AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_Amino_Acid_Transport_2_hpyl_reg_100.orf -o111_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 RHP01133 257 AE000511 #2 RHP00038 117 AE000511 #3 RHP00039 44 AE000511 #4 RHP00040 65 AE000511 #5 RHP00211 147 AE000511 Motif number 1 GTCATAGCGTCTTAAAACAAACACCCATTA 1 82 1 CTTAAAACAA 0.973888 -176 ACCCATTACTCTTAAATCATGCCAATTCAC 1 104 1 CTTAAATCAT 0.834818 -154 AATAACACAACTTAAAAAAAACTACCCTTA 1 160 1 CTTAAAAAAA 0.980569 -98 AAAAACTACCCTTAAAAAAATCAATCTAAA 1 176 1 CTTAAAAAAA 0.980569 -82 ATCTAAAATTCTTAAATTAAAATATAGCTA 1 199 1 CTTAAATTAA 0.90772 -59 TTTTAAGAAAGGTGTTTGTA 2 1 1 TTTTAAGAAA 0.85124 -117 AGAAGTAAAAATTAAAGCAAAAAGCCAACG 2 49 0 ATTAAAGCAA 0.794532 -69 TTTACTTCTTTTTTAATAAAATACTCTTTT 2 70 1 TTTTAATAAA 0.9166 -48 AATAACCGCCTATAATAAAAAGGAATCAA 2 99 0 CTATAATAAA 0.908781 -19 AATATTCATTTTAAAAAACAACTATGGA 4 9 1 TTTTAAAAAA 0.891356 -57 TATTCAAACCTTAAAACAATCTCTCATCT 5 10 1 CTTAAAACAA 0.973888 -138 AATCTCTCATCTTTAATAAAACCCTTTATT 5 28 1 CTTTAATAAA 0.981396 -120 TTTAGCATGGATAAAATAAAAGTCATGTAA 5 58 0 ATAAAATAAA 0.668992 -90 AAAACTGACGCTTTAATAAAATAAATGAGA 5 97 1 CTTTAATAAA 0.981396 -51 ********** Masking position 5 Map Score: 23.178 Number of sites scoring better than the average of aligned sites = 662 Number in coding regions = 534 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 2 GGTTTGGGTTTAGGGTTTGAATTATATTGATT 1 22 0 TAGGGTTTGT 0.985252 -236 TATATGAGAGAAAGGTTTGGGTTTAGGGTTTG 1 35 0 AAAGGTTTGT 0.987258 -223 GATTTAAGAGTAATGGGTGTTTGTTTTAAGAC 1 90 0 TAATGGGTGT 0.888999 -168 TTCAAGTCTAAAGAGTGTGAATTGGCATGATT 1 118 0 AAGAGTGTGT 0.758775 -140 TTGATTTTTTTAAGGGTAGTTTTTTTTAAGTT 1 168 0 TAAGGGTAGT 0.934688 -90 TTTTAAGAAAGGTGTTTGTATGGGGCTAA 2 8 1 AAAGGTGTTT 0.953614 -110 GCTAACGCTTTAAGCGTTGGCTTTTTGCTTTA 2 35 1 TAAGCGTTGT 0.963708 -83 CTTTTTATTATAGGCGGTTATT 2 106 1 TAGGCGGTTT 0.815261 -12 TTTGTCTAATTATGGTTTTTATACTCCATAGT 4 31 0 TATGGTTTTT 0.844316 -35 AAATCCTTAAAGGTTTGTCTAATTATGGTT 4 46 0 AAAGGTTTGT 0.987258 -20 GAGATTGTTTTAAGGTTTGAATA 5 2 0 TAAGGTTTGT 0.990712 -146 CATGTAAAATAAAGGGTTTTATTAAAGATGAG 5 33 0 AAAGGGTTTT 0.966609 -115 ********* * Masking position 2 Map Score: 15.2528 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 708 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 3 TTTGAAAATAATAACACAACTTAAAAAAAACTACC 1 151 1 ATAAATTAAA 0.919342 -107 CAACTTAAAAAAAACTACCCTTAAAAAAATCAATC 1 167 1 AAAACTTAAA 0.955393 -91 TACCCTTAAAAAAATCAATCTAAAATTCTTAAATT 1 182 1 AAAAATAAAA 0.988679 -76 TTCTTAAATTAAAATATAGCTATAATACACTAAAA 1 207 1 AAAAATATAA 0.946915 -51 GTATTTTATTAAAAAAGAAGTAAAAATTAAAGCAA 2 59 0 AAAAATAAAA 0.988679 -59 CGCCTATAATAAAAAGGAATCAAAAAGAGTATTTT 2 87 0 AAAAACAAAA 0.932317 -31 AATAACCGCCTATAATAAAAAGGAA 2 103 0 AATAGTATAA 0.605348 -15 GCTTAAGATTAAGAAAAATCTAAAAA 3 2 0 AAGAATAAAA 0.942683 -43 TAAAACGCCTTTTAAAAGGCTTAAGA 3 29 0 AAAACTTAAA 0.955393 -16 AATATTCATTTTAAAAAACAACTAT 4 1 1 AATAATTAAA 0.925946 -65 TGGATAAAATAAAAGTCATGTAAAATAAAGGGTTT 5 46 0 AAAAATAAAA 0.988679 -102 TATCCATGCTAAAATGGGATTAAAAACTGACGCTT 5 75 1 AAAAGTAAAA 0.97103 -73 CTTTAATAAAATAAATGAGATTAAAGCACTCTTAA 5 107 1 ATAAATTAAA 0.919334 -41 **** * ***** Masking position 4 Map Score: 19.2254 Number of sites scoring better than the average of aligned sites = 972 Number in coding regions = 715 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 4 TTGGGTTTAGGGTTTGAATTATATTGATTT 1 21 0 GGTTTGAATT 0.95857 -237 ATGAGAGAAAGGTTTGGGTTTAGGGTTTGA 1 34 0 GGTTTGGGTT 0.926398 -224 AAGAGTAATGGGTGTTTGTTTTAAGACGCT 1 87 0 GGTGTTTGTT 0.950227 -171 AAGTCTAAAGAGTGTGAATTGGCATGATTT 1 117 0 AGTGTGAATT 0.690643 -141 TTTTAAGGGTAGTTTTTTTTAAGTTGTGTT 1 163 0 AGTTTTTTTT 0.675765 -95 TTTTAAGAAAGGTGTTTGTATGGGGCTAAC 2 11 1 GGTGTTTGTA 0.941403 -107 TTTTTAGATTTTTCTTAATCTTAAGC 3 7 1 GATTTTTCTT 0.622476 -38 GTCTAATTATGGTTTTTATACTCCATAGTT 4 30 0 GGTTTTTATA 0.955038 -36 AATCCTTAAAGGTTTGTCTAATTATGGTTT 4 45 0 GGTTTGTCTA 0.959402 -21 ATTGTTTTAAGGTTTGAATA 5 1 0 GGTTTGAATA 0.951149 -147 TAAAATAAAGGGTTTTATTAAAGATGAGAG 5 31 0 GGTTTTATTA 0.886054 -117 ********** Masking position 5 Map Score: 9.71797 Number of sites scoring better than the average of aligned sites = 1044 Number in coding regions = 885 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 5 AAGTAACGCTAAATCAATAT 1 1 1 AAGTAACGCT 0.980257 -257 GTTTGTATGGGGCTAACGCTTTAAGCGTTG 2 24 1 GGCTAACGCT 0.991372 -94 TAAAGCAAAAAGCCAACGCTTAAAGCGTTA 2 37 0 AGCCAACGCT 0.986016 -81 TGGGATTAAAAACTGACGCTTTAATAAAAT 5 89 1 AACTGACGCT 0.987097 -59 ********** Masking position 6 Map Score: 2.09502 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 44 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 AAGTAACGCTAAATCAATATAATTCAAACC 1 10 1 TAAACAATAT 0.958033 -248 CATAGCGTCTTAAAACAAACACCCATTACTC 1 84 1 TAAACAAACA 0.803716 -174 TAACACAACTTAAAAAAAACTACCCTTAAAA 1 162 1 TAAAAAAACT 0.863866 -96 TACCCTTAAAAAAATCAATCTAAAATTCTTA 1 182 1 AAAACAATCT 0.952547 -76 CTAAAATTCTTAAATTAAAATATAGCTATAA 1 201 1 TAAATAAAAT 0.64164 -57 TATAATACACTAAAACAATCTCAAGGTTTCA 1 227 1 TAAACAATCT 0.987791 -31 TCTTTTTTAATAAAATACTCTTTTTGATTCC 2 76 1 TAAATACTCT 0.937103 -42 TTCATTTTAAAAAACAACTATGGAGTATAAA 4 15 1 AAAAAACTAT 0.51054 -51 ATTCAAACCTTAAAACAATCTCTCATCTTTA 5 12 1 TAAACAATCT 0.987791 -136 TCATCTTTAATAAAACCCTTTATTTTACATG 5 34 1 TAAACCCTTT 0.614073 -114 TAAATGAGATTAAAGCACTCTTAATAAGGTT 5 118 1 TAAACACTCT 0.986956 -30 **** ****** Masking position 4 Map Score: 13.2077 Number of sites scoring better than the average of aligned sites = 611 Number in coding regions = 500 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 AACACCCATTACTCTTAAATCATGCCAATT 1 101 1 ACTCTTAAAT 0.631347 -157 ATTATTTTCAAATTTCAAGTCTAAAGAGTG 1 133 0 AATTTCAAGT 0.620005 -125 TAAAAAAATCAATCTAAAATTCTTAAATTA 1 188 1 AATCTAAAAT 0.944072 -70 ACACTAAAACAATCTCAAGGTTTCAAAATT 1 233 1 AATCTCAAGG 0.968027 -25 GTAAAAATTAAAGCAAAAAGCCAACGCTTA 2 45 0 AAGCAAAAAG 0.810728 -73 AATAAAAAGGAATCAAAAAGAGTATTTTAT 2 85 0 AATCAAAAAG 0.948273 -33 AACCGCCTATAATAAAAAGGAATCAAAAAG 2 95 0 AATAAAAAGG 0.724941 -23 GATTAAGAAAAATCTAAAAA 3 1 0 AATCTAAAAA 0.870077 -44 GATTTTTCTTAATCTTAAGCCTTTTAAAAG 3 17 1 AATCTTAAGC 0.84753 -28 ********** Masking position 7 Map Score: 1.07237 Number of sites scoring better than the average of aligned sites = 894 Number in coding regions = 765 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 8 CCCAAACCTTTCTCTCATATATCTCGCATA 1 46 1 TCTCTCATAT 0.988133 -212 CTCTCATATATCTCGCATAAAGATAGTCAT 1 57 1 TCTCGCATAA 0.975409 -201 CTTAAAACAATCTCTCATCTTTAATAAAAC 5 20 1 TCTCTCATCT 0.985913 -128 ********** Masking position 7 Map Score: 0.282911 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 4 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ********** No masking Map Score: 1.63668e-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: 1.63668e-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: 1.63668e-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