AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i226_synecho_ctra_300.orf -o226_synecho_ctra_300.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 RCY00779 241 Synechocystis #2 RCY09718 300 Synechocystis #3 RCY10327 39 Synechocystis #4 RCT00762 300 Chlamydia_trachomatis Motif number 1 GATAACTGTTCACTGAACCCTAGACCCAACAAC 1 32 0 CACGACCTAG 0.849874 -210 CCCCTCAACAAATATAACGCTAGGGTCAATCCT 2 37 0 AATTACCTAG 0.982436 -264 GTAAAAAGGTAATAATCCCCCAGCCCCTCAACA 2 60 0 AATATCCCAG 0.940826 -241 CATGCCAAGGAAGATTCCCCCAGGTAAAAAGGT 2 83 0 AAGTTCCCAG 0.983526 -218 TTGCGGTCTGAATTTTACCCCAGCATTACCAAC 2 179 0 AATTTCCCAG 0.988854 -122 GCATTTCTAGAATTTATCGCCAGTCTTTCCCAT 4 29 1 AATTACCCAG 0.986304 -272 CTTTTTCAAAAACTTAGCACTAGTTCTCTCTAT 4 91 1 AACTACCTAG 0.974119 -210 TCAATTAATACAGCTTCCACTAGTATGTTCCTC 4 168 1 CAGTTCCTAG 0.963315 -133 CTTCCACTAGTATGTTCCTCTAGGAATATCAAG 4 181 1 TATTTCCTAG 0.934669 -120 *** ** * **** Masking position 2 Map Score: 10.0338 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 247 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 ACTGAACCCTAGACCCAACAACATAACCGCTATC 1 20 0 ACCCACACAT 0.97404 -222 GGCAGATGCTTACGCCATCATTTCTCGATTAGGT 1 99 0 TGCCACATTC 0.950054 -143 AAAATCTCTATGCCCCATCTCAACTTGCCTGATA 1 163 1 TCCCACTAAC 0.863715 -79 AGGGAAGGCAAAAGCCACCACCAATAAACATATC 1 193 0 AGCCACACAA 0.925653 -49 AAGGTAATAATCCCCCAGCCCCTCAACAAATATA 2 54 0 TCCCACCCTC 0.973521 -247 CTTCCTTGGCATGGCCGCCCTCACGGTCTTGGTG 2 103 1 AGCCGCCCAC 0.945411 -198 GCCGTACAACAGGGCCACCAAGACCGTGAGGGCG 2 118 0 AGCCACAGAC 0.962355 -183 CGGCTAGTCAATTCCCAGCCGTACAACAGGGCCA 2 135 0 ACCCACCTAC 0.982403 -166 GTCTGAATTTTACCCCAGCATTACCAACATTGAC 2 173 0 TCCCACATAC 0.982746 -128 AGAAAGCCAACAACTTGATGCTAAAT 3 24 0 AGCCACACTT 0.926093 -16 ATCGCCAGTCTTTCCCATCTATATTTGGAATAAA 4 44 1 TCCCACTTAT 0.85472 -257 * **** ** *** Masking position 6 Map Score: 7.81752 Number of sites scoring better than the average of aligned sites = 1678 Number in coding regions = 1578 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 3 ACATAACCGCTATCAAGATTTTT 1 3 0 TATCAAGATT 0.853089 -239 AATCGAATCGGAAACAGAGTTAAATGTTAAG 2 249 0 GAAACAGATT 0.901299 -52 CTCAGCAATTGAACCAGATTTAGATGAATCG 2 275 0 GAACCAGATT 0.965282 -26 CTAAGTTTTTGAAAAAGGATTTAGAATGTAT 4 77 0 GAAAAAGGTT 0.956045 -224 TGTATTAATTGAACAAGGCGAGAAATGCCCT 4 149 0 GAACAAGGGA 0.94535 -152 CCTCTAGGAATATCAAGGATTTCTTAATCCT 4 197 1 TATCAAGGTT 0.919241 -104 GGGCTCTGCAGAACAAGGATTAAGAAATCCT 4 212 0 GAACAAGGTT 0.98513 -89 GGATATCTGAGAAAAAGAAGAGCCTTACGGA 4 270 0 GAAAAAGAGA 0.742641 -31 TTTTCTCAGATATCCAGGAGTTTTT 4 286 1 TATCCAGGGT 0.885606 -15 ******** ** Masking position 6 Map Score: 6.26383 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 493 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 4 TAAAACCTAATCGAGAAATGATGGCGTAAG 1 95 1 TCGAGAAATG 0.976213 -147 TGCTAAGAATGAGAGAACTAA 4 2 0 GAGAGAACTA 0.927973 -299 GGCGATAAATTCTAGAAATGCTAAGAATGA 4 20 0 TCTAGAAATG 0.952085 -281 TATTGCAATAGAGAGAACTAGTGCTAAGTT 4 101 0 GAGAGAACTA 0.927973 -200 ATTGAACAAGGCGAGAAATGCCCTGTTTAT 4 143 0 GCGAGAAATG 0.98834 -158 AGTATGTTCCTCTAGGAATATCAAGGATTT 4 189 1 TCTAGGAATA 0.835065 -112 ACGGAATACGGCTTGAAATAGGAGCCGGGC 4 239 0 GCTTGAAATA 0.875857 -62 ********** Masking position 7 Map Score: 3.99918 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 202 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 ACTGTTCACTGAACCCTAGACCCAACAACATA 1 29 0 GAACCAGACC 0.932936 -213 CAGGAATCGGTCAACACTGACCATTAAAACCT 1 71 1 TCACATGACC 0.947762 -171 GTGGCTTTTGCCTTCCCTAACCGACCCATTGC 1 209 1 CCTCCTAACC 0.964909 -33 CCGACCCATTGCTCCCTTGCCCT 1 229 1 GCTCCTGCCC 0.992745 -13 TAGGGTCAATCCTACCAAACCCAATAGGGGTT 2 18 0 CCTCCAACCC 0.956287 -283 GTACAACAGGGCCACCAAGACCGTGAGGGCGG 2 117 0 GCCCCAGACC 0.97644 -184 CCCAGCATTACCAACATTGACCTAACGGCTAG 2 162 0 CCACATGACC 0.966135 -139 TAATCCTTGTTCTGCAGAGCCCGGCTCCTATT 4 221 1 TCTCAAGCCC 0.958602 -80 TTTCAAGCCGTATTCCGTGTCCGTAAGGCTCT 4 251 1 TATCCTGTCC 0.811824 -50 *** ** ***** Masking position 5 Map Score: 5.12412 Number of sites scoring better than the average of aligned sites = 2016 Number in coding regions = 1792 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 6 AAATCTTGATAGCGGTTATGTTGTTGGGTC 1 13 1 AGCGGTTATG 0.930228 -229 GGAGCAATGGGTCGGTTAGGGAAGGCAAAA 1 214 0 GTCGGTTAGG 0.99084 -28 GGGCCACCAAGACCGTGAGGGCGGCCATGC 2 111 0 GACCGTGAGG 0.961703 -190 GGAATTGACTAGCCGTTAGGTCAATGTTGG 2 154 1 AGCCGTTAGG 0.975282 -147 TTAGGTCAATGTTGGTAATGCTGGGGTAAA 2 169 1 GTTGGTAATG 0.797823 -132 CGTATTCCGTGTCCGTAAGGCTCTTCTTTT 4 259 1 GTCCGTAAGG 0.986926 -42 ********** Masking position 6 Map Score: 2.26943 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 180 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 ********** No masking Map Score: -1.44708e-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: -1.44708e-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: -1.44708e-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