AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i003_GMP_Biosynthesis_synecho_reg_300.orf -o003_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 RCY53439 283 Synechocystis #2 RCY05376 78 Synechocystis #3 RCY50998 180 Synechocystis #4 RCY13509 16 Synechocystis #5 RCY34085 102 Synechocystis #6 RCY46344 300 Synechocystis Motif number 1 GGAGTTGACATTGCCATGGGAAAACTTTTGCTA 1 15 1 TTGCATGGGA 0.879172 -269 TGGTTTTCGGTGGCGATCGGGCCTAGAACCTGG 1 134 0 TGGGATCGGC 0.972484 -150 GATCCCCCCTGGGCCATGAGCCCAGAAAAATTG 1 183 1 GGGCATGAGC 0.903202 -101 CCCATCTTATCGGTAGTGGGCCAACCCGGAAGA 1 225 0 CGGAGTGGGA 0.917217 -59 AAGCGTTAAATGGGAGTCGGAGCGGGTTCAGCA 3 52 0 TGGAGTCGGC 0.985857 -129 CCTAATCCAGTGGGGATCAGAGC 5 1 0 TGGGATCAGC 0.971985 -102 TCTGACCCTTTGGACGTCAGCACAGCCTAATAA 5 35 0 TGGCGTCAGC 0.995828 -68 TAGCGCAGATTTGCCGTGGGTTATTCTGGGCTT 6 130 1 TTGCGTGGGA 0.957531 -171 TGGGTTATTCTGGGCTTCAGGTATTGGGGTAGA 6 146 1 TGGCTTCAGA 0.945066 -155 GGCAAGGCCATGGTCGTCAACAATCCCCGTATT 6 178 0 TGGCGTCAAA 0.919048 -123 GACCATGGCCTTGCCGTCAGTTAGACCCAGAAA 6 196 1 TTGCGTCAGA 0.972145 -105 GAATTTATACTGGAGGTGAGGGCGAATCCCCAG 6 262 0 TGGGGTGAGC 0.985542 -39 GGCGATCGGCAGTCAGGAATTTATACTGG 6 282 0 CGGAGTCAGA 0.944934 -19 *** ****** * Masking position 7 Map Score: 16.9357 Number of sites scoring better than the average of aligned sites = 1154 Number in coding regions = 1052 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 2 CTAGAACCTGGCCAAAGTGCTGGACCTTAACTAAGC 1 109 0 GCCAAGGGCC 0.768458 -175 GCCACCGAAAACCAGTTTAAAGCCCATTGGGATCCC 1 153 1 ACCAGTACCA 0.887661 -131 GGGCTCATGGCCCAGGGGGGATCCCAATGGGCTTTA 1 170 0 CCCAGGGCCA 0.960262 -114 GGGCCATGAGCCCAGAAAAATTGGCCAATTCTTCTT 1 193 1 CCCAGAAGCC 0.992901 -91 GTTGTTCATTCCCCAAACAATCCGCCAAATCCT 1 261 1 CCCCAAACCC 0.986797 -23 TGTCTCCCCCAGATGGGTTGTCCGTAGGTCGCC 3 158 0 CCCAGTGGCC 0.981622 -23 AAATTAGCGTACCAAATAATCTGACCCTTTGGACGT 5 51 0 ACCAATAGCC 0.893401 -52 GGATTCGAACCCCCGTTGAGTTGCCCCAAAACAGAT 6 12 1 CCCCGTAGCC 0.991045 -289 CTCAAGAATTCCCTGGAGAGGTGGCAGAGCGGTTGA 6 64 0 CCCTGAAGCA 0.889928 -237 ATACCTGAAGCCCAGAATAACCCACGGCAAATCTGC 6 134 0 CCCAGAACCG 0.959361 -167 CGTCAACAATCCCCGTATTCTACCCCAATACCTGAA 6 161 0 CCCCGATCCC 0.963613 -140 CGTCAGTTAGACCCAGAAACGACACCACGAATCTAG 6 210 1 ACCCAAACCC 0.942889 -91 GAGGGCGAATCCCCAGGCACACCTCAGAGAGACTAG 6 242 0 CCCCAGACCA 0.952147 -59 ***** * * * ** Masking position 3 Map Score: 13.621 Number of sites scoring better than the average of aligned sites = 2225 Number in coding regions = 2047 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 197 Fraction of orfs with sites within 600 bp upstream = 0.0316415 Motif number 3 TTTTTAGCAAAAGTTTTCCCATGGCAATGT 1 22 0 AAGTTTTCCC 0.64088 -262 GGGAATAACCTGGTTTGCCAAAGTTTTTCA 1 73 0 TGGTTTGCCA 0.792358 -211 AAGCCCATTGGGATCCCCCCTGGGCCATGA 1 172 1 GGATCCCCCC 0.855037 -112 CCCGGAAGAAGAATTGGCCAATTTTTCTGG 1 204 0 GAATTGGCCA 0.906372 -80 TTCTTCTTCCGGGTTGGCCCACTACCGATA 1 221 1 GGGTTGGCCC 0.992293 -63 AGGATTTGGCGGATTGTTTGG 1 273 0 GGATTTGGCG 0.876134 -11 TCCCCCAGATGGGTTGTCCGTAGGTCGCCG 3 157 0 GGGTTGTCCG 0.966841 -24 AACCCCCGTTGAGTTGCCCCAAAACAGATT 6 19 1 GAGTTGCCCC 0.953576 -282 AACAGATTTCGAGTCTGCCGCATTCAACCG 6 41 1 GAGTCTGCCG 0.942007 -260 ATCTTAGCGCAGATTTGCCGTGGGTTATTC 6 126 1 AGATTTGCCG 0.912819 -175 GTGTGCCTGGGGATTCGCCCTCACCTCCAG 6 256 1 GGATTCGCCC 0.980573 -45 ********** Masking position 4 Map Score: 8.2873 Number of sites scoring better than the average of aligned sites = 2821 Number in coding regions = 2604 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 4 TGTCCTAGATTTTTAGCAAAAGTTTTCCCA 1 31 0 TTTTAGCAAA 0.945666 -253 AGTGTTTTAGCAATGATAGCTAGG 2 65 0 TTTTAGCAAT 0.982871 -14 AAGGTTTGGTGTTTAGCAATTTAGTGTTGA 3 13 1 GTTTAGCAAT 0.984122 -168 GTCGGAGCGGGTTCAGCAATTAGCCACTCA 3 40 0 GTTCAGCAAT 0.985274 -141 TTGAGAAGGATTTCTGCAATTTTCCGCCCC 6 95 1 TTTCTGCAAT 0.949591 -206 ********** Masking position 3 Map Score: 5.16224 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 90 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 ATGAACAACCCTCCCATCTTATCGGTAGTGG 1 239 0 CTCCCACTTA 0.990755 -45 GAGAAGAGAACTCAAAACTTAAATATAAAGA 2 23 0 CTCAAACTTA 0.958385 -56 CAATTAGCCACTCAACACTAAATTGCTAAAC 3 23 0 CTCAACCTAA 0.95023 -158 CCCGCTCCGACTCCCATTTAACGCTTACTTC 3 59 1 CTCCCATTAA 0.943114 -122 ACGCTTACTTCTCACCCCTAACTCCTGCTGT 3 79 1 CTCACCCTAA 0.98261 -102 CAATTTTCCGCCCCCATCTTAGCGCAGATTT 6 111 1 CCCCCACTTA 0.975116 -190 ****** **** Masking position 9 Map Score: 3.1451 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 107 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 GCTTTAAACTGGTTTTCGGTGGCGATCGGG 1 146 0 GGTTTTCGGT 0.924057 -138 TTTGGCGGATTGTTTGGGGAATGAACAACC 1 260 0 TGTTTGGGGA 0.878894 -24 CTAAGGTTTGGTGTTTAGCAATTT 3 5 1 GGTTTGGTGT 0.96784 -176 GAACAGCAGGAGTTAGGGGTGAGAAGTAAG 3 82 0 AGTTAGGGGT 0.878894 -99 GATCCCCACTGGATTAGGGTTATTAGGCTG 5 16 1 GGATTAGGGT 0.93851 -87 CTCGAAATCTGTTTTGGGGCAACTCAACGG 6 24 0 GTTTTGGGGC 0.970072 -277 TGGGCTTCAGGTATTGGGGTAGAATACGGG 6 156 1 GTATTGGGGT 0.974725 -145 TCGTGGTGTCGTTTCTGGGTCTAACTGACG 6 210 0 GTTTCTGGGT 0.898399 -91 ********** Masking position 4 Map Score: 3.00878 Number of sites scoring better than the average of aligned sites = 1717 Number in coding regions = 1529 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 182 Fraction of orfs with sites within 600 bp upstream = 0.0292323 Motif number 7 TTAGTGTTGAGTGGCTAATTGCTGAACCCGCTCC 3 33 1 GTGGAATGCG 0.98897 -148 ACTCATTATTGCGGCGACCTACGGACAACCCATC 3 146 1 GCGGACTACG 0.986145 -35 AGGTGGCAGAGCGGTTGAATGCGGCAGACTCGAA 6 48 0 GCGGGATGCG 0.997421 -253 TAAGATGGGGGCGGAAAATTGCAGAAATCCTTCT 6 98 0 GCGGAATGCG 0.997848 -203 CCCCATCTTAGCGCAGATTTGCCGTGGGTTATTC 6 122 1 GCGCATTGCG 0.961927 -179 TTCAGGTATTGGGGTAGAATACGGGGATTGTTGA 6 161 1 GGGGGATACG 0.973839 -140 **** ** *** * Masking position 10 Map Score: 4.81129 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 112 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 ********** No masking Map Score: -3.13817e-12 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: -3.13817e-12 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: -3.13817e-12 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