AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_hpyl_reg_100.orf -o00460_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 HP0181 257 H. pylori predicted coding region HP0181 #2 HP0723 128 L-asparaginase II (ansB) #3 HP0830 58 amidase #4 HP0832 91 spermidine synthase (speE) #5 HP0833 76 H. pylori predicted coding region HP0833 #6 HP1118 210 gamma-glutamyltranspeptidase (ggt) #7 HP1376 171 (3R)-hydroxymyristoyl-(acyl carrier protein) dehydratase (fabZ) Motif number 1 GAAACCTTGAGATTGTTTTAGTGTATTATA 1 22 1 GATTGTTTTA 0.970951 -236 ATTTTAGATTGATTTTTTTAAGGGTAGTTT 1 71 1 GATTTTTTTA 0.975979 -187 TTTAAGGGTAGTTTTTTTTAAGTTGTGTTA 1 87 1 GTTTTTTTTA 0.946454 -171 AGTAATGGGTGTTTGTTTTAAGACGCTATG 1 165 1 GTTTGTTTTA 0.935654 -93 TGAAATTGTTGATTCTTTTATTTTGTTTGA 2 98 1 GATTCTTTTA 0.904699 -31 GCTCGTTTTATCTCTAAGCA 3 1 1 GCTCGTTTTA 0.922912 -58 GCTTTTGTTACAATAATTTA 4 1 1 GCTTTTGTTA 0.975007 -91 TTAAGGCATGGATATTGTTAAAAAGTAAGC 4 60 1 GATATTGTTA 0.821289 -32 GATCAAATAAGCCTTATTTAACTTATTTTT 6 32 1 GCCTTATTTA 0.722077 -179 TCATTTTTGAGCCTTTTTTATAGCTAGCGC 6 84 1 GCCTTTTTTA 0.960652 -127 GTTTTGTAAAGCTTGTGTTATAATAACAAA 6 156 1 GCTTGTGTTA 0.969783 -55 TAATAGCGGTTATTTTTTTAGAATAACCAA 7 105 1 TATTTTTTTA 0.727977 -67 CAATTAAAGCGCTATTTTTAGCGTTGGTTA 7 128 0 GCTATTTTTA 0.945398 -44 ********** Masking position 10 Map Score: 18.4589 Number of sites scoring better than the average of aligned sites = 805 Number in coding regions = 709 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 2 ATAATACACTAAAACAATCTCAAGGTTTCAA 1 20 0 AAAAAATCTC 0.98907 -238 AACTACCCTTAAAAAAATCAATCTAAAATTC 1 69 0 AAAAAATCAA 0.965492 -189 AACACAACTTAAAAAAAACTACCCTTAAAAA 1 85 0 AAAAAAACTA 0.92979 -173 TTGAAATTTGAAAATAATAACACAACTTAAA 1 103 0 AAAAAATAAC 0.921458 -155 ATAGCGTCTTAAAACAAACACCCATTACTCT 1 163 0 AAAAAAACAC 0.968084 -95 AACAATTTCAAAAATATTCTCATTATGGACC 2 77 0 AAAAATTCTC 0.927183 -52 CAAACAAAATAAAAGAATCAACAATTTCAAA 2 96 0 AAAAAATCAA 0.965492 -33 ACATGCTAGCTAAAAAATCTAAATTATTGTA 4 19 0 TAAAAATCTA 0.808586 -73 CAAGCTTTACAAAACACTCTCTCGCTTATAA 6 140 0 AAAAACTCTC 0.949679 -71 TGGTTATTCTAAAAAAATAACCGCTATTATA 7 103 0 AAAAAATAAC 0.921458 -69 AAAATAAACTCCTTGTTTTGG 7 161 0 AAAAAAACTC 0.973006 -11 **** ****** Masking position 6 Map Score: 16.7791 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 464 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 CACTAAAACAATCTCAAGGTTTCAAAATTTAGCC 1 10 0 ATAAGTTCAA 0.827574 -248 TTAGTGTATTATAGCTATATTTTAATTTAAGAATT 1 39 1 ATTAATTTAA 0.962816 -219 TTGTGTTATTATTTTCAAATTTCAAGTCTAAAGAG 1 109 1 ATCAATTCAA 0.890858 -149 AAGAGTGTGAATTGGCATGATTTAAGAGTAATGGG 1 139 1 ATCAGTTTAA 0.890858 -119 GTAACGCTAAATCAATATAATTCAAACCCTAAACC 1 231 0 ATTAATTCAA 0.95908 -27 TAACCCTTTTTAAATTTATTTTAACGATGTTTTA 2 10 1 TTTTATTTAA 0.556958 -119 TTAACGATGTTTTACTATACTATAAAATCTTTTAA 2 31 1 TTTAATATAA 0.786758 -98 ATACTATAAAATCTTTTAATTTCAAAAGGTGGTCC 2 47 1 ATTTATTCAA 0.907792 -82 GTTTTTAGCCTTACAAAAAATTTAATGGTAGTTTA 3 34 0 TTAAATTTAA 0.809466 -25 CTTTTTTATCGCTTCAATTTAATCAAAATTAG 5 8 1 ATTTATTTAA 0.915428 -69 CGCTAGACCCTTATTTAAGCTTTAAATAACTATAA 5 52 0 TTTAGTTTAA 0.947041 -25 GAGTTTTAAAATAGATAGAGTTTAAAAAATAAGTT 6 51 0 ATTAATTTAA 0.962767 -160 AGCGAGCGGTTTTCTTATGGTATAATAGCGGTTAT 7 83 1 TTTAGTATAA 0.770425 -89 AATAAACTCCTTGTTTTGGATTCAATTAAAGCGCT 7 145 0 TTTTGTTCAA 0.869895 -27 ** ** * ***** Masking position 14 Map Score: 12.6619 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 144 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 TTATATTGATTTAGCGTTACTT 1 246 1 TTAGCGTTAC 0.937283 -12 TAACCCTTTTTAAATTTATT 2 1 1 TAACCCTTTT 0.836175 -128 GTTTTTAGCCTTACAAAAAATTTA 3 45 0 TTAGCCTTAC 0.904815 -14 CGCTAGACCCTTATTTAAGCTTTA 5 63 0 AGACCCTTAT 0.724755 -14 TTTTCTACCCATAGCGTTTTGATCAAATAA 6 12 1 ATAGCGTTTT 0.728536 -199 TTTGATCAAATAAGCCTTATTTAACTTATT 6 29 1 TAAGCCTTAT 0.962263 -182 AACTCATTTTTGAGCCTTTTTTATAGCTAG 6 81 1 TGAGCCTTTT 0.920697 -130 ATTAATGGTTTGAGCGCTAGCTATAAAAAA 6 97 0 TGAGCGCTAG 0.788888 -114 AAAGAAATTTTAAGCGTAACTGATTGAAAG 6 183 1 TAAGCGTAAC 0.779029 -28 TGCATAAGCGGTTTCTATGCAAAG 7 5 1 TAAGCGGTTT 0.786896 -167 GTTTCTATGCAAAGCGTTTCTTGAAGCTTA 7 21 1 AAAGCGTTTC 0.899453 -151 TCTAAAAAAATAACCGCTATTATACCATAA 7 97 0 TAACCGCTAT 0.842023 -75 GGATTCAATTAAAGCGCTATTTTTAGCGTT 7 133 0 AAAGCGCTAT 0.53658 -39 ********** Masking position 3 Map Score: 8.72841 Number of sites scoring better than the average of aligned sites = 1950 Number in coding regions = 1734 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 5 TATGACTATCTTTATGCGAGATATATGAGA 1 191 1 TTTATGCGAG 0.976586 -67 TTATGCGAGATATATGAGAGAAAGGTTTGG 1 202 1 TATATGAGAG 0.963671 -56 TCATGTAAGTTATAAGCGAGAGAGTGTTTT 6 131 1 TATAAGCGAG 0.990601 -80 TTTTTGCAAATACAAGCGAGCGGTTTTCTT 7 69 1 TACAAGCGAG 0.984081 -103 ********** Masking position 4 Map Score: 2.20225 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 12 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 AAATTAAAATATAGCTATAATACACTAAAAC 1 36 0 ATAGCTAAAT 0.956882 -222 CTAAGCATGTTAAACTACCATTAAATTTTTT 3 24 1 TAAACTACAT 0.642632 -35 TTTAGATTTTTTAGCTAGCATGTTAGCAATT 4 27 1 TTAGCTACAT 0.937452 -65 AAACACTCCTTAGCTTACTTTTTAACAATA 4 72 0 TTAGCTTCTT 0.744302 -20 CTTTTTTATCGCTTCAATTTAATCAAAA 5 8 1 ATCGCTTAAT 0.930382 -69 TAAGCTTTAAATAACTATAATATTGTAATCT 5 41 0 ATAACTAAAT 0.87913 -36 ATAGTTATTTAAAGCTTAAATAAGGGTCTAG 5 54 1 AAAGCTTAAT 0.909168 -23 TCTCTCGCTTATAACTTACATGATGCTATTA 6 123 0 ATAACTTCAT 0.920234 -88 CGCTAAAAATAGCGCTTTAATTGAATCCAAA 7 135 1 AGCGCTTAAT 0.804394 -37 ******* *** Masking position 6 Map Score: 1.73228 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 456 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 GGCTAAATTTTGAAACCTTGAGATT 1 5 1 AAATTTGAAA 0.892147 -253 AGCTATATTTTAATTTAAGAATTTTAGATTG 1 51 1 TAATTTAGAA 0.852344 -207 AATAATAACACAACTTAAAAAAAACTACCCT 1 91 0 CAACTTAAAA 0.928607 -167 TTTAGACTTGAAATTTGAAAATAATAACACA 1 110 0 AAATTTAAAA 0.968889 -148 TCGTTAAAATAAATTTAAAAAGGGTTA 2 7 0 AAATTTAAAA 0.968889 -122 TAAAATCTTTTAATTTCAAAAGGTGGTCCAT 2 53 1 TAATTTAAAA 0.956014 -76 AAAGAATCAACAATTTCAAAAATATTCTCAT 2 85 0 CAATTTAAAA 0.979988 -44 TAAACTCTATCTATTTTAAAACTCATTTTTG 6 62 1 CTATTTAAAA 0.897707 -149 ****** **** Masking position 3 Map Score: 8.23438 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 205 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 8 GTAGTTTTTTTTAAGTTGTGTTATTATTTTCA 1 94 1 TTAATGTGTT 0.821402 -164 AATTTCAAGTCTAAAGAGTGTGAATTGGCATG 1 126 1 CTAAGGTGTG 0.989881 -132 TGATTTAAGAGTAATGGGTGTTTGTTTTAAGA 1 156 1 GTAAGGTGTT 0.987818 -102 AAAAAGTAAGCTAAGGAGTGTTT 4 79 1 CTAAGGTGTT 0.991605 -13 AAGTTATAAGCGAGAGAGTGTTTTGTAAAGCT 6 137 1 CGAGGGTGTT 0.940447 -74 AGAGTGTTTTGTAAAGCTTGTGTTATAATAAC 6 151 1 GTAAGTTGTG 0.912276 -60 **** * ***** Masking position 9 Map Score: 0.812988 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 69 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 ********** No masking Map Score: 2.54618e-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: 2.54618e-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 11 ********** No masking Map Score: 2.54618e-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