AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_mjan_reg_300.orf -o00440_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 Input sequences: #1 MJ0102 300 Phenylacrylic acid decarboxylase #2 MJ0771 88 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #3 MJ1027 125 formate hydrogenlyase, subunit 5 #4 MJ1028 60 DNA topoisomerase VI, subunit B (top6B) #5 MJ1029 47 dimethyladenosine transferase (ksgA) #6 MJ1054 300 UDP-glucose dehydrogenase, putative #7 MJ1391 300 putative aminotransferase #8 MJ1521 88 Na+/H+ antiporter #9 MJ1522 146 cobalamin biosynthesis precorrin-6Y methylase (cbiE) #10 MJ1575 300 GMP synthase (guaA) #11 MJ1576 80 LemA protein #12 MJ1577 29 M. jannaschii predicted coding region MJ1577 #13 MJ1578 66 cobalamin biosynthesis precorrin-3 methylase (cbiF) #14 MJ1656 300 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE) Motif number 1 CGGTTAAATGAAAACTAAAAGAGTTTTCAT 1 83 0 AAAACTAAAA 0.91935 -218 AACCTAAAATAAAATAATAAAATGGTGCCG 1 189 0 AAAATAATAA 0.939211 -112 TAAATCTAAAAAAATAAATATAACAACCTA 1 213 0 AAAATAAATA 0.923003 -88 ATACTATTTAAAAATAGTTAATCCATAAAT 1 238 0 AAAATAGTTA 0.636877 -63 TAAGATTTAAAAAATAAATACTATTTAAAA 1 255 0 AAAATAAATA 0.923003 -46 TTCACCATTAAAAACTGTTAAGTTAAGATT 1 278 0 AAAACTGTTA 0.421512 -23 TTATAAAATTACAATTAAAAACTTTTTTAG 2 60 0 ACAATTAAAA 0.839468 -29 CCAACAATTATAAACATGATAAT 3 113 0 ACAATTATAA 0.746483 -13 ATAATGTAACAAAATAGAAATTAACTAAAC 4 23 0 AAAATAGAAA 0.876993 -38 AAATATCAGTAAAATAAATAATGTAACAAA 4 40 0 AAAATAAATA 0.923003 -21 AAGAGAAAAGAAAATAAAAAT 5 2 0 AAAATAAAAA 0.964837 -46 TTTTTTAGAATAAATAAAAAGTGAAACA 5 30 1 TAAATAAAAA 0.691254 -18 ATTGATAACGAAAATTATAAGTAATGCTAT 6 147 1 AAAATTATAA 0.939211 -154 ATGTAAGAGAAATATAATAATATTATACAA 6 252 1 AATATAATAA 0.557656 -49 ATAATATTATACAATTATTAATAAATAAAC 6 268 1 ACAATTATTA 0.562632 -33 GTATCTTTCAAAAATAATAAAAATTTTATA 7 68 0 AAAATAATAA 0.939211 -233 AATTTTAACAAATATAAAAATTTCGCTATT 7 144 0 AATATAAAAA 0.691254 -157 TACTTACATTAAAACAAGTAGTTTTTGCAA 7 174 1 AAAACAAGTA 0.492867 -127 AAAAGTTATTAAAATTAAAAAATACCTTAC 7 202 1 AAAATTAAAA 0.964837 -99 ATGCTCCGCAAAAACTAAAAATGCCAATTT 7 272 1 AAAACTAAAA 0.91935 -29 CCAGATATTAAAAACTAAAAGATTGGTGGG 8 66 1 AAAACTAAAA 0.91935 -23 TAAAAATTTAAAAATTGAAA 9 1 0 AAAATTGAAA 0.876993 -146 ATAAGAATATAAAATAAGAATATAAAAATA 9 48 0 AAAATAAGAA 0.842634 -99 AAATATCAATAAAATTAAAAAGATAAGGTA 9 89 0 AAAATTAAAA 0.964837 -58 CAAAGTTGTTAAAATTAATATTAATAATGG 10 74 1 AAAATTAATA 0.923003 -227 AAATCCCCTAAAAATTAAAATTAATAA 12 8 0 AAAATTAAAA 0.964837 -22 TAGGTCTTTCAAAATTAATAAAATTTACTT 13 18 0 AAAATTAATA 0.923003 -49 ACCTACTATAAAAACAAAAACAAGAGGAGA 13 43 1 AAAACAAAAA 0.91935 -24 AACAATCTCTTAAATAATAAGTTAATGATT 14 198 0 TAAATAATAA 0.557656 -103 ATAGTCCTCTAAAATTATAAAACAATCTCT 14 218 0 AAAATTATAA 0.939211 -83 ********** Masking position 4 Map Score: 44.3811 Number of sites scoring better than the average of aligned sites = 1632 Number in coding regions = 1065 Number in noncoding regions = 567 Number of orfs with sites within 600 bp upstream = 411 Fraction of orfs with sites within 600 bp upstream = 0.0660135 Motif number 2 GAGGGATACAAACGAAACTTTTAGAAAAAGTTAAAC 1 150 0 AAAATTTAAA 0.969901 -151 TAACAACCTAAAATAAAATAATAAAATGGTGCCGAG 1 187 0 AAAAAATAAA 0.760851 -114 CCATAAATCTAAAAAAATAAATATAACAACCTAAAA 1 210 0 AAAAAATAAA 0.760852 -91 TTTAAAAAATAAATACTATTTAAAAATAGTTAATCC 1 244 0 AAATTTAAAA 0.494975 -57 AAAAACTGTTAAGTTAAGATTTAAAAAATAAATACT 1 263 0 AATATTTAAA 0.917031 -38 AAATTCACCATTAAAAACTGTTAAGT 1 285 0 AATAATTAAA 0.790738 -16 AAAAGTTTTTAATTGTAATTTTATAAAATCGTAAG 2 64 1 AAGATTTAAA 0.887268 -25 AACTTTATTAAAACAAAACTATATAAAAGGTTAAGC 3 17 1 AAAATATAAA 0.90298 -109 TCATATACCTATTATCATGTTTATAATTGTTGG 3 103 1 ATTATTTAAA 0.55523 -23 TAATGTAACAAAATAGAAATTAACTAAACTATTTTT 4 16 0 AAAATTAATA 0.503089 -45 TAAATATCAGTAAAATAAATAATGTAAC 4 43 0 AATAAAAAAA 0.44238 -18 AATTATAAGTAATGCTATATTTACAATTAATTGTTG 6 159 1 AACATTTAAA 0.745938 -142 TCAGACATAAAATTACAGCTAAATAAACTCCAAAAT 6 207 0 AAAATAAAAA 0.871227 -94 TTATCGATGTAAGAGAAATATAATAATATTATACAA 6 246 1 AAGAATAAAA 0.661676 -55 CTTTCGCAGGAATAAAATCTTTAAAAGAAATC 7 7 0 AAAATTTAAA 0.969901 -294 TTTCAAAAATAATAAAAATTTTATAAAGATTATTAA 7 57 0 AAAATTTAAA 0.969901 -244 GTTTTAATGTAAGTAAATTTTAACAAATATAAAAAT 7 153 0 AAAATTAAAA 0.959054 -148 ATTAAAATTAAAAAATACCTTACTAAAGGAAGGCAT 7 209 1 AAAATTACAA 0.608111 -92 ACAGACACTAAACTTTACATTTAGAAAGCATATAAA 8 26 0 AATATTTAAA 0.917038 -63 GTGTCTGTATATCCAGATATTAAAAACTAAAAGATT 8 54 1 ATAATTAAAA 0.725683 -35 TTAAATTTTGAATTAAAAATTTAAAAATTGAAA 9 8 0 AAAATTTAAA 0.969888 -139 AAGAATATAAAATAAGAATATAAAAATATAAGTTAA 9 40 0 AAAAATAAAA 0.888982 -107 GTTTTTAAATATCAATAAAATTAAAAAGATAAGGTA 9 89 0 ATAAATTAAA 0.554367 -58 TAATCATAATAAAAGAAATTTTAAAATATAGTGTCT 10 36 1 AAGATTTAAA 0.887268 -265 AAAGTTGTTAAAATTAATATTAATAATGGATATTTG 10 75 1 AATATTAAAA 0.889323 -226 AATGTTTTTGAAAGATACTAATAAAATATAAGGTGA 10 271 1 AAAAAATAAA 0.760852 -30 CTAATAATAAAATTTATATAAGTTGATATCA 11 6 1 AAAATATAAA 0.902979 -75 AATCCCCTAAAAATTAAAATTAATAA 12 1 0 AATATTAAAA 0.889323 -29 TTTTCATAAGTAAATTTTATTAATTTTGAAAGA 13 8 1 AAAATTATAA 0.648651 -59 GGAGCTGTTAAAAAAGAGATTTTAAAGTTCCCAAAA 14 146 1 AAAATTTTAA 0.717493 -155 AAGTTCCCAAAAACAGAGGTTGATAATGAATCATTA 14 170 1 AAAATTGAAA 0.773607 -131 CAATCTCTTAAATAATAAGTTAATGATTCATTATCA 14 190 0 AAAATTAAGA 0.600088 -111 ** * * **** ** Masking position 1 Map Score: 36.8353 Number of sites scoring better than the average of aligned sites = 1680 Number in coding regions = 1237 Number in noncoding regions = 443 Number of orfs with sites within 600 bp upstream = 362 Fraction of orfs with sites within 600 bp upstream = 0.0581433 Motif number 3 GATTTTGTTTAACTTTTTCTAAAAGTTTCGTTTG 1 144 1 AATTCTAAAA 0.904377 -157 TTAAAAAATAAATACTATTTAAAAATAGTTAATC 1 245 0 AATTTTAAAA 0.947962 -56 ATTTATATAGTAAGTTATCTAAAAAAGTTTTTAA 2 42 1 TATTCTAAAA 0.924298 -47 CTCGATAACTTTATTAAAACAAAACTATA 3 6 1 TATATTAAAA 0.727875 -120 TTATTAAAACAAAACTATATAAAAGGTTAAGCTA 3 21 1 AATTATAAAA 0.720672 -105 ATATACCTATTATCATGTTTATAATTGTTGG 3 105 1 TATTTTATAA 0.872125 -21 AGAAATTAACTAAACTATTTTTAAACT 4 4 0 TATTTTTTAA 0.65753 -57 TTTCACTTTTTATTTATTCTAAAAAAGAGAAAAG 5 22 0 TAATCTAAAA 0.569621 -26 TATTACTTGGAAATCTATTTAAAACCTCTTTAAT 6 28 0 AATTTTAAAA 0.947962 -273 TTCGCAGGAATAAAATCTTTAAAAGAAATC 7 7 0 TATTTTAAAA 0.959212 -294 TAACTTTATTAATAATCTTTATAAAATTTTTATT 7 49 1 AATTTTATAA 0.840838 -252 GACTTTCGTATAGTATCTTTCAAAAATAATAAAA 7 76 0 TATTTTCAAA 0.913051 -225 GCGAAATTTTTATATTTGTTAAAATTTACTTACA 7 148 1 TATGTTAAAA 0.692135 -153 TAGTTTTTGCAAAAGTTATTAAAATTAAAAAATA 7 192 1 AATATTAAAA 0.674468 -109 TTACTACCCATATATTCTTTTAAAATGCTCCGCA 7 248 1 TATTTTTAAA 0.868774 -53 AATTTATTACTATTATGTTTTTAAATATCAATAA 9 107 0 TATTTTTTAA 0.65753 -40 ATCATAATAAAAGAAATTTTAAAATATAGTGTCT 10 38 1 AAATTTAAAA 0.663828 -263 TTTTAAAATATAGTGTCTTTCAAAGTTGTTAAAA 10 54 1 TATTTTCAAA 0.913051 -247 CTTTTACTAAAAGGTTCTTTCAAAATGTTTTTGA 10 248 1 AATTTTCAAA 0.890521 -53 TATATTTTATTAGTATCTTTCAAAAACATTTTGA 10 267 0 TATTTTCAAA 0.913051 -34 CTAATAATAAAATTTATATAAGTTGATATCA 11 8 1 TATTATATAA 0.491334 -73 CCTCATCTCTAAAAGTGTCTAAAATAATACACAA 14 48 0 AATTCTAAAA 0.904377 -253 AAAATTATAAAACAATCTCTTAAATAATAAGTTA 14 204 0 AATTCTTAAA 0.726962 -97 ** * ******* Masking position 10 Map Score: 24.7518 Number of sites scoring better than the average of aligned sites = 1233 Number in coding regions = 925 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 4 AAGATTTTGTTTAACTTTTTCTAAAAGTTT 1 142 1 TTAACTTTTT 0.946083 -159 TTTTAGGTTGTTATATTTATTTTTTTAGAT 1 210 1 TTATATTTAT 0.526196 -91 ATTTATTTTTTTAGATTTATGGATTAACTA 1 224 1 TTAGATTTAT 0.428267 -77 GATTTATGGATTAACTATTTTTAAATAGTA 1 237 1 TTAACTATTT 0.486226 -64 TAAATTGACAATAAATTTTTGGTGAC 2 7 0 ATAAATTTTT 0.703819 -82 AACTTACTATATAAATTTAGCTAAATTGAC 2 28 0 ATAAATTTAG 0.284823 -61 ATTACAATTAAAAACTTTTTTAGATAACTT 2 53 0 AAAACTTTTT 0.549974 -36 CTCGATAACTTTATTAAAACAAAA 3 5 1 ATAACTTTAT 0.717355 -121 GATAATTAGCTTAACCTTTTATATAGTTTT 3 31 0 TTAACCTTTT 0.583799 -95 TTATTTTCTTTTCTCTTTTTTAGAATAAAT 5 15 1 TTCTCTTTTT 0.554363 -33 TGTTTCACTTTTTATTTATTCTA 5 35 0 TTCACTTTTT 0.810946 -13 GAAAGCCCCATTAACTTTATTAATAATCTT 7 38 1 TTAACTTTAT 0.851333 -263 ATAATCTTTATAAAATTTTTATTATTTTTG 7 60 1 TAAAATTTTT 0.628359 -241 TTTAATTTTAATAACTTTTGCAAAAACTAC 7 191 0 ATAACTTTTG 0.662868 -110 TAGAAAGCATATAAATTTTTTGGTGGTAAT 8 11 0 ATAAATTTTT 0.703819 -78 TTTCAATTTTTAAATTTTTAATTCAAAAT 9 10 1 TTAAATTTTT 0.918113 -137 AAAATATAAGTTAAATTTTGAATTAAAAAT 9 24 0 TTAAATTTTG 0.732655 -123 AAAATTTAACTTATATTTTTATATTCTTAT 9 35 1 TTATATTTTT 0.773008 -112 TATCTTTACCTTATCTTTTTAATTTTATTG 9 83 1 TTATCTTTTT 0.835883 -64 CATAATAGTAATAAATTATTTGAATGTGAA 9 124 1 ATAAATTATT 0.352957 -23 CGAGGAGGTGTTAGATTTTTGATGAACCTT 10 221 1 TTAGATTTTT 0.696349 -80 CTAATAATAAAATTTATATAAGTTGAT 11 8 1 TAAAATTTAT 0.340996 -73 TTATTAATTTTAATTTTTAGGGGATTTT 12 9 1 TTTAATTTTT 0.419295 -21 GAACTTTAAAATCTCTTTTTTAACAGCTCC 14 146 0 ATCTCTTTTT 0.373902 -155 TAATGAATCATTAACTTATTATTTAAGAGA 14 193 1 TTAACTTATT 0.635094 -108 ********** Masking position 7 Map Score: 17.627 Number of sites scoring better than the average of aligned sites = 2202 Number in coding regions = 1653 Number in noncoding regions = 549 Number of orfs with sites within 600 bp upstream = 420 Fraction of orfs with sites within 600 bp upstream = 0.067459 Motif number 5 TCCAGCTATGAAAACTCTTTTAGTTTTCATTT 1 76 1 AAACTCTTTA 0.968354 -225 ATTACAATTAAAAACTTTTTTAGATAACTTAC 2 51 0 AAACTTTTTA 0.617948 -38 AATCTATTTAAAACCTCTTTAATCTTGTGATA 6 19 0 AAACTCTTAA 0.83164 -282 AGTTGAGTAAAAAGCTCCATAATGTTCTACAA 6 82 1 AAACTCCTAA 0.828731 -219 TATTCCTGCGAAAGCCCCATTAACTTTATTAA 7 29 1 AAACCCCTTA 0.882141 -272 AATCCCACCAATCTTTTAGTTTTTAATA 8 71 0 ACCATCTTTA 0.641022 -18 CTATATTTTAAAATTTCTTTTATTATGATTAT 10 35 0 AAATTCTTTA 0.727776 -266 GAGAGCGTTCAAATATCCATTATTAATATTAA 10 88 0 AAAATCCTTA 0.926549 -213 TGGATATTTGAACGCTCTCCTATAGGGAGGTG 10 101 1 AACCTCTCTA 0.904191 -200 AAAAATCCCCTAAAAATTAAAA 12 18 0 AAAATCCCTA 0.875084 -12 ATTAATTTTGAAAGACCTACTATAAAAACAAA 13 29 1 AAAACCTCTA 0.641022 -38 GATATTGAAGAACTATCTCTTAATATTGATTT 14 99 1 AACATCTTTA 0.877322 -202 CTCTTTTTTAACAGCTCCATTAATTCCTCCTC 14 132 0 ACACTCCTTA 0.882141 -169 GGGAACTTTAAAATCTCTTTTTTAACAGCTCC 14 146 0 AAACTCTTTT 0.723621 -155 AAAATTATAAAACAATCTCTTAAATAATAAGT 14 206 0 AACATCTTTA 0.877322 -95 AAATGCATCTAAAACTCCCCTACTGAATTCAT 14 273 0 AAACTCCCTA 0.943332 -28 *** **** *** Masking position 1 Map Score: 12.5294 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 550 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 ACCTAAAATAAAATAATAAAATGGTGCCGAG 1 187 0 AATAATAAAA 0.8011 -114 TTAGCTAAATTGACAATAAATTTTTGGTGAC 2 11 0 TGCAATAAAT 0.701815 -78 TGACTCACTAAGGTAATGAATAGATAATTTA 3 75 0 AGTAATGAAT 0.646989 -51 TTTAATCTTGTGATAATAAATTC 6 3 0 TGTAATAAAT 0.904085 -298 GATTTCCAAGTAATAGTAAATTCGATACGGT 6 47 1 TATAGTAAAT 0.68279 -254 ATTATACAATTATTAATAAATAAACTCAGGG 6 273 1 TATAATAAAT 0.944324 -28 TTATAAAGATTATTAATAAAGTTAATGGGGC 7 42 0 TATAATAAAG 0.779719 -259 TATCTTTCAAAAATAATAAAAATTTTATAAA 7 66 0 AATAATAAAA 0.8011 -235 AATATATGGGTAGTAATGAATGCCTTCCTTT 7 233 0 TATAATGAAT 0.904085 -68 TGTTTTTAAATATCAATAAAATTAAAAAGAT 9 95 0 TACAATAAAA 0.74172 -52 AAAAACATAATAGTAATAAATTATTTGAATG 9 119 1 TATAATAAAT 0.944361 -28 AAATTAATATTAATAATGGATATTTGAACGC 10 85 1 TATAATGGAT 0.544497 -216 TTTTGAAAGATACTAATAAAATATAAGGTGA 10 276 1 TATAATAAAA 0.920011 -25 CTAATAATAAAATTTATATAAG 11 2 1 TATAATAAAA 0.920022 -79 GGTCTTTCAAAATTAATAAAATTTACTTATG 13 15 0 AATAATAAAA 0.800971 -52 AAACAGAGGTTGATAATGAATCATTAACTTA 14 180 1 TGTAATGAAT 0.839606 -121 ** ******** Masking position 5 Map Score: 15.5046 Number of sites scoring better than the average of aligned sites = 378 Number in coding regions = 266 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 7 ACCATTTTATTATTTTATTTTAGGTTGTTA 1 193 1 TATTTTATTT 0.807343 -108 ACCTTTTATATAGTTTTGTTTTAATAAAGT 3 18 0 TAGTTTTGTT 0.764389 -108 AGTTTAAAAATAGTTTAGTTAATTTCTATT 4 11 1 TAGTTTAGTT 0.958431 -50 ATACGGTTGTTAGTTGAGTAAAAAGCTCCA 6 71 1 TAGTTGAGTA 0.766578 -230 GTTGGAGGAGTAGTTTATTTTGGAGTTTAT 6 191 1 TAGTTTATTT 0.955117 -110 GTTTATTTTGGAGTTTATTTAGCTGTAATT 6 203 1 GAGTTTATTT 0.901485 -98 TAAATCCCCTGAGTTTATTTATTAATAATT 6 280 0 GAGTTTATTT 0.901485 -21 CACATTCAAATAATTTATTACTATTATGTT 9 122 0 TAATTTATTA 0.617793 -25 TATCACCTTATATTTTATTAGTATCTTTCA 10 279 0 TATTTTATTA 0.741033 -22 ATTATTTGGATAGTTTAGTATGTTTGATAT 11 36 0 TAGTTTAGTA 0.940276 -45 ********** Masking position 5 Map Score: 5.67918 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 83 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 GCTTTCCATTTCATCAAAATAGGATGCATT 1 39 0 TCATCAAAAT 0.958094 -262 GTCACCAAAAATTTATTGTCA 2 2 1 TCACCAAAAA 0.926506 -87 GTTAACGACTTCACCCAATTGTAGAACATT 6 102 0 TCACCCAATT 0.75026 -199 TTTATCACCAAATTGGCATTTTTA 7 287 0 TCACCAAATT 0.841401 -14 ATTATGATTATCCTCCAAATTTATTGAAGT 10 16 0 TCCTCCAAAT 0.923709 -285 AGTAAAAGGTTCATCAAAAATCTAACACCT 10 226 0 TCATCAAAAA 0.93094 -75 AAAAATCCCCTAAAAATTAAAATTA 12 15 0 TCCCCTAAAA 0.860811 -15 CATTAATTCCTCCTCAAAATCAATATTAAG 14 117 0 TCCTCAAAAT 0.95532 -184 ATCAACATAGTCCTCTAAAATTATAAAACA 14 224 0 TCCTCTAAAA 0.868645 -77 ATCTAAATAATCATCAACATAGTCCTCTAA 14 236 0 TCATCAACAT 0.811519 -65 TTCATCACCCTCATCTAAATAATCATCAAC 14 248 0 TCATCTAAAT 0.923036 -53 ********** Masking position 7 Map Score: 10.6641 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 354 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 9 AGCTATGAAAACTCTTTTAGTTTTCATTTA 1 79 1 ACTCTTTTAG 0.967729 -222 AGTTAAACAAAATCTTTCAGATTTTGTAGC 1 128 0 AATCTTTCAG 0.890422 -173 GATACAAACGAAACTTTTAGAAAAAGTTAA 1 152 0 AAACTTTTAG 0.942519 -149 ACAATTAAAAACTTTTTTAGATAACTTACT 2 50 0 ACTTTTTTAG 0.770045 -39 TAATTAGCTTAACCTTTTATATAGTTTTGT 3 29 0 AACCTTTTAT 0.739062 -97 AATCCCACCAATCTTTTAGTTTTTAATAT 8 70 0 AATCTTTTAG 0.968348 -19 ATTTTGAAAGAACCTTTTAGTAAAAGGTTC 10 244 0 AACCTTTTAG 0.962069 -57 ATTATTTTAGACACTTTTAGAGATGAGGCT 14 54 1 ACACTTTTAG 0.941425 -247 ********** Masking position 9 Map Score: 7.49259 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 94 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 10 CAAAATCTTTCAGATTTTGTAGCCCGAAGC 1 121 0 CAGATTTTGT 0.372151 -180 CAAAATCTGAAAGATTTTGTTTAACTTTTT 1 132 1 AAGATTTTGT 0.832749 -169 CTGTTAAGTTAAGATTTAAAAAATAAATAC 1 264 0 AAGATTTAAA 0.609803 -37 GTCACCAAAAATTTATTGTCAATTTA 2 7 1 AAAAATTTAT 0.685991 -82 TTATCTAAAAAAGTTTTTAATTGTAATTTT 2 56 1 AAGTTTTTAA 0.455061 -33 CTTACGATTTTATAAAATTACAA 2 76 0 ACGATTTTAT 0.605605 -13 ATTTCTTTTAAAGATTTTATTCCTGCGAAA 7 12 1 AAGATTTTAT 0.931926 -289 AAATTTTATAAAGATTATTAATAAAGTTAA 7 48 0 AAGATTATTA 0.23327 -253 AAAAATAATAAAAATTTTATAAAGATTATT 7 59 0 AAAATTTTAT 0.732701 -242 ACTCGCATTAAAGATTTAATACAAAACAAT 7 117 1 AAGATTTAAT 0.65974 -184 AGCATTTTAAAAGAATATATGGGTAGTAAT 7 247 0 AAGAATATAT 0.768697 -54 ATTACCACCAAAAAATTTATATGCTTTCTA 8 11 1 AAAAATTTAT 0.685991 -78 ATTTTGAATTAAAAATTTAAAAATTGAAA 9 10 0 AAAAATTTAA 0.640399 -137 AATATAAAATAAGAATATAAAAATATAAGT 9 43 0 AAGAATATAA 0.728166 -104 ATATCAGAATAAGAATATAAAATAAGAATA 9 56 0 AAGAATATAA 0.728166 -91 TTCACATTCAAATAATTTATTACTATTATG 9 124 0 AATAATTTAT 0.401595 -23 CACCACAAAAAAGAATTTGAATTATTTGGA 11 56 0 AAGAATTTGA 0.763856 -25 TGTTAAAAAAGAGATTTTAAAGTTCCCAAA 14 151 1 GAGATTTTAA 0.567765 -150 ********** Masking position 6 Map Score: 5.73489 Number of sites scoring better than the average of aligned sites = 1488 Number in coding regions = 1260 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 11 AGGCATTGCCGAGCGTAGCGAGGCAATGCA 1 15 1 GAGCGTAGCG 0.926994 -286 CATAGCTGGAAAGCGTAGCTTTCCATTTCA 1 56 0 AAGCGTAGCT 0.918415 -245 GTTTTCATTTAACCGAAGCGTTAGCTTCGG 1 98 1 AACCGAAGCG 0.977034 -203 CTCAACTAACAACCGTATCGAATTTACTAT 6 59 0 AACCGTATCG 0.926927 -242 TTTAATACAAAACAATAGCGAAATTTTTAT 7 131 1 AACAATAGCG 0.859978 -170 TTATTCCAGAAACCATAGGGCTTCGCCTAT 10 149 1 AACCATAGGG 0.901017 -152 TCAATATCAAAACCAAAGCTTATAGCCTCA 14 77 0 AACCAAAGCT 0.848923 -224 ********** Masking position 7 Map Score: 0.779896 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 17 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 12 AGTTTCGTTTGTATCCCTCCCTCGGCACCA 1 167 1 GTATCCCTCC 0.839068 -134 CCAAAATAAACTACTCCTCCAACAATTAAT 6 184 0 CTACTCCTCC 0.925128 -117 AGGCATTAATGAACACCTCCCTATAGGAGA 10 116 0 GAACACCTCC 0.98222 -185 TCCTTCTGAGTTGCACCTCCGAGCGTAAGC 10 192 1 TTGCACCTCC 0.940287 -109 ATCAAAAATCTAACACCTCCTCGCTTACGC 10 214 0 TAACACCTCC 0.985215 -87 ACAGCTCCATTAATTCCTCCTCAAAATCAA 14 124 0 TAATTCCTCC 0.906916 -177 ATCTCTTTTTTAACAGCTCCATTAATTCCT 14 136 0 TAACAGCTCC 0.927593 -165 ********** Masking position 8 Map Score: 2.13773 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 120 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 AAGCTAATTATCATTATTAATTATGATAAA 3 49 1 TCATTATTAA 0.861923 -77 CTTATAATTTTCGTTATCAATACCAGAGGC 6 138 0 TCGTTATCAA 0.812947 -163 ATTATGTTTTTAAATATCAATAAAATTAAA 9 100 0 TAAATATCAA 0.70683 -47 ATATCCATTATTAATATTAATTTTAACAAC 10 78 0 TTAATATTAA 0.484387 -223 TTTATATAAGTTGATATCAAACATACTAAA 11 23 1 TTGATATCAA 0.471584 -58 CCCCTAAAAATTAAAATTAATAA 12 4 0 TTAAAATTAA 0.507354 -26 AGTAGGTCTTTCAAAATTAATAAAATTTAC 13 20 0 TCAAAATTAA 0.794718 -47 AGATAGTTCTTCAATATCAAAACCAAAGCT 14 87 0 TCAATATCAA 0.906386 -214 CTCCTCAAAATCAATATTAAGAGATAGTTC 14 108 0 TCAATATTAA 0.832823 -193 AGTTAATGATTCATTATCAACCTCTGTTTT 14 179 0 TCATTATCAA 0.909586 -122 ********** Masking position 6 Map Score: 6.65663 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 184 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 ********** No masking Map Score: -6.1574e-13 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: -6.1574e-13 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