AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00053_synecho_reg_300.orf -o00053_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 Input sequences: #1 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #2 sll1869 149 cbaB; 3-chlorobenzoate-3,4-dioxygenase. [EC:1.14.-.-] #3 slr1984 300 rps1b; 30S ribosomal protein S1 homolog B. [SP:RS1B_SYNY3] #4 slr0092 117 hisB; hypothetical protein. #5 slr0093 28 dnaJ-like protein slr0093. [SP:DNJH_SYNY3] #6 slr0095 161 hisB; O-methyltransferase. [EC:2.1.1.-] #7 slr0096 29 hisB; low affinity sulfate transporter. #8 slr0498 246 hisB; hypothetical protein. #9 sll0489 286 hisB; ABC transporter. #10 sll0488 116 hypothetical protein. #11 sll0487 109 hypothetical protein. #12 sll0486 173 hypothetical protein. #13 sll0485 247 hypothetical protein. #14 sll0484 130 ABC transporter. #15 slr0502 62 cobW; CobW. #16 slr0505 121 hypothetical protein. #17 slr0506 56 pcr; protochlorophyllide oxido-reductase. [EC:1.3.1.33] #18 sll0481 71 hypothetical protein. [SP:Y481_SYNY3] #19 sll0480 182 hypothetical protein. #20 slr0509 131 alkaline phosphatase-like. #21 slr0510 222 hypothetical protein. #22 ssr0871 55 transposase. #23 slr0511 300 transposase. #24 slr1556 152 ddh; 2-hydroxyaciddehydrogenase. [EC:1.1.1.-] #25 sll1498 50 carA; carbamoyl-phosphate synthetase subunit A. [EC:6.3.5.5] #26 slr1557 99 hypothetical protein. #27 sll1496 146 mannose-1-phosphate guanyltransferase. [EC:2.7.7.-] #28 sll1495 154 hypothetical protein. #29 tRNA-Val 51 tRNA-Val. #30 slr1559 126 aroE; shikimate 5-dehydrogenase. [EC:1.1.1.25] #31 slr1560 77 hiss2; probable histidyl-tRNA synthetase 2 (histidine--tRNA ligase #32 slr1562 30 probable glutaredoxin slr1562. [SP:GLR1_SYNY3] #33 slr1563 300 hypothetical protein. Motif number 1 CAATGCCAAACTTTGCCCACAGCCGCCGACA 1 100 1 CTTTGCCACA 0.940496 -201 TCACTAAAGCCTTTGTCCCCCAACTATTTTC 1 186 1 CTTTGCCCCC 0.956951 -115 GTTTGGTTATTTCTGTCCCCAATTT 3 5 0 TTCTGCCCCA 0.978961 -296 GAGAAACTCTCCCTGACTCCACCAAATGTTG 3 141 0 CCCTGCTCCA 0.950285 -160 AGGAATTAAGTTCTACCCCCGTCCACGTCCC 6 103 1 TTCTACCCCG 0.727132 -59 AAATCCCTGGCTCCGTGGCCATCAA 7 5 1 CCCTGCTCCG 0.826775 -25 GGAACCCATTCTTTGTCCCCATTGTCGCCGC 8 61 0 CTTTGCCCCA 0.978961 -186 CAATTTTAGTCCTTAGCCCCCGTCTGCGAAG 10 63 0 CCTTACCCCC 0.881161 -54 AGGGCGAAAATTTTGCCCCCATTCCTCTGGC 11 59 1 TTTTGCCCCA 0.95108 -51 TAATTCAGGTTACTGACCCCAGATTAATTGA 12 117 1 TACTGCCCCA 0.85533 -57 TGAACTGCCCCCCTGACCCCCCCAAGGCTGG 17 18 1 CCCTGCCCCC 0.987241 -39 GGTGAGTTACCCCTCGCCCCAGGGGAAATGG 19 127 0 CCCTCCCCCA 0.931425 -56 TAAAATCGGGTCTTGGCCACATTCAAACATC 20 32 0 TCTTGCCACA 0.905698 -100 TTACCCATCCCCCTATCCCCATGAACCTTAG 20 65 0 CCCTACCCCA 0.973786 -67 CTCCATTTTATCCTACCCACAATGATAGAAG 21 120 1 TCCTACCACA 0.840562 -103 ACGGAGGATTCCTTGGCCACAGGGAGATCGT 27 58 1 CCTTGCCACA 0.95831 -89 AGTGACGAATTTCTGTTCCCATCTTAAGGTA 27 115 0 TTCTGTCCCA 0.660654 -32 GAAATTTTTCCTTTAACCACAAAGGGATTTT 28 26 0 CTTTACCACA 0.783785 -129 TTTTGGATAATTCTGCCCACCAAGGAAAACC 30 89 0 TTCTGCCACC 0.883051 -38 GATGGTTGGACTCTGCCTACATCAGCAAATA 33 46 1 CTCTGCTACA 0.816997 -255 ***** ***** Masking position 4 Map Score: 26.3019 Number of sites scoring better than the average of aligned sites = 2127 Number in coding regions = 1837 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 CAAAGTTTGGCATTGCCGCCAGAAAAGCTGA 1 84 0 CATGCCGCCA 0.918727 -217 AAACTTTGCCCACAGCCGCCGACACTGGGCG 1 107 1 CAAGCCGCCG 0.941352 -194 TAAGCTAGAGAAAAACCGCCCAGTGTCGGCG 1 123 0 AAAACCGCCC 0.864386 -178 AGTGTAAGTCCAAATCCCCCAACCTTGCCGG 1 226 0 CAATCCCCCA 0.678069 -75 TGTGACCTGAAACTGCCGCCCTGGAGCAAAG 4 25 1 AATGCCGCCC 0.98896 -93 TCTTTGTCCCCATTGTCGCCGCACCGCCAGT 8 52 0 CATGTCGCCG 0.839016 -195 GAGAAGTCGTAAAAGCAGCCC 10 1 0 AAAGCAGCCC 0.800468 -116 ACTAAAATTGAAAAGTCCCCCTGGTTGCACA 10 84 1 AAAGTCCCCC 0.917567 -33 ATAATCACCTAATATCGGCCCACCGCCTAGG 11 20 0 AAATCGGCCC 0.723319 -90 ATGGGGGCAAAATTTTCGCCCTGGTTTTTAA 11 50 0 AATTTCGCCC 0.920311 -60 GCTAAACTTAAAGATCCGCCCCTAGATAGCC 14 44 0 AAATCCGCCC 0.972653 -87 TCGTTTTTGAACTGCCCCCCTGACCCCCCC 17 10 1 AATGCCCCCC 0.976766 -47 TTCACCGATAAATTCCCCCCAGCCTTGGGG 17 37 0 AATTCCCCCC 0.948677 -20 AGTAAGTTTCCCCAGAATCGGGAT 20 4 1 AATTTCCCCA 0.454624 -128 ATTAGCAGATTCGCCCCTGTCGTCTG 25 35 0 CAATTCGCCC 0.895353 -16 GATGATCACAAATTCCCGCCGTTGGCCGCAA 28 68 0 AATCCCGCCG 0.716724 -87 CGTAGCTGTACAATGCCGCCCTGTGGGAGAT 28 96 0 CATGCCGCCC 0.986576 -59 TTAAATTAACAATTGCTCCCC 29 1 0 AATGCTCCCC 0.675841 -51 TAAAGTTGATTAGAGTCGCCCAAACCTAAAA 33 13 0 TAAGTCGCCC 0.716238 -288 ** ******** Masking position 2 Map Score: 20.0479 Number of sites scoring better than the average of aligned sites = 1624 Number in coding regions = 1459 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 3 TGTCGGCGGCTGTGGGCAAAGTTTGGCATT 1 101 0 TGTGGGCAAA 0.497043 -200 CATCGTTCAAACTGGGGAGAGTCCTTTAAA 3 274 1 ACTGGGGAGA 0.902643 -27 TGGCTTTGCTCCAGGGCGGCAGTTTCAGGT 4 29 0 CCAGGGCGGC 0.863247 -89 TAGGGGTAAGGCTGGGGCAGTTTGATCAAC 4 87 0 GCTGGGGCAG 0.770526 -31 GGCAGGGGAAATTAGTGAGTA 9 276 0 GCAGGGGAAA 0.943613 -11 CTCTGTGCAACCAGGGGGACTTTTCAATTT 10 88 0 CCAGGGGGAC 0.892024 -29 TCCCCTAGGCGGTGGGCCGATATTAGGTGA 11 17 1 GGTGGGCCGA 0.910728 -93 TTATTAAAAACCAGGGCGAAAATTTTGCCC 11 47 1 CCAGGGCGAA 0.882792 -63 GACCTTTTGTCGAGGGGAAAACCACGGCTA 14 71 0 CGAGGGGAAA 0.842156 -60 CTTGGGGGGGTCAGGGGGGCAGTTCAAAAA 17 14 0 TCAGGGGGGC 0.813806 -43 CCCCCCCAAGGCTGGGGGGAATTTATCGGT 17 34 1 GCTGGGGGGA 0.97851 -23 TGCCATTTCCCCTGGGGCGAGGGGTAACTC 19 125 1 CCTGGGGCGA 0.968424 -58 ACATCCCGATTCTGGGGAAACTTACT 20 7 0 TCTGGGGAAA 0.815186 -125 TTTTGCTTCACGTGGGGCAACCATATACCA 21 68 1 CGTGGGGCAA 0.899929 -155 GGAACAGACGACAGGGGCGAATCTGCTAAT 25 31 1 ACAGGGGCGA 0.916401 -20 GACTATGACTGGTGGGGGGACGATCTCCCT 27 78 0 GGTGGGGGGA 0.955659 -69 ATCATCTCCCACAGGGCGGCATTGTACAGC 28 93 1 ACAGGGCGGC 0.729281 -62 TTTTCCAAGGAGTGGGGCAAAA 28 143 1 AGTGGGGCAA 0.793293 -12 CTTTGTTTCGGCAGGGGCAAGTTTAAACAT 30 16 1 GCAGGGGCAA 0.959389 -111 GGTTTTCCTTGGTGGGCAGAATTATCCAAA 30 89 1 GGTGGGCAGA 0.878441 -38 CCCAGCCAGAGCAGGGGAGAGGATGATGCC 33 162 0 GCAGGGGAGA 0.964304 -139 CCCTGCTCTGGCTGGGCAACTAGCTTGCGT 33 176 1 GCTGGGCAAC 0.830798 -125 ********** Masking position 5 Map Score: 26.4029 Number of sites scoring better than the average of aligned sites = 3406 Number in coding regions = 3063 Number in noncoding regions = 343 Number of orfs with sites within 600 bp upstream = 359 Fraction of orfs with sites within 600 bp upstream = 0.0576614 Motif number 4 ACAAAGGCTTTAGTGATCGCTCGGTGCGCCA 1 171 0 TAGTGATCGT 0.693674 -130 GCATCAAGATTGCTAATCGTCAGCATAGACC 6 29 1 TGCTAATCGC 0.791954 -133 TGTCCGGAAATGCTGATGGTTGTGGGTTCCA 6 73 0 TGCTGATGGT 0.903032 -89 CTTCCCAAACTGGCGATCGCCAAGGATCATC 8 110 0 TGGCGATCGC 0.964158 -137 TTTACCATTGTGCCAAGGGATGAATTTTCTC 8 217 1 TGCCAAGGGT 0.743899 -30 TGAAATTGAGTGGCAATGGCTTTTTTCAGAA 9 25 1 TGGCAATGGT 0.962193 -262 ACTGGAGCTTTGGCGATCGCCAGAGGAATGG 11 77 0 TGGCGATCGC 0.964158 -33 AATTCAGTTTTACCAATGGTTGA 16 109 1 TACCAATGGT 0.811823 -13 CAAACTGGAATGGCAATTGATAAAGGCGTAG 18 37 0 TGGCAATTGT 0.713887 -35 GGTTTAATCATGGTGACGGCCATAGCTAGTC 19 56 0 TGGTGACGGC 0.70523 -127 CCAGGGGAAATGGCAATGGGTTTATGCTCGC 19 109 0 TGGCAATGGT 0.962195 -74 CCTTTTATAATGGCGATCGCCCTTTAATCAC 19 156 1 TGGCGATCGC 0.964158 -27 GGCACTACCTTGGTGATCGATAGTACGATAA 24 34 0 TGGTGATCGT 0.912662 -119 CCAAAACCCTTACCAATGGGTCA 30 114 1 TACCAATGGT 0.811855 -13 TAATCAACTTTACCGATGGTTGGACTCTGCC 33 32 1 TACCGATGGT 0.874026 -269 AAAAACTTTCTGCCAACCGATGCCCTAGGCA 33 99 1 TGCCAACCGT 0.824344 -202 ********* * Masking position 6 Map Score: 13.4477 Number of sites scoring better than the average of aligned sites = 3961 Number in coding regions = 3584 Number in noncoding regions = 377 Number of orfs with sites within 600 bp upstream = 371 Fraction of orfs with sites within 600 bp upstream = 0.0595888 Motif number 5 AGGGCCGTCCCACACTGGAACTAGCTTGTC 2 75 0 CACACTGGAA 0.76555 -75 CATCCCTTGGCACAATGGTAAAAGCGAAAC 8 209 0 CACAATGGTA 0.909044 -38 CCCCTGGTTGCACAGAGGAAATTGCC 10 101 1 CACAGAGGAA 0.712597 -16 ATAAACCCCTCACCTTGGAACTTAGCCGTG 13 223 1 CACCTTGGAA 0.920613 -25 TGTTTCTCTGCTCCATGGTAGCCGATTCTG 15 26 1 CTCCATGGTA 0.8468 -37 AATCCCTCCCAAAGGTAGCTCTAGCTC 18 8 1 CCCAAAGGTA 0.862053 -64 TCCTTAACACCCCCATCGAACATTT 19 6 0 CCCCATCGAA 0.830512 -177 CTGAAAAATTCACCATCGAAATAGGATTGA 20 96 1 CACCATCGAA 0.856224 -36 TACTATCGATCACCAAGGTAGTGCCGTTAA 24 40 1 CACCAAGGTA 0.939432 -113 TTCCTTTAACCACAAAGGGATTTTCGGGGA 28 20 0 CACAAAGGGA 0.735275 -135 TTTTGCCCCACTCCTTGGAAAAATTACCAG 28 135 0 CTCCTTGGAA 0.764641 -20 TTTCCCGCAACCCCAAGGAACATTTCTCCG 30 60 1 CCCCAAGGAA 0.953732 -67 TAATTCTGCCCACCAAGGAAAACCGGAGAA 30 83 0 CACCAAGGAA 0.961216 -44 TGACCCATTGGTAAGGGTTTTGG 30 114 0 CCCATTGGTA 0.745285 -13 ********** Masking position 10 Map Score: 9.38191 Number of sites scoring better than the average of aligned sites = 1136 Number in coding regions = 1043 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 6 TAGTGAAAATAGTTGGGGGACAAAGGCTTT 1 191 0 AGTTGGGGGA 0.872208 -110 GCTCCGGCAAGGTTGGGGGATTTGGACTTA 1 223 1 GGTTGGGGGA 0.984517 -78 CTCCAAGCTGGGATTGGGGAGCCAAATACC 3 183 0 GGATTGGGGA 0.962949 -118 TTAGGGGTAAGGCTGGGGCAGTTTGATCAA 4 88 0 GGCTGGGGCA 0.90948 -30 GGAAAAGGAAGGGGAATTGCATCAAG 6 7 1 GGAAGGGGAA 0.603105 -155 CTTCCTCGTCGGATTCGGAACCCATTCTTT 8 78 0 GGATTCGGAA 0.626789 -169 GGCGATCGCCAGTTTGGGAAGTGGTTCTGT 8 120 1 AGTTTGGGAA 0.608913 -127 CAATACTGGAGTTTTGGGAAAACAGACTCT 9 101 0 GTTTTGGGAA 0.418384 -186 GATCGCCAGAGGAATGGGGGCAAAATTTTC 11 64 0 GGAATGGGGG 0.742665 -46 ACCCCCCCAAGGCTGGGGGGAATTTATCGG 17 33 1 GGCTGGGGGG 0.938115 -24 AGGTTCATGGGGATAGGGGGATGGGTAACT 20 68 1 GGATAGGGGG 0.715554 -64 TGTTTGGGGGTTGCCTAGTC 26 1 1 TGTTTGGGGG 0.788405 -99 GACTATGACTGGTGGGGGGACGATCTCCCT 27 78 0 GGTGGGGGGA 0.896128 -69 GACGGCTTTGTTTCGGCAGGGGCAAGTT 30 9 1 TGTTTCGGCA 0.356988 -118 TGTTCCTTGGGGTTGCGGGAAAACATTATA 30 52 0 GGTTGCGGGA 0.934616 -75 GGTTTTAGGTTTGGGCGACTCTAATCA 33 8 1 GGTTTGGGCG 0.94057 -293 GCTTTGTTTAGGTTTGGGCATCATCCTCTC 33 146 1 GGTTTGGGCA 0.958346 -155 ********** Masking position 7 Map Score: 12.9872 Number of sites scoring better than the average of aligned sites = 2312 Number in coding regions = 2049 Number in noncoding regions = 263 Number of orfs with sites within 600 bp upstream = 272 Fraction of orfs with sites within 600 bp upstream = 0.0436878 Motif number 7 AGTTTTGGGAAAACAGACTCTAACTTTTGGCAATCTTCTCTTTACC 9 76 0 AATATTTTCT 0.828495 -211 GAGTCACTCAGAATAGCTTCTAGATTTGCTCATTTTTTCAATAATC 9 180 0 GATATTTTTT 0.814948 -107 TTTTAACTAGATTAATAATCCATTATTTGATTGTTTTATTTAAATT 12 66 1 AATAATTTTT 0.748197 -108 ATAAGCTTTGACTAATCCTAAATATTTCTATGATTTAATTTGGGAT 13 70 0 AATATTTTTT 0.962407 -178 GCCCCTAGATAGCCACCATTTAATTTTTACAAATTTTTACGAAATC 14 12 0 AATATTTTTT 0.962481 -119 ATTGACCTTAAATAAACCTCCAGCTTTCCTATTTTTATGAAAGATC 21 164 0 AATATTTTTT 0.962471 -59 TAATTATGGTGAAAATTTTATTCTTTTCACCATTTTC 22 2 1 AATATTTTTT 0.962414 -54 TTTTGCATCTACATAGTTTTTAAATTCAAGCGATTTTCCAAAAGGA 23 62 1 AATATTCTTT 0.81488 -239 TTCATTAAATATCAACCATGCAATTTTATCTACTTTTTGTAAGAAA 23 251 1 AATATTTTTT 0.962479 -50 TGTTAACTAAAGATAACGTTAAATTTTTTAGCCTTTTATTACCAGA 24 101 0 AATATTTTTT 0.962401 -52 ATCGGTTGGCAGAAAGTTTTTATTTTTTCCAATTTTCTCCATGTAT 33 74 0 AATATTTTTT 0.962479 -227 TTGAAGAATTGTTGACTTTTTCTACATGTTATTGTTCGG 33 272 0 AATATTTTGT 0.828504 -29 * * * * *** *** Masking position 12 Map Score: 8.40493 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 24 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 8 TACTAAATTCGATTAATCGAGAATTGGATAATGG 6 138 1 GAATGTGTAA 0.934502 -24 CCATTTTAAAGGTAAAGAGAAGATTGCCAAAAGTTAGAGTC 9 66 1 GAAGGTGAAA 0.938549 -221 GATCAGATCTGGCTAACAGATTATTGAAAAAATGAGCAAAT 9 162 1 GAACGTGAAA 0.976158 -125 TTAAAACAAAGTGTAATAGGTTATAGTTAAACAACTAAACA 12 31 0 GAATGTGAAA 0.982907 -143 ACAAATTAAAGCACAATTAAAACTTGGCAAATAAGCTTTGA 13 105 0 GAATATGAAA 0.898569 -143 GGGCAAATAGATAGTGGGAAAAAGAGCTTGTA 14 109 0 GAATGTGAAA 0.982907 -22 ATAAATTTTTAATTAATTGTTAGTGGTTAAACTTTGCCATT 16 17 1 AAATGTGAAA 0.819196 -105 TCAACCATTGGTAAAACTGAATTTTGCTTAAAGCTCCTTCA 16 91 0 GAACGTGTAA 0.910383 -31 AAAGTAGGGTGAAGAATGGAAAATGGTGAAAAGAATAAAAT 22 25 0 GAATGTGAAA 0.982907 -31 AGGGGAAAACAGGACAGGGACAAATAATAC 32 4 1 GAACGGGAAA 0.885193 -27 TCTAAAATCCGAACAATAACATGTAGAAAAAGTCAACAATT 33 264 1 GAATATGAAA 0.898569 -37 * *** * * * *** Masking position 6 Map Score: 8.25928 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 93 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 9 AAACTGATCCTACCCAGGTAAGGGCCGTCCC 2 94 0 TACCAGGTAA 0.969426 -56 TAAAACAGGGTACCCAGGCAACTCAGTAAAA 3 241 0 TACCAGGCAA 0.904217 -60 CATAGGGACATTACCAGGTAAACCCCAGAGA 13 160 1 TTCCAGGTAA 0.584433 -88 CACGGCTAAGTTCCAAGGTGAGGGGTTTATG 13 222 0 TTCAAGGTGA 0.791036 -26 ACGATATTTACAACCAGCTAAAGTTAACATC 23 140 0 CACCAGCTAA 0.778138 -161 CTTGGAAAAATTACCAGCTAATTATCGTAGC 28 121 0 TTCCAGCTAA 0.910186 -34 CCAGTTCCAATTTCCAGGTGATGTC 31 5 0 TTCCAGGTGA 0.966049 -73 CCCGTTGCAGTTCCCAGGTAAAATTTCCAGT 31 31 0 TTCCAGGTAA 0.905327 -47 ** ******** Masking position 6 Map Score: 3.98823 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 126 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 GGGGAAAAGATTGGTGAAATTGAGTGGCA 9 5 1 AAAATGGAAA 0.668017 -282 AAAGGTAAAGAGAAGATTGCCAAAAGTTAGAGTCT 9 73 1 AGAATGAAAA 0.962819 -214 CCGCAATACTGGAGTTTTGGGAAAACAGACTCTAA 9 99 0 GGAGTGAAAA 0.751188 -188 TCTGGCTAACAGATTATTGAAAAAATGAGCAAATC 9 169 1 AGATTGAAAA 0.865323 -118 GATCGCCAGAGGAATGGGGGCAAAATTTTCGCCCT 11 59 0 GGAAGGAAAA 0.713074 -51 ACCGACATTAAAAACTTAGTTAAAAGCTCCATATA 13 21 1 AAAATGAAAA 0.921392 -227 AAGCACAATTAAAACTTGGCAAATAAGCTTTGACT 13 103 0 AAAATGAATA 0.575849 -145 GGATTTCGTAAAAATTTGTAAAAATTAAATGGTG 14 10 1 AAAATGAAAA 0.921392 -121 GGGCAAATAGATAGTGGGAAAAAGAGCTTGTAT 14 108 0 AGATTGAAAA 0.865323 -23 GGTGAAGAATGGAAAATGGTGAAAAGAATAAAATT 22 24 0 GGAATGAAAA 0.935387 -32 ACTTTCTTACAAAAAGTAGATAAAATTGCATGGTT 23 264 0 AAAATGAAAA 0.921392 -37 AAATACATGGAGAAAATTGGAAAAAATAAAAACTT 33 72 1 AGAATGAAAA 0.962819 -229 **** * * **** Masking position 3 Map Score: 4.75077 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 191 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 11 ATTAATTATCTTTGCTTGATTGTTTAG 12 6 1 TTATCTTGTT 0.75972 -168 GAGCTAGATTTAAGCATTGGCTTTATTTGTTA 12 146 1 TAAGCTTGCT 0.945354 -28 ACTTGGCAAATAAGCTTTGACTAATCCTAAAT 13 93 0 TAAGCTTGCT 0.945354 -155 ACCTTGGAACTTAGCCGTGATTAC 13 234 1 TTAGCGTGTT 0.941292 -14 ATCTTTAAGTTTAGCCGTGGTTTTCCCCTCGA 14 60 1 TTAGCGTGTT 0.941292 -71 CTTATTTTCATTAGCATTGCCTAGGGCATCGG 33 115 0 TTAGCTTGCT 0.965221 -186 CTAATGAAAATAAGCTTTGTTTAGGTTTGGGC 33 133 1 TAAGCTTGTT 0.946379 -168 AATCCTATAATTAGCGTGGGTTCCTATGCCAT 33 230 0 TTAGCTGGTT 0.882634 -71 ***** *** ** Masking position 3 Map Score: 2.9925 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 81 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 12 TTGCCCACAGCCGCCGACACTGGGCGGTTTTTC 1 112 1 CCGCCGATGG 0.956944 -189 ATCGCTCGGTGCGCCATGGTTGGGATTAGCCGT 1 154 0 GCGCCAGTGG 0.972115 -147 CACTAAAGCTCCGGCAAGGTTGGGGGATTTGGA 1 216 1 CCGGCAGTGG 0.953544 -85 TTTACCTTTACCGCTGTTGTTGGCTTGCTA 2 130 1 CCGCTGGTGG 0.884693 -20 AAGTTAGTTAGGGGTAAGGCTGGGGCAGTTTGA 4 92 0 GGGGTAGTGG 0.465599 -26 TTAGTAATGGGGGACGTGGACGGGGGTAGAACT 6 111 0 GGGACGGCGG 0.711419 -51 TGTCGCCGCACCGCCAGTAATGGTATTAAATGC 8 37 0 CCGCCAATGG 0.965384 -210 TACTGGCGGTGCGGCGACAATGGGGACAAAGAA 8 51 1 GCGGCGATGG 0.826282 -196 GGTTCCGAATCCGACGAGGAAGGTGATGATCCT 8 86 1 CCGACGGAGG 0.79362 -161 TTTGAGCGGCCGGCCGAGAAAGGGGCATAATGT 9 231 1 CGGCCGAAGG 0.910231 -56 CCTAGGCGGTGGGCCGATATTAGGTGATTATTA 11 20 1 GGGCCGATAG 0.692597 -90 ACCCCTTCGGCCATCAACAGAATCGGCTAC 15 43 0 CGGCCAACAG 0.660562 -20 CCCCCTGACCCCCCCAAGGCTGGGGGGAATTTA 17 26 1 CCCCCAGTGG 0.854705 -31 ATCATGGTGACGGCCATAGCTAGTCCAAATTTC 19 48 0 CGGCCAGTAG 0.910375 -135 AGAGGATTTGCGGCCAACGGCGGGAATTTGTGA 28 61 1 CGGCCAGCGG 0.691948 -94 GCTAGTTGCCCAGCCAGAGCAGGGGAGAGGATG 33 167 0 CAGCCAGAGG 0.703017 -134 ****** * *** Masking position 13 Map Score: 9.71248 Number of sites scoring better than the average of aligned sites = 2301 Number in coding regions = 2170 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 146 Fraction of orfs with sites within 600 bp upstream = 0.02345 Motif number 13 CGCCAGAAAAGCTGACGGGAGGTGGTTAAT 1 69 0 GCTGACGGGA 0.870233 -232 AATTTGCGTTGCTGACAGCGA 8 2 0 GCTGACAGCG 0.896571 -245 CTGAAACTTCGCAGACGGGGGCTAAGGACT 10 57 1 GCAGACGGGG 0.927185 -60 TTTCCTCTGTGCAACCAGGGGGACTTTTCA 10 92 0 GCAACCAGGG 0.675473 -25 AACAGAATCGGCTACCATGGAGCAGAGAAA 15 28 0 GCTACCATGG 0.414179 -35 TCTGTTGATGGCCGAAGGGGT 15 52 1 GCCGAAGGGG 0.968209 -11 AATGGCAATTGATAAAGGCGTAGAGCTAGA 18 30 0 GATAAAGGCG 0.49827 -42 GTTACCCCTCGCCCCAGGGGAAATGGCAAT 19 123 0 GCCCCAGGGG 0.805445 -60 AAAAGGATTTGCCGAAGTCGCTACTATTCC 23 216 0 GCCGAAGTCG 0.687684 -85 TAGTGGAACAGACGACAGGGGCGAATCTGC 25 27 1 GACGACAGGG 0.656188 -24 CAGCTTGATTGCTACAGGCGTTTGGCCCAA 26 33 0 GCTACAGGCG 0.883706 -67 TCGACCTACTGCTAACAGCGTTGACAGCTT 26 57 0 GCTAACAGCG 0.843789 -43 GGATTCCTTGGCCACAGGGAGATCGTCCCC 27 63 1 GCCACAGGGA 0.72176 -84 AGGATTTGCGGCCAACGGCGGGAATTTGTG 28 63 1 GCCAACGGCG 0.95896 -92 TGCTGAAGGGAAAGGACAAAG 31 67 0 GCTGAAGGGA 0.785801 -11 ********** Masking position 1 Map Score: 5.52099 Number of sites scoring better than the average of aligned sites = 2749 Number in coding regions = 2565 Number in noncoding regions = 184 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 14 GGTAAAGCAAAAAACTGATCCTACCCAGGTAAGGG 2 101 0 AAATACCTAC 0.792886 -49 AAAGCCAGGAAAAGTTTATCCAAACCGGCTATGGA 4 52 1 AAATACCAAC 0.967876 -66 CACAATGGTAAAAGCGAAACCAAGCCCAAACAGTA 8 194 0 AAAGACCAAC 0.949674 -53 ATCAGCCCTGTAAACTGACCCAATCAAGCGACCGC 9 130 0 TAATACCAAC 0.923082 -157 AGATTATTGAAAAAATGAGCAAATCTAGAAGCTAT 9 179 1 AAATACAAAC 0.89475 -108 GGCATAGCATTAAACTTAACTAACCCATAAACCCC 13 197 1 TAATACTAAC 0.572674 -51 GCGATTTTCCAAAAGGAAGCCAAACACTACAATTA 23 91 1 AAAGACCAAC 0.949674 -210 GGTATTCATTAAATATCAACCATGCAATTTTATCT 23 247 1 AAATACCATC 0.923082 -54 ATTGTTAATTTAAATGGAGCCATGCTATATTACTA 29 19 1 TAAGACCATC 0.749619 -33 GATGATGCCCAAACCTAAACAAAGCTTATTTTCAT 33 136 0 AAATACAAAC 0.89475 -165 AACATGTAGAAAAAGTCAACAATTCTTCAA 33 281 1 AAATACAATC 0.772009 -20 *** * * **** * Masking position 8 Map Score: 5.54238 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 80 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 15 AGGTGATGATCCTTGGCGATCGCCAGTTTGG 8 106 1 CCTTGGCGTC 0.871821 -141 CCGCTATCCCCTAGGCGGTGGGCCGATATT 11 10 1 CCTAGGCGTG 0.955364 -100 CGGCTAAGTTCCAAGGTGAGGGGTTTATGGG 13 220 0 CCAAGGTGGG 0.877851 -28 ATGGTGGCTATCTAGGGGCGGATCTTTAAGT 14 39 1 TCTAGGGGGG 0.881918 -92 TTCCCCCCAGCCTTGGGGGGGTCAGGGGGGC 17 24 0 CCTTGGGGGG 0.991181 -33 GCTAGAGCTACCTTTGGGAGGGATT 18 5 0 CCTTTGGGGG 0.898718 -67 TTGCCATTTCCCCTGGGGCGAGGGGTAACTC 19 124 1 CCCTGGGGGA 0.720673 -59 GGTAATTTTTCCAAGGAGTGGGGCAAAA 28 137 1 CCAAGGAGGG 0.802986 -18 GAGAAATGTTCCTTGGGGTTGCGGGAAAACA 30 57 0 CCTTGGGGTG 0.976406 -70 CTCCGGTTTTCCTTGGTGGGCAGAATTATCC 30 85 1 CCTTGGTGGC 0.891499 -42 CAACCGATGCCCTAGGCAATGCTAATGAAAA 33 112 1 CCTAGGCATG 0.627547 -189 ******** ** Masking position 2 Map Score: 3.62968 Number of sites scoring better than the average of aligned sites = 1143 Number in coding regions = 1057 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435