AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i263_tpal_bbur_300.orf -o263_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 RTP00501 73 AE000520 #2 RTP00500 127 AE000520 #3 RTP00498 117 AE000520 #4 RTP00497 30 AE000520 #5 RTP00495 106 AE000520 #6 RTP00493 88 AE000520 #7 RBB00736 178 3615 #8 RBB00735 61 3615 #9 RBB00734 56 3615 #10 RBB00725 54 3615 #11 RBB00716 39 3615 Motif number 1 GGTTCAGAGGACATTAAAAATTTTGCCAGC 1 49 1 ACATTAAAAA 0.89918 -25 CCTAGACAAAAAAATATAAAATTAAGCAAA 7 37 0 AAAATATAAA 0.886665 -142 TTTAATTATTAAGATAAAAACCTAGACAAA 7 57 0 AAGATAAAAA 0.882327 -122 TTAATAATTAAAATTATAAAATAAGTTGTA 7 75 1 AAATTATAAA 0.900628 -104 TAAGGCAGCTAATTTAAAAATTAGCCACAA 7 114 0 AATTTAAAAA 0.965778 -65 TTACATGAGTAATTTAAAAAAAGAGCTATA 7 141 1 AATTTAAAAA 0.965778 -38 ATATTTGAAAAATATATAAACATATAGATG 8 29 1 AATATATAAA 0.886662 -33 AATTTAATAAAAAAGAAAAGTCAAGCATTA 9 13 0 AAAAGAAAAG 0.795354 -44 AAACATTGTAAATTTAATAAAAAAGAAAAG 9 23 0 AATTTAATAA 0.750253 -34 TTTTAATTGAAAAGATTGGAGATT 10 5 1 AATTGAAAAG 0.818261 -50 TTTTGGTTTTAATTGAAAAATTGGAGAAAG 10 34 1 AATTGAAAAA 0.934432 -21 TAAAAAGCCCACAATAAAAATCAATTTTA 11 10 0 ACAATAAAAA 0.88504 -30 GTCTTAAAAATAAAAAGCCCACAATA 11 24 0 AAAATAAAAA 0.960581 -16 ********** Masking position 6 Map Score: 15.3293 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 105 Number in noncoding regions = 265 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 CAAGTCGTCTCTACGCTGAGCTCGGTTCAGA 1 26 1 CTACGCGAGC 0.852791 -48 AATTTTTAATGTCCTCTGAACCGAGCTCAGC 1 40 0 GTCCTCGAAC 0.59917 -34 GGAAGTGGCGCTTGCGCGCTA 2 1 1 GGAAGTGCGC 0.904186 -127 TTGTCGAAAAGTCCGTAGCGCGCAAGCGCCA 2 16 0 GTCCGTGCGC 0.834809 -112 TTTTCGACAAGGACGCTGCAGGCGCTTGTGC 2 37 1 GGACGCGCAG 0.972704 -91 ACGCTGCAGGCGCTTGTGCGGAGTATGCGCG 2 49 1 CGCTTGGCGG 0.767919 -79 GAAGGTACGCCTCTGCCGCGCATACTCCGCA 2 65 0 CTCTGCGCGC 0.897201 -63 CGTCGGGAATGGATGGAGAAGGTACGCCTCT 2 82 0 GGATGGGAAG 0.93673 -46 CATCCATTCCCGACGGGGAAGGAGGAAGCTG 2 98 1 CGACGGGAAG 0.872415 -30 CGGGGAAGGAGGAAGCTGCGCACCGCA 2 111 1 GGAAGCGCGC 0.96695 -17 AGGTGCTCTTGCGTGCTGAGGCAGAAAAGTT 3 54 0 GCGTGCGAGG 0.717285 -64 CCAGTGAACCGGATGTTGAGGTGCTCTTGCG 3 72 0 GGATGTGAGG 0.891174 -46 GGCCTGGTGCACGAAATAGTGA 3 106 0 GCCTGGGCAC 0.941392 -12 TCACCATGGAGAAGATTGTCGGTC 4 17 0 CCATGGGAAG 0.826505 -14 TGGGCTTTAGGGAATTAGAAGGGGT 5 5 0 GGAATTGAAG 0.419183 -102 GTTGGCGTACCCATGCTGCACATGAGTTGGC 5 80 0 CCATGCGCAC 0.940082 -27 ACATCTCTGTGCAATGCGCACCGTATTCAGC 6 13 1 GCAATGGCAC 0.726842 -76 AATGCGCACCGTATTCAGCACCATTTCAGGA 6 25 1 GTATTCGCAC 0.826938 -64 ****** **** Masking position 8 Map Score: 12.0193 Number of sites scoring better than the average of aligned sites = 4916 Number in coding regions = 1494 Number in noncoding regions = 3422 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 TCTAATTCCCTAAAGCCCATAGGGAATGCA 5 17 1 TAAAGCCCAT 0.95226 -90 AAAATTAAGCAAAAACACAACAGGCCAATT 7 20 0 AAAAACACAA 0.865893 -159 TCCTCCTTAAAACCAAATTATAGCTCT 7 162 0 TAAAACCAAA 0.963693 -17 TATCAAGACCAAAAGCCAAAT 8 2 0 AAAAGCCAAA 0.976601 -60 ATTTTTCAATTAAAACCAAAAATCTCCAAT 10 25 0 TAAAACCAAA 0.963693 -30 CTTAAAAATAAAAAGCCCACAATAAAAATC 11 18 0 AAAAGCCCAC 0.967282 -22 ********** Masking position 4 Map Score: 3.80981 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 106 Number in noncoding regions = 283 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 4 TGTGCGGAGTATGCGCGGCAGAGGCGTACC 2 63 1 ATGCGCGGCA 0.782243 -65 TACCTTCTCCATCCATTCCCGACGGGGAAG 2 89 1 ATCCATTCCC 0.759492 -39 TCAACATCCGGTTCACTGGCACTCACTATT 3 84 1 GTTCACTGGC 0.86818 -34 GACATTGAGTATGCATTCCCTATGGGCTTT 5 28 0 ATGCATTCCC 0.932306 -79 TTGGCTCATTATGCACGGGCTGCCTGTGAC 5 55 0 ATGCACGGGC 0.972402 -52 CATGCTGCACATGAGTTGGCTCATTATGCA 5 70 0 ATGAGTTGGC 0.959402 -37 ACATGCGTTGGCGTACCCATGC 5 95 0 ATGCGTTGGC 0.98632 -12 ATAACAATTAATTGGCCTGTTGTGTT 7 7 1 ATTAATTGGC 0.877705 -172 TAATTTTTAAATTAGCTGCCTTACATGAGT 7 121 1 ATTAGCTGCC 0.905693 -58 ********** Masking position 2 Map Score: 3.92499 Number of sites scoring better than the average of aligned sites = 1176 Number in coding regions = 324 Number in noncoding regions = 852 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 CTGAGGCAGAAAAGTTTGGAATAAAACTTG 3 40 0 AAAGTTTGGA 0.977957 -78 CCATTTCAGGATAGTGGGGAAACAGCTGAG 6 45 1 ATAGTGGGGA 0.930792 -44 AAAAAGAGCTATAATTTGGTTTTAAGGAGG 7 158 1 ATAATTTGGT 0.787165 -21 ATATAAACATATAGATGGGATAAGTAGGTT 8 42 1 ATAGATGGGA 0.973532 -20 TTTTAATTGAAAAGATTGGAGATTTTTGGT 10 11 1 AAAGATTGGA 0.977957 -44 GTTTTAATTGAAAAATTGGAGAAAGT 10 39 1 AAAAATTGGA 0.937466 -16 ********** Masking position 3 Map Score: 3.25305 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 30 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 AGGACATTAAAAATTTTGCCAGCGTTCT 1 56 1 AAATTTGCCA 0.943948 -18 TGGGCATGAGAAAATCACCAAGTTTTATTCC 3 22 1 AAAATACCAA 0.951189 -96 CAGCCCGTGCATAATGAGCCAACTCATGTGC 5 63 1 ATAATAGCCA 0.93533 -44 AAAAAATATAAAATTAAGCAAAAACACAACA 7 28 0 AAATTAGCAA 0.952341 -151 AGCTAATTTAAAAATTAGCCACAAACATCAT 7 107 0 AAAATAGCCA 0.983229 -72 ATTAAAACCAAAAATCTCCAATCTTTTCAAT 10 16 0 AAAATTCCAA 0.912621 -39 ***** ***** Masking position 5 Map Score: 2.95659 Number of sites scoring better than the average of aligned sites = 483 Number in coding regions = 138 Number in noncoding regions = 345 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 ********** No masking Map Score: -1.17788e-14 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 8 ********** No masking Map Score: -1.17788e-14 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: -1.17788e-14 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