AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i063_Glycine_Catabolism_synecho_reg_100.orf -o063_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 RCY06192 207 Synechocystis #2 RCY19916 97 Synechocystis #3 RCY47027 173 Synechocystis #4 RCY44761 150 Synechocystis Motif number 1 CAATCAAAACCGCCACGGCGATCGCCAAGG 1 68 1 CGCCACGGCG 0.626266 -140 GACAATTATTTTCCTTGGCGATCGCCGTGG 1 80 0 TTCCTTGGCG 0.951534 -128 TAATTGTCTTTTTCTCGGCGTTCCTGCTCC 1 102 1 TTTCTCGGCG 0.925805 -106 GCGTTCCTGCTCCTTGGGCCTTTTTTCTGC 1 119 1 TCCTTGGGCC 0.928262 -89 GAACGGTTAACTCCTGGGCGGGGCTACGAC 1 150 0 CTCCTGGGCG 0.962343 -58 CCTTTCGGCGATCGGTTCGG 1 198 0 CCTTTCGGCG 0.823987 -10 GCAGGGGTTGTTCCTGGGTCCACAAAGGAC 2 25 0 TTCCTGGGTC 0.808576 -73 GAACAACCCCTGCCTCCGCCATATTTTTGG 2 42 1 TGCCTCCGCC 0.969686 -56 GCCAAGGCGGCCCCATCCCCATAAAACTCG 3 38 0 CCCCATCCCC 0.624038 -136 GGGTCAGCATTGCCAAGGCGGCCCCATCCC 3 49 0 TGCCAAGGCG 0.591839 -125 GCAATGCTGACCCCTAGGCCTACCAAAATT 3 66 1 CCCCTAGGCC 0.966974 -108 CATCCTTTCCCTACTCCGCCATT 3 161 1 CTACTCCGCC 0.827131 -13 TATTGAAAGTCCCCTAGCCCCCAATACTGG 4 30 1 CCCCTAGCCC 0.958985 -121 ********** Masking position 9 Map Score: 15.5031 Number of sites scoring better than the average of aligned sites = 6591 Number in coding regions = 6071 Number in noncoding regions = 520 Number of orfs with sites within 600 bp upstream = 482 Fraction of orfs with sites within 600 bp upstream = 0.0774173 Motif number 2 ATTGCTGGACCTGCGGAAAAGCAGCTAAACA 1 19 0 CTCGGAAAAG 0.958762 -189 ACGGCGATCGCCAAGGAAAATAATTGTCTTT 1 82 1 CCAGGAAAAT 0.980796 -126 AGCAGGAACGCCGAGAAAAAGACAATTATTT 1 99 0 CCAGAAAAAG 0.986433 -109 GAAAAAAGGCCCAAGGAGCAGGAACGCCGAG 1 115 0 CCAGGAGCAG 0.982202 -93 GGGGCTACGACCGCAGAAAAAAGGCCCAAGG 1 130 0 CCCAGAAAAA 0.942961 -78 CCTTTGTGGACCCAGGAACAACCCCTGCCTC 2 27 1 CCAGGAACAA 0.983767 -71 ATAGATTTTTCCTAAAAAAAGCACAAAAAAT 4 97 0 CCAAAAAAAG 0.952001 -54 ** ******** Masking position 7 Map Score: 5.85057 Number of sites scoring better than the average of aligned sites = 878 Number in coding regions = 773 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 GCTGCAATCAAAACCGCCACGGCGATCGCCA 1 64 1 AACCGCCACG 0.934129 -144 AGAGGAACGGTTAACTCCTGGGCGGGGCTAC 1 153 0 TAACTCCTGG 0.884449 -55 GGACCCAGGAACAACCCCTGCCTCCGCCATA 2 34 1 AAACCCCTGC 0.971005 -64 TTGGCAATGCTGACCCCTAGGCCTACCAAAA 3 63 1 TACCCCTAGG 0.966612 -111 AGGGAAAGGATGAACGCCTGGACTGGATCTG 3 142 0 TAACGCCTGG 0.954291 -32 CTGTATTGAAAGTCCCCTAGCCCCCAATACT 4 27 1 ATCCCCTAGC 0.924336 -124 ATCGAATCTGATTCCCCCAGTATTGGGGGCT 4 45 0 ATCCCCCAGT 0.951413 -106 AAGCACAAAAAATCCCCCTGGTTAAAGGAGG 4 79 0 ATCCCCCTGG 0.992162 -72 * ********* Masking position 5 Map Score: 4.47128 Number of sites scoring better than the average of aligned sites = 3164 Number in coding regions = 2829 Number in noncoding regions = 335 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549 Motif number 4 AGGTCCAGCAATATTTTGAAATTGAAGCTG 1 38 1 ATATTTTGAA 0.91996 -170 CCTCCGCCATATTTTTGGTAAACTAACAAC 2 54 1 ATTTTTGGTA 0.971199 -44 CGTTTTAAGAATATTTGGACGAGTTTTATG 3 19 1 ATATTTGGAC 0.951243 -155 AAGCTTAACAAATTTTGGTAGGCCTAGGGG 3 76 0 AATTTTGGTA 0.892694 -98 AATCTGTAACATTTTTTGACAGATCCAGTC 3 123 1 ATTTTTTGAC 0.958592 -51 AACCAGGGGGATTTTTTGTGCTTTTTTTAG 4 87 1 ATTTTTTGTG 0.926359 -64 ********** Masking position 5 Map Score: 3.1262 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 304 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 ********** No masking Map Score: -7.08111e-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 6 ********** No masking Map Score: -7.08111e-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 7 ********** No masking Map Score: -7.08111e-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