AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_aful_reg_100.orf -o00720_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 AF0366 218 acetyl-CoA synthetase (acs-2) #4 AF0647 132 isocitrate dehydrogenase, NADP (icd) #5 AF0677 165 acetyl-CoA synthetase (acs-3) #6 AF0681 145 succinate dehydrogenase, flavoprotein subunit A (sdhA) #7 AF0710 88 phosphoenolpyruvate synthase (ppsA) #8 AF0973 108 bile acid-inducible operon protein F (baiF-1) #9 AF1099 122 fumarase (fum-2) #10 AF1287 300 acetyl-CoA synthetase (acs-6) #11 AF1462 136 A. fulgidus predicted coding region AF1462 #12 AF1540 143 succinyl-CoA synthetase, beta subunit (sucC-1) #13 AF1699 102 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #14 AF2186 65 succinyl-CoA synthetase, beta subunit (sucC-2) #15 AF2187 174 A. fulgidus predicted coding region AF2187 #16 AF2389-C 300 acetyl-CoA synthetase, putative Motif number 1 ATTATCATCTTAAAAAATTGAATTATGCTC 2 23 0 TAAAAAATTG 0.791788 -64 ACCTCCAATTTATAACATTTAATGAGCAAA 2 62 0 TATAACATTT 0.655504 -25 TTGCGAAAATTAAAACACTTTTGCGCAAAT 3 97 0 TAAAACACTT 0.894039 -122 TTAATTTTCGCAAAAATTTTCATTTTTAAT 3 114 1 CAAAAATTTT 0.750284 -105 AATTATACCGTAAAAACTTTTGCACATTTT 4 54 1 TAAAAACTTT 0.92856 -79 TGGTAGTTTATAAAATCCTTCCGCTCTTGG 4 101 0 TAAAATCCTT 0.76277 -32 GAGTATTAGACAAAACATTTTTAACTAACA 5 27 0 CAAAACATTT 0.894037 -139 AAATCTATTTTAAAAAACTTGCGAAAGCGT 5 110 0 TAAAAAACTT 0.911292 -56 GTTTGTTATATAAAATCTTTTTTCTCGTGC 6 25 1 TAAAATCTTT 0.844517 -121 GCCAAAGCCTTAAAAAATTTTAGGTGGAGC 7 47 0 TAAAAAATTT 0.945534 -42 TTTCAAACTTTAAAAAATTGTAGAAATA 8 9 0 TAAAAAATTG 0.791788 -100 ACTTATACCTTATAAACCTTTGCGGCTATG 9 53 1 TATAAACCTT 0.506518 -70 TCTGAAAACTTAAAACTTTTCATTTAATTC 10 211 1 TAAAACTTTT 0.806638 -90 CAATTCGAATCAAAATTCTTAAATACTATG 10 240 1 CAAAATTCTT 0.42644 -61 ATTTCTTTTCCAAAAAATTTAAATAGTAAC 12 11 0 CAAAAAATTT 0.91129 -133 TTTTTCAATATAAAAAATTTTCGGAATTTC 12 36 0 TAAAAAATTT 0.945534 -108 AATCGGCATTTAAAATATTTTTTTAGCTTT 13 32 1 TAAAATATTT 0.878844 -71 TTTTAGCTTTCAAAACCTTTTCCGTTAATT 13 52 1 CAAAACCTTT 0.863334 -51 CTTAAAAGAATAAAAAATTAACGGAAAAGG 13 67 0 TAAAAAATTA 0.582328 -36 ********** Masking position 9 Map Score: 16.4234 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 136 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 2 CACGATTTGTTTATTTATGATGATAAAGTATTTATG 1 62 1 TTATTTATAA 0.829913 -70 CATAATTCAATTTTTTAAGATGATAATGAATTTAAA 2 26 1 TTTTTTATAA 0.95148 -61 GCGCAAAAGTGTTTTAATTTTCGCAAAAATTTTCAT 3 101 1 GTTTTAATAA 0.961129 -118 ACTTTATTTGGGATTAACGATTAAAAATGAAAATTT 3 127 0 GGATTAATAA 0.622764 -92 ATGTGCAAAAGTTTTTACGGTATAATTGCTTTAAGC 4 45 0 GTTTTTATAT 0.679061 -88 ATAGATATATTTATTTATTGTTAAAATCTATTTTAA 5 127 0 TTATTTATAA 0.829823 -39 TACACCACCTTGTTTAACTCTATTAATCCCTCTATA 6 120 0 TGTTTAATAA 0.840269 -26 TTTCTACAATTTTTTAAAGTTTGAAATCGAAAAACT 8 13 1 TTTTTAATAA 0.944865 -96 TAAATGAAAAGTTTTAAGTTTTCAGAACAATGACAT 10 201 0 GTTTTAATGA 0.758215 -100 GTTTTTTTTTTTTTTTGCGGTAACAATTTACTCGCT 11 65 1 TTTTTTGTAA 0.713239 -72 ATTCCGAAAATTTTTTATATTGAAAAATTGAGAATG 12 39 1 TTTTTTATAA 0.944865 -105 TTTTAAGTTCGATTTAACATTCTCAATTTTTCAATA 12 56 0 GATTTAATAA 0.708776 -88 TTTAAAATATTTTTTTAGCTTTCAAAACCTTTTCCG 13 40 1 TTTTTTATAA 0.951386 -63 TTTCCGTTAATTTTTTATTCTTTTAAGCATCCTCAG 13 70 1 TTTTTTATAA 0.95151 -33 TTAAGTTTAGGTTTTAAGGTTCTAAATCGATCTGCC 14 16 0 GTTTTAATAA 0.960994 -50 GTTTTAATGTTGCGAAGTGGTAAATT 14 50 0 GTTTTAATAA 0.961129 -16 ******* * ** Masking position 11 Map Score: 13.0393 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 36 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 AGGTATGATTTATCTCAGCACGCTTTCGCAAGTTTT 5 91 1 TTCTCGCCTT 0.982807 -75 TTACTCACCTCGTTCTGAGTTTGCCA 7 73 0 TACTCCCCCT 0.982574 -16 TTCACTCACCACCAACTAACCAACAAT 9 2 1 TACTCCCCCT 0.982574 -121 GAAGTTACTCCGCACAGCCCTTAAAATAGT 9 103 0 TACTCGCCCC 0.950325 -20 GAACTTTTCTTCTCTCTGCCCAGCTTTTTGCAACCA 10 104 1 TTCTCGCCTT 0.982804 -197 GTTTGAGACATTTCTCTTCCCATTCTTTCCTTTTCT 10 142 1 TTCTCTCCCT 0.982227 -159 ATCGTTCTCTTTTCTCTGCTGTGTTT 15 1 0 TTCTCGCGTT 0.892495 -174 GATATAGCCTTTTCTCGTCGAATTCTATTAAGTTGT 15 108 0 TTCTCTCACT 0.844188 -67 GCTTAATCCTAATCTCCCCTCTAACTCCCTTAATCA 16 186 0 ATCTCCCCCT 0.946008 -115 ATGCTCTCTCAGCTCCTCCTTCAGCTCGTC 16 281 0 TTCTCGCCCT 0.995088 -20 * **** ** * ** Masking position 5 Map Score: 11.1453 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 178 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 TCAATAAAAAAGGGGTGGTGGT 1 120 1 AGGGGTGGTG 0.693093 -12 GGACTTTAAGGGGGGAGTTTAG 3 207 1 GGGGGAGTTT 0.86727 -12 TCAACCAAGAGCGGAAGGATTTTATAAACT 4 97 1 GCGGAAGGAT 0.820247 -36 AGCGGAAGGTTGTGGTAGTTT 4 122 0 GCGGAAGGTT 0.885576 -11 TGAGTAGTGTGGAGGAGTAT 8 99 1 GGAGGAGTAT 0.780285 -10 AAATGTAGGTAAGGGAGGTTGTT 10 288 1 AAGGGAGGTT 0.918746 -13 AAAAAAACGAACAGGAGGCTCTTCCAGAGG 11 43 0 ACAGGAGGCT 0.939252 -94 GGACTGCGTTAAAGGAGGCTATCTCCTTT 11 118 1 AAAGGAGGCT 0.906957 -19 ATCGAACTTAAAAGGTGGTTGGATGTGCAG 12 79 1 AAAGGTGGTT 0.643999 -65 TGTAGAGGGGGCAGAAGGTTCTGCCTATTG 15 81 0 GCAGAAGGTT 0.877066 -94 TGTTTCACCCAGAGGAGGCTTACGCCTCCT 16 58 1 AGAGGAGGCT 0.963678 -243 AAGTTATGTAGGAGGAGGCGTAAGCCTCCT 16 70 0 GGAGGAGGCG 0.953501 -231 TATTTCGGCTGGAGAAGGATTACTGGATGT 16 119 1 GGAGAAGGAT 0.87832 -182 AGGGAGTTAGAGGGGAGATTAGGATTAAGC 16 192 1 AGGGGAGATT 0.669647 -109 CGGACGAGCTGAAGGAGGAGCTGAGAGAGC 16 279 1 GAAGGAGGAG 0.826081 -22 ********** Masking position 4 Map Score: 10.8 Number of sites scoring better than the average of aligned sites = 2507 Number in coding regions = 2357 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 5 GCATAATTCAATTTTTTAAGATGATAATGA 2 25 1 ATTTTTTAAG 0.880058 -62 TGCTCATTAAATGTTATAAATTGGAGGTGA 2 64 1 ATGTTATAAA 0.753857 -23 TTGCGCAAAAGTGTTTTAATTTTCGCAAAA 3 99 1 GTGTTTTAAT 0.545556 -120 GAGCGGAAGGATTTTATAAACTACCACAAC 4 105 1 ATTTTATAAA 0.845616 -28 GCTTTCGCAAGTTTTTTAAAATAGATTTTA 5 112 1 GTTTTTTAAA 0.843534 -54 GAGAAAAAAGATTTTATATAACAAACCTAA 6 21 0 ATTTTATATA 0.637531 -125 TCCACCTAAAATTTTTTAAGGCTTTGGCAA 7 49 1 ATTTTTTAAG 0.880058 -40 TATTTCTACAATTTTTTAAAGTTTGAAATC 8 11 1 ATTTTTTAAA 0.944642 -98 AGTCGTAATTATGTTTTAATTGTTGGTTAG 9 26 0 ATGTTTTAAT 0.791658 -97 AGGAAACCGTATTTTTTCAAAAGCTCTTTC 11 16 0 ATTTTTTCAA 0.729105 -121 AATTCCGAAAATTTTTTATATTGAAAAATT 12 38 1 ATTTTTTATA 0.845643 -106 AGCTAAAAAAATATTTTAAATGCCGATTCT 13 30 0 ATATTTTAAA 0.705979 -73 TTTTCCGTTAATTTTTTATTCTTTTAAGCA 13 69 1 ATTTTTTATT 0.685749 -34 ********** Masking position 5 Map Score: 6.36919 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 60 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 TGTTCGGGGGAAAACGGTAACTTCCTGTTTT 1 14 0 AAAACGGTAC 0.808086 -118 TTTTATATAACAAACCTAAACTTCAAGCG 6 9 0 CAAACCTAAC 0.855535 -137 TGAGTTTGCCAAAGCCTTAAAAAATTTTAGG 7 53 0 AAAGCCTTAA 0.660319 -36 TTTTCGATTTCAAACTTTAAAAAATTGTAGA 8 15 0 CAAACTTTAA 0.492931 -94 TTGAAATCGAAAAACTTATACATTTGAAAAT 8 33 1 AAAACTTAAC 0.808894 -76 TGCTCCGGTAAAAACCGCTACTATTTTAAGG 9 84 1 AAAACCGCAC 0.942561 -39 CATTGTTCTGAAAACTTAAAACTTTTCATTT 10 205 1 AAAACTTAAA 0.657053 -96 TCCGCCTTGGAAAACCGTCAAGCGAGTAAAT 11 90 0 AAAACCGTAA 0.929165 -47 TTTAGCTTTCAAAACCTTTTCCGTTAATTTT 13 53 1 AAAACCTTTC 0.743429 -50 TTAGAACCTTAAAACCTAAACTTAATTTACC 14 27 1 AAAACCTAAC 0.944713 -39 GCTGCTTAGAAAAACCGTTACAAGACTCAAA 15 43 1 AAAACCGTAC 0.966634 -132 AAACCAATCAAAAACCGCAAAAGTTATGTAG 16 89 0 AAAACCGCAA 0.881348 -212 ******** ** Masking position 3 Map Score: 4.87746 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 226 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 GCTCATTTCGTCAGTTGTTGTTCGGGGGAAAACGG 1 28 0 TGTTGTGTGG 0.984095 -104 CGCTCTTGGTTGAGTCGAAGATTGTCAAAATGTGC 4 75 0 TGTCGAGTGT 0.742965 -58 GTATTTGTTTTGTAGTTGTTAGTTAAAAATGTT 5 9 1 TGTAGTGTGT 0.934083 -157 GGAGGGATTGTATTGAGTAGTGTGGAGGAGTAT 8 86 1 TTGAGTGGGG 0.760906 -23 TTTTAATTGTTGGTTAGTTGGTGGTGAGTGAA 9 8 0 TTTAGTGTGT 0.858103 -115 TCCTTTTGGTTTCGTTGAAAATGGGGTGGT 12 124 1 TGTTGAATGG 0.709958 -20 CGAATTCTATTAAGTTGTAGAGGGGGCAGAAGGTT 15 91 0 TGTTGTGGGG 0.977805 -84 AATTGCCATCTGTAGTCGTTTGGGTCGACTGCA 16 9 1 TGTAGTGTGG 0.980477 -292 ACTGGATGTCTCTTTTGATGGGAGGGTTGGATTGT 16 140 1 TTTTGAGGGG 0.894881 -161 GAGGGTTGGATTGTTTGTAGTTTGGTGATTAAGGG 16 161 1 TTTTGTGTGG 0.963511 -140 * ***** * * ** Masking position 1 Map Score: 2.92468 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 105 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 8 AGTTCACCTCCAATTTATAACA 2 75 0 TTCACCTCCA 0.952955 -12 CCGTCATCTATTCATCACCAAAAATAGGTT 3 179 0 TTCATCACCA 0.981209 -40 TTCATCACCTCTAATAGATA 5 156 0 TTCATCACCT 0.965501 -10 TACACCACCTTGTTTAACTC 6 136 0 TACACCACCT 0.915659 -10 TTCACTCACCACCAACTAACCAAC 9 5 1 CTCACCACCA 0.967765 -118 TCTAACTCCCTTAATCACCAAACTACAAAC 16 173 0 TTAATCACCA 0.889845 -128 ********** Masking position 4 Map Score: 3.0229 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 118 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 9 ACTGACGAAATGAGCACGATTTGTTTATTTA 1 48 1 TGAGCAGATT 0.964277 -84 GCTCACACTTTGAGCATAATTCAATTTTTTA 2 12 1 TGAGCAAATT 0.978731 -75 TAACATTTAATGAGCAAATTTAAATTCATTA 2 49 0 TGAGCAATTT 0.978731 -38 AGTGCAATTGTGAGCAAATTTGCGCAAAAGT 3 80 1 TGAGCAATTT 0.978731 -139 ****** **** Masking position 6 Map Score: 0.33842 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 12 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 ********** No masking Map Score: 3.57646e-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 GAATTTCGATGCTGAAAGCTT 4 1 0 GCTGAAAGCT 0.851749 -132 CGGTATAATTGCTTTAAGCCTCACATGAGCC 4 33 0 GCTTTAAGCT 0.569728 -100 TTAAAAAACTTGCGAAAGCGTGCTGAGATAA 5 100 0 TGCGAAAGCT 0.953831 -66 GTTCTGAGTTTGCCAAAGCCTTAAAAAATTT 7 57 0 TGCCAAAGCT 0.825691 -32 AAAGGAGATAGCCTCCTTTAACGC 11 123 0 GGAGATAGCT 0.939786 -14 TATATCTGGCTGATATAGCCTTTTCTCGTCG 15 124 0 TGATATAGCT 0.772214 -51 GGATAAAGCATAATCGATGGC 15 164 0 GGATAAAGCT 0.961742 -11 TGTAGGAGGAGGCGTAAGCCTCCTCTGGGTG 16 63 0 GGCGTAAGCT 0.956371 -238 GGGGAGATTAGGATTAAGCTTGAGTAAGCAC 16 203 1 GGATTAAGCT 0.919242 -98 AAGGAGGAGCTGAGAGAGCAT 16 290 1 TGAGAGAGCT 0.848444 -11 ********* * Masking position 7 Map Score: 1.71338 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 360 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 12 ********** No masking Map Score: 3.57646e-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: 3.57646e-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: 3.57646e-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