AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i147_bsub_mtub_300.orf -o147_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 cysH 300 phosphoadenosine phosphosulfate #2 nirA 300 nirA Motif number 1 ATAGGTCCAGTCCCTCAGCCGCTCTTGATAAG 1 46 0 TCTCAGCCGC 0.985297 -255 TACAAACTATGCAGGTTGCCGGGCTTCATAGG 1 73 0 GCGTTGCCGG 0.984334 -228 AAAATGGAATTCATTTTGCTGGAAGTAGCACC 1 106 0 TCTTTGCTGG 0.958648 -195 TTCCTGTCTTTCTTTCCGCCGGATTGAAAGTT 1 160 1 TCTCCGCCGG 0.996318 -141 ACAAACAGTAGCTTTCTGCCGGTTGTCTTTTC 1 253 0 GCTCTGCCGG 0.986458 -48 TTTGACCAGGTCGCGCAGCTGCACGCCATCCA 2 72 1 TCGCAGCTGC 0.976615 -229 GGGCGCGGGTTCTTGGCGGCGGTCACGGTGAC 2 113 0 TCGGCGGCGG 0.994066 -188 GATTCGCAGATCGGGGCGCGGGTTCTTGGCGG 2 126 0 TCGGCGCGGG 0.993106 -175 GATCTGCGAATCGCGCTGGTGGCTCGGCGGCA 2 146 1 TCGCTGGTGG 0.978485 -155 CCGCTTGAGGTCGATGTGCCGCCGAGCCACCA 2 162 0 TCTGTGCCGC 0.988611 -139 GAGGGGCAGATCCGGTCGCCGGCTGCAGATAC 2 242 0 TCGTCGCCGG 0.995719 -59 CGCCGCTTGTTCCGGGAGGGGCAGATCCGGTC 2 257 0 TCGGAGGGGC 0.926469 -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 0.947133 -257 GCAGGTTGCCGGGCTTCATAGGTCCAGTCC 1 65 0 GGGCTTCATA 0.92087 -236 TGAAAGATAAGGGCTGCATGCTGTTCCTGT 1 137 1 GGGCTGCATG 0.983889 -164 ACTTTCAATCCGGCGGAAAGAAAGACAGGA 1 161 0 CGGCGGAAAG 0.873802 -140 ATGTGATTCGCGGCTGCTGATATACAGATA 1 216 0 CGGCTGCTGA 0.989443 -85 CCAGGTCGCGCAGCTGCACGCCATCCATGG 2 77 1 CAGCTGCACG 0.976504 -224 GATCGGGGCGCGGGTTCTTGGCGGCGGTCA 2 120 0 CGGGTTCTTG 0.668149 -181 GCTGGTGGCTCGGCGGCACATCGACCTCAA 2 160 1 CGGCGGCACA 0.992299 -141 CCGACAGCCACAGCTGCAGACCCGCTTGAG 2 185 0 CAGCTGCAGA 0.988376 -116 GCTGGGTTTACGGCGTCAAGGCCGACAGCC 2 206 0 CGGCGTCAAG 0.955162 -95 ATCCGGTCGCCGGCTGCAGATACAGGTGGG 2 235 0 CGGCTGCAGA 0.996221 -66 CTTGTTCCGGGAGGGGCAGATCCGGTCGCC 2 254 0 GAGGGGCAGA 0.915467 -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 0.876996 -157 GTTCCTGTCTTTCTTTCCGCCGGATTGAAAGT 1 159 1 TCTTTCGCCG 0.866064 -142 AAGGCTATCTGTATATCAGCAGCCGCGAATCA 1 211 1 GATATCGCAG 0.84625 -90 AACAAACAGTAGCTTTCTGCCGGTTGTCTTTT 1 254 0 ACTTTCGCCG 0.866063 -47 CCGGGTCGGCCTATCCATCCAT 2 1 1 CGGGTCGCCT 0.981226 -300 CAGAATGTCACCGTGACCGCCGCCAAGAACCC 2 107 1 CGTGACGCCG 0.982143 -194 GAGCCACCAGCGCGATTCGCAGATCGGGGCGC 2 139 0 CCGATTGCAG 0.887943 -162 CCCGCTTGAGGTCGATGTGCCGCCGAGCCACC 2 163 0 GCGATGGCCG 0.945142 -138 TCGACCTCAAGCGGGTCTGCAGCTGTGGCTGT 2 180 1 GGGGTCGCAG 0.982087 -121 CTGCAGCTGTGGCTGTCGGCCTTGACGCCGTA 2 196 1 GCTGTCGCCT 0.956607 -105 CCCAGCCCACCTGTATCTGCAGCCGGCGACCG 2 230 1 CGTATCGCAG 0.986349 -71 CAGCCGGCGACCGGATCTGCCCCTCCCGGAAC 2 249 1 CGGATCGCCC 0.970395 -52 ACCTAGGACGCGCTAAACGCCGCTTGTTCCGG 2 274 0 CCTAAAGCCG 0.82245 -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 CAAACTATGCAGGTTGCCGGGCTTCATAGG 1 73 0 AGGTTGCCGG 0.985756 -228 TGAAAGATAAGGGCTGCATGCTGTTCCTGT 1 137 1 GGGCTGCATG 0.882334 -164 AGAGGTAAAAAGGCTATCTGTATATCAGCA 1 202 1 AGGCTATCTG 0.801303 -99 AGCTTTCTGCCGGTTGTCTTTTCCCATGTA 1 246 0 CGGTTGTCTT 0.878998 -55 GCAACAAGCCTGGATGGATGGATAGGCCGA 2 16 0 TGGATGGATG 0.850158 -285 CATTCTGCCATGGATGGCGTGCAGCTGCGC 2 84 0 TGGATGGCGT 0.879555 -217 TCTGCAGCTGTGGCTGTCGGCCTTGACGCC 2 195 1 TGGCTGTCGG 0.981509 -106 CTGCAGATACAGGTGGGCTGGGTTTACGGC 2 222 0 AGGTGGGCTG 0.934545 -79 GGGGCAGATCCGGTCGCCGGCTGCAGATAC 2 242 0 CGGTCGCCGG 0.951951 -59 ********** Masking position 3 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