AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_Polysaccharide_Biosynthesis_1_tpal_reg_300.orf -o047_tpal_300.ace -a/home/amcguire/alignace/lib/ORF_tpal.txt -z/skink1/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 RTP00395 300 AE000520 #2 RTP00396 118 AE000520 #3 RTP01065 39 AE000520 #4 RTP00398 40 AE000520 #5 RTP01119 127 AE000520 #6 RTP01036 45 AE000520 #7 RTP01121 16 AE000520 #8 RTP00834 177 AE000520 #9 RTP00833 104 AE000520 #10 RTP01019 170 AE000520 Motif number 1 CCGACGCGCCAGTCACTCCTCCC 1 4 1 ACGCGCCAGT 0.921681 -297 GCGCCAGTCACTCCTCCCCCCTGCTCCACC 1 16 1 CTCCTCCCCC 0.805938 -285 CTCCTCCCCCCTGCTCCACCGCGCGCAAAG 1 26 1 CTGCTCCACC 0.926261 -275 GTTGGTACACCCCCGCCAGCAGCAATACCA 1 74 1 CCCCGCCAGC 0.990655 -227 GGCGGCGGCAATGCTCACGCCAGGATTTTC 1 112 0 ATGCTCACGC 0.832184 -189 ATTGCCGCCGCCGCTAGCGCCCCTGCGCAC 1 130 1 CCGCTAGCGC 0.915031 -171 GCTAGCGCCCCTGCGCACACGGTCGCCACA 1 142 1 CTGCGCACAC 0.718558 -159 CGCCACAAATCCGCGCGTGTGTGCAGTAGT 1 165 1 CCGCGCGTGT 0.634682 -136 TCCTCTGCGACCGCCCCTGCGTCTGTTCAG 1 210 0 CCGCCCCTGC 0.965717 -91 AGGATGCGTCACGCGCGTGCTGCATGCGAG 1 236 1 ACGCGCGTGC 0.910599 -65 AGACGACGTGCCACTTGAGCTAACAGCTCA 2 41 1 CCACTTGAGC 0.560017 -78 AACATCGTAGCCGCGCGCCTCCTGCAAAAG 2 70 1 CCGCGCGCCT 0.83697 -49 TTGTTCCTCCTCCTGCGCGGTGTTCG 2 103 0 CTCCTCCTGC 0.899817 -16 ACACGACAGACCGCGCGCGCAAGATCAACA 3 11 1 CCGCGCGCGC 0.674671 -29 GCCAGCTGCGCCAGTGCTGAACCGA 4 6 1 CTGCGCCAGT 0.948545 -35 TTCATCAGCACCGCGTCCGCACGCCCTCTA 5 86 1 CCGCGTCCGC 0.977766 -42 GTAGATGGGTACGCGCCTGGGTAATGAGCT 8 34 0 ACGCGCCTGG 0.818658 -144 AGCCCCAAAGCCGCTCGCGCTCAAACCCCC 9 14 1 CCGCTCGCGC 0.964507 -91 ACAAAAACCACTGCGCAAGAAGTGCCGCTA 9 48 1 CTGCGCAAGA 0.665138 -57 AGGGGTTATTCCCCGCGTCGAGTATTC 9 88 1 CCCCGCGTCG 0.681484 -17 CACAGCAGGTCCGCGCGAGC 10 1 0 CCGCGCGAGC 0.988587 -170 CTTCATAACCACGCTCGAGCTGAATGCCAA 10 41 1 ACGCTCGAGC 0.976044 -130 CATGCTTTTTCCGCTCAGGCAATTGGCATT 10 63 0 CCGCTCAGGC 0.942144 -108 CATTGTAGAGCCACTCAAGCCCGGCGCCAA 10 139 1 CCACTCAAGC 0.858841 -32 ********** Masking position 4 Map Score: 45.7894 Number of sites scoring better than the average of aligned sites = 3093 Number in coding regions = 2834 Number in noncoding regions = 259 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 2 TGAGCGTGTTGTCTTTGCGCGCGGTGGAGCAGG 1 35 0 GTTTTGGCGG 0.954896 -266 TGTACCAACCGCTTTTGAGCGTGTTGTCTTTGC 1 50 0 GCTTTGGCGG 0.979467 -251 CCGGTTCATTGGTATTGCTGCTGGCGGGGGTGT 1 80 0 GGATTGTGCG 0.880808 -221 ACACACGCGCGGATTTGTGGCGACCGTGTGCGC 1 154 0 GGTTTGGGCA 0.923672 -147 TGTGCTGCTTGGGTTTGTGGCAGTGTGTGCGTT 1 268 0 GGTTTGGGCG 0.995346 -33 CACGTCGTCTCCATATGGACGTGCAGGTGAAAG 2 18 0 CCTATGACGG 0.538754 -101 GGTGTTCGTTGCTTTTGCAGGAGGCGCGCGGCT 2 78 0 GCTTTGAGGG 0.940496 -41 TGGTTTTGATGTTGATCTTGCGCG 3 26 0 GGTTTGTGTG 0.854045 -14 ATTTGATAATGGGAATGAGGGACTCAAAGAATT 5 14 0 GGAATGGGGC 0.731894 -114 TACGCGCCTGGGTAATGAGCTGGAGAAAATTTT 8 22 0 GGAATGGCTG 0.833747 -156 GAAAGTAGATGGGTACGCGCCTGGGTAATGAGC 8 35 0 GGTACGGCCG 0.928507 -143 GAGCGCGAGCGGCTTTGGGGCTGTG 9 3 0 GGTTTGGGCG 0.995346 -102 TTGTACCAGGGGGTTTGAGCGCGAGCGGCTTTG 9 19 0 GGTTTGGCGG 0.994059 -86 TTGCGCAGTGGTTTTTGTACCAGGGGGTTTGAG 9 33 0 GTTTTGACCG 0.845877 -72 GCTCGAGCGTGGTTATGAAGGGGATGGGTCCAC 10 28 0 GGTATGAGGG 0.971374 -143 CAATTCGCTCCGGTATGGGGCGGCGTTCATGCT 10 87 0 CGTATGGGCG 0.952834 -84 ** **** *** * Masking position 7 Map Score: 24.808 Number of sites scoring better than the average of aligned sites = 590 Number in coding regions = 550 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 3 GCTGCTGGCGGGGGTGTACCAACCGCTTTTGAGCGTGT 1 59 0 GGGGTCCCTT 0.96227 -242 GAGCATTGCCGCCGCCGCTAGCGCCCCTGCGCACACGG 1 126 1 GCGCGTCCCT 0.938233 -175 TGGGTTTGTGGCAGTGTGTGCGTTTTCTCGCATGCAGC 1 254 0 GCGGTTTTCT 0.960439 -47 ACGTCCATATGGAGACGACGTGCCACTTGAGCTAACAG 2 29 1 GGGCGCCCTT 0.786036 -90 CTCCTCCTGCGCGGTGTTCGTTGCTTTTGCAGGAGGCG 2 85 0 GCGGTCCTTT 0.977963 -34 GATGAACCATGCAGGATTTGATTTTTTTACCCTTGGCA 5 54 0 GCGATTTTTT 0.807376 -74 GTTCATCAGCACCGCGTCCGCACGCCCTCTAAAGAGGG 5 85 1 ACGGTCGCCT 0.639957 -43 GTACGCTGTATTCTACCCTCTTTAGAGGGCGT 5 106 0 GCGATCCCTT 0.973921 -22 TCATTACCCAGGCGCGTACCCATCTACTTTCGGGGAAA 8 37 1 GGGGTCCACT 0.820485 -141 TTGAAGACATTCAGTATTTTAATTACCTCATCCAAGAA 8 103 1 TCGATTTCCT 0.536171 -75 TTTAAAACGTGCGGCATGTTCGTTTTTTTGGAATTCTT 8 136 0 GCGATTTTTT 0.807376 -42 CACTTCTTGCGCAGTGGTTTTTGTACCAGGGGGTTTGA 9 34 0 GCGGGTTCCA 0.748975 -71 AATACTCGACGCGGGGAATAACCCCTCTTCGGCAAATA 9 76 0 GCGGATCTCT 0.836834 -29 GCGCGGACCTGCTGTGGACCCATCCCCTTCATAACCAC 10 15 1 GCGGGCCCCT 0.99241 -156 CCACGCTCGAGCTGAATGCCAATTGCCTGAGCGGAAAA 10 49 1 GCGATCTCCT 0.976693 -122 CCGGTATGGGGCGGCGTTCATGCTTTTTCCGCTCAGGC 10 73 0 GCGGTCTTTT 0.960439 -98 ** * ** * * *** Masking position 4 Map Score: 12.7697 Number of sites scoring better than the average of aligned sites = 1196 Number in coding regions = 1111 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 4 AATGCTCACGCCAGGATTTTCCGGTTCATT 1 103 0 CCAGGATTTT 0.96717 -198 ATGAGGGACTCAAAGAATTTCT 5 3 0 CAAAGAATTT 0.857175 -125 CCCTTGGCAATCACGAATTTGATAATGGGA 5 33 0 TCACGAATTT 0.83991 -95 GATGAACCATGCAGGATTTGATTTTTTTAC 5 62 0 GCAGGATTTG 0.915047 -66 TACCTTGTACGCAAGATTTTTCCCCGAAAG 8 63 0 GCAAGATTTT 0.972625 -115 ATTACCTCATCCAAGAATTCCAAAAAAACG 8 124 1 CCAAGAATTC 0.944188 -54 TCGATTTGCAAGAATTTAAAACGTGCG 8 161 0 GCAAGAATTT 0.978845 -17 ********** Masking position 6 Map Score: 2.82312 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 73 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 CGCGCCAGTCACTCCTCCCCCCTGCTCCAC 1 15 1 ACTCCTCCCC 0.987177 -286 CACGCGCGTGACGCATCCTCTGCGACCGCC 1 225 0 ACGCATCCTC 0.983408 -76 CCAGGCGCGTACCCATCTACTTTCGGGGAA 8 44 1 ACCCATCTAC 0.943 -134 GCGGGGAATAACCCCTCTTCGGCAAATAGC 9 74 0 ACCCCTCTTC 0.978665 -31 CCTGCTGTGGACCCATCCCCTTCATAACCA 10 22 1 ACCCATCCCC 0.994886 -149 AAAAGCATGAACGCCGCCCCATACCGGAGC 10 84 1 ACGCCGCCCC 0.987143 -87 ********** Masking position 1 Map Score: 7.22597 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 86 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 TTGTCTTTGCGCGCGGTGGAGCAGGGGGGA 1 30 0 GCGCGGTGGA 0.939886 -271 GGTGTACCAACCGCTTTTGAGCGTGTTGTC 1 55 0 CCGCTTTTGA 0.865588 -246 GGGGCGCTAGCGGCGGCGGCAATGCTCACG 1 123 0 CGGCGGCGGC 0.945965 -178 CGTGACGCATCCTCTGCGACCGCCCCTGCG 1 219 0 CCTCTGCGAC 0.862047 -82 TTCATCAGCACCGCGTCCGCACGCCCTCTA 5 86 1 CCGCGTCCGC 0.924914 -42 TGTATTCTACCCTCTTTAGAGGGCGTGCGG 5 102 0 CCTCTTTAGA 0.70291 -26 GCTCTTTGGCACGAAT 7 1 1 GCTCTTTGGC 0.916239 -16 TACCGCTGTGGAAAATTTTCTC 8 3 1 CCGCTGTGGA 0.990544 -175 GGGAATAACCCCTCTTCGGCAAATAGCGGC 9 71 0 CCTCTTCGGC 0.980288 -34 TCGCGCGGACCTGCTGTGGACCCATCCCCT 10 13 1 CTGCTGTGGA 0.901498 -158 CATGCTTTTTCCGCTCAGGCAATTGGCATT 10 63 0 CCGCTCAGGC 0.904618 -108 ********** Masking position 4 Map Score: 7.98677 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 702 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 GCCAGCAGCAATACCAATGAACCGGAAAATCC 1 88 1 AACAATGAAC 0.973219 -213 GCCTCCTGCAAAAGCAACGAACACCGCGCAGG 2 86 1 AACAACGAAC 0.990787 -33 TACATATCAACGATCATCATTCGCA 6 31 0 AACAACGATC 0.982947 -15 CAAGAATTCCAAAAAAACGAACATGCCGCACG 8 135 1 AAAAACGAAC 0.953721 -43 CATCCCCTTCATAACCACGCTCGAGCTGAATG 10 35 1 AACCACGCTC 0.945866 -136 CCTGAGCGGAAAAAGCATGAACGCCGCCCCAT 10 74 1 AAGCATGAAC 0.895357 -97 * * ******** Masking position 7 Map Score: 1.56354 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 31 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 ********** No masking Map Score: -2.98895e-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: -2.98895e-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: -2.98895e-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