AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_synecho_reg_300.orf -o00720_synecho_300.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.48 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.48 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 sll1682 221 alanine dehydrogenase. [EC:1.4.1.1] #2 slr1780 58 hypothetical protein. #3 sll1680 33 hypothetical protein. #4 sll1679 198 hhoA; protease HhoA. [EC:3.4.21.-] #5 slr1783 63 regulatory components of sensory transduction system. #6 sll1678 74 spore maturation protein A. #7 sll1677 65 spore maturation protein B. #8 sll1676 97 malQ; 4-alpha-glucanotransferase. [EC:2.4.1.25] #9 sll1675 49 hypothetical protein. #10 slr1787 300 hypothetical protein. #11 slr1290 63 hypothetical 21.6 kD protein slr1290. [SP:YC90_SYNY3] #12 sll1201 225 hypothetical protein. #13 slr1291 85 ndhD2; NADH dehydrogenase subunit 4. [EC:1.6.5.3] #14 sll1200 217 hypothetical protein. #15 slr1293 56 hypothetical protein. #16 ssr2142 300 ycf19; hypothetical protein. #17 sll1022 146 hypothetical protein. #18 sll1021 39 hypothetical protein. #19 sll1020 95 hypothetical protein. #20 slr1090 44 GTP-binding protein. #21 ssr1789 79 hliA; high light inducible protein. #22 sll1019 60 gloB; probable hydroxyacylglutathione hydrolase (glyoxalase II). #23 sll1018 119 pyrC; dihydroorotase. [EC:3.5.2.3] #24 sll1017 241 putative ammonium transporter sll1017. [SP:YA17_SYNY3] #25 slr1400 119 regulatory components of sensory transduction system. #26 slr0670 117 hypothetical protein. #27 sll0656 130 nucH; extracellular nuclease. #28 sll0654 300 alkaline phosphatase. [EC:3.1.3.1] #29 slr1233 47 frdA; succinate dehydrogenase flavoprotein subunit. [EC:1.3.99.1] #30 ssr2049 51 bchB; protochlorophillide reductase 57 kD subunit. #31 slr1234 45 hypothetical hit-like protein slr1234. [SP:YHIT_SYNY3] #32 slr1235 36 hypothetical protein. #33 slr1236 66 hypothetical protein. #34 ssl2250 221 glycoprotein 64. #35 sll1132 35 hypothetical protein. #36 sll1131 174 hypothetical protein. #37 slr1237 48 codA; cytosine deaminase. [EC:3.5.4.1] #38 ssl2245 300 hypothetical protein. #39 sll1625 293 sdhB; succinate dehydrogenase iron- sulphur protein subunit. #40 sll1623 163 phr; ABC transporter. #41 slr1736 58 phr; hypothetical protein. #42 slr1737 71 phr; hypothetical protein. #43 sll1621 300 phr; membrane protein. [SP:YG21_SYNY3] #44 sll1557 104 sucD; succinyl-CoA synthetase. [EC:6.2.1.5] #45 sll1556 171 hypothetical 37.5 kD protein sll1556. [SP:YF56_SYNY3] #46 sll1555 300 regulatory components of sensory transduction system. #47 sll0920 300 ppc; phosphoenolpyruvate carboxylase. [EC:4.1.1.31] #48 slr0018 55 fumC; fumarase. [EC:4.2.1.2] #49 sll0010 192 hypothetical protein. #50 tRNA-Gly-2 198 tRNA-Gly. #51 slr0019 28 hypothetical protein. #52 sll0008 35 hypothetical protein. #53 sll0007 51 hypothetical protein. #54 sll0006 103 aspC; aspartate aminotransferase. [EC:2.6.1.1] #55 sll0005 187 hypothetical 77.3 kD protein sll0005. [SP:Y005_SYNY3] #56 slr0020 100 recG; DNA recombinase. [EC:3.6.1.-] #57 slr0021 65 putative protease slr0021. [EC:3.4.-.-] [SP:Y021_SYNY3] #58 sll0002 226 ponA; penicillin-binding protein 1A. #59 tRNA-Ser-4 225 tRNA-Ser. #60 slr0213 87 guaA; probable GMP synthase (glutamine-hydrolysing) (glutamine #61 sll0210 114 bacA; bacitracin resistance; possibly phosphorylates undecaprenol. #62 slr0216 127 cobU; cobinamide kinase. #63 slr0217 238 hypothetical protein. #64 ssr0349 258 hypothetical protein. #65 sll0209 218 hypothetical protein. #66 sll0208 257 hypothetical protein. #67 sll0207 157 rfbA; glucose-1-phosphate thymidylyltransferase. [EC:2.7.7.24] #68 slr0220 175 glyS; glycyl-tRNA synthetase beta chain (glycine--tRNA ligase beta #69 sll0205 286 hypothetical protein. #70 sll0204 136 gidA; glucose inhibited division protein A. #71 sll0202 129 gidA; glucose inhibited division protein A. [SP:GIDA_SYNY3] #72 sll0200 300 transposase. #73 sll0542 245 acs; acetyl-coenzyme A synthetase. [EC:6.2.1.1] #74 slr0579 124 hypothetical protein. #75 sll0541 110 des9; acyl-CoA desaturase 1. [EC:1.14.99.5] #76 slr0580 129 hypothetical protein. #77 sll0540 112 hypothetical protein. #78 sll0539 192 hypothetical protein. #79 slr0583 25 hypothetical protein. #80 slr0825 94 hypothetical protein. #81 ssr1398 96 rpmG, rpl33; 50S ribosomal protein L33. [SP:RL33_SYNY3] #82 ssr1399 265 rpsR, rps18; 30S ribosomal protein S18. [SP:RS18_SYNY3] #83 slr0827 294 alr; probable alanine racemase. [EC:5.1.1.1] [SP:ALR_SYNY3] #84 sll0834 284 low affinity sulfate transporter. #85 sll0832 300 hypothetical protein. #86 sll0823 166 sdhB; succinate dehydrogenase iron-sulfur protein. [EC:1.3.99.1] #87 sll0822 163 hypothetical protein. #88 slr0846 61 hypothetical protein. #89 sll0821 300 hypothetical protein. #90 slr0301 261 ppsA; phosphoenolpyruvate synthase (pyruvate,water dikinase) (PEP #91 slr0302 300 pleD; PleD gene product. #92 slr0665 229 acnB; aconitate hydratase 2 (citrate hydro-lyase 2) (aconitase 2). #93 slr0666 300 hypothetical protein. Motif number 1 AAAAGTTTTGCCCGATCGCCATGGTTATTG 2 36 1 CCCGATCGCC 0.926458 -23 GTGGATCTATGGCGATCGCCTTTAGGATT 11 45 1 GGCGATCGCC 0.499996 -19 CCAATTTTCTGGCGATCGCCTGGCGGATCT 12 179 1 GGCGATCGCC 0.499996 -47 CCCTATCAGTAGCGATCGCCGTTGATCCCC 17 12 0 AGCGATCGCC 0.542997 -135 GCTGTCCGTTGGCGATCGCCAGCACCGATT 28 233 1 GGCGATCGCC 0.499996 -68 GGATTTTAGGGGCGATCGCCTTGGGAATTT 39 119 1 GGCGATCGCC 0.499996 -175 AACTGAGTTTGGCGATCGCCTGATATTCTG 46 168 1 GGCGATCGCC 0.499996 -133 TCGCATAGAAGGCGATCGCCGCAAAAGGAG 50 53 1 GGCGATCGCC 0.499996 -146 ATTCCTGACTGCCGATCGCC 59 1 0 GCCGATCGCC 0.551677 -225 CCCCTAGAATTGTGATCGCCCCACCGTTGC 61 17 0 TGTGATCGCC 0.869486 -98 GTGTTTGCTGTTCGATCGCCTTTGAGTAGA 63 199 0 TTCGATCGCC 0.839771 -40 AGTTAACGACTCCGATCGCCATAAAGCTTT 65 155 0 TCCGATCGCC 0.9314 -64 GCTTAAAAGATGCGATCGCCAAAACGCAGA 72 86 0 TGCGATCGCC 0.550864 -215 TTGTTTTTCGGGCGATCGCCTGTGGGTAAA 83 153 1 GGCGATCGCC 0.499996 -142 CCCGATCGCCTAACAATTAA 88 1 1 CCCGATCGCC 0.926458 -61 GCATTGGTTAGGTGATCGCCAACGTGGTCT 93 114 0 GGTGATCGCC 0.544384 -187 ********** Masking position 5 Map Score: 54.4982 Number of sites scoring better than the average of aligned sites = 6056 Number in coding regions = 5510 Number in noncoding regions = 546 Number of orfs with sites within 600 bp upstream = 338 Fraction of orfs with sites within 600 bp upstream = 0.0542885 Motif number 2 TAACCATGGCGATCGGGCAAAACTTTTCTCC 2 32 0 GATGGGCAAA 0.659298 -27 AGTACCTTGGGAAAAATCAAAAAAG 5 5 1 CCTGGGAAAA 0.732894 -59 TTTTCTATATCCTGGGGGAAGTAAAAAGCAC 6 51 0 CCTGGGGAAG 0.804293 -24 TTAACATATCCAACGGGCCAAGAAATGACTT 8 45 0 CAAGGGCCAA 0.584594 -53 CTTGAACAATGCCTGGGCCAGGAACCGTTGC 14 62 0 GCCGGGCCAG 0.906536 -156 CAATTTGCCGGCCCGGGAAAAGCAGTACTCT 24 118 0 GCCGGGAAAA 0.878993 -124 TCAATCTTGACCAAGGGCCAATGGGTTTAGA 25 77 0 CCAGGGCCAA 0.843438 -43 GCGTTACCCTGCAGGGGAAAAATTTAGCCCC 36 75 1 GCAGGGAAAA 0.881193 -100 TAAGCCCTTTGCCCGGGACGACAAGCTAAAG 38 33 0 GCCGGGACGA 0.815797 -268 GGGTTAATGCCCAGGGGGCAGCGAATGATTT 39 54 0 CCAGGGGCAG 0.844732 -240 AGGAAATACCCTGGGAAAAGCAATATGGG 39 275 0 CCCGGGAAAA 0.799618 -19 AACCCCTGGAGCAGGGGGAGGAAGAAGACAA 47 131 0 GCAGGGGAGG 0.883688 -170 TTTATTAATAGAATGGGGCAGGAC 48 4 0 GAAGGGGCAG 0.721219 -52 TCGCCTAGATGACCGGGAAAAATTCCAAAAT 49 47 1 GACGGGAAAA 0.65488 -146 CCTGGGTTAGGATGGGGAAAACCGTCTTTAG 55 14 0 GATGGGAAAA 0.566113 -174 AACCCAGGTAGCCAGGGCCAACCCATTCTCG 55 37 1 GCCGGGCCAA 0.905699 -151 CGGTGGATAGGCACGGGAAGGCCGAATTTGG 58 204 0 GCAGGGAAGG 0.836672 -23 TCTGCGCTAAGATGGGGGCGGAAAATTGCAG 59 183 1 GATGGGGCGG 0.543687 -43 TCAGAACAATGGGGAAGACATAAATAA 60 71 0 CAAGGGGAAG 0.614523 -17 TCTATGGAAAGCACGGGGAAATATTGACTAC 64 66 0 GCAGGGGAAA 0.916669 -193 CTTCCCGTTGGCATGGGCCAGCTTCCTAAAA 65 99 0 GCAGGGCCAG 0.908287 -120 ATTTTCATGGCATCGGGGAGAGCATTGATCT 69 100 0 CATGGGGAGA 0.42097 -187 ACATTTTAAAGCAGGGGACAGTCTACCGCCC 70 80 0 GCAGGGACAG 0.869748 -57 TGCTGTTTACCCTGGGGGCGATCTAGGATAG 73 121 0 CCTGGGGCGA 0.712736 -125 CAAATCTGGGGAAAGGGGAAAAATTTTTGCG 73 176 1 GAAGGGGAAA 0.741841 -70 CTTGTATGATGATAGGGCAAGAAAAGTTTCA 78 31 0 GATGGGCAAG 0.661503 -162 CGGCCAATGACCAGGGGCAGATTTTGTCCCA 80 74 0 CCAGGGCAGA 0.805177 -21 CTCAATGGGGGCTGGGGAAGATTTATGGTTG 84 25 1 GCTGGGAAGA 0.773547 -260 AGACTGACTGCCCAGGGAAAAATTCACTTTC 85 141 1 CCCGGGAAAA 0.799618 -160 TTACGGAAGGGCCGGGGGCAATAATTTTTAT 86 103 0 GCCGGGGCAA 0.905699 -64 GAATTGGTAAGCAAGGGAAGATTAGTCGAAG 87 115 0 GCAGGGAAGA 0.835324 -49 AACCATGGCTGCAAGGGCAAACCTTAAAATT 89 155 0 GCAGGGCAAA 0.916669 -146 TTGGATGATTGCCAGGGCAAGTCTTTGACAT 90 89 0 GCCGGGCAAG 0.915824 -173 ACAGTTCCTCCCTTGGGCAGGGGAGTTAGGA 91 158 0 CCTGGGCAGG 0.737577 -143 *** ******* Masking position 6 Map Score: 33.7847 Number of sites scoring better than the average of aligned sites = 2730 Number in coding regions = 2491 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 270 Fraction of orfs with sites within 600 bp upstream = 0.0433665 Motif number 3 ACTATGGATTGGTCATCAATTCCCTTAAAATAGT 1 117 0 GCTCATTCCC 0.597142 -105 CGCCAAGGCACTCCCAAATGCCCCAAACCTATGG 7 19 0 CCAAAGCCCC 0.970051 -47 TTAACAACAGCAACTTAAATCCCCCTTGAATAGG 14 180 1 CCTAATCCCC 0.974136 -38 GTAACCTGGACAAATAAAATCCCCCTGGCGTAAC 16 187 1 CAAAATCCCC 0.834262 -114 TCTCTGCAGGCCTCCACCTTCCCCT 17 132 1 CCACCTCCCC 0.898273 -15 GGGAACGACGGCACAAAAATCCCCCTAAAATCCT 23 78 0 GCAAATCCCC 0.965514 -42 CGCCAACGGACAGCAAAATTCCCCATCGGTGAAG 28 213 0 CCAAATCCCC 0.990244 -88 ACTAAGCCTGCCACTAAAATTCCCAAGGCGATCG 39 131 0 CCAAATTCCC 0.946384 -163 TCGTCAACCAGAGCAAAATGTCCC 44 1 0 GCAAAGTCCC 0.608415 -104 AGCAGCACCACCACAATATGCCCCCACCTTAATC 45 67 1 CCATAGCCCC 0.775121 -105 ATTCTGCCGCCCAGAAAACTCCCCTAACAAAAAA 46 192 1 CGAAATCCCC 0.93211 -109 CTACTTCACTCCCCAGAGGATTTA 53 38 0 CCTCATCCCC 0.968652 -14 AGGCTGGGACGATGGACATTCCCCATGTATCTCT 56 75 1 GGACATCCCC 0.75652 -26 AGGCCATGGTCGTCAACAATCCCCGTATTCTACC 59 115 1 CCACATCCCC 0.988134 -111 TAGTTAATAGCAACAAAAATCCCCGCTGAACTTA 74 93 0 CCAAATCCCC 0.990244 -32 TACTCCTCTGCACCCAAATTCCCCAAGGGGATAC 82 17 1 CCAAATCCCC 0.990244 -249 GGGGGACATCCTCCTACAATTCCCCATTGATCTA 86 47 1 CCACATTCCC 0.935407 -120 CTGTTTAATCCCTCCTAACTCCCCTGCCCAAGGG 91 146 1 CCTAATCCCC 0.974136 -155 AGGTATTTATCTCCCTAAATCCCCACTTAACAAG 91 202 0 CCTAATCCCC 0.974136 -99 * * *** ***** Masking position 12 Map Score: 27.4786 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 362 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 4 GAGCCAGTCTTTTTTGATTTTTCCCAAGGTACT 5 11 0 TTTATTTTTC 0.681168 -53 GTTGAGACTCGGCTAAATTTTTCTTCCTAATCC 16 70 0 GCTATTTTTC 0.945954 -231 ACTAAAAATAGACTTCAATTTTCCGAATAGCCT 19 40 1 GCTAATTTTC 0.945954 -56 TTCAGCCTAATACTCAATTTTTCTAACTCCCAT 33 11 0 TCTATTTTTC 0.932843 -56 TGCAAATAGGGGCTAAATTTTTCCCCTGCAGGG 36 81 0 GCTATTTTTC 0.945954 -94 AACCAAAAGAGTTTTAAATTTTCAACATTATCT 38 247 0 GTTAATTTTC 0.729146 -54 CTATCTAAACGACTAAATTTTTCTGAGGGGATG 43 266 0 GCTATTTTTC 0.945954 -35 AATCTTATTTTCCTTAAATTTTCCGTAATCTCT 46 34 1 TCTAATTTTC 0.932843 -267 GATTTGCCCTTACTGAAATTTTCCTTGACATAA 58 103 1 TCTAATTTTC 0.932843 -124 TGAGAAGGATTTCTGCAATTTTCCGCCCCCATC 59 193 0 TCTAATTTTC 0.932843 -33 AGGAGGAAACTTCTGGATTTTTCAGGAGTATTA 62 17 0 TCTATTTTTC 0.932843 -111 CAAAGTGTTCTACTTCAATTTTCATGGCATCGG 69 115 0 TCTAATTTTC 0.932843 -172 TCTCTAACTATTTTTGAATTTTCAAAGTTCCCT 70 114 1 TTTAATTTTC 0.681168 -23 CTTTTGTGGTTGCTGCATTTTTCTTTACTCGTG 82 141 0 TCTATTTTTC 0.932843 -125 TTGATATCCCGCCTTTATTTTTCGATCAA 88 43 1 GCTATTTTTC 0.945954 -19 CCTTAAGTCTGGCTCAAATTTTCTAACTATCCC 92 19 0 GCTAATTTTC 0.945954 -211 * ** ******* Masking position 7 Map Score: 20.8436 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 51 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 CACTGACTTGTGGGCAATAGACTAGCCCAAG 4 75 0 TGGGCAAAGA 0.89034 -124 GAACAATGCCTGGGCCAGGAACCGTTGCAAC 14 59 0 TGGGCCAGAA 0.654642 -159 ATGCATCAACAGGGCAGAAAAAACAATTTTT 34 138 0 AGGGCAGAAA 0.934272 -84 ATCACACCAATGGGCTACAAA 35 1 0 TGGGCTAAAA 0.868371 -35 AAGTCAGTAAAGGGCAGATAATCCGGCTATT 36 150 0 AGGGCAGTAA 0.565448 -25 TAATGCCCAGGGGGCAGCGAATGATTTGGAT 39 50 0 GGGGCAGGAA 0.835909 -244 GCTCTGGATTAGGGCAGGAAAATGGTCCGGC 40 64 0 AGGGCAGAAA 0.934272 -100 TGTGGGTCGATGGGCAATGGACTTTGCCTTT 40 95 0 TGGGCAAGGA 0.883471 -69 GGGAGTTTTCTGGGCGGCAGAATATCAGGCG 46 184 0 TGGGCGGAGA 0.810891 -117 CTCCCAGATTAGGGCAGAAAAAAACCCCTGG 47 153 0 AGGGCAGAAA 0.934272 -148 CTAGTCACCTTGGGCTGAAAAGCTCCGGTCT 50 93 1 TGGGCTGAAA 0.899092 -106 CGCTAAGATGGGGGCGGAAAATTGCAGAAAT 59 187 1 GGGGCGGAAA 0.680843 -39 GGACACTGGCTGGGCTAGAAATTTTCCAGCA 63 163 0 TGGGCTAAAA 0.868371 -76 AGGGCAAGGGAGCAATGGGTC 67 1 1 AGGGCAAGGA 0.851498 -157 GCCTTCTCCTTGGGCGGTAGACTGTCCCCTG 70 69 1 TGGGCGGAGA 0.810891 -68 AAATGGTAGCAGGGCTAAAAACTATATTTTA 71 97 0 AGGGCTAAAA 0.833038 -33 GATAAAATTTTGGGCACGGAAGATCCCACAT 72 193 0 TGGGCACGAA 0.67208 -108 GGTCTGTGGCAGGGCTAGGAAGACCATCGCC 76 79 0 AGGGCTAGAA 0.823293 -51 GTATGATGATAGGGCAAGAAAAGTTTCAGTA 78 28 0 AGGGCAAAAA 0.913227 -165 TTTCCGTCTTTGGGCTAAGAATAGTCTGAGA 82 243 0 TGGGCTAGAA 0.860343 -23 ATATGTTTTTTGGGCAAAAAATCAGCCAATG 83 42 1 TGGGCAAAAA 0.932956 -253 GGAAATCAACAGGGCAAAAAAGGCTCGACCT 86 139 0 AGGGCAAAAA 0.913227 -28 GTTCCTCCCTTGGGCAGGGGAGTTAGGAGGG 91 155 0 TGGGCAGGGA 0.911029 -146 ******* *** Masking position 11 Map Score: 21.4496 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 421 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 6 CCAGGCGATCGCCAGAAAATTGGCAAAAAT 12 172 0 GCCAGAAAAT 0.683431 -54 GCAGAGATAGACCGGAAAAACCAGGACTCA 17 109 0 ACCGGAAAAA 0.75869 -38 CAGCTTATTTCCCGGCAAAAAG 21 3 0 CCCGGCAAAA 0.95896 -77 CTTTTCCCGGGCCGGCAAATTGTGGACAAA 24 127 1 GCCGGCAAAT 0.871459 -115 ATCGCCAACGGACAGCAAAATTCCCCATCG 28 219 0 GACAGCAAAA 0.790886 -82 GGGGGTAGACCCCGGCAAAAGTAACTTGTA 34 69 1 CCCGGCAAAA 0.95896 -153 GCTCCATCCCCTCAGAAAAATTTAGTCGTT 43 262 1 CTCAGAAAAA 0.617215 -39 TTGATCTCGCCTCAGCAAAATTTTGACTGG 54 30 0 CTCAGCAAAA 0.77501 -74 CGCTGAACCAGCCAGCAAAATTAAGTAATT 55 153 1 GCCAGCAAAA 0.934063 -35 CAGAATAACCCACGGCAAATCTGCGCTAAG 59 164 1 CACGGCAAAT 0.670082 -62 CTAGAAGAAAACCAGAAAAACC 60 3 0 ACCAGAAAAA 0.681407 -85 CTGGATGCAAGCCAGAAAAAAGAAAAGACA 78 156 0 GCCAGAAAAA 0.868957 -37 TTAGCCCAAAGACGGAAAAA 82 256 1 GACGGAAAAA 0.722413 -10 ATAATTGCTGACCGGAAAAACTGCCCAGTT 83 249 0 ACCGGAAAAA 0.75869 -46 CCCCATTAGTCCCAGCAAATTAGCC 86 6 0 CCCAGCAAAT 0.838059 -161 TATTCCTGGTCCCGGCAAAATTCCATAGAT 86 76 0 CCCGGCAAAA 0.95896 -91 AATTACTAGGAACAGCAAAATCGATCAAAA 89 206 0 AACAGCAAAA 0.549524 -95 AGGGGCTTCGCCCGGCAAAACC 90 3 0 CCCGGCAAAA 0.95896 -259 TTTAGCCTTAGTCGGCAAAATAAACACCAT 90 239 1 GTCGGCAAAA 0.818599 -23 AGTAAATAAAGTCAGAAAAAATATTTTTGA 91 73 0 GTCAGAAAAA 0.589656 -228 TTAAGGACTACACAGAAAATCTTCAGTCTC 92 46 1 CACAGAAAAT 0.392745 -184 ********** Masking position 7 Map Score: 16.7504 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 732 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 TGCTAACATTGGGGGTCAACATCGATCACGTAG 1 37 0 GGGGGCACAC 0.947636 -185 CGGGGATCAACGGCGATCGCTACT 17 2 1 GGGGACACGC 0.982878 -145 CTTTGGTGATGGGGGTCTACCCCCCTATCAGTA 17 31 0 GGGGGCTCCC 0.941817 -116 TTTAACCTCGGGGGAACGACGGCACAAAAATCC 23 90 0 GGGGACGCGC 0.972949 -30 GGCAAACGGTGGGGATCAACCCCAAACCATAGG 32 11 1 GGGGACACCC 0.93975 -26 AAGGGCTATAGGGGGTAGACCCCGGCAAAAGTA 34 59 1 GGGGGAGCCC 0.872942 -163 CCTAATCTGGGAGGGGCATCGACAAATCGCTGG 47 171 1 GAGGGCACGC 0.908017 -130 TAAAACATTAGGGGAACTTCGCCTAGATGACCG 49 29 1 GGGGACTCGC 0.95392 -164 AAGACATAGTGGGGGGCGGCGACCTGGATTACA 49 86 0 GGGGGCGCGC 0.990251 -107 GGGTTAGGATGGGGAAAACCGTCTTTAGCTG 55 9 0 GGGGAAACGC 0.868973 -179 TCGTTAACATGGAGGCCAGCCGCACAGCAGGAG 62 45 0 GGAGGCACCC 0.894717 -83 TGAGTAGACTGGGGGACACTGGCTGGGCTAGAA 63 174 0 GGGGGCATGC 0.949585 -65 CGGCAATACTGGGGGACTTTCACTCAGTTTCCC 68 115 1 GGGGGCTTCC 0.865888 -61 TAAAATTTAAGGGGGACATCCTCCTACAATTCC 86 37 1 GGGGGCACCC 0.975006 -130 ***** ** ** * Masking position 13 Map Score: 20.4165 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 167 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 GGGCCAGGAACCGTTGCAACCAGTTACATTAA 14 47 0 CTTGCAACCA 0.941639 -171 TCGGCTCCAACAGTGGCAAGCATTGGTAAATA 14 138 1 CTGGCAAGCA 0.981227 -80 GAGCCATACTCCCTGGCAAGCATTTTTAGCTT 27 26 1 CTGGCAAGCA 0.981223 -105 TGACTGGAACCTATGGCAACCATGGC 54 5 0 CTGGCAACCA 0.988974 -99 CGGGAGCCAACATTGGCAAGGATTGAGGAGGA 55 123 0 CTGGCAAGGA 0.825054 -65 TATTGGCCAGCCTTGGCAATCAAAAATCCGGT 63 49 1 CTGGCAATCA 0.961991 -190 CAGATATCTTCTATGGAAAGCACGGGGAAATA 64 74 0 CTGGAAAGCA 0.760878 -185 CATGGTGAATCCCTTGCAACCATAATTGCTGA 83 268 0 CTTGCAACCA 0.941819 -27 CTGCTGTCGAGCTTGGCAACCATAAATCTTCC 84 40 0 GTGGCAACCA 0.890022 -245 CTATGCAAGGCAGTGGCAACCAACAAAAACGT 85 60 1 CTGGCAACCA 0.988973 -241 TTAAGGTTTGCCCTTGCAGCCATGGTTGCCAA 89 159 1 CTTGCAGCCA 0.703457 -142 TGGCTTATCCCTTTGGCAACCATGGCTGCAAG 89 171 0 CTGGCAACCA 0.988975 -130 CAAAGACTTGCCCTGGCAATCATCCAAAATTT 90 93 1 CTGGCAATCA 0.961985 -169 TTATAGACCACGTTGGCGATCACCTAACCAAT 93 110 1 CTGGCGATCA 0.786871 -191 * ********* Masking position 12 Map Score: 19.1263 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 120 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 TCGATGTTGACCCCCAATGTTAGCAAGGCAA 1 45 1 CCCCCAATTT 0.921647 -177 CCCACTCCGGCCCCCAAGTTTGCTTGGGCTA 4 53 1 CCCCCAAGTT 0.906563 -146 CTTTTTACTTCCCCCAGGATATAGAAAAATA 6 54 1 CCCCCAGGTA 0.836496 -21 TAAATATTAGCCCCCAGACTTGTTTTACTAA 10 49 0 CCCCCAGATT 0.976385 -252 GTACAGTTAACCCCCAGAATCCGGAAAGGTT 23 34 1 CCCCCAGATC 0.945891 -86 CACAAAAATCCCCCTAAAATCCTAGCAAAGT 23 70 0 CCCCTAAATC 0.751734 -50 ACTTCAACTTTCCCTAGAGTTAGCAAATTTG 28 105 1 TCCCTAGATT 0.750562 -196 AAGGCGATCGCCCCTAAAATCCAATCTAAAT 39 110 0 CCCCTAAATC 0.751734 -184 TGTCGAGAACCCCCTAGAATTGTGCCTATTT 39 196 0 CCCCTAGATT 0.933529 -98 GAAATCGAAATCCCTAATGTTTTTTGGTTTT 45 32 1 TCCCTAATTT 0.461223 -140 AGGCGAAGTTCCCCTAATGTTTTACGATGGT 49 22 0 CCCCTAATTT 0.799821 -171 AAAGGTTACGTCCCCAAATTGCCTTGGTA 54 85 1 TCCCCAAATG 0.567322 -19 ATAAATAAATTCCCCAATTTTTAAGCAACGA 60 48 0 TCCCCAATTT 0.715927 -40 TTTAAACTGTCCCCTAGAATTGTGATCGCCC 61 26 0 CCCCTAGATT 0.933529 -89 CAGCCAGTGTCCCCCAGTCTACTCAAAGGCG 63 182 1 CCCCCAGTTA 0.86116 -57 GAGTGAAAGTCCCCCAGTATTGCCGGAGCTT 68 109 0 CCCCCAGTTT 0.95845 -67 ACTCAGTTTCCCCCCAAATTGGAGGCCAGGA 68 136 1 CCCCCAAATG 0.859546 -40 TCCTAGATCGCCCCCAGGGTAAACAGCAGAG 73 124 1 CCCCCAGGTA 0.836494 -122 TTTTCCCCTTTCCCCAGATTTGTAACCTTTT 73 167 0 TCCCCAGATT 0.898565 -79 AGTTGCCAAGCCCCCAGAATTTCGCTCGAAG 83 222 0 CCCCCAGATT 0.976385 -73 ******** ** Masking position 10 Map Score: 19.2386 Number of sites scoring better than the average of aligned sites = 742 Number in coding regions = 542 Number in noncoding regions = 200 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 10 GTGATCGATGTTGACCCCCAATGTTAGCAA 1 41 1 TTGACCCCCA 0.684759 -181 GGGCAAAACTTTTCTCCCCATAGCTAAGGT 2 19 0 TTTCTCCCCA 0.921795 -40 GTAAAGAAAATTTCCCCACTGTCCTTTTCC 14 12 0 TTTCCCCACT 0.75368 -206 CAATGAACAATTTCTCCCCATCTTAACCCG 15 34 1 TTTCTCCCCA 0.921795 -23 ATTGAAGGTTTTGCCCCACTTTTTCCTGAT 28 260 1 TTGCCCCACT 0.788447 -41 TGGTTTGGGGTTGATCCCCACCGTTTGCC 32 10 0 TTGATCCCCA 0.767054 -27 AAAATTGTTTTTTCTGCCCTGTTGATGCAT 34 139 1 TTTCTGCCCT 0.819703 -83 AGGGGCTAAATTTTTCCCCTGCAGGGTAAC 36 77 0 TTTTTCCCCT 0.697173 -98 AAACTGTGGCTTGATGCCCTACTCCGCAGC 44 67 0 TTGATGCCCT 0.559491 -38 TTTTAAGTTATTGCTCCACTCCCTCCAGTT 45 110 1 TTGCTCCACT 0.849618 -62 CTTCTTAAAGTTGCTCCCCTACTCCCAAAA 46 65 1 TTGCTCCCCT 0.965642 -236 CAGGGGTTTTTTTCTGCCCTAATCTGGGAG 47 154 1 TTTCTGCCCT 0.819703 -147 AACCGACCCATTGCTCCCTTGCCCT 67 6 0 TTGCTCCCTT 0.527785 -152 TTTCACTCAGTTTCCCCCCAAATTGGAGGC 68 132 1 TTTCCCCCCA 0.886046 -44 TTCTTGATCTTTTCCCCACTGTCCAATTAA 73 65 1 TTTCCCCACT 0.75368 -181 GTCGCAAAAATTTTTCCCCTTTCCCCAGAT 73 179 0 TTTTTCCCCT 0.697173 -67 TTCCCCGTATTTGCTACCCTGAGGTAGAAA 82 183 1 TTGCTACCCT 0.710799 -83 TTGGGTACTAATTCTCCCCTTA 83 3 0 ATTCTCCCCT 0.598117 -292 AAATTAATTCTTTACCCACAGGCGATCGCC 83 163 0 TTTACCCACA 0.263885 -132 CCCCTTAAATTTTATCCCCATTAGTCCCAG 86 21 0 TTTATCCCCA 0.729976 -146 CTTTTGCTCCTTGCTACCCTGCTTATATTA 87 73 0 TTGCTACCCT 0.710799 -91 ********** Masking position 2 Map Score: 12.1012 Number of sites scoring better than the average of aligned sites = 1344 Number in coding regions = 1162 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 190 Fraction of orfs with sites within 600 bp upstream = 0.0305172 Motif number 11 GGGAAAAGGACAGTGGGGAAATTTTCTTT 14 9 1 GACAGTGGGA 0.902851 -209 GCTCGGCTCCAACAGTGGCAAGCATTGGTAA 14 136 1 AACAGTGGCA 0.881984 -82 CCCCTGGCGTAACAGAGGGAAGATTTGTGAA 16 208 1 AACAGAGGGA 0.923425 -93 ATATCATTTGGAGAGAGGCTATTCGGAAAAT 19 57 0 GAGAGAGGCA 0.566749 -39 GGTACACTGAAAAAGAGGGGAATGAATCCTC 24 45 0 AAAAGAGGGA 0.686153 -197 CAACCATGCCAGCGGAGGGCAGATTTTATT 25 10 0 AGCGGAGGGA 0.922518 -110 CTGCAAAATTAGGAGTGGGGATATTACTTGT 26 26 0 AGGAGTGGGA 0.846813 -92 CTAATTTTGCAGAGGTGGGGATTTTTTCGTA 26 45 1 AGAGGTGGGA 0.707457 -73 GGCAAACGGTGGGGATCAACCCCAA 32 5 1 AACGGTGGGA 0.902851 -32 AAGCAATATGGGCGGAGGCTACCTCACAGTT 39 256 0 GGCGGAGGCA 0.819186 -38 CTATTCTGAGAAAAGAGGGCAAGCATTGATG 43 225 1 AAAAGAGGGA 0.686153 -76 CAAGGTCTGAAACAGTGGCCAGTAGTCAATA 64 45 1 AACAGTGGCA 0.881984 -214 GGGTTAATTGGACAGTGGGGAAAAGATCAAG 73 67 0 GACAGTGGGA 0.902851 -179 CAGGGTAAACAGCAGAGGCAAAGAAATACAA 73 138 1 AGCAGAGGCA 0.905433 -108 AGGAGAGGGGAAACTAGTTAC 79 1 1 AGGAGAGGGA 0.831485 -25 CGCTATGCAAGGCAGTGGCAACCAACAAAAA 85 58 1 GGCAGTGGCA 0.88065 -243 GCGGGGATTAAGCGGTGGGAAGGATCTCGTT 89 269 0 AGCGGTGGGA 0.93026 -32 ********* * Masking position 11 Map Score: 11.695 Number of sites scoring better than the average of aligned sites = 475 Number in coding regions = 424 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 12 AAATTATTGAGAGGTTTGCCTTGCTAACATTG 1 59 0 GAGTTGCCTT 0.873695 -163 AATCTGGAAAGAGATTTTCCTTCCTAGGCTTG 8 75 1 GAGTTTCCTT 0.710118 -23 AATTTTTTTTGAGATTTTCCCTATAGAAGTCA 12 74 1 GAGTTTCCCT 0.931091 -152 CAAAGTTTTGGAGCTTGGCCCTGAATTGATGC 36 44 0 GAGTTGCCCT 0.97446 -131 CATGGTTCCTGAGGTTTGCCCAGAGGGACTTA 43 50 0 GAGTTGCCCA 0.802384 -251 AAGATACTACGGGATTATCCCTACCTCACTCC 47 220 0 GGGTTTCCCT 0.955915 -81 CTAACGAGAATGGGTTGGCCCTGGCTACCTGG 55 40 0 TGGTTGCCCT 0.946232 -148 ATCTGCACTTTAGATTTGCCCTTACTGAAATT 58 91 1 TAGTTGCCCT 0.916439 -136 GGTGTGCCTGGGGATTCGCCCTCACCTCCAGT 59 35 0 GGGTTGCCCT 0.983931 -191 TAGGATCTGTGGGTTTTTCCCTATTCTGGAGT 65 65 1 GGGTTTCCCT 0.955916 -154 TCAAAATTTTAAGGTTTGCCCTTGCAGCCATG 89 151 1 AAGTTGCCCT 0.769231 -150 ATCAAAATCCTGGCTTATCCCTTTGGCAACCA 89 181 0 TGGTTTCCCT 0.861741 -120 TCAGTTAAAGGGGCTTCGCCCGGCAAAACC 90 9 0 GGGTTGCCCG 0.906169 -253 GCTGTATTTATGGTTTAGCCTTAGTCGGCAAA 90 226 1 TGGTTGCCTT 0.761385 -36 *** ** ***** Masking position 6 Map Score: 15.2925 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 294 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 13 TAGTCTATTGCCCACAAGTCAGTGGCGTGGAAAAGCTTTGA 4 82 1 CCCATCCTGA 0.786863 -117 ATTCCCCCACTCCCCTTTATTTAATTTATTTAAG 13 4 1 CCCCCCATAA 0.908378 -82 GGTTAGAGGCCCCAACCTCCAGTTCCACTGACCATGGTTCA 16 235 0 CCCACCCCGA 0.976456 -66 GGGGGTAGACCCCCATCACCAAAGCCCCCAATAATGAGGGA 17 40 1 CCCCCCCCAA 0.945728 -107 CAATTAGATGCCAATTTTCCTAGAACATTGACCAGTATAAT 36 112 1 CCAACCCTGA 0.817243 -63 TAGAATTGTGCCTATTTTCCCAAGTCTTTGACACCATTGAG 39 172 0 CCTACCCTGA 0.817265 -122 TAAAGTTGCTCCCCTACTCCCAAAAACTTGATTCAAGTCCT 46 70 1 CCCCCCATGA 0.978847 -231 TCGCCGCCCCCCACTATGTCTTCAAAGCTGAAGAGGTTACT 49 97 1 CCACTCACGA 0.508623 -96 CCGTATTCTACCCCAATACCTGAAGCCCAGAATAACCCACG 59 137 1 CCCCCCCCGA 0.987854 -89 CCTCCCCCCCAGCAACTTAGACTAGTTTTGC 66 1 1 CCTCCCCTGA 0.897654 -257 TTTGTTCAGCCCCCTAAATCTCTTCACTAAAGCTCCGGCAA 68 80 1 CCCCTCATAA 0.539185 -96 TCAATGCTCTCCCCGATGCCATGAAAATTGAAGTAGAACAC 69 103 1 CCCCCCATGA 0.978847 -184 AAGGAGAAGGCCCCATCTCCTGAAGAATGGAATTTTCCTTG 70 39 0 CCCCCCATGA 0.978776 -98 TTACACGCAGCCCATAGCCCATTCACTCGGAGGATAAATCT 73 11 0 CCCACCCCGA 0.976456 -235 TGATCTTTTCCCCACTGTCCAATTAACCCGGACCAATACTA 73 69 1 CCCACCACGG 0.758772 -177 CCGGGATTTACCAACCATCCAAGAAAATCGAATCGGTGATG 75 78 0 CCAACCATGA 0.771353 -33 GGAAAAACTGCCCAGTTGCCAAGCCCCCAGAATTTCGCTCG 83 225 0 CCCACCCCGA 0.976455 -70 CATAAATCTTCCCCAGCCCCCATTGAGCAAATTTTTCTCTA 84 11 0 CCCCCCACAA 0.929299 -274 CGACCAACAACCCAAGACCCGAAAGAACAAATTACTAGGAA 89 224 0 CCCACCACAA 0.870173 -77 CATTTTAACCCCTCCTTACCCTTGGAATTGAACCAGCGGGA 90 177 1 CCTCCCATGA 0.868692 -85 **** ** * * ** Masking position 10 Map Score: 23.0582 Number of sites scoring better than the average of aligned sites = 700 Number in coding regions = 636 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 14 GATTTACAGAAATTTTCACTTTTGCCATTC 4 155 0 AATTTTCACT 0.814988 -44 ACTTCCTGTTAATTCTGACTAAAAATAGAC 19 23 1 AATTCTGACT 0.707149 -73 ATCTTGAGAAAAATTTCACTTTTCCAGGGA 24 204 1 AAATTTCACT 0.39927 -38 AGTAACTTGTAATTCTGTCTAGCCTTTGCA 34 88 1 AATTCTGTCT 0.510188 -134 AGGTTCTGTAAATATTGACAATACATGGTC 38 72 1 AATATTGACA 0.436605 -229 CTTCGATTAAAATTTTGTCAAGAAACAA 50 181 1 AATTTTGTCA 0.50795 -18 GCCTCAGCAAAATTTTGACTGGAACCTATG 54 22 0 AATTTTGACT 0.911866 -82 TCTAGCGCTTAAATTTGACTTCGTTGCTTA 60 28 1 AAATTTGACT 0.609539 -60 AGCACGGGGAAATATTGACTACTGGCCACT 64 58 0 AATATTGACT 0.770132 -201 ATTGCTCCTTAATTTTGACTTTGTATCGAT 69 42 0 AATTTTGACT 0.911866 -245 ACCTCCCATCAATTTTGTCTAGTTCCCTCG 77 18 0 AATTTTGTCT 0.816949 -95 CCAGCCCTAGAATATTCTCTATGGAAATCT 84 213 1 AATATTCTCT 0.38092 -72 TGCAAAGGAGAATTTTCACAAAACTTCTTG 85 181 0 AATTTTCACA 0.504685 -120 TACTTCCCATAATTTTCTCTGCGGGATGTC 90 64 1 AATTTTCTCT 0.65519 -198 ATCCACTCTTAATATTGACTGCATTTTAAC 90 156 1 AATATTGACT 0.770132 -106 TAACTGTATAAATTTTGACTAATTATCCAC 91 39 1 AATTTTGACT 0.911866 -262 GGCTCACCTTAATTTTGACTATTCATTTAA 92 183 0 AATTTTGACT 0.911866 -47 ********** Masking position 6 Map Score: 8.09418 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 219 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 15 CAAAACTTTTCTCCCCATAGCTAAGGTCAAT 2 15 0 CTCCCCATAC 0.892557 -44 TTTGGTAATACTCCCCTTTACCCTGGGTTGT 16 103 1 CTCCCCTTTC 0.900416 -198 CTTCCCTTAGCTTCAAACAAA 29 37 0 CTTCCCTTAC 0.910116 -11 GCCGGATTATCTGCCCTTTACTGACTTCGCC 36 154 1 CTGCCCTTTC 0.900416 -21 GACCATTTTCCTGCCCTAATCCAGAGCAAAG 40 68 1 CTGCCCTAAC 0.935573 -96 CTTAAAGTTGCTCCCCTACTCCCAAAAACTT 46 68 1 CTCCCCTACC 0.713703 -233 GGGTTTTTTTCTGCCCTAATCTGGGAGGGGC 47 157 1 CTGCCCTAAC 0.935573 -144 ATTTCGGATGCATCCCATAGCAGTGCATCTA 49 159 0 CATCCCATAC 0.468545 -34 TGGCTTTTGCCTTCCCTAACCGACCCATTGC 67 22 0 CTTCCCTAAC 0.861055 -136 CCTTTACACGCAGCCCATAGCCCATTCACTC 73 24 0 CAGCCCATAC 0.67383 -222 GCAAAAATTTTTCCCCTTTCCCCAGATTTGT 73 175 0 TTCCCCTTTC 0.474276 -71 CCACAGACCACTTCCCTAAACGGCTGATATG 76 101 1 CTTCCCTAAC 0.861055 -29 TTTTCCAACTTTGCCCTTATCTTAGGCGTAT 82 47 0 TTGCCCTTAC 0.703029 -219 TGGTGGATGACTGCCATTAACTTTTCAGTCG 83 112 0 CTGCCATTAC 0.55637 -183 AATCTTCAGTCTCCCCAATACAGTGATTGTG 92 63 1 CTCCCCAATC 0.659575 -167 TCATTTAATTCACCCCTTATCATCACCGAAG 92 160 0 CACCCCTTAC 0.855083 -70 ********* * Masking position 5 Map Score: 7.58433 Number of sites scoring better than the average of aligned sites = 417 Number in coding regions = 345 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813