AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i169_bsub_mtub_100.orf -o169_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 cysH 300 phosphoadenosine phosphosulfate #2 nirA 300 nirA Motif number 1 ATAGGTCCAGTCCCTCAGCCGCTCTTGATAAG 1 46 0 TCTCAGCCGC 0.985348 -255 TACAAACTATGCAGGTTGCCGGGCTTCATAGG 1 73 0 GCGTTGCCGG 0.984387 -228 AAAATGGAATTCATTTTGCTGGAAGTAGCACC 1 106 0 TCTTTGCTGG 0.958785 -195 TTCCTGTCTTTCTTTCCGCCGGATTGAAAGTT 1 160 1 TCTCCGCCGG 0.996331 -141 ACAAACAGTAGCTTTCTGCCGGTTGTCTTTTC 1 253 0 GCTCTGCCGG 0.986505 -48 TTTGACCAGGTCGCGCAGCTGCACGCCATCCA 2 72 1 TCGCAGCTGC 0.976694 -229 GGGCGCGGGTTCTTGGCGGCGGTCACGGTGAC 2 113 0 TCGGCGGCGG 0.994087 -188 GATTCGCAGATCGGGGCGCGGGTTCTTGGCGG 2 126 0 TCGGCGCGGG 0.993129 -175 GATCTGCGAATCGCGCTGGTGGCTCGGCGGCA 2 146 1 TCGCTGGTGG 0.978559 -155 CCGCTTGAGGTCGATGTGCCGCCGAGCCACCA 2 162 0 TCTGTGCCGC 0.98865 -139 GAGGGGCAGATCCGGTCGCCGGCTGCAGATAC 2 242 0 TCGTCGCCGG 0.995733 -59 CGCCGCTTGTTCCGGGAGGGGCAGATCCGGTC 2 257 0 TCGGAGGGGC 0.926705 -44 ** ******** Masking position 2 Map Score: 25.4363 Number of sites scoring better than the average of aligned sites = 1249 Number in coding regions = 1185 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 AACTTATCAAGAGCGGCTGAGGGACTGGAC 1 44 1 GAGCGGCTGA 0.950709 -257 GCAGGTTGCCGGGCTTCATAGGTCCAGTCC 1 65 0 GGGCTTCATA 0.926085 -236 TGAAAGATAAGGGCTGCATGCTGTTCCTGT 1 137 1 GGGCTGCATG 0.985018 -164 ACTTTCAATCCGGCGGAAAGAAAGACAGGA 1 161 0 CGGCGGAAAG 0.881719 -140 ATGTGATTCGCGGCTGCTGATATACAGATA 1 216 0 CGGCTGCTGA 0.990187 -85 CCAGGTCGCGCAGCTGCACGCCATCCATGG 2 77 1 CAGCTGCACG 0.97814 -224 GATCGGGGCGCGGGTTCTTGGCGGCGGTCA 2 120 0 CGGGTTCTTG 0.684308 -181 GCTGGTGGCTCGGCGGCACATCGACCTCAA 2 160 1 CGGCGGCACA 0.992843 -141 CCGACAGCCACAGCTGCAGACCCGCTTGAG 2 185 0 CAGCTGCAGA 0.989194 -116 GCTGGGTTTACGGCGTCAAGGCCGACAGCC 2 206 0 CGGCGTCAAG 0.958219 -95 ATCCGGTCGCCGGCTGCAGATACAGGTGGG 2 235 0 CGGCTGCAGA 0.996489 -66 CTTGTTCCGGGAGGGGCAGATCCGGTCGCC 2 254 0 GAGGGGCAGA 0.921007 -47 ********** Masking position 3 Map Score: 21.1464 Number of sites scoring better than the average of aligned sites = 3012 Number in coding regions = 2833 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 GAAAGAAAGACAGGAACAGCATGCAGCCCTTA 1 144 0 CGGAACGCAT 0.881183 -157 GTTCCTGTCTTTCTTTCCGCCGGATTGAAAGT 1 159 1 TCTTTCGCCG 0.870568 -142 AAGGCTATCTGTATATCAGCAGCCGCGAATCA 1 211 1 GATATCGCAG 0.851305 -90 AACAAACAGTAGCTTTCTGCCGGTTGTCTTTT 1 254 0 ACTTTCGCCG 0.870567 -47 CCGGGTCGGCCTATCCATCCAT 2 1 1 CGGGTCGCCT 0.981938 -300 CAGAATGTCACCGTGACCGCCGCCAAGAACCC 2 107 1 CGTGACGCCG 0.98282 -194 GAGCCACCAGCGCGATTCGCAGATCGGGGCGC 2 139 0 CCGATTGCAG 0.891801 -162 CCCGCTTGAGGTCGATGTGCCGCCGAGCCACC 2 163 0 GCGATGGCCG 0.947149 -138 TCGACCTCAAGCGGGTCTGCAGCTGTGGCTGT 2 180 1 GGGGTCGCAG 0.982767 -121 CTGCAGCTGTGGCTGTCGGCCTTGACGCCGTA 2 196 1 GCTGTCGCCT 0.958213 -105 CCCAGCCCACCTGTATCTGCAGCCGGCGACCG 2 230 1 CGTATCGCAG 0.986861 -71 CAGCCGGCGACCGGATCTGCCCCTCCCGGAAC 2 249 1 CGGATCGCCC 0.971506 -52 ACCTAGGACGCGCTAAACGCCGCTTGTTCCGG 2 274 0 CCTAAAGCCG 0.828123 -27 * ***** **** Masking position 10 Map Score: 12.478 Number of sites scoring better than the average of aligned sites = 3021 Number in coding regions = 2852 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 4 CCTATGAAGCCCGGCAACCTGCATAGTTTG 1 73 1 CCGGCAACCT 0.986711 -228 ACAGGAACAGCATGCAGCCCTTATCTTTCA 1 137 0 CATGCAGCCC 0.889449 -164 TGCTGATATACAGATAGCCTTTTTACCTCT 1 202 0 CAGATAGCCT 0.8122 -99 TACATGGGAAAAGACAACCGGCAGAAAGCT 1 246 1 AAGACAACCG 0.886282 -55 TCGGCCTATCCATCCATCCAGGCTTGTTGC 2 16 1 CATCCATCCA 0.858908 -285 GCGCAGCTGCACGCCATCCATGGCAGAATG 2 84 1 ACGCCATCCA 0.886812 -217 GGCGTCAAGGCCGACAGCCACAGCTGCAGA 2 195 0 CCGACAGCCA 0.982741 -106 GCCGTAAACCCAGCCCACCTGTATCTGCAG 2 222 1 CAGCCCACCT 0.938721 -79 GTATCTGCAGCCGGCGACCGGATCTGCCCC 2 242 1 CCGGCGACCG 0.95506 -59 ********** Masking position 8 Map Score: 2.74861 Number of sites scoring better than the average of aligned sites = 2270 Number in coding regions = 2116 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 5 ********** No masking Map Score: 1.30983e-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 6 ********** No masking Map Score: 1.30983e-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 7 ********** No masking Map Score: 1.30983e-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