AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ifnr_hpyl_opreg_300.orf -g0.389 -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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0144 300 cytochrome c oxidase, heme b and copper-binding subunit, membrane-bound (fixN) #2 HP0376 55 ferrochelatase (hemH) #3 HP0377 76 thiol:disulfide interchange protein (dsbC), putative #4 HP0723 128 L-asparaginase II (ansB) #5 HP0730 91 H. pylori predicted coding region HP0730 #6 HP0733 119 H. pylori predicted coding region HP0733 #7 HP0736 146 phosphoserine aminotransferase (serC) Motif number 1 CTTGGCTTTATTTTTGTATTTTCATGGGCATG 1 19 0 TTTTTTTTTT 0.835781 -282 TGAGGGTTTGTTTAATCATGTTTAACCTTTAG 1 123 1 TTTAACTGTT 0.967785 -178 AAGCTTAATTTTTAATCTTTTTCTGTAACATT 1 212 0 TTTAACTTTT 0.980682 -89 AAGATTAAAAATTAAGCTTTTTGAAAAAGATA 1 225 1 ATTAACTTTT 0.911364 -76 AATTATAAAATTTTATCTTTTTCAAAAAGCTT 1 238 0 TTTTACTTTT 0.978652 -63 AAAGATAAAATTTTATAATTATGTTTATCTTT 1 250 1 TTTTAATTAT 0.746235 -51 TATAATTATGTTTATCTTTGTTGAATTTACTA 1 263 1 TTTATTTGTT 0.769327 -38 TTTATTTTTTATTAATCGTTTTATTTTAGCAT 2 28 1 ATTAACTTTT 0.911525 -28 TAACCCTTTTTAAATTTATTTTAACGATG 4 8 1 TTTTAATTAT 0.746234 -121 TTAAATTTATTTTAACGATGTTTTACTATACT 4 20 1 TTTAAGTGTT 0.889294 -109 CCTTTTGAAATTAAAAGATTTTATAGTATAGT 4 44 0 TTAAAGTTTT 0.644317 -85 TTGTTGATTCTTTTATTTTGTTTGAAGGGGCA 4 103 1 TTTTATTGTT 0.936868 -26 TAAGCGGTGTTTTAAATCTTTTAAAGGAAAGG 5 68 1 TTTAATTTTT 0.965244 -24 TTAGCCGTGCTTTTAGCCTTATGGCTAACTT 6 10 0 TTTTACTTAT 0.944478 -110 GGGGTTTGCGTTTTTTTTTTTTTGTTAAAATG 6 70 1 TTTTTTTTTT 0.835781 -50 TCATTGCCTTAAATTCTTTTTAAATCATGG 7 9 1 TTAAATTTTT 0.78751 -138 AATCATGGCATTTTAGCATTTTATTTGCATTA 7 33 1 TTTTACTTTT 0.978652 -114 CGTGCTTAAAATTAAGCCTTATTGTTTAAGAA 7 75 0 ATTAACTTAT 0.792495 -72 TTTAAGCACGTTTTAGTATGATAACTTTTAAA 7 97 1 TTTTATTGAT 0.84631 -50 ***** * **** Masking position 9 Map Score: 24.5971 Number of sites scoring better than the average of aligned sites = 1871 Number in coding regions = 1434 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 2 CATTCTTGCCCCTTTTTTTATCGCAACGCT 1 92 0 CCTTTTTTTA 0.453838 -209 CCATTTGAATGGCATTTTTAAGCCAAATTG 1 168 0 GGCATTTTTA 0.859801 -133 CTACAATAATCGCTTTTTTATGCGCATTTT 3 12 0 CGCTTTTTTA 0.930801 -65 TAACCCTTTTTAAATTTATTTTA 4 4 1 CCCTTTTTAA 0.884629 -125 TGGCGCATTCGGTATTTTAACACAAAT 5 8 0 GGTATTTTAA 0.791798 -84 AAAACTAGCAAGCGTTTTAGCGTTGGCGCA 5 31 0 AGCGTTTTAG 0.856968 -61 GCTAGTAAGCGGTGTTTTAAATCTTTTAAA 5 63 1 GGTGTTTTAA 0.899107 -29 ACGCTTTAGCCGTGCTTTTAGCCTTATGGC 6 17 0 CGTGCTTTTA 0.789924 -103 ACGCTTTAGCCACGCTTTAGCCGTGCTTTT 6 28 0 CACGCTTTAG 0.874477 -92 ACGCTCCAGCCACGCTTTAGCCACGCTTTA 6 39 0 CACGCTTTAG 0.874477 -81 AATTTTCTGACGCATTTTAACAAAAAAAAA 6 84 0 CGCATTTTAA 0.969858 -36 TTTAAATCATGGCATTTTAGCATTTTATTT 7 29 1 GGCATTTTAG 0.930281 -118 TTAAGAAAATCGCTTTTTAATGCAAATAAA 7 52 0 CGCTTTTTAA 0.969858 -95 TAATTTTAAGCACGTTTTAGTATGATAACT 7 93 1 CACGTTTTAG 0.938037 -54 ********** Masking position 6 Map Score: 14.2604 Number of sites scoring better than the average of aligned sites = 2206 Number in coding regions = 2002 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 3 TGAAAATACAAAAATAAAGCCAAGCGTTAG 1 27 1 AAAATAAAGC 0.97907 -274 GTGCGCCTAAAAAATACAACAGCGTTGCGA 1 72 1 AAAATACAAC 0.957906 -229 AAAAAGATTAAAAATTAAGCTTTTTGAAAA 1 222 1 AAAATTAAGC 0.975225 -79 CTATTTGTAGTAAATTCAACAAAGATAAAC 1 272 0 TAAATTCAAC 0.708729 -29 CGATTAATAAAAAATAAATCGTTAGAAAGA 2 16 0 AAAATAAATC 0.899635 -40 GGTGCATGCTAAAATAAAACGATTAATAAA 2 35 0 AAAATAAAAC 0.973214 -21 CCCTTCAAACAAAATAAAAGAATCAACAAT 4 102 0 AAAATAAAAG 0.809272 -27 TTTAACAAAAAAAAAAAAACGCAAACCCCC 6 69 0 AAAAAAAAAC 0.821955 -51 AATGCGTCAGAAAATTCGGCATGAGGGCAA 6 98 1 AAAATTCGGC 0.822788 -22 AAACGTGCTTAAAATTAAGCCTTATTGTTT 7 80 0 AAAATTAAGC 0.975225 -67 TAAAATTAACCTTTAATTTTT 7 136 0 AAAATTAACC 0.917897 -11 ********** Masking position 4 Map Score: 15.7547 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 320 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 ATGTTTAACCTTTAGCCAAAGATAGTAGCA 1 140 1 TTTAGCCAAA 0.662236 -161 AATGGCATTTTTAAGCCAAATTGCTACTAT 1 161 0 TTAAGCCAAA 0.939382 -140 TGGGATTGAGTTATTACAATGTTACAGAAA 1 195 1 TTATTACAAT 0.696086 -106 TTTGTTGAATTTACTACAAATAGGAGTATT 1 279 1 TTACTACAAA 0.9137 -22 AATAAAACGATTAATAAAAAATAAATCGTT 2 23 0 TTAATAAAAA 0.858974 -33 ACTAGGTATCTTACTACAATAATCGCTTTT 3 25 0 TTACTACAAT 0.862025 -52 ATTCGGTATTTTAACACAAAT 5 2 0 TTAACACAAA 0.943094 -90 CTGACGCATTTTAACAAAAAAAAAAAAACG 6 78 0 TTAACAAAAA 0.804097 -42 TAAAAAGAATTTAAGGCAATGA 7 3 0 TTAAGGCAAT 0.901419 -144 AAATCGCTTTTTAATGCAAATAAAATGCTA 7 46 0 TTAATGCAAA 0.923303 -101 GCCTTATTGTTTAAGAAAATCGCTTTTTAA 7 62 0 TTAAGAAAAT 0.822496 -85 ********** Masking position 8 Map Score: 8.65546 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 263 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 5 TTAATCATGTTTAACCTTTAGCCAAAGATA 1 134 1 TTAACCTTTA 0.986413 -167 TTCAAAAAGCTTAATTTTTAATCTTTTTCT 1 220 0 TTAATTTTTA 0.866267 -81 GTAATAACCTTTATCTTTTAATA 3 64 0 ATAACCTTTA 0.981589 -13 TTTTAGTATGATAACTTTTAAATTCTCTCA 7 107 1 ATAACTTTTA 0.959501 -40 TAAAATTAACCTTTAATTTTTGAGA 7 132 0 TTAACCTTTA 0.986413 -15 ********** Masking position 4 Map Score: 5.93689 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 18 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 AAGACCTAACGCTTGGCTTTATTTTTGTAT 1 32 0 GCTTGGCTTT 0.934393 -269 AAATACAACAGCGTTGCGATAAAAAAAGGG 1 83 1 GCGTTGCGAT 0.964426 -218 CACGGCTAAAGCGTGGCTAAAGCGTGGCTG 6 33 1 GCGTGGCTAA 0.981086 -87 CGTGGCTAAAGCGTGGCTGGAGCGTGGGGG 6 44 1 GCGTGGCTGG 0.991661 -76 CGTGGCTGGAGCGTGGGGGTTTGCGTTTTT 6 55 1 GCGTGGGGGT 0.984166 -65 ********** Masking position 4 Map Score: 1.41666 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 183 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TTTTTGTATTTTCATGGGCATGATTATAGG 1 11 0 TTCATGGGCA 0.951942 -290 TGTTGTATTTTTTAGGCGCACCGGATGGGT 1 63 0 TTTAGGCGCA 0.990479 -238 TAATCGCTTTTTTATGCGCATTTTA 3 6 0 TTTATGCGCA 0.972339 -71 TTATTTTGTTTGAAGGGGCAGGTT 4 115 1 TGAAGGGGCA 0.946912 -14 AGCGTTTTAGCGTTGGCGCATTCGGTATTT 5 21 0 CGTTGGCGCA 0.944143 -71 ATGCCGAATTTTCTGACGCATTTTAACAAA 6 90 0 TTCTGACGCA 0.902922 -30 ********** Masking position 10 Map Score: 1.22689 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 184 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 ********** No masking Map Score: -8.78641e-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 ********** No masking Map Score: -8.78641e-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 10 ********** No masking Map Score: -8.78641e-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