AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i312_synecho_ctra_300.orf -o312_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 RCY33042 153 Synechocystis #2 RCY51152 40 Synechocystis #3 RCT00337 60 Chlamydia_trachomatis #4 RCT00338 300 Chlamydia_trachomatis Motif number 1 CTAGAAGATTTTTCCTGGACGGGTAGAGAAAGGAT 1 21 1 TCGGAGGGTA 0.996207 -133 AAGTTAGTTGAAACAAGGATGGGGGATAGGACAAA 1 66 1 ACGGAGGGGG 0.998151 -88 CTTCTGGCATTGCCCCGGCAGGGTAGTAAACCAAG 1 113 1 TCGGCGGGTA 0.900409 -41 AAAAGGCGGGGAAGGGTGGCACGGAGTT 3 4 1 ACGGAGGGTG 0.996374 -57 CACTTAAATATCGAAAAGAGGGGTAACTAAGAGCA 4 17 0 TAAGAGGGTA 0.895462 -284 AGGTAAAAGCTATAGGGGAGGAGGGACCCAGCCGT 4 126 0 TAGGAGAGGG 0.991035 -175 CTATAGCTTTTACCTAGGACGAGGGTAGGTTCTTT 4 146 1 TCGGAGAGGG 0.997043 -155 GTTTGCCACATCTCTAGGGAGGCGGTAAGATCCAA 4 209 1 TCGGGGGCGG 0.975438 -92 GATCCAAAGAAAAAGGGGAGGAGGAACAACCCAAA 4 237 1 AAGGAGAGGA 0.967228 -64 * * *** ***** Masking position 8 Map Score: 13.6336 Number of sites scoring better than the average of aligned sites = 958 Number in coding regions = 880 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 CATTGTACAATTTGTCCTATCCCCCATCCTTGTTTCA 1 74 0 TTGTTTCCCT 0.991197 -80 TTCCTTTGGCTTGAGGATATAACGCTTTTTTGTTAAA 4 80 1 TTAGTTACCT 0.97438 -221 GCTGCTTTGTTTGGGTGTTTGCCACATCTCTAGGGAG 4 193 1 TTGGTTCCCT 0.998593 -108 CCCCTTTTTCTTTGGATCTTACCGCCTCCCTAGAGAT 4 218 0 TTGGCTCCCT 0.996257 -83 CCTTAAGAATTTTGGGTTGTTCCTCCTCCCCTTTTTC 4 245 0 TTGGTTCCCT 0.998625 -56 CCCAAAATTCTTAAGGTTTTTCTACCTAAAAACTACA 4 266 1 TTAGTTCTCT 0.974391 -35 ** ** * * ** * * Masking position 10 Map Score: 7.46238 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 65 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 3 AACAAAAGAACTAGAAGATTT 1 2 1 ACAAAAGAAC 0.905858 -152 AGTTAGTTGAAACAAGGATGGGGGATAGGA 1 67 1 AACAAGGATG 0.773249 -87 TGATCTCAGAAAAGAAGTTAACTGTTC 3 44 0 AGAAAAGAAG 0.934277 -17 GGTAACTAAGAGCAAAACAC 4 1 0 AGCAAAACAC 0.858748 -300 AGCCAAAGGAAACAAAAATGTATTTTTCTG 4 61 0 AACAAAAATG 0.911141 -240 GAACACTTTTAACAAAAAAGCGTTATATCC 4 94 0 AACAAAAAAG 0.973606 -207 CTTATATTCTAAAAAAGAACCTACCCTCGT 4 164 0 AAAAAAGAAC 0.944421 -137 CAAACACCCAAACAAAGCAGCTTATATTCT 4 184 0 AACAAAGCAG 0.961967 -117 GGTAAGATCCAAAGAAAAAGGGGAGGAGGA 4 232 1 AAAGAAAAAG 0.786231 -69 AGGTTTTTCTACCTAAAAACTACAAATCAA 4 279 1 ACCTAAAAAC 0.690296 -22 ********** Masking position 5 Map Score: 6.74868 Number of sites scoring better than the average of aligned sites = 994 Number in coding regions = 855 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 4 ACTAACTTAACTCCGTCAATCCTTTCTCTACCC 1 41 0 CTCGTAACCT 0.991322 -113 TTCTATAGAACTCCGTGCCACCCTTCCCCGCCT 3 14 0 CTCGTCCCCC 0.992077 -47 GTGTTTTGCTCTTAGTTACCCCTCTTTTCGATA 4 11 1 CTAGTACCCT 0.989455 -290 GTTCTGACGGCTGGGTCCCTCCTCCCCTATAGC 4 120 1 CTGGTCCCCT 0.996385 -181 TACCCTCGTCCTAGGTAAAAGCTATAGGGGAGG 4 140 0 CTGGTAAGCT 0.970116 -161 ** *** ** *** Masking position 6 Map Score: 1.6929 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 62 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TGCCGGGGCAATGCCAGAAGCCCATTGTAC 1 103 0 ATGCCAGAAG 0.964963 -51 TCATTATCCCATAGGAATCTCCCCT 2 6 1 ATCCCATAGG 0.980659 -35 TTATATCCTCAAGCCAAAGGAAACAAAAAT 4 72 0 AAGCCAAAGG 0.990639 -229 TCCTAGGTAAAAGCTATAGGGGAGGAGGGA 4 135 0 AAGCTATAGG 0.953005 -166 GAGGAGGAACAACCCAAAATTCTTAAGGTT 4 254 1 AACCCAAAAT 0.860702 -47 ********** Masking position 6 Map Score: 0.95818 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 319 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 ********** No masking Map Score: -8.21797e-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 7 ********** No masking Map Score: -8.21797e-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 8 ********** No masking Map Score: -8.21797e-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