AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_synecho_reg_100.orf -o00310_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 slr1772 90 penicillin acylase (penicillin V amidase). [EC:3.5.1.11] #2 sll1686 300 hypothetical protein. #3 sll1682 221 alanine dehydrogenase. [EC:1.4.1.1] #4 sll1931 300 glyA; serine hydroxymethyltransferase (serine methylase) (SHMT). #5 sll2008 164 rpoD; processing protease. [EC:3.4.-.-] #6 sll1702 38 rpoD; hypothetical protein. #7 slr1807 25 rpoD; hypothetical protein. #8 slr1808 161 hemA; glutamyl-tRNA reductase (GLUTR). [EC:1.2.1.-] [SP:HEM1_SYNY3] #9 slr2001 147 pepE; peptidase E (alpha-aspartyl dipeptidase). [EC:3.4.-.-] #10 sll0809 140 putative lipoate-protein ligase A. [EC:6.-.-.-] #11 ssr1391 77 hypothetical protein. #12 slr0820 145 glucosyltransferase. #13 ssl1807 200 hypothetical protein. #14 slr0776 107 lpxD; UDP-3-o-[3-hydroxymyristoyl] glucosamine n-acyltransferase. #15 slr0021 65 putative protease slr0021. [EC:3.4.-.-] [SP:Y021_SYNY3] #16 sll0002 226 ponA; penicillin-binding protein 1A. #17 slr0092 117 hisB; hypothetical protein. #18 sll0290 300 ppk; polyphosphate kinase. [EC:2.7.4.1] #19 slr0319 78 blaOXA-3; beta-lactamase. [EC:3.5.2.6] #20 ssl0511 104 hypothetical protein. #21 slr1556 152 ddh; 2-hydroxyaciddehydrogenase. [EC:1.1.1.-] Motif number 1 CTTACTGCCACCAATGGGGATGGGCTGACA 2 106 0 CCAATGGGGA 0.602545 -195 TTACTATTCTGTCGGGGAAATTCGCTGAGA 2 227 0 GTCGGGGAAA 0.663016 -74 AGAATAGTAACCATGGGGGCACAGTAAACC 2 247 1 CCATGGGGGC 0.800184 -54 ACCAATCTCTGCAAGGGGGATACTATGCCG 3 202 0 GCAAGGGGGA 0.970677 -20 CAATTTCTTCCCAGACGGAAACTGTACTCA 4 84 1 CCAGACGGAA 0.466041 -217 CTGCACAGGCCCCTGTGGAAAAAGGGAGGA 5 17 0 CCCTGTGGAA 0.569654 -148 AGCCTTAGCTGTAGGGGGACAAAAAATTTT 5 49 1 GTAGGGGGAC 0.427729 -116 GCCCCGGCGGGATGGACCCTTG 7 14 0 CCCGGCGGGA 0.89841 -12 AGACATTAGCGCCGAGGACAACTAGGCC 8 9 0 GCCGAGGACA 0.648003 -153 CGGGGCTTTTGCCAGGGGCACCAAAGGGAA 8 68 1 GCCAGGGGCA 0.975678 -94 GCCAGGGGCACCAAAGGGAAAAACGACTCC 8 78 1 CCAAAGGGAA 0.889789 -84 AAAAACGACTCCATGGGGAACACAGAGCCA 8 96 1 CCATGGGGAA 0.948941 -66 GGTTCCCTGACCCTGGGGGCTGACTCGGAT 9 108 0 CCCTGGGGGC 0.895757 -40 CTAGACTTTTGTCAGGAGAACTTTCCCGTT 10 48 1 GTCAGGAGAA 0.571771 -93 GGGAAGGGTAGCCAACGGGAAAGTTCTCCT 10 61 0 GCCAACGGGA 0.675184 -80 GGAAGACTGAGCAGGGGGAAGGGTAGCCAA 10 76 0 GCAGGGGGAA 0.962823 -65 GGCAATAAACGCCAGGGGGAAGACTGAGCA 10 93 0 GCCAGGGGGA 0.986117 -48 CATTGCGCCCCCCAGGGACAACGG 11 5 0 CCCAGGGACA 0.920974 -73 CTTTCCATTACCCAGGGAAA 11 68 1 CCCAGGGAAA 0.951678 -10 CTGGCAGTAACCAAGGAGGAAGGGCTTGGC 13 90 0 CCAAGGAGGA 0.842522 -111 CCCGTTCACAGCCGAGAGAAATTACAAATA 13 129 1 GCCGAGAGAA 0.633798 -72 TTCCAAAACCCTCTGGGGGAAGCTCAACTA 13 171 0 CTCTGGGGGA 0.854324 -30 TCAGCCTTGCCCAAAGGGAAAATAAAGCTT 14 12 0 CCAAAGGGAA 0.889789 -96 CTACCATTATGTCAAGGAAAATTTCAGTAA 16 112 0 GTCAAGGAAA 0.347508 -115 GAAACTGCCGCCCTGGAGCAAAGCCAGGAA 17 33 1 CCCTGGAGCA 0.768088 -85 CTGGAGCAAAGCCAGGAAAAGTTTATCCAA 17 45 1 GCCAGGAAAA 0.705885 -73 TTTATATTTTCCATGGGAAATATATGCGAA 18 129 1 CCATGGGAAA 0.824204 -172 CAGATGGGGAGCAAGGGACATTGAAGTGAT 18 161 0 GCAAGGGACA 0.825051 -140 ********** Masking position 10 Map Score: 26.969 Number of sites scoring better than the average of aligned sites = 10801 Number in coding regions = 9751 Number in noncoding regions = 1050 Number of orfs with sites within 600 bp upstream = 756 Fraction of orfs with sites within 600 bp upstream = 0.121426 Motif number 2 TCTTACTGCCACCAATGGGGATGGGCTGAC 2 107 0 ACCAATGGGG 0.684643 -194 TTTTCGTAGAATAATGGGGGTTGACTAAGG 2 165 1 ATAATGGGGG 0.649778 -136 CAGAATAGTAACCATGGGGGCACAGTAAAC 2 246 1 ACCATGGGGG 0.949566 -55 CAGCTAGTGGTCGTTGGGGCGAT 2 288 1 TCGTTGGGGC 0.813952 -13 TGCCTTGCTAACATTGGGGGTCAACATCGA 3 45 0 ACATTGGGGG 0.853137 -177 ACCAATCTCTGCAAGGGGGATACTATGCC 3 203 0 TGCAAGGGGG 0.764223 -19 CCTGTAAACAGTGCTGGGGGCGGAAAGCAC 4 271 0 GTGCTGGGGG 0.765275 -30 CTCCCTTTTTCCACAGGGGCCTGTGCAGGT 5 19 1 CCACAGGGGC 0.89728 -146 GTAGCCTTAGCTGTAGGGGGACAAAAAATT 5 47 1 CTGTAGGGGG 0.870055 -118 GGCAGACAAAATGATGGGGGGTTAACCGAC 5 103 1 ATGATGGGGG 0.812998 -62 AGGGTCCATCCCGCCGGGGC 7 16 1 CCGCCGGGGC 0.886502 -10 GCGGGGCTTTTGCCAGGGGCACCAAAGGGA 8 67 1 TGCCAGGGGC 0.832908 -95 GGAAAAACGACTCCATGGGGAACACAGAGC 8 94 1 CTCCATGGGG 0.740945 -68 AGGTTCCCTGACCCTGGGGGCTGACTCGGA 9 109 0 ACCCTGGGGG 0.973547 -39 GGGCAATAAACGCCAGGGGGAAGACTGAGC 10 94 0 CGCCAGGGGG 0.902781 -47 CCGTTGTCCCTGGGGGGCGCAATGAA 11 7 1 TCCCTGGGGG 0.961215 -71 GGTTCCAAAACCCTCTGGGGGAAGCTCAAC 13 173 0 CCCTCTGGGG 0.570295 -28 GCTTTATTTTCCCTTTGGGCAAGGCTGACC 14 14 1 CCCTTTGGGC 0.783769 -94 GTTAGGGGTAAGGCTGGGGCAGTTTGATCA 17 89 0 AGGCTGGGGC 0.87879 -29 CCTTTAGCATCTATCGGGGCATCAATGCCT 19 19 1 CTATCGGGGC 0.525852 -60 ********** Masking position 7 Map Score: 15.6651 Number of sites scoring better than the average of aligned sites = 5621 Number in coding regions = 5088 Number in noncoding regions = 533 Number of orfs with sites within 600 bp upstream = 465 Fraction of orfs with sites within 600 bp upstream = 0.0746868 Motif number 3 TCCCAGTATTGCCCAACATCTGGTTGACTAA 1 8 0 GCCCACTGGT 0.967778 -83 CCGACATGACGCCCTCTTACTGCCACCAATGGGG 2 117 0 GCCTTCTGCC 0.957448 -184 TCGCCCCAACGACCACTAGCTGGCAATTATTTCG 2 276 0 GCCTACTGGC 0.991769 -25 GTCAATAAATGTCCCAAAACTGGCTCTGTGTTCC 8 112 0 GCCAACTGGC 0.993714 -50 CAGGGTCAGGGAACCTTACCTGCCTTGGGTCATG 9 123 1 GACTACTGCC 0.943902 -25 TGTTTCTCCAGTCCCTAATCTGCACTTTAGATTT 16 74 1 GCCAACTGCA 0.962192 -153 TCCCTCCTGTGACCTGAAACTGCCGCCCTGGAGC 17 18 1 GCCAACTGCC 0.994917 -100 AATGTCCCTTGCTCCCCATCTGCTACTTTTTCCA 18 169 1 GTCCACTGCT 0.805999 -132 GTTTTTTACCGTCCTTAAACTGGCCATAATTTTC 18 212 1 GCCAACTGGC 0.993714 -89 * ** ** ***** Masking position 11 Map Score: 9.72686 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 60 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 4 CGTTTGGCGGGCTTGGCGAATGGTGGCTACGTGATC 3 8 1 CGCTGGCAGG 0.995719 -214 ACAACGGCTTCACGCTCCGTAACAGGTGGCTTTGTAGAT 4 163 1 CGCTCGTAGG 0.949643 -138 CTATGCCTTCTATCCTAGGCGATCGCCGTCTTAACCGTC 5 130 0 TCCTGGCAGT 0.874331 -35 GCTTAGGAATCTGGCGGGGCTTTTGCCAGGGGCACCAAA 8 54 1 CGCGGGCTGG 0.931015 -108 CTATCATTCTCAAGCTAGGCCTCTGACTGAAACTGTTCG 9 56 1 CGCTGGCTGG 0.984775 -92 TTTCCCTGGGTAATGGAAAGGGTAGGCTTA 11 58 0 TCCTGGTAGG 0.961887 -20 CCAAGCCCTTCCTCCTTGGTTACTGCCAGCTTAACCATC 13 91 1 CCCTGGTAGG 0.993193 -110 AGAAACTCCCCACCCTAGGTAACTGGGATGGGGTTTTTC 14 69 1 CCCTGGTAGT 0.961887 -39 CGGCTCGTATCATGCTAGGCTATGCTGTGCTAGCATGAA 20 39 0 CGCTGGCACG 0.967894 -66 ATTAACGGCACTACCTTGGTGATCGATAGTACGATAAAT 21 32 0 CCCTGGTAGG 0.993196 -121 * *** *** * * * Masking position 5 Map Score: 9.52327 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 380 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 5 GGGGTTGACTAAGGCAAAATTTTTGATTTGTGA 2 181 1 AAGCAAATTT 0.704461 -120 CAATGTTAGCAAGGCAAACCTCTCAATAATTTT 3 59 1 AAGCAACTCT 0.911317 -163 TAGATCAACAAAATCCAAAATTATTGAGAGGTT 3 75 0 AAACAAATTA 0.460033 -147 CACCCCTATTAAATCAAACATTTCCACCGATGC 3 168 0 AAACAACTTT 0.940548 -54 TGATATCTACAAAGCCACCTGTTACGGAGCGTG 4 173 0 AAACACCGTT 0.927796 -128 CCCTACAGCTAAGGCTACCTGCACAGGCCCCTG 5 32 0 AAGCACCGCA 0.745042 -133 TTACGTCAACAAATCTAACAGAAA 6 2 0 AAACAACGAA 0.573801 -37 TCAATTGTTCACAGCGAACAGTTTCAGTCAGAG 9 76 0 ACACAACGTT 0.810799 -72 TAGCGTTTTTAAGACTAACATATTTTGCCTAGA 10 20 1 AAGCAACTAT 0.776403 -121 CGTTCAATCTAAGCCTACCCTTTCCATTACCCA 11 49 1 AAGCACCTTT 0.920654 -29 AGCCATGAATAAAACTACCCATTGATGGAAAAG 12 32 1 AAACACCATT 0.625006 -114 GCGAGCGATCAAGACCACCATTAGGGAGCTTTT 13 39 0 AAGCACCTTA 0.802471 -162 GGGCTTGGCAAAAGCAAAATTCTAAGGGCGAGC 13 66 0 AAACAAATCT 0.617369 -135 TTAAACTGGAAAAGCTAACCGTTGATTCCATAG 16 19 1 AAACAACGTT 0.94494 -208 TAAAAAGGACAAACCTAACAGCTAAATAGCTTC 16 170 0 AAACAACGCT 0.919224 -57 ACAGCAAACCTTTAGCATCTATC 19 1 1 ACACAACTTT 0.797996 -78 *** * *** *** Masking position 7 Map Score: 6.85669 Number of sites scoring better than the average of aligned sites = 441 Number in coding regions = 372 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 ATCTCTGCCTGGAATTAACCCCGTTCCAACTG 2 35 1 GAATAACCCC 0.940356 -266 CTATGGATTGGTCATCAATTCCCTTAAAATAG 3 118 0 GCATAATTCC 0.711667 -104 CGATGCCATGGACTAGAACCCCAACTATGGAT 3 142 0 GCTAAACCCC 0.95764 -80 GGAAAACCGGGTCTAAAACCCCGTCTTTCAGA 4 209 0 GCTAAACCCC 0.95764 -92 TAGGATAGAAGGCATAGACCCCA 5 152 1 GCATGACCCC 0.951623 -13 TGTCGAGAAAGACATTAGCGCCGAGGACAACT 8 16 0 GCATAGCGCC 0.970122 -146 TGGTGCCCCTGGCAAAAGCCCCGCCAGATTCC 8 59 0 GCAAAGCCCC 0.955491 -103 TGGATGTAGGGCAATAAACGCCAGGGGGAAGA 10 100 0 GAATAACGCC 0.929926 -41 TCTTTTAAAAGGCTGAAACGCCTATTTCTCAA 12 75 1 GCTGAACGCC 0.914487 -71 CATCTATCGGGGCATCAATGCCTATTTCTTTT 19 26 1 GCATAATGCC 0.548262 -53 * *** ****** Masking position 11 Map Score: 5.94588 Number of sites scoring better than the average of aligned sites = 550 Number in coding regions = 511 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 7 CCAGATGTTGGGCAATACTGGGAAAATTTG 1 19 1 GGCAATACTG 0.927477 -72 AAACGCCAGGGGGAAGACTGAGCAGGGGGA 10 87 0 GGGAAGACTG 0.932458 -54 TGAACGGGATGGTTAAGCTGGCAGTAACCA 13 107 0 GGTTAAGCTG 0.914546 -94 TACAAATAAAGGCTATATTGTAGTTGAGCT 13 151 1 GGCTATATTG 0.504369 -50 TTTCCCTTTGGGCAAGGCTGACCGATTTAG 14 21 1 GGCAAGGCTG 0.987744 -87 GGATAGGCACGGGAAGGCCGAATTTGGTTA 16 201 0 GGGAAGGCCG 0.907765 -26 GTTAGTTAGGGGTAAGGCTGGGGCAGTTTG 17 93 0 GGTAAGGCTG 0.975013 -25 ATTTTCGTCAGGTTAAGCTGGGGTAAGATC 18 240 1 GGTTAAGCTG 0.914546 -61 TATCATGCTAGGCTATGCTGTGCTAGCATG 20 41 0 GGCTATGCTG 0.969393 -64 ********** Masking position 5 Map Score: 7.1797 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 283 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 8 TTGGGCAATACTGGGAAAATTTGATCTCAT 1 26 1 CTGGGAAAAT 0.817003 -65 GGGGTTGACTAAGGCAAAATTTTTGATTTG 2 181 1 AAGGCAAAAT 0.711021 -120 TGACACTGAGTTGTCAAAAGATATTCGAGA 4 134 0 TTGTCAAAAG 0.719104 -167 ACAGGCCCCTGTGGAAAAAGGGAGGAAAAT 5 13 0 GTGGAAAAAG 0.768476 -152 TCACGAAAGGCAGACAAAATGATGGGGGGT 5 95 1 CAGACAAAAT 0.733292 -70 TTTGGTGCCCCTGGCAAAAGCCCCGCCAGA 8 63 0 CTGGCAAAAG 0.980882 -99 GACAAAAGTCTAGGCAAAATATGTTAGTCT 10 31 0 TAGGCAAAAT 0.890051 -110 GAAAGTTCTCCTGACAAAAGTCTAGGCAAA 10 43 0 CTGACAAAAG 0.898675 -98 GAGGAAGGGCTTGGCAAAAGCAAAATTCTA 13 75 0 TTGGCAAAAG 0.963118 -126 ACGAAATTAGCTGGAAAAAGTAGCAGATGG 18 184 0 CTGGAAAAAG 0.935385 -117 GCTTCATTTTTAGGAAAAATATCTGGTAAT 21 80 1 TAGGAAAAAT 0.695502 -73 ********** Masking position 6 Map Score: 4.65979 Number of sites scoring better than the average of aligned sites = 961 Number in coding regions = 819 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 164 Fraction of orfs with sites within 600 bp upstream = 0.0263412 Motif number 9 AACCTCCCAAGTTTTGGGAGAAATGAGATC 1 48 0 GTTTTGGGAG 0.931119 -43 CACAGAGCCAGTTTTGGGACATTTATTGAC 8 116 1 GTTTTGGGAC 0.983315 -46 CATGTTTGGAGTTTTGGAAAAAA 13 4 0 GTTTTGGAAA 0.86273 -197 CCCCCAGAGGGTTTTGGAACCATTTAGGA 13 182 1 GTTTTGGAAC 0.958258 -19 CTAAAGTGCAGATTAGGGACTGGAGAAACA 16 74 0 GATTAGGGAC 0.913534 -153 GTCTATTGTTTTTTAGGGACTCAATCAATT 18 52 1 TTTTAGGGAC 0.930961 -249 ATTATGGCCAGTTTAAGGACGGTAAAAAAC 18 212 0 GTTTAAGGAC 0.868119 -89 GTTGCTTCATTTTTAGGAAAAATATCTGGT 21 77 1 TTTTAGGAAA 0.58981 -76 ********** Masking position 9 Map Score: 3.46379 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 302 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 10 TTCAAAATCTCTGCCTGGAATTAACCCCGTT 2 29 1 CTGCCTGAAT 0.960915 -272 ATGACGCCCTCTTACTGCCACCAATGGGGAT 2 115 0 CTTACTGCAC 0.748038 -186 AATTTCTTCCCAGACGGAAACTGTACTCAGG 4 85 1 CAGACGGAAC 0.722123 -216 GTCTTATCTTCCTGTAAACAGTGCTGGG 4 283 0 CTTCCTGAAA 0.82666 -18 AAAAATTTTACTCCCGGCAACCTTGTCACGA 5 70 1 CTCCCGGAAC 0.970048 -95 AGCTAGGCCTCTGACTGAAACTGTTCGCTGT 9 68 1 CTGACTGAAC 0.952339 -80 TACATCCAAGCTCCCGGTAATTTACAA 10 124 1 CTCCCGGAAT 0.953293 -17 TAGATTTGCCCTTACTGAAATTTTCCTTGAC 16 101 1 CTTACTGAAT 0.889014 -126 TGATTAAAAACTCCCTGCAATTCAATCTCGC 18 12 1 CTCCCTGAAT 0.961172 -289 ******* *** Masking position 10 Map Score: 2.80672 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 212 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 GAGGGCGTCATGTCGGCAATAAATTAATCA 2 135 1 TGTCGGCAAT 0.789538 -166 TTGTGGATGATCTCAGCGAATTTCCCCGAC 2 217 1 TCTCAGCGAA 0.775398 -84 GTTACTATTCTGTCGGGGAAATTCGCTGAG 2 228 0 TGTCGGGGAA 0.984323 -73 TTAATAGGGGTGTCGGCATAGTATCCCCCT 3 189 1 TGTCGGCATA 0.807797 -33 CCGGCAACCTTGTCACGAAAGGCAGACAAA 5 83 1 TGTCACGAAA 0.802809 -82 AAGCTAGAATTGTCGAGAAAGACATTAGCG 8 28 0 TGTCGAGAAA 0.885628 -134 CAGCCCCCAGGGTCAGGGAACCTTACCTGC 9 116 1 GGTCAGGGAA 0.891471 -32 CCTAGACTTTTGTCAGGAGAACTTTCCCGT 10 47 1 TGTCAGGAGA 0.852148 -94 CCTACCATTATGTCAAGGAAAATTTCAGTA 16 113 0 TGTCAAGGAA 0.88579 -114 GGAAAGGGCTTGTCGGCGAAGCTATTTAGC 16 153 1 TGTCGGCGAA 0.97702 -74 ********** Masking position 3 Map Score: 2.95151 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 453 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 12 GTAACCATGGGGGCACAGTAAACCGAAATAATT 2 253 1 GGGACAGAAC 0.928241 -48 ACAGTGCTGGGGGCGGAAAGCACCGCGCTTCTT 4 261 0 GGGGGAAGAC 0.988126 -40 TGTGGAAAAAGGGAGGAAAATCC 5 1 0 GGGGGAAACC 0.950904 -164 TGTCCCTGGGGGGCGCAATGAACGATCGCCGTT 11 15 1 GGGGCAAGAC 0.993748 -63 GTAGCAGATGGGGAGCAAGGGACATTGAAGTGA 18 162 0 GGGGCAAGAC 0.993764 -139 GGGGGCAGGACACCAATGGCATA 18 288 0 GGGGCAGAAC 0.988081 -13 *** **** * ** Masking position 7 Map Score: 2.36405 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 64 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 AAAATGCCCAATAACCTCCCAAGTTTTGGGAG 1 58 0 AAACCTCCCA 0.970027 -33 GTTAGCAAGGCAAACCTCTCAATAATTTTGGA 3 63 1 CAACCTCTCA 0.779853 -159 TGCCCTACATCCAAGCTCCCGGTAATTTACAA 10 119 1 CAAGCTCCCG 0.947267 -22 TTTTTTCCAAAACTCCAAACATGTTACCA 13 8 1 CAAACTCCAA 0.897456 -193 ACATGTTACCAAAAGCTCCCTAATGGTGGTCT 13 29 1 AAAGCTCCCA 0.970027 -172 ACCAAGAAAAAGAAACTCCCCACCCTAGGTAA 14 59 1 AAAACTCCCA 0.975024 -49 GGGCAGTTTGATCAACTCCATAGCCGGTTTGG 17 71 0 ACAACTCCAA 0.703402 -47 TTGATTAAAAACTCCCTGCAATTCAATC 18 7 1 AAAACTCCCG 0.956721 -294 * ******** * Masking position 4 Map Score: 1.35344 Number of sites scoring better than the average of aligned sites = 203 Number in coding regions = 162 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 14 AAAATGATTAATTTATTGCCGACATGACGC 2 139 0 ATTTATTGCC 0.959567 -162 AGTAAACCGAAATAATTGCCAGCTAGTGGT 2 269 1 AATAATTGCC 0.927111 -32 GTTTTGGGACATTTATTGACAGTTAGCTGA 8 126 1 ATTTATTGAC 0.785932 -36 TCCCCCTGGCGTTTATTGCCCTACATCCAA 10 103 1 GTTTATTGCC 0.896663 -38 ACCTGACGAAAATTATGGCCAGTTTAAGGA 18 223 0 AATTATGGCC 0.951633 -78 CTAAGATACCAATAATGGCCCGGCTCGTAT 20 68 0 AATAATGGCC 0.913383 -37 ********** Masking position 5 Map Score: 0.414834 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 186 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 15 CTATCCTAGGCGATCGCCGTCTTAACCGTC 5 130 0 CGATCGCCGT 0.994001 -35 GCGCAATGAACGATCGCCGTTGCGTTCAAT 11 27 1 CGATCGCCGT 0.994001 -51 TGGTCTTGATCGCTCGCCCTTAGAATTTTG 13 55 1 CGCTCGCCCT 0.986939 -146 ********** Masking position 4 Map Score: 0.266864 Number of sites scoring better than the average of aligned sites = 799 Number in coding regions = 732 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918