AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i211_transcription_translation_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 argS 300 argS #2 thrB 217 thrB #3 rho 256 rho #4 rpmE 150 rpmE Motif number 1 CACCCGCGAGGGCGGCCGCATAGTTGGCTT 1 47 0 GGCGGCCGCA 0.813309 -254 GGCCGCCCTCGCGGGTGGCGCCGATCACAT 1 60 1 GCGGGTGGCG 0.971396 -241 TTCGAATCCTGCCGGGGGCACAAGGGTTGA 1 115 0 GCCGGGGGCA 0.982844 -186 CGCCCCCGTAGCTCAGGGGATAGAGCGTCT 1 169 0 GCTCAGGGGA 0.687709 -132 CCCTGAGCTACGGGGGCGCACGACGACACG 1 181 1 CGGGGGCGCA 0.872728 -120 CGCTACTCTGGCGGGGCCCCATGGCGCAAC 1 210 0 GCGGGGCCCC 0.90534 -91 CGCCAGAGTAGCGCATCGCGGCTACCCACT 1 227 1 GCGCATCGCG 0.962868 -74 CCGTTGCGGTGGTCAGTGGGTAGCCGCGAT 1 241 0 GGTCAGTGGG 0.674149 -60 TATGGGCTGAGGTGGTTGGGCTTCGAATCC 1 269 0 GGTGGTTGGG 0.918002 -32 AACCACCTCAGCCCATAGGATGGACGTTC 1 282 1 GCCCATAGGA 0.722427 -19 TGGCGATCGCAAGCGCGGCGG 2 2 1 GGCGATCGCA 0.846457 -216 GCGATCGCAAGCGCGGCGGAGCCGGGTGCG 2 13 1 GCGCGGCGGA 0.989986 -205 GCGCGGCGGAGCCGGGTGCGGCGGGTCGGC 2 23 1 GCCGGGTGCG 0.990574 -195 GCCGGGTGCGGCGGGTCGGCACGGTTTGGA 2 33 1 GCGGGTCGGC 0.692172 -185 TGGATTGGGTGGCGATCGCAAGCGCGGCGG 2 59 1 GGCGATCGCA 0.846457 -159 GCGATCGCAAGCGCGGCGGAGCCGGGTGCG 2 70 1 GCGCGGCGGA 0.989986 -148 GCGCGGCGGAGCCGGGTGCGGCGGGTCGGC 2 80 1 GCCGGGTGCG 0.990574 -138 GCCGGGTGCGGCGGGTCGGCACGGTTTGGA 2 90 1 GCGGGTCGGC 0.692172 -128 TGGATTGGGTGGCGATCGCAAGCGCGGCGG 2 116 1 GGCGATCGCA 0.846457 -102 GCGATCGCAAGCGCGGCGGAGCCGGGTGCG 2 127 1 GCGCGGCGGA 0.989986 -91 GCGCGGCGGAGCCGGGTGCGGCGGGTCGGC 2 137 1 GCCGGGTGCG 0.990574 -81 GCCGGGTGCGGCGGGTCGGCACGGTTTGGA 2 147 1 GCGGGTCGGC 0.692172 -71 TGGATTGGGTGGCGATCGCAAGCGCGGCGG 2 173 1 GGCGATCGCA 0.846457 -45 GCGATCGCAAGCGCGGCGGAGCCGGGTGCG 2 184 1 GCGCGGCGGA 0.989986 -34 GCGCGGCGGAGCCGGGTGCGGCGGGTCGGC 2 194 1 GCCGGGTGCG 0.990574 -24 GCCGGGTGCGGCGGGTCGGCACGC 2 204 1 GCGGGTCGGC 0.692172 -14 CCGCTTCCTGGCCGGAAGCAAGCAAACCCC 3 25 0 GCCGGAAGCA 0.875246 -232 TGCTGCGATTGCTGGACGGCTCCGAGGATA 3 57 0 GCTGGACGGC 0.931754 -200 ACTTTGCAACGGTGATCGCCATCAGCGGCG 3 155 0 GGTGATCGCC 0.810902 -102 CAGCCAAATCGCCGAGTGCGCCAATCATCG 3 185 0 GCCGAGTGCG 0.97165 -72 CGGCGATTTGGCTGACTGCAACAAAACCCC 3 201 1 GCTGACTGCA 0.797254 -56 CGTGATCAGCGGGGGAAGGAAAGGAAATCC 3 237 1 GGGGGAAGGA 0.735089 -20 CGGCGAGACGGCTCGCCGGGAATGTCCGCA 4 13 1 GCTCGCCGGG 0.932096 -138 CGGTGTTTGGGGTGATAGCGGTTGACCTGG 4 50 1 GGTGATAGCG 0.715249 -101 CTCTGTGATCGGTGGCCGCCCGTCGTGGCG 4 125 0 GGTGGCCGCC 0.789926 -26 ********** Masking position 8 Map Score: 85.5422 Number of sites scoring better than the average of aligned sites = 37930 Number in coding regions = 35205 Number in noncoding regions = 2725 Number of orfs with sites within 600 bp upstream = 1244 Fraction of orfs with sites within 600 bp upstream = 0.199807 Motif number 2 TATGCGGCCGCCCTCGCGGGTGGCGCCGAT 1 55 1 CCCTCGCGGG 0.729946 -246 ACCCTTGTGCCCCCGGCAGGATTCGAACCT 1 118 1 CCCCGGCAGG 0.78435 -183 AGAGCGTCTGCCTCCGGAGCAGAAGGCCGC 1 148 0 CCTCCGGAGC 0.827403 -153 TCGTCGTGCGCCCCCGTAGCTCAGGGGATA 1 177 0 CCCCCGTAGC 0.975808 -124 TGGGGCCCCGCCAGAGTAGCGCATCGCGGC 1 219 1 CCAGAGTAGC 0.737886 -82 CCAGAGTAGCGCATCGCGGCTACCCACTGA 1 229 1 GCATCGCGGC 0.912901 -72 TACCCACTGACCACCGCAACGGATTCGAAG 1 249 1 CCACCGCAAC 0.971073 -52 CGAAGCCCAACCACCTCAGCCCATAGGATG 1 274 1 CCACCTCAGC 0.936335 -27 TGGCGATCGCAAGCGCGGCGGAGCCGGGT 2 10 1 CAAGCGCGGC 0.983927 -208 CCGTGCCGACCCGCCGCACCCGGCTCCGCC 2 27 0 CCGCCGCACC 0.987879 -191 GTGGCGATCGCAAGCGCGGCGGAGCCGGGT 2 67 1 CAAGCGCGGC 0.983927 -151 CCGTGCCGACCCGCCGCACCCGGCTCCGCC 2 84 0 CCGCCGCACC 0.987879 -134 GTGGCGATCGCAAGCGCGGCGGAGCCGGGT 2 124 1 CAAGCGCGGC 0.983927 -94 CCGTGCCGACCCGCCGCACCCGGCTCCGCC 2 141 0 CCGCCGCACC 0.987879 -77 GTGGCGATCGCAAGCGCGGCGGAGCCGGGT 2 181 1 CAAGCGCGGC 0.983927 -37 GCGTGCCGACCCGCCGCACCCGGCTCCGCC 2 198 0 CCGCCGCACC 0.987879 -20 AGCAAGCAAACCCCCGCAACCTTGCGGA 3 9 0 CCCCCGCAAC 0.969282 -248 AAGCGGGCTATCCTCGGAGCCGTCCAGCAA 3 49 1 TCCTCGGAGC 0.729872 -208 AGCCGTCCAGCAATCGCAGCATCTGCATAC 3 66 1 CAATCGCAGC 0.969434 -191 TTGGTGGCTGTCCTAGCGGCAAGGCAGTAC 3 96 0 TCCTAGCGGC 0.658421 -161 CGGTGATCGCCATCAGCGGCGAATACGGCG 3 146 0 CATCAGCGGC 0.730725 -111 TATGACGTGATCAGCGGGGGAAGGAAAGGA 3 232 1 TCAGCGGGGG 0.434269 -25 CGGTGGCCGCCCGTCGTGGCGTGCCGAGAA 4 116 0 CCGTCGTGGC 0.944643 -35 ********** Masking position 6 Map Score: 49.4601 Number of sites scoring better than the average of aligned sites = 29469 Number in coding regions = 27687 Number in noncoding regions = 1782 Number of orfs with sites within 600 bp upstream = 921 Fraction of orfs with sites within 600 bp upstream = 0.147928 Motif number 3 TTCGTGGTCTCGCTCTCAAATTCGTCGGGGTAAG 1 15 0 CGTCAAATCG 0.943916 -286 TGGCGATCGCAAGCGCGGCGGAGCCGG 2 4 1 CGGCAAGGCG 0.991084 -214 GCGATCGCCACCCAATCCAAACCGTGCCGACCCG 2 44 0 CCTCCAACCG 0.990474 -174 GATTGGGTGGCGATCGCAAGCGCGGCGGAGCCGG 2 61 1 CGGCAAGGCG 0.991084 -157 GCGATCGCCACCCAATCCAAACCGTGCCGACCCG 2 101 0 CCTCCAACCG 0.990474 -117 GATTGGGTGGCGATCGCAAGCGCGGCGGAGCCGG 2 118 1 CGGCAAGGCG 0.991084 -100 GCGATCGCCACCCAATCCAAACCGTGCCGACCCG 2 158 0 CCTCCAACCG 0.990474 -60 GATTGGGTGGCGATCGCAAGCGCGGCGGAGCCGG 2 175 1 CGGCAAGGCG 0.991084 -43 CGAGGATAGCCCGCTTCCTGGCCGGAAGCAAGCA 3 31 0 CCTCCTGCCG 0.955897 -226 ATGGCGATCACCGTTGCAAAGTCGATGATTGGCG 3 163 1 CCGCAAATCG 0.990887 -94 GTTTTGTTGCAGTCAGCCAAATCGCCGAGTGCGC 3 194 0 AGGCCAATCG 0.942499 -63 ATAGCGGTTGACCTGGCATAATCGATGCTCAACG 4 64 1 ACGCATATCG 0.737848 -87 AGAACCTGGTCCGGTTCCAACTCGTTGAGCATCG 4 86 0 CCTCCAATCG 0.987232 -65 ** ***** *** Masking position 7 Map Score: 30.3138 Number of sites scoring better than the average of aligned sites = 3459 Number in coding regions = 3283 Number in noncoding regions = 176 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 4 CGCCACCCGCGAGGGCGGCCGCATAGTTGG 1 50 0 GAGGGCGGCC 0.966627 -251 CCTCGCGGGTGGCGCCGATCACATTGTTGT 1 66 1 GGCGCCGATC 0.943718 -235 CCTGAGCTACGGGGGCGCACGACGACACGT 1 182 1 GGGGGCGCAC 0.900766 -119 AGTAGCGCATCGCGGCTACCCACTGACCAC 1 233 1 CGCGGCTACC 0.585668 -68 GCTCCGCCGCGCTTGCGATCGCCA 2 5 0 GCTTGCGATC 0.921119 -213 CGGCGGAGCCGGGTGCGGCGGGTCGGCACG 2 26 1 GGGTGCGGCG 0.969838 -192 CAATCCAAACCGTGCCGACCCGCCGCACCC 2 36 0 CGTGCCGACC 0.96837 -182 GTTTGGATTGGGTGGCGATCGCAAGCGCGG 2 56 1 GGTGGCGATC 0.950462 -162 CGGCGGAGCCGGGTGCGGCGGGTCGGCACG 2 83 1 GGGTGCGGCG 0.969838 -135 CAATCCAAACCGTGCCGACCCGCCGCACCC 2 93 0 CGTGCCGACC 0.96837 -125 GTTTGGATTGGGTGGCGATCGCAAGCGCGG 2 113 1 GGTGGCGATC 0.950462 -105 CGGCGGAGCCGGGTGCGGCGGGTCGGCACG 2 140 1 GGGTGCGGCG 0.969838 -78 CAATCCAAACCGTGCCGACCCGCCGCACCC 2 150 0 CGTGCCGACC 0.96837 -68 GTTTGGATTGGGTGGCGATCGCAAGCGCGG 2 170 1 GGTGGCGATC 0.950462 -48 CGGCGGAGCCGGGTGCGGCGGGTCGGCACG 2 197 1 GGGTGCGGCG 0.969838 -21 GCGTGCCGACCCGCCGCACCC 2 207 0 CGTGCCGACC 0.96837 -11 CGGCCAGGAAGCGGGCTATCCTCGGAGCCG 3 41 1 GCGGGCTATC 0.877308 -216 AAGAAGAATTGGTGGCTGTCCTAGCGGCAA 3 104 0 GGTGGCTGTC 0.907248 -153 ATTCGCCGCTGATGGCGATCACCGTTGCAA 3 152 1 GATGGCGATC 0.917343 -105 GACATTCCCGGCGAGCCGTCTCGCCGGA 4 9 0 GCGAGCCGTC 0.331978 -142 ACACCGAGATGCGTGCGGACATTCCCGGCG 4 26 0 GCGTGCGGAC 0.824037 -125 CTCTGTGATCGGTGGCCGCCCGTCGTGGCG 4 125 0 GGTGGCCGCC 0.512034 -26 ********** Masking position 6 Map Score: 52.7803 Number of sites scoring better than the average of aligned sites = 20706 Number in coding regions = 19497 Number in noncoding regions = 1209 Number of orfs with sites within 600 bp upstream = 773 Fraction of orfs with sites within 600 bp upstream = 0.124157 Motif number 5 GAGGGCGGCCGCATAGTTGGCTTCGTGGTC 1 40 0 GCATAGTTGG 0.914081 -261 TGCCGGGGGCACAAGGGTTGATCTAGCCTC 1 106 0 ACAAGGGTTG 0.892236 -195 CGGCGGGTCGGCACGGTTTGGATTGGGTGG 2 41 1 GCACGGTTTG 0.996964 -177 CGGCGGGTCGGCACGGTTTGGATTGGGTGG 2 98 1 GCACGGTTTG 0.996964 -120 CGGCGGGTCGGCACGGTTTGGATTGGGTGG 2 155 1 GCACGGTTTG 0.996964 -63 TCCGCAAGGTTGCGGGGGTTTGC 3 4 1 GCAAGGTTGC 0.936932 -253 ********** Masking position 3 Map Score: 8.36175 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 221 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 6 GGCTACAACAATGTGATCGGCGCCACCCGC 1 70 0 ATGTGATCGG 0.512849 -231 TTCGAACCTGCGGCCTTCTGCTCCGGAGGC 1 139 1 CGGCCTTCTG 0.506647 -162 GAATCCGTTGCGGTGGTCAGTGGGTAGCCG 1 245 0 CGGTGGTCAG 0.556929 -56 CTATGGGCTGAGGTGGTTGGGCTTCGAATC 1 270 0 AGGTGGTTGG 0.423473 -31 TGGCGATCGCAAGCGCGGCG 2 1 1 TGGCGATCGC 0.948008 -217 CGCGGCGGAGCCGGGTGCGGCGGGTCGGCA 2 24 1 CCGGGTGCGG 0.953066 -194 TTGGATTGGGTGGCGATCGCAAGCGCGGCG 2 58 1 TGGCGATCGC 0.948008 -160 CGCGGCGGAGCCGGGTGCGGCGGGTCGGCA 2 81 1 CCGGGTGCGG 0.953066 -137 TTGGATTGGGTGGCGATCGCAAGCGCGGCG 2 115 1 TGGCGATCGC 0.948008 -103 CGCGGCGGAGCCGGGTGCGGCGGGTCGGCA 2 138 1 CCGGGTGCGG 0.953066 -80 TTGGATTGGGTGGCGATCGCAAGCGCGGCG 2 172 1 TGGCGATCGC 0.948008 -46 CGCGGCGGAGCCGGGTGCGGCGGGTCGGCA 2 195 1 CCGGGTGCGG 0.953066 -23 GCAAGGTTGCGGGGGTTTGCTTGCTTCCGG 3 14 1 GGGGGTTTGC 0.738416 -243 TGGACGGCTCCGAGGATAGCCCGCTTCCTG 3 45 0 CGAGGATAGC 0.509636 -212 TATGCAGATGCTGCGATTGCTGGACGGCTC 3 65 0 CTGCGATTGC 0.81489 -192 TTCTTGTGGACGAGGTTCGCCGTATTCGCC 3 129 1 CGAGGTTCGC 0.947157 -128 GACTTTGCAACGGTGATCGCCATCAGCGGC 3 156 0 CGGTGATCGC 0.985843 -101 GTTGCAAAGTCGATGATTGGCGCACTCGGC 3 175 1 CGATGATTGG 0.785397 -82 TTGGCGCACTCGGCGATTTGGCTGACTGCA 3 191 1 CGGCGATTTG 0.861035 -66 TCACGTCATACGGGGTTTTGTTGCAGTCAG 3 212 0 CGGGGTTTTG 0.878336 -45 GCACGCATCTCGGTGTTTGGGGTGATAGCG 4 40 1 CGGTGTTTGG 0.960374 -111 TGGAACCGGACCAGGTTCTCGGCACGCCAC 4 101 1 CCAGGTTCTC 0.470721 -50 GCTGCCCTCTGTGATCGGTGGCCGCCCG 4 133 0 CTGTGATCGG 0.923303 -18 ********** Masking position 5 Map Score: 33.4911 Number of sites scoring better than the average of aligned sites = 25082 Number in coding regions = 23334 Number in noncoding regions = 1748 Number of orfs with sites within 600 bp upstream = 971 Fraction of orfs with sites within 600 bp upstream = 0.155959 Motif number 7 ********** No masking Map Score: 1.58751e-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 8 ********** No masking Map Score: 1.58751e-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 9 ********** No masking Map Score: 1.58751e-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