AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icytR_tpal_opreg_300.orf -g0.528 -x5 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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0261 114 catabolite gene activator, putative #2 TP0734 81 purine nucleoside phosphorylase (deoD) #3 TP0736 233 hydrogenase, gamma chain (hydG) #4 TP1026 300 oligoendopeptidase F, putative #5 TP1027 121 uridine phosphorylase (udp) Motif number 1 CGCGCTCCTGCGCGCACACCTGCAGAGATC 1 39 0 CGCGCACACC 0.998073 -76 GAATTCACGTCACGCGCTCCTGCGCGCACA 1 51 0 CACGCGCTCC 0.973002 -64 CGTCACTCCCTCCCTTCGTGGGG 2 69 0 CACTCCCTCC 0.981461 -13 GCAGGTTTTGCGTGCAGTCCTCATTCAAGC 3 71 0 CGTGCAGTCC 0.932378 -163 AGGCAACTAACGCGCCGACCGCTGCTTTTC 3 117 0 CGCGCCGACC 0.998583 -117 CAGTGCATCCTGCGCCCACCCGAGACCACA 4 13 1 TGCGCCCACC 0.996362 -288 CGAAAACCGCCGCTCCCATCAGCAGCACAC 4 69 1 CGCTCCCATC 0.987262 -232 CAACCAAAACCGCGCCCACCACCGCCTCCC 4 99 1 CGCGCCCACC 0.999361 -202 CTTGAACAAACGCTCAGTCCGCCTGATGAT 4 268 1 CGCTCAGTCC 0.978037 -33 GCGTTATGCGCCCATCATCAGGCGGA 4 285 0 TGCGCCCATC 0.979374 -16 ********** Masking position 5 Map Score: 26.8512 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 359 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 2 CGCGCAGGAGCGCGTGACGTGAATTCTGGA 1 55 1 CGCGTGACGT 0.961963 -60 GTACGCTCAGCGCATGCAGCACCCG 2 6 0 CGCATGCAGC 0.86326 -76 TGAGCGTACACGCGCGAGGTTACCGAAACG 2 27 1 CGCGCGAGGT 0.974591 -55 CCCTTCTCGGCGCCGATGGCGTTTTGCTTG 3 46 1 CGCCGATGGC 0.945918 -188 GCAACTAACGCGCCGACCGCTGCTTTTCTC 3 115 0 CGCCGACCGC 0.954886 -119 TCAGCTCTGTCGCACAAGGCAACTAACGCG 3 133 0 CGCACAAGGC 0.983345 -101 AGAGTTTGGTCGAAGGAGGCATGGCT 3 218 1 CGAAGGAGGC 0.953348 -16 CTCGGGTGGGCGCAGGATGCACTGCG 4 7 0 CGCAGGATGC 0.983895 -294 GGAGATTTTGCGCGGGAGGCGGTGGTGGGC 4 112 0 CGCGGGAGGC 0.997034 -189 GATTTCTTTCAGCAGAAGGTTTCTTCAGGA 4 232 0 AGCAGAAGGT 0.871966 -69 ACGCTCAGTCCGCCTGATGATGGGCGCATA 4 277 1 CGCCTGATGA 0.722023 -24 TGATGATGGGCGCATAACGC 4 291 1 CGCATAACGC 0.974955 -10 TTCCCCTTTAAGCGTAAGGTGCACAGCACT 5 98 0 AGCGTAAGGT 0.795046 -24 ********** Masking position 2 Map Score: 17.2966 Number of sites scoring better than the average of aligned sites = 1358 Number in coding regions = 1247 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 3 GAGATCGTTCGCACGCCTTTTCCAGGAAAGGTGG 1 7 0 GGTTTTCGAA 0.995266 -108 GGTCATGCACTTAAGTCTTTTTCCAGAATTCACGTCAC 1 68 0 TGTTTTCGAA 0.970168 -47 TCTCGGCGCCGATGGCGTTTTGCTTGAATGAGGACTGC 3 50 1 GGTTTTCGAA 0.995266 -184 CAGAGCTGAAGAAAGGCTTTTCTTTGACAAATCTGCAT 3 154 1 GGTTTTTGAC 0.985765 -80 GCTTGACACAGAATGATTTTTATGAGACGATCGGGAGA 4 137 0 GGTTTTTGAC 0.985765 -164 TTCTTTCAGCAGAAGGTTTCTTCAGGAAGTTTTCCGCA 4 221 0 AGTTCTCGAA 0.956301 -80 GTCCCCCGTGGTCGGGATTCTTCGTGACTGGGGAGTGC 5 65 1 GGTTCTCGAC 0.99415 -57 * * **** * *** Masking position 17 Map Score: 7.34669 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 22 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 GGCGTGCGAACGATCTCTGCAGGTGTGCGC 1 28 1 CGATCTCTGC 0.816131 -87 TCAAGCAAAACGCCATCGGCGCCGAGAAGG 3 47 0 CGCCATCGGC 0.929422 -187 ACTAACGCGCCGACCGCTGCTTTTCTCATC 3 112 0 CGACCGCTGC 0.966392 -122 GTGCATCCTGCGCCCACCCGAGACCACAAC 4 15 1 CGCCCACCCG 0.895944 -286 CCACCCGAGACCACAACCGTACTCCATAGG 4 28 1 CCACAACCGT 0.921002 -273 GAAAGAAGAGCGAAAACCGCCGCTCCCATC 4 59 1 CGAAAACCGC 0.975545 -242 AGCACACCAACCAAAACCGCGCCCACCACC 4 92 1 CCAAAACCGC 0.953614 -209 AAAACCGCGCCCACCACCGCCTCCCGCGCA 4 104 1 CCACCACCGC 0.994369 -197 CGAAGAATCCCGACCACGGGGGACGGTGAC 5 59 0 CGACCACGGG 0.980819 -63 ********** Masking position 7 Map Score: 7.22465 Number of sites scoring better than the average of aligned sites = 542 Number in coding regions = 495 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 CCACCTTTCCTGGAAAAGGCGTGCGAACG 1 10 1 CTGGAAAAGG 0.946643 -105 GACGTGAATTCTGGAAAAAGACTTAAGTGC 1 70 1 CTGGAAAAAG 0.982948 -45 GGAAACAATGATGAGAAAAGCAGCGGTCGG 3 103 1 ATGAGAAAAG 0.874013 -131 TGCGACAGAGCTGAAGAAAGGCTTTTCTTT 3 149 1 CTGAAGAAAG 0.988233 -85 GGAAAACTTCCTGAAGAAACCTTCTGCTGA 4 224 1 CTGAAGAAAC 0.941679 -77 AAGAAACCTTCTGCTGAAAGAAATCAGCTA 4 237 1 CTGCTGAAAG 0.90322 -64 GTCTATGAAAAAAGGGTAAAAGAT 5 5 1 ATGAAAAAAG 0.949932 -117 ********** Masking position 7 Map Score: 5.57536 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 123 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 CACGTATATCTGTTCATCGGACCCTTCTCGGCGCC 3 25 1 TGTCACCCCT 0.992448 -209 ATTCGCTGTACTATCATCCATCCCTCCGAGAGTTT 3 190 1 CTTCACCCCT 0.992448 -44 CGGCGGTTTTCGCTCTTCTTTCCCCTATGGAGTAC 4 46 0 CGTCTCCCCC 0.993415 -255 ACCAAAACCGCGCCCACCACCGCCTCCCGCGCAAA 4 101 1 CGCCACGCCT 0.97571 -200 AGAGAACTACCTGTCACCGTCCCCCGTGGTCGGGA 5 47 1 CTTCACCCCC 0.995184 -75 AAGCGTAAGGTGCACAGCACTCCCCAGTCACGAAG 5 84 0 TGACACCCCC 0.984328 -38 ** *** * **** Masking position 8 Map Score: 3.27883 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 74 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 CGGGTGCTGCATGCGCTGAG 2 1 1 CGGGTGCTGC 0.976902 -81 CGGCGCCGATGGCGTTTTGCTTGAATGAGG 3 53 1 GGCGTTTTGC 0.984725 -181 TGTTTCCTGGCAGGTTTTGCGTGCAGTCCT 3 80 0 CAGGTTTTGC 0.934202 -154 TGATGGGAGCGGCGGTTTTCGCTCTTCTTT 4 60 0 GGCGGTTTTC 0.844026 -241 GGTTTTGGTTGGTGTGCTGCTGATGGGAGC 4 80 0 GGTGTGCTGC 0.95051 -221 AGACGATCGGGAGATTTTGCGCGGGAGGCG 4 121 0 GAGATTTTGC 0.901756 -180 CCCCGTGGTCGGGATTCTTCGTGACTGGGG 5 68 1 GGGATTCTTC 0.917243 -54 ********** Masking position 8 Map Score: 1.88101 Number of sites scoring better than the average of aligned sites = 517 Number in coding regions = 476 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 8 GAAAAGGCGTGCGAACGATCTCTGCAGGTG 1 23 1 GCGAACGATC 0.956185 -92 AAGTGCATGACCGTTCTATCGAAAATGTAC 1 94 1 CCGTTCTATC 0.802227 -21 AACCTCGCGCGTGTACGCTCAGCGCATGCA 2 18 0 GTGTACGCTC 0.976611 -64 TCTGCATTCGCTGTACTATCATCCATCCCT 3 185 1 CTGTACTATC 0.867257 -49 CCTCCTTCGACCAAACTCTCGGAGGGATGG 3 207 0 CCAAACTCTC 0.952476 -27 GGGAGCGGCGGTTTTCGCTCTTCTTTCCCC 4 56 0 GTTTTCGCTC 0.71659 -245 CGCCTCCCGCGCAAAATCTCCCGATCGTCT 4 121 1 GCAAAATCTC 0.761706 -180 GTTAGAATGCGTATACTCTCCAGATAGTTG 4 193 1 GTATACTCTC 0.953374 -108 GCTAACTTGAACAAACGCTCAGTCCGCCTG 4 263 1 ACAAACGCTC 0.866568 -38 ********** Masking position 9 Map Score: 3.10204 Number of sites scoring better than the average of aligned sites = 792 Number in coding regions = 736 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 ********** No masking Map Score: 6.56131e-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: 6.56131e-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 11 ********** No masking Map Score: 6.56131e-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