AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i149_synecho_ctra_300.orf -o149_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 RCY51535 95 Synechocystis #2 RCY29531 40 Synechocystis #3 RCY10065 104 Synechocystis #4 RCY35156 33 Synechocystis #5 RCY03241 110 Synechocystis #6 RCT00097 300 Chlamydia_trachomatis #7 RCT00513 300 Chlamydia_trachomatis Motif number 1 AAACCTGTCTAGGCATGGGTATCAAGCGGCGATCGCCTG 3 55 1 ACTGGGTAGG 0.961213 -50 CAAGCGGCGATCGCCTGGGGCAATTTCGGTGTTGAACC 3 77 1 TCTGGGATGG 0.982056 -28 TGACAGTCCTTTCCATGGGGATGTTTAGATGGAATATTT 6 123 0 TCTGGGTTGA 0.987112 -178 AGGACTGTCAATCCTTGAGATTTTCAAGGATATCGGAGG 6 152 1 ACTGAGTTGG 0.964598 -149 CGGGAACCTTTTTCCTGCGTATTTAAAGCTCTTTTATCT 6 251 1 TCTGCGTTGC 0.981122 -50 TATACTGGCCTCTCATGCAGCTATGGCGGAACCGGTAGA 7 38 1 TCTGCATTGG 0.981898 -263 CTAGAACCTGAATCTAGCGCGTCTACCGGTTCCGCCATA 7 59 0 ACAGCGTTGG 0.978229 -242 CAGATGCCCCTGTCCCGGGCGTTTGTTGAAAAGAAGTTT 7 137 0 TCCGGGTTGA 0.953147 -164 CTAGCCCCGTTTGCTTGCGGTTCTTAGGGAAGCCCTGAA 7 225 1 TCTGCGTTGG 0.996826 -76 ATGTAAATCCTTGCTAGGAGGTTTCAGGGCTTCCCTAAG 7 247 0 TCAGGATTGG 0.955052 -54 * * **** * * ** Masking position 4 Map Score: 10.8463 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 255 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 TTGGGAATTTTTTTCGCTAGAGACA 1 81 1 TTTTCGCTAG 0.983524 -15 GGTATTTTCCCTCGCAAAGATATT 2 27 0 TTTTCCCTCG 0.989459 -14 TCAGCGACAATTTTCCCTAGTCCCATTAAA 3 18 0 TTTTCCCTAG 0.99379 -87 AAAGGCAAGATTTCCCTTGCACTACAAGT 6 10 1 ATTTCCCTTG 0.961636 -291 ATTAAAAAAAGTTTCACTAGTTTCTGTGTA 6 58 1 GTTTCACTAG 0.959394 -243 ********** Masking position 4 Map Score: 4.25266 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 123 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 GGGAAAATTGTCGCTGAAAAATCCAAACCTGTCT 3 31 1 TGCGAAAATC 0.951001 -74 AACCCGACTTTTTCCGCAAACGACATTCATCCCC 6 190 0 TTCGAAACGC 0.995442 -111 ATAGTTCCTTTTTTTGTAAAAGCCGGGAACCTTT 6 228 1 TTTGAAAAGC 0.942385 -73 CAAGTCTTCTTAGCTGCAAACTTCTTTTCAACAA 7 120 1 TGCGAAACTC 0.975661 -181 GCAAACTTCTTTTCAACAAACGCCCGGGACAGGG 7 135 1 TTCAAAACGC 0.965899 -166 AGCCATAACCTCTACGAAAAAGTCAAGACAGATG 7 170 0 TTAGAAAAGC 0.942386 -131 CTAACTGGCCTTTCAGAACACGGCTAGCCCCGTT 7 202 1 TTCGACACGC 0.985336 -99 * ** * ***** * Masking position 8 Map Score: 3.47237 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 135 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 4 GCAAGGGAAATCTTGCCTTT 6 1 0 TCTTGCCTTT 0.976073 -300 ACTATAACCAACCCGACTTTTTCCGCAAAC 6 203 0 ACCCGACTTT 0.958708 -98 GGAAAAAGGTTCCCGGCTTTTACAAAAAAA 6 236 0 TCCCGGCTTT 0.951255 -65 TTCTCTCTATACTGGCCTCTCATGCAGCTA 7 31 1 ACTGGCCTCT 0.958077 -270 GGGGCATCTGTCTTGACTTTTTCGTAGAGG 7 166 1 TCTTGACTTT 0.947659 -135 GTTATGGCTAACTGGCCTTTCAGAACACGG 7 195 1 ACTGGCCTTT 0.984007 -106 ********** Masking position 8 Map Score: 3.07736 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 64 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 CGTTACACTGAAAATAAGCAGAGTATTAAG 1 25 1 AAAATAAGCA 0.946449 -71 TAAGAATTATTAAATAAGTATCACCATGGG 1 51 1 TAAATAAGTA 0.923545 -45 AATGGACAAATAAATACGGAGCTAGGTTTT 5 46 0 TAAATACGGA 0.9755 -65 CGGCTTTTACAAAAAAAGGAACTATAACCA 6 223 0 AAAAAAAGGA 0.863968 -78 AAAAGAGCTTTAAATACGCAGGAAAAAGGT 6 256 0 TAAATACGCA 0.964709 -45 ACATAGATTTTAAATTAGGAACAAGTTTT 7 282 1 TAAATTAGGA 0.922179 -19 ********** Masking position 4 Map Score: 2.74925 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 39 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 TTAAGCCGAGGAGAGGCCCC 5 101 1 GAGAGGCCCC 0.990799 -10 GGGAACCCCCAATATGAACT 6 291 0 GGGAACCCCC 0.961602 -10 AAAGTCAAGACAGATGCCCCTGTCCCGGGC 7 156 0 CAGATGCCCC 0.959647 -145 TTCAGAACACGGCTAGCCCCGTTTGCTTGC 7 213 1 GGCTAGCCCC 0.97609 -88 GCGGTTCTTAGGGAAGCCCTGAAACCTCCT 7 241 1 GGGAAGCCCT 0.988935 -60 ********** Masking position 7 Map Score: 2.66271 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 253 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 ATACGGAGCTAGGTTTTAGCTCATCCAAAG 5 33 0 AGGTTTTAGC 0.962543 -78 GAGATTTTCAAGGATATCGGAGGGGGATGA 6 168 1 AGGATATCGG 0.902135 -133 AAAGTCGGGTTGGTTATAGTTCCTTTTTTT 6 213 1 TGGTTATAGT 0.831708 -88 CGCAGGAAAAAGGTTCCCGGCTTTTACAAA 6 240 0 AGGTTCCCGG 0.96997 -61 CGCTAGATTCAGGTTCTAGTGAGCTTTTGC 7 79 1 AGGTTCTAGT 0.962543 -222 TTTTTCGTAGAGGTTATGGCTAACTGGCCT 7 183 1 AGGTTATGGC 0.943142 -118 CCTTGCTAGGAGGTTTCAGGGCTTCCCTAA 7 248 0 AGGTTTCAGG 0.961815 -53 ********** Masking position 5 Map Score: 2.16449 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 188 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 8 TATACTAAGAATAGAAACTTTGGATGAGCT 5 16 1 ATAGAAACTT 0.818934 -95 TCTCTTTATTAAAAAAAGTTTCACTAGTTT 6 51 1 AAAAAAAGTT 0.889231 -250 TTTTACAAAAAAAGGAACTATAACCAACCC 6 219 0 AAAGGAACTA 0.646714 -82 AAATACGCAGGAAAAAGGTTCCCGGCTTTT 6 245 0 GAAAAAGGTT 0.749442 -56 GAACTTAGATAAAAGAGCTTTAAATACGCA 6 266 0 AAAAGAGCTT 0.961762 -35 GGAACCCCCAATATGAACTTAGATAAAAGA 6 280 0 ATATGAACTT 0.691032 -21 AGCTGTTTTAATAAAAGGTT 7 1 0 ATAAAAGGTT 0.897376 -300 ACCTTTTATTAAAACAGCTTTCTCTCTATA 7 12 1 AAAACAGCTT 0.852225 -289 GCGTTTGTTGAAAAGAAGTTTGCAGCTAAG 7 128 0 AAAAGAAGTT 0.940378 -173 TAAATCCTTGCTAGGAGGTTTCAGGGCTTC 7 253 0 CTAGGAGGTT 0.76803 -48 ********** Masking position 6 Map Score: 1.06568 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 405 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 9 TGTTAGAACTGGATTAATATCTTTGCGAGG 2 12 1 GGATTAATAT 0.966748 -29 GGATTTATACTAAGAATAGA 5 1 1 GGATTTATAC 0.944707 -110 GCCTCTCCTCGGCTTAATATTGGTTAACTA 5 88 0 GGCTTAATAT 0.931702 -23 AAAATCTCAAGGATTGACAGTCCTTTCCAT 6 146 0 GGATTGACAG 0.941678 -155 CTCCTAGCAAGGATTTACATAGATTTTAAA 7 266 1 GGATTTACAT 0.970367 -35 ********** Masking position 5 Map Score: 0.314715 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 47 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ATACCCATGCCTAGACAGGTTTGGATTTTTCAGCGA 3 41 0 CTGAATTTGT 0.966512 -64 CGGCGATCGCCTGGGGCAATTTCGGTGTTGAACC 3 81 1 CTGGCTTTGT 0.992063 -24 CTCCGTATTTATTTGTCCATTTAGTTCTGTCATTAG 5 55 1 ATTGCTTTGT 0.934515 -56 TCACTAGTTTCTGTGTAATTTTAGTTTTAGATTTTG 6 71 1 CTTGATTTGT 0.980747 -230 AGTCCTTTCCATGGGGATGTTTAGATGGAATATTTA 6 122 0 ATGGATTTGT 0.980508 -179 GATTCAGGTTCTAGTGAGCTTTTGCTCATGGAAGTT 7 84 1 CTGTATTTGT 0.966543 -217 ** ** * *** * * Masking position 10 Map Score: 0.225832 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 108 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ********** No masking Map Score: 1.37378e-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: 1.37378e-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 13 ********** No masking Map Score: 1.37378e-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