AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_hpyl_reg_300.orf -o00620_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 HP0121 186 phosphoenolpyruvate synthase (ppsA) #2 HP0282 50 H. pylori predicted coding region HP0282 #3 HP0289 66 toxin-like outer membrane protein #4 HP0290 47 diaminopimelate decarboxylase (dap decarboxylase) (lysA) #5 HP0371 123 biotin carboxyl carrier protein (fabE) #6 HP0557 22 acetyl-coenzyme A carboxylase (accA) #7 HP0558 300 beta ketoacyl-acyl carrier protein synthase II (fabF) #8 HP0688 143 H. pylori predicted coding region HP0688 #9 HP0690 281 acetyl coenzyme A acetyltransferase (thiolase) (fadA) #10 HP0950 77 acetyl-CoA carboxylase beta subunit (accD) #11 HP1045 197 acetyl-CoA synthetase (acoE) #12 HP1222 65 D-lactate dehydrogenase (dld) #13 HP1483 26 gerC2 protein (gerC2) #14 HP1490 103 hemolysin #15 HP1491 138 phosphate permease Motif number 1 AGTTAGGTATTTTTGAATAGAAAGGGTGGTT 1 10 0 TTTTGATAAA 0.769277 -177 GGTGTATTCTTTTTGGTTTATGATTTTATTGT 1 55 0 TTTTGGTTTG 0.847073 -132 CATGATAGAGCTTTAGTTTTAGCTAGTTTGTA 1 109 0 CTTTAGTTAG 0.851101 -78 CATTGTTATATTTTTGTTTTAAGAAACTTAAT 1 145 1 TTTTTGTTAA 0.884713 -42 TAAGCCTTAATCTTGGATATAATGGCGTAATC 2 15 1 TCTTGGTAAA 0.78475 -36 ATGAGAGAGTTTTTGGCTACTATCTAGGAAAT 3 29 1 TTTTGGTATA 0.873258 -38 CTTTTTTGCTATAATGCTTCGTTC 4 3 1 TTTTTGTAAA 0.889397 -45 TAACAATAATTTTTTGCTAAAAACGCTTATGG 5 46 1 TTTTTGTAAA 0.71584 -78 AAAGCCAAATTTTTGACTAAAACCTGGAGACA 7 24 0 TTTTGATAAA 0.621457 -277 TAAAACTAGATTTTAGCTAAAGCCAAATTTTT 7 42 0 TTTTAGTAAG 0.518208 -259 AACTCCTATCCTTTAGGTAGAGATATAAGTGC 7 90 1 CTTTAGTAAG 0.847614 -211 TTTTAACCTCTTTTAGCTTGAATATAGCCTAA 7 129 0 TTTTAGTTAA 0.950984 -172 TTTTTCTAATTTTTAGTTATATCGTTTTTAGA 8 36 1 TTTTAGTAAT 0.699376 -108 GTTATATCGTTTTTAGATTAAAAGTCAGCACT 8 51 1 TTTTAGTTAA 0.951893 -93 TTAGGTTTTGTTTTGGATTGAGGGCGATCCGT 9 183 0 TTTTGGTTAG 0.968395 -99 TTGGATTTTATTTTAGGTTTTGTTTTGGATTG 9 195 0 TTTTAGTTTG 0.774734 -87 GTCTTTGCCTTTAAGTTGATTTAT 9 268 0 CTTTGCTTAA 0.673119 -14 TGTATCCAAGTTTTGCTTATAATAAACAAAAT 10 24 0 TTTTGCTAAA 0.882164 -54 AAGAGTGTGAGTTTGGATATAATAATAAAAAA 11 146 1 GTTTGGTAAA 0.81052 -52 TATCGTTAGGTTTTAGGTTTAAAGTT 14 88 1 TTTTAGTTAA 0.954783 -16 CTCTTTAAAATTTTACTTTAAGATACCATATA 15 22 1 TTTTACTTAG 0.782406 -117 ****** ** ** Masking position 8 Map Score: 22.0689 Number of sites scoring better than the average of aligned sites = 987 Number in coding regions = 814 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 2 ACTAAGCTTTTTAATAAGAGGGTGTATTCTTTTTGGTTTATGAT 1 63 0 TTTAGTTTTT 0.809793 -124 ATATTTTTGTTTTAAGAAACTTAATGATCATTTTAAGGGAGTTT 1 152 1 TTAATTTTTT 0.920351 -35 TAATGCTTCGTTCAAATTTTATGGTTAGGTTTTTCT 4 22 1 TTATTTTTTT 0.970591 -26 AAAGCCTTTAAAGTTTGTTAATAATTATGTTATTATAACAA 5 8 1 TTATTTTGTT 0.797108 -116 AACTTGGAGCGTTTGTCTCCAGGTTTTAGTCAAAAAT 7 4 1 TTATGTTTTT 0.974061 -297 GCACTTATATCTCTACCTAAAGGATAGGAGTTTTTCGTGCTGTT 7 78 0 CTAAGTTTTT 0.754209 -223 TGGGTTTGAATGCTCCGCATTAAAGTTTTTCTAATTTTT 8 6 1 TTATGTTTTT 0.974061 -138 TAAAGTTTTTCTAATTTTTAGTTATATCGTTTTTAGATTAAAAG 8 31 1 CTTTTTTTTT 0.71381 -113 TCCTTTCATTTTTTAACATTCTTGTCTCGCTTTTATTATATAAC 8 103 0 TTATTTTTTT 0.970591 -41 GCAATAATCATTGAACGATAAGAATAATATTTTTGTGAAAAAAA 9 136 1 TTATGTTTTT 0.974061 -146 TTTAAGTTGATTTATTATTCATAGTATCACTTTTAGGTGATTGA 9 239 0 TTTTTTTTTT 0.914434 -43 TTTTGCAGTTTTGTTAGGATTGTATCCAAGTTTTGCTTATAATA 10 32 0 TTTAGTTTTT 0.809793 -46 CCCCTTTAGGTTTCATCGTGCTATTTCCTTTTTTATCAGTCTCA 11 66 1 TTATTTTTTT 0.970591 -132 GCATCTCCTTTTTCATGGTTTTAAGCGCATTTTTTATTATTATA 11 163 0 TTATTGTTTT 0.797108 -35 AAGGCTTGATTTTTAAAGTTAGGCTTAATCTTTTATGTTAAAAT 14 19 1 TTATGTTTTT 0.974061 -85 ATTTTATATATTTTATATTTATCGTTAGGTTTTAGGTTTAAAGT 14 69 1 TTATTTTTTA 0.726084 -35 TTTTTAAAACTCTCTTTAAAATTTTACTTTAAGAT 15 2 1 TTACTTTTTT 0.838848 -137 ** * * * * **** Masking position 21 Map Score: 20.4638 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 342 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 3 AGAATACACCCTCTTATTAAAAAGCTTAGTAA 1 77 1 CTTATTAAAA 0.640246 -110 TAATTATTAACAAACTTTAAAGGCTTT 5 6 0 CACTTTAAAG 0.939035 -118 GTGTTTGTGGCATATTTTAAAATAATATAAGG 5 91 1 CATTTTAAAA 0.950918 -33 AATATCCATGCAGACTTTAAAGAACAAAGCCT 7 180 1 CACTTTAAAG 0.939035 -121 CAATAGCTCCTCATTTCAAAACTTTAATTCA 7 280 0 CTTTTCAAAA 0.852853 -21 ACGCTCCTTTCATTTTTTAACATTCTTGTCTC 8 119 0 CATTTTAACA 0.753435 -25 ATGTTTCTCTAACGCTTTAAAAAATTTCTTTC 9 50 0 AACTTTAAAA 0.860503 -232 AAAAGTATCCCTCCCTTTAAAAGAGTGTGAGT 11 126 1 CTCTTTAAAA 0.97679 -72 GTAACATAACCTTATTTTAAAAACTAAGGATA 12 14 0 CTTTTTAAAA 0.943578 -52 TTTAAAAATCAAGCCTTCAAAAACC 14 4 0 AACTTCAAAA 0.681313 -100 AAGATTAAGCCTAACTTTAAAAATCAAGCCTT 14 19 0 CTCTTTAAAA 0.97679 -85 TTTTTAAAACTCTCTTTAAAATTTTACTTTA 15 10 1 CTCTTTAAAA 0.97679 -129 GCCCTTGAGCCACTCTTAAAAAGCGTTGTTTG 15 69 0 CACTTAAAAA 0.861011 -70 ** ******** Masking position 9 Map Score: 14.3284 Number of sites scoring better than the average of aligned sites = 694 Number in coding regions = 557 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 4 AACCACCCTTTCTATTCAAAA 1 1 1 AACCCCCTTT 0.968524 -186 ATACCTAACTAACCGCCCATTATACAATAAA 1 32 1 AACCCCCATT 0.916249 -155 CAAAAAGAATACACCCTCTTATTAAAAAGCT 1 72 1 ACACCTCTTA 0.933963 -115 AAAACTCCCTTAAAATGATCAT 1 175 0 AAACCCCTTA 0.873725 -12 GTAGCCAAAAACTCTCTCATTTGATTAAATC 3 18 0 ACTCCTCATT 0.714053 -49 TAAATGCTACCCTCTCATTTCCTAGATAG 3 48 0 ACCCCTCATT 0.957195 -19 AGACTATTTTAACCTCTTTTAGCTTGAATAT 7 136 0 AACCCTTTTA 0.621591 -165 AATTCAGTGAAACCACCCCTTGCTTAAAGCA 7 255 0 AACCCCCCTT 0.921936 -46 TACACGCTCCTTTCATTTTTTA 8 132 0 ACACCTCCTT 0.928492 -12 ATCACCCTTTTTGTAGTCATAA 11 2 1 TCACCTTTTT 0.534879 -196 GAAAAAAGTATCCCTCCCTTTAAAAGAGTGT 11 123 1 TCCCCCCTTT 0.943638 -75 ATATCCAAACTCACACTCTTTTAAAGGGAGG 11 135 0 TCACCTCTTT 0.908267 -63 TTTTTAAAACTCTCTTTAAAATTTTAC 15 7 1 AAACCTCTTT 0.947909 -132 TTAGCCCTTGAGCCACTCTTAAAAAGCGTTG 15 73 0 AGCCCTCTTA 0.813147 -66 **** ****** Masking position 10 Map Score: 13.7302 Number of sites scoring better than the average of aligned sites = 875 Number in coding regions = 756 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 CGTTTAAGCCTTAATCTTGGATATAAT 2 6 1 AACCTTATCT 0.894528 -45 TCAAAATCCTAACTTTGTAAAA 6 7 0 AACCTAATTT 0.95894 -16 ATTTTAGCTAAAGCCAAATTTTTGACTAAAAC 7 33 0 AACCAAATTT 0.845617 -268 GCTTTAGCTAAAATCTAGTTTTATCCCAACAG 7 51 1 AATCTAGTTT 0.509289 -250 TACTCTTAAGCTAATTTTGTTTATTATA 10 7 1 TAGCTAATTT 0.808893 -71 GTTAGGATTGTATCCAAGTTTTGCTTATAATA 10 32 0 TACCAAGTTT 0.765971 -46 GTTTTTCCTTAATTTTGCAGTTTTG 10 63 0 TTCCTTATTT 0.673101 -15 GTTTATCCTTAGTTTTTAAAATAAG 12 4 1 TACCTTATTT 0.946701 -62 CATTGTAACATAACCTTATTTTAAAAACTAAG 12 18 0 TACCTTATTT 0.946709 -48 GGTTTTTGAAGGCTTGATTTTTAAAGTTAG 14 9 1 AAGCTTGTTT 0.819481 -95 ATAAAAGATTAAGCCTAACTTTAAAAATCAAG 14 23 0 AACCTAATTT 0.95894 -81 ATCGTCATAAAAACCTTGTTCTAATAGTGGTC 15 117 0 AACCTTGTCT 0.872423 -22 ** ***** *** Masking position 10 Map Score: 8.07927 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 253 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 ATTCAAAAATACCTAACTAACCGCCCATTAT 1 24 1 ACCTAACAAC 0.934717 -163 ACTTCCTAAAAAATGATTACGCCA 2 37 0 TCCTAAAAAT 0.663356 -14 AGAAAAACCTAACCATAAAATTTGAAC 4 31 0 ACCTAACATA 0.888766 -17 CATGGATATTTCCTACCCCAAAAAGACTATT 7 159 0 TCCTACCCAA 0.846269 -142 GCAAGGAGCTTCCTAACTAAAGCATTCCATT 7 227 0 TCCTAACAAA 0.979675 -74 TCGCCCTCAATCCAAAACAAAACCTAAAATA 9 188 1 TCCAAAAAAA 0.74996 -94 TTGGATACAATCCTAACAAAACTGCAAAATT 10 47 1 TCCTAACAAA 0.979675 -31 TATTATTATATCCAAACTCACACTCTTTTAA 11 142 0 TCCAAACCAC 0.808286 -56 TAAACCTAAAACCTAACGATAAATATAAAAT 14 78 0 ACCTAACATA 0.888766 -26 ******* *** Masking position 5 Map Score: 3.48493 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 112 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 CCATTATACAATAAAATCATAAACCAAAAA 1 48 1 ATAAAATCAT 0.693281 -139 AATCATAAACCAAAAAGAATACACCCTCTT 1 62 1 CAAAAAGAAT 0.562488 -125 TTTCTTAAAACAAAAATATAACAATGATAG 1 141 0 CAAAAATATA 0.714539 -46 ACTTCCTAAAAAATGATTACGCCATTA 2 34 0 AAAAAATGAT 0.585819 -17 CTCTCATTTGATTAAATCAAAGGGA 3 6 0 ATTAAATCAA 0.617528 -61 TTGGCTTTAGCTAAAATCTAGTTTTATCCC 7 48 1 CTAAAATCTA 0.740132 -253 CCACCCCTTGCTTAAAGCAAGGAGCTTCCT 7 244 0 CTTAAAGCAA 0.510988 -57 CAAGAATGTTAAAAAATGAAAGGAGCGTGT 8 123 1 AAAAAATGAA 0.813708 -21 GAGTGGGGATCTAAAATCAAGCAGATATGC 9 93 0 CTAAAATCAA 0.897912 -189 ATTTTTTTCACAAAAATATTATTCTTATCG 9 151 0 CAAAAATATT 0.447681 -131 ATTTTTGTGAAAAAAATAAACGGATCGCCC 9 164 1 AAAAAATAAA 0.85984 -118 AAAACAAAACCTAAAATAAAATCCAACCTG 9 201 1 CTAAAATAAA 0.845696 -81 TACTATGAATAATAAATCAACTTAAAGGCA 9 257 1 AATAAATCAA 0.694861 -25 TGAGACTGATAAAAAAGGAAATAGCACGAT 11 80 0 AAAAAAGGAA 0.691687 -118 ACAAGCCATGAAAAAAGAAAAGTC 13 13 1 AAAAAAGAAA 0.759089 -14 AGCCTAACTTTAAAAATCAAGCCTTCAAAA 14 14 0 TAAAAATCAA 0.58076 -90 AACGATAAATATAAAATATATAAAATCTCA 14 65 0 ATAAAATATA 0.5848 -39 ********** Masking position 5 Map Score: 5.70661 Number of sites scoring better than the average of aligned sites = 1978 Number in coding regions = 1653 Number in noncoding regions = 325 Number of orfs with sites within 600 bp upstream = 220 Fraction of orfs with sites within 600 bp upstream = 0.0353357 Motif number 8 GCGGTTAGTTAGGTATTTTTGAATAGAAAG 1 18 0 AGGTATTTTT 0.884095 -169 GATCATTTTAAGGGAGTTTT 1 177 1 AGGGAGTTTT 0.973406 -10 TAATCAAATGAGAGAGTTTTTGGCTACTAT 3 22 1 AGAGAGTTTT 0.946565 -45 CCTAAAGGATAGGAGTTTTTCGTGCTGTTG 7 77 0 AGGAGTTTTT 0.855703 -224 CTGCTTAGAAAGAAATTTTTTAAAGCGTTA 9 43 1 AGAAATTTTT 0.893983 -239 TTTGATAAATAGGAATGTTTAAGGA 12 51 1 AGGAATGTTT 0.855694 -15 AAAATTTTAAAGAGAGTTTTAAAAA 15 6 0 AGAGAGTTTT 0.946565 -133 ********** Masking position 1 Map Score: 2.97413 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 244 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 9 TTTTTGGTTTATGATTTTATTGTATAATGG 1 48 0 ATGATTTTAT 0.725305 -139 TGTATTACTAAGCTTTTTAATAAGAGGGTG 1 83 0 AGCTTTTTAA 0.749947 -104 TTACAAAGTTAGGATTTTGA 6 13 1 AGGATTTTGA 0.845547 -10 GCCTAGTTTCAGGGTTTTAATAGAATT 9 8 0 AGGGTTTTAA 0.966095 -274 CCTAACAGGTTGGATTTTATTTTAGGTTTT 9 206 0 TGGATTTTAT 0.809622 -76 CAGTTTTGTTAGGATTGTATCCAAGTTTTG 10 41 0 AGGATTGTAT 0.763469 -37 CTCCTTTTTCATGGTTTTAAGCGCATTTTT 11 173 0 ATGGTTTTAA 0.814462 -25 TTTGAAGGCTTGATTTTTAAAGTTAGGCTT 14 15 1 TGATTTTTAA 0.559204 -89 ATAAAATCTCAGAATTTTAACATAAAAGAT 14 46 0 AGAATTTTAA 0.891328 -58 AATTTTAAAGAGAGTTTTAAAAA 15 4 0 AGAGTTTTAA 0.889377 -135 TATTAGAACAAGGTTTTTATGACGAT 15 123 1 AGGTTTTTAT 0.914414 -16 ********** Masking position 5 Map Score: 3.46997 Number of sites scoring better than the average of aligned sites = 1119 Number in coding regions = 961 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 10 ACTAGCTAAAACTAAAGCTCTATCATGCTAT 1 114 1 ACTAAAGCCT 0.927324 -73 ATAAAATTTGAACGAAGCATTATAGCAAAAA 4 13 0 AACGAAGCTT 0.819876 -35 TTTTAGCTTGAATATAGCCTAACAGCTATGC 7 120 0 AATATAGCTA 0.635719 -181 GACTTTAAAGAACAAAGCCTTTCGTGTTAGC 7 192 1 AACAAAGCTT 0.951224 -109 GAGCTTCCTAACTAAAGCATTCCATTGAATG 7 222 0 ACTAAAGCTT 0.9674 -79 AAAAGTCAGCACTATAGCGCTATAAGACTAA 8 70 1 ACTATAGCCT 0.852456 -74 CTCATGTTTCTCTAACGCTTTAAAAAATTTC 9 54 0 TCTAACGCTT 0.64227 -228 ATTATTGCACAATATAGCTTTGAGTGGGGAT 9 113 0 AATATAGCTT 0.925387 -169 TAACTTTAAAAATCAAGCCTTCAAAAACC 14 9 0 AATCAAGCTT 0.864857 -95 ATTTTTATCAAACAACGCTTTTTAAGAGTGG 15 61 1 AACAACGCTT 0.893453 -78 ******** ** Masking position 8 Map Score: 3.24053 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 387 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 11 AAACAAAAATATAACAATGATAGCATGATA 1 134 0 ATAACAATGA 0.94432 -53 TTATGTTATTATAACAATAATTTTTTGCTA 5 35 1 ATAACAATAA 0.966565 -89 CTTTTATTATATAACAATTAGTCTTATAGC 8 88 0 ATAACAATTA 0.919632 -56 TCATTGAACGATAAGAATAATATTTTTGTG 9 143 1 ATAAGAATAA 0.915147 -139 GAGTTTGGATATAATAATAAAAAATGCGCT 11 154 1 ATAATAATAA 0.879112 -44 ********** Masking position 6 Map Score: 0.957568 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 21 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 ********** No masking Map Score: 2.89434e-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 13 ********** No masking Map Score: 2.89434e-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 14 ********** No masking Map Score: 2.89434e-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