AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -ifadR_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 MTH657 96 long-chain-fatty-acid-CoA ligase #2 MTH659 216 epoxidase #3 MTH1343 218 imidazoleglycerol-phosphate synthase (cyclase) Motif number 1 AAGCCTATACCTCCCGAGATAAGGAAGCAG 1 30 1 CTCCCGAGAT 0.970375 -67 AATCCATTACCCCCTCAGATATTACATGGA 2 15 1 CCCCTCAGAT 0.972482 -202 GGTTCAAATCCCCCCGGGTCCGCTTTTTTA 3 25 0 CCCCCGGGTC 0.989209 -194 GGGATTTGAACCCCCGACCTTGGGATCCGA 3 43 1 CCCCCGACCT 0.987467 -176 AGACTACGGGCCCCCTACACACATCTCTAT 3 96 1 CCCCCTACAC 0.982082 -123 TGTCTGCTGTCCCCTGAGTCTGGTCTTCGG 3 167 0 CCCCTGAGTC 0.993388 -52 ATACTAAATGCCCCTTAATTAATAAAT 3 202 1 CCCCTTAATT 0.889587 -17 ********** Masking position 4 Map Score: 7.1502 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 361 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 TATGTCAATGTTCACATCCCTGCAGAGATGCAACC 2 47 0 TTAATCTGCG 0.98361 -170 GATGTGAACATTGACATATTTTCAGATAACCGGAG 2 64 1 TTAATATTCG 0.981955 -153 AAAATTGCTGTTTAAAAATGTGCAGAGCATCAGCA 2 136 0 TTAAAATGCG 0.993944 -81 AAATCTCAGTTTAAAAAAATTGCTGTTTAAAAATG 2 151 0 TTAAAATGCG 0.993944 -66 TAAAAAGCAGTTAATAAAAAAGCGGACCCGGGGGG 3 11 1 TTAAAAAGCG 0.975899 -208 AAGTTAACCATTTAAATATTTTCTCATCAACGTGT 3 129 1 TTAATATTCC 0.927086 -90 ** * *** *** * Masking position 6 Map Score: 4.04649 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 36 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 GCTTCTTTCTCTGCTCTATGAAG 1 3 0 CTGCTTATGA 0.982638 -94 GATAAGGAAGCAGCTTGAGGAGCACCTCGTG 1 47 1 CAGCTGAGGA 0.982657 -50 TGAGGAGCACCTCGTGGAGGAAGATTAACTT 1 62 1 CTCGTGAGGA 0.990629 -35 GTTAAGTAATCTCCTAAATGATCTCCGGTTA 2 90 0 CTCCTAATGA 0.969784 -127 GTAGTCTAGCCTGGAATATGACGTGGGACTT 3 72 0 CTGGATATGA 0.933166 -147 CTTCGGCTGACACGTTGATGAGAAAATATTT 3 142 0 CACGTGATGA 0.985579 -77 ***** ***** Masking position 8 Map Score: 3.44588 Number of sites scoring better than the average of aligned sites = 376 Number in coding regions = 361 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 CGTGGAGGAAGATTAACTTATAAGGGTGGATTT 1 74 1 GATACTTTAG 0.939859 -23 AATGATCTCCGGTTATCTGAAAATATGTCAATGT 2 71 0 GGTACTGAAT 0.992546 -146 GCATATGCATGACGAACTGTTAAGTAATCTCCTA 2 105 0 GACACTGTAG 0.908521 -112 TGCATATGCTGATGCTCTGCACATTTTTAAACAG 2 130 1 GATCCTGAAT 0.971368 -87 TTAACATTATGGTAAGCTGTATCTATTATCTAAA 2 184 0 GGTACTGACT 0.976173 -33 GTGATCACCTTAACATTATGGTAAGC 2 201 0 GATACTTAAT 0.981612 -16 ATATTTAAATGGTTAACTTTAAATAGAGATGTGT 3 114 0 GGTACTTAAT 0.984723 -105 *** * *** * ** Masking position 8 Map Score: 3.3178 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 118 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TTTCAGATAACCGGAGATCATTTAGGAGAT 2 83 1 CCGGAGATCA 0.980588 -134 ACCTTGGGATCCGAAGTCCCACGTCATATT 3 59 1 CCGAAGTCCC 0.992902 -160 TGTAGGGGGCCCGTAGTCTAGCCTGGAATA 3 85 0 CCGTAGTCTA 0.971487 -134 AACGTGTCAGCCGAAGACCAGACTCAGGGG 3 157 1 CCGAAGACCA 0.995824 -62 ********** Masking position 5 Map Score: 2.4188 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 76 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 6 CATAGAGCAGAGAAAGAAGCCTATACCTCCC 1 14 1 AGAAAGAAGC 0.955172 -83 TCCCGAGATAAGGAAGCAGCTTGAGGAGCAC 1 41 1 AGGAAGCAGT 0.969722 -56 GCACATTTTTAAACAGCAATTTTTTTAAACT 2 148 1 AAACAGCAAT 0.877215 -69 TAAAAAGCAGTTAATAAAAAAG 3 2 1 AAAAAGCAGT 0.982365 -217 GCAGTTAATAAAAAAGCGGACCCGGGGGGAT 3 17 1 AAAAAGCGGC 0.969722 -202 CAGACTCAGGGGACAGCAGACAGCTTTATAC 3 175 1 GGACAGCAGC 0.976609 -44 ********* * Masking position 5 Map Score: 1.30217 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 179 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 ********** No masking Map Score: 1.50878e-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 8 ********** No masking Map Score: 1.50878e-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 9 ********** No masking Map Score: 1.50878e-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