AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00190_tpal_reg_100.orf -o00190_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -x5 -e 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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0399 116 flagellar basal-body M ring protein (fliF) #2 TP0401 47 flagellar assembly protein (fliH) #3 TP0402 27 flagellum-specific ATP synthase (fliI) #4 TP0426 141 V-type ATPase, subunit A (atpA-1) #5 TP0430 36 V-type ATPase, subunit K (atpK-1) #6 TP0527 94 V-type ATPase, subunit D (atpD-2) #7 TP0531 300 V-type ATPase, subunit F, putative #8 TP0535 140 T. pallidum predicted coding region TP0535 Motif number 1 TGAAAAGAGGGTGGGACGCGCTTAGTGCGCA 1 62 1 GGGGACGCGC 0.987389 -55 TATAGTGAGGGGAGGGGACACGC 1 104 1 GAGGGGACAC 0.795177 -13 TAGAGAAAGAGGCGTGGGTGTGCGT 3 5 1 GAAGAGGCGT 0.714215 -23 GCCGCTTGACCCGTTTTCCTCAGA 4 4 1 GTTGACCCGT 0.667856 -138 TGTTGCTTACGCATCGGTCGCGTTTCACAAT 4 64 1 GATCGGTCGC 0.957611 -78 GAAAAAGAGTGGAGGGCTCGTT 5 25 1 GAGGGCTCGT 0.953579 -12 TGATTTCTTTGCGGCGCTCCCTTGCTGTGTG 6 45 1 GGGCGCTCCC 0.807377 -50 TCCGCGTTAAGAAGCACGCACAAGCCAGCAA 7 47 0 GAGCACGCAC 0.955898 -254 TTAACGCGGAGAGTCAGCCGCCCTCTCATGT 7 68 1 GGTCAGCCGC 0.956873 -233 ATACATTGCCGCAGGACTCGCGGTGGGGCTC 7 114 1 GAGGACTCGC 0.985315 -187 AGGACTCGCGGTGGGGCTCGCTTGCGTTGGG 7 126 1 GGGGGCTCGC 0.965065 -175 CGCTTGCGTTGGGGGAGGCCTTGCAGTAGGT 7 144 1 GGGGAGGCCT 0.920469 -157 TGCCCCCATCGCTGCAGCCCCGATTTTACCT 7 171 0 GTGCAGCCCC 0.90417 -130 TATCGGTCTTGCAGAAGGCATTTGTCTGTGG 7 243 1 GAGAAGGCAT 0.540096 -58 GGAGTAGGTCGATGTGCTCGCTGAGTGTCGG 8 17 1 GTGTGCTCGC 0.802576 -124 TGCTCGCTGAGTGTCGGCCGCGTGGGTTGGT 8 31 1 GGTCGGCCGC 0.891152 -110 GGAGGTGGAGGATGCGGCCGCTGTCCTCGTG 8 94 1 GTGCGGCCGC 0.986437 -47 CTGTCCTCGTGGAGAAGGCGCAGGAGCAGGC 8 114 1 GAGAAGGCGC 0.970836 -27 AGAAGGCGCAGGAGCAGGCGCACGG 8 126 1 GAGCAGGCGC 0.994702 -15 * ********* Masking position 9 Map Score: 28.5076 Number of sites scoring better than the average of aligned sites = 2544 Number in coding regions = 2355 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 2 TATATCAGGTGAAAAGAGGGTGGGACGCGC 1 53 1 GAAAAGAGGG 0.808261 -64 GTTCTATAGTGAGGGGAGGGGACACGC 1 100 1 GAGGGGAGGG 0.989455 -17 AGAGAAAGAGGCGTGGGTGTGCGTGT 3 12 1 GCGTGGGTGT 0.769599 -16 GTTTCACAATGCAGGCGGGGTCCAAAGCAT 4 85 1 GCAGGCGGGG 0.91881 -57 GGTAGAAAAAGAGTGGAGGGCTCGTT 5 21 1 GAGTGGAGGG 0.973882 -16 AAGGCTCTTGGAGAAGGGTGATTTCTTTGC 6 27 1 GAGAAGGGTG 0.910264 -68 AAGACACACAGCAAGGGAGCGCCGCAAAGA 6 50 0 GCAAGGGAGC 0.470536 -45 TCTTGGCCACGCAGGGAGAGGATACAGAG 6 76 1 GCAGGGAGAG 0.665258 -19 GCTTCTTAACGCGGAGAGTCAGCCGCCCTC 7 63 1 GCGGAGAGTC 0.823454 -238 CCATCTACATGAGAGGGCGGCTGACTCTCC 7 75 0 GAGAGGGCGG 0.959341 -226 CGCAGGACTCGCGGTGGGGCTCGCTTGCGT 7 123 1 GCGGTGGGGC 0.979858 -178 GGGCTCGCTTGCGTTGGGGGAGGCCTTGCA 7 139 1 GCGTTGGGGG 0.984955 -162 CGGGGCTGCAGCGATGGGGGCAATGAGTGA 7 180 1 GCGATGGGGG 0.987309 -121 GGTACGGGAGTAGGTCGATGTGCTCGC 8 8 1 GAGTAGGTCG 0.728266 -133 AGTGTCGGCCGCGTGGGTTGGTAATATGGA 8 40 1 GCGTGGGTTG 0.900791 -101 TATGGATAAAGGGGTGATGGTCCGCCTAGC 8 64 1 GGGGTGATGG 0.672846 -77 GGTCCGCCTAGCGGAGGTGGAGGATGCGGC 8 82 1 GCGGAGGTGG 0.987845 -59 CCTTCTCCACGAGGACAGCGGCCGCATCCT 8 102 0 GAGGACAGCG 0.520574 -39 TGTCCTCGTGGAGAAGGCGCAGGAGCAGGC 8 115 1 GAGAAGGCGC 0.792155 -26 ********** Masking position 1 Map Score: 21.4218 Number of sites scoring better than the average of aligned sites = 2745 Number in coding regions = 2372 Number in noncoding regions = 373 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 3 CCGGGCTGTTCTGCAAAAAGAGTACCGACGGT 1 22 1 CTGCAAAGAG 0.666192 -95 TATCGCTTATCAGGAACAACAT 2 1 0 CAGGAAACAT 0.900796 -47 TGGGGTTCGAAAGGAAGCAGACAGT 2 33 1 AAGGAACGAC 0.961723 -15 ACCGATGCGTAAGCAACATCAGCTGCAGCCCG 4 50 0 AAGCAAACAG 0.939612 -92 GCGGGGTCCAAAGCATACGCAGCTCTTTATTA 4 99 1 AAGCATCCAG 0.937588 -43 CACGCAGGGAGAGGATACAGAG 6 83 1 GAGGATCGAG 0.802714 -12 ACGCACAAGCCAGCAAACACACCCGTAAACCA 7 31 0 CAGCAACCAC 0.991664 -270 CCTGAAATTTCAGGATCCTCACTCATTGCCCC 7 196 0 CAGGATCCAC 0.964041 -105 CCTGAAATTTCAGGAAAGGCACTTCCCTTTAT 7 214 1 CAGGAAGCAC 0.958263 -87 GCAAGATGATAAGCAATGCGACCAAAAAACCC 7 273 0 AAGCAAGGAC 0.923526 -28 GTCAAAGCAAGATGATAAGCAATGCG 7 285 0 AAGCAAAGAT 0.826813 -16 GGCCGACACTCAGCGAGCACATCGACCTACTC 8 18 0 CAGCGACCAT 0.860155 -123 GAAGGCGCAGGAGCAGGCGCACGG 8 127 1 GAGCAGCCAC 0.897739 -14 ****** * *** Masking position 11 Map Score: 8.74975 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 553 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 TCAGGTGAAAAGAGGGTGGGACGCGCTTAG 1 57 1 AGAGGGTGGG 0.986125 -60 TTCTATAGTGAGGGGAGGGGACACGC 1 101 1 AGGGGAGGGG 0.935385 -16 GAGAAAGAGGCGTGGGTGTGCGTGT 3 13 1 CGTGGGTGTG 0.859156 -15 GTAGAAAAAGAGTGGAGGGCTCGTT 5 22 1 AGTGGAGGGC 0.945833 -15 AGGCTCTTGGAGAAGGGTGATTTCTTTGCG 6 28 1 AGAAGGGTGA 0.704354 -67 CATCTACATGAGAGGGCGGCTGACTCTCCG 7 74 0 AGAGGGCGGC 0.983312 -227 CCTCTCATGTAGATGGCGGCTTAAAATACA 7 89 1 AGATGGCGGC 0.950767 -212 GGCTCGCTTGCGTTGGGGGAGGCCTTGCAG 7 140 1 CGTTGGGGGA 0.960217 -161 GGGGCTGCAGCGATGGGGGCAATGAGTGAG 7 181 1 CGATGGGGGC 0.983979 -120 GTGTCGGCCGCGTGGGTTGGTAATATGGAT 8 41 1 CGTGGGTTGG 0.922643 -100 GTCCGCCTAGCGGAGGTGGAGGATGCGGCC 8 83 1 CGGAGGTGGA 0.876662 -58 ********** Masking position 5 Map Score: 11.1853 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 619 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 5 GACGCGCTTAGTGCGCATTGGCTCGTTCTAT 1 76 1 GTGCGCTTGG 0.984039 -41 AAAGAGCTGCGTATGCTTTGGACCCCGCCTG 4 96 0 GTATGCTTGG 0.984453 -46 CTCCCTTGCTGTGTGTCTTGGCCACGCAGGG 6 61 1 GTGTGTTTGG 0.993271 -34 GTATGGGTTGGAAAAGAGCAT 7 1 1 GTATGGTTGG 0.977514 -300 GTTTACGGGTGTGTTTGCTGGCTTGTGCGTG 7 33 1 GTGTTTCTGG 0.89968 -268 GGTGGGGCTCGCTTGCGTTGGGGGAGGCCTT 7 135 1 GCTTGCTTGG 0.960261 -166 TTTGTCTGTGGGGTTTTTTGGTCGCATTGCT 7 263 1 GGGTTTTTGG 0.925071 -38 AGTGTCGGCCGCGTGGGTTGGTAATATGGAT 8 40 1 GCGTGGTTGG 0.990761 -101 ****** **** Masking position 9 Map Score: 9.80688 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 140 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 AAGGCCGGGCTGTTCTGCAAAAAGAGTACC 1 18 1 TGTTCTGCAA 0.794546 -99 TGTTTTTGTACGGGCTGCAGCTGATGTTGC 4 40 1 CGGGCTGCAG 0.977571 -102 GCTTTGGACCCCGCCTGCATTGTGAAACGC 4 83 0 CCGCCTGCAT 0.875551 -59 AAGAAATCACCCTTCTCCAAGAGCCTTATA 6 24 0 CCTTCTCCAA 0.975277 -71 CACCGCGAGTCCTGCGGCAATGTATTTTAA 7 109 0 CCTGCGGCAA 0.967113 -192 CCCGATTTTACCTACTGCAAGGCCTCCCCC 7 154 0 CCTACTGCAA 0.964317 -147 AGGTAAAATCGGGGCTGCAGCGATGGGGGC 7 171 1 GGGGCTGCAG 0.863836 -130 CAGACAAATGCCTTCTGCAAGACCGATAAA 7 241 0 CCTTCTGCAA 0.988878 -60 TGCTCCTGCGCCTTCTCCACGAGGACAGCG 8 112 0 CCTTCTCCAC 0.935166 -29 CCGTGCGCCTGCTCCTGCGCCTTCTCC 8 124 0 CCTGCTCCTG 0.896152 -17 ********** Masking position 5 Map Score: 9.10717 Number of sites scoring better than the average of aligned sites = 546 Number in coding regions = 509 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 TGCGCATTGGCTCGTTCTATAGTGAGGGGA 1 87 1 CTCGTTCTAT 0.980943 -30 ACACCCACGCCTCTTTCTCTA 3 2 0 CTCTTTCTCT 0.992688 -26 CTTTTTCTACCTCTTTCTATG 5 2 0 CTCTTTCTAT 0.988734 -35 GAGCCCTCCACTCTTTTTCTACCTCTTTCT 5 14 0 CTCTTTTTCT 0.971566 -23 ********** Masking position 5 Map Score: 4.13723 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 10 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 8 TGGGGTTCGAAAGGAAGCAGACAGT 2 33 1 AAGGAAGCAG 0.935347 -15 CACGCAGGGAGAGGATACAGAG 6 83 1 GAGGATACAG 0.984102 -12 AGGTAAAATCGGGGCTGCAGCGATGGGGGC 7 171 1 GGGGCTGCAG 0.980548 -130 GGCAATGAGTGAGGATCCTGAAATTTCAGG 7 198 1 GAGGATCCTG 0.920699 -103 AGCGGAGGTGGAGGATGCGGCCGCTGTCCT 8 91 1 GAGGATGCGG 0.993026 -50 ********** Masking position 4 Map Score: 2.27079 Number of sites scoring better than the average of aligned sites = 118 Number in coding regions = 111 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ********** No masking Map Score: -4.38104e-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: -4.38104e-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 11 ********** No masking Map Score: -4.38104e-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