AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i170_Urease_hpyl_reg_300.orf -o170_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 RHP01027 28 AE000511 #2 RHP01028 22 AE000511 #3 RHP01030 192 AE000511 #4 RHP01032 300 AE000511 Motif number 1 TTGTTATTTTTCTATTTCTTTT 2 8 0 ATTTTTCTAT 0.843086 -15 TAGCTCTCTGATTTTTTGTTTATCAAAAAA 3 49 1 ATTTTTTGTT 0.990639 -144 AAAGCCCCCAATTTTTTGATAAACAAAAAA 3 60 0 ATTTTTTGAT 0.986354 -133 AATTGGGGGCTTTTTTTGTTTTTATTTTTT 3 77 1 TTTTTTTGTT 0.93707 -116 TTTTGTTTTTATTTTTTGTCAATTTACTAT 3 90 1 ATTTTTTGTC 0.956653 -103 TCAATTTACTATTTTTCTTTATGATTAGCT 3 108 1 ATTTTTCTTT 0.887211 -85 CCTTACGAATAACTTTTGTTGCTTGAGCTA 3 133 0 AACTTTTGTT 0.886529 -60 TTGTTGTAAAAATTTTTGTTTGGAAGGAAA 3 168 1 AATTTTTGTT 0.970965 -25 TTTTTTTGCGAGTTTTTGATCTTTATAAAT 4 86 1 AGTTTTTGAT 0.950492 -215 AATTGTAGCAATGTTTTGATTTACTAAGAT 4 220 0 ATGTTTTGAT 0.944098 -81 ********** Masking position 5 Map Score: 14.3601 Number of sites scoring better than the average of aligned sites = 446 Number in coding regions = 365 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 AAAATTCCTTTCAATTTGAGATTAAA 1 13 0 TCCTTCAATT 0.945121 -16 GGAGCGTTGCTCCTAAAAAATC 3 2 0 TCCTAAAAAT 0.884297 -191 TTACTATTTTTCTTTATGATTAGCTCAAGCA 3 113 1 TCTTTTGATT 0.88118 -80 CAACAAACGCACCTTACGAATAACTTTTGTT 3 143 0 ACCTTCGAAT 0.934233 -50 TGCCTTTTCCTTCCAAACAAAAATTTTT 3 175 0 TCCTTCAAAC 0.927184 -18 GAGTTTTTGATCTTTATAAATTCTAAAGGGG 4 95 1 TCTTTTAAAT 0.965999 -206 TAACACTAATTCATTTTAAATAATAATTAGT 4 171 1 TCATTTAAAT 0.896349 -130 CTTCTGTTAATCTTAGTAAATCAAAACATTG 4 211 1 TCTTATAAAT 0.899827 -90 AAGGAAAAACACTTTAAGAATAGGAGAATAA 4 279 1 ACTTTAGAAT 0.798875 -22 ***** ***** Masking position 4 Map Score: 4.15108 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 324 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 3 AATTCCTTTCAATTTGAGATTAAAAT 1 3 0 AATGAATTAA 0.971677 -26 AAAAGAAATAGAAAAATAACAA 2 6 1 AATGAAAAAA 0.793062 -17 GAGAGCTAAAAACTAAGGATTTAAGGAGCGTTGC 3 23 0 AATAGATTAA 0.946466 -170 TCATAAAGAAAAATAGTAAATTGACAAAAAATAA 3 98 0 AATGTAATGA 0.94551 -95 ACTCGCAAAAAAATGAGAATTAAAATTGGAGTGA 4 65 0 AATAGATTAA 0.946466 -236 TATAAATTCTAAAGGGGTATTAAACGCACTTCTA 4 109 1 AAGGGATTAA 0.953555 -192 AAGCGCTATAAAATCGTTATTAGAAGTGCGTTTA 4 129 0 AATGTATTGA 0.965322 -172 TTTAAATAATAATTAGTTAATGAACGCTTCTGTT 4 185 1 AATGTAATAA 0.968397 -116 ** * ** *** ** Masking position 9 Map Score: 3.23913 Number of sites scoring better than the average of aligned sites = 232 Number in coding regions = 194 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 ********** No masking Map Score: 1.74326e-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 5 ********** No masking Map Score: 1.74326e-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 6 ********** No masking Map Score: 1.74326e-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