AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_aful_reg_100.orf -o00330_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 AF0645 232 translation initiation factor eIF-5A (eif5A) #2 AF0883 71 argininosuccinate lyase (argH) #3 AF0894 300 arginyl-tRNA synthetase (argS) #4 AF1215 101 cell division protein, putative #5 AF1252 194 oxaloacetate decarboxylase, subunit alpha (oadA) #6 AF1255 27 ornithine carbamoyltransferase (argF) #7 AF1259 36 inosine monophosphate dehydrogenase, putative #8 AF1260 207 phosphoribosylformylglycinamidine synthase I (purQ) #9 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #10 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #11 AF1420 216 membrane protein #12 AF1609 59 prolyl-tRNA synthetase (proS) #13 AF1665 147 ornithine cyclodeaminase (arcB) #14 AF2086 41 protease inhibitor, putative #15 AF2089 111 conserved hypothetical protein #16 AF2252 78 argininosuccinate synthetase (argG) #17 AF2334 33 spermidine synthase (speE) Motif number 1 ATCCTGCCAGAACGACTTCTGGAATC 1 3 1 CCGCCACGAC 0.948766 -230 TGCTTTACCTCTGGCCTCACGGGCCAAATCAGGG 1 53 0 CTGCCCGGGC 0.991041 -180 CGAGGGGAGGCCTGTCAAGCGGGCGGCAGCGGTT 3 27 1 CCGTCCGGGC 0.987106 -274 GCCATAACCGCCGGCCCTCCGGGACGAGGACTCT 3 72 0 CCGCCCGGGA 0.998297 -229 GACAGCCCCTCCGGGCAGCCCGGCCATAACCGCC 3 94 0 CCGGCCCGGC 0.992509 -207 CGGGCCTGGGCCGTTCCCCCCGGCTAATATGGCG 3 128 0 CCTTCCCGGC 0.962964 -173 GGGTTAGCCTGCTCCCTTCCGGGCCTGGGCCGTT 3 147 0 GCCCCCGGGC 0.969476 -154 CCCGGAAGCGCCGGTCGTCCGGGGTTAGCCTGCT 3 168 0 CCGTCCGGGG 0.992772 -133 GCACCTCCTCCCCGCACCCCCGGAAGCGCCGGTC 3 186 0 CCGCACCGGA 0.964085 -115 CTCGGGTCGACCTGCCTTACGGGCGGCTTGAAGC 3 225 0 CCGCCCGGGC 0.999428 -76 AGGAATCAGACCAGCCCCACCAGCTAAAAGAATT 8 87 1 CCGCCCCAGC 0.993741 -121 GAACATCAACGCTGCCGACACGGAAAAAGCTTAA 8 160 1 GCGCCACGGA 0.902241 -48 AACAATTTTGCCTGCCCTTCGAGAGCATCTATTG 13 36 1 CCGCCCGAGA 0.985517 -112 ACAATCCCGTCATGCGGAGAGGTTTAAAT 16 60 0 CCGTCCGGAG 0.912982 -19 ** *** ***** Masking position 6 Map Score: 30.2493 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 212 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 TCATCTCCAAAACATAAATACATTTGCGGTAAGAA 2 20 1 AATAATATTT 0.908307 -52 CTCAACGCTAAGATTTAATACGCTTTTTATTTAAA 4 77 0 AGTAATACTT 0.85711 -25 TACTGCCATCAACCTAAATAAACTTTCCTGAAGAA 5 29 1 AATAATACTT 0.833122 -166 AAGCAATATTAAAAACAAAAAATTTTTGTATTTCC 5 89 1 AAAAAAATTT 0.843967 -106 AGACATGGCAAAAGTAAAAATTGTTGACTTAACTC 5 135 1 AATAAAAGTT 0.795729 -60 AAATGACGGCAAGCTAAAAACTTTTG 7 2 0 AATAAAATTT 0.963913 -35 TAACGGCATCAATTTGAAAAGAATTCTTTTAGCTG 8 107 0 AATAAAAATT 0.724456 -101 GACACGGAAAAAGCTTAAAAGATTGCGGTTGATTG 8 176 1 AATAAAATTG 0.739085 -32 AAATTCAGGTAGGCATAAAAGTTTT 9 1 0 AGAAAAATTT 0.864959 -49 AAATAACAAGAGGCTAATAAGGTTTTTCATGAGTT 11 184 0 AGTATAATTT 0.808132 -33 CAATCCATTTTGTATAAAAAACTTTCGTGTCAGCC 12 21 1 TGTAAAATTT 0.864961 -39 GTAGATAAGAAAGATAAAACAATTTTGCCTGCCCT 13 19 1 AATAAACTTT 0.738952 -129 CTTGAGATGCTGTAAGAAAAATTTTTCTATTCAAT 13 78 0 TGAAAAATTT 0.5652 -70 ACTTGACATTAACTTTAATACTTTTCAAGAAGACA 13 116 1 AATAATATTT 0.905057 -32 CTAAACTTTATGATTAAAAAGCTTTGGTTTT 14 7 0 TGTAAAATTT 0.864961 -35 GCTTTAATATAGCGTAATTACTTTTAAGGGAGTTG 15 12 0 AGTATTATTT 0.609814 -100 TTCGATTTCAAGTTTAAAAACGCTTTTCAAAAGGT 15 79 0 AGTAAAACTT 0.941897 -33 AGATTAAACAAAAGTTAAAAAACTTCCTGGGTTTT 16 19 0 AATAAAACTT 0.91311 -60 ACTTTTGTTTAATCTCAAAAGATTTAAACCTCTCC 16 39 1 AATAAAATTT 0.963916 -40 ** * **** *** Masking position 14 Map Score: 16.4778 Number of sites scoring better than the average of aligned sites = 343 Number in coding regions = 182 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 3 TTCAGGAGTAATTATAGCCTTTACCGGAAT 1 89 0 ATTATAGCCT 0.6436 -144 CTCAGTCGCATTTTTAACTCTTCTTCAGAA 1 179 1 TTTTTAACTC 0.632643 -54 GCGGTAAGAATTAATAACCTCTGCACAAAC 2 45 1 TTAATAACCT 0.589765 -27 GCGTTGCTGTTTTTAAACTTGCCTTTATCG 4 24 1 TTTTAAACTT 0.932726 -78 TACGCTTTTTATTTAAACCTTTTTCCCAAC 4 64 0 ATTTAAACCT 0.858725 -38 TAAGTCAACAATTTTTACTTTTGCCATGTC 5 136 0 ATTTTTACTT 0.615957 -59 TAACCGGAAATTTTTAACCGGT 6 16 1 TTTTTAACCG 0.670478 -12 CAAAAGTTTTTAGCTTGCCGTCATTT 7 7 1 TTTTTAGCTT 0.936027 -30 AGGTTTTTCTTTTTTTACTTTTCCCTAGAC 8 40 1 TTTTTTACTT 0.812111 -168 AACCGCAATCTTTTAAGCTTTTTCCGTGTC 8 176 0 TTTTAAGCTT 0.929639 -32 AAAACTTTTATGCCTACCTGAATTT 9 6 1 TTTTATGCCT 0.814628 -44 ATGAAAAACCTTATTAGCCTCTTGTTATTT 11 189 1 TTATTAGCCT 0.829543 -28 TGACATTAACTTTAATACTTTTCAAGAAGA 13 119 1 TTTAATACTT 0.523531 -29 ATTACGCTATATTAAAGCTTTTAGCTAATG 15 29 1 ATTAAAGCTT 0.579866 -83 TGAAAAGCGTTTTTAAACTTGAAATCGAAA 15 85 1 TTTTAAACTT 0.932726 -27 CCCAGGAAGTTTTTTAACTTTTGTTTAATC 16 23 1 TTTTTAACTT 0.938852 -56 ATCTCAAAAGATTTAAACCTCTCCGCATGA 16 50 1 ATTTAAACCT 0.858725 -29 ATTGACGGGATTATAAACCT 17 1 0 TTATAAACCT 0.821792 -33 CGTCAATCCTTTATTAGCTT 17 24 1 TTATTAGCTT 0.80465 -10 ********** Masking position 2 Map Score: 17.2563 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 375 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 4 CGGGCCAAATCAGGGCAGCTGGTAATTCTCG 1 37 0 CAGGCAGCTG 0.871091 -196 AGAAGAAAAAGCATGAAGCTCGCAAAAATCA 1 150 0 GCTGAAGCTC 0.863102 -83 TTTTGGAGATGATGGCAGAGC 2 1 0 GAGGCAGAGC 0.885497 -71 CTGTCAAGCGGGCGGCAGCGGTTCCAGGCAC 3 38 1 GGGGCAGCGG 0.923241 -263 GGCAGCGGTTCCAGGCACCGCAGAGTCCTCG 3 51 1 CCGGCACCGC 0.991255 -250 GACAGCCCCTCCGGGCAGCCCGGCCATAACC 3 97 0 CCGGCAGCCC 0.992257 -204 GGCTAATATGGCGGACAGCCCCTCCGGGCAG 3 110 0 GCGACAGCCC 0.911666 -191 TCCCCGCACCCCCGGAAGCGCCGGTCGTCCG 3 181 0 CCGGAAGCGC 0.985 -120 GCTTGAAGCCCCAGGCACCTCCTCCCCGCAC 3 203 0 CCGGCACCTC 0.98608 -98 TTTTAATATTGCTTGCACCTCAAAAGATCAA 5 72 0 GCTGCACCTC 0.915869 -123 AACTTTCAAAGCTGGCAGATCTTTAATT 8 8 0 GCGGCAGATC 0.972048 -200 CTTTTTCCGTGTCGGCAGCGTTGATGTTCTG 8 158 0 GTGGCAGCGT 0.839909 -50 AATAGACTATCCGGGAAGCTTTGAAGCTGAG 11 59 0 CCGGAAGCTT 0.850754 -158 AAGTTATTCTGCTGGCAACGCTTCAAGACTT 11 120 1 GCGGCAACGC 0.97419 -97 ** ******** Masking position 7 Map Score: 17.4552 Number of sites scoring better than the average of aligned sites = 600 Number in coding regions = 563 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 5 AAATGCGACTGAGAAGAAAAAGCATGAAGCT 1 161 0 GAGAAGAAAA 0.819794 -72 CCATCATCTCCAAAACATAAATACATTTGCG 2 17 1 CAAAACTAAA 0.947795 -55 AACTTTCCTGAAGAACGTAAATCTTGATCTT 5 49 1 AAGAACTAAA 0.808215 -146 GCTTGCACCTCAAAAGATCAAGATTTACGTT 5 62 0 CAAAAGTCAA 0.862865 -133 AAGCAATATTAAAAACAAAAAATTTTTGTAT 5 89 1 AAAAACAAAA 0.836671 -106 TGAGACATGGCAAAAGTAAAAATTGTTGACT 5 133 1 CAAAAGAAAA 0.947795 -62 TACAGAAGAAAAATGACGGCAAG 7 24 0 CAGAAGAAAA 0.937247 -13 GTAAAAAAAGAAAAACCTAAACTTTCAAAGC 8 27 0 AAAAACTAAA 0.836671 -181 CCTGTCTAGGGAAAAGTAAAAAAAGAAAAAC 8 42 0 GAAAAGAAAA 0.846857 -166 CTAAAGAGTGCAGAACATCAACGCTGCCGAC 8 148 1 CAGAACTCAA 0.838089 -60 AATAACTTGACAAAACGAATAGCCCTGATGG 11 97 0 CAAAACAATA 0.677715 -120 TGAGATTAAACAAAAGTTAAAAAACTTCCTG 16 25 0 CAAAAGTAAA 0.947795 -54 ****** **** Masking position 5 Map Score: 9.90173 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 66 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 CCCTCGGCTTCGGCCCCCGCGT 3 2 0 CGCCCCCGCG 0.870803 -299 GCTTGACAGGCCTCCCCTCGGCTTCGGCCCC 3 16 0 CCCCCCTCGG 0.985316 -285 ACCGCAGAGTCCTCGTCCCGGAGGGCCGGCG 3 67 1 CCCGTCCCGG 0.991768 -234 ATGGCGGACAGCCCCTCCGGGCAGCCCGGCC 3 103 0 GCCCTCCGGG 0.988803 -198 GGCCTGGGCCGTTCCCCCCGGCTAATATGGC 3 129 0 GTCCCCCCGG 0.97458 -172 GGGGGAACGGCCCAGGCCCGGAAGGGAGCAG 3 142 1 CCAGGCCCGG 0.701321 -159 AAGGGAGCAGGCTAACCCCGGACGACCGGCG 3 163 1 GCAACCCCGG 0.912727 -138 CGGACGACCGGCGCTTCCGGGGGTGCGGGGA 3 181 1 GCCTTCCGGG 0.931795 -120 GCCCCAGGCACCTCCTCCCCGCACCCCCGGA 3 196 0 CCCCTCCCCG 0.981558 -105 GAAAAGGTGGGCACGCCTCGGGTCGACCTGC 3 244 0 GCCGCCTCGG 0.976393 -57 ** ******** Masking position 7 Map Score: 9.78774 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 235 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 CTGCCAGAACGACTTCTGGAATCCGAGAAT 1 14 1 GACTTCTGGA 0.815644 -219 GCATTTTTAACTCTTCTTCAGAAAAATTTA 1 186 1 CTCTTCTTCA 0.948339 -47 GACCCTTTTCTTCATCTCCAATCC 9 36 0 CTTTTCTTCA 0.938276 -14 AGCCCTTCCTCTTTTTTTGATTC 10 12 1 CTTTTTTTGA 0.721435 -13 TCGTGGATTCGTTTTCTGCAATATCTCAAT 11 150 1 GTTTTCTGCA 0.930727 -67 TTAATGTCAAGTTTTCTTGAGATGCTGTAA 13 98 0 GTTTTCTTGA 0.96327 -50 GATGTCCTGTCTTCTTGAAAAGTATTAA 13 130 0 GTCTTCTTGA 0.969391 -18 ********** Masking position 10 Map Score: 2.62299 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 184 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 ACCAGCTGCCCTGATTTGGCCCGTGAGGCC 1 45 1 CTGATTTGGC 0.857461 -188 AGCAGTATTCCGGTAAAGGCTATAATTACT 1 83 1 CGGTAAAGGC 0.948983 -150 GGAGGGCCGGCGGTTATGGCCGGGCTGCCC 3 86 1 CGGTTATGGC 0.963326 -215 TTCCCCCCGGCTAATATGGCGGACAGCCCC 3 119 0 CTAATATGGC 0.899067 -182 TTCAATTTAACTGAAAAGGTGGGCACGCCT 3 257 0 CTGAAAAGGT 0.863163 -44 CGGTCAGAATTGGCTGGAGGATTT 3 287 0 CAGAATTGGC 0.687718 -14 TTTGCAATCTCGATAAAGGCAAGTTTAAAA 4 34 0 CGATAAAGGC 0.872353 -68 GCTGCCGACACGGAAAAAGCTTAAAAGATT 8 170 1 CGGAAAAAGC 0.635258 -38 TAACAAGAGGCTAATAAGGTTTTTCATGAG 11 186 0 CTAATAAGGT 0.733618 -31 CAGTTATGGTAGATAAGAAA 13 1 1 CAGTTATGGT 0.765309 -147 TGCCTTATAACTATTATGGTCATTAGCTAA 15 49 0 CTATTATGGT 0.733618 -63 ********** Masking position 1 Map Score: 3.64947 Number of sites scoring better than the average of aligned sites = 975 Number in coding regions = 926 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 9 TAAATTAACGCAAAATTAGGCAGCAAGGT 1 214 1 CAAAATTAGG 0.805824 -19 AACCTCTGCACAAACTGAGTGC 2 60 1 CAAACTGAGT 0.769549 -12 CGGTCAAGCTGAGGCGTTGCTGTT 4 5 1 CAAGCTGAGG 0.977705 -97 AGTATCAAATCAAGGTGATGGT 5 3 0 CAAGGTGATG 0.842803 -192 GCCAGCTTTGAAAGTTTAGGTTTTTCTTTT 8 23 1 AAAGTTTAGG 0.7759 -185 GAATTCTTTTCAAATTGATGCCGTTACTAG 8 116 1 CAAATTGATG 0.902384 -92 ATCTCCAATCCAAATTCAGGTAGGCATAAA 9 17 0 CAAATTCAGG 0.936478 -33 ATCTCAATATCAAACTCATGAAAAACCTTA 11 172 1 CAAACTCATG 0.853638 -45 TTTTAATCATAAAGTTTAGGAGGAGAAGG 14 23 1 AAAGTTTAGG 0.7759 -19 ********** Masking position 6 Map Score: 1.29906 Number of sites scoring better than the average of aligned sites = 336 Number in coding regions = 312 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 GAGTAATTATAGCCTTTACCGGAATACTGC 1 84 0 AGCCTTTACC 0.930576 -149 GCGAGCTTCATGCTTTTTCTTCTCAGTCGC 1 158 1 TGCTTTTTCT 0.658438 -75 ACCTTGCTGCCTAATTTTGC 1 223 0 ACCTTGCTGC 0.7679 -10 GTCCGGGGTTAGCCTGCTCCCTTCCGGGCC 3 156 0 AGCCTGCTCC 0.945609 -145 TTTTATTTAAACCTTTTTCCCAACTTTGCA 4 58 0 ACCTTTTTCC 0.941056 -44 TTTTTAATATTGCTTGCACCTCAAAAGATC 5 74 0 TGCTTGCACC 0.777475 -121 CAATCTTTTAAGCTTTTTCCGTGTCGGCAG 8 171 0 AGCTTTTTCC 0.96873 -37 GACCCTTTTCTTCATCTCCAA 9 39 0 ACCCTTTTCT 0.721689 -11 GCTATATTAAAGCTTTTAGCTAATGACCAT 15 34 1 AGCTTTTAGC 0.831928 -78 ********** Masking position 5 Map Score: 1.61655 Number of sites scoring better than the average of aligned sites = 893 Number in coding regions = 838 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 ACTCTGCGGTGCCTGGAACCGCTGCCGCCC 3 47 0 GCCTGGAACC 0.916117 -254 CCTTACGGGCGGCTTGAAGCCCCAGGCACC 3 215 0 GGCTTGAAGC 0.984629 -86 GGTCAGAATTGGCTGGAGGATTTTTCAATT 3 280 0 GGCTGGAGGA 0.911926 -21 TTTCCCATCAGGCTTGAGACATGGCAAAAG 5 119 1 GGCTTGAGAC 0.928172 -76 TATCCGGGAAGCTTTGAAGCTGAGTGACAG 11 53 0 GCTTTGAAGC 0.892693 -164 AATCCACGAAGTCTTGAAGCGTTGCCAGCA 11 129 0 GTCTTGAAGC 0.957756 -88 ********** Masking position 4 Map Score: 0.679232 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 136 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 CTTCTTCAGAAAAATTTAAATTAACGCAAA 1 198 1 AAAATTTAAA 0.676943 -35 CCTTTTCAGTTAAATTGAAAAATCCTCCAG 3 268 1 TAAATTGAAA 0.689762 -33 TGCTGTTTTTAAACTTGCCTTTATCGAGAT 4 28 1 AAACTTGCCT 0.901663 -74 CAACCTAAATAAACTTTCCTGAAGAACGTA 5 38 1 AAACTTTCCT 0.796456 -157 AGAAAAACCTAAACTTTCAAAGCTGGCAGA 8 20 0 AAACTTTCAA 0.840958 -188 GCCAGCAGAATAACTTGACAAAACGAATAG 11 106 0 TAACTTGACA 0.895145 -111 TATTGAAGGAAAAATTGAATAGAAAAATTT 13 65 1 AAAATTGAAT 0.770317 -83 CATCTCAAGAAAACTTGACATTAACTTTAA 13 104 1 AAACTTGACA 0.949631 -44 AACTTGACATTAACTTTAATACTTTTCAAG 13 115 1 TAACTTTAAT 0.696684 -33 AAGCGTTTTTAAACTTGAAATCGAAATCCG 15 89 1 AAACTTGAAA 0.945659 -23 ********** Masking position 5 Map Score: 4.25308 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 105 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 13 ********** No masking Map Score: 1.20325e-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: 1.20325e-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: 1.20325e-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