AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i228_bsub_mtub_100.orf -o228_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 yacL 115 similar to hypothetical proteins #2 gltX 90 glutamyl-tRNA synthetase #3 ywfO 161 alternate gene name: ipa-93d; similar to hypothetical proteins #4 Rv2993c 275 hypothetical protein Rv2993c Motif number 1 CTTGTTTTGATGCCGGGTCTATTTGGTGG 2 10 1 ATGCCGGGTC 0.941095 -81 AAAGCCTGACCTGAGGGCCGAGGCTAAGAA 3 22 0 CTGAGGGCCG 0.922025 -140 ATCCTTGAATTTGCCCGGCGATTTGTTCCA 3 83 0 TTGCCCGGCG 0.981725 -79 ATCGGGCCCCGTGCCGGGTGACTGTGCCAG 4 20 0 GTGCCGGGTG 0.957457 -256 GGGCCCTCACCATCGGGCCCCGTGCCGGGT 4 31 0 CATCGGGCCC 0.822403 -245 CTGCCGGGCGCTGCGGGCCCTCACCATCGG 4 45 0 CTGCGGGCCC 0.923238 -231 CAATCAGACCCTGCCGGGCGCTGCGGGCCC 4 55 0 CTGCCGGGCG 0.975937 -221 CAGGGTCTGATTGCCGGGCTCCTCATCGGG 4 72 1 TTGCCGGGCT 0.994833 -204 TCATCGGGCCGTGCCGGCCCGAATCGTCGC 4 94 1 GTGCCGGCCC 0.67404 -182 CAATCAGACCCTGCCGGGCGACGATTCGGG 4 111 0 CTGCCGGGCG 0.975937 -165 CAGGGTCTGATTGCCGGGCTCCTCATCGGG 4 128 1 TTGCCGGGCT 0.994833 -148 TCATCGGGCCGTGCCGGCCCGAATCGTCGC 4 150 1 GTGCCGGCCC 0.67404 -126 TAGCCGGGCCCTGCCGGGCGACGATTCGGG 4 167 0 CTGCCGGGCG 0.975937 -109 TGGATGAGCTTAGCCGGGCCCTGCCGGGCG 4 177 0 TAGCCGGGCC 0.990996 -99 AAAGCGACACCGTCCGGGCTGGCGATTCGA 4 219 0 CGTCCGGGCT 0.886591 -57 CATCGACGGCGAGCTGGGCGAGCCGAGTGA 4 255 1 GAGCTGGGCG 0.949208 -21 ********** Masking position 7 Map Score: 52.3823 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 582 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 TTTTGATGCCGGGTCTATTTGGTGGTAGAATA 2 15 1 GGTCTTTTGG 0.591738 -76 GCCCTCAGGTCAGGCTTTTTTGCTTCACAAGA 3 34 1 CGGCTTTTTG 0.807844 -128 TTGAATTTGCCCGGCGATTTGTTCCATCTTCA 3 77 0 CGGCGTTTGT 0.771375 -85 CCCGTGCCGGGTGACTGTGCCAGCATGGGTGG 4 11 0 GGACTTGCCA 0.850054 -265 GCCCGGCAATCAGACCCTGCCGGGCGCTGCGG 4 59 0 CGACCTGCCG 0.995987 -217 GGCTCCTCATCGGGCCGTGCCGGCCCGAATCG 4 88 1 CGGCCTGCCG 0.997672 -188 ACCCTGCCGGGCGACGATTCGGGCCGGCACGG 4 102 0 GGACGTTCGG 0.978813 -174 GCCCGGCAATCAGACCCTGCCGGGCGACGATT 4 115 0 CGACCTGCCG 0.995987 -161 GGCTCCTCATCGGGCCGTGCCGGCCCGAATCG 4 144 1 CGGCCTGCCG 0.997672 -132 GCCCTGCCGGGCGACGATTCGGGCCGGCACGG 4 158 0 GGACGTTCGG 0.978813 -118 TGAGCTTAGCCGGGCCCTGCCGGGCGACGATT 4 171 0 CGGCCTGCCG 0.997654 -105 ACCGTCCGGGCTGGCGATTCGACCGATACGCA 4 209 0 CGGCGTTCGA 0.958246 -67 ATCGCCAGCCCGGACGGTGTCGCTTTTGCCAG 4 223 1 CGACGTGTCG 0.988506 -53 GCCCAGCTCGCCGTCGATGCTGGCAAAAGCGA 4 242 0 CGTCGTGCTG 0.959923 -34 * **** ***** Masking position 8 Map Score: 31.3517 Number of sites scoring better than the average of aligned sites = 1448 Number in coding regions = 1385 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 TTCTTAGCCTCGGCCCTCAGGTCAGGCTTT 3 22 1 CGGCCCTCAG 0.996284 -140 TGAATTTGCCCGGCGATTTGTTCCATCTTC 3 78 0 CGGCGATTTG 0.579501 -84 CACAGTCACCCGGCACGGGGCCCGATGGTG 4 24 1 CGGCACGGGG 0.898531 -252 CCGATGGTGAGGGCCCGCAGCGCCCGGCAG 4 45 1 GGGCCCGCAG 0.99081 -231 GGGCCCGCAGCGCCCGGCAGGGTCTGATTG 4 55 1 CGCCCGGCAG 0.958636 -221 ATGAGGAGCCCGGCAATCAGACCCTGCCGG 4 68 0 CGGCAATCAG 0.965666 -208 CGGGCCGGCACGGCCCGATGAGGAGCCCGG 4 85 0 CGGCCCGATG 0.993956 -191 CGGGCCGTGCCGGCCCGAATCGTCGCCCGG 4 98 1 CGGCCCGAAT 0.980423 -178 CCCGAATCGTCGCCCGGCAGGGTCTGATTG 4 111 1 CGCCCGGCAG 0.958636 -165 ATGAGGAGCCCGGCAATCAGACCCTGCCGG 4 124 0 CGGCAATCAG 0.965666 -152 CGGGCCGGCACGGCCCGATGAGGAGCCCGG 4 141 0 CGGCCCGATG 0.993956 -135 CGGGCCGTGCCGGCCCGAATCGTCGCCCGG 4 154 1 CGGCCCGAAT 0.980423 -122 CCCGAATCGTCGCCCGGCAGGGCCCGGCTA 4 167 1 CGCCCGGCAG 0.958636 -109 CCAGCATCGACGGCGAGCTGGGCGAGCCGA 4 251 1 CGGCGAGCTG 0.970078 -25 ********** Masking position 4 Map Score: 37.8375 Number of sites scoring better than the average of aligned sites = 865 Number in coding regions = 813 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 CATATTTTTTCTTAGCCTCGGCCCTCAGGTC 3 14 1 CTTACCTCGG 0.976121 -148 GCTGCGGGCCCTCACCATCGGGCCCCGTGCC 4 35 0 CTCACATCGG 0.997233 -241 GATTGCCGGGCTCCTCATCGGGCCGTGCCGG 4 80 1 CTCCCATCGG 0.998225 -196 GATTGCCGGGCTCCTCATCGGGCCGTGCCGG 4 136 1 CTCCCATCGG 0.998225 -140 GCTCGCCCAGCTCGCCGTCGATGCTGGCAAA 4 247 0 CTCGCGTCGA 0.97175 -29 **** ****** Masking position 8 Map Score: 7.24473 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 52 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 5 ACCCCCACCTCCTTTTTTAACATTTTAATTT 1 95 0 CTCTTTTTAC 0.975913 -21 CTTGTTTTGATGCCGGGTCTATTT 2 1 1 CTTTTTATGC 0.968862 -90 AGAATAGATTCATACATTTTTGCCTGAGGCCATA 2 41 1 CTCATTTTGC 0.94557 -50 TTTCAAATACTTCCTTTCATGTCATGTATGGCC 2 68 0 CTCTTTATGC 0.984678 -23 AAACATATTTTTTCTTAGCCTCGGCCCTC 3 6 1 TTTTTTTTAC 0.904744 -156 ATATCGACTCTATTCTTTGAAAACATCCTTGAAT 3 103 0 TTCTTTAAAC 0.867616 -59 CGTCATTCCCTCTTTTTTTTAGCCGTGTTTCTAT 3 138 0 TTTTTTTAGC 0.89511 -24 * * **** *** * Masking position 7 Map Score: 1.04987 Number of sites scoring better than the average of aligned sites = 692 Number in coding regions = 587 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 6 TTCTACCACCAAATAGACCCGGCATCAAAA 2 15 0 AAATAGACCC 0.962498 -76 GGGCCCTCACCATCGGGCCCCGTGCCGGGT 4 31 0 CATCGGGCCC 0.981132 -245 GGAGCCCGGCAATCAGACCCTGCCGGGCGC 4 64 0 AATCAGACCC 0.996134 -212 GGAGCCCGGCAATCAGACCCTGCCGGGCGA 4 120 0 AATCAGACCC 0.996134 -156 ********** Masking position 2 Map Score: 3.41464 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 32 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ********** No masking Map Score: -1.39734e-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: -1.39734e-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 9 ********** No masking Map Score: -1.39734e-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