AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i201_excinuclease_abc_hpyl_reg_300.orf -o201_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 Input sequences: #1 RHP00134 182 AE000511 #2 RHP00515 70 AE000511 #3 RHP00517 300 AE000511 Motif number 1 TATGAGACAATTTTAAAGATAGGAATGTAAA 1 14 0 TTTTAAAATA 0.594103 -169 AAGCAAATATTTTTAACTCTTATGAATAAGA 1 71 1 TTTTAACCTT 0.918377 -112 TAACACGCCTTATTCAATCTCAAAAAAAA 2 9 0 TATTCAACTC 0.811598 -62 TATAGTGGTTTTTTAACACGCCTTATTCAAT 2 22 0 TTTTAACCGC 0.990922 -49 GTTTTAAACTCGCATTTTTTAGG 2 58 0 TTTAAACCGC 0.986766 -13 ACCCCCTAAATTTACAAACTCCAAACAATAG 3 101 1 TTTACAACTC 0.954361 -200 TAGCGAGCGGTTTTCACAAGCTTTTTAAAAA 3 129 1 TTTTCACAGC 0.930728 -172 TCACAAGCTTTTTAAAAACGACGCTAAGATC 3 142 1 TTTAAAACGA 0.862366 -159 TGTAGCGGGCTTTAAACTCTCGGCGATCTTA 3 166 0 TTTAAACCTC 0.985678 -135 TCCACTGATACTTTAACGCTCCGCTGAGAGT 3 227 0 CTTTAACCTC 0.954571 -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 GGATAAACATGCTATTATTTTATGAGACAAT 1 34 0 GCTATTATTT 0.989557 -149 CCTTAATCAAGCAAATATTTTTAACTCTTAT 1 63 1 GCAAATATTT 0.862411 -120 AAAAAAGAATGGTTTTATTATCATTTCTTAT 1 96 0 GGTTTTATTT 0.973407 -87 ATTAAAAGGAGCTATTATACTTCAAAAAAGA 1 119 0 GCTATTATAT 0.96873 -64 AATGGTTTTATGTTGCAAGAGTTT 1 169 0 GGTTTTATGT 0.930485 -14 ATTTTTTAGGGGTATTATAGTGGTTTTTTAA 2 37 0 GGTATTATAT 0.949991 -34 AACATTGCTTGCTATAATTTTGCTGTTTGCC 3 41 1 GCTATAATTT 0.971976 -260 CTAAACCTTGGCTTAAATTTTTCGTTGTAGC 3 191 0 GCTTAAATTT 0.888667 -110 ********* * Masking position 7 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 CATAAAATAATAGCATGTTTATCCTTAATC 1 41 1 TAGCATGTTT 0.907084 -142 AGGGGTATTATAGTGGTTTTTTAACACGCC 2 31 0 TAGTGGTTTT 0.938816 -40 TCGCATTTTTTAGGGGTATTATAGTGGTTT 2 42 0 TAGGGGTATT 0.896789 -29 GTTTTAAACTCGCATTTTTTAGGGGTATT 2 52 0 TCGCATTTTT 0.85284 -19 TTTGTAAATTTAGGGGGTTTGTTAAGGCAG 3 89 0 TAGGGGGTTT 0.971848 -212 AAACAATAGCGAGCGGTTTTCACAAGCTTT 3 123 1 GAGCGGTTTT 0.983 -178 TTTTTCGTTGTAGCGGGCTTTAAACTCTCG 3 175 0 TAGCGGGCTT 0.982149 -126 CGTTTCTGTATAGCGTTCCTAAAGTGAATT 3 261 0 TAGCGTTCCT 0.943393 -40 ATGCGATCGGGCGCGTTTCTGTATAGCGTT 3 274 0 GCGCGTTTCT 0.875497 -27 ********** Masking position 10 Map Score: 7.34286 Number of sites scoring better than the average of aligned sites = 1495 Number in coding regions = 1355 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 4 AGAAAACATTGCTTGCTATAATTTTGCTGT 3 37 1 GCTTGCTATA 0.979935 -264 TGTGAAAACCGCTCGCTATTGTTTGGAGTT 3 117 0 GCTCGCTATT 0.98724 -184 AGAGTTTAAAGCCCGCTACAACGAAAAATT 3 177 1 GCCCGCTACA 0.988745 -124 CGCTGAGAGTGGTCGCTAAACCTTGGCTTA 3 207 0 GGTCGCTAAA 0.974104 -94 TTCACTTTAGGAACGCTATACAGAAACGCG 3 263 1 GAACGCTATA 0.962155 -38 ********** Masking position 7 Map Score: 3.10573 Number of sites scoring better than the average of aligned sites = 184 Number in coding regions = 170 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 5 AAAATTGTCTCATAAAATAATAGCATGTTT 1 31 1 CATAAAATAA 0.836686 -152 AGCTATTATACTTCAAAAAAGAATGGTTTT 1 111 0 CTTCAAAAAA 0.979074 -72 CAAGAGTTTCCTTAAAATAAGAAAATGGAT 1 148 0 CTTAAAATAA 0.954058 -35 CTTATTCAATCTCAAAAAAAA 2 2 0 CTCAAAAAAA 0.969809 -69 GTGGCTTTCTACCAAAAACTTTAGTCAG 3 9 1 CTACCAAAAA 0.871316 -292 AATTTACAAACTCCAAACAATAGCGAGCGG 3 109 1 CTCCAAACAA 0.96735 -192 ********** Masking position 6 Map Score: 3.03046 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 296 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 6 TTTTCTTATTTTAAGGAAACTCTTGCAACA 1 153 1 TTAAGGAAAC 0.92129 -30 TACCAAAAACTTTAGTCAGAAAACATTGCT 3 20 1 TTTAGTCAGA 0.851581 -281 AGGGGGAGTATTTAGGCAAGGCAAACAGCA 3 61 0 TTTAGGCAAG 0.990722 -240 AGGGGGTTTGTTAAGGCAGGGGGAGTATTT 3 78 0 TTAAGGCAGG 0.985519 -223 AACGAAAAATTTAAGCCAAGGTTTAGCGAC 3 196 1 TTAAGCCAAG 0.958855 -105 CTAAAGTGAATTTAGTCCACTGATACTTTA 3 243 0 TTTAGTCCAC 0.853134 -58 CTAAATTCACTTTAGGAACGCTATACAGAA 3 258 1 TTTAGGAACG 0.929259 -43 ********** Masking position 4 Map Score: 3.29555 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 478 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 TCATAAAATAATAGCATGTTTATCCTTAAT 1 40 1 ATAGCATGTT 0.95327 -143 GTTTTAAACTCGCATTTTTTAGGGGTAT 2 53 0 CTCGCATTTT 0.98813 -18 GCGGTTTTCACAAGCTTTTTAAAAACGACG 3 135 1 CAAGCTTTTT 0.893942 -166 AACGCGCCCGATCGCATTTTAGGA 3 287 1 ATCGCATTTT 0.98175 -14 ********** Masking position 7 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 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 Motif number 10 ********** 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