AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i118_synecho_ctra_100.orf -o118_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 RCY51088 297 Synechocystis #2 RCY15245 60 Synechocystis #3 RCT00429 300 Chlamydia_trachomatis Motif number 1 CAAGTTGCGCTTGCCCACGGAATAAATCCTA 1 43 1 TTGCCACGGA 0.967 -255 TGATCAGGCATCGACAAAAGCGAATTTTTGT 1 159 1 TCGCAAAAGC 0.787137 -139 CCCTAGGCGATCGCCTGGGGCCGAAAGCAAC 1 224 0 TCGCTGGGGC 0.864123 -74 CCCCAGGCGATCGCCTAGGGATCGACCCGTA 1 235 1 TCGCTAGGGA 0.966102 -63 GGGAAAGGAATTGATCGGGGACAATGTTCGA 1 277 0 TTGTCGGGGA 0.928168 -21 TTTTTGAGAATTGGTCAAAGAAAGCAAACAG 2 38 0 TTGTCAAAGA 0.837664 -23 GGGTGTGGTCCAGGGAACGCTTTCCT 3 6 1 TGGCCAGGGA 0.981735 -295 GCCCGGCGACTCGACCAGGAAAGCGTTCCCT 3 22 0 TCGCCAGGAA 0.967374 -279 CCGAAAACTCTCGCCCGGCGACTCGACCAGG 3 34 0 TCGCCGGCGA 0.714666 -267 AGCTACCGTGTTGTCCAAAAAATTGCAGAAA 3 90 1 TTGCCAAAAA 0.837665 -211 CCATTTTTTGATGTCCAGAGACAAATTTGGA 3 130 0 ATGCCAGAGA 0.962729 -171 AGCCCTCTCAATGACAAGAGAAGGAGCCCGG 3 169 0 ATGCAAGAGA 0.864837 -132 AACATATATGTTGACAAAAGAAAGCCCTCTC 3 191 0 TTGCAAAAGA 0.909927 -110 *** ******* Masking position 3 Map Score: 13.6628 Number of sites scoring better than the average of aligned sites = 2876 Number in coding regions = 2589 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 315 Fraction of orfs with sites within 600 bp upstream = 0.0505943 Motif number 2 TTACTTGGTAGGATTTATTCCGTGGGCAAGCGCAA 1 47 0 GGTTTTCTGG 0.971747 -251 ATTGATCGGGGACAATGTTCGATTCTATCGTGCTA 1 264 0 GAATTTCTTC 0.811212 -34 CCAGAATTCTGTTTGCTTTCTTTGACCAATTCTCA 2 30 1 GTGCTTCTGA 0.926251 -31 ACTCGACCAGGAAAGCGTTCCCTGGACCACACCC 3 10 0 GAGCTTCTGG 0.99627 -291 GTCGCCGGGCGAGAGTTTTCGGTTGGTTTTGGTAG 3 43 1 GAGTTTCTTG 0.985035 -258 TGGACAACACGGTAGCTTTCAATGCTTGTCTACCA 3 72 0 GGGCTTCTGC 0.992706 -229 GGGAGACTCCGGGCTCCTTCTCTTGTCATTGAGAG 3 161 1 GGTCTTCTTG 0.982293 -140 TTGTCATTGAGAGGGCTTTCTTTTGTCAACATATA 3 183 1 GAGCTTCTTG 0.994097 -118 ** ** *** *** Masking position 8 Map Score: 6.78332 Number of sites scoring better than the average of aligned sites = 290 Number in coding regions = 267 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 TTTAATTACTTTGTCCCCCATCGTTGCTTT 1 202 1 TTGTCCCCCA 0.996233 -96 CATCGTTGCTTTCGGCCCCAGGCGATCGCC 1 220 1 TTCGGCCCCA 0.965921 -78 GAATCGAACATTGTCCCCGATCAATTCCTT 1 274 1 TTGTCCCCGA 0.989559 -24 CTTTCAATGCTTGTCTACCAAAACCAACCG 3 62 0 TTGTCTACCA 0.931557 -239 GGAGCCCGGAGTCTCCCCCATTTTTTGATG 3 148 0 GTCTCCCCCA 0.991398 -153 ********** Masking position 2 Map Score: 3.84664 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 568 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 4 GAATTCATGACGAAGTTTTTTTACTTGGTA 1 72 0 CGAAGTTTTT 0.887448 -226 CTATGCATTGCAGTGTTTTGCAACATTTAA 1 106 0 CAGTGTTTTG 0.944666 -192 TCGACAAAAGCGAATTTTTGTATATCAAGA 1 169 1 CGAATTTTTG 0.966935 -129 ATCTTTTCTGCAATTTTTTGGACAACACGG 3 95 0 CAATTTTTTG 0.964979 -206 GGAGTCTCCCCCATTTTTTGATGTCCAGAG 3 141 0 CCATTTTTTG 0.967039 -160 ********** Masking position 6 Map Score: 0.965513 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 379 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 5 CATTTAATTAAGAATTCATGACGAAGTTTT 1 83 0 AGAATTCATG 0.975216 -215 TCGACAAAAGCGAATTTTTGTATATCAAGA 1 169 1 CGAATTTTTG 0.916536 -129 GAAAGCAAACAGAATTCTGGGTTGAAAAAT 2 20 0 AGAATTCTGG 0.979301 -41 TCGCCGGGCGAGAGTTTTCGGTTGGTTTTG 3 44 1 AGAGTTTTCG 0.941176 -257 CTGCATTCGCAGAATTCACGAATAACGAAG 3 272 1 AGAATTCACG 0.983781 -29 ********** Masking position 5 Map Score: 1.86303 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 43 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ********** No masking Map Score: 1.11798e-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 7 ********** No masking Map Score: 1.11798e-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 8 ********** No masking Map Score: 1.11798e-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