AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i312_synecho_ctra_100.orf -o312_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 RCY33042 153 Synechocystis #2 RCY51152 40 Synechocystis #3 RCT00337 60 Chlamydia_trachomatis #4 RCT00338 300 Chlamydia_trachomatis Motif number 1 ATCCTTTCTCTACCCGTCCAGGAAAAATCTTCTAG 1 21 0 TACCCTCCGA 0.994919 -133 TTTGTCCTATCCCCCATCCTTGTTTCAACTAACTT 1 66 0 CCCCCTCCGT 0.997505 -88 CTTGGTTTACTACCCTGCCGGGGCAATGCCAGAAG 1 113 0 TACCCGCCGA 0.915178 -41 AACTCCGTGCCACCCTTCCCCGCCTTTT 3 4 0 CACCCTCCGT 0.995109 -57 TGCTCTTAGTTACCCCTCTTTTCGATATTTAAGTG 4 17 1 TACCCTCTTA 0.863819 -284 ACGGCTGGGTCCCTCCTCCCCTATAGCTTTTACCT 4 126 1 CCCTCTCCTA 0.987931 -175 AAAGAACCTACCCTCGTCCTAGGTAAAAGCTATAG 4 146 0 CCCTCTCCGA 0.996011 -155 TTGGATCTTACCGCCTCCCTAGAGATGTGGCAAAC 4 209 0 CCGCCCCCGA 0.967115 -92 TTTGGGTTGTTCCTCCTCCCCTTTTTCTTTGGATC 4 237 0 TCCTCTCCTT 0.956246 -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 AAACAAGGATGGGGGATAGGACAAATTGTACAATGG 1 76 1 GGGAAACAAT 0.947988 -78 CTACCCTGCCGGGGCAATGCCAGAAGCCCATTGTAC 1 103 0 GGGATCAAAG 0.971334 -51 TTGCCCCGGCAGGGTAGTAAACCAAGCATTGATTAG 1 122 1 AGGATACAAG 0.910147 -32 ATCAGGTTTAAGGGGAGATTCCTATGGGATAATGA 2 10 0 AGGAACCATG 0.956805 -31 TAACAAAAAAGCGTTATATCCTCAAGCCAAAGGAAA 4 79 0 GGTAACTAAG 0.941179 -222 CCCTAGAGATGTGGCAAACACCCAAACAAAGCAGCT 4 192 0 GGGAACCAAA 0.99391 -109 CTCTAGGGAGGCGGTAAGATCCAAAGAAAAAGGGGA 4 220 1 GGGAGCCAAG 0.995466 -81 AAAAGGGGAGGAGGAACAACCCAAAATTCTTAAGGT 4 247 1 GGGAACCAAA 0.99391 -54 TAGTTTTTAGGTAGAAAAACCTTAAGAATTTTGGGT 4 265 0 GAGAACTAAG 0.941179 -36 * ** * * ** *** Masking position 6 Map Score: 7.56737 Number of sites scoring better than the average of aligned sites = 1033 Number in coding regions = 964 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 AAATCTTCTAGTTCTTTTGTT 1 2 0 GTTCTTTTGT 0.915939 -152 TCCTATCCCCCATCCTTGTTTCAACTAACT 1 67 0 CATCCTTGTT 0.794305 -87 GAACAGTTAACTTCTTTTCTGAGATCA 3 44 1 CTTCTTTTCT 0.941511 -17 GTGTTTTGCTCTTAGTTACC 4 1 1 GTGTTTTGCT 0.873167 -300 CAGAAAAATACATTTTTGTTTCCTTTGGCT 4 61 1 CATTTTTGTT 0.920705 -240 GGATATAACGCTTTTTTGTTAAAAGTGTTC 4 94 1 CTTTTTTGTT 0.976619 -207 ACGAGGGTAGGTTCTTTTTTAGAATATAAG 4 164 1 GTTCTTTTTT 0.950598 -137 AGAATATAAGCTGCTTTGTTTGGGTGTTTG 4 184 1 CTGCTTTGTT 0.966264 -117 TCCTCCTCCCCTTTTTCTTTGGATCTTACC 4 232 0 CTTTTTCTTT 0.806383 -69 TTGATTTGTAGTTTTTAGGTAGAAAAACCT 4 279 0 GTTTTTAGGT 0.716229 -22 ********** Masking position 6 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 0.991714 -113 TTCTATAGAACTCCGTGCCACCCTTCCCCGCCT 3 14 0 CTCGTCCCCC 0.992435 -47 GTGTTTTGCTCTTAGTTACCCCTCTTTTCGATA 4 11 1 CTAGTACCCT 0.989925 -290 GTTCTGACGGCTGGGTCCCTCCTCCCCTATAGC 4 120 1 CTGGTCCCCT 0.996547 -181 TACCCTCGTCCTAGGTAAAAGCTATAGGGGAGG 4 140 0 CTGGTAAGCT 0.971441 -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 0.966014 -51 TCATTATCCCATAGGAATCTCCCCT 2 6 1 ATCCCATAGG 0.981249 -35 TTATATCCTCAAGCCAAAGGAAACAAAAAT 4 72 0 AAGCCAAAGG 0.990927 -229 TCCTAGGTAAAAGCTATAGGGGAGGAGGGA 4 135 0 AAGCTATAGG 0.954399 -166 GAGGAGGAACAACCCAAAATTCTTAAGGTT 4 254 1 AACCCAAAAT 0.864445 -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