AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_aful_reg_100.orf -o00620_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 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #2 AF0197 86 acetyl-CoA synthetase (acs-1) #3 AF0219 180 2-isopropylmalate synthase (leuA-2) #4 AF0366 218 acetyl-CoA synthetase (acs-2) #5 AF0396 154 A. fulgidus predicted coding region AF0396 #6 AF0677 165 acetyl-CoA synthetase (acs-3) #7 AF0710 88 phosphoenolpyruvate synthase (ppsA) #8 AF0818 102 acylphosphatase (acyP) #9 AF0957 53 2-isopropylmalate synthase (leuA-1) #10 AF0973 108 bile acid-inducible operon protein F (baiF-1) #11 AF1215 101 cell division protein, putative #12 AF1252 194 oxaloacetate decarboxylase, subunit alpha (oadA) #13 AF1287 300 acetyl-CoA synthetase (acs-6) #14 AF1448 114 transcriptional regulatory protein, AsnC family #15 AF1449 33 pyruvate formate-lyase 2 (pflD) #16 AF1699 102 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #17 AF2086 41 protease inhibitor, putative #18 AF2089 111 conserved hypothetical protein #19 AF2389-C 300 acetyl-CoA synthetase, putative Motif number 1 TCACCTCCAATTTATAACATTTAATGAGCAAA 2 62 0 TTTATAATTT 0.736819 -25 AGCCACCGATTTAAAAACCTTTTTTCAAATAG 3 27 1 TTAAAAATTT 0.961668 -154 TTTATCGAAATAAATAAAATTCTCGGCAACTG 3 118 0 TAAATAATTC 0.487093 -63 TTTGCGAAAATTAAAACACTTTTGCGCAAATT 4 96 0 TTAAAACTTT 0.944451 -123 AGATAAAAACTTAAAACTAATTTGCTTTTTAA 5 69 1 TTAAAACATT 0.725341 -86 TAGTTGTTAGTTAAAAATGTTTTGTCTAATAC 6 23 1 TTAAAAATTT 0.961668 -143 AAAATCTATTTTAAAAAACTTGCGAAAGCGTG 6 109 0 TTAAAAATTG 0.815284 -57 TGCCAAAGCCTTAAAAAATTTTAGGTGGAGCG 7 46 0 TTAAAAATTT 0.961668 -43 AAAATATTCATACAAAAGAATTCAAACTTATA 8 58 1 TACAAAAATT 0.454205 -45 AACGAGTGGGTAAAAAAACTTTGGCCTTCCAG 9 20 0 TAAAAAATTT 0.927443 -34 GATTTCAAACTTTAAAAAATTGTAGAAATA 10 9 0 TTTAAAATTG 0.538394 -100 ACGCTTTTTATTTAAACCTTTTTCCCAACTTT 11 61 0 TTTAAACTTT 0.817947 -41 ACGCTAAGATTTAATACGCTTTTTATTTAAAC 11 76 0 TTAATACTTT 0.87775 -26 GCCATCAACCTAAATAAACTTTCCTGAAGAAC 12 33 1 TAAATAATTT 0.8437 -162 TGATGGGAAATACAAAAATTTTTTGTTTTTAA 12 97 0 TACAAAATTT 0.84271 -98 GGCATTGAAGTTAATACAGTTTATGATCCAAC 13 60 0 TTAATACTTT 0.87775 -241 TTCTGAAAACTTAAAACTTTTCATTTAATTCA 13 210 1 TTAAAACTTC 0.749449 -91 ACTTTCATTGTAAATAAAGTTTACCTTATAAA 14 79 0 TAAATAATTT 0.8437 -36 AAAAACCTAATTAAAAAAGATTACGATTT 15 8 0 TTAAAAAATT 0.795785 -26 AGAATCGGCATTTAAAATATTTTTTTAGCTTT 16 30 1 TTTAAAATTT 0.868931 -73 TTTTTTAGCTTTCAAAACCTTTTCCGTTAATT 16 50 1 TTCAAAATTT 0.913161 -53 AACTTTATGATTAAAAAGCTTTGGTTTT 17 7 0 TTAAAAATTT 0.961668 -35 ATTTCAAGTTTAAAAACGCTTTTCAAAAGGTT 18 78 0 TAAAAACTTT 0.896509 -34 CGCCTCCTCCTACATAACTTTTGCGGTTTTTG 19 80 1 TACATAATTT 0.693492 -221 ******* *** Masking position 11 Map Score: 28.0931 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 93 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 183 Fraction of orfs with sites within 600 bp upstream = 0.0293929 Motif number 2 ATAATTCAATTTTTTAAGATGATAATGAATT 2 27 1 TTTTTAAGTG 0.896802 -60 CCAGTTTTAAGGCTAAAGCCACCG 3 4 1 GTTTTAAGCT 0.863741 -177 TGAAAAAAGGTTTTTAAATCGGTGGCTTTAG 3 23 0 TTTTTAAACG 0.725282 -158 GCGCAAAAGTGTTTTAATTTTCGCAAAAATT 4 101 1 GTTTTAATTT 0.786399 -118 TCACTGACGATATTTAAATTTTTCTTTAAGA 5 41 1 TATTTAAATT 0.739441 -114 AAGCAAATTAGTTTTAAGTTTTTATCTTAAA 5 65 0 GTTTTAAGTT 0.919449 -90 ACTAATTTGCTTTTTAAGTTTGTAGCTTGAA 5 84 1 TTTTTAAGTT 0.962353 -71 TTTCGCAAGTTTTTTAAAATAGATTTTAACA 6 114 1 TTTTTAAATA 0.542228 -52 CACCTAAAATTTTTTAAGGCTTTGGCAAACT 7 51 1 TTTTTAAGCT 0.934194 -38 TTTCTACAATTTTTTAAAGTTTGAAATCGAA 10 13 1 TTTTTAAATT 0.933261 -96 GGCGTTGCTGTTTTTAAACTTGCCTTTATCG 11 23 1 TTTTTAAATT 0.933261 -79 ATACGCTTTTTATTTAAACCTTTTTCCCAAC 11 64 0 TATTTAAACT 0.611809 -38 AAATTTTTTGTTTTTAATATTGCTTGCACCT 12 83 0 TTTTTAATTT 0.891832 -112 TAAATGAAAAGTTTTAAGTTTTCAGAACAAT 13 206 0 GTTTTAAGTT 0.919449 -95 TTTTACATAGTATTTAAGAATTTTGATTCGA 13 244 0 TATTTAAGAT 0.582434 -57 ATCGTAATCTTTTTTAATTAGGTTTTTAAGG 15 13 1 TTTTTAATAG 0.42977 -21 TTTAAAATATTTTTTTAGCTTTCAAAACCTT 16 40 1 TTTTTTAGTT 0.646505 -63 AAACCAAAGCTTTTTAATCATAAAGTTTAGG 17 12 1 TTTTTAATAT 0.68915 -30 TTGAAAAGCGTTTTTAAACTTGAAATCGAAA 18 84 1 TTTTTAAATT 0.933261 -28 ******** ** Masking position 5 Map Score: 17.1732 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 87 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 AGTTCACCTCCAATTTATAACATT 2 73 0 TCCCTCCAAT 0.919397 -14 CCTATCCCCTCCGCACTGCTACTGT 5 5 1 TCCCTCCGCA 0.933351 -150 TTCATCACCTCTAATAGATATATTT 6 151 0 TCCCTCTAAT 0.691937 -15 CGCTTGCGATTCCGCTCCACCTAAAATTTTT 7 34 1 TCGCTCCACC 0.978502 -55 TTACTCACCTCGTTCTGAGTTTGCC 7 74 0 TCCCTCGTTC 0.821965 -15 ATACTCCTCCACACTACTCAATA 10 96 0 ACCCTCCACA 0.904787 -13 CCTTCTCCTCCTAAACTTTATGAT 17 28 0 TCCCTCCTAA 0.942344 -14 GAGGAGGCTTACGCCTCCTCCTACATAACTT 19 69 1 ACCCTCCTCC 0.966661 -232 AATCCTAATCTCCCCTCTAACTCCCTTAATC 19 187 0 TCCCTCTAAC 0.907579 -114 AGCTCCTCCTTCAGCTCGTCCGACGGCTGGT 19 270 0 TCGCTCGTCC 0.932722 -31 ATGCTCTCTCAGCTCCTCCTTCAGCTCGT 19 282 0 TCGCTCCTCC 0.978502 -19 ** ******** Masking position 6 Map Score: 7.74034 Number of sites scoring better than the average of aligned sites = 1383 Number in coding regions = 1316 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 TAAATACTTTATCATCATAAATAAACAAATCGTGC 1 61 0 ATAAAATAAA 0.830028 -71 ATACGAAATTATTATTCAATAAAAAAGGGGTGGTG 1 105 1 ATAATAAAAA 0.49367 -27 ATAACATTTAATGAGCAAATTTAAATTCATTATCA 2 46 0 ATAATTTAAA 0.374465 -41 TAACAATTTATCGAAATAAATAAAATTCTCGGCAA 3 121 0 TCAAATAAAA 0.69582 -60 TTTTTAATCGTTAATCCCAAATAAAGTTAAATATC 4 136 1 TTAAAATAAA 0.932982 -83 GTTTTAAGTTTTTATCTTAAAGAAAAATTTAAATA 5 51 0 TTAAAAGAAA 0.837052 -104 TGTCTAATACTCTAATTGAATAAAAGTTGACAGTT 6 45 1 TCAAATAAAA 0.694606 -121 AAAATAGATTTTAACAATAAATAAATATATCTATT 6 129 1 TTAAAATAAA 0.933059 -37 TTCGAACGAATTGAAATCATATAAATAGTTTGCCT 8 25 0 TTAATATAAA 0.80486 -78 TGATACTGCCATCAACCTAAATAAACTTTCCTGAA 12 26 1 ATAAAATAAA 0.830029 -169 GAATTTTGATTCGAATTGAATTAAATGAAAAGTTT 13 223 0 TCAAATTAAA 0.799027 -78 GACAGCTACTTCAATTACAAAGAAAAGACTGTCAT 14 13 0 TCAAAAGAAA 0.814698 -102 TTGTAACACTTTCATTGTAAATAAAGTTTACCTTA 14 83 0 TTAAAATAAA 0.928447 -32 GAAAAGGTTTTGAAAGCTAAAAAAATATTTTAAAT 16 39 0 TGAAAAAAAA 0.599697 -64 CTGAGGATGCTTAAAAGAATAAAAAATTAACGGAA 16 71 0 TTAATAAAAA 0.735809 -32 GTAATCCTTCTCCAGCCGAAATAAACCAATCAAAA 19 107 0 TCAAAATAAA 0.919715 -194 ** * ******* Masking position 9 Map Score: 6.93591 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 51 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 CCTGCTTAATATATCGCTTGCGATTCCGCTC 7 20 1 ATATCGCTGC 0.978972 -69 TCAAACTTATATACCGCAGGCAAAAGGTGGG 8 79 1 ATACCGCGGC 0.980537 -24 CAAATTATTAATACTGCATGGAGGGATTGTA 10 67 1 ATACTGCTGG 0.952586 -42 TTTGTTTTTAATATTGCTTGCACCTCAAAAG 12 77 0 ATATTGCTGC 0.967329 -118 GTCTTTATCCATACTGCATGCTCTCCAACGT 14 45 1 ATACTGCTGC 0.988716 -70 AACAATGCAGATCCCGCTTGCAGTCGACCCA 19 31 0 ATCCCGCTGC 0.980537 -270 ******* *** Masking position 2 Map Score: 4.63864 Number of sites scoring better than the average of aligned sites = 20 Number in coding regions = 16 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 6 GGAAAACAGGAAGTTACCGTTTTCCCCCGAACA 1 12 1 AAGTACTTTT 0.885168 -120 TTTAAGGCTAAAGCCACCGATTTAAAAACCTTT 3 16 1 AAGCACATTT 0.977956 -165 TTCGGTGCCTTAGATAACAATTTATCGAAATAA 3 137 0 TAGTACATTT 0.796638 -44 ATTTTTCTTTAAGATAAAAACTTAAAACTAATT 5 58 1 AAGTAAACTT 0.760726 -97 AGAAAAATTCAAGCTACAAACTTAAAAAGCAAA 5 89 0 AAGTAAACTT 0.77224 -66 TCTAAGAGTTAAGTCAACAATTTTTACTTTTGC 12 142 0 AAGCACATTT 0.977693 -53 AGTATGGATAAAGACAGCTACTTCAATTACAAA 14 27 0 AAGCACACTT 0.969095 -88 CTAATTAAAAAAGATTACGATTT 15 1 0 AAGTTCATTT 0.795891 -33 TAATAGTTATAAGGCAACCTTTTGAAAAGCGTT 18 63 1 AAGCACTTTT 0.925045 -49 GAGGATGACGAAGGCAACTATATAAGGTGCTTA 19 227 0 AAGCACATAT 0.862014 -74 *** ** * **** Masking position 2 Map Score: 5.11577 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 51 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 7 CTAAACTCCCCCCTTAAAGTCCGTCAT 4 202 0 CCCCCCTTAA 0.979963 -17 AACAACCTCCCTTACCTACATTTTT 13 286 0 CCTCCCTTAC 0.979963 -15 CCAACTCCCTTAAAAGTAATTAC 18 4 1 ACTCCCTTAA 0.979669 -108 ACAATCCAACCCTCCCATCAAAAGAGACAT 19 145 0 CCTCCCATCA 0.93697 -156 CTCCCCTCTAACTCCCTTAATCACCAAACT 19 179 0 ACTCCCTTAA 0.979669 -122 ********** Masking position 8 Map Score: 2.05988 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 CCGTTTTCCCCCGAACAACAACTGACGAAATG 1 28 1 CCGAACAAAC 0.976468 -104 GCAACTGCTACAAATCAAATACGTATTCTTGT 3 93 0 CAAATCAAAC 0.944629 -88 CTAACAACTACAAAACAAATAC 6 1 0 CAAAACAAAC 0.969541 -165 TTTAAGTTTTCAGAACAATGACATATGAACAA 13 193 0 CAGAACAAAC 0.963489 -108 TGCAGTCGACCCAAACGACTACAGATGGCAAT 19 12 0 CCAAACGAAC 0.948189 -289 CCGAAATAAACCAATCAAAAACCGCAAAAGTT 19 95 0 CCAATCAAAC 0.964062 -206 ******** ** Masking position 8 Map Score: 2.09468 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 6 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 9 AATATCGTCAGTGAGAGGCACAGTAGCAGTG 5 24 0 GTGGAGGCAC 0.963152 -131 TTCCCATCAGGCTTGAGACATGGCAAAAGTA 12 120 1 GCTGAGACAT 0.957685 -75 CATAGACTTTGTGAGAGACATCGGCTATCCG 13 17 0 GTGGAGACAT 0.981884 -284 GAGAAGAAAAGTTCGAGACACTATCCGGCAT 13 87 0 GTTGAGACAC 0.981821 -214 TGCAACCACGGTTTGAGACATTTCTCTTCCC 13 132 1 GTTGAGACAT 0.980478 -169 *** ******* Masking position 6 Map Score: 1.56485 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 CAATAAAAAAGGGGTGGTGGT 1 121 1 GGGGTGGTGG 0.939956 -11 GACTTTAAGGGGGGAGTTTAG 4 208 1 GGGGAGTTTA 0.935471 -11 AATACTGCATGGAGGGATTGTATTGAGTAG 10 76 1 GGAGGGATTG 0.839445 -33 AATGTAGGTAAGGGAGGTTGTT 13 289 1 AGGGAGGTTG 0.953574 -12 ATTACTTTTAAGGGAGTTGG 18 1 0 AGGGAGTTGG 0.967657 -111 TCTTTTGATGGGAGGGTTGGATTGTTTGTA 19 150 1 GGAGGGTTGG 0.921754 -151 TTGGTGATTAAGGGAGTTAGAGGGGAGATT 19 182 1 AGGGAGTTAG 0.88277 -119 GGGAGTTAGAGGGGAGATTAGGATTAAGCT 19 193 1 GGGGAGATTA 0.885972 -108 ********** Masking position 8 Map Score: 1.30138 Number of sites scoring better than the average of aligned sites = 578 Number in coding regions = 546 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 ATCAGCGATATTAAAAAGGAACA 4 4 0 TTAAAAAGGA 0.964376 -215 GGATTAACGATTAAAAATGAAAATTTTTGC 4 123 0 TTAAAAATGA 0.929114 -96 AGCTACAAACTTAAAAAGCAAATTAGTTTT 5 81 0 TTAAAAAGCA 0.905461 -74 TAGTTGTTAGTTAAAAATGTTTTGTCTAAT 6 23 1 TTAAAAATGT 0.929114 -143 AGATGTGTGATTAAAAATGTAGGTAAGGGA 13 274 1 TTAAAAATGT 0.929114 -27 AAAAACCTAATTAAAAAAGATTACGATTT 15 10 0 TTAAAAAAGA 0.838383 -24 AACTTTATGATTAAAAAGCTTTGGTTTT 17 9 0 TTAAAAAGCT 0.905461 -33 AAAAACGCTTTTCAAAAGGTTGCCTTATAA 18 69 0 TTCAAAAGGT 0.877903 -43 ********** Masking position 5 Map Score: 5.59134 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 56 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 12 CCGAACAACAACTGACGAAATGAGCACGAT 1 38 1 ACTGACGAAA 0.898111 -94 TGTGCCTCTCACTGACGATATTTAAATTTT 5 33 1 ACTGACGATA 0.966668 -122 TACCTTATAAACTGACGTTGGAGAGCATGC 14 60 0 ACTGACGTTG 0.952063 -55 CTCTTAACTGAGGATGCTTAAAAGAA 16 87 0 ACTGAGGATG 0.978194 -16 GGTATCCCTTCCTGAGGATGACGAAGGCAA 19 243 0 CCTGAGGATG 0.952848 -58 ********** Masking position 5 Map Score: 0.612502 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 22 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 13 TATGATGATAAAGTATTTATGAATACTCAT 1 77 1 AAGTATTTAT 0.624968 -55 ATTTTCGCAAAAATTTTCATTTTTAATCGT 4 117 1 AAATTTTCAT 0.848547 -102 GACGATATTTAAATTTTTCTTTAAGATAAA 5 46 1 AAATTTTTCT 0.79134 -109 AATTAGTTTTAAGTTTTTATCTTAAAGAAA 5 61 0 AAGTTTTTAT 0.905677 -94 TTTGCTTTTTAAGTTTGTAGCTTGAATTTT 5 89 1 AAGTTTGTAG 0.585623 -66 ATTGCAATATAAATTTTCCGACGTACAGAA 5 118 0 AAATTTTCCG 0.816948 -37 ATTCGTTCGAAAATATTCATACAAAAGAAT 8 49 1 AAATATTCAT 0.492995 -54 TGGAAGGCCAAAGTTTTTTTACCCACTCGT 9 21 1 AAGTTTTTTT 0.704353 -33 TCAAATGTATAAGTTTTTCGATTTCAAACT 10 30 0 AAGTTTTTCG 0.884374 -79 CAACCTAAATAAACTTTCCTGAAGAACGTA 12 38 1 AAACTTTCCT 0.524816 -157 GGAAATACAAAAATTTTTTGTTTTTAATAT 12 94 0 AAATTTTTTG 0.581616 -101 GAAAAGTTTTAAGTTTTCAGAACAATGACA 13 202 0 AAGTTTTCAG 0.918695 -99 GAAAACTTAAAACTTTTCATTTAATTCAAT 13 214 1 AACTTTTCAT 0.632887 -87 CTTTTCCGTTAATTTTTTATTCTTTTAAGC 16 68 1 AATTTTTTAT 0.517431 -35 CGCTATATTAAAGCTTTTAGCTAATGACCA 18 33 1 AAGCTTTTAG 0.736585 -79 ********** Masking position 2 Map Score: 3.32054 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 176 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 14 ********** No masking Map Score: 1.75037e-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 15 ********** No masking Map Score: 1.75037e-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