AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_trans4_aquae_reg_300.orf -o210_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RAA01489 30 Aquifex_aeolicus Input sequences: #1 RAA00853 79 Aquifex_aeolicus #2 RAA00925 58 Aquifex_aeolicus #3 RAA00927 105 Aquifex_aeolicus #4 RAA01787 33 Aquifex_aeolicus #5 RAA00958 300 Aquifex_aeolicus #6 RAA01180 38 Aquifex_aeolicus #7 RAA01137 30 Aquifex_aeolicus Motif number 1 AACAACTTATGAGTTTTCCACAATTCTCCAC 5 11 0 GAGTTTCCAC 0.976021 -290 GAAAACTCATAAGTTGTTCATATAACGACAC 5 24 1 AAGTTTTCAT 0.98716 -277 ATAACTTAAGAAGTTTTCCACATTTATCCAC 5 104 0 AAGTTTCCAC 0.994903 -197 AAAACTTCTTAAGTTATTCATACTACGAAAC 5 118 1 AAGTTTTCAT 0.98716 -183 TGAACAACTTAAGTTATTTATAATTCGTAAG 5 166 0 AAGTTTTTAT 0.870413 -135 TAAATAACTTAAGTTGTTCATGTGGAAAAGT 5 177 1 AAGTTTTCAT 0.98716 -124 AACTTTCCACAACTTTTCCACATGAACAACT 5 188 0 AACTTTCCAC 0.969973 -113 TTTTCCCGAAAAACTTTCCACAACTTTTCCA 5 199 0 AAACTTCCAC 0.94294 -102 ATTGATTTTCAAGCTTTTCCCGAAAAACTTT 5 213 0 AAGCTTTCCC 0.941706 -88 ATGGGTTTTGAAATTTGTCACATGAAAATAG 5 242 1 AAATTGTCAC 0.880925 -59 ***** ***** Masking position 5 Map Score: 15.6354 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 320 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 TTCAAGAATAAGGAGTGGAAG 1 2 0 AGGAGTGGAA 0.949655 -78 GTGGAGAATTGTGGAAAACTCATAAG 5 7 1 AATTGTGGAA 0.988272 -294 CTTACGTTAAAAATGTGGATAAATGTGGAA 5 90 1 AAATGTGGAT 0.967521 -211 AAATGTGGATAAATGTGGAAAACTTCTTAA 5 100 1 AAATGTGGAA 0.991786 -201 CTTAAGTTGTTCATGTGGAAAAGTTGTGGA 5 184 1 TCATGTGGAA 0.945869 -117 CATGTGGAAAAGTTGTGGAAAGTTTTTCGG 5 195 1 AGTTGTGGAA 0.989127 -106 ********** Masking position 6 Map Score: 7.56464 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 47 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 3 TTTATCCTAGTATTCATGTCGTCTAAACATGTATGAA 1 43 0 TATATGTTAA 0.973693 -37 CCTGAAGTTCAATCCATGCCCTTTTAACAGGGTGTTC 3 44 0 AACATGTTAA 0.989529 -62 TATCAATTAAATTTAAAACTTATGGAG 4 1 1 TACATTTTAA 0.930876 -33 TTATATGAACAACTTATGAGTTTTCCACAATTCTCCA 5 12 0 AATATGTTCA 0.940564 -289 ACTCAAAAGAAAACCACGGTGTATAAACTACTTACGT 5 60 1 AACACGTTAA 0.981656 -241 GGTGACTTAAAACTTACGAATTATAAATAACTTAAGT 5 154 1 AATACGTTAA 0.971213 -147 AAAGCTTGAAAATCAATGGGTTTTGAAATTTGTCACA 5 227 1 AACATGTTAA 0.989529 -74 ACTATTTATTTTGTATTAATAAGAATAAT 5 282 0 TATATTTTAA 0.894675 -19 ** * *** * * ** Masking position 6 Map Score: 6.928 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 25 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 TTGAATGTAATTTCTTTTCATACATGTTTAG 1 27 1 TTTCTTTTAT 0.959217 -53 AAATTCCTTATAATATTTATTTGC 2 4 1 TTCCTTATAT 0.903993 -55 ACCTCCGTCTTTTCTTAGAATTGAGCAAATA 2 28 0 TTTCTTAGAT 0.967822 -31 GAGTAGATTGTGTCGTTATATGAACAACTTA 5 33 0 TGTCGTTAAT 0.859138 -268 ACACCGTGGTTTTCTTTTGAGTAGATTGTGT 5 51 0 TTTCTTTTAG 0.878597 -250 CACCGGATTGTTTCGTAGTATGAATAACTTA 5 127 0 TTTCGTAGAT 0.975554 -174 ATTTAAACCATTTCGTAAAATAATCCTT 6 21 1 TTTCGTAAAT 0.962696 -18 ******** ** Masking position 10 Map Score: 3.11668 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 106 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 TTAACAGGGTGTTCTTCGGGAATTCCCTCG 3 28 0 GTTCTTCGGG 0.98686 -78 GGCATGGATTGAACTTCAGGTTCCCCAGTG 3 61 1 GAACTTCAGG 0.957171 -45 AATAACTTAAGTTGTTCATGTGGAAAAGTT 5 179 1 GTTGTTCATG 0.956198 -122 GTTGTGGAAAGTTTTTCGGGAAAAGCTTGA 5 206 1 GTTTTTCGGG 0.98583 -95 AAAACCCATTGATTTTCAAGCTTTTCCCGA 5 221 0 GATTTTCAAG 0.954793 -80 AATAGGCGGCTATTTTCATGTGACAAATTT 5 252 0 TATTTTCATG 0.852109 -49 ********** Masking position 5 Map Score: 2.7388 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 341 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 ********** No masking Map Score: 1.40931e-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 7 ********** No masking Map Score: 1.40931e-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 8 ********** No masking Map Score: 1.40931e-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