AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -ifadR_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 aq_990 48 hypothetical protein #2 fadD 300 long-chain-fatty-acid CoA ligase Motif number 1 CGTTTCGGGAGGATCGGGTGTCTAA 2 4 1 TTGGGGGATC 0.987601 -297 TCCCTCACTATTAGGGCGTAACCCTGCGTGCC 2 70 0 TTGGGGTAAC 0.996126 -231 TTTCTGTTTCTTCTGATGGAACAACTTGGACC 2 113 1 TTTGAGGAAC 0.993863 -188 TCCCTCACTATTAGGGCGTAACCGGTCCAAGT 2 136 0 TTGGGGTAAC 0.996126 -165 GATTGCGACCTTTTGATGGGACTTGTGATAGG 2 166 1 TTTGAGGGAC 0.987525 -135 TTGATGGGACTTGTGATAGGACCTGCTGGTGT 2 178 1 TTTGAAGGAC 0.939781 -123 TCCCTTATTGTTAGGGCGTAACTGACACCAGC 2 202 0 TTGGGGTAAC 0.996126 -99 CGATAGCGTATTTCCAAGGAACAATCCCTTAT 2 226 0 TTCCAGGAAC 0.955933 -75 TCGTTTCTCTTTCTCGCATAACTTTTCTTATC 2 255 1 TTTCGATAAC 0.906751 -46 ** *** ***** Masking position 2 Map Score: 17.5786 Number of sites scoring better than the average of aligned sites = 196 Number in coding regions = 173 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 GGCACGCAGGGTTACGCCCTAATAGTGAGG 2 70 1 GTTACGCCCT 0.99836 -231 ACTTGGACCGGTTACGCCCTAATAGTGAGG 2 136 1 GTTACGCCCT 0.99836 -165 ATAGTGAGGGATTGCGACCTTTTGATGGGA 2 157 1 ATTGCGACCT 0.980241 -144 GCGACCTTTTGATGGGACTTGTGATAGGAC 2 170 1 GATGGGACTT 0.932957 -131 TGGGACTTGTGATAGGACCTGCTGGTGTCA 2 182 1 GATAGGACCT 0.990868 -119 GCTGGTGTCAGTTACGCCCTAACAATAAGG 2 202 1 GTTACGCCCT 0.99836 -99 ********** Masking position 3 Map Score: 13.9542 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 26 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 ATTTTACAATTTGCCTTTCTTGAGCTTTAT 1 19 1 TTGCCTTTCT 0.966416 -30 TGGTGTCGCAATCCCTCACTATTAGGGCGT 2 83 0 ATCCCTCACT 0.995567 -218 AAAGGTCGCAATCCCTCACTATTAGGGCGT 2 149 0 ATCCCTCACT 0.995567 -152 CCAAGGAACAATCCCTTATTGTTAGGGCGT 2 215 0 ATCCCTTATT 0.975529 -86 ACGCTATCGTTTCTCTTTCTCGCATAACTT 2 249 1 TTCTCTTTCT 0.951018 -52 ********** Masking position 6 Map Score: 5.80939 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 247 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 GTTTCGGGAGGATCGGGTGTCTAATAAGTTG 2 12 1 GATCGGTGTC 0.994983 -289 GTAACCCTGCGTGCCTGTGTCTAAAAAATAA 2 54 0 GTGCTGTGTC 0.992695 -247 AGAAGAAACAGAAATGGTGTCGCAATCCCTC 2 96 0 GAAAGGTGTC 0.979322 -205 GTGATAGGACCTGCTGGTGTCAGTTACGCCC 2 190 1 CTGCGGTGTC 0.995172 -111 **** ****** Masking position 8 Map Score: 1.90959 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 17 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TGCCTTTCTTGAGCTTTATCATATAAATT 1 30 1 GAGCTTTATC 0.98942 -19 CTAAAAAATAACGCTTTATCAACAACTTAT 2 35 0 ACGCTTTATC 0.989642 -266 AAATACTTTAAAGCTAAATCTGGATAAGAA 2 279 0 AAGCTAAATC 0.973238 -22 ********** Masking position 8 Map Score: 0.0260016 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 28 Number in noncoding regions = 14 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: -3.17312e-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: -3.17312e-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: -3.17312e-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