AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -ilexA_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 AF0497 132 DNA polymerase B1 (polB) #2 AF0899 300 conserved hypothetical protein #3 AF0993 55 DNA repair protein RAD51 (radA) Motif number 1 TCATCTGCTCCCATCTCAATTAACAATACAGC 1 12 0 CCATCTCATA 0.991474 -121 ATCTTGCAGTCCCTCTCGCTCATCTGCTCCCA 1 31 0 CCCTCTCCTA 0.992119 -102 AAGATACAGCCAATCACACCAAACTTTAAATC 1 90 1 CAATCACCCA 0.978323 -43 GGGAAGGCTGCAATCTCAACTACAAAAGAGTC 2 111 0 CAATCTCACA 0.98408 -190 GCAGCCTTCCCCATCTCTCCCATGATTTGATT 2 132 1 CCATCTCCCA 0.998156 -169 CCACCTTGAACCATCTTCCTAATCTTGCTTTC 2 182 1 CCATCTTCTA 0.981572 -119 ******* ** * Masking position 4 Map Score: 8.13195 Number of sites scoring better than the average of aligned sites = 283 Number in coding regions = 269 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 TGCATGTTGGCAAGGCGGAGCTTCAGGT 2 7 1 TGGCAAGGCG 0.992548 -294 TACAAAAGAGTCTTGACGGCAGCTGGGTCGAC 2 91 0 TTTGACGGCG 0.98685 -210 ATGGGAGAGATGGGGAAGGCTGCAATCTCAAC 2 123 0 TGGGAAGGCG 0.996104 -178 ATCTTTTCCTCGTGACTGCTGGTTAAAAATT 2 280 0 TGTGACTGCG 0.993936 -21 TAAATTTTTTTGGTCTCGGCAGACGTAAAGG 3 10 0 TGTCTCGGCG 0.992657 -46 ATTTAATGGATTGTGTATGAGGTAGGGTA 3 37 1 TGTGTATGAG 0.896304 -19 * ******** * Masking position 1 Map Score: 5.43992 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 226 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 TAATGTGATCTTGCAGTCCCTCTCGCTCAT 1 40 0 TTGCAGTCCC 0.964728 -93 ACCTGAAGCTCCGCCTTGCCAACATGCA 2 9 0 CCGCCTTGCC 0.98194 -292 GTCGACCCAGCTGCCGTCAAGACTCTTTTG 2 91 1 CTGCCGTCAA 0.977701 -210 GTTGAGATTGCAGCCTTCCCCATCTCTCCC 2 123 1 CAGCCTTCCC 0.991982 -178 AATTTTTAACCAGCAGTCACGAGGAAAAGA 2 280 1 CAGCAGTCAC 0.987429 -21 CCTTTACGTCTGCCGAGACCAAAAAAATT 3 10 1 CTGCCGAGAC 0.977268 -46 ********** Masking position 4 Map Score: 4.84619 Number of sites scoring better than the average of aligned sites = 412 Number in coding regions = 393 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 CTTCGCAACTAAAATTAAGATAATGTGATC 1 60 0 AAAATTAAGA 0.964982 -73 AAAGGAAAGCAAGATTAGGAAGATGGTTCA 2 188 0 AAGATTAGGA 0.991472 -113 AGGTAATAAGAAAATTATGAAAAATTAAAG 2 214 0 AAAATTATGA 0.964982 -87 GGGTTTGGTAAAGGTTAGGAATCGGTAAAG 2 242 0 AAGGTTAGGA 0.985549 -59 ********** Masking position 5 Map Score: 2.79965 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 17 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 CTGCTCCCATCTCAATTAACAATACAGCG 1 9 0 CTCAATAACA 0.970321 -124 GTATCTTCTTCGCAACTAAAATTAAGATAAT 1 66 0 CGCAATAAAA 0.970321 -67 CGTTTTTGATCTCAGTTGCAAGATGTGTCTT 2 48 1 CTCAGTGCAA 0.966138 -253 AGGCTGCAATCTCAACTACAAAAGAGTCTTG 2 108 0 CTCAATACAA 0.992936 -193 ACACGATAAGCTCAAATCAAATCATGGGAGA 2 147 0 CTCAATCAAA 0.975774 -154 TACCCTACCTCATACACAATCCATTAAAT 3 37 0 CTCATCACAA 0.939851 -19 ***** ***** Masking position 4 Map Score: 2.51048 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 100 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 ACTTTAAATCCTTTTAAGCATAATTGGTTC 1 112 1 CTTTTAAGCA 0.948586 -21 TGTTTTCCCACCTTGAACCATCTTCCTAAT 2 175 1 CCTTGAACCA 0.985074 -126 TTTCTTATTACCTTTACCGATTCCTAACCT 2 231 1 CCTTTACCGA 0.983245 -70 CGATTCCTAACCTTTACCAAACCCAATCAG 2 248 1 CCTTTACCAA 0.975461 -53 AATCAGGAAATTTTTAACCAGCAGTCACGA 2 272 1 TTTTTAACCA 0.924699 -29 ********** Masking position 6 Map Score: 1.30329 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 228 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 CGCTGTATTGTTAATTGAGAT 1 2 1 GCTGTATTGT 0.967514 -131 GGTGTGATTGGCTGTATCTTCTTCGCAACT 1 80 0 GCTGTATCTT 0.987097 -53 TCAGTTGCAAGATGTGTCTTCGTCCTCAGG 2 59 1 GATGTGTCTT 0.967521 -242 CTTGACGGCAGCTGGGTCGACACCCTGAGG 2 82 0 GCTGGGTCGA 0.977012 -219 ********** Masking position 7 Map Score: 0.0781177 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 56 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 ********** No masking Map Score: 5.21128e-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: 5.21128e-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: 5.21128e-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