AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_tpal_reg_300.orf -o00710_tpal_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0218 300 sigma factor SigB regulation protein, putative #2 TP0220 28 anti-sigma F factor antagonist (spoIIAA-1) #3 TP0223 267 aspartate aminotransferase (tpaaT) #4 TP0537 150 triosephosphate isomerase (tpi) #5 TP0560 110 transketolase A (tktA) #6 TP0561 170 conserved hypothetical protein #7 TP0609 300 asparaginyl-tRNA synthetase (asnS) #8 TP0611 141 ABC transporter, ATP-binding protein #9 TP0612 80 conserved hypothetical protein #10 TP0613 26 conserved hypothetical protein #11 TP0615 50 nitrogen fixation protein (nifU) #12 TP0662 266 fructose-bisphosphate aldolase (cbbA) #13 TP0945 151 ribulose-phosphate 3-epimerase (cfxE) Motif number 1 CGCTTTCTGCACGGTCGCGTGCGCTCTTAGCG 1 37 1 AGGCGCGTGC 0.966398 -264 GGCTACAGAAAGGGGCGCGTGGGGTAAAAGGA 1 134 1 AGGCGCGTGG 0.983684 -167 TAAAAGGATTATTCTCGCGTGCGTGGTGTTTC 1 158 1 ATCCGCGTGC 0.794998 -143 CTTCATCGTGATGGGTGCGTGTGCTATCTGAG 1 217 1 AGGTGCGTGT 0.870532 -84 GCTCATCCGTGTGGCTGCGCGGGCTTGTGTGC 3 41 1 GGGTGCGCGG 0.989219 -227 TTGACAGGGTCAGGGGGCGTGTCTACACTGTG 3 110 1 CGGGGCGTGT 0.975658 -158 ATGGACCTCTCTGAAGGCGCGCGTGCGTTAAA 3 146 1 CGAGGCGCGC 0.954846 -122 TTGAAGGAACGGTGGTGCACGCGCTGTTATCT 3 186 1 GTGTGCACGC 0.576243 -82 TGCACAGAATGCAGAGGCGCGG 3 256 1 GAGGGCGCGG 0.982732 -12 GATATAGTGGTGCCGTGAGATTTTCCCT 4 7 1 GGGGCCGTGA 0.83417 -144 TTTCCCTTGGGTTGGGGCGAGATCTCCTGGCG 4 32 1 GTGGGCGAGA 0.795766 -119 GGGGCGAGATCTCCTGGCGAGGGTATGTCTCT 4 45 1 CCCGGCGAGG 0.823963 -106 TAGTGTGCTCGGTGACGCACGGGAAAAGCATA 5 76 1 GTGCGCACGG 0.797707 -35 GTCGGCCCTGCGGGTGCCGAGGATGAACGGC 6 150 1 CGGGCCGAGG 0.930852 -21 CTCCCGCAGAAAGGACGCGCGGGTGAACGATT 7 30 0 AGGCGCGCGG 0.987425 -271 TTTTCTATGTCGTACGGCGTGGTCCCGGTCAC 7 89 1 CTAGGCGTGG 0.918973 -212 ATGAGGAGCGGCCGAGGCGCGGTCTTCTGTGA 7 117 0 GCGGGCGCGG 0.979363 -184 CGCTCTCCCCAGTCCTGCGCGGCGTTCCATGC 7 197 1 ATCTGCGCGG 0.884444 -104 GCGTTCCATGCAGATGCCGCGCAGGGCGTGCG 7 218 1 CGAGCCGCGC 0.758635 -83 CCGCGCAGGGCGTGCGCCGTGGCGTCACAGCT 7 234 1 CTGGCCGTGG 0.927975 -67 CCCTCTTTGTGGAAGGGCGTGGACCGGCAAGC 7 266 0 GAAGGCGTGG 0.852183 -35 GTTTCCTGTGCAGGATGCGTGGTCTCTTTCCC 8 58 1 CGGTGCGTGG 0.984691 -84 TTATCCTTTTGTGGAGGCGCGCTGCCCCCACG 9 21 1 GGGGGCGCGC 0.994397 -60 GATATGCGGTCTGCTGGCGTGGGGGCAGCGCG 9 38 0 CGCGGCGTGG 0.990611 -43 CCACCGCTTAGAGGAAGCGCGT 9 69 1 GGGAGCGCGT 0.716465 -12 CGGCGAGCTGGCGCCTGCGAGGCGTTAGGGGT 12 30 0 GGCTGCGAGG 0.908303 -237 CATGCGCTAGAATGCGGCGAGCTGGCGCCTGC 12 44 0 ATGGGCGAGC 0.906926 -223 GCTTGTCAAACCTCCCGCGTGGTACCTGTCCA 12 84 1 CTCCGCGTGG 0.91265 -183 TGCCGTTCCAACGCCTGCGTGTGGACTCAAGC 12 127 1 AGCTGCGTGT 0.731704 -140 ACCCTCGGCAAGAGGGGCATGGTAGGGCGATC 12 188 0 AAGGGCATGG 0.718952 -79 CCTCTTGCCGAGGGTGGCACGCTTCTCTATTT 12 205 1 AGGGGCACGC 0.911529 -62 GTAAATATGGATACTGGCGTGAACAACCCCAA 13 99 0 AACGGCGTGA 0.566515 -53 * ** ******* Masking position 8 Map Score: 47.2363 Number of sites scoring better than the average of aligned sites = 2514 Number in coding regions = 2287 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 173 Fraction of orfs with sites within 600 bp upstream = 0.0277867 Motif number 2 TCCAACTACGCTTTCTGCACGGTCGCGTGC 1 29 1 CTTTCTGCAC 0.864029 -272 GTCGCGTGCGCTCTTAGCGGAGATTTCTCA 1 50 1 CTCTTAGCGG 0.934988 -251 CCACGCGCCCCTTTCTGTAGCCTACTTGAG 1 126 0 CTTTCTGTAG 0.682254 -175 CACGGATGAGCTTCCTGCGGCAAATGGTTA 3 22 0 CTTCCTGCGG 0.990501 -246 AGACATGGACCTCTCTGAAGGCGCGCGTGC 3 142 1 CTCTCTGAAG 0.861339 -126 GCGAGGGTATGTCTCTGCGGTGGCTCTATA 4 61 1 GTCTCTGCGG 0.96023 -90 CTGCTCCTAGCACAGCACGGTTT 5 4 1 CTCCTAGCAC 0.739961 -107 CCGTCGTGTCGGCCCTGCGGGTGCCGAGGA 6 143 1 GGCCCTGCGG 0.940636 -28 CCCGCGCGTCCTTTCTGCGGGAGTGTTTCT 7 39 1 CTTTCTGCGG 0.983016 -262 CCACGGCGCACGCCCTGCGCGGCATCTGCA 7 226 0 CGCCCTGCGC 0.972155 -75 CGCTTTTACCCTCTTTGTGGAAGGGCGTGG 7 276 0 CTCTTTGTGG 0.851659 -25 GCTCAGTTTACTCCTTGCAGGAGCCGCTC 8 123 1 CTCCTTGCAG 0.969967 -19 ACGCGCTTCCTCTAAGCGGTGGATATGCG 9 62 0 CTCTAAGCGG 0.862192 -19 CTCCCTTCCTGAGGGCGCACAGCA 10 5 1 CTTCCTGAGG 0.917831 -22 CCACCCCTAACGCCTCGCAGGCGCCAGCTC 12 28 1 CGCCTCGCAG 0.778824 -239 CAAGCTATTTCTCCATGCGCTAGAATGCGG 12 59 0 CTCCATGCGC 0.93024 -208 GAAAAATATCCTTCCCGCGGGTAGGCTGAC 13 17 0 CTTCCCGCGG 0.968063 -135 ********** Masking position 7 Map Score: 21.1098 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 893 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 3 TTCTCGCGTGCGTGGTGTTTCTTTCTCGTG 1 169 1 CGTGGTGTTT 0.933358 -132 TTGGCTTCATCGTGATGGGTGCGTGTGCTA 1 213 1 CGTGATGGGT 0.963818 -88 CGGTGTTTGTGTAACCATTT 3 1 1 CGGTGTTTGT 0.80407 -267 ATTTTCCCCACGGGATTGTTGCACAGAATG 3 237 1 CGGGATTGTT 0.965675 -31 GAGCTATCGGCGGGGTGTTTGTGGTGTGAA 4 106 1 CGGGGTGTTT 0.963818 -45 ACGCCAAACGCGTGATTGGTGTATAGCTTT 6 21 1 CGTGATTGGT 0.952038 -150 CAATCCTTGCCGTGGTTTGTATGGGTAAGA 6 64 1 CGTGGTTTGT 0.933358 -107 GTCCTTTCTGCGGGAGTGTTTCTGATACTC 7 46 1 CGGGAGTGTT 0.946295 -255 GCCTGCGAGGCGTTAGGGGTGGTGAAAAGG 12 20 0 CGTTAGGGGT 0.719914 -247 AGGTACCACGCGGGAGGTTTGACAAGCTAT 12 81 0 CGGGAGGTTT 0.925553 -186 CTTGAATGTTTGGGGTTGTTCACGCCAGTA 13 90 1 TGGGGTTGTT 0.748412 -62 ********** Masking position 10 Map Score: 10.0833 Number of sites scoring better than the average of aligned sites = 259 Number in coding regions = 229 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 ATTTCTCAAGAGGAAGGGGAAAACGCCCAT 1 72 1 AGGAAGGGGA 0.848574 -229 GAAAGTTCAAGCAACGGCGGATGGGCGTTT 1 92 0 GCAACGGCGG 0.91457 -209 AGTAGGCTACAGAAAGGGGCGCGTGGGGTA 1 130 1 AGAAAGGGGC 0.949841 -171 CCATACAAAGGGAACGGTAG 1 291 1 GGAACGGTAG 0.931723 -10 AAATTGACAGGGTCAGGGGGCGTGTCTACA 3 107 1 GGTCAGGGGG 0.767529 -161 TGCTCTTGAAGGAACGGTGGTGCACGCGCT 3 181 1 GGAACGGTGG 0.965494 -87 TATGGGTAAGAGGCAGGTGCTAAGATAGTG 6 83 1 AGGCAGGTGC 0.856988 -88 CAGGGCCGACACGACGGTACTGCAAAAATA 6 130 0 ACGACGGTAC 0.616016 -41 AACGCCGCGCAGGACTGGGGAGAGCGAACC 7 193 0 AGGACTGGGG 0.707831 -108 GGAAGGGCGTGGACCGGCAAGCAGCTGTGA 7 258 0 GGACCGGCAA 0.65053 -43 GTGCGCCCTCAGGAAGGGAG 10 1 0 AGGAAGGGAG 0.94662 -26 AGCGAATGCCAGGAAGGCGCACTGGC 11 7 0 AGGAAGGCGC 0.945125 -44 ATCTCCTTAGAGAAAGGCAGCGAATGCCAG 11 25 0 AGAAAGGCAG 0.932002 -26 AAGACGATTTGGACAGGTACCACGCGGGAG 12 95 0 GGACAGGTAC 0.772445 -172 CGCAGGCGTTGGAACGGCAGCAAGACGATT 12 116 0 GGAACGGCAG 0.956066 -151 AGCAATCCTAACAAAGGGGGTTCTC 12 252 1 ACAAAGGGGG 0.890225 -15 ********** Masking position 7 Map Score: 10.4685 Number of sites scoring better than the average of aligned sites = 1069 Number in coding regions = 921 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 5 TTCTGCACGGTCGCGTGCGCTCTTAGCGGA 1 41 1 TCGCGTGCGC 0.952758 -260 CGTGATGGGTGCGTGTGCTATCTGAGTTTT 1 223 1 GCGTGTGCTA 0.835222 -78 CTGCGCGGGCTTGTGTGCTCTGAAGTCGGG 3 55 1 TTGTGTGCTC 0.952409 -213 TATCTCCTCTTGGTTTGCGCGCGTATTTTC 3 213 1 TGGTTTGCGC 0.965643 -55 GTGAACGAAAGGATGTGCTAAGGAGGGGAT 4 131 1 GGATGTGCTA 0.649388 -20 AAAGAAACCGTGCTGTGCTAGGAGCAG 5 8 0 TGCTGTGCTA 0.862894 -103 GGTGTATCTATAGTGTGCTCGGTGACGCAC 5 66 1 TAGTGTGCTC 0.963029 -45 GGTGCTAAGATAGTGTGCGCTTGTCAGACA 6 98 1 TAGTGTGCGC 0.982189 -73 ATGCCGCGCAGGGCGTGCGCCGTGGCGTCA 7 231 1 GGGCGTGCGC 0.970534 -70 ACAGGTTTAATACCGTGCGCAGTGTATGTC 8 24 0 TACCGTGCGC 0.898105 -118 ACTGCTGTGCGCCCTCAGGAAG 10 15 0 TGCTGTGCGC 0.974117 -12 TGGTGAAAAGGAGTTTGCGA 12 1 0 GAGTTTGCGA 0.770564 -266 TTATCCTGTTTTATTTGCGCCTAAACCGAT 13 48 0 TTATTTGCGC 0.628611 -104 GGTGCTCGATTTGTTTGCTAGCATGGACCT 13 132 1 TTGTTTGCTA 0.647548 -20 ********** Masking position 6 Map Score: 15.0172 Number of sites scoring better than the average of aligned sites = 1133 Number in coding regions = 1034 Number in noncoding regions = 99 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 6 GCGTTTTCCCCTTCCTCTTGAGAAATCTCC 1 68 0 CTTCCTCTTG 0.965529 -233 CGTGGTGTTTCTTTCTCGTGTGTCGCAGGA 1 179 1 CTTTCTCGTG 0.965529 -122 GATGAGTTGGCTTCATCGTGATGGGTGCGT 1 207 1 CTTCATCGTG 0.718221 -94 CTACCGTTCCCTTTGTATGGCTGCT 1 286 0 GTTCCCTTTG 0.804123 -15 CGCGCTGTTATCTCCTCTTGGTTTGCGCGC 3 205 1 TCTCCTCTTG 0.775734 -63 TGCCGTGAGATTTTCCCTTGGGTTGGGGCG 4 21 1 TTTTCCCTTG 0.901767 -130 CTATAGAACAGTTTCTCGTGGAGCTATCGG 4 86 1 GTTTCTCGTG 0.965529 -65 TGTACGGGCAGTCTCTCTTGGAAGAGGTGT 5 41 1 GTCTCTCTTG 0.910989 -70 CTCCTTATGCTTTTCCCGTGCGTCACCGAG 5 83 0 TTTTCCCGTG 0.926916 -28 ACCTGTATGTGTTTCCTGTGCAGGATGCGT 8 48 1 GTTTCCTGTG 0.804123 -94 TGCGTGGTCTCTTTCCCTTGCAACATACAT 8 73 1 CTTTCCCTTG 0.959158 -69 CTTGTCAAACCTCCCGCGTGGTACCTGTCC 12 85 1 CTCCCGCGTG 0.838417 -182 GCCCTACCATGCCCCTCTTGCCGAGGGTGG 12 192 1 GCCCCTCTTG 0.817092 -75 ********** Masking position 9 Map Score: 12.3471 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 313 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 CAAGAGGAAGGGGAAAACGCCCATCCGCCG 1 78 1 GGGAAAACGC 0.952527 -223 GGGGCGCGTGGGGTAAAAGGATTATTCTCG 1 145 1 GGGTAAAAGG 0.965939 -156 GGTGTTTGTGGTGTGAACGAAAGGATGTGC 4 119 1 GTGTGAACGA 0.853446 -32 TGGTTTGTATGGGTAAGAGGCAGGTGCTAA 6 76 1 GGGTAAGAGG 0.959003 -95 CGGGTGCCGAGGATGAACGGC 6 160 1 GGATGAACGG 0.875504 -11 AAGGACGCGCGGGTGAACGATTACCGCGCC 7 22 0 GGGTGAACGA 0.983444 -279 CGCAGGACTGGGGAGAGCGAACCGTGCGAA 7 186 0 GGGAGAGCGA 0.96255 -115 TCCACAAAGAGGGTAAAAGCGTTAGA 7 285 1 GGGTAAAAGC 0.951146 -16 TATGTTGCAAGGGAAAGAGACCACGCATCC 8 70 0 GGGAAAGAGA 0.910404 -72 ********** Masking position 6 Map Score: 8.08696 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 162 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 CCGCGCCTCTGCATTCTGTGCAACAATCCCG 3 247 0 GCATTCTTGC 0.800781 -21 CACGCGTTTGGCGTACAATGCCCC 6 4 0 GCGTACATGC 0.948358 -167 TGATCGGTAGGCAATCCTTGCCGTGGTTTGT 6 53 1 GCAATCCTGC 0.856827 -118 ACTGGGGAGAGCGAACCGTGCGAAAAAGCGT 7 179 0 GCGAACCTGC 0.969867 -122 GTCCTGCGCGGCGTTCCATGCAGATGCCGCG 7 208 1 GCGTTCCTGC 0.9769 -93 ACGCCACGGCGCACGCCCTGCGCGGCATCTG 7 228 0 GCACGCCTGC 0.891823 -73 CCAAGGTAGGACATACACTGCGCACGGTATT 8 15 1 ACATACATGC 0.759028 -127 CGCCTTCCTGGCATTCGCTGCCTTTCTCTAA 11 18 1 GCATTCGTGC 0.965256 -33 ******* *** Masking position 9 Map Score: 6.00518 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 222 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 ACACGCCCCCTGACCCTGTCAATTTATGCA 3 102 0 TGACCCTGTC 0.971687 -166 CCTTCAGAGAGGTCCATGTCTCACAGTGTA 3 133 0 GGTCCATGTC 0.978112 -135 CGTACGGCGTGGTCCCGGTCACAGAAGACC 7 99 1 GGTCCCGGTC 0.986629 -202 GCTGCTTGCCGGTCCACGCCCTTCCACAAA 7 263 1 GGTCCACGCC 0.919351 -38 CCTCCCGCGTGGTACCTGTCCAAATCGTCT 12 94 1 GGTACCTGTC 0.955053 -173 GCGGGTAGGCTGACCCCGTC 13 1 0 TGACCCCGTC 0.966047 -151 AGGATAAGCAGGACACTGTCTTGAATGTTT 13 71 1 GGACACTGTC 0.942258 -81 ********** Masking position 8 Map Score: 6.3432 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 21 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 GTGTGGCTGCGCGGGCTTGTGTGCTCTGAAG 3 49 1 GCGGGCTGTG 0.986337 -219 GGGTTGGGGCGAGATCTCCTGGCGAGGGTAT 4 40 1 GAGATCTCTG 0.97282 -111 CGGCCGAGGCGCGGTCTTCTGTGACCGGGAC 7 110 0 GCGGTCTCTG 0.994033 -191 CGGTGGATATGCGGTCTGCTGGCGTGGGGGC 9 44 0 GCGGTCTCTG 0.994033 -37 AGGGAGATCTCCTTAGAGAAAGGC 11 37 0 GAGATCTCTT 0.847052 -14 CTAGAATGCGGCGAGCTGGCGCCTGCGAGGC 12 39 0 GCGAGCTGCG 0.943778 -228 ******* *** Masking position 7 Map Score: 2.84161 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 44 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 CGCGTGCGTGGTGTTTCTTTCTCGTGTGTCGC 1 173 1 GTGTCTTTCT 0.76824 -128 GCAGCCACACGGATGAGCTTCCTGCGGCAAAT 3 27 0 GGATGCTTCC 0.944452 -241 CGTGATTGGTGTATAGCTTTCCTGATCGGTAG 6 31 1 GTATCTTTCC 0.96805 -140 ACCACGGCAAGGATTGCCTACCGATCAGGAAA 6 48 0 GGATCCTACC 0.968524 -123 CGTGCGCAGTGTATGTCCTACCTTGGCGTT 8 9 0 GTATCCTACC 0.951235 -133 TATTAAACCTGTATGTGTTTCCTGTGCAGGAT 8 42 1 GTATGTTTCC 0.930848 -100 CTCCACAAAAGGATAACTTACTTTTT 9 5 0 GGATCTTACT 0.925025 -76 CCCGCGGGAAGGATATTTTTCTATCGGTTTAG 13 26 1 GGATTTTTCT 0.753794 -126 **** ****** Masking position 4 Map Score: 0.787229 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 58 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 ********** No masking Map Score: -5.32664e-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: -5.32664e-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 14 ********** No masking Map Score: -5.32664e-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