AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -idnaA_tpal_opreg_300.orf -g0.528 -x5 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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0002 242 DNA polymerase III, subunit beta (dnaN) #2 TP1008 126 ribonucleoside-diphosphate reductase, subunit alpha (nrdA) #3 TP1009 96 glycerol-3-phosphate dehydrogenase (gpsA) #4 TP1010 125 nucleoside-diphosphate kinase (ndk) #5 TP1011 34 peptidyl-tRNA hydrolase (pth) #6 TP1012 204 RNA polymerase sigma-43 factor (sigA) Motif number 1 AAGAAAGTATATTTTTTCTCTAAAAAAAGGG 1 92 0 ATTTTTCTCT 0.892068 -151 GAGAAAAAATATACTTTCTTCACAAGCTTGT 1 103 1 ATCTTTCTTC 0.899501 -140 CTCGTTCTTTACGCTTCCCCCACAGAGACGC 2 32 0 ACCTTCCCCC 0.971141 -95 CCACTCCTAGACTCGTTCTTTACGCTTCCCC 2 43 0 ACCGTTCTTT 0.876765 -84 TACGGTGATCATGTTTCCTCTTGCTGAAGAA 3 46 1 ATTTTCCTCT 0.948078 -51 GATTCCTAACCCCTCCCCTGATCCTCACC 3 78 0 ACCCTCCCCT 0.974161 -19 TTCTCTTTTTACCCTTCCTTCACCGTATGGT 4 25 0 ACCTTCCTTC 0.974099 -101 AGTCCTCCCCACACTTTCTCTTTTTACCCTT 4 40 0 ACCTTTCTCT 0.979895 -86 CGTACCCACCATTCTTTCTTTATGCAAGTCC 4 66 0 ATCTTTCTTT 0.941211 -60 CGCATTCTATACATTTCCTTTTGAAGAATCA 6 77 1 ACTTTCCTTT 0.955944 -128 CCCTCTGTGCATACCTCCCTTTCCCACGGCG 6 122 0 ATCCTCCCTT 0.925287 -83 GACACCGAACAGATCTCCTCTGGTTTATCGT 6 170 1 AGTCTCCTCT 0.80701 -35 ** ******** Masking position 1 Map Score: 14.0845 Number of sites scoring better than the average of aligned sites = 367 Number in coding regions = 325 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 2 AAGCTTGTGTGCGGTTTTTGTTTGGTAATT 1 126 1 GCGGTTTTTG 0.898046 -117 CCGTCCGAACGCGGATTATGGGCCAAAAAT 2 99 0 GCGGATTATG 0.952885 -28 TTTAGGGTCTGCGGTGCGTGTTCTTTTTCG 3 15 1 GCGGTGCGTG 0.993436 -82 GAAGAAAGGTGAGGATCAGGGGAGGGGTTA 3 71 1 GAGGATCAGG 0.714783 -26 GTACGCTGGCGCGCCACGTGTATTAGCTAG 4 92 1 GCGCCACGTG 0.961434 -34 ACATCAGAGGCGTATGAAATAGGAGC 5 7 1 GAGGCGTATG 0.967899 -28 CTTCACGTTTGCGCCGTATGCCTACACGCA 6 37 1 GCGCCGTATG 0.987486 -168 TGCGCCCCGCGCGGTGCGTGTAGGCATACG 6 51 0 GCGGTGCGTG 0.993436 -154 GAACTGTAGCGCGCCGTGGGAAAGGGAGGT 6 111 1 GCGCCGTGGG 0.983918 -94 ********** Masking position 3 Map Score: 11.3836 Number of sites scoring better than the average of aligned sites = 872 Number in coding regions = 812 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 AAAAAATATACTTTCTTCACAAGCTTGTGT 1 106 1 CTTTCTTCAC 0.934364 -137 AGTTAGTTTCCTCCTTATTAATCTTA 1 227 0 TTTCCTCCTT 0.89578 -16 CACGGGGGTGTTTTCTTCCGCGCGTCTCTG 2 11 1 TTTTCTTCCG 0.76366 -116 GTTCTTTACGCTTCCCCCACAGAGACGCGC 2 30 0 CTTCCCCCAC 0.910511 -97 AGAGTTCTCACTTCCACTCCTAGACTCGTT 2 57 0 CTTCCACTCC 0.783519 -70 GGTGATCATGTTTCCTCTTGCTGAAGAAAG 3 49 1 TTTCCTCTTG 0.9052 -48 TGATCCTCACCTTTCTTCAGCAAGAGGAAA 3 59 0 CTTTCTTCAG 0.892424 -38 TCTTTTTACCCTTCCTTCACCGTATGGTGA 4 23 0 CTTCCTTCAC 0.975727 -103 CCTCCCCACACTTTCTCTTTTTACCCTTCC 4 38 0 CTTTCTCTTT 0.804692 -88 ACCCACCATTCTTTCTTTATGCAAGTCCTC 4 64 0 CTTTCTTTAT 0.683595 -62 ATGATTTCCTCGTCCTAGCTAATA 4 112 0 TTTCCTCGTC 0.834483 -14 GCGTTCCTCCTCATAACGAGTC 6 3 1 GTTCCTCCTC 0.917616 -202 ATTCTATACATTTCCTTTTGAAGAATCAAG 6 80 1 TTTCCTTTTG 0.856115 -125 CTGTGCATACCTCCCTTTCCCACGGCGCGC 6 119 0 CTCCCTTTCC 0.755593 -86 ********** Masking position 2 Map Score: 8.95427 Number of sites scoring better than the average of aligned sites = 1186 Number in coding regions = 1063 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 4 TTTCTCTAAAAAAAGGGGGATATTCGTGAG 1 79 0 AAAAGGGGGA 0.899641 -164 TATAAGATTAATAAGGAGGAAACTAACT 1 225 1 ATAAGGAGGA 0.974598 -18 ACCTTTCTTCAGCAAGAGGAAACATGATCA 3 51 0 AGCAAGAGGA 0.983555 -46 AAGGAAGGGTAAAAAGAGAAAGTGTGGGGA 4 36 1 AAAAAGAGAA 0.826482 -90 TGTATTAGCTAGGACGAGGAAATCAT 4 110 1 AGGACGAGGA 0.964212 -16 CGTATGAAATAGGAGCAGGACGCG 5 21 1 AGGAGCAGGA 0.932357 -14 ATGACTCGTTATGAGGAGGAACGC 6 5 0 ATGAGGAGGA 0.983695 -200 CTTTTGAAGAATCAAGAGAACTGTAGCGCG 6 94 1 ATCAAGAGAA 0.882209 -111 ATTTACGATAAACCAGAGGAGATCTGTTCG 6 175 0 AACCAGAGGA 0.898853 -30 ********** Masking position 1 Map Score: 7.75709 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 260 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 5 GAATTCGATGGGGATAAGTGGTGGATAAAA 1 23 1 GGGATAAGTG 0.978643 -220 GGATAAGTGGTGGATAAAAGAATATAAATT 1 34 1 TGGATAAAAG 0.895295 -209 TGTGAATATCTGGATAAGTGCTTATGTCTC 1 159 0 TGGATAAGTG 0.982229 -84 GCGTCTCTGTGGGGGAAGCGTAAAGAACGA 2 32 1 GGGGGAAGCG 0.964641 -95 AAATAACATTTGGGTAAGAGTTCTCACTTC 2 73 0 TGGGTAAGAG 0.988625 -54 TAGCGCGCCGTGGGAAAGGGAGGTATGCAC 6 117 1 TGGGAAAGGG 0.956902 -88 ********** Masking position 6 Map Score: 4.56861 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 86 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 AATCCGCGTTCGGACGGAGAGATAT 2 112 1 CGGACGGAGA 0.936645 -15 GTTCTTTTTCGATACGGTGATCATGTTTCC 3 34 1 GATACGGTGA 0.978019 -63 GGACAGGGTGACTCACCATAC 4 2 1 GACAGGGTGA 0.957758 -124 GGTGACTCACCATACGGTGAAGGAAGGGTA 4 17 1 CATACGGTGA 0.986374 -109 TGCGTGTAGGCATACGGCGCAAACGTGAAG 6 37 0 CATACGGCGC 0.962886 -168 GAATGCGCCCCGCGCGGTGCGTGTAGGCAT 6 54 0 CGCGCGGTGC 0.898452 -151 GAGGTATGCACAGAGGGTCCAGTGGCGTGA 6 136 1 CAGAGGGTCC 0.927495 -69 CCAGTGGCGTGATAGGGACACCGAACAGAT 6 154 1 GATAGGGACA 0.808033 -51 ********** Masking position 6 Map Score: 3.19403 Number of sites scoring better than the average of aligned sites = 527 Number in coding regions = 481 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 ********** No masking Map Score: 5.63761e-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: 5.63761e-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: 5.63761e-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