AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i297_synecho_ctra_100.orf -o297_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 RCY04992 300 Synechocystis #2 RCY11382 300 Synechocystis #3 RCT00464 88 Chlamydia_trachomatis #4 RCT00465 300 Chlamydia_trachomatis Motif number 1 TTTCAGCGTGGTTAAATGCACTCTCTGAAGCACA 1 105 1 GAAATGCTCT 0.980036 -196 AAGGACATAGGAAAAACTGCCTCTCCAGCCAGGG 1 203 0 GAAACTCTCT 0.982973 -98 TATTCAATAGGTTAAATTTTATCTTCCTTTCCCA 2 71 0 GAAATTATCT 0.921444 -230 AATTTACTCAGCTAAATTGTCTCTATATCTTAAC 2 119 1 GAAATTCTCT 0.992607 -182 AATGAAGCCCCGCAAATTGGCTTTATTGTGGGGG 2 222 0 CAAATTCTTT 0.781315 -79 CACCCGTAACTTGAAATTACCTCTTCT 2 284 1 TAAATTCTCT 0.937471 -17 AGCTCGAAAAGAAAAATCCACTCT 3 1 0 GAAATCCTCT 0.994248 -88 TTGCTTGATAGAAGAATCAGCTCTTTATTTTGCC 3 57 0 GGAATCCTCT 0.99194 -32 GATTCCTCACCTTGAACCTCCTCTGCGGATCATT 4 44 0 CGAACCCTCT 0.941583 -257 GGTTCAAGGTGAGGAATCTGCTCTTGGATAGGTA 4 60 1 GGAATCCTCT 0.99194 -241 * ***** **** Masking position 6 Map Score: 13.9089 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 142 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 TATGGGAAAGGAAGATAAAATTTAACCTAT 2 69 1 GAAGATAAAA 0.874278 -232 TGAATAAAGTAAATGTAAAAAATTTACTCA 2 99 1 AAATGTAAAA 0.718271 -202 TCAACAGCTCGAAAAGAAAAATCCACTCT 3 10 0 GAAAAGAAAA 0.859496 -79 AGCTGTTGACAAAGGTAAAAGTGGTTGGCA 3 31 1 AAAGGTAAAA 0.874278 -58 CTTTTCCCATAAAAAGAAATGATCCGCAGA 4 27 1 AAAAAGAAAT 0.906694 -274 TAGATGTTTGAAAAATAAAAATTATCTAAT 4 178 0 AAAAATAAAA 0.970663 -123 TCAAACATCTAAAAATAAAATCGATTTATT 4 197 1 AAAAATAAAA 0.970663 -104 TTATTGCATGAATAATAAATCGATTTTATT 4 210 0 AATAATAAAT 0.760708 -91 AATAATTTTAAAAAATAAATTATTAAAAAA 4 261 0 AAAAATAAAT 0.957624 -40 CGCCACCATAAAAAATAATTTTAAAAAATA 4 274 0 AAAAATAATT 0.760708 -27 ********** Masking position 7 Map Score: 7.42237 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 302 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 GCAATTAGACTTATGGGAAAGGAAGATAAA 2 58 1 TTATGGGAAA 0.917128 -243 ATTTCCCCTCGGTTGGGAAAGTTGCACCTT 2 182 1 GGTTGGGAAA 0.979168 -119 CTTTTCGAGCTGTTGACAAAGGTAAAAGTG 3 24 1 TGTTGACAAA 0.96096 -65 AGGTAAAAGTGGTTGGCAAAATAAAGAGCT 3 43 1 GGTTGGCAAA 0.984061 -46 TCATTTCTTTTTATGGGAAAAGATTCTTAG 4 19 0 TTATGGGAAA 0.917128 -282 TCCACATCTTTGTTGGCATACCTATCCAAG 4 82 0 TGTTGGCATA 0.918618 -219 AATTATCTAATTTTGACAAAAAACGGACCC 4 159 0 TTTTGACAAA 0.93925 -142 ATTTTTAGATGTTTGAAAAATAAAAATTAT 4 183 0 GTTTGAAAAA 0.744427 -118 ********** Masking position 8 Map Score: 7.17279 Number of sites scoring better than the average of aligned sites = 699 Number in coding regions = 584 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 AACTATTCGAGGCAATGGTTCGG 1 1 0 GGATGGTCGG 0.985814 -300 TTTGGCGATCGCCCCTGGCTGGAGAGGCAGTTT 1 191 1 GCCTGGTGGA 0.979511 -110 CATGGTATTTCCCCTCGGTTGGGAAAGTTGCAC 2 176 1 CCCCGGTGGG 0.952651 -125 TGGGAAAGTTGCACCTTGGTCGGCTAGCCCCCA 2 195 1 GCCTTGTCGG 0.989185 -106 TCATTTCCCCGGTCTTGGTTCCGATAGTTTATA 2 251 1 GGCTGGTCCG 0.995605 -50 TGAGGAATCTGCTCTTGGATAGGTATGCCAACA 4 69 1 GCCTGGTAGG 0.992653 -232 TCTCTATAAAGGGCATGGGTCCGTTTTTTGTCA 4 143 1 GGCTGGTCCG 0.995603 -158 ** * *** **** Masking position 10 Map Score: 5.76735 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 305 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 CCGAACCATTGCCTCGAATAGTTCTTC 1 8 1 ATTGCCTCGA 0.910335 -293 GATCGCCAAACTGGCCCCGAAATATTAAGA 1 171 0 CTGGCCCCGA 0.98708 -130 CAGTTTGGCGATCGCCCCTGGCTGGAGAGG 1 188 1 ATCGCCCCTG 0.868277 -113 AAATTGACCCTCCCATCACTGA 1 289 0 ATTGACCCTC 0.674167 -12 TATGTTTACCCTATCCTCTAAGCAATTAGA 2 37 1 CTATCCTCTA 0.774296 -264 TTTTATCTTCCTTTCCCATAAGTCTAATTG 2 59 0 CTTTCCCATA 0.714973 -242 GACCCTAGTTCTGGCCTCAATTTTGTTAAG 2 147 0 CTGGCCTCAA 0.78387 -154 GGGTCATGGTATTTCCCCTCGGTTGGGAAA 2 172 1 ATTTCCCCTC 0.932461 -129 CCTTGGTCGGCTAGCCCCCACAATAAAGCC 2 208 1 CTAGCCCCCA 0.90594 -93 GCGGGGCTTCATTTCCCCGGTCTTGGTTCC 2 243 1 ATTTCCCCGG 0.924259 -58 CTGTCCCCGCCACCATAAAA 4 291 0 CTGTCCCCGC 0.970706 -10 ********** Masking position 2 Map Score: 5.29959 Number of sites scoring better than the average of aligned sites = 3630 Number in coding regions = 3200 Number in noncoding regions = 430 Number of orfs with sites within 600 bp upstream = 412 Fraction of orfs with sites within 600 bp upstream = 0.0661741 Motif number 6 GTGCCAGTCAAGCCACCACACCCCAGACTG 1 37 0 AGCCACCACA 0.945577 -264 TCGCCAAACTGGCCCCGAAATATTAAGAAT 1 169 0 GGCCCCGAAA 0.983518 -132 AAATTGACCCTCCCATCACTGACTG 1 286 0 GACCCTCCCA 0.891681 -15 TTGGTCGGCTAGCCCCCACAATAAAGCCAA 2 210 1 AGCCCCCACA 0.991175 -91 GGGGAAATGAAGCCCCGCAAATTGGCTTTA 2 231 0 AGCCCCGCAA 0.983518 -70 CTGTCCCCGCCACCATAAAAAA 4 289 0 GTCCCCGCCA 0.981553 -12 ********** Masking position 10 Map Score: 4.28423 Number of sites scoring better than the average of aligned sites = 806 Number in coding regions = 728 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 ATGCATCAGTGCCAGTCAAGCCACCACACCC 1 44 0 GCCAGCAAGC 0.989664 -257 ACGCTAACAGATCAAACAAGAAACAGCAACA 1 138 1 ATCAACAAGA 0.928149 -163 GTGGGGGCTAGCCGACCAAGGTGCAACTTTC 2 198 0 GCCGACAAGG 0.931302 -103 TGATTCTTCTATCAAGCAAGAGGTTTC 3 72 1 ATCAACAAGA 0.928149 -17 GGATAGGTATGCCAACAAAGATGTGGAATAG 4 85 1 GCCAAAAAGA 0.963872 -216 GCATAGGCGAGTCAGAAAAGAGTTCTTATCT 4 115 1 GTCAGAAAGA 0.939757 -186 TATTAAAAAAGCCAGACAAACAAAACTGTAA 4 240 0 GCCAGCAAAC 0.926906 -61 ***** ***** Masking position 8 Map Score: 1.64363 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 616 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 8 CAAGCCACCACACCCCAGACTGAAGAACTA 1 29 0 CACCCCAGAC 0.874423 -272 GTTTACCATGCTCCCCATGCATCAGTGCCA 1 61 0 CTCCCCATGC 0.984038 -240 GTTTGGCGATCGCCCCTGGCTGGAGAGGCA 1 190 1 CGCCCCTGGC 0.988619 -111 CCATCACTGACTGCCCAGGCAATCTCAGAA 1 269 0 CTGCCCAGGC 0.987177 -32 GTCATGGTATTTCCCCTCGGTTGGGAAAGT 2 174 1 TTCCCCTCGG 0.869503 -127 CACCTTGAACCTCCTCTGCGGATCATTTCT 4 41 0 CTCCTCTGCG 0.918768 -260 GGTGAGGAATCTGCTCTTGGATAGGTATGC 4 67 1 CTGCTCTTGG 0.875546 -234 ********** Masking position 6 Map Score: 0.822789 Number of sites scoring better than the average of aligned sites = 2495 Number in coding regions = 2275 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 9 TGATGCATGGGGAGCATGGTAAACGCCTCC 1 67 1 GGAGCATGGT 0.894571 -234 AGGGCGACAAAGGACATAGGAAAAACTGCC 1 216 0 AGGACATAGG 0.87792 -85 TAAACATAGACGGTCAGAGTCATCAAAATT 2 15 0 CGGTCAGAGT 0.917517 -286 AATTGCTTAGAGGATAGGGTAAACATAGAC 2 34 0 AGGATAGGGT 0.773723 -267 GCCAGAACTAGGGTCATGGTATTTCCCCTC 2 162 1 GGGTCATGGT 0.983766 -139 TTCATTTCCCCGGTCTTGGTTCCGATAGTT 2 250 1 CGGTCTTGGT 0.926365 -51 ATCTCTATAAAGGGCATGGGTCCGTTTTTT 4 142 1 AGGGCATGGG 0.976063 -159 ********** Masking position 2 Map Score: 0.168464 Number of sites scoring better than the average of aligned sites = 1760 Number in coding regions = 1616 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 10 ********** No masking Map Score: 3.05066e-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: 3.05066e-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: 3.05066e-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