AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i047_tpal_bbur_300.orf -o047_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 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 GGGAGGAGTGACTGGCGCGTCGG 1 2 0 ACGGCGCGTG 0.982972 -299 CTTTGCGCGCGGTGGAGCAGGGGGGAGGAGTG 1 24 0 GGGGAGCAGG 0.932696 -277 TGGTATTGCTGCTGGCGGGGGTGTACCAACCG 1 72 0 GCGGCGGGGT 0.944613 -229 GAAAATCCTGGCGTGAGCATTGCCGCCGCCGC 1 112 1 GCTGAGCATG 0.87376 -189 GTGCGCAGGGGCGCTAGCGGCGGCGGCAATGC 1 128 0 GCCTAGCGGG 0.967907 -173 TGTGGCGACCGTGTGCGCAGGGGCGCTAGCGG 1 140 0 GTTGCGCAGG 0.861737 -161 ACTACTGCACACACGCGCGGATTTGTGGCGAC 1 163 0 ACCGCGCGGT 0.667488 -138 CGTAGTCTGAACAGACGCAGGGGCGGTCGCAG 1 204 1 ACGACGCAGG 0.954207 -97 AGACGCAGGGGCGGTCGCAGAGGATGCGTCAC 1 216 1 GCGTCGCAGG 0.970972 -85 CTCGCATGCAGCACGCGCGTGACGCATCCTCT 1 234 0 GCCGCGCGTA 0.53646 -67 ACTGCCACAAACCCAAGCAGCACAAAGAAAAT 1 277 1 ACCAAGCAGA 0.477673 -24 CTTTTGCAGGAGGCGCGCGGCTACGATGTTGA 2 68 0 AGCGCGCGGT 0.830805 -51 TTGTTCCTCCTCCTGCGCGGTGTTCGTTGCTT 2 97 0 TCTGCGCGGG 0.907735 -22 TGTTGATCTTGCGCGCGCGGTCTGTCGTGT 3 9 0 GCCGCGCGGC 0.97162 -31 TCGGTTCAGCACTGGCGCAGCTGGC 4 4 0 ACGGCGCAGT 0.964347 -37 TAGAGGGCGTGCGGACGCGGTGCTGATGAACC 5 84 0 GCGACGCGGG 0.995926 -44 AGCTCATTACCCAGGCGCGTACCCATCTACTT 8 34 1 CCGGCGCGTC 0.783322 -144 GGGGGTTTGAGCGCGAGCGGCTTTGGGGCTGT 9 12 0 GCCGAGCGGT 0.988418 -93 TAGCGGCACTTCTTGCGCAGTGGTTTTTGTAC 9 46 0 TCTGCGCAGG 0.928019 -59 GCCGCTATTTGCCGAAGAGGGGTTATTCCCCG 9 71 1 GCGAAGAGGG 0.735631 -34 GAATACTCGACGCGGGGAATAACCCCT 9 88 0 CTGACGCGGG 0.713134 -17 GCTCGCGCGGACCTGCTGTGGA 10 1 1 GCCGCGCGGC 0.856465 -170 TTGGCATTCAGCTCGAGCGTGGTTATGAAGGG 10 39 0 GCCGAGCGTG 0.980855 -132 AATGCCAATTGCCTGAGCGGAAAAAGCATGAA 10 63 1 GCTGAGCGGA 0.947685 -108 ** ******* * Masking position 7 Map Score: 46.09 Number of sites scoring better than the average of aligned sites = 1061 Number in coding regions = 321 Number in noncoding regions = 740 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 2 CCTGCTCCACCGCGCGCAAAGACAACACGCTCA 1 35 1 CCGCCAAAAC 0.964248 -266 GCAAAGACAACACGCTCAAAAGCGGTTGGTACA 1 50 1 CCGCCAAAGC 0.98381 -251 ACACCCCCGCCAGCAGCAATACCAATGAACCGG 1 80 1 CGCACAATCC 0.903977 -221 GCGCACACGGTCGCCACAAATCCGCGCGTGTGT 1 154 1 TGCCCAAACC 0.939085 -147 AACGCACACACTGCCACAAACCCAAGCAGCACA 1 268 1 CGCCCAAACC 0.996343 -33 CTTTCACCTGCACGTCCATATGGAGACGACGTG 2 18 1 CCGTCATAGG 0.598071 -101 AGCCGCGCGCCTCCTGCAAAAGCAACGAACACC 2 78 1 CCCTCAAAGC 0.952686 -41 CGCGCAAGATCAACATCAAAACCA 3 26 1 CACACAAACC 0.881717 -14 AATTCTTTGAGTCCCTCATTCCCATTATCAAAT 5 14 1 GCCCCATTCC 0.776669 -114 AAAATTTTCTCCAGCTCATTACCCAGGCGCGTA 8 22 1 CAGCCATTCC 0.864658 -156 GCTCATTACCCAGGCGCGTACCCATCTACTTTC 8 35 1 CGGCCGTACC 0.943004 -143 CACAGCCCCAAAGCCGCTCGCGCTC 9 3 1 CGCCCAAACC 0.996343 -102 CAAAGCCGCTCGCGCTCAAACCCCCTGGTACAA 9 19 1 CCGCCAAACC 0.995331 -86 CTCAAACCCCCTGGTACAAAAACCACTGCGCAA 9 33 1 CGGTCAAAAC 0.874871 -72 GTGGACCCATCCCCTTCATAACCACGCTCGAGC 10 28 1 CCCTCATACC 0.97739 -143 AGCATGAACGCCGCCCCATACCGGAGCGAATTG 10 87 1 CGCCCATACG 0.962597 -84 * *** **** ** Masking position 7 Map Score: 24.808 Number of sites scoring better than the average of aligned sites = 1799 Number in coding regions = 529 Number in noncoding regions = 1270 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 3 GCGGTTGGTACACCCCCGCCAGCAGCAATA 1 71 1 CACCCCCGCC 0.915474 -230 GCGTGAGCATTGCCGCCGCCGCTAGCGCCC 1 122 1 TGCCGCCGCC 0.930966 -179 CAGTAGTAAGGACCGCCGTAGTCTGAACAG 1 188 1 GACCGCCGTA 0.889802 -113 CATCCTCTGCGACCGCCCCTGCGTCTGTTC 1 212 0 GACCGCCCCT 0.819752 -89 AGCTCAAGTGGCACGTCGTCTCCATATGGA 2 32 0 GCACGTCGTC 0.94537 -87 CATCGTAGCCGCGCGCCTCCTGCAAAAGCA 2 72 1 GCGCGCCTCC 0.952887 -47 TTGATCTTGCGCGCGCGGTCTGTCGTGT 3 9 0 GCGCGCGGTC 0.811758 -31 TGGTTCATCAGCACCGCGTCCGCACGCCCT 5 83 1 GCACCGCGTC 0.959659 -45 CACCGCGTCCGCACGCCCTCTAAAGAGGGT 5 94 1 GCACGCCCTC 0.976415 -34 GAGGGGTTATTCCCCGCGTCGAGTATTC 9 87 1 TCCCCGCGTC 0.895921 -18 GAAAAAGCATGAACGCCGCCCCATACCGGA 10 82 1 GAACGCCGCC 0.980831 -89 AGCCACTCAAGCCCGGCGCCAAAAAGAAAA 10 147 1 GCCCGGCGCC 0.994218 -24 ********** Masking position 4 Map Score: 14.4337 Number of sites scoring better than the average of aligned sites = 2087 Number in coding regions = 607 Number in noncoding regions = 1480 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 AATGCTCACGCCAGGATTTTCCGGTTCATT 1 103 0 CCAGGATTTT 0.948862 -198 ATGAGGGACTCAAAGAATTTCT 5 3 0 CAAAGAATTT 0.823225 -125 GATGAACCATGCAGGATTTGATTTTTTTAC 5 62 0 GCAGGATTTG 0.952835 -66 TACCTTGTACGCAAGATTTTTCCCCGAAAG 8 63 0 GCAAGATTTT 0.973127 -115 ATTACCTCATCCAAGAATTCCAAAAAAACG 8 124 1 CCAAGAATTC 0.941764 -54 TCGATTTGCAAGAATTTAAAACGTGCG 8 161 0 GCAAGAATTT 0.979236 -17 AAACCACTGCGCAAGAAGTGCCGCTATTTG 9 52 1 GCAAGAAGTG 0.923256 -53 ********** Masking position 6 Map Score: 4.46523 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 118 Number in noncoding regions = 281 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 5 GGTCGCAGAGGATGCGTCACGCGCGTGCTGC 1 228 1 GATGCTCACG 0.937958 -73 CGTTTTCTCGCATGCAGCACGCGCGTGACGC 1 241 0 CATGCGCACG 0.731343 -60 GCCACAAACCCAAGCAGCACAAAGAAAATAA 1 280 1 CAAGCGCACA 0.971986 -21 GCTGTTAGCTCAAGTGGCACGTCGTCTCCAT 2 37 0 CAAGTGCACG 0.973388 -82 AAAAAACGAACATGCCGCACGTTTTAAATTC 8 146 1 CATGCGCACG 0.731343 -32 CACAGCCCCAAAGCCGCTCGCGCTCAAACC 9 10 1 AAAGCGCTCG 0.95803 -95 AGGCAATTGGCATTCAGCTCGAGCGTGGTTA 10 46 0 CATTCGCTCG 0.955584 -125 ***** ***** Masking position 2 Map Score: 10.6929 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 10 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 6 CCGCCGCCGCTAGCGCCCCTGCGCACACGG 1 134 1 TAGCGCCCCT 0.995964 -167 CATCCTCTGCGACCGCCCCTGCGTCTGTTC 1 212 0 GACCGCCCCT 0.953917 -89 AGAAATTCTTTGAGTCCCTCATTCCCATT 5 10 1 TTGAGTCCCT 0.952028 -118 TTCAACAAATTTGCGTACCTTGTACGCAAG 8 78 0 TTGCGTACCT 0.900853 -100 CTTCGGCAAATAGCGGCACTTCTTGCGCAG 9 58 0 TAGCGGCACT 0.968869 -47 CCCCACATTGTAGAGCCACTCAAGCCCGGC 10 134 1 TAGAGCCACT 0.965743 -37 ********** Masking position 10 Map Score: 2.56834 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 93 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 7 ACGGCGGTCCTTACTACTGCACACACGCGC 1 177 0 TTACTACTGC 0.842426 -124 TGAACGACTTTCACCTGCACGTCCATAT 2 9 1 TTTCACCTGC 0.959005 -110 ATCCTGCATGGTTCATCAGCACCGCGTCCG 5 75 1 GTTCATCAGC 0.929885 -53 TGGAGAAAATTTTCCACAGCGGTA 8 5 0 TTTCCACAGC 0.984262 -173 TGTGGAAAATTTTCTCCAGCTCATTACCCA 8 17 1 TTTCTCCAGC 0.977602 -161 GAAGGGGATGGGTCCACAGCAGGTCCGCGC 10 15 0 GGTCCACAGC 0.949892 -156 ********** Masking position 4 Map Score: 1.19329 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 107 Number in noncoding regions = 225 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 GGATTTTCCGGTTCATTGGTATTGCTGCTGGC 1 88 0 GTTCATTGTT 0.976363 -213 CCTGCGCGGTGTTCGTTGCTTTTGCAGGAGGC 2 86 0 GTTCGTTGTT 0.991886 -33 TGCGAATGATGATCGTTGATATGTA 6 31 1 GATCGTTGTT 0.984967 -15 CGTGCGGCATGTTCGTTTTTTTGGAATTCTTG 8 135 0 GTTCGTTTTT 0.959058 -43 CATTCAGCTCGAGCGTGGTTATGAAGGGGATG 10 35 0 GAGCGTGGTT 0.952063 -136 ATGGGGCGGCGTTCATGCTTTTTCCGCTCAGG 10 74 0 GTTCATGCTT 0.906767 -97 ******** * * Masking position 6 Map Score: 1.56354 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 17 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 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 Motif number 11 ********** 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