AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_ctra_reg_300.orf -o057_ctra_300.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 RCT00348 169 Chlamydia_trachomatis #2 RCT00363 300 Chlamydia_trachomatis Motif number 1 GAAAAGGATTTTATTTTGTTGTTATAATTA 1 39 0 TTATTTTGTT 0.689053 -131 GAAATAAGTTCTATTTTTTTGTTATGAAAA 1 64 0 CTATTTTTTT 0.929614 -106 ATGCAAAAAACTCTTCCGAAGACTACATTA 1 115 1 CTCTTCCGAA 0.804485 -55 ACTACATTAGCTATTCATTTTTAACCTTTT 1 136 1 CTATTCATTT 0.880068 -34 ATGTCTATTTTCTAAAAAGGTTAA 1 156 0 CTATTTTCTA 0.865562 -14 GCATATTCAGCTCTTCCTTTGAGTAGTTTC 2 60 0 CTCTTCCTTT 0.983947 -241 TTTAATGATGCTATTCTGATCCGTTAGGCA 2 155 0 CTATTCTGAT 0.917212 -146 ATTAAACGTTCTCTTCTCTTCAAGAGAAGA 2 179 1 CTCTTCTCTT 0.992294 -122 AAAAAACGCCCTCTTCTCTTGAAGAGAAGA 2 190 0 CTCTTCTCTT 0.992294 -111 AAAAATCTTTCTATTTCTTTTCTCTTCCCT 2 226 1 CTATTTCTTT 0.925102 -75 TATTTCTTTTCTCTTCCCTGTGTGTATGAT 2 237 1 CTCTTCCCTG 0.961706 -64 TTTTCCTTGTTTCTTCTCTTAACTCATGAA 2 273 0 TTCTTCTCTT 0.947064 -28 ********** Masking position 5 Map Score: 17.689 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 781 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 2 ATTAATCTTGTTGAAAGATTTTATGTTTTTTT 1 11 0 TTGAAGATTT 0.989827 -159 CTTATTTCCCTCGTATGATCTTAAATATCATG 1 86 1 TCGATGATTT 0.976083 -84 GAAGAGTTTTTTGCATGATATTTAAGATCATA 1 99 0 TTGATGATTT 0.983779 -71 AATGTAGTCTTCGGAAGAGTTTTTTGCATGAT 1 112 0 TCGAAGAGTT 0.945621 -58 AGCTATTCATTTTTAACCTTTTTAGAAAATAG 1 144 1 TTTAACCTTT 0.780914 -26 TGAGGCGCTATTTCAAGCTTTTCTTACGACGC 2 93 1 TTTAAGCTTT 0.955627 -208 GAAGAGAACGTTTAATGATGCTATTCTGATCC 2 163 0 TTTATGATCT 0.862953 -138 AGAAAAGAAATAGAAAGATTTTTCAATGAAAA 2 217 0 TAGAAGATTT 0.960005 -84 *** ***** ** Masking position 5 Map Score: 5.72164 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 147 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 TAAATATCATGCAAAAAACTCTTCCGAAGAC 1 107 1 GAAAAAACTC 0.991185 -63 TGTTATTGTAGGAAACTACTCAAAGGAAGAG 2 49 1 GAAACTACTC 0.973616 -252 TATCAGCGTCGTAAGAAAAGCTTGAAATAGC 2 99 0 GAAGAAAAGC 0.960439 -202 ATTTTTCAATGAAAAAAACGCCCTCTTCTCT 2 201 0 GAAAAAACGC 0.991829 -100 AAGAAACAAGGAAAACAAATCTA 2 288 1 GAAACAAATC 0.98178 -13 * ********* Masking position 4 Map Score: 3.78917 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 32 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 TTATAATTAATCTTGTTGAAAGATTTTATG 1 18 0 TCTTGTTGAA 0.896056 -152 GATTTTATTTTGTTGTTATAATTAATCTTG 1 33 0 TGTTGTTATA 0.960469 -137 TCTATTTTTTTGTTATGAAAAGGATTTTAT 1 55 0 TGTTATGAAA 0.938582 -115 TTCCCTCGTATGATCTTAAATATCATGCAA 1 91 1 TGATCTTAAA 0.929614 -79 TAGTTTGCTTTGTTATTGTAGGAAACTACT 2 39 1 TGTTATTGTA 0.949131 -262 ATGTAATTTCTGATATTAAACAGTTGCCTA 2 131 1 TGATATTAAA 0.957454 -170 ********** Masking position 6 Map Score: 1.75191 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 113 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 AAAAAAACATAAAATCTTTCAACAAGA 1 7 1 ACATAAATCT 0.965733 -163 TATAACAACAAAATAAAATCCTTTTCATAAC 1 43 1 AAATAAATCC 0.878224 -127 CATACGAGGGAAATAAGTTCTATTTTTTTGT 1 72 0 AAATAAGTCT 0.973158 -98 TCCGAAGACTACATTAGCTATTCATTTTTAA 1 129 1 ACATTAGTAT 0.711856 -41 CAAGTTAAACACATAACGCCTTGTATAA 2 8 0 ACATAACCCT 0.977229 -293 GAAAAGCTTGAAATAGCGCCTCATCAGCATA 2 85 0 AAATAGCCCT 0.916211 -216 TTAATATCAGAAATTACATCTATCAGCGTCG 2 119 0 AAATTACTCT 0.958147 -182 ******* *** Masking position 3 Map Score: 1.81755 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 107 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: -1.32571e-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 7 ********** No masking Map Score: -1.32571e-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: -1.32571e-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