AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i337_tpal_bbur_100.orf -o337_tpal_bbur_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTP00846 300 AE000520 #2 RTP00843 73 AE000520 #3 RBB00058 61 3615 Motif number 1 GAACCCCCACACACAGAACCA 1 1 1 GAACCCCACA 0.993207 -300 TTGTGTAATGGTAGCACCGCAGATTCTGGTT 1 27 0 GTAGCACGCA 0.915846 -274 AGCAGATAACGAACACTCACTCAGATCAAAA 1 102 1 GAACACCACT 0.930242 -199 CTTGACCGACGCAGACTGGCAGCTGCCATCA 1 151 1 GCAGACGGCA 0.988988 -150 GCTGCCATCAGCAGCCCCACAGCACACGCGC 1 172 1 GCAGCCCACA 0.997783 -129 CAGCCCCACAGCACACGCGCATTCCGGCAAA 1 183 1 GCACACCGCA 0.993462 -118 GCATTCCGGCAAAGACACACAACTGCACATT 1 201 1 AAAGACCACA 0.934018 -100 TCCTTGTATCGCAGCCAGGCGCGCTTTGCAA 1 275 0 GCAGCCGGCG 0.979109 -26 TGGAAAAAACGACGCCCCACACTGAGGAAGT 2 23 0 GACGCCCACA 0.985137 -51 ****** **** Masking position 10 Map Score: 13.9966 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 80 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 2 CCAGAATCTGCGGTGCTACCATTACACAACC 1 29 1 CGGTCTACCA 0.98782 -272 AAAACTTACCCGGTACCTCCACTTGACCGAC 1 130 1 CGGTCCTCCA 0.988151 -171 GACGCAGACTGGCAGCTGCCATCAGCAGCCC 1 158 1 GGCACTGCCA 0.961497 -143 ATTGTGCAGTCGCTCCTTCCAGTCAGTAGCG 1 241 1 CGCTCTTCCA 0.997558 -60 CAGTCAGTAGCGCTATTGCAAAGCGCGCCTG 1 260 1 CGCTTTGCAA 0.958482 -41 TGTGGGGCGTCGTTTTTTCCAGATTTTTCAG 2 33 1 CGTTTTTCCA 0.972058 -41 **** ****** Masking position 11 Map Score: 4.48694 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 131 Number in noncoding regions = 352 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 3 CCCCCACACACAGAACCAGAATCTGCGGTG 1 14 1 CAGAACCAGA 0.896318 -287 GCTACCATTACACAACCAGGGAGGGAGGCC 1 43 1 CACAACCAGG 0.993741 -258 ACTTGACCGACGCAGACTGGCAGCTGCCAT 1 150 1 CGCAGACTGG 0.982186 -151 ACAGCACACGCGCATTCCGGCAAAGACACA 1 190 1 CGCATTCCGG 0.967696 -111 CTCCTTGTATCGCAGCCAGGCGCGCTTTGC 1 277 0 CGCAGCCAGG 0.998186 -24 ********** Masking position 4 Map Score: 2.78204 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 122 Number in noncoding regions = 291 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 GTTGTGTAATGGTAGCACCGCAGATTCTGG 1 29 0 GGTAGCACCG 0.975034 -272 AACCAGGGAGGGAGGCCCAGGCTAGTACGA 1 56 1 GGAGGCCCAG 0.931199 -245 TCGGTCAAGTGGAGGTACCGGGTAAGTTTT 1 130 0 GGAGGTACCG 0.982425 -171 TGTCTTTGCCGGAATGCGCGTGTGCTGTGG 1 188 0 GGAATGCGCG 0.974689 -113 GCTACTGACTGGAAGGAGCGACTGCACAAT 1 241 0 GGAAGGAGCG 0.995948 -60 GCTCCTTCCAGTCAGTAGCGCTATTGCAAA 1 252 1 GTCAGTAGCG 0.933307 -49 TTGTATCGCAGCCAGGCGCGCTTTGCAATA 1 273 0 GCCAGGCGCG 0.982585 -28 ********** Masking position 1 Map Score: 6.02788 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 198 Number in noncoding regions = 522 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 GAGCGACTGCACAATTGTATCGGCAATGTG 1 226 0 ACAATTGTAT 0.964727 -75 AAATTGATTTACAATTTTAATTTAT 3 6 0 ACAATTTTAA 0.958527 -56 AAATTGTAAATCAATTTTAGAAAAAAATTA 3 19 1 TCAATTTTAG 0.91611 -43 TATAGTGTAAATAATTTTTTTCTAAAATTG 3 30 0 ATAATTTTTT 0.881426 -32 ACACTATAATATAATTTTAT 3 52 1 ATAATTTTAT 0.889268 -10 ********** Masking position 5 Map Score: 1.69907 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 42 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 AGCTGCCATCAGCAGCCCCACAGCACACGC 1 171 1 AGCAGCCCCA 0.940155 -130 GCCCCACAGCACACGCGCATTCCGGCAAAG 1 185 1 ACACGCGCAT 0.926373 -116 ACAATTGTGCAGTCGCTCCTTCCAGTCAGT 1 238 1 AGTCGCTCCT 0.674481 -63 CCTTCCAGTCAGTAGCGCTATTGCAAAGCG 1 255 1 AGTAGCGCTA 0.893264 -46 TATCGCAGCCAGGCGCGCTTTGCAATAGCG 1 270 0 AGGCGCGCTT 0.54976 -31 ACACGCCCGTACACTTCCTC 2 1 1 ACACGCCCGT 0.944608 -73 CTGGAAAAAACGACGCCCCACACTGAGGAA 2 25 0 CGACGCCCCA 0.986299 -49 AGCTTTTGCGCGATGCGCCTCG 2 62 1 CGATGCGCCT 0.952824 -12 ********** Masking position 5 Map Score: 4.38487 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 119 Number in noncoding regions = 286 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 ********** No masking Map Score: -2.10731e-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 8 ********** No masking Map Score: -2.10731e-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 9 ********** No masking Map Score: -2.10731e-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