AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_mtub_reg_300.orf -o00052_mtub_300.ace -a/home/amcguire/genomes/ORF_mtub.txt -z/home/amcguire/genomes/mtub.fna -g0.66 -x5 -e 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 = 1 Input sequences: #1 PE_PGRS 277 PE_PGRS #2 Rv0110 147 hypothetical protein Rv0110 #3 Rv0111 180 hypothetical protein Rv0111 #4 gca 281 gca #5 gmhA 73 gmhA #6 Rv0114 31 hypothetical protein Rv0114 #7 PE_PGRS 300 PE_PGRS #8 pepA 151 pepA #9 Rv0126 108 hypothetical protein Rv0126 #10 galE1 300 galE1 #11 Rv0617 155 hypothetical protein Rv0617 #12 galT' 128 galT' #13 galU 100 galU #14 hspX 196 hspX #15 pfkA 95 pfkA #16 gatC 84 gatC #17 pgmA 69 pgmA #18 mhpE 60 mhpE #19 rmlB2 22 rmlB2 Motif number 1 GCCTCCGCGTCGAGGTGGCGCACCACGCAG 1 75 0 CGAGGTGGCG 0.927806 -203 GCCACCTCGACGCGGAGGCACCAGCGGGTT 1 86 1 CGCGGAGGCA 0.574181 -192 AGAGCGAGCCCGCCGCGGCCAACCCGCTGG 1 106 0 CGCCGCGGCC 0.503015 -172 GTGATTGTGACCAGCTGCCGGAGCGGGAAT 1 149 1 CCAGCTGCCG 0.897957 -129 GAATGCGTGTTGGACAGCCGAATCCCCGCA 1 175 1 TGGACAGCCG 0.589718 -103 GCAACGTGCCCCGGAAGCCGCGCTACATTT 1 211 1 CCGGAAGCCG 0.666038 -67 TTGCATCCCGCCCAACGGCGCAGGCAACAA 2 16 1 CCCAACGGCG 0.91307 -132 GCGACTCCGATGAGCTGGCGCCACTCATCG 2 51 0 TGAGCTGGCG 0.7605 -97 TATCGCCATCCCGGGCGCCGGACCTACGTC 2 89 1 CCGGGCGCCG 0.974007 -59 GACCACTTCGTCGTCCGGCGCAGTGCTTGC 3 117 0 TCGTCCGGCG 0.874762 -64 GGAGTGAATCCCGCCCGGCTCAGCTCTCGC 3 161 0 CCGCCCGGCT 0.889329 -20 CTCATCCGGAGCACACGGCGGA 4 3 0 GCACACGGCG 0.915933 -279 CCGTTTGACGAGCCGCGGCCTCGCTGCAAA 4 106 1 AGCCGCGGCC 0.586127 -176 CGCCAGATCGGGGAGCGCCCTCGTTGTGTA 4 166 0 GGGAGCGCCC 0.860932 -116 GGGCGCTCCCCGATCTGGCGCGCGCAACGA 4 176 1 CGATCTGGCG 0.867188 -106 CTCGACAAACCGCACCGGCCTGAGCATCAA 4 241 0 CGCACCGGCC 0.973951 -41 CTTCGCGACGTCGAGCGGCGGCTG 7 5 0 TCGAGCGGCG 0.918671 -296 GGGTGCGCGTGCACCTGGCCCGGGTGGTAA 7 94 1 GCACCTGGCC 0.915545 -207 ATCCATTGACGCGCACGGCAATTGGCCGGC 7 123 1 GCGCACGGCA 0.750699 -178 AGACCGAGACCGAGCCGGCCAATTGCCGTG 7 136 0 CGAGCCGGCC 0.988627 -165 ACCCGGCACCGCACACGGCCTTTTCGCCAA 7 194 0 GCACACGGCC 0.882598 -107 GAACGTAGCGCGACCCGGCACCGCACACGG 7 206 0 CGACCCGGCA 0.96416 -95 CGCCCGCCCCACCACCGGCGAACACGCTCG 7 264 0 ACCACCGGCG 0.870484 -37 CCTCCCCAACCCGCCCGCCCCACCACCGGC 7 275 0 CCGCCCGCCC 0.981214 -26 GGCCATGCCCCGGACCGGCACCGAAACCCT 8 23 0 CGGACCGGCA 0.965661 -129 TGCCGGTCCGGGGCATGGCCATCCGCTGAG 8 33 1 GGGCATGGCC 0.582917 -119 GGCCATCCGCTGAGCTGGCGATCTGGACTA 8 49 1 TGAGCTGGCG 0.7605 -103 CCTTAAGGGTCCGGGCGGCAGGATTTTTCT 8 88 0 CCGGGCGGCA 0.94628 -64 ATCCAATTGGCCGGCCGGCGGGTGGTATCC 9 20 0 CCGGCCGGCG 0.99549 -89 AATTGGATTGGCGCCAGCCGTGATTGCCGC 9 42 1 GCGCCAGCCG 0.896398 -67 ACTCGGGGGCTCACGCGGCAATCACGGCTG 9 56 0 TCACGCGGCA 0.645179 -53 CGTCTCCCGTGCGCGTGGCATCGTGGAAGC 9 88 1 GCGCGTGGCA 0.685611 -21 GCCGCACGCGGCCGGAGTCCGCC 10 4 1 GCACGCGGCC 0.96388 -297 ATTGCCAGATCGGTCAGGCGGACTCCGGCC 10 20 0 CGGTCAGGCG 0.912929 -281 ACACCAAACCGGCAGCGCCCGAGCATTGCC 10 44 0 GGCAGCGCCC 0.704044 -257 GGTGTTCCGTGCGACCGCCCGGGTAGAGTG 10 69 1 GCGACCGCCC 0.947431 -232 TCAGTAATCAAGAAGCGGCGCAAGCGCATG 10 138 1 AGAAGCGGCG 0.824025 -163 GCGTGACGGTCGAGCTGGCGGGGTCTGCTC 10 239 0 CGAGCTGGCG 0.962457 -62 GACAGCCTAACGGCCAGGCGAAACGGCGGC 10 278 0 CGGCCAGGCG 0.910901 -23 GGGCGGTTGGCGGCCAGGCCTCGTCGCATG 11 40 0 CGGCCAGGCC 0.943324 -116 GGCCTGGCCGCCAACCGCCCTACCGCGTTG 11 50 1 CCAACCGCCC 0.96079 -106 CGTCTCCCGGCGGCGCGGCGAGCCGCCCCA 12 18 1 CGGCGCGGCG 0.508989 -111 TAGGCATAGCTGAGGTGGCGTCGCGGCCCT 12 73 1 TGAGGTGGCG 0.614775 -56 CGTCGCGGCCCTCACCGGCGACACCACAGA 12 91 1 CTCACCGGCG 0.657962 -38 CGGATCGGCCCGAGATCCTC 12 119 0 CGGATCGGCC 0.731342 -10 GGCGCTCGCGCGGGACGGCCGGGGCTGTGT 13 24 0 CGGGACGGCC 0.95 -77 GCCGTCCCGCGCGAGCGCCGGGACAGCGCC 13 35 1 GCGAGCGCCG 0.928976 -66 ACAGCGCCAACGAAGAGGCGGGCAATCAGC 13 57 1 CGAAGAGGCG 0.906568 -44 CTGTTGTCTGCCAACCGCCGTTCAGAAAGA 14 42 0 CCAACCGCCG 0.972637 -155 AAGTGGATCACCGACGGGCGCGGACAAATG 14 86 1 CCGACGGGCG 0.939643 -111 TTCTGTCCCTAGCCCTGGCCACGATGGGCT 14 133 1 AGCCCTGGCC 0.616142 -64 GCCTTTGATCCGACCAGCCCATCGTGGCCA 14 148 0 CGACCAGCCC 0.889686 -49 ACACAGACTCGCATCCGGCGCCCCTCGCCC 15 21 1 GCATCCGGCG 0.931086 -75 GACACAGAATCGCACGGGCGAGGGGCGCCG 15 36 0 CGCACGGGCG 0.837386 -60 GCGCGGCCGCCGACCTGGCGCGAGCAGACA 15 62 0 CGACCTGGCG 0.96778 -34 CCTCATCTTGCCGCGCGGCCGCCGACCTGG 15 74 0 CCGCGCGGCC 0.964007 -22 CGCCGGCTGCCGAAACGCCGTGGATACATC 16 31 0 CGAAACGCCG 0.833074 -54 CGGCGTTTCGGCAGCCGGCGTCGGCCGTCC 16 41 1 GCAGCCGGCG 0.981504 -44 CCGGCGTCGGCCGTCCGGCCACCCATTAGG 16 55 1 CCGTCCGGCC 0.974926 -30 ACCAATTCTGCCCACAGGCCCTACAGTGCG 17 46 0 CCCACAGGCC 0.905686 -24 GACACCAGCCGCGCGTCCAAG 18 2 1 ACACCAGCCG 0.515064 -59 AATTCATCAAGGATCCGGCAAGGGTGCGGG 18 32 1 GGATCCGGCA 0.681297 -29 GCCCACCATACCGGCGGCCC 19 1 0 CCGGCGGCCC 0.818003 -22 ********** Masking position 7 Map Score: 102.65 Number of sites scoring better than the average of aligned sites = 65671 Number in coding regions = 61321 Number in noncoding regions = 4350 Number of orfs with sites within 600 bp upstream = 1450 Fraction of orfs with sites within 600 bp upstream = 0.232894 Motif number 2 CGTCGAGGTGGCGCACCACGCAGAGTGTTCC 1 67 0 GCGCACCAGC 0.919131 -211 GGTTGGCCGCGGCGGGCTCGCTCTTGGGTGG 1 112 1 GGCGGGCTGC 0.817183 -166 GCGGCTTCCGGGGCACGTTGCGCCAATTGCG 1 201 0 GGGCACGTGC 0.963446 -77 GCCAAATGTAGCGCGGCTTCCGGGGCACGTT 1 213 0 GCGCGGCTCC 0.579192 -65 CTGCGCCGTTGGGCGGGATGCAACACGC 2 8 0 GGGCGGGAGC 0.987318 -140 CCGCCCAACGGCGCAGGCAACAATGGTGCGA 2 23 1 GCGCAGGCAC 0.891278 -125 ACTCCGATGAGCTGGCGCCACTCATCGCACC 2 47 0 GCTGGCGCAC 0.620095 -101 TAGGTCCGGCGCCCGGGATGGCGATAGCAGG 2 84 0 GCCCGGGAGG 0.97619 -64 ATCGGGTGCAGCGGACGTAGGTCCGGCGCCC 2 101 0 GCGGACGTGG 0.796823 -47 GTTTAGATGTGACCGCGTCGGATTCCCCGAA 3 48 0 GACCGCGTGG 0.68657 -133 CTCGCTGTTAGCGCGCCCTGACCACTTCGTC 3 135 0 GCGCGCCCGA 0.8835 -46 GAGCTGAGCCGGGCGGGATTCACTCC 3 165 1 GGGCGGGATC 0.608664 -16 TGCTCCGGATGAGCGCGACGGTAACCCTGGA 4 20 1 GAGCGCGAGG 0.756162 -262 GACGAGCCGCGGCCTCGCTGCAAACATTGAA 4 112 1 GGCCTCGCGC 0.691626 -170 CCCCGATCTGGCGCGCGCAACGAGGTGCGCA 4 183 1 GCGCGCGCAC 0.969348 -99 ACTCCTTGATGCTCAGGCCGGTGCGGTTTGT 4 236 1 GCTCAGGCGG 0.831722 -46 CTTTCGAATGGCCGCGTAAGGATCGGCTTT 6 12 0 GGCCGCGTAG 0.9156 -20 CGCTGGTCACGGCTGCGACAGCTGACTGTCC 7 38 0 GGCTGCGAAG 0.480003 -263 CGGACATCTCGGGCAGCTAGCCCGACAGGGT 7 67 1 GGGCAGCTGC 0.889362 -234 CCAGGTGCACGCGCACCCTGTCGGGCTAGCT 7 81 0 GCGCACCCGT 0.67567 -220 CGTGCACCTGGCCCGGGTGGTAATCCATTGA 7 101 1 GCCCGGGTGT 0.882967 -200 CACGGCAATTGGCCGGCTCGGTCTCGGTCTG 7 136 1 GGCCGGCTGG 0.930079 -165 TGCGGTGCCGGGTCGCGCTACGTTCAGATTC 7 211 1 GGTCGCGCAC 0.880359 -90 ACGCTCGTTGGCGGACGACATTGTTAGGTGA 7 240 0 GCGGACGAAT 0.1933 -61 GCCGGTGGTGGGGCGGGCGGGTTGGGGAGGT 7 275 1 GGGCGGGCGG 0.985256 -26 TTAAGGGTCCGGGCGGCAGGATTTTTCTACA 8 85 0 GGGCGGCAGA 0.822638 -67 CAATCCAATTGGCCGGCCGGCGGGTGGTATC 9 21 0 GGCCGGCCGC 0.9645 -88 GAACTCGGGGGCTCACGCGGCAATCACGGCT 9 57 0 GCTCACGCGC 0.903933 -52 TCCGTCTCCCGTGCGCGTGGCATCGTGGAAG 9 86 1 GTGCGCGTGC 0.702273 -23 GGCGGACTCCGGCCGCGTGCGGC 10 3 0 GGCCGCGTCG 0.703847 -298 TTGCCAGATCGGTCAGGCGGACTCCGGCCGC 10 18 0 GGTCAGGCGA 0.549018 -283 CCGTGCGACCGCCCGGGTAGAGTGTCCGGGT 10 75 1 GCCCGGGTGA 0.897334 -226 CCGTATAGATGGCGGGGTCATGGGTTCAGTA 10 113 1 GGCGGGGTAT 0.302032 -188 TTGGACATGCGCTTGCGCCGCTTCTTGATTA 10 142 0 GCTTGCGCGC 0.547846 -159 CGACGCAGCAGCTTGCGATGCTTTTTCTTGG 10 169 0 GCTTGCGAGC 0.620354 -132 CGCTGCACCCGGGTGCGACGCAGCAGCTTGC 10 184 0 GGGTGCGAGC 0.869785 -117 CCCGGGTGCAGCGCAGGAAACTGGGCAAATA 10 202 1 GCGCAGGAAC 0.860384 -99 GGCGTTACAAGCGCGTGACGGTCGAGCTGGC 10 250 0 GCGCGTGAGG 0.606314 -51 CAGGCGAAACGGCGGCGTTACAAGCGCGTGA 10 263 0 GGCGGCGTAC 0.794949 -38 ACAGCCTAACGGCCAGGCGAAACGGCGGCGT 10 276 0 GGCCAGGCAA 0.515343 -25 TAGGGCGGTTGGCGGCCAGGCCTCGTCGCAT 11 41 0 GGCGGCCAGC 0.783988 -115 CGGTCCCGACGCTCACCAAAGGCAATCCCGT 11 95 0 GCTCACCAAG 0.29863 -61 CGTCCTCGGAGGTCACGACGGTCCCGACGCT 11 113 0 GGTCACGAGG 0.820358 -43 GTTGGTTTTGGGGCGGCTCGCCGCGCCGCCG 12 25 0 GGGCGGCTGC 0.961807 -104 CCAACGATTGGGCCACGATGCGTAGGCATAG 12 51 1 GGCCACGAGC 0.961318 -78 CGCCGGTGAGGGCCGCGACGCCACCTCAGCT 12 80 0 GGCCGCGAGC 0.987262 -49 CCCGGCGCTCGCGCGGGACGGCCGGGGCTGT 13 26 0 GCGCGGGAGG 0.980476 -75 ATATCGAACAGCGGAGGTTGATC 14 3 0 GCGGAGGTGA 0.440064 -194 CCATTTGTCCGCGCCCGTCGGTGATCCACTT 14 86 0 GCGCCCGTGG 0.758865 -111 AGTCCCCGAAGCGCGGGCCATTTGTCCGCGC 14 103 0 GCGCGGGCAT 0.779448 -94 CCCTAGCCCTGGCCACGATGGGCTGGTCGGA 14 139 1 GGCCACGAGG 0.941301 -58 CGGCGAGCAGACACAGACTCGC 15 2 1 GGCGAGCAAC 0.302989 -94 CGGGCGAGGGGCGCCGGATGCGAGTCTGTGT 15 21 0 GCGCCGGAGC 0.820903 -75 TTCTGTGTCTGCTCGCGCCAGGTCGGCGGCC 15 57 1 GCTCGCGCAG 0.826028 -39 CCAGGTCGGCGGCCGCGCGGCAAGATGAGGG 15 74 1 GGCCGCGCGC 0.990223 -22 CGTTTCGGCAGCCGGCGTCGGCCGTCCGGCC 16 44 1 GCCGGCGTGG 0.909534 -41 AAAGCCTAATGGGTGGCCGGACGGCCGACGC 16 58 0 GGGTGGCCGA 0.312077 -27 ATTCTTGGACGCGCGGCTGGTGTC 18 4 0 GCGCGGCTGT 0.776052 -57 CGGCCCACCATACCGGCGGCCC 19 10 0 GCCCACCAAC 0.698537 -13 ******** ** Masking position 1 Map Score: 81.8117 Number of sites scoring better than the average of aligned sites = 60887 Number in coding regions = 56933 Number in noncoding regions = 3954 Number of orfs with sites within 600 bp upstream = 1459 Fraction of orfs with sites within 600 bp upstream = 0.23434 Motif number 3 TGGTGCCTCCGCGTCGAGGTGGCGCACCAC 1 79 0 GCGTCGAGGT 0.776727 -199 CCCGCCGCGGCCAACCCGCTGGTGCCTCCG 1 98 0 CCAACCCGCT 0.797149 -180 TGACCAGCTGCCGGAGCGGGAATGCGTGTT 1 156 1 CCGGAGCGGG 0.802373 -122 CGCAATTGGCGCAACGTGCCCCGGAAGCCG 1 201 1 GCAACGTGCC 0.809858 -77 GGAGCCAAATGTAGCGCGGCTTCCGGGGCA 1 217 0 GTAGCGCGGC 0.705139 -61 GCGTGTTGCATCCCGCCCAACGGCGCA 2 8 1 GCATCCCGCC 0.908739 -140 CCTGCTATCGCCATCCCGGGCGCCGGACCT 2 84 1 CCATCCCGGG 0.920328 -64 TTCGGGGAATCCGACGCGGTCACATCTAAA 3 48 1 CCGACGCGGT 0.967521 -133 ACTTCGTCGTCCGGCGCAGTGCTTGCTGCC 3 113 0 CCGGCGCAGT 0.71193 -68 GGAGTGAATCCCGCCCGGCTCAGCTCTCG 3 162 0 CCCGCCCGGC 0.812466 -19 TCCAGGGTTACCGTCGCGCTCATCCGGAGC 4 21 0 CCGTCGCGCT 0.89608 -261 TTCAATGTTTGCAGCGAGGCCGCGGCTCGT 4 113 0 GCAGCGAGGC 0.884465 -169 TTGTATTTACACAACGAGGGCGCTCCCCGA 4 159 1 ACAACGAGGG 0.29343 -123 TCTGGCGCGCGCAACGAGGTGCGCACTATC 4 189 1 GCAACGAGGT 0.724526 -93 CAGACCGAGACCGAGCCGGCCAATTGCCGT 7 137 0 CCGAGCCGGC 0.720752 -164 TGAACGTAGCGCGACCCGGCACCGCACACG 7 207 0 GCGACCCGGC 0.982208 -94 ATGTCGTCCGCCAACGAGCGTGTTCGCCGG 7 250 1 CCAACGAGCG 0.603301 -51 ACACACCTCCCCAACCCGCCCGCCCCACCA 7 280 0 CCAACCCGCC 0.941074 -21 TGGCCATGCCCCGGACCGGCACCGAAACCC 8 24 0 CCGGACCGGC 0.887688 -128 TTTTTCTACACCAACGTAGTCCAGATCGCC 8 65 0 CCAACGTAGT 0.22293 -87 CGTGCGCGTGGCATCGTGGAAGCA 9 95 1 GCATCGTGGA 0.256383 -14 GCACGGAACACCAAACCGGCAGCGCCCGAG 10 51 0 CCAAACCGGC 0.813251 -250 GCACCCGGGTGCGACGCAGCAGCTTGCGAT 10 181 0 GCGACGCAGC 0.871778 -120 GCACCCGGGTGCAGCGCAGGAAACTGGGCA 10 199 1 GCAGCGCAGG 0.590711 -102 CGACAGCCTAACGGCCAGGCGAAACGGCGG 10 279 0 ACGGCCAGGC 0.595303 -22 CCGACCTCATGCGACGAGGCCTGGCCGCCA 11 33 1 GCGACGAGGC 0.936704 -123 GGGTCTGAGGACAACGCGGTAGGGCGGTTG 11 61 0 ACAACGCGGT 0.64096 -95 AGCGTCGGGACCGTCGTGACCTCCGAGGAC 11 113 1 CCGTCGTGAC 0.367599 -43 TCGTCTCCCGGCGGCGCGGCGAGCCGCCCC 12 17 1 GCGGCGCGGC 0.935163 -112 CTATGCCTACGCATCGTGGCCCAATCGTTG 12 52 0 GCATCGTGGC 0.899482 -77 AGCTGAGGTGGCGTCGCGGCCCTCACCGGC 12 80 1 GCGTCGCGGC 0.97587 -49 ACAGCCCCGGCCGTCCCGCGCGAGCGCCGG 13 26 1 CCGTCCCGCG 0.867584 -75 TTCGTTGGCGCTGTCCCGGCGCTCGCGCGG 13 41 0 CTGTCCCGGC 0.691755 -60 ACGATAACCCGCAGCGTGCTGATTGCCCGC 13 74 0 GCAGCGTGCT 0.539898 -27 ACAGAAGTCCCCGAAGCGCGGGCCATTTGT 14 109 0 CCGAAGCGCG 0.558963 -88 TCCGACCAGCCCATCGTGGCCAGGGCTAGG 14 140 0 CCATCGTGGC 0.92577 -57 CGCGCGGCCGCCGACCTGGCGCGAGCAGAC 15 63 0 CCGACCTGGC 0.939706 -33 CAGGTCGGCGGCCGCGCGGCAAGATGAGGG 15 75 1 GCCGCGCGGC 0.497044 -21 CCGGCGTCGGCCGTCCGGCCACCCATTAGG 16 55 1 CCGTCCGGCC 0.509703 -30 CGGCCCACCATACCGGCGGCCC 19 6 0 CCATACCGGC 0.780403 -17 ********** Masking position 2 Map Score: 57.1864 Number of sites scoring better than the average of aligned sites = 41045 Number in coding regions = 38241 Number in noncoding regions = 2804 Number of orfs with sites within 600 bp upstream = 1230 Fraction of orfs with sites within 600 bp upstream = 0.197559 Motif number 4 GCGGCTTCCGGGGCACGTTGCGCCAATTGCGG 1 200 0 GGGCGTTGCG 0.949566 -78 TGCCGTTTTCGGGCAAGCTGTCTGGTGGCTAG 1 246 0 GGGCGCTGTC 0.992815 -32 CAGGGACCTCTGCCGTTTTCGGGC 1 264 0 GGGATCTGCC 0.885011 -14 GTCCGGCGCAGTGCTTGCTGCCGATACGTCGC 3 103 0 GTGCGCTGCC 0.986506 -78 GAAGTGGTCAGGGCGCGCTAACAGCGAGAGCT 3 138 1 GGGCGCTAAC 0.889954 -43 CGCGCTAACAGCGAGAGCTGAGCCGGGCGGGA 3 151 1 GCGAGCTGAG 0.78007 -30 ATTGTGCTGTGTGCTGGCTGTGTCGTTGTGAT 4 51 1 GTGCGCTGTG 0.925496 -231 GCGCAACGAGGTGCGCACTATCCATTCGAGGT 4 197 1 GTGCACTATC 0.278981 -85 GCTCAGGCCGGTGCGGTTTGTCGAGAAAGGCG 4 246 1 GTGCTTTGTC 0.667344 -36 GGTCACGGCTGCGACAGCTGACTGTCCAGACT 7 33 0 GCGAGCTGAC 0.92044 -268 GCACCCTGTCGGGCTAGCTGCCCGAGATGTCC 7 68 0 GGGCGCTGCC 0.996005 -233 CCAGGTGCACGCGCACCCTGTCGGGCTAGCTG 7 80 0 GCGCCCTGTC 0.847016 -221 GAGACCGAGCCGGCCAATTGCCGTGCGCGTCA 7 129 0 CGGCATTGCC 0.664584 -172 GTGGTGGGGCGGGCGGGTTGGGGAGGTGTGTG 7 279 1 GGGCGTTGGG 0.709139 -22 AATTGGATTGGCGCCAGCCGTGATTGCCGCGT 9 42 1 GCGCGCCGTG 0.787177 -67 GCCATCTATACGGCTATCTGACCCGGACACTC 10 94 0 CGGCTCTGAC 0.84598 -207 CCCGGCGGCGCGGCGAGCCGCCCCAAAACCAA 12 23 1 CGGCGCCGCC 0.887593 -106 AACCCGCAGCGTGCTGATTGCCCGCCTCTTCG 13 67 0 GTGCATTGCC 0.746067 -34 GATCCACTTGGGGACCATTGACCCTGTTGTCT 14 63 0 GGGAATTGAC 0.460313 -134 CCCGAAGCGCGGGCCATTTGTCCGCGCCCGTC 14 98 0 GGGCTTTGTC 0.87248 -99 CCGCGCTTCGGGGACTTCTGTCCCTAGCCCTG 14 118 1 GGGATCTGTC 0.810115 -79 CGGCGAGCAGACACAGACTCGC 15 1 1 CGGCGCAGAC 0.738846 -95 CGGGCGAGGGGCGCCGGATGCGAGTCTGTGTC 15 20 0 GCGCGATGCG 0.647801 -76 CGCCGACCTGGCGCGAGCAGACACAGAATCGC 15 53 0 GCGCGCAGAC 0.886355 -43 CGGACGGCCGACGCCGGCTGCCGAAACGCCGT 16 40 0 ACGCGCTGCC 0.837396 -45 TCCGGCAAGGGTGCGGGCTGACACTG 18 45 1 GTGCGCTGAC 0.975913 -16 **** ****** Masking position 3 Map Score: 32.5176 Number of sites scoring better than the average of aligned sites = 11000 Number in coding regions = 10240 Number in noncoding regions = 760 Number of orfs with sites within 600 bp upstream = 544 Fraction of orfs with sites within 600 bp upstream = 0.0873755 Motif number 5 CGGCTTAATTGCCTTACTGTGTTTCGCGTGG 1 31 0 GCCTTACGTG 0.926726 -247 CACAATTCCAGGGTTACCGTCGCGCTCATCC 4 26 0 GGGTTACGTC 0.524828 -256 CCAGACGTGCGGGCTTCAATGTTTGCAGCGA 4 126 0 GGGCTTCATG 0.872959 -156 CGGGCAGCTAGCCCGACAGGGTGCGCGTGCA 7 76 1 GCCCGACGGG 0.931667 -225 CAATTGCCGTGCGCGTCAATGGATTACCACC 7 116 0 GCGCGTCATG 0.961817 -185 CAAAATTGTCGCCCTTCAGTGCGGTATCCGC 7 166 0 GCCCTTCGTG 0.982467 -135 CGATCAACGAGGGTTTCGGTGCCGGTCCGGG 8 14 1 GGGTTTCGTG 0.901133 -138 CGTTACAAGCGCGTGACGGTCGAGCTGGCGG 10 248 0 GCGTGACGTC 0.801324 -53 GCCGCCAACCGCCCTACCGCGTTGTCCTCAG 11 56 1 GCCCTACGCG 0.874051 -100 CCGCGCCGCCGGGAGACGATGCACA 12 5 0 GGGAGACATG 0.600119 -124 ATTTGTCCGCGCCCGTCGGTGATCCACTTGG 14 84 0 GCCCGTCGTG 0.985588 -113 CAAATGGCCCGCGCTTCGGGGACTTCTGTCC 14 110 1 GCGCTTCGGG 0.963994 -87 GGCGCCGGATGCGAGTCTGTGTCTGCTCGCC 15 12 0 GCGAGTCGTG 0.96249 -84 CCTCGCCCGTGCGATTCTGTGTCTGCTCGCG 15 43 1 GCGATTCGTG 0.953194 -53 CTGCCCACAGGCCCTACAGTGCGAAGCGCAG 17 38 0 GCCCTACGTG 0.977776 -32 GACACCAGCCGCGCGTCCAAGAATTCATCAA 18 11 1 GCGCGTCAAG 0.728308 -50 ******* *** Masking position 7 Map Score: 21.7167 Number of sites scoring better than the average of aligned sites = 4122 Number in coding regions = 3791 Number in noncoding regions = 331 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 6 ACTGTGTTTCGCGTGGAGTCAAACGGAAAT 1 17 0 GCGTGGAGTC 0.741086 -261 GGAGGCACCAGCGGGTTGGCCGCGGCGGGC 1 99 1 GCGGGTTGGC 0.931178 -179 GTTGGCCGCGGCGGGCTCGCTCTTGGGTGG 1 113 1 GCGGGCTCGC 0.96978 -165 GCTCGCTCTTGGGTGGTCGCCAGTGATTGT 1 127 1 GGGTGGTCGC 0.903432 -151 AGCTGCCGGAGCGGGAATGCGTGTTGGACA 1 161 1 GCGGGAATGC 0.605903 -117 TGCGCCAATTGCGGGGATTCGGCTGTCCAA 1 184 0 GCGGGGATTC 0.841856 -94 TCTGCCGTTTTCGGGCAAGCTGTCTGGTGG 1 250 0 TCGGGCAAGC 0.862731 -28 CGCCAGCTCATCGGAGTCGCCCACCTGCTA 2 61 1 TCGGAGTCGC 0.653628 -87 TCGCGTGTCTTCGGGGAATCCGACGCGGTC 3 39 1 TCGGGGAATC 0.855852 -142 TTGACGAGCCGCGGCCTCGCTGCAAACATT 4 110 1 GCGGCCTCGC 0.779753 -172 GCGCACCCTGTCGGGCTAGCTGCCCGAGAT 7 72 0 TCGGGCTAGC 0.929407 -229 CGTGTGCGGTGCCGGGTCGCGCTACGTTCA 7 207 1 GCCGGGTCGC 0.905794 -94 CCGCCAACGAGCGTGTTCGCCGGTGGTGGG 7 257 1 GCGTGTTCGC 0.888861 -44 GGTGGGGCGGGCGGGTTGGGGAGGTGTGTG 7 281 1 GCGGGTTGGG 0.583179 -20 ACCTCCTGTGTCGGGGTAGCTATCAGAAAT 8 126 0 TCGGGGTAGC 0.968675 -26 GCCGGCCGGCGGGTGGTATCCGCGACGAAA 9 11 0 GGGTGGTATC 0.700928 -98 GAGACGGAACTCGGGGGCTCACGCGGCAAT 9 64 0 TCGGGGGCTC 0.717499 -45 GCGCGTGGCATCGTGGAAGCA 9 98 1 TCGTGGAAGC 0.779074 -11 CACTCTACCCGGGCGGTCGCACGGAACACC 10 69 0 GGGCGGTCGC 0.742753 -232 GGTCGAGCTGGCGGGGTCTGCTCGCAACCT 10 232 0 GCGGGGTCTG 0.882068 -69 CAACGAAGAGGCGGGCAATCAGCACGCTGC 13 64 1 GCGGGCAATC 0.9013 -37 TCAGCACGCTGCGGGTTATCGTGTGAACG 13 82 1 GCGGGTTATC 0.906869 -19 AGAAAGATCGGGGTGATATCGAACAGCGGA 14 19 0 GGGTGATATC 0.213964 -178 ********** Masking position 3 Map Score: 25.0671 Number of sites scoring better than the average of aligned sites = 9322 Number in coding regions = 8570 Number in noncoding regions = 752 Number of orfs with sites within 600 bp upstream = 550 Fraction of orfs with sites within 600 bp upstream = 0.0883392 Motif number 7 AGGGAACACTCTGCGTGGTGCGCCACCTCGAC 1 65 1 CGGTGGTGCG 0.973105 -213 ATGAGTGGCGCCAGCTCATCGGAGTCGCCCAC 2 53 1 CACTCATCGG 0.453903 -95 CCGCTGCACCCGATGTGATCGGTACATCTGTG 2 118 1 CAGTGATCGG 0.749661 -30 CGAAGACACGCGAAGACAAGCGGCTATCGGTT 3 20 0 CAGACAAGCG 0.751237 -161 CGCCGGACGACGAAGTGGTCAGGGCGCGCTAA 3 127 1 CAGTGGTCAG 0.557508 -54 TCCGCCGTGTGCTCCGGATGAGCGCG 4 5 1 CGGTGCTCCG 0.628141 -277 ATGAGCCTGTCTAAGTGGTGCGTAACCGTTTG 4 81 1 CAGTGGTGCG 0.977858 -201 TAAATACAAACCCAGACGTGCGGGCTTCAATG 4 136 0 CCGACGTGCG 0.955103 -146 CTGGCGCGCGCAACGAGGTGCGCACTATCCAT 4 190 1 CAGAGGTGCG 0.972149 -92 GTTGGCAGGACAAAGACATTCGG 5 2 0 CAGACATTCG 0.413757 -72 CCAGACTTCGCGACGTCGAGCGGCGGCTG 7 8 0 CAGTCGAGCG 0.935027 -293 GGCTAGCTGCCCGAGATGTCCGCTGGTCACGG 7 57 0 CGGATGTCCG 0.603554 -244 GCAGCTAGCCCGACAGGGTGCGCGTGCACCTG 7 79 1 CAAGGGTGCG 0.562913 -222 ATTCACCTAACAATGTCGTCCGCCAACGAGCG 7 238 1 CAGTCGTCCG 0.980799 -63 CCGCGTGAGCCCCCGAGTTCCGTCTCCCGTGC 9 68 1 CCGAGTTCCG 0.31548 -41 AGGCGGACTCCGGCCGCGTGCGGC 10 3 0 CGCGCGTGCG 0.610663 -298 GTATAGATGGCGGGGTCATGGGTTCAGTAATC 10 115 1 CGGTCATGGG 0.833487 -186 GATGCTTTTTCTTGGACATGCGCTTGCGCCGC 10 152 0 CTGACATGCG 0.533377 -149 GCAGACCCCGCCAGCTCGACCGTCACGCGCTT 10 241 1 CACTCGACCG 0.661947 -60 AAACGGTCGCCGACCTCATGCGACGAGGCCTG 11 24 1 CACTCATGCG 0.76488 -132 TCGTGACCTCCGAGGACGTGCGTTCATTAGAG 11 126 1 CAGACGTGCG 0.981659 -30 GTGGTGTCGCCGGTGAGGGCCGCGACGCCACC 12 86 0 CGGAGGGCCG 0.878664 -43 ACAGCGCCAACGAAGAGGCGGGCAATCAGCAC 13 57 1 CAGAGGCGGG 0.530996 -44 CCAAGTGGATCACCGACGGGCGCGGACAAATG 14 84 1 CCGACGGGCG 0.883228 -113 CTGGTCGGATCAAAGGCATCCGTTTCCATCGA 14 161 1 CAGGCATCCG 0.86625 -36 CACAGAATCGCACGGGCGAGGGGCGCCGGATG 15 32 0 CCGGCGAGGG 0.494424 -64 TCTGCTCGCGCCAGGTCGGCGGCCGCGCGGCA 15 64 1 CAGTCGGCGG 0.853671 -32 TTTCGGCAGCCGGCGTCGGCCGTCCGGCCACC 16 46 1 CGGTCGGCCG 0.932941 -39 GGGCCGCCGGTATGGTGGGCCG 19 8 1 CGATGGTGGG 0.428422 -15 * * ******** Masking position 1 Map Score: 29.9603 Number of sites scoring better than the average of aligned sites = 12274 Number in coding regions = 11388 Number in noncoding regions = 886 Number of orfs with sites within 600 bp upstream = 659 Fraction of orfs with sites within 600 bp upstream = 0.105846 Motif number 8 GGGCAGCGACGTATCGGCAGCAAGCACTGC 3 98 1 GTATCGGCAG 0.988485 -83 CGGACTCTCAGTATCGACAAAAG 5 61 1 GTATCGACAA 0.907376 -13 CTTCAGTGCGGTATCCGCAGACCGAGACCG 7 154 0 GTATCCGCAG 0.988488 -147 CCGGCGGGTGGTATCCGCGACGAAA 9 6 0 GTATCCGCGA 0.960086 -103 GCACAACGATGTATCCACGGCGTTTCGGCA 16 24 1 GTATCCACGG 0.960086 -61 TATCCACGGCGTTTCGGCAGCCGGCGTCGG 16 35 1 GTTTCGGCAG 0.954918 -50 ********** Masking position 4 Map Score: 4.74382 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 80 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 9 CAGAGTGTTCCCTAGTCGGCTTAATTGCCT 1 48 0 CCTAGTCGGC 0.902533 -230 ACATTTGGCTCCTAGCCACCAGACAGCTTG 1 235 1 CCTAGCCACC 0.644569 -43 CTCATCGCACCATTGTTGCCTGCGCCGTTG 2 28 0 CATTGTTGCC 0.788734 -120 GCCAGCTCATCGGAGTCGCCCACCTGCTAT 2 62 1 CGGAGTCGCC 0.888471 -86 GGACTGTTCCTATTCGCCTTTCTCGACA 4 264 0 CCTATTCGCC 0.973224 -18 TTTTCGCCAAAATTGTCGCCCTTCAGTGCG 7 174 0 AATTGTCGCC 0.620586 -127 CCGCACACGGCCTTTTCGCCAAAATTGTCG 7 186 0 CCTTTTCGCC 0.967216 -115 CGCCAACGAGCGTGTTCGCCGGTGGTGGGG 7 258 1 CGTGTTCGCC 0.867378 -43 CTGCTCGCAACCTATTTGCCCAGTTTCCTG 10 215 0 CCTATTTGCC 0.834714 -86 TGTAACGCCGCCGTTTCGCCTGGCCGTTAG 10 272 1 CCGTTTCGCC 0.895436 -29 GGCGGCCAGGCCTCGTCGCATGAGGTCGGC 11 32 0 CCTCGTCGCA 0.859627 -124 TGCGACGAGGCCTGGCCGCCAACCGCCCTA 11 42 1 CCTGGCCGCC 0.952488 -114 TATGCCTACGCATCGTGGCCCAATCGTTGG 12 51 0 CATCGTGGCC 0.874587 -78 CCGACCAGCCCATCGTGGCCAGGGCTAGGG 14 139 0 CATCGTGGCC 0.874587 -58 ********** Masking position 8 Map Score: 10.4181 Number of sites scoring better than the average of aligned sites = 6062 Number in coding regions = 5713 Number in noncoding regions = 349 Number of orfs with sites within 600 bp upstream = 287 Fraction of orfs with sites within 600 bp upstream = 0.046097 Motif number 10 CGCGTGGAGTCAAACGGAAATCCGGAT 1 6 0 CAACGGAATC 0.967717 -272 TCGGAGTCGCCCACCTGCTATCGCCATCCCGG 2 71 1 CCACTGCATC 0.969129 -77 CACGCGAAGACAAGCGGCTATCGGTTTTGATG 3 14 0 CAACGGCATC 0.990982 -167 GCAGCCGTGACCAGCGGACATCTCGGGCAGCT 7 53 1 CCACGGAATC 0.987128 -248 GCCCGCCCCACCACCGGCGAACACGCTCGTTG 7 261 0 CCACGGCAAC 0.980537 -40 CTCGGGGGCTCACGCGGCAATCACGGCTGGCG 9 53 0 CACCGGCATC 0.971274 -56 CCGACGCTCACCAAAGGCAATCCCGTTCTGGG 11 89 0 CCAAGGCATC 0.969129 -67 TTGTCCGCGCCCGTCGGTGATCCACTTGGGGA 14 81 0 CCGCGGTATC 0.930468 -116 *** **** *** Masking position 10 Map Score: 8.8866 Number of sites scoring better than the average of aligned sites = 738 Number in coding regions = 685 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 11 ATCCGGATTTCCGTTTGACTCCACGCGAAA 1 11 1 CCGTTTGACT 0.981448 -267 GTTGCCTGCGCCGTTGGGCGGGATGCAACA 2 14 0 CCGTTGGGCG 0.962173 -134 AAACCGATAGCCGCTTGTCTTCGCGTGTCT 3 19 1 CCGCTTGTCT 0.941369 -162 TGGTGCGTAACCGTTTGACGAGCCGCGGCC 4 96 1 CCGTTTGACG 0.988223 -186 CAGGCCGGTGCGGTTTGTCGAGAAAGGCGA 4 249 1 CGGTTTGTCG 0.881561 -33 CAGCCGCCGCTCGACGTCGCGAAGTC 7 7 1 CCGCTCGACG 0.945573 -294 TTTCGCCTGGCCGTTAGGCTGTCGGA 10 285 1 CCGTTAGGCT 0.915397 -16 AGGTCGGCGACCGTTTCACTCAACGTGCG 11 10 0 CCGTTTCACT 0.897496 -146 ********** Masking position 5 Map Score: 5.28866 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 640 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 12 GACCACCCAAGAGCGAGCCCGCCGCGGCCAA 1 114 0 GGCGAGCCCG 0.694126 -164 CTGCCGATACGTCGCTGCCCCTCCTCTTGAT 3 87 0 GCGCTGCCCC 0.858555 -94 AATCCCGCCCGGCTCAGCTCTCGCTGTTAGC 3 154 0 GCTCAGCTCT 0.65133 -27 TCATCACAACGACACAGCCAGCACACAGCAC 4 54 0 GCACAGCCAG 0.572554 -228 TTGCAGCGAGGCCGCGGCTCGTCAAACGGTT 4 104 0 GCGCGGCTCG 0.969682 -178 ACACAACGAGGGCGCTCCCCGATCTGGCGCG 4 167 1 GCGCTCCCCG 0.841221 -115 CAGCCGCCGCTCGACGTCGCGAA 7 3 1 GCGCCGCTCG 0.969682 -298 CTCAGCGGATGGCCATGCCCCGGACCGGCAC 8 32 0 GCCATGCCCC 0.389385 -120 CGTGATTGCCGCGTGAGCCCCCGAGTTCCGT 9 60 1 GGTGAGCCCC 0.628076 -49 CGGTCAGGCGGACTCCGGCCGCGTGCGGC 10 9 0 GCTCCGGCCG 0.735074 -292 TGACCGATCTGGCAATGCTCGGGCGCTGCCG 10 34 1 GCAATGCTCG 0.533778 -267 GCAATGCTCGGGCGCTGCCGGTTTGGTGTTC 10 45 1 GCGCTGCCGG 0.824529 -256 GGTGTTCCGTGCGACCGCCCGGGTAGAGTGT 10 69 1 GGACCGCCCG 0.964995 -232 CGAGCTGGCGGGGTCTGCTCGCAACCTATTT 10 228 0 GGTCTGCTCG 0.952928 -73 CGTTGGTTTTGGGGCGGCTCGCCGCGCCGCC 12 26 0 GGGCGGCTCG 0.950619 -103 CTGAGGTGGCGTCGCGGCCCTCACCGGCGAC 12 82 1 GCGCGGCCCT 0.878154 -47 CGGATCGGCCCGAGATCCTCTG 12 117 0 GATCGGCCCG 0.772664 -12 CCTCAACGATGACACAGCCCCGGCCGTCCCG 13 13 1 GCACAGCCCC 0.918596 -88 CGCGAGCGCCGGGACAGCGCCAACGAAGAGG 13 44 1 GGACAGCGCC 0.513333 -57 ATGCGAGTCTGTGTCTGCTCGCCG 15 4 0 GGTCTGCTCG 0.953049 -92 GTGCGATTCTGTGTCTGCTCGCGCCAGGTCG 15 51 1 GGTCTGCTCG 0.953049 -45 CGCCAGGTCGGCGGCCGCGCGGCAAGATGAG 15 72 1 GGGCCGCGCG 0.90929 -24 CAGTGTCAGCCCGCACCCTTGCC 18 48 0 GGTCAGCCCG 0.978764 -13 * ********* Masking position 1 Map Score: 32.1634 Number of sites scoring better than the average of aligned sites = 9453 Number in coding regions = 8624 Number in noncoding regions = 829 Number of orfs with sites within 600 bp upstream = 567 Fraction of orfs with sites within 600 bp upstream = 0.0910697 Motif number 13 ********** No masking Map Score: 8.12451e-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 14 ********** No masking Map Score: 8.12451e-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 15 ********** No masking Map Score: 8.12451e-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