AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_aful_reg_300.orf -o00910_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 AF0154 139 conserved hypothetical protein #2 AF0155 62 A. fulgidus predicted coding region AF0155 #3 AF0157 99 molybdopterin oxidoreductase, iron-sulfur binding subunit #4 AF0162 241 A. fulgidus predicted coding region AF0162 #5 AF0163 157 A. fulgidus predicted coding region AF0163 #6 AF0164 60 ferredoxin-nitrite reductase (nirA) #7 AF0499 300 molybdopterin oxidoreductase, iron-sulfur binding subunit #8 AF0546 300 nitrate reductase, gamma subunit (narI) #9 AF0883 71 argininosuccinate lyase (argH) #10 AF0949_AF0950 177 AF0949: glutamine synthetase (glnA), AF0950: carbon monoxide dehydrogenase, iron sulfur subunit (cooF) #11 AF1439 31 asparagine synthetase (asnB) #12 AF1442 54 conserved hypothetical protein #13 AF1591 300 A. fulgidus predicted coding region AF1591 #14 AF2173 300 2-nitropropane dioxygenase (ncd2) #15 AF2332 238 flavodoxin, putative Motif number 1 GATTGCATTTTCAAAACCGATTTTAGGCCAACC 1 80 1 TCAAACCTTT 0.98429 -60 TTTAGGCCAACCAAAAACTTTTTAAATTTAGGC 1 101 1 CCAAAACTTT 0.833462 -39 GTGTTAATTTCCAAAACCCTTATATTTTATCAA 3 29 1 CCAAACCTAT 0.962805 -71 CCTCCTCTTGCCAGAACCTTTCTGGCTAACAAT 3 71 0 CCAAACCTCT 0.93821 -29 CTGGTCATTTTAACCACCACTTTTGTTTTTTCA 4 61 0 TAACACCTTT 0.862139 -181 TTGATGGTTTCCACAACCTCTTTATCTGCCCTG 4 180 0 CCAAACCTTT 0.98882 -62 ATCTCCATACTCATCACCAGATTATACTTATCC 7 62 1 TCACACCATT 0.832526 -239 CAAAATCTTATAATAACCATTATTATGAGGTCA 7 130 1 TAAAACCTAT 0.812338 -171 TTTTTATAGCTCATAACCTAAATTGCTGTTTTT 8 189 0 TCAAACCAAT 0.774822 -112 TACATACCAATACAAACCAATTTTAACAACACA 10 63 0 TACAACCTTT 0.862139 -115 CCCTAACCTATTTTTCCAAACTT 13 1 1 CCCAACCTTT 0.973956 -300 GAATTGCATGCCACCACCCCTTTGTTTCCTGTG 13 35 0 CCACACCTTT 0.973956 -266 TTTGCAGCTGTAAGAACCAATTTTCGATTTTCG 13 130 0 TAAAACCTTT 0.936672 -171 CAAATTGGTTTCAAAACCATCTTTAAATACTGA 15 76 1 TCAAACCCTT 0.908107 -163 TTTCCTATGCCCCAAACCTTTTTGAAAATCAAG 15 203 1 CCCAACCTTT 0.973956 -36 *** **** *** Masking position 6 Map Score: 19.2846 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 219 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 2 TAAAATCTTCGAATATGAAAAAAA 2 3 0 GAAATGAAAA 0.749893 -60 ACACCGTAAAAAAAACGAAAAA 3 1 0 AAAACGAAAA 0.702703 -99 TAAAAGCGGTAGAAATTTAAAAAGTAATGAAA 4 34 1 AGAATTAAAA 0.826104 -208 AAATTTAAAAAGTAATGAAAAAACAAAAGTGG 4 46 1 AGTATGAAAA 0.883674 -196 AAGGACTATCAGTTCAGGAAAAGCAGGGCAGA 4 157 1 AGTCAGAAAA 0.697664 -85 GAGGTTGTGGAAACCATCAAAAAAGAGAGAAA 4 193 1 AAACATAAAA 0.735414 -49 AAAGAAAATCGATAAAGTAAAACTGAAAGTCC 5 27 1 GATAAGAAAA 0.597905 -131 AGAATCGAATAAAAAAGCAAAAGGTTAATATA 7 215 1 AAAAAGAAAA 0.89898 -86 CTCTCTTTTGAATTATTTAAAATTTTCTCAAG 8 21 1 AATATTAAAA 0.892039 -280 TTTTTATCTTAATTATTAAAAACTTGAGAAAA 8 43 0 AATATTAAAA 0.892039 -258 GCATGTATATAAAAAATAAAAATTAAATTTTT 8 71 0 AAAAATAAAA 0.834034 -230 TTAGCATAATAATAATTTAAAAAAAGCATTAA 8 248 0 AATATTAAAA 0.892039 -53 AAGCGTAGGTAAATCTGAAAAATCTTCACCAA 10 104 0 AAACTGAAAA 0.899618 -74 TTCAACTATGAGTTATTAAAAAA 11 2 0 AGTATTAAAA 0.810957 -30 AGGAGTGCAGAAAGATGGAAAAGTTAAATTTG 13 159 0 AAAATGAAAA 0.941872 -142 TTCCTGTGGAAAATGTGGAAAAGGATACAGAA 13 236 0 AAAGTGAAAA 0.672654 -65 GCTATGTGCAAAGTATTAAAAAATTGCCTTAT 14 93 0 AAGATTAAAA 0.760258 -208 CCCTCAACCAAAACAATAAAAATTATCAACCT 15 28 0 AAAAATAAAA 0.834034 -211 CCAATTTGACAGGGCTTTAAAACTCCCTCAAC 15 52 0 AGGCTTAAAA 0.476611 -187 ACCATCTTTAAATACTGAAAAATATGGCACCA 15 91 1 AATCTGAAAA 0.890022 -148 CCTTTTTGAAAATCAAGCAAAACAAAGCTT 15 219 1 AATAAGAAAA 0.88933 -20 *** *** **** Masking position 9 Map Score: 16.8398 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 222 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 3 CACCACCCCAAACACTGTTACCTAACAGTG 1 16 1 AACACTGTTA 0.990889 -124 GTTAAATATAAACACTGTTAGGTAACAGTG 1 28 0 AACACTGTTA 0.990889 -112 TTTGGAAATTAACACCGTAAAAAAAACGAA 3 14 0 AACACCGTAA 0.907499 -86 TCAAGTAGTAAACATTGTTAGCCAGAAAGG 3 58 1 AACATTGTTA 0.943899 -42 CTTTTGCCTTAACTCTGTTAAATTTATAAA 6 11 0 AACTCTGTTA 0.964069 -50 AGGTTAATTAACACTGTTAAGTTAATAAA 6 42 0 AACACTGTTA 0.990889 -19 ********** Masking position 8 Map Score: 8.08833 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 3 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 4 ACCAAAAACTTTTTAAATTTAGGCTATCCTA 1 110 1 TTTTAATTTA 0.523915 -30 TTCATTACTTTTTAAATTTCTACCGCTTTTA 4 34 0 TTTAAATTCT 0.678073 -208 ATGGAGAGTGTTTAAAATTTTCCGTAAACGA 5 123 0 TTTAAATTTT 0.946506 -35 CCCCATTATATTTAAAGTTTTCCTCTATACA 7 94 1 TTTAAATTTT 0.946506 -207 AGACAGAGAATTTGAAGTTTACAGAAAAGCC 7 262 1 TTTGAATTTA 0.542953 -39 TTTTGAATTATTTAAAATTTTCTCAAGTTTT 8 26 1 TTTAAATTTT 0.946506 -275 AAATTTTTTATCTTAATTATTAAAAACTTGA 8 48 0 TCTTAATATT 0.532644 -253 AAAAATAAAAATTAAATTTTTTATCTTAATT 8 61 0 ATTAAATTTT 0.727494 -240 ATTAATAGACTTTAAATTATTAAATTTTCGT 8 222 0 TTTAAATATT 0.884147 -79 TAATGCTTTTTTTAAATTATTATTATGCTAA 8 249 1 TTTAAATATT 0.884147 -52 TTATAAAGTTTTCCAAAGATAA 8 289 0 TATAAATTTT 0.653129 -12 GCGTAAACAATTTAAACTTTAAGGTTTATGA 12 20 0 TTTAAATTTA 0.803639 -35 ACAGCTGCAAATTTAACTTTTCCATCTTTCT 13 152 1 ATTTAATTTT 0.417872 -149 TTAGATATTATCTAAACTTTT 14 1 0 TCTAAATTTT 0.907631 -300 TTAGATAATATCTAAATGTTTAGATGCGGGC 14 17 1 TCTAAAGTTT 0.539112 -284 ATTTGTTGCTTCTGAACTATTCCAGTAAATC 14 251 0 TCTGAATATT 0.551631 -50 CAACAAATGTTTTAAAATATTACTGACAAAT 14 274 1 TTTAAATATT 0.884156 -27 ****** **** Masking position 6 Map Score: 13.7767 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 83 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 166 Fraction of orfs with sites within 600 bp upstream = 0.0266624 Motif number 5 TTCGAAGATTTTAGGGAAAAGGTAGATGTTGA 2 22 1 TTGGGAAAGG 0.988416 -41 GGACTATCAGTTCAGGAAAAGCAGGGCAGATA 4 159 1 TTAGGAAAGC 0.783604 -83 TTTAACAGAGTTAAGGCAAAAGATTTATTAAC 6 19 1 TTAGGCAAAG 0.926011 -42 TTTAAATATAATGGGGGATAAGTATAATCTGG 7 78 0 ATGGGGAAAG 0.84729 -223 GCACTCAGTTTGTGCAGAGGTTATTAATTC 9 52 0 TTGTGCAAGG 0.959006 -20 TAATGGATTGTTTGTGAAGAGGAGTGCAGAAA 13 178 0 TTGTGAAAGG 0.93651 -123 GAAGGGCAAATTCGGGGACAGGAGCTTTATAA 13 207 0 TTGGGGAAGG 0.986061 -94 CCTGTGGAAAATGTGGAAAAGGATACAGAAGG 13 234 0 ATTGGAAAGG 0.754697 -67 TGGCACCAGTTTAAGGCAGAAGGGGCTGATGA 15 115 1 TTAGGCAAAG 0.926011 -124 TCAAAAAGGTTTGGGGCATAGGAAAGTCGGAT 15 196 0 TTGGGCAAGG 0.992665 -43 ** ***** *** Masking position 8 Map Score: 7.5568 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 317 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 AGTACATATTTTGGATTCTGGACTTTCAGT 5 48 0 TTGGATTCTG 0.975125 -110 GGTTTGGATCTTGGATGGAGAGT 5 145 0 TTGGATCTTG 0.913079 -13 TGCTTTTTTATTCGATTCTGAGCCGTCTGC 7 204 0 TTCGATTCTG 0.882888 -97 ACAAATCCTCATGTATCCTGACGGTAAGGT 10 36 0 ATGTATCCTG 0.890598 -142 CACCACCCCTTTGTTTCCTGTGGAAGTTTG 13 27 0 TTGTTTCCTG 0.944627 -274 CCTACCCCCTTTGTTTCCTGTGGAAAATGT 13 252 0 TTGTTTCCTG 0.944627 -49 TTCTACAAGGTTGGATTCTGTTCAATATAT 15 156 1 TTGGATTCTG 0.975125 -83 ********** Masking position 6 Map Score: 4.54358 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 45 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 ATTTAGGCTATCCTAAACATAACG 1 126 1 TCCTAAACAT 0.855813 -14 AAGTCCAGAATCCAAAATATGTACTGGACT 5 53 1 TCCAAAATAT 0.883389 -105 ACTTAGGAGAGCCAAAATATATCGAAAAAT 7 172 0 GCCAAAATAT 0.773378 -129 TGCCATCATCTCCAAAACATAAATACATTT 9 15 1 TCCAAAACAT 0.970692 -57 TCAAATACATACCAATACAAACCAATTTTA 10 71 0 ACCAATACAA 0.820089 -107 GTTTGAAGCTTCCAAAACAATCTCAACGTT 13 100 1 TCCAAAACAA 0.970692 -201 AACTCCCTCAACCAAAACAATAAAAATTAT 15 34 0 ACCAAAACAA 0.962173 -205 TTGAAAATCAAGCAAAACAAAGCTT 15 224 1 AGCAAAACAA 0.808056 -15 ********** Masking position 5 Map Score: 3.48249 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 42 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 CAACATCTACCTTTTCCCTAAAATCTTCGAA 2 22 0 CTTTCCCTAA 0.894109 -41 CAGCATAATACTTTCCGGTAACTGGATTGTA 4 119 0 CTTTCGGTAA 0.9679 -123 ATCTGCCCTGCTTTTCCTGAACTGATAGTCC 4 159 0 CTTTCCTGAA 0.763372 -83 TCGATATGGGATTTACTGTAAT 4 230 1 ATTTCTGTAA 0.946265 -12 AGTGTTTAAAATTTTCCGTAAACGAGTTAAT 5 117 0 ATTTCCGTAA 0.965145 -41 CCGATTACGGCTTTTCTGTAAACTTCAAATT 7 270 0 CTTTCTGTAA 0.965436 -31 ACATAAATACATTTGCGGTAAGAATTAATAA 9 31 1 ATTTCGGTAA 0.950025 -41 TGGGGTTTAGATTTACTGGAATAGTTCAGAA 14 242 1 ATTTCTGGAA 0.908859 -59 **** ****** Masking position 10 Map Score: 3.93462 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 97 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 9 AAAATCGGTTTTGAAAATGCAATCAAAAATG 1 73 0 TTGAAATGCA 0.983917 -67 TAAAGTAAAACTGAAAGTCCAGAATCCAAAA 5 39 1 CTGAAATCCA 0.949884 -119 TAAACCGATATTGAAATTGCAAACATTTGAT 8 129 0 TTGAAATGCA 0.982985 -172 ACATTCATTTTTGAAACTGCAGAATTGCATG 13 58 0 TTGAAATGCA 0.983917 -243 CCAAACCTTTTTGAAAATCAAGCAAAACAAA 15 214 1 TTGAAATCAA 0.866694 -25 ****** **** Masking position 6 Map Score: 1.63681 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 25 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 10 ACACCGTAAAAAAAACGAAAAA 3 1 0 AAAACGAAAA 0.961957 -99 ACCTTAGATTAAAAGCGGTAGAAATTTAAAAA 4 25 1 AAAACGGAGA 0.831413 -217 AAAGTAATGAAAAAACAAAAGTGGTGGTTAAA 4 54 1 AAAACAAAGT 0.610589 -188 AGAGAAAGAGAAAAAAGAGAATATACAATCCA 4 96 1 AAAAAGAAAT 0.900802 -146 AAACCATCAAAAAAGAGAGAAAAGAAATCGAT 4 203 1 AAAAAGAAAA 0.915189 -39 GCTGGTAAAGAAAATCGATAAAGTAAAACTGA 5 21 1 AAAACGAAAA 0.961957 -137 TCGATAAAGTAAAACTGAAAGTCCAGAATCCA 5 35 1 AAAATGAAGT 0.720765 -123 AGAATCGAATAAAAAAGCAAAAGGTTAATATA 7 215 1 AAAAAGCAAA 0.692349 -86 TAAATAATTCAAAAGAGAGAGATTTATTG 8 8 0 AAAAAGAAGA 0.909843 -293 ATGAGCTATAAAAAACGAAAATTTAATAATTT 8 208 1 AAAACGAAAT 0.955114 -93 TCAACGTTCGAAAATCGAAAATTGGTTCTTAC 13 122 1 AAAACGAAAT 0.955114 -179 **** *** *** Masking position 4 Map Score: 7.6812 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 87 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 11 TTTCCACCTCCTCTTGCCAGAACCTTT 3 83 0 CTCCTCTTGC 0.957091 -17 AGTTAATTATCTCCTCCTGCGTCTATTCCA 5 94 0 CTCCTCCTGC 0.972279 -64 AATGCTCCTACAGAGAGGACA 7 2 1 ATGCTCCTAC 0.866686 -299 AACAACACAAATCCTCATGTATCCTGACGG 10 42 0 ATCCTCATGT 0.812466 -136 ATCCATTATAAAGCTCCTGTCCCCGAATTT 13 202 1 AAGCTCCTGT 0.853242 -99 AGCATCAAATATGCTCATGCACCTGCTAAC 14 122 1 ATGCTCATGC 0.96274 -179 GAGGTGCTCAAAGCTCTTGCATCAGGTCCC 14 168 1 AAGCTCTTGC 0.93129 -133 TCAAACAGTTCTGCTCTTGGGACCTGATGC 14 186 0 CTGCTCTTGG 0.892713 -115 ********** Masking position 5 Map Score: 2.92181 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 253 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 AAAAGAAATCGATATGGGATTTACTGTAAT 4 222 1 GATGGTTTGT 0.991283 -20 ACATATTTTGGATTCTGGACTTTCAGTTTTACTTTAT 5 38 0 GATGGCTAGT 0.917067 -120 GGTTTGGATCTTGGATGGAGAGTGTTTAAAATT 5 135 0 GATGGTGAGT 0.927591 -23 GTTATTATAAGATTTTGGCTTATGTATAGAGGAAAAC 7 110 0 GATGGTTTAT 0.936513 -191 TTATTCCTCCGATTACGGCTTTTCTGTAAACTTCAAA 7 272 0 GATGGTTTGT 0.991283 -29 ACAGGAGCTTTATAATGGATTGTTTGTGAAGAGGAGT 13 185 0 TATGGTTTGT 0.927005 -116 TAAATGTTTAGATGCGGGCTAAACTGTTTAGACGTTA 14 29 1 GATGGTATGT 0.959366 -272 AACTCTGCGAGATTGGGGTTTAGATTTACTGGAATAG 14 229 1 GATGGTTTTT 0.936513 -72 *** ** ** *** Masking position 2 Map Score: 3.0656 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 37 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 13 TGAAAATGCAATCAAAAATGCATAATGCTT 1 63 0 ATCAAAAATG 0.938657 -77 TAAAATCGGTTTTGAAAATGCAATCAAAAA 1 75 0 TTTGAAAATG 0.702275 -65 CCCTAAAATCTTCGAATATGAAAAAAA 2 8 0 TTCGAATATG 0.926587 -55 TGTGGAAACCATCAAAAAAGAGAGAAAAGA 4 198 1 ATCAAAAAAG 0.732776 -44 GGATACCCTTCAACTATGAGTTATTAAA 11 14 0 TTCAACTATG 0.781429 -18 ATTCTGCAGTTTCAAAAATGAATGTTGGTG 13 64 1 TTCAAAAATG 0.966855 -237 AATCTCAACGTTCGAAAATCGAAAATTGGT 13 118 1 TTCGAAAATC 0.777582 -183 TGCACATAGCATCAAATATGCTCATGCACC 14 115 1 ATCAAATATG 0.889218 -186 TTGCTTGATTTTCAAAAAGGTTTGGGGCAT 15 209 0 TTCAAAAAGG 0.885686 -30 ********** Masking position 5 Map Score: 1.86063 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 134 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 CCCATCACCACCCCAAACACTG 1 3 1 CATCACCACC 0.973828 -137 GCTCTGCCATCATCTCCAAAACATAAA 9 8 1 CATCATCTCC 0.97791 -64 ATTGTTTACGCATCATCATCTTATC 12 40 1 CATCATCATC 0.894443 -15 AAAGCTCTTGCATCAGGTCCCAAGAGCAGA 14 177 1 CATCAGGTCC 0.951095 -124 CTCCACTGCTCATCAGCCCCTTCTGCCTTA 15 126 0 CATCAGCCCC 0.982922 -113 ********** Masking position 5 Map Score: 0.166429 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 131 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 ********** No masking Map Score: -2.56263e-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