AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i327_not_clear2_hpyl_reg_300.orf -o327_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 RHP01289 259 AE000511 #2 RHP01290 43 AE000511 #3 RHP01291 17 AE000511 #4 RHP00013 73 AE000511 #5 RHP00020 81 AE000511 #6 RHP00021 228 AE000511 Motif number 1 GAAGCAAAAATTAAAGGAACGCAATAACTT 1 6 0 TTAAAACAAT 0.706492 -254 TAGACTACAATTTAAGAAGCAAAAATTAAAGGAAC 1 21 0 TTTAAAAAAA 0.892327 -239 TTAAAAAGCTTTAAAAGAGGGCAAAAATTAAAGCG 1 63 1 TTAAAACAAA 0.963359 -197 TTAAAGCGATTTCAAAAAAAAAAAAAAACAATTTC 1 90 1 TTCAAAAAAA 0.962623 -170 ATAAAAGCTTTTCATTTTAATCAAACCTAGCTAAT 1 133 0 TTCATTCAAA 0.895458 -127 GACAATGAAGTTTAAACACATAAAAGCTTTTCATT 1 152 0 TTTAAAAAAA 0.902977 -108 GTGTTTAAACTTCATTGTCTTAAAACTTTTAAGAG 1 168 1 TTCATTAAAA 0.910755 -92 ACGAACGGCTTAAAAGAATGAAAATTTTATCAAG 2 10 1 TTAAAAAAAA 0.969683 -34 AATCATGCGTTTAATGGAATAAAAACCTAGTTTG 4 10 0 TTAATAAAAA 0.978458 -64 TAAAATCCTATTATTGTAGCAAAAATCATGCGTTT 4 33 0 TTATTAAAAA 0.902861 -41 TTGTCCTTTATATAATTAAAATCCTATTATT 4 53 0 TTTATAAAAA 0.924627 -21 TGGCTTTATTTGTTATAAAATTTATAGTAA 5 6 1 TTATTTAAAA 0.727176 -76 TTAAGATTTTATAATCAAAGTCAAATCATTCTTGA 5 43 1 ATAATACAAA 0.780287 -39 ATTGAACCCCTTCATGGATACCAAAAGAGAGAAAG 6 92 0 TTCATACAAA 0.969616 -137 TTCTTTTGCATTATTCCATGAAAAAAGCCACGCTT 6 130 1 TTATTAAAAA 0.902861 -99 ***** * **** Masking position 13 Map Score: 20.0605 Number of sites scoring better than the average of aligned sites = 669 Number in coding regions = 537 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 2 CTAAAAAGGGTTAAAAAGCTTTAAAAGAGGG 1 53 1 TTAAAAGCTT 0.922921 -207 AGGGCAAAAATTAAAGCGATTTCAAAAAAAA 1 80 1 TTAAGCGATT 0.921946 -180 TTTGATTAAAATGAAAAGCTTTTATGTGTTT 1 143 1 ATAAAAGCTT 0.922921 -117 GACAATGAAGTTTAAACACATAAAAGCTTTT 1 156 0 TTAAACACAT 0.67051 -104 TCTTAAAAGTTTTAAGACAATGAAGTTTAAA 1 171 0 TTAAGACAAT 0.66028 -89 TATTTAAAACCCTTTTTTTAGTAG 1 246 0 TTAAACCCTT 0.983903 -14 TTTTCATTCTTTTAAGCCGTTCGT 2 4 0 TTAAGCCGTT 0.887638 -40 TATTAAAACCTTGATAAAATTT 2 32 0 ATAAAACCTT 0.946743 -12 GTTTAATGGAATAAAAACCTAGTTTG 4 6 0 ATAAAACCTA 0.603345 -68 TTTTTATTCCATTAAACGCATGATTTTTGCT 4 20 1 ATAAACGCAT 0.94008 -54 ATGACGCTCAATGAAGCCATTAAAGACAAAG 6 12 1 ATAAGCCATT 0.946052 -217 GCTAACTGCGATGAAGCCCTTAAAAAACGCT 6 63 1 ATAAGCCCTT 0.986717 -166 TGAAGCCCTTAAAAAACGCTTTCTCTCTTTT 6 74 1 AAAAACGCTT 0.778891 -155 AAAGAATGCATTGAACCCCTTCATGGATACC 6 105 0 TTAACCCCTT 0.963345 -124 TTCGGTTAAAATCAACCGCATTCAAGTGGCT 6 164 1 ATAACCGCAT 0.870899 -65 TCATGGGATCTTAAAGCCACTTGAATGCGGT 6 178 0 TTAAGCCACT 0.75065 -51 ** ******** Masking position 5 Map Score: 19.6255 Number of sites scoring better than the average of aligned sites = 2782 Number in coding regions = 2485 Number in noncoding regions = 297 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 3 AGCTTTTTAACCCTTTTTAGACTACAATTTAAG 1 40 0 CCTTTTTAAT 0.959158 -220 AATTTTTGCCCTCTTTTAAAGCTTTTTAACCCT 1 59 0 CCTTTTAAGT 0.971852 -201 AAAATTAAAGCGATTTCAAAAAAAAAAAAAAAC 1 86 1 CATTTCAAAA 0.745995 -174 CTTTTAAGAGCAATTTTAAAATTCGTTGGCGTA 1 193 1 CATTTTAAAT 0.904602 -67 TATTTAAAACCCTTTTTTTAGTAGTTCATTCA 1 238 0 CCTTTTTTAT 0.92492 -22 AAAACTCTACTCTTTCAAGAATGATTTGACTT 5 60 0 CCTTTCAAAT 0.982698 -22 TCGCAGTTAGCGATTTCTACGATTTCATAAACT 6 41 0 CATTTCTAGT 0.951145 -188 ATGCATTGAACCCCTTCATGGATACCAAAAGAG 6 98 0 CCCTTCATGT 0.899682 -131 ACGCTTTCTTTGATGACAAGGTAT 6 215 0 CCTTTCTTGT 0.968906 -14 * ******* * * Masking position 6 Map Score: 6.90198 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 417 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 CCTTTAATTTTTGCTTCTTAAATTGTAGTCTA 1 24 1 TTGCTTTAAA 0.925066 -236 CTTCTTAAATTGTAGTCTAAAAAGGGTTAAAA 1 37 1 TGTAGTAAAA 0.742169 -223 TAATCAAACCTAGCTAATAAGAAACTGAAATT 1 119 0 TAGCTTAAGA 0.769752 -141 AATTTTAAAATTGCTCTTAAAAGTTTTAAGAC 1 184 0 TTGCTTAAAA 0.975051 -76 TTGTCCTTTATATAATTAAAATCCTATTAT 4 54 0 TATATTTAAA 0.688664 -20 TGGCTTTATTTGTTATAAAATTTATAGTAA 5 9 1 TTTGTTAAAA 0.896001 -73 TGTTATAAAATTTATAGTAAAATTAAGATTTT 5 21 1 TTTATTAAAA 0.949765 -61 TGATTTGACTTTGATTATAAAATCTTAATTTT 5 39 0 TTGATTAAAA 0.960982 -43 AAAGCCACGCTTTCGGTTAAAATCAACCGCAT 6 153 1 TTTCGTAAAA 0.93679 -76 ***** ***** Masking position 8 Map Score: 3.33831 Number of sites scoring better than the average of aligned sites = 839 Number in coding regions = 664 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 5 ACTACAATTTAAGAAGCAAAAATTAAAGGAA 1 22 0 AAGAGCAAAA 0.954785 -238 TTTTAATTATATAAAGGACAA 4 63 1 ATAAGGACAA 0.951764 -11 AATGACGCTCAATGAAGCCATT 6 2 1 ATGAGCTCAA 0.977769 -227 TTTTCATGGAATAATGCAAAAGAATGCATTG 6 123 0 ATAAGCAAAA 0.968588 -106 TTAAGATCCCATGAAGCACAATACCTTGTCA 6 195 1 ATGAGCACAA 0.993637 -34 **** ****** Masking position 4 Map Score: 2.48831 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 65 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 ********** No masking Map Score: -1.76682e-12 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: -1.76682e-12 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: -1.76682e-12 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