AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -icpxR9_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 senX3 173 senX3 #2 regX3 227 regX3 #3 tcrA 56 tcrA #4 phoP 141 phoP #5 phoR 44 phoR #6 Rv0903c 130 hypothetical protein Rv0903c #7 Rv0981 300 hypothetical protein Rv0981 #8 Rv0983 43 hypothetical protein Rv0983 #9 Rv1033c 181 hypothetical protein Rv1033c #10 Rv1222 157 hypothetical protein Rv1222 #11 Rv2723 25 hypothetical protein Rv2723 #12 mtrB 49 mtrB #13 mtrA 69 mtrA #14 tmk 96 tmk #15 sahH 104 sahH #16 Rv3764c 70 hypothetical protein Rv3764c #17 Rv3765c 300 hypothetical protein Rv3765c Motif number 1 GTTTGAGATCCCACCTGCCGGCGGTTTCGG 1 13 1 CCACCTGCCG 0.851495 -161 AAGCACACCATCAGCCGCCGAAACCGCCGG 1 30 0 TCAGCCGCCG 0.984883 -144 CGGTGAACGTCGCCCTAGCGCGGCAAGGCC 1 135 0 CGCCCTAGCG 0.55925 -39 CCTGCGCCGACGACGATGCAGA 2 3 1 TGCGCCGACG 0.990459 -225 AAGCGGGTGGTGCCCCCACCTCATCGCTAC 2 35 0 TGCCCCCACC 0.657918 -193 GCCACTCTCCCCCGCAAGCGGGTGGTGCCC 2 50 0 CCCGCAAGCG 0.943049 -178 GCTGATGACCTGCGCCGACGACGATGCAGA 2 80 1 TGCGCCGACG 0.990459 -148 AAGCGGGTGGTGCCCCCACCTCATCGCTAC 2 112 0 TGCCCCCACC 0.657918 -116 GCCACTCTCCCCCGCAAGCGGGTGGTGCCC 2 127 0 CCCGCAAGCG 0.943049 -101 GCTGATGACCTGCGCCGACGACGATGCAGA 2 157 1 TGCGCCGACG 0.990459 -71 AAGCGGGTGGTGCCCCCACCTCATCGCTAC 2 189 0 TGCCCCCACC 0.657918 -39 GCCACTCTCCCCCGCAAGCGGGTGGTGCCC 2 204 0 CCCGCAAGCG 0.943049 -24 TACCGTCGGAGCCGCACACCGTCACAGCGA 3 34 0 GCCGCACACC 0.753241 -23 GCGTTCTCCTCGGGCTGCCGATCCGATTAA 5 21 0 CGGGCTGCCG 0.912021 -24 CCCGCGCGCACCCCGCGAGCAGAC 6 5 1 CGCGCACCCC 0.891974 -126 GCGCACCCCGCGAGCAGACACAGAGTCGCA 6 16 1 CGAGCAGACA 0.855632 -115 GCGTGCTGGGCGAGCAGACACAGAGTCGCA 6 64 0 CGAGCAGACA 0.855632 -67 GTCTGCTCGCCCAGCACGCGACCCGGCGGC 6 75 1 CCAGCACGCG 0.962267 -56 GGTGGGAGGGTGAGCCGCCGGGTCGCGTGC 6 88 0 TGAGCCGCCG 0.987711 -43 TTTGTGCCTGCGCCCAGGCGTGGAACGGCA 7 37 0 CGCCCAGGCG 0.686146 -264 TCATCGTGTGTCAGCAGGCGAAACCCGCGC 7 118 1 TCAGCAGGCG 0.966309 -183 AGGCGAAACCCGCGCGGACGAGAACTCTTC 7 133 1 CGCGCGGACG 0.942269 -168 CACACCCATGCCAGTCCACGC 8 33 1 CCAGTCCACG 0.65029 -11 CCGGGTATACGGAGCCCCCGGTGGACCGG 9 10 0 GGAGCCCCCG 0.955178 -172 CCTGAAAAGGTGACCGGGCGGGATGTCGGG 9 70 0 TGACCGGGCG 0.726828 -112 ACCGACGCGCTCGGCGGCCGTTGAGTAGT 10 10 0 TCGGCGGCCG 0.855353 -148 ATGCGGTAGCCGAACCGACGCGCTCGGCGG 10 23 0 CGAACCGACG 0.739555 -135 TGGGGTTTTACCGGCTGGCGATGGTTTTCC 10 76 1 CCGGCTGGCG 0.871284 -82 CGCCACCTAGCGAGCCACCGGTATCTCGAA 10 125 0 CGAGCCACCG 0.961474 -33 TCCGCGCCGGCGACGATGCAGA 12 3 1 CGCGCCGGCG 0.972396 -47 CAAAACTGGCGCACCACACGGGCGTTTCTT 13 32 0 GCACCACACG 0.60157 -38 CTCCCACCCGCGAGCAGACGCAAAATCGCC 14 15 1 CGAGCAGACG 0.987354 -82 GGTGGCGGCGCGAGCAGACGCAAAATCGCC 14 63 0 CGAGCAGACG 0.987354 -34 GTCTGCTCGCGCCGCCACCGACAGGGCCGC 14 74 1 GCCGCCACCG 0.917917 -23 GGCGCGGCCCTGTCGGTGGC 14 87 0 GGCGCGGCCC 0.816359 -10 AGTCACTGTAGCCGCCGTCGGTCAGCCCCG 15 15 0 GCCGCCGTCG 0.812346 -90 CGGATCCCTGTGAGCCCCCAAAGAAGGATG 15 76 1 TGAGCCCCCA 0.691371 -29 CCGACCAGGAGCCGCAGCCGAAGCGACCAA 16 23 0 GCCGCAGCCG 0.980743 -48 CCGGGTCGGCGACTTCCACAA 17 2 1 CGGGTCGGCG 0.651149 -299 TTGGTCGCTCTCCGTCGCCGTTGTGGAAGT 17 22 0 TCCGTCGCCG 0.847836 -279 TGAAGCAAATCCCGCTGCCACGCTTGAGGC 17 73 0 CCCGCTGCCA 0.788982 -228 GGGATTTGCTTCAGCAGCCCGGTCGCCAGC 17 90 1 TCAGCAGCCC 0.898653 -211 AGCCCGGTCGCCAGCAGCCGCTACTGGTAC 17 105 1 CCAGCAGCCG 0.989257 -196 TACCAACATGCGCGCCGACGTGAGTGGGGT 17 132 1 CGCGCCGACG 0.995835 -169 TCGGAGCCTGCCAGCGGGCCGGATCCGGGC 17 165 0 CCAGCGGGCC 0.881551 -136 CGCACACGGCTGAGCAGACGCCATGCGGAT 17 232 0 TGAGCAGACG 0.970263 -69 GCGTCAAGTATCCGCACACGGCTGAGCAGA 17 244 0 TCCGCACACG 0.94801 -57 ********** Masking position 9 Map Score: 87.9985 Number of sites scoring better than the average of aligned sites = 52954 Number in coding regions = 49553 Number in noncoding regions = 3401 Number of orfs with sites within 600 bp upstream = 1352 Fraction of orfs with sites within 600 bp upstream = 0.217154 Motif number 2 TGATGGTGTGCTTTGGTGCGCTGTTTGCCAA 1 47 1 CTTGGTGCGC 0.667235 -127 CCGATTTTGGCCTTGCCGCGCTAGGGCGACG 1 127 1 CCTGCCGCGC 0.97134 -47 GCGCCGACGACGATGCAGAGCGTAGCGATGA 2 14 1 CGAGCAGAGC 0.967163 -214 CCCCGCAAGCGGGTGGTGCCCCCACCTCATC 2 40 0 GGGGGTGCCC 0.963158 -188 CACCCGCTTGCGGGGGAGAGTGGCGCTGATG 2 56 1 CGGGGAGAGT 0.95058 -172 GCATCGTCGTCGGCGCAGGTCATCAGCGCCA 2 76 0 CGGGCAGGTC 0.818975 -152 GCGCCGACGACGATGCAGAGCGTAGCGATGA 2 91 1 CGAGCAGAGC 0.967163 -137 CCCCGCAAGCGGGTGGTGCCCCCACCTCATC 2 117 0 GGGGGTGCCC 0.963158 -111 CACCCGCTTGCGGGGGAGAGTGGCGCTGATG 2 133 1 CGGGGAGAGT 0.95058 -95 GCATCGTCGTCGGCGCAGGTCATCAGCGCCA 2 153 0 CGGGCAGGTC 0.818975 -75 GCGCCGACGACGATGCAGAGCGTAGCGATGA 2 168 1 CGAGCAGAGC 0.967163 -60 CCCCGCAAGCGGGTGGTGCCCCCACCTCATC 2 194 0 GGGGGTGCCC 0.963158 -34 CACCCGCTTGCGGGGGAGAGTGGCGCTG 2 210 1 CGGGGAGAGT 0.95058 -18 CCCTACCGTCGGAGCCGCACACCGTCACAG 3 37 0 CGGGCCGCAC 0.980881 -20 GCCGCTCAATCCACGGCGCGCCGTGAATACA 4 19 0 CCAGGCGCGC 0.961669 -123 CAGCTTGGACCGTTGCCGCTCAATCCACGGC 4 33 0 CGTGCCGCTC 0.897786 -109 TTTGGCGATTCCTGGCAGACTGTTAGCAGAC 4 65 1 CCTGCAGACT 0.397517 -77 GATCGGCAGCCCGAGGAGAACGCGGCA 5 28 1 CCGGGAGAAC 0.851301 -17 GTGTCTGCTCGCGGGGTGCGCGCGGG 6 6 0 GCGGGTGCGC 0.963532 -125 CCGCCGGGTCGCGTGCTGGGCGAGCAGACAC 6 73 0 GCGGCTGGGC 0.848423 -58 CAGCAGGGTGGGAGGGTGAGCCGCCGGGTCG 6 93 0 GGAGGTGAGC 0.891082 -38 ACTGCACCTGGGGTTCTGCCCTCATCGTGTG 7 97 1 GGGTCTGCCC 0.761077 -204 GAAACCCGCGCGGACGAGAACTCTTCCGCCA 7 137 1 CGGCGAGAAC 0.66929 -164 AACTCTTCCGCCAAGCAGCACAAATCGCCCT 7 155 1 CCAGCAGCAC 0.748459 -146 AACCCGCATACCACGGCGCGCCTCTCAGGCC 7 255 1 CCAGGCGCGC 0.961669 -46 CAGTGTCGTCGCAGCGCCTGAGACTGG 7 284 0 CGTGCAGCGC 0.954356 -17 TGTCGGGCTTCGGCGGTGAGAAAGCGGATCT 9 46 0 CGGGGTGAGA 0.671433 -136 TACTCAACGGCCGCCGAGCGCGTCGGTTCGG 10 13 1 CCGCGAGCGC 0.923868 -145 GCAACCATGCGGTAGCCGAACCGACGCGCTC 10 28 0 GGTGCCGAAC 0.676148 -130 GGTTGCCAATCGGTCCCGAATCCTGGGGTTT 10 53 1 CGGCCCGAAT 0.354807 -105 TTTTCCGGCACCGCGCCGCGCTACATTCGAG 10 100 1 CCGGCCGCGC 0.616121 -58 TTCGAGATACCGGTGGCTCGCTAGGTGGCGG 10 125 1 CGGGGCTCGC 0.864797 -33 GCGCCGGCGACGATGCAGAGCGCAGCGATGC 12 14 1 CGAGCAGAGC 0.967163 -36 CGGCGCCGCTCCTTAGCATCG 12 39 0 CGGGCCGCTC 0.940953 -11 AGAAACGCCCGTGTGGTGCGCCAGTTTTGTC 13 33 1 GTGGGTGCGC 0.744555 -37 CCTGTCGGTGGCGGCGCGAGCAGACGCAAAA 14 68 0 GCGCGCGAGC 0.767855 -29 CCGCCACCGACAGGGCCGCGCC 14 85 1 CAGGCCGCGC 0.905629 -12 CCTGCGGGGCTGACCGACGGCGGCT 15 5 1 CGGGCTGACC 0.974638 -100 GGGGCTCACAGGGATCCGAGCGGGCTACTTA 15 63 0 GGGTCCGAGC 0.851086 -42 TTGGTCGCTTCGGCTGCGGCTCCTGGTCGGA 16 23 1 CGGTGCGGCT 0.355147 -48 AGGACGACAACCTGTCCGACCAGGAGCCGCA 16 37 0 CCTTCCGACC 0.430776 -34 CCGGGTCGGCGACTTCCACAACGG 17 4 1 GGTGGCGACT 0.452847 -297 TCCACAACGGCGACGGAGAGCGACCAATTGG 17 25 1 CGAGGAGAGC 0.965787 -276 CGTTGGTCCGGGACGCTGCCTCAAGCGTGGC 17 56 1 GGAGCTGCCT 0.516791 -245 CTGCCTCAAGCGTGGCAGCGGGATTTGCTTC 17 71 1 CGTGCAGCGG 0.652752 -230 ACCCCACTCACGTCGGCGCGCATGTTGGTAC 17 131 0 CGTGGCGCGC 0.80729 -170 GCCAGCGGGCCGGATCCGGGCGGTACCCCAC 17 155 0 CGGTCCGGGC 0.90547 -146 TGGCAGGCTCCGAACGTGCCCCAAATCGGGT 17 182 1 CGACGTGCCC 0.709837 -119 CCATGCGGATCCTATGTGCGCGCTATGAAAC 17 211 0 CCTTGTGCGC 0.681055 -90 AACCGAGATGCGGTGCTGCGTCACAGCGTCA 17 268 0 CGGGCTGCGT 0.972362 -33 CACCGCATCTCGGTTGAGCGTGTCGTA 17 284 1 CGGTGAGCGT 0.82227 -17 *** ******* Masking position 8 Map Score: 82.6688 Number of sites scoring better than the average of aligned sites = 51164 Number in coding regions = 47674 Number in noncoding regions = 3490 Number of orfs with sites within 600 bp upstream = 1336 Fraction of orfs with sites within 600 bp upstream = 0.214584 Motif number 3 TCACACACTACGCCACAGCTGTTCGGTTAC 1 92 0 CGCCACAGCT 0.890658 -82 GCCCCCACCTCATCGCTACGCTCTGCATCG 2 24 0 CATCGCTACG 0.826929 -204 CGCAGGTCATCAGCGCCACTCTCCCCCGCA 2 64 0 CAGCGCCACT 0.937597 -164 GCATCGTCGTCGGCGCAGGTCATCAGCGCC 2 77 0 CGGCGCAGGT 0.826076 -151 GCCCCCACCTCATCGCTACGCTCTGCATCG 2 101 0 CATCGCTACG 0.826929 -127 CGCAGGTCATCAGCGCCACTCTCCCCCGCA 2 141 0 CAGCGCCACT 0.937597 -87 GCATCGTCGTCGGCGCAGGTCATCAGCGCC 2 154 0 CGGCGCAGGT 0.826076 -74 GCCCCCACCTCATCGCTACGCTCTGCATCG 2 178 0 CATCGCTACG 0.826929 -50 CAGCGCCACTCTCCCCCGCA 2 218 0 CAGCGCCACT 0.937597 -10 AGCCGCACACCGTCACAGCGAGGTAGACAG 3 25 0 CGTCACAGCG 0.942278 -32 AGTGTATTCACGGCGCGCCGTGGATTGAGC 4 17 1 CGGCGCGCCG 0.495053 -125 CAGCTTGGACCGTTGCCGCTCAATCCACGG 4 34 0 CGTTGCCGCT 0.707273 -108 CCGCATACCACGGCGCGCCTCTCAGGCCAG 7 258 1 CGGCGCGCCT 0.761915 -43 CAGTGTCGTCGCAGCGCCTGAGACTG 7 285 0 CGTCGCAGCG 0.764007 -16 GATGGTTTTCCGGCACCGCGCCGCGCTACA 10 95 1 CGGCACCGCG 0.97792 -63 CACCACCTCCTTCCGCCACC 10 148 0 CACCACCTCC 0.243142 -10 TCTGCATCGTCGCCGGCGCGGA 12 3 0 CGCCGGCGCG 0.905766 -47 CGCTCCTTAGCATCGCTGCGCTCTGCATCG 12 24 0 CATCGCTGCG 0.943199 -26 CGGCGCCGCTCCTTAGCATC 12 40 0 CGGCGCCGCT 0.987821 -10 GGTGTCACCACATCGGGACAAAACT 13 55 0 CACCACATCG 0.510527 -15 CGTCTGCTCGCGCCGCCACCGACAGGGCCG 14 73 1 CGCCGCCACC 0.855892 -24 CCGCCACCGACAGGGCCGCGCC 14 85 1 CAGGGCCGCG 0.857961 -12 ACACACCACGGCGAGGACGACAA 16 58 0 CACCACGGCG 0.81434 -13 GGTCGCTCTCCGTCGCCGTTGTGGAAGTCG 17 20 0 CGTCGCCGTT 0.714244 -281 CTGCCTCAAGCGTGGCAGCGGGATTTGCTT 17 71 1 CGTGGCAGCG 0.559849 -230 ACCCCACTCACGTCGGCGCGCATGTTGGTA 17 132 0 CGTCGGCGCG 0.926352 -169 TGCGGTGCTGCGTCACAGCGTCAAGTATCC 17 261 0 CGTCACAGCG 0.942278 -40 TGTGACGCAGCACCGCATCTCGGTTGAGCG 17 274 1 CACCGCATCT 0.692416 -27 ********** Masking position 1 Map Score: 47.5901 Number of sites scoring better than the average of aligned sites = 29160 Number in coding regions = 27197 Number in noncoding regions = 1963 Number of orfs with sites within 600 bp upstream = 959 Fraction of orfs with sites within 600 bp upstream = 0.154031 Motif number 4 CCGCCGAAACCGCCGGCAGGTGGGATCTCA 1 16 0 CGCCGGCAGG 0.90004 -158 TTTTGGCCTTGCCGCGCTAGGGCGACGTTC 1 131 1 GCCGCGCTAG 0.412672 -43 TGCATCGTCGTCGGCGCAGG 2 1 0 TCGGCGCAGG 0.704011 -227 GCGCCACTCTCCCCCGCAAGCGGGTGGTGC 2 52 0 CCCCCGCAAG 0.917854 -176 TGCATCGTCGTCGGCGCAGGTCATCAGCGC 2 78 0 TCGGCGCAGG 0.704011 -150 GCGCCACTCTCCCCCGCAAGCGGGTGGTGC 2 129 0 CCCCCGCAAG 0.917854 -99 TGCATCGTCGTCGGCGCAGGTCATCAGCGC 2 155 0 TCGGCGCAGG 0.704011 -73 GCGCCACTCTCCCCCGCAAGCGGGTGGTGC 2 206 0 CCCCCGCAAG 0.917854 -22 GGATCGGCAGCCCGAGGAGAACGCGGCA 5 27 1 CCCGAGGAGA 0.6074 -18 GCTCGCGGGGTGCGCGCGGG 6 1 0 TGCGCGCGGG 0.614985 -130 GCGCGCACCCCGCGAGCAGACACAGAGTCG 6 14 1 CGCGAGCAGA 0.968721 -117 TCGCGTGCTGGGCGAGCAGACACAGAGTCG 6 66 0 GGCGAGCAGA 0.945854 -65 CCTGATTACCGTCCAGCAGGGTGGGAGGGT 6 107 0 GTCCAGCAGG 0.716256 -24 GTTCCACGCCTGGGCGCAGGCACAAACCGC 7 41 1 TGGGCGCAGG 0.933356 -260 CCTCATCGTGTGTCAGCAGGCGAAACCCGC 7 116 1 TGTCAGCAGG 0.708865 -185 GCAGGCGAAACCCGCGCGGACGAGAACTCT 7 131 1 CCCGCGCGGA 0.496364 -170 CTCAACGGCCGCCGAGCGCGTCGGTTCGGC 10 15 1 GCCGAGCGCG 0.662405 -143 GGAAAACCATCGCCAGCCGGTAAAACCCCA 10 76 0 CGCCAGCCGG 0.930043 -82 TGCATCGTCGCCGGCGCGGA 12 1 0 CCGGCGCGGA 0.48955 -49 GCCTCCCACCCGCGAGCAGACGCAAAATCG 14 13 1 CGCGAGCAGA 0.968721 -84 TCGGTGGCGGCGCGAGCAGACGCAAAATCG 14 65 0 CGCGAGCAGA 0.968721 -32 CCGTCGGTCAGCCCCGCAGG 15 1 0 GCCCCGCAGG 0.969088 -104 CTCACAGGGATCCGAGCGGGCTACTTAGCC 15 60 0 TCCGAGCGGG 0.838294 -45 CGACCAGGAGCCGCAGCCGAAGCGACCAAA 16 22 0 CCGCAGCCGA 0.610869 -49 CGACAACCTGTCCGACCAGGAGCCGCAGCC 16 34 0 TCCGACCAGG 0.730432 -37 GCCTCAAGCGTGGCAGCGGGATTTGCTTCA 17 73 1 TGGCAGCGGG 0.877093 -228 GCAGCCCGGTCGCCAGCAGCCGCTACTGGT 17 103 1 CGCCAGCAGC 0.817611 -198 CACTCACGTCGGCGCGCATGTTGGTACCAG 17 128 0 GGCGCGCATG 0.730295 -173 GTTCGGAGCCTGCCAGCGGGCCGGATCCGG 17 167 0 TGCCAGCGGG 0.954279 -134 TCCGCACACGGCTGAGCAGACGCCATGCGG 17 234 0 GCTGAGCAGA 0.587888 -67 ********** Masking position 6 Map Score: 52.656 Number of sites scoring better than the average of aligned sites = 16843 Number in coding regions = 15510 Number in noncoding regions = 1333 Number of orfs with sites within 600 bp upstream = 782 Fraction of orfs with sites within 600 bp upstream = 0.125602 Motif number 5 CCCACCTGCCGGCGGTTTCGGCGGCTGATG 1 22 1 GGCGGTTTCG 0.909851 -152 GTGTGACTTGTCCGATTTTGGCCTTGCCGC 1 116 1 TCCGATTTTG 0.820852 -58 GCGACGTTCACCGGATTTGTAGGATTTTCC 1 152 1 CCGGATTTGT 0.677328 -22 AACGGTCCAAGCTGATTTGGCGATTCCTGG 4 50 1 GCTGATTTGG 0.899338 -92 CATCAAAACCGCCGATTTTGTGCGACTCTG 6 36 0 GCCGATTTTG 0.97711 -95 CCAATGTTGGTGCGGTTTGTGCCTGCGCCC 7 52 0 TGCGGTTTGT 0.507508 -249 TCTCGTCCGCGCGGGTTTCGCCTGCTGACA 7 126 0 GCGGGTTTCG 0.890688 -175 TCAAGAGTAGGGCGATTTGTGCTGCTTGGC 7 164 0 GGCGATTTGT 0.914901 -137 CGTCCATGGGGCCAATGTGGCTGATGTGGC 7 209 1 GCCAATGTGG 0.909283 -92 GCCGTGGTATGCGGGTTTGTTCGACGAGGT 7 242 0 GCGGGTTTGT 0.885721 -59 AGCAAGAAACGCCCGTGTGGTGCGCCAGTT 13 29 1 GCCCGTGTGG 0.840019 -41 CGTGTGGTGCGCCAGTTTTGTCCCGATGTG 13 42 1 GCCAGTTTTG 0.844953 -28 CCAGTTTTGTCCCGATGTGGTGACACC 13 53 1 CCCGATGTGG 0.944299 -17 CATGAAAATGGGCGATTTTGCGTCTGCTCG 14 25 0 GGCGATTTTG 0.943809 -72 TGACGAAAAGGGCGATTTTGCGTCTGCTCG 14 53 1 GGCGATTTTG 0.943809 -44 CAGTCCGCGAATTTGGTCGCTTCGGC 16 7 1 GCGAATTTGG 0.869534 -64 GCTCTCCGTCGCCGTTGTGGAAGTCGCCGA 17 16 0 GCCGTTGTGG 0.890367 -285 CGCTATGAAACCCGATTTGGGGCACGTTCG 17 192 0 CCCGATTTGG 0.972574 -109 ********** Masking position 6 Map Score: 21.4812 Number of sites scoring better than the average of aligned sites = 6219 Number in coding regions = 5833 Number in noncoding regions = 386 Number of orfs with sites within 600 bp upstream = 310 Fraction of orfs with sites within 600 bp upstream = 0.0497912 Motif number 6 TTTGGCAAACAGCGCACCAAAGCACACCAT 1 49 0 AGCGCACCAA 0.938462 -125 ACGTCGCCCTAGCGCGGCAAGGCCAAAATC 1 129 0 AGCGCGGCAA 0.973146 -45 GACGATGCAGAGCGTAGCGATGAGGTGGGG 2 22 1 AGCGTAGCGA 0.988337 -206 GACGATGCAGAGCGTAGCGATGAGGTGGGG 2 99 1 AGCGTAGCGA 0.988337 -129 GACGATGCAGAGCGTAGCGATGAGGTGGGG 2 176 1 AGCGTAGCGA 0.988337 -52 GCCAGTCTCAGGCGCTGCGACGACACTG 7 283 1 GGCGCTGCGA 0.898952 -18 TCTCGAATGTAGCGCGGCGCGGTGCCGGAA 10 102 0 AGCGCGGCGC 0.971654 -56 GACGATGCAGAGCGCAGCGATGCTAAGGAG 12 22 1 AGCGCAGCGA 0.992681 -28 CCCTGTCGGTGGCGGCGCGAGCAGACGCAA 14 70 0 GGCGGCGCGA 0.895671 -27 TGACTGCAAGAGCGTACCTAGGCTAAGTAG 15 40 1 AGCGTACCTA 0.790398 -65 CGCTTGAGGCAGCGTCCCGGACCAACGCCA 17 53 0 AGCGTCCCGG 0.931886 -248 CGCTGCCTCAAGCGTGGCAGCGGGATTTGC 17 69 1 AGCGTGGCAG 0.919549 -232 GGTACCAACATGCGCGCCGACGTGAGTGGG 17 130 1 TGCGCGCCGA 0.922519 -171 GGAGCCTGCCAGCGGGCCGGATCCGGGCGG 17 163 0 AGCGGGCCGG 0.948347 -138 ********** Masking position 3 Map Score: 25.8643 Number of sites scoring better than the average of aligned sites = 3103 Number in coding regions = 2801 Number in noncoding regions = 302 Number of orfs with sites within 600 bp upstream = 247 Fraction of orfs with sites within 600 bp upstream = 0.0396723 Motif number 7 GTGAAGGTAACGTTCAACCA 4 132 1 CGTTCAACCA 0.913106 -10 GGCGGCTCACCCTCCCACCCTGCTGGACGG 6 99 1 CCTCCCACCC 0.990657 -32 CGATCCCTGCCGTTCCACGCCTGGGCGCAG 7 30 1 CGTTCCACGC 0.920692 -271 GTGTGCACCACGTTCCACCAATGTTGGTGC 7 69 0 CGTTCCACCA 0.985529 -232 GGACGAGAACTCTTCCGCCAAGCAGCACAA 7 148 1 TCTTCCGCCA 0.867732 -153 CCGGTCCACCGGGGGCTCCGT 9 2 1 CGGTCCACCG 0.910255 -180 CGAAGCCCGACATCCCGCCCGGTCACCTTT 9 65 1 CATCCCGCCC 0.931012 -117 CACCACCTCCTTCCGCCACCTAGCGAGC 10 140 0 CCTTCCGCCA 0.979254 -18 AGCCGGGATTCCTCTCACCGCA 11 3 0 CCTCTCACCG 0.762456 -23 GTGCCTCCCACCCGCGAGCAGAC 14 4 1 CCTCCCACCC 0.990657 -93 TAGCCGCCGTCGGTCAGCCCCGCAGG 15 7 0 CGGTCAGCCC 0.824819 -98 GACGACAACCTGTCCGACCAGGAGCCGCAG 16 36 0 TGTCCGACCA 0.584766 -35 ********** Masking position 8 Map Score: 10.9184 Number of sites scoring better than the average of aligned sites = 2583 Number in coding regions = 2356 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 8 CCGCAAGCGGGTGGTGCCCCCACCTCATCGCTA 2 36 0 GGGTGCCCCC 0.785971 -192 CCGCAAGCGGGTGGTGCCCCCACCTCATCGCTA 2 113 0 GGGTGCCCCC 0.785971 -115 CCGCAAGCGGGTGGTGCCCCCACCTCATCGCTA 2 190 0 GGGTGCCCCC 0.785971 -38 CCCTACCGTCGGAGCCGCACACCGTCACAG 3 37 0 GCGGACCGCC 0.782049 -20 AAGCTGATTTGGCGATTCCTGGCAGACTGTTAG 4 58 1 GCGATCCTGC 0.974893 -84 CGTTTATTCGGACGATCCCTGCCGTTCCACGCC 7 18 1 GCGATCCTGC 0.974893 -283 TGTGTCAGCAGGCGAAACCCGCGCGGACGAGAA 7 124 1 GCGAACCCGG 0.957348 -177 TTGACCACCAAACAAAACCCGTCCATGGGGCCA 7 190 1 ACAAACCCGC 0.30421 -111 CTTTCTCACCGCCGAAGCCCGACATCCCGCCCG 9 53 1 GCGAACCCGC 0.877896 -129 GCCAATCGGTCCCGAATCCTGGGGTTTTACCGG 10 57 1 CCGAACCTGG 0.527348 -101 TGCGGTGAGAGGAATCCCGGCTGAC 11 9 1 GGGAACCCGC 0.933844 -17 CCTGCGGGGCTGACCGACGGCGGCTACA 15 6 1 GGGCTACCGC 0.661121 -99 AGTAGCCCGCTCGGATCCCTGTGAGCCCCCAAA 15 65 1 TGGATCCTGG 0.483718 -40 ACGCCAATTGGTCGCTCTCCGTCGCCGTTGTGG 17 26 0 GCGCTTCCGC 0.712707 -275 GCCGGATCCGGGCGGTACCCCACTCACGTCGGC 17 145 0 GCGGTCCCCC 0.582101 -156 TTGGGGCACGTTCGGAGCCTGCCAGCGGGCCGG 17 173 0 TCGGACCTGC 0.766009 -128 TCAGCCGTGTGCGGATACTTGACGCTGTGACGC 17 249 1 GGGATCTTGC 0.654478 -52 * **** **** * Masking position 9 Map Score: 10.7036 Number of sites scoring better than the average of aligned sites = 10507 Number in coding regions = 9690 Number in noncoding regions = 817 Number of orfs with sites within 600 bp upstream = 592 Fraction of orfs with sites within 600 bp upstream = 0.0950851 Motif number 9 GCCGATTTTGTGCGACTCTGTGTCTGCTCGC 6 25 0 TGCACTCTGT 0.827846 -106 GCGGTTTTGATGCGACTCTGTGTCTGCTCGC 6 54 1 TGCACTCTGT 0.827846 -77 TCGCCCAGCACGCGACCCGGCGGCTCACCCT 6 81 1 CGCACCCGGC 0.925961 -50 CCCTGCTGGACGGTAATCAGGCAAA 6 116 1 CGGAATCAGG 0.552155 -15 TACCACGGCGCGCCTCTCAGGCCAGTCTCAG 7 263 1 CGCTCTCAGG 0.872852 -38 GGTGAGAAAGCGGATCTCGGTTTCCGGGTAT 9 32 0 CGGTCTCGGT 0.965632 -150 ACCGCATGGTTGCCAATCGGTCCCGAATCCT 10 46 1 TGCAATCGGT 0.867885 -112 GGAAAACCATCGCCAGCCGGTAAAACCCCAG 10 75 0 CGCAGCCGGT 0.945567 -83 TCGAATGTAGCGCGGCGCGGTGCCGGAAAAC 10 99 0 CGCGCGCGGT 0.811948 -59 GTAGCCCGCTCGGATCCCTGTGAGCCCCCAA 15 66 1 CGGTCCCTGT 0.814903 -39 CAGTCCGCGAATTTGGTCGCTTCGGC 16 6 1 CGCAATTTGG 0.591872 -65 GCTTCGGCTGCGGCTCCTGGTCGGACAGGTT 16 29 1 CGGTCCTGGT 0.786336 -42 CCCGGACCAACGCCAATTGGTCGCTCTCCGT 17 37 0 CGCAATTGGT 0.902491 -264 CACGTCGGCGCGCATGTTGGTACCAGTAGCG 17 123 0 CGCTGTTGGT 0.808469 -178 CCGAACGTGCCCCAAATCGGGTTTCATAGCG 17 191 1 CCCAATCGGG 0.653051 -110 GACGCAGCACCGCATCTCGGTTGAGCGTGTC 17 277 1 CGCTCTCGGT 0.987913 -24 *** ******* Masking position 10 Map Score: 9.21336 Number of sites scoring better than the average of aligned sites = 7675 Number in coding regions = 7035 Number in noncoding regions = 640 Number of orfs with sites within 600 bp upstream = 514 Fraction of orfs with sites within 600 bp upstream = 0.082557 Motif number 10 CAGCATGTGAACGGTAACCGAACAGCTGTG 1 79 1 ACGGTAACCG 0.969142 -95 CAGGAATTACACAATGACTGTGAAGGTAAC 4 113 1 ACAATGACTG 0.894417 -29 GTGGCTTTCAACAGTAACTGCACAA 8 6 0 ACAGTAACTG 0.948726 -38 TCGGCCTGAAAAGGTGACCGGGCGGGATGT 9 74 0 AAGGTGACCG 0.934977 -108 GACGGCGGCTACAGTGACTGCAAGAGCGTA 15 26 1 ACAGTGACTG 0.982065 -79 GACTTCCACAACGGCGACGGAGAGCGACCA 17 21 1 ACGGCGACGG 0.948585 -280 ********** Masking position 7 Map Score: 1.40245 Number of sites scoring better than the average of aligned sites = 537 Number in coding regions = 500 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 11 CCGATTTTGGCCTTGCCGCGCTAGGGCGAC 1 127 1 CCTTGCCGCG 0.899632 -47 CTACGCTCTGCATCGTCGTCGGCGCAGG 2 9 0 CATCGTCGTC 0.897244 -219 GGTGCCCCCACCTCATCGCTACGCTCTGCA 2 27 0 CCTCATCGCT 0.906225 -201 CTACGCTCTGCATCGTCGTCGGCGCAGGTC 2 86 0 CATCGTCGTC 0.897244 -142 GGTGCCCCCACCTCATCGCTACGCTCTGCA 2 104 0 CCTCATCGCT 0.906225 -124 CTACGCTCTGCATCGTCGTCGGCGCAGGTC 2 163 0 CATCGTCGTC 0.897244 -65 GGTGCCCCCACCTCATCGCTACGCTCTGCA 2 181 0 CCTCATCGCT 0.906225 -47 GATCTGTCTACCTCGCTGTGACGGTGTGCG 3 22 1 CCTCGCTGTG 0.939501 -35 TCAATCCACGGCGCGCCGTGAATACACTCG 4 15 0 GCGCGCCGTG 0.903783 -127 GGGGTTCTGCCCTCATCGTGTGTCAGCAGG 7 106 1 CCTCATCGTG 0.968742 -195 TGTGGCTAAACCTCGTCGAACAAACCCGCA 7 233 1 CCTCGTCGAA 0.587974 -68 GGCCTGAGAGGCGCGCCGTGGTATGCGGGT 7 256 0 GCGCGCCGTG 0.903783 -45 TTTTCCGGCACCGCGCCGCGCTACATTCGA 10 100 1 CCGCGCCGCG 0.986048 -58 CGCTCCTTAGCATCGCTGCGCTCTGCATCG 12 24 0 CATCGCTGCG 0.784975 -26 GGTGTCACCACATCGGGACAAAACTGG 13 53 0 CCACATCGGG 0.388801 -17 AGGTTGTCGTCCTCGCCGTGGTGTGT 16 55 1 CCTCGCCGTG 0.994034 -16 GGTCGCTCTCCGTCGCCGTTGTGGAAGTCG 17 20 0 CGTCGCCGTT 0.823796 -281 ********** Masking position 8 Map Score: 22.9184 Number of sites scoring better than the average of aligned sites = 10495 Number in coding regions = 9712 Number in noncoding regions = 783 Number of orfs with sites within 600 bp upstream = 586 Fraction of orfs with sites within 600 bp upstream = 0.0941214 Motif number 12 ********** No masking Map Score: 2.89434e-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 13 ********** No masking Map Score: 2.89434e-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 14 ********** No masking Map Score: 2.89434e-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