AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_hpyl_reg_100.orf -o00500_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 Purged sequences: HP1503 25 cation-transporting ATPase, P-type (copA) Input sequences: #1 HP0429 124 H. pylori predicted coding region HP0429 #2 HP0430 85 H. pylori predicted coding region HP0430 #3 HP0643 164 glutamyl-tRNA synthetase (gltX) #4 HP0791 24 cadmium-transporting ATPase, P-type (cadA) #5 HP0795 111 trigger factor (tig) #6 HP0906 259 H. pylori predicted coding region HP0906 #7 HP0907 50 hook assembly protein, flagella (flgD) #8 HP0909 51 H. pylori predicted coding region HP0909 #9 HP1101 65 glucose-6-phosphate dehydrogenase (g6pD) #10 HP1166 63 glucose-6-phosphate isomerase (pgi) #11 HP1365 83 response regulator #12 HP1368 300 type IIS restriction enzyme M2 protein (mod) #13 HP1483 26 gerC2 protein (gerC2) #14 HP1490 103 hemolysin #15 HP1506 127 glutamate permease (gltS) #16 HP1523 81 DNA recombinase (recG) Motif number 1 TTTACGCCACAAAAACGCTTTATTTATGGATT 1 27 1 AAAACCTTTA 0.973762 -98 AAACCCTTTAAATCCCACTTTTGTATATCTGT 2 42 0 AACCCCTTTT 0.934494 -44 AGCGTCTTCAAACTCCCCTTTTAAACCCTTTA 2 64 0 AATCCCTTTT 0.905884 -22 AGGTATAATCAAAAACTATTTTTAAATAAAGG 3 137 1 AAAACATTTT 0.795202 -28 AAAAACCCTTTATTTAAAAATA 3 153 0 AAAACCTTTA 0.973987 -12 AACTAGAATTAAAACCGCTTTTTATAAACTGG 5 28 1 AAACCCTTTT 0.97708 -84 CATAGTTTTAAAAACCTCTGTTCTCATTAAGC 6 77 1 AAACCCTGTT 0.934993 -183 TTTAAAACGAAAAACCCCATTTTTTAAAAATA 6 127 0 AAACCCATTT 0.956276 -133 TTTTCGTTTTAAAAACACCTTTAGCATTTTTA 6 146 1 AAAACCCTTT 0.96786 -114 ACGCGTCTTAAGGAACTCTTTTTGCTTAACTC 6 187 1 AGAACCTTTT 0.911699 -73 TCCTTTTTAAAACAACTCTTTTATTTCTTTAT 6 233 0 AAAACCTTTT 0.983804 -27 GCTCTATAATAAGACATCTTTAAGAAGGAAGA 7 25 1 AAACACTTTA 0.932072 -26 GAATACCCCTTTAATTAAGATTT 9 2 1 AAACCCTTTA 0.990068 -64 CAATAACCCTTTTAGAGTGTTTT 9 53 0 AAAACCTTTT 0.98401 -13 ACTAGCTTATAATACAGCATTATATCTTTTAT 10 29 1 AAACACATTA 0.64679 -35 CAATACCCCTTAAATAAAAGATA 10 51 0 AAACCCTTAA 0.848533 -13 CCTTAAAAAAGACACCGCTTTATTTTA 11 6 0 GAACCCTTTA 0.892507 -78 GTTATAAAAAAACACTCCCTTAAAAAAGACAC 11 23 0 AAACTCCTTA 0.671082 -61 GTGTTTTTTTATAACCGCTTTTAGTATAAAGG 11 40 1 ATACCCTTTT 0.908828 -44 ATGAAGTTTTAGAAAACCTTTTCATAG 12 6 0 AGAAACTTTT 0.587002 -295 TCTTCTAATAAAAAAATCTTTTTTTGCATGGG 12 129 0 AAAAACTTTT 0.892327 -172 ATTTTTTTAAAATACCCCCATTTCATTGTAAA 12 230 1 AAACCCCATT 0.831355 -71 GTATGCAAGGAACACCTACTTTCTAACTGATC 15 45 1 AAACCACTTT 0.836505 -83 ATTATAATATAATACCCCCCTAAAAGAACGAG 15 76 0 AAACCCCCTA 0.816276 -52 ** *** ***** Masking position 11 Map Score: 35.4331 Number of sites scoring better than the average of aligned sites = 1401 Number in coding regions = 1182 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 2 TCCATAAATAAAGCGTTTTTGTGGCGTAAA 1 27 0 AAGCGTTTTT 0.894439 -98 GGGTTTAAAAGGGGAGTTTGAAGACGCT 2 68 1 GGGGAGTTTG 0.800867 -18 TTTTTAAATAAAGGGTTTTT 3 155 1 AAGGGTTTTT 0.985187 -10 AAGGATTTTTATAAGGGAGA 4 1 1 AAGGATTTTT 0.940781 -24 AGTTTATAAAAAGCGGTTTTAATTCTAGTT 5 28 0 AAGCGGTTTT 0.866533 -84 TAATGAGAACAGAGGTTTTTAAAACTATGG 6 76 0 AGAGGTTTTT 0.804329 -184 TTTTTAAAAAATGGGGTTTTTCGTTTTAAA 6 129 1 ATGGGGTTTT 0.898421 -131 AAAATGCTAAAGGTGTTTTTAAAACGAAAA 6 146 0 AGGTGTTTTT 0.873706 -114 CCTTATTAAAAAGGATATTTTACCATACTT 8 25 0 AAGGATATTT 0.829714 -27 CCTTTTTAATAAGGATATTTA 8 41 1 AAGGATATTT 0.829714 -11 ATCTTAATTAAAGGGGTATTC 9 2 0 AAGGGGTATT 0.923052 -64 AACCCTTTTAGAGTGTTTTTGAGTTATTAT 9 42 0 GAGTGTTTTT 0.857434 -24 AACACTCTAAAAGGGTTATTG 9 55 1 AAGGGTTATT 0.93996 -11 TCTTTTATTTAAGGGGTATTG 10 53 1 AAGGGGTATT 0.923052 -11 TTTTTTAAGGGAGTGTTTTTTTATAACCGC 11 28 1 GAGTGTTTTT 0.857434 -56 GGGGGTATTGTAGCGCTAAT 11 74 0 GGGGGTATTG 0.870806 -10 TTTTTTGCATGGGGGTATTGTAGCGCTTAA 12 112 0 GGGGGTATTG 0.870806 -189 CCATGCAAAAAAAGATTTTTTTATTAGAAG 12 130 1 AAAGATTTTT 0.526868 -171 CGAGAGCGTTAAGGAGTTTGACTCATTGAA 12 176 1 AAGGAGTTTG 0.856222 -125 ACAATGAAATGGGGGTATTTTAAAAAAATG 12 229 0 GGGGGTATTT 0.932334 -72 TTAAACTTCAATGGGTTTTGCATGAAAGAA 12 263 0 ATGGGTTTTG 0.849549 -38 CGTTCTTTTAGGGGGGTATTATATTATAAT 15 78 1 GGGGGGTATT 0.890125 -50 ********** Masking position 9 Map Score: 28.1348 Number of sites scoring better than the average of aligned sites = 3274 Number in coding regions = 2822 Number in noncoding regions = 452 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 3 TGGATGATTTAAAATCTTTACGCCACAAAA 1 9 1 TTAAAACTTA 0.803909 -116 TTTAAAGGGTTTAAAATATCTATCAACTTCAT 1 65 0 TTAAAAATTA 0.76648 -60 TTTTAAACCCTTTAAAGAGAAAGCATGAAGAT 1 81 1 TTTAAAAGAA 0.793655 -44 ATGGTTGGTTATCAAAAAGCTAACAGCGTTT 3 10 0 ATCAAAAGTA 0.645012 -155 TTCTGTTTTTATCAAACATGAATAGGCATCAT 3 78 0 ATCAAAATAA 0.806038 -87 ATAGTTTTTGATTATACCTAAAGAATACTTAA 3 124 0 ATTATACTAA 0.603576 -41 AATTCTAGTTTTCAAAAATTTAAAAAA 5 6 0 TTCAAAATTA 0.627684 -106 TTTTTGTATCATTATAGCTTAATTTGTTTTAA 5 62 0 ATTATACTAA 0.603575 -50 TCCTTAATGGCTAAAAAATTAAATTTTTGTAT 5 85 0 CTAAAAATAA 0.74637 -27 CTACAATTAAATAAAAACGATAATTTTAGAGA 6 18 0 ATAAAACGTA 0.815461 -242 GCGAAATTTAATTAAACCTAAACGAAACCATA 6 49 1 ATTAAACTAA 0.895702 -211 AACCCCATTTTTTAAAAATAAAAGTTGTCGTT 6 115 0 TTTAAAATAA 0.831842 -145 TAAAGGTGTTTTTAAAACGAAAAACCCCATTT 6 137 0 TTTAAACGAA 0.82772 -123 AAGACGCGTGATCAAATCTAAAAATGCTAAAG 6 164 0 ATCAAACTAA 0.83846 -96 CTCCCACCATGTAAAATATAAAGAAATAAAAG 6 216 1 GTAAAAATAA 0.523188 -44 AAGAGTTGTTTTAAAAAGGATAACC 6 245 1 TTAAAAGGTA 0.618544 -15 AAGATGTCTTATTATAGAGCAAACTTGCTTAA 7 13 0 ATTATAAGAA 0.486255 -38 AATATCCTTATTAAAAAGGATATTTTACCATA 8 28 0 TTAAAAGGTA 0.618544 -24 ATTATTATATATTAAATCTTAATTAAAGGGGT 9 15 0 ATTAAACTAA 0.895685 -51 TTAATATATAATAATAACTCAAAAACACTCTA 9 32 1 ATAATACTAA 0.641811 -34 CAAAAACACTCTAAAAGGGTTATTG 9 51 1 CTAAAAGGTA 0.450124 -15 TACCCCTTAAATAAAAGATATAATGCTGTATT 10 39 0 ATAAAAATTA 0.820009 -25 AACGCTCTCGCTTAAAAGGTAATCGTCTTCTA 12 154 0 CTTAAAGGAA 0.552638 -147 TTGAAGTTTAATAAAAGGTAAAAATAAGA 12 282 1 ATAAAAGTAA 0.837332 -19 TAAGCCTAACTTTAAAAATCAAGCCTTCAAAA 14 14 0 TTTAAAATAA 0.832023 -90 GAATTTTAACATAAAAGATTAAGCCTAACTTT 14 33 0 ATAAAAATAA 0.889998 -71 AACGATAAATATAAAATATATAAAATCTCAGA 14 63 0 ATAAAAATTA 0.820007 -41 AACTTTAAACCTAAAACCTAACGAT 14 89 0 TTTAAACTAA 0.860853 -15 ****** ** ** Masking position 6 Map Score: 24.4227 Number of sites scoring better than the average of aligned sites = 1620 Number in coding regions = 1235 Number in noncoding regions = 385 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 4 ATTATACCTAAAGAATACTTAATTGTGTTGTG 3 114 0 AAGATCTTAA 0.861807 -51 AATTGTAGCGAAATTTAATTAAACCTAAACGA 6 42 1 AAATTATTAA 0.951394 -218 GATCAAATCTAAAAATGCTAAAGGTGTTTTTA 6 155 0 AAAATCTAAA 0.852441 -105 TTAAGCAAAAAGAGTTCCTTAAGACGCGTGAT 6 184 0 AGATTCTTAA 0.843216 -76 ATTATAGAGCAAACTTGCTTAAAA 7 3 0 AAATTCTTAA 0.969068 -48 TAAATATCCTTATTAAAAAGGAT 8 39 0 AAAATCTTAT 0.653025 -13 TTATATATTAAATCTTAATTAAAGGGGTATTC 9 11 0 AATTTATTAA 0.733633 -55 AGGTTTTCTAAAACTTCATAAAATTGCGCTTC 12 19 1 AAATTATAAA 0.874358 -282 AAACCCATTGAAGTTTAATAAAAGGTAAAAAT 12 275 1 AAGTTATAAA 0.727587 -26 ATAATAAGATAAATTTGATTAATAAGGATGCA 15 103 1 AAATTATTAA 0.951395 -25 CAATTAAATTTCCTTAAGTCAATGTAT 16 6 1 AAATTCTTAA 0.969068 -76 ATCTTATCATAAAAATGATTAAGGATTGGCTA 16 47 1 AAAATATTAA 0.91033 -35 *** ** ***** Masking position 11 Map Score: 9.99349 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 165 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 CATTATAGCTTAATTTGTTTTAATTCCAGT 5 55 0 TAATTTGTTT 0.757436 -57 AATGATACAAAAATTTAATTTTTTAGCCAT 5 81 1 AAATTTAATT 0.941683 -31 ATTATCGTTTTTATTTAATTGTAGCGAAAT 6 26 1 TTATTTAATT 0.721132 -234 AATTGTAGCGAAATTTAATTAAACCTAAAC 6 42 1 AAATTTAATT 0.941683 -218 ATAATAAGATAAATTTGATTAATAAGGATG 15 103 1 AAATTTGATT 0.951413 -25 TGACTTAAGGAAATTTAATTG 16 2 0 AAATTTAATT 0.941683 -80 AGTCAATGTATAATTTGACTATCTTATCAT 16 27 1 TAATTTGACT 0.822327 -55 ********** Masking position 3 Map Score: 3.07814 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 63 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TTGTGGTAGTTCTGTTTTTATCAAACATGAA 3 88 0 TTGTTTTTAT 0.895806 -77 TATAGCTTAATTTGTTTTAATTCCAGTTTAT 5 51 0 TTGTTTTAAT 0.895806 -61 TTTAAAAACCTCTGTTCTCATTAAGCGCGAA 6 83 1 TTGTTCTCAT 0.685739 -177 AACTCTTTTATTTCTTTATATTTTACATGGT 6 221 0 TTCTTTATAT 0.698046 -39 TTCTTAAAGATGTCTTATTATAGAGCAAACT 7 20 0 TTCTTATTAT 0.918848 -31 AGAGTGTTTTTGAGTTATTATTATATATTAA 9 32 0 TAGTTATTAT 0.527051 -34 TAATTAAAACTAGCTTATAATACAGCATTAT 10 21 1 TGCTTATAAT 0.622879 -43 TACAGCATTATATCTTTTATTTAAGGGGTAT 10 41 1 TTCTTTTATT 0.44042 -23 TTTAAGGGAGTGTTTTTTTATAACCGCTTTT 11 31 1 TTTTTTTTAT 0.738066 -53 ATGAGCGGGCTTTGTTATAATACTTCCTATG 12 82 0 TTGTTATAAT 0.918848 -219 ACTGACTCATTTTTTTAAAATACCCCCATTT 12 222 1 TTTTTAAAAT 0.499446 -79 GACTTTTCTTTTTTCATGGCTTGTCT 13 10 0 TTTTTTTCAT 0.699175 -17 CTTAATCTTTTATGTTAAAATTCTGAGATTT 14 42 1 TTGTTAAAAT 0.75275 -62 TAATCAAATTTATCTTATTATAATATAATAC 15 93 0 TTCTTATTAT 0.918848 -35 ATAATTTGACTATCTTATCATAAAAATGATT 16 36 1 TTCTTATCAT 0.903282 -46 * ********* Masking position 6 Map Score: 6.73061 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 250 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 7 TTCATCGTTTAAATCCATAAATAAAGCGTTT 1 39 0 AAATCCATAA 0.914498 -86 TAGATATTTTAAACCCTTTAAAGAGAAAGCA 1 75 1 AAACCCTTAA 0.980687 -50 CTCCCCTTTTAAACCCTTTAAATCCCACTTT 2 53 0 AAACCCTTAA 0.980687 -33 AAAAACCCTTTATTTAAAAATAG 3 152 0 AAACCCTTAT 0.948952 -13 CTTTCATGCAAAACCCATTGAAGTTTAATAA 12 265 1 AAACCCATGA 0.893699 -36 AGACAAGCCATGAAAAAAGAAAAG 13 4 1 CAAGCCATAA 0.941915 -23 CTTTAAAAATCAAGCCTTCAAAAACC 14 6 0 CAAGCCTTAA 0.962983 -98 TTACCCTAGCCAATCCTTAATCATTTTTATG 16 54 0 CAATCCTTAT 0.860274 -28 ******** ** Masking position 3 Map Score: 5.96902 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 250 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 8 GCCAAGTGCTAATCTCTTAAATGATGCCTA 3 58 1 AATCTCTTAA 0.657429 -107 TTTTTCTCCCTTATAAAAATCCTT 4 11 0 TCTCCCTTAT 0.884014 -14 TTTGTATCATTATAGCTTAATTTGTTTTAA 5 62 0 TATAGCTTAA 0.690763 -50 TTTAATTTTTTAGCCATTAAGGAAAAAA 5 94 1 TAGCCATTAA 0.661478 -18 GCCAATCTCTCTAAAATTATCGTTT 6 6 1 TCTCTCTAAA 0.72031 -254 TTGTCGTTATTCGCGCTTAATGAGAACAGA 6 93 0 TCGCGCTTAA 0.976316 -167 CAATACCCCTTAAATAAAAGATA 10 51 0 TACCCCTTAA 0.875672 -13 ATAAAAAAACACTCCCTTAAAAAAGACACC 11 22 0 ACTCCCTTAA 0.884014 -62 GGGGGTATTGTAGCGCTAATTGCCTTTATA 11 64 0 TAGCGCTAAT 0.654112 -20 GGGGGTATTGTAGCGCTTAATGAGCGGGCT 12 102 0 TAGCGCTTAA 0.968472 -199 TCCTTAACGCTCTCGCTTAAAAGGTAATCG 12 161 0 TCTCGCTTAA 0.97439 -140 ********** Masking position 9 Map Score: 5.25536 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 738 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 9 GTATTTTTTAGCCAATTGCTCAAAAGCTAA 2 14 0 GCCAATTGCT 0.973207 -72 CTTGGCTAACGCCAAGCTTTTTATGGTTGG 3 34 0 GCCAAGCTTT 0.96228 -131 CTTGGCGTTAGCCAAGTGCTAATCTCTTAA 3 48 1 GCCAAGTGCT 0.975275 -117 GCCAATCTCTCTAAAATTAT 6 1 1 GCCAATCTCT 0.981565 -259 TCTTACCCTAGCCAATCCTTAATCATTTTT 16 57 0 GCCAATCCTT 0.952069 -25 ********** Masking position 5 Map Score: 1.92177 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 100 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ********** No masking Map Score: -1.16996e-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 11 ********** No masking Map Score: -1.16996e-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 12 ********** No masking Map Score: -1.16996e-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