AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 leuA 92 2-isopropylmalate synthase #2 leuL_leuO 482 leuL: leu operon leader peptide, leuO: probable transcriptional activator for leuABCD operon #3 ilvI 227 acetolactate synthase III, valine sensitive, large subunit #4 acnB 300 aconitate hydrase B #5 yeaU 81 putative tartrate dehydrogenase #6 ilvB 105 acetolactate synthase I,valine-sensitive, large subunit #7 ivbL 300 ilvB operon leader peptide #8 ilvM 300 acetolactate synthase II, valine insensitive, small subunit #9 ilvD 95 dihydroxyacid dehydratase #10 ilvC 149 ketol-acid reductoisomerase #11 HI0682 300 ketol-acid reductoisomerase (ilvC) #12 HI0737 247 acetohydroxy acid synthase II, putative #13 HI0738 71 dihydroxyacid dehydratase (ilvD) #14 HI0986 300 2-isopropylmalate synthase (leuA) #15 HI0987 85 3-isopropylmalate dehydrogenase (beta-IPM dehydrogenase) (leuB) #16 HI0988 175 3-isopropylmalate dehydratase, alpha subunit (leuC) #17 HI0989 23 3-isopropylmalate dehydratase small subunit (leuD) #18 HI1585 266 acetolactate synthase III large subunit (ilvI) #19 HI1586 300 conserved hypothetical integral membrane protein Motif number 1 ATTATTGATCAATTAATGTTAAGAATTAATGCATT 2 135 0 AAAAGAAGAA 0.850919 -348 ATATTCACCAAATCAATATCAAAAAAAATCGCAAA 2 168 1 AAAAAAAAAA 0.958498 -315 TTTTGCATCTAATCAACGAGGAAAAAGGGGACAAA 2 252 0 AAAAGGAAAA 0.879804 -231 TAGATGCAAAAATTTATGCTGAAATATGTCAACCG 2 276 1 AATAGGAAAT 0.429755 -207 GGATTAATTAAAAAAATAGAGAAATTGCTGTAAGT 3 107 1 AAAAAGAAAT 0.694012 -121 GAAAGGTGAAAAGAAACGATAAAATCCTCCATTAC 3 180 0 AAAAGAAAAT 0.889316 -48 GTTTACAAAAAAGCAACATAAAAAAGTGGCTGAAT 4 142 0 AAAAAAAAAA 0.958498 -159 AAGAAAATTGAAACAAAGCAAAGAACAGCGATTTA 11 41 1 AAAAGAAGAA 0.850919 -260 CGTGTAAAAGAAAGTAGGCAAAGAAAACACGCCCC 11 79 0 AATAGAAGAA 0.641572 -222 ATACGATGCCAATTCACAAAAAAAAATAATTGCAC 11 146 1 AACAAAAAAA 0.837576 -155 TCCTATAATCAAACCACAACAAAAAAATATGCAAA 11 231 1 AACAAAAAAA 0.837576 -70 AACCTTACACAATTAAGGACAAAAA 11 286 1 AAAAGAAAAA 0.96074 -15 AAATTATCCTATGTAAAAAAATGAAAAGAG 12 6 1 ATTAGAAAAA 0.45595 -242 AAATAAGCCAAAAGAGCGGTAAAAATTCACTAAAT 12 74 1 AAAGGAAAAA 0.850919 -174 CTTGGAGAGAAAAAAACGAAAAAAAGTGCGGTGAA 12 149 0 AAAAGAAAAA 0.96074 -99 CCCAAAATAAAAACAACAGGAAACAAACACC 12 227 1 AAAAAAAACA 0.58121 -21 ATATTTTATCAATTAACGAAGAAATTAATCATACA 13 13 1 AAAAGGAAAT 0.706166 -59 TATTTTTAATATAAAATGCCAAAAAATAGTTTGAC 14 52 1 ATAAGAAAAA 0.727699 -249 AACAATACGAAACATAAATAAAAATCCTCTGTGTA 14 121 0 AATAAAAAAT 0.703962 -180 TTTTATCTAAAAAATACAGGAAAAACGCACCGCAC 14 269 1 AATAAAAAAA 0.878679 -32 CCTTTTTAGCAAAGAGGGGAAAAATACAAAAAAAC 15 24 1 AAAGGAAAAT 0.652056 -62 CTTTTGAAGTAAAAAATAGGAAAAATAAT 15 67 1 AAAAAAAAAA 0.958498 -19 CACTTCCCTTAACGAATAGAGAAAAATATT 16 156 1 AAAAAGAAAA 0.873546 -20 GGCTCAAAAGAGGAAAAAGAAAA 17 7 1 AAAGAAAGAA 0.556818 -17 CTCATTCAAAAATTTGAATAAAAAATAATATTTTT 18 20 1 AATGAAAAAA 0.628152 -247 GCCGCATTTTATAAAATAGTAAAAATATTATTTTT 18 40 0 ATAAAAAAAA 0.716078 -227 TTTTTCCATCAATAAAAATAAAAAAATGCGACAAA 18 77 0 AAAAAAAAAA 0.958498 -190 TAAAAAACCAAATATAAATGAAAATTTAGTTTTTT 18 117 0 AATAAAAAAT 0.703962 -150 AAATCAATTAAAAAAATATAAAAAACCAAATATAA 18 135 0 AAAAAAAAAA 0.958498 -132 CTAGCCACTAAAACAACAAAAAAATCAATTAAAAA 18 156 0 AAAAAAAAAT 0.883487 -111 TGTTTCACATAATACAAAGTAAAAAAAATTTGTCT 18 189 0 AACAAAAAAA 0.837576 -78 ATATAAAGAAAATAAACACAAAAAAATATAT 19 7 0 AAAAAAAAAA 0.958498 -294 CAGAGTGGATAACGAAGAAGAAAAAAGAAAGGAAT 19 153 1 AAAAAAAAAA 0.958498 -148 ** ** * ***** Masking position 12 Map Score: 40.8209 Number of sites scoring better than the average of aligned sites = 478 Number in coding regions = 293 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 206 Fraction of orfs with sites within 600 bp upstream = 0.0330871 Motif number 2 TCTCATTGTCATAGTGCGGCAGGCGATTCT 4 266 0 ATAGTGCGGC 0.946362 -35 AAATAAGCCAAAAGAGCGGTAAAAATTCAC 12 74 1 AAAGAGCGGT 0.973043 -174 AAAACGAAAAAAAGTGCGGTGAAAATTGGC 12 142 0 AAAGTGCGGT 0.996117 -106 CGCAACTTATAAAGTGCGGGTTTAAAATTG 14 235 0 AAAGTGCGGG 0.985536 -66 TCCAAAAGTGCGGTGCGTTTTTCC 14 287 0 AAAGTGCGGT 0.996117 -14 TTTTACTTCAAAAGTGCGGTTAGTTTTTTT 15 51 0 AAAGTGCGGT 0.996117 -35 CAAAGTATTTAAAGTGCGGTTGAAAAACAC 16 111 1 AAAGTGCGGT 0.996117 -65 TTCGTTAAGGGAAGTGCGGTTAAAATTCGA 16 142 0 GAAGTGCGGT 0.981651 -34 ACTATTTTATAAAATGCGGCATTTTGTCGC 18 55 1 AAAATGCGGC 0.916353 -212 CGTTTTTTTAAAAGTGCGGTGAATTTAAGG 18 239 1 AAAGTGCGGT 0.996117 -28 ********** Masking position 3 Map Score: 28.5634 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 GCAGTCAAACAAAAAACCCGCGCCATTGCGC 1 19 1 AAAAACCCGC 0.99422 -74 TTCGGGCATAAAAAAACCCGCGCAATGGCGC 1 38 0 AAAAACCCGC 0.99422 -55 ATCAATATCAAAAAAAATCGCAAAACATATA 2 179 1 AAAAAATCGC 0.73152 -304 AAAAGGGGACAAAATGCACGCGTTGCAAAAC 2 234 0 AAAATCACGC 0.753844 -249 GACGCAATAAAAACGTCCCGCCAGCGTGAGT 2 395 0 AAACGCCCGC 0.97087 -88 AACACCTCGTCAAAATCCTGCTATTCTGCCC 4 182 1 CAAAACCTGC 0.851184 -119 CACACGATTCCAAAACCCCGCCGGCGCAAAC 6 23 1 CAAAACCCGC 0.988616 -83 TGCTTAAACGAAAAACCCCGCCCGGTTTGCG 6 47 0 AAAAACCCGC 0.99422 -59 GCAGATAACAAAAAACCCCGCCGGAGCGAGG 7 160 0 AAAAACCCGC 0.99422 -141 TTTTTTAGATAAAAAACCCGCAACTTATAAA 14 252 0 AAAAACCCGC 0.99422 -49 AATACAGGAAAAACGCACCGCACTTTTGGA 14 281 1 AAACGACCGC 0.880345 -20 AAATACAAAAAAACTAACCGCACTTTTGAAG 15 45 1 AAACTACCGC 0.826282 -41 AAAAATGCGACAAAATGCCGCATTTTATAAA 18 60 0 CAAAAGCCGC 0.918332 -207 ***** ***** Masking position 3 Map Score: 22.4097 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 234 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 4 CCGCGCAATGGCGCGGGTTTTTTGTTTGAC 1 22 0 GCGCGGGTTT 0.99059 -71 CCGCGCCATTGCGCGGGTTTTTTTATGCCC 1 36 1 GCGCGGGTTT 0.99059 -57 CGGTTTGCGCCGGCGGGGTTTTGGAATCGT 6 26 0 CGGCGGGGTT 0.988138 -80 GGCGCAAACCGGGCGGGGTTTTTCGTTTAA 6 45 1 GGGCGGGGTT 0.99496 -61 AACCTCGCTCCGGCGGGGTTTTTTGTTATC 7 158 1 CGGCGGGGTT 0.988138 -143 GATTTAACTGGGGCGTGTTTTCTTTGCCTA 11 70 1 GGGCGTGTTT 0.957431 -231 AACTTATAAAGTGCGGGTTTAAAATTGGGT 14 232 0 GTGCGGGTTT 0.985519 -69 ACTTTATAAGTTGCGGGTTTTTTATCTAAA 14 250 1 TTGCGGGTTT 0.913258 -51 ********** Masking position 9 Map Score: 15.0007 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 117 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 TAGAGCGCCTCGCTTCGGGCATAAAAAAAC 1 52 0 CGCTTCGGGC 0.729379 -41 GCAGAACTCACGCTGGCGGGACGTTTTTAT 2 390 1 CGCTGGCGGG 0.950198 -93 TGAAGAGAATCGCCTGCCGCACTATGACAA 4 261 1 CGCCTGCCGC 0.993236 -40 GCCCGGTTTGCGCCGGCGGGGTTTTGGAAT 6 29 0 CGCCGGCGGG 0.992719 -77 AAACGAAAAACCCCGCCCGGTTTGCGCCGG 6 43 0 CCCCGCCCGG 0.929463 -63 TTCGTTTAAGCACCTCCCGGAAAGTCGGCC 6 66 1 CACCTCCCGG 0.902541 -40 TTTCGTCAGTCGCCTGCGGCTGGTAACCGC 7 130 0 CGCCTGCGGC 0.995109 -171 CGAAACCTCGCTCCGGCGGGGTTTTTTGTT 7 155 1 CTCCGGCGGG 0.938737 -146 TGTTAGCCAGCGCCTTCGGCATCCATGGCC 8 124 1 CGCCTTCGGC 0.975645 -177 CGCCAGGCGGCACCAGCGGCCAGACGTTCT 8 250 0 CACCAGCGGC 0.877736 -51 CCGCTGGTGCCGCCTGGCGCCAGTAATTCA 8 261 1 CGCCTGGCGC 0.969288 -40 TGGAGATTGCCCCCTTCCGCCCTTCAGGCA 16 41 0 CCCCTTCCGC 0.89804 -135 ********** Masking position 3 Map Score: 15.4204 Number of sites scoring better than the average of aligned sites = 1947 Number in coding regions = 1849 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 CATTGTCATAGTGCGGCAGGCGATTCTCTT 4 263 0 GTGCGGCAGG 0.933782 -38 CGTCAGTCGCCTGCGGCTGGTAACCGCAAA 7 127 0 CTGCGGCTGG 0.81813 -174 GCTTCTTATTGTTCGGTTCGCGTTTGCGAG 10 109 0 GTTCGGTTCG 0.768885 -41 TAAGCCAAAAGAGCGGTAAAAATTCACTAA 12 77 1 GAGCGGTAAA 0.721018 -171 ACGAAAAAAAGTGCGGTGAAAATTGGCTTA 12 139 0 GTGCGGTGAA 0.978646 -109 CACATTTTGTGTGCGGCTAAGTTGTGGATA 14 181 1 GTGCGGCTAA 0.972067 -120 TCCAAAAGTGCGGTGCGTTTTTCCTGT 14 284 0 GTGCGGTGCG 0.972088 -17 TACTTCAAAAGTGCGGTTAGTTTTTTTGTA 15 48 0 GTGCGGTTAG 0.986766 -38 AGTATTTAAAGTGCGGTTGAAAAACACATC 16 114 1 GTGCGGTTGA 0.978646 -62 GTTAAGGGAAGTGCGGTTAAAATTCGATGT 16 139 0 GTGCGGTTAA 0.98232 -37 TTTTTTAAAAGTGCGGTGAATTTAAGGAGT 18 242 1 GTGCGGTGAA 0.978646 -25 ********** Masking position 4 Map Score: 13.7376 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 341 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 7 TCGGTAGTTAAGCAGAAATTAATATCGCTTA 2 321 1 AGCGAAATTA 0.78801 -162 ATTTTACGGATGCAGAACTCACGCTGGCGGG 2 379 1 TGCGAACTCA 0.956398 -104 TCAAAATTCGTGCCGAAATTGCGCGTTCTGC 7 54 1 TGCGAAATTG 0.966818 -247 CTGGCTAACATGAGGAAATCGGGGTTATCAG 8 103 0 TGAGAAATCG 0.81018 -198 ACCAGGTTGAAGCGGCACTCGACACCATGCT 8 172 1 AGCGCACTCG 0.7365 -129 TCAGAAATGTTGGAGAAATTATC 8 288 1 TGGGAAATTA 0.713334 -13 ATGTTGACGTTGCAAAAATTGCAATGTGACG 10 25 1 TGCAAAATTG 0.676441 -125 GGAAATTTATTGCGGAAATTGATATATTCAC 10 58 0 TGCGAAATTG 0.966818 -92 AACGGCAATTTGCTGAACTCGCTACGCTCA 11 10 0 TGCGAACTCG 0.982206 -291 AAAAAATAATTGCACAAATCGCAACATTACA 11 166 1 TGCCAAATCG 0.852084 -135 TTCGCTACAATGCTGAACTTATCCCCAAAAT 12 204 1 TGCGAACTTA 0.921865 -44 TTTGCTAAAAAGGGGAACTCGATAAA 15 6 0 AGGGAACTCG 0.792039 -80 AAGGAATAGTTGCCGAAATCAAATAAAAGTC 19 181 1 TGCGAAATCA 0.955606 -120 *** ******* Masking position 7 Map Score: 10.8398 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 950 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 8 TTTTTGATATTGATTTGGTGAATATTATTG 2 163 0 TGATTTGGTG 0.829446 -320 AAACCTATCCTGATGATTTGTATTGAATTA 2 208 0 TGATGATTTG 0.839428 -275 AGCAGGATTTTGACGAGGTGTTAATCTGTT 4 174 0 TGACGAGGTG 0.927112 -127 TATAGGATGGTGATGTTGTCAATTTTGATG 5 43 1 TGATGTTGTC 0.880292 -39 TCTTTCCGGGTGATGTGTTGGCCATGGATG 8 143 0 TGATGTGTTG 0.907135 -158 AATTGCAATGTGACGTTGTGAATATATCAA 10 41 1 TGACGTTGTG 0.961148 -109 TGATTCCTCGTGATGTTGTGCTTCTTATTG 10 128 0 TGATGTTGTG 0.980624 -22 GATAATTGTATGATGTTGTGTTTGCATATT 11 256 0 TGATGTTGTG 0.980624 -45 AATGTATATTTGATGAAGTGTAAGTAGGTT 14 22 1 TGATGAAGTG 0.867543 -279 ********** Masking position 3 Map Score: 7.46148 Number of sites scoring better than the average of aligned sites = 340 Number in coding regions = 309 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 CAAAAACGGATGTCAACCCTGACGCAATAAA 2 415 0 TGTCACCCTG 0.991977 -68 CACTGTATTATGTCAACACTGAAAGTATACG 7 93 0 TGTCACACTG 0.950316 -208 AATTTTCCATTGTCTCCCCTGTAAAGCTGTG 7 238 1 TGTCCCCCTG 0.994883 -63 AAGGGGGCAATCTCCACCCTTAGTTATTTAG 16 55 1 TCTCACCCTT 0.905475 -121 TTAAATACTTTGTCCCCCCTGTTTATTGGGG 16 92 0 TGTCCCCCTG 0.994883 -84 ACTATGACAGTGTCGCCCCTTTCGAGCACGC 19 229 0 TGTCCCCCTT 0.985006 -72 **** ****** Masking position 3 Map Score: 6.58256 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 8 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 CAGCACGCAGTCAAACAAAAAACCCGCGCCATTGCGC 1 13 1 TAAAAAACGC 0.424831 -80 CCAAATCAATATCAAAAAAAATCGCAAAACATATAAT 2 175 1 AAAAAATCAA 0.465712 -308 TCAATAAAAAATGCAGAATAAACCAGACATTCATGTC 3 30 0 AAAAAAACGA 0.962567 -198 AGAGGATTAAATTGATAATAAATCGGCTGAATCCCAC 3 143 0 AAAAAAATGC 0.716605 -85 GGGGTAATAAGAATAAACAGGAGGAAAGGTGA 3 206 0 AAAAAAACGA 0.962567 -22 TAATCTGTTTACAAAAAAGCAACATAAAAAAGTGGCT 4 146 0 AAAACAACAA 0.85562 -155 ATATTGTTAAACACAAAACCAACAAGGTCCCCA 7 278 1 AAAACAACGG 0.699488 -23 ACGCGAACCGAACAATAAGAAGCACAACATCACGAGG 10 116 1 AAAAAAGCAA 0.775942 -34 AAAAGAAAGTAGGCAAAGAAAACACGCCCCAGTTAAA 11 72 0 AAAGAAACGC 0.511661 -229 ATCAAACCACAACAAAAAAATATGCAAACACAACATC 11 238 1 AAAAATATAA 0.219528 -63 GAGAGAAAAAAACGAAAAAAAGTGCGGTGAAAATTGG 12 143 0 AAAAAAGTGG 0.214722 -105 CTTATCCCCAAAATAAAAACAACAGGAAACAAACACC 12 221 1 AAAACAACGA 0.918542 -27 GGCATTTTATATTAAAAATAAACCTACTTACACTTCA 14 35 0 AAAAAAACAC 0.868609 -266 TTTCCATATTACGAATAAAAAACTGGCTGTCAAACTA 14 78 0 AAAAAAACGC 0.926357 -223 AGGTTGAGAGATAAAGAAACAATACGAAACATAAATA 14 136 0 AAAACAATGA 0.693885 -165 TAAGTTGTGGATAAAAAAACAGTCAGATGTAAATACC 14 198 1 AAAACAGTGA 0.367444 -103 CGGGTTTTTTATCTAAAAAATACAGGAAAAACGCACC 14 263 1 AAAAATACGA 0.726959 -38 AAGAGGGGAAAAATACAAAAAAACTAACCGCACTTTT 15 35 1 AAAAAAAAAA 0.628719 -51 TGATGGAAAAATTTATAAAAAACTAAATTTTCATTTA 18 101 1 AAAAAAACAA 0.9311 -166 TCAATTAAAAAAATATAAAAAACCAAATATAAATGAA 18 130 0 AAAAAAACAA 0.9311 -137 TAGCCACTAAAACAACAAAAAAATCAATTAAAAAAAT 18 153 0 AAAAAAAAAA 0.628719 -114 ATAAAAATATAAAGAAAATAAACACAAAAAAATATAT 19 11 0 AAAAAAACAA 0.9311 -290 GGGGAGATTACCGTAAAACAAACAAAATGCCAACAGA 19 73 0 CAAAAAACAA 0.540457 -228 AGAGTGGATAACGAAGAAGAAAAAAGAAAGGAATAGT 19 154 1 AAAAAAAAGA 0.763153 -147 * * ** **** ** Masking position 7 Map Score: 12.283 Number of sites scoring better than the average of aligned sites = 570 Number in coding regions = 440 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 11 GGAAAGGTGAAAAGAAACGATAAAATCCTC 3 186 0 AAAGAAACGA 0.813821 -42 GGTAATAAGAATAAACAGGAGGAAAGGTGA 3 206 0 ATAAACAGGA 0.634895 -22 GTCGGCCCAGAAGAAAAGGACTGGAGC 6 89 1 AAGAAAAGGA 0.882533 -17 TATCCTATGTAAAAAAATGAAAAGAGTTTC 12 15 1 AAAAAAATGA 0.661154 -233 TTTTTAGGGGAAGAACAGGAATATTCAAAA 12 109 1 AAGAACAGGA 0.875408 -139 GCTTGGAGAGAAAAAAACGAAAAAAAGTGC 12 155 0 AAAAAAACGA 0.926539 -93 CCAAAATAAAAACAACAGGAAACAAACACC 12 228 1 AACAACAGGA 0.910989 -20 GAGATAAAGAAACAATACGAAACATAAATA 14 136 0 AACAATACGA 0.713983 -165 TTTATCTAAAAAATACAGGAAAAACGCACC 14 270 1 AAATACAGGA 0.674931 -31 TTTTGAAGTAAAAAATAGGAAAAATAAT 15 68 1 AAAAATAGGA 0.846662 -18 CCGCACTTTTAAAAAAACGAACAGATTATG 18 228 0 AAAAAAACGA 0.926539 -39 GAAGAAGAAAAAAGAAAGGAATAGTTGCCG 19 166 1 AAAGAAAGGA 0.858269 -135 CCACCAACCAAACAAAACGACTTTTATTTG 19 200 0 AACAAAACGA 0.887635 -101 ********** Masking position 5 Map Score: 7.49437 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 101 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 12 ATTAGCTAATTTTACGGATGCAGAACTCAC 2 371 1 TTTACGGATG 0.884763 -112 TAACGAAGTTTTTACGGAGGGAAACAATCT 4 95 1 TTTACGGAGG 0.965687 -206 CTGGGCCGACTTTCCGGGAGGTGCTTAAAC 6 69 0 TTTCCGGGAG 0.915026 -37 CAAGCACAGCTTTACAGGGGAGACAATGGA 7 243 0 TTTACAGGGG 0.950091 -58 CAACCTGGTCTTTCCGGGTGATGTGTTGGC 8 151 0 TTTCCGGGTG 0.950018 -150 GAACAGCGATTTAACTGGGGCGTGTTTTCT 11 63 1 TTAACTGGGG 0.857461 -238 CCTTCCTCCGTTTACGGGGGAAGGTGCCTG 16 17 1 TTTACGGGGG 0.991939 -159 GTCCCCCCTGTTTATTGGGGATATTTCTAA 16 82 0 TTTATTGGGG 0.789409 -94 ********** Masking position 2 Map Score: 4.27219 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 112 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 13 CATAATGTTTTTGTTGCGAAAACAATCTAATC 2 30 1 TTGTGGAAAA 0.961289 -453 CCTCGTTGATTAGATGCAAAAATTTATGCTGA 2 266 1 TAGTGAAAAA 0.689256 -217 AGACAGCAGTTTGTAGGGTAAATGCCCAGTAC 4 219 0 TTGAGGTAAA 0.826819 -82 CAATTTTCCCTTGCTGAAAAATTTTCCATTGT 7 219 1 TTGTGAAAAT 0.814234 -82 CGCTGTATCGTTCCTGAAAAAACAGTTGCTGC 8 59 0 TTCTGAAAAA 0.671238 -242 GGATTTTTTGTTGTTGCGTAAAGTGATATTAT 11 202 0 TTGTGGTAAA 0.874419 -99 TTGGTAGGGCTTGGAGAGAAAAAAACGAAAAA 12 161 0 TTGAGGAAAA 0.94498 -87 AAGTTCAGCATTGTAGCGAAATTTCGAGTCAT 12 192 0 TTGAGGAAAT 0.826819 -56 AACCGCACTTTTGAAGTAAAAAATAGGAAAAA 15 60 1 TTGAGAAAAA 0.915036 -26 TTTATTTTTATTGATGGAAAAATTTATAAAAA 18 90 1 TTGTGAAAAA 0.940314 -177 *** ** ***** Masking position 10 Map Score: 4.30677 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 215 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 14 TATATAAATTAATTATTAAATAAGCACATTTAA 2 99 0 ATTATAATAA 0.448901 -384 GAATTAATGCATTAAATATATAAATTAATTATT 2 115 0 ATAATAATAA 0.767536 -368 ATATTCACCAAATCAATATCAAAAAAAATCGCA 2 168 1 ATCATACAAA 0.681742 -315 AAAACATATAATTCAATACAAATCATCAGGATA 2 200 1 ATCATAAAAT 0.59105 -283 AAAATTCTACATTCAATAAAAAATGCAGAATAA 3 46 0 ATCATAAAAA 0.944107 -182 GAGCCCACACATTCAGAATAAAATTCTACATTC 3 65 0 ATCAAAAAAA 0.855365 -163 CTATTTTAGGATTAATTAAAAAAATAGAGAAAT 3 99 1 ATAATAAAAA 0.843622 -129 ATTACAGAGGATTAAATTGATAATAAATCGGCT 3 152 0 ATAATTATAA 0.347678 -76 GTTATCTGCAATTCAGTACAAAACGTGATCAAC 7 182 1 ATCATAAAAA 0.944107 -119 GCGAGATTGAATTCACTATATGACAGGAAATTT 10 81 0 ATCATAATGA 0.567292 -69 TACGATGCCAATTCACAAAAAAAAATAATTGCA 11 147 1 ATCAAAAAAA 0.855365 -154 TCTAATCATCAGTCAATAAATAAGCCAAAAGAG 12 57 1 ATCATAATAA 0.9118 -191 TTTTTCCATCAATAAAAATAAAAAAATGCGACA 18 79 0 ATAAAAAAAA 0.653839 -188 ACAACAAAAAAATCAATTAAAAAAATATAAAAA 18 146 0 ATCATTAAAA 0.731664 -121 TATAAACTTTAATAAAAATATAAAGAAAATAAA 19 26 0 ATAAAAATAA 0.536181 -275 TAATCTCCCCAATCACTACAAAAGTAGAGGCGC 19 100 1 ATCATAAAAA 0.944107 -201 * *** ** **** Masking position 5 Map Score: 9.08367 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 88 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 15 TGATTGAGTATTCGCGGTAGTTATGATTAGATTGTTT 2 49 0 TCGGTGTTGT 0.959626 -434 CCGATGAAAAGCGTCGGTAGTTAAGCAGAAATTAATA 2 308 1 GCGGTGTTGA 0.987611 -175 AGCTAATTGTGCTGCGGTGGTTAAAGTAAGCGATATT 2 341 0 GCGGTGTTAT 0.980387 -142 CGAGTATAAAGAGGCGGTAGTTTAAATTTTGACTAAT 4 18 1 GCGGTGTTAT 0.980387 -283 GGGGTTATCAGTAAGGGTGGTTTCGCTGTATCGTTCC 8 77 0 GGGGTGTTGT 0.972397 -224 TGGTGGTGGCGGAACGGTACTTAGGCATACTTTATTT 9 66 0 GCGGTCTTGA 0.938744 -30 ACTATGGAGTGCTACGGTTGTTCTGGTCTTATTCTGT 19 271 1 GCGGTGTTGT 0.994572 -30 * **** *** * * Masking position 8 Map Score: 2.65158 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 85 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432