AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i164_NIF1_mthe_reg_300.orf -o164_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 RTH00742 300 M.thermo #2 RTH01812 104 M.thermo #3 RTH00789 78 M.thermo #4 RTH00588 38 M.thermo #5 RTH00837 72 M.thermo #6 RTH01538 300 M.thermo Motif number 1 AATCATAATTATTAAGATATTAATATCACGGATCT 1 61 0 AAATATTATA 0.984441 -240 ATAATATTATATGAAAATAATCATAATTATTAAGA 1 79 0 AAATAATATA 0.879931 -222 AGTCAATTTAAGCAATGTTTTCATTTTATCCTCCT 1 143 0 AAATTTTATT 0.959737 -158 AATTCTCCTTATAAGTTTTTTGATTTGAAAATTAT 1 204 1 AAGTTTTATT 0.803621 -97 AAAATTATCAAAAAATATATTTATATTGGAAACCG 1 231 1 AAATATTATA 0.984385 -70 AAAATCCCAGAAAAATTTATTTATTTTTTTATCCA 2 18 1 AAATATTATT 0.97445 -87 GATTGGCATAGGAATCTATTTATTGTATCCTACG 5 10 1 AAATATTATT 0.978702 -63 TCTTCCTTTTAATAAATTATTCGTAGGATACAATA 5 31 0 AAATATTGTA 0.955623 -42 TCAGGAGCTCACCAAGTCTTTTATAGACGGGGCGT 6 36 0 AAACTTTATA 0.849244 -265 AATATATAGTAATAACTTATTAGTTTTCAGGAGCT 6 62 0 AAATATTGTT 0.940112 -239 ATACTTTGATAATAAGATTTAAATATATAGTAATA 6 83 0 AAATTTAATA 0.791709 -218 AAATCTTATTATCAAAGTATTTATAGGGCCGGGTG 6 98 1 AAATATTATA 0.984431 -203 * ** **** *** Masking position 4 Map Score: 15.6706 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 35 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 2 CACTGGATTGAAGCAGCTCAGCCACAGATC 1 36 1 AAGCAGCTCA 0.978455 -265 AGGCTTCCCAAAGGAGGATAAAATGAAAAC 1 132 1 AAGGAGGATA 0.912185 -169 TTTCAATCCCAAGCAGCTGAAACTGGTGTT 2 82 1 AAGCAGCTGA 0.988622 -23 CCCCATCAAAGAACAGCAGAGAAAAACAGG 3 14 1 GAACAGCAGA 0.91267 -65 ATATAACAGGAAACAGCTGATCAAAA 3 63 1 AAACAGCTGA 0.971399 -16 AACTTAAGGGAAAGAGCAGAAA 4 27 1 AAAGAGCAGA 0.971399 -12 TATTAGTTTTCAGGAGCTCACCAAGTCTTT 6 50 0 CAGGAGCTCA 0.933218 -251 TATTCTGCTAAAGGAGGATAGAAG 6 287 1 AAGGAGGATA 0.912185 -14 ********** Masking position 5 Map Score: 6.9791 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 242 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 GCCTTTACCATCCATTATCCATATAATATTATATGAA 1 99 0 TCTTCCTAAT 0.966361 -202 AACCGATTAATCTGTACTACTAATAATATAAGTAGTA 1 261 1 TTTTACTAAT 0.984862 -40 TCCATTTCTGTAATACTACTTATATTATTAGTA 1 278 0 TTTTACTTAT 0.965874 -23 ATTTATTTATTTTTTTATCCAAGTAATTTTTACACTT 2 32 1 TTTTCCTAAT 0.987432 -73 TCCTGTTATATGGTTCATACTGTTTATGGACCTGTTT 3 37 0 TGTTACTTAT 0.911885 -42 ATCTATTTATTGTATCCTACGAATAATTTATTAAAAG 5 24 1 TTTTACTAAT 0.984862 -49 AACCACCACCTATTTCTTCCTTTTAATAAATTATTCG 5 43 0 TTTTCCTAAT 0.987432 -30 * * * *** **** Masking position 16 Map Score: 5.60089 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 TGCTTCAATCCAGTGATCCTAACTGGAAGGC 1 20 0 CGTGATCCTA 0.961022 -281 AGCCACAGATCCGTGATATTAATATCTTAAT 1 55 1 CGTGATATTA 0.962193 -246 ACCGATTAATCTGTACTACTAATAATATAAG 1 262 1 CGTACTACTA 0.771373 -39 TCCATTTCTGTAATACTACTTATATTAT 1 283 0 CGTAATACTA 0.941776 -18 GTAAATTGAAGTGTAAAAATTACTTGGATAA 2 46 0 GGTAAAAATT 0.581682 -59 TATAGACGGGGCGTGATATTATTAATCAAGT 6 19 0 GGTGATATTA 0.918642 -282 CCTATAAATACTTTGATAATAAGATTTAAAT 6 94 0 CTTGATAATA 0.836363 -207 TTATAGGGCCGGGTGAAAATATAGATGTAAA 6 118 1 GGTGAAAATA 0.946606 -183 GACAGTTATCCAGTGAACATATGGGGACATC 6 181 1 CGTGAACATA 0.945 -120 ATGGGGCAGTCTGTGAAAATTAGAGCCTCTT 6 221 0 CGTGAAAATT 0.917408 -80 * ********* Masking position 4 Map Score: 6.09712 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 286 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 CCAGTGATCCTAACTGGAAGGCTGCCCTTA 1 12 0 TAACTGGAAG 0.974737 -289 CAAAGGAGGATAAAATGAAAACATTGCTTA 1 140 1 TAAAATGAAA 0.909811 -161 GAAAAGTCAGTAAATTGAAGTGTAAAAATT 2 56 0 TAAATTGAAG 0.9407 -49 ATGAACCATATAACAGGAAACAGCTGATCA 3 56 1 TAACAGGAAA 0.960831 -23 AATAATTTATTAAAAGGAAGAAATAGGTGG 5 45 1 TAAAAGGAAG 0.980848 -28 ********** Masking position 3 Map Score: 3.21909 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 19 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 AGATCCGTGATATTAATATCTTAATAATTAT 1 61 1 TATTAATACT 0.867726 -240 CGGTTTCCAATATAAATATATTTTTTGATAA 1 235 0 TATAAATAAT 0.976325 -66 TGGATAAAAAAATAAATAAATTTTTCTGGGA 2 22 0 AATAAATAAT 0.945785 -83 CGTAGGATACAATAAATAGATTCCTATGCCA 5 14 0 AATAAATAAT 0.947147 -59 TATTTCTTCCTTTTAATAAATTATTCGTAGG 5 39 0 TTTTAATAAT 0.881089 -34 GATAATAAGATTTAAATATATAGTAATAACT 6 80 0 TTTAAATAAT 0.947198 -221 CACCCGGCCCTATAAATACTTTGATAATAAG 6 102 0 TATAAATATT 0.910509 -199 ******** ** Masking position 6 Map Score: 4.56064 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 19 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TGGATAATGGATGGTAAAGGCTTCCCAAAG 1 115 1 ATGGTAAAGG 0.927462 -186 TGGTAAAGGCTTCCCAAAGGAGGATAAAAT 1 126 1 TTCCCAAAGG 0.98053 -175 TACCCTGAAATTGCCACAGGTGAATAAATT 1 178 1 TTGCCACAGG 0.97748 -123 GATTGGCATAGGAATCTATTTA 5 3 1 TTGGCATAGG 0.952618 -70 AATTGAAGGGTTCATAAAGGTTCCAGCAAG 6 258 0 TTCATAAAGG 0.889637 -43 TTCAATTATTCTGCTAAAGGAGGATAGAAG 6 281 1 CTGCTAAAGG 0.965039 -20 ********** Masking position 6 Map Score: 2.00673 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 66 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TTAAGGGCAGCCTTCCAGTTAGGA 1 5 1 GGGCAGCCTT 0.997455 -296 ATCCTCCTTTGGGAAGCCTTTACCATCCAT 1 121 0 GGGAAGCCTT 0.993088 -180 GTGGTCCATGGGGCAGTCTGTGAAAATTAG 6 229 0 GGGCAGTCTG 0.991787 -72 ********** Masking position 5 Map Score: 1.63783 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 12 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 CTGCTGTTCTTTGATGGGGCCT 3 3 0 TTGATGGGGC 0.991807 -76 GTTCATACTGTTTATGGACCTGTTTTTCTC 3 32 0 TTTATGGACC 0.880792 -47 GTACATGGAACGCATGAACTT 4 2 1 TACATGGAAC 0.879341 -37 AAGTCTTTTATAGACGGGGCGTGATATTAT 6 28 0 TAGACGGGGC 0.952302 -273 TATCAAAGTATTTATAGGGCCGGGTGAAAA 6 107 1 TTTATAGGGC 0.874516 -194 CAGCAAGTGGTCCATGGGGCAGTCTGTGAA 6 235 0 TCCATGGGGC 0.973973 -66 CATGGACCACTTGCTGGAACCTTTATGAAC 6 249 1 TTGCTGGAAC 0.859036 -52 ********** Masking position 1 Map Score: 1.02064 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 290 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 10 ********** No masking Map Score: -8.07587e-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 11 ********** No masking Map Score: -8.07587e-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 12 ********** No masking Map Score: -8.07587e-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