AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00120_mtub_reg_300.orf -o00120_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 Rv0144 101 hypothetical protein Rv0144 #2 Rv0145 88 hypothetical protein Rv0145 #3 Rv0146 42 hypothetical protein Rv0146 #4 Rv0147 94 hypothetical protein Rv0147 #5 Rv0223c 98 hypothetical protein Rv0223c #6 Rv0224c 35 hypothetical protein Rv0224c #7 adhB 98 adhB #8 Rv0767c 201 hypothetical protein Rv0767c #9 fadA3 52 fadA3 #10 Rv1075c 300 hypothetical protein Rv1075c #11 Rv1861 300 hypothetical protein Rv1861 #12 adhA 73 adhA #13 adhE2 300 adhE2 #14 ltp1 32 ltp1 #15 Rv2792c 201 hypothetical protein Rv2792c #16 Rv2795c 144 hypothetical protein Rv2795c #17 Rv2798c 130 hypothetical protein Rv2798c #18 Rv3137 300 hypothetical protein Rv3137 #19 fadE24 79 fadE24 #20 Rv3292 30 hypothetical protein Rv3292 #21 aldB 26 aldB #22 Rv3545c_fadA5 111 Rv3545c: hypothetical protein Rv3545c, fadA5: fadA5 Motif number 1 CCGACGATCAGCAGCGCAACCATGGCCCAGG 1 32 1 GCAGCGCACC 0.930576 -70 CGGCGGTGATCGCGTACGTCCAGACCTGGGC 1 56 0 CGCGTACGCC 0.618151 -46 GATCACCGCCGCTGTGCGGCGAGGAGATCCG 1 76 1 GCTGTGCGCG 0.98514 -26 GGCGCTCATCCTGTGCTCCCT 3 32 0 GGCGCTCACC 0.753698 -11 CGAGCGCATCCGACTGACCTT 4 1 1 CGAGCGCACC 0.902999 -94 GTTCTCGTTTCGCGTTCGGCTTGGGTAGGGT 5 22 1 CGCGTTCGCT 0.542012 -77 ACGCCATGACCGCCGGCGACGATGCCGAGCG 5 54 1 CGCCGGCGCG 0.694189 -45 ATGCGCCGCTCCTCCTCATCGCTGCGCTCGG 5 78 0 CCTCCTCACG 0.973501 -21 ACTCGTAGCCGAAGTTCAACGATGAAAGCAG 7 71 1 GAAGTTCACG 0.536916 -28 ATCCGCAAGGCCGCTACACCGTCCTGACCGA 8 82 1 CCGCTACACG 0.825596 -120 GACGTGGCCCCTGGTGCATCGGTCAGGACGG 8 100 0 CTGGTGCACG 0.61331 -102 GATGCACCAGGGGCCACGTCGCGTCGCGGAC 8 111 1 GGGCCACGCG 0.855502 -91 AACATGGGACTGTCCGCGACGCGACGTGGCC 8 122 0 TGTCCGCGCG 0.880872 -80 GGCTTGCCTCCTGCCGCGACCATCCGATAGC 8 173 1 CTGCCGCGCC 0.734207 -29 TTGTCATTTCGCCGCGCGACGTGTTGAAGGC 10 21 0 GCCGCGCGCG 0.989564 -280 AGTAAGGTATCCGGCTCACCCAGAGTTGTCA 10 46 0 CCGGCTCACC 0.917031 -255 ATGCTGTATCGGACTACAACGGCGTAGGAAG 10 97 0 GGACTACACG 0.469106 -204 GGCTGAGCCAGAGGCTCAGCCGCTTCGTCAC 10 128 0 GAGGCTCACC 0.623459 -173 TACCACATTTGGTCCACACCGTGACGGGTTT 10 220 1 GGTCCACACG 0.807468 -81 TACAAGTCGCCAACCACGACCCAC 11 4 0 CAACCACGCC 0.537026 -297 CTGCCCGTCCCCGGCGCGACCTATGGAGAAC 11 44 0 CCGGCGCGCC 0.984792 -257 CACACGACCCGCTGCCCGTCCCCGGCGCGAC 11 55 0 GCTGCCCGCC 0.664603 -246 CAGCGGGTCGTGTGCGCGTCTTTCAGTGCAC 11 72 1 TGTGCGCGCT 0.458109 -229 TGCGCGTCTTTCAGTGCACCGTGCGAAACGC 11 84 1 TCAGTGCACG 0.633364 -217 GCTTTCAGGTGGAGTTCAACGGTGTCGGCGT 11 111 0 GGAGTTCACG 0.700086 -190 GCGCTTTTCTGCTGTTCAGCGGTGCTTTCAG 11 134 0 GCTGTTCACG 0.9188 -167 TGACTGCGGCGGCCGGCGACGGTAGCGGCAT 12 44 1 GGCCGGCGCG 0.739123 -30 ACTCATCTGCGCCGCTCCTCCTCA 13 4 1 CATCTGCGCG 0.958101 -297 CTGCGCCGCTCCTCCTCATCGCTTCGCTCTG 13 17 1 CCTCCTCACG 0.973501 -284 TCATCGCTTCGCTCTGCATCGTCACCGGCGC 13 32 1 GCTCTGCACG 0.971135 -269 TGCATCGTCACCGGCGCGACTCATCTGCGCC 13 46 1 CCGGCGCGCT 0.947147 -255 CGGCGCGACTCATCTGCGCCGCTCCTGCTCA 13 57 1 CATCTGCGCG 0.958101 -244 CTGCGCCGCTCCTGCTCATCGCTTCGCTCTG 13 70 1 CCTGCTCACG 0.973501 -231 TCATCGCTTCGCTCTGCATCGTCACCGGCGC 13 85 1 GCTCTGCACG 0.971135 -216 TGCATCGTCACCGGCGCGACTCATCTGCGCC 13 99 1 CCGGCGCGCT 0.947147 -202 CGGCGCGACTCATCTGCGCCGCTCCTGCTCA 13 110 1 CATCTGCGCG 0.958101 -191 CTGCGCCGCTCCTGCTCATCGCTTCGCTCTG 13 123 1 CCTGCTCACG 0.973501 -178 TCATCGCTTCGCTCTGCATCGTCACCGGCGC 13 138 1 GCTCTGCACG 0.971135 -163 TGCATCGTCACCGGCGCGACTCATCTGCGCC 13 152 1 CCGGCGCGCT 0.947147 -149 CGGCGCGACTCATCTGCGCCGCTCCTGCTCA 13 163 1 CATCTGCGCG 0.958101 -138 CTGCGCCGCTCCTGCTCATCGCTTCGCTCTG 13 176 1 CCTGCTCACG 0.973501 -125 TCATCGCTTCGCTCTGCATCGTCACCGGCGC 13 191 1 GCTCTGCACG 0.971135 -110 TGCATCGTCACCGGCGCGACTCATCTGCGCC 13 205 1 CCGGCGCGCT 0.947147 -96 CGGCGCGACTCATCTGCGCCGCTCCTCCTCA 13 216 1 CATCTGCGCG 0.958101 -85 CTGCGCCGCTCCTCCTCATCGCTTCGCTCTG 13 229 1 CCTCCTCACG 0.973501 -72 TCATCGCTTCGCTCTGCATCGTCACCGGCGC 13 244 1 GCTCTGCACG 0.971135 -57 CGTCGCTGACCATGCGCGCCGGTGACGATGC 13 259 0 CATGCGCGCG 0.979971 -42 CACTCACTTGCAACGGCAACG 14 22 1 CAACGGCACG 0.585572 -11 TCGCCCGGCTCCTCCTCACCCCG 15 3 0 CCTCCTCACC 0.938183 -199 TTGCCGTCCCGGACCGCATCCCCCTACATTG 15 53 0 GGACCGCACC 0.859839 -149 ATGCGGTCCGGGACGGCAACGGTGGCACACT 15 65 1 GGACGGCACG 0.651448 -137 GCGGCCCATCGCCGTGCGACGTAGGCCGTGT 15 101 0 GCCGTGCGCG 0.977935 -101 GGCTTTTGCGTCTGCTCGGCCAACCTAGCCC 16 16 0 TCTGCTCGCC 0.691825 -129 GTTCGACCAACCGCTACGGCGTGAGCAGACG 16 77 0 CCGCTACGCG 0.90315 -68 CGAAATCCAGCCAGTTCGACCAACCGCTACG 16 90 0 CCAGTTCGCC 0.863019 -55 GATTTCGTTCCCACTTCGCCGGGTCGTTAGG 16 114 1 CCACTTCGCG 0.938454 -31 GTCGGCTCCGCGTCGTCACAGTCAA 17 5 1 GCTCCGCGCG 0.992999 -126 TACTGCTGGCCGCCTGCGTCCGGTCGCGGGC 18 38 1 CGCCTGCGCC 0.926737 -263 CGCGGCTTATCCCGCGCGGCCCGCGGGGAGA 18 104 0 CCCGCGCGCC 0.983456 -197 GGTATTTCTTGCTCCGCGGCTTATCCCGCGC 18 118 0 GCTCCGCGCT 0.941914 -183 GCACTGAGTTCACGCTCGGCGTAATAACGGC 18 223 0 CACGCTCGCG 0.916674 -78 GCACTGGGTACACGCTCGGCGAAAGGATGGT 18 274 1 CACGCTCGCG 0.916674 -27 ******** ** Masking position 7 Map Score: 108.558 Number of sites scoring better than the average of aligned sites = 61329 Number in coding regions = 57402 Number in noncoding regions = 3927 Number of orfs with sites within 600 bp upstream = 1323 Fraction of orfs with sites within 600 bp upstream = 0.212496 Motif number 2 ATCCGACGATCAGCAGCGCAACCATGGCCC 1 30 1 CAGCAGCGCA 0.44011 -72 GGACGTACGCGATCACCGCCGCTGTGCGGC 1 66 1 GATCACCGCC 0.768295 -36 CTACGCTTCGGGGCCGCCGGTTAGGTCTCG 2 12 0 GGGCCGCCGG 0.917329 -77 GGGAGCACAGGATGAGCGCC 3 33 1 GATGAGCGCC 0.813861 -10 AGGGTGACGCCATGACCGCCGGCGACGATG 5 48 1 CATGACCGCC 0.611856 -51 CAGCGATGAGGAGGAGCGGCGCAT 5 85 1 GAGGAGCGGC 0.98955 -14 GCTGAGTGTAGGTCAACGGCGCTAGGGCGT 7 11 0 GGTCAACGGC 0.862156 -88 GTCGGCGTTCCGGCCGAGGCTAGGGACCAC 7 43 1 CGGCCGAGGC 0.927801 -56 GGTCAGGACGGTGTAGCGGCCTTGCGGATA 8 81 0 GTGTAGCGGC 0.662943 -121 GACGGCTCCCGGCATGGACAAGA 9 40 0 GGCTCCCGGC 0.719617 -13 CCTTCAACACGTCGCGCGGCGAAATGACAA 10 22 1 GTCGCGCGGC 0.574016 -279 GACAACTCTGGGTGAGCCGGATACCTTACT 10 47 1 GGTGAGCCGG 0.858951 -254 TGAGCCAGAGGCTCAGCCGCTTCGTCACAT 10 126 0 GCTCAGCCGC 0.78678 -175 CGCCGGGGACGGGCAGCGGGTCGTGTGCGC 11 59 1 GGGCAGCGGG 0.984782 -242 AAAACACCGTGGGGCGCCACACACGTTTGA 11 170 1 GGGGCGCCAC 0.570633 -131 TGGCTTAGCCCAGCACAGGGCCGTGATATC 11 261 0 CAGCACAGGG 0.545552 -40 CTACCGTCGCCGGCCGCCGCAGTCACACTC 12 39 0 CGGCCGCCGC 0.972474 -35 CGGCCGGCGACGGTAGCGGCATGATGGAGT 12 53 1 CGGTAGCGGC 0.957402 -21 AAGCGATGAGGAGGAGCGGCGCAGATGAGT 13 11 0 GAGGAGCGGC 0.98955 -290 CGCTCTGCATCGTCACCGGCGCGACTCATC 13 41 1 CGTCACCGGC 0.97821 -260 AAGCGATGAGCAGGAGCGGCGCAGATGAGT 13 64 0 CAGGAGCGGC 0.984628 -237 CGCTCTGCATCGTCACCGGCGCGACTCATC 13 94 1 CGTCACCGGC 0.97821 -207 AAGCGATGAGCAGGAGCGGCGCAGATGAGT 13 117 0 CAGGAGCGGC 0.984628 -184 CGCTCTGCATCGTCACCGGCGCGACTCATC 13 147 1 CGTCACCGGC 0.97821 -154 AAGCGATGAGCAGGAGCGGCGCAGATGAGT 13 170 0 CAGGAGCGGC 0.984628 -131 CGCTCTGCATCGTCACCGGCGCGACTCATC 13 200 1 CGTCACCGGC 0.97821 -101 AAGCGATGAGGAGGAGCGGCGCAGATGAGT 13 223 0 GAGGAGCGGC 0.98955 -78 CGCTCTGCATCGTCACCGGCGCGCATGGTC 13 253 1 CGTCACCGGC 0.97821 -48 CGGCGCGCATGGTCAGCGACGCTACACCGT 13 269 1 GGTCAGCGAC 0.871685 -32 CGGGGTGAGGAGGAGCCGGGCGATTCGGT 15 10 1 GAGGAGCCGG 0.868165 -192 CCCCTACATTGAGGCCAGGCTCCAACCGAA 15 34 0 GAGGCCAGGC 0.763368 -168 CTTCCGAATTGAACAGCGGCCCATCGCCGT 15 117 0 GAACAGCGGC 0.823741 -85 TAGGTTGGCCGAGCAGACGCAAAAGCCCCC 16 20 1 GAGCAGACGC 0.838261 -125 GCCCCCATTTCGGGCCCGAAATGGGGGCTT 16 42 0 CGGGCCCGAA 0.150252 -103 GCTACGGCGTGAGCAGACGCAAAAGCCCCC 16 66 0 GAGCAGACGC 0.838261 -79 CAGCCAGTTCGACCAACCGCTACGGCGTGA 16 84 0 GACCAACCGC 0.371958 -61 TCACATTATGCGTCAGCGGGAACTACCGCA 17 81 0 CGTCAGCGGG 0.946005 -50 GGAGTCAGCCCGCGACCGGACGCAGGCGGC 18 46 0 CGCGACCGGA 0.619187 -255 GCACGCTCCTGGTGACCGGAGTCAGCCCGC 18 63 0 GGTGACCGGA 0.786524 -238 GGGGAGATCTGGCCAGCGGCACGCTCCTGG 18 81 0 GGCCAGCGGC 0.987963 -220 TATCCCGCGCGGCCCGCGGGGAGATCTGGC 18 98 0 GGCCCGCGGG 0.900945 -203 GGTATTTCTTGCTCCGCGGCTTATCCCGCG 18 119 0 GCTCCGCGGC 0.857066 -182 AAATCGCACTGGGTACACGCTCGGCGAAAG 18 269 1 GGGTACACGC 0.410155 -32 ACGGCAGCCTCGGTCATCGGG 19 69 0 CGGCAGCCTC 0.592633 -11 GGGGCCAGGCTAGAACACGT 22 1 1 GGGGCCAGGC 0.880102 -111 ********** Masking position 7 Map Score: 70.9726 Number of sites scoring better than the average of aligned sites = 47598 Number in coding regions = 44709 Number in noncoding regions = 2889 Number of orfs with sites within 600 bp upstream = 1290 Fraction of orfs with sites within 600 bp upstream = 0.207196 Motif number 3 CAGAGTTGGCCAGCGCTATCCGACGATCAGCAG 1 13 1 CGGCTATCGA 0.840098 -89 CGCTATCCGACGATCAGCAGCGCAACCATGGCC 1 26 1 CACAGCACGC 0.763008 -76 CGCTGTGCGGCGAGGAGATCCGAAACG 1 85 1 CAGAGATCGA 0.596469 -17 CGGTGATAACCGCGATCCTAGTC 4 82 0 CGGATAACGC 0.913321 -13 TACCCAAGCCGAACGCGAAACGAGAACGTGTTC 5 16 0 GAGCGAACGA 0.751282 -83 GGCGACGATGCCGAGCGCAGCGATGAGGAGGAG 5 68 1 CGGCGCACGA 0.993134 -31 GGCCGCTACACCGTCCTGACCGATGCACCAGGG 8 90 1 CGCCTGACGA 0.78459 -112 TAACATGGGACTGTCCGCGACGCGACGTGGCCC 8 121 0 CGCCGCGCGC 0.893038 -81 TTTCAGTGCACCGTGCGAAACGCCGACACCGTT 11 92 1 CGGCGAACGC 0.996693 -209 TGAACTCCACCTGAAAGCACCGCTGAACAGCAG 11 124 1 CGAAGCACGC 0.699219 -177 CGGCCCTGTGCTGGGCTAAGCCAGCGTCTGCAA 11 268 1 CGGCTAACCA 0.817055 -33 CCAGCGTCTGCAAGGAGAACCGC 11 288 1 CAGAGAACGC 0.932597 -13 GGTGACGATGCAGAGCGAAGCGATGAGGAGGAG 13 25 0 CGGCGAACGA 0.995621 -276 GGTGACGATGCAGAGCGAAGCGATGAGCAGGAG 13 78 0 CGGCGAACGA 0.995621 -223 GGTGACGATGCAGAGCGAAGCGATGAGCAGGAG 13 131 0 CGGCGAACGA 0.995621 -170 GGTGACGATGCAGAGCGAAGCGATGAGCAGGAG 13 184 0 CGGCGAACGA 0.995621 -117 GGTGACGATGCAGAGCGAAGCGATGAGGAGGAG 13 237 0 CGGCGAACGA 0.995621 -64 AGGCCAGGCTCCAACCGAATCGCCCGGCTCCTC 15 20 0 CACCGAACGC 0.959382 -182 GTTGCCGTCCCGGACCGCATCCCCCTACATTGA 15 52 0 CGCCGCACCC 0.894113 -150 GCGGCTTATCCCGCGCGGCCCGCGGGGAGATCT 18 101 0 CGGCGGCCGC 0.905816 -200 * * ***** *** Masking position 11 Map Score: 38.9469 Number of sites scoring better than the average of aligned sites = 4920 Number in coding regions = 4491 Number in noncoding regions = 429 Number of orfs with sites within 600 bp upstream = 331 Fraction of orfs with sites within 600 bp upstream = 0.0531642 Motif number 4 GCAGCGCAACCATGGCCCAGGTCTGGACGT 1 42 1 CATGGCCCAG 0.787857 -60 CTCCTCATCGCTGCGCTCGGCATCGTCGCC 5 68 0 CTGCGCTCGG 0.960151 -31 GCCCCTGGTGCATCGGTCAGGACGGTGTAG 8 95 0 CATCGGTCAG 0.593616 -107 AATCAGACTCTTTGGCTGTGGCACCTAAAA 10 187 0 TTTGGCTGTG 0.530042 -114 TAGCCCAGCACAGGGCCGTGATATCGGTAT 11 256 0 CAGGGCCGTG 0.6421 -45 CAGACGCTGGCTTAGCCCAGCACAGGGCCG 11 268 0 CTTAGCCCAG 0.749785 -33 CTCCTCATCGCTTCGCTCTGCATCGTCACC 13 28 1 CTTCGCTCTG 0.983156 -273 CTGCTCATCGCTTCGCTCTGCATCGTCACC 13 81 1 CTTCGCTCTG 0.983156 -220 CTGCTCATCGCTTCGCTCTGCATCGTCACC 13 134 1 CTTCGCTCTG 0.983156 -167 CTGCTCATCGCTTCGCTCTGCATCGTCACC 13 187 1 CTTCGCTCTG 0.983156 -114 CTCCTCATCGCTTCGCTCTGCATCGTCACC 13 240 1 CTTCGCTCTG 0.983156 -61 GCTCCAACCGAATCGCCCGGCTCCTCCTCA 15 16 0 AATCGCCCGG 0.831216 -186 AACAGCGGCCCATCGCCGTGCGACGTAGGC 15 106 0 CATCGCCGTG 0.97995 -96 TTCGTTCCCACTTCGCCGGGTCGTTAGGGT 16 117 1 CTTCGCCGGG 0.989316 -28 AGTATGTCACCATCGCCGGGATCATCACTG 18 12 0 CATCGCCGGG 0.983564 -289 TGCTGGCCGCCTGCGTCCGGTCGCGGGCTG 18 41 1 CTGCGTCCGG 0.708458 -260 GCAGTCCTACCATGGCCGGGTGGGATGGGA 18 185 0 CATGGCCGGG 0.949706 -116 TGCACCATCCTTTCGCCGAGCGTGTACCCA 18 278 0 TTTCGCCGAG 0.786517 -23 ********** Masking position 5 Map Score: 31.8211 Number of sites scoring better than the average of aligned sites = 3809 Number in coding regions = 3452 Number in noncoding regions = 357 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 5 CGGCATCGTCGCCGGCGGTCATGGCGTCACCCTACC 5 45 0 GGGGGATGCG 0.794995 -54 AGCCTAGCGGGCCGTAGGGTGTGCCAG 6 19 1 GGTGGGTGCA 0.991452 -17 GAGAGTCGGAGAAGTTGGGAGCGGTAG 8 2 0 GGTGGGCGTA 0.933143 -200 GTCCAAGCTATCGGATGGTCGCGGCAGGAGGCAAGC 8 174 0 TGAGGGCGCA 0.915198 -28 GGACTACAACGGCGTAGGAAGTGTTGGGCATGACTG 10 82 0 GGTGGGTGTG 0.981314 -219 CTAAGTTCGCGGGGTTGGCTGAGCCAGAGGCTCAGC 10 139 0 GGTGGGAGCA 0.959496 -162 GGGATCAGTTTAGGACGGTTGTGCCGATTTCGTGGA 10 263 0 TGAGGGTGCG 0.975966 -38 CTTCCGGTTCTCCATAGGTCGCGCCGGGGACGGGCA 11 38 1 TATGGGCGCG 0.776622 -263 AGTGACGGTGTCGGTGGGTTGTGGCGTGATCAAACG 11 193 0 TGTGGGTGCG 0.991452 -108 TGCGTAACGATTTGAGGGTAGTGACGGTGTCGGTGG 11 212 0 TGAGGGTGCG 0.975966 -89 CGCCAAACTGTTGTCGGCCATGCAAATTGAGTGTG 12 10 1 GGTGGATGAA 0.737006 -64 TGCGGCGGCCGGCGACGGTAGCGGCATGATGGAGTG 12 48 1 GGAGGGCGCA 0.960854 -26 ATCGCCGTGCGACGTAGGCCGTGTAGCCCAGTGTGC 15 89 0 GGTGGGTGAG 0.985587 -113 TGAGTGGTCGGTAGTTGTCAGTGGCGTGCTGTAGGA 15 168 1 GGTGTGTGCG 0.928987 -34 CAGTTGGGCTAGGTTGGCCGAGCAGACGCAAAAGC 16 10 1 TGTGGGAGAG 0.859962 -135 GGGTGGGATGGGAGTTTGGCGTGCTACTCATACTGA 18 162 0 GGTTGGTGTA 0.682762 -139 TTCAATGCCTTTTGTCTGCGGTGAAGGCATGTTTTA 22 57 1 TGTTGGTGAG 0.73701 -55 * ** ** *** ** Masking position 13 Map Score: 23.8964 Number of sites scoring better than the average of aligned sites = 6990 Number in coding regions = 6661 Number in noncoding regions = 329 Number of orfs with sites within 600 bp upstream = 265 Fraction of orfs with sites within 600 bp upstream = 0.0425634 Motif number 6 CGTTCGGCTTGGGTAGGGTGACGCCATGAC 5 34 1 GGGTAGGGTG 0.97514 -65 GCCTAGCGGGCCGTAGGGTGTGCCAG 6 20 1 CCGTAGGGTG 0.982997 -16 AGGTCAACGGCGCTAGGGCGT 7 2 0 CGCTAGGGCG 0.976318 -97 AAGCTAAGTTCGCGGGGTTGGCTGAGCCAG 10 148 0 CGCGGGGTTG 0.857104 -153 TTCCGGTTCTCCATAGGTCGCGCCGGGGAC 11 39 1 CCATAGGTCG 0.798292 -262 CACGAAAACACCGTGGGGCGCCACACACGT 11 166 1 CCGTGGGGCG 0.978012 -135 GTGACGGTGTCGGTGGGTTGTGGCGTGATC 11 198 0 CGGTGGGTTG 0.987461 -103 CGACGCTACACCGTAGGTTGGACACC 13 285 1 CCGTAGGTTG 0.977314 -16 CAGTTGGGCTAGGTTGGCCGAGCAGA 16 7 1 GGCTAGGTTG 0.92841 -138 CACGCCGTAGCGGTTGGTCGAACTGGCTGG 16 85 1 CGGTTGGTCG 0.925454 -60 TTCGCCGGGTCGTTAGGGTGGTAAGTC 16 128 1 CGTTAGGGTG 0.926574 -17 TACCATGGCCGGGTGGGATGGGAGTTTGGC 18 178 0 GGGTGGGATG 0.85019 -123 ********** Masking position 6 Map Score: 13.8168 Number of sites scoring better than the average of aligned sites = 1433 Number in coding regions = 1301 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 7 GTCGGATAGCGCTGGCCAACTCTGGG 1 5 0 GCGGCCACTC 0.970877 -97 CTGGACGTACGCGATCACCGCCGCTGTGCGGC 1 64 1 GCATCACGCC 0.641939 -38 GGTGATAACCGCGATCCTAGTCACCCGGTTGA 4 72 0 GCATCCAGTC 0.863547 -23 ATCGTCGCCGGCGGTCATGGCGTCACCCTACC 5 45 0 GCGTCAGGCG 0.883119 -54 CAGCCAGTCGGCGTTCCGGCCGAGGCTAGGGA 7 37 1 GCTTCCGCCG 0.750227 -62 TAGCAGACTGGCTTGCCTCCTGCCGCGACCAT 8 164 1 GCTGCCCCTG 0.60124 -38 CAGTAAGGTATCCGGCTCACCCAGAGTTGTCA 10 46 0 TCGGCTACCC 0.504529 -255 CTTACTGGGTGCAGTCATGCCCAACACTTCCT 10 71 1 GCGTCAGCCC 0.900131 -230 CGGCTGAGCCTCTGGCTCAGCCAACCCCGCGA 10 137 1 TCGGCTAGCC 0.568607 -164 AGAACCGGAAGCTGTACAAGTCGCCAACCACG 11 17 0 GCGTACAGTC 0.724334 -284 CCTTGCAGACGCTGGCTTAGCCCAGCACAGGG 11 271 0 GCGGCTAGCC 0.953828 -30 GCCGGCCGCCGCAGTCACACTCAATTTGCATG 12 29 0 GCGTCAACTC 0.879474 -45 TGCCACCGTTGCCGTCCCGGACCGCATCCCCC 15 60 0 GCGTCCGGAC 0.755884 -142 GTCAGCTGTTGCGGTCTGAGTGGTCGGTAGTT 15 152 1 GCGTCTAGTG 0.859494 -50 CGTCTGCTCGGCCAACCTAGCCCAACTG 16 7 0 GCAACCAGCC 0.547365 -138 GTGACATACTGCTGGCCGCCTGCGTCCGGTCG 18 32 1 GCGGCCCCTG 0.92741 -269 GCGTCCGGTCGCGGGCTGACTCCGGTCACCAG 18 53 1 GCGGCTACTC 0.884338 -248 GGAGCGTGCCGCTGGCCAGATCTCCCCGCGGG 18 84 1 GCGGCCGATC 0.608511 -217 AGATCTCCCCGCGGGCCGCGCGGGATAAGCCG 18 101 1 GCGGCCCGCG 0.971846 -200 CATACTGATCGCGGTCCTAGCGGTATTTCTTG 18 138 0 GCGTCCAGCG 0.982355 -163 GCTCATGCCAGCAGTCCTACCATGGCCGGGTG 18 193 0 GCGTCCACCA 0.789811 -108 AGGGTGGTCCGCTATCACCCCGATGACCGAGG 19 51 1 GCATCACCCG 0.472856 -29 AACCACTGACGCGTTACGAGCCCAG 21 12 1 GCTTACAGCC 0.39294 -15 TAGCTGTCCTAGTGAGGACCTTCT 22 98 0 GCGTCCAGTG 0.963861 -14 ** **** **** Masking position 2 Map Score: 24.1414 Number of sites scoring better than the average of aligned sites = 21079 Number in coding regions = 19787 Number in noncoding regions = 1292 Number of orfs with sites within 600 bp upstream = 838 Fraction of orfs with sites within 600 bp upstream = 0.134597 Motif number 8 TCACCGGCGCGACTCATCTGCGCCGCTCCT 13 53 1 GACTCATCTG 0.996059 -248 TCACCGGCGCGACTCATCTGCGCCGCTCCT 13 106 1 GACTCATCTG 0.996059 -195 TCACCGGCGCGACTCATCTGCGCCGCTCCT 13 159 1 GACTCATCTG 0.996059 -142 TCACCGGCGCGACTCATCTGCGCCGCTCCT 13 212 1 GACTCATCTG 0.996059 -89 ********** Masking position 6 Map Score: 9.77556 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 CGGCTTGGGTAGGGTGACGCCATGACCGCC 5 38 1 AGGGTGACGC 0.732389 -61 GCCATGACCGCCGGCGACGATGCCGAGCGC 5 56 1 CCGGCGACGA 0.977622 -43 CCTTGCGGATACGGTCTCGATGAGGCAATA 8 62 0 ACGGTCTCGA 0.73254 -140 ATCGGTCAGGACGGTGTAGCGGCCTTGCGG 8 84 0 ACGGTGTAGC 0.788939 -118 TCGGACTACAACGGCGTAGGAAGTGTTGGG 10 90 0 ACGGCGTAGG 0.884356 -211 CCTAAAAAAGACTGTCAAGCTAAGTTCGCG 10 164 0 ACTGTCAAGC 0.109508 -137 TTTGGTCCACACCGTGACGGGTTTGTTCGT 10 227 1 ACCGTGACGG 0.942558 -74 ATAGGTCGCGCCGGGGACGGGCAGCGGGTC 11 51 1 CCGGGGACGG 0.94003 -250 GTGGAGTTCAACGGTGTCGGCGTTTCGCAC 11 104 0 ACGGTGTCGG 0.981377 -197 GAGGGTAGTGACGGTGTCGGTGGGTTGTGG 11 205 0 ACGGTGTCGG 0.981377 -96 ATTGAGTGTGACTGCGGCGGCCGGCGACGG 12 36 1 ACTGCGGCGG 0.580945 -38 ACTGCGGCGGCCGGCGACGGTAGCGGCATG 12 46 1 CCGGCGACGG 0.975263 -28 ATGAGTCGCGCCGGTGACGATGCAGAGCGA 13 40 0 CCGGTGACGA 0.983015 -261 ATGAGTCGCGCCGGTGACGATGCAGAGCGA 13 93 0 CCGGTGACGA 0.983015 -208 ATGAGTCGCGCCGGTGACGATGCAGAGCGA 13 146 0 CCGGTGACGA 0.983015 -155 ATGAGTCGCGCCGGTGACGATGCAGAGCGA 13 199 0 CCGGTGACGA 0.983015 -102 ACCATGCGCGCCGGTGACGATGCAGAGCGA 13 252 0 CCGGTGACGA 0.983015 -49 TGTCCAACCTACGGTGTAGCGTCGCTGACC 13 279 0 ACGGTGTAGC 0.788939 -22 GCGGTCCGGGACGGCAACGGTGGCACACTG 15 67 1 ACGGCAACGG 0.813483 -135 CCTACGTCGCACGGCGATGGGCCGCTGTTC 15 107 1 ACGGCGATGG 0.829863 -95 AGTTCGACCAACCGCTACGGCGTGAGCAGA 16 79 0 ACCGCTACGG 0.344713 -66 TTCTCGTTTGACTGTGACGACGCGGAGCCG 17 13 0 ACTGTGACGA 0.873714 -118 CCTTTTGTCTGCGGTGAAGGCATGTTTTAC 22 64 1 GCGGTGAAGG 0.777806 -48 ********** Masking position 4 Map Score: 44.4249 Number of sites scoring better than the average of aligned sites = 10787 Number in coding regions = 10273 Number in noncoding regions = 514 Number of orfs with sites within 600 bp upstream = 392 Fraction of orfs with sites within 600 bp upstream = 0.0629618 Motif number 10 GCAATATCGGACAAGTGTCCAATCGATGAT 8 38 0 ACAAGTGTCC 0.854074 -164 CGAAATCGGCACAACCGTCCTAAACTGATC 10 267 1 ACAACCGTCC 0.900529 -34 CGGAAGCTGTACAAGTCGCCAACCACGACC 11 14 0 ACAAGTCGCC 0.900529 -287 TGAACAGCAGAAAAGCGCCCACGAAAACAC 11 147 1 AAAAGCGCCC 0.978152 -154 TGATCACGCCACAACCCACCGACACCGTCA 11 197 1 ACAACCCACC 0.836976 -104 TTCCGAATTGAACAGCGGCCCATCGCCGTG 15 116 0 AACAGCGGCC 0.845379 -86 GAGCAGACGCAAAAGCCCCCATTTCGGGCC 16 30 1 AAAAGCCCCC 0.978152 -115 GAGCAGACGCAAAAGCCCCCATTTCGGGCC 16 56 0 AAAAGCCCCC 0.978152 -89 ACAACTTAACAAGCACCCCTATCTTACT 19 9 1 ACAAGCACCC 0.943995 -71 ********** Masking position 4 Map Score: 6.2396 Number of sites scoring better than the average of aligned sites = 386 Number in coding regions = 300 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 11 CACCGGCATCACGAGAACCAGAG 3 3 1 CCGGCACACG 0.982911 -40 TTTGACCTAAACTTCACCACGTCTTGTCCAT 9 19 1 ACTTCACACG 0.899409 -34 AGTCTACGTGCCTTCAACACGTCGCGCGGCG 10 12 1 CCTTCACACG 0.987662 -289 TAAACTGATCCCGTGAGCATGCGC 10 287 1 CCGTGACATG 0.866801 -14 CCCACCGACACCGTCACTACCCTCAAATCGT 11 211 1 CCGTCATACC 0.818212 -90 AAGCGGTATACCGATATCACGGCCCTGTGCT 11 249 1 CCGATACACG 0.963965 -52 ACTGTTGTTCCTACAGCACGCCACTGACAA 15 182 0 CCTACACACG 0.980268 -20 CTGGCATGAGCCGTTATTACGCCGAGCGTGA 18 214 1 CCGTTATACG 0.894184 -87 GGGGCCAGGCTAGAACACGTTTCATTACT 22 9 1 GCTAGACACG 0.777068 -103 ****** **** Masking position 6 Map Score: 2.46617 Number of sites scoring better than the average of aligned sites = 1767 Number in coding regions = 1676 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 12 AGCGGCGGTGATCGCGTACGTCCAGACCTG 1 59 0 ATCGCGTACG 0.369879 -43 ATCACTACGCTTCGGGGCCGCCGGTTAGGT 2 16 0 TTCGGGGCCG 0.890949 -73 TATAAGGTCAGTCGGATGCGCTCG 4 5 0 GTCGGATGCG 0.791491 -90 ACGTTCTCGTTTCGCGTTCGGCTTGGGTAG 5 20 1 TTCGCGTTCG 0.436001 -79 GCTCGGCATCGTCGCCGGCGGTCATGGCGT 5 54 0 GTCGCCGGCG 0.994161 -45 ATCGTTGAACTTCGGCTACGAGTGGTCCCT 7 64 0 TTCGGCTACG 0.810901 -35 AGTCGGAGAAGTTGGGAGCGGTAG 8 5 0 GTTGGGAGCG 0.421618 -197 ACATGGGACTGTCCGCGACGCGACGTGGCC 8 122 0 GTCCGCGACG 0.793404 -80 CTATCGGATGGTCGCGGCAGGAGGCAAGCC 8 173 0 GTCGCGGCAG 0.651818 -29 AGTTCGCGGGGTTGGCTGAGCCAGAGGCTC 10 142 0 GTTGGCTGAG 0.305929 -159 AATCAGACTCTTTGGCTGTGGCACCTAAAA 10 187 0 TTTGGCTGTG 0.0622164 -114 CATAGGTCGCGCCGGGGACGGGCAGCGGGT 11 50 1 GCCGGGGACG 0.794184 -251 CGGGCAGCGGGTCGTGTGCGCGTCTTTCAG 11 68 1 GTCGTGTGCG 0.905583 -233 CCACGGTGTTTTCGTGGGCGCTTTTCTGCT 11 152 0 TTCGTGGGCG 0.847984 -149 TGCCGCTACCGTCGCCGGCCGCCGCAGTCA 12 44 0 GTCGCCGGCC 0.885515 -30 GCTCTGCATCGTCACCGGCGCGACTCATCT 13 42 1 GTCACCGGCG 0.970251 -259 GCTCTGCATCGTCACCGGCGCGACTCATCT 13 95 1 GTCACCGGCG 0.970251 -206 GCTCTGCATCGTCACCGGCGCGACTCATCT 13 148 1 GTCACCGGCG 0.970251 -153 GCTCTGCATCGTCACCGGCGCGACTCATCT 13 201 1 GTCACCGGCG 0.970251 -100 GCTCTGCATCGTCACCGGCGCGCATGGTCA 13 254 1 GTCACCGGCG 0.970251 -47 GGCGCGCATGGTCAGCGACGCTACACCGTA 13 270 1 GTCAGCGACG 0.871496 -31 GGGGGATGCGGTCCGGGACGGCAACGGTGG 15 60 1 GTCCGGGACG 0.755016 -142 AAGCCCCCATTTCGGGCCCGAAATGGGGGC 16 44 0 TTCGGGCCCG 0.390261 -101 GTCGGCTCCGCGTCGTCACA 17 1 1 GTCGGCTCCG 0.94596 -130 CATACTGCTGGCCGCCTGCGTCCGGTCGCG 18 36 1 GCCGCCTGCG 0.913445 -265 CCTGCGTCCGGTCGCGGGCTGACTCCGGTC 18 50 1 GTCGCGGGCT 0.807292 -251 AGTGCGATTTTTCGCGTGCGTTCTTGCACT 18 249 0 TTCGCGTGCG 0.943023 -52 TTCAATGCCTTTTGTCTGCGGTGAAGGCAT 22 57 1 TTTGTCTGCG 0.257281 -55 ********** Masking position 2 Map Score: 37.8255 Number of sites scoring better than the average of aligned sites = 32961 Number in coding regions = 31358 Number in noncoding regions = 1603 Number of orfs with sites within 600 bp upstream = 845 Fraction of orfs with sites within 600 bp upstream = 0.135721 Motif number 13 GTATAGGTTACCTAACTTACTTAGGTAGCA 2 60 1 CCTAACTTAC 0.973759 -29 AACAAGCACCCCTATCTTACTCCGGAGTAA 19 18 1 CCTATCTTAC 0.984947 -62 AGCGGACCACCCTATCTTACTCCGGAGTAA 19 34 0 CCTATCTTAC 0.984947 -46 ********** Masking position 4 Map Score: 0.578275 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 14 ********** No masking Map Score: -6.55588e-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: -6.55588e-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