AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -inarL_mthe_opreg_100.orf -g0.495 -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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH170 141 phosphoribosylaminoimidazolesuccinocarboxamide synthase #2 MTH420 300 conserved protein #3 MTH1354 124 NADH oxidase #4 MTH1502 189 succinate dehydrogenase, flavoprotein subunit #5 MTH1567 235 catalytic subunit of nitrate reductase (flp) #6 MTH1850 105 fumarate reductase Motif number 1 TATATTGCGATTCAGTTATATAATCTTGCG 1 42 0 TTCAGTTATA 0.819246 -100 AAATTCTATTATGAGTTATATTGCGATTCA 1 58 0 ATGAGTTATA 0.78358 -84 TCATACTCAAATTCTTTAAAAGTGATAGT 1 123 1 ATTCTTTAAA 0.84635 -19 AGCATAGATTTTTGGTTAAATGCTGCATAT 2 128 0 TTTGGTTAAA 0.912054 -173 ATATATCTGAATTATTTATAAAATGAAGAA 3 67 1 ATTATTTATA 0.744552 -58 CCTAGGAGTTATCGGTTATAGGTCTCTTCT 3 93 0 ATCGGTTATA 0.942571 -32 TTTGAAATACGTTAAAATACCTGTAG 5 7 1 ATACGTTAAA 0.821959 -229 TAATAAGGATATTCCTTAAATAAGGAAATT 5 65 1 ATTCCTTAAA 0.763653 -171 CTATCTTCAGATCGGTTAAAGATTTCAGTA 5 180 0 ATCGGTTAAA 0.969367 -56 CATCCAGGTATTTAGTTAAATTAATTGAAC 5 209 0 TTTAGTTAAA 0.885548 -27 ATGTCTGTATTGTTTAAAAGATTATCAG 6 9 1 ATTGTTTAAA 0.878567 -97 TTAAAAGATTATCAGTTAAAATCACAAACC 6 24 1 ATCAGTTAAA 0.960904 -82 ********** Masking position 8 Map Score: 9.39158 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 53 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 ATCAGATTCATGCTTCTTAGGGTGAAATA 1 2 0 TGTCTTAAAT 0.921871 -140 GGATTGCCGGTGCTGCACCCGGAGAAATCAACCACAAA 2 23 0 TGTCAAAAAT 0.967242 -278 ACACACTCCGGGCTGCAGACTGACAGATAAATCCATGA 2 75 1 GGTCAAAGAT 0.945256 -226 CATATTTCGGTGTCCCTGTATCATGGATTTATCTGTCA 2 95 0 TGCCTAGGAT 0.746637 -206 ATCCATTCCCTGATACTGAAGGACAGATAATCACATCC 2 242 0 TGTCTAAGAT 0.96724 -59 GTTTGATGCTCCCTTATAACTACCACACAGA 3 4 1 TGTCTAAACT 0.972384 -121 TTATAAATTTGGATACATCAATAGATCTGTGTGGTAGT 3 29 0 GGTCAAATCT 0.786804 -96 ATCAGGCGACTGATCCTGATTGAAGGCTTAAATCCATA 4 41 1 TGTCTAGGCT 0.927991 -149 GACCGGGTGATGGTTCATCACCTGAGCTTGACTTTATT 4 109 1 TGTCATAGCT 0.956288 -81 TTCTCGGTTATGGTTCATCACCTTAACTATTGACTGCC 4 145 1 TGTCATAACT 0.949712 -45 CTGTAGATGGGGATACTCTTATAAAAATTGAATTTAAT 5 31 1 GGTCTAAAAT 0.927885 -205 AATGATAATGTGGTGCAACTCATAAAATTAGATGAATC 5 117 1 TGTCATAAAT 0.93183 -119 GCTGACTCATATGAAAAACTTCAGAATGAA 6 86 0 TGCCAAAACT 0.927995 -20 ** * ** * **** Masking position 18 Map Score: 12.0383 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 89 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 ATAGAATTTACACCTATATAAGTATTGGAGAGTTGAT 1 79 1 CTAAAAGTAG 0.883804 -63 AGTGTGTCCCCTCTGATACGGGGATTGCCGGTGCTGC 2 45 0 CGAAGGGGAG 0.996657 -256 ACAGATAAATCCATGATACAGGGACACCGAAATATGC 2 97 1 CGAAAGGGAC 0.98602 -204 AACACTGCAGCACTGATATGAGTAAAGGCAATAAAGC 2 163 1 CGAAGAGTAG 0.967615 -138 GACCAGAGATCTATGGTAAAGGGAAGGTAAGGATGTG 2 212 1 CGGAAGGGAG 0.981851 -89 AATCCATTCCCTGATACTGAAGGACAGATAATCACAT 2 244 0 CTATAAGGAG 0.858939 -57 GGATTGCTGGCGCAGACAGAAGGGCTGTTTTACTG 2 276 1 CGAAAAGGGG 0.964957 -25 CCGATAACTCCTAGGAGAAGGGGATAG 3 108 1 CGAAGGGGAG 0.996657 -17 CGTTAAAATACCTGTAGATGGGGATACTCTTATAAAA 5 20 1 CTAAGGGGAC 0.96749 -216 * ** * ***** * Masking position 1 Map Score: 7.61283 Number of sites scoring better than the average of aligned sites = 307 Number in coding regions = 285 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 ATTTCTCCGGGTGCAGCACCGGCAATCCCC 2 33 1 GTGCAGCACC 0.992464 -268 GCTTAAATCCATACATCACCCTCAGATTAG 4 66 1 ATACATCACC 0.956807 -124 TAGAACGTCCGTAGAGGACCGGGTGATGGT 4 93 1 GTAGAGGACC 0.935833 -97 CCGGGTGATGGTTCATCACCTGAGCTTGAC 4 111 1 GTTCATCACC 0.980564 -79 CTCGGTTATGGTTCATCACCTTAACTATTG 4 147 1 GTTCATCACC 0.980564 -43 AAAGATTTCAGTACAGTACCTTGCCACATA 5 163 0 GTACAGTACC 0.977352 -73 ********** Masking position 5 Map Score: 6.3924 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 49 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 GTGTAAATTCTATTATGAGTTATATTGCGA 1 62 0 TATTATGAGT 0.961026 -80 CACTTTTAAAGAATTTGAGTATGAAATCCT 1 117 0 GAATTTGAGT 0.829945 -25 TTGCCTTTACTCATATCAGTGCTGCAGTGT 2 164 0 TCATATCAGT 0.94239 -137 GTAAGGATGTGATTATCTGTCCTTCAGTAT 2 238 1 GATTATCTGT 0.767635 -63 AATTCAATTTTTATAAGAGTATCCCCATCT 5 35 0 TTATAAGAGT 0.6015 -201 CATTATCATTTCTTTTCAGTCTTATCCCAT 5 97 0 TCTTTTCAGT 0.819747 -139 ATTCATCTAATTTTATGAGTTGCACCACAT 5 124 0 TTTTATGAGT 0.914728 -112 TTGTTTAAAAGATTATCAGTTAAAATCACA 6 20 1 GATTATCAGT 0.922386 -86 TCACAAACCTTAATATGTGTTGATAAACAA 6 45 1 TAATATGTGT 0.872685 -61 CTGAAGTTTTTCATATGAGTCAGC 6 92 1 TCATATGAGT 0.960262 -14 ********** Masking position 4 Map Score: 6.80365 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 167 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 CACCGGCAATCCCCGTATCAGAGGGGACACA 2 49 1 CCCGTATCAG 0.990148 -252 ATTTCGGTGTCCCTGTATCATGGATTTATCT 2 99 0 CCCGTATCAT 0.991819 -202 AGCATATTAACCCGGGACCAGAGATCTATGG 2 197 1 CCCGGACCAG 0.98573 -104 TCCTTACCTTCCCTTTACCATAGATCTCTGG 2 214 0 CCCTTACCAT 0.984596 -87 ACAGAACCCCCAGTGATCATTATCGAATAA 4 10 1 CCATGATCAT 0.908158 -180 TGAGTTGCACCACATTATCATTTCTTTTCAG 5 108 0 CACTTATCAT 0.922645 -128 *** ******* Masking position 7 Map Score: 3.90596 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 118 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 TACACCTATATAAGTATTGGAGAGTTGATC 1 87 1 TAAGTATTGG 0.913619 -55 TCTATTTAAGTTTTTGTGGTTGATTT 2 7 1 TAAGTTTTTG 0.919382 -294 AAAGGGAAGGTAAGGATGTGATTATCTGTC 2 229 1 TAAGGATGTG 0.935331 -72 AGTCAATAGTTAAGGTGATGAACCATAACC 4 150 0 TAAGGTGATG 0.873329 -40 TCATTATTATAAGGTTTGGCAGTCAATAG 4 171 0 TAAGGTTTGG 0.980577 -19 TTGAATTTAATAAGGATATTCCTTAAATAA 5 58 1 TAAGGATATT 0.824383 -178 CAACACATATTAAGGTTTGTGATTTTAACT 6 37 0 TAAGGTTTGT 0.932305 -69 ********** Masking position 3 Map Score: 2.31395 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 69 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 TATTTCACCCTAAGAAGCATGAATCT 1 6 1 CACCCTAGAA 0.994604 -136 GCCGGTGCTGCACCCGGAGAAATCAACCACA 2 25 0 CACCCGAGAA 0.99083 -276 GTTTGATGCTCCCTTATAACTACCACACA 3 9 1 CTCCCTATAA 0.948356 -116 ATCCATACATCACCCTCAGATTAGAACGTCC 4 72 1 CACCCTAGAT 0.986479 -118 ****** **** Masking position 8 Map Score: 1.41812 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 32 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 CCTAAGAAGCATGAATCTGATTTCGCAAGA 1 19 1 ATGAATCTGA 0.982374 -123 TCGCAAGATTATATAACTGAATCGCAATAT 1 41 1 ATATAACTGA 0.806517 -101 ATCACTTTTAAAGAATTTGAGTATGAAATC 1 119 0 AAGAATTTGA 0.759414 -23 AGATATATTTATAAATTTGGATACATCAAT 3 45 0 ATAAATTTGG 0.894394 -80 AAATTTATAAATATATCTGAATTATTTATA 3 57 1 ATATATCTGA 0.952558 -68 TCATTATCGAATAAATCAGGCGACTGATCC 4 27 1 ATAAATCAGG 0.865732 -163 ATAAAATTAGATGAATCTGACTGTATATGT 5 138 1 ATGAATCTGA 0.982374 -98 ********** Masking position 5 Map Score: 2.60587 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 93 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 10 ********** No masking Map Score: -3.17312e-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 11 ********** No masking Map Score: -3.17312e-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 12 ********** No masking Map Score: -3.17312e-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