AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -irpoH_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 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 AF1298 300 A. fulgidus predicted coding region AF1298 #10 AF1448 114 transcriptional regulatory protein, AsnC family #11 AF1449 33 pyruvate formate-lyase 2 (pflD) #12 AF1451 88 thermosome, subunit beta (thsB) #13 AF1898 74 response regulator #14 AF1899 42 conserved hypothetical protein #15 AF1971 45 small heat shock protein (hsp20-2) #16 AF1976 93 26S protease regulatory subunit 4 #17 AF2098 59 cell division control protein 48, AAA family (cdc48-2) #18 AF2238 210 thermosome, subunit alpha (thsA) Motif number 1 TCGCTGACCTGTGCAGAAAAAGTATATAACAACTC 1 29 0 GGAAAAAGAT 0.957458 -31 CAACCTTCAATAGAGAAAAAAGATTTTTAA 3 6 0 TGAAAAAGTT 0.96763 -59 TTGATTTCAGGTGTAATAAAAGTATCCAAACCTGC 4 68 0 GGTAAAAGAT 0.848124 -34 GCACCTTGAAGGGGTGAAAAAGGACCCTCTCTGCT 8 190 1 GGAAAAAGAC 0.766524 -68 GCACATTCTTGCGAGAGTAAAGGTTGAGAGAGGGA 9 66 1 GGGTAAAGTT 0.926374 -235 GGTTGAGAGAGGGACTGGAAAGTTTGGCTCAGTTG 9 87 1 GGGGAAAGTT 0.931425 -214 GTTAGGTTTATGGTATATAAAGTTTTCGGTTATTT 9 251 0 TGATAAAGTT 0.913999 -50 AACACTTTCATTGTAAATAAAGTTTACCTTATAAA 10 79 0 TGATAAAGTT 0.913999 -36 CTTAAAAACCTAATTAAAAAAGATTACGATTT 11 8 0 TAAAAAAGTT 0.645344 -26 ATTTAAATTCGTGATAGAAAAGCTTATATAGAAAT 12 26 1 GGGAAAAGTT 0.97252 -63 TTAAGTAAGTTAGGAAAGAAAGGTTAGGGGGAGGT 15 20 1 TGAGAAAGTT 0.919825 -26 TTTTATTTTAGAGATAAAAAAGGCTTGTGGTGATT 17 13 0 GGAAAAAGCT 0.960468 -47 AAAAACTGTTTAGGTGTAAAAGATTG 17 44 1 TGTAAAAGTT 0.881193 -16 CCACCGCGCAGAGCTCAAAAAGCCTGACCGTAAAA 18 135 1 GGAAAAAGCT 0.960459 -76 * * ****** ** Masking position 9 Map Score: 16.9357 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 225 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 CACGTTTGTCCAATTTGTGAGAGG 2 21 1 CATTTGGAGG 0.934868 -14 TTCTCTATTGAAGGTTGCCTTAGGGCTATTTTAA 3 24 1 AGGTTGTAGG 0.979574 -41 AAGTACAAAAACGTTTGTAAGGGAACTCTATTTC 4 22 1 AGTTTGGGGA 0.959318 -80 CTGCATTTTTCGAGTTGAAATAGAGTTCCCTTAC 4 38 0 CAGTTGTAGA 0.626179 -64 GAAAAAAGTTGGTCGGGGGAATATAAAC 5 16 0 AAGTTGGGGG 0.98519 -18 TGCGAGAGTAAAGGTTGAGAGAGGGACTGGAAAG 9 75 1 AGGTTGGAGG 0.994861 -226 AGCCTCATAGAAGTTTGGAGTGGGATGAACTCTG 9 152 1 AGTTTGTGGG 0.959318 -149 TAGGAAAGAAAGGTTAGGGGGAGGTG 15 30 1 AGTTAGGAGG 0.928232 -16 TTGAGGCTACATGGTTTTTGGGGAGGTTGAATTG 18 92 0 AGGTTTGGGA 0.779438 -119 GCGCGGTGGAAGGGTTGATTGAGGCTACATGGTT 18 110 0 AGGTTGGAGG 0.994861 -101 CAATCCACCAATATTTGCAAGAGGGAGGTGAGTG 18 185 1 AATTTGGAGG 0.973957 -26 * ***** **** Masking position 5 Map Score: 11.9515 Number of sites scoring better than the average of aligned sites = 494 Number in coding regions = 458 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 GCTGCCCTAACAACTCCCCTGCGGAGTGCC 8 234 0 CAACTCCCCT 0.917599 -24 TCTCATTATGCCATCCAACAACTGCTTCAA 9 119 0 CCATCCAACA 0.784526 -182 AGAGTTCATCCCACTCCAAACTTCTATGAG 9 155 0 CCACTCCAAA 0.666518 -146 AATTGGGATGCACAGCCACACAAAATAACC 9 229 1 CACAGCCACA 0.684673 -72 GAAAGTGTTACAATCCAACC 10 105 1 CAATCCAACC 0.837005 -10 TATAGAAATACCAATCCACCAATTTCTGCA 12 52 1 CCAATCCACC 0.952173 -37 TTCACATCACCTCCTATTGCAG 12 77 0 CACATCACCT 0.772661 -12 CACCTCCCCCTAACCTTTCT 15 36 0 CACCTCCCCC 0.945115 -10 CAAATCACCACAAGCCTTTT 17 1 1 CAAATCACCA 0.925472 -59 AAAACAGACACAAATCCAAAT 18 2 0 CAAATCCAAA 0.691938 -209 GTAGCTGAACCAAATCCACAAAATTTTTTA 18 33 0 CAAATCCACA 0.95439 -178 GCTATTCGTTCAATTCAACCTCCCCAAAAA 18 82 1 CAATTCAACC 0.917755 -129 CCTCAATCAACCCTTCCACCGCGCAGAGCT 18 120 1 CCCTTCCACC 0.910126 -91 ATAGAAATTTCAATCCACCAATATTTGCAA 18 175 1 CAATCCACCA 0.82785 -36 CCCACTCACCTCCCTCTTGCA 18 200 0 CCACTCACCT 0.833427 -11 ********** Masking position 6 Map Score: 9.52419 Number of sites scoring better than the average of aligned sites = 1385 Number in coding regions = 1294 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 4 GCTTCTTCTGCTGAAAGAAGGGTGATAAAAAA 8 30 0 CTGAGAAGGG 0.892874 -228 TTTGAAAATACACACCAAAGAGCACCTTGAAG 8 169 1 CACAAAAGAG 0.866905 -89 CACCAAAGAGCACCTTGAAGGGGTGAAAAAGG 8 181 1 CACCGAAGGG 0.968748 -77 GACAGCCTGGCACTCCGCAGGGGAGTTGTTAG 8 226 1 CACTGCAGGG 0.944957 -32 TTCGTTGCTGCGAAAAGCAGAGAGAAGGTTAA 9 34 1 CGAAGCAGAG 0.941273 -267 TGTACCAGAACGCATTGCAGAGTTCATCCCAC 9 171 0 CGCAGCAGAG 0.989899 -130 AAGCTTCCTCCAGATTGAAGAGAAAATAATTG 9 202 1 CAGAGAAGAG 0.976157 -99 TGGAGGCTTCCGGAACGTAGAGGGAAGCAAAA 16 51 1 CGGAGTAGAG 0.924227 -43 TCAACCCTTCCACCGCGCAGAGCTCAAAAAGC 18 126 1 CACCGCAGAG 0.97501 -85 **** ****** Masking position 9 Map Score: 5.25673 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 316 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TTTGTAAGGGAACTCTATTTCAACTCGAAA 4 35 1 AACTCTATTT 0.828643 -67 ATTAAGTTTATATTCCCCCGACC 5 4 1 AAGTTTATAT 0.731229 -30 AAATTATTTAATTTTTATGTTTTGACTAAT 6 21 0 ATTTTTATGT 0.87942 -37 ATTTTTATGTTTACTGGTGT 8 1 1 ATTTTTATGT 0.87942 -257 AATAACCGAAAACTTTATATACCATAAACC 9 252 1 AACTTTATAT 0.905474 -49 GTCGGTTACTAACTTTATGTTAGGTTTATG 9 274 0 AACTTTATGT 0.90375 -27 TTATAAGGTAAACTTTATTTACAATGAAAG 10 80 1 AACTTTATTT 0.905471 -35 GTGGATTGGTATTTCTATATAAGCTTTTCT 12 41 0 ATTTCTATAT 0.789748 -48 AGCGAGTTAGAATTTTATTTGA 14 31 1 AATTTTATTT 0.920908 -12 TTTATCCCTCAATTTTATTTTTTGCTTCCC 16 72 0 AATTTTATTT 0.920908 -22 CACCTAAACAGTTTTTATTTTAGAGATAAA 17 30 0 GTTTTTATTT 0.53993 -30 AAATCCACAAAATTTTTTATAAAACAGACA 18 22 0 AATTTTTTAT 0.553409 -189 GTGGATTGAAATTTCTATATATATTTTACG 18 163 0 ATTTCTATAT 0.789748 -48 ********** Masking position 6 Map Score: 10.2828 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 60 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 6 GATAGCTTCTTCTGCTGAAAGAAGGGTGATA 8 35 0 TCTGCTGAAG 0.95234 -223 GCTCTCAATTTCTGCAAAAGCTTCGGGAAAG 8 91 0 TCTGCAAAGC 0.982239 -167 TGCAATGCGTTCTGGTACAAGCTTCCTCCAG 9 184 1 TCTGGTAAAG 0.926081 -117 TTCTCTTCAATCTGGAGGAAGCTTGTACCAG 9 195 0 TCTGGAGAAG 0.919244 -106 TCCACCAATTTCTGCAATAGGAGGTGATGTG 12 66 1 TCTGCAAAGG 0.988996 -23 TCTGCAATAACTATTTATAAA 14 1 1 TCTGCAAAAC 0.972162 -42 TGGATTTGGTTCAGCTACAGCTAAATGTTTC 18 45 1 TCAGCTAAGC 0.86082 -166 TCCACCAATATTTGCAAGAGGGAGGTGAGTG 18 188 1 TTTGCAAAGG 0.909606 -23 ******* *** Masking position 9 Map Score: 5.04773 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 243 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TGGGAAAGATTTTAAAATGAGTTGTTATA 1 10 1 TTTTAAAATG 0.911329 -50 TGGACAAACGTGTTAAAATAAC 2 3 0 TGTTAAAATA 0.66417 -32 TGTTTTTGCTTTTTAAAATAGCCCTAAGGC 3 40 0 TTTTAAAATA 0.904526 -25 TTCGATGAAATTTGAAATTATTTAATTTTT 6 35 0 TTTGAAATTA 0.911333 -23 AGGAGCTGATTTTGAAAATACACACCAAAG 8 159 1 TTTGAAAATA 0.911329 -99 CAGTCTTTTCTTTGTAATTGAAGTAGCTGT 10 17 1 TTTGTAATTG 0.834497 -98 TAACACTTTCATTGTAAATAAAGTTTACCT 10 85 0 ATTGTAAATA 0.564021 -30 ATCGTAATCTTTTTTAATTAGGTTTTTAAG 11 13 1 TTTTTAATTA 0.811062 -21 TCTATCACGAATTTAAATTGCAAGCATTTG 12 14 0 ATTTAAATTG 0.740738 -75 ATGACTAAGTTTTTAAATTGCCAAGTCTAA 13 36 1 TTTTAAATTG 0.911333 -39 ********** Masking position 6 Map Score: 5.15466 Number of sites scoring better than the average of aligned sites = 91 Number in coding regions = 57 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 8 TACTTTTATTACACCTGAAATCAAACTCCCACC 4 79 1 ACACCGAACA 0.992927 -23 GTGATAAAAAACACCAGTAAACATAAAAAT 8 8 0 ACACCGAACA 0.992927 -250 AAGCTATCTCACACTGGGAACAAGGCTGAGAGA 8 58 1 ACACTGAAAA 0.967913 -200 TTGAAAATACACACCAAAGAGCACCTTGAAGGG 8 170 1 ACACCAGACA 0.888148 -88 CTCAACCTTTACTCTCGCAAGAATGTGCTTAAC 9 61 0 ACTCTGAAAA 0.881542 -240 TTCCTGACACCTGTAAAAATTAGACTTGG 13 56 0 ACACCGAAAA 0.988922 -19 ***** * ** ** Masking position 10 Map Score: 2.37455 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 = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GGTTTTATTTCAAGTACAAAAACGTTTGTAAG 4 11 1 CAATCAAAAA 0.78413 -91 TTTGGGCTCTCAATTTCTGCAAAAGCTTCGGG 8 95 0 CAATCTGCAA 0.972171 -163 TGCCATCCAACAACTGCTTCAACTGAGCCAAA 9 109 0 CAATCTTCAA 0.966586 -192 TGGATAAAGACAGCTACTTCAATTACAAAGAA 10 24 0 CAGTCTTCAA 0.93395 -91 ACCAATCCACCAATTTCTGCAATAGGAGGTGA 12 61 1 CAATCTGCAA 0.972171 -28 CAGCAACAAGTTCTTATATGATGAGTGA 16 7 1 CAATCTTATA 0.885368 -87 CGGAAGCCTCCAAATACATATATATCACTCAT 16 31 0 CAATCATATA 0.86243 -63 GTAGCTGAACCAAATCCACAAAATTTTTTATA 18 31 0 CAATCACAAA 0.843351 -180 GGATTTGGTTCAGCTACAGCTAAATGTTTCCA 18 46 1 CAGTCAGCTA 0.878995 -165 *** * ****** Masking position 5 Map Score: 4.20288 Number of sites scoring better than the average of aligned sites = 299 Number in coding regions = 267 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 ********** No masking Map Score: 1.64379e-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 11 ********** No masking Map Score: 1.64379e-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 12 ********** No masking Map Score: 1.64379e-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