AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i012_Glycogen_Biosynthesis_ctra_reg_300.orf -o012_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 RCT00084 37 Chlamydia_trachomatis #2 RCT00085 17 Chlamydia_trachomatis #3 RCT00086 191 Chlamydia_trachomatis #4 RCT00237 155 Chlamydia_trachomatis #5 RCT00465 300 Chlamydia_trachomatis #6 RCT00764 300 Chlamydia_trachomatis #7 RCT00827 300 Chlamydia_trachomatis Motif number 1 AAAGCCTCCTTAACTAAAAAAGGCGAACA 4 10 1 TTAACTAAAA 0.712131 -146 AATATTAATATTAAAAGAAAGATTTCTATT 4 94 0 TTAAAAGAAA 0.956702 -62 TCTTTTCCCATAAAAAGAAATGATCCGCAG 5 26 1 TAAAAAGAAA 0.866082 -275 TTTAGATGTTTGAAAAATAAAAATTATCTA 5 180 0 TGAAAAATAA 0.802473 -121 TTTCAAACATCTAAAAATAAAATCGATTTA 5 195 1 CTAAAAATAA 0.762524 -106 AAAATAATTTTAAAAAATAAATTATTAAAA 5 263 0 TAAAAAATAA 0.873825 -38 CCCGCCACCATAAAAAATAATTTTAAAAAA 5 276 0 TAAAAAATAA 0.873825 -25 AAGATGCCCCTTAAATGTAAAAAACTTTGA 6 143 0 TTAAATGTAA 0.919948 -158 AAACTATCCATTAAATAAAAGTAATTAAAT 6 200 1 TTAAATAAAA 0.947167 -101 ATAAAAGTAATTAAATATAACAAAAACATC 6 214 1 TTAAATATAA 0.903224 -87 ATTATTTTTGTTAAAAGAAATAATTAATGA 6 247 1 TTAAAAGAAA 0.956702 -54 GTTTCGTTAATTAAATAAAACTCATTAATT 6 268 0 TTAAATAAAA 0.947167 -33 ATGTTTATCCTTATAAAAAATTGCTCGTGC 7 94 0 TTATAAAAAA 0.710777 -207 ACACTCGTAATTAAAAGAAATCTTATTTTG 7 157 0 TTAAAAGAAA 0.956702 -144 AGAAAGATGATTAAATATAAGGTCTGGAGA 7 254 1 TTAAATATAA 0.903224 -47 ********** Masking position 3 Map Score: 20.8176 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 117 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 TGTTGAGAATAGAAATCTTTCTTTTAATATTAA 4 87 1 AGAATTTCTT 0.8799 -69 TTCTTTTAATATTAATATTTCTTATTCACAAGC 4 105 1 ATTATTTCTT 0.753081 -51 GTCAAAATTAGATAATTTTTATTTTTCAAACAT 5 172 1 GATATTTATT 0.637869 -129 TCTAAAAATAAAATCGATTTATTATTCATGCAA 5 204 1 AAACTTTATT 0.883176 -97 GTACCTCACAAAACCTTTTTATCGGTAGAGAAA 6 99 1 AAACTTTATC 0.776737 -202 TTTTATCGGTAGAGAAATTTCTCAAAAATCAAA 6 115 1 AGAATTTCTC 0.771262 -186 CTTAAATGTAAAAAACTTTGATTTTTGAGAAAT 6 131 0 AAAATTGATT 0.815307 -170 TGTTATATTTAATTACTTTTATTTAATGGATAG 6 203 0 AATATTTATT 0.944151 -98 AATATAACAAAAACATCTTGATTATTTTTGTTA 6 227 1 AAAATTGATT 0.824217 -74 AGAAATAATTAATGAGTTTTATTTAATTAACGA 6 262 1 AATATTTATT 0.944151 -39 CTTCTATTCTAAAAATGTTTATCCTTATAAAAA 7 105 0 AAAATTTATC 0.889795 -196 GTCAGGAGGAAATACGCTTTCTTCTATTCTAAA 7 125 0 AATCTTTCTT 0.923568 -176 CTCCTGACAAAATAAGATTTCTTTTAATTACGA 7 150 1 AATATTTCTT 0.951938 -151 CTATGTTGATAATAACGTTTCTAAAAGGTACCA 7 196 1 AATATTTCTA 0.768465 -105 CCTTATATTTAATCATCTTTCTTTCAGTAGGAT 7 243 0 AATATTTCTT 0.962375 -58 *** * ****** Masking position 8 Map Score: 12.8609 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 220 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 AGACGATACTGCAGAGGGTCTTGATATTCGGTA 4 55 0 GCAGAGGTTG 0.985973 -101 GAAATGATCCGCAGAGGAGGTTCAAGGTGAGGA 5 42 1 GCAGAGGTTC 0.994028 -259 ATCTGCTCTTGGATAGGTATGCCAACAAAGATG 5 75 1 GGATAGGGCC 0.950397 -226 ATGTGGAATAGCATAGGCGAGTCAGAAAAGAGT 5 105 1 GCATAGGGTC 0.978109 -196 TTGGTACCGCGCATCGGAGGTTCGAATCCTTCC 6 18 0 GCATCGGTTC 0.963909 -283 AAGCGGTAAGGCAGCGGTTTTTGGTACCGCGCA 6 38 0 GCAGCGGTTG 0.971748 -263 GTGAAAGAGGGCAGAGGGAGTCATTTTGTTTAT 7 39 1 GCAGAGGTCA 0.974042 -262 TCAGTAGGATGGAGAGCTATTCCATGGTACCTT 7 220 0 GGAGAGCTCC 0.909773 -81 TATAAGGTCTGGAGAGGATAGTACAAAGGCGCT 7 269 1 GGAGAGGGTA 0.950828 -32 ******* *** Masking position 3 Map Score: 8.1834 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 95 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 4 TGGCAAAATGATCATCAAGACCACGCCTAACATCC 3 104 0 ACACAGCCCG 0.969865 -88 GTTAATGGTGATCATAAAGTCCACCATAGCTGGAG 3 143 0 ACAAAGCCCC 0.997096 -49 CAGCAGGAACACAGAGATCGCCAAGTTAATGG 3 170 0 ACAAGGTCCC 0.978011 -22 TAAAAAATCAAGTAAAATGTTCGCCTTTTTTAGTT 4 22 0 ATAAAGTCCC 0.947271 -134 TTTTTTACCGAATATCAAGACCCTCTGCAGTATCG 4 50 1 ATACAGCCTC 0.910499 -106 GCATCTTACCACCACAACGACCTTCTATGAGCAGA 6 166 1 ACAAAGCCTC 0.987428 -135 ATTCCTAATAAACAAAATGACTCCCTCTGCCCTCT 7 44 0 ACAAAGCTCC 0.974585 -257 CGTTATTATCAACATAGCGACCTCCTACACTCGTA 7 178 0 ACAAGGCCCC 0.994884 -123 * ** ** * ** ** Masking position 4 Map Score: 8.00826 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 43 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 CTACTCAACTTTGTCAGTAGAACATTCGGGGG 3 19 1 TTGTCAAGAA 0.954295 -173 GTTCGCCTTTTTTAGTTAAGGAGGCTTT 4 7 0 TTTAGTAGGA 0.608069 -149 GTATCGTCTGTTGAGAATAGAAATCTTTCTTT 4 79 1 TTGAGAAGAA 0.958158 -77 GTTTGTTTGCTTGTGAATAAGAAATATTAATA 4 114 0 TTGTGAAAGA 0.822061 -42 AAACAAACTCTTTACATGAGAAGCCTCT 4 138 1 TTTACAAGAA 0.89123 -18 ATGCCCTTTATAGAGATAAGAACTCTTTTCTG 5 127 0 TAGAGAAGAA 0.709046 -174 AATTATCTAATTTTGACAAAAAACGGACCCAT 5 157 0 TTTTGAAAAA 0.72906 -144 CAACGACCTTCTATGAGCAGAAACTATCCATT 6 180 1 CTATGAAGAA 0.59491 -121 TTGATTATTTTTGTTAAAAGAAATAATTAATG 6 244 1 TTGTTAAGAA 0.875543 -57 CACGAGCAATTTTTTATAAGGATAAACATTTT 7 95 1 TTTTTAAGGA 0.817384 -206 GATAAACATTTTTAGAATAGAAGAAAGCGTAT 7 115 1 TTTAGAAGAA 0.934665 -186 AAATCTTATTTTGTCAGGAGGAAATACGCTTT 7 138 0 TTGTCAAGGA 0.955114 -163 AATCATCTTTCTTTCAGTAGGATGGAGAGCTA 7 234 0 CTTTCAAGGA 0.807721 -67 ****** **** Masking position 9 Map Score: 6.61772 Number of sites scoring better than the average of aligned sites = 379 Number in coding regions = 379 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 TGACAAAGTTGAGTAGCTTGTTCA 3 3 0 GAGAGTTGTT 0.978024 -189 CTTCTCATGTAAAGAGTTTGTTTGCTTGTGAA 4 129 0 AAAAGTTGTT 0.844065 -27 CTTTTTATGGGAAAAGATTCTTAGGAATTTAC 5 11 0 GAAAGTTCTT 0.909205 -290 ACCTATCCAAGAGCAGATTCCTCACCTTGAAC 5 61 0 GAGAGTTCCT 0.961923 -240 TTTCTGCTCATAGAAGGTCGTTGTGGTGGTAA 6 171 0 TAGAGTCGTT 0.924936 -130 TTAACGAAACGAAAAGCTTGCTA 6 288 1 GAAAGTTGCT 0.978256 -13 TTTATCCTTATAAAAAATTGCTCGTGCTTTTA 7 89 0 TAAAATTGCT 0.708824 -212 ATTACGAGTGTAGGAGGTCGCTATGTTGATAA 7 176 1 TAGAGTCGCT 0.951407 -125 *** ** ***** Masking position 5 Map Score: 2.31738 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 192 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 7 AAGATTTCTATTCTCAACAGACGATACTGCAG 4 74 0 TTCCAAAGAC 0.969628 -82 ATATTTCTTATTCACAAGCAAACAAACTCTTT 4 119 1 TTCCAACAAA 0.913763 -37 GTAAATTCCTAAGAATCTTTTCCCATA 5 6 1 TTCTAAAATC 0.871014 -295 TAAGAATCTTTTCCCATAAAAAGAAATGATCC 5 20 1 TTCCATAAAA 0.669178 -281 TTATCTAATTTTGACAAAAAACGGACCCATGC 5 155 0 TTGCAAAAAC 0.915397 -146 TAATTTTTATTTTTCAAACATCTAAAAATAAA 5 184 1 TTTCAACATC 0.75954 -117 GTAGAGAAATTTCTCAAAAATCAAAGTTTTTT 6 123 1 TTCCAAAATC 0.971665 -178 TCTGCCCTCTTTCACAAACGACTAATAGAACA 7 22 0 TTCCAACGAC 0.963437 -279 CTTGCAAATATTCCTAATAAACAAAATGACTC 7 56 0 TTCTAAAAAC 0.927918 -245 *** *** **** Masking position 6 Map Score: 3.82606 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 172 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 8 AATAAAAAGAGCGCACTTCCTTT 1 25 1 GCGCACTTCC 0.967863 -13 CTCTTCTCACCTCACGG 2 4 0 TCTCACCTCA 0.85084 -14 ATATTCAGGGCCGCATCTCCCCCGAATGTT 3 39 0 CCGCATCTCC 0.918265 -153 ATTCCTCACCTTGAACCTCCTCTGCGGATC 5 47 0 TTGAACCTCC 0.917141 -254 GTGGAAGGATTCGAACCTCCGATGCGCGGT 6 16 1 TCGAACCTCC 0.979754 -285 AAGAGACCGAGTGTACCTCACAAAACCTTT 6 87 1 GTGTACCTCA 0.814152 -214 TTAAGGGGCATCTTACCACCACAACGACCT 6 159 1 TCTTACCACC 0.739738 -142 ATAGAAGAAAGCGTATTTCCTCCTGACAAA 7 131 1 GCGTATTTCC 0.814151 -170 ********** Masking position 5 Map Score: 0.708235 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 171 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 9 AAAACTGTAATAAAAAGAGCGCACTTCCTT 1 17 1 TAAAAAGAGC 0.904688 -21 TTGTTTATCATATTCAGGGCCGCATCTCCC 3 48 0 TATTCAGGGC 0.816423 -144 CTGAATATGATAAACAAGTCCAGTGACCTG 3 61 1 TAAACAAGTC 0.889579 -131 CCTCCTTAACTAAAAAAGGCGAACATTTTA 4 15 1 TAAAAAAGGC 0.972551 -141 TTCTTATCTCTATAAAGGGCATGGGTCCGT 5 137 1 TATAAAGGGC 0.969544 -164 AATAAATTATTAAAAAAGCCAGACAAACAA 5 248 0 TAAAAAAGCC 0.909607 -53 TCTCTACCGATAAAAAGGTTTTGTGAGGTA 6 100 0 TAAAAAGGTT 0.762319 -201 ********** Masking position 6 Map Score: 0.481229 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 121 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 10 ********** No masking Map Score: 2.24775e-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: 2.24775e-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: 2.24775e-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