AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i263_bsub_mtub_100.orf -o263_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 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 0.995502 -217 CACACCAAAAAGTGGATAACTTGTGAGTAT 1 100 1 AGTGGATAAC 0.980231 -201 GTGGATAACTTGTGAGTATCGTGTTTATAA 1 111 1 TGTGAGTATC 0.859904 -190 CTTCACCAGGTGTGGATAAATTTACACACA 1 175 0 TGTGGATAAA 0.940754 -126 GTATTATTCTTGTGAAGAACACATCGAAAC 2 70 1 TGTGAAGAAC 0.978121 -231 CTGTGAATTATGTGGAGACCCCGCAGTATA 2 182 1 TGTGGAGACC 0.966562 -119 CAGTATATATAGTGGGGAACGAATGATCTT 2 205 1 AGTGGGGAAC 0.914987 -96 TGTCCACAATTGTGGATATCTTTTCTGTAT 2 242 0 TGTGGATATC 0.982114 -59 TATCCACAATTGTGGACAACATATATGAAT 2 254 1 TGTGGACAAC 0.981026 -47 GGACAACATATATGAATAACTTGTTTTTAA 2 267 1 TATGAATAAC 0.908403 -34 GTTTTTAAAGTGGGGATGACCT 2 289 1 TGGGGATGAC 0.929411 -12 CGCAAAGGCTTAGGAATAACCAATCGTGCT 3 146 1 TAGGAATAAC 0.774628 -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 CGTCTATGTACATATCCAGCACCGTTTCGATGTG 2 89 0 CTACCGCCCG 0.975328 -212 CATAGACGACCACGAGCTGCCGCCCGAAATCAGA 2 115 1 CCGGCGCGCC 0.986667 -186 CGCGCCGCACTGCCCGCGGGTATC 3 1 1 CCGCGACGCC 0.977952 -274 CCGCACTGCCCGCGGGTATCACCGGTAGGCCATG 3 15 1 CCGGTTCCCG 0.903612 -260 ACCGGTAGGCCATGCCGCTCGCCGAGGGAGTCAC 3 35 1 CTGCGTCCCG 0.97387 -240 GACTGGGTGTCGCGACCCTCGCCGGTGACTCCCT 3 59 0 CCGCCTCCCG 0.993824 -216 GTCGCGACACCCAGTCCCGCCCCGTCGGCGACGA 3 77 1 CAGCCGCCCG 0.994981 -198 CGGGTGAGGTCGAGGTCGTCGCCGACGGGGCGGG 3 92 0 CAGTCTCCCG 0.952573 -183 TTAGGAATAACCAATCGTGCTGCCTTATCAATGG 3 155 1 CAACGGCGCC 0.975429 -120 GCCAGCCAGCCTAAGCGAGCAGCCATTGATAAGG 3 177 0 CAACGGCGCC 0.975423 -98 GCAGTTGCCGCGAACGGAACTGCGGCAAGATAAT 3 209 1 CAAGGACGCG 0.905055 -66 GACTCCCAATCGACGCCCATGCACGATT 3 257 0 CCATCACCCC 0.88952 -18 * ** ** ** *** Masking position 10 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 0.85881 -205 GATTGTCGAAAAAAATCGAACTTGCGCCTA 1 246 0 AAAAATCGAA 0.985936 -55 TGAAAGAAAGAAAAAGGGAAGGGTGCGGGT 1 280 1 AAAAAGGGAA 0.961022 -21 GAACATTTGTAAAAATGGAAGAAAACATCG 2 17 1 AAAAATGGAA 0.973433 -284 AAATGGAAGAAAACATCGGAGGATTTGAAC 2 29 1 AAACATCGGA 0.969459 -272 CTTGTGAAGAACACATCGAAACGGTGCTGG 2 78 1 ACACATCGAA 0.935546 -223 CCGAAATCAGAAAAATCGAACATACTAACA 2 138 1 AAAAATCGAA 0.985936 -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 GGATAACAGAACGATTGTTCTTATATGCAT 1 71 0 ACGATTGTTC 0.991518 -230 TTCCATTTTTACAAATGTTCTCTTCT 2 7 0 ACAAATGTTC 0.906474 -294 CAAGAATAATACGCTTGTTTCATGTTCAAA 2 52 0 ACGCTTGTTT 0.935237 -249 ATAGTGGGGAACGAATGATCTTACACAAAA 2 213 1 ACGAATGATC 0.961235 -88 ATAAGGCAGCACGATTGGTTATTCCTAAGC 3 153 0 ACGATTGGTT 0.977085 -122 ACGCCCATGCACGATTGGCCAGCTTACTGG 3 243 0 ACGATTGGCC 0.978787 -32 ********** Masking position 6 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 TACATCACTCTTTAGACAAATTATAAACAC 1 131 0 TTTAGACAAA 0.969812 -170 TGTGGATAAATTTACACACACTATCCACTC 1 165 0 TTTACACACA 0.92211 -136 AGCAAAAAAATTTCGACAAAAATTGGGTTT 1 205 0 TTTCGACAAA 0.980493 -96 GTTCGATTTTTTTCGACAATCATTTTGAAA 1 255 1 TTTCGACAAT 0.964676 -46 AACGAATGATCTTACACAAAATACAGAAAA 2 222 1 CTTACACAAA 0.922184 -79 TCATATATGTTGTCCACAATTGTGGATATC 2 252 0 TGTCCACAAT 0.909003 -49 ********** Masking position 6 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 TTCGACAAAAATTGGGTTTCTTCACCAGGT 1 194 0 ATTGGGTTTC 0.969951 -107 ACGGGGCGGGACTGGGTGTCGCGACCCTCG 3 72 0 ACTGGGTGTC 0.990808 -203 GCCAATCGTGCATGGGCGTCGATTGGGAGT 3 254 1 CATGGGCGTC 0.972866 -21 ATGGGCGTCGATTGGGAGTC 3 265 1 ATTGGGAGTC 0.986437 -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 7 GTAGATTAAAGATAACTTCAACCTCAGATG 1 35 0 GATAACTTCA 0.925701 -266 CCAAAAAGTGGATAACTTGTGAGTATCGTG 1 104 1 GATAACTTGT 0.984206 -197 ACCAGGTGTGGATAAATTTACACACACTAT 1 171 0 GATAAATTTA 0.833576 -130 CAGGCTGTGGGATAAACTGTTAGTATGTTC 2 155 0 GATAAACTGT 0.885047 -146 CACAATTGTGGATATCTTTTCTGTATTTTG 2 238 0 GATATCTTTT 0.872162 -63 AACATATATGAATAACTTGTTTTTAAAGTG 2 271 1 AATAACTTGT 0.906017 -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 8 ATTAAAGATAACTTCAACCTCAGATGAATG 1 31 0 ACTTCAACCT 0.677245 -270 AACCCGCACCCTTCCCTTTTTC 1 289 0 CCCGCACCCT 0.979019 -12 TACATAGACGACCACGAGCTGCCGCCCGAA 2 113 1 ACCACGAGCT 0.89509 -188 AACAGTTTATCCCACAGCCTGTGAATTATG 2 164 1 CCCACAGCCT 0.967925 -137 CACTATATATACTGCGGGGTCTCCACATAA 2 189 0 ACTGCGGGGT 0.824575 -112 ACCGGTGATACCCGCGGGCAGTGCGGCGCG 3 11 0 CCCGCGGGCA 0.973782 -264 GCCGGTGACTCCCTCGGCGAGCGGCATGGC 3 43 0 CCCTCGGCGA 0.947359 -232 GACACCCAGTCCCGCCCCGTCGGCGACGAC 3 82 1 CCCGCCCCGT 0.933473 -193 GTCGGCGACGACCTCGACCTCACCCGGAAC 3 100 1 ACCTCGACCT 0.960831 -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