AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i106_synecho_ctra_300.orf -o106_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 RCY37413 300 Synechocystis #2 RCY34719 56 Synechocystis #3 RCY30401 142 Synechocystis #4 RCY19962 189 Synechocystis #5 RCY15566 231 Synechocystis Motif number 1 AGGGGAAAAGTTGCAGGGGT 1 1 1 AGGGGAAAAG 0.951542 -300 TTGTTTTAGTATGGGCGGGAAGACCCCTGC 1 23 0 ATGGGCGGGA 0.888828 -278 ATCATTTGGTATAGGCAAAAGCTAAACAAC 1 86 1 ATAGGCAAAA 0.920965 -215 CAACTTTAATATAGGTAAGGAAATTGCTTA 1 112 1 ATAGGTAAGG 0.845444 -189 TGGATAAATTAGGGGCGGAATTTGATTTTT 1 218 1 AGGGGCGGAA 0.908419 -83 GTTACTGGCTATGGGAAAAAAATCAAATTC 1 235 0 ATGGGAAAAA 0.906467 -66 AATCGGATTTAAGGGTAGAGAAAAGGTAGC 2 24 0 AAGGGTAGAG 0.775424 -33 AATCTTAGGTAAAAATCGGATTTA 2 43 0 TTAGGTAAAA 0.63304 -14 GAAAAATCTCTGGGGAAAGGGCACAATGGC 3 33 0 TGGGGAAAGG 0.920048 -110 AAGGAGAAAGTAGGGAAAAATCTCTGGGGA 3 47 0 TAGGGAAAAA 0.581152 -96 AAAGATGCTTTTAGGCAAAATATCAGGTTA 4 56 0 TTAGGCAAAA 0.857172 -134 ATTTTTTTGGGGGGGCAGGGGGCGTTTGAA 4 84 0 GGGGGCAGGG 0.960089 -106 GGGAAATTTAGGGGGCAAAATAAAACCTTT 4 147 1 GGGGGCAAAA 0.942842 -43 TTGAAACATCAGAGGCAAGGGT 5 3 0 AGAGGCAAGG 0.964112 -229 GGTGTAGCTCATAGGTAAGGGAAGTTGAAT 5 94 0 ATAGGTAAGG 0.845444 -138 CTAAGTTTTCATGGGCAGGACGATAGGTCG 5 148 0 ATGGGCAGGA 0.971637 -84 GGTGATGGGGCAGAGGGGATTTGCA 5 217 0 TGGGGCAGAG 0.969153 -15 ********** Masking position 5 Map Score: 22.0154 Number of sites scoring better than the average of aligned sites = 4695 Number in coding regions = 4072 Number in noncoding regions = 623 Number of orfs with sites within 600 bp upstream = 596 Fraction of orfs with sites within 600 bp upstream = 0.0957276 Motif number 2 AGGTATAGAAGGGCATTTAAAAGGTATTTA 1 153 0 GGGCATTTAA 0.966424 -148 AAATTAGGGGCGGAATTTGATTTTTTTCCC 1 223 1 CGGAATTTGA 0.973782 -78 TAGAAAACATCGGAGTTGGAGTAAAGGAGA 3 70 0 CGGAGTTGGA 0.92254 -73 GGGGGGCAGGGGGCGTTTGAAAGATGCTTT 4 75 0 GGGCGTTTGA 0.971151 -115 AAAAATTAGGGGGAAGTTAAGTAAAAATCC 4 108 1 GGGAAGTTAA 0.971594 -82 CTCCATTATTGGGAAATTTAGGGGGCAAAA 4 137 1 GGGAAATTTA 0.832295 -53 TCATAGGTAAGGGAAGTTGAATGCAAACTC 5 86 0 GGGAAGTTGA 0.986042 -146 ACACCGGGTTGGGAATTGAAACCTTGATCC 5 119 1 GGGAATTGAA 0.966424 -113 ********** Masking position 10 Map Score: 8.86685 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 583 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 3 TATCTTTTTTGTTTTAGTATGGGCGGGAAGAC 1 29 0 GTTTAGATGG 0.89984 -272 TATTAAAGTTGTTTAGCTTTTGCCTATACCAA 1 91 0 GTTTGCTTTG 0.75648 -210 TGTCCGATGACTGCAAGGTTTTG 3 2 1 GTCCATACTG 0.782075 -141 TGACTGCAAGGTTTTGCCATTGTGCCCTTTCC 3 18 1 GTTTGCATTG 0.926035 -125 AAGATGATGCGGCCAATGACGGAGGTTTTAGA 3 102 0 GGCCATACGG 0.948923 -41 CAAAATATCAGGTTAGTAATGGAGCATAAAAA 4 39 0 GGTTGTATGG 0.95504 -151 AAATTCTTGTGGTTCACCACGGCGATCGCCTA 5 37 1 GGTTACACGG 0.984806 -195 TGCAAACTCTGGCTAACCATGGCCCGTAGGCG 5 63 0 GGCTACATGG 0.97834 -169 AGCTACACCGGGTTGGGAATTGAAACCTTGAT 5 115 1 GGTTGGATTG 0.893897 -117 AACTTAGACCGTTCAACGACGGACCGAGGCAG 5 171 1 GTTCACACGG 0.969576 -61 AAAGCAGAGGGGCCTGCCTCGGTCCGTCGTTG 5 184 0 GGCCGCTCGG 0.949685 -48 **** ** **** Masking position 1 Map Score: 7.06042 Number of sites scoring better than the average of aligned sites = 2284 Number in coding regions = 2085 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 219 Fraction of orfs with sites within 600 bp upstream = 0.0351751 Motif number 4 CAAGGTATAGAAGGGCATTTAAAAGGTATT 1 155 0 AAGGGCATTT 0.909201 -146 ATAAATTAGGGGCGGAATTTGATTTTTTTC 1 221 1 GGCGGAATTT 0.953894 -80 AAACAGGATAAGTGGGGGTTACTGGCTATG 1 252 0 AGTGGGGGTT 0.792597 -49 TGCGGCCAATGACGGAGGTTTTAGAAGTAG 3 97 0 GACGGAGGTT 0.952998 -46 TGGGGGGGCAGGGGGCGTTTGAAAGATGCT 4 77 0 GGGGGCGTTT 0.975516 -113 AAAAAAATTAGGGGGAAGTTAAGTAAAAAT 4 106 1 GGGGGAAGTT 0.987305 -84 GCTCATAGGTAAGGGAAGTTGAATGCAAAC 5 88 0 AAGGGAAGTT 0.950401 -144 TGATGGGGCAGAGGGGATTTGCAGAAAGCA 5 210 0 GAGGGGATTT 0.962444 -22 ********** Masking position 9 Map Score: 7.04422 Number of sites scoring better than the average of aligned sites = 1089 Number in coding regions = 940 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 5 TACTAAAACAAAAAAGATAGATCTATTCGT 1 42 1 AAAAAGATAG 0.855742 -259 TGATGATATGGATAAATTAGGGGCGGAATT 1 210 1 GATAAATTAG 0.81801 -91 TGGCTATGGGAAAAAAATCAAATTCCGCCC 1 230 0 AAAAAAATCA 0.563202 -71 TAAGGGTAGAGAAAAGGTAGCAACCAAGGA 2 15 0 GAAAAGGTAG 0.962105 -42 AATCTTAGGTAAAAATCGGATTTAAGGG 2 39 0 GTAAAAATCG 0.788117 -18 TGGAGTAAAGGAGAAAGTAGGGAAAAATCT 3 54 0 GAGAAAGTAG 0.912856 -89 TTTAGAAGTAGAAAACATCGGAGTTGGAGT 3 78 0 GAAAACATCG 0.937379 -65 AAACTAGTTTGAAAAAGTAACC 4 3 0 GAAAAAGTAA 0.885721 -187 TGCCCCCCCAAAAAAATTAGGGGGAAGTTA 4 97 1 AAAAAATTAG 0.889443 -93 TCCTGCCCATGAAAACTTAGACCGTTCAAC 5 158 1 GAAAACTTAG 0.941677 -74 ********** Masking position 5 Map Score: 3.44797 Number of sites scoring better than the average of aligned sites = 1130 Number in coding regions = 960 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 6 CCTATACCAAATGATATAGAAGTAATTAAA 1 71 0 ATGATATAGA 0.947432 -230 GAACTTTCACAAGGTATAGAAGGGCATTTA 1 164 0 AAGGTATAGA 0.965917 -137 CAGCAAACTGATGATATGGATAAATTAGGG 1 202 1 ATGATATGGA 0.923826 -99 TGTTTTGATGATGGTTTGGAGATGACAAAA 1 277 1 ATGGTTTGGA 0.954516 -24 ATCGGATTTAAGGGTAGAGAAAAGGTAGCA 2 23 0 AGGGTAGAGA 0.93098 -34 CCAATGACGGAGGTTTTAGAAGTAGAAAAC 3 92 0 AGGTTTTAGA 0.937272 -51 GGCAAAGTTTTAGAGTTTTTTTGA 4 176 0 AAGTTTTAGA 0.906188 -14 ********** Masking position 1 Map Score: 4.08166 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 129 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 GTGGGGGTTACTGGCTATGGGAAAAAAATC 1 241 0 CTGGCTATGG 0.904115 -60 CGATCGCCTACGGGCCATGGTTAGCCAGAG 5 59 1 CGGGCCATGG 0.994911 -173 GACGATAGGTCGGATCAAGGTTTCAATTCC 5 130 0 CGGATCAAGG 0.959718 -102 CGTTCAACGACGGACCGAGGCAGGCCCCTC 5 180 1 CGGACCGAGG 0.992604 -52 GGTGATGGGGCAGAGGGGATTTGCAG 5 216 0 GGGGCAGAGG 0.955786 -16 ********** Masking position 3 Map Score: 1.00896 Number of sites scoring better than the average of aligned sites = 716 Number in coding regions = 676 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 8 ********** No masking Map Score: -6.79689e-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: -6.79689e-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 10 ********** No masking Map Score: -6.79689e-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