AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_aful_reg_300.orf -o00010_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: AF1131 75 DNA-directed RNA polymerase, subunit K (rpoK) Input sequences: #1 AF0025 300 cyanate transport protein (cynX) #2 AF0818 102 acylphosphatase (acyP) #3 AF1127 213 LSU ribosomal protein L18E (rpl18E) #4 AF1132 108 enolase (eno) #5 AF1146 65 3-phosphoglycerate kinase (pgk) #6 AF1305 72 D-arabino 3-hexulose 6-phosphate formaldehyde lyase (hps-2) #7 AF1306 77 conserved hypothetical protein #8 AF2009 101 heme biosynthesis protein (nirJ-2) #9 AF2010 46 A. fulgidus predicted coding region AF2010 #10 AF2011 175 conserved hypothetical protein #11 AF2013 275 coenzyme F390 synthetase (ftsA-3) #12 AF2014 63 sugar transporter, putative #13 AF2100 106 acetolactate synthase, large subunit (ilvB-4) Motif number 1 AACGAATTGAAATCATATAAATAGTTTGCCTGC 2 23 0 AATATAAATA 0.631311 -80 CCGCGGAAGGAACATTAAAAATTAACATGCGGC 3 37 1 AATAAAAATT 0.869726 -177 AACATGCGGCAAAGATTTAAATTACGTAATGTA 3 60 1 AATTTAAATT 0.960235 -154 AAACTTTCTGAAAATTTTAATTTACCTGCTCAG 5 20 0 AATTTAATTT 0.856751 -46 AATTTTCAGAAAGTTTTTAATTTCACCTTCCGA 5 37 1 AATTTAATTT 0.854668 -29 TTAACGAAAAAAAATTTTAAAATGGCGGTTGTA 7 47 1 AATTTAAAAT 0.936631 -31 TTTAGTTCCAAAAGGTTAAATATCTGGATGCAC 8 23 0 AATTAAATAT 0.633164 -79 ACATGCTAACAAAAATAAAAATTTTACTATTTA 9 15 0 AATAAAAATT 0.873179 -32 TCTTTACTTCAAGTGTAAAAATTGAGTGCCCCA 10 78 0 AATAAAAATT 0.869726 -98 TTTCGATGTGAAGGTTATAAAACTTATTATTAA 10 143 0 AATATAAAAC 0.806342 -33 TTTGCAGCAAAAGGCTTTAAAAGCCACTGCCTT 11 183 0 AATTTAAAAG 0.717344 -93 CAGGATGGTGAAGTATTTAAATCCTGCCTCCCT 11 229 1 AATTTAAATC 0.917462 -47 AAAGAATTAAAAAGCTAAAAATTTTATGCAAAT 12 33 0 AATAAAAATT 0.873179 -31 TTAGCTTTTTAATTCTTTAAATTTCC 12 48 1 AATTTAAATT 0.957851 -16 GTCAGGCTGCAAGAGTTTAAAACCCATCGAATA 13 37 0 AATTTAAAAC 0.871847 -70 AACCTTAGCAAACTTTTTAAAATTATAATCATA 13 76 1 AATTTAAAAT 0.936588 -31 ** ******** Masking position 6 Map Score: 16.1919 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 46 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 2 GGCCAAAAGTTCAGGCATTCTTCGGAAATGA 1 191 1 TCAGGCATCT 0.975633 -110 CAATTGCTATGCAGGCAAACTATTTATATGA 2 13 1 GCAGGCAACT 0.984498 -90 CTTATATACCGCAGGCAAAAGGTGGGGTT 2 84 1 GCAGGCAAAG 0.975362 -19 AGATAAGGAAGCTGGCAGAGGAGGAAGTCAA 3 131 1 GCTGGCAAGG 0.939921 -83 TAGGAACAATTCAGGCGTAATGAATAAATAT 8 67 1 TCAGGCGAAT 0.871187 -35 GTTATGTAGCTCAGGCACTGGGGCACTCAAT 10 60 1 TCAGGCATGG 0.96421 -116 GGATAAAGGAGCAGGCAGTCTTGTCGTAAGC 10 112 1 GCAGGCATCT 0.984498 -64 TCAGACAGTATCTGGCAGTATTAAAAAACGG 11 45 1 TCTGGCATAT 0.903117 -231 ******* *** Masking position 6 Map Score: 6.566 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 100 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 GCAGTCCGACAATAAAAAAGATATACTGCT 1 76 0 AATAAAAAAG 0.903402 -225 AATCTATCTTTATCAAAAAGCGGTTTTTAT 1 230 0 TATCAAAAAG 0.958613 -71 CGGAAGGTGAAATTAAAAACTTTCTGAAAA 5 39 0 AATTAAAAAC 0.855393 -27 TATTAGCGTAAATCAAAAAGTCCTTC 7 7 0 AATCAAAAAG 0.973793 -71 TATCTGGCAGTATTAAAAAACGGTTTTCCC 11 53 1 TATTAAAAAA 0.713275 -223 AAATTTAAAGAATTAAAAAGCTAAAAATTT 12 42 0 AATTAAAAAG 0.968523 -22 GAATACGATTAATCAAAAAGAATAAATAAT 13 12 0 AATCAAAAAG 0.973793 -95 ATGATTATAATTTTAAAAAGTTTGCTAAGG 13 78 0 TTTTAAAAAG 0.774589 -29 ********** Masking position 5 Map Score: 6.93074 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 56 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 ATGGTAGTGGTCATTTCCGAAGAATGCCTGA 1 201 0 TCATTCCGAA 0.958704 -100 ATGATTTCAATTCGTTCGAAAATATTCATAC 2 40 1 TTCTTCGAAA 0.791805 -63 CTCATATCGAAATCGTTTTTAG 3 2 1 TCAATCGAAA 0.972068 -212 GAGGAGGAAGTCAAATCCAAACCTCGTTACT 3 148 1 TCAATCCAAA 0.96363 -66 TTCAATTCGGAAGGTGAAATTA 5 54 0 TCATTCGGAA 0.968247 -12 TATGAACTATTTAGTTCCAAAAGGTTAAATA 8 34 0 TTATTCCAAA 0.903949 -68 TTTATAACCTTCACATCGAAATTCATACCTA 10 155 1 TCAATCGAAA 0.972068 -21 *** ******* Masking position 10 Map Score: 4.17734 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 52 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 TCCAAGCTTTCCGAGGTACTCCGTTACATCTT 1 9 1 TCCGGACTCC 0.83851 -292 TAACTAATTATGTTGACAAGTTCCATCGAAGATG 1 37 0 TTTGCGTTCC 0.742843 -264 ATATCTTTTTTATTGTCGGACTGCGGTTTTATTT 1 82 1 TTTGCACTGC 0.933365 -219 TGATAAAAGTTATTGACTTACTGAAGTTAAATCT 1 255 0 TTTGCACTGA 0.882826 -46 CGAGGTTTGGATTTGACTTCCTCCTCTGCCAGCT 3 140 0 ATTGCCCTCC 0.970616 -74 CCTCATTTTTTGCTGACTCGCTCAGCAGTACATC 3 185 0 TCTGCGCTCA 0.922534 -29 CGCCGAATTGATTTGCCAAACTCAATTTTCCT 6 9 0 ATTGCACTCA 0.91764 -64 TGGCAAATCAATTCGGCGAACTCCAAAAAATTTA 6 25 1 ATCGCACTCC 0.93831 -48 TGTTCAAATCTATCGGGCCCCTCCCTTAATC 10 8 0 TTCGGCCTCC 0.942536 -168 CAAGTGTAAAAATTGAGTGCCCCAGTGCCTGAGC 10 68 0 ATTGGCCCCA 0.637324 -108 CGAGTTCAAATCTCGGCGGCCCCATCATTGAACT 11 86 0 TTCGCCCCCA 0.899023 -190 AGTATTTAAATCCTGCCTCCCTCATGACAGAAAG 11 240 1 TCTGCCCTCA 0.950921 -36 CTAAGGTTGATTTTGTCAGGCTGCAAGAGTTTAA 13 50 0 TTTGCGCTGC 0.932109 -57 * *** * ***** Masking position 5 Map Score: 7.22572 Number of sites scoring better than the average of aligned sites = 1083 Number in coding regions = 1040 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 AAAAAAGATATACTGCTGAGTGTAACTAAT 1 63 0 TACTGCTGAG 0.959735 -238 TCATATCAACTACACCTCAGCGTAGTTTTG 3 98 0 TACACCTCAG 0.936956 -116 AGCTTCCTTATCTTGCTCATATCAACTACA 3 114 0 TCTTGCTCAT 0.730203 -100 GGATTTGACTTCCTCCTCTGCCAGCTTCCT 3 136 0 TCCTCCTCTG 0.870439 -78 CTCATCGATGTACTGCTGAGCGAGTCAGCA 3 179 1 TACTGCTGAG 0.959735 -35 ATTTTAATTTACCTGCTCAGAATTGGTTC 5 10 0 ACCTGCTCAG 0.949973 -56 ATGAAGGTTATGTAGCTCAGGCACTGGGGC 10 54 1 TGTAGCTCAG 0.912064 -122 TTTCTGGAACTGCAGCTCAGACAGTATCTG 11 29 1 TGCAGCTCAG 0.978421 -247 ********** Masking position 7 Map Score: 3.09441 Number of sites scoring better than the average of aligned sites = 586 Number in coding regions = 548 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 TGCTGAGTGTAACTAATTATGTTGACAAGT 1 50 0 AACTAATTAT 0.867598 -251 AGGATTTAAAAACAAATTAGATTGCACATA 1 130 1 AACAAATTAG 0.806288 -171 TATGCAGGCAAACTATTTATATGATTTCAA 2 20 1 AACTATTTAT 0.942697 -83 ATTCGTTCGAAAATATTCATACAAAAGAAT 2 49 1 AAATATTCAT 0.609984 -54 GCGAACTCCAAAAAATTTATTACATATCCG 6 40 1 AAAAATTTAT 0.618029 -33 CCTATGTATGAACTATTTAGTTCCAAAAGG 8 41 0 AACTATTTAG 0.963283 -61 CATACATAGGAACAATTCAGGCGTAATGAA 8 61 1 AACAATTCAG 0.800424 -41 ATAAAAATTTTACTATTTAGGCC 9 4 0 TACTATTTAG 0.769237 -43 AAGGTTATAAAACTTATTATTAAGCTTACG 10 136 0 AACTTATTAT 0.722998 -40 TATTTGCATAAAATTTTTAGCTTTTTAATT 12 32 1 AAATTTTTAG 0.72133 -32 AACCTTAGCAAACTTTTTAAAATTATAATC 13 76 1 AACTTTTTAA 0.617825 -31 ********** Masking position 2 Map Score: 3.29962 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 37 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 GGAGTACCTCGGAAAGCTTGGA 1 3 0 GGAAAGCTTG 0.809602 -298 GAGCAAGATAAGGAAGCTGGCAGAGGAGGA 3 126 1 AGGAAGCTGG 0.844409 -88 GGTGGTAGCTTGATAATTGAGG 4 3 1 TGGTAGCTTG 0.947039 -106 AGTCGTTGCTGGGGAGGTTGTTGCGAAGGC 4 88 1 GGGGAGGTTG 0.961647 -21 CCAGAAAAGCTGACAGGTTGATTCT 11 6 0 TGACAGGTTG 0.737319 -270 CTCTCGGCTTTGGGAGCCGGTGACCCGAGT 11 115 0 TGGGAGCCGG 0.967076 -161 AGGGGCCGTAGGGTAGCCTGGTGATCCTCT 11 141 0 GGGTAGCCTG 0.965279 -135 TTCTGTCATGAGGGAGGCAGGATTTAAATA 11 242 0 AGGGAGGCAG 0.748391 -34 TTTTAAACTCTTGCAGCCTGACAAAATCAA 13 48 1 TTGCAGCCTG 0.777336 -59 ********** Masking position 5 Map Score: 0.820103 Number of sites scoring better than the average of aligned sites = 916 Number in coding regions = 864 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 TTGACAAGTTCCATCGAAGATGTAACGGAG 1 29 0 CCATCGAAGA 0.968458 -272 GCTCAGCAGTACATCGATGAGAGTAACGAG 3 170 0 ACATCGATGA 0.794953 -44 ATAGATTTGAACATCGAGGAGACGGATGAA 10 29 1 ACATCGAGGA 0.958327 -147 AGTTTAAAACCCATCGAATACGATTAATCA 13 27 0 CCATCGAATA 0.950938 -80 ********** Masking position 4 Map Score: 0.796362 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 64 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 10 TTCCATCGAAGATGTAACGGAGTACCTCGG 1 21 0 GATGTAACGG 0.978867 -280 TAAATTACGTAATGTAACGGTCAAAACTAC 3 77 1 AATGTAACGG 0.953613 -137 CAGCAGGGGAAACGAGACGGTTGAGTGTGA 4 58 1 AACGAGACGG 0.949903 -51 TTTGAACATCGAGGAGACGGATGAAGGTTA 10 34 1 GAGGAGACGG 0.977128 -142 TATGAATTTCGATGTGAAGGTTATAAAACT 10 152 0 GATGTGAAGG 0.952377 -24 ********** Masking position 7 Map Score: 0.307643 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 69 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 AACCCCACCTTTTGCCTGCGG 2 92 0 AACCCCACCT 0.897813 -11 TGGCGCCTCATTTTTTGCTGAC 3 202 0 GGCGCCTCAT 0.960797 -12 AAATCTATCGGGCCCCTCCCTTAATC 10 6 0 GGCCCCTCCT 0.997092 -170 AAATCTCGGCGGCCCCATCATTGAACTGGCG 11 82 0 GGCCCCATCT 0.978655 -194 GCTACCCTACGGCCCCTCTGTAATGATTAAA 11 154 1 GGCCCCTCTT 0.988544 -122 ********* * Masking position 11 Map Score: 0.390733 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 53 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 12 ********** No masking Map Score: 9.40348e-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 13 ********** No masking Map Score: 9.40348e-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 14 ********** No masking Map Score: 9.40348e-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