AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i223_synecho_ctra_100.orf -o223_synecho_ctra_100.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 RCY24465 237 Synechocystis #2 RCY17780 95 Synechocystis #3 RCY18001 37 Synechocystis #4 RCY20929 300 Synechocystis #5 RCY27839 51 Synechocystis #6 RCY11822 42 Synechocystis #7 RCT00692 296 Chlamydia_trachomatis Motif number 1 AACATCACAATTTGTTGCTAAACCCCCTCCCATCC 1 58 1 TTTGGTACCC 0.954527 -180 ATTATAGGTCTTTCCTCCCTTGTCCATGGGGATGG 1 87 0 TTTCCCTTCC 0.910181 -151 AGACCTATAATTTGGCCATGATCCCCGGGGATGTT 1 111 1 TTTGCTACCC 0.965246 -127 TTTGGTCTCGTTTCAAGTTTCCCCCGATGCCATGG 1 192 1 TTTCGTCCCC 0.921205 -46 AGCTTTCCATTTTCTACATAGGTCT 2 81 1 TTTCCTGTCT 0.826124 -15 TCTCCTCCCATTTCCCATCCACCCTA 4 2 0 TTTCACACCT 0.787394 -299 TAAGCGATCATTTCCCCCTCTCCTCCCATTTCCCA 4 20 0 TTTCCTTCTC 0.824119 -281 TTATGGCCAATTTCAGCCTATCCCTCCTTTTACTT 4 131 1 TTTCCTTCCT 0.965352 -170 TTCAGGGCTTTTTCCGCGTCTATCCAGAGATAGAT 4 172 1 TTTCCTTTCC 0.965352 -129 TCGTCCTAATTTTCCGGATTAATCTATCTCTGGAT 4 193 0 TTTCGTATCT 0.945112 -108 TATTGGGCAATTTGACGATAAATCCGCTGGTTCGT 4 224 0 TTTGGTATCC 0.920846 -77 TTGCCCAATATTTCCGGTTGTATCCACGGAAACTC 4 249 1 TTTCGTTTCC 0.954664 -52 ACGGACAATTTTTACTAATTATTCCTGAGGTTATT 5 27 1 TTTAATATCC 0.563003 -25 AGATGAAGCCTTTCGTAATCATCCTTAAATCTTGC 7 16 0 TTTCATACCT 0.910575 -281 ATCTTCCTTGTTTGCGGATTATCTTTGCAAAGATT 7 47 1 TTTGGTACTT 0.520228 -250 CAAATGAAGAGTTCCCCCCCTCCCTTATAAGGTAA 7 84 0 GTTCCCTCCT 0.546756 -213 CGTTTTTATTTTTACCCTTGAATCTAAGAGAGTTC 7 183 1 TTTACTATCT 0.742436 -114 **** * * * *** Masking position 3 Map Score: 14.3413 Number of sites scoring better than the average of aligned sites = 2019 Number in coding regions = 1747 Number in noncoding regions = 272 Number of orfs with sites within 600 bp upstream = 267 Fraction of orfs with sites within 600 bp upstream = 0.0428847 Motif number 2 GTCCATGGGGATGGGAGGGGGTTTAGCAACAAA 1 68 0 ATGGGGGGGT 0.979397 -170 TCCCATCCCCATGGACAAGGGAGGAAAGACCTA 1 85 1 ATGGAAAGGG 0.87113 -153 CCCCGATGCCATGGTGGGTTGCTAAACAAAGAA 1 213 1 ATGGTGGTGT 0.851018 -25 TATGTAGAAAATGGAAAGCTGAGCCGACTGGTC 2 68 0 ATGGAAGTGG 0.94479 -28 TAGGGTGGATGGGAAATGGGAGG 4 1 1 TAGGGGGTGG 0.927889 -300 TGGATGGGAAATGGGAGGAGAGGGGGAAATGAT 4 16 1 ATGGGGGGAG 0.986016 -285 TCGAAAGTAAAAGGAGGGATAGGCTGAAATTGG 4 137 0 AAGGAGGTAG 0.971705 -164 AGCAAGATTTAAGGATGATTACGAAAGGCTTCA 7 15 1 AAGGAGATAG 0.894813 -282 ATCCGCAAACAAGGAAGATGAAGCCTTTCGTAA 7 33 0 AAGGAGAGAG 0.931347 -264 TTTACCTTATAAGGGAGGGGGGGAACTCTTCAT 7 83 1 AAGGGGGGGG 0.993846 -214 TCTTGATATGATGGAGGGTCGTTTTTATTTTTA 7 164 1 ATGGAGGCGT 0.909587 -133 ***** ** ** * Masking position 4 Map Score: 10.5981 Number of sites scoring better than the average of aligned sites = 1229 Number in coding regions = 1098 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 3 TGGCCCGGTGACAGTTACGCCAG 1 4 1 CCCGGTGACA 0.965543 -234 CTCCCTTGTCCATGGGGATGGGAGGGGGTT 1 78 0 CATGGGGATG 0.903976 -160 GGCCATGATCCCCGGGGATGTTGTGACTCC 1 124 1 CCCGGGGATG 0.998216 -114 ATGTTGTGACTCCGGGGACGCCTTTTTTCG 1 141 1 TCCGGGGACG 0.992202 -97 ACGATTTTTTACCGGGGATGAAGTAGCCTT 2 27 1 ACCGGGGATG 0.99076 -69 AAGGGGAGTTTCCGTGGATACAACCGGAAA 4 259 0 TCCGTGGATA 0.869971 -42 TAAGAGAGTTCCCGGTGTTGTTTCGGAGAG 7 207 1 CCCGGTGTTG 0.969411 -90 ********** Masking position 4 Map Score: 9.40423 Number of sites scoring better than the average of aligned sites = 545 Number in coding regions = 511 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 AAGTCGGATTAATTGGTAGCAAACATCACA 1 37 1 AATTGGTAGC 0.894221 -201 GCTTCTTTGTTTAGCAACCCACCAT 1 223 0 TTTGTTTAGC 0.869677 -15 CAAAATAACGATTTTTTACCGGGGATGAAG 2 20 1 ATTTTTTACC 0.95189 -76 TATTAGAAGCAATGGTTAGCCTTTAAGAGT 4 61 1 AATGGTTAGC 0.947432 -240 GAGGTTGTTTATTTGTTAGCAAGGT 6 6 0 ATTTGTTAGC 0.980791 -37 CTTTGCAAAGATTTTTTACCTTATAAGGGA 7 69 1 ATTTTTTACC 0.95189 -228 GGAACTCTTCATTTGTGAGCCTCTTTGAGA 7 104 1 ATTTGTGAGC 0.931326 -193 GGGTCGTTTTTATTTTTACCCTTGAATCTA 7 179 1 TATTTTTACC 0.81868 -118 ********** Masking position 8 Map Score: 5.40164 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 292 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 GTTTGCTACCAATTAATCCGACTTAGCCTG 1 31 0 AATTAATCCG 0.96094 -207 CATTGCTTCTAATAAATACCTAAGCGATCA 4 45 0 AATAAATACC 0.780519 -256 TCCAGAGATAGATTAATCCGGAAAATTAGG 4 194 1 GATTAATCCG 0.974801 -107 GCAATTTGACGATAAATCCGCTGGTTCGTC 4 223 0 GATAAATCCG 0.986334 -78 AGTTTCCGTGGATACAACCGGAAATATTGG 4 253 0 GATACAACCG 0.93397 -48 CAAGGGTAAAAATAAAAACGACCCTCCATC 7 173 0 AATAAAAACG 0.892621 -124 ********** Masking position 6 Map Score: 2.48383 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 154 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 GGGTTGCTAAACAAAGAAGC 1 228 1 ACAAAGAAGC 0.968796 -10 AAATTACGGGACAAACAGACATTTACTCTT 4 85 0 ACAAACAGAC 0.898144 -216 ACCTTGCTAACAAATAAACAACCTCGATA 6 10 1 ACAAATAAAC 0.896774 -33 AGTTCTCCTCTCAAAGAGGCTCACAAATGA 7 112 0 TCAAAGAGGC 0.966436 -185 TACCCTTGAATCTAAGAGAGTTCCCGGTGT 7 195 1 TCTAAGAGAG 0.778778 -102 TAAGCGACTATCTAAGAAACCTTCTCTCCG 7 230 0 TCTAAGAAAC 0.938133 -67 TTTGAAGTTCACTAATAAGCGACTATCTAA 7 245 0 ACTAATAAGC 0.889558 -52 ********** Masking position 5 Map Score: 2.21396 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 198 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 ********** No masking Map Score: -8.07587e-13 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: -8.07587e-13 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: -8.07587e-13 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