AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i293_ecoli_mtub_300.orf -o293_ecoli_mtub_300.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 rpsB 300 30S ribosomal subunit protein S2 #5 tsf 257 protein chain elongation factor EF-Ts #6 pyrH 146 uridylate kinase #7 frr 291 ribosome releasing factor #8 yaeM 91 putative ATP-binding component of a transport system #9 yaeS 185 orf, hypothetical protein #10 cdsA 120 CDP-diglyceride synthetase #11 yaeT 29 orf, hypothetical protein #12 hlpA 121 histone-like protein, located in outer membrane or nucleoid #13 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #14 dnaE 36 DNA polymerase III, alpha subunit #15 ldcC 98 lysine decarboxylase 2, constitutive #16 yaeR 29 orf, hypothetical protein #17 mesJ 64 cell cycle protein #18 ychF 116 putative GTP-binding protein #19 pth 277 peptidyl-tRNA hydrolase #20 prsA 150 phosphoribosylpyrophosphate synthetase #21 hemM 213 an enzyme in main pathway of synthesis of 5-aminolevulinate, possibly glutamyl-tRNA dehydrogenase #22 yejH 148 putative ATP-dependent helicase #23 rplY 124 50S ribosomal subunit protein L25 #24 folP 44 7,8-dihydropteroate synthase #25 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #26 ftsJ 125 cell division protein #27 glmU 300 N-acetyl glucosamine-1-phosphate uridyltransferase #28 rplY 216 rplY #29 lpqT 35 lpqT #30 prsA 91 prsA #31 glmU 254 glmU #32 Rv1112 131 hypothetical protein Rv1112 #33 mrsA 124 mrsA #34 rplM 233 rplM #35 Rv3447c 113 hypothetical protein Rv3447c #36 ftsH 66 ftsH #37 Rv3627c 137 hypothetical protein Rv3627c Motif number 1 ATCACGTTTACCACAGGCGGGAA 2 24 1 CCACGGCGGG 0.9065 -13 CTATCGATCCCCATGTTCGGGGGAAAAATGA 3 136 0 CCATTTCGGG 0.352681 -42 CGACCCCAAAGGGCACCCCGGAATATGTGCC 4 226 0 GGGCCCCCGG 0.919728 -75 GGGAATTCTCGAGCTTGCCGCCTTTCTGCAA 5 44 0 GAGCTGCCGC 0.461864 -214 ATCTTCGCTCGCTCATCCCGGTCACTTACTG 5 87 0 GCTCTCCCGG 0.725197 -171 CGAAGATAACGCATCTGCGGCGCGAAATATG 5 111 1 GCATTGCGGC 0.417904 -147 TCGGAGATGTGATCTGCCCGGCATTAAACCG 5 227 0 GATCGCCCGG 0.574365 -31 AAGAAGCCGCCCTCAGGCGGCTCCTTTTTGA 6 14 0 CCTCGGCGGC 0.858485 -133 AACCCTTGTGGGGCTGCGCTGAAAAGCGACG 6 71 1 GGGCGCGCTG 0.402499 -76 GGTTGCTGCGCGCTGGCCGTGACCAAACTGC 7 94 0 CGCTGCCGTG 0.718058 -198 AGGATGGCGAGCACTGCCCGGGGCCAAAATG 7 145 1 GCACGCCCGG 0.916168 -147 CCTTGCGGATCGGCTGGCGGCGTTTTGCTTT 8 44 1 CGGCGGCGGC 0.979469 -48 ATGGCGAACCCCACCGGCGGCAACAGAAACA 10 81 0 CCACGGCGGC 0.873373 -40 GCAGTTCTTTGCGTGGCCCGGCGATCTTATA 12 65 0 GCGTGCCCGG 0.968122 -57 AATAATAACACGGCCTGCCGCAATCGTAAGA 13 52 0 CGGCTGCCGC 0.896048 -53 CTTGCCAGAGCGGCTTCCGGGCGAGTAAC 16 11 1 CGGCTCCGGG 0.975209 -19 GTCATCGCCGCATTTGCCCGGTAACGTGCCG 17 16 1 CATTGCCCGG 0.443518 -49 CTATTATACACGGCACTCGGCAAAAATGCCG 18 22 0 CGGCCTCGGC 0.75803 -95 CCGAAACTCAGCTTGCCCGGC 20 1 0 GCTTCCCGGC 0.427407 -150 AAAGGATCATGCCTGGCCCGCACAGTTTTCG 20 87 1 GCCTGCCCGC 0.854077 -64 CAGAATCTAACGGCTTTCGGCAATTACTCCA 21 100 0 CGGCTTCGGC 0.84996 -114 ATGGCGCTTTCGTCAGCGGGGATAATCCGTT 27 180 1 CGTCGCGGGG 0.56198 -121 CCATGGGTTAGCCTAGCCGGGCGTCACGGCG 28 78 1 GCCTGCCGGG 0.926566 -139 GTCACGGCGAGGGTGGTCGGCGGTCTACAGC 28 100 1 GGGTGTCGGC 0.886704 -117 CGGCGGTCTACAGCAGGCCGGCAGAACACCG 28 117 1 CAGCGGCCGG 0.845058 -100 GACAGCTTGTCGGCCTCCGTCGATAACGGTG 28 143 0 CGGCTCCGTC 0.800078 -74 GCTGTCGCGACCCTGGCCGTGCCCCCAAACG 28 168 1 CCCTGCCGTG 0.692718 -49 TCATCCTTGAGGGCATCCGGCGGGC 29 21 1 GGGCTCCGGC 0.957309 -15 ATTTGTCGCCGGGTAGCCGGGATGCGACT 30 9 0 GGGTGCCGGG 0.981932 -83 GGTACGTAGCGCACCGCCCGGATTTGTCGCC 30 30 0 GCACGCCCGG 0.9161 -62 CGCGCTGCCCTCGCCGTTTGGG 30 80 0 GCGCGCCCTC 0.871757 -12 CACCCGCGTCGGGTTTTCCGGCGCCTTATCC 31 23 1 GGGTTTCCGG 0.66527 -232 TTTTCCGGCGCCTTATCCGGCCCTTTATCCG 31 36 1 CCTTTCCGGC 0.627493 -219 TTGTTGATGTGGCCGGACCGGATAAAGGGCC 31 54 0 GGCCGACCGG 0.65028 -201 ACAAGGGTATCGGTTTGCGTGGGGCCGGTGG 31 81 1 CGGTTGCGTG 0.554669 -174 TGGGGCCGGTGGGTAGACGGCGACAGCGTTG 31 100 1 GGGTGACGGC 0.7837 -155 CCTTGAAGCTCCGTCGCCAGGACTCGAACCT 31 227 0 CCGTGCCAGG 0.599606 -28 CTTGCCTGTACCGCCGACCTCGCCCGCTGCG 32 42 1 CCGCGACCTC 0.442621 -90 ACGTGTGTCAGCGCAGCGGGCGAGGTCGGCG 32 53 0 GCGCGCGGGC 0.79985 -79 ATTGCCGGTACGGTCGACGTGTGTCAGCGCA 32 69 0 CGGTGACGTG 0.476133 -63 CGAGGCGGTGCCGCCTTCGGCGCCATTGCCG 32 93 0 CCGCTTCGGC 0.833683 -39 TGTTTGTGTGCGCTCGTCGGCGTGTCGGTGA 33 37 1 CGCTGTCGGC 0.719483 -88 GTGGATATGTGCGCAGCCGTCAACTGTGAAA 33 94 1 GCGCGCCGTC 0.911737 -31 GTTGCGCGCTCCGGGGCCCGGAA 34 3 0 CCGGGCCCGG 0.58885 -231 CGACGGCTCTCCCCCGTCGGGACCACACAGG 34 39 0 CCCCGTCGGG 0.865892 -195 CGACGGGGGAGAGCCGTCGGGACCACACAGT 34 51 1 GAGCGTCGGG 0.742557 -183 GTAAGCTGCTCGGTTGGCGTGCGGTACGCCG 34 109 1 CGGTGGCGTG 0.819435 -125 GGTTGGCGTGCGGTACGCCGGGACCTCGGGT 34 120 1 CGGTCGCCGG 0.760257 -114 CACGCCTGACCGGCGCCCGGGGCACCCCGGG 34 183 1 CGGCCCCGGG 0.955836 -51 ATCACCGGAACGGTAGCCGGTTCTCGATCGC 35 30 1 CGGTGCCGGT 0.635839 -84 AGCCGGTTCTCGATCGCCCGGTATTCGGTTG 35 44 1 CGATGCCCGG 0.879389 -70 TGTCCACAAGCGACTTGCGGCGGATTCTCGC 35 73 1 CGACTGCGGC 0.681358 -41 CGATCATCGGCCGTGCCGGCCAGGTCCTT 36 48 0 GGCCTGCCGG 0.718243 -19 TACCGTGGCAGCGTCGCCCGGCCGGTTCGGC 37 88 1 GCGTGCCCGG 0.9688 -50 **** ****** Masking position 8 Map Score: 50.8936 Number of sites scoring better than the average of aligned sites = 15109 Number in coding regions = 14190 Number in noncoding regions = 919 Number of orfs with sites within 600 bp upstream = 523 Fraction of orfs with sites within 600 bp upstream = 0.0840026 Motif number 2 GCCGCCCTCAGGCGGCTCCTTTTTGATAA 6 9 0 GGCGGTCCTT 0.914841 -138 GCCGCCTGAGGGCGGCTTCTTTTTGTGCCCA 6 24 1 GGCGGTTCTT 0.771164 -123 TATTGTTGCAGGCAGTTTGGTCACGGCCAGC 7 83 1 GGCAGTTGGT 0.816633 -209 TATTTTATTTGCCATTTTGGCCCCGGGCAGT 7 157 0 GCCATTTGGC 0.366041 -135 AGTAGATCCTTGCGGATCGGCTGGCGGCGTT 8 37 1 TGCGGTCGGC 0.740798 -55 CTTGCCAGAGCGGCTTCCGGGCGA 16 4 1 GCCAGGCGGC 0.92983 -26 TTTTTTGTCAAGCGGGGCCGCAACCAGTAAA 19 219 1 AGCGGGCCGC 0.816455 -59 CACAGTTTTCGGCAGATTCTTTCCACCAATG 20 107 1 GGCAGTTCTT 0.527997 -44 AGAAAATTAAGGCAGTACCTTAATTTAAGCG 27 120 0 GGCAGACCTT 0.729505 -181 AGCCTAGCCGGGCGTCACGGCGAGGGTGGTC 28 87 1 GGCGTACGGC 0.729328 -130 TGGGGGCACGGCCAGGGTCGCGACAGCTTGT 28 164 0 GCCAGGTCGC 0.824289 -53 GTCGCTCCTGGGTGGCTCGGTTACCTCGTTT 28 194 0 GGTGGTCGGT 0.567324 -23 GACAAATCCGGGCGGTGCGCTACGTACCATG 30 33 1 GGCGGGCGCT 0.685092 -59 TGGTGTAATCGGCAGCACCTCTGATTTTGGT 31 185 1 GGCAGACCTC 0.844472 -70 GCGGTGACTTGCCTGTACCGCCGACCTCGCC 32 35 1 GCCTGACCGC 0.659837 -97 CGGCGCCATTGCCGGTACGGTCGACGTGTGT 32 76 0 GCCGGACGGT 0.942429 -56 TTTAAGGCGAGGCGGTGCCGCCTTCGGCGCC 32 100 0 GGCGGGCCGC 0.987009 -32 TGCGCTCGTCGGCGTGTCGGTGAACCAACAG 33 45 1 GGCGTTCGGT 0.828751 -80 TGAACCAACAGGCATATTCGCTGCCAAGAGT 33 65 1 GGCATTTCGC 0.523536 -60 CGTGCGGTACGCCGGGACCTCGGGTCAATGT 34 126 1 GCCGGACCTC 0.906493 -108 AGGCGTGAACGGCGGGTTGGTCTCGGCGAAC 34 159 0 GGCGGTTGGT 0.930625 -75 TTCTCGGATCACCGGAACGGTAGCCGGTTCT 35 23 1 ACCGGACGGT 0.526584 -91 AGCGACTTGCGGCGGATTCTCGCGCTGCATA 35 81 1 GGCGGTTCTC 0.871543 -33 GAAGGACCTGGCCGGCACGGCCGATGATCG 36 47 1 GCCGGACGGC 0.864675 -20 CCCTAGTCGAGCCGGTACCGTGGCAGCGTCG 37 73 1 GCCGGACCGT 0.953705 -65 CCGGTACCGTGGCAGCGTCGCCCGGCCGGTT 37 84 1 GGCAGGTCGC 0.887818 -54 GCGTCGCCCGGCCGGTTCGGCAGAATGGGAC 37 98 1 GCCGGTCGGC 0.970671 -40 ***** ***** Masking position 3 Map Score: 30.5898 Number of sites scoring better than the average of aligned sites = 5248 Number in coding regions = 5025 Number in noncoding regions = 223 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 3 ATTTACATTCTGGTCGCGTGCGCAAATACGCTT 3 30 1 TGGTGTGCGC 0.955425 -148 GACGTATTTGTGGTATAAAGCGCGCCGGACTTC 4 124 1 TGGTAAGCGC 0.594778 -177 GTAAGTGACCGGGATGAGCGAGCGAAGATAACG 5 89 1 GGGAGCGAGC 0.788504 -169 TGTACGCTCCGGTTGCTGCGCGCTGGCCGTGAC 7 102 0 GGTTGCGCGC 0.981522 -190 TTTTGGCCCCGGGCAGTGCTCGCCATCCTCACG 7 141 0 GGGCGCTCGC 0.828534 -151 CTGTTGCCGCCGGTGGGGTTCGCCATTGTAACG 10 86 1 CGGTGTTCGC 0.854375 -35 AACACCCAGTGGGTTATGTGCGGGCGTGATCAC 19 79 1 GGGTGTGCGG 0.954046 -199 TTGTTCCAGACGTTGCATCGCGCTCTTTAATAC 20 45 1 CGTTTCGCGC 0.796425 -106 CGATAGCGGACGGTAACGCTAGCATTAAGGGTT 21 156 1 CGGTGCTAGC 0.668558 -58 TATTCAGGACGGGTCACACGCGC 27 1 0 GGGTACGCGC 0.966688 -300 CAGTAGCCATGGGTTAGCCTAGCCGGGCGTCAC 28 72 1 GGGTCCTAGC 0.756894 -145 GTCACGGCGAGGGTGGTCGGCGGTCTACAGCAG 28 100 1 GGGTCGGCGG 0.812051 -117 GGATTACCCATGGTACGTAGCGCACCGCCCGGA 30 39 0 TGGTTAGCGC 0.771376 -53 AACCCGACGCGGGTGACGCGCGCCAGG 31 5 0 GGGTGCGCGC 0.99601 -250 ACCCGCGTCGGGTTTTCCGGCGCCTTATCCGGC 31 24 1 GGTTCGGCGC 0.815719 -231 TGGGATGTGGGGGTGAATCGAGCGGTGACTTGC 32 14 1 GGGTTCGAGC 0.901793 -118 CAAGCGTGCATGTTTGTGTGCGCTCGTCGGCGT 33 27 1 TGTTGTGCGC 0.82005 -98 CTGCCAAGAGTGGATATGTGCGCAGCCGTCAAC 33 85 1 TGGAGTGCGC 0.699106 -40 GACCACACAGGGGTCTGTTGCGCGCTCCGGGGC 34 17 0 GGGTTTGCGC 0.96391 -217 TAAGCTGCTCGGTTGGCGTGCGGTACGCCGGGA 34 110 1 GGTTGTGCGG 0.815296 -124 CGTGAACGGCGGGTTGGTCTCGGCGAACCGACA 34 154 0 GGGTTCTCGG 0.746408 -80 GTGGATCCCGGGGTGCCCCGGGCGCCGGTCAGG 34 187 0 GGGTCCGGGC 0.868364 -47 AACGGTAGCCGGTTCTCGATCGCCCGGTATTCG 35 38 1 GGTTGATCGC 0.727246 -76 GCTGGGCGACGGTATGCAGCGCGAGAATCCGC 35 92 0 CGGTCAGCGC 0.873851 -22 **** ****** Masking position 2 Map Score: 22.8851 Number of sites scoring better than the average of aligned sites = 1930 Number in coding regions = 1841 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 4 CAATAATTGTTGGCGCTGTGTACAGCATCAG 4 85 0 TGGCGCTTGT 0.654709 -216 ATCGGAAGTCCGGCGCGCTTTATACCACAAA 4 130 0 CGGCGCGTTT 0.931806 -171 GGCCTGCATATGGCCCCCTTTTTCACTTTTA 5 188 1 TGGCCCCTTT 0.978099 -70 CGCCCTCAGGCGGCTCCTTTTTGATAA 6 7 0 CGGCTCCTTT 0.678854 -140 GCGGATCGGCTGGCGGCGTTTTGCTTTTTAT 8 48 1 TGGCGGCTTT 0.815202 -44 CTACAGAGAGTCGCGCTATTTGTTAGCGTAG 9 22 1 TCGCGCTTTT 0.925698 -164 GCCACCGAAGTGACCCTTTTTCAGAACTTTT 15 16 0 TGACCCTTTT 0.762124 -83 GTCACTTCGGTGGCCCTTTTTTATCGCCACG 15 33 1 TGGCCCTTTT 0.951541 -66 GGCTTGTCATCGCCGCATTTGCCCGGTAAC 17 10 1 TCGCCGCTTT 0.771437 -55 GATGGTGCGATTTTACAGTAGCA 17 52 0 TGGTGCGTTT 0.439729 -13 TTACTGGTTGCGGCCCCGCTTGACAAAAAAC 19 218 0 CGGCCCCCTT 0.728569 -60 AGACGTTGCATCGCGCTCTTTAATACACCGC 20 52 1 TCGCGCTTTT 0.925698 -99 ATAAAAGAGAGCGCCCCCTTTTGGAGTAATT 21 79 1 GCGCCCCTTT 0.79782 -135 GTATAGAATCTCGCCCGCTTTTGCATACGCA 23 43 1 TCGCCCGTTT 0.940647 -82 TAGAGTATCCTGACGCTGTTTTTAACACAGT 25 50 1 TGACGCTTTT 0.744738 -50 GGCGGTAGAATGACCCGTTTTCAATCCCAAC 26 27 0 TGACCCGTTT 0.787747 -99 TCGACCATCGTCACGCCTTTTGTCTGCAGAA 27 147 0 TCACGCCTTT 0.822169 -154 CGCGCTGCCCTCGCCGTTTGGGATCGAAT 30 73 0 CCTCGCCTTT 0.620436 -19 TCGGGTTTTCCGGCGCCTTATCCGGCCCTTT 31 31 1 CGGCGCCTAT 0.829054 -224 GCGCCTTATCCGGCCCTTTATCCGGTCCGGC 31 43 1 CGGCCCTTAT 0.700743 -212 TCTCCCCCTTTATTCTCGGAT 35 1 1 TCTCCCCTTT 0.731262 -113 CGGTTCTCGATCGCCCGGTATTCGGTTGTCC 35 47 1 TCGCCCGTAT 0.741266 -67 ******* *** Masking position 11 Map Score: 17.47 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 1160 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 170 Fraction of orfs with sites within 600 bp upstream = 0.0273049 Motif number 5 TTACATTCTGGTCGCGTGCGCAAATACGCTTT 3 32 1 GTGCGGCGCA 0.754296 -146 TACCACAAATACGTCGTGGACACCAATAATTG 4 107 0 ACTCGGGACA 0.84057 -194 CCCTTGTGGGGCTGCGCTGAAAAGCGACGTAC 6 73 1 GCGCGTGAAA 0.764392 -74 CCGCGTAAGTATCGCGGGGGCGTAAGTCTGGT 7 41 1 ATGCGGGGCG 0.777349 -251 GTACGTGAGGATGGCGAGCACTGCCCGGGGCC 7 138 1 ATGCGGCACT 0.722576 -154 TTACGATCAGATGGCGCAGACTATATCACTGA 9 57 0 ATGCGAGACT 0.582796 -129 CAGAAACAACGCCGCGATGACGACGGGTATTA 10 57 0 GCGCGTGACG 0.955101 -64 TAGTGGTAGTGTAGCGATGACTTTAGGCGATC 12 31 1 GTGCGTGACT 0.925977 -91 CCGGGCAAATGCGGCGATGACAAGCC 17 5 0 GCGCGTGACA 0.983969 -60 GGCAAGCTGAGTTTCGGTGACAACGTCACCTT 20 15 1 GTTCGTGACA 0.749099 -136 CCCGTCCTGAATAGCGTTCACATAGATCCTGC 27 21 1 ATGCGTCACA 0.851708 -280 CTGTGCCCCAACCGTGCGGACAA 28 2 0 ACGTGGGACA 0.736364 -215 TCGATCCCAAACGGCGAGGGCAGCGCG 30 75 1 ACGCGGGGCA 0.953839 -17 GTAGACGGCGACAGCGTTGACTGTGCTGACGG 31 112 1 ACGCGTGACT 0.953191 -143 GACTGTGCTGACGGCGTTGACACCGTCTAAAG 31 130 1 ACGCGTGACA 0.979884 -125 GACCTCGCCCGCTGCGCTGACACACGTCGACC 32 57 1 GCGCGTGACA 0.983969 -75 ** *** ***** Masking position 6 Map Score: 14.0511 Number of sites scoring better than the average of aligned sites = 1451 Number in coding regions = 1390 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 6 TAAGGCTTGATAACTCCCCCAAAATAGTTC 5 11 1 TAACTCCCCC 0.52432 -247 GTCTATAAGGGCTCTCCCCCTTCATATTTC 5 134 0 GCTCTCCCCC 0.972243 -124 GGGGCCATATGCAGGCCCCCTAACCAAACG 5 175 0 GCAGGCCCCC 0.953877 -83 GGGGCCTGCATATGGCCCCCTTTTTCACTT 5 186 1 TATGGCCCCC 0.81197 -72 TCGCTTTTCAGCGCAGCCCCACAAGGGTTA 6 70 0 GCGCAGCCCC 0.667848 -77 ATAACCAGACTTACGCCCCCGCGATACTTA 7 46 0 TTACGCCCCC 0.476859 -246 GTAATTGTGATCACGCCCGCACATAACCCA 19 88 0 TCACGCCCGC 0.933868 -190 TTTTTGTCAAGCGGGGCCGCAACCAGTAAA 19 220 1 GCGGGGCCGC 0.673832 -58 AAGGATCATGCCTGGCCCGCACAGTTTTCG 20 88 1 CCTGGCCCGC 0.893858 -63 CAATAAAAGAGAGCGCCCCCTTTTGGAGTA 21 77 1 GAGCGCCCCC 0.923963 -137 GAGTATAGAATCTCGCCCGCTTTTGCATAC 23 41 1 TCTCGCCCGC 0.961244 -84 TGCTCGGATAGCTGTGCCCCAACCGTGCGG 28 15 0 GCTGTGCCCC 0.926191 -202 GCGGTCTACAGCAGGCCGGCAGAACACCGT 28 119 1 GCAGGCCGGC 0.494146 -98 CGCGACCCTGGCCGTGCCCCCAAACGAGGT 28 173 1 GCCGTGCCCC 0.82806 -44 GTACCGCCGACCTCGCCCGCTGCGCTGACA 32 49 1 CCTCGCCCGC 0.933337 -83 TTAAGGCGAGGCGGTGCCGCCTTCGGCGCC 32 100 0 GCGGTGCCGC 0.87476 -32 TTCCGGGCCCCGGAGCGCGCA 34 2 1 TCCGGGCCCC 0.806097 -232 GGTCCCGACGGCTCTCCCCCGTCGGGACCA 34 45 0 GCTCTCCCCC 0.972243 -189 GCCGGTTCTCGATCGCCCGGTATTCGGTTG 35 45 1 GATCGCCCGG 0.457709 -69 GAGCTCTCCTGCCTTTCCGGTC 37 126 0 GCTCTCCTGC 0.559399 -12 ********** Masking position 7 Map Score: 18.067 Number of sites scoring better than the average of aligned sites = 1540 Number in coding regions = 1452 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 7 ATGAGCGAGCGAAGATAACGCATCTGCGGC 5 102 1 GAAGATAACG 0.498147 -156 TTAATGCCGGGCAGATCACATCTCCGAGGA 5 231 1 GCAGATCACA 0.956269 -27 TAACACAAAAGCAGATATCAGGCGATACTT 10 29 0 GCAGATATCA 0.702811 -92 GCAGACCACCAGCGTTACAA 10 111 0 GCAGACCACC 0.976948 -10 CAAAAATGCCGCAGACAACGAC 18 3 0 GCAGACAACG 0.955198 -114 GATCACGCCCGCACATAACCCACTGGGTGT 19 80 0 GCACATAACC 0.645678 -198 CGTATCAAATGCAGATAACGTAATAATTGC 19 186 0 GCAGATAACG 0.946071 -92 GCTATACTGGGCAGACAACAGTTCAGATTT 22 56 0 GCAGACAACA 0.943054 -93 CATACGCAAAGCAGATCACTTACCTGTTGC 23 66 1 GCAGATCACT 0.843621 -59 TTAATTTTCTGCAGACAAAAGGCGTGACGA 27 141 1 GCAGACAAAA 0.483744 -160 AGCTATCCGAGCAGCTCACAAGGATCGAAT 28 32 1 GCAGCTCACA 0.854448 -185 GCTGTAGACCGCCGACCACCCTCGCCGTGA 28 101 0 GCCGACCACC 0.919208 -116 CAGCAGGCCGGCAGAACACCGTTATCGACG 28 127 1 GCAGAACACC 0.846088 -90 TGCCTGTACCGCCGACCTCGCCCGCTGCGC 32 44 1 GCCGACCTCG 0.614515 -88 CGCCAACCGAGCAGCTTACCGACGAGCATC 34 98 0 GCAGCTTACC 0.511098 -136 ********** Masking position 1 Map Score: 8.43238 Number of sites scoring better than the average of aligned sites = 832 Number in coding regions = 777 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 8 AAATTCGACGTCTGATGCTGTACACAGCGCC 4 74 1 TCTGATGCGT 0.661592 -227 ATAAGGCGTTATTGTTGCAGGCAGTTTGGTC 7 74 1 ATTGTTGCGG 0.447584 -218 AGCGCGACTCTCTGTAGCCGGATTATCC 9 8 0 TCTGTAGCGG 0.902773 -178 CGGCGTTGTTTCTGTTGCCGCCGGTGGGGTT 10 75 1 TCTGTTGCGC 0.712405 -46 AGATCACTTACCTGTTGCTGGGTCGCCTGTA 23 78 1 CCTGTTGCGG 0.981567 -47 TGCTGGGTCGCCTGTAGCAGGATTAATTTAA 23 93 1 CCTGTAGCGG 0.932468 -32 AATACAGTCATCTGATGCGGGAAC 24 4 0 TCTGATGCGG 0.921536 -41 TATAGAGTATCCTGACGCTGTTTTTAACACA 25 48 1 CCTGACGCGT 0.897618 -52 ACCGCCCGGATTTGTCGCCGGGTAGCCGGGA 30 18 0 TTTGTCGCGG 0.892067 -74 CCTGGCGCGCGTCACCCGCGT 31 1 1 CCTGGCGCCG 0.938971 -254 CGCCGGAAAACCCGACGCGGGTGACGCGCGC 31 15 0 CCCGACGCGG 0.877145 -240 CACAGTCAACGCTGTCGCCGTCTACCCACCG 31 106 0 GCTGTCGCGT 0.733458 -149 AGGTTCGAGTCCTGGCGACGGAGCTTCAAGG 31 227 1 CCTGGCGAGG 0.770782 -28 AACATGCACGCTTGTCGCCCGAAAGTGATG 33 10 0 CTTGTCGCCG 0.808907 -115 CACACAGGGGTCTGTTGCGCGCTCCGGGGCC 34 16 0 TCTGTTGCCG 0.859884 -218 CCGGGGTGCCCCGGGCGCCGGTCAGGCGTGA 34 182 0 CCGGGCGCGG 0.896051 -52 ******** ** Masking position 7 Map Score: 10.5583 Number of sites scoring better than the average of aligned sites = 2923 Number in coding regions = 2791 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 103 Fraction of orfs with sites within 600 bp upstream = 0.0165435 Motif number 9 AATTCAGCTAACCCTTGTGGGGCTGCGCTGA 6 62 1 ACCCTTGGGG 0.987543 -85 TTCCCGTGATGGATAAATAAGG 7 2 1 TCCCGTGTGG 0.864025 -290 CGCTCAGTAGATCCTTGCGGATCGGCTGGCG 8 32 1 ATCCTTGGGA 0.832937 -60 ACCACTACATTCCTTTGTGGAGAACAC 12 7 0 TCCTTTGGGA 0.914164 -115 CAGGCATGCGTCCATTGGTGGAAAGAATCTG 20 119 0 TCCATTGTGG 0.746703 -32 TGGATCTTTTTCCCTTGAGGGATGTTATTAG 22 89 0 TCCCTTGGGG 0.993496 -60 AAGAGGTTAATCCCTTGAGTGAC 25 87 1 TCCCTTGGTG 0.916439 -13 TTAACTTTCCCATGGGGATAACTCATCG 26 108 0 TCCCATGGGA 0.897133 -18 CTCGGTTACCTCGTTTGGGGGCACGGCCAGG 28 179 0 TCGTTTGGGG 0.835007 -38 GGCAGCCGTCATCCTTGAGGGCATCCGGCGG 29 13 1 ATCCTTGGGG 0.916769 -23 GCAAACCGATACCCTTGTTGATGTGGCCGGA 31 68 0 ACCCTTGTGA 0.887911 -187 CCGCCGCAAGTCGCTTGTGGACAACCGAATA 35 65 0 TCGCTTGGGA 0.936984 -49 ******* *** Masking position 6 Map Score: 8.83791 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 178 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 10 CCCATGTTCGGGGGAAAAATGAGGCCGCTATAA 3 125 0 GGGGAAATGG 0.863213 -53 CCCTTTGGGGTCGGTAATATGGGATACGTGGAG 4 244 1 TCGGATATGG 0.841724 -57 TTATATCTGTGCGGTTTAATGCCGGGCAGATCA 5 216 1 GCGGTAATGC 0.965776 -42 CAGACCACCAGCGTTACAATGGCGAACCCCACC 10 97 0 GCGTAAATGC 0.913743 -24 CCTGCCGCAATCGTAAGAATGAGACAGGCCGTA 13 37 0 TCGTAAATGG 0.86916 -68 GTTCAGATTTTCGGGTCAATGCCCGACCTCCGT 22 33 0 TCGGTAATGC 0.95637 -116 ATGGGAGATGGCGGTAGAATGACCCGTTTTCAA 26 34 0 GCGGAAATGC 0.981751 -92 CGCCGGGACCTCGGGTCAATGTCGGTTCGCCGA 34 135 1 TCGGTAATGC 0.95637 -99 CCCGGCCGGTTCGGCAGAATGGGACCGGAAAGG 37 104 1 TCGGAAATGG 0.971211 -34 **** * **** * Masking position 9 Map Score: 4.66049 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 208 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 TTGCGCACGCGACCAGAATGTAAATTAACC 3 25 0 GACCAGAATG 0.733473 -153 CCATATTACCGACCCCAAAGGGCACCCCGG 4 236 0 GACCCCAAAG 0.9184 -65 CCCGGCATTAAACCGCACAGATATAAAAGT 5 212 0 AACCGCACAG 0.896042 -46 GTCTCAGTCAGACCAGACAGTCACACACAG 7 251 0 GACCAGACAG 0.975177 -41 ATCATGCCTGGCCCGCACAGTTTTCGGCAG 20 92 1 GCCCGCACAG 0.95349 -59 CCCCCGTCGGGACCACACAGGGGTCTGTTG 34 30 0 GACCACACAG 0.984596 -204 GAGCCGTCGGGACCACACAGTCATTTTGAC 34 61 1 GACCACACAG 0.984596 -173 GGCAGAATGGGACCGGAAAGGCAGGAGAGC 37 116 1 GACCGGAAAG 0.948834 -22 ********** Masking position 7 Map Score: 6.51268 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 85 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 12 TTACAGCCGTTCCATCACGTTTA 2 4 1 CAGCCGTTCC 0.971898 -33 TTAACACGCACTATCGATCCCCATGTTCGG 3 147 0 CTATCGATCC 0.712035 -31 GCGCGCCGGACTTCCGATCCATTTCGTATA 4 143 1 CTTCCGATCC 0.908947 -158 AAAACGCCGCCAGCCGATCCGCAAGGATCT 8 40 0 CAGCCGATCC 0.965602 -52 TGACACACGTCGACCGTACCGGCAATGGCG 32 74 1 CGACCGTACC 0.88446 -58 CGAGAACCGGCTACCGTTCCGGTGATCCGA 35 26 0 CTACCGTTCC 0.968824 -88 CGATCATCGGCCGTGCCGGCCAGGTCC 36 50 0 CGGCCGTGCC 0.942729 -17 CGGTCCCATTCTGCCGAACCGGCCGGGCGA 37 101 0 CTGCCGAACC 0.959387 -37 GAGCTCTCCTGCCTTTCCGGTCCCATTC 37 120 0 CTGCCTTTCC 0.886283 -18 ********** Masking position 5 Map Score: 6.32691 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 275 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 TGTCAAACATCATTCAGGACAAAAAAATAG 1 25 0 CATTCAGGAC 0.668831 -68 TGGTATAAAGCGCGCCGGACTTCCGATCCA 4 134 1 CGCGCCGGAC 0.972471 -167 GGTTTAATGCCGGGCAGATCACATCTCCGA 5 228 1 CGGGCAGATC 0.705976 -30 ATTTTGGCCCCGGGCAGTGCTCGCCATCCT 7 145 0 CGGGCAGTGC 0.755577 -147 TGCCCGGTAACGTGCCGGGCATTGCTACTG 17 30 1 CGTGCCGGGC 0.960204 -35 GTTATGTACACACTCAGGACAAAAAAAC 19 260 1 CACTCAGGAC 0.762098 -18 TGGAAAGGATCATGCCTGGCCCGCACAGTT 20 84 1 CATGCCTGGC 0.539946 -67 TCTCAAATTACAGTCAGGACGCGT 27 287 1 CAGTCAGGAC 0.875406 -14 GCCCTTTATCCGGTCCGGCCACATCAACAA 31 55 1 CGGTCCGGCC 0.921343 -200 GTCGGCGGTACAGGCAAGTCACCGCTCGAT 32 30 0 CAGGCAAGTC 0.556162 -102 GCGCCATTGCCGGTACGGTCGACGTGTGTC 32 75 0 CGGTACGGTC 0.618678 -57 GACGAGCATCCACGCAGGTCAAAATGACTG 34 78 0 CACGCAGGTC 0.909886 -156 ACCCGCCGTTCACGCCTGACCGGCGCCCGG 34 173 1 CACGCCTGAC 0.63212 -61 CTGCGTGTATCGGGAAGGACCTGGCCGGCA 36 34 1 CGGGAAGGAC 0.834199 -33 GATCATCGGCCGTGCCGGCCAGGTCCTTCC 36 46 0 CGTGCCGGCC 0.926531 -21 CATGGGACAACGGGCAGGTCCAATGCGTCC 37 36 1 CGGGCAGGTC 0.97846 -102 TTCTGCCGAACCGGCCGGGCGACGCTGCCA 37 93 0 CCGGCCGGGC 0.915749 -45 ********** Masking position 1 Map Score: 11.2968 Number of sites scoring better than the average of aligned sites = 1977 Number in coding regions = 1871 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 14 GATAGTGCGTGTTAAGGAGAAGCAAC 3 162 1 GTTAAGGAGA 0.749063 -16 TAAGTCTGGTTATAAGGCGTTATTGTTGCA 7 63 1 TATAAGGCGT 0.909476 -229 CAAAAGCAGATATCAGGCGATACTTCAGCA 10 24 0 TATCAGGCGA 0.892323 -97 CAAATGGGATGGTAAGGAGTTTATT 12 107 1 GGTAAGGAGT 0.763167 -15 AAGTCAAGGTGTTCAGGCGTTTATTTGTAA 19 139 0 GTTCAGGCGT 0.925948 -139 TTGATTGATGTATAAGGCGATTGAGTATAG 23 19 1 TATAAGGCGA 0.909476 -106 TAAAGGGCCGGATAAGGCGCCGGAAAACCC 31 33 0 GATAAGGCGC 0.89891 -222 GAGAGCCAAGTTTAAGGCGAGGCGGTGCCG 32 111 0 TTTAAGGCGA 0.885266 -21 CCCGGGCGCCGGTCAGGCGTGAACGGCGGG 34 174 0 GGTCAGGCGT 0.931025 -60 ********** Masking position 5 Map Score: 2.59148 Number of sites scoring better than the average of aligned sites = 568 Number in coding regions = 340 Number in noncoding regions = 228 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 15 TCAAACATCATTCAGGACAAAAAAATAGCGGC 1 21 0 TTCAGGCAAA 0.922871 -72 AAATTAGCGACTCGGGTAAAAATAGTACACCT 1 61 0 CTCGGGAAAA 0.962944 -32 GATCCCCATGTTCGGGGGAAAAATGAGGCCGC 3 130 0 TTCGGGGAAA 0.898992 -48 CGTTGACAGTCTCAGGAAAGAAAC 6 133 1 CTCAGGAAAA 0.959977 -14 CGTAAACCCTGTCAGGGAATAAAAAACGC 9 167 1 GTCAGGAAAA 0.846144 -19 TAATAGTCCACTCAGGCAATTATTACGTTATC 19 171 1 CTCAGGAATA 0.771427 -107 TATGTACACACTCAGGACAAAAAAAC 19 262 1 CTCAGGCAAA 0.9592 -16 GTCTGCGGGAAATAATACCAACGTT 21 4 1 TGCGGGAAAA 0.85046 -210 CATCACTTTCGGGCGACAAGCGTGCATGT 33 8 1 TTCGGGGAAA 0.898987 -117 CGAGCATCCACGCAGGTCAAAATGACTGTGTG 34 74 0 CGCAGGCAAA 0.909982 -160 ****** ** ** Masking position 9 Map Score: 4.42776 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 98 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419