AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_synecho_reg_100.orf -o00350_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 slr1099 300 ubiX; 3-octaprenyl-4-hydroxybenzoate carboxy-lyase. [EC:4.1.1.-] #5 sll1191 233 hypothetical protein. #6 sll0938 40 aspartate transaminase. [EC:2.6.1.1] #7 ssl1792 33 hypothetical protein. #8 sll0936 83 hypothetical protein. #9 slr0969 102 cbiH; precorrin methylase. #10 sll1713 61 hisC; histidinol-phosphate aminotransferase. [EC:2.6.1.9] #11 sll1712 170 DNA binding protein HU. [SP:DBH_SYNY3] #12 sll1958 138 hisC; histidinol phosphate aminotransferase. [EC:2.6.1.9] #13 sll1909 77 prmA; probable methyltransferase. [EC:2.1.1.-] [SP:PRMA_SYNY3] #14 sll1908 260 serA; phosphoglycerate dehydrogenase. [EC:1.1.1.95] #15 sll1605 262 fabZ; (3R)-hydroxymyristol acyl carrier protein dehydrase. #16 ssr1391 77 hypothetical protein. #17 slr0820 145 glucosyltransferase. #18 slr0370 171 gabD; succinate-semialdehyde dehydrogenase (NADP+). [EC:1.2.1.16] #19 slr0776 107 lpxD; UDP-3-o-[3-hydroxymyristoyl] glucosamine n-acyltransferase. #20 sll0006 103 aspC; aspartate aminotransferase. [EC:2.6.1.1] #21 sll0402 122 aspC; aspartate aminotransferase. [EC:2.6.1.1] #22 slr0092 117 hisB; hypothetical protein. #23 slr0095 161 hisB; O-methyltransferase. [EC:2.1.1.-] #24 sll0034 62 hypothetical protein. #25 sll0033 160 hypothetical protein. Motif number 1 GAAAAACCGCCCAGTGTCGGCGGCTGTGGGCA 4 113 0 CCGTGCGGCG 0.978741 -188 GCTCGGTGCGCCATGGTTGGGATTAGCCGTTA 4 152 0 CCTGGTGGGA 0.92152 -149 AAATCCCCCAACCTTGCCGGAGCTTTAGTGAA 4 214 0 ACTTGCGGAG 0.905348 -87 CTTGCTGCCACCGTTGTCGCCGTGGCTGACGG 5 178 1 CCTTGCGCCG 0.89965 -56 GTTTAGCCCGACCAGGATGGCGATCTCCAACG 8 24 0 ACAGGTGGCG 0.743142 -60 AGAAGTGAGTCCGTTGACCGGGAGTATTTTCC 9 12 0 CCTTGCCGGG 0.890775 -91 TTGCCACTGACCTTTGTTTGAGCGACCCCACC 10 11 1 CCTTGTTGAG 0.81695 -51 CCAAATTACCACCGTGGTGGGGTCGCTCAAAC 10 26 0 ACGTGTGGGG 0.955654 -36 GAAAGAATGCCCTTTGTTTGGGCTATTTTTTA 12 58 0 CCTTGTTGGG 0.938819 -81 TACAGCGGCAACGGTGTCGGGGTATGGTCTGT 12 116 1 ACGTGCGGGG 0.969079 -23 ATTCCTCCCCCCATTGACTTGGACCCTTGGTG 13 17 0 CCTTGCTTGG 0.510371 -61 TACGGGGGCTGAGTAAAGTTGGC 14 2 1 ACGGGCTGAG 0.741661 -259 TTTCTGATTCCCTGGGACTGGGGGGGCCAAAC 14 167 0 CCGGGCTGGG 0.968789 -94 CCGTTGTCCCTGGGGGGCGCAATGAACGA 16 8 1 CCTGGGGGCG 0.944207 -70 ATAAAACTACCCATTGATGGAAAAGCGATTGA 17 40 1 CCTTGTGGAA 0.699084 -106 ATCCCAGTTACCTAGGGTGGGGAGTTTCTTTT 19 66 0 CCAGGTGGGG 0.951821 -42 ACCCTAGGTAACTGGGATGGGGTTTTTCGTTG 19 80 1 ACGGGTGGGG 0.969399 -28 GCCATGGTTGCCATAGGTTCCAG 20 2 1 CCTGGTGCCA 0.502647 -102 AATTCCAGCTCCCTTGCTGGGGTTGGCATGCT 21 44 1 CCTTGTGGGG 0.986212 -79 TGGCTTTGCTCCAGGGCGGCAGTTTCAGGTCA 22 27 0 CCGGGGGCAG 0.652382 -91 GTAATGGGGGACGTGGACGGGGGTAGAACTTA 23 109 0 ACTGGCGGGG 0.979734 -53 ** *** ***** Masking position 6 Map Score: 25.1024 Number of sites scoring better than the average of aligned sites = 3840 Number in coding regions = 3558 Number in noncoding regions = 282 Number of orfs with sites within 600 bp upstream = 295 Fraction of orfs with sites within 600 bp upstream = 0.0473819 Motif number 2 GCCGCCGACACTGGGCGGTTTTTCTCTAGC 4 121 1 CTGGGCGGTT 0.904614 -180 TAATCCCAACCATGGCGCACCGAGCGATCA 4 159 1 CATGGCGCAC 0.549109 -142 AGTGAAAATAGTTGGGGGACAAAGGCTTTA 4 190 0 GTTGGGGGAC 0.977696 -111 CTCCGGCAAGGTTGGGGGATTTGGACTTAC 4 224 1 GTTGGGGGAT 0.957922 -77 AGTCCCATCTTTGGGGGGATGAACATGGAA 5 104 1 TTGGGGGGAT 0.849886 -130 GGTTAAAATAGTTGGCCGTCAGCCACGGCG 5 195 0 GTTGGCCGTC 0.803079 -39 GCCCGACCAGGATGGCGATCTCCAACGAGA 8 21 0 GATGGCGATC 0.466613 -63 GGTAATTTGGGTTGGGCAGCGCAG 10 48 1 GTTGGGCAGC 0.695823 -14 AACAGCCAGTCTGCGGGGATTTCAGGGGTT 11 134 1 CTGCGGGGAT 0.614942 -37 CTTCCCTACCGTTGGCGCACATAAGGGAGA 13 53 1 GTTGGCGCAC 0.724042 -25 AGATTTTGCTCTGGGGGAACAGTAACCAGG 14 54 1 CTGGGGGAAC 0.949055 -207 TTCCCTGGGACTGGGGGGGCCAAACCATAG 14 162 0 CTGGGGGGGC 0.965726 -99 ATTCTAGCGGCTTGGGGGATAACCGTTAGC 14 203 0 CTTGGGGGAT 0.961895 -58 AGTTAGTATCCTGGGCCGATCTCCGTAGCC 14 234 0 CTGGGCCGAT 0.877696 -27 AGGATTTGGCGGATTGTTTGGGGA 15 5 1 TTTGGCGGAT 0.807732 -258 TGGCGGATTGTTTGGGGAATGAACAACCCT 15 17 1 TTTGGGGAAT 0.630599 -246 CTTATCGGTAGTGGGCCAACCCGGAAGAAG 15 52 1 GTGGGCCAAC 0.518039 -211 GCTCATGGCCCAGGGGGGATCCCAATGGGC 15 101 1 CAGGGGGGAT 0.837155 -162 CCGTTGTCCCTGGGGGGCGCAATGAACG 16 9 1 CCTGGGGGGC 0.726194 -69 AGGGGTAAGGCTGGGGCAGTTTGATCAACT 22 86 0 CTGGGGCAGT 0.599669 -32 GCCAGAGAATGTTGGCGGTCA 24 2 0 GTTGGCGGTC 0.935255 -61 GCAGTTGGCGATCGTTGCAGCTC 24 50 0 GTTGGCGATC 0.80328 -13 ********** Masking position 5 Map Score: 18.9793 Number of sites scoring better than the average of aligned sites = 3590 Number in coding regions = 3188 Number in noncoding regions = 402 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 3 GAATTGCCTCAAATATTTTGCTCTAACTTCA 3 69 1 AAATTTTTGC 0.85903 -232 CGGCTGTGGGCAAAGTTTGGCATTGCCGCCA 4 94 0 CAAATTTGGC 0.893957 -207 ACGGAATAGTAGATTTTTTGCCA 7 21 1 AGATTTTTGC 0.868601 -13 CGATCTCCAACGAGAATTTGCCGCT 8 5 0 CGAGATTTGC 0.668619 -79 CTTTTCCCCACGAATTTTTGCAGTTTTGCGG 11 62 0 CGAATTTTGC 0.95581 -109 AGAAATTTGGCATTAAAAACC 11 160 0 AGAATTTGGC 0.909539 -11 GTTTAAAAAAAAAGATTTTGCTCTGGGGGAA 14 42 1 AAAGTTTTGC 0.957151 -219 CCAGGGAATCAGAAATATTGCTAACGGTTAT 14 184 1 AGAATATTGC 0.685234 -77 AAATTTTTGAAAAACTTTGGCAAACCAGGTT 15 208 0 AAAATTTGGC 0.902615 -55 AGGACAAACGAAAATTTTTGAAAAACTTTGG 15 219 0 AAAATTTTGA 0.701763 -44 GGGAAAACTTTTGCTAAAAATCTA 15 249 0 AAAATTTTGC 0.956373 -14 CCTATTTCTCAAAGATTTTGCTCTACTTTCC 17 95 1 AAAGTTTTGC 0.957151 -51 AATATGGCTTCGAGTTTTTGAAGCATAATTT 18 64 0 CGAGTTTTGA 0.702894 -108 AGGTTCCAGTCAAAATTTTGCTGAGGCGAGA 20 25 1 CAAATTTTGC 0.952241 -79 CTAATCAGTTTAAGGTTTTGCCGCCAAAAAA 25 86 0 TAAGTTTTGC 0.758638 -75 **** ****** Masking position 3 Map Score: 14.607 Number of sites scoring better than the average of aligned sites = 526 Number in coding regions = 437 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 4 TTCCAAATGGCGATCGCCAGTGTGAAAGACGG 3 274 1 CGATCGCCAG 0.99683 -27 GCGCACCGAGCGATCACTAAAGCCTTTGTCCC 4 173 1 CGATCACTAG 0.922487 -128 ACCAGGATGGCGATCTCCAACGAGAATTTGCC 8 14 0 CGATCTCCAG 0.988988 -70 TATCCTGGGCCGATCTCCGTAGCCCATTCTAG 14 226 0 CGATCTCCGG 0.993172 -35 GTTCTAGGCCCGATCGCCACCGAAAACCAGTT 15 135 0 CGATCGCCAG 0.988283 -128 GCGCAATGAACGATCGCCGTTGCGTTCAATCT 16 27 1 CGATCGCCGG 0.997923 -51 GCAGTTGGCGATCGTTGCAGCTCATTGCTT 24 43 0 CGATCGTTGG 0.931647 -20 AGGGAGCACTCGATCGCCGAGCCACCCCCTAC 25 52 0 CGATCGCCGC 0.988804 -109 ********* * Masking position 3 Map Score: 13.2203 Number of sites scoring better than the average of aligned sites = 2900 Number in coding regions = 2646 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 252 Fraction of orfs with sites within 600 bp upstream = 0.0404754 Motif number 5 ACTCATGAAGTTAGAGCAAAATATTTGAGG 3 75 0 TTAGAGCAAA 0.854086 -226 GTAAGAATCTGTAGAACAAACCGCTTGACA 4 28 1 GTAGAACAAA 0.724193 -273 AGCCGTTAAGCTAGAGAAAAACCGCCCAGT 4 130 0 CTAGAGAAAA 0.916118 -171 GCAAAAATTCGTGGGGAAAAGTGATCCTAC 11 72 1 GTGGGGAAAA 0.799696 -99 AAGGCGACGTCTAGGAAAAAACAGGGGAAA 12 86 0 CTAGGAAAAA 0.80168 -53 TACTGTTCCCCCAGAGCAAAATCTTTTTTT 14 48 0 CCAGAGCAAA 0.914512 -213 GGAACAGTAACCAGGGCAATTTTAAGTTTT 14 69 1 CCAGGGCAAT 0.679121 -192 TCTAGGCTTTCTAGGGAAAACTCCCTATGG 14 138 1 CTAGGGAAAA 0.953061 -123 TGCTAAAAATCTAGGACAAACGAAAATTTT 15 232 0 CTAGGACAAA 0.926106 -31 GTCCAGGAAAGTAGAGCAAAATCTTTGAGA 17 101 0 GTAGAGCAAA 0.929521 -45 CAAAACATCCCTGGGGTAAACAACAGCAAA 21 100 0 CTGGGGTAAA 0.757014 -23 AACTGCCGCCCTGGAGCAAAGCCAGGAAAA 22 35 1 CTGGAGCAAA 0.944732 -83 CTTGGTCTGGTTAGGGCAAAAAGTTAACAA 25 136 0 TTAGGGCAAA 0.915838 -25 ********** Masking position 8 Map Score: 10.6213 Number of sites scoring better than the average of aligned sites = 1038 Number in coding regions = 909 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 6 GGGACTGACATGCCCTGAAGAGAGCCCTATGG 5 78 0 TGCCCGAAAG 0.969945 -156 TGGGGGGATGAACATGGAAAAAAGTGGAATAG 5 115 1 AACATGAAAA 0.683635 -119 ATTTTCAAGGTACCCTGAATAGAAGTGAGTCC 9 32 0 TACCCGAAAG 0.944345 -71 CCACACTTTGTGCATAGAATAAGGCAGTGAAA 11 104 1 TGCATGAAAA 0.775716 -67 GTAGTGGGCCAACCCGGAAGAAGAATTGGCCA 15 59 1 AACCCGAAAA 0.955675 -204 CTGGGCCATGAGCCCAGAAAAATTGGCCAATT 15 82 0 AGCCCGAAAA 0.976195 -181 TATACTAATCAGCCATGAATAAAACTACCCAT 17 22 1 AGCCAGAAAA 0.95428 -124 CTTTACCGCCTACACTGAATAGAAGAGCGATA 18 131 1 TACACGAAAG 0.861764 -41 TAGATAATTGAACCAAGAAAAAGAAACTCCCC 19 48 1 AACCAGAAAA 0.916485 -60 TACCTGCAACGAAAAACCCCATCCCA 19 92 0 TGCAAGAAAA 0.865828 -16 CCTGGAGCAAAGCCAGGAAAAGTTTATCCAAA 22 44 1 AGCCAGAAAG 0.951266 -74 ***** *** ** Masking position 8 Map Score: 7.48267 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 282 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 AGTGGTCCCTCAGCCCATAAAACTA 1 6 1 TCCCTCAGCC 0.606078 -73 GAAGATATTTGCCCATCCCCTATTTCTTGA 2 27 0 GCCCATCCCC 0.946856 -57 GATTCCAAATGGCGATCGCCAGTGTGAAAG 3 272 1 GGCGATCGCC 0.467736 -29 GCCAAACTTTGCCCACAGCCGCCGACACTG 4 104 1 GCCCACAGCC 0.825834 -197 CTCATCAGAAGGACTTACCCTCAGAGCCTA 4 271 1 GGACTTACCC 0.879827 -30 AAGATGGGACTGACATGCCCTGAAGAGAGC 5 85 0 TGACATGCCC 0.816605 -149 CAACACCAGTGGACTTGCCCTATTCCACTT 5 136 0 GGACTTGCCC 0.885803 -98 CATGGAGATATGCCATGGCCAAACTGCCAA 12 11 0 TGCCATGGCC 0.719205 -128 TACAGACCATACCCCGACACCGTT 12 125 0 GACCATACCC 0.8073 -14 TAAATCGGTCAGCCTTGCCCAAAGGGAAAA 19 20 0 AGCCTTGCCC 0.948288 -88 AGACAGAGCATGCCAACCCCAGCAAGGGAG 21 52 0 TGCCAACCCC 0.757208 -71 CTGTCTGACTAGCCTTAGCCATTTTTTGCT 21 76 1 AGCCTTAGCC 0.90613 -47 AAACTGCCCCAGCCTTACCCCTAACTAACT 22 94 1 AGCCTTACCC 0.94516 -24 TCGATCGCCGAGCCACCCCCTACTGAATCC 25 45 0 AGCCACCCCC 0.925444 -116 ********** Masking position 9 Map Score: 6.76064 Number of sites scoring better than the average of aligned sites = 3152 Number in coding regions = 2928 Number in noncoding regions = 224 Number of orfs with sites within 600 bp upstream = 227 Fraction of orfs with sites within 600 bp upstream = 0.03646 Motif number 8 TATTGATTAATGGGTGGAAGATATTTGCCC 2 43 0 TGGGTGGAAG 0.841978 -41 TTACAGTTGGGTGGAGGGTAAGAATCT 4 8 1 TGGGTGGAGG 0.939086 -293 AGAGAGCCCTATGGTGGTAGTAGAGCAGTC 5 62 0 ATGGTGGTAG 0.795945 -172 GTCCCATCTTTGGGGGGATGAACATGGAAA 5 105 1 TGGGGGGATG 0.615431 -129 CACGGCGACAACGGTGGCAGCAAGAGTAAT 5 172 0 ACGGTGGCAG 0.957416 -62 CGACCCCACCACGGTGGTAATTTGGGTTGG 10 33 1 ACGGTGGTAA 0.586425 -29 TACAGCGGCAACGGTGTCGGGGTATGGTCT 12 116 1 ACGGTGTCGG 0.741697 -23 TCCAAGTCAATGGGGGGAGGAATTAATCTT 13 26 1 TGGGGGGAGG 0.926731 -52 TACGGGGGCTGAGTAAAGTTG 14 2 1 ACGGGGGCTG 0.871014 -259 TCCCATCTTATCGGTAGTGGGCCAACCCGG 15 46 1 TCGGTAGTGG 0.513197 -217 AAACTGGTTTTCGGTGGCGATCGGGCCTAG 15 134 1 TCGGTGGCGA 0.864561 -129 CCGTTGTCCCTGGGGGGCGCAATGAACGAT 16 11 1 TGGGGGGCGC 0.754427 -67 TAATTTTAAAATGGTGGCGGA 18 161 1 ATGGTGGCGG 0.95984 -11 CCAGTTACCTAGGGTGGGGAGTTTCTTTTT 19 65 0 AGGGTGGGGA 0.557989 -43 GCTTTGCTCCAGGGCGGCAGTTTCAGGTCA 22 27 0 AGGGCGGCAG 0.780033 -91 GGAAATGCTGATGGTTGTGGGTTCCAGATT 23 69 0 ATGGTTGTGG 0.345185 -93 GGGGACGTGGACGGGGGTAGAACTTAATTC 23 105 0 ACGGGGGTAG 0.897017 -57 GTGCCAGAGAATGTTGGCGGTCA 24 4 0 ATGTTGGCGG 0.513374 -59 AAGGATTCAGTAGGGGGTGGCTCGGCGATC 25 43 1 TAGGGGGTGG 0.674039 -118 ********** Masking position 3 Map Score: 10.8081 Number of sites scoring better than the average of aligned sites = 4411 Number in coding regions = 4173 Number in noncoding regions = 238 Number of orfs with sites within 600 bp upstream = 260 Fraction of orfs with sites within 600 bp upstream = 0.0417604 Motif number 9 GGCAAAGTTTGGCATTGCCGCCAGAAAAGCT 4 86 0 GGCATGCCGC 0.94403 -215 GCCATGGTTGGGATTAGCCGTTAAGCTAGAG 4 144 0 GGATTGCCGT 0.780223 -157 TCTCCAACGAGAATTTGCCGCT 8 2 0 GAATTGCCGC 0.930092 -82 TAGCTTAACGGGTTTAGCCCGACCAGGATGG 8 36 0 GGTTTGCCCG 0.95565 -48 CGAAAACTTGGATTTTACCCGGACTTAAAAG 11 11 0 GATTTACCCG 0.549479 -160 TCCCCCCATTGACTTGGACCCTTGGTGAGCT 13 13 0 GACTTGACCC 0.820892 -65 AACTCCCTATGGTTTGGCCCCCCCAGTCCCA 14 156 1 GGTTTGCCCC 0.987742 -105 AGTTCCCATAGACTTTACCGCCTACACTGAA 18 119 1 GACTTACCGC 0.882541 -53 AACTTTTCCTGGCTTTGCTCCAGGGCGGCAG 22 37 0 GGCTTGCTCC 0.92578 -81 TGCAGCTCATTGCTTGGCCCCATTGTGCCAG 24 27 0 TGCTTGCCCC 0.925787 -36 ATCAGTTTAAGGTTTTGCCGCCAAAAAAACA 25 83 0 GGTTTGCCGC 0.985415 -78 ***** ***** Masking position 5 Map Score: 7.01244 Number of sites scoring better than the average of aligned sites = 1090 Number in coding regions = 992 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 10 CGGTTTTTCTCTAGCTTAACGGCTAATCCCAAC 4 136 1 CTAGTTAAGC 0.894819 -165 CCACTTTTTTCCATGTTCATCCCCCCAAAGATG 5 109 0 CCATTTCACC 0.850614 -125 CCACCGAAAACCAGTTTAAAGCCCATTGGGATC 15 118 0 CCAGTTAAGC 0.987044 -145 AGCACTTTGGCCAGGTTCTAGGCCCGATCGCCA 15 148 0 CCAGTTCTGC 0.977895 -115 CTTTGGCAAACCAGGTTATTCCCAGCAACGCTT 15 192 0 CCAGTTATCC 0.921683 -71 ATGGGAACTTCCAGTTTAAGGGCTGTCCCGTTA 18 95 0 CCAGTTAAGC 0.987044 -77 CTCCAGGGCGGCAGTTTCAGGTCACAGGAGGGA 22 18 0 GCAGTTCAGC 0.952381 -100 GTTGTGGGTTCCAGATTCATAACCCTGGTCTAT 23 53 0 CCAGTTCAAC 0.949224 -109 **** **** * * Masking position 3 Map Score: 3.3807 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 183 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 CAGCTTCTCTCCTTGACACGTCCTAAC 5 8 1 TCTCCTTGAC 0.832082 -226 GCCACCGTTGTCGCCGTGGCTGACGGCCAA 5 184 1 TCGCCGTGGC 0.987716 -50 TTCCTAGACGTCGCCTTTACAGCGGCAACG 12 99 1 TCGCCTTTAC 0.921527 -40 CCTGGGCCGATCTCCGTAGCCCATTCTAGC 14 225 0 TCTCCGTAGC 0.953068 -36 CAATGAACGATCGCCGTTGCGTTCAATCTA 16 30 1 TCGCCGTTGC 0.981126 -48 TGGCTTGATCTCGCCTCAGCAAAATTTTGA 20 34 0 TCGCCTCAGC 0.94995 -70 TCTGTCTGACTAGCCTTAGCCATTTTTTGC 21 75 1 TAGCCTTAGC 0.888901 -48 ********** Masking position 1 Map Score: 3.4239 Number of sites scoring better than the average of aligned sites = 506 Number in coding regions = 476 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 12 GAGAAGTCTACCTGGGTTCTCAATATCGAAG 3 171 1 CCTGGGTCTC 0.962387 -130 TTAAAATTGCCCTGGTTACTGTTCCCCCAGA 14 63 0 CCTGGTTCTG 0.974165 -198 TGGGATCCCCCCTGGGCCATGAGCCCAGAAA 15 94 0 CCTGGGCATG 0.981998 -169 TTTCCCTGGGTAATGGAAAGGGTAG 16 63 0 CCTGGGTATG 0.986099 -15 AAGTGTCCCTCCTGTGACCTGAAACTGCCGC 22 13 1 CCTGTGACTG 0.872313 -105 GATTCATAACCCTGGTCTATGCTGACGATTA 23 42 0 CCTGGTCATG 0.962652 -120 ******* *** Masking position 3 Map Score: 1.47191 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 404 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 GTGTACTCATGAAGTTAGAGCAAAATATTTG 3 78 0 GAAGTAGAGC 0.978206 -223 ACACCGAGACCAAATTAGAGCTTTGACTGCT 5 38 1 CAAATAGAGC 0.92545 -196 GTCAGTCCAGGAAAGTAGAGCAAAATCTTTG 17 104 0 GAAATAGAGC 0.981865 -42 AGATTAGAAAATATAGCGATTGTCAGT 17 129 0 GAAATATAGC 0.931633 -17 TCGACCAACAGAAGGTCAAGCTATGCTTAAA 18 14 1 GAAGTCAAGC 0.879287 -158 TGCCCAAAGGGAAAATAAAGCTTT 19 4 0 GAAATAAAGC 0.960047 -104 **** ****** Masking position 6 Map Score: 0.627096 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 32 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 ACAAACCTCCACATTCGTTGACAAGACAA 1 60 0 CACATTCGTT 0.668313 -19 TATTTAGAATCTGATTCCTTCGATATTGAG 3 189 0 CTGATTCCTT 0.867951 -112 TAATTTTTCTCTCAATCTCTCAAGATTGGG 3 220 0 CTCAATCTCT 0.850927 -81 CGAGCGATCACTAAAGCCTTTGTCCCCCAA 4 179 1 CTAAAGCCTT 0.736372 -122 TGGAGCGGTGCTCAAGCCCTCTAATCCCAT 9 65 0 CTCAAGCCCT 0.875176 -38 GGGATTTTGTCACAATCCTTTACGAAAACT 11 34 0 CACAATCCTT 0.927296 -137 TCCCCCAGAGCAAAATCTTTTTTTTTAAAC 14 42 0 CAAAATCTTT 0.541168 -219 AGCAATATTTCTGATTCCCTGGGACTGGGG 14 176 0 CTGATTCCCT 0.843928 -85 TTAAAAGAGACTCAATCGCTTTTCCATCAA 17 53 0 CTCAATCGCT 0.860373 -93 GAAAGTAGAGCAAAATCTTTGAGAAATAGG 17 95 0 CAAAATCTTT 0.541168 -51 ATCGTTGCAGCTCATTGCTTGGCCCCATTG 24 33 0 CTCATTGCTT 0.575617 -30 CCACCCCCTACTGAATCCTTGAGAAGAGAA 25 33 0 CTGAATCCTT 0.926864 -128 ********** Masking position 4 Map Score: 1.39336 Number of sites scoring better than the average of aligned sites = 510 Number in coding regions = 431 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 15 CCGTCAGCTTTTCTGGCGGCAATGCCAAAC 4 81 1 TTCTGGCGGC 0.987021 -220 AACCGCCCAGTGTCGGCGGCTGTGGGCAAA 4 111 0 TGTCGGCGGC 0.975906 -190 GACGTCGCCTTTACAGCGGCAACGGTGTCG 12 105 1 TTACAGCGGC 0.936765 -34 CCGTAGCCCATTCTAGCGGCTTGGGGGATA 14 212 0 TTCTAGCGGC 0.962543 -49 TTAAACTGGTTTTCGGTGGCGATCGGGCCT 15 132 1 TTTCGGTGGC 0.944864 -131 CTCCCTGTTTTTTTGGCGGCAAAACCTTAA 25 78 1 TTTTGGCGGC 0.986004 -83 ********** Masking position 1 Map Score: 4.08894 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 211 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049