AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -intrC_mtub_opreg_100.orf -g0.656 -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 = 0.656 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv0072 300 hypothetical protein Rv0072 #2 Rv0986 300 hypothetical protein Rv0986 #3 glnA1 300 glnA1 #4 Rv2563 142 hypothetical protein Rv2563 #5 ftsE 43 ftsE #6 prfB 102 prfB Motif number 1 GATATCGGTTGAGCCGCCGGTTGCCCACTG 1 46 0 GAGCCGCCGG 0.925428 -255 CTTGTGGTTGGGTGTGCAGGTGAAGGTGAG 1 82 0 GGTGTGCAGG 0.734279 -219 ACAAGGAAACGGTCCGACGGCCAAACGGAA 1 133 1 GGTCCGACGG 0.940708 -168 CGGTCGAGGTGGGGTGGCGGGATCCATTCC 1 159 0 GGGGTGGCGG 0.995195 -142 CACCTCGACCGCGGTGCCCACACCAACGAC 1 178 1 GCGGTGCCCA 0.839819 -123 AGAGGCGTTCGGGGTGGTGGTAGTCGTTGG 1 200 0 GGGGTGGTGG 0.976084 -101 CCACTAGCGGGCCGCGCCCTGACCACAAAA 1 234 1 GCCGCGCCCT 0.886634 -67 GCACTTGTGGGGCCTGGTCTTGACGTTTTG 1 259 0 GGCCTGGTCT 0.781276 -42 TTCCACTCGCGGACTGCCGGCCG 2 4 0 GGACTGCCGG 0.934625 -297 CGATCCCAGCGTCGTGGCCATTGACACCAC 2 55 0 GTCGTGGCCA 0.810208 -246 CACGACGCTGGGATCGCCGTTGCCATGGGG 2 69 1 GGATCGCCGT 0.766045 -232 CCGTTGCCATGGGGAGCTGACGCTGCCGGG 2 85 1 GGGGAGCTGA 0.753708 -216 GTTTGTTGACGGGATGCCCTTGACTTCGCT 2 128 1 GGGATGCCCT 0.736031 -173 CGCTGACCGTGGTGTGCGCGTAACCGGCCG 2 154 1 GGTGTGCGCG 0.885972 -147 TGCGCGTAACCGGCCGGTCGGGAACGCGGC 2 168 1 CGGCCGGTCG 0.429783 -133 GGTCGGGAACGCGGCGACGGATGGCGCGGT 2 183 1 GCGGCGACGG 0.891612 -118 GGCGACGGATGGCGCGGTGGCCAGGACAGT 2 195 1 GGCGCGGTGG 0.984045 -106 AGGCGTTGTTGGCGTGATGTCATCTCGATC 2 225 0 GGCGTGATGT 0.663948 -76 TTCGGCGGTAGTCTAGCCCGGATCGCTCAC 2 261 0 GTCTAGCCCG 0.586668 -40 TGGCTCCGATGGGGCGCCGGCTGGCGGCTC 3 13 0 GGGGCGCCGG 0.984405 -288 CACCGGACCGGGTTCGCTGGCTCCGATGGG 3 30 0 GGTTCGCTGG 0.912929 -271 CAGCGAACCCGGTCCGGTGTCCGGCAAGCC 3 41 1 GGTCCGGTGT 0.817229 -260 CAAGACGCTGGGCTTGCCGGACACCGGACC 3 51 0 GGCTTGCCGG 0.98758 -250 CAAGCCCAGCGTCTTGCCGGGATAGTCGGG 3 65 1 GTCTTGCCGG 0.921884 -236 CCGGGATAGTCGGGCGGCGATTTCGCCGTC 3 81 1 CGGGCGGCGA 0.767431 -220 CTGGTTATCGGGTCTGCCCGATGACGGCGA 3 103 0 GGTCTGCCCG 0.971732 -198 CGTAACCGGTGGCATGCCGAACGGGAACCT 3 131 0 GGCATGCCGA 0.829207 -170 CCCCACAATAGGGCCGGGGAGACCCGGCGT 3 177 1 GGGCCGGGGA 0.893245 -124 GGGCCGGGGAGACCCGGCGTCAGTGGTGGG 3 187 1 GACCCGGCGT 0.720558 -114 GTTACTGACCGTGCCGCCCACCACTGACGC 3 203 0 GTGCCGCCCA 0.852365 -98 CGGCTCCATAGCGTCGGCCGCGGATACAGT 3 268 1 GCGTCGGCCG 0.877642 -33 GGGTTCGCTTGGCTCGATCGCCGATGATCT 4 13 1 GGCTCGATCG 0.675915 -130 GAGGGGGTCGGTCGTGGCGGTCGAGATCAT 4 36 0 GTCGTGGCGG 0.966749 -107 GTTCGACCGAGGTGAGGGGGTCGGTCGTGG 4 49 0 GGTGAGGGGG 0.723075 -94 GGTTCGCCGAGGTTCGACCGAGGTGAGGGG 4 60 0 GGTTCGACCG 0.816037 -83 TTGCCGCGTTGGTTCGCCGAGGTTCGACCG 4 70 0 GGTTCGCCGA 0.935959 -73 AAATGATCATGGGCTGGCGTTGCCGCGTTG 4 89 0 GGGCTGGCGT 0.973075 -54 TGAGATTAGCGGGCAGGCGAAA 5 3 0 GGGCAGGCGA 0.889702 -41 CCGCTACACTGGCGTGCCGTG 5 33 1 GGCGTGCCGT 0.98503 -11 GAGCCTCTGTGTTGTGCCCGGCTGCGGCGC 6 15 1 GTTGTGCCCG 0.889303 -88 TGCGGCGCAAGGGGCTGCGAATGGGCTGGG 6 37 1 GGGGCTGCGA 0.637051 -66 GCTGCGAATGGGCTGGGCCGCAGTCGTGCG 6 50 1 GGCTGGGCCG 0.777535 -53 CTGGGCCGCAGTCGTGCGGTGCACATGACG 6 62 1 GTCGTGCGGT 0.583648 -41 ********** Masking position 6 Map Score: 61.3912 Number of sites scoring better than the average of aligned sites = 66818 Number in coding regions = 62367 Number in noncoding regions = 4451 Number of orfs with sites within 600 bp upstream = 1531 Fraction of orfs with sites within 600 bp upstream = 0.245904 Motif number 2 CACCCGGTGACCGGTGCGAAGTCC 1 3 1 CCCGGTACCG 0.986142 -298 CGGTTGAGCCGCCGGTTGCCCACTGGTCGATA 1 39 0 GCCGGTGCCA 0.816804 -262 CGGCGGCTCAACCGATATCGACAAACTCACCT 1 57 1 ACCGATTCGC 0.773005 -244 GATCCCGCCACCCCACCTCGACCGCGGTGCCC 1 165 1 CCCCACTCGC 0.914297 -136 CTACCACCACCCCGAACGCCTCTTCGACCACT 1 207 1 CCCGAAGCCC 0.940681 -94 CAGGGCGCGGCCCGCTAGTGGTCGAAGAGGCG 1 223 0 CCCGCTGTGT 0.548276 -78 CGGCCGGCAGTCCGCGAGTGGAAC 2 3 1 GCCGGCGTCG 0.938993 -298 AAAAACTAGACCAGGTGGTGTCAATGGCCACG 2 41 1 CCAGGTGTGC 0.638256 -260 CAACGGCGATCCCAGCGTCGTGGCCATTGACA 2 59 0 CCCAGCTCGG 0.72688 -242 AGCGTCAGCTCCCCATGGCAACGGCGATCCCA 2 77 0 CCCCATGCAC 0.513758 -224 AGCACCGGATCCCGGCAGCGTCAGCTCCCCAT 2 93 0 CCCGGCGCGC 0.987346 -208 TTCCCGACCGGCCGGTTACGCGCACACCACGG 2 160 0 GCCGGTACGG 0.979162 -141 CGATCACTGTCCTGGCCACCGCGCCATCCGTC 2 198 0 CCTGGCACCC 0.879621 -103 ATGACATCACGCCAACAACGCCTTCAGCTGTG 2 232 1 GCCAACACGC 0.817327 -69 CAGAGCCGCCAGCCGGCGCCCCATCG 3 5 1 GCCGCCGCCG 0.543178 -296 CGCTGGGCTTGCCGGACACCGGACCGGGTTCG 3 44 0 GCCGGAACCG 0.855695 -257 GAAATCGCCGCCCGACTATCCCGGCAAGACGC 3 73 0 CCCGACATCC 0.972278 -228 ATCGGGTCTGCCCGATGACGGCGAAATCGCCG 3 95 0 CCCGATACGC 0.788501 -206 ATCGGGCAGACCCGATAACCAGGTTCCCGTTC 3 111 1 CCCGATACCG 0.976577 -190 TCGGCATGCCACCGGTTACGATCTTGCCGACC 3 141 1 ACCGGTACGT 0.534392 -160 TTACGATCTTGCCGACCATGGCCCCACAATAG 3 156 1 GCCGACATGC 0.954397 -145 ACCACTGACGCCGGGTCTCCCCGGCCCTATTG 3 182 0 CCGGGTTCCC 0.771827 -119 TACTGACCGTGCCGCCCACCACTGACGCCGGG 3 199 0 GCCGCCACCC 0.980317 -102 CGTCAGTCAACCCCGTGTTGCGCAGACGTTAC 3 228 0 CCCCGTTTGG 0.613348 -73 ACGCTATGGAGCCGATATTGCCCGTCAGTCAA 3 250 0 GCCGATTTGC 0.823474 -51 TGGCTCGATCGCCGATGATCTCGACCGCCACG 4 22 1 GCCGATATCC 0.933795 -121 CCACGACCGACCCCCTCACCTCGGTCGAACCT 4 49 1 CCCCCTACCC 0.922052 -94 GGCGAACCAACGCGGCAACGCCAGCCCATGAT 4 82 1 CGCGGCACGC 0.922193 -61 TTTCGCCTGCCCGCTAATCTCACCGCTACAC 5 10 1 CCCGCTATCC 0.948109 -34 CTGTGTTGTGCCCGGCTGCGGCGCAAGGGGCT 6 21 1 CCCGGCGCGC 0.951459 -82 ATGTGCACCGCACGACTGCGGCCCAGCCCATT 6 56 0 CACGACGCGC 0.565416 -47 ****** *** * Masking position 2 Map Score: 47.5502 Number of sites scoring better than the average of aligned sites = 50328 Number in coding regions = 47413 Number in noncoding regions = 2915 Number of orfs with sites within 600 bp upstream = 1316 Fraction of orfs with sites within 600 bp upstream = 0.211372 Motif number 3 GGCAACCGGCGGCTCAACCGATATCGACAA 1 51 1 GGCTCAACCG 0.344922 -250 TCCATTCCGTTTGGCCGTCGGACCGTTTCC 1 137 0 TTGGCCGTCG 0.806888 -164 TGTGGGCACCGCGGTCGAGGTGGGGTGGCG 1 170 0 GCGGTCGAGG 0.927186 -131 GTTCGGGGTGGTGGTAGTCGTTGGTGTGGG 1 194 0 GTGGTAGTCG 0.914608 -107 GGTCGAAGAGGCGTTCGGGGTGGTGGTAGT 1 206 0 GCGTTCGGGG 0.833744 -95 TTGACGTTTTGTGGTCAGGGCGCGGCCCGC 1 240 0 GTGGTCAGGG 0.713466 -61 AGACCAGGTGGTGTCAATGGCCACGACGCT 2 48 1 GTGTCAATGG 0.787851 -253 TGGGATCGCCGTTGCCATGGGGAGCTGACG 2 77 1 GTTGCCATGG 0.887571 -224 GGTCGGGAACGCGGCGACGGATGGCGCGGT 2 183 1 GCGGCGACGG 0.930167 -118 GGCGACGGATGGCGCGGTGGCCAGGACAGT 2 195 1 GGCGCGGTGG 0.90885 -106 GGATATTTCGGCGGTAGTCTAGCCCGGATC 2 267 0 GCGGTAGTCT 0.663712 -34 CGGCGATTTCGCCGTCATCGGGCAGACCCG 3 95 1 GCCGTCATCG 0.899815 -206 GCCCTATTGTGGGGCCATGGTCGGCAAGAT 3 161 0 GGGGCCATGG 0.962878 -140 GGGAGACCCGGCGTCAGTGGTGGGCGGCAC 3 193 1 GCGTCAGTGG 0.967079 -108 TACTGTATCCGCGGCCGACGCTATGGAGCC 3 269 0 GCGGCCGACG 0.978515 -32 GGGGTCGGTCGTGGCGGTCGAGATCATCGG 4 33 0 GTGGCGGTCG 0.967693 -110 ATGGGCTGGCGTTGCCGCGTTGGTTCGCCG 4 81 0 GTTGCCGCGT 0.486516 -62 GAAGCTACCTGCTTCCGTGGACCCAATCAA 4 117 0 GCTTCCGTGG 0.940826 -26 GAAGCAGGTAGCTTCCGTCGC 4 132 1 GCTTCCGTCG 0.935395 -11 AGCCCCTTGCGCCGCAGCCGGGCACAACAC 6 23 0 GCCGCAGCCG 0.958292 -80 AATGGGCTGGGCCGCAGTCGTGCGGTGCAC 6 56 1 GCCGCAGTCG 0.978135 -47 ********** Masking position 1 Map Score: 26.2815 Number of sites scoring better than the average of aligned sites = 58414 Number in coding regions = 55386 Number in noncoding regions = 3028 Number of orfs with sites within 600 bp upstream = 1210 Fraction of orfs with sites within 600 bp upstream = 0.194346 Motif number 4 CCTGCACACCCAACCACAAGCTAGTCGGGAA 1 92 1 CAACCACAAC 0.85444 -209 TCCCGCCACCCCACCTCGACCGCGGTGCCCA 1 167 1 CCACCTCGAC 0.965862 -134 GTGCCCACACCAACGACTACCACCACCCCGA 1 191 1 CAACGACTAC 0.835519 -110 ACGACTACCACCACCCCGAACGCCTCTTCGA 1 203 1 CCACCCCGAC 0.984555 -98 AACGCCTCTTCGACCACTAGCGGGCCGCGCC 1 221 1 CGACCACTAC 0.962496 -80 CTCCCCATGGCAACGGCGATCCCAGCGTCGT 2 70 0 CAACGGCGAC 0.881755 -231 GGTTACGCGCACACCACGGTCAGCGAAGTCA 2 148 0 ACACCACGGC 0.96628 -153 GATGTCATCTCGATCACTGTCCTGGCCACCG 2 209 0 CGATCACTGC 0.899776 -92 TCGGAGCCAGCGAACCCGGTCCGGTGTCCGG 3 34 1 CGAACCCGGC 0.883696 -267 CGGGTCTGCCCGATGACGGCGAAATCGCCGC 3 94 0 CGATGACGGG 0.564502 -207 ACGATCTTGCCGACCATGGCCCCACAATAGG 3 158 1 CGACCATGGC 0.924598 -143 ACCGTGCCGCCCACCACTGACGCCGGGTCTC 3 195 0 CCACCACTGC 0.985465 -106 ATGATCTCGACCGCCACGACCGACCCCCTCA 4 36 1 CCGCCACGAC 0.937626 -107 ACCGACCCCCTCACCTCGGTCGAACCTCGGC 4 54 1 TCACCTCGGC 0.78453 -89 ACCAACGCGGCAACGCCAGCCCATGATCATT 4 87 1 CAACGCCAGC 0.757629 -56 GTGCACCGCACGACTGCGGCCCAGCCCATTC 6 55 0 CGACTGCGGC 0.860113 -48 CGTGCGGTGCACATGACGGTCATCTGATGCT 6 74 1 ACATGACGGC 0.671506 -29 ********* * Masking position 3 Map Score: 17.6625 Number of sites scoring better than the average of aligned sites = 15442 Number in coding regions = 14625 Number in noncoding regions = 817 Number of orfs with sites within 600 bp upstream = 587 Fraction of orfs with sites within 600 bp upstream = 0.094282 Motif number 5 TGGACTTCGCACCGGTCACCGGGTG 1 6 0 ACCGGTCACC 0.892408 -295 TCGACAAACTCACCTTCACCTGCACACCCA 1 74 1 CACCTTCACC 0.900919 -227 CGGCCGGCAGTCCGCGAGTGG 2 2 1 GGCCGGCAGT 0.748615 -299 CGGATCCCGGCAGCGTCAGCTCCCCATGGC 2 90 0 CAGCGTCAGC 0.948091 -211 ACGCGCACACCACGGTCAGCGAAGTCAAGG 2 145 0 CACGGTCAGC 0.986683 -156 ACGCCAACAACGCCTTCAGCTGTGAGCGAT 2 240 1 CGCCTTCAGC 0.969516 -61 CAGAGCCGCCAGCCGGCGCCCCA 3 4 1 AGCCGCCAGC 0.809962 -297 CGCTGGGCTTGCCGGACACCGGACCGGGTT 3 46 0 GCCGGACACC 0.721122 -255 GCGGCGATTTCGCCGTCATCGGGCAGACCC 3 94 1 CGCCGTCATC 0.964319 -207 TAACCAGGTTCCCGTTCGGCATGCCACCGG 3 126 1 CCCGTTCGGC 0.74385 -175 CGGGGAGACCCGGCGTCAGTGGTGGGCGGC 3 191 1 CGGCGTCAGT 0.87303 -110 TGGTGGGCGGCACGGTCAGTAACGTCTGCG 3 210 1 CACGGTCAGT 0.94592 -91 AGCCGATATTGCCCGTCAGTCAACCCCGTG 3 243 0 GCCCGTCAGT 0.9497 -58 CCACGACCGACCCCCTCACCTCGGTCGAAC 4 49 1 CCCCCTCACC 0.894799 -94 CGGTGCACATGACGGTCATCTGATGCTAGA 6 78 1 GACGGTCATC 0.838801 -25 ********** Masking position 7 Map Score: 16.8126 Number of sites scoring better than the average of aligned sites = 17894 Number in coding regions = 16985 Number in noncoding regions = 909 Number of orfs with sites within 600 bp upstream = 640 Fraction of orfs with sites within 600 bp upstream = 0.102795 Motif number 6 TATGGTGGACTTCGCACCGGTCACCGGGTG 1 11 0 TTCGCACCGG 0.836472 -290 TATCGACCAGTGGGCAACCGGCGGCTCAAC 1 39 1 TGGGCAACCG 0.901341 -262 GCTGGCAGACAAGGAAACGGTCCGACGGCC 1 125 1 AAGGAAACGG 0.715531 -176 GCCAAACGGAATGGATCCCGCCACCCCACC 1 152 1 ATGGATCCCG 0.911424 -149 TCAGCTCCCCATGGCAACGGCGATCCCAGC 2 75 0 ATGGCAACGG 0.885836 -226 CTGACGCTGCCGGGATCCGGTGCTGTTGTT 2 101 1 CGGGATCCGG 0.653671 -200 CCGTGGTGTGCGCGTAACCGGCCGGTCGGG 2 160 1 CGCGTAACCG 0.939523 -141 CATCCGTCGCCGCGTTCCCGACCGGCCGGT 2 176 0 CGCGTTCCCG 0.657294 -125 GATCACTGTCCTGGCCACCGCGCCATCCGT 2 199 0 CTGGCCACCG 0.768453 -102 TTCAGCTGTGAGCGATCCGGGCTAGACTAC 2 254 1 AGCGATCCGG 0.945254 -47 CATCGGAGCCAGCGAACCCGGTCCGGTGTC 3 32 1 AGCGAACCCG 0.974099 -269 CTGGGCTTGCCGGACACCGGACCGGGTTCG 3 44 0 CGGACACCGG 0.783284 -257 ACCCGATAACCAGGTTCCCGTTCGGCATGC 3 120 1 CAGGTTCCCG 0.540897 -181 GGTCGGCAAGATCGTAACCGGTGGCATGCC 3 143 0 ATCGTAACCG 0.837331 -158 GATCGAGCCAAGCGAACCCGA 4 2 0 AGCGAACCCG 0.974099 -141 ********** Masking position 8 Map Score: 19.3967 Number of sites scoring better than the average of aligned sites = 8449 Number in coding regions = 7776 Number in noncoding regions = 673 Number of orfs with sites within 600 bp upstream = 505 Fraction of orfs with sites within 600 bp upstream = 0.0811115 Motif number 7 ATATCGGTTGAGCCGCCGGTTGCCCACTGG 1 45 0 AGCCGCCGGT 0.963152 -256 CCACGTTGGTAGCCTCTGGGA 1 290 1 AGCCTCTGGG 0.987925 -11 TCAATGGCCACGACGCTGGGATCGCCGTTG 2 61 1 CGACGCTGGG 0.995156 -240 TATCCCGGCAAGACGCTGGGCTTGCCGGAC 3 59 0 AGACGCTGGG 0.995989 -242 CGCCCACCACTGACGCCGGGTCTCCCCGGC 3 189 0 TGACGCCGGG 0.980695 -112 TATCCGCGGCCGACGCTATGGAGCCGATAT 3 264 0 CGACGCTATG 0.879317 -37 ACTCGAGCCTCTGTGTTGTGCCCGG 6 6 1 AGCCTCTGTG 0.957119 -97 ********** Masking position 6 Map Score: 9.88872 Number of sites scoring better than the average of aligned sites = 1958 Number in coding regions = 1794 Number in noncoding regions = 164 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 8 ********** No masking Map Score: 1.43062e-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: 1.43062e-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 10 ********** No masking Map Score: 1.43062e-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