AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00550_synecho_reg_100.orf -o00550_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 slr1118 38 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #2 sll1063 224 hypothetical protein. #3 sll0648 127 lim; lipophilic protein. [EC:2.4.1.-] #4 slr1756 218 glnA; glutamine synthetase (glutamate--ammonia ligase). [EC:6.3.1.2] #5 slr1910 23 amiA; N-acetylmuramoyl-L-alanine amidase. [EC:3.5.1.28] #6 sll1837 264 hypothetical protein. #7 sll0864 180 hypothetical protein. #8 slr1874 86 ddlA; D-alanine--D-alanine ligase (D-alanylalanine synthetase). #9 slr1875 119 exoD; exopolysaccharide synthesis protein ExoD. #10 sll2010 180 murD; UDP-N-acetylmuramoylalanine-D-glutamate ligase. [EC:6.3.2.9] #11 slr1734 57 opcA; putative oxppcycle protein opcA. [EC:3.5.1.28] [SP:OPCA_SYNY3] #12 slr1735 248 glnQ; glutamine transport ATP-binding protein. #13 slr1744 143 amiA; N-acetylmuramoyl-L-alanine amidase. [EC:3.5.1.28] #14 slr1351 170 murF; UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate--D- #15 slr1271 251 rffM; UDP-N-acetyl-D-mannosaminuronic acid transferase. [EC:2.4.1.-] #16 slr0288 163 glnN; glutamate-ammonia ligase. [EC:6.3.1.2] #17 sll0210 114 bacA; bacitracin resistance; possibly phosphorylates undecaprenol. #18 sll0657 112 mraY; phospho-N-acetylmuramoyl-pentapeptide-transferas e. #19 slr0528 128 murE; UDP-MurNac-tripeptide synthetase. [EC:6.3.2.13] #20 slr1423 71 murC; UDP-N-acetylmuramate-alanine ligase. [EC:6.3.2.8] #21 slr1424 21 hypothetical protein. #22 slr1425 134 hypothetical protein. #23 slr1656 300 murG; UDP-N-acetylglucosamine-N-acetylmuramyl-(pentape ptide) Motif number 1 TCAAAACCAATGGGATGGATTGTAACGAGATCT 2 42 1 TGGGAGGATT 0.602687 -183 GCGATCGCCGGGGGGCAAATGTGTATAAATGCT 2 101 0 GGGGGAAATG 0.982364 -124 ATCGCCAAATTGGGGCAAAAAATTAGATAATTG 2 129 1 TGGGGAAAAT 0.946068 -96 GGGGATAGGATGGGGCAAATGCGCCGCAATTAT 2 155 0 TGGGGAAATG 0.991294 -70 CGTACAAATATGGGGTAAACTTTATCCTAAACC 3 83 1 TGGGGAAACT 0.981659 -45 AATTTTTCTGGGGGGCGATTTTTCTTTTGGAAA 4 52 0 GGGGGGATTT 0.846053 -167 CCGGTGGCCCTGGGAAAAATCTGTTTCAATAAC 4 169 0 TGGGAAAATG 0.945941 -50 GGCTTACCCTGGGGATAAATAGTTTTTTGGTAT 6 165 0 GGGGAAAATT 0.841339 -100 CACCCAACTTTGGGGAGAAACTGGGTAAAGTTT 7 83 1 TGGGGGAAAG 0.936314 -98 GCTTTATCCCTGGGGGGGTTTTGGTTAGTTGGC 10 58 1 TGGGGGGTTG 0.830166 -123 ATTGAAAGTTGGGGGCAAAAAGGGAACGCCCCT 10 132 0 GGGGGAAAAG 0.932672 -49 AGGTTACGGCTGGGGGAAATTGGGTTACATTTA 15 152 0 TGGGGAAATG 0.991294 -100 GTTAATAATCGGGGGAAATTGTGGATAAAGGTT 15 180 0 GGGGGAATTG 0.944713 -72 TTTGGAAGTTTGGGGGGATTAATGATCGGGAAA 16 66 0 TGGGGGATTT 0.918263 -98 CTCCCAATGCTGGGGTAAACCAGCTTAAAGTCC 16 108 0 TGGGGAAACG 0.988559 -56 CCCAGGGGGATGGGTAAAACCATCTCCCAATGC 16 131 0 TGGGTAAACT 0.714284 -33 GGGAGATTTATGGGGTCATCGTTGCTTAAAACC 22 19 0 TGGGGCATCT 0.661539 -116 AGGGTTTTGCTGGGGTAGATTTTTGTTATGGAA 22 87 0 TGGGGAGATT 0.950032 -48 AACACCAATCTAGGGAAAATAGTCCTGGGTAAG 23 27 0 TAGGGAAATT 0.727726 -274 TGTGAATCTATGGGAAAAACAATGCCAGCTCCG 23 92 0 TGGGAAAACT 0.8916 -209 TCCCCAAGCTTGGGGGAAACTCGGGAAAGGTTT 23 207 0 TGGGGAAACG 0.988559 -94 CCCCCAAGCTTGGGGAAAATTAGGTTGGATTTT 23 224 1 TGGGGAAATG 0.991294 -77 ***** **** * Masking position 4 Map Score: 36.4733 Number of sites scoring better than the average of aligned sites = 1861 Number in coding regions = 1634 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 232 Fraction of orfs with sites within 600 bp upstream = 0.0372631 Motif number 2 TTTGCCCCCCGGCGATCGCCAAATTGGGGC 2 115 1 GGCGATCGCC 0.499998 -110 TTATCCGTTTGGCGATCGCCGTTTAATTTA 4 83 1 GGCGATCGCC 0.499998 -136 TAGTAATTTAGGCGATCGCCGTCAATTATG 6 64 1 GGCGATCGCC 0.499998 -201 GGTGATTCCGATGGATCACCAGCAAGCAC 8 68 1 ATGGATCACC 0.71625 -19 TAGCTTTGAGGGGGATCACCGCCAACTAAC 10 81 0 GGGGATCACC 0.760447 -100 GGGGGCAAAAAGGGAACGCCCCTGGCATCG 10 125 0 AGGGAACGCC 0.927042 -56 TCCCTAGGCTGGCGATCGCCTTTCGCTGGC 12 66 1 GGCGATCGCC 0.499998 -183 CGGAGGTGTGGGCGATCGCCTGCCAATCAA 15 97 1 GGCGATCGCC 0.499998 -155 TACATTTATTAGGTATCGCCGTCTAAATTG 15 130 0 AGGTATCGCC 0.894653 -122 GCAACGGTGGGGCGATCACAATTCTAGGGG 17 17 1 GGCGATCACA 0.717136 -98 ********** Masking position 5 Map Score: 26.2725 Number of sites scoring better than the average of aligned sites = 5993 Number in coding regions = 5430 Number in noncoding regions = 563 Number of orfs with sites within 600 bp upstream = 340 Fraction of orfs with sites within 600 bp upstream = 0.0546097 Motif number 3 TATCCCTAATGTTTTAGCAGTAAAAAGTAA 1 12 0 GTTTTAGCAG 0.46992 -27 GATGTCCTAGGGTCGGGCGGGTAAAATCAA 2 16 1 GGTCGGGCGG 0.772316 -209 TTTGGCTCCGATGCTGGGGG 3 1 0 ATGCTGGGGG 0.855713 -127 TCGGAGCCAAATTCTAGGGGCCATACCAAA 3 20 1 ATTCTAGGGG 0.898864 -108 ACGGATAATTTTTCTGGGGGGCGATTTTTC 4 61 0 TTTCTGGGGG 0.641262 -158 TCGACTGCGGTCGGGGGGTGAAC 5 9 1 GGTCGGGGGG 0.959342 -15 TTTTTCTTTTGTGTGAGGAGTCAGC 6 6 0 GTGTGAGGAG 0.7971 -259 ACTATTTTGTGTTTTGGGAGCGACAATTTC 6 105 1 GTTTTGGGAG 0.887231 -160 AATTTCTGTGGTTTGAGGAGTTTTT 6 250 1 GTTTGAGGAG 0.882509 -15 AAAGTTGGGTGGGTTGGGGGCTTTTAAAAG 7 64 0 GGGTTGGGGG 0.91681 -117 ACCCACCCAACTTTGGGGAGAAACTGGGTA 7 80 1 CTTTGGGGAG 0.698587 -101 TTACCGGAGTAATTTAGGGGCGGAATCAAA 7 124 1 AATTTAGGGG 0.676389 -57 AAAATTTAGCGTTTCAGCGGAGATTATCGG 8 40 1 GTTTCAGCGG 0.666534 -47 ACCATTTTAGCTTTGAGGGGGATCACCGCC 10 88 0 CTTTGAGGGG 0.880602 -93 TGCGACATCGATGCCAGGGGCGTTCCCTTT 10 117 1 ATGCCAGGGG 0.720784 -64 AAACTATTGAAAGTTGGGGGCAAAAAGGGA 10 140 0 AAGTTGGGGG 0.582415 -41 TGGTCATTTTGGTTGAGGAGTGTTCTGTA 15 10 0 GGTTGAGGAG 0.832072 -242 ATAAAGGTTACGGCTGGGGGAAATTGGGTT 15 159 0 CGGCTGGGGG 0.710167 -93 CAGTGGAAATGTTCCAGGGGTTAATAATCG 15 202 0 GTTCCAGGGG 0.927443 -50 GCTTTTGGAAGTTTGGGGGGATTAATGATC 16 72 0 GTTTGGGGGG 0.974942 -92 ACTTCCAAAAGCTTGAGGGGACTTTAAGCT 16 90 1 GCTTGAGGGG 0.794551 -74 GGCGATCACAATTCTAGGGGACAGTTTAAA 17 27 1 ATTCTAGGGG 0.898864 -88 TCAAAAAATTAGTTCAGGGGTTGATCAATG 18 91 0 AGTTCAGGGG 0.779817 -22 AGACCTAGGGATTTTAGGGGGGACGGTTTT 22 59 1 ATTTTAGGGG 0.906259 -76 GTTTTATCTTGATTTGGGAGGTGTTGGCAA 23 144 1 GATTTGGGAG 0.629765 -157 ********** Masking position 7 Map Score: 27.5835 Number of sites scoring better than the average of aligned sites = 3429 Number in coding regions = 2894 Number in noncoding regions = 535 Number of orfs with sites within 600 bp upstream = 348 Fraction of orfs with sites within 600 bp upstream = 0.0558946 Motif number 4 ATCTTTCCAAAAGAAAAATCGCCCCCCAGAAAA 4 49 1 AGAAAATGCC 0.788528 -170 AATCGCCCCCCAGAAAAATTATCCGTTTGGCGA 4 65 1 CGAAAATATC 0.885628 -154 CCTCACACAAAAGAAAAAAAGGCAACGGCAAAA 6 18 1 AGAAAAAGGC 0.787156 -247 AAAAAGGCAACGGCAAAACTGGCCTCAACTCTA 6 33 1 CGAAAACGGC 0.982772 -232 CGCTCCCAAAACACAAAATAGTCAGCACATCGA 6 94 0 AAAAAATGTC 0.708196 -171 ACCTTCCAAAACGAAAAATTAGCAAAA 7 164 1 AGAAAATAGC 0.910696 -17 AACGTATCTGGAAAATAGGCTTAGCCAGTA 9 8 1 CGAAAATGGC 0.984587 -112 TAGGCTTAGCCAGTAAAACCCGCAAGAGTTTAC 9 26 1 CGAAAACCGC 0.946971 -94 GCAAGACTAGACAAAAAACTCTCAGATTAAGGA 9 96 1 AAAAAACCTC 0.404211 -24 CCTAGATAGCCATAAAAACAGGCCAGCGAAAGG 12 84 0 CTAAAACGGC 0.776405 -165 GACCAACGGACTGGAAAATAAGCCGCAAAAGTT 15 35 1 CGAAAATAGC 0.953277 -217 TAATTCTTCAAACAAAATTGGCCCTTTATGCA 15 230 0 AAAAAATGGC 0.864767 -22 AAAGGTATATCTAAAAAATCAGCAATTTCCCGA 16 41 1 CAAAAATAGC 0.803386 -123 TTAAATCTGTCAGCAAAATCGACAGCCAAAGGC 18 23 1 CGAAAATGAC 0.834256 -90 GGCGGTTGGTCCGGAAAATTAGCGGGACAGGAA 20 11 1 CGAAAATAGC 0.953277 -61 GATTTTTGTTATGGAAAACCGTCCCCCCTAAAA 22 70 0 AGAAAACGTC 0.915406 -65 AAATCTACCCCAGCAAAACCCTCTGTCGAGATC 22 98 1 CGAAAACCTC 0.871425 -37 ACACCAATCTAGGGAAAATAGTCCTGGGTAAGC 23 26 0 AGAAAATGTC 0.92377 -275 * * ***** *** Masking position 7 Map Score: 20.8648 Number of sites scoring better than the average of aligned sites = 1041 Number in coding regions = 924 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 5 ATGGCCCCGACTAAGTTGGTCTAGAAATAA 4 121 0 CTAAGTTGGT 0.934408 -98 AATCGGTGAACTAGGCCGGTTATTGAAACA 4 151 1 CTAGGCCGGT 0.858053 -68 CTTACTAGAACTAGGCTGGCTTTGCCCACG 6 208 0 CTAGGCTGGC 0.973002 -57 TCTCCCCAAAGTTGGGTGGGTTGGGGGCTT 7 71 0 GTTGGGTGGG 0.807688 -110 TTTTTTGCCGCTTGATTGGGCA 10 3 0 CTTGATTGGG 0.88426 -178 GGGGGTTTTGGTTAGTTGGCGGTGATCCCC 10 71 1 GTTAGTTGGC 0.882494 -110 TGTTCTTAACCTTAGTCGGCC 11 2 0 CTTAGTCGGC 0.84337 -56 ACTTCTATCCCTAGGCTGGCGATCGCCTTT 12 59 1 CTAGGCTGGC 0.973002 -190 TTATGGCTATCTAGGGTGGTCACCGGGGCA 12 102 1 CTAGGGTGGT 0.939241 -147 TAGGTGTGGGGTTGGTTGGCAGTGGCATCC 14 85 0 GTTGGTTGGC 0.959208 -86 CTAAATTGGTGTTGATTGGCAGGCGATCGC 15 108 0 GTTGATTGGC 0.847354 -144 GTATCGCCGTCTAAATTGGTGTTGATTGGC 15 118 0 CTAAATTGGT 0.770799 -134 AAAGATAACCCTAGGTTAGTTTGCCCAGC 20 53 1 CTAGGTTAGT 0.716215 -19 ACTATTTTCCCTAGATTGGTGTTTAATTAT 23 37 1 CTAGATTGGT 0.913267 -264 TTATCCTCTGCTTAGTTGGGGCAGGGAAAC 23 63 1 CTTAGTTGGG 0.911788 -238 ********** Masking position 2 Map Score: 11.984 Number of sites scoring better than the average of aligned sites = 1299 Number in coding regions = 1181 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 6 GGTAAACTTTATCCTAAACCCTTCCCAATCCCATC 3 96 1 ATCAACCTCC 0.933594 -32 ATTTATCCCCAGGGTAAGCCCATCCCTGGCCGTGG 6 178 1 AGGAACCACC 0.983091 -87 TCCCTGGCCGTGGGCAAAGCCAGCCTAGTTCTAGT 6 200 1 TGGAACCACC 0.988477 -65 ACCACAGAAATTGTTAACGCCAATCTTACTAGAAC 6 227 0 TTGAACCATC 0.894603 -38 TGCAAAAAGGTTGAAAAATCCTGCCTGCT 7 5 0 TTGAACCTCC 0.976035 -176 GAATCAAACTTTCTGAAGACCTTCCAAAACGAAAA 7 146 1 TTCAACCTCC 0.954008 -35 GGCCAGCGAAAGGCGATCGCCAGCCTAGGGATAGA 12 62 0 AGGATCCACC 0.85124 -187 GGCGTTTTGTTTCAAAACCCCATCCCCCAAGAAAA 12 141 1 TTCAACCACC 0.975772 -108 CATTTGTTGGATGCCACTGCCAACCAACCCCACAC 14 77 1 ATGACCCACC 0.886597 -94 CCCAGGGGGATGGGTAAAACCATCTCCCAATGCTG 16 129 0 TGGAACCACT 0.839272 -35 CAAAATCGACAGCCAAAGGCCAGCAACCTTGATGC 18 36 1 AGCAACCACA 0.643181 -77 GGGTCATCGTTGCTTAAAACCAATCAAAC 22 5 0 TGCAACCATC 0.824244 -130 GATTTTTGTTATGGAAAACCGTCCCCCCTAAAATC 22 68 0 ATGAACGTCC 0.698328 -67 AACCCGAACTTTGCCAACACCTCCCAAATCAAGAT 23 149 0 TTGAACCTCC 0.976035 -152 CAAAAGACTGTTGTAAAATCCAACCTAATTTTCCC 23 236 0 TTGAACCACC 0.987512 -65 *** ** *** ** Masking position 6 Map Score: 18.0818 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 683 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 7 CCAAATTGGGGCAAAAAATTAGATAATTGC 2 133 1 GCAAAAAATT 0.640663 -92 GAAGGGTTTAGGATAAAGTTTACCCCATAT 3 90 0 GGATAAAGTT 0.669659 -38 TCACACAAAAGAAAAAAAGGCAACGGCAAA 6 20 1 GAAAAAAAGG 0.604656 -245 CAACAATTTTGCAAAAAGGTTGAAAAATCC 7 19 0 GCAAAAAGGT 0.972166 -162 AAAGTTGGGGGCAAAAAGGGAACGCCCCTG 10 131 0 GCAAAAAGGG 0.982426 -50 GCAGAATGGAGCAACAAGCGCCCTTTGCTT 11 36 0 GCAACAAGCG 0.762276 -22 AGGGATAGAAGTAAAAAGTTTTACCAGTGT 12 41 0 GTAAAAAGTT 0.588978 -208 CATCCCCCAAGAAAAAAGGGAGGAAAAGCA 12 161 1 GAAAAAAGGG 0.916721 -88 GGGAAATTGTGGATAAAGGTTACGGCTGGG 15 171 0 GGATAAAGGT 0.846569 -81 CATTTCCACTGCATAAAGGGCCAATTTTGT 15 221 1 GCATAAAGGG 0.96666 -31 CATCAGACTAGCATCAAGGTTGCTGGCCTT 18 51 0 GCATCAAGGT 0.862602 -62 AGTTTGCTCCGCAAAAAGTGACCACAATGG 19 74 0 GCAAAAAGTG 0.953571 -55 ********** Masking position 6 Map Score: 6.82909 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 537 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 8 TTAGCCACTGTTACCCAGGCAGTAAAGACT 3 49 0 TTACCCAGGC 0.946622 -79 CCAGTCCATCTCACCCAGTTTTAGCTCCGG 4 198 0 TCACCCAGTT 0.92347 -21 TGAGGAAACTTTACCCAGTTTCTCCCCAAA 7 91 0 TTACCCAGTT 0.961069 -90 GAAAATAGGCTTAGCCAGTAAAACCCGCAA 9 21 1 TTAGCCAGTA 0.925502 -99 CCGCAAGAGTTTACCCGGTTTACTAAAGGT 9 45 1 TTACCCGGTT 0.852241 -75 ATAGACGTTTTTAGCCATGTTCTTAACCAT 14 35 1 TTAGCCATGT 0.793331 -136 TAAGAACCTATTGGCCAGGTTTCAGTTTGC 19 97 0 TTGGCCAGGT 0.901464 -32 TCTGTCGAGATCAGCCAGGAAAAAAG 22 119 1 TCAGCCAGGA 0.922665 -16 GAATGACTGCTTACCCAGGACTATTTTCCC 23 18 1 TTACCCAGGA 0.967983 -283 ********** Masking position 1 Map Score: 5.43464 Number of sites scoring better than the average of aligned sites = 372 Number in coding regions = 343 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 9 CCTTCCCAATCCCATCTTTGCCC 3 115 1 CCCACTTTGC 0.970523 -13 GCCTAGTTCACCGATTATGGCCCCGACTAAGT 4 135 0 CCGATATGGC 0.611178 -84 GTCCATCTCACCCAGTTTTAGCTCCGGTGGCC 4 193 0 CCCATTTTAC 0.940463 -26 TAGAGTTGAGGCCAGTTTTGCCGTTGCCTTTT 6 34 0 GCCATTTTGC 0.637491 -231 CCCCAACCCACCCAACTTTGGGGAGAAACTGG 7 75 1 CCCACTTTGG 0.823517 -106 GTAAAGTTTCCTCAGTATTACCGGAGTAATTT 7 107 1 CTCATATTAC 0.471715 -74 GCCGAAATATCCCGGCTTTATCCCTGGGGGGG 10 44 1 CCCGCTTTAC 0.874384 -137 CCCGGCATTACCGGGAACAGCT 12 1 1 CCCGCATTAC 0.818148 -248 TGAGATTAACCCCATTTTTAACTGACTCAAGC 14 140 1 CCCATTTTAC 0.940468 -31 ATAAATGTAACCCAATTTCCCCCAGCCGTAAC 15 151 1 CCCATTTCCC 0.71186 -101 ACAATTTCCCCCGATTATTAACCCCTGGAACA 15 191 1 CCGATATTAC 0.878113 -61 CAGCAATTTCCCGATCATTAATCCCCCCAAAC 16 60 1 CCGACATTAT 0.330464 -104 GCTGGTTTACCCCAGCATTGGGAGATGGTTTT 16 117 1 CCCACATTGG 0.752907 -47 TCTTTGAGTCCCGATTATCATCGACAGTTA 17 95 1 CCGATATCAC 0.723788 -20 ATCAAGGTTGCTGGCCTTTGGCTGTCGATTTT 18 37 0 CTGGCTTTGC 0.408513 -76 GCCCGATGCTCCTAATTTTGGCTGAGGACTAT 19 28 1 CCTATTTTGC 0.664819 -101 AAGGGCAAACCCGAACTTTGCCAACACCTCCC 23 159 0 CCGACTTTGC 0.958731 -142 GAAACCTTTCCCGAGTTTCCCCCAAGCTTGGG 23 206 1 CCGATTTCCC 0.635472 -95 **** ***** * Masking position 8 Map Score: 7.9655 Number of sites scoring better than the average of aligned sites = 1928 Number in coding regions = 1687 Number in noncoding regions = 241 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 10 CCCCCAGCATCGGAGCCAAATTCTAGG 3 7 1 GCATCGGAGC 0.968776 -121 CCCAGTTTTAGCTCCGGTGGCCCTGGGAAAA 4 184 0 GCTCCGGTGC 0.963316 -35 AACGCCCCTGGCATCGATGTCGCACCATTTT 10 110 0 GCATCGATGC 0.960409 -71 TAGGACGAATGCCCCGGTGACCACCCTAGAT 12 110 0 GCCCCGGTGC 0.974476 -139 GGAGTTGCAACGGTGGGGCGATCACAA 17 7 1 GCAACGGTGG 0.951217 -108 TTGGTTTTAAGCAACGATGACCCCATAAATC 22 17 1 GCAACGATGC 0.972023 -118 CCAGCCTGCTGCAACGTAGTCACTGGGTTCA 23 273 0 GCAACGTAGC 0.895573 -28 ********* * Masking position 6 Map Score: 3.29141 Number of sites scoring better than the average of aligned sites = 306 Number in coding regions = 293 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 TACCAATAGGTTTAAGTATCGTT 2 212 0 CCAATAGTTT 0.957461 -13 ACCCTGGGGATAAATAGTTTTTTGGTATTAA 6 162 0 TAAATAGTTT 0.939528 -103 CCCCCAACTTTCAATAGTTTTTAACAGTAAA 10 150 1 TCAATAGTTT 0.975458 -31 GGGATAGAAGTAAAAAGTTTTACCAGTGTGG 12 39 0 TAAAAAGTTT 0.735749 -210 ATAGATGAAGTAAATAGGTTTTGGTCACCAT 13 69 1 TAAATAGTTT 0.939529 -75 TCAATCGAGATCAATAGGTGTGGGGTTGGTT 14 98 0 TCAATAGTGT 0.913473 -73 TTAAAATTGGTCAATAGATTTGATTAAAACC 16 12 0 TCAATAGTTT 0.975459 -152 TGAAACCTGGCCAATAGGTTCTTAGGGGTTG 19 103 1 CCAATAGTTC 0.856696 -26 ******* *** Masking position 6 Map Score: 4.81269 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 24 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 12 ATCTCGTTACAATCCATCCCATTGGTTTTG 2 43 0 AATCCATCCC 0.89438 -182 CATTTGCCCCATCCTATCCCCGATAAACTA 2 167 1 ATCCTATCCC 0.910383 -58 CTTTATCCTAAACCCTTCCCAATCCCATCT 3 102 1 AACCCTTCCC 0.926604 -26 CCCCAGGGTAAGCCCATCCCTGGCCGTGGG 6 184 1 AGCCCATCCC 0.905499 -81 AAAAGCCCCCAACCCACCCAACTTTGGGGA 7 69 1 AACCCACCCA 0.844874 -112 AGAAAGTTTGATTCCGCCCCTAAATTACTC 7 130 0 ATTCCGCCCC 0.688282 -51 AAGGCTTTATTCCCTATCCAT 8 2 0 TCCCTATCCA 0.425125 -85 TTGTTTCAAAACCCCATCCCCCAAGAAAAA 12 147 1 ACCCCATCCC 0.962527 -102 TGCCACTGCCAACCAACCCCACACCTATTG 14 88 1 AACCAACCCC 0.788791 -83 GAGATGGTTTTACCCATCCCCCTGGGGTGA 16 138 1 TACCCATCCC 0.942779 -26 AAACGTTTTTAAACTGTCCCCTAGAATTGT 17 34 0 AAACTGTCCC 0.799467 -81 AGCAAACTGAAACCTGGCCAATAGGTTCTT 19 96 1 AACCTGGCCA 0.457245 -33 TGACCGTTTCTTCCTGTCCCGCTAATTTTC 20 24 0 TTCCTGTCCC 0.781109 -48 TTGTTATGGAAAACCGTCCCCCCTAAAATC 22 68 0 AAACCGTCCC 0.86506 -67 CCATAACAAAAATCTACCCCAGCAAAACCC 22 89 1 AATCTACCCC 0.797682 -46 CAGCTCCGTTTCCCTGCCCCAACTAAGCAG 23 70 0 TCCCTGCCCC 0.807735 -231 CTGACTAGGAAACCTTTCCCGAGTTTCCCC 23 198 1 AACCTTTCCC 0.887019 -103 ********** Masking position 4 Map Score: 13.5786 Number of sites scoring better than the average of aligned sites = 1792 Number in coding regions = 1601 Number in noncoding regions = 191 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 13 AAAATCAAAACCAATGGGATGGATTGTAACGA 2 38 1 CCATGGGTGG 0.937333 -187 GATGGGCTTACCCTGGGGATAAATAGTTTTTT 6 170 0 CCCGGGGTAA 0.794542 -95 TGCTGGTGATCCATCGGAATCACCGATAATCT 8 60 0 CCACGGATCA 0.905493 -27 ACCAAAACCCCCCCAGGGATAAAGCCGGGATA 10 51 0 CCCAGGGTAA 0.722931 -130 AAAGGGAACGCCCCTGGCATCGATGTCGCACC 10 115 0 CCCTGGCTCG 0.873913 -66 TCCCTTGGGCTCACAAAAATTTC 12 236 0 CCCTGGGTCA 0.989664 -13 TAATCTCACTCCAGCGGGATCAATCGAGATCA 14 116 0 CCACGGGTCA 0.977477 -55 ACCAAAATGACCAACGGACTGGAAAATAAGCC 15 27 1 CCACGGATGG 0.673324 -225 TTTACCCATCCCCCTGGGGTGATATGCA 16 146 1 CCCTGGGTGA 0.973885 -18 AAGTCTCCAGCCATTGTGGTCACTTTTTGCGG 19 64 1 CCATGTGTCA 0.820288 -65 TGAAACCTGGCCAATAGGTTCTTAGGGGTTGC 19 103 1 CCATAGGTCT 0.552326 -26 CATTGTTTTTCCCATAGATTCACAAACTAAAA 23 101 1 CCCTAGATCA 0.727834 -200 TGCAACGTAGTCACTGGGTTCATCCAAAAGAC 23 263 0 TCATGGGTCA 0.82029 -38 *** **** *** Masking position 10 Map Score: 5.42264 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 895 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 14 GAGATTCTACAGGTTGACGTAAGCATTTAT 2 80 1 AGGTTGACGT 0.696653 -145 GATAAACTAAAGGTTGCAGTAAGCAACGAT 2 188 1 AGGTTGCAGT 0.684013 -37 GGGCAAAGATGGGATTGGGAAGGGTT 3 112 0 AGATGGGATT 0.636114 -16 TACTAGAACTAGGCTGGCTTTGCCCACGGC 6 206 0 AGGCTGGCTT 0.786699 -59 AGTTCTAGTAAGATTGGCGTTAACAATTTC 6 226 1 AGATTGGCGT 0.951427 -39 GGATAAGGCCAGATTGGTTTGGATAGACGT 14 13 1 AGATTGGTTT 0.937071 -158 ATCGCCGTCTAAATTGGTGTTGATTGGCAG 15 116 0 AAATTGGTGT 0.611586 -136 AGATAACCCTAGGTTAGTTTGCCCAGC 20 55 1 AGGTTAGTTT 0.611547 -17 GTTTGATTGGTTTTAAGCAACGA 22 4 1 TGATTGGTTT 0.654234 -131 TATTTTCCCTAGATTGGTGTTTAATTATCC 23 39 1 AGATTGGTGT 0.952344 -262 GGGGAAAATTAGGTTGGATTTTACAACAGT 23 235 1 AGGTTGGATT 0.92569 -66 ********** Masking position 10 Map Score: 0.671215 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 417 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 15 CACTGTTACCCAGGCAGTAAAGACTTTGGT 3 44 0 CAGGCAGTAA 0.982991 -84 TTAAACTAAACAGGCCGTAACGGACAATAC 6 136 0 CAGGCCGTAA 0.96301 -129 AGCAGGCAGGATTTTTCAACCT 7 3 1 CAGGCAGGAT 0.949905 -178 AAAATAGGCTTAGCCAGTAAAACCCGCAAG 9 22 1 TAGCCAGTAA 0.883757 -98 CTGTCGAGATCAGCCAGGAAAAAAG 22 120 1 CAGCCAGGAA 0.977184 -15 ********** Masking position 2 Map Score: 0.0932804 Number of sites scoring better than the average of aligned sites = 55 Number in coding regions = 42 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