AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00052_synecho_reg_300.orf -o00052_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: slr1078 33 galE; UDPglucose 4-epimerase. [EC:5.1.3.2] sll0744 21 hypothetical protein. Input sequences: #1 sll1196 112 pfkA; phosphofructokinase. [EC:2.7.1.11] #2 slr1298 149 hypothetical 84.3 kD protein slr1298. [SP:YC98_SYNY3] #3 sll1194 194 psbU; photosystem II 12 kD extrinsic protein precursor. #4 sll1193 300 putative deoxyribonuclease. [EC:3.1.21.4] #5 slr1067 300 galE; UDP-glucose 4-epimerase. [EC:5.1.3.2] #6 slr1079 255 hypothetical protein. #7 ssr1768 95 hypothetical protein. #8 slr1082 76 hypothetical protein. #9 slr1083 164 hypothetical protein. #10 slr1084 63 hypothetical protein. #11 slr1085 160 hypothetical protein. #12 ssl1972 270 hypothetical protein. #13 sll1024 169 hypothetical protein. #14 sll1022 146 hypothetical protein. #15 sll1021 39 hypothetical protein. #16 sll1020 95 hypothetical protein. #17 slr1090 44 GTP-binding protein. #18 ssr1789 79 hliA; high light inducible protein. #19 sll1019 60 gloB; probable hydroxyacylglutathione hydrolase (glyoxalase II). #20 sll1018 119 pyrC; dihydroorotase. [EC:3.5.2.3] #21 sll1017 241 putative ammonium transporter sll1017. [SP:YA17_SYNY3] #22 slr1400 119 regulatory components of sensory transduction system. #23 slr0670 117 hypothetical protein. #24 sll0656 130 nucH; extracellular nuclease. #25 sll0654 300 alkaline phosphatase. [EC:3.1.3.1] #26 sll1757 144 hypothetical protein. [EC:2.7.1.69] #27 ssr3188 159 hypothetical protein. #28 ssl3364 164 hypothetical protein. #29 slr1884 150 trpS; tryptophanyl-tRNA synthetase (tryptophan--tRNA ligase) #30 ssr3189 125 hypothetical protein. #31 slr1885 85 hypothetical protein. #32 slr1886 32 iojap protein. #33 sll1755 76 hypothetical protein. #34 slr1887 129 hemC; porphobilinogen deaminase (PBG) (hydroxymethylbilane synthase) #35 slr1888 265 hypothetical protein. #36 slr2132 57 pta; phosphotransacetylase. [EC:2.3.1.8] #37 sll2015 61 hypothetical protein. #38 sll2014 53 sfsA; sugar fermentation stimulation protein. #39 sll2013 159 hypothetical protein. #40 sll2012 300 rpoD; RNA polymerase sigma factor. #41 slr0862 87 lmbP; LmbP protein. [EC:2.7.1.6] #42 sll0844 113 probable tRNA (5-methylaminomethyl-2-thiouridylate)- #43 sll0842 61 nplT; neopullulanase. [EC:3.2.1.135] #44 slr0864 100 ABC transporter. #45 sll0838 46 pyrF; orotidine 5'-phosphate decarboxylase (OMP decarboxylase). #46 sll0837 107 hypothetical protein. #47 slr0867 248 hypothetical protein. #48 slr0868 300 hypothetical protein. #49 sll0244 73 galE; UDP-glucose 4-epimerase. [EC:5.1.3.2] #50 slr0269 90 hypothetical protein. [SP:Y269_SYNY3] #51 slr0270 216 hypothetical protein. [SP:Y270_SYNY3] #52 ssl0453 86 phycobilisome degradation protein nblA homolog 2. [SP:NBL2_SYNY3] #53 ssl0452 300 phycobilisome degradation protein nblA homolog 1. [SP:NBL1_SYNY3] #54 sll0593 206 glk; glucokinase. [EC:2.7.1.2] #55 slr0615 300 ABC transporter. #56 sll0745 111 pfkA; phosphofructokinase. [EC:2.7.1.11] #57 sll0742 73 hypothetical protein. #58 sll0741 300 nifJ; putative pyruvate-flavodoxin oxidoreductase. [EC:1.-.-.-] #59 slr1556 152 ddh; 2-hydroxyaciddehydrogenase. [EC:1.1.1.-] #60 sll1498 50 carA; carbamoyl-phosphate synthetase subunit A. [EC:6.3.5.5] #61 slr1557 99 hypothetical protein. #62 sll1496 146 mannose-1-phosphate guanyltransferase. [EC:2.7.7.-] #63 sll1495 154 hypothetical protein. #64 tRNA-Val 51 tRNA-Val. #65 slr1559 126 aroE; shikimate 5-dehydrogenase. [EC:1.1.1.25] #66 slr1560 77 hiss2; probable histidyl-tRNA synthetase 2 (histidine--tRNA ligase #67 slr1562 30 probable glutaredoxin slr1562. [SP:GLR1_SYNY3] #68 slr1563 300 hypothetical protein. #69 sll0726 300 pgm; phosphoglucomutase. [EC:5.4.2.2] Motif number 1 GGTCTGCCATCGCTGAATTTTTTT 4 287 0 TGCCATCGCT 0.661193 -14 TTAGCTAACCGGCGATCGCC 7 86 1 GGCGATCGCC 0.499997 -10 GAAAGGGTTGGGCGATCGCCTAT 8 64 1 GGCGATCGCC 0.499997 -13 CCATATGCGGGGCGATCGGGATGGATGGTG 13 96 0 GGCGATCGGG 0.92225 -74 CCGTTATTCCGGCGATCGCCTCCCGG 13 154 1 GGCGATCGCC 0.499997 -16 GGGGATCAACGGCGATCGCTACTGATAGGG 14 12 1 GGCGATCGCT 0.540589 -135 GCTGTCCGTTGGCGATCGCCAGCACCGATT 25 233 1 GGCGATCGCC 0.499997 -68 GGCCGCAACTGGCGATCGCCAGGATTTCCA 27 33 1 GGCGATCGCC 0.499997 -127 CATAAAAAACGGCGATCGGTGGGTTTCGGC 30 69 0 GGCGATCGGT 0.919889 -57 TAGCATCAGAGGCTATCGGCCTTGGTTTTC 33 52 1 GGCTATCGGC 0.914132 -25 CTCCTCCAGAGGCTATCGTCTGGGTTAAGA 40 48 0 GGCTATCGTC 0.73208 -253 CATTGACTGTGGCGATCGCCTTTTTTTGCT 47 88 1 GGCGATCGCC 0.499997 -161 AGCACCAACAGGCCAACGCCTGCAAGAAAG 47 170 0 GGCCAACGCC 0.906231 -79 TTTCCGCCAGGGCCAACGGGTACCCATTTC 47 225 0 GGCCAACGGG 0.689663 -24 TTTTCAGGAGTGCGATCGCC 52 77 1 TGCGATCGCC 0.529307 -10 CCTCCTCCTCGGCGATCGCCAAGCGAAATG 53 28 1 GGCGATCGCC 0.499997 -273 GGCGATCGCCAGGATCATTA 55 1 1 GGCGATCGCC 0.499997 -300 GAGGATTTGCGGCCAACGGCGGGAATTTGT 63 62 1 GGCCAACGGC 0.929757 -93 ********** Masking position 5 Map Score: 53.9629 Number of sites scoring better than the average of aligned sites = 6206 Number in coding regions = 5638 Number in noncoding regions = 568 Number of orfs with sites within 600 bp upstream = 362 Fraction of orfs with sites within 600 bp upstream = 0.0581433 Motif number 2 CTCAGTCAATCCAGGGAAGATGGTCAGCCG 3 56 1 CCAGGGAAGA 0.938446 -139 GCTACTAACTCCCTGGAAAAATAGGCGAGT 4 186 0 CCCTGGAAAA 0.869188 -115 GTGCTAGCATCTAGGGAAAAAAATTCAGCG 4 271 1 CTAGGGAAAA 0.786835 -30 AATTACGCCAGGTAAAAACTAACTTTT 10 47 0 CCAGGTAAAA 0.799855 -17 TTTACGTCTTCCATGGAAAAGGTATTTCAA 12 97 1 CCATGGAAAA 0.946798 -174 GGGATTTCCTGGGATAATTAACTTAGT 17 8 1 CCTGGGATAA 0.604316 -37 CAGCTTATTTCCCGGCAAAAAG 18 3 0 CCCGGCAAAA 0.697705 -77 AATTTGCCGGCCCGGGAAAAGCAGTACTCT 21 118 0 CCCGGGAAAA 0.962255 -124 TAAATCAACTCCCTGGAAAAGTGAAATTTT 21 213 0 CCCTGGAAAA 0.869188 -29 TTTGCTAACTCTAGGGAAAGTTGAAGTAAA 25 102 0 CTAGGGAAAG 0.680719 -199 GTTAACCCCAGGGAAGATATCCTTTAC 27 143 0 CCAGGGAAGA 0.938446 -17 GGGGCCACCACCGGGGATAGT 28 2 0 CCGGGGATAG 0.723043 -163 AGTTCTTGACCGGGGAAGATATGAGTGAA 34 10 1 CCGGGGAAGA 0.850575 -120 ACCAATAAACCCAGGGAACGCCATGTTAGT 40 242 0 CCAGGGAACG 0.858067 -59 CCGTCAGGGTCCATGGAAATAAACAGCTTT 41 64 1 CCATGGAAAT 0.534423 -24 GATCGACAGACCAGGGATAGATTCAGAATT 44 65 1 CCAGGGATAG 0.874879 -36 ATACGGCCAGGGTAAAAATTCTGAAT 44 85 0 CCAGGGTAAA 0.766098 -16 TGTGCCACTCCCATGGAAAAAACGCCCCGT 48 53 1 CCATGGAAAA 0.946798 -248 ACCTAGCAACCCAGGGAAAAAATAGGTTTT 53 159 0 CCAGGGAAAA 0.985566 -142 GAAAGGGTCACCAAGCAAAAAGCTAAAATT 54 126 0 CCAAGCAAAA 0.487167 -81 GTTTAGGTCACCGAGGAAAGGGTCACCAAG 54 141 0 CCGAGGAAAG 0.693519 -66 TACAATAGAGCCAGGGAAAAAATTACAGCT 55 107 1 CCAGGGAAAA 0.985566 -194 TTAATTAAGGCCGGGGAAAGAGATAGCCCA 58 101 0 CCGGGGAAAG 0.936408 -200 TTGCCCCACTCCTTGGAAAAATTACCAGCT 63 133 0 CCTTGGAAAA 0.691853 -22 TCCCGCAACCCCAAGGAACATTTCTCCGGT 65 62 1 CCAAGGAACA 0.616628 -65 ATTCTGCCCACCAAGGAAAACCGGAGAAAT 65 81 0 CCAAGGAAAA 0.912989 -46 GTTGCAGTTCCCAGGTAAAATTTCCAGTTC 66 29 0 CCAGGTAAAA 0.799855 -49 ATCTCTTTGCCCATGGATAGCCCTTGGCTA 69 255 1 CCATGGATAG 0.645688 -46 ********** Masking position 5 Map Score: 33.9245 Number of sites scoring better than the average of aligned sites = 1224 Number in coding regions = 1096 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 149 Fraction of orfs with sites within 600 bp upstream = 0.0239319 Motif number 3 GCCGATTTTGGGAGGTCAAACCAGCGCTAAT 3 113 0 GGGGTCAAAC 0.939197 -82 ATTGAGTCAGGGGGGACAAAATAGCCAGAGC 4 102 0 GGGGACAAAA 0.848041 -199 GGTTTGAAGGAGCGGTCAAAAAATGCATTAT 6 11 1 AGGGTCAAAA 0.593622 -245 CTCTCCGACCATTGGCCAAACTGAAACCATG 9 144 0 ATGGCCAAAC 0.426736 -21 TCAATGCAATTTTGGTCAAAATGTTGGTCAG 11 43 1 TTGGTCAAAA 0.415181 -118 GCTACTGATAGGGGGGTAGACCCCCATCACC 14 29 1 GGGGGTAGAC 0.629157 -118 GTGTGCCTCCGGAGGATAAAAGTTGTAGTTG 15 18 0 GGGGATAAAA 0.473568 -22 TTAAAATACTTGCAGGCAAACACTGAGATTA 19 24 1 TGAGGCAAAC 0.641949 -37 TCCTAGCAAAGTTGGGCAACCTTTCCGGATT 20 51 0 GTGGGCAACC 0.744999 -69 GCCGGCAAATTGTGGACAAACAGTAACAAAA 21 137 1 TGGGACAAAC 0.804773 -105 GGATATTACTTGTGGGAAAACTAGGAGC 23 8 0 TGGGGAAAAC 0.856292 -110 TGTCAGTTAATGTGGGCAAAACGGAAAACTC 24 68 0 TGGGGCAAAA 0.955393 -63 TCAGGAAAAAGTGGGGCAAAACCTTCAATCG 25 258 0 GTGGGCAAAA 0.902607 -43 GGGCTGATGGGGCAAACCCAATGGCCG 27 7 1 ATGGGCAAAC 0.722917 -153 GACAATCGTAGGCGGTTAAACTTT 28 151 1 GGGGTTAAAC 0.713461 -14 CGCTCCTAAGGGTGGCTAAAACTTTGCATAA 30 94 0 GGGGCTAAAA 0.697096 -32 CTGGCCTTGATGGGGGAAACAGCTTCACTCA 34 32 0 TGGGGAAACA 0.38835 -98 GGAATATCGCTGTGGGAAAAATCGAGATCAT 35 56 0 TGGGGAAAAA 0.775458 -210 TTTGGAGGGCAAAATCAAGGTAAT 36 4 1 GGGGGCAAAA 0.980407 -54 GGAATAGGGCTGGGGGGAAACTGAGCTTCCA 43 12 1 TGGGGGAAAC 0.685408 -50 GCACAGGCAGGCAAAAAAATTAGCTT 52 6 1 GGAGGCAAAA 0.708199 -81 GAAAAAATGGGGCGGTCAAAAATTGTAACTA 52 51 0 GGGGTCAAAA 0.899524 -36 CCGAGGAGGAGGAGGCTAAACTGTTCGTC 53 9 0 GGGGCTAAAC 0.798821 -292 TGCCCAAAACGGGGGGCAAACCTAGCAACCC 53 177 0 GGGGGCAAAC 0.988549 -124 TAGTCGCCTTGGAGGGCAACAGCT 53 287 1 GGGGGCAACA 0.901954 -14 AATCGGCATTAGGGGGCAAACGTTAATCGGT 57 11 1 AGGGGCAAAC 0.933716 -63 CGGGCAAATATGAGGCAAAACGG 57 61 1 TGGGCAAAAC 0.629644 -13 GCCTAGTCCTTTGGGCCAAACGCCTGTAGCA 61 23 1 TTGGCCAAAC 0.661407 -77 TTTCCAAGGAGTGGGGCAAAA 63 144 1 GTGGGCAAAA 0.902607 -11 TCCTTGGGGTTGCGGGAAAACATTATATTGA 65 48 0 TGGGGAAAAC 0.856292 -79 GGTTTTCCTTGGTGGGCAGAATTATCCAAAA 65 89 1 GGGGGCAGAA 0.859138 -38 ** ******** Masking position 8 Map Score: 25.8586 Number of sites scoring better than the average of aligned sites = 1594 Number in coding regions = 1431 Number in noncoding regions = 163 Number of orfs with sites within 600 bp upstream = 175 Fraction of orfs with sites within 600 bp upstream = 0.0281079 Motif number 4 AACAACAAAAAACCACCCCAAACAAGGCAAAGT 2 103 0 ACACCCCAAC 0.809014 -47 GCTGACCTCAACTTGCCCCATACGGCCCTGGGG 28 29 0 ATGCCCCATC 0.833229 -136 AAAATTTACTACTAGCCCCAGTCTCCAAAAACC 30 18 1 ATGCCCCAGC 0.986988 -108 CCCAGTCTCCAAAAACCCCAGACAACAAACGGC 30 34 1 AAACCCCAGC 0.864981 -92 TAGATCCCACACTGATCCCTGCCTAG 32 4 0 ATATCCCTGC 0.913624 -29 TTATTAGTGGATTGATCCCAGTCATTCCCCATC 40 125 1 ATATCCCAGC 0.939781 -176 GTCCGTTTCCAGTTGTCCCAAACGCCCCCATCG 40 162 1 ATGTCCCAAC 0.765952 -139 TCCGTCATTTACCTAGCCCAGTCCGTCTCGAAT 40 206 1 ACAGCCCAGC 0.845447 -95 TGCTTTAACAAATAGGCCCTAACCCAGCTTAAC 42 56 0 ATGGCCCTAC 0.647744 -58 TATTTGTTAAAGCAACCCCTGTCAATTTGGAGC 42 75 1 ACACCCCTGC 0.945209 -39 TTAGCGCTCCATTAACCCCCGGCAGTATCCCCA 58 198 1 ATACCCCCGC 0.926224 -103 ATTAGCAGATTCGCCCCTGTCGTCTGTTCCA 60 30 0 ATGCCCCTGC 0.98092 -21 GATTTAAATAATTGACCCCAGTCTT 62 3 0 ATACCCCAGC 0.98366 -144 GAATGTTTAAACTTGCCCCTGCCGAAACAAAGC 65 15 0 ATGCCCCTGC 0.98092 -112 GTATTATTTGTCCCTGTCCTGTTTTCCC 67 13 0 ATGTCCCTGC 0.930206 -18 AAATTGCCAAAGTTACCCCAGGCCATACACGGC 69 185 0 ATACCCCAGC 0.98366 -116 * * ******* * Masking position 1 Map Score: 19.1416 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 325 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 ATAGGCGAGTGTCCCTGGCGGTTGGTTTTGC 4 165 0 GTCCCTGGGG 0.963975 -136 TGCCCCATACGGCCCTGGGGGCCACCACCGG 28 18 0 GGCCCTGGGG 0.996498 -147 GGAAATATTCGGCCGTGGAGGCGCATCCCAA 29 89 1 GGCCGTGGGG 0.993705 -62 GAGATAATCTGGCCTTGATGGGGGAAACAGC 34 40 0 GGCCTTGAGG 0.939269 -90 TATTTCCATGGACCCTGACGGTCAAGCAAGG 41 54 0 GACCCTGAGG 0.879082 -34 TAGGGCCCAACACCTTGGTGGT 46 2 0 CACCTTGGGG 0.917786 -106 TGTTTTGAGCCGTCGTGGGGGAACGTTACAG 46 80 0 CGTCGTGGGG 0.890797 -28 GGTACCCGTTGGCCCTGGCGGAAATGAG 47 231 1 GGCCCTGGGG 0.996742 -18 GCTTGGCGATCGCCGAGGAGGAGGAGGCTAA 53 21 0 CGCCGAGGGG 0.96223 -280 GAAAGGTAGTCGCCTTGGAGGGCAACAGCT 53 281 1 CGCCTTGGGG 0.986371 -20 AATTTCCTCTGGCCCAGGTGGAGGAACTGCT 54 61 1 GGCCCAGGGG 0.98562 -146 TGTACAATGCCGCCCTGTGGGAGATGATCAC 63 90 0 CGCCCTGTGG 0.950545 -65 ******** ** Masking position 4 Map Score: 17.8346 Number of sites scoring better than the average of aligned sites = 774 Number in coding regions = 742 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 6 ATTATTGACTTCCCCAATTCCATAAATATCCA 2 60 1 TCCCCAATCA 0.878109 -90 TGGTTTGACCTCCCAAAATCGGCGCAGTCGGC 3 121 1 TCCCAAAACG 0.894492 -74 GCCCTCTGAATCCCAAAAGCTGATTGTGCTAG 4 246 1 TCCCAAAACG 0.894492 -55 CGCAGCATTCTCCCAAATTCTAAATAAATTCC 9 57 0 TCCCAAATCA 0.772823 -108 CTCAGTTGGTTACCAAAAACAAAGGAGCAAGA 9 93 1 TACCAAAACA 0.61301 -72 CTGATAGCTCTGCCTAAATCAGCTTATTTCCC 18 20 0 TGCCTAAACG 0.848065 -60 ATAGGAGGCACCCCCAAAGCTGAAATTGCGCC 26 121 1 CCCCCAAACG 0.895584 -24 TGGTTCCTTCTACCCAAAGCCAACCAAATTCG 28 91 1 TACCCAAACA 0.770354 -74 CACGTCCGGATGCCAAATCCAGCCTCCGCTTA 34 96 1 TGCCAAATCG 0.758719 -34 TCCACTGAAATCCCTAATCCAAG 40 288 1 TCCCTAATCA 0.741116 -13 TCTCCCAGCTTACCCAAAGCAAAACCTAATCA 46 48 0 TACCCAAACA 0.770354 -60 TAATTTGGTCCGCCAAAACCGAAATGGGTACC 47 205 1 CGCCAAAACA 0.728409 -44 CCTTGCTTGATGCCTAAACCTAGAGTTGTG 51 9 0 TGCCTAAACA 0.825308 -208 TATACAAGCTTGCCCAAAACGGGGGGCAAACC 53 186 0 TGCCCAAACG 0.93354 -115 GGCCCCAAAGCCATTGAAAAACT 54 194 0 GCCCCAAACA 0.673392 -13 CTATCGCCAATCCCTAATCCGGCGGTTTA 56 8 0 TCCCTAATCG 0.771808 -104 TAACGTTTGCCCCCTAATGCCGATT 57 4 0 CCCCTAATCG 0.61771 -70 TGATTAGAGTCGCCCAAACCTAAAACC 68 6 0 CGCCCAAACA 0.850292 -295 GAGAGGATGATGCCCAAACCTAAACAAAGCTT 68 144 0 TGCCCAAACA 0.922414 -157 ******** * * Masking position 6 Map Score: 15.692 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 492 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 TTGTCCTCAATCCTTAACCTACTTTTAACT 1 12 0 TCCTTAACCT 0.864587 -101 ACTGCCCCGGTCCTTGACCACTTTCCTTTA 7 27 0 TCCTTGACCA 0.777137 -69 GCCAATCGTTTGCTTTACCCTG 11 3 0 TGCTTTACCC 0.887364 -158 TGGGAACTGGTGCTTTCCCCCCTTCTTGGC 12 183 1 TGCTTTCCCC 0.647722 -88 TAGTTTACAATTCTTTACCTT 17 34 1 TTCTTTACCT 0.822107 -11 TTAGCAAATTTGCTTAACCTTTTCATAGTC 25 124 1 TGCTTAACCT 0.881179 -177 CAAGTGATCGTCCTTCACCGATGGGGAATT 25 201 1 TCCTTCACCG 0.702928 -100 AGGGAAGATATCCTTTACCACCATCCCTTA 27 131 0 TCCTTTACCA 0.750638 -29 AGTTCTTGACCGGGGAAGATAT 34 3 1 TTCTTGACCG 0.814952 -127 TTTTATTGCCTTCTTAACCCAGACGATAGC 40 37 1 TTCTTAACCC 0.63053 -264 TTCCTGCCCTTGCTTGACCGTCAGGGTCCA 41 47 1 TGCTTGACCG 0.922999 -41 GGCCTGTTGGTGCTTTACCTAATTTGGTCC 47 186 1 TGCTTTACCT 0.926354 -63 TTCTTAACCTTGCTTGACCTTAGCTTTTT 49 10 0 TGCTTGACCT 0.935778 -64 GAGCATACCATTCTTAACCTTGCTTGACCT 49 20 0 TTCTTAACCT 0.731526 -54 CTGACCACCTTGCTTGACCGGCCAGAGAGC 51 74 1 TGCTTGACCG 0.922999 -143 TCCTTTACCTCAGTGACGAA 62 137 0 TCCTTTACCT 0.915462 -10 GTTGTCTTTGTCCTTTCCCTTCAGCA 66 62 1 TCCTTTCCCT 0.716502 -16 ********** Masking position 5 Map Score: 13.7638 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 144 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 AAGTAGGTTAAGGATTGAGGACAATTTTAAG 1 18 1 AGGATGAGGA 0.732448 -95 TTAGGGAATATGGACGGAGGAAACCATCGAC 4 65 0 TGGACGAGGA 0.759716 -236 AAAGTGGTCAAGGACCGGGGCAGTAGGGCCA 7 33 1 AGGACGGGGC 0.913773 -63 TTTTTTGCCAAGAAGGGGGGAAAGCACCAGT 12 188 0 AGAAGGGGGA 0.922228 -83 TTATATCATTTGGAGAGAGGCTATTCGGAAA 16 59 0 TGGAGGAGGC 0.899928 -37 GGTACACTGAAAAAGAGGGGAATGAATCCTC 21 45 0 AAAAGGGGGA 0.688232 -197 CTGCAAAATTAGGAGTGGGGATATTACTTGT 23 26 0 AGGAGGGGGA 0.984544 -92 CTAATTTTGCAGAGGTGGGGATTTTTTCGTA 23 45 1 AGAGGGGGGA 0.898768 -73 TATGAAAAACTGGAGCGGGGCCAAGTGATCG 25 180 1 TGGAGGGGGC 0.957375 -121 TCAATCAGGAAAAAGTGGGGCAAAACCTTCA 25 262 0 AAAAGGGGGC 0.602941 -39 CTTTTATTCCAGGGGTGAGGTTTGCTGAAAA 39 124 0 AGGGGGAGGT 0.67019 -36 GTTCAGGTTATGGTGCGAGGATGTGTTAGTT 44 24 0 TGGTGGAGGA 0.727529 -77 AAAGGAAAGAGAGAGGAAAGCAATAAA 51 200 0 AAGAGGAGGA 0.826021 -17 ATTTGCCCGATGGGTAGGGGAACAAATAACC 57 39 0 TGGGTGGGGA 0.724066 -35 ATTCTTAATTAAGGCCGGGGAAAGAGATAGC 58 104 0 AAGGCGGGGA 0.682259 -197 TGACTATGACTGGTGGGGGGACGATCTCCCT 62 78 0 TGGTGGGGGA 0.869602 -69 AATTTTTCCAAGGAGTGGGGCAAAA 63 140 1 AGGAGGGGGC 0.977687 -15 CAGCCAGAGCAGGGGAGAGGATGATGCCCAA 68 159 0 AGGGGGAGGA 0.950237 -142 ***** ***** Masking position 7 Map Score: 14.2609 Number of sites scoring better than the average of aligned sites = 965 Number in coding regions = 856 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 9 GCACGGCTGACCATCTTCCCTGGATTGACTG 3 58 0 CCATCTCCCT 0.899058 -137 TTTCCTCCGTCCATATTCCCTAATGCCTAGC 4 73 1 CCATATCCCT 0.903346 -228 ACCCCCATCACCAAAGCCCCCAATAATGAGG 14 48 1 CCAAACCCCC 0.923485 -99 TCCAGTCATACCATCTTCCCTCATTATTGGG 14 66 0 CCATCTCCCT 0.899058 -81 CTGCAGGCCTCCACCTTCCCCT 14 135 1 CCACCTCCCC 0.892698 -12 AACGACGGCACAAAAATCCCCCTAAAATCCT 20 78 0 CAAAATCCCC 0.892945 -42 ACGATTAGAGCCATACTCCCTGGCAAGCATT 24 19 1 CCATATCCCT 0.903346 -112 GGGCAAAACGGAAAACTCCCTGGTTATTAAG 24 55 0 GAAAATCCCT 0.527206 -76 CAACGGACAGCAAAATTCCCCATCGGTGAAG 25 213 0 CAAAATCCCC 0.892945 -88 ATATCCTTTACCACCATCCCTTAAACAAAAC 27 123 0 CCACCTCCCT 0.897226 -37 ATTTCCTGTGCAAACTTCCCTTAGCACGACG 29 64 0 CAAACTCCCT 0.892945 -87 GCCCCAGTCTCCAAAAACCCCAGACAACAAA 30 32 1 CCAAAACCCC 0.65122 -94 TTTCCCACAGCGATATTCCCTAAAAAGTTAA 35 68 1 CGATATCCCT 0.667626 -198 ATAAAAAACGCAAAAATCCCCCATAAAGCTT 40 12 0 CAAAATCCCC 0.892945 -289 CCAGTTGTCCCAAACGCCCCCATCGGACAGG 40 170 1 CAAACCCCCC 0.834902 -131 TATCGAAAATCAACAACCCCTACTCCTCACA 51 135 1 CAACACCCCT 0.719303 -82 ACCAAACCCCCTTAATTTATCC 56 100 0 CCAAACCCCT 0.92682 -12 ACTTGTTCCCCGAAAATCCCTTTGTGGTTAA 63 14 1 CGAAATCCCT 0.810546 -141 ATTGTGTTAAGCAACTCCCCTGAACGTTAAC 69 75 1 GCAACCCCCT 0.60593 -226 ***** ***** Masking position 3 Map Score: 19.2846 Number of sites scoring better than the average of aligned sites = 852 Number in coding regions = 742 Number in noncoding regions = 110 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 10 GAAAAAGTATTTTTGTTGCTTAATCTTATGCT 5 100 1 TTTTTTGCTA 0.648055 -201 CTATGGCAAGTTTTCTGGCCCTACTGCCCCGG 7 47 0 TTTTTGGCCT 0.951622 -49 CCATGGCAAGTTTTCTGGCCGTATTCTTGCTC 9 117 0 TTTTTGGCCT 0.951622 -48 TACCTTAGGATTTTATGGCTAACTAAAATAAA 12 47 1 TTTTTGGCTA 0.676914 -224 TAGGTTATAGTTTTTTTGCCAAGAAGGGGGGA 12 198 0 TTTTTTGCCA 0.873368 -73 TTTAGGGGGATTTTTGTGCCGTCGTTCCCCCG 20 83 1 TTTTGTGCCT 0.672985 -37 TAGCGGTTTATTTTCTGGCTAAAAGCGCTATC 35 140 0 TTTTTGGCTA 0.676914 -126 GATTATACGGTTTTTAGGCCATTGATCCCGTC 39 47 0 TTTTAGGCCT 0.61239 -113 TTTTTGCGTTTTTTATTGCCTTCTTAACCCAG 40 27 1 TTTTTTGCCT 0.945318 -274 TCCATGATACTTTTCCTGCCCTTGCTTGACCG 41 35 1 TTTTCTGCCT 0.672985 -53 TTCATGCTCATTTTCTGGCGGTAGTTTTTCTA 42 23 1 TTTTTGGCGT 0.77944 -91 GGCGATCGCCTTTTTTTGCTGTAGCCTAAGCA 47 98 1 TTTTTTGCTT 0.821922 -151 TGTCATTCGTTTTTATTGCTTTCCTCTCTCTT 51 189 1 TTTTTTGCTT 0.821922 -28 AGCAAGCTAATTTTTTTGCCTGCCTGTGC 52 8 0 TTTTTTGCCG 0.716056 -79 CTCGACTAAGTTTTTTGGGCTATCTCTTTCCC 58 86 1 TTTTTGGGCA 0.499943 -215 GTTGTTTAATTTTTCTTGGCATTAGTGTTATT 58 154 1 TTTTTTGGCT 0.687739 -147 TTTTCAACAATTTTTTAGCGCTCCATTAACCC 58 184 1 TTTTTAGCGT 0.410334 -117 TATTTCTGGCTTTTGTTGCCATTGCAGAAACC 58 261 1 TTTTTTGCCT 0.945318 -40 TAACGTTAAATTTTTTAGCCTTTTATTACCAG 59 102 0 TTTTTAGCCT 0.794804 -51 **** ***** * Masking position 4 Map Score: 12.0439 Number of sites scoring better than the average of aligned sites = 427 Number in coding regions = 361 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 AACTTTGCCTTGTTTGGGGTGGTTTTTTGT 2 102 1 TGTTTGGGGT 0.85502 -48 AACAGCATTGAGTCAGGGGGGACAAAATAG 4 109 0 AGTCAGGGGG 0.706361 -192 GACTCAATGCTGTTGGGGGGTTCACCTATG 4 125 1 TGTTGGGGGG 0.945607 -176 TTTTTTGCCAAGAAGGGGGGAAAGCACCAG 12 189 0 AGAAGGGGGG 0.620946 -82 ACTATAACCTAGATAGGGAGAGTCGCAAGA 12 219 1 AGATAGGGAG 0.541512 -52 TGTTTATCTAAGTTGGGGGAGAGCAAATTT 13 40 1 AGTTGGGGGA 0.765084 -130 CGATCGCTACTGATAGGGGGGTAGACCCCC 14 24 1 TGATAGGGGG 0.859821 -123 GGGGCTTTGGTGATGGGGGTCTACCCCCCT 14 38 0 TGATGGGGGT 0.948067 -109 GTTAGGATGAAGTTTGGGATGCGCCTCCAC 29 103 0 AGTTTGGGAT 0.531747 -48 CGCCGTTTGTTGTCTGGGGTTTTTGGAGAC 30 38 0 TGTCTGGGGT 0.806286 -88 AATCTGGCCTTGATGGGGGAAACAGCTTCA 34 36 0 TGATGGGGGA 0.854247 -94 TGATGGGGAATGACTGGGATCAATCCACTA 40 129 0 TGACTGGGAT 0.590549 -172 AACGGACGATTGATGGGGAATGACTGGGAT 40 139 0 TGATGGGGAA 0.598749 -162 CGCTCCAAATTGACAGGGGTTGCTTTAACA 42 79 0 TGACAGGGGT 0.769587 -35 GATTGGCGATAGATTGGGGTTCGATTTTGA 56 28 1 AGATTGGGGT 0.858567 -84 TTGGGGATACTGCCGGGGGTTAATGGAGCG 58 202 0 TGCCGGGGGT 0.688649 -99 GTTTGTTAACAGTTGGGGATACTGCCGGGG 58 214 0 AGTTGGGGAT 0.720888 -87 TGTTTGGGGGTTGCCTAGTC 61 1 1 TGTTTGGGGG 0.884309 -99 AAGACTGGGGTCAATTATTTA 62 2 1 AGACTGGGGT 0.810761 -145 TGACTATGACTGGTGGGGGGACGATCTCCC 62 79 0 TGGTGGGGGG 0.802443 -68 CCCAGCGCCAAGATGGGGAGCACAAATTCA 69 156 0 AGATGGGGAG 0.820015 -145 ********** Masking position 6 Map Score: 13.3128 Number of sites scoring better than the average of aligned sites = 1534 Number in coding regions = 1343 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 12 TGGTGTTCAACCCTTTGACGGTGAGATTTTAG 4 14 1 CCCTTTGGGT 0.926651 -287 TGACTAGTCCCCCGTTGCCTGTGAAATAACC 8 10 0 CCCGTTGTGT 0.952122 -67 CTAAATAAATTCCGTTGTTTTTGCTGTCGAAC 9 38 0 TCCGTTGTTT 0.690376 -127 TTCACCACTTCCCGTTTACGGTTCCCCT 12 253 1 CCCGTTTGGT 0.966317 -18 AATTTTGCTGTCCGTTGGCGATCGCCAGCACC 25 227 1 TCCGTTGGAT 0.734255 -74 ACCGCATATTCCCGTTGTGGTTCCTTCTACCC 28 74 1 CCCGTTGGTT 0.978361 -91 CACTGCTGAGTCCGTTTGCGGTCGTCGTGCTA 29 42 1 TCCGTTTGGT 0.876728 -109 GTTTCGGCCCGCCGTTTGTTGTCTGGGGTTTT 30 45 0 GCCGTTTTGT 0.604512 -81 AGGTTTGCCCCCCGTTTTGGGCAAGCTTGTAT 53 185 1 CCCGTTTGGC 0.819122 -116 CTAAGCCGTTGAAGTTAAAACTTTCG 61 84 0 GCCGTTGGTT 0.923606 -16 CCCCGAAAATCCCTTTGTGGTTAAAGGAAAAA 63 21 1 CCCTTTGGTT 0.851204 -134 CAAAGACAACCCCGTTGCAGTTCCCAGGTAAA 66 40 0 CCCGTTGGTT 0.978361 -38 GCCATATCTTCCCGTTGCTGGTAATTCCAACG 68 203 0 CCCGTTGGGT 0.990088 -98 ******* *** Masking position 6 Map Score: 9.72572 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 313 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 13 CAGAACTATATCGGCAAGGAAAACC 1 98 1 TGGCAAGGAA 0.556955 -15 CTCGCCTATTTTTCCAGGGAGTTAGTAGCAGA 4 187 1 TTCCAGGGAT 0.715262 -114 GGCGGTTTAGTGCCCTGGGAACTGGTGCTTTC 12 168 1 TCCCTGGGAC 0.661444 -103 AAATTTCACTTTTCCAGGGAGTTGATTTAGTA 21 214 1 TTCCAGGGAT 0.715262 -28 AGGTCAATCTTGACCAAGGGCCAATGGGTTTA 22 79 0 TACCAAGGGC 0.715504 -41 CTAAAAATGCTTGCCAGGGAGTATGGCTCTAA 24 23 0 TGCCAGGGAT 0.952048 -108 TTTAGCTTAATAACCAGGGAGTTTTCCGTTTT 24 50 1 TACCAGGGAT 0.88826 -81 GCAGTGACAATTACCTGGGGGTTGTTACTGCT 27 83 1 TACCTGGGGT 0.864849 -77 AAAGGATATCTTCCCTGGGGTTAAC 27 145 1 TCCCTGGGGT 0.819778 -15 GCACAATATTCCCAGGGGTTCTAGCTACAC 31 66 0 TCCCAGGGGT 0.893544 -20 CTAGGCAGGGATCAGTGTGGGAT 32 2 1 TGGCAGGGAC 0.856711 -31 GCGCTCCAAATTGACAGGGGTTGCTTTAACAA 42 78 0 TGACAGGGGT 0.608834 -36 TTGCTTTGGGTAAGCTGGGAGACTGTAACGTT 46 58 1 TAGCTGGGAA 0.448971 -50 CATTATTCCTTTGGCAAGGGGCGGTAGTAATG 48 187 1 TGGCAAGGGC 0.748319 -114 GTGGTTTGTTTTAGCAAGGGCTTTTAGAAAAA 53 85 0 TAGCAAGGGT 0.651712 -216 GATCTCCCTGTGGCCAAGGAATCCTCCGTTCC 62 55 0 TGCCAAGGAT 0.869401 -92 CGGCTTTGTTTCGGCAGGGGCAAGTTTAAACA 65 13 1 TGGCAGGGGA 0.847574 -114 ACTGGAAATTTTACCTGGGAACTGCAACGGGG 66 31 1 TACCTGGGAC 0.732981 -47 TTCATTAGCATTGCCTAGGGCATCGGTTGGCA 68 109 0 TGCCTAGGGA 0.674451 -192 GGGCCGTGTATGGCCTGGGGTAACTTTGGCAA 69 183 1 TGCCTGGGGA 0.864099 -118 TTTTTCTCTATGACCAGGGATTTGGAGACTTT 69 216 1 TACCAGGGAT 0.88826 -85 AAGGGTTAACTAGCCAAGGGCTATCCATGGGC 69 263 0 TGCCAAGGGT 0.908028 -38 TTAACCCTTTTTGGCTAGGATTTGG 69 286 1 TGGCTAGGAT 0.631043 -15 * ******** * Masking position 1 Map Score: 17.4242 Number of sites scoring better than the average of aligned sites = 2055 Number in coding regions = 1839 Number in noncoding regions = 216 Number of orfs with sites within 600 bp upstream = 236 Fraction of orfs with sites within 600 bp upstream = 0.0379056 Motif number 14 CCCCAAACAAGGCAAAGTTCAGAGCGGTGTGG 2 89 0 GGCAAAGTTG 0.935992 -61 CTGCTGCGTTGGCAAGGTTCCGTTATTCCGGC 13 135 1 GGCAAGGTTG 0.973349 -35 ACCAGGACTCAGCAAGGTTTAGTTCCAGTCAT 14 88 0 AGCAAGGTTG 0.935992 -59 AGGGGAAGGTGGAGGCCTGCAGAG 14 133 0 GGGAAGGTGG 0.674722 -14 CTAAAATCCTAGCAAAGTTGGGCAACCTTTCC 20 56 0 AGCAAAGTTG 0.854118 -64 TTCCCGGGCCGGCAAATTGTGGACAAACAGTA 21 130 1 GGCAAATTGG 0.690727 -112 AAACAAAACCAGCAAAGAGCAGTAACAACCCC 27 100 0 AGCAAAGAGG 0.674481 -60 GGCCGTATGGGGCAAGTTGAGGTCAGCAAAGT 28 35 1 GGCAAGTTGG 0.84798 -130 AGTTGAGGTCAGCAAAGTGAGGAAAACCGCAT 28 49 1 AGCAAAGTGG 0.82769 -116 CTAGGCAGGGATCAGTGTGGGATCT 32 4 1 GGCAGGGATG 0.842662 -29 TTCTAGGTTAAGCTGGGTTAGGGCCTATTTGT 42 50 1 AGCTGGGTTG 0.413172 -64 GGCAAAGTTGAGGAGTTATGGC 45 35 0 GGCAAAGTTG 0.935992 -12 CACGAACGACGGCAGGGATGGGAATACGGGGC 48 76 0 GGCAGGGATG 0.842662 -225 TTATTCCTTTGGCAAGGGGCGGTAGTAATGAC 48 189 1 GGCAAGGGGG 0.825359 -112 GCTAAGGTCAAGCAAGGTTAAGAATGGTATGC 49 16 1 AGCAAGGTTG 0.935992 -58 CTCCCGTTTCAGCAAGTTTTAGCAACTTTAGG 54 94 0 AGCAAGTTTG 0.731344 -113 CTACCCATCGGGCAAATATGAGGCAAAACGG 57 53 1 GGCAAATATG 0.540071 -21 AACCCTTTTTGGCTAGGATTTGG 69 288 1 GGCTAGGATG 0.690525 -13 ********* * Masking position 2 Map Score: 13.9406 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 463 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 15 ATGGTGGCTGAAAAAGCTCAAGAATTTGCT 13 72 0 AAAAAGCTCA 0.769033 -98 CAAGTATTTTAAAAAGCTGACCAAA 19 6 0 AAAAAGCTGA 0.859701 -55 CCCCGAGGTTAAAAGGTTAA 20 110 1 AAAAGGTTAA 0.766316 -10 ACGGGGAACGAAAAAGCTAAGCTCAAGGGC 25 59 0 AAAAAGCTAA 0.93443 -242 TTAGACTATGAAAAGGTTAAGCAAATTTGC 25 127 0 AAAAGGTTAA 0.766316 -174 GATATTCCCTAAAAAGTTAAGTATCAACTA 35 79 1 AAAAAGTTAA 0.839635 -187 AGAAAAGCTAACTTTCATTAC 39 2 1 GAAAAGCTAA 0.728536 -158 AAAAAGCTAAGGTCAAGCAA 49 1 1 AAAAAGCTAA 0.93443 -73 TAAATGTAACAAAAAGTTGACCCAATTAAC 53 228 0 AAAAAGTTGA 0.692431 -73 GTCACCAAGCAAAAAGCTAAAATTCTCCCG 54 120 0 AAAAAGCTAA 0.93443 -87 ATCTGGTAATAAAAGGCTAAAAAATTTAAC 59 100 1 AAAAGGCTAA 0.899251 -53 ********** Masking position 4 Map Score: 6.99604 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 81 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295