AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00710_tpal_reg_100.orf -o00710_tpal_100.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 TP0223 267 aspartate aminotransferase (tpaaT) #2 TP0537 150 triosephosphate isomerase (tpi) #3 TP0560 110 transketolase A (tktA) #4 TP0611 141 ABC transporter, ATP-binding protein #5 TP0612 80 conserved hypothetical protein #6 TP0613 26 conserved hypothetical protein #7 TP0615 50 nitrogen fixation protein (nifU) #8 TP0662 266 fructose-bisphosphate aldolase (cbbA) #9 TP0945 151 ribulose-phosphate 3-epimerase (cfxE) Motif number 1 GGAAGCTCATCCGTGTGGCTGCGCGGGCTTGTGTGCT 1 37 1 CTGTGCGCGG 0.990985 -231 GTCGGGCTGTCGATTCACTGGGGTGCATAAATTGACA 1 79 1 CTAGGGGTGA 0.905784 -189 CATAAATTGACAGGGTCAGGGGGCGTGTCTACACTGT 1 104 1 CGCGGGGCGG 0.992 -164 AGACATGGACCTCTCTGAAGGCGCGCGTGCGTTAAAC 1 142 1 CTGGGCGCGG 0.991533 -126 CTGTTATCTCCTCTTGGTTTGCGCGCGTATTTTCCCC 1 209 1 CTGTGCGCGG 0.990889 -59 GATTGTTGCACAGAATGCAGAGGCGCGG 1 250 1 CAGGAGGCGG 0.993318 -18 TGAGATTTTCCCTTGGGTTGGGGCGAGATCTCCTGGC 2 26 1 CTGGGGGCGG 0.999309 -125 CGGGCAGTCTCTCTTGGAAGAGGTGTATCTATAGTGT 3 45 1 CTGGAGGTGA 0.963526 -66 GTATGTGTTTCCTGTGCAGGATGCGTGGTCTCTTTCC 4 52 1 CGCGATGCGG 0.862795 -90 AGTAAGTTATCCTTTTGTGGAGGCGCGCTGCCCCCAC 5 15 1 CTGGAGGCGG 0.99874 -66 GGTGGATATGCGGTCTGCTGGCGTGGGGGCAGCGCGC 5 37 0 CTGGGCGTGG 0.989935 -44 GCATATCCACCGCTTAGAGGAAGCGCGT 5 63 1 CTGGAAGCGG 0.991874 -18 CTCCCTTCCTGAGGGCGCACAGCAGT 6 3 1 CTCAGGGCGA 0.866183 -24 TTTCTCCATGCGCTAGAATGCGGCGAGCTGGCGCCTG 8 45 0 CTAGCGGCGG 0.976574 -222 AGAAGAGTCACGAAATAGAGAAGCGTGCCACCCTCGG 8 212 0 CAAGAAGCGG 0.820199 -55 GGATATTTTTCTATCGGTTTAGGCGCAAATAAAACAG 9 36 1 CTGTAGGCGA 0.966198 -116 * * * ****** * Masking position 13 Map Score: 33.0378 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 413 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 2 CACGGATGAGCTTCCTGCGGCAAATGGTTA 1 22 0 CTTCCTGCGG 0.961874 -246 GCGCTGTTATCTCCTCTTGGTTTGCGCGCG 1 206 1 CTCCTCTTGG 0.940163 -62 CGCGCGTATTTTCCCCACGGGATTGTTGCA 1 230 1 TTCCCCACGG 0.813002 -38 GCCGTGAGATTTTCCCTTGGGTTGGGGCGA 2 22 1 TTTCCCTTGG 0.974104 -129 TATAGAACAGTTTCTCGTGGAGCTATCGGC 2 87 1 TTTCTCGTGG 0.934111 -64 ATCCCCTCCTTAGCACATCCTTTC 2 137 0 CCTCCTTAGC 0.78412 -14 GTACGGGCAGTCTCTCTTGGAAGAGGTGTA 3 42 1 TCTCTCTTGG 0.899676 -69 TCCTTATGCTTTTCCCGTGCGTCACCGAGC 3 82 0 TTTCCCGTGC 0.972801 -29 TGTTCTCACTCCTTATGCTTTTCCCGTG 3 93 0 CTCCTTATGC 0.504149 -18 CAGTGTATGTCCTACCTTGGCGTT 4 5 0 CCTACCTTGG 0.791168 -137 CCTGTATGTGTTTCCTGTGCAGGATGCGTG 4 49 1 TTTCCTGTGC 0.925158 -93 GCGTGGTCTCTTTCCCTTGCAACATACATT 4 74 1 TTTCCCTTGC 0.962029 -68 CTCCCTTCCTGAGGGCGCACAGCA 6 5 1 CTTCCTGAGG 0.894958 -22 GCTTGTCAAACCTCCCGCGTGGTACCTGTC 8 84 1 CCTCCCGCGT 0.90944 -183 CCCTACCATGCCCCTCTTGCCGAGGGTGGC 8 193 1 CCCCTCTTGC 0.904308 -74 GAGAACCCCCTTTGTTAGGATTGCT 8 252 0 CCCCCTTTGT 0.736711 -15 GAAAAATATCCTTCCCGCGGGTAGGCTGAC 9 17 0 CTTCCCGCGG 0.986485 -135 ********** Masking position 9 Map Score: 19.6653 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 998 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 3 CACACAAGCCCGCGCAGCCACACGGATGAG 1 42 0 CGCGCAGCCA 0.960568 -226 GCTCTGAAGTCGGGCTGTCGATTCACTGGG 1 71 1 CGGGCTGTCG 0.925227 -197 TCTCTGAAGGCGCGCGTGCGTTAAACGCTG 1 153 1 CGCGCGTGCG 0.879271 -115 TTTTTCTGTACGGGCAGTCTCTCTTGGAAG 3 35 1 CGGGCAGTCT 0.931842 -76 GGAAAGAGACCACGCATCCTGCACAGGAAA 4 59 0 CACGCATCCT 0.81307 -83 CAGTTTACTCCTTGCAGGAGCCGCTC 4 126 1 CTTGCAGGAG 0.69639 -16 TTTGTGGAGGCGCGCTGCCCCCACGCCAGC 5 28 1 CGCGCTGCCC 0.932239 -53 ACGCGCTTCCTCTAAGCGGTG 5 70 0 CGCGCTTCCT 0.86469 -11 TTCCTGAGGGCGCACAGCAGT 6 16 1 CGCACAGCAG 0.733744 -11 CAGCGAATGCCAGGAAGGCGCACTGGC 7 8 0 CAGGAAGGCG 0.893696 -43 CCCCTAACGCCTCGCAGGCGCCAGCTCGCC 8 31 1 CTCGCAGGCG 0.987766 -236 GGACAGGTACCACGCGGGAGGTTTGACAAG 8 85 0 CACGCGGGAG 0.871599 -182 TCCAAATCGTCTTGCTGCCGTTCCAACGCC 8 112 1 CTTGCTGCCG 0.746169 -155 CTTGAGTCCACACGCAGGCGTTGGAACGGC 8 128 0 CACGCAGGCG 0.990751 -139 TCAACCGAAGCGCGAAGGCTTGAGTCCACA 8 146 0 CGCGAAGGCT 0.964011 -121 ATCCTTCCCGCGGGTAGGCTGACCCCGTC 9 10 0 CGGGTAGGCT 0.843774 -142 AGCCTACCCGCGGGAAGGATATTTTTCTAT 9 20 1 CGGGAAGGAT 0.732161 -132 ********** Masking position 1 Map Score: 20.9016 Number of sites scoring better than the average of aligned sites = 2041 Number in coding regions = 1858 Number in noncoding regions = 183 Number of orfs with sites within 600 bp upstream = 120 Fraction of orfs with sites within 600 bp upstream = 0.019274 Motif number 4 GAGCACACAAGCCCGCGCAGCCACACGGAT 1 45 0 GCCCGCGCAG 0.931001 -223 CTGAAGGCGCGCGTGCGTTAAACGCTGCTC 1 156 1 GCGTGCGTTA 0.937046 -112 GAACGGTGGTGCACGCGCTGTTATCTCCTC 1 192 1 GCACGCGCTG 0.989837 -76 TATGCTTTTCCCGTGCGTCACCGAGCACAC 3 78 0 CCGTGCGTCA 0.866141 -33 AGGTTTAATACCGTGCGCAGTGTATGTCCT 4 22 0 CCGTGCGCAG 0.959056 -120 TTTACTCCTTGCAGGAGCCGCTC 4 129 1 GCAGGAGCCG 0.92636 -13 CGCCTTCCTGGCATTCGCTGCCTTTCTCTA 7 18 1 GCATTCGCTG 0.929045 -33 CTAACGCCTCGCAGGCGCCAGCTCGCCGCA 8 34 1 GCAGGCGCCA 0.983986 -233 AGCTATTTCTCCATGCGCTAGAATGCGGCG 8 57 0 CCATGCGCTA 0.965947 -210 GAGTCCACACGCAGGCGTTGGAACGGCAGC 8 125 0 GCAGGCGTTG 0.976434 -142 ********** Masking position 2 Map Score: 10.9182 Number of sites scoring better than the average of aligned sites = 1360 Number in coding regions = 1272 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 5 AAATGGTTACACAAACACCG 1 1 0 ACAAACACCG 0.950115 -267 CACCGCAGAGACATACCCTCGCCAGGAGAT 2 53 0 ACATACCCTC 0.968848 -98 CGTTCACACCACAAACACCCCGCCGATAGC 2 108 0 ACAAACACCC 0.981763 -43 CCAAGGTAGGACATACACTGCGCACGGTAT 4 15 1 ACATACACTG 0.951056 -127 TTCCCTTGCAACATACATTCGAATGTACGT 4 85 1 ACATACATTC 0.971931 -57 GCAGGAGTATACGTACATTCGAATGTATGT 4 95 0 ACGTACATTC 0.901932 -47 AAATAGCTTGTCAAACCTCCCGCGTGGTAC 8 79 1 TCAAACCTCC 0.799601 -188 GTGAACAACCCCAAACATTCAAGACAGTGT 9 83 0 CCAAACATTC 0.914196 -69 ********** Masking position 5 Map Score: 4.90042 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 95 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 6 GCATAAATTGACAGGGTCAGGGGGCGTGTCT 1 103 1 ACAGGGTCGG 0.962404 -165 GCGCCTTCAGAGAGGTCCATGTCTCACAGTG 1 135 0 AGAGGTCCTG 0.838758 -133 TGCACAGAATGCAGAGGCGCGG 1 256 1 GCAGAGGCCG 0.887998 -12 GCTCTATAGAACAGTTTCTCGTGGAGCTATC 2 83 1 ACAGTTTCCG 0.946567 -68 TCGGTTGACTAGAGCGTCCCGATCGCCCTAC 8 168 1 AGAGCGTCCG 0.96226 -99 ACCCTCGGCAAGAGGGGCATGGTAGGGCGAT 8 189 0 AGAGGGGCTG 0.98242 -78 CCTCTTGCCGAGGGTGGCACGCTTCTCTATT 8 205 1 AGGGTGGCCG 0.94177 -62 AACATTCAAGACAGTGTCCTGCTTATCCTGT 9 69 0 ACAGTGTCTG 0.954814 -83 ATCCATATTTACAGGTGCTCGATTTGTTTGC 9 119 1 ACAGGTGCCG 0.983001 -33 ******** ** Masking position 8 Map Score: 5.40569 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 174 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 7 GCTCATCCGTGTGGCTGCGCGGGCTTGTGT 1 41 1 GTGGCTGCGC 0.813029 -227 ACAGGGTCAGGGGGCGTGTCTACACTGTGA 1 113 1 GGGGCGTGTC 0.825336 -155 CTCTCTGAAGGCGCGCGTGCGTTAAACGCT 1 152 1 GCGCGCGTGC 0.526189 -116 GTATGTCTCTGCGGTGGCTCTATAGAACAG 2 67 1 GCGGTGGCTC 0.958516 -84 TTCTGTACGGGCAGTCTCTCTTGGAAGAGG 3 38 1 GCAGTCTCTC 0.836706 -73 CAGGATGCGTGGTCTCTTTCCCTTGCAACA 4 68 1 GGTCTCTTTC 0.509961 -74 ACTCCTTGCAGGAGCCGCTC 4 132 1 GGAGCCGCTC 0.972239 -10 TGCTGGCGTGGGGGCAGCGCGCCTCCACAA 5 29 0 GGGGCAGCGC 0.953633 -52 CCTGGCATTCGCTGCCTTTCTCTAAGGAGA 7 24 1 GCTGCCTTTC 0.900477 -27 CGCCTCGCAGGCGCCAGCTCGCCGCATTCT 8 38 1 GCGCCAGCTC 0.840936 -229 AAATCGTCTTGCTGCCGTTCCAACGCCTGC 8 115 1 GCTGCCGTTC 0.957918 -152 TCCTAACAAAGGGGGTTCTC 8 257 1 GGGGGTTCTC 0.88957 -10 TTGAATGTTTGGGGTTGTTCACGCCAGTAT 9 91 1 GGGGTTGTTC 0.917137 -61 ********** Masking position 10 Map Score: 5.47122 Number of sites scoring better than the average of aligned sites = 1439 Number in coding regions = 1312 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 8 AGCCCGACTTCAGAGCACACAAGCCCGCGC 1 57 0 CAGAGCACAC 0.972983 -211 CCGTGCGTCACCGAGCACACTATAGATACA 3 68 0 CCGAGCACAC 0.972452 -43 GTAGGACATACACTGCGCACGGTATTAAAC 4 20 1 CACTGCGCAC 0.90879 -122 GGCGTGGGGGCAGCGCGCCTCCACAAAAGG 5 25 0 CAGCGCGCCT 0.975603 -56 CCCACGCCAGCAGACCGCATATCCACCGCT 5 47 1 CAGACCGCAT 0.902605 -34 ACTGCTGTGCGCCCTCAGGAAGGG 6 13 0 CTGTGCGCCC 0.97016 -14 GCCAGTGCGCCTTCCTGGCATT 7 3 1 CAGTGCGCCT 0.985581 -48 CTAGAGCGTCCCGATCGCCCTACCATGCCC 8 176 1 CCGATCGCCC 0.959445 -91 AGCAAACAAATCGAGCACCTGTAAATATGG 9 121 0 TCGAGCACCT 0.776012 -31 ********** Masking position 6 Map Score: 8.68951 Number of sites scoring better than the average of aligned sites = 809 Number in coding regions = 731 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 9 TGCACGCGCTGTTATCTCCTCTTGGTTTGC 1 201 1 GTTATCTCCT 0.972524 -67 GGGTTGGGGCGAGATCTCCTGGCGAGGGTA 2 40 1 GAGATCTCCT 0.974495 -111 TCGAATGTACGTATACTCCTGCTCAGTTTA 4 103 1 GTATACTCCT 0.949927 -39 CTCCTGCTCAGTTTACTCCTTGCAGGAGCC 4 118 1 GTTTACTCCT 0.949927 -24 AGGGAGATCTCCTTAGAGAAAGG 7 38 0 GAGATCTCCT 0.974495 -13 TCGCAAACTCCTTTTCACCACC 8 3 1 GCAAACTCCT 0.954049 -264 ********** Masking position 7 Map Score: 5.10257 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 ATTGACAGGGTCAGGGGGCGTGTCTACACT 1 109 1 TCAGGGGGCG 0.964943 -159 AGGGTATGTCTCTGCGGTGGCTCTATAGAA 2 64 1 TCTGCGGTGG 0.94979 -87 AAGGATGTGCTAAGGAGGGGAT 2 139 1 TAAGGAGGGG 0.972672 -12 GGGAAAAGCATAAGGAGTGAGAACA 3 96 1 TAAGGAGTGA 0.802173 -15 GCGCTTCCTCTAAGCGGTGGATATGCGGTC 5 59 0 TAAGCGGTGG 0.970456 -22 CTGTGCGCCCTCAGGAAGGGAG 6 3 0 TCAGGAAGGG 0.862063 -24 CTGCGAGGCGTTAGGGGTGGTGAAAAGGAG 8 18 0 TTAGGGGTGG 0.984809 -249 GTCTTGAATGTTTGGGGTTGTTCACGCCAG 9 88 1 TTTGGGGTTG 0.754811 -64 ********** Masking position 1 Map Score: 4.02439 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 222 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 CTGTCAATTTATGCACCCCAGTGAATCGAC 1 87 0 ATGCACCCCA 0.915625 -181 ACAGCGCGTGCACCACCGTTCCTTCAAGAG 1 183 0 CACCACCGTT 0.854395 -85 TGTTCTATAGAGCCACCGCAGAGACATACC 2 66 0 AGCCACCGCA 0.968036 -85 TTCACACCACAAACACCCCGCCGATAGCTC 2 106 0 AAACACCCCG 0.889053 -45 CAGACCGCATATCCACCGCTTAGAGGAAGC 5 57 1 ATCCACCGCT 0.972996 -24 AACTCCTTTTCACCACCCCTAACGCCTCGC 8 16 1 CACCACCCCT 0.983449 -251 TACTGGCGTGAACAACCCCAAACATTCAAG 9 90 0 AACAACCCCA 0.919706 -62 ********** Masking position 5 Map Score: 1.75413 Number of sites scoring better than the average of aligned sites = 297 Number in coding regions = 275 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ********** No masking Map Score: -3.47212e-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: -3.47212e-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: -3.47212e-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