AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iphoB_ecoli_bsub_100.orf -g0.5 -x5 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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 phoE 287 outer membrane pore protein E (E,Ic,NmpAB) #2 yaiB 300 orf, hypothetical protein #3 phoA 31 alkaline phosphatase #4 psiF 100 induced by phosphate starvation #5 phoB 189 positive response regulator for pho regulon, sensor is PhoR (or CreC) #6 phoR 57 positive and negative sensor protein for pho regulon #7 phoH 300 PhoB-dependent, ATP-binding pho regulon component; may be helicase; induced by P starvation #8 ugpA 97 sn-glycerol 3-phosphate transport system, integral membrane protein #9 ugpB 300 sn-glycerol 3-phosphate transport system; periplasmic binding protein #10 pstB 182 ATP-binding component of high-affinity phosphate-specific transport system #11 pstC 86 high-affinity phosphate-specific transport system, cytoplasmic membrane component #12 pstS 300 high-affinity phosphate-specific transport system; periplasmic phosphate-binding protein #13 phnQ 125 orf, hypothetical protein #14 phnL 110 ATP-binding component of phosphonate transport #15 phnE 54 membrane channel protein component of Pn transporter #16 phnD 24 periplasmic binding protein component of Pn transporter #17 phnC 132 ATP-binding component of phosphonate transport #18 glpQ 98 glycerophosphoryl diester phosphodiesterase #19 glpT 296 glycerol-3-phosphate permease #20 yczA 300 yczA #21 ycbL 96 similar to two-component response regulator [YcbM] #22 yclJ 212 similar to two-component response regulator [YclK] #23 phoB 300 alkaline phosphatase III #24 yesO 148 similar to sugar-binding protein #25 phoA 300 alkaline phosphatase A #26 yhdW 233 similar to glycerophosphodiester phosphodiesterase #27 ykoG 300 similar to two-component response regulator [YkoH] #28 resD 80 two-component response regulator #29 resC 135 essential protein similar to cytochrome c biogenesis protein #30 yqgH 68 alternate gene name: yzmC; similar to phosphate ABC transporter (permease) #31 yqgG 153 alternate gene name: yzmB; similar to phosphate ABC transporter (binding protein) #32 yrkP 267 similar to two-component response regulator [YrkQ] #33 araP 35 integral membrane protein #34 araN 30 sugar-binding protein #35 araA 207 L-arabinose isomerase #36 phoP 211 two-component response regulator #37 msmR 217 transcriptional regulator (LacI family) #38 msmE 33 multiple sugar-binding protein #39 yurJ 181 similar to multiple sugar ABC transporter (ATP-binding protein) #40 yurN 57 similar to sugar permease #41 yurO 80 similar to multiple sugar-binding protein #42 yurP 215 similar to opine catabolism #43 yvrI 300 yvrI #44 yvcP 300 similar to two-component response regulator [YvcQ] #45 ywnF 242 ywnF #46 msmX 120 multiple sugar-binding transport ATP-binding protein #47 yxdL 143 similar to ABC transporter (ATP-binding protein) #48 yxdJ 108 similar to two-component response regulator [YxdK] #49 yycF 300 similar to two-component response regulator [YycG] Motif number 1 CTGATTGTAGGCATGATAAGACGCGCAAGCGT 7 10 0 GCATGATGCG 0.825108 -291 GGTTTGGTAGGCTGGATAAGGCGTTCACGCCGC 7 47 1 GCTGGATGCG 0.9842 -254 GTGCACGATCGCCGGATGCGGCGTGAACGCCTT 7 64 0 GCCGGATGCG 0.998506 -237 TCGCGTGTAGGCCGGATAAGCGAAGCGCATCCG 8 52 1 GCCGGATGGA 0.924661 -46 GATCTTGTAGGCCTGATAAGGCGTTTACGCCGC 9 33 1 GCCTGATGCG 0.98892 -268 ATCGTTTCATGCCGGATGCGGCGTAAACGCCTT 9 50 0 GCCGGATGCG 0.998506 -251 TTAACACTTTGCCGGATGCGGCGTGAACGCCTG 10 99 1 GCCGGATGCG 0.998506 -84 CTTACCGTAGGCCGGATCAGGCGTTCACGCCGC 10 116 0 GCCGGATGCG 0.998506 -67 CCTACGGTAAGCCTGATTAGCGAAGTGCATCAG 10 138 1 GCCTGATGGA 0.621093 -45 ATTTTGTAATGCCGGATGCGGCGTAAAACACCG 11 30 0 GCCGGATGCG 0.998506 -57 GCCGGTGCCGGATGCGGCGTAAACGCCTT 14 7 1 GCCGGATGCG 0.998506 -104 GCATTTGTAGGCCGGATAAGGCGTTTACGCCGC 14 24 0 GCCGGATGCG 0.998506 -87 CTCCCCGTAGGTCGGATAAGACGCGTCAGCGTC 14 58 1 GTCGGATGCG 0.993972 -53 TGGTTCGGGTGTCGGATGCGACGCTGACGCGTC 14 77 0 GTCGGATGCG 0.993972 -34 ATCGTAGGTCGGATAAGACGCCCCGGCGTC 15 8 1 GTCGGATGCG 0.993972 -47 CCTGCACATTGTCGGATGCGACGCCGGGGCGTC 15 27 0 GTCGGATGCG 0.993972 -28 TGCTGTTTGTGCTGGATGTGTGGCGTGCCTCCT 19 257 0 GCTGGATGGG 0.928984 -40 TTTTAAAGCGTTCGGATAGGGCGAAACACTCAA 24 45 0 TTCGGATGCG 0.885083 -104 ******* * ** Masking position 7 Map Score: 61.8002 Number of sites scoring better than the average of aligned sites = 658 Number in coding regions = 223 Number in noncoding regions = 435 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 TTATCCGTGCCCCATCTCCCATTTTCCCTCAC 9 127 1 CCCATCCCCT 0.960717 -174 TCTCCCATTTTCCCTCACCCACGCCGTCACCG 9 141 1 TCCCTCCCCC 0.83387 -160 ACACGGTTTTCCCCTCACCCTAACCCTCTCCC 10 19 1 CCCCTCCCCA 0.995661 -164 CCTCACCCTAACCCTCTCCCCAGAGGGGCGAG 10 31 1 ACCCTCCCCA 0.986451 -152 CTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAG 10 44 0 CCCCTCCCCT 0.995198 -139 GCGCGCTGGCCCCCTCACCCTAACCCTCTCCC 13 24 1 CCCCTCCCCA 0.995661 -102 CCTCACCCTAACCCTCTCCCCAGAGGGGCGAG 13 36 1 ACCCTCCCCA 0.986451 -90 CACAATCGGTCCCCTCGCCCCTCTGGGGAGAG 13 49 0 CCCCTCCCCT 0.995198 -77 GCTCGTTTTCTCCCTCTCCCCATTGGGGTGAG 13 99 1 TCCCTCCCCA 0.963838 -27 CGCCCCTCACCCCAATGGGGAGAG 13 112 0 CCCCTCCCCA 0.995661 -14 TGTGGCGTGCCTCCTTTCCCGAAAAACAAAAA 19 240 0 CTCCTTCCCA 0.858501 -57 GTGTGAACCGATCCTCCCCTGATGCCGAATGG 20 27 1 ATCCTCCCTA 0.756032 -274 GTACCGCGAGACCCTCGTCCTTTGCATAGGAC 20 189 1 ACCCTCTCCT 0.733386 -112 TGCGCTGCATCTCCTCACCTAACCTTTACAAA 21 73 0 CTCCTCCCTA 0.907129 -24 ATTTGACCATCCTCTCCCGTCCCTATATGA 27 281 0 ATCCTCCCCT 0.95714 -20 ATCAATACTCCTTTCCCATTTATCACGGC 32 8 1 CTCCTTCCCT 0.845649 -260 CCCATCACCCTTCCTTATTCGC 37 1 1 CCCATCCCCT 0.960717 -217 GGGTATCTCATCTCCTTTATAAAAAGAA 40 40 0 CTCATCCCTT 0.51003 -18 ATAATCCTCCCCCTTTATTTGATGT 45 228 0 ATCCTCCCCT 0.95714 -15 ATTGAAACCTCCCCTCACCGGAGTGCGTCTTT 49 59 0 CCCCTCCCGA 0.944033 -242 ****** *** * Masking position 5 Map Score: 42.4407 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 84 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 AATTAAGAGAAAAAAACTCACCGCATGGCCA 2 46 0 AAAAAACTCC 0.876839 -255 CTAACAGCAAAAAAACCACCCGGCAGCGAAA 4 31 0 AAAAACCACC 0.700015 -70 TGTAGGCATGATAAGACGCGCAAGCGT 7 7 0 ATAAGACGCC 0.896468 -294 CCCCGCGAGCATAAAACGCGTGAATTCGCGC 9 254 1 ATAAAACGCT 0.814497 -47 CGTAGGTCGGATAAGACGCGTCAGCGTCGCA 14 63 1 ATAAGACGCT 0.621119 -48 CGTAGGTCGGATAAGACGCCCCGGCGTCGCA 15 13 1 ATAAGACGCC 0.896468 -42 AAAAAGAGCCAGAAAACACCCCTTGTCAAAA 19 214 0 AGAAAACACC 0.764595 -83 TAAGAAACACAAAAAACCCCCGTCCTATGCA 20 211 0 AAAAAACCCC 0.856815 -90 TTTTTATAAAACACACACGTTTTTCA 21 6 1 ATAAAACACC 0.913463 -91 TTACAAAATCAAAAAACACACACGTAATTAC 21 49 0 AAAAAACACC 0.962422 -48 TAAGGAAATGAAAAAACGCTTTTCGTTATCT 25 194 0 AAAAAACGCT 0.914187 -107 TATAACTAAAAAAAGACACTCAGCGTATCAG 26 96 0 AAAAGACACC 0.905325 -138 GATATGGCAGAAAAAATTCACCAGTTTGTAT 26 152 1 AAAAAATTCC 0.429435 -82 TAAGCGCACAAAAAAATACACCATTCGGTCA 27 74 1 AAAAAATACC 0.730283 -227 TAAAGCGCGGAAGAAACGCGCTTTGATCCCT 27 147 0 AAGAAACGCC 0.836782 -154 AAAAAACGCTCACATGATGTG 31 1 1 AAAAAACGCC 0.982539 -153 TTTTGTATAAAAAAAACGCCCACATCATGTG 31 21 0 AAAAAACGCC 0.982539 -133 TTTTTATACAAAAAAACGCACTGATTTACAA 31 39 1 AAAAAACGCC 0.982539 -115 TTCTCATAAAATAAAACGCTTTCAAATACAA 35 174 0 ATAAAACGCT 0.814497 -34 TCTATATGCGAAAAAATGCCCAAATCAAAAG 42 63 0 AAAAAATGCC 0.856087 -153 ACACCGCACAAAAAAACACGCCATCTCGGCG 48 24 0 AAAAAACACC 0.962422 -85 AGGTTTAGAAAAAAAACACATGTTTCACCTT 49 150 0 AAAAAACACT 0.829029 -151 ********* * Masking position 4 Map Score: 26.0247 Number of sites scoring better than the average of aligned sites = 481 Number in coding regions = 325 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 4 GCGCGTCTTATCATGCCTACAATCAGTGCG 7 17 1 TCATGCCTAC 0.947695 -284 GAACGCCTTATCCAGCCTACCAAACCCGCA 7 43 0 TCCAGCCTAC 0.956957 -258 GCTTCGCTTATCCGGCCTACACGCGATGCC 8 48 0 TCCGGCCTAC 0.995609 -50 AAACGCCTTATCAGGCCTACAAGATCGTGC 9 29 0 TCAGGCCTAC 0.9865 -272 AGAGTTTGATTCAGACCTTCTATATTTTCC 9 94 1 TCAGACCTTC 0.78345 -207 GAACGCCTGATCCGGCCTACGGTAAGCCTG 10 123 1 TCCGGCCTAC 0.995609 -60 ACTTCGCTAATCAGGCTTACCGTAGGCCGG 10 134 0 TCAGGCTTAC 0.910418 -49 TAATCAAACATCCTGCCAACTCCATGTGAC 12 47 1 TCCTGCCAAC 0.866784 -254 AAACGCCTTATCCGGCCTACAAATGCGCTC 14 31 1 TCCGGCCTAC 0.995609 -80 ACGCGTCTTATCCGACCTACGGGGAGCGCA 14 54 0 TCCGACCTAC 0.980416 -57 GGGCGTCTTATCCGACCTACGAT 15 4 0 TCCGACCTAC 0.980416 -51 TGTCGGAATGTCCTGCTTTCGCTAAAATAA 36 118 1 TCCTGCTTTC 0.636199 -94 ********** Masking position 1 Map Score: 20.2676 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 102 Number in noncoding regions = 364 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 5 GCCACTTTTTTAGGGAGGCTGCATC 17 118 1 TAGGGAGGCT 0.695162 -15 TGCTTATCTATAAGGAGGAGAAATC 18 84 1 TAAGGAGGAG 0.955535 -15 GTTTTTCGGGAAAGGAGGCACGCCACACAT 19 245 1 AAAGGAGGCA 0.730748 -52 CACAAACAGCAAAGGGGGATAATTATTA 19 279 1 AAAGGGGGAT 0.946121 -18 CCTCTCTTGGTAACGGGGAGAGAAACCCGG 20 97 0 TAACGGGGAG 0.78831 -204 CCCCGTTACCAAGAGAGGAGTATCGAAACA 20 109 1 AAGAGAGGAG 0.644558 -192 CGTCCTATGCAAAGGACGAGGGTCTCGCGG 20 192 0 AAAGGACGAG 0.716518 -109 TGTGTTTCTTAAAGGAGGTGACGGCCAATG 20 231 1 AAAGGAGGTG 0.783313 -70 GATGAGTTAGAAAGGAGGATATCAA 20 286 1 AAAGGAGGAT 0.949508 -15 ACTTACATTAAAGGGGGGATTGGTTTGAAG 24 90 1 AAGGGGGGAT 0.895727 -59 TAATAGCAAAAAAGGAGGCGAGATC 26 6 0 AAAGGAGGCG 0.958961 -228 TCTTAATAAAAAGAGGAGTGCGGGGACA 30 9 1 AAAAGAGGAG 0.787547 -60 CAAAAAGTGAAAGCGGGGAGGTTCTC 33 20 1 AAGCGGGGAG 0.79233 -16 ATTTTATGAGAAAGGGGCAGTTTAC 35 193 1 AAAGGGGCAG 0.702401 -15 ATCACGATGATAAGGAGGAAAAG 38 21 1 TAAGGAGGAA 0.713951 -13 TAATAGGTTAAAAGGAGGCTACCCT 39 6 0 AAAGGAGGCT 0.907092 -176 TATATAATAAAAACGAGGAGTGAAGGAT 42 198 1 AAACGAGGAG 0.893073 -18 TTTAATTTAGTAGGGAGGCGGT 43 289 1 TAGGGAGGCG 0.845152 -12 GATGTACATATAAGGGGGATCAAC 44 287 1 TAAGGGGGAT 0.89344 -14 AACATCAAATAAAGGGGGAGGATTAT 45 227 1 AAAGGGGGAG 0.976759 -16 TTACAATAACAAAGGGGGATGTTAG 46 106 1 AAAGGGGGAT 0.946121 -15 AATAAAACCATAAGGAGGATTTTC 47 130 1 TAAGGAGGAT 0.899787 -14 ********** Masking position 2 Map Score: 24.8414 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 96 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 GCCTAGCGGCAGTTGTTTACGCTTTTATTACA 1 129 1 AGTGTTACGC 0.912163 -159 AGGCTGGATAAGGCGTTCACGCCGCATCCGGC 7 55 1 AGGGTTACGC 0.99247 -246 AGGCCTGATAAGGCGTTTACGCCGCATCCGGC 9 41 1 AGGGTTACGC 0.99247 -260 AAAGATGACAAGGCGGTGACGGCGTGGGTGAG 9 154 0 AGGGGTACGG 0.988125 -147 AGGCCGGATCAGGCGTTCACGCCGCATCCGGC 10 109 0 AGGGTTACGC 0.99247 -74 AGGCCGGATAAGGCGTTTACGCCGCATCCGGC 14 17 0 AGGGTTACGC 0.99247 -94 CTAACAGATGAAGAGTTAACGGGAATTCGATG 17 41 0 AAGGTTACGG 0.922074 -92 AACGGATAGTAGGCGATGCCGGGTTTCTCTCC 20 79 1 AGGGATCCGG 0.859547 -222 CTGTTAATAAAGGTGGTACCGCGAGACCCTCG 20 174 1 AGGGGTCCGC 0.98208 -127 TGTTTCTTAAAGGAGGTGACGGCCAATGTACG 20 233 1 AGGGGTACGG 0.988125 -68 CCTCGAATGGAAGGGGTAACGCAG 34 17 1 AAGGGTACGC 0.956519 -14 *** *** **** Masking position 1 Map Score: 17.7984 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 103 Number in noncoding regions = 167 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 7 ATCGCCGGATGCGGCGTGAACGCCTTATCCAGCC 7 56 0 GCGCGACGCC 0.995316 -245 CTTCGCTTATCCGGCCTACACGCGATGCCAGGTC 8 43 0 CCGCCCCGCG 0.851089 -55 CATGCCGGATGCGGCGTAAACGCCTTATCAGGCC 9 42 0 GCGCGACGCC 0.995316 -259 TCCCTCACCCACGCCGTCACCGCCTTGTCATCTT 9 151 1 ACGCGACGCC 0.964136 -150 CCCCAGAGGGGCGAGGGGACCGACCGAGCGCCTT 10 48 1 GCGGGACGAC 0.796125 -135 TTTGCCGGATGCGGCGTGAACGCCTGATCCGGCC 10 106 1 GCGCGACGCC 0.995316 -77 GAGGGAATGTGCGCGCTGGCCCCCTCACCCTAAC 13 14 1 GCGGCGCCCC 0.843324 -112 GGTGCCGGATGCGGCGTAAACGCCTTATCCGGCC 14 14 1 GCGCGACGCC 0.995316 -97 GGTGTCGGATGCGACGCTGACGCGTCTTATCCGA 14 69 0 GCGCGGCGCG 0.983585 -42 ATTGTCGGATGCGACGCCGGGGCGTCTTATCCGA 15 19 0 GCGCGGGGCG 0.970713 -36 CCCGCCGGGAGGCCCGCCCTCCCGC 17 2 1 CCGCGAGCCC 0.941501 -131 TATGCAAAGGACGAGGGTCTCGCGGTACCACCTT 20 183 0 ACGGGCCGCG 0.609243 -118 GCAAGGGGACGCGCCCCAGAGGCGGTCTTATCAA 22 38 0 GCGCCGGGCG 0.928785 -175 TTAAAAAAAGCCGGGGGCAGAGCCCGGCTTTTTA 35 41 0 CCGGGAAGCC 0.735609 -167 ATTGCAATCAGCGCGGGAAACCCCAAATTGCCGA 43 85 1 GCGGGACCCC 0.961069 -216 AGACCAGAAACCGCCGAGATGGCGTGTTTTTTTG 48 13 1 CCGCGAGGCG 0.965134 -96 GTGCGGTGTTGCGTCCATACGCCCAAAACGATTA 48 46 1 GCGCCAGCCC 0.931767 -63 CTTCTTTGAACCGGCCGCAGGGCCGGTTCTCCCT 49 11 0 CCGCCAGGCC 0.955456 -290 *** ** * **** Masking position 3 Map Score: 24.7273 Number of sites scoring better than the average of aligned sites = 1973 Number in coding regions = 1620 Number in noncoding regions = 353 Number of orfs with sites within 600 bp upstream = 137 Fraction of orfs with sites within 600 bp upstream = 0.0220045 Motif number 8 AAAATTCACTGCCGGGCGCGGTT 4 3 0 GCCGGCGCGG 0.911989 -98 AGACTTAATGGCAGATCACGGGCGCATACGC 4 67 1 GCAGTCACGG 0.909045 -34 CTCATCGGACGCAGAGCAGGGCTTATGATTT 6 18 1 GCAGGCAGGG 0.66487 -40 GGCTGGATAAGGCGTTCACGCCGCATCCGGC 7 56 1 GGCGTCACGC 0.959925 -245 CGCCGCATCCGGCGATCGTGCACTGATGCCT 7 74 1 GGCGTCGTGC 0.551993 -227 AGTAGCAGCGGAAGTTCCCGGCAGTGATAGT 7 259 1 GAAGTCCCGG 0.66442 -42 CAGTCACTATGGAGATCGCGG 7 290 1 GGAGTCGCGG 0.95669 -11 GGCCTGATAAGGCGTTTACGCCGCATCCGGC 9 42 1 GGCGTTACGC 0.799452 -259 AGGGAAAATGGGAGATGGGGCACGGATAAGC 9 125 0 GGAGTGGGGC 0.74425 -176 AAGATGACAAGGCGGTGACGGCGTGGGTGAG 9 154 0 GGCGTGACGG 0.953002 -147 GGCCGGATCAGGCGTTCACGCCGCATCCGGC 10 109 0 GGCGTCACGC 0.959925 -74 AAAACTCCAGGCCGGGTACGGTGTTTTACGC 11 12 1 GCCGGTACGG 0.624431 -75 AAAAGTAGCCGAAGATGACGGTTTGTCACAT 12 70 0 GAAGTGACGG 0.658939 -231 GCCGGTGCCGGATGCGGCGTA 14 1 1 GCCGTGCCGG 0.851891 -110 GGCCGGATAAGGCGTTTACGCCGCATCCGGC 14 17 0 GGCGTTACGC 0.799452 -94 TGTCGGATGCGACGCTGACGCGTCTTATCCG 14 70 0 GACGTGACGC 0.684841 -41 TGACAGTGCGGGAGGGCGGGCCTCCCGGCGG 17 12 0 GGAGGCGGGC 0.753396 -121 ACGGATAGTAGGCGATGCCGGGTTTCTCTCC 20 80 1 GGCGTGCCGG 0.924566 -221 GTTTCTTAAAGGAGGTGACGGCCAATGTACG 20 234 1 GGAGTGACGG 0.926261 -67 AATAAAAAGAGGAGTGCGGGGACAACCGTTT 30 15 1 GGAGGCGGGG 0.814293 -54 ATTGGAGCTCGGGCTGGCCGTCCT 35 4 1 GGAGTCGGGC 0.831473 -204 AAAGCCGGGGGCAGAGCCCGGCTTTTTATTC 35 38 0 GCAGGCCCGG 0.789064 -170 **** ****** Masking position 4 Map Score: 23.2365 Number of sites scoring better than the average of aligned sites = 2674 Number in coding regions = 2425 Number in noncoding regions = 249 Number of orfs with sites within 600 bp upstream = 126 Fraction of orfs with sites within 600 bp upstream = 0.0202377 Motif number 9 TCGTTTGATATCATTTTTCCTAAAATTGAATGGC 1 19 0 TCATTTTTAA 0.931007 -269 TTCATAACTTTTATTTATAATAAAGGTTGATAAT 2 100 1 TTATTTATAA 0.786764 -201 GTGTGGGTAATTATTTAAATAAGAGAAACGTTTC 2 150 1 TTATTTAAAA 0.577884 -151 TCTGGAAGTATTATTTTTATGACAAAGGAAATAC 2 216 0 TTATTTTTAA 0.893254 -85 CACCGCCTTGTCATCTTTCTGACACCTTACTATC 9 168 1 TCATCTTTAA 0.80227 -133 ATATCAACGCTTATTTAAATCAGACTGAAGACTT 12 164 1 TTATTTAAAA 0.577916 -137 ACTTTATCACTCATTTTTCCGATATATGAGCCGA 25 45 0 TCATTTTTAA 0.931007 -256 TGTAAAGCATTCATTTTTCAGAAAAATCTTTACC 25 148 0 TCATTTTTAA 0.931006 -153 ATGCAGTTTTTTATTTTACCAAAAAAACAGGA 27 9 0 TTATTTTAAA 0.756401 -292 ATGATAAGAATCATTTTGTAAACAACGAAATCAT 27 242 1 TCATTTTGAA 0.646753 -59 AACAACGAAATCATTTTTTTCATATAGGGACGGG 27 262 1 TCATTTTTAA 0.931007 -39 TGAAGAGTCATCATTTTTTTTAGAAAATGTGACA 32 112 1 TCATTTTTAA 0.931007 -156 GATAGCGCTTTCATTTATAGTAAAAAGAGAAAGG 36 41 0 TCATTTATAA 0.856117 -171 GCCTTTTACATCATTTTTAAAAGAAATAAAGACG 36 80 0 TCATTTTTAA 0.930528 -132 TTTCATGATTTTATTTTAGCGAAAGCAGGACATT 36 124 0 TTATTTTAAA 0.756401 -88 GGGTTCCCCTTTATTTTTCCAACATAAATCACAT 37 59 1 TTATTTTTAA 0.893254 -159 TTTTAACCTATTATTTATATTATAATGTATTATG 39 23 1 TTATTTATAA 0.786774 -159 TTTACATTTTTTATTTTAGAAATATAGCAAAAAT 39 72 1 TTATTTTAAA 0.756401 -110 TTCAATAAAGTTATCTTTTTTAAAAAAAGTTGAC 49 85 1 TTATCTTTAA 0.715592 -216 TGACTTCATTTCATCTATATAACATTCGTTTCAT 49 253 0 TCATCTATAA 0.641462 -48 ******** * * Masking position 6 Map Score: 16.9126 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 34 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 10 CTAAAATTGAATGGCAGAGAATC 1 4 0 ATGGCAGAGA 0.939285 -284 TGACAGAGTGATGACAGTGATGAAAAAAGC 7 131 0 ATGACAGTGA 0.907737 -170 TACTGGAAAGATGACAGAGTGATGACAGTG 7 142 0 ATGACAGAGT 0.808066 -159 TTTTCATTCTGTGACAGAGAAAAAGTAGCC 12 91 0 GTGACAGAGA 0.833809 -210 TAACGAAGAGATGACAGAAAAATTTTCATT 12 113 0 ATGACAGAAA 0.926662 -188 TGACAGTTTTATGACAGAGAGATAAAGTCT 12 192 0 ATGACAGAGA 0.975347 -109 CGGGAATTCGATGACAGTGCGGGAGGGCGG 17 24 0 ATGACAGTGC 0.806194 -109 GAAAGTCAAAAAAACAGAGATGG 24 4 0 AAAACAGAGA 0.580527 -145 ATATCATGCAAAGACAGAGAGGTAAAGATT 25 128 1 AAGACAGAGA 0.864615 -173 CCATTCCGATATGGCAGAAAAAATTCACCA 26 145 1 ATGGCAGAAA 0.831678 -89 ATTTGATACAATAACAGAAATGCCCATACG 26 199 1 ATAACAGAAA 0.732488 -35 GAGTGATGTCATGGCAGAGCTGAGCGGAAA 29 20 1 ATGGCAGAGC 0.867391 -116 TACTCTAAAAATAACAGAAAGACCAAGTTG 39 116 1 ATAACAGAAA 0.732488 -66 ATTTATTCGGATGACAGACAAAGGGTCTAT 42 89 0 ATGACAGACA 0.822068 -127 AATAGAACTAATGACAGAACTGAAAGATCA 43 16 0 ATGACAGAAC 0.84233 -285 TATTCCATGAATAACAGTGATCTGATTCCC 45 56 1 ATAACAGTGA 0.680719 -187 ********** Masking position 6 Map Score: 13.3697 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 172 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 11 TCTTCGGCTACTTTTTCTCTGTCACAGAATGA 12 86 1 CTTTTTCTGT 0.742799 -215 AGACTGAAGACTTTATCTCTCTGTCATAAAAC 12 185 1 CTTTTTCTCT 0.742799 -116 TTTTCTGGCTCTTTTTGTTTTTCGGGAAAGGA 19 229 1 CTTTTTTTTT 0.952854 -68 CCATCTCTGTTTTTTTGACTTTCGCC 24 5 1 CTCTTTTTTT 0.834616 -144 AAATCTTTACCTCTCTGTCTTTGCATGATATG 25 127 0 CTCTTTCTTT 0.831749 -174 TTGGCCTGCCCTTTTTATCTTTATTCCCGCGT 29 110 0 CTTTTTCTTT 0.951918 -26 AAGATTCGGTCTTTATATTTATCCATTGTAAG 32 71 0 CTTTTTTTAT 0.66546 -197 AACCTCCCCGCTTTCACTTTTTGAATGGGATT 33 11 0 CTTTATTTTT 0.633609 -25 TTAAGCAAGCCTTTCTCTCTTTTTA 36 4 0 CTTTTTCTTT 0.951918 -208 TTAATACAGCCTTTCTCTTTTTACTATAAATG 36 32 1 CTTTTTTTTT 0.952854 -180 TCATAAACGTCTTTATTTCTTTTAAAAATGAT 36 73 1 CTTTTTCTTT 0.951918 -139 ACAACTTGGTCTTTCTGTTATTTTTAGAGTAA 39 115 0 CTTTTTTATT 0.633609 -67 AAGCTTCGCACCTTTTCTTTTTATAAAGGAGA 40 26 1 CCTTTTTTTT 0.719343 -32 GTAAATCGGTCTTTTTCTTTTTGTTATGATAG 44 205 0 CTTTTTTTTT 0.952854 -96 GATCGCCGCTCTTTATTCTTTTAAAATGTGAG 45 102 0 CTTTTCTTTT 0.719343 -141 TTTTCTAAACCTTTATTTTTTTTATCTTTTGA 49 169 1 CTTTTTTTTT 0.952854 -132 **** * ***** Masking position 4 Map Score: 11.3656 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 37 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 12 GCGAATATTCAGCGGGAGAGTCCCGTTGAA 1 243 0 AGCGGGAGAG 0.829612 -45 GGCACGGATAAGCGGGAAAATATAGAAGGT 9 108 0 AGCGGGAAAA 0.678417 -193 ATCAGGCACGATGAGGAAAAGATTGCA 10 166 1 ATGAGGAAAA 0.62661 -17 CCTCACCCCAATGGGGAGAGGGAGAAAACG 13 102 0 ATGGGGAGAG 0.829943 -24 CTTATCTATAAGGAGGAGAAATC 18 86 1 AGGAGGAGAA 0.94191 -13 TTGGATGGAGATGAGGAGAGCCAGGAATCC 19 178 1 ATGAGGAGAG 0.794795 -119 CAAACAGCAAAGGGGGATAATTATTA 19 281 1 AGGGGGATAA 0.666997 -16 TCTCTTGGTAACGGGGAGAGAAACCCGGCA 20 95 0 ACGGGGAGAG 0.741116 -206 GAGAAGTTTTAGAAGGAAAGAGCGATAGTA 23 139 0 AGAAGGAAAG 0.608385 -162 ATAGCAAAAAAGGAGGCGAGATC 26 4 0 AGGAGGCGAG 0.73478 -230 TGAAAGTAACAGAAGGAAAGCAGGGGGAAA 28 59 1 AGAAGGAAAG 0.608385 -22 GAAGGAAAGCAGGGGGAAAAC 28 70 1 AGGGGGAAAA 0.927039 -11 TGAATGTGTTAAGAGGAGAAACGGTTGTCC 30 34 0 AAGAGGAGAA 0.516439 -35 CACGATGATAAGGAGGAAAAG 38 23 1 AGGAGGAAAA 0.909777 -11 GGAAGACACTAGGCGGAAAGTAGTAGTTTA 43 239 1 AGGCGGAAAG 0.75114 -62 CATCAAATAAAGGGGGAGGATTAT 45 229 1 AGGGGGAGGA 0.708641 -14 GTCATTCGGCAGGAGGAAAATCAAAATG 49 283 1 AGGAGGAAAA 0.909777 -18 ********** Masking position 1 Map Score: 10.2389 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 123 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 13 CCGCACTGATTGTAGGCATGATAAGACGCG 7 18 0 TGTAGGCATG 0.711391 -283 TGGCATCGCGTGTAGGCCGGATAAGCGAAG 8 47 1 TGTAGGCCGG 0.989744 -51 TGCACGATCTTGTAGGCCTGATAAGGCGTT 9 28 1 TGTAGGCCTG 0.950008 -273 TCAGGCTTACCGTAGGCCGGATCAGGCGTT 10 124 0 CGTAGGCCGG 0.992016 -59 TGCGTAAGCGGGGCATTTTTCT 12 3 1 CGTAAGCGGG 0.896435 -298 GGAGCGCATTTGTAGGCCGGATAAGGCGTT 14 32 0 TGTAGGCCGG 0.989744 -79 ATGCGCTCCCCGTAGGTCGGATAAGACGCG 14 53 1 CGTAGGTCGG 0.960731 -58 ATCGTAGGTCGGATAAGACGCC 15 3 1 CGTAGGTCGG 0.960731 -52 TTGTTCAAGATGTAAGCGGGTTGCTTCTAT 23 42 1 TGTAAGCGGG 0.870521 -259 ********** Masking position 4 Map Score: 11.4809 Number of sites scoring better than the average of aligned sites = 295 Number in coding regions = 83 Number in noncoding regions = 212 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 14 TGGCAATATGTTGAATTTGCACGATCTTGTAGGCC 9 6 1 ATTATTGAGT 0.603583 -295 AAAATAACTTTTTTGTTACATTTGTAAGATAGTAAGGTGT 9 189 0 TTTATTGAGT 0.915404 -112 GTTAAGCTAGTATTAATCGATTTTAAAGATTGGATTTACA 23 212 0 TTTATTTAGT 0.945286 -89 AACCCAATTATATTTTTAAACTGTTAAGCTAGTATTAATC 23 234 0 TTTACTTAGT 0.764904 -67 AAAATGATTCTTATCATCTATTATGATGTTAAAATAAAAA 27 219 0 TTTATTTAGT 0.945286 -82 TCGGTCTTTATATTTATCCATTGTAAGGCTCAAGTTTTTC 32 58 0 TTTATTTAGT 0.945286 -210 AAATGATGACTCTTCATAAATTGTTAAGATTCGGTCTTTA 32 88 0 TTTATTTAGT 0.945286 -180 CGAGCATCAGCTTTCATAAATTGGTAAGATTTACGTAGTA 32 155 1 CTTATTGAGT 0.692938 -113 ATTATTTATATTATAATGTATTATGACGTTATAATACAAA 39 32 1 TTTATTTAGT 0.945286 -150 TATCGCCAGTTGTTTATCTATTGTCATGCTGGTCAACTTT 49 110 0 TTTATTTAGT 0.945286 -191 AAAGAATGGGTCCTTGTCTATTATAACGGTTTAAGGTCAA 49 197 0 TTTATTTAGT 0.945286 -104 * * * *** * * * * Masking position 10 Map Score: 5.13774 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 8 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 TACGGTTAATTCCTGAACTGTGCCGGATGCGCTT 8 74 0 TTTGAAGGCC 0.923184 -24 ATATCAACGCTTATTTAAATCAGACTGAAGACTTT 12 164 1 TTTTAACGAC 0.685097 -137 CAAACAATGCTTTATGAATCCTCCCAGGAGACATT 12 276 1 TTTGAACCCC 0.950553 -25 AGAATAACCATTATTTAAGGGTGCCAGTTCATTAT 23 174 1 TTTTAAGGCC 0.866031 -127 GAGCGGAAATTTTCTTTATGCGGCCTTTCTTGTGT 29 41 1 TTTTTACGCC 0.792781 -95 TTCCTGAATTCCCCCTGCGTATAAT 31 139 0 TTTGAACCCC 0.950553 -15 AGAGAAAGGCTTGCTTAATACAGCCTTTCTCTTTT 36 18 1 TTTTAACGCC 0.970615 -194 CAAGCTGGTTTTAAAGAAATCTGCCCGTATTTTTC 45 146 0 TTAGAACGCC 0.867284 -97 GCTGGGTGATTTTATGAACGCTGCCCATTTTAGCG 46 34 1 TTTGAACGCC 0.983976 -87 GCTATGTTGTTTTCTTAACGCAGCC 47 1 0 TTTTAACGCC 0.970615 -143 GTCCCGGCACTACATGAAAGCAGCCCAGATCAACA 47 93 1 TATGAACGCC 0.867284 -51 TGACGTCTTCTTCTTTGAACCGGCCGCAGGGCCGG 49 19 0 TTTTGACGCC 0.850082 -282 AAAGATAACTTTATTGAAACCTCCCCTCACCGGAG 49 68 0 TTTGAACCCC 0.950553 -233 ** **** * *** Masking position 8 Map Score: 11.4541 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 185 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987