AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_hpyl_reg_100.orf -o00630_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 HP0026 198 citrate synthase (gltA) #2 HP0577 73 methylene-tetrahydrofolate dehydrogenase (folD) #3 HP0584 81 flagellar switch protein (fliN) #4 HP0585 228 endonuclease III (nth) #5 HP0779 127 aconitase B (acnB) #6 HP0795 111 trigger factor (tig) #7 HP1100 65 6-phosphogluconate dehydratase #8 HP1435 70 protease IV (PspA) Motif number 1 ACACGCATTCAAAAAAAGATTTTTAAGGGTTATAT 1 61 0 AAAAGTTTTA 0.942599 -138 TTTCTTTTAAAAACATTGCGTTTTTTCAAGTTATT 1 114 0 AAATGTTTTT 0.91234 -85 AATGTTTTTAAAAGAAATCATTTAATTTTTTGGCT 1 132 1 AAAATTTTAA 0.87095 -67 TTTTGGCTTATAATTAGGAGTTGAATGCTATCAAA 1 159 1 TAAAGTTGAA 0.69359 -40 CAAACTAGGTTTTTATTCCATTAAAC 2 2 1 AAAAGTTTAT 0.981508 -72 ATTGTAGCAAAAATCATGCGTTTAATGGAATAAAA 2 21 0 AAAAGTTTAA 0.985434 -53 TTTTGCTACAATAATAGGATTTTAATTATATAAAG 2 44 1 ATAAGTTTAA 0.860888 -30 ATTTATAGTAAAATTAAGATTTTATAATCAAAGTC 3 30 1 AAAAGTTTAT 0.981508 -52 ACGATTTCATAAACTTTGTCTTTAATGGCTTCATT 4 21 0 AAATGTTTAA 0.955985 -208 ATACCAAAAGAGAGAAAGCGTTTTTTAAGGGCTTC 4 75 0 AGAAGTTTTT 0.815181 -154 GAATAATGCAAAAGAATGCATTGAACCCCTTCATG 4 111 0 AAAAGTTGAA 0.963576 -118 ATTTTAACCGAAAGCGTGGCTTTTTTCATGGAATA 4 141 0 AAAGGTTTTT 0.942493 -88 CATGCGATACAAAAAAGGATTTTAA 5 1 0 AAAAGTTTAA 0.982097 -127 AACTAAAAGTAAAAAGAGTTTTGTTATCATGGGGC 5 59 1 AAAGGTTGTT 0.858155 -69 TCCAGTTTATAAAAAGCGGTTTTAATTCTAGTTTT 6 26 0 AAAGGTTTAA 0.968263 -86 ATAATGATACAAAAATTTAATTTTTTAGCCATTAA 6 79 1 AAATTTTTTT 0.459707 -33 *** * * ***** Masking position 11 Map Score: 22.7807 Number of sites scoring better than the average of aligned sites = 1601 Number in coding regions = 1302 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 2 AAAAAAGATTTTTAAGGGTTATATAGTATTT 1 54 0 TTAAGGGTTA 0.97264 -145 ATCATTTAATTTTTTGGCTTATAATTAGGAG 1 148 1 TTTTGGCTTA 0.874745 -51 AATCATGCGTTTAATGGAATAAAAACCTAGT 2 14 0 TTATGGAATA 0.938047 -60 AACTTTGTCTTTAATGGCTTCATTGAGCGTC 4 14 0 TTATGGCTTC 0.980238 -215 AAAGCGTTTTTTAAGGGCTTCATCGCAGTTA 4 65 0 TTAGGGCTTC 0.929451 -164 ATTGAACCCCTTCATGGATACCAAAAGAGAG 4 96 0 TTATGGATAC 0.875103 -133 CGTGGCTTTTTTCATGGAATAATGCAAAAGA 4 131 0 TTATGGAATA 0.938047 -98 GGTATTGTGCTTCATGGGATCTTAAAGCCAC 4 189 0 TTATGGGATC 0.951824 -40 TTTTTTCCTTAATGGCTAAAAAATTAAAT 6 93 0 TTATGGCTAA 0.931078 -19 AAAAACACTCTAAAAGGGTTATTG 7 4 0 TAAAGGGTTA 0.804597 -62 TAAATCTTAATTAAAGGGGTATTC 7 52 1 TTAAGGGGTA 0.892542 -14 CTTCAAATGTTTTAAGGATTAAATC 8 5 0 TTAAGGATTA 0.957288 -66 ** ******** Masking position 1 Map Score: 13.6879 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 334 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 AACGCAATGTTTTTAAAAGAAATCATTTAATTTTT 1 127 1 TTTAAGAATA 0.928884 -72 AGGAGTTGAATGCTATCAAAACTTAAGGAAGTCAA 1 174 1 TGTAAAAATA 0.974858 -25 AATCCTATTATTGTAGCAAAAATCATGCGTTTAAT 2 30 0 TTTAAAAATA 0.985786 -44 TTACTATAAATTTTATAACAAATAAAGCCA 3 6 0 TTTAACAATA 0.928873 -76 GTTATAAAATTTATAGTAAAATTAAGATTTTATAA 3 22 1 TTTAAAAATA 0.985777 -60 AATTAAGATTTTATAATCAAAGTCAAATCATTCTT 3 41 1 TTTACAAATA 0.922515 -41 TTTAGTTAAGTTGTAAGAAACTTTAGCTACCATGC 5 31 0 TTTAAAACTA 0.967556 -97 GTTTGCCCCATGATAACAAAACTCTTTTTACTTTT 5 63 0 TGTAAAAATT 0.817887 -65 TTAATTCTAGTTTTCAAAAATTTAAAAAA 6 5 0 TTTCAAATTA 0.869824 -107 TAAGCTATAATGATACAAAAATTTAATTTTTTAGC 6 73 1 TGTAAAAATA 0.974858 -39 AGTTATTATTATATATTAAATCTTAATTAAAGGGG 7 36 1 ATTAAAATTA 0.690668 -30 GCAGCTTTTCCTAAACTTAATATTTGACCA 8 51 0 TTTCAAACTA 0.911783 -20 ** ** **** * * Masking position 10 Map Score: 11.4171 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 147 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 4 TTTTCTAAAGTTTGAGTAACTATACTAGCGCAAA 1 21 1 TTTGTACATA 0.934866 -178 CATTTAATTTTTTGGCTTATAATTAGGAGTTGAA 1 150 1 TTTGTATATT 0.969936 -49 AACTCTACTCTTTCAAGAATGATTTGACTTTGAT 3 56 0 TTTCGATATT 0.847642 -26 AATGCATTCTTTTGCATTATTCCATGAAAAAAGC 4 124 1 TTTGTATCCA 0.875374 -105 ACGCTTTCTTTGATGACAAGGTATTGTG 4 211 0 TTTCTATACA 0.901271 -18 GCCCTAATCGTTTGCCCCATGATAACAAAACTCT 5 73 0 TTTGCATATA 0.949792 -55 AAATTAAATTTTTGTATCATTATAGCTTAATTTG 6 68 0 TTTGTATATA 0.983999 -44 TTAGAGTGTTTTTGAGTTATTATTATATATTAAA 7 22 1 TTTGTATATT 0.969936 -44 CCTTAAAACATTTGAAGTATAATACACTCTTATG 8 19 1 TTTGGATATA 0.972085 -52 **** * ** *** Masking position 9 Map Score: 5.49847 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 103 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 TGTTTATCCTTTTTCTAAAGTTT 1 4 1 TTATCCTTTT 0.924932 -195 AAATACTATATAACCCTTAAAAATCTTTTT 1 54 1 TAACCCTTAA 0.951315 -145 TTGTCCTTTATATAATTAAA 2 64 0 TTGTCCTTTA 0.923889 -10 AACTGCGATGAAGCCCTTAAAAAACGCTTT 4 66 1 AAGCCCTTAA 0.785213 -163 TTAAAATCCTTTTTTGTATCGCA 5 4 1 AAATCCTTTT 0.833734 -124 TTCTCCTTTTTAAATCGCAT 5 118 0 TTCTCCTTTT 0.892373 -10 TTTTTTCCTTAATGGCTAAAAA 6 100 0 TTTTCCTTAA 0.752462 -12 CAATAACCCTTTTAGAGTGTTTT 7 4 1 TAACCCTTTT 0.95132 -62 GAATACCCCTTTAATTAAGATTT 7 53 0 TACCCCTTTA 0.950627 -13 GATTTAATCCTTAAAACATTTGAA 8 5 1 TAATCCTTAA 0.947468 -66 ********** Masking position 7 Map Score: 8.66142 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 421 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 6 AAATCTTTTTTTGAATGCGTGTTTAAAAGT 1 74 1 TTGAATGCGT 0.972509 -125 CAAATCATTCTTGAAAGAGTAGAGTTTT 3 64 1 TTGAAAGAGT 0.93126 -18 GACAAAGTTTATGAAATCGTAGAAATCGCT 4 36 1 ATGAAATCGT 0.808331 -193 TACCAAAAGAGAGAAAGCGTTTTTTAAGGG 4 79 0 GAGAAAGCGT 0.972454 -150 AATAATGCAAAAGAATGCATTGAACCCCTT 4 115 0 AAGAATGCAT 0.703383 -114 TTGATTTTAACCGAAAGCGTGGCTTTTTTC 4 149 0 CCGAAAGCGT 0.927789 -80 TTAAAGCCACTTGAATGCGGTTGATTTTAA 4 169 0 TTGAATGCGG 0.938446 -60 CTTGTCATCAAAGAAAGCGT 4 219 1 AAGAAAGCGT 0.98364 -10 TAACTAAAAGTAAAAAGAGTTTTGTTATCA 5 58 1 TAAAAAGAGT 0.742624 -70 TTCCAGTTTATAAAAAGCGGTTTTAATTCT 6 32 0 TAAAAAGCGG 0.877703 -80 ********** Masking position 5 Map Score: 7.50124 Number of sites scoring better than the average of aligned sites = 933 Number in coding regions = 858 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TGGCTTTATTTGTTATAAAA 3 1 1 TGGCTTTATT 0.979931 -81 TGGCTTCATTGAGCGTCATT 4 1 0 GAGCGTCATT 0.918494 -228 TTGTCTTTAATGGCTTCATTGAGCGTCATT 4 11 0 TGGCTTCATT 0.990992 -218 CGTTTTTTAAGGGCTTCATCGCAGTTAGCG 4 62 0 GGGCTTCATC 0.970888 -167 ACCGAAAGCGTGGCTTTTTTCATGGAATAA 4 140 0 TGGCTTTTTT 0.923349 -89 TGTATCATTATAGCTTAATTTGTTTTAATT 6 60 0 TAGCTTAATT 0.903444 -52 ********** Masking position 6 Map Score: 3.26344 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 262 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 ********** No masking Map Score: -1.66734e-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: -1.66734e-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: -1.66734e-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