AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -imalT_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 TP0074 300 sugar ABC transporter, periplasmic binding protein (y4oP) #2 TP0075 118 sugar ABC transporter, permease protein (y4oQ) #3 TP0076 39 sugar ABC transporter, permease protein (y4oR) #4 TP0652 175 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #5 TP0802 45 T. pallidum predicted coding region TP0802 #6 TP0804 77 sugar ABC transporter, ATP-binding protein (ugpC) Motif number 1 TCAACAAAGACATACACCGCACCCACACGCGTTTGCATTCTGGCA 1 18 0 CCCCACGCTG 0.975648 -283 TTCAACCTAACGGGGCAGATTCTCGTACGCTTTTCTCCCCGTTGT 1 62 0 CTCCGCGCTC 0.989648 -239 GTATCCACCGCGCGCATCGCACCCCATATCGATACGGGAAAACAA 1 139 0 CCCCCATCTC 0.919018 -162 GCGATGCGCGCGGTGGATACGCTCCTTCTCGACTGAGGTCGCAAG 1 164 1 CCCCCCTCCG 0.980429 -137 CACCACACCAATCGACGCACGCCCCTACGCAGTCCTACAAAATCT 1 207 0 ACCCCCGCTC 0.987407 -94 CACCCCAGTCCTGATACATCAAACCAGCACGACACATAGCACCAC 1 246 0 CCACCCACCC 0.954323 -55 GCACTCCCCCTCTTACGCTACCCAACGTAACGCGCTCCACAGA 2 86 0 CCACCCGTCC 0.928094 -33 TCTGCTCCTGCTCTTATCTAACCCGTACGCAACCC 3 1 0 CACCGCGCCC 0.991468 -39 ACGGGGTGGTCCTTTCTTCCTCATGCGCACTTCTCGCGCCAGCGA 4 21 1 CCCTGCACCC 0.931016 -155 CTCGCGCCAGCGAGCGTAACACGCCAGCGGTAATCTGTCCAGCAA 4 53 1 CCCCCCGGAC 0.993565 -123 GTAATCTGTCCAGCAAGGACACACGGACGCCTTGCGTACCCCAAC 4 82 1 CCCCGCGCTC 0.999408 -94 TGGGTATGTTCTGTCAAGGCTCGCGGTTGGGGTACGCAAGGCGTC 4 107 0 CCCCGTGGTC 0.986569 -69 ACAGAACATACCCAAATACCGCACCATCGGCCTCCGCAATGAGAA 4 138 1 CCCCCCGGTC 0.998203 -38 TTCCTCTCCATACCCTCGTGGGGGATGCCCCCCTGTGT 5 4 1 CCCCGGGGTC 0.984068 -42 CATGACAACACCACCTCCCGTTTGCGTAAGGAAAGTAGTG 6 6 1 CCCCGTGCAG 0.929447 -72 GTTTACATTCCTTTTGAAACACGGGTGCGCAACACACTACTTTCC 6 40 0 CCCGGCGCCC 0.994225 -38 * * * ** *** * * Masking position 1 Map Score: 29.4704 Number of sites scoring better than the average of aligned sites = 1015 Number in coding regions = 901 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 ATACACCGCACCCACACGCGTTTGCATTCTGGCA 1 18 0 CCCCACGCTG 0.990575 -283 GGGGCAGATTCTCGTACGCTTTTCTCCCCGTTGT 1 62 0 CTCTACGCTC 0.996532 -239 AGGAGCGTATCCACCGCGCGCATCGCACCCCATA 1 156 0 CCACGCGCTC 0.924544 -145 TCGACGCACGCCCCTACGCAGTCCTACAAAATCT 1 207 0 CCCTACGCCC 0.998403 -94 CGTTTTTCCCCTCACACCCCAGTCCTGATACATC 1 271 0 CTCCACCCTC 0.984271 -30 GCACTCCCCCTCTTACGCTACCCAACGTAACGC 2 96 0 CTCTACGCCC 0.997005 -23 TCTTATCTAACCCGTACGCAACCC 3 1 0 CCCTACGCCC 0.998418 -39 GCTATCTGCTCCTGCTCTTATCTAACCCGTAC 3 18 0 CTCTGCTCTC 0.940299 -22 TCCTTTCTTCCTCATGCGCACTTCTCGCGCCAGC 4 30 1 CTCTGCGCTC 0.993611 -146 ACGGACGCCTTGCGTACCCCAACCGCGAGCCTTG 4 104 1 TGCTACCCCC 0.912786 -72 TTCCTCTCCATACCCTCGTGGGGGATGCCC 5 7 1 TCCTACCCTG 0.942241 -39 CACACTACTTTCCTTACGCAAACGGGAGGTGGTG 6 19 0 TCCTACGCCG 0.979792 -59 *** ***** ** Masking position 7 Map Score: 25.1422 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 434 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 3 CAAAGACATACACCGCACCCACACGCGTTTG 1 28 0 CACCGCCCCA 0.914847 -273 TTCTCGTACGCTTTTCTCCCCGTTGTCAACA 1 57 0 CTTTTCCCCC 0.990204 -244 AGCACGTACAGTTTGCTCCCCCTTCAACCTA 1 98 0 GTTTGCCCCC 0.983285 -203 CCACCGCGCGCATCGCACCCCATATCGATAC 1 149 0 CATCGCCCCC 0.991023 -152 ACGCACGCCCCTACGCAGTCCTACAAAATCT 1 207 0 CTACGCGTCC 0.794562 -94 CCACACCAATCGACGCACGCCCCTACGCAGT 1 219 0 CGACGCCGCC 0.985261 -82 CCTGTCCGTTTTTCCCCTCACACCCCA 1 284 0 CGTTTTCCCC 0.922841 -17 TTTCTGCCCTCTCTTCCCCCAAGAAGAAGAG 2 16 0 CTCTTCCCCA 0.907719 -103 TATCCAGCATCTTTTCTGCCCTCTCTTCCCC 2 28 0 CTTTTCGCCC 0.955993 -91 TATCTAACCCGTACGCAACCC 3 1 0 GTACGCACCC 0.835546 -39 AGGACCACCCCGTCTTACGCATT 4 3 0 CGTCTTCGCA 0.605775 -173 CTCATGCGCACTTCTCGCGCCAGCGAGCGTA 4 40 1 CTTCTCCGCC 0.984901 -136 CCCTCGTGGGGGATGCCCCCCTGTGTACGCT 5 23 1 GGATGCCCCC 0.970081 -23 ****** **** Masking position 10 Map Score: 14.735 Number of sites scoring better than the average of aligned sites = 1289 Number in coding regions = 1122 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 4 ACAAAGACATACACCGCACCCACACGCGTT 1 30 0 ACACCGCACC 0.988779 -271 TCCACCGCGCGCATCGCACCCCATATCGAT 1 151 0 GCATCGCACC 0.978788 -150 ACGACACATAGCACCACACCAATCGACGCA 1 233 0 GCACCACACC 0.996242 -68 CATCAAACCAGCACGACACATAGCACCACA 1 245 0 GCACGACACA 0.860978 -56 GCTACCCAACGTAACGCGCTCCACAGATAG 2 83 0 GTAACGCGCT 0.859315 -36 GAGGAAGAAAGGACCACCCCGTCTTACGCA 4 13 0 GGACCACCCC 0.961307 -163 GCCAGCGAGCGTAACACGCCAGCGGTAATC 4 58 1 GTAACACGCC 0.963409 -118 GTTGGGGTACGCAAGGCGTCCGTGTGTCCT 4 97 0 GCAAGGCGTC 0.821346 -79 ACATACCCAAATACCGCACCATCGGCCTCC 4 143 1 ATACCGCACC 0.961336 -33 CATGACAACACCACCTCCCGTTTGCGT 6 8 1 ACACCACCTC 0.851381 -70 ACACGGGTGCGCAACACACTACTTTCCTTA 6 37 0 GCAACACACT 0.951355 -41 ********** Masking position 3 Map Score: 13.9132 Number of sites scoring better than the average of aligned sites = 1184 Number in coding regions = 1061 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 5 TTGACAACGGGGAGAAAAGCGTACGAGAATC 1 59 1 GGAGAAAACG 0.96105 -242 TCAACCTAACGGGGCAGATTCTCGTACGCTT 1 75 0 GGGGCAGATC 0.956188 -226 GGTTGAAGGGGGAGCAAACTGTACGTGCTCA 1 100 1 GGAGCAAATG 0.961185 -201 TATCGATACGGGAAAACAAAGATTACATGAG 1 127 0 GGAAAACAAG 0.788054 -174 TGGGGTGTGAGGGGAAAAACGGACAGG 1 284 1 GGGGAAAACG 0.963941 -17 CTTCCCCCAAGAAGAAGAGACTTT 2 4 0 GAAGAAGAAC 0.894082 -115 CTTCTTCTTGGGGGAAGAGAGGGCAGAAAAG 2 18 1 GGGGAAGAAG 0.991818 -101 GATATGAGCGGAAACAGAATGACGTGTTCTA 2 55 1 GAAACAGATG 0.786574 -64 GATAAGAGCAGGAGCAGATAGC 3 28 1 GGAGCAGAAG 0.991817 -12 AAGTGCGCATGAGGAAGAAAGGACCACCCCG 4 22 0 GAGGAAGAAG 0.971592 -154 ******** ** Masking position 6 Map Score: 12.2893 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 371 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 6 CACCGCACCCACACGCGTTTGCATTCTGGC 1 19 0 ACACGCGTTT 0.726192 -282 CGTACAGTTTGCTCCCCCTTCAACCTAACG 1 95 0 GCTCCCCCTT 0.80923 -206 GGGGTGCGATGCGCGCGGTGGATACGCTCC 1 159 1 GCGCGCGGTG 0.932504 -142 GGGTTGCGTACGGGTTAGATAAGAG 3 6 1 GCGTACGGGT 0.793794 -34 ACAGATTACCGCTGGCGTGTTACGCTCGCT 4 61 0 GCTGGCGTGT 0.938405 -115 GGTACGCAAGGCGTCCGTGTGTCCTTGCTG 4 92 0 GCGTCCGTGT 0.958252 -84 TTCTGTCAAGGCTCGCGGTTGGGGTACGCA 4 114 0 GCTCGCGGTT 0.984176 -62 GGGGCATCCCCCACGAGGGTATGGAGAGGA 5 12 0 CCACGAGGGT 0.638227 -34 CGTGGGGGATGCCCCCCTGTGTACGCTTC 5 27 1 GCCCCCCTGT 0.921274 -19 GACAACACCACCTCCCGTTTGCGTAAGGAA 6 14 1 CCTCCCGTTT 0.939258 -64 AGTGTGTTGCGCACCCGTGTTTCAAAAGGA 6 47 1 GCACCCGTGT 0.983757 -31 ********** Masking position 2 Map Score: 6.86504 Number of sites scoring better than the average of aligned sites = 1821 Number in coding regions = 1673 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 7 CCCTGTGCCAGAATGCAAACGCGTGTGGGT 1 13 1 GAATGCAAAC 0.892911 -288 GACATACACCGCACCCACACGCGTTTGCAT 1 25 0 GCACCCACAC 0.926933 -276 GATTACATGAGCACGTACAGTTTGCTCCCC 1 108 0 GCACGTACAG 0.961743 -193 GTGAGGGGAAAAACGGACAGG 1 290 1 AAACGGACAG 0.902192 -11 TGCTGGATATGAGCGGAAACAGAATGACGT 2 50 1 GAGCGGAAAC 0.961864 -69 AATCTGTCCAGCAAGGACACACGGACGCCT 4 84 1 GCAAGGACAC 0.945304 -92 GAAGCGTACACAGGGGGGCAT 5 35 0 AAGCGTACAC 0.903745 -11 GTTTCAAAAGGAATGTAAACGCT 6 65 1 GAATGTAAAC 0.88545 -13 ********** Masking position 7 Map Score: 1.8305 Number of sites scoring better than the average of aligned sites = 1038 Number in coding regions = 953 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 8 ********** No masking Map Score: 6.91659e-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: 6.91659e-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: 6.91659e-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