AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i030_Glycerol_Uptake_synecho_reg_300.orf -o030_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RCY34833 127 Synechocystis #2 RCY49702 300 Synechocystis #3 RCY25232 300 Synechocystis #4 RCY02659 52 Synechocystis Motif number 1 AACTCTAACTTTGGGCAATTTTTAGGGGGT 1 67 0 TTGGGCAATT 0.863953 -61 TTAGAGTTTAGGGGGCTTTTTTCCATTCAA 1 89 1 GGGGGCTTTT 0.980567 -39 GTTCCCCTGTGGGGGCAATTACGGTAACGG 2 112 0 GGGGGCAATT 0.99685 -189 TAATTCCCGCCGGGGCATTTTAGTACGTTG 2 213 0 CGGGGCATTT 0.982372 -88 CCGGGAAGTCGGGTGCATTAGCCGTACTAG 2 252 1 GGGTGCATTA 0.944121 -49 GGCGATCGCCGGGGGCAAAGCTCAATGTTA 3 126 0 GGGGGCAAAG 0.984132 -175 GCTGACTTAGGGGGGCAAAAACAATGTCAA 3 207 0 GGGGGCAAAA 0.986629 -94 ********** Masking position 5 Map Score: 9.46916 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 978 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 2 GTGTTACGGCATTTTACTGACGGGTTAAGT 2 59 1 ATTTTACTGA 0.943152 -242 GACGTAATCAATTTTTCTGTACCGATATTA 2 165 1 ATTTTTCTGT 0.961723 -136 GTAAATTGATTTTTTCTTGTTGTTTGATCC 3 29 1 TTTTTCTTGT 0.839133 -272 GTTTGATCCCATTTTCCAGTCTTTTTGACT 3 50 1 ATTTTCCAGT 0.929574 -251 AACTGCAAAAATTATCCTGACTGAATGGAA 3 79 0 ATTATCCTGA 0.854921 -222 TTTTGCAGTTTTTTTATGGAGTTTTGATAA 3 99 1 TTTTTATGGA 0.657456 -202 TTTTGAGCTTATTTTTCAGTATGAAAACA 3 282 1 ATTTTTCAGT 0.916179 -19 AGAGCAAGGATTTTTTTTGATTAATTTTTC 4 19 1 TTTTTTTTGA 0.841817 -34 TTTTTGATTAATTTTTCGGAGGTTACCGTC 4 32 1 ATTTTTCGGA 0.954191 -21 ********** Masking position 5 Map Score: 5.48031 Number of sites scoring better than the average of aligned sites = 1043 Number in coding regions = 845 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 3 CTGGAGTAAGGGGAAAAGGTAATTAGTGTTACGG 2 34 1 GGGAAAGAAT 0.990273 -267 AAGGTAATTAGTGTTACGGCATTTTACTGACGGG 2 49 1 GTGTACGATT 0.926093 -252 TTTTACTGACGGGTTAAGTAATCTTTAACAAAGA 2 70 1 GGGTAAGATT 0.990256 -231 TGCCCCCACAGGGGAACGCGATGTCTGTGGACTC 2 125 1 GGGAACGATT 0.990665 -176 CCGCTAATATCGGTACAGAAAAATTGATTACGTC 2 165 0 CGGACAGAAT 0.850037 -136 GATATTAGCGGTGAAAAGTTTTATTCAACGTACT 2 188 1 GTGAAAGTTT 0.802439 -113 GAATTAACTTGGGTTCCGGGAAGTCGGGTGCATT 2 237 1 GGGTCCGAAT 0.955134 -64 GCCATGGGCAGGGTAAATTGATTTTTTCTTGTTG 3 17 1 GGGAAATATT 0.928682 -284 CGATCGCCGGGGGCAAAGCTCAATGTTATCAAAA 3 120 0 GGGAAAGCAT 0.959655 -181 AAATTGCTGGGGAGTAAGGGATTTTCAACTCTGT 3 241 0 GGATAAGATT 0.898933 -60 *** **** ** * Masking position 14 Map Score: 7.751 Number of sites scoring better than the average of aligned sites = 1017 Number in coding regions = 869 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 4 GCGATCGCCAATGCCAGTTGTGG 1 2 1 CGATCGCCTG 0.995185 -126 TGGCTTGCCGCTGCTGTTCTCCT 2 2 1 GGCTTGCCTG 0.987855 -299 ACAGACATCGCGTTCCCCTGTGGGGGCAATTA 2 121 0 CGTTCCCCTG 0.93958 -180 GATGTCTGTGGACTCGCCCAGGACGTAATCAA 2 144 1 GACTCGCCGG 0.969116 -157 ACTATTGCCATGGGCAGGGTAAA 3 2 1 CTATTGCCGG 0.959314 -299 TATCCCTAGGCGATCGCCGGGGGCAAAGCTCA 3 132 0 CGATCGCCGG 0.996869 -169 ATTTATCCCTGGATTGACATTGTTTTTGCCCC 3 194 1 GGATTGACTG 0.927142 -107 ******** ** Masking position 4 Map Score: 5.02902 Number of sites scoring better than the average of aligned sites = 3328 Number in coding regions = 3043 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 5 AAAAAGCCCCCTAAACTCTAACTTTGGGCA 1 80 0 CTAAACTCTA 0.893395 -48 AAACAACAAGAAAAAATCAATTTACCCTGC 3 24 0 AAAAAATCAA 0.794091 -277 AACTCCATAAAAAAACTGCAAAAATTATCC 3 92 0 AAAAACTGCA 0.912288 -209 TCAATGTTATCAAAACTCCATAAAAAAACT 3 105 0 CAAAACTCCA 0.967496 -196 TCGCCGGGGGCAAAGCTCAATGTTATCAAA 3 121 0 CAAAGCTCAA 0.977417 -180 TAAGCTCAAAATAAGCTGAAATTGCTGGGG 3 263 0 ATAAGCTGAA 0.920735 -38 ATACTGAAAAATAAGCTCAAAATAAGCTGA 3 274 0 ATAAGCTCAA 0.964877 -27 ********** Masking position 4 Map Score: 3.47081 Number of sites scoring better than the average of aligned sites = 331 Number in coding regions = 261 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 TTACTCCAGAGGAGAACAGCAGCGGCAAGC 2 13 0 GGAGAACAGC 0.943045 -288 GTTCTCCTCTGGAGTAAGGGGAAAAGGTAA 2 26 1 GGAGTAAGGG 0.972667 -275 AAGGTAATTAGTGTTACGGCATTTTACTGA 2 49 1 GTGTTACGGC 0.944748 -252 GGGGCAATTACGGTAACGGCTCATAAATCT 2 101 0 CGGTAACGGC 0.942856 -200 TGCCCCCACAGGGGAACGCGATGTCTGTGG 2 125 1 GGGGAACGCG 0.950557 -176 GAATTAACTTGGGTTCCGGGAAGTCGGGTG 2 237 1 GGGTTCCGGG 0.942505 -64 TTGGGTTAGTCTAGTACGGCTAATGCACCC 2 262 0 CTAGTACGGC 0.889946 -39 GCGATCGCCGGGGGCAAAGCTCAATGTTAT 3 125 0 GGGGCAAAGC 0.86221 -176 AAATTGCTGGGGAGTAAGGGATTTTCAACT 3 245 0 GGAGTAAGGG 0.972667 -56 ********** Masking position 6 Map Score: 5.01143 Number of sites scoring better than the average of aligned sites = 2874 Number in coding regions = 2631 Number in noncoding regions = 243 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 7 CAATTGCACGATTTATTCCTCA 1 116 1 ATTTATTCCT 0.950451 -12 CGGAACCCAAGTTAATTCCCGCCGGGGCAT 2 225 0 GTTAATTCCC 0.934071 -76 CACGTTTATTGTTTATCCCTAGGCGATCGC 3 147 0 GTTTATCCCT 0.985262 -154 ATATGCCTGGATTTATCCCTGGATTGACAT 3 184 1 ATTTATCCCT 0.967397 -117 GATTGACATTGTTTTTGCCCCCCTAAGTCA 3 205 1 GTTTTTGCCC 0.9226 -96 ********** Masking position 6 Map Score: 1.42111 Number of sites scoring better than the average of aligned sites = 390 Number in coding regions = 327 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 8 CGACCACAACTGGCATTGGCGATCGC 1 6 0 TGCATTGGCG 0.956633 -122 TGGCTTGCCGCTGCTGTTCTCCTCTG 2 6 1 TGCGCTGCTG 0.9804 -295 ATCCCTGGATTGACATTGTTTTTGCCCCCCT 3 198 1 TGCATTGTTT 0.922292 -103 TTTTCAACTCTGTCATTGCTGACTTAGGGGG 3 223 0 TGCATTGCTG 0.995917 -78 CAAAATAAGCTGAAATTGCTGGGGAGTAAGG 3 256 0 TGAATTGCTG 0.979278 -45 ** ******** Masking position 7 Map Score: 0.817777 Number of sites scoring better than the average of aligned sites = 612 Number in coding regions = 565 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 9 ********** No masking Map Score: -3.17312e-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: -3.17312e-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 11 ********** No masking Map Score: -3.17312e-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