AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i074_Fatty_Acid_Metabolism_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -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 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #2 yusM 300 similar to proline dehydrogenase Motif number 1 GCTGCTTCCCACGGCTGCTT 1 1 0 ACGGCTGCTT 0.990502 -267 GGACAATCATAATGCAGCTGCTTCCCACGG 1 17 0 AATGCAGCTG 0.939937 -251 TGTTTTTTATACTGCTGATTTTGACTTGTC 1 54 1 ACTGCTGATT 0.95094 -214 ACTCAGCATTACGGCGGCGGAAAACGGACA 1 80 0 ACGGCGGCGG 0.993997 -188 CCGCCGCCGTAATGCTGAGTCGGACCGGCA 1 90 1 AATGCTGAGT 0.861614 -178 CGCCGCGCTGACTGCCGCTGAAGACGGATT 1 134 1 ACTGCCGCTG 0.986066 -134 TGATCCTGGCACTGCTGCGCCATGAAATGC 2 80 1 ACTGCTGCGC 0.977524 -221 GAAATAACGGAAGGCGGCATTTGAGATTGC 2 173 1 AAGGCGGCAT 0.93279 -128 GGCATTTGAGATTGCTGCTGATTATCCATT 2 188 1 ATTGCTGCTG 0.961694 -113 TTTGAAGATGACGGCGGGAGGGAGTCGG 2 283 1 ACGGCGGGAG 0.936699 -18 ********** Masking position 1 Map Score: 13.4967 Number of sites scoring better than the average of aligned sites = 1603 Number in coding regions = 1450 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 2 GACTTGTCCGTTTTCCGCCGCCGTAATGCTGAG 1 76 1 TTTCCGCGCG 0.984779 -192 GGCATCTCCCTTTACGCTCGCCGCGCTGACTGC 1 116 1 TTTCGCCGCG 0.992098 -152 GCTCGCCGCGCTGACTGCCGCTGAAGACGGATT 1 131 1 CTGCTGCGTG 0.927893 -137 GACGGATTTTTTTTCTCTCGTACCATTCCCTTC 1 156 1 TTTCTCCGAC 0.929206 -112 AGTCGGGCAACTTAAGCCCGGAGGTGAAGGGAA 1 181 0 CTTAGCCGAG 0.962186 -87 AAAGCAAGAACTCGACCGCGTCGGACACATGCA 2 41 0 CTCACCCGCG 0.967738 -260 AAAAAGCGCATTTCATGGCGCAGCAGTGCCAGG 2 84 0 TTTATGCGAG 0.938157 -217 TGAACTGGAATTTGCTCGCGATGAAAAAAGCGC 2 108 0 TTTCTCCGTG 0.984385 -193 CCGACTCCCTCCCGCCGTCATCTTCAA 2 284 0 CTCCTCCGCG 0.992441 -17 *** *** ** ** Masking position 2 Map Score: 7.56034 Number of sites scoring better than the average of aligned sites = 605 Number in coding regions = 544 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 CAGCTGCTTCCCACGGCTGCTT 1 3 0 CCACGGCTGC 0.871258 -265 GACAATCATAATGCAGCTGCTTCCCACGGC 1 16 0 ATGCAGCTGC 0.865158 -252 TTTTATACTGCTGATTTTGACTTGTCCGTT 1 58 1 CTGATTTTGA 0.494928 -210 CTCAGCATTACGGCGGCGGAAAACGGACAA 1 79 0 CGGCGGCGGA 0.99207 -189 CGCCGTAATGCTGAGTCGGACCGGCATCTC 1 94 1 CTGAGTCGGA 0.924731 -174 TGAGTCGGACCGGCATCTCCCTTTACGCTC 1 105 1 CGGCATCTCC 0.883579 -163 GCCGCGCTGACTGCCGCTGAAGACGGATTT 1 135 1 CTGCCGCTGA 0.978751 -133 AAGAACTCGACCGCGTCGGACACATGCATC 2 39 0 CCGCGTCGGA 0.978335 -262 GATCCTGGCACTGCTGCGCCATGAAATGCG 2 81 1 CTGCTGCGCC 0.942418 -220 TAACGGAAGGCGGCATTTGAGATTGCTGCT 2 177 1 CGGCATTTGA 0.83991 -124 GCATTTGAGATTGCTGCTGATTATCCATTG 2 189 1 TTGCTGCTGA 0.872784 -112 ********** Masking position 3 Map Score: 6.58337 Number of sites scoring better than the average of aligned sites = 6253 Number in coding regions = 5878 Number in noncoding regions = 375 Number of orfs with sites within 600 bp upstream = 208 Fraction of orfs with sites within 600 bp upstream = 0.0334083 Motif number 4 AAAAAACATAACATGGGACAATCATAATGCAGC 1 29 0 ACATGGAATC 0.988962 -239 CGGAAAACGGACAAGTCAAAATCAGCAGTATAA 1 60 0 ACAATCAATC 0.941321 -208 CGTTATTTCGACAAAGGATCATTTGTATCTCAA 2 149 0 ACAAGGAATT 0.982604 -152 AAGGAGGATCACAATGGATAATCAGCAGCAATC 2 197 0 ACAAGGAATC 0.996619 -104 TGAACAGAAACCAAAGGAGGATCACAATGGATA 2 210 0 CCAAGGAATC 0.992526 -91 **** *** *** Masking position 8 Map Score: 3.18056 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 58 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 CGGCGGCGGAAAACGGACAAGTCAAAATCA 1 69 0 AAACGGACAA 0.891469 -199 CGTAATGCTGAGTCGGACCGGCATCTCCCT 1 97 1 AGTCGGACCG 0.995771 -171 AGCCTATAAAAGTCGGGCAACTTAAGCCCG 1 194 0 AGTCGGGCAA 0.984503 -74 TAGCTATTGAAGTCGAACCGGAAATCTTTT 1 245 1 AGTCGAACCG 0.978319 -23 AACTCGACCGCGTCGGACACATGCATCATG 2 36 0 CGTCGGACAC 0.981617 -265 ********** Masking position 5 Map Score: 2.09603 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 212 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ********** No masking Map Score: 1.67221e-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: 1.67221e-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: 1.67221e-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