AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00630_synecho_reg_300.orf -o00630_synecho_300.ace -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/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 Purged sequences: slr0049 25 hypothetical protein. sll0320 33 rnd; ribonuclease D. [EC:3.1.26.3] Input sequences: #1 slr1549 115 def; polypeptide deformylase (PDF) (formylmethionine deformylase). #2 ssr2611 55 hypothetical protein. #3 slr1550 42 lysS; lysyl-tRNA synthetase (lysine--tRNA ligase) (lysRS). #4 sll1457 203 rfbJ; RfbJ protein. #5 sll1456 110 hypothetical protein. #6 slr1552 75 hypothetical protein. #7 sll1455 300 hypothetical protein. #8 sll1138 111 gph; phosphoglycolate phosphatase. [EC:3.1.3.18] #9 slr1226 212 purC; phosphoribosyl aminoidazole succinocarboxamide synthetase. #10 slr1227 114 IAP75; chloroplast import-associated channel IAP75. #11 slr1228 47 prfC; peptide chain release factor 3 (RF-3). [SP:RF3_SYNY3] #12 slr1229 99 hypothetical protein. #13 sll1135 153 hypothetical protein. #14 slr1232 300 hypothetical protein. #15 sll1349 35 cbbZp; phosphoglycolate phosphatase. [EC:3.1.3.18] #16 sll1348 153 glgP; hypothetical protein. #17 sll1282 104 ribH; 6,7-dimethyl-8-ribityllumazine synthase (dmrl synthase) #18 sll1281 140 ycf9; Ycf9. [SP:YCF9_SYNY3] #19 sll1280 300 glgP; hypothetical protein. #20 sll1223 26 hoxU; hydrogenase subunit. [EC:1.12.1.2] #21 sll1222 40 hypothetical protein. #22 sll1221 76 hoxF; hydrogenase subunit. #23 sll1220 300 potential NAD-reducing hydrogenase subunit. [EC:1.6.5.3] #24 sll0753 73 folD; methylenetetrahydrofolate dehydrogenase. [EC:1.5.1.5] #25 sll0751 135 ycf22; hypothetical protein. #26 slr0782 90 hypothetical protein. [SP:Y782_SYNY3] #27 sll0750 145 sensory transduction histidine kinase. [EC:2.7.-.-] #28 sll0749 188 hypothetical protein. #29 sll0325 222 hypothetical protein. #30 slr0342 130 petB; cytochrome b6. [EC:1.10.99.1] [SP:CYB6_SYNY3] #31 slr0343 251 petD; cytochrome b6-F complex subunit 4 (17 kD polypeptide). #32 slr0344 127 rfbW; mannosyl transferase. #33 slr0345 204 hypothetical protein. #34 sll0322 45 hypF; transcriptional regulatory protein hypF. [SP:HYPF_SYNY3] #35 sll0321 138 hypothetical protein. #36 sll0319 276 hypothetical protein. #37 sll0318 164 hypothetical protein. #38 slr0350 174 transposase. #39 slr0351 152 hypothetical protein. #40 sll0317 139 transposase. #41 sll0315 123 transposase. #42 slr0353 300 hypothetical protein. #43 slr0009 201 rbcL; ribulose bisphosphate carboxylase large chain precursor. #44 slr0011 32 rbcX; #45 slr0012 300 rbcS; ribulose bisphosphate carboxylase small chain. [EC:4.1.1.39] #46 sll0401 193 gltA; citrate synthase. [EC:4.1.3.7] [SP:CISY_SYNY3] #47 sll0400 62 hypothetical protein. [SP:Y400_SYNY3] #48 slr0440 93 hypothetical protein. #49 ssr0102 74 ycf40; hypothetical protein. #50 sll0072 31 hypothetical protein. #51 sll0071 93 hypothetical protein. #52 sll0070 90 purU; formyltetrahydrofolate deformylase (formyl-fh(4) hydrolase). #53 sll0069 26 hypothetical protein. #54 sll0068 157 hypothetical protein. #55 sll0067 93 gst; glutathione S-transferase. [EC:2.5.1.18] #56 sll0066 99 hypothetical protein. #57 sll0065 181 ilvN; acetolactate synthase. [EC:4.1.3.18] #58 slr0053 64 hypothetical 20.1 kD protein slr0053. [SP:Y053_SYNY3] #59 slr0054 135 dgkA; probable diacylglycerol kinase (DAGK) (diglyceride kinase) #60 slr0055 143 trpG; anthranilate synthase component II. [EC:4.1.3.27] #61 slr0056 146 G4; chlorophyll synthase 33 kD subunit. #62 sll0064 300 hypothetical protein. #63 sll0107 119 eda; 4-hydroxy-2-oxoglutarate aldolase. [EC:4.1.3.16] #64 slr0103 45 hypothetical protein. #65 slr0104 37 hypothetical 90.3 kD protein slr0104. [SP:Y104_SYNY3] #66 sll0103 82 hypothetical 45.8 kD protein sll0103. [SP:Y103_SYNY3] #67 sll0102 300 hypothetical protein. #68 slr0665 229 acnB; aconitate hydratase 2 (citrate hydro-lyase 2) (aconitase 2). #69 slr0666 300 hypothetical protein. Motif number 1 GAGAACCATTGGCACAGGCCTCTATTAAAA 4 99 1 GGCACAGGCC 0.907897 -105 TGTCATTTGAGGAGATGACCAAGCAAAATT 7 47 1 GGAGATGACC 0.750182 -254 TGATTTTAGCGGAGATGGGCATTAATCCCT 8 11 1 GGAGATGGGC 0.918269 -101 CGAAATTGGGGGAACTGGCCACGCTTTTTT 12 54 0 GGAACTGGCC 0.833837 -46 CCCTCAACCGGGCGCTGTCCGCTAGTTAAA 14 171 1 GGCGCTGTCC 0.705733 -130 GGGAGGCGATCGCCCTATCCCGGT 17 5 1 GGCGATCGCC 0.499871 -100 CACAGAGCTAGGCGATCGCCTCTGGGTAAT 18 115 1 GGCGATCGCC 0.499871 -26 TTTAGCCTCAGGCGATCGCCGGGTGAAATG 19 86 1 GGCGATCGCC 0.499871 -215 AGCATATTTGGGCGCAGAGCTGGAGGTTTA 25 36 0 GGCGCAGAGC 0.787708 -100 AGATAAAGGGGGCGATCGCCGATCCTTGGG 33 31 1 GGCGATCGCC 0.499871 -174 ATCGAGCAACGGCAATGGGCTTTGAGCTTG 36 78 0 GGCAATGGGC 0.952323 -199 TTGAAGGAAGGGCACAGGCCAAAAGCTCAA 38 24 1 GGCACAGGCC 0.907897 -151 ATGGCCAATGGGAGCTGGGAAAGTCCAAAT 42 101 1 GGAGCTGGGA 0.56409 -200 GGGACAGGCTGGCCCGGGCCGGCGCAATTT 46 122 1 GGCCCGGGCC 0.477452 -72 GGAAGTTAGAGGCGATGGGCCGGCAAACTC 47 23 0 GGCGATGGGC 0.945207 -40 ACAGGTTTATGGCGCGGGGCTTCTCGCGTT 48 60 0 GGCGCGGGGC 0.949146 -34 GCAAATACTGGGCAAAGAGCTCAGGACAAC 56 70 0 GGCAAAGAGC 0.501821 -30 AAAAATCTATGGCAAGGGCAAAAACAATCG 57 11 1 GGCAAGGGCA 0.571786 -171 ATTTTAGGACGGCGATCGCCGGGGATAATT 61 11 1 GGCGATCGCC 0.499871 -136 TTTTAACCATGGCGATCGGAGGGCGGAGAT 63 100 0 GGCGATCGGA 0.805577 -20 AGACCACGTTGGCGATCACCTAACCAATGC 69 114 1 GGCGATCACC 0.654813 -187 ********** Masking position 2 Map Score: 27.0802 Number of sites scoring better than the average of aligned sites = 7154 Number in coding regions = 6523 Number in noncoding regions = 631 Number of orfs with sites within 600 bp upstream = 400 Fraction of orfs with sites within 600 bp upstream = 0.0642467 Motif number 2 GTTTACCGTTAAGCGGGGGCTAGGGTTGAGCCAG 1 52 1 AACGGGGGAG 0.847461 -64 ATGGTTCTCAGAACTGGGGCTAATTTTATCTGGC 4 74 0 GACTGGGGAT 0.827866 -130 ATTAATACGGACACGGGGGGTATGGAAAAATACC 9 39 1 ACCGGGGGAG 0.952553 -174 CACAGCCCAGGCCATGGGGAAATTACCGGGATAG 17 25 0 GCATGGGGAT 0.64755 -80 CATGGCCTGGGCTGTGGGGGATAGCCCCGAAAAA 17 43 1 GCGTGGGGTG 0.757481 -62 GGGTGAAATGGCGCTTGGGCTTTGTTTGCAAAAT 19 106 1 GCCTTGGGTG 0.918909 -195 CTTTGATGTTGCCCGGGGGCCCTGGTTAATAGTT 19 232 1 GCCGGGGGCG 0.979107 -69 GTGGAACTTTGACCGGGGGAATAGAGTTTAATAG 25 71 1 GACGGGGGTG 0.890499 -65 CGGACGACGTAAACTGGGGGTTGGCAAATTTTGT 28 40 0 AACTGGGGTG 0.791618 -149 ACAGCTTCAAGCCCTGGGGAAAGGGAAGTCCGGC 29 166 1 GCCTGGGGAG 0.992142 -57 AAGATTTTCCACTCTTGGGTAAGGTCGACAGTAG 31 226 0 ACCTTGGGAG 0.885602 -26 CATGGGTAAAGCCCTGGGGGCCCGTTTGGTAGAA 36 116 1 GCCTGGGGCG 0.987703 -161 GCAGACTGTCTCTCTGGGGCTCCGTTGGGGAACA 36 201 1 TCCTGGGGCG 0.919894 -76 AATGATCGAAGCTCGTCGGACCAGTACTGGGCTC 46 31 1 GCCGTCGGCG 0.624885 -163 CCCTAATATGGATATGGGGACAGGCTGGCCCGGG 46 106 1 GAATGGGGAG 0.786942 -88 TCAGAAAAATTCCCTGGGGGCACTAAGTGGGAAA 52 13 1 TCCTGGGGAT 0.713029 -78 CTATGATGGGGCCATGGGGTTAGGGTTTCCCAGG 54 27 0 GCATGGGGAG 0.930299 -131 GCTCAGGACAACCCTGGGGAGACGTGCTTGAGGC 56 48 0 ACCTGGGGAG 0.971759 -52 ATGCAAGCTTGCCCGGCGGGCATGGTAGGATATA 57 99 1 GCCGGCGGAG 0.920876 -83 CTTCAGATCTTCGGCTACGGCGTATTTCT 59 6 1 GACTTCGGAG 0.553957 -130 CCAGCCTATCACCCTTGGGGCTAGGAATGCCATG 60 52 1 ACCTTGGGTG 0.755407 -92 CGCAATTAGTTCGCTTGGGCCCAGATAAAATCCC 62 219 0 TCCTTGGGCG 0.720947 -82 TTTATTTTTAGAGCTGGGGAGATTTCACCTCGGC 67 156 1 GACTGGGGAT 0.827866 -145 ** ****** * * Masking position 8 Map Score: 25.8887 Number of sites scoring better than the average of aligned sites = 1253 Number in coding regions = 1156 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 3 TGGCTTTGGCTGGACAAACTTGCAGAGGGACAACCGG 4 38 1 TGGCAATCAG 0.906813 -166 TTAGCGGAGATGGGCATTAATCCCTGGTAGGAGGAAA 8 16 1 TGGCATTCGG 0.953886 -96 GACTCGATAATGGGCAAGCAATCGCGGCGAATCTCTA 9 94 0 TGGCAAACGG 0.917976 -119 AAAAAATAAGCGGGCATTAGCAATGGGCCCACTCTTT 10 19 1 CGGCATCAGG 0.696047 -96 ATTAATTCATCGGACATCTATCCCTGGCTACCCGCGA 14 130 1 CGGCATTCGG 0.964041 -171 TTAACCTTCATGGCCAAGGCTGGTTGGAAGTAATTTG 14 202 1 TGGCAATGGG 0.949864 -99 CGCCCTATCCCGGTAATTTCCCCATGGCCTGGGCTGT 17 21 1 CGGAATCCGG 0.536791 -84 AATTTTTCCCCGGTCAATGAAACCAGGGTAATTAAGG 18 71 0 CGGCAAACGG 0.935506 -70 CCAGGGCCCCCGGGCAACATCAAAGGGCGGGTTTGAG 19 220 0 CGGCAACAGG 0.868465 -81 TCTATTCCCCCGGTCAAAGTTCCACAGAGGAGCATAT 25 59 0 CGGCAATCAG 0.926537 -77 TTTCCACCCTTGGTCAAACCGTCATAGTACGCTGATT 29 81 0 TGGCAAGCAG 0.738534 -142 TCTTGAATTTTGGCCAATCGTTCTGGGAGTTAGCTAA 31 121 1 TGGCAATCGG 0.983509 -131 TGCTTATGCATGGCCATGGTTTACCGGATTGAATCTA 35 68 1 TGGCATTAGG 0.760852 -71 GGAAGGGCACAGGCCAAAAGCTCAAGGGGACGGAATG 38 29 1 AGGCAACCGG 0.881248 -146 ACGGAATTGATGGCCAATGGGAGCTGGGAAAGTCCAA 42 92 1 TGGCAAGGGG 0.846136 -209 TTATTTGCCCCGGCCAACGGTTCTAGGGTAGGTAGAT 54 119 1 CGGCAATCGG 0.987228 -39 CAAAGAGCTCAGGACAACCCTGGGGAGACGTGCTTGA 56 51 0 AGGCAATGAG 0.409194 -49 TGCTCCTTTACGGTCAAATGTGGACGGGGA 59 116 1 CGGCAATGGG 0.960829 -20 GAGAAATGGTTGGTCAATTATCCCCGGCGATCGCCGT 61 19 0 TGGCAATCGG 0.983509 -128 ATTGATTTCTTGGTAAATGTTCCCGGGGATTATGCCG 62 157 1 TGGAAATCGG 0.82276 -144 *** *** * * ** Masking position 6 Map Score: 22.318 Number of sites scoring better than the average of aligned sites = 561 Number in coding regions = 512 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 TTTCCTCCTACCAGGGATTAATGCCCATCTC 8 22 0 CCGGGATTAA 0.937901 -90 TCGCGGGTAGCCAGGGATAGATGTCCGATGA 14 136 0 CCGGGATAGA 0.925399 -165 ACCGGTTAACCCTGGGAAATTGTAGCTCTCA 16 49 1 CCGGGAAATT 0.715818 -105 GTTTCATTGACCGGGGAAAAATTTCCCACCC 18 85 1 CCGGGAAAAA 0.776166 -56 TTCCCTTTCCCCAGGGCTTGAAGCTGTGTTA 29 162 0 CCGGGCTTGA 0.923283 -61 GTTAAAGCTCCCATGGATAAATTCAGCATAG 35 115 1 CCTGGATAAA 0.604895 -24 AAACGGGCCCCCAGGGCTTTACCCATGGCCG 36 112 0 CCGGGCTTTA 0.882998 -165 TTTCCTCCATGGATTGAAGGAAGGGCA 38 7 1 CCTGGATTGA 0.714392 -168 TTACCTTCACCCCTGGATTGAGCCCAGTACT 46 53 0 CCTGGATTGA 0.714392 -141 CTTAGTGCCCCCAGGGAATTTTTCTGACT 52 9 0 CCGGGAATTT 0.780346 -82 GAACCGTTGGCCGGGGCAAATAATTACCGAC 54 111 0 CCGGGCAAAT 0.704607 -47 ACGGCGATCGCCGGGGATAATTGACCAACCA 61 19 1 CCGGGATAAT 0.914592 -128 TTGCTAGCTTCCTGGGCTTGGAATTGCACGC 61 91 1 CCGGGCTTGG 0.737659 -56 CTACGCCGGGCCGGGGATTTTAAGGCCTATG 62 90 1 CCGGGATTTT 0.916465 -211 GTAAATGTTCCCGGGGATTATGCCGTTTTAG 62 169 1 CCGGGATTAT 0.937901 -132 GATTTTTGCCCCTGGGATTTTCCACCGATGA 66 24 0 CCGGGATTTT 0.916465 -59 AAATCCACATCCCGGGCTAATTCGCATAATC 67 65 1 CCGGGCTAAT 0.880472 -236 ** ******** Masking position 6 Map Score: 14.2692 Number of sites scoring better than the average of aligned sites = 680 Number in coding regions = 607 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 5 CGTTAATTTAGCCAAAAATTCGGTA 4 189 0 AATTAGCCAA 0.849189 -15 TTGTGGGAGAATGTTAGCCAACCTGAGGATA 5 61 1 ATTTAGCCAA 0.849189 -50 ACAAACTAAGAATTTTGCAAACAAAGCCCAA 19 120 0 AATTTGCAAA 0.811583 -181 GGTCACAACAAAATTTGCCAACCCCCAGTTT 28 33 1 AATTTGCCAA 0.92403 -156 AGTAGTTCTCATTTTTGCCAAGTTTGGGAGC 29 119 0 ATTTTGCCAA 0.92403 -104 TCAGCTTATTTTGTTTGCAAAGGAATTTTTT 31 65 0 TTTTTGCAAA 0.642942 -187 GATATCTTGAATTTTGGCCAATCGTTCTGGG 31 117 1 ATTTGGCCAA 0.717241 -135 TAGATTAAACTATTTTGCCAACCATGAACCT 32 72 1 TATTTGCCAA 0.835652 -56 AAAGCTAGAAAAATTAGCCAATGATAACTAT 40 119 1 AATTAGCCAA 0.849189 -21 GGCGATAACTTTTTTGCAAAACTCTGCTGG 55 10 1 TTTTTGCAAA 0.642942 -84 GGAGATGTTTGCAAATACTGGGCAA 56 85 0 ATTTTGCAAA 0.811583 -15 TCTAGTGAGGAATTTTGCAAAATGCAAGCTT 57 78 1 AATTTGCAAA 0.811583 -104 GTTTTTATGTAACTTTGCCAACACGTCATAG 62 116 0 AATTTGCCAA 0.92403 -185 ATTGCCTAGATTTTTAGCCAACG 67 288 1 TTTTAGCCAA 0.70184 -13 ** ******** Masking position 10 Map Score: 11.6303 Number of sites scoring better than the average of aligned sites = 444 Number in coding regions = 379 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 GGTGGTGGTCTTGCCCCCTTTGTCCAACGC 19 20 0 TTGCCCCCTT 0.652088 -281 TTAGCCTGATTTTCACCCTTAGTCGGGAAA 23 200 0 TTTCACCCTT 0.746117 -101 GATTCCAATCTTTAACGATGAA 28 3 1 TTCCAATCTT 0.76951 -186 TTGGGAGCTTTTCCACCCTTGGTCAAACCG 29 97 0 TTCCACCCTT 0.971103 -126 TTCTAATCTGTTCCAATCTTTAGCAATTTG 30 56 1 TTCCAATCTT 0.76951 -75 TGAAGATTTTCCACTCTTGGGTAAGGTC 31 234 0 TTCCACTCTT 0.90619 -18 AGACGTTCTGTTCCAACCTGCAGACTGTCT 36 182 1 TTCCAACCTG 0.787524 -95 TTTCACCATTTTCCATTCTTCACCCTACTT 37 35 1 TTCCATTCTT 0.549997 -130 ATAACTATCGTTCAACACTTCTGATTTCAT 41 40 0 TTCAACACTT 0.805699 -84 ATTTTCTCCATTCAACCCTTATTTTCAATC 45 45 1 TTCAACCCTT 0.907864 -256 CAATTGACAATTCCCCACTTAGATAAAAAA 45 118 1 TTCCCCACTT 0.914756 -183 GAAATTTACCTTCACCCCTGGATTGAGCCC 46 59 0 TTCACCCCTG 0.704661 -135 ACCTTGTCATTTTCCCACTTAGTGCCCCCA 52 27 0 TTTCCCACTT 0.484118 -64 AAATTTCAATCCTTAAATTCGCTT 62 287 0 TTCAATCCTT 0.554906 -14 ACTTCCTACATTCAACACTGTTCCAGATTA 63 21 0 TTCAACACTG 0.56957 -99 GATGGACAAATTCCAAACTTCCTACATTCA 63 37 0 TTCCAAACTT 0.830157 -83 TCCTAGGGCTTTCCCAACTTGAGTTCCGC 65 19 1 TTCCCAACTT 0.787632 -19 ATTCATTTAATTCACCCCTTATCATCACCG 68 163 0 TTCACCCCTT 0.882031 -67 GAATAATTCATTCCAACCTTTCAGCATTTA 69 262 1 TTCCAACCTT 0.920727 -39 ********** Masking position 2 Map Score: 11.1219 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 398 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 7 TTGGCTAACATTCTCCCACAAAAATCAACCC 5 51 0 TTTCCCACAA 0.687347 -60 GTCCTGACACCCAATTCAAGCCAT 9 4 1 CTACACCCAA 0.744689 -209 ATCTGGAGCACTGTGCCGCAAAGATACTTAG 14 80 0 CTTGCCGCAA 0.862836 -221 TTTTTCGGGGCTATCCCCCACAGCCCAGGCC 17 46 0 CTTCCCCCAC 0.859407 -59 TAATTAAGGACTCACCCCGAAGGAGACGAGT 18 49 0 CTACCCCGAA 0.697791 -92 CCTCCACAATCTTGCCCACAATAACGAATGG 23 158 0 CTGCCCACAA 0.80365 -143 CAACGAGGAACTAACCCCCAAACTCAACTGC 28 91 1 CTACCCCCAA 0.970891 -98 GCCTTAATTGTTTTCACCCAAGGATCGGCGA 33 46 0 TTTCACCCAA 0.470114 -159 ATATTTTTTTCTTTGCCGCAAGAAACCCCAA 33 116 1 CTTGCCGCAA 0.862844 -89 AAATAACCTGCTATGCCACAA 34 1 0 CTTGCCACAA 0.883559 -45 TTTTGCCATCCTCTCCCCCCAACCGCTAGAC 36 48 1 CTTCCCCCCA 0.859407 -229 ATCTAGCCCACAATTGATCGAAT 46 3 1 CTGCCCACAA 0.80365 -191 TTAAACCCTCCAGTGCCCCAAAAGCTGTCCC 48 13 1 CATGCCCCAA 0.737704 -81 GCCCCAAAAGCTGTCCCCCAAATATTAGCTT 48 27 1 CTTCCCCCAA 0.98198 -67 TAGAATGGTTCTTAGCCCCAAATTTTTTTTG 49 25 0 CTAGCCCCAA 0.955419 -50 TACGGCGTATTTCTGCCCCAATTCGCCTAAA 59 26 1 TTTGCCCCAA 0.866654 -110 CCATGGCATTCCTAGCCCCAAGGGTGATAGG 60 56 0 CCAGCCCCAA 0.718407 -88 CGGTCAAGGTTTAACCCCCAACCAAGTTACC 60 96 0 TTACCCCCAA 0.861288 -48 ** ******** Masking position 7 Map Score: 13.8438 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 686 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 8 AGGCCTCTATTAAAATCCTGAATTATGAAC 4 114 1 TAAAATCCTG 0.714129 -90 GCGTTTCCCAAAAAATCCGATGGTTTATCC 5 87 0 AAAAATCCGA 0.817936 -24 AATTCTCGCGAAAAATCTTGTAAAAGACTA 11 27 0 AAAAATCTTG 0.715884 -21 TCTTTTCCTCAATAATCCTAAAACAACACT 14 253 0 AATAATCCTA 0.648397 -48 GGAAAAATCCTCAAAAAGGAGC 23 289 0 AAAAATCCTC 0.912396 -12 CAAAATGCTTCAAAATCCGCCGATAACTGG 26 19 0 CAAAATCCGC 0.561054 -72 TTGCATTGCCAAACATCCTCTCAATCTTGA 31 17 0 AAACATCCTC 0.736563 -235 TTTTGCTGGTAAAAATCCTGATTGCATTGC 31 38 0 AAAAATCCTG 0.959141 -214 ATAAGTTCAACAAAATCCTAATCCATCTTT 31 183 0 CAAAATCCTA 0.755155 -69 AAGAAACCCCAAACATCCTGCAATAATTCA 33 135 1 AAACATCCTG 0.863049 -70 AACAATCGTTAAAAATCCTAGTCAGTGGCC 38 70 0 AAAAATCCTA 0.913983 -105 AAATAGACAGAATAATCCTACAGCAAAGCA 39 17 0 AATAATCCTA 0.648397 -136 CACTTAGATAAAAAATCCGGTCAGGATGCG 45 133 1 AAAAATCCGG 0.908468 -168 TCCCAGGGGCAAAAATCTTGGAGTAAGCTA 66 38 1 AAAAATCTTG 0.715884 -45 AAGCTGAAGGAAAAATCCTGCCAAATCCAC 67 43 1 AAAAATCCTG 0.959141 -258 ********** Masking position 5 Map Score: 7.71861 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 312 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 9 AGGAAAAATACAGGCGCTCTGACCCTTTCT 4 148 1 CAGGCGCTCT 0.736711 -56 AATATCACAGGGGATTGCATTTTTTAG 5 8 1 CAGGGGATTG 0.910765 -103 GGGAGGCGATCGCCCTATCCCG 17 3 1 GAGGCGATCG 0.905494 -102 CCCACAGAGCTAGGCGATCGCCTCTGGGTA 18 113 1 TAGGCGATCG 0.955095 -28 ACTTTAGCCTCAGGCGATCGCCGGGTGAAA 19 84 1 CAGGCGATCG 0.986665 -217 TATTAAGTATCAGGTGATTGCTTGATCTTT 22 15 1 CAGGTGATTG 0.866503 -62 CTTAATAATTCAGGTGATTGATATGGCACA 24 37 0 CAGGTGATTG 0.866503 -37 CACCCAAGGATCGGCGATCGCCCCCTTTAT 33 33 0 TCGGCGATCG 0.9148 -172 CAAAACTCTGCTGGGGATCGGTTTCCCAAG 55 27 1 CTGGGGATCG 0.785498 -67 TCAATTATCCCCGGCGATCGCCGTCCTAAA 61 13 0 CCGGCGATCG 0.973927 -134 GTAGAAACCTCAGGCGATTTTCAATTAATA 62 64 0 CAGGCGATTT 0.871679 -237 CTACGCCGGGCCGGGGATTTTAAGGCCTAT 62 90 1 CCGGGGATTT 0.571861 -211 GAGCATTGGTTAGGTGATCGCCAACGTGGT 69 116 0 TAGGTGATCG 0.840471 -185 ATTTGTTTGATAGGCGATCTATTTCTGTCC 69 164 0 TAGGCGATCT 0.846477 -137 ********** Masking position 8 Map Score: 13.1941 Number of sites scoring better than the average of aligned sites = 3723 Number in coding regions = 3407 Number in noncoding regions = 316 Number of orfs with sites within 600 bp upstream = 311 Fraction of orfs with sites within 600 bp upstream = 0.0499518 Motif number 10 TCAGAACTGGGGCTAATTTTATCTGGCCGG 4 71 0 GGCTAATTTT 0.85777 -133 TCCTCAGGTTGGCTAACATTCTCCCACAAA 5 60 0 GGCTAACATT 0.958787 -51 TAGTTTTTAATGCTAACATTGGATGTTGAG 7 256 0 TGCTAACATT 0.85777 -45 AGGCTCTAGCTGCAAACATTGTCTCAAGTT 10 58 1 TGCAAACATT 0.574694 -57 TGGCCATGAAGGTTAACTTTAACTAGCGGA 14 188 0 GGTTAACTTT 0.729876 -113 GTGAAAATCAGGCTAACTTTCGCAATCAAA 23 214 1 GGCTAACTTT 0.958787 -87 ACACCTCGAAGGCTAATTTTAGGGGTTTC 24 10 0 GGCTAATTTT 0.85777 -64 ACTGGGGGTTGGCAAATTTTGTTGTGACCT 28 32 0 GGCAAATTTT 0.574694 -157 CCATAACAATTGCCAACATTTATTGTTTAA 37 88 1 TGCCAACATT 0.67639 -77 AGTTATCATTGGCTAATTTTTCTAGCTTTA 40 118 0 GGCTAATTTT 0.85777 -22 TGTCATGGCAGGCTACCTTTTTT 42 4 0 GGCTACCTTT 0.772397 -297 GTCAGGATGCGGTCAACATTATACAAAAAC 45 152 1 GGTCAACATT 0.483588 -149 CGCGGGAGCGGGCTAACATTGAATTGAAGT 45 251 1 GGCTAACATT 0.958787 -50 AAACATTTATTGCTAACATTATAGACCACG 69 92 1 TGCTAACATT 0.85777 -209 ********** Masking position 5 Map Score: 9.21422 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 279 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 11 GGTTTGATGACCCCATTGGCCTAGGGAGAAAGA 8 77 1 CCCCATTCTA 0.94729 -35 TAGCAATGGGCCCACTCTTTCTAGGCTCTAGCT 10 36 1 CCCACTCCTA 0.661803 -79 GGCCAGTTCCCCCAATTTCGCTCTAGTTCAGTA 12 64 1 CCCAATTCTC 0.64562 -36 CTTTCACCTTGCCCATCTGGCTAAGTATCTTTG 14 60 1 GCCCATCCTA 0.701829 -241 CAATATCATTTCCCATTTTTCCA 14 288 1 TCCCATTCCA 0.641994 -13 CAACTATTTGGCCCATCCTCCTCACC 15 20 1 GCCCATCCTC 0.608259 -16 ATTTTTCCTGCGCCCTTGTCCCAAGCATCCCTA 16 86 1 CGCCCTTCCA 0.877344 -68 TCGGGGCTATCCCCCACAGCCCAGGCCATGGGG 17 40 0 CCCCCACCCA 0.648569 -65 GGTGGTCTTGCCCCCTTTGTCCAACGCGTACTG 19 14 0 CCCCCTTCCA 0.974712 -287 AAAGCCCAAGCGCCATTTCACCCGGCGATCGCC 19 96 0 CGCCATTCCC 0.82456 -205 GTAAGAATAACCCCATTTACCTAGATTCAGACT 27 74 1 CCCCATTCTA 0.94729 -72 CCGGAGTCAACCCCCTCCATCCCTGATCCTTAA 29 27 0 CCCCCTCCCC 0.947216 -196 TCGGCGATCGCCCCCTTTATCTACACTCTCTTT 33 20 0 CCCCCTTCTA 0.947487 -185 GGAGCTTTAACCCCCCTATTCTAGATTCAATCC 35 93 0 CCCCCCTCTA 0.644656 -46 AAGATTGCTAGCCCATTCTACCAAACGGGCCCC 36 132 0 GCCCATTCCA 0.876919 -145 GGATTGTTAACCCCATCAAGCCCGAAAATGTTC 36 230 0 CCCCATCCCC 0.947019 -47 TCAAAATTTTCTCCATTCAACCCTTATTTTCAA 45 40 1 CTCCATTCCC 0.541903 -261 GAAACCCTAACCCCATGGCCCCATCATAGTTTA 54 32 1 CCCCATGCCA 0.838948 -126 CCGACAAATTCGCACTTCCACCAATCATGTAGT 54 83 0 CGCACTTCCA 0.523628 -75 GTATTTCTGCCCCAATTCGCCTAAATACTGAAC 59 32 1 CCCAATTCTA 0.734167 -104 ACCAAGTTACCCCCATTGTTCCATGGCATTCCT 60 74 0 CCCCATTCCA 0.974615 -70 ******* *** Masking position 3 Map Score: 17.8713 Number of sites scoring better than the average of aligned sites = 1294 Number in coding regions = 1033 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 192 Fraction of orfs with sites within 600 bp upstream = 0.0308384 Motif number 12 CCTTTCCAACGGGTCTGGGTCAACCTACCA 9 172 0 GGGTCTGGGT 0.953667 -41 ATAAAAAATCCGGTCAGGATGCGGTCAACA 45 140 1 CGGTCAGGAT 0.88776 -161 TGGGGCCATGGGGTTAGGGTTTCCCAGGTT 54 25 0 GGGTTAGGGT 0.8646 -133 CGGTCTGGGTTAGGGCCCAG 57 172 0 CGGTCTGGGT 0.962258 -10 GTGATAGGCTGGGTCAGTGTTTTTGGGTAC 60 34 0 GGGTCAGTGT 0.927673 -110 CGGCCTAAGTCGGTCAAGGTTTAACCCCCA 60 107 0 CGGTCAAGGT 0.88776 -37 GGTTTATCCAGGCTCAGGGTAGCGCAATTA 62 245 0 GGCTCAGGGT 0.952014 -56 ACCTCGGCTACGGTCAGGGTTTCCATAGCG 67 182 1 CGGTCAGGGT 0.987757 -119 ACTGACGAAGCGCTCAGTGTTAATTTGTTT 69 186 0 CGCTCAGTGT 0.828739 -115 ********** Masking position 4 Map Score: 7.44083 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 182 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 AAATTCGGTAAAAATAAGCTGAGAAAGGGT 4 169 0 AAAATAAGCT 0.772505 -35 TTCTCCCACAAAAATCAACCCCATCTAGGG 5 42 0 AAAATCAACC 0.690976 -69 TTGTTACAGGAAAATCAACTTAGTTTTTAA 7 276 0 AAAATCAACT 0.92232 -25 AACAAATCAAAAAATCAACTAGAAAAGATC 22 38 0 AAAATCAACT 0.92232 -39 ACTAACCCCCAAACTCAACTGCTTGAAGCC 28 100 1 AAACTCAACT 0.690976 -89 TCCAATCGAGAAGATAAACTGGAATTAGTT 28 160 1 AAGATAAACT 0.624933 -29 CTTTGCAAACAAAATAAGCTGACAAAGGAA 31 74 1 AAAATAAGCT 0.772505 -178 TTTGACTATAAAAATAAACTATGATGGGGC 54 49 0 AAAATAAACT 0.898453 -109 TTTTATAGTCAAAATAAACTACATGATTGG 54 66 1 AAAATAAACT 0.898453 -92 ATCTATGACCAGAATCAACTGGAATGCTCC 59 92 1 AGAATCAACT 0.690976 -44 CCCAGCTCTAAAAATAAACTTATAATTTAC 67 144 0 AAAATAAACT 0.898453 -157 ********** Masking position 7 Map Score: 4.66032 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 58 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 TTTTATCTGGCCGGTTGTCCCTCTGCAAGTT 4 54 0 CCGGTGTCCC 0.851855 -150 GACATCTATCCCTGGCTACCCGCGAAATACC 14 142 1 CCTGCTACCC 0.923092 -159 AAGTCAGTCACCGGTTAACCCTGGGAAATTG 16 40 1 CCGGTAACCC 0.907432 -114 AGCCGGATTACCCAGAGGCGATC 18 128 0 CCGGTTACCC 0.960954 -13 AGAATCACAGCCGGACTTCCCTTTCCCCAGG 29 178 0 CCGGCTTCCC 0.98194 -45 TTCCTGTCTTCCCACCGATCTGA 30 118 0 CCTGCTTCCC 0.923092 -13 ATCTTTAAGACCTGGTATCTCGGGATATTTG 31 158 0 CCTGTATCTC 0.411064 -94 GTTTATGGCGCGGGGCTTCTCGCGTTTTAAG 48 55 0 CGGGCTTCTC 0.806916 -39 GCAAAGAGCTCAGGACAACCCTGGGGAGACG 56 58 0 CAGGCAACCC 0.654229 -42 TTAAGATCCGACGGACTACTCTTCAGCTTCC 57 42 1 ACGGCTACTC 0.709014 -140 AAAACCAAGCCCGGTCTACTCTTTTGCTAGC 61 68 1 CCGGCTACTC 0.946054 -79 CAGATATCCTAGGGCTTTCCCAACTTGAGTT 65 13 1 AGGGTTTCCC 0.448993 -25 **** ****** Masking position 9 Map Score: 3.05797 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 439 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 15 AAGCAATCGCGGCGAATCTCTAGCCATCGCGGC 9 83 0 GGGAATCTAG 0.883802 -130 ATGAATTAATTGAAAATCTTTAGAGATAAATCT 14 107 0 TGAAATCTAG 0.623012 -194 CTAAATTTTGGGAAAAGTTAGAGAAAACTCTCC 19 172 0 GGAAAGTTAG 0.736457 -129 AAAATCAACTAGAAAAGATCAAGCAATCACCTG 22 25 0 AGAAAGATAG 0.57557 -52 TTAAAAAGTGAGCAAATCTTTAGCTTTCTTCAA 23 88 0 AGAAATCTAG 0.912917 -213 GGTTGAATGGAGAAAATTTTGAGCCTTTGTCAA 45 29 0 AGAAATTTAG 0.793882 -272 CAGGGGTGAAGGTAAATTTCCAGAATTCCTTCA 46 69 1 GGAAATTTAG 0.706945 -125 TATCCATATTAGGGAATCTGAAGGAATTCTGGA 46 87 0 AGGAATCTAG 0.923919 -107 CCGATAAAATAGGGAAGTTAGAGGCGATGGGCC 47 32 0 AGGAAGTTAG 0.837883 -31 CACTAGAGTTAGGGAAGCTGAAGAGTAGTCCGT 57 52 0 AGGAAGCTAG 0.933632 -130 GTAACTTACCAGAGAAGCTGAAGGAAAAATCCT 67 29 1 AGGAAGCTAG 0.933632 -272 AGGACTACACAGAAAATCTTCAGTCTCCCCAAT 68 49 1 AGAAATCTAG 0.912917 -181 ** ****** ** Masking position 6 Map Score: 3.46581 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 63 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789