AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_mthe_reg_300.orf -o02010_mthe_300.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 MTH604 116 adhesion protein #2 MTH606 102 manganese transport system membrane protein #3 MTH1093 96 ABC transporter (ATP-binding #4 MTH1370 137 ABC transporter (ATP-binding protein) #5 MTH1488 178 unknown Motif number 1 TCCTATCTTAATAAATGTTTATATATTTTA 1 17 1 ATAAATGTTT 0.725349 -100 ATAAATGTTTATATATTTTATGTTAAAATT 1 27 1 ATATATTTTA 0.840852 -90 ATAAAATTTAATAAATTTTAACATAAAATA 1 40 0 ATAAATTTTA 0.87773 -77 AATATAAACGATAAAATTTAATAAATTTTA 1 50 0 ATAAAATTTA 0.842228 -67 CCCTGATAGTATAAATTGTTATAGTGATGC 3 27 0 ATAAATTGTT 0.939139 -70 GGGGTCCTTTATATATAGGTCCATATAAGA 4 35 0 ATATATAGGT 0.771327 -103 AAGGACCCCCATATAATTAATTCAGGAATT 4 56 1 ATATAATTAA 0.636156 -82 GATGCACTCGATAAAAATGTTATCGCTACA 4 86 1 ATAAAAATGT 0.677951 -52 ATAAGCCCCGATAAATAGAAGATCTACCGG 5 19 0 ATAAATAGAA 0.756959 -160 AAAGTTTGTGATATATTGATGAGGCGTCCT 5 138 0 ATATATTGAT 0.792113 -41 TGTTCATGATATATAAAGTTTGTGATATAT 5 152 0 ATATAAAGTT 0.834411 -27 AATAAAATGTTCATGATATAT 5 168 0 ATAAAATGTT 0.92161 -11 ********** Masking position 5 Map Score: 8.13558 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 86 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 2 TCATTGTACTCGGATACCGGGAATTCAGCATTTCAA 2 7 0 CGATCCGTCA 0.995036 -96 TGTGATTCAGCTGATGCTGTCATCTTCTCATTGTACTCGG 2 34 0 CGATCTGTCA 0.995134 -69 AGCTGAATCACAGATACTGAATCCTTATGACGTGAACGAT 2 62 1 CGATCTGTGA 0.986367 -41 AATTGTTATAGTGATGCTGTGGAGGGTGCATGA 3 4 0 GGATCTGGCA 0.991438 -93 CAAATCCTCCGCGACCCTGAAGCATCGGGTATTATGGTTA 3 66 0 GGACCTGTGT 0.957013 -31 ATCAGATCCCGGTAGATCTTCTATTTATCGGG 5 3 1 CGATCCGTCT 0.995036 -176 GCGGTATCCCGTGAAACTGCGCGGGTAACTTGTGGGTACT 5 69 0 GGAACTGGCT 0.960063 -110 GCAGTTTCACGGGATACCGCCAGATTCCCTCCCCATCATC 5 89 1 GGATCCGTCT 0.995033 -90 * *** *** * ** Masking position 4 Map Score: 8.08943 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 83 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 AAATCTAACCATAATACCCGATGCTTCAGG 3 61 1 ATAATACCCG 0.973773 -36 CCAAATCCTCCGCGACCCTGAAGC 3 83 0 ATCCTCCGCG 0.982411 -14 GTGATCATCACCGCTTAACTACT 4 4 1 ATCATCACCG 0.994865 -134 GGAAAGACTCATAAGCCCCGATAAATAGAA 5 29 0 ATAAGCCCCG 0.988673 -150 TTCCCTCCCCATCATCACCGGTTAAAGGAC 5 113 1 ATCATCACCG 0.994865 -66 ********** Masking position 2 Map Score: 5.5516 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 137 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 GTACTCGGATACCGGGAATTCAGCATTTCA 2 12 0 ACCGGGAATT 0.984875 -91 AGGATTCAGTATCTGTGATTCAGCTGATGC 2 57 0 ATCTGTGATT 0.788734 -46 ACCCTGAAGCATCGGGTATTATGGTTAGAT 3 63 0 ATCGGGTATT 0.942494 -34 AGAGTAGTTAAGCGGTGATGATCAC 4 6 0 AGCGGTGATG 0.953351 -132 TTATCGCTACAGCGGGACCTCCAGTGGCTG 4 105 1 AGCGGGACCT 0.94455 -33 TAGAAGATCTACCGGGATCTGAT 5 4 0 ACCGGGATCT 0.900959 -175 TCTTCTATTTATCGGGGCTTATGAGTCTTT 5 27 1 ATCGGGGCTT 0.982922 -152 GCGTCCTTTAACCGGTGATGATGGGGAGGG 5 115 0 ACCGGTGATG 0.967499 -64 ********** Masking position 1 Map Score: 6.39001 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 334 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TCCTTCCTTGGATCGTTCACGTCATAAGG 2 84 0 GGATCGTTCA 0.861419 -19 TCATGCACCCTCCACAGCATCACT 3 5 1 GCACCCTCCA 0.926662 -92 CAAATCCTCCGCGACCCTGAAGCATCGGGT 3 76 0 GCGACCCTGA 0.876037 -21 AATTATATGGGGGTCCTTTATATATAGGTC 4 44 0 GGGTCCTTTA 0.97818 -94 TCGCTACAGCGGGACCTCCAGTGGCTGACT 4 108 1 GGGACCTCCA 0.988227 -30 TGAGTCCCCCAGTCAGCCACT 4 127 0 GAGTCCCCCA 0.955623 -11 GGTAACTTGTGGGTACTGCAATCAAATGGA 5 56 0 GGGTACTGCA 0.892091 -123 TATTGATGAGGCGTCCTTTAACCGGTGATG 5 125 0 GCGTCCTTTA 0.971535 -54 ********** Masking position 10 Map Score: 3.53463 Number of sites scoring better than the average of aligned sites = 1316 Number in coding regions = 1262 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 GTGATTCAGCTGATGCTGTCATCTTCTCAT 2 43 0 TGATGCTGTC 0.937393 -60 TCATGCACCCTCCACAGCAT 3 1 1 TCATGCACCC 0.924403 -96 ATTCAGGAATTGATGCACTCGATAAAAATG 4 75 1 TGATGCACTC 0.98135 -63 TGAGTCCCCCAGTCAGCCAC 4 128 0 TGAGTCCCCC 0.982872 -10 TCGGGGCTTATGAGTCTTTCCATTTGATTG 5 38 1 TGAGTCTTTC 0.912401 -141 GGATACCGCCAGATTCCCTCCCCATCATCA 5 100 1 AGATTCCCTC 0.891272 -79 GATATATTGATGAGGCGTCCTTTAACCGGT 5 129 0 TGAGGCGTCC 0.953256 -50 ********** Masking position 3 Map Score: 2.38727 Number of sites scoring better than the average of aligned sites = 963 Number in coding regions = 929 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 7 ********** No masking Map Score: -2.10731e-13 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: -2.10731e-13 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: -2.10731e-13 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