AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i207_holliday_junction_hpyl_reg_100.orf -o207_hpyl_100.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 0.958347 -47 GCATTAAGAATTTTAAAAAATTTAGCGTAT 2 28 0 TTTTAAAAAA 0.93802 -103 TTGTATTTTATTCTAACAAGAAACATGGAT 2 62 1 TTCTAACAAG 0.951439 -69 TAATTGCAAGGTTTAAAAAACGCTATTATT 2 94 0 GTTTAAAAAA 0.917484 -37 AAAAAAATATTTTTAACCAACAGCTTAGGG 3 50 0 TTTTAACCAA 0.961457 -118 ACAACCAGTATGCTAAAAAAAATATTTTTA 3 65 0 TGCTAAAAAA 0.976903 -103 AAAAGAAATATGCTAACAAAAAAACACTGA 3 111 0 TGCTAACAAA 0.978682 -57 AATATAAGAATTTGAAAAAAGAAATATGCT 3 127 0 TTTGAAAAAA 0.874925 -41 TGAAAGAAACTTTTAACAAACAATTCAAGG 4 23 0 TTTTAACAAA 0.973434 -126 GTAATTTTCTTTCTAAACAAGA 5 3 0 TTCTAAACAA 0.973783 -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 0.867303 -36 GCGTATAAATAAGGGAGCAATAA 2 2 0 AAGGGCAATA 0.932589 -129 TTATACGCTAAATTTTTTAAAATTCTTAATGC 2 26 1 AATTTTAAAA 0.764658 -105 AACAAGAAACATGGATATAATAATAGCGTTTT 2 76 1 ATGGATAATA 0.787761 -55 ATTTAATTGCAAGGTTTAAAAAACGCTATTAT 2 95 0 AAGGTAAAAA 0.823215 -36 TAAACCTTGCAATTAAATAATAGGAATGGTTG 2 109 1 AATTATAATA 0.89197 -22 AAACACTGAAAATTAGGTAATAAATACAACCA 3 88 0 AATTATAATA 0.89197 -80 TTAATCCTTAAATGGTATAATATAAGAATTTG 3 143 0 AATGGTAATA 0.976417 -25 TATACCATTTAAGGATTAAAAA 3 156 1 AAGGAAAAAA 0.91456 -12 AATTATACTAAAATAATTAAAATGACCGGTTA 4 52 1 AAATATAAAA 0.608118 -97 GACCGGTTAAAATGGAGTAAAATTTTTACCCA 4 75 1 AATGGTAAAA 0.972807 -74 TAAAAATCCTAAGTGTTAAATATAGTGGCATT 4 127 0 AAGTGAAATA 0.903579 -22 TAAAATTTTAAAGGGTGTAAAAGTAGATTGTT 5 46 1 AAGGGTAAAA 0.982836 -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 0.771917 -14 TTTATACGCTAAATTTTTTAAAATTCTTAA 2 25 1 AAATTTTTTA 0.701387 -106 AAATTTTTTAAAATTCTTAATGCAATCTTG 2 35 1 AAATTCTTAA 0.97454 -96 CAAATCCCGTAAAAAGCCAAA 3 2 1 AAATCCCGTA 0.83795 -166 TAAAAAGCCAAAAATCCTAGAGCATAAAAT 3 20 1 AAAATCCTAG 0.909102 -148 CTAGAGCATAAAATCCCTAAGCTGTTGGTT 3 36 1 AAATCCCTAA 0.985701 -132 TTCTTTTTTCAAATTCTTATATTATACCAT 3 134 1 AAATTCTTAT 0.857837 -34 TTTTTAATCCTTAAATGGTATAAT 3 154 0 TAATCCTTAA 0.927247 -14 AATCGCCAAATCCCTTGAATTGTTTGT 4 8 1 AAATCCCTTG 0.921914 -141 TAAAAATCCTAAGTGTTAAATA 4 137 0 AAAATCCTAA 0.958776 -12 CAATAACGATAAAATTTTAAAGGGTGTAAA 5 37 1 AAAATTTTAA 0.727534 -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 TTTATACGCTAAATTTTTTAAAATTCTTAA 2 25 1 AAATTTTTTA 0.762368 -106 TATTATATCCATGTTTCTTGTTAGAATAAA 2 68 0 ATGTTTCTTG 0.952624 -63 TTGGTTAAAAATATTTTTTTTAGCATACTG 3 60 1 ATATTTTTTT 0.944234 -108 CTAATTTTCAGTGTTTTTTTGTTAGCATAT 3 104 1 GTGTTTTTTT 0.89122 -64 TTTTGTTAGCATATTTCTTTTTTCAAATTC 3 120 1 ATATTTCTTT 0.972198 -48 TGTTTGTTAAAAGTTTCTTTCAATTATACT 4 31 1 AAGTTTCTTT 0.976866 -118 ATTGTAGTGTAATTTTCTTTCTAAACAAGA 5 11 0 AATTTTCTTT 0.914011 -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 0.981729 -32 TTTTTAAACCTTGCAATTAAATAATAGGAAT 2 105 1 TTCAATTAAA 0.802175 -26 TTCTTATATTATACCATTTAAGGATTAAAAA 3 147 1 ATCCATTTAA 0.963294 -21 TAAAAGTTTCTTTCAATTATACTAAAATAAT 4 38 1 TTCAATTATA 0.840763 -111 TAAAAATTTTACTCCATTTTAACCGGTCATT 4 72 0 ACCCATTTTA 0.97634 -77 TCATGCTACAATGCCACTATATTTAACACTT 4 118 1 ATCCACTATA 0.931932 -31 ATCTACTTTTACACCCTTTAAAATTTTATCG 5 43 0 ACCCCTTTAA 0.906989 -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