AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_aful_reg_300.orf -o00550_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -x5 -e 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 = 1 Input sequences: #1 AF0045 300 mannosyltransferase A (mtfA) #2 AF0949 177 glutamine synthetase (glnA) Motif number 1 TTTTAGCTTCGACGATCTCGCTCGGGTTC 1 10 0 GACGATCTCG 0.935182 -291 AACAGTCGTTGACGAGCTGATGCTGAAAGA 1 62 1 GACGAGCTGA 0.993272 -239 GATGCTGAAAGACGAGCTGTCGTTTGAGCT 1 80 1 GACGAGCTGT 0.978202 -221 TTCCTTTATCTTCCAGCTCAAACGACAGCT 1 94 0 TTCCAGCTCA 0.85618 -207 AACAGATTCAGACCGGCAGAAGTTCCGATA 1 171 1 GACCGGCAGA 0.990173 -130 CATAATCCGCGACCAGCTGAACTACTATTT 1 263 1 GACCAGCTGA 0.995854 -38 ATTTAAACCTTACCGTCAGGATACATGAGG 2 30 1 TACCGTCAGG 0.915814 -148 TTTGTTAAATTACCTGCAGGCAAGCGTAGG 2 127 0 TACCTGCAGG 0.945761 -51 ********** Masking position 7 Map Score: 8.58876 Number of sites scoring better than the average of aligned sites = 633 Number in coding regions = 605 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 GTCGAAGCTAAAATCTTCGGGGTTAAGTTCGAAG 1 27 1 AAATCTCGTT 0.972953 -274 GTTAGGGTCGAACTCTACCGGAATCTTACCTTTG 1 140 0 AACTCTCGAT 0.995516 -161 GGGCTTCAACTCTAAGTGTATTTAAACCTTA 2 8 1 AACTCTAGAT 0.97171 -170 TTAACAACACAAATCCTCATGTATCCTGACGGTA 2 40 0 AAATCCCGAT 0.99549 -138 TAAATCTGAAAAATCTTCACCAATTCTCAAATAC 2 93 0 AAATCTCCAT 0.983977 -85 GTAATTTAACAAATCCCCTTGAATGCAAAAAAAT 2 144 1 AAATCCCGAT 0.995517 -34 ****** * * ** Masking position 4 Map Score: 7.09199 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 25 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 3 CGAGATCGTCGAAGCTAAAATCTTCGGGGT 1 20 1 GAAGCTAAAA 0.982003 -281 GGTTAAGTTCGAAGCAACAGTCGTTGACGA 1 47 1 GAAGCAACAG 0.893853 -254 TTGACGAGCTGATGCTGAAAGACGAGCTGT 1 70 1 GATGCTGAAA 0.924681 -231 GTTTGAGCTGGAAGATAAAGGAATACTTGT 1 101 1 GAAGATAAAG 0.884632 -200 CTTTACAGACAAAGGTAAGATTCCGGTAGA 1 131 1 AAAGGTAAGA 0.895225 -170 GGACACAACAAAAGCAAAGGAGATAGGCTT 1 209 1 AAAGCAAAGG 0.924637 -92 TTAGATGCCAGAAGGAGAAA 1 291 1 GAAGGAGAAA 0.931859 -10 CATGTATCCTGACGGTAAGGTTTAAATACA 2 27 0 GACGGTAAGG 0.852101 -151 AAGCGTAGGTAAATCTGAAAAATCTTCACC 2 106 0 AAATCTGAAA 0.591588 -72 AATCCCCTTGAATGCAAAAAAATATATATC 2 155 1 AATGCAAAAA 0.834056 -23 ********** Masking position 2 Map Score: 4.50532 Number of sites scoring better than the average of aligned sites = 2309 Number in coding regions = 2148 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 CAGCATCAGCTCGTCAACGACTGTTGCTTCG 1 56 0 TCGTCAAGAC 0.959828 -245 GACGAGCTGATGCTGAAAGACGAGCTGTCGT 1 72 1 TGCTGAAGAC 0.97878 -229 GGAATACTTGTCTTTACAGACAAAGGTAAGA 1 120 1 TCTTTACGAC 0.721916 -181 GTTCCGATACTGCTCTCGGACACAACAAAAG 1 192 1 TGCTCTCGAC 0.869237 -109 ATAGGCTTCAGGGTCAACCACAGCCTCAAGG 1 231 1 GGGTCAACAC 0.897627 -70 GTCAACCACAGCCTCAAGGACATAATCCGCG 1 243 1 GCCTCAAGAC 0.979023 -58 ATCCGCGACCAGCTGAACTACTATTTAGATG 1 267 1 AGCTGAATAC 0.830482 -34 CTGACGGTAAGGTTTAAATACACTTAGAGTT 2 18 0 GGTTTAATAC 0.83103 -160 TCTTCACCAATTCTCAAATACATACCAATAC 2 83 0 TTCTCAATAC 0.878834 -95 CAAGGGGATTTGTTAAATTACCTGCAGGCAA 2 134 0 TGTTAAATAC 0.771781 -44 ******* *** Masking position 4 Map Score: 2.48468 Number of sites scoring better than the average of aligned sites = 849 Number in coding regions = 799 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 AAGATAAAGGAATACTTGTCTTTACAGACA 1 112 1 AATACTTGTC 0.909828 -189 CAATTTTAACAACACAAATCCTCATGTATC 2 49 0 AACACAAATC 0.958669 -129 AATACATACCAATACAAACCAATTTTAACA 2 68 0 AATACAAACC 0.982344 -110 CCAATTCTCAAATACATACCAATACAAACC 2 78 0 AATACATACC 0.987491 -100 AATGCAAAAAAATATATATCGAA 2 165 1 AATATATATC 0.90743 -13 ********** Masking position 4 Map Score: 2.48446 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 11 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 6 ********** No masking Map Score: 2.29806e-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 7 ********** No masking Map Score: 2.29806e-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 8 ********** No masking Map Score: 2.29806e-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