AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i105_synecho_ctra_100.orf -o105_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 RCY20071 98 Synechocystis #2 RCY34291 164 Synechocystis #3 RCT00066 300 Chlamydia_trachomatis #4 RCT00396 300 Chlamydia_trachomatis Motif number 1 TTGACACGTTGAGTTTTTCTGTAATCAACT 1 26 1 GAGTTTTTCT 0.96861 -73 TAAGCTCGTGGGCTTTTTCTGA 2 3 0 GGCTTTTTCT 0.986359 -162 ATAGTGATAATGGTCTTTCATGATCATCTC 2 102 0 TGGTCTTTCA 0.789593 -63 ATAAGCGAGGTTCTTTTTTTGGAGGGGGAG 3 43 1 TTCTTTTTTT 0.805722 -258 CTTTAAAATAGAGTTTTTCTTATGATCCCA 3 95 1 GAGTTTTTCT 0.96861 -206 AAATATCGGTTGGTTTTTGTCCTTAGGGGA 3 159 1 TGGTTTTTGT 0.882034 -142 GGGGATCGTATACTTTTTCAAAGTATGTCC 3 184 1 TACTTTTTCA 0.916132 -117 AGGCTCTTATGTCTTTTTTTCATACTAGAA 3 231 1 GTCTTTTTTT 0.84769 -70 GTGTTTAGCAGGCTGTTTCTTA 3 289 1 GGCTGTTTCT 0.937809 -12 AGAATATTCTTAGTTTTTTAAGATTTTATC 4 63 1 TAGTTTTTTA 0.721 -238 GTACAATTTTTGCTTTTTCTTTAAAAAACT 4 106 1 TGCTTTTTCT 0.981779 -195 ********** Masking position 6 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 0.973133 -19 AAAGAACCTCGCTTATCGCAAAGATACTTT 3 29 0 GCTTATCGCA 0.85957 -272 CCTCCTGTAAGGAGCTCCCCCTCCAAAAAA 3 57 0 GGAGCTCCCC 0.824833 -244 GAGTTTTTCTTATGATCCCATGTGGCGATA 3 105 1 TATGATCCCA 0.759339 -196 GCTAGACCCGGCCTATCGCCACATGGGATC 3 118 0 GCCTATCGCC 0.969053 -183 TGAAAAAGTATACGATCCCCTAAGGACAAA 3 174 0 TACGATCCCC 0.942936 -127 GAAAATATAAGCTTATCCTCAGAGGACTCT 3 258 1 GCTTATCCTC 0.874843 -43 CAAACAACTCGGCTATCGCCGGCAAAAAGA 4 25 1 GGCTATCGCC 0.71437 -276 AAAAAACTGTTCCTCACCCCGTTTTCTAAA 4 128 1 TCCTCACCCC 0.926349 -173 GCTTCTCTGCTCTGAACCCCATATTACTAA 4 158 1 TCTGAACCCC 0.973133 -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 AAGATTAAGTCCAGTTGATTACAGAAAAACTCAA 1 34 0 CCAGTTTAAG 0.995366 -65 CACGAGCTTACCAGTTGGTAAAAGTTAAGAAATT 2 23 1 CCAGTTAAAG 0.981476 -142 CGGCGATAGCCGAGTTGTTTGGAGAGTAGTAGTT 4 12 0 CGAGTTTGAG 0.97622 -289 GGGGTGAGGAACAGTTTTTTAAAGAAAAAGCAAA 4 114 0 ACAGTTTAAG 0.970787 -187 TGTTCCTCACCCCGTTTTCTAAAGCTTCTCTGCT 4 135 1 CCCGTTTAAG 0.987428 -166 TGATTTAACGCGATTTCCCTAAAGAATGAAATTG 4 204 1 CGATTTTAAG 0.945558 -97 ****** ** ** Masking position 6 Map Score: 2.76547 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 81 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 TTTACCAACTGGTAAGCTCGTGGGCTTTTTCTG 2 12 0 GGAAGCTTGG 0.971175 -153 CTGCAATTATGAGAAGATAATGAAAAATGAGAT 2 74 1 GAAAGATTGA 0.977969 -91 AATGAAAAATGAGATGATCATGAAAGACCATTA 2 92 1 GAATGATTGA 0.902111 -73 AGTCCTCCCCGGGAAGCAAATGATGTTGCCATA 2 129 0 GGAAGCATGA 0.964303 -36 AATTGTACGAAAAAAGCTGGAGATAAAATCTTA 4 81 0 AAAAGCTAGA 0.901788 -220 GTTCAGAGCAGAGAAGCTTTAGAAAACGGGGTG 4 142 0 GAAAGCTAGA 0.98607 -159 TTGTTTGGAAGACAAGCCATTGAACAAAATTAC 4 235 1 GAAAGCCTGA 0.983471 -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 CAGATTTTAGGTAGTGGTAAATCGTCAAGA 1 64 0 GTAGTGGTAA 0.938455 -35 TCTCATAATTGCAGTGAAAACGGGGAGTTA 2 58 0 GCAGTGAAAA 0.919499 -107 TTATGAGAAGATAATGAAAAATGAGATGAT 2 80 1 ATAATGAAAA 0.796018 -85 TGATGTTGCCATAGTGATAATGGTCTTTCA 2 112 0 ATAGTGATAA 0.916482 -53 TCTAGCGCCGATAGTAGAAATATCGGTTGG 3 142 1 ATAGTAGAAA 0.961857 -159 TCTTTTTTTCATACTAGAAAATATAAGCTT 3 242 1 ATACTAGAAA 0.852365 -59 CGGCAAAAAGACAGTAGAAAGAATATTCTT 4 44 1 ACAGTAGAAA 0.944365 -257 ********** Masking position 3 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 6 GAGGTTCTTTTTTTGGAGGGGGAGCTCCTT 3 49 1 TTTTGGAGGG 0.968526 -252 GGGAGCTCCTTACAGGAGGCTTGTATCCTT 3 68 1 TACAGGAGGC 0.961255 -233 CGTATCGATTATCTGGAGGCTCTTATGTCT 3 215 1 ATCTGGAGGC 0.972617 -86 GACTCTTGTGTTTAGCAGGCTGTTTCTTA 3 282 1 TTTAGCAGGC 0.981099 -19 TCTACTGTCTTTTTGCCGGCGATAGCCGAG 4 32 0 TTTTGCCGGC 0.97102 -269 ********** Masking position 5 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 7 ********** 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 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