AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -igcvA_aquae_opreg_100.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 gcsH4 269 glycine cleavage system protein H #2 gcvT 144 aminomethyltransferase (glycine cleavage system T protein) #3 putative 27 putative protein Motif number 1 TTAATTCGTAAGATGGTGGAGATAAGGTACTTT 1 11 1 AGATTGGAGT 0.961807 -259 CTCTTCCTTTTCTTTACCGAGCTTCTCCCTGAG 1 50 0 TCTTCCGAGT 0.965613 -220 ACTCAGTAGTAGTTTCCTGAGCTCAGATACGGT 1 98 0 AGTTCTGAGT 0.983011 -172 CTACTGAGTAAGTATCCCGAGATAGAAAATATA 1 122 1 AGTACCGAGT 0.964516 -148 TTAACGGCAAACTTAACGGAGTTCAATATATTT 1 148 0 ACTTCGGAGT 0.996034 -122 TAATACCTCCAGTTAGCGGTGGTTAAAACTTCT 1 234 1 AGTTCGGTGT 0.987144 -36 GGTGGTTAAAACTTCTTGGAGGTGGAAGG 1 251 1 ACTTTGGAGT 0.98777 -19 TGCCTTCAGGTGTTTATGGACATAGTAAAGGGG 2 36 0 TGTTTGGACT 0.93894 -109 CTGAAGGCAAAGTTCACGAACTTCGCAGGCTGG 2 60 1 AGTTCGAACT 0.935661 -85 **** ***** * Masking position 13 Map Score: 11.0184 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 320 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 GAGATAAGGTACTTTTCCATTCTCAGGGAG 1 29 1 ACTTTTCCAT 0.969422 -241 TCTTTACCGAGCTTCTCCCTGAGAATGGAA 1 43 0 GCTTCTCCCT 0.947104 -227 TCAAACTCAAACTCTTCCTTTTCTTTACCG 1 64 0 ACTCTTCCTT 0.99394 -206 GAGCTCAGATACGGTGCCTTCAAACTCAAA 1 83 0 ACGGTGCCTT 0.926244 -187 TCATCCACGTACTCTTCGTTAACGGCAAAC 1 169 0 ACTCTTCGTT 0.96926 -101 AAGTTCGTGAACTTTGCCTTCAGGTGTTTA 2 53 0 ACTTTGCCTT 0.985952 -92 TCCGGCTCTTCCCTTACAGCCCTT 2 131 0 GCTCTTCCCT 0.989189 -14 ********** Masking position 10 Map Score: 8.09589 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 577 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 GGAGATAAGGTACTTTTCCATTCTCAGGGA 1 28 1 TACTTTTCCA 0.931796 -242 TTCAAACTCAAACTCTTCCTTTTCTTTACC 1 65 0 AACTCTTCCT 0.969097 -205 CTCATCCACGTACTCTTCGTTAACGGCAAA 1 170 0 TACTCTTCGT 0.929738 -100 CGGTGGTTAAAACTTCTTGGAGGTGGAAGG 1 250 1 AACTTCTTGG 0.90697 -20 GAAGTTCGTGAACTTTGCCTTCAGGTGTTT 2 54 0 AACTTTGCCT 0.969097 -91 AAAGTTCACGAACTTCGCAGGCTGGACAAT 2 68 1 AACTTCGCAG 0.838134 -77 TTACAGCCCTTACTTCTTCTATTATTGAGG 2 112 0 TACTTCTTCT 0.971699 -33 TAAGATAAAATACTTCTTCTA 3 2 0 TACTTCTTCT 0.971699 -26 ********** Masking position 2 Map Score: 5.54301 Number of sites scoring better than the average of aligned sites = 1087 Number in coding regions = 1027 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 4 CAGGGAGAAGCTCGGTAAAGAAAAGGAAGA 1 52 1 CTCGGTAAAG 0.979342 -218 CGTATCTGAGCTCAGGAAACTACTACTGAG 1 100 1 CTCAGGAAAC 0.965056 -170 TATTTTCTATCTCGGGATACTTACTCAGTA 1 123 0 CTCGGGATAC 0.970398 -147 ATATATTGAACTCCGTTAAGTTTGCCGTTA 1 150 1 CTCCGTTAAG 0.985693 -120 TCCACGTACTCTTCGTTAACGGCAAACTTA 1 166 0 CTTCGTTAAC 0.921872 -104 GCTTTAATACCTCCAGTTAGCGGTGGTTAA 1 230 1 CTCCAGTTAG 0.909047 -40 CCTTTACTATGTCCATAAACACCTGAAGGC 2 38 1 GTCCATAAAC 0.862147 -107 ********** Masking position 9 Map Score: 4.60413 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 614 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 5 ********** No masking Map Score: 1.01908e-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 6 ********** No masking Map Score: 1.01908e-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 7 ********** No masking Map Score: 1.01908e-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