AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i162_synecho_ctra_300.orf -o162_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 RCY03451 139 Synechocystis #2 RCY20878 101 Synechocystis #3 RCY23470 133 Synechocystis #4 RCY29017 300 Synechocystis #5 RCY39499 300 Synechocystis #6 RCT00201 196 Chlamydia_trachomatis #7 RCT00285 300 Chlamydia_trachomatis #8 RCT00286 163 Chlamydia_trachomatis #9 RCT00603 300 Chlamydia_trachomatis #10 RCT00632 300 Chlamydia_trachomatis Motif number 1 TAAAAAATATTGTTAAAAATAGACTCGATCT 1 113 0 TTTAAAAATA 0.804442 -27 GAAACTTAAAAAATATTGTTAAAAA 1 125 0 CTAAAAAATA 0.84705 -15 ACTTTAAAAACTTTAAAAAAATCCATTAAGC 4 261 1 CTTAAAAAAA 0.956025 -40 TTTGGTGCTCCATTGAACAAACTTCTGACAC 5 183 0 CTTGAACAAA 0.711646 -118 CCTGTGCCCACATCAAAAAAACAGACGGGGA 5 233 0 CTCAAAAAAA 0.916503 -68 GGAGAGAAAACCTTAAAAATAACAACAGGTT 6 18 0 CTTAAAAATA 0.961116 -179 GAGAAATAAGCGTCAAACATACACTATGTCT 6 71 1 CTCAAACATA 0.770105 -126 ACCAGGATCGCATTAAAAAAAAGATGATGGA 6 135 0 CTTAAAAAAA 0.956024 -62 CGGCAACCTCCTTTAGAAATAGCTTCAACTC 7 67 1 CTTAGAAATA 0.912664 -234 GTGCCCATGATTTTGGAAATAACGCTTGTGC 7 149 1 TTTGGAAATA 0.423733 -152 ATTTTGTATTCTTAAAAAATAGTT 7 287 1 CTAAAAAATA 0.84705 -14 CTTTAGAAAAATAATGTAAGG 10 1 1 CTTAGAAAAA 0.901889 -300 ATAGAAAAACCGTTAAAAAAGGCGTTTCCAC 10 106 0 CTTAAAAAAG 0.746841 -195 TCGTTCTCTGCATTGAAAAAATTTTGTAGTC 10 148 0 CTTGAAAAAA 0.901888 -153 ACGAAGAGAGTCTCAAAAATATTGGTATAAA 10 175 1 TTCAAAAATA 0.674971 -126 * ********* Masking position 7 Map Score: 12.9966 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 232 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 TTAGTTAATCTTCATCCCCCCGATCGCCGCA 2 55 1 TTCATCCCCC 0.954187 -47 ACAATCAAGGGTCCATCCCGCCGGGGC 3 7 0 GTCCATCCCC 0.958586 -127 TCGAAATCAAGTCCTCTCCAGTCTGCGAATC 6 106 1 GTCCTCTCCG 0.852714 -91 GGTATACACTTCCCTTTCCCCAATCTTTACA 6 163 1 TCCCTTTCCC 0.9247 -34 TAGAAATAGCTTCAACTCCGCTTCCAACTGT 7 80 1 TTCAACTCCC 0.939774 -221 AGAAACAGGAGCCAACCCCTCGAATAGGATG 7 119 1 GCCAACCCCC 0.955843 -182 GCTCTTCTATTCCCATACCACTAAACAAT 8 145 1 TCCCATACCC 0.91808 -19 TATAAACAATTTCCACACCCCTTAAAGAAGA 9 28 1 TTCCACACCC 0.979748 -273 TATCGAAAGTTTCCACCCCCCTAGAAGAAGA 9 84 0 TTCCACCCCC 0.990091 -217 AGTATCTCAAGTCCTCACCGCTCACACTGCT 10 64 0 GTCCTCACCC 0.974407 -237 CTCCTTAAGCTCCCTCTCATCATTCCCTTTC 10 264 0 TCCCTCTCAC 0.796178 -37 ********* * Masking position 8 Map Score: 10.7145 Number of sites scoring better than the average of aligned sites = 1022 Number in coding regions = 909 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 GCGGGATGGACCCTTGATTGTGGTCTGCCATTC 3 17 1 CCCGATTGGG 0.983427 -117 GGCACCTTAACCAGTTCTTGGGGGCAAAAACTA 4 176 1 CCATCTTGGG 0.925842 -125 ATCCATTAAGCAAAATATTTAGGCACCATT 4 281 1 CAATATTTGG 0.84828 -20 GTGACAGTCCCCCAGTATTGCGGTCGCTTTAGT 5 17 0 CCCTATTGGG 0.983748 -284 CCCCCTGACCCCCCAGATTTTGGGGGAAACTGA 5 50 0 CCCGATTTGG 0.982501 -251 CTGTTAACCTCCATTTGTTTGGGCCAAGACTCT 5 102 0 CCATGTTTGG 0.938017 -199 ATAGGATGTGCCCATGATTTTGGAAATAACGCT 7 142 1 CCCGATTTGG 0.986142 -159 GCCCTCATACTCACTTATTTAGGCGAATAAACT 7 195 1 TCATATTTGG 0.848285 -106 GAACATTGTCCCAACCATTTTGGAGAATGTGTG 8 38 0 CCACATTTGG 0.954093 -126 *** ***** ** Masking position 8 Map Score: 7.23168 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 275 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 CAATGTAGTCCGAATGGCAGACCACAATCAAGG 3 28 0 CGAGCAGACC 0.994786 -106 AACCGCAGACCGTAAAGCAGACCAAGGGTGACC 4 32 0 CGAGCAGACC 0.994793 -269 AGCCTGGCAACCCAACCCAGACCAGTTCTCAGT 4 96 0 CCACCAGACC 0.986358 -205 CAGGCTTTTCCCCAGGGCTGACCGAATTCTGCT 4 123 1 CCAGCTGACC 0.991571 -178 CTAACTAATCCCTAAGGCTGAACTTTTACTTTA 4 234 1 CCAGCTGAAC 0.969777 -67 CCGTTTTAAACGCCCCCCTGACCCCCCAGATTT 5 63 0 CGCCCTGACC 0.968986 -238 AATTATAGATCGAACGGCTGCACTTTTTCGGTT 9 164 0 CGAGCTGCAC 0.932739 -137 TATTTCTTCTCGAATTCCAGAGCCATCTTTAAG 9 242 0 CGACCAGAGC 0.964251 -59 ** * ******* Masking position 8 Map Score: 8.23023 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 55 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 GATAACAATAGAAGCCAAGATTAGGGAGTTTCCTCCA 1 28 1 GAGCAAGTGA 0.930585 -112 GGTCAGCCCTGGGGAAAAGCCTGGCAACCCAACCCAG 4 109 0 GGGAAAGTGA 0.98965 -192 GCAATGGTTTGAAGCAGAATTCGGTCAGCCCTGGGGA 4 131 0 GAGAGAACGA 0.754529 -170 AACTGGTTAAGGTGCCAAATTCCGGCAATGGTTTGAA 4 155 0 GGGCAAACGA 0.957873 -146 CCAGTTCTTGGGGGCAAAAACTAGTCAATTAGCAACG 4 186 1 GGGAAAATGA 0.986715 -115 GTCTCCTTAGGGTGTAAAGACTGGCTATGGGAATTTA 5 269 0 GGGAAAGTGA 0.98965 -32 GGAGGTTGCCGTGGTAAAGGATCGACATCTTCAGCGT 7 41 0 GTGAAAGTGA 0.914367 -260 CACTTATTTAGGCGAATAAACTCGAAAGTACTATAGA 7 206 1 GGGATAATGA 0.930117 -95 CTTCTAGGGGGGTGGAAACTTTCGATAAGTGTACAAC 9 88 1 GGGAAACTGA 0.964481 -213 TTTGTAGTCTGGAGACGAAAATAGAAAAACCGTTAAA 10 120 0 GGGCGAATGA 0.962754 -181 ** * **** * * * Masking position 8 Map Score: 6.79646 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 338 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 TTAGAGAATCCTTTAGGAGAACCC 3 120 1 CTTAGGAGAA 0.974416 -14 TCTAACCCATCTTCAGGTTAACTGAGAACTG 4 76 1 CTTAGGTTAA 0.880378 -225 AAAGTTCAGCCTTAGGGATTAGTTAGTGCTT 4 229 0 CTTGGGATTA 0.944267 -72 TTCGCGTCTCCTTAGGGTGTAAAGACTGGCT 5 280 0 CTTGGGTGTA 0.947304 -21 CCGCCTTGCACTTAGAGAGAAATAAGCGTCA 6 55 1 CTTGAGAGAA 0.842266 -142 AACGCTTGTGCTCTAGGTGTAAAACTGCCCT 7 169 1 CTCAGGTGTA 0.855053 -132 GTACTATAGACTTTAAGATTATTTCCGCCTA 7 233 1 CTTAAGATTA 0.82412 -68 AATAGAAGAGCTAGAGGAGTAAGAAGATGTG 8 125 0 CTAAGGAGTA 0.897855 -39 AAGTGTACAACTTTATGATAAGGCTTCCATT 9 114 1 CTTATGATAA 0.644763 -187 TGAGAGGGAGCTTAAGGAGTAAAGAAGAAAC 10 276 1 CTTAGGAGTA 0.982382 -25 *** ******* Masking position 2 Map Score: 5.47898 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 184 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 AACAAATCTAACAGAAAATGCAGTTAGTTA 2 32 1 ACAGAAAATG 0.799842 -70 TAAAGTTTTTAAAGTAAAAGTTCAGCCTTA 4 246 0 AAAGTAAAAG 0.638799 -55 GCATTAAAAAAAAGATGATGGATTCGCAGA 6 127 0 AAAGATGATG 0.821688 -70 TCAGCGTTGGAGAGAGAATGTTCATCGAAC 7 18 0 AGAGAGAATG 0.873057 -283 GCTAGAGGAGTAAGAAGATGTGTTTAGTTT 8 117 0 TAAGAAGATG 0.748642 -47 CACACCCCTTAAAGAAGAAGAAACTAATAA 9 41 1 AAAGAAGAAG 0.949184 -260 GAGAAGAAATAAAGAGTATGCCTGGAGTAT 9 264 1 AAAGAGTATG 0.788147 -37 AATACGAAACAAAGAGAATGAGCCAACCGA 10 206 1 AAAGAGAATG 0.947145 -95 GAGCCAACCGAGAGAAGAAGCATACAATCT 10 225 1 AGAGAAGAAG 0.877584 -76 TTCCCTTTCTAAAGAAAAAGATTGTATGCT 10 243 0 AAAGAAAAAG 0.932971 -58 TTTTCTTTAGAAAGGGAATGATGAGAGGGA 10 255 1 AAAGGGAATG 0.771409 -46 CTTAAGGAGTAAAGAAGAAACCGTG 10 286 1 AAAGAAGAAA 0.572693 -15 ********** Masking position 3 Map Score: 5.72961 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 263 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GGCGATCGGGTTGGGATGAT 1 1 1 GGCGATCGGG 0.990352 -139 TAGCATCAGAGGCTATCGGCCTTGGTTTTC 1 79 0 GGCTATCGGC 0.977275 -61 CTTGCCCTGCGGCGATCGGGGGGATGAAGA 2 63 0 GGCGATCGGG 0.990352 -39 TGTAAAGACTGGCTATGGGAATTTATTGAA 5 264 0 GGCTATGGGA 0.923618 -37 AATCTTGAGAGTCAATCGGGTTTTTATAGG 7 260 0 GTCAATCGGG 0.948167 -41 ********** Masking position 5 Map Score: 3.86518 Number of sites scoring better than the average of aligned sites = 768 Number in coding regions = 701 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 9 GGCGATCGGGTTGGGATGATAACAATAG 1 9 1 GGTTGGGATG 0.921158 -131 AGGTAGGGAGAGAATTACGTC 2 2 1 GGTAGGGAGA 0.796193 -100 CCTGAAGATGGGTTAGATCAGCTTGACAAA 4 63 0 GGTTAGATCA 0.703041 -238 AACTGGTCTGGGTTGGGTTGCCAGGCTTTT 4 102 1 GGTTGGGTTG 0.94935 -199 AATAACAACAGGTTAGGTGCT 6 2 0 GGTTAGGTGC 0.868961 -195 CTATTCGAGGGGTTGGCTCCTGTTTCTGAC 7 116 0 GGTTGGCTCC 0.959021 -185 TCTCCAAAATGGTTGGGACAATGTTCTGGA 8 45 1 GGTTGGGACA 0.976581 -119 TTCTTCTCTCGGTTGGCTCATTCTCTTTGT 10 214 0 GGTTGGCTCA 0.965792 -87 ********** Masking position 3 Map Score: 2.28234 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 490 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 10 CTAACTGCATTTTCTGTTAGATTTGTTGAC 2 29 0 TTTCTGTTAG 0.58068 -73 AACGTCGTAATTTCTGCGACCACCACCTTA 3 90 1 TTTCTGCGAC 0.905531 -44 GGCTGACCGAATTCTGCTTCAAACCATTGC 4 138 1 ATTCTGCTTC 0.46526 -163 TACTTTCGAGTTTATTCGCCTAAATAAGTG 7 206 0 TTTATTCGCC 0.482274 -95 GGAGCTGTTCTTTCTTCGACTAGTGTATTC 8 86 0 TTTCTTCGAC 0.928846 -78 TATTTATTAGTTTCTTCTTCTTTAAGGGGT 9 44 0 TTTCTTCTTC 0.903152 -257 CTCTACGAATCTTCTTCTAGGGGGGTGGAA 9 75 1 CTTCTTCTAG 0.837816 -226 ACTTTTTCGGTTTCTGCGAGGTCGTTTTAG 9 146 0 TTTCTGCGAG 0.889343 -155 ATACTCTTTATTTCTTCTCGAATTCCAGAG 9 253 0 TTTCTTCTCG 0.941687 -48 AGGCGTAGTATTTCTTTTAGTCTTCTGTCT 10 29 1 TTTCTTTTAG 0.653488 -272 GTTTTTCTATTTTCGTCTCCAGACTACAAA 10 127 1 TTTCGTCTCC 0.75234 -174 AGATTGTATGCTTCTTCTCTCGGTTGGCTC 10 225 0 CTTCTTCTCT 0.604235 -76 CACGGTTTCTTCTTTACTCCTTAAG 10 286 0 TTTCTTCTTT 0.680812 -15 ********** Masking position 3 Map Score: 3.4458 Number of sites scoring better than the average of aligned sites = 1020 Number in coding regions = 905 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 11 AGCCAAGATTAGGGAGTTTCCTCCATTGCT 1 40 1 AGGGAGTTTC 0.948567 -100 GGGGGTCAGGGGGGCGTTTAAAACGGGCTC 5 70 1 GGGGCGTTTA 0.852757 -231 GCCCAAACAAATGGAGGTTAACAGCTATAA 5 111 1 ATGGAGGTTA 0.922619 -190 CTCTAAGTGCAAGGCGGTTGTAAGGAGAGA 6 42 0 AAGGCGGTTG 0.932808 -155 GCTATTTCTAAAGGAGGTTGCCGTGGTAAA 7 60 0 AAGGAGGTTG 0.934053 -241 GAGTATACAGATGGAGTTTAGAC 9 288 1 ATGGAGTTTA 0.908032 -13 ACCGTTAAAAAAGGCGTTTCCACGGCTTAA 10 99 0 AAGGCGTTTC 0.919974 -202 GAATGATGAGAGGGAGCTTAAGGAGTAAAG 10 270 1 AGGGAGCTTA 0.909267 -31 ********** Masking position 8 Map Score: 2.49736 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 135 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 12 AGGTAGGGAGAGAATTACGTCAACA 2 5 1 AGGAGAGAAT 0.949868 -97 AAAAAAACAGACGGGGAGAACTCCACTCTAC 5 219 0 AGGGGAGAAC 0.973085 -82 AGGCGGTTGTAAGGAGAGAAAACCTTAAAAA 6 30 0 AGGAGAGAAA 0.949868 -167 GATTCGCAGACTGGAGAGGACTTGATTTCGA 6 106 0 CGGAGAGGAC 0.929675 -91 AAGCAGAGATCTCTGTAAAGA 6 186 0 AGCAGAGATC 0.927272 -11 AATTTTTTCAATGCAGAGAACGAAGAGAGTC 10 156 1 AGCAGAGAAC 0.981018 -145 * ********* Masking position 7 Map Score: 0.509409 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 62 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 13 ********** No masking Map Score: 9.26138e-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: 9.26138e-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 15 ********** No masking Map Score: 9.26138e-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