AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_soj_synecho_reg_300.orf -o254_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 RCY29546 300 Synechocystis #2 RCY03338 300 Synechocystis #3 RCY11382 300 Synechocystis #4 RCY49571 65 Synechocystis #5 RCY41531 22 Synechocystis Motif number 1 TCTTTTTGAAGAAGACGGAAGTAGGGATAT 1 21 0 GAAGACGGAA 0.985568 -280 CGCACTCGTGGAAAACGGAACTCTGAAGCA 1 173 0 GAAAACGGAA 0.913532 -128 AGGCCCCAGGGAACAGGCAAAAGTAACCCT 1 244 0 GAACAGGCAA 0.971727 -57 CGAAGAGGGAATATTAATGGG 2 2 1 GAAGAGGGAA 0.994846 -299 TTTTCTAATTGCGGGGGGAACCTATGCTTT 2 75 0 GCGGGGGGAA 0.948386 -226 TCGGAACCAAGACCGGGGAAATGAAGCCCC 3 245 0 GACCGGGGAA 0.981724 -56 AGAAGAGGTAATTTCAAGTTA 3 290 0 GAAGAGGTAA 0.967597 -11 CTAGGCGCTTGACGGGGCAAATAGAACGAA 4 38 0 GACGGGGCAA 0.981726 -28 ********** Masking position 9 Map Score: 9.41606 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 461 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 2 GTTTTCCACGAGTGCGAGGGAGATGGAACT 1 187 1 AGTGCGAGGG 0.94411 -114 ATATTTTCTAATTGCGGGGGGAACCTATGC 2 78 0 ATTGCGGGGG 0.996663 -223 TCGAAGGGTCATGGCGGCGCACTAAAATGG 2 275 0 ATGGCGGCGC 0.982688 -26 AATTGGCTTTATTGTGGGGGCTAGCCGACC 3 212 0 ATTGTGGGGG 0.978813 -89 ATAAAGCCAATTTGCGGGGCTTCATTTCCC 3 230 1 TTTGCGGGGC 0.993791 -71 ATCTAGGCGCTTGACGGGGCAAATAGAACG 4 40 0 TTGACGGGGC 0.953548 -26 ********** Masking position 6 Map Score: 5.70658 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 575 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 GCAGTCTTTAAAATAACCTCATTTCC 1 285 1 AAAACCATTT 0.841362 -16 GTTATGGCATTATTAGCCTAATTTATGGATCATT 2 154 0 TTAGCAATTT 0.948622 -147 CTTTTAGAGAATTAAACTGAATTTCAGACAAATA 2 203 0 ATAACAATTT 0.982244 -98 GTAGCAGGGCTAAAAACTATATTTTAGTCTTTAG 2 242 0 TAAACTATTT 0.729511 -59 AGACGGTCAGAGTCATCAAAATTTTAA 3 4 0 ATATCAATTT 0.908372 -297 TAAAAAATTTACTCAGCTAAATTGTCTCTATATC 3 114 1 ATAGCAATTG 0.920804 -187 TGTCTCTATATCTTAACAAAATTGAGGCCAGAAC 3 136 1 TTAACAATTG 0.94202 -165 TAGCCCCCACAATAAAGCCAATTTGCGGGGCTTC 3 219 1 ATAAGAATTT 0.877494 -82 TTTAAAACAGTTTTAACGCAATTTAT 4 3 0 TTAACAATTT 0.974215 -63 GACGGGGCAAATAGAACGAAATTTAAAACAGTTT 4 24 0 AAAACAATTT 0.961592 -42 * * *** ***** Masking position 5 Map Score: 5.19191 Number of sites scoring better than the average of aligned sites = 316 Number in coding regions = 234 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 GGATACAGAAAGTAAATCGTTCATCTTCTCT 1 48 0 AGTAATCGTT 0.967307 -253 CCGAATGATCAGTAAATCTTACATGAATGTT 1 136 0 AGTAATCTTA 0.849731 -165 AATATTAATGGGTAAATGGTTCTTAAGTAAC 2 20 1 GGTAATGGTT 0.897268 -281 CTCCCCTTGGGGTCAATCGTTACTTAAGAAC 2 38 0 GGTAATCGTT 0.97442 -263 CAAGTCAATTAGTTAATATTTGTCTGAAATT 2 187 1 AGTAATATTT 0.847311 -114 TTTAGTCTTTAGTTCAACTTTTAGAGAATTA 2 223 0 AGTCAACTTT 0.901938 -78 TTATTCAATAGGTTAAATTTTATCTTCCTTT 3 75 0 GGTAAATTTT 0.868568 -226 AATTTAGCTGAGTAAATTTTTTACATTTACT 3 106 0 AGTAATTTTT 0.907281 -195 AGCCGACCAAGGTGCAACTTTCCCAACCGAG 3 189 0 GGTCAACTTT 0.922127 -112 *** ******* Masking position 6 Map Score: 5.58335 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 263 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 5 CACGAGTGCGAGGGAGATGGAACTTGGGCT 1 193 1 AGGGAGATGG 0.989686 -108 TGGCGATCGAAGGGTCATGGCGGCGCACTA 2 281 0 AGGGTCATGG 0.996799 -20 GGCCAGAACTAGGGTCATGGTATTTCCCCT 3 161 1 AGGGTCATGG 0.996799 -140 ********** Masking position 7 Map Score: 2.89847 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 15 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 CCAACGATCTGCTAGAAGGGTTACTTTTGC 1 228 1 GCTAGAAGGG 0.970439 -73 GCAATGTTAAGGCCCCAGGGAACAGGCAAA 1 253 0 GGCCCCAGGG 0.957733 -48 GTAACGATTGACCCCAAGGGGAGTAAAAAA 2 46 1 ACCCCAAGGG 0.929399 -255 GATATTTTCTAATTGCGGGGGGAACCTATG 2 79 0 AATTGCGGGG 0.843295 -222 GCACTAAAATGGTAGCAGGGCTAAAAACTA 2 257 0 GGTAGCAGGG 0.956694 -44 TGGCGATCGAAGGGTCATGGCGGC 2 287 0 GATCGAAGGG 0.984073 -14 CAACTTTCCCAACCGAGGGGAAATACCATG 3 176 0 AACCGAGGGG 0.940899 -125 TTATCTAGGCGCTTGACGGGGCAAATAGAA 4 42 0 GCTTGACGGG 0.923099 -24 ********** Masking position 8 Map Score: 2.66342 Number of sites scoring better than the average of aligned sites = 1117 Number in coding regions = 1010 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 7 ********** No masking Map Score: 9.48026e-14 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: 9.48026e-14 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: 9.48026e-14 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