AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00220_hpyl_reg_300.orf -o00220_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 Purged sequences: HP1157 22 H. pylori predicted coding region HP1157 Input sequences: #1 HP0073 300 urease alpha subunit (ureA) (urea amidohydrolase) #2 HP0832 91 spermidine synthase (speE) #3 HP0833 76 H. pylori predicted coding region HP0833 #4 HP1154 130 H. pylori predicted coding region HP1154 #5 HP1156 107 H. pylori predicted coding region HP1156 #6 HP1399 201 arginase (rocF) Motif number 1 ATAAATTCTAAAGGGGTATTAAACGCACTTCTA 1 110 1 AAGGTTTAAA 0.827077 -191 TATATCTTTGAAGCGCTATAAAATCGTTATTAG 1 140 0 AACGTTAAAA 0.930747 -161 TTCATTAACTAATTATTATTTAAAATGAATTAG 1 176 0 AATATTTTAA 0.502539 -125 AGATTAACAGAAGCGTTCATTAACTAATTATTA 1 191 0 AACGTATTAA 0.983376 -110 GATTAAATTGAAGCGATAAAAAAG 3 2 0 AACGTAAAAA 0.972427 -75 ACCCTTATTTAAGCTTTAAATAACTATAATATT 3 48 0 AACTTAATAA 0.928003 -29 TTCCAAATCCAACCATTTTTTAAGGAACGCTCT 4 25 0 AACATTTTAA 0.879092 -106 TTAGTCGCTTAATTGTTGATTAAAATGGGCTAT 5 12 0 AATGTATTAA 0.891527 -96 CATTAAACTTAAGCGATAAATAAGATAAAATTT 5 46 1 AACGTAATAA 0.981145 -62 GGATAGCTCAAATCTTTTAAAAAGAAAAGGATA 5 80 1 AACTTAAAAA 0.897288 -28 GTTAATCCTTTAAATAATAGTGTCAGT 6 5 1 ATCTTAATAA 0.691073 -197 TTATGATTATATTCGCTCAATAAGACTATTGGG 6 37 1 ATCGTAATAA 0.900308 -165 TTAATAAGCAAATGGATAATAAATAGAACAATT 6 118 0 AAGGTATAAA 0.926205 -84 CAAAATTAACAACCAATTATTAATAAGCAAATG 6 137 0 AACATATTAA 0.950198 -65 AGGGGATTTAAAGGAGTTATAAA 6 189 1 AAGATATAAA 0.80191 -13 ** ** * ***** Masking position 12 Map Score: 16.4016 Number of sites scoring better than the average of aligned sites = 1130 Number in coding regions = 958 Number in noncoding regions = 172 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 CGTGGCCACCATTATCACTCCAATTTTAATTCTCAT 1 51 1 ATTATACTTT 0.884461 -250 TAATTCTCATTTTTTTGCGAGTTTTTGATCTTTATA 1 77 1 TTTTTGCTTT 0.97339 -224 GTTGGATGTAATTGTAGCAATGTTTTGATTTACTAA 1 223 0 ATTGTGCTTT 0.989506 -78 GCTTTTGTTACAATAATTTAGATTTTTTA 2 4 1 TTTGTACTTT 0.975379 -88 TAATTTAGATTTTTTAGCTAGCATGTTAGCAATTCA 2 24 1 TTTTTGCTGT 0.933507 -68 CTTTTTTATCGCTTCAATTTAATCAAAATT 3 5 1 TTTATGCTTT 0.981279 -72 TAACTATAATATTGTAATCTAATTTTGATTAAATTG 3 25 0 ATTGTATTTT 0.782534 -52 TACGCTTTTAATTGTTGCGTATTTTTTCAAAATTAT 4 71 1 ATTGTGCTTT 0.989506 -60 ATTTAAATGCTTTGTTGTATAATTTTGAAAAAATAC 4 89 0 TTTGTGTTTT 0.960996 -42 AGTTTAATGGTTAGTCGCTTAATTGTTGATTAAAAT 5 19 0 TTAGTGCTGT 0.886351 -89 TTTTATCTTATTTATCGCTTAAGTTTAATGGTTAGT 5 40 0 TTTATGCTTT 0.981279 -68 ***** ** *** Masking position 5 Map Score: 13.2873 Number of sites scoring better than the average of aligned sites = 762 Number in coding regions = 684 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 GTGCGTTTAATACCCCTTTAGAATTTATAAA 1 107 0 TACCCTTTAG 0.967746 -194 TTCAAGGAAAAACACTTTAAGAATAGGAGAA 1 276 1 AACCTTTAAG 0.886513 -25 GACCCTTATTTAAGCTTTAAATAACTATAAT 3 51 0 TAACTTTAAA 0.872688 -26 TTGGATTTGGAACGCCTTTTGCTTTTACGCT 4 46 1 AACCCTTTTG 0.762365 -85 CTTTTGCTTTTACGCTTTTAATTGTTGCGTA 4 61 1 TACCTTTTAA 0.970354 -70 ATTATACAACAAAGCATTTAAATTAAAAAGG 4 102 1 AAACATTTAA 0.863015 -29 ATTAAGCGACTAACCATTAAACTTAAGCGAT 5 32 1 TAACATTAAA 0.748869 -76 AGGATAGCTCAAATCTTTTAAAAAGAAAAGG 5 79 1 AAACTTTTAA 0.935409 -29 GTTAATCCTTTAAATAATAGTGT 6 3 1 TAACCTTTAA 0.956814 -199 TGAATGGTTTTACTCTTTTACACAATGAAAT 6 90 1 TACCTTTTAC 0.89684 -112 TTTATAACTCCTTTAAATCCCCTCTA 6 186 0 AACCCTTTAA 0.972574 -16 *** ******* Masking position 2 Map Score: 10.4664 Number of sites scoring better than the average of aligned sites = 848 Number in coding regions = 722 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 CCACCATTATCACTCCAATTTTAATTCTCATT 1 56 1 CCTCAATTTT 0.94933 -245 TTTAATACCCCTTTAGAATTTATAAAGATCAA 1 101 0 CTTAAATTTA 0.841999 -200 CTTTTTTATCGCTTCAATTTAATCAAAATTA 3 10 1 CCTTAATTTA 0.96909 -67 TTTTAAGGAACGCTCTATTTTAGGATAATA 4 9 0 CCTCATTTTA 0.96105 -122 TTTGGAACGCCTTTTGCTTTTACGCTTTTAAT 4 51 1 CTTTCTTTTA 0.727706 -80 TGCTTTTACGCTTTTAATTGTTGCGTATTTTT 4 65 1 CTTTATTGTT 0.820717 -66 TGGACTATCCTTTTTAATTTAAATGCTTTGT 4 110 0 CTTTAATTTA 0.944021 -21 AATGGTTAGTCGCTTAATTGTTGATTAAAATG 5 18 0 CCTTATTGTT 0.894855 -90 TCTTATTTATCGCTTAAGTTTAATGGTTAGTC 5 39 0 CCTTAGTTTA 0.946677 -69 GGGGTTATCCTTTTCTTTTTAAAAGATTTGA 5 87 0 CTTTTTTTTA 0.760744 -21 TCATAACTGACACTATTATTTAAAGGATTAAC 6 11 0 CCTATATTTA 0.689421 -191 AGAGTAAAACCATTCAAGTTTTTGATAGAAAA 6 74 0 CTTCAGTTTT 0.850893 -128 CCTTTAAATCCCCTCTAATGTTCTATTCTAAA 6 171 0 CCTCAATGTT 0.90438 -31 * *** ****** Masking position 4 Map Score: 10.0412 Number of sites scoring better than the average of aligned sites = 729 Number in coding regions = 603 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 TTTTTTTGCGAGTTTTTGATCTTTATAAAT 1 86 1 AGTTTTTGAT 0.832462 -215 AATTGTAGCAATGTTTTGATTTACTAAGAT 1 220 0 ATGTTTTGAT 0.789643 -81 TAACGAAATCAAGGTTGGATGTAATTGTAG 1 242 0 AAGGTTGGAT 0.921221 -59 TTGTTACAATAATTTAGATTTTTTAGCTAG 2 15 1 AATTTAGATT 0.633305 -77 ATTGTAATCTAATTTTGATTAAATTGAAGC 3 21 0 AATTTTGATT 0.813178 -56 GGAACGCTCTATTTTAGGATAATA 4 5 0 ATTTTAGGAT 0.905924 -126 TCCTTAAAAAATGGTTGGATTTGGAACGCC 4 32 1 ATGGTTGGAT 0.904685 -99 TAGTCGCTTAATTGTTGATTAAAATGGGCT 5 14 0 ATTGTTGATT 0.688743 -94 AATAAGATAAAATTTAGGATAGCTCAAATC 5 64 1 AATTTAGGAT 0.92228 -44 AAACCATTCAAGTTTTTGATAGAAAAACAC 6 70 0 AGTTTTTGAT 0.832462 -132 ATTGGTTGTTAATTTTGGTTTAGAATAGAA 6 153 1 AATTTTGGTT 0.946165 -49 ********** Masking position 1 Map Score: 6.76803 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 542 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 CTTATTCTCCTATTCTTAAAGTGTTTTTC 1 282 0 CTATTCTTAA 0.900435 -19 TCGCTTCAATTTAATCAAAATTAGATTACA 3 19 1 TTAATCAAAA 0.723276 -58 TATTATCCTAAAATAGAGCGTT 4 3 1 TTATCCTAAA 0.923114 -128 TGTTGCGTATTTTTTCAAAATTATACAACA 4 83 1 TTTTTCAAAA 0.785647 -48 AAGATTTGAGCTATCCTAAATTTTATCTTA 5 66 0 CTATCCTAAA 0.959534 -42 TAGCTCAAATCTTTTAAAAAGAAAAGGATA 5 83 1 CTTTTAAAAA 0.743022 -25 GGGTGTTTTTCTATCAAAAACTTGAATGGT 6 68 1 CTATCAAAAA 0.903804 -134 ATCCATTTGCTTATTAATAATTGGTTGTTA 6 134 1 TTATTAATAA 0.439199 -68 CTCTAATGTTCTATTCTAAACCAAAATTAA 6 161 0 CTATTCTAAA 0.966248 -41 ********** Masking position 2 Map Score: 4.93043 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 485 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 7 GGCCACTACCATGTCAAGGTAGT 1 4 0 ATGTCAAGGT 0.907857 -297 TCAAGGTTGGATGTAATTGTAGCAATGTTT 1 234 0 ATGTAATTGT 0.892788 -67 TATTATAGTTATTTAAAGCTTAAATAAGGG 3 50 1 ATTTAAAGCT 0.856972 -27 GCTTTTACGCTTTTAATTGTTGCGTATTTT 4 66 1 TTTTAATTGT 0.753267 -65 ATCCTTTTTAATTTAAATGCTTTGTTGTAT 4 105 0 ATTTAAATGC 0.865919 -26 TATCGCTTAAGTTTAATGGTTAGTCGCTTA 5 34 0 GTTTAATGGT 0.898888 -74 TGACACTATTATTTAAAGGATTAAC 6 6 0 ATTTAAAGGA 0.937873 -196 AAATAGAACAATTTCATTGTGTAAAAGAGT 6 101 0 ATTTCATTGT 0.892788 -101 ATTAGAGGGGATTTAAAGGAGTTATAAA 6 184 1 ATTTAAAGGA 0.937873 -18 ********** Masking position 6 Map Score: 3.38629 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 307 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 8 ********** No masking Map Score: 6.77448e-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: 6.77448e-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: 6.77448e-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