AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i298_mixed13_synecho_reg_300.orf -o298_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 RCY20391 256 Synechocystis #2 RCY49700 117 Synechocystis #3 RCY39680 96 Synechocystis #4 RCY41334 295 Synechocystis #5 RCY24823 47 Synechocystis #6 RCY42786 46 Synechocystis #7 RCY33128 300 Synechocystis Motif number 1 TAGCCCATTTAGTCTCCCCTTACCC 1 6 0 AGTCTCCCCT 0.948892 -251 GGGTAACGGATCTTTTCCCCGGAGCGCTTC 1 72 1 TCTTTTCCCC 0.897469 -185 TATATTGCTATCTAGCCCCTGTTTTTGCTT 1 186 1 TCTAGCCCCT 0.947072 -71 GTTGTTTAAATCCTTCCCCACCAGAAACTT 2 40 1 TCCTTCCCCA 0.919419 -78 TGGCCACCGCTGTCGCCCCTCACCCCATTG 2 71 1 TGTCGCCCCT 0.970099 -47 CCCCTCACCCCATTGCCCCCGTAGTTGACT 2 86 1 CATTGCCCCC 0.865346 -32 AATGCTGGCCTCATTCCCCCATTTGTCTGG 3 31 0 TCATTCCCCC 0.974453 -66 AGGCCAGCATTTTCTCCCCTTCCACTAGAA 3 50 1 TTTCTCCCCT 0.950365 -47 CCGTAAAAAGAATTTCCCCCATTCTAGTGG 3 71 0 AATTTCCCCC 0.92089 -26 ACGTATAAACTCCATCCCCCAATGGTTAGC 4 82 1 TCCATCCCCC 0.948313 -214 GCAAGAATTAAGTCTTCCCTCGGAGCAAGC 4 110 1 AGTCTTCCCT 0.618848 -186 TAGCTCCGGCATTTTCCCCTGGGTAATCTA 4 172 1 ATTTTCCCCT 0.864277 -124 CCCTGGGTAATCTATCCCCAATTTCCCGAT 4 188 1 TCTATCCCCA 0.908052 -108 CCGATGTCCATCATGCCCCCTCCTCCGTCT 4 213 1 TCATGCCCCC 0.969035 -83 CCGTCTTCGGTTCCGCCCCATCAGGGGCAT 4 237 1 TTCCGCCCCA 0.765991 -59 CCGCCAAAACCCATGCCCCTGATGGGGCGG 4 249 0 CCATGCCCCT 0.843957 -47 CCAAGTCGGCTAACTCCCCCATTTTTAGGC 7 100 1 TAACTCCCCC 0.930256 -201 ATAAATTTTTAGTCTCCCCCGGCGCTGGAG 7 223 1 AGTCTCCCCC 0.971379 -78 ********** Masking position 7 Map Score: 24.343 Number of sites scoring better than the average of aligned sites = 3781 Number in coding regions = 3249 Number in noncoding regions = 532 Number of orfs with sites within 600 bp upstream = 486 Fraction of orfs with sites within 600 bp upstream = 0.0780597 Motif number 2 GACTTTTTAGTAAGCACAACCTTAAAATCCT 1 120 0 TAAGCAAACC 0.915013 -137 AAGGAATTAACAAGCAAAAACAGGGGCTAGA 1 196 0 CAAGCAAAAC 0.967902 -61 AGGATTTAAACAACCATAACCAGCCCAAAGA 2 23 0 CAACCAAACC 0.976829 -95 AAATCCTTCCCCACCAGAAACTTGTGGCCAC 2 47 1 CCACCAAAAC 0.970195 -71 GGGAATGAGGCCAGCATTTTCTCCCCTTCCA 3 43 1 CCAGCATTTC 0.858214 -54 AATGGTAGCTCCGGCATTTTCCCCTGGGTAA 4 167 1 CCGGCATTTC 0.867686 -129 AAACCGCTCCCCGCCAAAACCCATGCCCCTG 4 258 0 CCGCCAAACC 0.986457 -38 AAAATCAAGACAAGCAAAACCGCTCCCCGCC 4 274 0 CAAGCAAACC 0.984197 -22 CCCCCATTTTTAGGCAAAATCATATACAGAC 7 115 1 TAGGCAAATC 0.849572 -186 TCACATTATACCGCCATTAACTACAAAAAAA 7 253 0 CCGCCATAAC 0.941068 -48 ****** **** Masking position 6 Map Score: 9.80001 Number of sites scoring better than the average of aligned sites = 1098 Number in coding regions = 1001 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 TAAAATCCTCAAATACTCCCTAGGAACGAA 1 99 0 AAATACTCCC 0.98649 -158 ATGGTTGTTTAAATCCTTCCCCACCAGAAA 2 37 1 AAATCCTTCC 0.897773 -81 GGAGAAACGTATAAACTCCATCCCCCAATG 4 76 1 ATAAACTCCA 0.891367 -220 AAAAGCTTCACTTCGGTTTT 7 1 1 AAAAGCTTCA 0.846163 -300 AAGGCAGCGGAAAAACTCCCTAGAGCAGAT 7 55 0 AAAAACTCCC 0.991535 -246 GACTTGGAGAAAATACTCTCTAAAGGCAGC 7 77 0 AAATACTCTC 0.943505 -224 TTAACTACAAAAAAACTCCAGCGCCGGGGG 7 238 0 AAAAACTCCA 0.978626 -63 TAAATAGATAAAAAACTTTCACATTATACC 7 272 0 AAAAACTTTC 0.912743 -29 ********** Masking position 3 Map Score: 8.06795 Number of sites scoring better than the average of aligned sites = 595 Number in coding regions = 472 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 4 GATCCGTTACCCTAGGAATTTACATCCGTG 1 54 0 CCTAGGAATT 0.977248 -203 GCGCTTCGTTCCTAGGGAGTATTTGAGGAT 1 95 1 CCTAGGGAGT 0.98418 -162 GAGTAACCCCCGAAGGAATTAACAAGCAAA 1 209 0 CGAAGGAATT 0.921078 -48 AGTTGGCCGAACGGATTAACCCAGACA 3 8 1 CGAACGGATT 0.831694 -89 TTGGGTTGAGACAAGGAATTAATCACAGCA 5 12 0 ACAAGGAATT 0.899987 -36 CATTGCCTTGGGATTGAAGCAAAAT 6 6 1 CCTTGGGATT 0.951672 -41 AGATTTACGAGGGATTTTGCCATTTT 6 31 0 ACGAGGGATT 0.931053 -16 AGGCATCTGCTCTAGGGAGTTTTTCCGCTG 7 51 1 TCTAGGGAGT 0.905891 -250 ********** Masking position 8 Map Score: 5.17578 Number of sites scoring better than the average of aligned sites = 1041 Number in coding regions = 924 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 TTTCTTAAAGATTAGCCCATTTAGTCTCCCC 1 17 0 ATTACCCATT 0.979289 -240 AACAACCATAACCAGCCCAAAGATTAATGAA 2 15 0 ACCACCCAAA 0.910609 -103 GCTGTCGCCCCTCACCCCATTGCCCCCGTAG 2 79 1 CTCACCCATT 0.950257 -39 GGCCGAACGGATTAACCCAGACAAATGGGGG 3 15 1 ATTACCCAGA 0.870883 -82 TGCTGGCCTCATTCCCCCATTTGTCTGGGTT 3 28 0 ATTCCCCATT 0.958609 -69 ACAGTATTAGCCCTATCAAAAATTCA 4 6 1 ATTACCCTAT 0.881888 -290 AATTCCTTGTCTCAACCCAATGTTACATCAA 5 22 1 CTCACCCAAT 0.950257 -26 AAGTCGGCTAACTCCCCCATTTTTAGGCAAA 7 102 1 ACTCCCCATT 0.950257 -199 TCATATACAGACTATCCCAATATTGCCAGAG 7 134 1 ACTACCCAAT 0.975043 -167 **** ****** Masking position 6 Map Score: 7.90352 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 229 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 GGTGGAAGTTCAGTTTGGCTCGACTTTTTA 1 142 0 CAGTTTGGCT 0.978881 -115 AACTTCCACCCAGTATTGCCCAGCTATATT 1 162 1 CAGTATTGCC 0.926708 -95 GGCTAGATAGCAATATAGCTGGGCAATACT 1 173 0 CAATATAGCT 0.783501 -84 CTGGGTTAATCCGTTCGGCCAACT 3 5 0 CCGTTCGGCC 0.948234 -92 CCTCATTCCCCCATTTGTCTGGGTTAATCC 3 23 0 CCATTTGTCT 0.775762 -74 TGGCGGGGAGCGGTTTTGCTTGTCTTGATT 4 273 1 CGGTTTTGCT 0.914421 -23 AGGGATTTTGCCATTTTGCTTCAATCCCAA 6 18 0 CCATTTTGCT 0.956986 -29 GTATTTTCTCCAAGTCGGCTAACTCCCCCA 7 91 1 CAAGTCGGCT 0.804371 -210 CAGACTATCCCAATATTGCCAGAGCTTTGA 7 141 1 CAATATTGCC 0.907588 -160 ********** Masking position 9 Map Score: 3.12678 Number of sites scoring better than the average of aligned sites = 1210 Number in coding regions = 1062 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137 Motif number 7 AGATTAGCCCATTTAGTCTCCCCTTACCC 1 10 0 ATTTAGTCTC 0.980386 -247 GTTAGCAAGAATTAAGTCTTCCCTCGGAGC 4 106 1 ATTAAGTCTT 0.878825 -190 ATTGCTAGAATTTTAGTCTGCCTTCTACAG 7 178 0 TTTTAGTCTG 0.964489 -123 TGGAATAAATTTTTAGTCTCCCCCGGCGCT 7 219 1 TTTTAGTCTC 0.980386 -82 ********** Masking position 5 Map Score: 0.179591 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 14 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 ********** No masking Map Score: 3.21409e-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: 3.21409e-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: 3.21409e-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