AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -imalT_ecoli_hinf_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 malP 300 maltodextrin phosphorylase #2 malS 300 alpha-amylase #3 malF 153 part of maltose permease, periplasmic #4 malE_malK 364 malE: periplasmic maltose-binding protein; substrate recognition for transport and chemotaxis, malK: ATP-binding component of transport system for maltose #5 lamB 71 phage lambda receptor protein; maltose high-affinity receptor #6 malM 242 periplasmic protein of mal regulon #7 HI0096 300 H. influenzae predicted coding region HI0096 #8 HI0097 272 iron(III) ABC transporter, periplasmic-binding protein (hitA) #9 HI0098 216 iron(III) ABC transporter, permease protein (hitB) #10 HI1354 300 glutaminyl-tRNA synthetase (glnS) #11 HI1355 65 conserved hypothetical protein #12 HI1356 61 4-alpha-glucanotransferase (malQ) Motif number 1 ACTCCTCCCTGCCTAATCCCCCGCAGGATGAG 1 209 1 GCCTATCCCC 0.993891 -92 CAGCAATAAGGACTCATCCGCC 2 289 1 GACTATCCGC 0.847281 -12 AGGCGTTCACGCCGCATCCGGCATTTCACAGC 3 12 0 GCCGATCCGC 0.501278 -142 CGGCGTGAACGCCTTGTCCGGCCTACAAAACC 3 30 1 GCCTGTCCGC 0.892006 -124 ACGTATGTAGGCCTGATAAGACGCGTCAGCGT 3 65 1 GCCTATAAGC 0.597776 -89 GACAACAACTGCCTGATGCGACGCTGACGCGT 3 85 0 GCCTATGCGC 0.723233 -69 AGGCTTTCACGCCTTATCCGACAACAACTGCC 3 104 0 GCCTATCCGC 0.926647 -50 AGGCGTGAAAGCCTTATCCGTCCTGGAATGAG 3 122 1 GCCTATCCGC 0.790648 -32 TCATCCTCCCGCCTCCTCCCCCATAAAAAAGC 4 107 0 GCCTCTCCCC 0.960426 -258 CGGCGTAAACGCCTTATCCGGCCCAGGTTTTG 6 14 0 GCCTATCCGC 0.536303 -229 GGCGTTGGTTGCCGAATGCGGCGTAAACGCCT 6 32 0 GCCGATGCGC 0.527417 -211 GGCAACCAACGCCTGATGCGACGCTTGCGCGT 6 51 1 GCCTATGCGC 0.723233 -192 GCCGTTGTAGGCCTGATAAGACGCGCAAGCGT 6 71 0 GCCTATAAGC 0.597776 -172 CGGCGTAAACGCCTTATCCGGCCTACATTTGA 6 105 0 GCCTATCCGC 0.536303 -138 AGGCGTTTACGCCGCATCCGGCATAAAAACAG 6 123 1 GCCGATCCGC 0.501278 -120 **** ***** * Masking position 7 Map Score: 56.4124 Number of sites scoring better than the average of aligned sites = 686 Number in coding regions = 144 Number in noncoding regions = 542 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 2 AATGCCGGATGCGGCGTGAACGCCTTGTCCGGCCT 3 19 1 GCGGCGCGCT 0.999514 -135 ACTGCCTGATGCGACGCTGACGCGTCTTATCAGGC 3 75 0 GCGACGCGCT 0.998518 -79 ATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGG 4 256 1 GCGACGGGCT 0.991096 -109 GTTGCCGAATGCGGCGTAAACGCCTTATCCGGCCC 6 22 0 GCGGCGCGCT 0.999514 -221 AACGCCTGATGCGACGCTTGCGCGTCTTATCAGGC 6 58 1 GCGACGCGCT 0.998518 -185 TATGCCGGATGCGGCGTAAACGCCTTATCCGGCCT 6 113 0 GCGGCGCGCT 0.999514 -130 TTATCTGAAAGGGGCGAAAGCCCCTCTGATTATCG 6 162 1 GGGGCGCCCT 0.977472 -81 TGCTACCCTTGCGGCACACTTGCTTTTTCTGCTAA 8 193 1 GCGGCATGCT 0.957466 -80 GCCTGCATTCACGGCGATACCGCTTTTTAATGTGA 10 31 0 ACGGCGCGCT 0.994993 -270 ****** *** * Masking position 15 Map Score: 24.3877 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 171 Number in noncoding regions = 271 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 3 TCATCCTGCGGGGGATTAGGCAGGGAGGAGTT 1 208 0 GGGGTAGGCA 0.835043 -93 AGAAAATGTGGGGGTTATCGCAAAATTCAGCC 2 156 1 GGGGTTCGCA 0.895384 -145 AGCAAGGGTGAGCGATCTCGCGCAAAAAACGG 2 186 0 AGCGTTCGCG 0.945357 -115 GGCCGGACAAGGCGTTCACGCCGCATCCGGCA 3 21 0 GGCGTACGCC 0.538506 -133 TGCCTGATGCGACGCTGACGCGTCTTATCAGG 3 76 0 GACGTACGCG 0.975284 -78 GGACGGATAAGGCTTTCACGCCTTATCCGACA 3 113 0 GGCTTACGCC 0.889853 -41 CACACAAAGCGACGGTGGGGCGTAGGGGCAAG 4 258 1 GACGTGGGCG 0.869865 -107 GGCCGGATAAGGCGTTTACGCCGCATTCGGCA 6 23 1 GGCGTACGCC 0.538506 -220 CGCCTGATGCGACGCTTGCGCGTCTTATCAGG 6 60 1 GACGTGCGCG 0.970424 -183 GGCCGGATAAGGCGTTTACGCCGCATCCGGCA 6 114 1 GGCGTACGCC 0.538506 -129 GATAATCAGAGGGGCTTTCGCCCCTTTCAGAT 6 164 0 GGGGTTCGCC 0.927679 -79 TCTGATTATCGGGTTTAGCGCGCTATTGCCTG 6 186 1 GGGTTGCGCG 0.907292 -57 CACATTAAAAAGCGGTATCGCCGTGAATGCAG 10 32 1 AGCGTTCGCC 0.753008 -269 **** * ***** Masking position 6 Map Score: 24.8102 Number of sites scoring better than the average of aligned sites = 1525 Number in coding regions = 1088 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 4 GCAAGGAAATGTGATCTCAACCACTTAAAGCT 1 166 0 GTGATCAACC 0.834155 -135 AGCGATAACGTTGTGTTGAAAATCTAAGAAAA 1 268 1 TTGTTGAAAA 0.660766 -33 GTTTGGCTTATCGCTGGCAAACTGTCTGAAAT 2 255 1 TCGCGCAAAC 0.812296 -46 CAACCTGTCATCGACAGCAACATTCATGATGG 4 29 1 TCGAGCAACA 0.663268 -336 CACGGCTTCTGTGAACTAAACCGAGGTCATGT 4 142 1 GTGATAAACC 0.500339 -223 TTTCGTGATGTTGCTTGCAAAAATCGTGGCGA 4 180 1 TTGCGCAAAA 0.908632 -185 CCTGTCACAGGTGATGTGAAAAAAGAAAAGCA 5 33 1 GTGATGAAAA 0.902816 -39 CCAGGCAATAGCGCGCTAAACCCGATAATCAG 6 187 0 GCGCTAAACC 0.592049 -56 GCTCCAGATTTTGAGGTGAAAACA 6 229 1 TTGATGAAAA 0.875112 -14 CGTGAATTACTTGAATTGAAAAAAGCATTGAA 7 93 0 TTGATGAAAA 0.875113 -208 GAAATGGAAAGCGAATTGAAACAGTTACGTCG 7 123 0 GCGATGAAAC 0.801687 -178 TAGTGATGATGCGCTCTCAACAAGCAGAAACC 7 179 0 GCGCTCAACA 0.917016 -122 TGACCGCACTTTGTGTTGAAACTTAATCTCTC 7 244 1 TTGTTGAAAC 0.562345 -57 ACTGAATAATTTGCACTCAACATAAGGAGCTT 8 134 1 TTGCTCAACA 0.926663 -139 AATGTTTAAATTGCATTGAAAAGCTCCTTATG 8 154 0 TTGCTGAAAA 0.939006 -119 GCTTGCGTGCGTGAACTGAAAAGTTCACATTC 9 80 1 GTGATGAAAA 0.902816 -137 TTCTGTCGCACGCAAAATGACATACAG 9 200 0 TCGCGCAAAA 0.867728 -17 ATCGCCGTGAATGCAGGCAAAAACAGCAAAAT 10 48 1 ATGCGCAAAA 0.535287 -253 TTGTAAAAACTTGCCATAAAAAACCGCCACGA 10 171 0 TTGCTAAAAA 0.792246 -130 AATCAACCAAGTGCGGTCAAAACAAACGTGAT 11 15 1 GTGCTCAAAA 0.962113 -51 CAAATAAAAAGTGCGGTCAAAATCACGTTTGT 11 36 0 GTGCTCAAAA 0.962113 -30 **** ****** Masking position 9 Map Score: 16.3268 Number of sites scoring better than the average of aligned sites = 1069 Number in coding regions = 936 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 5 GCGTATTTTCAAAAAGCGGAAGGTAACTCTA 1 56 0 AAAAGCGGAA 0.926401 -245 ATCATATCAAAAATAGCTGTCAAGAGCACCC 2 62 1 AAAAGCTGTC 0.882058 -239 CTCGCGCAAAAAACGGCTGAATTTTGCGATA 2 171 0 AAAGGCTGAA 0.884342 -130 TCTGTTACAGAATTGGCGGTAATGTGGAGAT 4 224 0 AATGGCGGTA 0.898255 -141 ATCAGGCCTACAACGGCTGTCAAATGTAGGC 6 86 1 CAAGGCTGTC 0.887744 -157 GATCAAATAAATAAGGCGGAATAATTGTTCC 7 44 1 ATAGGCGGAA 0.803424 -257 AAATAATAGGAAAAGGCGGAACAATTATTCC 7 61 0 AAAGGCGGAA 0.974623 -240 GTTTCAACACAAAGTGCGGTCAATTCTGCGG 7 235 0 AAATGCGGTC 0.979966 -66 AAGTGAGCCAGAATGGCGGTCTGCGAGGCAA 9 128 0 GAAGGCGGTC 0.955721 -89 ACATCACATTAAAAAGCGGTATCGCCGTGAA 10 28 1 AAAAGCGGTA 0.964526 -273 ATAAATGCACAAAGTGCGGTAAGTTTTTTGA 10 123 0 AAATGCGGTA 0.97253 -178 TTTAATCAACCAAGTGCGGTCAAAACAAACG 11 12 1 CAATGCGGTC 0.944297 -54 ATACAAATAAAAAGTGCGGTCAAAATCACGT 11 40 0 AAATGCGGTC 0.979966 -26 *** ******* Masking position 7 Map Score: 18.0959 Number of sites scoring better than the average of aligned sites = 535 Number in coding regions = 488 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 CTCATCCCCGCAACTCCTCCCTGCCTAATCCCC 1 197 1 CAACCCCCTG 0.965992 -104 GAGGAAGGTCAACATCGAGCCTGGCAAACTAGC 1 238 1 AACACGCCTG 0.925371 -63 CGATCTCGCGCAAAAAACGGCTGAATTTTGCGA 2 173 0 CAAAAGGCTG 0.795192 -128 AAGCCAAACAAAACTCATCCCTGAGCGGTAAGT 2 231 0 AAACCCCCTG 0.892042 -70 CCTTATCCGACAACAACTGCCTGATGCGACGCT 3 92 0 CAACAGCCTG 0.954893 -62 CGGTTTAGTTCACAGAAGCCGTGTTCTCATCCT 4 132 0 CACAACCGTG 0.833535 -233 AGAGATCACACAAAGCGACGGTGGGGCGTAGGG 4 252 1 CAAACCGGTG 0.838086 -113 CCCCACAAAACACACAAAGCCTGTCACAGGTGA 5 14 1 CACAAGCCTG 0.9417 -58 TTTCTTTTTTCACATCACCTGTGACAGGCTTTG 5 28 0 CACACCTGTG 0.710951 -44 CCGCATTCGGCAACCAACGCCTGATGCGACGCT 6 43 1 CAACAGCCTG 0.954891 -200 TATTAGCAGAAAAAGCAAGTGTGCCGCAAGGGT 8 197 0 AAAACGTGTG 0.657938 -76 TCCAAATATTGCGTGCGTGTATTTG 9 3 1 CAAAAGCGTG 0.955676 -214 AGAGAATTGTAAACGCGTGCGTGAATTTTTTCA 9 34 0 AAACCGCGTG 0.941927 -183 TAACAAAATTAACCGCTTGCGTGCGTGAACTGA 9 66 1 AACCCGCGTG 0.923452 -151 TTTAGCTTACCAAACCCAGCCAGCTCCCATTTG 10 87 0 CAAACGCCAG 0.82971 -214 CAAGTGCGGTCAAAACAAACGTGATTTTGACCG 11 22 1 CAAACACGTG 0.817741 -44 **** * ***** Masking position 2 Map Score: 16.4095 Number of sites scoring better than the average of aligned sites = 1629 Number in coding regions = 1520 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 7 CCTGCGGGGGATTAGGCAGGGAGGAGTTGC 1 206 0 ATTAGGCAGG 0.548339 -95 GTTTCGGTTTTGTAGGCCGGACAAGGCGTT 3 37 0 TGTAGGCCGG 0.99369 -117 CCGAAACGTATGTAGGCCTGATAAGACGCG 3 60 1 TGTAGGCCTG 0.977991 -94 GGATAAGGCGTTTACGCCGCATTCGGCAAC 6 27 1 TTTACGCCGC 0.926969 -216 TGACAGCCGTTGTAGGCCTGATAAGACGCG 6 78 0 TGTAGGCCTG 0.977991 -165 GGCTGTCAAATGTAGGCCGGATAAGGCGTT 6 100 1 TGTAGGCCGG 0.99369 -143 GGATAAGGCGTTTACGCCGCATCCGGCATA 6 118 1 TTTACGCCGC 0.926969 -125 ACAACCTGTTTTTATGCCGGATGCGGCGTA 6 130 0 TTTATGCCGG 0.974749 -113 GCTTCCGTTATGTTTGCCGTTTCTGTATGT 9 178 1 TGTTTGCCGT 0.656468 -39 AATTTTGCTGTTTTTGCCTGCATTCACGGC 10 51 0 TTTTTGCCTG 0.751723 -250 ********** Masking position 3 Map Score: 10.5396 Number of sites scoring better than the average of aligned sites = 512 Number in coding regions = 207 Number in noncoding regions = 305 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 8 CATTTCCTTGCTCATCCCCGCAACTCCTCCC 1 187 1 CTCATCCCGC 0.993376 -114 ATCCCCGCAACTCCTCCCTGCCTAATCCCCC 1 200 1 CTCCTCCCGC 0.994277 -101 GTTGACCTTCCTCATCCTGCGGGGGATTAGG 1 220 0 CTCATCCTCG 0.960357 -81 CGCGAGATCGCTCACCCTTGCTTCTCATCCT 2 196 1 CTCACCCTGC 0.970126 -105 ACCCTTGCTTCTCATCCTGTGGACTTACCGC 2 209 1 CTCATCCTTG 0.822766 -92 CCAAACAAAACTCATCCCTGAGCGGTAAGTC 2 230 0 CTCATCCCGA 0.967247 -71 GGGGTTCTTCCTCATTCCAGGACGGATAAGG 3 133 0 CTCATTCCGG 0.826816 -21 TTAAATCCTCCACCCCCTGGCTTTTTTATGG 4 88 1 CACCCCCTGC 0.82698 -277 ATCCTCCCGCCTCCTCCCCCATAAAAAAGCC 4 106 0 CTCCTCCCCA 0.952234 -259 AAGCCGTGTTCTCATCCTCCCGCCTCCTCCC 4 119 0 CTCATCCTCC 0.982016 -246 ACCTCTTTCCATCCTCCTTGCCCCTACGCCC 4 275 0 ATCCTCCTGC 0.886209 -90 ATACGCCTCCCTCCACTACATCAC 10 4 1 CGCCTCCCCC 0.950163 -297 ******** ** Masking position 7 Map Score: 13.7829 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 265 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 AAATACGCAACGGCCATTTTTTGCACTTAGATA 1 79 1 CGGCATTTTG 0.975192 -222 GCGCAAAAAACGGCTGAATTTTGCGATAACCCC 2 166 0 CGGCGATTTG 0.703163 -135 GAGTTTTGTTTGGCTTATCGCTGGCAAACTGTC 2 248 1 TGGCTTCGTG 0.793721 -53 CTCCACCCCCTGGCTTTTTTATGGGGGAGGAGG 4 95 1 TGGCTTTTTG 0.959909 -270 GCAAAAATCGTGGCGATTTTATGTGCGCATCTC 4 196 1 TGGCATTTTG 0.966046 -169 TCCACATTACCGCCAATTCTGTAACAGAGATCA 4 227 1 CGCCATCTTA 0.808295 -138 CTTTCCATTTCAGCTTGTTTATACAGTTTTTTG 7 144 1 CAGCTTTTTA 0.539589 -157 GCCTGAATTGTGGCTATTCTATGCCTAATTTTA 8 98 0 TGGCATCTTG 0.966659 -175 AGCCGTAGCGGCTTCTTTGTGCTGACCATTA 8 252 0 CGGCTTTTTG 0.970657 -21 CCGTTATGTTTGCCGTTTCTGTATGTCATTTTG 9 182 1 TGCCTTCTTA 0.719763 -35 GATAATTTCGTGGCGGTTTTTTATGGCAAGTTT 10 164 1 TGGCGTTTTA 0.896548 -137 CGGTTTTTTATGGCAAGTTTTTACAATCTTTTA 10 177 1 TGGCATTTTA 0.938665 -124 AAAAAATATTCGGCTATTCTATACAAATCTAAG 10 261 0 CGGCATCTTA 0.955646 -40 **** * *** ** Masking position 12 Map Score: 10.1553 Number of sites scoring better than the average of aligned sites = 485 Number in coding regions = 414 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 10 GCTTTTTGAAAATACGCAACGGCCATTTTTT 1 70 1 AATACGCACG 0.935645 -231 CCGGCCTACAAAACCGAAACGTATGTAGGCC 3 47 1 AAACCGAACG 0.964043 -107 TGCGCACATAAAATCGCCACGATTTTTGCAA 4 194 0 AAATCGCACG 0.978727 -171 CAGAGATCACACAAAGCGACGGTGGGGCGTA 4 251 1 ACAAAGCACG 0.741063 -114 GCTCGTGAAAACACCTAAACGGACTCTAGTT 4 319 0 ACACCTAACG 0.680688 -46 CAATTCAAGTAATTCACGACGTAACTGTTTC 7 107 1 AATTCACACG 0.741125 -194 ATTTAGATGAAAAACAAAACGGTACATTAAA 8 34 0 AAAACAAACG 0.718803 -239 CAGCACAAAGAAGCCGCTACGGCT 8 259 1 AAGCCGCACG 0.961888 -14 GTGCATTTATACATCGCCACGATAATTTCGT 10 144 1 ACATCGCACG 0.970377 -157 TTGCCATAAAAAACCGCCACGAAATTATCGT 10 162 0 AAACCGCACG 0.989586 -139 ******* *** Masking position 9 Map Score: 6.69979 Number of sites scoring better than the average of aligned sites = 645 Number in coding regions = 615 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 GCCTGATAAGACGCGCAAGCGTCGCATCAG 6 63 0 ACGCGCAAGC 0.94778 -180 TGAAACTTAATCTCTCAAGCGGTTTATTAT 7 260 1 TCTCTCAAGC 0.862652 -41 TTTTTCAAATACACGCACGCAATATTTGGA 9 11 0 ACACGCACGC 0.989264 -206 TTGAAAAAATTCACGCACGCGTTTACAATT 9 33 1 TCACGCACGC 0.99421 -184 ACTTTTCAGTTCACGCACGCAAGCGGTTAA 9 74 0 TCACGCACGC 0.99421 -143 TTCTGTCGCACGCAAAATGACAT 9 204 0 TGTCGCACGC 0.96497 -13 ********** Masking position 7 Map Score: 6.40624 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 139 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 12 GTGAAAAATATAAGGTGTTGGAATGATTA 2 10 0 TAAGGTGTTG 0.860011 -291 CTATGCGTCATCAGGAGATGGCTTAAATCC 4 66 1 TCAGGAGATG 0.935993 -299 ATCACCTGTGACAGGCTTTGTGTGTTTTGT 5 18 0 ACAGGCTTTG 0.86973 -54 AAAGCCTGTCACAGGTGATGTGAAAAAAGA 5 29 1 ACAGGTGATG 0.908994 -43 AAGCAATGACTCAGGAGATAGA 5 60 1 TCAGGAGATA 0.589083 -12 CTTATCCGGCCCAGGTTTTGCTA 6 4 0 CCAGGTTTTG 0.540378 -239 CTGGGCCGGATAAGGCGTTTACGCCGCATT 6 20 1 TAAGGCGTTT 0.730695 -223 AAGCGTCGCATCAGGCGTTGGTTGCCGAAT 6 47 0 TCAGGCGTTG 0.98448 -196 CCTACATTTGACAGCCGTTGTAGGCCTGAT 6 86 0 ACAGCCGTTG 0.835015 -157 GTAGGCCGGATAAGGCGTTTACGCCGCATC 6 111 1 TAAGGCGTTT 0.730695 -132 TATGGCAAGAACAGGAGATGAACCTTTATT 10 227 1 ACAGGAGATG 0.908994 -74 ********** Masking position 3 Map Score: 5.03264 Number of sites scoring better than the average of aligned sites = 2131 Number in coding regions = 2010 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 13 GTTTCATAAGTAAAATATCCA 1 2 0 TAAAATATCC 0.901828 -299 TCCTCCCCCATAAAAAAGCCAGGGGGTGGA 4 96 0 TAAAAAAGCC 0.935777 -269 GATGCGCACATAAAATCGCCACGATTTTTG 4 197 0 TAAAATCGCC 0.955743 -168 AAATTAGGCATAGAATAGCCACAATTCAGG 8 100 1 TAGAATAGCC 0.981043 -173 TAGATTTGTATAGAATAGCCGAATATTTTT 10 263 1 TAGAATAGCC 0.981043 -38 ********** Masking position 5 Map Score: 1.79518 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 14 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 TAGATACAGATTTTCTGCGCTGTATTGCATTGA 1 106 1 TTTCTGCTGT 0.875344 -195 TCTGCGCTGTATTGCATTGATTTGATGCTAATC 1 119 1 ATTCAGATTT 0.59652 -182 GGAGTTCCACTTTTCTTAGATTTTCAACACAAC 1 277 0 TTTCTGATTT 0.966901 -24 GACAGCTATTTTTGATATGATTTGAGATTCAAC 2 50 0 TTTATGATTT 0.878582 -251 AACCCCCACATTTTCTGCGATTTAGCGCCAATC 2 139 0 TTTCTGATTT 0.966901 -162 ATGAGTCCTTATTGCTGCGATTTCAGACAGTTT 2 273 0 ATTCTGATTT 0.920859 -28 CTCCTGAGTCATTGCTTTTCTTTTTTCACATCA 5 44 0 ATTCTTCTTT 0.528909 -28 TGTTCCGCCTTTTCCTATTATTTCTTCAATGCT 7 69 1 TTTCTTATTT 0.818195 -232 ACGTAACTGTTTCAATTCGCTTTCCATTTCAGC 7 125 1 TTCATGCTTT 0.634957 -176 GATACCGCTTTTTAATGTGATGTAGTGGAGGGA 10 18 0 TTTATGATGT 0.735252 -283 AACCTTTATTTTCCCTTAGATTTGTATAGAATA 10 247 1 TTCCTGATTT 0.91811 -54 *** ** ***** Masking position 11 Map Score: 2.84728 Number of sites scoring better than the average of aligned sites = 275 Number in coding regions = 211 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 15 CAGCGCAGAAAATCTGTATCTAAGTGCAAA 1 98 0 AATCTGTATC 0.816121 -203 GAATAGTCCAAATCTGAAACTATGTCACGT 2 97 1 AATCTGAAAC 0.97069 -204 ATTTAGCGCCAATCTGAATCGTTAACACGT 2 123 0 AATCTGAATC 0.923803 -178 ATTACCGCCAATTCTGTAACAGAGATCACA 4 232 1 ATTCTGTAAC 0.684809 -133 AGGTTGTCATTATCTGAAAGGGGCGAAAGC 6 153 1 TATCTGAAAG 0.714637 -90 CTGTATAAACAAGCTGAAATGGAAAGCGAA 7 140 0 AAGCTGAAAT 0.833936 -161 CGCTCTCAACAAGCAGAAACCGACAAAAAA 7 170 0 AAGCAGAAAC 0.853313 -131 GATTATAGCTAAGCTGAAAGTGATGACAAC 12 16 0 AAGCTGAAAG 0.931961 -46 ********** Masking position 8 Map Score: 0.40444 Number of sites scoring better than the average of aligned sites = 416 Number in coding regions = 370 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529