AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_aful_reg_100.orf -o00260_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: AF1510 24 long-chain-fatty-acid--CoA ligase (fadD-6) Input sequences: #1 AF0273 137 sarcosine oxidase, subunit alpha (soxA) #2 AF0274 300 sarcosine oxidase, subunit beta (soxB) #3 AF0546 300 nitrate reductase, gamma subunit (narI) #4 AF0548 59 threonyl-tRNA synthetase (thrS) #5 AF0551 108 threonine synthase (thrC-1) #6 AF0700 41 aspartate kinase (lysC) #7 AF0703 38 A. fulgidus predicted coding region AF0703 #8 AF0813 72 phosphoglycerate dehydrogenase (serA) #9 AF0916 59 glycyl-tRNA synthetase (glyS) #10 AF0932 41 conserved hypothetical protein #11 AF0933 22 branched-chain amino acid aminotransferase (ilvE) #12 AF1316 48 threonine synthase (thrC-2) #13 AF1506 30 aspartate-semialdehyde dehydrogenase (asd) #14 AF1507 62 A. fulgidus predicted coding region AF1507 #15 AF1508 61 A. fulgidus predicted coding region AF1508 #16 AF1512 71 conserved hypothetical protein #17 AF1513 257 A. fulgidus predicted coding region AF1513 #18 AF2035 23 seryl-tRNA synthetase (serS) #19 AF2036 62 cytochrome C oxidase folding protein (coxD) #20 AF2037 54 translation initiation factor eIF-2B, subunit delta (eif2BD) #21 AF2046 26 cytochrome oxidase, subunit I, putative #22 AF2138 195 phosphoserine phosphatase (serB) Motif number 1 CACTATAAATTTAAATTTTTGCTTTTGGTT 1 25 1 TTAAATTTTT 0.93175 -113 TGAGAAAATTTTAAATAATTCAAAAGAGAG 3 21 0 TTAAATAATT 0.774101 -280 AAAATAAAAATTAAATTTTTTATCTTAATT 3 61 0 TTAAATTTTT 0.93175 -240 TTAATAGACTTTAAATTATTAAATTTTCGT 3 222 0 TTAAATTATT 0.899903 -79 AATAATTTAAAAAAAGCATTAATAGACTTT 3 240 0 AAAAAGCATT 0.632965 -61 AATGCTTTTTTTAAATTATTATTATGCTAA 3 250 1 TTAAATTATT 0.899903 -51 TTATAAAGTTTTCCAAAGATAA 3 289 0 ATAAAGTTTT 0.934429 -12 TGGAGGAGTAATAAATTTTTCTAAGCAATT 4 26 0 ATAAATTTTT 0.858085 -34 AACACTGACCAAAAATTATTAATACTCATA 5 73 1 AAAAATTATT 0.695243 -36 GGTGGACGAGTAAAAGTTTTTATCGTAAAA 8 22 1 TAAAAGTTTT 0.876835 -51 GTTTTTATCGTAAAAGTTTTTAGCTCTGCC 8 37 1 TAAAAGTTTT 0.876835 -36 AGAAGTAATGATAAATCTTTCCATTTATTA 15 28 0 ATAAATCTTT 0.836605 -34 GTTGAGAATAATAAAGCTTTGATTTTGGTG 16 40 0 ATAAAGCTTT 0.869916 -32 TAATTACTATTTAAAGTTTTCCTTTCTTTT 17 223 0 TTAAAGTTTT 0.947437 -35 GAATTTCCCGATAAATAATTACTATTTAAA 17 238 0 ATAAATAATT 0.734169 -20 TTTGAGGGCAAAAAAGTTTTCGGAATTTAT 19 30 0 AAAAAGTTTT 0.797432 -33 TTTTCAAAGGTTAAAGAATTTTAACCTGAA 20 25 0 TTAAAGAATT 0.816223 -30 GGAGAAGGTGTTAAATATTTTCAGACTAAG 22 17 0 TTAAATATTT 0.841299 -179 ********** Masking position 9 Map Score: 22.9248 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 84 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 CCTTTCACCTCTGCAACAAGTATTTTA 1 121 0 CCACCCTCAC 0.962087 -17 TGCAAACAACCTTCCTGTCCTTCACGCTTATCACCC 2 25 0 CCTGTCTCAG 0.97812 -276 CCGAGGAGGAGATAATCCACGCCATCGAGCTTGGCT 2 76 1 GATCCCGCAC 0.829546 -225 TCTTTATCACCCTTCCCTGCAGCGAGTATGTAA 2 278 0 CCTTCCTCAC 0.964492 -23 ATTTTAGTGGCTGCGCGGCACCATAAGAAGAT 9 7 1 GCTGCCGCAC 0.941704 -53 TTTTAAATTGCCCCCTGTCCTTCAACC 13 14 1 CCTGTCTCAC 0.987169 -17 AGGCGTGCGCCTTACCGCTCGGCAACCCCGGCCTAA 17 33 0 CCCGCCGCAC 0.984401 -225 GGGCGAACGCCCACACGCTCTCCAGGCGTGCGCCTT 17 56 0 CACGCCTCAG 0.930483 -202 GTTCCCACCTCTGCTTCAGGTTAAAATTCT 20 5 1 CCTCTCTCAG 0.9681 -50 ATATTTAACACCTTCTCCACGACACCTTTAAATTTG 22 29 1 CCTCCCGCAC 0.992511 -167 TGATATTGAGCAGACCGTCCTGCAGGGC 22 178 1 CCCGTCTCAG 0.969382 -18 * **** ** ** * Masking position 14 Map Score: 10.7773 Number of sites scoring better than the average of aligned sites = 946 Number in coding regions = 915 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 ACTTAGGAAAGTTTAAATAAGCATTCTAAT 1 82 1 GTTTAAATAA 0.716842 -56 TAATTCACGATTTTAAAATACTTGTTGCAG 1 108 1 TTTTAAAATA 0.621799 -30 CTTGAGAAAATTTTAAATAATTCAAAAGAG 3 23 0 TTTTAAATAA 0.923742 -278 TTTTCTCAAGTTTTTAATAATTAAGATAAA 3 43 1 TTTTTAATAA 0.774542 -258 CATTAATAGACTTTAAATTATTAAATTTTC 3 224 0 CTTTAAATTA 0.924647 -77 TTAATGCTTTTTTTAAATTATTATTATGCT 3 248 1 TTTTAAATTA 0.943537 -53 ACTTTTTTCTTTTTTAATTGCTTAGAAAAA 4 11 1 TTTTTAATTG 0.832782 -49 ACCTGAACTTTAAATCGGCGGAGATAA 7 8 1 CTTTAAATCG 0.859396 -31 GAAGATAACCTTTTAAGTTGCATTCTGCAC 9 37 1 TTTTAAGTTG 0.712984 -23 CGGAAAAACGTTTTAAATCAGCTGATTAAC 10 13 1 TTTTAAATCA 0.890931 -29 CTTTTTTAAATTGCCCCCTGTCC 13 4 1 TTTTAAATTG 0.944532 -27 TTCGTATTAATTTTTAATAAATGGAAAGAT 15 14 1 TTTTTAATAA 0.774542 -48 GAAAGGAAAACTTTAAATAGTAATTATTTA 17 227 1 CTTTAAATAG 0.900716 -31 TCCACGACACCTTTAAATTTGGTGAGTTAA 22 44 1 CTTTAAATTT 0.659224 -152 ********** Masking position 6 Map Score: 9.74588 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 32 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 4 CTTCCACTATAAATTTAAATTTTTGCTTTTGG 1 21 1 AAATTTATTT 0.49896 -117 TTAAGATAAAAAATTTAATTTTTATTTTTTAT 3 63 1 AAATTTATTT 0.680386 -238 TTAAATTATTAAATTTTCGTTTTTTATAGCTC 3 210 0 AAATTTTTTT 0.76669 -91 TCCAAAGATAAGATTCATCTTTAGCATAATAA 3 268 0 AGATTCATTT 0.905675 -33 CTCAGCAAGATTTATATTTCTTGCTTAGG 6 8 1 AGATTTATTT 0.95462 -34 AACAACCAGAAGATTTATCTTTAGCCTCGCTT 14 28 1 AGATTTATTT 0.975499 -35 ATAAATGGAAAGATTTATCATTACTTCTTCCT 15 30 1 AGATTTAATT 0.866293 -32 ATAGAAAATTTAGTTTGAGGGCAAAAA 19 46 0 AAATTTATTG 0.910229 -17 GCTTTTCCCAAGATTTACATTGTTT 21 4 0 AGATTTATTG 0.951858 -23 ******* *** Masking position 5 Map Score: 8.50617 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 17 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 5 CCTTTCACCTCTGCAACAAGTATT 1 124 0 TCACCTCTGC 0.963813 -14 GGTCAGATCCTCACACCTGCAAACAACCTT 2 48 0 TCACACCTGC 0.736962 -253 TACGCCAATCTCATCAACGCTCTTGCCAGT 2 213 0 TCATCAACGC 0.687838 -88 TCTTTATCACCCTTCCCTGCAGCGAGTATG 2 281 0 CCTTCCCTGC 0.753177 -20 CAAAAGAATTTTATCCCAGCAGTCAGGATA 5 18 0 TTATCCCAGC 0.687632 -91 GCAACCGTTTTTATCTCCGCCGATTTAAAG 7 18 0 TTATCTCCGC 0.913819 -21 GTAAAAGTTTTTAGCTCTGCCCCTGAGCGT 8 46 1 TTAGCTCTGC 0.926291 -27 TAAGTTGCATTCTGCACTGC 9 50 1 TCTGCACTGC 0.729952 -10 GTGTTCAGCTATGCACAAACAACC 14 5 1 TCAGCTATGC 0.877035 -58 AGATTTATCTTTAGCCTCGCTTACAATCAC 14 38 1 TTAGCCTCGC 0.729015 -25 ATTCAGCCCCGGCTATGAGGCG 17 3 1 TCAGCCCCGG 0.951196 -255 GGTTCGAATCCCACCCCCGGCGCTGTTGTA 17 97 1 CCACCCCCGG 0.847987 -161 GTTCCCACCTCTGCTTCAGGTTAA 20 5 1 CCACCTCTGC 0.918435 -50 AAACCGGGAATCATCCACGCGATTTCGAAA 22 119 1 TCATCCACGC 0.917966 -77 ATCAACTATGTTCGCTCCGCAGTCAGCGAG 22 152 0 TTCGCTCCGC 0.760816 -44 ********** Masking position 9 Map Score: 8.40203 Number of sites scoring better than the average of aligned sites = 2022 Number in coding regions = 1936 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 6 TTATCTCCTCCTCGGTCAGATCCTCACACC 2 61 0 CTCGGTCAGA 0.921271 -240 CCTAAGAATACTCAGCCAGAAGACTGGCAA 2 191 1 CTCAGCCAGA 0.992596 -110 CTCAGCAAGATTTATATTTC 6 1 1 CTCAGCAAGA 0.983472 -41 ATTTCCTGCCCTAAGCAAGAAATATAAATC 6 19 0 CTAAGCAAGA 0.885296 -23 ACTCGGCGAGTTAATCAGCTG 10 31 0 CTCGGCGAGT 0.964213 -11 CTTTATTATTCTCAACCAGATTGTTTCT 16 54 1 CTCAACCAGA 0.945622 -18 TCGCTCCGCAGTCAGCGAGTGCTTTCGAAA 22 141 0 GTCAGCGAGT 0.885025 -55 ********** Masking position 8 Map Score: 4.43519 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 332 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TACTTGTTGCAGAGGTGAAAGG 1 126 1 AGAGGTGAAA 0.971998 -12 CGCTGCAGGGAAGGGTGATAAAGA 2 287 1 AAGGGTGATA 0.800626 -14 AATAGTCTAAAAAGGTCAAATCAAATGTTT 3 110 1 AAAGGTCAAA 0.966381 -191 GCAGTAATAAAGAGGACAAAAGAATTTTAT 5 34 0 AGAGGACAAA 0.937891 -75 ACCAGAAATGAAGGGTGAAA 11 1 0 AAGGGTGAAA 0.950843 -22 CAATTTTTTCAAAGGTTAAAGAATTTTAAC 20 30 0 AAAGGTTAAA 0.878566 -25 CAGTGTACGGAGAGGACAAACCGGGAATCA 22 102 1 AGAGGACAAA 0.937891 -94 ********** Masking position 8 Map Score: 4.11112 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 100 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 AAATTTAATTTTTATTTTTTATATACATGC 3 73 1 TTTATTTTTT 0.805733 -228 ATAACCTAAATTGCTGTTTTTTTCGCCTTA 3 180 0 TTGCTGTTTT 0.922369 -121 ATTATTAAATTTTCGTTTTTTATAGCTCAT 3 208 0 TTTCGTTTTT 0.90774 -93 AAGTCTATTAATGCTTTTTTTAAATTATTA 3 241 1 ATGCTTTTTT 0.889092 -60 ACTTTTTTCTTTTTTAATTGCTTAG 4 6 1 TTTCTTTTTT 0.969675 -54 GTTTTTATGCTTGCTTTTTTGGAAATTCCA 17 163 0 TTGCTTTTTT 0.974756 -95 AAAGTTTTCCTTTCTTTTTTGATTGATTAT 17 211 0 TTTCTTTTTT 0.969675 -47 ********** Masking position 7 Map Score: 6.09781 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 22 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 9 CTTATCACCCCACTGGCCTTACAG 2 4 0 CACTGCCTTA 0.962087 -297 CAAACAACCTTCCTGTCCTTCACGCTTATCA 2 28 0 TCCTGCCTTC 0.968398 -273 TCTTTATCACCCTTCCCTGCAGCGAGTATG 2 281 0 CCCTTCCTGC 0.895255 -20 ATGAATTTAACACTGACCAAAAATTATTAAT 5 65 1 CACTGCCAAA 0.840468 -44 CCTATTTCCTGCCCTAAGCAAGAAATA 6 25 0 TCCTGCCTAA 0.962086 -17 TTAAATTGCCCCCTGTCCTTCAACC 13 16 1 CCCTGCCTTC 0.991177 -15 CGCTCGGCAACCCCGGCCTAACGCCTCATAG 17 23 0 CCCCGCCTAA 0.966243 -235 ***** ***** Masking position 7 Map Score: 2.29592 Number of sites scoring better than the average of aligned sites = 250 Number in coding regions = 236 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 GATAGAGACTTAAGGCGAAAAAAACAGCAATT 3 170 1 TAACGAAAAA 0.964456 -131 AGCTAAAAACTTTTACGATAAAAACTTTTACT 8 30 0 TTTCGATAAA 0.666419 -43 TATTAAAAATTAATACGAAAAA 15 1 0 TAACGAAAAA 0.959322 -61 GTTTAGAAAATAATTCGAAAAAAG 16 3 0 TAACGAAAAA 0.861548 -69 TGATTGATTATTATACGAATAAAACATGAGTT 17 190 0 TTACGAATAA 0.715358 -68 GAATTTCCCGATAAATAATTACTAT 17 243 0 TTTCGATAAA 0.88291 -15 ATGGTTGCTGTTAATCGATAAATTCCGAAAAC 19 13 1 TTACGATAAA 0.569374 -50 *** ******* Masking position 8 Map Score: 4.37062 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 16 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 ACCTCTTGAGGCTCTCAAGGTCGTCGTAGCC 2 108 0 GCTCTCAAGT 0.936055 -193 GCATCAGACAGCTCTTACCCTGACATGGGCC 2 156 0 GCTCTTACCT 0.971366 -145 GTTTTTTATAGCTCATAACCTAAATTGCTGT 3 193 0 GCTCATAACT 0.9204 -108 ACCTCTCACGCTCAGGGGCAGA 8 61 0 CCTCTCACCT 0.958366 -12 GCGGGCGAACGCCCACACGCTCTCCAGGCGT 17 63 0 GCCCACACCT 0.978074 -195 AAACTTTTTTGCCCTCAAACTAAATTTTCTA 19 41 1 GCCCTCAACT 0.981458 -22 ******** ** Masking position 7 Map Score: 0.901441 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 152 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 12 AGAGGTTTACCGGAGCAACGACTGGCCCAT 2 133 1 CGGAGCAACG 0.969416 -168 ATGAGATTGGCGTAACAACGCAGAGGCAGC 2 229 1 CGTAACAACG 0.973558 -72 CTCATAGCATCTTAACAACGTT 5 97 1 CTTAACAACG 0.955746 -12 AACGGAAAAACGTTTTAAATCA 10 3 1 CGGAAAAACG 0.971215 -39 ********** Masking position 4 Map Score: 0.608473 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 9 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 ********** No masking Map Score: -7.8627e-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 14 ********** No masking Map Score: -7.8627e-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 15 ********** No masking Map Score: -7.8627e-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