AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_mthe_reg_100.orf -o199_mthe_100.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 Purged sequences: RTH00858 16 M.thermo RTH00618 16 M.thermo RTH01420 17 M.thermo RTH01010 21 M.thermo RTH01561 41 M.thermo Input sequences: #1 RTH01790 170 M.thermo #2 RTH00571 19 M.thermo #3 RTH02039 22 M.thermo #4 RTH00851 46 M.thermo #5 RTH00189 109 M.thermo #6 RTH00952 236 M.thermo #7 RTH00723 62 M.thermo #8 RTH01329 300 M.thermo #9 RTH01081 40 M.thermo #10 RTH00257 22 M.thermo #11 RTH00964 38 M.thermo #12 RTH00179 113 M.thermo #13 RTH00330 34 M.thermo #14 RTH01858 70 M.thermo #15 RTH00707 98 M.thermo #16 RTH01259 73 M.thermo #17 RTH00422 120 M.thermo #18 RTH00483 26 M.thermo #19 RTH01562 52 M.thermo #20 RTH00987 33 M.thermo #21 RTH00617 300 M.thermo Motif number 1 CCCCTTAAAAAGTTTTTTCGCTGGACTGGAAAATATGCCC 5 24 0 AGTCGCTGGA 0.983773 -86 TACAGTTATATGATACATCCTGTGCCGGGATAGCCTAGCC 6 49 1 TGACGCGGGA 0.993042 -188 TAGCCTAGCCAGGTAAGGCGCAAGACTGGAAATCTTGTGG 6 79 1 AGACGCTGGA 0.988859 -158 GCAACAGGGTTGCTTTAACCGACGCCGGGACTGGGATTTG 6 139 0 TGTCGCGGGA 0.989846 -98 CTCCAGTAAGAGTGAATTCGCGGGACGGGGGTTTGCGAAT 6 199 0 AGACGCGGGG 0.997272 -38 AGGATCACCTGGTGTGGAGATAAGAGAAAC 7 43 0 AGTCGGGAGA 0.89122 -20 ACGGGCCCTCAGGAAACGCCCTGGCCGGGAATTGAACCCG 8 163 0 AGACGCGGGA 0.998056 -138 CCGTAAAATTAGATAGCGGGCCCGACGGGAATTGAACCCG 8 245 0 AGAGGCGGGA 0.985182 -56 AGATTTATAAAGGTTTTCCTTGAGTGGGGGTGTGTGGAAG 17 15 0 AGTCGGGGGG 0.985244 -106 CCCTGAGCGGAGGGATGACCATTGCCGGGGGTCTCAGGGT 21 152 0 AGACGCGGGG 0.997272 -149 ** * * * ***** Masking position 14 Map Score: 19.144 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 42 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 TGTAAGGAGGTAAAGTTAA 2 1 1 TTAAGGAGGT 0.95445 -19 AAATAACCAGGAGGATATTCGG 3 5 1 ACCAGGAGGA 0.958613 -18 AAATGCTGAATACAAGGAGGTTTCTTGA 5 92 1 TCAAGGAGGT 0.965659 -18 TGGGATTTGAACCCAGGAGGAGCAAAGCTCC 6 117 0 ACCAGGAGGA 0.95861 -120 GAATTCACTCTTACTGGAGGTTAATGA 6 220 1 TACTGGAGGT 0.910261 -17 TGGAAAAGTATATAAGCAGGTAACTAGAGAA 8 56 1 TTAAGCAGGT 0.856598 -245 TGTAGGGGCTATCATGCGGGCCTGTCGAGCC 8 125 1 ACATGCGGGC 0.610283 -176 GGTGACTTTTTATCTGGAGGACTGAATT 8 283 1 TTCTGGAGGA 0.958296 -18 TTTAAGATCAACACTGCAGGATCATTTCATC 9 13 1 AACTGCAGGA 0.662147 -28 TAAACCATCATATATGGAGGTATATT 12 98 1 TTATGGAGGT 0.940866 -16 CTTCCCTTTTTTACAGGAGGATTTAA 13 19 1 TACAGGAGGA 0.940738 -16 CTTGTTTACATTTATGGGGGATCATTAATTA 15 60 0 TTATGGGGGA 0.896916 -39 GATAATACTATGCAAGGGGGCAGTAT 16 6 0 TCAAGGGGGC 0.926921 -68 TTAAAAAAAGATTAAGGAGGCGAATAGC 21 283 1 ATAAGGAGGC 0.921347 -18 * ********* Masking position 6 Map Score: 12.905 Number of sites scoring better than the average of aligned sites = 1436 Number in coding regions = 1328 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 3 TTCAATCCCTTTCTATTATT 4 37 0 TTCAATCCCT 0.79999 -10 AATATGCCCCTTCCAGTCCTCC 5 3 0 TTCCAGTCCT 0.981907 -107 GGGGCATATTTTCCAGTCCAGCGAAAAAAC 5 23 1 TTCCAGTCCA 0.930502 -87 TCCACAAGATTTCCAGTCTTGCGCCTTACC 6 90 0 TTCCAGTCTT 0.841784 -147 TCCTCCTGGGTTCAAATCCCAGTCCCGGCG 6 127 1 TTCAAATCCC 0.949907 -110 TTATATACTTTTCCATTCCTATATGACATG 8 41 0 TTCCATTCCT 0.978233 -260 GCGACTCGGGTTCAATTCCCGGCCAGGGCG 8 157 1 TTCAATTCCC 0.961077 -144 TGGTCGCGGGTTCAATTCCCGTCGGGCCCG 8 239 1 TTCAATTCCC 0.961077 -62 CCATCACTCATCCCAATCCTAGCCCTTGTT 17 71 1 TCCCAATCCT 0.878017 -50 CTTTTTTTAATTCCAATCACTATATCAAAC 21 263 0 TTCCAATCAC 0.8133 -38 ********** Masking position 5 Map Score: 11.2956 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 122 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 GTATCAGAGCATACAATGTGAGCGGATCCACCGCAGA 1 68 0 ATAATGGGAT 0.964437 -103 CTATTAATATCTGTCCGGATTTATTTATAA 1 151 0 TTATTGGGAT 0.758606 -20 TTCAATCCCTTTCTATTATTCACTGATATGAATCTGT 4 20 0 TTCATTTGAT 0.737625 -27 ACCTCCTTGTATTCAGCATTTGCTGATAAACCCGAAA 5 76 0 ATTATTTGAT 0.654588 -34 AGATGTCATAATATACAGTTATATGATACATCCTGTG 6 36 1 ATAATTTGAT 0.937222 -201 ATTAGATGATGAAATGATCCTGCAGTGT 9 23 0 TTAATGTGAT 0.970573 -18 TAATTATTATTTATAAGGTGTGCTGATGAACTGAAGG 14 43 1 TTAATGTGAT 0.970574 -28 AGCTTCTTGTTTACATTTATGGGGGATCATTAATTAA 15 59 0 TTAAATGGAT 0.813667 -40 TTTTTTAACTATATAAATAGCGGGGATAAACC 17 99 1 ATAAAGGGAT 0.906076 -22 CCCATAAAAAATAAAATTTGAGGTGATCAT 19 33 1 ATAATGTGAT 0.97055 -20 TTCATATAATATAAAGGTTGAAGTGATTATTACTAAT 21 225 0 ATAATGTGAT 0.97055 -76 AACCTTTATATTATATGAATGTTTGATATAGTGATTG 21 243 1 TTAAATTGAT 0.841439 -58 *** * ** **** Masking position 16 Map Score: 7.69626 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 40 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 GTCCGGATTTATTTATAAATATTTCCACAAT 1 138 0 ATTATAAATA 0.71491 -33 ATTATGACATCTATTTAAGTATTGCTGCCGT 6 17 0 CTTTTAAGTA 0.782759 -220 TAAAAAGTCACCGTAAAATTAGATAGCGGGC 8 264 0 CCTAAAATTA 0.797239 -37 TTCCTATATTCTTTTTAATTATATAAGTTTA 12 17 0 CTTTTAATTA 0.842634 -97 CAATAAATTTCTCTATAATTATTATTTATAA 14 28 1 CTTATAATTA 0.943435 -43 CATCAGCACACCTTATAAATAATAATTATAG 14 40 0 CCTATAAATA 0.935706 -31 TAATGATCCCCCATAAATGTAAACAAGAAGC 15 64 1 CCTAAATGTA 0.550535 -35 GTATTATCTACTGTATATATAACTCCTTATT 16 29 1 CTTATATATA 0.901723 -45 TCCTGTTCTGCTATTTATTTAAATAAGGAGT 16 50 0 CTTTTATTTA 0.712552 -24 CAAGGAAAACCTTTATAAATCTTGAAGGATA 17 33 1 CTTATAAATC 0.757636 -88 TGTTTTTTAACTATATAAATAGCGGGGATAA 17 97 1 CTTATAAATA 0.951968 -24 TATATAGATTCCATAAAATTAAAAACATCAT 21 24 0 CCTAAAATTA 0.797239 -277 ATTTTATGGAATCTATATATAAACTTTGTGC 21 36 1 ATTATATATA 0.537231 -265 ** ******** Masking position 7 Map Score: 4.87485 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 41 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 6 CAGACTGGGCAAGTAAAACCACAGACCACA 1 107 0 AAGTAAAACC 0.881822 -64 AAACTTTTTAAGGGGATACCTGAAATTTTT 5 49 1 AGGGGATACC 0.981824 -61 GTGTGGAGATAAGAGAAACCTGTAGTTAGA 7 32 0 AAGAGAAACC 0.900108 -31 AATGGATTTAAGGGAATAACAAAAAGGAGA 11 12 1 AGGGAATAAC 0.852989 -27 AACAAAAAGGAGAGAATACC 11 29 1 AGAGAATACC 0.852989 -10 ACCCCCACTCAAGGAAAACCTTTATAAATC 17 24 1 AAGGAAAACC 0.979689 -97 ACCACAATATAAGGGAAACCGAAGATTAGT 21 201 1 AAGGGAAACC 0.983121 -100 ********** Masking position 6 Map Score: 3.94575 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 234 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 GCAAGTAAAACCACAGACCACATCGTATCAG 1 98 0 CCCAGACCAC 0.992936 -73 TATGAAGAATTCGCAAACCCCCGTCCCGCGA 6 191 1 TCCAAACCCC 0.895902 -46 GCATGATAGCCCCTACACCACCAGGGCAAGT 8 111 0 CCTACACCAC 0.960457 -190 GGGAATTGAACCCGCGACCACTTGGTTAAAA 8 228 0 CCGCGACCAC 0.972441 -73 TATTCTTCCACACACCCCCACTCAAGGA 17 8 1 CCCACACCCC 0.993453 -113 CATTATACACCCTGAGACCCCCGGCAATGGT 21 144 1 CCGAGACCCC 0.993453 -157 ** ******** Masking position 7 Map Score: 3.88764 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 114 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 8 TTCAATCCCTTTCTATTATTCACTGATA 4 29 0 CCTTTTATTA 0.939575 -18 CTTTTCCATTCCTATATGACATGCATGCTAT 8 33 0 CCTATTGACA 0.934461 -268 GGTATTCTCTCCTTTTTGTTATTCCCTTAAA 11 18 0 CCTTTTGTTA 0.949437 -21 CCACCTCTTCCCTTTTTTACAGGAGGATTTA 13 13 1 CCTTTTTACA 0.852007 -22 AAGCCTATATATCTCATCAATAAA 14 4 1 CCTATTATCT 0.733699 -67 AAGACATGGACCTTTTTAATAAATGGTGGGG 21 85 1 CCTTTTAATA 0.92273 -216 TAATCCTCCGCCTATCTGGCACATCCCCACC 21 109 0 CCTATTGGCA 0.893203 -192 ATCACTTCAACCTTTATATTATATGAATGTT 21 235 1 CCTTTTATTA 0.939575 -66 ***** ***** Masking position 5 Map Score: 1.36425 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 72 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 GATCCGCTCACATTGTATGCTCTGATACGATGTGG 1 77 1 CTGATGCTTA 0.887538 -94 CGTAGGTGCAACAGGGTTGCTTTAACCGACGCCGG 6 151 0 AGGTTGCTTA 0.976134 -86 TTCCTATATGACATGCATGCTATGAGTTACATTTT 8 21 0 ATGATGCTTA 0.962474 -280 ACTAGAGAACAATGGAATGCTCTCATTCTAGAGAC 8 78 1 AGGATGCTTA 0.989476 -223 AGTCTGGCAGAGCGCTTGGCTTTTAACCAAGTGGT 8 208 1 AGCTGGCTTA 0.841047 -93 TTTTCCACCGGGAGGCTGTTAA 10 7 1 AGGAGGCTTA 0.98444 -16 GATCCAGCAAATGGGCATGCTGTTTGTCTAAGGTA 12 50 0 AGGATGCTTT 0.951265 -64 * ** ***** * * Masking position 11 Map Score: 1.12632 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 51 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 CAATCTGCGGTGGATCCGCTCACATTGTAT 1 65 1 TGGATCCGCT 0.850377 -106 GACTGGGATTTGAACCCAGGAGGAGCAAAG 6 121 0 TGAACCCAGG 0.827109 -116 GAAGAATTCGCAAACCCCCGTCCCGCGAAT 6 194 1 CAAACCCCCG 0.801468 -43 CCAGTAAGAGTGAATTCGCGGGACGGGGGT 6 207 0 TGAATTCGCG 0.830513 -30 GCGGGCCTGTCGAGCCCGCGACTCGGGTTC 8 140 1 CGAGCCCGCG 0.990567 -161 GGCCGGGAATTGAACCCGAGTCGCGGGCTC 8 151 0 TGAACCCGAG 0.961367 -150 CGACGGGAATTGAACCCGCGACCACTTGGT 8 233 0 TGAACCCGCG 0.994815 -68 CAATTCCCGTCGGGCCCGCTATCTAATTTT 8 251 1 CGGGCCCGCT 0.93235 -50 ********** Masking position 7 Map Score: 1.80511 Number of sites scoring better than the average of aligned sites = 191 Number in coding regions = 160 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 ********** No masking Map Score: -3.03159e-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: -3.03159e-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: -3.03159e-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