AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -icpxR_aful_opreg_100.orf -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 AF1045 86 methyl-accepting chemotaxis protein (tlpC-2) #2 AF1049 102 type II secretion system protein (gspE-4) #3 AF1351 238 ISA1083-2, ISORF2 #4 AF1354 68 membrane protein, putative #5 AF2013 275 coenzyme F390 synthetase (ftsA-3) #6 AF2014 63 sugar transporter, putative Motif number 1 CTTTATAGAGAAAATTTTATTTTTTATTTT 1 44 1 AAAATTTTAT 0.929929 -43 AAAAATCCATAACATTTAAACCCTACGAAT 3 58 0 AACATTTAAA 0.891468 -181 AGTTAAATGCAACATTTTAATAAAATATTA 3 111 1 AACATTTTAA 0.953749 -128 ACATTTTAATAAAATATTATGAAAACTCAA 3 122 1 AAAATATTAT 0.630548 -117 GGCTTTTGTGAAAATTTTAAAAGGACACAT 3 159 0 AAAATTTTAA 0.941209 -80 TCCTGAGCAAAACTATTTATACTATAGATA 3 206 1 AACTATTTAT 0.853294 -33 TGATGGTAACAAAAATTAAA 4 1 0 AAAAATTAAA 0.842975 -68 TTTTATGCTTAACTATTTATACCCCCATGT 4 43 1 AACTATTTAT 0.853294 -26 CAGGATGGTGAAGTATTTAAATCCTGCCTC 5 229 1 AAGTATTTAA 0.783211 -47 TAAAAAGCTAAAAATTTTATGCAAATAAAT 6 29 0 AAAATTTTAT 0.929929 -35 GGAAATTTAAAGAATTAAAAAGCTAAAAA 6 45 0 AAGAATTAAA 0.783211 -19 ********** Masking position 2 Map Score: 9.51367 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 106 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 2 TTTCGCAATCTACTTTCGGTGGTGTT 1 71 1 TCTTCGGTTG 0.992154 -16 TATTAACCTTTGCTTTCATTTTTGGGATTACACT 2 29 0 TCTTCATTTG 0.947783 -74 TAAATTCCCCTTCTGGCTTTTGTGAAAATTTTAA 3 169 0 TCTGCTTTTG 0.951318 -70 CATCATAAACTGCTATCTTTTATGCTTAACTATT 4 26 1 TCTTCTTTTG 0.98659 -43 TACTGCCAGATACTGTCTGAGCTGCAGTTCCAGA 5 31 0 TCTTCTGATG 0.975048 -245 AGCCTGGTGATCCTCTCGGCTTTGGGAGCCGGTG 5 123 0 TCTTCGGCTG 0.974983 -153 CTACCCTACGGCCCCTCTGTAATGATTAAAGGCA 5 155 1 GCCTCTGTTG 0.93896 -121 GATAAAGTGTATCTTTCTGTCATGAGGGAGGCAG 5 252 0 ACTTCTGTTG 0.975048 -24 * ** ***** ** Masking position 13 Map Score: 6.57233 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 80 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 ACTTATTTTAAGGTTTTCAAATTGTATGAAT 3 29 1 AGGTTTCAAA 0.962878 -210 ATGAATTCGTAGGGTTTAAATGTTATGGATT 3 54 1 AGGTTTAAAT 0.988024 -185 AAACAACATGGGGGTATAAATAGTTAAGCAT 4 47 0 GGGTATAAAT 0.918676 -22 TTGCAGCAAAAGGCTTTAAAAGCCACTGCCT 5 184 0 AGGTTTAAAA 0.982929 -92 TGAGGGAGGCAGGATTTAAATACTTCACCAT 5 233 0 AGGTTTAAAT 0.988024 -43 *** ******* Masking position 5 Map Score: 3.90801 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 13 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 TATTATAATGAAGGGGGGAGGAT 2 90 1 AAGGGGGAGG 0.994296 -13 ATTTTCACAAAAGCCAGAAGGGGAATTTATT 3 174 1 AAGCAGAAGG 0.946919 -65 AGTTCCAGAAAAGCTGACAGGTTGATTCT 5 9 0 AAGCGACAGG 0.991205 -267 CCGGCTCCCAAAGCCGAGAGGATCACCAGGC 5 125 1 AAGCGAGAGG 0.991205 -151 TTCTGTCATGAGGGAGGCAGGATTTAAATAC 5 241 0 AGGGGGCAGG 0.987426 -35 **** ****** Masking position 9 Map Score: 3.2793 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 126 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ACCCTACGAATTCATACAATTTGAAAACCT 3 39 0 TTCATACAAT 0.962444 -200 TCGCAAAAAATCCATAACATTTAAACCCTA 3 63 0 TCCATAACAT 0.914066 -176 AGCTTGAGTTTTCATAATATTTTATTAAAA 3 125 0 TTCATAATAT 0.955702 -114 AGCAAAACTATTTATACTATAGATAATAGA 3 211 1 TTTATACTAT 0.734532 -28 CAAATAAATATGCATAAAATGCACACT 6 8 0 TGCATAAAAT 0.970907 -56 CATATTTATTTGCATAAAATTTTTAGCTTT 6 26 1 TGCATAAAAT 0.970907 -38 ********** Masking position 5 Map Score: 2.93529 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 45 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 6 TTTTCTTATTCGAAATTTTACTTTATAGAG 1 24 1 CGAAATTTTA 0.922421 -63 AAGTAGATTGCGAAAATAAAAAATAAAATT 1 56 0 CGAAAATAAA 0.935017 -31 AACACCACCGAAAGTAGATTGCGAAAAT 1 69 0 CGAAAGTAGA 0.813493 -18 GGATTTTTTGCGACAATTAATCGTAGATAT 3 80 1 CGACAATTAA 0.96414 -159 TAGTTAAATGCAACATTTTAATAAAATATT 3 110 1 CAACATTTTA 0.69721 -129 GTTTTGCTCAGGACAATAAATTCCCCTTCT 3 189 0 GGACAATAAA 0.811171 -50 ATGATGGTAACAAAAATTAAA 4 2 0 CAAAAATTAA 0.843774 -67 ATGGGGCCGCCGAGATTTGAACTCGGGTCA 5 95 1 CGAGATTTGA 0.870951 -181 GGAAATTTAAAGAATTAAAA 6 54 0 GGAAATTTAA 0.893071 -10 ********** Masking position 5 Map Score: 2.82136 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 187 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 TTACACTGCACCTTGTGACCAAAGG 2 6 0 CCTTGTGACC 0.981269 -97 GAGTTCAAATCTCGGCGGCCCCATCATTGA 5 89 0 CTCGGCGGCC 0.983428 -187 GGCTTTGGGAGCCGGTGACCCGAGTTCAAA 5 110 0 GCCGGTGACC 0.986902 -166 CGTAGGGTAGCCTGGTGATCCTCTCGGCTT 5 135 0 CCTGGTGATC 0.957662 -141 CACCAGGCTACCCTACGGCCCCTCTGTAAT 5 148 1 CCCTACGGCC 0.963438 -128 ********** Masking position 7 Map Score: 0.332335 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 112 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 ********** No masking Map Score: -9.49695e-13 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: -9.49695e-13 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: -9.49695e-13 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