AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ipurR_aful_opreg_100.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF0252 251 CTP synthase (pyrG) #2 AF0841 80 adenylosuccinate synthetase (purA) #3 AF0842 65 A. fulgidus predicted coding region AF0842 #4 AF0875 300 snRNP, putative #5 AF0977 173 ammonium transporter (amt-1) #6 AF1157 163 phosphoribosylamine--glycine ligase (purD) #7 AF1186 139 conserved hypothetical protein #8 AF1215 101 cell division protein, putative #9 AF1269 300 A. fulgidus predicted coding region AF1269 #10 AF1270 33 transcriptional regulatory protein, ArsR family #11 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #12 AF1420 216 membrane protein #13 AF1693 45 phosphoribosylformylglycinamidine cyclo-ligase (purM) #14 AF1746 122 ammonium transporter (amt-2) #15 AF1749 95 ammonium transporter (amt-3) #16 AF1941 201 conserved hypothetical protein #17 AF2242 61 adenylosuccinate lyase (purB) #18 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #19 AF2244 300 acyl-CoA dehydrogenase (acd-11) Motif number 1 GTTCTCCTCAACCACTTCAACTTCCAATTCCGA 1 128 0 ACCTTCACTT 0.936222 -124 CTTTCCAGATATAATCTCCTCTTCGTTCTCCTC 1 152 0 AATCTCCCTT 0.790055 -100 CCAACCACCTCATGTTTTATCACTAC 3 50 0 ACCCTCAGTT 0.977761 -16 ATTTTTAAATAACTCCTCCTGCAACGAACCTTA 4 256 1 ACCCTCCGCA 0.86463 -45 TAAAAACAGCAACGCCTCAGCTTGACCG 8 6 0 ACCCTCACTT 0.980795 -96 TAGACAGTAGAAAATTTCCTGTTAAAGGGTTCT 9 273 1 AATTTCCGTT 0.482202 -28 AAGCCCTTCCTCTTTTTTTGATTC 11 2 1 ACCTTCCCTT 0.964653 -23 GTAACCTTTTATCGCCCCCTGTTAACTTCGCTT 17 38 1 ACCCCCCGTT 0.928016 -24 GACCTTCTCCACCGCCTCAGCCTGAGGCGGAAA 19 64 1 ACCCTCACCT 0.974026 -237 CAGCTCTTCTATACCCTCCTCCTTTAAAATGCC 19 97 1 AACCTCCCCT 0.932794 -204 GCTTGCTGAAAGCATCTCAAGTTATGCTGTTGG 19 128 0 ACTCTCAGTT 0.897425 -173 GCTTTCAGCAAGCTCCTCCACCTTCACCACTTC 19 148 1 ACCCTCCCCT 0.985859 -153 CTCCACCTTCACCACTTCAAGTTTTCAACGGTG 19 163 1 ACCTTCAGTT 0.926674 -138 * * ***** *** Masking position 1 Map Score: 14.79 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 987 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 2 AACCTACCATTTTTCCAAAAATCGCAAACCAAATAAA 2 30 1 TTTTCAAAAA 0.898348 -51 AAAATATTCTTTTTAAAAAAAGAAAAA 5 1 0 TTTTAAAAAA 0.950482 -173 ACTGAAGAATTTTTAAGAAAATTTGTAGAAATTGAAG 5 93 0 TTTTAAAATA 0.935823 -81 AACTCTAAACTTTAAAGACATTCGAAAGCCTTACAAA 6 19 1 TTTAAAATAA 0.713399 -145 AATCCTCGTTTTTAATTACAAATTCTACCTGTGTAAA 6 77 0 TTTAAAAATA 0.950499 -87 GGGAAAAAGGTTTAAATAAAAAGCGTATTAAATCTTA 8 67 1 TTTAAAAATA 0.950505 -35 TTAAAAGATTTTTAAAAACAACACTAAAACTTGAGTT 14 95 1 TTTAAAAAAA 0.961964 -28 AAACTTTTTAGAAAAAAACTAAAAAACTGAAG 15 6 1 TTTTAAAAAA 0.950505 -90 TAAAAAAATATTTAACAAAAACTCATAACTTTTCACA 15 46 0 TTTAAAAATA 0.950504 -50 AGTAAAAAAATTTTACTAAAATAAAAATTGAGGATAG 16 78 0 TTTTAAAAAA 0.95027 -124 GTAAAATTTTTTTACTTATAAATTTTATCCTTCAGAT 16 99 1 TTTACAAATA 0.898343 -103 CTTTTTTCTTTTTAACGAAAAGGAGTAACCTTTTATC 17 14 1 TTTAAAAATA 0.950505 -48 CTGCAAACGTTTTTCAAATAATAAAAAAT 18 3 0 TTTTCAAAAA 0.898326 -36 TGAAAAAGGATTTAAATAGAACACAATTGTAGTTATA 19 229 0 TTTAAAAAAT 0.713399 -72 ***** * ** ** Masking position 8 Map Score: 14.3726 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 26 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 ACACAAGTCGAAAACATTTTTAACCCTGAAGCT 4 180 0 AAATTTTTAA 0.9567 -121 AAAATAAAAAATATTCTTTTTAAAAAAAGAAAA 5 12 0 ATATTTTTAA 0.88553 -162 AGAATTTACTGAAGAATTTTTAAGAAAATTTGT 5 104 0 GAATTTTTAA 0.724535 -70 GCCAGATTTAAAAGTTTTTTGCATGAATTAGAG 5 135 0 AAATTTTGCA 0.892956 -39 AAAGCCTTACAAATCGTATTTAAGCTTTGTTAT 6 43 1 AAATATTTAA 0.877371 -121 GATATAATAAAAATAATATTGCCAAGAA 7 6 0 AAATATTGCC 0.58114 -134 CTTTTTATTTAAACCTTTTTCCCAACTTTGCAA 8 57 0 AAATTTTCCC 0.746288 -45 AGCTTCCCGGATAGTCTATTTCACACTCCATCA 12 70 1 ATATATTTCA 0.691063 -147 CAAGAGGCTAATAAGGTTTTTCATGAGTTTGAT 12 180 0 ATATTTTTCA 0.873545 -37 TCAAGTCGGAAAAGTCTTTTTAAAAGGTTGCCC 13 20 0 AAATTTTTAA 0.9567 -26 AGAGTTATTCACAAAATTTTTAAACAGCCTTGT 14 23 0 ACATTTTTAA 0.777028 -100 AAATCTTTTAATATTTTTTTGACATTTCTAAGA 14 73 0 ATATTTTGAC 0.626859 -50 AAAAAATATTAAAAGATTTTTAAAAACAACACT 14 87 1 AAATTTTTAA 0.9567 -36 CCCGAATTTAAAAAAATATTTAACAAAAACTCA 15 58 0 AAATATTTAA 0.87737 -38 TTATTTTAGTAAAATTTTTTTACTTATAAATTT 16 91 1 AAATTTTTAC 0.919018 -111 ATCACCCTGCAAACGTTTTTCAAATAATAAAAA 18 13 0 AAATTTTCAA 0.865109 -26 TGTTCTATTTAAATCCTTTTTCAATTGTTTAAC 19 243 1 AAATTTTTCA 0.951761 -58 *** ******* Masking position 7 Map Score: 11.8052 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 140 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 4 CCAACCACCTCATGTTTTATCACTACAT 3 48 0 CTCATGTTTT 0.965873 -18 TTTTTCTTTTTTTAAAAAGAATA 5 4 1 TTCTTTTTTT 0.443537 -170 GTACTCAGGATTTCATGCCAGAT 5 161 0 CTCAGGATTT 0.795491 -13 AAGCCCTTCCTCTTTTTTTGATTC 11 10 1 CTCTTTTTTT 0.783112 -15 TATTCGTTTTGTCAAGTTATTCTGCTGGCA 12 107 1 GTCAAGTTAT 0.668445 -110 CCTTATTAGCCTCTTGTTATTTATTTGCGT 12 197 1 CTCTTGTTAT 0.80793 -20 GTGAATAACTCTCAATTTTTGTGAAGAAAT 14 44 1 CTCAATTTTT 0.930384 -79 GAACTCAAGTTTTAGTGTTGTTT 14 110 0 CTCAAGTTTT 0.971125 -13 TTCACAATTCTTCAGTTTTTTAGTTTTTTT 15 22 0 TTCAGTTTTT 0.625557 -74 GCAAGCTATCCTCAATTTTTATTTTAGTAA 16 73 1 CTCAATTTTT 0.930384 -129 CTGAAAGCATCTCAAGTTATGCTGTTGGCA 19 126 0 CTCAAGTTAT 0.939649 -175 CCTTCACCACTTCAAGTTTTCAACGGTGCA 19 168 1 TTCAAGTTTT 0.881296 -133 CCTCGTTAAACTCATGATATATAACTACAA 19 210 1 CTCATGATAT 0.727969 -91 ********** Masking position 8 Map Score: 8.47977 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 309 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 ATTTAAAATTAAGGCGGAAATCGTTATTTA 1 32 1 AAGGCGGAAA 0.980556 -220 TCCTCTCTGCAAGTCGGAATTGGAAGTTGA 1 115 1 AAGTCGGAAT 0.801831 -137 TCAACTCCGGAGGGCGCAAATCTGGAATCC 1 228 0 AGGGCGCAAA 0.925823 -24 AAAGGCACACAAGTCGAAAACATTTTTAAC 4 189 0 AAGTCGAAAA 0.854455 -112 TCGGTCAGCAGGGGCGGATATATAATTAAT 6 111 0 GGGGCGGATA 0.929461 -53 TTCAACTGCGGGCTCGGAAAATCTCACGAT 12 20 1 GGCTCGGAAA 0.860754 -197 GATTCAAGTCGGAAAAGTCTTTTTA 13 31 0 AAGTCGGAAA 0.962501 -15 AAGTTAACAGGGGGCGATAAAAGGTTACTC 17 36 0 GGGGCGATAA 0.75086 -26 GCCTCAGCCTGAGGCGGAAACAGCTCTTCT 19 77 1 GAGGCGGAAA 0.984831 -224 ********** Masking position 5 Map Score: 4.85392 Number of sites scoring better than the average of aligned sites = 467 Number in coding regions = 449 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CAGATTTGCGCCCTCCGGAGTTGAGACA 1 234 1 CCCTCCGGAG 0.983024 -18 CCAAATAAACCCCTGCGAAGGACTGTCAGT 2 58 1 CCCTGCGAAG 0.977642 -23 TTAATTGCCTCCATCCGAAGAAACTTTTAT 4 57 0 CCATCCGAAG 0.982362 -244 AGGACAACGCCCTTCCGAGGCGTTAGCCCG 4 118 0 CCTTCCGAGG 0.980775 -183 TTTTTACCTTACGGAGAAGATTGACG 9 7 1 CCTTACGGAG 0.911318 -294 AAAAGGTTGCCCATCTGAAGT 13 2 0 CCATCTGAAG 0.878421 -44 CCGCTGTGGGCATTGCGAGGAGCAGATTTT 19 24 1 CATTGCGAGG 0.782413 -277 ********** Masking position 4 Map Score: 3.44832 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 178 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 7 TTTTAACATTTTCTAAATTGGCCGCGTTCTTGA 5 55 1 TTTAATGGCC 0.92639 -119 TTTGTAGAAATTGAAGATTTCTCAAGAACGCGG 5 76 0 TTAAGTTCTC 0.705397 -98 GCAAAAAACTTTTAAATCTGGCATGAAATCCTG 5 146 1 TTAAATGGCA 0.796095 -28 GCGTTGCTGTTTTTAAACTTGCCTTTATCGAGA 8 24 1 TTTAATTGCC 0.93849 -78 GTCACTCAGCTTCAAAGCTTCCCGGATAGTCTA 12 55 1 TTAAATTCCC 0.961299 -162 CCACGAAGTCTTGAAGCGTTGCCAGCAGAATAA 12 123 0 TTAAGTTGCC 0.959348 -94 AAAAGTCTTTTTAAAAGGTTGCCCATCTGAAGT 13 11 0 TTAAATTGCC 0.979709 -35 CAACGGTGCATTAAAAATTGCTCCTCGTTAAAC 19 188 1 TTAAATGCTC 0.801644 -113 TTTGTGATTATTTAAATTTTGCCAAGTTAAACA 19 268 0 TTAAATTGCC 0.979705 -33 ** *** ***** Masking position 5 Map Score: 3.41549 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 67 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 GCTGGTAGGCTTTTTTGCGGTATT 1 1 1 GCGTGCTTTT 0.966695 -251 CCCGGCCCGCGCACATTGGTTTTTAATTGCCTCC 4 75 0 GCCTGTTTTT 0.951418 -226 CCATAAACTAGCACATAGTCTTTTGTGGTTATCT 9 46 0 GCCTTCTTTT 0.987731 -255 GATGATGGAAGCCCTTGAGCTTTTTGGATTGGGC 9 119 1 GCCTGCTTTT 0.992162 -182 AAGCCCTTCCTCTTTTTTTGATTC 11 3 1 GCCTTCTTTT 0.987731 -22 GTTGTTTTTTGCTCATGCTCTTTAAAAATCAAGC 16 177 0 GCCTTCTTTA 0.952065 -25 ** * * ****** Masking position 6 Map Score: 2.74269 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 9 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 TAAATACCGCAAAAAAGCCTACCAGC 1 7 0 AAAAAAGCCT 0.871285 -245 CATTCATGAAAAGGAAGCTTCTGGAAATCC 1 78 1 AAGGAAGCTT 0.701903 -174 CAACTGCTGCAAACGAGCTTTCCAGATATA 1 172 0 AAACGAGCTT 0.72564 -80 CTCCTCCTGCAACGAACCTTAGATAATTCT 4 268 1 AACGAACCTT 0.857516 -33 TAATTCATGCAAAAAACTTTTAAATCTGGC 5 138 1 AAAAAACTTT 0.699718 -36 GTGTAAAAATAACAAAGCTTAAATACGATT 6 54 0 AACAAAGCTT 0.822918 -110 CTGAATAAACAAAGAACCTTAGTTAGGATG 9 93 1 AAAGAACCTT 0.939673 -208 AGAAAAGAACCCTTTAACAGGAA 9 288 0 AAAGAACCCT 0.897636 -13 TCAAACTCATGAAAAACCTTATTAGCCTCT 12 181 1 GAAAAACCTT 0.742243 -36 CAACCTTTTAAAAAGACTTTTCCGACTTGA 13 23 1 AAAAGACTTT 0.657183 -23 TTTTTGCCGGAAAAGACCTTCTCCACCGCC 19 50 1 AAAAGACCTT 0.93242 -251 AATAATCACAAAAAGAGCCTGC 19 289 1 AAAAGAGCCT 0.847762 -12 ********** Masking position 6 Map Score: 4.47405 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 266 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 GGTTGAGGAGAACGAAGAGGAGATTATATC 1 148 1 AACGAAGAGG 0.956975 -104 ATCGCTAACGAGAAGTTACTAACAAC 3 7 1 AACGAGAAGT 0.915033 -59 AGGTTCGTTGCAGGAGGAGTTATTTAAAAA 4 257 0 CAGGAGGAGT 0.88488 -44 TGTAATTAAAAACGAGGATTAATTATATAT 6 94 1 AACGAGGATT 0.8402 -70 TTTTCTTTTTAACGAAAAGGAGTAACCTTT 17 17 1 AACGAAAAGG 0.835725 -45 TGGCATTTTAAAGGAGGAGGGTATAGAAGA 19 101 0 AAGGAGGAGG 0.983545 -200 TGAAGTGGTGAAGGTGGAGGAGCTTGCTGA 19 152 0 AAGGTGGAGG 0.914613 -149 TCATGAGTTTAACGAGGAGCAATTTTTAAT 19 197 0 AACGAGGAGC 0.965058 -104 ********** Masking position 8 Map Score: 4.61717 Number of sites scoring better than the average of aligned sites = 587 Number in coding regions = 557 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 TGTCTCAACTCCGGAGGGCGC 1 241 0 TTCTCAACTC 0.942858 -11 ATTTTTATTATATCACACTTCTTTGCTCAAT 7 25 1 TTCACACTTC 0.969036 -115 TGCTCAATCTTATCTCAATCCTTAAGAATTT 7 48 1 TTCTCAATCC 0.942858 -92 GATTGCAAGCTCTCTCACCTCTCACAGGGAC 9 162 1 TTCTCACCTC 0.962888 -139 GGATAGTCTATTTCACACTCCATCAGGGCTA 12 78 1 TTCACACTCC 0.962888 -139 ACTCATAACTTTTCACAATTCTTCAGTTTTT 15 32 0 TTCACAATTC 0.95216 -64 * ********* Masking position 7 Map Score: 2.1897 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 38 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 GGAATTGGAAGTTGAAGTGGTTGAGGAGAA 1 130 1 GTTGAAGTGG 0.962292 -122 GGGAATCATGCTAGAATTGGTGGTATGTAC 4 26 0 CTAGAATTGG 0.925127 -275 AAGAAAATTTGTAGAAATTGAAGATTTCTC 5 86 0 GTAGAAATTG 0.856115 -88 TTTTACACAGGTAGAATTTGTAATTAAAAA 6 76 1 GTAGAATTTG 0.937632 -88 CGAGCCCGCAGTTGAATTTGGACAG 12 6 0 GTTGAATTTG 0.937632 -211 CCGTTGAAAACTTGAAGTGGTGAAGGTGGA 19 164 0 CTTGAAGTGG 0.930257 -137 ********** Masking position 5 Map Score: 1.04551 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 59 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 13 ACTCATACCTCCAACAGCATTCATGAAAAG 1 61 1 CCAACAGCAT 0.902242 -191 TGCCTTTAAGCTCTCAGCATCTGGCAAAAT 4 212 1 CTCTCAGCAT 0.945513 -89 AAACAGCAACGCCTCAGCTTGACCG 8 6 0 GCCTCAGCTT 0.883561 -96 TCAAGGGCTTCCATCATCCTAACTAAGGTT 9 107 0 CCATCATCCT 0.945235 -194 GATACTCTGTCACTCAGCTTCAAAGCTTCC 12 47 1 CACTCAGCTT 0.786364 -170 CCATCATACACTATCATCATACACCGAATC 16 147 1 CTATCATCAT 0.781005 -55 TCTATCACCCTGCAAACGTTT 18 28 0 CTATCACCCT 0.768417 -11 CTTCTCCACCGCCTCAGCCTGAGGCGGAAA 19 67 1 GCCTCAGCCT 0.957368 -234 CTCTTCTATACCCTCCTCCTTTAAAATGCC 19 100 1 CCCTCCTCCT 0.851635 -201 CTTTAAAATGCCAACAGCATAACTTGAGAT 19 118 1 CCAACAGCAT 0.902242 -183 ********** Masking position 10 Map Score: 2.13949 Number of sites scoring better than the average of aligned sites = 1381 Number in coding regions = 1327 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 14 ATTAAACCTTAACTCAAACCTACCATTTTTCCAAA 2 14 1 AACCAATACA 0.94319 -67 AGTTACTAACAACACTAAAGTAAAATGTAGTGATA 3 24 1 AACCAATAAA 0.944253 -42 AATATCGCTGAACCCGAATTTTGCCAGATGCTGAG 4 224 0 AACCAATTCC 0.876149 -77 CCTGATCAAACTCTAAACTTTAAAGACATTCGA 6 9 1 AACCAATTAA 0.964505 -155 AATTTAAAGCAGCTCAAACATTACAAAAGTTTATA 7 92 1 AGCCAATTCA 0.963108 -48 CTCAACGCTAAGATTTAATACGCTTTTT 8 84 0 AACCAATTAA 0.964505 -18 TATATTTTGCAGCGCAAAGTATAAATCTCCTTGAC 9 222 1 AGCCAAATAA 0.826781 -79 TCAGAAATTAAGCCCGAATTTAAAAAAATATTTAA 15 68 0 AGCCAATAAA 0.94319 -28 *** * ** ** ** Masking position 8 Map Score: 1.31255 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 26 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 ATGAATGCTGTTGGAGGTATGAGTAAATAA 1 55 0 TTGGAGGTAT 0.742307 -197 CATGCTAGAATTGGTGGTATGTACAGAGCA 4 20 0 TTGGTGGTAT 0.921112 -281 CTTTAAATTACTGTTGGTAATCAAATTCTT 7 71 0 CTGTTGGTAA 0.906701 -69 TCAAGTTATTCTGCTGGCAACGCTTCAAGA 12 118 1 CTGCTGGCAA 0.925667 -99 TCCGTTAACCTTGCTGGTATTAGTT 16 6 0 TTGCTGGTAT 0.921091 -196 TTACCCGCCGCTGTGGGCATTGCGAGGAGC 19 17 1 CTGTGGGCAT 0.907951 -284 TCAAGTTATGCTGTTGGCATTTTAAAGGAG 19 115 0 CTGTTGGCAT 0.964254 -186 ********** Masking position 9 Map Score: 0.627739 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 114 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185