AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i320_mixed5_mthe_reg_300.orf -o320_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 RTH02062 231 M.thermo #2 RTH02064 195 M.thermo #3 RTH01737 64 M.thermo #4 RTH00128 23 M.thermo #5 RTH00136 54 M.thermo #6 RTH02067 22 M.thermo #7 RTH01815 75 M.thermo #8 RTH00552 206 M.thermo #9 RTH01769 269 M.thermo #10 RTH00704 49 M.thermo #11 RTH02072 18 M.thermo Motif number 1 GGGCGAGAGGCTGTGCCCAGGGGATGGCCCATG 1 14 1 CGTCCCAGGG 0.954218 -218 ACACATGTAACCGGAATCATGGGCCATCCCCTG 1 31 0 CGGATCAGGG 0.972692 -201 GATTCTTTGCCTGTAATGCCGGGGTGATAAACT 1 77 0 CGTATGCGGG 0.982772 -155 CATAGGTTACCTATAATCCAGGGGAGAGTGTGA 1 208 1 CATATCCGGG 0.989372 -24 CCCGGGCATCACGGGACCCGGGGCCCCTCAAGG 2 51 0 AGGACCCGGG 0.948803 -145 AGGAACACGGAAGGCCTCCCGGGCATCACGGGA 2 68 0 AGGCTCCGGG 0.991031 -128 GGGAGGCCTTCCGTGTTCCTGGGGAATATTCCG 2 81 1 CGTTTCCGGG 0.993502 -115 GGAGGGGTGCTGGTTTTCCAGGGAACTCTATCT 2 116 1 TGTTTCCGGG 0.974275 -80 CCTCCAGGGGAAATCCTTCAGGGCGCTGACACC 2 151 0 AATCTTCGGG 0.858766 -45 TCTCAAACCCTGACCCTCCAGGGGAAATCCTTC 2 165 0 TACCTCCGGG 0.934059 -31 TCGCTGCAGTCATCCATGGAAGACCCCTT 3 7 1 CGTATCCTGG 0.942831 -58 CTCAACCAGCACTCACGGGAGGT 4 7 1 CGCCTCAGGG 0.96753 -17 AAGGTATCTTCAAGAATTCAGGGGG 8 3 0 CAGATTCGGG 0.89636 -204 GCACTCGTGGATATACTGCTGGGTTGAAGGTGC 8 98 1 AATCTGCGGG 0.903896 -109 CTATTAATCCTTGTTTTCCTGGGCGTCTTACTG 9 84 1 TGTTTCCGGG 0.974275 -186 * ** **** *** Masking position 12 Map Score: 24.2665 Number of sites scoring better than the average of aligned sites = 1063 Number in coding regions = 1013 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 TATGGGCGAGAGGCTGTGCCCAGGGGAT 1 9 1 AGAGGCTGTG 0.955843 -223 ATAATCCAGGGGAGAGTGTGAC 1 220 1 GGAGAGTGTG 0.967912 -12 GATTTCCCCTGGAGGGTCAGGGTTTGAGAT 2 169 1 GGAGGGTCAG 0.992235 -27 ATGAGAAATAAGAAGGTCAG 6 13 1 AGAAGGTCAG 0.944062 -10 ACGAGTGCTTGGAGGGTGAGAAATTAACTT 8 76 0 GGAGGGTGAG 0.996708 -131 ATTAACATGAAGTGGGTGAGTACCTTTATA 9 190 0 AGTGGGTGAG 0.968192 -80 TCAGGAAGGTGTTTACCA 11 4 1 GGAAGGTGTT 0.891643 -15 ********** Masking position 7 Map Score: 7.35535 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 456 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 TATTCCCCAGGAACACGGAAGGCCTCCCGGGC 2 77 0 GAACGGAAGG 0.977028 -119 AAATGAGAAATAAGAAGGTCAG 6 7 1 GAAAAGAAGG 0.974165 -16 ATTAACCAGGGAAATTAAACGGGGT 7 4 0 GAAAAAACGG 0.905731 -72 AAAAGCTTAAAAAAGAGAAAGGTATCTTCAAG 8 22 0 AAAAGAAAGG 0.982276 -185 TGTCCGATGAAAAATAGAAAAGCTTAAAAAAG 8 39 0 AAAAGAAAAG 0.877879 -168 GCTGCCAATTAAAAAGGGAAGGAATAATGGAT 9 22 0 AAAAGGAAGG 0.985278 -248 TTATTAAATTGAAATTGAAAGGCTTTTAGTGC 10 18 0 GAAAGAAAGG 0.991339 -32 **** ****** Masking position 9 Map Score: 5.38854 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 146 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 AAACTGATAACTGGAAAAACACATGTAACC 1 52 0 CTGGAAAAAC 0.865527 -180 TAATATTCCTCAGGAACTCAACACTCTGTC 2 19 0 CAGGAACTCA 0.84372 -177 GAATATTCCCCAGGAACACGGAAGGCCTCC 2 82 0 CAGGAACACG 0.962008 -114 ATAGAGTTCCCTGGAAAACCAGCACCCCTC 2 117 0 CTGGAAAACC 0.982946 -79 ACCGATGGCTCAGAAAAACCTTAAAATTAG 8 142 1 CAGAAAAACC 0.977247 -65 TTTTAATTGGCAGCAAAACTTTATATGTGA 9 40 1 CAGCAAAACT 0.8737 -230 GTAAGACGCCCAGGAAAACAAGGATTAATA 9 85 0 CAGGAAAACA 0.98155 -185 CGATGGATGGTAGAAAAACCAG 9 258 1 TAGAAAAACC 0.827474 -12 ********** Masking position 5 Map Score: 5.09209 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 403 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 TATGGCAACAATATTTATCGCTGATGGTAAATAA 1 178 0 ATTTATCCTA 0.905817 -54 AATTAGCGATATATTTATATAGGATTATATGAAT 8 166 1 ATTTATAAGA 0.851533 -41 ATATAGGATTATATGAATAGATAATATCACATAA 8 182 1 ATTGATAATA 0.946086 -25 CTCTCATCTGCATCCATTATTCCTTCCCT 9 6 1 ATTGATCATA 0.984627 -264 TCTCATGAAAATCTGTATCCAGCAAGTTTTATAT 9 146 1 ATTGATCAGA 0.976617 -124 CACCCACTTCATGTTAATCCATAACTTGGATTAT 9 202 1 ATTTATCATA 0.968759 -68 AATTACACCAATCTGGATCAATAATCCAAGTTAT 9 222 0 ATTGATCATA 0.950135 -48 ** ** *** ** * Masking position 7 Map Score: 4.4584 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 20 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ATCTGATTTTTTTTCTCATGGTACTTACAA 1 145 1 TTTTCTCATG 0.854161 -87 AAGGTATAATATTCCTCAGGAACTCAACAC 2 25 0 ATTCCTCAGG 0.981648 -171 CCAGCGGAATATTCCCCAGGAACACGGAAG 2 88 0 ATTCCCCAGG 0.985687 -108 CCTGGGGAATATTCCGCTGGAGGGGTGCTG 2 98 1 ATTCCGCTGG 0.951358 -98 CCCCAGATAGAGTTCCCTGGAAAACCAGCA 2 123 0 AGTTCCCTGG 0.929854 -73 CCCTGAAGGATTTCCCCTGGAGGGTCAGGG 2 161 1 TTTCCCCTGG 0.950355 -35 TTATTAAGTCATTTCTGTTGCTTAAGCCGT 5 24 0 ATTTCTGTTG 0.731779 -31 TGACCTTCTTATTTCTCATTT 6 2 0 ATTTCTCATT 0.647985 -21 ACCCCGTTTAATTTCCCTGGTTAATTCAGG 7 11 1 ATTTCCCTGG 0.984511 -65 TCAGAATACGATTTCTCATGAAAATCTGTA 9 133 1 ATTTCTCATG 0.954689 -137 ********** Masking position 3 Map Score: 11.7811 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 316 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 CATAGGTTACCTATAATCCAGGGGAGAGTG 1 208 1 CTATAATCCA 0.904443 -24 GGAAAACCAGCACCCCTCCAGCGGAATATT 2 105 0 CACCCCTCCA 0.946311 -91 TCGCTGCAGTCATCCATGGAAGACCC 3 7 1 CAGTCATCCA 0.982584 -58 TTAACAGATGCAGCCATACACAAGTACTGA 3 39 1 CAGCCATACA 0.932084 -26 CAATCTGGATCAATAATCCAAGTTATGGAT 9 218 0 CAATAATCCA 0.946409 -52 CTGGTTTTTCTACCATCCATCGGTAATTA 9 251 0 CTACCATCCA 0.9778 -19 ********** Masking position 7 Map Score: 2.07413 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 206 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 8 AAGAGATTCTTTGCCTGTAATGCCGGGGTG 1 84 0 TTGCCTGTAA 0.832574 -148 TTTAGATGCTGCACCGGTCAGTATAGAATC 1 118 1 GCACCGGTCA 0.891617 -114 TTGCCATAGGTTACCTATAATCCAGGGGAG 1 204 1 TTACCTATAA 0.74762 -28 TCATATCACCGTTATTAAGTCATTT 5 40 0 TCACCGTTAT 0.864921 -15 TTATCAATATGTACCTGAATTAACCAGGGA 7 24 0 GTACCTGAAT 0.729391 -52 TTTACCGGTAAGAATAAAGTT 7 65 0 TTACCGGTAA 0.496628 -11 GGTTCATGGGGCACCTTCAACCCAGCAGTA 8 111 0 GCACCTTCAA 0.83114 -96 AAGTGGGTGAGTACCTTTATATGTTCTCGG 9 181 0 GTACCTTTAT 0.92997 -89 AAGGCTTTTAGTGCCTTTCAT 10 2 0 GTGCCTTTCA 0.782375 -48 TAAATCACCTTTATTAAATTGAAA 10 36 0 TCACCTTTAT 0.900226 -14 ********** Masking position 5 Map Score: 1.64347 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 331 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 AGGTCAGACAGAGTGTTGAGTTCCTGAGGA 2 13 1 GAGTGTTGAG 0.92502 -183 TCCGCTGGAGGGGTGCTGGTTTTCCAGGGA 2 110 1 GGGTGCTGGT 0.985331 -86 ACCTCCCGTGAGTGCTGGTTGAG 4 5 0 GAGTGCTGGT 0.993338 -19 GTATATCCACGAGTGCTTGGAGGGTGAGAA 8 84 0 GAGTGCTTGG 0.984705 -123 CTCGTGGATATACTGCTGGGTTGAAGGTGC 8 101 1 TACTGCTGGG 0.948143 -106 ********** Masking position 4 Map Score: 1.88729 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 106 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 TTTAGATGCTGCACCGGTCAGTATAGAATC 1 118 1 GCACCGGTCA 0.951762 -114 AATATTGTTGCCATAGGTTACCTATAATCC 1 197 1 CCATAGGTTA 0.954847 -35 GTGTATGGCTGCATCTGTTAAAGGGGTCTT 3 30 0 GCATCTGTTA 0.935595 -35 TTTTTCTGAGCCATCGGTTGGTTCATGGGG 8 130 0 CCATCGGTTG 0.977553 -77 TTTCTACCATCCATCGGTAATTACACCAAT 9 244 0 CCATCGGTAA 0.977468 -26 ********** Masking position 3 Map Score: 0.441468 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 59 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 ********** No masking Map Score: 3.35619e-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 12 ********** No masking Map Score: 3.35619e-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 13 ********** No masking Map Score: 3.35619e-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