AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00350_ecoli_reg_100.orf -o00350_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 surA 52 survival protein #2 imp 254 organic solvent tolerance #3 hlpA 121 histone-like protein, located in outer membrane or nucleoid #4 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #5 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #6 adhC 34 alcohol dehydrogenase class III; formaldehyde dehydrogenase, glutathione-dependent #7 yaiN 166 putative alpha helix chain #8 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #9 ybeX 89 putative transport protein #10 ybeZ 113 putative ATP-binding protein in pho regulon #11 potF 300 periplasmic putrescine-binding protein; permease protein #12 ybjO 59 orf, hypothetical protein #13 ybjF 40 putative enzyme #14 ybjU 36 putative arylsulfatase #15 poxB 132 pyruvate oxidase #16 aspC 184 aspartate aminotransferase #17 htrB 224 heat shock protein #18 adhE 300 CoA-linked acetaldehyde dehydrogenase and iron-dependent alcohol dehydrogenase; pyruvate-formate-lyase deactivase #19 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #20 tynA 247 copper amine oxidase (tyramine oxidase) #21 ydcH 72 orf, hypothetical protein #22 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #23 msbB 119 suppressor of htrB, heat shock protein #24 hisG 145 ATP phosphoribosyltransferase #25 wcaA 34 putative regulator #26 BIME92 24 BIME #27 wza 300 putative polysaccharide export protein #28 gatY 197 tagatose-bisphosphate aldolase 1 #29 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #30 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #31 cvpA 165 membrane protein required for colicin V production #32 b2659 230 orf, hypothetical protein #33 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #34 ygcA 56 putative enzyme #35 pepP 25 proline aminopeptidase P II #36 ygfB 161 orf, hypothetical protein #37 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #38 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #39 agaC 38 PTS system N-acetylgalactosamine-specific IIC component 1 #40 yhdT 108 orf, hypothetical protein #41 yiaM 117 orf, hypothetical protein #42 yiaY 189 putative oxidoreductase #43 yigN 140 putative alpha helix chain #44 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone #45 tyrB 192 tyrosine aminotransferase, tyrosine repressible #46 sgaT 291 orf, hypothetical protein Motif number 1 CACGACTCGGACAAAATGTCGTTGCGCGCAC 5 46 0 ACAAAAGTCG 0.825545 -31 TGTTAGTTAATCAAAACGCCGTCGTTAATCA 9 50 0 TCAAAAGCCG 0.971635 -40 AAGAGAGAAAAAACAAGGCCCACCGGAACGG 10 23 0 AAACAAGCCC 0.856052 -91 CAACCTGGCTACATAATGCCGCGCATGTCGC 12 27 1 ACATAAGCCG 0.874313 -33 GAAAACAATGCCGCGACATGCGC 12 47 0 AAACAAGCCG 0.954256 -13 ATGCAGTTGTTAAAAAAGCCGCCTGGCTGGC 22 24 0 TAAAAAGCCG 0.974134 -39 CGCACCAAATAAAAAAAGCCGGTACTGACTG 23 36 0 AAAAAAGCCG 0.985081 -84 AACCGCGCAATAAAAAAGCCCCCGGAAGGTG 24 88 0 TAAAAAGCCC 0.914793 -58 GTGAAAGGCAAAAAAACGGCCTCCCGATAGG 28 76 0 AAAAAAGGCC 0.854921 -122 CGCGCATCAATAAAAATGGCGCTGAAAAAAT 31 59 0 TAAAAAGGCG 0.921812 -107 TGCTAAAGCGTCAAAAGGCCGGATTTTCCGG 40 14 1 TCAAAAGCCG 0.971635 -95 CCCCAGTAATAAAAAAGGCCGGAAAATCCGG 40 32 0 AAAAAAGCCG 0.985081 -77 CTGAAAGTGTAAAAAAGGGCGGGCAGCTTAC 42 160 0 AAAAAAGGCG 0.953855 -30 ACGCAAAAATACAAAAGGCCGAACGCGTCGG 43 32 0 ACAAAAGCCG 0.983622 -109 ****** **** Masking position 6 Map Score: 20.4009 Number of sites scoring better than the average of aligned sites = 436 Number in coding regions = 354 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 TAGTGTTAATCCTGTCCGAATAGCGTCAGTGGTGTTAGG 2 146 0 CCTGCAACAG 0.927238 -109 CTTTGCGTGGCCCGGCGATCTTATATTGATCGCCTAAAG 3 51 0 CCCGCTCTGA 0.496237 -71 AATAACACGGCCTGCCGCAATCGTAAGAATGAGACAGGC 4 41 0 CCTGCAATAA 0.917464 -64 GATACTCTTCCTGTCAAAATATAAGAAACGACAATAAT 4 77 0 CCTGCAAAAA 0.853609 -28 GGCGGCCTTCCCTGCCGATTAGCCCCCCCCCCTTTCCTC 7 35 1 CCTGCTTCCC 0.683363 -132 TTCTCAGGCCTGCCGTTCCGGTGGGCCTTGTTTTTTC 10 9 1 CCTGCTCTCC 0.749599 -105 ATTGCGCTTACCCGGCTTACAGAACAAAAAGA 19 4 0 CCCGCACAAA 0.744814 -271 GCGCAATGCGCCCGGCAATCTATACACAAAATCATTCAA 19 36 1 CCCGCTCAAA 0.598549 -239 AGCTGGCACACCTGCCAAACAACCTGGCAGGTGCAGGCA 20 125 1 CCTGCACCCA 0.974789 -123 ATAATGTGAACCTGACTAAACCGCCCACAGAGCGCGGTT 20 185 1 CCTGCAACCA 0.980753 -63 GATTTAATATCCCGTCTGAAAAACGAAAATCCTCGCTTT 21 44 1 CCCGCAACAA 0.958528 -29 CCTCTTTAAACCTGTCTGAACCGTTATCAACCGCGCAAT 24 108 0 CCTGCAATCA 0.941747 -38 CGCTACCGCCCCTGGCTTTTTAGCTACCAATACACTGAT 27 92 0 CCTGCTTCCA 0.818761 -209 ACTTGCAACTCCCGCCGAAATCCTGCAAAGTCTGCCTGC 29 44 1 CCCGCAATAA 0.879993 -51 AAATAGTTGCCCTGTCAGACTTGCAGGCAGACTTTGCAG 29 66 0 CCTGCACCCA 0.974789 -29 TTCTCTTCTCCTGTCTGAAGGCCGACGCGTTCGGCCTT 43 10 1 CCTGCAACGC 0.852964 -131 AACGCCTCCTGACGCAACAACTTACCCGCACAAAAT 43 115 0 CCTGCAACCC 0.960542 -26 TAGATTTCTACCCGGCTTAACTACTCCCAATGGG 44 6 0 CCCGCAACCA 0.97111 -89 GTTTTAACCACCTGCCCGTAAACCTGGAGAACCATCGC 45 165 1 CCTGCTACAG 0.86684 -28 TTTGATTAATCCTGACACTATTTTTTCAGGAAGGCAATG 46 53 1 CCTGCTATAG 0.673768 -239 CAACAACTTCCCTGGCAAAAAGTCAAAAAATGGTCATTG 46 87 0 CCTGCAACAA 0.972251 -205 **** * ** * ** Masking position 6 Map Score: 19.6277 Number of sites scoring better than the average of aligned sites = 720 Number in coding regions = 649 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 GTTGATTTACCACGTAATCCGCAGTGCGGTT 1 14 1 CACGAATCCG 0.822678 -39 GGCTAATCGGCAGGGAAGGCCGCCCCGGATA 7 28 0 CAGGAAGGCC 0.929522 -139 GGCCCACCGGAACGGCAGGCCTGAGAA 10 7 0 AACGCAGGCC 0.556776 -107 AAAACAATGCCGCGACATGCGCGGCATTATG 12 38 0 CGCGCATGCG 0.890404 -22 CTTATTATGACGGGAAATGCCACCCTTT 14 8 0 CGGGAATGCC 0.981582 -29 CCGTCATAATAAGGACATGCC 14 26 1 AAGGCATGCC 0.925908 -11 TGGTTACAGAAGGGAAGTCCGCTATCAGGGT 16 149 0 AGGGAGTCCG 0.773708 -36 AAGCCGGGTAAGCGCAATGCGCCCGGCAATC 19 25 1 AGCGAATGCG 0.849769 -250 CTGGCAGGTGCAGGCAATCCCCTTTGCATCA 20 148 1 CAGGAATCCC 0.948442 -100 TAACAGGGAGTGCGTATGTTTCCA 21 4 1 CAGGAGTGCG 0.952385 -69 TTTGCGGCATCGGGCAATGCGT 31 2 0 CGGGAATGCG 0.972874 -164 GATGCGCGGGAAGGAAATCCCTACGCAAACG 31 82 1 AAGGAATCCC 0.885603 -84 CGATTAATATCGGGGAGTGCCTTAATGGAAA 38 47 1 CGGGAGTGCC 0.969892 -120 TAGCGCCTCGCAGGAAATGCCTTTCCAACTG 43 62 1 CAGGAATGCC 0.980051 -79 TGCTCTTATAAAGGTCGTGCCTCTGGCGGAT 45 47 1 AAGGCGTGCC 0.883091 -146 **** ****** Masking position 4 Map Score: 13.679 Number of sites scoring better than the average of aligned sites = 981 Number in coding regions = 902 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 4 CCTTACCATCCCATTTGCACCGGAGGGTGCA 3 93 0 CCTTTGCACC 0.932257 -29 ATCCGGGGCGGCCTTCCCTGCCGATTAGCCC 7 29 1 GCTTCCCTGC 0.727382 -138 GTTAGTGCCTCCTTTCTCTCCCATCCCTTCC 15 55 1 CCTTCTCTCC 0.929546 -78 AAAACAGCCTGCGTTTTCATCAGTAATAGTT 16 96 1 GCTTTTCATC 0.423194 -89 TGCCTTGGCTGCGTTCGCTCCCCCGAATCAC 19 125 0 GCTTCGCTCC 0.971225 -150 GCAGGCAATCCCCTTTGCATCAGTACTGATA 20 157 1 CCTTTGCATC 0.878575 -91 TTAACATCCATTCGCAGCCGGTACGCAG 23 8 1 CCTTCGCAGC 0.975284 -112 CGACGCCTGCATTCGCACCGCCCC 26 9 1 GCTTCGCACC 0.967417 -16 CCGTAATAACCCTTTCTCATCAACGACTGCA 27 32 1 CCTTCTCATC 0.859196 -269 CGTTTTTTTGCCTTTCACTCCTCGAATAATT 28 89 1 CCTTCACTCC 0.839271 -109 TGCCTTCGCTGAGGGTGCCGGT 29 2 1 GCTTCGCTGA 0.710348 -93 ATAGTGTCGCCCCTTCGCAGACCATGGGTCT 36 50 0 CCTTCGCAGA 0.809001 -112 ATCCCTTTTGCTTCCTTTATCTTT 37 4 1 CCTTTGCTTC 0.891603 -188 CTTTCACTTGCCTTTCGTTTCATTTCACTTG 37 128 0 CCTTCGTTTC 0.663469 -64 TTGCTAATTGCCGTTCGCTCCTGAACATCCA 45 104 1 CCTTCGCTCC 0.985135 -89 ** ******** Masking position 5 Map Score: 12.6039 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 613 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 ACAATTGACCGCAGCCGGAAAACGGTAAAAGCACC 2 62 0 GCCCGGAAGG 0.989167 -193 GCCCCGGATAGCGGGCGGCAGAAGGAA 7 3 0 GCGCGGAAGG 0.933743 -164 AATTATTCACGCCACAGGAAAAAGGCGCAAGCATT 10 72 0 GCCAGGAAGG 0.951895 -42 TCTTGCTTACGCCACCTGGAAGTGACGCATTAGAG 18 113 1 GCCCTGAGGA 0.867583 -188 AAGCCGCCTGGCTGGCGGCTTAGGAAAGT 22 5 0 GCGCGGTAGA 0.840025 -58 ACATCCATTCGCAGCCGGTACGCAGTCAGTACCGG 23 14 1 GCCCGGAGAG 0.946515 -106 CAATAAAAAAGCCCCCGGAAGGTGATCTTCCGGGG 24 77 0 GCCCGGAGGA 0.989167 -69 AGGTTGTTCTCCCGGCTTATGAGCTGGTTTGC 25 13 0 TCCCGGTAGA 0.839553 -22 TGTTTACACCGCATCCGGCATAAAAACACGCGCAC 28 27 1 GCCCGGAAAA 0.917669 -171 CAAAAAAACGGCCTCCCGATAGGGAAGCCGTAGCA 28 64 0 GCCCCGTGGA 0.941358 -134 CTGTTAGAATGCGCCCCGAACAGGATGACAGGGCG 31 123 1 GCCCCGAAGA 0.964457 -43 AATAACTAAAGCAACAGGTTAGGGGGAGTTAACAT 32 126 0 GCCAGGTGGG 0.921299 -105 GCGCAGTCAATCAGCAGGAAGGTGGC 36 2 0 TCCAGGAGGG 0.793173 -160 CGACACTATAGCTACCCTGATGAGAAGAGACAAGC 36 72 1 GCCCCTAGGA 0.643782 -90 GCGATGGTTCTCCAGGTTTACGGGCAGGTGGTT 45 170 0 TCCAGGTAGG 0.588293 -23 TAAATGTGACGCGACCCGCAAATAATTCCACATGG 46 223 0 GCCCCGAAAA 0.806709 -69 ** **** * * ** Masking position 2 Map Score: 14.357 Number of sites scoring better than the average of aligned sites = 1556 Number in coding regions = 1370 Number in noncoding regions = 186 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 6 CAGACGTCCCCGCCGTTGGTGATTAACGACGG 9 31 1 CGCGTTGTGA 0.975397 -59 TTAATCAAAACGCCGTCGTTAATCACCAACGG 9 43 0 CGCGTCGTAA 0.963703 -47 ATTATCTGCTGTTTTTAACCTTTTCTTA 11 7 1 TGCGTTTTAA 0.886682 -294 ATCAGATATATGCAGTTTGTGAACGTCAGGGC 19 232 0 TGCGTTTTGA 0.879775 -43 GCCCACAGAGCGCGGTTGCTAACAAGAACACA 20 207 1 CGCGTTGTAA 0.976954 -41 AGTCAATCCATGCAGTTGTTAAAAAAGCCGCC 22 32 0 TGCGTTGTAA 0.969315 -31 TTTTTTATTGCGCGGTTGATAACGGTTCAGAC 24 102 1 CGCGTTGTAA 0.976954 -44 CCTCTCAGCATGCAGTCGTTGATGAGAAAGGG 27 41 0 TGCGTCGTGA 0.948725 -260 TGCCTTCGCTGAGGGTGCCGGT 29 1 1 TGCTTCGTGA 0.740295 -94 TTAAACAATGTGCTTTTTTTAAATTCATAAGA 42 52 0 TGCTTTTTAA 0.546583 -138 ATGAGTCTCACTCTGTTGCTAATTGCCGTTCG 45 89 1 CTCGTTGTAA 0.769595 -104 *** **** *** Masking position 12 Map Score: 8.41718 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 462 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 7 ACCGCAGCCGGAAAACGGTAAAAGCACCTT 2 60 0 GAAAACGGTA 0.618363 -195 AGAAAAGGTTAAAAACAGCAGATAAT 11 7 0 AAAAACAGCA 0.951734 -294 GCTCGGATTAAAAAACGGTATTTAACAAAT 11 101 0 AAAAACGGTA 0.857865 -200 TAAATGCCGAAAAAACAGGACTTTGGTCCT 16 27 1 AAAAACAGGA 0.934356 -158 AAGGTATAAAAAAAACAGGACCAAAGTCCT 16 43 0 AAAAACAGGA 0.934356 -142 CACGTCTTGCAAAAACAGCCTGCGTTTTCA 16 85 1 AAAAACAGCC 0.941845 -100 GAATAGGTTGAAAAACAGGATTGAT 17 210 1 AAAAACAGGA 0.934356 -15 CGCACCAAATAAAAAAAGCCGGTACTGACT 23 37 0 AAAAAAAGCC 0.792671 -83 TGAAAGGCAAAAAAACGGCCTCCCGATAGG 28 76 0 AAAAACGGCC 0.946146 -122 TAACGATCACAAAAACGACAATATGAAAAT 28 117 0 AAAAACGACA 0.547581 -81 CTGGTCGATAAAAAACAGTAAATGGCTTCA 32 81 0 AAAAACAGTA 0.847649 -150 CCTTTGAAAACAGGATGTAGCG 33 6 1 GAAAACAGGA 0.792579 -17 CCCCAGTAATAAAAAAGGCCGGAAAATCCG 40 33 0 AAAAAAGGCC 0.80573 -76 TTATGAATTTAAAAAAAGCACATTGTTTAA 42 54 1 AAAAAAAGCA 0.823164 -136 CTGAAAGTGTAAAAAAGGGCGGGCAGCTTA 42 161 0 AAAAAAGGGC 0.749611 -29 ********** Masking position 5 Map Score: 13.8045 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 414 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 8 ACGGTCAGAGACTAACGTACTCGTCATCTCT 2 189 0 ACTAACGTCT 0.743647 -66 GTTGCGCGTGACAAACGGTCAGAGACTAACG 2 203 0 ACAAACGGCA 0.982345 -52 AAGATATGCAATAAACGTGCATATTTTTTAT 11 227 0 ATAAACGTCA 0.873542 -74 AAGTTCGTTAACAAACGAACAAAAGTTGTCA 11 264 0 ACAAACGACA 0.914254 -37 GAAAGGAGGCACTAACGGTTAAATAGCCCGA 15 40 0 ACTAACGGTA 0.741029 -93 GTCGCCAGAAATAAACGGGCATACGGCCCGG 19 191 1 ATAAACGGCA 0.916365 -84 TGTTTAGTTTACTAACGGTCATTTTGCAGTG 32 52 1 ACTAACGGCA 0.966874 -179 ATTGTGCTGTACAAACGTCCAGTTGGAAAGG 43 81 0 ACAAACGTCA 0.972284 -60 GAGACTCATGACAAACGTACATCCGCCAGAG 45 67 0 ACAAACGTCA 0.972284 -126 ******** ** Masking position 5 Map Score: 6.81116 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 59 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 ATTACGTGGTAAATCAACAAA 1 2 0 AAATCAACAA 0.860944 -51 ATATTCCCCAAATCGACACACGGATATCA 2 10 1 AAATCGACAC 0.927493 -245 TGATAAAGCCAAATCGACACAAGAGAAGTG 11 49 0 AAATCGACAC 0.927493 -252 CGGGCGAAAAAATGCGACAATACATACAAT 17 175 1 AATGCGACAA 0.853563 -50 TATTATCTCTAATGCGTCACTTCCAGGTGG 18 124 0 AATGCGTCAC 0.65964 -177 TAGGTTAAGCAAATCATCACCGCACTGACT 18 221 1 AAATCATCAC 0.673051 -80 AACGATCACAAAAACGACAATATGAAAATT 28 116 0 AAAACGACAA 0.771401 -82 ATGAATAACTAAAGCAACAGGTTAGGGGGA 32 134 0 AAAGCAACAG 0.757735 -97 ATTGTGATCAAAAGCAACAAATTAGTAACA 32 200 0 AAAGCAACAA 0.921727 -31 AAGGCAAGTGAAAGCGACAACGCCCGACGT 37 145 1 AAAGCGACAA 0.962984 -47 GACTGCTAAAGCGTCAAAAGGCCGGAT 40 8 1 AAAGCGTCAA 0.902433 -101 TCCATACTCAAAATCAACAACAACTTCCCT 46 113 0 AAATCAACAA 0.860944 -179 ********** Masking position 2 Map Score: 7.8643 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 172 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 AAAGAACTGCACCCTCCGGTGCAAATGGGAT 3 86 1 ACCCTCCGGG 0.925343 -36 GAGAATAAAATTTATCCGGTGAATGTGGTCG 7 83 0 TTTATCCGGG 0.547575 -84 GATAAATTTTATTCTCCAGTGTTATATACTA 7 98 1 ATTCTCCAGG 0.55454 -69 TGACCTTCACATCATCAGGGGCGACGATTAT 13 16 0 ATCATCAGGG 0.850001 -25 TACCGTTATCACATTCAGGAGATGGAGAACC 15 112 1 ACATTCAGGG 0.759884 -21 TTTTTTTTATACCTTCCAGAGCAATCTCACG 16 58 1 ACCTTCCAGG 0.857837 -127 CTAATGCGTCACTTCCAGGTGGCGTAAGCAA 18 115 0 ACTTCCAGGG 0.717982 -186 AAAGTTTAACATTATCAGGAGAGCATT 18 284 1 ATTATCAGGG 0.823405 -17 GTGTACATCTATTTTCAGGGCATCCACTGTA 20 89 1 ATTTTCAGGC 0.710886 -159 TCTTTCAGGCGATGTGTGCTG 24 1 1 TCTTTCAGGG 0.764186 -145 AGACATTCAGATCTTCCAGTGGTGCATGAAC 24 34 1 ATCTTCCAGG 0.827255 -112 CCGGAAGGTGATCTTCCGGGGGCTTTCTCAT 24 67 0 ATCTTCCGGG 0.968882 -79 CCGGAAGATCACCTTCCGGGGGCTTTTTTAT 24 79 1 ACCTTCCGGG 0.975144 -67 AAAAGGCCGGATTTTCCGGCCTTTTTTATTA 40 26 1 ATTTTCCGGC 0.798137 -83 CCTTTTTTACACTTTCAGGAGTGTGTT 42 173 1 ACTTTCAGGG 0.95255 -17 GATCGAGTGGATGTTCAGGAGCGAACGGCAA 45 111 0 ATGTTCAGGG 0.788243 -82 ********* * Masking position 6 Map Score: 8.57441 Number of sites scoring better than the average of aligned sites = 1029 Number in coding regions = 944 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 11 TCATCGGTAACGTTGCGCGTGACAAACGGT 2 215 0 CGTTGCGCGT 0.95602 -40 CAGTTCTTTGCGTGGCCCGGCGATCTTATA 3 65 0 CGTGGCCCGG 0.824448 -57 TAACAAAATAAGTTGCGCTGTACTGTGCGC 5 22 1 AGTTGCGCTG 0.845688 -55 GACAAAATGTCGTTGCGCGCACAGTACAGC 5 38 0 CGTTGCGCGC 0.819277 -39 TGTGTATAATCGTCGCCCCTGATGATGTGA 13 11 1 CGTCGCCCCT 0.947611 -30 GTAAATCTCCCGTTACCCTGATAGCGGACT 16 135 1 CGTTACCCTG 0.576738 -50 TTGCCGGGCGCATTGCGCTTACCCGGCTTA 19 24 0 CATTGCGCTT 0.568069 -251 AACTATTCGCCGTTGCCCTTCATTCACCGA 20 11 0 CGTTGCCCTT 0.963605 -237 AACGGCGAATAGTTGCCCTTTTATTTCACT 20 27 1 AGTTGCCCTT 0.872833 -221 GTGCGGGGCAAGTTGCGCCGCTACACTATC 23 62 1 AGTTGCGCCG 0.836658 -58 AAATAGTTGCCCTGTCAGACTTGC 29 81 0 AGTTGCCCTG 0.861931 -14 GTAGCTATAGTGTCGCCCCTTCGCAGACCA 36 57 0 TGTCGCCCCT 0.588913 -105 ATGAACTTGACGTCGGGCGTTGTCGCTTTC 37 154 0 CGTCGGGCGT 0.726045 -38 AGGCCGAACGCGTCGGCCTTCAGACAGGAG 43 18 0 CGTCGGCCTT 0.763482 -123 TGTATTTTTGCGTAGCGCCTCGCAGGAAAT 43 50 1 CGTAGCGCCT 0.753595 -91 ********** Masking position 3 Map Score: 7.20331 Number of sites scoring better than the average of aligned sites = 1311 Number in coding regions = 1252 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 12 TCTGCCAGTCAAATGCCTGGCAAA 9 3 0 AATCCTGGCA 0.744995 -87 CAATGCCGCGACATGCGCGGCATTATGTAGCC 12 33 0 AATCGCGGCA 0.97899 -27 GGGAAAGTAAAAATCCGCGGCATGATATAGCA 17 32 1 AATCGCGGCA 0.978991 -193 TTTGTTATTTACAAGCGCGGCAATTTCGCCCA 17 119 1 AAACGCGGCA 0.95475 -106 CTCAGGTAAGTGATTCGGGGGAGCGAACGCAG 19 116 1 TATCGGGGGA 0.914901 -159 TTTTTTTATTTGGTGCGGGGCAAGTTGCGCCG 23 50 1 TGTCGGGGCA 0.834795 -70 TGCGGTGTAAACATACGTGGCAGTGCTAT 28 8 0 AATCGTGGCA 0.957558 -190 CCATTTTTATTGATGCGCGGGAAGGAAATCCC 31 71 1 TATCGCGGGA 0.933854 -95 GACAGGGCGTAAAATCGTGGGACACAT 31 149 1 AAACGTGGGA 0.819252 -17 TCTGCCCCGATAAAACGGGGCAGATAATATGT 32 23 1 TAACGGGGCA 0.916474 -208 * ** ******* Masking position 12 Map Score: 5.74274 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 269 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 GTTATATACTATAGGGGGGTATGCATTGACAT 7 118 1 ATAGGGGGAT 0.962827 -49 GCAATATACTATAGGGGGGTATTCTATATGTC 7 145 0 ATAGGGGGAT 0.962827 -22 GCATTGCAATAAAGATGGGGATAAAGAGAGAA 10 45 0 AAAGATGGAT 0.670827 -69 GTTTGAGACTATAGCTCGGATTAAAAAACGGT 11 112 0 ATAGCTGGTT 0.681591 -189 AAAGGGTGGCATTTCCCGTCAT 14 1 1 AAAGGGGGAT 0.974318 -36 AAAGCGAGGATTTTCGTTTTTC 21 61 0 AAAGCGGGTT 0.940894 -12 TCGTCGTCAAAGGGAGGAATATTCATGATA 36 142 0 AAAGGGGGAT 0.974318 -20 TAAAGCGTCAAAAGGCCGGATTTTCCGGCCTT 40 17 1 AAAGGCGGTT 0.810921 -92 ATGGGTGAAGAAAGCGGGGATTGTACCTTATG 40 75 0 AAAGCGGGTT 0.940899 -34 TTCCACATGGATAGAGTGGGATTCACACAACG 46 201 0 ATAGAGGGAT 0.876069 -91 ****** ** ** Masking position 3 Map Score: 6.52034 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 83 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 GTTCGCCAAACTTTACGGCCTGTCTCATTCT 4 24 1 CTTTCGGCCT 0.983946 -81 TTCTCAGGCCTGCCGTTCCGG 10 1 1 TTCTAGGCCT 0.681331 -113 AAAGTCCTGTTTTTTCGGCATTTAACAAAGA 16 20 0 TTTTCGGCAT 0.922116 -165 ATTGTCGCATTTTTTCGCCCGCAACCAAAAT 17 165 0 TTTTCGCCCG 0.835749 -60 TTCAGCATCGCTTTTCGCCATTATAGCTAAC 18 22 0 CTTTCGCCAT 0.9497 -279 GCCCGGGGATCTCTGCGCCCTGACGTTCACA 19 216 1 CTCTCGCCCT 0.951745 -59 TCAGACTGGTCTTTCAGGCATCCAGACACGC 27 128 0 CTTTAGGCAT 0.795617 -173 CTTTTTATGCCTTTGCGGCATCGGGCAATGC 31 13 0 CTTTCGGCAT 0.95748 -153 TGTCCCACGATTTTACGCCCTGTCATCCTGT 31 142 0 TTTTCGCCCT 0.96431 -24 TATGCTACCACTTTGGGCCCTGGTGGACCAG 36 113 0 CTTTGGCCCT 0.881893 -49 AAAGGCCGGATTTTCCGGCCTTTTTTATTAC 40 27 1 TTTTCGGCCT 0.969902 -82 **** ****** Masking position 4 Map Score: 8.98636 Number of sites scoring better than the average of aligned sites = 244 Number in coding regions = 208 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 15 AGGTGCTTTTACCGTTTTCCGGCTGCGGTCAA 2 61 1 ACCGTTTCCG 0.82414 -194 CAACGGCGGGGACGTCTGCCAGTCAAATGCCT 9 17 0 GACGTTGCCG 0.956002 -73 CAATGCTTGCGCCTTTTTCCTGTGGCGTGAAT 10 71 1 GCCTTTTCCG 0.976561 -43 TCGCCTTATGCCCGATGATATTCC 15 3 1 GCCTTTGCCG 0.989861 -130 AGATCCCCGGGCCGTATGCCCGTTTATTTCTG 19 196 0 GCCGTTGCCG 0.992107 -79 ACTTTCCTAAGCCGCCAGCCAGGCGGCTTTTT 22 11 1 GCCGCAGCCG 0.944686 -52 ATTTTTTTAGGACTGATGCCAGTTAAATTTTT 27 191 1 GACTGTGCCG 0.817607 -110 GCCACCTTCCTGCTGATTGACT 36 1 1 GCCACTTCCG 0.834004 -161 GAACGCGTCGGCCTTCAGACAGGAGAAGAGAA 43 11 0 GCCTTAGACG 0.703355 -130 CTCGATCTTCGCCTTCTTCCGGTTTATTGTGT 45 135 1 GCCTTTTCCG 0.976561 -58 ***** **** * Masking position 3 Map Score: 6.23327 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 580 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822