AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_tpal_reg_100.orf -o00630_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 TP0407 127 phosphoglycolate phosphatase (gph-1) #2 TP0553 243 conserved hypothetical integral membrane protein #3 TP0554 34 phosphoglycolate phosphatase (gph-2) #4 TP0568 121 4-hydroxy-2-oxoglutarate aldolase/2-dehydro-3-deoxyphosphogluconate aldolase (eda) #5 TP0732 95 methylenetetrahydrofolate dehydrogenase (folD) #6 TP0757 40 polypeptide deformylase (def) #7 TP0758 118 ribosomal protein S21 (rpsU) Motif number 1 TGGATATCGGGTGCGTGCACTGTGTGTGTT 1 20 1 GTGCGTGCAC 0.949888 -108 CAGCGCGGTGCTGCGTGCGTACAATGGGCC 1 84 1 CTGCGTGCGT 0.989523 -44 CACGAAACCTCGGCTTCCCCATGGCCCATT 1 106 0 CGGCTTCCCC 0.96644 -22 TATTGTCACGGAGTTTGCGTTAC 2 4 0 GAGTTTGCGT 0.865416 -240 CGCCTTCGTTCGGCCTGCGCGTGTCTTGGC 2 61 0 CGGCCTGCGC 0.992482 -183 GGGTCCTCGGCGCCGTGCCCAAGTGGTAAG 2 136 0 CGCCGTGCCC 0.988559 -108 CGCAAGGTCACAGCGTGCCTGGAGTATCGG 2 210 0 CAGCGTGCCT 0.973285 -34 GGCACGCTGTGACCTTGCGCAAAGGGGATT 2 221 1 GACCTTGCGC 0.979061 -23 GGTGTTTCTTGGGCTTCCGTCTAGTGTCCG 5 27 1 GGGCTTCCGT 0.966014 -69 TCCGTCTAGTGTCCGTGCGTGTTCGGTCTT 5 42 1 GTCCGTGCGT 0.984532 -54 TGCGTGTTCGGTCTTTGCGCTGTTGCGTGC 5 57 1 GTCTTTGCGC 0.919315 -39 CTTTGCGCTGTTGCGTGCGCGTGTCTATAC 5 69 1 TTGCGTGCGC 0.966778 -27 GACACGTAGGGTGTGCGTGCAGGGGAGG 7 9 1 GGGTGTGCGT 0.965409 -110 GAAAGCACTCCTGCCTCCCCTGCACGCACA 7 22 0 CTGCCTCCCC 0.954659 -97 CGACCCTCCCCTGAAAAAAAC 7 108 0 GACCCTCCCC 0.906477 -11 ********** Masking position 6 Map Score: 26.683 Number of sites scoring better than the average of aligned sites = 2828 Number in coding regions = 2658 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 TCCCCATGGCCCATTGTACGCACGCAGCACC 1 90 0 CCATTTACGC 0.775709 -38 CAGTTCGATTCTGATCGGCGCCTTCGTTCGG 2 78 0 CTGATGGCGC 0.9715 -166 AGCCTGAGGGGTCCTCGGCGCCGTGCCCAAG 2 143 0 GTCCTGGCGC 0.987076 -101 GGTAATCCCCTTTGCGCAAGGTCACAG 2 227 0 CCCCTTGCGC 0.990276 -17 GGATATCTTGCTGCTCGGCGCCCTTTTTATT 3 11 1 CTGCTGGCGC 0.993327 -24 CTGTTGATTGGTGTTATACGCAGATCTTGAT 4 18 1 GTGTTTACGC 0.828652 -104 AATTCCCTCCTCTTGCCCGCGGACATCTTT 4 102 0 CTCTTCCCGC 0.984524 -20 GGTCTTTGCGCTGTTGCGTGCGCGTGTCTAT 5 66 1 CTGTTCGTGC 0.864735 -30 GCGCGTGTCTATACTGGGCGC 5 85 1 ATACTGGCGC 0.814807 -11 CCAAGAGAAACTCATACCCGC 6 1 0 CTCATCCCGC 0.965127 -40 CGCCTCTTCCCGCTCTTACCCAA 6 28 0 CCTCTCCCGC 0.920157 -13 ACTCCTGCCTCCCCTGCACGCACACCCTACG 7 15 0 CCCCTCACGC 0.982606 -104 GACAGGGGACGTCTTTTGCGCTAGCCTACCC 7 65 1 GTCTTTGCGC 0.962023 -54 ***** ***** Masking position 5 Map Score: 17.939 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 937 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 3 GCCTCCACACAAACACACACAGTGCACGCA 1 31 0 AAACACACAC 0.940384 -97 GGGAAAAGAGAGAAGCACCCGCCAAGACAC 2 41 1 AGAAGCACCC 0.97021 -203 GCACCCGCCAAGACACGCGCAGGCCGAACG 2 55 1 AGACACGCGC 0.989741 -189 AGGCTAACAAAAAAAGACGCAATCGTTCAA 2 169 1 AAAAAGACGC 0.950463 -75 GGTAATAAAAAGGGCGCCGAGCAGCAA 3 18 0 AAAAGGGCGC 0.936711 -17 CGGAAGCCCAAGAAACACCGTATGCTCGGC 5 16 0 AGAAACACCG 0.93025 -80 CACGGACACTAGACGGAAGCCCAAGAAACA 5 29 0 AGACGGAAGC 0.850527 -67 CAAAGACCGAACACGCACGGACACTAGACG 5 44 0 ACACGCACGG 0.937238 -52 CGCCCAGTATAGACACGCGCACGCAACAGC 5 75 0 AGACACGCGC 0.989741 -21 CTCCCCTGAAAAAAACACAGCCTACCAGGG 7 94 0 AAAAACACAG 0.814421 -25 ********** Masking position 3 Map Score: 8.82657 Number of sites scoring better than the average of aligned sites = 1117 Number in coding regions = 1023 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 GTCTATCAGCCTCTCTTATCTACCGCCTCC 1 55 0 CTCTCTTATC 0.962769 -73 GTAACGCAAACTCCGTGACAATACAAAACT 2 11 1 CTCCGTGACA 0.891303 -233 GCGGGTGCTTCTCTCTTTTCCCAGTTTTGT 2 33 0 CTCTCTTTTC 0.918364 -211 TTGCAGACCTCTCCCTTACCACTTGGGCAC 2 122 1 CTCCCTTACC 0.99056 -122 GGGTCCTCGGCGCCGTGCCCAAGTGGTAAG 2 136 0 CGCCGTGCCC 0.973449 -108 ACTCCAGGCACGCTGTGACCTTGCGCAAAG 2 215 1 CGCTGTGACC 0.984428 -29 TGCTGCTCGGCGCCCTTTTTATTACC 3 19 1 CGCCCTTTTT 0.785918 -16 CGCCTCTTCCCGCTCTTACCCAAGAGAAAC 6 21 0 CGCTCTTACC 0.99056 -20 ********** Masking position 6 Map Score: 7.54482 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 280 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 5 CACAGTGCACGCACCCGATATCCAGTGCCG 1 14 0 GCACCCGATA 0.994658 -114 AAAGAGAGAAGCACCCGCCAAGACACGCGC 2 45 1 GCACCCGCCA 0.997832 -199 CAAGGGTAAACCAACCGATACTCCAGGCAC 2 196 1 CCAACCGATA 0.868497 -48 CACATGCAGTGCACCCGCCTAAGCTAATGT 4 64 0 GCACCCGCCT 0.991272 -58 ATAGACACGCGCACGCAACAGCGCAAAGAC 5 67 0 GCACGCAACA 0.940945 -29 TCCCCTGCACGCACACCCTACGTGTC 7 7 0 GCACACCCTA 0.940945 -112 ********** Masking position 3 Map Score: 4.47034 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 169 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 ACACGGCACTGGATATCGGGTGCGTGC 1 6 1 GCACTGTATC 0.988876 -122 TCGGGTGCGTGCACTGTGTGTGTTTGTGTGGA 1 26 1 GCACTGTGTG 0.996584 -102 ACGCAGCACCGCGCTGTCTATCAGCCTCTCTT 1 68 0 GCGCTGTATC 0.989687 -60 AGACAGCGCGGTGCTGCGTGCGTACAATGGGC 1 81 1 GTGCTGTGCG 0.964524 -47 TTAGGCGGGTGCACTGCATGTGGTGTCTGAAA 4 72 1 GCACTGTGTG 0.996584 -50 ****** **** Masking position 5 Map Score: 3.77291 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 93 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 7 ACACGGCACTGGATATCGGGTGCGTGCACT 1 11 1 GGATATCGGG 0.954722 -117 GCGTACAATGGGCCATGGGGAAGCCGAGGT 1 100 1 GGCCATGGGG 0.907098 -28 TTCGGCCTGCGCGTGTCTTGGCGGGTGCTT 2 53 0 GCGTGTCTTG 0.918252 -191 TCGGCGCCGTGCCCAAGTGGTAAGGGAGAG 2 130 0 GCCCAAGTGG 0.852055 -114 TTTTTTGTTAGCCTGAGGGGTCCTCGGCGC 2 153 0 GCCTGAGGGG 0.95239 -91 CAAGGTCACAGCGTGCCTGGAGTATCGGTT 2 208 0 GCGTGCCTGG 0.946298 -36 GGATATCTTGCTGCTCGGCG 3 1 1 GGATATCTTG 0.874251 -34 GGTGTTATACGCAGATCTTGATTTTTGATC 4 27 1 GCAGATCTTG 0.806549 -95 CGGGTGCACTGCATGTGGTGTCTGAAAAGA 4 77 1 GCATGTGGTG 0.957115 -45 ACGACGCCGAGCATACGGTGTTTCTTGGGC 5 11 1 GCATACGGTG 0.951654 -85 AAAAAACACAGCCTACCAGGGGTAGGCTAG 7 85 0 GCCTACCAGG 0.898924 -34 ********** Masking position 1 Map Score: 5.73692 Number of sites scoring better than the average of aligned sites = 804 Number in coding regions = 730 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 ********** No masking Map Score: 1.40931e-12 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: 1.40931e-12 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: 1.40931e-12 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