AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -inarL_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 nirB 213 nirB #2 nirD 25 nirD #3 narK3 140 narK3 #4 narU 176 narU #5 hemL 113 hemL #6 Rv0528 32 hypothetical protein Rv0528 #7 narG 300 narG #8 narH 38 narH #9 narJ 56 narJ #10 Rv1458c 102 hypothetical protein Rv1458c #11 frdA 300 frdA #12 Rv1676 71 hypothetical protein Rv1676 #13 narK1 233 narK1 #14 cysG2 276 cysG2 Motif number 1 AGTTAGCTGTGTCCGGCGCGTTGCCGGCCC 1 36 1 GTCCGGCGCG 0.940153 -178 TCCGGCGCGTTGCCGGCCCGCTATACCAAG 1 47 1 TGCCGGCCCG 0.960521 -167 TCACACAGCCGGTCGCCAGGTGTGATCACA 1 133 1 GGTCGCCAGG 0.989476 -81 TCCGCTGCACGGCCGCCCTCACACGCTGGC 3 16 1 GGCCGCCCTC 0.686513 -125 CTCACACGGTTACCGCCAGCGTGTGAGGGC 3 30 0 TACCGCCAGC 0.802148 -111 TTCCGGTAGTGACCCCGGCGTGAACTTTCG 3 60 0 GACCCCGGCG 0.850916 -81 AATCCTTTGTTGCCCGGGCGCTTCCGGTAG 3 81 0 TGCCCGGGCG 0.764794 -60 GGACGGGACCGGCTGCGAGCGTGAAGGGGG 4 18 0 GGCTGCGAGC 0.704332 -159 GAGACCCTGTTACCGGCCCGGATGCGCGCT 4 97 0 TACCGGCCCG 0.839504 -80 TTACCGCTGATGTCGCCCGCTTGTCGACAG 4 145 1 TGTCGCCCGC 0.895782 -32 GTTTGCTTGATGCCGCGGCCGGTCCACGAG 5 24 0 TGCCGCGGCC 0.597309 -90 TGTAAGAGTTTGCCGCAGCCACCAGAGGTT 5 51 0 TGCCGCAGCC 0.620251 -63 GTGGGCAGGGTGCCGCGCAAAAGGCGC 6 8 1 GGGTGCCGCG 0.975478 -25 TGTGGTTGACGGTGGCCGCCGTCAACTTGG 7 15 1 GGTGGCCGCC 0.499166 -286 GCCCGGAAGTTGTCGCCACGCGTCCAGAAA 7 104 0 TGTCGCCACG 0.987352 -197 TCAAGCCCCGGTCCGCCGGGTCGGGGACCC 7 179 0 GTCCGCCGGG 0.929484 -122 CGGGCTGGCCGGCCGCGCCGCATTGCGCCC 7 210 0 GGCCGCGCCG 0.546189 -91 CAGCGAGTGCGGTCGCGCGCCGACGGCCCG 7 247 1 GGTCGCGCGC 0.770123 -54 AGCGGTGTGGGGCCGGGCCGTCGGCGCGCG 7 260 0 GGCCGGGCCG 0.657348 -41 CCAATGAAGGGCCCGAGCGACGCTTGCG 8 9 1 GGGCCCGAGC 0.663246 -30 GAGAGCGGTCGAGCGCCACCACAATGAGGG 9 29 1 GAGCGCCACC 0.938711 -28 TCTGCATCGTCGTCGGCGCGGC 10 3 0 CGTCGGCGCG 0.87782 -100 CGCGGTTCACGAGCGCCGCTCCTCCTCATC 10 40 0 GAGCGCCGCT 0.941587 -63 TCTGCATCGTCGTCGGCGCGGTTCACGAGC 10 56 0 CGTCGGCGCG 0.87782 -47 GAGCGCCGCTCCTCCTCATC 10 93 0 GAGCGCCGCT 0.941587 -10 CCTCCTCCGGTGCTGGCACGTGACCTAGAT 11 31 0 TGCTGGCACG 0.804156 -270 GCGGGACTATGGTCGCGACCACTACGCACT 11 60 1 GGTCGCGACC 0.499893 -241 GTCAACCATGTGCCCGCAGGGCGCTTTTTG 11 98 0 TGCCCGCAGG 0.641535 -203 TCGATGTGGTGATCGCCGTCAACCATGTGC 11 115 0 GATCGCCGTC 0.742079 -186 TCACCACATCGAGCGCGACGACGAAGGCCT 11 133 1 GAGCGCGACG 0.874618 -168 GTTTTCCTGCGGCTGCCGCGAAATCCGGCA 11 181 1 GGCTGCCGCG 0.97428 -120 CACGCTTCGTGATCGCCGCTGTGCTCGTCC 11 271 0 GATCGCCGCT 0.957417 -30 GCTGTTTTCTTGCTGCGAGGACAACAGCGC 13 32 1 TGCTGCGAGG 0.476564 -202 AGGAGTTTCAGGCTGCCAGGAAACAACTTC 13 147 1 GGCTGCCAGG 0.942773 -87 GTACACGCAAGGCTGGCACCCTGGTAGGCC 13 177 1 GGCTGGCACC 0.887506 -57 CACCCTGGTAGGCCGGCCCGCATTCGCACC 13 193 1 GGCCGGCCCG 0.968473 -41 CACCCTCCTTGTTCCCACCCTGGTGCGAA 13 215 0 TGTTCCCACC 0.548203 -19 CACTGCGAATTTCCGGCCCGGCTTTTCGCA 14 17 0 TTCCGGCCCG 0.565379 -260 GGGCGCCGCGGGTCGCCACCCCTTTGGCCG 14 59 0 GGTCGCCACC 0.607966 -218 CGCGGGGACCGGGCGCCGCGGGTCGCCACC 14 69 0 GGGCGCCGCG 0.915503 -208 CGCGGCGCCCGGTCCCCGCGCTTGCGATCG 14 79 1 GGTCCCCGCG 0.954006 -198 CCGCGCTTGCGATCGCCACTGGCCCTGATG 14 94 1 GATCGCCACT 0.930248 -183 GGGCGCCGCGGGTCGCCACCATCAGGGCCA 14 113 0 GGTCGCCACC 0.607966 -164 CGCGGGGACCGGGCGCCGCGGGTCGCCACC 14 123 0 GGGCGCCGCG 0.915503 -154 CGCGGCGCCCGGTCCCCGCGCTTGCGATCG 14 133 1 GGTCCCCGCG 0.954006 -144 CCGCGCTTGCGATCGCCACTGGCCCTGATG 14 148 1 GATCGCCACT 0.930248 -129 GGGCGCCGCGGGTCGCCACCATCAGGGCCA 14 167 0 GGTCGCCACC 0.607966 -110 CGCGGGGACCGGGCGCCGCGGGTCGCCACC 14 177 0 GGGCGCCGCG 0.915503 -100 CGCGGCGCCCGGTCCCCGCGCTTGCGATCG 14 187 1 GGTCCCCGCG 0.954006 -90 CCGCGCTTGCGATCGCCACTGGCCCTGATG 14 202 1 GATCGCCACT 0.930248 -75 GGGCGCCGCGGGTCGCCACCATCAGGGCCA 14 221 0 GGTCGCCACC 0.607966 -56 CGCGGGGACCGGGCGCCGCGGGTCGCCACC 14 231 0 GGGCGCCGCG 0.915503 -46 CGCGGCGCCCGGTCCCCGCGCTTGCGATCG 14 241 1 GGTCCCCGCG 0.954006 -36 CCGCGCTTGCGATCGCCACTAGGCTTGGCG 14 256 1 GATCGCCACT 0.930248 -21 ********** Masking position 5 Map Score: 129.763 Number of sites scoring better than the average of aligned sites = 44634 Number in coding regions = 41801 Number in noncoding regions = 2833 Number of orfs with sites within 600 bp upstream = 1217 Fraction of orfs with sites within 600 bp upstream = 0.195471 Motif number 2 GCTGTGTCCGGCGCGTTGCCGGCCCGCTATACCA 1 41 1 GCGCGTCGGC 0.824247 -173 TTCCGGTGAACGCCGAGGTGGAACTTAAGCGTGG 1 89 0 CGCCGAGGAC 0.915459 -125 GCGAACACTGTCACACAGCCGGTCGCCAGGTGTG 1 123 1 TCACACCGGC 0.543357 -91 GTGAGGGCGGCCGTGCAGCGGAGCGGA 3 4 0 CCGTGCGGAC 0.7565 -137 TTTGTTGCCCGGGCGCTTCCGGTAGTGACCCCGG 3 72 0 GGGCGCCGGA 0.903941 -69 CTATCGTGATCGACGTTCTCGATCACGCTAGAAA 3 109 0 CGACGTCGAC 0.777348 -32 AGAACGTCGATCACGATAGGGGTCAGT 3 124 1 TCACGAGGGC 0.916925 -17 CCCCCTTCACGCTCGCAGCCGGTCCCGTCCTCAC 4 18 1 GCTCGCCGGC 0.858895 -159 CGCTGTAACAGCGCGCATCCGGGCCGGTAACAGG 4 88 1 GCGCGCCGGC 0.923349 -89 AATGACGGCTCGACGCTAAAGAGACCCTGTTACC 4 113 0 CGACGCAGAA 0.324296 -64 CCGTCATTACCGCTGATGTCGCCCGCTTGTCGAC 4 139 1 CGCTGACGCC 0.36751 -38 GTTTGCTTGATGCCGCGGCCGGTCCACGAGTTGG 5 20 0 TGCCGCCGGC 0.941703 -94 TGTTCCAGCCTGCCCAGGTCGCTCAACTACAGGG 5 81 0 TGCCCACGCC 0.27598 -33 GGGCAGGGTGCCGCGCAAAAGGCGCGCAAC 6 13 1 CCGCGCAGGG 0.697272 -20 ATGGTTTTCTGGACGCGTGGCGACAACTTCCGGG 7 99 1 GGACGCGCGC 0.79027 -202 CTTCCGGGCAGGACGCTGACGCCCATCCATCGAG 7 125 1 GGACGCCGCC 0.91666 -176 TACCCGATGTTGACGAGAGGGGTCCCCGACCCGG 7 160 1 TGACGAGGGC 0.919948 -141 GAGGGGTCCCCGACCCGGCGGACCGGGGCTTGAC 7 176 1 CGACCCGGAC 0.921056 -125 GGGCGCAATGCGGCGCGGCCGGCCAGCCCGTAAC 7 210 1 CGGCGCCGGC 0.990327 -91 CCGTAACGTCCAGCGAGTGCGGTCGCGCGCCGAC 7 237 1 CAGCGACGGC 0.847173 -64 GAGTGCGGTCGCGCGCCGACGGCCCGGCCCCACA 7 251 1 GCGCGCCGGC 0.715425 -50 CGACGGCCCGGCCCCACACCGCTCATGACGAGGA 7 267 1 GCCCCACGCC 0.583391 -34 ACACCGCTCATGACGAGGAGGGTCATCCC 7 282 1 TGACGAGGGC 0.920235 -19 AGGGCCCGAGCGACGCTTGCGGAGCGAGACG 8 18 1 CGACGCCGGG 0.939346 -21 GGTGGCGCTCGACCGCTCTCGGACACGAGACAGC 9 15 0 GACCGCCGGC 0.655782 -42 TCGAGCGCCACCACAATGAGGGACCGACTG 9 37 1 CCACAAGGGC 0.715815 -20 GCCGCGCCGACGACGATGCAGAGCGAAGCGATGA 10 11 1 CGACGAAGAC 0.801492 -92 CAGAGCGAAGCGATGAGGAGGAGCGGCGCTCGTG 10 29 1 CGATGAGGAC 0.558157 -74 ACCGCGCCGACGACGATGCAGAGCGAAGCGATGA 10 64 1 CGACGAAGAC 0.801492 -39 CAGAGCGAAGCGATGAGGAGGAGCGGCGCTC 10 82 1 CGATGAGGAC 0.558157 -21 ACTATGGTCGCGACCACTACGCACTTCCCGAAGC 11 65 1 CGACCACGCC 0.852618 -236 GAAGCAAAAAGCGCCCTGCGGGCACATGGTTGAC 11 94 1 GCGCCCGGGA 0.611985 -207 TTGACGGCGATCACCACATCGAGCGCGACGACGA 11 123 1 TCACCACGAC 0.571939 -178 ACATCGAGCGCGACGACGAAGGCCTTGCCTACGA 11 138 1 CGACGAAGGC 0.928515 -163 CCTGCGGCTGCCGCGAAATCCGGCATTTCTACCA 11 186 1 CCGCGACCGC 0.857683 -115 ACGAGCACAGCGGCGATCACGAAGCGTGAACCAG 11 273 1 CGGCGACGAG 0.758183 -28 ACAATTGGCAGCACGATGACGGCATCGCCTGCTC 12 24 0 GCACGACGGA 0.777379 -48 CGCACGCAATCCACGCGCGCTGACAATTGGCAGC 12 46 0 CCACGCCTGC 0.775422 -26 TGGTAGGCCGGCCCGCATTCGCACCAGGGTGGGA 13 198 1 GCCCGCCGCC 0.675042 -36 CCGCGGGTCGCCACCCCTTTGGCCGCGAATGTAA 14 50 0 CCACCCTGGC 0.613873 -227 CGCGGGGACCGGGCGCCGCGGGTCGCCACCCCTT 14 65 0 GGGCGCGGGC 0.989485 -212 CGCCCGGTCCCCGCGCTTGCGATCGCCACTGGCC 14 84 1 CCGCGCCGAC 0.98266 -193 CCGCGGGTCGCCACCATCAGGGCCAGTGGCGATC 14 104 0 CCACCAGGGC 0.94749 -173 CGCGGGGACCGGGCGCCGCGGGTCGCCACCATCA 14 119 0 GGGCGCGGGC 0.989485 -158 CGCCCGGTCCCCGCGCTTGCGATCGCCACTGGCC 14 138 1 CCGCGCCGAC 0.98266 -139 CCGCGGGTCGCCACCATCAGGGCCAGTGGCGATC 14 158 0 CCACCAGGGC 0.94749 -119 CGCGGGGACCGGGCGCCGCGGGTCGCCACCATCA 14 173 0 GGGCGCGGGC 0.989485 -104 CGCCCGGTCCCCGCGCTTGCGATCGCCACTGGCC 14 192 1 CCGCGCCGAC 0.98266 -85 CCGCGGGTCGCCACCATCAGGGCCAGTGGCGATC 14 212 0 CCACCAGGGC 0.94749 -65 CGCGGGGACCGGGCGCCGCGGGTCGCCACCATCA 14 227 0 GGGCGCGGGC 0.989485 -50 CGCCCGGTCCCCGCGCTTGCGATCGCCACTAGGC 14 246 1 CCGCGCCGAC 0.98266 -31 ****** *** * Masking position 11 Map Score: 106.931 Number of sites scoring better than the average of aligned sites = 38290 Number in coding regions = 35863 Number in noncoding regions = 2427 Number of orfs with sites within 600 bp upstream = 1128 Fraction of orfs with sites within 600 bp upstream = 0.181176 Motif number 3 AGCGGGCCGGCAACGCGCCGGACACAGCTA 1 39 0 CAACGCGCCG 0.677554 -175 GGCGTTCACCGGAAGCGAACACTGTCACAC 1 109 1 GGAAGCGAAC 0.589956 -105 GGTCACTACCGGAAGCGCCCGGGCAACAAA 3 76 1 GGAAGCGCCC 0.969744 -65 TTACCGGCCCGGATGCGCGCTGTTACAGCG 4 88 0 GGATGCGCGC 0.95395 -89 ATGGTTTTCTGGACGCGTGGCGACAACTTC 7 99 1 GGACGCGTGG 0.582022 -202 CGGGCTGGCCGGCCGCGCCGCATTGCGCCC 7 210 0 GGCCGCGCCG 0.887609 -91 GCGCGCGACCGCACTCGCTGGACGTTACGG 7 237 0 GCACTCGCTG 0.769893 -64 CAGCGAGTGCGGTCGCGCGCCGACGGCCCG 7 247 1 GGTCGCGCGC 0.920281 -54 GTCTCGCTCCGCAAGCGTCGCTCGGGCCCT 8 18 0 GCAAGCGTCG 0.724565 -21 CCCTCATTGTGGTGGCGCTCGACCGCTCTC 9 29 0 GGTGGCGCTC 0.723226 -28 CGATGCAGAGCGAAGCGATGAGGAGGAGCG 10 24 1 CGAAGCGATG 0.81159 -79 GAAGCGATGAGGAGGAGCGGCGCTCGTGAA 10 35 1 GGAGGAGCGG 0.851523 -68 CGATGCAGAGCGAAGCGATGAGGAGGAGCG 10 77 1 CGAAGCGATG 0.81159 -26 GAAGCGATGAGGAGGAGCGGCGCTC 10 88 1 GGAGGAGCGG 0.851523 -15 AGTGCGTAGTGGTCGCGACCATAGTCCCGC 11 60 0 GGTCGCGACC 0.428514 -241 AGGCCTTCGTCGTCGCGCTCGATGTGGTGA 11 133 0 CGTCGCGCTC 0.816718 -168 GCCGTCGTGTCGAATCGTGCGTACCCGCAT 11 230 0 CGAATCGTGC 0.42804 -71 GCGGCGATCACGAAGCGTGAACCAGCGCG 11 282 1 CGAAGCGTGA 0.392822 -19 CTCCTTGAGAGCAGGCGATGCCGTCATCGT 12 16 1 GCAGGCGATG 0.669633 -56 CGCACGCAATCCACGCGCGCTGACAATTGG 12 50 0 CCACGCGCGC 0.81578 -22 AGGCCGGCCCGCATTCGCACCAGGGTGGGA 13 202 1 GCATTCGCAC 0.0739309 -32 AAAGGGGTGGCGACCCGCGGCGCCCGGTCC 14 64 1 CGACCCGCGG 0.973496 -213 AGTGGCGATCGCAAGCGCGGGGACCGGGCG 14 84 0 GCAAGCGCGG 0.988104 -193 CTGATGGTGGCGACCCGCGGCGCCCGGTCC 14 118 1 CGACCCGCGG 0.973496 -159 AGTGGCGATCGCAAGCGCGGGGACCGGGCG 14 138 0 GCAAGCGCGG 0.988104 -139 CTGATGGTGGCGACCCGCGGCGCCCGGTCC 14 172 1 CGACCCGCGG 0.973496 -105 AGTGGCGATCGCAAGCGCGGGGACCGGGCG 14 192 0 GCAAGCGCGG 0.988104 -85 CTGATGGTGGCGACCCGCGGCGCCCGGTCC 14 226 1 CGACCCGCGG 0.973496 -51 AGTGGCGATCGCAAGCGCGGGGACCGGGCG 14 246 0 GCAAGCGCGG 0.988104 -31 ********** Masking position 7 Map Score: 46.3982 Number of sites scoring better than the average of aligned sites = 15967 Number in coding regions = 14758 Number in noncoding regions = 1209 Number of orfs with sites within 600 bp upstream = 799 Fraction of orfs with sites within 600 bp upstream = 0.128333 Motif number 4 TTCGCTTCCGGTGAACGCCGAGGTGGAACT 1 98 0 GTGAACGCCG 0.902813 -116 CGCCAGGTGTGATCACAGCGTCATATGTGC 1 146 1 GATCACAGCG 0.928833 -68 GTGAGCGAAAGTTCACGCCGGGGTCACTAC 3 55 1 GTTCACGCCG 0.831327 -86 TAGCGTGATCGAGAACGTCGATCACGATAG 3 113 1 GAGAACGTCG 0.895891 -28 ACAAGCGGGCGACATCAGCGGTAATGACGG 4 139 0 GACATCAGCG 0.92129 -38 ACGGTGTGGTTGACGGTGGCCGCCGTCA 7 9 1 GTTGACGGTG 0.780685 -292 TTCTAACCAAGTTGACGGCGGCCACCGTCA 7 21 0 GTTGACGGCG 0.987049 -280 TCGATGGATGGGCGTCAGCGTCCTGCCCGG 7 128 0 GGCGTCAGCG 0.833309 -173 GACCCCTCTCGTCAACATCGGGTATCTCGA 7 154 0 GTCAACATCG 0.818597 -147 GTGGGGCCGGGCCGTCGGCGCGCGACCGCA 7 254 0 GCCGTCGGCG 0.919159 -47 GCTCTGCATCGTCGTCGGCGCGGC 10 5 0 GTCGTCGGCG 0.979865 -98 AGCGGCGCTCGTGAACCGCGCCGACGACGA 10 50 1 GTGAACCGCG 0.867264 -53 CGGGCACATGGTTGACGGCGATCACCACAT 11 112 1 GTTGACGGCG 0.987049 -189 AGGAAAACTTGAGGTCGTCGTAGGCAAGGC 11 159 0 GAGGTCGTCG 0.862555 -142 GTTGAAGGACGAGCACAGCGGCGATCACGA 11 265 1 GAGCACAGCG 0.945989 -36 TTGGCAGCACGATGACGGCATCGCCTGCTC 12 24 0 GATGACGGCA 0.780685 -48 CTCGCAGCAAGAAAACAGCGAAAGCTATTG 13 21 0 GAAAACAGCG 0.791909 -213 TTGCTGCGAGGACAACAGCGCAGCTTTACA 13 41 1 GACAACAGCG 0.967039 -193 ********** Masking position 6 Map Score: 21.8611 Number of sites scoring better than the average of aligned sites = 18944 Number in coding regions = 18048 Number in noncoding regions = 896 Number of orfs with sites within 600 bp upstream = 595 Fraction of orfs with sites within 600 bp upstream = 0.095567 Motif number 5 GGTCTGAGGGTATGAGGGGCAAATTACC 1 196 0 GGGTAGAGGG 0.821104 -18 GTCCTCACAACGGCAGACGGGCCGAAGCCAC 4 44 1 CGGCAACGGG 0.958461 -133 GCGGTAATGACGGCTCGACGCTAAAGAGACC 4 121 0 CGGCTGACGC 0.953922 -56 GGTCTCCTGTCGACAAGCGGGCGACATCAGC 4 150 0 CGACAGCGGG 0.988209 -27 TCCAACTCGTGGACCGGCCGCGGCATCAAGC 5 19 1 GGACCGCCGC 0.972555 -95 TGAGCGACCTGGGCAGGCTGGAACACTAGTC 5 90 1 GGGCAGCTGG 0.890939 -24 GACAACTTCCGGGCAGGACGCTGACGCCCAT 7 120 1 GGGCAGACGC 0.952986 -181 CGTCAAGCCCCGGTCCGCCGGGTCGGGGACC 7 180 0 CGGTCGCCGG 0.971888 -121 CGGCGGACCGGGGCTTGACGGGCGCAATGCG 7 191 1 GGGCTGACGG 0.946874 -110 TGGACGTTACGGGCTGGCCGGCCGCGCCGCA 7 218 0 GGGCTGCCGG 0.979796 -83 ACGCACGATTCGACACGACGGCAAGGTGTTG 11 238 1 CGACAGACGG 0.968558 -63 TAGGTCTTCTCGGCTCAAGGGCGAGCCCAAT 13 80 1 CGGCTAAGGG 0.814762 -154 GCTGGCACCCTGGTAGGCCGGCCCGCATTCG 13 188 1 TGGTAGCCGG 0.618294 -46 CGGCACTGCGAAAAGCCGGGCCGGAAATT 14 9 1 CGAAAGCCGG 0.815841 -268 GTTACATTCGCGGCCAAAGGGGTGGCGACCC 14 49 1 CGGCCAAGGG 0.922909 -228 AAAGGGGTGGCGACCCGCGGCGCCCGGTCCC 14 64 1 CGACCGCGGC 0.985873 -213 CTGATGGTGGCGACCCGCGGCGCCCGGTCCC 14 118 1 CGACCGCGGC 0.985873 -159 CTGATGGTGGCGACCCGCGGCGCCCGGTCCC 14 172 1 CGACCGCGGC 0.985873 -105 CTGATGGTGGCGACCCGCGGCGCCCGGTCCC 14 226 1 CGACCGCGGC 0.985873 -51 ***** ***** Masking position 2 Map Score: 39.6403 Number of sites scoring better than the average of aligned sites = 13818 Number in coding regions = 12899 Number in noncoding regions = 919 Number of orfs with sites within 600 bp upstream = 598 Fraction of orfs with sites within 600 bp upstream = 0.0960488 Motif number 6 GTGGAACTTAAGCGTGGTCGACTCAGGTTC 1 76 0 AGCGTGGTCG 0.71776 -138 GTCCACGAGTTGGATGGTGGGC 5 3 0 TGGATGGTGG 0.971951 -111 ACGGTGTGGTTGACGGTGGCCGCCGTCAA 7 10 1 TTGACGGTGG 0.850797 -291 GGTATCTCGATGGATGGGCGTCAGCGTCCT 7 134 0 TGGATGGGCG 0.89167 -167 CCCGGTCCGCCGGGTCGGGGACCCCTCTCG 7 173 0 CGGGTCGGGG 0.949336 -128 CCCGACCCGGCGGACCGGGGCTTGACGGGC 7 184 1 CGGACCGGGG 0.882074 -117 GGTGTGGGGCCGGGCCGTCGGCGCGCGACC 7 257 0 CGGGCCGTCG 0.91924 -44 CAGTCGGTCCCTCATTGTGGTGGCGCTCGA 9 37 0 CTCATTGTGG 0.642665 -20 CGCTTCGCTCTGCATCGTCGTCGGCGCGGC 10 11 0 TGCATCGTCG 0.942754 -92 CGCTTCGCTCTGCATCGTCGTCGGCGCGGT 10 64 0 TGCATCGTCG 0.942754 -39 CTTCGGGAAGTGCGTAGTGGTCGCGACCAT 11 68 0 TGCGTAGTGG 0.747829 -233 AGGCAAGGCCTTCGTCGTCGCGCTCGATGT 11 138 0 TTCGTCGTCG 0.871611 -163 CCCGCATGGATCCGTCGTGGTAGAAATGCC 11 207 0 TCCGTCGTGG 0.774713 -94 GCCACTGGCCCTGATGGTGGCGACCCGCGG 14 108 1 CTGATGGTGG 0.953673 -169 GCCACTGGCCCTGATGGTGGCGACCCGCGG 14 162 1 CTGATGGTGG 0.953673 -115 GCCACTGGCCCTGATGGTGGCGACCCGCGG 14 216 1 CTGATGGTGG 0.953673 -61 ********** Masking position 7 Map Score: 18.2436 Number of sites scoring better than the average of aligned sites = 4888 Number in coding regions = 4480 Number in noncoding regions = 408 Number of orfs with sites within 600 bp upstream = 332 Fraction of orfs with sites within 600 bp upstream = 0.0533248 Motif number 7 TCACAACGAAGCATGAGGAGATAACC 1 7 0 GCATGAGGAG 0.726075 -207 GGTCTGAGGGTATGAGGGGCAAATTACCG 1 195 0 GTATGAGGGG 0.402253 -19 CTGCGAGCGTGAAGGGGGAGTCCGG 4 6 0 GAAGGGGGAG 0.922714 -171 TCTGCCGTTGTGAGGACGGGACCGGCTGCG 4 31 0 TGAGGACGGG 0.925344 -146 TCCACGAGTTGGATGGTGGGC 5 2 0 GGATGGTGGG 0.5671 -112 ACGGTGTGGTTGACGGTGGCCGCCGTC 7 8 1 GGTTGACGGT 0.222096 -293 ACGATGGTTTTCTGGACGCGTGGCGACAAC 7 96 1 TCTGGACGCG 0.554886 -205 CAACTTCCGGGCAGGACGCTGACGCCCATC 7 122 1 GCAGGACGCT 0.800666 -179 CGGGTATCTCGATGGATGGGCGTCAGCGTC 7 136 0 GATGGATGGG 0.592078 -165 GCGGACCGGGGCTTGACGGGCGCAATGCGG 7 193 1 GCTTGACGGG 0.710944 -108 CCCACACCGCTCATGACGAGGAGGGTCATC 7 279 1 TCATGACGAG 0.548127 -22 CCAATGAAGGGCCCGAGCGACGCTT 8 6 1 GAAGGGCCCG 0.515958 -33 AGCGAAGCGATGAGGAGGAGCGGCGCTCGT 10 32 1 TGAGGAGGAG 0.720714 -71 AGCGAAGCGATGAGGAGGAGCGGCGCTC 10 85 1 TGAGGAGGAG 0.720714 -18 TGCCAGCACCGGAGGAGGCGGGACTATGGT 11 43 1 GGAGGAGGCG 0.914217 -258 CCATGTGCCCGCAGGGCGCTTTTTGCTTCG 11 93 0 GCAGGGCGCT 0.803708 -208 GCAAGGTGTTGAAGGACGAGCACAGCGGCG 11 258 1 GAAGGACGAG 0.955991 -43 CGCCTGCTCTCAAGGAGGGGCC 12 3 0 CAAGGAGGGG 0.94958 -69 CTGACAATTGGCAGCACGATGACGGCATCG 12 31 0 GCAGCACGAT 0.491211 -41 CTTCTCGGCTCAAGGGCGAGCCCAATTGTG 13 85 1 CAAGGGCGAG 0.9322 -149 CGCATTCGCACCAGGGTGGGAACAAGGAGG 13 211 1 CCAGGGTGGG 0.848908 -23 AGGGTGGGAACAAGGAGGGTG 13 223 1 CAAGGAGGGT 0.743099 -11 GTGGCGATCGCAAGCGCGGGGACCGGGCGC 14 83 0 CAAGCGCGGG 0.897116 -194 GTGGCGATCGCAAGCGCGGGGACCGGGCGC 14 137 0 CAAGCGCGGG 0.897116 -140 GTGGCGATCGCAAGCGCGGGGACCGGGCGC 14 191 0 CAAGCGCGGG 0.897116 -86 GTGGCGATCGCAAGCGCGGGGACCGGGCGC 14 245 0 CAAGCGCGGG 0.897116 -32 ********** Masking position 8 Map Score: 24.7744 Number of sites scoring better than the average of aligned sites = 11626 Number in coding regions = 10666 Number in noncoding regions = 960 Number of orfs with sites within 600 bp upstream = 682 Fraction of orfs with sites within 600 bp upstream = 0.109541 Motif number 8 GGGCAACAAAGGATTTCTAGCGTGATCGAGA 3 96 1 GGATTTCAGC 0.930714 -45 AGCCACCAGAGGTTTGCTTGATGCCGCGGCC 5 34 0 GGTTTGCTGA 0.951416 -80 CGTTAACTTGGGTTTGCATGCCCGTAGCGAT 7 64 1 GGTTTGCTGC 0.988455 -237 CGATTACGATGGTTTTCTGGACGCGTGGCGA 7 91 1 GGTTTTCGGA 0.930768 -210 GACGACCTCAAGTTTTCCTGCGGCTGCCGCG 11 170 1 AGTTTTCTGC 0.918898 -131 CAGCGCGCGTGGATTGCGTGCGGG 12 58 1 GGATTGCTGC 0.981608 -14 TAGCTTTCGCTGTTTTCTTGCTGCGAGGACA 13 24 1 TGTTTTCTGC 0.918898 -210 ACGCCACTGCGAATTTCCGGCCCGGCTTTTC 14 20 0 GAATTTCGGC 0.803597 -257 ******* *** Masking position 5 Map Score: 5.05222 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 479 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 9 ACGGTTACCGCCAGCGTGTGAGGGCGGCCGTG 3 23 0 CAGCGTGTAG 0.850137 -118 CAAAGGATTTCTAGCGTGATCGAGAACGTCGA 3 102 1 CAGCGTGACG 0.990255 -39 ACTGACCCCTATCGTGATCGACGTTCTCGA 3 121 0 CATCGTGACG 0.896383 -20 GGACCGGCTGCGAGCGTGAAGGGGGAGTCCGG 4 11 0 CAGCGTGAGG 0.931537 -166 GTCCAGAAAACCATCGTAATCGCTACGGGCAT 7 81 0 CATCGTAACG 0.977561 -220 CCCGTAACGTCCAGCGAGTGCGGTCGCGCGCC 7 236 1 CAGCGAGTCG 0.934069 -65 ACGACGGATCCATGCGGGTACGCACGATTCGA 11 219 1 CTGCGGGTCG 0.870824 -82 GCTGGTTCACGCTTCGTGATCGCCGCTGTGCT 11 276 0 GTTCGTGACG 0.792824 -25 GGGTGCCAGCCTTGCGTGTACGAAGTTGTTTC 13 166 0 CTGCGTGTCG 0.962046 -68 GGGCCAGTGGCGATCGCAAGCGCGGGGACCGG 14 87 0 CATCGCAACG 0.934196 -190 GGGCCAGTGGCGATCGCAAGCGCGGGGACCGG 14 141 0 CATCGCAACG 0.934196 -136 GGGCCAGTGGCGATCGCAAGCGCGGGGACCGG 14 195 0 CATCGCAACG 0.934196 -82 AGCCTAGTGGCGATCGCAAGCGCGGGGACCGG 14 249 0 CATCGCAACG 0.934196 -28 * ******* ** Masking position 5 Map Score: 23.7073 Number of sites scoring better than the average of aligned sites = 1810 Number in coding regions = 1654 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 10 ********** No masking Map Score: -5.49717e-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 11 ********** No masking Map Score: -5.49717e-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 12 ********** No masking Map Score: -5.49717e-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