AlignACE version 2.2 July 7, 1998 alignACE -aORF_aful.txt -zaful.fna -icpxR_aful_opreg_300.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 AF1052 32 A. fulgidus predicted coding region AF1052 #4 AF1053 34 A. fulgidus predicted coding region AF1053 #5 AF1055 111 flagellin (flaB1-2) #6 AF1057 39 cytochrome C-type biogenesis protein (ccdA) #7 AF1058 293 A. fulgidus predicted coding region AF1058 #8 AF1351 238 ISA1083-2, ISORF2 #9 AF1354 68 membrane protein, putative #10 AF2009 101 heme biosynthesis protein (nirJ-2) #11 AF2010 46 A. fulgidus predicted coding region AF2010 #12 AF2011 175 conserved hypothetical protein #13 AF2013 275 coenzyme F390 synthetase (ftsA-3) #14 AF2014 63 sugar transporter, putative Motif number 1 TGCGAAAATAAAAAATAAAATTTTCTCTATAA 1 46 0 AAATAAAATT 0.757051 -41 AAATGAAAGCAAAGGTTAATAGCAACATCAGT 2 42 1 AAATTAATAG 0.708875 -61 TCACCTCTAAAAAATTAAAAATTTGGGGGA 4 9 0 AAATAAAAAT 0.969355 -26 CTCAAGCATAAAAATTGAAAAAGAA 6 25 0 AAGTAAAAAT 0.966478 -15 CTTCAGAGGGAAACCTTAATATAGTCTTGAAA 7 239 1 AAATTAATAT 0.841048 -55 AGAGTGCTGGAAATTTAAAAAGGGTGATTTGA 7 272 1 AAATAAAAAG 0.935833 -22 TACAATTTGAAAACCTTAAAATAAGTCAACAA 8 23 0 AAATTAAAAT 0.947588 -216 GCTTTTGTGAAAATTTTAAAAGGACACATATA 8 156 0 AAATTAAAAG 0.892704 -83 TTAGTTCCAAAAGGTTAAATATCTGGATGCAC 10 23 0 AAGTAAATAT 0.894006 -79 ACATGCTAACAAAAATAAAAATTTTACTATTT 11 16 0 AAATAAAAAT 0.969412 -31 TCTTTACTTCAAGTGTAAAAATTGAGTGCCCC 12 79 0 AAGTAAAAAT 0.966477 -97 GTCTTGTCGTAAGCTTAATAATAAGTTTTATA 12 129 1 AAGTAATAAT 0.739425 -47 CAGGATGGTGAAGTATTTAAATCCTGCCTCCC 13 229 1 AAGTTTAAAT 0.618099 -47 AAAGAATTAAAAAGCTAAAAATTTTATGCAAA 14 34 0 AAATAAAAAT 0.969418 -30 *** ******* Masking position 2 Map Score: 17.1733 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 65 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 2 AATTTCGAATAAGAAAATTCAGAAGTGTAA 1 11 0 AAGAAAATTC 0.832877 -76 TTCTCTATAAAGTAAAATTTCGAATAAGAA 1 26 0 AGTAAAATTT 0.871579 -61 GAAAATAAAAAATAAAATTTTCTCTATAAA 1 45 0 AATAAAATTT 0.955521 -42 TTCAACATATAAGAAAATTCTTATATATTG 5 49 1 AAGAAAATTC 0.832877 -63 CTCAAGCATAAAAATTGAAAAAGAAA 6 24 0 CATAAAAATT 0.809529 -16 TAAGGGAGTTCATAAAATTTTTTGAAACAT 7 24 1 CATAAAATTT 0.975573 -270 GTGAACAACCAATACAATTCAATGTTTCAA 7 45 0 AATACAATTC 0.832877 -249 CCTACGAATTCATACAATTTGAAAACCTTA 8 37 0 CATACAATTT 0.926566 -202 GCAAAAAATCCATAACATTTAAACCCTACG 8 61 0 CATAACATTT 0.872712 -178 CTTGAGTTTTCATAATATTTTATTAAAATG 8 123 0 CATAATATTT 0.822251 -116 GGCCTAAATAGTAAAATTTTTATTTTTGT 11 10 1 AGTAAAATTT 0.871579 -37 AATAAATATGCATAAAATGCACACT 14 6 0 CATAAAATGC 0.822238 -58 TATTTATTTGCATAAAATTTTTAGCTTTTT 14 28 1 CATAAAATTT 0.975573 -36 ********** Masking position 4 Map Score: 12.636 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 52 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 ATCCTCCCCCCTTCATTATAAT 2 91 0 TCCTCCCCCT 0.896314 -12 CCTCAGCGCAGCCGCTCTCACGGCC 3 5 0 GCCGCTCTCC 0.920639 -28 ATTTGAACCCGCGGCCTCCGCCTCGCGAAGG 7 106 1 GCGGCCTCCC 0.981498 -188 GCGGGAGAGCGCCGCCTTCGCGAGGCGGAGG 7 120 0 GCCGCCTTCC 0.975363 -174 GTGTGAGTTATACGGTTCCTCATTCAGGGAC 7 209 1 TACGGTTCCC 0.738678 -85 TTCAAATCTATCGGGCCCCTCCCTTAATC 12 9 0 TCGGGCCCCC 0.981202 -167 ATAACCTTCATCCGTCTCCTCGATGTTCAAA 12 34 0 TCCGTCTCCC 0.94852 -142 CGACAAGACTGCCTGCTCCTTTATCCTTCTT 12 107 0 GCCTGCTCCT 0.859142 -69 TCAAATCTCGGCGGCCCCATCATTGAACTGG 13 84 0 GCGGCCCCAC 0.902568 -192 CAGGCTACCCTACGGCCCCTCTGTAATGATT 13 151 1 TACGGCCCCC 0.972002 -125 AGTATTTAAATCCTGCCTCCCTCATGACAGA 13 240 1 TCCTGCCTCC 0.932882 -36 ********* * Masking position 9 Map Score: 8.9598 Number of sites scoring better than the average of aligned sites = 1259 Number in coding regions = 1195 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 CATGGACTCGGCGGGATTTGAACCCGCGGCCT 7 91 1 GGGGTTTGAA 0.958423 -203 TTTTGACCTCAGGGGTTATAAAGGTTTACGTC 7 173 1 AGGGTATAAA 0.900137 -121 TGACTTATTTTAAGGTTTTCAAATTGTATGAA 8 27 1 TAGGTTTCAA 0.805547 -212 GTATGAATTCGTAGGGTTTAAATGTTATGGAT 8 52 1 GAGGTTTAAA 0.98014 -187 CAAACAACATGGGGGTATAAATAGTTAAGCA 9 48 0 TGGGTATAAA 0.900137 -21 GGAGACGGATGAAGGTTATGTAGCTCAGGCAC 12 46 1 GAGGTATGTA 0.781465 -130 ATTTCGATGTGAAGGTTATAAAACTTATTATT 12 145 0 GAGGTATAAA 0.975645 -31 GTTTGCAGCAAAAGGCTTTAAAAGCCACTGCC 13 185 0 AAGGTTTAAA 0.930859 -91 CATGAGGGAGGCAGGATTTAAATACTTCACCA 13 234 0 GAGGTTTAAA 0.98014 -42 * *** ****** Masking position 7 Map Score: 6.4392 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 182 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 GCCGTGAGAGCGGCTGCGCTGAGGTATTAC 3 12 1 CGGCTGCGCT 0.956973 -21 CGGCGCTCTCCCGCTGAGCTACGAGCCCTT 7 137 1 CCGCTGAGCT 0.980941 -157 ACCTTTATAACCCCTGAGGTCAAAAAGGTT 7 168 0 CCCCTGAGGT 0.982782 -126 TAAAGGTTTACGTCTTAGGTGTGAGTTATA 7 191 1 CGTCTTAGGT 0.868333 -103 TTAAGGTTTCCCTCTGAAGTCCCTGAATGA 7 228 0 CCTCTGAAGT 0.892503 -66 TTATTCATTACGCCTGAATTGTTCCTATGT 10 64 0 CGCCTGAATT 0.842422 -38 AGTGCCCCAGTGCCTGAGCTACATAACCTT 12 57 0 TGCCTGAGCT 0.965396 -119 TGCCAGATACTGTCTGAGCTGCAGTTCCAG 13 32 0 TGTCTGAGCT 0.946645 -244 ********** Masking position 5 Map Score: 4.73089 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 261 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 AAAATAAAAAATAAAATTTTCTCTATAAAG 1 44 0 ATAAAATTTT 0.809641 -43 CTCTAAAAAATTAAAAATTTGGGGGA 4 7 0 TTAAAAATTT 0.868326 -28 TTAGCAATATATAAGAATTTTCTTATATGT 5 53 0 ATAAGAATTT 0.6967 -59 CTCAAGCATAAAAATTGAAAAAGAAAT 6 23 0 ATAAAAATTG 0.696694 -17 TTCAATGTTTCAAAAAATTTTATGAACTCC 7 28 0 CAAAAAATTT 0.572709 -266 TAATATTTTATTAAAATGTTGCATTTAACT 8 111 0 TTAAAATGTT 0.701098 -128 ATGTGTCCTTTTAAAATTTTCACAAAAGCC 8 159 1 TTAAAATTTT 0.658672 -80 TATCTATAGTATAAATAGTTTTGCTCAGGA 8 206 0 ATAAATAGTT 0.880941 -33 ACATGGGGGTATAAATAGTTAAGCATAAAA 9 43 0 ATAAATAGTT 0.880941 -26 CCTTTTGGAACTAAATAGTTCATACATAGG 10 41 1 CTAAATAGTT 0.873735 -61 GGCCTAAATAGTAAAATTTTTAT 11 4 1 CTAAATAGTA 0.424094 -43 GCTAACAAAAATAAAAATTTTACTATTTAG 11 14 0 ATAAAAATTT 0.93574 -33 CGTAAGCTTAATAATAAGTTTTATAACCTT 12 136 1 ATAATAAGTT 0.65321 -40 AATTAAAAAGCTAAAAATTTTATGCAAATA 14 32 0 CTAAAAATTT 0.9316 -32 ********** Masking position 4 Map Score: 7.06148 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 59 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 7 AACACCACCGAAAGTAGATTGCGAAAATAAAA 1 65 0 AAAGAGATGC 0.959233 -22 GTGTAATCCCAAAAATGAAAGCAAAGGTTAAT 2 30 1 AAAATGAAGC 0.958604 -73 ATATAGTCTTGAAAGAGAGTGCTGGAAATTTA 7 257 1 GAAAAGATGC 0.869549 -37 ATAGTTAAGCATAAAAGATAGCAGTTTATGAT 9 27 0 ATAAAGAAGC 0.784967 -42 TTCAAGTGTAAAAATTGAGTGCCCCAGTGCCT 12 72 0 AAAATGATGC 0.966135 -104 CAGTTCCAGAAAAGCTGACAGGTTGATTCT 13 9 0 AAAGTGAAGG 0.853326 -267 ACCGGCTCCCAAAGCCGAGAGGATCACCAGGC 13 124 1 AAAGCGAAGG 0.901459 -152 AAAAGGCTTTAAAAGCCACTGCCTTTAATCAT 13 176 0 AAAACCATGC 0.866989 -100 CACCATCCTGAAAAACGAATGCGTTTGCAGCA 13 207 0 AAAACGATGC 0.978194 -69 **** *** *** Masking position 8 Map Score: 3.18356 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 151 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 AATTACGTAAAGGAAATTTCAACTTAGAA 5 9 1 AAAGGAATTT 0.975217 -103 CAACTTAGAAAAAGGTAATTTCAACATATAA 5 30 1 AAAGGAATTT 0.975217 -82 GAAATTTAAAAAGGGTGATTTGA 7 281 1 AAGGGGATTT 0.973312 -13 CAAAAGCCAGAAGGGGAATTTATTGTCCTGA 8 181 1 AAGGGAATTT 0.984155 -58 ***** ***** Masking position 8 Map Score: 1.02675 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 = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 TTTTTGATAAGGGAGTTCATAAAATTTTTT 7 17 1 GGGAGTTCAT 0.947707 -277 TCAAATCCCGCCGAGTCCATGTTTTTTCTT 7 82 0 CCGAGTCCAT 0.951773 -212 GGCGGAGGCCGCGGGTTCAAATCCCGCCGA 7 98 0 GCGGGTTCAA 0.976298 -196 CGGTTTTCCCGCCAGTTCAATGATGGGGCC 13 73 1 GCCAGTTCAA 0.962922 -203 AGCCGGTGACCCGAGTTCAAATCTCGGCGG 13 101 0 CCGAGTTCAA 0.984317 -175 ********** Masking position 6 Map Score: 0.230843 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 48 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ********** No masking Map Score: 2.72438e-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 11 ********** No masking Map Score: 2.72438e-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 12 ********** No masking Map Score: 2.72438e-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