AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i270_hypothetical15_mtub_reg_300.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 ftsZ 172 ftsZ #2 murE 22 murE #3 hypothetical 267 hypothetical protein Rv2160c #4 Rv2161c 102 hypothetical protein Rv2161c #5 PE_PGRS 209 PE_PGRS #6 Rv2166c 300 hypothetical protein Rv2166c Motif number 1 CGCGCCGATACGCGGCGGGCATTTTTTCGG 1 11 0 CGCGGCGGGC 0.866698 -162 CGCCGCGTATCGGCGCGCCTGCACGGTTAG 1 24 1 CGGCGCGCCT 0.614895 -149 CGTTCGGCTTCCTCCCTGGTGGGG 1 159 0 CGGCTTCCTC 0.902796 -14 CCTACCGACAGGGCGCGCACAC 2 3 0 GGGCGCGCAC 0.647309 -20 CGCCGACGTCGGCCGCCAAA 3 1 1 CGCCGACGTC 0.833294 -267 CGCGCAGGATCTGCGCCCGGGTTTGGCGGC 3 22 0 CTGCGCCCGG 0.891072 -246 ATATCCATCGCGGCGCGCAGGATCTGCGCC 3 35 0 CGGCGCGCAG 0.558222 -233 CGATGGATATCGCCTCGGTGAAGGGGCTCT 3 55 1 CGCCTCGGTG 0.671321 -213 CTCGGTGAAGGGGCTCTCGGGGCTGTCCAT 3 68 1 GGGCTCTCGG 0.827035 -200 TCGGCGAGCTTGCCGGGCGGCTGGGCATGA 3 97 1 TGCCGGGCGG 0.819379 -171 TCCGGCATTTCGGCGCCAAGGAGCAGCTGC 3 142 1 CGGCGCCAAG 0.951749 -126 CGCCAAGGAGCAGCTGCAGCTGGCGACCGT 3 155 1 CAGCTGCAGC 0.787067 -113 AACACGCTCACGGCGGCCTCGACGGTCGCC 3 176 0 CGGCGGCCTC 0.986455 -92 GCCGAGGTCGTGGCTCCCGCGATGGCAGCG 3 210 1 TGGCTCCCGC 0.941687 -58 GCGATGGCAGCGCCGCCCGGGGTGGACCGG 3 228 1 CGCCGCCCGG 0.966593 -40 GCATGCATGAGGGCGCGCACCCGGTCCACC 3 248 0 GGGCGCGCAC 0.647309 -20 ACCGCTCGCTCGGGGCCCGGG 4 2 0 CGGGGCCCGG 0.907721 -101 CGGATTGCGTGACCGCTCGCTCGGGGCCCG 4 13 0 GACCGCTCGC 0.646903 -90 AACGATGGTCCGCCTGGGGCGTGCTGTCAA 4 46 0 CGCCTGGGGC 0.963197 -57 CGGCGGCGGCTTTCATTAAG 4 93 0 CGGCGGCGGC 0.994013 -10 GCGCCGTTACCGGCGCCGCCGCC 5 4 0 CGGCGCCGCC 0.693645 -206 GCGCCGGTAACGGCGCGCGCCGGTTCGTTT 5 18 1 CGGCGCGCGC 0.873042 -192 CGGTTCGTTTCGGCTCCAACAACTTTTGCG 5 38 1 CGGCTCCAAC 0.923812 -172 ACCCGATCGTCAGCGCGCACATGTTGCGCA 5 64 0 CAGCGCGCAC 0.682128 -146 TTCCTTAAAAGAGCTTCCGCCAACCCGATC 5 86 0 GAGCTTCCGC 0.568599 -124 AGACCTGCGACACCGTCGGCAGGGCTTTCG 5 150 0 CACCGTCGGC 0.815066 -60 CCCGCACCTCCGACCAGCTCAGCA 5 196 0 CACCTCCGAC 0.831226 -14 TCTCCGGACTCACCGGGGCGGTTCACCCAG 6 28 1 CACCGGGGCG 0.597748 -273 GGTGACGACCCGGCTGGGTGAACCGCCCCG 6 41 0 CGGCTGGGTG 0.903164 -260 GGGTCGTCACCGGCTGTCGGCGATATTGAG 6 60 1 CGGCTGTCGG 0.911851 -241 CCCATTTGCCCGGCGACATGCGGTTTTCTG 6 134 1 CGGCGACATG 0.682 -167 CTGAAGCGCGCGGCTAGCCCGGCTACGACC 6 165 0 CGGCTAGCCC 0.602039 -136 GGGGCACCTCCCTGCCAAATCCAT 6 287 0 CACCTCCCTG 0.796923 -14 ********** Masking position 4 Map Score: 56.3999 Number of sites scoring better than the average of aligned sites = 95479 Number in coding regions = 89859 Number in noncoding regions = 5620 Number of orfs with sites within 600 bp upstream = 1581 Fraction of orfs with sites within 600 bp upstream = 0.253935 Motif number 2 CCGAAAAAATGCCCGCCGCGTATC 1 1 1 CCGAAAGCCC 0.858482 -172 AAAATGCCCGCCGCGTATCGGCGCGCCTGCACGG 1 16 1 CCGCACGCGC 0.923375 -157 AGCAGACACACCGAAGAACCGAGCCCCACCAGGG 1 136 1 CCGAACGAGC 0.944825 -37 CCTACCGACAGGGCGCGCACAC 2 5 0 CCGAGGGCGC 0.944241 -18 CGCCGACGTCGGCCGCCAAACCCGGG 3 3 1 CCGATGCCGC 0.981503 -265 CATCGCGGCGCGCAGGATCTGCGCCCGGGTTTGG 3 26 0 CGCAACGCGC 0.840411 -242 GCCCAGCCGCCCGGCAAGCTCGCCGATGGACAGC 3 89 0 CCGGACCGCC 0.9522 -179 GGGCCTGTTCCGGCATTTCGGCGCCAAGGAGCAG 3 134 1 CGGCTCGCGC 0.904692 -134 ACGGCGGCCTCGACGGTCGCCAGCTGCAGCTGCT 3 163 0 CGACTGCAGC 0.419083 -105 GGCTTCGAACACGCTCACGGCGGCCTCGACGGTC 3 179 0 ACGCAGCGGC 0.708655 -89 GGTCGTGGCTCCCGCGATGGCAGCGCCGCCCGGG 3 215 1 CCCGAGCAGC 0.960695 -53 GCAGCGCCGCCCGGGGTGGACCGGGTGCGCGCCC 3 234 1 CCGGTGCCGG 0.655476 -34 CCCGGGCCCCGAGCGAGCGGTCACGCAATC 4 7 1 CCCCGGGCGG 0.703052 -96 GTCACGCAATCCGGCATTGACAGCACGCCCCAGG 4 30 1 CCGGTGCAGC 0.966321 -73 GGCGGCGGCGCCGGTAACGGCGCGCGCCGGTTCG 5 11 1 CCGGAGCGCG 0.844787 -199 ACAACTTTTGCGCAACATGTGCGCGCTGACGATC 5 56 1 CGCAAGGCGC 0.879701 -154 AAAAGAGCTTCCGCCAACCCGATCGTCAGCGCGC 5 76 0 CCGCACGATC 0.725217 -134 CCCGCACCTCCGACCAGCTCAGCACAACTTCAC 5 187 0 CCGAACCAGC 0.960249 -23 CAGAGAGTCTCCGGACTCACCGGGGCGGTTCACC 6 21 1 CCGGTACGGG 0.418292 -280 TCGCCGACAGCCGGTGACGACCCGGCTGGGTGAA 6 49 0 CCGGAGCCCG 0.573065 -252 GATATTGAGTCCGGTTTGAGCCCCAGTTGTGCCC 6 81 1 CCGGTACCCC 0.880167 -220 CCCAGTTGTGCCCCACTTGGCCCCACTTGCCACC 6 102 1 CCCCTGCCCC 0.91897 -199 ACCCATTTGCCCGGCGACATGCGGTTTTCTGAGG 6 133 1 CCGGAAGCGG 0.494884 -168 CGCGGCTAGCCCGGCTACGACCTCAGAAAACCGC 6 153 0 CCGGAGCCTC 0.947521 -148 CGTCTCTGTACCACTGAAGCGCGCGGCTAGCCCG 6 174 0 CCACAGGCGC 0.953645 -127 GGTACAGAGACGGCAAAACGCCGCTTTGATACCC 6 196 1 CGGCACCCGC 0.974257 -105 CCCCACTTTGCCCCATAACTGGGGTATCAAAGCG 6 217 0 CCCCACGGGG 0.624452 -84 AGCCACCATACCCCACAATCCCCCACTTTGCCCC 6 237 0 CCCCATCCCC 0.674219 -64 TCCATCTCACCCAAACACCTCAGCCACCATACCC 6 258 0 CCAAACCAGC 0.718613 -43 **** * * **** Masking position 1 Map Score: 47.167 Number of sites scoring better than the average of aligned sites = 46380 Number in coding regions = 43355 Number in noncoding regions = 3025 Number of orfs with sites within 600 bp upstream = 1304 Fraction of orfs with sites within 600 bp upstream = 0.209444 Motif number 3 TGCTAACCGTGCAGGCGCGCCGATACGCGG 1 26 0 GCAGGCGCGC 0.518965 -147 TGCACGGTTAGCAACCGTCGTAGCCATACG 1 43 1 GCAACCGTCG 0.779509 -130 CGGCTTCCTCCCTGGTGGGGCTCGGTTCTT 1 149 0 CCTGGTGGGG 0.790504 -24 CCTACCGACAGGGCGCGCACAC 2 6 0 ACAGGGCGCG 0.469755 -17 CCCGGGTTTGGCGGCCGACGTCGGCG 3 7 0 GCGGCCGACG 0.842991 -261 CGTCGGCCGCCAAACCCGGGCGCAGATCCT 3 17 1 CAAACCCGGG 0.842568 -251 CGCAGATCCTGCGCGCCGCGATGGATATCG 3 37 1 GCGCGCCGCG 0.771911 -231 CCTCGGTGAAGGGGCTCTCGGGGCTGTCCA 3 67 1 GGGGCTCTCG 0.317864 -201 AGCCGCCCGGCAAGCTCGCCGATGGACAGC 3 89 0 CAAGCTCGCC 0.743833 -179 AGCTTGCCGGGCGGCTGGGCATGAGCAAGT 3 103 1 GCGGCTGGGC 0.926992 -165 CTGGGCATGAGCAAGTCGGGCCTGTTCCGG 3 117 1 GCAAGTCGGG 0.927826 -151 AGGAGCAGCTGCAGCTGGCGACCGTCGAGG 3 160 1 GCAGCTGGCG 0.981856 -108 TGGCGACCGTCGAGGCCGCCGTGAGCGTGT 3 175 1 CGAGGCCGCC 0.765631 -93 GAGCGTGTTCGAAGCCGAGGTCGTGGCTCC 3 197 1 GAAGCCGAGG 0.689537 -71 GGCGGCGCTGCCATCGCGGGAGCCACGACC 3 215 0 CCATCGCGGG 0.516022 -53 CCGGTCCACCCCGGGCGGCGCTGCCATCGC 3 228 0 CCGGGCGGCG 0.970363 -40 CCGCTCGCTCGGGGCCCGGG 4 1 0 GGGGCCCGGG 0.894099 -102 GAGCGGTCACGCAATCCGGCATTGACAGCA 4 25 1 GCAATCCGGC 0.322867 -78 TAACGATGGTCCGCCTGGGGCGTGCTGTCA 4 47 0 CCGCCTGGGG 0.771186 -56 CGTGCTTAATGAAAGCCGCCGCCG 4 89 1 GAAAGCCGCC 0.602289 -14 GGAGCCGAAACGAACCGGCGCGCGCCGTTA 5 25 0 CGAACCGGCG 0.849122 -185 GATCGAAAGCCCTGCCGACGGTGTCGCAGG 5 147 1 CCTGCCGACG 0.45019 -63 CGACGGTGTCGCAGGTCTGGGATTCGTGAA 5 162 1 GCAGGTCTGG 0.767262 -48 GCACCTCCGACCAGCTCAGCACAACTTCAC 5 187 0 CCAGCTCAGC 0.627855 -23 GGCGGTTCACCCAGCCGGGTCGTCACCGGC 6 44 1 CCAGCCGGGT 0.754609 -257 CGGGTCGTCACCGGCTGTCGGCGATATTGA 6 59 1 CCGGCTGTCG 0.733701 -242 CAAGTGGGGCACAACTGGGGCTCAAACCGG 6 91 0 ACAACTGGGG 0.644007 -210 GCAAGTGGGGCCAAGTGGGGCACAACTGGG 6 102 0 CCAAGTGGGG 0.93486 -199 CAAATGGGTGGCAAGTGGGGCCAAGTGGGG 6 112 0 GCAAGTGGGG 0.942 -189 TCAGAAAACCGCATGTCGCCGGGCAAATGG 6 135 0 GCATGTCGCC 0.470305 -166 TTCTGAGGTCGTAGCCGGGCTAGCCGCGCG 6 159 1 GTAGCCGGGC 0.590519 -142 CTGTACCACTGAAGCGCGCGGCTAGCCCGG 6 173 0 GAAGCGCGCG 0.746212 -128 ACTGGGGTATCAAAGCGGCGTTTTGCCGTC 6 204 0 CAAAGCGGCG 0.816513 -97 AGTTATGGGGCAAAGTGGGGGATTGTGGGG 6 231 1 CAAAGTGGGG 0.743443 -70 ********** Masking position 7 Map Score: 36.6858 Number of sites scoring better than the average of aligned sites = 80731 Number in coding regions = 75279 Number in noncoding regions = 5452 Number of orfs with sites within 600 bp upstream = 1594 Fraction of orfs with sites within 600 bp upstream = 0.256023 Motif number 4 TGGTGGGGCTCGGTTCTTCGGTGTGTCTGC 1 137 0 CGGTTCTTCG 0.731022 -36 GCTCTCGGGGCTGTCCATCGGCGAGCTTGC 3 80 1 CTGTCCATCG 0.980937 -188 GCAGCTGCAGCTGGCGACCGTCGAGGCCGC 3 164 1 CTGGCGACCG 0.935389 -104 GGCGCGCACCCGGTCCACCCCGGGCGGCGC 3 237 0 CGGTCCACCC 0.854331 -31 ACGCCCCAGGCGGACCATCGTTAAACACGA 4 54 1 CGGACCATCG 0.973959 -49 CATGTGCGCGCTGACGATCGGGTTGGCGGA 5 71 1 CTGACGATCG 0.954488 -139 GTCGGCAGGGCTTTCGATCCTATAACAATC 5 136 0 CTTTCGATCC 0.818036 -74 CCCGCACCTCCGACCAGCTCAG 5 198 0 CGCACCTCCG 0.791194 -12 CTCACCGGGGCGGTTCACCCAGCCGGGTCG 6 36 1 CGGTTCACCC 0.938055 -265 CCGACAGCCGGTGACGACCCGGCTGGGTGA 6 50 0 GTGACGACCC 0.799175 -251 CTTGGCCCCACTTGCCACCCATTTGCCCGG 6 117 1 CTTGCCACCC 0.90808 -184 ********** Masking position 9 Map Score: 10.9336 Number of sites scoring better than the average of aligned sites = 8040 Number in coding regions = 7492 Number in noncoding regions = 548 Number of orfs with sites within 600 bp upstream = 430 Fraction of orfs with sites within 600 bp upstream = 0.0690652 Motif number 5 ACACACCGAAGAACCGAGCCCCACCAGGGA 1 141 1 GAACCGAGCC 0.982834 -32 CGGCGCGCAGGATCTGCGCCCGGGTTTGGC 3 25 0 GATCTGCGCC 0.943588 -243 GCTCGCCGATGGACAGCCCCGAGAGCCCCT 3 76 0 GGACAGCCCC 0.979808 -192 CGAAATGCCGGAACAGGCCCGACTTGCTCA 3 124 0 GAACAGGCCC 0.886408 -144 GCGCGCACCCGGTCCACCCCGGGCGGCGCT 3 236 0 GGTCCACCCC 0.901965 -32 GGGTGGACCGGGTGCGCGCCCTCATGCATG 3 247 1 GGTGCGCGCC 0.526289 -21 GAAACGAACCGGCGCGCGCCGTTACCGGCG 5 19 0 GGCGCGCGCC 0.499815 -191 TGTTGGAGCCGAAACGAACCGGCGCGCGCC 5 29 0 GAAACGAACC 0.539605 -181 CCGGCTGGGTGAACCGCCCCGGTGAGTCCG 6 32 0 GAACCGCCCC 0.994928 -269 CTGTACCACTGAAGCGCGCGGCTAGCCCGG 6 173 0 GAAGCGCGCG 0.951302 -128 ********** Masking position 9 Map Score: 11.9704 Number of sites scoring better than the average of aligned sites = 4693 Number in coding regions = 4287 Number in noncoding regions = 406 Number of orfs with sites within 600 bp upstream = 363 Fraction of orfs with sites within 600 bp upstream = 0.0583039 Motif number 6 CAAACTCTCAACCTCAACCATAGGCTTAGA 1 104 0 ACCTCAACCA 0.849219 -69 GGCGCGCAGGATCTGCGCCCGGGTTTGGCG 3 24 0 ATCTGCGCCC 0.960842 -244 GCGCGCCGTTACCGGCGCCGCCGCC 5 6 0 ACCGGCGCCG 0.916019 -204 CCTTAAAAGAGCTTCCGCCAACCCGATCGT 5 84 0 GCTTCCGCCA 0.622649 -126 CGAATCCCAGACCTGCGACACCGTCGGCAG 5 158 0 ACCTGCGACA 0.980292 -52 ACCTCCGACCAGCTCAGCACAACTTCACGA 5 185 0 AGCTCAGCAC 0.542779 -25 CCCGCACCTCCGACCAGCTCAGCAC 5 195 0 ACCTCCGACC 0.98475 -15 AGACTCTCTGATCTGAGACC 6 1 0 ATCTGAGACC 0.876534 -300 CGGACTCAATATCGCCGACAGCCGGTGACG 6 64 0 ATCGCCGACA 0.927436 -237 CACCCATTTGCCCGGCGACATGCGGTTTTC 6 132 1 CCCGGCGACA 0.811703 -169 CCCGGCTACGACCTCAGAAAACCGCATGTC 6 148 0 ACCTCAGAAA 0.842321 -153 TCACCCAAACACCTCAGCCACCATACCCCA 6 256 0 ACCTCAGCCA 0.987421 -45 TGCCAAATCCATCTCACCCAAACACCTCAG 6 269 0 ATCTCACCCA 0.729174 -32 ********** Masking position 3 Map Score: 10.0744 Number of sites scoring better than the average of aligned sites = 9626 Number in coding regions = 9023 Number in noncoding regions = 603 Number of orfs with sites within 600 bp upstream = 452 Fraction of orfs with sites within 600 bp upstream = 0.0725988 Motif number 7 ********** No masking Map Score: 2.73092e-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 8 ********** No masking Map Score: 2.73092e-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 9 ********** No masking Map Score: 2.73092e-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