AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_tpal_reg_100.orf -o00230_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0002 242 DNA polymerase III, subunit beta (dnaN) #2 TP0045 300 adenosine deaminase, putative #3 TP0053 170 ribonucleoside-diphosphate reductase, subunit beta (nrdB) #4 TP0104 246 5'-nucleotidase (ushA) #5 TP0105 166 DNA polymerase I (polA) #6 TP0207 187 ribosomal protein L15 (rplO) #7 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #8 TP0284 104 T. pallidum predicted coding region TP0284 #9 TP0289 22 T. pallidum predicted coding region TP0289 #10 TP0290 54 conserved hypothetical protein #11 TP0291 36 T. pallidum predicted coding region TP0291 #12 TP0524 135 ATP-dependent protease LA (lon-2) #13 TP0595 23 adenylate kinase (adk) #14 TP0596 107 polynucleotide adenylyltransferase (pcnB) #15 TP0642 140 phosphomannomutase (manB) #16 TP0669 153 DNA polymerase III, subunit alpha (dnaE) #17 TP0734 81 purine nucleoside phosphorylase (deoD) #18 TP0736 233 hydrogenase, gamma chain (hydG) #19 TP0886 147 polyribonucleotide nucleotidyltransferase (pnp) #20 TP1005 58 DNA polymerase III, subunits gamma and tau (dnaH) #21 TP1006 108 DNA gyrase, subunit B (gyrB) #22 TP1008 126 ribonucleoside-diphosphate reductase, subunit alpha (nrdA) #23 TP1010 125 nucleoside-diphosphate kinase (ndk) #24 TP1039 226 adenine phosphoribosyltransferase (apt) Motif number 1 CACAAGCTTGTGTGCGGTTTTTGTTTGGTAAT 1 123 1 TGTGCGTTTT 0.592864 -120 TCACATGTGCAGTGTGTTCGCGTGTAC 2 6 1 TGTGCGTTGT 0.910598 -295 ATGTGAGCGTGGTGGGGTTTGTTAGCAAGGGG 2 43 1 GGTGGGTTGT 0.977705 -258 TCCTAGAGGAGGTGGGCTAAGTAATGGTATTG 2 145 0 GGTGGCTAGT 0.734752 -156 TGTCTTGTGTGGTGGTCCCTGTTTTGTGGGTA 3 49 0 GGTGGCCTGT 0.971021 -122 AAAGCAGATTGGCACAGCCTGTAAAGAACGTA 5 46 0 GGCACGCTGT 0.875714 -121 CGGAAAGAAGGGTGCTGCACATAACCTTATCT 5 112 1 GGTGCGCCAT 0.941757 -55 GGAGTATTACGGTAGAGCGTGTGGTATAGGGA 7 203 1 GGTAGGCTGT 0.882128 -60 GAACCGACACGGTGCTCCCTATACCACACGCT 7 218 0 GGTGCCCTAT 0.962199 -45 GTGTCGGTTCGGTGCAGCTTGAGGGGGGAGTG 7 240 1 GGTGCGCTGA 0.970767 -23 TGGTGCAGTACGCTGAAGTAAT 9 10 0 GGTGCGTCGC 0.948201 -13 GACCTGCGGGGGCGCAGTATACCGCGCAGGTA 12 48 1 GGCGCGTTAC 0.798757 -88 GAAGATAAGGTGGAGTTTGTTTC 13 9 1 GGTGGGTTGT 0.977705 -15 GGGTACACAAGGTGCGGTGTATTTTGTAATTC 14 13 1 GGTGCGTTAT 0.970857 -95 CCCCCGAGAAGGAGCTCCCTGTCAAGACCAAC 14 70 0 GGAGCCCTGT 0.888148 -38 TAGTGGCTCTGGTACACTTTTTCAAGACATGC 15 16 1 GGTACCTTTT 0.509591 -125 TCTATCCTGTGGTGCCGTAAATAGTCCAGTAC 15 97 1 GGTGCGTAAT 0.816365 -44 CTGCTTATCGGGTGCACCGTTTTTTGTTATA 16 133 1 GGTGCCCTTT 0.940713 -21 CGGGTGCTGCATGCGCTGAGCGTA 17 3 1 GGTGCGCTGC 0.989927 -79 GCCAGGGCTTGGTGCGGCCTGCGATACATTCT 19 111 1 GGTGCGCTGC 0.989927 -37 CCATGTGAGTGGTGCCGTCTGACAGGGGGAAG 20 32 1 GGTGCGTTGA 0.953643 -27 TGGGTACGCTGGCGCGCCACGTGTATTAGCTA 23 89 1 GGCGCCCCGT 0.904632 -37 ***** ** *** Masking position 2 Map Score: 29.4338 Number of sites scoring better than the average of aligned sites = 717 Number in coding regions = 658 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 GGGTTTGTTAGCAAGGGGACGTTGATCTGTTCGT 2 57 1 GCGGGGAGTG 0.964546 -244 ACGAAAATTTCCTAGAGGAGGTGGGCTAAGTAAT 2 152 0 CCGAGGAGTG 0.759986 -149 ATTGTTTTACGCAAGAGGATGCAGA 2 286 1 GCGAGGAGCG 0.926487 -15 GTGCCCGCACTCAGGAGGAGGTTTCATC 3 153 1 TCGAGGAGTT 0.823171 -18 ACGGAACACATCGAGCGGACGCGTCTGTTCGTGG 4 215 1 TCGCGGAGCT 0.841043 -32 AGTACGATCGGTCAGAGGGAGCCGGTGCGTCGGA 6 46 1 GTGAGGGGCG 0.59576 -142 AGGGAGCCGGTGCGTCGGACGGTTCGGTCTTTGG 6 61 1 TGTCGGAGGT 0.687753 -127 CGGTCTTTGGGTTTGAGGAAGTTGCATTCAATGG 6 85 1 GTGAGGAGTG 0.692383 -103 AGTCCTGCCGTCTTGGGGATGGTGCGAGCTGTTT 6 133 1 TCGGGGAGGG 0.987095 -55 GTTTCGCACCTGGTGCGGGTGGAGGAGTTAGGTT 6 163 1 TGGCGGGGGG 0.874478 -25 GACACCCTTTCGTGTGGGAGGGCGTCGCGCTTTT 7 57 1 CGTGGGAGGG 0.844513 -206 CTCACTTGAGTGGAGGGGACGGCGTCTCCCCTGT 7 165 1 TGGGGGAGGG 0.981581 -98 GCGTCTCCCCTGTGTGGGGAGTATTACGGTAGAG 7 186 1 TGTGGGGGTT 0.544392 -77 GTTCGGTGCAGCTTGAGGGGGGAGTGC 7 246 1 GCGAGGGGGG 0.931938 -17 CTTGCACGACCTGCGGGGGCGCAGTATACCGCGC 12 41 1 CTGGGGGGCG 0.604072 -95 GGGAGCTCCTTCTCGGGGGAGGATGGGCGGGGTA 14 83 1 TCGGGGGGGT 0.954212 -25 GAGGGGCATTGTAATGGGAAGGTGCTGCTCTGTG 15 65 0 GTTGGGAGGG 0.847124 -76 TCTAGGCCCCACGAAGGGAGGGAGTGACG 17 63 1 ACAGGGAGGG 0.610383 -19 CAGATATACGTGTCGGGGAGGTTTAC 18 3 0 TGGGGGAGTT 0.906308 -231 GACCAAACTCTCGGAGGGATGGATGATAGTACAG 18 195 0 TCAGGGAGGT 0.838434 -39 GGGCTTTGCATGGGGAAGTTTCGCAGTGCGT 19 8 1 GCGGGGAGTT 0.939905 -140 CGAGGGGTTGTGCATAGGACGGTTGTCCGTTCTG 19 47 1 TGTAGGAGGT 0.728069 -101 GTGCCGTCTGACAGGGGGAAGGATCA 20 43 1 ACGGGGAGGT 0.884145 -16 CGCGCGTCTCTGTGGGGGAAGCGTAAAGAACGAG 22 29 1 TGGGGGAGCT 0.930384 -98 CCCATAATCCGCGTTCGGACGGAGAGATAT 22 107 1 GCTCGGAGGG 0.861009 -20 CTCACCATACGGTGAAGGAAGGGTAAAAAGAGAA 23 22 1 GGAAGGAGGT 0.5773 -104 TCTTACCGGTTTGTTGGGAGGCTTGGTGGATTGA 24 195 0 TTTGGGAGCT 0.552283 -32 ** ***** ** * Masking position 7 Map Score: 29.8579 Number of sites scoring better than the average of aligned sites = 1150 Number in coding regions = 1000 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 3 AATTCTCAATTGCGGCGGGCGTAAAAATGTC 3 97 0 TGCGCGGGCG 0.987723 -74 AGGGAGCCGGTGCGTCGGACGGTTCGGTCTT 6 61 1 TGCGCGGACG 0.857295 -127 TTTTTTTGCATGCGTCCGGCGCGTCGTTGTG 7 19 1 TGCGCCGGCG 0.995104 -244 AAACGTCTTGCACGACCTGCGGGGGCGCAGT 12 35 1 CACGCCTGCG 0.751003 -101 GGGTGCTGCATGCGCTGAGCGTACACGCGCG 17 12 1 TGCGTGAGCG 0.853496 -70 TCAAGCAAAACGCCATCGGCGCCGAGAAGGG 18 46 0 CGCCTCGGCG 0.944821 -188 TGAGAAAAGCAGCGGTCGGCGCGTTAGTTGC 18 114 1 AGCGTCGGCG 0.974836 -120 GCGCGTTAGTTGCCTTGTGCGACAGAGCTGA 18 132 1 TGCCTGTGCG 0.940635 -102 AGCCATGCCTCCTTCGACCAAACTCT 18 218 0 TGCCCCTTCG 0.886698 -16 CCTATGCACAACCCCTCGGCGGCACGCACTG 19 34 0 ACCCTCGGCG 0.832321 -114 AGGACGGTTGTCCGTTCTGCTTTCTTTGTCT 19 62 1 TCCGTCTGCT 0.608049 -86 GCCCTGGCACAGCCACCTGCGAAGCTAGACA 19 88 0 AGCCCCTGCG 0.956416 -60 CAGGGCTTGGTGCGGCCTGCGATACATTCTG 19 113 1 TGCGCCTGCG 0.990935 -35 AAGTCTATAGTGCGCTCGTCTGTGTGAGCAG 21 11 1 TGCGTCGTCT 0.650903 -98 **** ****** Masking position 3 Map Score: 14.5565 Number of sites scoring better than the average of aligned sites = 666 Number in coding regions = 611 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 AACGTCCCCTTGCTAACAAACCCCACCACGCT 2 48 0 TGCACAAACC 0.975285 -253 TCCCCAAACCTACCCACAAAACAGGGACCACC 3 39 1 TACACAAAAC 0.847601 -132 CACAGAGCCCTGCAGACAGACATTTTTACGCC 3 79 1 TGCACAGACA 0.832047 -92 CGATTCTGCGAGCAAATCGTATCTGCAG 4 7 1 TGCGCAAATC 0.879418 -240 TATATAAAATTGCATAAAAAACCTGTAGAAGT 4 124 0 TGCAAAAAAC 0.933568 -123 GCCGGACGCATGCAAAAAAAACCAGACA 7 7 0 TGCAAAAAAC 0.933568 -256 CTCTGTGCAATGCTCACAAAAAGTGCATGTCT 15 40 0 TGCACAAAAA 0.965576 -101 CGTGGTACGCTGCGAGCAAAAACCCTGCAAGG 16 45 1 TGCGCAAAAA 0.953696 -109 GCAGTCCTCATTCAAGCAAAACGCCATCGGCG 18 56 0 TTCGCAAAAC 0.803303 -178 GAATGAGGACTGCACGCAAAACCTGCCAGGAA 18 75 1 TGCGCAAAAC 0.981072 -159 GGGGAGGACTTGCATAAAGAAAGAATGGTGGG 23 61 1 TGCAAAGAAA 0.638237 -65 GCAAAAACCATGCCAACAAAAAATCGAAAGAA 24 36 1 TGCACAAAAA 0.965576 -191 CCACCAAGCCTCCCAACAAACCGGTAAGATCA 24 200 1 TCCACAAACC 0.821693 -27 *** ******* Masking position 8 Map Score: 11.3602 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 136 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TATGTGATACGACTACATTCTTTATACTTA 1 197 1 GACTACATTC 0.598518 -46 TTGTACACGCGAACACACTGCACATGTGA 2 10 0 GAACACACTG 0.930003 -291 CCGTCGTATAGAACACACTCGCAGGTTTCC 2 110 1 GAACACACTC 0.951696 -191 ACTACCCTGTGCCCGCACTCAGGAGGAGGT 3 145 1 GCCCGCACTC 0.981869 -26 ACGGAACCTAGACCACACCGTATCGGAGAC 4 174 0 GACCACACCG 0.969197 -73 TGTGTTCCGTGCCCGCACGGTACGGAACCT 4 195 0 GCCCGCACGG 0.953769 -52 TGCGGGCACGGAACACATCGAGCGGACGCG 4 208 1 GAACACATCG 0.552803 -39 CAAACCCAAAGACCGAACCGTCCGACGCAC 6 70 0 GACCGAACCG 0.78558 -118 AGAAATAGAAGCCCACGCTCTACTCAAAAG 7 86 0 GCCCACGCTC 0.880467 -177 GTGCTCCCTATACCACACGCTCTACCGTAA 7 209 0 TACCACACGC 0.725513 -54 CTTGAATGAGGACTGCACGCAAAACCTGCC 18 72 1 GACTGCACGC 0.843395 -162 TGCCTCCTTCGACCAAACTCTCGGAGGGAT 18 209 0 GACCAAACTC 0.89969 -25 CCCCTCGGCGGCACGCACTGCGAAACTTCC 19 24 0 GCACGCACTG 0.897007 -124 GCATACCTATGACCACATTCACCTTTTTAA 21 65 0 GACCACATTC 0.932844 -44 AACTGACCGCTCTCCTTTTCATCA 21 95 0 GACCGCTCTC 0.899163 -14 ********** Masking position 1 Map Score: 10.9085 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 426 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 AAAAAATATACTTTCTTCACAAGCTTGTGTG 1 106 1 CTTTCTCACA 0.89987 -137 TTGATCTGTTCGTGCTGCTGATTGTCTTTGT 2 78 1 CGTGCTCTGA 0.804618 -223 CAGCACCCTTCTTTCCGCTCCTAACGTGGCA 5 98 0 CTTTCCCTCC 0.797342 -69 CGGAAAGAAGGGTGCTGCACATAACCTTATC 5 112 1 GGTGCTCACA 0.675531 -55 TCTGACCGATCGTACTCCTCACCAGCGTTAT 6 31 0 CGTACTCTCA 0.952395 -157 GGACTCCCGTCTTTCTCCACCATTGAATGCA 6 107 0 CTTTCTCACC 0.947314 -81 TAACCTAACTCCTCCACCCGCACCA 6 173 0 CTAACTCTCC 0.616401 -15 TAGAAGCCCACGCTCTACTCAAAAGCGCGAC 7 80 0 CGCTCTCTCA 0.806788 -183 GGTTGGGTCGCGTTCTCCTCACTTGAGTGGA 7 148 1 CGTTCTCTCA 0.972282 -115 CACGCTCTACCGTAATACTCCCCACACAGGG 7 193 0 CGTAATCTCC 0.842415 -70 TTTTGAGCAAGGTTCTCCTGC 8 94 1 GGTTCTCTGC 0.755804 -11 ATTACTTCAGCGTACTGCACCA 9 11 1 CGTACTCACC 0.953512 -12 AAAGAAAAGCCTTTCTTCAGCTCTGTCGCAC 18 148 0 CTTTCTCAGC 0.790618 -86 AGGCAATACTCTTGCTGCTCACACAGACGAG 21 25 0 CTTGCTCTCA 0.90742 -84 TCTTTTTACCCTTCCTTCACCGTATGGTGAG 23 22 0 CTTCCTCACC 0.789462 -104 CGTTCTTTCTCCTCCAAACTTTAAA 24 5 1 CTTTCTCTCC 0.972282 -222 AAAAGACAGTGGTTATGCTCCATTTCTTTCG 24 60 0 GGTTATCTCC 0.663069 -167 TTCCAGGAGACGTAATTCTCAATCCACCAAG 24 177 1 CGTAATCTCA 0.727666 -50 ****** **** Masking position 8 Map Score: 15.1344 Number of sites scoring better than the average of aligned sites = 479 Number in coding regions = 434 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 7 ATAGAACACACTCGCAGGTTTCCCTGCCCA 2 117 1 CTCGCAGGTT 0.863359 -184 AAAATGTCTGTCTGCAGGGCTCTGTGTCTT 3 75 0 TCTGCAGGGC 0.76539 -96 CCTTGTATATTCCGCGAGTTACGCGCATTT 4 72 1 TCCGCGAGTT 0.772927 -175 GTGTTCCGTGCCCGCACGGTACGGAACCTA 4 194 0 CCCGCACGGT 0.982401 -53 TTGCATGCGTCCGGCGCGTCGTTGTGTGCC 7 24 1 CCGGCGCGTC 0.961801 -239 GGCATTTTGGCATGCGGGTTGGGTCGCGTT 7 132 1 CATGCGGGTT 0.568717 -131 CTGCACCGAACCGACACGGTGCTCCCTATA 7 227 0 CCGACACGGT 0.820537 -36 ATACTGCGCCCCCGCAGGTCGTGCAAGACG 12 38 0 CCCGCAGGTC 0.947091 -98 AAAAAATATACCTGCGCGGTATACTGCGCC 12 58 0 CCTGCGCGGT 0.967445 -78 ATTTTGTAATTCGGCACGGTGGTATGAATG 14 33 1 TCGGCACGGT 0.944298 -75 CGGGGGAGGATGGGCGGGGTAG 14 96 1 TGGGCGGGGT 0.806984 -12 TTTATCCACCCTTGCAGGGTTTTTGCTCGC 16 56 0 CTTGCAGGGT 0.769154 -98 TGAGCGTACACGCGCGAGGTTACCGAAACG 17 27 1 CGCGCGAGGT 0.734522 -55 GGGGCCTAGACCCACACGTTTCGGTAACCT 17 43 0 CCCACACGTT 0.787241 -39 TCATTGTTTCCTGGCAGGTTTTGCGTGCAG 18 84 0 CTGGCAGGTT 0.844712 -150 AAAGCAGCGGTCGGCGCGTTAGTTGCCTTG 18 119 1 TCGGCGCGTT 0.944278 -115 GGTGTTTTCTTCCGCGCGTCTCTGTGGGGG 22 17 1 TCCGCGCGTC 0.907927 -110 ********** Masking position 8 Map Score: 13.353 Number of sites scoring better than the average of aligned sites = 1067 Number in coding regions = 964 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 8 TGTACACGCGAACACACTGCACATGTGA 2 8 0 AACACACGCA 0.963596 -293 ATACCCGTTAAAAGCATAGCATTGCTCGACA 2 249 1 AAAGCATGCA 0.625562 -52 AGTAATGCTAACCACTCGGCCATAAAAATGC 4 96 0 ACCACTCGCC 0.818612 -151 CGGAACCTAGACCACACCGTATCGGAGACAC 4 172 0 ACCACACGTA 0.809892 -75 TGCTCCCTATACCACACGCTCTACCGTAATA 7 207 0 ACCACACCTC 0.514707 -56 CTGAACTTTAAAAGCACAGCCCCGAAGATCA 8 58 0 AAAGCACGCC 0.96425 -47 CACCCAAAAAACAACACGGCAACT 10 4 0 ACAACACGCA 0.970402 -51 TTTCCCTAAAAAAGCACTGCCCTCT 11 5 0 AAAGCACGCC 0.96425 -32 CGAATTACAAAATACACCGCACCTTGTGTAC 14 15 0 AATACACGCA 0.835313 -93 GCTGCGAGCAAAAACCCTGCAAGGGTGGATA 16 53 1 AAAACCCGCA 0.842024 -101 AGTCGGAGCTACAGCACAGCATTCTAGGATT 16 104 0 ACAGCACGCA 0.96425 -50 CGCGCGGAAGAAAACACCCCCGTG 22 4 0 AAAACACCCC 0.87572 -123 ******* *** Masking position 1 Map Score: 6.27141 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 271 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 CCTTTTTTTAGAGAAAAAATATACTTTCTTC 1 93 1 GAGAAAAAAA 0.757879 -150 TATACGACGGGACAAAGACAATCAGCAGCAC 2 89 0 GACAAAGACA 0.866626 -212 TTCCGGGAAAGACAAAGGGTATGCCACGTTA 5 77 1 GACAAAGGGA 0.729462 -90 GCATGACAAAGAGGGTGCGTATAAC 6 5 1 GACAAAGAGG 0.960159 -183 TTCAATGGTGGAGAAAGACGGGAGTCCTGCC 6 111 1 GAGAAAGACG 0.960437 -77 TCAACCGAGTGAGAAAAAGAATCATCACATA 8 26 0 GAGAAAAAGA 0.745374 -79 AAACAATGATGAGAAAAGCAGCGGTCGGCGC 18 105 1 GAGAAAAGCG 0.665354 -129 ATGCAGATTTGTCAAAGAAAAGCCTTTCTTC 18 161 0 GTCAAAGAAA 0.631338 -73 TGCGAAGCTAGACAAAGAAAGCAGAACGGAC 19 71 0 GACAAAGAAG 0.962644 -77 ACCTTTTTAAGACACAGAAAGGCAATACTCT 21 44 0 GACACAGAAG 0.789877 -65 AGGGTAAAAAGAGAAAGTGTGGGGAGGACTT 23 41 1 GAGAAAGTGG 0.78693 -85 GACTTGCATAAAGAAAGAATGGTGGGTACGC 23 67 1 AAGAAAGAAG 0.674848 -59 AAGTTTGGAGGAGAAAGAACG 24 1 0 GAGAAAGAAG 0.971507 -226 TTACCAATCGGTGAAAAAAAGCCGGGAAAAG 24 95 0 GTGAAAAAAG 0.623867 -132 ********* * Masking position 6 Map Score: 5.77632 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 236 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 AGAACGTAGTTCTTTACAGGCCTCTAATGT 5 24 0 TCTTTACAGG 0.951888 -143 AGAACTACGTTCTTTACAGGCTGTGCCAAT 5 41 1 TCTTTACAGG 0.951888 -126 ATACCCTTTGTCTTTCCCGGAAAAGCAGAT 5 69 0 TCTTTCCCGG 0.976826 -98 ACTTTTCGTCCCTTGCCTGGATACTAGGCG 12 112 1 CCTTGCCTGG 0.896857 -24 TCCTAGTTGGTCTTGACAGGGAGCTCCTTC 14 65 1 TCTTGACAGG 0.917879 -43 TTCTCATCATTGTTTCCTGGCAGGTTTTGC 18 90 0 TGTTTCCTGG 0.862057 -144 TCTTTTTGGACTTTTCCCGGCTTTTTTTCA 24 85 1 CTTTTCCCGG 0.866887 -142 AGCGAAATCTTTTTTCCAGGAGACGTAATT 24 164 1 TTTTTCCAGG 0.93276 -63 ********** Masking position 4 Map Score: 4.02241 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 42 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 11 AGATAATGTCGAGCAATGCTATGCTTTTAA 2 256 0 GAGCAATGCT 0.800729 -45 GTGATCTTCGGGGCTGTGCTTTTAAAGTTC 8 57 1 GGGCTGTGCT 0.978235 -48 AGAGGGCAGTGCTTTTTTAGGGA 11 4 1 GGGCAGTGCT 0.9832 -33 CACTTTTTGTGAGCATTGCACAGAGCAGCA 15 47 1 GAGCATTGCA 0.929679 -94 CAGGATAGAGGGGCATTGTAATGGGAAGGT 15 76 0 GGGCATTGTA 0.862753 -65 GGGCTTTGCATGGGGAAGTT 19 1 1 GGGCTTTGCA 0.973835 -147 TGCCGCCGAGGGGTTGTGCATAGGACGGTT 19 41 1 GGGTTGTGCA 0.883601 -107 ********** Masking position 7 Map Score: 3.40802 Number of sites scoring better than the average of aligned sites = 93 Number in coding regions = 83 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 GGAACACATCGAGCGGACGCGTCTGTTCGT 4 217 1 GAGCGGACGC 0.953279 -30 CCCTCTGACCGATCGTACTCCTCACCAGCG 6 35 0 GATCGTACTC 0.92203 -153 ATTACTTCAGCGTACTGCACCA 9 8 1 CAGCGTACTG 0.922134 -15 TTTTTGCTCGCAGCGTACCACGGGATCATA 16 37 0 CAGCGTACCA 0.956859 -117 TGCATGCGCTGAGCGTACACGCGCGAGGTT 17 18 1 GAGCGTACAC 0.953397 -64 TATATCTGTTCATCGGACCCTTCTCGGCGC 18 29 1 CATCGGACCC 0.926002 -205 TCACACAGACGAGCGCACTATAGACTT 21 8 0 GAGCGCACTA 0.836979 -101 CGTGGCGCGCCAGCGTACCCACCATTCTTT 23 80 0 CAGCGTACCC 0.987847 -46 ********** Masking position 7 Map Score: 2.19075 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 184 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 13 TATTTTTTCTCTAAAAAAAGGGGGATATTCGT 1 82 0 CTAAAAAGGG 0.783758 -161 GTTAGCATTACTTCTACAGGTTTTTTATGCAA 4 115 1 CTTTACAGTT 0.735675 -132 CACCTCTGAACTTGAACAAGTGCACACCCAAA 10 27 0 CTTAACAGTG 0.955471 -28 CTCTTATCTCCTAGTAAACGTCTTGCACGACC 12 20 1 CTATAAAGTC 0.724015 -116 AAGTGCATGTCTTGAAAAAGTGTACCAGAGCC 15 20 0 CTTAAAAGTG 0.956315 -121 TAGTCCAGTACTTTTAAAGGTGAGGAAGCGCT 15 118 1 CTTTAAAGTG 0.956315 -23 CTTTCTGTGTCTTAAAAAGGTGAATGTGGTCA 21 54 1 CTTAAAAGTG 0.956315 -55 CTCGTCCTAGCTAATACACGTGGCGCGCCAGC 23 96 0 CTATACAGTG 0.930437 -30 *** **** *** Masking position 6 Map Score: 0.629043 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 11 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 ********** No masking Map Score: 4.73465e-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 GTCGTATAGAACACACTCGCAGGTTTCCCTGC 2 112 1 ACCATCGCAG 0.932159 -189 CCTAGACCACACCGTATCGGAGACACATGAAC 4 166 0 ACGTTCGGAG 0.958454 -81 GATGGTGCGAGCTGTTTCGCACCTGGTGCGGG 6 150 1 GCGTTCGCAC 0.928652 -38 TGCACCCGATAAGCAGTCGGAGCTACAGCACA 16 117 0 AACATCGGAG 0.841883 -37 CCTTTCTTCAGCTCTGTCGCACAAGGCAACTA 18 138 0 GCCTTCGCAC 0.928652 -96 TCCTTCGACCAAACTCTCGGAGGGATGGATGA 18 203 0 AACTTCGGAG 0.935668 -31 TTTGCATGGGGAAGTTTCGCAGTGCGTGCCGC 19 15 1 GAGTTCGCAG 0.958667 -133 CTAAGAACAGAATGTATCGCAGGCCGCACCAA 19 119 0 AAGTTCGCAG 0.959453 -29 ** ** ****** Masking position 11 Map Score: 1.48293 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 57 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493