AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_synecho_ctra_300.orf -o111_synecho_ctra_300.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 RCY29694 187 Synechocystis #2 RCY03689 300 Synechocystis #3 RCY50298 300 Synechocystis #4 RCY17260 138 Synechocystis #5 RCT00147 300 Chlamydia_trachomatis #6 RCT00148 35 Chlamydia_trachomatis Motif number 1 GCTTTTCTAGGTCACTTGGCCTGGCTAAAACT 2 201 1 GTCCTTGCCT 0.803223 -100 AATTCTAAGGCTGGTATTGACTTTCCTTCCTG 2 234 1 CTGTATGACT 0.720704 -67 ACTTTCCTTCCTGTCCTAGCCCGCTAATTCGG 2 253 1 CTGCCTGCCC 0.988925 -48 CGGTACTATTCTTCCCTCGCATCGTTTTT 2 282 1 CTTCCTGCAT 0.932376 -19 ATTTCTACCTGTTCTTGGCTATAGGCAGGG 3 9 1 CTGTCTGGCT 0.985196 -292 GTTTTTTTTTCTTTCCTGCCCTGCCTATAGCC 3 27 0 CTTCCTCCCT 0.90526 -274 CCACCATGCGCTGCCCTTGGCTATTAATTCTT 3 60 0 CTGCCTGGCT 0.990723 -241 CTTCCCCTAGCTGATCTCGACTAATTCTGACT 3 106 0 CTGTCTGACT 0.967251 -195 ATAGTTTTTGCTCACTTCCCCTAGCTGATCTC 3 120 0 CTCCTTCCCT 0.890451 -181 TCAATTTGACCGCCCCTGGCCCTAGGATTAAG 4 69 0 CGCCCTGCCC 0.929758 -70 CGTTACCTCGGTTCTAGGATCTTTAGCTAG 4 119 0 CGGTCTGGAT 0.833541 -20 GATAAAACAACTCTTTTTGCCTGGCATCAAAT 5 21 1 CTCTTTGCCT 0.965745 -280 TAATCAAGATCTGCTCTCGCATTTATTCAAAG 5 218 0 CTGTCTGCAT 0.980275 -83 AGCATAGGGGCTGATTTAGCATTTTCTTGAGA 5 267 1 CTGTTTGCAT 0.93458 -34 *** *** **** Masking position 7 Map Score: 14.7103 Number of sites scoring better than the average of aligned sites = 1113 Number in coding regions = 968 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 AACAATAGTGTTAATGGAGACTGTTAAGTT 1 15 1 TTAATGGAGA 0.81467 -173 TCGAGTCTTTTGACTGGGAAAATGTCGGAG 1 95 0 TGACTGGGAA 0.922909 -93 GAGGCAATAATTCCTGGGGAAAGGAAAAAT 1 142 0 TTCCTGGGGA 0.990974 -46 AGGGGCTGGGGGGATGGGGAAC 1 176 0 GGGCTGGGGG 0.906713 -12 ATTTGCCAACTTGCTGGGGGTTTTTACGGA 2 61 1 TTGCTGGGGG 0.982203 -240 TAAAGCAATATTACTGGGCTTTTCTAGGTC 2 184 1 TTACTGGGCT 0.862776 -117 TTCTGACTTTTGCCTGGAGAAACCACCATG 3 84 0 TGCCTGGAGA 0.96301 -217 ATTGTTCCTGTTACTGGGCAGTCCCCCAGG 3 178 1 TTACTGGGCA 0.972164 -123 TTCTAGAATTTTCCTGGGGGACTGCCCAGT 3 190 0 TTCCTGGGGG 0.987706 -111 GGATGTATGGGGATTGCAGAAGG 4 4 1 TGTATGGGGA 0.8037 -135 TAAATTACTGGATAAAACAACTCT 5 5 1 TTACTGGATA 0.761122 -296 ********** Masking position 5 Map Score: 10.7191 Number of sites scoring better than the average of aligned sites = 1945 Number in coding regions = 1722 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 3 CAGGAACAATAGTGTTAATGG 1 2 1 AGGAACAATA 0.90656 -186 TGGAGCTAAAACGAACAAAAACTTAACAGT 1 34 0 ACGAACAAAA 0.8514 -154 TAATTCCTGGGGAAAGGAAAAATTTCAATG 1 135 0 GGAAAGGAAA 0.840367 -53 GGGGGTTTTTACGGAGAAAAAATGGACTGA 2 76 1 ACGGAGAAAA 0.901909 -225 GGGCTAGGACAGGAAGGAAAGTCAATACCA 2 245 0 AGGAAGGAAA 0.954056 -56 AACGATGCGAGGGAAGAATAGTACCGAATT 2 278 0 GGGAAGAATA 0.965699 -23 AGGCAGGGCAGGAAAGAAAAAAAAACTAAG 3 33 1 GGAAAGAAAA 0.924489 -268 GCCCAGTAACAGGAACAATAGCCTATCAAT 3 167 0 AGGAACAATA 0.90656 -134 CTTAGATGCTCGGGAGAAAATTTTAACTTA 4 43 1 CGGGAGAAAA 0.926324 -96 CTTTAGACACGGTGAGAAAATGATTTTTTG 5 97 0 GGTGAGAAAA 0.831749 -204 ********** Masking position 5 Map Score: 5.71508 Number of sites scoring better than the average of aligned sites = 1300 Number in coding regions = 1102 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 203 Fraction of orfs with sites within 600 bp upstream = 0.0326052 Motif number 4 TTCCAGTGGAGCTAAAACGAACAAAAACTT 1 40 0 GCTAAAACGA 0.981387 -148 ACTTGGCCTGGCTAAAACTAAATTCTAAGG 2 214 1 GCTAAAACTA 0.971498 -87 GGGCAGGAAAGAAAAAAAAACTAAGAATTA 3 38 1 GAAAAAAAAA 0.737284 -263 GGGGAAGTGAGCAAAAACTATAATTATTAG 3 131 1 GCAAAAACTA 0.936822 -170 TAAATTACTGGATAAAACAACTCTTTTTGC 5 11 1 GATAAAACAA 0.959429 -290 TTCTCTTACACCTAAAACGACAAATAATTA 5 52 0 CCTAAAACGA 0.910202 -249 ATGATTTTTTGATAAAAAAATCTTTCTTCT 5 78 0 GATAAAAAAA 0.865791 -223 ********** Masking position 5 Map Score: 4.01091 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 217 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 TTGAAATTTTTCCTTTCCCCAGGAATTATTGCC 1 137 1 TCTTCCCAGG 0.594572 -51 TTCCTTGGACTTCTTTGCCCAAATTTGCCAACT 2 39 1 TCTTCCCAAA 0.740081 -262 GCCTGGCTAAAACTAAATTCTAAGGCTGGTATT 2 219 1 ACTATTCTAA 0.91285 -82 ATAGCTCCCATGCTTGATTCAAACTCGTTA 3 281 1 TCTTTTCAAA 0.878912 -20 AGAAAATTTTAACTTAATCCTAGGGCCAGGGGC 4 57 1 ACTTTCCTAG 0.928002 -82 CGTTACCTCGGTTCTAGGATCTTTAGC 4 122 0 ACTCTTCTAG 0.863616 -17 CCAAGATCTTACCTAAATTCTAGCAATATCTTT 5 157 0 ACTATTCTAG 0.933584 -144 TTTAGGTAAGATCTTGGTTCAGAAAGTGCAACG 5 173 1 ACTTTTCAGA 0.874905 -128 CCTATGCTATACCTATTTTCAAAAATAATCAAG 5 242 0 ACTATTCAAA 0.925634 -59 GAATGAACCTTTTCTCAAGAAAATGCTAA 5 282 0 ACTTCTCAAG 0.938713 -19 GCTTTTATCTAGCTTCTAAGATTCCCAAG 6 7 1 ACTATTCTAA 0.91285 -29 * *** ****** Masking position 4 Map Score: 3.68581 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 214 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 TTAACAAAGTAACAAATAAGTTTACAAAAC 2 152 0 AACAAATAAG 0.804211 -149 GGCTAAAACTAAATTCTAAGGCTGGTATTG 2 223 1 AAATTCTAAG 0.899717 -78 GGAAAGAAAAAAAAACTAAGAATTAATAGC 3 43 1 AAAAACTAAG 0.899717 -258 AAAATTCTAGAACATCAAAGTCGTTATGAT 3 208 1 AACATCAAAG 0.924366 -93 TTTTCTCCCGAGCATCTAAGATAGAATCTC 4 33 0 AGCATCTAAG 0.97623 -106 GCTTTTATCTAGCTTCTAAGATTCCCAAGG 6 11 1 AGCTTCTAAG 0.956545 -25 ********** Masking position 8 Map Score: 1.24415 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 107 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 GGAGAAACCACCATGCGCTGCCCTTGGCTA 3 69 0 CCATGCGCTG 0.987742 -232 TTGTTGTTTGCCGTTCGCTCTAGATAGCTC 3 258 1 CCGTTCGCTC 0.993363 -43 TCTATTTTATCCATTCGCTCAATTTGACCG 4 89 0 CCATTCGCTC 0.994422 -50 ********** Masking position 4 Map Score: 0.142961 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 ********** No masking Map Score: -1.19839e-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: -1.19839e-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: -1.19839e-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