AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yfnH 235 similar to glucose-1-phosphate cytidylyltransferase #2 spsI 24 alternate gene name: ipa-71d #3 spsA 300 alternate gene name: ipa-63d Motif number 1 CCCGCTCAAGGCTCTTTTTCATC 1 4 0 GCTCTTTTTC 0.99535 -232 TTCGCTCAAGGCTCTTTTTTTGGTTATACA 1 43 1 GCTCTTTTTT 0.959848 -193 GGTCACCAAGGCTGGCTTTCTCTCATATCA 1 100 1 GCTGGCTTTC 0.976749 -136 CAGCGACTAAGATCGTTTTCCATCGGAGGT 3 64 0 GATCGTTTTC 0.990227 -237 GTGCGATTTTTATCTCTTTCACCTTATGAG 3 94 1 TATCTCTTTC 0.930674 -207 TCGGTCCGCTGTTCTTTTTCAGCATAATCC 3 134 0 GTTCTTTTTC 0.976203 -167 CTGGGCAGCCGCTGTTTTTCAGAAACATAC 3 176 1 GCTGTTTTTC 0.986969 -125 CACCTGAAACTATCGTTATCTTATGTTGCT 3 254 0 TATCGTTATC 0.806348 -47 ********** Masking position 7 Map Score: 11.5352 Number of sites scoring better than the average of aligned sites = 1320 Number in coding regions = 1181 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 GCAATGCGCCCGCTCAAGGCTCTTTTTCAT 1 12 0 CGCTCAAGGC 0.999011 -224 GCATTGCCTTCGCTCAAGGCTCTTTTTTTG 1 35 1 CGCTCAAGGC 0.999011 -201 TCTTCACAATCTATCAAGGCATTTCCCCGA 1 171 0 CTATCAAGGC 0.984993 -65 GATCAGATTTCGCTCTGGGCAGCCGCTGTT 3 162 1 CGCTCTGGGC 0.995858 -139 ********** Masking position 4 Map Score: 8.41692 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 7 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 3 CAGTAGATTTTGAAACCGGATTGAAATCGG 1 133 1 TGAAACCGGA 0.9898 -103 GAAACCGGATTGAAATCGGACAAATTATCG 1 144 1 TGAAATCGGA 0.977079 -92 ATATTGAGTTCGAAACCTGGTACATCTTCA 1 195 0 CGAAACCTGG 0.98914 -41 CTGCCCAGAGCGAAATCTGATCGGTCCGCT 3 154 0 CGAAATCTGA 0.988748 -147 GTATCCCTAGCGCAACTTGAGCATAAGCAA 3 229 1 CGCAACTTGA 0.945702 -72 ********** Masking position 5 Map Score: 4.20946 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 133 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 GATGAAAAAGAGCCTTGAGCGGGCGCA 1 8 1 AAGAGCCTTG 0.996071 -228 TAACCAAAAAAAGAGCCTTGAGCGAAGGCA 1 39 0 AAGAGCCTTG 0.996071 -197 ATGAGAGAAAGCCAGCCTTGGTGACCAAAT 1 96 0 GCCAGCCTTG 0.979969 -140 ATTATCGGGGAAATGCCTTGATAGATTGTG 1 167 1 AAATGCCTTG 0.972669 -69 ********** Masking position 8 Map Score: 3.86031 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 29 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 TTCCCCGATAATTTGTCCGATTTCAATCCG 1 149 0 ATTTGTCCGA 0.898976 -87 CTTTCACCTTATGAGGCTGATGCTTGGATT 3 109 1 ATGAGGCTGA 0.985912 -192 TGATGCTTGGATTATGCTGAAAAAGAACAG 3 126 1 ATTATGCTGA 0.966413 -175 AAGTTTGTGTATGTTTCTGAAAAACAGCGG 3 184 0 ATGTTTCTGA 0.97632 -117 TCGTTATCTTATGTTGCTTATGCTCAAGTT 3 242 0 ATGTTGCTTA 0.946811 -59 ********** Masking position 2 Map Score: 1.53893 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 571 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 ATTTTTTCAAGTTGGTTGTATAACCAAAAAA 1 58 0 GTGGTTGTAT 0.80172 -178 AACGATCTTAGTCGCTGGTGCGATTTTTATC 3 77 1 GTGCTGGTGC 0.995608 -224 TTCACCTTATGAGGCTGATGCTTGGATTATG 3 111 1 GAGCTGATGC 0.976711 -190 GTTATCTTATGTTGCTTATGCTCAAGTTGCG 3 239 0 GTGCTTATGC 0.963707 -62 GATAACGATAGTTTCAGGTGTGAAGTTCCAA 3 264 1 GTTCAGGTGT 0.9246 -37 GAAGTTCCAAGAAGGAGGTGTAGGAT 3 285 1 GAGGAGGTGT 0.956931 -16 ** ******** Masking position 9 Map Score: 0.762248 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 746 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 7 TACAACCAACTTGAAAAAATAGATTCCATT 1 69 1 TTGAAAAAAT 0.797124 -167 TCAATCCGGTTTCAAAATCTACTGTAATGA 1 127 0 TTCAAAATCT 0.980663 -109 CTGGTACATCTTCACAATCTATCAAGGCAT 1 179 0 TTCACAATCT 0.976768 -57 GAATATTGAGTTCGAAACCTGGTACATCTT 1 197 0 TTCGAAACCT 0.966311 -39 AAAACCATTCAAAACATGTTCTGGATG 3 8 1 TTCAAAACAT 0.963645 -293 TTCAGAAACATACACAAACTTTTCGCATAT 3 193 1 TACACAAACT 0.912068 -108 ********** Masking position 6 Map Score: 2.6489 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 298 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 ********** No masking Map Score: 1.48747e-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 9 ********** No masking Map Score: 1.48747e-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: 1.48747e-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