AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i224_Holliday_Junction_enzyme_hpyl_reg_100.orf -o224_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 GGCGTAATCATTTTTTAGGAAGT 1 4 0 TTTTTTAGGA 0.954779 -47 ATACGCTAAATTTTTTAAAATTCTTAATGC 2 28 1 TTTTTTAAAA 0.939819 -103 ATCCATGTTTCTTGTTAGAATAAAATACAA 2 62 0 CTTGTTAGAA 0.947304 -69 AATAATAGCGTTTTTTAAACCTTGCAATTA 2 94 1 TTTTTTAAAC 0.91097 -37 CCCTAAGCTGTTGGTTAAAAATATTTTTTT 3 50 1 TTGGTTAAAA 0.958232 -118 TAAAAATATTTTTTTTAGCATACTGGTTGT 3 65 1 TTTTTTAGCA 0.974888 -103 TCAGTGTTTTTTTGTTAGCATATTTCTTTT 3 111 1 TTTGTTAGCA 0.976811 -57 AGCATATTTCTTTTTTCAAATTCTTATATT 3 127 1 TTTTTTCAAA 0.871886 -41 CCTTGAATTGTTTGTTAAAAGTTTCTTTCA 4 23 1 TTTGTTAAAA 0.972774 -126 TCTTGTTTAGAAAGAAAATTAC 5 3 1 TTGTTTAGAA 0.97151 -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 CGTTTAAGCCTTAATCTTGGATA 1 38 0 TTAAGCCTTA 0.886538 -13 CTAAATTTTTTAAAATTCTTAATGCAATCTT 2 33 1 TAAATTCTTA 0.874291 -98 AATAGCGTTTTTTAAACCTTGCAATTAAATA 2 97 1 TTAAACCTTG 0.783418 -34 CGTAAAAAGCCAAAAATCCTAGAGCATAAAA 3 18 1 CAAAATCCTA 0.919496 -150 TCCTAGAGCATAAAATCCCTAAGCTGTTGGT 3 34 1 TAAATCCCTA 0.983366 -134 ATTTCTTTTTTCAAATTCTTATATTATACCA 3 132 1 TAAATTCTTA 0.975734 -36 TTTTTAATCCTTAAATGGTATAA 3 155 0 TTAATCCTTA 0.962108 -13 AATCGCCAAATCCCTTGAATTGTTTG 4 6 1 CAAATCCCTT 0.76302 -143 TAAAATGGAGTAAAATTTTTACCCACCCTAA 4 82 1 TAAATTTTTA 0.503276 -67 TAAAAATCCTAAGTGTTAAAT 4 138 0 TAAAATCCTA 0.960962 -11 TTTACACCCTTTAAAATTTTATCGTTATTGT 5 36 0 TAAAATTTTA 0.717328 -32 * ********* Masking position 5 Map Score: 11.5531 Number of sites scoring better than the average of aligned sites = 1099 Number in coding regions = 963 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 CTAAAAAATGATTACGCCATTATATCCAAGA 1 16 1 ATTACCCATT 0.992059 -35 TTATTGCTCCCTTATTTATACGC 2 3 1 ATTGCCCCTT 0.970193 -128 AAACGCTATTATTATATCCATGTTTCTTGTT 2 76 0 ATTATTCCAT 0.770465 -55 AACCATTCCTATTATTTAATTGCAAGGTTTA 2 109 0 ATTATTAATT 0.813812 -22 GGTTGTATTTATTACCTAATTTTCAGTGTTT 3 89 1 ATTACTAATT 0.917911 -79 AAATTCTTATATTATACCATTTAAGGATTAA 3 144 1 ATTATCCATT 0.979947 -24 GGGTAAAAATTTTACTCCATTTTAACCGGTC 4 75 0 TTTACCCATT 0.978626 -74 ACAATCTACTTTTACACCCTTTAAAATTTTA 5 46 0 TTTACCCCTT 0.978204 -22 ***** ***** Masking position 3 Map Score: 7.97665 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 361 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 4 AATCTTGGATATAATGGCGTAATCATTTTT 1 19 0 ATAATGGCGT 0.837464 -32 AATTTTAAAAAATTTAGCGTATAAATAAGG 2 20 0 AATTTAGCGT 0.934747 -111 CATGGATATAATAATAGCGTTTTTTAAACC 2 85 1 ATAATAGCGT 0.956511 -46 AAAAATATTTTTTTTAGCATACTGGTTGTA 3 66 1 TTTTTAGCAT 0.879387 -102 AAATTCTTATATTATACCATTTAAGGATTA 3 144 1 ATTATACCAT 0.850569 -24 CATTTTAATTATTTTAGTATAATTGAAAGA 4 46 0 ATTTTAGTAT 0.900404 -103 ATATAGTGGCATTGTAGCATGACTTTATTA 4 110 0 ATTGTAGCAT 0.973983 -39 TTTTATCGTTATTGTAGTGTAATTTTCTTT 5 21 0 ATTGTAGTGT 0.936687 -47 ACCCTTTAAAATTTTATCGTTATTGTAGTG 5 32 0 ATTTTATCGT 0.910258 -36 ********** Masking position 5 Map Score: 7.63301 Number of sites scoring better than the average of aligned sites = 1144 Number in coding regions = 996 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 5 ATTTATACGCTAAATTTTTTAAAATTCTTA 2 24 1 TAAATTTTTT 0.690891 -107 TTATTATATCCATGTTTCTTGTTAGAATAA 2 69 0 CATGTTTCTT 0.966011 -62 ATATAATAATAGCGTTTTTTAAACCTTGCA 2 90 1 AGCGTTTTTT 0.895894 -41 GTTGGTTAAAAATATTTTTTTTAGCATACT 3 59 1 AATATTTTTT 0.931296 -109 CCTAATTTTCAGTGTTTTTTTGTTAGCATA 3 103 1 AGTGTTTTTT 0.950256 -65 TTTTTGTTAGCATATTTCTTTTTTCAAATT 3 119 1 CATATTTCTT 0.93225 -49 TTGTTTGTTAAAAGTTTCTTTCAATTATAC 4 30 1 AAAGTTTCTT 0.948314 -119 ********** Masking position 5 Map Score: 3.54976 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 326 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 TAATGCAATCTTGTATTTTATTCTAACAAG 2 52 1 TTGTATTTTA 0.875465 -79 TTTTTAAACCTTGCAATTAAATAATAGGAA 2 105 1 TTGCAATTAA 0.87326 -26 AGCATACTGGTTGTATTTATTACCTAATTT 3 81 1 TTGTATTTAT 0.950501 -87 CTAATTTTCAGTGTTTTTTTGTTAGCATAT 3 104 1 GTGTTTTTTT 0.79923 -64 TGTTAGCATATTTCTTTTTTCAAATTCTTA 3 123 1 TTTCTTTTTT 0.72925 -45 TAAAAGTTTCTTTCAATTATACTAAAATAA 4 38 1 TTTCAATTAT 0.880345 -111 TAACCGGTCATTTTAATTATTTTAGTATAA 4 54 0 TTTTAATTAT 0.882438 -95 CGTTATTGTAGTGTAATTTTCTTTCTAAAC 5 15 0 GTGTAATTTT 0.915783 -53 ********** Masking position 7 Map Score: 2.02979 Number of sites scoring better than the average of aligned sites = 769 Number in coding regions = 641 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 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