AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -inarP_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 TP0100 194 thioredoxin, putative #2 TP0278 127 T. pallidum predicted coding region TP0278 #3 TP0279 45 ribosomal protein S1 (rpsA) #4 TP0382 83 T. pallidum predicted coding region TP0382 #5 TP0383 27 conserved hypothetical protein #6 TP0390 45 cell division protein (ftsZ) Motif number 1 TTTGGATCCAGGCCCTGTGTGTATCTGGCAT 1 48 1 GGCCCTGGTG 0.969969 -147 CGTGCACGCTGGGACGCAATGCCAGATACAC 1 66 0 GGGACGCATG 0.989027 -129 CGTGCACGGGGCGATGGAGTGTTCTACACGG 1 89 1 GCGATGGGTG 0.974269 -106 TACAAGAACTAGGAGTCTGTGTCGCCCGTGT 1 114 0 AGGAGTCGTG 0.856506 -81 CGTCTTCCTCGGAAGACTGTGGCAAATAAGC 2 16 1 GGAAGACGTG 0.93342 -112 GCAAATAAGCGGCAGTCCATGTGGGGAAGGG 2 37 1 GGCAGTCATG 0.966747 -91 GTCCATGTGGGGAAGGGAGTGCGCTGGTGAT 2 51 1 GGAAGGGGTG 0.995588 -77 TCCATCATCCGCCCATGAGTGTTCTGAGACT 2 107 0 GCCCATGGTG 0.773603 -21 CTCGTCGGGGGGGGGGGGGTGGACGT 4 6 0 GGGGGGGGTG 0.988165 -78 TGGACAACCGGCAACGGTATGGGTGACAATG 4 45 0 GCAACGGATG 0.957742 -39 AAAAATATAGGGGAAGGTAGGAAATC 5 12 1 GGGAAGGAGG 0.938212 -16 CACAGCATGCGGCACGCGGTGTAGGGGAATG 6 17 1 GGCACGCGTG 0.994569 -29 GCGGTGTAGGGGAATGGGAGGGGA 6 32 1 GGAATGGAGG 0.885434 -14 ******* *** Masking position 11 Map Score: 16.0462 Number of sites scoring better than the average of aligned sites = 1466 Number in coding regions = 1240 Number in noncoding regions = 226 Number of orfs with sites within 600 bp upstream = 148 Fraction of orfs with sites within 600 bp upstream = 0.0237713 Motif number 2 GAAACCCTCTCGCCGGCATCGTAA 1 4 1 ACCCTTCGCC 0.980072 -191 CGTGTAGAACACTCCATCGCCCCGTGCACGC 1 88 0 ACTCCTCGCC 0.986424 -107 CACCAGCGCACTCCCTTCCCCACATGGACTG 2 49 0 CTCCCTCCCC 0.998827 -79 ACGTCCACCCCCCCCCCCCCGACGAGAA 4 8 1 CCCCCCCCCC 0.99685 -76 ATTGTCACCCATACCGTTGCCGGTTGTCCAG 4 46 1 ATACCTTGCC 0.966603 -38 GATTTCCTACCTTCCCCTATATTTTTC 5 11 0 CTACCTCCCC 0.996538 -17 TCCCCTCCCATTCCCCTACACCGCG 6 31 0 CTCCCTTCCC 0.995715 -15 ***** ***** Masking position 4 Map Score: 12.7548 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 209 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 TTTTTGCACAGAATACAAGAACTAGGAGTCT 1 127 0 GAAACAAGAA 0.743938 -68 TATTCTGTGCAAAAACCGACGTAAAAACTGT 1 143 1 AAAACCGACG 0.920738 -52 ACACTCACTAGACTACGGAGATACAGTTTTT 1 165 0 GACACGGAGA 0.899976 -30 GTCTTCCGAGGAAGACGAGCGC 2 2 0 GAAACGAGCG 0.983993 -126 TCTGTTGTCTGATCACCAGCGCACTCCCTTC 2 62 0 GATACCAGCG 0.927339 -66 CTGGTGATCAGACAACAGACGAGGAGCGCAA 2 74 1 GACACAGACG 0.973724 -54 GTACAGGGCAGAAAACGGAAG 3 1 0 GAAACGGAAG 0.977567 -45 AGGGGTGAAAAACGAAGAAGGGAAGTA 3 29 0 GAAAACGAAG 0.882809 -17 CCCCCGACGAGAAAAAGAACATTGTCACCCA 4 26 1 GAAAAGAACA 0.807173 -58 AAATTTACTGGACAACCGGCAACGGTATGGG 4 53 0 GACACCGGCA 0.98066 -31 *** ******* Masking position 5 Map Score: 7.40543 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 578 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 4 GCATCGTAACGCAAAGAGACCCTTTGGATC 1 26 1 GCAAAGAGAC 0.904112 -169 TGCCAGATACACACAGGGCCTGGATCCAAA 1 48 0 ACACAGGGCC 0.977482 -147 CGCCCCGTGCACGCTGGGACGCAATGCCAG 1 72 0 ACGCTGGGAC 0.832483 -123 GTCCCAGCGTGCACGGGGCGATGGAGTGTT 1 82 1 GCACGGGGCG 0.994036 -113 GCACAGAGAACACTCACTAG 1 185 0 GCACAGAGAA 0.95506 -10 AGTCCATGTGGGGAAGGGAGTGCGCTGGTG 2 50 1 GGGAAGGGAG 0.820414 -78 CAGACAACAGACGAGGAGCGCAAACAGTCT 2 82 1 ACGAGGAGCG 0.859851 -46 AAGAAGGGAAGTACAGGGCAGAAAACGGAA 3 12 0 GTACAGGGCA 0.905586 -34 ACCGCGCACAGCATGCGGCACGC 6 4 1 GCGCACAGCA 0.923642 -42 ACAGCATGCGGCACGCGGTGTAGGGGAATG 6 18 1 GCACGCGGTG 0.873338 -28 ********** Masking position 8 Map Score: 5.84863 Number of sites scoring better than the average of aligned sites = 2941 Number in coding regions = 2708 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 5 CGTTACGATGCCGGCGAGAGGGTTTC 1 7 0 CCGGCGAGAG 0.986898 -188 TGTGCAAAAACCGACGTAAAAACTGTATCT 1 148 1 CCGACGTAAA 0.980359 -47 CCACAGTCTTCCGAGGAAGACGAGCGC 2 8 0 CCGAGGAAGA 0.980708 -120 GATCAGACAACAGACGAGGAGCGCAAACAG 2 79 1 CAGACGAGGA 0.987206 -49 CCCCCCCCCCCCGACGAGAAAAAGAACATT 4 19 1 CCGACGAGAA 0.997318 -65 ********** Masking position 6 Map Score: 5.3635 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 57 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 6 ********** No masking Map Score: 5.21128e-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 7 ********** No masking Map Score: 5.21128e-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: 5.21128e-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