AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_hpyl_reg_100.orf -o00640_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -0.39 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HP0371 123 biotin carboxyl carrier protein (fabE) #2 HP0557 22 acetyl-coenzyme A carboxylase (accA) #3 HP0558 300 beta ketoacyl-acyl carrier protein synthase II (fabF) #4 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #5 HP0950 77 acetyl-CoA carboxylase beta subunit (accD) #6 HP1045 197 acetyl-CoA synthetase (acoE) Motif number 1 GGGATAAAACTAGATTTTAGCTAAAGCCAAAT 3 46 0 TATTTTAGCT 0.945263 -255 GAAAAACTCCTATCCTTTAGGTAGAGATATAA 3 86 1 TCCTTTAGGT 0.9931 -215 TATAAGTGCATAGCTGTTAGGCTATATTCAAG 3 113 1 TCTGTTAGGC 0.922561 -188 ACTATTTTAACCTCTTTTAGCTTGAATATAGC 3 133 0 CCTTTTAGCT 0.894059 -168 CAAGCAGATATGCACTTTAGGCTCATGTTTCT 4 74 0 TACTTTAGGC 0.96352 -208 GCATATCTGCTTGATTTTAGATCCCCACTCAA 4 93 1 TATTTTAGAT 0.863599 -189 CAGGTTGGATTTTATTTTAGGTTTTGTTTTGG 4 199 0 TATTTTAGGT 0.982668 -83 ATTCATAGTATCACTTTTAGGTGATTGACACC 4 235 0 TCTTTTAGGT 0.992529 -47 GTCTTTGCCTTTAAGTTGATTTATTA 4 266 0 TCCTTTAAGT 0.926337 -16 AACGCTAATATCCCCTTTAGGTTTCATCGTGC 6 55 1 TCCTTTAGGT 0.9931 -143 * ********* Masking position 7 Map Score: 12.8736 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 129 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 GCCTTTAAAGTTTGTTAATAATTATGTTATTA 1 14 1 TTTGAATAAT 0.924726 -110 TTAATAATTATGTTATTATAACAATAATTTTT 1 28 1 TGTTTATAAC 0.812323 -96 ACAATAATTTTTTGCTAAAAACGCTTATGGCT 1 48 1 TTTGAAAAAC 0.951635 -76 TTGTGGCATATTTTAAAATAATATAAGGAATA 1 95 1 TTTTAATAAT 0.798568 -29 AAGCCAAATTTTTGACTAAAACCTGGAGACAA 3 23 0 TTTGTAAAAC 0.968548 -278 AAAATTTGGCTTTAGCTAAAATCTAGTTTTAT 3 43 1 TTTATAAAAT 0.686039 -258 TTTCGTGCTGTTGGGATAAAACTAGATTTTAG 3 58 0 TTGGTAAAAC 0.921991 -243 AATTCTATTAAAACCCTGAAACTA 4 3 1 TTCTTAAAAC 0.792191 -279 CAAAGCTATATTGTGCAATAATCATTGAACGA 4 122 1 TTGTAATAAT 0.603478 -160 ATAATATTTTTGTGAAAAAAATAAACGGATCG 4 159 1 TGTGAAAAAT 0.877901 -123 GTATCCAAGTTTTGCTTATAATAAACAAAATT 5 23 0 TTTGTATAAT 0.950592 -55 AGAGTGTGAGTTTGGATATAATAATAAAAAAT 6 147 1 TTTGTATAAT 0.950592 -51 TAATAAAAAATGCGCTTAAAACCATGAAAAAG 6 168 1 TGCGTAAAAC 0.856458 -30 **** ****** Masking position 8 Map Score: 9.05556 Number of sites scoring better than the average of aligned sites = 746 Number in coding regions = 642 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 GAGTTTTTCGTGCTGTTGGGATAAAACTAGAT 3 63 0 TGCGTTGGAT 0.959635 -238 AATAGTCTTTTTGGGGTAGGAAATATCCATGC 3 159 1 TTGGGTGGAA 0.926882 -142 AATGGAATGCTTTAGTTAGGAAGCTCCTTGCT 3 227 1 TTTGTTGGAA 0.968102 -74 CAATATAGCTTTGAGTGGGGATCTAAAATCAA 4 103 0 TTGGTGGGAT 0.986636 -179 TATTTTAGGTTTTGTTTTGGATTGAGGGCGAT 4 187 0 TTTTTTGGAT 0.902526 -95 AATTTTGCAGTTTTGTTAGGATTGTATCCAAG 5 46 0 TTTGTTGGAT 0.988083 -32 ACTTTTTTCTTTCTGTGTGGATTGAGACTGAT 6 100 0 TTCGTGGGAT 0.98065 -98 TTAAAAGAGTGTGAGTTTGGATATAATAATAA 6 142 1 GTGGTTGGAT 0.971933 -56 *** *** **** Masking position 11 Map Score: 6.82154 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 95 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 4 TAATTATTAACAAACTTTAAAGGCTTT 1 3 0 CAAACTAACT 0.914303 -121 AAATATGCCACAAACACATAATCTTACTAGCCATA 1 73 0 CAAACCAATT 0.983706 -51 TCAAAATCCTAACTTTGTAAAA 2 7 0 CAAAACAATT 0.978255 -16 AACCTGGAGACAAACGCTCCAAGTT 3 1 0 CAAACCCATT 0.941298 -300 TAGATTTTAGCTAAAGCCAAATTTTTGACTAAAAC 3 33 0 CTAAACAATT 0.947143 -268 TTTCCTACCCCAAAAAGACTATTTTAACCTCTTTT 3 147 0 CAAAAGTATT 0.771242 -154 CCATTGAATGCTAACACGAAAGGCTTTGTTCTTTA 3 197 0 CTAACCAACT 0.937738 -104 AGCTTCCTAACTAAAGCATTCCATTGAATGCTAAC 3 217 0 CTAAACTCTT 0.756932 -84 ATTTTTTTCACAAAAATATTATTCTTATCGTTCAA 4 146 0 CAAAATTACT 0.782603 -136 ACAATCCTAACAAAACTGCAAAATTAAGGAAAAAC 5 53 1 CAAAATAATT 0.926973 -25 TTATTATATCCAAACTCACACTCTTTTAAAGGGAG 6 136 0 CAAACCACTT 0.958627 -62 ***** * ** ** Masking position 4 Map Score: 7.18905 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 443 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 TTTTAAAATAATATAAGGAATAGATCGTT 1 105 1 ATAAGAATAG 0.830837 -19 TTTTATCCCAACAGCACGAAAAACTCCTATCCT 3 69 1 ACAAGAAAAA 0.97541 -232 TAAAACCCTGAAACTAGGCAAAGACTGCTTAGA 4 19 1 AAAAGCAAAG 0.767439 -263 TAATCATTGAACGATAAGAATAATATTTTTGTG 4 140 1 ACGAGAATAA 0.789285 -142 CCTAAAAGTGATACTATGAATAATAAATCAACT 4 246 1 ATAAGAATAA 0.9195 -36 CAAAACTGCAAAATTAAGGAAAAAC 5 63 1 AAAAGGAAAA 0.884721 -15 TGAGACTGATAAAAAAGGAAATAGCACGATGAA 6 77 0 AAAAGAAATA 0.822125 -121 CTCAATCCACACAGAAAGAAAAAAGTATCCCTC 6 106 1 ACAAGAAAAA 0.97541 -92 GAGTTTGGATATAATAATAAAAAATGCGCTTAA 6 154 1 ATAATAAAAA 0.687884 -44 AATGCGCTTAAAACCATGAAAAAGGAGATGCG 6 176 1 AAAAGAAAAA 0.970456 -22 *** * ****** Masking position 6 Map Score: 3.87542 Number of sites scoring better than the average of aligned sites = 443 Number in coding regions = 382 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 TATTAACAAACTTTAAAGGCTTT 1 4 0 CTTTAAAGGC 0.914523 -120 AAAATCCTAACTTTGTAAAA 2 1 0 CTTTGTAAAA 0.819221 -22 TCCATGCAGACTTTAAAGAACAAAGCCTTT 3 184 1 CTTTAAAGAA 0.94897 -117 GCAAAGACTGCTTAGAAAGAAATTTTTTAA 4 36 1 CTTAGAAAGA 0.878329 -246 TTCTCTAACGCTTTAAAAAATTTCTTTCTA 4 48 0 CTTTAAAAAA 0.956667 -234 GTATCCCTCCCTTTAAAAGAGTGTGAGTTT 6 130 1 CTTTAAAAGA 0.972414 -68 ********** Masking position 7 Map Score: 1.74153 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 418 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 7 TGTTAATAATTATGTTATTATAACAATAATT 1 26 1 TAGTTATTAT 0.556334 -98 GATTTTAGCTAAAGCCAAATTTTTGACTAAA 3 35 0 AAGCCAAATT 0.819366 -266 GCATAGCTGTTAGGCTATATTCAAGCTAAAA 3 120 1 TAGCTATATT 0.927488 -181 CTACCCCAAAAAGACTATTTTAACCTCTTTT 3 147 0 AAACTATTTT 0.684338 -154 ATCCCCACTCAAAGCTATATTGTGCAATAAT 4 113 1 AAGCTATATT 0.940311 -169 ATCCAAAACAAAACCTAAAATAAAATCCAAC 4 197 1 AACCTAAAAT 0.722851 -85 TACTCTTAAGCTAATTTTGTTTATTAT 5 7 1 TAGCTAATTT 0.951016 -71 TTAGCGTTAATATGCTAATATAGTAGAACAT 6 32 0 TAGCTAATAT 0.940329 -166 TTAGCATATTAACGCTAATATCCCCTTTAGG 6 45 1 AAGCTAATAT 0.951016 -153 ** ******** Masking position 7 Map Score: 2.21231 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 432 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 8 ********** No masking Map Score: 1.77879e-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: 1.77879e-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 10 ********** No masking Map Score: 1.77879e-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