AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i226_synecho_ctra_100.orf -o226_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 RCY00779 241 Synechocystis #2 RCY09718 300 Synechocystis #3 RCY10327 39 Synechocystis #4 RCT00762 300 Chlamydia_trachomatis Motif number 1 GATAACTGTTCACTGAACCCTAGACCCAACAAC 1 32 0 CACGACCTAG 0.849253 -210 CCCCTCAACAAATATAACGCTAGGGTCAATCCT 2 37 0 AATTACCTAG 0.982352 -264 GTAAAAAGGTAATAATCCCCCAGCCCCTCAACA 2 60 0 AATATCCCAG 0.940555 -241 CATGCCAAGGAAGATTCCCCCAGGTAAAAAGGT 2 83 0 AAGTTCCCAG 0.983447 -218 TTGCGGTCTGAATTTTACCCCAGCATTACCAAC 2 179 0 AATTTCCCAG 0.988801 -122 GCATTTCTAGAATTTATCGCCAGTCTTTCCCAT 4 29 1 AATTACCCAG 0.986238 -272 CTTTTTCAAAAACTTAGCACTAGTTCTCTCTAT 4 91 1 AACTACCTAG 0.973997 -210 TCAATTAATACAGCTTCCACTAGTATGTTCCTC 4 168 1 CAGTTCCTAG 0.963143 -133 CTTCCACTAGTATGTTCCTCTAGGAATATCAAG 4 181 1 TATTTCCTAG 0.934372 -120 *** ** * **** Masking position 2 Map Score: 10.0338 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 247 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 TATGTTGTTGGGTCTAGGGTTCAGTGAACAGTT 1 29 1 GGTCTGGTCA 0.938531 -213 AGGTTTTAATGGTCAGTGTTGACCGATTCCTGC 1 70 0 GGTCATGGAC 0.974681 -172 GCAATGGGTCGGTTAGGGAAGGCAAAAGCCACC 1 208 0 GGTTAGGGGC 0.962096 -34 AGGGCAAGGGAGCAATGGGTCGGT 1 228 0 GGGCAGGGCA 0.994539 -14 AACCCCTATTGGGTTTGGTAGGATTGACCCTAG 2 18 1 GGGTTGGGGA 0.910454 -283 GAATCTTCCTTGGCATGGCCGCCCTCACGGTCT 2 99 1 TGGCAGGGCC 0.958129 -202 CCGCCCTCACGGTCTTGGTGGCCCTGTTGTACG 2 117 1 GGTCTGGGCC 0.993591 -184 CTAGCCGTTAGGTCAATGTTGGTAATGCTGGGG 2 162 1 GGTCATGGGT 0.903517 -139 AAACTGTTGTGATCATTGCCGCAGGTTTGTTCG 2 210 1 GATCATGGCA 0.829527 -91 AATAGGAGCCGGGCTCTGCAGAACAAGGATTAA 4 220 0 GGGCTTGGAA 0.939099 -81 AGAGCCTTACGGACACGGAATACGGCTTGAAAT 4 250 0 GGACAGGTAC 0.769887 -51 ***** ** *** Masking position 8 Map Score: 8.46368 Number of sites scoring better than the average of aligned sites = 3109 Number in coding regions = 2843 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 253 Fraction of orfs with sites within 600 bp upstream = 0.040636 Motif number 3 CTTGATAGCGGTTATGTTGTTGGGTCTAGGGTTC 1 17 1 GTTGTGTGGG 0.995326 -225 TCTCGATTAGGTTTTAATGGTCAGTGTTGACCGA 1 77 0 GTTATGTCAG 0.837703 -165 GGCATAGAGATTTTTGATGATGACACGAAATCAG 1 143 0 TTTGTGTGAC 0.933595 -99 CCTGATATGTTTATTGGTGGTGGCTTTTGCCTTC 1 190 1 TTTGTGTGGC 0.97722 -52 CGTTATATTTGTTGAGGGGCTGGGGGATTATTAC 2 51 1 GTAGGGTGGG 0.982015 -250 TGGTGGCCCTGTTGTACGGCTGGGAATTGACTAG 2 132 1 GTTAGGTGGG 0.981475 -169 TAGGTCAATGTTGGTAATGCTGGGGTAAAATTCA 2 170 1 TTTATGTGGG 0.976942 -131 TCTAAATCTGGTTCAATTGCTGAGTTGCC 2 282 1 GTAATGTGAG 0.949069 -19 ATCATTTAGCATCAAGTTGTTGGCTTTCT 3 21 1 ATAGTGTGGC 0.899049 -19 ** ** ** **** Masking position 11 Map Score: 6.73178 Number of sites scoring better than the average of aligned sites = 1103 Number in coding regions = 1039 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 4 ACATAACCGCTATCAAGATTTTT 1 3 0 TATCAAGATT 0.858005 -239 AATCGAATCGGAAACAGAGTTAAATGTTAAG 2 249 0 GAAACAGATT 0.904782 -52 CTCAGCAATTGAACCAGATTTAGATGAATCG 2 275 0 GAACCAGATT 0.966586 -26 CTAAGTTTTTGAAAAAGGATTTAGAATGTAT 4 77 0 GAAAAAGGTT 0.957686 -224 TGTATTAATTGAACAAGGCGAGAAATGCCCT 4 149 0 GAACAAGGGA 0.947369 -152 CCTCTAGGAATATCAAGGATTTCTTAATCCT 4 197 1 TATCAAGGTT 0.922133 -104 GGGCTCTGCAGAACAAGGATTAAGAAATCCT 4 212 0 GAACAAGGTT 0.9857 -89 GGATATCTGAGAAAAAGAAGAGCCTTACGGA 4 270 0 GAAAAAGAGA 0.750172 -31 TTTTCTCAGATATCCAGGAGTTTTT 4 286 1 TATCCAGGGT 0.889555 -15 ******** ** Masking position 6 Map Score: 6.26383 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 493 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 CTTACGCCATCATTTCTCGATTAGGTTTTA 1 95 0 CATTTCTCGA 0.974241 -147 TTAGTTCTCTCATTCTTAGCA 4 2 1 TAGTTCTCTC 0.922321 -299 TCATTCTTAGCATTTCTAGAATTTATCGCC 4 20 1 CATTTCTAGA 0.948219 -281 AACTTAGCACTAGTTCTCTCTATTGCAATA 4 101 1 TAGTTCTCTC 0.922321 -200 ATAAACAGGGCATTTCTCGCCTTGTTCAAT 4 143 1 CATTTCTCGC 0.98736 -158 AAATCCTTGATATTCCTAGAGGAACATACT 4 189 0 TATTCCTAGA 0.823508 -112 GCCCGGCTCCTATTTCAAGCCGTATTCCGT 4 239 1 TATTTCAAGC 0.866702 -62 ********** Masking position 2 Map Score: 3.99918 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 202 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 GACCCAACAACATAACCGCTATCAAGATTT 1 13 0 CATAACCGCT 0.920567 -229 TTTTGCCTTCCCTAACCGACCCATTGCTCC 1 214 1 CCTAACCGAC 0.989477 -28 GCATGGCCGCCCTCACGGTCTTGGTGGCCC 2 111 1 CCTCACGGTC 0.956195 -190 CCAACATTGACCTAACGGCTAGTCAATTCC 2 154 0 CCTAACGGCT 0.97167 -147 TTTACCCCAGCATTACCAACATTGACCTAA 2 169 0 CATTACCAAC 0.774277 -132 AAAAGAAGAGCCTTACGGACACGGAATACG 4 259 0 CCTTACGGAC 0.984989 -42 ********** Masking position 5 Map Score: 2.26943 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 180 Number in noncoding regions = 18 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: -1.44708e-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 8 ********** No masking Map Score: -1.44708e-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 9 ********** No masking Map Score: -1.44708e-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