AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_fla_operon_hpyl_reg_100.orf -o259_hpyl_100.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RHP00808 16 AE000511 Input sequences: #1 RHP01127 300 AE000511 #2 RHP01289 259 AE000511 #3 RHP01290 43 AE000511 #4 RHP01291 17 AE000511 #5 RHP00195 87 AE000511 #6 RHP00290 207 AE000511 #7 RHP00443 128 AE000511 #8 RHP00446 140 AE000511 #9 RHP00809 24 AE000511 #10 RHP00810 101 AE000511 #11 RHP00937 207 AE000511 #12 RHP00963 179 AE000511 Motif number 1 TTTGAATCTTCTTTAACATTTTTTTTCTTTCC 1 91 0 CTTTAACTTT 0.804362 -210 GCATCGAGAATTTTTGAATCTTCTTTAACATT 1 103 0 TTTTTGATTT 0.68269 -198 GTTCCTTTAATTTTTGCTTCTTAAATTGTAGT 2 21 1 TTTTTGCTTT 0.906944 -239 TTTTAAAGCTTTTTAACCCTTTTTAGACTACA 2 47 0 TTTTAACCTT 0.948623 -213 ATCGCTTTAATTTTTGCCCTCTTTTAAAGCTT 2 68 0 TTTTTGCCCT 0.653913 -192 CTCTTAAAAGTTTTAAGACAATGAAGTTTAAA 2 171 0 TTTTAAGCAT 0.819579 -89 TAAAACCCTTTTTTTAGTAGTTCATTCAAAAC 2 234 0 TTTTTAGATT 0.630344 -26 ATTTTCATTCTTTTAAGCCGTTCGT 3 4 0 TTTTAAGCTT 0.963637 -40 TTTTAACCTTCTATCTT 4 6 0 TTTTAACTCT 0.873726 -12 ATGCCCTTTTATTTAAGCTTTTAGTGTAACAT 5 25 1 ATTTAAGTTT 0.683889 -63 TGTTTGATGTTGTTAAGTCGTTGTTTATTATG 5 54 0 TGTTAAGCTT 0.688216 -34 TGGTTGCGGATTTTAAAGTTTTGTTAATCAAA 6 108 0 TTTTAAATTT 0.850006 -100 CTAAATAGCTTTTTAGAATGATTGGTTGCGGA 6 130 0 TTTTAGATAT 0.530206 -78 TGGTTTGTCTTTTTAGGCTTATTATAATATAA 8 89 0 TTTTAGGTAT 0.880064 -52 CCACCACTCTTTTTAAGGAATTTGT 10 4 0 TTTTAAGATT 0.839185 -98 AGGGTTTTAGTTTTAGCATGTTAGCATTCAGC 10 35 0 TTTTAGCTTT 0.967559 -67 TTACCCTATTCTTTAAGTTTTTATCCATAACT 10 71 0 CTTTAAGTTT 0.855094 -31 GCGTTTATTTTACCCTATTCTTTAAGTTT 10 83 0 TTTTACCTTT 0.776938 -19 GATTTCCTTATTTTTGGTTTTTGAATAGGCGT 11 14 1 TTTTTGGTTT 0.933281 -194 ATAGGCGTTCTCTTAAGGTATTTTATGGGTAT 11 38 1 TCTTAAGTTT 0.754235 -170 ATTGGAATGCTTTTTGCATGTTATGAATTTGC 11 161 1 TTTTTGCTTT 0.906944 -47 TATTGATAAATTTTAGGGCGTTTTATCATGCG 12 29 0 TTTTAGGCTT 0.968543 -151 ACACCCTCTTTTTTAAGCTCTTGCCTCAAAAT 12 77 0 TTTTAAGTTT 0.973576 -103 AAACGCGCTTTTTTAACACCCTCTTTTTTAAG 12 92 0 TTTTAACCCT 0.832685 -88 TTGGTTACAATTTTAGGTTATTAAGTTTTAGT 12 144 1 TTTTAGGTTT 0.977173 -36 ******* * ** Masking position 4 Map Score: 27.1258 Number of sites scoring better than the average of aligned sites = 1752 Number in coding regions = 1440 Number in noncoding regions = 312 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 2 CTTGGTTACCAGGGTTATTATTCTTTATATTT 1 182 1 AGGGTTATAT 0.803755 -119 CTTACATAGTAAGCTTATCAATATGAGATTGA 1 268 0 AAGCTTATAT 0.843692 -33 GTAGTCTAAAAAGGGTTAAAAAGCTTTAAAAG 2 48 1 AAGGGTTAAA 0.910404 -212 AAACACATAAAAGCTTTTCATTTTAATCAAAC 2 142 0 AAGCTTTTAT 0.843692 -118 TAAAATTCGTTGGCGTATAATATCCGTTTTGA 2 209 1 TGGCGTATAA 0.854534 -51 CTACTAAAAAAAGGGTTTTAAATA 2 246 1 AAGGGTTTAA 0.966994 -14 AAATTTTATCAAGGTTTTAATA 3 32 1 AAGGTTTTAA 0.924477 -12 GTTATCGCTCAAGCTTAAGAATCTAACTCGCT 6 11 0 AAGCTTAAAT 0.651815 -197 CCACCCCATAACGCTTTTTAAAGGTTATCGCT 6 34 0 ACGCTTTTAA 0.641014 -174 TGTTCCTAAATAGCTTTTTAGAATGATTGGTT 6 135 0 TAGCTTTTAA 0.763857 -73 CATCAAGGGGTTTGACATTAGTCAAGC 7 6 1 AGGGGTTTAA 0.956953 -123 GGGGGATTTAAGGGGTAAGATAAAAACTTATG 7 63 1 AGGGGTAAAA 0.885188 -66 GTTCGCATTATAGCGTAAAATAAGCTTTTTTG 8 40 1 TAGCGTAAAA 0.72864 -101 TATAAAGTTTAAGCGTATGATACAAAAAAGCT 8 62 0 AAGCGTATAA 0.966993 -79 TTGTCTTTTTAGGCTTATTATAATATAAAGTT 8 85 0 AGGCTTATAA 0.902802 -56 CATAACTTATAAGGGTTTTAGTTTTAGCATGT 10 46 0 AAGGGTTTAT 0.928154 -56 ACTTAAAGAATAGGGTAAAATAAACGC 10 85 1 TAGGGTAAAA 0.72864 -17 ATGAATTTGCAAGGGTTTGAAAAAGGGGTTTT 11 183 1 AAGGGTTTAA 0.966994 -25 GGTTTGAAAAAGGGGTTTTATT 11 196 1 AGGGGTTTAT 0.907428 -12 TACAAAAAGAAAGCGCATGATAAAACGCCCTA 12 16 1 AAGCGCATAA 0.746563 -164 ******** * * Masking position 10 Map Score: 24.5616 Number of sites scoring better than the average of aligned sites = 1254 Number in coding regions = 1107 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 3 AAAAAGGGTTAAAAAGCTTTAAAAGAGGGC 2 55 1 AAAAAGCTTT 0.615862 -205 TTTTTTTTTGAAATCGCTTTAATTTTTGCC 2 82 0 AAATCGCTTT 0.800975 -178 TATTTAAAACCCTTTTTTTAGTAGT 2 245 0 AAAACCCTTT 0.978892 -15 ACACCACCCCATAACGCTTTTTAAAGGTTA 6 39 0 ATAACGCTTT 0.721546 -169 GTGGTGTTGCAAAACCCCCTATTTTCTTAT 6 62 1 AAAACCCCCT 0.987402 -146 TGACTAATGTCAAACCCCTTGATG 7 5 0 CAAACCCCTT 0.967403 -124 CTTACCCCTTAAATCCCCCTAAGAACGAAT 7 52 0 AAATCCCCCT 0.936338 -77 CCTAAAAAGACAAACCACCTACCAGATTAA 8 104 1 CAAACCACCT 0.687071 -37 TGCTAAAACTAAAACCCTTATAAGTTATGG 10 49 1 AAAACCCTTA 0.832422 -53 ACCCCTTTTTCAAACCCTTGCAAATTCATA 11 182 0 CAAACCCTTG 0.772103 -26 AATAAAACCCCTTTTTCAAACCC 11 195 0 AAAACCCCTT 0.984728 -13 AGCGCATGATAAAACGCCCTAAAATTTATC 12 27 1 AAAACGCCCT 0.977902 -153 GCGCTTTTTTAACACCCTCTTTTTTAAGCT 12 90 0 AACACCCTCT 0.892189 -90 AAATTTGACTAAAACGCGCTTTTTTAACAC 12 105 0 AAAACGCGCT 0.894814 -75 ********** Masking position 2 Map Score: 16.2657 Number of sites scoring better than the average of aligned sites = 1651 Number in coding regions = 1397 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 ATCTGAGGCGAACACTTTTACCCGCTTTGA 1 13 0 AACACTTTTA 0.808721 -288 AATCTTCTTTAACATTTTTTTTCTTTCCAA 1 89 0 AACATTTTTT 0.64633 -212 AAAGCTTTTTAACCCTTTTTAGACTACAAT 2 45 0 AACCCTTTTT 0.980842 -215 GCCCTCTTTTAAAGCTTTTTAACCCTTTTT 2 55 0 AAAGCTTTTT 0.662726 -205 TATTTAAAACCCTTTTTTTAGTAGTTC 2 243 0 AACCCTTTTT 0.980842 -17 ACCACCCCATAACGCTTTTTAAAGGTTATC 6 37 0 AACGCTTTTT 0.967571 -171 GTGTTGCAAAACCCCCTATTTTCTTATGAA 6 65 1 ACCCCCTATT 0.840919 -143 GCTATTTAGGAACAACTTTTGCTTTATTTT 6 153 1 AACAACTTTT 0.557235 -55 ACTAATGTCAAACCCCTTGATG 7 3 0 AACCCCTTGA 0.726518 -126 CTAAAACTAAAACCCTTATAAGTTATGGAT 10 51 1 AACCCTTATA 0.814312 -51 ACCTTAAGAGAACGCCTATTCAAAAACCAA 11 27 0 AACGCCTATT 0.913887 -181 CGATTATTGGAATGCTTTTTGCATGTTATG 11 156 1 AATGCTTTTT 0.662752 -52 AATAAAACCCCTTTTTCAAACCCTT 11 193 0 AACCCCTTTT 0.984183 -15 CTTTTTTAACACCCTCTTTTTTAAGCTCTT 12 87 0 ACCCTCTTTT 0.695614 -93 ********** Masking position 1 Map Score: 12.3368 Number of sites scoring better than the average of aligned sites = 1573 Number in coding regions = 1304 Number in noncoding regions = 269 Number of orfs with sites within 600 bp upstream = 188 Fraction of orfs with sites within 600 bp upstream = 0.030196 Motif number 5 AACTAACACCAAAAAAGACAATAAATATTATT 1 48 0 AAAAAACAAT 0.882865 -253 TTCTTTTTGGAAAGAAAAAAAATGTTAAAGAA 1 83 1 AAAAAAAAAA 0.783879 -218 CCTGGTAACCAAGGAAAGAGAATGCATACAAC 1 163 0 AAGAAGAGAA 0.827439 -138 ATGCAATGCTAAAAAACCAAATATAAAGAATA 1 200 0 AAAAACAAAT 0.650035 -101 GCAAAAATTAAAGGAACGCAATAACTT 2 6 0 AAGAAGCAAT 0.901821 -254 AAAAGCTTTAAAAGAGGGCAAAAATTAAAGCG 2 66 1 AAAAGGCAAA 0.776293 -194 AGAGGGCAAAAATTAAAGCGATTTCAAAAAAA 2 78 1 AATAAGCGAT 0.865625 -182 TTCAAAAAAAAAAAAAAACAATTTCAGTTTCT 2 100 1 AAAAAACAAT 0.882865 -160 GAACGGCTTAAAAGAATGAAAATTTTATCAAG 3 13 1 AAAAAGAAAA 0.933294 -31 AAGTTTTGTTAATCAAAAAGATCGACCAAATT 6 93 0 AATAAAAGAT 0.477412 -115 AATCTATGCAAAATAAAGCAAAAGTTGTTCCT 6 160 0 AAAAAGCAAA 0.962372 -48 ATTCCATATTAAACAAGGAGAAATAAATA 7 110 1 AAAAAGAGAA 0.938186 -19 CAAAAACCAAAAATAAGGAAATCCTA 11 5 0 AAAAAGAAAT 0.940847 -203 TTTTCTCATCAAAGAATGCGATCAATTCAAAG 11 119 0 AAAAAGCGAT 0.969269 -89 ATGGATACAAAAAGAAAGCGCATGATAAAACG 12 11 1 AAAAAGCGCA 0.79011 -169 *** ** ***** Masking position 5 Map Score: 11.4971 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 721 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 TTGCTTCTTAAATTGTAGTCTAAAAAGGGTTAAA 2 34 1 ATTAGTTAAA 0.89115 -226 AGTTTTAAGACAATGAAGTTTAAACACATAAAAG 2 161 0 CTAAGTTAAA 0.947477 -99 ATTATGTTACACTAAAAGCTTAAATAAAAGGGCA 5 26 0 AAAAGCTAAA 0.847997 -62 TAAAGGTTATCGCTCAAGCTTAAGAATCTAACTC 6 14 0 CTAAGCTAAG 0.978798 -194 AATCTATGCAAAATAAAGCAAAAGTTGTTCCTAA 6 158 0 ATAAGCAAAG 0.76963 -50 AATGAGACCACATTATAGCATAAGTTTTTATCTT 7 79 0 CTTAGCTAAG 0.971044 -50 ATAAAGTTCGCATTATAGCGTAAAATAAGCTTTT 8 35 1 CTTAGCTAAA 0.96661 -106 GCTTATTATAATATAAAGTTTAAGCGTATGATAC 8 71 0 ATAAGTTAAG 0.928855 -70 ACTTTATATTATAATAAGCCTAAAAAGACAAACC 8 86 1 AAAAGCTAAA 0.847997 -55 AATTCAGAGCCATTATAGTGTAAAATACCCATAA 11 60 0 CTTAGTTAAA 0.929097 -148 ATTGGCTTATCGCTCAAGCTTAAGCATGCTTTGA 11 91 1 CTAAGCTAAG 0.978798 -117 TAGGTTATTAAGTTTTAGTTTAAAGGGAAAATC 12 157 1 ATTAGTTAAA 0.89115 -23 * * **** **** Masking position 7 Map Score: 13.2391 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 161 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 AAACCAAATATAAAGAATAATAACCCTGGT 1 189 0 TAAAGAATAA 0.718788 -112 AGTTATTTAATATGGGATAACATGCAATGC 1 223 0 TATGGGATAA 0.937488 -78 TAAAAGGGCATAAGGGATAAAGGGA 5 6 0 TAAGGGATAA 0.986342 -82 TTCTTAAGCTTGAGCGATAACCTTTAAAAA 6 22 1 TGAGCGATAA 0.953383 -186 TTCTTTAAATTAAAGGATAACC 6 196 1 TAAAGGATAA 0.951701 -12 TAGGGGGATTTAAGGGGTAAGATAAAAACT 7 61 1 TAAGGGGTAA 0.956943 -68 TGCTTAAGCTTGAGCGATAAGCCAATTCAG 11 87 0 TGAGCGATAA 0.953383 -121 ********** Masking position 9 Map Score: 5.51389 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 164 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 TTACGAATATTATATTCATAATTGCATCGAG 1 127 0 TATATTCAAA 0.889782 -174 TAATCAATCTCATATTGATAAGCTTACTATG 1 265 1 CATATTGAAA 0.773664 -36 AAAGATCGACCAAATTCATAAGAAAATAGGG 6 78 0 CAAATTCAAA 0.953817 -130 AGAAATTCAATCTATGCAAAATAAAGCAAAA 6 169 0 TCTATGCAAA 0.772782 -39 TAAGAGAACGCCTATTCAAAAACCAAAAATA 11 22 0 CCTATTCAAA 0.970378 -186 GAGCGATAAGCCAATTCAGAGCCATTATAGT 11 75 0 CCAATTCAAG 0.948849 -133 AAGAATGCGATCAATTCAAAGCATGCTTAAG 11 109 0 TCAATTCAAG 0.878803 -99 CAAACCCTTGCAAATTCATAACATGCAAAAA 11 171 0 CAAATTCAAA 0.953817 -37 ******** ** Masking position 4 Map Score: 2.68494 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 111 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 AACATTTTTTTTCTTTCCAAAAAGAATAAA 1 79 0 TTCTTTCCAA 0.599307 -222 GTAATTATTGTTGTATGCATTCTCTTTCCT 1 154 1 TTGTATGCAT 0.833801 -147 ATAATAACCCTGGTAACCAAGGAAAGAGAA 1 173 0 TGGTAACCAA 0.774549 -128 TTTTAAAGCTTTTTAACCCTTTTTAGACTA 2 49 0 TTTTAACCCT 0.78328 -211 TTTTAACCTTCTATCTT 4 8 0 TTTTAACCTT 0.709182 -10 AAGTTCTATCCATGTTTGATGTT 5 75 0 TTCTATCCAT 0.947629 -13 TTCTTTAAGTTTTTATCCATAACTTATAAG 10 65 0 TTTTATCCAT 0.9437 -37 CGCTTTCTTTTTGTATCCAT 12 1 0 TTGTATCCAT 0.971476 -179 TAACCTAAAATTGTAACCAAGATAAGATTA 12 134 0 TTGTAACCAA 0.934416 -46 ********** Masking position 4 Map Score: 2.4119 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 231 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 10 CCTCTTTTAAAGCTTTTTAACCCTTTTTAG 2 53 0 AGCTTTTTAA 0.825505 -207 AATCAAACCTAGCTAATAAGAAACTGAAAT 2 120 0 AGCTAATAAG 0.810934 -140 TAAAATGAAAAGCTTTTATGTGTTTAAACT 2 149 1 AGCTTTTATG 0.953832 -111 ATTGTCTTAAAACTTTTAAGAGCAATTTTA 2 181 1 AACTTTTAAG 0.928343 -79 GTTCCTAAATAGCTTTTTAGAATGATTGGT 6 136 0 AGCTTTTTAG 0.973314 -72 GCGTAAAATAAGCTTTTTTGTATCATACGC 8 52 1 AGCTTTTTTG 0.940711 -89 TTTTATCCATAACTTATAAGGGTTTTAGTT 10 55 0 AACTTATAAG 0.849306 -47 ********** Masking position 1 Map Score: 3.64073 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 202 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 AGTCCCTTAATCTTACATAGTAAG 1 287 0 CCTTAATCTT 0.980684 -14 CGAGTTAGATTCTTAAGCTTGAGCGATAAC 6 13 1 TCTTAAGCTT 0.840898 -195 TGTATCATACGCTTAAACTTTATATTATAA 8 70 1 GCTTAAACTT 0.840898 -71 AAAATCAATGCCTTAATCTGGTAGGTGGTT 8 116 0 CCTTAATCTG 0.930963 -25 TGATTAATCCTTAGTCTTTTGTCT 9 7 0 CCTTAGTCTT 0.948886 -18 GTTTATTTTACCCTATTCTTTAAGTTTTTA 10 80 0 CCCTATTCTT 0.854362 -22 TAGGATTTCCTTATTTTTGGTTTTTGAA 11 9 1 CCTTATTTTT 0.711517 -199 TTCAAAGCATGCTTAAGCTTGAGCGATAAG 11 96 0 GCTTAAGCTT 0.935133 -112 ********** Masking position 5 Map Score: 3.1606 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 92 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 12 ********** No masking Map Score: -1.25466e-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 13 ********** No masking Map Score: -1.25466e-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 14 ********** No masking Map Score: -1.25466e-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