AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i282_synecho_ctra_100.orf -o282_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 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 0.979917 -275 GTCTGAAAAGTCTAAATTCTCCCTGTACATCTC 1 57 0 TTAATCTCCC 0.923298 -244 ATTTAGACTTTTCAGACCCTCTCTAGGAAAGTG 1 73 1 TCAGCCTCTC 0.94797 -228 ACTCAAATTTTTAAACACTTTCCTAGAGAGGGT 1 88 0 TAAACTTTCC 0.846215 -213 AGGTCTTTTGTAACAGTTCTCCCCTTCCCAAGG 1 147 0 TACATCTCCC 0.90247 -154 TATTCATCCTTCCAAATCCTCCCACTAAAGCTC 1 193 0 TCAACCTCCC 0.995818 -108 CTTTGCACTTTTCAGACCCTCTCTAAAGCTAAA 1 231 1 TCAGCCTCTC 0.94797 -70 TGATTAACTGTGAAAAATCTCCCCTTAACTTAG 1 271 0 TAAATCTCCC 0.975348 -30 TCTAGATATTTACAAGCCTTCTCATAGGCTCTC 2 45 1 TCAACTTCTC 0.959666 -256 CGTTCCTATATTCGACACCTCCCGCGTTTCATT 2 80 1 TCGACCTCCC 0.99334 -221 GAAGCCCTTGTTAGATTCTTTCCTTTGAGAGGT 4 70 1 TAGACTTTCC 0.775099 -25 TGAAAGACTCTGCGATTTTTCCCCGTTCTAAAG 5 207 1 TCGATTTCCC 0.968314 -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 GGGGAGAACTGTTACAAAAGACCTCCTTTTT 1 156 1 GTTACAAAGA 0.907678 -145 AAAGCTCCGGCTTAAAAAGGAGGTCTTTTGT 1 169 0 CTTAAAAGGA 0.925501 -132 TCCAAATCCTCCCACTAAAGCTCCGGCTTAA 1 185 0 CCCACAAAGC 0.975328 -116 AGGTATTCATCCTTCCAAATCCTCCCACTAA 1 198 0 CCTTCAAATC 0.775752 -103 TTTTCAGACCCTCTCTAAAGCTAAAATTTCA 1 239 1 CTCTCAAAGC 0.91149 -62 TATCCAATAAGTTAAGAAAGCTAGTAGCTCT 2 135 1 GTTAAAAAGC 0.853682 -166 ACCCGACCATCCTAACAAGGAGATCGTTAAC 2 182 0 CCTAAAAGGA 0.952236 -119 ACAGTAGGCCCTTACCAAACATATTCATATG 2 234 0 CTTACAAACA 0.88028 -67 TGACGTCCCACCTAAGAAGCAAAACTTCTTA 2 266 0 CCTAAAAGCA 0.795991 -35 GTCTTGATAAAGCTTTGAAGGAA 4 3 1 CTTGAAAAGC 0.807642 -92 AAACCTCTCAAAGGAAAGAATCTAA 4 80 0 CTCTCAAGGA 0.851593 -15 ATGGTGAAAACCCAAAAAAGCGCAACACACT 5 31 1 CCCAAAAAGC 0.955803 -270 ATGTTTGCATGCTAAGAAAGATTTATAGACA 5 92 0 GCTAAAAAGA 0.896167 -209 GAGGTTTTCTCCTACGAAATAAATGTTTGCA 5 114 0 CCTACAAATA 0.884103 -187 GATTTTTCCCCGTTCTAAAGATCAGTTATAT 5 220 1 CGTTCAAAGA 0.806633 -81 ***** ***** Masking position 7 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 CTAGAGAGGGTCTGAAAAGTCTAAATTCTC 1 69 0 TCTGAAAAGT 0.976164 -232 TTAGAGAGGGTCTGAAAAGTGCAAAGCTAG 1 227 0 TCTGAAAAGT 0.976164 -74 CATGATTAACTGTGAAAAATCTCCCCTTAA 1 276 0 TGTGAAAAAT 0.982227 -25 GCGTTTCATTCGTGAAAAATAATCAAATAC 2 103 1 CGTGAAAAAT 0.961383 -198 CTAGTAGCTCTGTGAATAATCTTGATTGTT 2 155 1 TGTGAATAAT 0.943811 -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 0.91075 -286 GCCCTTACCAAACATATTCATATGACTAGG 2 228 0 AACATATTCA 0.810971 -73 TAAGAAGCAAAACTTCTTATACAGTAGGCC 2 255 0 AACTTCTTAT 0.866652 -46 AACATCTTATTGTAACAAT 3 10 0 AACATCTTAT 0.955322 -10 GTAATCCTACAACCTCTTCAAGATTCCTTC 4 27 0 AACCTCTTCA 0.964815 -68 AAACCTCTCAAAGGAAAGAAT 4 84 0 AACCTCTCAA 0.926137 -11 CACCTTCTCAAAGATCTTAACTAAAGACTC 5 165 0 AAGATCTTAA 0.904301 -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 ATTGAATTCCCTACATAATTGAGGGA 1 7 0 CTACATAATT 0.750815 -294 AGGGAATTCAATTCAAAATTTCCCAGTATG 1 25 1 ATTCAAAATT 0.812528 -276 AACTACATGATTAACTGTGAAA 1 289 0 CTACATGATT 0.916817 -12 AAATCATACACTTCTAGATATTTACAAGCC 2 33 1 CTTCTAGATA 0.840313 -268 GATCGTTAACAATCAAGATTATTCACAGAG 2 162 0 AATCAAGATT 0.639968 -139 CCTACAACCTCTTCAAGATTCCTTCAAAGC 4 22 0 CTTCAAGATT 0.982293 -73 TAGGAGAAAACCTCAAGATAAACGATCTTT 5 131 1 CCTCAAGATA 0.902653 -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 6 ********** 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 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