AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i326_not_clear1_hpyl_reg_300.orf -o326_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 RHP01340 80 AE000511 #2 RHP00173 300 AE000511 Motif number 1 CTTTTAAGGTTTTTCTTTTATTAAAGTTGTATTA 1 24 1 TTTTTATTAA 0.993204 -57 TAAAGTTGTATTATAGCTTTTTAAAAATAAAATA 1 45 1 TTATTTTTAA 0.972727 -36 TCATGATTGGTTTTTCTTTTTTAATGGCTTCGCG 2 18 1 TTTTTTTTAA 0.991392 -283 CTTCGCGCAATTTTTCCATATTCAATCCTCCTTC 2 45 1 TTTTTATTCA 0.974932 -256 ATTTTCGTTGTTTTCCATTATAAAACCCCTTTTA 2 142 1 TTTTTATAAA 0.958444 -159 GGCACACAGATTATAGCGTATTAAACCAACTAAT 2 201 1 TTATTATTAA 0.977499 -100 AAAAATCATGTTTTTATTTATTAATTTATTAGTT 2 228 0 TTTTTATTAA 0.985312 -73 AAAACATGATTTTTAAGGTTTTGAGTAAAATAAT 2 248 1 TTTTTTTTGA 0.969094 -53 CCAAACTCTTTTTTGCTTTTTTAAAAACCATTAT 2 277 0 TTTTTTTTAA 0.991644 -24 **** ****** Masking position 9 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 0.933001 -78 ACTTTAATAAAAGAAAAACCTTAAAAGGGA 1 21 0 AAGAAAAACC 0.977155 -60 GCCATTAAAAAAGAAAAACCAATCATGAAT 2 16 0 AAGAAAAACC 0.977155 -285 CTAAAAACTTGCGCAAAACGCCATTCAATT 2 105 1 GCGCAAAACG 0.970838 -196 ATGGAAAACAACGAAAATCATGAGAAATTG 2 130 0 ACGAAAATCA 0.946678 -171 ACATTGTGTGGCTCAAATCATTTTTAAAAG 2 170 0 GCTCAAATCA 0.904119 -131 TAAATTAATAAATAAAAACATGATTTTTAA 2 234 1 AATAAAAACA 0.93465 -67 CCATTATTTTACTCAAAACCTTAAAAATCA 2 254 0 ACTCAAAACC 0.972572 -47 GTTTTTAAAAAAGCAAAAAAGAGTTTGG 2 283 1 AAGCAAAAAA 0.94408 -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 0.95666 -70 TCCTTATATTTTATTTTTAAAAAGCTATAA 1 55 0 TTATTTTTAA 0.962657 -26 GATTGGTTTTTCTTTTTTAATGGCTTCGCG 2 22 1 TCTTTTTTAA 0.976037 -279 GTGGCTCAAATCATTTTTAAAAGGGGTTTT 2 163 0 TCATTTTTAA 0.990368 -138 AATAAAAACATGATTTTTAAGGTTTTGAGT 2 244 1 TGATTTTTAA 0.986035 -57 AGTAAAATAATGGTTTTTAAAAAAGCAAAA 2 271 1 TGGTTTTTAA 0.976439 -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 0.962764 -66 GTTTTTCTTTTTTAATGGCTTCGCGCAATT 2 27 1 TTTAATGGCT 0.976197 -274 TTTGCGCAAGTTTTTAGGCGATGCGTTCAC 2 92 0 TTTTTAGGCG 0.950693 -209 TCATGAGAAATTGAATGGCGTTTTGCGCAA 2 113 0 TTGAATGGCG 0.965738 -188 TGTGCCAACATTGTGTGGCTCAAATCATTT 2 177 0 TTGTGTGGCT 0.96619 -124 AAAACATGATTTTTAAGGTTTTGAGTAAAA 2 248 1 TTTTAAGGTT 0.962764 -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 0.955639 -44 TTCCATATTCAATCCTCCTTCTTTCCCATC 2 58 1 AATCCTCCTT 0.854228 -243 TTTATAATGGAAAACAACGAAAATCATGAG 2 136 0 AAAACAACGA 0.936295 -165 TTTCCATTATAAAACCCCTTTTAAAAATGA 2 153 1 AAAACCCCTT 0.972947 -148 ATAGCGTATTAAACCAACTAATAAATTAAT 2 213 1 AAACCAACTA 0.970865 -88 TGCTTTTTTAAAAACCATTATTTTACTCAA 2 268 0 AAAACCATTA 0.870339 -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