AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i231_tpal_bbur_100.orf -o231_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00221 300 AE000520 #2 RTP01008 135 AE000520 #3 RBB00489 275 3615 #4 RBB00148 300 3615 #5 RBB00146 23 3615 Motif number 1 TGGGGGGGGGCGGGAACGGCGTGCTGTCCT 1 9 1 GGGGGACGGC 0.923338 -292 ACTTCGGGTGGGGTGTTTTCCCTTTGAAGAAC 1 61 1 GGTGTTTCCC 0.973475 -240 CTGGGCAAACGGCTGGTATCGCGCGAAATCCT 1 92 1 GGTGGTTCGC 0.977888 -209 GTCCCGGCGCGGGGGATGTGCCCCGTGTCTTT 1 124 1 GGGGATTGCC 0.76587 -177 CGCGCTCAGGGGAGGTTTTCCCTTCAGGAGCC 1 157 1 GGGGTTTCCC 0.984757 -144 GAGCGCATTCTGCGCATCTGCCTCTTGCATAT 2 62 1 TGGCATTGCC 0.795246 -74 GGTTCGACTCCTGCTGAGTGCG 4 1 1 GGTCGATCCT 0.86041 -300 TGCCAGGAGTGGTGGAATTGGCAGACACGCTA 4 111 1 GGGGAATGGC 0.982023 -190 GCTAGACTTAGGATCTAGTGCCTTTGGCGTGT 4 139 1 GGTCTATGCC 0.966339 -162 TTGGCGTGTGGGTTCGACTCCCACCTTCTGTA 4 162 1 GGTCGATCCC 0.988407 -139 ACCTTGCCAAGGTGGAAGTCGCGGGTTCAAAT 4 226 1 GGGGAATCGC 0.986857 -75 GGAAGTCGCGGGTTCAAATCCCGTCTTTCGCT 4 239 1 GGTCAATCCC 0.985196 -62 ** **** **** Masking position 2 Map Score: 17.3573 Number of sites scoring better than the average of aligned sites = 1196 Number in coding regions = 366 Number in noncoding regions = 830 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 TGGGGGGGGGCGGGAACGGCGTGCTGTCCTGTT 1 11 1 CGGGCGCGTG 0.996664 -290 GCGTGCTGTCCTGTTCCTACGCGTTTTTCCTCA 1 29 1 CTGTCACGCG 0.969678 -272 GGGCAAACGGCTGGTATCGCGCGAAATCCTGTC 1 94 1 CTGGTGCGCG 0.994483 -207 GCGCGAAATCCTGTCCCGGCGCGGGGGATGTGC 1 112 1 CTGTCGCGCG 0.994749 -189 GATGTGCCCCGTGTCTTTGCGCGCTCAGGGGAG 1 138 1 GTGTTGCGCG 0.963051 -163 TTCAGGAGCCCGGGGACGGGGTGCTCTCCGTGA 1 179 1 CGGGCGGGTG 0.978907 -122 CTCCGTGAAGGTGTCGCCGTGTGATCCGCAGGT 1 204 1 GTGTCGTGTG 0.752978 -97 CAGTCTCAGGCAGGAGCAGCGTGCACCTGCGGA 1 228 0 CAGGCGCGTG 0.990688 -73 GCACCATCATCGGGCTTGACGAGGCAAGGAGAC 1 271 0 CGGGTACGAG 0.844786 -30 GCGCAGAATGCGCTCATTGCGCGCTGCGTTGCG 2 44 0 CGCTTGCGCG 0.819395 -92 GAAAGTAACTCAGGGGTAGAGTGTCACCTTGCC 4 201 1 CAGGTGAGTG 0.847608 -100 **** * ***** Masking position 11 Map Score: 13.373 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 106 Number in noncoding regions = 204 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 3 CGCGCGATACCAGCCGTTTGCCCAGTTCTTC 1 86 0 CAGCCTTTGC 0.902416 -215 CGCGGGGGATGTGCCCCGTGTCTTTGCGCGC 1 131 1 GTGCCCGTGT 0.71814 -170 TTCACGGAGAGCACCCCGTCCCCGGGCTCCT 1 182 0 GCACCCGTCC 0.781445 -119 CAGGTGCACGCTGCTCCTGCCTGAGACTGAG 1 232 1 CTGCTCTGCC 0.945974 -69 GCACAGGATACTGCCTTTTCCTAC 2 4 0 CTGCCTTTCC 0.970327 -132 GCGCTGCGTTGCGCTGTTTGCGGCACAGGAT 2 26 0 GCGCTTTTGC 0.944872 -110 TGCGCAGAATGCGCTCATTGCGCGCTGCGTT 2 47 0 GCGCTATTGC 0.92908 -89 TTCTGCGCATCTGCCTCTTGCATATGGTGCC 2 69 1 CTGCCCTTGC 0.991798 -67 GGTTCGACTCCTGCTGAGTGCGAAATTATTA 4 11 1 CTGCTAGTGC 0.900545 -290 GCCAATTCCACCACTCCTGGCATACTTCATA 4 102 0 CCACTCTGGC 0.801961 -199 TCTAGCGTGTCTGCCAATTCCACCACTCCTG 4 114 0 CTGCCATTCC 0.961706 -187 TTAGGATCTAGTGCCTTTGGCGTGTGGGTTC 4 146 1 GTGCCTTGGC 0.942883 -155 GGATTTGAACCCGCGACTTCCACCTTGGCAA 4 229 0 CCGCGCTTCC 0.936269 -72 ***** ***** Masking position 4 Map Score: 13.3094 Number of sites scoring better than the average of aligned sites = 2182 Number in coding regions = 643 Number in noncoding regions = 1539 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 AGCATAATAACTACTACTTAAAATTAATTAATCTAT 3 72 0 CTATAAAATA 0.931088 -204 ATACCATTCGATAATAAGCATAATAACTACTACTTA 3 88 0 ATATAATATA 0.896909 -188 ATTAATTTGGATTATAGTAAAAATTACAATCCGCTA 3 129 0 ATTTAAAATA 0.981376 -147 TTATTATTTTATAATAAAAAAAATTATTATTAAATG 3 196 1 ATATAAAATA 0.965085 -80 CAAAACAAATATTTTATGGAAATTCATTTAATAATA 3 220 0 ATTTAAAATA 0.981361 -56 TCCTAAGCTAATTATAACAAAACAAATATTTTATGG 3 237 0 ATTTAAAAAA 0.892549 -39 TACTCAAAATAGTATACAAAAACTTAAAAGCTTTTG 4 68 0 AGTTAAAATA 0.924879 -233 CCTCAATTAAATTTTATTGATAATTATTAAAAAGCG 4 267 0 ATTTAATATA 0.94328 -34 AAAAACTTTTACCGAAAATAAAA 5 3 0 CTTTAAAATA 0.962625 -21 *** ** *** * * Masking position 10 Map Score: 7.15118 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 16 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 5 CTTCTCTAGAATTCATTTTTAATCGATTTTTCA 3 14 1 ATTCATTTAT 0.80986 -262 TTTTTCAAGGATTATTCTTTACTAACTTCACCA 3 40 1 ATTATTTTAT 0.968711 -236 CTTAAAATTAATTAATCTATGGTGAAGTTAGTA 3 59 0 ATTAATTTGT 0.875522 -217 AGTTATTATGCTTATTATCGAATGGTATAGTTT 3 96 1 CTTATTTGAT 0.83088 -180 AATTATGACCATTAATTTGGATTATAGTAAAAA 3 142 0 ATTAATTGAT 0.944596 -134 TTCTCATTTTATTATTTTATAATAAAAAAAATT 3 188 1 ATTATTTTAT 0.837684 -88 AATAAAAAAAATTATTATTAAATGAATTTCCAT 3 208 1 ATTATTTAAT 0.880069 -68 TGAGTGCGAAATTATTATTTATTTAGTAGATTA 4 25 1 ATTATTTTAT 0.968711 -276 TAATGCCTCAATTAAATTTTATTGATAATTATT 4 275 0 ATTAAATTAT 0.72932 -26 ****** * ** * Masking position 8 Map Score: 4.85607 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 19 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 GTTCCTACGCGTTTTTCCTCACTTCGGGTG 1 41 1 GTTTTTCCTC 0.973161 -260 CGGGTGGGGTGTTTTCCCTTTGAAGAACTG 1 65 1 GTTTTCCCTT 0.989377 -236 CTCAGGGGAGGTTTTCCCTTCAGGAGCCCG 1 161 1 GTTTTCCCTT 0.989377 -140 CAAGGAGACGTATTTCCCTCAGTCTCAGGC 1 250 0 TATTTCCCTC 0.934855 -51 ********** Masking position 5 Map Score: 1.89026 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 24 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 GGATGTGCCCCGTGTCTTTGCGCGCTCAGGG 1 137 1 CGTTCTTTGC 0.981686 -164 GAGGGAAATACGTCTCCTTGCCTCGTCAAGC 1 260 1 CGTTCCTTGC 0.978287 -41 GCTCATTGCGCGCTGCGTTGCGCTGTTTGCG 2 35 0 CGCGCGTTGC 0.993672 -101 GCGATATACACGCAGCATTGCACGCCATTCG 2 99 0 CGCGCATTGC 0.99065 -37 TTAAAAACGGTGCTCTGCGATATACACG 2 118 0 CGGGCTCTGC 0.978601 -18 *** ******* Masking position 9 Map Score: 1.82987 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 31 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 8 ATTCGGCACCATATGCAAGAGGCAGATGCGC 2 73 0 ATATGCAGAG 0.949679 -63 GATTAGGCATACTTGCAAAAGCTTTTAAGTT 4 53 1 ACTTGCAAAG 0.957105 -248 GAATTGGCAGACACGCTAGACTTAGGATCTA 4 125 1 ACACGCAGAC 0.948873 -176 AGTCGAACCCACACGCCAAAGGCACTAGATC 4 150 0 ACACGCAAAG 0.989862 -151 CCTTCTGTAAAAATGCGAAAGTAACTCAGGG 4 185 1 AAATGCAAAG 0.975694 -116 ATAATTATTAAAAAGCGAAAGACGGGATTTG 4 253 0 AAAAGCAAAG 0.940782 -48 ****** **** Masking position 8 Map Score: 1.73013 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 17 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 CGGCGTGCTGTCCTGTTCCTACGCGTTTTT 1 27 1 TCCTGTTCCT 0.981777 -274 TCGCGCGAAATCCTGTCCCGGCGCGGGGGA 1 110 1 TCCTGTCCCG 0.991969 -191 AAAGGCAGTATCCTGTGCCGCAAACAGCGC 2 17 1 TCCTGTGCCG 0.99562 -119 AGACTTAGGATCTAGTGCCTTTGGCGTGTG 4 142 1 TCTAGTGCCT 0.936055 -159 ********** Masking position 6 Map Score: 2.01022 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 14 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 TGACGAGGCAAGGAGACGTATTTCCCTCAG 1 258 0 AGGAGACGTA 0.946724 -43 CGCACTCAGCAGGAGTCGAACC 4 3 0 AGGAGTCGAA 0.991263 -298 TACAGAAGGTGGGAGTCGAACCCACACGCC 4 164 0 GGGAGTCGAA 0.994334 -137 AGCGAAAGACGGGATTTGAACCCGCGACTT 4 241 0 GGGATTTGAA 0.917471 -60 ********** Masking position 4 Map Score: 0.804425 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 18 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 GGAAAACACCCCACCCGAAGTGAGGAAAAA 1 52 0 CCACCCGAAG 0.90517 -249 CCGTCCCCGGGCTCCTGAAGGGAAAACCTC 1 168 0 GCTCCTGAAG 0.942956 -133 TCACACGGCGACACCTTCACGGAGAGCACC 1 198 0 ACACCTTCAC 0.910461 -103 GGAGCAGCGTGCACCTGCGGATCACACGGC 1 219 0 GCACCTGCGG 0.981136 -82 TACACCTGCACCATCATCGGG 1 290 0 ACACCTGCAC 0.962981 -11 ACGCCATTCGGCACCATATGCAAGAGGCAG 2 79 0 GCACCATATG 0.73798 -57 GGTTCGACTCCTGCTGAGTGCGAAAT 4 7 1 ACTCCTGCTG 0.953856 -294 GGTTCGACTCCCACCTTCTGTAAAAATGCG 4 172 1 CCACCTTCTG 0.959721 -129 ********** Masking position 5 Map Score: 3.48606 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 184 Number in noncoding regions = 380 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 ********** No masking Map Score: 5.35339e-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 13 ********** No masking Map Score: 5.35339e-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 14 ********** No masking Map Score: 5.35339e-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