AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_hpyl_reg_300.orf -o00052_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) #5 HP1101 65 glucose-6-phosphate dehydrogenase (g6pD) Motif number 1 ATGTTATACCAAAAACCCTAAAAATTTAAGC 1 41 1 AAAACCCTAA 0.954238 -260 TATATTGCGCAAAATCTCTTTTGCTTTATAA 1 124 0 AAAACTCTTT 0.985629 -177 CACCTGAGCTATAAGCCCTTAAAAGCCAATA 2 95 1 ATAACCCTTA 0.95423 -122 AATTTTCTTAAAAAATCCTTAAATAATAAAT 2 145 1 AAAATCCTTA 0.975971 -72 AAAACCCCTTTTAAAATGAAA 2 206 0 AAAACCCTTT 0.996344 -11 CAAAATTCCTTAAAAATTCTAA 3 2 1 AAAATCCTTA 0.975991 -61 TTTTACTCTTAAAATTTCTTTGTGTTATTAT 3 39 0 AAAATTCTTT 0.944617 -24 AGGTATAATCAAAAACTATTTTTAAATAAAG 4 137 1 AAAACTATTT 0.843861 -28 AAAAACCCTTTATTTAAAAAT 4 154 0 AAAACCCTTT 0.995607 -11 GAATACCCCTTTAATTAAGATT 5 2 1 AATACCCTTT 0.985726 -64 CAATAACCCTTTTAGAGTGTTT 5 54 0 AATACCCTTT 0.985706 -12 **** ****** Masking position 4 Map Score: 24.1349 Number of sites scoring better than the average of aligned sites = 857 Number in coding regions = 738 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 2 ATCGGCTTATATTTGTTCTAAGGAGCTTAAA 1 65 0 ATTTTTCTAA 0.820628 -236 TTTTTATTTGCTTTGTTCTTTATATTGCGCA 1 144 0 CTTTTTCTTT 0.938922 -157 TTGGATTGAGATTTTTTATTTGCTTTGTTCT 1 156 0 ATTTTTATTT 0.952858 -145 TCTCAATCCAATTTAATCTTCCATCAAGGAG 1 176 1 ATTTATCTTC 0.93475 -125 TTCTCCTTAAATTTTTTCTTTTTATCAGTCG 1 276 0 ATTTTTCTTT 0.987897 -25 TTAATCTATAATTTCATCTTTATTGGCTTTT 2 115 0 ATTTATCTTT 0.985651 -102 TTTTAAGAAAATTTAATCTATAATTTCATCT 2 127 0 ATTTATCTAT 0.963929 -90 TCTTAATCCCATTTATTATTTAAGGATTTTT 2 155 0 ATTTTTATTT 0.952259 -62 AATAGTTGTTATTTTTTCATTTTAAAAGGGG 2 192 1 ATTTTTCATT 0.912046 -25 TCTTTGTGTTATTATATCTTTTTAGAATTTT 3 23 0 ATTAATCTTT 0.897206 -40 TTTAATTAAGATTTAATATATAATAATAACT 5 20 1 ATTTATATAT 0.848371 -46 **** ****** Masking position 7 Map Score: 15.0536 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 297 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 AGGAGCTTAAATTTTTAGGGTTTTTGGTATAACA 1 42 0 ATTTTGTTTT 0.823946 -259 TCTTTGGCGGCTTTATCGGCTTATATTTGTTCTA 1 76 0 CTTTTGTTAT 0.985074 -225 TAACTTTTCGCTTTCTATCTTTGGCGGCTTTATC 1 93 0 CTTTTTTTGG 0.924978 -208 TGCGCAAAATCTCTTTTGCTTTATAACTTTTCGC 1 116 0 CTCTTGTTAT 0.912352 -185 ATTGAGATTTTTTATTTGCTTTGTTCTTTATATT 1 149 0 TTTATGTTGT 0.793001 -152 TCTCCTTAAATTTTTTCTTTTTATCAGTCGTGTC 1 272 0 TTTTTTTTAT 0.807238 -29 TTTTTACAATCTTTGGGGAATTAGC 2 2 0 CTTTGGTTAG 0.913236 -215 ATAATTTCATCTTTATTGGCTTTTAAGGGCTTAT 2 105 0 CTTTTGTTTT 0.981674 -112 GTTATTATATCTTTTTAGAATTTTTAAGGAATTT 3 13 0 CTTTTGTTTT 0.981674 -50 CTTAAAATTTCTTTGTGTTATTATATCTTTTTAG 3 29 0 CTTTTTTTAT 0.949926 -34 TAACGCCAAGCTTTTTATGGTTGGTTATCAAAAA 4 24 0 CTTTTTTTGG 0.924978 -141 CTAAAGAATACTTAATTGTGTTGTGGTAGTTCTG 4 105 0 CTTATGTTGT 0.945516 -60 CAATAACCCTTTTAGAGTGTTTTTGAGTTATTA 5 43 0 TTTTGGTTTT 0.788849 -23 **** * * **** Masking position 11 Map Score: 13.8235 Number of sites scoring better than the average of aligned sites = 904 Number in coding regions = 789 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 TTATACCAAAAACCCTAAAAATTTAAGCTC 1 44 1 AACCCTAAAA 0.526344 -257 CGAAAAGTTATAAAGCAAAAGAGATTTTGC 1 117 1 TAAAGCAAAA 0.543857 -184 CAATTTAATCTTCCATCAAGGAGCTTTGAG 1 184 1 TTCCATCAAG 0.760486 -117 GCAAGTCTTTTAACTCAAAGCTCCTTGATG 1 197 0 TAACTCAAAG 0.939996 -104 ACTTGCGGCGTTAAACAAAGACGATCCAAT 1 221 1 TTAAACAAAG 0.833425 -80 GCTAATTCCCCAAAGATTGTAAAAA 2 6 1 TTCCCCAAAG 0.945074 -211 CAAAATTCCTTAAAAATTCTAAAAA 3 6 1 TTCCTTAAAA 0.758703 -57 AAAGATATAATAACACAAAGAAATTTTAAG 3 33 1 TAACACAAAG 0.950739 -30 TTTGATAACCAACCATAAAAAGCTTGGCGT 4 26 1 AACCATAAAA 0.531333 -139 AGCACTTGGCTAACGCCAAGCTTTTTATGG 4 38 0 TAACGCCAAG 0.790345 -127 GTTTTTGATTATACCTAAAGAATACTTAAT 4 123 0 ATACCTAAAG 0.775277 -42 AAAACTATTTTTAAATAAAGGGTTTTT 4 148 1 TTAAATAAAG 0.757147 -17 ATATTAAATCTTAATTAAAGGGGTATTC 5 9 0 TTAATTAAAG 0.71676 -57 TATATAATAATAACTCAAAAACACTCTAAA 5 36 1 TAACTCAAAA 0.847275 -30 ********** Masking position 8 Map Score: 6.25817 Number of sites scoring better than the average of aligned sites = 1338 Number in coding regions = 1185 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 5 ATATTTGTTCTAAGGAGCTTAAATTTTTAGG 1 57 0 TAAGGAGTTA 0.871389 -244 TTGCGCAATATAAAGAACAAAGCAAATAAAA 1 143 1 TAAAGAAAAA 0.770126 -158 ACACGACTGATAAAAAGAAAAAATTTAAGGA 1 273 1 TAAAAAGAAA 0.749989 -28 AGAAAAAATTTAAGGAGAAAACG 1 288 1 TAAGGAGAAA 0.922398 -13 TTATTGGCTTTTAAGGGCTTATAGCTCAGGT 2 96 0 TTAAGGGTTA 0.619946 -121 TAAAAGCCAATAAAGATGAAATTATAGATTA 2 114 1 TAAAGATAAA 0.949224 -103 AAGATGAAATTATAGATTAAATTTTCTTAAA 2 126 1 TATAGATAAA 0.64783 -91 ATTTATTATTTAAGGATTTTTTAAGAAAATT 2 145 0 TAAGGATTTT 0.325629 -72 ATAAATGGGATTAAGATGTTATAATAGTTGT 2 170 1 TTAAGATTTA 0.890016 -47 AAAACCCCTTTTAAAATGAAAAAATAACAAC 2 196 0 TTAAAATAAA 0.6224 -21 AAAAATTCTAAAAAGATATAATAACACAAAG 3 22 1 AAAAGATTAA 0.647888 -41 CAAAGAAATTTTAAGAGTAAAAAGC 3 48 1 TTAAGAGAAA 0.951466 -15 TAGGCATCATTTAAGAGATTAGCACTTGGCT 4 57 0 TTAAGAGTTA 0.917933 -108 ACCCCTTTAATTAAGATTTAATATATAATAA 5 15 1 TTAAGATTAA 0.932676 -51 ******* *** Masking position 3 Map Score: 8.24543 Number of sites scoring better than the average of aligned sites = 1082 Number in coding regions = 905 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 154 Fraction of orfs with sites within 600 bp upstream = 0.024735 Motif number 6 GGGTTTTTGGTATAACATTTCTCACTGGCA 1 29 0 TATAACATTT 0.940679 -272 TCTTTTGCTTTATAACTTTTCGCTTTCTAT 1 109 0 TATAACTTTT 0.796415 -192 TAACAACTATTATAACATCTTAATCCCATT 2 173 0 TATAACATCT 0.979139 -44 AAAATGAAAAAATAACAACTATTATAACAT 2 185 0 AATAACAACT 0.930744 -32 TTCTTTGTGTTATTATATCTTTTTAGAATT 3 25 0 TATTATATCT 0.796415 -38 TTTAATATATAATAATAACTCAAAAACACT 5 31 1 AATAATAACT 0.816278 -35 ********** Masking position 5 Map Score: 0.959231 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 37 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 ********** No masking Map Score: 1.793e-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 8 ********** No masking Map Score: 1.793e-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 9 ********** No masking Map Score: 1.793e-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