AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02030_ecoli_reg_300.orf -o02030_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 trg 300 methyl-accepting chemotaxis protein III, ribose sensor receptor #2 tap 45 methyl-accepting chemotaxis protein IV, peptide sensor receptor #3 tar 144 methyl-accepting chemotaxis protein II, aspartate sensor receptor #4 motA 126 proton conductor component of motor; no effect on switching #5 flhD 300 regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor #6 fliF 214 flagellar biosynthesis; basal-body MS(membrane and supramembrane)-ring and collar protein #7 fliL 104 flagellar biosynthesis #8 mglB 279 galactose-binding transport protein; receptor for galactose taxis #9 galS 141 mgl repressor, galactose operon inducer #10 folE 257 GTP cyclohydrolase I #11 aer 300 aerotaxis sensor receptor, flavoprotein #12 dppA 300 dipeptide transport protein #13 rbsD 300 D-ribose high-affinity transport system; membrane-associated protein #14 rbsB 24 D-ribose periplasmic binding protein #15 malE 300 periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis #16 tsr 300 methyl-accepting chemotaxis protein I, serine sensor receptor Motif number 1 AGAAAGTCTCAGGCACCCGCAGGCATCCTATGAGGTTTCCTTA 1 41 1 ACCCGCCCCA 0.971969 -260 TGGTCATAAGTAATTACCGTCAAGTGCCGATGACTTTCTATCA 1 239 1 TTCCGTGCCA 0.766853 -62 TCAGCAATAAAGTTTCCCCCCTCCTTGCCGATAACGAGATCAA 3 90 1 ATCCCCCGCA 0.988916 -55 CCGCTGCTTTTTTTTGCCCCAATCGCGCGTTAACGCCTGACGA 4 54 1 TTCCCCCGCA 0.972707 -73 GCACCCCGTGATGTCGCCGGGAAGCCCCGGTAAAAAATAATTA 5 232 0 ATCCGGGCCA 0.920686 -69 AATCCGCGTCTTTTCCCCGCTTTGTTGCGCTCAAGACGCAGGA 7 29 1 TTCCGCGGCA 0.98505 -76 AGTGCTGACAAAATAGCCGCCAGCAAGCAGTCATTTACTGCAA 9 89 1 ATCCGCCGCA 0.993662 -53 CAGCTTAATAACTTTGCCCCCACGCAGGGCGGAGGCGTCACAC 10 207 1 ATCCCCGGGA 0.887599 -51 AATCGGTTAAAGATAACCGCAGCGGGGCCGACATAAACTCTGA 11 228 1 ATCCGCGGCA 0.97891 -73 CCACCTCATAACGTTGACCCGACCGGGCAAAAAACAAAAAAGG 12 206 1 ATACCCCGCA 0.837665 -95 CAGCAAGTACAGCTTGCCGCGCAGACGCAAATACCACGGGCGT 13 51 0 ATCCGCGGCA 0.99193 -250 CCGTGTTCTCATCCTCCCGCCTCCTCCCCCATAAAAAAGCCAG 15 40 0 ACCCGCCCCA 0.971969 -261 CTTTCCATCCTCCTTGCCCCTACGCCCCACCGTCGCTTTGTGT 15 195 0 TTCCCCGCCT 0.734589 -106 TCAACCGCAAAACTGACCGCTTACATCCCTAAAATAACCACTC 16 70 0 ATCCGCCCCA 0.991698 -231 * * **** * ** * Masking position 8 Map Score: 17.272 Number of sites scoring better than the average of aligned sites = 572 Number in coding regions = 544 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 2 AATTGAGTGTTTTGTGTGATCTGCATCACGCATTATTGA 5 29 1 TTTGTGTCAC 0.986241 -272 CCCCCTCCGTTGTATGTGCGTGTAGTGACGAGTACAGTT 5 78 1 TTTGTGTGAC 0.927961 -223 TAACCAACTTTATTTTTATGCGGTTTCACCGCACCCCGT 5 266 0 TTTTTATCAC 0.828135 -35 GGGAGCGTCAATTTTTCGAGTTTGCTGACCCGGGAGTGA 6 133 1 ATTTCGTGAC 0.627049 -82 CCGCTTTCAATCTGTGAGTGATTTCACAGTATCTTAA 8 9 1 ATTGTGTCAC 0.981964 -271 ACCGTTTCCATTGCTGTGACTCGATTCACGAAGTCCTGT 9 46 1 TGTGTGTCAC 0.954153 -96 TGAATACTGGATTATGTGCGCCGCCTCACGCACAATAAT 10 156 1 ATTGTGTCAC 0.981962 -102 TTTTTTAATCTTTGTGTGTGGATTCTCACCGTTGGTGTA 12 54 1 TTTGTGTCAC 0.986245 -247 GGGGCGTTTTTGTTTTCATGGTTAATCACCATGTAAAAC 13 207 1 TTTTCATCAC 0.761623 -94 ACCATGTAAAACGTTTCGAGGTTGATCACATTTCCGTAA 13 234 1 AGTTCGTCAC 0.730927 -67 ATCGCCACGATTTTTGCAAGCAACATCACGAAATTCCTT 15 110 0 TTTGCATCAC 0.924952 -191 TCGTGGCGATTTTATGTGCGCATCTCCACATTACCGCCA 15 139 1 TTTGTGCCAC 0.912734 -162 ATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGAC 15 168 1 ATTGTATCAC 0.933836 -133 TCACAATATAAATATGTGATATGAATCACATATTTATCG 16 137 0 ATTGTGTCAC 0.981964 -164 * * **** **** Masking position 18 Map Score: 12.9094 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 124 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 3 TTACCGTCAAGTGCCGATGACTTTCTATCA 1 252 1 GTGCCGATGA 0.854228 -49 GGAAACTTTATTGCTGATGCCACCCGCCGC 3 77 0 TTGCTGATGC 0.79838 -68 TCCCCCCTCCTTGCCGATAACGAGATCAAC 3 104 1 TTGCCGATAA 0.713681 -41 CGGTACGTCGTTACCGCTGCTGGAATGTTG 4 27 0 TTACCGCTGC 0.971494 -100 CGGTAACGACGTACCGCTGCTTTTTTTTGC 4 41 1 GTACCGCTGC 0.957597 -86 ACTCGAAAAATTGACGCTCCCATTATTTGT 6 124 0 TTGACGCTCC 0.938372 -91 CGGTCTTCCTGTGTCGCTACTGCTTATCGG 7 79 0 GTGTCGCTAC 0.829759 -26 TCCATGCCCGGTAACGCTCCAGAAAACGGC 8 148 0 GTAACGCTCC 0.646669 -132 ATTATTGTAATTGCCGCTGCCTTTCATCAG 10 118 0 TTGCCGCTGC 0.99471 -140 TTGCAGTGGGTTGTCGCTGCCTGACCTTTT 12 243 0 TTGTCGCTGC 0.963136 -58 CAAGTACAGCTTGCCGCGCAGACGCAAATA 13 61 0 TTGCCGCGCA 0.805607 -240 CAAGCTGTACTTGCTGCTGCAACGTAATGC 13 78 1 TTGCTGCTGC 0.95622 -223 TCCATCCTCCTTGCCCCTACGCCCCACCGT 15 205 0 TTGCCCCTAC 0.827204 -96 AACGACGCCTTTGCCGCTCAACCGCAAAAC 16 100 0 TTGCCGCTCA 0.965997 -201 ********** Masking position 2 Map Score: 13.1855 Number of sites scoring better than the average of aligned sites = 2438 Number in coding regions = 2325 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 4 CGTCACTACACGCACATACAACGGAGGGGGGCTG 5 74 0 CGCCATACCG 0.990025 -227 TTTTTCTATCCGCCAATAAACCCGTTTTTTTGTT 6 81 0 CGCAATAACG 0.984876 -134 TGTTCCACTTTGCCAATAACGCCGTCCATAATCA 6 176 1 TGCAATAACG 0.918429 -39 CGCTTTGTTGCGCTCAAGACGCAGGATAATTAGC 7 46 1 CGCCAAGACG 0.960663 -59 CGTGAGGCGGCGCACATAATCCAGTATTCACAGC 10 152 0 CGCCATAACG 0.995686 -106 CGCCGCCTCACGCACAATAATCAGGCTGTAAATC 10 174 1 CGCCAATACG 0.942782 -84 TTAATTATCTTGCCCAAAAATCAGGCAATTATTG 11 107 0 TGCCAAAACG 0.947559 -194 GCCGCGCAGACGCAAATACCACGGGCGTTTGCGA 13 45 0 CGCAATACCG 0.965523 -256 TGTGGAGATGCGCACATAAAATCGCCACGATTTT 15 135 0 CGCCATAATG 0.952755 -166 TTACTTTACGCGCGCGTAACTCTGGCAACATCAC 16 25 0 CGCCGTAACG 0.979649 -276 *** ***** * * Masking position 3 Map Score: 10.7563 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 253 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 TCCCGGTTAGCCTGAAAACAGAAAGTCTCA 1 22 1 CCTGAAAACA 0.968737 -279 AAGGCACCTTCCTGAAAACAAGTTGATCTC 3 125 0 CCTGAAAACA 0.968737 -20 CGGGTTACAACGTTAAAACGGTGCAATCAT 8 61 0 CGTTAAAACG 0.741077 -219 GAGGTAACAGCGTCATAACAACAATTAAAG 8 119 1 CGTCATAACA 0.785959 -161 CGGTAACGCTCCAGAAAACGGCTTTAATTG 8 140 0 CCAGAAAACG 0.851739 -140 TTTACTGCAATCTCATAACAGGTAGTGAAT 9 122 1 TCTCATAACA 0.471458 -20 CAATTATTGCCCTGAAAACGTGCATTTGCG 11 86 0 CCTGAAAACG 0.980225 -215 GTCAACAGAATGTGAAAACGTCAATACAGC 12 104 0 TGTGAAAACG 0.80024 -197 GGCATCCCCACCTCATAACGTTGACCCGAC 12 199 1 CCTCATAACG 0.910908 -102 GGTGATTAACCATGAAAACAAAAACGCCCC 13 207 0 CATGAAAACA 0.775808 -94 ATGTGATCAACCTCGAAACGTTTTACATGG 13 235 0 CCTCGAAACG 0.832268 -66 GTGAAGTGCTCGTGAAAACACCTAAACGGA 15 263 0 CGTGAAAACA 0.947426 -38 ********** Masking position 7 Map Score: 10.4589 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 535 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 6 TGGAATGTTGCGCCTCACCGTATCAG 4 1 0 CGCCCACTCG 0.907181 -126 TATTGAAAATCGCAGCCCCCCTCCGTTGTATGTGCG 5 62 1 CGCACCCCCT 0.988901 -239 TTTTTACCGGGGCTTCCCGGCGACATCACGGGGTGC 5 239 1 GGCTCCGCCT 0.71804 -62 CTTCCTGTGTCGCTACTGCTTATCGGCTAATTATCC 7 69 0 CGCTCTCTCG 0.776372 -36 ACTTCATTAACTCTACTGCCCCGCCGAGCATTTATC 8 217 1 CTCTCTCCCG 0.7597 -63 TTGTAATTGCCGCTGCCTTTCATCAGCAGATGTTAA 10 108 0 CGCTCCTCCG 0.90217 -150 GCAGGTGTGACGCCTCCGCCCTGCGTGGGGGCAAAG 10 218 0 CGCCCCCCCT 0.991706 -40 CAGAGTTTATGTCGGCCCCGCTGCGGTTATCTTTAA 11 234 0 GTCGCCCCCG 0.839247 -67 TAATTAGTACGGCATCCCCACCTCATAACGTTGACC 12 189 1 GGCACCCCCT 0.976373 -112 TAACGCCAGACGCCTCCTTTCTTCATAAGGGGGCGT 13 178 1 CGCCCCTCCT 0.927717 -123 GGCTTAAATCCTCCACCCCCTGGCTTTTTTATGGGG 15 21 1 CTCCCCCTCT 0.917402 -280 AAGCCGTGTTCTCATCCTCCCGCCTCCTCCCCCATA 15 50 0 CTCACCCCCC 0.858248 -251 CTTGCCCCTACGCCCCACCGTCGCTTTGTGTGATCT 15 190 0 CGCCCACTCT 0.873792 -111 TTCTTTATACGGCAACCTCTTTCCATCCTCCTTGCC 15 220 0 GGCACCCTCT 0.92957 -81 GCGTAACTCTGGCAACATCACTACAGGATAGCGGT 16 10 0 GGCACACCCG 0.913617 -291 GCCTTTGCCGCTCAACCGCAAAACTGACCGCTTACA 16 88 0 CTCACCCACG 0.742428 -213 **** ** * * * * Masking position 6 Map Score: 13.0515 Number of sites scoring better than the average of aligned sites = 1542 Number in coding regions = 1456 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 CCCGATGATCTGCGCATCGGGTTTTTTATTT 3 39 1 TGCCATCGGG 0.922726 -106 TTATTTCAATTTCGCGGCGGGTGGCATCAGC 3 64 1 TTCCGGCGGG 0.938951 -81 GCGGTTTCACCGCACCCCGTGATGTCGCCGG 5 255 0 CGCCCCCGTG 0.965284 -46 CGCGCACCTCGTGGCTGATTATG 6 202 0 CGCCCTCGTG 0.979323 -13 TTGAGATAAATGCTCGGCGGGGCAGTAGAGT 8 226 0 TGCCGGCGGG 0.988066 -54 GTGACGCCTCCGCCCTGCGTGGGGGCAAAGT 10 217 0 CGCCTGCGTG 0.975482 -41 CTCCATAAAATGCCCCTCGTGACCTACAATC 12 135 0 TGCCCTCGTG 0.979764 -166 TGCAACGTAATGCGCTGCGTGCACCAGATCA 13 95 1 TGCCTGCGTG 0.975942 -206 ACTCGGCGTAATCTCCGCGGGATATTCATAA 16 226 1 ATCCCGCGGG 0.885639 -75 *** ******* Masking position 5 Map Score: 9.15521 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 459 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 ATTACTTATGACCAAAAACCTCTTTGCGTC 1 223 0 ACCAAAAACC 0.791446 -78 CGAAATTGAAATAAAAAACCCGATGCGCAG 3 48 0 ATAAAAAACC 0.508239 -97 CGATTGGGGCAAAAAAAAGCAGCGGTACGT 4 49 0 AAAAAAAAGC 0.783802 -78 GACATATTAAACCAAAAAGGTGGTTCTGCT 5 172 1 ACCAAAAAGG 0.930129 -129 AAATAGCAACAAAAAAACGGGTTTATTGGC 6 74 1 AAAAAAACGG 0.815023 -141 CACATTCGTTAACAAAACGGCTGTAACCGT 9 21 1 AACAAAACGG 0.800301 -121 TTCAGTGCTGACAAAATAGCCGCCAGCAAG 9 86 1 ACAAAATAGC 0.73308 -56 TCCATACCCGACAAAAACCGTGCAAAATAA 11 42 0 ACAAAAACCG 0.835277 -259 CGGGCAAAAAACAAAAAAGGTCAGGCAGCG 12 229 1 ACAAAAAAGG 0.936044 -72 AACCATGAAAACAAAAACGCCCCCTTATGA 13 200 0 ACAAAAACGC 0.946773 -101 CTCCTCCCCCATAAAAAAGCCAGGGGGTGG 15 33 0 ATAAAAAAGC 0.783802 -268 AGATGCGCACATAAAATCGCCACGATTTTT 15 134 0 ATAAAATCGC 0.452597 -167 TCGTGAAAACACCTAAACGGACTCTAGTTT 15 254 0 ACCTAAACGG 0.614247 -47 CGAGCACTTCACCAACAAGGACCATAGATT 15 281 1 ACCAACAAGG 0.66008 -20 ********** Masking position 5 Map Score: 5.80451 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 603 Number in noncoding regions = 157 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 9 CTCGTCCAGGTTTACTCCTGATAGAAAGTCA 1 269 0 TTTATCCTGA 0.846314 -32 AACGCGGTCATTGCCGCCTGATGGGGAGCGT 2 23 1 TTGCGCCTGA 0.986734 -23 CAATCGCGCGTTAACGCCTGACGACTGAACA 4 73 1 TTAAGCCTGA 0.915392 -54 CTGGTAGGCTTTGCTACCAGAAATTATCCGG 6 20 0 TTGCACCAGA 0.761826 -195 TTAAGCTGATTTACAGCCTGATTATTGTGCG 10 184 0 TTACGCCTGA 0.970598 -74 CAGTGGGTTGTCGCTGCCTGACCTTTTTTGT 12 239 0 TCGCGCCTGA 0.945588 -62 TGGCGTTAGATTTCGACCTGAGTACCCAGTT 13 155 0 TTTCACCTGA 0.943823 -146 AGTTTAATCCTGACTGAGTTGGG 13 288 0 TTTATCCTGA 0.846314 -13 GATGCAAGATTTTCGGCCTGGAAAGGAAAAA 16 259 0 TTTCGCCTGG 0.935026 -42 **** ****** Masking position 1 Map Score: 4.37881 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 529 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 10 CAGGAGTAAACCTGGACGAGAGACAACGGTA 1 280 1 CCTGGAGAGA 0.96407 -21 CGCAACAAAGCGGGGAAAAGACGCGGATTAC 7 27 0 CGGGGAAAGA 0.866873 -78 CAAGCACTACCCTGCATAAGAAAAACCGGAG 8 254 1 CCTGCAAAGA 0.984824 -26 AGGCGTCACACCTGCAGGAGAAATCATAA 10 239 1 CCTGCAGAGA 0.977595 -19 CGACAAAAACCGTGCAAAATAACAACAAATG 11 33 0 CGTGCAAATA 0.816653 -268 AACCATATAACCTGCACAGGACGCGAAC 11 283 1 CCTGCAAGGA 0.973508 -18 TAATGCGCTGCGTGCACCAGATCAATTTGAA 13 102 1 CGTGCACAGA 0.935822 -199 AGATTTTCGGCCTGGAAAGGAAAAACTTTAT 16 253 0 CCTGGAAGGA 0.957603 -48 ****** **** Masking position 6 Map Score: 4.13296 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 109 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 11 AGTGATTATTCACTGTTACATACGGGTTAC 8 83 0 CACTGTTACA 0.976852 -197 GTTGTTATGACGCTGTTACCTCGGCAAAAG 8 111 0 CGCTGTTACC 0.95414 -169 AATACTTTCACTCTGTTACTATACGAAAAC 11 142 0 CTCTGTTACT 0.943507 -159 GGAGGATCCGCACTGTTACACTGATGTTAA 12 162 1 CACTGTTACA 0.976852 -139 TTTGTGTGATCTCTGTTACAGAATTGGCGG 15 172 0 CTCTGTTACA 0.976852 -129 ********** Masking position 6 Map Score: 3.18891 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 24 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 12 AAACTTTATTGCTGATGCCACCCGCCGCGA 3 75 0 GCTGATGCCA 0.867057 -70 CGTCGTTACCGCTGCTGGAATGTTGCGCCT 4 22 0 GCTGCTGGAA 0.960961 -105 TTTAACATCTGCTGATGAAAGGCAGCGGCA 10 107 1 GCTGATGAAA 0.870106 -151 CTGATGAAAGGCAGCGGCAATTACAATAAT 10 118 1 GCAGCGGCAA 0.915928 -140 TTTGATGATTGCTGCGCAAATGCACGTTTT 11 72 1 GCTGCGCAAA 0.854342 -229 CACAAATTTCTCTGCTGCAAATAGCTGTTT 12 19 1 TCTGCTGCAA 0.960869 -282 TATTCTGCTCCAATTGTGATGTT 12 288 0 TCTGCTCCAA 0.896764 -13 AGCTGTACTTGCTGCTGCAACGTAATGCGC 13 80 1 GCTGCTGCAA 0.990771 -221 ********** Masking position 10 Map Score: 3.77052 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 1025 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 13 GTCTTTCTGATTCCCGGTTAGCCTGA 1 4 1 TTCTGATTCG 0.923012 -297 TGCCTGAGACTTTCTGTTTTCAGGCTAACCGGG 1 23 0 TTCTGTTTCG 0.682389 -278 AAGGCACCTTCCTGAAAACAAGTT 3 131 0 AGCACCTTCG 0.44608 -14 GTTCTGCTTATTGCAGCTTATCGCAACTATTCT 5 194 1 TTCAGCTTTG 0.886019 -107 GCGCACCTCGTGGCTGATTATGGACGGCGTTAT 6 191 0 TGCTGATTTG 0.954318 -24 TCCTGTGTCGCTACTGCTTATCGGCTAATTATC 7 70 0 CTCTGCTTTG 0.719623 -35 TTGCAGTAAATGACTGCTTGCTGGCGGCTATTT 9 99 0 TGCTGCTTCG 0.972282 -43 GCGTGGCTCCTTGTTGTGTTGTTTGC 10 4 1 TGCTCCTTTG 0.838325 -254 GCTGATTTACAGCCTGATTATTGTGCGTGAGGC 10 178 0 AGCTGATTTG 0.823962 -80 GGGTATGGATTTGATGATTGCTGCGCAAATGCA 11 63 1 TTATGATTCG 0.58202 -238 GGGCAATAATTGCCTGATTTTTGGGCAAGATAA 11 104 1 TGCTGATTTG 0.954318 -197 CACATTCTGTTGACAGATTGTAGGTCACGAGGG 12 120 1 TGCAGATTTG 0.92257 -181 GCAGCAGCAAGTACAGCTTGCCGCGCAGACGCA 13 65 0 GTCAGCTTCG 0.640174 -236 TGTGGACCGATGCAAGATTTTCGGCCTGGAAAG 16 265 0 TGAAGATTTG 0.580512 -36 ** ****** * * Masking position 8 Map Score: 4.52178 Number of sites scoring better than the average of aligned sites = 1174 Number in coding regions = 1058 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 14 AAATTCTGGAAAACAGCACGCAATTTCGTGAAG 1 100 0 AAACGCACAA 0.845483 -201 ACCCGCCGCGAAATTGAAATAAAAAACCCGATG 3 53 0 AAATGAAAAA 0.694613 -92 TGCGTGATGCAGATCACACAAAACACTCAATTA 5 28 0 AGATACAAAA 0.839491 -273 GGGTGCGGTGAAACCGCATAAAAATAAAGTTGG 5 269 1 AAACGCAAAA 0.927144 -32 CAAAGGCGCTAAATAGCAACAAAAAAACGGGTT 6 64 1 AAATGCAAAA 0.96301 -151 ACCTGTTATGAGATTGCAGTAAATGACTGCTTG 9 112 0 AGATGCAAAA 0.948814 -30 TATGATGAAGAAATTGCAAACAACACAACAAGG 10 19 0 AAATGCACAA 0.917994 -239 AAATGTTAACAGATAGCATTAAATATT 11 5 0 AGATGCAAAA 0.948814 -296 AAACCGTGCAAAATAACAACAAATGTTAACAGA 11 25 0 AAATACAAAA 0.880178 -276 CCGACCGGGCAAAAAACAAAAAAGGTCAGGCAG 12 224 1 AAAAACAAAA 0.568296 -77 **** *** *** Masking position 8 Map Score: 4.49186 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 122 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 15 CGAGTATTTACTAACGCGGTCA 2 3 1 AGTATTTACT 0.741989 -43 GGCAAAAGTGATTATTCACTGTTACATACG 8 89 0 ATTATTCACT 0.913432 -191 CACATAATCCAGTATTCACAGCGATAATTA 10 144 0 AGTATTCACA 0.942193 -114 ATTTACATAAATTATTCACAATATAAATAT 16 161 0 ATTATTCACA 0.951664 -140 TTAAAAAGCCATTATTTACATAAATTATTC 16 174 0 ATTATTTACA 0.869288 -127 CCGAGTGAATTTTATTCACACTCTGAATTT 16 202 0 TTTATTCACA 0.829275 -99 ********** Masking position 5 Map Score: 0.323978 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 28 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802