AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -iphoB_ecoli_hinf_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 HI0362 300 iron (chelated) ABC transporter, periplasmic-binding protein (yfeA) #19 HI1379 300 phosphate regulon transcriptional regulatory protein (phoB) #20 HI1382 90 phosphate ABC transporter, permease protein (pstC) #21 HI1383 300 phosphate ABC transporter, periplasmic-binding protein (pstS) Motif number 1 GCGGCGTGAACGCCTTATCCAGCCTACCAAACC 7 47 0 CGCCATCCAC 0.987745 -254 AAGGCGTTCACGCCGCATCCGGCGATCGTGCAC 7 64 1 CGCCATCCGC 0.999345 -237 GCGGCGTAAACGCCTTATCAGGCCTACAAGATC 9 33 0 CGCCATCAGC 0.986154 -268 AAGGCGTTTACGCCGCATCCGGCATGAAACGAT 9 50 1 CGCCATCCGC 0.999345 -251 CCCTCACCCACGCCGTCACCGCCTTGTCATCTT 9 152 1 CGCCCACCGC 0.982264 -149 GTTTTCCCCTCACCCTAACCCTCTCCCCAGAGG 10 24 1 CACCAACCCC 0.90483 -159 CAGGCGTTCACGCCGCATCCGGCAAAGTGTTAA 10 99 0 CGCCATCCGC 0.999345 -84 GCGGCGTGAACGCCTGATCCGGCCTACGGTAAG 10 116 1 CGCCATCCGC 0.999345 -67 CGGCGTAAAACACCGTACCCGGCCTGGAGTTTT 11 12 0 CACCACCCGC 0.967434 -75 CGGTGTTTTACGCCGCATCCGGCATTACAAAAT 11 30 1 CGCCATCCGC 0.999345 -57 CTGGCCCCCTCACCCTAACCCTCTCCCCAGAGG 13 29 1 CACCAACCCC 0.90483 -97 AAGGCGTTTACGCCGCATCCGGCACCGGC 14 7 0 CGCCATCCGC 0.999345 -104 GCGGCGTAAACGCCTTATCCGGCCTACAAATGC 14 24 1 CGCCATCCGC 0.999345 -87 GACGCTGACGCGTCTTATCCGACCTACGGGGAG 14 58 0 CGTCATCCGC 0.99649 -53 GACGCGTCAGCGTCGCATCCGACACCCGAACCA 14 77 1 CGTCATCCGC 0.99649 -34 GACGCCGGGGCGTCTTATCCGACCTACGAT 15 8 0 CGTCATCCGC 0.99649 -47 GACGCCCCGGCGTCGCATCCGACAATGTGCAGG 15 27 1 CGTCATCCGC 0.99649 -28 TGTTGTCCGCCGCCCGAACCGATGGATTGATAA 21 232 0 CGCCAACCGT 0.958441 -69 **** ***** * Masking position 9 Map Score: 73.206 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 199 Number in noncoding regions = 395 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 2 TTATCCGTGCCCCATCTCCCATTTTCCCTC 9 127 1 CCCATCTCCC 0.969636 -174 TCTCCCATTTTCCCTCACCCACGCCGTCAC 9 141 1 TCCCTCACCC 0.993329 -160 ACACGGTTTTCCCCTCACCCTAACCCTCTC 10 19 1 CCCCTCACCC 0.997539 -164 CCTCACCCTAACCCTCTCCCCAGAGGGGCG 10 31 1 ACCCTCTCCC 0.987625 -152 CTCGGTCGGTCCCCTCGCCCCTCTGGGGAG 10 46 0 CCCCTCGCCC 0.997489 -137 GCGCGCTGGCCCCCTCACCCTAACCCTCTC 13 24 1 CCCCTCACCC 0.997539 -102 CCTCACCCTAACCCTCTCCCCAGAGGGGCG 13 36 1 ACCCTCTCCC 0.987625 -90 CACAATCGGTCCCCTCGCCCCTCTGGGGAG 13 51 0 CCCCTCGCCC 0.997489 -75 GCTCGTTTTCTCCCTCTCCCCATTGGGGTG 13 99 1 TCCCTCTCCC 0.993329 -27 CGCCCCTCACCCCAATGGGGAG 13 114 0 CCCCTCACCC 0.997539 -12 CAGCGTCGCATCCGACACCCGAACCACGAG 14 84 1 TCCGACACCC 0.802612 -27 GCCGGGAGGCCCGCCCTCCCGCACTGTCAT 17 14 1 CCGCCCTCCC 0.932028 -119 TTTGCTGTTGTCCGCCGCCCGAACCGATGG 21 240 0 TCCGCCGCCC 0.915761 -61 ********** Masking position 6 Map Score: 37.5517 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 59 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 GACGCATAATGACGTCGCATTAATGATCGC 5 143 1 GACGTCGCAT 0.916316 -47 ACGCTTGCGCGTCTTATCATGCCTACA 7 8 1 CGCGTCTTAT 0.769301 -293 ATGCGGCGTGAACGCCTTATCCAGCCTACC 7 52 0 AACGCCTTAT 0.905798 -249 ATAAGGCGTTCACGCCGCATCCGGCGATCG 7 62 1 CACGCCGCAT 0.975568 -239 ATCGTGCACTGATGCCTGATGCAAATCCTG 7 88 1 GATGCCTGAT 0.690578 -213 TCAGTGTAATGTCGGATGCGTTTCGCT 8 8 1 AATGTCGGAT 0.613851 -90 ATTCCTGAACTGTGCCGGATGCGCTTCGCT 8 70 0 TGTGCCGGAT 0.708625 -28 ATGCGGCGTAAACGCCTTATCAGGCCTACA 9 38 0 AACGCCTTAT 0.905798 -263 ATAAGGCGTTTACGCCGCATCCGGCATGAA 9 48 1 TACGCCGCAT 0.953103 -253 ATCAGGCGTTCACGCCGCATCCGGCAAAGT 10 104 0 CACGCCGCAT 0.975568 -79 ATGCGGCGTGAACGCCTGATCCGGCCTACG 10 114 1 AACGCCTGAT 0.917618 -69 TTTTCCTCATCGTGCCTGATGCACTTCGCT 10 156 0 CGTGCCTGAT 0.709009 -27 TACGGTGTTTTACGCCGCATCCGGCATTAC 11 28 1 TACGCCGCAT 0.953103 -59 ATAAGGCGTTTACGCCGCATCCGGCACCGG 14 12 0 TACGCCGCAT 0.953103 -99 ATGCGGCGTAAACGCCTTATCCGGCCTACA 14 22 1 AACGCCTTAT 0.905798 -89 GCGACGCTGACGCGTCTTATCCGACCTACG 14 63 0 CGCGTCTTAT 0.769301 -48 AAGACGCGTCAGCGTCGCATCCGACACCCG 14 75 1 AGCGTCGCAT 0.911656 -36 GCGACGCCGGGGCGTCTTATCCGACCTACG 15 13 0 GGCGTCTTAT 0.729154 -42 AAGACGCCCCGGCGTCGCATCCGACAATGT 15 25 1 GGCGTCGCAT 0.90611 -30 CAAATACATAAATGCCGTATAGTCGGAGCA 19 94 0 AATGCCGTAT 0.801589 -207 ********** Masking position 10 Map Score: 27.3986 Number of sites scoring better than the average of aligned sites = 1859 Number in coding regions = 1173 Number in noncoding regions = 686 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 4 TGGCAGATCACGGGCGCATACGCTCATGGTTAA 4 75 1 CGGCGCTAGC 0.980124 -26 TTTGGGTATAATCGCGCCCATGCTTTTTCGCCA 5 21 0 ACGCGCCAGC 0.98526 -169 TAGGCATGATAAGACGCGCAAGCGT 7 3 0 AGACGCCAGC 0.983687 -298 TAGGCTGGATAAGGCGTTCACGCCGCATCCGGC 7 54 1 AGGCGTCAGC 0.991777 -247 CACGCCGCATCCGGCGATCGTGCACTGATGCCT 7 72 1 CGGCGACGGC 0.853139 -229 CTGACCTGGCATCGCGTGTAGGCCGGATAAGCG 8 41 1 ACGCGTTAGC 0.909757 -57 TAGGCCTGATAAGGCGTTTACGCCGCATCCGGC 9 40 1 AGGCGTTAGC 0.974698 -261 CAGAGTCAAAAAGGCGCTCGGTCGGTCCCCTCG 10 59 0 AGGCGCCGTC 0.913216 -124 TAGGCCGGATCAGGCGTTCACGCCGCATCCGGC 10 109 0 CGGCGTCAGC 0.986469 -74 TGAGGGGGCCAGCGCGCACATTCCCTCTCA 13 8 0 ACGCGCCATC 0.877675 -118 TAGGCCGGATAAGGCGTTTACGCCGCATCCGGC 14 17 0 AGGCGTTAGC 0.974698 -94 TAGGTCGGATAAGACGCGTCAGCGTCGCATCCG 14 65 1 AGACGCTCGC 0.933956 -46 TAGGTCGGATAAGACGCCCCGGCGTCGCATCCG 15 15 1 AGACGCCCGC 0.977914 -40 TGCGGGAGGGCGGGCCTCCCGGCGGG 17 4 0 CGGCCTCCGC 0.817837 -129 GGATAAGGGAAAGACGCTCCAGCACCAGTGATG 21 145 0 AGACGCCCGC 0.977914 -156 * ***** ** ** Masking position 5 Map Score: 23.8969 Number of sites scoring better than the average of aligned sites = 1435 Number in coding regions = 1156 Number in noncoding regions = 279 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 5 CCTAAAATTGAATGGCAGAGAATC 1 5 0 AATGGCAGAG 0.833435 -283 TTTACGCTTTTATTACAGATTTAATAAATT 1 144 1 TATTACAGAT 0.786442 -144 GTTAAAGATATATTACAGATTAATAATATT 1 187 0 TATTACAGAT 0.786442 -101 GTATTATTTTTATGACAAAGGAAATACTTT 2 213 0 TATGACAAAG 0.672129 -88 CTTTATGACAGCTGTTGAAAAGA 3 19 0 TATGACAGCT 0.802476 -13 AACCAGACTTAATGGCAGATCACGGGCGCA 4 63 1 AATGGCAGAT 0.75716 -38 GCGTCAGATTTATGACAGATTTATGAAAAG 5 118 0 TATGACAGAT 0.962628 -72 ATGACAGAGTGATGACAGTGATGAAAAAAG 7 132 0 GATGACAGTG 0.936499 -169 CTACTGGAAAGATGACAGAGTGATGACAGT 7 143 0 GATGACAGAG 0.97681 -158 GACATGCTCGAATTACAGAAAAATAACTTT 9 218 0 AATTACAGAA 0.463763 -83 ATTTTCATTCTGTGACAGAGAAAAAGTAGC 12 92 0 TGTGACAGAG 0.906081 -209 ATAACGAAGAGATGACAGAAAAATTTTCAT 12 114 0 GATGACAGAA 0.92239 -187 ATGACAGTTTTATGACAGAGAGATAAAGTC 12 193 0 TATGACAGAG 0.97638 -108 ATGTAAGGAATATGACAGTTTTATGACAGA 12 204 0 TATGACAGTT 0.900185 -97 AGGACAAACAGGTGACAGTTATATGTAAGG 12 226 0 GGTGACAGTT 0.682014 -75 ACGGGAATTCGATGACAGTGCGGGAGGGCG 17 25 0 GATGACAGTG 0.936499 -108 ATAAACCTAAAATGACAGAACAAACCAAAA 18 46 0 AATGACAGAA 0.858141 -255 ********** Masking position 7 Map Score: 18.9975 Number of sites scoring better than the average of aligned sites = 233 Number in coding regions = 197 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 AAACCACCCGGCAGCGAAAATTCACTGCCG 4 20 0 GCAGCGAAAA 0.907243 -81 ATCGCCGGATGCGGCGTGAACGCCTTATCC 7 60 0 GCGGCGTGAA 0.98922 -241 CATGCCGGATGCGGCGTAAACGCCTTATCA 9 46 0 GCGGCGTAAA 0.995336 -255 TTTTATGCTCGCGGGGTAACATGACATGCT 9 240 0 GCGGGGTAAC 0.922488 -61 GGGTTAGGGTGAGGGGAAAACCGTGTCAGC 10 15 0 GAGGGGAAAA 0.838056 -168 TTTGCCGGATGCGGCGTGAACGCCTGATCC 10 106 1 GCGGCGTGAA 0.98922 -77 AATGCCGGATGCGGCGTAAAACACCGTACC 11 26 0 GCGGCGTAAA 0.995336 -61 GGTGCCGGATGCGGCGTAAACGCCTTATCC 14 14 1 GCGGCGTAAA 0.995336 -97 CCCGAACCACGAGGCGAAAA 14 101 1 GAGGCGAAAA 0.950867 -10 ATCGGTTCGGGCGGCGGACAACAGCAAATT 21 242 1 GCGGCGGACA 0.931949 -59 ********** Masking position 6 Map Score: 18.5091 Number of sites scoring better than the average of aligned sites = 690 Number in coding regions = 494 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 AATACTTCCAGACACTATGAAGTTGTGAAACA 2 238 1 GCACTATGAG 0.953109 -63 GTGATAGTCAGTCACTATGGAGATCGCGG 7 282 1 GCACTATGGG 0.970072 -19 CGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAG 10 38 0 GCCCTCTGGG 0.987982 -145 AAGTGCATCAGGCACGATGAGGAAAAGATTGC 10 160 1 GCACGATGAG 0.970072 -23 GAAGAAAAATGCCCCGCTTACGCA 12 3 0 GCCCGCTTAG 0.877891 -298 CGGTCCCCTCGCCCCTCTGGGGAGAGGGTTAG 13 43 0 GCCCTCTGGG 0.987982 -83 GGTGTCGGATGCGACGCTGACGCGTCTTATCC 14 71 0 GGACGCTGAG 0.971181 -40 ATTGTCGGATGCGACGCCGGGGCGTCTTATCC 15 21 0 GGACGCCGGG 0.918082 -34 ACAATAATCCGCCACGATGGAGCCACTTTTTT 17 97 1 GCACGATGGG 0.98102 -36 GTTGATTTTGGTGCCTCTGACGATCCA 21 284 1 GGCCTCTGAG 0.958149 -17 * ******** * Masking position 5 Map Score: 11.7801 Number of sites scoring better than the average of aligned sites = 786 Number in coding regions = 724 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 8 TGCCGCTAGGCTTGCTGATCCCGCGCAACA 1 110 0 CTTGCTGATC 0.794602 -178 GTCTGTATTTCCTTATCCAAAGTATGG 2 284 0 TTTCCTTATC 0.835345 -17 CGCCTTGCTCATCGGACGCAGAG 6 4 1 CTTGCTCATC 0.952659 -54 TCGGATGCGTTTCGCTTATCTGACCTGGCA 8 22 1 TTCGCTTATC 0.963138 -76 CCGGATGCGCTTCGCTTATCCGGCCTACAC 8 56 0 TTCGCTTATC 0.963138 -42 AACTCTACAGATTGCTCATCGTTTCATGCC 9 70 0 ATTGCTCATC 0.756874 -231 TCTATATTTTCCCGCTTATCCGTGCCCCAT 9 112 1 CCCGCTTATC 0.795245 -189 ATCTCCCATTTTCCCTCACCCACGCCGTCA 9 140 1 TTCCCTCACC 0.714972 -161 GGTCGGTCCCCTCGCCCCTCTGGGGAGAGG 10 43 0 CTCGCCCCTC 0.850575 -140 CCTGATGCACTTCGCTAATCAGGCTTACCG 10 142 0 TTCGCTAATC 0.844345 -41 TGCAATCTTTTCCTCATCGTGCCTGATG 10 165 0 TTTCCTCATC 0.890352 -18 TTTGTCCTATTTTGCTTCTCGTAGCCAACA 12 248 1 TTTGCTTCTC 0.850253 -53 AATCGGTCCCCTCGCCCCTCTGGGGAGAGG 13 48 0 CTCGCCCCTC 0.850575 -78 TGGAGCGTCTTTCCCTTATCCAATTTATGC 21 157 1 TTCCCTTATC 0.914848 -144 ********** Masking position 5 Map Score: 9.21159 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 569 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 9 GCGTCTTATCATGCCTACAATCAGTGCGGG 7 19 1 ATGCCTACAA 0.770602 -282 TTCGCTTATCCGGCCTACACGCGATGCCAG 8 46 0 CGGCCTACAC 0.977152 -52 ACGCCTTATCAGGCCTACAAGATCGTGCAA 9 27 0 AGGCCTACAA 0.962823 -274 ACGCCTGATCCGGCCTACGGTAAGCCTGAT 10 125 1 CGGCCTACGG 0.989588 -58 ACGCCTTATCCGGCCTACAAATGCGCTCCC 14 33 1 CGGCCTACAA 0.989576 -78 GCGTCTTATCCGACCTACGGGGAGCGCATT 14 52 0 CGACCTACGG 0.962863 -59 GCGTCTTATCCGACCTACGAT 15 2 0 CGACCTACGA 0.969016 -53 ********** Masking position 7 Map Score: 6.82924 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 44 Number in noncoding regions = 148 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 10 GAGTTTTTTTCTCTTAATTATAAGTTAACGA 2 58 1 CTCTTATTAT 0.935431 -243 GAAATATATTCTCTTCGTTAACTTATAATTA 2 72 0 CTCTTCTTAA 0.938985 -229 TATTTCATAACTTTTATTTATAATAAAGGTT 2 97 1 CTTTTATTAT 0.88395 -204 AAAATATAGGCTTTTAATTATCAACCTTTAT 2 119 0 CTTTTATTAT 0.88395 -182 CGAAACGTTTCTCTTATTTAAATAATTACCC 2 154 0 CTCTTATTAA 0.960894 -147 GTGCGACGAGCTTTTCATAAATCTGTCATAA 5 108 1 CTTTTCTAAA 0.667512 -82 AATATATTTACTTATATTTAACTATAAAACA 7 194 0 CTTATATTAA 0.621424 -107 TTTCTGTCATCTCTTCGTTATTAATGTTTGT 12 123 1 CTCTTCTTAT 0.900732 -178 TGAATATCAACGCTTATTTAAATCAGACTGA 12 161 1 CGCTTATTAA 0.822294 -140 CTGTTAGTCACTTTTAATTAACCAAATCGTC 17 66 1 CTTTTATTAA 0.928155 -67 ATTTTGAGTTCTCTTATTAAAAAGTAAAAGT 19 219 1 CTCTTATAAA 0.859088 -82 ****** **** Masking position 10 Map Score: 6.87388 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 41 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 GCGTAAACAACTGCCGCTAGGCTTGCTGAT 1 121 0 CTGCCGCTAG 0.84483 -167 CGAAAATTCACTGCCGGGCGCGGTT 4 6 0 CTGCCGGGCG 0.540161 -95 TGAATTTTCGCTGCCGGGTGGTTTTTTTGC 4 26 1 CTGCCGGGTG 0.725165 -75 AACGGTTCCCTGGCGAAAAAGCATG 5 6 1 TTCCCTGGCG 0.529407 -184 CTGACTATCACTGCCGGGAACTTCCGCTGC 7 263 0 CTGCCGGGAA 0.613061 -38 ATGTCATGTTACCCCGCGAGCATAAAACGC 9 243 1 ACCCCGCGAG 0.619939 -58 CCCTAACCCTCTCCCCAGAGGGGCGAGGGG 10 36 1 CTCCCCAGAG 0.899757 -147 ACACCGTACCCGGCCTGGAGTTTTA 11 6 0 CGGCCTGGAG 0.811658 -81 TTTATGAATCCTCCCAGGAGACATT 12 286 1 CTCCCAGGAG 0.582426 -15 CCCTAACCCTCTCCCCAGAGGGGCGAGGGG 13 41 1 CTCCCCAGAG 0.899757 -85 TACAAATGCGCTCCCCGTAGGTCGGATAAG 14 48 1 CTCCCCGTAG 0.866768 -63 TCGGATAAGACGCCCCGGCGTCGCATCCGA 15 19 1 CGCCCCGGCG 0.722848 -36 CCCGCCGGGAGGCCCGCCCTC 17 2 1 CCGCCGGGAG 0.752625 -131 TTGCTGTTGTCCGCCGCCCGAACCGATGGA 21 239 0 CCGCCGCCCG 0.658111 -62 ********** Masking position 5 Map Score: 9.38611 Number of sites scoring better than the average of aligned sites = 1396 Number in coding regions = 1299 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 12 AAAGTTAATCTTTTCAACAGCTGTCATAA 3 7 1 AATTTCAACA 0.908507 -25 ATCGCAACCTATTTATTACAACAGGGCAAATC 5 168 1 ATTTTCAACA 0.956388 -22 CAGATCTCGCATTTATTGCAACAATATATTTAC 7 214 0 ATTTTCAACA 0.956388 -87 GCTGCTACTTAATAAGTACAACAGATCTCGCAT 7 235 0 AATGTCAACA 0.9406 -66 GAATTCGCGCATTCGGTACAACAAGAGAGATAA 9 275 1 ATTGTCAACA 0.9722 -26 TTTGGTTAGTATTAAGTTCAGCAATAGTCTTGG 18 88 0 ATTGTCAGCA 0.879419 -213 ATTTATAATTATTTCGTACAAAATGTATTGAAT 18 143 0 ATTGTCAAAA 0.858063 -158 AATTAGTTGAATTTGGTCAAACACAACAAATTT 19 128 1 ATTGTAAACA 0.753405 -173 CACAATTATTTTCTACACTTCGCTACG 21 5 1 ATTTTCTACA 0.755243 -296 GACAACAGCAAATTATTGCAAAAACGGTTGATT 21 258 1 AATTTCAAAA 0.631888 -43 *** ** ***** Masking position 7 Map Score: 5.3311 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 78 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 ATGGCCATGCGGTGAGTTTTTTTCTCTTAATTA 2 45 1 GGTGTTTTTT 0.961116 -256 TTTCGCTGCCGGGTGGTTTTTTTGCTGTTAGCA 4 31 1 GGGGTTTTTT 0.975258 -70 CTCCAGGCCGGGTACGGTGTTTTACGCCGCATC 11 16 1 GGTGGTTTTT 0.837526 -71 TGCGTAAGCGGGGCATTTTTCTTCCTGTTATGT 12 11 1 GGGTTTTCTT 0.880704 -290 CTGTTCTACAGTGACTTTTTCTTGGTCAGTTGT 18 14 1 GTGTTTTCTT 0.675643 -287 ACTTTTTCTTGGTCAGTTGTTTTGGTTTGTTCT 18 27 1 GGTGTTTTTT 0.961116 -274 TAACCAAAATGTTTTGTTCTTTTTTCATACATT 18 113 1 GTTGTTTTTT 0.874597 -188 CGGTAAAATGGGGTAGTTATTTTGAGTTCTCTT 19 201 1 GGGGTTTTTT 0.975258 -100 CATTAATAAAGTGCGGTTATCTTAAATAATTTT 20 57 1 GTGGTTTCTT 0.92337 -34 TTTAACCTTAGGTACGTTACCTTTTGCTCAAGC 21 106 1 GGTGTTCCTT 0.848135 -195 *** *** **** Masking position 8 Map Score: 6.12601 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 83 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 TTTCATTCCTGATTTTAATTAACGCGCGA 1 269 0 TTTCCTTTAT 0.926846 -19 GGAAGCTAATTTATTCCTGGCTTAAATGGCCATGCGG 2 20 1 TTTCCTTTAT 0.926846 -281 GAAGAGAATATATTTCATAACTTTTATTTATAATAAA 2 87 1 TTTCATTTAT 0.967176 -214 TAATGTTAACTTCTCCATACTTTGGATAAGGAAATAC 2 270 1 TTCCATTTAT 0.860043 -31 GCACACAGCTTTTTTCATCACTGTCATCACTCTGTCA 7 124 1 TTTCATTGAT 0.860043 -177 CTGTAGAGTTTGATTCAGACCTTCTATATTTTCCCGC 9 90 1 TTTCAGTTAT 0.926846 -211 GTTTTGTTCTTTTTTCATACATTCAATACATTTTGTA 18 123 1 TTTCATTTAT 0.967176 -178 TATTGAACAATTATTCAGGCATTCAATCTATCTTTTT 18 258 1 TTTCAGTTAT 0.926846 -43 AATACTCCTTCATTTGATTTATGGCATAAAAG 19 279 0 TTTCATATAT 0.891197 -22 AATAAGATTTTTTTTCATTTTATGCATAAACATAACA 21 65 0 TTTCATATAT 0.891197 -236 * ***** ** ** Masking position 4 Map Score: 4.84387 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 23 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 ATTACCCACACAAAATATAGGCTTTTAATTATCAA 2 126 0 CAAAATAGTT 0.755195 -175 CGCTGGTAATCAAACAAAAAATATTTGCGCAAAGT 2 183 1 CAAAAAAATT 0.683149 -118 ATTTTTATGACAAAGGAAATACTTTGCGCAAATAT 2 203 0 CAAAAAATTT 0.683148 -98 CAAGATCGTGCAAATTCAACATATTGCCA 9 5 0 CAAACAACTT 0.977024 -296 AGGTCTGAATCAAACTCTACAGATTGCTCATCGTT 9 77 0 CAAACTACTT 0.957094 -224 TGTGTTTGACCAAATTCAACTAATTCACCCAAATA 19 118 0 CAAACAACTT 0.977024 -183 TGAATTTGGTCAAACACAACAAATTTTTGATAGAC 19 135 1 CAAACAACTT 0.977024 -166 GCACTTTATACAAAACCTAGCACTTAACATTAATA 20 30 1 CAAACTAGTT 0.903963 -61 TCAGAGGCACCAAAATCAACCGTTTTTGCAATAAT 21 269 0 CAAACAACTT 0.977024 -32 **** **** ** Masking position 9 Map Score: 3.91806 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 41 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555