AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_ecoli_mtub_100.orf -o293_ecoli_mtub_100.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.58 -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 = 0.58 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 pcnB 92 poly(A) polymerase I #2 yadB 36 putative tRNA synthetase #3 dksA 177 dnaK suppressor protein #4 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #5 dnaE 36 DNA polymerase III, alpha subunit #6 ldcC 98 lysine decarboxylase 2, constitutive #7 yaeR 29 orf, hypothetical protein #8 mesJ 64 cell cycle protein #9 ychF 116 putative GTP-binding protein #10 pth 277 peptidyl-tRNA hydrolase #11 prsA 150 phosphoribosylpyrophosphate synthetase #12 rplY 124 50S ribosomal subunit protein L25 #13 folP 44 7,8-dihydropteroate synthase #14 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #15 ftsJ 125 cell division protein #16 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #17 rplY 216 rplY #18 prsA 91 prsA #19 glmU 254 glmU #20 Rv1112 131 hypothetical protein Rv1112 #21 mrsA 124 mrsA #22 ftsH 66 ftsH #23 Rv3627c 137 hypothetical protein Rv3627c Motif number 1 AATGCCCGGCACGTTACCGGGCAAATGCGG 8 23 0 ACGTTACCGG 0.937223 -42 TTTTTGTCAAGCGGGGCCGCAACCAGTAAA 10 220 1 GCGGGGCCGC 0.847806 -58 ACCGAAACTCAGCTTGCCCGGC 11 3 0 AGCTTGCCCG 0.928454 -148 AAAGGATCATGCCTGGCCCGCACAGTTTTC 11 87 1 GCCTGGCCCG 0.974711 -64 TGAGTATAGAATCTCGCCCGCTTTTGCATA 12 40 1 ATCTCGCCCG 0.681557 -85 GCGCGTGTGACCCGTCCTGAATAG 16 5 1 GTGTGACCCG 0.733211 -296 CCATGGGTTAGCCTAGCCGGGCGTCACGGC 17 78 1 GCCTAGCCGG 0.947313 -139 GTCACGGCGAGGGTGGTCGGCGGTCTACAG 17 100 1 GGGTGGTCGG 0.883531 -117 GGCGGTCTACAGCAGGCCGGCAGAACACCG 17 118 1 AGCAGGCCGG 0.677353 -99 GGGTCGCGACAGCTTGTCGGCCTCCGTCGA 17 151 0 AGCTTGTCGG 0.802982 -66 CGCGACCCTGGCCGTGCCCCCAAACGAGGT 17 173 1 GCCGTGCCCC 0.898763 -44 ATTTGTCGCCGGGTAGCCGGGATGCGACT 18 10 0 GGGTAGCCGG 0.918477 -82 CATGGTACGTAGCGCACCGCCCGGATTTGT 18 34 0 AGCGCACCGC 0.671272 -58 CCTGGCGCGCGTCACCCGCGTCGGGTTT 19 9 1 GCGTCACCCG 0.90802 -246 GTTTTCCGGCGCCTTATCCGGCCCTTTATC 19 35 1 GCCTTATCCG 0.737544 -220 TGTTGATGTGGCCGGACCGGATAAAGGGCC 19 54 0 GCCGGACCGG 0.978141 -201 CACATCAACAAGGGTATCGGTTTGCGTGGG 19 74 1 AGGGTATCGG 0.701313 -181 ATCGGTTTGCGTGGGGCCGGTGGGTAGACG 19 89 1 GTGGGGCCGG 0.943087 -166 TGTACCGCCGACCTCGCCCGCTGCGCTGAC 20 48 1 ACCTCGCCCG 0.924852 -84 ACACACGTCGACCGTACCGGCAATGGCGCC 20 76 1 ACCGTACCGG 0.957379 -56 TTAAGGCGAGGCGGTGCCGCCTTCGGCGCC 20 100 0 GCGGTGCCGC 0.52478 -32 TGCGCTCGTCGGCGTGTCGGTGAACCAACA 21 45 1 GGCGTGTCGG 0.919145 -80 CAACTGTGAAAGGTTGTCCGT 21 114 1 AGGTTGTCCG 0.669063 -11 TGGAAAGTCCAGGTTACCGCTC 22 3 0 AGGTTACCGC 0.681556 -64 CGATCATCGGCCGTGCCGGCCAGGTCCTT 22 48 0 GCCGTGCCGG 0.989826 -19 CGACGCTGCCACGGTACCGGCTCGACTAGG 23 74 0 ACGGTACCGG 0.9509 -64 TACCGTGGCAGCGTCGCCCGGCCGGTTCGG 23 88 1 GCGTCGCCCG 0.957214 -50 GTCCCATTCTGCCGAACCGGCCGGGCGACG 23 99 0 GCCGAACCGG 0.91729 -39 GTTCGGCAGAATGGGACCGGAAAGGCAGGA 23 112 1 ATGGGACCGG 0.785672 -26 ********** Masking position 8 Map Score: 41.7459 Number of sites scoring better than the average of aligned sites = 6555 Number in coding regions = 6196 Number in noncoding regions = 359 Number of orfs with sites within 600 bp upstream = 276 Fraction of orfs with sites within 600 bp upstream = 0.0443302 Motif number 2 TTTACATTCTGGTCGCGTGCGCAAATACGCTT 3 31 1 GGTCGGGCGC 0.94014 -147 CTCATTCTTACGATTGCGGCAGGCCGTGTTAT 4 47 1 CGATTCGCAG 0.618308 -58 TTTATCGCCACGGTTTGAGCAGGCTATGATTA 6 52 1 CGGTTGGCAG 0.787787 -47 CTTGCCAGAGCGGCTTCCGGGCGAGTAAC 7 11 1 CGGCTCGGGC 0.921306 -19 GTCGTTGTCTGCGGCATTTTTGCC 9 3 1 CGTTGCGCGG 0.922317 -114 GGTTATGTGCGGGCGTGATCACAATTACAACC 10 90 1 GGGCGGTCAC 0.606354 -188 CCTGTTGCTGGGTCGCCTGTAGCAGGATTAAT 12 88 1 GGTCGCGTAG 0.830106 -37 GCCCCGGGGTTTTCGGTACAAATACAGTC 13 26 0 GGTTTCGTAC 0.392107 -19 TTGTCCGCACGGTTGGGGCACAGCTATCCGA 17 10 1 CGGTTGGCAC 0.851437 -207 CCGGGCGTCACGGCGAGGGTGGTCGGCGGTCT 17 94 1 CGGCGGGTGG 0.920513 -123 GGTGGTCGGCGGTCTACAGCAGGCCGGCAGAA 17 111 1 GGTCTCGCAG 0.885277 -106 CGATCCCAAACGGCGAGGGCAGCGCG 18 76 1 CGGCGGGCAG 0.9774 -16 ACAAGGGTATCGGTTTGCGTGGGGCCGGTGGG 19 81 1 CGGTTGGTGG 0.497576 -174 GGTGGGTAGACGGCGACAGCGTTGACTGTGCT 19 107 1 CGGCGCGCGT 0.887098 -148 ACGGTGTCAACGCCGTCAGCACAGTCAACGCT 19 124 0 CGCCGCGCAC 0.978693 -131 CTTGAAGCTCCGTCGCCAGGACTCGAACCTGA 19 225 0 CGTCGCGGAC 0.945273 -30 CAGCGGGCGAGGTCGGCGGTACAGGCAAGTCA 20 39 0 GGTCGCGTAC 0.882955 -93 CCGCCGACCTCGCCCGCTGCGCTGACACACGT 20 52 1 CGCCCCGCGC 0.801611 -80 CGCTGACACACGTCGACCGTACCGGCAATGGC 20 71 1 CGTCGCGTAC 0.954444 -61 GAGGCGGTGCCGCCTTCGGCGCCATTGCCGGT 20 91 0 CGCCTCGCGC 0.950935 -41 ACCGACACGCCGACGAGCGCACACAAACATGC 21 34 0 CGACGGGCAC 0.936617 -91 CTTTCACAGTTGACGGCTGCGCACATATCCAC 21 94 0 TGACGCGCGC 0.588791 -31 GCGTCGGCTCCTTCAGATCAGAGTGC 23 5 1 CGGCTCTCAG 0.687714 -133 ACCGTGGCAGCGTCGCCCGGCCGGTTCGGCAG 23 89 1 CGTCGCGGCC 0.69471 -49 ***** * **** Masking position 2 Map Score: 22.1547 Number of sites scoring better than the average of aligned sites = 8088 Number in coding regions = 7788 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 226 Fraction of orfs with sites within 600 bp upstream = 0.0362994 Motif number 3 GTTACTCGCCCGGAAGCCGCTCTGGCA 7 13 0 CGCCGGAAGC 0.991544 -17 TCGCCGCATTTGCCCGGTAACGTGCCGGGCA 8 20 1 TGCCGGTAAC 0.451514 -45 ATTGTGATCACGCCCGCACATAACCCACTGG 10 84 0 CGCCGCACAT 0.872962 -194 TACAAATAAACGCCTGAACACCTTGACTTTC 10 140 1 CGCCGAACAC 0.982556 -138 TTTAATACACCGCCTGGAAAGGATCATGCCT 11 70 1 CGCCGGAAAG 0.964917 -81 TTCAAACTTTCGTCTGAAATCTCCCGG 14 7 0 CGTCGAAATC 0.726754 -93 TTAAAAACAGCGTCAGGATACTCTATATCCA 14 44 0 CGTCGGATAC 0.868538 -56 CTCAAATTACAGTCAGGACGCGT 16 288 1 AGTCGGACGC 0.710574 -13 CGACCACCCTCGCCGTGACGCCCGGCTAGGC 17 88 0 CGCCTGACGC 0.914012 -129 TACAGCAGGCCGGCAGAACACCGTTATCGAC 17 125 1 CGGCGAACAC 0.846122 -92 CCGGATTTGTCGCCGGGTAGCCGGGATGCGA 18 13 0 CGCCGGTAGC 0.949819 -79 CGTAGCGCACCGCCCGGATTTGTCGCCGGGT 18 26 0 CGCCGGATTT 0.687657 -66 CCGGATAAGGCGCCGGAAAACCCGACGCGGG 19 25 0 CGCCGAAAAC 0.968567 -230 GTGTCAACGCCGTCAGCACAGTCAACGCTGT 19 122 0 CGTCGCACAG 0.700735 -133 GAAGCTCCGTCGCCAGGACTCGAACCTGAAC 19 223 0 CGCCGGACTC 0.985964 -32 GCACGCTTGTCGCCCGAAAGTGATG 21 5 0 CGCCGAAAGT 0.871619 -120 GTGGCAGCGTCGCCCGGCCGGTTCGGCAGAA 23 92 1 CGCCGGCCGG 0.892362 -46 **** ****** Masking position 2 Map Score: 16.8496 Number of sites scoring better than the average of aligned sites = 2739 Number in coding regions = 2623 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 4 TGTTCCTCCTGGAAAATCCTTCCTTAATCAT 6 77 0 GGAAAATCCT 0.95942 -22 GTTGTAACAGGGAATACCCCTCTTCCTTATG 10 34 1 GGAATACCCT 0.95679 -244 TGTAATAAGAGGTTAATCCCTTGAGTGAC 14 81 1 GGTTAATCCT 0.887314 -19 TTTCCCATGGGGATAACTCATCGTAACCAAT 15 100 0 GGATAACTCT 0.915508 -26 TCGTCAGCGGGGATAATCCGTTATTGAACAA 16 189 1 GGATAATCCT 0.974312 -112 CGCCCGGCTAGGCTAACCCATGGCTACTGCA 17 70 0 GGCTAACCCT 0.967592 -147 GGATCGAATTGGATTACCCATGGTACGTAGC 18 51 0 GGATTACCCT 0.972619 -41 ATAAGGCGCCGGAAAACCCGACGCGGGTGAC 19 21 0 GGAAAACCCA 0.915536 -234 ********* * Masking position 6 Map Score: 6.16278 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 95 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 5 TTCCCGCCTGTGGTAAACGTGAT 2 24 0 CCGCCTGTGG 0.731148 -13 TACATTCTGGTCGCGTGCGCAAATACGCTT 3 33 1 TCGCGTGCGC 0.855824 -145 GTCGTTGTCTGCGGCATTTTTGCC 9 5 1 TTGTCTGCGG 0.889532 -112 AATTGTGATCACGCCCGCACATAACCCACT 10 86 0 ACGCCCGCAC 0.824883 -192 GGATCATGCCTGGCCCGCACAGTTTTCGGC 11 90 1 TGGCCCGCAC 0.760568 -61 TGTTGCTGGGTCGCCTGTAGCAGGATTAAT 12 90 1 TCGCCTGTAG 0.821786 -35 GTCACGCCTTTTGTCTGCAGAAAATTAAGG 16 139 0 TTGTCTGCAG 0.785644 -162 AATGGCGCTTTCGTCAGCGGGGATAATCCG 16 179 1 TCGTCAGCGG 0.851362 -122 TTGTCCGCACGGTTGGGGCA 17 1 1 TTGTCCGCAC 0.907755 -216 TGTCGCGACCCTGGCCGTGCCCCCAAACGA 17 170 1 CTGGCCGTGC 0.711869 -47 GGCGACAGCGTTGACTGTGCTGACGGCGTT 19 118 1 TTGACTGTGC 0.711647 -137 CGTGGTGTAATCGGCAGCACCTCTGATTTT 19 183 1 TCGGCAGCAC 0.838587 -72 GAGCGGTGACTTGCCTGTACCGCCGACCTC 20 33 1 TTGCCTGTAC 0.83083 -99 CGGTCGACGTGTGTCAGCGCAGCGGGCGAG 20 60 0 GTGTCAGCGC 0.620869 -72 CTGACACACGTCGACCGTACCGGCAATGGC 20 73 1 TCGACCGTAC 0.73903 -59 GCGTGCATGTTTGTGTGCGCTCGTCGGCGT 21 30 1 TTGTGTGCGC 0.686119 -95 TTCACAGTTGACGGCTGCGCACATATCCAC 21 94 0 ACGGCTGCGC 0.847836 -31 CGATCATCGGCCGTGCCGGCCAGGTC 22 51 0 TCGGCCGTGC 0.948487 -16 CAGGTCCAATGCGTCCGTGGACACCCTAGT 23 50 1 GCGTCCGTGG 0.712679 -88 ********** Masking position 7 Map Score: 10.1675 Number of sites scoring better than the average of aligned sites = 5915 Number in coding regions = 5719 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 207 Fraction of orfs with sites within 600 bp upstream = 0.0332477 Motif number 6 TAGCCGCTATTTTTTTGTCCTGAATGATGT 1 19 1 TTTTTTGTCC 0.941717 -74 GAGGTGTACTATTTTTACCCGAGTCGCTAA 1 60 1 ATTTTTACCC 0.854267 -33 CGAGTCGCTAATTTTTGCCGCAAG 1 79 1 ATTTTTGCCG 0.962446 -14 TAGCGGCCTCATTTTTCCCCCGAACATGGG 3 128 1 ATTTTTCCCC 0.83128 -50 AGGCCGTGTTATTATTGTCGTTTCTTATAT 4 67 1 ATTATTGTCG 0.758343 -38 TCGGTGGCCCTTTTTTATCGCCACGGTTTG 6 39 1 TTTTTTATCG 0.787037 -60 TGTCTGCGGCATTTTTGCCGAGTGCCGTGT 9 16 1 ATTTTTGCCG 0.962446 -101 TGATACGCAGTTTTTTGTCAAGCGGGGCCG 10 209 1 TTTTTTGTCA 0.755871 -69 GTTTTTTTGTCCTGAGTGTGTA 10 266 0 TTTTTTGTCC 0.941717 -12 ********** Masking position 5 Map Score: 4.33524 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 406 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 CTTCAGATTCCGGTTTACTTAATCTC 5 21 0 CTCAGATGTT 0.980257 -16 GAGAAGAACCTCAGGCATGCGTCCATTGGTGGAA 11 127 0 CTCAGGCGTC 0.975198 -24 GTTCCCGCATCAGATGACTGTATTTGTACCGAA 13 8 1 CTCAGATGTT 0.980255 -37 CCGGGAGATTTCAGACGAAAGTTTGAAAGATGCT 14 9 1 TTCAGACGTT 0.758923 -91 TTAATTTAAGCGTCAGGTGGATGTTTTTGCTCTTAT 16 96 0 CTCAGGTGTT 0.976165 -205 CTTGTGAGCTGCTCGGATAGCTGTGCCCCAACCGTG 17 18 0 GTCGGATGTC 0.899954 -199 ATCGGCAGCACCTCTGATTTTGGTTCAGATAGTTCA 19 192 1 CTCTGATGTC 0.945893 -63 GGTTCAGATAGTTCAGGTTCGAGTCCTGGCGACGGA 19 213 1 GTCAGGTGTC 0.96606 -42 GCGTCGGCTCCTTCAGATCAGAGTGCATGGGACAAC 23 11 1 CTCAGATGTC 0.989853 -127 * ****** ** * Masking position 3 Map Score: 4.99727 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 97 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 8 CAAACTTTACGGCCTGTCTCATTCTTACGATTGC 4 30 1 GGCCGTCTTC 0.795095 -75 GTGTATAATAGGCAAAGTTATTTCCATTTCTGCA 9 42 1 GGCAAGTTTC 0.916865 -75 GTGCGGGCCAGGCATGATCCTTTCCAGGCGGTGT 11 76 0 GGCAGATCTC 0.922941 -75 CACAGTTTTCGGCAGATTCTTTCCACCAATGGAC 11 107 1 GGCAATTCTC 0.975925 -44 GCAAAAGCGGGCGAGATTCTATACTCAATCGCCT 12 33 0 GCGAATTCTC 0.830613 -92 CCGGGAGATTTCAGACGAAAGTTTGA 14 3 1 GGGAATTTGC 0.587235 -97 TACTGCATTGGGGAAATTCGATCCTTGTGAGCTG 17 43 0 GGGAATTCTC 0.922633 -174 TGGGGGCACGGCCAGGGTCGCGACAGCTTGTCGG 17 161 0 GCCAGGTCGC 0.935843 -56 CGCCTTCGGCGCCATTGCCGGTACGGTCGACGTG 20 79 0 GCCATGCCTC 0.706964 -53 AGAGAGCCAAGTTTAAGGCGAGGCGGTGC 20 113 0 GCCAGTTTGC 0.791569 -19 TGAACCAACAGGCATATTCGCTGCCAAGAGTGGA 21 65 1 GGCAATTCTC 0.976646 -60 CGGCCGTGCCGGCCAGGTCCTTCCCGATACACGC 22 36 0 GGCCGGTCTC 0.904458 -31 GGACCTGGCCGGCACGGCCGATGATCG 22 50 1 GGCAGGCCTA 0.761791 -17 TGGGACAACGGGCAGGTCCAATGCGTCCGTGGAC 23 38 1 GGCAGTCCTC 0.980788 -100 **** **** * * Masking position 1 Map Score: 6.44413 Number of sites scoring better than the average of aligned sites = 1119 Number in coding regions = 1062 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 CTTTTCCTCACACAGTTGTCAAGTGTTACG 3 60 1 CACAGTTGTC 0.988099 -118 GCCTGGCCCGCACAGTTTTCGGCAGATTCT 11 97 1 CACAGTTTTC 0.947033 -54 CTGTTTTTAACACAGTTGTAATAAGAGGTT 14 65 1 CACAGTTGTA 0.92267 -35 ACGGTTGGGGCACAGCTATCCGAGCAGCTC 17 19 1 CACAGCTATC 0.953636 -198 GCCGGCAGAACACCGTTATCGACGGAGGCC 17 133 1 CACCGTTATC 0.955128 -84 TCAGCACAGTCAACGCTGTCGCCGTCTACC 19 111 0 CAACGCTGTC 0.845766 -144 GACAACCTTTCACAGTTGACGGCTGCGCAC 21 102 0 CACAGTTGAC 0.951011 -23 ********** Masking position 2 Map Score: 4.54357 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 94 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 Motif number 10 AACACGCACTATCGATCCCCATGTTCGGGGG 3 144 0 ATCGTCCCCA 0.88243 -34 CAAGCTGAGTTTCGGTGACAACGTCACCTTG 11 17 1 TTCGTGACAA 0.884565 -134 ATGACCCGTTTTCAATCCCAACGTAAGCAAA 15 18 0 TTCATCCCAA 0.938406 -108 GCGGTTTAAATTCGTTCTCAAATTACAGTCA 16 272 1 TTCGTCTCAA 0.947838 -29 GGTAATCCAATTCGATCCCAAACGGCGAGGG 18 64 1 TTCGTCCCAA 0.991435 -28 AACAGGCATATTCGCTGCCAAGAGTGGATAT 21 71 1 TTCGTGCCAA 0.978794 -54 CTCCTGCCTTTCCGGTCCCATTCTGCCGAAC 23 112 0 TCCGTCCCAT 0.8824 -26 **** ****** Masking position 6 Map Score: 1.58511 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 89 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 GCAAAAATTAGCGACTCGGGTAAAAATAGT 1 67 0 GCGACTCGGG 0.978282 -26 TCGCCCGGAAGCCGCTCTGGCAAG 7 5 0 GCCGCTCTGG 0.923524 -25 TTTCTAATAGTCCACTCAGGCAATTATTAC 10 167 1 TCCACTCAGG 0.971636 -111 GCAGATTCTTTCCACCAATGGACGCATGCC 11 118 1 TCCACCAATG 0.631007 -33 CCTGCTACAGGCGACCCAGCAACAGGTAAG 12 84 0 GCGACCCAGC 0.910428 -41 ACAAGCTGTCGCGACCCTGGCCGTGCCCCC 17 164 1 GCGACCCTGG 0.981726 -53 AGGTAACCGAGCCACCCAGGAGCGACAT 17 199 1 GCCACCCAGG 0.988591 -18 TGCGCACATATCCACTCTTGGCAGCGAATA 21 79 0 TCCACTCTTG 0.838198 -46 CGGTACCGGCTCGACTAGGGTGTCCACGGA 23 63 0 TCGACTAGGG 0.818668 -75 ********** Masking position 5 Map Score: 4.17143 Number of sites scoring better than the average of aligned sites = 836 Number in coding regions = 768 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 12 CGGATAGCAATTATCTAAACGTAACACTTGACAAC 3 74 0 TCAACGTAAC 0.921991 -104 CCATCTTTTGTTCGCCAAACTTTACGGCCTGTCTC 4 15 1 TCAACTTTAC 0.979229 -90 ACAGTAGCAATGCCCGGCACGTTACCGGGCAAATG 8 26 0 TCGACGTTAC 0.97456 -39 CCACTGGGTGTTGTCTATACTTTACACATAAGGAA 10 56 0 TCAACTTTAC 0.979229 -222 AACCCTTATTTCAACAAAACTTTACAAATAAACGC 10 118 1 TCAACTTTAC 0.979229 -160 AACGTCACCTTGTTCCAGACGTTGCATCGCGCTCT 11 36 1 TCAACGTTGC 0.954163 -115 GAGCGGTAACCTGGACTTTCCAGCTGCGTGT 22 7 1 TCGACTTTCC 0.920632 -60 * * * ******* Masking position 9 Map Score: 1.699 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 33 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 GTTGCTTCTCCTTAACACGCACTAT 3 163 0 CTCTCCTTAA 0.922276 -15 GATTTAAATCACCTTAATATCTTAATA 9 100 0 ATCACCTTAA 0.872736 -17 TCGGTGACAACGTCACCTTGTTCCAGACGTT 11 28 1 CTCACCTTGT 0.948238 -123 TTCTATACTCAATCGCCTTATACATCAATCA 12 20 0 ATCGCCTTAT 0.898259 -105 ATTTAAACCGCTTCACCTTGAAAAAACTACA 16 252 0 CTCACCTTGA 0.967092 -49 CGCCGACCACCCTCGCCGTGACGCCCGGCTA 17 91 0 CTCGCCGTGA 0.941592 -126 TCGGGTTTTCCGGCGCCTTATCCGGCCCTTT 19 31 1 CGCGCCTTAT 0.911131 -224 GGCGGCACCGCCTCGCCTTAAACTTGGCTCT 20 109 1 CTCGCCTTAA 0.984108 -23 * ********* Masking position 9 Map Score: 4.03755 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 222 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 ********** No masking Map Score: 4.42911e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: 4.42911e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0