AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i255_heat_shock_hpyl_reg_100.orf -o255_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 RHP01066 29 AE000511 #2 RHP01068 300 AE000511 #3 RHP00429 167 AE000511 #4 RHP00723 124 AE000511 Motif number 1 AACATTTATTTTAAAAGAAAGGATAA 1 4 1 ATTTTTAAAA 0.968796 -26 GTAGGGGGAGAGTTATTTCAAAATACCCCACTA 2 46 1 ATTTTCAAAA 0.901371 -255 TAAGAGAATGAGTTTCATTATAAAACAAAAAGG 2 85 1 ATTATTATAA 0.736688 -216 TTTAGATCTGATCTCATTTAAATATGGATAATC 2 117 0 ACTTTTAAAT 0.882498 -184 ATGAGATCAGATCTAAATTAAATCAACTCTATA 2 133 1 ACTATTAAAT 0.531902 -168 AAATTAAATCAACTCTATAAAAAATCCTAATTT 2 147 1 ACTATAAAAA 0.845553 -154 AAATCTATTTACTAGCATTAAATTAGGATTTTT 2 166 0 ATAATTAAAT 0.789588 -135 ATAATCTATCACTTGTTTTAAAAAAGTGATAAA 2 238 0 ATTTTTAAAA 0.973296 -63 TAACTAAAATATTGAGTTTAAATCCACGATGAG 3 17 0 ATGTTTAAAT 0.943926 -151 TAAACTCAATATTTTAGTTAAAATTCCTTTTAA 3 30 1 ATTGTTAAAA 0.882749 -138 AACCCGTTTCAGCGCAATTAAAAGGAATTTTAA 3 47 0 ACGATTAAAA 0.970779 -121 ATTGCGCTGAAACGGGTTTAAAATCTGCATTAT 3 62 1 ACGTTTAAAA 0.973836 -106 GTTTATTGATAATGCTTTTAGATAATGCAGATT 3 83 0 ATGTTTAGAT 0.811067 -85 CCTTTAAAATAGTTTTATTAGAATACTATCATA 3 139 0 ATTATTAGAA 0.884127 -29 GGATCACCTTTAAAATAGTTTTATT 3 153 0 ACATTTAAAA 0.894883 -15 GCATGCCAAAACTTAGATAAAATAACACGATAA 4 35 0 ATTATAAAAT 0.70613 -90 ACGCAAAATTATCGCTTTTAAGATAAAATAAGC 4 76 1 ACGTTTAAGA 0.806757 -49 TCGCTCCAAAAATGGCATCAAAACGCTTATTTT 4 100 0 ATGATCAAAA 0.888861 -25 * ** ******* Masking position 8 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 TCTTGGGTTAGGGGGATTTTAAGGGGGGTT 2 16 1 GGGGGATTTT 0.994972 -285 GGGATTTTAAGGGGGGTTGTAGGGGGAGAG 2 28 1 GGGGGGTTGT 0.98096 -273 GGGGGTTGTAGGGGGAGAGTTATTTCAAAA 2 39 1 GGGGGAGAGT 0.957289 -262 AGGGGATAGTGGGGTATTTTGAAATAACTC 2 55 0 GGGGTATTTT 0.989671 -246 CATTCTCTTAAGGGGATAGTGGGGTATTTT 2 65 0 AGGGGATAGT 0.904061 -236 AAGAAAAATCGGGTAATTTTTATCACTTTT 2 220 1 GGGTAATTTT 0.936803 -81 GGGGTTATCTTTATTACTATG 4 2 1 GGGTTATCTT 0.93195 -123 TGGTTTTATCGTGTTATTTTATCTAAGTTT 4 30 1 GTGTTATTTT 0.807045 -95 ********** Masking position 10 Map Score: 7.88595 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 692 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 ACCCCCCTTAAAATCCCCCTAACCCAAGAA 2 15 0 AAATCCCCCT 0.992563 -286 TCTCCCCCTACAACCCCCCTTAAAATCCCC 2 27 0 CAACCCCCCT 0.992672 -274 TTTGAAATAACTCTCCCCCTACAACCCCCC 2 38 0 CTCTCCCCCT 0.989533 -263 AGTTATTTCAAAATACCCCACTATCCCCTT 2 56 1 AAATACCCCA 0.886017 -245 AAATACCCCACTATCCCCTTAAGAGAATGA 2 66 1 CTATCCCCTT 0.975736 -235 ********** Masking position 6 Map Score: 3.83341 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 183 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 AACAAAAAGGATTATCCATATTTAAATGAGATCA 2 108 1 ATTATCTTTA 0.964457 -193 AACTCTATAAAAAATCCTAATTTAATGCTAGTAA 2 157 1 AAAATCTTTA 0.655926 -144 AGTGATAAAAATTACCCGATTTTTCTTTAAAGTT 2 213 0 ATTACCTTTT 0.969385 -88 TCGGGTAATTTTTATCACTTTTTTAAAACAAGTG 2 228 1 TTTATATTTT 0.682492 -73 CAAGTGATAGATTATTAACTTTTTATGCTATAAT 2 256 1 ATTATATTTT 0.944165 -45 ATGCTTTTAGATAATGCAGATTTTAAACCCGTTT 3 71 0 ATAATCTTTT 0.96377 -97 TTAGAATACTATCATAAATCTTTAGTGTTAGTCA 3 121 0 ATCATATTTA 0.754257 -47 TAGTATTCTAATAAAACTATTTTAAAGGTGATCC 3 144 1 ATAAACTTTA 0.767328 -24 GGTTATCTTTATTACTATGGTTTTATCGTGTTAT 4 13 1 ATTACATTTT 0.921935 -112 AAAAGCGATAATTTTGCGTGTTTTGGCGCATGCC 4 61 0 ATTTTCTTTT 0.853937 -64 AAATGGCATCAAAACGCTTATTTTATCTTAAAAG 4 90 0 AAAACCTTTT 0.512341 -35 ***** * **** Masking position 11 Map Score: 5.43055 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 379 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 GCGTTATCCTTTCTTTTAAA 1 20 0 GCGTTATCCT 0.984487 -10 AAAACAAAAAGGATTATCCATATTTAAATG 2 106 1 GGATTATCCA 0.983044 -195 TTTAAAATCTGCATTATCTAAAAGCATTAT 3 78 1 GCATTATCTA 0.98204 -90 TTATCTAAAAGCATTATCAATAAACTTGAT 3 91 1 GCATTATCAA 0.968759 -77 GGGGTTATCTTTATTACTATG 4 2 1 GGGTTATCTT 0.965787 -123 ********** Masking position 5 Map Score: 4.73972 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 46 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 ********** 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 7 ********** 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 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