AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i181_pantotenate_Biosynthesis_synecho_reg_100.orf -o181_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 RCY37956 139 Synechocystis #2 RCY07064 50 Synechocystis #3 RCY31978 37 Synechocystis #4 RCY28308 300 Synechocystis #5 RCY48903 300 Synechocystis Motif number 1 CTGTCCTAGACCCCCCGCCGCAAGTCTTCA 1 19 0 CCCCCCGCCG 0.992528 -121 CCAGACAAATTGCCCCGCTGTCCTAGACCC 1 36 0 TGCCCCGCTG 0.936206 -104 CCACCATCAACACCCCGGAGGGTGCC 3 22 1 CACCCCGGAG 0.920249 -16 TTTCTGGGATTCCCCAGGCGGCGATCGCCA 4 80 1 TCCCCAGGCG 0.995428 -221 CCTAAAAAATTCCCCCACCCCTAGGGTGCC 4 143 1 TCCCCCACCC 0.988032 -158 CCCCTAGGGTGCCCACGGCCCAGTCAGGGT 4 160 1 GCCCACGGCC 0.889867 -141 GCGGATTTTATCCCCAGGAGGTTAAGGTTT 4 205 0 TCCCCAGGAG 0.991345 -96 CCCCAGTGATTCCCCCAGTTAGCGGATTTT 4 226 0 TCCCCCAGTT 0.919169 -75 TCCCCAGACTTTCCCCAGTGATTCCCCCAG 4 238 0 TTCCCCAGTG 0.9476 -63 CCCCAGGCCATTCCCCAGACTTTCCCCAGT 4 249 0 TTCCCCAGAC 0.92971 -52 GGCTAGTTTCTCCCCAGGCCATTCCCCAGA 4 260 0 TCCCCAGGCC 0.990034 -41 GTGTTACTATGCCCCCATAGAGTAATGATC 5 117 0 GCCCCCATAG 0.863432 -184 AGACCTAATATCCCCAGCCGAGGGGAGAAC 5 147 0 TCCCCAGCCG 0.99004 -154 CGAAAGTTCCTCCCCCAGAGTAACCAGAAA 5 198 1 TCCCCCAGAG 0.995234 -103 ********** Masking position 4 Map Score: 27.9756 Number of sites scoring better than the average of aligned sites = 3349 Number in coding regions = 3107 Number in noncoding regions = 242 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 2 TGTTGATGGTGGAGAAAAGCAAC 3 4 0 GGAGAAAAGC 0.991448 -34 AACCTCCTGGGGATAAAATCCGCTAACTGG 4 212 1 GGATAAAATC 0.938807 -89 GGGAATCACTGGGGAAAGTCTGGGGAATGG 4 242 1 GGGGAAAGTC 0.948527 -59 AATGGCCTGGGGAGAAACTAGCCAAAAATA 4 267 1 GGAGAAACTA 0.960198 -34 CTCAGTTTTTGGAGAAAATC 5 1 0 GGAGAAAATC 0.991616 -300 GGGTGATTTCGGAGAAATGCCTGTCAATGG 5 42 1 GGAGAAATGC 0.97867 -259 GCCTGTCAATGGAAAAACGCGAAAAACCGT 5 60 1 GGAAAAACGC 0.959425 -241 TTACTCTGGGGGAGGAACTTTCGTGGTTCC 5 191 0 GGAGGAACTT 0.865002 -110 ********** Masking position 6 Map Score: 10.2895 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 342 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 AAACGGTATTGGCACTGTCCGTTATCGTG 2 9 0 GGCACGTCCG 0.997322 -42 GGCACCCTCCGGGGTGTTGAT 3 27 0 GGCACCTCCG 0.998471 -11 ATATTTTTCTGGCGATCGCCGCCTGGGGAAT 4 88 0 GGCGACGCCG 0.974473 -213 CTGGGCCGTGGGCACCCTAGGGGTGGGGGAA 4 152 0 GGCACCTAGG 0.966699 -149 GGGTGCCCACGGCCCAGTCAGGGTTAAGAAA 4 166 1 GGCCCGTCAG 0.975085 -135 ATAAGCTATAGGCACGAGCCGTCTAAGCAAT 5 239 0 GGCACAGCCG 0.992791 -62 ***** ***** Masking position 3 Map Score: 6.06371 Number of sites scoring better than the average of aligned sites = 172 Number in coding regions = 166 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 CATTGATATCCCAGACAAATTGCCCCGCTG 1 46 0 CCAGACAAAT 0.975626 -94 CTGGGGAATCCCAGAAAAAATTAGAGAGAG 4 67 0 CCAGAAAAAA 0.990948 -234 GCGGCGATCGCCAGAAAAATATTCCTACTA 4 97 1 CCAGAAAAAT 0.990948 -204 GCGTCAAAACCCTAAAAAATTCCCCCACCC 4 133 1 CCTAAAAAAT 0.901242 -168 GAGAAACTAGCCAAAAATAAGAATTACAAA 4 278 1 CCAAAAATAA 0.901242 -23 CCCAGAGTAACCAGAAAAGAATGGTACCAT 5 211 1 CCAGAAAAGA 0.975626 -90 ********** Masking position 5 Map Score: 5.97019 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 165 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TGAAGACTTGCGGCGGGGGGTCTAGGACAGC 1 19 1 CGGCGGGGGT 0.946124 -121 TTTTTCACCGAGGTTAGGGCTTA 2 38 1 AGGTTAGGGT 0.986874 -13 TAGGGTTTTGACGCTAGGGATAGTAGGAATA 4 116 0 ACGCTAGGGT 0.976104 -185 GGCCGTGGGCACCCTAGGGGTGGGGGAATTT 4 149 0 ACCCTAGGGT 0.952103 -152 TATCCCCAGGAGGTTAAGGTTTTTAGGCTAT 4 196 0 AGGTTAAGGT 0.936749 -105 AAAATCCGCTAACTGGGGGAATCACTGGGGA 4 226 1 AACTGGGGGA 0.802495 -75 TTTCTCCAAAAACTGAGGGATATGTAGAGGG 5 14 1 AACTGAGGGT 0.963372 -287 TAATATCCCCAGCCGAGGGGAGAACGTGTTA 5 141 0 AGCCGAGGGA 0.975046 -160 AATTTGAGTTAGGTAAAGGTTGGTATAAGCT 5 263 0 AGGTAAAGGT 0.818401 -38 ********* * Masking position 8 Map Score: 5.32764 Number of sites scoring better than the average of aligned sites = 912 Number in coding regions = 798 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 CCGCAAGTCTTCAATGATACA 1 2 0 TCAATGATAC 0.960619 -138 GTCTGGGATATCAATGAAACTTCGGCCATG 1 60 1 TCAATGAAAC 0.972186 -80 TGAAACTTCGGCCATGGAAAGGTTTTAATG 1 74 1 GCCATGGAAA 0.944437 -66 GAAATGCCTGTCAATGGAAAAACGCGAAAA 5 55 1 TCAATGGAAA 0.972186 -246 AGCCGTCTAAGCAATGGTACCATTCTTTTC 5 224 0 GCAATGGTAC 0.983424 -77 ********** Masking position 5 Map Score: 2.68657 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 264 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 7 GCAAACGATGGAGGTCATTAAAACCTTTCCAT 1 87 0 GAGGTATAAA 0.98104 -53 TTGTTAAGTTGAGTTAAGTAAAAATAGCTCAA 4 17 0 GAGTTATAAA 0.988791 -284 AAATTAGAGAGAGTTGGTTAAAGCCCTTTTAT 4 48 0 GAGTTGTAAA 0.992725 -253 TCGAAAATTTGAGTTAGGTAAAGGTTGGTATA 5 267 0 GAGTTGTAAA 0.992725 -34 ***** * **** Masking position 5 Map Score: 2.16226 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 24 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 8 AATGACCTCCATCGTTTGCACACAATCCAAAGA 1 100 1 ACGTTGACAC 0.974587 -40 CAGTGCCAATACCGTTTTTTCACCGAGGTTAGG 2 23 1 ACGTTTTCAC 0.978839 -28 GGAATTTTTTAGGGTTTTGACGCTAGGGATAGT 4 123 0 AGGTTTACGC 0.986217 -178 CCAGGAGGTTAAGGTTTTTAGGCTATTTCTTAA 4 189 0 AGGTTTAGGC 0.953099 -112 TTCTAGTATTAACGGTTTTTCGCGTTTTTCCAT 5 68 0 ACGTTTTCGC 0.992748 -233 TAGAGTAATGATCGGTTGGTAGCATTTGTTTCT 5 97 0 ACGTTGTAGC 0.95604 -204 * ** *** **** Masking position 7 Map Score: 2.16031 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 69 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 ********** No masking Map Score: -1.62471e-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: -1.62471e-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 11 ********** No masking Map Score: -1.62471e-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