AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i063_Glycine_Catabolism_pyro_reg_300.orf -o063_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RPH00018 118 Pyrococcus_OT3 #2 RPH01216 70 Pyrococcus_OT3 #3 RPH01044 61 Pyrococcus_OT3 #4 RPH01043 165 Pyrococcus_OT3 Motif number 1 CGTTCCAACTATACCTCCTTCACTTT 1 5 1 CCAACAACCT 0.996625 -114 ATAATTATAACCACCAACAACTTGAACGTTTA 1 37 1 CCACCAAACT 0.994567 -82 TTGGATCACCAAACCCTAATTCTTTTT 1 102 0 TCACCACCCT 0.983781 -17 AACAACCACCACCTTCCAATTTAG 2 57 0 CAACCCACCT 0.967336 -14 TGCAAATCCCCGACTAAAAATTTAGTAAGAT 3 41 0 CCGACAAAAT 0.937298 -21 TTTATCACCGAAACCTTTATTACGCT 4 5 1 TCACCAACCT 0.990751 -161 GCTCCGAAGGCCGACGCCCCATCCAGGCTAGG 4 69 0 CCGACCCCAT 0.924601 -97 GGCCGGCCCGCCAACAATAACTTTAAAACTTC 4 124 1 CCAACAAACT 0.99141 -42 ***** * **** Masking position 12 Map Score: 11.218 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 248 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 TTATAATTATAACCACCAACAACTTGAACG 1 35 1 AACCACCAAC 0.988763 -84 TTGGATCACCAAACCCTAATTCT 1 106 0 GATCACCAAA 0.887232 -13 TGTTAACTCCCCAGCCTTTTTACTG 2 6 1 ACTCCCCAGC 0.951539 -65 AACAACCACCACCTTCCAATTTA 2 58 0 AACCACCACC 0.980325 -13 TGCAAATCCCCGACTAAAAATTTA 3 48 0 AATCCCCGAC 0.991249 -14 TTTATCACCGAAACCTTTATTA 4 3 1 TATCACCGAA 0.759498 -163 ATCCAGGCTAGGCCACCGGCCCTCAGAAAA 4 51 0 GGCCACCGGC 0.944538 -115 CCGGGATTTGAACCCGGGACCTTCGGCTCC 4 96 0 AACCCGGGAC 0.861954 -70 CCCGGGTTCAAATCCCGGCCGGCCCGCCAA 4 108 1 AATCCCGGCC 0.944652 -58 ATCCCGGCCGGCCCGCCAACAATAACTTTA 4 119 1 GCCCGCCAAC 0.925498 -47 ********** Masking position 4 Map Score: 8.34993 Number of sites scoring better than the average of aligned sites = 626 Number in coding regions = 519 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 3 AAATACCTTTCCTAAGGTTGATTA 3 5 0 CCTAAGGTTG 0.976603 -57 AAAGCCTTTTCTGAGGGCCGGTGGCCTAGC 4 45 1 CTGAGGGCCG 0.993348 -121 ACCTTCGGCTCCGAAGGCCGACGCCCCATC 4 78 0 CCGAAGGCCG 0.99897 -88 GCCTTCGGAGCCGAAGGTCCCGGGTTCAAA 4 90 1 CCGAAGGTCC 0.995948 -76 ********** Masking position 4 Map Score: 3.99521 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 24 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 4 TTGTTGGTGGTTATAATTATAAAGTGAAGG 1 27 0 TTATAATTAT 0.76468 -92 TTTTTAGTCCTTAAAATATTTAGTCAATAA 1 77 0 TTAAAATATT 0.933053 -42 GCAGCAACCTTTAAAATCTTTACAGTAAAA 2 28 0 TTAAAATCTT 0.982261 -43 AAGGTATTTATTATAATCTTACTAAATTTT 3 26 1 TTATAATCTT 0.967404 -36 CGCTTTCAATTTAAAGCCTTTTCTGAGGGC 4 33 1 TTAAAGCCTT 0.943775 -133 AACAATAACTTTAAAACTTCCACAAATGTG 4 136 1 TTAAAACTTC 0.881656 -30 ********** Masking position 5 Map Score: 2.71769 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 191 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 5 GTCCTTAAAATATTTAGTCAATAATTTATC 1 71 0 TATTTAGTCA 0.975682 -48 ACCCTAATTCTTTTTAGTCCTTAAAATATT 1 87 0 TTTTTAGTCC 0.990562 -32 TCTTACTAAATTTTTAGTCGGGGATTTGCA 3 42 1 TTTTTAGTCG 0.990562 -20 ********** Masking position 6 Map Score: 1.35464 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ********** No masking Map Score: 5.42445e-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: 5.42445e-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: 5.42445e-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