AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_synecho_ctra_100.orf -o060_synecho_ctra_100.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 RCY32906 29 Synechocystis #2 RCY06983 300 Synechocystis #3 RCY44336 300 Synechocystis #4 RCY38981 59 Synechocystis #5 RCY43130 300 Synechocystis #6 RCT00346 236 Chlamydia_trachomatis Motif number 1 CCGTTAACCCAGGGCAAGCACTGGATG 1 13 0 GACCGGGCAA 0.977339 -17 TGGACGTAGATTTGACCTTGGACATCATCAAACAT 2 87 1 TACCGGACAT 0.978839 -214 TAAGATTCAGTACAAACTAGGGGAAAACGTTCAGG 2 122 0 TAACGGGGAA 0.962615 -179 TTTTGCTAGCCCAGACGACGGGCGATCGCCGTGAA 2 185 0 CACGGGGCGA 0.937573 -116 TCTGGGCTAGCAAAACCAAGGGGATCAGTTGGGAT 2 205 1 CACCGGGGAT 0.973849 -96 TCGAAAATGGTTGTAGCATGGACAACAAGGGATCA 2 257 1 TAGCGGACAA 0.904493 -44 CGGGTGCCATTTTTTCCTAGGGCGAGAATCTTTTC 3 32 1 TTCCGGGCGA 0.967984 -269 ATCAATGATTTTTCTAGCTGGACAATTCAATAATG 3 110 1 TTAGGGACAA 0.735132 -191 AAAAACTAATTGTGACGCAGGGCATTGCCCCCTAA 3 155 0 TACGGGGCAT 0.981721 -146 CTAATCGGGATCGAAAGATGGGCAACGCAGTCAGA 3 258 0 TAAGGGGCAA 0.949361 -43 AGGCAAATTACTCCTAGGAGAAATTTGCCGAG 5 8 1 TTCCGGAGAA 0.950331 -293 AGTTAGAATGCGGAACCCGGGACTTGAACCCGGAA 5 73 1 CACCGGACTT 0.730075 -228 TGACTTCCAGTCAATCCTGGGGGATGATGGTCTTT 5 186 0 TTCCGGGGAT 0.96859 -115 TTAATTTTTTTGATACCATGGGGAACTGCCGACTT 5 250 1 TACCGGGGAA 0.992327 -51 * *** ****** Masking position 10 Map Score: 14.6917 Number of sites scoring better than the average of aligned sites = 2494 Number in coding regions = 2275 Number in noncoding regions = 219 Number of orfs with sites within 600 bp upstream = 228 Fraction of orfs with sites within 600 bp upstream = 0.0366206 Motif number 2 AAAACCAAGGGGATCAGTTGGGATCAGTCCTCC 2 216 1 GGAAGTGGGA 0.991118 -85 GTTGTAGCATGGACAACAAGGGATCAGTCCGCT 2 266 1 GGAACAGGGA 0.816819 -35 TCTCGCCCTAGGAAAAAATGGCACCCGGCTTAT 3 26 0 GGAAATGGCA 0.987766 -275 CAGGCCGGTTTGAGAGAATGGGACTAAATCAAT 3 83 1 TGAGATGGGA 0.921898 -218 CCAACAACTTTGACCAACTGGGCTTAACTAAGC 3 213 1 TGAAATGGGC 0.902611 -88 AAGTAACCATGGATGGGTTGGGAAAAATT 4 7 0 GGAGGTGGGA 0.98757 -53 ATTTCTCCTAGGAGTAATTTGCCT 5 2 0 GGAAATTGCC 0.862514 -299 ATTACTCCTAGGAGAAATTTGCCGAGTTGATAG 5 17 1 GGAAATTGCC 0.862504 -284 CACCGCAAGCGGAACTGGCGGAATTGGTAGACG 5 140 0 GGATGCGGAA 0.755828 -161 TCATCCCCCAGGATTGACTGGAAGTCAACAGGC 5 194 1 GGAGATGGAA 0.951056 -107 ATAGGGCCGGGGAAAAGTCGGCAGTTCCCCATG 5 266 0 GGAAGCGGCA 0.966567 -35 AGGCCTTGTCGGAGATACTGGGAGG 6 222 1 GGATATGGGA 0.974164 -15 *** ** ***** Masking position 3 Map Score: 11.3805 Number of sites scoring better than the average of aligned sites = 1179 Number in coding regions = 1058 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 3 CGTCTGGGCTAGCAAAACCAAGGGGATCAG 2 203 1 AGCAAAACCA 0.957657 -98 CGCCCTAGGAAAAAATGGCACCCGGCTTAT 3 26 0 AAAAATGGCA 0.652116 -275 TTGTCCAGCTAGAAAAATCATTGATTTAGT 3 105 0 AGAAAAATCA 0.830911 -196 CCCCCTAAACCGCAAAGCCATTATTGAATT 3 133 0 CGCAAAGCCA 0.844638 -168 TATCTCAACGAAAAAGGGCAGCGGGCAAGT 4 36 0 AAAAAGGGCA 0.881624 -24 TCTTTCGGTAAGCAAAACCACCGCAAGCGG 5 161 0 AGCAAAACCA 0.957657 -140 TTTTGCTTACCGAAAGACCATCATCCCCCA 5 174 1 CGAAAGACCA 0.896696 -127 ATAAATTAGGAAAAAGAGCAAGTTTGCGAA 6 50 1 AAAAAGAGCA 0.922427 -187 TAGCTCCAACAGGAAAAGCAAAGCAAATTC 6 77 0 AGGAAAAGCA 0.894033 -160 AAAATGGCTAAAAGAAACCACTGCAGCAGT 6 125 0 AAAGAAACCA 0.758752 -112 TAGTATTATGAAAAAAAGCATAGGCCTTGT 6 201 1 AAAAAAAGCA 0.943506 -36 ********** Masking position 5 Map Score: 7.0468 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 437 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 ATCTACGTCCAGATCGGGCCAATAAAAATG 2 68 0 AGATCGGGCC 0.943245 -233 AAAACCAAGGGGATCAGTTGGGATCAGTCC 2 216 1 GGATCAGTTG 0.880939 -85 GGATCAGTTGGGATCAGTCCTCCCTTTGGG 2 226 1 GGATCAGTCC 0.955969 -75 GGACAACAAGGGATCAGTCCGCTAGAAACA 2 276 1 GGATCAGTCC 0.955969 -25 ATAGGGCCGGGGAAAAGTCGGCAGTTCCCC 5 269 0 GGAAAAGTCG 0.871555 -32 GGTGATTTCGGGATAGGGCCGGGGAAAAGT 5 281 0 GGATAGGGCC 0.978422 -20 CCAGTATCTCCGACAAGGCCTATGCTTTTT 6 213 0 CGACAAGGCC 0.867083 -24 ********** Masking position 3 Map Score: 3.77985 Number of sites scoring better than the average of aligned sites = 375 Number in coding regions = 343 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 ATGTCATTGAGCCAACCGCCAATCATTTTT 2 45 1 GCCAACCGCC 0.672165 -256 GCCACTTCACGGCGATCGCCCGTCGTCTGG 2 180 1 GGCGATCGCC 0.499863 -121 CATAATATAAGCCGGGTGCCATTTTTTCCT 3 20 1 GCCGGGTGCC 0.862675 -281 AACCGGCCTGGGGGACCCCCCGGCGGGAAA 3 63 0 GGGGACCCCC 0.526973 -238 TTGTGACGCAGGGCATTGCCCCCTAAACCG 3 151 0 GGGCATTGCC 0.782636 -150 ATGGTTACTTGCCCGCTGCCCTTTTTCGTT 4 30 1 GCCCGCTGCC 0.911354 -30 TGATACCATGGGGAACTGCCGACTTTTCCC 5 260 1 GGGAACTGCC 0.567272 -41 ********** Masking position 9 Map Score: 4.09447 Number of sites scoring better than the average of aligned sites = 6784 Number in coding regions = 6194 Number in noncoding regions = 590 Number of orfs with sites within 600 bp upstream = 372 Fraction of orfs with sites within 600 bp upstream = 0.0597494 Motif number 6 CATTGAAAATATGTTTTACCAGAGCGTTTT 2 18 0 ATGTTTTACC 0.940915 -283 AACATCCTGAACGTTTTCCCCTAGTTTGTA 2 117 1 ACGTTTTCCC 0.979756 -184 GCCGGGTGCCATTTTTTCCTAGGGCGAGAA 3 30 1 ATTTTTTCCT 0.901317 -271 TAGGGCGAGAATCTTTTCCCGCCGGGGGGT 3 49 1 ATCTTTTCCC 0.969438 -252 TTTTTGGCTGATTTTTTACCCCAACAACTT 3 193 1 ATTTTTTACC 0.950517 -108 AATTTTTCCCAACCCATCCA 4 1 1 AATTTTTCCC 0.955361 -59 GGAACTGCCGACTTTTCCCCGGCCCTATCC 5 271 1 ACTTTTCCCC 0.947264 -30 ********** Masking position 1 Map Score: 6.33451 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 520 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 7 TGGTTTAAAAACGCTCTGGTA 2 1 1 TGGTTAAAAA 0.914135 -300 GCCCGTCGTCTGGGCTAGCAAAACCAAGGGG 2 197 1 TGGGTAGCAA 0.967184 -104 GTCCTCCCTTTGGGGTCGAAAATGGTTGTAG 2 242 1 TGGGTCGAAA 0.992172 -59 TCAAAGTTGTTGGGGTAAAAAATCAGCCAAA 3 195 0 TGGGTAAAAA 0.975017 -106 AGTAGCTAATCGGGATCGAAAGATGGGCAAC 3 267 0 CGGGTCGAAA 0.975 -34 TAACCATGGATGGGTTGGGAAAAATT 4 6 0 TGGGTGGGAA 0.945322 -54 CAGTTCCCCATGGTATCAAAAAAATTAAGCC 5 247 0 TGGTTCAAAA 0.943634 -54 **** ****** Masking position 10 Map Score: 4.77687 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 176 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 CAGTCCGCTAGAAACATGCCC 2 290 1 GAAACATGCC 0.972775 -11 CCCATCCATGGTTACTTGCCCGCTGCCCTT 4 23 1 GTTACTTGCC 0.972895 -37 TCTCCTAGGAGTAATTTGCCT 5 2 0 GTAATTTGCC 0.983163 -299 ACTCCTAGGAGAAATTTGCCGAGTTGATAG 5 20 1 GAAATTTGCC 0.983163 -281 ********** Masking position 4 Map Score: 1.54658 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 71 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 GGCCTTTAACAAGCCAGGTAATTAATTAAG 2 153 0 AAGCCAGGTA 0.895919 -148 ATCATAATATAAGCCGGGTGCCATTTTTTC 3 18 1 AAGCCGGGTG 0.947842 -283 GGGGTCCCCCAGGCCGGTTTGAGAGAATGG 3 74 1 AGGCCGGTTT 0.913248 -227 AGCTTAGTTAAGCCCAGTTGGTCAAAGTTG 3 217 0 AGCCCAGTTG 0.936725 -84 TAGAATGCGGAACCCGGGACTTGAACCCGG 5 76 1 AACCCGGGAC 0.885885 -225 CCGGGACTTGAACCCGGAAGTCCTTACGAA 5 89 1 AACCCGGAAG 0.915545 -212 TTCTTGACAAAAGCCTGTTGACTTCCAGTC 5 209 0 AAGCCTGTTG 0.942478 -92 ********** Masking position 1 Map Score: 0.585929 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 373 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 ********** No masking Map Score: 2.09143e-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: 2.09143e-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: 2.09143e-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