AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_mjan_reg_300.orf -o057_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 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 0.978356 -143 CATTAGAGACAAGAATTAAGAATCGGGTATAT 1 42 1 AAAATTAAAA 0.939677 -119 ATCGGGTATATAGAATTATCATAATTTCATTT 1 63 1 TAAATTATAT 0.958385 -98 ATCAACAGAGTATAATTTAAATGTGATATATT 1 123 0 TAAATTTAAT 0.958386 -38 GTTATAATTTAATAATTTAGAAC 2 2 0 AAAATTTAAA 0.888102 -144 AGTTATAATTTATAGTTATAATTTAATAATTT 2 16 0 TAAGTTATAT 0.893349 -130 ATTAAACTTGAATAGTTATAATTTATAGTTAT 2 29 0 AAAGTTATAT 0.893349 -117 ATTCAAGTTTAATATTTAAAATTTAATTAAGG 2 48 1 AAATTTAAAT 0.95849 -98 AATACCCAATTAAATTTTTGATATGTTTTTGA 2 95 0 TAATTTTTAT 0.85702 -51 TATCACCAACAAGATTTTATATCCGCAATACC 2 121 0 AAATTTTAAT 0.921658 -25 AGAGAAGGTAAAAAATAAATATCAAATAACAC 5 20 0 AAAATAAAAT 0.880476 -69 AATTAGTTTTTATAATTAAAAATTGTAAATTA 5 55 0 TAAATTAAAA 0.939677 -34 AAAATAGTCAAAAAATAAAAAAGGT 6 4 0 AAAATAAAAA 0.717409 -74 CATTTAAAATAAAAATTAAAATAGTCAAAAAA 6 21 0 AAAATTAAAT 0.978356 -57 TGCTTAGTTTTACATTTAAAATAAAAATTAAA 6 33 0 TAATTTAAAT 0.95849 -45 AATGTCACCAAAAATTTTTAATTGCTTAGTTT 6 55 0 AAATTTTTAT 0.857015 -23 ACATAAAATTTAAATATAAGAATTT 7 4 1 TAAATTTAAT 0.958386 -118 ATTTAAATATAAGAATTTTTATTATAATTCCA 7 18 1 AAAATTTTAT 0.921466 -104 CATAATAAAATAAAATGATTATAATATTCCCT 7 71 1 TAAATGATAT 0.687659 -51 TAATGCAATATAAAATTAAGCTAAAAAATAGA 8 15 0 TAAATTAACT 0.790136 -90 TATATTGCATTAAATTTAAAATATTTTGCTTT 8 35 1 TAATTTAAAT 0.95849 -70 TTATTTAATTAAAAATTAAAAAGCAAAATATT 8 54 0 AAAATTAAAA 0.939677 -51 CATAGATTTTTAATTGACAAAGTT 9 3 1 TAATTTTTAT 0.85702 -78 TTTTTTCTTATACAGTAAATAATATAAGCACT 9 46 0 TAAGTAAAAA 0.480076 -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 0.924376 -73 CTGTGTAATTATAACAACCTTAATATATCACAT 1 102 1 ATAACAACAA 0.891265 -59 CAACCTTAATATATCACATTTAAATTATACTCT 1 116 1 ATATCACAAA 0.985462 -45 CAAGTTTAATATTTAAAATTTAATTAAGGTCTT 2 51 1 ATTTAAAAAA 0.797415 -95 AATTAAGGTCTTATCACATCAAATCAAAAACAT 2 72 1 TTATCACAAA 0.959569 -74 TTTTATCACCAACAAGATTTTATAT 2 131 0 TTATCACCAA 0.929474 -15 GATATCACAATGAAATAA 3 5 0 ATATCACAAA 0.985462 -14 TAAAAAATAAATATCAAATAACACAAAAGTGTT 5 11 0 ATATCAAACA 0.842422 -78 AAAATTGTAAATTACAAAGAGAAGGTAAAAAAT 5 36 0 ATTACAAAAA 0.883743 -53 CAATTTTTAATTATAAAAACTAATTTAATGTGA 5 62 1 TTATAAAAAA 0.727954 -27 ATTATCACATTAAATTAGTTTTTA 5 75 0 TTATCACAAA 0.959561 -14 TTAGTTTTACATTTAAAATAAAAATTAAAATAG 6 29 0 ATTTAAAAAA 0.797415 -49 TAATGTCACCAAAAATTTTTAATTG 6 63 0 ATGTCACCAA 0.87638 -15 ATGATAATCCATAATAAAATAAAATGATTATAA 7 62 1 ATAATAAAAA 0.651257 -60 AATATCACCGGTAAATTTAAGTTA 7 108 0 ATATCACCAA 0.974123 -14 AAAGCAAAATATTTTAAATTTAATGCAATATAA 8 34 0 ATTTTAAAAA 0.733122 -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 AACATTTATAAATTAAGTAAGT 1 3 0 AATTAAGTAA 0.909833 -158 AGTTAATACAAATGAAATTATGATAATTCT 1 74 0 AATGAAATTA 0.925465 -87 AATATATCACATTTAAATTATACTCTGTTG 1 123 1 ATTTAAATTA 0.920011 -38 TTATAGTTATAATTTAATAATTTAGAAC 2 9 0 AATTTAATAA 0.865141 -137 TAATATTTAAAATTTAATTAAGGTCTTATC 2 57 1 AATTTAATTA 0.919849 -89 CGCAATACCCAATTAAATTTTTGATATGTT 2 100 0 AATTAAATTT 0.882262 -46 GATATCACAATGAAATAA 3 1 0 AATGAAATAA 0.873854 -18 ATTATCACATTAAATTAGTTTTTATAA 5 72 0 CATTAAATTA 0.947605 -17 TTAAAATAAAAATTAAAATAGTCAAAAAAT 6 20 0 AATTAAAATA 0.925029 -58 TTAGTTTTACATTTAAAATAAAAATTAAAA 6 32 0 ATTTAAAATA 0.740889 -46 ACATAAAATTTAAATATAAGAATTTT 7 7 1 AATTTAAATA 0.73418 -115 GATAATCCATAATAAAATAAAATGATTATA 7 64 1 AATAAAATAA 0.717491 -58 TCACCGGTAAATTTAAGTTAAGTGAAGGGA 7 98 0 ATTTAAGTTA 0.807078 -24 TGCAATATAAAATTAAGCTAAAAAATAGAA 8 14 0 AATTAAGCTA 0.725145 -91 TTTTATATTGCATTAAATTTAAAATATTTT 8 32 1 CATTAAATTT 0.731807 -73 TTTAATTTTTAATTAAATAAAACTTTTAAG 8 66 1 AATTAAATAA 0.965208 -39 TTTTCTTATACAGTAAATAATATAAGCACT 9 46 0 CAGTAAATAA 0.545701 -35 ********** Masking position 6 Map Score: 19.2077 Number of sites scoring better than the average of aligned sites = 1426 Number in coding regions = 1003 Number in noncoding regions = 423 Number of orfs with sites within 600 bp upstream = 298 Fraction of orfs with sites within 600 bp upstream = 0.0478638 Motif number 4 AAAATCTTGTTGGTGATAAAA 2 135 1 TGGTGATAAA 0.889271 -11 AAAATACATTAGGTCAGAATTTATGTCCAT 4 38 1 AGGTCAGAAT 0.922498 -32 TTATGTCCATAGGTGAGAGAGT 4 58 1 AGGTGAGAGA 0.99295 -12 TACAAAGAGAAGGTAAAAAATAAATATCAA 5 27 0 AGGTAAAAAA 0.86184 -62 AAAACTTTTAAGGGGAGAGAATATGATATG 8 84 1 AGGGGAGAGA 0.980951 -21 GAAAAAATCAAGGTGAGAAA 9 71 1 AGGTGAGAAA 0.994148 -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 TGAGAAAAATTAACATTTATAAATTAAGTAA 1 13 0 TACATTTATA 0.944594 -148 ATTATCATAATTTCATTTGTATTAACTGTGT 1 77 1 TTCATTTGTA 0.504885 -84 ATCAACAGAGTATAATTTAAATGTGATATAT 1 124 0 TAAATTTAAA 0.784863 -37 AATTTATAGTTATAATTTAATAATTTAGAAC 2 11 0 TAAATTTAAT 0.510571 -135 CTTGAATAGTTATAATTTATAGTTATAATTT 2 24 0 TAAATTTATA 0.706325 -122 TATTCAAGTTTAATATTTAAAATTTAATTAA 2 47 1 TATATTTAAA 0.717819 -99 TATCACCAACAAGATTTTATATCCGCAATAC 2 122 0 AAATTTTATA 0.614904 -24 TACATTAGGTCAGAATTTATGTCCATAGGTG 4 42 1 CAAATTTATG 0.475308 -28 CTTTGTAATTTACAATTTTTAATTATAAAAA 5 50 1 TAAATTTTTA 0.879037 -39 CACATTAAATTAGTTTTTATAATTAAAAATT 5 63 0 TATTTTTATA 0.542788 -26 TTTTGACTATTTTAATTTTTATTTTAAATGT 6 23 1 TTAATTTTTA 0.734965 -55 TTGCTTAGTTTTACATTTAAAATAAAAATTA 6 35 0 TTCATTTAAA 0.756827 -43 TAATGTCACCAAAAATTTTTAATTGCTTAGT 6 57 0 AAAATTTTTA 0.772256 -21 ACATAAAATTTAAATATAAGAATT 7 4 1 TAAATTTAAA 0.857043 -118 ATTTAAATATAAGAATTTTTATTATAATTCC 7 18 1 AAAATTTTTA 0.785703 -104 TATTATGGATTATCATTTATATACCATATGG 7 47 0 TACATTTATA 0.939878 -75 ATTTTTTAGCTTAATTTTATATTGCATTAAA 8 18 1 TTATTTTATA 0.763048 -87 TTATATTGCATTAAATTTAAAATATTTTGCT 8 34 1 TTAATTTAAA 0.837452 -71 TATTTTGCTTTTTAATTTTTAATTAAATAAA 8 56 1 TTAATTTTTA 0.734965 -49 TCTCTCCCCTTAAAAGTTTTATTTAATTAAA 8 73 0 TAAAGTTTTA 0.531791 -32 TTTTAATTGACAAAGTTTATATATAGTCAGT 9 18 1 CAAGTTTATA 0.502562 -63 ** ******** Masking position 7 Map Score: 21.842 Number of sites scoring better than the average of aligned sites = 1512 Number in coding regions = 1006 Number in noncoding regions = 506 Number of orfs with sites within 600 bp upstream = 396 Fraction of orfs with sites within 600 bp upstream = 0.0636042 Motif number 6 ********** 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 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