AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i225_synecho_ctra_300.orf -o225_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 RCY16794 188 Synechocystis #2 RCY17332 228 Synechocystis #3 RCY32570 127 Synechocystis #4 RCY19563 100 Synechocystis #5 RCY22523 192 Synechocystis #6 RCY03497 49 Synechocystis #7 RCY41630 300 Synechocystis #8 RCY48213 282 Synechocystis #9 RCY50646 95 Synechocystis #10 RCY28122 56 Synechocystis #11 RCT00002 300 Chlamydia_trachomatis Motif number 1 AATCCCTTTTCCTGGCGATCGTCGTTGGCATAGC 1 68 0 CCTGGGCGTG 0.903321 -121 TTAAATTTTTCCGGGAGTCGGGCCCTAAGGCAGA 1 100 1 CCGGGGGGGC 0.979399 -89 GGTCAGTTGACCGGGCGCTGGGGAGGGTTTTGGC 2 11 1 CCGGGGGGGA 0.996402 -218 TTGCTGATAGACTGGGGGAGGTAAATCTGGCTCT 3 98 1 ACTGGGGGTA 0.909687 -30 TCCGATCGCCGCTGGGGGTTAGTGAGGGAGAAAA 4 18 1 GCTGGGTAGG 0.800105 -83 CCGTTGGACGGCGGGAGTATGGCAGAATGGGAGG 4 56 1 GCGGGGTGGA 0.965513 -45 AATTCCATTTCCTGGCGTGAGGAAGTTCTTACAC 5 168 1 CCTGGGAGGA 0.960572 -25 GTGACGTCTCCATGGTTCCGGGCA 6 36 1 CATGGTGGGA 0.953387 -14 ATTTCCGCCCGAGGGGGAAGGTTATTATGTGCCA 7 129 1 GAGGGGGGTA 0.9699 -172 TTTCCATCGCCATGGTGATGGTGGCTATGGGCAA 7 192 0 CATGGGGGTG 0.981497 -109 TCATGGTCATCATGGCTGTGGGCAAAATTTCCAT 7 219 0 CATGGTGGGA 0.953387 -82 TGATGTTCTTGCTGGTCATGGTCATCATGGCTGT 7 234 0 GCTGGCGGTA 0.866885 -67 CTGTAGTTGCCATGGTGGTGATGATGTTCTTGCT 7 255 0 CATGGGGATA 0.910145 -46 CAGGTCAACAGCAGGAGGGGGGCATATCTATAGC 8 28 1 GCAGGGGGGA 0.962997 -255 GAGTAGGGAGCATGGTGGCTGGAGAAGTTTGCCT 8 239 0 CATGGGTGGG 0.962325 -44 TGGTAGTGCAGATGGGGGAGAGTAGGGAGCATGG 8 258 0 GATGGGGAGA 0.946817 -25 GGGTTAAGTCCAGGGAGTAGGGAGTACAAGTCTT 9 57 1 CAGGGGGGGG 0.991373 -39 ***** * *** * Masking position 5 Map Score: 22.6882 Number of sites scoring better than the average of aligned sites = 2770 Number in coding regions = 2595 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 2 GATCGTCGTTGGCATAGCTCGATCCTATGATCAAC 1 51 0 GGCAACTACC 0.97277 -138 CCCGACTCCCGGAAAAATTTAATCCCTTTTCCTGG 1 87 0 GGAAATTACC 0.906307 -102 AGACTGTTTTGGCACAGTTCAATCTTTATTCTGCC 1 128 0 GGCAATTACT 0.930091 -61 GAAAATTTTAGCCAAAACCCTCCCCAGCGCCCGGT 2 20 0 GCCAACCCCC 0.864091 -209 GGTTACGCTTAGCAGGCTTCTCTCCGAAACCCACT 2 172 1 AGCAGTTCCC 0.899888 -57 AGGGAAAGAGCCAGATTTACCTCCCCCAGTCTAT 3 104 0 GCCAATTCCC 0.972762 -24 CCGTCCAACGGGCACTTTTCTCCCTCACTAACCCC 4 32 0 GGCATTTCCT 0.924703 -69 TTTTGGCAAAAAATCCCCTCTAAGCGAGC 5 5 1 GGCAAAACCT 0.813482 -188 CTACTCCCCAGGAACAATTTTCCCCGGAATTAATC 5 100 0 GGAAATTCCC 0.969139 -93 CCTGGCGTGAGGAAGTTCTTACACC 5 178 1 GGAATCTCCC 0.86002 -15 AAAAGATTATGGCAGTGACGTCTCCATGGTTCCGG 6 22 1 GGCATACCCC 0.84811 -28 CCGCAGTTTTGGCACATAATAACCTTCCCCCTCGG 7 137 0 GGCAAAAACT 0.580547 -164 GTGGCTATGGGCAACGGTTCCCACCGCACTACAAC 7 171 0 GCAAGTTCCC 0.800757 -130 CATGGCTGTGGGCAAAATTTCCATCGCCATGGTGA 7 208 0 GGCAATTCTC 0.888188 -93 GCAGGAGGGGGGCATATCTATAGCTTGCCCTGAAA 8 38 1 GGCAACTACT 0.898242 -245 CACCGTTGATGGCAGGGATCAATCCTGGTAATCCT 8 173 0 GGCAGATACC 0.930408 -110 AAACACGGGTAGCACACTATTCCCCTTTGGATGAC 9 20 1 AGCAATACCC 0.787173 -76 TTTTTCCTGGCAAGATTAGCGCCTTTAAACTGA 10 9 1 GGCAGTTCCC 0.984988 -48 **** * ** * ** Masking position 4 Map Score: 18.2598 Number of sites scoring better than the average of aligned sites = 2726 Number in coding regions = 2501 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 246 Fraction of orfs with sites within 600 bp upstream = 0.0395117 Motif number 3 GAGTCGGGCCCTAAGGCAGAATAAAGATTGAA 1 114 1 CTAGCAGAAT 0.976091 -75 CCAAAACAGTCTGAAGCAAAAGAGATTATCAG 1 151 1 CTAGCAAAAG 0.98109 -38 GACGGCGGGAGTATGGCAGAATGGGAGGAAGC 4 62 1 GTTGCAGAAT 0.83875 -39 ACCATGGCAACTACAGCAAAAGTCCAAGTCAG 7 273 1 CTCGCAAAAG 0.908736 -28 ACCGAGGGGACTTTGGCAAAAGCTTTTGTATT 8 117 1 CTTGCAAAAG 0.59561 -166 GAGACAGTTACTAAGGCAAACTTCTCCAGCCA 8 226 1 CTAGCAAACT 0.9173 -57 ATGCGTTTTGCTGTCGCAAAAGACGCTTCAGT 11 201 1 CTTGCAAAAG 0.919977 -100 CAATCATGATCTTATGCAGAATAAAATCCTTC 11 260 0 CTAGCAGAAT 0.935046 -41 ** * ******* Masking position 8 Map Score: 7.3684 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 118 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 CGACGATCGCCAGGAAAAGGGATTAAATTT 1 78 1 CAGGAAAAGG 0.827127 -111 ATGTCTTCACAAGGGAAAATTTTAGCCAAA 2 39 0 AAGGGAAAAT 0.920982 -190 AAACCAGAGAAAAGAAAGAGAGTGGGTTTC 2 197 0 AAAGAAAGAG 0.800551 -32 TTCGTTGTAGAAGGGAAGGTGTTTGAGTCA 3 44 1 AAGGGAAGGT 0.958839 -84 CCTAGCAAAAAAGGAAAGATGACTCAAACA 3 63 0 AAGGAAAGAT 0.944641 -65 AGGGAAAGAGCCAGATTTAC 3 118 0 AGGGAAAGAG 0.958839 -10 AGATTAATTCCGGGGAAAATTGTTCCTGGG 5 99 1 CGGGGAAAAT 0.827127 -94 TTCCTCACGCCAGGAAATGGAATTTGTAAC 5 162 0 CAGGAAATGG 0.719446 -31 GAGTTGAAGGAAAAAGATTATGGCAG 6 7 1 AAGGAAAAAG 0.920982 -43 TTCCGCCCGAGGGGGAAGGTTATTATGTGC 7 131 1 GGGGGAAGGT 0.78105 -170 TTAATCAAAGGAAGAGGCAGGTCAAC 8 7 1 AAAGGAAGAG 0.881827 -276 GGTCATCCAAAGGGGAATAGTGTGCTACCC 9 26 0 AGGGGAATAG 0.895045 -70 GAACAACAATAAGAGAAGATAATCCTCTAC 11 65 1 AAGAGAAGAT 0.676324 -236 ********** Masking position 6 Map Score: 7.19208 Number of sites scoring better than the average of aligned sites = 2034 Number in coding regions = 1767 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 5 AATTGATGGTGGAGACCCAGGTTTGTCTTTTCTG 7 16 0 GGACCCGGTT 0.989318 -285 AGATTAAATAGGATTACCAGGATTGATCCCTGCC 8 164 1 GGAACCGGTT 0.996068 -119 TGCCCTGGAAAACACGGGTAGCACACTATT 9 7 1 GGAACAGGTA 0.978665 -89 ATTCCCCTTTGGATGACCGGGGTTAAGTCCAGGG 9 38 1 GGAACCGGTT 0.996068 -58 CAGGGAGTAGGGAGTACAAGTCTTTTTTTTGATT 9 67 1 GGAACAGTTT 0.929779 -29 TGGAATTTTAGGAGTAACAGGGTATAAGGTAAAC 11 15 0 GGAAACGGTA 0.954549 -286 *** *** ** ** Masking position 3 Map Score: 3.70341 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 78 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 CACAGTTCAATCTTTATTCTGCCTTAGGGC 1 121 0 TCTTTATTCT 0.699175 -68 AATCTGATAATCTCTTTTGCTTCAGACTGT 1 156 0 TCTCTTTTGC 0.752759 -33 CCACTCTCTTTCTTTTCTCTGGTTTTGGAG 2 202 1 TCTTTTCTCT 0.876579 -27 GAGTCATCTTTCCTTTTTTGCTAGGCAGGC 3 68 1 TCCTTTTTTG 0.815745 -60 ACTGCCATAATCTTTTTCCTTCAACTC 6 8 0 TCTTTTTCCT 0.775014 -42 CCCAGGTTTGTCTTTTCTGGCTCC 7 5 0 TCTTTTCTGG 0.901418 -296 AGTAACTGTCTCCTTTTTGTACCGCATTTA 8 208 0 TCCTTTTTGT 0.903183 -75 GGAGTACAAGTCTTTTTTTTGATTTTCTG 9 77 1 TCTTTTTTTT 0.913078 -19 TGACTTTTAATCTTTTTTGCAATTTAATAA 11 144 1 TCTTTTTTGC 0.935894 -157 TTTAATAAAGTCTTTTTTTGTTCTCTCTAT 11 166 1 TCTTTTTTTG 0.911476 -135 ********** Masking position 5 Map Score: 2.61222 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 287 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 7 GCAGGCTTCTCTCCGAAACCCACTCTCTTT 2 183 1 CTCCGAAACC 0.971392 -46 AAATTAGCTCCAAAACCAGAGAAAAGA 2 212 0 CTCCAAAACC 0.976166 -17 GTTCCCACCGCACTACAACCGCAGTTTTGG 7 160 0 CACTACAACC 0.920469 -141 GTGTTTATAGCTCCGAGAACAACAATAAGA 11 49 1 CTCCGAGAAC 0.887588 -252 GAAGATAATCCTCTACAAACTTTACAAAGC 11 79 1 CTCTACAAAC 0.932124 -222 TACTTTTTTACACTAAAAACACTCTTACTG 11 229 0 CACTAAAAAC 0.898768 -72 ********** Masking position 8 Map Score: 0.304131 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 157 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 CACCTGCCGCCAGAATTTGATGGCCAATTT 2 75 0 CAGAATTTGA 0.742979 -154 GCCTAATTACCTGAATTTAAGATTTCATTC 3 17 1 CTGAATTTAA 0.919796 -111 ACAATTTTCCCCGGAATTAATCTTAGTTTA 5 92 0 CCGGAATTAA 0.890425 -101 GCACAGTAATCTGGAATTGATGGTGGAGAC 7 34 0 CTGGAATTGA 0.937324 -267 TCCCTACTCCCTGGACTTAACCCCGGTCAT 9 50 0 CTGGACTTAA 0.965401 -46 CGCCTTTAAACTGAACTTAAAGAATTAGAG 10 30 1 CTGAACTTAA 0.946652 -27 ********** Masking position 5 Map Score: 0.119755 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 88 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 CCTTAGGGCCCGACTCCCGGAAAAATTTAA 1 100 0 CGACTCCCGG 0.850641 -89 GCTTAGCAGGCTTCTCTCCGAAACCCACTC 2 178 1 CTTCTCTCCG 0.980463 -51 CACTCTCTTTCTTTTCTCTGGTTTTGGAGC 2 203 1 CTTTTCTCTG 0.861047 -26 CCAACGGGCACTTTTCTCCCTCACTAACCC 4 33 0 CTTTTCTCCC 0.929966 -68 CCCAGGAACAATTTTCCCCGGAATTAATCT 5 99 0 ATTTTCCCCG 0.814279 -94 TTAAAATTAGCTACTCCCCAGGAACAATTT 5 115 0 CTACTCCCCA 0.956201 -78 ACCATGCTCCCTACTCTCCCCCATCTGCAC 8 257 1 CTACTCTCCC 0.954906 -26 GGGTAGCACACTATTCCCCTTTGGATGACC 9 26 1 CTATTCCCCT 0.885891 -70 CTTGTACTCCCTACTCCCTGGACTTAACCC 9 57 0 CTACTCCCTG 0.94033 -39 CAAAGCATGACGTTTCTCCAACGTAGATGT 11 103 1 CGTTTCTCCA 0.786836 -198 ********** Masking position 5 Map Score: 6.22977 Number of sites scoring better than the average of aligned sites = 1008 Number in coding regions = 891 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 10 ********** No masking Map Score: -4.13293e-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: -4.13293e-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: -4.13293e-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