AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i064_Histidine_Biosynthesis_aquae_reg_300.orf -o064_aquae_300.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RAA01515 16 Aquifex_aeolicus RAA01159 17 Aquifex_aeolicus Input sequences: #1 RAA01000 32 Aquifex_aeolicus #2 RAA01002 61 Aquifex_aeolicus #3 RAA01003 294 Aquifex_aeolicus #4 RAA01004 125 Aquifex_aeolicus #5 RAA00890 49 Aquifex_aeolicus #6 RAA01502 110 Aquifex_aeolicus #7 RAA01514 35 Aquifex_aeolicus #8 RAA01558 69 Aquifex_aeolicus #9 RAA00241 67 Aquifex_aeolicus #10 RAA00567 43 Aquifex_aeolicus #11 RAA01625 61 Aquifex_aeolicus Motif number 1 AAAGAAGTTAGCACCGGTGCGTGTATGTG 2 43 0 ATTCACGGTG 0.90411 -19 GTATAAATAGAGGTCTCGGTGGTGGTCCTCCTAT 3 190 0 AGTCGGGGTG 0.989398 -105 TGCCCTCTAACTTTTGAGGAGGTATAAATAGAGG 3 211 0 CTTAGGGGTA 0.972616 -84 AGGGCAATAAACTTATCGTCGGTGTTGAGGGATT 3 239 1 ATTCGTGGTG 0.977714 -56 AAAGGAACTCATATAAAGGAGGTGGGAAT 3 276 1 AATAGGGGTG 0.979133 -19 ACTATATTTTACTACTCGGCGGTGAAAATTTTTA 4 71 0 ATACGGGGTG 0.991074 -55 GGTTTACTTAAATTTCAGGAGGTGGTATT 4 107 1 ATTAGGGGTG 0.99701 -19 GTTAGAATATACTAACCGGAGGTGGAAAG 8 6 0 ATACGGGGTG 0.991074 -64 TTTAAAATTAAGTTTCAGGAGGAAGGAGA 9 6 0 ATTAGGGGAA 0.913009 -62 TATTATTAGTTTTTAAAGCTGGTGAGGTGATAGC 10 20 1 TTTAGCGGTG 0.933584 -24 TTACCGAGAGCTTTGAAGGAGGTAATGGA 11 6 0 CTTAGGGGTA 0.972616 -56 * ** *** **** Masking position 11 Map Score: 16.6217 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 186 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 2 GTTAGGAAGTTAAAATAAACTTG 4 1 0 TAAATAATTG 0.957022 -125 CTTCCTAACCTTTAATTAACTTTATGTATATAT 4 25 1 TTAATAATTT 0.957679 -101 TTTATGTATATATAACGAAATTTTTATAAAAAT 4 45 1 TAAACAATTT 0.917473 -81 CGCCGAGTAGTAAAATATAGTTTGGTTTACTTA 4 84 1 TAAATTATTT 0.935049 -42 TATAGTTTGGTTTACTTAAATTTCAGGAGGTGG 4 99 1 TTACTAATTT 0.781141 -27 CAGAAAATTATAACATAAATTTG 5 37 1 TACATAATTG 0.792627 -13 AGCAGTTTTTTAAAATGAATCTTGTGAGGTCAC 6 15 0 TAAATAACTT 0.917444 -96 TTAATTATCCTTTAATTTATTTTTATTATGTAG 8 43 0 TTAATTATTT 0.822124 -27 AATGTTGTTTTAAAATTAAGTTTCAGGAGGAAG 9 15 0 TAAATAATTT 0.986006 -53 TTAATTAAAATACAATAAAATGTTGTTTTAAAA 9 33 0 TAAATAATGT 0.957023 -35 CTCGTATTATATTATTAGTTTTTAAAGCTGGT 10 10 1 TATATAGTTT 0.720611 -34 TTTTAGCGGTTATAATTAAATGTTTACCGAGAG 11 30 0 TAAATAATGT 0.957023 -32 TTATAACCGCTAAAATAAGTTTTT 11 48 1 TAAATAGTTT 0.956837 -14 ** *** ** *** Masking position 1 Map Score: 12.7602 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 72 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 TTAGGAAGTTAAAATAAACTTG 4 2 0 AAAATAAATT 0.975481 -124 TCGTTATATATACATAAAGTTAATTAAAGGT 4 32 0 TACATAAATT 0.760792 -94 GCCGAGTAGTAAAATATAGTTTGGTTTACTT 4 85 1 AAAATATATT 0.918001 -41 AGAAAATTATAACATAAATTTG 5 38 1 AACATAAATT 0.953211 -12 GCAGTTTTTTAAAATGAATCTTGTGAGGTCA 6 16 0 AAAATGAACT 0.78345 -95 CTACATAATAAAAATAAATTAAAGGATAATT 8 43 1 AAAATAAATA 0.940324 -27 ATGTTGTTTTAAAATTAAGTTTCAGGAGGAA 9 16 0 AAAATTAATT 0.89982 -52 TATTTTAATTAAAATACAATAAAATGTTGTT 9 39 0 AAAATACATA 0.789707 -29 TATTTTAATTAAAATAAATCAAGT 9 54 1 AAAATAAACA 0.860477 -14 GCTCTCGGTAAACATTTAATTATAACCGCTA 11 29 1 AACATTTATT 0.661329 -33 TATAACCGCTAAAATAAGTTTTT 11 49 1 AAAATAAGTT 0.875697 -13 ******** ** Masking position 4 Map Score: 7.37499 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 135 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 4 TTTAAAAAGCCCCAAAGGGGCGGA 1 2 0 CCAAGGGCGG 0.987508 -31 ACTCTAAGGGGACGACTAATTACG 3 2 1 CCAAGGGACG 0.998359 -293 TTACGAAATACTCAAAGGTCACGATGTCTTTGC 3 30 1 CCAAGGCACG 0.991495 -265 CCTGTGGAAGCCTCAAGGAGAGGGGGGTATTAA 3 99 1 CTAAGGGAGG 0.959488 -196 GTTATACACACCCTACGGAGACGTAATAGGAGG 3 165 1 CCACGGGACG 0.998053 -130 ATAGGAGGACCACCACCGAGACCTCTATTTATA 3 190 1 CCACCGGACC 0.96989 -105 TTACAAATCCCTCAACACCGACGATAAGTTTAT 3 245 0 CCACACGACG 0.956281 -50 * * **** **** Masking position 5 Map Score: 6.76148 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 90 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 TGGGAGAAATTCCCTTCGGATGGCT 2 2 1 GAGAAACCCT 0.928112 -60 TAGCACCGGTGCGTGTATGTGCCTGAAGAGCCAT 2 30 0 GTGTATGCCT 0.991684 -32 CACGCACCTCGGATGTATTCCCCTGTGGAAGCCT 3 78 1 GTGTATCCCT 0.993611 -217 GGAGAGGGGGGTATTAATAAGCCTGTCTTCCACT 3 115 1 GTTAATGCCT 0.961516 -180 TCTCCGTAGGGTGTGTATAACCCTCCGTGACAAG 3 152 0 GTGTATCCCT 0.99364 -143 CACCGACGATAAGTTTATTGCCCTCTAACTTTTG 3 229 0 ATTTATCCCT 0.847125 -66 ATGATACGGGGACAGAAGCCGCCTGTGTAAGCAG 6 43 0 GAGAAGGCCT 0.935769 -68 * ***** **** Masking position 7 Map Score: 3.55794 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 68 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 CCTGAAGAGCCATCCGAAGGGAATTTCTCCC 2 12 0 CATCCGAGGG 0.987155 -50 CAGGGGAATACATCCGAGGTGCGTGCAAACT 3 72 0 CATCCGAGTG 0.962911 -223 CTCCTTGAGGCTTCCACAGGGGAATACATCC 3 88 0 CTTCCACGGG 0.993134 -207 ATAAGCCTGTCTTCCACTGTCCTTGTCACGG 3 131 1 CTTCCACGTC 0.97995 -164 TAAAAAACTGCTTACACAGGCGGCTTCTGTC 6 36 1 CTTACACGGC 0.957223 -75 TTTTATAGTAAATCCGCGGGCTAAAACCGCG 6 82 0 AATCCGCGGC 0.972365 -29 ******* *** Masking position 3 Map Score: 3.48584 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 135 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TTTGGGGCTTTTTAAAAACTTTTT 1 19 1 TTTAAAAACT 0.969418 -14 TGAAAATTTTTATAAAAATTTCGTTATATA 4 53 0 TATAAAAATT 0.921792 -73 AAGATTCATTTTAAAAAACTGCTTACACAG 6 25 1 TTAAAAAACT 0.868091 -86 TAAATACTTTTATAGATATTTGCT 7 5 0 TATAGATATT 0.612059 -31 TCCGATAAATATAAATACTTTTATAGATA 7 17 0 TATAAATACT 0.913721 -19 TAAAATGTTGTTTTAAAATTAAGTTTCAGG 9 21 0 TTTTAAAATT 0.761129 -47 CCTCACCAGCTTTAAAAACTAATAATATAA 10 17 0 TTTAAAAACT 0.969418 -27 ********** Masking position 6 Map Score: 3.48051 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 202 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 ********** No masking Map Score: -1.80235e-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 9 ********** No masking Map Score: -1.80235e-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 10 ********** No masking Map Score: -1.80235e-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