AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i298_bsub_mtub_100.orf -o298_bsub_mtub_100.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yloB 115 similar to calcium-transporting ATPase #2 yloC 82 similar to hypothetical proteins #3 yloD 233 similar to guanylate kinase #4 yloI 80 similar to pantothenate metabolism flavoprotein #5 gmk 134 gmk #6 Rv1401 133 hypothetical protein Rv1401 #7 priA 80 priA Motif number 1 GTTTGATTGGCGCAGACTCCGGGCTGACAAT 3 150 0 CGCAGACCCG 0.517757 -84 TGCAAGAGACCGCGGAATGCTAATTGACGCT 3 194 1 CGCGGAAGCT 0.904176 -40 CCCCGCCGGCCGACGATGCGG 5 1 1 CCCCGCCGCC 0.932852 -134 GACGATGCGGGCCGGAAGGCCTGTGGTGGGC 5 22 1 GCCGGAAGCC 0.982662 -113 GGCCTGTGGTGGGCGTACCCCCGCATACGGG 5 39 1 GGGCGTACCC 0.799067 -96 GCCGCCTCTCCCCCGTATGCGGGGGTACGCC 5 50 0 CCCCGTAGCG 0.980385 -85 ACGGGGGAGAGGCGGCCTGACAGGGCCAGCT 5 65 1 GGCGGCCGAC 0.863014 -70 TCACAATTCAGGCCGAACGCCCCGTGGGGGG 5 95 1 GGCCGAAGCC 0.763932 -40 ACGCCCCGTGGGGGGAACCCGCCCAGGAGCG 5 111 1 GGGGGAACCG 0.904064 -24 CCAGCCGCCGGCCAGCAAGCGAGGTGCGTAC 6 20 0 GCCAGCAGCG 0.994823 -114 CCGGCGACCACCCAGCCGCCGGCCAGCAAGC 6 31 0 CCCAGCCCCG 0.966419 -103 GCGAGGCCCGCCCAGCCGGCGACCACCCAGC 6 46 0 CCCAGCCGCG 0.937598 -88 GTCAAGTACACGCCGTAGGCGAGGCCCGCCC 6 64 0 CGCCGTAGCG 0.661355 -70 CTCGCTGCCCGGTGGCAAGCGCAATGCGATC 6 98 0 GGTGGCAGCG 0.961561 -36 AGCGAGTTGACCGGGCACGCG 6 123 1 CCGGGCAGCG 0.987211 -11 TCGCGGTCAAGCCCGCACGCCCGTCGAAGTA 7 36 1 GCCCGCAGCC 0.995069 -45 CGGCAGCACCCGCGCGATCGGC 7 69 0 GGCAGCACCG 0.981021 -12 ******* *** Masking position 5 Map Score: 35.4553 Number of sites scoring better than the average of aligned sites = 2309 Number in coding regions = 2117 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 TCCGCTCGTCCACTCCCCTGCT 1 104 0 CGCTCGTCCA 0.611877 -12 TGATTAATATCGGATTTGGCAATATCATCT 3 100 1 CGGATTTGGC 0.548437 -134 ACGCTACATACGGACGAAGAACCC 3 220 1 CGGACGAAGA 0.57569 -14 TGAATTCTCCCCCTCTGCACTTTACAAAA 4 62 0 CCCCTCTGCA 0.494701 -19 CCCCGCCGGCCGACGATGCGGGCCGG 5 7 1 CGGCCGACGA 0.968006 -128 CCTGTCAGGCCGCCTCTCCCCCGTATGCGG 5 59 0 CGCCTCTCCC 0.885377 -76 GCGGGTTCCCCCCACGGGGCGTTCGGCCTG 5 103 0 CCCACGGGGC 0.880531 -32 TGGGGGGAACCCGCCCAGGAGCGCCA 5 119 1 CCGCCCAGGA 0.877362 -16 CGGTACCGTACGCACCTCGCTTGCTGGCCG 6 13 1 CGCACCTCGC 0.976156 -121 GACCACCCAGCCGCCGGCCAGCAAGCGAGG 6 27 0 CCGCCGGCCA 0.910197 -107 GCCCGCCCAGCCGGCGACCACCCAGCCGCC 6 42 0 CCGGCGACCA 0.840446 -92 GCCGGCTGGGCGGGCCTCGCCTACGGCGTG 6 57 1 CGGGCCTCGC 0.983553 -77 TGACCGTGATCGCATTGCGCTTGCCACCGG 6 91 1 CGCATTGCGC 0.714554 -43 CGCTTGCCACCGGGCAGCGAGTTGACCGGG 6 108 1 CGGGCAGCGA 0.787736 -26 AGCGAGTTGACCGGGCACGCG 6 123 1 CCGGGCACGC 0.72322 -11 TGTCTAGCAGCGGATCTCGCGGTCAAGCCC 7 20 1 CGGATCTCGC 0.956707 -61 CAAGCCCGCACGCCCGTCGAAGTAGAGCCG 7 43 1 CGCCCGTCGA 0.967757 -38 CGAAGTAGAGCCGATCGCGCGGGTGCTGCC 7 60 1 CCGATCGCGC 0.935285 -21 ********** Masking position 1 Map Score: 14.6755 Number of sites scoring better than the average of aligned sites = 3918 Number in coding regions = 3645 Number in noncoding regions = 273 Number of orfs with sites within 600 bp upstream = 168 Fraction of orfs with sites within 600 bp upstream = 0.0269836 Motif number 3 ATCGAATGCAGGAAGAATGAGAGGGTGTA 1 8 0 GGAAGAATGA 0.977437 -108 GCATGAAATGGGACGAGTCAGAATAAGCATGC 1 47 1 GGACGAGTGA 0.968441 -69 ATGAGAACAGGGAAGAATTGGGTGTTTTAAA 2 62 1 GGAAGAATGG 0.976992 -21 ACAGGGGGAACGTAGAAGATGACGATTAAACT 3 69 1 CGTAGAAGGA 0.905254 -165 TCCGCCAATCGGATGATTTCGATTGTCAGCCC 3 129 1 GGATGATTGA 0.958709 -105 CCAATCAAACGGATGATTCAGGATGCAAGAGA 3 171 1 GGATGATTGG 0.957909 -63 CCCCGCCGGCCGACGATGCGGGCCGGAAGGCC 5 11 1 CGACGATGGG 0.968645 -124 CCCGCACGCCCGTCGAAGTAGAGCCGATCGCG 7 47 1 CGTCGAAGGA 0.937593 -34 ******** ** Masking position 6 Map Score: 4.6795 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 508 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TAAGAGAGCAGGGGAGTGGACGAGCGGA 1 98 1 GGGGAGTGGA 0.956044 -18 CATCCGATTGGCGGAGATGATATTGCCAAA 3 114 0 GCGGAGATGA 0.84251 -120 CCCGCATACGGGGGAGAGGCGGCCTGACAG 5 58 1 GGGGAGAGGC 0.982335 -77 GGCGCTCCTGGGCGGGTTCCCCCCACGGGG 5 114 0 GGCGGGTTCC 0.956447 -21 CCGGCCAGCAAGCGAGGTGCGTACGGTACC 6 14 0 AGCGAGGTGC 0.97538 -120 ACACGCCGTAGGCGAGGCCCGCCCAGCCGG 6 58 0 GGCGAGGCCC 0.970202 -76 GCCACCGGGCAGCGAGTTGACCGGGCACGC 6 113 1 AGCGAGTTGA 0.934834 -21 CGGGCTTGACCGCGAGATCCGCTGCTAGAC 7 21 0 CGCGAGATCC 0.949899 -60 ********** Masking position 6 Map Score: 3.6897 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 498 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 5 CATAATAAAAGGGCAATAGACACGCTATTACCCC 2 31 0 GGCAATAACG 0.925534 -52 GTAAGACCGTCTGTAAACAATACGCACAGTCA 3 9 0 CGTAAAAACG 0.985652 -225 TACGTTCCCCCTGTAAAATAGACGTCTCTAGTTT 3 49 0 CGTAAAAACG 0.985646 -185 AATATCATCTCCGCCAATCGGATGATTTCGATTG 3 120 1 CGCCAAGATG 0.920214 -114 CCCGGAGTCTGCGCCAATCAAACGGATGATTCAG 3 158 1 GGCCAAAACG 0.991977 -76 CCCCGCCGGCCGACGATGCGGGCCGGAAGG 5 7 1 CGCCGAAGCG 0.965209 -128 AATGCGATCACGGTCAAGTACACGCCGTAGGCGA 6 73 0 CGTCAAAACG 0.992989 -61 * ***** * *** Masking position 3 Map Score: 2.95169 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 320 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ATATCTCTATAAGAGAGCAGGGGAGTGGACG 1 89 1 AAGAGAGCGG 0.981291 -27 CCCTTTTATTATGAGAACAGGGAAGAATTGG 2 52 1 ATGAGAACGG 0.971253 -31 ATGATTTCGATTGTCAGCCCGGAGTCTGCGC 3 141 1 TTGTCAGCCG 0.920332 -93 TTCAGGATGCAAGAGACCGCGGAATGCTAAT 3 187 1 AAGAGACCCG 0.933896 -47 CCGGCCGACGATGCGGGCCGGAAGGCCTGTG 5 16 1 ATGCGGGCGG 0.965766 -119 TCGGCCTGAATTGTGAGCTGGCCCTGTCAGG 5 80 0 TTGTGAGCGG 0.977527 -55 GGCAAGCGCAATGCGATCACGGTCAAGTACA 6 85 0 ATGCGATCCG 0.922623 -49 CGCATTGCGCTTGCCACCGGGCAGCGAGTTG 6 101 1 TTGCCACCGG 0.963501 -33 GATCCGCTGCTAGACAACCGGTCCG 7 5 0 TAGACAACGG 0.881141 -76 ******** ** Masking position 8 Map Score: 6.5235 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 504 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 CATGCTATAATTATCGAATGCAGGAAGAAT 1 22 0 TTATCGAATG 0.915335 -94 CATTCGATAATTATAGCATGAAATGGGACG 1 32 1 TTATAGCATG 0.988704 -84 ATAAGCATGCTTATAGAGTGATATCTCTAT 1 69 1 TTATAGAGTG 0.960807 -47 ACCCCTAAGATTATATCATATGAAT 2 6 0 TTATATCATA 0.820644 -77 ATCTTAGGGGTAATAGCGTGTCTATTGCCC 2 25 1 TAATAGCGTG 0.947088 -58 AAGTAGCAACCTATATCATGTAGGTTGTTA 4 17 1 CTATATCATG 0.915352 -64 ********** Masking position 4 Map Score: 1.19684 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 153 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 8 ********** No masking Map Score: 6.20604e-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: 6.20604e-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 10 ********** No masking Map Score: 6.20604e-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