AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i181_pantotenate_Biosynthesis_synecho_reg_300.orf -o181_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 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 0.994035 -121 CCAGACAAATTGCCCCGCTGTCCTAGACCC 1 36 0 TGCCCCGCTG 0.96473 -104 CCACCATCAACACCCCGGAGGGTGCC 3 22 1 CACCCCGGAG 0.934743 -16 TTTCTGGGATTCCCCAGGCGGCGATCGCCA 4 80 1 TCCCCAGGCG 0.996703 -221 CCTAAAAAATTCCCCCACCCCTAGGGTGCC 4 143 1 TCCCCCACCC 0.988361 -158 GCGGATTTTATCCCCAGGAGGTTAAGGTTT 4 205 0 TCCCCAGGAG 0.993554 -96 CCCCAGTGATTCCCCCAGTTAGCGGATTTT 4 226 0 TCCCCCAGTT 0.942298 -75 TCCCCAGACTTTCCCCAGTGATTCCCCCAG 4 238 0 TTCCCCAGTG 0.966437 -63 CCCCAGGCCATTCCCCAGACTTTCCCCAGT 4 249 0 TTCCCCAGAC 0.935916 -52 GGCTAGTTTCTCCCCAGGCCATTCCCCAGA 4 260 0 TCCCCAGGCC 0.991615 -41 AGACCTAATATCCCCAGCCGAGGGGAGAAC 5 147 0 TCCCCAGCCG 0.993604 -154 CGAAAGTTCCTCCCCCAGAGTAACCAGAAA 5 198 1 TCCCCCAGAG 0.995411 -103 ********** Masking position 5 Map Score: 27.7606 Number of sites scoring better than the average of aligned sites = 2007 Number in coding regions = 1870 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 2 GTTGCTTTTCTCCACCATCAACA 3 4 1 GCTTTTCTCC 0.992372 -34 CCAGTTAGCGGATTTTATCCCCAGGAGGTT 4 212 0 GATTTTATCC 0.945105 -89 CCATTCCCCAGACTTTCCCCAGTGATTCCC 4 242 0 GACTTTCCCC 0.953874 -59 TATTTTTGGCTAGTTTCTCCCCAGGCCATT 4 267 0 TAGTTTCTCC 0.964378 -34 GATTTTCTCCAAAAACTGAG 5 1 1 GATTTTCTCC 0.992522 -300 CCATTGACAGGCATTTCTCCGAAATCACCC 5 42 0 GCATTTCTCC 0.980948 -259 ACGGTTTTTCGCGTTTTTCCATTGACAGGC 5 60 0 GCGTTTTTCC 0.963683 -241 GGAACCACGAAAGTTCCTCCCCCAGAGTAA 5 191 1 AAGTTCCTCC 0.877908 -110 ********** Masking position 5 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 CACGATAACGGACAGTGCCAATACCGTTT 2 9 1 CGGACGTGCC 0.99731 -42 ATCAACACCCCGGAGGGTGCC 3 27 1 CGGAGGTGCC 0.998462 -11 ATTCCCCAGGCGGCGATCGCCAGAAAAATAT 4 88 1 CGGCGTCGCC 0.974312 -213 TTCCCCCACCCCTAGGGTGCCCACGGCCCAG 4 152 1 CCTAGGTGCC 0.966491 -149 TTTCTTAACCCTGACTGGGCCGTGGGCACCC 4 166 0 CTGACGGGCC 0.974928 -135 ATTGCTTAGACGGCTCGTGCCTATAGCTTAT 5 239 1 CGGCTGTGCC 0.992745 -62 ***** ***** Masking position 9 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 0.972028 -94 CTGGGGAATCCCAGAAAAAATTAGAGAGAG 4 67 0 CCAGAAAAAA 0.989587 -234 GCGGCGATCGCCAGAAAAATATTCCTACTA 4 97 1 CCAGAAAAAT 0.989587 -204 GCGTCAAAACCCTAAAAAATTCCCCCACCC 4 133 1 CCTAAAAAAT 0.887923 -168 GAGAAACTAGCCAAAAATAAGAATTACAAA 4 278 1 CCAAAAATAA 0.887923 -23 CCCAGAGTAACCAGAAAAGAATGGTACCAT 5 211 1 CCAGAAAAGA 0.972028 -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 GCTGTCCTAGACCCCCCGCCGCAAGTCTTCA 1 19 0 ACCCCCGCCG 0.939548 -121 TAAGCCCTAACCTCGGTGAAAAA 2 38 0 ACCCTAACCT 0.985199 -13 TATTCCTACTATCCCTAGCGTCAAAACCCTA 4 116 1 ACCCTAGCGT 0.973091 -185 AAATTCCCCCACCCCTAGGGTGCCCACGGCC 4 149 1 ACCCTAGGGT 0.950529 -152 ATAGCCTAAAAACCTTAACCTCCTGGGGATA 4 196 1 ACCTTAACCT 0.929131 -105 TCCCCAGTGATTCCCCCAGTTAGCGGATTTT 4 226 0 TCCCCCAGTT 0.782418 -75 CCCTCTACATATCCCTCAGTTTTTGGAGAAA 5 14 0 ACCCTCAGTT 0.95881 -287 TAACACGTTCTCCCCTCGGCTGGGGATATTA 5 141 1 TCCCTCGGCT 0.971919 -160 AGCTTATACCAACCTTTACCTAACTCAAATT 5 263 1 ACCTTTACCT 0.799539 -38 * ********* Masking position 4 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 0.965837 -138 GTCTGGGATATCAATGAAACTTCGGCCATG 1 60 1 TCAATGAAAC 0.97591 -80 TGAAACTTCGGCCATGGAAAGGTTTTAATG 1 74 1 GCCATGGAAA 0.951692 -66 GAAATGCCTGTCAATGGAAAAACGCGAAAA 5 55 1 TCAATGGAAA 0.97591 -246 AGCCGTCTAAGCAATGGTACCATTCTTTTC 5 224 0 GCAATGGTAC 0.985665 -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 ATGGAAAGGTTTTAATGACCTCCATCGTTTGC 1 87 1 TTTATACCTC 0.979347 -53 TTGAGCTATTTTTACTTAACTCAACTTAACAA 4 17 1 TTTATAACTC 0.987781 -284 ATAAAAGGGCTTTAACCAACTCTCTCTAATTT 4 48 1 TTTACAACTC 0.992066 -253 TATACCAACCTTTACCTAACTCAAATTTTCGA 5 267 1 TTTACAACTC 0.992066 -34 **** * ***** Masking position 8 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 TCTTTGGATTGTGTGCAAACGATGGAGGTCATT 1 100 0 GTGCAAACGT 0.979403 -40 CCTAACCTCGGTGAAAAAACGGTATTGGCACTG 2 23 0 GTGAAAACGT 0.982864 -28 ACTATCCCTAGCGTCAAAACCCTAAAAAATTCC 4 123 1 GCGAAAACCT 0.988854 -178 TTAAGAAATAGCCTAAAAACCTTAACCTCCTGG 4 189 1 GCCAAAACCT 0.961829 -112 ATGGAAAAACGCGAAAAACCGTTAATACTAGAA 5 68 1 GCGAAACCGT 0.992944 -233 AGAAACAAATGCTACCAACCGATCATTACTCTA 5 97 1 GCTCAACCGT 0.957185 -204 *** ****** * Masking position 7 Map Score: 2.91348 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 90 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 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