AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_hpyl_reg_300.orf -o224_hpyl_300.ace -a/home/amcguire/genomes/ORF_hpyl.txt -z/home/amcguire/genomes/hpyl.fna -g0.39 -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 = 0.39 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RHP00299 25 AE000511 Input sequences: #1 RHP01228 50 AE000511 #2 RHP00296 130 AE000511 #3 RHP00300 167 AE000511 #4 RHP00462 148 AE000511 #5 RHP00464 67 AE000511 Motif number 1 ACTTCCTAAAAAATGATTACGCC 1 4 1 TCCTAAAAAA 0.950699 -47 GCATTAAGAATTTTAAAAAATTTAGCGTAT 2 28 0 TTTTAAAAAA 0.941313 -103 TTGTATTTTATTCTAACAAGAAACATGGAT 2 62 1 TTCTAACAAG 0.942583 -69 TAATTGCAAGGTTTAAAAAACGCTATTATT 2 94 0 GTTTAAAAAA 0.903556 -37 AAAAAAATATTTTTAACCAACAGCTTAGGG 3 50 0 TTTTAACCAA 0.954534 -118 ACAACCAGTATGCTAAAAAAAATATTTTTA 3 65 0 TGCTAAAAAA 0.972574 -103 AAAAGAAATATGCTAACAAAAAAACACTGA 3 111 0 TGCTAACAAA 0.974664 -57 AATATAAGAATTTGAAAAAAGAAATATGCT 3 127 0 TTTGAAAAAA 0.867877 -41 TGAAAGAAACTTTTAACAAACAATTCAAGG 4 23 0 TTTTAACAAA 0.97187 -126 GTAATTTTCTTTCTAAACAAGA 5 3 0 TTCTAAACAA 0.968903 -65 ********** Masking position 5 Map Score: 15.6897 Number of sites scoring better than the average of aligned sites = 755 Number in coding regions = 593 Number in noncoding regions = 162 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 TCTTGGATATAATGGCGTAATCATTTTTTAGG 1 15 0 AATGGTAATC 0.887395 -36 GCGTATAAATAAGGGAGCAATAA 2 2 0 AAGGGCAATA 0.943444 -129 TTATACGCTAAATTTTTTAAAATTCTTAATGC 2 26 1 AATTTTAAAA 0.796607 -105 AACAAGAAACATGGATATAATAATAGCGTTTT 2 76 1 ATGGATAATA 0.81737 -55 ATTTAATTGCAAGGTTTAAAAAACGCTATTAT 2 95 0 AAGGTAAAAA 0.848828 -36 TAAACCTTGCAATTAAATAATAGGAATGGTTG 2 109 1 AATTATAATA 0.907083 -22 AAACACTGAAAATTAGGTAATAAATACAACCA 3 88 0 AATTATAATA 0.907083 -80 TTAATCCTTAAATGGTATAATATAAGAATTTG 3 143 0 AATGGTAATA 0.980354 -25 TATACCATTTAAGGATTAAAAA 3 156 1 AAGGAAAAAA 0.928094 -12 AATTATACTAAAATAATTAAAATGACCGGTTA 4 52 1 AAATATAAAA 0.651707 -97 GACCGGTTAAAATGGAGTAAAATTTTTACCCA 4 75 1 AATGGTAAAA 0.977342 -74 TAAAAATCCTAAGTGTTAAATATAGTGGCATT 4 127 0 AAGTGAAATA 0.918695 -22 TAAAATTTTAAAGGGTGTAAAAGTAGATTGTT 5 46 1 AAGGGTAAAA 0.985724 -22 ***** ***** Masking position 9 Map Score: 13.127 Number of sites scoring better than the average of aligned sites = 945 Number in coding regions = 804 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 CGTTTAAGCCTTAATCTTGGATAT 1 37 0 TAAGCCTTAA 0.754076 -14 TTTATACGCTAAATTTTTTAAAATTCTTAA 2 25 1 AAATTTTTTA 0.680305 -106 AAATTTTTTAAAATTCTTAATGCAATCTTG 2 35 1 AAATTCTTAA 0.971972 -96 CAAATCCCGTAAAAAGCCAAA 3 2 1 AAATCCCGTA 0.82409 -166 TAAAAAGCCAAAAATCCTAGAGCATAAAAT 3 20 1 AAAATCCTAG 0.900606 -148 CTAGAGCATAAAATCCCTAAGCTGTTGGTT 3 36 1 AAATCCCTAA 0.98424 -132 TTCTTTTTTCAAATTCTTATATTATACCAT 3 134 1 AAATTCTTAT 0.845365 -34 TTTTTAATCCTTAAATGGTATAAT 3 154 0 TAATCCTTAA 0.920299 -14 AATCGCCAAATCCCTTGAATTGTTTGT 4 8 1 AAATCCCTTG 0.914503 -141 TAAAAATCCTAAGTGTTAAATA 4 137 0 AAAATCCTAA 0.954692 -12 CAATAACGATAAAATTTTAAAGGGTGTAAA 5 37 1 AAAATTTTAA 0.707528 -31 ********** Masking position 3 Map Score: 9.01502 Number of sites scoring better than the average of aligned sites = 1972 Number in coding regions = 1735 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 4 TTAAGAATTTTAAAAAATTTAGCGTATAAA 2 25 0 TAAAAAATTT 0.768293 -106 TTTATTCTAACAAGAAACATGGATATAATA 2 68 1 CAAGAAACAT 0.954091 -63 CAGTATGCTAAAAAAAATATTTTTAACCAA 3 60 0 AAAAAAATAT 0.945946 -108 ATATGCTAACAAAAAAACACTGAAAATTAG 3 104 0 AAAAAAACAC 0.894378 -64 GAATTTGAAAAAAGAAATATGCTAACAAAA 3 120 0 AAAGAAATAT 0.973075 -48 AGTATAATTGAAAGAAACTTTTAACAAACA 4 31 0 AAAGAAACTT 0.9776 -118 TCTTGTTTAGAAAGAAAATTACACTACAAT 5 11 1 AAAGAAAATT 0.916569 -57 ********** Masking position 5 Map Score: 4.99358 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 368 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 AAAATGATTACGCCATTATATCCAAGATTA 1 20 1 CGCCATTATA 0.987164 -31 TTATTGCTCCCTTATTTATACGCTAA 2 7 1 CTCCCTTATT 0.880526 -124 GTTTAAAAAACGCTATTATTATATCCATGT 2 84 0 CGCTATTATT 0.704784 -47 TTTTAAACCTTGCAATTAAATAATAGGAAT 2 106 1 TGCAATTAAA 0.745237 -25 TCTTATATTATACCATTTAAGGATTAAAAA 3 148 1 TACCATTTAA 0.765096 -20 AAAAGTTTCTTTCAATTATACTAAAATAAT 4 39 1 TTCAATTATA 0.756975 -110 AAAAATTTTACTCCATTTTAACCGGTCATT 4 72 0 CTCCATTTTA 0.944011 -77 AATTTTTACCCACCCTAATAAAGTCATGCT 4 95 1 CACCCTAATA 0.788611 -54 CATGCTACAATGCCACTATATTTAACACTT 4 119 1 TGCCACTATA 0.872526 -30 TCTACTTTTACACCCTTTAAAATTTTATCG 5 43 0 CACCCTTTAA 0.844624 -25 ********** Masking position 3 Map Score: 2.99941 Number of sites scoring better than the average of aligned sites = 1611 Number in coding regions = 1447 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 6 TGGCGTAATCATTTTTTAGGAAGT 1 5 0 ATTTTTTAGG 0.839497 -46 TTGCTCCCTTATTTATACGCTAAATTTTTT 2 14 1 ATTTATACGC 0.924941 -117 ATAATAGCGTTTTTTAAACCTTGCAATTAA 2 95 1 TTTTTAAACC 0.710766 -36 GGATTTTTGGCTTTTTACGGGATTTG 3 7 0 CTTTTTACGG 0.874606 -161 TAAAAAAAATATTTTTAACCAACAGCTTAG 3 52 0 ATTTTTAACC 0.971757 -116 TACTGGTTGTATTTATTACCTAATTTTCAG 3 85 1 ATTTATTACC 0.726855 -83 ATTTTACTCCATTTTAACCGGTCATTTTAA 4 68 0 ATTTTAACCG 0.943906 -81 ATGGAGTAAAATTTTTACCCACCCTAATAA 4 86 1 ATTTTTACCC 0.982116 -63 TAACGATAAAATTTTAAAGGGTGTAAAAGT 5 40 1 ATTTTAAAGG 0.89177 -28 AACAATCTACTTTTACACCCTTTAAAAT 5 50 0 ACTTTTACAC 0.639148 -18 ********** Masking position 4 Map Score: 7.12363 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 987 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 7 ********** No masking Map Score: -8.21797e-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 8 ********** No masking Map Score: -8.21797e-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 9 ********** No masking Map Score: -8.21797e-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