AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_aful_reg_100.orf -o00860_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 AF0114 63 transcriptional regulatory protein, putative #2 AF0260 30 glutamyl-tRNA synthetase (gltX) #3 AF0422 138 uroporphyrin-III C-methyltransferase (cysG-1) #4 AF0727 97 cobalamin biosynthesis precorrin-2 methyltransferase (cbiL) #5 AF1241 81 glutamate-1-semialdehyde aminotransferase (hemL) #6 AF1778 105 stage V sporulation protein (spoVG) #7 AF1779 57 2-hydroxyacid dehydrogenase, putative #8 AF1975 99 glutamyl-tRNA reductase (hemA) #9 AF1976 93 26S protease regulatory subunit 4 Motif number 1 TGAGCTAAGATTTTAACTTTTCGAATGGTTTA 1 28 0 TTTTACTTTC 0.984161 -36 CCTTTTAAACTTGTTGAGCTAAGAT 1 49 0 TTTAACTTTT 0.98124 -15 CTTTATATTTCTCAACTTCCCAG 2 2 1 TTTATTTTTC 0.925405 -29 CGCTTTCTGGTTTAAGCTTACCTAAAAATATC 3 76 1 TTTAACTTCC 0.979995 -63 CGAGAAGTTTTTTAACCTTCCCACAACTCCCC 3 114 1 TTTAACTTCC 0.980036 -25 ATTGACTTTATTTAAATTTTTTGGATTTTCAG 4 42 1 TTTAATTTTT 0.954096 -56 TCATTTTATTTAAGTTTTTTCCCATTAAAT 5 9 1 TTTAATTTTT 0.954095 -73 TCCAATTCGTTTTAAATGTTTTCTTGCTGAGA 5 49 0 TTTAATGTTT 0.781091 -33 TTCAAAACCTTTTTATCTTTTCTGGGTTCAAT 7 30 1 TTTTACTTTC 0.984161 -28 GTCTCCACCATTTTATCATTTTAATTTTTGCT 8 22 1 TTTTACATTT 0.794712 -78 ATCATTTTAATTTTTGCTTTTCAGCATTGCTG 8 36 1 TTTTTCTTTC 0.952264 -64 ACAAGTGCTTTTTAAGTTTTTTATTCAGCAAT 8 61 0 TTTAATTTTT 0.954095 -39 TCAATTTTATTTTTTGCTTCCCTCTACGTTCC 9 62 0 TTTTTCTTCC 0.90967 -32 ***** *** ** Masking position 9 Map Score: 21.8949 Number of sites scoring better than the average of aligned sites = 335 Number in coding regions = 228 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 2 TTTTAACTTTTCGAATGGTTTATATAACCTTCACG 1 15 0 TCATTTATAT 0.949656 -49 AAATCTTAGCTCAACAAGTTTAAAAGG 1 47 1 TCAATTAAAA 0.855469 -17 AGCGCAAATTTCGAAATTCTTATATATTGCCTAAA 3 45 0 TCAATTATAT 0.973239 -94 ATATCTGCAATCGAGAAGTTTTTTAACCTTCCCAC 3 103 1 TCAATTTTTA 0.890686 -36 TTACTGAAAATCCAAAAAATTTAAATAAAGTCAAT 4 42 0 TCAATTTAAA 0.890242 -56 CTTCGCTCTCTCCAATTCGTTTTAAATGTTTTCTT 5 56 0 TCATTTTTAA 0.9496 -26 TTTCCTGCAATCAAAATTCTTATATACCACTTTGT 6 47 1 TCAATTATAT 0.973188 -59 GGCTTTTGCTTCAAAACCTTTTTATCTTTTCTGGG 7 21 1 TCAATTTTAT 0.978491 -37 GTTCCGGGAGTCTCCACCATTTTATCATTTTAATT 8 13 1 TCCATTTTAT 0.895782 -87 TTCAGAATTCACAAGTGCTTTTTAAGTTTTTTATT 8 68 0 ACATTTTTAA 0.685972 -32 TCCGGAAGCCTCCAAATACATATATATCACTCATC 9 30 0 TCAAATATAT 0.808159 -64 ATTTTATCCCTCAATTTTATTTTTTGCTTCCCTCT 9 69 0 TCATTTTTTT 0.853332 -25 ** * * ****** Masking position 11 Map Score: 12.6644 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 69 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 CTTTATATTTCTCAACTTCCCAGGTGGGCC 2 9 1 TTCCATTCCA 0.826613 -22 TCGTTCACCTCCTGTAATTGCAAGTCCCCCTCT 3 10 1 TCCGATTCAA 0.984785 -129 GTAAGCTTAAACCAGAAAGCGCAAATTTCGAAAT 3 63 0 ACCGAGCCAA 0.939769 -76 ATCTAACGTTTCCTGCAATCAAAATTCTTATATA 6 39 1 TCCGATCAAA 0.969282 -67 CCTTTCAAATTTCGTTACTCTCAAACAAAGTGGT 6 72 0 TTCTATCCAA 0.934841 -34 CCGTTCCGGGAGTCTCCACCATTTTATC 8 5 1 TCCGATCCCA 0.996403 -95 CTTATAGTTCAGAATTCACAAGTGCTTTTTA 8 79 0 TTCGATCCAA 0.931894 -21 CCCTCTACGTTCCGGAAGCCTCCAAATACATATA 9 41 0 TCCGACCCCA 0.988405 -53 *** * * ** *** Masking position 7 Map Score: 6.33112 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 324 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 TTCTTATATATTGCCTAAAAAGAGGGGGAC 3 34 0 TTGCCTAAAA 0.971398 -105 TGGTTTAAGCTTACCTAAAAATATCTGCAA 3 83 1 TTACCTAAAA 0.903566 -56 TAAATAAATCTTACTGAAAATCCAAAAAAT 4 57 0 TTACTGAAAA 0.959051 -41 AAATGTTTTCTTGCTGAGAATGTTCCCATT 5 38 0 TTGCTGAGAA 0.963521 -44 AGAATTTTGATTGCAGGAAACGTTAGATTA 6 37 0 TTGCAGGAAA 0.885648 -69 AGTTTGGCTTTTGCTTCAAAACCTTTTTAT 7 16 1 TTGCTTCAAA 0.93833 -42 CTTTTCAGCATTGCTGAATAAAAAACTTAA 8 52 1 TTGCTGAATA 0.946943 -48 ********** Masking position 10 Map Score: 4.98354 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 374 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 CGTTCGTGAAGGTTATATAAACCATTCG 1 8 1 GAAGGTTAAT 0.92359 -56 TGCCTAAAAAGAGGGGGACTTGCAATTACAG 3 22 0 GAGGGGGATT 0.945134 -117 GGAGTTGTGGGAAGGTTAAAAAACTTCTCGA 3 113 0 GAAGGTTAAA 0.891963 -26 AAGGGGGAGTTGTGGGAAGGT 3 128 0 AAGGGGGATT 0.829367 -11 TATTATGAGAGCGTGGTAATTTAATCTAACG 6 16 1 GCGTGGTATT 0.780968 -90 CTCTCAAACAAAGTGGTATATAAGAATTTTG 6 58 0 AAGTGGTAAT 0.914189 -48 AATTTGAAAGGAGGGTTAGAA 6 95 1 GAGGGTTAAA 0.966954 -11 GCAAAAATTAAAATGATAAAATGGTGGAGAC 8 22 0 AAATGATAAA 0.498529 -78 CTTATATGATGAGTGATATATATGTATTTGG 9 23 1 GAGTGATAAT 0.948137 -71 AAATAAAATTGAGGGATAAAAT 9 82 1 GAGGGATAAA 0.966954 -12 ******** ** Masking position 8 Map Score: 5.13367 Number of sites scoring better than the average of aligned sites = 1048 Number in coding regions = 970 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 ********** No masking Map Score: 1.67931e-12 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: 1.67931e-12 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: 1.67931e-12 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