AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i088_bsub_mtub_300.orf -o088_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 yeeG 135 yeeG #2 rapH 161 response regulator aspartate phosphatase #3 yeeI 160 similar to hypothetical proteins #4 yeeK 134 similar to hypothetical proteins #5 yesE 78 alternate gene name: yeeL #6 cotJA 126 cotJA #7 yesJ 124 alternate gene name: yeeN, yfxC, yfxD; similar to hypothetical proteins #8 yesL 114 similar to hypothetical proteins from B. subtilis #9 yesO 148 similar to sugar-binding protein #10 yesS 22 similar to transcriptional regulator (AraC/XylS family) #11 yesW 120 similar to hypothetical proteins from B. subtilis #12 yesX 45 similar to hypothetical proteins from B. subtilis #13 yesY 157 similar to rhamnogalacturonan acetylesterase #14 yetA 43 yetA #15 lplA 121 lipoprotein #16 lplB 54 transmembrane lipoprotein Motif number 1 TGAGCGAACAAAAGAAGGGAAATGGTC 1 8 0 AAAGAAGGGA 0.926656 -128 TCGTGGAGGGATTGGAGGAAAC 1 124 1 ATTGGAGGAA 0.845956 -12 TGAAAACAATATAGAAGGAAGAAATTGTTT 2 90 0 ATAGAAGGAA 0.914393 -72 ATCTCATAGAGAAGGAGGGAAGCCG 2 147 1 GAAGGAGGGA 0.94989 -15 TGCGTTAGAAATAGAAGGAATGCCGCGATG 3 50 0 ATAGAAGGAA 0.914393 -111 TAACCTATGTGAAGGAGAGAGTAAAT 4 119 1 GAAGGAGAGA 0.846467 -16 TGTTTTTGAGAAAGGAGGAGCCGGA 6 112 1 AAAGGAGGAG 0.952247 -15 TTTTCTTTCGAAAGGAGAAATACATATTAC 8 60 1 AAAGGAGAAA 0.975465 -55 AGCGTTTTCCAAAGCAGGAAGGTG 8 101 1 AAAGCAGGAA 0.930289 -14 AAGCGTTCGGATAGGGCGAAACACTCAAAA 9 43 0 ATAGGGCGAA 0.790115 -106 CACTTACATTAAAGGGGGGATTGGTTTGAA 9 89 1 AAAGGGGGGA 0.982711 -60 CTGAAAGGGGGAAGGAACGGGCT 12 4 1 AAAGGGGGAA 0.990324 -42 CCGGAATTTCATAGGAGAAATGGTGCAAAA 15 14 1 ATAGGAGAAA 0.949152 -108 TGAGAGGGGCAAAGGGGAAATGCAAATTGA 15 81 1 AAAGGGGAAA 0.967498 -41 CAAATTGAAAAAAGGGGGACTTACGCAAC 15 103 1 AAAGGGGGAC 0.964883 -19 CGGTATCACGAAAGGAGAACAGAT 16 41 1 AAAGGAGAAC 0.914336 -14 ********** Masking position 4 Map Score: 26.3623 Number of sites scoring better than the average of aligned sites = 1010 Number in coding regions = 569 Number in noncoding regions = 441 Number of orfs with sites within 600 bp upstream = 508 Fraction of orfs with sites within 600 bp upstream = 0.0815933 Motif number 2 ATACTATATGAAATAGAATGACAAAG 2 5 1 TTATGAAATG 0.89256 -157 AAAAGAACCCTTTATGCAAGGGTCTTTGTCAT 2 28 0 TTATGCAAGG 0.972042 -134 TAGATTGATATATATGAAAGAGAGTGGAACAT 3 138 1 TTATGAAAGG 0.989593 -23 TTGTTTTAGCTGTATGTAGGCGGCCGCCTATA 4 55 1 TTATGTAGGG 0.973329 -80 GACTGTAACCTATGTGAAGGAGAGAGTAAAT 4 114 1 TTGTGAAGGG 0.872978 -21 TGTAAAAGGGTGTATGAAAGAGAGGCCAATCT 7 16 0 TTATGAAAGG 0.989593 -109 CCATTTTCTCTGTATGTAAAAGGGTGTATGAA 7 30 0 TTATGTAAAG 0.89256 -95 ATATTACTTTAAAATGAAAGCGTTTTCCAAAG 8 83 1 AAATGAAAGG 0.749861 -32 AATCCCCCCTTTAATGTAAGTGCTTACATTTT 9 79 0 TAATGTAAGG 0.959338 -70 TAAAATCCAATTTAAGTAAGCGCTTACAGATA 11 98 1 TTAAGTAAGG 0.923559 -23 ATTGCAAGAATTTATGTAAGCGCTTTATATTG 15 51 1 TTATGTAAGG 0.989593 -71 * ******** * Masking position 8 Map Score: 15.1327 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 97 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 3 TATCCCGACCCGTGGTAAAATTTTGATATTGAGCGA 1 31 0 CGTATTTTGA 0.860489 -105 ACACATGCCAAATGACTCATTTTTCCACCAAAACAC 1 82 0 AACTTTTTCC 0.902301 -54 TTCATCCTGTCAATTTGTTTTTTTCATAAAAAAGAA 2 53 0 CATTTTTTCA 0.925159 -109 TATAGAAGGAAGAAATTGTTTTTTCATCCTGTCAAT 2 75 0 AGTTTTTTCA 0.865131 -87 CATATTCTATCAATCCCAAATTTTGAAAACAATATA 2 107 0 CACATTTTGA 0.915422 -55 TCATCATCACCTCATTTTTATTTCTAGACT 5 59 0 CACATTTTTA 0.625111 -20 GACTAAAACACGACTTAGCTTTTTCAATAAGAAGAC 6 39 0 CGTTTTTTCA 0.941252 -88 ATACCTATTAAGGTCATTGTTTTTGAGAAAGGAGGA 6 95 1 AGATTTTTGA 0.595038 -32 ATACAGAGAAAATGGTCTGTTTTTGCAGTTTGGTCT 7 47 1 AATTTTTTGC 0.838454 -78 GGTGTGTGTGCAAGCTTACTTTTTGATTGGGAGGCC 7 96 1 CATTTTTTGA 0.940477 -29 CGTCTCTCAACAGGTCGAAATTTTCACAGACCGGCA 8 20 1 CACATTTTCA 0.894381 -95 TTTTGACTTTCGCCACTGTTTTTTGAGTGTTTCGCC 9 23 1 CGCTTTTTGA 0.978981 -126 CTATTTCGGACACTGCACTTTTTTGCTTATTTGTCA 11 19 0 CACTTTTTGC 0.967195 -102 AGCTGTCTTCAATTTCACTTTTTTGCATCTGCCTAT 11 51 0 AACTTTTTGC 0.921903 -70 AAGCGCTGTACGCACCGGTTTTTTCAAGGGAAGAGC 13 88 1 CGCTTTTTCA 0.97329 -70 TTCTTTGTATCGAATCAGCTTTTTTCTATGGAGGGA 14 11 1 CGCTTTTTTC 0.854798 -33 AAATTCTTGCAATCTTCATTTTTTGCACCATTTCTC 15 28 0 AATTTTTTGC 0.838454 -94 GTTGCGTAAGTCCCCCTTTTTTCAATTTGCATTT 15 98 0 AGCTTTTTCA 0.935856 -24 ** * ******* Masking position 11 Map Score: 20.9148 Number of sites scoring better than the average of aligned sites = 1456 Number in coding regions = 1233 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 235 Fraction of orfs with sites within 600 bp upstream = 0.0377449 Motif number 4 GCTGTATGTAGGCGGCCGCCTATACGATCT 4 63 1 GGCGGCCGCC 0.499911 -72 ATAGGTATGAGGCAGGAGGCATGATTATGA 6 73 0 GGCAGGAGGC 0.987436 -54 GTTGAGAGACGGCAGCAGCC 8 1 0 GGCAGCAGCC 0.523665 -114 AGATAGCGGCGGGGGGAGAGGG 10 8 1 GGCGGGGGGA 0.97241 -15 GTCCGAAATAGGCAGATGCAAAAAAGTGAA 11 44 1 GGCAGATGCA 0.777515 -77 GATGGGAACGGGCTGCGCGCAGCCCGTTCC 12 24 0 GGCTGCGCGC 0.907992 -22 AAGACGCAAAGGCTGAACGCTACGCCAAGA 13 25 1 GGCTGAACGC 0.842542 -133 TTAGAGAACTGGCAGGACGAACCAATGCTC 13 58 1 GGCAGGACGA 0.950649 -100 CCCGCCGAAAGGCAGGCGCATCGGT 16 6 0 GGCAGGCGCA 0.975011 -49 CCTGCCTTTCGGCGGGCGCCCCGGTATCAC 16 20 1 GGCGGGCGCC 0.628862 -35 ********** Masking position 3 Map Score: 13.1156 Number of sites scoring better than the average of aligned sites = 867 Number in coding regions = 788 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 5 GACCATTTCCCTTCTTTTGTT 1 2 1 ACCATTTCCC 0.982406 -134 TTCTCACCCCACCTTATCCCGACCCGTGGT 1 51 0 ACCTTATCCC 0.864449 -85 GGAAAATGGAACCGTCTTCCGTAAAGCAAG 3 19 0 ACCGTCTTCC 0.853783 -142 GGAAGACGGTTCCATTTTCCACATCGCGGC 3 29 1 TCCATTTTCC 0.911692 -132 AACACGACTTAGCTTTTTCAATAAGAAGAC 6 39 0 AGCTTTTTCA 0.712144 -88 GCAAAAACAGACCATTTTCTCTGTATGTAA 7 43 0 ACCATTTTCT 0.784262 -82 TTAAAATGAAAGCGTTTTCCAAAGCAGGAA 8 91 1 AGCGTTTTCC 0.959143 -24 CATCACGGATAGCTCTTCCCTTGAAAAAAC 13 105 0 AGCTCTTCCC 0.877395 -53 GTATCGAATCAGCTTTTTTCTATGGAGGGA 14 17 1 AGCTTTTTTC 0.813519 -27 CATTTTTTGCACCATTTCTCCTATGAAATT 15 18 0 ACCATTTCTC 0.89586 -104 TTTTTCAATTTGCATTTCCCCTTTGCCCCT 15 85 0 TGCATTTCCC 0.920738 -37 ********** Masking position 7 Map Score: 6.53159 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 856 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 6 CATAAAGGGTTCTTTTTTATGAAAAAAACAA 2 44 1 TCTTTTTATG 0.858636 -118 GGCTTTTTCTTGCTTTACGGAA 3 2 1 GCTTTTTTTG 0.981739 -159 GTTATGGCCTGCTTTTTTTTGTCCCGGAAAT 4 25 1 GCTTTTTTTG 0.981739 -110 CTTCCGAAGGTCTTCTTATTGAAAAAGCTAA 6 30 1 TCTTCTTTTG 0.900023 -97 TGCTTATTTGTCATTTTTTTG 11 1 0 TCATTTTTTG 0.954808 -120 TTCGGACACTGCACTTTTTTGCTTATTTGTC 11 20 0 GCACTTTTTG 0.949941 -101 GTCTTCAATTTCACTTTTTTGCATCTGCCTA 11 52 0 TCACTTTTTG 0.922863 -69 TTATGTAAGCGCTTTATATTGAGAGGGGCAA 15 62 1 GCTTTATTTG 0.905964 -60 ******* *** Masking position 7 Map Score: 7.1854 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 179 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 7 GGGATAAGGTGGGGTGAGAACGTGTTTTGG 1 61 1 GGGGTGAGAA 0.926427 -75 CTTTATTCGTGGAGGGATTGGAGGAAAC 1 118 1 GGAGGGATTG 0.905712 -18 GGAGTGAGCAGGCTGTTATG 4 1 1 GGAGTGAGCA 0.90764 -134 GTAACCTATGTGAAGGAGAGAGTAAAT 4 118 1 TGAAGGAGAG 0.864776 -17 ATTTTCTTTCGAAAGGAGAAATACATATTA 8 59 1 GAAAGGAGAA 0.867973 -56 TTACATTAAAGGGGGGATTGGTTTGAAGAA 9 92 1 GGGGGGATTG 0.857476 -57 AGATAGCGGCGGGGGGAGAGGG 10 11 1 GGGGGGAGAG 0.989763 -12 CTGAAAGGGGGAAGGAACGGGCTGCGCGC 12 10 1 GGAAGGAACG 0.88652 -36 AAAACGAGGAGGAATGAAAAA 13 147 1 GGAATGAAAA 0.675478 -11 TTTTTTCTATGGAGGGAGAGACAG 14 30 1 GGAGGGAGAG 0.993564 -14 CCGGTATCACGAAAGGAGAACAGAT 16 40 1 GAAAGGAGAA 0.867973 -15 ********** Masking position 7 Map Score: 9.18688 Number of sites scoring better than the average of aligned sites = 699 Number in coding regions = 508 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 8 TACAGCGCTTGAGCATTGGTTCGTCCTGCC 13 68 0 GAGCATTGGT 0.915944 -90 CAAGCGCTGTACGCACCGGTTTTTTCAAGG 13 87 1 ACGCACCGGT 0.985265 -71 CGAAAGGCAGGCGCATCGGT 16 1 0 GCGCATCGGT 0.994203 -54 CTTTCGGCGGGCGCCCCGGTATCACGAAAG 16 25 1 GCGCCCCGGT 0.993633 -30 ********** Masking position 10 Map Score: 0.979869 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 40 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 9 TCTAGAAAGACCTTCGGCGCTTCCGAAG 6 9 1 GACCTTCGGC 0.992525 -118 TCAATAAGAAGACCTTCGGAAGCGCCGAAG 6 22 0 GACCTTCGGA 0.983761 -105 CTGTTTTTTTGACTTTCGCCACTGTTTTTT 9 17 1 GACTTTCGCC 0.988584 -132 AAAAAAGGGGGACTTACGCAAC 15 110 1 GACTTACGCA 0.921335 -12 CGATGCGCCTGCCTTTCGGCGGGCGCCCCG 16 13 1 GCCTTTCGGC 0.979371 -42 ********** Masking position 5 Map Score: 3.88614 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 41 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 AAAGACCTTCGGCGCTTCCGAAGGTCTTCT 6 16 1 GGCGCTTCCG 0.921653 -111 TAAGGGATAAGACGCAAAGGCTGAACGCTA 13 17 1 GACGCAAAGG 0.950673 -141 TCAAGCGCTGTACGCACCGGTTTTTTCAAG 13 86 1 TACGCACCGG 0.931735 -72 TATATTGAGAGGGGCAAAGGGGAAATGCAA 15 76 1 GGGGCAAAGG 0.928967 -46 CCGAAAGGCAGGCGCATCGGT 16 2 0 GGCGCATCGG 0.994111 -53 CCTTTCGGCGGGCGCCCCGGTATCACGAAA 16 24 1 GGCGCCCCGG 0.99157 -31 ********** Masking position 5 Map Score: 1.51758 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 188 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 ********** No masking Map Score: 1.18193e-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: 1.18193e-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 13 ********** No masking Map Score: 1.18193e-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