AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iphoB_ecoli_bsub_300.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 phnB 300 orf, hypothetical protein #19 glpQ 98 glycerophosphoryl diester phosphodiesterase #20 glpT 296 glycerol-3-phosphate permease #21 yczA 300 yczA #22 ycbL 96 similar to two-component response regulator [YcbM] #23 yclJ 212 similar to two-component response regulator [YclK] #24 phoB 300 alkaline phosphatase III #25 yeeG 135 yeeG #26 rapH 161 response regulator aspartate phosphatase #27 yeeI 160 similar to hypothetical proteins #28 yeeK 134 similar to hypothetical proteins #29 yesE 78 alternate gene name: yeeL #30 cotJA 126 cotJA #31 yesJ 124 alternate gene name: yeeN, yfxC, yfxD; similar to hypothetical proteins #32 yesL 114 similar to hypothetical proteins from B. subtilis #33 yesO 148 similar to sugar-binding protein #34 phoA 300 alkaline phosphatase A #35 yhdW 233 similar to glycerophosphodiester phosphodiesterase #36 ykoG 300 similar to two-component response regulator [YkoH] #37 resD 80 two-component response regulator #38 resC 135 essential protein similar to cytochrome c biogenesis protein #39 resA 131 essential protein similar to cytochrome c biogenesis protein #40 ypuL 91 similar to hypothetical proteins #41 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #42 ypuI 54 similar to hypothetical proteins from B. subtilis #43 ypuG 280 similar to hypothetical proteins #44 yqgH 68 alternate gene name: yzmC; similar to phosphate ABC transporter (permease) #45 yqgG 153 alternate gene name: yzmB; similar to phosphate ABC transporter (binding protein) #46 pbpA 113 penicillin-binding protein 2A #47 yqgE 33 similar to hypothetical proteins #48 sodA 178 superoxide dismutase #49 yqgC 109 yqgC #50 yrkP 267 similar to two-component response regulator [YrkQ] #51 araP 35 integral membrane protein #52 araN 30 sugar-binding protein #53 araA 207 L-arabinose isomerase #54 abnA 196 arabinan-endo 1,5-alpha-L-arabinase #55 ysdC 183 similar to endo-1,4-beta-glucanase #56 phoP 211 two-component response regulator #57 citH 43 malate dehydrogenase #58 citC 163 isocitrate dehydrogenase #59 citZ 300 citrate synthase II #60 msmR 217 transcriptional regulator (LacI family) #61 msmE 33 multiple sugar-binding protein #62 yurJ 181 similar to multiple sugar ABC transporter (ATP-binding protein) #63 yurN 57 similar to sugar permease #64 yurO 80 similar to multiple sugar-binding protein #65 yurP 215 similar to opine catabolism #66 yurQ 102 yurQ #67 yurR 300 similar to opine catabolism #68 yvrI 300 yvrI #69 yvcP 300 similar to two-component response regulator [YvcQ] #70 ywnF 242 ywnF #71 msmX 120 multiple sugar-binding transport ATP-binding protein #72 yxkF 183 similar to hypothetical proteins #73 yxdL 143 similar to ABC transporter (ATP-binding protein) #74 yxdJ 108 similar to two-component response regulator [YxdK] #75 iolI 85 alternate gene name: yxdH; myo-inositol catabolism #76 iolG 22 myo-inositol 2-dehydrogenase #77 iolD 203 alternate gene name: yxdD; myo-inositol catabolism #78 iolC 23 alternate gene name: yxdC; myo-inositol catabolism #79 iolB 74 alternate gene name: yxdB; myo-inositol catabolism #80 iolA 300 methylmalonate-semialdehyde dehydrogenase #81 yycF 300 similar to two-component response regulator [YycG] Motif number 1 CTGATTGTAGGCATGATAAGACGCGCAAGCGT 7 10 0 GCATGATGCG 0.914626 -291 GGTTTGGTAGGCTGGATAAGGCGTTCACGCCGC 7 47 1 GCTGGATGCG 0.97453 -254 GTGCACGATCGCCGGATGCGGCGTGAACGCCTT 7 64 0 GCCGGATGCG 0.999096 -237 GATCTTGTAGGCCTGATAAGGCGTTTACGCCGC 9 33 1 GCCTGATGCG 0.996779 -268 ATCGTTTCATGCCGGATGCGGCGTAAACGCCTT 9 50 0 GCCGGATGCG 0.999096 -251 TTAACACTTTGCCGGATGCGGCGTGAACGCCTG 10 99 1 GCCGGATGCG 0.999096 -84 CTTACCGTAGGCCGGATCAGGCGTTCACGCCGC 10 116 0 GCCGGATGCG 0.999096 -67 ATTTTGTAATGCCGGATGCGGCGTAAAACACCG 11 30 0 GCCGGATGCG 0.999096 -57 GCCGGTGCCGGATGCGGCGTAAACGCCTT 14 7 1 GCCGGATGCG 0.999096 -104 GCATTTGTAGGCCGGATAAGGCGTTTACGCCGC 14 24 0 GCCGGATGCG 0.999096 -87 CTCCCCGTAGGTCGGATAAGACGCGTCAGCGTC 14 58 1 GTCGGATGCG 0.994143 -53 TGGTTCGGGTGTCGGATGCGACGCTGACGCGTC 14 77 0 GTCGGATGCG 0.994143 -34 ATCGTAGGTCGGATAAGACGCCCCGGCGTC 15 8 1 GTCGGATGCG 0.994143 -47 CCTGCACATTGTCGGATGCGACGCCGGGGCGTC 15 27 0 GTCGGATGCG 0.994143 -28 GACTGCCTGATGCGACGCTTGCGCGTC 18 5 1 GCCTGATGCG 0.996779 -296 GAATTTGTAGGCCTGATAAGACGCGCAAGCGTC 18 24 0 GCCTGATGCG 0.996779 -277 CCCTCCGTAGGCCGGATAAGGCGTTTACGCCGC 18 62 1 GCCGGATGCG 0.999096 -239 CGGCACCATTGCCGGATGCGGCGTAAACGCCTT 18 79 0 GCCGGATGCG 0.999096 -222 GGTGCCGACTGCCTGATGCGACGCTTGCGCGTC 18 105 1 GCCTGATGCG 0.996779 -196 GAATTTGTAGGCCTGATAAGACGCGCAAGCGTC 18 124 0 GCCTGATGCG 0.996779 -177 CCCTCCGTAGGCCGGATAAGGCGTTTACGCCGC 18 162 1 GCCGGATGCG 0.999096 -139 CGGCACTGTTGCCGGATGCGGCGTAAACGCCTT 18 179 0 GCCGGATGCG 0.999096 -122 AGTGCCGACTGCCTGATGCGACGCTCGCGCGTC 18 205 1 GCCTGATGCG 0.996779 -96 ATGAGAGGCGGCCTGATAAGACGCGCGAGCGTC 18 224 0 GCCTGATGCG 0.996779 -77 TTTTAAAGCGTTCGGATAGGGCGAAACACTCAA 33 45 0 TTCGGATGCG 0.843991 -104 ATGGAGTTCGGCGGGATATGGCGACAGCCTTCC 75 18 1 GCGGGATGCG 0.982671 -68 ******* * ** Masking position 7 Map Score: 121.95 Number of sites scoring better than the average of aligned sites = 382 Number in coding regions = 46 Number in noncoding regions = 336 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 2 ATCGCCGGATGCGGCGTGAACGCCTTATCCAGCCT 7 55 0 GCGCGCGCCT 0.998886 -246 CATGCCGGATGCGGCGTAAACGCCTTATCAGGCCT 9 41 0 GCGCGCGCCT 0.998886 -260 TCCCTCACCCACGCCGTCACCGCCTTGTCATCTTT 9 151 1 ACGCGCGCCT 0.982487 -150 TTTGCCGGATGCGGCGTGAACGCCTGATCCGGCCT 10 106 1 GCGCGCGCCT 0.998886 -77 GGTGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 14 14 1 GCGCGCGCCT 0.998886 -97 GGTGTCGGATGCGACGCTGACGCGTCTTATCCGAC 14 68 0 GCGCGCGCGT 0.998705 -43 ATTGTCGGATGCGACGCCGGGGCGTCTTATCCGAC 15 18 0 GCGCGGGCGT 0.993371 -37 ACTGCCTGATGCGACGCTTGCGCGTCTTATCAGGC 18 12 1 GCGCGCGCGT 0.998705 -289 ATTGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 18 70 0 GCGCGCGCCT 0.998886 -231 ACTGCCTGATGCGACGCTTGCGCGTCTTATCAGGC 18 112 1 GCGCGCGCGT 0.998705 -189 GTTGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 18 170 0 GCGCGCGCCT 0.998886 -131 ACTGCCTGATGCGACGCTCGCGCGTCTTATCAGGC 18 212 1 GCGCGCGCGT 0.998705 -89 AGACCAGAAACCGCCGAGATGGCGTGTTTTTTTGT 74 13 1 CCGCGGGCGT 0.937997 -96 *** ** ***** Masking position 15 Map Score: 48.7343 Number of sites scoring better than the average of aligned sites = 300 Number in coding regions = 45 Number in noncoding regions = 255 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 TGGCAGATCACGGGCGCATACGCTCATGGTTAA 4 75 1 CGGGCGACGC 0.941876 -26 ATCGCCGGATGCGGCGTGAACGCCTTATCCAGC 7 57 0 GCGGCGACGC 0.997153 -244 CACGCCGCATCCGGCGATCGTGCACTGATGCCT 7 72 1 CCGGCGGTGC 0.882094 -229 CTTCGCTTATCCGGCCTACACGCGATGCCAGGT 8 44 0 CCGGCCACGC 0.970626 -54 TTCCTGAACTGTGCCGGATGCGCTTCGCTTATC 8 66 0 GTGCCGGCGC 0.878693 -32 CATGCCGGATGCGGCGTAAACGCCTTATCAGGC 9 43 0 GCGGCGACGC 0.997678 -258 TTTGCCGGATGCGGCGTGAACGCCTGATCCGGC 10 106 1 GCGGCGACGC 0.997153 -77 GAAGAAAAATGCCCCGCTTACGCA 12 2 0 GCCCCGACGC 0.889903 -299 TTAGGGTGAGGGGGCCAGCGCGCACATTCCCTC 13 14 0 GGGGCCGCGC 0.950274 -112 GGTGCCGGATGCGGCGTAAACGCCTTATCCGGC 14 14 1 GCGGCGACGC 0.997678 -97 GGTGTCGGATGCGACGCTGACGCGTCTTATCCG 14 70 0 GCGACGACGC 0.98965 -41 ATTGTCGGATGCGACGCCGGGGCGTCTTATCCG 15 20 0 GCGACGGGGC 0.820819 -35 ACTGCCTGATGCGACGCTTGCGCGTCTTATCAG 18 12 1 GCGACGGCGC 0.992927 -289 ATTGCCGGATGCGGCGTAAACGCCTTATCCGGC 18 72 0 GCGGCGACGC 0.997678 -229 ACTGCCTGATGCGACGCTTGCGCGTCTTATCAG 18 112 1 GCGACGGCGC 0.992927 -189 GTTGCCGGATGCGGCGTAAACGCCTTATCCGGC 18 172 0 GCGGCGACGC 0.997678 -129 ACTGCCTGATGCGACGCTCGCGCGTCTTATCAG 18 212 1 GCGACGGCGC 0.992927 -89 GCAAGGGGACGCGCCCCAGAGGCGGTCTTATCA 23 39 0 GCGCCCAGGC 0.871467 -174 CTTCTTTGAACCGGCCGCAGGGCCGGTTCTCCC 81 12 0 CCGGCCGGGC 0.891273 -289 ****** **** Masking position 5 Map Score: 43.3804 Number of sites scoring better than the average of aligned sites = 748 Number in coding regions = 476 Number in noncoding regions = 272 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 TTATCCGTGCCCCATCTCCCATTTTCCCTCAC 9 127 1 CCCATCCCCT 0.967022 -174 TCTCCCATTTTCCCTCACCCACGCCGTCACCG 9 141 1 TCCCTCCCCC 0.788169 -160 ACACGGTTTTCCCCTCACCCTAACCCTCTCCC 10 19 1 CCCCTCCCCA 0.994597 -164 CCTCACCCTAACCCTCTCCCCAGAGGGGCGAG 10 31 1 ACCCTCCCCA 0.984258 -152 CTCGGTCGGTCCCCTCGCCCCTCTGGGGAGAG 10 44 0 CCCCTCCCCT 0.995072 -139 GCGCGCTGGCCCCCTCACCCTAACCCTCTCCC 13 24 1 CCCCTCCCCA 0.994597 -102 CCTCACCCTAACCCTCTCCCCAGAGGGGCGAG 13 36 1 ACCCTCCCCA 0.984258 -90 CACAATCGGTCCCCTCGCCCCTCTGGGGAGAG 13 49 0 CCCCTCCCCT 0.995072 -77 GCTCGTTTTCTCCCTCTCCCCATTGGGGTGAG 13 99 1 TCCCTCCCCA 0.951825 -27 CGCCCCTCACCCCAATGGGGAGAG 13 112 0 CCCCTCCCCA 0.994597 -14 TGTGGCGTGCCTCCTTTCCCGAAAAACAAAAA 20 240 0 CTCCTTCCCA 0.887441 -57 GTGTGAACCGATCCTCCCCTGATGCCGAATGG 21 27 1 ATCCTCCCTA 0.672853 -274 GTACCGCGAGACCCTCGTCCTTTGCATAGGAC 21 189 1 ACCCTCTCCT 0.72213 -112 TGCGCTGCATCTCCTCACCTAACCTTTACAAA 22 73 0 CTCCTCCCTA 0.858256 -24 GACCATTTCCCTTCTTTTGTTCG 25 2 1 ACCATTCCCT 0.591251 -134 ATTTGACCATCCTCTCCCGTCCCTATATGA 36 281 0 ATCCTCCCCT 0.952897 -20 TGCCCCCTTCCCCCTATTGCAGATC 39 117 0 CCCCTTCCCT 0.967022 -15 ATCAATACTCCTTTCCCATTTATCACGGC 50 8 1 CTCCTTCCCT 0.896362 -260 CCCATCACCCTTCCTTATTCGC 60 1 1 CCCATCCCCT 0.967022 -217 GGGTATCTCATCTCCTTTATAAAAAGAA 63 40 0 CTCATCCCTT 0.490994 -18 ATAATCCTCCCCCTTTATTTGATGT 70 228 0 ATCCTCCCCT 0.952897 -15 ATTGAAACCTCCCCTCACCGGAGTGCGTCTTT 81 59 0 CCCCTCCCGA 0.923323 -242 ****** *** * Masking position 5 Map Score: 37.9011 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 96 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 5 CGCACTGATTGTAGGCATGATAAGACGCGC 7 17 0 GTAGGCATGA 0.923066 -284 TGCGGGTTTGGTAGGCTGGATAAGGCGTTC 7 43 1 GTAGGCTGGA 0.950528 -258 GGCATCGCGTGTAGGCCGGATAAGCGAAGC 8 48 1 GTAGGCCGGA 0.996279 -50 GCACGATCTTGTAGGCCTGATAAGGCGTTT 9 29 1 GTAGGCCTGA 0.989557 -272 CAGGCTTACCGTAGGCCGGATCAGGCGTTC 10 123 0 GTAGGCCGGA 0.996279 -60 CCGGCCTACGGTAAGCCTGATTAGCGAAGT 10 134 1 GTAAGCCTGA 0.852343 -49 GTCACATGGAGTTGGCAGGATGTTTGATTA 12 47 0 GTTGGCAGGA 0.769297 -254 GAGCGCATTTGTAGGCCGGATAAGGCGTTT 14 31 0 GTAGGCCGGA 0.996279 -80 TGCGCTCCCCGTAGGTCGGATAAGACGCGT 14 54 1 GTAGGTCGGA 0.968848 -57 ATCGTAGGTCGGATAAGACGCCC 15 4 1 GTAGGTCGGA 0.968848 -51 GCGGGAATTTGTAGGCCTGATAAGACGCGC 18 31 0 GTAGGCCTGA 0.989557 -270 CGCACCCTCCGTAGGCCGGATAAGGCGTTT 18 58 1 GTAGGCCGGA 0.996279 -243 GCGGGAATTTGTAGGCCTGATAAGACGCGC 18 131 0 GTAGGCCTGA 0.989557 -170 CGCACCCTCCGTAGGCCGGATAAGGCGTTT 18 158 1 GTAGGCCGGA 0.996279 -143 ********** Masking position 10 Map Score: 38.6373 Number of sites scoring better than the average of aligned sites = 310 Number in coding regions = 30 Number in noncoding regions = 280 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 6 TAATAATTATCCCCCTTTGCTGTTTGTGCTGGA 20 274 0 CCCCCTTTTT 0.971772 -23 TTGATATCCTCCTTTCTAACTCATCTGCTA 21 281 0 CCTCCTTTAC 0.700213 -20 ATAGAAGCAACCCGCTTACATCTTGAACAATTT 24 39 0 CCCGCTTATT 0.424593 -262 CGGCTTCCCTCCTTCTCTATGAGATATGTC 26 142 0 CCTCCTTCTT 0.818983 -20 GCTGTTATGGCCTGCTTTTTTTTGTCCCGGAAA 28 22 1 CCTGCTTTTT 0.842158 -113 CAAACCAATCCCCCCTTTAATGTAAGTGCTTAC 33 84 0 CCCCCTTTTT 0.971772 -65 GCCTCCTTTAATGTATTCCGTTTA 34 287 0 CCTCCTTTTT 0.964264 -14 GATCTCGCCTCCTTTTTTGCTATTATAAAG 35 8 1 CCTCCTTTTC 0.940274 -226 GTTTTCCCCCTGCTTTCCTTCTGTTACTTTC 37 60 0 CCTGCTTTTC 0.756865 -21 GGTGCTTCCTCCTTTAATGTGCTTTTAGTG 43 8 1 CCTCCTTTTT 0.964264 -273 TACTGACTCCCCTTTACTATCCCTTAGTCT 47 14 0 TCCCCTTTTT 0.811023 -20 ATTTTCGGTATCCCCTTTATTGTAGTCACTATG 54 71 0 TCCCCTTTTT 0.811023 -126 GATTATTTATCCTCCCTTCCTGTCAAATCGACT 54 132 0 CCTCCCTTTT 0.805302 -65 TTTTGTTCAACCTCCTTTATTTTAGAAAGCGCT 54 174 0 CCTCCTTTTT 0.964264 -23 ATATAACATCTCCTTTTCAATAAATTTCCCC 59 280 0 TCTCCTTTAT 0.332916 -21 AGATCTGGGTTCCCCTTTATTTTTCCAACATAA 60 53 1 TCCCCTTTTT 0.811023 -165 AGGGTAGCCTCCTTTTAACCTATTATTTAT 62 8 1 CCTCCTTTAC 0.700213 -174 CAGAAAAGTCCCCCTATCTTTTGACCCGTTAT 62 160 0 CCCCCTATTT 0.649752 -22 TAGGAAAATACCTCCCTTCTTTTTCTGCAGTCA 68 155 1 CCTCCCTTTT 0.805302 -146 GTTGATCCCCCTTATATGTACATCACGAT 69 282 0 CCCCCTTATT 0.788662 -19 ATAATCCTCCCCCTTTATTTGATGTTTCAAG 70 222 0 CCCCCTTTTG 0.876639 -21 CTAACATCCCCCTTTGTTATTGTAAACGCT 71 101 0 CCCCCTTTTT 0.971772 -20 AAGATGACCCTCCTTTGGTCCTGCATGTCTT 72 9 1 CCTCCTTTTC 0.940274 -175 AACAACATAGCCCGCTTTGTTTCCCCTTGATAA 73 25 1 CCCGCTTTTC 0.798859 -119 TCTTATTGCCTCCTTCATTAGTAAACACATA 80 280 0 CCTCCTTCTG 0.482916 -21 ******** * * Masking position 5 Map Score: 32.206 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 57 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 7 CGCGTCTTATCATGCCTACAATCAGTGCGGG 7 18 1 CATGCCTACA 0.868775 -283 AACGCCTTATCCAGCCTACCAAACCCGCACT 7 41 0 CCAGCCTACA 0.912338 -260 CTTCGCTTATCCGGCCTACACGCGATGCCAG 8 46 0 CCGGCCTACC 0.938961 -52 AACGCCTTATCAGGCCTACAAGATCGTGCAA 9 27 0 CAGGCCTACA 0.947404 -274 AACGCCTGATCCGGCCTACGGTAAGCCTGAT 10 124 1 CCGGCCTACG 0.991643 -59 AACGCCTTATCCGGCCTACAAATGCGCTCCC 14 32 1 CCGGCCTACA 0.988963 -79 CGCGTCTTATCCGACCTACGGGGAGCGCATT 14 52 0 CCGACCTACG 0.912194 -59 GGCGTCTTATCCGACCTACGAT 15 2 0 CCGACCTACA 0.886828 -53 GCCGGGAGGCCCGCCCTCCCGCACTGTCATC 17 14 1 CCGCCCTCCG 0.950467 -119 CGCGTCTTATCAGGCCTACAAATTCCCGCAC 18 32 1 CAGGCCTACA 0.947404 -269 AACGCCTTATCCGGCCTACGGAGGGTGCGGG 18 56 0 CCGGCCTACG 0.991643 -245 CGCGTCTTATCAGGCCTACAAATTCCCGCAC 18 132 1 CAGGCCTACA 0.947404 -169 AACGCCTTATCCGGCCTACGGAGGGTGCGGG 18 156 0 CCGGCCTACG 0.991643 -145 CTTTAAACAGCCTCCCTCCAGATTTTTATGT 20 11 1 CCTCCCTCCG 0.875817 -286 TCGGTTCACACCTGCCACCGACTCTCT 21 7 0 CCTGCCACCA 0.646846 -294 TAGTCATAATCATGCCTCCTGCCTCATACCT 30 70 1 CATGCCTCCG 0.877977 -57 AAAAGAACGCCCGGCCTCTAGTGCTTCTTAG 43 64 1 CCGGCCTCTG 0.877826 -217 CCCCATTAAACCTGCCGCCAGCATTTC 48 7 0 CCTGCCGCCG 0.782553 -172 TTGACGCAAGCCAGCCTCCAATGGTTCT 58 8 0 CCAGCCTCCA 0.895088 -156 ACCGCCTCCCTACTAAATTAAATGA 68 286 0 CCTCCCTACA 0.866475 -15 CATCACGACACCTGCCTATTATGAAAATTTT 69 162 1 CCTGCCTATA 0.708442 -139 ********* * Masking position 6 Map Score: 30.8105 Number of sites scoring better than the average of aligned sites = 381 Number in coding regions = 187 Number in noncoding regions = 194 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 8 TGGCCATGCGGTGAGTTTTTTTCTCTTAATT 2 46 1 GTGGTTTTTT 0.947168 -255 TTTCGCTGCCGGGTGGTTTTTTTGCTGTTAG 4 31 1 GGGGGTTTTT 0.871872 -70 GGGACCGACCGAGCGCCTTTTTGACTCTGTA 10 63 1 GAGGCCTTTT 0.541332 -120 TTTTGACAAGGGGTGTTTTCTGGCTCTTTTT 20 214 1 GGGGTTTTCT 0.753879 -83 TGCATAGGACGGGGGTTTTTTGTGTTTCTTA 21 211 1 GGGGTTTTTT 0.973527 -90 GTAATTACGTGTGTGTTTTTTGATTTTGTAA 22 49 1 GTGGTTTTTT 0.947168 -48 AGATAACGAAAAGCGTTTTTTCATTTCCTTA 34 194 1 AAGGTTTTTT 0.64304 -107 CTGATACGCTGAGTGTCTTTTTTTAGTTATA 35 96 1 GAGGTCTTTT 0.814083 -138 ATACAAACTGGTGAATTTTTTCTGCCATATC 35 152 0 GTGATTTTTT 0.631868 -82 TGACCGAATGGTGTATTTTTTTGTGCGCTTA 36 74 0 GTGATTTTTT 0.631868 -227 AAACGGCGTTTTTTTTAGATTTGG 40 4 1 CGGGTTTTTT 0.68429 -88 CTTTTTCAGGGAGAGTTTTTTTATGTTTGCT 41 23 1 GAGGTTTTTT 0.947168 -100 ACTAGAGGCCGGGCGTTCTTTTTTCCTTTTA 43 55 0 GGGGTTCTTT 0.753879 -226 AGTATTGGACGAGAGCTTTTTGGTGGCTTAT 43 203 1 GAGGCTTTTT 0.82854 -78 CACATCATGTGAGCGTTTTTT 45 1 0 GAGGTTTTTT 0.947168 -153 CACATGATGTGGGCGTTTTTTTTATACAAAA 45 21 1 GGGGTTTTTT 0.973527 -133 TTGTAAATCAGTGCGTTTTTTTGTATAAAAA 45 39 0 GTGGTTTTTT 0.947168 -115 ACTCTTACTTGAGTGTCTTTTCTTTCTGTAA 46 76 1 GAGGTCTTTT 0.814083 -38 GAGCCAAATCGTGAGCTTTTTCATTGATTAC 48 75 1 GTGGCTTTTT 0.82854 -104 ATTACATACTGGGAGGTTTTTATT 58 150 1 GGGGGTTTTT 0.871872 -14 CCGCAAATAAAGGCGTTTTTTCGGGGAAATC 59 18 1 AGGGTTTTTT 0.787011 -283 CTTTTGATTTGGGCATTTTTTCGCATATAGA 65 63 1 GGGATTTTTT 0.778795 -153 CGCCGAGATGGCGTGTTTTTTTGTGCGGTGT 74 24 1 GCGGTTTTTT 0.826443 -85 AAGGTGAAACATGTGTTTTTTTTCTAAACCT 81 150 1 ATGGTTTTTT 0.64304 -151 *** ******* Masking position 9 Map Score: 23.5271 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 122 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 9 AAGCCTAGCGGCAGTTGTTTACGCTTTTATTACAGAT 1 127 1 GAGTTCCTTT 0.971874 -161 TTGCTTTACGGAAGACGGTTCCATTTTCCACATCGCG 27 20 1 GAGTTCTTTT 0.978792 -141 CAAGGTGTGTGTGCAAGCTTACTTTTTGATTGGGAGG 31 93 1 GGGTTCTTTT 0.920152 -32 TCCTGCTTTGGAAAACGCTTTCATTTTAAAGTAATAT 32 83 0 GAGTTCTTTT 0.978792 -32 CCCCTTTAATGTAAGTGCTTACATTTTATTTTAAAGC 33 69 0 GAGTTCTTTT 0.978792 -80 TTCACCTCAAGTATTATCTTACTTTTTTCAACCTTAA 40 61 0 GATTTCTTTT 0.695935 -31 TCAAGTAAGAGTGCCAGTTTTCATTTTAAAGGTTTTT 46 51 0 GGGTTCTTTT 0.920152 -63 GAAAAGCATAGAAAAAGGTTTCACTTTTTCTAAAAGA 55 54 1 GAGTTCCTTT 0.971874 -130 TCAGACATCAAAATTGGGTTACACTTTAAATTGAATG 58 56 1 AAGTTCCTTT 0.763064 -108 CCCCCAAAAAGAAAATGCTTACATTTTACTGGCTGCT 59 184 0 GAGTTCTTTT 0.978792 -117 TTACGAGACAGATCTGGGTTCCCCTTTATTTTTCCAA 60 44 1 GTGTTCCTTT 0.759801 -174 AACAATTATTGTAACCGCTTACTTTTATATGATAATA 60 134 1 GAGTTCTTTA 0.787543 -84 TATTTTTAGAGTAATCGATTCCCATTTTTGCTATATT 62 92 0 GAGTTCATTT 0.84241 -90 AAAATACTTTGCAGCAGTTTACGTTTTATCGGTTTTC 68 202 0 GAGTTCTTTT 0.978792 -99 TAGGCGGAAAGTAGTAGTTTACTTTTTTTTGCTTTCC 68 248 1 GAGTTCTTTT 0.978792 -53 ATATGTAAACGAATGAGGTTTCCCTTTCAGTTTCTCG 72 63 1 GAGTTCCTTT 0.971874 -121 CATTTCATGCACAACAGGTTACTTTTTGGTCATTTCT 80 121 0 AAGTTCTTTT 0.811378 -180 * * * ** * **** Masking position 9 Map Score: 23.3527 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 29 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 GCAAAGTATTTCCTTTGTCATAAAAATAATACTTCC 2 211 1 TCTTTAAAAA 0.948864 -90 GCACTACCTGTCTTTCATAATAAAAAACGGATGTAA 19 51 0 TCTCTAAAAA 0.596773 -48 CATAAAGGGTTCTTTTTTATGAAAAAAACAAATTGA 26 44 1 TCTTTAAAAA 0.944129 -118 TCCGGCTCCTCCTTTCTCAAAAACAATGACCTTAA 30 102 0 TCTTTAAACA 0.812352 -25 AATATGTATTTCTCCTTTCGAAAGAAAATTCCTGCC 32 52 0 TCCTTAAGAA 0.693774 -63 CGGGGTCGGCTCATATATCGGAAAAATGAGTGATAA 34 40 1 TCTTTAAAAA 0.948896 -261 TGTAAAGCATTCATTTTTCAGAAAAATCTTTACCTC 34 146 0 TCTTTAAAAA 0.94889 -155 CCTCTCCCGTCCCTATATGAAAAAAATGATTTCGTT 36 265 0 CCTTTAAAAA 0.812443 -36 CTTCTGGTTTTCCTTTCTAAGAAGCACTAGAGGCCG 43 75 0 TCTTTAAGCA 0.693697 -206 TGTGGGCGTTTTTTTTATACAAAAAAACGCACTGAT 45 28 1 TTTTTAAAAA 0.483904 -126 TACAGATAACCCCTTTTTGGCAAAAAAA 46 3 0 CCTTTAAAAA 0.812443 -111 CAAAAAGGGGTTATCTGTAGAAAAAAGTCGAAAAAA 46 20 1 TTTTTAAAAA 0.81984 -94 CACAAATTTGTCACATTTTCTAAAAAAAATGATGAC 50 118 0 TCCTTAAAAA 0.812443 -150 GGGCTGGCCGTCCTATTGAATAAAAAGCCGGGCTCT 53 21 1 TCTTGAAAAA 0.597253 -187 ATACTGTCAATCTTTTCTTTTAAAAAAAGCCGGGGG 53 58 0 TCTTTAAAAA 0.948886 -150 GTTTTTACAGCTTTCTTTTAGAAAAAGTGAAACCTT 55 68 0 CTTTTAAAAA 0.516191 -116 TAGCGCCATGTTTTGTATAATAAGAATGCAGGACTG 55 139 1 TTTTTAAGAA 0.704683 -45 GATAGCGCTTTCATTTATAGTAAAAAGAGAAAGGCT 56 39 0 TCTTTAAAAA 0.948883 -173 ATAAACGTCTTTATTTCTTTTAAAAATGATGTAAAA 56 75 1 TTTTTAAAAA 0.820566 -137 TCATTTTATTTTCTATATAAGAAAAATAAAATGTTT 58 103 1 TTTTTAAAAA 0.818666 -61 AGTATGTAATTCATATTTAGAAAACATTTTATTTTT 58 124 0 TCTTTAAACA 0.812443 -40 GTATCTCATCTCCTTTATAAAAAGAAAAGGTGCGAA 63 30 0 TCTTTAAGAA 0.878476 -28 CCCCGCTCATTCATATTTATCAAGAAGATTGCCATT 70 18 1 TCTTTAAGAA 0.906641 -225 ATTATAACACTCACATTTTAAAAGAATAAAGAGCGG 70 93 1 TCCTTAAGAA 0.693775 -150 TTCAATAAAGTTATCTTTTTTAAAAAAAGTTGACCA 81 85 1 TTTTTAAAAA 0.820576 -216 ** * * * ***** Masking position 12 Map Score: 21.6642 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 12 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 CAGCGAAAATTCACTGCCGGGCGCGGTT 4 8 0 TCATGCCGGG 0.973395 -93 CAGTGAATTTTCGCTGCCGGGTGGTTTTTTT 4 23 1 TCGTGCCGGG 0.978769 -78 TGACTGACTATCACTGCCGGGAACTTCCGCT 7 265 0 TCATGCCGGG 0.973395 -36 CGGCCTACACGCGATGCCAGGTCAGATAAGC 8 35 0 GCGTGCCAGG 0.919022 -63 AAGTCATTTTGTAATGCCGGATGCGGCGTAA 11 37 0 GTATGCCGGA 0.848512 -50 GCCGGTGCCGGATGCGGCGTAA 14 2 1 CCGTGCCGGA 0.968809 -109 ATTGTCGGATGCGACGCCGGGGCGTCTTATC 15 22 0 GCGCGCCGGG 0.903452 -33 GCAGTCGGCACCATTGCCGGATGCGGCGTAA 18 86 0 CCATGCCGGA 0.961014 -215 GCAGTCGGCACTGTTGCCGGATGCGGCGTAA 18 186 0 CTGTGCCGGA 0.826911 -115 AGAGAGTCGGTGGCAGGTGTGAACCGA 21 7 1 TCGTGGCAGG 0.52252 -294 CGGATAGTAGGCGATGCCGGGTTTCTCTCCC 21 81 1 GCGTGCCGGG 0.986629 -220 AAGGCTCAGAGCACTGGCGGATCACGGTAAA 39 12 1 GCATGGCGGA 0.848951 -120 AGTATCACTCTCATTGCCGGAAAAACTGGCT 43 244 0 TCATGCCGGA 0.9579 -37 TGGACTTTTGCCACTGCCGCATCGCGTCTGT 67 91 1 CCATGCCGCA 0.658837 -210 AGAATTGACGTCATTGCCAGAAACAGCATGA 69 124 1 TCATGCCAGA 0.777754 -177 CTGCTTTCATGTAGTGCCGGGACGTTCAACA 73 85 0 GTATGCCGGG 0.900068 -59 *** ******* Masking position 6 Map Score: 16.9481 Number of sites scoring better than the average of aligned sites = 1103 Number in coding regions = 1024 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 12 GATAATTTAAGAAAGCGCTATCATGATAAG 20 140 1 GAAAGCGCTA 0.943573 -157 ACTTTAAAATGAAAGCGTTTTCCAAAGCAG 32 88 1 GAAAGCGTTT 0.978136 -27 CAAGATAACGAAAAGCGTTTTTTCATTTCC 34 192 1 AAAAGCGTTT 0.778039 -109 ATTGTATACGGAAAGCACTAGGGGTGCTGT 36 189 0 GAAAGCACTA 0.720372 -112 GTGAAATTTAGAAAGCGTTTTTACCGTGAT 39 32 0 GAAAGCGTTT 0.978136 -100 TTTTGTATTTGAAAGCGTTTTATTTTATGA 53 172 1 GAAAGCGTTT 0.978136 -36 CTTTATTTTAGAAAGCGCTTACAAATTAGA 54 163 0 GAAAGCGCTT 0.976732 -34 TACTATAAATGAAAGCGCTATCATAAACGT 56 53 1 GAAAGCGCTA 0.943573 -159 AAGGTCGAAGGAAAGCATTTGATTTGGTAA 67 245 1 GAAAGCATTT 0.873606 -56 CTCAATATAAGAAAGCGTTTACAATAACAA 71 88 1 GAAAGCGTTT 0.978136 -33 TGGTGTTTTTGAAAGCGTTTAATTCTTGGC 80 197 1 GAAAGCGTTT 0.978136 -104 ********** Masking position 4 Map Score: 17.0351 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 46 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 ATTGTTAGTTTTTATTTCATCAACTAGAAAT 23 120 0 TTTATTTCAC 0.818179 -93 AATACTGTTATTCACTTTATCCATTATACCT 27 107 0 TTCACTTTAC 0.822079 -54 GGAAAACGCTTTCATTTTAAAGTAATATGTA 32 80 0 TTCATTTTAA 0.875357 -35 GTGCTTACATTTTATTTTAAAGCGTTCGGAT 33 61 0 TTTATTTTAA 0.813665 -88 TATGCAGTTTTTTATTTTACCAAAAAAACAG 36 13 0 TTTATTTTAC 0.920048 -288 TATACAATTTTTTATTTTAACATCATAATAG 36 211 1 TTTATTTTAC 0.920048 -90 TTCTGTTACTTTCATTTTATCAAATCGTGAG 37 42 0 TTCATTTTAC 0.948729 -39 TCATTGCACGTTCATTTCACATTTCTTACTT 39 74 0 TTCATTTCAA 0.733067 -58 AGTGCCAGTTTTCATTTTAAAGGTTTTTTCG 46 48 0 TTCATTTTAA 0.875357 -66 GCGGACATATTTCACTTTAACCGATAATCTG 48 38 0 TTCACTTTAC 0.822079 -141 TTCAACCTCCTTTATTTTAGAAAGCGCTTAC 54 171 0 TTTATTTTAA 0.813692 -26 GTTTCATGATTTTATTTTAGCGAAAGCAGGA 56 128 0 TTTATTTTAC 0.920048 -84 ATTTACATTTTTTATTTTAGAAATATAGCAA 62 71 1 TTTATTTTAA 0.813692 -111 ATAATGTCTATTCATTTTACCAAATCAAATG 67 260 0 TTCATTTTAC 0.948729 -41 ATCATATGTGTTTATTTTAACGCAGGTGCAA 70 178 0 TTTATTTTAC 0.920048 -65 GCCGAATGACTTCATTTCATCTATATAACAT 81 262 0 TTCATTTCAC 0.878581 -39 ********* * Masking position 6 Map Score: 12.3916 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 49 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 AGTGATGACAGTGATGAAAAAAGCTGTGTG 7 125 0 GTGATGAAAA 0.436089 -176 ATCAGGCACGATGAGGAAAAGATTGCA 10 166 1 ATGAGGAAAA 0.922762 -17 AAAACATAACAGGAAGAAAAATGCCCCGCT 12 17 0 AGGAAGAAAA 0.832999 -284 CAATGGGGAGAGGGAGAAAACGAGCGCAAT 13 94 0 AGGGAGAAAA 0.591477 -32 ATCCCCATCATTGAGGAAAACGA 16 12 1 TTGAGGAAAA 0.658534 -13 CTTATCTATAAGGAGGAGAAATC 19 86 1 AGGAGGAGAA 0.683363 -13 GAACGTGTTTTGGTGGAAAAATGAGTCATT 25 78 1 TGGTGGAAAA 0.520954 -58 ACAAATTGACAGGATGAAAAAACAATTTCT 26 71 1 AGGATGAAAA 0.832999 -91 GAATGCCGCGATGTGGAAAATGGAACCGTC 27 33 0 ATGTGGAAAA 0.807058 -128 GAAGGAAAGCAGGGGGAAAAC 37 70 1 AGGGGGAAAA 0.84814 -11 TTGTTTGTTAAGGTTGAAAAAAGTAAGATA 40 54 1 AGGTTGAAAA 0.635888 -38 ATATCTTATGATGATGAAAAAGCGCGATTC 42 20 0 ATGATGAAAA 0.755924 -35 CACGATGATAAGGAGGAAAAG 61 23 1 AGGAGGAAAA 0.950596 -11 CGTCATGAAAATGAAGAAAACAGACGCGAT 67 111 0 ATGAAGAAAA 0.755924 -190 TTTTGCCCTAATGTGGAAAAACCGCGAAGT 67 217 0 ATGTGGAAAA 0.807058 -84 ATGTATGTAAGTGAGGAAAACCGATAAAAC 68 187 1 GTGAGGAAAA 0.74894 -114 AGGTGTCGTGATGAAGAAAATCATGCTGTT 69 145 0 ATGAAGAAAA 0.755924 -156 GTCATTCGGCAGGAGGAAAATCAAAATG 81 283 1 AGGAGGAAAA 0.950596 -18 ********** Masking position 7 Map Score: 11.5788 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 140 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 15 CCGACGACAGTCCTGCTAAAACGTTCGTTT 1 47 0 TCCTGCTAAA 0.69194 -241 GGCTTGCTGATCCCGCGCAACAAAACGCCA 1 102 0 TCCCGCGCAA 0.781537 -186 AGCGGGAGAGTCCCGTTGAAAACAGGAAAG 1 233 0 TCCCGTTGAA 0.774439 -55 AACGGGACTCTCCCGCTGAATATTCGCGCG 1 246 1 TCCCGCTGAA 0.9767 -42 CTGATGCAAATCCTGCTGAAAGCACACAGC 7 103 1 TCCTGCTGAA 0.958044 -198 CCGCGTATGGCCCCGCCGAAGATTGGGACA 38 86 0 CCCCGCCGAA 0.898876 -50 CTTCTTCTATTTCCGCTGAAGCCAATATGT 72 39 1 TTCCGCTGAA 0.751072 -145 TGTCGCCATATCCCGCCGAACTCCATGCTC 75 14 0 TCCCGCCGAA 0.97839 -72 GCGACAGCCTTCCTGCCGAACTCCCTTCAT 75 38 1 TCCTGCCGAA 0.961138 -48 ATGGCCTGCATCCTGCTCAAGCGCCTGCCC 77 184 0 TCCTGCTCAA 0.859678 -20 TTGATTTTCCTCCTGCCGAATGACTTCATT 81 277 0 TCCTGCCGAA 0.961138 -24 ********** Masking position 9 Map Score: 8.785 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 88 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548