AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -irpoN_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 MJ0443 43 conserved hypothetical protein #2 MJ0444 265 conserved hypothetical protein #3 MJ0445 300 translation initiation factor aIF-1A #4 MJ0516 113 carbon monoxide dehydrogenase, hydrogenase subunit CooL (cooL) #5 MJ0519 181 M. jannaschii predicted coding region MJ0519 #6 MJ0520 192 NADH-ubiquinone oxidoreductase, subunit 1 #7 MJ0522 108 NADH dehydrogenase I #8 MJ0524 123 conserved hypothetical protein #9 MJ0525 122 conserved hypothetical protein #10 MJ0528 74 conserved hypothetical protein #11 MJ0529 132 repressor protein, putative #12 MJ0676 108 hydrogenase expression/formation protein (hypE) #13 MJ0677 69 ethylene-inducible protein #14 MJ0678 62 conserved hypothetical protein #15 MJ0679 39 transketolase'' #16 MJ0680 23 pentose-5-phosphate-3-epimerase #17 MJ0681 156 transketolase' #18 MJ0682 26 conserved hypothetical protein #19 MJ0683 29 conserved hypothetical protein #20 MJ0684 68 aspartate aminotransferase (aspB2) #21 MJ0792 300 M. jannaschii predicted coding region MJ0792 #22 MJ0792.1 68 M. jannaschii predicted coding region MJ0792.1 #23 MJ0793 60 M. jannaschii predicted coding region MJ0793 #24 MJ0794 48 M. jannaschii predicted coding region MJ0794 #25 MJ0795 79 M. jannaschii predicted coding region MJ0795 #26 MJ0995 57 VAR1 protein isolog #27 MJ1027 125 formate hydrogenlyase, subunit 5 #28 MJ1089 40 cobalt transport protein (cbiQ) #29 MJ1091 281 cobalamin biosynthesis protein (cbiM) #30 MJ1309 37 carbon monoxide dehydrogenase, hydrogenase anchor subunit CooM (cooM) #31 MJ1310 83 conserved hypothetical protein #32 MJ1345 300 O-linked GlnNAc transferase #33 MJ1346 87 glutamine synthetase (glnA) #34 MJ1363 300 formate hydrogenlyase, subunit 7 Motif number 1 AGTTCTGTGCCAATAGGGGGCGAAGCCCCC 2 223 1 CAATAGGGGG 0.99795 -43 CCTTTTCTTTCCATAGGGGGCTTCGCCCCC 2 238 0 CCATAGGGGG 0.998368 -28 TATTCAGAAACCATAGGGCTTCGCCCTATT 4 26 1 CCATAGGGCT 0.907165 -88 CTGGGTATCCCAATAGGGCGAAGCCCTATG 4 37 0 CAATAGGGCG 0.991578 -77 TACATTGTATCCATAGGGGAAACCCCCTAT 5 21 1 CCATAGGGGA 0.9903 -161 AGGTTCATCCCAATAGGGGGTTTCCCCTAT 5 33 0 CAATAGGGGG 0.99795 -149 GGGAGTATCCCAATAGAGGGGCGAAGCCCC 5 133 1 CAATAGAGGG 0.994613 -49 TGTATAAGACCCATAGAGGGGCTTCGCCCC 5 150 0 CCATAGAGGG 0.995473 -32 GGTGGTATAGCAATAGGAGGTCTCCTCCTA 7 22 0 CAATAGGAGG 0.964969 -87 AACTTGGAAACCATAGAGGGAAACCCTCTA 8 29 1 CCATAGAGGG 0.995473 -95 GGGTGTATCCCAATAGAGGGTTTCCCTCTA 8 42 0 CAATAGAGGG 0.994613 -82 CTGGGTATCCCAATAGGGCGAAGCCCT 10 58 1 CAATAGGGCG 0.991578 -17 TTAAAAGTTCCCATAGGTGATAAA 11 5 0 CCATAGGTGA 0.852429 -128 AATAGATAGTAAATAGAGGAAGT 17 4 0 AAATAGAGGA 0.754184 -153 TGGCTCAGCTCCATATAGGGAGCGTCATCG 21 249 0 CCATATAGGG 0.912935 -52 GAAATTCGTAAAATAGGGGGATTAAAATCG 32 266 1 AAATAGGGGG 0.979828 -35 ********** Masking position 5 Map Score: 38.436 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 38 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 2 ATCAAAGCTAACACCTCCTTGCTACGCTCGGA 2 77 1 ACACCTCCGC 0.999634 -189 AATTTAATTTACACCTCCGAGCGTAGCAAGGA 2 92 0 ACACCTCCGC 0.999634 -174 CCAAAACCTAACACCTCCTCGCTTACGCTCGG 5 79 1 ACACCTCCGC 0.999634 -103 TTACTAATTTACACCTCCGAGCGTAAGCGAGG 5 95 0 ACACCTCCGC 0.999634 -87 TCAAAAACTAACACCTCCTCGCTTCGCTCGGA 6 142 1 ACACCTCCGC 0.999634 -51 TTGTAAATTTACACTTCCGAGCGAAGCGAGGA 6 157 0 ACACTTCCGC 0.996729 -36 ATACACCCTAACACCTCCTCGCTTACGCTCGG 8 64 1 ACACCTCCGC 0.999634 -60 AAATTAATTTACACCTCCGAGCGTAAGCGAGG 8 80 0 ACACCTCCGC 0.999634 -44 ******** ** Masking position 3 Map Score: 34.7677 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 0 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 TGCCAATAGGGGGCGAAGCCCCCTATGGAAA 2 230 1 GGGGAAGCCC 0.772459 -36 TATCCCAATAGGGCGAAGCCCTATGGTTTCT 4 31 0 GGGGAAGCCC 0.772459 -83 GCAATGCATCCTGGGTATCCCAATAGGGCGA 4 46 0 CTGGTATCCC 0.966334 -68 CATCCCAATAGGGGGTTTCCCCTATGGATAC 5 27 0 GGGGTTTCCC 0.980328 -155 GTAAGATTTGGGGAGTATCCCAATAGAGGGG 5 123 1 GGGGTATCCC 0.827749 -59 CCCAATAGAGGGGCGAAGCCCCTCTATGGGT 5 141 1 GGGGAAGCCC 0.772459 -41 TATCCCAATAGAGGGTTTCCCTCTATGGTTT 8 36 0 GAGGTTTCCC 0.963608 -88 GGAGGTGTTAGGGTGTATCCCAATAGAGGGT 8 51 0 GGGGTATCCC 0.985766 -73 GGGCTGAACGTAGTGAAGCCCCGCTCTGGGT 10 33 1 TAGGAAGCCC 0.922388 -42 AAGCCCCGCTCTGGGTATCCCAATAGGGCGA 10 48 1 CTGGTATCCC 0.966334 -27 TATCCCAATAGGGCGAAGCCCT 10 63 1 GGGGAAGCCC 0.772459 -12 *** ******* Masking position 9 Map Score: 23.353 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 11 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 CTTATTTCTAATTTTTATTTTATATGGTTTT 1 20 1 ATTTTATTTT 0.936466 -24 ATATACCCCCAAATTTAATTTACACCTCCGA 2 104 0 AATTTAATTT 0.592836 -162 AAATTTAGTGTTATTTAAATTTCTT 3 5 0 TTTTTAAATT 0.799793 -296 TATTTTTAATATTTTTATTTTGTGTTTGTTG 3 264 0 ATTTTATTTT 0.936466 -37 TTATCACCTTTTTTTTATTTTTAATATTTTT 3 279 0 TTTTTATTTT 0.958573 -22 CCTCACCCAGATTTTTATTTTAATATTT 6 8 0 ATTTTATTTT 0.936466 -185 TAAATTAATTTTGATTAATTTGTTTGGAAAA 8 101 1 TTATTAATTT 0.857917 -23 ATGGAACTCGTTGAATATATTCTCTATATTG 9 32 1 TTAATATATT 0.527718 -91 TGTGGGTAACTTTTATATATTTCCCAGAGGA 11 69 1 TTTATATATT 0.714618 -64 TTCATAATCAATCATTATATTATCGCCATGG 11 110 0 ATATTATATT 0.660093 -23 TTTACTTCATTTTTTTAATTTTGTTTTAAAA 12 19 1 TTTTTAATTT 0.931184 -90 TATTGAATACTTAAATATTTTGATATATTTT 12 69 0 TTAATATTTT 0.791008 -40 TAATTTTATTTTATTTATTTTATTT 14 5 0 TTTTTATTTT 0.958573 -58 AAATAATTAATTTATTATTTTTGTTT 15 6 0 TTATTATTTT 0.911701 -34 AAATAATAAATTAATTATTTTGGGTGAAAAA 15 17 1 TTATTATTTT 0.911701 -23 AATTTTATTTTTTGGTGATTT 16 1 1 AATTTATTTT 0.717182 -23 TCATTATGGATTTTTTGTTTTTGCTTTTTTT 17 84 1 TTTTTGTTTT 0.89591 -73 TTTTTAACTATTTTATAATTTTATATCAAAA 21 34 0 TTTATAATTT 0.832221 -267 TTTAAAAAAGTAAATTATTTTTAACTATTTT 21 51 0 TAATTATTTT 0.640764 -250 TTTTAAAGTTATAATTGTTTTATTATTAAAA 21 75 1 ATATTGTTTT 0.709879 -226 AAATTTTAACATATATAATTTACTATTTAAC 21 121 1 ATTATAATTT 0.759619 -180 TCGCCAACTATTCTTTAATTTTTTGTATGGT 21 221 0 TTTTTAATTT 0.931184 -80 AATGTTTTTCTTTTTTAATTTTAATAATTTT 22 12 1 TTTTTAATTT 0.931184 -57 GTTAAAGTTATTATTTATTTTATCATCATTA 23 28 0 TTTTTATTTT 0.958573 -33 AGATTTTTCAATGATTGTATTTGTTACTTCA 24 23 0 ATATTGTATT 0.419403 -26 TAATAATAGTTAAAATATTTTATAAAAAGTA 26 33 0 TAAATATTTT 0.395376 -25 TTCTTTAATTTTTTACTTTTT 28 1 1 TTTTTAATTT 0.931184 -40 AATTTTTTACTTTTTTAAATTTTAAAATTTA 28 17 1 TTTTTAAATT 0.799793 -24 CTTTTTATATATCTTTATTTTTAGTAATACT 29 19 1 ATTTTATTTT 0.936473 -263 ATTTTTAATAATGATTAATTTTTCTTTTTTA 29 92 0 ATATTAATTT 0.793678 -190 TTTTTATTACTTATTTAAATTAAAGACATTT 29 119 0 TTTTTAAATT 0.799793 -163 ATTAATGAGTTATTTTGTTTTTTTCATATTT 29 148 0 TATTTGTTTT 0.597919 -134 AACAAAATTAAAGTTTATTTTATTAATAATA 29 182 1 AATTTATTTT 0.718041 -100 ACTCTTTATCTTATATAAATTTAACGGTATT 29 214 0 TTTATAAATT 0.594217 -68 TGTGTTAAGTTTTTTTGAATTATATTCAGGG 29 253 1 TTTTTGAATT 0.597743 -29 ATTAATATTTATGTTTTTAATAGCTTT 31 7 1 ATTATGTTTT 0.667778 -77 ATCCCAATATTTGTTTATTTTGCATTTCC 32 9 0 TTTTTATTTT 0.958573 -292 TTATAATTAAATTTTTATATTTATAATTATA 32 61 1 ATTTTATATT 0.813148 -240 TTTTATATTTATAATTATATTATAGCGTATA 32 73 1 ATATTATATT 0.660064 -228 GATTGGGGTATTAATTGTTTTATGACATTAT 32 101 0 TTATTGTTTT 0.793418 -200 AGATAGAAAAATTTATATTTTACACTAAAAT 32 197 1 ATTATATTTT 0.843841 -104 ATTATTTATTAAAATTATTTTAGTGTAAAAT 32 213 0 AAATTATTTT 0.528221 -88 ATTTTTATATTTTAATTTAAATT 33 3 1 TTTATATTTT 0.894536 -85 ACTTCCATATATATATAATTTACGGTATATT 33 35 0 ATTATAATTT 0.759619 -53 TGTTTTTATTTTGTATGTTTTAGGGTTCGAA 34 20 0 TTTATGTTTT 0.759329 -281 AGTAATACTTTTTATTAATTTTCCAATACCA 34 96 1 TTATTAATTT 0.857917 -205 TATAAGTAGGTTGTTTGATTTTGGTATTGGA 34 117 0 TTTTTGATTT 0.834256 -184 GCATAATAGATTTTTTAATTTAATTTCTTGC 34 199 0 TTTTTAATTT 0.931184 -102 AGCATAATCTATTTATATTTTATACATCACT 34 249 1 ATTATATTTT 0.843841 -52 ** ******** Masking position 6 Map Score: 61.3426 Number of sites scoring better than the average of aligned sites = 2460 Number in coding regions = 1678 Number in noncoding regions = 782 Number of orfs with sites within 600 bp upstream = 533 Fraction of orfs with sites within 600 bp upstream = 0.0856087 Motif number 5 AAACACTCAATTTTGAAATTTTGATAGGAT 3 217 1 TTTTGAAATT 0.575433 -84 TTTTTTTTATTTTTAATATTTTTATTTTGT 3 272 0 TTTTAATATT 0.859399 -29 GGGATGAACCTTTTAGTAAAAGCTTCACCA 5 52 1 TTTTAGTAAA 0.83122 -130 AGGTGTTAGGTTTTGGTGAAGCTTTTACTA 5 65 0 TTTTGGTGAA 0.609249 -117 CAGATTTTTATTTTAATATTT 6 2 0 TTTTAATATT 0.859399 -191 TAAACGAAACTTTTAGAAAAAGTTGAACGA 6 66 1 TTTTAGAAAA 0.695858 -127 AGGTGTTAGTTTTTGATGAAATGGAGAGCT 6 128 0 TTTTGATGAA 0.582092 -65 TCTCACCTAATTTTATTAAATAATGGACAT 7 85 0 TTTTATTAAA 0.727603 -24 TTTAATTTTGTTTTAAAATTTTATTGAAAG 12 32 1 TTTTAAAATT 0.748291 -77 TACTTAAATATTTTGATATATTTTTTACAA 12 63 0 TTTTGATATA 0.631095 -46 ACTCTTTAACTTTTATTGAATACTTAAATA 12 83 0 TTTTATTGAA 0.658787 -26 TCAAATAAACTTTTATTGTTGGGATT 14 47 1 TTTTATTGTT 0.728349 -16 AATTTTATTTTTTGGTGATTTAA 16 10 1 TTTTGGTGAT 0.717497 -14 TTTTTGCTTTTTTTATTAATTCATTGAGTA 17 101 1 TTTTATTAAT 0.819203 -56 TAATAATTCCTTTTAGTGTTTATAAATGGT 20 43 1 TTTTAGTGTT 0.826026 -26 ATATTTCATTTTTTGATATAAAATTATAAA 21 24 1 TTTTGATATA 0.631095 -277 TTTTTAACTATTTTATAATTTTATATCAAA 21 35 0 TTTTATAATT 0.652623 -266 TAATTTACTTTTTTAAAGTTATAATTGTTT 21 65 1 TTTTAAAGTT 0.673518 -236 TTATTAGAATTTTTAATAATAAAACAATTA 21 86 0 TTTTAATAAT 0.877625 -215 TCTTTTTTAATTTTAATAATTTTTTGATAT 22 20 1 TTTTAATAAT 0.877625 -49 TTTAATAATTTTTTGATATTTTTTAGGTGA 22 31 1 TTTTGATATT 0.735915 -38 TTTTCCCTCATTTTATAGTAACTTTAATAC 25 58 0 TTTTATAGTA 0.444575 -22 TTAAAATACTTTTTATAAAATATTTTAACT 26 27 1 TTTTATAAAA 0.409737 -31 TATAGTTTTGTTTTAATAAAGTTATCGAG 27 10 0 TTTTAATAAA 0.81481 -116 CTTTAAATTTTAAAATTTAAAAAAGTA 28 24 0 TTTTAAAATT 0.748291 -17 ATATCTTTATTTTTAGTAATACTTAATATT 29 27 1 TTTTAGTAAT 0.889232 -255 AATTTTTCTTTTTTAGTAATAAACTATTTA 29 77 0 TTTTAGTAAT 0.889232 -205 TTAAAGACATTTTTAATAATGATTAATTTT 29 101 0 TTTTAATAAT 0.877625 -181 TTAAAGTTTATTTTATTAATAATAAAATAC 29 189 1 TTTTATTAAT 0.819203 -93 CCCTCCAATCTTTTAGAGAAAGTTAAATAG 30 13 0 TTTTAGAGAA 0.624459 -25 ATTTATGGACTTTTATAATTAAATTTTTAT 32 49 1 TTTTATAATT 0.652623 -252 ATTAAAATTATTTTAGTGTAAAATATAAAT 32 207 0 TTTTAGTGTA 0.744558 -94 ACTAAAATAATTTTAATAAATAATATCATA 32 220 1 TTTTAATAAA 0.81481 -81 AATTTTTCAATTTTAAAGTTTTATTTTTAA 34 66 0 TTTTAAAGTT 0.673518 -235 TAGTAATACTTTTTATTAATTTTCCAATAC 34 95 1 TTTTATTAAT 0.819203 -206 GGTTGTTTGATTTTGGTATTGGAAAATTAA 34 110 0 TTTTGGTATT 0.757245 -191 AGCGAACAGGTTTTAGAAATCTTTCGGATT 34 156 0 TTTTAGAAAT 0.796013 -145 ********** Masking position 4 Map Score: 36.583 Number of sites scoring better than the average of aligned sites = 1669 Number in coding regions = 1148 Number in noncoding regions = 521 Number of orfs with sites within 600 bp upstream = 371 Fraction of orfs with sites within 600 bp upstream = 0.0595888 Motif number 6 CTCCGAGCGTAGCAAGGAGGTGTTAGCTTT 2 80 0 AGCAAGGAGG 0.97397 -186 CTCCTTGCTACGCTCGGAGGTGTAAATTAA 2 91 1 CGCTCGGAGG 0.996781 -175 TCCGAGCGTAAGCGAGGAGGTGTTAGGTTT 5 82 0 AGCGAGGAGG 0.993318 -100 TCCTCGCTTACGCTCGGAGGTGTAAATTAG 5 94 1 CGCTCGGAGG 0.996781 -88 TTCCGAGCGAAGCGAGGAGGTGTTAGTTTT 6 145 0 AGCGAGGAGG 0.993318 -48 CTCCTCGCTTCGCTCGGAAGTGTAAATTTA 6 156 1 CGCTCGGAAG 0.971899 -37 TCCGAGCGTAAGCGAGGAGGTGTTAGGGTG 8 67 0 AGCGAGGAGG 0.993318 -57 TCCTCGCTTACGCTCGGAGGTGTAAATTAA 8 79 1 CGCTCGGAGG 0.996781 -45 ********** Masking position 8 Map Score: 18.8151 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 0 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 AGAATTCTTATTTCTAATTTTTATTTTATATG 1 14 1 TTTCATTTTT 0.921759 -30 TTATCACCTTTTTTTTATTTTTAATATTTTTA 3 278 0 TTTTATTTTT 0.915603 -23 AAGAGTTTTCGTTCAACTTTTTCTAAAAGTTT 6 72 0 GTTCCTTTTT 0.624091 -121 GTTTCCAAGTTTTTTCATTATTTCCCCCT 8 8 0 TTTTATTATT 0.812425 -116 TATATAAACTTTTCGTCTTATTTTTTGTGGGT 11 44 1 TTTCCTTATT 0.812171 -89 ATTTGAATTTTACTTCATTTTTTTAATTTTGT 12 11 1 TACTATTTTT 0.565651 -98 CCAAAATAATTAATTTATTATTTTTGTTT 15 8 0 TAATATTATT 0.346592 -32 CATAACATCATTATGGATTTTTTGTTTTTGCT 17 77 1 TTATATTTTT 0.768943 -80 GGATTTTTTGTTTTTGCTTTTTTTATTAATTC 17 91 1 TTTTCTTTTT 0.908871 -66 AGTTTCACCTTTTTAAGATTTAAA 17 143 0 TTTCCTTTTT 0.915474 -14 GATTATGTTATATTTCATTTTTTGATATAAAA 21 15 1 TATTATTTTT 0.812425 -286 ATGTTAAAATTTTTAACTTATTAGAATTTTTA 21 101 0 TTTTCTTATT 0.799269 -200 TATATAGAGGTTTTGTATTATTACATTTGTGA 21 166 1 TTTTATTATT 0.812425 -135 CCCTATTATTTTCCACATTTTTCACAAATGTA 21 187 0 TTCCATTTTT 0.779848 -114 AAATGTTTTTCTTTTTTAATTTTAAT 22 5 1 GTTTCTTTTT 0.60456 -64 CTATTAGATTTTTCAATGATTGT 24 36 0 TATTATTTTT 0.812425 -13 TTCTTTAATTTTTTACTTTTTTAAATTTTAA 28 10 1 TTTTCTTTTT 0.908871 -31 AATAACTACTTTTTATATATCTTT 29 3 1 TAACCTTTTT 0.570155 -279 ATTTTGTTTTTTTCATATTTTTTATTACTTAT 29 136 0 TTTCATTTTT 0.921759 -146 AATTTAACGGTATTTTATTATTAATAAAATAA 29 196 0 TATTATTATT 0.633588 -86 TTTTAATAGCTTTTAGCTTTTTGGTTGCTAAC 31 25 1 TTTTCTTTTT 0.908871 -59 TTTCTTTTATTTCCATATTATTTCCACATTAG 32 150 0 TTCCATTATT 0.585787 -151 ATAAAAAGTATTACTAATTTTTCAATTTTAAA 34 79 0 TTACATTTTT 0.783266 -222 TTTAGAAATCTTTCGGATTTTTAAGATTATAA 34 143 0 TTTCATTTTT 0.921759 -158 TTAATATGCATAATAGATTTTTTAATTTAATT 34 205 0 TAATATTTTT 0.570563 -96 **** ****** Masking position 8 Map Score: 24.2619 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 982 Number in noncoding regions = 365 Number of orfs with sites within 600 bp upstream = 293 Fraction of orfs with sites within 600 bp upstream = 0.0470607 Motif number 8 AACCATATAAAATAAAAATTAGAAATAAGAA 1 18 0 AATAAAATTA 0.818485 -26 GTTGATTGACAATAAAATTTAGTGTTATTTA 3 19 0 AATAAAATTA 0.818485 -282 CTTACGCAGTAATAAATCTTTTCTATTGAAT 3 178 0 AATAAATTTT 0.842791 -123 GTTTGTTGATATTAATAGTTTTGTTATCCTA 3 241 0 ATTAATATTT 0.810558 -60 ATGGTTTCTGAATAATTCTTTCATCATGG 4 9 0 AATAATTTTT 0.888404 -105 TATTCCTCCCAATAAATTTTAAGAGGCATTG 4 90 0 AATAAATTTA 0.720182 -24 TGAACCTTTTAGTAAAAGCTTCACCAAAACC 5 56 1 AGTAAAACTT 0.397177 -126 ACAATCTTTCAATAAAATTTTAAAACAAAAT 12 36 0 AATAAAATTT 0.903764 -73 TTAAGTATTCAATAAAAGTTAAAGAGTGAGA 12 86 1 AATAAAATTA 0.818485 -23 TTGAAAATAGAATAATAATTTTATTTTATTT 14 20 0 AATAATATTT 0.933101 -43 AATCCCAACAATAAAAGTTTATTTGAAAAT 14 43 0 AATAAAATTT 0.903779 -20 AAAATAATAAATTAATTATTTTGGGTGAAAA 15 16 1 ATTAATTTTT 0.709498 -24 GTTATGCTAAAATAATTGTTAGTCATATTTA 17 52 0 AATAATTTTA 0.792624 -105 ATTATTAATTAATAATACTTTTCGTGGTGGC 20 16 0 AATAATATTT 0.933101 -53 ATTAATTAATAATAATTCCTTTTAGTGTTTA 20 34 1 AATAATTCTT 0.650024 -35 TTTTAATTTTAATAATTTTTTGATATTTTTT 22 24 1 AATAATTTTT 0.887605 -45 TGATAAAATAAATAATAACTTTAACAATTGT 23 34 1 AATAATACTT 0.764924 -27 CTTATAATAATAGTTAAAATATTTTA 26 42 0 AATAATATTA 0.870062 -16 CTTTATTTTTAGTAATACTTAATATTACCTA 29 31 1 AGTAATATTA 0.668142 -251 ATTAATATTTATGTTTTTAAT 31 1 1 ATTAATATTA 0.672566 -83 GACTTTTATAATTAAATTTTTATATTTATAA 32 56 1 ATTAAATTTT 0.621875 -245 AGATTGGGGTATTAATTGTTTTATGACATTA 32 102 0 ATTAATTTTT 0.709498 -199 ATATCATAGTAATAATAATTTAACGAAATTC 32 242 1 AATAATATTT 0.933101 -59 TTCTCTTAAAAATAAAACTTTAAAATTGAAA 34 61 1 AATAAAATTT 0.903779 -240 TTGAAAAATTAGTAATACTTTTTATTAATTT 34 86 1 AGTAATATTT 0.807464 -215 ******* *** Masking position 3 Map Score: 30.4934 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 391 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 211 Fraction of orfs with sites within 600 bp upstream = 0.0338901 Motif number 9 ATTAGAAATAAGAATTCTAAT 1 1 0 AGAATTTAAT 0.899951 -43 AAACTCTTTAAGAGTTTTCATGTAACTTTCT 2 18 0 AGAGTTTCAT 0.969975 -248 AAACTCTTAAAGAGTTTTCATAGCCCGAAGC 2 32 1 AGAGTTTCAT 0.969975 -234 TTCAAAATTGAGTGTTTTAATAGGTCTTACG 3 203 0 AGTGTTTAAT 0.86204 -98 GAAAACTCTAAGAGTTTTCGTTCAACTTTTT 6 82 0 AGAGTTTCGT 0.847233 -111 GAAAACTCTTAGAGTTTTCATAGCTGGAAAG 6 94 1 AGAGTTTCAT 0.969975 -99 AACAGTTCCAAGAGTTCCAATAATTAATAGT 9 70 0 AGAGTTCAAT 0.906238 -53 AGATTGATTAAAAGTTCCCATAGGTGATAAA 11 11 0 AAAGTTCCAT 0.711948 -122 TTACTTTTTTAAAGTTATAATTGTTTTATTA 21 69 1 AAAGTTTAAT 0.860264 -232 TTTATTATTAAAAATTCTAATAAGTTAAAAA 21 93 1 AAAATTTAAT 0.665069 -208 TTTTATAAAAAGTATTTTAATGTCTTTGGTG 26 16 0 AGTATTTAAT 0.668368 -42 TGCTTTATTGAGAATTTTAATATGCATAATA 34 222 0 AGAATTTAAT 0.899951 -79 ****** **** Masking position 1 Map Score: 8.68204 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 95 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ACCATATAAAATAAAAATTAGAAATAAGAA 1 18 0 ATAAAAATTA 0.645827 -26 TCCATTATTTAATAAAATTAGGTGAGATAA 7 88 1 AATAAAATTA 0.82714 -21 AAACAAATTAATCAAAATTAATTTACACCT 8 96 0 ATCAAAATTA 0.832304 -28 ATCGCCATGGAATAACATTATCCTCTGGGA 11 90 0 AATAACATTA 0.885378 -43 AAAATTTTAAAACAAAATTAAAAAAATGAA 12 24 0 AACAAAATTA 0.832304 -85 AAATAAATAAAATAAAATTATTATTCTATT 14 16 1 AATAAAATTA 0.82714 -47 TTTTTCACCCAAAATAATTAATTTATTATT 15 18 0 AAAATAATTA 0.532377 -22 ATTTTAGCATAACATCATTATGGATTTTTT 17 70 1 AACATCATTA 0.833394 -87 TTTAAAAAATAATATCATTACTCAATGAAT 17 119 0 AATATCATTA 0.828256 -38 TATGCATCACCATTAATGTGTTTTT 18 12 0 ATCACCATTA 0.5389 -15 ATAAGCAAAAACTTTATAAGGGGCTA 19 7 1 AAAAACTTTA 0.335358 -23 TCAAAAAATTATTAAAATTAAAAAAGAAAA 22 17 0 ATTAAAATTA 0.82714 -52 TATTTATTTTATCATCATTATTGTATAGTA 23 18 0 ATCATCATTA 0.833394 -43 TAAAATAAATAATAACTTTAACAATTGTGA 23 37 1 AATAACTTTA 0.569718 -24 GGTTAAGCTAATTATCATTATTAATTATGA 27 45 1 ATTATCATTA 0.828256 -81 TAGATAATTTATCATAATTAATAATGATAA 27 56 0 ATCATAATTA 0.756022 -70 CATTAATAGTAACAAAATTAAAGTTTATTT 29 172 1 AACAAAATTA 0.832304 -110 TTAACAGTATATAAACATTACGTTAGCAAC 31 48 0 ATAAACATTA 0.746423 -36 TATACGCTATAATATAATTATAAATATAAA 32 74 0 AATATAATTA 0.749217 -227 CCCCAATCTTATTAACTTTAAATAAACTAA 32 124 1 ATTAACTTTA 0.569718 -177 GATATTATTTATTAAAATTATTTTAGTGTA 32 217 0 ATTAAAATTA 0.82714 -84 GTAATTTATCATTATCATTAATGACAAATA 34 279 0 ATTATCATTA 0.828256 -22 ********** Masking position 8 Map Score: 19.9735 Number of sites scoring better than the average of aligned sites = 665 Number in coding regions = 511 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 11 AAATTTAGTGTTATTTAAATTTCTT 3 6 0 TTATTTAAAT 0.608129 -295 TATACTCTCACTATATATATGTGTTGATTG 3 42 0 CTATATATAT 0.66313 -259 AGGACTTAAGCACTTTATATTGGACATTTG 3 123 1 CACTTTATAT 0.618203 -178 GATAACAAAACTATTAATATCAACAAACAC 3 244 1 CTATTAATAT 0.66313 -57 GAAGCAATGCCTCTTAAAATTTATTGGGAG 4 86 1 CTCTTAAAAT 0.673436 -28 AATCTCACTCTTTAACTTTTATTGAAT 12 92 0 CTCTTTAACT 0.87646 -17 ATATAATTTACTATTTAACTTTAAATCATA 21 133 1 CTATTTAACT 0.896242 -168 AATACAAAACCTCTATATATATTATGATTT 21 155 0 CTCTATATAT 0.61819 -146 GTTACTTCAACTATTTAAATC 24 2 0 CTATTTAAAT 0.939582 -47 AATAACTACTTTTTATATATCTTTATTT 29 9 1 CTTTTTATAT 0.60805 -273 TAGTAATAAACTATTTAAATAGTAAGGCAA 29 64 0 CTATTTAAAT 0.939582 -218 TTTTTATTACTTATTTAAATTAAAGACATT 29 120 0 TTATTTAAAT 0.608129 -162 ATTTATAGTACTCTTTATCTTATATAAATT 29 224 0 CTCTTTATCT 0.847803 -58 TTCTATTTAACTTTCTCTAAAA 30 3 1 CTATTTAACT 0.896242 -35 ACGGTATATTCAATTTAAATTAAAATATAA 33 15 0 CAATTTAAAT 0.715166 -73 AAAGCATAATCTATTTATATTTTATACATC 34 247 1 CTATTTATAT 0.92424 -54 ********** Masking position 4 Map Score: 11.0461 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 358 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 12 TTGATGAAACCGAAGCGTAGCTTCGGGCTAT 2 51 0 CAAGCGTAGC 0.974134 -215 ATTTACACCTCCGAGCGTAGCAAGGAGGTGT 2 87 0 CGAGCGTAGC 0.991372 -179 TGTGCCAATAGGGGGCGAAGCCCCCTATGGA 2 228 1 GGGGCGAAGC 0.813857 -38 ATTTACACCTCCGAGCGTAAGCGAGGAGGTG 5 90 0 CGAGCGTAAG 0.921015 -92 TTCATAGCTGGAAAGCATAGCTCTCCATTTC 6 110 1 GAAGCATAGC 0.864145 -83 ATTTACACTTCCGAGCGAAGCGAGGAGGTGT 6 152 0 CGAGCGAAGC 0.973199 -41 TTGACAAAGCATAGGAGGAGACCTC 7 5 1 CAAGCATAGG 0.864145 -104 ATTTACACCTCCGAGCGTAAGCGAGGAGGTG 8 75 0 CGAGCGTAAG 0.921015 -49 CTTGCTTCTTGTGAGCATAGCGAACAGGTTT 34 173 0 GGAGCATAGC 0.951 -128 * ********* Masking position 9 Map Score: 5.89221 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 8 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 ATTAGAATTCTTATTTCTAA 1 1 1 ATTAGAATTC 0.584632 -43 AGAAAGTTACATGAAAACTCTTAAAGAGTT 2 18 1 ATGAAAACTC 0.93571 -248 GCTTCGGGCTATGAAAACTCTTTAAGAGTT 2 33 0 ATGAAAACTC 0.93571 -233 CGTAAGACCTATTAAAACACTCAATTTTGA 3 203 1 ATTAAAACAC 0.868633 -98 AAAAAGTTGAACGAAAACTCTTAGAGTTTT 6 82 1 ACGAAAACTC 0.714168 -111 CTTTCCAGCTATGAAAACTCTAAGAGTTTT 6 95 0 ATGAAAACTC 0.93571 -98 GGGGGAAATAATGAAAAAACTTGGAAACCA 8 12 1 ATGAAAAAAC 0.466374 -112 AAAAAAATGAAGTAAAATTCAAAT 12 5 0 AGTAAAATTC 0.605048 -104 TCAAAAAATTATTAAAATTAAAAAAGAAAA 22 17 0 ATTAAAATTA 0.639852 -52 CACCAAAGACATTAAAATACTTTTTATAAA 26 16 1 ATTAAAATAC 0.805115 -42 CGATAACTTTATTAAAACAAAACTATATAA 27 13 1 ATTAAAACAA 0.5683 -113 GATATTATTTATTAAAATTATTTTAGTGTA 32 217 0 ATTAAAATTA 0.639852 -84 TATTATGCATATTAAAATTCTCAATAAAGC 34 222 1 ATTAAAATTC 0.899233 -79 ********** Masking position 6 Map Score: 5.58761 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 251 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 14 CTAAATAACCTTTTCTTTCCATAGGGGG 2 248 0 CCTTTTCTTT 0.800654 -18 CAGTAATAAATCTTTTCTATTGAATATTGG 3 173 0 TCTTTTCTAT 0.55858 -128 TTTATCACCTTTTTTTTATTTTTAATA 3 284 0 CCTTTTTTTT 0.595552 -17 CTAATTAATGTCCATTATTTAATAAAATTA 7 78 1 TCCATTATTT 0.624535 -31 AGCCCCACTTTCTTTTATTTCCCTGAT 10 8 0 TCTTTTATTT 0.919178 -67 CTATTTACTATCTATTATTTTTAGGTGTAA 17 18 1 TCTATTATTT 0.840383 -139 GTATGGTGCCCCTATTATTTTCCACATTTT 21 198 0 CCTATTATTT 0.842892 -103 CGCCAACTATTCTTTAATTTTTTGTATGGT 21 221 0 TCTTTAATTT 0.785003 -80 GTATTATCACCCATTATATCACCTAAAAA 22 50 0 CCCATTATAT 0.352401 -19 ATTAGCTTAACCTTTTATATAGTTTTGTTT 27 27 0 CCTTTTATAT 0.788163 -99 TTCTTTAATTTTTTACTTTTT 28 2 1 TCTTTAATTT 0.785003 -39 ATTAAAAATGTCTTTAATTTAAATAAGTAA 29 114 1 TCTTTAATTT 0.785003 -168 CTGGATATTTTCTTTTATTTCCATATTATT 32 160 0 TCTTTTATTT 0.919178 -141 ********** Masking position 5 Map Score: 6.40562 Number of sites scoring better than the average of aligned sites = 615 Number in coding regions = 538 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 15 TTTATCACCTTTTTTTTATTT 3 290 0 TTATCACCTT 0.810428 -11 AGTATCCATATCCTCACCCAGATTTTTATT 6 20 0 TCCTCACCCA 0.833506 -173 TTTATCTCACCTAATTTTATTAA 7 96 0 ATCTCACCTA 0.810203 -13 TTTATCACCTATGGGAACTTT 11 2 1 TTATCACCTA 0.959767 -131 GATTTTTCACCCAAAATAATTAA 15 27 0 TTTTCACCCA 0.887076 -13 ATCACCCATTATATCACCTAAAAAATATCA 22 44 0 ATATCACCTA 0.882883 -25 GTATTATCACCCATTATATCACC 22 56 0 TTATCACCCA 0.974252 -13 GTTATCACCAAAGACATTAAA 26 2 1 TTATCACCAA 0.878798 -56 GTTATCACCCCTGAATATAAT 29 271 0 TTATCACCCC 0.909503 -11 ********** Masking position 6 Map Score: 5.60249 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 39 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459