AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ilexA_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 AF0481 64 proteasome, subunit beta (psmB) #2 AF0483 101 conserved hypothetical protein #3 AF0484 33 GTP cyclohydrolase II (ribA-1) #4 AF0487 57 penicillin G acylase #5 AF0495 265 A. fulgidus predicted coding region AF0495 #6 AF0496 57 conserved hypothetical transmembrane protein #7 AF0497 132 DNA polymerase B1 (polB) #8 AF0899 300 conserved hypothetical protein #9 AF0993 55 DNA repair protein RAD51 (radA) Motif number 1 ACAAACGTTTTTGTACTTGAAATAAAACC 2 7 0 TTATTGAAAT 0.985037 -95 ACCTGCATTTTTCGAGTTGAAATAGAGTTCCCT 2 41 0 TTATTGAAAT 0.985037 -61 GATACTTTTATTACACCTGAAATCAAACTCCCA 2 77 1 TTACTGAAAT 0.973876 -25 AGCTTCGATGAAATTTGAAATTATTTAATTT 4 37 0 TGATTGAAAT 0.973876 -21 CGCTGTATTGTTAATTGAGATGGGAGCAGAT 7 9 1 TGATTGAGAT 0.983368 -124 AAGACACATCTTGCAACTGAGATCAAAAACGCT 8 46 0 TTACTGAGAT 0.983369 -255 CAAGACTCTTTTGTAGTTGAGATTGCAGCCTTC 8 108 1 TTATTGAGAT 0.990514 -193 TCTCCCATGATTTGATTTGAGCTTATCGTGTTT 8 147 1 TTATTGAGCT 0.965199 -154 ** * ******* Masking position 5 Map Score: 12.7289 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 33 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 CAATAGAGAAAAAAGATTTTTAA 1 1 0 AAAAATTTAA 0.894243 -64 TTCAAGTACAAAAACGTTTGTAAGGGAACTCTA 2 19 1 AAAAGTTTAA 0.875161 -83 CAGGTGTAATAAAAGTATCCAAACCTGCATTTT 2 63 0 AAAATATAAA 0.903686 -39 GTCAAAACATAAAAATTAAATAATTTCAAATTT 4 25 1 AAAATTATAA 0.826734 -33 AAACAACAACAAAATAATAAAGAAAA 5 4 0 AAAAAATAGA 0.691306 -262 TTGGACTAAAAAAATTTTCATAAACAACAACAA 5 25 0 AAAATTTTAA 0.942209 -241 TTTTTAGTCCAAAATTGTTGTAAAGGAAACGCA 5 46 1 AAAATGTTAA 0.916465 -220 TAATCTGCTCCAAACTATAATAAGCAGTCCCAG 5 162 1 CAAATATTAA 0.86693 -104 CTTCGCAACTAAAATTAAGATAATGTGATCTTG 7 57 0 AAAATAATAA 0.867876 -76 AATTATGCTTAAAAGGATTTAAAGTTTGGTGTG 7 104 0 AAAAGATAAA 0.801367 -29 TCTCAACTACAAAAGAGTCTTGACGGCAGCTGG 8 97 0 AAAAAGTTGA 0.723645 -204 AGGTAATAAGAAAATTATGAAAAATTAAAGGAA 8 211 0 AAAATATAAA 0.903686 -90 ACTGCTGGTTAAAAATTTCCTGATTGGGTTTGG 8 264 0 AAAATTTTGA 0.882392 -37 CTGCCGAGACCAAAAAAATTTAATGGATTGTGT 9 20 1 CAAAAAATAA 0.497203 -36 **** *** *** Masking position 4 Map Score: 8.81936 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 153 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 3 AAAGTATCCAAACCTGCATTTTTCGAGTTGA 2 54 0 ACCTGCATTT 0.912475 -48 GTTTTGACTAATCCAGCCTCCG 4 2 0 ACCAGCCTCC 0.940409 -56 AAAACCAGCATTGATCGTTCTCG 6 3 1 ACCAGCATTG 0.816252 -55 GCAATTTCGCTCCTTGCAGCCCTCTACCAGT 6 33 1 TCTTGCAGCC 0.902648 -25 AGATAATGTGATCTTGCAGTCCCTCTCGCTC 7 42 0 ACTTGCAGTC 0.973142 -91 CGCTCTGATCAACCTGAAGCTCCGCCTTGCC 8 19 0 ACCTGAAGCT 0.758333 -282 ACGAAGACACATCTTGCAACTGAGATCAAAA 8 51 0 ACTTGCAACT 0.720045 -250 CAGGGTGTCGACCCAGCTGCCGTCAAGACTC 8 85 1 ACCAGCTGCC 0.980832 -216 TTTGTAGTTGAGATTGCAGCCTTCCCCATCT 8 117 1 AATTGCAGCC 0.851703 -184 TCCCACCTTGAACCATCTTCCTAATCTTGCT 8 180 1 ACCATCTTCC 0.658746 -121 CATCTTCCTAATCTTGCTTTCCTTTAATTTT 8 193 1 ACTTGCTTTC 0.883563 -108 GGAAATTTTTAACCAGCAGTCACGAGGAAAA 8 277 1 ACCAGCAGTC 0.983093 -24 * ********* Masking position 1 Map Score: 6.87662 Number of sites scoring better than the average of aligned sites = 1331 Number in coding regions = 1256 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 CTATTTGCCCCGTTAATCTGCTCCAAACTATAATAA 5 149 1 CGTTATCCCA 0.994126 -117 TTCTTCTTTGCGTTCATGTTTTCCCACGCGTAGAAT 5 237 1 CGTTATGCCA 0.988821 -29 CAGTCCCTCTCGCTCATCTGCTCCCATCTCAATTAA 7 21 0 CGCTATCCCA 0.984097 -112 TTTCTTATTACCTTTACCGATTCCTAACCTTTACCA 8 231 1 CCTTACCCCA 0.996256 -70 CGATTCCTAACCTTTACCAAACCCAATCAGGAAATT 8 248 1 CCTTACCCCA 0.996256 -53 CCTTTACGTCTGCCGAGACCAAAAAA 9 1 1 CCTTACGCCA 0.992862 -55 **** *** ** * Masking position 6 Map Score: 6.13461 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 26 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 GGAAACGCAATTGTATCCATGTATGGATGC 5 70 1 TTGTATCCAT 0.904443 -196 TTCGTGGTGTTTGCATCCATACATGGATAC 5 82 0 TTGCATCCAT 0.986302 -184 AAATTCTTCTTTGCGTTCATGTTTTCCCAC 5 234 1 TTGCGTTCAT 0.928287 -32 ATTTCGCTCCTTGCAGCCCTCTACCAGTAC 6 36 1 TTGCAGCCCT 0.99285 -22 TAATGTGATCTTGCAGTCCCTCTCGCTCAT 7 40 0 TTGCAGTCCC 0.953893 -93 GTAGTTGAGATTGCAGCCTTCCCCATCTCT 8 120 1 TTGCAGCCTT 0.972185 -181 CTTCCTAATCTTGCTTTCCTTTAATTTTTC 8 196 1 TTGCTTTCCT 0.932139 -105 ********** Masking position 2 Map Score: 5.82634 Number of sites scoring better than the average of aligned sites = 304 Number in coding regions = 290 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 CTTTTTTCTCTATTGAAGGTTGCCTTAGGGCTA 1 19 1 TTGAGGTTGC 0.970187 -46 GACTGCTTATTATAGTTTGGAGCAGATTAACGG 5 158 0 TTGTTGGAGC 0.794265 -108 CTGTACTGGTAGAGGGCTGCAAGGAGCGAA 6 38 0 GTGAGGCTGC 0.981222 -20 GTATTGTTAATTGAGATGGGAGCAGATGAGCGA 7 15 1 TGGAGGGAGC 0.987998 -118 TACAAAAGAGTCTTGACGGCAGCTGGGTCGACA 8 90 0 TTGAGGCAGC 0.99239 -211 ATGGGAGAGATGGGGAAGGCTGCAATCTCAACT 8 122 0 TGGAGGCTGC 0.995147 -179 ATCTTTTCCTCGTGACTGCTGGTTAAAAATTT 8 279 0 TGGATGCTGG 0.91493 -22 * * ** ****** Masking position 5 Map Score: 3.69278 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 339 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 7 ATTAAGTTTATATTCCCCCGACCAACTTT 3 9 1 TTATTCCCCC 0.974989 -25 ATCTTCGTGGTGTTTGCATCCATACATGGAT 5 84 0 TTTTGCATCC 0.872575 -182 CGTACTTTGCTATTTGCCCCGTTAATCTGCT 5 140 1 TTTTGCCCCG 0.985605 -126 TTTGCGTTCATGTTTTCCCACGCGTAGAATA 5 243 1 TTTTTCCCAC 0.981615 -23 GAGCTTATCGTGTTTTCCCACCTTGAACCAT 8 165 1 TTTTTCCCAC 0.981615 -136 ATCTTTTCCTCGTGACTGCTGG 8 289 0 TTTTTCCTCG 0.965406 -12 * ********* Masking position 5 Map Score: 3.29731 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 158 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 ********** No masking Map Score: 6.56131e-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 9 ********** No masking Map Score: 6.56131e-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 10 ********** No masking Map Score: 6.56131e-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