AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -ilexA_hpyl_opreg_100.orf -g0.389 -x5 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 = 0.389 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 HP0153 98 recombinase (recA) #2 HP0705 182 excinuclease ABC subunit A (uvrA) #3 HP0883 25 Holliday junction DNA helicase (ruvA) #4 HP0884 167 H. pylori predicted coding region HP0884 #5 HP1058 148 3-methyl-2-oxobutanoate hydroxymethyltransferase (panB) #6 HP1085 66 H. pylori predicted coding region HP1085 #7 HP1088 46 transketolase A (tktA) #8 HP1114 69 excinuclease ABC subunit B (uvrB) #9 HP1116 300 H. pylori predicted coding region HP1116 #10 HP1394 187 conserved hypothetical protein #11 HP1483 26 gerC2 protein (gerC2) #12 HP1490 103 hemolysin Motif number 1 ATCCTAGCCTAAAATCTATTATAATAAAAGGACT 1 36 0 AAAAATATAA 0.896418 -63 TTTCTTATTCATAAGAGTTAAAAATATTTGCTTG 2 70 0 ATAATTAAAA 0.941834 -113 ACTCTTATGAATAAGAAATGATAATAAAACCATT 2 86 1 ATAAATATAA 0.804012 -97 AAAAGGAGCTATTATACTTCAAAAAAGAATGGTT 2 113 0 ATTATTAAAA 0.715513 -70 TTAAAATAAGAAAATGGATTAAAAGGAGCTATTA 2 133 0 AAAAATAAAA 0.976066 -50 AACAAGAAATAAAAAAGGGATAAAA 3 2 1 ACAAATAAAA 0.962888 -24 GTATGCTAAAAAAAATATTTTTAACCAACAGCTT 4 54 0 AAAATTTTAA 0.617998 -114 ATGCTAACAAAAAAACACTGAAAATTAGGTAATA 4 98 0 AAAACTAAAA 0.922102 -70 ATGGTATAATATAAGAATTTGAAAAAAGAAATAT 4 130 0 ATAATTGAAA 0.619496 -38 ATTATACCATTTAAGGATTAAAAA 4 154 1 TTAATTAAAA 0.715511 -14 TCAATTATACTAAAATAATTAAAATGACCGGTTA 5 50 1 TAAAATAAAA 0.863655 -99 ATGACCGGTTAAAATGGAGTAAAATTTTTACCCA 5 73 1 AAAAAGAAAA 0.772562 -76 AATGACTCTCAAAAACCTTAAAAATGGAAAAATT 7 21 1 AAAATTAAAA 0.971555 -26 AAACCACTATAATACCCCTAAAAAATGCGAGTTT 8 41 1 AATACTAAAA 0.647719 -29 AGCGGTTTTCACAAGCTTTTTAAAAACGACGCTA 9 134 1 ACAATTTAAA 0.829063 -167 CAAGTAACAAAAAATTATTTTTAAGGAATCACAC 10 11 0 AAAATTTTAA 0.617998 -177 AGAATACCCAAAAAATAATTAAAAACGATTAAAT 10 48 1 AAAAATAAAA 0.976066 -140 ATGAAACATTAATAAAAATAAAAACTTTTCATGA 10 83 1 AATAATAAAA 0.863655 -105 CATCTTATGTAAAATTCATGAAAAGTTTTTATTT 10 98 0 AAAAATAAAA 0.976066 -90 AAGATGATAAAAAAGCAATTAAAACCCCCTTTTT 10 126 1 AAAAATAAAA 0.976066 -62 AAAGCTTGAAACAAAATTTTAAAAAAGGGGGTTT 10 147 0 ACAATTAAAA 0.956005 -41 AGACAAGCCATGAAAAAAGAAAAGTC 11 3 1 ACAAATAAAA 0.962888 -24 ACTTTAAAAATCAAGCCTTCAAAAACC 12 4 0 TCAATTAAAA 0.77144 -100 AACGATAAATATAAAATATATAAAATCTCAGAAT 12 61 0 ATAAATTAAA 0.811633 -43 **** ** **** Masking position 4 Map Score: 31.704 Number of sites scoring better than the average of aligned sites = 1542 Number in coding regions = 1208 Number in noncoding regions = 334 Number of orfs with sites within 600 bp upstream = 224 Fraction of orfs with sites within 600 bp upstream = 0.0359782 Motif number 2 AAGGAAACTCTTGCAACATAAAACCATT 2 165 1 TTGCAACAAA 0.806347 -18 GATTTTTGGCTTTTTACGGGATTTG 4 4 0 TTTTTACGAT 0.653737 -164 AAAAAAATATTTTTAACCAACAGCTTAGGGAT 4 48 0 TTTTAACACA 0.964519 -120 AAAATATTTTTTTTAGCATACTGGTTGTATTT 4 67 1 TTTTAGCACT 0.870292 -101 TGAAAGAAACTTTTAACAAACAATTCAAGGGA 5 21 0 TTTTAACACA 0.963922 -128 TGGAGTAAAATTTTTACCCACCCTAATAAAGT 5 87 1 TTTTTACACC 0.71141 -62 TATAGTGGCATTGTAGCATGACTTTATTAGGG 5 107 0 TTGTAGCGAC 0.850646 -42 AAAATCTATATTATAACTAAAAGGGGGTTTT 6 10 0 TTATAACAAA 0.8097 -57 ATAGATTTTATTTTAGCTAAAAATGGCATGGG 6 33 1 TTTTAGCAAA 0.498924 -34 ATGGCATGGGTTTTAGCAAGGA 6 55 1 TTTTAGCGGA 0.76367 -12 TTGAGAGTCATTTTAACACAAA 7 1 0 TTTTAACAAA 0.960814 -46 TATAGTGGTTTTTTAACACGCCTTATTCAATC 8 20 0 TTTTAACGCC 0.90859 -50 GTTTTAAACTCGCATTTTTTAGGG 8 56 0 TTTAAACGCA 0.847236 -14 GTGGCTTTCTACCAAAAACTTTAGTCA 9 6 1 TTTCTACAAA 0.575789 -295 AACAGCAAAATTATAGCAAGCAATGTTTTCTG 9 36 0 TTATAGCGCA 0.795392 -265 AAATTTTTCGTTGTAGCGGGCTTTAAACTCTC 9 176 0 TTGTAGCGCT 0.836601 -125 AAATAATTTTTTGTTACTTGAAAAGAATACCC 10 25 1 TTGTTACGAA 0.826264 -163 AGCTTAAAGCTTGAAACAAAATTTTAAAAAAG 10 154 0 TTGAAACAAT 0.537681 -34 ACATACTATTGTAGCTTAAAGCTTGAAACA 10 168 0 TTGTAGCAAA 0.863695 -20 AATCTCAGAATTTTAACATAAAAGATTAAGCC 12 40 0 TTTTAACAAA 0.952861 -64 AACTTTAAACCTAAAACCTAACGAT 12 89 0 TTTAAACAAA 0.835213 -15 ******* *** Masking position 2 Map Score: 19.9643 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 465 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 3 AGTAAAATCCTTTTGTGATAGGGTAAGTC 1 4 1 ATCTTTGTAT 0.714692 -95 TAAATTACCTTATTGAATTTGATTTGT 1 82 0 ATCTTATTAA 0.960064 -17 CTATTATTTTATGAGACAATTTTAAAGATAGGAATG 2 18 0 AGCATTTTAA 0.866848 -165 TGATAATAAAACCATTCTTTTTTGAAGTATAATAGC 2 104 1 ATCTTTTTAA 0.984396 -79 TTTTATCCCTTTTTTATTTCTTGTT 3 9 0 TTCTTTTTAT 0.762144 -17 TTTTGTTAGCATATTTCTTTTTTCAAATTCTTATAT 4 120 1 ATCTTTTTAA 0.984396 -48 TCATGCTACAATGCCACTATATTTAACACTTAGGAT 5 118 1 ACCATATTAA 0.825983 -31 CAAATTTTTCCATTTTTAAGGTTTTTGAG 7 28 0 ATCATTTTAA 0.944329 -19 GTGGTTTTTTAACACGCCTTATTCAATCTCAAAAAA 8 12 0 ACCTTATTAA 0.946388 -58 GTTTTAAACTCGCATTTTTTAGGGGTATTATA 8 48 0 ACCTTTTTAG 0.888296 -22 TCGGCGATCTTAGCGTCGTTTTTAAAAAGCTTGTGA 9 142 0 TGCTTTTTAA 0.807768 -159 ATTTTTATTAATGTTTCATTATTTAATCGTTTTTAA 10 66 0 ATCTTATTAA 0.960064 -122 AAGCAATTAAAACCCCCTTTTTTAAAATTTTGTTTC 10 138 1 ACCTTTTTAA 0.978869 -50 GACTTTTCTTTTTTCATGGCTTGTCT 11 10 0 ATCTTTTTAT 0.948619 -17 GGTTTTTGAAGGCTTGATTTTTAAAGTTAGGCTTA 12 10 1 ATGTTTTTAA 0.841027 -94 * * * ***** ** Masking position 15 Map Score: 16.2244 Number of sites scoring better than the average of aligned sites = 789 Number in coding regions = 623 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 AGTAAAATCCTTTTGTGATAGGG 1 4 1 AAAATCCTTT 0.92214 -95 TTTATTCTATCAAATCCTAGCCTAAAATCT 1 53 0 CAAATCCTAG 0.913477 -46 CAAATCCCGTAAAAAGCCAA 4 1 1 CAAATCCCGT 0.92277 -167 TAAAAAGCCAAAAATCCTAGAGCATAAAAT 4 20 1 AAAATCCTAG 0.927711 -148 CCTAGAGCATAAAATCCCTAAGCTGTTGGT 4 35 1 AAAATCCCTA 0.921894 -133 AATCGCCAAATCCCTTGAATTGTTTG 5 7 1 CAAATCCCTT 0.963667 -142 TAAAAATCCTAAGTGTTAAATA 5 137 0 AAAATCCTAA 0.81261 -12 AAAACCCCCTTTTAGTTATA 6 1 1 AAAACCCCCT 0.969724 -66 TCCTTGCTAAAACCCATGCCATTTTTAG 6 49 0 AAAACCCATG 0.762409 -18 CCTGCCTTAACAAACCCCCTAAATTTACAA 9 88 1 CAAACCCCCT 0.963436 -213 AAAAGCAATTAAAACCCCCTTTTTTAAAAT 10 136 1 AAAACCCCCT 0.969724 -52 TAAAATATATAAAATCTCAGAATTTTAACA 12 54 0 AAAATCTCAG 0.714801 -50 ********** Masking position 4 Map Score: 10.5626 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 993 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 5 ATTATACTTCAAAAAAGAATGGTTTTATTA 2 107 0 AAAAAAGAAT 0.677537 -76 AGTTTCCTTAAAATAAGAAAATGGATTAAA 2 144 0 AAATAAGAAA 0.640986 -39 AACAAGAAATAAAAAAGGGATAAAA 3 11 1 AAAAAAGGGA 0.947022 -15 TAAGAATTTGAAAAAAGAAATATGCTAACA 4 123 0 AAAAAAGAAA 0.947754 -45 AATGACCGGTTAAAATGGAGTAAAATTTTT 5 72 1 TAAAATGGAG 0.590705 -77 TATTTTAGCTAAAAATGGCATGGGTTTTAG 6 41 1 AAAAATGGCA 0.835442 -26 CAAAAACCTTAAAAATGGAAAAATTTG 7 30 1 AAAAATGGAA 0.960543 -17 AATACCCCTAAAAAATGCGAGTTTAAAAC 8 51 1 AAAAATGCGA 0.916578 -19 TCCTAAAATGCGATCGGGCGCGT 9 288 0 TAAAATGCGA 0.673392 -13 AAAACGATTAAATAATGAAACATTAATAAA 10 69 1 AATAATGAAA 0.640986 -119 AAACATTAATAAAAATAAAAACTTTTCATG 10 86 1 AAAAATAAAA 0.524769 -102 ATAAGATGATAAAAAAGCAATTAAAACCCC 10 124 1 AAAAAAGCAA 0.937354 -64 ACAAAATTTTAAAAAAGGGGGTTTTAATTG 10 141 0 AAAAAAGGGG 0.849566 -47 ACAAGCCATGAAAAAAGAAAAGTC 11 13 1 AAAAAAGAAA 0.947754 -14 ********** Masking position 5 Map Score: 11.0469 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 762 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 6 TCTATCAAATCCTAGCCTAAAATCTATTAT 1 48 0 CCTAGCCTAA 0.986286 -51 AAAATTTTTACCCACCCTAATAAAGTCATG 5 93 1 CCCACCCTAA 0.956616 -56 TTGCTGTTTGCCTTGCCTAAATACTCCCCC 9 60 1 CCTTGCCTAA 0.99039 -241 TAAATACTCCCCCTGCCTTAACAAACCCCC 9 77 1 CCCTGCCTTA 0.987283 -224 GGTCGCTAAACCTTGGCTTAAATTTTTCGT 9 197 0 CCTTGGCTTA 0.953328 -104 ********** Masking position 8 Map Score: 3.65772 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 45 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 TTACATTCCTATCTTTAAAATTGTCTCATA 2 15 1 ATCTTTAAAA 0.654579 -168 AGGAGCTATTATACTTCAAAAAAGAATGGT 2 114 0 ATACTTCAAA 0.730823 -69 TTGCAAGAGTTTCCTTAAAATAAGAAAATG 2 151 0 TTCCTTAAAA 0.883643 -32 CTAACAAAAAAACACTGAAAATTAGGTAAT 4 99 0 AACACTGAAA 0.461043 -69 TTTTTAATCCTTAAATGGTATAATAT 4 152 0 ATCCTTAAAT 0.649851 -16 TTATTTTAGTATAATTGAAAGAAACTTTTA 5 38 0 ATAATTGAAA 0.720471 -111 TTATACTAAAATAATTAAAATGACCGGTTA 5 54 1 ATAATTAAAA 0.859077 -95 AATCTATATTATAACTAAAAGGGGGTTTT 6 10 0 ATAACTAAAA 0.85656 -57 CATGCCATTTTTAGCTAAAATAAAATCTAT 6 33 0 TTAGCTAAAA 0.433262 -34 GACTCTCAAAAACCTTAAAAATGGAAAAAT 7 24 1 AACCTTAAAA 0.853635 -23 CCACTATAATACCCCTAAAAAATGCGAGTT 8 44 1 ACCCCTAAAA 0.770179 -26 GTGTGATTCCTTAAAAATAATTTTTT 10 7 1 TTCCTTAAAA 0.883643 -181 TAATTTTTTGTTACTTGAAAAGAATACCCA 10 28 1 TTACTTGAAA 0.718168 -160 CTTGAAAAGAATACCCAAAAAATAATTAAA 10 41 1 ATACCCAAAA 0.681371 -147 TACCCAAAAAATAATTAAAAACGATTAAAT 10 52 1 ATAATTAAAA 0.859077 -136 AACTTTAAACCTAAAACCTAACGATA 12 88 0 AAACCTAAAA 0.819301 -16 ********** Masking position 8 Map Score: 7.97367 Number of sites scoring better than the average of aligned sites = 1685 Number in coding regions = 1421 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 8 AATCAAATTCAATAAGGTAATTTA 1 85 1 AATAAGGTAT 0.90385 -14 AAAATTGTCTCATAAAATAATAGCATGTTTA 2 31 1 CATAAAATAT 0.941487 -152 AAGAAATGATAATAAAACCATTCTTTTTTGA 2 98 1 AATAAAACAT 0.896904 -85 GTTTCCTTAAAATAAGAAAATGGATTAAAAG 2 142 0 AATAAGAAAT 0.643029 -41 ACTCTTGCAACATAAAACCATT 2 171 1 CATAAAACAT 0.909729 -12 AAACACTGAAAATTAGGTAATAAATACAACC 4 89 0 AATTAGGTAT 0.521262 -79 TTTCAATTATACTAAAATAATTAAAATGACC 5 48 1 ACTAAAATAT 0.704536 -101 TACCCACCCTAATAAAGTCATGCTACAATGC 5 101 1 AATAAAGTAT 0.919529 -48 TTTCAAGTAACAAAAAATTATTTTTAAGGAA 10 17 0 CAAAAAATAT 0.851204 -171 AAAGAATACCCAAAAAATAATTAAAAACGAT 10 46 1 CAAAAAATAT 0.851204 -142 ATGAATTTTACATAAGATGATAAAAAAGCAA 10 113 1 CATAAGATAT 0.92976 -75 ATAAGATGATAAAAAAGCAATTAAAACCCCC 10 124 1 AAAAAAGCAT 0.717873 -64 ******** ** Masking position 5 Map Score: 7.12946 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 217 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 AGGACTTACCCTATCACAAAAGGATTTTAC 1 12 0 CTATCACAAA 0.670406 -87 AAAAATATTTTTAACCAACAGCTTAGGGAT 4 48 0 TTAACCAACA 0.78541 -120 AACCAGTATGCTAAAAAAAATATTTTTAAC 4 63 0 CTAAAAAAAA 0.746013 -105 AAGAAATATGCTAACAAAAAAACACTGAAA 4 109 0 CTAACAAAAA 0.971114 -59 AAAGAAACTTTTAACAAACAATTCAAGGGA 5 21 0 TTAACAAACA 0.951065 -128 GAGAGTCATTTTAACACAAA 7 1 0 TTAACACAAA 0.930278 -46 GTGGCTTTCTACCAAAAACTTTAGTCAG 9 9 1 CTACCAAAAA 0.875175 -292 TCCCCCTGCCTTAACAAACCCCCTAAATTT 9 84 1 TTAACAAACC 0.78541 -217 TTCTTTTCAAGTAACAAAAAATTATTTTTA 10 22 0 GTAACAAAAA 0.905197 -166 TAATGAAACATTAATAAAAATAAAAACTTT 10 81 1 TTAATAAAAA 0.730503 -107 TCTCAGAATTTTAACATAAAAGATTAAGCC 12 40 0 TTAACATAAA 0.830263 -64 ********** Masking position 3 Map Score: 6.10734 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 208 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 10 ********** No masking Map Score: 3.7902e-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 11 ********** No masking Map Score: 3.7902e-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 12 ********** No masking Map Score: 3.7902e-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