AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i260_flagella_hpyl_reg_300.orf -o260_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 RHP00037 163 AE000511 #2 RHP00173 300 AE000511 #3 RHP00179 92 AE000511 #4 RHP00180 16 AE000511 #5 RHP00181 71 AE000511 Motif number 1 AAAATGGGCTATAATAAAGAAAATTTATACCAA 1 21 0 ATAAAAAAAA 0.969017 -143 AGGGCTTTGTTTTAAAAGCAAAATTTAAAGGAG 1 58 0 TTTAAAAAAA 0.90881 -106 ACAAAGCCCTTTAAAATTTCAAACTTTAACCGA 1 81 1 TTAAATCAAA 0.922034 -83 CTCCTTGTTATAAAAAACCCAAAGGCATCCTTG 1 133 0 TAAAAACAAA 0.95367 -31 CGCGAAGCCATTAAAAAAGAAAAACCAATCATG 2 19 0 TTAAAAAAAA 0.987412 -282 GAAGGAGGATTGAATATGGAAAAATTGCGCGAA 2 46 0 TGAAATAAAA 0.90587 -255 TTTATAATGGAAAACAACGAAAATCATGAGAAA 2 133 0 AAAAAAAAAA 0.955283 -168 AACTAATAAATTAATAAATAAAAACATGATTTT 2 228 1 TTAAAAAAAA 0.987412 -73 TAATGGTTTTTAAAAAAGCAAAAAAGAGTTTGG 2 278 1 TAAAAAAAAA 0.981696 -23 GCGGCGGCTAAAAAGAATTAAAAACAGAGAGTT 5 22 1 AAAAAAAAAA 0.955283 -50 CCTTTATCCTTTAAAATTGATAACTCTCTGTTT 5 43 0 TTAAATATAA 0.791826 -29 **** ** **** Masking position 6 Map Score: 14.6307 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 388 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 TTTGAAATTTTAAAGGGCTTTGTTTTAAAAG 1 73 0 TAAAGGCTTT 0.777948 -91 GGTTTTTTATAACAAGGAGTTACAACA 1 147 1 AACAAGAGTT 0.954363 -17 AATCATTTTTAAAAGGGGTTTTATAATGGAA 2 154 0 AAAAGGGTTT 0.941565 -147 AACCCCTTTTAAAAATGATTTGAGCCACACA 2 165 1 AAAAAGATTT 0.983593 -136 TAATAAATAAAAACATGATTTTTAAGGTTTT 2 239 1 AAACAGATTT 0.918374 -62 TTTTGAGTAAAATAATGGTTTTTAAAAAAGC 2 266 1 AATAAGGTTT 0.890871 -35 TTAAAAAAGCAAAAAAGAGTTTGG 2 287 1 AAAAAGAGTT 0.977146 -14 TATCGGCAATAAAAACGATTTGT 3 3 0 AAAAAGATTT 0.983593 -90 TGCCTACAAGTATAATGATTTATTTGTTTGC 3 51 0 TATAAGATTT 0.883253 -42 AAGCGGCGGCTAAAAAGAATTAAAAACAGAG 5 20 1 TAAAAGAATT 0.810979 -52 AAGAATTAAAAACAGAGAGTTATCAATTTTA 5 34 1 AACAGGAGTT 0.929074 -38 ***** ***** Masking position 2 Map Score: 14.3726 Number of sites scoring better than the average of aligned sites = 1034 Number in coding regions = 817 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 AAAATATTCATGATTGGTTTTTCTTTT 2 8 1 TCATGATTGG 0.948266 -293 ATTCAATTTCTCATGATTTTCGTTGTTTTC 2 127 1 TCATGATTTT 0.974275 -174 CCCCTTTTAAAAATGATTTGAGCCACACAA 2 167 1 AAATGATTTG 0.974277 -134 ATAAATAAAAACATGATTTTTAAGGTTTTG 2 241 1 ACATGATTTT 0.966752 -60 TTGAGTAAAATAATGGTTTTTAAAAAAGCA 2 268 1 TAATGGTTTT 0.906107 -33 TCGGCAATAAAAACGATTTGT 3 2 0 AAACGATTTG 0.920987 -91 CCTACAAGTATAATGATTTATTTGTTTGCA 3 50 0 TAATGATTTA 0.925431 -43 ********** Masking position 3 Map Score: 6.02572 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 182 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 GAGCATGAAAATGGGCTATAATAAAGAAAA 1 31 0 ATGGGCTATA 0.977433 -133 TGGAACTATAATCGGTTAAAGTTTGAAATT 1 95 0 ATCGGTTAAA 0.962627 -69 GCGTGAACGCATCGCCTAAAAACTTGCGCA 2 90 1 ATCGCCTAAA 0.974474 -211 AGTTGGTTTAATACGCTATAATCTGTGTGC 2 202 0 ATACGCTATA 0.8489 -99 TTTAGCCAATATCGGCAATAAAAACGATTT 3 13 0 ATCGGCAATA 0.969382 -80 TATTGCCGATATTGGCTAAAGAATTTATGC 3 23 1 ATTGGCTAAA 0.974277 -70 TCGATCAAGCGGCGGCTAAAAAGAATTAAA 5 14 1 GGCGGCTAAA 0.949498 -58 ********** Masking position 8 Map Score: 4.51402 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 318 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 CATTTTCATGCTCCTTTAAATTTTGCTTTT 1 48 1 CTCCTTTAAA 0.939448 -116 AATTGCGCGAAGCCATTAAAAAAGAAAAAC 2 27 0 AGCCATTAAA 0.966888 -274 GTGAACGCATCGCCTAAAAACTTGCGCAAA 2 92 1 CGCCTAAAAA 0.8969 -209 TTGCGCAAAACGCCATTCAATTTCTCATGA 2 113 1 CGCCATTCAA 0.941885 -188 AAATGATTTGAGCCACACAATGTTGGCACA 2 177 1 AGCCACACAA 0.895234 -124 TTTTACTCAAAACCTTAAAAATCATGTTTT 2 248 0 AACCTTAAAA 0.92399 -53 AAAAACCTCCAAATTTTTCCATG 3 80 0 AACCTCCAAA 0.827533 -13 ATGTTCCTTTATCCTTTAAAATTGATAACT 5 51 0 ATCCTTTAAA 0.940577 -21 ********** Masking position 9 Map Score: 3.68777 Number of sites scoring better than the average of aligned sites = 1111 Number in coding regions = 989 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 6 TTTTTTAATGGCTTCGCGCAATTTTTCCATA 2 34 1 GTTCGCGCAA 0.993813 -267 ATTGAATGGCGTTTTGCGCAAGTTTTTAGGC 2 103 0 GTTTGCGCAA 0.996361 -198 TTTTAAAAATGATTTGAGCCACACAATGTTG 2 171 1 GTTTGAGCCA 0.990462 -130 GATTTTTAAGGTTTTGAGTAAAATAATGGTT 2 255 1 GTTTGAGTAA 0.978049 -46 * ********* Masking position 4 Map Score: 2.21765 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 42 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 GCAAAATTTAAAGGAGCATGAAAATGGGCT 1 44 0 AAGGAGCATG 0.9829 -120 TGAAATTTTAAAGGGCTTTGTTTTAAAAGC 1 72 0 AAGGGCTTTG 0.926034 -92 GATGGGAAAGAAGGAGGATTGAATATGGAA 2 58 0 AAGGAGGATT 0.952109 -243 TCATTTTTAAAAGGGGTTTTATAATGGAAA 2 153 0 AAGGGGTTTT 0.965322 -148 AAAAAGCAAAAAAGAGTTTGG 2 290 1 AAAGAGTTTG 0.89183 -11 TTAAAGGATAAAGGAACATT 5 62 1 AAGGAACATT 0.874843 -10 ********** Masking position 2 Map Score: 1.01117 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 436 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 8 GCAATAAGATTTGGTATAAATTTTCTTTA 1 10 1 TTTGGTATAA 0.937769 -154 TTTAAAGGGCTTTGTTTTAAAAGCAAAATT 1 66 0 TTTGTTTTAA 0.966312 -98 CATCCTTGCTTTTGGTTGGAACTATAATCG 1 111 0 TTTGGTTGGA 0.913047 -53 GTTGTAACTCCTTGTTATAAAAAACCCAAA 1 143 0 CTTGTTATAA 0.848975 -21 CATGATTTTCGTTGTTTTCCATTATAAAAC 2 138 1 GTTGTTTTCC 0.858484 -163 TAATTTATTAGTTGGTTTAATACGCTATAA 2 211 0 GTTGGTTTAA 0.96635 -90 TAATGATTTATTTGTTTGCATAAATTCTTT 3 40 0 TTTGTTTGCA 0.941185 -53 ********** Masking position 6 Map Score: 1.92861 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 390 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 9 ********** No masking Map Score: 1.82142e-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 10 ********** No masking Map Score: 1.82142e-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 11 ********** No masking Map Score: 1.82142e-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