AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -irpoH_aful_opreg_300.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 AF0362 59 snRNP, putative #2 AF0364 34 ATP-dependent protease La (lon) #3 AF0481 64 proteasome, subunit beta (psmB) #4 AF0483 101 conserved hypothetical protein #5 AF0484 33 GTP cyclohydrolase II (ribA-1) #6 AF0487 57 penicillin G acylase #7 AF1285 42 cell division control protein, AAA family, putative #8 AF1286 257 acetoin utilization protein, putative #9 AF1287 300 acetyl-CoA synthetase (acs-6) #10 AF1298 300 A. fulgidus predicted coding region AF1298 #11 AF1446 63 A. fulgidus predicted coding region AF1446 #12 AF1448 114 transcriptional regulatory protein, AsnC family #13 AF1449 33 pyruvate formate-lyase 2 (pflD) #14 AF1451 88 thermosome, subunit beta (thsB) #15 AF1898 74 response regulator #16 AF1899 42 conserved hypothetical protein #17 AF1971 45 small heat shock protein (hsp20-2) #18 AF1976 93 26S protease regulatory subunit 4 #19 AF2098 59 cell division control protein 48, AAA family (cdc48-2) #20 AF2238 210 thermosome, subunit alpha (thsA) Motif number 1 CAAGTACAAAAACGTTTGTAAGGGAACTCTATTTC 4 21 1 AAGTTGGGGA 0.976229 -81 GAAAAAAGTTGGTCGGGGGAATATAAACT 5 15 0 AAGTGGGGGG 0.995036 -19 GTGGTTGCAAAAAGCTGGGCAGAGAGAAGAAAAGT 9 106 0 AAGTGGGAGA 0.985424 -195 GAGAAAAGGAAAGAATGGGAAGAGAAATGTCTCAA 9 144 0 AAATGGGAGA 0.961299 -157 TGTGATTAAAAATGTAGGTAAGGGAGGTTGTT 9 279 1 AAGAGGGGGA 0.969931 -22 TTGCGAGAGTAAAGGTTGAGAGAGGGACTGGAAAG 10 74 1 AAGTTGGAGG 0.985424 -227 AGCCTCATAGAAGTTTGGAGTGGGATGAACTCTGC 10 152 1 AATTGGGGGA 0.910166 -149 TGTACTGGTGAAAGTTTTTAAGAGGGAAAAATCCA 11 17 1 AAGTTTGAGG 0.82909 -47 TAAGTTAGGAAAGAAAGGTTAGGGGGAGGTG 17 25 1 AAAAGGGGGG 0.963211 -21 TTTTAGAGATAAAAAAGGCTTGTGGTGATTTG 19 8 0 AAAAGGGTGG 0.801998 -52 TGCGCGGTGGAAGGGTTGATTGAGGCTACATGGTT 20 110 0 AAGTTGGAGG 0.985424 -101 TCAATCCACCAATATTTGCAAGAGGGAGGTGAGTG 20 184 1 AAATTGGAGG 0.961299 -27 ** * *** **** Masking position 2 Map Score: 16.3796 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 275 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 ACCTGTGCAGAAAAAGTATATAACAACTCATTTTA 1 23 0 AAATATTACA 0.965614 -37 CAAAATTCTTAAATACTATGTAAAAGATGTGTGAT 9 250 1 AAATATTAAA 0.975272 -51 AAATAACCGAAAACTTTATATACCATAAACCTAAC 10 251 1 AAATATTACA 0.965614 -50 TTTATAAGGTAAACTTTATTTACAATGAAAGTGTT 12 79 1 AAATATTAAA 0.975272 -36 CCTTAAAAACCTAATTAAAAAAGATTACGA 13 14 0 AAATAATAAA 0.847319 -20 TCGTGATAGAAAAGCTTATATAGAAATACCAATCC 14 34 1 AAATATTAAA 0.975272 -55 TCTGCAATAACTATTTATAAAGCGAGTTAG 16 6 1 AATTATTAAA 0.916413 -37 GAAGCCTCCAAATACATATATATCACTCATCATAT 18 26 0 AATTATTACA 0.886442 -68 CAAATCCACAAAATTTTTTATAAAACAGACACAAA 20 18 0 AAATTTTAAA 0.847319 -193 GCCTGACCGTAAAATATATATAGAAATTTCAATCC 20 156 1 AAATATTAAA 0.975272 -55 *** *** ** ** Masking position 7 Map Score: 12.7249 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 4 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 3 GTTTGTCCAATTTGTGAGAGG 2 24 1 TTTGGAGAGG 0.984142 -11 AGCTTCTTCTGCTGAAAGAAGGGTGATAAAA 8 32 0 GCTGAAGAAG 0.91052 -226 ACACATAGACTTTGTGAGAGACATCGGCTAT 9 20 0 TTTGGAGAGA 0.803436 -281 AAAAAGCTGGGCAGAGAGAAGAAAAGTTCGA 9 102 0 GCAGGAGAAG 0.922207 -199 GCTGCGAAAAGCAGAGAGAAGGTTAAGCACA 10 40 1 GCAGGAGAAG 0.922207 -261 GAGAGTAAAGGTTGAGAGAGGGACTGGAAAG 10 78 1 GTTGGAGAGG 0.984433 -223 TTCTCTTCAATCTGGAGGAAGCTTGTACCAG 10 195 0 TCTGAGGAAG 0.879991 -106 CTGGTGAAAGTTTTTAAGAGGGAAAAATCCA 11 21 1 TTTTAAGAGG 0.757295 -43 TCCACCAATTTCTGCAATAGGAGGTGATGTG 14 66 1 TCTGAATAGG 0.623379 -23 GAAAGAAAGGTTAGGGGGAGGTG 17 33 1 TTAGGGGAGG 0.954744 -13 CTTCCGGAACGTAGAGGGAAGCAAAAAATAA 18 57 1 GTAGGGGAAG 0.895206 -37 GCTACATGGTTTTTGGGGAGGTTGAATTGAA 20 90 0 TTTTGGGAGG 0.852197 -121 TCCACCAATATTTGCAAGAGGGAGGTGAGTG 20 188 1 TTTGAAGAGG 0.96103 -23 **** ****** Masking position 9 Map Score: 12.3635 Number of sites scoring better than the average of aligned sites = 1526 Number in coding regions = 1438 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 ATCACCTCGCTGACCTGTGCAGAAA 1 45 0 CTCGCTGACC 0.905542 -15 CAATATTTGCTCCTCTGCTTAATATGTCTT 7 18 0 TCCTCTGCTT 0.842427 -25 TCGGGAAAGTCTCTCAGCCTTGTTCCCAGT 8 70 0 CTCTCAGCCT 0.969859 -188 AAAAAGGACCCTCTCTGCTCGACAGCCTGG 8 206 1 CTCTCTGCTC 0.984977 -52 CTCCGCTGCCCTAACAACTCC 8 247 0 TCCGCTGCCC 0.939997 -11 AACTTTTCTTCTCTCTGCCCAGCTTTTTGC 9 105 1 CTCTCTGCCC 0.995026 -196 TTTGAGACATTTCTCTTCCCATTCTTTCCT 9 143 1 TTCTCTTCCC 0.879834 -158 GCTTAACCTTCTCTCTGCTTTTCGCAGCAA 10 38 0 CTCTCTGCTT 0.970907 -263 TCCAGTCCCTCTCTCAACCTTTACTCTCGC 10 76 0 CTCTCAACCT 0.782288 -225 ********** Masking position 5 Map Score: 7.9936 Number of sites scoring better than the average of aligned sites = 902 Number in coding regions = 860 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TTGAAGCAGTTGTTGGATGGCATAATGAGA 10 119 1 TGTTGGATGG 0.943053 -182 GGTTGGATTGTAACACTTTC 12 105 0 GGTTGGATTG 0.984847 -10 TTGCAGAAATTGGTGGATTGGTATTTCTAT 14 53 0 TGGTGGATTG 0.991084 -36 AAAAGGCTTGTGGTGATTTG 19 1 0 TGGTGATTTG 0.862925 -59 TTTTTGGGGAGGTTGAATTGAACGAATAGC 20 82 0 GGTTGAATTG 0.946609 -129 CGCGGTGGAAGGGTTGATTGAGGCTACATG 20 113 0 GGGTTGATTG 0.945686 -98 TTGCAAATATTGGTGGATTGAAATTTCTAT 20 175 0 TGGTGGATTG 0.991084 -36 ********** Masking position 4 Map Score: 7.97398 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 74 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 TTTGTAAGGGAACTCTATTTCAACTCGAAA 4 35 1 AACTCTATTT 0.858568 -67 ATTAAGTTTATATTCCCCCGACC 5 4 1 AAGTTTATAT 0.756918 -30 AAATTATTTAATTTTTATGTTTTGACTAAT 6 21 0 ATTTTTATGT 0.852815 -37 ATTTTTATGTTTACTGGTGT 8 1 1 ATTTTTATGT 0.852815 -257 GTCTCTCACAAAGTCTATGTGTTCAATGTC 9 29 1 AAGTCTATGT 0.861766 -272 AAAATTCTTAAATACTATGTAAAAGATGTG 9 251 1 AATACTATGT 0.575772 -50 AATAACCGAAAACTTTATATACCATAAACC 10 252 1 AACTTTATAT 0.85627 -49 GTCGGTTACTAACTTTATGTTAGGTTTATG 10 274 0 AACTTTATGT 0.92129 -27 TTATAAGGTAAACTTTATTTACAATGAAAG 12 80 1 AACTTTATTT 0.856267 -35 GTGGATTGGTATTTCTATATAAGCTTTTCT 14 41 0 ATTTCTATAT 0.75032 -48 AGCGAGTTAGAATTTTATTTGA 16 31 1 AATTTTATTT 0.864317 -12 TTTATCCCTCAATTTTATTTTTTGCTTCCC 18 72 0 AATTTTATTT 0.864317 -22 GTGGATTGAAATTTCTATATATATTTTACG 20 163 0 ATTTCTATAT 0.75032 -48 ********** Masking position 7 Map Score: 10.5305 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 66 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 TTGTTATATACTTTTTCTGCACAGGTCAGCGA 1 32 1 CTTTCTGCAC 0.885012 -28 GAGATAGCTTCTTCTGCTGAAAGAAGGGTGAT 8 36 0 CTCTCTGAAA 0.727053 -222 TTTGGGCTCTCAATTTCTGCAAAAGCTTCGGG 8 95 0 CATTCTGCAA 0.984325 -163 TAAAACTTTTCATTTAATTCAATTCGAATCAA 9 221 1 CATTATTCAA 0.844887 -80 TGCCATCCAACAACTGCTTCAACTGAGCCAAA 10 109 0 CACTCTTCAA 0.975748 -192 GGGAAAAATCCAATTACTTCGAAGGTGGAGCA 11 40 1 CATTCTTCGA 0.919332 -24 TGGATAAAGACAGCTACTTCAATTACAAAGAA 12 24 0 CACTCTTCAA 0.975748 -91 ACCAATCCACCAATTTCTGCAATAGGAGGTGA 14 61 1 CATTCTGCAA 0.984325 -28 TTCCATGCAGCTATTCGTTCAATTCAACCTCC 20 73 1 CTTTGTTCAA 0.808971 -138 ** ** ****** Masking position 5 Map Score: 4.35907 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 265 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 AATAGAGTTCCCTTACAAACGTTTTTGTAC 4 24 0 CCTTACAAAC 0.967239 -78 TTTATATTCCCCCGACCAACTTTTTTC 5 17 1 CCCGACCAAC 0.858137 -17 AAAATCAGCTCCTCATCGACTGCTGGCGAT 8 142 0 CCTCATCGAC 0.648275 -116 CTCCGCTGCCCTAACAACTCCCCTGCGG 8 240 0 CCCTAACAAC 0.958738 -18 GAATCAAAATTCTTAAATACTATGTAAAAG 9 246 1 TCTTAAATAC 0.621994 -55 AACAACCTCCCTTACCTACATTTTTAATC 9 282 0 CCTTACCTAC 0.909975 -19 GATTTTTCCCTCTTAAAAACTTTCACCAGT 11 20 0 TCTTAAAAAC 0.838893 -44 ATAAAGTTTACCTTATAAACTGACGTTGGA 12 68 0 CCTTATAAAC 0.929093 -47 CCTTAAAAACCTAATTAAAA 13 24 0 CCTTAAAAAC 0.967868 -10 AATTCAACCTCCCCAAAAACCATGTAGCCT 20 93 1 CCCCAAAAAC 0.912915 -118 ********** Masking position 5 Map Score: 5.3304 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 376 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 TACTTTTATTACACCTGAAATCAAACTCCCACC 4 79 1 ACACCGAACA 0.991918 -23 GTGATAAAAAACACCAGTAAACATAAAAAT 8 8 0 ACACCGAACA 0.991918 -250 AAGCTATCTCACACTGGGAACAAGGCTGAGAGA 8 58 1 ACACTGAAAA 0.963467 -200 CTCAACCTTTACTCTCGCAAGAATGTGCTTAAC 10 61 0 ACTCTGAAAA 0.866778 -240 TTAAAAACTTTCACCAGTACACACTCA 11 5 0 TCACCGACCA 0.917154 -59 TTCCTGACACCTGTAAAAATTAGACTTGG 15 56 0 ACACCGAAAA 0.98735 -19 ***** * ** ** Masking position 9 Map Score: 1.604 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 22 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 CTTCAAGGTGCTCTTTGGTGTGTATTTTCAAA 8 169 0 CTCTTTGGTG 0.87253 -89 CCTTTTTCACCCCTTCAAGGTGCTCTTTGGTG 8 181 0 CCCTTCAGTG 0.955751 -77 ACCCTCTCTGCTCGACAGCCTGGCACTCCGCA 8 213 1 CTCGACACTG 0.815345 -45 CTAACAACTCCCCTGCGGAGTGCCAGGCTGTC 8 226 0 CCCTGCGGTG 0.968784 -32 GTGGGATGAACTCTGCAATGCGTTCTGGTACA 10 171 1 CTCTGCAGCG 0.971157 -130 CAATTATTTTCTCTTCAATCTGGAGGAAGCTT 10 202 0 CTCTTCACTG 0.959698 -99 TTTTGCTTCCCTCTACGTTCCGGAAGCCTCCA 18 51 0 CTCTACGCCG 0.93714 -43 GCTTTTTGAGCTCTGCGCGGTGGAAGGGTTGA 20 126 0 CTCTGCGGTG 0.980159 -85 ******* *** Masking position 3 Map Score: 3.26083 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 194 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 CTCATTTTAAAATCTTTCCCA 1 1 0 AATCTTTCCA 0.949663 -59 TTAAAAATCTTTTTTCTCTATTGAAG 3 6 1 AATCTTTTTC 0.823735 -59 TTGTAAGGGAACTCTATTTCAACTCGAAAAA 4 36 1 ACTCTATTCA 0.58463 -66 TCAGCAGAAGAAGCTATCTCACACTGGGAAC 8 48 1 AAGCTATCCA 0.835297 -210 GACTTTCCCGAAGCTTTTGCAGAAATTGAGA 8 89 1 AAGCTTTTCA 0.970269 -169 TTTAATCACACATCTTTTACATAGTATTTAA 9 258 0 CATCTTTTCA 0.850134 -43 AATCTGGAGGAAGCTTGTACCAGAACGCATT 10 187 0 AAGCTTGTCC 0.793782 -114 TCCCTCTTAAAAACTTTCACCAGTACACACT 11 13 0 AAACTTTCCC 0.71041 -51 AAATCGTAATCTTTTTTAATTAGGTTTT 13 8 1 AATCTTTTTA 0.881817 -26 ATTTCTATATAAGCTTTTCTATCACGAATTT 14 30 0 AAGCTTTTTA 0.889914 -59 CAATCTTTTACACCTAAACAGT 19 48 0 AATCTTTTCA 0.967869 -12 ******** ** Masking position 5 Map Score: 4.62578 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 320 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 12 TGGGAAAGATTTTAAAATGAGTTGTTAT 1 8 1 GTTTTAAAAT 0.791674 -52 GCTTCGATGAAATTTGAAATTATTTAATTTT 6 36 0 ATTTGAAATT 0.729434 -22 TGAGAGCCCAAAATTGAAGATTATCGAATCG 8 115 1 AATTGAAGAT 0.726176 -143 TGAGGAGCTGATTTTGAAAATACACACCAAA 8 157 1 ATTTGAAAAT 0.711375 -101 ACACTATCCGGCATTGAAGTTAATACAGTTT 9 70 0 GATTGAAGTT 0.908771 -231 TTAAATGAAAAGTTTTAAGTTTTCAGAACAA 9 207 0 ATTTTAAGTT 0.76013 -94 TTTCTATCACGAATTTAAATTGCAAGCATTT 14 15 0 GATTTAAATT 0.859691 -74 GAATGACTAAGTTTTTAAATTGCCAAGTCTA 15 34 1 GTTTTAAATT 0.879123 -41 AAATATTGGTGGATTGAAATTTCTATATATA 20 170 0 GATTGAAATT 0.92351 -41 * ********* Masking position 5 Map Score: 1.95736 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 139 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 13 TTGATTTCAGGTGTAATAAAAGTATCCAAA 4 73 0 GTGTAATAAA 0.819697 -29 AAGTTGGTCGGGGGAATATAAACTTAAT 5 9 0 GGGGAATATA 0.729235 -25 GCTGAAAGAAGGGTGATAAAAAACACCAGT 8 23 0 GGGTGATAAA 0.969473 -235 CTTGTTCCCAGTGTGAGATAGCTTCTTCTG 8 52 0 GTGTGAGATA 0.75978 -206 CACCTTGAAGGGGTGAAAAAGGACCCTCTC 8 191 1 GGGTGAAAAA 0.909385 -67 TGTAAAAGATGTGTGATTAAAAATGTAGGT 9 268 1 GTGTGATTAA 0.805664 -33 GAAGTTTGGAGTGGGATGAACTCTGCAATG 10 161 1 GTGGGATGAA 0.8694 -140 AAGTTTTTAAGAGGGAAAAATCCAATTACT 11 28 1 GAGGGAAAAA 0.873652 -36 CTTATATGATGAGTGATATATATGTATTTG 18 23 1 GAGTGATATA 0.901431 -71 AAATAAAATTGAGGGATAAAAT 18 82 1 GAGGGATAAA 0.956296 -12 ********** Masking position 6 Map Score: 5.20278 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 296 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 14 TTTTAAAAAGCAAAAACAAAGTG 3 52 1 CAAAAACAAA 0.841503 -13 GGTTTTATTTCAAGTACAAAAACGTTTGTA 4 11 1 CAAGTACAAA 0.952235 -91 GCTGATTTTGAAAATACACACCAAAGAGCA 8 163 1 AAAATACACA 0.799807 -95 AAAACTTTCACCAGTACACACTCA 11 5 0 CCAGTACACA 0.864762 -59 ACAGCTACTTCAATTACAAAGAAAAGACTG 12 17 0 CAATTACAAA 0.879649 -98 CGGAAGCCTCCAAATACATATATATCACTC 18 33 0 CAAATACATA 0.900048 -61 AAAACAGACACAAATCCAAAT 20 2 0 CAAATCCAAA 0.943746 -209 GTAGCTGAACCAAATCCACAAAATTTTTTA 20 33 0 CAAATCCACA 0.952962 -178 ********** Masking position 3 Map Score: 3.05196 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 43 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 AGGCTGAGAGACTTTCCCGAAGCTTTTGCAG 8 80 1 ACTTTCCCGA 0.949792 -178 AGAGACATCGGCTATCCGGGAGAG 9 4 0 GCTATCCGGA 0.980461 -297 AGTTCGAGACACTATCCGGCATTGAAGTTAA 9 78 0 ACTATCCGGA 0.978941 -223 ACTCTGCAATGCGTTCTGGTACAAGCTTCCT 10 180 1 GCGTTCTGGA 0.937003 -121 GCTTCCCTCTACGTTCCGGAAGCCTCCAAAT 18 48 0 ACGTTCCGGA 0.986283 -46 ********* * Masking position 5 Map Score: 0.0660629 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 45 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