AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_hpyl_reg_300.orf -o00520_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 HP0359 300 H. pylori predicted coding region HP0359 #2 HP0360 216 UDP-glucose 4-epimerase #3 HP0640 62 poly(A) polymerase (papS) #4 HP0643 164 glutamyl-tRNA synthetase (gltX) Motif number 1 ATGTTATACCAAAAACCCTAAAAATTTAAG 1 41 1 AAAAACCCTA 0.972252 -260 TATATTGCGCAAAATCTCTTTTGCTTTATA 1 125 0 AAAATCTCTT 0.968194 -176 CTTTTAACTCAAAGCTCCTTGATGGAAGAT 1 191 0 AAAGCTCCTT 0.90047 -110 GTCTTGGTTGAGAAATCCTAAACGATTGGA 1 245 0 AGAAATCCTA 0.838531 -56 ATTATAGATTAAATTTTCTTAAAAAATCCT 2 134 1 AAATTTTCTT 0.769691 -83 AATTTTCTTAAAAAATCCTTAAATAATAAA 2 145 1 AAAAATCCTT 0.985338 -72 AAAACCCCTTTTAAAATGAA 2 207 0 AAAACCCCTT 0.982392 -10 CAAAATTCCTTAAAAATTCTA 3 2 1 AAAATTCCTT 0.982955 -61 AAAATTCCTTAAAAATTCTAAAAAGATATA 3 12 1 AAAAATTCTA 0.931554 -51 TTTTACTCTTAAAATTTCTTTGTGTTATTA 3 40 0 AAAATTTCTT 0.962707 -23 AGGTATAATCAAAAACTATTTTTAAATAAA 4 137 1 AAAAACTATT 0.761357 -28 AAAAACCCTTTATTTAAAAA 4 155 0 AAAAACCCTT 0.989805 -10 ********** Masking position 3 Map Score: 18.9411 Number of sites scoring better than the average of aligned sites = 1455 Number in coding regions = 1277 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 2 CTATATTTTGACCCTTGATGCCAGTG 1 3 1 ATATTTGCTT 0.873617 -298 TAAGGAGCTTAAATTTTTAGGGTTTTTGGTATAA 1 44 0 AAATTTTGTT 0.869702 -257 TTCGCTTTCTATCTTTGGCGGCTTTATCGGCTTA 1 87 0 ATCTTTGGTT 0.973643 -214 ATTGCGCAAAATCTCTTTTGCTTTATAACTTTTC 1 118 0 ATCTCTTGTT 0.958841 -183 CAAATAAAAAATCTCAATCCAATTTAATCTTCCA 1 165 1 ATCTCATCTT 0.831138 -136 TTTTCTCCTTAAATTTTTTCTTTTTATCAGTCGT 1 275 0 AAATTTTCTT 0.828249 -26 CATTTTTACAATCTTTGGGGAATTAGC 2 4 0 ATCTTTGGTT 0.973643 -213 CTATAATTTCATCTTTATTGGCTTTTAAGGGCTT 2 107 0 ATCTTTTGTT 0.987695 -110 CTATTATAACATCTTAATCCCATTTATTATTTAA 2 163 0 ATCTTATCTT 0.944313 -54 ATAATAGTTGTTATTTTTTCATTTTAAAAGGGGT 2 190 1 TTATTTTCTT 0.814678 -27 GTGTTATTATATCTTTTTAGAATTTTTAAGGAAT 3 15 0 ATCTTTTGTT 0.987693 -48 CTCTTAAAATTTCTTTGTGTTATTATATCTTTTT 3 31 0 TTCTTTTTTT 0.822252 -32 GCTAACGCCAAGCTTTTTATGGTTGGTTATCAAA 4 26 0 AGCTTTTTTT 0.748534 -139 ACCTAAAGAATACTTAATTGTGTTGTGGTAGTTC 4 107 0 TACTTATGTT 0.688192 -58 ****** * * ** Masking position 4 Map Score: 15.3755 Number of sites scoring better than the average of aligned sites = 986 Number in coding regions = 878 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 TTAGAACAAATATAAGCCGATAAAGCCGCCAA 1 75 1 TAAACCGATA 0.927615 -226 CCGCCAAAGATAGAAAGCGAAAAGTTATAAAG 1 100 1 TAAAGCGAAA 0.982229 -201 AGCGAAAAGTTATAAAGCAAAAGAGATTTTGC 1 115 1 TAAAGCAAAA 0.980775 -186 TTTTGCGCAATATAAAGAACAAAGCAAATAAA 1 141 1 TAAAGAACAA 0.911294 -160 ACACGACTGATAAAAAGAAAAAATTTAAGGAG 1 273 1 TAAAGAAAAA 0.981999 -28 AAAGAAAAAATTTAAGGAGAAAACG 1 286 1 TTAAGAGAAA 0.882462 -15 TATAAGCCCTTAAAAGCCAATAAAGATGAAAT 2 104 1 TAAACCAATA 0.922129 -113 AAACCCCTTTTAAAATGAAAAAATAACAACTA 2 194 0 TAAAGAAAAA 0.981999 -23 TTAAAAATTCTAAAAAGATATAATAACACAAA 3 20 1 TAAAGATATA 0.818544 -43 TCATGTTTGATAAAAACAGAACTACCACAACA 4 89 1 TAAACAGAAC 0.866419 -76 ATTCTTTAGGTATAATCAAAAACTATTTTTAA 4 130 1 TAAACAAAAA 0.969503 -35 ** ** ****** Masking position 5 Map Score: 13.6664 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 278 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 TTATACCAAAAACCCTAAAAATTTAAGCTC 1 44 1 AACCCTAAAA 0.978151 -257 TTGGTTGAGAAATCCTAAACGATTGGATCG 1 242 0 AATCCTAAAC 0.808652 -59 CTGAGCTATAAGCCCTTAAAAGCCAATAAA 2 98 1 AGCCCTTAAA 0.973764 -119 AGCCCTTAAAAGCCAATAAAGATGAAATTA 2 108 1 AGCCAATAAA 0.373941 -109 TTTCTTAAAAAATCCTTAAATAATAAATGG 2 148 1 AATCCTTAAA 0.975044 -69 CAAAATTCCTTAAAAATTCTAAAA 3 5 1 ATTCCTTAAA 0.915686 -58 ATTCCTTAAAAATTCTAAAAAGATATAATA 3 15 1 AATTCTAAAA 0.833873 -48 GCTTTTTACTCTTAAAATTTCTTTGT 3 47 0 TACTCTTAAA 0.712357 -16 TTTGATAACCAACCATAAAAAGCTTGGCGT 4 26 1 AACCATAAAA 0.8615 -139 CCAAGTGCTAATCTCTTAAATGATGCCTAT 4 59 1 ATCTCTTAAA 0.85598 -106 ATACCTAAAGAATACTTAATTGTGTTGTGG 4 113 0 AATACTTAAT 0.487267 -52 AAAAACCCTTTATTTAAAAATAG 4 152 0 AACCCTTTAT 0.712699 -13 ********** Masking position 9 Map Score: 7.69228 Number of sites scoring better than the average of aligned sites = 2120 Number in coding regions = 1843 Number in noncoding regions = 277 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 5 CAACCAAGACACGACTGATAAAAAGAAAAAAT 1 265 1 ACACTATAAA 0.957019 -36 TCCTAAGCCCACCATTTTTACAATCTTTGGGG 2 18 0 ACATTTTACA 0.860259 -199 CGGAGGTTCAACTCCTCCTAAGCCCACCATTT 2 33 0 ACCCTCTAAG 0.947314 -184 GTTAGAGCGCACCCCTGATAAGGGTGAGGTCG 2 63 0 ACCCTATAAG 0.955341 -154 TGAAAAAATAACAACTATTATAACATCTTAAT 2 179 0 ACACTTTATA 0.913986 -38 AAAACCCCTTTTAAAATGAAAAAAT 2 202 0 ACCCTTTAAA 0.980457 -15 ATATCTTTTTAGAATTTTTAAGGAATTTTG 3 9 0 AGATTTTAAG 0.764465 -54 ATAATCAAAAACTATTTTTAAATAAAGGGTTT 4 141 1 ACATTTTAAA 0.952397 -24 ** *** ***** Masking position 10 Map Score: 2.28529 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 248 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 AAAGATAGAAAGCGAAAAGTTATAAAGCAA 1 105 1 AGCGAAAAGT 0.938011 -196 AGGAGCTTTGAGTTAAAAGACTTGCGGCGT 1 202 1 AGTTAAAAGA 0.919668 -99 TAACCACCTGAGCTATAAGCCCTTAAAAGC 2 91 1 AGCTATAAGC 0.968886 -126 AAATTTTAAGAGTAAAAAGC 3 53 1 AGTAAAAAGC 0.947382 -10 GTTATCAAAAAGCTAACAGCGTTT 4 5 0 AGCTAACAGC 0.978802 -160 ********** Masking position 5 Map Score: 0.848318 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 148 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 ********** No masking Map Score: -7.57276e-14 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: -7.57276e-14 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: -7.57276e-14 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