AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i066_Lysine_Biosynthesis_synecho_reg_100.orf -o066_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 RCY33655 258 Synechocystis #2 RCY52095 117 Synechocystis Motif number 1 GTGGAGAGCATGGCAGGGGGATTTTTAATAC 1 159 0 TGGAGGGGGA 0.999165 -100 TTCCGGTGGTTGGAAGGGGCATTTCAGTGGA 1 185 0 TGGAGGGGCA 0.997783 -74 ATTTTGGTTGGGGGAGGGGGAGGCCGGGGTT 1 229 0 GGGAGGGGGA 0.999467 -30 GGGATCAGGTTAGAGGGAAACTAAAGTC 2 100 0 GGTAGAGGGA 0.991651 -18 *** ******* Masking position 5 Map Score: 7.24394 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 131 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 CAATAACTCTTGTAATATCCCAGTTTATCAA 1 55 0 TGTAATTCCC 0.978166 -204 TTTAGGGTTTTGCTTTGCCCCCGGTTGTTGT 1 91 1 TGCTTTCCCC 0.914074 -168 TTTATCTGTATTAAAAATCCCCCTGCCATGC 1 152 1 TTAAAATCCC 0.981594 -107 TGCTCTCCACTGAAATGCCCCTTCCAACCAC 1 180 1 TGAAATCCCC 0.990222 -79 AAGCACCTTATTAAAAACCCCGGCCTCCCCC 1 214 1 TTAAAACCCC 0.984712 -45 AATAGTTTCTTTATTATTCCCAACGGCGATC 2 65 1 TTATTATCCC 0.925574 -53 ATCGCCTGACTTTAGTTTCCCTCTAACCTGA 2 93 1 TTTAGTTCCC 0.943718 -25 ****** **** Masking position 1 Map Score: 5.80534 Number of sites scoring better than the average of aligned sites = 831 Number in coding regions = 651 Number in noncoding regions = 180 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 3 ATCAATCTTAGGGATGATTGTTTTCCTTCT 1 30 0 GGGATGATTG 0.923095 -229 ATTGATAAACTGGGATATTACAAGAGTTAT 1 54 1 TGGGATATTA 0.890316 -205 GCATGGCAGGGGGATTTTTAATACAGATAA 1 153 0 GGGATTTTTA 0.986925 -106 TGGTTGGAAGGGGCATTTCAGTGGAGAGCA 1 180 0 GGGCATTTCA 0.931597 -79 GGGGGAGGCCGGGGTTTTTAATAAGGTGCT 1 215 0 GGGGTTTTTA 0.984272 -44 AGTATTTTACGGCAATTTTGTCAGGAAAAG 2 29 0 GGCAATTTTG 0.927085 -89 GATCGCCGTTGGGAATAATAAAGAAACTAT 2 66 0 GGGAATAATA 0.940015 -52 ********** Masking position 2 Map Score: 3.16413 Number of sites scoring better than the average of aligned sites = 2071 Number in coding regions = 1760 Number in noncoding regions = 311 Number of orfs with sites within 600 bp upstream = 280 Fraction of orfs with sites within 600 bp upstream = 0.0449727 Motif number 4 CCATAGTTACAGCCAAAAAAGAAGGAAAA 1 10 1 CAGCCAAAAA 0.986089 -249 ATTTTTAATACAGATAAAATTTAGTCGGAC 1 140 0 CAGATAAAAT 0.966826 -119 CCCCCTCCCCCAACCAAAATCTTTTACCG 1 240 1 CAACCAAAAT 0.978299 -19 CTTTCTTTTCCTGACAAAATTGCCGTAAAA 2 25 1 CTGACAAAAT 0.978645 -93 ********** Masking position 6 Map Score: 2.37345 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 339 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 5 AGAAGGAAAACAATCATCCCTAAGATTGAT 1 30 1 CAATCATCCC 0.888395 -229 ATCGGAGCTACAACAACCGGGGGCAAAGCA 1 101 0 CAACAACCGG 0.959916 -158 TCGGACTGGTCGGACATCGGAGCTACAACA 1 116 0 CGGACATCGG 0.971127 -143 ATGCCCCTTCCAACCACCGGAAGCACCTTA 1 194 1 CAACCACCGG 0.992062 -65 TTAAAAACCCCGGCCTCCCCCTCCCCCAAC 1 224 1 CGGCCTCCCC 0.975371 -35 TTATTCCCAACGGCGATCGCCTGACTTTAG 2 78 1 CGGCGATCGC 0.982389 -40 ********** Masking position 8 Map Score: 2.25688 Number of sites scoring better than the average of aligned sites = 3362 Number in coding regions = 3154 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 6 TTAGGGATGATTGTTTTCCTTCTTTTTTGG 1 23 0 TTGTTTTCCT 0.99329 -236 GTAATTCTCTTTCTTTTCCTGACAAAATTG 2 17 1 TTCTTTTCCT 0.987723 -101 CGCCTGACTTTAGTTTCCCTCTAACCTGAT 2 95 1 TAGTTTCCCT 0.986027 -23 ********** Masking position 5 Map Score: 1.35638 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 40 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 ********** No masking Map Score: 4.64285e-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 8 ********** No masking Map Score: 4.64285e-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 9 ********** No masking Map Score: 4.64285e-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