AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i263_synecho_ctra_300.orf -o263_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 RCY05387 284 Synechocystis #2 RCY20297 90 Synechocystis #3 RCY31385 125 Synechocystis #4 RCY08522 85 Synechocystis #5 RCT00738 300 Chlamydia_trachomatis Motif number 1 GCAAAGTGAGGAAAACCGCATATTCCCGTTGTGGTTC 1 89 0 GACCATATTC 0.935367 -196 TCCTCACTTTGCTGACCTCAACTTGCCCCATACGGCC 1 114 1 GGCCAACTTC 0.996346 -171 AATCGGTGTAGTTGACCCCATGCTTTCCCGGAGGAAA 1 212 0 GGCCATGCTC 0.978634 -73 GCCGTGGAGGCGCATCCCAAACTTCATCCTAACACGG 2 35 0 CACCAACTTT 0.885622 -56 GATGCGCCTCCACGGCCGAATATTTCCTGTGCAAACT 2 56 1 CGCCATATTC 0.957909 -35 CGCTCCTAAGGGTGGCTAAAACTTTGCATAAAAAACG 3 22 1 GGCTAACTTC 0.957222 -104 ACAACAAACGGCGGGCCGAAACCCACCGATCGCCGTT 3 55 0 GGCCAACCCC 0.980412 -71 CACTAGAAAAGTAACCCTTAACCTGTCCATCGTTTTT 4 38 1 GACCAACCTC 0.985016 -48 GTTTTTTGGAGTTGACCGAATCCTAAT 4 69 1 GGCCATCCTT 0.988912 -17 GGATAGCAGAGAAGTCCTAATCTTGCTCTGGCATGGA 5 90 1 GGCCATCTTT 0.989623 -211 AGAAAAAAAGCTCGACCTTATCTTAGATAATCGGGTA 5 258 1 CGCCATCTTA 0.93631 -43 * * ** ***** * Masking position 10 Map Score: 11.812 Number of sites scoring better than the average of aligned sites = 584 Number in coding regions = 531 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 CCGGTGGTGGCCCCCAGGGCCGTATGGGGCAA 1 136 0 CCCCAGGCCG 0.991656 -149 GCCCTGGGGGCCACCACCGGGGATAGTATGAA 1 148 1 CCACACGGGG 0.591577 -137 AGCAGTGGTTGACCTATGAGCGAAATTAAACT 1 263 0 GACCAGAGCG 0.929616 -22 GCTCCTGGTGCCCCGATGACGGGCC 2 4 0 CCCCAGACGG 0.798234 -87 GTCATCGGGGCACCAGGAGCCGTGTTAGGATG 2 16 1 CACCGAGCCG 0.925614 -75 TTGGGATGCGCCTCCACGGCCGAATATTTCCT 2 52 1 CCTCAGGCCG 0.986783 -39 GTTTTAGCCACCCTTAGGAGCGCTAAAAATAG 3 12 0 CCCTAGAGCG 0.945025 -114 GGCCGAAACCCACCGATCGCCGTTTTTTATGC 3 47 0 CACCACGCCG 0.98557 -79 AAACCCCAGACAACAAACGGCGGGCCGAAACC 3 69 0 CAACACGGCG 0.97502 -57 **** * ***** Masking position 12 Map Score: 8.92053 Number of sites scoring better than the average of aligned sites = 1438 Number in coding regions = 1366 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 TGGGTAGAAGGAACCACAACGGGAATATGC 1 79 1 GAACCACAAC 0.900615 -206 ACGGCCCTGGGGGCCACCACCGGGGATAGT 1 145 1 GGGCCACCAC 0.987038 -140 AATGATCACAGGTTCACAACAGTTTCCTCC 1 190 1 GGTTCACAAC 0.945842 -95 GAAAGCATGGGGTCAACTACACCGATTCCC 1 222 1 GGTCAACTAC 0.989408 -63 TTCGCTCATAGGTCAACCACTGCT 1 271 1 GGTCAACCAC 0.99018 -14 ATTAGGATTCGGTCAACTCCAAAAAACGAT 4 66 0 GGTCAACTCC 0.966362 -20 CCTCTAGCGAGATCCCCTACTCTTTGAAGA 5 165 0 GATCCCCTAC 0.941844 -136 ********** Masking position 7 Map Score: 7.14752 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 300 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 TCAGCAAAGTGAGGAAAACCGCATATTCCC 1 99 0 GAGGAAAACC 0.951209 -186 GAAGAATTGTGAAAATGATCACAGGTTCAC 1 177 1 GAAAATGATC 0.855563 -108 TGTTCATGATGAGAACGATCGCAAAATGTT 5 17 1 GAGAACGATC 0.956063 -284 AAAATGTTGCGAGAAAAGCCTTAGCTCTTT 5 39 1 GAGAAAAGCC 0.964078 -262 CTAGGTTTTTGAGAAAGCTCTTCAAAGAGT 5 147 1 GAGAAAGCTC 0.974066 -154 TTTTTCTAAAGAGAAAAATCCCTTTGAGCC 5 235 0 GAGAAAAATC 0.983765 -66 TTTCTCTTTAGAAAAAAAGCTCGACCTTAT 5 249 1 GAAAAAAAGC 0.862315 -52 AAACTGGCCTGAGAATACCCGATTATCTAA 5 280 0 GAGAATACCC 0.953966 -21 ********** Masking position 5 Map Score: 5.89014 Number of sites scoring better than the average of aligned sites = 339 Number in coding regions = 281 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 CCCCATACGGCCCTGGGGGCCACCACCGGG 1 139 1 CCCTGGGGGC 0.99309 -146 ACTGTTGTGAACCTGTGATCATTTTCACAA 1 183 0 ACCTGTGATC 0.922997 -102 ACTTAATTAAACTTGGGAATCGGTGTAGTT 1 236 0 ACTTGGGAAT 0.811141 -49 GCAGTGGTTGACCTATGAGCGAAATTAAAC 1 264 0 ACCTATGAGC 0.967917 -21 TTTTAGCCACCCTTAGGAGCGCTAAAAATA 3 13 0 CCTTAGGAGC 0.979605 -113 TAGCTAGAACCCCTGGGAATATTGTGC 4 8 0 CCCTGGGAAT 0.965647 -78 TCTCTGCTATCCTTATGGACATATTTTTAT 5 72 0 CCTTATGGAC 0.892516 -229 AGAGAAAAATCCCTTTGAGCCCTAGCTCTC 5 226 0 CCCTTTGAGC 0.968418 -75 ********** Masking position 4 Map Score: 5.54866 Number of sites scoring better than the average of aligned sites = 1399 Number in coding regions = 1258 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 6 GGGGGCCACCACCGGGGATAGTATGAAGAAT 1 153 1 ACCGGGATAG 0.899651 -132 CTAAGGGAAGTTTGCACAGGAAAT 2 77 0 AGGGAGTTTG 0.855715 -14 AGCGCTCCTAAGGGTGGCTAAAACTTTGCAT 3 20 1 AGGGGGCTAA 0.955532 -106 GTTTTTGGAGACTGGGGCTAGTAGTAAATTT 3 97 1 ACTGGGCTAG 0.985704 -29 TTACTTTTCTAGTGTAGCTAGAACCCCTGGG 4 21 0 AGTGAGCTAG 0.97067 -65 TTGCTCTGGCATGGAAGTTAGCTTGAGTACG 5 112 1 ATGGAGTTAG 0.892815 -189 TAGCTTGAGTACGGTGACTAGGTTTTTGAGA 5 130 1 ACGGGACTAG 0.965782 -171 AAGAATATCCACGAGAGCTAGGGCTCAAAGG 5 214 1 ACGAAGCTAG 0.946792 -87 **** ****** Masking position 1 Map Score: 3.08153 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 450 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 7 CCTACGATTGTCTACAGAGAGTAAGGCTCA 1 23 1 TCTACAGAGA 0.972738 -262 ACTTTTCTAGTGTAGCTAGAACCCCTGGGA 4 20 0 TGTAGCTAGA 0.670368 -66 GATCGCAAAATGTTGCGAGAAAAGCCTTAG 5 33 1 TGTTGCGAGA 0.927944 -268 TTGAGAAAGCTCTTCAAAGAGTAGGGGATC 5 155 1 TCTTCAAAGA 0.789146 -146 GCCTCTTTCCTCTAGCGAGATCCCCTACTC 5 173 0 TCTAGCGAGA 0.628888 -128 GAGCTTTTTTTCTAAAGAGAAAAATCCCTT 5 241 0 TCTAAAGAGA 0.936239 -60 ********** Masking position 3 Map Score: 2.51271 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 33 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 TTTTTATGCAAAGTTTTAGCCACCCTTAGGA 3 25 0 AAGTTTAGCC 0.893817 -101 ATATTCCCAGGGGTTCTAGCTACACTAGAAA 4 16 1 GGGTCTAGCT 0.988862 -70 GTTGCGAGAAAAGCCTTAGCTCTTTGAAATA 5 44 1 AAGCTTAGCT 0.950213 -257 CAAAGAGTAGGGGATCTCGCTAGAGGAAAGA 5 169 1 GGGTCTCGCT 0.970127 -132 AAATCCCTTTGAGCCCTAGCTCTCGTGGATA 5 219 0 GAGCCTAGCT 0.988866 -82 TATCTAAGATAAGGTCGAGCTTTTTTTCTAA 5 256 0 AAGTCGAGCT 0.961406 -45 *** ******* Masking position 3 Map Score: 1.97905 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 79 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 ********** No masking Map Score: -1.51813e-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: -1.51813e-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: -1.51813e-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