AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00251_aful_reg_100.orf -o00251_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 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 Motif number 1 AGCTTCCTTTTCATGAATGCTGTTGGAGGT 1 67 0 TCATGAATGC 0.905087 -185 AAAGGAAGCTTCTGGAAATCCTCGCGTGTC 1 87 1 TCTGGAAATC 0.867556 -165 GCGTGTCCTCTCTGCAAGTCGGAATTGGAA 1 110 1 TCTGCAAGTC 0.892876 -142 GGAGATTATATCTGGAAAGCTCGTTTGCAG 1 166 1 TCTGGAAAGC 0.883558 -86 AGGGCGCAAATCTGGAATCCCATCCTCAAT 1 218 0 TCTGGAATCC 0.954162 -34 TCTGTACATACCACCAATTCTAGCATGATT 3 23 1 CCACCAATTC 0.802369 -278 ACACAAATCCTCATGTATCCTGACGGTAAG 4 38 0 TCATGTATCC 0.504287 -140 TGAAAAATCTTCACCAATTCTCAAATACAT 4 91 0 TCACCAATTC 0.905682 -87 TAACAAATCCCCTTGAATGCAAAAAAATAT 4 150 1 CCTTGAATGC 0.780068 -28 GAGCTTGCAATCTGTAATGCTGCCCAATCC 8 144 0 TCTGTAATGC 0.747399 -157 GATAAAGGTATCAGCAATTCCATATTA 10 8 0 TCAGCAATTC 0.949417 -293 TGTAAGAAGTTCAGGAATTCTATATTAATA 10 66 0 TCAGGAATTC 0.97079 -235 CAATCCAAATTCAGGTAGGCATAAAAGTTT 12 12 0 TCAGGTAGGC 0.771329 -38 CTTTTCTTCATCTCCAATCCAAATTCAGGT 12 26 0 TCTCCAATCC 0.857432 -24 GAAAACGAATCCACGAAGTCTTGAAGCGTT 14 136 0 CCACGAAGTC 0.783979 -81 ********** Masking position 7 Map Score: 11.0537 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 657 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 2 AGCTTCAGGGTTAAAAATGTTTTCGACTTGTG 3 180 1 TTAAAATGTT 0.971011 -121 ATTTGTGTTGTTAAAATTGGTTTGTATTGGTA 4 60 1 TTAAAATGTT 0.971011 -118 GGAGTGGGGATTAAAATCTTTTTACCAGTTAA 5 23 0 TTAAAACTTT 0.900757 -35 TTGGCTTAGTTGAAAAATTTTTTACAAAGCTT 6 22 1 TGAAAATTTT 0.900757 -48 ATAACTCCTCCTAAAACTTGTTTTCATCACAT 10 138 1 CTAAAATTTT 0.90076 -163 CAGTCCAAGATTAAAATTTATTTAGCCAAACC 10 178 0 TTAAAATTTT 0.971566 -123 TCCAGCTAAGTTAAAAATGGTTATATTTATTT 10 230 1 TTAAAATGTT 0.971011 -71 GGTTAAAACTTGTTGGTGAATTAA 10 287 0 TTAAAATTTT 0.971569 -14 ****** ** ** Masking position 6 Map Score: 8.16764 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 7 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 3 TGTCTCAACTCCGGAGGGCGCAAATCTG 1 234 0 TTACTCGGGG 0.879452 -18 TTCCCTATAAAAGTTTCTTCGGATGGAGGCAATTAA 3 51 1 AGTCTTGGGG 0.957596 -250 ATTAAAAACCAATGTGCGCGGGCCGGGATTCGAACC 3 82 1 ATTCGCGGGG 0.945197 -219 TTCCCTCCAGAATTATCTAAGGTTCGTTGCAGGAGG 3 270 0 ATACTAGGCG 0.672503 -31 CGGGCACGTCAATCTTCTCCGTAAGGTAAAAA 8 7 0 ATTCTCGTGG 0.982824 -294 CTTTTGTGGTTATCTGCTCGGGCACGTCAATCTTCT 8 25 0 TTTCTCGGCG 0.936757 -276 GTGCTAGTTTATGGTGCTCTGTACGGTCTGAATAAA 8 66 1 AGTCTCGTGG 0.989199 -235 TGAATAAACAAAGAACCTTAGTTAGGATGATGGAAG 8 94 1 AGACTTGTGG 0.833786 -207 GAGCTGCACCATTCTTCTCTGTCCCTGTGAGAGGTG 8 177 0 ATTCTCGTCT 0.851606 -124 AATCTCCTTGACGATCCTCTGGTTGGGATAGACAGT 8 245 1 AGTCTCGGGG 0.993224 -56 CCGTTATAAGTTGCACCGTTGCGCAACCAAACA 9 8 1 AGTCACGTCG 0.893616 -26 GGAAAATCTCACGATACTCTGTCACTCAGCTTCAAA 14 35 1 AGTCTCGTCT 0.901818 -182 * * * *** ** ** Masking position 7 Map Score: 8.30333 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 309 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 4 CACCTGGGAAGTTGAGAAATATAAAG 2 7 0 GTTGAGAAAT 0.82785 -24 AGATAATTCTGGAGGGAAAGAAT 3 288 1 GGAGGGAAAG 0.893112 -13 GTATTTGAGAATTGGTGAAGATTTTTCAGA 4 93 1 ATTGGTGAAG 0.804817 -85 GCAGGCAAGCGTAGGTAAATCTGAAAAATC 4 112 0 GTAGGTAAAT 0.895063 -66 GGAAAGCTGTAGGGGAGTGGGGATTAAA 5 40 0 GTAGGGGAGT 0.803917 -18 AATTTTTGTTGATAAAGATGTATATAA 6 53 0 GTTGATAAAG 0.872048 -17 TCTTCTTTGCGTTGGGGAATGCTTATTAGG 7 36 1 GTTGGGGAAT 0.973632 -40 CGATCCTCTGGTTGGGATAGACAGTAGAAA 8 256 1 GTTGGGATAG 0.824305 -45 GTTAAAACTTGTTGGTGAATTAAATAAAGG 10 280 0 GTTGGTGAAT 0.96493 -21 GCCCTTAAGTTGGTGAAGGAAAAA 11 7 0 GTTGGTGAAG 0.98125 -18 AATTTGGATTGGAGATGAAGAAAAGGGTC 12 31 1 GGAGATGAAG 0.745767 -19 ********** Masking position 4 Map Score: 7.83124 Number of sites scoring better than the average of aligned sites = 866 Number in coding regions = 820 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 GCCTTAATTTTAAATACCGCAAAAAAGCCT 1 17 0 TAAATACCGC 0.944509 -235 GAGGTATGAGTAAATAACGATTTCCGCCTT 1 42 0 TAAATAACGA 0.870206 -210 CTTTGCTCTGTACATACCACCAATTCTAGC 3 17 1 TACATACCAC 0.957186 -284 TGGAGGCAATTAAAAACCAATGTGCGCGGG 3 74 1 TAAAAACCAA 0.896098 -227 GCGATATTTTTAAATAACTCCTCCTGCAAC 3 251 1 TAAATAACTC 0.646423 -50 TACATACCAATACAAACCAATTTTAACAAC 4 66 0 TACAAACCAA 0.903324 -112 AATTCTCAAATACATACCAATACAAACCAA 4 76 0 TACATACCAA 0.953779 -102 AGTTATCATGGAAATACCACTCAGTTCGGG 10 114 0 GAAATACCAC 0.898712 -187 AGAATAACTTGACAAAACGAATAGCCCTGA 14 100 0 GACAAAACGA 0.585791 -117 ACGCAAATAAATAACAAGAGGCTAATA 14 200 0 TAAATAACAA 0.89045 -17 ********** Masking position 6 Map Score: 5.45814 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 6 ATGAAAAGGAAGCTTCTGGAAATCCTCGCG 1 83 1 AGCTTCTGGA 0.760365 -169 AAGAGGAGATTATATCTGGAAAGCTCGTTT 1 162 1 TATATCTGGA 0.936023 -90 CCGGAGGGCGCAAATCTGGAATCCCATCCT 1 222 0 CAAATCTGGA 0.950111 -30 GAACCTTAGATAATTCTGGAGGGAAAGAAT 3 281 1 TAATTCTGGA 0.946357 -20 CAAGCGTAGGTAAATCTGAAAAATCTTCAC 4 107 0 TAAATCTGAA 0.767282 -71 ATACCTTTATCGTTTCTGGATAGTTAACGA 10 27 1 CGTTTCTGGA 0.848374 -274 CTGAACTTCTTACATCTGGAGTGTTCACAT 10 82 1 TACATCTGGA 0.957657 -219 TATGCCTACCTGAATTTGGATTGGAGATGA 12 19 1 TGAATTTGGA 0.895024 -31 AGCCCGCAGTTGAATTTGGACAG 14 4 0 TGAATTTGGA 0.895024 -213 ********** Masking position 5 Map Score: 5.05651 Number of sites scoring better than the average of aligned sites = 206 Number in coding regions = 182 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 AATGGGAAATTCAGCACGACAACTGCTGCAAACGAGC 1 184 0 TCCAAAATCT 0.965928 -68 CAAACCAATTTTAACAACACAAATCCTCATGTATCCT 4 47 0 TTCAAAATCT 0.980417 -131 TGGGGAATGCTTATTAGGAAAAATGCTGAGTATTAAA 7 48 1 TTTAAAATCT 0.848269 -28 AAAGAACCCTTTAACAGGAAATTTTCTACTGTCTATC 8 271 0 TTCAAATTCT 0.968951 -30 CTGAGTGGTATTTCCATGATAACTCCTCCTAAAACTT 10 120 1 TTCAAAATCT 0.980417 -181 CTAAAACTTGTTTTCATCACATCAACTTAGGGTTTGG 10 148 1 TTCAAATACT 0.951108 -153 TTATTTTTTATCCTCAAAAAATTACCTTTATTTAATT 10 256 1 TCCAAATACT 0.916776 -45 TCTTGAAGCGTTGCCAGCAGAATAACTTGACAAAACG 14 111 0 TTCAAAAACT 0.968951 -106 ** ** * ** * ** Masking position 9 Map Score: 4.95441 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 22 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 AACATTTTTAACCCTGAAGCTCCAGCAATG 3 171 0 ACCCTGAAGC 0.965116 -130 CGACTTGTGTGCCTTTAAGCTCTCAGCATC 3 203 1 GCCTTTAAGC 0.979187 -98 GATGATGGAAGCCCTTGAGCTTTTTGGATT 8 119 1 GCCCTTGAGC 0.968762 -182 GCCCTTAAGTTGGTGAAGGA 11 15 0 GCCCTTAAGT 0.941144 -10 TATCCGGGAAGCTTTGAAGCTGAGTGACAG 14 53 0 GCTTTGAAGC 0.907851 -164 AAAACGAATAGCCCTGATGGAGTGTGAAAT 14 87 0 GCCCTGATGG 0.910478 -130 AATCCACGAAGTCTTGAAGCGTTGCCAGCA 14 129 0 GTCTTGAAGC 0.930615 -88 ********** Masking position 5 Map Score: 3.11697 Number of sites scoring better than the average of aligned sites = 413 Number in coding regions = 392 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 TTTTAAATACCGCAAAAAAGCCTACCAGC 1 10 0 CGCAAAAAAG 0.894267 -242 ACAGCATTCATGAAAAGGAAGCTTCTGGAA 1 74 1 TGAAAAGGAA 0.54973 -178 AATTCCGACTTGCAGAGAGGACACGCGAGG 1 106 0 TGCAGAGAGG 0.842563 -146 TTGAGGAGAACGAAGAGGAGATTATATCTG 1 150 1 CGAAGAGGAG 0.815164 -102 CGACAACTGCTGCAAACGAGCTTTCCAGAT 1 175 0 TGCAAACGAG 0.892358 -77 TTAAATTACCTGCAGGCAAGCGTAGGTAAA 4 123 0 TGCAGGCAAG 0.891607 -55 TCCCCTTGAATGCAAAAAAATATATATCGA 4 157 1 TGCAAAAAAA 0.789363 -21 CATTCCCCAACGCAAAGAAGATAAGAAGGT 7 27 0 CGCAAAGAAG 0.915888 -49 GTTGATGTGATGAAAACAAGTTTTAGGAGG 10 144 0 TGAAAACAAG 0.870336 -157 CTTAAGTTGGTGAAGGAAAAA 11 2 0 TGAAGGAAAA 0.484786 -23 GGATTGGAGATGAAGAAAAGGGTC 12 36 1 TGAAGAAAAG 0.916392 -14 ATTGAGATATTGCAGAAAACGAATCCACGA 14 150 0 TGCAGAAAAC 0.77868 -67 ********** Masking position 4 Map Score: 2.2621 Number of sites scoring better than the average of aligned sites = 1373 Number in coding regions = 1289 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 10 GAGAGGACACGCGAGGATTTCCAGAAGCTT 1 92 0 GCGAGGATTT 0.922717 -160 GGAGAACGAAGAGGAGATTATATCTGGAAA 1 154 1 GAGGAGATTA 0.92019 -98 GTCAGGATACATGAGGATTTGTGTTGTTAA 4 44 1 ATGAGGATTT 0.888346 -134 TTGAGAATTGGTGAAGATTTTTCAGATTTA 4 97 1 GTGAAGATTT 0.927706 -81 TTTTGCATTCAAGGGGATTTGTTAAATTAC 4 144 0 AAGGGGATTT 0.942636 -34 CTGTAGGGGAGTGGGGATTAAAATCTTTTT 5 32 0 GTGGGGATTA 0.933532 -26 TTACCTTACGGAGAAGATTGACGTGCCCGA 8 14 1 GAGAAGATTG 0.859347 -287 GAGGATCGTCAAGGAGATTTATACTTTGCG 8 234 0 AAGGAGATTT 0.911971 -67 ********** Masking position 7 Map Score: 3.68579 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 451 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 TGCGGTATTTAAAATTAAGGCGGAAATCGT 1 26 1 AAAATTAAGG 0.91982 -226 TACCAGTTAAAAAATAAAGGGG 5 3 0 AAAATAAAGG 0.974189 -55 TTTGCGCTGCAAAATATAGGCGACGGAGAG 8 210 0 AAAATATAGG 0.937256 -91 GTTGGTGAATTAAATAAAGGTAATTTTTTG 10 270 0 TAAATAAAGG 0.91982 -31 GAATCAAAAAAAGAGGAAGGGCTT 13 9 0 AAAAAAGAGG 0.870621 -16 ********** Masking position 4 Map Score: 0.458129 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 35 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 GCTGGTAGGCTTTTTTGCGGTAT 1 4 1 GGTAGGCTTT 0.969413 -248 CTAACGCCTCGGAAGGGCGTTGTCCTACCG 3 122 1 GGAAGGGCGT 0.973393 -179 GTATCCTGACGGTAAGGTTTAAATACACTT 4 24 0 GGTAAGGTTT 0.921153 -154 GGAAAGCTGTAGGGGAGTGG 5 48 0 GGAAAGCTGT 0.950657 -10 TTAGGATGATGGAAGCCCTTGAGCTTTTTG 8 115 1 GGAAGCCCTT 0.932102 -186 CAAAAAAAGAGGAAGGGCTT 13 1 0 GGAAGGGCTT 0.981938 -24 TAGACTATCCGGGAAGCTTTGAAGCTGAGT 14 58 0 GGGAAGCTTT 0.928046 -159 ********** Masking position 4 Map Score: 3.09915 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 251 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 ********** No masking Map Score: 5.23913e-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: 5.23913e-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: 5.23913e-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