AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_hpyl_reg_100.orf -o02020_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 Input sequences: #1 HP0019 107 chemotaxis protein (cheV) #2 HP0165 25 H. pylori predicted coding region HP0165 #3 HP0166 235 response regulator (ompR) #4 HP0246 188 flagellar basal-body P-ring protein (flgI) #5 HP0616 77 chemotaxis protein (cheV) #6 HP0698 187 H. pylori predicted coding region HP0698 #7 HP0699 39 H. pylori predicted coding region HP0699 #8 HP1365 83 response regulator #9 HP1368 300 type IIS restriction enzyme M2 protein (mod) Motif number 1 GTTTAATGCCAACGACACTTAAAAACTAAAATTCCTTTGGT 1 24 0 AATAATAAAA 0.983599 -84 CATTAAACGCAAACACGATATAATTATAAAACGATACGAAA 1 57 1 AATAATAAAA 0.983613 -51 CGATCAAAGGAATTGTTTAAAAACATTAAAAAATAAGACTT 3 15 1 AAAAATAAAA 0.940693 -221 CTTTGTTTTCATGGAATATTGAAAAATAAAGTCTTATTTTT 3 43 0 ATTAATAAAG 0.698208 -193 AGATACCTTGAAAATATCTTAAAAATAAAAATTCAAAACAT 3 112 0 AATAAAAAAA 0.940667 -124 AGATATTTTCAAGGTATCTTTAATAATAAAATGCTAGAATT 3 134 1 AATAATAAAA 0.983609 -102 AACTCCTTCAATGATTTCTGCAACTTTAAAAACGATTAACT 3 196 0 ATTAATAAAA 0.940692 -40 TTCATACCTCAATTTAATTTGAAACTTTATAAAAAGCTAAT 4 17 1 AATAATTATA 0.744272 -172 AACTTTATAAAAAGCTAATAAAAGGCTAAAATTAAAATCTT 4 39 1 AATAATAAAA 0.983613 -150 GCTATACTCAAAAATCTTATAAACTTTAAATCAAAGATTTT 4 72 0 AAAAATAAAT 0.882599 -117 TAAGCCTTTTATAAAAACTTTAAACCTAATTGAGCGTATTT 4 117 0 ATTAATAATT 0.742898 -72 GTTTGTAAAAACCTTTTAAACTAAATTAGGGTAGTAT 5 7 1 AATAAAAATT 0.761785 -71 TTTTCCCCTAAAGCCCTATCAAAGATTAAATGCTATAATAC 5 44 0 AATAATAAAT 0.966051 -34 TAACTCAAGCAAATTTTCTTCAATCCTAACAAATTTGGCTG 6 75 1 AATAATAACA 0.897483 -113 AATCCTAACAAATTTGGCTGCAAATTAAAAAATTTAAGCTT 6 96 1 AATAAAAAAA 0.940487 -92 TTAAATCAAAAAAAAAGAAAAAAGCTTAAATTTTTTAATTT 6 117 0 AAAAATAAAT 0.882622 -71 TTTTGATTTAATACTAGGTATAATTTTAATTCCACCTAACA 6 147 1 ATTAATAATT 0.780914 -41 ACGCTCCTTAAAAAACATAGGAAGTATTATAACAAAGCCCG 9 67 1 AAAAATTATA 0.486831 -234 CTTAAAAGGTAATCGTCTTCTAATAAAAAAATCTTTTTTTG 9 135 0 AATAAAAAAA 0.940693 -166 TCTTTCATGCAAAACCCATTGAAGTTTAATAAAAGGTAAAA 9 264 1 AATAATAATA 0.966044 -37 ** * ** ***** Masking position 12 Map Score: 27.534 Number of sites scoring better than the average of aligned sites = 765 Number in coding regions = 539 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 2 TTAAAAACTAAAATTCCTTTGGTGGGGGTT 1 17 0 AAATTCCTTT 0.909904 -91 TGTTTTTAAACAATTCCTTTGATCGTTTT 3 10 0 CAATTCCTTT 0.810718 -226 ATTGAAAAATAAAGTCTTATTTTTTAATGT 3 37 0 AAAGTCTTAT 0.804841 -199 GGCTAAAATTAAAATCTTTGATTTAAAGTT 4 62 1 AAAATCTTTG 0.737769 -127 GCTATACTCAAAAATCTTATAAACTTTAAA 4 83 0 AAAATCTTAT 0.848853 -106 TATTTTAGCATAAGCCTTTTATAAAAACTT 4 138 0 TAAGCCTTTT 0.783553 -51 TCAAACCCTTTCTTATTCCCT 4 178 0 CAAACCCTTT 0.960042 -11 GTTTGTAAAAACCTTTTAAACTAAATT 5 8 1 AAAACCTTTT 0.967434 -70 ATTTTCCCCTAAAGCCCTATCAAAGATTAA 5 56 0 AAAGCCCTAT 0.914152 -22 GATTGCTCAATCCTTTTTATGAAAGAG 6 8 1 CAATCCTTTT 0.874544 -180 CAAGAGGCATAAAGCCTCTTTCATAAAAAG 6 23 0 AAAGCCTCTT 0.901172 -165 AAAAAACCCCTTATTTTATTGA 7 28 0 AAAACCCCTT 0.939937 -12 GAAGTTTTAGAAAACCTTTTCATAG 9 6 0 AAAACCTTTT 0.967434 -295 TTCTAATAAAAAAATCTTTTTTTGCATGGG 9 129 0 AAAATCTTTT 0.946444 -172 ATTTCATTGTAAAATTCTTTCATGCAAAAC 9 249 1 AAAATTCTTT 0.595844 -52 TCTTTCATGCAAAACCCATTGAAGTTTAAT 9 264 1 AAAACCCATT 0.851784 -37 ********** Masking position 3 Map Score: 19.3065 Number of sites scoring better than the average of aligned sites = 1929 Number in coding regions = 1671 Number in noncoding regions = 258 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 GTTTTCGTATCGTTTTATAATTATATCGTG 1 70 0 CGTTTTATAA 0.926476 -38 TATTTTTTAATGTTTTTAAACAATTCCTTT 3 20 0 TGTTTTTAAA 0.482482 -216 AATAAAGTCTTATTTTTTAATGTTTTTAAA 3 30 0 TATTTTTTAA 0.718643 -206 GTTTTGAATTTTTATTTTTAAGATATTTTC 3 114 1 TTTATTTTTA 0.581217 -122 CTAATTCTAGCATTTTATTATTAAAGATAC 3 147 0 CATTTTATTA 0.84896 -89 CAAAGTTAATCGTTTTTAAAGTTGCAGAAA 3 193 1 CGTTTTTAAA 0.707124 -43 CTTTTATTAGCTTTTTATAAAGTTTCAAAT 4 33 0 CTTTTTATAA 0.901192 -156 TTAATTTTAGCCTTTTATTAGCTTTTTATA 4 44 0 CCTTTTATTA 0.934978 -145 CCTAATTGAGCGTATTTTTATGCTATACTC 4 104 0 CGTATTTTTA 0.832376 -85 TTAGCATAAGCCTTTTATAAAAACTTTAAA 4 134 0 CCTTTTATAA 0.913534 -55 TTGCTCAATCCTTTTTATGAAAGAGGCTTT 6 13 1 CTTTTTATGA 0.796818 -175 GCTTTTTTCTTTTTTTTTGATTTAATACTA 6 133 1 TTTTTTTTGA 0.70807 -55 AAAAAACCCCTTATTTTATTGAAAGTAT 7 22 0 CCTTATTTTA 0.733701 -18 AAAGACACCGCTTTATTTTA 8 1 0 CTTTATTTTA 0.704005 -83 TAAAGCGGTGTCTTTTTTAAGGGAGTGTTT 8 16 1 TCTTTTTTAA 0.867275 -68 TTTAAGGGAGTGTTTTTTTATAACCGCTTT 8 31 1 TGTTTTTTTA 0.913845 -53 ATACTTCCTATGTTTTTTAAGGAGCGTTAT 9 64 0 TGTTTTTTAA 0.886279 -237 AAAAAAAGATTTTTTTATTAGAAGACGATT 9 136 1 TTTTTTATTA 0.827382 -165 TTGACTGACTCATTTTTTTAAAATACCCCC 9 219 1 CATTTTTTTA 0.900027 -82 CTTATTTTTACCTTTTATTAAACTTCAATG 9 280 0 CCTTTTATTA 0.934978 -21 TCTTATTTTTACCTTTTATTA 9 290 0 CTTATTTTTA 0.782334 -11 ********** Masking position 6 Map Score: 23.314 Number of sites scoring better than the average of aligned sites = 1482 Number in coding regions = 1179 Number in noncoding regions = 303 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 4 TTTCAAAACCCCCACCAAAGGAA 1 2 1 TTAAACCCCC 0.970713 -106 CGTGTTTGCGTTTAATGCCAACGACACTTAAA 1 42 0 TTAATCCAAC 0.912979 -66 TAAATTGAGGTATGAATCTCCC 4 1 0 TAGAACTCCC 0.811986 -188 GATTAAATGCTATAATACTACCCTAATTTAGT 5 30 0 TAAATCTACC 0.974305 -48 GCAAATTTTCTTCAATCCTAACAAATTTGGCT 6 83 1 TTAATCTAAC 0.817427 -105 TAGGTATAATTTTAATTCCACCTAACAAGGAA 6 161 1 TTAATCCACC 0.98379 -27 CAATTAGCGCTACAATACCCCC 8 72 1 TAAATCCCCC 0.994304 -12 CGGGCTTTGTTATAATACTTCCTATGTTTTTT 9 76 0 TAAATCTTCC 0.920159 -225 CATTAAGCGCTACAATACCCCCATGCAAAAAA 9 110 1 TAAATCCCCC 0.994304 -191 CTCATTTTTTTAAAATACCCCCATTTCATTGT 9 227 1 TAAATCCCCC 0.994304 -74 ** *** ***** Masking position 5 Map Score: 15.6516 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 156 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 GACTTCCCCTTAATTTAGGTTTT 1 95 0 TTCCCCTTAA 0.967962 -13 AACCCCTTAACTCCTTATTA 2 16 0 AACCCCTTAA 0.881709 -10 AAGCCTTAAATTTCCATTAATAACTATGAT 3 81 1 TTTCCATTAA 0.787566 -155 TGCTAGAATTAGTCCCCTAAAACATTAACA 3 165 1 AGTCCCCTAA 0.943852 -71 ACCCTTTCTTATTCCCTAAATTCTAATTAT 4 165 0 ATTCCCTAAA 0.856544 -24 ATGCTATAATACTACCCTAATTTAGTTTAA 5 26 0 ACTACCCTAA 0.797446 -52 CTATTTTCCCCTAAAGCCCTATCA 5 64 0 TTTCCCCTAA 0.978711 -14 ATAATTTTAATTCCACCTAACAAGGAAAAG 6 166 1 TTCCACCTAA 0.762414 -22 ATAAAAAAACACTCCCTTAAAAAAGACACC 8 22 0 ACTCCCTTAA 0.976522 -62 TCCTTAACGCTCTCGCTTAAAAGGTAATCG 9 161 0 TCTCGCTTAA 0.85802 -140 ********** Masking position 9 Map Score: 5.36068 Number of sites scoring better than the average of aligned sites = 887 Number in coding regions = 740 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 6 TTTTTCAATATTCCATGAAAACAAAGCCTT 3 58 1 TTCCATGAAA 0.76555 -178 ACCTTGAAAATATCTTAAAAATAAAAATTC 3 119 0 TATCTTAAAA 0.723596 -117 TTATTAAAGATACCTTGAAAATATCTTAAA 3 130 0 TACCTTGAAA 0.898508 -106 ATTAAAATCTTTGATTTAAAGTTTATAAGA 4 69 1 TTGATTTAAA 0.334914 -120 TTTTTGAGTATAGCATAAAAATACGCTCAA 4 99 1 TAGCATAAAA 0.739804 -90 GCTCAATCCTTTTTATGAAAGAGGCTTTAT 6 15 1 TTTTATGAAA 0.401149 -173 AACCCCTTATTTTATTGAAAGTATAGTGAT 7 16 0 TTTATTGAAA 0.835613 -24 TTTTCTAAAACTTCATAAAATTGCGCTTCG 9 22 1 CTTCATAAAA 0.711141 -279 TAAGGAGCGTTATAATGAAAACGAACGAAG 9 47 0 TATAATGAAA 0.799043 -254 CATTATAACGCTCCTTAAAAAACATAGGAA 9 60 1 CTCCTTAAAA 0.73976 -241 AGGAGTTTGACTCATTGAAAATTTAGATTG 9 187 1 CTCATTGAAA 0.793717 -114 GAAAGAATTTTACAATGAAATGGGGGTATT 9 240 0 TACAATGAAA 0.862048 -61 TCAATGGGTTTTGCATGAAAGAATTTTACA 9 256 0 TTGCATGAAA 0.744927 -45 CCCATTGAAGTTTAATAAAAGGTAAAAATA 9 278 1 TTTAATAAAA 0.673035 -23 ********** Masking position 8 Map Score: 8.37856 Number of sites scoring better than the average of aligned sites = 847 Number in coding regions = 739 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 7 CACCAAAGGAATTTTAGTTTTTAAGTGTCG 1 23 1 ATTTTAGTTT 0.744286 -85 TAGGGGACTAATTCTAGCATTTTATTATTA 3 154 0 ATTCTAGCAT 0.930013 -82 AAAGATTTTAATTTTAGCCTTTTATTAGCT 4 51 0 ATTTTAGCCT 0.949635 -138 AATTCTAATTATTTTAGCATAAGCCTTTTA 4 147 0 ATTTTAGCAT 0.983456 -42 TTAGGGTAGTATTATAGCATTTAATCTTTG 5 36 1 ATTATAGCAT 0.926683 -42 TCAACCCAAGCTTTTAGCACCAAGAGGCAT 6 43 0 CTTTTAGCAC 0.91636 -145 TTTATAACCGCTTTTAGTATAAAGGCAATT 8 47 1 CTTTTAGTAT 0.904147 -37 AAAAAAATCTTTTTTTGCATGGGGGTATTG 9 122 0 TTTTTTGCAT 0.730468 -179 ********** Masking position 5 Map Score: 4.289 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 240 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 8 ATTATATCGTGTTTGCGTTTAATGCCAACG 1 51 0 GTTTGCGTTT 0.926387 -57 CTTTAAAAACGATTAACTTTGTTAATGTTT 3 184 0 GATTAACTTT 0.811516 -52 TTGTAGCGCTAATTGCCTTTATACTAAAAG 8 57 0 AATTGCCTTT 0.958546 -27 AACTTCATAAAATTGCGCTTCGTTCGTTTT 9 30 1 AATTGCGCTT 0.750425 -271 ATTAGAAGACGATTACCTTTTAAGCGAGAG 9 152 1 GATTACCTTT 0.970754 -149 TGAAAATTTAGATTGCCTTGACTGACTCAT 9 202 1 GATTGCCTTG 0.954739 -99 TCTTATTTTTACCTTTTATTAAACTT 9 285 0 TTTTACCTTT 0.73454 -16 ********** Masking position 4 Map Score: 0.467753 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 247 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 ********** No masking Map Score: -3.47212e-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 10 ********** No masking Map Score: -3.47212e-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: -3.47212e-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