AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i299_synecho_ctra_300.orf -o299_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 RCY49210 300 Synechocystis #2 RCY35846 218 Synechocystis #3 RCY33500 23 Synechocystis #4 RCT00579 80 Chlamydia_trachomatis #5 RCT00626 300 Chlamydia_trachomatis Motif number 1 CACTGAAAAGGGTAAGGGTGCAAAGGTGCGG 1 54 1 GGTAAGGGGC 0.931935 -247 GCAAAGGTGCGGTAAGAGCGCACCAGCAGTA 1 73 1 GGTAAGAGGC 0.970045 -228 AAGGTCGGAGGGGCAAAGGTTGGTCTTTTTC 1 141 1 GGGCAAAGTT 0.913481 -160 TGAGGAATTTGGTAACAAATTTCCCAGATAG 1 197 1 GGTAACAATT 0.613088 -104 GGGTCGCTAAGGTCAGAAATCCATCCTCCAC 2 39 0 GGTCAGAATC 0.900742 -180 AAGAAAGCAGGGGAAGATTGTCAACCCAATA 2 102 0 GGGAAGATGT 0.875643 -117 GGCAAGCTTAGGGAAGAAAGCAGGGGAAGAT 2 115 0 GGGAAGAAGC 0.979542 -104 AAATGGGAGGGGGAAAAACGTTGAGGGAATA 2 176 0 GGGAAAAAGT 0.893632 -43 CCTTAATCTAAGGCATAGAGTATATGCATTC 4 18 1 AGGCATAGGT 0.850036 -63 GAATAGAAGAAGGAAGAGTGCTTCCAGAAAA 5 59 0 AGGAAGAGGC 0.977101 -242 AATGGGTTATGGGCAAGGATTCGGCGGATTA 5 113 0 GGGCAAGGTT 0.816985 -188 AGTGAATCCAAGGAATGGGTTATGGGCAAGG 5 126 0 AGGAATGGTT 0.547216 -175 ATAAAATCCTAGGAAGAAGGTTTTTTAAAGA 5 163 0 AGGAAGAAGT 0.934526 -138 TTGTGCCTTTAGTCAGAGTTCTTAACGATCT 5 253 0 AGTCAGAGTC 0.889957 -48 CTCTGACTAAAGGCACAATTCCACTCTAAAA 5 266 1 AGGCACAATC 0.761754 -35 ******** ** Masking position 5 Map Score: 13.3377 Number of sites scoring better than the average of aligned sites = 3229 Number in coding regions = 2887 Number in noncoding regions = 342 Number of orfs with sites within 600 bp upstream = 356 Fraction of orfs with sites within 600 bp upstream = 0.0571796 Motif number 2 GCTCGGTAAACCCCGGTTGGAAGCAAGGTCGG 1 117 1 CCCGGTGGAA 0.963664 -184 CCGGTTGGAAGCAAGGTCGGAGGGGCAAAGGT 1 129 1 GCAGGTGGAG 0.983171 -172 TTTTCCTGCCCCATGATTGGTGGAACCGCTTG 1 167 1 CCAGATGGTG 0.95519 -134 GGGTTCTGTTCCAGGATGCGAGGCACCCTTGG 1 236 0 CCAGATCGAG 0.987316 -65 CTTTTTTTGTCCATGGGTCCAGTGGC 1 285 1 CCAGGGCCAG 0.981723 -16 CGTCCAAAACCCAGGGGTGGAGGATGGATTTC 2 23 1 CCAGGGGGAG 0.997282 -196 CCAACCCCAGTGACGAGATAGCAAATG 2 202 0 CCCGTGCGAG 0.972991 -17 *** *** **** Masking position 5 Map Score: 4.78594 Number of sites scoring better than the average of aligned sites = 559 Number in coding regions = 501 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 TAACAGGGTTTTTCTGCTGACTAACTGGTAA 1 18 1 TTTCTGCGAC 0.950448 -283 TTCTGCTGACTAACTGGTAACTGACCACTGA 1 29 1 TAACTGGAAC 0.876772 -272 CCCTCCGACCTTGCTTCCAACCGGGGTTTAC 1 122 0 TTGCTTCAAC 0.896755 -179 GGGAGTTATCTATCTGGGAAATTTGTTACCA 1 206 0 TATCTGGAAA 0.792813 -95 TCTCGAAAATTTTCTTCGAACCCGAAAATAT 4 47 1 TTTCTTCAAC 0.965768 -34 TAAGGTATAGTATCTTCCAGCACTATGGAAG 5 20 0 TATCTTCAGC 0.945197 -281 AGACTTCGATTTTCTGGAAGCACTCTTCCTT 5 50 1 TTTCTGGAGC 0.981782 -251 TATAGTCAAATTTCTGTCAGCTGAGAAGATC 5 227 1 TTTCTGTAGC 0.931336 -74 ******* *** Masking position 5 Map Score: 2.75467 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 401 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 GTTACCAAATTCCTCAAGCGGTTCCACCAA 1 183 0 TCCTCAAGCG 0.975442 -118 GATAGATAACTCCCCAAGGGTGCCTCGCAT 1 223 1 TCCCCAAGGG 0.983861 -78 TCTGTTTGGGTCGCTAAGGTCAGAAATCCA 2 47 0 TCGCTAAGGT 0.915567 -172 CCTGCTTTCTTCCCTAAGCTTGCCTGTTAG 2 122 1 TCCCTAAGCT 0.98898 -97 CTCATGGTATTCCCTCAACGTTTTTCCCCC 2 169 1 TCCCTCAACG 0.908994 -50 ACACTCTCCTTAATCTAAGGCATAGA 4 7 1 TCCTTAATCT 0.854372 -74 ********** Masking position 7 Map Score: 1.13394 Number of sites scoring better than the average of aligned sites = 525 Number in coding regions = 462 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 CCCTTTTCAGTGGTCAGTTACCAGTTAGTC 1 36 0 TGGTCAGTTA 0.892185 -265 AAGGGTGCAAAGGTGCGGTAAGAGCGCACC 1 67 1 AGGTGCGGTA 0.947975 -234 TCGATACTGCTGGTGCGCTCTTACCGCACC 1 78 0 TGGTGCGCTC 0.96973 -223 CGAGAGGTACTGGCTCGGTAAACCCCGGTT 1 105 1 TGGCTCGGTA 0.96145 -196 GAGGCACCCTTGGGGAGTTATCTATCTGGG 1 219 0 TGGGGAGTTA 0.94841 -82 GCAATCTGTTTGGGTCGCTAAGGTCAGAAA 2 51 0 TGGGTCGCTA 0.978538 -168 TTAGCGATTATGGTTCGTTTGCTCATGGTA 2 148 1 TGGTTCGTTT 0.927315 -71 ********** Masking position 9 Map Score: 1.57983 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 353 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TTAGTCAGCAGAAAAACCCTGTTAACTGTT 1 12 0 GAAAAACCCT 0.969919 -289 CGCTAAGGTCAGAAATCCATCCTCCACCCC 2 36 0 AGAAATCCAT 0.71946 -183 AAACGTTGAGGGAATACCATGAGCAAACGA 2 162 0 GGAATACCAT 0.892587 -57 ATGGGAGGGGGAAAAACGTTGAGGGAATAC 2 175 0 GAAAAACGTT 0.797662 -44 AAGGAAACACTTCCATAGTGC 5 2 1 AGGAAACACT 0.803817 -299 TTTCCTCTTTAAAAAACCTTCTTCCTAGGA 5 158 1 AAAAAACCTT 0.928183 -143 TGATTGGTACGAGAAACCTTATAAAATCCT 5 184 0 GAGAAACCTT 0.95258 -117 ACTCTAAAAAAGGATACCCTTTT 5 288 1 AGGATACCCT 0.911419 -13 ********** Masking position 4 Map Score: 0.946967 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 854 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 7 ********** No masking Map Score: -1.13444e-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 TGGTCAGTTACCAGTTAGTCAGCAGAAAAAC 1 25 0 CAGTTAGTCA 0.824487 -276 GTTTACCGAGCCAGTACCTCTCGATACTGCT 1 97 0 CAGTACCTCT 0.902768 -204 AATTTGTTACCAAATTCCTCAAGCGGTTCCA 1 187 0 CAATTCCTCA 0.968508 -114 AATTTGGTAACAAATTTCCCAGATAGATAAC 1 202 1 CAATTTCCCA 0.798184 -99 CTCCCATTTGCTATCTCGTCACTGGGGTTGG 2 198 1 CATCTCGTCA 0.938582 -21 GCAGTTTGAACAAGCATCTCAAGGAATAGAA 5 82 0 CAGCATCTCA 0.923301 -219 CTTGGATTCACTATTTCCTCTTTAAAAAACC 5 145 1 CATTTCCTCT 0.941631 -156 GAGTTCTTAACGATCTTCTCAGCTGACAGAA 5 238 0 CATCTTCTCA 0.954364 -63 * ********* Masking position 3 Map Score: 1.23024 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 429 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 9 ********** No masking Map Score: -1.13444e-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: -1.13444e-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: -1.13444e-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