AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_excinuclease_abc_hpyl_reg_100.orf -o201_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 RHP00134 182 AE000511 #2 RHP00515 70 AE000511 #3 RHP00517 300 AE000511 Motif number 1 TTTACATTCCTATCTTTAAAATTGTCTCATA 1 14 1 TATTTTAAAA 0.599258 -169 TCTTATTCATAAGAGTTAAAAATATTTGCTT 1 71 0 AAGGTTAAAA 0.919968 -112 TTTTTTTTGAGATTGAATAAGGCGTGTTA 2 9 1 GAGTTGAATA 0.814851 -62 ATTGAATAAGGCGTGTTAAAAAACCACTATA 2 22 1 GCGGTTAAAA 0.991113 -49 CCTAAAAAATGCGAGTTTAAAAC 2 58 1 GCGGTTTAAA 0.987043 -13 CTATTGTTTGGAGTTTGTAAATTTAGGGGGT 3 101 0 GAGTTGTAAA 0.955285 -200 TTTTTAAAAAGCTTGTGAAAACCGCTCGCTA 3 129 0 GCTGTGAAAA 0.932097 -172 GATCTTAGCGTCGTTTTTAAAAAGCTTGTGA 3 142 0 TCGTTTTAAA 0.864889 -159 TAAGATCGCCGAGAGTTTAAAGCCCGCTACA 3 166 1 GAGGTTTAAA 0.985977 -135 ACTCTCAGCGGAGCGTTAAAGTATCAGTGGA 3 227 1 GAGGTTAAAG 0.955491 -74 *** ******* Masking position 6 Map Score: 9.90054 Number of sites scoring better than the average of aligned sites = 1633 Number in coding regions = 1474 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 2 ATTGTCTCATAAAATAATAGCATGTTTATCC 1 34 1 AAATAATAGC 0.988898 -149 ATAAGAGTTAAAAATATTTGCTTGATTAAGG 1 63 0 AAATATTTGC 0.85479 -120 ATAAGAAATGATAATAAAACCATTCTTTTTT 1 96 1 AAATAAAACC 0.971732 -87 TCTTTTTTGAAGTATAATAGCTCCTTTTAAT 1 119 1 ATATAATAGC 0.967723 -64 AAACTCTTGCAACATAAAACCATT 1 169 1 ACATAAAACC 0.926312 -14 TTAAAAAACCACTATAATACCCCTAAAAAAT 2 37 1 ATATAATACC 0.948409 -34 GGCAAACAGCAAAATTATAGCAAGCAATGTT 3 41 0 AAATTATAGC 0.970243 -260 GCTACAACGAAAAATTTAAGCCAAGGTTTAG 3 191 1 AAATTTAAGC 0.882301 -110 * ********* Masking position 4 Map Score: 8.17093 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 138 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 GAAATGATAATAAAACCATTCTTTTTTGAA 1 100 1 TAAAACCATT 0.93584 -83 TCTTGCAACATAAAACCATT 1 173 1 TAAAACCATT 0.93584 -10 AGGCGTGTTAAAAAACCACTATAATACCCC 2 30 1 AAAAACCACT 0.971574 -41 AAAACCACTATAATACCCCTAAAAAATGCG 2 41 1 TAATACCCCT 0.97759 -30 CTTGCCTAAATACTCCCCCTGCCTTAACAA 3 71 1 TACTCCCCCT 0.919073 -230 CCTGCCTTAACAAACCCCCTAAATTTACAA 3 88 1 CAAACCCCCT 0.977914 -213 AAAAGCTTGTGAAAACCGCTCGCTATTGTT 3 124 0 GAAAACCGCT 0.968761 -177 CCGAGAGTTTAAAGCCCGCTACAACGAAAA 3 174 1 AAAGCCCGCT 0.929691 -127 ********** Masking position 2 Map Score: 6.13306 Number of sites scoring better than the average of aligned sites = 1022 Number in coding regions = 890 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 4 ATGTTTATCCTTAATCAAGCAAATATTTTT 1 55 1 TTAATCAAGC 0.793199 -128 TTTTCTTATTTTAAGGAAACTCTTGCAACA 1 153 1 TTAAGGAAAC 0.938625 -30 ACAGCAAAATTATAGCAAGCAATGTTTTCT 3 37 0 TATAGCAAGC 0.909381 -264 AGGGGGAGTATTTAGGCAAGGCAAACAGCA 3 61 0 TTTAGGCAAG 0.940812 -240 AGGGGGTTTGTTAAGGCAGGGGGAGTATTT 3 78 0 TTAAGGCAGG 0.975873 -223 GCCGAGAGTTTAAAGCCCGCTACAACGAAA 3 173 1 TAAAGCCCGC 0.820849 -128 AACGAAAAATTTAAGCCAAGGTTTAGCGAC 3 196 1 TTAAGCCAAG 0.960406 -105 TAAGCCAAGGTTTAGCGACCACTCTCAGCG 3 207 1 TTTAGCGACC 0.882035 -94 CTAAATTCACTTTAGGAACGCTATACAGAA 3 258 1 TTTAGGAACG 0.915385 -43 ********** Masking position 4 Map Score: 4.81481 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 659 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 5 TTAAAATTGTCTCATAAAATAATAGCATGT 1 29 1 CTCATAAAAT 0.840167 -154 AGCTATTATACTTCAAAAAAGAATGGTTTT 1 111 0 CTTCAAAAAA 0.97056 -72 CAAGAGTTTCCTTAAAATAAGAAAATGGAT 1 148 0 CTTAAAATAA 0.797495 -35 CTTATTCAATCTCAAAAAAAA 2 2 0 CTCAAAAAAA 0.979271 -69 CACTATAATACCCCTAAAAAATGCGAGTTT 2 46 1 CCCCTAAAAA 0.94149 -25 GTGGCTTTCTACCAAAAACTTTAGTCAG 3 9 1 CTACCAAAAA 0.893872 -292 AATTTACAAACTCCAAACAATAGCGAGCGG 3 109 1 CTCCAAACAA 0.972735 -192 ********** Masking position 6 Map Score: 3.35547 Number of sites scoring better than the average of aligned sites = 784 Number in coding regions = 693 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 6 ATTAAGGATAAACATGCTATTATTTTATGA 1 40 0 AACATGCTAT 0.957114 -143 ATACCCCTAAAAAATGCGAGTTTAAAAC 2 53 1 AAAATGCGAG 0.98914 -18 CGTCGTTTTTAAAAAGCTTGTGAAAACCGC 3 135 0 AAAAAGCTTG 0.90217 -166 TCCTAAAATGCGATCGGGCGCGTT 3 287 0 AAAATGCGAT 0.983292 -14 ********** Masking position 4 Map Score: 0.248896 Number of sites scoring better than the average of aligned sites = 137 Number in coding regions = 128 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 7 ********** No masking Map Score: -5.44113e-14 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: -5.44113e-14 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: -5.44113e-14 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