AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i325_not_clear_mjan_reg_300.orf -o325_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 RMJ08781 131 M_jannaschii_chromosome #2 RMJ12462 83 M_jannaschii_chromosome #3 RMJ06449 72 M_jannaschii_chromosome Motif number 1 CTTAGGTATTAAAAAATTAGAAAAAT 1 5 0 AAAATTAGAA 0.9624 -127 AGATTGGATGAAAACCTTAAAACTTAGGTATT 1 27 0 AAAATTAAAA 0.989731 -105 TTTCTTGTAAAACATTTTGAAAGAAACTTTTA 1 63 0 AACATTGAAA 0.973111 -69 TAAAATAGAAAAAAAGTTGAAATATAGTTTCT 1 90 0 AAAATTGAAA 0.970933 -42 CTCACCTAATTAAACATTAAAATAGAAAAAAA 1 107 0 TAAATTAAAA 0.980388 -25 AGTTTATTATAAAAATTCATAATTAAAGTATT 2 26 1 AAAATCATAA 0.907025 -58 TTCATAATTAAAGTATTTAAAAATATCTATTA 2 41 1 AAGTTTAAAA 0.950991 -43 ATTATATAACAAATTATCACCTAATAGAT 2 65 0 AACATTATCA 0.913562 -19 ATAATCACCATACATCTTATAATAATAGTTAA 3 11 1 TACATTATAA 0.969635 -62 CATCTTATAATAATAGTTAAAATATTTTATAA 3 23 1 TAATTTAAAA 0.946723 -50 GACATTAAAATACTTTTTATAAAATATTTTAA 3 39 0 TACTTTATAA 0.919045 -34 GTTATCACCAAAGACATTAAAATACTTTTTAT 3 51 0 AAGATTAAAA 0.982007 -22 **** ****** Masking position 2 Map Score: 19.7454 Number of sites scoring better than the average of aligned sites = 1750 Number in coding regions = 1324 Number in noncoding regions = 426 Number of orfs with sites within 600 bp upstream = 341 Fraction of orfs with sites within 600 bp upstream = 0.0547703 Motif number 2 AAACTTAGGTATTAAAAAATTAGAAAAAT 1 9 0 ATTAAAAATT 0.917616 -123 GAAAGAAACTTTTAGGAAAGATTGGATGAAA 1 46 0 TTTAGAAAGA 0.944179 -86 CTTGTAAAACATTTTGAAAGAAACTTTTAGG 1 61 0 ATTTGAAAGA 0.913913 -71 TTCAAAATGTTTTACAAGAAACTATATTTCA 1 74 1 TTTAAAGAAA 0.866596 -58 CTAATTAAACATTAAAATAGAAAAAAAGTTG 1 103 0 ATTAAATAGA 0.911919 -29 TTAATGTTTAATTAGGTGAGATT 1 119 1 ATTAGTGAGA 0.94055 -13 CTCCAAGTTTATTATAAAAATTCATAATTAA 2 21 1 ATTAAAAAAT 0.823113 -63 TAATTAAAGTATTTAAAAATATCTATTAGGT 2 45 1 ATTTAAAATA 0.909515 -39 AAAAATATCTATTAGGTGATAATTTGTTATA 2 59 1 ATTAGTGATA 0.924747 -25 ATTATATAACAAATTATCACC 2 73 0 ATTAATAACA 0.853753 -11 TTTAACTATTATTATAAGATGTATGGTGATT 3 13 0 ATTAAAGATG 0.897563 -60 TAAAATACTTTTTATAAAATATTTTAACTAT 3 35 0 TTTAAAAATA 0.940835 -38 **** ****** Masking position 9 Map Score: 11.2226 Number of sites scoring better than the average of aligned sites = 2500 Number in coding regions = 2129 Number in noncoding regions = 371 Number of orfs with sites within 600 bp upstream = 321 Fraction of orfs with sites within 600 bp upstream = 0.051558 Motif number 3 TAGGTATTAAAAAATTAGAAAAAT 1 5 0 AAAATTAGAA 0.930473 -127 ATTGGATGAAAACCTTAAAACTTAGGTATT 1 27 0 AACCTTAAAA 0.968562 -105 AAATAGAAAAAAAGTTGAAATATAGTTTCT 1 90 0 AAAGTTGAAA 0.935262 -42 CACCTAATTAAACATTAAAATAGAAAAAAA 1 107 0 AACATTAAAA 0.981316 -25 CATAATTAAAGTATTTAAAAATATCTATTA 2 43 1 GTATTTAAAA 0.834409 -41 TCTTATAATAATAGTTAAAATATTTTATAA 3 25 1 ATAGTTAAAA 0.953326 -48 TATCACCAAAGACATTAAAATACTTTTTAT 3 51 0 GACATTAAAA 0.972484 -22 ********** Masking position 9 Map Score: 6.50169 Number of sites scoring better than the average of aligned sites = 1041 Number in coding regions = 786 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 221 Fraction of orfs with sites within 600 bp upstream = 0.0354963 Motif number 4 GGATGAAAACCTTAAAACTTAGGTATTAAA 1 24 0 CTTAAAACTT 0.943296 -108 TCCAATCTTTCCTAAAAGTTTCTTTCAAAA 1 51 1 CCTAAAAGTT 0.994388 -81 ATAACTTCACCTCCAAGTTTATTATAAAA 2 10 1 CCTCCAAGTT 0.983861 -74 CAAATTATCACCTAATAGATATTTTTAAAT 2 55 0 CCTAATAGAT 0.965219 -29 ********** Masking position 7 Map Score: 1.49978 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 103 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 ********** No masking Map Score: -2.39152e-13 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 6 ********** No masking Map Score: -2.39152e-13 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: -2.39152e-13 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