AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_synecho_reg_300.orf -o060_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 RCY32906 29 Synechocystis #2 RCY06983 300 Synechocystis #3 RCY44336 300 Synechocystis #4 RCY38981 59 Synechocystis #5 RCY43130 300 Synechocystis Motif number 1 CATCCAGTGCTTGCCCTGGGTTAACGG 1 13 1 TTGCCCGGGT 0.994247 -17 ATGTTTGATGATGTCCAAGGTCAAATCTACG 2 91 0 ATGTCCAGGT 0.925566 -210 CCTGAACGTTTTCCCCTAGTTTGTACTGAAT 2 122 1 TTCCCCAGTT 0.934144 -179 TTCACGGCGATCGCCCGTCGTCTGGGCTAGC 2 185 1 TCGCCCTCGT 0.94572 -116 ATCCCAACTGATCCCCTTGGTTTTGCTAGCC 2 209 0 ATCCCCTGGT 0.970973 -92 TGATCCCTTGTTGTCCATGCTACAACCATTT 2 261 0 TTGTCCTGCT 0.892378 -40 GAAAAGATTCTCGCCCTAGGAAAAAATGGCA 3 36 0 TCGCCCAGGA 0.94109 -265 CGCCGGGGGGTCCCCCAGGCCGGTTTGAGAG 3 68 1 TCCCCCGGCC 0.861423 -233 CATTATTGAATTGTCCAGCTAGAAAAATCAT 3 114 0 TTGTCCGCTA 0.660395 -187 TTAGGGGGCAATGCCCTGCGTCACAATTAGT 3 155 1 ATGCCCGCGT 0.974132 -146 TCTGACTGCGTTGCCCATCTTTCGATCCCGA 3 258 1 TTGCCCTCTT 0.893722 -43 CTCGGCAAATTTCTCCTAGGAGTAATTTGCC 5 12 0 TTCTCCAGGA 0.896503 -289 TTCCGGGTTCAAGTCCCGGGTTCCGCATTCT 5 77 0 AAGTCCGGGT 0.715537 -224 AAAGACCATCATCCCCCAGGATTGACTGGAA 5 186 1 ATCCCCAGGA 0.933223 -115 AAGTCGGCAGTTCCCCATGGTATCAAAAAAA 5 254 0 TTCCCCTGGT 0.986159 -47 CTGCCGACTTTTCCCCGGCCCTATCCCGAAA 5 275 1 TTCCCCGCCC 0.872102 -26 ****** **** Masking position 6 Map Score: 18.8629 Number of sites scoring better than the average of aligned sites = 5990 Number in coding regions = 5474 Number in noncoding regions = 516 Number of orfs with sites within 600 bp upstream = 472 Fraction of orfs with sites within 600 bp upstream = 0.0758111 Motif number 2 TACAAACTAGGGGAAAACGTTCAGGATGTT 2 117 0 GGGAAAACGT 0.836076 -184 CAAAACCAAGGGGATCAGTTGGGATCAGTC 2 215 1 GGGATCAGTT 0.969509 -86 GGGATCAGTTGGGATCAGTCCTCCCTTTGG 2 225 1 GGGATCAGTC 0.988576 -76 TGGACAACAAGGGATCAGTCCGCTAGAAAC 2 275 1 GGGATCAGTC 0.988576 -26 ACCCCCCGGCGGGAAAAGATTCTCGCCCTA 3 49 0 GGGAAAAGAT 0.908374 -252 GCGGTTTAGGGGGCAATGCCCTGCGTCACA 3 150 1 GGGCAATGCC 0.861494 -151 TGGATGGGTTGGGAAAAATT 4 1 0 GGGAAAAATT 0.778315 -59 CCACCGCAAGCGGAACTGGCGGAATTGGTA 5 144 0 CGGAACTGGC 0.883828 -157 TGATACCATGGGGAACTGCCGACTTTTCCC 5 260 1 GGGAACTGCC 0.977981 -41 GATAGGGCCGGGGAAAAGTCGGCAGTTCCC 5 270 0 GGGAAAAGTC 0.990939 -31 GGTGATTTCGGGATAGGGCCGGGGAAAAG 5 282 0 GGGATAGGGC 0.943656 -19 ********** Masking position 3 Map Score: 11.896 Number of sites scoring better than the average of aligned sites = 1418 Number in coding regions = 1258 Number in noncoding regions = 160 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 TACCAGAGCGTTTTTAAACCA 2 1 0 TTTTTAACCA 0.934722 -300 CCCCTTGGTTTTGCTAGCCCAGACGACGGGC 2 197 0 TTGCTACCCA 0.975394 -104 CTACAACCATTTTCGACCCCAAAGGGAGGAC 2 242 0 TTTCGACCCA 0.994169 -59 TTTGGCTGATTTTTTACCCCAACAACTTTGA 3 195 1 TTTTTACCCA 0.981306 -106 GTTGCCCATCTTTCGATCCCGATTAGCTACT 3 267 1 TTTCGACCCG 0.981294 -34 AATTTTTCCCAACCCATCCATGGTTA 4 6 1 TTCCCACCCA 0.95877 -54 GGCTTAATTTTTTTGATACCATGGGGAACTG 5 247 1 TTTTGAACCA 0.957479 -54 ****** **** Masking position 6 Map Score: 6.30081 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 176 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 CGGCTTATATTATGATCAATTGG 3 1 0 TATGAAATGG 0.980426 -300 ATTCTCGCCCTAGGAAAAAATGGCACCCGGCTT 3 28 0 TAGGAAATGG 0.990426 -273 CCCAGGCCGGTTTGAGAGAATGGGACTAAATCA 3 81 1 TTTGAGATGG 0.962805 -220 CCCCAACAACTTTGACCAACTGGGCTTAACTAA 3 211 1 TTTGAAATGG 0.974662 -90 AAATTTCTCCTAGGAGTAATTTGCCT 5 4 0 TAGGAAATTG 0.930645 -297 GCAAGCGGAACTGGCGGAATTGGTAGACGCGCT 5 136 0 CTGGCAATGG 0.942694 -165 CATCATCCCCCAGGATTGACTGGAAGTCAACAG 5 192 1 CAGGAGATGG 0.979096 -109 ***** ** *** Masking position 9 Map Score: 4.68781 Number of sites scoring better than the average of aligned sites = 296 Number in coding regions = 262 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 CGTCTGGGCTAGCAAAACCAAGGGGATCAG 2 203 1 AGCAAAACCA 0.991579 -98 TTGTCCAGCTAGAAAAATCATTGATTTAGT 3 105 0 AGAAAAATCA 0.90921 -196 CCCCCTAAACCGCAAAGCCATTATTGAATT 3 133 0 CGCAAAGCCA 0.982836 -168 TCTTTCGGTAAGCAAAACCACCGCAAGCGG 5 161 0 AGCAAAACCA 0.991579 -140 TTTTGCTTACCGAAAGACCATCATCCCCCA 5 174 1 CGAAAGACCA 0.962142 -127 ********** Masking position 5 Map Score: 4.04103 Number of sites scoring better than the average of aligned sites = 234 Number in coding regions = 216 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 ATGTCATTGAGCCAACCGCCAATCATTTTT 2 45 1 GCCAACCGCC 0.92142 -256 AGGAAAAAATGGCACCCGGCTTATATTATG 3 20 0 GGCACCCGGC 0.994777 -281 GGCCTGGGGGACCCCCCGGCGGGAAAAGAT 3 59 0 ACCCCCCGGC 0.978075 -242 TCCCATTCTCTCAAACCGGCCTGGGGGACC 3 76 0 TCAAACCGGC 0.973946 -225 AGGTTTACTATCAACTCGGCAAATTTCTCC 5 27 0 TCAACTCGGC 0.948057 -274 GTTAGAATGCGGAACCCGGGACTTGAACCC 5 74 1 GGAACCCGGG 0.965307 -227 ACCCGGGACTTGAACCCGGAAGTCCTTACG 5 87 1 TGAACCCGGA 0.964805 -214 AAGACCATCATCCCCCAGGATTGACTGGAA 5 187 1 TCCCCCAGGA 0.817238 -114 ********** Masking position 8 Map Score: 5.2947 Number of sites scoring better than the average of aligned sites = 1276 Number in coding regions = 1194 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 GGTCGAAAATGGTTGTAGCATGGACAACAA 2 255 1 GGTTGTAGCA 0.893685 -46 GGGCATGTTTCTAGCGGACTGATCCC 2 285 0 GTTTCTAGCG 0.97345 -16 GGCGGGAAAAGATTCTCGCCCTAGGAAAAA 3 42 0 GATTCTCGCC 0.941955 -259 AGGACTTCCGGGTTCAAGTCCCGGGTTCCG 5 83 0 GGTTCAAGTC 0.892746 -218 GCTAGATTCAGGTTCTAGTGTTCGTAAGGA 5 109 0 GGTTCTAGTG 0.980084 -192 ACTAGAACCTGAATCTAGCGCGTCTACCAA 5 120 1 GAATCTAGCG 0.941001 -181 ********** Masking position 4 Map Score: 0.215837 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 195 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 ********** No masking Map Score: -2.90369e-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: -2.90369e-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: -2.90369e-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