AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i156_HYP_operon_hpyl_reg_300.orf -o156_hpyl_300.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 Input sequences: #1 RHP01009 51 AE000511 #2 RHP01011 174 AE000511 #3 RHP01012 194 AE000511 #4 RHP01014 37 AE000511 #5 RHP01015 26 AE000511 #6 RHP01016 300 AE000511 #7 RHP00289 58 AE000511 #8 RHP00290 207 AE000511 #9 RHP00291 300 AE000511 #10 RHP00314 108 AE000511 #11 RHP00315 300 AE000511 Motif number 1 TGTGTTATAGTTATTTAAAAGGATATTTTG 1 31 1 TTATTTAAAA 0.928388 -21 GCTAGATCCTTTTTTTAAAGCCCTATGACA 2 24 0 TTTTTTAAAG 0.901035 -151 GCAATAAAGACAATTTAGAGTTTGCGCAAT 2 97 1 CAATTTAGAG 0.769177 -78 TCATTAGTTTTTGTTTAAAGGTTTTAGAAT 3 88 0 TTGTTTAAAG 0.778572 -107 TAACCTTTTATTTTTTAAAAGGATTATAAG 3 125 0 TTTTTTAAAA 0.892903 -70 TTGACCCTTTTAATTTAGGG 3 185 1 TAATTTAGGG 0.808358 -10 TTTGATCTCCTTATTTAATACAATAT 5 7 0 TTATTTAATA 0.724635 -20 TAAATCCGTTTAATTTAAAATCGTTTCGTT 6 20 1 TAATTTAAAA 0.923035 -281 TCGCATCGTGTAATTTAAAACCATTGAACG 6 46 0 TAATTTAAAA 0.923035 -255 CGCTAGAACAAAATTTAAAATTAAAAAACA 6 202 1 AAATTTAAAA 0.696361 -99 AGCTTACCTTTTATTTAAGAATTTGACTTG 6 280 0 TTATTTAAGA 0.889256 -21 TAATAGGGGCTAATTTAAAGATTAAGGTTT 7 36 1 TAATTTAAAG 0.928693 -23 CCCCATAACGCTTTTTAAAGGTTATCGCTC 8 33 0 CTTTTTAAAG 0.817032 -175 TCCTAAATAGCTTTTTAGAATGATTGGTTG 8 134 0 CTTTTTAGAA 0.683372 -74 TTCTAAAAAGCTATTTAGGAACAACTTTTG 8 144 1 CTATTTAGGA 0.672614 -64 GGTTATCCTTTAATTTAAAGAAATTCAATC 8 188 0 TAATTTAAAG 0.928693 -20 AGCTATTTAATTTTTTAAAAAATTCTTTTA 9 86 1 TTTTTTAAAA 0.892903 -215 TTCTTTTAGCTTTTTTAATGTTATCAATTT 9 108 1 TTTTTTAATG 0.649896 -193 TCAAAAATCTCTTTTTAAAAATAGGTTACT 9 158 1 CTTTTTAAAA 0.803858 -143 TCATTATGATTATTTTAATGAATTTTAACT 9 202 0 TATTTTAATG 0.63223 -99 ACGATACGAAAATTTTAAAAGAAAGGAACA 10 87 1 AATTTTAAAA 0.598722 -22 AAGGCTTAGAAAATTTAGGGATCGCTTTAT 11 41 1 AAATTTAGGG 0.446466 -260 GAATAAAGAATTGTTTAAGAAATCTATAAG 11 208 1 TTGTTTAAGA 0.667225 -93 ATTTAGAACTTAATTTAAGAAAGCTAATTT 11 253 0 TAATTTAAGA 0.881328 -48 GATATTTTCTTAATTTAGAACTTAATTTAA 11 265 0 TAATTTAGAA 0.862501 -36 ********** Masking position 5 Map Score: 26.7881 Number of sites scoring better than the average of aligned sites = 1511 Number in coding regions = 1144 Number in noncoding regions = 367 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 2 ATAGTTATTTAAAAGGATATTTTGA 1 37 1 AAAAGGATAT 0.959356 -15 GGGCTTTAAAAAAAGGATCTAGCGAAGAGG 2 31 1 AAAAGGATCT 0.878983 -144 ATGGCTTAAGAAAAGGATAAGATAAGTCAA 3 44 0 AAAAGGATAA 0.907987 -151 AGTTTTTGTTTAAAGGTTTTAGAATGCTAT 3 83 0 TAAAGGTTTT 0.937084 -112 TTTATTTTTTAAAAGGATTATAAGATAGCG 3 119 0 AAAAGGATTA 0.919474 -76 TTTAAAAAATAAAAGGTTATTGTTGCTTGT 3 136 1 AAAAGGTTAT 0.959218 -59 ATTTTAAATTAAACGGATTTACAAAAAATT 6 11 0 AAACGGATTT 0.88811 -290 CCATTGAACGAAACGATTTTAAATTAAACG 6 26 0 AAACGATTTT 0.672772 -275 GGGGCTAATTTAAAGATTAAGGTTTAGT 7 41 1 TAAAGATTAA 0.593325 -18 TAACGCTTTTTAAAGGTTATCGCTCAAGCT 8 28 0 TAAAGGTTAT 0.930804 -180 TTCTTTAAATTAAAGGATAACC 8 196 1 TAAAGGATAA 0.849134 -12 TAAAAAAGCTAAAAGAATTTTTTAAAAAAT 9 95 0 AAAAGAATTT 0.87623 -206 TCATAATGATTAAAGATTTTAACCACTATT 9 223 1 TAAAGATTTT 0.799449 -78 TTGCAAACCAAAAAGGTTTTGGAAAAAACA 11 178 1 AAAAGGTTTT 0.958227 -123 ********** Masking position 3 Map Score: 16.9268 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 593 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 TAGATCCTTTTTTTAAAGCCCTATGACAAGTAGG 2 18 0 TTAAAGCCCT 0.930357 -157 GAAGAGGAGTTTCAAAAACGCTTGATTAGAAACA 2 54 1 TTAAAACGCG 0.923235 -121 ATTAGAAACATTCTCAATCGCAATAAAGACAATT 2 78 1 TTCAATCGCT 0.955171 -97 AAATCATCGGTTTCAAAACGCAATTGCGCAAACT 2 115 0 TTAAAACGCT 0.988844 -60 TGAAACTGGCTATAAAAACCCGCTTGACTTATCT 3 21 1 TAAAAACCCT 0.876905 -174 AATTTTTTGTAAATCCGTTTAATTTAAAAT 6 7 1 TTAAATCCGT 0.656346 -294 TGGGGTGGTGTTGCAAAACCCCCTATTTTCTTAT 8 58 1 TTAAAACCCT 0.987313 -150 CAACCAATCATTCTAAAAAGCTATTTAGGAACAA 8 134 1 TTAAAAAGCT 0.936516 -74 TTATAAAACGCTTTATTTTGACAA 9 1 1 TTAAAACGCT 0.988844 -300 AATGAGAGTTTTTGCAAACCCTCTTGTTATTTTT 9 257 0 TTCAAACCCT 0.984595 -44 TTTCTAAGCCTTCACACACGCTCTCTCTTAAAGC 11 19 0 TTCACACGCT 0.908071 -282 GTTGGTGGGCTTACATAAAGCGATCCCTAAATTT 11 51 0 TTATAAAGCT 0.719123 -250 TTGGCTTAAATTCACTAACCCACTGCCCGGATTG 11 87 0 TTCTAACCCT 0.917305 -214 TGATGAAGAATTAGAAATCGCTTTGCAAACCAAA 11 156 1 TTAAATCGCT 0.962883 -145 TATTCTGTTTTTTCCAAAACCTTTTTGGTTTGCA 11 179 0 TTCAAAACCT 0.914066 -122 ** ******* * Masking position 1 Map Score: 20.2121 Number of sites scoring better than the average of aligned sites = 766 Number in coding regions = 673 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 GGGCTTTAAAAAAAGGATCTAGCGAAGAGGAGTT 2 31 1 AAAAATAGCG 0.913454 -144 ATAGCATTCTAAAACCTTTAAACAAAAACTAATG 3 83 1 AAAATTAACA 0.691071 -112 CCTTTAAACAAAAACTAATGAGCGCTATCTTATA 3 97 1 AAAAAAAGCG 0.949794 -98 AATAGCGTTAAAAAGCAAGAAACAAGCAACAATA 3 153 0 AAAAAAAACA 0.961298 -42 CGTGTAATTTAAAACCATTGAACGAAACGATTTT 6 36 0 AAAAATAACG 0.893348 -265 AATGAAGCTAAAAACAATACAAATTATCACTCAA 6 106 1 AAAAATAAAT 0.554455 -195 AACAAAATTTAAAATTAAAAAACATTACCAATAA 6 208 1 AAAAAAAACA 0.961298 -93 TTTGTTAATCAAAAAGATCGACCAAATTCATAAG 8 87 0 AAAAATACCA 0.74293 -121 CAATCTATGCAAAATAAAGCAAAAGTTGTTCCTA 8 159 0 AAAAAAAAAA 0.916114 -49 AATTTTTTAAAAAATTAAATAGCTTGCACTAAGC 9 76 0 AAAAAAAGCT 0.864725 -225 ATAACATTAAAAAAGCTAAAAGAATTTTTTAAAA 9 98 0 AAAATAAGAA 0.689572 -203 GAGATTTTTGAATACTAACTAGAAAAAAATTAAA 9 135 0 AATAAAAGAA 0.524999 -166 CTAATAAGTTAAAATTCATTAAAATAATCATAAT 9 196 1 AAAACAAAAA 0.597058 -105 ACTATTGTAGAAAAATAACAAGAGGGTTTGCAAA 9 247 1 AAAAAAAGAG 0.892678 -54 AACTCTCATTAAAAACAAGGAGCAAAAAAG 9 281 1 AAAAAAAGCA 0.969038 -20 AAAATCAGCCAAAAAGATAAAAAAAGTCGCTAAA 10 28 1 AAAAATAAAA 0.859014 -81 CGAAAATTTTAAAAGAAAGGAACAAC 10 93 1 AAAAAAAACA 0.961298 -16 **** ** **** Masking position 4 Map Score: 15.2524 Number of sites scoring better than the average of aligned sites = 897 Number in coding regions = 687 Number in noncoding regions = 210 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 5 AATCTCATTCAAATAGCGTTT 1 2 0 AAATAGCGTT 0.966406 -50 AGGAGTTTCAAAAACGCTTGATTAGAAACA 2 58 1 AAAACGCTTG 0.920511 -117 AGAGTTTGCGCAATTGCGTTTTGAAACCGA 2 113 1 CAATTGCGTT 0.718752 -62 AAATACGATCAATAAGCGTTGAAAAATCAT 2 142 0 AATAAGCGTT 0.822915 -33 TTAAAAGGGTCAATAGCGTTAAAAAGCAAG 3 168 0 CAATAGCGTT 0.87786 -27 TCATTGTGTAAAAATGCGTGATAAACTCAA 6 147 1 AAAATGCGTG 0.850386 -154 TGATAAACTCAAAAAGGTTGGAATGAGAAT 6 165 1 AAAAAGGTTG 0.715617 -136 GATAACCTTTAAAAAGCGTTATGGGGTGGT 8 37 1 AAAAAGCGTT 0.966406 -171 AGTTGTTCCTAAATAGCTTTTTAGAATGAT 8 140 0 AAATAGCTTT 0.966054 -68 TTATAAAACGCTTTATTTTGACAA 9 5 1 AAAACGCTTT 0.945632 -296 TTAAAAAATTAAATAGCTTGCACTAAGCAG 9 74 0 AAATAGCTTG 0.942011 -227 AATTTTTTAAAAAATTCTTTTAGCTTTTTT 9 94 1 AAAATTCTTT 0.510295 -207 TAGTATTCAAAAATCTCTTTTTAAAAATAG 9 152 1 AAATCTCTTT 0.673174 -149 GAAGAATTAGAAATCGCTTTGCAAACCAAA 11 160 1 AAATCGCTTT 0.945632 -141 TTTGCAAACCAAAAAGGTTTTGGAAAAAAC 11 177 1 AAAAAGGTTT 0.818468 -124 TTGGGTAAAAAATTAGCTTTCTTAAATTAA 11 244 1 AATTAGCTTT 0.825875 -57 ********** Masking position 2 Map Score: 19.2165 Number of sites scoring better than the average of aligned sites = 1909 Number in coding regions = 1676 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 6 CTGGCTATAAAAACCCGCTTGACTTATCTT 3 26 1 AAACCCGCTT 0.974472 -169 AGACTTAAAGCCACCCGCTTAAAACATGCT 6 245 1 CCACCCGCTT 0.980349 -56 TTTTGCAACACCACCCCATAACGCTTTTTA 8 46 0 CCACCCCATA 0.918314 -162 TGGTGTTGCAAAACCCCCTATTTTCTTATG 8 63 1 AAACCCCCTA 0.982377 -145 TGACAAGTATCAACCCCCTAAGATCGCATG 9 29 1 CAACCCCCTA 0.98872 -272 GAGTTTTTGCAAACCCTCTTGTTATTTTTC 9 256 0 AAACCCTCTT 0.933467 -45 ********** Masking position 3 Map Score: 4.27411 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 163 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 7 AACTATAACACAATCTCATTCAAATAGCGTT 1 12 0 CATCTCATTC 0.960404 -40 TGATTAGAAACATTCTCAATCGCAATAAAGA 2 76 1 CATCTCAATC 0.77347 -99 ATTAAGGATTAAACCAAATTCATTTGAAGCA 4 11 0 AACCAAATTC 0.862572 -27 TACAAATTATCACTCAAATTCTTATCATTGT 6 123 1 CATCAAATTC 0.912231 -178 AGCGGTAATTAATTCTCATTCCAACCTTTTT 6 175 0 AATCTCATTC 0.971477 -126 GGGTGGCTTTAAGTCTCATTTATTGGTAATG 6 230 0 AATCTCATTT 0.870226 -71 TGCTACAATCAAGTCAAATTCTTAAATAAAA 6 271 1 AATCAAATTC 0.935882 -30 GGTTTGCAAAAACTCTCATTAAAAACAAGGA 9 271 1 AATCTCATTA 0.791918 -30 CTGACGCTAAAATCCAAATTTTACGCATCCC 11 122 1 AACCAAATTT 0.552759 -179 TTGCAAAGCGATTTCTAATTCTTCATCAGTA 11 153 0 ATTCTAATTC 0.750448 -148 ** ******** Masking position 8 Map Score: 4.73616 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 203 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 AATGTTTCTAATCAAGCGTTTTTGAAACTC 2 60 0 ATCAAGCGTT 0.897799 -115 TTCAAGCTTTCACAAATACG 2 165 0 TTCAAGCTTT 0.899628 -10 TAGTTTTTGTTTAAAGGTTTTAGAATGCTA 3 84 0 TTAAAGGTTT 0.699656 -111 TTCTTGCTTTTTAACGCTATTGACCCTTTT 3 166 1 TTAACGCTAT 0.760936 -29 TTTTGAGTTTATCACGCATTTTTACACAAT 6 149 0 ATCACGCATT 0.685495 -152 ACACCACCCCATAACGCTTTTTAAAGGTTA 8 39 0 ATAACGCTTT 0.923874 -169 GTTGCGGATTTTAAAGTTTTGTTAATCAAA 8 108 0 TTAAAGTTTT 0.611147 -100 CAATCATTCTAAAAAGCTATTTAGGAACAA 8 138 1 AAAAAGCTAT 0.475911 -70 ACTTGTCAAAATAAAGCGTTTTATAA 9 7 0 ATAAAGCGTT 0.940162 -294 ATCATAATGATTAAAGATTTTAACCACTAT 9 222 1 TTAAAGATTT 0.734857 -79 GTGGGCTTACATAAAGCGATCCCTAAATTT 11 51 0 ATAAAGCGAT 0.848108 -250 AAAAAACAGAATAAAGAATTGTTTAAGAAA 11 200 1 ATAAAGAATT 0.54663 -101 ********** Masking position 4 Map Score: 3.31024 Number of sites scoring better than the average of aligned sites = 1353 Number in coding regions = 1187 Number in noncoding regions = 166 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 9 TTTGAAACCGATGATTTTTCAACGCTTATTG 2 132 1 ATGATTTTCA 0.751559 -43 ATATTGTATTAAATAAGGAGA 5 1 1 ATATTGTTTA 0.792574 -26 TGCGAATGTTATAATTTATTATTAAACGAAA 6 71 1 ATAATTTTTA 0.929398 -230 TTTATTGGTAATGTTTTTTAATTTTAAATTT 6 212 0 ATGTTTTTAA 0.661669 -89 AGCCCCTATTATATTGTATTAGAGTAATCTT 7 16 0 ATATTGTTTA 0.792574 -43 GCAAAACCCCCTATTTTCTTATGAATTTGGT 8 70 1 CTATTTTTTA 0.869203 -138 GCGGATTTTAAAGTTTTGTTAATCAAAAAGA 8 104 0 AAGTTTTTTA 0.718669 -104 TAAGCAGGCGATAATTTTTCACCATGCGATC 9 50 0 ATAATTTTCA 0.820216 -251 TGCAAGCTATTTAATTTTTTAAAAAATTCTT 9 82 1 TTAATTTTTA 0.625833 -219 ATCTTTTTGGCTGATTTTTTAGATCAGAAAT 10 15 0 CTGATTTTTA 0.815035 -94 AGCGATCCCTAAATTTTCTAAGCCTTCACAC 11 36 0 AAATTTTTAA 0.463283 -265 TTTTTACCCAAAAATTTCTTATAGATTTCTT 11 224 0 AAAATTTTTA 0.793923 -77 TTTAAGAAAGCTAATTTTTTACCCAAAAATT 11 239 0 CTAATTTTTA 0.869203 -62 TCCTAGTGTGATATTTTCTTAATTTAGAACT 11 273 0 ATATTTTTTA 0.929398 -28 ******* *** Masking position 11 Map Score: 8.18278 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 147 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 CGTTTTGAAACCGATGATTTTTCAACGCTTAT 2 129 1 CCATGATTTT 0.840339 -46 CTTTTCTTAAGCCATGCTTTGTTCATAGCATT 3 59 1 GCATGCTTTT 0.924998 -136 CGATGCGAATGTTATAATTTATTATTAAACGA 6 68 1 GTATAATTTT 0.949428 -233 AAGAATTTGAGTGATAATTTGTATTGTTTTTA 6 114 0 GTATAATTTT 0.949428 -187 TCATTTATTGGTAATGTTTTTTAATTTTAAAT 6 214 0 GTATGTTTTT 0.923959 -87 CACTAAGCAGGCGATAATTTTTCACCATGCGA 9 52 0 GCATAATTTT 0.957755 -249 AACTCCTAGTGTGATATTTTCTTAATTTAGAA 11 275 0 GTATATTTTT 0.909602 -26 ** ******* * Masking position 4 Map Score: 1.02081 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 119 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 AACGAAAAGTAAATGAAGCTAAAAACAATACAA 6 95 1 AATGGCTAAA 0.968315 -206 AATACAATATAATAGGGGCTAATTTAAAGATTA 7 27 1 AAAGGCTAAT 0.966077 -32 ATAGGTTACTAAAAGTTACTAATAAGTTAAAAT 9 178 1 AAAGACTAAT 0.798221 -123 ATTTTTCTACAATAGTGGTTAAAATCTTTAATC 9 230 0 AAAGGTTAAA 0.9011 -71 CTCATTAAAAACAAGGAGCAAAAAAG 9 285 1 ACAGGCAAAA 0.907527 -16 AAAAGATAAAAAAAGTCGCTAAATCATAGTCGT 10 39 1 AAAGGCTAAA 0.985948 -70 ATTTAAGCCAACCTGACGCTAAAATCCAAATTT 11 110 1 ACTGGCTAAA 0.953628 -191 ** ** ****** Masking position 11 Map Score: 1.247 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 247 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 ********** No masking Map Score: -1.91603e-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 13 ********** No masking Map Score: -1.91603e-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 14 ********** No masking Map Score: -1.91603e-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