AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i079_bsub_mtub_300.orf -o079_bsub_mtub_300.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 purT 230 phosphoribosylglycinamide formyltransferase 2 #2 mpr 143 extracellular metalloprotease #3 ybfK 165 similar to carboxylesterase #4 pssA 195 phosphatidylserine synthase #5 psd 60 psd #6 Rv0439c 293 hypothetical protein Rv0439c Motif number 1 GGGATGCCTCCTGTCGGTGTGGTGGTCTTGGATTAAGTG 1 10 1 CCTCGTGTCT 0.843046 -221 TTGTCATCTCCCTCCTTTAGTGTCAACCACCCGTATCGAT 2 113 0 CCTTGTGCCC 0.895801 -31 CCGGACCGATCCTAGTGCCGTGCACCCAACCTGCG 5 6 1 CCGCGTGCCC 0.996733 -55 GGTCATCTTACGGAGCTTCGTGCCGCAGGTTGGGTGCACG 5 29 0 CGGCGTGCGT 0.998066 -32 GCGGGGTTGCCGTCACCCGGTGACCCCCGTTTCATCCCCG 6 32 0 CGTCGTGCCT 0.988395 -262 CTTACGCTGGCCGGGCGCAGTGCCCGCGACGGACGGCTCA 6 74 1 CCGCGTGCGC 0.998326 -220 CCGCGACGGACGGCTCAAGTTGTCCTCGCTGCCACTCGCT 6 97 1 CGGCTTGCGT 0.986248 -197 AGTGCTAGGTCGGGACGGTGAGGCCAGGCCCGTCGTCGCA 6 136 0 CGGCGAGCGC 0.989657 -158 TAGCACTCACCGGTCGCGAGTGCCAACGTTATTCTTAGCA 6 169 1 CGGGGTGCGT 0.991935 -125 TGACCCGGTGCGGGGCTTCTTGCACTCGGCATAGGCGAGT 6 208 0 CGGCTTGAGC 0.909323 -86 TCATGCCCCTCGTTCGACCGTGTCCTCGGCCCTCCGATCC 6 245 1 CGTGGTGCGC 0.984496 -49 CCTCGGCCCTCCGATCCGGGTGAGTATGTTCGGCCC 6 268 1 CCGCGTGGGT 0.979693 -26 *** * *** * * * Masking position 1 Map Score: 20.1892 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 233 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 AGTAGCGGGGTTGCCGTCACCCGGTGACCC 6 46 0 TTGCCGTCAC 0.878201 -248 ACGGCTCAAGTTGTCCTCGCTGCCACTCGC 6 106 1 TTGTCCTCGC 0.955098 -188 TTGTCCTCGCTGCCACTCGCTGCGACGACG 6 116 1 TGCCACTCGC 0.990835 -178 CGTCCCGACCTAGCACTCACCGGTCGCGAG 6 159 1 TAGCACTCAC 0.968769 -135 AGAATAACGTTGGCACTCGCGACCGGTGAG 6 174 0 TGGCACTCGC 0.996738 -120 ACGTTATTCTTAGCACTCGCCTATGCCGAG 6 194 1 TAGCACTCGC 0.992681 -100 GCGGGGCTTCTTGCACTCGGCATAGGCGAG 6 209 0 TTGCACTCGG 0.973931 -85 CACCGGGTCATGCCCCTCGTTCGACCGTGT 6 238 1 TGCCCCTCGT 0.932181 -56 ********** Masking position 7 Map Score: 10.999 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 123 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 TAAACAGCAACATCATACAAGAAATCCCCCAAA 1 59 0 CTCTCAAGAA 0.874016 -172 ATTTGTCTGCTTTCGTTTAAGAATTTAAAAGAT 1 114 1 TTCTTAAGAA 0.971431 -117 TAAAAGATTTTAACCCTCAATAATAATTTTATC 1 139 1 TACCCAATAA 0.823968 -92 AATAATTTTATCTTTTTTAATAAAAATTTATTT 1 160 1 TTTTTAATAA 0.911169 -71 CCGTAAAAGTTTTATCATAAGAATCAGAAACCT 2 58 1 TTACTAAGAA 0.780269 -86 TATAGTTTGGTTTCCTGCAATAAATAAAAAAGG 3 37 0 TTCTCAATAA 0.975242 -129 TTTCTTATTATCTCACATAATAAATTTCCAGTA 3 70 0 TTCCTAATAA 0.971431 -96 ACGCCCCTTTTGTCTCGTAAGAAAAAATACCTA 3 103 0 TTCCTAAGAA 0.969512 -63 AGGTAACAAATGTTGTATAATAATAGAATTTGA 4 47 1 TTTTTAATAA 0.911181 -149 CAGGAAAAATTTTTCTCCAATAAGCATGATAAC 4 107 0 TTTTCAATAA 0.917443 -89 ATTCGATCACTATCGTCAAATAATATAGATGGT 4 147 1 TTCTAAATAA 0.883018 -49 * ** * ****** Masking position 9 Map Score: 8.55746 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 136 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 CTTTGCCCCTCCTATCTGTTCCAAAC 1 215 0 CCCTCCTATC 0.974723 -16 TAGTGTCAACCACCCGTATCGATGGAAGAC 2 106 0 CACCCGTATC 0.984296 -38 TTTGTCATCTCCCTCCTTTAGTGTCAACCA 2 124 0 CCCTCCTTTA 0.728572 -20 GGGTGCACGGCACTAGGATCGGTCCGG 5 8 0 CACTAGGATC 0.834585 -53 CGAAGTGATTCCTCCGGATCGGGGATGAAA 6 13 1 CCTCCGGATC 0.965774 -281 CACCCGGTGACCCCCGTTTCATCCCCGATC 6 29 0 CCCCCGTTTC 0.990104 -265 CCGGGTCATGCCCCTCGTTCGACCGTGTCC 6 240 1 CCCCTCGTTC 0.926749 -54 CGAACATACTCACCCGGATCGGAGGGCCGA 6 270 0 CACCCGGATC 0.989657 -24 ********** Masking position 9 Map Score: 7.93387 Number of sites scoring better than the average of aligned sites = 315 Number in coding regions = 260 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 GAAAAAAACAGGCCTTGTCCCATGACAAGA 2 23 0 GGCCTTGTCC 0.963607 -121 AAATAAAAAAGGCAGTTCCCTTAAAATCAA 3 19 0 GGCAGTTCCC 0.972773 -147 CCGATCCTAGTGCCGTGCACCCAACCTGCG 5 16 1 TGCCGTGCAC 0.954076 -45 GCTGGCCGGGCGCAGTGCCCGCGACGGACG 6 79 1 CGCAGTGCCC 0.984733 -215 GGGACGGTGAGGCCAGGCCCGTCGTCGCAG 6 135 0 GGCCAGGCCC 0.943524 -159 CCCCGCACCGGGTCATGCCCCTCGTTCGAC 6 233 1 GGTCATGCCC 0.764107 -61 CCCCTCGTTCGACCGTGTCCTCGGCCCTCC 6 250 1 GACCGTGTCC 0.972861 -44 ********** Masking position 10 Map Score: 5.57167 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 284 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 AAATAACGGTCTGCTTTCTCTATTCCTAAA 1 88 0 CTGCTTTCTC 0.987174 -143 CGTTATTTGTCTGCTTTCGTTTAAGAATTT 1 110 1 CTGCTTTCGT 0.971384 -121 GGGACAAGGCCTGTTTTTTTCTTTCTCCGT 2 32 1 CTGTTTTTTT 0.945426 -112 TTTAAGGGAACTGCCTTTTTTATTTATTGC 3 24 1 CTGCCTTTTT 0.976159 -142 CTTCTTCTTTTTCCTCCGGGTTT 3 153 0 CTTCTTTTTC 0.934904 -13 AATTTGAATGCTGCTTTTTTTGGGAGCATT 4 73 1 CTGCTTTTTT 0.991149 -123 ********** Masking position 6 Map Score: 5.42298 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 458 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 CTTGTCCCATGACAAGACCTGTTCAAACT 2 10 0 GACAAGACCT 0.98307 -134 CTTGTCATGGGACAAGGCCTGTTTTTTTCT 2 24 1 GACAAGGCCT 0.984297 -120 TGCGACGACGGGCCTGGCCTCACCGTCCCG 6 136 1 GGCCTGGCCT 0.990466 -158 TGGCCTCACCGTCCCGACCTAGCACTCACC 6 150 1 GTCCCGACCT 0.967609 -144 TCGAACGAGGGGCATGACCCGGTGCGGGGC 6 232 0 GGCATGACCC 0.975867 -62 ********** Masking position 6 Map Score: 1.62122 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 78 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TTGAGGGTTAAAATCTTTTAAATTCTTAAA 1 129 0 AAATCTTTTA 0.913628 -102 TAAAAAAGATAAAATTATTATTGAGGGTTA 1 149 0 AAAATTATTA 0.89758 -82 ATTTGAAAAATAAATTTTTATTAAAAAAGA 1 170 0 TAAATTTTTA 0.79741 -61 TTCTTATGATAAAACTTTTACGGAGAAAGA 2 51 0 AAAACTTTTA 0.960015 -93 GTATCGATGGAAGACTTTTACATTATAATC 2 91 0 AAGACTTTTA 0.882405 -53 TATATACTGGAAATTTATTATGTGAGATAA 3 66 1 AAATTTATTA 0.792552 -100 TTATTGGAGAAAAATTTTTCCTGTAACGCT 4 117 1 AAAATTTTTC 0.861276 -79 ********** Masking position 2 Map Score: 2.25555 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 118 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 9 TATATAGTTTGGTTTCCTGCAATAAATAAA 3 42 0 GGTTTCCTGC 0.958896 -124 GACCGATCCTAGTGCCGTGCACCCAACCTG 5 14 1 AGTGCCGTGC 0.97001 -47 CATCTTACGGAGCTTCGTGCCGCAGGTTGG 5 36 0 AGCTTCGTGC 0.984261 -25 ACGCTGGCCGGGCGCAGTGCCCGCGACGGA 6 77 1 GGCGCAGTGC 0.969196 -217 CCCGGTGCGGGGCTTCTTGCACTCGGCATA 6 215 0 GGCTTCTTGC 0.972576 -79 ********** Masking position 8 Map Score: 0.528464 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 221 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 TGTTTTTTTCTTTCTCCGTAAAAGTTTTAT 2 43 1 TTTCTCCGTA 0.95074 -101 CTTCTTCTTTTTCCTCCGGGTTTGATTGAT 3 146 0 TTCCTCCGGG 0.994576 -20 TGCGAAGTGATTCCTCCGGATCGGGGATGA 6 11 1 TTCCTCCGGA 0.991587 -283 ATGCCCCTCGTTCGACCGTGTCCTCGGCCC 6 247 1 TTCGACCGTG 0.945903 -47 ********** Masking position 2 Map Score: 0.454914 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 106 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 ********** No masking Map Score: 4.07441e-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 12 ********** No masking Map Score: 4.07441e-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 13 ********** No masking Map Score: 4.07441e-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