AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i254_soj_synecho_reg_100.orf -o254_synecho_100.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 ATATCCCTACTTCCGTCTTCTTCAAAAAGA 1 21 1 TTCCGTCTTC 0.984199 -280 TGCTTCAGAGTTCCGTTTTCCACGAGTGCG 1 173 1 TTCCGTTTTC 0.905981 -128 AGGGTTACTTTTGCCTGTTCCCTGGGGCCT 1 244 1 TTGCCTGTTC 0.969086 -57 CCCATTAATATTCCCTCTTCG 2 2 0 TTCCCTCTTC 0.994352 -299 AAAGCATAGGTTCCCCCCGCAATTAGAAAA 2 75 1 TTCCCCCCGC 0.943692 -226 GGGGCTTCATTTCCCCGGTCTTGGTTCCGA 3 245 1 TTCCCCGGTC 0.979999 -56 TAACTTGAAATTACCTCTTCT 3 290 1 TTACCTCTTC 0.964585 -11 TTCGTTCTATTTGCCCCGTCAAGCGCCTAG 4 38 1 TTGCCCCGTC 0.98 -28 ********** Masking position 2 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 AGTTCCATCTCCCTCGCACTCGTGGAAAAC 1 187 0 CCCTCGCACT 0.946658 -114 GCATAGGTTCCCCCCGCAATTAGAAAATAT 2 78 1 CCCCCGCAAT 0.996823 -223 CCATTTTAGTGCGCCGCCATGACCCTTCGA 2 275 1 GCGCCGCCAT 0.983508 -26 GGTCGGCTAGCCCCCACAATAAAGCCAATT 3 212 1 CCCCCACAAT 0.979813 -89 GGGAAATGAAGCCCCGCAAATTGGCTTTAT 3 230 0 GCCCCGCAAA 0.994088 -71 CGTTCTATTTGCCCCGTCAAGCGCCTAGAT 4 40 1 GCCCCGTCAA 0.955686 -26 ********** Masking position 5 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 TTTTGCTATTATTTTGTTTAGATATTTTCTAATTG 2 94 0 ATGTTTAATT 0.939885 -207 TTATGGCATTATTAGCCTAATTTATGGATCATTTA 2 152 0 ATCCTAATTT 0.851422 -149 ATAACAAGTCAATTAGTTAATATTTGTCTGAAATT 2 183 1 ATGTTAAATT 0.967537 -118 TTTGTCTGAAATTCAGTTTAATTCTCTAAAAGTTG 2 205 1 ATGTTTATTT 0.961659 -96 TACTTTATTCAATAGGTTAAATTTTATCTTCCTTT 3 75 0 ATGTTAATTT 0.979513 -226 TAAAAAATTTACTCAGCTAAATTGTCTCTATATCT 3 114 1 ATGCTAATTT 0.975271 -187 TCTGGCCTCAATTTTGTTAAGATATAGAGACAATT 3 133 0 ATGTTAAATT 0.967537 -168 AAGCCCCGCAAATTGGCTTTATTGTGGGGGCTAGC 3 217 0 ATGCTTTTTT 0.867332 -84 GCTGAAGTAAGTTATTGTGTCA 5 6 1 ATGTTATGTT 0.846736 -17 * * ***** ** * Masking position 8 Map Score: 5.41603 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 92 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 4 GAGAAGATGAACGATTTACTTTCTGTATCC 1 49 1 ACGATTTACT 0.976449 -252 ACATTCATGTAAGATTTACTGATCATTCGG 1 137 1 AAGATTTACT 0.963154 -164 TTACTTAAGAACCATTTACCCATTAATATT 2 20 0 ACCATTTACC 0.978331 -281 TTCTTAAGTAACGATTGACCCCAAGGGGAG 2 39 1 ACGATTGACC 0.945851 -262 AAAGGAAGATAAAATTTAACCTATTGAATA 3 75 1 AAAATTTAAC 0.773767 -226 GTAAATTTTTTACATTTACTTTATTCAATA 3 96 0 TACATTTACT 0.762808 -205 GTAAATGTAAAAAATTTACTCAGCTAAATT 3 107 1 AAAATTTACT 0.943259 -194 AGATATAGAGACAATTTAGCTGAGTAAATT 3 119 0 ACAATTTAGC 0.889386 -182 ********** Masking position 4 Map Score: 3.90724 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 384 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 CACGAGTGCGAGGGAGATGGAACTTGGGCT 1 193 1 AGGGAGATGG 0.990131 -108 TGGCGATCGAAGGGTCATGGCGGCGCACTA 2 281 0 AGGGTCATGG 0.996938 -20 GGCCAGAACTAGGGTCATGGTATTTCCCCT 3 161 1 AGGGTCATGG 0.996938 -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 ACTTCCGTCTTCTTCAAAAAGAGAAGATGA 1 29 1 TCTTCAAAAA 0.931838 -272 CTTGACATGATCTTGAAAAACCGTAAAAAT 1 79 0 TCTTGAAAAA 0.759285 -222 CAAGGAATGGTCAACAAAATACGAATTTCT 1 105 1 TCAACAAAAT 0.96942 -196 TTGCTTGCAGTCTTTAAAATAACCTCATTT 1 279 1 TCTTTAAAAT 0.830138 -22 AGAAAATATCTAAACAAAATAATAGCAAAA 2 99 1 TAAACAAAAT 0.83063 -202 ACGGTCAGAGTCATCAAAATTTTAA 3 6 0 TCATCAAAAT 0.976346 -295 TCTCTATATCTTAACAAAATTGAGGCCAGA 3 138 1 TTAACAAAAT 0.830629 -163 ********** Masking position 6 Map Score: 2.26566 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 442 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 7 CCAACGATCTGCTAGAAGGGTTACTTTTGC 1 228 1 GCTAGAAGGG 0.967832 -73 GCAATGTTAAGGCCCCAGGGAACAGGCAAA 1 253 0 GGCCCCAGGG 0.954061 -48 GTAACGATTGACCCCAAGGGGAGTAAAAAA 2 46 1 ACCCCAAGGG 0.923461 -255 GATATTTTCTAATTGCGGGGGGAACCTATG 2 79 0 AATTGCGGGG 0.831426 -222 GCACTAAAATGGTAGCAGGGCTAAAAACTA 2 257 0 GGTAGCAGGG 0.952932 -44 TGGCGATCGAAGGGTCATGGCGGC 2 287 0 GATCGAAGGG 0.982647 -14 CAACTTTCCCAACCGAGGGGAAATACCATG 3 176 0 AACCGAGGGG 0.935864 -125 TTATCTAGGCGCTTGACGGGGCAAATAGAA 4 42 0 GCTTGACGGG 0.916675 -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 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 Motif number 10 ********** 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