AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_soj_ctra_reg_100.orf -o254_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 RCT00473 293 Chlamydia_trachomatis #2 RCT00554 300 Chlamydia_trachomatis #3 RCT00657 135 Chlamydia_trachomatis Motif number 1 CTGTCAATTTTTGGGAATAAACTTGT 1 6 0 TTGGGAAAAA 0.988678 -288 TCACCAGGCGATGGGAAGAAGTTTACAATGG 1 37 0 ATGGGAAAAG 0.930986 -257 GCGATACACTTTGAGAAGAAAACCTATGAGG 1 74 1 TTGAGAAAAA 0.97154 -220 GCGTAAACCATTAAGAAGAAAACCATGTCAT 1 172 1 TTAAGAAAAA 0.963657 -122 ATGTCATCTGTTAAGAAAAAACGAAGACTTA 1 196 1 TTAAGAAAAA 0.963656 -98 AGCAACTACCATGGGAAGAAAAATCGTATAG 2 49 0 ATGGGAAAAA 0.965032 -252 AAGTCTATTTTTAGGGATAAGTCTTTTGTAA 2 98 0 TTAGGGAAAG 0.941886 -203 TCGTCCATGCTTATGGACAAATCAATATAAA 2 215 1 TTATGGAAAA 0.836853 -86 GGGCTGAGAATTAGGAAAATATT 3 123 1 TTAGGAAATA 0.914482 -13 ******* *** Masking position 7 Map Score: 11.8455 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 170 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 CACTTTGAGAAGAAAACCTATGAGGATCGG 1 80 1 AGAAAACCTA 0.776936 -214 AAGTCTTTTGAAAAGACTCAGCTAATGCCT 1 128 0 AAAAGACTCA 0.963669 -166 GAGTCTTTTCAAAAGACTTACCAATTATTC 1 139 1 AAAAGACTTA 0.984048 -155 TAAGAAAAAACGAAGACTTAAGATCGCCAA 1 207 1 CGAAGACTTA 0.949713 -87 TAAGCGTAAAAAAAGACGTCGAAGAGATCG 1 240 1 AAAAGACGTC 0.913878 -54 CCATGGGAAGAAAAATCGTATAGTTAACTC 2 42 0 AAAAATCGTA 0.857877 -259 TTCCGTTTACAAAAGACTTATCCCTAAAAA 2 92 1 AAAAGACTTA 0.984048 -209 AATAATATAGAAAAGAGGTATCTGGAGAGC 2 153 1 AAAAGAGGTA 0.868226 -148 ACTCAAGATACAAAATCTTATAATGCAAAT 3 54 0 CAAAATCTTA 0.838975 -82 CCCCAGAATACAAAAACTCAAGATACAAAA 3 69 0 CAAAAACTCA 0.889619 -67 ********** Masking position 4 Map Score: 9.82232 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 149 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 CAAGTTTATTCCCAAAAATTGACAGCCATTGT 1 12 1 CCAAAATTGA 0.977918 -282 AAGAGATCGGCATAAAAATAGATAGTTAAATT 1 261 1 CAAAAATAGA 0.980077 -33 AGAACCCAAACAATTTAACTATCTATT 1 277 0 CCAAAATTTA 0.955433 -17 AAGACTTATCCCTAAAAATAGACTTTTCTACC 2 104 1 CCAAAATAGA 0.990186 -197 GGATACTGTACCCAATAATATAGAAAAGAGGT 2 140 1 CCAAAATATA 0.980061 -161 TGCTTATGGACAAATCAATATAAAGGAATTAA 2 222 1 CAATAATATA 0.911964 -79 TCTTATAATGCAAATCAAGAGATGCCCACTCC 3 37 0 CAATAAGAGA 0.868392 -99 ** ** ****** Masking position 7 Map Score: 6.65116 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 54 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 TCGCCTGGTGAAAGCCGGCGATACACTTTGA 1 57 1 AAAGCCGCGA 0.971817 -237 AACGAAGACTTAAGATCGCCAAGCATAAGCG 1 215 1 TAAGATCCCA 0.865447 -79 AAGCGTAAAAAAAGACGTCGAAGAGATCGGC 1 241 1 AAAGACGCGA 0.972361 -53 AAGACGTCGAAGAGATCGGCATAAAAATAGA 1 252 1 AGAGATCGCA 0.972216 -42 ATGAGATTTTAGAGCCCTGGACCTGCCTGT 2 10 0 AGAGCCCGGA 0.971113 -291 ATAAAGTAAGAAAGCTCTCCAGATACCTCTT 2 165 0 AAAGCTCCCA 0.972361 -136 TGTTGTCAAGAGAGATGCGGAGTGGGCATCT 3 19 1 AGAGATGGGA 0.972216 -117 ATGCAAATCAAGAGATGCCCACTCCGCATCT 3 31 0 AGAGATGCCA 0.982736 -105 ******* *** Masking position 3 Map Score: 7.86934 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 108 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 GAAAACCTATGAGGATCGGGTGCTTGCCCG 1 91 1 GAGGATCGGG 0.985241 -203 TCTTTTGTAAACGGAACAGGATTACTGTAG 2 78 0 ACGGAACAGG 0.943843 -223 ATAAGCATGGACGAATGAGGTTAAAGGAGA 2 199 0 ACGAATGAGG 0.908999 -102 AGCAACTAAAAAGGAGCGAGGCTTCCTCCC 2 254 1 AAGGAGCGAG 0.856065 -47 CAAGAGAGATGCGGAGTGGGCATCTCTTGA 3 25 1 GCGGAGTGGG 0.986432 -111 GTAGAATACAACGAATTGGGCTGAGAATTA 3 106 1 ACGAATTGGG 0.972278 -30 GAATTGGGCTGAGAATTAGGAAAATATT 3 118 1 GAGAATTAGG 0.908737 -18 ********** Masking position 5 Map Score: 2.92586 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 126 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 6 AGACTCAGCTAATGCCTATGAGAACGGGCA 1 115 0 AATGCCTATG 0.949552 -179 CGTCTTTTTTTACGCTTATGCTTGGCGATC 1 228 0 TACGCTTATG 0.988708 -66 CTCATTCGTCCATGCTTATGGACAAATCAA 2 210 1 CATGCTTATG 0.978774 -91 TACGCTTCTGTTGTCAAGAG 3 1 1 TACGCTTCTG 0.980905 -135 ********** Masking position 7 Map Score: 0.891708 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 14 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: 1.65857e-13 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: 1.65857e-13 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: 1.65857e-13 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