AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i175_synecho_ctra_100.orf -o175_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 RCY00022 120 Synechocystis #2 RCY52230 73 Synechocystis #3 RCY23132 293 Synechocystis #4 RCY41564 233 Synechocystis Motif number 1 AGGCGATCGCCGGGGGAAAAAAATGAT 1 104 0 CGCCGGGGGA 0.98334 -17 TGGGCAGAGGTGCCAGGAGAGG 2 3 0 TGCCAGGAGA 0.807553 -71 TTCCTAGGTTTGGCTCGGGATTACCATTTG 3 38 0 TGGCTCGGGA 0.975387 -256 TTTTTTTTAATGGCGGGAGGCGGATTTGAA 3 213 0 TGGCGGGAGG 0.970315 -81 AACCATTATCCGGCGGGGGGAATTTTTTTC 3 244 0 CGGCGGGGGG 0.997491 -50 CGCCGGATAATGGTTGGGGGGTTTGTTTTA 3 259 1 TGGTTGGGGG 0.932634 -35 TAATCTGCCATGACATGGGGGTAAA 4 6 0 TGACATGGGG 0.960543 -228 TCCGGGCACCCGACTAAGGGAAACACCAGT 4 35 0 CGACTAAGGG 0.802125 -199 GGGAAAAATTCGACATGGGGAGCAAAAACT 4 167 0 CGACATGGGG 0.978679 -67 TTTTGGTCAACGGCTCGGGAAAAATTCGAC 4 183 0 CGGCTCGGGA 0.986841 -51 TTGCGGGTTGCGACACAGGG 4 224 1 CGACACAGGG 0.941522 -10 ********** Masking position 2 Map Score: 16.2967 Number of sites scoring better than the average of aligned sites = 2563 Number in coding regions = 2332 Number in noncoding regions = 231 Number of orfs with sites within 600 bp upstream = 253 Fraction of orfs with sites within 600 bp upstream = 0.040636 Motif number 2 ATGGGCGGTTAAAGCAGAGGCCCCCACATT 1 25 1 AAAGCAGAGG 0.922754 -96 CCCCACATTATAACCAAGGGATCTTTTCCT 1 46 1 TAACCAAGGG 0.938607 -75 TTTAAGCCAGAAACCCAGGAAAAGATCCCT 1 62 0 AAACCCAGGA 0.955486 -59 GTTTCTGGCTTAAACTGAGGCTGACCATCA 1 78 1 TAAACTGAGG 0.889359 -43 ATCCCGAGCCAAACCTAGGAATGCTTGGTG 3 47 1 AAACCTAGGA 0.95633 -247 CCCTAACAGAAAAGCTGAGGGTGAAGAGAA 3 111 1 AAAGCTGAGG 0.964862 -183 TTGGTAAGCATAACCCGAAGGTCGGTGGTT 3 185 1 TAACCCGAAG 0.856216 -109 GCCCGGAAGCAAACCCAGGGTTTTCGATCC 4 58 1 AAACCCAGGG 0.987026 -176 AAGTTTTGCAAAACCTAAAGAGATTGGCGA 4 108 0 AAACCTAAAG 0.89377 -126 ATGGGGAGCAAAAACTGGGAAGAGAAATTT 4 153 0 AAAACTGGGA 0.888737 -81 ********** Masking position 3 Map Score: 10.7171 Number of sites scoring better than the average of aligned sites = 2134 Number in coding regions = 1879 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 263 Fraction of orfs with sites within 600 bp upstream = 0.0422422 Motif number 3 CCATCATTTTTTTCCCCCGGCGATCGCCT 1 102 1 TTTCCCCCGG 0.950648 -19 CTGGCACCTCTGCCCACCGTGATAAAATGC 2 17 1 TGCCCACCGT 0.942591 -57 TCTGTTAGGGTGTCTCCCATTAAGTCTCTA 3 91 0 TGTCTCCCAT 0.951704 -203 CTTCGGGTTATGCTTACCAACTACAGTTTT 3 175 0 TGCTTACCAA 0.669474 -119 GGTTCAAATCCGCCTCCCGCCATTAAAAAA 3 211 1 CGCCTCCCGC 0.959662 -83 AAGAAAAAAATTCCCCCCGCCGGATAATGG 3 242 1 TTCCCCCCGC 0.972969 -52 TTTACCCCCATGTCATGGCAG 4 2 1 TTACCCCCAT 0.758484 -232 AGATTACTGGTGTTTCCCTTAGTCGGGTGC 4 30 1 TGTTTCCCTT 0.752315 -204 ACCCTGGGTTTGCTTCCGGGCACCCGACTA 4 49 0 TGCTTCCGGG 0.869173 -185 CAATAAATTTCTCTTCCCAGTTTTTGCTCC 4 149 1 CTCTTCCCAG 0.83747 -85 TCCCAGTTTTTGCTCCCCATGTCGAATTTT 4 163 1 TGCTCCCCAT 0.974886 -71 CCATGTCGAATTTTTCCCGAGCCGTTGACC 4 179 1 TTTTTCCCGA 0.821781 -55 ********** Masking position 7 Map Score: 8.17393 Number of sites scoring better than the average of aligned sites = 4894 Number in coding regions = 4431 Number in noncoding regions = 463 Number of orfs with sites within 600 bp upstream = 424 Fraction of orfs with sites within 600 bp upstream = 0.0681015 Motif number 4 AACCGTTGAAATGGGCGGTTAAAGCAGAGG 1 15 1 ATGGGCGGTT 0.974471 -106 GGCAATATGGGGTTAGGGGTCTGG 2 60 0 ATATGGGGTT 0.862673 -14 TTAATGGCGGGAGGCGGATTTGAACCACCG 3 207 0 GAGGCGGATT 0.886966 -87 CGGATAATGGTTGGGGGGTTTGTTTTATTC 3 262 1 TTGGGGGGTT 0.976231 -32 CCCCCATGTCATGGCAGATTACTGGTGTTT 4 15 1 ATGGCAGATT 0.946673 -219 CGATCCAATCATAGCGGATTCTTTCCTCGC 4 82 1 ATAGCGGATT 0.956493 -152 AGAGAAATTTATTGGAGGTTAATTTAAGTT 4 133 0 ATTGGAGGTT 0.938823 -101 AACTTTATTAGTTGCGGGTTGCGACACAGG 4 213 1 GTTGCGGGTT 0.974262 -21 ********** Masking position 9 Map Score: 5.72296 Number of sites scoring better than the average of aligned sites = 976 Number in coding regions = 862 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 5 CACCTTCCCAGAAACACCAAGCATTCCTAG 3 61 0 GAAACACCAA 0.990573 -233 AGGGTGAAGAGAAAGTCCAGACCACAAACT 3 128 1 GAAAGTCCAG 0.957418 -166 AGGCGGATTTGAACCACCGACCTTCGGGTT 3 196 0 GAACCACCGA 0.980807 -98 CCGACTAAGGGAAACACCAGTAATCTGCCA 4 26 0 GAAACACCAG 0.991262 -208 AAACTTAAATTAACCTCCAATAAATTTCTC 4 132 1 TAACCTCCAA 0.938158 -102 ********** Masking position 3 Map Score: 2.95849 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 145 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CCGCCCATTTCAACGGTTTTCC 1 2 0 CACGGTTTTC 0.996481 -119 TGCTTACCAACTACAGTTTTCACTGCCTGAC 3 164 0 CACAGTTTTC 0.990488 -130 GGAAGCAAACCCAGGGTTTTCGATCCAATCA 4 62 1 CAGGGTTTTC 0.993572 -172 * ********* Masking position 3 Map Score: 0.427994 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 12 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ********** No masking Map Score: 9.90086e-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: 9.90086e-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 9 ********** No masking Map Score: 9.90086e-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