AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00130_synecho_reg_100.orf -o00130_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 slr0723 78 hypothetical protein. #2 slr0724 83 sohA; HtaR suppressor protein. #3 slr0725 300 hypothetical protein. #4 slr0738 89 trpE; probable anthranilate synthase component I. [EC:4.1.3.27] #5 slr0739 80 crtE; geranylgeranyl pyrophosphate synthase. [EC:2.5.1.29] #6 sll0696 76 hypothetical protein. #7 slr0741 86 phoU; a negative regulator of pho regulon. #8 slr0742 75 hypothetical protein. #9 slr0743 300 nusA; N utilization substance protein. #10 sll0223 141 ndhB; NADH-plastoquinone oxidoreductase chain 2. [EC:1.6.5.3] #11 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #12 slr1291 85 ndhD2; NADH dehydrogenase subunit 4. [EC:1.6.5.3] #13 sll1200 217 hypothetical protein. #14 sll1191 233 hypothetical protein. #15 slr2007 111 ndhD; NADH dehydrogenase subunit 4. [EC:1.6.5.3] #16 slr2012 247 hypothetical protein. #17 sll1733 116 ndhD; NADH dehydrogenase subunit 4. [EC:1.6.5.3] #18 sll1732 300 ndhF; NADH dehydrogenase subunit 5. [EC:1.6.5.3] #19 sll1127 200 menB; naphthoate synthase. [EC:4.1.3.36] #20 slr1255 176 crtB, pys; phytoene synthase. [EC:2.5.1.-] [SP:CRTB_SYNY3] #21 sll1909 77 prmA; probable methyltransferase. [EC:2.1.1.-] [SP:PRMA_SYNY3] #22 sll1908 260 serA; phosphoglycerate dehydrogenase. [EC:1.1.1.95] #23 slr0261 42 ndhH; NADH-plastoquinone oxidoreductase 49 kD subunit. [EC:1.6.5.3] #24 slr0262 50 hypothetical protein. #25 slr0263 38 hypothetical protein. #26 slr0264 99 hypothetical 41.0 kD protein slr0264. [SP:Y264_SYNY3] #27 slr0265 119 transposase. #28 slr1519 109 hglK; HglK. #29 sll1220 300 potential NAD-reducing hydrogenase subunit. [EC:1.6.5.3] #30 sll0809 140 putative lipoate-protein ligase A. [EC:6.-.-.-] #31 slr0817 68 entC; isochorismate synthase. [EC:5.4.99.6] #32 slr0818 93 hypothetical protein. #33 ssr1391 77 hypothetical protein. #34 slr0820 145 glucosyltransferase. #35 slr1980 61 hypothetical protein. #36 sll1876 260 hemN; oxygen independent coprophorphyrinogen III oxidase. #37 sll1868 152 dnaG; DNA primase. [EC:2.7.7.-] [SP:PRIM_SYNY3] #38 slr1279 71 ndhC; NADH-plastoquinone oxidoreductase chain 3. [EC:1.6.5.3] #39 slr1281 300 ndhJ; NADH-plastoquinone oxidoreductase subunit J (orf 155). #40 ssl1807 200 hypothetical protein. #41 slr0331 178 ndhD; NADH-plastoquinone oxidoreductase chain 4. [EC:1.6.5.3] #42 slr0055 143 trpG; anthranilate synthase component II. [EC:4.1.3.27] #43 slr0492 187 menE; O-succinylbenzoic acid-CoA ligase. [EC:6.2.1.26] #44 sll0602 130 hypothetical protein. [EC:3.1.3.16] #45 sll0829 112 rapQ; methyltransferase. [EC:2.1.1.64] #46 slr0844 151 ndhF; NADH-plastoquinone oxidoreductase chain 5. [EC:1.6.5.3] #47 slr0095 161 hisB; O-methyltransferase. [EC:2.1.1.-] #48 sll0027 164 ndhD; NADH dehydrogenase subunit 4. [EC:1.6.5.3] #49 sll0026 244 ndhF; NADH dehydrogenase subunit 5. [EC:1.6.5.3] #50 slr0926 189 ubiA; 4-hydroxybenzoate-octaprenyl transferase. [EC:2.5.1.-] #51 sll0522 139 ndhE; NADH-plastoquinone oxidoreductase chain 4l. [EC:1.6.5.3] #52 sll0521 94 ndhG; NADH-plastoquinone oxidoreductase chain 6. [EC:1.6.5.3] #53 sll0520 110 ndhI; NADH-plastoquinone oxidoreductase subunit I (frxb protein). #54 sll0519 254 ndhA; NADH-plastoquinone oxidoreductase chain 1. [EC:1.6.5.3] #55 sll1496 146 mannose-1-phosphate guanyltransferase. [EC:2.7.7.-] Motif number 1 GTGGAAGATATTTGCCCATCCCCTATTTCTTGA 2 27 0 TTGCCCCCCC 0.963966 -57 CTCCCGGCCATTGCCCAACCCCGTTATTTAGTA 4 23 0 TTCCCACCCG 0.919354 -67 GTTTCTTCCATCACCCCTACCTGTAA 4 74 0 TCTCCAACCC 0.830446 -16 AGTCGATTTCTTTCCCCATCCCCCTAGTATC 6 9 0 TTCCCCCCCC 0.986391 -68 TCCGGTCTTTTCCCATACCCGTAGGTGGTCC 6 56 0 TTCCCACCCG 0.919354 -21 CCGACCTAATCTCCCCACTCCCCCATTAATCAC 7 58 1 CTCCCACCCC 0.985531 -29 CGATAAAGCTCTAGCCCTTCCCCAGACCTAGGC 8 33 1 CTGCCCCCCC 0.970291 -43 TTGGGGCGGGCCCTCCGAGCCCCAGTTCCCAGC 9 38 0 CCTCCGCCCC 0.746762 -263 AATAAGCCGATCGCCCCGCACCGTGATCTAATT 9 118 1 TCCCCCACCG 0.79268 -183 TTTGTCCTGACCACTCCTTGCCCACCGTTGACC 9 248 0 CCCTCCGCCC 0.808055 -53 ACTGGGGCCCTTTGCCATGGCCCAAAACCAGGA 10 30 1 TTGCCAGCCC 0.828074 -112 CTACAGATTCTTACCCTCCACCCAACTGTAA 11 9 0 TTCCCTACCC 0.930605 -292 ATGCCAAACTTTGCCCACAGCCGCCGACACTGG 11 102 1 TTCCCAGCCG 0.727246 -199 ATTCCCCCACTCCCCTTTATTTAAT 12 3 1 TCCCCACCCC 0.982462 -83 AATTTCCCCACTGTCCTTTTCCC 13 1 0 CTTCCTTCCC 0.790481 -217 TCAAATGCCATCGTTCTTTGCCCAATGGGATGG 15 49 1 TCTTCTGCCC 0.457578 -63 GCCGTTTAATCCCCCCTAGCCCCCCTTGGGAAG 16 84 1 CCCCCTCCCC 0.984597 -164 TTGGTAACATTTCCTCCCTTCCCAAGGGGGGCT 16 101 0 TTCTCCTCCC 0.719048 -147 ATGGCTGATCTTATCCAGGCCCCAAAGGGGCAT 18 127 0 TTTCCACCCC 0.949927 -174 GTTAACAAAATTTCCCACAACCCCC 18 286 1 TTCCCAACCC 0.934843 -15 GGTCAAACCTTTACGCTGTCCCCGTAAGATGGG 19 154 1 TTCGCTCCCC 0.665518 -47 TTAGCCAACTTTACTCAGCCCCCGTA 22 4 0 TTCTCACCCC 0.918725 -257 TATGGTTTGGCCCCCCCAGTCCCAGGGAATCAG 22 163 1 CCCCCCTCCC 0.939335 -98 CTAACGGTTATCCCCCAAGCCGCTAGAATGGGC 22 204 1 TCCCCACCGC 0.618084 -57 ATTAAATTTTTCTCCCTTTTCCC 23 1 0 TCCCCTTCCC 0.901239 -42 TCACCATTTTCCATTCTTCACCCTACTTTTCAA 26 37 1 CCTTCTACCC 0.531021 -63 AAAGCCCCCCTGACCCCCCAAATTTGG 27 5 1 CCCCCTCCCC 0.984597 -115 TTCCCGTTGGCTACCCTTCCCCCTGCTCAGTCT 30 70 1 CTCCCTCCCC 0.984536 -71 TTCCCCCTGCTCAGTCTTCCCCCTGGCGTTTAT 30 86 1 TCGTCTCCCC 0.796549 -55 TAAGCCTACCCTTTCCATTACCCAGGGAAA 33 58 1 CTTCCAACCC 0.85623 -20 GCAAATTGCACTCTCCTTCACCGGGGGGTGCTT 37 41 1 CTTCCTACCG 0.532133 -112 TTGTCCTTGCCTTGCCTGCCCCCCCTATTGTCT 38 24 0 CTGCCTCCCC 0.959181 -48 TTAGTTTTAGCTCCCCCTTCCCCCACTGTTGCC 39 244 0 CTCCCCCCCC 0.988825 -57 GCTAAGCTTTCCAGCCAAACCCGGTAAATATTT 46 72 0 CCGCCACCCG 0.83759 -80 AGTTCTACCCCCGTCCACGTCCCCCATTACTAA 47 111 1 CCTCCATCCC 0.802084 -51 CCATTGCGGTTTTTCCAGACCCCAAGGAGCAAC 49 16 0 TTTCCACCCC 0.949927 -229 GTAATAAAACCTCCCCCAGACCGACAACGGCGA 49 121 1 CTCCCCACCG 0.822984 -124 TCTAGTTAAATTTCTCTTACCCCACT 51 124 1 TTCTCTCCCC 0.913536 -16 GTCACTGAAATTTGTCTTAGCCCAGCTTCTAAC 53 39 1 TTGTCTGCCC 0.477006 -72 AATCATTTGCTTATCCCAATCCCAAATCT 53 92 1 TTTCCCTCCC 0.81115 -19 CCTCTAGTAACCAGTCCTGCCCCTATCAAAACT 54 26 0 CCGTCCCCCC 0.869165 -229 TCCCTAGGGTTTTTTCCCTACCCTGGGCAGCCC 54 57 0 TTTTCCACCC 0.562157 -198 ** **** **** Masking position 6 Map Score: 58.0805 Number of sites scoring better than the average of aligned sites = 3805 Number in coding regions = 3319 Number in noncoding regions = 486 Number of orfs with sites within 600 bp upstream = 410 Fraction of orfs with sites within 600 bp upstream = 0.0658529 Motif number 2 TAAAGCCTTTGTCCCCCAACTATTTTCACTA 11 190 1 GTCCCCCACT 0.820158 -111 ATTCCCCCACTCCCCTTTATTT 12 2 1 TTCCCCCATC 0.841393 -84 GTAAAGAAAATTTCCCCACTGTCCTTTTCCC 13 11 0 TTTCCCCATG 0.931726 -207 TCCATGTTCATCCCCCCAAAGATGGGACTGA 14 102 0 TCCCCCCAAG 0.982037 -132 GTTTGATTAATCTCCCCAGGTTATCAAATGC 15 26 1 TCTCCCCAGT 0.577028 -86 ATCCCCCCTAGCCCCCCTTGGGAAGGGAGGA 16 92 1 GCCCCCCTGG 0.834545 -156 TAACCGCAAATTTCCCCACTGGAAAGTGTTT 16 200 0 TTTCCCCATG 0.931726 -48 TGGAATTTTATTTCCCCTATGATATGGTGTA 18 40 1 TTTCCCCTTG 0.734051 -261 CGCCCCGATGTTTCCCCTTAGGTGAAGAGAA 20 25 0 TTTCCCCTAG 0.640798 -152 GATTAATTCCTCCCCCCATTGACTTGGACCC 21 23 0 TCCCCCCATG 0.988316 -55 CTGGTTACTGTTCCCCCAGAGCAAAATCTTT 22 52 0 TTCCCCCAAG 0.977662 -209 TGACTGTGTTTCCCCCCAAATTTGGGGGGTC 27 22 0 TCCCCCCAAT 0.904828 -98 CACAGTCAAAGTCCCCCAGTATTGAGGGATT 27 45 1 GTCCCCCATA 0.902868 -75 TTGGCTACCCTTCCCCCTGCTCAGTCTTCCC 30 76 1 TTCCCCCTCT 0.590102 -65 GGCAATGCCCCCCAATAGTAAGGGCAA 32 7 1 GCCCCCCATA 0.920704 -87 CGTTCATTGCGCCCCCCAGGGACAACGG 33 8 0 GCCCCCCAGG 0.961448 -70 GACAAGTATCTCTCCCCATCGTCACTCTTAG 37 110 1 TCTCCCCACG 0.911534 -43 CACAAAAATATTCCCCCAAAGTTTTCAGTCC 39 210 1 TTCCCCCAAG 0.977662 -91 TAGCTCCCCCTTCCCCCACTGTTGCCAATGG 39 239 0 TTCCCCCATG 0.985447 -62 GTAGTTGAGCTTCCCCCAGAGGGTTTTGGAA 40 170 1 TTCCCCCAAG 0.977662 -31 CCAACCAAGTTACCCCCATTGTTCCATGGCA 42 79 0 TACCCCCATG 0.921582 -65 TAGCATTGTCTCCCCCCAAAAAGGGGCTAAG 46 99 0 TCCCCCCAAA 0.921341 -53 CCCCGTCCACGTCCCCCATTACTAAATTCGA 47 119 1 GTCCCCCATA 0.902868 -43 GGCCCATTTTGACCCCCATTGCGGTTTTTCC 49 33 0 GACCCCCATG 0.882761 -212 AGGGAGATCGTCCCCCCACCAGTCATAGTCA 55 78 1 TCCCCCCACA 0.916347 -69 ******** ** Masking position 6 Map Score: 36.8938 Number of sites scoring better than the average of aligned sites = 1478 Number in coding regions = 1329 Number in noncoding regions = 149 Number of orfs with sites within 600 bp upstream = 153 Fraction of orfs with sites within 600 bp upstream = 0.0245744 Motif number 3 GATTCCAAATGGCGATCGCCAGTGTGAAAG 3 272 1 GGCGATCGCC 0.499995 -29 ACATAAATAAGCCGATCGCCCCGCACCGTG 9 113 1 GCCGATCGCC 0.5418 -188 CAAAATTGTCGGCGATCGCCTACTTTGCGA 9 186 1 GGCGATCGCC 0.499995 -115 TGCATAGTAAGGCGATCGCCAAAGTTTGGG 19 46 1 GGCGATCGCC 0.499995 -155 GAAACATCGGGGCGATCGCCTTTGTTCGCT 20 42 1 GGCGATCGCC 0.499995 -135 AGTATCCTGGGCCGATCTCCGTAGCCCATT 22 230 0 GCCGATCTCC 0.900706 -31 GGGCGCAATGAACGATCGCCGTTGCGTTCA 33 25 1 AACGATCGCC 0.825517 -53 TCCCGGTCGCCCACGGCAAAA 39 290 0 CCCGGTCGCC 0.924645 -11 GACCGACAACGGCGATCGCCAAAGTCAGAA 49 139 1 GGCGATCGCC 0.499995 -106 AATTTTCTCTCCCGATCGCCGACCCATGGT 50 46 1 CCCGATCGCC 0.910338 -144 CTGGTGGGGGGACGATCTCCCTGTGGCCAA 55 70 0 GACGATCTCC 0.858716 -77 ********** Masking position 6 Map Score: 30.5044 Number of sites scoring better than the average of aligned sites = 5973 Number in coding regions = 5425 Number in noncoding regions = 548 Number of orfs with sites within 600 bp upstream = 344 Fraction of orfs with sites within 600 bp upstream = 0.0552522 Motif number 4 CGGACAATTCGCCAAAATTGTCGGCGATCGC 9 174 1 GCCAAAATGT 0.589342 -127 GGCGGCTGTGGGCAAAGTTTGGCATTGCCGC 11 96 0 GGCAAAGTTG 0.869764 -205 CTAAAGCTCCGGCAAGGTTGGGGGATTTGGA 11 218 1 GGCAAGGTGG 0.896636 -83 TTGTAGTAGTGGCAAAAGTAG 15 101 1 GGCAAAAGAG 0.842561 -11 ATTTTCCATTGGCAAGATTTACCTTCATCCA 17 72 1 GGCAAGATTA 0.57621 -45 GGCAAAAAGAGGTGATAAGTC 17 106 0 GGCAAAAAAG 0.573921 -11 TAAGGCGATCGCCAAAGTTTGGGGCCAATCC 19 53 1 GCCAAAGTTG 0.731288 -148 GGATTTAGGGGGCAAAATAAGACTTTGCAAA 27 71 1 GGCAAAATAG 0.949564 -49 CGTTATTGTGGGCAAGATTGTGGAGGCACAC 29 163 1 GGCAAGATGT 0.568013 -138 CAAAAGTCTAGGCAAAATATGTTAGTCTTAA 30 28 0 GGCAAAATTG 0.897075 -113 ACAATGGCGGGGCAAAATAGAATATGGGTAG 31 34 0 GGCAAAATGA 0.926842 -35 ATATTGAGTTGCCAAAATCAAGCAATAGTAA 36 126 0 GCCAAAATAA 0.762219 -135 GGTCGCCCACGGCAAAATTAAACATCAAAAT 39 276 0 GGCAAAATAA 0.887213 -25 GGAAGGGCTTGGCAAAAGCAAAATTCTAAGG 40 72 0 GGCAAAAGAA 0.69098 -129 TTGAATCCTAGGCAAAGTCGGTAAATAAACC 43 147 1 GGCAAAGTGG 0.958735 -41 CGCAATGGGGGTCAAAATGGGCCTCCCAATC 49 41 1 GTCAAAATGG 0.615787 -204 TTTGTGGATTGCCAAAGTTGATTGGGAGGCC 49 60 0 GCCAAAGTGA 0.798217 -185 AACGGCGATCGCCAAAGTCAGAATTGAGGCA 49 146 1 GCCAAAGTAG 0.854622 -99 CCAATTAACCGGCAAGATTGAAGAAGCTGCC 51 32 0 GGCAAGATGA 0.825485 -108 ATAGTGGAAGGGCAAAATTGGTTCACAACGA 52 51 0 GGCAAAATGG 0.968073 -44 GTTTAAGTCGGCCAAAGTTAGAAGCTGGGCT 53 57 0 GCCAAAGTAG 0.854622 -54 AGGGCGGCAAAAGGAAGTTTTGATAG 54 6 1 GGCAAAAGAA 0.69098 -249 ******** ** Masking position 5 Map Score: 18.9959 Number of sites scoring better than the average of aligned sites = 1013 Number in coding regions = 863 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 5 CTAGGGACAGTTTTATCTGTTCATTGCATTAAT 5 28 0 TTTTTCTGTA 0.502974 -53 ATTTATTAGTATTTTCCTGGTTTTGGGCCATGG 10 44 0 ATTTCCTGTT 0.955679 -98 ATTCGTGAGCATTTCTCGGTTGTACCT 10 125 1 ATTTTCGGTT 0.851861 -17 TGTAAAGAAAATTTCCCCACTGTCCTTTTCCC 13 10 0 ATTTCCCATT 0.617634 -208 TAATCAAATTTTTTCCCCGTTTTCGGTAAGGCC 16 11 0 TTTTCCCGTT 0.89429 -237 CTTGCAGTTGATTTTCCTGGTCTTGGGC 17 6 0 ATTTCCTGTT 0.955679 -111 TCACCGAAGAATTTTCCGGCTTACTCGGTGCTA 18 221 0 ATTTCCGGTA 0.87919 -80 ACCAATCTGAATTTATCTGTTTTTTCCCTGGGC 28 14 0 ATTTTCTGTT 0.863431 -96 TCGCAATCAAATTTACCTGGTTTAGGCTCTCCC 29 233 1 ATTTCCTGTT 0.955679 -68 CCCAATCATCTTTTATCTGCTGTATTGCTCCTT 29 263 1 TTTTTCTGTT 0.731699 -38 CACTCTCTTAATTTTCCCGTTTAAC 36 3 0 ATTTCCCGTA 0.87919 -258 ATCAAAGCCTTTTTTTCTGTTGTTTTAACCGAT 39 163 1 TTTTTCTGTT 0.731699 -138 AGTATGGTTTATTTACCGACTTTGCCTAGGATT 43 150 0 ATTTCCGATT 0.617634 -38 TAAAAAAAATATTTACCGGGTTTGGCTGGAAAG 46 66 1 ATTTCCGGTT 0.951485 -86 TTAAAACTAACTTTTTCTGATTTGCTTGATGTT 48 43 1 CTTTTCTGTT 0.647283 -122 CGACCCATGGTTTTGCCCGTTGTTGGGACAAAA 50 65 1 TTTTCCCGTT 0.89429 -125 AAAAATTAAGATTTCCCGGTTCTTTCTCATTTT 50 95 0 ATTTCCGGTT 0.951485 -95 TATTCCTTGGCTTTACCCGTTAAAGTAAACTCG 52 21 1 CTTTCCCGTA 0.678703 -74 TTGTAATGAAATTTACCTGCTTAGTATAGTCCC 54 168 0 ATTTCCTGTA 0.888903 -87 **** **** * * Masking position 4 Map Score: 16.5458 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 379 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 GTCGTTGCCTCAGCTGTCGCAAAGTAGGCG 9 202 0 CAGCTGTCGC 0.727003 -99 CCCCTGGATACCGTCGTTGCCTCAGCTGTC 9 214 0 CCGTCGTTGC 0.890816 -87 GAAAAACCGCCCAGTGTCGGCGGCTGTGGG 11 115 0 CCAGTGTCGG 0.74964 -186 CCAATGCTTGCCACTGTTGGAGCCGAGCCT 13 134 0 CCACTGTTGG 0.864194 -84 CTTGCTGCCACCGTTGTCGCCGTGGCTGAC 14 178 1 CCGTTGTCGC 0.986248 -56 AATTTTTTCCCCGTTTTCGGTAAGGCC 16 8 0 CCGTTTTCGG 0.787135 -240 CTAGGTTATACCATTGTCGCTTGACTATGG 18 95 1 CCATTGTCGC 0.969263 -206 TAACAAGATTCCACTTTCGCCGTCCAAACA 18 260 0 CCACTTTCGC 0.68756 -41 AAGCCCCCAACCGTTGTAGGCTAAGGACTC 20 101 0 CCGTTGTAGG 0.776097 -76 ATCTTCCCTACCGTTGGCGCACATAAGGGA 21 51 1 CCGTTGGCGC 0.895139 -27 TATGGGTAGTCCGCCGTTGCGTTTCAGTCT 31 13 0 CCGCCGTTGC 0.859225 -56 TTTTGCCCCGCCATTGTTGCGAGATTATTA 31 48 1 CCATTGTTGC 0.938926 -21 CCGTTGTCCCTGGGGGGCGC 33 1 1 CCGTTGTCCC 0.911819 -77 CCCCCTTCCCCCACTGTTGCCAATGGACTG 39 235 0 CCACTGTTGC 0.920066 -66 CAAGTTACCCCCATTGTTCCATGGCATTCC 42 75 0 CCATTGTTCC 0.689102 -69 TTGGCGATCGCCGTTGTCGGTCTGGGGGAG 49 131 0 CCGTTGTCGG 0.975356 -114 ATGGTTTTGCCCGTTGTTGGGACAAAAATG 50 71 1 CCGTTGTTGG 0.950816 -119 ********** Masking position 1 Map Score: 19.1046 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 429 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 7 AGGGGGCAATCATGCCATTACTGG 10 2 1 GGGGCAACTG 0.963237 -140 CCATCTTTGGGGGGATGAACATGGAAAAAAGTG 14 108 1 GGGGTGACTG 0.781246 -126 CTCAGACTCTGGGGTTTAGCCATCCCATTGGGC 15 68 0 GGGGTTACAT 0.861605 -44 GCCAAAGTTTGGGGCCAATCCTTTGCATTGCTT 19 63 1 GGGGCAACTT 0.988086 -138 GAATAGGAATTGGGTCAAACCTTTACGCTGTCC 19 142 1 TGGGCAACTT 0.84526 -59 ACTTTATGAAGGGTTCAAACTATCAGTGTAGCG 20 68 0 GGGTCAACAT 0.716618 -109 TGGGACTGGGGGGGCCAAACCATAGGGAGTTTT 22 154 0 GGGGCAACAT 0.974615 -107 TAGCGGCTTGGGGGATAACCGTTAGCAATATTT 22 196 0 GGGGTAACTT 0.983614 -65 GAACGCTAAGGGAGGTAAGCCTTATGTCGTAGT 39 122 0 GGAGTAACTT 0.798129 -179 AACTTGGTTGGGGGTTAAACCTTGACCGACTTA 42 99 1 GGGGTAACTT 0.983611 -45 CCCCCAAAAAGGGGCTAAGCTTTCCAGCCAAAC 46 85 0 GGGGTAACTT 0.983614 -67 CCACAAAGCCGGGGTTTACCTATAGAGTTAAAC 49 84 1 GGGGTTACAT 0.861615 -161 AAGACTGGGGTCAATTATTTAAATCGATG 55 7 1 GGGGCAATTT 0.84526 -140 **** *** * ** Masking position 8 Map Score: 12.023 Number of sites scoring better than the average of aligned sites = 404 Number in coding regions = 363 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 GGATGGCCACGAAGATTTGCTAAACTGGACGCA 7 27 0 GAATTTGTAA 0.796796 -60 CAACAGTGGCAAGCATTGGTAAATAGTTTTCAA 13 145 1 AAGTTGGAAA 0.813452 -73 TTTAAAAAGGGAGACTTTGGTAACATTTCCTCC 16 117 0 GAGTTTGTAA 0.943215 -131 CCCCACTGGAAAGTGTTTGAAAAGTGCAAGGCT 16 185 0 AAGTTTGAAA 0.911609 -63 GGGGTTGTGGGAAATTTTGTTAACAAGATTCCA 18 277 0 GAATTTGTAA 0.796796 -24 CGTTCTAAGAGCGTGTTTGAAAAGTAGGGTGAA 26 53 0 GCGTTTGAAA 0.911986 -47 CGCTCTTAGAACGGATTTGAAAATTGTGAATGA 26 73 1 ACGTTTGAAA 0.813452 -27 GGGGCAAAATAAGACTTTGCAAACAGGCTCTTA 27 79 1 AAGTTTGAAA 0.911609 -41 GGCTCTTAGAAAGTGTTTGAAAAGTT 27 104 1 AAGTTTGAAA 0.911609 -16 GTTAATTCAAGAGAATTTGCAAAATATTTTCCC 36 160 1 GAGTTTGAAA 0.960796 -101 AACATGTTTGGAGTTTTGGAAAAAA 40 3 0 GAGTTGGAAA 0.911986 -198 CACCATTAGGGAGCTTTTGGTAACATGTTTGGA 40 24 0 GAGTTTGTAA 0.943215 -177 TCCTCGTGGGGCAATTTTGCAAACAATGGCGGT 44 13 1 GCATTTGAAA 0.709818 -118 TCGATTAATCGAGAATTGGATAATGG 47 146 1 GAGTTGGTAA 0.875357 -16 ATCAAGCTAAAAAAATTTGATAAAAATTAGGTT 48 76 0 AAATTTGTAA 0.622661 -89 *** **** *** Masking position 12 Map Score: 11.2411 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 134 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 9 TAACAATGTTAATTTTTCTCTCAATCTCTCA 3 228 0 AATTTTCTCT 0.425071 -73 GACACTGGGCGGTTTTTCTCTAGCTTAACGG 11 127 1 GGTTTTCTCT 0.945434 -174 TGCAAGGCTAGGTATTTCTCTAAATCTCCTC 16 163 0 GGTTTTCTCT 0.945434 -85 TAAGCAAATGGTTGTTGATCTGGAATTTTAT 18 20 1 GTTTTGATCT 0.865793 -281 TAAACACGGAGGTCTTGATCTGCATAGTAAG 19 26 1 GGTTTGATCT 0.958096 -175 TAAAAAAAAAGATTTTGCTCTGGGGGAACAG 22 45 1 GATTTGCTCT 0.930942 -216 ATGAAAAGATTTTGATCTCAACTCTGAT 28 92 0 GATTTGATCT 0.893619 -18 ATTTCTCAAAGATTTTGCTCTACTTTCCTGG 34 98 1 GATTTGCTCT 0.930942 -48 ACATTTGATTGTTTTTTATCTAGATTGTGTC 36 75 0 GTTTTTATCT 0.752863 -186 CCCTAATGGTGGTCTTGATCGCTCGCCCTTA 40 46 1 GGTTTGATCG 0.769332 -155 CTTAATTGTTGGTATTTATCTACCCTCTTCT 41 119 0 GGTTTTATCT 0.91523 -60 AACAATGGCGGTTTTTTCTCTTTTAGCCTAT 44 34 1 GTTTTTCTCT 0.830185 -97 AAGATTAATTAGTTTTGATCTTCCCTCAA 48 9 0 AGTTTGATCT 0.726441 -156 ATTCTTGAAGGGTATAGCTCTCTTGGGGTCG 54 112 0 GGTTAGCTCT 0.783141 -143 *** ******* Masking position 5 Map Score: 9.49633 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 192 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 10 AATTAGTTTGAGGCAAGGGA 5 71 1 AGGCAAGGGA 0.655683 -10 CGGTATCCAGGGGCCATGGTCAACGGTGGG 9 231 1 GGGCCATGGT 0.750128 -70 AACAATGCCTGGGCCAGGAACCGTTGCAAC 13 59 0 GGGCCAGGAA 0.898515 -159 TGCAAGCCAAGGCCAATGAATGCAATCTGT 17 33 1 GGCCAATGAA 0.79723 -84 AGGTAAATCTTGCCAATGGAAAATCAAATT 17 66 0 TGCCAATGGA 0.830272 -51 GGCCCCCCCAGTCCCAGGGAATCAGAAATA 22 171 1 GTCCCAGGGA 0.727966 -90 TACGGAGATCGGCCCAGGATACTAACTCCA 22 237 1 GGCCCAGGAT 0.8997 -24 GGTGCCCAGGGAAAAAACAGAT 28 3 1 TGCCCAGGGA 0.962769 -107 CCCTTTCCATTACCCAGGGAAA 33 66 1 TACCCAGGGA 0.720774 -12 TTGGGATTATTGGCAATGGAGGCCAATACT 39 73 0 TGGCAATGGA 0.675612 -228 CCCCCACTGTTGCCAATGGACTGAAAACTT 39 228 0 TGCCAATGGA 0.830272 -73 ATCACCCTTGGGGCTAGGAATGCCATGGAA 42 59 1 GGGCTAGGAA 0.604827 -85 TTACCGACTTTGCCTAGGATTCAAGTAAGT 43 141 0 TGCCTAGGAT 0.458278 -47 CCCGATCGCCGACCCATGGTTTTGCCCGTT 50 56 1 GACCCATGGT 0.41298 -134 TAACGGGTAAAGCCAAGGAATAAATCATCA 52 13 0 AGCCAAGGAA 0.662885 -82 ACTAGAGGGCTGCCCAGGGTAGGGAAAAAA 54 51 1 TGCCCAGGGT 0.917762 -204 ATCTCCCTGTGGCCAAGGAATCCTCCGTTC 55 56 0 GGCCAAGGAA 0.919196 -91 ********** Masking position 6 Map Score: 8.16264 Number of sites scoring better than the average of aligned sites = 2583 Number in coding regions = 2363 Number in noncoding regions = 220 Number of orfs with sites within 600 bp upstream = 241 Fraction of orfs with sites within 600 bp upstream = 0.0387086 Motif number 11 TTACGAAATGTTTGAATTGCCTCAAATATT 3 56 1 TTTGAATTGC 0.616387 -245 TGTGATAATATTGGGATAGCCTTATTATTA 3 118 0 TTGGGATAGC 0.694798 -183 TGGGCAAAGTTTGGCATTGCCGCCAGAAAA 11 89 0 TTGGCATTGC 0.922023 -212 GTTGGGGGATTTGGACTTACACTTCCCTCA 11 234 1 TTGGACTTAC 0.457489 -67 TGAATAGGATTTGGAATTACCC 13 206 1 TTGGAATTAC 0.683194 -12 AACAACACCAGTGGACTTGCCCTATTCCAC 14 138 0 GTGGACTTGC 0.785105 -96 AGGCCCCAAAGGGGCATTACCATAGTCAAG 18 114 0 GGGGCATTAC 0.809336 -187 GGGCCAATCCTTTGCATTGCTTTATATTTG 19 74 1 TTTGCATTGC 0.719287 -127 CTAGCGGCTTGGGGGATAACCGTTAGCAAT 22 200 0 GGGGGATAAC 0.449718 -61 TCGCTGACTAGGGGGCTTGCAGCATTAGAA 24 30 1 GGGGGCTTGC 0.871907 -21 CGGGTTGGATTGCATAGCCCTTA 25 26 0 GTTGGATTGC 0.793849 -13 TTACTATTGGGGGGCATTGCC 32 2 0 GGGGCATTGC 0.935877 -92 GATTATTCAGTTGGCATTACACCAAGGAA 37 10 0 TTGGCATTAC 0.774724 -143 GGAAAAGGAAGGGGAATTGCATCAAGATTG 47 11 1 GGGGAATTGC 0.901498 -151 ACCCCGGCTTTGTGGATTGCCAAAGTTGAT 49 69 0 TGTGGATTGC 0.749604 -176 TGAGCTTGGGATTGCGAGGAATTTT 49 230 0 TTGGGATTGC 0.933786 -15 ********** Masking position 7 Map Score: 8.7135 Number of sites scoring better than the average of aligned sites = 887 Number in coding regions = 816 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 12 CATTCTAATTCTCCTTTGCGGCAAACCTGCGC 10 86 1 CCCTTGCGGC 0.988695 -56 TATGGTAATGCCCCTTTGGGGCCTGGATAAGA 18 120 1 CCCTTGGGGC 0.986033 -181 GCTCAGTCTTCCCCCTGGCGTTTATTGCCCTA 30 94 1 CCCTGGCGTT 0.944136 -47 ATGGGTAGTCCGCCGTTGCGTTTCAGTCTAA 31 10 0 CCCTTGCGTT 0.971892 -59 AATGAACGATCGCCGTTGCGTTCAATCTAAGC 33 31 1 CCCTTGCGTT 0.971892 -47 CCCAGCCTATCACCCTTGGGGCTAGGAATGCC 42 51 1 CCCTTGGGGC 0.985988 -93 ACATTGTTGCTCCTTGGGGTCTGGAAAAACC 49 10 1 CCCTGGGGTC 0.94614 -235 CCATTTTGACCCCCATTGCGGTTTTTCCAGAC 49 29 0 CCCTTGCGGT 0.985493 -216 AAGGGTATAGCTCTCTTGGGGTCGGTGGTGTC 54 104 0 CCTTTGGGGT 0.843177 -151 * ** ******* Masking position 6 Map Score: 11.0339 Number of sites scoring better than the average of aligned sites = 208 Number in coding regions = 193 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 13 TCTAGCCCTTCCCCAGACCTAGGCTGGCTA 8 42 1 CCCCAGACCT 0.913349 -34 TTTGCCATGGCCCAAAACCAGGAAAATACT 10 40 1 CCCAAAACCA 0.932772 -102 AAGCCTTTGTCCCCCAACTATTTTCACTAA 11 192 1 CCCCCAACTA 0.768851 -109 AAGTCCAAATCCCCCAACCTTGCCGGAGCT 11 222 0 CCCCCAACCT 0.923116 -79 GGTTAGCTAACCCCAGACCAACGCATCTCA 16 226 1 CCCCAGACCA 0.980991 -22 GCCCAAGACCAGGAAAATCAA 17 2 1 CCCAAGACCA 0.951425 -115 AACAAAATTTCCCACAACCCCC 18 289 1 CCCACAACCC 0.792964 -12 TGAAAAAAAGCCCCCAACCGTTGTAGGCTA 20 108 0 CCCCCAACCG 0.948907 -69 GTTACTGTTCCCCCAGAGCAAAATCTTTTT 22 50 0 CCCCAGAGCA 0.812309 -211 TGCCAATAATCCCAAGACAAGCTCCTGAAA 39 88 1 CCCAAGACAA 0.525675 -213 GACTAGCGTACCCAAAAACACTGACCCAGC 42 27 1 CCCAAAAACA 0.439796 -117 CAAGGTTTAACCCCCAACCAAGTTACCCCC 42 93 0 CCCCCAACCA 0.983273 -51 GAATCTGGAACCCACAACCATCAGCATTTC 47 68 1 CCCACAACCA 0.957102 -94 TTAAGTTCTACCCCCGTCCACGTCCCCCAT 47 108 1 CCCCCGTCCA 0.876554 -54 ATAAAACCTCCCCCAGACCGACAACGGCGA 49 124 1 CCCCAGACCG 0.942211 -121 GGGAGATCGTCCCCCCACCAGTCATAGTCA 55 79 1 CCCCCCACCA 0.932134 -68 ********** Masking position 3 Map Score: 20.9631 Number of sites scoring better than the average of aligned sites = 628 Number in coding regions = 566 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 14 ATCACCCATTCTAATTCTCCTTTGCGGCAA 10 80 1 CTAATTCTCC 0.812743 -62 ACTATTTTCACTAAAGCTCCGGCAAGGTTG 11 208 1 CTAAAGCTCC 0.935531 -93 GAAATGTTACCAAAGTCTCCCTTTTTAAAC 16 121 1 CAAAGTCTCC 0.955047 -127 AATCTCCTCACTAAGGCTCCGGTTTAAAAA 16 142 0 CTAAGGCTCC 0.934313 -106 AGGTATTTCTCTAAATCTCCTCACTAAGGC 16 155 0 CTAAATCTCC 0.946216 -93 ATCTTGTTAACAAAATTTCCCACAACCCCC 18 281 1 CAAAATTTCC 0.679988 -20 GAAACACAGTCAAAGTCCCCCAGTATTGAG 27 41 1 CAAAGTCCCC 0.832322 -79 AACATGTTACCAAAAGCTCCCTAATGGTGG 40 28 1 CAAAAGCTCC 0.947029 -173 GGCGCAAAATCTCCAAAATAATAA 50 5 1 CAAAATCTCC 0.955898 -185 ********** Masking position 4 Map Score: 6.12277 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 122 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 15 TAGGTCTGGGGAAGGGCTAGAGCTTTATCGC 8 32 0 GAAGGGCTGA 0.449722 -44 CTGGAGTCTAGCCAGCCTAGGTCTGGGGAAG 8 49 0 GCCAGCCTGG 0.916357 -27 GTTCGAGATGGATAGACTCGGACAATTCGCC 9 156 1 GATAGACTGG 0.555644 -145 TAAAGCTCCGGCAAGGTTGGGGGATTTGGAC 11 219 1 GCAAGGTTGG 0.69298 -82 GAGTAAATGCGATAGGCTCGGCTCCAACAGT 13 121 1 GATAGGCTGG 0.927298 -97 TCCAACAGTGGCAAGCATTGGTAAATAGTTT 13 143 1 GCAAGCATGG 0.66457 -75 ATAGTTGGCCGTCAGCCACGGCGACAACGGT 14 187 0 GTCAGCCAGG 0.474656 -47 TTTGAAAAGTGCAAGGCTAGGTATTTCTCTA 16 172 0 GCAAGGCTGG 0.971668 -76 AAAATCAACTGCAAGCCAAGGCCAATGAATG 17 24 1 GCAAGCCAGG 0.919122 -93 GTTTTCCCTAGAAAGCCTAGAAGTTTTTGGA 22 128 0 GAAAGCCTGA 0.727692 -133 CTGGGTAATGGAAAGGGTAGGCTTAGATTGA 33 52 0 GAAAGGGTGG 0.73353 -26 GGGGGGGCAGGCAAGGCAAGGACAATGGATT 38 32 1 GCAAGGCAGG 0.928291 -40 AACCAAGGAGGAAGGGCTTGGCAAAAGCAAA 40 81 0 GAAGGGCTGG 0.891198 -120 CCCCAAGGGTGATAGGCTGGGTCAGTGTTTT 42 41 0 GATAGGCTGG 0.927281 -103 TTGGGGCTAGGAATGCCATGGAACAATGGGG 42 66 1 GAATGCCAGG 0.479991 -78 AAGCCGTTGTGTTAGCCTGGGTTAGAAAAAA 43 49 0 GTTAGCCTGG 0.756835 -139 ******** ** Masking position 5 Map Score: 6.19528 Number of sites scoring better than the average of aligned sites = 524 Number in coding regions = 451 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301