AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00460_synecho_reg_300.orf -o00460_synecho_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.48 -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 = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 sll1931 300 glyA; serine hydroxymethyltransferase (serine methylase) (SHMT). #2 slr0877 207 amidase. [EC:3.5.1.4] #3 slr0878 97 hypothetical protein. #4 slr0879 93 gcvH; glycine decarboxylase complex H-protein. #5 slr0880 22 secreted protein MPB70 precursor. #6 sll0873 142 napC; carboxynorspermidine decarboxylase. #7 ssl1633 85 CAB/ELIP/HLIP superfamily. #8 slr0881 88 hypothetical protein. #9 sll0872 153 hypothetical protein. #10 slr0882 300 hypothetical protein. #11 sll1605 262 fabZ; (3R)-hydroxymyristol acyl carrier protein dehydrase. #12 slr1718 78 hypothetical protein. #13 slr1719 129 drgA; drgA protein. [SP:DRGA_SYNY3] #14 slr1720 25 aspS; aspartyl-tRNA synthetase (aspartate--tRNA ligase) (aspRS). #15 slr1721 102 hypothetical protein. #16 slr1722 126 guaB; IMP dehydrogenase subunit. [EC:1.1.1.205] #17 sll1601 96 hypothetical protein. #18 slr1724 167 hypothetical protein. #19 ssl3127 285 hypothetical protein. #20 sll1599 98 mntA; manganese transport system ATP-binding protein mntA. #21 sll1598 143 mntC; Mn transporter MntC. #22 ssr2898 300 transposase. #23 slr1269 96 ggt; gamma-glutamyltranspeptidase precursor. [EC:2.3.2.2] #24 slr1270 197 hypothetical protein. #25 slr1271 251 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #26 slr1272 29 hypothetical protein. #27 slr1273 184 hypothetical protein. #28 slr1274 81 pilM; membrane protein. #29 slr1275 39 hypothetical protein. #30 slr1276 80 hypothetical protein. #31 sll1173 66 hypothetical protein. #32 slr1278 49 hypothetical protein. #33 sll1172 282 thrC; threonine synthase. [EC:4.2.99.2] #34 slr1279 71 ndhC; NADH-plastoquinone oxidoreductase chain 3. [EC:1.6.5.3] #35 slr1281 300 ndhJ; NADH-plastoquinone oxidoreductase subunit J (orf 155). #36 sll1538 116 bgl; beta-glucosidase. [EC:3.2.1.21] #37 slr1627 118 hypothetical 22.0 kD protein slr1627. [SP:YG27_SYNY3] #38 sll1536 135 moeB; molybdopterin biosynthesis MoeB protein. #39 slr1629 124 hypothetical protein. #40 sll1535 99 rfbP; galactosyl-1-phosphate transferase. #41 sll1533 300 pilT; twitching mobility protein. #42 sll0422 120 asparaginase. [EC:3.5.1.1] #43 sll0421 109 purB; adenylosuccinate lyase (adenylosuccinase) (ASL). [EC:4.3.2.2] #44 slr0445 56 hypothetical protein. #45 sll0420 35 ureB; urease beta subunit (ureA amidohydrolase). [EC:3.5.1.5] #46 sll0419 77 hypothetical protein. #47 sll0418 68 sterol-C-methyltransferase. [EC:2.1.1.41] #48 slr0446 300 dnaX_and_dnaZ; DNA polymerase III subunit. [EC:2.7.7.7] #49 sll0827 266 hypothetical protein. #50 slr0841 300 hypothetical protein. Motif number 1 CCTTTCGGCGATCGGTTCGGGACACA 2 7 1 GGCGATCGGT 0.724436 -201 TATTTTCCTTGGCGATCGCCGTGGCGGTTT 2 125 1 GGCGATCGCC 0.499945 -83 CCAAAAATATGGCGGAGGCAGGGGTTGTTC 3 47 1 GGCGGAGGCA 0.826012 -51 TGGTGAAAAAGGCAACGGGAGGATAATGTT 7 56 0 GGCAACGGGA 0.770756 -30 GGCAATGGCAGGCACTGGAA 8 79 0 GGCAATGGCA 0.950282 -10 GGTTTTATCAAGCGAAGGCATTATACTATT 10 86 0 AGCGAAGGCA 0.553686 -215 CAAACCCGCTGGCGATCGCCAAAAACAGGT 10 158 1 GGCGATCGCC 0.499945 -143 AACTAGAACTGGCAACGGGCATCGGCACAA 10 279 1 GGCAACGGGC 0.857195 -22 GGTTTTCGGTGGCGATCGGGCCTAGAACCT 11 139 1 GGCGATCGGG 0.936056 -124 CAACTATTATGGCGATCGCCAGTTTGGTGG 19 186 1 GGCGATCGCC 0.499945 -100 TGATGGTCGGAGCGATGGGCACCATGGACG 22 186 1 AGCGATGGGC 0.777606 -115 CGGAGGTGTGGGCGATCGCCTGCCAATCAA 25 97 1 GGCGATCGCC 0.499945 -155 CGGACTTGTGGGCGATCGCCTGGGGGCATT 33 99 1 GGCGATCGCC 0.499945 -184 GGGGGGCAATGGCCCGAGGTTCCA 33 269 0 GGCAATGGCC 0.953452 -14 TTTTGCCGTGGGCGACCGGGA 35 290 1 GGCGACCGGG 0.870484 -11 TGATCATATTGGCGATCGCCATTTTCCTGG 37 43 1 GGCGATCGCC 0.499945 -76 TCCTGGTAGTGGAGATGGCGGTCACTTTTT 37 67 1 GGAGATGGCG 0.83794 -52 TAGTCTTTTTGGCGGCGGCACTACCATGGT 38 59 0 GGCGGCGGCA 0.881997 -77 TGGCGGTGGGAGTCCTCAGTT 40 2 1 GGCGGTGGGA 0.882559 -98 AGACGGCATGGAGAAGGCAATTAATGCAA 41 10 1 GGAGAAGGCA 0.650539 -291 CAACTGCCAAGGCAATGGCGTTTTCCAGGT 43 21 0 GGCAATGGCG 0.933541 -89 ATTAAAATCAGGCGATCGCCGC 44 45 1 GGCGATCGCC 0.499945 -12 AGCCTCTAATGGCAAAGGCAAAAACAATTG 49 109 0 GGCAAAGGCA 0.835194 -158 AGTTGGAAATGGCAAAATGCTTGA 49 253 0 GGAAATGGCA 0.647397 -14 ********** Masking position 8 Map Score: 45.6926 Number of sites scoring better than the average of aligned sites = 7243 Number in coding regions = 6610 Number in noncoding regions = 633 Number of orfs with sites within 600 bp upstream = 403 Fraction of orfs with sites within 600 bp upstream = 0.0647286 Motif number 2 CGGTCGTAGCCCCGCCCAGGAGTTAACCGTTCCTCTC 2 44 0 CCCCCCAATC 0.936867 -164 CGTTGCCTTTTTCACCACAGACTTGCC 7 69 1 TTCCCACATC 0.791778 -17 TGGAAACTAACCCGCCAATAATTCCCCCTAGCAGCTT 8 47 0 CCCCCAAATC 0.77304 -42 AACTGGCAATCCCTCCCCCTTATTAGCTGGAGATTTT 9 90 0 CCCCCCCTTC 0.88393 -64 TCCGATTAACCCCTCCCCTCCCTCTCCAGGTCAACCA 10 13 0 CCCCCCCCTC 0.914898 -288 GGGTTGTTCATTCCCCAAACAATCCGCCAAATCCT 11 9 0 TTCCCAAATC 0.800868 -254 CCCAGAAAAATTGGCCAATTCTTCTTCCGGGTTGGCC 11 65 0 TTGCCAACTC 0.60866 -198 ACGCTTACTTCTCACCCCTAACTCCTGCTGTTCAACG 13 35 0 CTCCCCCATG 0.906577 -95 TTGTTGACCAATGCCCCACCACTACCCGCTATTACCC 16 18 0 ATGCCCAATC 0.856526 -109 CCCAATAAAAATCCCCCCAGAATAATCCCAGGGGGTT 16 80 1 ATCCCCCATC 0.917923 -47 AAATTTTATTCCGCCCCCTAAATCTCCTTACTAACGC 18 63 1 CCGCCCCATC 0.876257 -105 AGTCCCCCTAATCCCCCCAAAATTTGGAGAGAAACTG 18 127 0 ATCCCCCATG 0.829069 -41 CAGTCTAGTATTCTCCCAGAATTGCCGGAGTTTAAGT 24 80 1 TTCCCCAATG 0.883711 -118 CGAGGGAAGAATCGCCAATTTCTCAAGGAAACTTTGA 24 127 1 ATCCCAATTG 0.389912 -71 TTGGCAGGCGATCGCCCACACCTCCGGTTACGCTGAC 25 86 0 ATCCCCACTG 0.797191 -166 GTAACCCAATTTCCCCCAGCCGTAACCTTTATCCACA 25 157 1 TTCCCCACTC 0.930681 -95 GATATTCTCTCCCTCCCATCCTTACTCCTTAATAATT 27 46 0 CCCCCCACTC 0.919163 -139 TATATTATTTTTGTCCACTAAATTTTCAATTTTTCCC 31 12 1 TTGCCACATC 0.657437 -55 TCCGGTAAGCTTGACCCAGGTGTAATCCCTTGGGGTG 33 66 0 TTGCCCATTC 0.827589 -217 CCCCCAGGCGATCGCCCACAAGTCCGGTAAGCTTGAC 33 88 0 ATCCCCAATG 0.836866 -195 CTTGCCTTGCCTGCCCCCCCTATTGTCTTCTCCTATT 34 15 0 CTGCCCCTTC 0.859739 -57 ACAAAAATATTCCCCCAAAGTTTTCAGTCCATTGGCA 35 211 1 TCCCCAATTG 0.372515 -90 CTATTAAATAATGTCCCCAATGTCCCCATTGAATTCG 41 169 1 ATGCCCCTTC 0.753919 -132 TGATCTATCCTTCACCCAAGCCTTTACCTAAAATTCT 42 94 1 TTCCCCACTC 0.930681 -27 TGCGCCTGTTTTGTCCCCATTGTCAGGGAGGCTTAGC 48 227 1 TTGCCCCTTG 0.663106 -74 TTCCCCAATAACTAGCCCCAAGATTGT 48 284 0 TTCCCAAATC 0.800868 -17 AAGATATCTATACCCCCATGATTTTACCATTGGGAAT 49 40 1 TACCCCAATC 0.518569 -227 GGAAACTGTTCCGTCCCAATTCTAGGCAAGAAATTCC 49 72 0 CCGCCCATTC 0.802574 -195 CTCCGAGCTAATCTCCCAAAACTTCTGCCAGGGAGGC 49 176 1 ATCCCCAATG 0.836866 -91 CTTTTCCCCTCTGTCCCATGCTTTGTCTATAGCTTGC 50 259 1 CTGCCCACTC 0.901496 -42 *** **** * * * Masking position 13 Map Score: 30.4096 Number of sites scoring better than the average of aligned sites = 1768 Number in coding regions = 1479 Number in noncoding regions = 289 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 3 TCGCCAGCGGGTTTGGCAAGAACGGCAGAT 10 143 0 GTTTGGCAAG 0.558682 -158 GTAAACCTGTTTTTGGCGATCGCCAGCGGG 10 162 0 TTTTGGCGAT 0.772063 -139 GTATTGCACTTGTTGGGGAGTTGCGTAAAC 10 186 0 TGTTGGGGAG 0.637818 -115 AGCTCCAGACCTGTGGCAATAAGGACAACT 10 253 1 CTGTGGCAAT 0.772869 -48 TGGCGGATTGTTTGGGGAATGAACAACCCT 11 17 1 TTTGGGGAAT 0.864184 -246 AACTGGTTTTCGGTGGCGATCGGGCCTAGA 11 135 1 CGGTGGCGAT 0.79032 -128 AGGTCCAGCACTTTGGCCAGGTTCTAGGCC 11 157 0 CTTTGGCCAG 0.419548 -106 AATTTAAACAGTTTGGGAATAGTAAGTAAG 15 12 0 GTTTGGGAAT 0.678672 -91 AGCGGGTAGTGGTGGGGCATTGGTCAACAA 16 25 1 GGTGGGGCAT 0.784001 -102 TGGGATTATTCTGGGGGGATTTTTATTGGG 16 80 0 CTGGGGGGAT 0.864046 -47 TCTCCAAATTTTGGGGGGATTAGGGGGACT 18 134 1 TTGGGGGGAT 0.920287 -34 GTTTTCATTATTGTGGCGATACAAACCAA 19 10 0 TTGTGGCGAT 0.860403 -276 GAGACAACTATTATGGCGATCGCCAGTTTG 19 182 1 TTATGGCGAT 0.407374 -104 CGCCAGTTTGGTGGGGGCATTATTTGCTTG 19 202 1 GTGGGGGCAT 0.856021 -84 GTTACAATTCTTAGGGCAATGCGGTAAGTT 23 72 0 TTAGGGCAAT 0.593715 -25 TAACCGGAGGTGTGGGCGATCGCCTGCCAA 25 93 1 TGTGGGCGAT 0.888593 -159 AGGTTACGGCTGGGGGAAATTGGGTTACAT 25 155 0 TGGGGGAAAT 0.733741 -97 GGTTAATAATCGGGGGAAATTGTGGATAAA 25 184 0 CGGGGGAAAT 0.602705 -68 TAATCCAGTCGGAGGGCAATCAACAAAGC 27 166 1 GGAGGGCAAT 0.533197 -19 AAGCAATAGGTGTGGGCAAGGTGAACAAAC 28 55 1 TGTGGGCAAG 0.809039 -27 TTACCGGACTTGTGGGCGATCGCCTGGGGG 33 95 1 TGTGGGCGAT 0.888593 -188 GGGCGATCGCCTGGGGGCATTCTGCCAATT 33 108 1 CTGGGGGCAT 0.823058 -175 TTATTAATCGTTTGGGCAATAATCCAATTC 33 200 1 TTTGGGCAAT 0.878059 -83 GGGGGGCAATGGCCCGAGGT 33 273 0 GGGGGGCAAT 0.911045 -10 GAAGACAATAGGGGGGGCAGGCAAGGCAAG 34 22 1 GGGGGGGCAG 0.777686 -50 GACAATGGATTGGTGGCCATTACTAAACTT 34 52 1 TGGTGGCCAT 0.833645 -20 TCAGAGCGACTTGTGGAAATTAGCTACTAA 35 43 0 TTGTGGAAAT 0.539228 -258 AAGGCTTTGATGGTGGCAAGAACGCTAAGG 35 144 0 TGGTGGCAAG 0.784337 -157 ACTGAAAACTTTGGGGGAATATTTTTGTGT 35 209 0 TTGGGGGAAT 0.920498 -92 ATTGGCAACAGTGGGGGAAGGGGGAGCTAA 35 241 1 GTGGGGGAAG 0.811848 -60 AATCAGTTTTTTTTGGCAATCAATGAAACT 36 21 1 TTTTGGCAAT 0.77257 -96 AATGGGGACATTGGGGACATTATTTAATAG 41 169 0 TTGGGGACAT 0.644179 -132 AAACCTAATCTTTTGGGCAGATTCTCT 44 8 0 TTTTGGGCAG 0.537094 -49 GCTTGTTGGCTGGTGGGGAGGAGTTTATTG 48 30 1 TGGTGGGGAG 0.762158 -271 TGGCAGAAGTTTTGGGAGATTAGCTCGGAG 49 176 0 TTTGGGAGAT 0.576156 -91 GTTCACCGCCGTTGGGGAATGGAGGCGTCA 50 219 0 GTTGGGGAAT 0.817421 -82 AGCTTGCCTTCGTTGGGAATTA 50 289 1 CGTTGGGAAT 0.647348 -12 ********** Masking position 9 Map Score: 29.4059 Number of sites scoring better than the average of aligned sites = 4800 Number in coding regions = 4308 Number in noncoding regions = 492 Number of orfs with sites within 600 bp upstream = 459 Fraction of orfs with sites within 600 bp upstream = 0.0737231 Motif number 4 GGTGCTTTCCGCCCCCAGCACTGTTTACAG 1 270 1 GCCCCCAGCA 0.944845 -31 TGCGGTCGTAGCCCCGCCCAGGAGTTAACC 2 53 0 GCCCCGCCCA 0.986279 -155 AACAACCCCTGCCTCCGCCATATTTTTGGT 3 46 0 GCCTCCGCCA 0.753927 -52 TAACCTCTAACCCCCGCCCAGACTGC 4 78 1 CCCCCGCCCA 0.983866 -16 ACTACAGGTACCCCAGGCCAGAAAACCTAA 6 34 0 CCCCAGGCCA 0.9357 -109 TGTAGTAAATCTCCCCGGCAACCTCCGTTA 6 58 1 CTCCCCGGCA 0.576804 -85 GCCAATAATTCCCCCTAGCAGCTTCTCTGG 8 41 0 CCCCCTAGCA 0.758999 -48 GTAAGGTCTCCCCCATCCCAATCAACCAAT 9 53 0 CCCCATCCCA 0.861307 -101 TTCCGATTAACCCCTCCCCTCCCTCTCCAG 10 21 0 CCCCTCCCCT 0.668386 -280 GGTCAACAAGGCCCAGACCAGGGTAACAAA 16 46 1 GCCCAGACCA 0.945977 -81 AGCAAATAATGCCCCCACCAAACTGGCGAT 19 200 0 GCCCCCACCA 0.98803 -86 CCAAAAGTATGCTCCGCCCAATGGATAAAA 22 69 1 GCTCCGCCCA 0.820988 -232 GGTGCCCATCGCTCCGACCATCAGGGTCTG 22 179 0 GCTCCGACCA 0.779664 -122 GCAGGCGATCGCCCACACCTCCGGTTACGC 25 90 0 GCCCACACCT 0.801911 -162 TAGATATTCTCTCCCTCCCATCCTTACTCC 27 55 0 CTCCCTCCCA 0.653148 -130 TGTTCACCTTGCCCACACCTATTGCTTCAC 28 52 0 GCCCACACCT 0.801911 -30 CGCTGGACCCCCCCTGACCACCATTAGCCG 33 30 0 CCCCTGACCA 0.870577 -253 TGCCTTGCCTGCCCCCCCTATTGTCTTCTC 34 20 0 GCCCCCCCTA 0.872223 -52 TCCCGGTCGCCCACGGCAAAATTAAACA 35 283 0 GCCCACGGCA 0.841228 -18 CCATGGTAGTGCCGCCGCCAAAAAGACTAA 38 60 1 GCCGCCGCCA 0.819527 -76 ACTGAGGACTCCCACCGCCA 40 1 0 CCCACCGCCA 0.722166 -99 GGCCCTGCCCAACTTTGTTAC 47 2 1 GCCCTGCCCA 0.91132 -67 CAATAAACTCCTCCCCACCAGCCAACAAGC 48 30 0 CTCCCCACCA 0.870206 -271 ACAAATAAGACCCCATACTACGAGTAGGTT 48 146 1 CCCCATACTA 0.234137 -155 ********** Masking position 3 Map Score: 21.8767 Number of sites scoring better than the average of aligned sites = 3129 Number in coding regions = 2948 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 5 CTGCTCCTTGGGCCTTTTTTCTGCGGTCGTAG 2 72 0 GGCTTTTTCT 0.83318 -136 TGCCTTGTTCTCCGAAGGTTAGT 7 2 1 GCCTGTTTCC 0.978194 -84 TCCTCCCGTTGCCTTTTTCACCACAGACTTGC 7 63 1 GCCTTTTACC 0.948602 -23 AGAAGAATTGGCCAATTTTTCTGGGCTCATGG 11 77 1 GCCATTTTCT 0.914695 -186 CCTGGTCTGGGCCTTGTTGACCAATGCCCCAC 16 36 0 GCCTGTTACC 0.917735 -91 GGACTTCAAAGCCTTTTTGTCCCTACTTTTTG 22 16 1 GCCTTTTTCC 0.986705 -285 TACGACCATTGACCTTTTTTCCACCGTCATAG 22 262 1 GACTTTTTCC 0.841899 -39 GGGAAGAATCGCCAATTTCTCAAGGAAACTTT 24 130 1 GCCATTTTCA 0.765208 -68 TAACTTTTGCGGCTTATTTTCCAGTCCGTTGG 25 37 0 GGCTATTTCC 0.710184 -215 CTAAATTTCAGCCAATTTATCCATAGTTTAGC 32 12 1 GCCATTTTCC 0.978458 -38 GGGGCATTCTGCCAATTTTTCTGATTATAGGA 33 121 1 GCCATTTTCT 0.914695 -162 CACCATCAAAGCCTTTTTTTCTGTTGTTTTAA 35 159 1 GCCTTTTTCT 0.946004 -142 TTTGGTTAGAGTCTATTTATCCCTTCCTTGCA 39 90 1 GTCATTTTCC 0.765208 -35 AGGGCCAGTTCTCCAAATAACCGC 43 96 0 GGCAGTTTCC 0.886701 -14 GAAATCCACTGCCTTGTTGACCAAAATAAACT 48 95 0 GCCTGTTACC 0.917735 -206 AGCATAGGATACCGTTTTGTCCGACTAAGCCC 48 191 1 ACCTTTTTCC 0.796864 -110 *** **** *** Masking position 7 Map Score: 16.3919 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 423 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 CAGAAAAAAGGCCCAAGGAGCAGGAACGCC 2 81 1 GCCCAAGGAG 0.924772 -127 CCACGGCGATCGCCAAGGAAAATAATTGTC 2 119 0 CGCCAAGGAA 0.580515 -89 TTTTGACGACCCCAATGGTTCG 5 4 0 CCCCAATGGT 0.866341 -19 TGGGCTCATGGCCCAGGGGGGATCCCAATG 11 98 1 GCCCAGGGGG 0.95083 -165 CCAGGGGGGATCCCAATGGGCTTTAAACTG 11 110 1 TCCCAATGGG 0.964133 -153 TGTGCTGACGTCCAAAGGGTCAGATTATTT 15 50 0 TCCAAAGGGT 0.606987 -53 GCTCTGATCCCCACTGGATTAGGGTTAT 15 85 0 CCCCACTGGA 0.716857 -18 CCCAGAATAATCCCAGGGGGTTGATAGTTG 16 95 1 TCCCAGGGGG 0.948351 -32 GCTCCTCTGATCCCAATGAGTTGATAGCAA 19 44 0 TCCCAATGAG 0.871057 -242 AATAGTTGTCTCCCAAGGAGAACTGTTTTT 19 164 0 TCCCAAGGAG 0.931019 -122 AGTATGCTCCGCCCAATGGATAAAATCCTT 22 74 1 GCCCAATGGA 0.921589 -227 TGCAGGCACTGCCAAAGGGGAGCAAACCAG 22 135 1 GCCAAAGGGG 0.813184 -166 TTTCAATTTTTCCCACGGGAAACATCAAGA 31 35 1 TCCCACGGGA 0.865398 -32 AGGGCCAATGGTCTCCTCACGG 33 3 1 GGCCAATGGT 0.703423 -280 CGGTGTTGCACCCCAAGGGATTACACCTGG 33 58 1 CCCCAAGGGA 0.930337 -225 CCCCCACTGTTGCCAATGGACTGAAAACTT 35 228 0 TGCCAATGGA 0.792424 -73 GGCAAGAAATTCCCAATGGTAAAATCATGG 49 55 0 TCCCAATGGT 0.898257 -212 CCAAAACTTCTGCCAGGGAGGCTTTCCATG 49 191 1 TGCCAGGGAG 0.609477 -76 ********** Masking position 5 Map Score: 15.3327 Number of sites scoring better than the average of aligned sites = 1803 Number in coding regions = 1606 Number in noncoding regions = 197 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 7 TAATCCTTTTCCCACCTAATGGATACTTTGTGA 4 47 0 CCCCCATGGA 0.826684 -47 CCGTTCTTGCCAAACCCGCTGGCGATCGCCAAA 10 148 1 CAACCCTGGC 0.92483 -153 GTCCTTATTGCCACAGGTCTGGAGCTGACGCAG 10 246 0 CCAAGCTGGA 0.916472 -55 TAGAACCTGGCCAAAGTGCTGGACCTTAACTAA 11 161 1 CCAAGCTGGA 0.916472 -102 GACAGAAGATCCAACCCGATGGAGATGATAGTT 19 131 0 CCACCATGGA 0.937879 -155 AATAATGCCCCCACCAAACTGGCGATCGCCATA 19 193 0 CCACACTGGC 0.842575 -93 CGTAAACGTACAATCCTTGTGGATACCATGGGA 22 233 0 CAACCGTGGA 0.902725 -68 AGACTGAGTCCCATCCCTCTGGACAATGCGGAG 24 53 0 CCACCCTGGA 0.989899 -145 ACCAAAATGACCAACGGACTGGAAAATAAGCCG 25 27 1 CCACGCTGGA 0.974471 -225 TTGTTGATTGCCCTCCGACTGGATTACAGTAAG 27 159 0 CCCCCCTGGA 0.968712 -26 CCTTGGGGTGCAACACCGCTGGACCCCCCCTGA 33 43 0 CAAACCTGGA 0.917992 -240 ATTACAAAAAACCTGGAAAACGCCATT 43 5 1 CAAAACTGGA 0.659295 -105 ATGGAGGCGTCAATCCATGTGGAACGCGAACCA 50 198 0 CAACCGTGGA 0.902725 -103 *** ** ***** Masking position 10 Map Score: 12.4038 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 303 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 TTTTTTATAAAGGGTTTTATCAAGCGAAGGCAT 10 95 0 AGGTTTTACA 0.951282 -206 CGTTTGTCCTAGATTTTTAGCAAAAGTTTTCCC 11 240 1 AGATTTTACA 0.841939 -23 AGTGTTTTAGCAATGATAGCTAG 12 1 1 AGTTTTTACA 0.943997 -78 AGAGGTGTTAATCAAGCAAAATTTC 13 3 1 AGGGTTAACA 0.696503 -127 CTAAGGTTTGGTGTTTAGCAATTTAGTGTTG 13 109 0 TGGGTTTACA 0.836401 -21 TTTGGCGGAAAGGATTTTATCCATTGGGCGGAG 22 80 0 AGGTTTTACA 0.951267 -221 CAATGCGGTAAGTTATTTAGCGAACAGCGTTTC 23 53 0 AGTATTTACA 0.870367 -44 AACTAGAAATTGATTTTTAACTATTTAGTATTT 36 71 1 TGATTTTACA 0.690091 -46 TTAACTATTTAGTATTTTAACAATAAGCAAAGC 36 87 1 AGTTTTTACA 0.943997 -30 CTTTTTTGTATGGAATTTACCCAATTGATTGAC 37 91 1 TGGATTTACA 0.764769 -28 GGGAGTCCTCAGTTATTTAGCAAAGAATCGTAA 40 18 1 AGTATTTACA 0.870367 -82 GTTTTTCGTCAGTTGTTTAACAAAACGACGCAT 41 119 0 AGTGTTTACA 0.913476 -182 AACAGAAAAAAGTCTTTAACCTATTAAATAATG 41 149 1 AGTTTTAACA 0.759795 -152 ATAGATATCTTGTTTTTTAGCTAATTGCAATAC 49 18 0 TGTTTTTACA 0.875724 -249 *** ***** * * Masking position 9 Map Score: 8.97829 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 136 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 9 GGGTTTTAGACCCGGTTTTCCGATAAACTTA 1 220 1 CCGGTTTTCC 0.848658 -81 GTTGCCTTTAGCGGTTTTGCC 3 1 0 GCGTTTTGCC 0.938174 -97 CCTGGTTGACCTGGAGAGGGA 10 1 1 CCGGTTGACC 0.720711 -300 GCGATCGCCAGCGGGTTTGGCAAGAACGGCA 10 146 0 GCGGTTTGGC 0.773622 -155 AATTCTTCTTCCGGGTTGGCCCACTACCGAT 11 55 0 CCGGTTGGCC 0.972947 -208 TTAAGGTCCAGCACTTTGGCCAGGTTCTAGG 11 159 0 GCCTTTGGCC 0.84071 -104 CTGGGAATAACCTGGTTTGCCAAAGTTTTTC 11 200 1 CCGGTTTGCC 0.987366 -63 AATCTGAACCCCTCTTTTGCC 20 88 1 CCCTTTTGCC 0.965389 -11 CTACTTGGCACCTGGTTTGCTCCCCTTTGGC 22 145 0 CCGGTTTGCT 0.837333 -156 GGCCCTAACGCTCGTTTCCCTTTGAATCT 26 10 0 GCCGTTTCCC 0.720894 -20 CCCCCTTCCCCCACTGTTGCCAATGGACTGA 35 234 0 CCCTGTTGCC 0.802712 -67 ATTTGTTTCCCCACGTTTGTCCCTATGTCCT 41 90 0 CCCGTTTGTC 0.881984 -211 TCCGACTAAGCCCCTTTTGCGCCTGTTTTGT 48 210 1 CCCTTTTGCG 0.73139 -91 CCCTTTTGCGCCTGTTTTGTCCCCATTGTCA 48 221 1 CCGTTTTGTC 0.823611 -80 ** ******** Masking position 7 Map Score: 7.57183 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 639 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 10 GGTCGTAGCCCCGCCCAGGAGTTAACCGTT 2 50 0 CCGCCCAGGA 0.871625 -158 GGGGCTACGACCGCAGAAAAAAGGCCCAAG 2 68 1 CCGCAGAAAA 0.56675 -140 AGGAGCAGGAACGCCGAGAAAAAGACAATT 2 96 1 ACGCCGAGAA 0.414802 -112 CCTCTAACCCCCGCCCAGACTGC 4 81 1 CCGCCCAGAC 0.845183 -13 GGAAACTAACCCGCCAATAATTCCCCCTAG 8 53 0 CCGCCAATAA 0.807032 -36 CCGCTGGCGATCGCCAAAAACAGGTTTACG 10 163 1 TCGCCAAAAA 0.42605 -138 CCCAAACAATCCGCCAAATCCT 11 3 0 CCGCCAAATC 0.711494 -260 GGCCCGATCGCCACCGAAAACCAGTTTAAA 11 131 0 CCACCGAAAA 0.623012 -132 CAATAAAAATCCCCCCAGAATAATCCCAGG 16 82 1 CCCCCCAGAA 0.815824 -45 TACCCTCGTACCGCCGGAGCGTTAGTAAGG 18 88 0 CCGCCGGAGC 0.574689 -80 TCCCCCTAATCCCCCCAAAATTTGGAGAGA 18 132 0 CCCCCCAAAA 0.896096 -36 AAAGTATGCTCCGCCCAATGGATAAAATCC 22 72 1 CCGCCCAATG 0.758896 -229 AAAATCCTTTCCGCCAAAGGTACTGTCAGT 22 95 1 CCGCCAAAGG 0.623988 -206 TCCACAATTTCCCCCGATTATTAACCCCTG 25 188 1 CCCCCGATTA 0.480557 -64 GGTAGTGCCGCCGCCAAAAAGACTAAAATG 38 64 1 CCGCCAAAAA 0.943875 -72 GCACAGCTAACCCCCGGTAAACCTTTGATG 41 251 0 CCCCCGGTAA 0.392031 -50 ACGATGGTTGCCGCCAAATAGTAAAATTAA 43 66 1 CCGCCAAATA 0.87885 -44 AGAGAATCTGCCCAAAAGATTAGGTTT 44 8 1 CTGCCCAAAA 0.56675 -49 AGCACTGTTTCCGCCCAATAAACTCCTCCC 48 45 0 CCGCCCAATA 0.93097 -256 CAGGGTAAATCCGCCGGAAACAAATAAGAC 48 127 1 CCGCCGGAAA 0.903853 -174 ********** Masking position 4 Map Score: 7.84679 Number of sites scoring better than the average of aligned sites = 1394 Number in coding regions = 1304 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 11 TACGACAAGAAAAATCAGTTAATTATCAGT 9 21 1 AAAATCAGTT 0.943643 -133 GGCGATCGCCAAAAACAGGTTTACGCAACT 10 168 1 AAAAACAGGT 0.698017 -133 ATCGCCACCGAAAACCAGTTTAAAGCCCAT 11 125 0 AAAACCAGTT 0.796423 -138 ATCTTCTGTCAAAAACAGTTCTCCTTGGGA 19 154 1 AAAAACAGTT 0.869612 -132 ACACCAATTAAAATCAATTATTGAATAAT 30 10 1 AAAATCAATT 0.843766 -71 TAACCGATTGAAAATCAGTCAACACAAAAA 35 188 1 AAAATCAGTC 0.853007 -113 ATTAAACATCAAAATTAGTTTTAGCTCCCC 35 261 0 AAAATTAGTT 0.699378 -40 TGATTACTAAAATCAGTTTTTTTTGGCA 36 9 1 AAAATCAGTT 0.943643 -108 TAAATAGTTAAAAATCAATTTCTAGTTGGG 36 68 0 AAAATCAATT 0.843766 -49 GGAAGGCTCGAAAATTAATTAAATTAGGAG 39 30 0 AAAATTAATT 0.428693 -95 AGATCACATTAAAATCAGGCGATCGCCGC 44 38 1 AAAATCAGGC 0.667903 -19 TGGCAAAGGCAAAAACAATTGGGAAACTGT 49 100 0 AAAAACAATT 0.682657 -167 ********** Masking position 4 Map Score: 6.03392 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 173 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 AAAGACAATTATTTTCCTTGGCGATCGCCG 2 116 1 ATTTTCCTTG 0.961359 -92 TAATTAACTGATTTTTCTTGTCGTAACCTC 9 16 0 ATTTTTCTTG 0.758908 -138 AGCCAGACTCATTTTCCTGGCTCTGTTTTT 9 132 1 ATTTTCCTGG 0.957678 -22 GAATTGGCCAATTTTTCTGGGCTCATGGCC 11 81 1 ATTTTTCTGG 0.741138 -182 TCTCCTAATCATTTTCCTAGCTATCATTGC 12 20 0 ATTTTCCTAG 0.777812 -59 GTTCAACGAAATTTTGCTTGATTAACACCT 13 13 0 ATTTTGCTTG 0.829615 -117 TTTGACCAGTATTTACCCGGGTAATTTTGA 19 235 1 ATTTACCCGG 0.722537 -51 TGCTGATCAAAGTTTCCTTGAGAAATTGGC 24 140 0 AGTTTCCTTG 0.771459 -58 AGGGTAATTTTGCTGGTAGATTATCG 30 65 0 ATTTTGCTGG 0.815792 -16 CCACCAATCCATTGTCCTTGCCTTGCCTGC 34 38 0 ATTGTCCTTG 0.771459 -34 GGCGATCGCCATTTTCCTGGTAGTGGAGAT 37 53 1 ATTTTCCTGG 0.957678 -66 CCCGACGATGATTTTCCGTGAACAACAGCA 38 116 1 ATTTTCCGTG 0.824105 -20 TTAATACTTAATTTTCCCTGCTGTTTTAAC 47 43 1 ATTTTCCCTG 0.942846 -26 TTTCCGGCGGATTTACCCTGGAAATCCACT 48 117 0 ATTTACCCTG 0.741138 -184 TGAAACCTTATTTTTCCCTGCAATGGTGAG 49 144 1 TTTTTCCCTG 0.601621 -123 ********** Masking position 3 Map Score: 13.0035 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 264 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 13 ATCCATTAGGTGGGAAAAGGATTAACCTCTAA 4 56 1 TGGAAAGGAT 0.825226 -38 TGATCCCCACTGGATTAGGGTTATTAGGCTGT 15 77 0 TGGTAGGGTT 0.916995 -26 GGATGATGGGTGGTTAAAGGTGCTGATCAAAG 24 158 0 TGGTAAGGTG 0.916995 -40 GGGGAAATTGTGGATAAAGGTTACGGCTGGGG 25 170 0 TGGTAAGGTT 0.979289 -82 GGATTACACCTGGGTCAAGCTTACCGGACTTG 33 75 1 TGGTAAGCTT 0.943594 -208 AATTTCTAGTTGGGTCAAGCTTAACGAATTTA 36 50 0 TGGTAAGCTT 0.943594 -67 GGTAAAGGCTTGGGTGAAGGATAGATCAGCAC 42 90 0 TGGTAAGGAT 0.937272 -31 AAAGCCTCCCTGGCAGAAGTTTTGGGAGATTA 49 184 0 TGGAAAGTTT 0.659644 -83 TTTGCCCCCATGGTTGAAGGTTAACGGATTTA 50 37 1 TGGTAAGGTT 0.979289 -264 *** * ****** Masking position 7 Map Score: 4.86708 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 42 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 GAGTTGATAGCAAGGAAGTTTTCATTATTG 19 27 0 CAAGGAAGTT 0.791964 -259 TGGCATCGGACAAGGAGAGGAGTGAAGCAA 28 31 1 CAAGGAGAGG 0.911537 -51 GGGGGGCAGGCAAGGCAAGGACAATGGATT 34 33 1 CAAGGCAAGG 0.946908 -39 TTGGCCACATCAAGGAAGGCTCGAAAATTA 39 43 0 CAAGGAAGGC 0.899492 -82 GCTATGGATGCAAGGAAGGGATAAATAGAC 39 100 0 CAAGGAAGGG 0.97897 -25 TTCCAACTGCCAAGGCAATGGCGTTTTCCA 43 24 0 CAAGGCAATG 0.918292 -86 TTTTGGTCAACAAGGCAGTGGATTTCCAGG 48 101 1 CAAGGCAGTG 0.966363 -200 GTCATACAATCAAGGAGGTGTTAGGGTTTA 50 86 0 CAAGGAGGTG 0.943244 -215 ********** Masking position 3 Map Score: 3.3667 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 144 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 TTTTTCCATAGTTCCTAAATTTTTTAGGTTTTCTGGCCTGG 6 8 1 ATTAATTGTT 0.945321 -135 AAAAAACACAAACTTTTGTGACAATGTTCCGATTAACCCCTCCC 10 33 0 ATTACTTGTT 0.957004 -268 CTGGTTTGCCAAAGTTTTTCAAAAATTTTCGTTTGTCCTAGATT 11 211 1 ATTAAATGTT 0.731573 -52 CAACCTGACAATTTTTGATTAAAGTTTAAGGATTTAGAACGTAT 18 14 1 ATTAATTGTT 0.945321 -154 ACGACATATTAAATTTTATTAACTTTTGCGGCTTATTTTCCAGT 25 44 0 ATTAATTGTT 0.945318 -208 TTTCAGTTGAAGCTTAGTTAACACTTTGTTGCTTATTGTTGACA 27 114 0 ATTACTTGTT 0.957004 -71 TTGCTGGTAGATTATCGCTAACGGTCTTACGATTTTTGAATAAT 30 38 0 ATTACTTGTT 0.957004 -43 AGTTAGTTTTACATTTGTTAACAATTTGTCGCTTGAATCTCATT 41 45 1 ATTACTTGTT 0.957004 -256 CTAATTTCTTAATTTAGCTGAATATTTGAGGTTTTTGACTGCAT 46 30 1 ATTAATTGTT 0.945321 -48 * * * ** * * * ** Masking position 11 Map Score: 3.10585 Number of sites scoring better than the average of aligned sites = 29 Number in coding regions = 17 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863