AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i217_tpal_bbur_100.orf -o217_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 RTP00715 275 AE000520 #2 RTP00717 119 AE000520 #3 RBB00314 240 3615 #4 RBB00313 90 3615 #5 RBB00312 91 3615 Motif number 1 ACTCGGCACTGCGCGCGTTCACGGTCATTGAA 1 40 0 GGCGCGTCAC 0.811567 -236 GCCGAGTAGGGGGAGCGATCGCTCCGACGCGT 1 65 1 GGAGCGTCGC 0.562041 -211 GCGATCGCTCCGACGCGTTTCCCACGCTACCT 1 79 1 CACGCGTTCC 0.980411 -197 CGGAGCCTGCGTGCACGATTGCAGGAAGGAAC 1 122 0 GGCACGTTGC 0.950106 -154 TCACAAGCGGGGACGCGTTTGCATCCATGTTT 1 189 1 GACGCGTTGC 0.867746 -87 GAATAGTGACGAACGCGGTTGCC 2 2 0 GACGCGTTGC 0.9951 -118 TTGCGAATAAGCACTCGGTAGCTCACCGCCCC 2 45 1 GACTCGTAGC 0.95594 -75 CTGCCAGCTGATACGCGCTTCCTGTTCTTTTA 2 86 1 AACGCGTTCC 0.965978 -34 * ***** **** Masking position 9 Map Score: 12.8176 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 5 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 2 TTAATTGAAGAATCAAAAATTATTTTAAAC 3 13 1 AATCAAAAAT 0.908049 -228 CAAAAATTATTTTAAACAATTGAACCAAAT 3 26 1 TTTAAACAAT 0.942541 -215 CCAAATAATTTATCAAAAATACAACAAAAA 3 50 1 TATCAAAAAT 0.892592 -191 AAATACAACAAAAAAACAACCTACAATTTA 3 66 1 AAAAAACAAC 0.785911 -175 ATTAAATACAATTAAACAATCAAACAGTAG 3 123 1 ATTAAACAAT 0.951188 -118 ACTATATATCTATAAAAAATAAAAATACAA 3 168 1 TATAAAAAAT 0.955855 -73 AAAAAATAAAAATACAAAATCCACAAAATC 3 181 1 AATACAAAAT 0.828931 -60 ACCACAATGCAAAAAACAATATTGAATAAA 4 58 0 AAAAAACAAT 0.951203 -33 TGCATTGTGGTATAAAAAATTGAT 4 77 1 TATAAAAAAT 0.955855 -14 CAAGCTACAAATTAAACACTAACATGGTAT 5 39 0 ATTAAACACT 0.785909 -53 GCTCCTCCATTAAAAACAATTTTATGCTGC 5 69 0 TAAAAACAAT 0.942542 -23 ********** Masking position 6 Map Score: 10.0335 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 127 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 GAAGGAATGCACGCGTGGGAAGAGGAGCCA 1 13 0 ACGCGTGGGA 0.995669 -263 AGCGTGGGAAACGCGTCGGAGCGATCGCTC 1 77 0 ACGCGTCGGA 0.978994 -199 CAGTGGCAGGTAGCGTGGGAAACGCGTCGG 1 88 0 TAGCGTGGGA 0.98875 -188 CACGCAGGCTCCGCATGGGAACGGTAAGAA 1 141 1 CCGCATGGGA 0.988812 -135 AAACGCGTCCCCGCTTGTGACTACCACGTC 1 179 0 CCGCTTGTGA 0.955526 -97 AATCGCATGGTAATCTTTACCT 1 264 0 TCGCATGGTA 0.929153 -12 GTTTAATTTGTAGCTTGGCAGCATAAAATT 5 52 1 TAGCTTGGCA 0.906042 -40 ********** Masking position 10 Map Score: 8.65352 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 32 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 4 CCCCCTACTCGGCACTGCGCGCGTTCACGG 1 48 0 GGCACTGCGC 0.892653 -228 ACATATCAGTGGCAGGTAGCGTGGGAAACG 1 94 0 GGCAGGTAGC 0.950664 -182 CGTGCACGATTGCAGGAAGGAACATATCAG 1 115 0 TGCAGGAAGG 0.857302 -161 CCTGCAATCGTGCACGCAGGCTCCGCATGG 1 129 1 TGCACGCAGG 0.983828 -147 GCTTGTGACTACCACGTCGGTACCCTTTCT 1 167 0 ACCACGTCGG 0.877658 -109 CAATACCAGAAGCACGGCGCTATGTCTGGA 1 228 0 AGCACGGCGC 0.984042 -48 TTCTGGTATTGGCTCGCAGGTAAAGATTAC 1 247 1 GGCTCGCAGG 0.986283 -29 AGCACTCGGTAGCTCACCGCCCCCGGCACT 2 54 1 AGCTCACCGC 0.873594 -66 AGCGCGTATCAGCTGGCAGGAAGTGCCGGG 2 75 0 AGCTGGCAGG 0.96844 -45 ********** Masking position 3 Map Score: 5.47172 Number of sites scoring better than the average of aligned sites = 681 Number in coding regions = 194 Number in noncoding regions = 487 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 ACTTAATTGAAGAATCAAAAAT 3 3 1 TTAATTGAAG 0.780378 -238 AGGTTGTTTTTTTGTTGTATTTTTGATAAA 3 58 0 TTTGTTGTAT 0.728806 -183 AATATCTTGTTAAATTGTAGGTTGTTTTTT 3 76 0 TAAATTGTAG 0.923379 -165 TTAATTGTATTTAATACTATATGATGCAAG 3 108 0 TTAATACTAT 0.802236 -133 GTTTGATTGTTTAATTGTATTTAATACTAT 3 118 0 TTAATTGTAT 0.938699 -123 TTTTTATAGATATATAGTAGTAATAGTAGT 3 156 0 TATATAGTAG 0.762173 -85 TGCCTCCTTATATATTCTATTACATTTTAT 3 219 0 TATATTCTAT 0.900914 -22 AGTGAGTTATTAATGCTATTTTGAATATT 4 10 1 TTAATGCTAT 0.862558 -81 CTTTTCTAGGTTTATTCAATATTGTTTTTT 4 48 1 TTTATTCAAT 0.728321 -43 CAATTGCATTTATATGCTATACCATGTTAG 5 21 1 TATATGCTAT 0.816322 -71 TGTTAGTGTTTAATTTGTAGCTTGGCAGCA 5 45 1 TAATTTGTAG 0.629041 -47 ********** Masking position 9 Map Score: 4.22676 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 57 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 GGCTCCTCTTCCCACGCGTGCATTCCTTCA 1 14 1 CCCACGCGTG 0.979166 -262 AGCGATCGCTCCCCCTACTCGGCACTGCGC 1 58 0 CCCCCTACTC 0.889067 -218 CGACGCGTTTCCCACGCTACCTGCCACTGA 1 89 1 CCCACGCTAC 0.983078 -187 TGCAAACGCGTCCCCGCTTGTGACTACCAC 1 182 0 TCCCCGCTTG 0.933901 -94 ATTCGCAATGCCCACGGCAGAATAGTGACG 2 23 0 CCCACGGCAG 0.988596 -97 TAGCTCACCGCCCCCGGCACTTCCTGCCAG 2 63 1 CCCCCGGCAC 0.992804 -57 ********** Masking position 5 Map Score: 3.14417 Number of sites scoring better than the average of aligned sites = 884 Number in coding regions = 280 Number in noncoding regions = 604 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 ********** No masking Map Score: -1.28365e-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: -1.28365e-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: -1.28365e-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