AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00360_ecoli_reg_100.orf -o00360_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 caiA 30 probable carnitine operon oxidoreductase #2 caiT 300 probable carnitine transporter #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 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #7 ybeX 89 putative transport protein #8 ybeZ 113 putative ATP-binding protein in pho regulon #9 ybjU 36 putative arylsulfatase #10 poxB 132 pyruvate oxidase #11 aspC 184 aspartate aminotransferase #12 b0968 181 orf, hypothetical protein #13 htrB 224 heat shock protein #14 dadA 300 D-amino acid dehydrogenase subunit #15 hemA 213 enzyme in alternate path of synthesis of 5-aminolevulinate #16 feaB 232 phenylacetaldehyde dehydrogenase #17 tynA 247 copper amine oxidase (tyramine oxidase) #18 ydcH 72 orf, hypothetical protein #19 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #20 rspA 205 starvation sensing protein #21 msbB 119 suppressor of htrB, heat shock protein #22 hisG 145 ATP phosphoribosyltransferase #23 wcaA 34 putative regulator #24 BIME92 24 BIME #25 wza 300 putative polysaccharide export protein #26 gatD 47 galactitol-1-phosphate dehydrogenase #27 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #28 gatZ 28 putative tagatose 6-phosphate kinase 1 #29 gatY 197 tagatose-bisphosphate aldolase 1 #30 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #31 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #32 cvpA 165 membrane protein required for colicin V production #33 pdxB 98 erythronate-4-phosphate dehyrogenase #34 pepP 25 proline aminopeptidase P II #35 ygfB 161 orf, hypothetical protein #36 epd 284 D-erythrose 4-phosphate dehydrogenase #37 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #38 yiaM 117 orf, hypothetical protein #39 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #40 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #41 tyrB 192 tyrosine aminotransferase, tyrosine repressible #42 sgaT 291 orf, hypothetical protein Motif number 1 AATTAACGAAAAAACGCCCTCTATTCACCC 2 116 1 AAAACGCCCT 0.861339 -185 GATCAATATAAGATCGCCGGGCCACGCAAA 3 59 1 AGATCGCCGG 0.58972 -63 TTAGTTAATCAAAACGCCGTCGTTAATCAC 7 49 0 AAAACGCCGT 0.94043 -41 ACGCCACAGGAAAAAGGCGCAAGCATTGCA 8 69 0 AAAAAGGCGC 0.926273 -45 ACTAACGGTTAAATAGCCCGATGAAAGGAA 10 31 0 AAATAGCCCG 0.721212 -102 ATTACTGATGAAAACGCAGGCTGTTTTTGC 11 93 0 AAAACGCAGG 0.630829 -92 AAATCCATGGAAAACTCCGGACAATGACGC 12 129 0 AAAACTCCGG 0.760203 -53 ATGGGAAAGTAAAAATCCGCGGCATGATAT 13 30 1 AAAAATCCGC 0.791787 -195 AGACTGGGCGAAATTGCCGCGCTTGTAAAT 13 125 0 AAATTGCCGC 0.655541 -100 GCTCACCATAAAAAAGCCGCATGTTGAATA 14 207 1 AAAAAGCCGC 0.980968 -94 GCAGTTGTTAAAAAAGCCGCCTGGCTGGCG 19 23 0 AAAAAGCCGC 0.980968 -40 GTGATCACAAAAAAAGGCGTATATTTGCGC 20 97 0 AAAAAGGCGT 0.765088 -109 TAAAGATCGAAAAAAGCCGGAGTGATCACA 20 118 0 AAAAAGCCGG 0.97324 -88 CACCAAATAAAAAAAGCCGGTACTGACTGC 21 35 0 AAAAAGCCGG 0.97324 -85 TGAACGCATGAGAAAGCCCCCGGAAGATCA 22 60 1 AGAAAGCCCC 0.789601 -86 CCGCGCAATAAAAAAGCCCCCGGAAGGTGA 22 87 0 AAAAAGCCCC 0.95301 -59 ATTGGTAGCTAAAAAGCCAGGGGCGGTAGC 25 100 1 AAAAAGCCAG 0.848341 -201 GAAAGGCAAAAAAACGGCCTCCCGATAGGG 29 75 0 AAAACGGCCT 0.602245 -123 CGCATCAATAAAAATGGCGCTGAAAAAATA 32 58 0 AAAATGGCGC 0.719575 -108 TCTTATGCCAAAAACGCCACGTGTTTACGT 39 16 1 AAAACGCCAC 0.903535 -224 ATATAAAAGCAAAACGCCACGTAAACACGT 39 34 0 AAAACGCCAC 0.903535 -206 ********** Masking position 3 Map Score: 24.8781 Number of sites scoring better than the average of aligned sites = 1625 Number in coding regions = 1392 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 213 Fraction of orfs with sites within 600 bp upstream = 0.0342114 Motif number 2 GCCAGTCAAATGCCTGGCAAA 7 2 0 TGCCTGGCAA 0.658743 -88 ACGGCGGGGACGTCTGCCAGTCAAATGCCT 7 17 0 CGTCTGCCAG 0.817207 -73 GGTGTACGGTTCCTGCGAGATGGGAAAGT 13 10 1 TTCCTGCGAG 0.525505 -215 TATGTCTCTATGCCTGACAAGACTTATTTC 16 91 0 TGCCTGACAA 0.773185 -142 AAAGCTGGCACACCTGCCAAACAACCTGGC 17 123 1 CACCTGCCAA 0.715764 -125 GGATTGCCTGCACCTGCCAGGTTGTTTGGC 17 138 0 CACCTGCCAG 0.935402 -110 TTTCCTAAGCCGCCAGCCAGGCGGCTTTTT 19 13 1 CGCCAGCCAG 0.983646 -50 CAGCACACATCGCCTGAAAGA 22 2 0 CGCCTGAAAG 0.923654 -144 CGTGTCTGGATGCCTGAAAGACCAGTCTGA 25 129 1 TGCCTGAAAG 0.871378 -172 CAAGTCAGGGTGCCAGACCGGCACCCTCAG 30 19 0 TGCCAGACCG 0.881031 -76 CTGCAAAGTCTGCCTGCAAGTCTGACAGGG 30 66 1 TGCCTGCAAG 0.951461 -29 TTCGCAAGTATGCCTGGCCGCGAGATTATG 33 34 1 TGCCTGGCCG 0.875959 -65 GTTATTATTACGCCAGCCTGGAATAAAGCT 36 34 1 CGCCAGCCTG 0.855484 -251 TGAGCAAATTTGCCAGACAGAGTAATCCAG 36 243 0 TGCCAGACAG 0.920887 -42 AGATCTCCTGCAAGGTTTTCCCTG 36 271 0 CTCCTGCAAG 0.777414 -14 TAATCGTCTACGCCAGAACGCCTGGGTAAT 38 16 1 CGCCAGAACG 0.820489 -102 TTCCTAACATCGCCAGCGCGGCATTAAGAT 39 69 0 CGCCAGCGCG 0.882193 -171 TTGCATAACATGCCAGCAAATTCCAGGAAT 39 100 0 TGCCAGCAAA 0.669343 -140 GTGTTTTAACCACCTGCCCGTAAACCTGGA 41 163 1 CACCTGCCCG 0.902081 -30 ********** Masking position 6 Map Score: 17.1136 Number of sites scoring better than the average of aligned sites = 4091 Number in coding regions = 3910 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 174 Fraction of orfs with sites within 600 bp upstream = 0.0279473 Motif number 3 ATCCCATTTGCACCGGAGGGTGCAGTTCTTT 3 86 0 CCCGGAGGGT 0.973246 -36 TCACCGGCCTATAAGGAAATTA 8 102 0 CCCGGCCTAT 0.78101 -12 TCCCTTCCCCCTCCGTCAGATGAACTAAACT 10 78 1 CCCGTCAGAT 0.759603 -55 CGTGAGATTGCTCTGGAAGGTATAAAAAAAA 11 58 0 CCTGGAAGGT 0.906851 -127 CGGGCAACGGCCCCGGAAAAGACCCACGGAT 12 12 1 CCCGGAAAAG 0.770365 -170 CCATGGAAAACTCCGGACAATGACGCCCATT 12 124 0 CCCGGACAAT 0.941586 -58 AAAACCGCGTCGCCGGAGAATTTTTTTCTTT 14 50 1 CCCGGAGAAT 0.941586 -251 GTTCATGCACCACTGGAAGATCTGAATGTCT 22 34 0 CCTGGAAGAT 0.945698 -112 ATGAGAAAGCCCCCGGAAGATCACCTTCCGG 22 67 1 CCCGGAAGAT 0.98748 -79 ATAAAAAAGCCCCCGGAAGGTGATCTTCCGG 22 79 0 CCCGGAAGGT 0.977826 -67 GGTAAGGTTTCCCCGGACGATTTGCTGGATT 36 219 1 CCCGGACGAT 0.984865 -66 AAGGTCGTGCCTCTGGCGGATGTACGTTTGT 41 57 1 CCTGGCGGAT 0.887493 -136 * ********* Masking position 3 Map Score: 11.6686 Number of sites scoring better than the average of aligned sites = 492 Number in coding regions = 454 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 TTCGGGTGAATAGAGGGCGTTTTTTCGTTA 2 119 0 TAGAGGGCGT 0.827477 -182 GTAAGAATGAGACAGGCCGTAAAGTTTGGC 4 28 0 GACAGGCCGT 0.977935 -77 TTACGATTGCGGCAGGCCGTGTTATTATTG 4 54 1 GGCAGGCCGT 0.986049 -51 TAACAGGGAGTGCGTATGTTTCCAG 18 6 1 GGGAGTGCGT 0.961093 -67 ACTGCATGCTGAGAGGGTGTGAAAAATTAA 25 57 1 GAGAGGGTGT 0.827477 -244 CCTCCCGATAGGGAAGCCGTAGCAAAGTGC 29 58 0 GGGAAGCCGT 0.93802 -140 CTTCCCTATCGGGAGGCCGTTTTTTTGCCT 29 72 1 GGGAGGCCGT 0.988707 -126 TGCGGCATCGGGCAATGCGT 32 1 0 GGCAATGCGT 0.775153 -165 CGAACAGGATGACAGGGCGTAAAATCGTGG 32 139 1 GACAGGGCGT 0.977935 -27 ATTCAGAAGGGAAAGTCCGTTCCAAACCCA 39 167 0 GAAAGTCCGT 0.705565 -73 ********** Masking position 4 Map Score: 8.70704 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 326 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 ATATAAGATCGCCGGGCCACGCAAAGAACTGCAC 3 64 1 GCCGGAGCAA 0.884497 -58 GTCTGCCAGTCAAATGCCTGGCAAA 7 2 0 CAAAGTGCAA 0.502464 -88 AGGAAAAAGGCGCAAGCATTGCAATAAAGATGGG 8 58 0 CGCAGTGCAA 0.843316 -56 TCCTTATTATGACGGGAAATGCCACCCTTT 9 7 0 GACGGAGCCA 0.807905 -30 ATTTGTTATTTACAAGCGCGGCAATTTCGCCCAG 13 118 1 TACAGCGCAA 0.714974 -107 TGTCAGCTGTGACAAGCTCCGCAAATCGTGACAA 16 129 0 GACAGCGCAA 0.969545 -104 CATGCATCACGACAAGCGATGCAAGGAATCGAAC 20 182 1 GACAGAGCAA 0.959552 -24 AATTATTCGAGGAGTGAAAGGCAAAAAAACGGCC 29 86 0 GGAGGAGCAA 0.91171 -112 GCAGGATTTCGGCGGGAGTTGCAAGTCAGGGTGC 30 36 0 GGCGGTGCAA 0.954328 -59 CAAGTGAAATGAAACGAAAGGCAAGTGAAAGCGA 37 128 1 GAAAGAGCAA 0.860137 -64 TAATTCAAGTCGCATGTGCAGCAACCTGAATTAT 38 67 0 CGCAGCGCAA 0.932292 -51 GGAATTTGCTGGCATGTTATGCAATTTGCATATC 39 106 1 GGCAGAGCAA 0.970393 -134 TGGATGTTCAGGAGCGAACGGCAATTAGCAACAG 41 101 0 GGAGGCGCAA 0.932695 -92 GATTAAATGTGACGCGACCCGCAAATAATTCCAC 42 227 0 GACGGCGCAA 0.974806 -65 **** * * **** Masking position 14 Map Score: 10.8621 Number of sites scoring better than the average of aligned sites = 470 Number in coding regions = 442 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 ATAAAGATGGGGATAAAGAGAGAAAAAACAAGGCCC 8 33 0 GTAAGAAAAA 0.865529 -81 AGGGATGGGAGAGAAAGGAGGCACTAACGGTTAAAT 10 47 0 GAAAGGACTA 0.584459 -86 ACACCTCTTTGTTAAATGCCGAAAAAACAGGACTTT 11 15 1 GAAAGGAAAA 0.971766 -170 TTTAGTGTTAGCCAAAGGGCGCGAAAAATCATTACT 12 51 0 GAAAGGGAAA 0.921264 -131 GTTGCGGGCGAAAAAATGCGACAATACATACAATTG 13 171 1 AAAAGAAATA 0.46226 -54 GTGAATGGTTGACAAAAGATGAAATAGAATACCTTT 20 60 0 GAAAGGAATA 0.912021 -146 GTTCAGACAGGTTTAAAGAGGAATAACAAA 22 126 1 GTAAGGATAA 0.705692 -20 TATTCGAGGAGTGAAAGGCAAAAAAACGGCCTCCCG 29 81 0 GAAAGAAAAA 0.955298 -117 CTGAGATGTGGCTTAACGAGGAAAAAGACGT 31 16 1 GTAAGGAAAA 0.912021 -21 TCGTCGTCAAAGGGAGGAATATTCATGATAT 35 141 0 GAAAGGAATA 0.912021 -21 AAAGCTTCCCACAAAAGGGGATAAAAGTGTGATGTG 36 58 1 AAAAGAAAAA 0.740539 -227 GCTAGGATAAGCGAAACGTGGAATAAAAGGAATGTT 36 124 0 GAAAGGATAA 0.888407 -161 TGAAAGAAAAGATAAAGGAAGCAAAAGGGAT 37 6 0 GAAAGGAAAA 0.971766 -186 GTTCAATGGAGAAAAAAGAAATAAAACGAAATTTGT 37 48 0 GAAAGAAAAA 0.955298 -144 ACATCACCAAGTGAAATGAAACGAAAGGCAAGTGAA 37 121 1 GAAAGAGAAA 0.879008 -71 AGATATAAAAGCAAAACGCCACGTAAACACGTGGCG 39 30 0 GAAAGAGTAA 0.626929 -210 AGATGCGGAGACTTAAGGTCAAAAAAACAGAAGGGT 40 16 0 ATAAGAAAAA 0.46226 -174 AACTTCCCTGGCAAAAAGTCAAAAAATGGTCATTGC 42 86 0 GAAAGAAAAA 0.955298 -206 * *** * * **** Masking position 6 Map Score: 15.6518 Number of sites scoring better than the average of aligned sites = 438 Number in coding regions = 361 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 7 CAGACGTCCCCGCCGTTGGTGATTAACGACGG 7 31 1 CGCGTTGTGA 0.974622 -59 TTAATCAAAACGCCGTCGTTAATCACCAACGG 7 43 0 CGCGTCGTAA 0.974622 -47 GCGAAATTGCCGCGCTTGTAAATAACAAATAA 13 116 0 CGCCTTGAAA 0.762746 -109 TCTCCGGCGACGCGGTTTTTAACAGGTGTTCT 14 37 0 CGCGTTTTAA 0.886405 -264 ATCTTGATAACTCAGTTGAAAATATTATTCAA 14 230 0 CTCGTTGAAA 0.811034 -71 GCCCACAGAGCGCGGTTGCTAACAAGAACACA 17 207 1 CGCGTTGTAA 0.988928 -41 AGTCAATCCATGCAGTTGTTAAAAAAGCCGCC 19 32 0 TGCGTTGTAA 0.939172 -31 TTTTTTATTGCGCGGTTGATAACGGTTCAGAC 22 102 1 CGCGTTGTAA 0.988928 -44 CCTCTCAGCATGCAGTCGTTGATGAGAAAGGG 25 41 0 TGCGTCGTGA 0.740571 -260 ATGAGTCTCACTCTGTTGCTAATTGCCGTTCG 41 89 1 CTCGTTGTAA 0.939172 -104 *** **** *** Masking position 6 Map Score: 7.85734 Number of sites scoring better than the average of aligned sites = 389 Number in coding regions = 363 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 TTATTTTGCGTTCCCGTTTGTTTTATTTTT 2 253 0 TTCCCGTTTG 0.944849 -48 ACTCCTTACCATCCCATTTGCACCGGAGGG 3 97 0 ATCCCATTTG 0.862655 -25 GATAGCGGACTTCCCTTCTGTAACCATAAT 11 154 1 TTCCCTTCTG 0.970395 -31 GGTGCAGGCAATCCCCTTTGCATCAGTACT 17 154 1 ATCCCCTTTG 0.902999 -94 GAGATTTAATATCCCGTCTGAAAAACGAAA 18 42 1 ATCCCGTCTG 0.948878 -31 ATGAAATAGAATACCTTTTGTCAGCTGACA 20 48 0 ATACCTTTTG 0.725516 -158 CACACTTTTATCCCCTTTTGTGGGAAGCTT 36 59 0 TCCCCTTTTG 0.876064 -226 ATCCCTTTTGCTTCCTTTAT 37 1 1 ATCCCTTTTG 0.968004 -191 GGAACGGACTTTCCCTTCTGAATAAAGGTC 39 174 1 TTCCCTTCTG 0.970395 -66 TTTTTACCCTTCTGTTTTTTTGAC 40 5 1 TACCCTTCTG 0.837849 -185 ********** Masking position 7 Map Score: 7.90922 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 70 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 9 TATAAGATCGCCGGGCCACGCAAAGAACTG 3 65 1 CCGGGCCACG 0.92464 -57 GCGCACAGTACAGCGCAACTTATTTTGTTA 5 22 0 CAGCGCAACT 0.968049 -55 GCTGTACTGTGCGCGCAACGACATTTTGTC 5 38 1 GCGCGCAACG 0.933774 -39 AGTCCGCTATCAGGGTAACGGGAGATTTAC 11 135 0 CAGGGTAACG 0.861804 -50 GCGGGCAACGGCCCCGGAAA 12 1 1 GCGGGCAACG 0.954191 -181 TCGGTGAATGAAGGGCAACGGCGAATAGTT 17 11 1 AAGGGCAACG 0.942282 -237 AGTGAAATAAAAGGGCAACTATTCGCCGTT 17 27 0 AAGGGCAACT 0.911013 -221 CAACCATTCACAGCGCAAATATACGCCTTT 20 85 1 CAGCGCAAAT 0.725803 -121 GATAGTGTAGCGGCGCAACTTGCCCCGCAC 21 62 0 CGGCGCAACT 0.903122 -58 GCAAGTCTGACAGGGCAACTATTT 30 81 1 CAGGGCAACT 0.978146 -14 ********** Masking position 8 Map Score: 6.33908 Number of sites scoring better than the average of aligned sites = 529 Number in coding regions = 497 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 TTACGGCCTGTCTCATTCTTACGATTGCGGCAGGCCG 4 36 1 TCCTTTTATG 0.915266 -69 TCGCCTTATGCCCGATGATATTCCTTT 10 1 1 TCCTTTGCTG 0.972661 -132 GGTTCTCCATCTCCTGAATGTGATAACGGT 10 113 0 TCCATTCCTG 0.914753 -20 TGCTGCTCTCCTTATCCTTAATGGACGCGTTGC 12 159 0 TCCTTTCCTG 0.985522 -23 GCTGTGACATTCGCTTTGTCAGCTGTGACAAGCTCCG 16 142 0 TCCTTTCATG 0.957098 -91 ACAAGAAAAGTCACTTTTTTCGCTGTGACATTCGCTT 16 163 0 TCCTTTTCTG 0.970552 -70 TGTGACGTTGTCACATTATGCATGATGTGTACATCTA 17 63 1 TCCTTTGCTG 0.972661 -185 TTAGTCAGGTTCACATTATCAGTACTGATGCAAAGGG 17 167 0 TCCTTTCATG 0.957098 -81 CACTCGATCTTCGCCTTCTTCCGGTTTATTGTGTTTT 41 133 1 TCCTTTTCTT 0.763649 -60 ** * ** *** ** Masking position 9 Map Score: 4.83446 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 34 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 ATTTCCCGTCATAATAAGGACATGCC 9 21 1 ATAATAAGGA 0.855623 -16 TAAATGCCGAAAAAACAGGACTTTGGTCCT 11 27 1 AAAAACAGGA 0.916307 -158 AAGGTATAAAAAAAACAGGACCAAAGTCCT 11 43 0 AAAAACAGGA 0.916307 -142 GAATAGGTTGAAAAACAGGATTGAT 13 210 1 AAAAACAGGA 0.916307 -15 TTTATGCTGGATAAAAAGGGCGTTCAGCAG 14 128 1 ATAAAAAGGG 0.731866 -173 CACTGGGTAAATAATAAGGAAAA 16 220 1 ATAATAAGGA 0.855623 -13 TATCTTATTGATAAAATGGATTTATGTTC 20 10 0 ATAAAATGGA 0.673545 -196 ATCCCCCTTAACAATCAGGAGTTTTT 26 32 1 ACAATCAGGA 0.744113 -16 CTCTGTAACAATAAAAAGGACTATTT 27 15 1 ATAAAAAGGA 0.929018 -16 TTAAAACACAATAAACCGGAAGAAGGCGAA 41 142 0 ATAAACCGGA 0.829831 -51 ********** Masking position 4 Map Score: 2.8968 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 106 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 12 CAAAAATGTGATACCAATCACAGAATACAGCT 2 150 1 AACAATCACA 0.911164 -151 ATAAGAAACGACAATAATAACACGGCCTGCCG 4 63 0 AAAAATAACA 0.617284 -42 GGGGATAAAGAGAGAAAAAACAAGGCCCACCG 8 29 0 AAGAAAAACA 0.65584 -85 TAGCCCGATGAAAGGAATATCATCGGGCATAA 10 16 0 AAGAATATCA 0.786609 -117 TATACCTTCCAGAGCAATCTCACGTCTTGCAA 11 65 1 AAGAATCTCA 0.855072 -120 AAAGAATAATAATCTAATCACATCTTGATAAC 14 251 0 ATCAATCACA 0.69679 -50 CGCTGCGTACACTGAAATCACACTGGGTAAAT 16 200 1 ATGAATCACA 0.855072 -33 ACAGGTTTAAAGAGGAATAACAAA 22 132 1 AAGAATAACA 0.942701 -14 AATGGAGAAAAAAGAAATAAAACGAAATTTGT 37 48 0 AAGAATAAAA 0.541387 -144 TAATATAGTTAGAGCAATAACATTACCCAGGC 38 35 0 AAGAATAACA 0.942701 -83 GGATTAATCAAAACCAATCACATATTGATTCG 42 33 0 AACAATCACA 0.911164 -259 CTAATTTTCAAAAGTAATCACAACAAGATTAT 42 265 0 AAGAATCACA 0.963414 -27 * ** ******* Masking position 6 Map Score: 5.29047 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 63 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 13 TAAAGTCATCGCTACACTACCACTACATTCCTT 3 23 0 GCACACTCAC 0.952291 -99 CATCTTTATTGCAATGCTTGCGCCTTTTTCCTG 8 60 1 GCATGCTCGC 0.961469 -54 CACATTTTACGCTACATTTGCGCATTAAAAATT 13 85 1 GCACATTCGC 0.955824 -140 TGAAGACTGGGCGAAATTGCCGCGCTTGTAAAT 13 125 0 GCAAATTCGC 0.715396 -100 TACTAAAGACGCCATATTGCCGCAGAGTCAGGG 14 162 1 GCATATTCGC 0.86453 -139 GGCACGTTTTCGCTCTGTGAAAT 16 1 1 GGACGTTCGC 0.841474 -232 ACTAAGTTTTGTGACGTTGTCACATTATGCATG 17 54 1 GTACGTTCAC 0.598943 -194 TCCACTGTATGAAAAGCTGGCACACCTGCCAAA 17 111 1 GAAAGCTCAC 0.618003 -137 AAGTTGCGCCGCTACACTATCACCAGATTGATT 21 71 1 GCACACTCAC 0.949537 -49 CAGGCATCCAGACACGCTACCGCCCCTGGCTTT 25 112 0 GAACGCTCGC 0.96147 -189 GGACAAGTGTGCCATAATCTCGCGGCCAGGCAT 33 43 0 GCATAATCGC 0.568579 -56 CTGCGAAGGGGCGACACTATAGCTACCCTGATG 35 61 1 GCACACTAGC 0.679852 -101 GAATATTCATGATATGCTACCACTTTGGGCCCT 35 123 0 GAATGCTCAC 0.751153 -39 TTAATCGACTGAAACGCTTCAGCTAGGATAAGC 36 148 0 GAACGCTAGC 0.728152 -137 AAAGCAAAACGCCACGTAAACACGTGGCGTTTT 39 26 0 GCACGTACAC 0.612294 -214 ** ***** *** Masking position 4 Map Score: 5.99076 Number of sites scoring better than the average of aligned sites = 1472 Number in coding regions = 1293 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 14 AAATGTCGTTGCGCGCACAGTACAGCGCAACTTATTT 5 27 0 GCGCAATGCG 0.771947 -50 CAATCTCACGTCTTGCAAAAACAGCCTGCGTTTTCAT 11 79 1 TCGCAAACCT 0.975435 -106 GCACCTCATTTCAAGCATAGAACACCTGTTAAAAACC 14 19 1 TCGCAAACCT 0.975435 -282 GCCCTTTTTATCCAGCATAAAATTCCGTTCAGAAGCG 14 112 0 TCGCAAACCG 0.984454 -189 CCTGTATGATGCAAGCAGACTAACCCTATCAACGTTG 15 169 1 GCGCAATCCT 0.927667 -45 GATGTACACATCATGCATAATGTGACAACGTCACAAA 17 61 0 TCGCAATACA 0.699343 -187 CTGAATGTCTTCCAGCACACATCGCCTGAAAGA 22 7 0 TCGCAAACCT 0.975435 -139 GACTGGTCTTTCAGGCATCCAGACACGCTACCGCCCC 25 119 0 TCGCACAACG 0.770893 -182 TTACACCGCATCCGGCATAAAAACACGCGCACTTTGC 29 30 1 TCGCAAAACG 0.946998 -168 CCCGCCGAAATCCTGCAAAGTCTGCCTGCAAGTCTGA 30 54 1 TCGCAATCCT 0.970944 -41 GCCGCGAGATTATGGCACACTTGTCCGGTTAACTCTC 33 50 1 TAGCAATCCG 0.807647 -49 ** *** * * *** Masking position 7 Map Score: 4.2919 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 184 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 15 AGTTAATTCCACTGTGAAAACGAATATTTATT 2 278 0 ATGTGAAACG 0.974262 -23 CCATCTCCTGAATGTGATAACGGTAACAAGTT 10 105 0 ATGTGAAACG 0.974262 -28 AGCCACTCCGATAACGGTAGATACAG 14 285 0 ATCCGAAACG 0.931729 -16 TACATTTCACAGAGCGAAAACGTGCC 16 5 0 AAGCGAAACG 0.969606 -228 CATCATGCATAATGTGACAACGTCACAAAACT 17 58 0 ATGTGAAACG 0.974262 -190 AAGGCAAGTGAAAGCGACAACGCCCGACGTCA 37 145 1 AAGCGAAACG 0.969606 -47 * ***** **** Masking position 7 Map Score: 2.42989 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 46 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802