AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_aful_reg_300.orf -o00251_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 AF0252 251 CTP synthase (pyrG) #2 AF0260 30 glutamyl-tRNA synthetase (gltX) #3 AF0875 300 snRNP, putative #4 AF0949_AF0950 177 AF0949: glutamine synthetase (glnA), AF0950: carbon monoxide dehydrogenase, iron sulfur subunit (cooF) #5 AF1000 57 NH(3)-dependent NAD+ synthetase (nadE) #6 AF1001 69 A. fulgidus predicted coding region AF1001 #7 AF1002 75 conserved hypothetical protein #8 AF1269 300 A. fulgidus predicted coding region AF1269 #9 AF1270 33 transcriptional regulatory protein, ArsR family #10 AF1319 300 A. fulgidus predicted coding region AF1319 #11 AF1320 24 GMP synthase (guaA-2) #12 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #13 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #14 AF1420 216 membrane protein #15 AF1421 49 conserved hypothetical protein #16 AF1422 35 aspartate racemase #17 AF1423 112 conserved hypothetical protein Motif number 1 TTAAGGCGGAAATCGTTATTTACTCATACCTCC 1 40 1 AACTATTTAC 0.770209 -212 CACAAGTCGAAAACATTTTTAACCCTGAAGCTC 3 179 0 AACTTTTAAC 0.981346 -122 TACCAATACAAACCAATTTTAACAACACAAATC 4 59 0 AACTTTTAAC 0.981346 -119 AGTGGGGATTAAAATCTTTTTACCAGTTAAAAA 5 20 0 AAATTTTTAC 0.956497 -38 GGCTTAGTTGAAAAATTTTTTACAAAGCTTTAT 6 24 1 AAATTTTTAC 0.956497 -46 GGTTTGGCTAAATAAATTTTAATCTTGGACTGG 10 178 1 AAATTTTAAT 0.80915 -123 AAATAAATATAACCATTTTTAACTTAGCTGGAA 10 229 0 AACTTTTAAC 0.981346 -72 TTAATTCACCAACAAGTTTTAACC 10 287 1 AAATTTTAAC 0.979821 -14 GGTAGCACAGCAAACTTTTTAACATTCAAAGCA 15 17 1 CAATTTTAAC 0.910124 -33 CACCCAACCTAAAAAATTTTAACCTCAACTTCA 17 22 0 AAATTTTAAC 0.979819 -91 ** * ******* Masking position 7 Map Score: 13.0661 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 18 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 2 GAATTTCCCATTGAGGATGGGATTCCAGATTTGC 1 209 1 TTGGATGGGT 0.957987 -43 TGGTATGTATTTGAGAATTGGTGAAGATTTTTCA 4 87 1 TTGAATTGGA 0.843566 -91 TCTTATCTTCTTTGCGTTGGGGAATGCTTATTAG 7 31 1 TTCGTTGGGA 0.974784 -45 CCCTTGAGCTTTTTGGATTGGGCAGCATTACAGA 8 130 1 TTGGATTGGA 0.984057 -171 CTTGACGATCCTCTGGTTGGGATAGACAGTAGAA 8 251 1 CTGGTTGGGA 0.971261 -50 TTCTGGATAGTTAACGATGGGGTAAATATTAATA 10 40 1 TTCGATGGGA 0.974784 -261 TCACATCAACTTAGGGTTTGGCTAAATAAATTTT 10 164 1 TTGGTTTGGA 0.984058 -137 GCCTACCTGAATTTGGATTGGAGATGAAGAAAAG 12 22 1 ATGGATTGGA 0.906811 -28 GTTAAAATTTTTTAGGTTGGGTGATGCGCTAAAT 17 32 1 TTGGTTGGGA 0.993134 -81 TGATGTTGTTCTGGTTGGGCCGATAAAAATTT 17 91 0 TTGGTTGGGG 0.971261 -22 ** ******* * Masking position 8 Map Score: 12.0627 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 94 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 3 CAAGTCGGAATTGGAAGTTGAAGTGGTTGAGG 1 124 1 TGAAGTTGAA 0.919652 -128 CCATCCTCAATGGGAAATTCAGCACGACAACT 1 197 0 TGAAATTCAG 0.875044 -55 ATTTGCGCCCTCCGGAGTTGAGACA 1 237 1 TGGAGTTGAG 0.964639 -15 GGCCCACCTGGGAAGTTGAGAAATATAAAG 2 11 0 TGAAGTTGAG 0.991508 -20 CCGAATTTTGCCAGATGCTGAGAGCTTAAAGG 3 214 0 CGATGCTGAG 0.89812 -87 ACTCCAGATGTAAGAAGTTCAGGAATTCTATA 10 72 0 TGAAGTTCAG 0.97265 -229 TCCGGGAAGCTTTGAAGCTGAGTGACAGAGTA 14 49 0 TGAAGCTGAG 0.98278 -168 TTTTCATGAGTTTGATATTGAGATATTGCAGA 14 164 0 TGATATTGAG 0.879006 -53 TGGATTTTGCTTGAAGTTGAGGTTAAAATTT 17 10 1 CGAAGTTGAG 0.982779 -103 * ********* Masking position 9 Map Score: 9.00012 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 260 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 GAAAAGGAAGCTTCTGGAAATCCTCGCGTG 1 85 1 CTTCTGGAAA 0.975929 -167 GAGGAGATTATATCTGGAAAGCTCGTTTGC 1 164 1 TATCTGGAAA 0.919833 -88 AGCACGACAACTGCTGCAAACGAGCTTTCC 1 179 0 CTGCTGCAAA 0.923345 -73 AAGCTCTCAGCATCTGGCAAAATTCGGGTT 3 219 1 CATCTGGCAA 0.953185 -82 GTTAAATTACCTGCAGGCAAGCGTAGGTAA 4 124 0 CTGCAGGCAA 0.87229 -54 TTTCTGGCAATTTGGCTTAG 6 1 1 TTTCTGGCAA 0.949458 -69 ACCTTTATCGTTTCTGGATAGTTAACGATG 10 29 1 TTTCTGGATA 0.780168 -272 ATTTTTAACTTAGCTGGAATTGCAATTTAA 10 218 0 TAGCTGGAAT 0.780402 -83 TCAAGTTATTCTGCTGGCAACGCTTCAAGA 14 118 1 CTGCTGGCAA 0.979231 -99 GTGGATTCGTTTTCTGCAATATCTCAATAT 14 152 1 TTTCTGCAAT 0.659661 -65 ********** Masking position 4 Map Score: 7.66078 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 369 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 AACATTTTTAACCCTGAAGCTCCAGCAATG 3 171 0 ACCCTGAAGC 0.929491 -130 CGACTTGTGTGCCTTTAAGCTCTCAGCATC 3 203 1 GCCTTTAAGC 0.986175 -98 GATGATGGAAGCCCTTGAGCTTTTTGGATT 8 119 1 GCCCTTGAGC 0.957949 -182 GCCCTTAAGTTGGTGAAGGA 11 15 0 GCCCTTAAGT 0.944532 -10 TATCCGGGAAGCTTTGAAGCTGAGTGACAG 14 53 0 GCTTTGAAGC 0.910607 -164 AATCCACGAAGTCTTGAAGCGTTGCCAGCA 14 129 0 GTCTTGAAGC 0.96498 -88 TAAAAGGCCTGTCTTGAAGTATTTAGCGCA 17 56 0 GTCTTGAAGT 0.863125 -57 TTCAAGACAGGCCTTTTAGCGGTAAATTTT 17 68 1 GCCTTTTAGC 0.940348 -45 ********** Masking position 8 Map Score: 7.02781 Number of sites scoring better than the average of aligned sites = 347 Number in coding regions = 327 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 6 AGAGAGGACACGCGAGGATTTCCAGAAGCTT 1 92 0 CGGAGGATTT 0.983115 -160 TGAGGAGAACGAAGAGGAGATTATATCTGGA 1 151 1 GAGAGGAGAT 0.764557 -101 AGGTTCGTTGCAGGAGGAGTTATTTAAAAAT 3 256 0 CAGAGGAGTT 0.983115 -45 CGTCAGGATACATGAGGATTTGTGTTGTTAA 4 43 1 CAGAGGATTT 0.986031 -135 TTTGAGAATTGGTGAAGATTTTTCAGATTTA 4 96 1 GGGAAGATTT 0.870988 -82 TTTTTGCATTCAAGGGGATTTGTTAAATTAC 4 144 0 CAGGGGATTT 0.971834 -34 AGAGGATCGTCAAGGAGATTTATACTTTGCG 8 234 0 CAGGAGATTT 0.918754 -67 AAACAAGTTTTAGGAGGAGTTATCATGGAAA 10 130 0 TAGAGGAGTT 0.883071 -171 ATAGACTATCCGGGAAGCTTTGAAGCTGAGT 14 58 0 CGGAAGCTTT 0.816798 -159 ** ******** Masking position 11 Map Score: 5.30181 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 265 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 TGTCTCAACTCCGGAGGGCGCAAATCTGGAATCC 1 228 0 CTCGGAGGAA 0.99533 -24 ATAAAAGTTTCTTCGGATGGAGGCAATTAAAAACCA 3 57 1 CTTGGAGGAA 0.95968 -244 CCTTAGATAATTCTGGAGGGAAAGAAT 3 284 1 TTCGGAGGAA 0.988126 -17 CGTCAATCTTCTCCGTAAGGTAAAAA 8 1 0 CTCGTAGGAA 0.9799 -300 GTTTATGGTGCTCTGTACGGTCTGAATAAACAAAGA 8 72 1 CTCGTAGGAA 0.979756 -229 CTTGACGATCCTCTGGTTGGGATAGACAGTAGAAAA 8 251 1 CTCGGTGGGA 0.972444 -50 CCAATCCAAATTCAGGTAGGCATAAAAGTTTT 12 7 0 TTCGGTGGAA 0.981102 -43 TGATGTTGTTCTGGTTGGGCCGATAAAAATTTAC 17 89 0 TTCGGTGGAT 0.902973 -24 *** *** ** ** Masking position 2 Map Score: 8.51055 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 93 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 GTATGAGTAAATAACGATTTCCGCCTTAAT 1 39 0 ATAACGATTT 0.805519 -213 ATGATTCCCTATAAAAGTTTCTTCGGATGG 3 47 1 ATAAAAGTTT 0.899058 -254 TTTAACTGGTAAAAAGATTTTAATCCCCAC 5 22 1 AAAAAGATTT 0.73684 -36 AAAGATGTATATAAAGCTTTGTAAAAAATT 6 37 0 ATAAAGCTTT 0.942844 -33 ATTTTTGTTGATAAAGATGTATATAAAGCT 6 49 0 ATAAAGATGT 0.840913 -21 TCCAGAAACGATAAAGGTATCAGCAATTCC 10 17 0 ATAAAGGTAT 0.908818 -284 GGTGAATTAAATAAAGGTAATTTTTTGAGG 10 267 0 ATAAAGGTAA 0.583958 -34 TCAGGTAGGCATAAAAGTTTT 12 2 0 ATAAAAGTTT 0.899058 -48 GCCTAACAAGATAAAGCTTTGG 16 3 0 ATAAAGCTTT 0.942844 -33 GGTTGGGCCGATAAAAATTTACCGCTAAAA 17 81 0 ATAAAAATTT 0.848835 -32 ********** Masking position 4 Map Score: 4.90919 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 80 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 AGGCTTTTTTGCGGTATTTAAAATTAAGGC 1 17 1 GCGGTATTTA 0.927222 -235 AAGGCGGAAATCGTTATTTACTCATACCTC 1 42 1 TCGTTATTTA 0.833843 -210 GCTAGAATTGGTGGTATGTACAGAGCAAAG 3 17 0 GTGGTATGTA 0.943612 -284 CCCGCGCACATTGGTTTTTAATTGCCTCCA 3 74 0 TTGGTTTTTA 0.865871 -227 GTTGCAGGAGGAGTTATTTAAAAATATCGC 3 251 0 GAGTTATTTA 0.577784 -50 GTTGTTAAAATTGGTTTGTATTGGTATGTA 4 66 1 TTGGTTTGTA 0.874905 -112 TTGGTTTGTATTGGTATGTATTTGAGAATT 4 76 1 TTGGTATGTA 0.939194 -102 CCCGAACTGAGTGGTATTTCCATGATAACT 10 114 1 GTGGTATTTC 0.869135 -187 TCAGGGCTATTCGTTTTGTCAAGTTATTCT 14 100 1 TCGTTTTGTC 0.514227 -117 TATTAGCCTCTTGTTATTTATTTGCGT 14 200 1 TTGTTATTTA 0.858839 -17 ********** Masking position 5 Map Score: 4.54617 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 53 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 ATGACAAGCGCGGGTAGTCTAGCGGTAGGA 3 144 0 CGGGTAGTCT 0.981842 -157 CGCTTGCCTGCAGGTAATTTAACAAATCCC 4 131 1 CAGGTAATTT 0.858288 -47 CATAAACTAGCACATAGTCTTTTGTGGTTA 8 49 0 CACATAGTCT 0.807425 -252 AACCCTTTAACAGGAAATTTTCTACTGTCT 8 274 0 CAGGAAATTT 0.830966 -27 GTAAGAAGTTCAGGAATTCTATATTAATAT 10 65 0 CAGGAATTCT 0.867245 -236 CCACTCAGTTCGGGTAATGTGAACACTCCA 10 98 0 CGGGTAATGT 0.867618 -203 ACTGCGGGCTCGGAAAATCTCACGATACTC 14 24 1 CGGAAAATCT 0.900684 -193 CAAAGCTTCCCGGATAGTCTATTTCACACT 14 67 1 CGGATAGTCT 0.946587 -150 AAAACGAATCCACGAAGTCTTGAAGCGTTG 14 135 0 CACGAAGTCT 0.912156 -82 ********** Masking position 6 Map Score: 3.49803 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 178 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 ATTTTAAATACCGCAAAAAAGCCTACCAGC 1 10 0 CCGCAAAAAG 0.89991 -242 CTTCGGATGGAGGCAATTAAAAACCAATGTG 3 67 1 AGGCAATAAA 0.808133 -234 GAGAGCTTAAAGGCACACAAGTCGAAAACAT 3 196 0 AGGCACAAAG 0.94249 -105 ATCCCCTTGAATGCAAAAAAATATATATCGA 4 156 1 ATGCAAAAAA 0.890898 -22 GCATTCCCCAACGCAAAGAAGATAAGAAGGT 7 27 0 ACGCAAAAAG 0.977331 -49 AGTTGATGTGATGAAAACAAGTTTTAGGAGG 10 144 0 ATGAAAAAAG 0.767862 -157 TAATTTTTTGAGGATAAAAAATAAATATAAC 10 249 0 AGGATAAAAA 0.589901 -52 AAATTCAGGTAGGCATAAAAGTTTT 12 5 0 AGGCATAAAG 0.917063 -45 AAATAACAAGAGGCTAATAAGGTTTTTCATG 14 188 0 AGGCTAAAAG 0.951215 -29 ACGCAAATAAATAACAAGAGG 14 206 0 ACGCAAAAAA 0.94845 -11 ******* *** Masking position 9 Map Score: 4.72694 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 319 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 CTCTGCAAGTCGGAATTGGAAGTTGAAGTG 1 119 1 CGGAATTGGA 0.920413 -133 GGAATCATGCTAGAATTGGTGGTATGTACA 3 25 0 TAGAATTGGT 0.965833 -276 TTTGTGTTGTTAAAATTGGTTTGTATTGGT 4 61 1 TAAAATTGGT 0.759487 -117 GTATGTATTTGAGAATTGGTGAAGATTTTT 4 89 1 GAGAATTGGT 0.911814 -89 TAATATGGAATTGCTGATACCTTTA 10 6 1 TGGAATTGCT 0.960958 -295 AATATTAATATAGAATTCCTGAACTTCTTA 10 64 1 TAGAATTCCT 0.817816 -237 TTAACTTAGCTGGAATTGCAATTTAATAAG 10 214 0 TGGAATTGCA 0.88347 -87 ACATTCAAAGCAGAATTGCATT 15 38 1 CAGAATTGCA 0.921953 -12 ********** Masking position 5 Map Score: 3.62997 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 119 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 CGTTATTTACTCATACCTCCAACAGCATTCATGAAA 1 53 1 TATCTCACAC 0.902081 -199 GTCGAAAACATTTTTAACCCTGAAGCTCCAGCAATG 3 171 0 TTTACCTAAC 0.641419 -130 TTGTGTGCCTTTAAGCTCTCAGCATCTGGCAAAATT 3 207 1 TAACCCACAC 0.83732 -94 CTAAAACTTGTTTTCATCACATCAACTTAGGGTTTG 10 148 1 TTTACCACAC 0.986605 -153 AAATTACCTTTATTTAATTCACCAACAAGTTTTAAC 10 274 1 TTTATCACAC 0.954091 -27 TTTTTCCTTCACCAACTTAAGGGC 11 1 1 TTTCTCACAC 0.97071 -24 CTCACGATACTCTGTCACTCAGCTTCAAAGCTTCCC 14 42 1 TTGCCCACTC 0.884106 -175 CCGGATAGTCTATTTCACACTCCATCAGGGCTATTC 14 76 1 TTTCCCTCAC 0.970282 -141 ACCTAAAAAATTTTAACCTCAACTTCAAGCAAAATC 17 13 0 TTTACCACTC 0.953433 -100 TGTCTTGAAGTATTTAGCGCATCACCCAACCTAAAA 17 41 0 TTTACCACAC 0.986591 -72 * ** * * ** ** * Masking position 1 Map Score: 5.94683 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 389 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 TTTACTCATACCTCCAACAGCATTCATGAA 1 58 1 CCTCCAACAG 0.991138 -194 TTTTTAATTGCCTCCATCCGAAGAAACTTT 3 60 0 CCTCCATCCG 0.972347 -241 AGCTCTCTCACCTCTCACAGGGACAGAGAA 8 169 1 CCTCTCACAG 0.957195 -132 AGAAAAGAACCCTTTAACAGGAAATTTTCT 8 281 0 CCTTTAACAG 0.904825 -20 TCTATTTCACACTCCATCAGGGCTATTCGT 14 84 1 ACTCCATCAG 0.937333 -133 ********** Masking position 3 Map Score: 0.390191 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 135 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 TCGAATCCCGGCCCGCGCACATTGGTTTTTA 3 84 0 GCCCGCGCAA 0.987658 -217 CGGGATTCGAACCCGGGCTAACGCCTCGGAA 3 105 1 ACCCGGGCTA 0.972544 -196 CCGCTAGACTACCCGCGCTTGTCATTGCTGG 3 149 1 ACCCGCGCTG 0.987456 -152 AGATTGACGTGCCCGAGCAGATAACCACAAA 8 28 1 GCCCGAGCAA 0.972615 -273 TGTTCACATTACCCGAACTGAGTGGTATTTC 10 103 1 ACCCGAACTA 0.934384 -198 GATTTTCCGAGCCCGCAGTTGAATTTGGACA 14 12 0 GCCCGCAGTG 0.905573 -205 ********* * Masking position 5 Map Score: 0.577713 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 40 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701