AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i262_synecho_ctra_300.orf -o262_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 RCY35276 173 Synechocystis #2 RCT00511 62 Chlamydia_trachomatis #3 RCT00512 300 Chlamydia_trachomatis Motif number 1 AATTTTGGTAGGCCTAGGGGTCAGCATTGCC 1 99 1 GGCTAGGGGT 0.938013 -75 GAGTTTTATGGGGATGGGGCCGCCTTGGCAA 1 125 0 GGGTGGGGCC 0.996962 -49 ACCAAGAGTTAGGTCCCGACCAACCC 2 47 0 GAGTAGGTCC 0.980613 -16 AAAACGTAATGAGCTTGTGCCTAACGGAAAA 3 69 1 GAGTTGTGCC 0.963072 -232 CCATGCTCTAGGGGTAGGGGCATCCTGAATC 3 118 0 GGGTAGGGGC 0.998349 -183 AGAGCATGGGGAGGTTAGGCCTGTTTTGCTT 3 140 1 GAGTTAGGCC 0.969015 -161 GTAGAGAACAGGGATATGGGCGGAAAGGCTT 3 206 1 GGGTATGGGC 0.989473 -95 *** ******* Masking position 5 Map Score: 8.83112 Number of sites scoring better than the average of aligned sites = 1127 Number in coding regions = 1056 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 2 GGAGTAGGGAAAGGATGAACGCCTGGACTG 1 17 1 AAGGATGAAC 0.931155 -157 AATTAGATACAAAGCTTAACAAATTTTGGT 1 78 1 AAAGCTTAAC 0.856275 -96 TGCTGACCCCTAGGCCTACCAAAATTTGTT 1 95 0 TAGGCCTACC 0.942778 -79 CCGCCTTGGCAATGCTGACCCCTAGGCCTA 1 107 0 AATGCTGACC 0.959022 -67 CAGCATTGCCAAGGCGGCCCCATCCCCATA 1 120 1 AAGGCGGCCC 0.986202 -54 ATATTCTTAAAACGTTTCCCAT 1 162 1 AACGTTTCCC 0.818155 -12 GTAGTCGATTCAGGATGCCCCTACCCCTAG 3 112 1 CAGGATGCCC 0.967832 -189 AAAAGCAAAACAGGCCTAACCTCCCCATGC 3 143 0 CAGGCCTAAC 0.93642 -158 TATGGGCGGAAAGGCTTCCCTTTAGAAGGA 3 220 1 AAGGCTTCCC 0.994488 -81 ********** Masking position 2 Map Score: 7.88633 Number of sites scoring better than the average of aligned sites = 1103 Number in coding regions = 1013 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 AAAGTCTTATTGAAAAACGTAATGAGCTTGTG 3 56 1 TGAAAAGTAA 0.960609 -245 AATGAGCTTGTGCCTAACGGAAAATCATGATA 3 76 1 TGCTAAGGAA 0.985567 -225 AAAAGTATTTTTACAAAAAGCAAAACAGGCCT 3 156 0 TTAAAAAGCA 0.786976 -145 ACCAGCCTCCTTCTAAAGGGAAGCCTTTCCGC 3 225 0 TTCAAAGGAA 0.966172 -76 AGGAGGCTGGTGATTAAAAGAAGAATCAGTTT 3 246 1 TGATAAAGAA 0.947411 -55 TTTTTTCAGTTGCTTAATGGCAAACTGATTCT 3 267 0 TGCTAAGGCA 0.949721 -34 ATTAAGCAACTGAAAAAAGTAAGGATAAGT 3 281 1 TGAAAAGTAA 0.960412 -20 *** *** **** Masking position 6 Map Score: 4.35923 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 368 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 4 GTTCATCCTTTCCCTACTCCGCCATT 1 7 0 TCCCTACTCC 0.9905 -167 CTGAATCGACTACATGCTATCATGATTTTC 3 95 0 TACATGCTAT 0.777427 -206 ATTCAGGATGCCCCTACCCCTAGAGCATGG 3 119 1 CCCCTACCCC 0.96933 -182 GCCTAACCTCCCCATGCTCTAGGGGTAGGG 3 130 0 CCCATGCTCT 0.982268 -171 CCCTGTTCTCTACCTACTCTCACTTCCTTG 3 189 0 TACCTACTCT 0.977008 -112 TCCGCCCATATCCCTGTTCTCTACCTACTC 3 200 0 TCCCTGTTCT 0.968346 -101 ********** Masking position 5 Map Score: 3.50875 Number of sites scoring better than the average of aligned sites = 921 Number in coding regions = 816 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 5 GCCAATCTGTAACATTTTTTGACAGATCCA 1 45 0 AACATTTTTT 0.804823 -129 TAGGCCTACCAAAATTTGTTAAGCTTTGTA 1 85 0 AAAATTTGTT 0.904371 -89 GTCGAGCAAGAAAATCATTTCT 3 3 0 AAAATCATTT 0.890813 -298 TGCTCGACATAGAAGTTTTTCATTTGAATT 3 25 1 AGAAGTTTTT 0.878439 -276 ACTTCCTTGCAAAAGTATTTTTACAAAAAG 3 168 0 AAAAGTATTT 0.890813 -133 GATTAAAAGAAGAATCAGTTTGCCATTAAG 3 257 1 AGAATCAGTT 0.902632 -44 ********** Masking position 4 Map Score: 0.885462 Number of sites scoring better than the average of aligned sites = 728 Number in coding regions = 565 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 6 ********** No masking Map Score: -1.75204e-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 7 ********** No masking Map Score: -1.75204e-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: -1.75204e-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