AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_ecoli_reg_100.orf -o00970_ecoli_100.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 b0024 102 orf, hypothetical protein #2 ileS 42 isoleucine tRNA synthetase #3 proS 111 proline tRNA synthetase #4 cysS 173 cysteine tRNA synthetase #5 leuS 234 leucine tRNA synthetase #6 glnS 202 glutamine tRNA synthetase #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 asnS 168 asparagine tRNA synthetase #10 tyrS 128 tyrosine tRNA synthetase #11 pheS 283 phenylalanine tRNA synthetase, alpha-subunit #12 thrS 300 threonine tRNA synthetase #13 aspS 276 aspartate tRNA synthetase #14 argS 209 arginine tRNA synthetase #15 metG 101 methionine tRNA synthetase #16 gltX 258 glutamate tRNA synthetase, catalytic subunit #17 hisS 110 histidine tRNA synthetase #18 alaS 128 alanyl-tRNA synthetase #19 prfB 90 peptide chain release factor RF-2 #20 dsbC 24 protein disulfide isomerase II #21 xerD 111 site-specific recombinase #22 def 129 peptide deformylase #23 dam 106 DNA adenine methylase #24 glyQ 300 glycine tRNA synthetase, alpha subunit #25 lysU 236 lysine tRNA synthetase, inducible; heat shock protein #26 yjeA 294 putative lysyl-tRNA synthetase #27 holC 52 DNA polymerase III, chi subunit #28 BIME233 22 BIME #29 pepA 266 aminopeptidase A/I Motif number 1 GCTCAAGGCGAGCCTGGGACAAAAAAAAGTGATTT 3 55 0 AGCCGGAAAA 0.892573 -57 GGTCATATATAGGGTGGTGTTATAGCATAACCGCA 4 54 1 AGGGGTGAAG 0.799234 -120 ATGTGGCCACAGCCTGCGACCACAGGGATACAGTA 8 34 0 AGCCGGAAAG 0.980363 -57 TGATTGCAGATGCCAGGTAACATAGGTATCCCCCC 9 91 1 TGCCGTAAAG 0.680225 -78 CACGACTTTTCGCCAGATGCGAAAGAGACATAGAA 10 64 0 CGCCGTGAAG 0.90727 -65 CCAGGAGGCTAGCGCGTGAGAAGAGAAACGGAAAA 11 13 1 AGCGGGAAAG 0.902579 -271 TTTCGAGCACAGCCCGGGACCAAAATGGCAAGTAA 11 192 1 AGCCGGAAAA 0.892573 -92 CAAGTAAAATAGCCTGATGGGATAGGCTCTAAGTC 11 220 1 AGCCGTGAAG 0.946288 -64 CTTTATATCGGGCCTGAAATCAGACTCTACGCCAG 13 89 0 GGCCGAAAAC 0.532073 -188 GAATGAAAAAAGGCGGCTATTATACTGGAAATTCT 13 169 0 AGGCGTAAAC 0.911993 -108 TAAAGAAATTAGGGCGGGAGTATACTGCAAATGGC 14 138 0 AGGGGGAAAC 0.827674 -72 TTGAGGAATCAGGCGGGAGTGATAGAATATCGCCC 16 176 1 AGGCGAGAAG 0.871448 -83 GTTACCAGCCCGGCGGTTAAGACACGCTGGAGCTG 18 68 1 CGGCGTAAAC 0.851959 -61 GCTAGTCAAAATGCGGTGATAAGAGCGGGATTGTA 19 46 0 ATGCGGAAAG 0.877664 -45 ATGCCTTATTGTGCCGTGACTAAAGCGATTCTGAT 21 54 0 GTGCGGAAAG 0.752064 -58 ACACCTTCTCCGGCTGTGGAGAAAGCTCCGACAGC 23 67 0 CGGCGGGAAG 0.967484 -40 TATATCTTCCATCCAGCGGGTATACTGATCCCTTC 24 243 1 ATCCGGGAAC 0.688567 -58 CTAATAGTCGAGGCAGATAATACAGTGTACCGATC 25 164 1 AGGCGTAAAG 0.960536 -73 AAACAGCGGTGGGCAGTGACTAAAAAAAGCACGAT 26 223 0 GGGCGGAAAA 0.810515 -72 TTAAAGACAACGGCGGTGGCTACAGATAGAATTGC 29 224 0 CGGCGGGAAG 0.967484 -43 **** * ** * ** Masking position 12 Map Score: 17.5387 Number of sites scoring better than the average of aligned sites = 1016 Number in coding regions = 935 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 2 AGAGAAGATCTCCACCGCTTGTCATTGTTG 6 49 0 TCCACCGCTT 0.880745 -154 GGGAGATGTGGCCACAGCCTGCGACCACAG 8 44 0 GCCACAGCCT 0.88392 -47 TACAAAAAAAGCCTCCACTGGGAGGCTTTC 11 56 0 GCCTCCACTG 0.782441 -228 ACTGGACACGGCCAGCGCGGAGAAACCGGA 11 141 1 GCCAGCGCGG 0.947206 -143 ACGAACCAGTGTCACCACTGACACAATGAG 11 257 1 GTCACCACTG 0.862364 -27 TTTCGTGTGGGTCACCACTGCAAATAAGGA 12 275 1 GTCACCACTG 0.862364 -26 AACGAGGCGTTCCAGCGCGGGCCAGGCTCT 13 128 1 TCCAGCGCGG 0.83918 -149 TTAGCTGTATGTCACAACTGAATGAAAAAA 13 193 0 GTCACAACTG 0.607221 -84 GCAGCAGGGGGCATCCGCCGGCAGCTAAGT 13 244 1 GCATCCGCCG 0.813812 -33 CCTGTGCCAACCAACCGCTGATTTCACGCC 14 50 1 CCAACCGCTG 0.832487 -160 CCAGCGTGTCTTAACCGCCGGGCTGGTAAC 18 68 0 TTAACCGCCG 0.688927 -61 AGCCGCAAAAGCCACAGCAGAATCGAGAAG 21 19 0 GCCACAGCAG 0.841413 -93 TCCGACAGCATCCAGCGCTTCAGGCAACTC 23 46 0 TCCAGCGCTT 0.607993 -61 CGGAGCTTTCTCCACAGCCGGAGAAGGTGT 23 72 1 TCCACAGCCG 0.92246 -35 AAAAATCGACGTCACCGCCTTCGAACAGTT 24 87 1 GTCACCGCCT 0.88392 -214 TTAGTCACTGCCCACCGCTGTTTGATTCCT 26 235 1 CCCACCGCTG 0.963893 -60 CGAAGTCATCGCAACAGCGGACATGAGTTA 29 185 1 GCAACAGCGG 0.796923 -82 TCTATCTGTAGCCACCGCCGTTGTCTTTAA 29 229 1 GCCACCGCCG 0.994004 -38 ********** Masking position 8 Map Score: 16.6974 Number of sites scoring better than the average of aligned sites = 3345 Number in coding regions = 3231 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 3 GATCGGATCATCACGCAATGTATGCTGATT 4 90 1 TCACGCAATG 0.918742 -84 CGTGGATTCCTCAAAGCGTAAACAAC 6 187 0 TTCCTCAAAG 0.816863 -16 GTAACAACATTACCGCAACGATAACA 8 7 0 TACCGCAACG 0.919256 -84 GGTTTTCCTCATTGTGTCAGTGGT 11 270 0 TTCCTCATTG 0.713345 -14 GGCTAGATGGTTTCGCAATGAACTGTTAAT 12 219 1 TTTCGCAATG 0.856003 -82 TCCCGCCTGATTCCTCAATGTAGTTCGGGT 16 164 0 TTCCTCAATG 0.955525 -95 CCTCAACGCTTCCCTCAATGTTTCGGGAGC 17 60 0 TCCCTCAATG 0.976113 -51 ATAAAAATGAACCCTCAACGCTTCCCTCAA 17 72 0 ACCCTCAACG 0.951212 -39 CAAGGTTATCTCCCGCAATGGTTTATCGTT 23 12 1 TCCCGCAATG 0.984941 -95 TTCAGGCAACTCCCGCAACGATAAACCATT 23 28 0 TCCCGCAACG 0.988735 -79 GAAGTCTACTCGCAACGCGACGGCGAG 26 278 0 ACTCGCAACG 0.843615 -17 TAAGATAATTATACTCAACGGATTCACCTC 29 106 1 ATACTCAACG 0.639256 -161 ********** Masking position 7 Map Score: 9.76865 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 454 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 4 GCTCAAGCGTCGCATCAGGCATAAAGCAGA 6 11 0 CGCATCAGGC 0.986617 -192 TATCATCAGGGAGCTAATCGG 9 2 1 ATCATCAGGG 0.647962 -167 ATGTCTCTTTCGCATCTGGCGAAAAGTCGT 10 68 1 CGCATCTGGC 0.886928 -61 AAAAGCCTGTCTCATCAGGTGTAATTGTCG 11 104 1 CTCATCAGGT 0.887449 -180 TAGAGCCTATCCCATCAGGCTATTTTACTT 11 221 0 CCCATCAGGC 0.94608 -63 GTTAACATCGCTCAACCGGGTGGAAGGTGA 12 135 1 CTCAACCGGG 0.737971 -166 TGGTCACCTGCGCAGCAGGGGGCATCCGCC 13 233 1 CGCAGCAGGG 0.960939 -44 GTTGGCACAGGGCAACAGGGTAAATTAACG 14 31 0 GGCAACAGGG 0.887547 -179 TGACAAATTGCGCAACACGGTCTGTTTTGC 16 107 0 CGCAACACGG 0.935617 -152 CGAGGCGCTTCCCATCACGTTA 17 3 0 CCCATCACGT 0.604616 -108 CAGCATCCAGCGCTTCAGGCAACTCCCGCA 23 41 0 CGCTTCAGGC 0.878868 -66 TTTTTTAGTGCGCAAGAGGGCTAAATTATC 26 158 1 CGCAAGAGGG 0.879474 -137 GATTTAAATACGCATCAGGTATACACCGCA 27 13 0 CGCATCAGGT 0.97276 -40 ACGAAGTCATCGCAACAGCGGACATGAGTT 29 184 1 CGCAACAGCG 0.879134 -83 ********** Masking position 3 Map Score: 11.3201 Number of sites scoring better than the average of aligned sites = 1448 Number in coding regions = 941 Number in noncoding regions = 507 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 5 GGCATATTCCTCGGCCTTTGAATTGTCCATATAGAA 1 30 0 TCGCCTTTTT 0.468588 -73 ATTCACGCCCTTCTCTTTTGACATTTCT 3 3 1 TCCGCCTCTT 0.979673 -109 GATCGGATCATCACGCAATGTATGCTGATTCGCGCG 4 90 1 TCCGCATTGT 0.822777 -84 AAACAGCCTTTCGCGCACTCGACGTTGAAATGATGC 5 117 0 TCCGCCTCGT 0.960522 -118 GGAGATCTTCTCTGCCGCTTTTTTTTTCATCAATCA 6 66 1 TCGCCCTTTT 0.924752 -137 TACTCCTGATTCTGGCACTTTATTCTATGTCTCTTT 10 42 1 TCGGCCTTTT 0.967624 -87 GTTTCTCTTCTCACGCGCTAGCCTCCTGGAT 11 6 0 TCCGCCTCTC 0.969658 -278 TGGGAGGCTTTCAGGCGCTGTTTTCCGTTTCTCTTC 11 32 0 TCGGCCTTTC 0.951964 -252 TGCAGTATACTCCCGCCCTAATTTCTTTAACTGGTG 14 144 1 TCCGCCTTTT 0.986429 -66 TGATAGAATATCGCCCACTTAATTTTTCCAGGATTT 16 195 1 TCCCCCTTTT 0.967624 -64 TGTACCCAATCCACGCTCTTTTTTATAGAGAAGATG 19 14 0 CCCGCCTTTT 0.913815 -77 TTGGGTACAATCCCGCTCTTATCACCGCATTTTGAC 19 41 1 TCCGCCTCAC 0.802394 -50 TCTAGACAAATCCCCCTCTGATTGACAGCATCACTG 22 57 0 TCCCCCTTGC 0.909127 -73 CAAGGTTATCTCCCGCAATGGTTTATCGTTGCGGGA 23 12 1 TCCGCATTTT 0.901927 -95 ** *** ** ** * Masking position 9 Map Score: 12.846 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 276 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 6 CAAAAGAGAAGGGCGTGAAT 3 1 0 GGGCGTGAAT 0.934901 -111 ATGCTGATTCGCGCGGGAAATATGGGTATT 4 111 1 GCGCGGGAAA 0.97043 -63 GCCCAAACGTCCGCGTCAAAACAGCCTTTC 5 141 0 CCGCGTCAAA 0.900545 -94 CAGGAGGCTAGCGCGTGAGAAGAGAAACGG 11 14 1 GCGCGTGAGA 0.97043 -270 ACGGAAAACAGCGCCTGAAAGCCTCCCAGT 11 40 1 GCGCCTGAAA 0.971316 -244 ACATCACGGTGCGTCTGAAAGGTT 12 5 0 GCGTCTGAAA 0.747377 -296 ACTTTATATCGGGCCTGAAATCAGACTCTA 13 95 0 GGGCCTGAAA 0.958196 -182 GCATCAGAAGCGGCGTGAAATCAGCGGTTG 14 61 0 CGGCGTGAAA 0.958196 -149 AAAGAAATTAGGGCGGGAGTATACTGCAAA 14 142 0 GGGCGGGAGT 0.726415 -68 AAATGGCCATCCGCGTCAAAAGAACAGACA 24 165 0 CCGCGTCAAA 0.900545 -136 ********** Masking position 8 Map Score: 6.82389 Number of sites scoring better than the average of aligned sites = 781 Number in coding regions = 728 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 CTTGAGCCTGTTCTACCTTCCAACTGGAACC 3 83 1 TTTACCTTCC 0.984768 -29 AAAAGGGAGATTGTACCTTTCCGTTTCACAT 12 98 0 TTTACCTTTC 0.893458 -203 GACATTAACCTCTCACCTTCCACCCGGTTGA 12 146 0 TCCACCTTCC 0.953983 -155 TAGTTCGGGTTTCTACCTTACGCATTATTGT 16 143 0 TTTACCTTAC 0.893458 -116 GCATACGGTATTTTACCTTCCCAGTCAAGAA 18 13 1 TTTACCTTCC 0.984768 -116 GACTAACTAATTACACCTTCTCCGGCTGTGG 23 83 0 TTCACCTTCT 0.803468 -24 ACCGCGCATTTCATAGCTTCCCTGGAACTGT 24 111 0 TCTAGCTTCC 0.858342 -190 AAATGCGCGGTTATACCTTCCGTAAAGAGCA 24 131 1 TTTACCTTCC 0.984768 -170 ** ******** Masking position 5 Map Score: 6.21786 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 90 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 GTTAACGACCCGGGAGATGAAACG 5 5 0 CGGGAGATGA 0.947511 -230 AAAAAAAAAGCGGCAGAGAAGATCTCCACC 6 63 0 CGGCAGAGAA 0.854145 -140 TATCATCAGGGAGCTAATCGGCTCCCT 9 8 1 AGGGAGCTAA 0.960317 -161 AGGTAAAAAAAGGGAGCCGATTAGCTCCCT 9 18 0 AGGGAGCCGA 0.870103 -151 GGGCATCCGCCGGCAGCTAAGTTAAGGGAT 13 252 1 CGGCAGCTAA 0.960788 -25 CTCAATGTTTCGGGAGCCATGCGGGTTCAA 17 47 0 CGGGAGCCAT 0.809316 -64 TGCTTATGGCAGGGAGATAAGG 22 3 0 AGGGAGATAA 0.949487 -127 TAAACCATTGCGGGAGATAACCTTGA 23 7 0 CGGGAGATAA 0.973636 -100 CTAATAGTCGAGGCAGATAATACAGTGTAC 25 164 1 AGGCAGATAA 0.906427 -73 ********** Masking position 5 Map Score: 6.03766 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 117 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 TTAAAAAACTAACAGTTGTCAGCCTGTCCCGCTTATA 6 131 1 AAATGCCTGT 0.960064 -72 GGAAAAAATAAACACTTGTCCACCCGTAAATGGGGGG 9 120 0 AAATGCCCGT 0.988781 -49 AAAAATTAACAAAATTTGTCGTTCCGCCATCGGCTAA 13 23 0 AAATGCCCGC 0.990692 -254 ATTATACTGGAAATTCTGCCGCACCGTAAGAGCCTGG 13 149 0 AATTGCCCGT 0.948178 -128 TCCGCGTCAAAAGAACAGACAAACTGCTCTTTACGGA 24 149 0 AAAAGCCTGC 0.857701 -152 GGAAAGATGCAAAAAATGGCCATCCGCGTCAAAAGAA 24 171 0 AAATGCCCGC 0.990692 -130 ATTCCTGCGTAAAATTTGTCTCGCCGTCGCGTTGCGA 26 259 1 AAATGCCCGT 0.988774 -36 ** * ** * **** Masking position 2 Map Score: 3.52647 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 26 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 10 GTTGTTACGGTTCCAGTTGG 3 102 0 GTTGTTACGG 0.965561 -10 TTGCGGTAATGTTGTTACTGTATCCCTGTG 8 19 1 GTTGTTACTG 0.846645 -72 CGCGGGCCAGGCTCTTACGGTGCGGCAGAA 13 143 1 GCTCTTACGG 0.930869 -134 GTAAATTAACGCTTTTACTGAAAGACGAAG 14 12 0 GCTTTTACTG 0.854775 -198 TTCTGCTGTGGCTTTTGCGGCTAGTGTATC 21 27 1 GCTTTTGCGG 0.935941 -85 ATAACCAATTGTTTTTACGACAG 25 4 0 GTTTTTACGA 0.820523 -233 CAAAAGACGAGTTTTTACGGGCGTATTTAA 29 12 0 GTTTTTACGG 0.958707 -255 TAATCTTAACGTTATTACGGCATTGGCACG 29 152 0 GTTATTACGG 0.87588 -115 ACTCATGTCCGCTGTTGCGATGACTTCGTG 29 183 0 GCTGTTGCGA 0.776501 -84 ********** Masking position 5 Map Score: 5.72952 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 226 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 CTTCAACCCAGTTCGGGTCATATATAGGGTG 4 39 1 GTTCGGGTAT 0.967431 -135 GTTTAGACATGTGTGGGTAATTGAGTTGCGT 4 143 0 GTGTGGGTAT 0.945557 -31 TGACGCGGACGTTTGGGCTATGCTATGCGGA 5 153 1 GTTTGGGCAT 0.945557 -82 GTGATCTTTCGTGTGGGTCACCACTGCAAAT 12 269 1 GTGTGGGTAC 0.954488 -32 ATTTTTATGAGTTCGGGCAACACCTTTATAG 13 54 1 GTTCGGGCAC 0.977433 -223 TCTTTAACTGGTGCGGGCAATTTTTGCTCGC 14 167 1 GTGCGGGCAT 0.977435 -43 CCTCAATGTAGTTCGGGTTTCTACCTTACGC 16 151 0 GTTCGGGTTC 0.881615 -108 ******** ** Masking position 2 Map Score: 3.3278 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 97 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 CGTCGAGTGCGCGAAAGGCTGTTTTGACGCGGAC 5 129 1 GCGAGGCTTT 0.991496 -106 CGTGCGCGTGGCGTATTGCCGTTTTCACTATTGC 14 89 0 GCGATGCTTT 0.969518 -121 GGAGTATACTGCAAATGGCTGTTTTCGTCAGCAA 14 123 0 GCAAGGCTTT 0.982594 -87 ATCTTTCTAAACGTAAGGCCATTTC 16 244 1 ACGAGGCTTT 0.969518 -15 ACGCATACGGTATTTTACCTTCCCAG 18 3 1 GCAAGGTTTT 0.879841 -126 AAAAGAACAGACAAACTGCTCTTTACGGAAGGTA 24 144 0 ACAATGCTTT 0.807728 -157 TTCTTTTGACGCGGATGGCCATTTTTTGCATCTT 24 171 1 GCGAGGCTTT 0.991496 -130 *** * *** *** Masking position 5 Map Score: 3.59289 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 72 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 AGCACCAATCAAACGGAACAGGATGCAAAA 4 11 0 AAACGGAACA 0.562716 -163 GTGAGAAGAGAAACGGAAAACAGCGCCTGA 11 28 1 AAACGGAAAA 0.890816 -256 CCCGGGACCAAAATGGCAAGTAAAATAGCC 11 204 1 AAATGGCAAG 0.892371 -80 AATCAATGTGAAACGGAAAGGTACAATCTC 12 93 1 AAACGGAAAG 0.961971 -208 GCAATAGTGAAAACGGCAATACGCCACGCG 14 89 1 AAACGGCAAT 0.671643 -121 AGATAGTACCAAATGGGAAAATGTTAAGTA 15 48 0 AAATGGGAAA 0.778396 -54 GTTCAATCATACACGGGAAGCGAGGCGCTT 17 23 0 ACACGGGAAG 0.896461 -88 TGTCTGAAAAGAACGGGAAGATTT 20 11 1 GAACGGGAAG 0.932591 -14 AGGGCTTAACGCATGGAAAGATGCAAAAAA 24 192 0 GCATGGAAAG 0.615851 -109 ATACAGTACGAAACGGGAAAAAGCAGGGCT 24 216 0 AAACGGGAAA 0.898367 -85 TTAGTGTTATAAACTGAAAGTTAATTTATT 25 35 0 AAACTGAAAG 0.834328 -202 TATCTACGCTAAATTGAAAGCTGGATTTAG 25 207 1 AAATTGAAAG 0.6668 -30 GCTACAGATAGAATTGCAAGCTTTCGTAAC 29 211 0 GAATTGCAAG 0.454535 -56 ********** Masking position 3 Map Score: 3.70001 Number of sites scoring better than the average of aligned sites = 808 Number in coding regions = 711 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 14 TCTGCTTTATGCCTGATGCGACGCTTG 6 7 1 TTTGCCTGAT 0.95239 -196 TTAATCGCTGGTACTCCTGATTCTGGCACTT 10 31 1 GTCTCCTGAT 0.901036 -98 GTACACGACTTTTCGCCAGATGCGAAAGAGA 10 71 0 TTCGCCAGAT 0.928726 -58 GCTGCGACAATTACACCTGATGAGACAGGCT 11 107 0 TTCACCTGAT 0.948249 -177 TCTTTCATTTGTGTACCTGATTGCGAACCAA 12 175 1 GTTACCTGAT 0.847735 -126 ATTCTATCACTCCCGCCTGATTCCTCAATGT 16 173 0 TCCGCCTGAT 0.916334 -86 ATTTGATCCATTATGCCTTATTGTGCCGTGA 21 70 0 TTTGCCTTAT 0.636063 -42 TATAACGTTTTGCCGCCTGATCCTTGCATAA 24 43 0 TGCGCCTGAT 0.916334 -258 GACATTCCTCCAGATTGTTTTTATC 26 5 1 TTCTCCAGAT 0.780443 -290 GCTGCGGTGTATACCTGATGCGTATTTAA 27 9 1 GTTACCTGAT 0.847735 -44 ** ******** Masking position 10 Map Score: 3.37986 Number of sites scoring better than the average of aligned sites = 523 Number in coding regions = 456 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 15 TTTTTTTTGTCCCAGGCTCGCCTTGAGCCTGTTCT 3 62 1 CCCGGCCTTG 0.843797 -50 ATAGCATAACCGCACGATCGGATCATCACGCAATG 4 75 1 CGCCGACTCA 0.665949 -99 TCCCTGTGGTCGCAGGCTGTGGCCACATCTCCCAT 8 41 1 CGCGGCGCCA 0.886463 -50 TATCATCAGGGAGCTAATCGGCTCCCTTTT 9 6 1 TCAGGACTCG 0.351366 -163 ATCCAGGAGGCTAGCGCGTGAGAAGA 11 2 1 TCCGGAGGCG 0.73071 -282 GGTTTCTCCGCGCTGGCCGTGTCCAGTCTGGCTGC 11 133 0 CGCGGCGCCA 0.886463 -151 CCATTTTGGTCCCGGGCTGTGCTCGAAATTCTCAC 11 185 0 CCCGGCGTCG 0.98436 -99 GCCTGGCCCGCGCTGGAACGCCTCGTTACCACTTT 13 120 0 CGCGGACTCG 0.990039 -157 CCGCTGTGTGGAGTCGCATTATAGGG 16 2 1 CGCGTGGTCG 0.74737 -257 GGTTAAGACACGCTGGAGCTGGTGGCGATATTTCG 18 82 1 CGCGGACTGG 0.916008 -47 TTGCCTGAAGCGCTGGATGCTGTCGGAGCTTTCTC 23 49 1 CGCGGAGTCG 0.987583 -58 TTCATAGCTTCCCTGGAACTGTTCGAAGGCGGTGA 24 98 0 CCCGGACTCG 0.984846 -203 AAATTTGTCTCGCCGTCGCGTTGCGAGTAGACTTC 26 270 1 CGCGTCCGCG 0.85027 -25 *** *** * *** Masking position 3 Map Score: 1.7265 Number of sites scoring better than the average of aligned sites = 2354 Number in coding regions = 2292 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219