AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -inarL_tpal_opreg_100.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 GCGTTACGATGCCGGCGAGAGGGTTTC 1 5 0 GCCGGAAGGG 0.953662 -190 AGCGTGCACGGGGCGATGGAGTGTTCTACACGG 1 87 1 GGGGTGAGTG 0.989021 -108 CAGTCCATGTGGGGAAGGGAGTGCGCTGGTGAT 2 49 1 GGGAGGAGTG 0.995338 -79 AACACTCATGGGCGGATGATGGA 2 115 1 GGCGTGTGGA 0.960657 -13 AAACGAAGAAGGGAAGTACAGGGCAGAAAACGG 3 14 0 GGGATAAGGG 0.98591 -32 CTCGTCGGGGGGGGGGGGGTGGACGT 4 4 0 GGGGGGTGGA 0.99313 -80 CTGGACAACCGGCAACGGTATGGGTGACAATGT 4 44 0 GGCAGGATGG 0.982071 -40 GAAAAATATAGGGGAAGGTAGGAAATC 5 11 1 GGGAGGAGGA 0.997194 -17 CGCGGTGTAGGGGAATGGGAGGGGA 6 31 1 GGGAGGAGGG 0.999079 -15 *** * ** **** Masking position 1 Map Score: 17.0982 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 353 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 TGGATCCAAAGGGTCTCTTTGCGTTACGATGC 1 26 0 GGTCTCTTGC 0.914107 -169 TTTGGATCCAGGCCCTGTGTGTATCTGGCATT 1 48 1 GGCCTGGTGT 0.932708 -147 CGTGCACGCTGGGACGCAATGCCAGATACACA 1 65 0 GGACGCATGC 0.984685 -130 TACAAGAACTAGGAGTCTGTGTCGCCCGTGTA 1 113 0 AGAGTCGTGT 0.939995 -82 TCCTAGTTCTTGTATTCTGTGCAAAAACCGAC 1 131 1 TGATTCGTGC 0.851055 -64 GTCTAGTGAGTGTTCTCTGTGC 1 183 1 TGTCTCGTGC 0.94358 -12 CGTCTTCCTCGGAAGACTGTGGCAAATAAGCG 2 16 1 GGAGACGTGG 0.977862 -112 GCAAATAAGCGGCAGTCCATGTGGGGAAGGGA 2 37 1 GGAGTCATGT 0.977981 -91 GTCCATGTGGGGAAGGGAGTGCGCTGGTGATC 2 51 1 GGAGGGGTGC 0.990775 -77 CTCGTCGGGGGGGGGGGGGTGGACGT 4 5 0 GGGGGGGTGG 0.923383 -79 GCAACGGTATGGGTGACAATGTTCTTTTTCTC 4 34 0 GGTGACATGT 0.880417 -50 CACAGCATGCGGCACGCGGTGTAGGGGAATGG 6 17 1 GGACGCGTGT 0.993894 -29 ** **** **** Masking position 10 Map Score: 13.7931 Number of sites scoring better than the average of aligned sites = 840 Number in coding regions = 751 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 3 ACGGGGCGATGGAGTGTTCTACACGGGCGA 1 94 1 GGAGTGTTCT 0.940996 -101 CGACACAGACTCCTAGTTCTTGTATTCTGT 1 121 1 TCCTAGTTCT 0.869737 -74 AAACTGTATCTCCGTAGTCTAGTGAGTGTT 1 167 1 TCCGTAGTCT 0.946454 -28 CGTAGTCTAGTGAGTGTTCTCTGTGC 1 179 1 TGAGTGTTCT 0.983618 -16 GCGCTCCTCGTCTGTTGTCTGATCACCAGC 2 73 0 TCTGTTGTCT 0.895376 -55 CATCCGCCCATGAGTGTTCTGAGACTGTTT 2 103 0 TGAGTGTTCT 0.983618 -25 CTTCCGTTTTCTGCCCTGTACT 3 3 1 TCCGTTTTCT 0.987479 -43 GGTGACAATGTTCTTTTTCTCGTCGGGGGG 4 25 0 TTCTTTTTCT 0.775621 -59 ********** Masking position 8 Map Score: 6.93392 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 203 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 4 GCGTGCACGGGGCGATGGAGTGTTCTACAC 1 88 1 GGCGATGGAG 0.962243 -107 AGTCCATGTGGGGAAGGGAGTGCGCTGGTG 2 50 1 GGGAAGGGAG 0.998126 -78 TCGTCGGGGGGGGGGGGGTGGACGT 4 6 0 GGGGGGGGTG 0.992849 -78 AACCGGCAACGGTATGGGTGACAATGTTCT 4 41 0 GGTATGGGTG 0.980449 -43 AAAAATATAGGGGAAGGTAGGAAATC 5 12 1 GGGAAGGTAG 0.98801 -16 GCGGTGTAGGGGAATGGGAGGGGA 6 32 1 GGAATGGGAG 0.989425 -14 ********** Masking position 7 Map Score: 8.75037 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 193 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 GTCTTCCGAGGAAGACGAGCGC 2 1 0 GAGAGAGCGC 0.99857 -127 TCTGTTGTCTGATCACCAGCGCACTCCCTTCC 2 61 0 GACACAGCGC 0.994856 -67 TCAGACAACAGACGAGGAGCGCAAACAGTCTC 2 81 1 GAGAGAGCGC 0.99821 -47 ACGAAGAAGGGAAGTACAGGGCAGAAAACGGA 3 13 0 GAGTCAGGGC 0.99077 -33 ** ** ****** Masking position 8 Map Score: 4.18408 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 29 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 GAAACCCTCTCGCCGGCATCGTAAC 1 6 1 CCTCTCGCCG 0.946376 -189 CTCTCGCCGGCATCGTAACGCAAAGAGACC 1 17 1 CATCGTAACG 0.862006 -178 CATTGCGTCCCAGCGTGCACGGGGCGATGG 1 76 1 CAGCGTGCAC 0.970084 -119 GTCTGATCACCAGCGCACTCCCTTCCCCAC 2 57 0 CAGCGCACTC 0.902151 -71 ACCGCGCACAGCATGCGGCAC 6 2 1 CCGCGCACAG 0.946752 -44 TTCCCCTACACCGCGTGCCGCATGCTGTGC 6 16 0 CCGCGTGCCG 0.942845 -30 ********** Masking position 4 Map Score: 4.05026 Number of sites scoring better than the average of aligned sites = 1095 Number in coding regions = 1008 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 7 TAACGCAAAGAGACCCTTTGGATCCAGGCC 1 32 1 AGACCCTTTG 0.989009 -163 CTTTGGATCCAGGCCCTGTGTGTATCTGGC 1 47 1 AGGCCCTGTG 0.993552 -148 GAACACTCCATCGCCCCGTGCACGCTGGGA 1 83 0 TCGCCCCGTG 0.942196 -112 CGGGCGACACAGACTCCTAGTTCTTGTATT 1 117 1 AGACTCCTAG 0.860222 -78 AATAAGCGGCAGTCCATGTGGGGAAGGGAG 2 40 1 AGTCCATGTG 0.91543 -88 GAGTGTTCTGAGACTGTTTGCGCTCCTCGT 2 92 0 AGACTGTTTG 0.927695 -36 CCATTCCCCTACACCGCGTGCCGCATGCTG 6 19 0 ACACCGCGTG 0.980197 -27 ********** Masking position 4 Map Score: 4.3595 Number of sites scoring better than the average of aligned sites = 211 Number in coding regions = 183 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 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 Motif number 9 ********** 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 10 ********** 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