AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i105_synecho_ctra_300.orf -o105_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 RCY20071 98 Synechocystis #2 RCY34291 164 Synechocystis #3 RCT00066 300 Chlamydia_trachomatis #4 RCT00396 300 Chlamydia_trachomatis Motif number 1 AGTTGATTACAGAAAAACTCAACGTGTCAA 1 26 0 AGAAAAACTC 0.960611 -73 TCAGAAAAAGCCCACGAGCTTA 2 3 1 AGAAAAAGCC 0.982802 -162 GAGATGATCATGAAAGACCATTATCACTAT 2 102 1 TGAAAGACCA 0.747852 -63 CTCCCCCTCCAAAAAAAGAACCTCGCTTAT 3 43 0 AAAAAAAGAA 0.766233 -258 TGGGATCATAAGAAAAACTCTATTTTAAAG 3 95 0 AGAAAAACTC 0.960611 -206 TCCCCTAAGGACAAAAACCAACCGATATTT 3 159 0 ACAAAAACCA 0.85527 -142 GGACATACTTTGAAAAAGTATACGATCCCC 3 184 0 TGAAAAAGTA 0.896194 -117 TTCTAGTATGAAAAAAAGACATAAGAGCCT 3 231 0 AAAAAAAGAC 0.81477 -70 TAAGAAACAGCCTGCTAAACAC 3 289 0 AGAAACAGCC 0.922589 -12 GATAAAATCTTAAAAAACTAAGAATATTCT 4 63 0 TAAAAAACTA 0.671316 -238 AGTTTTTTAAAGAAAAAGCAAAAATTGTAC 4 106 0 AGAAAAAGCA 0.977056 -195 ********** Masking position 5 Map Score: 10.7308 Number of sites scoring better than the average of aligned sites = 863 Number in coding regions = 709 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 2 CTACCTAAAATCTGAACCCCTCTTTTGCC 1 80 1 TCTGAACCCC 0.974673 -19 AAAGAACCTCGCTTATCGCAAAGATACTTT 3 29 0 GCTTATCGCA 0.866698 -272 CCTCCTGTAAGGAGCTCCCCCTCCAAAAAA 3 57 0 GGAGCTCCCC 0.833153 -244 GAGTTTTTCTTATGATCCCATGTGGCGATA 3 105 1 TATGATCCCA 0.770196 -196 GCTAGACCCGGCCTATCGCCACATGGGATC 3 118 0 GCCTATCGCC 0.969691 -183 TGAAAAAGTATACGATCCCCTAAGGACAAA 3 174 0 TACGATCCCC 0.944213 -127 GAAAATATAAGCTTATCCTCAGAGGACTCT 3 258 1 GCTTATCCTC 0.881334 -43 CAAACAACTCGGCTATCGCCGGCAAAAAGA 4 25 1 GGCTATCGCC 0.709664 -276 AAAAAACTGTTCCTCACCCCGTTTTCTAAA 4 128 1 TCCTCACCCC 0.930382 -173 GCTTCTCTGCTCTGAACCCCATATTACTAA 4 158 1 TCTGAACCCC 0.974673 -143 ********** Masking position 7 Map Score: 6.37211 Number of sites scoring better than the average of aligned sites = 9147 Number in coding regions = 8278 Number in noncoding regions = 869 Number of orfs with sites within 600 bp upstream = 617 Fraction of orfs with sites within 600 bp upstream = 0.0991005 Motif number 3 TTGAGTTTTTCTGTAATCAACTGGACTTAATCTT 1 34 1 CTAAAACTGG 0.994544 -65 AATTTCTTAACTTTTACCAACTGGTAAGCTCGTG 2 23 0 CTTAAACTGG 0.978246 -142 AACTACTACTCTCCAAACAACTCGGCTATCGCCG 4 12 1 CTAAAACTCG 0.989614 -289 TTTGCTTTTTCTTTAAAAAACTGTTCCTCACCCC 4 114 1 CTAAAACTGT 0.965756 -187 AGCAGAGAAGCTTTAGAAAACGGGGTGAGGAACA 4 135 0 CTAGAACGGG 0.982226 -166 CAATTTCATTCTTTAGGGAAATCGCGTTAAATCA 4 204 0 CTAGAAATCG 0.92436 -97 ** ** ****** Masking position 9 Map Score: 1.96803 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 82 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 4 TTTACCAACTGGTAAGCTCGTGGGCTTTTTCTG 2 12 0 GGAAGCTTGG 0.97061 -153 CTGCAATTATGAGAAGATAATGAAAAATGAGAT 2 74 1 GAAAGATTGA 0.977534 -91 AATGAAAAATGAGATGATCATGAAAGACCATTA 2 92 1 GAATGATTGA 0.900331 -73 AGTCCTCCCCGGGAAGCAAATGATGTTGCCATA 2 129 0 GGAAGCATGA 0.963608 -36 AATTGTACGAAAAAAGCTGGAGATAAAATCTTA 4 81 0 AAAAGCTAGA 0.900003 -220 GTTCAGAGCAGAGAAGCTTTAGAAAACGGGGTG 4 142 0 GAAAGCTAGA 0.985793 -159 TTGTTTGGAAGACAAGCCATTGAACAAAATTAC 4 235 1 GAAAGCCTGA 0.983143 -66 ** ***** *** Masking position 4 Map Score: 2.47539 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 119 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 ATCATCTCATTTTTCATTATCTTCTCATAA 2 80 0 TTTTCATTAT 0.906295 -85 TATAAATTCATTCTGTTAAAAGTA 3 5 1 AATTCATTCT 0.960911 -296 TTATGTCTTTTTTTCATACTAGAAAATATA 3 237 1 TTTTCATACT 0.938804 -64 AAACTAAGAATATTCTTTCTACTGTCTTTT 4 49 0 TATTCTTTCT 0.914575 -252 CTTCCAAACAATTTCATTCTTTAGGGAAAT 4 216 0 ATTTCATTCT 0.972394 -85 ********** Masking position 4 Map Score: 1.74315 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 55 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 TCTTGACGATTTACCACTACCTAAAATCTG 1 64 1 TTACCACTAC 0.940159 -35 TAACTCCCCGTTTTCACTGCAATTATGAGA 2 58 1 TTTTCACTGC 0.921685 -107 ATCATCTCATTTTTCATTATCTTCTCATAA 2 80 0 TTTTCATTAT 0.80083 -85 TGAAAGACCATTATCACTATGGCAACATCA 2 112 1 TTATCACTAT 0.918742 -53 CCAACCGATATTTCTACTATCGGCGCTAGA 3 142 0 TTTCTACTAT 0.962939 -159 AAGCTTATATTTTCTAGTATGAAAAAAAGA 3 242 0 TTTCTAGTAT 0.856076 -59 AAGAATATTCTTTCTACTGTCTTTTTGCCG 4 44 0 TTTCTACTGT 0.945915 -257 ********** Masking position 6 Map Score: 1.83107 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 413 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 7 AAGGAGCTCCCCCTCCAAAAAAAGAACCTC 3 49 0 CCCTCCAAAA 0.965133 -252 AAGGATACAAGCCTCCTGTAAGGAGCTCCC 3 68 0 GCCTCCTGTA 0.957113 -233 AGACATAAGAGCCTCCAGATAATCGATACG 3 215 0 GCCTCCAGAT 0.969656 -86 TAAGAAACAGCCTGCTAAACACAAGAGTC 3 282 0 GCCTGCTAAA 0.979033 -19 CTCGGCTATCGCCGGCAAAAAGACAGTAGA 4 32 1 GCCGGCAAAA 0.967888 -269 ********** Masking position 6 Map Score: 0.655828 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 140 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 8 ********** No masking Map Score: -1.23391e-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: -1.23391e-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: -1.23391e-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