AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_mixed_mthe_reg_100.orf -o293_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 Input sequences: #1 RTH01746 83 M.thermo #2 RTH00902 142 M.thermo #3 RTH00250 30 M.thermo #4 RTH00057 21 M.thermo #5 RTH01659 205 M.thermo #6 RTH00097 230 M.thermo Motif number 1 GAAAAATCACCTTCCGGTAATTAACAATTTTT 1 62 0 AATCCGAATT 0.807369 -22 CAGATGATTCAAGTTAGTTACCATCATTTCCTGGAGGTA 2 15 0 AATCCAATTT 0.968473 -128 AACTAACTTGAATCATCTGACCTAAAGGTTTATACAGAC 2 35 1 AACCCTAGGT 0.880491 -108 TTCTGAGATATATCACAGTATCAGAATTTGTTTCTGAAG 2 104 1 TACTCAATTT 0.934238 -39 GATTAACCCACCTTCCTAGATTTATGATCT 3 8 0 AACCCTATTT 0.987642 -23 CAGCACCCCAAACCACCATGTCAAGATTTAAATACTCCC 5 45 1 AACTCAATTT 0.968464 -161 ATTCATATTTAACTGGTTAACCATGATTTAGAGTTACAT 5 119 0 AATCCAATTT 0.930123 -87 CAGCTGGATTTAACATAAATTCAAAAAATTCATATTTAA 5 146 0 TACTCAAAAT 0.652707 -60 CAAACTCCTTAAACCCATACCCATCATTTAACC 6 5 0 AACCCAATTT 0.992508 -226 TTTGTAGGATAACCTGCCCACCATAATTTCATTCCATTT 6 40 1 AACCCAATTT 0.993542 -191 GGGAACATGTTATCTCTGTTCCTTTAATTAGTTTTTTCA 6 95 0 TACCCTAATT 0.956066 -136 TAAAGTTAGTTATCTCTATTCCTTTAATTAGTTTTTCCG 6 150 0 TACCCTAATT 0.956239 -81 ACTAACTTTAAAGCATACATCCAGCAGATGTCTTAAAAT 6 179 1 AACCCAAGAT 0.94415 -52 ** * *** **** Masking position 16 Map Score: 16.2859 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 115 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 TCAAGTTAGTTACCATCATTTCCTGGAGGTATTC 2 12 0 TCATCATCCT 0.919662 -131 AAGATTTAAATACTCCCTTATCCTATTATAGAGT 5 67 1 TTCCCTTCCT 0.995334 -139 GGGCAGGTTATCCTACAAACTCCTTAAACCCATA 6 25 0 TTACAATCCT 0.853531 -206 TTTCATTCCATTTTATCTTCTCCTCTAAATGAAA 6 66 1 TTATCTTCCT 0.988442 -165 AGGGAACATGTTATCTCTGTTCCTTTAATTAGTT 6 101 0 TTCTCTTCCT 0.99437 -130 AGAGATAACATGTTCCCTTCTCCATCCAGATCCC 6 117 1 TTCCCTTCCA 0.977916 -114 TTAAAGTTAGTTATCTCTATTCCTTTAATTAGTT 6 156 0 TTCTCTTCCT 0.99437 -75 * ***** **** Masking position 11 Map Score: 7.74072 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 108 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 3 GATAACTCTATTAATTCTAATTATAAAATT 1 27 0 TTAATTCTAA 0.659582 -57 ATTAATAGAGTTATCTATATAAAAATTGTT 1 42 1 TTATCTATAT 0.882657 -42 AATTGTGCAGTTGTCTGTATAAACCTTTAG 2 56 0 TTGTCTGTAT 0.861445 -87 ACTGCACAATTTATCTATGATGACCTTGTT 2 75 1 TTATCTATGA 0.922546 -68 TATGATGACCTTGTTTCTGAGATATATCAC 2 90 1 TTGTTTCTGA 0.943858 -53 GTATCAGAATTTGTTTCTGAAGAACAGGTG 2 121 1 TTGTTTCTGA 0.943858 -22 AGGGAACATGTTATCTCTGTTCCTTTAATT 6 105 0 TTATCTCTGT 0.977718 -126 TTAAAGTTAGTTATCTCTATTCCTTTAATT 6 160 0 TTATCTCTAT 0.965098 -71 ********** Masking position 6 Map Score: 6.17916 Number of sites scoring better than the average of aligned sites = 190 Number in coding regions = 165 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 4 GAAAAATCACCTTCCGGTAATTA 1 71 0 AAATCACCTT 0.990859 -13 GATTAACCCACCTTCCTAGATTTA 3 17 0 AACCCACCTT 0.992145 -14 ACAGCACCCCAAACCACCATGTCAAGATTT 5 44 1 AAACCACCAT 0.972662 -162 TATATCACCTTAATCTTTAAC 5 195 0 ATATCACCTT 0.970553 -11 CTCAACTCTCCTTGATGTGCTTG 6 218 0 AACTCTCCTT 0.97266 -13 ********** Masking position 1 Map Score: 5.89312 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 9 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 5 GAAAAATCACCTTCCGGTAATTAACAA 1 67 0 CACCTTCCGG 0.880609 -17 GGAATACCTCCAGGAAATGATGGT 2 5 1 TACCTCCAGG 0.9898 -138 AGATCATAAATCTAGGAAGGTGGGTT 3 7 1 TAAATCTAGG 0.750307 -24 CATGAATATGAACAGCCAGTTATGCGGG 5 9 0 AACAGCCAGT 0.826634 -197 GAGTTACATACACCGCCAGTATGGAATACT 5 98 0 CACCGCCAGT 0.953541 -108 GAATTTATGTTAAATCCAGCTGTTTTTACG 5 163 1 TAAATCCAGC 0.919059 -43 CTTCTCCATCCAGATCCCGGAAAAACTAAT 6 133 1 CAGATCCCGG 0.946049 -98 CTTTAAAGCATACATCCAGCAGATGTCTTA 6 184 1 TACATCCAGC 0.980254 -47 TAAAATCAAGCACATCAAGGAGAGTTGAG 6 212 1 CACATCAAGG 0.954209 -19 ********** Masking position 2 Map Score: 5.18812 Number of sites scoring better than the average of aligned sites = 1255 Number in coding regions = 1174 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 GAAAAATCACCTTCCGGTAATTAACA 1 68 0 ATCACCTTCG 0.944543 -16 ACTAACTTGAATCATCTGACCTAAAGGTTTA 2 36 1 ATCATCTGCC 0.983598 -107 ATCACCTGTTCTTCAGAAACA 2 132 0 ATCACCTGTC 0.992852 -11 AGTTTGTAGGATAACCTGCCCACCATAATTT 6 38 1 ATAACCTGCC 0.992852 -193 AGGAACAGAGATAACATGTTCCCTTCTCCAT 6 111 1 ATAACATGTC 0.921954 -120 ******** ** Masking position 7 Map Score: 1.88103 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 147 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 TCACCTTCCGGTAATTAACAATTTTTATAT 1 58 0 GTAATTAACA 0.923437 -26 GGAAATGATGGTAACTAACTTGAATCATCT 2 23 1 GTAACTAACT 0.981404 -120 GGATAAGGGAGTATTTAAATCTTGACATGG 5 60 0 GTATTTAAAT 0.88322 -146 TACTGGCGGTGTATGTAACTCTAAATCATG 5 107 1 GTATGTAACT 0.966304 -99 CAAAAAATTCATATTTAACTGGTTAACCAT 5 134 0 ATATTTAACT 0.94292 -72 AGGAATAGAGATAACTAACTTTAAAGCATA 6 166 1 ATAACTAACT 0.946902 -65 ********** Masking position 6 Map Score: 4.01853 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 13 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 8 ********** No masking Map Score: -1.80235e-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: -1.80235e-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: -1.80235e-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