AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_bsub_mtub_300.orf -o294_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: yqfA 21 yqfA kasB 30 kasB Input sequences: #1 yhfB 125 similar to 3-oxoacyl- acyl-carrier protein synthase #2 yjaX 164 similar to 3-oxoacyl- acyl-carrier protein synthase #3 yjaY 22 similar to 3-oxoacyl- acyl-carrier protein synthase #4 yloU 276 similar to alkaline-shock protein #5 yloW 138 similar to phosphoglycerate dehydrogenase #6 ylpA 25 similar to L-serine dehydratase #7 ylpC 108 ylpC #8 acpA 83 acyl carrier protein #9 rncS 139 ribonuclease III #10 flgB 300 flagellar basal-body rod protein #11 fliF 45 flagellar basal-body M-ring protein #12 fliH 117 flagellar assembly protein #13 fliK 160 fliK #14 flgE 21 flagellar hook protein #15 fliL 251 flagellar protein #16 fliM 33 flagellar motor switch protein #17 cheY 25 two-component response regulator #18 flhA 32 flagella-associated protein #19 cheW 21 cheW #20 sigD 22 RNA polymerase sigma-28 factor (sigma-D) #21 ylxL 28 ylxL #22 rpsB 143 ribosomal protein S2 #23 tsf 101 elongation factor Ts #24 smbA 145 uridylate kinase #25 yluA 130 similar to hypothetical proteins #26 yluB 61 similar to hypothetical proteins #27 cdd 118 cytidine/deoxycytidine deaminase #28 yqfF 78 yqfF #29 yqfC 56 yqfC #30 yqfB 24 yqfB #31 yqeZ 130 yqeZ #32 rpsU 163 ribosomal protein S21 #33 yrkA 300 similar to hemolysin-like #34 yttI 300 similar to acetyl-CoA carboxylase #35 ywpB 191 similar to hydroxymyristoyl-(acyl carrier protein) dehydratase #36 fadD30 300 fadD30 #37 fabH 81 fabH #38 accD3 26 accD3 #39 Rv1348 300 hypothetical protein Rv1348 #40 fabG2 128 fabG2 #41 aceE 51 aceE #42 Rv2242 59 hypothetical protein Rv2242 #43 fabD 238 fabD #44 acpM 75 acpM #45 Rv2362c 61 hypothetical protein Rv2362c #46 bex 73 bex #47 Rv2370c 194 hypothetical protein Rv2370c #48 Rv2870c 57 hypothetical protein Rv2870c #49 cdsA 22 cdsA #50 frr 171 frr #51 pyrH 234 pyrH #52 rpsB 283 rpsB #53 Rv2926c 50 hypothetical protein Rv2926c #54 Rv2927c 238 hypothetical protein Rv2927c #55 echA20 54 echA20 #56 Rv3553 97 hypothetical protein Rv3553 Motif number 1 TTTCGTCGAGACCGACGACGGGTTCTGCCG 13 23 1 ACCGACGACG 0.656155 -138 CTTCAACAAGCCGCCGCGTGAGGACGAAC 36 10 1 GCCGCCGCGT 0.952034 -291 GACGAACCCTACCGGGGAGACGCCACTCGT 36 33 1 ACCGGGGAGA 0.734834 -268 TGGCCACCAGGCCGCCGAGCTGTCTGGGCA 36 248 0 GCCGCCGAGC 0.984899 -53 GGTTTTAGGTGCCGGTGCTCGAAAGAGTTT 39 21 1 GCCGGTGCTC 0.804274 -280 TATCAGCGCGGTCGCGGCGCAGCTCGGGGT 39 171 1 GTCGCGGCGC 0.9432 -130 TTACCGGCCAACCGGCGTGCAACGGCGTCG 39 213 0 ACCGGCGTGC 0.872216 -88 GGCGGATTAGGCCGCCGCGAGAGAGGACCG 39 278 1 GCCGCCGCGA 0.992961 -23 CGCGAGAAACCACCGCGCCACGCAGATA 40 9 1 ACCACCGCGC 0.913412 -120 GAAGAGCTTCGCCGCCGACGGTGCAAAATA 40 99 1 GCCGCCGACG 0.968189 -30 CGCCGGCGAGCCGACCGCCTT 42 2 1 GCCGGCGAGC 0.985763 -58 ACCCCCTCTGACCGGCGAGGGAATCTATGA 43 32 0 ACCGGCGAGG 0.933602 -207 CTGGTATCTTTCCGGGGCCCCTGCTGGACC 43 59 0 TCCGGGGCCC 0.879759 -180 CTTTCCGTCCGACGGCGCCCCTGGTATCTT 43 79 0 GACGGCGCCC 0.889714 -160 GTACGAGACTATCGGCGCGGATACCCGCGA 45 14 1 ATCGGCGCGG 0.902551 -48 ACGGCCCGCTGCCGCCGCGGTGGGTAACCG 47 53 1 GCCGCCGCGG 0.996398 -142 TGGACGTTTAGCCGGTGTGGCGCGTTCGGG 47 97 0 GCCGGTGTGG 0.773966 -98 CTGCATCGTCGCCGGCGCGAAGCAGCGCGT 50 18 0 GCCGGCGCGA 0.993367 -154 GCTCCTCCTCATCGCTGCGCTCTGCATCGT 50 39 0 ATCGCTGCGC 0.763083 -133 CTGCATCGTCGCCGGCGCCAACCATCTGCG 50 71 0 GCCGGCGCCA 0.990772 -101 GCTCCTCCTCATCGCTGCGCTCTGCATCGT 50 92 0 ATCGCTGCGC 0.763083 -80 CTGCATCGTCGCCGGCGCCAACCATCTGCG 50 124 0 GCCGGCGCCA 0.990772 -48 GCTCCTCCTCATCGCTGCGCTCTGCATCGT 50 145 0 ATCGCTGCGC 0.763083 -27 CGAGGGGCCGGCCGAGGCCAGGCCCGTCGA 51 107 0 GCCGAGGCCA 0.887086 -128 CCCCGCCCACGCCGGAGCGCGGCTATTGAG 51 156 1 GCCGGAGCGC 0.944739 -79 TCGCCGCCGCCCGTTTTGTGGA 52 3 1 GCCGCCGCCC 0.996728 -281 CGCTGTGGATTCCGCTGCCGGGAAAATCAC 52 42 1 TCCGCTGCCG 0.736121 -242 AAGTCAGCCCGCCGATGCGAGCTGCGCCGA 52 94 0 GCCGATGCGA 0.87205 -190 GCGTGTCTGCACCGCGGCCCGCCTTTCCGG 52 125 1 ACCGCGGCCC 0.97349 -159 GCAACAGCATGCCGGGGCGGTCCCGCGGCG 52 160 1 GCCGGGGCGG 0.991268 -124 CCCGAAGGGAACCGCCGCGGGACCGCCCCG 52 172 0 ACCGCCGCGG 0.988542 -112 CGCGGCAGACGCCAGGGCCCGGCTTCAGCC 52 224 1 GCCAGGGCCC 0.908672 -60 CCCGGCTTCAGCCGATGCCGGGCGAACAAC 52 241 1 GCCGATGCCG 0.905492 -43 TCAAGCGCCGGCCAACGCCCAACGCGGC 53 33 1 GCCAACGCCC 0.829751 -18 TCACCCGTCAGCCGCCGAACGGTCTACGAC 54 63 1 GCCGCCGAAC 0.711931 -176 TATTCGACGAGCCCGGGCGACCACTCAGAT 54 114 0 GCCCGGGCGA 0.674829 -125 GTCCCGACACACCGGCGCCACCAGTGCAGT 54 153 1 ACCGGCGCCA 0.971003 -86 AGCCACCGCCGACAATGCAGT 56 87 0 GCCACCGCCG 0.940414 -11 ********** Masking position 7 Map Score: 57.6247 Number of sites scoring better than the average of aligned sites = 1855 Number in coding regions = 1719 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 GCAGGCTGAAGAGAACCCGGAGCGCTT 12 101 1 GAGACCGGGC 0.935406 -17 TTCGACCACAGGCTGGTCGAAGCGGCTCTGGATCG 36 158 0 GGCTGCGGGG 0.608761 -143 AACGATCCTGGCCACCAGGCCGCCGAGCTGTCTGG 36 251 0 GCCACGGGCG 0.677456 -50 CTACGGCGACGACACGCCGACGGAGCCCGCCCTGA 37 25 0 GACAGCGGAG 0.668252 -57 GTCAAACTCGGGGACCATGGAGTGCGGGCGGAGGG 39 63 0 GGGACTGGGC 0.844642 -238 CTGAGTATCAGCGCGGTCGCGGCGCAGCTCGGGGT 39 166 1 GCGCGCGGGC 0.727183 -135 TCGGCGGAGCGCGACGCCGTTGCACGCCGGTTGGC 39 202 1 GCGAGCGGAC 0.975941 -99 CGCCCGATCTGAGAAGTCGTGGCGGATTAGGCCGC 39 258 1 GAGAGCGGGG 0.970937 -43 AATCTGCATCGCGAGGTCGGCCACCTTGCCAGCTA 40 54 1 GCGAGCGCCC 0.923135 -75 AACAGCGCAAGCGAACCCGACCGAGTTCGGGTGAT 41 17 1 GCGACCGCAG 0.804223 -35 AAGTGATCCAGACAACAGGTCGCGGGACGATCTCA 43 106 1 GACACGGGGG 0.65456 -133 GCGGATACCCGCGATGTCGTGGCGGGGTGCAAAAC 45 30 1 GCGAGCGGGG 0.993992 -32 CCACCGCGGCGGCAGCGGGCCGTGCGCCTGCCGAG 47 41 0 GGCACGGGGC 0.772445 -154 CACGTTCTGGGGAATGTTGGTGAGGTTTACTCCTT 47 136 0 GGAAGTGGGG 0.492278 -59 CTTCGCGCCGGCGACGATGCAGAGCGCAGCGATGA 50 26 1 GCGAGTGGGC 0.977337 -146 GCAGAGCGCAGCGATGAGGAGGAGCGGCGCAGATG 50 44 1 GCGAGGGGGC 0.989907 -128 GTTGGCGCCGGCGACGATGCAGAGCGCAGCGATGA 50 79 1 GCGAGTGGGC 0.977337 -93 GCAGAGCGCAGCGATGAGGAGGAGCGGCGCAGATG 50 97 1 GCGAGGGGGC 0.989907 -75 GTTGGCGCCGGCGACGATGCAGAGCGCAGCGATGA 50 132 1 GCGAGTGGGC 0.977337 -40 GCAGAGCGCAGCGATGAGGAGGAGCGGCGCAG 50 150 1 GCGAGGGGGC 0.989907 -22 CCGCGCTCCGGCGTGGGCGGGGTGCGTTAGTCACG 51 143 0 GCGTGCGGGC 0.951277 -92 GGCAGGATGTGAGATGCCGTCCTGGTGGTGCCGGG 51 185 1 GAGAGCGCGG 0.906593 -50 TGGTGGTGCCGGGATGGCACTGTCGTGCGAGGAGT 51 207 1 GGGAGCAGCG 0.423102 -28 GGAATCCACAGCGACGACATTGTCCACAAAACGGG 52 20 0 GCGAGCAGCC 0.716458 -264 GTGCAGACACGCGAAGTCAGCCCGCCGATGCGAGC 52 102 0 GCGAGCACGC 0.765618 -182 TGCGGATCCCGGAAAGGCGGGCCGCGGTGCAGACA 52 128 0 GGAAGCGCGC 0.573896 -156 GGACCGCCCCGGCATGCTGTTGCGGATCCCGGAAA 52 148 0 GGCAGTGGGG 0.774588 -136 GCATGCCGGGGCGGTCCCGCGGCGGTTCCCTTCGG 52 166 1 GCGGCCGGGG 0.792418 -118 GGCGTCTGCCGCGATGCCGGACCCGGGAGGAAATC 52 202 0 GCGAGCGCCG 0.91493 -82 CGTCGTCTGGGCGATCTTGCCCGAGCGTGCCGACA 54 23 0 GCGACTGCAG 0.489553 -216 CGCGTGATCTGAGTGGTCGCCCGGGCTCGTCGAAT 54 108 1 GAGTGCGCGG 0.506435 -131 CTTGCAAGATGCCAGGAGGGTGTGGCC 54 222 1 GCCAGGGGGG 0.960192 -17 TGCTTAGGTAGCGAACCCGCAGGAGTGCA 55 36 1 GCGACCGGAG 0.933946 -19 GCTTGCGGGGGAGAGGAGGCGGAACAA 56 3 0 GAGAGGGGAC 0.813066 -95 AGGGGACGAAGCGATGTGGGCGCACCTCCCGCTTG 56 33 0 GCGAGGGGAC 0.955623 -65 TTCGTCCCCTGCAAGCGGGTGGTACCCCCACTGCA 56 58 1 GCAACGGGAC 0.393662 -40 **** * ** * ** Masking position 1 Map Score: 53.3777 Number of sites scoring better than the average of aligned sites = 1081 Number in coding regions = 994 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 3 TGTGCAAGTGAGGAGGGAAACAA 4 2 0 AGGAGGGACA 0.874903 -275 ATGCATTCGAAGGAGGAACTAGT 4 264 1 AGGAGGAAAG 0.757926 -13 CTGGTTCATAAGGAGGAATAGC 5 127 1 AGGAGGAAGC 0.955329 -12 GAAAAGGGTCAGGAGGAGCCAGTT 6 12 1 AGGAGGAGAG 0.811134 -14 GGAGGGAGGGGAGGCGAGTAATCGC 15 4 1 GGGAGGGGGC 0.912988 -248 TGACAGAATACGGAGGTGAGGAAA 16 20 1 CGGAGGTGGA 0.90845 -14 CCATTCGAGGAGGTGTCTCAC 19 8 1 AGGAGGTGTC 0.60198 -14 ATGACCTAAGCGGAGGAAAAAAACCATTATAT 22 108 1 CGGAGGAAAA 0.834816 -36 CCATTATATTAGGAGGAAATAAC 22 131 1 AGGAGGAAAA 0.79219 -13 TAAACATATAAGGAGGAATACAA 23 89 1 AGGAGGAACA 0.92199 -13 TTTTGGGTGACGGAGGAATCTC 25 119 1 CGGAGGAATC 0.797544 -12 TATAAAAGGAAGGAGGGATACACCGCCC 31 113 1 AGGAGGGACA 0.874903 -18 TTGGTGTATTCGGAGGGAGGGAAAGAGA 32 146 1 CGGAGGGAGA 0.920231 -18 ATATTTACATCGGAGGTGTACGCCTTACTAGG 33 267 1 CGGAGGTGCG 0.867557 -34 CTTCACAAAAGGGAGGTAATCATTTGTTAAAG 34 204 1 GGGAGGTACA 0.726094 -97 TCAGTTGAACCGGAGGAGTGGAAACATGAGCG 36 198 1 CGGAGGAGGA 0.963953 -103 GGAGTGCGGGCGGAGGGACTCGAACCCTCAAA 39 48 0 CGGAGGGACG 0.883928 -253 TGCAGATTCACGGAGGAAGTGGCTATCTGCGT 40 30 0 CGGAGGAAGG 0.941218 -99 CGCAGCGATGAGGAGGAGCGGCGCAGATGGTT 50 50 1 AGGAGGAGGC 0.967035 -122 CGCAGCGATGAGGAGGAGCGGCGCAGATGGTT 50 103 1 AGGAGGAGGC 0.967035 -69 CGCAGCGATGAGGAGGAGCGGCGCAG 50 156 1 AGGAGGAGGC 0.967035 -16 TGCCGGACCCGGGAGGAAATCCCCGAAGGGAA 52 191 0 GGGAGGAACC 0.912201 -93 CTCCCGCTTGCGGGGGAGAGGAGGCGGAACAA 56 11 0 CGGGGGAGGA 0.690155 -87 CCCCGCAAGCGGGAGGTGCGCCCACATCGCTT 56 28 1 GGGAGGTGCC 0.840975 -70 ******** ** Masking position 6 Map Score: 30.1574 Number of sites scoring better than the average of aligned sites = 579 Number in coding regions = 431 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 4 GACCCGATAACGGGCGATCGGGTCATTCAGCA 28 11 0 CGGCGATCGG 0.537366 -68 CGCGTGAGGACGAACCCTACCGGGGAGACGCC 36 25 1 CGACCCTACG 0.741525 -276 CTATAGTCATCGATCCAGAGCCGCTTCGACCA 36 148 1 CGACCAGACC 0.832146 -153 GACGACACGCCGACGGAGCCCGCCCTGAGTGC 37 21 0 CGAGGAGCCG 0.965935 -61 CGGCCCCAGTCGGACGATCTCGTCCAAACTAA 39 115 0 CGGCGATCCG 0.707699 -186 AGCGCGGTCGCGGCGCAGCTCGGGGTATCGGC 39 175 1 CGGGCAGCCG 0.990722 -126 CTCGGGGTATCGGCGGAGCGCGACGCCGTTGC 39 193 1 CGGGGAGCCG 0.97081 -108 TCAGATCGGGCGACCACGAACGCTGGGTTACC 39 238 0 CGACACGACG 0.723455 -63 TCTTCTACACCGAACTAGCTGGCAAGGTGGCC 40 72 0 CGACTAGCGG 0.632578 -57 AGAAGAGCTTCGCCGCCGACGGTGCAAAATAT 40 98 1 CGCGCCGAGG 0.869807 -31 ACAGCGCAAGCGAACCCGACCGAGTTCGGGTG 41 18 1 CGACCCGACG 0.966577 -34 CGGTCAGAGGGGGTCCAGCAGGGGCCCCGGAA 43 48 1 GGGCCAGCGG 0.661857 -191 ACTTTCCGTCCGACGGCGCCCCTGGTATCTTT 43 78 0 CGAGGCGCCC 0.785001 -161 GTCGCCGGCGCGAAGCAGCGCGTAGTCCCC 50 9 0 CGAGCAGCCG 0.990002 -163 GCGCCGGCGACGATGCAGAGCGCAGCGATGAG 50 30 1 CGAGCAGACG 0.978283 -142 TGAGGAGGAGCGGCGCAGATGGTTGGCGCCGG 50 58 1 CGGGCAGAGG 0.959189 -114 GCGCCGGCGACGATGCAGAGCGCAGCGATGAG 50 83 1 CGAGCAGACG 0.978283 -89 TGAGGAGGAGCGGCGCAGATGGTTGGCGCCGG 50 111 1 CGGGCAGAGG 0.959189 -61 GCGCCGGCGACGATGCAGAGCGCAGCGATGAG 50 136 1 CGAGCAGACG 0.978283 -36 ACCCCGCCCACGCCGGAGCGCGGCTATTGAGG 51 155 1 CGCGGAGCCG 0.91458 -80 TCGCCGCCGCCCGTTTTGTGGAC 52 2 1 CGCGCCGCCG 0.967789 -282 TAGTTTACACCGACCCAGCTGGTGATTTTCCC 52 61 0 CGACCAGCGG 0.976236 -223 GTAAACTACTCGGCGCAGCTCGCATCGGCGGG 52 85 1 CGGGCAGCCG 0.990722 -199 CATGCCGGGGCGGTCCCGCGGCGGTTCCCTTC 52 167 1 CGGCCCGCGC 0.837184 -117 CGGCTTCAGCCGATGCCGGGCGAACAACCGAC 52 243 1 CGAGCCGGCG 0.927883 -41 TCGGCACGCTCGGGCAAGATCGCCCAGACGAC 54 25 1 CGGCAAGACG 0.7182 -214 TCATATTCGACGAGCCCGGGCGACCACTCAGA 54 115 0 CGACCCGGCG 0.808459 -124 GCTTAGGTAGCGAACCCGCAGGAGTGCA 55 37 1 CGACCCGCGG 0.973954 -18 *** ***** ** Masking position 2 Map Score: 51.2663 Number of sites scoring better than the average of aligned sites = 589 Number in coding regions = 561 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 ATATGTAGAGGTACGGCCAGCGATTATTGCCT 4 187 1 GACGGCCGCG 0.926498 -90 TAACCCGTTTGAACGGGCAGCCCTTTACACTG 15 60 1 GACGGGCGCC 0.960216 -192 GCAGAGGGTGCTGCAGGCGGCAGTTCTGTACA 22 73 1 CGCAGGCGCA 0.434414 -71 CTTCAACAAGCCGCCGCGTGAGGACGAACCCT 36 11 1 CGCCGCGGAG 0.861001 -290 TCGGTTAATCGTACAGGCTGCCGCTCGGTCAT 36 116 1 GACAGGCGCC 0.787785 -185 CGGATCAGTTGAACCGGAGGAGTGGAAACATG 36 194 1 GACCGGAGAG 0.492116 -107 GTGGAAACATGAGCGGCCCGACGGGAAATTCG 36 215 1 GGCGGCCGAC 0.953852 -86 CGTGCACTCAGGGCGGGCTCCGTCGGCGTGTC 37 18 1 GGCGGGCCCG 0.936996 -64 GGACCATGGAGTGCGGGCGGAGGGACTCGAAC 39 55 0 GGCGGGCGAG 0.990278 -246 TGGGTTGTATGCGCGGGCTGAGTATCAGCGCG 39 149 1 GGCGGGCGAG 0.990305 -152 ACCCCGAGCTGCGCCGCGACCGCGCTGATACT 39 169 0 GGCCGCGCCG 0.690393 -132 GCAGCTCGGGGTATCGGCGGAGCGCGACGCCG 39 189 1 GATCGGCGAG 0.435211 -112 ACCGGCCAACCGGCGTGCAACGGCGTCGCGCT 39 209 0 CGCGTGCACG 0.502651 -92 GCGGATTAGGCCGCCGCGAGAGAGGACCGCTG 39 279 1 CGCCGCGGAG 0.861 -22 AAGTGGCTATCTGCGTGGCGCGGTGGTTTCTC 40 14 0 CGCGTGGGCG 0.648812 -115 ATCATATTTTGCACCGTCGGCGGCGAAGCTCT 40 101 0 GACCGTCGCG 0.769367 -28 CGCCGGCGAGCCGACCGCCTTTGGCCGAA 42 8 1 GGCCGACGCC 0.84874 -52 GATACCAGGGGCGCCGTCGGACGGAAAGTGAT 43 81 1 GGCCGTCGAC 0.845446 -158 AGCGGGCCGTGCGCCTGCCGAGTCGTCGACAT 47 31 0 GGCCTGCGAG 0.927699 -164 GTTACCCACCGCGGCGGCAGCGGGCCGTGCGC 47 49 0 GGGCGGCGCG 0.907779 -146 GCGCTGCTTCGCGCCGGCGACGATGCAGAGCG 50 20 1 GGCCGGCACG 0.978992 -152 CAGATGGTTGGCGCCGGCGACGATGCAGAGCG 50 73 1 GGCCGGCACG 0.978992 -99 CAGATGGTTGGCGCCGGCGACGATGCAGAGCG 50 126 1 GGCCGGCACG 0.978992 -46 GTACCCAGGGGTACCGGCAGACATCTCCGCGA 51 14 0 GACCGGCGAC 0.953326 -221 GTTCTGTTCTGAACCGGGTACCCAGGGGTACC 51 31 0 GACCGGGACC 0.647102 -204 CAACAACGAGGGGCCGGCCGAGGCCAGGCCCG 51 111 0 GGCCGGCGAG 0.993644 -124 GCTCCGGCGTGGGCGGGGTGCGTTAGTCACGC 51 142 0 GGCGGGGGCG 0.982348 -93 ATTGTCCACAAAACGGGCGGCGGCGA 52 5 0 AACGGGCGCG 0.55275 -279 CAGCTCGCATCGGCGGGCTGACTTCGCGTGTC 52 100 1 CGCGGGCGAC 0.962575 -184 CGTGTCTGCACCGCGGCCCGCCTTTCCGGGAT 52 126 1 CGCGGCCGCC 0.937978 -158 CCGAAGGGAACCGCCGCGGGACCGCCCCGGCA 52 169 0 CGCCGCGGAC 0.793935 -115 CTTGATCCTTGCGCCGGGTGAATGGTG 53 6 0 GGCCGGGGAA 0.758848 -45 CAAGGATCAAGCGCCGGCCAACGCCCAACGCG 53 27 1 GGCCGGCAAC 0.941305 -24 GATCTTGCCCGAGCGTGCCGACAACGTAGGTG 54 14 0 GGCGTGCGAC 0.839171 -225 GCTCACCCGTCAGCCGCCGAACGGTCTACGAC 54 61 1 CGCCGCCAAC 0.678313 -178 GACACGCGCCCAGCAGGCCGCGTGATCTGAGT 54 90 1 CGCAGGCGCG 0.919972 -149 * ****** *** Masking position 4 Map Score: 53.3185 Number of sites scoring better than the average of aligned sites = 2231 Number in coding regions = 2062 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 6 AGCTTATTAGCGCTTTGCTTCTAGACTAAT 5 97 0 CGCTTTGCTT 0.760384 -42 CGCTTTTACGCGCGCTGTATCCGGTTTAGT 9 79 1 CGCGCTGTAT 0.871091 -61 GCCTGCAGCACCCTCTGCATAAATCGTTAA 22 61 0 CCCTCTGCAT 0.968944 -83 TCCCTCCGCCCGCACTCCATGGTCCCCGAG 39 62 1 CGCACTCCAT 0.866217 -239 GGGGACTACGCGCTGCTTCGCGCCGGCG 50 9 1 CGCGCTGCTT 0.956106 -163 CTCATCGCTGCGCTCTGCATCGTCGCCGGC 50 32 0 CGCTCTGCAT 0.990332 -140 CTCATCGCTGCGCTCTGCATCGTCGCCGGC 50 85 0 CGCTCTGCAT 0.990332 -87 CTCATCGCTGCGCTCTGCATCGTCGCCGGC 50 138 0 CGCTCTGCAT 0.990332 -34 GGGTGGTACCCCCACTGCATTGTCGGCGGT 56 74 1 CCCACTGCAT 0.93138 -24 ********** Masking position 6 Map Score: 11.1414 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 61 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 7 ATATTGCCATGTGAAAAAAAATAGGATAGA 2 70 1 GTGAAAAAAA 0.940322 -95 TGAAATTTTCGAGAAAAAAC 8 1 0 GAGAAAAAAC 0.945977 -83 GAAAAGAAAGGAGAAAAAACAGAAATTCTG 10 74 1 GAGAAAAAAC 0.945977 -227 TATGAAGTTCGTGTAAAAAAATGTCCTCAC 10 184 0 GTGTAAAAAA 0.689161 -117 GATATTGAGGGTGAAAAAAACTGAAATGGA 10 270 1 GTGAAAAAAA 0.940322 -31 TTTAAAAGGAGAGAAAAAACAGC 18 20 1 GAGAAAAAAC 0.945977 -13 GACCTAAGCGGAGGAAAAAAACCATTATAT 22 110 1 GAGGAAAAAA 0.79612 -34 TATTATGCAAGAGAAAAAAAGGTTTGTAAA 24 94 0 GAGAAAAAAA 0.9493 -52 ATAGATAATAGTGAAAAGACCCTCTCATGT 25 27 1 GTGAAAAGAC 0.7351 -104 AGAAATGGGCGTGAAAAAAAGCGCGCGATT 27 45 1 GTGAAAAAAA 0.940322 -74 GACAGCGTTTGACAAAAAAAGTACAATAGT 34 119 1 GACAAAAAAA 0.686187 -182 ********** Masking position 5 Map Score: 9.98895 Number of sites scoring better than the average of aligned sites = 260 Number in coding regions = 213 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 TGAAAAAGAAAAAGGAGGCTGAAAA 1 6 0 AAAGGAGGCT 0.688702 -120 TGGTATATGGAAAGGAGGCGT 2 2 0 AAAGGAGGCG 0.910787 -163 AAAAAGGTGAGGTGCACACAAG 3 5 1 AGGTGAGGTG 0.910586 -18 TGTTTTGTGCAAGTGAGGAGGGAAACAA 4 9 0 AAGTGAGGAG 0.641742 -268 ATAATACTTGAGGGGAGGTGAATTGCT 8 67 1 AGGGGAGGTG 0.954315 -17 GGAGGGAGGGGAGGCGAGTAATCGCT 15 7 1 AGGGGAGGCG 0.978791 -245 CCATTCGAGGAGGTGTCTCAC 19 6 1 CGAGGAGGTG 0.964119 -16 TGATGTTTCAAGAGGAGGTTCTT 28 66 1 AGAGGAGGTT 0.8221 -13 GTATGATTTGAAAGGAGGTTCTAACACT 29 9 0 AAAGGAGGTT 0.500353 -48 CGAACCCTACCGGGGAGACGCCACTCGTTG 36 35 1 CGGGGAGACG 0.754521 -266 GCGATGAGGCTATATAGGCTG 38 16 0 CGATGAGGCT 0.862477 -11 GACGTTTAGCCGGTGTGGCGCGTTCGGGAT 47 95 0 CGGTGTGGCG 0.708091 -100 CAGAGCGCAGCGATGAGGAGGAGCGGCGCA 50 45 1 CGATGAGGAG 0.914036 -127 CAGAGCGCAGCGATGAGGAGGAGCGGCGCA 50 98 1 CGATGAGGAG 0.914036 -74 CAGAGCGCAGCGATGAGGAGGAGCGGCGCA 50 151 1 CGATGAGGAG 0.914036 -21 CTTGCGGGGGAGAGGAGGCGGAACAA 56 7 0 AGAGGAGGCG 0.979215 -91 ********** Masking position 5 Map Score: 17.1152 Number of sites scoring better than the average of aligned sites = 395 Number in coding regions = 294 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 9 TACAGCGCGCGTAAAAGCGGCATGCTGTAA 9 68 0 GTAAAAGCGG 0.229816 -72 AATAAGAATAGGAGTAGTGGCAACT 26 47 1 GGAGTAGTGG 0.820285 -15 CCACAGGCTGGTCGAAGCGGCTCTGGATCG 36 158 0 GTCGAAGCGG 0.793944 -143 CCAGCCTGTGGTCGAAGCGGATCAGTTGAA 36 177 1 GTCGAAGCGG 0.793944 -124 ACAGCTCGGCGGCCTGGTGGCCAGGATCGT 36 255 1 GGCCTGGTGG 0.926766 -46 TGGGAGTGGCGATCCCTTACCC 36 289 0 GGAGTGGCGA 0.579747 -12 GATCTGAGAAGTCGTGGCGGATTAGGCCGC 39 263 1 GTCGTGGCGG 0.964492 -38 CTATCTGCGTGGCGCGGTGGTTTCTCGCG 40 10 0 GGCGCGGTGG 0.9149 -119 CGAACTAGCTGGCAAGGTGGCCGACCTCGC 40 64 0 GGCAAGGTGG 0.767532 -65 TACCCGCGATGTCGTGGCGGGGTGCAAAAC 45 35 1 GTCGTGGCGG 0.964492 -27 GCCCGCTGCCGCCGCGGTGGGTAACCGTTC 47 56 1 GCCGCGGTGG 0.845182 -139 TACTCCTTCAGCCGTGGTGGACGTTTAGCC 47 114 0 GCCGTGGTGG 0.949515 -81 GCAGCGATGAGGAGGAGCGGCGCAGATGGT 50 51 1 GGAGGAGCGG 0.854213 -121 GCAGCGATGAGGAGGAGCGGCGCAGATGGT 50 104 1 GGAGGAGCGG 0.854213 -68 GCAGCGATGAGGAGGAGCGGCGCAG 50 157 1 GGAGGAGCGG 0.854213 -15 GTGAGATGCCGTCCTGGTGGTGCCGGGATG 51 193 1 GTCCTGGTGG 0.800595 -42 TGCGGATCCCGGAAAGGCGGGCCGCGGTGC 52 133 0 GGAAAGGCGG 0.772657 -151 GCAACAGCATGCCGGGGCGGTCCCGCGGCG 52 160 1 GCCGGGGCGG 0.960229 -124 TCCCGGGTCCGGCATCGCGGCAGACGCCAG 52 209 1 GGCATCGCGG 0.52253 -75 CTGAAGCCGGGCCCTGGCGTCTGCCGCGAT 52 222 0 GCCCTGGCGT 0.349582 -62 CAGATCACGCGGCCTGCTGGGCGCGTGTCG 54 89 0 GGCCTGCTGG 0.393716 -150 GTCTGTGACTGCACTGGTGGCGCCGGTGTG 54 160 0 GCACTGGTGG 0.741031 -79 CGCTTGCGGGGGAGAGGAGGCGGAACAA 56 9 0 GGAGAGGAGG 0.543302 -89 CGCCGACAATGCAGTGGGGGTACCACCCGC 56 72 0 GCAGTGGGGG 0.635922 -26 ********** Masking position 9 Map Score: 20.7853 Number of sites scoring better than the average of aligned sites = 871 Number in coding regions = 798 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 AGACCGACGACGGGTTCTGCCGCTAAAAAC 13 31 1 CGGGTTCTGC 0.694559 -130 TGAGTATCAGCGCGGTCGCGGCGCAGCTCG 39 167 1 CGCGGTCGCG 0.782319 -134 GCAACGGCGTCGCGCTCCGCCGATACCCCG 39 195 0 CGCGCTCCGC 0.892069 -106 ATCTGCATCGCGAGGTCGGCCACCTTGCCA 40 55 1 CGAGGTCGGC 0.960254 -74 TCATATTTTGCACCGTCGGCGGCGAAGCTC 40 102 0 CACCGTCGGC 0.660837 -27 CGAACCCGACCGAGTTCGGGTGATCCGCGA 41 28 1 CGAGTTCGGG 0.918794 -24 TTCGGCCAAAGGCGGTCGGCTCGCCGGCG 42 10 0 GGCGGTCGGC 0.887341 -50 TTGTTCTGGCCGAGTCCGCGG 44 2 0 CGAGTCCGCG 0.507923 -74 GCCGTGAATGCACGTTCGGCG 46 2 0 CACGTTCGGC 0.95941 -72 TCCCTGTGTTCACGTTCGGCGAGGAAACCG 46 52 1 CACGTTCGGC 0.95941 -22 GCCGGTGTGGCGCGTTCGGGATTATTGGGA 47 87 0 CGCGTTCGGG 0.982531 -108 CGTTGTGCACCACGTTCTGGGGAATGTTGG 47 151 0 CACGTTCTGG 0.665907 -44 CGGGCCTGGCCTCGGCCGGCCCCTCGTTGT 51 111 1 CTCGGCCGGC 0.84744 -124 GTGTCTGCACCGCGGCCCGCCTTTCCGGGA 52 127 1 CGCGGCCCGC 0.932927 -157 GATTTCCTCCCGGGTCCGGCATCGCGGCAG 52 202 1 CGGGTCCGGC 0.923454 -82 GCCGCGTTGGGCGTTGGCCGGC 53 39 0 CGCGTTGGGC 0.862391 -12 ACGTTGTCGGCACGCTCGGGCAAGATCGCC 54 19 1 CACGCTCGGG 0.88628 -220 ACTCAGATCACGCGGCCTGCTGGGCGCGTG 54 92 0 CGCGGCCTGC 0.927847 -147 TCATATTCGACGAGCCCGGGCGACCACTCA 54 117 0 CGAGCCCGGG 0.827234 -122 ********** Masking position 7 Map Score: 21.0836 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 507 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 CAGCCTCCTTTTTCTTTTTCATAGATTCCT 1 15 1 TTTCTTTTTC 0.907274 -111 TATCTACACTTCTCTTTTTTTGTAAAAAAC 1 44 1 TCTCTTTTTT 0.87042 -82 AATAGCAGAATTTCTGTTTTTTCTCCTTTC 10 79 0 TTTCTGTTTT 0.85526 -222 CTTACCTCCATTTCAGTTTTTTTCACCCTC 10 276 0 TTTCAGTTTT 0.621578 -25 TATAGAAAGTTTTCTTTTTTCCTTTTGTGG 12 39 0 TTTCTTTTTT 0.932168 -79 CTAAGAGAGATGTCTTTTTTTATACATAAA 31 34 1 TGTCTTTTTT 0.784947 -97 GTATCAAAGGTTTCATTTTTTTATGTATAA 31 53 0 TTTCATTTTT 0.792533 -78 TTTATTTTGCTTTCTTTTTTAAGCCTTAAA 33 99 1 TTTCTTTTTT 0.932168 -202 AAGCATACTTTTTCTTTTTCGTGAATATAT 34 237 0 TTTCTTTTTC 0.907274 -64 TATGAATTAATCTCTTTTTCAACCGCGCTA 35 94 0 TCTCTTTTTC 0.827071 -98 ********** Masking position 7 Map Score: 5.19111 Number of sites scoring better than the average of aligned sites = 592 Number in coding regions = 454 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 12 AAAAAGGTGAGGTGCACACAA 3 2 1 AAAAGGTGAG 0.925347 -21 ATGAATGTTAAAAAGTAGATGTTTTGTGCA 4 28 0 AAAAGTAGAT 0.549448 -249 GAATTTTCTTGAAAGATGATGAAACAATAG 4 123 0 GAAAGATGAT 0.65481 -154 TTTGTGGAGAAATAGATGATTCTTGTTTAA 12 16 0 AATAGATGAT 0.561382 -102 TTCAGCCTGCAAAAGGTGAGAATGATCAAT 12 81 0 AAAAGGTGAG 0.925347 -37 CTGCTAAAAGCTGATCTTCAGAATT 13 146 0 AAAAGCTGAT 0.819419 -15 AGTTTGTAGTAAAAGAAGATGAAGAAGCTG 15 159 1 AAAAGAAGAT 0.800488 -93 TTTTCGATTTAAAAGGAGAGAAAAAACAGC 18 13 1 AAAAGGAGAG 0.831571 -20 CCTATTCAAAAGGTGATAAGAGGGACT 23 8 1 AAAAGGTGAT 0.951901 -94 TTTTCTTGAAAAAAGGTGATAAAAGGCAGT 23 35 0 AAAAGGTGAT 0.951901 -67 TCCATACGGAAAAAGATGATTATTTACATC 33 168 1 AAAAGATGAT 0.90969 -133 ********** Masking position 4 Map Score: 7.23817 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 227 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 13 TATACTATAGCGCTGCTGTTTCCGCAAGATGT 4 158 0 CGCTGTGTTC 0.905152 -119 AAGGGCTAAAGCCCCGCGTTTCGGCGGGACTT 9 22 0 GCCCCCGTTC 0.848226 -118 TAGACTTTATGCCTGTTATTTCTTACAATAAG 10 212 1 GCCTGTATTC 0.638623 -89 TTGCTTATGGGCTTGATGTTTCAAGAGGAGGT 28 53 1 GCTTGTGTTC 0.865024 -26 GCGCTGTCAACCTTGTCGTTTCAACACCTTAT 34 27 1 CCTTGCGTTC 0.822095 -274 ATCAAGCGAAGCACGATGTTCCGGAAGGCATT 34 279 1 GCACGTGTTC 0.900464 -22 CCCGTCGGGCCGCTCATGTTTCCACTCCTCCG 36 208 0 CGCTCTGTTC 0.613079 -93 CGGCGGAGCGCGACGCCGTTGCACGCCGGTTG 39 203 1 CGACGCGTTC 0.709522 -98 TCGGCCGGCCCCTCGTTGTTGCGTGACTAACG 51 122 1 CCTCGTGTTC 0.888173 -113 CGCGAAGTCAGCCCGCCGATGCGAGCTGCGCC 52 96 0 GCCCGCGATC 0.754986 -188 CTGCACCGCGGCCCGCCTTTCCGGGATCCGCA 52 131 1 GCCCGCTTTC 0.672021 -153 GACCGCCCCGGCATGCTGTTGCGGATCCCGGA 52 150 0 GCATGTGTTC 0.865022 -134 GCACTGGTGGCGCCGGTGTGTCGGGACACAAT 54 148 0 CGCCGTGTGC 0.646378 -91 TTACCAGTGTGCCTGGTGTTTCGTCTGTGACT 54 180 0 GCCTGTGTTC 0.966701 -59 CTTGCAAGATCCCTGTTGTTACCAGTGTGCCT 54 198 0 CCCTGTGTTC 0.962245 -41 ***** **** * Masking position 12 Map Score: 5.91038 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 555 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 14 CTTGTGTGCACCTCACCTTTT 3 12 0 TTGTGTGCAC 0.885661 -11 GGTCAACTAAGTGAGTTCACTTTTCCGTCA 32 52 0 GTGAGTTCAC 0.866281 -112 GGAGCCCGCCCTGAGTGCACGTTCGAAG 37 9 0 CTGAGTGCAC 0.954708 -73 TGTTCTCGTCGAGTGTGCACCTACGGCGAC 37 50 0 GAGTGTGCAC 0.899718 -32 TTTTTCCGCCGTGAATGCACGTTCGGCG 46 9 0 GTGAATGCAC 0.796889 -65 AAAAGTCTCCCTGTGTTCACGTTCGGCGAG 46 45 1 CTGTGTTCAC 0.828394 -29 CTGACTTCGCGTGTCTGCACCGCGGCCCGC 52 117 1 GTGTCTGCAC 0.954205 -167 TGTTTCGTCTGTGACTGCACTGGTGGCGCC 54 166 0 GTGACTGCAC 0.950318 -73 ********** Masking position 9 Map Score: 2.91565 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 13 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 15 TATACTATAGCGCTGCTGTTTCCGCAAGAT 4 160 0 CGCTGCTGTT 0.931698 -117 AATATATTCCCCCAGATGTTT 14 2 0 CCCAGATGTT 0.914829 -20 AGGTTACATTCCCTGCTGATAATCAATGTA 25 89 0 CCCTGCTGAT 0.897734 -42 TTTCCGGGGCCCCTGCTGGACCCCCTCTGA 43 51 0 CCCTGCTGGA 0.889982 -188 GGAGGAGCGGCGCAGATGGTTGGCGCCGGC 50 61 1 CGCAGATGGT 0.931656 -111 GGAGGAGCGGCGCAGATGGTTGGCGCCGGC 50 114 1 CGCAGATGGT 0.931656 -58 TTTACACCGACCCAGCTGGTGATTTTCCCG 52 60 0 CCCAGCTGGT 0.938204 -224 CTTGCAAGATCCCTGTTGTTACCAGTGTGC 54 200 0 CCCTGTTGTT 0.809628 -39 ********** Masking position 7 Map Score: 2.64299 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 136 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234