AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -imetR_mthe_opreg_100.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 MTH124 126 conserved protein #2 MTH777 48 conserved protein #3 MTH778 68 unknown #4 MTH779 300 conserved protein #5 MTH1380 167 serine hydroxymethyltransferase Motif number 1 ATCTAGTTGCAACCCCATATCTCTGGTTTCAGG 3 24 1 AACCCCACTC 0.9856 -45 TCAGGGCAAAAATCCGGACCCTGAAACCAGAGA 3 43 0 AATCCGGCTG 0.9856 -26 GGACATCCCGGTGACTCCCTTTAAACT 4 5 1 ATCCCGGCTC 0.997892 -296 CCGGGTTCAAATCCCGGCCAGTCCACTCAAAAC 4 160 0 ATCCCGGGTC 0.990872 -141 CCGGGATTTGAACCCGGGGCCTCCGCCATGCCA 4 176 1 AACCCGGCTC 0.998864 -125 GGGGATTCCGAATCCGATTGCTCGGAGTATTAT 5 54 0 AATCCGACTC 0.990183 -114 ******* *** Masking position 12 Map Score: 7.67078 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 75 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 AGATAAGAGATTTATCATTTTCACAGGAGAT 1 12 0 TTTATATTTT 0.943435 -115 TGCCCAATGATTTTTAAGTTTAAAGGGAGTC 4 23 0 TTTTTAGTTT 0.944289 -278 CTGGAATGATTTTTTTATTTTAATAAGGAAA 4 66 1 TTTTTATTTT 0.953594 -235 TTAAATGAAGTTTTTCAGGTTTCCTTATTAA 4 85 0 TTTTTAGGTT 0.970846 -216 CCTGCATTTATTTTTACTGATTAAATGAAGT 4 105 0 TTTTTCTGAT 0.839991 -196 AAAACTGTTTTTTAAACTGTTTTTATTGTCC 4 134 0 TTTAACTGTT 0.809922 -167 CGTCGAAGATTTAATAAGGTTAACTTTAAAT 4 270 0 TTAATAGGTT 0.809922 -31 CATCAAATCCTTTATCCTTTTTCTAACTTAC 5 23 1 TTTATCTTTT 0.932238 -145 TCAACACGCGTTTTTTATGTTGACATCGCAA 5 94 1 TTTTTATGTT 0.97583 -74 ***** ***** Masking position 2 Map Score: 7.12028 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 108 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 3 CGAACTGTAATGGACAGGAATGCAGTTGTAG 1 81 1 TGGACGGAAT 0.977031 -46 TCTGGTTTCAGGGTCCGGATTTTTGCCCTGA 3 45 1 GGGTCGGATT 0.985029 -24 CACTTCCCTGTGGCCTGGAATGATTTTTTTA 4 52 1 TGGCCGGAAT 0.99548 -249 CTGTTTTTATTGTCCTGCATTTATTTTTACT 4 118 0 TGTCCGCATT 0.947886 -183 TTGAGTGGACTGGCCGGGATTTGAACCCGGG 4 163 1 TGGCCGGATT 0.997555 -138 GCATGGCGGAGGCCCCGGGTTCAAATCCCGG 4 176 0 GGCCCGGGTT 0.972396 -125 ***** ***** Masking position 11 Map Score: 5.52974 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 131 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 GATCTCCTGTGAAAATGATAAATCTCTTAT 1 1 1 GTTAAATATA 0.972483 -126 ACATCCCGGTGACTCCCTTTAAACTTAAAAATCATTGGGC 4 13 1 GCTAATTAAA 0.928185 -288 AGTTTTTCAGGTTTCCTTATTAAAATAAAAAAATCATTCC 4 68 0 GTTAAATAAA 0.993039 -233 GATTTAATAAGGTTAACTTTAAATATTAAAAGGCTTAATG 4 254 0 GTTAAATAAA 0.989998 -47 TCCATTACCAGTTGCGATGTCAACATAAAAAACGCGTGTT 5 96 0 GTTAAATAAA 0.993039 -72 TAGGAAAATAGTTGCAATGACAATATAAAATTGGTGTTAA 5 138 0 GTTAAATAAA 0.992942 -30 * * * ** ** *** Masking position 12 Map Score: 4.51691 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 5 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ATCAAGCCCCCTCCAAATAGTATTTAAGAT 1 50 0 CTCCAAATAG 0.75924 -77 CCATTACAGTTCGCATCAAGCCCCCTCCAA 1 64 0 TCGCATCAAG 0.933531 -63 GCGGTCCCAGCTGGTGAATGATCA 2 5 1 TCCCAGCTGG 0.96165 -44 AGATATGGGGTTGCAACTAGATCATATATT 3 16 0 TTGCAACTAG 0.952766 -53 GAGCTACCAGCCCCAACAAAGTATACATTA 4 229 1 CCCCAACAAA 0.933533 -72 ATGGGTTAACCCCATCAAATCCTTTATCC 5 10 1 CCCCATCAAA 0.859348 -158 TTCGGAATCCCCCCAGCTATCAACACGCGT 5 75 1 CCCCAGCTAT 0.947415 -93 TATGTTGACATCGCAACTGGTAATGGAAGT 5 109 1 TCGCAACTGG 0.967829 -59 TATATTGTCATTGCAACTATTTTCCTA 5 151 1 TTGCAACTAT 0.846216 -17 ********** Masking position 5 Map Score: 4.40487 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 324 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 TACAACTGCATTCCTGTCCATTACAGTTCG 1 81 0 TTCCTGTCCA 0.948602 -46 GTTTCAGGGCAAAAATCCGGA 3 58 0 TTTCAGGGCA 0.955434 -11 AAAAAAATCATTCCAGGCCACAGGGAAGTG 4 52 0 TTCCAGGCCA 0.994367 -249 GTAAAAATAAATGCAGGACAATAAAAACAG 4 119 1 ATGCAGGACA 0.940897 -182 CCGGGTTCAAATCCCGGCCAGTCCACTCAA 4 163 0 ATCCCGGCCA 0.987628 -138 ********** Masking position 2 Map Score: 1.81666 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 234 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 AGCCCCCTCCAAATAGTATTTAAGATGAAA 1 46 0 AAATAGTATT 0.700983 -81 TTTTTATTTTAATAAGGAAACCTGAAAAAC 4 77 1 AATAAGGAAA 0.825013 -224 AACTTCATTTAATCAGTAAAAATAAATGCA 4 104 1 AATCAGTAAA 0.853128 -197 AGGACAATAAAAACAGTTTAAAAAACAGTT 4 133 1 AAACAGTTTA 0.940572 -168 ACAGTTTAAAAAACAGTTTTGAGTGGACTG 4 145 1 AAACAGTTTT 0.849683 -156 ACCAGCCCCAACAAAGTATACATTAAGCCT 4 234 1 ACAAAGTATA 0.848453 -67 TCGAAGATTTAATAAGGTTAACTTTAAATA 4 269 0 AATAAGGTTA 0.888971 -32 TGTAAGTTAGAAAAAGGATAAAGGATTTGA 5 25 0 AAAAAGGATA 0.953723 -143 ********** Masking position 5 Map Score: 1.31112 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 180 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 8 CAGTTGTAGGGAGGTTTACAGAGATCTTGA 1 103 1 GAGGTTTACA 0.960396 -24 TTTAATATTTAAAGTTAACCTTATTAAATC 4 264 1 AAAGTTAACC 0.914308 -37 AGGATTTGATGGGGTTAACCCAT 5 4 0 GGGGTTAACC 0.974865 -164 TACCAGTTGCGATGTCAACATAAAAAACGC 5 101 0 GATGTCAACA 0.929463 -67 ACTGGTAATGGAAGTTAACACCAATTTTAT 5 124 1 GAAGTTAACA 0.980981 -44 ********** Masking position 5 Map Score: 0.737568 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 171 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 ********** No masking Map Score: 1.57984e-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: 1.57984e-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 11 ********** No masking Map Score: 1.57984e-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