AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i197_replication1_hpyl_reg_100.orf -o197_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 Input sequences: #1 RHP01419 228 AE000511 #2 RHP01422 57 AE000511 #3 RHP00129 300 AE000511 #4 RHP00131 19 AE000511 #5 RHP00907 152 AE000511 Motif number 1 ATTCCCCTTACTTAAATAATGAAATTTTCT 1 13 1 CTTAAATAAT 0.811162 -216 ATGAAATTTTCTTAAAATTATACAATATGT 1 31 1 CTTAAAATTA 0.961115 -198 TTAGATTATACTATAGTTAAGTTACATATT 1 54 0 CTATAGTTAA 0.611478 -175 TTAAAAATACCTAAAAAATACAGAGCAACG 1 87 0 CTAAAAAATA 0.726135 -142 AAAAAACCCACTTTAAAAATACCTAAAAAA 1 99 0 CTTTAAAAAT 0.714459 -130 CTTTAAAGATCTTAAGATTTAAGAAAAAAC 1 122 0 CTTAAGATTT 0.844501 -107 TTTTTAAAATCTTTAAAGATCTTAAGATTT 1 132 0 CTTTAAAGAT 0.797342 -97 GGACATCGCTCTTTAATTTTAATCATTGAC 1 189 1 CTTTAATTTT 0.858063 -40 TTAATTATAGCTAAAAGAACGCTTTT 2 8 0 CTAAAAGAA 0.180003 -50 TTCTTTTAYGCTATAATTAAGACCAAAAAT 2 18 1 CTATAATTAA 0.822366 -40 AAATAATCCCCTTGAATTTTTGGTCTTAAT 2 33 0 CTTGAATTTT 0.802684 -25 AGTTAAAATAATCCCCTTGAA 2 47 0 GTTAAAATAA 0.679782 -11 AGAAAATTTGCTTGAGTTAAATCAACCCAA 3 48 0 CTTGAGTTAA 0.726376 -253 AAGAAAAAAGCTTAAATTTTTTAATTTGCA 3 98 0 CTTAAATTTT 0.927935 -203 ATTTTCTATCCTAAAAATAAGAAAATGTAT 3 235 1 CTAAAAATAA 0.924437 -66 GTGTCTCCCTAAAATTTAA 4 2 0 CTAAAATTTA 0.888242 -18 TAGACAAACCCTTAAAAGAAACACCTTAAT 5 58 1 CTTAAAAGAA 0.928396 -95 TGAATGAAGCCTTAAAATTAAGGTGTTTCT 5 74 0 CTTAAAATTA 0.961115 -79 ********** Masking position 2 Map Score: 17.9119 Number of sites scoring better than the average of aligned sites = 1671 Number in coding regions = 1292 Number in noncoding regions = 379 Number of orfs with sites within 600 bp upstream = 293 Fraction of orfs with sites within 600 bp upstream = 0.0470607 Motif number 2 AGTTACATATTGTATAATTTTAAGAAAATT 1 35 0 TGTATAATTT 0.791339 -194 GGCGTTGCTCTGTATTTTTTAGGTATTTTT 1 85 1 TGTATTTTTT 0.958851 -144 GTATTTTTTAGGTATTTTTAAAGTGGGTTT 1 96 1 GGTATTTTTA 0.783643 -133 ATTTTTAAAGTGGGTTTTTTCTTAAATCTT 1 109 1 TGGGTTTTTT 0.937851 -120 CAACTATTGCTGTATTAGTTTTTAAAATCT 1 150 0 TGTATTAGTT 0.8792 -79 AAAATTCAAGGGGATTATTTTAACT 2 43 1 GGGATTATTT 0.927001 -15 TTTAATACTAGGTATAATTTTAATTCCACC 3 137 1 GGTATAATTT 0.835781 -164 AGCAATGCCTTGTGTTACTTTCATAGCTTT 3 176 0 TGTGTTACTT 0.893966 -125 TAGAAAATATCGTGTTTGTTAGGGCAAAAA 3 213 0 CGTGTTTGTT 0.781244 -88 AATAAGAAAATGTATTTTATGAGTTCTATC 3 250 1 TGTATTTTAT 0.729655 -51 AATAAAATAAGGGGTTTTTT 3 291 1 GGGGTTTTTT 0.952943 -10 TTAAAATTAAGGTGTTTCTTTTAAGGGTTT 5 63 0 GGTGTTTCTT 0.939671 -90 ********** Masking position 5 Map Score: 11.3428 Number of sites scoring better than the average of aligned sites = 901 Number in coding regions = 795 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 TTAAAGATCTTAAGATTTAAGAAAAAACCC 1 120 0 TAAGATTTAA 0.677491 -109 AAAAGCTTGGGTTGATTTAACTCAAGCAAA 3 42 1 GTTGATTTAA 0.903682 -259 CCAAATTTGTTAGGATTGAAGAAAATTTGC 3 67 0 TAGGATTGAA 0.951363 -234 TTTCTTTTTTTTTGATTTAATACTAGGTAT 3 122 1 TTTGATTTAA 0.929342 -179 TCCTTGTTAGGTGGAATTAAAATTATACCT 3 146 0 GTGGAATTAA 0.840922 -155 TTCTTATTTTTAGGATAGAAAATATCGTGT 3 228 0 TAGGATAGAA 0.7335 -73 AAACCCCTTATTTTATTGAAAGTATAGTGA 3 278 0 TTTTATTGAA 0.729473 -23 GTGAATGAAATGTGAATGAAGCCTTAAAAT 5 86 0 TGTGAATGAA 0.962222 -67 AGGAATAACATGTGAATGAAATGTGAATGA 5 97 0 TGTGAATGAA 0.962222 -56 GTGAATAAGTGGTGAATGAAAAAGGAATAA 5 119 0 GGTGAATGAA 0.94774 -34 ********** Masking position 5 Map Score: 6.9855 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 486 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 4 TTATTTAAGTAAGGGGAATTA 1 2 0 AAGGGGAATT 0.951129 -227 TAGTATAATCTAAGGGCGTTGCTCTGTATT 1 71 1 TAAGGGCGTT 0.836393 -158 TTAATCATTGACAAGGAGTTTGGTAGTTAA 1 207 1 ACAAGGAGTT 0.918106 -22 CCAAAAATTCAAGGGGATTATTTTAACT 2 40 1 AAGGGGATTA 0.87569 -18 TTATGAAAGAGGCTTTATGCCTCTTG 3 7 1 AAGAGGCTTT 0.967707 -294 TGAAAGTAACACAAGGCATTGCTAACGACT 3 183 1 ACAAGGCATT 0.901756 -118 GTTAGGGCAAAAAAGTCGTTAGCAATGCCT 3 196 0 AAAAGTCGTT 0.745638 -105 TCAATAAAATAAGGGGTTTTTT 3 289 1 AAGGGGTTTT 0.861446 -12 TGGATGCGAAAAAAGGATTTTC 5 3 0 AAAAGGATTT 0.955638 -150 TGGTGAATGAAAAAGGAATAACATGTGAAT 5 110 0 AAAAGGAATA 0.821722 -43 ********** Masking position 9 Map Score: 6.89109 Number of sites scoring better than the average of aligned sites = 1621 Number in coding regions = 1433 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 5 AAATAATGAAATTTTCTTAAAATTATACAAT 1 26 1 ATTTTCTTAA 0.955037 -203 TAAAGTGGGTTTTTTCTTAAATCTTAAGATC 1 114 1 TTTTTCTTAA 0.955037 -115 TTAAAGAGCGATGTCCTTAATCGTCCAACTA 1 174 0 ATGTCCTTAT 0.759267 -55 ACTCAAGCAAATTTTCTTCAATCCTAACAAA 3 61 1 ATTTTCTTAA 0.955038 -240 AATTTAAGCTTTTTTCTTTTTTTTTGATTTA 3 110 1 TTTTTCTTTT 0.955038 -191 CTTTCATAGCTTTTCCTTGTTAGGTGGAATT 3 158 0 TTTTCCTTTT 0.937979 -143 CATAAAATACATTTTCTTATTTTTAGGATAG 3 240 0 ATTTTCTTTT 0.955038 -61 AAAACCCCTTATTTTATTGAAAGTATAGTGA 3 278 0 ATTTTATTAA 0.64983 -23 AAAATTAAGGTGTTTCTTTTAAGGGTTTGTC 5 60 0 TGTTTCTTTA 0.832294 -93 ATTCACATGTTATTCCTTTTTCATTCACCAC 5 110 1 TATTCCTTTT 0.7045 -43 ******** ** Masking position 7 Map Score: 7.47965 Number of sites scoring better than the average of aligned sites = 876 Number in coding regions = 719 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 6 ********** No masking Map Score: 1.37435e-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 7 ********** No masking Map Score: 1.37435e-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: 1.37435e-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