AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i334_synecho_ctra_100.orf -o334_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY03368 177 Synechocystis #2 RCY22330 51 Synechocystis #3 RCY11539 185 Synechocystis #4 RCY06664 88 Synechocystis #5 RCT00023 187 Chlamydia_trachomatis Motif number 1 AGGTGGAAGTAGAATACAGTGGAGTGTCCCCTGGAA 1 49 0 AGAACAGAGG 0.972685 -129 AACAGGTCAAAGACAAATGTTGAGCGGAACAACGGC 3 144 0 AGAAATGAGG 0.98764 -42 CCATTTGGCGATCAATGCAAGGGGAAAAAGCAGG 4 9 1 CGAAATGGGG 0.995079 -80 TCTGTTATCTAGAGAAAAGCGGGGCGAACACCCCGC 5 25 1 AGAAAAGGGG 0.996672 -163 CTTATTAAAACAAAAAAAGCGGGGTGTTCGCCCCGC 5 43 0 CAAAAAGGGG 0.988786 -145 CTGACTTTTCAGAGTAAAGTCTAGTGTTCCCCAAAA 5 94 1 AGAAAAGAGG 0.993481 -94 TGTACATTGGCAATCAATTTTTGGGGAACACTAGAC 5 112 0 CAAAATTGGG 0.819226 -76 TAGTATCTCTCTAACAAAGACCAGAGTGTACATTGG 5 138 0 CTAAAAGAGG 0.962195 -50 GAGAGATACTAGAGTAAAGGCAGAAGAAGTCGTTC 5 163 1 AGAAAAGGAG 0.967057 -25 *** **** ** * Masking position 6 Map Score: 11.7315 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 210 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 GGCGCAGGACCGGGGGAGGAATAACCGTTT 1 10 1 CCGGGGGAGA 0.950831 -168 AAGTAGAATACAGTGGAGTGTCCCCTGGAAC 1 48 0 CAGTGGAGGT 0.953158 -130 CGCTCTCCGAAAGGTGGAAGTAGAATACAGT 1 65 0 AAGGTGGAGT 0.776063 -113 ACCTTTCGGAGAGCGAAAAGAATTAATTAAT 1 81 1 GAGCGAAAGA 0.759111 -97 TTATTATTACCAGCGGAATATGT 2 3 0 CAGCGGAAAT 0.957456 -49 ATCCAGTATCCAGTGGAAAGAAGCAAAATAA 3 59 0 CAGTGGAAGA 0.962764 -127 GACAAATGTTGAGCGGAACAACGGCTATTTC 3 138 0 GAGCGGAAAA 0.918598 -48 CGATCAATGCAAGGGGAAAAAGCAGGGGGGT 4 19 1 AAGGGGAAAA 0.916591 -70 GGGGAAAAAGCAGGGGGGTCTTGGGGGAGTT 4 31 1 CAGGGGGGCT 0.930436 -58 ATCTAGAGAAAAGCGGGGCGAACACCCCGCT 5 31 1 AAGCGGGGGA 0.983751 -157 AAAACAAAAAAAGCGGGGTGTTCGCCCCGCT 5 42 0 AAGCGGGGGT 0.980751 -146 ******** ** Masking position 3 Map Score: 8.60285 Number of sites scoring better than the average of aligned sites = 2421 Number in coding regions = 2196 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 243 Fraction of orfs with sites within 600 bp upstream = 0.0390299 Motif number 3 TAACCGTTTGCTTGGCGTTCCAGGGGACAC 1 32 1 CTTGGCGTTC 0.962381 -146 CATACATGGCATGGGCAAACTTTGGCGCTT 1 127 0 ATGGGCAAAC 0.935982 -51 CTGACTCAGGTTTGGGGACCATGGCATATA 3 96 0 TTTGGGGACC 0.965815 -90 CCATTTGGCGATCAATGCAAGGG 4 4 1 TTTGGCGATC 0.991302 -85 TAGAGAAAAGCGGGGCGAACACCCCGCTTT 5 34 1 CGGGGCGAAC 0.962277 -154 GCAATCAATTTTTGGGGAACACTAGACTTT 5 109 0 TTTGGGGAAC 0.979654 -79 CAGAGTGTACATTGGCAATCAATTTTTGGG 5 123 0 ATTGGCAATC 0.955996 -65 ********** Masking position 5 Map Score: 5.74411 Number of sites scoring better than the average of aligned sites = 2304 Number in coding regions = 2065 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 4 CAGGACCGGGGGAGGAATAACCGTTTGCTT 1 15 1 GGAGGAATAA 0.912897 -163 TCCGAAAGGTGGAAGTAGAATACAGTGGAG 1 61 0 GGAAGTAGAA 0.989272 -117 CTATCATTTTGGTATTAGAAAGGGTTTATT 3 34 1 GGTATTAGAA 0.88489 -152 GTATCCAGTGGAAAGAAGCAAAATAAACCC 3 55 0 GAAAGAAGCA 0.912897 -131 CAATGCAAGGGGAAAAAGCAGGGGGGTCTT 4 23 1 GGAAAAAGCA 0.93933 -66 GGGTCTTGGGGGAGTTAGAATAGAAGACTG 4 46 1 GGAGTTAGAA 0.954479 -43 CTAGAGTAAAGGCAGAAGAAGTCGTTC 5 171 1 GGCAGAAGAA 0.977731 -17 ********** Masking position 7 Map Score: 4.05886 Number of sites scoring better than the average of aligned sites = 824 Number in coding regions = 753 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 CCACCATCAACCGTAAACCCCCGTAAACAC 1 157 1 CCGTAAACCC 0.973691 -21 CCGTAAACCCCCGTAAACACA 1 167 1 CCGTAAACAC 0.968403 -11 CCAAAATCACTCAGTTATTC 3 1 1 CCAAAATCAC 0.951958 -185 TAGATATATGCCATGGTCCCCAAACCTGAG 3 92 1 CCATGGTCCC 0.87226 -94 CTTCAGCTTACCAAAAACAGGTCAAAGACA 3 165 0 CCAAAAACAG 0.93976 -21 TTCTAACTCCCCCAAGACCCCCCTGCTTTT 4 36 0 CCCAAGACCC 0.983108 -53 AGCATTTTGACCCAAGGCAGACC 4 76 1 CCCAAGGCAG 0.901589 -13 ********** Masking position 8 Map Score: 2.74892 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 752 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 6 CCAAAATCACTCAGTTATTCCCACTATC 3 9 1 ACTCAGTTAT 0.960629 -177 ATTGGCTCTGACTCAGGTTTGGGGACCATG 3 103 0 ACTCAGGTTT 0.982111 -83 GCCAATGTACACTCTGGTCTTTGTTAGAGA 5 137 1 ACTCTGGTCT 0.987774 -51 TTCTGCCTTTACTCTAGTATCTCTCTAACA 5 158 0 ACTCTAGTAT 0.959893 -30 ********** Masking position 3 Map Score: 1.22517 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 38 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 TTGAATTTTATGAGTCGGACTTAACC 2 36 1 TGAGTCGGAC 0.973412 -16 TTCTTAAGATTGGCTCTGACTCAGGTTTGG 3 111 0 TGGCTCTGAC 0.992235 -75 GCTCAACATTTGTCTTTGACCTGTTTTTGG 3 155 1 TGTCTTTGAC 0.942929 -31 TCTCTCTTTTTGAATCTGACTTTTCAGAGT 5 79 1 TGAATCTGAC 0.98209 -109 ACACTAGACTTTACTCTGAAAAGTCAGATT 5 91 0 TTACTCTGAA 0.888877 -97 ********** Masking position 5 Map Score: 0.890123 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 133 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 8 ********** No masking Map Score: -1.25523e-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: -1.25523e-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 10 ********** No masking Map Score: -1.25523e-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