AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_soj_ctra_reg_300.orf -o254_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 RCT00472 300 Chlamydia_trachomatis #2 RCT00473 293 Chlamydia_trachomatis #3 RCT00554 300 Chlamydia_trachomatis #4 RCT00653 300 Chlamydia_trachomatis #5 RCT00657 135 Chlamydia_trachomatis Motif number 1 CACGAGAGTTTTTTTTTTGAAAAGCATAAGA 1 110 1 TTTTTTTTAA 0.872749 -191 AGAAAACGATATTTTTCTTCCCCTCCCCTTT 1 200 1 ATTTTTCTCC 0.894391 -101 ATGGCTGTCAATTTTTGGGAATAAACTTGT 2 10 0 ATTTTTGGAA 0.478185 -284 CCTCATAGGTTTTCTTCTCAAAGTGTATCGC 2 74 0 TTTCTTCTAA 0.867253 -220 ATTAGCTGAGTCTTTTCAAAAGACTTACCAA 2 132 1 TCTTTTCAAA 0.783711 -162 ATGACATGGTTTTCTTCTTAATGGTTTACGC 2 172 0 TTTCTTCTAA 0.867253 -122 TAAGTCTTCGTTTTTTCTTAACAGATGACAT 2 196 0 TTTTTTCTAA 0.969371 -98 CTCTTCGACGTCTTTTTTTACGCTTATGCTT 2 235 0 TCTTTTTTAC 0.860114 -59 TAACTATACGATTTTTCTTCCCATGGTAGTT 3 46 1 ATTTTTCTCC 0.894391 -255 TAGGGATAAGTCTTTTGTAAACGGAACAGGA 3 87 0 TCTTTTGTAA 0.862723 -214 CTAAAAATAGACTTTTCTACCGGAGGGATAC 3 115 1 ACTTTTCTCC 0.86534 -186 TCCAGATACCTCTTTTCTATATTATTGGGTA 3 148 0 TCTTTTCTTA 0.687349 -153 AAAAAATGGAATTTTTCTACAACACAAACAA 4 35 0 ATTTTTCTCA 0.877571 -266 GAAAAATTCCATTTTTTTTACGATTCGTAGC 4 49 1 ATTTTTTTAC 0.793456 -252 GCCAACAAGTTTTTTTCTTAAGGGCTGTTTG 4 78 1 TTTTTTCTAA 0.969371 -223 CTGTCTTTCTTTTTTTTTCAAGAAGGTGTTC 4 155 1 TTTTTTTTAA 0.872749 -146 TTCGAGATATTTTTTTCGAACACCTTCTTGA 4 172 0 TTTTTTCGAC 0.897195 -129 TTGTTTTGCCTTTTTTGAGACAGAGGAGATA 4 217 1 TTTTTTGAAC 0.596196 -84 GATAATAGGCTCTTTTCTCACGAGCTCCACT 4 244 1 TCTTTTCTAC 0.965956 -57 ******** ** Masking position 6 Map Score: 20.5634 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 640 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 TTTTCTTCCCCTCCCCTTTCCTCTTGAGGA 1 212 1 CTCCCCTTTC 0.974927 -89 TGAGGATATATTCCCCTATACCCTAACCTG 1 236 1 TTCCCCTATA 0.872687 -65 CCGAGAGAGCTTCCTTTACCAACCATAAAA 1 267 1 TTCCTTTACC 0.842511 -34 CATAAAAATAATCCTCTAACT 1 290 1 ATCCTCTAAC 0.86789 -11 CTTTATTCATCTCCTTTAACCTCATTCGTC 3 190 1 CTCCTTTAAC 0.913439 -111 GTTGCTTTAATTCCTTTATATTGATTTGTC 3 230 0 TTCCTTTATA 0.800835 -71 GGAAGCCTCGCTCCTTTTTAGTTGCTTTAA 3 250 0 CTCCTTTTTA 0.893391 -51 GCGAGGCTTCCTCCCCTACAAGGGCTTCAC 3 269 1 CTCCCCTACA 0.9109 -32 AGGGAGAGACATCCTCTTTCCCTAGGCTGT 4 129 1 ATCCTCTTTC 0.93421 -172 AGCCTATTATCTCCTCTGTCTCAAAAAAGG 4 225 0 CTCCTCTGTC 0.965478 -76 GATCCTCCTCTTTCATCAGGATGC 4 287 0 CTCCTCTTTC 0.984148 -14 ********** Masking position 7 Map Score: 10.705 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 297 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 AAATTTACACGAGAGTTTTTTTTTTGAAAAGC 1 103 1 GAGAGTTTTT 0.803351 -198 GGGGTTTTTAGACAGTCAACTTCTTTTTTAGG 1 157 0 GACAGCACTT 0.947347 -144 ACCTGGCCGAGAGAGCTTCCTTTACCAACCAT 1 261 1 GAGAGTTCTT 0.973392 -40 GAGGTATCTGGAGAGCTTTCTTACTTTATTCA 3 167 1 GAGAGTTCTT 0.973387 -134 CTAAAAAGGAGCGAGGCTTCCTCCCCTACAAG 3 259 1 GCGAGCTCCT 0.975265 -42 TGGGTCTAGGGAGAGACATCCTCTTTCCCTAG 4 122 1 GAGAGCACCT 0.993306 -179 GAAAAAAAAAGAAAGACAGCCTAGGGAAAGAG 4 142 0 GAAAGCACCT 0.95063 -159 ACTCCAAATAGAGTGGCATCCTGATGAAAGAG 4 272 1 GAGTGCACCT 0.963766 -29 ***** ** *** Masking position 12 Map Score: 6.29646 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 76 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 ACTCAGTCATCTTTCCAACGAAACAACCGG 1 52 1 CTTTCCAACG 0.919677 -249 CGATATTTTTCTTCCCCTCCCCTTTCCTCT 1 206 1 CTTCCCCTCC 0.971973 -95 TTGTAAACTTCTTCCCATCGCCTGGTGAAA 2 40 1 CTTCCCATCG 0.990239 -254 TACGATTTTTCTTCCCATGGTAGTTGCTAC 3 52 1 CTTCCCATGG 0.98149 -249 CCTACAAGGGCTTCACCTCGTGATAAAC 3 283 1 CTTCACCTCG 0.959014 -18 TTTGACAGTCCTTTCCTTGGGTCTAGGGAG 4 105 1 CTTTCCTTGG 0.929731 -196 AAGAGGATGTCTCTCCCTAGACCCAAGGAA 4 117 0 CTCTCCCTAG 0.922214 -184 GAGACATCCTCTTTCCCTAGGCTGTCTTTC 4 134 1 CTTTCCCTAG 0.978081 -167 ********** Masking position 2 Map Score: 9.17074 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 66 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 AATTTATCCCTTCGGAGCTTTTTGGGCCGGT 1 77 0 TTCGAGCTTT 0.680841 -224 CTGTCTAAAAACCCCGTCTCTAACCAAGAAA 1 174 1 ACCCGTCTCT 0.744491 -127 TCAAAGTGTATCGCCGGCTTTCACCAGGCGA 2 57 0 TCGCGGCTTT 0.946992 -237 CGCTTATGCTTGGCGATCTTAAGTCTTCGTT 2 215 0 TGGGATCTTA 0.610499 -79 GCCGATCTCTTCGACGTCTTTTTTTACGCTT 2 241 0 TCGCGTCTTT 0.955979 -53 TCTATTTTTATGCCGATCTCTTCGACGTCTT 2 252 0 TGCGATCTCT 0.940032 -42 ACAGGCAGGTCCAGGGCTCTAAAATCTCAT 3 10 1 TCCGGGCTCT 0.953907 -291 AAGAGGTATCTGGAGAGCTTTCTTACTTTAT 3 165 1 TGGGAGCTTT 0.917576 -136 GAACTGCAATTCGAGATATTTTTTTCGAACA 4 181 0 TCGGATATTT 0.624928 -120 GATCCTCCTCTTTCATCAGGATG 4 288 0 TCCCCTCTTT 0.860484 -13 AGATGCCCACTCCGCATCTCTCTTGACAACA 5 19 0 TCCCATCTCT 0.964157 -117 AGATGCGGAGTGGGCATCTCTTGATTTGCAT 5 31 1 TGGCATCTCT 0.940032 -105 *** ******* Masking position 9 Map Score: 6.01925 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 238 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 6 ATCTGTTAAGAAAAAACGAAGACTTAAGATCGCC 2 201 1 AAACGAAACT 0.820799 -93 AGAACCCAAACAATTTAACTATCT 2 280 0 AAACAAAAAT 0.9686 -14 TATAAAGGAATTAAAGCAACTAAAAAGGAGCGAG 3 240 1 TAACAACAAA 0.651119 -61 CAAACAAATAAAAAATCAAAAAATCGCTAGA 4 8 0 AAACAAAAAT 0.9686 -293 GAATTTTTCTACAACACAAACAAATAAAAAATCA 4 24 0 AAACAAAAAA 0.9686 -277 CTTCTTGAAAAAAAAAGAAAGACAGCCTAGGGAA 4 146 0 AAAGAAAACA 0.739852 -155 TCTGTCTCAAAAAAGGCAAAACAAATCCTGAACT 4 207 0 AAACAAACAA 0.929892 -94 ACAAAATCTTATAATGCAAATCAAGAGATGCCCA 5 41 0 AAACAAACAA 0.929891 -95 GACCGTCCCCAGAATACAAAAACTCAAGATACAA 5 71 0 AAACAAAACT 0.956452 -65 GACGGTCTGTAGAATACAACGAATTGGGCTGAGA 5 98 1 AAACAACAAT 0.929891 -38 * ** **** *** Masking position 9 Map Score: 5.68586 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 7 TTTTTGAAAAGCATAAGAGTCAGAATCCTT 1 123 1 GCATAAGAGT 0.966469 -178 CCTTTACCAACCATAAAAATAATCCTCTAA 1 279 1 CCATAAAAAT 0.956729 -22 AGATCGCCAAGCATAAGCGTAAAAAAAGAC 2 227 1 GCATAAGCGT 0.959832 -67 GAAGAGATCGGCATAAAAATAGATAGTTAA 2 260 1 GCATAAAAAT 0.956729 -34 AAAGACTTATCCCTAAAAATAGACTTTTCT 3 103 1 CCCTAAAAAT 0.889922 -198 ATTGATTTGTCCATAAGCATGGACGAATGA 3 211 0 CCATAAGCAT 0.966469 -90 ********** Masking position 5 Map Score: 2.84815 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 46 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 TCTTTTTTAGGAAGCAAGGATTCTGACTCT 1 138 0 GAAGCAAGGA 0.972797 -163 ACCCCGTCTCTAACCAAGAAAACGATATTT 1 184 1 TAACCAAGAA 0.935795 -117 CTTAATGGTTTACGCAAGGAATAATTGGTA 2 157 0 TACGCAAGGA 0.98547 -137 AGGGATACTGTACCCAATAATATAGAAAAG 3 138 1 TACCCAATAA 0.780004 -163 GATTTGTCCATAAGCATGGACGAATGAGGT 3 208 0 TAAGCATGGA 0.9141 -93 TCTCTCCCTAGACCCAAGGAAAGGACTGTC 4 108 0 GACCCAAGGA 0.982527 -193 ********** Masking position 6 Map Score: 2.63981 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 44 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 TTCAAAAAAAAAACTCTCGTGTAAATTTAT 1 101 0 AAACTCTCGT 0.86497 -200 GAGGGGAAGAAAAATATCGTTTTCTTGGTT 1 195 0 AAAATATCGT 0.702696 -106 ATTTTTGGGAATAAACTTGT 2 1 0 ATAAACTTGT 0.705102 -293 CCAGGGCTCTAAAATCTCATCGAGTTAACT 3 21 1 AAAATCTCAT 0.9493 -280 CATGGGAAGAAAAATCGTATAGTTAACTCG 3 41 0 AAAATCGTAT 0.772553 -260 TCCGTTTACAAAAGACTTATCCCTAAAAAT 3 93 1 AAAGACTTAT 0.758269 -208 CCCTTAAGAAAAAAACTTGTTGGCTACGAA 4 72 0 AAAAACTTGT 0.938251 -229 CTCAAGATACAAAATCTTATAATGCAAATC 5 53 0 AAAATCTTAT 0.934978 -83 CCCAGAATACAAAAACTCAAGATACAAAAT 5 68 0 AAAAACTCAA 0.70562 -68 ********** Masking position 3 Map Score: 1.37867 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 212 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 ********** No masking Map Score: -2.76868e-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 11 ********** No masking Map Score: -2.76868e-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: -2.76868e-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