AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i013_Glycolysis___PPS_ctra_reg_300.orf -o013_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 RCT00174 300 Chlamydia_trachomatis #2 RCT00177 116 Chlamydia_trachomatis #3 RCT00178 24 Chlamydia_trachomatis #4 RCT00359 112 Chlamydia_trachomatis #5 RCT00361 28 Chlamydia_trachomatis #6 RCT00362 68 Chlamydia_trachomatis #7 RCT00363 300 Chlamydia_trachomatis Motif number 1 CTAGATATTTACAAGCCTTCTCATAGGCTCTC 1 46 1 AAAGCTTCTC 0.908103 -255 AAGCCTTCTCATAGGCTCTCTTCGTTCCTATA 1 58 1 AAGGTCTCTT 0.871864 -243 TCGTTCCTATATTCGACACCTCCCGCGTTTCA 1 79 1 ATCGCACCTC 0.684376 -222 TCACAGAGCTACTAGCTTTCTTAACTTATTGG 1 138 0 ATAGTTTCTT 0.924598 -163 GGTTCTGTGTACTAGATCCCTAGTCATATGAA 1 210 1 ATAGTCCCTA 0.918797 -91 CTTCTTATACAGTAGGCCCTTACCAAACATAT 1 241 0 ATAGCCCTTA 0.630263 -60 TATGTGCCTAAAAAGATTTCTCTCTCATAAAA 2 33 0 AAAGTTTCTC 0.909657 -84 TTAGGCACATATTCGTTTTTTTGGTATTGTGG 2 54 1 ATCGTTTTTT 0.726959 -63 GTATACAACCTCTTGCAAAACAAA 3 11 0 AACACCTCTT 0.68047 -14 TTTGTAGAACAATCGATCTTTTCATCTA 4 7 0 ATCGTCTTTT 0.853819 -106 GTAAAAAGAAAGAAGGTCTCTCGTATCACATT 4 74 1 AAAGTCTCTC 0.959897 -39 AAGGCCCCTTAATCGTTTTCTAAAA 5 4 0 ATCGTTTCTA 0.89978 -25 AATAAGGCCCCTTAATCGTTTTC 5 16 0 AAAGCCCCTT 0.954605 -13 TCTTCCTTTGAGTAGTTTCCTACAATAACAAA 7 47 0 ATAGTTCCTA 0.82644 -254 TAGCATCATTAAACGTTCTCTTCTCTTCAAGA 7 172 1 AACGTCTCTT 0.976132 -129 TCAATGAAAAAAACGCCCTCTTCTCTTGAAGA 7 195 0 AACGCCTCTT 0.975649 -106 * *** ****** Masking position 11 Map Score: 14.0482 Number of sites scoring better than the average of aligned sites = 627 Number in coding regions = 627 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 TGATGTTATTTACTATTTTTC 1 1 0 TACTTTTTTC 0.967743 -300 TAATGTATTTGATTATTTTTCACGAATGAAA 1 106 0 GATTTTTTTC 0.94315 -195 TTCACAGAGCTACTAGCTTTCTTAACTTATT 1 140 0 TACTGCTTTC 0.96491 -161 TTTAGGCACATATTCGTTTTTTTGGTATTGT 2 53 1 TATTGTTTTT 0.746271 -64 TTTTTACTTGTACTATCTTTCGTGATCTTTC 4 50 0 TACTTCTTTC 0.955279 -63 TGATACGAGAGACCTTCTTTCTTTTTACTTG 4 71 0 GACCTCTTTC 0.760299 -42 TAAGGCCCCTTAATCGTTTTCTAAAA 5 6 0 TAATGTTTTC 0.880969 -23 ATTCTTATTTTTTTTAAGAATCATGT 6 6 1 TATTTTTTTA 0.695544 -63 AAAATCTTTCTATTTCTTTTCTCTTCCCTGT 7 227 1 TATTCTTTTC 0.894966 -74 TAGATTTGTTTTCCTTGTTTCTT 7 288 0 GATTGTTTTC 0.955278 -13 **** ****** Masking position 8 Map Score: 7.18493 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 123 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 ACCCGACCATCCTAACAAGGAGATCGTTAACAA 1 180 0 CCTAAAGGAA 0.992349 -121 TGACGTCCCACCTAAGAAGCAAAACTTCTTATA 1 264 0 CCTAAAGCAA 0.994735 -37 TATCACATTTCCTCAAAAGGAGAATC 4 97 1 CCTAAAGGAA 0.992346 -16 TGAAATAGCGCCTCATCAGCATATTCAGCTCTT 7 75 0 CCTACAGCAA 0.99511 -226 TCTCTTAACTCATGAACAGCAAATCATACACAC 7 256 0 CATACAGCAA 0.975052 -45 *** * ***** * Masking position 8 Map Score: 5.03448 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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 TATGATTTATGATGTTATTTACTATTTTTC 1 11 0 GATGTTATTT 0.96453 -290 TTATACAAGGCGTTATGTGTTTAACTTG 7 9 1 GGCGTTATGT 0.960914 -292 ATGCTGATGAGGCGCTATTTCAAGCTTTTC 7 86 1 GGCGCTATTT 0.982376 -215 GACGCTGATAGATGTAATTTCTGATATTAA 7 120 1 GATGTAATTT 0.870274 -181 AACGTTTAATGATGCTATTCTGATCCGTTA 7 159 0 GATGCTATTC 0.891811 -142 AAGAGAAGAGGGCGTTTTTTTCATTGAAAA 7 200 1 GGCGTTTTTT 0.943141 -101 ********** Masking position 8 Map Score: 1.59133 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 45 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 AGTAAATAACATCATAAATCATACACTTCTAG 1 18 1 ATCTAAACAT 0.967051 -283 TAACAAGGAGATCGTTAACAATCAAGATTATT 1 169 0 ATCTTAAAAT 0.807975 -132 AGATTTCTCTCTCATAAAACATGGCTTTGCCA 2 20 0 CTCTAAACAT 0.987755 -97 TGTGGGCTCTCTCTTAAAAAATTAACACTCTA 2 81 1 CTCTAAAAAT 0.948871 -36 AAGAAGGTCTCTCGTATCACATTTCCTCAAAA 4 83 1 CTCTATCCAT 0.891876 -30 AATAAGGCCCCTTAATCGTTTTCTAAAA 5 10 0 CCCTTAACGT 0.883937 -19 TCAGAATAGCATCATTAAACGTTCTCTTCTCT 7 166 1 ATCTTAACGT 0.914727 -135 CTTGTTTCTTCTCTTAACTCATGAACAGCAAA 7 266 0 CTCTAACCAT 0.978734 -35 *** **** *** Masking position 5 Map Score: 4.25821 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 72 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 TAACATCATAAATCATACACTTCTAGATAT 1 24 1 AATCATACAC 0.981315 -277 ATTTTTCACGAATGAAACGCGGGAGGTGTC 1 93 0 AATGAAACGC 0.92672 -208 CGTGAAAAATAATCAAATACATTATCCAAT 1 113 1 AATCAAATAC 0.935151 -188 GCAAACTACAAGTTAAACACATAACGCCTT 7 17 0 AGTTAAACAC 0.895097 -284 ATGAACAGCAAATCATACACACAGGGAAGA 7 248 0 AATCATACAC 0.981315 -53 ********** Masking position 5 Map Score: 0.783144 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 18 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: -1.16996e-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: -1.16996e-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 9 ********** No masking Map Score: -1.16996e-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