AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_hpyl_reg_100.orf -o00680_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 HP0875 300 catalase Motif number 1 GCTATAATACACTAAAACAATCTCAAGGTT 1 24 0 ACTAAAACAA 0.867189 -234 AAATTCTTAAATTAAAATATAGCTATAATA 1 45 0 ATTAAAATAT 0.743245 -213 AAAAACTACCCTTAAAAAAATCAATCTAAA 1 73 0 CTTAAAAAAA 0.986012 -185 AATAACACAACTTAAAAAAAACTACCCTTA 1 89 0 CTTAAAAAAA 0.986012 -169 ACCCATTACTCTTAAATCATGCCAATTCAC 1 145 0 CTTAAATCAT 0.849283 -113 GTCATAGCGTCTTAAAACAAACACCCATTA 1 167 0 CTTAAAACAA 0.98627 -91 AAATTTAAAAAATAAAAATCAA 2 3 1 ATTTAAAAAA 0.81212 -298 AAAAATAAAAATCAAAAAAAAAAAAAAAAC 2 18 1 ATCAAAAAAA 0.865006 -283 AATAATTATTATTAAAACCAGATTAAAAAT 2 81 1 ATTAAAACCA 0.939442 -220 TTAAAACCAGATTAAAAATAAAATTTTGTT 2 92 1 ATTAAAAATA 0.907766 -209 AATAAGAAAGATTAAAAACAAAATTTTATT 2 108 0 ATTAAAAACA 0.938362 -193 GTTTTTCATTCTTAAAAAAAGGATTTTTTA 2 173 1 CTTAAAAAAA 0.986012 -128 ATTCAATTTCCTTAAAAAATCCTTTTTTTA 2 185 0 CTTAAAAAAT 0.967169 -116 CTTTTATGATCTTAAATCTTCGTAATATGA 2 273 0 CTTAAATCTT 0.558021 -28 ********** Masking position 5 Map Score: 22.7064 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 590 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 2 TTTGAAACCTTGAGATTGTTTTAGTGTATTA 1 19 1 TGAGATTTTT 0.680024 -239 TATTATAGCTATATTTTAATTTAAGAATTTT 1 45 1 ATATTTTATT 0.758439 -213 AATTTTAGATTGATTTTTTTAAGGGTAGTTT 1 70 1 TGATTTTTTA 0.758051 -188 TAAGGGTAGTTTTTTTTAAGTTGTGTTATTA 1 89 1 TTTTTTTAGT 0.742786 -169 TTTTAAGTTGTGTTATTATTTTCAAATTTCA 1 102 1 TGTTATTTTT 0.869839 -156 AAGAGTAATGGGTGTTTGTTTTAAGACGCTA 1 162 1 GGTGTTTTTT 0.80221 -96 AGGGTTTGAATTATATTGATTTAGCGTTACT 1 236 1 TTATATTATT 0.870821 -22 TTTTTTTTTTTGATTTTTATTTTTTAAATTT 2 11 0 TGATTTTATT 0.977573 -290 ATTTTGTTTTTTTTTTTTTTTTGATTTTTAT 2 22 0 TTTTTTTTTT 0.94354 -279 ATGCATTGACGGATTTTGTTTTTTTTTTTTT 2 34 0 GGATTTTTTT 0.95389 -267 AAACAAAATTTTATTTTTAATCTGGTTTTAA 2 92 0 TTATTTTAAT 0.712769 -209 AATAAAATTTTGTTTTTAATCTTTCTTATTT 2 108 1 TGTTTTTATC 0.82281 -193 TTAATCTTTCTTATTTTCATTAATTGTTACG 2 123 1 TTATTTTATT 0.964422 -178 ACCCCCTTAAGTATTTCTATTCGTAACAATT 2 144 0 GTATTTCATT 0.803585 -157 TACTTAAGGGGGTTTTTCATTCTTAAAAAAA 2 162 1 GGTTTTTATT 0.95389 -139 CTTTTTTCCTTTTATGATCTTA 2 289 0 TTTTTTCTTT 0.806683 -12 ******* *** Masking position 6 Map Score: 12.9787 Number of sites scoring better than the average of aligned sites = 1973 Number in coding regions = 1564 Number in noncoding regions = 409 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 3 GAGATTGTTTTAGTGTATTATAGCTATATT 1 30 1 TAGTGTATTA 0.975063 -228 AAGATAGTCATAGCGTCTTAAAACAAACAC 1 173 0 TAGCGTCTTA 0.978383 -85 TGAGATAGAATAGTATAATAATTATTATTA 2 65 1 TAGTATAATA 0.865197 -236 GTAATCGGCTTAGTGTCATATTACGAAGAT 2 258 1 TAGTGTCATA 0.986737 -43 ********** Masking position 6 Map Score: 1.66395 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 15 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 4 TAATACACTAAAACAATCTCAAGGTTTCAA 1 20 0 AAACAATCTC 0.942387 -238 CCCTTAAAAAAATCAATCTAAAATTCTTAA 1 65 0 AATCAATCTA 0.955542 -193 AATCATGCCAATTCACACTCTTTAGACTTG 1 131 0 ATTCACACTC 0.932124 -127 AATCAATATAATTCAAACCCTAAACCCAAA 1 227 0 ATTCAAACCC 0.932124 -31 AGTAACGCTAAATCAATATAATTCAAACCC 1 237 0 AATCAATATA 0.768788 -21 TTATTATACTATTCTATCTCAATGCATTGA 2 56 0 ATTCTATCTC 0.955155 -245 GACTAACAAGATTCAATTTCCTTAAAAAAT 2 195 0 ATTCAATTTC 0.940727 -106 ********** Masking position 1 Map Score: 3.32837 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 373 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 AAATCAATCTAAAATTCTTAAATTAAAATA 1 56 0 AAAATTCTTA 0.720522 -202 CTTAAAAAAAACTACCCTTAAAAAAATCAA 1 79 0 ACTACCCTTA 0.964993 -179 ATGCCAATTCACACTCTTTAGACTTGAAAT 1 127 0 ACACTCTTTA 0.923451 -131 CTTAAAACAAACACCCATTACTCTTAAATC 1 157 0 ACACCCATTA 0.870225 -101 AGACGCTATGACTATCTTTATGCGAGATAT 1 185 1 ACTATCTTTA 0.884685 -73 AAGAATGAAAAACCCCCTTAAGTATTTCTA 2 156 0 AACCCCCTTA 0.924871 -145 ATTTCCTTAAAAAATCCTTTTTTTAAGAAT 2 180 0 AAAATCCTTT 0.805248 -121 AACAAGATTCAATTTCCTTAAAAAATCCTT 2 191 0 AATTTCCTTA 0.843484 -110 ********** Masking position 1 Map Score: 1.39303 Number of sites scoring better than the average of aligned sites = 896 Number in coding regions = 748 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 6 ********** No masking Map Score: -1.12023e-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 7 ********** No masking Map Score: -1.12023e-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: -1.12023e-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