AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00730_mthe_reg_300.orf -o00730_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 Purged sequences: MTH1576 23 thiamine biosynthesis protein Input sequences: #1 MTH1543 229 thiamine biosynthesis protein #2 MTH1544 219 ribokinase #3 MTH1545 63 conserved protein #4 MTH1621 83 GTP-binding protein, GTP1/OBG family Motif number 1 TGTCAGAGTCTGGGGGGGCCCCA 1 4 0 TGGGGGGGCC 0.997079 -226 TCTCCCCTAGTTGAGGGGCCACGGCTTGCT 1 60 0 TTGAGGGGCC 0.981618 -170 TTTTTATAACTGGATGGAACCAATCAATAT 1 134 1 TGGATGGAAC 0.990564 -96 ATCACCCTTCTGGTTTGACCCTTAACCCGT 1 207 0 TGGTTTGACC 0.931909 -23 TCAAATTTCATGCAGGGAACTGATCCCATA 2 37 0 TGCAGGGAAC 0.960584 -183 CATCCTTTATTGGGTGGGACTTTATACTTT 2 103 0 TGGGTGGGAC 0.994467 -117 TCGTTATAGATGGATTGGGCCTGGTTCTGT 2 137 0 TGGATTGGGC 0.971983 -83 ********** Masking position 1 Map Score: 8.58201 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 402 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 GGGTATGATCTGGATCAGCGGAAATGAGATATA 1 172 0 TGATCACGAA 0.979457 -58 GCATGAAAACCCGCTGAAAAACCATTTA 2 6 1 AAACCCCGAA 0.97707 -214 ACATTTTATAAAAATCACCTTAATCCGCCTCAA 2 72 1 AAATCACTAA 0.937858 -148 CCAATAAAGGATGCTCAACAGAACCAGGCCCAA 2 120 1 AGCTCACGAA 0.986624 -100 ATTATAAACCAACCCCAACAGAATTAACCCCAT 2 180 1 ACCCCACGAA 0.939689 -40 ATGATCACCTGAAAAATATGGGG 2 207 0 AGATCACGAA 0.993417 -13 TCAGGGTTTCATAATCAACCGGACCATATTCCA 3 22 0 AAATCACGGA 0.976128 -42 TATGAAACCCTGAAACCACAGAAACACCATAG 3 42 1 TAAACCCGAA 0.831558 -22 AAAATCACCTGCATATAATATGA 4 1 1 AAATCACGCA 0.976128 -83 * ***** * *** Masking position 13 Map Score: 8.17462 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 143 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 3 ATCCAGTTATAAAAACTACTGTTTCAGTCCC 1 118 0 AAAAACTACG 0.658464 -112 ACCAATCAATATGATATCCATATATCTCATT 1 152 1 ATGATATCCT 0.696593 -78 GTAATCACCCTTCTGGTTTGA 1 219 0 GTAATCACCT 0.902058 -11 GCATGAAAACCCGCTGAAAAACC 2 3 1 ATGAAAACCG 0.897708 -217 ACATTTTATAAAAATCACCTTAATCCGCCTC 2 72 1 AAAATCACCT 0.958611 -148 CCAATAAAGGATGCTCAACAGAACCAGGCCC 2 120 1 ATGCTCAACG 0.868348 -100 ATGATCACCTGAAAAATATGG 2 209 0 ATGATCACCG 0.991143 -11 TCAGGGTTTCATAATCAACCGGACCATATTC 3 24 0 ATAATCAACG 0.966887 -40 CTGAAACCACAGAAACACCATAG 3 51 1 AGAAACACCT 0.860197 -13 AAAATCACCTGCATATAATAT 4 1 1 AAAATCACCG 0.981912 -83 ********* * Masking position 9 Map Score: 6.96146 Number of sites scoring better than the average of aligned sites = 822 Number in coding regions = 729 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 TGGGGCCCCCCCAGACTCTGAC 1 3 1 GGGCCCCCCC 0.995297 -227 CCTAGTTGAGGGGCCACGGCTTGCTGCCTG 1 55 0 GGGCCACGGC 0.966134 -175 CATATTGATTGGTTCCATCCAGTTATAAAA 1 135 0 GGTTCCATCC 0.981157 -95 CACGGGTTAAGGGTCAAACCAGAAGGGTGA 1 206 1 GGGTCAAACC 0.884051 -24 TTATGGGATCAGTTCCCTGCATGAAATTTG 2 36 1 AGTTCCCTGC 0.894061 -184 CAAAGTATAAAGTCCCACCCAATAAAGGAT 2 102 1 AGTCCCACCC 0.973549 -118 AACAGAACCAGGCCCAATCCATCTATAACG 2 136 1 GGCCCAATCC 0.972408 -84 ********** Masking position 5 Map Score: 4.47049 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 767 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 CAAGCCGTGGCCCCTCAACTAGGGGAGACA 1 62 1 CCCCTCAACT 0.93194 -168 TTCTGGTTTGACCCTTAACCCGTGAGGGTA 1 200 0 ACCCTTAACC 0.98925 -30 AGGGAACTGATCCCATAAATGGTTTTTCAG 2 24 0 TCCCATAAAT 0.930782 -196 CATATTCCAGGCCCTTTACC 3 1 0 GCCCTTTACC 0.941374 -63 TGATTATGAAACCCTGAAACCACAGAAACA 3 38 1 ACCCTGAAAC 0.942167 -26 ATATTTTATATCCCATAACCTTCATATTAT 4 25 0 TCCCATAACC 0.982865 -59 TTAAATATTTTCCCTTATATTTTATATCCC 4 41 0 TCCCTTATAT 0.865181 -43 ********** Masking position 4 Map Score: 3.5104 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 591 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 AATGTGGTCCTCAAATTTCATGCAGGGAAC 2 47 0 TCAAATTTCA 0.888207 -173 AATTTGAGGACCACATTTTATAAAAATCAC 2 60 1 CCACATTTTA 0.963402 -160 TTAATCCGCCTCAAAGTATAAAGTCCCACC 2 91 1 TCAAAGTATA 0.779956 -129 AATAATCCAATCACATTATAAACCAACCCC 2 166 1 TCACATTATA 0.953771 -54 AGAATTAACCCCATATTTTTCAGGTGATCA 2 199 1 CCATATTTTT 0.850651 -21 ATCAACCGGACCATATTCCAGGCCCTTTAC 3 12 0 CCATATTCCA 0.890203 -52 CCCATAACCTTCATATTATATGCAGGTGAT 4 14 0 TCATATTATA 0.961364 -70 ATATTTTCCCTTATATTTTATATCCCATAA 4 37 0 TTATATTTTA 0.78294 -47 ********** Masking position 5 Map Score: 2.98467 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 105 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ********** No masking Map Score: 2.227e-13 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 8 ********** No masking Map Score: 2.227e-13 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: 2.227e-13 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