AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_hpyl_reg_300.orf -o255_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 RHP01066 29 AE000511 #2 RHP01068 300 AE000511 #3 RHP00429 167 AE000511 #4 RHP00723 124 AE000511 Motif number 1 TTATCCTTTCTTTTAAAATAAATGTT 1 4 0 TTTTAAAAAT 0.968008 -26 TAGTGGGGTATTTTGAAATAACTCTCCCCCTAC 2 46 0 TTTTGAAAAT 0.898101 -255 CCTTTTTGTTTTATAATGAAACTCATTCTCTTA 2 85 0 TTATAATAAT 0.729583 -216 GATTATCCATATTTAAATGAGATCAGATCTAAA 2 117 1 ATTTAAAAGT 0.88301 -184 TATAGAGTTGATTTAATTTAGATCTGATCTCAT 2 133 0 ATTTAATAGT 0.532734 -168 AAATTAGGATTTTTTATAGAGTTGATTTAATTT 2 147 0 TTTTTATAGT 0.840751 -154 AAAAATCCTAATTTAATGCTAGTAAATAGATTT 2 166 1 ATTTAATTAT 0.783499 -135 TTTATCACTTTTTTAAAACAAGTGATAGATTAT 2 238 1 TTTTAAAAAT 0.972345 -63 CTCATCGTGGATTTAAACTCAATATTTTAGTTA 3 17 1 ATTTAAACAT 0.942288 -151 TTAAAAGGAATTTTAACTAAAATATTGAGTTTA 3 30 0 TTTTAACAAT 0.879039 -138 TTAAAATTCCTTTTAATTGCGCTGAAACGGGTT 3 47 1 TTTTAATCGT 0.969731 -121 ATAATGCAGATTTTAAACCCGTTTCAGCGCAAT 3 62 0 TTTTAAACGT 0.972894 -106 AATCTGCATTATCTAAAAGCATTATCAATAAAC 3 83 1 ATCTAAACAT 0.80544 -85 TATGATAGTATTCTAATAAAACTATTTTAAAGG 3 139 1 TTCTAATAAT 0.880356 -29 AATAAAACTATTTTAAAGGTGATCC 3 153 1 TTTTAAATGT 0.891417 -15 TTATCGTGTTATTTTATCTAAGTTTTGGCATGC 4 35 1 ATTTTATAAT 0.699946 -90 GCTTATTTTATCTTAAAAGCGATAATTTTGCGT 4 76 0 TCTTAAACGT 0.801032 -49 AAAATAAGCGTTTTGATGCCATTTTTGGAGCGA 4 100 1 TTTTGATCAT 0.885223 -25 ******* ** * Masking position 4 Map Score: 22.246 Number of sites scoring better than the average of aligned sites = 1226 Number in coding regions = 989 Number in noncoding regions = 237 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 2 TTATTTTAAAAGAAAGGATAACGC 1 16 1 AGAAAGATAA 0.91239 -14 ATTATAAAACAAAAAGGATTATCCATATTTA 2 101 1 AAAAAGATTA 0.958979 -200 CTTGTTTTAAAAAAGTGATAAAAATTACCCG 2 229 0 AAAAGGATAA 0.973521 -72 CATTATAGCATAAAAAGTTAATAATCTATCA 2 260 0 TAAAAGTTAA 0.880663 -41 AATTGCGCTGAAACGGGTTTAAAATCTGCAT 3 61 1 AAACGGTTTA 0.892977 -107 AGTGTTAGTCAATCAAGTTTATTGATAATGC 3 101 0 AATCAGTTTA 0.761732 -67 AAACCATAGTAATAAAGATAACCCC 4 5 0 AATAAGATAA 0.933711 -120 TTAGATAAAATAACACGATAAAACCATAGTA 4 25 0 TAACAGATAA 0.920749 -100 ATTTTATCTTAAAAGCGATAATTTTGCGTGT 4 74 0 AAAAGGATAA 0.973521 -51 ***** ***** Masking position 9 Map Score: 7.67842 Number of sites scoring better than the average of aligned sites = 384 Number in coding regions = 289 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 3 CCCCCTTAAAATCCCCCTAACCCAAGAAGA 2 13 0 ATCCCCCTAA 0.993463 -288 CCCCCTACAACCCCCCTTAAAATCCCCCTA 2 24 0 CCCCCCTTAA 0.985604 -277 TGAAATAACTCTCCCCCTACAACCCCCCTT 2 36 0 CTCCCCCTAC 0.98665 -265 ATACCCCACTATCCCCTTAAGAGAATGAGT 2 68 1 ATCCCCTTAA 0.992947 -233 GGATCACCTTTAAAATAGTTTT 3 156 0 ATCACCTTTA 0.891305 -12 ********** Masking position 8 Map Score: 5.14051 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 126 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 TCTTGGGTTAGGGGGATTTTAAGGGGGGTT 2 16 1 GGGGGATTTT 0.995005 -285 GGGATTTTAAGGGGGGTTGTAGGGGGAGAG 2 28 1 GGGGGGTTGT 0.991344 -273 GGGGGTTGTAGGGGGAGAGTTATTTCAAAA 2 39 1 GGGGGAGAGT 0.983969 -262 AGGGGATAGTGGGGTATTTTGAAATAACTC 2 55 0 GGGGTATTTT 0.97447 -246 CATTCTCTTAAGGGGATAGTGGGGTATTTT 2 65 0 AGGGGATAGT 0.962921 -236 AAGAAAAATCGGGTAATTTTTATCACTTTT 2 220 1 GGGTAATTTT 0.855174 -81 ********** Masking position 10 Map Score: 6.58108 Number of sites scoring better than the average of aligned sites = 334 Number in coding regions = 290 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TCCCCTTAAGAGAATGAGTTTCATTATAAAA 2 79 1 AAATGAGTTT 0.972158 -222 TTAAATATGGATAATCCTTTTTGTTTTATAA 2 102 0 AAATCCTTTT 0.626312 -199 CTAGCATTAAATTAGGATTTTTTATAGAGTT 2 157 0 ATAGGATTTT 0.885559 -144 GTTTAAATCCACGATGAGTTTTTA 3 4 0 AGATGAGTTT 0.934627 -164 TTTAACTAAAATATTGAGTTTAAATCCACGA 3 21 0 AATTGAGTTT 0.915567 -147 CAGCGCAATTAAAAGGAATTTTAACTAAAAT 3 40 0 AAAGGAATTT 0.529324 -128 AAGTTTATTGATAATGCTTTTAGATAATGCA 3 87 0 AAATGCTTTT 0.925251 -81 TATCTTTATTACTATGGTTTTATCGTGTTAT 4 16 1 ATATGGTTTT 0.855769 -109 AAAAGCGATAATTTTGCGTGTTTTGGCGCAT 4 64 0 ATTTGCGTGT 0.705084 -61 TTTAAGATAAAATAAGCGTTTTGATGCCATT 4 92 1 ATAAGCGTTT 0.880751 -33 * ********* Masking position 9 Map Score: 3.60005 Number of sites scoring better than the average of aligned sites = 1102 Number in coding regions = 912 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 6 GGTATTTTGAAATAACTCTCCCCCTACAAC 2 43 0 AATAACTCTC 0.94228 -258 AGTCTATATCACTAAATCTATTTACTAGCA 2 182 0 ACTAAATCTA 0.945542 -119 AACTTGATTGACTAACACTAAAGATTTATG 3 113 1 ACTAACACTA 0.982474 -55 ATAGTATTCTAATAAAACTATTTTAAAGGT 3 143 1 AATAAAACTA 0.958415 -25 ACTTAGATAAAATAACACGATAAAACCATA 4 28 0 AATAACACGA 0.959004 -97 ********** Masking position 5 Map Score: 2.5124 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 23 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 TTTTAAAAAAGTGATAAAAATTACCCGATT 2 226 0 GTGATAAAAA 0.749841 -75 CCTTTTAATTGCGCTGAAACGGGTTTAAAA 3 55 1 GCGCTGAAAC 0.973319 -113 ATAAAATAACACGATAAAACCATAGTAATA 4 22 0 ACGATAAAAC 0.9166 -103 GTTTTGGCGCATGCCAAAACTTAGATAAAA 4 46 0 ATGCCAAAAC 0.948238 -79 GTTTTGGCATGCGCCAAAACACGCAAAATT 4 56 1 GCGCCAAAAC 0.995933 -69 TCCAAAAATGGCATCAAAACGCTTATTTTA 4 99 0 GCATCAAAAC 0.879053 -26 GATCGCTCCAAAAATGGCATCAAA 4 111 0 GCTCCAAAAA 0.912206 -14 ********** Masking position 7 Map Score: 3.71136 Number of sites scoring better than the average of aligned sites = 730 Number in coding regions = 693 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 ********** No masking Map Score: -2.10731e-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 9 ********** No masking Map Score: -2.10731e-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 10 ********** No masking Map Score: -2.10731e-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