AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i232_synecho_ctra_100.orf -o232_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 RCY28443 110 Synechocystis #2 RCY06942 53 Synechocystis #3 RCY41351 138 Synechocystis #4 RCY10129 213 Synechocystis #5 RCT00336 274 Chlamydia_trachomatis #6 RCT00507 100 Chlamydia_trachomatis Motif number 1 CTGGAATCAACTTTTCCAGGCTTGTTAGGATTG 1 16 1 CTTTCAGGTT 0.990445 -95 TTTTAGGCATCTTCCCCAGGATTGAGTCCGGTT 1 69 1 CTTCCAGGTT 0.983244 -42 TAAATCTACCCTTTTTGAGGATATACCCCA 4 8 0 CTTTGAGGTA 0.975436 -206 TGCATTAATCCTTCTAGTGAATTAAAAGTACAA 4 95 0 CTTCGTGATT 0.934112 -119 AGAAGTCTTCCTTTCGCTGAATAGCGAAAACCT 5 12 0 CTTTCTGATA 0.962105 -263 TCCGTGAAGTCGTTCACTGACTAGTATCGTCAA 5 146 0 CGTTCTGATA 0.870871 -129 AACGGCCTATCTTTTTGAGACTTTGTATAGGGA 5 241 1 CTTTGAGATT 0.975708 -34 TACGGGGTCTCTTTGTCAGGGTTTTGC 6 84 1 CTTTCAGGTT 0.990444 -17 **** **** ** Masking position 3 Map Score: 7.3799 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 186 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 TGTCGAGCCGAAATCATAGGCAATGCAGTT 2 33 0 AAATCATAGG 0.984766 -21 AAAATTCATAGGATGTGTAACT 3 3 1 AATTCATAGG 0.984766 -136 CAAACCTTTTAAACCATAGCGAAAATTGTC 3 54 1 AAACCATAGC 0.925116 -85 GTACAGTCGTAGTTCATCGGACTAAATCTA 4 33 0 AGTTCATCGG 0.962286 -181 GGTGTCTTGGATTTCATAGCACTCTTCTCG 5 85 1 ATTTCATAGC 0.930419 -190 GGAATTTTTTAGATCATAGGTTTATCGGAA 5 213 1 AGATCATAGG 0.985872 -62 ********** Masking position 6 Map Score: 5.64063 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 33 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 AAAATCACGGCCTGGACAATTTTCGCTATGGT 3 66 0 CCTACAATTT 0.956705 -73 TTGGACTACATCTTAACAAAATCACGGCCTGG 3 83 0 TCTACAAAAT 0.82236 -56 TACGGGCCTATCTCAACAATGGGGTCTTGGAC 3 109 0 TCTACAATGG 0.934403 -30 TCTTAATTACCCTTAACAATGTAAAGAATTGT 4 143 0 CCTACAATGT 0.993031 -71 ATCTTCTTTTCCATCACAATGTCTGCTCTAGG 5 55 1 CCAACAATGT 0.972383 -220 CCCACAGATCCCTATACAAAGTCTCAAAAAGA 5 250 0 CCTACAAAGT 0.990897 -25 GCAAAACCCTGACAAAGAGACCCCGTAT 6 83 0 CCCACAAAGA 0.908173 -18 *** ******* Masking position 6 Map Score: 3.96627 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 132 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 4 AGATGCCTAAAAATAGGCTCAATCAACCTC 1 51 0 AAATAGGCTC 0.941484 -60 ATTGCCTATGATTTCGGCTCGACAA 2 39 1 ATTTCGGCTC 0.910352 -15 CCCATTGTTGAGATAGGCCCGTAGAACGTC 3 118 1 AGATAGGCCC 0.977987 -21 TCATCGGACTAAATCTACCCTTTTTGAGGA 4 20 0 AAATCTACCC 0.821289 -194 ATTTGCTTAACTATCGGCCCGAATTGTACT 4 72 1 CTATCGGCCC 0.965479 -142 AATATCTAGAAAGTCTGCCCAGTTCATTAC 4 192 0 AAGTCTGCCC 0.965102 -22 TTCCATCACAATGTCTGCTCTAGGTGTCTT 5 63 1 ATGTCTGCTC 0.915442 -212 AGTCTCAAAAAGATAGGCCGTTCCGATAAA 5 233 0 AGATAGGCCG 0.880282 -42 ********** Masking position 4 Map Score: 3.82908 Number of sites scoring better than the average of aligned sites = 1003 Number in coding regions = 908 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 5 TGGGGAGGTTGATTGAGCCTATTTTTAGGCATCT 1 47 1 GTTGGCTTTT 0.858265 -64 TTGATTGATAGTAATTGGCTGAAACTGCAT 2 7 1 GTAGAATGCT 0.95394 -47 ACGGGCAACGGTAAGCAAACCTTTTAAACCATAG 3 39 1 GAAGAACTTT 0.86264 -100 GACTGTACTTGGTTGTAATTTGCTTAACTATCGG 4 55 1 GTTGAATGCT 0.92811 -159 GTGTTTGTATGAATGAAACTTTTTCTTCACTTTG 5 115 1 GATGAATTTT 0.936463 -160 GTCAGAAGACGCTAGGGAATTTTTTAGATCATAG 5 198 1 GTAGGATTTT 0.973386 -77 GATAGCAAGTGTTTTAGAACTAGG 6 1 1 GTAGAATTTT 0.984753 -100 TTTAGAACTAGGTAGTAATTTTTTGATATCGCTT 6 23 1 GTAGAATTTT 0.984753 -78 * *** ** * *** Masking position 14 Map Score: 2.87295 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 147 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 TTGATTGATAGTAATTGGCTGAAACT 2 7 1 GATAGTAATT 0.937751 -47 AAATTGTCCAGGCCGTGATTTTGTTAAGAT 3 76 1 GGCCGTGATT 0.961057 -63 GACTGTACTTGGTTGTAATTTGCTTAACTA 4 55 1 GGTTGTAATT 0.97806 -159 TAACTACCATGGTCTTAATTACCCTTAACA 4 157 0 GGTCTTAATT 0.958852 -57 TTTAGAACTAGGTAGTAATTTTTTGATATC 6 23 1 GGTAGTAATT 0.98744 -78 ********** Masking position 6 Map Score: 2.28871 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 119 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 AAAATAGGCTCAATCAACCTCCCCAATCCT 1 42 0 CAATCAACCT 0.965481 -69 GGCATCTCTGCATTAATCCTTCTAGTGAAT 4 106 0 CATTAATCCT 0.929428 -108 CTGCCCAGTTCATTACACCTTTAACTACCA 4 178 0 CATTACACCT 0.979068 -36 CTATGAAATCCAAGACACCTAGAGCAGACA 5 74 0 CAAGACACCT 0.967942 -201 TAGGCCGTTCCGATAAACCTATGATCTAAA 5 220 0 CGATAAACCT 0.965479 -55 ********** Masking position 10 Map Score: 1.66072 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 31 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TCTCAACAATGGGGTCTTGGACTACATCTTA 3 100 0 GGGTCTTGGA 0.991 -39 TTCACTAGAAGGATTAATGCAGAGATGCCGT 4 107 1 GGTTAATGCA 0.926729 -107 GGTAGTTAAAGGTGTAATGAACTGGGCAGAC 4 179 1 GGGTAATGAA 0.930645 -35 GTCTGCTCTAGGTGTCTTGGATTTCATAGCA 5 75 1 GGGTCTTGGA 0.991 -200 GTCAGTGAACGACTTCACGGAAGAATAACCT 5 158 1 GATTCACGGA 0.89981 -117 TTAGATCATAGGTTTATCGGAACGGCCTATC 5 221 1 GGTTATCGGA 0.973629 -54 ** ******** Masking position 5 Map Score: 1.4816 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 254 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 9 GTGATGGGAAGGAGAAAAAACCGGACTCAATCCT 1 86 0 GGAAAAACGG 0.990187 -25 AAAATTCATAGGATGTGTAACTAGTCAAACGGGC 3 11 1 GGAGTAACAG 0.975572 -128 GGACGTTCTACGGGCCTATCTCAA 3 125 0 GGAGTTACGG 0.99105 -14 ACGACTTCACGGAAGAATAACCTGTAATTTATGT 5 166 1 GGAGAAACTG 0.982825 -109 AAAAAAAAAAGGATAATATACGGGGTCTCTTTGT 6 66 1 GGAAATACGG 0.985999 -35 *** ** *** ** Masking position 10 Map Score: 0.582382 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 142 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 GCCTATTTTTAGGCATCTTCCCCAGGATTG 1 63 1 AGGCATCTTC 0.931637 -48 ATCATAGGCAATGCAGTTTCAGCCAATTAC 2 21 0 ATGCAGTTTC 0.983519 -33 TAATGCAGAGATGCCGTTTCTCACAATTCT 4 121 1 ATGCCGTTTC 0.989282 -93 TCAAAAAGATAGGCCGTTCCGATAAACCTA 5 229 0 AGGCCGTTCC 0.988197 -46 ********** Masking position 8 Map Score: 0.485214 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 65 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 11 AATGCAGTTTCAGCCAATTACTATCAATCAA 2 11 0 CAGCCATTAC 0.909459 -43 CGGACTAAATCTACCCTTTTTGAGGATATAC 4 15 0 CTACCTTTTT 0.777639 -199 AAGCAAATTACAACCAAGTACAGTCGTAGTT 4 49 0 CAACCAGTAC 0.972567 -165 ACACCTTTAACTACCATGGTCTTAATTACCC 4 163 0 CTACCTGGTC 0.96072 -51 TCTAGAAAGTCTGCCCAGTTCATTACACCTT 4 187 0 CTGCCAGTTC 0.990424 -27 CAAAAAATTACTACCTAGTTCTAAAACACTT 6 17 0 CTACCAGTTC 0.991964 -84 ***** ***** Masking position 5 Map Score: 1.71208 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 159 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ********** No masking Map Score: 1.43062e-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 13 ********** No masking Map Score: 1.43062e-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 14 ********** No masking Map Score: 1.43062e-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