AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i194_dna_replication_ctra_reg_300.orf -o194_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 RCT00229 119 Chlamydia_trachomatis #2 RCT00313 295 Chlamydia_trachomatis #3 RCT00316 275 Chlamydia_trachomatis #4 RCT00317 96 Chlamydia_trachomatis #5 RCT00318 22 Chlamydia_trachomatis #6 RCT00319 292 Chlamydia_trachomatis Motif number 1 CCGCAAACAAAAAGAAAAAACCGAGTATAC 1 7 1 AAAAGAAAAA 0.946117 -113 ATTTAAGCAAATTCACAGAAAAAAGTAAGACAAG 2 35 1 ATAAGAAAAA 0.986144 -261 TTTATATCAAAGCAATAGAAAATAAATCATATAA 2 90 1 ACAAGAAAAA 0.985868 -206 AGACAAAGAAACTCACAGAAAACCATTTCCAACT 2 215 1 ATAAGAAAAC 0.943276 -81 TTTCCAATTACCGAAAACAAATTGCTTTG 2 277 0 ATACGAAAAA 0.972058 -19 CTCCTTCTTGAATAAGAGAAAACATTTCCTCATA 3 131 0 ATAAGAAAAA 0.986144 -145 AGAAGCCTTCAACTATACAAAATATTTAGCAACC 4 18 0 ACAACAAAAA 0.930611 -79 ATTATGAGACAGCTATAAAAAATATACTCTCTCT 6 76 1 ACAAAAAAAA 0.941025 -217 TGCGTAAACTAATCAGCAAAAAGATTAATGAAAC 6 145 1 ATACAAAAAA 0.888359 -148 * * * ****** * Masking position 9 Map Score: 8.85004 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 101 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 TTTGATATAAATCTCTTGGATATGCTAATC 2 71 0 ATCTCTTGGA 0.944173 -225 TTTATTTTCTATTGCTTTGATATAAATCTC 2 86 0 ATTGCTTTGA 0.958161 -210 GTAATACTCGATTTCTTGCAAGGAAGGCTT 2 128 0 ATTTCTTGCA 0.964117 -168 CCGAAAACAAATTGCTTTGATGGCTCAGAG 2 266 0 ATTGCTTTGA 0.958161 -30 GGGTACCGAGATTTCCTGCATGACCGG 3 8 0 ATTTCCTGCA 0.94759 -268 GAGGACTGTCATTCCGTGGAAGCTATCTTG 3 95 1 ATTCCGTGGA 0.961735 -181 GCTTAATGGGATTGCCTGAAGTATCTACTG 3 231 0 ATTGCCTGAA 0.912457 -45 ACGCTTGCCTATTCCTTGGATTAGCTAGAT 6 38 1 ATTCCTTGGA 0.98566 -255 ********** Masking position 1 Map Score: 7.30195 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 72 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 GATATGCTAATCTTCTTGTCTTACTTTTTTC 2 52 0 TCTTCTGTCT 0.929504 -244 CTTGGGCCCACCTTCTCCACTCTGAGCCATC 2 247 1 CCTTCTCACT 0.970812 -49 TTATACAGCGCCTTCTGGTTTTACAGAAGGC 3 60 1 CCTTCTGTTT 0.925187 -216 ATTGGTTTCTCCTTCTTGAATAAGAGAAAAC 3 142 0 CCTTCTGAAT 0.987717 -134 ATGAAAGAAGCCTTCAACTATACAAAATATT 4 26 0 CCTTCACTAT 0.918562 -71 GAGTAGAATATCTTCTAGAATATCCGAAATG 4 54 0 TCTTCTGAAT 0.969168 -43 TTCATAGTTTTCTTCATCAAGAATAGTATAG 6 182 1 TCTTCACAAG 0.800208 -111 TCGGGCGGTACCTTCTTGAAGAAACTTGATA 6 237 0 CCTTCTGAAG 0.978511 -56 ****** **** Masking position 4 Map Score: 5.87515 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 173 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 AGATTAGCATATCCAAGAGATTTATATCAA 2 70 1 ATCCAAGAGA 0.913258 -226 AGAGATTTATATCAAAGCAATAGAAAATAA 2 85 1 ATCAAAGCAA 0.983833 -211 TGTAAGATAGATCAAAGCGTAATACTCGAT 2 146 0 ATCAAAGCGT 0.96434 -150 ACTCTGAGCCATCAAAGCAATTTGTTTTCG 2 265 1 ATCAAAGCAA 0.983833 -31 TTCCCCAGGGATAAAAGGATGCTTAATGGG 3 251 0 ATAAAAGGAT 0.775921 -25 CATCTAGCTAATCCAAGGAATAGGCAAGCG 6 39 0 ATCCAAGGAA 0.969812 -254 ********** Masking position 5 Map Score: 2.9176 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 67 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 ATTTAGGTCTAGCACCTAGATAATCGATTATGA 1 84 0 AGCACTGTAA 0.990539 -36 AGTTGGTTTTAGCCCCTTTGTTAT 2 2 0 AGCCCTTTTA 0.920598 -294 AGGGGCTAAAACCAACTATTTAAGCAAATTCAC 2 18 1 ACCACTTTAA 0.916139 -278 TAAAACCAGAAGGCGCTGTATAACGGTGTCCAG 3 50 0 AGGCCTTTAA 0.936846 -226 AGCCTCACTTTAAATAAAATTTG 6 1 1 AGCCCATTAA 0.920598 -292 ATAATTTAACAGCATCTAGCTAATCCAAGGAAT 6 48 0 AGCACTGTAA 0.990539 -245 ACCTTCTTGAAGAAACTTGATAAGAGGTCATAA 6 226 0 AGAACTGTAA 0.966171 -67 ATCCTGGCCAAGAATCTCGGAAAAATTGTTCGG 6 264 0 AGAACTGAAA 0.836553 -29 **** ** * *** Masking position 1 Map Score: 3.46317 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 110 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 TGCAAAATAAAGGTTAGGGTATAAACCTCCCTA 1 44 0 AGGAGGTATA 0.982697 -76 TAAGACAAGAAGATTAGCATATCCAAGAGATTT 2 60 1 AGAAGATATC 0.956897 -236 CCGGTATTAGTGAGTAGAATATCTTCTAGAATA 4 63 0 TGAAGATATC 0.890438 -34 TCCAAGGAATAGGCAAGCGTATCTCAAATTTTA 6 25 0 AGGAGGTATC 0.989021 -268 AACTTCGTAAAAGAGAGAGTATATTTTTTATAG 6 88 0 AAGAGGTATA 0.928522 -205 CTCTTTTACGAAGTTAGAGTAGATTAATACAGG 6 106 1 AAGAGGTAGA 0.880326 -187 TTCTTCATCAAGAATAGTATAGCACGATTCTTT 6 191 1 AGAAGATAGC 0.926315 -102 CCGAGATTCTTGGCCAGGATATAGTC 6 277 1 TGGAGATATA 0.929119 -16 *** ** ***** Masking position 6 Map Score: 4.02746 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 92 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 7 AAAGAAAAAACCGAGTATACTGCTAGGGAGGT 1 21 1 CCGAGTACTG 0.961987 -99 AATACATGCACAGGTTATTCAGCAAATCTCAT 2 177 1 CAGGTTTCAG 0.93165 -119 CCGGTCATGCAGGAAATCTCGG 3 1 1 CCGGTTGCAG 0.974828 -275 ACAGCGCCTTCTGGTTTTACAGAAGGCGCTTG 3 64 1 CTGGTTACAG 0.968649 -212 TGTCGAACAGCTGAGTTTTCAGCTACAATTAA 3 181 1 CTGAGTTCAG 0.906067 -95 CAATTAAACCCCGATGGTTCTGTCGCAGTAGA 3 206 1 CCGATTTCTG 0.966518 -70 CCTTTTATCCCTGGGGAATCTGT 3 263 1 CTGGGATCTG 0.863388 -13 AATCGGGATACCGGTATTAGTGAGTAGAATAT 4 74 0 CCGGTTAGTG 0.916408 -23 ***** ***** Masking position 3 Map Score: 2.95801 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 94 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 CTTGCAAGGAAGGCTTATTTTTATATGATT 2 114 0 AGGCTTATTT 0.904219 -182 GGTTTTCTGTGAGTTTCTTTGTCTGTAAAC 2 209 0 GAGTTTCTTT 0.966638 -87 AGAACCATCGGGGTTTAATTGTAGCTGAAA 3 197 0 GGGTTTAATT 0.926498 -79 GTATAGTTGAAGGCTTCTTTCATTTCGGAT 4 34 1 AGGCTTCTTT 0.951215 -63 GTAAAAGAGAGAGTATATTTTTTATAGCTG 6 85 0 GAGTATATTT 0.743917 -208 AACTATGAATGGGTTTCATTAATCTTTTTG 6 161 0 GGGTTTCATT 0.96301 -132 ACCTCTTATCAAGTTTCTTCAAGAAGGTAC 6 231 1 AAGTTTCTTC 0.811908 -62 ********** Masking position 6 Map Score: 1.19868 Number of sites scoring better than the average of aligned sites = 257 Number in coding regions = 257 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 AAAAACCGAGTATACTGCTAGGGAGGTTTA 1 26 1 TATACTGCTA 0.705028 -94 CCCTAACCTTTATTTTGCATCTATCCTCAT 1 58 1 TATTTTGCAT 0.831399 -62 TAATACTCGATTTCTTGCAAGGAAGGCTTA 2 127 0 TTTCTTGCAA 0.888856 -169 CGCTTTGATCTATCTTACAAAATACATGCA 2 157 1 TATCTTACAA 0.599847 -139 ATGCACAGGTTATTCAGCAAATCTCATGTT 2 182 1 TATTCAGCAA 0.961357 -114 GGTACCGAGATTTCCTGCATGACCGG 3 7 0 TTTCCTGCAT 0.832815 -269 AACAGCTGAGTTTTCAGCTACAATTAAACC 3 186 1 TTTTCAGCTA 0.804826 -90 CTATACAAAATATTTAGCAACCGCAATCG 4 10 0 TATTTAGCAA 0.926681 -87 ATGCGTAAACTAATCAGCAAAAAGATTAAT 6 144 1 TAATCAGCAA 0.796859 -149 ********** Masking position 1 Map Score: 1.50692 Number of sites scoring better than the average of aligned sites = 383 Number in coding regions = 382 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 10 TAGGTCTAGCACCTAGATAATCGATTATGAGG 1 82 0 ACTAATAATC 0.965708 -38 TAGGTGCTAGACCTAAATAGGCTTAAAAGAC 1 99 1 ACTAATAGGC 0.95332 -21 GGCTAAAACCAACTATTTAAGCAAATTCACAG 2 21 1 ACTATTAAGC 0.947828 -275 ATTCCGTGGAAGCTATCTTGGCTATCTATGAG 3 105 1 ACTACTTGGC 0.91183 -171 ATTTAACAGCATCTAGCTAATCCAAGGAATAG 6 46 0 ACTACTAATC 0.969785 -247 AAGAGGTCATAACTAAAGAATCGTGCTATACT 6 206 0 ACTAAGAATC 0.916039 -87 * *** ****** Masking position 5 Map Score: 0.0852429 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 21 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 11 ********** No masking Map Score: -2.61947e-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 12 ********** No masking Map Score: -2.61947e-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 13 ********** No masking Map Score: -2.61947e-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