AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i335_2_7_7_40_ctra_reg_300.orf -o335_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 RCT00415 300 Chlamydia_trachomatis #2 RCT00441 300 Chlamydia_trachomatis #3 RCT00442 69 Chlamydia_trachomatis Motif number 1 CAAACAGATATTTCACACTCCTCCTTCCAAAATTC 1 142 1 TTTCTCTCCT 0.992626 -159 ATAGAAAGATTGTTATCAACATCCTGTCGGTTCTT 1 189 0 TGTAACTCCT 0.887572 -112 AGGTAAGATCTCTTCACAACTTCTTGAAGAGATCT 1 236 0 TCTAACTCTT 0.838728 -65 AAATATCCAACTTTAAACTCTTCTTTTTCAAAGAG 2 12 1 CTTCTCTCTT 0.992626 -289 CTAATTCGCTTTTACCTCTCTTCTTGCTGAAGACT 2 171 1 TTTCTCTCTT 0.99391 -130 ATAAGAAAAGTTTAGGGCTCTTCCTTCGCAACTCT 2 251 0 TTTCTCTCCT 0.992626 -50 AGCCCTAAACTTTTCTTATCATCTTCTTTAACTAG 2 267 1 TTTATCTCTT 0.981647 -34 AATTGACTCACGTGTTCCTCGTCTTTAAGATGAGG 3 17 1 CGTCTCTCTT 0.987051 -53 AAAGAATGAACTAGTTCCTCATCTTAAAGACGAGG 3 33 0 CTACTCTCTT 0.954996 -37 *** *** **** Masking position 12 Map Score: 11.2355 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 98 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 TATTATTCTCACTAGCCCTTCTATCGTTCGT 1 37 1 ACTAGCCTTC 0.96635 -264 CAACTTCTTGAAGAGATCTTCATTAAAATAA 1 224 0 AAGAGTCTTC 0.988673 -77 TAAAAGAGGTAAGATCTCTTCACAACTTCTT 1 246 0 AAGATTCTTC 0.952301 -55 TGGCAAGGAAAATAGCTCTTTGAAAAAGAAG 2 31 0 AATAGTCTTT 0.825158 -270 GCTCATGGTAACATGATCTTCTCTTAGGGAT 2 102 1 ACATGTCTTC 0.939994 -199 GAATTAGAAAACGATTTATTCCTCGGACTAT 2 147 0 ACGATTATTC 0.850826 -154 AAATTGACTCACGTGTTCCTCGTCTTTAAGA 3 16 1 ACGTGTCCTC 0.978854 -54 AAAAGAATGAACTAGTTCCTCATCTTAAAGA 3 38 0 ACTAGTCCTC 0.983929 -32 ***** ***** Masking position 1 Map Score: 5.67951 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 228 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 ACTATTTCCCTGCCTCCCTGATAAAGAACACTGGTG 1 79 1 TGCCCCTGAG 0.959712 -222 AGGAATTATATGCCCTCTAAAAGAGGTAAGATCTCT 1 258 0 TGCCCTAAAG 0.988162 -43 ACAGTGGCGGTGACAGCTAAAACACGCTCATGGTAA 2 77 1 TGACCTAAAG 0.992003 -224 CGCAAGAAATTGATCCCTAAGAGAAGATCATGTTAC 2 109 0 TGATCTAAAG 0.976698 -192 CTCTTCTTGCTGAAGACTTGGCTATGTTTTTTATTT 2 188 1 TGAACTTGAG 0.956609 -113 CGCAACTCTTTTATGCCTTAACTAGGTTTATCGTCA 2 224 0 TTATCTTAAG 0.806788 -77 GGATGACTCCTAGTTAAAGAAGATGATAA 2 282 0 TGACCTAGAG 0.993351 -19 **** **** * * Masking position 14 Map Score: 2.40137 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 19 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 GTAAGTACCTTTCTTCCCCATAAAACTAT 1 10 1 TTTCTTCCCC 0.943001 -291 CTATGCACAACTATTTCCCTGCCTCCCTGA 1 70 1 CTATTTCCCT 0.802172 -231 TCCAAAATTCTTTTTTCAACTAAAGAACCG 1 167 1 TTTTTTCAAC 0.726125 -134 TCCTTGCCAGTTATTTCCACTATTACAGTG 2 53 1 TTATTTCCAC 0.936709 -248 TAGAAAACGATTTATTCCTCGGACTATTAC 2 144 0 TTTATTCCTC 0.930864 -157 TTCTAATTCGCTTTTACCTCTCTTCTTGCT 2 169 1 CTTTTACCTC 0.926427 -132 AATTGACTCACGTGTTCCTCGTCTTTAAGA 3 17 1 CGTGTTCCTC 0.939291 -53 AAAGAATGAACTAGTTCCTCATCTTAAAGA 3 38 0 CTAGTTCCTC 0.973199 -32 ********** Masking position 5 Map Score: 1.86761 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 357 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 GCAGGGAAATAGTTGTGCATAGGCACGAAC 1 62 0 AGTTGTGCAT 0.976267 -239 TCTAGGAGAGATTAGTGCAGCAGAATTCAA 1 115 1 ATTAGTGCAG 0.942135 -186 CTCTTCAAGAAGTTGTGAAGAGATCTTACC 1 240 1 AGTTGTGAAG 0.990622 -61 GGCATAAAAGAGTTGCGAAGGAAGAGCCCT 2 243 1 AGTTGCGAAG 0.984039 -58 ********** Masking position 3 Map Score: 1.26526 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 28 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: 4.35863e-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: 4.35863e-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: 4.35863e-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