AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i117_Oligopeptide_Transport_ctra_reg_100.orf -o117_ctra_100.ace -a/home/amcguire/alignace/lib/ORF_ctra.txt -z/skink1/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCT00189 215 Chlamydia_trachomatis #2 RCT00457 300 Chlamydia_trachomatis #3 RCT00659 160 Chlamydia_trachomatis Motif number 1 CGCACGGAGTAAAAACATCTT 1 2 0 AAAAACATCT 0.930381 -214 CCGTGCGTAGAAAAGATTCTCTCTTTAAAA 1 25 1 AAAAGATTCT 0.952201 -191 ACTCTCTAGACAAGACCTCTCCGCATTTTA 1 50 0 CAAGACCTCT 0.892689 -166 CACTCTTGGCAAAGGCCTTTTATGTTTTCA 1 90 1 AAAGGCCTTT 0.493033 -126 TACAATATACAAAGGAATCTACTATGCTCA 1 146 1 AAAGGAATCT 0.948603 -70 TCTCTTTTAGAAAAAACTATAGAATAATAG 2 47 0 AAAAAACTAT 0.871321 -254 TTTTTTTCTTAAAAGATTCTCTATACCAGC 2 97 1 AAAAGATTCT 0.952201 -204 AGAAATATTTCAAAAAATATTTAGGAAGGA 2 127 0 CAAAAAATAT 0.739249 -174 CGACTTACTGAAAGAAATATTTCAAAAAAT 2 139 0 AAAGAAATAT 0.851244 -162 TGTAAGAGGAAAAAGCTTTTCTTTTGCTAT 2 180 1 AAAAGCTTTT 0.493048 -121 GAAAACGCACCAAAAAGTCTCAAGACAGGT 2 260 0 CAAAAAGTCT 0.749543 -41 GACAATTAAAAAAGGCTTAT 3 1 0 AAAGGCTTAT 0.794291 -160 AGAAAAAAACAAAAAATTTTGGTTCTTAGT 3 91 0 AAAAAATTTT 0.834666 -70 ********** Masking position 3 Map Score: 11.9373 Number of sites scoring better than the average of aligned sites = 631 Number in coding regions = 631 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 2 GAGTGATAATTTAACACTCTCTAGACAAGACC 1 63 0 TTACACTCTT 0.977271 -153 GAGTGTTAAATTATCACTCTTGGCAAAGGCCT 1 76 1 TTACACTCTG 0.988301 -140 TGTTGTTTAATTTGCTTTCTTTATGGGTAGTA 1 194 1 TTTCTTTCTT 0.778989 -22 AGAGTTGAAAATTCAACTCTCTTTTAGAAAAA 2 62 0 ATTAACTCTT 0.80897 -239 AGAGTTGAATTTTCAACTCTCTTTTTTTTTCT 2 74 1 TTTAACTCTT 0.964111 -227 CAATCTGGGTTTTGAATTCTAGTAACTAGCGA 2 213 0 TTTAATTCTG 0.934735 -88 TAGAATACTCTTATCAATCTGGGTTTTGAATT 2 227 0 TTACAATCTG 0.95841 -74 CATATATATATTTGCAATCTAGAATGTACTAA 3 64 1 TTTCAATCTG 0.977731 -97 TTTCTAAGATTTTTCACGCTCGAGGTCCCCTT 3 116 1 TTTCACGCTG 0.974111 -45 *** ****** * Masking position 10 Map Score: 8.73721 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 80 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 3 CCTCTCCGCATTTTAAAGAGAGAATCTTTT 1 35 0 TTTTAAAGAG 0.922651 -181 TATAGTTTTTTCTAAAAGAGAGTTGAATTT 2 56 1 TCTAAAAGAG 0.904539 -245 AAAAAATATTTAGGAAGGAGCTGGTATAGA 2 116 0 TAGGAAGGAG 0.964427 -185 GATCATCTTGTTTGTAAGAGGAAAAAGCTT 2 168 1 TTTGTAAGAG 0.964387 -133 AAAACCCAGATTGATAAGAGTATTCTAGAC 2 232 1 TTGATAAGAG 0.860285 -69 CAAATATATATATGAAGGAGGTATATTTTG 3 48 0 TATGAAGGAG 0.975781 -113 TCTCCTACTATTTGAAGGGGACCTCGAGCG 3 132 0 TTTGAAGGGG 0.958558 -29 ********** Masking position 6 Map Score: 4.52255 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 196 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 4 CCATAAAGAAAGCAAATTAAACAACAGCCGC 1 189 0 AGCAAATAAA 0.97426 -27 GAATCTTTTAAGAAAAAAAAAGAGAGTTGAA 2 85 0 AGAAAAAAAA 0.980485 -216 AGCGAATTATAGCAAAAGAAAAGCTTTTTCC 2 187 0 AGCAAAAAAA 0.981896 -114 TTTTTCTCAAAGACAATTAAAAAAGGCTTAT 3 11 0 AGACAATAAA 0.94046 -150 GAAAAATCTTAGAAAAAAACAAAAAATTTTG 3 100 0 AGAAAAAACA 0.957687 -61 ******* *** Masking position 6 Map Score: 2.54073 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 81 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 5 TTACTCCGTGCGTAGAAAAGATTCTCTCTT 1 20 1 CGTAGAAAAG 0.890569 -196 ACAGATAACAAGTTGAAAACATAAAAGGCC 1 103 0 AGTTGAAAAC 0.982283 -113 AAGGGGAAGAAGGTGGAGACGAAACTAGAG 2 14 1 AGGTGGAGAC 0.944119 -287 AAAAAAAGAGAGTTGAAAATTCAACTCTCT 2 72 0 AGTTGAAAAT 0.949301 -229 CTCCTCTATTCGTTGAAAACGCACCAAAAA 2 274 0 CGTTGAAAAC 0.973897 -27 CAACGAATAGAGGAGACAACGC 2 289 1 AGGAGACAAC 0.898136 -12 CCCTTCAAATAGTAGGAGATACATAGCT 3 143 1 AGTAGGAGAT 0.866941 -18 ********** Masking position 9 Map Score: 3.09253 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 79 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 ********** No masking Map Score: -1.0918e-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: -1.0918e-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: -1.0918e-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