AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02020_mthe_reg_300.orf -o02020_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 MTH442 195 excinuclease ABC subunit B #2 MTH443 41 excinuclease ABC subunit A #3 MTH444 133 sensory transduction histidine kinase #4 MTH446 97 sensory transduction regulatory protein #5 MTH447 109 sensory transduction regulatory protein #6 MTH448 74 unknown #7 MTH449 38 unknown #8 MTH451 132 magnesium chelatase subunit ChlI #9 MTH452 45 unknown #10 MTH456 238 magnesium chelatase subunit #11 MTH457 194 sensory transduction regulatory protein #12 MTH459 54 sensory transduction histidine kinase #13 MTH549 126 sensory transduction regulatory protein #14 MTH550 118 DNA-dependent DNA polymerase family X #15 MTH902 126 sensory transduction histidine kinase Motif number 1 AGCAGAGATCCGTGAAGAGCCATGCGTTTC 3 70 0 CGTGAAGAGC 0.909307 -64 CTCTGCTCTTCCAGAGGTCCGGCTGATTTT 3 93 1 CCAGAGGTCC 0.977378 -41 GACCAGAAGAGGAGAGTCAGAA 3 122 0 CCAGAAGAGG 0.962913 -12 GCATGTCTTGAAGACCAGACACCAGT 4 7 1 CTTGAAGACC 0.863159 -91 CGGGCCAGAGGACGCTCTTTGACT 7 5 1 CCAGAGGACG 0.991821 -34 TCTCGACGTCCGAGAAGACCACGGTGCAGT 10 11 0 CGAGAAGACC 0.953369 -228 TCGAGAACAACCTGAGGGCCATCGAGGAGT 10 35 1 CCTGAGGGCC 0.994757 -204 GGGTCGCCGCCCAGGGGGCCCGGTTCAGCT 10 107 0 CCAGGGGGCC 0.97699 -132 CAAGGAGGCTCCTGAGGAGGATAGGCGCCC 10 145 1 CCTGAGGAGG 0.98345 -94 ACCTCATCTGCCTGAGGGGCTATGAGACAG 10 178 1 CCTGAGGGGC 0.991037 -61 TCCGGGAATCCCAGAGGGCGCTGATAAGG 12 36 1 CCAGAGGGCG 0.992447 -19 ********** Masking position 1 Map Score: 20.5706 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 666 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 AAACATAAATCAGAGGATGGTAATGATAAA 1 9 0 CAGAGGGGTA 0.878839 -187 TCTGGAAGAGCAGAGATCCGTGAAGAGCCATG 3 76 0 CAGAGACGTG 0.874601 -58 TCTGCTCTTCCAGAGGTCCGGCTGATTTTTCT 3 94 1 CAGAGGCGGC 0.971887 -40 AACCGTAATGAAGAGGAACCGGA 4 85 1 AAGAGGCCGG 0.967735 -13 CATTAGTCCTCAGTGATAGCGGTTCCATAAAG 5 78 1 CAGTGAGCGG 0.872664 -32 CGGGCCAGAGGACGCTCTTTGACTTCA 7 6 1 CAGAGGGCTC 0.972392 -33 ATCACCGGTTCAGTGGTTGGTCTAATCATTAT 8 108 0 CAGTGGGGTC 0.926775 -25 CGAGGAGTACATGGGGGACGTGGACCTCTTTG 10 57 1 ATGGGGCGTG 0.830572 -182 GGTCGCCGCCCAGGGGGCCCGGTTCAGCTGGA 10 104 0 CAGGGGCCGG 0.948444 -135 CTTGTGGCCTCAGGGTCGCCGCCCAGGGGGCC 10 117 0 CAGGGTCCGC 0.800017 -122 TGAGGCCACAAGGAGGCTCCTGAGGAGGATAG 10 137 1 AGGAGGCCTG 0.882618 -102 CAGATGAGGTATGGGGCGCCTATCCTCCTCAG 10 156 0 ATGGGGCCTA 0.528575 -83 ATTATGTGTGCAGTGGTGCCGGGTTCTGTACC 11 90 0 CAGTGGCCGG 0.987805 -105 CCGGGAATCCCAGAGGGCGCTGATAAGG 12 37 1 CAGAGGGCTG 0.98713 -18 TTTTAAGTTCCGGGGGTGGCTGGCA 13 112 1 CGGGGGGCTG 0.968996 -15 AATGAATATACTGTGGTGGGGGTTTTCAT 14 8 0 CTGTGGGGGG 0.919034 -111 ****** **** Masking position 5 Map Score: 19.7448 Number of sites scoring better than the average of aligned sites = 1772 Number in coding regions = 1683 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 CGTGTTCCATAATCCTGTGATGATACCCCC 1 55 0 AATCCTGTGA 0.814219 -141 TATATAAGTTGACCCTGAAATATAATCCCA 1 144 1 GACCCTGAAA 0.97015 -52 AGACACCTTAAGCCTGGAAATTTTATTGTG 4 45 0 AGCCTGGAAA 0.733874 -53 TCAACACTGAAACCCGGTAA 6 1 0 AACCCGGTAA 0.975152 -74 ACCAACCACTGAACCGGTGATAGC 8 119 1 GAACCGGTGA 0.932855 -14 CCTGGGCGGCGACCCTGAGGCCACAAGGAG 10 122 1 GACCCTGAGG 0.891467 -117 GCAGAATATGGACCCGGAAAGGATATCCGG 11 62 1 GACCCGGAAA 0.977586 -133 TGAACTTCAGAAACTTGAGAAACTCCGGGA 12 13 1 AAACTTGAGA 0.669675 -42 CCAATCCCTGAGCCCTGTAATGTTTCAGGT 13 48 1 AGCCCTGTAA 0.918197 -79 CATCCTATTTAAACCTGAAACATTACAGGG 13 60 0 AAACCTGAAA 0.907458 -67 GCCTTATTGGAACCCGGTGATTAAGTTCCA 15 41 1 AACCCGGTGA 0.981366 -86 ********** Masking position 4 Map Score: 9.72998 Number of sites scoring better than the average of aligned sites = 763 Number in coding regions = 711 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 TTATGTTTAAAACAAGTTCAGTGGGGGTATCAT 1 33 1 AAAAGTTGTG 0.975233 -163 GCCAGGATACATAAAGTTGAGTCTGGAGTCTCA 1 104 0 ATAAGTTGTC 0.957171 -92 TTTCATGGATAAGAGGTTCCATGAAACGCATGG 3 48 1 AAAGGTTATG 0.933589 -86 TCACTGCAGAATAAGGTTTAATGTGACGCCGTG 5 17 0 ATAGGTTATG 0.95754 -93 TATTGAAAGAAAAAAGTTGAATGTATATCTGTA 11 135 0 AAAAGTTATG 0.961278 -60 CCAGCTCCTGATTAAGTTCTGTCCCGAAGCTTA 13 15 0 ATAAGTTGTC 0.957171 -112 GAACCCGGTGATTAAGTTCCATGGATATACTTG 15 50 1 ATAAGTTATG 0.975505 -77 GTAAACAGTAATCAAGATATGTGACATGGTTCA 15 85 1 ATAAGATGTG 0.918833 -42 ** ***** *** Masking position 4 Map Score: 5.53162 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 36 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 ATCAGAGGATGGTAATGATAAA 1 2 0 GGTATGATAA 0.899749 -194 TCCATAATCCTGTGATGATACCCCCACTGAA 1 49 0 TGTATGATAC 0.910899 -147 ATACCCTGTCAGATATGAGACTCCAGACTCA 1 89 1 AGAATGAGAC 0.693429 -107 TATATACCTTTGCCAGGATACATAAAGTTGA 1 117 0 TGCAGGATAC 0.831231 -79 ACATTTTCTGGTAATGAGAATTAAGGCAGG 2 10 1 GGTATGAGAA 0.833816 -32 TGATAAGAGTGGATCAGATACCTCACTGATG 3 17 0 GGACAGATAC 0.781314 -117 CTCTTATCCATGAAATGATAAGAGTGGATCA 3 32 0 TGAATGATAA 0.811092 -102 TCTGGACATTGCCCCTGATACTTTGATGTCA 5 47 0 GCCCTGATAC 0.861625 -63 TCTTTATACTTGCTCTGATACGCTCAACACT 6 23 0 TGCCTGATAC 0.955308 -52 CTGCCTGAGGGGCTATGAGACAGACCTCGAC 10 185 1 GGCATGAGAC 0.975364 -54 TAGCCCGGATGGAAATTATACGGTTGTAGCA 11 34 1 GGAATTATAC 0.722199 -161 AATCCCAGAGGGCGCTGATAAGG 12 42 1 GGCCTGATAA 0.949712 -13 *** ******* Masking position 8 Map Score: 5.61022 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 494 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 TCATCACAGGATTATGGAACACGTGGGATA 1 62 1 ATTATGGAAC 0.889393 -134 CAGACTCAACTTTATGTATCCTGGCAAAGG 1 112 1 TTTATGTATC 0.690539 -84 CTCTTATCATTTCATGGATAAGAGGTTCCA 3 39 1 TTCATGGATA 0.928102 -95 AGCCATGCGTTTCATGGAACCTCTTATCCA 3 53 0 TTCATGGAAC 0.984035 -81 CGCATGGCTCTTCACGGATCTCTGCTCTTC 3 74 1 TTCACGGATC 0.836607 -60 ATAAACCTCCTTTATGGAACCGCTATCACT 5 89 0 TTTATGGAAC 0.970057 -21 ACTTTGGGAGTTTATGAAAAAACATGACAC 9 12 1 TTTATGAAAA 0.625331 -34 TATTAATTTTTTTATTGAAAGAAAAAAGTT 11 150 0 TTTATTGAAA 0.573089 -45 GATTGAATTAATCATGTAAATGAATATACT 14 28 0 ATCATGTAAA 0.58159 -91 AGACTTTTGGTTCAGGGAAACAGTAAATTT 14 70 0 TTCAGGGAAA 0.871103 -49 AGCAAGTATATCCATGGAACTTAATCACCG 15 55 0 TCCATGGAAC 0.920684 -72 ********** Masking position 4 Map Score: 5.68889 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 437 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 7 GGATACATAAAGTTGAGTCTGGAGTCTCATAT 1 101 0 ATGAGTCTGG 0.975814 -95 TGGTAATGAGAATTAAGGCAGGATTAAAGAGT 2 19 1 ATAAGGCAGG 0.909073 -23 GACCAGAAGAGGAGAGTCAGAAAAATCAGCC 3 113 0 AGGAGTCAGA 0.917508 -21 TGGGCTCTTCACTGGTGTCTGGTCTTCAAGAC 4 15 0 ATGTGTCTGG 0.964983 -83 ATCACTGAGGACTAATGTCTGGACATTGCCCC 5 63 0 ATATGTCTGG 0.863073 -47 GTATAAAGAGACGTCAGGCTGAAGTTATGATG 6 45 1 AGCAGGCTGA 0.810005 -30 TATTACTTTTAATACAGTCAGGTACATATTAG 8 46 1 ATCAGTCAGG 0.93453 -87 TCACACCTCCATGCGTGTCATGTTTTTTCATA 9 24 0 AGGTGTCATG 0.793367 -22 ACCTCGACGAATGGGAGGCAGGTGGTGATGGC 10 208 1 AGGAGGCAGG 0.985857 -31 TTTAAGTTCCGGGGGTGGCTGGCA 13 113 1 GGGTGGCTGG 0.908504 -14 * * ******** Masking position 9 Map Score: 5.08953 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 418 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 AATGTCCAGACATTAGTCCTCAGTGATAGCGGT 5 68 1 CTTGCCTCAG 0.994899 -42 ATGTACTCCTCGATGGCCCTCAGGTTGTTCTCG 10 36 0 CATGCCTCAG 0.991855 -203 CAGGAGCCTCCTTGTGGCCTCAGGGTCGCCGCC 10 126 0 CTGGCCTCAG 0.990828 -113 TATGGGGCGCCTATCCTCCTCAGGAGCCTCCTT 10 146 0 CATCCCTCAG 0.98946 -93 AGGTCTGTCTCATAGCCCCTCAGGCAGATGAGG 10 179 0 CTACCCTCAG 0.98104 -60 * ** * ****** Masking position 10 Map Score: 3.30956 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 34 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 9 TCCCTGCATCAGTGAGGTATCT 3 2 1 CCCGCATCAG 0.937003 -132 TTAATGTGACGCCGTGACCAGA 5 2 0 GCCTGACCAG 0.976961 -108 AGTATCAGGGGCAATGTCCAGACATTAGTCC 5 56 1 GCATGTCCAG 0.88368 -54 GCTATCACCGGTTCAGTGGTTGGTCT 8 117 0 CACGGTTCAG 0.812561 -16 CGCCCAGGGGGCCCGGTTCAGCTGGAAGTAC 10 99 0 GCCGGTTCAG 0.990969 -140 CGGGTTGAGGCCATCACCACCTGCCTCCCA 10 219 0 GCCTCACCAC 0.811815 -20 GTGCAGTGGTGCCGGGTTCTGTACCGGATAT 11 84 0 GCCGGTTCTG 0.97571 -111 TCAGGGATTGGCCAGCTCCTGATTAAGTTCT 13 28 0 GCCGCTCCTG 0.9751 -99 *** ******* Masking position 9 Map Score: 2.79985 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 514 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 ********** No masking Map Score: 2.62433e-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: 2.62433e-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 12 ********** No masking Map Score: 2.62433e-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