AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_aful_reg_100.orf -o00272_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 AF0409 74 aspartate aminotransferase (aspB-4) #2 AF0410 56 signal-transducing histidine kinase, putative #3 AF0411 30 cysteinyl-tRNA synthetase (cysS) #4 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #5 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #6 AF1420 216 membrane protein Motif number 1 CCGAATAACGTAAATATCAGAAGCTTGAGG 1 18 0 TAAATATCAG 0.810525 -57 GCTGTTCAGTTAAATAAAAA 2 1 0 TAAATAAAAA 0.91491 -56 TTCTGGACGATGAATATAAACTTTGCTGTT 2 25 0 TGAATATAAA 0.898419 -32 ATATTCATCGTCCAGAAAAGTCAGCATAA 2 38 1 TCCAGAAAAG 0.96005 -19 AATTCAGGTAGGCATAAAAGTTTT 4 5 0 GGCATAAAAG 0.806843 -45 GGATTGGAGATGAAGAAAAGGGTC 4 36 1 TGAAGAAAAG 0.974599 -14 GAATCAAAAAAAGAGGAAGGGCT 5 12 0 TCAAAAAAAG 0.880274 -13 ATTGAGATATTGCAGAAAACGAATCCACGA 6 150 0 TGCAGAAAAC 0.846391 -67 CTGCAATATCTCAATATCAAACTCATGAAA 6 165 1 TCAATATCAA 0.847088 -52 AATATCAAACTCATGAAAAACCTTATTAGC 6 177 1 TCATGAAAAA 0.753519 -40 ACGCAAATAAATAACAAGAGGCTAATA 6 200 0 TAAATAACAA 0.870708 -17 ********** Masking position 6 Map Score: 6.32594 Number of sites scoring better than the average of aligned sites = 688 Number in coding regions = 597 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 2 ATCAACTTTTACCCGAATAACGTAAATATCA 1 29 0 ACCGAATAAC 0.971116 -46 TTTTTATTTAACTGAACAGCAAAGTTTATA 2 10 1 AACGAACAGC 0.95358 -47 TTTGGATTGGAGATGAAGAAAAGGGTC 4 33 1 AGAGAAGAAA 0.848674 -17 AATCAAAAAAAGAGGAAGGGCTT 5 3 0 AGAGAAGGGC 0.965368 -22 GAAGCTTTGAAGCTGAGTGACAGAGTATCGT 6 45 0 AGCGAGTGAC 0.946823 -172 TAACTTGACAAAACGAATAGCCCTGATGGAG 6 95 0 AAAGAATAGC 0.972542 -122 AAGCGTTGCCAGCAGAATAACTTGACAAAAC 6 112 0 AGCGAATAAC 0.991623 -105 ACGCAAATAAATAACAAGAGGCTAA 6 202 0 AAAAAATAAC 0.801402 -15 *** ******* Masking position 6 Map Score: 4.3375 Number of sites scoring better than the average of aligned sites = 620 Number in coding regions = 572 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 3 GCGATTTGTTGGAGCTTTCGAATATAT 1 58 0 GTTGGAGCTT 0.983481 -17 CCTACCTGAATTTGGATTGGAGATGAAGAA 4 23 1 TTTGGATTGG 0.93351 -27 CGAGCCCGCAGTTGAATTTGGACAG 6 6 0 GTTGAATTTG 0.927505 -211 TCCGGGAAGCTTTGAAGCTGAGTGACAGAG 6 51 0 TTTGAAGCTG 0.963536 -166 GAATAGCCCTGATGGAGTGTGAAATAGACT 6 82 0 GATGGAGTGT 0.936258 -135 TCCACGAAGTCTTGAAGCGTTGCCAGCAGA 6 127 0 CTTGAAGCGT 0.956915 -90 ********** Masking position 6 Map Score: 1.01318 Number of sites scoring better than the average of aligned sites = 927 Number in coding regions = 864 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 GCAAGAACCTCAAGCTTCTGATA 1 4 1 AGAACCTCAA 0.959997 -71 GGAGCTTTCGAATATATCAACTTTTACCCG 1 45 0 AATATATCAA 0.946102 -30 GCGGGCTCGGAAAATCTCACGATACTCTGT 6 27 1 AAAATCTCAC 0.97614 -190 CGTTTTCTGCAATATCTCAATATCAAACTC 6 159 1 AATATCTCAA 0.985865 -58 ********** Masking position 4 Map Score: 0.73632 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 98 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 ATATCAACTTTTACCCGAATAACGTAAATA 1 32 0 TTACCCGAAT 0.966474 -43 ACTTTTATGCCTACCTGAATTTGGATTGGA 4 14 1 CTACCTGAAT 0.987208 -36 AGCTTCAAAGCTTCCCGGATAGTCTATTTC 6 62 1 CTTCCCGGAT 0.992502 -155 CGCTTCAAGACTTCGTGGATTCGTTTTCTG 6 138 1 CTTCGTGGAT 0.974567 -79 ********** Masking position 2 Map Score: 2.5008 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 49 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 AATTTTTAAACCCATGACCGTTCTCT 3 7 1 TAAACCCATG 0.945417 -24 ATCTCCAATCCAAATTCAGGTAGGCATAAA 4 17 0 CAAATTCAGG 0.984893 -33 CTGTCCAAATTCAACTGCGGGCTCG 6 6 1 CAAATTCAAC 0.925887 -211 TTGCAGAAAACGAATCCACGAAGTCTTGAA 6 141 0 CGAATCCACG 0.969421 -76 ATCTCAATATCAAACTCATGAAAAACCTTA 6 172 1 CAAACTCATG 0.988193 -45 ********** Masking position 4 Map Score: 0.54999 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 105 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ********** No masking Map Score: -7.64954e-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: -7.64954e-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: -7.64954e-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