AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i258_synecho_ctra_300.orf -o258_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 RCY00673 300 Synechocystis #2 RCT00206 300 Chlamydia_trachomatis #3 RCT00208 93 Chlamydia_trachomatis #4 RCT00209 130 Chlamydia_trachomatis Motif number 1 TAATATTTCTTTAAAAAAACAAGATGGTTTCTCA 1 23 1 TTAAAAAAGA 0.987373 -278 AAAAAAGATTTTAATAGGAAAAAATAAATCATTA 1 82 1 TTAATAAAAA 0.881003 -219 AAATAAATCATTAAAAAATAAAAATTTTTCTCGT 1 103 1 TTAAAAAAAA 0.983121 -198 AGAATAAAAATTAAAAAGAGAAAATAGTT 2 6 0 TTAAAAAAAA 0.983127 -295 TAACTGATCTTTAGAACGGGGAAAAATCGCAGAG 2 71 1 TTAGAAGAAA 0.895648 -230 ATTTCGTAGGAGAAAACCTCAAGATAAACGATCT 2 160 0 AGAAAAAAGA 0.86155 -141 TTAAATATGGTGAAAACCCAAAAAAGCGCAACAC 2 260 0 TGAAAAAAAA 0.973329 -41 CAGGTAAGTCTTAGAAAGAAAAGAGCTTCTTTAC 3 36 0 TTAGAAAAGA 0.967753 -58 AAATTTTTATTTAAATCTAGGAAAGGA 4 4 0 TTAAATGAAA 0.739684 -127 TTAGATCTTTTTAAAATAATAAGAAAAATAAACC 4 56 0 TTAAAAAAGA 0.987373 -75 TTATGCGCAATGAAAAGTATAAGAGGGGGCTC 4 109 1 TGAAAAAAGA 0.97999 -22 ****** **** Masking position 3 Map Score: 13.7703 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 96 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 2 TTGGTTTCCAAAGGTAAAAAAAAGATTTTAA 1 65 1 AGGTAAAAAA 0.838465 -236 AAAGATTTTAATAGGAAAAAATAAATCATTA 1 85 1 AAGGAAAAAA 0.939813 -216 TCTGGCATTTACGAGAAAAATTTTTATTTTT 1 116 0 AGAGAAAAAT 0.950808 -185 ATGGGGCGATCGGGGAAAAATGGCTTGATCT 1 144 0 CGGGAAAAAT 0.986033 -157 CCCATTGGCCAAAGGAACAAAATACTGCCTG 1 170 1 AAGGAACAAA 0.765061 -131 CAGGAGTTACCTGGTAAGAATCAGAGTTTAA 1 220 1 CGGTAAGAAT 0.78481 -81 CAATGTGTGCAGAATAAAAATTAAAAAGAGA 2 19 0 AAATAAAAAT 0.78107 -282 ATCTTTAGAACGGGGAAAAATCGCAGAGTCT 2 77 1 CGGGAAAAAT 0.986033 -224 ACTAAAGACTCCAGGAAAGATCGTTTATCTT 2 143 1 CAGGAAAGAT 0.95281 -158 TGTTTGCATGCTAAGAAAGATTTATAGACAA 2 197 1 CAAGAAAGAT 0.88121 -104 TTTTAAAATAATAAGAAAAATAAACCAAGTA 4 51 0 AAAGAAAAAT 0.935077 -80 * ********* Masking position 6 Map Score: 10.8296 Number of sites scoring better than the average of aligned sites = 2051 Number in coding regions = 1703 Number in noncoding regions = 348 Number of orfs with sites within 600 bp upstream = 380 Fraction of orfs with sites within 600 bp upstream = 0.0610344 Motif number 3 GCAATCTGAGAAACCATCTTGTTTTTTTAA 1 33 0 AAACCATCTT 0.87211 -268 AAAGGTAAAAAAAAGATTTTAATAGGAAAA 1 74 1 AAAAGATTTT 0.85074 -227 CGATCGGGGAAAAATGGCTTGATCTGGCAT 1 139 0 AAAATGGCTT 0.817496 -162 CTCACCTTCTCAAAGATCTTAACTAAAGAC 2 122 1 CAAAGATCTT 0.952327 -179 ACCTCAAGATAAACGATCTTTCCTGGAGTC 2 149 0 AAACGATCTT 0.97519 -152 TTTTGCACAGAAAAGGGCTTTGTAAAGAAG 3 15 1 AAAAGGGCTT 0.975012 -79 TCTTAGAAAGAAAAGAGCTTCTTTACAAAG 3 32 0 AAAAGAGCTT 0.985525 -62 TATTATTTTAAAAAGATCTAATAGCTCATT 4 69 1 AAAAGATCTA 0.930966 -62 ********** Masking position 3 Map Score: 8.46131 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 222 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 TTGTTTTTTTAAAGAAATATTATTAATCTGA 1 14 0 AAAGAAATTT 0.924581 -287 TTCCAAAGGTAAAAAAAAGATTTTAATAGGA 1 70 1 AAAAAAAAAT 0.826823 -231 TAATAGGAAAAAATAAATCATTAAAAAATAA 1 93 1 AAATAAATAT 0.910328 -208 AATCATTAAAAAATAAAAATTTTTCTCGTAA 1 108 1 AAATAAAATT 0.959716 -193 TAAAAATTAAAAAGAGAAAATAGTT 2 5 0 AAAGAGAAAT 0.815907 -296 AATGTGTGCAGAATAAAAATTAAAAAGAGAA 2 18 0 GAATAAAATT 0.847811 -283 TTCTCCTACGAAATAAATGTTTGCATGCTAA 2 180 1 AAATAAATTT 0.925958 -121 TAAGTCTTAGAAAGAAAAGAGCTTCTTTACA 3 35 0 AAAGAAAAAG 0.815907 -59 TCCTAGATTTAAATAAAAATTTGTATTAATC 4 16 1 AAATAAAATT 0.959716 -115 ******** ** Masking position 5 Map Score: 6.62022 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 221 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 5 ATGGTTTCTCAGATTGCAGTTGGTTTCCAAAGGTA 1 46 1 AATGCAGGTT 0.972189 -255 TGGGGCCACAACCAGGCAGTATTTTGTTCCTTTGG 1 178 0 ACAGCAGTTT 0.950669 -123 GAACGGGGAAAAATCGCAGAGTCTTTCATTTTCTT 2 84 1 AATGCAGTTT 0.990962 -217 AGCGGATGCGACATGGCAGATTGTCTATAAATCTT 2 213 0 AATGCAGTTC 0.972219 -88 ACCATATTTAAAATAGGAGCATCTTCGA 2 283 1 AATGGAGTTT 0.979316 -18 AGTCTTAGAAAGAAAAGAGCTTCTTTACAAAGCCC 3 29 0 AAAAGAGTTT 0.826826 -65 CTAATAGCTCATTACGCAGGTTTTTATGCGCAATG 4 86 1 ATAGCAGTTT 0.951093 -45 * ** **** * ** Masking position 8 Map Score: 1.95082 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 85 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 AAAAAAACAAGATGGTTTCTCAGATTGCAG 1 35 1 GATGGTTTCT 0.762493 -266 TCAGATTGCAGTTGGTTTCCAAAGGTAAAA 1 54 1 GTTGGTTTCC 0.962359 -247 CCAGGTAACTCCTGGGCTCCATGGGGCCAC 1 204 0 CCTGGGCTCC 0.935949 -97 ATCTCGATTCTTTGGTGTCCT 1 290 1 TTTGGTGTCC 0.941864 -11 TTAAAATAACCTTGGTGTTCAATGTGTGCA 2 39 0 CTTGGTGTTC 0.958702 -262 AACGATCTTTCCTGGAGTCTTTAGTTAAGA 2 138 0 CCTGGAGTCT 0.928002 -163 GTTGCGCTTTTTTGGGTTTTCACCATATTT 2 262 1 TTTGGGTTTT 0.68875 -39 CTAAGACTTACCTGGATTTCTAATTCGCAA 3 56 1 CCTGGATTTC 0.909902 -38 AATCATAATACTTGGTTTATTTTTCTTATT 4 43 1 CTTGGTTTAT 0.826717 -88 ********** Masking position 3 Map Score: 2.20594 Number of sites scoring better than the average of aligned sites = 1175 Number in coding regions = 1074 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 7 CTCGTAAATGCCAGATCAAGCCATTTTTCCCC 1 132 1 CCAGATAGCC 0.993128 -169 GCCATTTTTCCCCGATCGCCCCATTGGCCAAA 1 151 1 CCCGATGCCC 0.985971 -150 CTGGTTGTGGCCCCATGGAGCCCAGGAGTTAC 1 198 1 CCCCATGGCC 0.977375 -103 CTGATTCTTACCAGGTAACTCCTGGGCTCCAT 1 212 0 CCAGGTATCC 0.981539 -89 ACCAAAGAATCGAGATTGTGCCTGCCAGCCTT 1 274 0 CGAGATGGCC 0.98117 -27 AATTAGAAATCCAGGTAAGTCTTAGAAAGAAA 3 49 0 CCAGGTATCT 0.891618 -45 ****** * *** Masking position 6 Map Score: 0.983193 Number of sites scoring better than the average of aligned sites = 487 Number in coding regions = 456 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 ********** No masking Map Score: -1.18417e-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 9 ********** No masking Map Score: -1.18417e-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 10 ********** No masking Map Score: -1.18417e-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