AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_rpxx_reg_100.orf -o00230_rpxx_100.ace -a/home/amcguire/genomes/ORF_rpxx.txt -z/home/amcguire/genomes/rpxx.fna -g0.29 -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 = 0.29 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RP636 23 30S RIBOSOMAL PROTEIN S11 (rpsK) RP655 24 30S RIBOSOMAL PROTEIN S19 (rpsS) Input sequences: #1 RP055 162 NUCLEOSIDE DIPHOSPHATE KINASE (ndk) #2 RP064 249 DEOXYGUANOSINETRIPHOSPHATE TRIPHOSPHOHYDROLASE (dgtP) #3 RP140 300 DNA-DIRECTED RNA POLYMERASE BETA CHAIN (rpoB) #4 RP141 156 DNA-DIRECTED RNA POLYMERASE BETA PRIME CHAIN (rpoC) #5 RP172 110 DNA POLYMERASE III, DELTA SUBUNIT (holB) #6 RP220 133 PHOSPHORIBOSYLAMINOIMIDAZOLE-SUCCINOCARBOXAMIDE SYNTHASE (purC) #7 RP303 89 RNA POLYMERASE SIGMA-32 FACTOR (rpoH) #8 RP417 106 PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN (pheS) #9 RP504 154 POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE (pnp) #10 RP512 164 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE BETA CHAIN (nrdB) #11 RP513 300 RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE ALPHA CHAIN (nrdA) #12 RP541 62 3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE (ubiX) #13 RP637 57 30S RIBOSOMAL PROTEIN S13 (rpsM) #14 RP641 24 50S RIBOSOMAL PROTEIN L30 (rpmD) #15 RP649 60 50S RIBOSOMAL PROTEIN L14 (rplN) #16 RP658 241 50S RIBOSOMAL PROTEIN L4 (rplD) #17 RP730 300 unknown #18 RP765 116 GUANYLATE KINASE (gmk) #19 RP776 153 DNA POLYMERASE I (polA) #20 RP778 127 DNA POLYMERASE III, ALPHA CHAIN (dnaE) #21 RP865 149 DNA POLYMERASE III SUBUNITS GAMMA AND TAU (dnaX) Motif number 1 AGGCTCAAGATATAAATTTTAACACAGAGATT 1 10 0 TATAATTTAC 0.555804 -153 GTAAAAATCTTATAAATTATATAATATATCTTA 2 24 1 TATAATTTAA 0.775111 -226 ATAATATATCTTAATATTTTTCAAGATGGTGTT 2 44 1 TTAAATTTTA 0.721641 -206 ACTTTTATCTTTAAAATTCTTGTATTTTAAGTT 2 154 1 TTAAATTTTT 0.582598 -96 AATTTAAATTATTATATTTTAAACAGTAAAGCT 3 64 0 ATTAATTTAA 0.736145 -237 AATATAATAATTTAAATTTTATATAGAACCTAG 3 79 1 TTTAATTTAA 0.93135 -222 ACACTTTTGATTAATATTATATTAGGCAATATT 3 118 1 TTAAATTTAT 0.690042 -183 AATAACAATTTTTAAATTATACAACAAGACAAA 4 33 0 TTTAATTTAA 0.966922 -124 AAAAGTTTATTTTAGATCATATATATGTTAGTA 7 40 1 TTTAATCTAA 0.813394 -50 TTATATATTGTATACAGGATCAAC 8 2 1 TATAATTTAA 0.775111 -105 ATTTTTTGTTTTTAGATTTTATCTCAACATTGT 8 80 0 TTTAATTTAC 0.908946 -27 CATTTCATAATTTATATTCTATTAAAGATATCA 9 122 0 TTTAATTTAT 0.940208 -33 TATTACTAATATTACATTGTTTAAAGGTTTTTT 10 138 0 ATTAATTTTA 0.776101 -27 CTTTTGTATTATTTTTTTCAACAAT 11 3 1 TTTGATTTTT 0.794444 -298 TTTATTTTTTTTTAGATTTTTGACTTGACAAAA 11 158 0 TTTAATTTTA 0.95327 -143 AAATAAAATATTTATATTGAATAAATTATTATT 11 184 1 TTTAATTAAA 0.738148 -117 ATAAATATATTTTATATTGTTTTTATTATATAC 12 13 1 TTTAATTTTT 0.916456 -50 ATCAAAGATTTTTATATTATTTTCTAGTTACTA 13 15 1 TTTAATTTTT 0.916456 -43 AAATAAACAATTTACATTATTAAGTCAAAAG 15 9 0 TTTAATTTTA 0.914919 -52 ATATTTGATTAGATTGTTTTGATTCCAAGA 16 8 1 ATTAATTTTT 0.653587 -234 CTTTGTTAATTTTAAATCCTAAATCTGAATAAC 16 155 0 TTTAATCTAA 0.81076 -87 GCTGTTGCTCTTTGTATTGTTGACTCATTGTTC 17 16 0 TTTGATTTTA 0.877839 -285 TTATTTTACCTTTACATTTTAATTAAATTCAGG 17 210 0 TTTAATTTAT 0.896555 -91 GAATTCTAGATTTATATTAAAAATTGGCTTATA 17 243 1 TTTAATTAAA 0.735274 -58 ACAAGTGAATTTTGTATTATTAATGCATTTGAC 18 19 1 TTTGATTTTA 0.877402 -98 CTTCCAGGGCTTTGCATTTTAAATTCATCTTGT 18 58 1 TTTGATTTAA 0.917187 -59 GATTTCAGCTATTATATTGTATCTTGACCATGT 19 91 0 ATTAATTTAC 0.630827 -63 GGTCATATCATTTGCATTGTAGATTTCAGCTAT 19 112 0 TTTGATTTAA 0.920805 -42 TTTAGATTTTATTTATATAGGTC 19 141 0 TTTAATTTAT 0.940208 -13 **** *** ** * Masking position 7 Map Score: 32.7477 Number of sites scoring better than the average of aligned sites = 558 Number in coding regions = 341 Number in noncoding regions = 217 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 2 TTATAACCTTTATATATAATAAATTATTAGATTTACTG 1 133 0 TTAAATTATT 0.841037 -30 TCTTATAAATTATATAATATATCTTAATATTTTTCAAG 2 31 1 TTAAATTAAT 0.729194 -219 TTAATCACAGTATAAAGCAACTTAAAATACAAGAATTT 2 167 0 TTAAAAAAAT 0.848646 -83 ATTTATTATAAATTATAAGTAATTTATTGGAAAT 3 7 1 TTAAATAATT 0.884284 -294 AGCTTTACTGTTTAAAATATAATAATTTAAATTTTATA 3 64 1 TTAAAAATTT 0.867866 -237 TCCTTGTAGCTGTAAATCATAAGATTTTTTTGAAAAAG 3 189 0 TTAAAATTTT 0.819968 -112 ATTTTTAAATTATACAACAAGACAAATTATGTACAACA 4 21 0 TTAAAAAATT 0.916858 -136 GGAGTAACATTTTAGAGTAGGAGTAATTTTTAGGGAAA 4 122 1 TTAAATAATT 0.884352 -35 ATTCACTTATTGTATAGTACTGATAATTTCTAAAACCC 5 14 1 TTAAATAATT 0.884352 -97 GTTTTTTGTTTTTATCACATCGCTTAATCATAGGATAT 6 22 1 TTACATTAAT 0.505684 -112 TTAAAAAAATTATAGAAAAAGTTTATTTTAGATCATAT 7 24 1 TTAAATATTT 0.819969 -66 ACTATTTTCGTTTATACTAACATATATATGATCTAAAA 7 49 0 TTAAAATATA 0.68487 -41 GTATTATACTTATACCGCAACTTAAATTAGTGTAAGCA 9 16 1 TTACAAAATT 0.807157 -139 CTATTTATCTCATTTCATAATTTATATTCTA 9 134 0 TTACAATAAT 0.59598 -21 ACATAAATCATATACCAAATCGTAATTTGTAAGCAGTG 10 21 1 TTACAAATTT 0.71371 -144 CTATAATTTCTCTAGCTCACGATAAAAAACCTTTAAAC 10 115 1 TTACAAAAAA 0.386569 -50 ATAAAAAACCTTTAAACAATGTAATATTAGTAATAAAT 10 136 1 TTAAAATATT 0.884241 -29 ATCAAAATTTTTTAAAAAAACTGTTTAAGTATCGCATT 11 36 0 TTAAATTTAA 0.322258 -265 AAGTCAAAAATCTAAAAAAAAATAAAATATTTATATTG 11 165 1 TTAAAAAAAT 0.848648 -136 ACCATTTTAGTGTATAGAACTTCAATTAAGTAGACACG 11 219 0 TTAAAAATTA 0.660424 -82 ATAAAAACAATATAAAATATATTTATAT 12 1 0 TTAAATATAT 0.698417 -62 TACTTCCTTTTATACATGAGAGTTAAAATAAACAATTT 15 29 0 TTAAATAAAA 0.535165 -32 TATTTTGCACTATAAATCACTAAATATTTATAGTATTT 16 76 0 TTAAAATATT 0.88435 -166 AAAACTTCTATATAAATCATTTAATATTGCATGACGCT 16 186 0 TTAAAATATT 0.884133 -56 CAACCTCTATTCTAAATTACGTTTATTACTATAGCTAT 17 153 1 TTAAATATTA 0.574221 -148 AGCTTTATACAAGTGAATTTTGTATTATTAA 18 4 1 TTAAAATTTT 0.819969 -113 AGACAGCAGATTTAGACAAGATGAATTTAAAATGCAAA 18 68 0 TTAAAAATTT 0.867867 -49 * ** * * ***** Masking position 9 Map Score: 22.2602 Number of sites scoring better than the average of aligned sites = 1027 Number in coding regions = 618 Number in noncoding regions = 409 Number of orfs with sites within 600 bp upstream = 189 Fraction of orfs with sites within 600 bp upstream = 0.0303566 Motif number 3 GATGGTGTTGTTTTGTAGTTTAGAAATTGCCA 2 68 1 TTTTTGTTTA 0.876161 -182 GATAATCAACTTTTATCTTTAAAATTCTTGTA 2 146 1 TTTTTTTTAA 0.818155 -104 TCTTTAAAATTCTTGTATTTTAAGTTGCTTTA 2 161 1 TCTTTTTTTA 0.725219 -89 AAATTTAAATTATTATATTTTAAACAGTAAAG 3 66 0 TATTTTTTTA 0.640381 -235 ATCGTATTAATTTTCGCTTTAAAATATTGCCT 3 141 0 TTTTGTTTAA 0.878566 -160 CATAATGTTATTTTGTATTTAAGCTATGGAGT 4 95 1 TTTTTTTTAA 0.818162 -62 CATTTCTAGTTTTTTGTTTTTATCACATCGCT 6 14 1 TTTTGTTTTA 0.96677 -120 TGTTTGATTTTATTTAAAAAAA 7 1 1 TGTTGTTTTA 0.809305 -89 TGAAAAACTATTTTCGTTTATACTAACATATA 7 61 0 TTTTGTTATA 0.824452 -29 TATTTTTTGTTTTTAGATTTTATCTCAACATT 8 82 0 TTTTGTTTTA 0.96677 -25 TTACACCAAATTTTTGAGTTTAACATGCAGTA 10 62 0 TTTTGGTTTA 0.919203 -103 TTTTATTTTTTTTTAGATTTTTGACTTGACAA 11 160 0 TTTTGTTTTT 0.713417 -141 AATGACACCATTTTAGTGTATAGAACTTCAAT 11 231 0 TTTTGGTATA 0.647452 -70 ATAATGTAAATTGTTTATTTTAACTCTCATGT 15 22 1 TTGTTTTTTA 0.696463 -39 ATTTTATGTTTTAGTTCATAGAG 18 104 0 TTTTTTTTTA 0.947624 -13 ATCTAGTCTGTTTTATGTTTTACACAGTAAAA 19 13 0 TTTTTTTTTA 0.947624 -141 **** * ***** Masking position 4 Map Score: 12.5847 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 134 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 4 AATCTCTGTGTTAAAATTTATATCTTGAGCCTATA 1 11 1 TTAATTTTAT 0.519169 -152 TTTTATAACCTTTATATATAATAAATTAT 1 144 0 ATAATTTTAT 0.940878 -19 TATATAATTTATAAGATTTTTACAAGGTAATTTTA 2 12 0 ATAATTTTAA 0.752683 -238 AGAAATTGCCATATTCATTATACCTTGGCTTAAAA 2 89 1 ATATATTTAT 0.752679 -161 TTAAGCTGCAATAAAAATTGGAGCTACATGGGCAA 2 201 1 ATAAATTGAT 0.627934 -49 TGTTTAAAATATAATAATTTAAATTTTATATAGAA 3 72 1 ATAAATTAAT 0.532426 -229 AACACTTTTGATTAATATTATATTAGGCAATATTT 3 117 1 ATTAATTTAA 0.445746 -184 AACTTTTTCTATAATTTTTTTAAATAAAATCAAAC 7 12 0 ATAATTTTAT 0.940883 -78 TTGTTACAACATAACTTTGCTAAATAGTCCAGTGA 8 49 0 ATAATTGTAT 0.615428 -58 TATAAGTATTATACTTATACCGCAAC 9 2 1 ATAAATTTAT 0.940884 -153 AAATTATTCTATAATTTCTCTAGCTCACGATAAAA 10 107 1 ATAATCTTAT 0.777124 -58 TTTATTCAATATAAATATTTTATTTTTTTTTAGAT 11 174 0 ATAAATTTAT 0.94083 -127 AATATATTTTATATTGTTTTTATTATATACTAAAT 12 16 1 ATATTTTTAA 0.367871 -47 GAGAGTTAAAATAAACAATTTACATTATTAAGTCA 15 15 0 ATAAAATTAT 0.560589 -46 TTTTTACGAAATAAGGTGTTTACATTACATAAATA 16 46 1 ATAATGTTAT 0.654535 -196 TTTACATTACATAAATACTATAAATATTTAGTGAT 16 64 1 ATAAACTTAT 0.775992 -178 TAAAGGTAAAATAAGAATTCTAGATTTATATTAAA 17 229 1 ATAAATTTAT 0.940882 -72 AATTAAGTTTTTAATTGAGCATTCTA 17 285 0 ATTATTTTAT 0.807907 -16 AGGTCATATCATTTGCATTGTAGATTTCAGCTATT 19 111 0 ATTTATTTAT 0.445713 -43 ATACTGTTTGATTAGATTTTTAGGTTCTCTACGTT 20 68 1 ATTATTTTAT 0.807907 -60 **** *** ** * Masking position 2 Map Score: 8.85351 Number of sites scoring better than the average of aligned sites = 457 Number in coding regions = 280 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 5 TATTAGATTTACTGCATAAACTATCTTATA 1 117 0 ACTGCATAAA 0.926142 -46 AACACTAGATACAGTGTAAAGCTAGATAAT 2 122 1 ACAGTGTAAA 0.933384 -128 CAGCTTAATCACAGTATAAAGCAACTTAAA 2 179 0 ACAGTATAAA 0.954175 -71 CAAAAGCTTTACTGTTTAAAATATAATAAT 3 60 1 ACTGTTTAAA 0.917763 -241 TTTTAAAAAAACTGTTTAAGTATCGCATTA 11 35 0 ACTGTTTAAG 0.845082 -266 TATAATAAAAACAATATAAAATATATTTAT 12 13 0 ACAATATAAA 0.671193 -50 TTTAGATAAGACTGCATAAGGTTAAATAAA 16 221 1 ACTGCATAAG 0.859734 -21 GGTTTTACTGTGTAAAACATAAAACA 19 7 1 ACTGTGTAAA 0.945243 -147 ATCTAATCAAACAGTATAAAACCTGAGATT 20 55 0 ACAGTATAAA 0.954175 -73 ********** Masking position 7 Map Score: 5.72251 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 20 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 ATAATGTTACTTTTTCAAAAAAATCTTATGATTT 3 180 1 TTTTAAAAAT 0.960545 -121 ATACAATAAGTTCTTAAACACAATTT 5 95 1 TTTTAAACAT 0.91369 -16 TTCTATAATTTTTTTAAATAAAATCAAACA 7 7 0 TTTTAAAAAT 0.960545 -83 TATCGCATTATTGTTGAAAAAAATAATACAAAAG 11 11 0 TTTTAAAAAT 0.960955 -290 ATATCAAAATTTTTTAAAAAAACTGTTTAAGTAT 11 42 0 TTTTAAAAAT 0.960955 -259 TAAAATATTTATATTGAATAAATTATTATTCTCG 11 187 1 ATTTAAAAAT 0.775988 -114 TTAAATTTCTTTAATTCATTAAATTTAGTA 12 43 0 TTTTAATCAT 0.827392 -20 TAAGAGATTATTATTAAATAAACTTACGATAATT 16 118 0 TTTTAAAAAT 0.960968 -124 TATAAGCCAATTTTTAATATAAATCTAGAATTCT 17 242 0 TTTTATTAAT 0.610418 -59 CACTGAATACTTATTAAATTAATTTTAAA 20 109 1 TTTTAATAAT 0.917682 -19 ** ** ** *** * Masking position 7 Map Score: 8.25448 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 85 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 7 AAAATCGAATCATAACTTATATCTATGTAC 1 45 1 CATAACTTAT 0.566037 -118 CAGTAAATCTAATAATTTATTATATATAAA 1 133 1 AATAATTTAT 0.934007 -30 AGATATATTATATAATTTATAAGATTTTTA 2 25 0 TATAATTTAT 0.819674 -225 ATAAATTACTTATAATTTATAATAAAT 3 8 0 TATAATTTAT 0.819674 -293 ATAAATTATAAGTAATTTATTGGAAATAGG 3 18 1 AGTAATTTAT 0.920734 -283 TTTAAAATATAATAATTTAAATTTTATATA 3 74 1 AATAATTTAA 0.532093 -227 AAATACGGGCAGTAATTTATCAGTTAGGAG 3 276 1 AGTAATTTAT 0.920734 -25 ATATGTTGTACATAATTTGTCTTGTTGTAT 4 18 1 CATAATTTGT 0.757387 -139 TTAGAGTAGGAGTAATTTTTAGGGAAAAGT 4 133 1 AGTAATTTTT 0.742777 -24 AAACTTTTTCTATAATTTTTTTAAATAAAA 7 18 0 TATAATTTTT 0.530564 -72 TATCTCATTTCATAATTTATATTCTATTAA 9 130 0 CATAATTTAT 0.920813 -25 TATACCAAATCGTAATTTGTAAGCAGTGAT 10 31 1 CGTAATTTGT 0.719198 -134 GAAATTATAGAATAATTTTTTGCATGTAAT 10 95 0 AATAATTTTT 0.778026 -70 ATTCAATATAAATATTTTATTTTTTTTTAG 11 176 0 AATATTTTAT 0.517258 -125 ACACGAGAATAATAATTTATTCAATATAAA 11 194 0 AATAATTTAT 0.934007 -107 ATAAATATTTAGTGATTTATAGTGCAAAAT 16 83 1 AGTGATTTAT 0.717898 -159 TGCAATATTAAATGATTTATATAGAAGTTT 16 193 1 AATGATTTAT 0.756205 -49 TAGTAATAAACGTAATTTAGAATAGAGGTT 17 154 0 CGTAATTTAG 0.531777 -147 ********** Masking position 7 Map Score: 14.1493 Number of sites scoring better than the average of aligned sites = 280 Number in coding regions = 182 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 AAACAACACCATCTTGAAAAATATTAAGAT 2 51 0 ATCTTGAAAA 0.755317 -199 CATTTTAGTGCACTTGACCACTATATCTTA 6 79 0 CACTTGACCA 0.964119 -55 AATAACCTGAAAAACTATTTTCG 7 77 0 AACCTGAAAA 0.737135 -13 GTAAGCACGTAACTTGACCATTTGATCTCA 9 47 1 AACTTGACCA 0.970069 -108 TTAGATTTTTGACTTGACAAAAATAAGATT 11 150 0 GACTTGACAA 0.913066 -151 GTCATCTATCCTCTTGAACACGTGGATTCA 19 45 1 CTCTTGAACA 0.867499 -109 ATTATATTGTATCTTGACCATGTATAGCGA 19 84 0 ATCTTGACCA 0.952837 -70 CTTCTTTTCAGACCTGACCAACTAAGCAAG 21 48 0 GACCTGACCA 0.93833 -102 ********** Masking position 7 Map Score: 2.58863 Number of sites scoring better than the average of aligned sites = 25 Number in coding regions = 14 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 CTCATACTGCAGTACATAGATATAAGTTAT 1 56 0 AGTACATAGA 0.927521 -107 ATTTATTAAGAGTGCATAGAGCCTAATCAA 3 242 1 AGTGCATAGA 0.980711 -59 AGTGTATATATGTTGTACAT 4 1 1 AGTGTATATA 0.726613 -156 ACACCATTTTAGTGTATAGAACTTCAATTA 11 229 0 AGTGTATAGA 0.944995 -72 AAATTTTTGAAGTTCATCGAGTATTGGTGG 17 96 1 AGTTCATCGA 0.891905 -205 TTTATGTTTTAGTTCATAGAGACAGCAGAT 18 95 0 AGTTCATAGA 0.957566 -22 ********** Masking position 6 Map Score: 1.8358 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 9 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 10 AGTTTATGCAGTAAATCTAATAATTTATTAT 1 125 1 GTAAATCTAT 0.82728 -38 CACTTGACCACTATATCTTAAGATACAGTCT 6 68 0 CTATATCTAA 0.651181 -66 TCATCAAACACTTAATCTCATATTGCAATAT 9 83 0 CTTAATCTAT 0.838622 -72 TATCTCGTATCTAGATCTAATAAAATACCAA 11 73 1 CTAGATCTAT 0.897496 -228 TGTATAGTAACTAAATCTTATTTTTGTCAAG 11 137 1 CTAAATCTAT 0.970542 -164 TTATTATATACTAAATTTAATGAATTAAAGA 12 35 1 CTAAATTTAT 0.763629 -28 ATTTTAAATCCTAAATCTGAATAACATCTAA 16 149 0 CTAAATCTAA 0.912412 -93 GCAGTCTTATCTAAAACTTCTATATAAATCA 16 205 0 CTAAAACTCT 0.717523 -37 TTCATCTTGTCTAAATCTGCTGTCTCTATGA 18 81 1 CTAAATCTCT 0.941566 -36 ******** ** Masking position 5 Map Score: 1.91739 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 109 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 11 TAATGAATATGGCAATTTCTAAACTACAAAA 2 78 0 GGCAATTTTA 0.763448 -172 AGTGTTTTAAGCCAAGGTATAATGAATATGG 2 97 0 GCCAAGGTTA 0.820168 -153 CCCATGTAGCTCCAATTTTTATTGCAGCTTA 2 202 0 TCCAATTTTA 0.903201 -48 GGCTTGCAATAACAATTTTTAAATTATACAA 4 42 0 AACAATTTTA 0.667712 -115 CTAATAAAATACCAATCTTTATGGAGAAATG 11 89 1 ACCAATCTTA 0.841767 -212 GCTTTTAATTACCAATGTATAGTAACTAAAT 11 122 1 ACCAATGTTA 0.907324 -179 AACGACTATAACCAATTAGTATCTATA 11 284 1 ACCAATTATA 0.900684 -17 AAATAATCTCCAAATTTTACTAGTAACTA 13 39 0 TCCAAATTTA 0.721695 -19 CTATATTAGCACCAAATATTATGCCTGAATT 17 187 1 ACCAAATATA 0.715993 -114 TTTATTATAAGCCAATTTTTAATATAAATCT 17 250 0 GCCAATTTTA 0.965078 -51 CTAAATAAGCCAAGTTGTAATTAGATGTG 20 9 1 GCCAAGTTTA 0.922364 -119 TCATTGCTTAACCAATTAATAGTCATTGCCA 21 113 1 ACCAATTATA 0.900687 -37 ******** ** Masking position 5 Map Score: 5.31568 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 79 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 AGGCTCAAGATATAAATTTTAACACAGAGA 1 13 0 TATAAATTTT 0.433168 -150 AATTACCTTGTAAAAATCTTATAAATTATA 2 15 1 TAAAAATCTT 0.928614 -235 CTTTTATCTTTAAAATTCTTGTATTTTAAG 2 155 1 TAAAATTCTT 0.579394 -95 TACTTTTTCAAAAAAATCTTATGATTTACA 3 187 1 AAAAAATCTT 0.82227 -114 AGCTCACGATAAAAAACCTTTAAACAATGT 10 128 1 AAAAAACCTT 0.700326 -37 CAGTTTTTTTAAAAAATTTTGATATCTCGT 11 51 1 AAAAAATTTT 0.568745 -250 TTTGTCAAGTCAAAAATCTAAAAAAAAATA 11 159 1 CAAAAATCTA 0.634381 -142 GAAAATAATATAAAAATCTTTGATGAAG 13 9 0 TAAAAATCTT 0.928614 -49 TTATGTAATGTAAACACCTTATTTCGTAAA 16 48 0 TAAACACCTT 0.674972 -194 CAATTTTTAATATAAATCTAGAATTCTTAT 17 239 0 TATAAATCTA 0.62953 -62 TTGAGCATTCTAAACATTTATTATAAGCCA 17 267 0 TAAACATTTA 0.429677 -34 AATGCTCAATTAAAAACTTAATT 17 288 1 TAAAAACTTA 0.546874 -13 GTAGAGAACCTAAAAATCTAATCAAACAGT 20 70 0 TAAAAATCTA 0.892535 -58 ********** Masking position 4 Map Score: 2.56019 Number of sites scoring better than the average of aligned sites = 565 Number in coding regions = 367 Number in noncoding regions = 198 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 13 ATCTATGTACTGCAGTATGAGGTATGTGAT 1 65 1 TGCAGTATGA 0.886379 -98 TTAGGCTCTATGCACTCTTAATAAATAACC 3 238 0 TGCACTCTTA 0.880059 -63 TTATATATATTGCAATATGAGATTAAGTGT 9 77 1 TGCAATATGA 0.903938 -78 ATTTTTTGCATGTAATCTTACACCAAATTT 10 81 0 TGTAATCTTA 0.864255 -84 CTTTAAACAATGTAATATTAGTAATAAATT 10 145 1 TGTAATATTA 0.866587 -20 CAAAGCGTCATGCAATATTAAATGATTTAT 16 183 1 TGCAATATTA 0.943238 -59 TTTAACCTTATGCAGTCTTATCTAAAACTT 16 217 0 TGCAGTCTTA 0.93105 -25 AAGTGAATTTTGTATTATTAATGCATTTGA 18 21 1 TGTATTATTA 0.663784 -96 ********** Masking position 4 Map Score: 2.25125 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 78 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 14 ********** No masking Map Score: 7.11496e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 AAATCTAATAATTTATTATATATAAAGGTT 1 137 1 ATTTATTATA 0.917627 -26 AAATATTAAGATATATTATATAATTTATAA 2 33 0 ATATATTATA 0.542442 -217 AAATTGCCATATTCATTATACCTTGGCTTA 2 91 1 ATTCATTATA 0.849029 -159 ATTTATTATAAATTATAAGT 3 1 1 ATTTATTATA 0.917627 -300 ATAAAATTTAAATTATTATATTTTAAACAG 3 71 0 AATTATTATA 0.666259 -230 AGCATTCACTTATTGTATAGTACTGAT 5 8 1 ACTTATTGTA 0.817266 -103 GTGTTTAAGAACTTATTGTATGATATTACT 5 86 0 ACTTATTGTA 0.817266 -25 GACCATTTGATCTCATTATATATATTGCAA 9 62 1 TCTCATTATA 0.676526 -93 TTTATATTGTTTTTATTATATACTAAATTT 12 23 1 TTTTATTATA 0.781423 -40 AATTTCTTTAATTCATTAAATTTAGTATAT 12 40 0 ATTCATTAAA 0.534583 -23 AATCTAGAATTCTTATTTTACCTTTACATT 17 225 0 TCTTATTTTA 0.344873 -76 CATTCTAAACATTTATTATAAGCCAATTTT 17 262 0 ATTTATTATA 0.917627 -39 GACACTGAATACTTATTAAATTAATTTTAA 20 107 1 ACTTATTAAA 0.724951 -21 ********** Masking position 5 Map Score: 5.77996 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 166 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301