AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_mjan_pyro_300.orf -o057_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ00806 160 M_jannaschii_chromosome #2 RMJ03296 145 M_jannaschii_chromosome #3 RMJ10951 18 M_jannaschii_chromosome #4 RMJ07886 69 M_jannaschii_chromosome #5 RMJ00483 88 M_jannaschii_chromosome #6 RMJ07769 77 M_jannaschii_chromosome #7 RMJ04015 121 M_jannaschii_chromosome #8 RMJ05308 104 M_jannaschii_chromosome #9 RMJ03826 80 M_jannaschii_chromosome Motif number 1 CTCTAATGAGAAAAATTAACATTTATAAATTA 1 18 0 AAAATTAAAT 0.9788 -143 CATTAGAGACAAGAATTAAGAATCGGGTATAT 1 42 1 AAAATTAAAA 0.940866 -119 ATCGGGTATATAGAATTATCATAATTTCATTT 1 63 1 TAAATTATAT 0.959222 -98 ATCAACAGAGTATAATTTAAATGTGATATATT 1 123 0 TAAATTTAAT 0.959222 -38 GTTATAATTTAATAATTTAGAAC 2 2 0 AAAATTTAAA 0.89019 -144 AGTTATAATTTATAGTTATAATTTAATAATTT 2 16 0 TAAGTTATAT 0.895351 -130 ATTAAACTTGAATAGTTATAATTTATAGTTAT 2 29 0 AAAGTTATAT 0.895351 -117 ATTCAAGTTTAATATTTAAAATTTAATTAAGG 2 48 1 AAATTTAAAT 0.959324 -98 AATACCCAATTAAATTTTTGATATGTTTTTGA 2 95 0 TAATTTTTAT 0.859596 -51 TATCACCAACAAGATTTTATATCCGCAATACC 2 121 0 AAATTTTAAT 0.923174 -25 AGAGAAGGTAAAAAATAAATATCAAATAACAC 5 20 0 AAAATAAAAT 0.882687 -69 AATTAGTTTTTATAATTAAAAATTGTAAATTA 5 55 0 TAAATTAAAA 0.940866 -34 AAAATAGTCAAAAAATAAAAAAGGT 6 4 0 AAAATAAAAA 0.721683 -74 CATTTAAAATAAAAATTAAAATAGTCAAAAAA 6 21 0 AAAATTAAAT 0.9788 -57 TGCTTAGTTTTACATTTAAAATAAAAATTAAA 6 33 0 TAATTTAAAT 0.959324 -45 AATGTCACCAAAAATTTTTAATTGCTTAGTTT 6 55 0 AAATTTTTAT 0.859591 -23 ACATAAAATTTAAATATAAGAATTT 7 4 1 TAAATTTAAT 0.959222 -118 ATTTAAATATAAGAATTTTTATTATAATTCCA 7 18 1 AAAATTTTAT 0.922985 -104 CATAATAAAATAAAATGATTATAATATTCCCT 7 71 1 TAAATGATAT 0.69219 -51 TAATGCAATATAAAATTAAGCTAAAAAATAGA 8 15 0 TAAATTAACT 0.793627 -90 TATATTGCATTAAATTTAAAATATTTTGCTTT 8 35 1 TAATTTAAAT 0.959324 -70 TTATTTAATTAAAAATTAAAAAGCAAAATATT 8 54 0 AAAATTAAAA 0.940866 -51 CATAGATTTTTAATTGACAAAGTT 9 3 1 TAATTTTTAT 0.859596 -78 TTTTTTCTTATACAGTAAATAATATAAGCACT 9 46 0 TAAGTAAAAA 0.485365 -35 ** ****** ** Masking position 6 Map Score: 38.7161 Number of sites scoring better than the average of aligned sites = 1365 Number in coding regions = 914 Number in noncoding regions = 451 Number of orfs with sites within 600 bp upstream = 356 Fraction of orfs with sites within 600 bp upstream = 0.0571796 Motif number 2 GGTTGTTATAATTACACAGTTAATACAAATGAA 1 88 0 ATTACACAAA 0.926882 -73 CTGTGTAATTATAACAACCTTAATATATCACAT 1 102 1 ATAACAACAA 0.894743 -59 CAACCTTAATATATCACATTTAAATTATACTCT 1 116 1 ATATCACAAA 0.985974 -45 CAAGTTTAATATTTAAAATTTAATTAAGGTCTT 2 51 1 ATTTAAAAAA 0.803233 -95 AATTAAGGTCTTATCACATCAAATCAAAAACAT 2 72 1 TTATCACAAA 0.960958 -74 TTTTATCACCAACAAGATTTTATAT 2 131 0 TTATCACCAA 0.931823 -15 GATATCACAATGAAATAA 3 5 0 ATATCACAAA 0.985975 -14 TAAAAAATAAATATCAAATAACACAAAAGTGTT 5 11 0 ATATCAAACA 0.847195 -78 AAAATTGTAAATTACAAAGAGAAGGTAAAAAAT 5 36 0 ATTACAAAAA 0.887432 -53 CAATTTTTAATTATAAAAACTAATTTAATGTGA 5 62 1 TTATAAAAAA 0.735104 -27 ATTATCACATTAAATTAGTTTTTA 5 75 0 TTATCACAAA 0.96095 -14 TTAGTTTTACATTTAAAATAAAAATTAAAATAG 6 29 0 ATTTAAAAAA 0.803233 -49 TAATGTCACCAAAAATTTTTAATTG 6 63 0 ATGTCACCAA 0.880271 -15 ATGATAATCCATAATAAAATAAAATGATTATAA 7 62 1 ATAATAAAAA 0.65948 -60 AATATCACCGGTAAATTTAAGTTA 7 108 0 ATATCACCAA 0.975025 -14 AAAGCAAAATATTTTAAATTTAATGCAATATAA 8 34 0 ATTTTAAAAA 0.740184 -71 ******** ** Masking position 6 Map Score: 20.4661 Number of sites scoring better than the average of aligned sites = 556 Number in coding regions = 436 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 3 ACTTACTTAATTTATAAATGTTAATTT 1 6 1 CTTAATTAAA 0.85651 -155 ATAGAATTATCATAATTTCATTTGTATTAACT 1 72 1 CATAATTCTT 0.583017 -89 TTAAGGTTGTTATAATTACACAGTTAATACAA 1 93 0 TATAATTCCA 0.682669 -68 ATCAACAGAGTATAATTTAAATGTGATATATT 1 123 0 TATAATTAAT 0.869315 -38 AATTTATAGTTATAATTTAATAATTTAGAAC 2 10 0 TATAATTATA 0.960587 -136 CTTGAATAGTTATAATTTATAGTTATAATTTA 2 23 0 TATAATTAAG 0.70865 -123 GTGATAAGACCTTAATTAAATTTTAAATATTA 2 57 0 CTTAATTATT 0.750909 -89 ATATCAAAAATTTAATTGGGTATTGCGGATAT 2 103 1 TTTAATTGTA 0.878839 -43 ACCTTCTCTTTGTAATTTACAATTTTTAATTA 5 43 1 TGTAATTAAA 0.788966 -46 AATTAGTTTTTATAATTAAAAATTGTAAATTA 5 55 0 TATAATTAAA 0.947159 -34 TAAAAACTAATTTAATGTGATAAT 5 75 1 TTTAATGGTA 0.586003 -14 TTTTGACTATTTTAATTTTTATTTTAAATGTA 6 23 1 TTTAATTTAT 0.420301 -55 ACCAAAAATTTTTAATTGCTTAGTTTTACATT 6 49 0 TTTAATTCTA 0.932785 -29 TAAAAATTCTTATATTTAAATTTTATGT 7 7 0 TATATTTATT 0.53319 -115 GAATTTTTATTATAATTCCATATGGTATATAA 7 30 1 TATAATTCTA 0.926098 -92 CCATATGGTATATAAATGATAATCCATAATAA 7 47 1 TATAAATAAA 0.548768 -75 TTATAATCATTTTATTTTATTATGGATTATCA 7 63 0 TTTATTTATA 0.773178 -59 ATATTTTAAATTTAATGCAATATAAAATTAAG 8 27 0 TTTAATGATA 0.84058 -78 CTTTTTAATTTTTAATTAAATAAAACTTTTAA 8 63 1 TTTAATTATA 0.964306 -42 CATAGATTTTTAATTGACAAAGTTTATATA 9 9 1 TTTAATTAAA 0.952044 -72 ******* * ** Masking position 3 Map Score: 17.6473 Number of sites scoring better than the average of aligned sites = 1268 Number in coding regions = 923 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 266 Fraction of orfs with sites within 600 bp upstream = 0.0427241 Motif number 4 AAAATCTTGTTGGTGATAAAA 2 135 1 TGGTGATAAA 0.884419 -11 AAAATACATTAGGTCAGAATTTATGTCCAT 4 38 1 AGGTCAGAAT 0.91897 -32 TTATGTCCATAGGTGAGAGAGT 4 58 1 AGGTGAGAGA 0.992603 -12 TACAAAGAGAAGGTAAAAAATAAATATCAA 5 27 0 AGGTAAAAAA 0.855981 -62 AAAACTTTTAAGGGGAGAGAATATGATATG 8 84 1 AGGGGAGAGA 0.980026 -21 GAAAAAATCAAGGTGAGAAA 9 71 1 AGGTGAGAAA 0.99386 -10 ********** Masking position 6 Map Score: 3.93234 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 96 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 5 ACTTACTTAATTTATAAATGTT 1 3 1 TTACTTAATT 0.690438 -158 AGAATTATCATAATTTCATTTGTATTAACT 1 74 1 TAATTTCATT 0.637331 -87 ACTCTGTTGATTAAAAAATTAGTGGTG 1 144 1 TTAAAAAATT 0.696102 -17 GTTCTAAATTATTAAATTATAACTATAA 2 9 1 TTATTAAATT 0.951154 -137 GATAAGACCTTAATTAAATTTTAAATATTA 2 57 0 TAATTAAATT 0.758648 -89 TTATTTCATTGTGATATC 3 1 1 TTATTTCATT 0.91587 -18 TTAAATTAGTTTTTATAATTAAAAATTGTA 5 60 0 TTTTATAATT 0.486817 -29 ATTATCACATTAAATTAGTTT 5 78 0 TTATCACATT 0.743028 -11 ATAATAAAAATTCTTATATTTAAATTTTAT 7 13 0 TTCTTATATT 0.695183 -109 ATAAGAATTTTTATTATAATTCCATATGGT 7 26 1 TTATTATAAT 0.589873 -96 TATAATCATTTTATTTTATTATGGATTATC 7 64 0 TTATTTTATT 0.929568 -58 AATAAAATGATTATAATATTCCCTTCACTT 7 79 1 TTATAATATT 0.919307 -43 ATTTAATGCAATATAAAATTAAGCTAAAAA 8 20 0 ATATAAAATT 0.530345 -85 TGCATTAAATTTAAAATATTTTGCTTTTTA 8 40 1 TTAAAATATT 0.664118 -65 CTTAAAAGTTTTATTTAATTAAAAATTAAA 8 66 0 TTATTTAATT 0.938611 -39 TAGTCAGTGCTTATATTATTTACTGTATAA 9 41 1 TTATATTATT 0.899449 -40 ********** Masking position 8 Map Score: 12.9668 Number of sites scoring better than the average of aligned sites = 1163 Number in coding regions = 838 Number in noncoding regions = 325 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 6 TGAGAAAAATTAACATTTATAAATTAAGTAAGT 1 11 0 TAACATTAAA 0.762393 -150 TTAAGGTTGTTATAATTACACAGTTAATACAAA 1 92 0 TATAATACAG 0.48402 -69 AACTATAAATTATAACTATTCAAGTTTAATATT 2 31 1 TATAATACAA 0.777494 -115 CATCAAATCAAAAACATATCAAAAATTTAATTG 2 88 1 AAAACTAAAA 0.806091 -58 GAAAAACTATTAAAACCTATTTCT 4 2 1 AAAAATAAAA 0.939339 -68 GAAGGTAAAAAATAAATATCAAATAACACAAAA 5 16 0 AATAATAAAA 0.793852 -73 TTTTTATAATTAAAAATTGTAAATTACAAAGAG 5 48 0 TAAAATTAAA 0.961978 -41 TAAAATAGTCAAAAAATAAAAAAGGT 6 4 0 AAAAATAAAA 0.939339 -74 ACATTTAAAATAAAAATTAAAATAGTCAAAAAA 6 21 0 TAAAATTAAT 0.713484 -57 ATTTTAAATGTAAAACTAAGCAATTAAAAATTT 6 43 1 TAAAATACAA 0.933559 -35 ACATAAAATTTAAATATAAGAATTTT 7 4 1 TAAAATTATA 0.684034 -118 AAATTAAGCTAAAAAATAGAAAAT 8 2 0 AAAAATAAAA 0.939339 -103 ATTAAAAAGCAAAATATTTTAAATTTAATGCAA 8 39 0 AAAATTTAAA 0.603815 -66 TTTATTTAATTAAAAATTAAAAAGCAAAATATT 8 54 0 TAAAATTAAA 0.961979 -51 TTTAATTAAATAAAACTTTTAAGGGGAGAGAAT 8 73 1 TAAAATTAAG 0.871668 -32 TGACTATATATAAACTTTGTCAATTAAAAATCT 9 14 0 TAAACTTCAA 0.790447 -67 ***** ** *** Masking position 7 Map Score: 16.9048 Number of sites scoring better than the average of aligned sites = 2043 Number in coding regions = 1434 Number in noncoding regions = 609 Number of orfs with sites within 600 bp upstream = 429 Fraction of orfs with sites within 600 bp upstream = 0.0689046 Motif number 7 ********** No masking Map Score: -1.62471e-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 8 ********** No masking Map Score: -1.62471e-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: -1.62471e-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