AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i263_bsub_mtub_300.orf -o263_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 yqeG 300 similar to hypothetical proteins #2 yydA 300 similar to hypothetical proteins #3 Rv2421c 274 hypothetical protein Rv2421c Motif number 1 CACTTTTTGGTGTGGATAACAGAACGATTG 1 84 0 TGTGGATAAC 0.995908 -217 CACACCAAAAAGTGGATAACTTGTGAGTAT 1 100 1 AGTGGATAAC 0.98199 -201 GTGGATAACTTGTGAGTATCGTGTTTATAA 1 111 1 TGTGAGTATC 0.870962 -190 CTTCACCAGGTGTGGATAAATTTACACACA 1 175 0 TGTGGATAAA 0.945832 -126 GTATTATTCTTGTGAAGAACACATCGAAAC 2 70 1 TGTGAAGAAC 0.980064 -231 CTGTGAATTATGTGGAGACCCCGCAGTATA 2 182 1 TGTGGAGACC 0.9695 -119 CAGTATATATAGTGGGGAACGAATGATCTT 2 205 1 AGTGGGGAAC 0.922091 -96 TGTCCACAATTGTGGATATCTTTTCTGTAT 2 242 0 TGTGGATATC 0.983708 -59 TATCCACAATTGTGGACAACATATATGAAT 2 254 1 TGTGGACAAC 0.982716 -47 GGACAACATATATGAATAACTTGTTTTTAA 2 267 1 TATGAATAAC 0.916007 -34 GTTTTTAAAGTGGGGATGACCT 2 289 1 TGGGGATGAC 0.935395 -12 CGCAAAGGCTTAGGAATAACCAATCGTGCT 3 146 1 TAGGAATAAC 0.790779 -129 ********** Masking position 4 Map Score: 19.6974 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 185 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 2 CACATCGAAACGGTGCTGGATATGTACATAGACG 2 89 1 CGGGCGGTAG 0.974613 -212 TCTGATTTCGGGCGGCAGCTCGTGGTCGTCTATG 2 115 0 GGCGCGCCGG 0.986277 -186 GATACCCGCGGGCAGTGCGGCGCG 3 1 0 GGCGTCGCGG 0.977547 -274 CATGGCCTACCGGTGATACCCGCGGGCAGTGCGG 3 15 0 CGGGAACCGG 0.901033 -260 GTGACTCCCTCGGCGAGCGGCATGGCCTACCGGT 3 35 0 CGGGACGCAG 0.973115 -240 AGGGAGTCACCGGCGAGGGTCGCGACACCCAGTC 3 59 1 CGGGAGGCGG 0.993646 -216 TCGTCGCCGACGGGGCGGGACTGGGTGTCGCGAC 3 77 0 CGGGCGGCTG 0.994836 -198 CCCGCCCCGTCGGCGACGACCTCGACCTCACCCG 3 92 1 CGGGAGACTG 0.951237 -183 CCATTGATAAGGCAGCACGATTGGTTATTCCTAA 3 155 0 GGCGCCGTTG 0.974717 -120 CCTTATCAATGGCTGCTCGCTTAGGCTGGCTGGC 3 177 1 GGCGCCGTTG 0.974711 -98 ATTATCTTGCCGCAGTTCCGTTCGCGGCAACTGC 3 209 0 CGCGTCCTTG 0.902511 -66 AATCGTGCATGGGCGTCGATTGGGAGTC 3 257 1 GGGGTGATGG 0.88661 -18 *** ** ** ** * Masking position 5 Map Score: 14.4843 Number of sites scoring better than the average of aligned sites = 940 Number in coding regions = 878 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TATCCACACCAAAAAGTGGATAACTTGTGA 1 96 1 AAAAAGTGGA 0.854002 -205 GATTGTCGAAAAAAATCGAACTTGCGCCTA 1 246 0 AAAAATCGAA 0.985383 -55 TGAAAGAAAGAAAAAGGGAAGGGTGCGGGT 1 280 1 AAAAAGGGAA 0.959531 -21 GAACATTTGTAAAAATGGAAGAAAACATCG 2 17 1 AAAAATGGAA 0.972402 -284 AAATGGAAGAAAACATCGGAGGATTTGAAC 2 29 1 AAACATCGGA 0.968279 -272 CTTGTGAAGAACACATCGAAACGGTGCTGG 2 78 1 ACACATCGAA 0.933147 -223 CCGAAATCAGAAAAATCGAACATACTAACA 2 138 1 AAAAATCGAA 0.985383 -163 ********** Masking position 5 Map Score: 7.96407 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 353 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 ATGCATATAAGAACAATCGTTCTGTTATCC 1 71 1 GAACAATCGT 0.99112 -230 AGAAGAGAACATTTGTAAAAATGGAA 2 7 1 GAACATTTGT 0.902479 -294 TTTGAACATGAAACAAGCGTATTATTCTTG 2 52 1 AAACAAGCGT 0.932379 -249 TTTTGTGTAAGATCATTCGTTCCCCACTAT 2 213 0 GATCATTCGT 0.959474 -88 GCTTAGGAATAACCAATCGTGCTGCCTTAT 3 153 1 AACCAATCGT 0.976027 -122 CCAGTAAGCTGGCCAATCGTGCATGGGCGT 3 243 1 GGCCAATCGT 0.977805 -32 ********** Masking position 5 Map Score: 4.41592 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 126 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 GTGTTTATAATTTGTCTAAAGAGTGATGTA 1 131 1 TTTGTCTAAA 0.971644 -170 GAGTGGATAGTGTGTGTAAATTTATCCACA 1 165 1 TGTGTGTAAA 0.926689 -136 AAACCCAATTTTTGTCGAAATTTTTTTGCT 1 205 1 TTTGTCGAAA 0.981676 -96 TTTCAAAATGATTGTCGAAAAAAATCGAAC 1 255 0 ATTGTCGAAA 0.966846 -46 TTTTCTGTATTTTGTGTAAGATCATTCGTT 2 222 0 TTTGTGTAAG 0.926769 -79 GATATCCACAATTGTGGACAACATATATGA 2 252 1 ATTGTGGACA 0.914293 -49 ********** Masking position 5 Map Score: 2.924 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 75 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 6 GTAGATTAAAGATAACTTCAACCTCAGATG 1 35 0 GATAACTTCA 0.922266 -266 CCAAAAAGTGGATAACTTGTGAGTATCGTG 1 104 1 GATAACTTGT 0.983427 -197 ACCAGGTGTGGATAAATTTACACACACTAT 1 171 0 GATAAATTTA 0.82668 -130 CAGGCTGTGGGATAAACTGTTAGTATGTTC 2 155 0 GATAAACTGT 0.879977 -146 CACAATTGTGGATATCTTTTCTGTATTTTG 2 238 0 GATATCTTTT 0.86661 -63 AACATATATGAATAACTTGTTTTTAAAGTG 2 271 1 AATAACTTGT 0.901769 -30 ********** Masking position 4 Map Score: 0.431524 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 202 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TTCGACAAAAATTGGGTTTCTTCACCAGGT 1 194 0 ATTGGGTTTC 0.968516 -107 ACGGGGCGGGACTGGGTGTCGCGACCCTCG 3 72 0 ACTGGGTGTC 0.990359 -203 GCCAATCGTGCATGGGCGTCGATTGGGAGT 3 254 1 CATGGGCGTC 0.971566 -21 ATGGGCGTCGATTGGGAGTC 3 265 1 ATTGGGAGTC 0.985777 -10 ********** Masking position 3 Map Score: 0.403772 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 35 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 8 ATTAAAGATAACTTCAACCTCAGATGAATG 1 31 0 ACTTCAACCT 0.678022 -270 AACCCGCACCCTTCCCTTTTTC 1 289 0 CCCGCACCCT 0.979092 -12 TACATAGACGACCACGAGCTGCCGCCCGAA 2 113 1 ACCACGAGCT 0.895342 -188 AACAGTTTATCCCACAGCCTGTGAATTATG 2 164 1 CCCACAGCCT 0.968036 -137 CACTATATATACTGCGGGGTCTCCACATAA 2 189 0 ACTGCGGGGT 0.824876 -112 ACCGGTGATACCCGCGGGCAGTGCGGCGCG 3 11 0 CCCGCGGGCA 0.973873 -264 GCCGGTGACTCCCTCGGCGAGCGGCATGGC 3 43 0 CCCTCGGCGA 0.947535 -232 GACACCCAGTCCCGCCCCGTCGGCGACGAC 3 82 1 CCCGCCCCGT 0.933691 -193 GTCGGCGACGACCTCGACCTCACCCGGAAC 3 100 1 ACCTCGACCT 0.960939 -175 ********** Masking position 5 Map Score: 3.48452 Number of sites scoring better than the average of aligned sites = 1249 Number in coding regions = 1111 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 9 ********** No masking Map Score: -1.80235e-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 10 ********** No masking Map Score: -1.80235e-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 11 ********** No masking Map Score: -1.80235e-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