAT 0.873964 -164 TTTTACAATATTTATATATTTAACTATTATTA 8 143 0 TTTATATTTA 0.764673 -42 TTGAGATAGTTTTAAAAGATATTGAAAATAAA 9 89 1 TTTAAAATAT 0.717963 -36 AAGCTCCAAATTTATACATAAACTGCGAAAGT 10 44 0 TTTATATAAA 0.814975 -108 ****** **** Masking position 6 Map Score: 41.4724 Number of sites scoring better than the average of aligned sites = 2110 Number in coding regions = 1491 Number in noncoding regions = 619 Number of orfs with sites within 600 bp upstream = 481 Fraction of orfs with sites within 600 bp upstream = 0.0772567 Motif number 6 AAATTTCTATTTAGATTGATTATTGACAGTTATTA 2 22 1 TTTGTTATTG 0.983108 -146 ACTTTTTGTATTTTATTGCTTATAGTTTTGGAGTA 2 90 0 TTTGTTATAG 0.880881 -78 TGTGAAAGTATTTTTATTAATATTGCTATAATTAA 3 28 0 TTTTATATTG 0.827631 -167 TTGTTGAGTATTTTAATCATTTTTGATATGGTTTA 3 85 0 TTTCTTTTTG 0.771081 -110 TATTTATATTTTGTGTTGTTTTTTGTTGAGTATTT 3 107 0 TTTGTTTTTG 0.958648 -88 TAATTGTTAATTCCCATAAATATTGCCCTTATTTA 5 142 1 TTTAATATTG 0.827631 -159 AAATTACACGTTTATGTGGTTATTGAATGAAATTA 5 179 0 TTTGTTATTG 0.983108 -122 TATGTGATAGTTTATAGGTATTTTGGTGAAATAT 6 109 1 TTGGATTTTG 0.786044 -24 TAAAATATTATTGTGGTGGATATTG 8 170 1 TTTGATATTG 0.979991 -15 TTATCATCACTTAAACTGGTGATTGACT 10 4 0 TTTGTGATTG 0.916391 -148 GGAAAAATATTTTTATTGAATATTGACACTCTTTG 10 83 0 TTTGATATTG 0.979991 -69 ** ** ****** Masking position 13 Map Score: 8.66063 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 120 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 AATAACTTTAAATAATAGAAGCCGTAACTAA 1 72 0 AATAATAGAG 0.837134 -74 ATAAACTGCTAATAATAACTGTCAATAATCA 2 38 0 AATAATAATG 0.789349 -130 GCAGTTTATATATAATAGGTGAGTTATATAT 2 60 1 TATAATAGTG 0.952157 -108 CAAAAAATTAAAGAATAGTTGGCGATGACGC 4 29 0 AAGAATAGTG 0.942854 -272 AAATGTGGAAAATAATAGGGGCACCATACAA 4 57 0 AATAATAGGG 0.883966 -244 TTAAATAGTAAATTATATATGTTAAAATTTT 4 136 1 AATTATATTG 0.621673 -165 ATTAACTATTAATAATATTTGATGTTTTTGT 5 115 0 AATAATATTG 0.904471 -186 TTTTTAATAGTATAAAAGGTGATAAA 5 285 1 TATAAAAGTG 0.645625 -16 TATGGTTGTTAATAATTGATGAAATGGTGAA 6 16 0 AATAATTGTG 0.900632 -117 TTATGCATTTTATAATTTATGGTTGTTAATA 6 33 0 TATAATTTTG 0.384898 -100 TAAAAAATAAAAGAATAGATAAAAAATTAAA 7 18 0 AAGAATAGTA 0.63912 -204 TCCTTTTAAATCTAATAGATGCTCTTTATAA 7 60 0 TCTAATAGTG 0.729747 -162 TAATCTGAATAATAATAGTTAAATATATAAA 8 134 1 AATAATAGTA 0.848616 -51 ATTGAAAATAAAAAATAGGTGATTAT 9 109 1 AAAAATAGTG 0.914284 -16 TCATGAATATAAATATAGTTGCCTTATTAAT 10 130 0 AAATATAGTG 0.649271 -22 ******** ** Masking position 5 Map Score: 9.50231 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 489 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 8 ATTAATAAAAATTAAGATTTTAGATAAAACGA 1 36 0 ATAGATTTTA 0.62753 -110 TGTAAGATATAAAAATATTTTGTGAGGGATTG 2 144 1 AAATATTTTG 0.757621 -24 CAATATTAATAAAAATACTTTCACATAAAAAT 3 38 1 AAATACTTTC 0.872224 -157 TTAATCACCAAAATGATTTTAAAATTAAAAA 3 174 0 AAAGATTTTA 0.947869 -21 TAAAATAGTTAAAAATAATTTACTTTTTTAAA 4 205 0 AAATAATTTA 0.578792 -96 TAACATAATCAATATTATTTAAACACGATTAA 4 262 1 AAATATTTAA 0.625405 -39 ATTAACTATTAATAATATTTGATGTTTTTGTA 5 114 0 AAATATTTGA 0.712142 -187 TATACTATTAAAAACTATTTTATATTATCATG 5 267 0 AAATATTTTA 0.93749 -34 AGATGCTCTTTATAATATTTTCAGTTTAAAAA 7 43 0 TAATATTTTC 0.608325 -179 TTTGTAAAAAAACAGGATTTTAGATGGATTCC 7 88 0 AAAGATTTTA 0.948402 -134 TATCCACCACAATAATATTTTACAATATTTAT 8 160 0 AAATATTTTA 0.939704 -25 AAGATAGTTAAAGAAGACGTTCCTAAAATAAA 9 49 1 AAAGACGTTC 0.62787 -76 AGTGATGATAAATAGGACTTTCGCAGTTTATG 10 28 1 AAAGACTTTC 0.925555 -124 AATATTCAATAAAAATATTTTTCCTGCGAAAG 10 94 1 AAATATTTTT 0.462968 -58 TTGCCTTATTAATAGGACTTTCGCAGGAAAAA 10 111 0 AAAGACTTTC 0.925555 -41 ** * ******* Masking position 7 Map Score: 10.1162 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 224 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 9 TAAAACGAGATTTTTGGTAGTTGGTGAGATAA 1 12 0 TTTTTGGAGT 0.972288 -134 TTATTTAAAGTTATTGTTTGATAAATTTTAAA 1 88 1 TTATTGTTGT 0.78547 -58 TTTAGATTGATTATTGACAGTTATTATTAGCA 2 31 1 TTATTGAAGT 0.710789 -137 GATTTATAATTTTATGTAAGATATAAAAATAT 2 130 1 TTTATGTAGT 0.946971 -38 ATTCTTTAATTTTTTGTATGGTGCCCCTATTA 4 44 1 TTTTTGTTGT 0.88994 -257 AAGGGCAATATTTATGGGAATTAACAATTAAC 5 140 0 TTTATGGAAT 0.774751 -161 CATTTTATAATTTATGGTTGTTAATAATTGAT 6 27 0 TTTATGGTGT 0.940781 -106 GTTTTTAAAGTTAATGGTAGGTAAATGGTGAT 8 14 0 TTAATGGAGT 0.940781 -171 CATAACTATATTTATGTTACTTAACTTTAAGT 8 71 0 TTTATGTACT 0.721811 -114 ATTATATCCTTCTTTGGAAGATAGTTAAAGAA 9 32 1 TCTTTGGAGT 0.879762 -93 ******* ** * Masking position 5 Map Score: 2.55546 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 253 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 CTAAGGTAATTAATAAAAATTAAGATTTTA 1 46 0 TAATAAAAAT 0.652453 -100 TAACTGTCAATAATCAATCTAAATAGAAAT 2 24 0 TAATCAATCT 0.887887 -144 AATATTGCTATAATTAATCTTTTTGGTGAT 3 15 0 TAATTAATCT 0.55059 -180 ATAGCAATATTAATAAAAATACTTTCACAT 3 34 1 TAATAAAAAT 0.652453 -161 CTTTAAATCATAATATATATAGAGGTTTTG 4 106 0 TAATATATAT 0.743053 -195 AAATATAACATAATCAATATTATTTAAACA 4 257 1 TAATCAATAT 0.913626 -44 AACACAAAGTTAATAAATAAAAAGAATTAC 5 87 1 TAATAAATAA 0.515632 -214 TTGTTAATTCCCATAAATATTGCCCTTATT 5 145 1 CCATAAATAT 0.665353 -156 ATTGGGATAATCATCTATCTACTGCTTTTA 6 71 0 TCATCTATCT 0.712777 -62 ATTATCCCAATCATATATATATGTGATAGT 6 90 1 TCATATATAT 0.784659 -43 AAAGGTTTTATAAAAAATCTTAAATTATAC 7 201 1 TAAAAAATCT 0.426943 -21 AAGTTAAGTAACATAAATATAGTTATGCAA 8 76 1 ACATAAATAT 0.572899 -109 TAAAAGCTCATCCTCAATATTAAGATAATC 8 109 1 TCCTCAATAT 0.62829 -76 TTCATAAATATTTTGGGATTG 9 2 1 TCATAAATAT 0.936115 -123 AAGAAGGATATAATCAATCCCAAAATATTT 9 16 0 TAATCAATCC 0.517962 -109 TTCATGAATATAAATATAGTT 10 141 0 TCATGAATAT 0.753452 -11 ********** Masking position 7 Map Score: 3.08472 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 587 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 11 TCACCAAAATGATTTTAAAATTAAAAATAA 3 171 0 GATTTTAAAA 0.817281 -24 ACTTATTAGAATTTTTAATAATAAAACAAT 4 169 1 ATTTTTAATA 0.665136 -132 TAATAAAACAGTTCTTAAAAAACTTATAGC 5 45 1 GTTCTTAAAA 0.933929 -256 ATATAAAATAGTTTTTAATAGTATAAAAGG 5 274 1 GTTTTTAATA 0.952962 -27 ATAATTTATGGTTGTTAATAATTGATGAAA 6 23 0 GTTGTTAATA 0.861771 -110 GATTTTATTAGTTTTTAATAAACTTTTTGT 7 115 0 GTTTTTAATA 0.952962 -107 ATCAGTTAAGGTTTTTAAAGTTAATGGTAG 8 26 0 GTTTTTAAAG 0.853614 -159 TTGAGGATGAGCTTTTAAAATTGCATAACT 8 96 0 GCTTTTAAAA 0.86894 -89 TAAAGAAGACGTTCCTAAAATAAAGAAAGA 9 57 1 GTTCCTAAAA 0.767585 -68 ********** Masking position 6 Map Score: 4.24067 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 264 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 12 AAGGGAAGTAATGCATTATAAGTATTTATA 3 134 0 ATGCATTATA 0.844067 -61 TATTTCACCAATGCATTTTAATCGTGTTTA 4 281 0 ATGCATTTTA 0.963063 -20 TGTTTTTGTAATTCTTTTTATTTATTAACT 5 94 0 ATTCTTTTTA 0.898066 -207 AGAGGACATTATGCATTTTATAATTTATGG 6 42 0 ATGCATTTTA 0.963063 -91 AATCTAATAGATGCTCTTTATAATATTTTC 7 53 0 ATGCTCTTTA 0.848461 -169 TTTTAGATGGATTCCTTTTAAATCTAATAG 7 73 0 ATTCCTTTTA 0.931637 -149 CATTCATTATATTCCTCTTACTATAAGGTT 7 166 1 ATTCCTCTTA 0.807443 -56 ********** Masking position 1 Map Score: 2.6079 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 67 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 13 ********** No masking Map Score: -2.31394e-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: -2.31394e-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: -2.31394e-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