AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i033_Pyruvate_Synthase_1_mjan_reg_100.orf -o033_mjan_100.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ04092 288 M_jannaschii_chromosome #2 RMJ11171 119 M_jannaschii_chromosome #3 RMJ01908 43 M_jannaschii_chromosome #4 RMJ08206 98 M_jannaschii_chromosome #5 RMJ10471 175 M_jannaschii_chromosome #6 RMJ10373 276 M_jannaschii_chromosome Motif number 1 AATTTAGAAGCCCAAAGGGCTTCTATATGT 1 67 1 CCCAAAGGGC 0.980687 -222 TTATTCAGAAACCATAGGGCTTCGCCCTAT 4 25 1 ACCATAGGGC 0.986021 -74 CCTGGGTATCCCAATAGGGCGAAGCCCTAT 4 38 0 CCAATAGGGC 0.996913 -61 CTACATTGTATCCATAGGGGAAACCCCCTA 5 20 1 TCCATAGGGG 0.941635 -156 AAGGTTCATCCCAATAGGGGGTTTCCCCTA 5 34 0 CCAATAGGGG 0.992028 -142 GGGGAGTATCCCAATAGAGGGGCGAAGCCC 5 132 1 CCAATAGAGG 0.986885 -44 CTGTATAAGACCCATAGAGGGGCTTCGCCC 5 151 0 CCCATAGAGG 0.980803 -25 AATAGGTATCCCAATAGGGCGAAGCTATGG 6 69 0 CCAATAGGGC 0.996913 -208 TCGTTTGATTAAAATAGGGCTTAACTCTAT 6 208 1 AAAATAGGGC 0.919458 -69 ATGGATACCCCAAATAGAGATAGAGTTAAG 6 227 0 CAAATAGAGA 0.716762 -50 ********** Masking position 6 Map Score: 24.5689 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 43 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 2 ATGTGCCTTATTTAATTAAAAACTTTGATAA 1 93 1 TTTATTAAAA 0.841399 -196 AACGCTTCGGTTTCATCAAAACTCGTCCATT 1 131 0 TTTATCAAAA 0.975812 -158 TTTAGTAAAAGTTGAACAAAAACTCTTCGAG 1 180 0 GTTAACAAAA 0.881468 -109 TTTGTTCAACTTTTACTAAAAGTTTCTTTTA 1 191 1 TTTACTAAAA 0.607887 -98 GAAATACTATTTCATAAAAAGTCATAATAG 3 10 1 TTTATAAAAA 0.882357 -34 TTGGTGAAGCTTTTACTAAAAGGTTCATCCC 5 52 0 TTTACTAAAA 0.607887 -124 TTAGTAAAAGCTTCACCAAAACCTAACACCT 5 64 1 CTTACCAAAA 0.93569 -112 GCTATGGTGCGTTGATCAAAACAGATGCATT 6 45 0 GTTATCAAAA 0.972854 -232 TTTAGAAAAGGTTGATCAAAACTTAGTTAAA 6 97 0 GTTATCAAAA 0.972854 -180 TCGAGTAACCTTTTACTAAAAGGTTGGGAGC 6 135 1 TTTACTAAAA 0.607887 -142 GATGAGTTCGTTTGATTAAAATAGGGCTTAA 6 201 1 TTTATTAAAA 0.841399 -76 *** ******* Masking position 5 Map Score: 20.972 Number of sites scoring better than the average of aligned sites = 355 Number in coding regions = 212 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 3 TACTATGGAATTTAGAAGCCCAAAGGGCTTC 1 59 1 TTTGAAGCCC 0.865682 -230 ATAAGGCACATATAGAAGCCCTTTGGGCTTC 1 73 0 TATGAAGCCC 0.91174 -216 CTCTTCGAGTTTTTGTAGCCCGAAGCTAACG 1 158 0 TTTGTAGCCC 0.894616 -131 TATCCCAATAGGGCGAAGCCCTATGGTTTCT 4 31 0 GGGGAAGCCC 0.684354 -68 GCAATGCATCCTGGGTATCCCAATAGGGCGA 4 46 0 CTGGTATCCC 0.905784 -53 TGAAAAGCTACATTGTATCCATAGGGGAAAC 5 13 1 CATGTATCCA 0.586086 -163 CATCCCAATAGGGGGTTTCCCCTATGGATAC 5 27 0 GGGGTTTCCC 0.913626 -149 GTAAGATTTGGGGAGTATCCCAATAGAGGGG 5 123 1 GGGGTATCCC 0.837253 -53 CCCAATAGAGGGGCGAAGCCCCTCTATGGGT 5 141 1 GGGGAAGCCC 0.684354 -35 AGGCATTACCGAGCGTAGCGAGGTAATGCAT 6 21 1 GAGGTAGCGA 0.848836 -256 TATCCCAATAGGGCGAAGCTATGGTGCGTTG 6 62 0 GGGGAAGCTA 0.754091 -215 AGCAATGTTTGAGCTTAGCCATGCGGTAGTT 6 163 1 GAGTTAGCCA 0.645408 -114 AATAGAGATAGAGTTAAGCCCTATTTTAATC 6 214 0 GAGTAAGCCC 0.893324 -63 TATCTCTATTTGGGGTATCCATTATAAATTA 6 235 1 TGGGTATCCA 0.924708 -42 *** ******* Masking position 9 Map Score: 17.2765 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 105 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 CCCAACTTATAACCAATTATCAAAGGATAT 1 25 1 AACCAATTAT 0.948332 -264 TCGTCCATTTAACCAATTATCAAAGTTTTT 1 110 0 AACCAATTAT 0.948332 -179 GTTTTAAAAGAAACTTTTAGTAAAAGTTGA 1 196 0 AAACTTTTAG 0.968704 -93 CTTTCAATGCAAACTATTATGACTTTTTAT 3 24 0 AAACTATTAT 0.920042 -20 TATTGGGATGAACCTTTTAGTAAAAGCTTC 5 48 1 AACCTTTTAG 0.991264 -128 TTACTCGAACAACCTTTTAGAAAAGGTTGA 6 113 0 AACCTTTTAG 0.991264 -164 CATTGCTCCCAACCTTTTAGTAAAAGGTTA 6 140 0 AACCTTTTAG 0.991264 -137 ********** Masking position 2 Map Score: 11.7578 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 51 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TGTAGCCCGAAGCTAACGCTTCGGTTTCATCA 1 144 0 AGCAACGCTC 0.991337 -145 ATAAATTAGCCCATGCTTCTATTTTTTTA 2 8 1 AGCCATGCTC 0.97834 -112 TTCTTTGCAGAAGCAATGCATCCTGGGTATCC 4 57 0 AAGAATGCTC 0.988666 -42 TTCTGCAAAGAAGCAATGCCTCTTAAAATTTA 4 77 1 AAGAATGCTC 0.988618 -22 TGAACCTTTTAGTAAAAGCTTCACCAAAACCT 5 56 1 AGTAAAGCTC 0.913494 -120 TCGCTACGCTCGGTAATGCCTCTTAGCATAG 6 10 0 CGGAATGCTC 0.983422 -267 GAGCGTAGCGAGGTAATGCATCTGTTTTGATC 6 31 1 AGGAATGCTC 0.995543 -246 ATTTTAATCAAACGAACTCATCTCCTCATAAC 6 191 0 AACAACTCTC 0.833143 -86 *** ***** ** Masking position 6 Map Score: 9.87685 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 64 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 AAGAGTGTTATAACACATCAAAAACTACTT 1 257 1 TAACACATCA 0.880791 -32 TATTATCCCTCCAAGTAGTTTT 1 277 0 TTATCCCTCC 0.906682 -12 TAAACCCCCTCCTTCTAAGCTA 2 108 0 AACCCCCTCC 0.959947 -12 CACCAAAACCTAACACCTCCTCGCTTACGC 5 77 1 TAACACCTCC 0.992975 -99 TCTTACTAATTTACACCTCCGAGCGTAAGC 5 99 0 TTACACCTCC 0.986972 -77 TTTACCACCTCAAATAATTTTT 6 265 0 TACCACCTCA 0.975367 -12 ********** Masking position 8 Map Score: 4.22609 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 95 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 CAACTTATAACCAATTATCAAAGGATATTATTT 1 27 1 CCTTACAAAG 0.995186 -262 GTCCATTTAACCAATTATCAAAGTTTTTAATTA 1 105 0 CCTTACAAAG 0.995186 -184 TTGGGATGAACCTTTTAGTAAAAGCTTCACCAA 5 50 1 CCTTATAAAA 0.950144 -126 CTCGGTAATGCCTCTTAGCATAG 6 1 0 CCTTACATAG 0.977232 -276 ATTGGGATACCTATTTAACTAAGTTTTGATCAA 6 84 1 CTTTACTAAG 0.846116 -193 ACTCGAACAACCTTTTAGAAAAGGTTGATCAAA 6 108 0 CCTTAAAAAG 0.974999 -169 TTGCTCCCAACCTTTTAGTAAAAGGTTACTCGA 6 135 0 CCTTATAAAA 0.950144 -142 ** *** ***** Masking position 7 Map Score: 7.39915 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 52 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 CTTATTTAATTAAAAACTTTGATAATTGGT 1 99 1 TAAAAACTTT 0.86852 -190 TTCGGTTTCATCAAAACTCGTCCATTTAAC 1 127 0 TCAAAACTCG 0.947475 -162 CTTCGGGCTACAAAAACTCGAAGAGTTTTT 1 164 1 CAAAAACTCG 0.956939 -125 AAAAGTTGAACAAAAACTCTTCGAGTTTTT 1 175 0 CAAAAACTCT 0.953676 -114 ATTCCAGATTAAAAAACTCTGTGGTTTTAA 1 219 0 AAAAAACTCT 0.797776 -70 TACTATTTCATAAAAAGTCATAATAGTTTG 3 15 1 TAAAAAGTCA 0.710618 -29 AAAAGCTTCACCAAAACCTAACACCTCCTC 5 69 1 CCAAAACCTA 0.804084 -107 GGGATACTCCCCAAATCTTACTAATTTACA 5 114 0 CCAAATCTTA 0.734643 -62 AAAAGGTTGATCAAAACTTAGTTAAATAGG 6 93 0 TCAAAACTTA 0.91718 -184 ********** Masking position 5 Map Score: 3.35163 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 440 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 GCCCTTTGGGCTTCTAAATTCCATAGTAAA 1 57 0 CTTCTAAATT 0.955435 -232 GCCCAAAGGGCTTCTATATGTGCCTTATTT 1 76 1 CTTCTATATG 0.968834 -213 TTAGCCCATGCTTCTATTTTTTTAAATTGT 2 16 1 CTTCTATTTT 0.955463 -104 TTGTTATTTTCTTCTCTATTATATTATAGT 2 42 1 CTTCTCTATT 0.969508 -78 ********** Masking position 5 Map Score: 0.584222 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 34 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ********** No masking Map Score: 2.17669e-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: 2.17669e-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: 2.17669e-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