AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i257_tpal_bbur_100.orf -o257_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 RTP00362 118 AE000520 #2 RTP00772 204 AE000520 #3 RBB00112 194 3615 #4 RBB00025 66 3615 Motif number 1 ACTACTACCGGTGCTCCTTCCTGTTCTCCTC 1 17 1 GTGCTCTTCC 0.998412 -102 GCTCCTTCCTGTTCTCCTCCCTTGCCCTCTC 1 29 1 GTTCTCTCCC 0.985676 -90 TTGCCCTCTCCTGCTGCATCCTTCTCGCTCA 1 50 1 CTGCTCATCC 0.975526 -69 ACTGTGCCTTGTGCTAGTCCCTGAGCGAGAA 1 71 0 GTGCTGTCCC 0.990285 -48 CCGGTCACATGTGCTTCTTCCGTCCTATCCC 2 18 1 GTGCTCTTCC 0.998412 -187 ATCCCTACCCGCGATCCTTTCCTCACCCGTG 2 44 1 GCGATCTTTC 0.915557 -161 GAAACCCACCGTGCTGCTCGCCTTTGACTCG 2 106 1 GTGCTCTCGC 0.992913 -99 TCCCCGCCCTCCGCTTCTTTCAAAACGCACC 2 180 1 CCGCTCTTTC 0.971719 -25 ***** ***** Masking position 5 Map Score: 14.9878 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 72 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 CAGCAGGAGAGGGCAAGGGAGGAGAACAGG 1 36 0 GGGCAAGGGA 0.986085 -83 CACATGTGACCGGTAAGGAA 2 1 0 CGGTAAGGAA 0.965825 -204 AAAGGATCGCGGGTAGGGATAGGACGGAAG 2 34 0 GGGTAGGGAT 0.990465 -171 TCGTAGGCACGGGTGAGGAAAGGATCGCGG 2 52 0 GGGTGAGGAA 0.994867 -153 GGGTTTCTGTGTGCGGGGATGTGGGGAGAT 2 83 0 GTGCGGGGAT 0.975449 -122 AAGAAGCGGAGGGCGGGGAAATCTGTTGGT 2 169 0 GGGCGGGGAA 0.997917 -36 ********** Masking position 7 Map Score: 9.10935 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 167 Number in noncoding regions = 456 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 CAGTAAAAATTTTTATTATATAATGTAAATA 3 46 0 TTTTTTATAT 0.980806 -149 ATTTTTACTGGTTTTGTATATTTTGTATTTT 3 67 1 GTTTGTATAT 0.913694 -128 GTTAATCTTATATTGTTATATGTAAATTATT 3 146 1 TATTTTATAT 0.985202 -49 ATATGTAAATTATTTTTATTTATAGAAAGGG 3 163 1 TATTTTATTT 0.932533 -32 GTTGAGTCAATATATTTATATGGTGC 4 6 0 TATATTATAT 0.932533 -61 ACTCTCAGTTTTTTCGTATATTTAATATTAT 4 35 1 TTTTGTATAT 0.971756 -32 GTATATTTAATATTATTATATAAGGAG 4 50 1 TATTTTATAT 0.9852 -17 **** ****** Masking position 8 Map Score: 8.59756 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 11 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 TATATAATGTAAATATTGACTAATCTTTAA 3 31 0 AAATATTGAC 0.981389 -164 TATATAATAAAAATTTTTACTGGTTTTGTA 3 55 1 AAATTTTTAC 0.971506 -140 TATAAATAAAAATAATTTACATATAACAAT 3 157 0 AATAATTTAC 0.911898 -38 AAAAATTTTACCCCTTTCTAT 3 184 0 AAAATTTTAC 0.959602 -11 CACCATATAAATATATTGACTCAACTCTCA 4 12 1 ATATATTGAC 0.941201 -55 ********** Masking position 6 Map Score: 2.02433 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 81 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 ACAGGAAGGAGCACCGGTAGTAGTTGATGG 1 11 0 GCACCGGTAG 0.963465 -108 CAAGGGAGGAGAACAGGAAGGAGCACCGGT 1 23 0 GAACAGGAAG 0.790538 -96 GCAGGAGAGGGCAAGGGAGGAGAACAGGAA 1 34 0 GCAAGGGAGG 0.907578 -85 CATCCTTCTCGCTCAGGGACTAGCACAAGG 1 66 1 GCTCAGGGAC 0.899706 -53 AAGGCACAGTGCTCCGTTACACTCGGCCGT 1 92 1 GCTCCGTTAC 0.709913 -27 GACGGAAGAAGCACATGTGACCGGTAAGGA 2 12 0 GCACATGTGA 0.58532 -193 GAGGAAAGGATCGCGGGTAGGGATAGGACG 2 38 0 TCGCGGGTAG 0.846478 -167 GATTTCGTAGGCACGGGTGAGGAAAGGATC 2 56 0 GCACGGGTGA 0.890761 -149 AAGGCGAGCAGCACGGTGGGTTTCTGTGTG 2 100 0 GCACGGTGGG 0.968801 -105 ********** Masking position 6 Map Score: 1.72445 Number of sites scoring better than the average of aligned sites = 2582 Number in coding regions = 770 Number in noncoding regions = 1812 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 CTTTGTCTTTATAATTTAAAGATTAGTCAA 3 16 1 ATAATTTAAA 0.873317 -179 TTTTTATTATATAATGTAAATATTGACTAA 3 38 0 ATAATGTAAA 0.911483 -157 TTTACATTATATAATAAAAATTTTTACTGG 3 48 1 ATAATAAAAA 0.908692 -147 TAAGATTAACATAAACTTAATACATTCGCT 3 126 0 ATAAACTTAA 0.871696 -69 ATATAACAATATAAGATTAACATAAACTTA 3 137 0 ATAAGATTAA 0.909303 -58 CTTTCTATAAATAAAAATAATTTACATATA 3 162 0 ATAAAAATAA 0.873652 -33 TCCTTATATAATAATATTAAATATACGAAA 4 46 0 ATAATATTAA 0.920768 -21 ********** Masking position 4 Map Score: 3.85773 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 50 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 7 ********** No masking Map Score: -1.17707e-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 8 ********** No masking Map Score: -1.17707e-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: -1.17707e-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