AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icpxR6_tpal_opreg_100.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 TP0773 300 periplasmic serine protease DO (htrA-1) #2 TP0841 300 periplasmic serine protease DO (htrA-2) #3 TP0949 275 membrane protein #4 TP1016 72 basic membrane protein (tpn39b) #5 TP1017 171 alanyl-tRNA synthetase (alaS) Motif number 1 CGATGGTGGAATTGGCAGACACGCTAGCTTCA 1 47 0 ATGCAGACAC 0.864361 -254 CCACGCGCAGCGCCGCGGGCAGCGTGTATTGG 1 188 0 CCGCGGGCAG 0.968417 -113 TAGCCCACGGCGCCACGCGCAGCGCCGCGGGC 1 200 0 CCACGCGCAG 0.978931 -101 ACTATCAGCACACCGCGCACACTT 2 3 0 CCGCGCACAC 0.992839 -298 ACGCTGCCTACCGTGCACAAACTGCTCCCTGC 2 39 0 CGGCACAAAC 0.813983 -262 CGCCACGTACACTTACACGCTGCCTACCGTGC 2 55 0 ATACACGCTG 0.645637 -246 TGTAAGTGTACGTGGCGGGCACAGGTGAAGAG 2 70 1 CTGCGGGCAC 0.946273 -231 CCGGGTTAAAAGCAGCACACAGCGATATGGTT 2 115 0 ACGCACACAG 0.981672 -186 CCCTCCACGTCCCTGCGCGTACCCAAACCCCT 2 158 0 CCGCGCGTAC 0.936341 -143 ACCGCATGTACCCCACACACAAACGAGGTAAA 2 206 0 CCACACACAA 0.648235 -95 AGCTGTCTTCCACAACGGAAACCAAGAGGACC 3 14 0 CCACGGAAAC 0.671736 -262 CGCGCGATCACACAACACGCACAGCAGCCGCT 3 57 0 CCACACGCAC 0.986054 -219 CAGAGAACAGACGCGCGCGATCACACAACACG 3 70 0 AGGCGCGATC 0.739033 -206 CATGCACACAAGCGACGCACACTCACGGCCTA 3 125 0 ACACGCACAC 0.98254 -151 TCCACTAAATACCCATGCACACAAGCGACGCA 3 138 0 ACATGCACAC 0.782154 -138 GTAAAAACGGATCAGCGCGAGCAACAATCCAC 3 165 0 ACGCGCGAGC 0.859608 -111 ATCCGTTTTTACCAGCGCGCTCTTTCCCCTCA 3 185 1 ACGCGCGCTC 0.987007 -91 CTCGGATAATAACGGCACGAAGGCAAAAGATG 3 215 0 ACGCACGAAG 0.948008 -61 TTATTATCCGAGTTGCTCGCAGTATGCCTATG 3 235 1 ATGCTCGCAG 0.734129 -41 CCATGTACTCGCACGCTCTCATAGGCAT 3 258 0 ATGCACGCTC 0.928763 -18 ACGCCGGAGAAACTATACGCAGCAGGGCAAG 4 10 0 ACATACGCAG 0.671664 -63 CGACTCAGTCACCAGCACACACGCCGGAGAAA 4 30 0 ACGCACACAC 0.991777 -43 AAAAAATATAAGGAGCACACAC 5 1 0 AGGCACACAC 0.962018 -171 CCTTGACAGAATTCGCACACACCTCTAGCCTC 5 56 0 ATGCACACAC 0.968273 -116 * * ******** Masking position 6 Map Score: 37.6453 Number of sites scoring better than the average of aligned sites = 4685 Number in coding regions = 4362 Number in noncoding regions = 323 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 TTGAACTCCCACGCCGGTGAAGGCACTAGC 1 14 1 ACGCCGGTGA 0.947356 -287 GCCACGCGCAGCGCCGCGGGCAGCGTGTAT 1 191 0 GCGCCGCGGG 0.995383 -110 GCTGCGCGTGGCGCCGTGGGCTATTAGCTC 1 209 1 GCGCCGTGGG 0.956136 -92 TGGGCTATTAGCTCAGCTGGTAGAGCAACG 1 225 1 GCTCAGCTGG 0.91302 -76 TACGTGGCGGGCACAGGTGAAGAGGGGATA 2 78 1 GCACAGGTGA 0.800202 -223 GTTTGGGTACGCGCAGGGACGTGGAGGGAC 2 162 1 GCGCAGGGAC 0.843436 -139 AAAACGAGCAACGCCGCTGCTGTAAAAAAA 2 247 0 ACGCCGCTGC 0.976918 -54 TGGATGACCAGAGCAGCAGATAAAAACGAG 2 269 0 GAGCAGCAGA 0.846244 -32 AGCCGCTGATACGCCGCAAGCTGTCTTCCA 3 34 0 ACGCCGCAAG 0.939368 -242 CACACAACACGCACAGCAGCCGCTGATACG 3 51 0 GCACAGCAGC 0.932681 -225 GAGAAACTATACGCAGCAGGGCAAG 4 6 0 ACGCAGCAGG 0.988843 -67 ACCAGCACACACGCCGGAGAAACTATACGC 4 22 0 ACGCCGGAGA 0.963526 -51 CAGATGTTGACCGCAGCAGGGAAAAGGCGA 5 141 1 CCGCAGCAGG 0.970049 -31 ********** Masking position 4 Map Score: 19.2894 Number of sites scoring better than the average of aligned sites = 1473 Number in coding regions = 1372 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 3 GGGCACAGGTGAAGAGGGGATAAACTCGTA 2 86 1 GAAGAGGGGA 0.992727 -215 GAAGGCAAAAGATGAGGGGAAAGAGCGCGC 3 199 0 GATGAGGGGA 0.989612 -77 AGTCGCGGTTGTTACGGGGAGTTCTC 4 57 1 GTTACGGGGA 0.966616 -16 ACGGGAAAAAGAAACGGGGACTCTCTGAGC 5 104 0 GAAACGGGGA 0.992727 -68 CCGCAGCAGGGAAAAGGCGATAATACCCTC 5 151 1 GAAAAGGCGA 0.972909 -21 ********** Masking position 10 Map Score: 5.51381 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 26 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 4 AGGGTTTTCTTGCCTCGATGGTGGAATTGGCAGACACG 1 56 0 TGCTGGGATT 0.967745 -245 CGCGCAGCGCCGCGGGCAGCGTGTATTGGAATTGGCAT 1 179 0 CGGGGGTTTG 0.914437 -122 CATCGACCCACGCCTTAAAAGGGCGTTGCTCTACCAGC 1 240 0 CGCTGGCTTG 0.965415 -61 GAATCCATCATGGCTCAGAGGTGGGATTG 1 282 1 TGCTGGGATT 0.967745 -19 TAACCCGGGCTGTGTCGGTAGGGGTTTGGGTACGCGCA 2 139 1 TGGTGGGTTG 0.994228 -162 CGTTTGTGTGTGGGGTACATGCGGTATGCCGCAGTTTT 2 213 1 TGGGGGGATG 0.974985 -88 GGCGTATCAGCGGCTGCTGTGCGTGTTGTGTGATCGCG 3 49 1 CGCTGGTTTG 0.97077 -227 CTTGTGTGCATGGGTATTTAGTGGATTGTTGCTCGCGC 3 145 1 TGGTGGGTTG 0.994228 -131 CGTTATTATCCGAGTTGCTCGCAGTATGCCTATGAGAG 3 233 1 CGGTGAGATG 0.882121 -43 TGTGTGCTGGTGACTGAGTCGCGGTTGTTACGGGGAGT 4 41 1 TGCTGGGTGT 0.913884 -32 GGTGCGAAACTGTCTTGCGAGAGGCTAGAGGTGTGTGC 5 36 1 TGCTGGGTAG 0.966562 -136 ** ** * ** *** Masking position 11 Map Score: 10.8464 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 155 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 GCTTCAGGTGCTAGTGCCTTCACCGGCGTGG 1 22 0 CTATGCCTTC 0.878304 -279 GAAAGCTGCTCTAATCCCTTGACTAGAAAAA 1 113 0 CTATCCCTTG 0.672123 -188 CCTTTGCATCCCGTGCCCTGAAAGCTGCTCT 1 132 0 CCGGCCCTGA 0.942326 -169 AATCCCACCTCTGAGCCATGATGGATTCGAA 1 279 0 CTGGCCATGA 0.652672 -22 CGTGCACAAACTGCTCCCTGCATGTACTATC 2 29 0 CTGTCCCTGC 0.995161 -272 CCCCTCTTCACCTGTGCCCGCCACGTACACT 2 74 0 CCTTGCCCGC 0.867499 -227 TGAGTCCCTCCACGTCCCTGCGCGTACCCAA 2 164 0 CACTCCCTGC 0.881429 -137 TCGCGCGCGTCTGTTCTCTGAATTTACCGCT 3 82 1 CTGTCTCTGA 0.856201 -194 ACACTCACGGCCTATTCCTGCCTTTCAGCGG 3 108 0 CCTTTCCTGC 0.879835 -168 TTCCCCTCATCTTTTGCCTTCGTGCCGTTAT 3 208 1 CTTTGCCTTC 0.930879 -68 GGCGTGTGTGCTGGTGACTGAGTCGCGGTTG 4 37 1 CTGTGACTGA 0.776256 -36 GTATTATCGCCTTTTCCCTGCTGCGGTCAAC 5 146 0 CTTTCCCTGC 0.990538 -26 *** ******* Masking position 1 Map Score: 5.20361 Number of sites scoring better than the average of aligned sites = 768 Number in coding regions = 698 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 AGAGCAGCTTTCAGGGCACGGGATGCAAAG 1 132 1 TCAGGGCACG 0.948191 -169 TATTAGCTCAGCTGGTAGAGCAACGCCCTT 1 230 1 GCTGGTAGAG 0.781877 -71 GATAGTACATGCAGGGAGCAGTTTGTGCAC 2 29 1 GCAGGGAGCA 0.975214 -272 CGGGTTAAAAGCAGCACACAGCGATATGGT 2 116 0 GCAGCACACA 0.733153 -185 GACCAGAGCAGCAGATAAAAACGAGCAACG 2 264 0 GCAGATAAAA 0.792683 -37 AGCGGTAAATTCAGAGAACAGACGCGCGCG 3 83 0 TCAGAGAACA 0.781004 -193 TAAAAACGGATCAGCGCGAGCAACAATCCA 3 166 0 TCAGCGCGAG 0.809716 -110 GAAAGAGCGCGCTGGTAAAAACGGATCAGC 3 181 0 GCTGGTAAAA 0.822911 -95 ACTATACGCAGCAGGGCAAG 4 1 0 GCAGGGCAAG 0.983571 -72 GTTGACCGCAGCAGGGAAAAGGCGATAATA 5 146 1 GCAGGGAAAA 0.980771 -26 ********** Masking position 2 Map Score: 4.44249 Number of sites scoring better than the average of aligned sites = 1208 Number in coding regions = 1096 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 7 CACTTACACGCTGCCTACCGTGCACAAACT 2 48 0 CTGCCTACCG 0.975665 -253 ACGCCGCAAGCTGTCTTCCACAACGGAAAC 3 24 0 CTGTCTTCCA 0.949017 -252 GTATCAGCGGCTGCTGTGCGTGTTGTGTGA 3 52 1 CTGCTGTGCG 0.930714 -224 CGGCCTATTCCTGCCTTTCAGCGGTAAATT 3 102 0 CTGCCTTTCA 0.952823 -174 GGGTGCGAAACTGTCTTGCGAGAGGCTAGA 5 35 1 CTGTCTTGCG 0.98769 -137 ACTCTCTGAGCAACCTTGCGACAAGATCCT 5 85 0 CAACCTTGCG 0.900631 -87 ********** Masking position 9 Map Score: 1.15777 Number of sites scoring better than the average of aligned sites = 241 Number in coding regions = 219 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 GTGGGAAATATAGTTTTTCTAGTCAAGGGA 1 100 1 TAGTTTTTCT 0.88167 -201 CGGTATGCCGCAGTTTTTTTACAGCAGCGG 2 234 1 CAGTTTTTTT 0.908665 -67 GCGGCGTTGCTCGTTTTTATCTGCTGCTCT 2 260 1 TCGTTTTTAT 0.93445 -41 TCGCGCTGATCCGTTTTTACCAGCGCGCTC 3 177 1 CCGTTTTTAC 0.951951 -99 TGCCTTCGTGCCGTTATTATCCGAGTTGCT 3 222 1 CCGTTATTAT 0.859403 -54 CTGCTGCGTATAGTTTCTCCGGCGTGTGTG 4 17 1 TAGTTTCTCC 0.77137 -56 CAGAGAGTCCCCGTTTCTTTTTCCCGTTTA 5 107 1 CCGTTTCTTT 0.932554 -65 ********** Masking position 5 Map Score: 0.594654 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 134 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 AGAGCAGCTTTCAGGGCACGGGATGCAAAG 1 132 1 TCAGGGCACG 0.935705 -169 CAGGGAGCAGTTTGTGCACGGTAGGCAGCG 2 40 1 TTTGTGCACG 0.926622 -261 AGGCAGCGTGTAAGTGTACGTGGCGGGCAC 2 62 1 TAAGTGTACG 0.960877 -239 CACACAGCGATATGGTTACGAGTTTATCCC 2 102 0 TATGGTTACG 0.808275 -199 TCGGTAGGGGTTTGGGTACGCGCAGGGACG 2 153 1 TTTGGGTACG 0.967824 -148 GTTTACCTCGTTTGTGTGTGGGGTACATGC 2 205 1 TTTGTGTGTG 0.591692 -96 GAATAGGCCGTGAGTGTGCGTCGCTTGTGT 3 122 1 TGAGTGTGCG 0.906798 -154 ACTCGGATAATAACGGCACGAAGGCAAAAG 3 218 0 TAACGGCACG 0.8375 -58 GCAGTATGCCTATGAGAGCGTGCGAGTACA 3 253 1 TATGAGAGCG 0.626733 -23 TTATATTTTTTAAGGGTGCGAAACTGTCTT 5 22 1 TAAGGGTGCG 0.981231 -150 ********** Masking position 1 Map Score: 5.4308 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 429 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 10 ATTGGCAGACACGCTAGCTTCAGGTGCTAG 1 39 0 ACGCTAGCTT 0.765226 -262 CGTGCCCTGAAAGCTGCTCTAATCCCTTGA 1 122 0 AAGCTGCTCT 0.821971 -179 TTTGTCAAGTACGCCGCCTTTGCATCCCGT 1 149 0 ACGCCGCCTT 0.970568 -152 ATTCCAATACACGCTGCCCGCGGCGCTGCG 1 185 1 ACGCTGCCCG 0.970212 -116 GTACACTTACACGCTGCCTACCGTGCACAA 2 51 0 ACGCTGCCTA 0.970262 -250 GATACGCCGCAAGCTGTCTTCCACAACGGA 3 27 0 AAGCTGTCTT 0.954373 -249 ATGTACTCGCACGCTCTCATAGGCATACTG 3 254 0 ACGCTCTCAT 0.783191 -22 TAAGGGTGCGAAACTGTCTTGCGAGAGGCT 5 32 1 AAACTGTCTT 0.767583 -140 ********** Masking position 1 Map Score: 1.11514 Number of sites scoring better than the average of aligned sites = 274 Number in coding regions = 249 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 ********** No masking Map Score: 6.49026e-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 12 ********** No masking Map Score: 6.49026e-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 13 ********** No masking Map Score: 6.49026e-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