AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i168_Nitrogenase_2_mthe_reg_300.orf -o168_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RTH01904 139 M.thermo #2 RTH01526 71 M.thermo #3 RTH00989 16 M.thermo #4 RTH00935 20 M.thermo #5 RTH00563 107 M.thermo #6 RTH02097 37 M.thermo Motif number 1 GGGGACTGTTAAATTTAGAATAGATGGAAGGGA 1 98 1 AAATTGAAAG 0.988699 -42 AATTTTCTACAAAAATCAAATAGAAAAATATAT 2 25 0 AAAAAAAAAG 0.982442 -47 TCATGAGAAGAAAATGGGAAAAATAGAATTTAT 5 23 0 AAAATGAAAA 0.982442 -85 ACAAAAAAGCAAAAACTGAACAGTTTTCATGAG 5 49 0 AAAAAGAAAG 0.993997 -59 TAAATGGTTAAAATAAAGAACAAAAAAGCAAAA 5 68 0 AAATAGAAAA 0.967731 -40 CATTTACCAAAAAATTTAAATAG 5 95 1 AAAATAAAAG 0.982434 -13 ***** *** ** Masking position 9 Map Score: 6.51605 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 34 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 2 TATCTTCAGTGTCCTTTTTATGGTGAAACTT 1 60 0 GTCCTTTTAT 0.987871 -80 AAATTTAACAGTCCCCTTCATGTTATCTTCA 1 83 0 GTCCCCTTAT 0.98784 -57 CAGCCTCAAGTTCCCTTCCATCTATTCTAAA 1 111 0 TTCCCTTCAT 0.984186 -29 ATATATATTTTTCTATTTGATTTTTGTAGAA 2 23 1 TTCTATTTAT 0.91489 -49 TTTAGCCGCCGTCCATATAATAATTTTCTAC 2 48 0 GTCCATATAT 0.980684 -24 CTTCAAGTAAGTCCATTCAATTCACT 6 6 0 GTCCATTCAT 0.994171 -32 ******** ** Masking position 2 Map Score: 6.15588 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 81 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 CCTCTTCACCTCACTCTCTACTC 1 2 1 CTCTTCACTA 0.992751 -138 TCACCTCACTCTCTACTCATAACCTTTATCTG 1 16 1 CTCTACTCTA 0.938418 -124 TTTAACAGTCCCCTTCATGTTATCTTCAGTGT 1 79 0 CCCTTCATTA 0.986148 -61 GCCTCAAGTTCCCTTCCATCTATTCTAAATTT 1 108 0 CCCTTCCACA 0.961441 -32 TTTTCCCATTTTCTTCTCATGAAAACTGTTCA 5 34 1 TTCTTCTCTA 0.952406 -74 TCAAGTAAGTCCATTCAATTCACT 6 3 0 CCATTCAATA 0.958902 -35 TTTAAATCATCCTTCAAGTAAGTCCATTCAA 6 17 0 TCCTTCAATA 0.980016 -21 ******** * * Masking position 12 Map Score: 4.57129 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 333 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 CCTCTTCACCTCACTCTCTAC 1 1 1 CCTCTTCACT 0.979249 -139 CTCTACTCATAACCTTTATCTGTGCATCATG 1 26 1 AACCTTTACT 0.883089 -114 ATTTAACAGTCCCCTTCATGTTATCTTCAGT 1 81 0 CCCCTTCAGT 0.993767 -59 GCCTCAAGTTCCCTTCCATCTATTCTAAATT 1 109 0 CCCTTCCACT 0.975076 -31 TTGAATCCTCCCGCTGAGCT 4 6 0 ATCCTCCCCT 0.963099 -15 TTTAAATCATCCTTCAAGTAAGTCCATTC 6 19 0 ATCCTTCAGT 0.97826 -19 ******** ** Masking position 5 Map Score: 1.85999 Number of sites scoring better than the average of aligned sites = 991 Number in coding regions = 923 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 5 TAAAGTTTCACCATAAAAAGGACACTGAAG 1 58 1 CCATAAAAAG 0.947721 -82 CCACACACCTATATATATATTTTTCTAT 2 9 1 CTATATATAT 0.800377 -63 TAATAATTTTCTACAAAAATCAAATAGAAA 2 32 0 CTACAAAAAT 0.938094 -40 TAGCCGCCGTCCATATAATAATTTTCTACA 2 47 0 CCATATAATA 0.868715 -25 GTCCGATCCTAAATAAATTCTATTTTTC 5 9 1 CTAAATAAAT 0.947255 -99 TAACCATTTACCAAAAAATTTAAATAG 5 91 1 CCAAAAAATT 0.938259 -17 ********** Masking position 5 Map Score: 0.716479 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 99 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 6 TCCTTTTTATGGTGAAACTTTATCATGATG 1 50 0 GGTGAAACTT 0.962353 -90 GGAACTTGAGGCTGAACCTGGA 1 128 1 GCTGAACCTG 0.979487 -12 TTTGATTTTTGTAGAAAATTATTATATGGA 2 38 1 GTAGAAAATT 0.916449 -34 GTTTTCATGAGAAGAAAATGGGAAAAATAG 5 30 0 GAAGAAAATG 0.96111 -78 GAACAAAAAAGCAAAAACTGAACAGTTTTC 5 54 0 GCAAAAACTG 0.966782 -54 ********** Masking position 5 Map Score: 0.435103 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 329 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 ********** No masking Map Score: -7.57276e-14 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: -7.57276e-14 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: -7.57276e-14 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