AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i301_synecho_ctra_100.orf -o301_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 RCY23791 159 Synechocystis #2 RCY43755 46 Synechocystis #3 RCT00547 294 Chlamydia_trachomatis #4 RCT00722 219 Chlamydia_trachomatis Motif number 1 TAGTAGTAATTTGTTATTTTTATTTTTTTAGGAATT 3 17 0 TTTATTTTTT 0.930864 -278 AAATCAGATCGTTAGAATTTAATATTGTTAGTAGTA 3 45 0 GTAATTTATT 0.925589 -250 AAAAACGTTTTTAATATTTTGCTTTTAATAAAACAT 3 96 1 TTAATTTTTT 0.986865 -199 GCAAAAAGAATTAATTATGTTTTATTAAAAGCAAAA 3 112 0 TTATTTTATT 0.893511 -183 CGCTATGATTTTAAGACTTTACTATTCAGTGAGAGA 3 259 0 TTAATTTATT 0.979094 -36 TTATAATGGTTAGAGAATCTTTTTTTCTAAAAACAT 4 23 1 TAAATTTTTT 0.930821 -197 TTGTTCCATCTTCATACTATGTTTTTAGAAAAAAAG 4 41 0 TTAATTTTTT 0.986865 -179 GTTGGGCTACTTAAAAGTATAGTTTTCTTTTGCAAG 4 98 1 TTAATTTTTT 0.98686 -122 ** * * * * **** Masking position 8 Map Score: 7.87491 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 38 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 AGGATTGGTTCCATTGTGGATTAATGG 1 143 0 GTTCCATTGT 0.899074 -17 AGGAGGTAACGGTACCTCCTGTTAAAAAAA 3 191 0 GGTACCTCCT 0.922022 -104 AGGAGGTACCGTTACCTCCTGCGCGAAAGG 3 201 1 GTTACCTCCT 0.980623 -94 GACTTCACGCTTTCTCTCGTGCTGTCTCTC 3 235 1 TTTCTCTCGT 0.899074 -60 AGAACAACTTGTTCCATCTTCATACTATGT 4 55 0 GTTCCATCTT 0.954774 -165 TAAAAGTATAGTTTTCTTTTGCAAGAAAGA 4 109 1 GTTTTCTTTT 0.811205 -111 AAACAAACGCTTTCCCTCTTTCTTGCAAAA 4 125 0 TTTCCCTCTT 0.954774 -95 CTATGTTATCGTTCTCTTCTAAGCTTTGTC 4 170 0 GTTCTCTTCT 0.971048 -50 CGCTTAACCCGTTATCTTTTCTCCATCTAT 4 196 0 GTTATCTTTT 0.915659 -24 ********** Masking position 7 Map Score: 7.10597 Number of sites scoring better than the average of aligned sites = 460 Number in coding regions = 390 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 GTTATTTTTATTTTTTTAGGAATTATCGCG 3 10 0 TTTTTTTAGA 0.940724 -285 TTAATAAAAACGTTTTTAATATTTTGCTTTT 3 91 1 CGTTTTTAAA 0.954036 -204 TTTAATATTTTGCTTTTAATAAAACATAATT 3 105 1 TGCTTTTAAA 0.962134 -190 GCCTTGCAATTTTTTTTAACAGGAGGTACCG 3 181 1 TTTTTTTAAA 0.944151 -114 ATCTCCGCTATGATTTTAAGACTTTACTATT 3 269 0 TGATTTTAAA 0.945212 -26 CTTCATACTATGTTTTTAGAAAAAAAGATTC 4 37 0 TGTTTTTAGA 0.978198 -183 ********* * Masking position 6 Map Score: 4.01382 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 35 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 4 GTTCTTACTCTGGCGGTAATGCTGGGGCTAAAA 1 29 0 TGCGTATGCT 0.977667 -131 TCCATGGCCCTAGGGGATTTGCTGAAAATGGTT 1 101 0 TGGGATTGCT 0.989595 -59 TGTGGATTAATGGCAGAATGGCTCCATGGCCCT 1 123 0 TGCGATGGCT 0.987449 -37 CGTTACCTCCTGCGCGAAAGGCTTGGACTTCAC 3 210 1 TCGGAAGGCT 0.987153 -85 CTTAAAATCATAGCGGAGATGCTTT 3 280 1 TGCGAATGCT 0.994396 -15 AAGCGTTTGTTTCGCGACATTCTTCTGGACAAA 4 143 1 TCGGAATTCT 0.934847 -77 * ** ** ***** Masking position 1 Map Score: 3.60333 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 90 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 CTGGGGCTAAAACTGTTTTTGCCCAGTCCA 1 10 0 AACTGTTTTG 0.909612 -150 TTGGACTAGAAATTGGTTTGGTTTTTCGTGC 1 68 0 AATTGGTTTG 0.956537 -92 GAAAATGGTTAATTGGACTAGAAATTGGTTT 1 80 0 AATTGGACTG 0.951862 -80 GTTCACCCAACATTCTACTAGGGG 2 4 0 CATTCTACTG 0.937712 -43 AAACATAATTAATTCTTTTTGCGTAAGTTAA 3 126 1 AATTCTTTTG 0.96139 -169 AGATGGAACAAGTTGTTCTCGTGAGGGTAAT 4 66 1 AGTTGTTCTG 0.954096 -154 TGTTTCGCGACATTCTTCTGGACAAAGCTTA 4 150 1 CATTCTTCTG 0.971915 -70 ********* * Masking position 4 Map Score: 2.62663 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 314 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 6 CTTGGACTTCACGCTTTCTCTCGTGCTGTC 3 231 1 ACGCTTTCTC 0.985399 -64 AAGTAGCCCAACTATTACCCTCACGAGAAC 4 80 0 ACTATTACCC 0.944405 -140 CGCGAAACAAACGCTTTCCCTCTTTCTTGC 4 129 0 ACGCTTTCCC 0.996284 -91 AACACGCTTAACCCGTTATCTTT 4 207 0 ACGCTTAACC 0.9854 -13 ********** Masking position 5 Map Score: 2.28622 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 65 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 7 TCTTACTCTGGCGGTAATGCTGGGGCTAAAA 1 29 0 GCGGTATGCT 0.989956 -131 CATGGCCCTAGGGGATTTGCTGAAAATGGTT 1 101 0 GGGGATTGCT 0.989348 -59 TGGATTAATGGCAGAATGGCTCCATGGCCCT 1 123 0 GCAGATGGCT 0.973523 -37 TAAAATCATAGCGGAGATGCTTT 3 282 1 GCGGAATGCT 0.996001 -13 ***** ***** Masking position 11 Map Score: 1.01807 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 65 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 8 ATTGGACTAGAAATTGGTTTGGTTTTTCGT 1 70 0 AAATTGGTTT 0.848846 -90 GGATTTGCTGAAAATGGTTAATTGGACTAG 1 90 0 AAAATGGTTA 0.974548 -70 TTGTTAGTAGTAATTTGTTATTTTTATTTT 3 27 0 TAATTTGTTA 0.908129 -268 GTTAGAATTTAATATTGTTAGTAGTAATTT 3 41 0 AATATTGTTA 0.796294 -254 TTTTATTAATTAACTTGTTAAATCAGATCG 3 70 0 TAACTTGTTA 0.88101 -225 CACAGATATTATAATGGTTAGAGAATCTTT 4 15 1 ATAATGGTTA 0.889783 -205 GGAGAAAAGATAACGGGTTAAGCGTGTT 4 202 1 TAACGGGTTA 0.851737 -18 ********** Masking position 8 Map Score: 1.51677 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 284 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 9 ********** No masking Map Score: 1.67931e-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 10 ********** No masking Map Score: 1.67931e-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: 1.67931e-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