AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00680_mtub_reg_300.orf -o00680_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 glyA2 300 glyA2 #2 Rv0079 300 hypothetical protein Rv0079 #3 Rv0081 94 hypothetical protein Rv0081 #4 adhB 98 adhB #5 Rv0767c 201 hypothetical protein Rv0767c #6 glyA 300 glyA #7 katG 37 katG #8 furA 104 furA #9 Rv1910c 82 hypothetical protein Rv1910c #10 lppC 99 lppC #11 fadB5 99 fadB5 #12 adhE2 300 adhE2 Motif number 1 CCTTCGGTCAGGCACGGTCGGTGCGACCGTCCCT 1 18 0 GGCGGTCGTC 0.920568 -283 CTGACCGAAGGTGTAGAGCGGCGCCATGATGCGA 1 41 1 GTGGAGCGCC 0.97071 -260 AAACCTGAGAGTCTGCGGCGTCGCATCATGGCGC 1 61 0 GTCCGGCGCC 0.991965 -240 GTTTCGACGAGCCCGGATCGCGCCGGGCTGGTTG 1 116 0 GCCGATCGGC 0.835901 -185 ACATCGTTTCGGCCACGGCGAGGTCGCCAACAGT 1 183 0 GGCCGGCGGT 0.772826 -118 ATCCGGCGGCCGCGACATCGTTTCGGCCACGGCG 1 197 0 CGCCATCGTC 0.984309 -104 TCCGGGAACACCCTTGACCGCCCCCGAGTACGCC 1 257 1 CCCGACCGCC 0.930715 -44 ATGAGGCTGGGTCGTGAACGGCCCAA 2 3 0 GTCGAACGCC 0.743194 -298 CAGCCTCATGCGCTGCATCTGCTCGCCAACCTCG 2 28 1 CGCCATCTCC 0.746247 -273 CCTCGTACATGTCCAGAGCGAGCCTCAGCTTCTG 2 57 1 GTCGAGCGGC 0.974778 -244 GCCTCAGCTTCTGCGCAGCGACGGAAACTGCCAC 2 78 1 CTGCAGCGCG 0.952289 -223 GCGGCATTTCGTGTGGATCGACTCGTTGCCACAC 2 134 0 GTGGATCGCC 0.950795 -167 TAGTCCGCGGCCCAACGGCGGCATTTCGTGTGGA 2 151 0 CCCCGGCGCT 0.834486 -150 GGGACTTTCGGCCCTGTCCGCGTCCGTGTCGGCC 2 225 1 GCCGTCCGGC 0.622782 -76 CCGATTGGCCGCGGGCGGCCCGCACGCATCC 3 8 1 GCCGGGCGCC 0.925479 -87 GTCTCCTGAGAGCTTCAGCGTTACATCGGTTGAC 3 68 0 AGCCAGCGTC 0.834873 -27 CTGAGTGTAGGTCAACGGCGCTAGGGCGT 4 6 0 GTCCGGCGTG 0.897539 -93 TAGCCTCGGCCGGAACGCCGACTGGCTGAGTGTA 4 31 0 CGGCGCCGCG 0.826 -68 TTCTCCGACTCTCATCATCGATTGGACACTTGTC 5 25 1 CTCCATCGTG 0.918915 -177 TGTCCGATATTGCCTCATCGAGACCGTATCCGCA 5 55 1 TGCCATCGGC 0.691775 -147 AGACCGTATCCGCAAGGCCGCTACACCGTCCTGA 5 75 1 CGCGGCCGTC 0.938119 -127 CCGCTACACCGTCCTGACCGATGCACCAGGGGCC 5 92 1 GTCGACCGTC 0.903162 -110 ATGCACCAGGGGCCACGTCGCGTCGCGGACAGTC 5 112 1 GGCCGTCGGC 0.974322 -90 TCCAAGCTATCGGATGGTCGCGGCAGGAGGCAAG 5 175 0 CGGGGTCGGC 0.904278 -27 TGGGCACTGGGGCCAGGGCGCGGTGTTTCGATGG 6 35 1 GGCGGGCGGT 0.687652 -266 AGCATCAACCGGCGTCAGCGTGCGAAATTCACAG 6 84 0 GGCCAGCGGG 0.945578 -217 CGGGCACAAACCGCCCACCGCTACTCGTGACCTA 6 124 1 CCGCACCGTC 0.802188 -177 GGGTAATCAGCCCGGGAGCGGCTCGCTGGATACA 6 232 1 CCCGAGCGCC 0.987929 -69 AGGTGCAGCAGTCACGGGCGCCAGTGTATCCAGC 6 256 0 GTCGGGCGCG 0.872905 -45 TACCGCGGTAGTGCGAGCGTCAGGTGCAG 6 282 0 CGGGTGCGGG 0.66646 -19 GCCCCGGGGCCGCTGGATCGTGGGATGGCGGGTG 8 13 0 CGCGATCGGG 0.904424 -92 CAGCGGCCCCGGGGCGATCGGGTCCTAGCAGACG 8 32 1 GGGGATCGGC 0.659479 -73 CGCCGCGGCATCCCTGGCGAGGTG 9 1 1 CGCCGGCACC 0.804859 -82 TCAGGAGGTTCGGCGGGGCGTTACCTTTGCGGTT 11 11 0 CGGGGGCGTC 0.95162 -89 GAGGGGTGTTCGCGGGTGCGACCCGTCAAGCCTG 11 62 1 CGCGTGCGCC 0.983247 -38 ACTCATCTGCGCCGCTCCTCCTCAT 12 2 1 CTCCTGCGCC 0.987716 -299 TGCGCCGCTCCTCCTCATCGCTTCGCTCTGCATC 12 18 1 CTCCATCGTC 0.982336 -283 CATCGCTTCGCTCTGCATCGTCACCGGCGCGACT 12 33 1 CTCCATCGCC 0.99375 -268 ACCGGCGCGACTCATCTGCGCCGCTCCTGCTCAT 12 55 1 CTCCTGCGCC 0.987716 -246 TGCGCCGCTCCTGCTCATCGCTTCGCTCTGCATC 12 71 1 CTGCATCGTC 0.950513 -230 CATCGCTTCGCTCTGCATCGTCACCGGCGCGACT 12 86 1 CTCCATCGCC 0.99375 -215 ACCGGCGCGACTCATCTGCGCCGCTCCTGCTCAT 12 108 1 CTCCTGCGCC 0.987716 -193 TGCGCCGCTCCTGCTCATCGCTTCGCTCTGCATC 12 124 1 CTGCATCGTC 0.950513 -177 CATCGCTTCGCTCTGCATCGTCACCGGCGCGACT 12 139 1 CTCCATCGCC 0.99375 -162 ACCGGCGCGACTCATCTGCGCCGCTCCTGCTCAT 12 161 1 CTCCTGCGCC 0.987716 -140 TGCGCCGCTCCTGCTCATCGCTTCGCTCTGCATC 12 177 1 CTGCATCGTC 0.950513 -124 CATCGCTTCGCTCTGCATCGTCACCGGCGCGACT 12 192 1 CTCCATCGCC 0.99375 -109 ACCGGCGCGACTCATCTGCGCCGCTCCTCCTCAT 12 214 1 CTCCTGCGCC 0.987716 -87 TGCGCCGCTCCTCCTCATCGCTTCGCTCTGCATC 12 230 1 CTCCATCGTC 0.982336 -71 CATCGCTTCGCTCTGCATCGTCACCGGCGCGCAT 12 245 1 CTCCATCGCC 0.99375 -56 ACCGGCGCGCATGGTCAGCGACGCTACACCGTAG 12 267 1 ATGCAGCGCC 0.816381 -34 *** ***** * * Masking position 9 Map Score: 116.816 Number of sites scoring better than the average of aligned sites = 34610 Number in coding regions = 32317 Number in noncoding regions = 2293 Number of orfs with sites within 600 bp upstream = 1050 Fraction of orfs with sites within 600 bp upstream = 0.168648 Motif number 2 CCTGAAACCTGAGAGTCTGCGGCGTCGCATCAT 1 66 0 GGAGTCGGGC 0.776044 -235 TTTCAGGACAGAGCGGGGAGGGCGCAACCAGCC 1 92 1 GGCGGGAGGC 0.963789 -209 CGCGACATCGTTTCGGCCACGGCGAGGTCGCCA 1 188 0 TTCGGCAGGC 0.801793 -113 AATGGGCATCCGGCGGCCGCGACATCGTTTCGG 1 205 0 CGCGGCGGAC 0.983247 -96 CGAGCAGATGCAGCGCATGAGGCTGGGTCGTGA 2 20 0 CGCGCAGGGC 0.901447 -281 CGTCGCTGCGCAGAAGCTGAGGCTCGCTCTGGA 2 68 0 CGAAGCGGGC 0.888819 -233 AGCCTACTGGGCGCACGTGTGGCAACGAGTCGA 2 118 1 GGCACGGGGC 0.994257 -183 CGGCTAGTCCGCGGCCCAACGGCGGCATTTCGT 2 156 0 GGGCCCAGGC 0.689567 -145 GATGCGTGCGGGCCGCCCGCGGCCAATCGG 3 8 0 GCCGCCGGGC 0.990986 -87 ACGCTGAAGCTCTCAGGAGACGCG 3 81 1 TTCAGGGCGC 0.528781 -14 ACGCCCTAGCGCCGTTGACCTACACTCAG 4 7 1 TGCGCCTGAC 0.763414 -92 CCAGTCGGCGTTCCGGCCGAGGCTAGGGACCAC 4 40 1 TCCGGCGGGC 0.983334 -59 GTCCTGACCGATGCACCAGGGGCCACGTCGCGT 5 102 1 AGCACCGGGC 0.973701 -100 CACCGCGCCCTGGCCCCAGTGCCCAGCTAAGCC 6 27 0 TGCCCCGGCC 0.81609 -274 TTTCGATGGAATTCAGCTGTGGCCCTGTGAATT 6 60 1 ATCAGCGGGC 0.812505 -241 GTGACCTACGTGGCAGCTGGGGCACTAGTGGCT 6 150 1 TGCAGCGGGC 0.995048 -151 AGGGTAATCAGCCCGGGAGCGGCTCGCTGGATA 6 231 1 GCCGGGGGGC 0.978542 -70 CTGGATACACTGGCGCCCGTGACTGCTGCACCT 6 257 1 TGCGCCGGAC 0.991825 -44 CCCGTGACTGCTGCACCTGACGCTCGCACTACC 6 272 1 CGCACCGCGC 0.918082 -29 CCACGATCCAGCGGCCCCGGGGCGATCGGGTCC 8 24 1 GGGCCCGGGC 0.666005 -81 CACCTCGCCAGGGATGCCGCGGCG 9 2 0 GGATGCGGGC 0.754724 -81 TATTGATCATTGTCGCCAGGCGCAATTGGAGAA 9 49 0 TTCGCCGCGC 0.867324 -34 GGCGATGGGTGGCCCGGGGCCCGGCTGTCT 10 8 1 GTGGCCGGGC 0.959309 -92 AGAGGGGTGTTCGCGGGTGCGACCCGTCAAGCC 11 61 1 TGCGGGGGAC 0.980473 -39 GCGAAGCGATGAGGAGGAGCGGCGCAGATGAGT 12 11 0 GGGAGGGGGC 0.970216 -290 CGCAGATGAGTCGCGCCGGTGACGATGCAGAGC 12 42 0 TGCGCCGGAC 0.991823 -259 GCGAAGCGATGAGCAGGAGCGGCGCAGATGAGT 12 64 0 GGCAGGGGGC 0.99395 -237 CGCAGATGAGTCGCGCCGGTGACGATGCAGAGC 12 95 0 TGCGCCGGAC 0.991823 -206 GCGAAGCGATGAGCAGGAGCGGCGCAGATGAGT 12 117 0 GGCAGGGGGC 0.99395 -184 CGCAGATGAGTCGCGCCGGTGACGATGCAGAGC 12 148 0 TGCGCCGGAC 0.991823 -153 GCGAAGCGATGAGCAGGAGCGGCGCAGATGAGT 12 170 0 GGCAGGGGGC 0.99395 -131 CGCAGATGAGTCGCGCCGGTGACGATGCAGAGC 12 201 0 TGCGCCGGAC 0.991823 -100 GCGAAGCGATGAGGAGGAGCGGCGCAGATGAGT 12 223 0 GGGAGGGGGC 0.970216 -78 CGCTGACCATGCGCGCCGGTGACGATGCAGAGC 12 254 0 GGCGCCGGAC 0.995147 -47 * ***** * *** Masking position 13 Map Score: 82.4436 Number of sites scoring better than the average of aligned sites = 18833 Number in coding regions = 17765 Number in noncoding regions = 1068 Number of orfs with sites within 600 bp upstream = 661 Fraction of orfs with sites within 600 bp upstream = 0.106168 Motif number 3 GTCCTGAAACCTGAGAGTCTGCGGCGTCGCATCA 1 67 0 CTGAGCGCGG 0.987861 -234 CTCAGGTTTCAGGACAGAGCGGGGAGGGCGCAAC 1 86 1 AGGACGGGGG 0.863822 -215 CGGATCGCGCCGGGCTGGTTGCGCCCTCCCCGCT 1 103 0 CGGGCTGCGC 0.592086 -198 GGTTCAGACAAGGGCCAACTCCGGTTTCGACGAG 1 139 0 AGGGCCCCGG 0.959038 -162 GCCCGGCCAAATGGGCATCCGGCGGCCGCGACAT 1 213 0 ATGGGCGGCG 0.93263 -88 TCCCGGAGCAATCGGCTGCCCGGCCAAATGGGCA 1 230 0 ATCGGCCGGC 0.916171 -71 GGGGGCGGTCAAGGGTGTTCCCGGAGCAATCGGC 1 248 0 AAGGGTCCGG 0.755105 -53 GAGGTTGGCGAGCAGATGCAGCGCATGAGGCTGG 2 27 0 AGCAGCGCGC 0.956698 -274 CAGAGCGAGCCTCAGCTTCTGCGCAGCGACGGAA 2 70 1 CTCAGCGCGC 0.929627 -231 CACATTTGGCATGGGACTTTCGGCCCTGTCCGCG 2 213 1 ATGGGTCGGC 0.847853 -88 CGGATGCGTGCGGGCCGCCCGCGGCCAATCGG 3 9 0 CGGGCCGCGG 0.944993 -86 TGAAGAATTTATCAGATAGTGCGGATGCGTGCGG 3 30 0 ATCAGGGCGG 0.97507 -65 TTGACCTACACTCAGCCAGTCGGCGTTCCGGCCG 4 25 1 CTCAGGCGGC 0.700557 -74 CCCCTGGTGCATCGGTCAGGACGGTGTAGCGGCC 5 90 0 ATCGGGACGG 0.704361 -112 CCGATGCACCAGGGGCCACGTCGCGTCGCGGACA 5 109 1 AGGGGCTCGC 0.793192 -93 TGCAGCTAACATGGGACTGTCCGCGACGCGACGT 5 126 0 ATGGGGCCGC 0.980988 -76 TGTCCAAGCTATCGGATGGTCGCGGCAGGAGGCA 5 177 0 ATCGGGCGCG 0.6802 -25 AGCTAAGCCCAGGGGGTACCCCCGG 6 2 0 AGGGGCCCCG 0.889921 -299 CTGGGCTTAGCTGGGCACTGGGGCCAGGGCGCGG 6 24 1 CTGGGTGGGC 0.806714 -277 CGTCAGGTGCAGCAGTCACGGGCGCCAGTGTATC 6 260 0 AGCAGCGGCG 0.721875 -41 CCCACGATCCAGCGGCCCCGGGGCGATCGGGTCC 8 23 1 AGCGGCGGGC 0.931928 -82 ACCACCTCGCCAGGGATGCCGCGGCG 9 3 0 CAGGGCGCGG 0.928083 -80 GGCGATGGGTGGCCCGGGGCCCGGCTGT 10 5 1 ATGGGCCGGG 0.985365 -95 ACGAGTTATCAGGAGGTTCGGCGGGGCGTTACCT 11 19 0 AGGAGCGCGG 0.992707 -81 GCTATCACAGAGGGGTGTTCGCGGGTGCGACCCG 11 53 1 AGGGGTGCGG 0.973892 -47 GAGCGAAGCGATGAGGAGGAGCGGCGCAGATGAG 12 12 0 ATGAGGGCGG 0.991108 -289 AGCGGCGCAGATGAGTCGCGCCGGTGACGATGCA 12 46 0 ATGAGCCCGG 0.990881 -255 GAGCGAAGCGATGAGCAGGAGCGGCGCAGATGAG 12 65 0 ATGAGGGCGG 0.991108 -236 AGCGGCGCAGATGAGTCGCGCCGGTGACGATGCA 12 99 0 ATGAGCCCGG 0.990881 -202 GAGCGAAGCGATGAGCAGGAGCGGCGCAGATGAG 12 118 0 ATGAGGGCGG 0.991108 -183 AGCGGCGCAGATGAGTCGCGCCGGTGACGATGCA 12 152 0 ATGAGCCCGG 0.990881 -149 GAGCGAAGCGATGAGCAGGAGCGGCGCAGATGAG 12 171 0 ATGAGGGCGG 0.991108 -130 AGCGGCGCAGATGAGTCGCGCCGGTGACGATGCA 12 205 0 ATGAGCCCGG 0.990881 -96 GAGCGAAGCGATGAGGAGGAGCGGCGCAGATGAG 12 224 0 ATGAGGGCGG 0.991108 -77 TGTAGCGTCGCTGACCATGCGCGCCGGTGACGAT 12 261 0 CTGACGGCGC 0.812632 -40 ***** * **** Masking position 13 Map Score: 76.9946 Number of sites scoring better than the average of aligned sites = 12442 Number in coding regions = 11451 Number in noncoding regions = 991 Number of orfs with sites within 600 bp upstream = 643 Fraction of orfs with sites within 600 bp upstream = 0.103277 Motif number 4 GCATCATGGCGCCGCTCTACACCTTCGGTCAG 1 41 0 GCGCTTACAC 0.610576 -260 CTGAGAGTCTGCGGCGTCGCATCATGGCGCCG 1 59 0 GGGCGCGCAT 0.936524 -242 TTGGCGAGCAGATGCAGCGCATGAGGCTGGGT 2 25 0 GTGCACGCAT 0.824584 -276 GGCAGTTTCCGTCGCTGCGCAGAAGCTGAGGC 2 78 0 GCGCTCGCAG 0.95463 -223 ATTCAGCTGTGGCCCTGTGAATTTCGCACGCT 6 70 1 GCCCTTGAAT 0.691299 -231 GGGCGGTTTGTGCCCGACTCACAGCATCAACC 6 108 0 TCCCGCTCAC 0.852743 -193 CAAAGGTAACGCCCCGCCGAACCTCCTGATAA 11 16 1 GCCCGCGAAC 0.750644 -84 TGTCAGGCTTGACGGGTCGCACCCGCGAACAC 11 67 0 GCGGGCGCAC 0.806837 -33 CATCTGCGCCGCTCCTCCTCATCGCTTCGCTC 12 14 1 GTCCTCTCAT 0.939638 -287 TCCTCATCGCTTCGCTCTGCATCGTCACCGGC 12 29 1 TCGCTTGCAT 0.929662 -272 CATCGTCACCGGCGCGACTCATCTGCGCCGCT 12 48 1 GCGCGCTCAT 0.990685 -253 CATCTGCGCCGCTCCTGCTCATCGCTTCGCTC 12 67 1 GTCCTCTCAT 0.939638 -234 TGCTCATCGCTTCGCTCTGCATCGTCACCGGC 12 82 1 TCGCTTGCAT 0.929662 -219 CATCGTCACCGGCGCGACTCATCTGCGCCGCT 12 101 1 GCGCGCTCAT 0.990685 -200 CATCTGCGCCGCTCCTGCTCATCGCTTCGCTC 12 120 1 GTCCTCTCAT 0.939638 -181 TGCTCATCGCTTCGCTCTGCATCGTCACCGGC 12 135 1 TCGCTTGCAT 0.929662 -166 CATCGTCACCGGCGCGACTCATCTGCGCCGCT 12 154 1 GCGCGCTCAT 0.990685 -147 CATCTGCGCCGCTCCTGCTCATCGCTTCGCTC 12 173 1 GTCCTCTCAT 0.939638 -128 TGCTCATCGCTTCGCTCTGCATCGTCACCGGC 12 188 1 TCGCTTGCAT 0.929662 -113 CATCGTCACCGGCGCGACTCATCTGCGCCGCT 12 207 1 GCGCGCTCAT 0.990685 -94 CATCTGCGCCGCTCCTCCTCATCGCTTCGCTC 12 226 1 GTCCTCTCAT 0.939638 -75 TCCTCATCGCTTCGCTCTGCATCGTCACCGGC 12 241 1 TCGCTTGCAT 0.929662 -60 * **** ***** Masking position 11 Map Score: 39.7995 Number of sites scoring better than the average of aligned sites = 3319 Number in coding regions = 3018 Number in noncoding regions = 301 Number of orfs with sites within 600 bp upstream = 244 Fraction of orfs with sites within 600 bp upstream = 0.0391905 Motif number 5 CCGAAGGTGTAGAGCGGCGCCATGATGCGA 1 45 1 AGAGCGGCGC 0.995185 -256 GGGCGCAACCAGCCCGGCGCGATCCGGGCT 1 111 1 AGCCCGGCGC 0.982979 -190 GGTTTCGACGAGCCCGGATCGCGCCGGGCT 1 121 0 AGCCCGGATC 0.85723 -180 CATTTCGTGTGGATCGACTCGTTGCCACAC 2 134 0 GGATCGACTC 0.854257 -167 TGCCTCATCGAGACCGTATCCGCAAGGCCG 5 65 1 AGACCGTATC 0.325719 -137 CATGGGACTGTCCGCGACGCGACGTGGCCC 5 121 0 TCCGCGACGC 0.850443 -81 GGGCGGTTTGTGCCCGACTCACAGCATCAA 6 110 0 TGCCCGACTC 0.860637 -191 AATCAGCCCGGGAGCGGCTCGCTGGATACA 6 236 1 GGAGCGGCTC 0.994007 -65 GGCGATGGGTGGCCCGGGGCCCGGCTGTCT 10 11 1 GGCCCGGGGC 0.890838 -89 GCGATGAGGAGGAGCGGCGCAGATGAGT 12 9 0 GGAGCGGCGC 0.99774 -292 GTGACGATGCAGAGCGAAGCGATGAGGAGG 12 27 0 AGAGCGAAGC 0.978629 -274 CATCGTCACCGGCGCGACTCATCTGCGCCG 12 48 1 GGCGCGACTC 0.992369 -253 GCGATGAGCAGGAGCGGCGCAGATGAGTCG 12 62 0 GGAGCGGCGC 0.99774 -239 GTGACGATGCAGAGCGAAGCGATGAGCAGG 12 80 0 AGAGCGAAGC 0.978629 -221 CATCGTCACCGGCGCGACTCATCTGCGCCG 12 101 1 GGCGCGACTC 0.992369 -200 GCGATGAGCAGGAGCGGCGCAGATGAGTCG 12 115 0 GGAGCGGCGC 0.99774 -186 GTGACGATGCAGAGCGAAGCGATGAGCAGG 12 133 0 AGAGCGAAGC 0.978629 -168 CATCGTCACCGGCGCGACTCATCTGCGCCG 12 154 1 GGCGCGACTC 0.992369 -147 GCGATGAGCAGGAGCGGCGCAGATGAGTCG 12 168 0 GGAGCGGCGC 0.99774 -133 GTGACGATGCAGAGCGAAGCGATGAGCAGG 12 186 0 AGAGCGAAGC 0.978629 -115 CATCGTCACCGGCGCGACTCATCTGCGCCG 12 207 1 GGCGCGACTC 0.992369 -94 GCGATGAGGAGGAGCGGCGCAGATGAGTCG 12 221 0 GGAGCGGCGC 0.99774 -80 GTGACGATGCAGAGCGAAGCGATGAGGAGG 12 239 0 AGAGCGAAGC 0.978629 -62 GCGCGCATGGTCAGCGACGCTACACCGTAG 12 271 1 TCAGCGACGC 0.853075 -30 ********** Masking position 5 Map Score: 81.6806 Number of sites scoring better than the average of aligned sites = 2724 Number in coding regions = 2437 Number in noncoding regions = 287 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 6 ACCGACCGTGCCTGACCGAAGGTGTAGAGCG 1 30 1 CCTGACCGAG 0.815166 -271 CGCCATGATGCGACGCCGCAGACTCTCAGGT 1 62 1 CGACGCCGCG 0.849715 -239 GCGACCTCGCCGTGGCCGAAACGATGTCGCG 1 190 1 CGTGGCCGAA 0.95322 -111 GAAACGATGTCGCGGCCGCCGGATGCCCATT 1 207 1 CGCGGCCGCG 0.957112 -94 GCCCATTTGGCCGGGCAGCCGATTGCTCCGG 1 231 1 CCGGGCAGCG 0.982493 -70 TGGGCGCACGTGTGGCAACGAGTCGATCCAC 2 125 1 TGTGGCAACA 0.0872225 -176 AATGCCGCCGTTGGGCCGCGGACTAGCCGAA 2 160 1 TTGGGCCGCG 0.772097 -141 CGGACGCGGACAGGGCCGAAAGTCCCATGCC 2 220 0 CAGGGCCGAA 0.739628 -81 CCAAAGCTTGTCTGGCCGACACGGACGCGGA 2 241 0 TCTGGCCGAA 0.540353 -60 GTGGCCCGATTGTGGCCAATGCCCAAAGCTT 2 263 0 TGTGGCCAAG 0.654582 -38 TTGGCCACAATCGGGCCACAATCGAAAGCCG 2 275 1 TCGGGCCACA 0.230805 -26 CCGATTGGCCGCGGGCGGCCCGCA 3 4 1 ATTGGCCGCG 0.263295 -91 CAGTCGGCGTTCCGGCCGAGGCTAGGGACCA 4 41 1 TCCGGCCGAG 0.857738 -58 AGGGACCACTCGTAGCCGAAGTTCAACGATG 4 64 1 CGTAGCCGAG 0.911272 -35 GCTACACCGTCCTGACCGATGCACCAGGGGC 5 94 1 CCTGACCGAG 0.815166 -108 CGCGACGCGACGTGGCCCCTGGTGCATCGGT 5 108 0 CGTGGCCCCG 0.883888 -94 ATCGGATGGTCGCGGCAGGAGGCAAGCCAGT 5 170 0 CGCGGCAGGG 0.762755 -32 AACACCGCGCCCTGGCCCCAGTGCCCAGCTA 6 31 0 CCTGGCCCCG 0.840089 -270 GCGAAATTCACAGGGCCACAGCTGAATTCCA 6 66 0 CAGGGCCACG 0.710255 -235 TCGTGACCTACGTGGCAGCTGGGGCACTAGT 6 148 1 CGTGGCAGCG 0.985528 -153 CTGCCGTTTGCGGTGCAGACGTGCAACGGTG 6 181 1 CGGTGCAGAG 0.950556 -120 GGGTAATCAGCCCGGGAGCGGCTCGCTGGAT 6 232 1 CCCGGGAGCG 0.422032 -69 CACTGGCGCCCGTGACTGCTGCACCTGACGC 6 264 1 CGTGACTGCG 0.302704 -37 CCGATCGCCCCGGGGCCGCTGGATCGTGGGA 8 22 0 CGGGGCCGCG 0.9677 -83 GCGATCGGGTCCTAGCAGACGCCTGTCACGC 8 45 1 CCTAGCAGAG 0.58643 -60 TACCAGACAGCCGGGCCCCGGGCCACCCATC 10 14 0 CCGGGCCCCG 0.657917 -86 GTCTGGTAAGCGCGGCCGCAAAACAGCTGTA 10 37 1 CGCGGCCGCA 0.945334 -63 TGAGGAGGAGCGGCGCAGATGAGT 12 4 0 CGGCGCAGAG 0.968459 -297 TGAGTCGCGCCGGTGACGATGCAGAGCGAAG 12 38 0 CGGTGACGAG 0.866357 -263 TGAGCAGGAGCGGCGCAGATGAGTCGCGCCG 12 57 0 CGGCGCAGAG 0.968459 -244 TGAGTCGCGCCGGTGACGATGCAGAGCGAAG 12 91 0 CGGTGACGAG 0.866357 -210 TGAGCAGGAGCGGCGCAGATGAGTCGCGCCG 12 110 0 CGGCGCAGAG 0.968459 -191 TGAGTCGCGCCGGTGACGATGCAGAGCGAAG 12 144 0 CGGTGACGAG 0.866357 -157 TGAGCAGGAGCGGCGCAGATGAGTCGCGCCG 12 163 0 CGGCGCAGAG 0.968459 -138 TGAGTCGCGCCGGTGACGATGCAGAGCGAAG 12 197 0 CGGTGACGAG 0.866357 -104 TGAGGAGGAGCGGCGCAGATGAGTCGCGCCG 12 216 0 CGGCGCAGAG 0.968459 -85 CCATGCGCGCCGGTGACGATGCAGAGCGAAG 12 250 0 CGGTGACGAG 0.866357 -51 ********* * Masking position 5 Map Score: 65.4695 Number of sites scoring better than the average of aligned sites = 40149 Number in coding regions = 37987 Number in noncoding regions = 2162 Number of orfs with sites within 600 bp upstream = 1073 Fraction of orfs with sites within 600 bp upstream = 0.172342 Motif number 7 ACGATCGAACTGTTGGCGACCTCGCCGTGG 1 175 1 TGTTGGCGAC 0.854387 -126 ATCGTTTCGGCCACGGCGAGGTCGCCAACA 1 185 0 CCACGGCGAG 0.851381 -116 ACATGTACGAGGTTGGCGAGCAGATGCAGC 2 39 0 GGTTGGCGAG 0.993534 -262 GCGTTACATCGGTTGACGAGTTGAAGAATT 3 55 0 GGTTGACGAG 0.95947 -40 GTGCAACGGTGGATGGCGTGTGCTGCATTA 6 201 1 GGATGGCGTG 0.968019 -100 CTGGATCGTGGGATGGCGGGTGGA 8 5 0 GGATGGCGGG 0.979088 -100 TCAAGACTTTGGCTAGCGTGACAGGCGTCT 8 61 0 GGCTAGCGTG 0.879988 -44 GCCGCGGCATCCCTGGCGAGGTGGTCGAAA 9 12 1 CCCTGGCGAG 0.959134 -71 CTCCAATTGCGCCTGGCGACAATGATCAAT 9 51 1 GCCTGGCGAC 0.97158 -32 TCCTTGTCAGGCTTGACGGGTCGCACCCGC 11 73 0 GCTTGACGGG 0.870857 -27 CGGCGCGCATGGTCAGCGACGCTACACCGT 12 269 1 GGTCAGCGAC 0.779681 -32 ********** Masking position 7 Map Score: 10.0044 Number of sites scoring better than the average of aligned sites = 5179 Number in coding regions = 4771 Number in noncoding regions = 408 Number of orfs with sites within 600 bp upstream = 352 Fraction of orfs with sites within 600 bp upstream = 0.0565371 Motif number 8 CGGGCTGGTTGCGCCCTCCCCGCTCTGTCC 1 97 0 GCGCCCTCCC 0.723768 -204 GTTCAGACAAGGGCCAACTCCGGTTTCGAC 1 142 0 GGGCCAACTC 0.573221 -159 CGATTGCTCCGGGAACACCCTTGACCGCCC 1 250 1 GGGAACACCC 0.881478 -51 TGTGGGCTGTGTCACCACCCGGAAAATTCG 2 187 0 GTCACCACCC 0.782472 -114 TTTGGGCATTGGCCACAATCGGGCCACAAT 2 267 1 GGCCACAATC 0.571481 -34 GCCACAATCGGGCCACAATCGAAAGCCGAG 2 278 1 GGCCACAATC 0.571481 -23 CGGGCCGCCCGCGGCCAATCGG 3 3 0 GCGGCCAATC 0.843689 -92 GCCGAGGCTAGGGACCACTCGTAGCCGAAG 4 55 1 GGGACCACTC 0.960352 -44 TATCGGACAAGTGTCCAATCGATGATGAGA 5 34 0 GTGTCCAATC 0.704614 -168 GCCTCCTGCCGCGACCATCCGATAGCTTGG 5 178 1 GCGACCATCC 0.831966 -24 TAAGCCCAGGGGGTACCCCCGG 6 3 0 GGGTACCCCC 0.734264 -298 CTGTGAGTCGGGCACAAACCGCCCACCGCT 6 116 1 GGCACAAACC 0.621773 -185 TGCAGCACACGCCATCCACCGTTGCACGTC 6 198 0 GCCATCCACC 0.540488 -103 CGGGCCCCGGGCCACCCATCGCC 10 4 0 GCCACCCATC 0.938034 -96 GGTCGCACCCGCGAACACCCCTCTGTGATA 11 55 0 GCGAACACCC 0.904706 -45 CAGGCTTGACGGGTCGCACCCGCGAACACC 11 66 0 GGGTCGCACC 0.5598 -34 CGTCACCGGCGCGACTCATCTGCGCCGCTC 12 51 1 GCGACTCATC 0.873664 -250 CGTCACCGGCGCGACTCATCTGCGCCGCTC 12 104 1 GCGACTCATC 0.873664 -197 CGTCACCGGCGCGACTCATCTGCGCCGCTC 12 157 1 GCGACTCATC 0.873664 -144 CGTCACCGGCGCGACTCATCTGCGCCGCTC 12 210 1 GCGACTCATC 0.873664 -91 GGTGTCCAACCTACGGTGTAG 12 290 0 GTGTCCAACC 0.778099 -11 ********** Masking position 1 Map Score: 16.5327 Number of sites scoring better than the average of aligned sites = 8482 Number in coding regions = 7764 Number in noncoding regions = 718 Number of orfs with sites within 600 bp upstream = 541 Fraction of orfs with sites within 600 bp upstream = 0.0868937 Motif number 9 TAGCCTCGGCCGGAACGCCGACTGGCTGAG 4 35 0 CGGAACGCCG 0.773971 -64 CGCAAACCTGCTTTCATCGT 4 89 0 CGCAAACCTG 0.915375 -10 TCCGCAAGGCCGCTACACCGTCCTGACCGA 5 83 1 CGCTACACCG 0.971472 -119 TGAATTCCATCGAAACACCGCGCCCTGGCC 6 45 0 CGAAACACCG 0.9682 -256 GGTTTGTGCCCGACTCACAGCATCAACCGG 6 106 0 CGACTCACAG 0.725618 -195 GCGGCTCGCTGGATACACTGGCGCCCGTGA 6 249 1 GGATACACTG 0.708678 -52 CGCCGCGGCATCCCTGGCGAGGTGGT 9 7 1 GGCATCCCTG 0.845246 -76 GCGAGGTGGTCGAAACCCTGGCTTCTCCAA 9 27 1 CGAAACCCTG 0.962635 -56 TTTGCGGCCGCGCTTACCAGACAGCCGGGC 10 29 0 CGCTTACCAG 0.767852 -71 TAAGCGCGGCCGCAAAACAGCTGTACTCTC 10 43 1 CGCAAAACAG 0.889628 -57 GCTGTACTCTCGAATCCCAGTTAGTAACAA 10 62 1 CGAATCCCAG 0.930371 -38 TGGTCAGCGACGCTACACCGTAGGTTGGAC 12 278 1 CGCTACACCG 0.971472 -23 ********** Masking position 8 Map Score: 8.47445 Number of sites scoring better than the average of aligned sites = 4483 Number in coding regions = 4147 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 275 Fraction of orfs with sites within 600 bp upstream = 0.0441696 Motif number 10 TGGAGACAGGGACGGTCGCACCGACCGT 1 9 1 GGGACGGTCG 0.990786 -292 CCTTCGGTCAGGCACGGTCGGTGCGACCGT 1 22 0 GGCACGGTCG 0.954327 -279 AGGACAGAGCGGGGAGGGCGCAACCAGCCC 1 96 1 GGGGAGGGCG 0.945689 -205 GGATCGCGCCGGGCTGGTTGCGCCCTCCCC 1 106 0 GGGCTGGTTG 0.695877 -195 CAACCAGCCCGGCGCGATCCGGGCTCGTCG 1 116 1 GGCGCGATCC 0.742103 -185 GGCGCGATCCGGGCTCGTCGAAACCGGAGT 1 126 1 GGGCTCGTCG 0.791049 -175 TTTCGGCCACGGCGAGGTCGCCAACAGTTC 1 181 0 GGCGAGGTCG 0.910593 -120 GGGGCGGTCAAGGGTGTTCCCGGAGCAATC 1 251 0 AGGGTGTTCC 0.648616 -50 GGCGTACTCGGGGGCGGTCAAGGGTGTTCC 1 261 0 GGGGCGGTCA 0.976583 -40 TTGGGCCGTTCACGACCCAGCC 2 3 1 GGGCCGTTCA 0.761482 -298 GGACATGTACGAGGTTGGCGAGCAGATGCA 2 41 0 GAGGTTGGCG 0.365968 -260 CATTTGGCATGGGACTTTCGGCCCTGTCCG 2 215 1 GGGACTTTCG 0.820875 -86 CGATTGGCCGCGGGCGGCCCGCACGCATCC 3 12 1 CGGGCGGCCC 0.601506 -83 CAGCTAACATGGGACTGTCCGCGACGCGAC 5 128 0 GGGACTGTCC 0.849702 -74 TCCAAGCTATCGGATGGTCGCGGCAGGAGG 5 179 0 CGGATGGTCG 0.894099 -23 GTCACGAGTAGCGGTGGGCGGTTTGTGCCC 6 125 0 GCGGTGGGCG 0.804338 -176 CAGCGGCCCCGGGGCGATCGGGTCCTAGCA 8 32 1 GGGGCGATCG 0.978199 -73 CATCCCTGGCGAGGTGGTCGAAACCCTGGC 9 19 1 GAGGTGGTCG 0.942083 -64 GAGGTTCGGCGGGGCGTTACCTTTGCGGTT 11 11 0 GGGGCGTTAC 0.652296 -89 ACGAGTTATCAGGAGGTTCGGCGGGGCGTT 11 23 0 AGGAGGTTCG 0.272251 -77 CTATCACAGAGGGGTGTTCGCGGGTGCGAC 11 54 1 GGGGTGTTCG 0.983941 -46 ********** Masking position 9 Map Score: 19.0159 Number of sites scoring better than the average of aligned sites = 13068 Number in coding regions = 12178 Number in noncoding regions = 890 Number of orfs with sites within 600 bp upstream = 650 Fraction of orfs with sites within 600 bp upstream = 0.104401 Motif number 11 ATCGCGCCGGGCTGGTTGCGCCCTCCCCGCT 1 103 0 GCTGGTTGCC 0.728977 -198 TTCGACGAGCCCGGATCGCGCCGGGCTGGTT 1 117 0 CCGGATCGCC 0.911202 -184 TGGCCGGGCAGCCGATTGCTCCGGGAACACC 1 238 1 GCCGATTGCC 0.97983 -63 CTTGACCGCCCCCGAGTACGCCGAACAGACC 1 269 1 CCCGAGTACC 0.973256 -32 CGCGTCTCCTGAGAGCTTCAGCGTTACA 3 77 0 CCTGAGAGCT 0.758749 -18 GCCGCGACCATCCGATAGCTTGGACAT 5 185 1 TCCGATAGCT 0.696562 -17 CGCGCCCTGGCCCCAGTGCCCAGCTAAGCCC 6 26 0 CCCCAGTGCC 0.906883 -275 CCGCTCCCGGGCTGATTACCCTTAATGCAGC 6 222 0 GCTGATTACC 0.861616 -79 TCACAGCCCGATAACACCAACTCCTGG 7 7 1 CCCGATAACC 0.976584 -31 TCTGCTAGGACCCGATCGCCCCGGGGCCGCT 8 33 0 CCCGATCGCC 0.986038 -72 CCCTGGCTTCTCCAATTGCGCCTGGCGACAA 9 42 1 TCCAATTGCC 0.607378 -41 CGCCGAACCTCCTGATAACTCGTGCTATCAC 11 30 1 CCTGATAACC 0.930805 -70 ACGGGTCGCACCCGCGAACACCCCTCTGTGA 11 57 0 CCCGCGAACC 0.840187 -43 ********* * Masking position 9 Map Score: 8.8649 Number of sites scoring better than the average of aligned sites = 3216 Number in coding regions = 2923 Number in noncoding regions = 293 Number of orfs with sites within 600 bp upstream = 264 Fraction of orfs with sites within 600 bp upstream = 0.0424028 Motif number 12 GAGGTCGCCAACAGTTCGATCGTGCGGTTC 1 168 0 ACAGTTCGAT 0.908125 -133 CAGCTCAGTCCGGTCTGTTCGGCG 1 287 0 TCAGTCCGGT 0.965961 -14 GACAGGGCCGAAAGTCCCATGCCAAATGTG 2 213 0 AAAGTCCCAT 0.837843 -88 CGCGTCGCGGACAGTCCCATGTTAGCTGCA 5 130 1 ACAGTCCCAT 0.970918 -72 TTAAGGGTAATCAGCCCGGGAGCGGCTCGC 6 228 1 TCAGCCCGGG 0.895907 -73 TCACAGCCCGATAACACCAACT 7 3 1 ACAGCCCGAT 0.981462 -35 ********** Masking position 3 Map Score: 0.382055 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 485 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 13 ********** No masking Map Score: 3.98858e-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: 3.98858e-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: 3.98858e-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