AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_synecho_ctra_300.orf -o259_synecho_ctra_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCT00059 217 Chlamydia_trachomatis #2 RCT00060 179 Chlamydia_trachomatis #3 RCT00530 300 Chlamydia_trachomatis #4 RCT00532 181 Chlamydia_trachomatis #5 RCT00534 275 Chlamydia_trachomatis #6 RCT00633 300 Chlamydia_trachomatis #7 RCT00635 43 Chlamydia_trachomatis #8 RCT00636 296 Chlamydia_trachomatis #9 RCT00637 19 Chlamydia_trachomatis Motif number 1 ACTCCAGAAGGAAAAAGAAAAGATTAGTTA 1 14 1 GAAAAAGAAA 0.937868 -204 TATATACTAGACAAGAGAAAGATACTGTAA 1 162 1 ACAAGAGAAA 0.908189 -56 TTTTTAGTTTGTAAAAGAAATTTTTTTTGT 2 90 1 GTAAAAGAAA 0.867842 -90 GTGAGTCTTCACAAAAAAAATTTCTTTTAC 2 100 0 ACAAAAAAAA 0.892362 -80 ATATTGGTCGACAAAAGAAATCCATCATAG 2 153 1 ACAAAAGAAA 0.95393 -27 TGGTAGCAGGAGAGAAAAAATAGGAACGTA 3 109 0 AGAGAAAAAA 0.754522 -192 TTCTAGGAAAGGAAAAGAGAGGTCCTTCAG 3 195 0 GGAAAAGAGA 0.809795 -106 GAAAGGCTTGGAAGGAGAATCCTCTTCCCT 3 222 1 GAAGGAGAAT 0.58015 -79 AGCATTCTCTGCAGAAAAAATGTTCCCGAT 4 33 1 GCAGAAAAAA 0.894678 -149 CACAAGCCGAGCAGAAGAAAAGAGCCAAAA 4 151 0 GCAGAAGAAA 0.954988 -31 TCCCATATATACAAAAAAAAGAAGCACCAA 5 41 1 ACAAAAAAAA 0.892362 -235 CATAGCCATCGGAGAAAAAATCTACAATGC 5 74 0 GGAGAAAAAA 0.831942 -202 ATCTCTGTGTAAAAAAGAATGCGATCCTTG 5 141 1 AAAAAAGAAT 0.738417 -135 AAAGAATTTTAGAAAAAAATCGGGCACGAA 6 58 0 AGAAAAAAAT 0.592688 -243 AATTTAAAGTACAAAAGAATTTTAGAAAAA 6 71 0 ACAAAAGAAT 0.86181 -230 TGAAAGGGATGAAAGAGAAAACAGAAAAGG 6 100 1 GAAAGAGAAA 0.878216 -201 ACCTACTTTAAAAAGAAAAACGATTTCTCA 6 144 0 AAAAGAAAAA 0.641928 -157 TGTAAACGGTAAAAGAGAGGGTATCTAT 8 9 1 GTAAAAGAGA 0.589931 -288 ********** Masking position 6 Map Score: 15.3594 Number of sites scoring better than the average of aligned sites = 856 Number in coding regions = 682 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 2 GCAGCCTGGTTAGCGCGGTTGCTTTGGGAG 1 82 0 TAGCGCGGTT 0.934177 -136 GTATCTGCGAGATCGTGAGTCTTCACAAAA 2 114 0 GATCGTGAGT 0.907962 -66 TCTGCTTGCTTATCGTGGGTACCGCTCTCT 3 54 1 TATCGTGGGT 0.907972 -247 GACAAATACATTTCCCGGGTTGTACATCTG 3 166 0 TTTCCCGGGT 0.869776 -135 CAGAAAAAATGTTCCCGATTGGCACTAATC 4 44 1 GTTCCCGATT 0.832676 -138 GTGAAAAGGTGTGCGTGGGTTATGTTTCGT 4 93 1 GTGCGTGGGT 0.969085 -89 AAACGAGAGCGATCGAGGGTCAGGAAAACC 5 108 1 GATCGAGGGT 0.981083 -168 TTTACACAGAGATCGAGGTTTTCCTGACCC 5 124 0 GATCGAGGTT 0.974768 -152 ACGAGCAAAGGAGCGAGGTTCCCTGCCTGT 5 221 1 GAGCGAGGTT 0.973076 -55 CGAGTCGTTCGTGCCCGATTTTTTTCTAAA 6 51 1 GTGCCCGATT 0.823149 -250 GCAGTTCGAGGTTTATTTAATTC 7 4 1 GTTCGAGGTT 0.970169 -40 ********** Masking position 10 Map Score: 11.3435 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 306 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 CTAATCTTTTCTTTTTCCTTCTGGAGTCCT 1 11 0 CTTTTTCCTT 0.692465 -207 GTGGGTACCGCTCTCTCCCTGAGCATTCGA 3 68 1 CTCTCTCCCT 0.974086 -233 TGAAGGACCTCTCTTTTCCTTTCCTAGAAA 3 196 1 CTCTTTTCCT 0.86893 -105 TATACTCTTTCTCGATCCTTATTTTTCATT 4 123 1 CTCGATCCTT 0.976604 -59 TTCATTTTGGCTCTTTTCTTCTGCTCGGCT 4 147 1 CTCTTTTCTT 0.831652 -35 TTTCCTGACCCTCGATCGCTCTCGTTTTTA 5 105 0 CTCGATCGCT 0.890577 -171 TCAGGAAAACCTCGATCTCTGTGTAAAAAA 5 127 1 CTCGATCTCT 0.906398 -149 CGCTCCTTTGCTCGTTACTTTATTCCCAAC 5 206 0 CTCGTTACTT 0.867807 -70 GGCAGGGAACCTCGCTCCTTTGCTCGTTAC 5 218 0 CTCGCTCCTT 0.984993 -58 GCACGAACGACTCGTTCTTTTGATTTCTAA 6 35 0 CTCGTTCTTT 0.920483 -266 GTCCGAAATACTCCCTCCCTAGCTATTGGA 6 210 0 CTCCCTCCCT 0.944238 -91 ********** Masking position 6 Map Score: 11.7519 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 188 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 GGTTCGAATCCCTCTACTCCGATTCTTAACTAATC 1 35 0 CCTCTCCATC 0.973201 -183 ACCAGGCTGCGCTATACTCCGATTTAAAAAAGTAG 1 102 1 GCTCTCCATT 0.947954 -116 ATGCTAACTTCCTTAGCTCCTACTTTTTTAAATCG 1 121 0 CCACTCCATT 0.990373 -97 CACAACTAACACATAACTCCTAATCAATAACTCTT 2 11 0 ACACTCCATC 0.965762 -169 TCTCCTGCTACCACTTCTCCTCATTGAGATTTTAT 3 126 1 CCTCTCCCTT 0.973201 -175 CCCGATTGGCACTAATCTCCCCATTTGCTATGGTG 4 57 1 ACACTCCCTT 0.965762 -125 TATTTCGGACCCAGAGCTCTCAGTTAGAGATGAGC 6 230 1 CCACTCTATT 0.959236 -71 GACCCATCTCTTATTTTATTAACTTC 8 281 0 ACACTCTATT 0.919311 -16 ** * **** * ** Masking position 8 Map Score: 5.12545 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 97 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 AGACAAGAGAAAGATACTGTAAATGCAAAA 1 170 1 AAGATACTGT 0.856153 -48 TGTGTAAGGGTAGATATTGTTTAAAAATTT 2 42 1 TAGATATTGT 0.968123 -138 CTTTTTAAAGTAGGTATTGGCATAACTCAG 6 159 1 TAGGTATTGG 0.955586 -142 ACTCCCTCCCTAGCTATTGGAATGGGCCCC 6 201 0 TAGCTATTGG 0.955586 -100 CTAATTCTGTTAGATATTGTTGTACTCCCT 8 104 0 TAGATATTGT 0.968123 -193 CACCGCAGTCAAGATATTGGATACAGACTC 8 214 0 AAGATATTGG 0.962399 -83 ********** Masking position 5 Map Score: 3.76172 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 56 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 6 TCGAACTTCTTCTTGCAGATAT 1 206 1 TCTTCAGATA 0.98296 -12 AGACTCACGATCTCGCAGATACTTGGCAGCT 2 122 1 TCTCCAGATA 0.983862 -58 AAAAGAGAGGTCCTTCAGACAAATACATTTC 3 182 0 TCCTCAGACA 0.965509 -119 AGAATCCTCTTCCCTCAGATAATCATCTCAT 3 237 1 TCCCCAGATA 0.982701 -64 TTTATTTAATTCTTCCAGGTAGGAATAAATC 7 22 1 TCTTCAGGTA 0.962958 -22 **** ****** Masking position 7 Map Score: 1.47522 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 21 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 7 ATTGCAACGATCCATATGAGATGATTATCTGAGGGAA 3 246 0 TCCAGAATGA 0.769954 -55 CACTAATCTCCCCATTTGCTATGGTGAGTGAAAAGGT 4 66 1 CCCTGCATGA 0.99272 -116 AAAAGAAGCACCAAATAGCATTGTAGATTTTTTCTCC 5 57 1 CCATGCTTGA 0.925504 -219 AGATTTTTTCTCCGATGGCTATGTTAAAAACGAGAGC 5 81 1 TCCTGCATGA 0.986244 -195 AAATGACATGCCTCATCGCGTTGGGAATAAAGTAACG 5 187 1 CCTTGCTTGA 0.946813 -89 AGGTTCCCTGCCTGTTGGCTTTGCCAAAGGATCCCTA 5 236 1 CCTTGCTTGA 0.946813 -40 GAAAAGGCTCCTCTATCGAGATGAGAAATCGTTTTTC 6 123 1 CTCTGAATGA 0.885302 -178 GAAATACTCCCTCCCTAGCTATTGGAATGGGCCCCGC 6 199 0 CTCTGCATTA 0.784098 -102 CCCAGAGCTCTCAGTTAGAGATGAGCACGTGAATACA 6 239 1 TCATGAATGA 0.857651 -62 CCGAACAACTTCCGCTCGCCATAGATACCCTCTCTTT 8 22 0 TCCTGCATAA 0.875447 -275 CCATCCAGCATCTGGTTGAAATTAAAAGCCGAACAAC 8 50 0 TCTTGAATTA 0.598784 -247 *** * ** *** * Masking position 17 Map Score: 2.4691 Number of sites scoring better than the average of aligned sites = 836 Number in coding regions = 760 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 8 ATAGGTCGGGGGTTCGAATCCCTCTACTCCGATT 1 46 0 GGCGAACCTC 0.988029 -172 TTGTACATCTGGGTGGATAAAATCTCAATGAGGA 3 143 0 GGGGATAATC 0.956866 -158 CATCTCATATGGATCGTTGCAATCCTAAACACTC 3 260 1 GGCGTTAATC 0.929694 -41 CGTGGGTTATGTTTCGTTATACTCTTTCTCGATC 4 106 1 GTCGTTACTC 0.88563 -76 GCGATCGAGGGTCAGGAAAACCTCGATCTCTGTG 5 116 1 GTGGAACCTC 0.921975 -160 AAAAAAATCGGGCACGAACGACTCGTTCTTTTGA 6 42 0 GGCGAAACTC 0.993239 -259 GAGAGCTCTGGGTCCGAAATACTCCCTCCCTAGC 6 217 0 GGCGAAACTC 0.993307 -84 AATTCTTCCAGGTAGGAATAAATCT 7 29 1 GGGGAAAATC 0.972723 -15 ** **** **** Masking position 13 Map Score: 5.74646 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 75 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 GATGTACAACCCGGGAAATGTATTTGTCTG 3 168 1 CCGGGAAATG 0.729904 -133 CCAAGCCTTTCTAGGAAAGGAAAAGAGAGG 3 203 0 CTAGGAAAGG 0.955167 -98 CACTCATTGAAGAGGAAATGTT 3 289 1 AGAGGAAATG 0.646873 -12 CTAGGGATAGCCAGACAAGGATCGCATTCT 5 156 0 CCAGACAAGG 0.940391 -120 AATAAAGTAACGAGCAAAGGAGCGAGGTTC 5 212 1 CGAGCAAAGG 0.874604 -64 GGCAAAGCCAACAGGCAGGGAACCTCGCTC 5 231 0 ACAGGCAGGG 0.954852 -45 CCTTCTGACGAGGTAGGGATCCTTTGGC 5 258 0 CGAGGTAGGG 0.951289 -18 GAAAGAGAAAACAGAAAAGGCTCCTCTATC 6 110 1 ACAGAAAAGG 0.799543 -191 ATTCCAATAGCTAGGGAGGGAGTATTTCGG 6 208 1 CTAGGGAGGG 0.879303 -93 TTTAATTCTTCCAGGTAGGAATAAATCT 7 26 1 CCAGGTAGGA 0.749115 -18 TTAGAAACATCCACGCAAGGAACTGTAGAC 8 130 1 CCACGCAAGG 0.914197 -167 ********** Masking position 7 Map Score: 2.2514 Number of sites scoring better than the average of aligned sites = 1754 Number in coding regions = 1595 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 10 AACATCCCTATGATGGATTTCT 2 168 0 CATCCCTATG 0.886039 -12 AGATTTTATCCACCCAGATGTACAACCCGG 3 152 1 CACCCAGATG 0.964981 -149 GGATTGCAACGATCCATATGAGATGATTAT 3 255 0 GATCCATATG 0.865575 -46 ACTTTATTCCCAACGCGATGAGGCATGTCA 5 190 0 CAACGCGATG 0.606295 -86 AAGGCTCCTCTATCGAGATGAGAAATCGTT 6 126 1 TATCGAGATG 0.812772 -175 CTTTTAATTTCAACCAGATGCTGGATGGCG 8 59 1 CAACCAGATG 0.968804 -238 ********** Masking position 8 Map Score: 0.334855 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 120 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 CCCAAAGCAACCGCGCTAACCAGGCTGCGCT 1 84 1 CCCGCTAACC 0.983678 -134 AGAGCGGTACCCACGATAAGCAAGCAGAATC 3 51 0 CCCGATAAGC 0.930761 -250 ATCGTGGGTACCGCTCTCTCCCTGAGCATTC 3 65 1 CCCTCTCTCC 0.949866 -236 GAAACATAACCCACGCACACCTTTTCACTCA 4 90 0 CCCGCACACC 0.987787 -92 TTTTCCTGACCCTCGATCGCTCTCGTTTTTA 5 105 0 CCCGATCGCT 0.934859 -171 GTCAGGAAAACCTCGATCTCTGTGTAAAAAA 5 126 1 CCCGATCTCT 0.960732 -150 TTGGAATGGGCCCCGCTGACCTTATGCTGAG 6 184 0 CCCGCTGACC 0.980641 -117 ATTAAATAAACCTCGAACTGC 7 1 0 CCCGAACTGC 0.932679 -43 ** ******** Masking position 4 Map Score: 5.16154 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 489 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 ********** No masking Map Score: 1.41641e-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: 1.41641e-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 14 ********** No masking Map Score: 1.41641e-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