AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i209_synecho_ctra_300.orf -o209_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 RCY17385 152 Synechocystis #2 RCY16671 240 Synechocystis #3 RCY22330 51 Synechocystis #4 RCY11539 185 Synechocystis #5 RCY38294 42 Synechocystis #6 RCY35677 300 Synechocystis #7 RCT00586 154 Chlamydia_trachomatis #8 RCT00587 300 Chlamydia_trachomatis #9 RCT00759 300 Chlamydia_trachomatis Motif number 1 CGATCGGCAACCCCTAGCAACCACCGGCTA 2 75 1 CCCCTAGCAA 0.971072 -166 CATAACCGGCTCCCAAGCAAAGAAATCTCT 2 166 1 TCCCAAGCAA 0.975898 -75 AAAAAAACTGGGCCCAGCTAGGGAGCCCAG 6 108 0 GGCCCAGCTA 0.899911 -193 CCATATCTGTGGCCTAGCAAAACACGAGTG 6 265 0 GGCCTAGCAA 0.981768 -36 ATCAGATTTAGGCCTAGAAAAACCCCTCCC 7 28 0 GGCCTAGAAA 0.965885 -127 AGGAAAAATCGGCCTAGAAAGTGACAGTTT 7 111 0 GGCCTAGAAA 0.965885 -44 CCAAACTATATCCCTACAAATCGCGAATTT 8 92 0 TCCCTACAAA 0.812774 -209 TGCAGTGCATCCCCAAACTATATCCCTACA 8 104 0 CCCCAAACTA 0.656072 -197 AATGTAGGACTGCCAAACAAAAAATACACT 8 207 1 TGCCAAACAA 0.905477 -94 AGTCTTGTATTCCCCAAAAATTCAACACCG 9 75 0 TCCCCAAAAA 0.832777 -226 AAGCACACATTCCCAAGAAAATTATAGTGC 9 153 1 TCCCAAGAAA 0.955135 -148 ********** Masking position 6 Map Score: 9.29929 Number of sites scoring better than the average of aligned sites = 872 Number in coding regions = 766 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 AACCCCTAGCAACCACCGGCTAGACAGATTT 2 83 1 AACACCGGCT 0.968106 -158 TACTCATATACATAACCGGCTCCCAAGCAAA 2 156 1 CAAACCGGCT 0.968108 -85 GGGGGCGAGGATAATCCGGCTAG 5 3 0 ATATCCGGCT 0.972789 -40 GCGTGATGCAAAAAACGGGCTTGGAGGGACT 6 60 0 AAAACGGGCT 0.978708 -241 GCCCGATGATAATAATCGGCGTGATGCAAAA 6 78 0 AAAATCGGCG 0.918763 -223 GCCGATTATTATCATCGGGCTGGGCTCCCTA 6 89 1 ATATCGGGCT 0.926731 -212 GACCAAACCAAAGATTCGGCTATCTACAGAG 6 201 1 AAATTCGGCT 0.957148 -100 CCTAAATCTGATCAACAGGCTTTTTTTTATC 7 46 1 ATAACAGGCT 0.898374 -109 AAAACTAAGGAAAAATCGGCCTAGAAAGTGA 7 117 0 AAAATCGGCC 0.918763 -38 ** ******** Masking position 10 Map Score: 6.94714 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 217 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 CTTAAGTTGACAAGTATCTCTCCCCATCGTCAC 1 102 1 CAGTTCCTCC 0.833484 -51 GTATCTCTCCCCATCGTCACTCTTAGAAGGAGA 1 115 1 CATCTCCTCT 0.930666 -38 GATAAATCAACCTACTCTCCTTCTAAGAGT 1 133 0 CACCACCTCC 0.909473 -20 TGGCTTTCCATCTCCCCACCACCACAGACT 2 8 1 CATCCCCACC 0.976209 -233 CCAACGGAATCAATCACCCCTCTAATGGCGATC 2 47 1 CATCCCCTCT 0.976169 -194 CATATATCTACTATCCAGTATCCAGTGGAAAGA 4 69 0 CATCAGATCC 0.825756 -117 TATGAATTTCCCAGGACCAAACCAAAGATTCGG 6 187 1 CAGGCCAACC 0.91226 -114 TTCAAAAAAACAATGATCAATCCCAAAATTCGC 8 67 1 CATGTCATCC 0.950712 -234 TAGTGCGTTACCATGGCGGATCCTTTATCGCCG 9 177 1 CATGCGATCC 0.933428 -124 TTTTTACACGCGATGCCCGCTCTTCGGCGATAA 9 201 0 CATGCCCTCT 0.965019 -100 ACTAGCCTAGCTCCAATCCTCTTGTTGCT 9 282 0 CAGCCCATCC 0.984103 -19 * *** ** **** Masking position 3 Map Score: 6.96152 Number of sites scoring better than the average of aligned sites = 1140 Number in coding regions = 1055 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 ACAAATACATAAGGAATTATAACCAA 2 225 1 AAGGAATTAT 0.80547 -16 TGGTATTAGAAAGGGTTTATTTTGCTTCTT 4 43 1 AAGGGTTTAT 0.917596 -143 AAAATAGGGAAATTTAAGCGGGGGC 5 28 0 AGGGAAATTT 0.829812 -15 GCCTGAGCACAGGGGACTATGAATTTCCCA 6 170 1 AGGGGACTAT 0.91976 -131 AAAAGACGGGAGGGGTTTTTCTAGGCCTAA 7 21 1 AGGGGTTTTT 0.981533 -134 CAAGAAATCTAGGGATTTTTAGATAAAAAA 7 68 0 AGGGATTTTT 0.962591 -87 TAGTATGACAAGGGGTTTTTTGAATAAGCG 8 163 1 AGGGGTTTTT 0.981533 -138 ********** Masking position 1 Map Score: 4.06114 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 394 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 GCACCCCCCGGTGAAGGAGAGTGCAATTTGC 1 41 0 GGAAGGAGAG 0.859882 -112 TAAGAGTGACGATGGGGAGAGATACTTGTCA 1 109 0 GTGGGGAGAG 0.926872 -44 TCAGTCTGTGGTGGTGGGGAGATGGAAAGCC 2 12 0 GGGTGGGGAG 0.985652 -229 TGTCTAGCCGGTGGTTGCTAGGGGTTGCCGA 2 78 0 GGGTTGCTAG 0.839508 -163 GGAAATTTAAGCGGGGGCGAGGATAATCCGG 5 15 0 GGGGGGCGAG 0.995105 -28 GCTTAGTGGATTAGAGCGCGTGGCTA 6 6 1 GGGATTAGAG 0.940953 -295 CCACGAGGTCGGGGGTTCGAGTCCCTCCAAG 6 41 1 GGGGTTCGAG 0.981044 -260 AATCGCCAAAACGGGTGGGAGGTAATGAAAG 8 253 0 AGGGTGGGAG 0.939322 -48 AGAGCAACAAGAGGATTGGAGCTAGGCTAGT 9 280 1 GGGATTGGAG 0.961623 -21 * ********* Masking position 10 Map Score: 6.90909 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 351 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 CAGATTATTCAGTTGGCATTACACCAAGGA 1 12 0 AGTTGGCATT 0.824164 -141 TGTTCAAAGGATTTGGCCTCAAGCTCAGAG 2 192 0 ATTTGGCCTC 0.976926 -49 GAAAGGGTTTATTTTGCTTCTTTCCACTGG 4 51 1 ATTTTGCTTC 0.88905 -135 TCCGCTCAACATTTGTCTTTGACCTGTTTT 4 152 1 ATTTGTCTTT 0.891009 -34 TTCTAGGCCGATTTTTCCTTAGTTTTAATT 7 122 1 ATTTTTCCTT 0.86842 -33 TTGTCATACTATTGGTCCTTCCCATCACAT 8 144 0 ATTGGTCCTT 0.817671 -157 GCCTATAGGGAGTTGGCCTTTT 8 289 1 AGTTGGCCTT 0.960723 -12 TCTCTTAAGAATTTTGCTTCCCAAAGTCTT 9 99 0 ATTTTGCTTC 0.88905 -202 ********** Masking position 1 Map Score: 3.06448 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 311 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 ACAACGGCTATTTCTTAAGATTGGCTCTGA 4 122 0 TTTCTTAAGA 0.979268 -64 ATTTCTTGTTTTTCTTAAGATAAACTGTCA 7 90 1 TTTCTTAAGA 0.979268 -65 GATTCCTTTTTCTCTTAAGAATTTTGCTTC 9 109 0 TCTCTTAAGA 0.978052 -192 GCACTATAATTTTCTTGGGAATGTGTGCTT 9 153 0 TTTCTTGGGA 0.926017 -148 TTGTTGCTCTTCTCTTATGATCCACTATTC 9 260 0 TCTCTTATGA 0.952854 -41 ********** Masking position 5 Map Score: 2.95645 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 5 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 TTCAGCTTACCAAAAACAGGTCAAAGACAA 4 164 0 CAAAAACAGG 0.959119 -22 GGCGTGATGCAAAAAACGGGCTTGGAGGGA 6 62 0 AAAAAACGGG 0.988552 -239 CATAGCTATAAAAAAACTGGGCCCAGCTAG 6 117 0 AAAAAACTGG 0.956012 -184 GGATAAGTAGAAAAGACGGGAGGGGTTTTT 7 11 1 AAAAGACGGG 0.974937 -144 AGGAGAATCGCCAAAACGGGTGGGAGGTAA 8 259 0 CCAAAACGGG 0.976734 -42 ********** Masking position 6 Map Score: 2.89762 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 72 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 ACATATTCCGCTGGTAATAAT 3 2 1 CATATTCCGC 0.961297 -50 AGATATATGCCATGGTCCCCAAACCTGAGT 4 93 1 CATGGTCCCC 0.991561 -93 CCCCCGACCTCGTGGTCCGTAGCCACGCGC 6 26 0 CGTGGTCCGT 0.911157 -275 CTGGGAAATTCATAGTCCCCTGTGCTCAGG 6 171 0 CATAGTCCCC 0.986794 -130 TACATAAGAGCCTGTTCCCCTACTACGAAT 9 15 0 CCTGTTCCCC 0.977693 -286 CCCAAAGTCTTGTATTCCCCAAAAATTCAA 9 80 0 TGTATTCCCC 0.888093 -221 ********** Masking position 6 Map Score: 2.29648 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 284 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 AGAGATACTTGTCAACTTAAGCTCTACTCAAG 1 91 0 GTAATTAAGC 0.954765 -62 CCAGTATCCAGTGGAAAGAAGCAAAATAAACC 4 56 0 GTGAAGAAGC 0.974489 -130 ATACTGGATAGTAGATATATGCCATGGTCCCC 4 81 1 GTGAATATGC 0.921747 -105 AAAATAGGGAAATTTAAGCGGGGGCGAGG 5 24 0 GGAATTAAGC 0.934068 -19 CTATGGAGTTGTAGACTTTAGCTTTCCGGCCT 6 142 1 GTGATTTAGC 0.900478 -159 AATCCATCAGGGAGAAAGAAGCACACATTCCC 9 135 1 GGGAAGAAGC 0.962552 -166 TCCACTATTCGTGAATATAAGCATCGTACAAT 9 238 0 GTAAATAAGC 0.964855 -63 ** ** ****** Masking position 5 Map Score: 2.50714 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 77 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TTGATTCCGTTGGGGCTTCAGTCTGTGGTG 2 30 0 TGGGGCTTCA 0.91299 -211 GCCACAGATATGGGGCAGGAGTTTCCACC 6 282 1 TGGGGCAGGA 0.973744 -19 ATCGCGAATTTTGGGATTGATCATTGTTTT 8 73 0 TTGGGATTGA 0.944361 -228 GGATATAGTTTGGGGATGCACTGCAGGCAT 8 109 1 TGGGGATGCA 0.969905 -192 GCAGTATGTGATGGGAAGGACCAATAGTAT 8 139 1 ATGGGAAGGA 0.904548 -162 ATACAAGACTTTGGGAAGCAAAATTCTTAA 9 95 1 TTGGGAAGCA 0.972029 -206 TATAATTTTCTTGGGAATGTGTGCTTCTTT 9 149 0 TTGGGAATGT 0.821055 -152 ********** Masking position 5 Map Score: 3.12418 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 376 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 12 GTAATAATAATTTTGAATTTTATGAGTCGGA 3 24 1 TTTGAATTTT 0.94627 -28 AAAATAGGGAAATTTAAGCGGGGGC 5 28 0 TGGGAAATTT 0.84385 -15 ACAAGAAATCTAGGGATTTTTAGATAAAAAA 7 68 0 TGGGATTTTT 0.84385 -87 ATCATTGTTTTTTTGAATTTTGGAATATCAA 8 53 0 TTTGAATTTT 0.94627 -248 TCCCTACAAATCGCGAATTTTGGGATTGATC 8 81 0 TGCGAATTTT 0.942482 -220 CGAAATACAATAGTGTATTTTTTGTTTGGCA 8 217 0 TGTGTATTTT 0.866995 -84 TGTACAACGGTGTTGAATTTTTGGGGAATAC 9 68 1 TTTGAATTTT 0.94627 -233 CCTTTTTCTCTTAAGAATTTTGCTTCCCAAA 9 104 0 TAAGAATTTT 0.679338 -197 * ********* Masking position 9 Map Score: 1.49544 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 189 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 13 CCAAAATCACTCAGTTATTCCCACTATCA 4 8 1 CACTCATATT 0.841538 -178 CAGTTATTCCCACTATCATTTTGGTATTAGAA 4 22 1 CACTATTTTT 0.9724 -164 GAGTTTGACGCACTCGTGTTTTGCTAGGCCAC 6 255 1 CACTCGTTTT 0.958742 -46 TTTTAGAATCTACTATGATATTGGCAACTACT 8 18 0 TACTATTATT 0.710352 -283 ACAAAAAATACACTATTGTATTTCGCGATACT 8 223 1 CACTATTATT 0.956449 -78 CACCGTTGTACACTCGCGTTTCGAAGGTTTTC 9 48 0 CACTCGTTTC 0.860571 -253 CATGGTAACGCACTATAATTTTCTTGGGAATG 9 160 0 CACTATTTTT 0.9724 -141 AAGCATCGTACAATATTTTTTTTACACGCGAT 9 220 0 CAATATTTTT 0.797337 -81 ****** **** Masking position 2 Map Score: 1.38482 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 131 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 ********** No masking Map Score: 2.23354e-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 15 ********** No masking Map Score: 2.23354e-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