AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -icpxR6_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 mtrB 49 mtrB #12 mtrA 69 mtrA #13 tmk 96 tmk #14 sahH 104 sahH #15 Rv3764c 70 hypothetical protein Rv3764c #16 Rv3765c 300 hypothetical protein Rv3765c Motif number 1 CCGCCGAAACCGCCGGCAGGTGGGATCTCA 1 16 0 CGCCGGCAGG 0.823728 -158 TGCATCGTCGTCGGCGCAGG 2 1 0 TCGGCGCAGG 0.747335 -227 CACTCTCCCCCGCAAGCGGGTGGTGCCCCC 2 48 0 CGCAAGCGGG 0.962144 -180 TGCATCGTCGTCGGCGCAGGTCATCAGCGC 2 78 0 TCGGCGCAGG 0.747335 -150 CACTCTCCCCCGCAAGCGGGTGGTGCCCCC 2 125 0 CGCAAGCGGG 0.962144 -103 TGCATCGTCGTCGGCGCAGGTCATCAGCGC 2 155 0 TCGGCGCAGG 0.747335 -73 CACTCTCCCCCGCAAGCGGGTGGTGCCCCC 2 202 0 CGCAAGCGGG 0.962144 -26 GTGTATTCACGGCGCGCCGTGGATTGAGCG 4 18 1 GGCGCGCCGT 0.976727 -124 GCTCGCGGGGTGCGCGCGGG 6 1 0 TGCGCGCGGG 0.80475 -130 ACTCTGTGTCTGCTCGCGGGGTGCGCGCGG 6 12 0 TGCTCGCGGG 0.979882 -119 TCGCGTGCTGGGCGAGCAGACACAGAGTCG 6 66 0 GGCGAGCAGA 0.909269 -65 TCGCCCAGCACGCGACCCGGCGGCTCACCC 6 81 1 CGCGACCCGG 0.976876 -50 GTTCCACGCCTGGGCGCAGGCACAAACCGC 7 41 1 TGGGCGCAGG 0.98266 -260 AGAGTTCTCGTCCGCGCGGGTTTCGCCTGC 7 131 0 TCCGCGCGGG 0.503221 -170 TGGCCTGAGAGGCGCGCCGTGGTATGCGGG 7 257 0 GGCGCGCCGT 0.976727 -44 AGCCCGACATCCCGCCCGGTCACCTTTTCA 9 68 1 CCCGCCCGGT 0.734394 -114 ACTACTCAACGGCCGCCGAGCGCGTCGGT 10 10 1 CGGCCGCCGA 0.924133 -148 GGCAACCATGCGGTAGCCGAACCGACGCGC 10 30 0 CGGTAGCCGA 0.760059 -128 GGAAAACCATCGCCAGCCGGTAAAACCCCA 10 76 0 CGCCAGCCGG 0.988973 -82 CGAATGTAGCGCGGCGCGGTGCCGGAAAAC 10 99 0 GCGGCGCGGT 0.900666 -59 TCCGCGCCGGCGACGATGCA 11 1 1 TCCGCGCCGG 0.508042 -49 ATTTTGCGTCTGCTCGCGGGTGGGAGGCAC 13 11 0 TGCTCGCGGG 0.979882 -86 TCGGTGGCGGCGCGAGCAGACGCAAAATCG 13 65 0 CGCGAGCAGA 0.948139 -32 CCGTCGGTCAGCCCCGCAGG 14 1 0 GCCCCGCAGG 0.966877 -104 CTCACAGGGATCCGAGCGGGCTACTTAGCC 14 60 0 TCCGAGCGGG 0.615578 -45 CGACCAGGAGCCGCAGCCGAAGCGACCAAA 15 22 0 CCGCAGCCGA 0.826623 -49 CGACAACCTGTCCGACCAGGAGCCGCAGCC 15 34 0 TCCGACCAGG 0.912226 -37 CAGGTTGTCGTCCTCGCCGTGGTGTGT 15 54 1 TCCTCGCCGT 0.867841 -17 TGTGGAAGTCGCCGACCCGG 16 1 0 GCCGACCCGG 0.946685 -300 TGGTCGCTCTCCGTCGCCGTTGTGGAAGTC 16 21 0 CCGTCGCCGT 0.802752 -280 GCCTCAAGCGTGGCAGCGGGATTTGCTTCA 16 73 1 TGGCAGCGGG 0.967555 -228 AGCGGCTGCTGGCGACCGGGCTGCTGAAGC 16 97 0 GGCGACCGGG 0.96106 -204 GGTACCAACATGCGCGCCGACGTGAGTGGG 16 130 1 TGCGCGCCGA 0.898142 -171 GGGGTACCGCCCGGATCCGGCCCGCTGGCA 16 157 1 CCGGATCCGG 0.457734 -144 GTTCGGAGCCTGCCAGCGGGCCGGATCCGG 16 167 0 TGCCAGCGGG 0.984701 -134 ********** Masking position 7 Map Score: 76.8921 Number of sites scoring better than the average of aligned sites = 24630 Number in coding regions = 22732 Number in noncoding regions = 1898 Number of orfs with sites within 600 bp upstream = 1008 Fraction of orfs with sites within 600 bp upstream = 0.161902 Motif number 2 TTCGGCGGCTGATGGTGTGCTTTGGTGCGCTGTTTGCC 1 38 1 GTGTGCTGGC 0.942654 -136 TTTTGGCCTTGCCGCGCTAGGGCGACGTTCACCGGATT 1 131 1 GCGGCGGGGT 0.984998 -43 CTGCGCCGACGACGATGCAGAGCGTAGCGATGAGGTGG 2 12 1 GCGTGGGGGC 0.997885 -216 GCACCACCCGCTTGCGGGGGAGAGTGGCGCTGATGACC 2 52 1 CTGGGGGGGC 0.98731 -176 GGAGAGTGGCGCTGATGACCTGCGCCGACGACGATGCA 2 70 1 GTGTGCGGGA 0.935053 -158 CTGCGCCGACGACGATGCAGAGCGTAGCGATGAGGTGG 2 89 1 GCGTGGGGGC 0.997885 -139 GCACCACCCGCTTGCGGGGGAGAGTGGCGCTGATGACC 2 129 1 CTGGGGGGGC 0.98731 -99 GGAGAGTGGCGCTGATGACCTGCGCCGACGACGATGCA 2 147 1 GTGTGCGGGA 0.935053 -81 CTGCGCCGACGACGATGCAGAGCGTAGCGATGAGGTGG 2 166 1 GCGTGGGGGC 0.997885 -62 GCACCACCCGCTTGCGGGGGAGAGTGGCGCTG 2 206 1 CTGGGGGGGC 0.98731 -22 TGTCTACCTCGCTGTGACGGTGTGCGGCTCCGACGGTA 3 26 1 GTGGAGGGGC 0.923038 -31 TGCGACTCTGTGTCTGCTCGCGGGGTGCGCGCGGG 6 8 0 TTCGCGGGGC 0.601157 -123 AGGGTGGGAGGGTGAGCCGCCGGGTCGCGTGCTGGGCG 6 82 0 GTGGCCGGGC 0.993946 -49 CCTGCGCCCAGGCGTGGAACGGCAGGGATCGTCCGAAT 7 23 0 GCGGGCGAGA 0.838088 -278 TTCCACCAATGTTGGTGCGGTTTGTGCCTGCGCCCAGG 7 49 0 GTGTGGTGCC 0.704913 -252 GGTTTTGTTTGGTGGTCAAGAGTAGGGCGATTTGTGCT 7 171 0 GTGTCGGAGC 0.915797 -130 CAGCGCCTGAGACTGGCCTGAGAGGCGCGCCGTGGTAT 7 262 0 GCTGCGGGGC 0.987501 -39 GCGTGGACTGGCATGGGTGTGGCTTTCAACAGT 8 21 0 GCTGCGGGGC 0.987501 -23 CGGGCGGGATGTCGGGCTTCGGCGGTGAGAAAGCGGAT 9 48 0 GCGGCCGGGA 0.983222 -134 TAGCCGAACCGACGCGCTCGGCGGCCGTTGAGTAGT 10 9 0 GCGGCGCGGT 0.764279 -149 AATGTAGCGCGGCGCGGTGCCGGAAAACCATCGCCAGC 10 89 0 GCGGGCGAAC 0.657116 -69 AGATACCGGTGGCTCGCTAGGTGGCGGAAGGAGGTGGT 10 129 1 GCTGCGTGGA 0.639321 -29 CCGCGCCGGCGACGATGCAGAGCGCAGCGATGCTAAGG 11 12 1 GCGTGGGGGC 0.997879 -38 AGAGCGCAGCGATGCTAAGGAGCGGCGCCG 11 30 1 GTGTAGGGGC 0.941559 -20 TTTGCGTCTGCTCGCGGGTGGGAGGCAC 13 1 0 CCGGGGGGAC 0.91175 -96 GGCGCGGCCCTGTCGGTGGCGGCGCGAGCAGAC 13 74 0 GCCTGGTGGC 0.864646 -23 ACGCCAATTGGTCGCTCTCCGTCGCCGTTGTGGAAGTC 16 21 0 GCGTCCTGGT 0.748486 -280 GCGACCAATTGGCGTTGGTCCGGGACGCTGCCTCAAGC 16 44 1 GCGTGCGGGC 0.996191 -257 CAGTAGCGGCTGCTGGCGACCGGGCTGCTGAAGCAAAT 16 93 0 TCTGCCGGGC 0.719332 -208 CACTCACGTCGGCGCGCATGTTGGTACCAGTAGCGGCT 16 120 0 GCGGCGTGCC 0.906556 -181 TACGACACGCTCAACCGAGATGCGGTGCTGCGT 16 278 0 CCGTCCGGGC 0.978591 -23 * ** ** * * * ** Masking position 14 Map Score: 70.5129 Number of sites scoring better than the average of aligned sites = 16767 Number in coding regions = 15518 Number in noncoding regions = 1249 Number of orfs with sites within 600 bp upstream = 718 Fraction of orfs with sites within 600 bp upstream = 0.115323 Motif number 3 GCCGAAACCGCCGGCAGGTGGGATCTCAAACAA 1 7 0 CCGGGGGTCC 0.810501 -167 CCTGCGCCGACGACGATGCAGAGCGTAGCGATGA 2 8 1 CGAGTGCGAC 0.967938 -220 CAGAGCGTAGCGATGAGGTGGGGGCACCACCCGCTTG 2 29 1 CGAGGGGGCC 0.995457 -199 TGACCTGCGCCGACGACGATGCAGAGCGTAGCGATGA 2 85 1 CGAGTGCGAC 0.967938 -143 CAGAGCGTAGCGATGAGGTGGGGGCACCACCCGCTTG 2 106 1 CGAGGGGGCC 0.995457 -122 TGACCTGCGCCGACGACGATGCAGAGCGTAGCGATGA 2 162 1 CGAGTGCGAC 0.967938 -66 CAGAGCGTAGCGATGAGGTGGGGGCACCACCCGCTTG 2 183 1 CGAGGGGGCC 0.995457 -45 ACCGTCGGAGCCGCACACCGTCACAGCGAGGTAGACA 3 26 0 CCGCGTCCAC 0.793995 -31 CGATTTTGTGCGACTCTGTGTCTGCTCGCGGGGTGCG 6 17 0 CGAGGTCGCC 0.995379 -114 GGTTTTGATGCGACTCTGTGTCTGCTCGCCCAGCACG 6 56 1 CGAGGTCGCC 0.995379 -75 GCCCAGCACGCGACCCGGCGGCTCACCCTCCCACCCT 6 83 1 CGAGGGCCAC 0.960909 -48 GGGCAGAACCCCAGGTGCAGTGTGCACCACGTTCCAC 7 81 0 CCACGTGGCC 0.961137 -220 CCGGTCCACCGGGGGCTCCGTATACCCG 9 2 1 CGGCGGGGCC 0.994172 -180 CCCCAGGATTCGGGACCGATTGGCAACCATGCGGTAG 10 44 0 CGGGTTGCAC 0.655469 -114 CGATGGTTTTCCGGCACCGCGCCGCGCTACATTCGAG 10 94 1 CCGCCGCGCC 0.889708 -64 GCGCTACATTCGAGATACCGGTGGCTCGCTAGGTGGC 10 117 1 CGACGGTGCC 0.914704 -41 TCCGCGCCGGCGACGATGCAGAGCGCAGCGATGC 11 8 1 CGGGTGCGAC 0.976723 -42 TGAAAATGGGCGATTTTGCGTCTGCTCGCGGGTGGGA 13 16 0 CGAGGTCGCC 0.995379 -81 ACGAAAAGGGCGATTTTGCGTCTGCTCGCGCCGCCAC 13 55 1 CGAGGTCGCC 0.995379 -42 GGCGCGGCCCTGTCGGTGGCGGCGCGAGCAGACGC 13 72 0 CCTGGGCGCC 0.941537 -25 GTCACTGTAGCCGCCGTCGGTCAGCCCCGCAGG 14 7 0 CCGCGTCGCC 0.984717 -98 GTAGCCCGCTCGGATCCCTGTGAGCCCCCAAAGAAGG 14 66 1 CGGCGTGGCC 0.988071 -39 CGAATTTGGTCGCTTCGGCTGCGGCTCCTGGTCGGAC 15 18 1 CGCGTGCGCC 0.928865 -53 ACGGCGAGGACGACAACCTGTCCGACCAGGAGCCGCA 15 37 0 CGACGTCGAC 0.974261 -34 TGCCAGCGGGCCGGATCCGGGCGGTACCCCACTCACG 16 150 0 CCGCGGCGTC 0.858077 -151 TGCCCCAAATCGGGTTTCATAGCGCGCACATAGGATC 16 198 1 CGGCTAGGCC 0.666783 -103 CACATAGGATCCGCATGGCGTCTGCTCAGCCGTGTGC 16 224 1 CCGGGTCGCC 0.991833 -77 AACCGAGATGCGGTGCTGCGTCACAGCGTCAAGTATC 16 262 0 CGGGGTCCAC 0.94435 -39 *** * *** ** * Masking position 1 Map Score: 74.1872 Number of sites scoring better than the average of aligned sites = 11304 Number in coding regions = 10523 Number in noncoding regions = 781 Number of orfs with sites within 600 bp upstream = 535 Fraction of orfs with sites within 600 bp upstream = 0.08593 Motif number 4 GGTTTCGGCGGCTGATGGTGTGCTTTGGTGCGC 1 35 1 GTGATGTGGC 0.765027 -139 TTACCGTTCACATGCTGTTTGGCAAACAGCGCA 1 63 0 CTGCTGTTGC 0.299074 -111 TTTTGGCCTTGCCGCGCTAGGGCGACGTTCACC 1 131 1 GCGCGCAGGC 0.849908 -43 CTGCGCCGACGACGATGCAGAGCGTAGCGATGA 2 12 1 GCGATGAGGC 0.92431 -216 AGAGCGTAGCGATGAGGTGGGGGCACCACCCGC 2 30 1 GTGAGGGGGG 0.942843 -198 GCACCACCCGCTTGCGGGGGAGAGTGGCGCTGA 2 52 1 CTGCGGGGGA 0.953054 -176 GGGGGAGAGTGGCGCTGATGACCTGCGCCGACG 2 67 1 GCGCTGTGCC 0.858884 -161 CTGCGCCGACGACGATGCAGAGCGTAGCGATGA 2 89 1 GCGATGAGGC 0.92431 -139 AGAGCGTAGCGATGAGGTGGGGGCACCACCCGC 2 107 1 GTGAGGGGGG 0.942843 -121 GCACCACCCGCTTGCGGGGGAGAGTGGCGCTGA 2 129 1 CTGCGGGGGA 0.953054 -99 GGGGGAGAGTGGCGCTGATGACCTGCGCCGACG 2 144 1 GCGCTGTGCC 0.858884 -84 CTGCGCCGACGACGATGCAGAGCGTAGCGATGA 2 166 1 GCGATGAGGC 0.92431 -62 AGAGCGTAGCGATGAGGTGGGGGCACCACCCGC 2 184 1 GTGAGGGGGG 0.942843 -44 GCACCACCCGCTTGCGGGGGAGAGTGGCGCTG 2 206 1 CTGCGGGGGA 0.953054 -22 ATCTGTCTACCTCGCTGTGACGGTGTGCGGCTC 3 23 1 CCGCTGGAGG 0.899547 -34 GTGTATTCACGGCGCGCCGTGGATTGAGCGGCA 4 18 1 GCGCGCGTGA 0.595938 -124 AACGGTCCAAGCTGATTTGGCGATTCCTGGCAG 4 50 1 GTGATTGGGA 0.29859 -92 GGATCGGCAGCCCGAGGAGAACGCGGCA 5 27 1 CCGAGGGACG 0.739953 -18 TCTGTGTCTGCTCGCGGGGTGCGCGCGGG 6 7 0 CCGCGGGTCG 0.721267 -124 CATCAAAACCGCCGATTTTGTGCGACTCTGTGT 6 33 0 GCGATTTGGC 0.37558 -98 CCCAGCACGCGACCCGGCGGCTCACCCTCCCAC 6 84 1 GCCCGGGGTC 0.462678 -47 TTGTGCCTGCGCCCAGGCGTGGAACGGCAGGGA 7 33 0 GCCAGGGTGA 0.450379 -268 CCTGCTGACACACGATGAGGGCAGAACCCCAGG 7 103 0 CCGATGGGCA 0.887196 -198 GCAGGCGAAACCCGCGCGGACGAGAACTCTTCC 7 131 1 CCGCGCGAGA 0.685362 -170 AACAAAACCCGTCCATGGGGCCAATGTGGCTGA 7 200 1 GCCATGGGCA 0.602855 -101 GGGTTTGTTCGACGAGGTTTAGCCACATCAGCC 7 227 0 GCGAGGTTGC 0.677931 -74 GCCAGTCTCAGGCGCTGCGACGACACTG 7 283 1 GCGCTGGAGA 0.915592 -18 GTATACGGAGCCCCCGGTGGACCGG 9 3 0 CCCCGGGGCC 0.904511 -179 GGGATGTCGGGCTTCGGCGGTGAGAAAGCGGAT 9 48 0 GTTCGGGGGA 0.562096 -134 CGAACCGACGCGCTCGGCGGCCGTTGAGTAGT 10 10 0 CCTCGGGGCG 0.558931 -148 GATTGGCAACCATGCGGTAGCCGAACCGACGCG 10 31 0 CTGCGGAGCG 0.487154 -127 AATGTAGCGCGGCGCGGTGCCGGAAAACCATCG 10 94 0 GCGCGGGCGG 0.912651 -64 ACCGGTGGCTCGCTAGGTGGCGGAAGGAGGTGG 10 133 1 CCTAGGGGGG 0.693407 -25 CCGCGCCGGCGACGATGCAGAGCGCAGCGATGC 11 12 1 GCGATGAGGC 0.92431 -38 AGAGCGCAGCGATGCTAAGGAGCGGCGCCG 11 30 1 GTGCTAGGGC 0.452243 -20 AGCAAGAAACGCCCGTGTGGTGCGCCAGTTTTG 12 29 1 GCCGTGGGGC 0.514521 -41 CCAGTTTTGTCCCGATGTGGTGACACC 12 53 1 CCGATGGGGA 0.960999 -17 TTTGCGTCTGCTCGCGGGTGGGAGGCAC 13 6 0 CCGCGGTGGA 0.911325 -91 TCGGTGGCGGCGCGAGCAGACGCAAAATCGCCC 13 62 0 CCGAGCGAGC 0.775671 -35 CCTGCGGGGCTGACCGACGGCGG 14 1 1 CTGCGGGCGA 0.661147 -104 GGCTAAGTAGCCCGCTCGGATCCCTGTGAGCCC 14 60 1 CCGCTCGACC 0.524445 -45 CAACCTGTCCGACCAGGAGCCGCAGCCGAAGCG 15 28 0 GCCAGGGCGC 0.691337 -43 ACACACCACGGCGAGGACGACAACCTGTCCGA 15 49 0 GCGAGGCGCA 0.696589 -22 CTTCCACAACGGCGACGGAGAGCGACCAATTGG 16 23 1 GCGACGAGGC 0.493764 -278 TGAAGCAAATCCCGCTGCCACGCTTGAGGCAGC 16 70 0 CCGCTGCAGC 0.74394 -231 ACCAGTAGCGGCTGCTGGCGACCGGGCTGCTGA 16 100 0 GTGCTGCGCC 0.630613 -201 CCGGATCCGGCCCGCTGGCAGGCTCCGAACGTG 16 167 1 CCGCTGCAGC 0.743838 -134 CGCTATGAAACCCGATTTGGGGCACGTTCGGAG 16 189 0 CCGATTGGGC 0.772044 -112 TCCGCACACGGCTGAGCAGACGCCATGCGGATC 16 231 0 GTGAGCGAGC 0.54788 -70 GCGGATACTTGACGCTGTGACGCAGCACCGCAT 16 259 1 GCGCTGGAGC 0.968026 -42 CACGCTCAACCGAGATGCGGTGCTGCGTCACAG 16 273 0 CAGATGGGGC 0.610627 -28 * ***** ** ** Masking position 4 Map Score: 65.0692 Number of sites scoring better than the average of aligned sites = 64077 Number in coding regions = 59604 Number in noncoding regions = 4473 Number of orfs with sites within 600 bp upstream = 1453 Fraction of orfs with sites within 600 bp upstream = 0.233376 Motif number 5 CCGGCGGTTTCGGCGGCTGATGGTGTGCTT 1 30 1 CGGCGGCTGA 0.771784 -144 AGCGATGAGGTGGGGGCACCACCCGCTTGC 2 37 1 TGGGGGCACC 0.990988 -191 AGCGATGAGGTGGGGGCACCACCCGCTTGC 2 114 1 TGGGGGCACC 0.990988 -114 AGCGATGAGGTGGGGGCACCACCCGCTTGC 2 191 1 TGGGGGCACC 0.990988 -37 CTGTGACGGTGTGCGGCTCCGACGGTAGGG 3 37 1 GTGCGGCTCC 0.841323 -20 GCTTGGACCGTTGCCGCTCAATCCACGGCG 4 32 0 TTGCCGCTCA 0.763749 -110 TCTCCTCGGGCTGCCGATCCGATTAACTAC 5 17 0 CTGCCGATCC 0.548531 -28 CCCGCGCGCACCCCGCGAGCAG 6 3 1 CGCGCGCACC 0.84649 -128 GCACGCGACCCGGCGGCTCACCCTCCCACC 6 88 1 CGGCGGCTCA 0.967355 -43 GTTCCACGCCTGGGCGCAGGCACAAACCGC 7 41 1 TGGGCGCAGG 0.686864 -260 GCACCAACATTGGTGGAACGTGGTGCACAC 7 69 1 TGGTGGAACG 0.505973 -232 CCGGTCCACCGGGGGCTCCGTATACCCGG 9 10 1 CGGGGGCTCC 0.993281 -172 GGCGATGGTTTTCCGGCACCGCGCCGCGCT 10 92 1 TTCCGGCACC 0.758816 -66 TTCGAGATACCGGTGGCTCGCTAGGTGGCG 10 125 1 CGGTGGCTCG 0.953739 -33 CGGGACAAAACTGGCGCACCACACGGGCGT 12 37 0 CTGGCGCACC 0.938356 -33 TGTCCCGATGTGGTGACACC 12 60 1 TGGTGACACC 0.584989 -10 GCCCTGTCGGTGGCGGCGCGAGCAGACGCA 13 71 0 TGGCGGCGCG 0.890724 -26 GGCTGACCGACGGCGGCTACAGTGACTGCA 14 18 1 CGGCGGCTAC 0.860933 -87 CATCCTTCTTTGGGGGCTCACAGGGATCCG 14 76 0 TGGGGGCTCA 0.963355 -29 TCCGCGAATTTGGTCGCTTCGGCTGCGGCT 15 14 1 TGGTCGCTTC 0.463598 -57 GTCGCTTCGGCTGCGGCTCCTGGTCGGACA 15 26 1 CTGCGGCTCC 0.97616 -45 CAACGCCAATTGGTCGCTCTCCGTCGCCGT 16 31 0 TGGTCGCTCT 0.557015 -270 GAAACCCGATTTGGGGCACGTTCGGAGCCT 16 186 0 TTGGGGCACG 0.922948 -115 ********** Masking position 6 Map Score: 34.4234 Number of sites scoring better than the average of aligned sites = 12802 Number in coding regions = 12001 Number in noncoding regions = 801 Number of orfs with sites within 600 bp upstream = 609 Fraction of orfs with sites within 600 bp upstream = 0.0978156 Motif number 6 GAACAGCTGTGGCGTAGTGTGTGACTTGTCC 1 98 1 GGCGAGTGTG 0.947431 -76 ACCTCGCTGTGACGGTGTGCGGCTCCGACGG 3 31 1 GACGTGTGCG 0.677726 -26 AAGCTGATTTGGCGATTCCTGGCAGACTGTT 4 58 1 GGCGTTCCTG 0.741038 -84 GATTTTGTGCGACTCTGTGTCTGCTCGCGGG 6 22 0 GACTTGTGTC 0.847973 -109 GTTTTGATGCGACTCTGTGTCTGCTCGCCCA 6 57 1 GACTTGTGTC 0.847973 -74 CACCAATGTTGGTGCGGTTTGTGCCTGCGCC 7 53 0 GGTGGGTTTG 0.493854 -248 CACCAACATTGGTGGAACGTGGTGCACACTG 7 70 1 GGTGAACGTG 0.530835 -231 CAGAACCCCAGGTGCAGTGTGCACCACGTTC 7 84 0 GGTGAGTGTG 0.90904 -217 TCAAGAGTAGGGCGATTTGTGCTGCTTGGCG 7 163 0 GGCGTTTGTG 0.888397 -138 CCCATGGACGGGTTTTGTTTGGTGGTCAAGA 7 188 0 GGTTTGTTTG 0.72812 -113 GCCAGTCTCAGGCGCTGCGACGACACTG 7 283 1 GGCGTGCGAC 0.835581 -18 GCACCACACGGGCGTTTCTTGCTTGATTAGG 12 21 0 GGCGTTCTTG 0.775345 -49 GAAAATGGGCGATTTTGCGTCTGCTCGCGGG 13 21 0 GATTTGCGTC 0.862972 -76 CGAAAAGGGCGATTTTGCGTCTGCTCGCGCC 13 56 1 GATTTGCGTC 0.862972 -41 GTTGGTCCGGGACGCTGCCTCAAGCGTGGCA 16 57 1 GACGTGCCTC 0.723992 -244 CGTGGCAGCGGGATTTGCTTCAGCAGCCCGG 16 81 1 GGATTGCTTC 0.404352 -220 ACCGAGATGCGGTGCTGCGTCACAGCGTCAA 16 267 0 GGTGTGCGTC 0.964074 -34 ACCGCATCTCGGTTGAGCGTGTCGTA 16 285 1 GGTTAGCGTG 0.888968 -16 **** ****** Masking position 1 Map Score: 10.3937 Number of sites scoring better than the average of aligned sites = 9366 Number in coding regions = 8595 Number in noncoding regions = 771 Number of orfs with sites within 600 bp upstream = 541 Fraction of orfs with sites within 600 bp upstream = 0.0868937 Motif number 7 AAAGCACACCATCAGCCGCCGAAACCGCCG 1 31 0 ATCAGCCGCC 0.848703 -143 CCTGCGCCGACGACGATGCAGAGC 2 5 1 CGCCGACGAC 0.91493 -223 TGATGACCTGCGCCGACGACGATGCAGAGC 2 82 1 CGCCGACGAC 0.91493 -146 TGATGACCTGCGCCGACGACGATGCAGAGC 2 159 1 CGCCGACGAC 0.91493 -69 GCAGACTGTTAGCAGACTACTGGCAACGAG 4 79 1 AGCAGACTAC 0.912569 -63 GCACCCCGCGAGCAGACACAGAGTCGCACA 6 18 1 AGCAGACACA 0.937771 -113 GTGCTGGGCGAGCAGACACAGAGTCGCATC 6 62 0 AGCAGACACA 0.937771 -69 CTGCTCGCCCAGCACGCGACCCGGCGGCTC 6 77 1 AGCACGCGAC 0.81214 -54 CTGGACGGTAATCAGGCAAA 6 121 1 ATCAGGCAAA 0.416756 -10 CACGCCTGGGCGCAGGCACAAACCGCACCA 7 45 1 CGCAGGCACA 0.893578 -256 ATCGTGTGTCAGCAGGCGAAACCCGCGCGG 7 120 1 AGCAGGCGAA 0.971919 -181 CCCACCCGCGAGCAGACGCAAAATCGCCCA 13 17 1 AGCAGACGCA 0.984574 -80 TGGCGGCGCGAGCAGACGCAAAATCGCCCT 13 61 0 AGCAGACGCA 0.984574 -36 CAGGGATCCGAGCGGGCTACTTAGCCTAGG 14 56 0 AGCGGGCTAC 0.605713 -49 CTGTCCGACCAGGAGCCGCAGCCGAAGCGA 15 27 0 AGGAGCCGCA 0.711856 -44 CCCGGTCGCCAGCAGCCGCTACTGGTACCA 16 107 1 AGCAGCCGCT 0.842421 -194 CCGGCCCGCTGGCAGGCTCCGAACGTGCCC 16 173 1 GGCAGGCTCC 0.767677 -128 CACACGGCTGAGCAGACGCCATGCGGATCC 16 230 0 AGCAGACGCC 0.99138 -71 ********** Masking position 7 Map Score: 25.7189 Number of sites scoring better than the average of aligned sites = 7367 Number in coding regions = 6766 Number in noncoding regions = 601 Number of orfs with sites within 600 bp upstream = 398 Fraction of orfs with sites within 600 bp upstream = 0.0639255 Motif number 8 CGACGTTCACCGGATTTGTAGGATTTTCCTT 1 153 1 CGGTTTGTAG 0.907636 -21 GGTAGTTAATCGGATCGGCAGCCCGAGGAGA 5 16 1 CGGTCGGCAG 0.890667 -29 ACAAAATCGGCGGTTTTGATGCGACTCTGTG 6 45 1 CGGTTTGATG 0.786785 -86 CCGTGGTATGCGGGTTTGTTCGACGAGGTTT 7 240 0 CGGTTTGTTC 0.5327 -61 AAAAGGTGACCGGGCGGGATGTCGGGCTTCG 9 65 0 CGGCGGGATG 0.806788 -117 TTTCAAATGTCGCTTATGTAGTTACTTCGGC 9 99 0 CGCTATGTAG 0.894292 -83 CCTGTGCAAGCGCACATGCAGTTGTCACGGG 9 141 0 CGCCATGCAG 0.936341 -41 AAGCAAGAAACGCCCGTGTGGTGCGCCAGTT 12 28 1 CGCCGTGTGG 0.82662 -42 GGCGCGGCCCTGTCGGTGGCGGCGC 13 82 0 CGGCCTGTCG 0.887357 -15 AGCCTAGGTACGCTCTTGCAGTCACTGTAGC 14 33 0 CGCCTTGCAG 0.936341 -72 CGAATTTGGTCGCTTCGGCTGCGGCTCCTGG 15 18 1 CGCTCGGCTG 0.892897 -53 GGCTCCTGGTCGGACAGGTTGTCGTCCTCGC 15 40 1 CGGCAGGTTG 0.940949 -31 CTCACGTCGGCGCGCATGTTGGTACCAGTAG 16 125 0 CGCCATGTTG 0.949213 -176 *** ******* Masking position 1 Map Score: 7.17549 Number of sites scoring better than the average of aligned sites = 5733 Number in coding regions = 5348 Number in noncoding regions = 385 Number of orfs with sites within 600 bp upstream = 338 Fraction of orfs with sites within 600 bp upstream = 0.0542885 Motif number 9 CCAAAGCACACCATCAGCCGCCGAAACCGCC 1 32 0 CCATCGCCGC 0.796132 -142 GCGCACCCCGCGAGCAGACACAGAGTCGCAC 6 16 1 CGAGCGACAC 0.949534 -115 GCGTGCTGGGCGAGCAGACACAGAGTCGCAT 6 63 0 CGAGCGACAC 0.949534 -68 ACCGTTTATTCGGACGATCCCTGCCGTTCCA 7 16 1 CGGACATCCC 0.864999 -285 TAAACCTCGTCGAACAAACCCGCATACCACG 7 239 1 CGAACAACCC 0.96211 -62 CCGGTCCACCGGGGGCTCCGTA 9 2 1 CGGTCACCGG 0.560959 -180 ATGCGGTAGCCGAACCGACGCGCTCGGCGGC 10 22 0 CGAACGACGC 0.984568 -136 GCATGGTTGCCAATCGGTCCCGAATCCTGGG 10 49 1 CAATCGTCCC 0.539172 -109 CATCGCCAGCCGGTAAAACCCCAGGATTCGG 10 68 0 CGGTAAACCC 0.584319 -90 CTCCCACCCGCGAGCAGACGCAAAATCGCCC 13 15 1 CGAGCGACGC 0.987935 -82 GGTGGCGGCGCGAGCAGACGCAAAATCGCCC 13 62 0 CGAGCGACGC 0.987935 -35 TAGCCGCCGTCGGTCAGCCCCGCAGG 14 6 0 CGGTCGCCCC 0.89891 -99 GGCAGCGTCCCGGACCAACGCCAATTGGTCG 16 45 0 CGGACAACGC 0.958476 -256 TGGCAGGCTCCGAACGTGCCCCAAATCGGGT 16 182 1 CGAACTGCCC 0.594121 -119 ***** ***** Masking position 9 Map Score: 13.2136 Number of sites scoring better than the average of aligned sites = 6109 Number in coding regions = 5548 Number in noncoding regions = 561 Number of orfs with sites within 600 bp upstream = 370 Fraction of orfs with sites within 600 bp upstream = 0.0594282 Motif number 10 CGCTTTCTCCTGATCTGTCT 3 1 1 CGCTTTCTCC 0.979311 -56 TGCCGCGTTCTCCTCGGGCTGCC 5 32 0 CGCGTTCTCC 0.945377 -13 AACCGAGATCCGCTTTCTCACCGCCGAAGC 9 41 1 CGCTTTCTCA 0.967849 -141 ACTGCATGTGCGCTTGCACAGGACTTGAGA 9 150 1 CGCTTGCACA 0.931323 -32 CGTCTGCTCGCGCCGCCACCGACAGGGCCG 13 73 1 CGCCGCCACC 0.961875 -24 TGGTCCGGGACGCTGCCTCAAGCGTGGCAG 16 59 1 CGCTGCCTCA 0.982791 -242 AAGCAAATCCCGCTGCCACGCTTGAGGCAG 16 71 0 CGCTGCCACG 0.962025 -230 ********** Masking position 7 Map Score: 4.83724 Number of sites scoring better than the average of aligned sites = 1454 Number in coding regions = 1354 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 11 GGTGCGCTGTTTGCCAAACAGCATGTGAAC 1 61 1 TTGCCAAACA 0.780527 -113 CTGTGTCTGCTCGCCCAGCACGCGACCCGG 6 71 1 TCGCCCAGCA 0.983905 -60 TGCCTGATTACCGTCCAGCAGGGTGGGAGG 6 109 0 CCGTCCAGCA 0.971784 -22 GAGAACTCTTCCGCCAAGCAGCACAAATCG 7 152 1 CCGCCAAGCA 0.991522 -149 CTACTCTTGACCACCAAACAAAACCCGTCC 7 184 1 CCACCAAACA 0.88017 -117 TGGCTAAACCTCGTCGAACAAACCCGCATA 7 235 1 TCGTCGAACA 0.88978 -66 TACTCAACGGCCGCCGAGCGCGTCGGTTCG 10 13 1 CCGCCGAGCG 0.974904 -145 ********** Masking position 7 Map Score: 3.06075 Number of sites scoring better than the average of aligned sites = 3272 Number in coding regions = 3031 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 12 CGATTTTGGCCTTGCCGCGCTAGGGCGACG 1 128 1 CTTGCCGCGC 0.847226 -46 CCCTACCGTCGGAGCCGCACACCGT 3 42 0 CCGTCGGAGC 0.667802 -15 CGTTGCCGCTCAATCCACGGCGCGCCGTGA 4 24 0 CAATCCACGG 0.371882 -118 TGAGCGGCAACGGTCCAAGCTGATTTGGCG 4 42 1 CGGTCCAAGC 0.966117 -100 TCTGCTCGCGGGGTGCGCGCGGG 6 4 0 GGGTGCGCGC 0.714269 -127 CGATCCCTGCCGTTCCACGCCTGGGCGCAG 7 30 1 CGTTCCACGC 0.97111 -271 GTGTGCACCACGTTCCACCAATGTTGGTGC 7 69 0 CGTTCCACCA 0.52137 -232 GGAAGAGTTCTCGTCCGCGCGGGTTTCGCC 7 134 0 TCGTCCGCGC 0.749381 -167 AACAAACCCGCATACCACGGCGCGCCTCTC 7 251 1 CATACCACGG 0.180125 -50 ACACCCATGCCAGTCCACGC 8 34 1 CAGTCCACGC 0.97139 -10 CCGGTCCACCGGGGGCTCCGT 9 2 1 CGGTCCACCG 0.784955 -180 CTCTCAAGTCCTGTGCAAGCGCACATGCAG 9 151 0 CTGTGCAAGC 0.466411 -31 TTTCCGGCACCGCGCCGCGCTACATTCGAG 10 101 1 CGCGCCGCGC 0.901822 -57 CGCCACCGACAGGGCCGCGCC 13 86 1 AGGGCCGCGC 0.820323 -11 TAGCCGCCGTCGGTCAGCCCCGCAGG 14 7 0 CGGTCAGCCC 0.78751 -98 CAGTCCGCGAATTTGGTCGC 15 1 1 CAGTCCGCGA 0.879911 -70 GGACGACAACCTGTCCGACCAGGAGCCGCA 15 37 0 CTGTCCGACC 0.792507 -34 ATTTGGGGCACGTTCGGAGCCTGCCAGCGG 16 178 0 CGTTCGGAGC 0.710711 -123 ********** Masking position 5 Map Score: 7.12799 Number of sites scoring better than the average of aligned sites = 18198 Number in coding regions = 16849 Number in noncoding regions = 1349 Number of orfs with sites within 600 bp upstream = 860 Fraction of orfs with sites within 600 bp upstream = 0.13813 Motif number 13 ********** No masking Map Score: -5.51138e-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: -5.51138e-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 15 ********** No masking Map Score: -5.51138e-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