AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_hpyl_reg_300.orf -o00280_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 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0688 143 H. pylori predicted coding region HP0688 #4 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #5 HP1468 51 branched-chain-amino-acid aminotransferase (ilvE) #6 HP1469 114 H. pylori predicted coding region HP1469 #7 HP1470 67 DNA polymerase I (polA) #8 HP1471 65 type IIS restriction enzyme R protein (BCGIB) #9 HP1472 30 type IIS restriction enzyme M protein (mod) #10 HP1483 26 gerC2 protein (gerC2) #11 HP1490 103 hemolysin #12 HP1491 138 phosphate permease Motif number 1 TGAGAGAAAGGTTTGGGTTTAGGGTTTGAATTATAT 1 27 0 GTTTTTAGTT 0.940537 -231 ATTCACACTCTTTAGACTTGAAATTTGAAAATAATA 1 128 1 TTTTTGATTT 0.958728 -130 AATTTAAGAATTTTAGATTGATTTTTTTAAGGGTAG 1 181 0 TTTTTGATTT 0.958728 -77 GCGATTTTAGGTTAATTTTGAGTTTTTAGGAGCAGT 2 15 0 GTTTTGATTT 0.907593 -200 ATTGAATTTTTTCTCAATTTAGGTTTTGTTTATAAG 2 99 0 TTCTTTATTT 0.806303 -116 ACAATAGCCCCTTTGAATTGAATTTTTTCTCAATTT 2 115 0 CTTTTGATTT 0.92806 -100 GGGGCTATTGTTTAAAATTTACATTTTTTAAACGCT 2 140 1 TTTTTTATTT 0.975159 -75 CATTAAAGTTTTTCTAATTTTTAGTTATATCGTTTT 3 28 1 TTTTTTTGTT 0.932803 -116 TTGGATTTTATTTTAGGTTTTGTTTTGGATTGAGGG 4 191 0 TTTTTTTTTT 0.935761 -91 GTCTTTGCCTTTAAGTTGATTTATTATT 4 264 0 CTTTTTATTG 0.721852 -18 TTTTTTAATTGAGTTTAAGAAAAAATA 6 2 1 TTTTTGATTA 0.766902 -113 TCAGTCTTTTCCCTTTATTTTTTGATAATCGC 6 93 0 TTTTTTATTT 0.975159 -22 ATCAAGCGAATTTTAAGTTTATTGTAACACAAGCTA 7 29 0 TTTTTTAGTA 0.84123 -39 GTTATAATTTTATTTTTTAAAAGGAT 9 1 1 GTTTTTTTTT 0.860314 -30 TTTTTGAAGGCTTGATTTTTAAAGTTAGGCTTAATC 11 13 1 CTTTTTAGTT 0.954077 -91 TAAAGTTAGGCTTAATCTTTTATGTTAAAATTCTGA 11 32 1 CTTTTTTGTT 0.885178 -72 ATTTTATATATTTTATATTTATCGTTAGGTTTTAGG 11 69 1 TTTTTTAGTT 0.973965 -35 TATCGTTAGGTTTTAGGTTTAAAGTT 11 88 1 TTTTTTAGTT 0.973965 -16 TAAAACTCTCTTTAAAATTTTACTTTAAGATACCAT 12 15 1 TTTTTTTTTT 0.935761 -124 *** **** *** Masking position 8 Map Score: 28.7979 Number of sites scoring better than the average of aligned sites = 665 Number in coding regions = 480 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 2 GACTTGAAATTTGAAAATAATAACACAACTT 1 142 1 TTGAAAAAAT 0.594716 -116 TTCTACTACATTTGAAATAATTTTTCTTATA 2 74 1 TTTGAAAAAT 0.960877 -141 ATAATTTTTCTTATAAACAAAACCTAAATTG 2 90 1 TTATAAAAAA 0.788074 -125 AAACCTAAATTGAGAAAAAATTCAATTCAAA 2 109 1 TGAGAAAAAT 0.926556 -106 AAAATGTAAATTTTAAACAATAGCCCCTTTG 2 136 0 TTTTAAAAAT 0.903099 -79 TTAAACGCTATTAGATATAATAAGGGATAGT 2 167 1 TTAGATAAAT 0.926419 -48 TAACTAAAAATTAGAAAAACTTTAATGCGGA 3 24 0 TTAGAAAACT 0.733691 -120 TAAGACTAATTGTTATATAATAAAAGCGAGA 3 92 1 TGTTATAAAT 0.710507 -52 GAGACAAGAATGTTAAAAAATGAAAGGAGCG 3 119 1 TGTTAAAAAT 0.82723 -25 GTTTCAGGGTTTTAATAGAATT 4 2 0 TTTAATAAAT 0.636274 -280 CAAAGACTGCTTAGAAAGAAATTTTTTAAAG 4 37 1 TTAGAAAAAA 0.907399 -245 ATAATATTTTTGTGAAAAAAATAAACGGATC 4 159 1 TGTGAAAAAA 0.834195 -123 CCCCTTTTTAGATACAATCACGCCTGAA 5 8 1 TTAGATAAAT 0.926418 -44 TAATTGAGTTTAAGAAAAAATATATTATTAT 6 16 1 TAAGAAAAAT 0.707386 -99 TAAGTATTACTTATAAAGAAATAATAATATA 6 36 0 TTATAAAAAA 0.788093 -79 GGGTATCCTTTTAAAAAATAAAATTATAA 9 12 0 TTTTAAAAAT 0.903113 -19 AAAAGCGTTGTTTGATAAAAATGGCTCATTA 12 52 0 TTTGATAAAA 0.833081 -87 CAAGGGCTAATTGGATAGAATAAGACCACTA 12 94 1 TTGGATAAAT 0.844083 -45 ******* *** Masking position 1 Map Score: 18.5621 Number of sites scoring better than the average of aligned sites = 895 Number in coding regions = 728 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 3 CATAGCGTCTTAAAACAAACACCCATTACTCT 1 84 1 TAAAACAAAC 0.586815 -174 ACTTGAAATTTGAAAATAATAACACAACTTAA 1 143 1 TGAAAATAAA 0.780053 -115 TAACACAACTTAAAAAAAACTACCCTTAAAAA 1 162 1 TAAAAAAAAA 0.732999 -96 AAAACTACCCTTAAAAAAATCAATCTAAAATT 1 177 1 TTAAAAAAAA 0.903665 -81 AATTCTTAAATTAAAATATAGCTATAATACAC 1 205 1 TTAAAATATC 0.797542 -53 TATAATACACTAAAACAATCTCAAGGTTTCAA 1 227 1 TAAAACAATC 0.694634 -31 AATTTTTCTTATAAACAAAACCTAAATTGAGA 2 92 1 ATAAACAAAC 0.584603 -123 ACCTAAATTGAGAAAAAATTCAATTCAAAGGG 2 111 1 AGAAAAAATA 0.818822 -104 AATGTAAATTTTAAACAATAGCCCCTTTGAAT 2 133 0 TTAAACAATC 0.886009 -82 CTAATAGCGTTTAAAAAATGTAAATTTTAAAC 2 149 0 TTAAAAAATA 0.937596 -66 GTTACCACCTATAAAATAAGGATCGTTCA 2 196 1 ATAAAATAAA 0.497907 -19 GACAAGAATGTTAAAAAATGAAAGGAGCGTGT 3 121 1 TTAAAAAATA 0.937596 -23 ATTAAAACCCTGAAACTAGGCAAAGACTGCTT 4 17 1 TGAAACTAGA 0.523105 -265 CTCTAACGCTTTAAAAAATTTCTTTCTAAGCA 4 44 0 TTAAAAAATC 0.915301 -238 AATATTTTTGTGAAAAAAATAAACGGATCGCC 4 161 1 TGAAAAAAAA 0.906801 -121 CAATCACGCCTGAAACTATCCATTTAAAGGTG 5 25 1 TGAAACTATA 0.803379 -27 ATTGAGTTTAAGAAAAAATATATTATTATTTC 6 18 1 AGAAAAAATA 0.818822 -97 AGAGCGATTATCAAAAAATAAAGGGAAAAGAC 6 90 1 TCAAAAAATA 0.825986 -25 TTCAAACAAATCCCCCAATCTGA 8 53 0 TCAAACAAAC 0.605233 -13 GGGTATCCTTTTAAAAAATAAAATTATAAC 9 9 0 TTAAAAAATA 0.937595 -22 AGACAAGCCATGAAAAAAGAAAAGTC 10 11 1 TGAAAAAAGA 0.807084 -16 TAAGCCTAACTTTAAAAATCAAGCCTTCAAAA 11 14 0 TTTAAAAATA 0.468711 -90 AACGATAAATATAAAATATATAAAATCTCAGA 11 63 0 ATAAAATATA 0.613651 -41 ********* * Masking position 5 Map Score: 20.1448 Number of sites scoring better than the average of aligned sites = 1765 Number in coding regions = 1464 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 4 AGATAGTCATAGCGTCTTAAAACAAACACCCA 1 77 1 ACGCTTAAAA 0.715881 -181 ATTTTAATTTAAGAATTTTAGATTGATTTTTT 1 190 0 AGATTTTAGA 0.735375 -68 TTTTGCGTCAAGCGATTTTAGGTTAATTTTGA 2 30 0 ACGTTTTAGG 0.975386 -185 ACATTTTTTAAACGCTATTAGATATAATAAGG 2 160 1 ACGTATTAGA 0.866556 -55 TTTTAGTTATATCGTTTTTAGATTAAAAGTCA 3 46 1 ACGTTTTAGA 0.960898 -98 TCAGCACTATAGCGCTATAAGACTAATTGTTA 3 75 1 ACGTATAAGA 0.781012 -69 GCCTAGTTTCAGGGTTTTAATAGAATT 4 6 0 AGGTTTAATA 0.475618 -276 ATGTTTCTCTAACGCTTTAAAAAATTTCTTTC 4 50 0 ACGTTTAAAA 0.893389 -232 TCAAGCAGATATGCACTTTAGGCTCATGTTTC 4 75 0 AGCCTTTAGG 0.759463 -207 TATTCATAGTATCACTTTTAGGTGATTGACAC 4 236 0 ACATTTTAGG 0.911292 -46 TGAATAATAAATCAACTTAAAGGCAAAGAC 4 262 1 ACACTTAAAG 0.512984 -20 CCCCTTTTTAGATACAATCACG 5 1 1 CCCTTTTAGA 0.600151 -51 GCCTGAAACTATCCATTTAAAGGTGTGAAA 5 32 1 ACCTTTAAAG 0.891408 -20 AGTAATACTTAGCCATTTTAAGCTAATATAAT 6 56 1 ACCTTTTAAG 0.93729 -59 AAGGGGTTTTAAGCGCGCTAGCT 7 2 1 AGGTTTTAAG 0.914772 -66 TAGCCAACTCAACGCTATTAAGTGGGGCGAGT 8 21 1 ACGTATTAAG 0.866702 -45 GGGTATCCTTTTAAAAAATAAAATTA 9 15 0 ACCTTTAAAA 0.835809 -16 TTATCAAACAACGCTTTTTAAGAGTGGCTCAA 12 65 1 AGCTTTTAAG 0.867022 -74 ATAGAATAAGACCACTATTAGAACAAGGTTTT 12 108 1 ACATATTAGA 0.627341 -31 CTATTAGAACAAGGTTTTTATGACGAT 12 122 1 AGGTTTTATG 0.72701 -17 * ** ******* Masking position 8 Map Score: 19.1373 Number of sites scoring better than the average of aligned sites = 1993 Number in coding regions = 1752 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 5 ATCAATATAATTCAAACCCTAAACCCAAAC 1 23 1 TTCAAACCCT 0.98163 -235 ATCATGCCAATTCACACTCTTTAGACTTGA 1 119 1 TTCACACTCT 0.910594 -139 GGCTAAATTTTGAAACCTTGAGATTGTTT 1 239 0 TTGAAACCTT 0.878647 -19 ATTTACATTTTTTAAACGCTATTAGATATA 2 156 1 TTTAAACGCT 0.700427 -59 ATGCGGAGCATTCAAACCCA 3 1 0 TTCAAACCCA 0.916066 -143 CTTTCATTTTTTAACATTCTTGTCTCGCTT 3 115 0 TTAACATTCT 0.521955 -29 AATTCTATTAAAACCCTGAAACTAGGC 4 8 1 TTAAAACCCT 0.980128 -274 TTTTAGGTGATTGACACCCTAACAGGTTGG 4 223 0 TTGACACCCT 0.94877 -59 TTTCACACCTTTAAATGGATA 5 41 0 TTCACACCTT 0.90182 -11 GCTAGCGCGCTTAAAACCCCTT 7 3 0 TTAAAACCCC 0.894372 -65 ATCTTTTATGTTAAAATTCTGAGATTTTAT 11 46 1 TTAAAATTCT 0.622164 -58 AACTTTAAACCTAAAACCTAACG 11 91 0 TTTAAACCTA 0.488762 -13 TTTTTAAAACTCTCTTTAAAATT 12 4 1 TTAAAACTCT 0.934113 -135 ATCGTCATAAAAACCTTGTTCTAATAG 12 122 0 TAAAAACCTT 0.557218 -17 ********** Masking position 6 Map Score: 13.2155 Number of sites scoring better than the average of aligned sites = 1353 Number in coding regions = 1168 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 6 GTGTATTATAGCTATATTTTAATTTAAGAAT 1 206 0 GCTTATTTTA 0.928134 -52 GGCTAAATTTTGAAACCTTGAG 1 246 0 GCTAATTTTG 0.857043 -12 GCGCTATAGTGCTGACTTTTAATCTAAAAAC 3 59 0 GCTACTTTTA 0.879271 -85 AACATTCTTGTCTCGCTTTTATTATATAACA 3 102 0 TCTGCTTTTA 0.63555 -42 GTGCATATCTGCTTGATTTTAGATCCCCACT 4 91 1 GCTGATTTTA 0.978228 -191 CCCACTCAAAGCTATATTGTGCAATAATCAT 4 116 1 GCTTATTGTG 0.812566 -166 TTTATTTTAGGTTTTGTTTTGGATTGAGGGC 4 190 0 GTTTGTTTTG 0.486051 -92 ACCCTAACAGGTTGGATTTTATTTTAGGTTT 4 207 0 GTTGATTTTA 0.906859 -75 ATAGTTTCAGGCGTGATTGTATCTAAAAAGG 5 13 0 GCGGATTGTA 0.759864 -39 GCTTAAAATGGCTAAGTATTACTTATAAAGA 6 48 0 GCTAGTATTA 0.57964 -67 TTTGATAATCGCTCTATATTATATTAGCTTA 6 74 0 GCTTATATTA 0.762567 -41 TTTTAAGCGCGCTAGCTTGTGTTACAATAAA 7 17 1 GCTGCTTGTG 0.917182 -51 CTTAAAATTCGCTTGATTGAAGAGGGTTGA 7 48 1 GCTGATTGAA 0.681019 -20 ATAGCGTTGAGTTGGCTATTAAGGGGGC 8 8 0 GTTGCTATTA 0.640024 -58 GTTTTTGAAGGCTTGATTTTTAAAGTTAGGC 11 12 1 GCTGATTTTT 0.838815 -92 TATATTTATCGTTAGGTTTTAGGTTTAAAGT 11 82 1 GTTGGTTTTA 0.844796 -22 *** ******* Masking position 7 Map Score: 11.5377 Number of sites scoring better than the average of aligned sites = 1239 Number in coding regions = 1095 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 7 ********** No masking Map Score: -1.58208e-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: -1.58208e-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: -1.58208e-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