AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i143_synecho_ctra_300.orf -o143_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 RCY35517 107 Synechocystis #2 RCY39915 204 Synechocystis #3 RCY29136 46 Synechocystis #4 RCY46165 41 Synechocystis #5 RCY08256 276 Synechocystis #6 RCT00013 300 Chlamydia_trachomatis Motif number 1 CTGTGCCATTGGGGGGAGAAGAATTAGCCATT 1 28 1 GGGGGAGAGA 0.970017 -80 GAAAAATCCCTGATGGGGAAAGCTTACGAGAA 2 55 0 TGAGGGGAAG 0.832221 -150 AGTAGCATATGGATCGAGAGAAAAATCCCTGA 2 74 0 GGACGAGAAA 0.937378 -131 GGTTGGTGCCGGATGGGCCAAAAAAAGTAGCA 2 99 0 GGAGGGCCAA 0.992576 -106 TGGGAGGACGGGACGGGGCGAAACAGGGCCTT 2 162 0 GGAGGGGCAA 0.99566 -43 AGTGGGGCCGGGAAAAATAGGGGAAT 3 31 0 GGGCGGGAAA 0.982039 -16 AATCACCACTGTGCGGAGAGAATCAAATAATT 4 20 1 GTGGGAGAAA 0.869143 -22 GTCTCAGCCAGGATGGGGCGGAGAGTTTGGTA 5 50 1 GGAGGGGCGA 0.988771 -227 GCAGGGGATAGGGTGGGCACAACTCTCTTCTT 5 207 1 GGGGGGCAAA 0.992576 -70 AACTTATTACGGATGAACCGAAGTCAAGGAAG 6 112 1 GGAGAACCAA 0.883286 -189 GTTTTTGATTTGGAGAGCCAAAT 6 288 1 TGGGAGCCAA 0.809837 -13 *** ***** ** Masking position 12 Map Score: 13.222 Number of sites scoring better than the average of aligned sites = 2418 Number in coding regions = 2194 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 229 Fraction of orfs with sites within 600 bp upstream = 0.0367812 Motif number 2 GCTAATTCTTCTCCCCCCAATGGCACAGGTA 1 25 0 CTCCCCCAAT 0.933671 -83 TTGTAAACACCCCACACCACCAGCAATGGCT 1 53 0 CCCCACCACC 0.988414 -55 TTTGGCCCATCCGGCACCAACCTCCCACCAG 2 109 1 CCGCACCAAC 0.969463 -96 CGGCACCAACCTCCCACCAGTACCCTCCAAG 2 120 1 CTCCACCAGT 0.943424 -85 CTGTTTCGCCCCGTCCCGTCCTCCCACTGCT 2 168 1 CCGCCCGTCC 0.931583 -37 CCTATTTTTCCCGGCCCCACT 3 36 1 CCGCCCCACT 0.994942 -11 ATTATAAGCAATCACCACTGTGCGGAGAG 4 9 1 CAACACCACT 0.916868 -33 AGACGCGATACAACCCCCACTTTTTGTCTTG 5 23 0 CAACCCCACT 0.954498 -254 ACCAAACTCTCCGCCCCATCCTGGCTGAGAC 5 50 0 CCGCCCATCC 0.901835 -227 TGTGCCCACCCTATCCCCTGCTCAAAACTAA 5 197 0 CTACCCCTGC 0.915121 -80 GCACGTTTCCCTGTCACCAGTTGTTAAAACA 6 227 0 CTGCACCAGT 0.964451 -74 *** ******* Masking position 5 Map Score: 12.0923 Number of sites scoring better than the average of aligned sites = 2869 Number in coding regions = 2705 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 3 AATAACAGGGCAACCAGTTGGAGTAATTGA 1 82 1 CAACCAGTTG 0.882913 -26 CCACTGCTATCTAGGAGCTTGCCC 2 191 1 CTAGGAGCTT 0.961436 -14 TAAGATAACCCTAGCAGTTGAAGTGTTTTC 6 42 1 CTAGCAGTTG 0.988759 -259 TTCAGCAAAACAAGAAGCTGTACCAACTCC 6 78 1 CAAGAAGCTG 0.979337 -223 TAATAAGTTTCAAGGAGTTGGTACAGCTTC 6 91 0 CAAGGAGTTG 0.986263 -210 AAAAAGAATACTAGAAGTTTTTGATTTGGA 6 272 1 CTAGAAGTTT 0.951076 -29 ********** Masking position 6 Map Score: 5.42483 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 127 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 TTCTTCTCCCCCCAATGGCACAGGTAATTC 1 21 0 CCCAATGGCA 0.979543 -87 AAGACGGATACCCTAAGGCCCTGTTTCGCC 2 148 1 CCCTAAGGCC 0.994776 -57 TCAATTATTCACCTATGGCGTGAGTCAGCA 5 120 1 ACCTATGGCG 0.951159 -157 GTTGTGCCCACCCTATCCCCTGCTCAAAAC 5 200 0 CCCTATCCCC 0.956552 -77 TGAGTCCTTTCCCAAAGGCCTTCTTAAGAC 6 144 0 CCCAAAGGCC 0.992532 -157 ********** Masking position 5 Map Score: 3.08012 Number of sites scoring better than the average of aligned sites = 403 Number in coding regions = 355 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 5 GGGTGTTTACAATAACAGGGCAACCAGTTGGAGT 1 72 1 ATACAGCAAC 0.976251 -36 TAGAGGCTTAACTATAAGTCCACCAAAAGATAGA 5 80 1 ATAAAGCACC 0.95861 -197 CCTGCTCAAAACTAACAGAAATCCCAGGTAAAGT 5 178 0 ATACAGATCC 0.963227 -99 TTAAACTCTAACTATCAGAAAACCATTTAGGAGC 5 242 1 ATACAGAACC 0.992136 -35 TACGAACATCTATATAAGATAACCCTAGCAGTTG 6 28 1 TTAAAGAACC 0.937394 -273 TGTTTTCATTATTTTCAGCAAAACAAGAAGCTGT 6 65 1 ATTCAGAAAC 0.963734 -236 CCATTAACTGTCTTCCAGCTAAACTAGGGATGAG 6 170 0 TTTCAGAAAC 0.920388 -131 * ** *** **** Masking position 7 Map Score: 2.20119 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 129 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 CTCCCCCCAATGGCACAGGTAATTCGATACCA 1 14 0 TGGACAGGAA 0.946716 -94 ACTGGAACAGATTAAAATAAATTC 3 3 1 TGGACAGATA 0.918043 -44 GCGGAGAGTTTGGTAGAGGCTTAACTATAAGT 5 67 1 TGGAGAGGTT 0.976011 -210 TTCAAGGAGTTGGTACAGCTTCTTGTTTTGCT 6 81 0 TGGACAGCTC 0.933129 -220 AGAAGGCCTTTGGGAAAGGACTCATCCCTAGT 6 150 1 TGGAAAGGCT 0.982907 -151 AGACAGTTAATGGCAAAGTATTTTGTGGAAAA 6 191 1 TGGAAAGTTT 0.930028 -110 AAGTATTTTGTGGAAAAGGGCTGTTTTAACAA 6 206 1 TGGAAAGGCT 0.982907 -95 *** ***** ** Masking position 7 Map Score: 1.99226 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 342 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ********** No masking Map Score: -3.39396e-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 ********** No masking Map Score: -3.39396e-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 9 ********** No masking Map Score: -3.39396e-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