AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00400_synecho_reg_100.orf -o00400_synecho_100.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 Input sequences: #1 slr0738 89 trpE; probable anthranilate synthase component I. [EC:4.1.3.27] #2 slr0739 80 crtE; geranylgeranyl pyrophosphate synthase. [EC:2.5.1.29] #3 sll0696 76 hypothetical protein. #4 slr0741 86 phoU; a negative regulator of pho regulon. #5 slr0742 75 hypothetical protein. #6 slr0743 300 nusA; N utilization substance protein. #7 sll1669 191 aroK; shikimate kinase (SK). [EC:2.7.1.71] [SP:AROK_SYNY3] #8 sll1662 61 pheA; chorismate mutase. [EC:5.4.99.5] #9 tRNA-Thr-1 97 tRNA-Thr. #10 slr1798 300 pleD; PleD. #11 slr0966 155 trpA; tryptophan synthase alpha chain. [EC:4.2.1.20] [SP:TRPA_SYNY3] #12 sll0938 40 aspartate transaminase. [EC:2.6.1.1] #13 ssl1792 33 hypothetical protein. #14 sll0936 83 hypothetical protein. #15 slr0969 102 cbiH; precorrin methylase. #16 sll0934 195 ccmA; carboxysome formation protein. [EC:5.4.99.5] #17 slr1031 187 tyrS; tyrosyl-tRNA synthetase (tyrosine--tRNA ligase) (tyrRS). #18 ssr1720 153 tyrS; tyrosyl tRNA synthetase. [EC:6.1.1.1] #19 sll1112 300 aroQ; carbonic 3-dehydroquinase. [EC:4.2.1.10] #20 sll1747 206 aroC; chorismate synthase (5-enolpyruvylshikimate-3-phosphate #21 sll1713 61 hisC; histidinol-phosphate aminotransferase. [EC:2.6.1.9] #22 sll1712 170 DNA binding protein HU. [SP:DBH_SYNY3] #23 slr1867 26 trpD; anthranilate phosphoribosyltransferase. [EC:2.4.2.18] #24 sll1776 51 deoC; deoxyribose-phosphate aldolase. [EC:4.1.2.4] #25 sll1775 300 hypothetical protein. #26 sll1958 138 hisC; histidinol phosphate aminotransferase. [EC:2.6.1.9] #27 slr2081 133 tyrA; prephenate dehydrogenase. [EC:1.3.1.12] #28 slr2130 137 aroB; 3-dehydroquinate synthase. [EC:4.6.1.3] #29 slr1980 61 hypothetical protein. #30 sll1876 260 hemN; oxygen independent coprophorphyrinogen III oxidase. #31 sll1553 283 pheT; phenylalanyl-tRNA synthetase beta chain (phenylalanine--tRNA #32 sll0424 80 hypothetical protein. #33 sll0423 221 hypothetical protein. #34 sll0356 100 trpF; N-(5'-phosphoribosyl)anthranilate isomerase (PRAI). #35 sll0006 103 aspC; aspartate aminotransferase. [EC:2.6.1.1] #36 sll0402 122 aspC; aspartate aminotransferase. [EC:2.6.1.1] #37 slr0055 143 trpG; anthranilate synthase component II. [EC:4.1.3.27] #38 sll0454 202 pheS; phenylalanyl-tRNA synthetase alpha chain (phenylalanine--tRNA #39 sll0109 197 aroH; chorismate mutase. [EC:5.4.99.5] #40 sll0034 62 hypothetical protein. #41 sll0033 160 hypothetical protein. #42 slr0543 70 trpB; tryptophan synthase beta chain. [EC:4.2.1.20] [SP:TRPB_SYNY3] #43 sll0499 300 clpP; hypothetical protein. #44 sll0536 297 clpP; hypothetical protein. #45 sll0622 92 nadA; quinolinate synthetase. [EC:4.6.1.3] [SP:NADA_SYNY3] #46 sll0621 284 dsbD; thiol:disulfide interchange protein DsbD. #47 slr1559 126 aroE; shikimate 5-dehydrogenase. [EC:1.1.1.25] #48 slr0752 192 eno; enolase (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate Motif number 1 CTCCCGGCCATTGCCCAACCCCGTTATTTAGT 1 24 0 TTGCCCACCC 0.991145 -66 GTTTCTTCCATCACCCCTACCTGTAA 1 74 0 CTTCCATCCC 0.534472 -16 GTCGATTTCTTTCCCCATCCCCCTAGTATC 3 9 0 TTCCCCACCC 0.982623 -68 TCCGGTCTTTTCCCATACCCGTAGGTGGTC 3 57 0 TTTCCCACCC 0.974926 -20 CCGACCTAATCTCCCCACTCCCCCATTAATCA 4 58 1 CTCCCCACCC 0.983585 -29 GATAAAGCTCTAGCCCTTCCCCAGACCTAGGC 5 34 1 TAGCCCTCCC 0.921265 -42 TTGCCCACCGTTGACCATGGCCCCTGGATACC 6 232 0 TTGACCAGCC 0.638722 -69 CTAATTTGTCCTGACCACTCCTTGCCCACCGT 6 253 0 CTGACCACCT 0.53048 -48 AACCCGCTTTTTTCCCAAGGCCGACACAACAC 10 47 1 TTTCCCAGCC 0.885276 -254 AATAGGTAATCCGCCCAATGCCTAACTGGGGC 10 263 1 CCGCCCAGCC 0.828771 -38 AAGGGCGGAAATCCCCATCCCCCAAGGAAATT 11 81 0 ATCCCCACCC 0.923077 -75 TCAATAATAATTGCCCAGTCCTGTTGGTCAAA 16 58 1 TTGCCCACCT 0.930541 -138 AGCTTTTAACCCTCCCTGTCCCAACCTATCGA 16 158 1 CCTCCCTCCC 0.838739 -38 CCGGTCAATCCTGCCCATTCCTGCCTGATCCG 18 61 0 CTGCCCACCT 0.934191 -93 GCCAGAACTAATTCCCATTCCCGTTAACGATC 19 242 1 ATTCCCACCC 0.891906 -59 GGCTAGGATATTTCCTTGGCCCGTTTATTTTT 20 122 1 TTTCCTTCCC 0.669053 -85 CTGCGCTGCCCAACCCAAATTACCACC 21 45 0 CTGCCCACCA 0.934191 -17 GTCGAGTAATTGCCCCTGTCCTTGCCATTTCA 24 26 1 TGCCCCTCCT 0.581618 -26 TCCTAATCGCTGTCCCTTCCCCCATATTCCCG 25 224 1 TGTCCCTCCC 0.888716 -77 ATCTCCATGTCGTCCCAATCCATCCCTAAAAA 26 32 1 CGTCCCACCA 0.622625 -107 TACAGACCATACCCCGACACCGTT 26 125 0 CAGACCACCC 0.616476 -14 TAAACAAGCACTGCCCTTTCCCGCTCAGAGCG 27 12 0 CTGCCCTCCC 0.986451 -122 TCTTTAACAATTGCCTAACCCCACCTTGGGCT 28 82 1 TTGCCTACCC 0.904576 -56 TAGAGTGGCCTTCCCCATCCCATCAACCCTCG 31 82 0 TTCCCCACCA 0.871275 -202 CTGAAGGCATTACCCCAGGCCACTCCGGGTCA 31 189 0 TACCCCACCA 0.535442 -95 GTTCCATGGCATTCCTAGCCCCAAGGGTGATA 37 58 0 ATTCCTACCC 0.41136 -86 GATGTTGGCCTTGACCATGGCCGAGGAAAGAC 38 77 1 TTGACCAGCC 0.638722 -126 CAAGCAAAATAGTCCCTTACCCTTGGGCTAGG 39 80 1 AGTCCCTCCC 0.628904 -118 GTTCCCCGTTTAGCCCTAGCCCAAGGGTAAGG 39 94 0 TAGCCCTCCC 0.921265 -104 TGTTAACTTTTTGCCCTAACCAGACCAAGAAA 41 137 1 TTGCCCTCCA 0.891593 -24 ATGGATTAATTTCCCCAGGCCCAGGGAAAAAG 42 16 0 TTCCCCACCC 0.982623 -55 CCACCATGCGCTGCCCTTGGCTATTAATTCTT 43 82 1 CTGCCCTGCT 0.633635 -219 CTTTCCTGCCCTGCCTATAGCCAAGAACAGGT 43 125 1 CTGCCTAGCC 0.665937 -176 CTGGTTGGAATTGCCATAACCCAAAACTGCCA 44 42 1 TTGCCATCCC 0.757224 -256 GATGAAGCGCTGGCCCATGCCCCACTGATTTT 45 15 1 TGGCCCACCC 0.97399 -78 TTAGACATTCCCCCCCTGCCCCTCAATGGAGA 46 106 0 CCCCCCTCCC 0.883235 -179 TGTTTTAAAGTTCCCCTAGCCCAAGGGTTGGG 48 167 0 TTCCCCTCCC 0.972 -26 ******* *** Masking position 5 Map Score: 52.458 Number of sites scoring better than the average of aligned sites = 3531 Number in coding regions = 3167 Number in noncoding regions = 364 Number of orfs with sites within 600 bp upstream = 362 Fraction of orfs with sites within 600 bp upstream = 0.0581433 Motif number 2 CACGGTGCGGGGCGATCGGCTTATTTATGT 6 113 0 GGCGATCGGC 0.547017 -188 CAAAATTGTCGGCGATCGCCTACTTTGCGA 6 186 1 GGCGATCGCC 0.499996 -115 TAATCATATAGGCGACCGCTCACGATAAAT 10 116 0 GGCGACCGCT 0.861768 -185 CGACCAGGATGGCGATCTCCAACGAGAATT 14 18 0 GGCGATCTCC 0.534911 -66 TCTCCAAGGCGATCAGCTTCTTAACTT 17 171 0 GGCGATCAGC 0.911783 -17 GGGGCGATAACCTCAATTCTAA 18 3 1 GGCGATAACC 0.687161 -151 TCTCTCCGTCGGCGATCGAGGTAGAATTGG 18 108 0 GGCGATCGAG 0.896646 -46 CGACGGGAACGGCGATCGTTAACGGGAATG 19 257 0 GGCGATCGTT 0.905021 -44 TTATTCTCCAGGCGATCGCCATTGGT 27 118 1 GGCGATCGCC 0.499996 -16 CGGGGAAAAAGGCGATTGGTTGGCACAGAC 28 13 1 GGCGATTGGT 0.790455 -125 CCAACTCCCTGGCGATCGCCGTTGTTTTAT 32 13 1 GGCGATCGCC 0.499996 -68 GCAGTTGGCGATCGTTGCAGCTCATT 40 47 0 GGCGATCGTT 0.905021 -16 GGGGTGGCTCGGCGATCGAGTGCTCCCTGT 41 56 1 GGCGATCGAG 0.896646 -105 CGGACTAAACGGCGATCGGCAAAGCCCAAG 44 271 0 GGCGATCGGC 0.547017 -27 ACTCCATCTAGGCGATCGCCGTCCGGAAAC 46 49 1 GGCGATCGCC 0.499996 -236 ********** Masking position 5 Map Score: 36.9218 Number of sites scoring better than the average of aligned sites = 6404 Number in coding regions = 5830 Number in noncoding regions = 574 Number of orfs with sites within 600 bp upstream = 364 Fraction of orfs with sites within 600 bp upstream = 0.0584645 Motif number 3 TCTTCCATCACCCCTACCTGTAAAATGGGC 1 67 0 CCCCTACCTG 0.460858 -23 GGAGGGCCCGCCCCAACAGATTTTTGTGGC 6 55 1 CCCCAACAGA 0.730818 -246 TTGACCATGGCCCCTGGATACCGTCGTTGC 6 224 0 CCCCTGGATA 0.844095 -77 GCCAATTTGCCCCCTAGGGTTCGGCAACGC 7 117 0 CCCCTAGGGT 0.752433 -75 AAATTCTCCCCAGGAAAGCTGGTACAG 8 45 0 CCCCAGGAAA 0.957608 -17 GCTAGCAGACCCCCCGGCGAAATTCATGGG 10 180 1 CCCCCGGCGA 0.835405 -121 AATCCCCATCCCCCAAGGAAATTAGCCCGT 11 74 0 CCCCAAGGAA 0.949053 -82 TGGGACAAACCCCCCGGCAGTGATTCCAGT 19 19 0 CCCCCGGCAG 0.804981 -282 GCTCCGGTTCCCCCTGGGGGCCGAGCAAAC 19 214 0 CCCCTGGGGG 0.573459 -87 AAAATAAACGGGCCAAGGAAATATCCTAGC 20 123 0 GGCCAAGGAA 0.529569 -84 AATCCCCAGGAAAAAGTCGAGTA 24 4 1 CCCCAGGAAA 0.957608 -48 AGCTGAAATGCGCCAGGAAATTGCCATTAT 25 33 0 CGCCAGGAAA 0.78458 -268 CAATGGCGATCGCCTGGAGAATAAATTTAG 27 112 0 CGCCTGGAGA 0.635891 -22 CTGAAGATCAGCCCAAGGTGGGGTTAGGCA 28 93 0 GCCCAAGGTG 0.700535 -45 ATCTTCAGTCCCCCAGGATTACAGTTTTAC 28 115 1 CCCCAGGATT 0.807499 -23 GAAGGCATTACCCCAGGCCACTCCGGGTCA 31 189 0 CCCCAGGCCA 0.794666 -95 CAACGGCGATCGCCAGGGAGTTGGGG 32 7 0 CGCCAGGGAG 0.824561 -74 AGCAAATTGGCCCCAAGCTGGGAACCGGCC 33 90 0 CCCCAAGCTG 0.852264 -132 CTGCCATAGGGCCCTGGGAGCAAATTGGCC 33 108 0 GCCCTGGGAG 0.852096 -114 CAACATTGGCCCCCTGCCATAGGGCCCTGG 33 121 0 CCCCTGCCAT 0.688732 -101 TGTTTGTCATCCCCTGGATAGATAGGCTGA 33 174 1 CCCCTGGATA 0.844095 -48 AACCTAAAATCCCCAGGAAATTTGCCCT 34 83 1 CCCCAGGAAA 0.957608 -18 AGCATGCCAACCCCAGCAAGGGAGCTGGAA 36 46 0 CCCCAGCAAG 0.823918 -77 CTGTTGTTTACCCCAGGGATGTTTTGATT 36 104 1 CCCCAGGGAT 0.941717 -19 GCATTCCTAGCCCCAAGGGTGATAGGCTGG 37 52 0 CCCCAAGGGT 0.872997 -92 AAGGTTTAACCCCCAACCAAGTTACCCCCA 37 92 0 CCCCAACCAA 0.828498 -52 ACCGATTCTACCCCAGCAGAGAGCGCAAAT 38 20 0 CCCCAGCAGA 0.851962 -183 TCGTAATTCCGCCCTAGCAAAGGCCTTGTT 38 168 0 GCCCTAGCAA 0.773121 -35 TTTAGCCCTAGCCCAAGGGTAAGGGACTAT 39 88 0 GCCCAAGGGT 0.721743 -110 GGCACAATGGGGCCAAGCAATGAGCTGCAA 40 29 1 GGCCAAGCAA 0.509891 -34 ATTTCCCCAGGCCCAGGGAAAAAGAATAA 42 10 0 GCCCAGGGAA 0.936709 -61 TTGCTCACTTCCCCTAGCTGATCTCGACTA 43 29 1 CCCCTAGCTG 0.752729 -272 TTTCTTTCCTGCCCTGCCTATAGCCAAGAA 43 122 1 GCCCTGCCTA 0.479117 -179 GATCGGCAAAGCCCAAGAATGGAAAAACAC 44 258 0 GCCCAAGAAT 0.620362 -40 TTTAAACTTGCCCCTGCCGAAACAAAGCCG 47 13 0 CCCCTGCCGA 0.830807 -114 TTTCCCGCAACCCCAAGGAACATTTCTCCG 47 60 1 CCCCAAGGAA 0.949053 -67 AGTTCCCCTAGCCCAAGGGTTGGGGTTACT 48 161 0 GCCCAAGGGT 0.721743 -32 ********** Masking position 4 Map Score: 36.4653 Number of sites scoring better than the average of aligned sites = 6147 Number in coding regions = 5603 Number in noncoding regions = 544 Number of orfs with sites within 600 bp upstream = 516 Fraction of orfs with sites within 600 bp upstream = 0.0828783 Motif number 4 AATCTTCGTGGCCATCCGACCTAATCTCCCC 4 43 1 GCCATCGACC 0.641973 -44 TCAGTCCGAAGCCAATTTGCCCCCTAGGGTT 7 126 0 GCCAATTGCC 0.954259 -66 AAAAGTCTAAGCAATTAGGCCTATACTTACT 9 14 0 GCAATTGGCC 0.848415 -84 TCAGTTCGCCCCAATTCTACCTCGATCGCCG 18 98 1 CCAATTTACC 0.813657 -56 ACTAAACCAAACAGCCCTGATTAACGA 19 284 0 CCAAACGCCC 0.461608 -17 TAGGCAAATAGCAAATATGCCAAACGA 20 7 0 GCAAATTGCC 0.904295 -200 CGCTGCCCAACCCAAATTACCACCGTGGTGG 21 38 0 CCCAAATACC 0.835739 -24 TGTCCCTTCCCCCATATTCCCGGTTCGATTA 25 234 1 CCCATATCCC 0.851977 -67 ATATGCCATGGCCAAACTGCCAA 26 3 0 GCCAAATGCC 0.930209 -136 TGCCGTGGGCCCCATTGTTCCTAAATTTGTT 27 61 1 CCCATTTTCC 0.851643 -73 CCTTCCCCATCCCATCAACCCTCGGAAAATT 31 75 0 CCCATCACCC 0.632792 -209 GGCCCTGGGAGCAAATTGGCCCCAAGCTGGG 33 98 0 GCAAATGGCC 0.822284 -124 TTGGCCCCCTGCCATAGGGCCCTGGGAGCAA 33 115 0 GCCATAGGCC 0.887501 -107 GTGAGGAAAAGCAAATCAGCCTATCTATCCA 33 188 0 GCAAATAGCC 0.775174 -34 AGGTTACGTCCCCAAATTGCCTTGGTA 35 87 1 CCCAAATGCC 0.94841 -17 CCAAGTTACCCCCATTGTTCCATGGCATTCC 37 75 0 CCCATTTTCC 0.851643 -69 CGAGGAAAGACCAATTATCCCCTGTTGATCA 38 98 1 CCAATTTCCC 0.803285 -105 TTACGAGAGACCCATTTTTCC 38 192 1 CCCATTTTCC 0.851642 -11 TGACCTTTTGCCAATTTTGCCTGA 39 4 0 CCAATTTGCC 0.940399 -194 GGAAACCACACCCATCTTACCGGACAATTCG 39 50 0 CCCATCTACC 0.834844 -148 AGTTACGGGGGCAAAAGTTCCCCGTTTAGCC 39 111 0 GCAAAATTCC 0.493809 -87 ATTGCTTGGCCCCATTGTGCCAGAGAATGTT 40 19 0 CCCATTTGCC 0.972362 -44 TTGCCATAACCCAAAACTGCCATATCAAATG 44 52 1 CCAAAATGCC 0.891838 -246 AATCTCGGCGGCAATTTAGCCCTACTTTCAA 44 127 0 GCAATTAGCC 0.806602 -171 ACACTAAATTCCCAATTCGCCAACTCCAGAC 44 177 0 CCCAATCGCC 0.897386 -121 TACAACAAAACCAATACCACCATAACAAACT 46 21 1 CCAATACACC 0.453526 -264 GCAATTCCCAGCCATCTTGCCAAAGCTCATC 46 147 0 GCCATCTGCC 0.929787 -138 GTTTGACCCCGCCAATAAACCAGGGGCGAAA 46 213 1 GCCAATAACC 0.680259 -72 TTTGCCGGCTGCCATTTCGCCCCTGGTTTAT 46 227 0 GCCATTCGCC 0.884666 -58 TACACAGTTGCCCAAAAAGCCAAAAATAAGT 46 264 0 CCCAAAAGCC 0.870164 -21 AACAACCTAACCAAAAGAACCTGTTGGCAAT 48 112 1 CCAAAAAACC 0.454082 -81 ****** **** Masking position 4 Map Score: 31.1524 Number of sites scoring better than the average of aligned sites = 1823 Number in coding regions = 1637 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 5 TAAATAACGGGGTTGGGCAATGGCCGGGAG 1 26 1 GGTTGGGCAA 0.908915 -64 CCCAGACCTAGGCTGGCTAGACTCCAGGGT 5 53 1 GGCTGGCTAG 0.776197 -23 TCAAAGAGATGGCTGGGAACTGGGGCTCGG 6 27 1 GGCTGGGAAC 0.729669 -274 CATGGTCAACGGTGGGCAAGGAGTGGTCAG 6 245 1 GGTGGGCAAG 0.873497 -56 GACACAACACCGTTGGGAAGCAAAAGTCAT 10 69 1 CGTTGGGAAG 0.884122 -232 AAGTTAGTACGGTTGGCAAGGCTTAAAAGA 11 133 0 GGTTGGCAAG 0.905662 -23 CTATTCGATAGGTTGGGACAGGGAGGGTTA 16 164 0 GGTTGGGACA 0.951232 -32 TCAATTCTAAGGTTGGGCAGTAATTGGTTG 18 23 1 GGTTGGGCAG 0.930926 -131 TAGCCACAACCGTTGGGACAAACCCCCCGG 19 32 0 CGTTGGGACA 0.840643 -269 TTACCACCGTGGTGGGGTCGCTCAAACAAA 21 23 0 GGTGGGGTCG 0.893105 -39 TGGTAATTTGGGTTGGGCAGCGCAG 21 47 1 GGTTGGGCAG 0.930926 -15 TGCAAAAATTCGTGGGGAAAAGTGATCCTA 22 71 1 CGTGGGGAAA 0.802498 -100 TTTAGGGATGGATTGGGACGACATGGAGAT 26 32 0 GATTGGGACG 0.626979 -107 GGCGGGGAAAAAGGCGATTG 28 1 1 GGCGGGGAAA 0.924862 -137 AAAGGCGATTGGTTGGCACAGACTGGCTCA 28 20 1 GGTTGGCACA 0.869068 -118 ATCAGCCCAAGGTGGGGTTAGGCAATTGTT 28 87 0 GGTGGGGTTA 0.516769 -51 CTGTTTTCATCGCTGGGAAAATATTTTGCA 30 177 0 CGCTGGGAAA 0.822328 -84 GGGTTGATGGGATGGGGAAGGCCACTCTAT 31 85 1 GATGGGGAAG 0.564202 -199 CCCTTGCTGGGGTTGGCATGCTCTGTCTGA 36 54 1 GGTTGGCATG 0.607798 -69 AAGGGTGATAGGCTGGGTCAGTGTTTTTGG 37 38 0 GGCTGGGTCA 0.875723 -106 CTAGATGAAGCGCTGGCCCATGCCCCACTG 45 12 1 CGCTGGCCCA 0.412669 -81 TTGGCAAGATGGCTGGGAATTGCTTAGCAT 46 155 1 GGCTGGGAAT 0.645535 -130 CTGGTTTATTGGCGGGGTCAAACCAGAGGA 46 206 0 GGCGGGGTCA 0.835208 -79 ACAGTTCACCGGTAGGGTAACCATGGGAAA 48 35 1 GGTAGGGTAA 0.425215 -158 ********** Masking position 5 Map Score: 20.4793 Number of sites scoring better than the average of aligned sites = 2109 Number in coding regions = 1919 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 6 ACTGTCCCTAGCTTAACGGGAAATTAGTTT 2 50 1 GCTTAACGGG 0.979885 -31 ACGAAGATTTGCTAAACTGGACGCAGAGTA 4 22 0 GCTAAACTGG 0.948151 -65 AAAAAAGCGGGTTAAACGGGTATATTCACC 10 30 0 GTTAAACGGG 0.968189 -271 TCCGCCCAATGCCTAACTGGGGCGGTGAAT 10 272 1 GCCTAACTGG 0.824218 -29 GCTGTCTTCACCCAAACGGGCTAATTTCCT 11 59 1 CCCAAACGGG 0.868339 -97 ACGCTCTCTAGCTTAACGGGTTTAGCCCGA 14 45 0 GCTTAACGGG 0.979885 -39 GTTAAACGGGAAAATTAAGA 30 1 1 GTTAAACGGG 0.968189 -260 TTGGGCTAGGGCTAAACGGGGAACTTTTGC 39 102 1 GCTAAACGGG 0.989347 -96 AGTTAAACGGACTAAACGGCG 44 287 0 GTTAAACGGA 0.748982 -11 ********** Masking position 5 Map Score: 9.95899 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 103 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 CAAATATTTTGGAGGATTTTCC 5 1 0 GGGATTTTCC 0.948397 -75 CGACAATTTTGGCGAATTGTCCGAGTCTATCC 6 165 0 GGGATTGTCC 0.907203 -136 TCACCCAAACGGGCTAATTTCCTTGGGGGATG 11 66 1 GGCAATTTCC 0.969407 -90 CCGTTGACCGGGAGTATTTTCCA 15 2 0 GGGATTTTCC 0.948397 -101 CCCTTTGTTTGGGCTATTTTTTAGGGATGGAT 26 49 0 GGCATTTTTT 0.668313 -90 AATTTGTTCTGGATCAATGTCTAGTCTCCTAA 27 84 1 GGTAATGTCT 0.47102 -50 TCCCAGCTTGGGGCCAATTTGCTCCCAGGGCC 33 97 1 GGCAATTTGC 0.894448 -125 AGGGCAAATTTCCTGGGGATTTT 34 88 0 GGCAATTTCC 0.969274 -13 AATCGGTAACGGGCGATTTTTCCTAGGTTTAG 38 43 1 GGCATTTTTC 0.895123 -160 CAAGGGTAAGGGACTATTTTGCTTGGAAACCA 39 73 0 GGCATTTTGC 0.851633 -125 CTTTGACAATGGATTAATTTCCCCAGGCCCAG 42 24 0 GGTAATTTCC 0.861878 -47 CCGGTCAAATTTTCCTTAAAAGTG 42 57 0 GGCAATTTTC 0.926432 -14 TGCGGACAATGGAGTAATTTTTGACCTTTATC 43 205 1 GGGAATTTTT 0.719051 -96 GAGGGGCAGGGGGGGAATGTCTAACTTTAGGA 46 114 1 GGGAATGTCT 0.795628 -171 AAGGAAAACCGGAGAAATGTTCCTTGGGGTTG 47 67 0 GGGAATGTTC 0.867476 -60 ** * ******* Masking position 6 Map Score: 12.0786 Number of sites scoring better than the average of aligned sites = 607 Number in coding regions = 530 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 8 CGGCCTTGGGAAAAAAGCGGGTTAAACGGG 10 40 0 AAAAAAGCGG 0.820035 -261 TGGGCCTTTTAAAACAGAGGAAGGATGTGT 10 206 1 AAAACAGAGG 0.956876 -95 CTCACACTCGAAAAAAGAGGTTTAACGCTT 17 109 0 AAAAAAGAGG 0.846066 -79 CGGGCTAACAAAAACAGGGATTGAACGACT 25 171 1 AAAACAGGGA 0.870401 -130 AAAATAGCCCAAACAAAGGGCATTCTTTCC 26 61 1 AAACAAAGGG 0.510275 -78 CGTCTAGGAAAAAACAGGGGAAAGAATGCC 26 79 0 AAAACAGGGG 0.977576 -60 GATCAACAATAAAACAACGGCGATCGCCAG 32 21 0 AAAACAACGG 0.739174 -60 TGCCGCCAAAAAAACAGGGAGCACTCGATC 41 69 0 AAAACAGGGA 0.870401 -92 TGGCGGGGTCAAACCAGAGGAAAGATTAAC 46 197 0 AAACCAGAGG 0.932874 -88 CCCCGCCAATAAACCAGGGGCGAAATGGCA 46 219 1 AAACCAGGGG 0.964669 -66 TCTTGAATAAAAAACTGAGGAATTTTAGAC 48 72 1 AAAACTGAGG 0.738173 -121 ********** Masking position 3 Map Score: 6.82719 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 398 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 9 GAAAGAAATCGACTGAACAGACTATTTAGGAC 3 28 1 GACGAACAGC 0.838568 -49 TGACCAACAGGACTGGGCAATTATTATTGACC 16 56 0 GACGGGCAAT 0.710967 -140 GTTGAATCTGGACGGATCAGGCAGGAATGGGC 18 49 1 GACGATCAGC 0.936232 -105 GAACTGATTTGACCGGTCAATCCTGCCCATTC 18 73 0 GACGGTCAAC 0.945627 -81 TCCCCCTGGGGGCCGAGCAAACCCTCAATCAG 19 204 0 GGCGAGCAAC 0.965679 -97 TAAAATAAGAGACTGGTCAGTCAGCATTGGTT 20 180 1 GACGGTCAGC 0.594911 -27 TTAAATCAATGGCAGATCAAACGGATCAACAA 32 42 0 GGCGATCAAC 0.945838 -39 AGGCTAGTCAGACAGAGCATGCCAACCCCAGC 36 59 0 GACGAGCATC 0.881323 -64 TAACAACGGACACGGAGCAATCCAACTAATCA 41 110 0 CACGAGCAAC 0.778559 -51 CTTGGCTATAGGCAGGGCAGGAAAGAAAAAAA 43 118 0 GGCGGGCAGA 0.78581 -183 TCAAATTAACGGCGGATCAGCCCGTCTTAATT 43 240 1 GGCGATCAGC 0.67581 -61 *** ****** * Masking position 9 Map Score: 5.6231 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 165 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 10 GGCTCTAGTTGCCGCTCCCGGCCATTGCCC 1 40 0 GCCGCTCCCG 0.969874 -50 TCCCTTGCCTCAAACTAATT 2 71 0 TCCCTTGCCT 0.671074 -10 TAAAGCTCTAGCCCTTCCCCAGACCTAGGC 5 36 1 GCCCTTCCCC 0.849624 -40 CCTGGATACCGTCGTTGCCTCAGCTGTCGC 6 212 0 GTCGTTGCCT 0.525595 -89 GCAACGCATCGGCGTTCCCTAGCTTAAATT 7 94 0 GGCGTTCCCT 0.851602 -98 GGAACGCCGATGCGTTGCCGAACCCTAGGG 7 106 1 TGCGTTGCCG 0.926895 -86 CATATAGGCGACCGCTCACGATAAATACCT 10 112 0 ACCGCTCACG 0.262653 -189 GTTAACGATCGCCGTTCCCGTCGTTAATCA 19 264 1 GCCGTTCCCG 0.9613 -37 CTGCGCTGCCCAACCCAAATT 21 51 0 TGCGCTGCCC 0.871085 -11 TTCAGTCATGGGGGTTGCCGTCAAAATATC 25 62 1 GGGGTTGCCG 0.751109 -239 CCAATCCACAGCCCCTGCCGCCA 25 288 1 GCCCCTGCCG 0.972277 -13 ATACCCCGACACCGTTGCCGCTGTAAAGGC 26 111 0 ACCGTTGCCG 0.860902 -28 AAAATAGAGTGGCCTTCCCCATCCCATCAA 31 88 0 GGCCTTCCCC 0.834299 -196 TACAATAGATGCCGCTGACGCCATCGCAAA 31 224 1 GCCGCTGACG 0.847196 -60 GAAACCACCATGCGCTGCCCTTGGCTATTA 43 78 1 TGCGCTGCCC 0.871085 -223 TTTTCTTTCCTGCCCTGCCTATAGCCAAGA 43 121 1 TGCCCTGCCT 0.702073 -180 TCCATTCTTGGGCTTTGCCGATCGCCGTTT 44 265 1 GGCTTTGCCG 0.75775 -33 GTTTAAACTTGCCCCTGCCGAAACAAAGCC 47 14 0 GCCCCTGCCG 0.972277 -113 ********** Masking position 6 Map Score: 16.3039 Number of sites scoring better than the average of aligned sites = 1402 Number in coding regions = 1320 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 11 CGGACAATTCGCCAAAATTGTCGGCGATCGCC 6 174 1 GCCAAAATTC 0.74122 -127 AGCAAATTTAGGGAAAATTGTGTAGGCGGACT 9 66 1 GGGAAAATTG 0.924591 -32 AGACCCCCCGGCGAAATTCATGGGCCTTTTAA 10 186 1 GCGAAATTCG 0.469478 -115 GCATAATTTCGGCAAAATTAAGGGCGGAAATC 11 100 0 GGCAAAATTG 0.972745 -56 AGCGGCAAATTCTCGTTGGAGATCG 14 4 1 GGCAAATTCG 0.820091 -80 AAAGGATTGTGACAAAATCCCGCAAAACTGCA 22 43 1 GACAAAATCG 0.738503 -128 GTTAAACGGGAAAATTAAGAGAGTGTTTA 30 8 1 GGGAAAATTG 0.924629 -253 ATATTGAGTTGCCAAAATCAAGCAATAGTAAA 30 125 0 GCCAAAATCG 0.911915 -136 GCTAGTTAGTGGGAAACTTTGGTTCATTGAGC 31 120 1 GGGAAACTTG 0.641479 -164 ATAGGTTCCAGTCAAAATTTTGCTGAGGCGAG 35 23 1 GTCAAAATTG 0.757174 -81 TCAGGCAAAATTGGCAAAAGGTCAG 39 4 1 GGCAAAATTC 0.82612 -194 GGTTTCTCCAGGCAAAAGTCAGAATTAGTCGA 43 52 0 GGCAAAAGTG 0.819045 -249 TACCTAGAAAGCCAAGATTTTGATCCTTATTT 43 272 1 GCCAAGATTG 0.705833 -29 GCCAACTCCAGACAAAATTATGAAAAAATGCA 44 158 0 GACAAAATTG 0.846118 -140 AATGGCAGCCGGCAAATTTCAGACTTATTTTT 46 242 1 GGCAAATTTG 0.898361 -43 TGCCCAAAAAGCCAAAAATAAGTCTGAAATTT 46 255 0 GCCAAAAATG 0.632982 -30 GGTAACCATGGGAAAAATTAAGTCTTGAATAA 48 50 1 GGAAAAATTG 0.701564 -143 ********* * Masking position 5 Map Score: 8.216 Number of sites scoring better than the average of aligned sites = 911 Number in coding regions = 788 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 138 Fraction of orfs with sites within 600 bp upstream = 0.0221651 Motif number 12 TAAATAACGGGGTTGGGCAATGGCCGGGAGCGG 1 26 1 GGTGGAATGG 0.754855 -64 GATAGGGTGATTAATGGGGGAGTGGGG 4 70 0 GGTGAAATGG 0.889172 -17 AAGTTACAGAGGTTGAAAAATAGTGAACAGTAA 7 164 0 GGTGAAATAG 0.922618 -28 GCTGTGGATTGGTTAGTTAACTGTCTGCATCAT 25 267 0 GGTAGAACTG 0.669746 -34 TCTATCCAGGGGATGACAAACAGGATTCTGTTT 33 163 0 GGTGAAACAG 0.976882 -59 AAAACTTGACGGGTGAGGAAAAGCAAATCAGCC 33 198 0 GGTGAAAAAG 0.825135 -24 AACATCCCTGGGGTAAACAACAGCAAAAAATGG 36 94 0 GGTAAAACAG 0.866843 -29 CTAGCCCCAAGGGTGATAGGCTGGGTCAGTGTT 37 43 0 GGTGAGGCTG 0.712558 -101 GCGCTGGTCAGGTTGATCAACAGGGGATAATTG 38 109 0 GGTGAAACAG 0.976882 -94 AATTCGGTTAGGATGATTGACTGACCTTTTGCC 39 23 0 GGTGAGACTG 0.929396 -175 TCTAAATTAGGGTTGATAAACTGCCTATACGGA 44 223 1 GGTGAAACTG 0.97167 -75 ** *** ***** Masking position 4 Map Score: 3.35678 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 99 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 13 AGTAGTGAGTTCAATTAATGCAATGAACAG 2 15 1 TCAATTAATG 0.496322 -66 TTATGTCCGACCCATGACTGTCTGCGTAAA 6 89 0 CCCATGACTG 0.944364 -212 GGACTGACATCCAATTACTGTTCACTATTT 7 150 1 CCAATTACTG 0.940006 -42 AAAAAAACAGTCAATTACTGGAGCGGTGCT 15 83 0 TCAATTACTG 0.876424 -20 CCAGATTCAACCAATTACTGCCCAACCTTA 18 30 0 CCAATTACTG 0.940006 -124 GTCAATCCTGCCCATTCCTGCCTGATCCGT 18 60 0 CCCATTCCTG 0.757036 -94 GACGGCAACCCCCATGACTGAAGCTGAAAT 25 54 0 CCCATGACTG 0.944364 -247 TGGGGATGGATCAAATACTGATTAGCGCTG 38 136 0 TCAAATACTG 0.786251 -67 TTTTCAGTAATCAAAGACTGGTTGGAATTG 44 25 1 TCAAAGACTG 0.774776 -273 ATTGCCATAACCCAAAACTGCCATATCAAA 44 51 1 CCCAAAACTG 0.627836 -247 AGCCCTACTTTCAATTACTAACTATCTTCA 44 111 0 TCAATTACTA 0.337256 -187 ATCGGCAAAGCCCAAGAATGGAAAAACACC 44 257 0 CCCAAGAATG 0.550195 -41 ********** Masking position 4 Map Score: 3.85871 Number of sites scoring better than the average of aligned sites = 302 Number in coding regions = 262 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 14 CTTGAAGTGTCTTTCCCAAACAAAATAGGTAA 10 240 1 CTTCCAAACA 0.724858 -61 AGGTTTAACGCTTTCCCAAAAATCGCACTGCG 17 90 0 CTTCCAAAAA 0.938824 -98 AGCTTCTTAACTTTCACAAAAAGCGATCATTC 17 152 0 CTTCAAAAAA 0.874157 -36 AATAATTTAGCTTCCAAAAAAAGTGAACAGAA 20 60 0 CTCCAAAAAA 0.917202 -147 TGGAACGAGGCATAGATAAAAATAAACGGGCC 20 139 0 CTAGAAAAAA 0.511945 -68 ATCTATGCCTCGTTCCAAAAAATACTTAAAAT 20 154 1 CTTCCAAAAA 0.938824 -53 CGTCCCAATCCATCCCTAAAAAATAGCCCAAA 26 42 1 CTCCCAAAAA 0.960743 -97 TCTCTAAATACTTCGATAAAAATTCATTTAAA 30 216 1 CTCGAAAAAA 0.79361 -45 TACACAAGCCCCTTGCTAAAAAAATTACTAAA 33 52 1 CTTGCAAAAA 0.841946 -170 GGTTGACTAGCGTACCCAAAAACACTGACCCA 37 23 1 CTACCAAAAA 0.869725 -121 GTATTTGATCCATCCCCATAAACAAGGCCTTT 38 148 1 CTCCCATAAA 0.739218 -55 TAAGGTTTTGCCGCCAAAAAAACAGGGAGCAC 41 75 0 CGCCAAAAAA 0.655371 -86 * **** ***** Masking position 8 Map Score: 4.41743 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 123 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 15 TGATTAATGGGGGAGTGGGGAGATTAGGTC 4 60 0 GGGAGTGGGG 0.869961 -27 AGAGATGGCTGGGAACTGGGGCTCGGAGGG 6 31 1 GGGAACTGGG 0.957503 -270 GATAAACTCAGAGAACTGGCCCAGAAGCTG 19 177 1 GAGAACTGGC 0.77634 -124 GGCCCCCAGGGGGAACCGGAGCCAGAACTA 19 222 1 GGGAACCGGA 0.967314 -79 GATCGTTAACGGGAATGGGAATTAGTTCTG 19 244 0 GGGAATGGGA 0.875025 -57 AGAAATTATTGGGAATTGGAGTCTAATAAT 20 86 0 GGGAATTGGA 0.925175 -121 ACACCATCTGGTGAACCGGA 31 1 0 GTGAACCGGA 0.721106 -283 GCGATCGCCAGGGAGTTGGGG 32 2 0 GGGAGTTGGG 0.921961 -79 GCCCCAAGCTGGGAACCGGCCTAAGAATTT 33 81 0 GGGAACCGGC 0.960646 -141 ACCCCAGCAAGGGAGCTGGAATTGAGCCGA 36 37 0 GGGAGCTGGA 0.969365 -86 AGCGCCGTCGGAGAGTTGGAAGCGGGGGAT 43 170 1 GAGAGTTGGA 0.688143 -131 GGGGCGAAATGGCAGCCGGCAAATTTCAGA 46 235 1 GGCAGCCGGC 0.750429 -50 ********** Masking position 4 Map Score: 9.0891 Number of sites scoring better than the average of aligned sites = 809 Number in coding regions = 742 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795