AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_synecho.txt -z/skink1/amcguire/genomes/synecho.fna -ipurR_synecho_opreg_300.orf -g0.48 -x5 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 = 0 Input sequences: #1 psbA2 300 photosystem II D1 protein #2 speA 180 arginine decarboxylase #3 purL 137 phosphoribosylformyl glycinamidine synthetase II #4 1651827 181 hypothetical protein #5 phdD 86 dihydrolipoamide dehydrogenase #6 1651830 57 hypothetical protein #7 ubiX 67 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #8 gylA 300 serine hydroxymethyltransferase #9 purA 238 adenylosuccinate synthetase #10 1652397 300 hypothetical protein #11 purC 111 phosphoribosyl aminoidazole succinocarboxamide synthetase #12 codA 174 cytosine deaminase #13 1652676 188 hypothetical protein #14 1652677 228 RNA-binding protein #15 1652678 127 amidase #16 1652679 207 hypothetical protein #17 gcvH 97 glycine decarboxylase complex H-protein #18 1652991 262 hypothetical protein #19 drgA 78 DrgA #20 aspS 129 aspartyl-tRNA synthetase #21 1652994 25 hypothetical protein #22 guaB 102 IMP dehydrogenase subunit #23 purD 111 glycinamide ribonucleotide synthetase #24 purB 109 adenylosuccinate lyase #25 gcvP 179 P protein of glycine cleavage complex #26 glnB 300 nitrogen regulatory protein P-II #27 pyrC 300 dihydroorotase #28 gcvT 168 aminomethyltransferase #29 dnaK 205 DnaK protein #30 1001436 187 hypothetical protein #31 1001437 88 hypothetical protein #32 1001440 300 beta transducin-like protein #33 purF 270 amidophosphoribosyltransferase #34 guaA 300 GMP synthetase #35 carB 46 carbamoyl-phosphate synthase, pyrimidine-specific, large chain #36 pyrR 300 pyrimidine operon regulatory protein PyrR #37 purM 133 phosphoribosyl formylglycinamidine cyclo-ligase #38 prsA 170 ribose-phosphate pyrophosphokinase #39 purE 100 phosphoribosylaminoimidazole carboxylase #40 pyrD 254 dihydroorotate dehydrogenase #41 speA 300 arginine decarboxylase #42 carA 50 carbamoyl-phosphate synthetase subunit A #43 purK 75 phosphoribosyl aminoimidazole carboxylase #44 1653935 195 hypothetical protein #45 1653950 142 hypothetical protein Motif number 1 GTAAACAGAGGGCGTTTTGGGGGTTGAGAAGA 1 112 0 GGCGTTGGGG 0.693729 -189 CGATCGCCGGGGAGTCCGGGGCAGTTACCATT 2 119 1 GGAGCGGGGC 0.972291 -62 TTCCCCCCTGGCGATCGGGTCTTTGTGGAAA 4 10 1 GGCGTGGGTC 0.97699 -172 CTTTAGTTTAGGGGTTAAGGGCAACCTCTGGA 5 50 0 GGGGTAGGGC 0.981209 -37 CCCTAGGCTAGGGGCCGGGGTTAGTCCGTCCT 6 25 0 GGGGCGGGTT 0.702477 -33 TATTGTTATCGGCGCTCAGTGGGGCGACGAGG 9 176 1 GGCGTAGTGG 0.536434 -63 CGCTCAGTGGGGCGACGAGGGAAAAGGTAAAA 9 188 1 GGCGCAGGGA 0.863817 -51 AAATTTTTCCGGGAGTCGGGCCCTAAGGCAGA 13 102 1 GGGATGGGCC 0.850737 -87 CAGTTGACCGGGCGCTGGGGAGGGTTTTGGCT 14 14 1 GGCGTGGGAG 0.729192 -215 ATCAAATTCTGGCGGCAGGTGCTATGATCAGC 14 84 1 GGCGCGGTGC 0.929527 -145 CCTTTCGGCGATCGGTTCGGGACACAGG 16 190 0 GGCGTGGTTC 0.773731 -18 AAAATATGGCGGAGGCAGGGGTTGTTCCTGGG 17 37 0 GGAGCGGGGT 0.779046 -61 GGTTTTCGGTGGCGATCGGGCCTAGAACCTGG 18 113 0 GGCGTGGGCC 0.98945 -150 AGCGTTAAATGGGAGTCGGAGCGGGTTCAGCA 20 52 0 GGGATGGAGC 0.720587 -78 TTGAACAGCAGGAGTTAGGGGTGAGAAGTAAG 20 82 0 GGAGTGGGGT 0.856147 -48 CTAATCCAGTGGGGATCAGAGC 22 1 0 GGGGTAGAGC 0.889096 -102 CGAGTTTTATGGGGATGGGGCCGCCTTGGCAA 25 44 1 GGGGTGGGCC 0.988716 -136 GCCCATGGCCGGAGATGAGGCATTTTAGTGAC 26 85 0 GGAGTAGGCA 0.437691 -216 GCTTGGAGACGGCGATCGGGTAATTACTTCAT 27 207 0 GGCGTGGGTA 0.890508 -94 CAAGATTTAGGGGGCTTGGAGACGGCGATCGG 27 220 0 GGGGTGGAGA 0.883651 -81 CCCAGTATTGGGGGCTAGGGGACTTTCAATAC 28 29 0 GGGGTGGGGA 0.980186 -140 CTCTTATAGTGACGGTAGGGGCTTAGTTCTCG 29 85 0 GACGTGGGGC 0.968576 -121 TGCCAGGGACGGGGATAGGGGGGACTAAATCA 32 110 0 GGGGTGGGGG 0.98516 -191 CTAGTTGTCAGGGGACAGGGGAATGTATAGAT 33 49 0 GGGGCGGGGA 0.967003 -222 AATTGATTAAGGGGTCTAGACCCGTTCGTCAT 33 152 1 GGGGCAGACC 0.617077 -119 GGGTCTAACTGACGGCAAGGCCATGGTCGTCA 34 192 0 GACGCAGGCC 0.556091 -109 AATTTATACTGGAGGTGAGGGCGAATCCCCAG 34 262 0 GGAGTAGGGC 0.922934 -39 ATACAATCAAGGCGATTGGAGCATT 36 4 0 GGCGTGGAGC 0.976982 -297 GGTAAACTCCGGGGCTGGAGCCATAAAGATTA 36 138 1 GGGGTGAGCC 0.793976 -163 CACCCTGCCGGACAGTGGGGGCGTGGTATGAT 36 206 0 GACATGGGGC 0.667201 -95 AGATTGCGGAGAGGTTTGAGGCCGGGAATTCT 37 51 0 GAGGTGAGGC 0.558775 -83 CCAAACTTGGGGGGCTAGGGGGGCATTTAAAA 41 41 1 GGGGTGGGGG 0.98516 -260 TAGTGGAACAGACGACAGGGGCGAATCTGCTA 42 27 1 GACGCGGGGC 0.948079 -24 AAGCAGTCTGGGCGATGGGATCCATCATAGTC 45 30 1 GGCGTGGATC 0.866999 -113 **** * ***** Masking position 1 Map Score: 45.775 Number of sites scoring better than the average of aligned sites = 3020 Number in coding regions = 2728 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 275 Fraction of orfs with sites within 600 bp upstream = 0.0441696 Motif number 2 AACAGAGGGCGTTTTGGGGGTTGAGAAGAG 1 111 0 GTTTTGGGGG 0.447461 -190 AGACCCGATCGCCAGGGGGGAA 4 3 0 GCCAGGGGGG 0.986185 -179 GCTCGGCCAAGCTTGGGGAGCAATACTGCA 4 48 1 GCTTGGGGAG 0.948236 -134 GGCCTGGGGCTCCAAACGCTC 4 171 0 GCCTGGGGCT 0.934595 -11 CCGGCCCCTAGCCTAGGGGGGGAAATTTC 6 39 1 GCCTAGGGGG 0.9736 -19 TGTAAACAGTGCTGGGGGCGGAAAGCACCG 8 269 0 GCTGGGGGCG 0.850832 -32 TATTTACCGACCTTGGGCAGAGCTTTCCTA 10 58 0 CCTTGGGCAG 0.678997 -243 TGGGGGGCGACACTGGGCCGGAGTTGTTGG 10 198 0 CACTGGGCCG 0.671821 -103 GATGGCGATCGCCTGGGGGGCGACACTGGG 10 211 0 GCCTGGGGGG 0.993525 -90 GACCCCATTGGCCTAGGGAGAAAGAGGAGC 11 18 0 GCCTAGGGAG 0.923919 -94 CTTGCTGATAGACTGGGGGAGGTAAATCTG 15 97 1 GACTGGGGGA 0.531595 -31 CTTGGCGATCGCCGTGGCGGTTTTGATTGC 16 67 0 GCCGTGGCGG 0.784507 -141 CGTTCCTGCTCCTTGGGCCTTTTTTCTGCG 16 120 1 CCTTGGGCCT 0.374315 -88 AACGGTTAACTCCTGGGCGGGGCTACGACC 16 149 0 TCCTGGGCGG 0.634619 -59 GGGCTCATGGCCCAGGGGGGATCCCAATGG 18 155 0 CCCAGGGGGG 0.952445 -108 AGGATTTGGCGGATTGTTTGGG 18 251 0 GATTTGGCGG 0.597991 -12 AAACGCCATTGCCTTGGCAGTTGGAATGCC 24 28 1 GCCTTGGCAG 0.848466 -82 GGTCAGCATTGCCAAGGCGGCCCCATCCCC 25 54 0 GCCAAGGCGG 0.875949 -126 ATTTTGGTAGGCCTAGGGGTCAGCATTGCC 25 71 0 GCCTAGGGGT 0.87763 -109 CTCATCTCCGGCCATGGGCGCTGCCAAACG 26 98 1 GCCATGGGCG 0.902013 -203 AGTATTGGGGGCTAGGGGACTTTCAATACA 28 28 0 GCTAGGGGAC 0.509337 -141 GGTTTCCGTACCTATGGGGGCATCTAGCCG 29 47 0 CCTATGGGGG 0.661644 -159 CCAATCCATTGCCTGGGGCCGACACGTTCA 29 119 0 GCCTGGGGCC 0.899495 -87 CGGAAAAAGCCTTGGCAGGACAGGTTCA 30 170 0 GCCTTGGCAG 0.848466 -18 CAGGGACGGGGATAGGGGGGACTAAATCAC 32 109 0 GATAGGGGGG 0.861966 -192 TGAAGCTAACGCCTAGGGCTTTCCTCGCTA 32 172 1 GCCTAGGGCT 0.774501 -129 TCTGCGCTAAGATGGGGGCGGAAAATTGCA 34 109 0 GATGGGGGCG 0.579161 -192 TCTGAGGTGTGCCTGGGGATTCGCCCTCAC 34 250 1 GCCTGGGGAT 0.907625 -51 AATCTGCCATGACATGGGGGTAAA 38 157 1 GACATGGGGG 0.822629 -14 AGGGAAAAAACCCTAGGGATCTTGAAGAAC 40 175 0 CCCTAGGGAT 0.398538 -80 TTTTTCCCTACCCTGGGCAGCCCTCTAGTA 40 196 1 CCCTGGGCAG 0.853672 -59 AGCCCCCCAAGTTTGGGGGGAAAGTATTAA 41 27 0 GTTTGGGGGG 0.750457 -274 AACTTGGGGGGCTAGGGGGGCATTTAAAAC 41 44 1 GCTAGGGGGG 0.9628 -257 AGACTCTAACGACTTGGGGTAATGACATTA 41 74 1 GACTTGGGGT 0.659708 -227 TGGAACAGACGACAGGGGCGAATCTGCTAA 42 30 1 GACAGGGGCG 0.891869 -21 CTTCGCCATTGATTAGGCGGTAGTCTGTAG 43 52 1 GATTAGGCGG 0.570398 -24 CTCTCCCTGCCATTGGGGGTATGCCCGCGC 44 114 1 CATTGGGGGT 0.422759 -82 CAACTGCTGAGCCAAGGGACTATGATGGAT 45 49 0 GCCAAGGGAC 0.407638 -94 ********** Masking position 6 Map Score: 38.9838 Number of sites scoring better than the average of aligned sites = 5096 Number in coding regions = 4569 Number in noncoding regions = 527 Number of orfs with sites within 600 bp upstream = 454 Fraction of orfs with sites within 600 bp upstream = 0.07292 Motif number 3 CCGGACTCCCCGGCGATCGATGGCAATCAA 2 108 0 CGGCGATCGA 0.902199 -73 TTCCACAAAGACCCGATCGCCAGGGGGGAA 4 11 0 ACCCGATCGC 0.97728 -171 CGAAGACAATGGGCGATCGCCAGGACGGGG 5 12 1 GGGCGATCGC 0.991531 -75 GTCGCCCCCCAGGCGATCGCCATCAGAGTT 10 217 1 AGGCGATCGC 0.989791 -84 GCTATGCCAACGACGATCGCCAGGAAAAGG 13 68 1 CGACGATCGC 0.947677 -121 AAAACCGCCACGGCGATCGCCAAGGAAAAT 16 73 1 CGGCGATCGC 0.991531 -135 CTGTGTCCCGAACCGATCGCCGAAAGG 16 191 1 AACCGATCGC 0.915444 -17 CAGGTTCTAGGCCCGATCGCCACCGAAAAC 18 114 1 GCCCGATCGC 0.981112 -149 TGAAGTAATTACCCGATCGCCGTCTCCAAG 27 208 1 ACCCGATCGC 0.97728 -93 AATTCCTGACTGCCGATCGCC 34 290 1 TGCCGATCGC 0.967178 -11 GACTCTGAGGGGGCGATCGCTGTTTAACCC 41 207 0 GGGCGATCGC 0.991531 -94 ********** Masking position 6 Map Score: 19.6335 Number of sites scoring better than the average of aligned sites = 6194 Number in coding regions = 5641 Number in noncoding regions = 553 Number of orfs with sites within 600 bp upstream = 350 Fraction of orfs with sites within 600 bp upstream = 0.0562159 Motif number 4 TGTGTCGCCCCTCTACACAGCCCAGAACTATGGTA 1 49 1 CTTCCCCCAG 0.991582 -252 TTTTCACTGTTTTTCCTTCTCCCTGGTAGTCTAAA 4 97 0 TTTCTCCCTG 0.922651 -85 ACGACGGTCACTATGCTCAACTCTGATGGCGATCG 10 230 0 CTTCCCTCTG 0.824402 -71 CAGCAAAAATTAATTCTTGCCCCAGGAGCAGTCC 10 277 1 TATCTCCCAG 0.79914 -24 GTAATCTTTCCTTTCCTCCTACCAGGGATTAATGC 11 69 1 CTTCCACCAG 0.906553 -43 AGCTCCAAAACTTTGCGTTACCCTGCAGGGGAAAA 12 100 0 CTTCTCCCTG 0.983488 -75 AAATTTTAGCCAAAACCCTCCCCAGCGCCCGGTCA 14 18 0 CAACCCCCAG 0.929399 -211 AAAGAGCCAGATTTACCTCCCCCAGTCTATCAGCA 15 99 0 ATTCTCCCAG 0.876236 -29 TTTCTGCGGTCGTAGCCCCGCCCAGGAGTTAACCG 16 142 1 CGACCCCCAG 0.855703 -66 AGACTTTTAACTAAACCTAAACCAGCTTATGATTA 27 272 1 CTACTACCAG 0.668414 -29 AGCTTATTCCCTCTACTTTTCCCTGATCTTCCGTA 31 41 1 CTTCTCCCTG 0.983488 -48 TTAGTCCCCCCTATCCCCGTCCCTGGCAGTGTCAA 32 114 1 CTTCCCCCTG 0.990686 -187 GTCGAATAGGCTTTTCCCTGCCCATAATTGTACTA 32 265 1 CTTCCCCCAT 0.838687 -36 ACACACTAATCTATACATTCCCCTGTCCCCTGACA 33 41 1 CTTCTCCCTG 0.983488 -230 TCTGTACCCGTTTTTCTCTACCCTGATCCAGGAAG 33 237 1 TTTCCCCCTG 0.95516 -34 GCTCTTATTGCTGAGCCTAACCCAGAATTCCCGGC 37 28 1 CTACTCCCAG 0.960726 -106 ACCTCCAATAAATTTCTCTTCCCAGTTTTTGCTCC 38 13 0 AATCCCCCAG 0.792013 -158 TCCCTAGGGTTTTTTCCCTACCCTGGGCAGCCCTC 40 186 1 TTTCCCCCTG 0.95516 -69 ATCAGTGGAACATAACCTCTCCCTGCCATTGGGGG 44 98 1 CAACTCCCTG 0.869393 -98 ** * * * ***** Masking position 6 Map Score: 25.0966 Number of sites scoring better than the average of aligned sites = 541 Number in coding regions = 493 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 5 GGGGTTTTAGACCCGGTTTTCCGATAAACTTA 8 219 1 ACCGTTTTCC 0.894874 -82 CTGATTGGCTCCTCTTTCTCCCTAGGCCAAT 11 10 1 TCCCTTCTCC 0.401636 -102 GGGTTTGATGACCCCATTGGCCTAGGGAGAAA 11 25 0 ACCCTTGGCC 0.903403 -87 TGCAATTAGATGCCAATTTTCCTAGAACATTG 12 54 0 TGCATTTTCC 0.510436 -121 TGATTTAGTTTGCCAGTTTGCCGTTGCATCAA 12 145 0 TGCATTTGCC 0.808431 -30 CCAGTCTATCAGCAAGCCTGCCTAGCAAAAAA 15 81 0 AGCACCTGCC 0.7399 -47 TTTATTGTTTAGCTGCTTTTCCGCAGGTCCAG 16 14 1 AGCGTTTTCC 0.828531 -194 TGTTGCCTTTAGCGGTTTTGCC 17 86 1 AGCGTTTGCC 0.951494 -12 GCTGGGAATAACCTGGTTTGCCAAAGTTTTTC 18 53 0 ACCGTTTGCC 0.971879 -210 GTTAAGGTCCAGCACTTTGGCCAGGTTCTAGG 18 93 1 AGCCTTGGCC 0.841487 -170 CAATTCTTCTTCCGGGTTGGCCCACTACCGAT 18 197 1 TCCGTTGGCC 0.889074 -66 TATCTCCGCCCCCCCACTTTCC 23 1 0 CCCCCTTTCC 0.733917 -111 TTCATCCTTTCCCTACTCCGCCATT 25 165 1 CCCATCCGCC 0.599412 -15 AAAACCAAAAACCTGCTTTGCCAGCCTAAATC 30 17 0 ACCGTTTGCC 0.971879 -171 TTTAAACTGAACCTGTCCTGCCAAGGCTTTTT 30 163 1 ACCGCCTGCC 0.917515 -25 CTCTACTTTTCCCTGATCTTCCGTAGTTGCAC 31 51 1 CCCGTCTTCC 0.729219 -38 GGCTCATTATCCCGAATTTGCCATCAAACCAG 32 65 0 CCCATTTGCC 0.922693 -236 TGACAACTAGACCGACTTGGCCAAGAACCAAA 33 71 1 ACCATTGGCC 0.884994 -200 CCCATCTTAGCGCAGATTTGCCGTGGGTTATT 34 123 1 CGCGTTTGCC 0.936438 -178 TCATACCACGCCCCCACTGTCCGGCAGGGTGA 36 207 1 CCCCCTGTCC 0.574341 -94 GTCTCAGCTCAGCAAGCTTGCCGATTATTGTA 40 48 1 AGCACTTGCC 0.87225 -207 CCCTCTAGTAACCAGTCCTGCCCCTATCAAAA 40 216 1 ACCGCCTGCC 0.917515 -39 CAAACCGTACTCCACTCTTGCCGTGATAGAGT 41 138 0 TCCCCTTGCC 0.874946 -163 CAGTGAACTATCCCAACTTGCCCAGTGACTCT 41 231 0 TCCACTTGCC 0.851998 -70 ATTAGCAGATTCGCCCCTGTCGTCT 42 36 0 AGCGTTCGCC 0.854484 -15 *** * ****** Masking position 3 Map Score: 23.9925 Number of sites scoring better than the average of aligned sites = 1376 Number in coding regions = 1236 Number in noncoding regions = 140 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 6 TCAGGGACAATGGAGATGAAATAATGAAAA 1 10 0 TGAGATGAAA 0.528765 -291 GCGCTAGGCGTTGACATCAAATCCCAAAAGT 9 91 1 TGACATCAAA 0.799639 -148 AGAGCTTTCCTAGCCAGCAAAAAAACCAGAC 10 39 0 TGCCAGCAAA 0.978712 -262 CCCCAGGCGATCGCCATCAGAGTTGAGCATA 10 223 1 TGCCATCAGA 0.831397 -78 GTTACTAGAGTTGCCAGCAAAAATTAATTCT 10 263 1 TGCCAGCAAA 0.978705 -38 CCAACGACGATCGCCAGGAAAAGGGATTAAA 13 74 1 TGCCAGGAAA 0.970689 -115 CTAGACAAATTGGCCATCAAATTCTGGCGGC 14 69 1 TGCCATCAAA 0.966358 -160 TTAGCAATGATAGCTAGGAAAATGATTAGGA 19 52 0 TGCTAGGAAA 0.764894 -27 TATCCCGAATTTGCCATCAAACCAGGCGGCA 32 59 0 TGCCATCAAA 0.966357 -242 TAGTCAAAAATAGCGAGGAAAGCCCTAGGCG 32 181 0 TGCGAGGAAA 0.928192 -120 CTAAAGAGATTGGCGAGGAAAGAATCCGCTA 38 68 1 TGCGAGGAAA 0.928192 -103 ATTCTAATCATAACCATCAAAACTATTGGGA 40 104 0 TACCATCAAA 0.673312 -151 * ********* Masking position 6 Map Score: 8.98692 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 207 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 7 GCAACCTCTGGAAAGTTGACCCCCGTCCTGGCG 5 29 0 GAATTACCCC 0.849339 -58 GAAATTTCCCCCCCTAGGCTAGG 6 45 0 GAATTCCCCC 0.968843 -13 CAAGAAGCGCGGTGCTTTCCGCCCCCAGCACTG 8 260 1 GTGTTCCGCC 0.985342 -41 TCTGCAATGGGGTATTTACCGACCTTGGGCAGA 10 67 0 GTATTCCGAC 0.743674 -234 TGAATTGTATGTTAATTGCCGTCTGCGCTTTCC 10 143 1 GTATTCCGTC 0.743676 -158 AGTATCTGACGATGGTTGCCGCCAAATAGTAAA 24 58 1 GTGTTCCGCC 0.985354 -52 TGGTCAAAAGGGGAGTTAACGCCACGCA 29 6 0 GGATTACGCC 0.808126 -200 ATGGCATACGGCTAGATGCCCCCATAGGTACGG 29 39 1 GTAATCCCCC 0.767319 -167 ATGGGAATTGGTGGATTCCCGCCAGACAGGGAA 33 188 0 GGGTTCCGCC 0.970491 -83 CCTGATCCAGGAAGATTGCCGCC 33 258 1 GAGTTCCGCC 0.983074 -13 AAGGATTTCTGCAATTTTCCGCCCCCATCTTAG 34 100 1 GAATTCCGCC 0.976271 -201 CTCCAGCCCCGGAGTTTACCTCCAGGGGTAGTC 36 125 0 GAGTTCCTCC 0.833603 -176 GGGGACTTTTAATACTTTCCCCCCAAACTTGGG 41 19 1 ATATTCCCCC 0.670866 -282 GGGGGCGATCGCTGTTTAACCCCTGATTAAATT 41 196 0 GTGTTACCCC 0.902112 -105 ATTAGCAGATTCGCCCCTGTCGTCTGT 42 34 0 GAGTTGCCCC 0.823576 -17 * ** ** ***** Masking position 7 Map Score: 12.1842 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 540 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 GGGAGTCCGGGGCAGTTACCATTAGAGAGT 2 128 1 GGCAGTTACC 0.659086 -53 TGGCCGAGCCGGCAGTTTCCACAAAGACCC 4 27 0 GGCAGTTTCC 0.947828 -155 ATCAAAGTTTGGCATTTTCACTGTTTTTCC 4 116 0 GGCATTTTCA 0.790578 -66 CAAGAAGCGCGGTGCTTTCCGCCCCCAGCA 8 260 1 GGTGCTTTCC 0.586799 -41 TTTTCAGCCAGGCGTTTTCACGGTCTGGTT 10 17 1 GGCGTTTTCA 0.787243 -284 CGATGCTTCTGGCATTTTTCCC 13 3 0 GGCATTTTTC 0.681612 -186 AGGTAAATCTGGCTCTTTCCCT 15 116 1 GGCTCTTTCC 0.936804 -12 CCAAGGCAATGGCGTTTTCCAGGTTTTTTG 24 15 0 GGCGTTTTCC 0.969566 -95 TTAGTTAAAAGTCTTTTTCCCCTTCCTTAA 27 256 0 GTCTTTTTCC 0.701592 -45 GTCCTGCCAAGGCTTTTTCCG 30 177 1 GGCTTTTTCC 0.974763 -11 AAATTCGGGCGGCTTTTTCCGCATTTCATC 32 14 0 GGCTTTTTCC 0.974763 -287 AGGTCGAATAGGCTTTTCCCTGCCCATAAT 32 263 1 GGCTTTTCCC 0.858994 -38 AGATCCCTAGGGTTTTTTCCCTACCCTGGG 40 183 1 GGTTTTTTCC 0.817716 -72 TAAAATCAAAGGCAGTTTACTTACCGCTGG 41 273 1 GGCAGTTTAC 0.544797 -28 ********** Masking position 6 Map Score: 11.0239 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 553 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 9 TTGAAATCTGAGCCCCAACCCGGAATACCTT 3 35 0 AGCCCCAACC 0.959846 -103 GGCCTGGGGCTCCAAACGCTCAAATGTG 4 164 0 GGCTCCAACG 0.948389 -18 GACTAACCCCGGCCCCTAGCCTAGGGGGGGA 6 31 1 GGCCCCTACC 0.916546 -27 TTCAGGGCCAAGCTCCAAAACTTTGCGTTAC 12 114 0 AGCTCCAAAC 0.875587 -61 AAATTAGCTCCAAAACCAGAGAAAAG 14 213 0 AGCTCCAAAC 0.875587 -16 TTGCCAAGGCGGCCCCATCCCCATAAAACTC 25 45 0 GGCCCCATCC 0.92198 -135 GTCTTTAAGTGGCTCAAATACACCTGTAAAT 27 88 0 GGCTCAAAAC 0.666685 -213 CCCGATCGCCGTCTCCAAGCCCCCTAAATCT 27 219 1 GTCTCCAACC 0.869802 -82 AAGTCCCCTAGCCCCCAATACTGGGGGAATC 28 36 1 GCCCCCAAAC 0.77577 -133 GAAAAGCCATGGTTCCAATCCATTGCCTGGG 29 132 0 GGTTCCAACC 0.862269 -74 CCCGTTGAGTTGCCCCAAAACAGATTTCGAG 34 23 1 TGCCCCAAAC 0.841973 -278 AATGCTCCAATCGCCTTGATTGT 36 3 1 TGCTCCAACG 0.718573 -298 TAATCTTTATGGCTCCAGCCCCGGAGTTTAC 36 139 0 GGCTCCAGCC 0.941629 -162 CAGAATTCCCGGCCTCAAACCTCTCCGCAAT 37 50 1 GGCCTCAACC 0.92678 -84 TGCTGGAATGGGCTTCAAACCGTACTCCACT 41 154 0 GGCTTCAACC 0.914214 -147 ******** ** Masking position 7 Map Score: 10.6325 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 593 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 10 CCTCTACACAGCCCAGAACTATGGTAAAGGC 1 58 1 GCCAGAACTA 0.847352 -243 ATCTGACATTGCCTAAAAACAATCCGGTTAG 3 103 0 GCCAAAAACA 0.679988 -35 CCCACTGAGCGCCGATAACAATAACGTTAGC 9 168 0 GCCATAACAA 0.774558 -71 ATGCCAATTTTCCTAGAACATTGACCAGTAT 12 46 0 TCCAGAACAT 0.646242 -129 CAGCAAGCCTGCCTAGCAAAAAAGGAAAGAT 15 73 0 GCCAGCAAAA 0.803816 -55 CACGGCGATCGCCAAGGAAAATAATTGTCTT 16 81 1 GCCAGGAAAA 0.882909 -127 GAGCAGGAACGCCGAGAAAAAGACAATTATT 16 100 0 GCCAGAAAAA 0.967947 -108 TGGCGATCGGGCCTAGAACCTGGCCAAAGTG 18 105 0 GCCAGAACCT 0.743128 -158 TGGGCCATGAGCCCAGAAAAATTGGCCAATT 18 171 1 GCCAGAAAAA 0.967947 -92 GGGGGCCAATAAAAAACAGGGCTAC 21 11 0 GCCATAAAAA 0.77814 -15 AATAGATTTTTCCTAAAAAAAGCACAAAAAA 28 98 0 TCCAAAAAAA 0.572972 -71 AACCTGCACTTCCGAGAACTAAGCCCCTACC 29 73 1 TCCAGAACTA 0.597103 -133 GACTAATAATTCCAAAAAAAACCAAAAACCT 30 35 0 TCCAAAAAAA 0.572972 -153 GACCGACTTGGCCAAGAACCAAACACTGCGG 33 80 1 GCCAGAACCA 0.925965 -191 AATACCTGAAGCCCAGAATAACCCACGGCAA 34 140 0 GCCAGAATAA 0.79326 -161 AATTCTTGCCGCCGAGGAAATCAGTGGAACA 44 79 1 GCCAGGAAAT 0.635586 -117 TGAGAATAGATCCTAGAAAAAGTTTTATTTA 45 96 1 TCCAGAAAAA 0.889653 -47 *** ******* Masking position 5 Map Score: 9.45983 Number of sites scoring better than the average of aligned sites = 411 Number in coding regions = 356 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 11 TTGAAATCTGAGCCCCAACCCGGAATACCT 3 36 0 AGCCCCAACC 0.502794 -102 TGGAAAGTTGACCCCCGTCCTGGCGATCGC 5 24 0 ACCCCCGTCC 0.905588 -63 AGGACGGACTAACCCCGGCCCCTAGCCTAG 6 25 1 AACCCCGGCC 0.985563 -33 CCGGGTCTAAAACCCCGTCTTTCAGAGTGT 8 205 0 AACCCCGTCT 0.631815 -96 CTATTCCAACAACTCCGGCCCAGTGTCGCC 10 193 1 AACTCCGGCC 0.966363 -108 GGCTGATCATAGCACCTGCCGCCAGAATTT 14 87 0 AGCACCTGCC 0.829669 -142 AGATGACTCAAACACCTTCCCTTCTACAAC 15 47 0 AACACCTTCC 0.599541 -81 CTGCGGTCGTAGCCCCGCCCAGGAGTTAAC 16 145 1 AGCCCCGCCC 0.938325 -63 ACCCAGGAACAACCCCTGCCTCCGCCATAT 17 36 1 AACCCCTGCC 0.95934 -62 TCTCACCCCTAACTCCTGCTGTTCAACGAA 20 88 1 AACTCCTGCT 0.464752 -42 GGAGTTATTTATCTCCGCCCCCCCACTTTC 23 12 0 ATCTCCGCCC 0.832582 -100 AACTCCAGTCAACTCCGGCCATTCTGTTAA 23 36 1 AACTCCGGCC 0.966363 -76 AAAATGCCTCATCTCCGGCCATGGGCGCTG 26 91 1 ATCTCCGGCC 0.954273 -210 CCGAGAACTAAGCCCCTACCGTCACTATAA 29 84 1 AGCCCCTACC 0.829669 -122 AGTCCCCCCTATCCCCGTCCCTGGCAGTGT 32 116 1 ATCCCCGTCC 0.934444 -185 CTAACCCAGAATTCCCGGCCTCAAACCTCT 37 44 1 ATTCCCGGCC 0.69845 -90 AGAGTTAACAATCTCCTGCCCGAATTTTAC 37 86 0 ATCTCCTGCC 0.878235 -48 GAACGAGGACACCACCGACCCCAAGAGAGC 40 149 0 ACCACCGACC 0.619212 -106 ********** Masking position 1 Map Score: 20.4266 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 725 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 12 TTTTTTTGCTGGCTAGGAAAGCTCTGCCCAA 10 45 1 GGCTAGGAAG 0.920962 -256 CGAAACCTAGGACTAGGAAAGCGCAGACGGC 10 160 0 GACTAGGAAG 0.89194 -141 TGGGGGGCGACACTGGGCCGGAGTTGTTGGA 10 197 0 CACTGGGCGG 0.691599 -104 GTTGACCGGGCGCTGGGGAGGGTTTTGGCTA 14 16 1 CGCTGGGAGG 0.938195 -213 CTTGCTGATAGACTGGGGGAGGTAAATCTGG 15 97 1 GACTGGGGAG 0.962511 -31 GCGCGATTTAGGCTGGCAAAGCAGGTTTTTG 30 13 1 GGCTGGCAAG 0.805423 -175 CACTGCCAGGGACGGGGATAGGGGGGACTAA 32 114 0 GACGGGGTAG 0.712946 -187 ACTGTGACAAGACTGGGCAAGCCTAGTCAAA 32 204 0 GACTGGGAAG 0.972195 -97 ATTCCCGCCAGACAGGGAAGGCAATGACGAA 33 176 0 GACAGGGAGG 0.865488 -95 TAAAGAGATTGGCGAGGAAAGAATCCGCTAT 38 69 1 GGCGAGGAAG 0.8547 -102 GGTGCCGTCCGCTGGGAGGGTTGAAATGAT 40 10 1 CGCTGGGGGG 0.917672 -245 AAACTTGGGGGGCTAGGGGGGCATTTAAAAC 41 43 1 GGCTAGGGGG 0.875427 -258 CCCTCAGAGTCACTGGGCAAGTTGGGATAGT 41 226 1 CACTGGGAAG 0.929039 -75 TACCCCCAATGGCAGGGAGAGGTTATGTTCC 44 104 0 GGCAGGGGAG 0.890359 -92 CAGATTTTCAGACGGGGGAAGATAAATAAAA 45 118 0 GACGGGGAAG 0.946384 -25 ******* *** Masking position 6 Map Score: 14.4754 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 635 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 13 GGGGGGTGCTTTTTGCTTGACTGAGTAATC 2 63 1 TTTTGCTTGA 0.838955 -118 AAACCGTTATTTTTGCTTCACCTGCAGTAT 4 70 0 TTTTGCTTCA 0.883561 -112 CTTCAGACTGTTTTGGCACAGTTCAATCTT 13 137 0 TTTTGGCACA 0.495645 -52 TGATAATCTCTTTTGCTTCAGACTGTTTTG 13 152 0 TTTTGCTTCA 0.883561 -37 CTGGGGAGGGTTTTGGCTAAAATTTTCCCT 14 28 1 TTTTGGCTAA 0.752976 -201 GTTTTTGCCTAATTACCTGAAT 15 3 1 TTTTGCCTAA 0.856197 -125 TCCGCCATATTTTTGGTAAACTAACAACGC 17 56 1 TTTTGGTAAA 0.71168 -42 GGGAAAACTTTTGCTAAAAATCTAGGAC 18 9 1 TTTTGCTAAA 0.825029 -254 TTCAACGAAATTTTGCTTGATTAACACCTC 20 109 1 TTTTGCTTGA 0.838955 -21 ACCTTGAATATTTTGCTCAAGTCAAAATCA 27 117 1 TTTTGCTCAA 0.838872 -184 ACCTGTAACATTTTGCTTAATTGACGGTGG 32 237 0 TTTTGCTTAA 0.914127 -64 GGACCCGGATTTTTGGTCAATAAACCTGGA 35 16 1 TTTTGGTCAA 0.727162 -31 ********** Masking position 10 Map Score: 4.97188 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 219 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 14 AACTATCTAACCGGATTGTTTTTAGGCAATG 3 97 1 CCGGATTTTT 0.955128 -41 AGTATAATAGCCGGATTATCTGCCCTTTACT 12 20 0 CCGGATTTCT 0.832587 -155 AGGATTTGGCGGATTGTTTGGGGAATGAA 18 244 0 GCGGATTTTT 0.963458 -19 GTTCCAAGTTCCGGATTGATTTTGACTTGAG 27 132 0 CCGGATTATT 0.770405 -169 CTTTAACCAGGGGGATTTTTTGTGCTTTTTT 28 83 1 GGGGATTTTT 0.889267 -86 GGTAGAATACGGGGATTGTTGACGACCATGG 34 173 1 GGGGATTTTG 0.868836 -128 GATTCGGACCCGGATTTTTGGTCAATAAAC 35 10 1 CCGGATTTTG 0.946113 -37 TCCAATCATAGCGGATTCTTTCCTCGCCAAT 38 76 0 GCGGATTTTT 0.963458 -95 CAGCAAGCTTGCCGATTATTGTAATGAAATT 40 57 1 GCCGATTTTG 0.759609 -198 ******* *** Masking position 6 Map Score: 3.03287 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 65 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 15 AAAATCAGTTGTGTCGCCCCTCTACACAGC 1 40 1 GTGTCGCCCC 0.978851 -261 TGGGGTGTTAGAATCGGGCCACATTTGAGC 4 145 1 GAATCGGGCC 0.568315 -37 ACCTTTTCCCTCGTCGCCCCACTGAGCGCC 9 186 0 TCGTCGCCCC 0.799896 -53 CTAGTCCTAGGTTTCGCCCTATTCCAACAA 10 175 1 GTTTCGCCCT 0.755952 -126 CTCCGGCCCAGTGTCGCCCCCCAGGCGATC 10 205 1 GTGTCGCCCC 0.978851 -96 ATTTTTCCGGGAGTCGGGCCCTAAGGCAGA 13 104 1 GAGTCGGGCC 0.921809 -85 TAGAAGCGATTATTCGCCCCTTTAAACTAG 26 240 1 TATTCGCCCC 0.922745 -61 GAGTGTGAACGTGTCGGCCCCAGGCAATGG 29 114 1 GTGTCGGCCC 0.959316 -92 GAACCATGGCTTTTCGGCCCATCGTTGTGT 29 148 1 TTTTCGGCCC 0.776271 -58 AGTGGTGATTTAGTCCCCCCTATCCCCGTC 32 105 1 TAGTCCCCCC 0.76091 -196 GGAATTGGTGGATTCCCGCCAGACAGGGAA 33 188 0 GATTCCCGCC 0.705434 -83 AACCCCCGTTGAGTTGCCCCAAAACAGATT 34 19 1 GAGTTGCCCC 0.821245 -282 TGTGCCTGGGGATTCGCCCTCACCTCCAGT 34 257 1 GATTCGCCCT 0.844501 -44 GATTCGGACCCGGATTTTTG 35 1 1 GATTCGGACC 0.649001 -46 ATTAGCAGATTCGCCCCTGTCGTCTGT 42 34 0 GATTCGCCCC 0.980618 -17 ********** Masking position 4 Map Score: 14.8785 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 241 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652