AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i066_Lysine_Biosynthesis_synecho_reg_300.orf -o066_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 RCY33655 258 Synechocystis #2 RCY27198 197 Synechocystis #3 RCY30985 201 Synechocystis #4 RCY15108 176 Synechocystis #5 RCY52095 117 Synechocystis Motif number 1 GTATTAAAAATCCCCCTGCCATGCTCTCCACTGAAA 1 159 1 TCCCCTCCCC 0.999085 -100 TCCACTGAAATGCCCCTTCCAACCACCGGAAGCACC 1 185 1 TCCCCTCCCC 0.999085 -74 AACCCCGGCCTCCCCCTCCCCCAACCAAAATCTTTT 1 229 1 TCCCCTCCAC 0.998896 -30 TAACGTTCACTTCCCCTAACATCATCGTCC 2 178 1 TCCCCTACAC 0.99519 -20 GCTACGGAATTACCCAAGCCAGTGCCGAGGAACGAA 3 41 1 TCCCAACCGC 0.943516 -161 GAACCTACTGTTACCATGCCGATCGCCAGTGGTCTA 3 85 0 TACCATCCCC 0.970069 -117 AACATGACTCTCTCCCTCCCTGGAGCAACCTAGTCT 4 70 1 TTCCCTCCAC 0.991549 -107 GACTTTAGTTTCCCTCTAACCTGATCCC 5 100 1 TCCTCTACAC 0.958517 -18 * ***** ** * * Masking position 1 Map Score: 13.2289 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 402 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 AGGGGCATTTCAGTGGAGAGCATGGCAGGG 1 172 0 CAGTGGAGAG 0.97068 -87 CCAGGGTAATCAATGGCCATAAAAATGCCA 2 20 0 CAATGGCCAT 0.95591 -178 TTACCCAAGCCAGTGCCGAGGAACGAAATT 3 50 1 CAGTGCCGAG 0.967137 -152 ATTTATAGACCACTGGCGATCGGCATGGTA 3 80 1 CACTGGCGAT 0.979546 -122 TAGTTAGAATCAATGCAGTTGGTTAATGGA 3 119 0 CAATGCAGTT 0.916384 -83 CGCCGTTGCCCAATGGAGTGATCTAGTTAG 3 142 0 CAATGGAGTG 0.966635 -60 CTCCATTGGGCAACGGCGTTAATGCACTGA 3 154 1 CAACGGCGTT 0.978831 -48 TTATTATTCCCAACGGCGATCGCCTGACTT 5 75 1 CAACGGCGAT 0.986699 -43 ********** Masking position 2 Map Score: 9.57657 Number of sites scoring better than the average of aligned sites = 1268 Number in coding regions = 1151 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 TTTCAGTGGAGAGCATGGCAGGGGGATTTTTAATA 1 160 0 GGGGAGGGGG 0.998931 -99 GGTGCTTCCGGTGGTTGGAAGGGGCATTTCAGTGG 1 186 0 GGGGAGGGGC 0.995378 -73 AAAAGATTTTGGTTGGGGGAGGGGGAGGCCGGGGT 1 230 0 GTGGAGGGGG 0.998314 -29 GGTTACATCGGGGCTTATCATGGGGCATTATTGTC 2 116 1 GGATATGGGG 0.903638 -82 GGACGATGATGTTAGGGGAAGTGAACGTT 2 179 0 GTGTAGGGGA 0.98441 -19 TAGACCACTGGCGATCGGCATGGTAACAGTAGGTT 3 85 1 GGGGATGGTA 0.883744 -117 AGACTAGGTTGCTCCAGGGAGGGAGAGAGTCATGT 4 71 0 GTGGAGGGAG 0.987148 -106 GGGATCAGGTTAGAGGGAAACTAAAGT 5 101 0 GTGTAGAGGG 0.962754 -17 * * ** ****** Masking position 10 Map Score: 9.24912 Number of sites scoring better than the average of aligned sites = 548 Number in coding regions = 500 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 CATGCTCTCCACTGAAATGCCCCTTCCAACC 1 178 1 ATGAAATGCC 0.853694 -81 ATCAATGGCCATAAAAATGCCATATTTCCGC 2 11 0 AAAAAATGCC 0.981059 -187 GCTGGGCTGGACAATAATGCCCCATGATAAG 2 129 0 AAATAATGCC 0.969961 -69 GAATATTTCCAGAAAATTACCAT 3 3 0 AAAAATTACC 0.914985 -199 TAGCATTTCCAGAATATTTCCAGAAAATTAC 3 14 0 AAATATTTCC 0.870261 -188 TAATGCACTGACTAAATTGACAGGAAATAAG 3 173 1 ATAAATTGAC 0.772579 -29 TCTTTTCCTGACAAAATTGCCGTAAAATACT 5 28 1 AAAAATTGCC 0.988109 -90 AATAATAAAGAAACTATTGCCATCAGTATTT 5 52 0 AACTATTGCC 0.940964 -66 * ********* Masking position 6 Map Score: 6.04004 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 579 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 CCCTAAAAGTATCAATAACTCTTGTAATATCCCA 1 64 0 ATAATACTTG 0.932221 -195 GAAGCACCTTATTAAAAACCCCGGCCTCCCCCTC 1 213 1 ATAAAACCGG 0.976778 -46 CGGTAAAAGATTTTGGTTGGGGGAGG 1 243 0 GTAAAATTGG 0.932366 -16 TTTTATGGCCATTGATTACCCTGGAAGTTAGTGT 2 26 1 ATGATACCGG 0.888604 -172 ATTCTATTGTATAAATCACTTAGGGCAACTAATC 2 73 1 ATAATACTGG 0.985885 -125 ACGTTAAATAATCAAAAACTAAGGGCTGGGCTGG 2 150 0 ATAAAACTGG 0.988513 -48 CCAGTGGTCTATAAATAATTTCGTTCCTCGGCAC 3 62 0 ATAATATTGT 0.69175 -140 CTTGCTGATGATCAAAAATTAAGGACAAAAACTA 4 147 0 ATAAAATTGG 0.965757 -30 CAAAATTGCCGTAAAATACTGATGGCAATAGTTT 5 39 1 GTAAAACTTG 0.892273 -79 ** *** *** ** Masking position 8 Map Score: 6.62946 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 257 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 GCTACAACAACCGGGGGCAAAGCAAAACCC 1 95 0 CCGGGGGCAA 0.982666 -164 ATATGGCATTTTTATGGCCATTGATTACCC 2 17 1 TTTATGGCCA 0.848544 -181 GTATAAATCACTTAGGGCAACTAATCTAAT 2 81 1 CTTAGGGCAA 0.975489 -117 TGTTACCATGCCGATCGCCAGTGGTCTATA 3 83 0 CCGATCGCCA 0.873935 -119 GGGTGTACAATCGAAGGCAAACTTTGTTTA 4 29 1 TCGAAGGCAA 0.907833 -148 TCTCTCCCTCCCTGGAGCAACCTAGTCTCA 4 78 1 CCTGGAGCAA 0.822598 -99 CCATCAGTATTTTACGGCAATTTTGTCAGG 5 34 0 TTTACGGCAA 0.852812 -84 CCGTAAAATACTGATGGCAATAGTTTCTTT 5 47 1 CTGATGGCAA 0.975648 -71 ********** Masking position 10 Map Score: 2.53392 Number of sites scoring better than the average of aligned sites = 2137 Number in coding regions = 1964 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 7 ATGGTAATTTTCTGGAAATATTCTGGAA 3 9 1 TTTCTGGAAA 0.804111 -193 TTCTGGAAATATTCTGGAAATGCTACGGAA 3 20 1 ATTCTGGAAA 0.929492 -182 CTGACTAAATTGACAGGAAATAAGTTACAT 3 180 1 TGACAGGAAA 0.964198 -22 ACGGCAATTTTGTCAGGAAAAGAAAGAGAA 5 21 0 TGTCAGGAAA 0.967077 -97 ********** Masking position 8 Map Score: 1.30462 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 52 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 ATCGGAGCTACAACAACCGGGGGCAAAGCA 1 101 0 CAACAACCGG 0.979724 -158 ATGCCCCTTCCAACCACCGGAAGCACCTTA 1 194 1 CAACCACCGG 0.990898 -65 AATTATTTATAGACCACTGGCGATCGGCAT 3 76 1 AGACCACTGG 0.952749 -126 AGGTTCCATTAACCAACTGCATTGATTCTA 3 115 1 AACCAACTGC 0.936397 -87 TTCGATTGTACACCCACTGCTAAAATTCCT 4 14 0 CACCCACTGC 0.986797 -163 ********** Masking position 6 Map Score: 1.74893 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 280 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 CCATAGTTACAGCCAAAAAAGAAGGAAA 1 9 1 ACAGCCAAAA 0.957062 -250 TCCCCCTCCCCCAACCAAAATCTTTTACCG 1 239 1 CCAACCAAAA 0.957062 -20 ATTGTCCAGCCCAGCCCTTAGTTTTTGATT 2 145 1 CCAGCCCTTA 0.962294 -53 CTAGTCTCAGCCAGCCATTACACACAGAAT 4 99 1 CCAGCCATTA 0.982655 -78 TCTTTCTTTTCCTGACAAAATTGCCGTAAA 5 24 1 CCTGACAAAA 0.871379 -94 ********** Masking position 10 Map Score: 0.3314 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 477 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 10 ********** No masking Map Score: 6.70342e-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: 6.70342e-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 12 ********** No masking Map Score: 6.70342e-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