AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i204_dna_repair1_hpyl_reg_300.orf -o204_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 Purged sequences: RHP01386 47 AE000511 Input sequences: #1 RHP01384 159 AE000511 #2 RHP01387 24 AE000511 #3 RHP01392 97 AE000511 #4 RHP01393 300 AE000511 #5 RHP00791 66 AE000511 Motif number 1 TGCAACAATATTCAAGCGAACTGACAAGCCTT 1 80 1 TTCAACAACT 0.953566 -80 TGGCGCAAAAACCAAATGATAAGTTTG 3 6 1 CAAAACAAAT 0.926821 -92 ACACTCACAATACAAGCAAACTTATCATTTGG 3 22 0 TACAACAACT 0.969823 -76 TATGTTAAAATACAAGCATATTTTAACTCCAA 3 54 1 TACAACTATT 0.579725 -44 CAAGCATATTTTAACTCCAAATTGATATAAAA 3 66 1 TTAACCAAAT 0.95343 -32 TTCATCCAATTAAACCCTAACCGACTCTTGAA 4 14 1 TAAACCAACC 0.971431 -287 AAAAGATTTTTGAACCCCAACCTTTCAAGAGT 4 37 0 TGAACCAACC 0.888201 -264 TTATACTGCGTTAAGGCAAACTTTCTATTTAT 4 71 0 TTAAGCAACT 0.902973 -230 TCTATTTTAGTAAAATAAAAATTAAAACGCTA 4 106 0 TAAAAAAAAT 0.72648 -195 TATTCAAACGCAAACACCAAACGCTCTATTTT 4 130 0 CAAACCAAAC 0.860464 -171 AATTTATTATTTAAATCTTACTAAACCCATAT 4 159 0 TTAAACTACT 0.893322 -142 TTTAAAGAAATAAAAGCGAAACTATCCTATTA 4 249 0 TAAAACAAAC 0.966591 -52 TTTTATTTCTTTAAAACAAATTGATTCTACTG 4 266 1 TTAAACAATT 0.910769 -35 ATTATAATCCTAAAAACAAAATAGGGCGGTTA 5 13 0 TAAAACAAAT 0.977595 -54 ***** * **** Masking position 4 Map Score: 13.1887 Number of sites scoring better than the average of aligned sites = 816 Number in coding regions = 679 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 2 AAGCGAACTGACAAGCCTTTTTGATGAAAGCCAG 1 93 1 ACCCTTTTTA 0.894557 -67 TCAATAGCCTTTTTCACAAGACCC 2 9 0 AACCTTTTTA 0.976008 -16 GAAATCCCCTTTTTATATCAATTTG 3 83 0 AACCCTTTTA 0.993112 -15 GTTGGGGTTCAAAAATCTTTTTCATAAATAGAAA 4 48 1 AATCTTTTTA 0.919861 -253 GCGTTAAGGCAAACTTTCTATTTATGAAAAAGAT 4 62 0 AATTCTATTA 0.902956 -239 CGCAAACACCAAACGCTCTATTTTAGTAAAATAA 4 120 0 AACTCTATTT 0.901641 -181 TGATCCATTAAATAACACTATTGAACAAAATAAT 4 212 0 AACACTATTA 0.949241 -89 ATAAAAGCGAAACTATCCTATTAAATTGATCCAT 4 238 0 AATCCTATTA 0.976008 -63 TTTAACCGCCCTATTTTGTTTTTAGGA 5 4 1 AACCCTATTT 0.975656 -63 AAACCCCTTAAGAACGCTTTTTATCGCTTTATA 5 44 0 AACGCTTTTA 0.965172 -23 ** ******* * Masking position 9 Map Score: 10.0918 Number of sites scoring better than the average of aligned sites = 1464 Number in coding regions = 1237 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 3 ACCCTGGGCAGTATTTCATTATAGAAGACACG 1 11 1 GATTTATTAT 0.933857 -149 CAGCCAAGCGGAGTTTGAAAATTTAATGCAAC 1 54 1 GGTTTAAAAT 0.969894 -106 AAATATGCTTGTATTTTAACATAACACTCACA 3 45 0 GATTTAACAT 0.91263 -53 TATCAATTTGGAGTTAAAATATGCTTGTATTT 3 61 0 GGTTAAATAT 0.968479 -37 TGAAAGGTTGGGGTTCAAAAATCTTTTTCATA 4 42 1 GGTTCAAAAT 0.908434 -259 TATAATCCTAGCGTTTTAATTTTTATTTTACT 4 98 1 GGTTTAATTT 0.932712 -203 TTTGGTGTTTGCGTTTGAATATGGGTTTAGTA 4 141 1 GGTTTAATAT 0.988669 -160 ATATATATAAGTAATTTATTATTTAAATCTTA 4 171 0 GAATTATTAT 0.690376 -130 TTTGTTTTTAGGATTATAATATAAAGCGATAA 5 25 1 GATTAAATAT 0.942183 -42 * **** ***** Masking position 5 Map Score: 9.22397 Number of sites scoring better than the average of aligned sites = 261 Number in coding regions = 219 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 4 TCACAATACAAGCAAACTTATCATTTGGTTT 3 19 0 ACAAACTTAT 0.947627 -79 ATATTTTAACTCCAAATTGATATAAAAAGGG 3 71 1 TCAAATTGAT 0.947311 -27 AATAATATCTATCAAATATATATAAGTAATT 4 187 0 ACAAATATAT 0.901759 -114 AACACTATTGAACAAAATAATATCTATCAAA 4 202 0 ACAAAATAAT 0.873163 -99 AAACTATCCTATTAAATTGATCCATTAAATA 4 232 0 ATAAATTGAT 0.618092 -69 ATTTCTTTAAAACAAATTGATTCTACTGGGG 4 270 1 ACAAATTGAT 0.838244 -31 * ********* Masking position 6 Map Score: 1.67752 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 123 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 TAATCCCTTTTAAAGTTTCTAAAATTTCTT 1 137 0 TAAAGTTTCT 0.765974 -23 ACCGACTCTTGAAAGGTTGGGGTTCAAAAA 4 33 1 GAAAGGTTGG 0.979413 -268 TTCATAAATAGAAAGTTTGCCTTAACGCAG 4 68 1 GAAAGTTTGC 0.951106 -233 TACTAAAATAGAGCGTTTGGTGTTTGCGTT 4 126 1 GAGCGTTTGG 0.934305 -175 AATTTAATAGGATAGTTTCGCTTTTATTTC 4 245 1 GATAGTTTCG 0.907313 -56 TTCTACTGGGGAAAGGTTTTT 4 290 1 GAAAGGTTTT 0.927923 -11 AACCCCTTAAGAACGCTTTTTATCGCTTTA 5 46 0 GAACGCTTTT 0.827197 -21 ********** Masking position 2 Map Score: 0.18488 Number of sites scoring better than the average of aligned sites = 431 Number in coding regions = 383 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 CGCTTGAATATTGTTGCATTAAATTTTCAA 1 68 0 TTGTTGCATT 0.961819 -92 ACAAGCCTTTTTGATGAAAGCCAGAGCTTG 1 103 1 TTGATGAAAG 0.901853 -57 CTAAAATTTCTTGTTGCAAGCTCTGGCTTT 1 119 0 TTGTTGCAAG 0.964531 -41 TTCTTCATCCAATTAAACCCTAA 4 4 1 TTCATCCAAT 0.852419 -297 AGATATTATTTTGTTCAATAGTGTTATTTA 4 208 1 TTGTTCAATA 0.771104 -93 TCCTATTAAATTGATCCATTAAATAACACT 4 227 0 TTGATCCATT 0.961819 -74 ********** Masking position 5 Map Score: 0.277928 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 316 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 ********** No masking Map Score: 8.76972e-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: 8.76972e-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: 8.76972e-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