AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00740_aful_reg_300.orf -o00740_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 AF0481 64 proteasome, subunit beta (psmB) #2 AF0483 101 conserved hypothetical protein #3 AF0484 33 GTP cyclohydrolase II (ribA-1) #4 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #5 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #6 AF1420 216 membrane protein #7 AF1421 49 conserved hypothetical protein #8 AF1422 35 aspartate racemase #9 AF1423 112 conserved hypothetical protein #10 AF2106 39 conserved hypothetical protein #11 AF2128 104 riboflavin synthase, subunit beta (ribE) Motif number 1 TTAAAAATCTTTTTTCTCTATTGAA 1 6 1 AATCTTTTTT 0.934549 -59 GTTCCCTTACAAACGTTTTTGTACTTGAAA 2 18 0 AAACGTTTTT 0.954081 -84 GCAGGTTTGGATACTTTTATTACACCTGAA 2 68 1 ATACTTTTAT 0.882198 -34 TTCCCCCGACCAACTTTTTTC 3 23 1 CAACTTTTTT 0.954867 -11 AAAACTTTTATGCCTACCTGA 4 2 1 AAACTTTTAT 0.979264 -48 GTAGCACAGCAAACTTTTTAACATTCAAAG 7 18 1 AAACTTTTTA 0.934546 -32 AGTTGAGGTTAAAATTTTTTAGGTTGGGTG 9 25 1 AAAATTTTTT 0.930643 -88 TTTTAGCGGTAAATTTTTATCGGCCCAACC 9 81 1 AAATTTTTAT 0.860328 -32 TGGTTTTAAAATTTTTTGAATTTTTAT 11 8 1 AAAATTTTTT 0.930643 -97 ********** Masking position 6 Map Score: 11.6144 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 78 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 GTACAAAAACGTTTGTAAGGGAACTCTATTTCAAC 2 24 1 GTTTGTGGAT 0.972977 -78 CTCGAAAAATGCAGGTTTGGATACTTTTATTACAC 2 58 1 GCAGGTGGAT 0.981065 -44 GAAAAAAGTTGGTCGGGGGAATATAAACTTAA 3 12 0 GTTGGTGGAT 0.989899 -22 CCTACCTGAATTTGGATTGGAGATGAAGAAAAGGG 4 23 1 TTTGGAGGAG 0.863762 -27 AAATTCAACTGCGGGCTCGGAAAATCTCACGATAC 6 17 1 GCGGGCGGAT 0.9493 -200 GGGCTATTCGTTTTGTCAAGTTATTCTGCTGGCAA 6 103 1 TTTTGTAGAT 0.75208 -114 CAAAGCTTTATCTTGTTAGGCGATTAGTCTATTT 8 12 1 TCTTGTGGAT 0.986528 -24 TTAAAATTTTTTAGGTTGGGTGATGCGCTAAATAC 9 33 1 TTAGGTGGAG 0.917897 -80 TGATGTTGTTCTGGTTGGGCCGATAAAAATTTAC 9 89 0 TCTGGTGGGT 0.987093 -24 ATTGCCTCAATCTGTCACGGATAATAAAAATTCAA 11 26 0 TCTGTCGGAT 0.871008 -79 TGACGGAGATTCTTGTCAGGTGGTTTCAA 11 86 1 TCTTGTGGGT 0.965641 -19 ****** ** * * Masking position 10 Map Score: 8.79914 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 365 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 3 GGTTTTATTTCAAGTACAAAAACGTTTGT 2 9 1 TTCAATACAA 0.923058 -93 TGTAAGGGAACTCTATTTCAACTCGAAAAAT 2 37 1 CTCTATTCAA 0.962943 -65 TCATCTCCAATCCAAATTCAGGTAGGCATAA 4 18 0 TCCAATTCAG 0.927885 -32 CTGTCCAAATTCAACTGCGGGCTC 6 4 1 TCCAATTCAA 0.97601 -213 TACTCTGTCACTCAGCTTCAAAGCTTCCCGG 6 49 1 CTCAGTTCAA 0.975961 -168 TCTGCAATATCTCAATATCAAACTCATGAAA 6 164 1 CTCAAATCAA 0.965091 -53 AAATTTTAACCTCAACTTCAAGCAAAATCCA 9 11 0 CTCAATTCAA 0.979049 -102 ***** ***** Masking position 10 Map Score: 7.23759 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 122 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 CACTTTGTTTTTGCTTTTTAAAATAGCCC 1 46 0 GTTGCTTTTT 0.869307 -19 ACGTTTGTAAGGGAACTCTATTTCAACTCGAAA 2 32 1 GAATCTATTT 0.907501 -70 AAAGCTTCCCGGATAGTCTATTTCACACTCCAT 6 68 1 GTATCTATTT 0.979 -149 ACTCCATCAGGGCTATTCGTTTTGTCAAGTTAT 6 94 1 GTATCGTTTT 0.977795 -123 TCAAGACTTCGTGGATTCGTTTTCTGCAATATC 6 142 1 GGATCGTTTT 0.961444 -75 CCAAAGCTTTATCTTGTTAGGCGATTAG 8 6 1 GTTTCTTGTT 0.932956 -30 CTTGTTAGGCGATTAGTCTATTT 8 23 1 GTATCTATTT 0.978924 -13 ATTGGCTCTGGACTACTCTTTTT 10 1 0 GTATCTTTTT 0.989004 -39 AATAACTGACGGAGATTCTTGTCAGGTGGTTTC 11 80 1 GGATCTTGTC 0.8535 -25 * ** ******* Masking position 12 Map Score: 8.00171 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 44 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 CGGAAAATCTCACGATACTCTGTCACTCAGCTT 6 34 1 CACGAACTGT 0.913851 -183 ATATCAAACTCATGAAAAACCTTATTAGCCTCT 6 178 1 CATGAACCTT 0.982412 -39 AATCGCCTAACAAGATAAAGCTTTGG 8 4 0 CAAGAAGCTT 0.976828 -32 CTAAATACTTCAAGACAGGCCTTTTAGCGGTAA 9 60 1 CAAGAACCTT 0.994553 -53 AGTCCAGAGCCAATAAAAGCCTTCCTCACG 10 20 1 CAATAACCTT 0.966036 -20 AACCACCTGACAAGAATCTCCGTCAGTTATTTA 11 78 0 CAAGATCCGT 0.973949 -27 ***** * **** Masking position 5 Map Score: 2.63154 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 110 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TCTCACGATACTCTGTCACTCAGCTTCAAA 6 41 1 CTCTGTCACT 0.983343 -176 CTATTTCACACTCCATCAGGGCTATTCGTT 6 85 1 CTCCATCAGG 0.981049 -132 CAATAAAAGCCTTCCTCACG 10 30 1 CTTCCTCACG 0.955397 -10 CATTGCCTCAATCTGTCACGGATAATAAAA 11 32 0 ATCTGTCACG 0.962247 -73 TGACAAGAATCTCCGTCAGTTATTTAATAA 11 74 0 CTCCGTCAGT 0.989167 -31 ********** Masking position 6 Map Score: 1.45596 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 249 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 7 TAGCCCTAAGGCAACCTTCAATAGAGAAAA 1 22 0 GCAACCTTCA 0.885234 -43 TAAAAGTATCCAAACCTGCATTTTTCGAGT 2 57 0 CAAACCTGCA 0.984942 -45 AACTTTTATGCCTACCTGAATTTGGATTGG 4 13 1 CCTACCTGAA 0.893269 -37 CACTCAGCTTCAAAGCTTCCCGGATAGTCT 6 57 1 CAAAGCTTCC 0.884304 -160 ATTCTGCTGGCAACGCTTCAAGACTTCGTG 6 125 1 CAACGCTTCA 0.886073 -92 TTTTAACATTCAAAGCAGAATTGCATT 7 33 1 CAAAGCAGAA 0.913197 -17 CCAAAGCTTTATCTTGTTAGG 8 2 1 CAAAGCTTTA 0.859773 -34 AGCGCATCACCCAACCTAAAAAATTTTAAC 9 32 0 CCAACCTAAA 0.910502 -81 TTTTATCGGCCCAACCAGAACAACATCA 9 95 1 CCAACCAGAA 0.943748 -18 ********** Masking position 6 Map Score: 4.16813 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 639 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 ATAGCCCTAAGGCAACCTTCAATAGAGAAA 1 23 0 GGCAACCTTC 0.79984 -42 TACACCTGAAATCAAACTCCCACC 2 88 1 ATCAAACTCC 0.972214 -14 TTCATCTCCAATCCAAATTCAGGTAGGCAT 4 20 0 ATCCAAATTC 0.941539 -30 CTGTCCAAATTCAACTGCGGGC 6 3 1 GTCCAAATTC 0.887291 -214 ATATCTCAATATCAAACTCATGAAAAACCT 6 170 1 ATCAAACTCA 0.819444 -47 TTGGTAGCACAGCAAACTTTTTAACATTCA 7 15 1 AGCAAACTTT 0.888925 -35 CTCAACTTCAAGCAAAATCCA 9 2 0 AGCAAAATCC 0.957296 -111 GGTTGGGCCGATAAAAATTTACCGCTAAAA 9 81 0 ATAAAAATTT 0.59742 -32 GTCACGGATAATAAAAATTCAAAAAATTTT 11 18 0 ATAAAAATTC 0.866454 -87 ********** Masking position 5 Map Score: 3.65654 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 674 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 AAGGTTGCCTTAGGGCTATTTTAAAAAGCA 1 34 1 TAGGGCTATT 0.981257 -31 CACACTCCATCAGGGCTATTCGTTTTGTCA 6 91 1 CAGGGCTATT 0.993031 -126 TACTTCAAGACAGGCCTTTTAGCGGTAAAT 9 65 1 CAGGCCTTTT 0.981592 -48 CGTGAGGAAGGCTTTTATTGGCTCTG 10 24 0 GAAGGCTTTT 0.950653 -16 ********** Masking position 7 Map Score: 1.12133 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 77 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 10 ********** No masking Map Score: -4.87842e-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 11 ********** No masking Map Score: -4.87842e-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 12 ********** No masking Map Score: -4.87842e-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