AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i326_not_clear1_hpyl_reg_100.orf -o326_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 RHP01340 80 AE000511 #2 RHP00173 300 AE000511 Motif number 1 TAATACAACTTTAATAAAAGAAAAACCTTAAAAG 1 24 0 TTAATAAAAA 0.992662 -57 TATTTTATTTTTAAAAAGCTATAATACAACTTTA 1 45 0 TTAAAAATAA 0.970798 -36 CGCGAAGCCATTAAAAAAGAAAAACCAATCATGA 2 18 0 TTAAAAAAAA 0.990746 -283 GAAGGAGGATTGAATATGGAAAAATTGCGCGAAG 2 45 0 TGAATAAAAA 0.972967 -256 TAAAAGGGGTTTTATAATGGAAAACAACGAAAAT 2 142 0 TTTATAAAAA 0.95525 -159 ATTAGTTGGTTTAATACGCTATAATCTGTGTGCC 2 201 0 TTAATAATAA 0.975936 -100 AACTAATAAATTAATAAATAAAAACATGATTTTT 2 228 1 TTAATAAAAA 0.985355 -73 ATTATTTTACTCAAAACCTTAAAAATCATGTTTT 2 248 0 TCAAAAAAAA 0.966717 -53 ATAATGGTTTTTAAAAAAGCAAAAAAGAGTTTGG 2 277 1 TTAAAAAAAA 0.990978 -24 ****** **** Masking position 6 Map Score: 19.0421 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 177 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 2 CCTTAAAAGGGAGCAAAAAAGC 1 3 0 GAGCAAAAAA 0.942382 -78 ACTTTAATAAAAGAAAAACCTTAAAAGGGA 1 21 0 AAGAAAAACC 0.980483 -60 GCCATTAAAAAAGAAAAACCAATCATGAAT 2 16 0 AAGAAAAACC 0.980483 -285 CTAAAAACTTGCGCAAAACGCCATTCAATT 2 105 1 GCGCAAAACG 0.975063 -196 ATGGAAAACAACGAAAATCATGAGAAATTG 2 130 0 ACGAAAATCA 0.954238 -171 ACATTGTGTGGCTCAAATCATTTTTAAAAG 2 170 0 GCTCAAATCA 0.917185 -131 TAAATTAATAAATAAAAACATGATTTTTAA 2 234 1 AATAAAAACA 0.943814 -67 CCATTATTTTACTCAAAACCTTAAAAATCA 2 254 0 ACTCAAAACC 0.976552 -47 GTTTTTAAAAAAGCAAAAAAGAGTTTGG 2 283 1 AAGCAAAAAA 0.95199 -18 ********** Masking position 5 Map Score: 11.982 Number of sites scoring better than the average of aligned sites = 771 Number in coding regions = 705 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 3 GCTTTTTTGCTCCCTTTTAAGGTTTTTCTT 1 11 1 TCCCTTTTAA 0.959792 -70 TCCTTATATTTTATTTTTAAAAAGCTATAA 1 55 0 TTATTTTTAA 0.965345 -26 GATTGGTTTTTCTTTTTTAATGGCTTCGCG 2 22 1 TCTTTTTTAA 0.977801 -279 GTGGCTCAAATCATTTTTAAAAGGGGTTTT 2 163 0 TCATTTTTAA 0.991086 -138 AATAAAAACATGATTTTTAAGGTTTTGAGT 2 244 1 TGATTTTTAA 0.987072 -57 AGTAAAATAATGGTTTTTAAAAAAGCAAAA 2 271 1 TGGTTTTTAA 0.978174 -30 ********** Masking position 5 Map Score: 8.88734 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 270 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 TTTTGCTCCCTTTTAAGGTTTTTCTTTTAT 1 15 1 TTTTAAGGTT 0.964292 -66 GTTTTTCTTTTTTAATGGCTTCGCGCAATT 2 27 1 TTTAATGGCT 0.977187 -274 TTTGCGCAAGTTTTTAGGCGATGCGTTCAC 2 92 0 TTTTTAGGCG 0.952693 -209 TCATGAGAAATTGAATGGCGTTTTGCGCAA 2 113 0 TTGAATGGCG 0.967149 -188 TGTGCCAACATTGTGTGGCTCAAATCATTT 2 177 0 TTGTGTGGCT 0.967582 -124 AAAACATGATTTTTAAGGTTTTGAGTAAAA 2 248 1 TTTTAAGGTT 0.964292 -53 ********** Masking position 2 Map Score: 5.24463 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 649 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 AAAAAGCTATAATACAACTTTAATAAAAGA 1 37 0 AATACAACTT 0.953512 -44 TTCCATATTCAATCCTCCTTCTTTCCCATC 2 58 1 AATCCTCCTT 0.848011 -243 TTTATAATGGAAAACAACGAAAATCATGAG 2 136 0 AAAACAACGA 0.933304 -165 TTTCCATTATAAAACCCCTTTTAAAAATGA 2 153 1 AAAACCCCTT 0.971625 -148 ATAGCGTATTAAACCAACTAATAAATTAAT 2 213 1 AAACCAACTA 0.969445 -88 TGCTTTTTTAAAAACCATTATTTTACTCAA 2 268 0 AAAACCATTA 0.864701 -33 ********** Masking position 2 Map Score: 1.31233 Number of sites scoring better than the average of aligned sites = 671 Number in coding regions = 555 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 6 ********** No masking Map Score: -6.79689e-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: -6.79689e-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: -6.79689e-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