AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i282_synecho_ctra_300.orf -o282_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 RCY21802 300 Synechocystis #2 RCT00174 300 Chlamydia_trachomatis #3 RCT00202 19 Chlamydia_trachomatis #4 RCT00204 94 Chlamydia_trachomatis #5 RCT00205 300 Chlamydia_trachomatis Motif number 1 GGGAATTCAATTCAAAATTTCCCAGTATGATGA 1 26 1 TCAATTTCCC 0.982127 -275 GTCTGAAAAGTCTAAATTCTCCCTGTACATCTC 1 57 0 TTAATCTCCC 0.931301 -244 ATTTAGACTTTTCAGACCCTCTCTAGGAAAGTG 1 73 1 TCAGCCTCTC 0.953528 -228 ACTCAAATTTTTAAACACTTTCCTAGAGAGGGT 1 88 0 TAAACTTTCC 0.861051 -213 AGGTCTTTTGTAACAGTTCTCCCCTTCCCAAGG 1 147 0 TACATCTCCC 0.91244 -154 TATTCATCCTTCCAAATCCTCCCACTAAAGCTC 1 193 0 TCAACCTCCC 0.996285 -108 CTTTGCACTTTTCAGACCCTCTCTAAAGCTAAA 1 231 1 TCAGCCTCTC 0.953528 -70 TGATTAACTGTGAAAAATCTCCCCTTAACTTAG 1 271 0 TAAATCTCCC 0.978044 -30 TCTAGATATTTACAAGCCTTCTCATAGGCTCTC 2 45 1 TCAACTTCTC 0.964022 -256 CGTTCCTATATTCGACACCTCCCGCGTTTCATT 2 80 1 TCGACCTCCC 0.994082 -221 GAAGCCCTTGTTAGATTCTTTCCTTTGAGAGGT 4 70 1 TAGACTTTCC 0.795136 -25 TGAAAGACTCTGCGATTTTTCCCCGTTCTAAAG 5 207 1 TCGATTTCCC 0.971764 -94 * *** ****** Masking position 10 Map Score: 17.0585 Number of sites scoring better than the average of aligned sites = 687 Number in coding regions = 603 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 AAAAAGGAGGTCTTTTGTAACAGTTCTCCCC 1 156 0 TCTTTGTAAC 0.882129 -145 ACAAAAGACCTCCTTTTTAAGCCGGAGCTTT 1 169 1 TCCTTTTAAG 0.904365 -132 TTAAGCCGGAGCTTTAGTGGGAGGATTTGGA 1 185 1 GCTTTGTGGG 0.967838 -116 TTAGTGGGAGGATTTGGAAGGATGAATACCT 1 198 1 GATTTGAAGG 0.724767 -103 TGAAATTTTAGCTTTAGAGAGGGTCTGAAAA 1 239 0 GCTTTGAGAG 0.886866 -62 AGAGCTACTAGCTTTCTTAACTTATTGGATA 2 135 0 GCTTTTTAAC 0.816217 -166 GTTAACGATCTCCTTGTTAGGATGGTCGGGT 2 182 1 TCCTTTTAGG 0.938178 -119 CATATGAATATGTTTGGTAAGGGCCTACTGT 2 234 1 TGTTTGTAAG 0.848416 -67 TAAGAAGTTTTGCTTCTTAGGTGGGACGTCA 2 266 1 TGCTTTTAGG 0.748112 -35 TTCCTTCAAAGCTTTATCAAGAC 4 3 0 GCTTTTCAAG 0.761679 -92 TTAGATTCTTTCCTTTGAGAGGTTT 4 80 1 TCCTTGAGAG 0.813709 -15 AGTGTGTTGCGCTTTTTTGGGTTTTCACCAT 5 31 0 GCTTTTTGGG 0.942733 -270 TGTCTATAAATCTTTCTTAGCATGCAAACAT 5 92 1 TCTTTTTAGC 0.867899 -209 TGCAAACATTTATTTCGTAGGAGAAAACCTC 5 114 1 TATTTGTAGG 0.853087 -187 ATATAACTGATCTTTAGAACGGGGAAAAATC 5 220 0 TCTTTGAACG 0.7605 -81 ***** ***** Masking position 5 Map Score: 10.5897 Number of sites scoring better than the average of aligned sites = 1256 Number in coding regions = 1050 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 3 GAGAATTTAGACTTTTCAGACCCTCTCTAG 1 69 1 ACTTTTCAGA 0.974979 -232 CTAGCTTTGCACTTTTCAGACCCTCTCTAA 1 227 1 ACTTTTCAGA 0.974979 -74 TTAAGGGGAGATTTTTCACAGTTAATCATG 1 276 1 ATTTTTCACA 0.981337 -25 GTATTTGATTATTTTTCACGAATGAAACGC 2 103 0 ATTTTTCACG 0.959493 -198 AACAATCAAGATTATTCACAGAGCTACTAG 2 155 0 ATTATTCACA 0.941114 -146 ********** Masking position 5 Map Score: 3.9087 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 14 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 AATAGTAAATAACATCATAAATCATACACT 2 15 1 AACATCATAA 0.908584 -286 GCCCTTACCAAACATATTCATATGACTAGG 2 228 0 AACATATTCA 0.806897 -73 TAAGAAGCAAAACTTCTTATACAGTAGGCC 2 255 0 AACTTCTTAT 0.863576 -46 AACATCTTATTGTAACAAT 3 10 0 AACATCTTAT 0.954184 -10 GTAATCCTACAACCTCTTCAAGATTCCTTC 4 27 0 AACCTCTTCA 0.963909 -68 AAACCTCTCAAAGGAAAGAAT 4 84 0 AACCTCTCAA 0.924313 -11 CACCTTCTCAAAGATCTTAACTAAAGACTC 5 165 0 AAGATCTTAA 0.901995 -136 ********** Masking position 2 Map Score: 2.0638 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 81 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 5 ********** No masking Map Score: -3.15948e-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 6 ATTGAATTCCCTACATAATTGAGGGA 1 7 0 CTACATAATT 0.761909 -294 AGGGAATTCAATTCAAAATTTCCCAGTATG 1 25 1 ATTCAAAATT 0.821491 -276 AACTACATGATTAACTGTGAAA 1 289 0 CTACATGATT 0.921276 -12 AAATCATACACTTCTAGATATTTACAAGCC 2 33 1 CTTCTAGATA 0.848202 -268 GATCGTTAACAATCAAGATTATTCACAGAG 2 162 0 AATCAAGATT 0.641813 -139 CCTACAACCTCTTCAAGATTCCTTCAAAGC 4 22 0 CTTCAAGATT 0.983207 -73 TAGGAGAAAACCTCAAGATAAACGATCTTT 5 131 1 CCTCAAGATA 0.907805 -170 ********** Masking position 8 Map Score: 0.0163355 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 171 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 7 ********** No masking Map Score: -3.15948e-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: -3.15948e-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: -3.15948e-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