AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_mjan_reg_100.orf -o057_mjan_100.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 Motif number 1 TAATTTATAAATGTTAATTTTTCTCATTAGAG 1 18 1 ATTTAATTTT 0.982651 -143 ATATACCCGATTCTTAATTCTTGTCTCTAATG 1 42 0 TTTTAATTTT 0.966593 -119 AAATGAAATTATGATAATTCTATATACCCGAT 1 63 0 ATATAATTTA 0.88495 -98 AATATATCACATTTAAATTATACTCTGTTGAT 1 123 1 ATTAAATTTA 0.975169 -38 GTTCTAAATTATTAAATTATAAC 2 2 1 TTTAAATTTT 0.943828 -144 TAAATTATAACTATAAATTATAACTATTCAAG 2 23 1 CTTAAATTTA 0.841985 -123 CCTTAATTAAATTTTAAATATTAAACTTGAAT 2 48 0 ATTTAAATTT 0.945579 -98 TCAAAAACATATCAAAAATTTAATTGGGTATT 2 95 1 ATAAAAATTA 0.578098 -51 GGTATTGCGGATATAAAATCTTGTTGGTGATA 2 121 1 ATTAAAATTT 0.909828 -25 GTGTTATTTGATATTTATTTTTTACCTTCTCT 5 20 1 ATTTTATTTT 0.90662 -69 TAATTAAAAATTGTAAATTACAAAGAGAAGGT 5 43 0 TTTAAATTCA 0.779224 -46 TAATTTACAATTTTTAATTATAAAAACTAATT 5 55 1 TTTTAATTTA 0.971868 -34 ACCTTTTTTATTTTTTGACTATTTT 6 4 1 TTTTTATTTT 0.832205 -74 TTTTTTGACTATTTTAATTTTTATTTTAAATG 6 21 1 ATTTAATTTT 0.982651 -57 TTTAATTTTTATTTTAAATGTAAAACTAAGCA 6 33 1 ATTTAAATTA 0.954014 -45 TCACCAAAAATTTTTAATTGCTTAGTTTTACA 6 51 0 TTTTAATTCT 0.835807 -27 AAATTCTTATATTTAAATTTTATGT 7 4 0 ATTAAATTTA 0.975169 -118 AAATATAAGAATTTTTATTATAATTCCATATG 7 22 1 ATTTTATTTA 0.920587 -100 TCCATATGGTATATAAATGATAATCCATAATA 7 46 1 ATTAAATGTA 0.781573 -76 TCTATTTTTTAGCTTAATTTTATATTGCATTA 8 15 1 AGTTAATTTA 0.860369 -90 AAAGCAAAATATTTTAAATTTAATGCAATATA 8 35 0 ATTTAAATTA 0.954014 -70 AATATTTTGCTTTTTAATTTTTAATTAAATAA 8 54 1 TTTTAATTTT 0.966593 -51 ** ****** ** Masking position 7 Map Score: 37.1179 Number of sites scoring better than the average of aligned sites = 1226 Number in coding regions = 853 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 302 Fraction of orfs with sites within 600 bp upstream = 0.0485063 Motif number 2 TTCATTTGTATTAACTGTGTAATTATAACAACC 1 88 1 TTTGTGTAAT 0.927633 -73 ATGTGATATATTAAGGTTGTTATAATTACACAG 1 102 0 TTGTTGTTAT 0.914415 -59 AGAGTATAATTTAAATGTGATATATTAAGGTTG 1 116 0 TTTGTGATAT 0.991438 -45 ATGTTTTTGATTTGATGTGATAAGACCTTAATT 2 72 0 TTTGTGATAA 0.978778 -74 ATATAAAATCTTGTTGGTGATAAAA 2 131 1 TTGGTGATAA 0.977337 -15 TTATTTCATTGTGATATC 3 5 1 TTTGTGATAT 0.991438 -14 AACACTTTTGTGTTATTTGATATTTATTTTTTA 5 11 1 TGTTTGATAT 0.843786 -78 ATTTTTTACCTTCTCTTTGTAATTTACAATTTT 5 36 1 TTTTTGTAAT 0.760524 -53 TAAAAACTAATTTAATGTGATAAT 5 75 1 TTTGTGATAA 0.978776 -14 CAATTAAAAATTTTTGGTGACATTA 6 63 1 TTGGTGACAT 0.961979 -15 TAACTTAAATTTACCGGTGATATT 7 108 1 TTGGTGATAT 0.990849 -14 ** ******** Masking position 12 Map Score: 17.9044 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 112 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 3 AATTTATAAATGTTAATTTTTCTCATTAGAG 1 19 1 TGTAATTTTT 0.830564 -142 AATTATAACTATTCAAGTTTAATATTTAAAA 2 38 1 ATTAAGTTTA 0.724089 -108 TAAGACCTTAATTAAATTTTAAATATTAAAC 2 54 0 ATTAATTTTA 0.862263 -92 GCAATACCCAATTAAATTTTTGATATGTTTT 2 98 0 ATTAATTTTT 0.902666 -48 GAAATAGGTTTTAATAGTTTTTC 4 3 0 TTATAGTTTT 0.826942 -67 ATTCTGACCTAATGTATTTTATCAGAAATAG 4 27 0 AATTATTTTA 0.762437 -43 TGTTATTTGATATTTATTTTTTACCTTCTCT 5 21 1 TATTATTTTT 0.896443 -68 TCTTTGTAATTTACAATTTTTAATTATAAAA 5 49 1 TTAAATTTTT 0.91935 -40 TTATCACATTAAATTAGTTTTTATAATTAAA 5 67 0 AAATAGTTTT 0.573601 -22 ACCTTTTTTATTTTTTGACTATTTT 6 5 1 TTTTATTTTT 0.944096 -73 TTTTATTTTTTGACTATTTTAATTTTTATTT 6 16 1 TGATATTTTA 0.690771 -62 ACTATTTTAATTTTTATTTTAAATGTAAAAC 6 28 1 TTTTATTTTA 0.919357 -50 ACTAAGCAATTAAAAATTTTTGGTGACATTA 6 57 1 TAAAATTTTT 0.827535 -21 AATTCTTATATTTAAATTTTATGT 7 4 0 TTTAATTTTA 0.919344 -118 AATTTAAATATAAGAATTTTTATTATAATTC 7 17 1 TAAAATTTTT 0.85345 -105 TATTATAATCATTTTATTTTATTATGGATTA 7 66 0 ATTTATTTTA 0.862281 -56 ATTTTCTATTTTTTAGCTTAATT 8 3 1 TTTTATTTTT 0.944096 -102 ATTAAAAAGCAAAATATTTTAAATTTAATGC 8 41 0 AAATATTTTA 0.683044 -64 ATATTTTGCTTTTTAATTTTTAATTAAATAA 8 55 1 TTTAATTTTT 0.944096 -50 TTCTCTCCCCTTAAAAGTTTTATTTAATTAA 8 74 0 TTAAAGTTTT 0.82693 -31 *** ******* Masking position 8 Map Score: 32.7791 Number of sites scoring better than the average of aligned sites = 2129 Number in coding regions = 1337 Number in noncoding regions = 792 Number of orfs with sites within 600 bp upstream = 517 Fraction of orfs with sites within 600 bp upstream = 0.0830389 Motif number 4 ATAGAATTATCATAATTTCATTTGTATTAAC 1 72 1 CATAATTCAT 0.903948 -89 TTAAGGTTGTTATAATTACACAGTTAATACA 1 94 0 TATAATTCAC 0.764538 -67 AGAGTATAATTTAAATGTGATATATTAAGGT 1 118 0 TTAAATGGAT 0.559693 -43 AATTTATAGTTATAATTTAATAATTTAGAAC 2 11 0 TATAATTAAT 0.953443 -135 GTGATAAGACCTTAATTAAATTTTAAATATT 2 58 0 CTTAATTAAT 0.927616 -88 TTGATATGTTTTTGATTTGATGTGATAAGAC 2 79 0 TTTGATTGAT 0.816686 -67 ATATCAAAAATTTAATTGGGTATTGCGGATA 2 103 1 TTTAATTGGT 0.827309 -43 AATTAGTTTTTATAATTAAAAATTGTAAATT 5 56 0 TATAATTAAA 0.669018 -33 TAAAAACTAATTTAATGTGATAAT 5 75 1 TTTAATGGAT 0.93282 -14 ACCAAAAATTTTTAATTGCTTAGTTTTACAT 6 50 0 TTTAATTCTT 0.763723 -28 TAAAAATTCTTATATTTAAATTTTATGT 7 8 0 TATATTTAAT 0.652873 -114 GAATTTTTATTATAATTCCATATGGTATATA 7 30 1 TATAATTCAT 0.957005 -92 TATTTTTTAGCTTAATTTTATATTGCATTAA 8 17 1 CTTAATTTAT 0.726811 -88 ATATTTTAAATTTAATGCAATATAAAATTAA 8 28 0 TTTAATGAAT 0.927619 -77 CTTTTTAATTTTTAATTAAATAAAACTTTTA 8 63 1 TTTAATTAAT 0.968032 -42 ******* *** Masking position 6 Map Score: 11.36 Number of sites scoring better than the average of aligned sites = 735 Number in coding regions = 581 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 5 ACAAATGAAATTATGATAATTCTATATACC 1 67 0 TTATGATAAT 0.618872 -94 ATTAAGGTTGTTATAATTACACAGTTAATA 1 96 0 TTATAATTAC 0.811481 -65 ACCACTAATTTTTTAATCAACAGAGTATAA 1 140 0 TTTTAATCAA 0.841976 -21 AATTATTAAATTATAACTATAAATTATAAC 2 17 1 TTATAACTAT 0.954599 -129 TAACTATAAATTATAACTATTCAAGTTTAA 2 30 1 TTATAACTAT 0.954599 -116 CTTAATTAAATTTTAAATATTAAACTTGAA 2 49 0 TTTTAAATAT 0.711806 -97 TTTTATCACCAACAAGATTTTA 2 134 0 TTATCACCAA 0.598587 -12 AGGTCAGAATTTATGTCCATAGGTGAGAGA 4 48 1 TTATGTCCAT 0.618373 -22 AATTTACAATTTTTAATTATAAAAACTAAT 5 56 1 TTTTAATTAT 0.940025 -33 CTTTTTTATTTTTTGACTATTTTAATTTTT 6 13 1 TTTTGACTAT 0.899287 -65 ATAAAAATTCTTATATTTAAATTTTATGT 7 10 0 TTATATTTAA 0.638124 -112 AATATAAGAATTTTTATTATAATTCCATAT 7 23 1 TTTTTATTAT 0.688029 -99 GAAGGGAATATTATAATCATTTTATTTTAT 7 75 0 TTATAATCAT 0.938109 -47 GCTTTTTAATTTTTAATTAAATAAAACTTT 8 62 1 TTTTAATTAA 0.878774 -43 ********** Masking position 9 Map Score: 10.8881 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 754 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 6 TGATAATTCTATATACCCGATTCTTAATTCTTGTCT 1 48 0 ATATCCCTTA 0.994708 -113 ACAAGATTTTATATCCGCAATACCCAATTAAATTTT 2 109 0 ATATCCCCCA 0.984775 -37 AATGATTATAATATTCCCTTCACTTAACTTAAATTT 7 84 1 ATATCCCTTA 0.994708 -38 ACATATCATATTCTCTCCCCTTAAAAGTTTTAT 8 82 0 ATATCCCTTA 0.994708 -23 **** * * **** Masking position 4 Map Score: 0.0346427 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 12 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ********** No masking Map Score: -1.28365e-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: -1.28365e-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: -1.28365e-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