AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_hpyl_reg_300.orf -o207_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 0.960697 -47 GCATTAAGAATTTTAAAAAATTTAGCGTAT 2 28 0 TTTTAAAAAA 0.936527 -103 TTGTATTTTATTCTAACAAGAAACATGGAT 2 62 1 TTCTAACAAG 0.954166 -69 TAATTGCAAGGTTTAAAAAACGCTATTATT 2 94 0 GTTTAAAAAA 0.921788 -37 AAAAAAATATTTTTAACCAACAGCTTAGGG 3 50 0 TTTTAACCAA 0.963575 -118 ACAACCAGTATGCTAAAAAAAATATTTTTA 3 65 0 TGCTAAAAAA 0.978227 -103 AAAAGAAATATGCTAACAAAAAAACACTGA 3 111 0 TGCTAACAAA 0.979911 -57 AATATAAGAATTTGAAAAAAGAAATATGCT 3 127 0 TTTGAAAAAA 0.87663 -41 TGAAAGAAACTTTTAACAAACAATTCAAGG 4 23 0 TTTTAACAAA 0.973786 -126 GTAATTTTCTTTCTAAACAAGA 5 3 0 TTCTAAACAA 0.975276 -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 CCTAAAAAATGATTACGCCATTATATCCAAGA 1 15 1 GATTACCATT 0.880849 -36 TTATTGCTCCCTTATTTATACGC 2 2 1 TATTGCCCTT 0.939935 -129 GCATTAAGAATTTTAAAAAATTTAGCGTATAA 2 26 0 TTTTAAAATT 0.786072 -105 AAAACGCTATTATTATATCCATGTTTCTTGTT 2 76 0 TATTATCCAT 0.807632 -55 ATAATAGCGTTTTTTAAACCTTGCAATTAAAT 2 95 1 TTTTTACCTT 0.84044 -36 CAACCATTCCTATTATTTAATTGCAAGGTTTA 2 109 0 TATTATAATT 0.902214 -22 TGGTTGTATTTATTACCTAATTTTCAGTGTTT 3 88 1 TATTATAATT 0.902214 -80 CAAATTCTTATATTATACCATTTAAGGATTAA 3 143 1 TATTACCATT 0.979088 -25 TTTTTAATCCTTAAATGGTATA 3 156 0 TTTTTTCCTT 0.923709 -12 TAACCGGTCATTTTAATTATTTTAGTATAATT 4 52 0 TTTTATATTT 0.637059 -97 TGGGTAAAAATTTTACTCCATTTTAACCGGTC 4 75 0 TTTTACCATT 0.975883 -74 AATGCCACTATATTTAACACTTAGGATTTTTA 4 127 1 TATTTCACTT 0.913792 -22 AACAATCTACTTTTACACCCTTTAAAATTTTA 5 46 0 TTTTACCCTT 0.984796 -22 ***** ***** Masking position 4 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 ATATCCAAGATTAAGGCTTAAACG 1 37 1 TTAAGGCTTA 0.770446 -14 TTAAGAATTTTAAAAAATTTAGCGTATAAA 2 25 0 TAAAAAATTT 0.699637 -106 CAAGATTGCATTAAGAATTTTAAAAAATTT 2 35 0 TTAAGAATTT 0.974333 -96 TTTGGCTTTTTACGGGATTTG 3 2 0 TACGGGATTT 0.836814 -166 ATTTTATGCTCTAGGATTTTTGGCTTTTTA 3 20 0 CTAGGATTTT 0.90841 -148 AACCAACAGCTTAGGGATTTTATGCTCTAG 3 36 0 TTAGGGATTT 0.985583 -132 ATGGTATAATATAAGAATTTGAAAAAAGAA 3 134 0 ATAAGAATTT 0.856817 -34 ATTATACCATTTAAGGATTAAAAA 3 154 1 TTAAGGATTA 0.926683 -14 ACAAACAATTCAAGGGATTTGGCGATT 4 8 0 CAAGGGATTT 0.921312 -141 TATTTAACACTTAGGATTTTTA 4 137 1 TTAGGATTTT 0.958445 -12 TTTACACCCTTTAAAATTTTATCGTTATTG 5 37 0 TTAAAATTTT 0.725877 -31 ********** Masking position 8 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 0.775514 -106 TTTATTCTAACAAGAAACATGGATATAATA 2 68 1 CAAGAAACAT 0.955855 -63 CAGTATGCTAAAAAAAATATTTTTAACCAA 3 60 0 AAAAAAATAT 0.948005 -108 ATATGCTAACAAAAAAACACTGAAAATTAG 3 104 0 AAAAAAACAC 0.89819 -64 GAATTTGAAAAAAGAAATATGCTAACAAAA 3 120 0 AAAGAAATAT 0.974129 -48 AGTATAATTGAAAGAAACTTTTAACAAACA 4 31 0 AAAGAAACTT 0.97848 -118 TCTTGTTTAGAAAGAAAATTACACTACAAT 5 11 1 AAAGAAAATT 0.919652 -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 AAAAATGATTACGCCATTATATCCAAGATTA 1 19 1 ACCCATTATA 0.985324 -32 TTTTTAAACCTTGCAATTAAATAATAGGAAT 2 105 1 TTCAATTAAA 0.835156 -26 TTCTTATATTATACCATTTAAGGATTAAAAA 3 147 1 ATCCATTTAA 0.970405 -21 TAAAAGTTTCTTTCAATTATACTAAAATAAT 4 38 1 TTCAATTATA 0.868365 -111 TAAAAATTTTACTCCATTTTAACCGGTCATT 4 72 0 ACCCATTTTA 0.980974 -77 TCATGCTACAATGCCACTATATTTAACACTT 4 118 1 ATCCACTATA 0.944772 -31 ATCTACTTTTACACCCTTTAAAATTTTATCG 5 43 0 ACCCCTTTAA 0.92415 -25 ** ******** Masking position 11 Map Score: 2.39067 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 360 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 AATCTTGGATATAATGGCGTAATCATTTTT 1 19 0 ATAATGGCGT 0.993973 -32 TAGCGTATAAATAAGGGAGCAATAA 2 6 0 ATAAGGGAGC 0.936926 -125 CATGGATATAATAATAGCGTTTTTTAAACC 2 85 1 ATAATAGCGT 0.969324 -46 ATGACCGGTTAAAATGGAGTAAAATTTTTA 4 73 1 AAAATGGAGT 0.956985 -76 AGTGTTAAATATAGTGGCATTGTAGCATGA 4 118 0 ATAGTGGCAT 0.934365 -31 ********** Masking position 3 Map Score: 1.8921 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 328 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 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