AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i196_synecho_ctra_300.orf -o196_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 RCY15861 300 Synechocystis #2 RCY20831 142 Synechocystis #3 RCY03076 153 Synechocystis #4 RCY36462 103 Synechocystis #5 RCY12866 27 Synechocystis #6 RCY21740 300 Synechocystis #7 RCT00614 300 Chlamydia_trachomatis Motif number 1 GATGTTGGATTTTTGCCCCTAGATGGAGAG 1 157 1 TTTTGCCCCT 0.930303 -144 CACATAACAACTTCTTCCCT 1 291 1 CTTCTTCCCT 0.952906 -10 TCACCACTCCCCTTGACCCC 2 1 0 CCTTGACCCC 0.802712 -142 TACGGAGCCCCTTCTCCTCCCTTTCTAAGC 2 53 0 CTTCTCCTCC 0.878807 -90 GATTTTTCCCTGGGCAACTAT 2 132 0 ATTTTTCCCT 0.93372 -11 AATTGCGCTGATTTGTCTCCGACTCGTTGC 3 89 1 ATTTGTCTCC 0.840853 -65 GTTTTCTCTGTCCCCATCATTTTCC 4 6 1 CTCTGTCCCC 0.919584 -98 TGTCCCCATCATTTTCCCCTATGTATCCAT 4 19 1 ATTTTCCCCT 0.935947 -85 ATGTATCCATCCTCGTCCCCGGGCCATCGG 4 39 1 CCTCGTCCCC 0.92332 -65 GGTAAGCTAGATTTTACTCCCAGGAAATAT 4 71 0 ATTTTACTCC 0.498525 -33 CCCCCCTAGCCCCCCTTGGGATGG 6 5 1 CCTAGCCCCC 0.906551 -296 CTTTTGTCACAGTTTCCCCCATCCCAAGGG 6 23 0 AGTTTCCCCC 0.846138 -278 AGGCTAAGTATTTATCCCCCTAAATCTCCT 6 80 0 TTTATCCCCC 0.903003 -221 CCTTTTTTCGTTTCTTCCCCCGTTTCCCCT 6 276 1 TTTCTTCCCC 0.920353 -25 TTTCTTCCCCCGTTTCCCCTTCCCT 6 286 1 CGTTTCCCCT 0.890154 -15 AGAATGTTGTTTCTTTCCCTATGAGCCGTT 7 64 0 TTCTTTCCCT 0.698202 -237 CCAGAGGACGCTTTTTCTCTAATGACTCTT 7 158 0 CTTTTTCTCT 0.877635 -143 TTTTATGATTTTTATTCCCTTCCAGAGGAC 7 179 0 TTTATTCCCT 0.847697 -122 ATACGATTATATTAGTCCCTCTTCATTTAA 7 210 0 ATTAGTCCCT 0.877745 -91 TAAGCGGGATCTTAGTCTCTCGCACAAAAG 7 269 0 CTTAGTCTCT 0.785191 -32 ********** Masking position 7 Map Score: 22.8764 Number of sites scoring better than the average of aligned sites = 5338 Number in coding regions = 4601 Number in noncoding regions = 737 Number of orfs with sites within 600 bp upstream = 605 Fraction of orfs with sites within 600 bp upstream = 0.0971731 Motif number 2 ATCCGAGCCTGATTAACGTCGATTTTTTTATCAAGCCC 1 41 1 GAAATCTTTT 0.975501 -260 GTCGAATTGTGAGAAACTTTCGGGATTTTTCGGTTGTC 3 43 1 GAAATTGTTT 0.940576 -111 GTTGTCGCCTGAGCAATTGCGCTGATTTGTCTCCGACT 3 75 1 GAAAGCGTTT 0.956643 -79 GGGAAACTGTGACAAAAGTCCCCTTTTTAAGCCGGAGC 6 35 1 GAAATCTTTT 0.975538 -266 TATTTGAAAAGCGCAAGGCTAAGTATTTATCCCCCTAA 6 87 0 GCAACTTTTT 0.85267 -214 GAATGATAAAGACCAAAAGTTGATTTTTGGCAAGTTCT 6 141 0 GAAAGTTTTT 0.979334 -160 CAAACATTGAGAAGAATGTTGTTTCTTTCCCTATGAGC 7 68 0 GAAATTTTTT 0.973495 -233 AAGTGGGTGTGAAGAACCGTAATTTTTTAAAAAAGAGT 7 126 1 GAAAGTTTTT 0.97806 -175 AATCGTATAAGAAAAAGGTTTTTTTTTTAAAAAAAAGC 7 232 1 GAAATTTTTT 0.973495 -69 TTAGTCTCTCGCACAAAAGCTTTTTTTTAAAAAAAAAA 7 250 0 GCAAGCTTTT 0.955841 -51 ** ** ** * *** Masking position 6 Map Score: 12.034 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 67 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 AGCAGAAAAGAAGAAGCTGTAAACTCTCTCCAT 1 179 0 AAGAACTAAA 0.865824 -122 TCCGTTACCCTAAAAGCAGAAAAGAAGAAGCTG 1 193 0 TAAAACAAAA 0.877658 -108 GTGAAAGAGTAAGAATCACATAACAACTTCTTC 1 275 1 AAGAACATAA 0.976153 -26 CGACCTAATAAAAAACCCAATAAAAATAAATAG 3 14 0 AAAAACATAA 0.962696 -140 GCGACAACCGAAAAATCCCGAAAGTTTCTCACA 3 50 0 AAAAACGAAA 0.857746 -104 AATCCTGGCTAATAACCATATAACCAATACTTA 6 215 0 AATAACATAA 0.932576 -86 GAAACGGGGGAAGAAACGAAAAAAGGAGGGCGA 6 269 0 AAGAACAAAA 0.976153 -32 AACGAAGCAGAAGTATCCTATAATTCGTAAGCA 7 13 0 AAGTACATAA 0.852066 -288 GGAAGGGAATAAAAATCATAAAAGTTAAATGAA 7 186 1 AAAAACAAAA 0.962696 -115 GAGGGACTAATATAATCGTATAAGAAAAAGGTT 7 219 1 TATAACATAA 0.793595 -82 ***** * **** Masking position 5 Map Score: 7.79019 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 183 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 GGGACCGAGTCTGATCCGTTACCCTAAAAGCAGAA 1 205 0 CGCCTTCCCT 0.925726 -96 TTATGTGATTCTTACTCTTTCACCATCAAAAAGGG 1 263 0 CTTCTTACCA 0.950848 -38 GGATGCAAAGCCGTCTCCTTTAGCTTAGAAAGGGA 2 31 1 CGTCTTAGCT 0.98591 -112 TATCTGATGACCGCATAGTTGCCCAGGGAAAAATC 2 118 1 CGTATTCCCA 0.873075 -25 CGGTTGTCGCCTGAGCAATTGCGCTGATTTGTCTC 3 73 1 CGCATTCGCT 0.796048 -81 TGATTTGTCTCCGACTCGTTGCGCTTGAAAATTAA 3 97 1 CGTCTTCGCT 0.987813 -57 AACTTTTGGTCTTTATCATTCAGTAAGGCGGGGTT 6 158 1 CTTCTTAGTA 0.81041 -143 CAATACTTATCTTAATCTTTCCGGAAAATCAAACC 6 189 0 CTTCTTCGGA 0.951628 -112 TAGGATACTTCTGCTTCGTTCAGGAAGTCCTCAAA 7 26 1 CGTCTTAGGA 0.974039 -275 CCCTATGAGCCGTTTTCTTTGAGGACTTCCTGAAC 7 43 0 CTTCTTAGGA 0.944392 -258 ATGTTTGCTGCTGTTTCATTAAACAAAAAGTGGGT 7 99 1 CGTCTTAACA 0.949921 -202 TATATTAGTCCCTCTTCATTTAACTTTTATGATTT 7 198 0 CTTCTTAACT 0.861818 -103 * * ** ** **** Masking position 9 Map Score: 8.98735 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 408 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 5 CAAACTATGTGACCCTTTTTGATGGTGAAA 1 251 1 GACCCTTTTT 0.971462 -50 GTGACAAAAGTCCCCTTTTTAAGCCGGAGC 6 43 1 TCCCCTTTTT 0.943463 -258 CCTCCGTCGCCCTCCTTTTTTCGTTTCTTC 6 263 1 CCTCCTTTTT 0.938137 -38 CTCAATGTTTGCTGCTGTTTCATTAAACAA 7 95 1 GCTGCTGTTT 0.84103 -206 GTTCTTCACACCCACTTTTTGTTTAATGAA 7 113 0 CCCACTTTTT 0.943463 -188 TTTCTCTAATGACTCTTTTTTAAAAAATTA 7 145 0 GACTCTTTTT 0.895483 -156 CCTTCCAGAGGACGCTTTTTCTCTAATGAC 7 162 0 GACGCTTTTT 0.971462 -139 AGACTAAGATCCCGCTTATTGGCATTGTGT 7 281 1 CCCGCTTATT 0.92237 -20 ********** Masking position 6 Map Score: 4.32503 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 418 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 GGCTTGATAAAAAAATCGACGTTAATCAGG 1 48 0 AAAAATCGAC 0.89655 -253 TCTAGGGGCAAAAATCCAACATCTAATGTC 1 150 0 AAAATCCAAC 0.928825 -151 AAAGTTTCTCACAATTCGACCTAATAAAAA 3 33 0 ACAATTCGAC 0.66229 -121 CGAGTCGGAGACAAATCAGCGCAATTGCTC 3 85 0 ACAAATCAGC 0.844431 -69 AATGACGTTTAAAAATTAACTATCTCCCCA 3 130 1 AAAAATTAAC 0.837789 -24 TCCTGGGAGTAAAATCTAGCTTACCTCTGC 4 76 1 AAAATCTAGC 0.651502 -28 AGAACTTGCCAAAAATCAACTTTTGGTCTT 6 141 1 AAAAATCAAC 0.957593 -160 ATCTTTCCGGAAAATCAAACCCCGCCTTAC 6 180 0 AAAATCAAAC 0.810496 -121 CTCATAGGGAAAGAAACAACATTCTTCTCA 7 69 1 AAGAAACAAC 0.726084 -232 CTTTTTTTTAAAAAAAAAACCTTTTTCTTA 7 239 0 AAAAAAAAAC 0.821849 -62 TTTTTTTTTTAAAAAAAAGCTTTTGTGCGA 7 250 1 AAAAAAAAGC 0.742888 -51 ********** Masking position 4 Map Score: 3.98351 Number of sites scoring better than the average of aligned sites = 889 Number in coding regions = 704 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 7 ********** No masking Map Score: -3.61423e-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: -3.61423e-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: -3.61423e-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