AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_mthe_reg_100.orf -o02020_mthe_100.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 MTH444 133 sensory transduction histidine kinase #2 MTH446 97 sensory transduction regulatory protein #3 MTH447 109 sensory transduction regulatory protein #4 MTH457 194 sensory transduction regulatory protein #5 MTH459 54 sensory transduction histidine kinase #6 MTH549 126 sensory transduction regulatory protein #7 MTH902 126 sensory transduction histidine kinase Motif number 1 TCCCTGCATCAGTGAGGTATCTGATCC 1 1 1 TCTACATGAG 0.941919 -133 CCTCTGGAAGAGCAGAGATCCGTGAAGAGCCATGCGT 1 73 0 ACGACCTGAG 0.99597 -61 TGTCTTGAAGACCAGACACCAGTGAAGAGCCCACAAT 2 14 1 ACGACATGAG 0.99623 -84 TCCTTTATGGAACCGCTATCACTGAGGACTAATGTCT 3 75 0 ACGACATGAG 0.99623 -35 CGGGTTCTGTACCGGATATCCTTTCCGGGTCCATATT 4 66 0 ACGACCTTCG 0.951576 -129 CCGGTACAGAACCCGGCACCACTGCACACATAATCAA 4 88 1 ACGACATGCC 0.978185 -107 TTGAATGTATATCTGTAAACCATGTGGTTGATTATGT 4 115 0 ACGACCTGTG 0.977921 -80 CTTGAGAAACTCCGGGAATCCCAGAGGGCGCTGATAA 5 26 1 TCGACCAGAG 0.925973 -29 ATCCTATTTAAACCTGAAACATTACAGGGCTCAGGGA 6 52 0 ACTACATACG 0.891061 -75 GAACTTAATCACCGGGTTCCAATAAGGCTTATCTATG 7 32 0 ACGTCATAAG 0.904532 -95 TGGATATACTTGCTGTAAACAGTAATCAAGATATGTG 7 71 1 TCGACATAAC 0.876207 -56 * * * * ** *** * Masking position 10 Map Score: 14.1825 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 430 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 CCATGCGTTTCATGGAACCTCTTATCCATG 1 51 0 CATGGAACCT 0.899582 -83 ACACCTTAAGCCTGGAAATTTTATTGTGGG 2 43 0 CCTGGAAATT 0.97511 -55 GGACATTGCCCCTGATACTTTGATGTCACT 3 45 0 CCTGATACTT 0.946637 -65 CTCTGGGATTCCCGGAGTTTCTCAAGTTTC 5 22 0 CCCGGAGTTT 0.959338 -33 TAAGTTCTGTCCCGAAGCTTAAGCA 6 6 0 CCCGAAGCTT 0.983502 -121 CCTATTTAAACCTGAAACATTACAGGGCTC 6 57 0 CCTGAAACAT 0.909584 -70 GCCAGCCACCCCCGGAACTTAAAACATGCT 6 106 0 CCCGGAACTT 0.995486 -21 CTTATTGGAACCCGGTGATTAAGTTCCATG 7 43 1 CCCGGTGATT 0.929313 -84 CAAGTATATCCATGGAACTTAATCACCGGG 7 53 0 CATGGAACTT 0.971205 -74 ********** Masking position 10 Map Score: 12.7608 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 411 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 3 TGAAGAGCCATGCGTTTCATGGAACCTCTTA 1 57 0 TGCGTTTCAG 0.922818 -77 TGAAACGCATGGCTCTTCACGGATCTCTGCT 1 69 1 GGCTCTTCAG 0.995064 -65 CACGGATCTCTGCTCTTCCAGAGGTCCGGCT 1 86 1 TGCTCTTCCG 0.990953 -48 TTTCTGACTCTCCTCTTCTGGTC 1 121 1 TCCTCTTCTG 0.96893 -13 CACTGGTGTCTGGTCTTCAAGACATGC 2 7 0 TGGTCTTCAG 0.982933 -91 TTTTATTGTGGGCTCTTCACTGGTGTCTGGT 2 24 0 GGCTCTTCAT 0.98214 -74 TCCGGTTCCTCTTCATTACGGTTAATG 2 81 0 TCCTCTTCAT 0.971818 -17 ********* * Masking position 6 Map Score: 7.45341 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 186 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 CACTGCAGAATAAGGTTTAATGTGACGCCGT 3 18 0 TAAGGTTAAT 0.752374 -92 CATCAAAGTATCAGGGGCAATGTCCAGACAT 3 50 1 TCAGGGCAAT 0.987606 -60 ATAATTTCCATCCGGGCTAATAATGCAGAGC 4 22 0 TCCGGGTAAT 0.980162 -173 GGATATCCTTTCCGGGTCCATATTCTGCTAC 4 59 0 TCCGGGCCAT 0.971076 -136 GGAAAGGATATCCGGTACAGAACCCGGCACC 4 77 1 TCCGGTCAGA 0.97818 -118 TGCTTAAGCTTCGGGACAGAACTTAATCAG 6 10 1 TTCGGGCAGA 0.951041 -117 CTGTAATGTTTCAGGTTTAAATAGGATGGGG 6 62 1 TCAGGTTAAA 0.951549 -65 AAACTATATTTAGGTCCAAATCATAGATAA 7 10 1 TTAGGTCAAA 0.929217 -117 ****** **** Masking position 1 Map Score: 4.86355 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 379 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TCCCTGCATCAGTGAGGTATCT 1 3 1 CCTGCATCAG 0.895334 -131 CTTATCATTTCATGGATAAGAGGTTCCATG 1 41 1 CATGGATAAG 0.85774 -93 CCATGAAACGCATGGCTCTTCACGGATCTC 1 66 1 CATGGCTCTT 0.711881 -68 ATAAAATTTCCAGGCTTAAGGTGTCTTGAG 2 49 1 CAGGCTTAAG 0.898197 -49 TAATGTGACGCCGTGACCAGA 3 2 0 CCGTGACCAG 0.700184 -108 ATCAAAGTATCAGGGGCAATGTCCAGACAT 3 51 1 CAGGGGCAAT 0.691689 -59 TAATTTCCATCCGGGCTAATAATGCAGAGC 4 22 0 CCGGGCTAAT 0.935835 -173 GATATCCTTTCCGGGTCCATATTCTGCTAC 4 59 0 CCGGGTCCAT 0.974546 -136 TGCAGTGGTGCCGGGTTCTGTACCGGATAT 4 84 0 CCGGGTTCTG 0.961978 -111 TTGGCCAGCTCCTGATTAAGTTCTGTCCCG 6 22 0 CCTGATTAAG 0.627401 -105 TGAAACATTACAGGGCTCAGGGATTGGCCA 6 45 0 CAGGGCTCAG 0.978103 -82 GAACTTAAAACATGCTCCATCAACTATTCC 6 92 0 CATGCTCCAT 0.779372 -35 AACTTAATCACCGGGTTCCAATAAGGCTTA 7 38 0 CCGGGTTCCA 0.812031 -89 AGATATGTGACATGGTTCAAAAATGATCAG 7 99 1 CATGGTTCAA 0.881018 -28 ********** Masking position 1 Map Score: 9.30281 Number of sites scoring better than the average of aligned sites = 2911 Number in coding regions = 2710 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 6 GCCATGCGTTTCATGGAACCTCTTATCCAT 1 52 0 TCATGGAACC 0.986914 -82 TCACGGCGTCACATTAAACCTTATTCTGCA 3 16 1 ACATTAAACC 0.707877 -94 TAATGTCTGGACATTGCCCCTGATACTTTG 3 53 0 ACATTGCCCC 0.826498 -57 TAAACCTCCTTTATGGAACCGCTATCACTG 3 88 0 TTATGGAACC 0.979402 -22 TTGTAGCAGAATATGGACCCGGAAAGGATA 4 57 1 ATATGGACCC 0.975137 -138 CTTATCTATGATTTGGACCTAAATATAGTT 7 12 0 ATTTGGACCT 0.802026 -115 AGATAAGCCTTATTGGAACCCGGTGATTAA 7 35 1 TATTGGAACC 0.883465 -92 GCAAGTATATCCATGGAACTTAATCACCGG 7 54 0 CCATGGAACT 0.869964 -73 CATCTGATCATTTTTGAACCATGTCACATA 7 102 0 TTTTTGAACC 0.891003 -25 ********** Masking position 4 Map Score: 5.21392 Number of sites scoring better than the average of aligned sites = 831 Number in coding regions = 785 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 GCATGTCTTGAAGACCAGACA 2 2 1 CATGTCTTGA 0.986119 -96 GCTCTTCACTGGTGTCTGGTCTTCAAGACA 2 14 0 GGTGTCTGGT 0.961777 -84 CCAGGCTTAAGGTGTCTTGAGCTCATTAAC 2 58 1 GGTGTCTTGA 0.987128 -40 ACTGAGGACTAATGTCTGGACATTGCCCCT 3 62 0 AATGTCTGGA 0.965654 -48 AACCATGTCACATATCTTGATTACTGTTTA 7 86 0 CATATCTTGA 0.931568 -41 ********** Masking position 5 Map Score: 2.4409 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 39 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 8 ********** No masking Map Score: -3.03101e-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: -3.03101e-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 10 ********** No masking Map Score: -3.03101e-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