AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_hpyl_reg_300.orf -o111_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 RHP01133 257 AE000511 #2 RHP00037 163 AE000511 #3 RHP00038 117 AE000511 #4 RHP00039 44 AE000511 #5 RHP00040 65 AE000511 #6 RHP00211 147 AE000511 Motif number 1 TAATGGGTGTTTGTTTTAAGACGCTATGAC 1 82 0 TTGTTTTAAG 0.968117 -176 GTGAATTGGCATGATTTAAGAGTAATGGGT 1 104 0 ATGATTTAAG 0.734931 -154 TAAGGGTAGTTTTTTTTAAGTTGTGTTATT 1 160 0 TTTTTTTAAG 0.975859 -98 TTTAGATTGATTTTTTTAAGGGTAGTTTTT 1 176 0 TTTTTTTAAG 0.975859 -82 TAGCTATATTTTAATTTAAGAATTTTAGAT 1 199 0 TTAATTTAAG 0.842255 -59 ATAAATTTTCTTTATTATAGCCCATTTTCA 2 26 1 TTTATTATAG 0.93019 -138 TTAAAGGGCTTTGTTTTAAAAGCAAAATTT 2 65 0 TTGTTTTAAA 0.906439 -99 TGCCTTTGGGTTTTTTATAACAAGGAGTTA 2 139 1 TTTTTTATAA 0.78887 -25 TACAAACACCTTTCTTAAAA 3 1 0 TTTCTTAAAA 0.849543 -117 CGTTGGCTTTTTGCTTTAATTTTTACTTCT 3 49 1 TTGCTTTAAT 0.673448 -69 AAAAGAGTATTTTATTAAAAAAGAAGTAAA 3 70 0 TTTATTAAAA 0.92547 -48 TTGATTCCTTTTTATTATAGGCGGTTATT 3 99 1 TTTATTATAG 0.93019 -19 TCCATAGTTGTTTTTTAAAATGAATATT 5 9 0 TTTTTTAAAA 0.917009 -57 AGATGAGAGATTGTTTTAAGGTTTGAATA 6 10 0 TTGTTTTAAG 0.968117 -138 AATAAAGGGTTTTATTAAAGATGAGAGATT 6 28 0 TTTATTAAAG 0.9762 -120 TTACATGACTTTTATTTTATCCATGCTAAA 6 58 1 TTTATTTTAT 0.674701 -90 TCTCATTTATTTTATTAAAGCGTCAGTTTT 6 97 0 TTTATTAAAG 0.9762 -51 ********** Masking position 5 Map Score: 27.8279 Number of sites scoring better than the average of aligned sites = 864 Number in coding regions = 693 Number in noncoding regions = 171 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 2 TTCAAACCCTAAACCCAAACCTTTCTCTCATATAT 1 33 1 AAACAACTTC 0.881136 -225 ATTATTTTCAAATTTCAAGTCTAAAGAGTGTGAAT 1 128 0 AATCAACTAA 0.865352 -130 ATTTGAAAATAATAACACAACTTAAAAAAAACTAC 1 150 1 AATCACCTTA 0.968217 -108 ACAACTTAAAAAAAACTACCCTTAAAAAAATCAAT 1 166 1 AAACTACTTA 0.968906 -92 TTTAGTGTATTATAGCTATATTTTAATTTAAGAAT 1 206 0 TATCTATTTA 0.575349 -52 ACACTAAAACAATCTCAAGGTTTCAAAATTTAGCC 1 233 1 AATCAATTTA 0.963278 -25 GCTTTGTTTTAAAAGCAAAATTTAAAGGAGCATGA 2 53 0 AAACAATTTA 0.974806 -111 AGCCCTTTAAAATTTCAAACTTTAACCGATTATAG 2 85 1 AATCAATTTA 0.963278 -79 AGCCCCATACAAACACCTTTCTTAAAA 3 3 0 AAACCTCTTA 0.819445 -115 ATTAAAGCAAAAAGCCAACGCTTAAAGCGTTAGCC 3 34 0 AAACAACTTA 0.982026 -84 TTTTTTAATAAAATACTCTTTTTGATTCCTTTTTA 3 78 1 AAACTCTTTA 0.947807 -40 ATGGAGTATAAAAACCATAATTAGACAAACCTTTA 5 34 1 AAACATTTAA 0.727928 -32 ACCTTAAAACAATCTCTCATCTTTAATAAAACCCT 6 18 1 AATCTCCTTA 0.945578 -130 ATCTTTAATAAAACCCTTTATTTTACATGACTTTT 6 36 1 AAACTTTTTA 0.897881 -112 ATGGGATTAAAAACTGACGCTTTAATAAAATAAAT 6 88 1 AAAGACTTTA 0.727529 -60 *** *** *** * Masking position 2 Map Score: 16.4052 Number of sites scoring better than the average of aligned sites = 1079 Number in coding regions = 925 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 GGTTTGGGTTTAGGGTTTGAATTATATTGATT 1 22 0 TAGGGTTTGT 0.955436 -236 TATATGAGAGAAAGGTTTGGGTTTAGGGTTTG 1 35 0 AAAGGTTTGT 0.976265 -223 GATTTAAGAGTAATGGGTGTTTGTTTTAAGAC 1 90 0 TAATGGGTGT 0.696883 -168 TTCAAGTCTAAAGAGTGTGAATTGGCATGATT 1 118 0 AAGAGTGTGT 0.633731 -140 TAGTTTTTTTTAAGTTGTGTTATTATTTTCAA 1 152 0 TAAGTTGTGA 0.785516 -106 TTGATTTTTTTAAGGGTAGTTTTTTTTAAGTT 1 168 0 TAAGGGTAGT 0.815467 -90 GGCTAAATTTTGAAACCTTGAGATT 1 243 0 TAAATTTTGA 0.611003 -15 GCAATAAGATTTGGTATAAATTTTCT 2 5 1 TAAGATTTGA 0.705707 -159 CATGCTCCTTTAAATTTTGCTTTTAAAACAAA 2 54 1 TAAATTTTGT 0.804754 -110 TATAATCGGTTAAAGTTTGAAATTTTAAAGGG 2 87 0 TAAAGTTTGA 0.887508 -77 TTTTAAGAAAGGTGTTTGTATGGGGCTAA 3 8 1 AAAGGTGTTT 0.727422 -110 GCTAACGCTTTAAGCGTTGGCTTTTTGCTTTA 3 35 1 TAAGCGTTGT 0.849337 -83 AAATCCTTAAAGGTTTGTCTAATTATGGTT 5 46 0 AAAGGTTTGT 0.976265 -20 GAGATTGTTTTAAGGTTTGAATA 6 2 0 TAAGGTTTGT 0.987633 -146 CATGTAAAATAAAGGGTTTTATTAAAGATGAG 6 33 0 AAAGGGTTTT 0.727422 -115 ********* * Masking position 2 Map Score: 13.4249 Number of sites scoring better than the average of aligned sites = 922 Number in coding regions = 785 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 4 AAGTAACGCTAAATCAATATAATTCAAACCCT 1 10 1 TAAATATTAA 0.766702 -248 TACCCTTAAAAAAATCAATCTAAAATTCTTAAA 1 182 1 AAAATATTAA 0.912278 -76 GCTTTTAAAACAAAGCCCTTTAAAATTTCAAAC 2 72 1 CAAAGCTTAA 0.913839 -92 ATTTTATTAAAAAAGAAGTAAAAATTAAAGCAA 3 59 0 AAAAGATAAA 0.961796 -59 GCCTATAATAAAAAGGAATCAAAAAGAGTATTT 3 88 0 AAAAGATAAA 0.961796 -30 AACGCCTTTTAAAAGGCTTAAGATTAAGAAAAA 4 19 0 AAAAGCTAGA 0.939192 -26 TAAGCCTTTTAAAAGGCGTTTTA 4 32 1 AAAAGCTTTA 0.935969 -13 TGGATAAAATAAAAGTCATGTAAAATAAAGGGT 6 48 0 AAAAGCTTAA 0.975569 -100 ACGCTTTAATAAAATAAATGAGATTAAAGCACT 6 104 1 AAAATATAGA 0.800894 -44 TAAATGAGATTAAAGCACTCTTAATAAGGTTAT 6 118 1 TAAAGATTTA 0.810023 -30 ***** * * *** Masking position 9 Map Score: 7.03201 Number of sites scoring better than the average of aligned sites = 710 Number in coding regions = 613 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 5 AATCAATATAATTCAAACCCTAAACCCAAA 1 22 1 ATTCAAACCC 0.988244 -236 CAAACCCTAAACCCAAACCTTTCTCTCATA 1 35 1 ACCCAAACCT 0.906097 -223 AATCATGCCAATTCACACTCTTTAGACTTG 1 118 1 ATTCACACTC 0.858976 -140 GGCTAAATTTTGAAACCTTGAGATTGTT 1 240 0 TTTGAAACCT 0.838618 -18 CCCTTTAAAATTTCAAACTTTAACCGATTA 2 87 1 TTTCAAACTT 0.895452 -77 CGTTAGCCCCATACAAACACCTTTCTTAAA 3 12 0 ATACAAACAC 0.849794 -106 AACCATAATTAGACAAACCTTTAAGGATTT 5 46 1 AGACAAACCT 0.919874 -20 TATTCAAACCTTAAAACAATC 6 2 1 ATTCAAACCT 0.988475 -146 ********** Masking position 5 Map Score: 3.61705 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 359 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 6 ********** No masking Map Score: -1.61761e-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 7 ********** No masking Map Score: -1.61761e-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: -1.61761e-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