AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i321_tpal_bbur_300.orf -o321_tpal_bbur_300.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 RTP00893 262 AE000520 #2 RTP00740 47 AE000520 #3 RTP00743 169 AE000520 #4 RBB00547 300 3615 Motif number 1 GCGGGTGCGCATGTGCTGCAGGGCCTC 1 2 0 AGGCTGCCCT 0.816197 -261 AATATGCTGACGCTGCTTCCAGCCCCTGTGCAAGTG 1 38 1 CCGCTTCCCC 0.998028 -225 GTGCAAGGGACAGCGCTGCAAAACCCACTTGCACAG 1 63 0 CGGCTGCCCC 0.998726 -200 CTTGCACATCCACGGCTTCCTTTGGAGAGACGCGGG 1 92 1 CCGCTTCGGA 0.934567 -171 ATATCGGGCAAACACCTGCTCTACCCCGCGTCTCTC 1 116 0 ACCCTGCCCC 0.988207 -147 GCAGCGGCGCCTCGGCTGCACCTCGCGCTCGAGGCG 2 11 0 CCGCTGCCGC 0.998477 -37 GCAGCCGAGGCGCCGCTGCCACTGGCGCAG 2 28 1 CCGCTGCGGC 0.996019 -20 GTGATAGGTAAAGCGCTTCTTTTCCCGGAAATCCCG 3 15 0 AGGCTTCCCC 0.991847 -155 * * ***** *** Masking position 7 Map Score: 11.4838 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 71 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 2 AGGCCCTGCAGCACATGCGCACCCGCAATA 1 12 1 GCACATGCGC 0.940579 -251 GCTGCAAAACCCACTTGCACAGGGGCTGGA 1 55 0 CCACTTGCAC 0.963716 -208 GCTGTCCCTTGCACATCCACGGCTTCCTTT 1 85 1 GCACATCCAC 0.968709 -178 ATTCACCCTGCCAGATCCAGTACATGGCAT 1 208 1 CCAGATCCAG 0.941921 -55 TTACCGCGATCCAAATCCGC 1 253 1 CCAAATCCGC 0.963695 -10 GCGAGGTGCAGCCGAGGCGCCGCTGCCACT 2 21 1 GCCGAGGCGC 0.897727 -27 GGCGCCGCTGCCACTGGCGCAG 2 36 1 CCACTGGCGC 0.941752 -12 CGTGTACATACCAGATGCCGTCGCGGGAGG 3 55 0 CCAGATGCCG 0.934184 -115 CATTCTGTTCCCAAATTCTCAACTACGTAA 3 86 0 CCAAATTCTC 0.815993 -84 ACTTTTAGTCGCAGATGATCCCGTTTCGGT 3 124 1 GCAGATGATC 0.765094 -46 TTTTCAAATACCAGATTCACCGAAACGGGA 3 142 0 CCAGATTCAC 0.968047 -28 ********** Masking position 2 Map Score: 8.61049 Number of sites scoring better than the average of aligned sites = 1139 Number in coding regions = 337 Number in noncoding regions = 802 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 TTAAAAAGTCTAACAAAAAAATCTAAAATT 4 4 0 TAAAAATAAA 0.978389 -297 ATGGGAATCTACACAAAACTTATTAAAAAGTCTAACA 4 26 0 AAAAATTAAA 0.954797 -275 AAAAAGAATGTTAAAATAAAACATAAATATGGGAATC 4 54 0 TAAAAATAAA 0.978388 -247 TATTTATTTAATAAAAGCAGTTTTAAAAAAGAATGTT 4 79 0 AAAACTTAAA 0.900707 -222 TAAGCGTGATTAAAAAAATCAATTATATTTTTTCATG 4 119 1 TAAAAATATA 0.926383 -182 ATTTATTATATAAAAAAACATGAAAAAATATAATTGA 4 137 0 TAAAATAAAA 0.81313 -164 ATATCCAACTTAATAACATTTATTATATAAAAAAACA 4 154 0 TAAAATTATA 0.895791 -147 TTATATATAAATACAACAAAACCTAATTTAACTTTAA 4 190 0 AAAAAATAAT 0.81313 -111 AACACACCGCAAATAATAATACGTAAAGCTCAATTTA 4 224 0 AAAAAATAAA 0.968676 -77 GTTATATCTTTGATAAACCGATTTAAAAGGGGTATTT 4 274 1 TAAACATAAA 0.951081 -27 * * ** * * **** Masking position 6 Map Score: 6.99443 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 29 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 4 GAGGCCCTGCAGCACATGCG 1 1 1 GAGGCCCTGC 0.972305 -262 CCGCAATATGCTGACGCTGCTTCCAGCCCC 1 34 1 CTGACGCTGC 0.944828 -229 CCCACTTGCACAGGGGCTGGAAGCAGCGTC 1 46 0 CAGGGGCTGG 0.968857 -217 TTCCTTTGGAGAGACGCGGGGTAGAGCAGG 1 108 1 GAGACGCGGG 0.986212 -155 CCTCGAGCGCGAGGTGCAGCCGAGGCGCCG 2 13 1 GAGGTGCAGC 0.942544 -35 AGGTGCAGCCGAGGCGCCGCTGCCACTGGC 2 24 1 GAGGCGCCGC 0.618837 -24 ATACCAGATGCCGTCGCGGGAGGACAGGTG 3 48 0 CCGTCGCGGG 0.902215 -122 ********** Masking position 7 Map Score: 3.30384 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 75 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 AAAGAAGCGCTTTACCTATCACCTGTCCTCC 3 29 1 TTTACTATCA 0.925108 -141 GATTCCCATATTTATGTTTTATTTTAACATT 4 54 1 TTTATTTTTA 0.890818 -247 GCTTATTCTATTTATTTAATAAAAGCAGTTT 4 93 0 TTTATTAATA 0.946591 -208 TTCATGTTTTTTTATATAATAAATGTTATTA 4 150 1 TTTATTAATA 0.946591 -151 TTTTGTTGTATTTATATATAAATTGAGCTTT 4 206 1 TTTATTATAA 0.909517 -95 TAAATTGAGCTTTACGTATTATTATTTGCGG 4 224 1 TTTACTATTA 0.964814 -77 ***** ***** Masking position 7 Map Score: 2.21641 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 6 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 CCACCTATCGTTCGAATTTTTTCCCAAAAC 1 166 0 TTCGAATTTT 0.846034 -97 AATTTTAGATTTTTTTGTTAGACT 4 5 1 TTAGATTTTT 0.964099 -296 GATTTTTTTGTTAGACTTTTTAATAAGTTT 4 18 1 TTAGACTTTT 0.907609 -283 ATCACGCTTATTCTATTTATTTAATAAAAG 4 99 0 TTCTATTTAT 0.88918 -202 AAAAAATCAATTATATTTTTTCATGTTTTT 4 131 1 TTATATTTTT 0.956983 -170 TTAGGTTTTGTTGTATTTATATATAAATTG 4 201 1 TTGTATTTAT 0.81343 -100 GTAGTTGAAGTTATATCTTTGATAAACCGA 4 265 1 TTATATCTTT 0.872503 -36 ********** Masking position 5 Map Score: 2.52235 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 52 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 7 TAAGTACTGAGCCGTTTTGGGAAAAAATTC 1 153 1 GCCGTTTTGG 0.991754 -110 GCGGATTTGGATCGCGGTAA 1 253 0 GCGGATTTGG 0.916925 -10 AATGATGAAGGCACTTTTAGTCGCAGATGA 3 112 1 GCACTTTTAG 0.946658 -58 CGCAGATGATCCCGTTTCGGTGAATCTGGT 3 133 1 CCCGTTTCGG 0.958282 -37 TTTAATAAAAGCAGTTTTAAAAAAGAATGT 4 80 0 GCAGTTTTAA 0.919829 -221 AAATACCCCTTTTAAATCGGTTTAT 4 286 0 CCCCTTTTAA 0.875964 -15 ********** Masking position 6 Map Score: 0.300064 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 238 Number in noncoding regions = 533 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 ********** No masking Map Score: -9.4259e-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 GAGGCCCTGCAGCACATGCGCACCC 1 6 1 CCTGCAGCAC 0.93478 -257 GGATGTGCAAGGGACAGCGCTGCAAAACCC 1 73 0 GGGACAGCGC 0.946586 -190 CTTAGATATCGGGCAAACACCTGCTCTACC 1 127 0 GGGCAAACAC 0.887178 -136 GGTGAATGCACCGTAAGCACCACCTATCGT 1 185 0 CCGTAAGCAC 0.933693 -78 CGCCTCGAGCGCGAGGTGCAGC 2 3 1 CCTCGAGCGC 0.961802 -45 ACAGGTGATAGGTAAAGCGCTTCTTTTCCC 3 25 0 GGTAAAGCGC 0.96422 -145 AATAATAATACGTAAAGCTCAATTTATATA 4 220 0 CGTAAAGCTC 0.91692 -81 ACTTCAACTACCTCAAACACACCGCAAATA 4 246 0 CCTCAAACAC 0.928873 -55 ********** Masking position 6 Map Score: 1.62666 Number of sites scoring better than the average of aligned sites = 581 Number in coding regions = 171 Number in noncoding regions = 410 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 ********** No masking Map Score: -9.4259e-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: -9.4259e-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: -9.4259e-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