AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i063_synecho_ctra_100.orf -o063_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 RCY06192 207 Synechocystis #2 RCY19916 97 Synechocystis #3 RCY47027 173 Synechocystis #4 RCY44761 150 Synechocystis #5 RCT00269 19 Chlamydia_trachomatis #6 RCT00270 194 Chlamydia_trachomatis Motif number 1 TTAGCTGCTTTTCCGCAGGTCCAGCAATATTTTGAAA 1 22 1 TCCGCGCCCA 0.847644 -186 CGGCGTTCCTGCTCCTTGGGCCTTTTTTCTGCGGTCG 1 117 1 GTCCTGCCTT 0.975265 -91 TTTTTTCTGCGGTCGTAGCCCCGCCCAGGAGTTAACC 1 139 1 GTCGTCCCCA 0.973879 -69 GGAGTTAACCGTTCCTCTCACTGACCTGTGTCCCGAA 1 166 1 GTCCTCCTCT 0.94486 -42 GGCAGGGGTTGTTCCTGGGTCCACAAAGGACTGAAAA 2 19 0 GTCCTGCCAA 0.981631 -79 CCCAGGAACAACCCCTGCCTCCGCCATATTTTTGGTA 2 37 1 ACCCTCCCCT 0.960269 -61 TTGCCAAGGCGGCCCCATCCCCATAAAACTCGTCCAA 3 33 0 GCCCCCCCAA 0.990034 -141 TGGCAATGCTGACCCCTAGGCCTACCAAAATTTGTTA 3 64 1 GCCCCGCCCA 0.994084 -110 GCGTTCATCCTTTCCCTACTCCGCCATT 3 156 1 TTCCCCCCCT 0.977075 -18 TGTATTGAAAGTCCCCTAGCCCCCAATACTGGGGGAA 4 28 1 GCCCCGCCAT 0.989972 -123 GATCTGTACAGATCCTCCCTCCCTATTAGAAGAG 6 8 0 GTCCTCCCAT 0.990283 -187 GATCTGTACAGATCCTCCCTTCGGTCTTTGTCCATGA 6 31 1 GTCCTCTCTT 0.796719 -164 * **** * ** * * Masking position 4 Map Score: 15.0383 Number of sites scoring better than the average of aligned sites = 1589 Number in coding regions = 1430 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 TGCAATCAAAACCGCCACGGCGATCGCCAA 1 66 1 ACCGCCACGG 0.96964 -142 CGCCACGGCGATCGCCAAGGAAAATAATTG 1 78 1 ATCGCCAAGG 0.992466 -130 AAGGAGCAGGAACGCCGAGAAAAAGACAAT 1 104 0 AACGCCGAGA 0.948121 -104 CCGCAGAAAAAAGGCCCAAGGAGCAGGAAC 1 121 0 AAGGCCCAAG 0.899954 -87 CGGGGCTACGACCGCAGAAAAAAGGCCCAA 1 132 0 ACCGCAGAAA 0.735993 -76 CGGTCGTAGCCCCGCCCAGGAGTTAACCGT 1 148 1 CCCGCCCAGG 0.955353 -60 TCCCGAACCGATCGCCGAAAGG 1 196 1 ATCGCCGAAA 0.956687 -12 TACCAAAAATATGGCGGAGGCAGGGGTTGT 2 44 0 ATGGCGGAGG 0.916187 -54 GGCAAAACCGCTAAAGGCAACAGCGT 2 82 0 ACCGCTAAAG 0.897348 -16 AGGGGTCAGCATTGCCAAGGCGGCCCCATC 3 51 0 ATTGCCAAGG 0.936347 -123 TCAAGTTTTCATGGACAAAGACCGAAGGGA 6 46 0 ATGGACAAAG 0.707709 -149 ********** Masking position 4 Map Score: 7.00237 Number of sites scoring better than the average of aligned sites = 4601 Number in coding regions = 4259 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 351 Fraction of orfs with sites within 600 bp upstream = 0.0563765 Motif number 3 GCTACGACCGCAGAAAAAAGGCCCAAGGAG 1 128 0 CAGAAAAAAG 0.958917 -80 GACTGGATCTGTCAAAAAATGTTACAGATT 3 123 0 GTCAAAAAAT 0.917017 -51 CTAAAAAAAGCACAAAAAATCCCCCTGGTT 4 87 0 CACAAAAAAT 0.954838 -64 TAGATTTTTCCTAAAAAAAGCACAAAAAAT 4 97 0 CTAAAAAAAG 0.965241 -54 ATCCTTTTAAGAAAAAAAAGGAAAACTACT 6 152 0 GAAAAAAAAG 0.935545 -43 AAGGATTGTTCTCAAAAAAGAAGGGTCTC 6 176 1 CTCAAAAAAG 0.984268 -19 ********** Masking position 5 Map Score: 4.94792 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 230 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 ATGGGAAACGTTTTAAGAATATTTGGACG 3 6 1 AAATTTAGAA 0.974827 -168 AGGCCTACCAAAATTTGTTAAGCTTTGTATCTAA 3 81 1 AAATTTAGCT 0.937589 -93 TTTTTAGGAAAAATCTATTATGCAGAAAGGACTT 4 110 1 AAATTTAGCA 0.983843 -41 AAAACTTGATAATAATCTTACGCAACAAGTACCA 6 67 1 AATTTTAGCA 0.983843 -128 ACTTCTACAGAATTCCTTTACGAAGAGAGAAAGA 6 121 0 AATCTTAGAA 0.934037 -74 TTTTGAGAACAATCCTTTTAAGAAAAAAAAGGAA 6 159 0 AATTTTAGAA 0.974827 -36 *** * *** *** Masking position 8 Map Score: 2.57402 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 38 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TTCCTTGGCGATCGCCGTGGCGGTTTTGAT 1 70 0 ATCGCCGTGG 0.977264 -138 TCCCGAACCGATCGCCGAAAGG 1 196 1 ATCGCCGAAA 0.81355 -12 AGGCGGCCCCATCCCCATAAAACTCGTCCA 3 34 0 ATCCCCATAA 0.913419 -140 AGGGGTCAGCATTGCCAAGGCGGCCCCATC 3 51 0 ATTGCCAAGG 0.825337 -123 CTGTATTGAAAGTCCCCTAGCCCCCAATAC 4 27 1 AGTCCCCTAG 0.93409 -124 ATCGAATCTGATTCCCCCAGTATTGGGGGC 4 46 0 ATTCCCCCAG 0.951243 -105 AGCACAAAAAATCCCCCTGGTTAAAGGAGG 4 79 0 ATCCCCCTGG 0.992581 -72 AGAGAAAGAGATCCCTCTAGAATATCTCAT 6 100 0 ATCCCTCTAG 0.938436 -95 ********** Masking position 1 Map Score: 3.43038 Number of sites scoring better than the average of aligned sites = 3002 Number in coding regions = 2703 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 305 Fraction of orfs with sites within 600 bp upstream = 0.0489881 Motif number 6 ATGCTGACCCCTAGGCCTACCAAAATTTGT 3 69 1 CTAGGCCTAC 0.92259 -105 CATCCTTTCCCTACTCCGCCATT 3 161 1 CTACTCCGCC 0.956979 -13 ATCAGATTCGATAATCCTCCTTTAACCAGG 4 64 1 ATAATCCTCC 0.975299 -87 AATAGTCCTACTCAATCCT 5 9 0 ATAGTCCTAC 0.953487 -11 AGGATCTGTACAGATCCTCCCTCCCTATTA 6 17 0 CAGATCCTCC 0.954425 -178 AGGATCTGTACAGATCCTCCCTTCGGTCTT 6 29 1 CAGATCCTCC 0.954425 -166 AAACTTGATAATAATCTTACGCAACAAGTA 6 68 1 ATAATCTTAC 0.735421 -127 AAAAGGAAAACTACTTCTACAGAATTCCTT 6 137 0 CTACTTCTAC 0.854992 -58 ********** Masking position 10 Map Score: 3.10552 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 588 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 7 ********** No masking Map Score: -2.24942e-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: -2.24942e-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: -2.24942e-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