AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_aful_reg_300.orf -o00400_aful_300.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 AF0230 232 conserved hypothetical protein #2 AF0667 69 A. fulgidus predicted coding region AF0667 #3 AF0669 35 4-oxalocrotonate tautomerase, putative #4 AF0776 135 tyrosyl-tRNA synthetase (tyrS) #5 AF1127 213 LSU ribosomal protein L18E (rpl18E) #6 AF1131 75 DNA-directed RNA polymerase, subunit K (rpoK) #7 AF1132 108 enolase (eno) #8 AF1240 81 tryptophan synthase, subunit beta (trpB-1) #9 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #10 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #11 AF1420 216 membrane protein #12 AF1421 49 conserved hypothetical protein #13 AF1422 35 aspartate racemase #14 AF1423_AF1424 112 AF1423: conserved hypothetical protein, AF1424: phenylalanyl-tRNA synthetase, subunit beta (pheT) #15 AF1495 73 conserved hypothetical protein #16 AF1604 300 anthranilate synthase component II (trpD) #17 AF1955 68 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #18 AF2327 72 shikimate 5-dehydrogenase (aroE) Motif number 1 AATTTTTTAAGTTTTAAAAATTGTGAGCCCTC 1 9 0 GTTTAAATGT 0.927328 -224 TTAGCAGCATGTATTTAAGCTTTTCCAATTTTTG 1 57 0 GTTTAAGTTT 0.985692 -176 CAATAGCAAAGTATTTAAATTTTGCGACATGTTT 2 18 0 GTTTAAATTG 0.952121 -52 TGGCAATTGGGTAATAAAACGTTTTT 3 3 0 GTATAAATTT 0.891885 -33 GTATAAATATATTTTCAAGCCTTTGCAACCTTTT 4 32 1 ATTTAAGTTT 0.913765 -104 GCTTTGGAGGGCTTTTAAACATTTAAACAACTTT 4 86 1 GCTTAAATTT 0.881211 -50 AACCCAGGCTGTTTTTAAAGTTGTTTAAATGTTT 4 102 0 GTTTAAATGT 0.927328 -34 TCTCCAATTCGTTTTAAATGTTTTCTTGCTGAGA 8 20 1 GTTTAATTTT 0.884968 -62 TCATTTTATTTAAGTTTTTTCCCATTAAA 8 63 0 TTTTAAGTTT 0.807457 -19 AATTCAGGTAGGCATAAAAGTTTT 9 1 0 GGATAAATTT 0.673187 -49 AATCCACGAAGTCTTGAAGCGTTGCCAGCAGAAT 11 125 0 GTTTAAGTTG 0.961623 -92 TCTGCTTTGAATGTTAAAAAGTTTGCTGTGCTAC 12 18 0 ATTTAAATTT 0.893723 -32 CTTGAAGTTGAGGTTAAAATTTTTTAGGTTGGGT 14 20 1 AGTTAAATTT 0.677397 -93 TAAAAGGCCTGTCTTGAAGTATTTAGCGCATCAC 14 52 0 GTTTAAGTTT 0.985692 -61 AGAGCCGGATGTATTTAAAGCTTGTTCAGAAAGG 15 21 1 GTTTAAATTG 0.952121 -53 CCCGCGAAGTGTATTTAAGCTTTTTGCTATAGTA 16 253 0 GTTTAAGTTT 0.985692 -48 TAGTAGAAATGTTTTAAAGTGTTTCTTCAGAGAT 17 37 0 GTTTAAGTTT 0.985692 -32 ** ** *** *** Masking position 7 Map Score: 25.7136 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 72 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 2 CCTTTGCAACCTTTTTCATCATTAGCAGGT 4 51 1 CTTTTTCATC 0.969919 -85 CCTCTGCCAGCTTCCTTATCTTGCTCATAT 5 122 0 CTTCCTTATC 0.939137 -92 TTGGATTTGACTTCCTCCTCTGCCAGCTTC 5 138 0 CTTCCTCCTC 0.992671 -76 GACCCTTTTCTTCATCTCCAATCCAA 9 34 0 TTTCTTCATC 0.940271 -16 TGAACCAAAGCTTCTTCATCAGGTCTTCGG 16 45 0 CTTCTTCATC 0.992956 -256 TTCCTCCTCGCTTCTTCATCCAGCTGAGGT 16 76 0 CTTCTTCATC 0.992956 -225 GATTTTCTATCTTCCTCCTCGCTTCTTCAT 16 87 0 CTTCCTCCTC 0.992671 -214 GTTTAGGTGACTTTTACCTCTTTTTTGCCA 16 223 1 CTTTTACCTC 0.849935 -78 ********** Masking position 3 Map Score: 13.0817 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 395 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 TACACCATGCATTGGAGGAAGGTTTAGCAGCAT 1 81 0 ATTGAGGGGT 0.946024 -152 GGTGTAGCCAAAACCAGGGTGTTTGGATTTTAT 1 108 1 AAACAGGGTT 0.964628 -125 TTAGCTTCTAATTAGCGGGAGGTGTTCTGCAGT 1 166 1 ATTGCGGGGT 0.835726 -67 ACCGAACGAAAACCCAGGCTGTTTTTAAAGTTG 4 113 0 AACCAGGGTT 0.878197 -23 GGAAGCTGGCAGAGGAGGAAGTCAAATCCAAAC 5 137 1 AGAGAGGGTC 0.742831 -77 CACCCCTTAAAGCAGATGGGGCCGCCGAGAT 6 55 0 AAACAGAGGG 0.682779 -21 GTAGCTTGATAATTGAGGACGTTCACTACAGAG 7 15 1 AATGAGGGTT 0.968897 -94 ACAGCAGGGGAAACGAGACGGTTGAGTGTGAAG 7 57 1 AAAGAGAGTT 0.807375 -52 CTCCAATCCAAATTCAGGTAGGCATAAAAGTTT 9 12 0 AATCAGGGGC 0.916542 -38 GAATCAAAAAAAGAGGAAGGGCTT 10 4 0 AAAGAGGGGG 0.960814 -21 GAAAGGTATTATAGCAGGTTGTGTGAAGAATTA 15 49 1 ATACAGGGTG 0.875916 -25 AGGTGCTTGAAAACCCGGCAGTTTACGTTCCCG 16 15 1 AAACCGGGTT 0.887413 -286 GCATTCCGGGATTTGAGGTCGGTGCAGCCTTAA 16 159 1 ATTGAGGGGT 0.946024 -142 TTAAACAATTAATTGAGGTGGTTAG 17 3 0 AATGAGGGTT 0.968897 -66 *** **** *** Masking position 1 Map Score: 12.9494 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 532 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 AGGAAGGTTTAGCAGCATGTATTTAAGCTTTTC 1 66 0 AGCAGAGTTT 0.967124 -167 GCTTCTAATTAGCGGGAGGTGTTCTGCAGTGGC 1 169 1 AGCGGAGTTT 0.992285 -64 AAAATTAACATGCGGCAAAGATTTAAATTACGT 5 54 1 TGCGGAAGTT 0.910031 -160 AATCAAAAAAAGAGGAAGGGCTT 10 1 0 AGAGGAGGTT 0.925142 -24 AAGCGTTGCCAGCAGAATAACTTGACAAAACGA 11 110 0 AGCAGAAATT 0.786955 -107 CAGGCCTTTTAGCGGTAAATTTTTATCGGCCCA 14 75 1 AGCGGAATTT 0.984954 -38 TTAAAAAAAGAGCCGGATGTATTTAAAGCTTGT 15 13 1 AGCCGAGTTT 0.961128 -61 ATTTATCCAAAGCGGCAGAGTATCG 18 3 0 AGCGGAAGAT 0.910031 -70 GGGTTTTCGGAGCGGTAAGTATTTATCCAAAGC 18 23 0 AGCGGAGTTT 0.992285 -50 ***** * ** ** Masking position 7 Map Score: 8.8761 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 66 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 5 TTTTAGGTTTAGCTTTGGCTACTGGTTTAG 1 140 1 AGCTTTGGCT 0.807808 -93 TTCAAATAGGAGGTGAGAAT 2 60 1 AGGTGAGAAT 0.630904 -10 GCAGGTAGCAAGCTTTGGAGGGCTTTTAAA 4 75 1 AGCTTTGGAG 0.970072 -61 GTCAAAACTACGCTGAGGTGTAGTTGATAT 5 96 1 CGCTGAGGTG 0.897388 -118 GAGAGTAACGAGGTTTGGATTTGACTTCCT 5 152 0 AGGTTTGGAT 0.851773 -62 GTGAAGTCGTTGCTGGGGAGGTTGTTGCGA 7 84 1 TGCTGGGGAG 0.853859 -25 AATGTTTTCTTGCTGAGAATGTTCCCATTT 8 36 1 TGCTGAGAAT 0.636998 -46 CTATCCGGGAAGCTTTGAAGCTGAGTGACA 11 54 0 AGCTTTGAAG 0.884418 -163 AATGCAATTCTGCTTTGAATGTTAAAAAGT 12 30 0 TGCTTTGAAT 0.582053 -20 TTTTGCTTGAAGTTGAGGTTAAAATTTTTT 14 15 1 AGTTGAGGTT 0.685346 -98 AAAATTTTTTAGGTTGGGTGATGCGCTAAA 14 35 1 AGGTTGGGTG 0.753772 -78 CTGATGAAGAAGCTTTGGTTCACACCTCAG 16 53 1 AGCTTTGGTT 0.931796 -248 TTCTTCATCCAGCTGAGGTGTGAACCAAAG 16 65 0 AGCTGAGGTG 0.965135 -236 CTTATCAGAAAGTTTAGGTGACTTTTACCT 16 212 1 AGTTTAGGTG 0.735421 -89 AAGCTGAGTAGTAGAAATGTT 17 58 0 AGCTGAGTAG 0.745582 -11 GATACTCTGCCGCTTTGGATAAATACTTAC 18 12 1 CGCTTTGGAT 0.864284 -61 ********** Masking position 4 Map Score: 10.0605 Number of sites scoring better than the average of aligned sites = 1613 Number in coding regions = 1509 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 6 ATGCTGCTAAACCTTCCTCCAATGCATGGT 1 81 1 ACCTTCCTCC 0.92979 -152 GTTTGGATTTGACTTCCTCCTCTGCCAGCT 5 140 0 GACTTCCTCC 0.852943 -74 CTCTGTAGTGAACGTCCTCAATTATCAAGC 7 18 0 AACGTCCTCA 0.973037 -91 CCTCCCCAGCAACGACTTCACACTCAACCG 7 75 0 AACGACTTCA 0.789326 -34 CGCCTTCGCAACAACCTCCCCAGCAACGA 7 90 0 AACAACCTCC 0.973404 -19 ATTAAATGGGAACATTCTCAGCAAGAAAAC 8 39 0 AACATTCTCA 0.643918 -43 GCCCAACCAGAACAACATCA 14 103 1 AACAACATCA 0.70438 -10 CCGGGTTTTCAAGCACCTCCTC 16 3 0 AAGCACCTCC 0.821871 -298 GAGATTTTCTATCTTCCTCCTCGCTTCTTC 16 89 0 ATCTTCCTCC 0.829212 -212 TTAAGGCTGCACCGACCTCAAATCCCGGAA 16 162 0 ACCGACCTCA 0.948558 -139 CTAACCACCTCAATTAATTGTT 17 3 1 AACCACCTCA 0.967149 -66 ********** Masking position 8 Map Score: 5.32078 Number of sites scoring better than the average of aligned sites = 1296 Number in coding regions = 1217 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 AAAAACGTTTTATTACCCAAT 3 2 1 AAAACGTTTT 0.488856 -34 CGGAAGGCTAAAAACGATTTCGATATGAG 5 10 0 AAAACGATTT 0.787809 -204 CCTGCTGTCGAAAACGACTCTGTAGTGAAC 7 35 0 AAAACGACTC 0.953814 -74 GAAAACATTTAAAACGAATTGGAGAGAGCG 8 15 0 AAAACGAATT 0.957684 -67 ATAACTTGACAAAACGAATAGCCCTGATGG 11 97 0 AAAACGAATA 0.928445 -120 GATATTGCAGAAAACGAATCCACGAAGTCT 11 145 0 AAAACGAATC 0.972117 -72 ********** Masking position 4 Map Score: 4.23302 Number of sites scoring better than the average of aligned sites = 45 Number in coding regions = 38 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 GTGATCCTGCGGCGTTCGGGACGCCGTGACC 6 15 1 GGCTTCGGGA 0.98357 -61 AGTATCGTGAGATTTTCCGAGCCCGCAGTTG 11 22 0 GATTTCCGAG 0.881749 -195 GTGTGAAATAGACTATCCGGGAAGCTTTGAA 11 65 0 GACATCCGGG 0.918327 -152 TTCTTCATCAGGTCTTCGGGAACGTAAACTG 16 33 0 GGTTTCGGGA 0.96665 -268 GCCTGAAGGAGGCATTCCGGGATTTGAGGTC 16 148 1 GGCTTCCGGG 0.99405 -153 CAGCCTTAACGGCTCTCGGTGGATCATCTCT 16 183 1 GGCCTCGGTG 0.938935 -118 AGTAAAAAAGGGTTTTCGGAGCGGTAAGTAT 18 34 0 GGTTTCGGAG 0.972902 -39 *** ******* Masking position 6 Map Score: 2.75315 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 190 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 CGAAAACCCAGGCTGTTTTTAAAGTTGTTT 4 110 0 GGCTGTTTTT 0.901739 -26 TTAAATCTTTGCCGCATGTTAATTTTTAAT 5 50 0 GCCGCATGTT 0.91093 -164 TGGCGCCTCATTTTTTGCTGACTC 5 200 0 GCCTCATTTT 0.969599 -14 AAGCCCTTCCTCTTTTTTTGATTC 10 8 1 TCCTCTTTTT 0.904849 -17 AACCTTATTAGCCTCTTGTTATTTATTTGC 11 195 1 GCCTCTTGTT 0.976479 -22 AAATACATCCGGCTCTTTTTTTAATC 15 7 0 GGCTCTTTTT 0.962878 -67 AACGTAAACTGCCGGGTTTTCAAGCACCTC 16 14 0 GCCGGGTTTT 0.843031 -287 GGTGACTTTTACCTCTTTTTTGCCATACTA 16 228 1 ACCTCTTTTT 0.904849 -73 ********** Masking position 7 Map Score: 4.7219 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 153 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 AACGAATAGCCCTGATGGAGTGTGAAATAG 11 85 0 CCTGATGGAG 0.994306 -132 TTCCCGAAGACCTGATGAAGAAGCTTTGGT 16 42 1 CCTGATGAAG 0.977396 -259 TAGAAAATCTCATGATTGAGGTTAAGGCCA 16 108 1 CATGATTGAG 0.917559 -193 CACAGTAAAGCCTGAAGGAGGCATTCCGGG 16 139 1 CCTGAAGGAG 0.985826 -162 ********** Masking position 5 Map Score: 1.7968 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 68 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 CCAATGCATGGTGTAGCCAAAACCAGGGTG 1 99 1 GTGTAGCCAA 0.842772 -134 GAAGCTAAACCAGTAGCCAAAGCTAAACCT 1 144 0 CAGTAGCCAA 0.977588 -89 AAATATGTTTCAATAGCAAAGTATTTAAAT 2 32 0 CAATAGCAAA 0.97098 -38 TTTTATTACCCAATTGCCAACACACTTT 3 18 1 CAATTGCCAA 0.928468 -18 TGCAATATCTCAATATCAAACTCATGAAAA 11 166 1 CAATATCAAA 0.83809 -51 TTTTGCCATACTATAGCAAAAAGCTTAAAT 16 245 1 CTATAGCAAA 0.947182 -56 ********** Masking position 4 Map Score: 1.00295 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 67 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 ********** No masking Map Score: 4.98334e-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 13 ********** No masking Map Score: 4.98334e-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 14 ********** No masking Map Score: 4.98334e-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