AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i327_synecho_ctra_100.orf -o327_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 RCY39915 204 Synechocystis #2 RCY29136 46 Synechocystis #3 RCY05183 198 Synechocystis #4 RCT00063 185 Chlamydia_trachomatis Motif number 1 TCTCGTAAGCTTTCCCCATCAGGGATTTTTC 1 56 1 TTCCCCATCA 0.911483 -149 CAGGGATTTTTCTCTCGATCCATATGCTACT 1 75 1 TTCTCGATCC 0.841437 -130 GCTACTTTTTTTGGCCCATCCGGCACCAACC 1 100 1 TGGCCCATCC 0.972798 -105 AGGCCCTGTTTCGCCCCGTCCCGTCCTCCCA 1 163 1 TGCCCCGTCC 0.998157 -42 TTCCCCTATTTTTCCCGGCCCCACT 2 32 1 TTCCCGGCCC 0.988343 -15 TGAAGCACAAATGCCCGATGCAAGACTGTTG 3 39 1 AGCCCGATGC 0.967332 -160 CACACTTCCATTGCCCTGCCCCCC 3 185 1 TGCCCTGCCC 0.980427 -14 CTCTAAAAAGAAGCCCCGTTCTATCTCGGAC 4 29 1 AGCCCCGTTC 0.976408 -157 GACAAAAGAAAAGCCCCGTCCGAGATAGAAC 4 46 0 AGCCCCGTCC 0.997309 -140 TGTCTTTAAAAATCCCCTCGCCTTTTTTATA 4 73 1 ATCCCCTCGC 0.841435 -113 * ********* Masking position 6 Map Score: 13.928 Number of sites scoring better than the average of aligned sites = 2096 Number in coding regions = 1934 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 176 Fraction of orfs with sites within 600 bp upstream = 0.0282686 Motif number 2 GATTTGCGTTAAAATTCTCGTAAGCTTTCCCCA 1 41 1 AAAATCCGAA 0.984461 -164 GGATCGAGAGAAAAATCCCTGATGGGGAAAGCT 1 63 0 AAAATCCTAT 0.970798 -142 ATGGGCCAAAAAAAGTAGCATATGGATCGAGAG 1 86 0 AAAATACAAT 0.73379 -119 TGGGGCCGGGAAAAATAGGGGAATTTATTTTAA 2 22 0 AAAATAGGAA 0.929369 -25 AGACTTTCTAAAAATTCTCTAAAAAGAAGCCCC 4 13 1 AAAATCCTAA 0.987083 -173 TAGACAACTCACAATTCCGTTAACATGTCCTTT 4 137 1 ACAATCGTAA 0.947096 -49 TTTCGAAGCAAAAACTCGGTTAAAAACA 4 168 1 AAAATCGTAA 0.983099 -18 **** ** ** ** Masking position 4 Map Score: 3.57026 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 159 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 CCTCCCACTGCTATCTAGGAGCTTGCCC 1 187 1 CTATCTAGGA 0.978712 -18 TAAGACTTTCTAAAAATTCTCTAAA 4 6 1 CTTTCTAAAA 0.895188 -180 AACGGGGCTTCTTTTTAGAGAATTTTTAGA 4 19 0 CTTTTTAGAG 0.938142 -167 AAGCCCCGTTCTATCTCGGACGGGGCTTTT 4 39 1 CTATCTCGGA 0.974439 -147 TGTGAGTTGTCTATCTAGAGAAAAGTAATC 4 120 0 CTATCTAGAG 0.978372 -66 GTTAACATGTCCTTTTCGAAGCAAAAACTC 4 155 1 CCTTTTCGAA 0.850327 -31 ********** Masking position 6 Map Score: 1.90324 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 74 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 4 GAGGGTACTGGTGGGAGGTTGGTGCCGGATGG 1 115 0 GGGGAGGTGG 0.998296 -90 CTAGATAGCAGTGGGAGGACGGGACGGGGCGA 1 173 0 GGGGAGGCGG 0.998419 -32 TTCAAATTGGGACGCAGTTTGGTACATAATAT 3 11 0 GCGCAGTTGG 0.981451 -188 ATCAATTAATGACTGAGGATGGAGTCCGCAAT 3 110 1 GCTGAGGTGG 0.987191 -89 GGGGGGCAGGGCAATGGAAGTGTG 3 185 0 GGGCAGGCAA 0.940975 -14 * ****** *** Masking position 6 Map Score: 1.88766 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 241 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 GCAAATCAGCGGAAACCTGATTCCCTTCGT 1 18 0 GGAAACCTGA 0.923201 -187 TCCCTGATGGGGAAAGCTTACGAGAATTTT 1 51 0 GGAAAGCTTA 0.97048 -154 ACTGGAACAGATTAAAATAAATTC 2 5 1 GAACAGATTA 0.763554 -42 TCTAACCGAGGAAAGGATTACAATGTGAAG 3 142 1 GAAAGGATTA 0.873218 -57 GCAGGGCAATGGAAGTGTGATCAATAAATC 3 174 0 GGAAGTGTGA 0.969901 -25 AGAATTTTTAGAAAGTCTTA 4 1 0 GAAAGTCTTA 0.927791 -185 ACATGTTAACGGAATTGTGAGTTGTCTATC 4 135 0 GGAATTGTGA 0.890238 -51 GCTTCGAAAAGGACATGTTAACGGAATTGT 4 147 0 GGACATGTTA 0.938799 -39 ********** Masking position 3 Map Score: 2.93728 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 527 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 TTGCATCGGGCATTTGTGCTTCAAATTGGGAC 3 30 0 CATTTGCTTC 0.984826 -169 CACTTAGCAACAGTCTTGCATCGGGCATTTGT 3 45 0 CAGTTGCATC 0.976662 -154 GGGAGCTTTTCATTTCTGGTTCATCACTTAGC 3 69 0 CATTTGGTTC 0.989532 -130 CATCCTCAGTCATTAATTGATCTGAATGTAGG 3 99 0 CATTTTGATC 0.981512 -100 ATGTGAAGGCGATTTATTGATCACACTTCCAT 3 164 1 GATTTTGATC 0.937273 -35 **** ****** Masking position 7 Map Score: 0.774448 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 83 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 ********** No masking Map Score: 1.82142e-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: 1.82142e-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 GACTGCAACGAAGGGAATCAGGTTTCCGCTG 1 10 1 GAGGGAATCG 0.990268 -195 ACTGGTGGGAGGTTGGTGCCGGATGGGCCAAA 1 109 0 GTTGGTGCCG 0.916269 -96 TATCCGTCTTGGAGGGTACTGGTGGGAGGTTG 1 126 0 GAGGGTACTG 0.987254 -79 AAACAGGGCCTTAGGGTATCCGTCTTGGAGGG 1 142 0 TAGGGTATCG 0.929572 -63 TGATCTGAATGTAGGGAGCTTTTCATTTCTGG 3 82 0 GAGGGAGCTT 0.923865 -117 TAATGACTGAGGATGGAGTCCGCAATTCTAAC 3 116 1 GATGGAGTCG 0.971033 -83 GGGGGGCAGGGCAATGGAAGTGTGATC 3 182 0 GAGGGCAATG 0.91958 -17 * ******** * Masking position 6 Map Score: 0.62448 Number of sites scoring better than the average of aligned sites = 766 Number in coding regions = 703 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 10 ********** No masking Map Score: 1.82142e-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 11 ********** No masking Map Score: 1.82142e-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 12 ********** No masking Map Score: 1.82142e-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