AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_hpyl_reg_100.orf -o00280_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 HP0180 257 apolipoprotein N-acyltransferase (cute) #2 HP0194 214 triosephosphate isomerase (tpi) #3 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #4 HP1468 51 branched-chain-amino-acid aminotransferase (ilvE) #5 HP1469 114 H. pylori predicted coding region HP1469 Motif number 1 AAGTAACGCTAAATCAATATAAT 1 1 1 AATAGCTAAA 0.880949 -257 ACGCTAAATCAATATAATTCAAACCCTAAACCC 1 16 1 AAAATTCAAA 0.795056 -242 ATAATTCAAACCCTAAACCCAAACCTTTCTCTC 1 29 1 CCTACCCAAA 0.731315 -229 AACAAACACCCATTACTCTTAAATCATGCCAAT 1 97 1 CATCCTTAAA 0.901399 -161 TGAAAATAATAACACAACTTAAAAAAAACTACC 1 153 1 AAAACTTAAA 0.959688 -105 ACTTAAAAAAAACTACCCTTAAAAAAATCAATC 1 169 1 AATCCTTAAA 0.966271 -89 ACCCTTAAAAAAATCAATCTAAAATTCTTAAAT 1 183 1 AATATCTAAA 0.960078 -75 AAAAACTGCTCCTAAAAACTCAAAAT 2 4 1 AATCCCTAAA 0.971303 -211 TAAAAACTCAAAATTAACCTAAAATCGCTTGAC 2 23 1 AATACCTAAA 0.986979 -192 TTTATAAGAAAAATTATTTCAAATGTAGTAGAA 2 74 0 AATATTCAAA 0.912699 -141 TTTTCTTATAAACAAAACCTAAATTGAGAAAAA 2 95 1 AAAACCTAAA 0.965668 -120 ATTGAGAAAAAATTCAATTCAAAGGGGCTATTG 2 117 1 AATATTCAAA 0.912699 -98 TATTATATCTAATAGCGTTTAAAAAATGTAAAT 2 156 0 AAACTTTAAA 0.771302 -59 CGTTAGAGAAACATGAGCCTAAAGTGCATATCT 3 68 1 ACTACCTAAA 0.943202 -214 CTCAATCCAAAACAAAACCTAAAATAAAATCCA 3 193 1 AAAACCTAAA 0.965668 -89 GTTAGGGTGTCAATCACCTAAAAGTGATACTAT 3 230 1 CATACTAAAA 0.780376 -52 TATGAATAATAAATCAACTTAAAGGCAAAGAC 3 260 1 AATACTTAAA 0.984652 -22 TTTTTTCTTAAACTCAATTAAAAAA 5 3 0 AATATTAAAA 0.779377 -112 GCTCTATATTATATTAGCTTAAAATGGCTAAGT 5 62 0 ATTACTTAAA 0.837478 -53 ** * * ****** Masking position 11 Map Score: 27.2462 Number of sites scoring better than the average of aligned sites = 778 Number in coding regions = 621 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 2 AGTAACGCTAAATCAATATAATTCAAACCC 1 12 1 AATCAATATA 0.530945 -246 TAGCGTCTTAAAACAAACACCCATTACTCT 1 86 1 AAACAAACAC 0.873521 -172 TGAAATTTGAAAATAATAACACAACTTAAA 1 146 1 AAATAATAAC 0.582984 -112 ACACAACTTAAAAAAAACTACCCTTAAAAA 1 164 1 AAAAAAACTA 0.729498 -94 ACTACCCTTAAAAAAATCAATCTAAAATTC 1 180 1 AAAAAATCAA 0.924962 -78 TAATACACTAAAACAATCTCAAGGTTTCAA 1 229 1 AAACAATCTC 0.943365 -29 TTTTTCTTATAAACAAAACCTAAATTGAGA 2 94 1 AAACAAAACC 0.832645 -121 CTAAATTGAGAAAAAATTCAATTCAAAGGG 2 113 1 AAAAAATTCA 0.711684 -102 TGTAAATTTTAAACAATAGCCCCTTTGAAT 2 133 0 AAACAATAGC 0.791126 -82 CTAACGCTTTAAAAAATTTCTTTCTAAGCA 3 44 0 AAAAAATTTC 0.667351 -238 ATTTTTGTGAAAAAAATAAACGGATCGCCC 3 164 1 AAAAAATAAA 0.884602 -118 CCTCAATCCAAAACAAAACCTAAAATAAAA 3 192 1 AAACAAAACC 0.832645 -90 AAAACCTAAAATAAAATCCAACCTGTTAGG 3 206 1 ATAAAATCCA 0.669131 -76 TACTATGAATAATAAATCAACTTAAAGGCA 3 257 1 AATAAATCAA 0.635809 -25 CCCTTTTTAGATACAATCACGCCTGAAACT 4 12 1 ATACAATCAC 0.764577 -40 ATCACGCCTGAAACTATCCATTTAAAGGTG 4 27 1 AAACTATCCA 0.607998 -25 TGAGTTTAAGAAAAAATATATTATTATTTC 5 20 1 AAAAAATATA 0.847754 -95 AGCGATTATCAAAAAATAAAGGGAAAAGAC 5 92 1 AAAAAATAAA 0.884602 -23 ********** Masking position 6 Map Score: 13.2665 Number of sites scoring better than the average of aligned sites = 1765 Number in coding regions = 1512 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 3 TTCTCTCATATATCTCGCATAAAGATAGTCATAGC 1 55 1 TTTCCTAAAA 0.926981 -203 AACAAACACCCATTACTCTTAAATCATGCCAATTC 1 97 1 CTACCTAAAC 0.79491 -161 TATTTTCAAATTTCAAGTCTAAAGAGTGTGAATTG 1 126 0 TTAATTAAAA 0.863691 -132 AAAATAATAACACAACTTAAAAAAAACTACCCTTA 1 155 1 CCACTAAAAA 0.606704 -103 AATCTAAAATTCTTAAATTAAAATATAGCTATAAT 1 198 1 TTAATAAAAA 0.847482 -60 AATATAGCTATAATACACTAAAACAATCTCAAGGT 1 219 1 TAACCAAAAA 0.803603 -39 CCTAAAATCGCTTGACGCAAAAACACTGCCTTAAT 2 40 1 CTACCAAAAA 0.961728 -175 TTTGAAATAATTTTTCTTATAAACAAAACCTAAAT 2 84 1 TTTCTTAAAA 0.839846 -131 GTTTAAAAAATGTAAATTTTAAACAATAGCCCCTT 2 138 0 TTAATTAAAA 0.861812 -77 CTCATGTTTCTCTAACGCTTTAAAAAATTTCTTTC 3 50 0 TTACCTTAAA 0.891019 -232 TCCGTTTATTTTTTTCACAAAAATATTATTCTTAT 3 153 0 TTTCCAAAAA 0.917721 -129 AACGGATCGCCCTCAATCCAAAACAAAACCTAAAA 3 182 1 CTAACAAAAA 0.889206 -100 TTTCACACCTTTAAATGGATAGTTT 4 37 0 TTACCTTTAA 0.587351 -15 AATGGCTAAGTATTACTTATAAAGAAATAATAATA 5 38 0 TTACTTAAAA 0.95161 -77 TACTTAGCCATTTTAAGCTAATATAATATAGAGCG 5 61 1 TTAACAATAA 0.696783 -54 * * ** * **** * Masking position 13 Map Score: 8.98092 Number of sites scoring better than the average of aligned sites = 1019 Number in coding regions = 875 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 4 TGCGAGATATATGAGAGAAAGGTTTGGGTT 1 44 0 ATGAGAGAAA 0.923408 -214 TTGGCATGATTTAAGAGTAATGGGTGTTTG 1 99 0 TTAAGAGTAA 0.903492 -159 GACTTGAAATTTGAAAATAATAACACAACT 1 142 1 TTGAAAATAA 0.829249 -116 ATAACACAACTTAAAAAAAACTACCCTTAA 1 161 1 TTAAAAAAAA 0.877918 -97 GGTTTTGTTTATAAGAAAAATTATTTCAAA 2 84 0 ATAAGAAAAA 0.950391 -131 AAAACCTAAATTGAGAAAAAATTCAATTCA 2 108 1 TTGAGAAAAA 0.979174 -107 TCATTGAACGATAAGAATAATATTTTTGTG 3 143 1 ATAAGAATAA 0.909495 -139 AATAATATTTTTGTGAAAAAAATAAACGGA 3 158 1 TTGTGAAAAA 0.881112 -124 TTAATTGAGTTTAAGAAAAAATATATTATT 5 15 1 TTAAGAAAAA 0.973342 -100 ********** Masking position 6 Map Score: 10.7669 Number of sites scoring better than the average of aligned sites = 553 Number in coding regions = 490 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 AAATCGCTTGACGCAAAAACACTGCCTTAA 2 44 1 ACGCAAAAAC 0.955183 -171 CCCTGAAACTAGGCAAAGACTGCTTAGAAA 3 24 1 AGGCAAAGAC 0.995614 -258 ATCAACTTAAAGGCAAAGAC 3 272 1 AGGCAAAGAC 0.995614 -10 AAAAAATAAAGGGAAAAGACTGA 5 102 1 GGGAAAAGAC 0.971025 -13 ********** Masking position 5 Map Score: 3.39787 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 18 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ATCAATATAATTCAAACCCTAAACCCAAAC 1 23 1 TTCAAACCCT 0.989 -235 GGTGTTTGTTTTAAGACGCTATGACTATCT 1 77 0 TTAAGACGCT 0.883523 -181 ATCATGCCAATTCACACTCTTTAGACTTGA 1 119 1 TTCACACTCT 0.94381 -139 GGCTAAATTTTGAAACCTTGAGATTGTTT 1 239 0 TTGAAACCTT 0.933854 -19 ATTTACATTTTTTAAACGCTATTAGATATA 2 156 1 TTTAAACGCT 0.905204 -59 AATTCTATTAAAACCCTGAAACTAGGC 3 8 1 TTAAAACCCT 0.975553 -274 TTTTAGGTGATTGACACCCTAACAGGTTGG 3 223 0 TTGACACCCT 0.986762 -59 TTTCACACCTTTAAATGGATA 4 41 0 TTCACACCTT 0.961291 -11 ********** Masking position 6 Map Score: 9.72797 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 248 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 ********** No masking Map Score: 6.56131e-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 8 ********** No masking Map Score: 6.56131e-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: 6.56131e-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