AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_aful_reg_100.orf -o00710_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/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 Purged sequences: AF1638 31 ribulose bisphosphate carboxylase, large subunit (rbcL-2) Input sequences: #1 AF0941 52 A. fulgidus predicted coding region AF0941 #2 AF1146 65 3-phosphoglycerate kinase (pgk) #3 AF1305 72 D-arabino 3-hexulose 6-phosphate formaldehyde lyase (hps-2) #4 AF1306 77 conserved hypothetical protein #5 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #6 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #7 AF1420 216 membrane protein #8 AF1588 51 conserved hypothetical protein #9 AF1590 300 A. fulgidus predicted coding region AF1590 Motif number 1 GAGCAGGTAAATTAAAATTTTCAGAAAGTTT 2 22 1 ATAAAATTTT 0.944771 -44 TAAAATTTTCAGAAAGTTTTTAATTTCACCT 2 34 1 AAAAGTTTTT 0.923884 -32 CCGGATATGTAATAAATTTTTTGGAGTTCGC 3 40 0 ATAAATTTTT 0.868862 -33 TGCTTAACGAAAAAAAATTTTAAAATGGCGG 4 44 1 AAAAAATTTT 0.929597 -34 TCAGGTAGGCATAAAAGTTTT 5 1 0 AAAAAGTTTT 0.956529 -49 ACAAGAGGCTAATAAGGTTTTTCATGAGTTT 7 183 0 ATAAGGTTTT 0.956071 -34 GTCAGCAAATATAAAGATTTTGATTTAATGT 8 17 0 AAAAGATTTT 0.976128 -35 CATCTGGCTTACAAAGAGTTTCTTTAATTTT 9 191 1 AAAAGAGTTT 0.920413 -110 * ********* Masking position 5 Map Score: 8.50613 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 63 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 2 TTCAATTCGGAAGGTGAAATT 2 55 0 TCAATTCGGA 0.963983 -11 AGGAAAATTGAGTTTGGCAAATCAATTC 3 9 1 TGAGTTTGGC 0.97307 -64 GTTTGGCAAATCAATTCGGCGAACTCCAAA 3 22 1 TCAATTCGGC 0.956905 -51 TATGCCTACCTGAATTTGGATTGGAGATGA 5 19 1 TGAATTTGGA 0.987172 -31 AGCCCGCAGTTGAATTTGGACAG 7 4 0 TGAATTTGGA 0.987172 -213 AGGTTTTTCATGAGTTTGATATTGAGATAT 7 170 0 TGAGTTTGAT 0.75186 -47 ATAAAGCCAATCAATTTGTAGAGGCTTCAA 9 19 1 TCAATTTGTA 0.859868 -282 GCATTATTGCGGAATTTGGTGAGACCTTTA 9 141 1 GGAATTTGGT 0.916365 -160 ********** Masking position 3 Map Score: 8.24657 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 77 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 CAATTCGGCGAACTCCAAAAAATTTATTACA 3 33 1 AACTCCAAAA 0.904681 -40 GGCCTTACGTCTCCGGATATGTAATAAAT 3 54 0 GTCTCCGATA 0.780184 -19 GAATCAAAAAAAGAGGAAGGG 6 14 0 GAATCAAAAA 0.802588 -11 GGCTCGGAAAATCTCACGATACTCTGTCACT 7 30 1 ATCTCACATA 0.933264 -187 GTTTTCTGCAATATCTCAATATCAAACTCAT 7 160 1 ATATCTCATA 0.618229 -57 CTCAATATCAAACTCATGAAAAACCTTATTA 7 174 1 AACTCATAAA 0.777647 -43 GTTGCTTGAAGCCTCTACAAATTGATTGGCT 9 23 0 GCCTCTAAAA 0.866682 -278 TGCTCCCGAGAACTCACAAAAAAGACGGTTT 9 62 1 AACTCACAAA 0.964238 -239 TCGAGTAAAAATCTCCCTAAAATCGCATGGG 9 92 1 ATCTCCCAAA 0.956971 -209 ATCAATAAAGGTCTCACCAAATTCCGCAATA 9 145 0 GTCTCACAAA 0.977353 -156 ATTCAATAGCGCATCAATAAAGGTCTCACCA 9 157 0 GCATCAAAAA 0.732316 -144 AGTTAATCTTGACTCTCAATAGTAGAAAAGA 9 280 0 GACTCTCATA 0.921514 -21 ******* *** Masking position 9 Map Score: 7.1457 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 395 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 4 ATAAATCCGTTGCGATAATGCATTTTTA 1 9 0 TGCGATAATG 0.976948 -44 CAGATTGAGTTATTGGTAAGGGCTA 1 38 0 TGAGTTATTG 0.982534 -15 AGTTTGATATTGAGATATTGCAGAAAACGA 7 158 0 TGAGATATTG 0.982531 -59 ATAAAGATTTTGATTTAATGTTATAAA 8 8 0 TGATTTAATG 0.882669 -44 CCTTTATTGATGCGCTATTGAATTTACATC 9 165 1 TGCGCTATTG 0.980784 -136 ********** Masking position 6 Map Score: 3.58312 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 31 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 TGAGTTATTGGTAAGGGCTATAAATCCGTT 1 28 0 GTAAGGGCTA 0.993393 -25 AATGGCGGTTGTAAGGGCTGC 4 67 1 GTAAGGGCTG 0.992149 -11 CAAAAAAAGAGGAAGGGCTT 6 1 0 GGAAGGGCTT 0.98545 -24 TTCACACTCCATCAGGGCTATTCGTTTTGT 7 89 1 ATCAGGGCTA 0.928463 -128 CAATCAATTTGTAGAGGCTTCAAGCAACCA 9 26 1 GTAGAGGCTT 0.928463 -275 ********** Masking position 9 Map Score: 2.80515 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 77 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 AATCAATTCGGCGAACTCCAAAAAATTTATTA 3 30 1 GCGAACTAAA 0.920264 -43 AAATTCAACTGCGGGCTCGGAAAATCTCACGA 7 17 1 GCGGGCTGAA 0.957785 -200 AGACTATCCGGGAAGCTTTGAAGCTGAGTGAC 7 55 0 GGAAGCTGAA 0.86651 -162 TTGAAGCGTTGCCAGCAGAATAACTTGACAAA 7 114 0 GCCAGCAATA 0.867831 -103 GGCGAGAAATAAAGCCAATCAAT 9 2 1 GCGAGAAAAA 0.964193 -299 GTGAGTTCTCGGGAGCAAAGAAGTGGTTGCTT 9 47 0 GGGAGCAGAA 0.980409 -254 CTCTTTGTAAGCCAGATGTAAATTCAATAGCG 9 177 0 GCCAGATAAA 0.905005 -124 GGAAAACTTAGGGAGGATAAAATTAAAGAAAC 9 208 0 GGGAGGAAAA 0.921034 -93 TTGGGGGGAAGCGAGCGGGAAAACTTAGGGAG 9 225 0 GCGAGCGAAA 0.981493 -76 ******* *** Masking position 12 Map Score: 3.53858 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 474 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 AGATTGAGTTATTGGTAAGGGCTATAAATCC 1 31 0 ATTGTAAGGG 0.953451 -22 TTCAATTCGGAAGGTGAAATTAAAA 2 51 0 ATTGGAAGGT 0.906883 -15 TTAAAATGGCGGTTGTAAGGGCTGC 4 63 1 GGTGTAAGGG 0.953501 -15 GAATCAAAAAAAGAGGAAGGGCTT 6 4 0 AAGGGAAGGG 0.972889 -21 AATCCACGAAGTCTTGAAGCGTTGCCAGCAG 7 128 0 GTCTGAAGCG 0.85957 -89 TTCCGCAATAATGCTGAAGGGAAGCAGCTGA 9 124 0 ATGTGAAGGG 0.969886 -177 CCCTAGTTTTGGGGGGAAGCGAGCGGGAAAA 9 234 0 GGGGGAAGCG 0.980344 -67 *** ******* Masking position 7 Map Score: 0.620595 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 713 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 ********** No masking Map Score: -1.46839e-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: -1.46839e-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 10 ********** No masking Map Score: -1.46839e-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