AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i110_Amino_Acid_Transport_1_hpyl_reg_100.orf -o110_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 RHP00355 67 AE000511 #2 RHP00357 40 AE000511 #3 RHP00358 21 AE000511 #4 RHP00359 300 AE000511 #5 RHP00568 212 AE000511 #6 RHP00571 48 AE000511 Motif number 1 TGTTTGAAAAAATTCAGGYTTAAAATATAAA 1 47 1 AATGGTTAAA 0.966103 -21 CTCCTTAATAAACTAGGGTTTAAAAAAGAAATTC 2 12 0 AATGGTTAAA 0.966112 -29 AAAAACTCCTTAATAAACTAGGGTT 2 26 0 AAACCTAATA 0.887092 -15 CATTGCCACTAAAAGAGGGCAAAGCCGCAATCTG 4 12 0 AAAGGCAAAG 0.848376 -289 GAGTGTCTGTAAAAATGCTCAAAAGCATTTTCTA 4 45 1 AAAGCCAAAA 0.957278 -256 CATTTTCTATAATAAGCCATAATAAAAGGGCTTG 4 70 1 AAACCTAATA 0.882276 -231 AATTGATGACAACAAAGCCTAAAACTCAAACAAA 4 124 1 AAAGCTAAAA 0.979875 -177 AAACTCAAACAAAACCCGTTTAAGAATTTCTAAA 4 145 1 AAACGTTAAG 0.682785 -156 AAGAATTTCTAAATATGGGTAAAAAATATACAAT 4 166 1 AATGGTAAAA 0.982254 -135 AAGAAATAAAAAATGAGCGCAAAACGCCATGAAT 4 219 0 AATGCCAAAA 0.962225 -82 TTATAATAAAAAAACTGGCTGAAATTAACAACAA 5 40 0 AAAGGTGAAA 0.901671 -173 TATTCAAAGAAATTTTGGATTATAATAAAAAAAC 5 59 0 AATGGTTATA 0.930136 -154 ACGGCTCATAAACTTCCCATAATAAGGGCTTGGG 5 101 1 AATCCTAATA 0.899305 -112 AACTTCTAACAATTGGGGTGAATAAGAGCTGTTT 5 142 1 AATGGGAATA 0.815522 -71 CTTAAAAATTAATGACGCTTTAAAGCACCATGTT 5 179 0 AAGGCTTAAA 0.869466 -34 ATAAAGTTTGCTAAAAAGATGATTCTA 6 4 1 AATGCAAAAA 0.865076 -45 ** * ** ***** Masking position 12 Map Score: 17.5607 Number of sites scoring better than the average of aligned sites = 1951 Number in coding regions = 1677 Number in noncoding regions = 274 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 2 AAAAACTCCTTAATAAACTAG 2 30 0 AAAACTCCTT 0.977393 -11 GAGTGTCTGTAAAAATGCTCAAAAGCATTT 4 45 1 AAAAATGCTC 0.923407 -256 GCTTATTATAGAAAATGCTTTTGAGCATTT 4 57 0 GAAAATGCTT 0.862726 -244 AAGCCATAATAAAAGGGCTTGCAAGCGAGT 4 83 1 AAAAGGGCTT 0.97287 -218 AAATGAGCGCAAAACGCCATGAATTTTCAT 4 213 0 AAAACGCCAT 0.906136 -88 GATTGAAACTCCTATGATGATGTG 4 287 0 GAAACTCCTA 0.794302 -14 GAATAGTGGCAAAACGGCTCATAAACTTCC 5 88 1 AAAACGGCTC 0.988159 -125 ACTTCCCATAATAAGGGCTTGGGTTTTCCA 5 112 1 ATAAGGGCTT 0.834605 -101 ACCATGTTTAAAAACAGCTCTTATTCACCC 5 157 0 AAAACAGCTC 0.965813 -56 AAAAACACCTTTTTTTGAAAT 6 38 0 AAAACACCTT 0.95865 -11 ********** Masking position 4 Map Score: 11.1029 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 713 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 AATCAAACCATGCAAAATTTTTATTTTGTGT 1 11 1 TGCAAATTTT 0.865836 -57 TATATTTTAACCTGAATTTTTTCAAACATT 1 45 0 CCTAATTTT 0.695472 -23 GGCTTTGTTGTCATCAATTTTAAAGCTACCA 4 112 0 TCATAATTTT 0.982124 -189 CAAAACCCGTTTAAGAATTTCTAAATATGGG 4 154 1 TTAAAATTTC 0.813233 -147 GCGCAAAACGCCATGAATTTTCATCTTATTA 4 206 0 CCATAATTTT 0.935868 -95 TTTATTATAATCCAAAATTTCTTTGAATAGT 5 64 1 TCCAAATTTC 0.970505 -149 GCAAAACGGCTCATAAACTTCCCATAATAAG 5 96 1 TCATAACTTC 0.934656 -117 CTTTAAAGCGTCATTAATTTTTAAGGTATAG 5 188 1 TCATAATTTT 0.982124 -25 **** ****** Masking position 6 Map Score: 6.95061 Number of sites scoring better than the average of aligned sites = 311 Number in coding regions = 260 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 4 ACCATGCAAAATTTTTATTTTGTGTTAGAA 1 17 1 ATTTTTATTT 0.692976 -51 TTTATATTTTAACCTGAATTTT 1 55 0 ATATTTTAA 0.0441184 -13 GGAATTTCTTTTTTAAACCCTAG 2 4 1 ATTTCTTTTT 0.841337 -37 CCCTTTTATTATGGCTTATTATAGAAAATG 4 70 0 ATGGCTTATT 0.788397 -231 CCGTTTAAGAATTTCTAAATATGGGTAAAA 4 160 1 ATTTCTAAAT 0.811505 -141 ATTATAAGGTATTGTATATTTTTTACCCAT 4 180 0 ATTGTATATT 0.825659 -121 TTTTGCGCTCATTTTTTATTTCTTTATTAA 4 229 1 ATTTTTTATT 0.9343 -72 TATTAATTTGATTGCATAATAATAGCTGAC 4 253 1 ATTGCATAAT 0.788022 -48 CCATTTAATGATTGTTTAATCATTGTTGTT 5 18 1 ATTGTTTAAT 0.941221 -195 TTTAATCATTGTTGTTAATTTCAGCCAGTT 5 32 1 GTTGTTAATT 0.744921 -181 ATTTCAGCCAGTTTTTTTATTATAATCCAA 5 49 1 GTTTTTTTAT 0.6468 -164 ********** Masking position 2 Map Score: 3.61857 Number of sites scoring better than the average of aligned sites = 1384 Number in coding regions = 1096 Number in noncoding regions = 288 Number of orfs with sites within 600 bp upstream = 248 Fraction of orfs with sites within 600 bp upstream = 0.039833 Motif number 5 TTTTCAAACATTCTAACACAAAATAAAAAT 1 27 0 TTCTAACACA 0.864744 -41 GTTAGAATGTTTGAAAAAATTCAGGYTTAA 1 40 1 TTGAAAAAAT 0.875811 -28 CAATGAGTGTCTGTAAAAATGCTCAAAAGC 4 41 1 CTGTAAAAAT 0.799738 -260 AAGCCTAAAACTCAAACAAAACCCGTTTAA 4 138 1 CTCAAACAAA 0.93165 -163 GTTTAAGAATTTCTAAATATGGGTAAAAAA 4 162 1 TTCTAAATAT 0.781282 -139 TTTGCCACTATTCAAAGAAATTTTGGATTA 5 71 0 TTCAAAGAAA 0.899794 -142 TTTTCCAAACTTCTAACAATTGGGGTGAAT 5 135 1 TTCTAACAAT 0.960113 -78 TGATTCTAATTTCAAAAAAAGGTGTTTTT 6 30 1 TTCAAAAAAA 0.952226 -19 ********** Masking position 5 Map Score: 2.57653 Number of sites scoring better than the average of aligned sites = 921 Number in coding regions = 818 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 6 AAACCCTAGTTTATTAAGGAGTTTTT 2 25 1 TTATTAAGGA 0.900362 -16 TTTATTAAAGGGACTATCAGC 3 2 1 TTATTAAAGG 0.979804 -20 TTATTATGGCTTATTATAGAAAATGCTTTT 4 65 0 TTATTATAGA 0.958697 -236 AATTTTCATCTTATTATAAGGTATTGTATA 4 192 0 TTATTATAAG 0.932125 -109 TGCAATCAAATTAATAAAGAAATAAAAAAT 4 239 0 TTAATAAAGA 0.747518 -62 ACATAACACATCATCATAGGAGTTTCAATC 4 281 1 TCATCATAGG 0.872776 -20 GATTAAACAATCATTAAATGGAGAGGAC 5 9 0 TCATTAAATG 0.755552 -204 GCCAGTTTTTTTATTATAATCCAAAATTTC 5 55 1 TTATTATAAT 0.68003 -158 ACCCAAGCCCTTATTATGGGAAGTTTATGA 5 106 0 TTATTATGGG 0.967049 -107 ********** Masking position 6 Map Score: 5.9175 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 313 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 7 ********** No masking Map Score: -1.42576e-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 8 ********** No masking Map Score: -1.42576e-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 9 ********** No masking Map Score: -1.42576e-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