AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_bsub_reg_300.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 yfnI 300 alternate gene name: yetP; similar to hypothetical proteins #2 yfnH 235 similar to glucose-1-phosphate cytidylyltransferase #3 spsI 24 alternate gene name: ipa-71d #4 spsA 300 alternate gene name: ipa-63d Motif number 1 TAGCAAAAACGAAAAATAGGTTTTGCAGACAG 1 11 0 GAAAAAAGGT 0.96851 -290 CACACATGACAAAAGAAATCCTTTTTTTATTT 1 88 1 AAAAGAATCT 0.85398 -213 TTATTTCCGAGAAAAAAATGTGAAACGAAATG 1 114 1 GAAAAAATGG 0.863264 -187 ATCACTGGACGAAAGAAACCTTCATTTCGTTT 1 136 0 GAAAGAACCT 0.932657 -165 GATGAAAAAGAGCCTTGAGCGGGCG 2 4 1 GAAAAAAGCT 0.991381 -232 TGTATAACCAAAAAAAGAGCCTTGAGCGAAGG 2 41 0 AAAAAAAGCT 0.966091 -195 AACCAACTTGAAAAAATAGATTCCATTTGGTC 2 72 1 AAAAAAAGAT 0.736364 -164 TGATATGAGAGAAAGCCAGCCTTGGTGACCAA 2 98 0 GAAAGCAGCT 0.965094 -138 ACCTCCGATGGAAAACGATCTTAGTCGCTGGT 4 64 1 GAAAACATCT 0.93535 -237 GGATTATGCTGAAAAAGAACAGCGGACCGATC 4 134 1 GAAAAAAACG 0.903328 -167 GTATGTTTCTGAAAAACAGCGGCTGCCCAGAG 4 174 0 GAAAAAAGCG 0.986309 -127 ****** *** * Masking position 8 Map Score: 11.887 Number of sites scoring better than the average of aligned sites = 1570 Number in coding regions = 1339 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 2 GTTGTGTGATGCCTTGATTTTGTTTGGAAA 1 243 1 GCCTTGATTT 0.925153 -58 ATGAAAAAGAGCCTTGAGCGGGCGCATTGC 2 12 1 GCCTTGAGCG 0.998266 -224 CAAAAAAAGAGCCTTGAGCGAAGGCAATGC 2 35 0 GCCTTGAGCG 0.998266 -201 TCGGGGAAATGCCTTGATAGATTGTGAAGA 2 171 1 GCCTTGATAG 0.984734 -65 AACAGCGGCTGCCCAGAGCGAAATCTGATC 4 162 0 GCCCAGAGCG 0.98751 -139 ********** Masking position 7 Map Score: 7.2105 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 49 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 CTGTCTGCAAAACCTATTTTT 1 1 1 CTGCTGCAAA 0.876498 -300 GTATCTATTTCTTTTTTCAAAGGCACACATG 1 65 1 CTTTTTCAAA 0.924459 -236 CGTCCAGTGATTGGTTTCCAAATGGTTGTAA 1 157 1 TTGTTTCCAA 0.950037 -144 CTTCCAATTCCTTCTTTCCAAACAAAATCAA 1 256 0 CTTTTTCCAA 0.951007 -45 TCTTTATATCCTGCCTTCCAATTCCTTCTTT 1 270 0 CTGCTTCCAA 0.979663 -31 CGATTTCAATCCGGTTTCAAAATCTACTGTA 2 131 0 CCGTTTCAAA 0.983849 -105 GATAATTTGTCCGATTTCAATCCGGTTTCAA 2 142 0 CCGTTTCAAT 0.950617 -94 GAAGATGTACCAGGTTTCGAACTCAATATTC 2 196 1 CAGTTTCGAA 0.873529 -40 GCGACTAAGATCGTTTTCCATCGGAGGTGAG 4 61 0 TCGTTTCCAT 0.857396 -240 *** ******* Masking position 6 Map Score: 6.80324 Number of sites scoring better than the average of aligned sites = 766 Number in coding regions = 687 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 ACATAAACTAGCAAAAACGAAAAATAGGTTTTGC 1 17 0 GCAAACAAAA 0.965146 -284 TAGATACCGAGTATAAGAATAACATAAACTAGCA 1 38 0 GTATAATAAA 0.592104 -263 TTTGAAAAAAGAAATAGATACCGAGTATAAGAAT 1 52 0 GAAAAAACCA 0.803749 -249 TTTTTTCTCGGAAATAAAAAAAGGATTTCTTTTG 1 97 0 GAAAAAAAAG 0.71148 -204 ATGATATGGTGCGAAACATAAATATTCCGGCTTG 1 193 1 GCGAAAAAAA 0.852473 -108 CAAAATCAAGGCATCACACAACAATAAATACACC 1 231 0 GCATAAAACA 0.907552 -70 GAATTGGAAGGCAGGATATAAAGAGCAGGTAAAT 1 277 1 GCAGAAAAAA 0.91195 -24 CAAGTTGGTTGTATAACCAAAAAAAGAGCCTTGA 2 48 0 GTATACAAAA 0.842019 -188 CTCATAAGGTGAAAGAGATAAAAATCGCACCAGC 4 90 0 GAAAAAAAAA 0.934916 -211 CATAATCCAAGCATCAGCCTCATAAGGTGAAAGA 4 108 0 GCATACTCAA 0.811148 -193 CTGTTTTTCAGAAACATACACAAACTTTTCGCAT 4 187 1 GAAAAAACAA 0.92198 -114 CGCAACTTGAGCATAAGCAACATAAGATAACGAT 4 239 1 GCATACACAA 0.950422 -62 **** * * *** * Masking position 6 Map Score: 4.31729 Number of sites scoring better than the average of aligned sites = 1319 Number in coding regions = 1057 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 260 Fraction of orfs with sites within 600 bp upstream = 0.0417604 Motif number 5 TCCTGCCTTCCAATTCCTTCTTTCCAAACA 1 263 0 CAATTCCTTC 0.976273 -38 GCTCTTTATATCCTGCCTTCCAATTCCTTC 1 273 0 TCCTGCCTTC 0.938419 -28 TGAGCGGGCGCATTGCCTTCGCTCAAGGCT 2 26 1 CATTGCCTTC 0.977976 -210 ATTAACACTTCCTTACATGCATTT 3 10 0 CACTTCCTTA 0.969074 -15 ATCCTACACCTCCTTCTTGGAACTTC 4 285 0 CACCTCCTTC 0.986607 -16 ********** Masking position 8 Map Score: 1.93726 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 318 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 AATGTGAAACGAAATGAAGGTTTCTTTCGT 1 130 1 GAAATGAAGG 0.95251 -171 CTACTGTAATGATATGAGAGAAAGCCAGCC 2 109 0 GATATGAGAG 0.908322 -127 AATATTCATAGAGATGAGGGGTAGAG 2 220 1 GAGATGAGGG 0.985089 -16 ACATGTTCTGGATGTATAGGTGAACGCTCC 4 24 1 GATGTATAGG 0.821782 -277 TCAGCCTCATAAGGTGAAAGAGATAAAAAT 4 99 0 AAGGTGAAAG 0.867552 -202 TTCCAAGAAGGAGGTGTAGGAT 4 289 1 GAGGTGTAGG 0.985328 -12 ********** Masking position 5 Map Score: 0.200568 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 511 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 7 ********** No masking Map Score: -3.30951e-14 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 8 ********** No masking Map Score: -3.30951e-14 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: -3.30951e-14 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