AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_aful_reg_100.orf -o00550_aful_100.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 GAACCCGAGCGAGATCGTCGAAGCTAAAA 1 10 1 CGAGATCGTC 0.932036 -291 TCTTTCAGCATCAGCTCGTCAACGACTGTT 1 62 0 TCAGCTCGTC 0.992925 -239 AGCTCAAACGACAGCTCGTCTTTCAGCATC 1 80 0 ACAGCTCGTC 0.977093 -221 AGCTGTCGTTTGAGCTGGAAGATAAAGGAA 1 94 1 TGAGCTGGAA 0.849816 -207 TATCGGAACTTCTGCCGGTCTGAATCTGTT 1 171 0 TCTGCCGGTC 0.989666 -130 AAATAGTAGTTCAGCTGGTCGCGGATTATG 1 263 0 TCAGCTGGTC 0.995639 -38 CCTCATGTATCCTGACGGTAAGGTTTAAAT 2 30 0 CCTGACGGTA 0.911817 -148 CCTACGCTTGCCTGCAGGTAATTTAACAAA 2 127 1 CCTGCAGGTA 0.943098 -51 ********** Masking position 4 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 CTTCGAACTTAACCCCGAAGATTTTAGCTTCGAC 1 27 0 AACGAGATTT 0.973069 -274 CAAAGGTAAGATTCCGGTAGAGTTCGACCCTAAC 1 140 1 ATCGAGAGTT 0.995783 -161 TAAGGTTTAAATACACTTAGAGTTGAAGCCC 2 8 0 ATCTAGAGTT 0.973354 -170 TACCGTCAGGATACATGAGGATTTGTGTTGTTAA 2 40 1 ATCGGGATTT 0.995754 -138 GTATTTGAGAATTGGTGAAGATTTTTCAGATTTA 2 93 1 ATGGAGATTT 0.98492 -85 ATTTTTTTGCATTCAAGGGGATTTGTTAAATTAC 2 144 0 ATCGGGATTT 0.995784 -34 ** * * ****** Masking position 11 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 ACCCCGAAGATTTTAGCTTCGACGATCTCG 1 20 0 TTTTAGCTTC 0.982081 -281 TCGTCAACGACTGTTGCTTCGAACTTAACC 1 47 0 CTGTTGCTTC 0.894273 -254 ACAGCTCGTCTTTCAGCATCAGCTCGTCAA 1 70 0 TTTCAGCATC 0.924989 -231 ACAAGTATTCCTTTATCTTCCAGCTCAAAC 1 101 0 CTTTATCTTC 0.885084 -200 TCTACCGGAATCTTACCTTTGTCTGTAAAG 1 131 0 TCTTACCTTT 0.895639 -170 AAGCCTATCTCCTTTGCTTTTGTTGTGTCC 1 209 0 CCTTTGCTTT 0.924945 -92 TTTCTCCTTCTGGCATCTAA 1 291 0 TTTCTCCTTC 0.93214 -10 TGTATTTAAACCTTACCGTCAGGATACATG 2 27 1 CCTTACCGTC 0.852658 -151 GGTGAAGATTTTTCAGATTTACCTACGCTT 2 106 1 TTTCAGATTT 0.592658 -72 GATATATATTTTTTTGCATTCAAGGGGATT 2 155 0 TTTTTGCATT 0.834668 -23 ********** Masking position 9 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 CGAGCTGATGCTGAAAGACGAGCTGTCGTT 1 74 1 CTGAAAGACG 0.902348 -227 AATACTTGTCTTTACAGACAAAGGTAAGAT 1 122 1 TTTACAGACA 0.957361 -179 TCCGATACTGCTCTCGGACACAACAAAAGC 1 194 1 CTCTCGGACA 0.911569 -107 CAACCACAGCCTCAAGGACATAATCCGCGA 1 245 1 CTCAAGGACA 0.973165 -56 GACGGTAAGGTTTAAATACACTTAGAGTTG 2 17 0 TTTAAATACA 0.846951 -161 GTATTTAAACCTTACCGTCAGGATACATGA 2 28 1 CTTACCGTCA 0.895137 -150 TTCACCAATTCTCAAATACATACCAATACA 2 82 0 CTCAAATACA 0.944747 -96 ATTTTTCAGATTTACCTACGCTTGCCTGCA 2 113 1 TTTACCTACG 0.804153 -65 ********** Masking position 2 Map Score: 1.97782 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 580 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 TGTCTGTAAAGACAAGTATTCCTTTATCTT 1 112 0 GACAAGTATT 0.909828 -189 GATACATGAGGATTTGTGTTGTTAAAATTG 2 49 1 GATTTGTGTT 0.958669 -129 TGTTAAAATTGGTTTGTATTGGTATGTATT 2 68 1 GGTTTGTATT 0.982344 -110 GGTTTGTATTGGTATGTATTTGAGAATTGG 2 78 1 GGTATGTATT 0.987491 -100 TTCGATATATATTTTTTTGCATT 2 165 0 GATATATATT 0.90743 -13 ********** Masking position 7 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