AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_hpyl_reg_300.orf -o00440_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 HP1067 290 chemotaxis protein (cheY) #2 HP1483 26 gerC2 protein (gerC2) #3 HP1490 103 hemolysin #4 HP1491 138 phosphate permease Motif number 1 TTACTTGTAAAATCCTTGTCTT 1 3 1 ACTTGTAAAA 0.900059 -288 TCATTGGATGGTTTGAAAAAAGAAAGACAA 1 26 0 GTTTGAAAAA 0.781117 -265 TTATTTTATTACTTTTAAACGATTATCATA 1 77 1 ACTTTTAAAC 0.895388 -214 GAGCGTTCTTATTTGTAAAAAAATTCAGTT 1 114 0 ATTTGTAAAA 0.908268 -177 GGTCAAGGTAATTTTAATCAAAACATGCTA 1 177 1 ATTTTAATCA 0.79967 -114 AAATTAGGCTCTTTTTAAACAGCCAAAGCG 1 244 0 CTTTTTAAAC 0.842299 -47 AGTGCTTCTCCTTTTAAGATTGCATTTAA 1 272 0 CCTTTTAAGA 0.917353 -19 ATTAAGCCTAACTTTAAAAATCAAGCCTTC 3 18 0 ACTTTAAAAA 0.923878 -86 AAAATCTCAGAATTTTAACATAAAAGATTA 3 44 0 AATTTTAACA 0.755031 -60 AACTTTAAACCTAAAACCTAA 3 93 0 ACTTTAAACC 0.845118 -11 TTTAAAGAGAGTTTTAAAAA 4 1 0 GTTTTAAAAA 0.762294 -138 TTAAAGTAAAATTTTAAAGAGAGTTTTAAA 4 13 0 ATTTTAAAGA 0.925827 -126 ATAATGAGCCATTTTTATCAAACAACGCTT 4 51 1 ATTTTTATCA 0.854859 -88 TCAAACAACGCTTTTTAAGAGTGGCTCAAG 4 68 1 CTTTTTAAGA 0.924222 -71 TTAGAACAAGGTTTTTATGACGAT 4 125 1 GTTTTTATGA 0.766967 -14 ********** Masking position 7 Map Score: 15.1705 Number of sites scoring better than the average of aligned sites = 3105 Number in coding regions = 2496 Number in noncoding regions = 609 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 CAAACCATCCAATGACCCTTTATCGCACTC 1 41 1 AATGACCCTT 0.916353 -250 TGGAGCGTTCAATGAGCGTTCTTATTTGTA 1 127 0 AATGAGCGTT 0.981875 -164 CATTGGCTAAATGGAGCGTTCAATGAGCGT 1 138 0 ATGGAGCGTT 0.950113 -153 CCTTATAATAATAAATCGTTCCAAATAATA 1 205 0 ATAAATCGTT 0.766027 -86 ATTTATTATTATAAGGCGTTAGAGACGCTT 1 219 1 ATAAGGCGTT 0.928531 -72 GGCTGTTTAAAAAGAGCCTAATTTAAATGC 1 250 1 AAAGAGCCTA 0.930732 -41 AACTTTAAAAATCAAGCCTTCAAAAACC 3 9 0 ATCAAGCCTT 0.931909 -95 AACATAAAAGATTAAGCCTAACTTTAAAAA 3 28 0 ATTAAGCCTA 0.893621 -76 GTAAAATTTTAAAGAGAGTTTTAAAAA 4 8 0 AAAGAGAGTT 0.811481 -131 GATACCATATAATGAGCCATTTTTATCAAA 4 43 1 AATGAGCCAT 0.872683 -96 AGCCACTCTTAAAAAGCGTTGTTTGATAAA 4 64 0 AAAAAGCGTT 0.973992 -75 ATTCTATCCAATTAGCCCTTGAGCCACTCT 4 85 0 ATTAGCCCTT 0.755805 -54 ********** Masking position 1 Map Score: 11.976 Number of sites scoring better than the average of aligned sites = 2555 Number in coding regions = 2314 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 3 TGAGTGCGATAAAGGGTCATTGGATGGTTTG 1 41 0 AAAGGGTCTT 0.868607 -250 TATCGCACTCAAAGAGTTATTTTATTACTTT 1 61 1 AAAGAGTTTT 0.815863 -230 GAGCGTTCAATGAGCGTTCTTATTTGTAAAA 1 124 0 TGAGCGTTTT 0.97278 -167 TTAAACAGCCAAAGCGTCTCTAACGCCTTAT 1 229 0 AAAGCGTCCT 0.83923 -62 CTGTTTAAAAAGAGCCTAATTTAAATGCAAT 1 252 1 AGAGCCTATT 0.957856 -39 CATAAAAGATTAAGCCTAACTTTAAAAATCA 3 25 0 TAAGCCTACT 0.910878 -79 TACCATATAATGAGCCATTTTTATCAAACAA 4 45 1 TGAGCCATTT 0.908506 -94 CCACTCTTAAAAAGCGTTGTTTGATAAAAAT 4 61 0 AAAGCGTTTT 0.979275 -78 AATTAGCCCTTGAGCCACTCTTAAAAAGCGT 4 75 0 TGAGCCACCT 0.873157 -64 ATCGTCATAAAAACCTTGTTCTAATAGTGG 4 119 0 AAAACCTTTT 0.808084 -20 ******** ** Masking position 3 Map Score: 7.15135 Number of sites scoring better than the average of aligned sites = 1736 Number in coding regions = 1572 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 4 CTTTCTTTTTTCAAACCATCCAATGACCCT 1 30 1 TCAAACCATC 0.985982 -261 GTAATTTTAATCAAAACATGCTATTATTTG 1 184 1 TCAAAACATG 0.954167 -107 AGACAAGCCATGAAAAAAGAAA 2 3 1 ACAAGCCATG 0.983551 -24 ACTTTAAAAATCAAGCCTTCAAAAACC 3 8 0 TCAAGCCTTC 0.968992 -96 GCCATTTTTATCAAACAACGCTTTTTAAGA 4 58 1 TCAAACAACG 0.883884 -81 ATCGTCATAAAAACCTTGTTCTAATAGT 4 121 0 AAAAACCTTG 0.856735 -18 ********** Masking position 4 Map Score: 2.32648 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 309 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TGTAAAATCCTTGTCTTTCTTTTTTCAAACC 1 16 1 TTTCTTTCTT 0.945949 -275 CAAAGAGTTATTTTATTACTTTTAAACGATT 1 70 1 TTTATTACTT 0.9169 -221 GTTCAATGAGCGTTCTTATTTGTAAAAAAAT 1 120 0 CGTCTTATTT 0.926382 -171 AATCAAAACATGCTATTATTTGGAACGATTT 1 192 1 TGTATTATTT 0.951925 -99 GACTTTTCTTTTTTCATGGCTTGT 2 13 0 TTTCTTTTTT 0.962974 -14 TTCTGAGATTTTATATATTTTATATTTATCG 3 62 1 TTTATATTTT 0.723321 -42 GTTCTAATAGTGGTCTTATTCTATCCAATTA 4 101 0 TGTCTTATTC 0.926381 -38 ** ******** Masking position 6 Map Score: 0.972538 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 449 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 6 ********** No masking Map Score: -1.25523e-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 7 ********** No masking Map Score: -1.25523e-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: -1.25523e-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