AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_hpyl_reg_300.orf -o00640_hpyl_300.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 HP0688 143 H. pylori predicted coding region HP0688 #5 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #6 HP0950 77 acetyl-CoA carboxylase beta subunit (accD) #7 HP1045 197 acetyl-CoA synthetase (acoE) Motif number 1 ACTAGCCATAAGCGTTTTTAGCAAAAAATTA 1 52 0 AGGTTTTTAG 0.84212 -72 TGGGATAAAACTAGATTTTAGCTAAAGCCAA 3 48 0 CTGATTTTAG 0.960269 -253 ATATAAGTGCATAGCTGTTAGGCTATATTCA 3 112 1 ATGCTGTTAG 0.925715 -189 TAGGAAGCTCCTTGCTTTAAGCAAGGGGTGG 3 243 1 CTGCTTTAAG 0.966417 -58 TAAAGTTTTTCTAATTTTTAGTTATATCGTT 4 31 1 CTATTTTTAG 0.912823 -113 TTTTAGTTATATCGTTTTTAGATTAAAAGTC 4 46 1 ATGTTTTTAG 0.968817 -98 CGCTATAGTGCTGACTTTTAATCTAAAAACG 4 58 0 CTACTTTTAA 0.669615 -86 ACATTCTTGTCTCGCTTTTATTATATAACAA 4 101 0 CTGCTTTTAT 0.901711 -43 TGCATATCTGCTTGATTTTAGATCCCCACTC 5 92 1 CTGATTTTAG 0.962948 -190 ATTGCACAATATAGCTTTGAGTGGGGATCTA 5 110 0 ATGCTTTGAG 0.938162 -172 TATTCATAGTATCACTTTTAGGTGATTGACA 5 237 0 ATACTTTTAG 0.941033 -45 CTCCTTTTTCATGGTTTTAAGCGCATTTTTT 7 172 0 ATGTTTTAAG 0.88518 -26 ** ******** Masking position 10 Map Score: 13.6876 Number of sites scoring better than the average of aligned sites = 711 Number in coding regions = 638 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 2 AAAACGCTTATGGCTAGTAAGATTATGTGTTTGTGGCATATTT 1 65 1 TGGTGGTTTG 0.991278 -59 AACTTGGAGCGTTTGTCTCCAGGTTTTAGTCAAAAAT 3 5 1 TGGTAGTTTT 0.992159 -296 CACTTATATCTCTACCTAAAGGATAGGAGTTTTTCGTGCTGTT 3 78 0 TCGTGGTTTT 0.991958 -223 AAGCAAGGGGTGGTTTCACTGAATTAAAGTTTTGAAATGAGGA 3 261 1 TGGTAGTTTT 0.992159 -40 TGGGTTTGAATGCTCCGCATTAAAGTTTTTCTAATTTTT 4 7 1 TGGTAGTTTT 0.992159 -137 TTCTAAGCAGTCTTTGCCTAGTTTCAGGGTTTTAATAGAATT 5 10 0 TCGTGGTTTT 0.991959 -272 TTTGCAGTTTTGTTAGGATTGTATCCAAGTTTTGCTTATAATA 6 32 0 TGGTAGTTTT 0.992159 -46 AAGTATCCCTCCCTTTAAAAGAGTGTGAGTTTGGATATAATAA 7 128 1 CCGTGGTTTG 0.948859 -70 ** * * * ***** Masking position 14 Map Score: 9.83858 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 62 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 ATTCAAGCTAAAAGAGGTTAAAATAGTCTT 3 138 1 AAAGAGGTTA 0.838767 -163 CTTTTAATCTAAAAACGATATAACTAAAAA 4 45 0 AAAAACGATA 0.934259 -99 GTTATATAATAAAAGCGAGACAAGAATGTT 4 103 1 AAAAGCGAGA 0.9567 -41 AAGAATGTTAAAAAATGAAAGGAGCGTGTA 4 124 1 AAAAATGAAA 0.831199 -20 TCAATCACCTAAAAGTGATACTATGAATAA 5 239 1 AAAAGTGATA 0.922047 -43 TATGACTACAAAAAGGGTGAT 7 2 0 AAAAGGGTGA 0.943008 -196 GATGAAACCTAAAGGGGATATTAGCGTTAA 7 53 0 AAAGGGGATA 0.954944 -145 GAGACTGATAAAAAAGGAAATAGCACGATG 7 79 0 AAAAAGGAAA 0.947508 -119 TAAAACCATGAAAAAGGAGATGCG 7 184 1 AAAAAGGAGA 0.976002 -14 ********** Masking position 3 Map Score: 8.58726 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 216 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 TCAAAATCCTAACTTTGTAAAA 2 10 0 CAAATCCAAC 0.978731 -13 TAAAATCTAGTTTTATCCCAACAGCACGAAAA 3 59 1 TTTATCCAAC 0.974958 -242 AAGCATTCCATTGAATGCTAACACGAAAGGCT 3 207 0 TTAATGCAAC 0.93922 -94 CTGCTTGATTTTAGATCCCCACTCAAAGCTAT 5 99 1 TTGATCCCAC 0.941161 -183 ACGGATCGCCCTCAATCCAAAACAAAACCTAA 5 183 1 CTAATCCAAA 0.895832 -99 AAACCTAAAATAAAATCCAACCTGTTAGGGTG 5 207 1 TAAATCCACC 0.928747 -75 AAAACTTGGATACAATCCTAACAAAACTGCAA 6 42 1 TAAATCCAAC 0.982391 -36 TTTTATCAGTCTCAATCCACACAGAAAGAAAA 7 96 1 CTAATCCCAC 0.97721 -102 TTTTTTATTATTATATCCAAACTCACACTCTT 7 146 0 TTTATCCAAC 0.974958 -52 ** ***** *** Masking position 6 Map Score: 8.83275 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 126 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 AAATTATTGTTATAATAACATAATTATTAACAA 1 25 0 TATAATAAAA 0.966384 -99 TGGCATATTTTAAAATAATATAAGGAATAGATC 1 98 1 TAAAATAAAA 0.958747 -26 CGATATAACTAAAAATTAGAAAAACTTTAATGC 4 27 0 AAAAATTAAA 0.837472 -117 TATATTGTGCAATAATCATTGAACGATAAGAAT 5 128 1 AATAATCAAA 0.903927 -154 TTTTTGTGAAAAAAATAAACGGATCGCCCTCAA 5 165 1 AAAAATAAGA 0.870434 -117 TGATACTATGAATAATAAATCAACTTAAAGGCA 5 254 1 AATAATAAAA 0.972544 -28 AAGTTTTGCTTATAATAAACAAAATTAGCTTAA 6 16 0 TATAATAAAA 0.966358 -62 ACAAAACTGCAAAATTAAGGAAAAAC 6 62 1 AAAATTAAAA 0.819258 -16 TGAGTTTGGATATAATAATAAAAAATGCGCTTA 7 153 1 TATAATAAAA 0.966185 -45 ******** ** Masking position 6 Map Score: 5.35751 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 117 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 ATAATTATTAACAAACTTTAAAGGCTTT 1 9 0 ACAAACTTTA 0.799498 -115 TGTGTTTGTGGCATATTTTAAAATAATATA 1 90 1 GCATATTTTA 0.785731 -34 TCAAAATCCTAACTTTGTAAAA 2 6 0 CCTAACTTTG 0.833259 -17 GCGTTTGTCTCCAGGTTTTAGTCAAAAATT 3 19 1 CCAGGTTTTA 0.903091 -282 TTAGCTAAAGCCAAATTTTTGACTAAAACC 3 32 0 CCAAATTTTT 0.578265 -269 AAATATCCATGCAGACTTTAAAGAACAAAG 3 179 1 GCAGACTTTA 0.951322 -122 TGCTAACACGAAAGGCTTTGTTCTTTAAAG 3 194 0 AAAGGCTTTG 0.5585 -107 GCATTCAATGGAATGCTTTAGTTAGGAAGC 3 221 1 GAATGCTTTA 0.707179 -80 TTAGGAAGCTCCTTGCTTTAAGCAAGGGGT 3 242 1 CCTTGCTTTA 0.796031 -59 CTCCTCATTTCAAAACTTTAATTCAGTGAA 3 275 0 CAAAACTTTA 0.762251 -26 TAAAAATTAGAAAAACTTTAATGCGGAGCA 4 21 0 AAAAACTTTA 0.510545 -123 GCGCTATAGTGCTGACTTTTAATCTAAAAA 4 60 0 GCTGACTTTT 0.653839 -84 TTCTTTCTAAGCAGTCTTTGCCTAGTTTCA 5 27 0 GCAGTCTTTG 0.799307 -255 TACTCTTAAGCTAATTTTGTTTATTATAA 6 10 1 GCTAATTTTG 0.687829 -68 AGGATTGTATCCAAGTTTTGCTTATAATAA 6 31 0 CCAAGTTTTG 0.805154 -47 GGTTTTAAGCGCATTTTTTATTATTATATC 7 161 0 GCATTTTTTA 0.476404 -37 TCTCCTTTTTCATGGTTTTAAGCGCATTTT 7 174 0 CATGGTTTTA 0.517713 -24 ********** Masking position 7 Map Score: 5.46854 Number of sites scoring better than the average of aligned sites = 1751 Number in coding regions = 1593 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 7 AACGATCTATTCCTTATATT 1 114 0 AACGATCTAT 0.892766 -10 CCTGGAGACAAACGCTCCAAGTT 3 4 0 AACGCTCCAA 0.924205 -297 TCCTTTAGGTAGAGATATAAGTGCATAGCT 3 98 1 AGAGATATAA 0.809462 -203 TTAATCTAAAAACGATATAACTAAAAATTA 4 42 0 AACGATATAA 0.958581 -102 TCAGCACTATAGCGCTATAAGACTAATTGT 4 75 1 AGCGCTATAA 0.969848 -69 ATGTTTCTCTAACGCTTTAAAAAATTTCTT 5 52 0 AACGCTTTAA 0.935602 -230 ATCCCCACTCAAAGCTATATTGTGCAATAA 5 113 1 AAAGCTATAT 0.850128 -169 ********** Masking position 9 Map Score: 2.16721 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 491 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 ********** No masking Map Score: 3.07965e-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 9 ATAACAATAATTTTTTGCTAAAAACGCTTA 1 45 1 TTTTTTGCTA 0.831837 -79 GATAGGAGTTTTTCGTGCTGTTGGGATAAA 3 70 0 TTTCGTGCTG 0.981956 -231 GAACAAAGCCTTTCGTGTTAGCATTCAATG 3 201 1 TTTCGTGTTA 0.866104 -100 CTTATAGCGCTATAGTGCTGACTTTTAATC 4 66 0 TATAGTGCTG 0.85142 -78 CTTTAAAAAATTTCTTTCTAAGCAGTCTTT 5 38 0 TTTCTTTCTA 0.876359 -244 CTCAAAGCTATATTGTGCAATAATCATTGA 5 120 1 TATTGTGCAA 0.794715 -162 ATATTATTCTTATCGTTCAATGATTATTGC 5 136 0 TATCGTTCAA 0.847257 -146 CTTTAGGTTTCATCGTGCTATTTCCTTTTT 7 69 1 CATCGTGCTA 0.925972 -129 GGGATACTTTTTTCTTTCTGTGTGGATTGA 7 107 0 TTTCTTTCTG 0.853939 -91 ********** Masking position 6 Map Score: 2.76663 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 272 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 ********** No masking Map Score: 3.07965e-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: 3.07965e-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: 3.07965e-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