AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00010_mpneu_reg_100.orf -o00010_mpneu_100.ace -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: K04_orf430 21 pgi; glucose-6-phosphate isomerase (GPI) (phosphoglucose isomerase) Input sequences: #1 R02_orf694 50 fruA; PTS system, fructose-specific IIABC component (EIIABC-Fru) #2 MPNtRNA-Ser01 300 mptgsb; tRNA-Ser. #3 D12_orf390o 45 dnaJ; dnaJ protein. [SP:DNAJ_MYCPN] #4 D12_orf623 133 pmd1; transport ATP-binding protein. #5 K05_orf312 170 ldh; L-lactate dehydrogenase. [EC:1.1.1.27] [SP:LDH_MYCPN] #6 E09_orf379 300 mtlA; PTS system mannitol-specific component IIA(EIIA-MTL). #7 C12_orf172 134 hypothetical protein. #8 C12_orf456 300 eno; enolase (2-phosphoglycerate dehydratase) (2-phospho-D-glycerate #9 H03_orf351 203 adh; probable NADP-dependent alcohol dehydrogenase. [EC:1.1.1.2] #10 P02_orf305 138 yjfW; #11 A05_orf409 37 pgk; phosphoglycerate kinase. [EC:2.7.2.3] [SP:PGK_MYCPN] #12 A05_orf290 184 yidA; #13 F11_orf358a 21 pdhA; pyruvate dehydrogenase E1 component, alpha subunit. #14 F11_orf327 300 pdhB; pyruvate dehydrogenase E1 component, beta subunit. #15 F11_orf457 26 pdhD; lipoamide dehydrogenase component (E3) of pyruvate #16 F11_orf339 300 lplA; probable lipoate-protein ligase A. [EC:6.-.-.-] #17 H10_orf149 206 hypothetical protein. #18 K04_orf726 273 vacB; vacB protein homolog. [SP:VACB_MYCPN] #19 GT9_orf940o 51 ptsG; PTS system, glucose-specific IIABC component (EIIABC-Glc) #20 GT9_orf113 54 hypothetical protein. #21 GT9_orf438V 300 hypothetical protein. Motif number 1 AATTTATAAAAATTTTTGCGTTTTCTTTTATTACTGAA 2 144 0 ATTTGGTTTT 0.778403 -157 TGCTTACAATTTATATTGAGAAATTTTTA 2 282 1 TTATGGATTT 0.710438 -19 TTGCTTGGGGACTTTTAGCTTCTTTTTTTATTCCATCT 6 77 1 ATTTGTTTTT 0.742524 -224 TTTTTTCAGCATTTTTCGCTCGTTTTTTACCCAA 7 7 0 ATTTGTTTTT 0.742524 -128 AATACCTGAGTCTTTCAGGTATTTTTTTATGCAAAATT 7 43 1 TTTCGTTTTT 0.827486 -92 AATTTACTCTTTTTTTAGGGCAAATTTTGCATAAAAAA 7 65 0 TTTTGGATTT 0.974384 -70 GATCCGTTGTTCATTCCGGGATAATTTTCCCGT 7 112 1 TTTCGGATTT 0.919597 -23 AGTTACGGTTTTCTTTGGTTCCTTTTTTGTGGCACGGT 8 44 0 TTTTGTTTTT 0.941012 -257 CCGTAACTCGTTGTTTTGATAAATGCTTAAACTTTTCA 8 74 1 TTTTGTACTT 0.852478 -227 TTTTAGTGGGTATTTTAGTTTGAGCTTTAACTACCCAA 8 198 0 TTTTGTATTT 0.968972 -103 ATTATCTTGGTGCTTTGGTTAGTGGTTTTAGTGGGTAT 8 223 0 TTTTGTTTTT 0.941012 -78 TGAGGGCAATTGCTTTAGTGAGTTTTTTATTGGTCCAG 8 260 1 TTTTGGTTTT 0.951055 -41 GGTTGAGCTCGCTTGGTTTTAATTTTCGTATTGCTT 9 9 1 TCTTGTATTT 0.852478 -195 AAAAACCTGCTTACTTAGTTTTACTCTTTACTTTAAT 11 11 1 TCTTGTACTT 0.516743 -27 ACTTAATTAAGCTTAATTTTTTTAACTGAAC 12 164 0 TTTAGTATTT 0.702679 -21 TTATTTGCATTACTTTTGCTTTAAATCTAAAAT 14 6 0 TTTTGTATCT 0.758443 -295 TTAAAAACGATGATTTAGAGTTAGCTTTAAAAAAGTTT 17 26 1 TTTTGGATTT 0.974384 -181 CTTACGGCGTTTCTTCTGCGCAATCTTTCGCTTTTCAC 17 137 0 TTTCGGATTT 0.919597 -70 CCGCGGTCTTTGGTTTTGCGAAAAATTTCCAAATCTTG 18 151 0 TTTTGGATTT 0.974368 -123 TGCTTTTTCTTATTTTAGGGTTAGTTTTTCATTTTGCG 18 230 1 TTTTGGATTT 0.974384 -44 AATTTGTTTTTTGTTTAGCTAAATATGTGCTGAAAGCC 21 54 1 TTTTGTATGT 0.758454 -247 * *** * * * *** Masking position 18 Map Score: 21.6916 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 82 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 ATTCTGTAAAAAAACCAAGCGACCTGAGGCT 2 106 0 AAAACCAGCG 0.962991 -195 AAGACCGCTTAAAAACTAGCTTTGGCTAAAT 4 91 0 AAAAACAGCT 0.976938 -43 TTGATCTAAATAAAACCTGCTGCCAAGCTTT 5 76 0 TAAAACTGCT 0.704199 -95 GATGGAATAAAAAAAGAAGCTAAAAGTCCCC 6 83 0 AAAAAGAGCT 0.90497 -218 ACACCTGATAAAAACCTAGCTTTAATGGTGG 6 121 1 AAAACCAGCT 0.966821 -180 TTGGGTAAAAAACGAGCGAAAAATGCTG 7 8 1 AAAAACAGCG 0.974245 -127 GTTGGTTTATTAAAACTAGGGGACTTTTTTG 8 110 0 TAAAACAGGG 0.871395 -191 TGGACCAATAAAAAACTCACTAAAGCAATTG 8 266 0 AAAAACCACT 0.619168 -35 TACGAAAATTAAAACCAAGCGAGCTCAACC 9 10 0 AAAACCAGCG 0.962991 -194 TGTTGGTTATTAAAACCAGGTTAGTAAGTTT 9 48 1 TAAAACAGGT 0.883557 -156 TTTATTAATTAAAAAGCAGCTTGACATGAGA 9 76 1 AAAAAGAGCT 0.90497 -128 AAAAACCTGCTTACTTAGTTT 11 1 1 AAAAACTGCT 0.880266 -37 AAGTAAAGAGTAAAACTAAGTAAGCAGGTTT 11 13 0 TAAAACAAGT 0.520344 -25 TTTTAGTTAAAAAAACTAGGTGCAATTATTC 14 229 1 AAAAACAGGT 0.959071 -72 ACTAGTAAACAAAAAGAAGGGGATTTTGCTC 16 49 1 AAAAAGAGGG 0.824685 -252 GGCGGTTTTTAAAACCCAACTCAATTTATTT 21 204 0 AAAACCAACT 0.806426 -97 CTCACGAGTGAAAACCCCGGGGCGTGGGCCT 21 278 1 AAAACCCGGG 0.794413 -23 ****** **** Masking position 4 Map Score: 19.0281 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 181 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 3 AATCCAATATTTATAATAAATTTAGATTCCAGTTCCT 1 5 0 TTTAATTTGT 0.956413 -46 TGCAAACAATTTATAAAAATTTTTGCGTTTTCTTTTATTACTG 2 146 0 TTAAATTTGT 0.855075 -155 TCGCTTCATAATTATATTAATTTAGCCAAAGCTAGTTTTTAAG 4 72 1 ATTTATTTGT 0.795927 -62 GTGGTATCTGTTAATTATACTTTTGCCACCCCCTTTTCCTTTT 5 12 1 TTATATTTGC 0.754624 -159 CAAGCTTGCCTTCATTTTAATTTGGTTTAAGCCACCAATCATT 5 126 0 TTTTATTTGC 0.919598 -45 TTTCTCAAATTTACTCTTTTTTTAGGGCAAATTTTGCATAAAA 7 67 0 TTTTTTTTGT 0.88087 -68 TTGAGCTCGCTTGGTTTTAATTTTCGTATTGCTTATGTTGGTT 9 13 1 TTTTATTTCT 0.793549 -191 TGGTTTTTTATTTGCATTACTTTTGCTTTAAATCTAAAAT 14 8 0 TTTTATTTGT 0.977067 -293 TAAGGCGAAATTTCTCTAAATTTCGTTTTAGATAAAAAGCCAG 14 60 0 TTTAATTTGT 0.956413 -241 TTAGAGAAATTTCGCCTTATTTTTGGCAGCATTTGCAACCGCC 14 84 1 TTTTATTTGT 0.977067 -217 ATCAAGCCATTTGAAATAAGTTTGGGGTTTGTTAGAATAATTG 14 251 0 TTTAATTTGT 0.956413 -50 ATTAACGGTTTTATTGAAACTTTAGACCAAATTGACGCAGCTG 16 252 0 TTAAATTTGT 0.855075 -49 TTAGTAGTGCTTTTTCTTATTTTAGGGTTAGTTTTTCATTTTG 18 223 1 TTTTATTTGT 0.977067 -51 CTTTAAAAATTTGTTTTTTGTTTAGCTAAATATGTGCTGAAAG 21 47 1 TTTTTTTTGT 0.88087 -254 GCCAAAAATTTTTAATTTAGTTTTTGCTACTTTCTCCTCCCTC 21 232 1 TTTTATTTTT 0.721714 -69 ** *** *** * * Masking position 12 Map Score: 11.7313 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 45 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 4 CGGTCTTATAATTAAAGCAAGTAGTTTTT 4 115 1 ATTAAAGCAA 0.949119 -19 CCAAATTAAAATGAAGGCAAGCTTGAATAA 5 144 1 ATGAAGGCAA 0.781317 -27 ATCGTCATTGATGAAAGCAATGAATCCAAA 6 27 0 ATGAAAGCAA 0.963414 -274 CTATTCCACCATTAAAGCTAGGTTTTTATC 6 127 0 ATTAAAGCTA 0.881378 -174 AATGGCAATAATGACAGCAATCACACCACC 6 221 0 ATGACAGCAA 0.876072 -80 ACCAGCAGCTATTACAGCAATGGCAATAAT 6 239 0 ATTACAGCAA 0.833548 -62 TAAAAAACTCACTAAAGCAATTGCCCTCAT 8 259 0 ACTAAAGCAA 0.71679 -42 CATGCTTTTTTTGAAAGCTAACTTAATTTG 9 183 1 TTGAAAGCTA 0.844723 -21 TAAACCTTTCCTTAAAGCCAACTAGAATAA 12 49 0 CTTAAAGCCA 0.879772 -136 ATTTTAGATTTAAAGCAAAAGTAATGCA 14 9 1 TTTAAAGCAA 0.906322 -292 TTTAAACTTTTTTAAAGCTAACTCTAAATC 17 37 0 TTTAAAGCTA 0.793969 -170 ATTAACACACATTAAAGCATGGACGCAATT 18 25 1 ATTAAAGCAT 0.764009 -249 AAATCTTGACCTGAAAGCGAAGCAAGTCCG 18 129 0 CTGAAAGCGA 0.793963 -145 TAAATATGTGCTGAAAGCCATTGCGTTAAC 21 73 1 CTGAAAGCCA 0.911739 -228 AAATTTTGTGTTGAAAGCCTGATTTTCTGT 21 155 0 TTGAAAGCCT 0.597522 -146 ********** Masking position 4 Map Score: 11.2574 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 146 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TATACTTTTGCCACCCCCTTTTCCTTTTATGT 5 27 1 CCACCCCCTT 0.956945 -144 TTGGTTTAAGCCACCAATCATTTACTGTTCCC 5 116 0 CCACCAATTT 0.926353 -55 ATATGTGATTCCGACCATAATTGTTTTTTTGG 6 164 1 CCGACCATTT 0.749782 -137 AGCAATCACACCACCACGTATTTCATAAATCT 6 204 0 CCACCACGTT 0.943201 -97 TGATTTTTGACCAACAATTTTTGTAAATGCTT 6 276 0 CCAACAATTT 0.944842 -25 TTTTAATAAACCAACCACGCTTAACGCTACAA 8 126 1 CCAACCACTT 0.949777 -175 GGACCATGTACCAACATGCTTTTTTTGAAAGC 9 169 1 CCAACATGTT 0.745763 -35 ACTAGTTGCACCAACCACTTGTCTTTGGCAAA 12 89 1 CCAACCACGT 0.856622 -96 ACATACTGCCCAACACTGTTAAAGATTGCTA 16 10 1 CCAACACTTA 0.744745 -291 CTAACCCGTTCCACCACCCAGTCATACGGAAA 16 182 1 CCACCACCGT 0.873271 -119 TTCAACGCATCCAACACGACTTTGACCCTAAC 16 217 0 CCAACACGTT 0.957653 -84 TTATTGCTATCCAACCATGGTTCTACTGGCGG 18 100 1 CCAACCATTT 0.945815 -174 ATTTTCTGTTCCCACACTTATTTGATTAATGT 21 132 0 CCCACACTTT 0.824766 -169 ******** ** Masking position 5 Map Score: 7.03959 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 113 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TTTATAAATTGTTTGCAACAGCAAATTCCGGAATT 2 172 1 GTTGCACCAA 0.917658 -129 TTAATCATTCGAGTGTTAATTATAAAACTGCTTTG 3 13 0 GGTGTAAAAA 0.711266 -33 CTTATCAGGGGTGTGCTCTAACCAACTGAGCTATA 4 11 1 GGTGCCTCAA 0.816121 -123 GTAAATGATTGGTGGCTTAAACCAAATTAAAATGA 5 123 1 GTGGCTACAA 0.705387 -48 TGTAATAGCTGCTGGTCAAACCGAAGCATTTACAA 6 253 1 GTGGTAACAA 0.830075 -48 CTTGACATGAGATTGTTCAAACAAAGAGCAGCTAT 9 95 1 GTTGTCACAA 0.894691 -109 AGTAATGCACTATTGCAAAATCTAACCTGATTTAA 12 11 0 TTTGCAACAA 0.798051 -174 ACAAGTACTAGTTTGCCAAAGACAAGTGGTTGGTG 12 97 0 GTTGCAAAAA 0.934772 -88 GAAATGCTGTGGTTGCAAAACCGAAACAGCTAACT 14 144 0 GTTGCAACAA 0.98483 -157 CACTGTTAAAGATTGCTAACACAAAACTAGTAAAC 16 24 1 GTTGCAACAA 0.98483 -277 AAAGTACTATGCGTGCTAAGATTAAGCACTTTTAT 16 91 0 GGTGCAATAA 0.868967 -210 AAAAGCGAAAGATTGCGCAGAAGAAACGCCGTAAG 17 140 1 GTTGCCAAAA 0.878561 -67 ATGCTTTAATGTGTGTTAATTTTAAACTAATGCT 18 10 0 GGTGTAATAA 0.63224 -264 TTAAACAAAGGATTGCCATTACAAACATTACTATT 18 57 0 GTTGCATCAA 0.92987 -217 * **** ** * ** Masking position 14 Map Score: 6.83678 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 105 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TTATTACTGAAGTGCAAAATTCTGTAAAAA 2 125 0 AGTGCAAAAT 0.781011 -176 GTTAACAAAAAGCGCAATAAAAAAGCAGAC 2 241 1 AGCGCAATAA 0.837085 -60 TTATGTTGAGAGCTAAAAAAGACAAAGCTT 5 53 1 AGCTAAAAAA 0.577411 -118 GTAAAAAACGAGCGAAAAATGCTGAAAAAA 7 15 1 AGCGAAAAAT 0.945713 -120 GGGTAGTTAAAGCTCAAACTAAAATACCCA 8 200 1 AGCTCAAACT 0.831991 -101 GTTAATTAACAGCGCAAAATATAAACATGG 10 11 1 AGCGCAAAAT 0.976089 -128 GCGTTTCTTCTGCGCAATCTTTCGCTTTTC 17 139 0 TGCGCAATCT 0.688408 -68 TCTTTGGTTTTGCGAAAAATTTCCAAATCT 18 153 0 TGCGAAAAAT 0.828842 -121 TAGATTTTAAAGCGCAAAATGAAAAACTAA 18 250 0 AGCGCAAAAT 0.976089 -24 TTTTTTGTTTAGCTAAATATGTGCTGAAAG 21 60 1 AGCTAAATAT 0.68999 -241 ********** Masking position 6 Map Score: 5.2674 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 126 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 8 TGATTGAATGGTTTGTGATTGACTTCATTA 2 32 0 GTTTGTGATT 0.87675 -269 GTTATGTGTTGTTTGTGATTGAATGGTTTG 2 47 0 GTTTGTGATT 0.87675 -254 CAGTGGTCTGCTTTTTTATTGCGCTTTTTG 2 246 0 CTTTTTTATT 0.651974 -55 TTTTAGCTTCTTTTTTTATTCCATCTGGTT 6 89 1 TTTTTTTATT 0.558297 -212 AAATTGATCCGTTGTTCATTCCGGGATAAT 7 107 1 GTTGTTCATT 0.870111 -28 GTTTTATACGGTTGGTTACTACCCTTTCCG 8 159 0 GTTGGTTACT 0.628013 -142 GCTTTAGTGAGTTTTTTATTGGTCCAGTTG 8 271 1 GTTTTTTATT 0.950471 -30 TATTGCTTATGTTGGTTATTAAAACCAGGT 9 39 1 GTTGGTTATT 0.920468 -165 GAAACCGGGAGTTTTTTATTGCTAAAGAAT 10 92 1 GTTTTTTATT 0.950471 -47 CGTAAGACTGGTTTTTTATTTGCATTACTT 14 29 0 GTTTTTTATT 0.950471 -272 ATTCAGTTGTTGATTAGTTAGACAG 15 6 1 GTTGTTGATT 0.907044 -21 TCCAAATTACGATGTTTATTTTAGTAGTGC 18 203 1 GATGTTTATT 0.632067 -71 TTTAGGGTTAGTTTTTCATTTTGCGCTTTA 18 243 1 GTTTTTCATT 0.880455 -31 TTAAAAATTTGTTTTTTGTTTAGCTAAATA 21 49 1 GTTTTTTGTT 0.736795 -252 ********** Masking position 6 Map Score: 12.0146 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 59 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 9 CTGAAGTGCAAAATTCTGTAAAAAAACCAAGCG 2 116 0 AATTCTAAAA 0.752785 -185 AAAACGCAAAAATTTTTATAAATTGTTTGCAAC 2 158 1 AATTTTAAAT 0.931823 -143 AAAGAAACGGAATTTTTAGAAGAGCTCGCTTAA 2 205 0 AATTTTAAGA 0.669275 -96 TAAAAATTTCTCAATATAAATTGTAAG 2 284 0 AATTCTATAT 0.652804 -17 TTTGACCAACAATTTTTGTAAATGCTTCGGTTT 6 270 0 AATTTTAAAT 0.931828 -31 TTTTTAGGGCAAATTTTGCATAAAAAAATACCT 7 59 0 AATTTTATAA 0.508549 -76 ACAACGGATCAATTTCTCAAATTTACTCTTTTT 7 89 0 AATTCTAATT 0.619441 -46 TAAATGCTTAAACTTTTCAAAAAAGTCCCCTAG 8 93 1 AATTTTAAAA 0.827178 -208 AATTAAGCTTAATTTTTTTAACTGAACCGCTCA 12 158 0 AATTTTAACT 0.683157 -27 AATAAGGCGAAATTTCTCTAAATTTCGTTTTAG 14 72 0 AATTCTAAAT 0.896877 -229 ACTAACGACTTTTCTAAATCAAGCCATTT 14 282 0 GATTTTAAAT 0.605264 -19 GCGATGTAGAAACTTTTAAAAGTACTATGCGTG 16 111 0 AATTTTAAGT 0.852421 -190 AACCCGTTTAAACTTTTTTAAAGCTAACTCTAA 17 40 0 AATTTTAAAG 0.798713 -167 CTTTCAGGTCAAGATTTGGAAATTTTTCGCAAA 18 142 1 AAATTTAAAT 0.508493 -132 GGAATTGTCAAAATTCTCCAAATTACGATGTTT 18 187 1 AATTCTAAAT 0.896877 -87 AAATGAACCTTTTTTAAATCCTTAAATTT 19 33 0 ACTTTTAAAT 0.605264 -19 AACAAAAAACAAATTTTTAAAGGAACAAACATT 21 36 0 AATTTTAAGG 0.626545 -265 AAACCGCCAAAAATTTTTAATTTAGTTTTTGCT 21 227 1 AATTTTATTT 0.356674 -74 ** **** **** Masking position 7 Map Score: 7.52603 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 97 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 10 TAAATTTAGATTCCAGTTCCT 1 1 0 TTCAGTTCCT 0.860305 -50 CACCAATCATTTACTGTTCCCAATTGAGATT 5 106 0 TTCTGTTCCC 0.981094 -65 GGCACGGTATTTGCTGTACCTGATTCCCGTA 8 21 0 TTCTGTACCT 0.860305 -280 CACTAACCCGTTCCACCACCCAGTCATACGG 16 180 1 TTCACCACCC 0.833455 -121 AAAGCCTGATTTTCTGTTCCCACACTTATTT 21 141 0 TTCTGTTCCC 0.981094 -160 AATTTTCGTTTTTCTGCTCCCACTAAATAAA 21 180 1 TTCTGCTCCC 0.984293 -121 TTTTTGCTACTTTCTCCTCCCTCCCCCTCAC 21 252 1 TTCTCCTCCC 0.963561 -49 ** ******** Masking position 2 Map Score: 3.98509 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 10 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 11 ATATTAATTTAGCCAAAGCTAGTTTTTAAG 4 85 1 AGCCAAAGCT 0.954127 -49 GAGCTAAAAAAGACAAAGCTTGGCAGCAGG 5 62 1 AGACAAAGCT 0.645097 -109 AAAGCAATGAATCCAAAGACTGAATGTGAA 6 14 0 ATCCAAAGAC 0.797203 -287 CTGCTGGTCAAACCGAAGCATTTACAAAAA 6 261 1 AACCGAAGCA 0.814412 -40 ACAAAAAAGGAACCAAAGAAAACCGTAACT 8 52 1 AACCAAAGAA 0.929553 -249 TAAAACCACTAACCAAAGCACCAAGATAAT 8 231 1 AACCAAAGCA 0.954632 -70 AGTACTAGTTTGCCAAAGACAAGTGGTTGG 12 99 0 TGCCAAAGAC 0.850803 -86 TCGGTTTTGCAACCACAGCATTTCTTGTCT 14 155 1 AACCACAGCA 0.814412 -146 TGCCAAAGATTGAAGTTAAA 17 1 1 TGCCAAAGAT 0.783856 -206 TTTTTCGCAAAACCAAAGACCGCGGAATTG 18 164 1 AACCAAAGAC 0.940948 -110 ********** Masking position 7 Map Score: 2.90746 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 124 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 GTTAATTATAAAACTGCTTTGAT 3 4 0 AAACTGCTTT 0.920437 -42 AAACAACGAGTTACGGTTTTCTTTGGTTCC 8 60 0 TTACGGTTTT 0.759621 -241 ATCTCATGTCAAGCTGCTTTTTAATTAATA 9 78 0 AAGCTGCTTT 0.730986 -126 GAATACAAGTAAACGGCTTTTTAGGCAAAA 10 118 1 AAACGGCTTT 0.972496 -21 ACTAACGACTTTTCTAAATCAA 14 289 0 TAACGACTTT 0.810799 -12 AGAAATACATTAACGGTTTTATTGAAACTT 16 273 0 TAACGGTTTT 0.909089 -28 AAAAAAGTTTAAACGGGTTTCGCTAGAAAT 17 54 1 AAACGGGTTT 0.867968 -153 ATTACGAAACTTACGGCGTTTCTTCTGCGC 17 154 0 TTACGGCGTT 0.763485 -53 CAAACATTCATAACTGCTTTACAACTCAAA 21 14 0 TAACTGCTTT 0.934752 -287 ********** Masking position 9 Map Score: 1.89084 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 175 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 13 TAGAGGTAGTGCGGCTTCCCTTT 2 4 0 GCGGCTTCCC 0.935491 -297 ATTTGCTGTACCTGATTCCCGTATTGCTCG 8 14 0 CCTGATTCCC 0.936519 -287 TTTATGGTTGCCTGTTTCCCCGTACTTGAA 9 138 0 CCTGTTTCCC 0.983555 -66 TAAAAAACTCCCGGTTTCCCGAGCGCCCTT 10 80 0 CCGGTTTCCC 0.989463 -59 ACTGCAGTTAGCTGTTTCGGTTTTGCAACC 14 139 1 GCTGTTTCGG 0.817961 -162 TTGACCCTAACCAGTTTCCGTATGACTGGG 16 198 0 CCAGTTTCCG 0.908992 -103 AAAGTTTAAACGGGTTTCGCTAGAAATTCG 17 57 1 CGGGTTTCGC 0.883939 -150 ********** Masking position 6 Map Score: 1.37554 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 13 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 14 ATTTTTAGAAGAGCTCGCTTAATTCCGGAA 2 197 0 GAGCTCGCTT 0.925906 -104 ATCTTCGTACAGGTTCGCTTCATAATTATA 4 58 1 AGGTTCGCTT 0.917328 -76 AATTTAGCCAAAGCTAGTTTTTAAGCGGTC 4 90 1 AAGCTAGTTT 0.654452 -44 ATTAAAATGAAGGCAAGCTTGAATAAATTA 5 148 1 AGGCAAGCTT 0.757076 -23 TCCACCATTAAAGCTAGGTTTTTATCAGGT 6 123 0 AAGCTAGGTT 0.636668 -178 GGTTGAGCTCGCTTGGTTTTAATT 9 5 1 GAGCTCGCTT 0.925906 -199 CCAAATTAAGTTAGCTTTCAAAAAAAG 9 187 0 AAGTTAGCTT 0.722503 -17 TTAAATCAGGTTAGATTTTGCAATAGT 12 8 1 AGGTTAGATT 0.670021 -177 CGATGATTTAGAGTTAGCTTTAAAAAAGTT 17 33 1 GAGTTAGCTT 0.92816 -174 TCTTATTTTAGGGTTAGTTTTTCATTTTGC 18 237 1 GGGTTAGTTT 0.795159 -37 ********** Masking position 9 Map Score: 4.23267 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 74 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 15 AATCATTCGAGTGTTAATTATAAAACTGCT 3 16 0 GTGTTAATTA 0.947445 -30 CGTGGTATCTGTTAATTATACTTTTGCC 5 9 1 CTGTTAATTA 0.883816 -162 AGCTCGCTTGGTTTTAATTTTCGTATTGCT 9 16 1 GTTTTAATTT 0.784087 -188 ATATTTTGCGCTGTTAATTAAC 10 3 0 CTGTTAATTA 0.883816 -136 GCTTTAATGTGTGTTAATTTTAAACTAATG 18 13 0 GTGTTAATTT 0.95914 -261 CATTTTTTATGTCTTAATTTACTTATGTTA 21 99 0 GTCTTAATTT 0.843317 -202 TTTGATTAATGTGTTCATTTTTTATGTCTT 21 114 0 GTGTTCATTT 0.87839 -187 ********** Masking position 7 Map Score: 1.63762 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 32 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617