AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_synecho_ctra_300.orf -o201_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 RCY22255 300 Synechocystis #2 RCY49058 126 Synechocystis #3 RCY53506 106 Synechocystis #4 RCY46170 157 Synechocystis #5 RCY38700 191 Synechocystis #6 RCT00554 300 Chlamydia_trachomatis #7 RCT00557 198 Chlamydia_trachomatis #8 RCT00558 24 Chlamydia_trachomatis Motif number 1 TGCTTAGCCTAGCATCTACCATGAATCTAAAGAAAATTGTC 1 143 1 AGCCCCAGAA 0.996504 -158 TAACAGGGACTTCCAAGATAGTTTAAGCATTTTTA 1 276 0 AGGCCCAGTA 0.988661 -25 AGGTAAGGGCCCACCAAGAAGGGAAATCTGCCTGCA 2 101 0 AGGCCCAGAA 0.998195 -26 GTAAATGGCGATCGCCAGCCAAGATTAGCAAAGACAGTTTA 4 90 1 ATCCCCAGAA 0.982481 -68 AGGGGGAGACAAGGCTCTTAACTTTTCTTCA 4 137 0 AGGGACAGAA 0.965449 -21 ACACCGCTGAATGGCCAGCCACGATAGTTATCTTTAATCAG 5 127 1 ATGCCCAGAT 0.944948 -65 ACAGGCAGGTCCAGGGCTCTAAAATCTCATCGA 6 3 1 AGGGCCAGAA 0.996503 -298 GGATTACTGTAGCAACTACCATGGGAAGAAAAATCGTATAG 6 49 0 AGCCCCAGAA 0.996504 -252 CTGACTCACGAGGCGGGACCCTGTTTGGGAAAAAACCTCGC 7 166 0 AGGGCCCGAA 0.985206 -33 *** * *** * ** Masking position 1 Map Score: 12.7653 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 61 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 2 TCAGTGTTGGTAAAGAAAAACCGCCTACAG 1 65 0 TAAAGAAAAA 0.949093 -236 ACCATGAATCTAAAGAAAATTGTCAACTTC 1 160 1 TAAAGAAAAT 0.821413 -141 TTATTAGGTGTGAGGAAAAGCTAAAAATGC 1 255 1 TGAGGAAAAG 0.967422 -46 GGCAAAGTTTTCAGGAAAAATTTCTTTCTC 3 16 0 TCAGGAAAAA 0.810234 -91 TTTAAAATCGTGAAGAAAAGTTAAGAGCCT 4 127 1 TGAAGAAAAG 0.979344 -31 GGTGTATCTTTGAAGACAAGCAGAGTAATG 5 102 0 TGAAGACAAG 0.947908 -90 AACTACCATGGGAAGAAAAATCGTATAGTT 6 47 0 GGAAGAAAAA 0.919425 -254 GTATCCCTCCGGTAGAAAAGTCTATTTTTA 6 116 0 GGTAGAAAAG 0.87876 -185 TACCCAATAATATAGAAAAGAGGTATCTGG 6 148 1 TATAGAAAAG 0.922133 -153 CGTCCATGCTTATGGACAAATCAATATAAA 6 216 1 TATGGACAAA 0.640945 -85 AATTAAGAATTAAAGAAAAAGCAAGGAGCG 7 139 1 TAAAGAAAAA 0.949093 -60 ********** Masking position 6 Map Score: 10.4148 Number of sites scoring better than the average of aligned sites = 318 Number in coding regions = 259 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 3 TGATTGTGGTCCTGGCTCCCTGAGCTAGCC 1 92 1 CCTGGCTCCC 0.997116 -209 GAGTATAGGACTTGGTTCCCGTAGTCATTA 1 228 1 CTTGGTTCCC 0.949228 -73 CTTTGCTAATCTTGGCTGGCGATCGCCATT 4 93 0 CTTGGCTGGC 0.977489 -65 AGTTAAGAGCCTTGTCTCCCCCT 4 145 1 CTTGTCTCCC 0.97455 -13 CGGTGGGTGGCCTGTCTGTCTCGCACAGTG 5 61 0 CCTGTCTGTC 0.882633 -131 AGATAACTATCGTGGCTGGCCATTCAGCGG 5 130 0 CGTGGCTGGC 0.962222 -62 GGGGAGGAAGCCTCGCTCCTTTTTAGTTGC 6 255 0 CCTCGCTCCT 0.965495 -46 TGGGAAAAAACCTCGCTCCTTGCTTTTTCT 7 152 0 CCTCGCTCCT 0.965495 -47 ********** Masking position 7 Map Score: 8.5619 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 517 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 4 TTAATAACAGATTATAGTTGCTAT 1 4 0 ATTTAGTTGC 0.967531 -297 CTTTAGATTCATGGTAGATGCTAGGCTAAGC 1 144 0 ATGTAGATGC 0.979281 -157 GGGTTTTTCGTTGTAAGATGCAGGCAGATTT 2 83 1 TTGAAGATGC 0.899548 -44 ATCGCTTTCGATGACCGTTGCAGT 4 4 0 ATGCCGTTGC 0.938053 -154 TTTTCTTCCCATGGTAGTTGCTACAGTAATC 6 58 1 ATGTAGTTGC 0.984011 -243 GCCTCGCTCCTTTTTAGTTGCTTTAATTCCT 6 245 0 TTTTAGTTGC 0.958132 -56 TAATTCTTAATTTATCGATGCAAGACATCTC 7 120 0 TTTTCGATGC 0.922036 -79 *** ******* Masking position 9 Map Score: 4.72523 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 58 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 5 ATAGCAACTATAATCTGTTATTAACCATCAA 1 8 1 CTAATCGTAT 0.857157 -293 TGAGCAGAAGCTGTAGGCGGTTTTTCTTTACCAA 1 55 1 CTAGGCGTTT 0.976249 -246 GGAGCCAGGACCACAATCAGTGTTGGTAAAGAAA 1 77 0 CCAATCGTTT 0.976708 -224 GACTTGGTTCCCGTAGTCATTATTAGGTGTGAGG 1 236 1 CCAGTCTTTT 0.960842 -65 GCCTGAGTCCGTCTTCTTAAGACAC 2 2 1 CCAGTCGTTT 0.990765 -125 AAAAACCCCACCAGAGGCGGGGTTAAAGAGTTAT 2 57 0 CCAGGCGGTT 0.990391 -70 GGCAAAGGAGCTATAGTCTGGGATAATAGGGCTG 5 165 0 CTAGTCGGAT 0.937684 -27 AAAATAAGCCCCTAAAGCCTGCTTTTTAAAAATA 7 73 0 CCAAGCTGTT 0.90207 -126 ** **** ** ** Masking position 5 Map Score: 4.33497 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 223 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 ATAGCAACTATAATCTGTTATTAACCA 1 8 1 CTATAATCTG 0.784294 -293 TCTAATAACTCTTTAACCCCGCCTCTGGTG 2 53 1 CTTTAACCCC 0.975763 -74 TAGAAATAGGCTTAAAACCCAGAACAGTTT 4 59 0 CTTAAAACCC 0.823456 -99 TTAATCAGCCCTATTATCCCAGACTATAGC 5 160 1 CTATTATCCC 0.900962 -32 GTCCAGGGCTCTAAAATCTCATCGAGTTAA 6 19 1 CTAAAATCTC 0.856664 -282 TATTCATCTCCTTTAACCTCATTCGTCCAT 6 193 1 CTTTAACCTC 0.929552 -108 TTTTTAGTTGCTTTAATTCCTTTATATTGA 6 236 0 CTTTAATTCC 0.933333 -65 TCTATAATCCTTCCTAACAAT 7 2 1 CTATAATCCT 0.929573 -197 CTTGCTTTTTCTTTAATTCTTAATTTATCG 7 134 0 CTTTAATTCT 0.762025 -65 ********** Masking position 6 Map Score: 3.67271 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 646 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 GACAATTTTCTTTAGATTCATGGTAGATGCTA 1 152 0 TTTAGATCTG 0.980994 -149 GTCCGTCTTCTTAAGACACTTGTTTGAAAGTT 2 17 1 TTAAGAACTG 0.965113 -110 GCAAAGACAGTTTAAAATCGTGAAGAAAAGTT 4 117 1 TTTAAATCTG 0.888703 -41 TGAAGAAAAGTTAAGAGCCTTGTCTCCCCCT 4 137 1 TTAAGACCTG 0.977164 -21 TCGATGAGATTTTAGAGCCCTGGACCTGCCTG 6 12 0 TTTAGACCTG 0.98763 -289 TAACATCATCTTTAGAAAGATGATTGTTAGGA 7 22 0 TTTAGAAGTG 0.922086 -177 ****** ** ** Masking position 6 Map Score: 2.50864 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 15 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GGGAGAAGTTGACAATTTTCTTTAGATTCATG 1 162 0 GAAATTTCTT 0.829164 -139 CCAAGATAGTTTAAGCATTTTTAGCTTTTCCT 1 267 0 TTAGATTTTT 0.467041 -34 GAACTGAGAAAGAAATTTTTCCTGAAAAC 3 8 1 GAAGAATTTT 0.864406 -99 CACAATTCCCGAAAGTTTTCTTTTTCTGGCAA 3 41 0 GAAGTTTCTT 0.980158 -66 TTCGGGAATTGTGAGTTATTTTAAAGCGTAAG 3 60 1 GTAGTATTTT 0.880773 -47 ACGAAATTGATACAGATTTTTTTGATCGCTTT 4 27 0 TAAGTTTTTT 0.883374 -131 GGCCAGCCACGATAGTTATCTTTAATCAGCCC 5 139 1 GAAGTATCTT 0.962935 -53 GAGGTATCTGGAGAGCTTTCTTACTTTATTCA 6 167 1 GAAGTTTCTT 0.9802 -134 AAAGCAAGGAGCGAGGTTTTTTCCCAAACAGG 7 156 1 GCAGTTTTTT 0.922099 -43 ** ** ****** Masking position 4 Map Score: 3.99012 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 232 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 CTGTTTTGCGGGCTAGCTCAGGGAGCCAGGAC 1 100 0 GGCTAGTCAG 0.88441 -201 TAGCCCGCAAAACAGACCAATGGCCTTGCTTA 1 117 1 AACAGACAAG 0.669518 -184 GTAGATGCTAGGCTAAGCAAGGCCATTGGTCT 1 130 0 GGCTAACAAG 0.888203 -171 GTCTTAAGAAGACGGACTCAGGC 2 2 0 GACGGATCAG 0.861818 -125 TTTGAAGACAAGCAGAGTAATGCTAACAAAAC 5 92 0 AGCAGATAAG 0.935274 -100 GGGATAATAGGGCTGATTAAAGATAACTATCG 5 148 0 GGCTGATAAG 0.984744 -44 ACAGGCAGGTCCAGGGCTCTAAAAT 6 4 1 GGCAGGCCAG 0.942957 -297 AGGTTAAAGGAGATGAATAAAGTAAGAAAGCT 6 180 0 AGATGATAAG 0.706454 -121 TTTAAAAATAGTCTGATTCAGGGGCTATGTAA 7 51 0 GTCTGATCAG 0.919966 -148 AGCTGACTCACGAGGCGGGACC 7 187 0 AGCTGATCAG 0.977742 -12 ****** *** * Masking position 10 Map Score: 3.11752 Number of sites scoring better than the average of aligned sites = 746 Number in coding regions = 656 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 10 TGGCGATCGCCATTTACTTAGAAATAGGCTTAAAACCCA 4 68 0 CATAAAATAC 0.965203 -90 GCTGTTTATCTCCTTAATATAAATATTCGATTAATTGA 5 10 1 CTTAAAATAC 0.986974 -182 CATTACTCTGCTTGTCTTCAAAGATACACCGCTGAATGG 5 102 1 CTTAAGATAC 0.952663 -90 GCTCTAAAATCTCATCGAGTTAACTATACGATTTTTCTT 6 26 1 CTTTAACTAC 0.884914 -275 TTACAAAAGACTTATCCCTAAAAATAGACTTTTCTACCG 6 98 1 CTTAAAATAC 0.986974 -203 CCCCTAAAGCCTGCTTTTTAAAAATAGTCTGATTCAGGG 7 60 0 CTTAAAATAC 0.986974 -139 ACATCTCTGGATTTTTACGAAAAATAAGCCCCTAAAGCC 7 88 0 ATTAAAATAC 0.945446 -111 AAAATCTTAACAACTATCCATTGT 8 1 1 AATAAACTAC 0.782262 -24 ** * * ***** * Masking position 12 Map Score: 3.99244 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 34 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 11 ********** No masking Map Score: 3.45567e-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: 3.45567e-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: 3.45567e-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