AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -isoxS_mthe_opreg_300.orf -g0.495 -x5 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 = 0.495 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 MTH151 75 methyl coenzyme M reductase system, component A2 homolog #2 MTH155 228 rubredoxin #3 MTH1009 300 glyceraldehyde 3-phosphate dehydrogenase Motif number 1 ATATATTCATGGAGCCGGTGGCGA 1 62 1 GGACCGGGGC 0.993903 -14 AATATCTGCAGGACCCGGAGGTCCTTAAAAAA 2 16 0 GGACCGGGGT 0.998145 -213 GGCTGCCATAGGAGCAGGGTACCTGCTGATAA 2 101 0 GGACAGGTAC 0.865432 -128 CATCCACAGAGAAACCGCAGTTATTGTTCAGC 3 42 0 GAACCGCGTT 0.970204 -259 GGATTTAAAGGAAATAGGGGGTGCAGCTTCAT 3 71 0 GAATAGGGGT 0.911337 -230 ATACCTCTAAGGACCCGGGATTTAAAGGAAAT 3 88 0 GGACCGGATT 0.989582 -213 GGCGGATCCGGGATCAGGGGTTCCCGTGATAA 3 156 0 GGACAGGGTT 0.996266 -145 CCCTGATCCCGGATCCGCCATTCACCGCACTT 3 169 1 GGACCGCATT 0.977387 -132 GGTTTCCCTGGGAACAGCGTTTTTCAGGGGAT 3 264 1 GGACAGCTTT 0.964423 -37 CGTTTTTCAGGGGATAGGAGGTTTTTTTAA 3 281 1 GGGTAGGGGT 0.925373 -20 *** **** *** Masking position 7 Map Score: 16.2259 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 501 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 2 AGCAGGGTACCTGCTGATAAAAAGAAGATC 2 91 0 CTGCTGATAA 0.834728 -138 TCTATAAAATTCACTGCGAAAGCTTTATAG 2 173 0 TCACTGCGAA 0.960865 -56 TTGCTACTGATCGCTGCTAACCAGCTGAAC 3 19 1 TCGCTGCTAA 0.936903 -282 GCAGCTTCATCCACAGAGAAACCGCAGTTA 3 51 0 CCACAGAGAA 0.93071 -250 GGTATCCTTTTCCCTCAGAAGCCCATGAGA 3 115 1 TCCCTCAGAA 0.958502 -186 CCCTCAGAAGCCCATGAGAAGCATTAAAGA 3 126 1 CCCATGAGAA 0.972129 -175 ATCAGGGGTTCCCGTGATAATCTTTAATGC 3 146 0 CCCGTGATAA 0.952846 -155 CAAAGAGGTTTCCCTGGGAACAGCGTTTTT 3 258 1 TCCCTGGGAA 0.979832 -43 AACCTCCTATCCCCTGAAAAACGCTGTTCC 3 274 0 CCCCTGAAAA 0.979724 -27 ********** Masking position 9 Map Score: 7.91615 Number of sites scoring better than the average of aligned sites = 1164 Number in coding regions = 1107 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 TTACTGACATAATAACTTTATGCG 1 1 0 AAAATTATCG 0.951238 -75 TTATTATGTCAGTAAAACTATTAGAACTATGGTG 1 20 1 AGAAATATAG 0.964015 -56 TTAATCTCAAAAAAATAATATCTGCAGGACCCGG 2 30 0 AAAAATATTG 0.983807 -199 ATCTGAAGCAAAGAATAATATACGTCCAGATTAA 2 60 0 AAAAATATCG 0.989472 -169 ACCTGCTGATAAAAAGAAGATCTGAAGCAAAGAA 2 79 0 AAAAAGATTG 0.949227 -150 GCAGCCCATTAAACAAATTATCAGATGTATGCCG 2 127 1 AACAATATAG 0.964015 -102 ATAATCCATTAAAAATAGTATCAGGTTAGGAATT 3 218 1 AAAAATATAG 0.988645 -83 ** ** * *** ** Masking position 5 Map Score: 5.45206 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 10 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 GGACCTCCGGGTCCTGCAGATATTATTTTTT 2 24 1 GTCCTCAGAT 0.986173 -205 AAGAATAATATACGTCCAGATTAATCTCAAA 2 53 0 TACGTCAGAT 0.959962 -176 ATATTATTCTTTGCTTCAGATCTTCTTTTTA 2 73 1 TTGCTCAGAT 0.990289 -156 AGGAGCAGGGTACCTGCTGATAAAAAGAAGA 2 93 0 TACCTCTGAT 0.98247 -136 AAAACTGATTGCTACTGATCGCTGCTAAC 3 9 1 TTGCTCTGAT 0.982032 -292 AGGTATCCTTTTCCCTCAGAAGCCCATGAGA 3 114 1 TTCCCCAGAA 0.946021 -187 ***** ***** Masking position 10 Map Score: 4.12079 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 139 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 5 AACTCTTTTTTAAGGACCTCCGGGTCCTG 2 9 1 TTAAGGACCT 0.947148 -220 AAAATAATATCTGCAGGACCCGGAGGTCCTT 2 22 0 CTCAGGACCC 0.973307 -207 CTTTATAGTGTTGAGAGACCCGGCATACATC 2 150 0 TTAGAGACCC 0.92086 -79 GACCCGGGATTTAAAGGAAATAGGGGGTGCA 3 78 0 TTAAGGAAAT 0.815374 -223 AAAGGATACCTCTAAGGACCCGGGATTTAAA 3 94 0 TCAAGGACCC 0.984707 -207 TCATGGGCTTCTGAGGGAAAAGGATACCTCT 3 112 0 CTAGGGAAAA 0.795659 -189 TTAAAGATTATCACGGGAACCCCTGATCCCG 3 149 1 TCCGGGAACC 0.973307 -152 AAACGCTGTTCCCAGGGAAACCTCTTTGAGT 3 255 0 CCAGGGAAAC 0.961045 -46 ** ******** Masking position 8 Map Score: 3.13476 Number of sites scoring better than the average of aligned sites = 1525 Number in coding regions = 1460 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 ACGTCCAGATTAATCTCAAAAAAATAATAT 2 43 0 TAATCTCAAA 0.979012 -186 AAATTTAAAATTATCTATAAAATTCACTGC 2 186 0 TTATCTATAA 0.908668 -43 GTTCCCGTGATAATCTTTAATGCTTCTCAT 3 139 0 TAATCTTTAA 0.922201 -162 TTTTATATACTTATCTAAAAGTGCGGTGAA 3 189 0 TTATCTAAAA 0.952911 -112 GTTAGGAATTTAAACTCAAAGAGGTTTCCC 3 242 1 TAAACTCAAA 0.934132 -59 ********** Masking position 6 Map Score: 2.37641 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 29 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 7 ATATACTAGAAGCACCATAGTTCTAATAGT 1 36 0 AGCACCATAG 0.875628 -40 CTCCTATGGCAGCCCATTAAACAAATTATC 2 119 1 AGCCCATTAA 0.927189 -110 GTGCAGCTTCATCCACAGAGAAACCGCAGT 3 53 0 ATCCACAGAG 0.902409 -248 TTCCCTCAGAAGCCCATGAGAAGCATTAAA 3 124 1 AGCCCATGAG 0.988359 -177 TTATCACGGGAACCCCTGATCCCGGATCCG 3 156 1 AACCCCTGAT 0.940872 -145 AAAACCTCCTATCCCCTGAAAAACGCTGTT 3 276 0 ATCCCCTGAA 0.980173 -25 ********** Masking position 9 Map Score: 1.2496 Number of sites scoring better than the average of aligned sites = 880 Number in coding regions = 821 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 ********** No masking Map Score: 1.18904e-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: 1.18904e-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 10 ********** No masking Map Score: 1.18904e-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