AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i308_synecho_ctra_100.orf -o308_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 RCY18056 198 Synechocystis #2 RCY08755 34 Synechocystis #3 RCY51306 167 Synechocystis #4 RCY51398 55 Synechocystis #5 RCY29713 300 Synechocystis #6 RCT00361 28 Chlamydia_trachomatis #7 RCT00362 68 Chlamydia_trachomatis #8 RCT00363 300 Chlamydia_trachomatis #9 RCT00547 294 Chlamydia_trachomatis #10 RCT00734 153 Chlamydia_trachomatis Motif number 1 ACCCGCCAGCAAAAAAATTACAATCGTTTA 5 14 0 AAAAAAATTA 0.841663 -287 ATGATTCTTAAAAAAAATAAGAAT 7 5 0 AAAAAAATAA 0.879776 -64 GAAACTACTCAAAGGAAGAGCTGAATATGC 8 60 1 AAAGGAAGAG 0.91219 -241 TCTTCTCTTGAAGAGAAGAGAACGTTTAAT 8 179 0 AAGAGAAGAG 0.943684 -122 TCTTCTCTTCAAGAGAAGAGGGCGTTTTTT 8 190 1 AAGAGAAGAG 0.943684 -111 AGGGAAGAGAAAAGAAATAGAAAGATTTTT 8 226 0 AAAGAAATAG 0.848552 -75 TTCATGAGTTAAGAGAAGAAACAAGGAAAA 8 273 1 AAGAGAAGAA 0.883518 -28 GATAATTCCTAAAAAAATAAAAATAACAAA 9 14 1 AAAAAAATAA 0.879776 -281 AACTTACGCAAAAAGAATTAATTATGTTTT 9 125 0 AAAAGAATTA 0.894825 -170 CCTCCTGTTAAAAAAAATTGCAAGGCAACG 9 177 0 AAAAAAATTG 0.921529 -118 GAAGAATCTAAAAAGAATTGCTTTTTTAAA 10 33 1 AAAAGAATTG 0.949485 -121 TTTTAAATAGAAAAAAAGTGAGAAACCCTT 10 56 1 AAAAAAAGTG 0.931524 -98 ********** Masking position 6 Map Score: 12.3781 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 287 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 2 GCTGTTGATAGAGGCGCTTTAGTTGCTTAA 3 122 0 GAGGCGCTTT 0.985096 -46 GATCGCCGGGGAGACGCTGTTGATAGAGGC 3 137 0 GAGACGCTGT 0.933834 -31 TCATTGCAAAGGGGCGTTGTAGGATGGAAT 5 80 1 GGGGCGTTGT 0.990899 -221 AAACGATTAAGGGGCCTTATT 6 18 1 GGGGCCTTAT 0.950964 -11 TTATACAAGGCGTTATGTGTTTAACT 8 7 1 AAGGCGTTAT 0.95777 -294 ATATGCTGATGAGGCGCTATTTCAAGCTTT 8 84 1 GAGGCGCTAT 0.990119 -217 TCAAGAGAAGAGGGCGTTTTTTTCATTGAA 8 198 1 AGGGCGTTTT 0.950151 -103 ********** Masking position 8 Map Score: 6.75259 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 133 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 CCTTTGACCTAAGGCGATCGCCTTACCCCA 1 14 1 AAGGCGATCG 0.987956 -185 ATTAGGACTAAAGCCTATCGATACCATCTA 3 60 1 AAGCCTATCG 0.967096 -108 GACTGGTTTTAAGCCGTTGGGTTTGGCCGT 3 89 0 AAGCCGTTGG 0.94993 -79 CGTTAGCAGGCGATCGCCGGGGAGAC 3 152 0 CAGGCGATCG 0.990005 -16 CCAGGCGAAGCTGGCGATCGAGTGTAAAAG 5 228 1 CTGGCGATCG 0.977316 -73 GGTATAGTCCCTGCCGTTAGACCATTGAGT 7 39 1 CTGCCGTTAG 0.870516 -30 CGTGAAGTCCAAGCCTTTCGCGCAGGAGGT 9 214 0 AAGCCTTTCG 0.957577 -81 ********** Masking position 8 Map Score: 6.34009 Number of sites scoring better than the average of aligned sites = 2617 Number in coding regions = 2377 Number in noncoding regions = 240 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 4 AGTTAGTCTGGGGTAAGGCGATCGCCTTAG 1 22 0 GGGTAAGGCG 0.984191 -177 TTAAGCCGTTGGGTTTGGCCGTAGATGGTA 3 81 0 GGGTTTGGCC 0.946733 -87 GGGTAATGCTCAAAGTTTGA 4 46 0 GGGTAATGCT 0.973234 -10 TTTTGCTGGCGGGTATGACTTTCCATTTTT 5 30 1 GGGTATGACT 0.949068 -271 CATTCAGACAGGGTATTGCGGGGTAAGTCT 5 158 1 GGGTATTGCG 0.979728 -143 GGGTATTGCGGGGTAAGTCTCCAAACATCG 5 168 1 GGGTAAGTCT 0.95346 -133 AGCTTCGCCTGGGTATTTTTTATGGAGTAG 5 210 0 GGGTATTTTT 0.784478 -91 GAATCATGTTGGGTATAGTCCCTGCCGTTA 7 28 1 GGGTATAGTC 0.813749 -41 ********** Masking position 4 Map Score: 4.88964 Number of sites scoring better than the average of aligned sites = 606 Number in coding regions = 554 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 GAATTGTTAGAAAACGCAAAATTGTCAGGAA 1 102 0 AAAAGCAAAA 0.932978 -97 AGTTCCTAATACAATGCAAAATGGGGATCTT 1 171 0 ACAAGCAAAA 0.98078 -28 AAGACTCAACTCAACGCAGACCTGCAATAGG 5 255 1 TCAAGCAGAC 0.93574 -46 TCCTACAATAACAAAGCAAACTACAAGTTAA 8 31 0 ACAAGCAAAC 0.984031 -270 GAAAGATTTTTCAATGAAAAAAACGCCCTCT 8 206 0 TCAAGAAAAA 0.914461 -95 AAGAGAAGAAACAAGGAAAACAAATCTA 8 283 1 ACAAGAAAAC 0.943852 -18 TATGTTTTATTAAAAGCAAAATATTAAAAAC 9 102 0 TAAAGCAAAA 0.914461 -193 **** ****** Masking position 4 Map Score: 4.59382 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 144 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 CAAAATTGTCAGGAAAAGACTGGCATTGACG 1 86 0 AGGAAAGACT 0.936307 -113 CTATGGCGGCAGGTGACGGTTGCTGACATTC 5 106 0 AGGGACGGTT 0.92997 -195 TTTTAGAAAACGATTAAGGGGCCTT 6 5 1 AGAAACGATT 0.919474 -24 TTGTTATTGTAGGAAACTACTCAAAGGAAGA 8 48 1 AGGAACTACT 0.936303 -253 CTGATCCGTTAGGCAACTGTTTAATATCAGA 8 139 0 AGGAACTGTT 0.917979 -162 CTTGAAGAGAAGAGAACGTTTAATGATGCTA 8 172 0 AGAAACGTTT 0.738012 -129 AAAAATTGCAAGGCAACGACACACGCTGCTG 9 164 0 AGGAACGACA 0.959334 -131 TTCGCGCAGGAGGTAACGGTACCTCCTGTTA 9 197 0 AGGAACGGTA 0.94726 -98 GGAAGATAAAAGGTAGAGACTTCTTCCGTCA 10 89 1 AGGAGAGACT 0.774505 -65 *** ******* Masking position 1 Map Score: 2.96051 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 434 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 CCCCGGCGATCGCCTGCTAACG 3 156 1 CGCCTGCTAA 0.993071 -12 GTTTCTCTGTCCCCTTCAAACTTTGAGCAT 4 31 1 CCCCTTCAAA 0.94305 -25 AAGTCATACCCGCCAGCAAAAAAATTACAA 5 21 0 CGCCAGCAAA 0.968152 -280 GTAACGGTACCTCCTGTTAAAAAAAATTGC 9 186 0 CTCCTGTTAA 0.873612 -109 AATCTCGCCTTCTAATTCAGCTTGT 10 139 0 CGCCTTCTAA 0.984522 -15 ********** Masking position 9 Map Score: 1.49146 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 116 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TCAAACTTGGCATTTAAAAATGGAAAGTCATAC 5 42 0 CATAAAATGG 0.813834 -259 TTGAGTAGATCATTGCAAAGGGGCGTTGTAGGA 5 71 1 CATCAAGGGG 0.933206 -230 GCCATAGGTACTTTACCTCGGGGACTTACATTC 5 130 1 CTTCTCGGGG 0.954706 -171 CGGGGACTTACATTCAGACAGGGTATTGCGGGG 5 148 1 CATAACAGGG 0.977588 -153 TCAACGCAGACCTGCAATAGGGGGGATACCGGC 5 265 1 CCTATAGGGG 0.9279 -36 GCCGTTAGACCATTGAGTCGGAGTGAGT 7 51 1 CATATCGGAG 0.930894 -18 AACAGCAAATCATACACACAGGGAAGAGAAAAG 8 242 0 CATAACAGGG 0.977588 -59 ATAGTAAAGTCTTAAAATCATAGCGGAGATGCT 9 270 1 CTTATCATAG 0.565006 -25 TACCTTTTATCTTCCAATAAGGGTTTCTCACTT 10 71 0 CTTATAAGGG 0.944448 -83 *** * ****** Masking position 3 Map Score: 1.04334 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 586 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 GCCAACAATCTCAAAAGATTGGCT 2 21 0 ACAATCTCAA 0.855868 -14 GGCAAAAAACAGAAGTTGAATTTATAGCCT 3 16 0 AGAAGTTGAA 0.905742 -152 AAAGCAAACTACAAGTTAAACACATAACGC 8 20 0 ACAAGTTAAA 0.920577 -281 TCAGATCGTTAGAATTTAATATTGTTAGTA 9 48 0 AGAATTTAAT 0.819987 -247 ATCTGATTTAACAAGTTAATTAATAAAAAC 9 72 1 ACAAGTTAAT 0.87842 -223 TGCATCTAGAAGAATCTAAAAAGAATTGCT 10 25 1 AGAATCTAAA 0.87749 -129 TCTTCCGTCAAGAATTTCATCATTAGATTA 10 110 1 AGAATTTCAT 0.790637 -44 TCATTAGATTACAAGCTGAATTAGAAGGCG 10 129 1 ACAAGCTGAA 0.904018 -25 ********** Masking position 4 Map Score: 1.30973 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 154 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 ********** No masking Map Score: 3.71914e-13 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 CGTCAATGCCAGTCTTTTCCTGACAATTTT 1 86 1 AGTCTTTTCC 0.966328 -113 CGTTGAGTTGAGTCTTTTACACTCGATCGC 5 241 0 AGTCTTTTAC 0.849649 -60 TGTTGGGTATAGTCCCTGCCGTTAGACCAT 7 34 1 AGTCCCTGCC 0.921101 -35 TCTTCCTTTGAGTAGTTTCCTACAATAACA 8 49 0 AGTAGTTTCC 0.761902 -252 TTCTATTTCTTTTCTCTTCCCTGTGTGTAT 8 234 1 TTTCTCTTCC 0.900118 -67 CAGCAGCGTGTGTCGTTGCCTTGCAATTTT 9 164 1 TGTCGTTGCC 0.898745 -131 TCTCTCGTGCTGTCTCTCACTGAATAGTAA 9 247 1 TGTCTCTCAC 0.767178 -48 GTCTCTACCTTTTATCTTCCAATAAGGGTT 10 79 0 TTTATCTTCC 0.63958 -75 TGACGGAAGAAGTCTCTACCTTTTATCTTC 10 90 0 AGTCTCTACC 0.932929 -64 ********** Masking position 7 Map Score: 0.586177 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 467 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 12 ********** No masking Map Score: 3.71914e-13 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 13 ********** No masking Map Score: 3.71914e-13 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 14 ********** No masking Map Score: 3.71914e-13 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