AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00860_synecho_reg_300.orf -o00860_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 Purged sequences: slr0265 119 transposase. slr0536 146 hemE; uroporphyrinogen decarboxylase. [EC:4.1.1.37] [SP:DCUP_SYNY3] slr1811 122 rpoD; hypothetical protein. ssr0871 55 transposase. Input sequences: #1 sll1678 74 spore maturation protein A. #2 sll1677 65 spore maturation protein B. #3 sll1676 97 malQ; 4-alpha-glucanotransferase. [EC:2.4.1.25] #4 sll1675 49 hypothetical protein. #5 slr1787 300 hypothetical protein. #6 sll1185 222 hemF; coproporphyrinogen III oxidase, aerobic #7 sll1184 134 ho; heme oxygenase. [EC:1.14.99.3] #8 slr1307 89 hypothetical protein. #9 ssr1604 198 rpmB, rpl28; 50S ribosomal protein L28. [SP:RL28_SYNY3] #10 slr0962 52 hypothetical protein. #11 tRNA-Pro-2 129 tRNA-Pro. #12 sll0943 251 hypothetical protein. #13 slr0963 198 sir; sulfite reductase (ferredoxin). [EC:1.8.7.1] [SP:SIR_SYNY3] #14 slr0964 99 hypothetical protein. #15 slr0965 143 dnaN; DNA polymerase III, beta chain. [EC:2.7.7.7] [SP:DP3B_SYNY3] #16 slr0966 155 trpA; tryptophan synthase alpha chain. [EC:4.2.1.20] [SP:TRPA_SYNY3] #17 slr0967 51 hypothetical protein. #18 sll0939 24 hypothetical protein. #19 sll0938 40 aspartate transaminase. [EC:2.6.1.1] #20 ssl1792 33 hypothetical protein. #21 sll0936 83 hypothetical protein. #22 slr0969 102 cbiH; precorrin methylase. #23 slr0971 82 hypothetical protein. #24 sll0934 195 ccmA; carboxysome formation protein. [EC:5.4.99.5] #25 ssl1784 164 rpsO, rps15; 30S ribosomal protein S15. [SP:RS15_SYNY3] #26 sll0932 100 hypothetical protein. #27 sll0931 171 hypothetical protein. [EC:2.1.1.45] #28 sll0930 43 hypothetical protein. #29 sll0928 111 apcD; allophycocyanin-B. #30 sll0927 168 metX; S-adenosylmethionine synthetase. [EC:2.5.1.6] #31 sll0925 266 hypothetical 23.0 kD protein sll0925. [SP:Y925_SYNY3] #32 slr0974 300 infC; translation initiation factor IF-3. [SP:IF3_SYNY3] #33 slr1887 129 hemC; porphobilinogen deaminase (PBG) (hydroxymethylbilane synthase) #34 slr1888 265 hypothetical protein. #35 slr2132 57 pta; phosphotransacetylase. [EC:2.3.1.8] #36 sll2015 61 hypothetical protein. #37 sll2014 53 sfsA; sugar fermentation stimulation protein. #38 sll2013 159 hypothetical protein. #39 sll2012 300 rpoD; RNA polymerase sigma factor. #40 slr1808 161 hemA; glutamyl-tRNA reductase (GLUTR). [EC:1.2.1.-] [SP:HEM1_SYNY3] #41 sll1698 276 rpoD; hypothetical protein. #42 sll1697 123 rpoD; hypothetical protein. #43 slr1812 74 hypothetical protein. #44 slr1813 122 rpoD; hypothetical protein. #45 slr1814 140 rpoD; hypothetical protein. #46 slr1815 41 rpoD; hypothetical protein. #47 sll1695 98 hofG; general secretion pathway protein G. #48 sll1694 143 hofG; general secretion pathway protein G. #49 sll1693 154 rpoD; hypothetical protein. #50 sll1691 49 rpoD; hypothetical protein. #51 sll1689 300 rpoD; RNA polymerase sigma factor. #52 slr0260 78 cobA; cob(I)alamin adenosyltransferase. [EC:2.5.1.17] #53 ssl0467 95 hypothetical protein. #54 sll0252 221 hypothetical protein. #55 slr0261 42 ndhH; NADH-plastoquinone oxidoreductase 49 kD subunit. [EC:1.6.5.3] #56 slr0262 50 hypothetical protein. #57 slr0263 38 hypothetical protein. #58 slr0264 99 hypothetical 41.0 kD protein slr0264. [SP:Y264_SYNY3] #59 ssl0461 66 hypothetical 9.5 kD protein ssl0461. [SP:Y461_SYNY3] #60 sll0249 234 hypothetical 28.9 kD protein ssl0249. [SP:Y249_SYNY3] #61 sll0248 300 isiB; flavodoxin. [SP:FLAV_SYNY3] #62 sll1994 300 hemB; delta-aminolevulinic acid dehydratase (porphobilinogen #63 sll1237 105 hemK protein homolog. [EC:1.3.3.4] [SP:HEMK_SYNY3] #64 slr1324 278 sensory transduction histidine kinase. #65 ssr2194 148 hypothetical protein. #66 sll1236 300 hypothetical protein. [EC:3.1.4.46] #67 sll1875 64 ho; heme oxygenase. [EC:1.14.99.3] #68 sll1874 300 AT103; AT103. #69 slr1643 91 petH; ferredoxin--NADP reductase (FNR). [EC:1.18.1.2] #70 sll1524 300 hypothetical protein. #71 sll0163 300 beta transducin-like protein. [SP:Y163_SYNY3] #72 slr0772 131 chlB; protochlorophyllide reductase ChlB subunit. [EC:1.3.1.33] #73 slr0773 36 hypothetical protein. #74 sll0772 91 hypothetical 59.1 kD protein sll0772. [SP:Y772_SYNY3] #75 sll0771 297 gtr, glcP; glucose transport protein. [SP:GLCP_SYNY3] #76 slr0774 60 secD; protein-export membrane protein SecD. #77 slr0775 132 secF; protein-export membrane protein SecF. #78 slr0776 107 lpxD; UDP-3-o-[3-hydroxymyristoyl] glucosamine n-acyltransferase. #79 sll0767 140 rplT, rpl20; 50S ribosomal protein L20. [SP:RL20_SYNY3] #80 ssl1426 96 rpmI, rpl35; 50S ribosomal protein L35. [SP:RL35_SYNY3] #81 sll0765 91 hypothetical protein. #82 tRNA-Ala-2 300 tRNA-Ala. #83 sll0017 300 hemL, gsa; glutamate-1-semialdehyde 2,1-aminomutase (GSA) #84 sll0461 300 proA; gamma-glutamyl phosphate reductase. [EC:1.2.1.41] #85 sll0378 195 cysG; uroporphyrin-III C-methyltransferase. [EC:2.1.1.107] #86 sll0377 147 mfd; transcription-repair coupling factor. #87 sll0376 300 hypothetical protein. #88 sll0373 125 proA; probable gamma-glutamyl phosphate reductase (GPR) (glutamate- #89 sll0372 300 hypothetical protein. #90 sll0179 169 gltX; glutamyl-tRNA synthetase (glutamate--tRNA ligase) (gluRS). #91 slr0207 69 putative gluconokinase 2. [EC:2.7.1.12] #92 slr0208 167 hypothetical protein. #93 ssr0330 126 ftrV; ferredoxin-thioredoxin reductase, variable chain (FTR-V) #94 slr0209 269 hypothetical protein. #95 slr0210 88 sensory transduction histidine kinase. #96 ssr0332 71 hypothetical protein. #97 slr0211 135 hypothetical protein. #98 ssl0331 209 hypothetical protein. #99 slr0212 236 metH; 5-methyltetrahydrofolate-homocysteine methyltransferase. #100 ssr0336 300 hypothetical protein. #101 slr0839 71 hemH; probable ferrochelatase (protoheme ferro-lyase) (hemE #102 sll0827 266 hypothetical protein. #103 slr0841 300 hypothetical protein. #104 slr0506 56 pcr; protochlorophyllide oxido-reductase. [EC:1.3.1.33] #105 sll0481 71 hypothetical protein. [SP:Y481_SYNY3] #106 sll0480 182 hypothetical protein. #107 slr0509 131 alkaline phosphatase-like. #108 slr0510 222 hypothetical protein. #109 slr0511 300 transposase. #110 sll0509 101 Ap-4-A phosphorylase II. #111 sll0508 235 hypothetical protein. #112 sll0507 131 magnesium and cobalt transport protein. #113 sll0505 42 hypothetical protein. #114 sll0504 168 lysA; diaminopimelate decarboxylase (dap decarboxylase). #115 sll0502 197 argS; arginyl-tRNA synthetase (arginine--tRNA ligase) (argRS). #116 sll0501 201 hypothetical 36.7 kD protein sll0501. [SP:Y501_SYNY3] #117 slr0541 79 hypothetical protein. #118 slr0542 77 clpP1; ATP-dependent clp protease proteolytic subunit 1 #119 slr0543 70 trpB; tryptophan synthase beta chain. [EC:4.2.1.20] [SP:TRPB_SYNY3] #120 sll0499 300 clpP; hypothetical protein. #121 slr0750 119 chlN; protochlorophyllide reductase 46 kD chain (orf 469). #122 sll0733 124 hypothetical protein. #123 slr0751 124 hypothetical 27.8 kD protein slr0751. [SP:Y751_SYNY3] #124 slr0752 192 eno; enolase (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate #125 sll0732 300 hypothetical protein. Motif number 1 TGCGAGACTAGGAGATCGGCTTAAATAAGC 6 104 0 GGAGATCGGC 0.76987 -119 CTGATCATAAGGAGATCTGCC 8 2 0 GGAGATCTGC 0.824675 -88 ATTATGGGCGGGCGATCGCCATTCTCTGGC 8 62 1 GGCGATCGCC 0.499995 -28 AGCGATCGGCTGTAGTTTTT 9 189 0 AGCGATCGGC 0.852882 -10 CCGGTCAAGCGGCGATCGCCAAATCTGTTT 12 106 1 GGCGATCGCC 0.499995 -146 ACCAAACTTGGGAGATCGGGCGGTTTAGCC 13 148 1 GGAGATCGGG 0.89178 -51 CAAATCCTTTGGGGATTGGCCATGGGACTA 15 118 0 GGGGATTGGC 0.916706 -26 CTTGGGGGATGGGGATTTCCGCCCTTAATT 16 87 1 GGGGATTTCC 0.733653 -69 ATTGAGCCATGGCGATCGCCTTTTCCTCGC 17 13 1 GGCGATCGCC 0.499995 -39 AATTCTCGTTGGAGATCGCCATCCTGGTCG 21 18 1 GGAGATCGCC 0.501997 -66 GGTTACCAGGGGCGATCGCCGTGGTGGGGG 41 213 1 GGCGATCGCC 0.499995 -64 TGAATTATCTGGCGATCTCGCAGAGATCCG 44 90 1 GGCGATCTCG 0.628162 -33 AAAGGCCGGCGGGGATCACCAAAGAGCAGT 54 111 0 GGGGATCACC 0.756243 -111 GCCAGATGCAGGCGATCGCCAACGATGGCA 61 164 1 GGCGATCGCC 0.499995 -137 GACATGCCCTGGAGATTTCCCTATGCTGTA 64 39 0 GGAGATTTCC 0.683402 -240 ACTCTCCCCAGGAGATTTCCCAGGGAGTTG 66 185 1 GGAGATTTCC 0.683402 -116 AAACCTTGGTGGGGATTGGCCACCATCAAT 72 59 0 GGGGATTGGC 0.916706 -73 TCGATCCCTAGGCGATCGCCTGGGGCCGAA 75 59 1 GGCGATCGCC 0.499995 -239 GGGAGATCGGCGGAGCTAAAC 77 2 1 GGAGATCGGC 0.76987 -131 ACTGTCCCTTGGCGATCGCCATTTTGACTA 84 110 1 GGCGATCGCC 0.499995 -191 CTGTCAATCCGGCGATTGGCTACCTCTAAC 84 172 1 GGCGATTGGC 0.959152 -129 CACCACCGGAGGCGATCGGGTAATGGTAAA 90 63 1 GGCGATCGGG 0.949431 -107 CTTAGGACTCGGCGATCGCCGGT 96 59 1 GGCGATCGCC 0.499995 -13 CTTTTATAATGGCGATCGCCCTTTAATCAC 106 157 1 GGCGATCGCC 0.499995 -26 ATAGACCACTGGCGATCGGCATGGTAACAG 116 84 1 GGCGATCGGC 0.584062 -118 CATTGCCCCAGGCGATCGCCATTCAACCTG 121 50 1 GGCGATCGCC 0.499995 -70 ********** Masking position 6 Map Score: 70.6614 Number of sites scoring better than the average of aligned sites = 6270 Number in coding regions = 5688 Number in noncoding regions = 582 Number of orfs with sites within 600 bp upstream = 370 Fraction of orfs with sites within 600 bp upstream = 0.0594282 Motif number 2 TTCTGCCATCATCCCTTTGGTAGAT 5 4 1 TGCCATTCCC 0.481652 -297 GGGCGAGAGATACCATTCCCCCGGTCAAGCGG 12 86 1 TACCATCCCC 0.676466 -166 GGCTAAACCGCCCGATCTCCCAAGTTTGGTGG 13 146 0 CCCGATCCCA 0.529539 -53 GGTTTCTTTCCCCCCTTTTCCCGTGCGTAT 14 9 0 CCCCCTTCCC 0.958575 -91 TCACATATTTTGCCATAGTCCCATGGCCAATC 15 103 1 TGCCATTCCC 0.481652 -41 GGGCGGAAATCCCCATCCCCCAAGGAAATTAG 16 79 0 CCCCATCCCA 0.946156 -77 GGTGCTCAAGCCCTCTAATCCCATAATTTTCA 22 57 0 CCCTCTTCCC 0.752005 -46 GCTTTTAACCCTCCCTGTCCCAACCTATCGAA 24 159 1 CTCCCTCCCA 0.907283 -37 CTGCAATTTACTCGCTCTCCCCTAGGGTACTC 31 102 1 CTCGCTCCCC 0.835065 -165 GGCCGGATAACCCCATTTACCCTTTCCCAAAG 31 137 0 CCCCATACCC 0.753961 -130 ATTGCCTTCATTCTATGGCCCCACACCATTGC 31 220 0 TTCTATCCCC 0.572921 -47 CTTTAAAAGCCCCCCTGACCCCCAAATTTAGG 32 131 1 CCCCCTCCCC 0.996232 -170 TCTTAACAAAACCCCTGCCCCCACCACGGCGA 41 228 0 ACCCCTCCCC 0.978372 -49 GCTGTAACTTACCCATCGCCCCTCATTTGCCT 48 67 0 ACCCATCCCC 0.960446 -77 GGAAGAATAGCGCCCTAACCCCTAGGGTAACC 52 47 0 CGCCCTCCCC 0.98795 -32 TTAAATTTTTCTCCCTTTTCCC 55 1 0 CTCCCTTCCC 0.87369 -42 TCCAATCTGCCCCTACATCCCCCAACACTAGA 64 240 0 CCCTACCCCC 0.653047 -39 GGTCTTTTATCCCCATTACTCCATAGCCCGCT 65 115 0 CCCCATCTCC 0.8299 -34 AACCTTGATTCGCCCAACCCCCGTCAAATTCA 66 271 1 CGCCCACCCC 0.936106 -30 TTTTAAGAACCCCCCTGGCCTCCAAATTTGGT 68 34 0 CCCCCTCCTC 0.900883 -267 TGATTTAGTCCCCCCTATCCCCGTCCCTGGCA 71 110 1 CCCCCTCCCC 0.996232 -191 TACCTCTAACCTCCAAAACCCCTAGCCTTTCC 84 192 1 CTCCAACCCC 0.883479 -109 TTTTAAAAGCCCCTCTGGCCCCTCAAATTAGG 85 122 0 CCCTCTCCCC 0.97195 -74 TTAGTCTTACCCCCCAGACCCCAAGCAGTTAC 87 187 1 CCCCCACCCC 0.979276 -114 CGTAGCATAACTCCCTGCCCTCTTTGGTAAGG 87 218 0 CTCCCTCCTC 0.730958 -83 AGCCATTCCCCCAGGTTCAAGC 88 1 1 AGCCATCCCC 0.882746 -125 TCATATAATATGCCATAACCCCGATCCAATCT 98 34 0 TGCCATCCCC 0.913928 -176 TATGGCTTAGCCCTAAATCCCCAACGTGCATT 100 75 1 CCCTAACCCC 0.768728 -226 TTTTGAAAGTCCCCAAACCCCCAATGATGGGG 101 45 0 CCCCAACCCC 0.962071 -27 AAAACAAGATATCTATACCCCCATGATTTTAC 102 35 1 ATCTATCCCC 0.48748 -232 GGATTGACGCCTCCATTCCCCAACGGCGGTGA 103 215 1 CTCCATCCCA 0.840069 -86 AGAGCTTTTCCCCTCTGTCCCATGCTTTGTCT 103 255 1 CCCTCTCCCA 0.810957 -46 TTTGAACTGCCCCCCTGACCCCCCCAAGGCTG 104 16 1 CCCCCTCCCC 0.996232 -41 ATAAACCCATTGCCATTTCCCCTGGGGCGAGG 106 115 1 TGCCATCCCC 0.913928 -68 AAGGTGAGTTACCCCTCGCCCCAGGGGAAATG 106 128 0 ACCCCTCCCC 0.978372 -55 AGTTACCCATCCCCCTATCCCCATGAACCTTA 107 66 0 CCCCCTCCCC 0.996232 -66 ACCTTTCCCTACCCCCACCCTAACGA 113 5 1 TTCCCTCCCC 0.950177 -38 ACGGTAACAACACCATCTCCCC 117 1 0 CACCATCCCC 0.896543 -79 TCCCCTGGCTCCCAATCCCTAG 117 68 0 TCCCCTCTCC 0.686813 -12 TGGATTAATTTCCCCAGGCCCAGGGAAAAAGA 119 15 0 TCCCCACCCA 0.585317 -56 CTCTAAAGAAATCCATTGCCCCAGGCGATCGC 121 37 1 ATCCATCCCC 0.87891 -83 TTATAGGGGCATCCCCTTCCCCTCTCCGGTAT 123 48 1 ATCCCCCCCC 0.577761 -77 GTTTTAAAGTTCCCCTAGCCCAAGGGTTGGGG 124 166 0 TCCCCTCCCA 0.887621 -27 ****** **** Masking position 3 Map Score: 60.833 Number of sites scoring better than the average of aligned sites = 2075 Number in coding regions = 1781 Number in noncoding regions = 294 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 3 CACGGGAAAAGGGGGGAAAGAAACCCTACC 14 16 1 GGGGGGAAAG 0.91132 -84 AAAGACGTTGGGGGGCAAATCATTCCAGAT 25 22 0 GGGGGCAAAT 0.915954 -143 AGAAAAGGGGAAAATTCCCAATAACA 27 156 0 GGGGAAAATT 0.843878 -16 TGGGGCAGTATGGGGCAACTCAGGCTAAAC 29 61 1 TGGGGCAACT 0.748844 -51 TGTCCTAGAATGGGGAAATTAGCAGAGCCC 32 13 0 TGGGGAAATT 0.87852 -288 CCCAAATTTAGGGGGAAACTGACTGAAAGT 32 151 1 GGGGGAAACT 0.829287 -150 ATGATTTTTCTGGGAAAATGATCTCGATTT 34 39 1 TGGGAAAATG 0.807615 -227 AATATCGCTGTGGGAAAAATCGAGATCATT 34 55 0 TGGGAAAAAT 0.812425 -211 TGGGGGCGTTTGGGACAACTGGAAACGGAC 39 162 0 TGGGACAACT 0.605415 -139 TGCCAATTTTGGGGACAATTTTTGCTAAGG 42 32 0 GGGGACAATT 0.82814 -92 TTCCTTCTGTAGGGGAAATTTAAATAACTG 48 114 0 AGGGGAAATT 0.756821 -30 AATTTTGAGAGGGGAAAAATCAAATCAACT 50 12 1 GGGGAAAAAT 0.862842 -38 CGGTCAGCCCTGGGGAAAAGCCTGGCAACC 62 117 0 TGGGGAAAAG 0.90471 -184 CTGAATAAGATGGGACAAAGGATGGATAGG 64 162 0 TGGGACAAAG 0.813277 -117 TCTAGGGAACGGGGAAAATTTTATCAATGG 64 195 0 GGGGAAAATT 0.843878 -84 CCAATTAACGGGGGAAAAATAGTATCAGCT 66 19 1 GGGGAAAAAT 0.862842 -282 AGTTTCCAAAGGGGAAAAATTATTACCTGG 68 127 0 GGGGAAAAAT 0.862842 -174 GTGAAAACCCAGGGAAAATTTTTGATGTTG 68 215 0 AGGGAAAATT 0.61561 -86 GGTTAAATGGAGGGGGAAATATAAATCATT 70 207 1 AGGGGGAAAT 0.729676 -94 CAAGGTTTGATGGGGAAATTTGAGGGTTGA 72 81 1 TGGGGAAATT 0.87852 -51 GGAATTGATCGGGGACAATGTTCGATTCTA 75 17 1 GGGGACAATG 0.844614 -281 AGCAACGATGGGGGACAAAGTAATTAAATT 75 89 1 GGGGACAAAG 0.863504 -209 CAAAGCCTTATGGGAAAATGGCCACAATTT 77 35 0 TGGGAAAATG 0.807615 -98 AAAGTTGGGATGGGGAAAATCCCGCTAGGG 79 59 1 TGGGGAAAAT 0.893806 -82 AAAAACAGACGGGGAGAACTCCACTCTACA 83 152 0 GGGGAGAACT 0.650702 -149 GAAAATTATAGGGGGCAAAGCCCACCCGCA 84 280 0 GGGGGCAAAG 0.924776 -21 GGCTTGAACCTGGGGGAATGGCT 88 4 0 TGGGGGAATG 0.858742 -122 GACAAAACCAAGGGGCAATGCACACCAAAA 89 263 0 AGGGGCAATG 0.75785 -38 GGGGTTACGATGGGAGAAAGGAATTGCCTC 90 34 0 TGGGAGAAAG 0.784526 -136 GGGCGAAGCTTGGGAGAAATTTCCAGTGTT 93 11 1 TGGGAGAAAT 0.763464 -116 ACTCCCGATATGGGGGAATTAGTTGCCCAA 97 87 1 TGGGGGAATT 0.843488 -49 CCCCCAATGATGGGGGAATTAGATTATTGC 101 30 0 TGGGGGAATT 0.843488 -42 TCACCATTGCAGGGAAAAATAAGGTTTCAG 102 143 0 AGGGAAAAAT 0.650829 -124 CTTCAACCATGGGGGCAAAGCAACAAGCCC 103 26 0 GGGGGCAAAG 0.924776 -275 CATGGGACAGAGGGGAAAAGCTCTCCTCCG 103 249 0 AGGGGAAAAG 0.803376 -52 CCCCAAGGCTGGGGGGAATTTATCGGTGAA 104 37 1 GGGGGGAATT 0.88672 -20 CCCTCGCCCCAGGGGAAATGGCAATGGGTT 106 118 0 AGGGGAAATG 0.778302 -65 ATCCCGATTCTGGGGAAACTTACT 107 5 0 TGGGGAAACT 0.769826 -127 TACAACAACCGGGGGCAAAGCAAAACCCTA 114 93 0 GGGGGCAAAG 0.924776 -76 CCCCAGGCCCAGGGAAAAAGAATAA 119 6 0 AGGGAAAAAG 0.677685 -65 TCCCTGGGCCTGGGGAAATTAATCCATTGT 119 21 1 TGGGGAAATT 0.87852 -50 GGCGATCGCCTGGGGCAATGGATTTCTTTA 121 40 0 TGGGGCAATG 0.879117 -80 CCCTGGATACGGGGGGAAAGTTGTCGCTCT 123 85 1 GGGGGGAAAG 0.91132 -40 AGGGTAACCATGGGAAAAATTAAGTCTTGA 124 48 1 TGGGAAAAAT 0.812425 -145 ********** Masking position 7 Map Score: 56.9526 Number of sites scoring better than the average of aligned sites = 1983 Number in coding regions = 1684 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 4 CCTAACCCTTGCCATACTAATT 11 1 1 CCTAACCCGC 0.809857 -129 GATACCATTCCCCCGGTCAAGCGGCGATCGCC 12 94 1 CCCCGGTCGC 0.416584 -158 GGGAGATGATCCCAATCCCACCTTCCTTTTTG 15 29 0 CCCAATCCCC 0.501527 -115 CTGCTAATTTCCCCATTCTAGGACAGGGGCCG 32 18 1 CCCCATTCGG 0.777299 -283 AAGCTGTTTCCCCCATCAAGGCCAGATTATCT 33 38 1 CCCCATCAGC 0.86262 -92 TTTCAGCAAACCTCACCCCTGGAATAAAAGGA 38 125 1 CCTCACCCGG 0.951944 -35 CCCAGTCATTCCCCATCAATCGTCCGTTTCCA 39 141 1 CCCCATCACG 0.566677 -160 AAACCCCTGCCCCCACCACGGCGATCGCCCCT 41 220 0 CCCCACCAGC 0.94078 -57 CTAGCTTCTACCCAATCAATGGTAATACCATC 44 46 1 CCCAATCAGG 0.809689 -77 AGAATAGCGCCCTAACCCCTAGGGTAACCACT 52 44 0 CCTAACCCAG 0.677215 -35 GTTTTCTCACCCCCAGCAAAACT 53 83 1 CCCCAGCAAC 0.551508 -13 TCAAACCACACCCCGCTCCAGCCCATTGGAAG 54 183 0 CCCCGCTCGC 0.719079 -39 AAGAATCTCCCCCCAGCCGGACTCCTACC 60 216 1 CCCCAGCCAC 0.814816 -19 AGCCTGGCAACCCAACCCAGACCAGTTCTCAG 62 97 0 CCCAACCCAC 0.857562 -204 ATTAATTAATCCCCATCCGCAGTAAAAGCGCC 63 30 1 CCCCATCCAG 0.917132 -76 CCTTGATTCGCCCAACCCCCGTCAAATTCATC 66 273 1 CCCAACCCGT 0.756214 -28 TCCCCCCTATCCCCGTCCCTGGCAGTGTCAAC 71 118 1 CCCCGTCCGG 0.953536 -183 GGTGGCCAATCCCCACCAAGGTTTGATGGGGA 72 65 1 CCCCACCAGT 0.694304 -67 TCTCTCTCAGCCTCACCCAGGGGAACGCAAAA 77 110 1 CCTCACCCGG 0.951941 -23 AAAAGAAACTCCCCACCCTAGGTAACTGGGAT 78 66 1 CCCCACCCGG 0.990152 -42 CAACGAAAAACCCCATCCCAGTTACCTAGGGT 78 80 0 CCCCATCCGT 0.762593 -28 GCGGGATTTTCCCCATCCCAACTTTCCATGGC 79 52 0 CCCCATCCAC 0.861774 -89 AGTGAAAGTCCCCCATTATTGGGGAATTTAGG 85 80 0 CCCCATTAGG 0.493785 -116 ACAGCAAGAACCCCATCCCAACTCCTAGCAAA 86 57 0 CCCCATCCAC 0.861774 -91 CCCATCGTAACCCCACCACCGGAGGCGATCGG 90 50 1 CCCCACCAGG 0.965755 -120 GGTTATCCATCCTAACCCAAAGCTTTGCCTCC 90 110 0 CCTAACCCAG 0.677215 -60 GCTCCATAACCCTAGCCCAAGCTGACCTAAAC 91 47 1 CCTAGCCCGC 0.686683 -23 TATTTATTAGCCCAGCCATTGCCGATGGCGTC 94 38 0 CCCAGCCAGC 0.757292 -232 AGCTGGTTAGCCTCACCCTAGGCGGACAATTC 94 122 0 CCTCACCCGG 0.951909 -148 CTCAAACAAACCCCACCAATCGAGATTGCCGT 100 35 1 CCCCACCACG 0.767908 -266 AATCTAATTCCCCCATCATTGGGGGTTTGGGG 101 35 1 CCCCATCAGG 0.917672 -37 ACTGTTCCGTCCCAATTCTAGGCAAGAAATTC 102 73 0 CCCAATTCGG 0.571224 -194 GATAAATTCCCCCCAGCCTTGGGGGGGTCAGG 104 29 0 CCCCAGCCGG 0.965489 -28 GTGAGTTACCCCTCGCCCCAGGGGAAATGGCA 106 125 0 CCTCGCCCGG 0.910564 -58 TCAAGTAAAACCCAGCCCCTGGCCGTATTTTC 110 54 1 CCCAGCCCGG 0.951965 -48 CTTTCCCTACCCCCACCCTAACGACCATCTCC 113 13 1 CCCCACCCAC 0.940382 -30 TATTGTCCAGCCCAGCCCTTAGTTTTTGATTA 115 144 1 CCCAGCCCAG 0.846143 -54 TAATTTCGTTCCTCGGCACTGGCTTGGGTAAT 116 49 0 CCTCGGCAGG 0.442784 -153 TCCCCTGGCTCCCAATCCCTAGAAGCGGAGAA 117 58 0 CCCAATCCAG 0.808588 -22 GATTAATTTCCCCAGGCCCAGGGAAAAAGAAT 119 13 0 CCCAGGCCGG 0.830113 -58 TAAGCAACAACCTAACCAAAAGAACCTGTTGG 124 107 1 CCTAACCAAG 0.369618 -86 CCGAAGTAACCCCAACCCTTGGGCTAGGGGAA 124 157 1 CCCAACCCGG 0.974693 -36 ******** ** Masking position 2 Map Score: 53.749 Number of sites scoring better than the average of aligned sites = 2605 Number in coding regions = 2399 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 225 Fraction of orfs with sites within 600 bp upstream = 0.0361388 Motif number 5 GAGATTTTCCTTCCTAGGCTTGC 3 85 1 TTCCTAGGCT 0.400822 -13 TCTGCCATCATCCCTTTGGTAGATATTTAA 5 12 1 TCCCTTTGGT 0.642728 -289 TTTAACGTCCTCCCTTTGGCC 7 2 0 TCCCTTTGGC 0.673894 -133 GGGGGGTAAAACCACTGGGTTAACAGGGGA 9 80 0 ACCACTGGGT 0.453992 -119 CCTGCTCCTTGCCATTGGGGGGTAAAACCA 9 96 0 GCCATTGGGG 0.672783 -103 ACGGGCTAATTTCCTTGGGGGATGGGGATT 16 74 1 TTCCTTGGGG 0.676817 -82 GAAGTTTTTGTCCCCTGGGCTGACTCTGCC 26 64 1 TCCCCTGGGC 0.931963 -37 GCCCCATACTGCCCCAGGCTAAATACCCTC 29 47 0 GCCCCAGGCT 0.83198 -65 AAGCCAGAGTACCCTAGGGGAGAGCGAGTA 31 110 0 ACCCTAGGGG 0.739915 -157 CTTTACGATCGCCATTGGCTAGCCATGGGA 31 181 0 GCCATTGGCT 0.541458 -86 TAACATGGCGTTCCCTGGGTTTATTGGTCT 39 244 1 TTCCCTGGGT 0.620227 -57 GAGTCGTTTTTCCCTTTGGTGCCCCTGGCA 40 77 0 TCCCTTTGGT 0.642728 -85 TGTTTTCTGTTTCCTTGGGTGGCCTTGTTG 51 231 1 TTCCTTGGGT 0.578474 -70 TTCAGTGGTTACCCTAGGGGTTAGGGCGCT 52 41 1 ACCCTAGGGG 0.739915 -38 ATATGGCATGGCCATTGGGGAGGCAAGGCG 54 76 1 GCCATTGGGG 0.672783 -146 GCCAGGCTTTTCCCCAGGGCTGACCGAATT 62 121 1 TCCCCAGGGC 0.882625 -180 CCTGGAGATTTCCCTATGCTGTAGTTATTG 64 32 0 TCCCTATGCT 0.467254 -247 ATCAAAAATTTTCCCTGGGTTTTCACCCTG 68 219 1 TTCCCTGGGT 0.620227 -82 AGCGAGGAAAGCCCTAGGCGTTAGCTTCAA 71 171 0 GCCCTAGGCG 0.863755 -130 TACGGGTCGATCCCTAGGCGATCGCCTGGG 75 53 1 TCCCTAGGCG 0.881707 -245 GTTGCTTTCGGCCCCAGGCGATCGCCTAGG 75 65 0 GCCCCAGGCG 0.883289 -233 AGCGCAACTTGCCATAGGCTAACTTCTTCA 75 265 1 GCCATAGGCT 0.395526 -33 TTTTTGCGTTCCCCTGGGTGAGGCTGAGA 77 114 0 TCCCCTGGGT 0.922622 -19 AGCTTTATTTTCCCTTTGGGCAAGGCTGAC 78 13 1 TCCCTTTGGG 0.73304 -95 TGCATGTTACGCCCTTTGGTAACAAACCTC 81 20 1 GCCCTTTGGT 0.602428 -72 TGGCTGACTGTCCCTTGGCGATCGCCATTT 84 104 1 TCCCTTGGCG 0.930532 -197 GGCAAAAGTTTTCCTAGGGGTCGACCTTAC 86 113 1 TTCCTAGGGG 0.538177 -35 AACTCTCCCGACCCTTTGCCAAGACTGGCT 87 116 0 ACCCTTTGCC 0.444746 -185 TTATGCTACGATCCTTGGCCAATAGCCCCA 87 240 1 ATCCTTGGCC 0.379239 -61 CACCAAGTCAACCACTGGGGCTATTGGCCA 87 255 0 ACCACTGGGG 0.55929 -46 GGTGTGCATTGCCCCTTGGTTTTGTCAAAT 89 267 1 GCCCCTTGGT 0.646215 -34 GGTTAGCCTCACCCTAGGCGGACAATTCTC 94 120 0 ACCCTAGGCG 0.766983 -150 TTTGTATGACTCCCCTTGCCCGATTTACAG 99 137 1 TCCCCTTGCC 0.683069 -100 CATTGCCATTTCCCCTGGGGCGAGGGGTAA 106 122 1 TCCCCTGGGG 0.94791 -61 GTAAAACCCAGCCCCTGGCCGTATTTTCGG 110 58 1 GCCCCTGGCC 0.911034 -44 AACGAATGTTATCCTAGGGCAGAATGGCTT 111 36 1 ATCCTAGGGC 0.270664 -200 TTTGACTGGTTCCACTGGCCCATCAGGCCG 112 32 1 TCCACTGGCC 0.654271 -100 TTATTTATAGACCACTGGCGATCGGCATGG 116 78 1 ACCACTGGCG 0.526445 -124 ACTAGATCACTCCATTGGGCAACGGCGTTA 116 145 1 TCCATTGGGC 0.644691 -57 TCCCCTGGCTCCCAATCCCT 117 70 0 TCCCCTGGCT 0.912634 -10 TGGATTAATTTCCCCAGGCCCAGGGAAAAA 119 17 0 TCCCCAGGCC 0.869766 -54 ACCATGCGCTGCCCTTGGCTATTAATTCTT 120 84 1 GCCCTTGGCT 0.882059 -217 GAAATCCATTGCCCCAGGCGATCGCCATTC 121 44 1 GCCCCAGGCG 0.883289 -76 AGTAACCCCAACCCTTGGGCTAGGGGAACT 124 161 1 ACCCTTGGGC 0.794142 -32 ATCATCTCCTTCCCCATGCTTCTTCGTT 125 283 1 TCCCCATGCT 0.510719 -18 ********** Masking position 3 Map Score: 39.6413 Number of sites scoring better than the average of aligned sites = 4351 Number in coding regions = 3898 Number in noncoding regions = 453 Number of orfs with sites within 600 bp upstream = 424 Fraction of orfs with sites within 600 bp upstream = 0.0681015 Motif number 6 TAAATATTAGCCCCCAGACTTGTTTTACTAAG 5 48 0 CCCCCAATTG 0.971121 -253 GTCTGATCCATCCCAATAATTGCGAGACTAGG 6 122 0 TCCCAAATTG 0.843393 -101 GACCCAAAATTCCCCAAGATTGATTGGCGGAC 6 151 1 TCCCCAGTTG 0.88619 -72 GACCAAAGCGCCACCAAACTTGGGAGATCGGG 13 136 1 CCACCAATTG 0.611949 -63 TTTCCTAACCTCCCTAAAATGGTAGGGTTTCT 14 34 0 TCCCTAATGG 0.598809 -66 AGTCAGTTTCCCCCTAAATTTGGGGGTCAGGG 32 143 0 CCCCTAATTG 0.817885 -158 TCAATAAATGTCCCAAAACTGGCTCTGTGTTC 40 113 0 TCCCAAATGG 0.857181 -49 AAAACCCCTGCCCCCACCACGGCGATCGCCCC 41 221 0 CCCCCACCGG 0.86013 -56 CAAAAATTGTCCCCAAAATTGGCATCTTGAGC 42 38 1 CCCCAAATGG 0.952666 -86 TGCAGGCGATCGCCAACGATGGCATCAGTCCC 61 170 1 CGCCAAGTGG 0.78695 -131 GCCAGGCTTTTCCCCAGGGCTGACCGAATTCT 62 121 1 TCCCCAGCTG 0.783035 -180 TAGTTTTTGCCCCCAAGAACTGGTTAAGGTGC 62 177 0 CCCCAAACTG 0.89328 -124 GCAGTAAAAGCGCCAAAGTTTGCCCATGCCAT 63 48 1 CGCCAAGTTG 0.768214 -58 ATCTAGCTTTCCACCAAATTTGGAGGCCAGGG 68 22 1 CCACCAATTG 0.611949 -279 GGCTTTTCCCTGCCCATAATTGTACTAACTTC 71 273 1 TGCCCAATTG 0.70327 -28 ATTACTTTGTCCCCCATCGTTGCTTTCGGCCC 75 81 0 CCCCCACTTG 0.922501 -217 CCCCGATAATGGCCACAATCAA 82 1 1 CCCCGAATGG 0.745926 -300 ATCAATGTAATGCCCATATCTGACGGTTTTGA 82 28 1 TGCCCAACTG 0.523472 -273 CCCCTAAATTCCCCAATAATGGGGGACTTTCA 85 78 1 CCCCAAATGG 0.952666 -118 CCCGACCCTTTGCCAAGACTGGCTAAGCATAC 87 108 0 TGCCAAATGG 0.586528 -193 TGCTGTTTGCCCCCCAAAGTTGCCCTGTCCGA 88 66 1 CCCCCAATTG 0.97112 -60 AAAATGTGAACCCCCAGCTTTGCTAGGCTACC 89 235 0 CCCCCACTTG 0.92251 -66 GCAACTAATTCCCCCATATCGGGAGTTTTTTG 97 81 0 CCCCCAACGG 0.945562 -55 GGGAATTAGTTGCCCAAAATGGAACATTACAA 97 100 1 TGCCCAATGG 0.725379 -36 GTCCCCAAACCCCCAATGATGGGGGAATTAGA 101 37 0 CCCCAAGTGG 0.939859 -35 TGTTGCTTTGCCCCCATGGTTGAAGGTTAACG 103 31 1 CCCCCAGTTG 0.962998 -270 CGCCTCCATTCCCCAACGGCGGTGAACCGGAG 103 222 1 CCCCAAGCGG 0.878693 -79 CCCCTGACCCCCCCAAGGCTGGGGGGAATTTA 104 27 1 CCCCAAGTGG 0.939861 -30 AAAACAATCATCCCTAAGATTGATAAACTGGG 114 36 1 TCCCTAGTTG 0.50979 -133 TGTATTAGCTCCCCAATAGCTGTTACAAATTG 118 52 0 CCCCAAACTG 0.89328 -26 CCCGAAGTAACCCCAACCCTTGGGCTAGGGGA 124 156 1 CCCCAACTTG 0.864746 -37 TTAGAAATAAGCCCCAGAATTGGTTCCCCCGC 125 139 1 GCCCCAATTG 0.653791 -162 ****** * *** Masking position 6 Map Score: 32.9369 Number of sites scoring better than the average of aligned sites = 1362 Number in coding regions = 1011 Number in noncoding regions = 351 Number of orfs with sites within 600 bp upstream = 195 Fraction of orfs with sites within 600 bp upstream = 0.0313203 Motif number 7 CCTAACCCTTGCCATACTAATTT 11 1 1 CCACCTTGCC 0.957846 -129 TTATGCTTCTTTTAAGCCTTGCCAACCGTACTA 16 126 1 TTAGCTTGCC 0.891959 -30 AGTTTTATTCCTTTGCCTTTTAGT 18 8 0 TTTCCTTGCC 0.914124 -17 GGCCGGGAAACTAAAACTTTGCCGACAGGCCCT 27 67 1 CTAACTTGCC 0.643611 -105 GGAACAAATTTTAGCCCTTTCCGTTCCCGTAC 30 10 1 TTACCTTTCC 0.664261 -159 GATAACCCCATTTACCCTTTCCCAAAGCCAGAG 31 131 0 TTACCTTCCC 0.537155 -136 ACTGAAAGTCCTCTAGTATTGCCGGAGCTTTAG 32 172 1 CTTGTTTGCC 0.278687 -129 CTAGCTGTAACTTACCCATCGCCCCTCATTTGC 48 69 0 CTACCTCGCC 0.657855 -75 TTAAAAAAAACTAAAGTTTTGCCATTTTTGGAA 51 55 1 CTAGTTTGCC 0.540198 -246 TTTTTCCTAAACCCTTGCCTCAATAGTTT 52 7 1 CTACCTTGCC 0.972942 -72 AATTAAATTTTTCTCCCTTTTCCC 55 2 0 TTTCCTTTCC 0.394178 -41 GTAACCTAAGCTTTTGCCGGCTGATCAC 60 6 1 CTACTTTGCC 0.821628 -229 TCTTGAAAATCTGATCTTTTGTCAGGGTTGTTT 60 95 1 CTACTTTGTC 0.317736 -140 CTTTTCTTTTTATTACCTTGCCTAAGTTAATG 61 10 1 TTTACTTGCC 0.348372 -291 TGAATTTTCACTCTCCCATTGCCTAAAAAATTA 61 41 1 CTTCCTTGCC 0.922027 -260 TCACACTTGTTTGTGCTGTTGCCATTGTCTTTT 61 84 1 TTTCTTTGCC 0.57692 -217 GAATTCTGCTTCAAACCATTGCCGGAATTTGGC 62 146 1 TCACCTTGCC 0.953389 -155 TCCACTCCTATCCATCCTTTGTCCCATCTTATT 64 156 1 TCACCTTGTC 0.674055 -123 TTTTGCCCAACTAATCCGTTGCCAGGGAGTTTA 70 275 1 CTACCTTGCC 0.972942 -26 TTGCACTAACTTTAACCATTGCTATGCATTGCA 75 162 1 TTACCTTGCT 0.41797 -136 TGGGAATTTATTGAACCTGTGCCCACATCAAAA 83 180 0 TTACCGTGCC 0.830802 -121 ACCAACTCTCCCGACCCTTTGCCAAGACTGGCT 87 116 0 CCACCTTGCC 0.957846 -185 ACTGGAATTGTTGAAGCTGTGCCTCGACATACA 89 89 1 TTAGCGTGCC 0.556025 -212 CCATCCTAACCCAAAGCTTTGCCTCCATTAATA 90 103 0 CCAGCTTGCC 0.852842 -67 TATTTATTAGCCCAGCCATTGCCGATGGCGTCA 94 37 0 CCACCTTGCC 0.957846 -233 TCCCAATTGTTTTTGCCTTTGCCATTAGAGGCT 102 106 1 TTTCCTTGCC 0.914124 -161 CATTCAAGCATTTTGCCATTTCCAACT 102 250 1 TTTCCTTTCC 0.394178 -17 CTTGGAGGGCTTGTTGCTTTGCCCCCATGGTTG 103 20 1 TTTGCTTGCC 0.73082 -281 TCCCCTCTGTCCCATGCTTTGTCTATAGCTTGC 103 263 1 CCAGCTTGTC 0.369458 -38 GCTCTACGCCTTTATCAATTGCCATTCCAGTTT 105 34 1 TTACATTGCC 0.46261 -38 GGAGCGAGCATAAACCCATTGCCATTTCCCCTG 106 106 1 TAACCTTGCC 0.617103 -77 GGTAAATTAATCTAACCATTGTCAGTCAAGCCA 111 60 0 TCACCTTGTC 0.674055 -176 ACTAGTTTTCTTGAGCCTTTGCC 112 119 1 TTACCTTGCC 0.970032 -13 ACGGAATTACCCAAGCCAGTGCCGAGGAACGAA 116 44 1 CCACCGTGCC 0.775125 -158 CCTGGGGAAATTAATCCATTGTCAAAGCCACTT 119 29 1 TTACCTTGTC 0.765949 -42 CTTTAGAGATTTCAGCTATTGCCCAAAAAGCTT 121 12 0 TTACTTTGCC 0.805694 -108 CGGGAGATAATCAAACCATTGCCAACAGGTTCT 124 127 0 TCACCTTGCC 0.953389 -66 ** * ** ***** Masking position 10 Map Score: 36.4184 Number of sites scoring better than the average of aligned sites = 1154 Number in coding regions = 1034 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 8 CGATCGCCGCTTGACCGGGGGAATGGTATC 12 94 0 TTGACCGGGG 0.954333 -158 AGTGAGTCCGTTGACCGGGAGTATTTTCCA 22 11 0 TTGACCGGGA 0.711507 -92 AGTTCTTGACCGGGGAAGATATGAG 33 6 1 TTGACCGGGG 0.954333 -124 TAATCTGGCCTTGATGGGGGAAACAGCTTC 33 37 0 TTGATGGGGG 0.977843 -93 CAAGCTTTATGGGGGATTTTTGCGT 39 6 1 TTTATGGGGG 0.846862 -295 AAACGGACGATTGATGGGGAATGACTGGGA 39 140 0 TTGATGGGGA 0.838927 -161 AGTTTTGCTGGGGGTGAGAAAACT 53 82 0 TTGCTGGGGG 0.816089 -14 TATTGCTGTTTTTACCGGGGTCACCCTTGG 62 14 1 TTTACCGGGG 0.723652 -287 GGGTTTACGGTTGATGGTGGCATACATGGC 63 75 0 TTGATGGTGG 0.838927 -31 TGTGTTTACGGGGGTTTACGGTTG 63 92 0 TTTACGGGGG 0.857203 -14 TAATTGCCAATTAACGGGGGAAAAATAGTA 66 13 1 TTAACGGGGG 0.703773 -288 TCCGATGAATTTGACGGGGGTTGGGCGAAT 66 278 0 TTGACGGGGG 0.979553 -23 TTTTGCTTAATTGACGGTGGGCACTGTGAC 71 227 0 TTGACGGTGG 0.849708 -74 TTCACGAAAATTGATGGTGGCCAATCCCCA 72 50 1 TTGATGGTGG 0.838927 -82 CCACCAAGGTTTGATGGGGAAATTTGAGGG 72 77 1 TTGATGGGGA 0.838927 -55 GGGAAAGGAATTGATCGGGGACAATGTTCG 75 11 1 TTGATCGGGG 0.950621 -287 GTCTGTTTTTTTGATGTGGGCACAGGTTCA 83 172 1 TTGATGTGGG 0.64869 -129 GAAGCTAGATTGGATCGGGGTTATGGCATA 98 28 1 TGGATCGGGG 0.671206 -182 CAAACCCCCAATGATGGGGGAATTAGATTA 101 34 0 ATGATGGGGG 0.749622 -38 AAATGTTCGATGGGGGTGTTAAGGAT 106 7 1 TCGATGGGGG 0.823936 -176 ********** Masking position 9 Map Score: 25.6083 Number of sites scoring better than the average of aligned sites = 562 Number in coding regions = 506 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 CCAGTAAAGTCATTTCTTGGCCCGTTGGATAT 3 39 1 CATTCTGGCC 0.893163 -59 GATTCGGAATGGGTTCTAGCCCGATAGAGAGA 5 80 0 GGTTCTGCCC 0.751892 -221 TTTATCTTCACACTTTTTGGCCTAAGTCTGAA 5 190 1 CATTTTGGCC 0.929281 -111 TCTAGCTTAACGGGTTTAGCCCGACCAGGATG 21 37 0 CGGTTTGCCC 0.84292 -47 GAGCTTCAGGAAGTTTTTGTCCCCTGGGCTGA 26 55 1 AATTTTGTCC 0.367852 -46 TATTTAGTGCCAAGTTTTGGCCGGGAAACTAA 27 49 1 CAGTTTGGCC 0.893163 -123 GGAACAAATTTTAGCCCTTTCCGTTCC 30 6 1 AATTTTGCCC 0.747165 -163 CGATTCTCTCGGATTTTCGGCCTGCAATTTAC 31 81 1 GGTTTTGGCC 0.858925 -186 AGGGCCGCACAAGTTTTCGGCCCCTGTCCTAG 32 35 0 AATTTTGGCC 0.790671 -266 GGGATTATACGGTTTTTAGGCCATTGATCCCG 38 49 0 GGTTTTGGCC 0.858925 -111 GGCTCCTTTTCAGTTTTGGGCCAACAA 69 6 0 CATTTTGGCC 0.929281 -86 CTTTCTAACAGAATTTTTGCCCAACTAATCCG 70 261 1 GATTTTGCCC 0.853071 -40 TAAGCAACTAGAATTTTGGCCCACAGACCC 72 112 1 GATTTTGCCC 0.853071 -20 ACGGGCTCTCAGAGTCTTGGCCCAAACAAATG 83 26 1 AGGTCTGGCC 0.556403 -275 GCGATTGAGCCATTTTTGGTCCATGTATCAGA 87 15 1 CATTTTGTCC 0.669358 -286 ACAAGCCCTCCAAGTTTAGCCCC 103 2 0 CAGTTTGCCC 0.867386 -299 AGACTAAAATCGGGTCTTGGCCACATTCAAAC 107 35 0 CGGTCTGGCC 0.813559 -97 GAAAAACTCTCATTTCTAGCCCGTCAGCTAAC 125 94 0 CATTCTGCCC 0.867386 -207 ** **** **** Masking position 7 Map Score: 10.8494 Number of sites scoring better than the average of aligned sites = 245 Number in coding regions = 203 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 GGTGAGAGAAAGGGCTCAACGAT 4 37 0 GGAGAGAAAG 0.690062 -13 ACTGGAGTTGGGCGAGGAAAAGGCGATCGCCAT 17 21 0 GGAGGAAAAG 0.588285 -31 AGGGTTAAAAGCTTAGCTAAAGGTCTGACAGTA 24 138 0 GCAGCTAAAG 0.5486 -58 TATTTTCCCTGGTACGGGAACGGAAAGGGCTAA 30 21 0 GGCGGGAACG 0.882707 -148 GGGTACTCTGGCTTTGGGAAAGGGTAAATGGGG 31 126 1 GCTGGGAAAG 0.684566 -141 AGACGGACTGGGCTAGGTAAATGACGGATAATG 39 201 0 GGAGGTAAAG 0.900636 -100 ACACAATCTAGCCACGGGGACTGGTATCTGGTT 51 96 1 GCCGGGGACG 0.732491 -205 ACCGCAGTGCGCATAGCTGAAAGTGGAGAGCCT 51 142 1 GCAGCTGAAG 0.498925 -159 AAGTGTTGAAGGAAAGGGGACTGATGCCATCGT 61 185 0 GGAGGGGACG 0.955929 -116 CTTTCGGAGAGCGAAAAGAATTAATTAA 63 6 1 GGAGCGAAAG 0.890849 -100 CTTTTACTAGGGACAGGTAAAAGCGATACTCTC 66 158 1 GGAGGTAAAG 0.900636 -143 GTACAATTATGGGCAGGGAAAAGCCTATTCGAC 71 265 0 GGAGGGAAAG 0.964327 -36 GGGAGATCGGCGGAGCTAAACGCTAAATTGTG 77 10 1 GCAGCTAAAG 0.5486 -123 CCGGCGAAAAGGGACGGGAAAGGTCAAAGCCTT 77 56 0 GGCGGGAAAG 0.884848 -77 CGAGTTAATCGCCTAGAGGACAGTCAAAACCGT 82 50 0 GCAGAGGACG 0.442394 -251 TGCCCTCTTTGGTAAGGTAACTGCTTGGGGTCT 87 202 0 GGAGGTAACG 0.898755 -99 AAACAGCAAAGCGCAGGGGAAAGTATTTAAAAA 88 41 0 GCAGGGGAAG 0.907713 -85 AGGTTCATGGGGATAGGGGGATGGGTAACTGAA 107 68 1 GGAGGGGGAG 0.648475 -64 GTTAGGGTGGGGGTAGGGAAAGGT 113 2 0 GGAGGGAAAG 0.964327 -41 ACTGGCGATCGGCATGGTAACAGTAGGTTCCAT 116 91 1 GGTGGTAACG 0.616087 -111 AAGAGAAAATGGATTGGGAACTGTGCCAAAGAT 122 70 1 GGTGGGAACG 0.827169 -55 CAGAAATACCGGAGAGGGGAAGGGGATGCCCCT 123 52 0 GGAGGGGAAG 0.956799 -73 ATGCCTACGGGGTTAGCTGACGGGCTAGAAATG 125 83 1 GGAGCTGACG 0.687092 -218 GAACGGTGGCGTGGAGGGAACAGAAAGCGGGGG 125 164 0 GTAGGGAACG 0.567653 -137 ** ******* * Masking position 6 Map Score: 17.129 Number of sites scoring better than the average of aligned sites = 848 Number in coding regions = 730 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 11 GTTGGCAGGACCCTAATTTTTCTCCCAATA 13 67 1 CCCTAATTTT 0.744751 -132 GGATTTCCGCCCTTAATTTTGCCGAAATTA 16 99 1 CCTTAATTTT 0.798935 -57 CCCTCTAATCCCATAATTTTCAAGGTACCC 22 49 0 CCATAATTTT 0.585528 -54 CCTTGAATTACCTTGATTTTGCCCTCCAAA 35 11 0 CCTTGATTTT 0.890716 -47 ATTACGTTACCCCTGGTTTTGACGGGATCA 38 27 1 CCCTGGTTTT 0.817548 -133 CAAGACCCCTTGATTTTCGTCGCTGAC 56 8 1 CCTTGATTTT 0.890716 -43 TGAGGATGATCCATAATTTTTTAGGCAATG 61 57 0 CCATAATTTT 0.585528 -244 ACGCTGAAACCCTTGATTTTACAGGTTTTT 64 76 0 CCTTGATTTT 0.890716 -203 TATTACCTGGCCTGGGTTTTGATTATTTGT 68 107 0 CCTGGGTTTT 0.704687 -194 AAAAATTTTCCCTGGGTTTTCACCCTGATT 68 222 1 CCTGGGTTTT 0.704687 -79 TGGGTTTTCACCCTGATTTTCTTTTAGGCT 68 234 1 CCCTGATTTT 0.856833 -67 GTGCATTGCCCCTTGGTTTTGTCAAATTTT 89 270 1 CCTTGGTTTT 0.8592 -31 GTTTTTAATTCCCTAATTTTCTTAGGCATA 99 191 1 CCCTAATTTT 0.744751 -46 ATCTATACCCCCATGATTTTACCATTGGGA 102 45 1 CCATGATTTT 0.743441 -222 CCAGCCCAGCCCTTAGTTTTTGATTATTTA 115 150 1 CCTTAGTTTT 0.748428 -48 TTCAATACGCCCTGAATTTTCTGAACGGTG 125 189 0 CCTGAATTTT 0.608427 -112 ********** Masking position 7 Map Score: 11.8742 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 165 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 12 TTGTTAGTGCTTTTTACTTCCCCCAGGATAT 1 45 1 TTTTACTTCC 0.83722 -30 GTCGGCAAAGTTTTAGTTTCCCGGCCAAAAC 27 62 0 TTTTGTTTCC 0.916185 -110 CCGGCCTGTATTTTAGCTTCCCATGGCTAGC 31 163 1 TTTTGCTTCC 0.967482 -104 GTCAATCTTATTTTAGCTTCCACTCAATGAG 43 34 1 TTTTGCTTCC 0.967482 -41 AAGTTTTGTTGTTTTGCTTCCAATGGGCTGG 54 167 1 GTTTGCTTCC 0.949069 -55 TAACGAAGCTTTTTTATTTCCAAACCGCAAC 84 16 1 TTTTATTTCC 0.653937 -285 TGCAGAATTTGTTTAGCTTCCCTCCACCCTG 86 23 1 GTTTGCTTCC 0.949069 -125 CAAAGTAGTCTTTTTGTTTCCACTGAATGAC 89 168 1 TTTTGTTTCC 0.916185 -133 CGGCGCCATTTTTTGGTTTCCTGGCCCCTAG 92 51 0 TTTTGTTTCC 0.916185 -117 TAATTGTAGTGTTTGGCTTCCTTTTGGAAAA 109 95 0 GTTTGCTTCC 0.949069 -206 TCCCAATCCATTTTCTCTTCCTTTGTTTACC 122 58 0 TTTTTCTTCC 0.744686 -67 **** ****** Masking position 4 Map Score: 8.47725 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 60 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 CAATTAGACAAATTTGGCAAGGCAG 31 252 1 AATTTGGCAG 0.643645 -15 CCAGATACCAAATTTGGGTAGTCTGAGGAAA 49 90 1 AATTTGGGAG 0.499784 -65 AAATTTTGAGAGGGGAAAAATCA 50 3 1 ATTTTGAGGG 0.801515 -47 TAAATACGGGATTTTGACAAGCTAATAGCTG 66 44 0 ATTTTGACAG 0.734789 -257 TGCTCCGATGAATTTGACGGGGGTTGGGCGA 66 280 0 AATTTGACGG 0.929 -21 GGATCCGGGGAATTGGACAGGATGAAAGGCA 68 186 1 AATTGGACGG 0.753315 -115 TTAATTTTTTATTTTGAGGGGAATTAATTGA 74 11 1 ATTTTGAGGG 0.801515 -81 ATTTTAGCCAAAATTGACGAGAGACTAGACC 82 145 0 AAATTGACAG 0.428334 -156 AAATGTTAAAAATTTGACGTGAATGACGTAA 85 20 1 AATTTGACTG 0.507625 -176 TATTCCTCCTAATTTGAGGGGCCAGAGGGGC 85 115 1 AATTTGAGGG 0.878611 -81 AGCTTAAATAATTTTGAGCAGCGTGTTCTGC 100 174 0 ATTTTGAGAG 0.60515 -127 TTTAGCAGAAATTTGGACTAGCTATGGCCGT 106 41 1 ATTTGGACAG 0.392695 -142 CCAGAAATTAAATTTGACTGGTTCCACTGGC 112 20 1 AATTTGACGG 0.929 -112 ACACTTTACGATTTTGGCCGGCCTGATGGGC 112 49 0 ATTTTGGCGG 0.726411 -83 TGCACTGACTAAATTGACAGGAAATAAGTTA 116 176 1 AAATTGACGG 0.663777 -26 TTTTAAGGAAAATTTGACCGG 119 60 1 AATTTGACGG 0.929 -11 ATCCGCCGTTAATTTGAGGGGATAAAGGTCA 120 226 0 AATTTGAGGG 0.878611 -75 ******** ** Masking position 4 Map Score: 6.52403 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 179 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 14 ATCTGTTTATACTTTGGCCCTTGTCAGCGGTAA 12 128 1 ACTTTGGCCG 0.705863 -124 GAGATCGGGCGGTTTAGCCGACGGAACTTTAGG 13 159 1 GGTTTAGCCG 0.858521 -40 TTACTATATCACGTTTGCCGGAGGGCTCCTTTC 25 82 0 ACGTTTGCCG 0.906273 -83 ATCATACTGTAGTTTAGCCTGAGTTGCCCCATA 29 69 0 AGTTTAGCCG 0.931459 -43 AAAGTCCTCTAGTATTGCCGGAGCTTTAGTGAG 32 176 1 AGTATTGCCG 0.54675 -125 ATCTGGCGGGGCTTTTGCCAGGGGCACCAAAGG 40 62 1 GCTTTTGCCG 0.850526 -100 GTTGGCCCAGTTTAGCCCCGGTTTGCTCTAT 59 9 1 AGTTTAGCCG 0.931459 -58 TTAAAGTAAAAGTTCAGCCTTAGGGATTAGTTA 62 235 0 AGTTCAGCCG 0.812617 -66 AAAAGCGCCAAAGTTTGCCCATGCCATGTATGC 63 53 1 AAGTTTGCCG 0.68863 -53 GGACTTTTGCCTGGGCATTAAGTAG 69 77 0 ACTTTTGCCG 0.927236 -15 GAAATTGAAGAAGTTAGCCTATGGCAAGTTGCG 75 267 0 AAGTTAGCCG 0.640622 -31 TCCAACAGCAGGGTTAGCCATGGTATAGTGGAA 80 48 1 GGGTTAGCCG 0.82157 -49 ATCAGAAGAGATTTTTGCCGCCGCTCAACATTT 83 277 1 ATTTTTGCCG 0.806816 -24 CCCTAGGAAAACTTTTGCCCTTGTTCAGTTATC 86 99 0 ACTTTTGCCG 0.927236 -49 ATTTTTGCATAGGTTAGCCACCGCTAAGCAAGC 92 98 1 AGGTTAGCCG 0.911596 -70 TTTCCCAATTGTTTTTGCCTTTGCCATTAGAGG 102 104 1 GTTTTTGCCG 0.650945 -163 ATCTCCCAAAACTTCTGCCAGGGAGGCTTTCCA 102 186 1 ACTTCTGCCG 0.802625 -81 CCAGACTTTAAGGTTAGCCATGGAAAGCCTCCC 102 206 0 AGGTTAGCCG 0.911596 -61 CCTCTCCGGTATTTCTGCCCTGGATACGGGGGG 123 68 1 ATTTCTGCCG 0.571321 -57 ********* * Masking position 7 Map Score: 10.276 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 367 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 15 TTTAACATATCCAACGGGCCAAGAAATGAC 3 47 0 CCAACGGGCC 0.948701 -51 GCTGGTTTTTCCGTCGGGCCTGGTTTAATC 23 36 0 CCGTCGGGCC 0.94534 -47 GACGGAAAAACCAGCGGGCCTTTTTTTGTT 23 51 1 CCAGCGGGCC 0.979301 -32 ATCACGTTTGCCGGAGGGCTCCTTTCCATC 25 78 0 CCGGAGGGCT 0.852123 -87 TAAAACTTTGCCGACAGGCCCTCGCGTTAT 27 78 1 CCGACAGGCC 0.864024 -94 GTCAATGTTGCCGGAGGGCCGCACAAGTTT 32 51 0 CCGGAGGGCC 0.958785 -250 CCGGTTTCCCCCAAAAGGCCGGCGGGGATC 54 124 0 CCAAAAGGCC 0.781294 -98 GGCCATTTTCCCATAAGGCTTTGACCTTTC 77 42 1 CCATAAGGCT 0.469465 -91 ATTTGAGGGGCCAGAGGGGCTTTTAAAACA 85 126 1 CCAGAGGGGC 0.743912 -70 AACCATCTATCCAGCGGGCTACAACTATTT 94 178 0 CCAGCGGGCT 0.921379 -92 TTCCACTGGCCCATCAGGCCGGCCAAAATC 112 41 1 CCATCAGGCC 0.871704 -91 ********** Masking position 2 Map Score: 5.75891 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 273 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234