AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_ecoli_reg_300.orf -o00260_ecoli_300.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 thrL 189 thr operon leader peptide #2 thrA 81 aspartokinase I, homoserine dehydrogenase I #3 lpdA 300 lipoamide dehydrogenase (NADH); component of 2-oxodehydrogenase and pyruvate complexes; L-protein of glycine cleavage complex #4 betI 128 probably transcriptional repressor of bet genes #5 lrp 300 regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system #6 ftsK 134 cell division protein #7 lolA 108 periplasmic protein effects translocation of lipoproteins from inner membrane to outer #8 serS 90 serine tRNA synthetase; also charges selenocystein tRNA with serine #9 ycaP 120 orf, hypothetical protein #10 serC 198 3-phosphoserine aminotransferase #11 solA 114 sarcosine oxidase-like protein #12 yceP 286 orf, hypothetical protein #13 dinI 73 damage-inducible protein I #14 pyrC 105 dihydro-orotase #15 yceB 133 orf, hypothetical protein #16 grxB 63 glutaredoxin 2 #17 yceL 205 orf, hypothetical protein #18 tynA 247 copper amine oxidase (tyramine oxidase) #19 maoC 284 putative aldehyde dehydrogenase #20 rspA 205 starvation sensing protein #21 b1582 134 orf, hypothetical protein #22 thrS 300 threonine tRNA synthetase #23 pabB 73 p-aminobenzoate synthetase, component I #24 sdaA 183 L-serine deaminase #25 purT 133 phosphoribosylglycinamide formyltransferase 2 #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 BIME96 27 BIME #31 b2097 184 orf, hypothetical protein #32 pdxB 98 erythronate-4-phosphate dehyrogenase #33 dsdX 217 transport system permease (serine?) #34 glyA 300 serine hydroxymethyltransferase #35 trxC 206 putative thioredoxin-like protein #36 yfiP 44 orf, hypothetical protein #37 yfiQ 31 orf, hypothetical protein #38 pssA 110 phosphatidylserine synthase; phospholipid synthesis #39 sdaC 300 probable serine transporter #40 sdaB 57 L-serine dehydratase (deaminase), L-SD2 #41 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #42 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #43 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #44 serA 255 D-3-phosphoglycerate dehydrogenase #45 rpiA 55 ribosephosphate isomerase, constitutive #46 yqfE 141 orf, hypothetical protein #47 yhaP 119 putative L-serine dehydratase #48 yhaQ 65 putative L-serine dehydratase #49 tdcE 33 probable formate acetyltransferase 3 #50 tdcC 21 anaerobically inducible L-threonine, L-serine permease #51 tdcB 98 threonine dehydratase, catabolic #52 tdcA 188 transcriptional activator of tdc operon #53 asd 192 aspartate-semialdehyde dehydrogenase #54 glyQ 300 glycine tRNA synthetase, alpha subunit #55 kbl 274 2-amino-3-ketobutyrate CoA ligase (glycine acetyltransferase) #56 htrL 288 involved in lipopolysaccharide biosynthesis #57 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #58 ilvD 95 dihydroxyacid dehydratase #59 trxA 76 thioredoxin 1 #60 rhoL 140 rho operon leader peptide #61 rho 84 transcription termination factor Rho; polarity suppressor #62 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #63 metB 276 cystathionine gamma-synthase #64 lysC 300 aspartokinase III, lysine sensitive #65 psd 96 phosphatidylserine decarboxylase; phospholipid synthesis #66 yjeQ 64 orf, hypothetical protein #67 serB 105 3-phosphoserine phosphatase Motif number 1 TCGTCTTTCAGGCCGCAGCGGCGTTAGCTTCAC 3 240 0 GGCGCACGCG 0.976811 -61 GAAAGACGACGGGTATGACCGCCGGAGATAAAT 3 264 1 GGGATGCGCC 0.419236 -37 CGCAGGCTGTGGCCACATCTCCCATTTAATTCG 8 51 1 GGCACACCCC 0.804435 -40 TCGGCATGGCGGCGGTGATAGCGCCTTTGAGAT 9 48 0 GGCGTGTGCG 0.781299 -73 TCACGAGGGCGCATTCGCGCCCTTTATTT 14 7 1 GGGGCATGCG 0.799683 -99 CGCGAATACAGGCTGCCGCGGCGGGTCAGGA 15 9 0 GGCGCCCGCG 0.746107 -125 AAAGGGGATTGCCTGCACCTGCCAGGTTGTTTG 18 140 0 GCCGCACGCC 0.914739 -108 GAATAGTTAAGCCAGTCGCCGCGTTCCCTCTTA 24 101 1 GCCGTCCGCG 0.859205 -83 GAGACTTATCGGCAACGACGCCGGTATGTTTCT 35 162 0 GGCACGCCCG 0.958759 -45 TTAAAACGGAGGAAGCGCCGCCCGAAAGCGGCG 40 20 0 GGAGCGCCCC 0.681305 -38 GTTGGGGACCGGGAGTGGCTCCGATGCTGGGTT 43 219 1 GGGGTGCCCG 0.857983 -82 TCTGACGGGGGAACCTCCCCCGTTAAAAAAA 44 9 1 GGGACCCCCC 0.627888 -247 AATGTTACCCGCCGACGGCTTCGGTATATGCAA 46 71 0 GCCACGCTCG 0.798878 -71 ACTGTTCGAAGGCGGTGACGTCGATTTTTTGCT 54 83 0 GGCGTGCTCG 0.89852 -218 CCTCATGTTAGCCAGCGCCTTCGGCATCCATGG 57 119 1 GCCGCGCTCG 0.948823 -182 ACTGGCGCCAGGCGGCACCAGCGGCCAGACGTT 57 252 0 GGCGCACGCG 0.986196 -49 TTTCATGTTCGGGTGCCCCGTCGCTAAAAACTG 60 16 1 GGGGCCCTCG 0.900677 -125 GCCTCTTCTGGCCTGCGCTAGCGCAGG 64 5 0 GCCGCGTGCG 0.883882 -296 ACACCTGAGGGGGTGCATCGCCGAGGTGATTGA 64 81 1 GGGGCACCCG 0.96355 -220 CTCTCCAAAGGCCAGCAGCGCCGC 66 51 1 GCCGCACCCG 0.960899 -14 *** *** * *** Masking position 12 Map Score: 17.8422 Number of sites scoring better than the average of aligned sites = 3060 Number in coding regions = 2940 Number in noncoding regions = 120 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 2 AAAGACGTTACGGGAAGGAGTAGGTATAGA 17 7 0 CGAAGATAGG 0.851002 -199 GCCAAACAACCTGGCAGGTGCAGGCAATCCCCTT 18 138 1 CGCAGTCAGG 0.827518 -110 ATACTGCGCGCGGAATTAATCAGGGGATATTCGT 25 109 1 CGATAACAGG 0.766036 -25 AGGTTATCCCCCTTAACAATCAGGAGTTTTT 26 27 1 CTAAAACAGG 0.849517 -21 AAAAACTCGCCCGTAACGACCAGGATT 31 168 1 CGAAGACAGG 0.990828 -17 GCGATGGTTCCTGAAACGTGCAGTGAATTGTGAA 41 93 0 CGAAGTCAGT 0.853347 -26 AAAAGCGCAGCTTAAAAGATCAGGGATTTGCGCT 46 117 1 CTAAGACAGG 0.9432 -25 GTGTATCAAAATGAAATGAACAGGATATGTGCGA 52 129 0 AGAAGACAGG 0.915119 -60 AGAAAGTCCGCGGCAATTATCAGGGAATTTGAGT 53 12 0 CGAATACAGG 0.943332 -181 TGGAAGCGTTATGCAAGGATCAGGCGGCAAAACG 54 35 1 AGAAGACAGG 0.915119 -266 GTTATACCTTCCGTAAAGAGCAGTTTGTCTGTTC 54 140 1 CGAAGACAGT 0.943245 -161 CAGTACGAAACGGGAAAAAGCAGGGCTTAACGCA 54 209 0 CGAAAACAGG 0.974531 -92 GTTAACACTTCTGCAAAATTCAGGATAAATAACG 55 182 0 CGAAATCAGG 0.930543 -93 CTGTATCGTTCCTGAAAAAACAGTTGCTGCCATT 57 55 0 CTAAAACAGT 0.475059 -246 AACACATCACCCGGAAAGACCAGGTTGAAGCGGC 57 154 1 CGAAGACAGG 0.990801 -147 CATAACATGCCAGCAAATTCCAGGAATTTTCCTA 62 93 0 CGAATTCAGG 0.853554 -147 * * ** ** **** Masking position 12 Map Score: 15.9058 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 331 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 3 CGTCGTCTTTCAGGCCGCAGCGGCGTTAGCTTC 3 242 0 CGGCGCAGCG 0.973074 -59 ACAACAGTACCAGGTTACCCCAGTACTGTTGCT 6 65 0 CGGTACCCCG 0.936144 -70 TTTTTTTTGCCGGGTCGCCCCGGCTTTTTTATT 12 21 1 CGGTGCCCCG 0.987593 -266 CCCGCGAATACAGGCTGCCGCGGCGGGTCAGGA 15 11 0 CGGCGCCGCG 0.992496 -123 CCTGTATTCGCGGGTTGCCGCCGTTTTCAGTTT 15 30 1 CGGTGCCGCG 0.991473 -104 GAGTTTATCGCTGGTGACACATGCTGCGTTGTG 15 74 1 CGGTACACAG 0.582988 -60 TTCACAGGGTCTGGTTGCGCAGGTATAGTAATA 17 54 0 CGGTGCGCAG 0.924175 -152 GCCAAACAACCTGGCAGGTGCAGGCAATCCCCT 18 138 1 CGGCGGTGCG 0.736726 -110 CGATTACCTTCAGGCTACGCAAGGCTTTGGAGA 34 153 0 CGGCACGCAG 0.668089 -148 ACCTATTACTCTGTCGGCGGCGGGTTTATTGTC 47 16 1 CGTCGCGGCG 0.695001 -104 CCGGAAAGACCAGGTTGAAGCGGCACTCGACAC 57 164 1 CGGTGAAGCG 0.670491 -137 TTACTGGCGCCAGGCGGCACCAGCGGCCAGACG 57 254 0 CGGCGCACCG 0.734663 -47 ATCTTAATGCCGCGCTGGCGATGTTAGGAAAAT 62 69 1 CCGCGGCGAG 0.630787 -171 CCAGAAGAGGCGCGTTGCCCAAGTAACGGTGTT 64 27 1 CCGTGCCCAG 0.846927 -274 GGATTCAGCCCCTGTAGCCGATGATGAACGTGG 64 122 0 CTGTGCCGAG 0.694764 -179 GAGCGGAAGACGGGTGGGCGCAGAGCGATACTT 64 231 0 CGGTGGCGCG 0.965558 -70 GTACAGACTCCTGGTCGCCCCTG 66 1 0 CGGTGCCCCG 0.987593 -64 * *** ***** * Masking position 13 Map Score: 15.2816 Number of sites scoring better than the average of aligned sites = 1680 Number in coding regions = 1614 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 ACCCAGGCATTGCGCGCCGTGAATCTTCAT 5 190 1 TGCGCGCCGT 0.965889 -111 TGTTCAGAGTCGCTACCCGTCACGATAGAC 5 227 0 CGCTACCCGT 0.842669 -74 AAAAAGCCGGGGCGACCCGGCAAAAAAAAT 12 20 0 GGCGACCCGG 0.947895 -267 AATTATTTCATGCTACCCGGCACATAGCCA 23 39 1 TGCTACCCGG 0.861357 -35 TGATTAATTCCGCGCGCAGTATAAACGAAA 25 101 0 CGCGCGCAGT 0.815058 -33 TCGGTTATACTGTTCGCCGTTGTCCAACAG 34 229 1 TGTTCGCCGT 0.600812 -72 GGGCACAAGATGCGCCCCGGTAAGA 36 6 0 TGCGCCCCGG 0.983689 -39 GGGCGCATCTTGTGCCCCGTTTTCTCCTCT 36 19 1 TGTGCCCCGT 0.902462 -26 TTGCGCGCCCCGGAAGAAGTCAG 39 4 1 CGCGCCCCGG 0.982579 -297 GTCGATTTTTTGCTCGCCGGTGTTATAACG 54 67 0 TGCTCGCCGG 0.907498 -234 AATGGGACGGTGCGTGCCGTCCCATTTTTT 58 15 0 TGCGTGCCGT 0.875219 -81 TTCATGTTCGGGTGCCCCGTCGCTAAAAAC 60 17 1 GGTGCCCCGT 0.896404 -124 ACTCACGCCGGGCGTCCAGTTTTTAGCGAC 60 35 0 GGCGTCCAGT 0.68187 -106 TAATTTCCAACGCTTCCCGTTTTATCTTAA 60 121 1 CGCTTCCCGT 0.804433 -20 CAGGGGCGACCAGGAGTCTGTACG 66 5 1 GGCGACCAGG 0.751712 -60 ********** Masking position 7 Map Score: 11.3085 Number of sites scoring better than the average of aligned sites = 1042 Number in coding regions = 966 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 CGTCGTCTTTCAGGCCGCAGCGGCGTTAGCTT 3 243 0 CAGGCGCAGG 0.980942 -58 TCTCTATGCTCCGGCTGAAGGGATGTTTTTGC 14 81 0 CCGGCGAAGG 0.985217 -25 CCCGCGAATACAGGCTGCCGCGGCGGGTCAGG 15 12 0 CAGGCGCCGG 0.932513 -122 CCTGACTAAACCGCCCACAGAGCGCGGTTGCT 18 195 1 CCGCCACAGG 0.888164 -53 ACCGGTCTCCCGCAGAAGTGACCGAATGAT 37 12 0 CCCGCGAAGG 0.961472 -20 CTGATCCTCTCCCGCAGAAGAGGAATAAAGCC 41 12 0 CCCGCGAAGG 0.961474 -107 GTGGTAAGTTCAGGCAAAAGAGAACGATTGCG 43 188 1 CAGGCAAAGG 0.921631 -113 AATAAACCCGCCGCCGACAGAGTAATAGGTTT 47 14 0 CCGCCACAGG 0.888164 -106 CATCGTGCGACAGGCCGAAGTGTTCTTCTTCG 47 48 0 CAGGCGAAGG 0.973304 -72 TTACGACCGTCCCGCTCACGAGGCT 48 4 0 CCCGCCACGG 0.722882 -62 CCGGAAAGACCAGGTTGAAGCGGCACTCGACA 57 164 1 CAGGTGAAGG 0.673527 -137 CTGGCGCCAGGCGGCACCAGCGGCCAGACGTT 57 252 0 GCGGCCCAGG 0.767784 -49 GGTGAAATGTCAGGCACCAGAGTAAACATTGT 63 230 0 CAGGCCCAGG 0.95249 -47 ACGTTCATCATCGGCTACAGGGGCTGAATCCC 64 124 1 TCGGCACAGG 0.648793 -177 CTACTATTTTCACCCAGAAGTGCTCCACCACT 64 197 0 CACCCGAAGG 0.781312 -104 ***** **** * Masking position 10 Map Score: 13.3324 Number of sites scoring better than the average of aligned sites = 1113 Number in coding regions = 1029 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 CACTGCGGACGCAAAACGTACCAGGAGGGTG 21 55 1 GCAAAACGTC 0.707327 -80 ACAGTTCATTGCGAAACCATCTAGCCAACAA 22 214 0 GCGAAACCAC 0.978533 -87 CCAGCGCTGCGCGAAGCGCGCAGATTACCCG 35 22 1 GCGAAGCGCC 0.964469 -185 CGAAATCATGGCGAACCGCGCGGACTTCGGG 35 49 0 GCGAACCGCC 0.936506 -158 CATACCACAGGCGAAACGATC 45 45 1 GCGAAACGAC 0.985367 -11 GTGAAGTGGAGCGGAACGACCTTACGACCGT 48 26 0 GCGGAACGAC 0.933527 -40 ATCAATGATAGCGAAGCCATCAGTAATGCGA 53 69 0 GCGAAGCCAC 0.957047 -124 CTATTCACATGCAAAACCAACATCCGCCATG 56 159 0 GCAAAACCAC 0.887386 -130 GAACGATACAGCGAAACCACCCTTACTGATA 57 78 1 GCGAAACCAC 0.978533 -223 TCCACCACTTGCGAAACGCCCGACTGCGAAC 64 175 0 GCGAAACGCC 0.982315 -126 ********* * Masking position 5 Map Score: 9.19358 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 147 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TTCTGAACTGGTTACCTGCCGTGAGTAAAT 1 81 1 GTTACCTGCC 0.584767 -109 GAAAAAAGCCCGCACCTGACAGTGCGGGCT 2 28 1 CGCACCTGAC 0.929754 -54 AAATCGTAGCTTCCTGTTGTCATT 13 5 1 CGTAGCTTCC 0.835614 -69 GAAAAGCTGGCACACCTGCCAAACAACCTG 18 121 1 CACACCTGCC 0.920094 -127 GGGGATTGCCTGCACCTGCCAGGTTGTTTG 18 140 0 TGCACCTGCC 0.839488 -108 ACATTAACCTCTCACCTTCCACCCGGTTGA 22 146 0 CTCACCTTCC 0.941837 -155 CGCACCTGCCATTTAACAAG 28 1 1 CGCACCTGCC 0.984639 -28 ATTGTCATCGCGTACCTTACATTACCTGTC 31 27 0 CGTACCTTAC 0.83798 -158 ATCTCACCTTCCCCTGTGATTA 33 206 0 CTCACCTTCC 0.941837 -12 TTTACGGTCAGGCACCTTCCCGGGCTGAAC 39 239 1 GGCACCTTCC 0.932684 -62 TCGAAACGTCCGTACCTTACGATTTCCACT 47 80 1 CGTACCTTAC 0.83798 -40 CCGCGCATTTCATAGCTTCCCTGGAACTGT 54 111 0 CATAGCTTCC 0.467781 -190 TGGGACGGCACGCACCGTCCCATTTACGAG 58 21 1 CGCACCGTCC 0.911593 -75 ********** Masking position 4 Map Score: 9.22524 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 537 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 8 TCAGGTGCGGGCTTTTTTCTGTGTTTCCTG 2 17 0 GCTTTTTTCT 0.880312 -65 GACAGTGCGGGCTTTTTTTTTCGACCAAAG 2 45 1 GCTTTTTTTT 0.871394 -37 GCTTTTTTCTGGTAATCTCA 3 1 1 GCTTTTTTCT 0.880312 -300 CAAATCGGTTGCCGTTTGTTGTTTAAAAAT 3 60 1 GCCGTTTGTT 0.525646 -241 AAAAACATCGGCTTTTTGCTAATAATCCGA 10 15 1 GCTTTTTGCT 0.782516 -184 GGTCGCCCCGGCTTTTTTATTTTACTTACG 12 33 1 GCTTTTTTAT 0.703468 -254 TGAATGACATGCTGTTTTATTGTTCATATA 12 124 1 GCTGTTTTAT 0.514398 -163 GAGGTTCAATGCGTTTTTATCTGAAGCAAC 12 229 0 GCGTTTTTAT 0.73704 -58 AGTCCAAAATGCCATTTTCTGCATTATTCA 17 88 1 GCCATTTTCT 0.65635 -118 GCAAATATACGCCTTTTTTTGTGATCACTC 20 99 1 GCCTTTTTTT 0.835337 -107 GATCACTCCGGCTTTTTTCGATCTTTATAC 20 121 1 GCTTTTTTCG 0.763335 -85 TGTTCTTTAAGCGTTTTGCTGGTGTACTCA 22 42 1 GCGTTTTGCT 0.809561 -259 TAGTTAAATCGCGGTTTTTGATTAGTTTAA 24 64 1 GCGGTTTTTG 0.610524 -120 CTATCGGGAGGCCGTTTTTTTGCCTTTCAC 29 77 1 GCCGTTTTTT 0.693743 -121 TGTTTTTTCAGCGTTTTCTGTTGGCTCGAT 31 126 0 GCGTTTTCTG 0.420174 -59 AAATTTTGCCGCTATTTTTTTACACTTAAG 33 28 0 GCTATTTTTT 0.701495 -190 ACATTGCAGGGCTATTTTTTATAAGATGCA 34 25 0 GCTATTTTTT 0.701495 -276 TTATTCTGTCGCGATTTTTGCATTTTTTAA 43 106 1 GCGATTTTTG 0.549057 -195 ATCGCTTTTTTTGTATATAATGC 45 4 1 GCTTTTTTTG 0.748193 -52 CCTGGTAAATGCTTTTTCCTGCACTATGAC 46 25 1 GCTTTTTCCT 0.602898 -117 AAGCGTTTTTTTCCTGCAAAGA 53 181 0 GCGTTTTTTT 0.888955 -12 GACGCGGATGGCCATTTTTTGCATCTTTCC 54 178 1 GCCATTTTTT 0.637613 -123 TTAGTGGGTAGCGTTTTGATACCAACTGAG 55 22 1 GCGTTTTGAT 0.578261 -253 TGTTTACGTGGCGTTTTGCTTTTATATCTG 62 37 1 GCGTTTTGCT 0.809561 -203 ********** Masking position 5 Map Score: 12.8303 Number of sites scoring better than the average of aligned sites = 809 Number in coding regions = 613 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 198 Fraction of orfs with sites within 600 bp upstream = 0.0318021 Motif number 9 CCCGCGGTCAATCGATTGCGACCACAGGTA 10 150 0 ATCGATTGCG 0.882534 -49 TGCAAAGGAAAACGTTTCCGCTTATCCTTT 14 44 1 AACGTTTCCG 0.763526 -62 GTTTCCGCTTATCCTTTGTGTCCGGCAAAA 14 57 1 ATCCTTTGTG 0.591415 -49 TCGTTAAAAGATCCTTTGCTTTTTATGATT 19 216 1 ATCCTTTGCT 0.73417 -69 ATTCTACACCATCCACTGCGGACGCAAAAC 21 42 1 ATCCACTGCG 0.742626 -93 AGGGAGATTGTACCTTTCCGTTTCACATTG 22 96 0 TACCTTTCCG 0.555606 -205 TATAAACGAAAACGTTTGCGTGTGTCTTTA 25 82 0 AACGTTTGCG 0.947291 -52 ACCTTTTAAATACCTTTGCGGTGAAAACTT 31 70 1 TACCTTTGCG 0.874359 -115 CCTGAAGGTAATCGTTTGCGTAAATTCCTT 34 172 1 ATCGTTTGCG 0.947291 -129 GGCAAAAGAGAACGATTGCGTTGGGGACCG 43 200 1 AACGATTGCG 0.882534 -101 ATCCAAGAATTACCTTTGCGTGATATTTCC 44 130 1 TACCTTTGCG 0.874359 -126 CGGCAATATGAACGTTTGCGTCGCGATGTT 44 162 0 AACGTTTGCG 0.947291 -94 TTGATCCTCTGCGTTCGTTGAAT 54 4 1 ATCCTCTGCG 0.873453 -297 GCTACCTTGTATCCATTGCTTCTGGCAACA 67 40 0 ATCCATTGCT 0.535865 -66 ********** Masking position 7 Map Score: 7.45548 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 327 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 10 CTGAACAGTGATGTTTCAGGGTCAGACAGG 5 250 1 ATGTTTCAGG 0.662335 -51 CGCTTATCCTTTGTGTCCGGCAAAAACATC 14 62 1 TTGTGTCCGG 0.731117 -44 ACATGCTGCGTTGTGTCAGGATATTGACGC 15 92 1 TTGTGTCAGG 0.955439 -42 TGTGTACATCTATTTTCAGGGCATCCACTG 18 88 1 TATTTTCAGG 0.592911 -160 CTGTGGGCGGTTTAGTCAGGTTCACATTAT 18 185 0 TTTAGTCAGG 0.768299 -63 ATAGAATACCTTTTGTCAGCTGACACTTCC 20 43 0 TTTTGTCAGC 0.672974 -163 ACATAGCCAGTAGAGTCAGGACTG 23 60 1 TAGAGTCAGG 0.544351 -14 AGTCCAGTCACCTTGTCAGGAGTATTATC 24 165 1 CCTTGTCAGG 0.719599 -19 CTTTTGGATGTTTTTTCAGCGTTTTCTGTT 31 134 0 TTTTTTCAGC 0.500811 -51 GAAACGGATTTCTTTTCAGGTTTGTGATGC 34 105 0 TCTTTTCAGG 0.811688 -196 TTATTGTTAGCTGAGTCAGGAGATGCGG 34 283 1 CTGAGTCAGG 0.60749 -18 AATTCACTGCACGTTTCAGGAACCATCGCT 41 98 1 ACGTTTCAGG 0.565338 -21 TGACACAATTTTGTGTCAGGTTGCATATAC 46 51 1 TTGTGTCAGG 0.955439 -91 GCAGCAACTGTTTTTTCAGGAACGATACAG 57 59 1 TTTTTTCAGG 0.866676 -242 AACTACCTCGTGTCAGGGGATCCATTT 64 284 0 TCGTGTCAGG 0.934284 -17 ATCGTCCCCTTTTTTTCAGGATCCGGCATG 65 34 1 TTTTTTCAGG 0.866676 -63 ********** Masking position 6 Map Score: 7.08569 Number of sites scoring better than the average of aligned sites = 265 Number in coding regions = 190 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 11 GAAGGGATGTTTTTGCCGGACACAAAGGATA 14 66 0 TTTTGCGGAC 0.832164 -40 AAAACATCCCTTCAGCCGGAGCATAGAGATT 14 84 1 TTCAGCGGAG 0.957796 -22 TTTCAGTTTTTTCTGCTGGCGAGTTTATCGC 15 54 1 TTCTGCGGCG 0.922375 -80 TCTTTAAGCGTTTTGCTGGTGTACTCACTAC 22 45 1 TTTTGCGGTG 0.856613 -256 GCGCCAACAATTTAGCAGGAGTTAACA 23 7 0 TTTAGCGGAG 0.94417 -67 ATTCGGTCACTTCTGCGGGAGACCGGT 37 15 1 TTCTGCGGAG 0.982752 -17 CTATTTCTCCTGGAGGAATGCAAAT 39 286 0 TTCTCCGGAG 0.938407 -15 TTTATTCCTCTTCTGCGGGAGAGGATCAGGG 41 15 1 TTCTGCGGAG 0.982752 -104 GGAAAAAGCATTTACCAGGAGCAGACAACAG 46 13 0 TTTACCGGAG 0.818909 -129 TTATCCTGAATTTTGCAGAAGTGTTAACGCG 55 188 1 TTTTGCGAAG 0.769869 -87 CTTCGAACGATTTTACAGGAGCCTTA 67 90 1 TTTTACGGAG 0.806287 -16 ****** **** Masking position 2 Map Score: 7.95511 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 221 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 12 AGTGACTGGGGTGAGGGCGTGAAGCTAACGC 3 222 1 GTGAGGGGTG 0.939438 -79 TCAGTTTTTTCTGCTGGCGAGTTTATCGCTG 15 56 1 CTGCTGGGAG 0.929757 -78 TTTTTACCTGAGGGGGAGGTTATCCCCC 26 8 1 CTGAGGGGAG 0.988303 -40 TCGGTCACTTCTGCGGGAGACCGGT 37 17 1 CTGCGGGGAC 0.951498 -15 TATTCCTCTTCTGCGGGAGAGGATCAGGGTG 41 17 1 CTGCGGGGAG 0.990295 -102 TACGAAGAGAGTGAGGGTGAGGCATAAATTT 41 52 0 GTGAGGGGAG 0.97272 -67 GTGATAACACCTGAGGGGGTGCATCGCCGAG 64 75 1 CTGAGGGGTG 0.973518 -226 ******* *** Masking position 2 Map Score: 4.65958 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 68 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 13 ATAGCAGCTTCTGAACTGGTTACCTGCCGTG 1 73 1 CGAACTGGTT 0.803499 -117 CCGCTGATGAATGGAGTGGCGAAA 4 115 1 AGGAGTGGCG 0.657226 -14 CACGGAACAGGTGCAAAATCGGC 6 3 1 CGAACAGGTG 0.821946 -132 CATACAGCAACAGTACTGGGGTAACCTGGTA 6 60 1 CGTACTGGGG 0.751577 -75 AACTCCCGATCGGGAGTGACGTAATTTGAGG 7 84 1 CGGAGTGACG 0.850977 -25 AATATTGTCCCCGAAGTGATGGGAAAAGTCT 17 163 1 CGAAGTGATG 0.617587 -43 TTCACATTATCAGTACTGATGCAAAGGGGAT 18 164 0 CGTACTGATG 0.64062 -84 ACCACTTAATCGGGACTGGTGTTATTATTGC 38 31 1 CGGACTGGTG 0.96774 -80 CCTTCCCGGGCTGAACTGGCTAAAAGCTGAA 39 253 1 CGAACTGGCT 0.883748 -48 CGTTGGGGACCGGGAGTGGCTCCGATGCTGG 43 218 1 CGGAGTGGCT 0.890895 -83 AATTTTTGCACAGGACTGGTGGGTTTGGAAC 62 148 1 CGGACTGGTG 0.967741 -92 GCATAGTTTACCGTACAGGCGTTACCGTGAC 63 84 1 CGTACAGGCG 0.842513 -193 TAGCGCAGGCCAGAAGAGGCGCGTTGCCCAA 64 18 1 CGAAGAGGCG 0.828964 -283 GGTGTTATCACAGGACTGGCTCCTCCAACAC 64 55 0 CGGACTGGCT 0.935312 -246 * ********* Masking position 5 Map Score: 6.39293 Number of sites scoring better than the average of aligned sites = 1150 Number in coding regions = 1092 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 14 CACAGAGACATATTGCCCGTTGCAGTCAGAATGAA 1 16 0 TATTCCCGTG 0.86876 -174 ACTCTGTAATTTTTATCTGTCTGTGCGCTATGCCT 1 154 0 TTTTTCTGTG 0.635101 -36 CTTTTTTCTGTGTTTCCTGTACGCG 2 1 0 TGTTCCTGTG 0.926575 -81 GTAAATACCATGTTTACCGTGCTAGTGAAATCTAC 5 87 1 TGTTACCGTG 0.907646 -214 AACCTGGTACTGTTGTCCGTTTTAGCATCGGGCAG 6 82 1 TGTTTCCGTG 0.949329 -53 AGGAATAATGTATTACCTGTGGTCGCAATCGATTG 10 137 1 TATTCCTGTG 0.735851 -62 CCGTTTTCAGTTTTTTCTGCTGGCGAGTTTATCGC 15 50 1 TTTTTCTGCG 0.653749 -84 AGTGCATTAATGTTTTCCGCAGTTGCTATACAGAT 19 166 1 TGTTTCCGCG 0.953105 -119 GGGGTGGTGTTGTTCGTATAAGGCGTA 30 6 0 TGTTTTCGTG 0.514584 -22 CGCGGTCAAGTTTTCACCGCAAAGGTATTTAAAAG 31 72 0 TTTTACCGCG 0.701803 -113 GTTTGTGTTACCTGTATGAGACGAGAGTTA 32 79 0 TGTTCCTGTG 0.926575 -20 CTGGTGTTATTATTGCCCGCTTATGTCGTCTGCAT 38 46 1 TATTCCCGCG 0.877765 -65 TGCTGTTGTCTGCTCCTGGTAAATGCTT 46 4 1 TGTTTCTGCG 0.89532 -138 CGGATACAAATGTTACCCGCCGACGGCTTCGGTAT 46 77 0 TGTTCCCGCG 0.970176 -65 AAACCCGCATAGTTTACCGTACAGGCGTTACCGTG 63 78 1 AGTTACCGTG 0.473597 -199 **** ***** * Masking position 4 Map Score: 6.22471 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 344 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 15 AACAGTTCATCGGCATGGCGGCGGTGATAG 9 60 0 CGGCATGGCG 0.647488 -61 CCTGTATTCGCGGGTTGCCGCCGTTTTCAG 15 30 1 CGGGTTGCCG 0.931731 -104 GCTTCCCTATCGGGAGGCCGTTTTTTTGCC 29 71 1 CGGGAGGCCG 0.95674 -127 GTCACTTCTGCGGGAGACCGGT 37 20 1 CGGGAGACCG 0.87262 -12 CGACATCGTGCGACAGGCCGAAGTGTTCTT 47 53 0 CGACAGGCCG 0.855426 -67 ACCCTCGGATTGCCGTTCAGTGAAG 48 51 0 CGGATTGCCG 0.880731 -15 TCTTTTGACGCGGATGGCCATTTTTTGCAT 54 172 1 CGGATGGCCA 0.87151 -129 AACTTGAGAACGTCTGGCCGCTGGTGCCGC 57 244 1 CGTCTGGCCG 0.916087 -57 GGTGATTGAACGGCTGGCCACGTTCATCAT 64 105 1 CGGCTGGCCA 0.949903 -196 GAGCGGAAGACGGGTGGGCGCAGAGCGATA 64 234 0 CGGGTGGGCG 0.968742 -67 ********** Masking position 9 Map Score: 6.47939 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 305 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419