AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -icpxR6_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 HP0166 235 response regulator (ompR) #2 HP0977 128 conserved hypothetical secreted protein #3 HP1015 111 H. pylori predicted coding region HP1015 #4 HP1017 97 amino acid permease (rocE) #5 HP1018 47 H. pylori predicted coding region HP1018 #6 HP1441 120 peptidyl-prolyl cis-trans isomerase B, cyclosporin-type rotamase (ppi) Motif number 1 ATTGTTTAAAAACATTAAAAAATAAGACTT 1 26 1 AACATTAAAA 0.963039 -210 TTTTCAATATTCCATGAAAACAAAGCCTTA 1 59 1 TCCATGAAAA 0.762496 -177 GCCTTAAATTTCCATTAATAACTATGATAA 1 83 1 TCCATTAATA 0.73448 -153 CCTTGAAAATATCTTAAAAATAAAAATTCA 1 118 0 ATCTTAAAAA 0.805663 -118 TATTAAAGATACCTTGAAAATATCTTAAAA 1 129 0 ACCTTGAAAA 0.924566 -107 TTTTCAAGGTATCTTTAATAATAAAATGCT 1 139 1 ATCTTTAATA 0.906953 -97 AGTCCCCTAAAACATTAACAAAGTTAATCG 1 175 1 AACATTAACA 0.779505 -61 TGATTTCTGCAACTTTAAAAACGATTAACT 1 196 0 AACTTTAAAA 0.9823 -40 TAATAAGGATAATTTTAATAACCTTTGGTT 2 26 1 AATTTTAATA 0.631584 -103 GAACTCTAATCCCTTTAAAAAATCAAAAAT 2 107 0 CCCTTTAAAA 0.886848 -22 AGAGTTGCAATTCATTAAAAAATGCTTGTT 3 52 1 TTCATTAAAA 0.91693 -60 TATTTTAAAAGAAGTTTTTA 4 1 1 TATTTTAAAA 0.804296 -97 GTTTTTAGCGTTCTTTAAAAAAACCTTAAA 4 24 1 TTCTTTAAAA 0.959117 -74 TCTTTAAAAAAACCTTAAAACGCTTAAAAA 4 35 1 AACCTTAAAA 0.946043 -63 TTACTATTTAATCTTTAAAAA 4 87 1 ATCTTTAAAA 0.976819 -11 AAATTTGCTAAACTTCAAAATTAAGAAAAG 5 12 0 AACTTCAAAA 0.937101 -36 CATGGTTACTTCCTTAAAATTTGCTAAAC 5 29 0 TTCCTTAAAA 0.881343 -19 TTACCGCTTAAATTTCAAAAGTATCCTACA 6 19 1 AATTTCAAAA 0.665516 -102 ********** Masking position 5 Map Score: 23.2466 Number of sites scoring better than the average of aligned sites = 1832 Number in coding regions = 1524 Number in noncoding regions = 308 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 2 AAAAACATTAAAAAATAAGACTTTATTTTT 1 33 1 AAAAATAAGA 0.977865 -203 TGGAATATTGAAAAATAAAGTCTTATTTTT 1 43 0 AAAAATAAAG 0.966703 -193 AAAATATCTTAAAAATAAAAATTCAAAACA 1 113 0 AAAAATAAAA 0.976063 -123 AGGTATCTTTAATAATAAAATGCTAGAATT 1 145 1 AATAATAAAA 0.948621 -91 AAAAACTCTCTATAATAAGGATAATTTTAA 2 14 1 TATAATAAGG 0.865754 -115 AACCTTTGGTTAAAATAAGGTTATTTGATT 2 45 1 TAAAATAAGG 0.934394 -84 AACCTTATAGTAAAATCAAATAACCTTATT 2 58 0 TAAAATCAAA 0.88813 -71 AATCCCTTTAAAAAATCAAAAATATGAAAT 2 100 0 AAAAATCAAA 0.946042 -29 TTAAAGATTAAATAGTAAAAGAGCTTGATC 4 75 0 AATAGTAAAA 0.811813 -23 GCTAAACTTCAAAATTAAGAAAAGA 5 6 0 AAAATTAAGA 0.874436 -42 ********** Masking position 6 Map Score: 11.5159 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 519 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 AACAATTCCTTTGATCGTTTT 1 1 0 TTGATCTTTT 0.841918 -235 GTCTTATTTTTTAATGTTTTTAAACAATTCC 1 23 0 TTAATGTTTT 0.93476 -213 TAATGGAAATTTAAGGCTTTGTTTTCATGGA 1 69 0 TTAAGGTTTG 0.966433 -167 AATAACTATGATAATGTTTTGAATTTTTATT 1 99 1 ATAATGTTTG 0.915332 -137 GGGGACTAATTCTAGCATTTTATTATTAAAG 1 151 0 TCTAGCTTTT 0.780819 -85 ATTAACTTTGTTAATGTTTTAGGGGACTAAT 1 172 0 TTAATGTTTA 0.719899 -64 ATTAACAAAGTTAATCGTTTTTAAAGTTGCA 1 188 1 TTAATCTTTT 0.948224 -48 ATTAACTCCTTCAATGATTTCTGCAACTTTA 1 209 0 TCAATGTTTC 0.757799 -27 GTGGATGTGGATAATGTTTTGCAAGAAATAT 3 13 0 ATAATGTTTG 0.915332 -99 CAAGCATTTTTTAATGAATTGCAACTCTTTG 3 49 0 TTAATGATTG 0.693942 -63 AAATAGCCCAACAAGCATTTTTTAATGAATT 3 60 0 ACAAGCTTTT 0.884997 -52 CGATAGTTTTTTAAGCGTTTTAAGGTTTTTT 4 41 0 TTAAGCTTTT 0.958447 -57 CGCTTAAAAAACTATCGCTTGATCAAGCTCT 4 55 1 ACTATCCTTG 0.363868 -43 TATCGCTTGATCAAGCTCTTTTACTATTTAA 4 67 1 TCAAGCCTTT 0.836003 -31 GTTGCTATAATAGAGCATTTGAATGACAAAA 6 83 1 TAGAGCTTTG 0.577676 -38 AACCTTTGCGATAAGCTTTTGTCATTCAAAT 6 99 0 ATAAGCTTTG 0.94568 -22 ****** **** Masking position 4 Map Score: 14.3981 Number of sites scoring better than the average of aligned sites = 1852 Number in coding regions = 1585 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 4 ACAAAGCCTTAAATTTCCATTAATAACTAT 1 78 1 AAATTTCCAT 0.754999 -158 GATACCTTGAAAATATCTTAAAAATAAAAA 1 122 0 AAATATCTTA 0.49192 -114 TTTATTATTAAAGATACCTTGAAAATATCT 1 134 0 AAGATACCTT 0.800506 -102 AGGTTATTAAAATTATCCTTATTATAGAGA 2 20 0 AATTATCCTT 0.891794 -109 AGGATAATTTTAATAACCTTTGGTTAAAAT 2 31 1 TAATAACCTT 0.891369 -98 TAGTAAAATCAAATAACCTTATTTTAACCA 2 51 0 AAATAACCTT 0.982547 -78 ATTCAGGTTTAAACAACCTTATAGTAAAAT 2 72 0 AAACAACCTT 0.938852 -57 GCGTTCTTTAAAAAAACCTTAAAACGCTTA 4 31 1 AAAAAACCTT 0.948008 -67 AATTTTAAGGAAGTAACCATG 5 37 1 AAGTAACCAT 0.930318 -11 TAAATTTCAAAAGTATCCTACAACACTATC 6 27 1 AAGTATCCTA 0.898181 -94 ********** Masking position 2 Map Score: 8.34095 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 376 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 TTAATGTTTTTAAACAATTCCTTTGATCGT 1 14 0 TAAACAATTC 0.588818 -222 AAAAACATTAAAAAATAAGACTTTATTTTT 1 33 1 AAAAATAAGA 0.692768 -203 ATATTCCATGAAAACAAAGCCTTAAATTTC 1 65 1 AAAACAAAGC 0.929304 -171 TAAAAATTCAAAACATTATCATAGTTATTA 1 98 0 AAACATTATC 0.593951 -138 TATCTTTAATAATAAAATGCTAGAATTAGT 1 148 1 AATAAAATGC 0.521127 -88 CAAAGGTTATTAAAATTATCCTTATTATAG 2 23 0 TAAAATTATC 0.537095 -106 AACCTTATTTTAACCAAAGGTTATTAAAAT 2 37 0 TAACCAAAGG 0.599231 -92 TTAAAAAATCAAAAATATGAAATTCAGGTT 2 93 0 AAAAATATGA 0.615196 -36 ATTTCTTGCAAAACATTATCCACATCCACC 3 15 1 AAACATTATC 0.593951 -97 CACATCCACCAAAACAAAGAGTTGCAATTC 3 35 1 AAAACAAAGA 0.686291 -77 TGCAATTCATTAAAAAATGCTTGTTGGGCT 3 57 1 TAAAAAATGC 0.905718 -55 CAAAGGGGCGAAAAAATAGCCCAACAAGCA 3 74 0 AAAAAATAGC 0.914247 -38 TAGCGTTCTTTAAAAAAACCTTAAAACGCT 4 29 1 TAAAAAAACC 0.56946 -69 GTTACTTCCTTAAAATTTGCTAAACTTCAA 5 24 0 TAAAATTTGC 0.791582 -24 CAACAAATTAAAACAAATGGTATTTTAGCC 6 57 0 AAACAAATGG 0.684902 -64 AGCATTTGAATGACAAAAGCTTATCGCAAA 6 96 1 TGACAAAAGC 0.590209 -25 AAACCTTTGCGATAAGCTTT 6 111 0 AAACCTTTGC 0.767019 -10 ********** Masking position 3 Map Score: 6.11695 Number of sites scoring better than the average of aligned sites = 5543 Number in coding regions = 4889 Number in noncoding regions = 654 Number of orfs with sites within 600 bp upstream = 363 Fraction of orfs with sites within 600 bp upstream = 0.0583039 Motif number 6 TTAATGGAAATTTAAGGCTTTGTTTTCATG 1 71 0 TTTAAGGCTT 0.916585 -165 TTTGTTAATGTTTTAGGGGACTAATTCTAG 1 167 0 TTTTAGGGGA 0.969439 -69 TTTTTGATTTTTTAAAGGGATTAGAGTTCT 2 108 1 TTTAAAGGGA 0.842708 -21 TAAAAGAAGTTTTTAGCGTTCTTTAAAAAA 4 16 1 TTTTAGCGTT 0.963327 -82 GCGATAGTTTTTTAAGCGTTTTAAGGTTTT 4 43 0 TTTAAGCGTT 0.971594 -55 ACTTTTGAAATTTAAGCGGTAAGTTGGATA 6 11 0 TTTAAGCGGT 0.986042 -110 ACAAATGGTATTTTAGCCGATAGTGTTGTA 6 45 0 TTTTAGCCGA 0.946182 -76 ********** Masking position 5 Map Score: 7.40709 Number of sites scoring better than the average of aligned sites = 759 Number in coding regions = 635 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 ********** No masking Map Score: -5.94424e-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 8 ********** No masking Map Score: -5.94424e-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 9 ********** No masking Map Score: -5.94424e-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