AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_aful_reg_100.orf -o00252_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 Input sequences: #1 AF0106 116 aspartate carbamoyltransferase, catalytic subunit (pyrB) #2 AF0841 80 adenylosuccinate synthetase (purA) #3 AF0842 65 A. fulgidus predicted coding region AF0842 #4 AF0883 71 argininosuccinate lyase (argH) #5 AF0916 59 glycyl-tRNA synthetase (glyS) #6 AF0919 30 conserved hypothetical protein #7 AF0920 36 aspartyl-tRNA synthetase (aspS) #8 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #9 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #10 AF1420 216 membrane protein #11 AF1422 35 aspartate racemase #12 AF1423 112 conserved hypothetical protein #13 AF1439 31 asparagine synthetase (asnB) #14 AF1442 54 conserved hypothetical protein #15 AF2242 61 adenylosuccinate lyase (purB) #16 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #17 AF2244 300 acyl-CoA dehydrogenase (acd-11) #18 AF2252 78 argininosuccinate synthetase (argG) #19 AF2254 207 ATP-dependent RNA helicase, DEAD-family (deaD) #20 AF2255 53 alanyl-tRNA synthetase (alaS) Motif number 1 TTCATAATTATTTAAGCTTTTGCTTGGTTA 1 42 1 TTTAAGCTTT 0.894036 -75 CTTTTACGGTTTTAAACTTTCTCCCGTATG 1 87 0 TTTAAACTTT 0.937857 -30 GTAGGTTTGAGTTAAGGTTTAATAGA 2 7 0 GTTAAGGTTT 0.761495 -74 GAAGATAACCTTTTAAGTTGCATTCTGCAC 5 37 1 TTTTAAGTTG 0.920442 -23 TCAGGCAGTTTTTTAAGTTTAGCC 7 5 0 TTTTAAGTTT 0.933614 -32 GGTTAAAATTTTTTAGGTTGGGTGATGCGC 12 31 1 TTTTAGGTTG 0.866094 -82 GCGTAAACAATTTAAACTTTAAGGTTTATG 14 21 0 TTTAAACTTT 0.937857 -34 TTTTTCAATTGTTTAACTTGGCAAAATTTA 17 259 1 GTTTAACTTG 0.90526 -42 TTTGTGATTATTTAAATTTTGCCAAGTTAA 17 271 0 TTTAAATTTT 0.775378 -30 CCAGGAAGTTTTTTAACTTTTGTTTAATCT 18 24 1 TTTTAACTTT 0.954079 -55 CACTCCTTAATTTTAACTTTACAAAACTTT 19 28 0 TTTTAACTTT 0.954079 -180 ATGTTTAGAAGTTTAATTTGCATCTCGGAG 19 96 1 GTTTAATTTG 0.686079 -112 ********** Masking position 5 Map Score: 14.3378 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 51 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 2 ACCTCCTCTCCTTTTACGGTTTT 1 104 0 ACCCTCTCTT 0.942161 -13 CCAACCACCTCATGTTTTATCACTAC 3 50 0 ACCCTCAGTT 0.977886 -16 GCTCTTACACCTTCAGGCAGTTTTTTAAG 7 18 0 AACTTCAGCA 0.604467 -19 AAGCCCTTCCTCTTTTTTTGATTC 9 2 1 ACCTTCCCTT 0.944666 -23 AAAAACCTTATTAGCCTCTTGTTATTTATTTGC 10 192 1 TACCTCTGTT 0.496737 -25 CTAAAAAATTTTAACCTCAACTTCAAGCAAAAT 12 14 0 TACCTCACTT 0.855199 -99 TGAAGTATTTAGCGCATCACCCAACCTAAAAAA 12 39 0 ACCATCACCA 0.703362 -74 GGATACCCTTCAACTATGAGTTATTA 13 16 0 TCCTTCACTA 0.771497 -16 GTAACCTTTTATCGCCCCCTGTTAACTTCGCTT 15 38 1 ACCCCCCGTT 0.815006 -24 GACCTTCTCCACCGCCTCAGCCTGAGGCGGAAA 17 64 1 ACCCTCACCT 0.986153 -237 CAGCTCTTCTATACCCTCCTCCTTTAAAATGCC 17 97 1 AACCTCCCCT 0.925067 -204 GCTTGCTGAAAGCATCTCAAGTTATGCTGTTGG 17 128 0 ACTCTCAGTT 0.714443 -173 GCTTTCAGCAAGCTCCTCCACCTTCACCACTTC 17 148 1 ACCCTCCCCT 0.981237 -153 CTCCACCTTCACCACTTCAAGTTTTCAACGGTG 17 163 1 ACCTTCAGTT 0.939975 -138 AAGACTTATATACCCTTCAGCCAAGCGTTGGGA 19 153 1 TCCTTCACCA 0.785528 -55 * * ***** *** Masking position 8 Map Score: 11.8287 Number of sites scoring better than the average of aligned sites = 2601 Number in coding regions = 2473 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 3 ACGGTTTTAAACTTTCTCCCGTATGCTATT 1 82 0 ACTTTCTCCC 0.944197 -35 GCTCTGCCATCATCTCCAAAACATAAAT 4 9 1 ATCATCTCCA 0.772684 -63 CTTTTAAGTTGCATTCTGCACTGC 5 46 1 GCATTCTGCA 0.796037 -14 GACCCTTTTCTTCATCTCCAATCCAAATTC 8 30 0 TTCATCTCCA 0.679372 -20 TCGTGGATTCGTTTTCTGCAATATCTCAAT 10 150 1 GTTTTCTGCA 0.78915 -67 TCTATCACCCTGCAAACGTT 16 29 0 TCTATCACCC 0.757282 -10 GCCGGAAAAGACCTTCTCCACCGCCTCAGC 17 55 1 ACCTTCTCCA 0.973601 -246 AACTTGAGATGCTTTCAGCAAGCTCCTCCA 17 138 1 GCTTTCAGCA 0.923151 -163 AAGCTCCTCCACCTTCACCACTTCAAGTTT 17 157 1 ACCTTCACCA 0.959294 -144 ACTTTACAAAACTTTCACCATGAAAAAGAG 19 13 0 ACTTTCACCA 0.936403 -195 GACTTATATACCCTTCAGCCAAGCGTTGGG 19 155 1 CCCTTCAGCC 0.800386 -53 AACGTTCCACTCTATCTCCCAACGCTTGGC 19 172 0 TCTATCTCCC 0.830011 -36 CGGATGCCTTCTGCATTGGATGTTT 20 39 0 GCCTTCTGCA 0.967834 -15 ********** Masking position 5 Map Score: 10.5418 Number of sites scoring better than the average of aligned sites = 1685 Number in coding regions = 1595 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 CTTAAATAATTATGAAGAAATTATACTCCATG 1 26 0 TTGAGAAATT 0.754605 -91 ATCGCTAACGAGAAGTTACTAACAACA 3 6 1 TACAGAAGTT 0.74847 -60 GCACTCAGTTTGTGCAGAGGTTATTAATTCTT 4 50 0 TTGAGAGGTT 0.960123 -22 AGTGACAGAGTATCGTGAGATTTTCCGAGCCC 10 29 0 TTCTGAGATT 0.92949 -188 TAATAAGGTTTTTCATGAGTTTGATATTGAGA 10 173 0 TTCTGAGTTT 0.901959 -44 TGGATTTTGCTTGAAGTTGAGGTTAAAA 12 7 1 TGCTGAAGTT 0.815167 -106 CTAAAAGGCCTGTCTTGAAGTATTTAGCGCAT 12 55 0 TTCTGAAGTA 0.710099 -58 TGTAGTTATATATCATGAGTTTAACGAGGAGC 17 207 0 TTCTGAGTTT 0.901959 -94 ACTTCCTGGGTTTTCAGAGGTT 18 1 0 TTTAGAGGTT 0.938696 -78 GAGGTTTAAATCTTTTGAGATTAAACAAAAGT 18 39 0 TTTTGAGATT 0.812044 -40 AATCCCGTCATGCGGAGAGGTTTAAATCTTTT 18 55 0 TCGAGAGGTT 0.833921 -24 CGTTCAGACATGTTTAGAAGTTTAATTTGCAT 19 87 1 TTTAGAAGTT 0.873911 -121 * ** ******* Masking position 8 Map Score: 4.76394 Number of sites scoring better than the average of aligned sites = 374 Number in coding regions = 335 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 AACTCAAACCTACCATTTTTCCAAAAATCGC 2 24 1 TACCTTTTTC 0.910344 -57 AAAACTTTTATGCCTACCTGAA 8 2 1 AAACTTTATG 0.879074 -48 AAGAGGCTAATAAGGTTTTTCATGAGTTTGA 10 181 0 TAAGTTTTTC 0.883262 -36 CCAAAGCTTTATCTTGTTAGGCG 11 3 1 AAAGTTTATC 0.943534 -33 TTTTAGCGGTAAATTTTTATCGGCCCAACCA 12 81 1 AAATTTTATC 0.881182 -32 ATTTAAACTTTAAGGTTTATGATAGAAAGAC 14 11 0 TAAGTTTATG 0.669225 -44 GAAAAGGAGTAACCTTTTATCGCCCCCTGTT 15 30 1 AACCTTTATC 0.957309 -32 ATCACCCTGCAAACGTTTTTCAAATAATAAA 16 15 0 AAACTTTTTC 0.964521 -24 GTTCTATTTAAATCCTTTTTCAATTGTTTAA 17 244 1 AATCTTTTTC 0.849488 -57 AACTCTTTTTCATGGTGAAAG 19 1 1 AACTTTTTTC 0.859495 -207 **** ****** Masking position 6 Map Score: 4.7936 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 196 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 6 CTTACCGCAAATGTATTTATGTTTTGGAGATGA 4 20 0 ATGTATTTGT 0.911475 -52 TTAAAAGGTTATCTTCTTATGGTGCCGCGCAGC 5 20 0 ATCTTTTTGT 0.974149 -40 AAGCCCTTCCTCTTTTTTTGATTC 9 10 1 CTCTTTTTGT 0.962132 -15 TCGTTTTGTCAAGTTATTCTGCTGGCAACGCTT 10 110 1 AAGTTTTTGT 0.955704 -107 TGATGTTGTTCTGGTTGGGCCGATA 12 98 0 ATGTTTTTGT 0.980235 -15 AAAGCATCTCAAGTTATGCTGTTGGCATTTTAA 17 120 0 AAGTTTGTGT 0.869087 -181 GCAGGCTCTTTTTGTGATTATTTAAATT 17 283 0 CTCTTTTTGT 0.962133 -18 ***** ** ** * Masking position 7 Map Score: 2.00116 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 33 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ATTTTAGTGGCTGCGCGGCACCATAAGAAG 5 6 1 ATGGTCGCCA 0.995636 -54 AATGGTTGTTCGACAGAGGAAAGAA 6 16 0 ATGGTTTCCA 0.845286 -15 AAGTTATTCTGCTGGCAACGCTTCAAGACTTCGTG 10 120 1 GTGGACGCCA 0.979029 -97 TAAAGTTTAAATTGTTTACGCATCATCATCTTATC 14 30 1 ATGTTCGCCA 0.987202 -25 GTATAGAAGAGCTGTTTCCGCCTCAGGCTGAGGCG 17 76 0 GTGTTCGCCA 0.984604 -225 AAAATTAAGGAGTGGATTCGCCCGATTTGAGCCGA 19 44 1 ATGGTCGCGA 0.981241 -164 * *** * *** ** Masking position 3 Map Score: 1.11333 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 27 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 AATTATTTAAGCTTTTGCTTGGTTATATCA 1 47 1 GCTTTTGCTT 0.985152 -70 TGGATTTTGCTTGAAGTTGAGG 12 3 1 GATTTTGCTT 0.943502 -110 AAGTTTTTTAACTTTTGTTTAATCTCAAAA 18 29 1 ACTTTTGTTT 0.849462 -50 GGGTATATAAGTCTTTGTTTGAATCCCTCA 19 138 0 GTCTTTGTTT 0.888902 -70 TATATCTCTTGCCTTTGCTTATTTCGATG 20 10 0 GCCTTTGCTT 0.986231 -44 ********** Masking position 5 Map Score: 0.937271 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 43 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 9 ********** No masking Map Score: 1.99195e-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: 1.99195e-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 11 ********** No masking Map Score: 1.99195e-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