AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icspA_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 TP0005 126 DNA gyrase, subunit A (gyrA) #3 TP0848 32 ribosomal protein L20 (rplT) #4 TP0849 52 ribosomal protein L35 (rpmI) #5 TP0850 162 translation initiation factor 3 (infC) Motif number 1 TTATCCACCACTTATCCCCATCGAATTCAG 1 21 0 CTTATCCCCA 0.94638 -222 TTTACTCACGAATATCCCCCTTTTTTTAGA 1 75 1 AATATCCCCC 0.936693 -168 ATTACCAAACAAAAACCGCACACAAGCTTG 1 125 0 AAAAACCGCA 0.965654 -118 TCCGTCGAATCCCATCCGCAAAA 2 4 0 CCCATCCGCA 0.988036 -123 TGCACGCAAGAAAAACCGCAGTCCTATGGA 2 45 0 AAAAACCGCA 0.965654 -82 CCATCCCCATCACAACCCCAATTCCTTATT 5 56 0 CACAACCCCA 0.990146 -107 GCAGGAAATCACCATCCCCATCACAACCCC 5 67 0 ACCATCCCCA 0.988989 -96 ********** Masking position 4 Map Score: 7.61171 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 133 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 2 AAAAACCGCACACAAGCTTGTGAAGAAAGT 1 115 0 CACAAGCTTG 0.975256 -128 CAAGGAGAGACACAGTCGTGCATAGGCTGC 2 72 0 CACAGTCGTG 0.964048 -55 CCTCCGTCCTCTCACGCTTGCCAC 3 5 0 CTCACGCTTG 0.972953 -28 CTTTTGGATGCCCACTATAGGTGGTGAATT 5 16 1 CCCACTATAG 0.936176 -147 AAGACTGGGCCCCAATCTAGCCATTCCTAA 5 118 0 CCCAATCTAG 0.983915 -45 TAGATTGGGGCCCAGTCTTGTTTTTTAGCG 5 129 1 CCCAGTCTTG 0.994377 -34 ********** Masking position 4 Map Score: 5.25171 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 65 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 3 CTCACGAATATCCCCCTTTTTTTAGAGAAA 1 79 1 TCCCCCTTTT 0.994316 -164 AGTTAGTTTCCTCCTTATTAATCTTATA 1 225 0 TCCTCCTTAT 0.910622 -18 CACGACTGTGTCTCTCCTTGAACGCAGTAT 2 82 1 TCTCTCCTTG 0.93789 -45 ATACTTTCTCCCCTTTATCCAACAAC 4 37 0 TCTCCCCTTT 0.994316 -16 TCTCCCTTTTGGATGCCCAC 5 1 1 TCTCCCTTTT 0.993867 -162 ********** Masking position 8 Map Score: 4.81127 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 58 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 4 TTATATTCTTTTATCCACCACTTATCCCCA 1 31 0 TTATCCACCA 0.974417 -212 TCATTACACTTTACTCACGAATATCCCCCT 1 66 1 TTACTCACGA 0.897259 -177 GTCTCGAGAATTACCAAACAAAAACCGCAC 1 134 0 TTACCAAACA 0.963035 -109 CGAACTGCAGTTACCCGACACTCCA 4 6 0 TTACCCGACA 0.991205 -47 TTTCTCCCCTTTATCCAACAACACGAACTG 4 29 0 TTATCCAACA 0.978697 -24 TCCTGCATGTTTACTTGACATGACATATTA 5 91 1 TTACTTGACA 0.879496 -72 ********** Masking position 3 Map Score: 3.91591 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 72 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 GTGGTGGATAAAAGAATATAAATTAGTCAT 1 40 1 AAAGAATATA 0.933402 -203 CCCTTTTTTTAGAGAAAAAATATACTTTCT 1 92 1 AGAGAAAAAA 0.868235 -151 ACAAGCTTGTGAAGAAAGTATATTTTTTCT 1 104 0 GAAGAAAGTA 0.979938 -139 TTATAAGTATAAAGAATGTAGTCGTATCAC 1 200 0 AAAGAATGTA 0.969305 -43 TGGATAAAGGGGAGAAAGTAT 4 42 1 GGAGAAAGTA 0.981388 -11 ********** Masking position 5 Map Score: 2.11102 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 31 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 6 TTGTGTGCGGTTTTTGTTTGGTAATTCTCG 1 130 1 TTTTTGTTTG 0.87749 -113 ACTGCGGTTTTTCTTGCGTGCAGCCTATGC 2 53 1 TTCTTGCGTG 0.990996 -74 AGGTGGTGAATTTTTACATGTAAATAAGGA 5 34 1 TTTTTACATG 0.926633 -129 GGATGGTGATTTCCTGCATGTTTACTTGAC 5 80 1 TTCCTGCATG 0.969745 -83 CAGTCTTGTTTTTTAGCGTGCATTAGAAGT 5 141 1 TTTTAGCGTG 0.968738 -22 ********** Masking position 2 Map Score: 1.05923 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 142 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 TATCTGGATAAGTGCTTATGTCTCGAGAAT 1 153 0 AGTGCTTATG 0.950661 -90 ATCTGTTCAAAGTCCATAGGACTGCGGTTT 2 33 1 AGTCCATAGG 0.980212 -94 GAGACACAGTCGTGCATAGGCTGCACGCAA 2 66 0 CGTGCATAGG 0.995141 -61 TGTTTTTTAGCGTGCATTAGAAGTGG 5 147 1 CGTGCATTAG 0.967536 -16 ********** Masking position 7 Map Score: 0.592644 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 39 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 8 ********** No masking Map Score: 6.06393e-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: 6.06393e-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 10 ********** No masking Map Score: 6.06393e-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