AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00150_aful_reg_100.orf -o00150_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 AF0140 123 ubiquinone/menaquinone biosynthesis methyltransferase (ubiE) #2 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #3 AF1778 105 stage V sporulation protein (spoVG) #4 AF1779 57 2-hydroxyacid dehydrogenase, putative Motif number 1 CTTAAATCGCCCATTGAATTTACAGGCTGCATGT 1 32 1 CCAGAATTAA 0.958728 -92 ATCTTTTTACCCAAAAAACATGCAGCCTGTAAAT 1 49 0 CCAAAACTGA 0.98425 -75 CCAGGATGGTAAACGAAAGGTATAAATGAATCCT 1 84 1 AAAAAAGTAA 0.86462 -40 TGACACAAGCTCAAGAAATCTGGAGGTGTT 2 7 0 TCAAAATTGA 0.974168 -91 TACTGAAAATCCAAAAAATTTAAATAAAGTCAAT 2 42 0 CCAAAATTAA 0.988695 -56 TCGTTACTCTCAAACAAAGTGGTATATAAGAATT 3 61 0 CAAAAAGGGA 0.94563 -45 TGTTTGAGAGTAACGAAATTTGAAAGGAGGGTTA 3 79 1 TAAAAATTGA 0.936677 -27 AGAATTGAACCCAGAAAAGATAAAAAGGTTTTGA 4 31 0 CCAAAAGTAA 0.99062 -27 *** **** ** * Masking position 7 Map Score: 5.62927 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 135 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 2 TTTTCGCTCCTTTGCTTAAATCGCCCATTGA 1 18 1 TTTGTTAAAT 0.971006 -106 CTGCATGTTTTTTGGGTAAAAAGATGCCAGG 1 58 1 TTTGGTAAAA 0.828986 -66 TCAGATTGACTTTATTTAAATTTTTTGGATT 2 38 1 TTTATTAAAT 0.930515 -60 TTAAATAAATCTTACTGAAAATCCAAAAAAT 2 57 0 CTTATGAAAA 0.809896 -41 CAACTCTAAACTCAGTTAAATAAATCTTACT 2 72 0 CTCATTAAAT 0.891493 -26 GCAGGAAACGTTAGATTAAATTACCACGCTC 3 24 0 TTAGTTAAAT 0.876696 -82 TAATCTAACGTTTCCTGCAATCAAAATTCTT 3 37 1 TTTCTGCAAT 0.870008 -69 TTCTAACCCTCCTTTCAAATTTCGTTACT 3 87 0 CTCCTTCAAA 0.867781 -19 GAGTTTGGCTTTTGCTTCAAAACCTTTTTAT 4 15 1 TTTGTTCAAA 0.761389 -43 TTTATCTTTTCTGGGTTCAATTCTGTC 4 41 1 CTGGTTCAAT 0.925224 -17 **** ****** Masking position 9 Map Score: 5.53107 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 263 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 AATTTTCGCTCCTTTGCTTAAATCGCCCAT 1 16 1 CCTTTGCTTA 0.991152 -108 TCATTTATACCTTTCGTTTACCATCCTGGC 1 83 0 CTTTCGTTTA 0.908594 -41 ATCCTTAAGCCCTTTTCTTCT 1 113 1 CCTTTTCTTC 0.991152 -11 AAGAGTTTGGCTTTTGCTTCAAAACCTTTT 4 13 1 CTTTTGCTTC 0.991152 -45 TGCTTCAAAACCTTTTTATCTTTTCTGGGT 4 27 1 CCTTTTTATC 0.937931 -31 ********** Masking position 4 Map Score: 3.71789 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 302 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 ATTTAAGCAAAGGAGCGAAAATTTAAAA 1 9 0 AGGAGCGAAA 0.97295 -115 AAAAGATGCCAGGATGGTAAACGAAAGGTA 1 76 1 AGGATGGTAA 0.993691 -48 TTATTATGAGAGCGTGGTAATTTAATCTAA 3 15 1 AGCGTGGTAA 0.971803 -91 GAAATTTGAAAGGAGGGTTAGAA 3 93 1 AGGAGGGTTA 0.989735 -13 ********** Masking position 1 Map Score: 1.4159 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 198 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 ********** No masking Map Score: -7.29427e-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 6 ********** No masking Map Score: -7.29427e-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: -7.29427e-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