AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00272_pyro_reg_300.orf -o00272_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 PH0636 128 476aa long hypothetical cysteinyl-tRNA synthetase #2 PH0770 167 154aa long hypothetical protein #3 PH0771 46 391aa long hypothetical aspartate aminotransferase #4 PH1308 38 386aa long hypothetical serine aminotransferase #5 PH1371 191 389aa long hypothetical aspartate aminotransferase Motif number 1 TCATCACCAAAAAGAATTTACCTTCTTTAGG 1 14 1 AAAAATTTAC 0.748892 -115 TTACCTTCTTTAGGTATTTAAAGCTTGCTTT 1 31 1 TAGTATTTAA 0.947416 -98 TTTAAGCCAAAAAATATTTAACTAGATAAAC 2 54 0 AAATATTTAA 0.961463 -114 AATATCACAAAAATAATTTAAGCCAAAAAAT 2 70 0 AAAAATTTAA 0.873928 -98 ATAAATTTAAAAGTTTTTTAAGTTCATAATA 2 97 0 AAGTTTTTAA 0.975484 -71 AAAAAACTTTTAAATTTATACCGGTCAAAAT 2 109 1 TAATTTATAC 0.768417 -59 TGTGTTGCTAAAAATTTTTAAATTTTGACCG 2 130 0 AAATTTTTAA 0.961463 -38 AAAGTTTTATAAATTTTTCATG 3 2 1 AAGTTTATAA 0.964512 -45 TATACTTCCATAGGTATATAATTGTGG 4 22 1 TAGTATATAA 0.924849 -17 TAAGTTTGTCAAGCTTTATAAAGGTTATCTG 5 50 1 AAGTTTATAA 0.964512 -142 *** ******* Masking position 7 Map Score: 11.4678 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 183 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 ACCTCAAGCCAAAAGCAAGCTTTAAATACCT 1 42 0 AAAGCAAGCT 0.896589 -87 GCAACTATGAAACCTCAAGCCAAAAGCAAGC 1 53 0 AACTCAAGCC 0.992241 -76 TAGTTGCCAAAACCGACATCCTAATAAAATT 1 77 1 AACGACATCC 0.922487 -52 TCACCTCCTTAATCTCCATCCAGGAATTTTA 1 101 0 AACTCCATCC 0.986162 -28 TTAACTAGATAAACTCAAGCCTTAGAATAGG 2 37 0 AACTCAAGCC 0.992241 -131 ACTCCAATTCAATCCTAATCTTTCGATAGTT 5 83 0 AACCTAATCT 0.895432 -109 ATCGAGTTTAAAACCCAATCTGTCCTCGATA 5 144 0 AACCCAATCT 0.982255 -48 ** ******** Masking position 8 Map Score: 5.59003 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 198 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 3 TCTTCATCACCAAAAAGAATTTAC 1 4 1 TCATCACCAA 0.946671 -125 TCACCCTTCACCTCCTTAATCTCCATCC 1 111 0 TCACCTCCTA 0.9967 -18 TTCTCCCCCTCACCAATTGTGT 2 156 0 TCTCCCCCTA 0.987321 -12 GTCACCTCCTCAATCGAGGACA 5 2 1 TCACCTCCTA 0.9967 -190 CTTCAATCACCACTTGAGAATATGATA 5 175 0 TCACCACTTA 0.982345 -17 ********* * Masking position 1 Map Score: 5.57881 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 81 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TCACCCTTCACCTCCTTAATCTCCATCC 1 111 0 CACCTCCTTA 0.981106 -18 TTCTCCCCCTCACCAATTGTGT 2 156 0 CTCCCCCTCA 0.991804 -12 GTCACCTCCTCAATCGAGGACA 5 3 1 CACCTCCTCA 0.995176 -189 AAAGATATCACTCCAATTCAATCCTAATCT 5 93 0 CTCCAATTCA 0.924501 -99 CTTCAATCACCACTTGAGAATATGATA 5 175 0 CACCACTTGA 0.971557 -17 ********** Masking position 8 Map Score: 3.88247 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 159 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 TTGAGGTTTCATAGTTGCCAAAACCGACATCC 1 66 1 ATAGTGCAAA 0.985071 -63 TTTTAAATTTATACCGGTCAAAATTTAAAAAT 2 116 1 ATACGGCAAA 0.968993 -52 CACCTCCTCAATCGAGGACAAAGTGGGACATA 5 13 1 ATCGGGCAAA 0.993951 -179 TAATCTTTCGATAGTTCCCAGATAACCTTTAT 5 67 0 ATAGTCCAGA 0.926534 -125 CTCGATACGAATATTTTACAAACAAGTAAAAG 5 119 0 ATATTTCAAA 0.775264 -73 AAATATTCGTATCGAGGACAGATTGGGTTTTA 5 135 1 ATCGGGCAGA 0.991051 -57 GAATATGATAATCGAGTTTAAAACCCAATCTG 5 153 0 ATCGGTTAAA 0.878254 -39 **** ** **** Masking position 10 Map Score: 2.79102 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 109 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 AGCTTTAAATACCTAAAGAAGGTAAATTCT 1 26 0 ACCTAAAGAA 0.958145 -103 CGGTTTTGGCAACTATGAAACCTCAAGCCA 1 62 0 AACTATGAAA 0.928777 -67 AAAAATATTTAACTAGATAAACTCAAGCCT 2 46 0 AACTAGATAA 0.876327 -122 TGATATTATGAACTTAAAAAACTTTTAAAT 2 94 1 AACTTAAAAA 0.78575 -74 ACAATTATATACCTATGGAAGTATAAAAAC 4 17 0 ACCTATGGAA 0.972581 -22 TTCCCAGATAACCTTTATAAAGCTTGACAA 5 55 0 ACCTTTATAA 0.892045 -137 GTTATCTGGGAACTATCGAAAGATTAGGAT 5 73 1 AACTATCGAA 0.941049 -119 ********** Masking position 9 Map Score: 2.33962 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 217 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 ********** No masking Map Score: -5.44113e-14 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: -5.44113e-14 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: -5.44113e-14 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