AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i016_Pentose_Phosphate_Shunt_aful_reg_300.orf -o016_aful_300.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RAG21749 39 Archaeoglobus_fulgidus #2 RAG45764 139 Archaeoglobus_fulgidus #3 RAG21865 126 Archaeoglobus_fulgidus #4 RAG21863 300 Archaeoglobus_fulgidus Motif number 1 TCCACCTGAAATTGCGTCTGATTTCCTTTGAAAT 2 43 1 ATTGTTGTTT 0.992566 -97 CCAAAGATTAATTGTATTTACTTTGAGACATATA 3 45 0 ATTGTTATTT 0.993775 -82 ATCTTATATTGCTTTTGCTTTTCTGGAACCA 4 8 1 ATTGTTGTTT 0.992564 -293 CTCTTGCGCTATTGCGCTTATTTTACTGCTGACA 4 69 0 ATTGCTATTT 0.983303 -232 TTTTGAGTGCATTCGGTTTAATTTGTATAATAAA 4 160 0 ATTCTTATTT 0.973635 -141 GTGGCTTAGTATTGGCTGTAATTTCTGCCACCGC 4 228 1 ATTGTTATTT 0.993829 -73 **** * ** *** Masking position 9 Map Score: 8.38303 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 6 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 2 AAAGATTAAAATTTTTCGCAG 1 2 0 ATTTTTCGCA 0.964388 -38 TTTTAATCTTTTTTCTGCCAAGACCAGAC 1 21 1 TTTTCTGCCA 0.969637 -19 TTTCATTTTTCTGTCAGAATGAGCTT 2 7 1 TTTTCTGTCA 0.921309 -133 AATACAATTAATCTTTGGCAAGAGTATTAA 3 61 1 ATCTTTGGCA 0.953118 -66 TGAACTAAAAATTTTTCGAAACAGACCATT 3 90 0 ATTTTTCGAA 0.913685 -37 TTGCTTTTGCTTTTCTGGAACCAATGCTCA 4 19 1 TTTTCTGGAA 0.967301 -282 AGGCTTATAAATTTTTGGACTCTTGCGCTA 4 92 0 ATTTTTGGAC 0.888229 -209 ATTGGCTGTAATTTCTGCCACCGCTGCTGC 4 238 1 ATTTCTGCCA 0.980854 -63 ********** Masking position 6 Map Score: 7.46437 Number of sites scoring better than the average of aligned sites = 504 Number in coding regions = 457 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 TTCTGTCAGAATGAGCTTCAGAATTCCACCTGAAAT 2 19 1 ATGCTTAATC 0.974326 -121 ATTGCGTCTGATTTCCTTTGAAATTCTATCCAGCTC 2 53 1 ATCCTTAATC 0.993994 -87 ATCTTCGGTGTTTACCTCTCAAACTCAATAAGGCTT 2 89 1 TTCCTCAATC 0.98863 -51 GGCTTTATGCATTCCCTCAGCAAATCTGCT 2 120 1 ATCCTCAATC 0.995022 -20 CAAAAATTTATAAGCCTTACGAATTCGTTCAAAGAT 4 105 1 TACCTTAATC 0.969062 -196 TAAACCAACGAAAACGTTCGAAAATCTTTGAACGAA 4 128 0 AACGTTAATC 0.932625 -173 ATTAAACCGAATGCACTCAAAAAGTCGGGGGTGAGT 4 172 1 ATACTCAATC 0.968672 -129 ** **** ** ** Masking position 12 Map Score: 5.59163 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 195 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 AGAAAAAAGATTAAAATTTTTCGCAG 1 7 0 TTAAAATTTT 0.970014 -33 CATATAATTCTTAAAATGTTTTTAAAGTTG 3 21 0 TTAAAATGTT 0.950032 -106 TCACTTGAACTAAAAATTTTTCGAAACAGA 3 95 0 TAAAAATTTT 0.969235 -32 TCGTAAGGCTTATAAATTTTTGGACTCTTG 4 97 0 TATAAATTTT 0.927616 -204 ********** Masking position 5 Map Score: 1.88096 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 34 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 5 GTTCAAGTGATGACATAGTAGC 3 115 1 TGACATAGTA 0.94083 -12 ACGTTTTCGTTGGTTTATTATACAAATTAA 4 147 1 TGGTTTATTA 0.910593 -154 AGGGTAAGTGTGGCTTAGTATTGGCTGTAA 4 219 1 TGGCTTAGTA 0.993814 -82 CTGCATACGATGGCTTGGTAGATAGAACGA 4 264 1 TGGCTTGGTA 0.989483 -37 ********** Masking position 6 Map Score: 1.48325 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 17 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 TAACTGCGATCAACTTTAAAAA 3 3 1 ACTGCGATCA 0.89704 -124 CGACTTTTTGAGTGCATTCGGTTTAATTTG 4 169 0 AGTGCATTCG 0.971985 -132 AAAAGTCGGGGGTGAGTTCGTGAAACACAG 4 191 1 GGTGAGTTCG 0.971229 -110 TGCCACCGCTGCTGCATACGATGGCTTGGT 4 253 1 GCTGCATACG 0.971923 -48 CGGTTCTTGCTGCGTTCTCGTTCTATCT 4 283 0 GCTGCGTTCT 0.984746 -18 ********** Masking position 3 Map Score: 0.535963 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 131 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 ********** No masking Map Score: 1.77879e-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: 1.77879e-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 9 ********** No masking Map Score: 1.77879e-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