AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_mthe_reg_100.orf -o00970_mthe_100.ace -a/home/amcguire/genomes/ORF_mthe.txt -z/home/amcguire/genomes/mthe.fna -g0.50 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MTH1680 41 ribosomal protein L10a (E.coli L1) Input sequences: #1 MTH42 171 DNA-dependent RNA polymerase, subunit K #2 MTH43 51 enolase #3 MTH44 27 ribosomal protein Sa (E.coli S2) #4 MTH47 21 conserved protein #5 MTH48 73 conserved protein #6 MTH225 300 histidinol dehydrogenase #7 MTH226 93 aspartyl-tRNA synthetase #8 MTH243 231 conserved protein #9 MTH248 195 conserved protein #10 MTH249 64 conserved protein #11 MTH250 23 tRNA intron endonuclease #12 MTH251 54 tryptophanyl-tRNA synthetase #13 MTH587 263 methionyl-tRNA synthetase #14 MTH611 84 prolyl-tRNA synthetase #15 MTH742 34 phenylalanyl-tRNA synthetase #16 MTH744 124 porphobilinogen synthase #17 MTH767 83 valyl-tRNA synthetase #18 MTH770 32 phenylalanyl-tRNA synthetase #19 MTH1120 132 nifH / minD related protein #20 MTH1122 39 seryl-tRNA synthetase #21 MTH1375 22 isoleucyl-tRNA synthetase #22 MTH1376 65 conserved protein #23 MTH1449 135 dihydroxy-acid dehydratase #24 MTH1455 192 threonyl-tRNA synthetase #25 MTH1501 189 phenylalanyl-tRNA synthetase alpha subunit #26 MTH1510 109 NH(3)-dependent NAD+ synthetase #27 MTH1542 37 conserved protein #28 MTH1543 229 thiamine biosynthesis protein #29 MTH1677 120 protein translocation complex sec61 gamma subunit related protein #30 MTH1678 26 transcription termination factor NusG #31 MTH1682 52 ribosomal protein Lp1 #32 MTH1683 89 alanyl-tRNA synthetase #33 MTH1768 26 conserved protein #34 MTH1769 37 translation initiation factor eIF-2, beta subunit #35 MTH1770 30 DNA replication initiator (Cdc21/Cdc54) #36 MTH1850 105 fumarate reductase Motif number 1 GTCAGCACCGGAACGCTGGAGACCCGAGTTCA 1 86 1 GACGCGGAGA 0.77479 -86 GCCCTAACTTTTTCACTGGAGG 6 289 1 TTCACGGAGG 0.989366 -12 GCGAGAGGCTGTGCCCAGGGGATGGCCCATGA 8 16 1 GTCCCGGGGA 0.810499 -216 TGAGGAATATTATACCTTGAGGGGCCCCGGGT 9 37 1 TAACCTGAGG 0.542203 -159 GGGTCCCGTGATGCCCGGGAGGCCTTCCGTGT 9 65 1 ATCCCGGAGG 0.984288 -131 TATTCCCCAGGAACACGGAAGGCCTCCCGGGC 9 77 0 GACACGAAGG 0.903933 -119 CTGGGGAATATTCCGCTGGAGGGGTGCTGGTT 9 99 1 TTCGCGGAGG 0.969928 -97 TGGGGTGTCAGCGCCCTGAAGGATTTCCCCTG 9 148 1 GCCCCGAAGG 0.906918 -48 CCTGAAGGATTTCCCCTGGAGGGTCAGGGTTT 9 162 1 TTCCCGGAGG 0.992663 -34 CTCAACCAGCACTCACGGGAGGT 11 11 1 ACCACGGAGG 0.944415 -13 AAATATATTTTTCCCTGGAGATAAACACTAA 14 64 0 TTCCCGGAGA 0.937431 -21 GCTTATTTGAGTAAACTGGAGGAGAATTATT 15 14 1 GTAACGGAGG 0.92105 -21 GTTATGTTTTTTACCCTTGAGGATGTAATAAG 16 74 1 TTCCCTGAGG 0.962441 -51 ATTCTCACAGGATCACAGGAGGATTATTT 19 8 0 GACACGGAGG 0.988888 -125 CAGGCCGCAGGCCCTCAGGAGGGATCG 23 6 0 GCCTCGGAGG 0.889527 -130 TCCCGGCCACATCCACCTGAGGGAACTTGCAG 23 97 1 ATCACTGAGG 0.890792 -39 AGGTTCAGGAGATCCCTTAAGGGTCATCATCT 24 76 1 GACCCTAAGG 0.721512 -117 GGGTTTAAAGATCCACCGGAGCAATATTTAAA 24 120 1 ATCACGGAGC 0.738119 -73 ATTCGATAATGATCACTGGGGGTTCTGT 25 172 1 GACACGGGGG 0.93997 -18 CGATGATTAATTTTACAGGAGGAGTATA 26 7 0 TTTACGGAGG 0.878694 -103 GTTTGACCCTTAACCCGTGAGGGTATGATCTG 28 193 0 TACCCTGAGG 0.938317 -37 ATTTACACACTTTTACTGGAGGTATCAGTT 34 18 1 TTTACGGAGG 0.878694 -20 ** *** ***** Masking position 6 Map Score: 30.1777 Number of sites scoring better than the average of aligned sites = 980 Number in coding regions = 928 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 2 CTCGGCGGTCCCATCAAATCGAATCCAAGAA 1 121 1 CCATCAAATG 0.734742 -51 TCTATCACCTCAAATAAGTTTC 3 16 0 CTATCACCTA 0.899632 -12 TAAAAATTTTCCATCACCCTATAAATTCCTT 5 40 0 CCATCACCCA 0.983918 -34 TGAATTCCAACCATCAACCAATGTTTAAGTG 6 150 1 CCATCAACCA 0.910572 -151 GAATCATGGGCCATCCCCTGGGCACAGCCTC 8 20 0 CCATCCCCTG 0.933237 -212 AGTTATCAGTTTATCACCCCGGCATTACAGG 8 70 1 TTATCACCCG 0.701036 -162 TCGAAGTGTTCCATCACATCGAACCGCAGTT 13 45 1 CCATCACATG 0.94329 -219 GTGTTTCTCCCTCAGCTGGATA 21 4 0 CCCTCAGCTG 0.914492 -19 CTTATTTATATCATCACCCCAAAACCATAAA 22 37 1 TCATCACCCA 0.951006 -29 CCCTTAAGGGTCATCATCTGAACATTACTAG 24 89 1 TCATCATCTA 0.667725 -104 TATTTAAAAACCCTCACCTTAAAAACAATAA 24 144 1 CCCTCACCTA 0.978697 -49 GCCATCACCTTGGTAAGAATAA 24 181 0 CCATCACCTG 0.992041 -12 CGGTTATGGTTCATCACCTTAACTATTGACT 25 31 0 TCATCACCTA 0.968264 -159 GGGTGATGGTTCATCACCTGAGCTTGACTTT 25 67 0 TCATCACCTA 0.968262 -123 AGGTGATGAACCATCACCCGGTCCTCTACGG 25 79 1 CCATCACCCG 0.987546 -111 CCATACATCACCCTCAGATTAGAACGTCCGT 25 106 0 CCCTCAGATA 0.524335 -84 AAGCCGTGGCCCCTCAACTAGGGGAGACATC 28 63 1 CCCTCAACTG 0.908338 -167 ATGATCACCTCAAATTTTATTT 31 41 0 TGATCACCTA 0.705032 -12 ********* * Masking position 4 Map Score: 24.4834 Number of sites scoring better than the average of aligned sites = 667 Number in coding regions = 629 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 CTACCATTTGCAATTTTTATATTAATCTGT 6 106 0 CAATTTTTAT 0.718909 -195 AACCATCAACCAATGTTTAAGTGAAAGCAT 6 158 1 CAATGTTTAA 0.814518 -143 AGTTTAAAGTGAATATTTAAGGTCTCTGAT 7 58 0 GAATATTTAA 0.731412 -36 ATGGTACTTACAATATTTATTTACCATCAG 8 162 1 CAATATTTAT 0.952671 -70 CCTATGGCAACAATATTTATCGCTGATGGT 8 184 0 CAATATTTAT 0.952671 -48 TCAACCGGTATAAGATTTAAAC 13 3 0 TAAGATTTAA 0.505826 -261 TACCCAATCTTTATAAAGATGTTT 17 70 0 CAATCTTTAT 0.791259 -14 AAGAAATCTCTAATATTTAA 18 23 1 TAATATTTAA 0.764145 -10 CTGTCCAAGACAATATTTATTAATGGTTAC 19 61 0 CAATATTTAT 0.952671 -72 TCCACCGGAGCAATATTTAAAAACCCTCAC 24 131 1 CAATATTTAA 0.958879 -62 GTTTGGCAGTCAATAGTTAAGGTGATGAAC 25 24 1 CAATAGTTAA 0.880483 -166 ATCTATCCTTCAAGATTTATAAAGGTTTTC 29 37 0 CAAGATTTAT 0.864116 -84 ACTTTACTGGCAATAGTTAACCCATAAAAA 31 13 1 CAATAGTTAA 0.880483 -40 ********** Masking position 3 Map Score: 11.3982 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 13 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 TCAAATCTCGGCGGTCCCATCAAATCGAATC 1 115 1 GCGGTCCCTC 0.600051 -57 ATTTGGATTAGGGGGCATCTAATGGACCAAA 6 63 0 GGGGGCATTA 0.749721 -238 ATATTAATCTGTGGTCATTCCTTAATTTGGA 6 87 0 GTGGTCATCC 0.673522 -214 TAAGAATTTAGGGGGCACACCGGATCATTTA 6 227 0 GGGGGCACCC 0.96513 -74 TTAGTTTTATGGAGCCATTCCCTTTTAAGAA 6 252 0 GGAGCCATCC 0.969481 -49 ACCGGAATCATGGGCCATCCCCTGGGCACAG 8 24 0 TGGGCCATCC 0.782005 -208 CACGGGACCCGGGGCCCCTCAAGGTATAATA 9 44 0 GGGGCCCCCA 0.979674 -152 GTGATGCCCGGGAGGCCTTCCGTGTTCCTGG 9 72 1 GGAGGCCTCC 0.944584 -124 TCGCTGCAGTCATCCATGGAAGACCC 10 6 1 GCAGTCATCA 0.803322 -59 ATCTGTTAAAGGGGTCTTCCATGGATGACTG 10 17 0 GGGGTCTTCA 0.832507 -48 TTTAACAGATGCAGCCATACACAAGTACTGA 10 38 1 GCAGCCATCA 0.911353 -27 AATAAATTCCGGGGCCCTTCATGAACACCAC 16 27 0 GGGGCCCTCA 0.98204 -98 CTGTCAGGCCGCAGGCCCTCAGGAGGGATCG 23 11 0 GCAGGCCCCA 0.834048 -125 TGGGGCCCCCCCAGACTCTGAC 28 2 1 GGGGCCCCCC 0.974226 -228 CCCTAGTTGAGGGGCCACGGCTTGCTGCCTG 28 55 0 GGGGCCACGC 0.944085 -175 ATACTCTTAAGGAGTCTTTGATGTCTCCCCT 28 82 0 GGAGTCTTGA 0.363835 -148 ACAGAGAGGAGCAGCCATAGAAA 33 14 1 GCAGCCATGA 0.729023 -13 ******** ** Masking position 4 Map Score: 14.5441 Number of sites scoring better than the average of aligned sites = 1258 Number in coding regions = 1209 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TAAAACACCTCATAATAAACTCTAG 2 37 0 CACCTCATAA 0.864562 -15 TCTATCACCTCAAATAAGTTTCAAT 3 13 0 CACCTCAAAT 0.969338 -15 AATTTTCCATCACCCTATAAATTCCTTTGA 5 37 0 CACCCTATAA 0.767194 -37 ATCCGGTGTGCCCCCTAAATTCTTAAAAGG 6 233 1 CCCCCTAAAT 0.849762 -68 AGGGCGCTGACACCCCAGATAGAGTTCCCT 9 135 0 CACCCCAGAT 0.922009 -61 ATTACACCCCCCAAGAAATCTCTA 18 5 1 CACCCCCCAA 0.748504 -28 TTTATATCATCACCCCAAAACCATAAACCA 22 41 1 CACCCCAAAA 0.973513 -25 TAAAAACCCTCACCTTAAAAACAATAACAT 24 148 1 CACCTTAAAA 0.881049 -45 TATGGTTCATCACCTTAACTATTGACTGCC 25 28 0 CACCTTAACT 0.850755 -162 CAAGCCGTGGCCCCTCAACTAGGGGAGACA 28 62 1 CCCCTCAACT 0.859651 -168 TTCTTCCACACACCCCCACTCAAGGAAAAC 29 13 1 CACCCCCACT 0.907437 -108 ATGATCACCTCAAATTTTATTTTTT 31 38 0 CACCTCAAAT 0.969338 -15 ********** Masking position 4 Map Score: 8.50768 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 191 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 TCATGATTCAAGGAGGAGTTTGAG 13 250 1 AGGAGGAGTT 0.94002 -14 TATTTTAAGTAGGAGTAATAAAATAATTTT 14 31 1 AGGAGTAATA 0.893612 -54 AGTAAACTGGAGGAGAATTATT 15 23 1 AGGAGAATTA 0.936755 -12 CTAACCTTGTAGGAGAAATAAGGGGAAGCA 17 33 0 AGGAGAAATA 0.955002 -51 ACAGGATCACAGGAGGATTATTT 19 4 0 AGGAGGATTA 0.958831 -129 CATCCAGTTCAGGAGAAATT 22 1 0 AGGAGAAATT 0.902275 -65 TTAATTTTACAGGAGGAGTATA 26 3 0 AGGAGGAGTA 0.972992 -107 ********** Masking position 4 Map Score: 5.76949 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 68 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 GGTGCTGACCATCCCCGTTCCAGTTGAAAA 1 65 0 ATCCCCGTTC 0.906635 -107 AAAATTTTCCATCACCCTATAAATTCCTTT 5 39 0 ATCACCCTAT 0.776411 -35 GGTCCATTAGATGCCCCCTAATCCAAATTA 6 66 1 ATGCCCCCTA 0.788937 -235 TCAAATCACCTCTAACAGTTTAAA 7 80 0 ATCACCTCTA 0.825736 -14 CTGGAAAACCAGCACCCCTCCAGCGGAATA 9 107 0 AGCACCCCTC 0.675231 -89 TCATATCACCGTTATTAAGTCATT 12 41 0 ATCACCGTTA 0.95485 -14 CCGATCACCGTTTATTTATTCAC 20 27 0 ATCACCGTTT 0.882615 -13 TATTTATATCATCACCCCAAAACCATAAAC 22 39 1 ATCACCCCAA 0.889159 -27 TGTTCAGATGATGACCCTTAAGGGATCTCC 24 83 0 ATGACCCTTA 0.847121 -110 GTTATGGTTCATCACCTTAACTATTGACTG 25 30 0 ATCACCTTAA 0.628035 -160 AAATCCATACATCACCCTCAGATTAGAACG 25 111 0 ATCACCCTCA 0.851393 -79 TACTGTTTCAGTCCCCGTTAATACTCTTAA 28 103 0 GTCCCCGTTA 0.702092 -127 GTAATCACCCTTCTGGTTTGACC 28 217 0 ATCACCCTTC 0.949128 -13 GGTTTATCCCCGCTATTTATATAGT 29 106 0 ATCCCCGCTA 0.934497 -15 ATCCCCCTTTATTTTTTTCC 32 1 1 ATCCCCCTTT 0.906935 -89 ********** Masking position 5 Map Score: 11.6994 Number of sites scoring better than the average of aligned sites = 350 Number in coding regions = 301 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 8 TTGGAATTCATCCCATGGATATGACTACCA 6 130 0 TCCCATGGAT 0.920158 -171 TCATGGGCCATCCCCTGGGCACAGCCTCTC 8 18 0 TCCCCTGGGC 0.895939 -214 GTCACACTCTCCCCTGGATTATAGGTAAC 8 213 0 TCCCCTGGAT 0.989672 -19 GGTATAATATTCCTCAGGAACTCAACACTC 9 23 0 TCCTCAGGAA 0.632895 -173 AGCGGAATATTCCCCAGGAACACGGAAGGC 9 86 0 TCCCCAGGAA 0.948198 -110 TGGGGAATATTCCGCTGGAGGGGTGCTGGT 9 100 1 TCCGCTGGAG 0.941835 -96 CCAGATAGAGTTCCCTGGAAAACCAGCACC 9 121 0 TTCCCTGGAA 0.855834 -75 CTGAAGGATTTCCCCTGGAGGGTCAGGGTT 9 163 1 TCCCCTGGAG 0.991302 -33 TAAAGGGGTCTTCCATGGATGACTGCAGCG 10 12 0 TTCCATGGAT 0.771131 -53 AGGTTGTGGTTTCCCTGAATCCAGTACCTC 13 99 1 TTCCCTGAAT 0.749846 -165 AAATATATTTTTCCCTGGAGATAAACACTA 14 65 0 TTCCCTGGAG 0.974714 -20 ********** Masking position 1 Map Score: 13.5665 Number of sites scoring better than the average of aligned sites = 402 Number in coding regions = 375 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 TGCCTCCAAGAAAAACATTAAAATAGAGGTT 1 150 0 AAAAACATAA 0.894533 -22 TTCCAGTAATATAAACATTTATTTATATGCT 6 183 0 ATAAACATTA 0.81978 -118 TTATATAGAAGTAAACCGTAAATTAAACTGG 13 178 1 GTAAACCTAA 0.878882 -86 TTCCCTGGAGATAAACACTAATCAAAAATTA 14 54 0 ATAAACATAA 0.907628 -31 CCTCAAGGGTAAAAAACATAACCATGTCCCG 16 65 0 AAAAAACTAA 0.711622 -60 CCCCAAAACCATAAACCATTACT 22 53 1 ATAAACCTTA 0.879516 -13 AGCAATATTTAAAAACCCTCACCTTAAAAAC 24 139 1 AAAAACCTCA 0.739488 -54 CCCTCACCTTAAAAACAATAACATTAGTTAT 24 154 1 AAAAACATAA 0.894533 -39 AGTTAAGGTGATGAACCATAACCGAGAATAA 25 38 1 ATGAACCTAA 0.696987 -152 CCCACTCAAGGAAAACCTTTATAAATCTTGA 29 27 1 GAAAACCTTA 0.743574 -94 TAGTTAACCCATAAAAAATAAAATTTGAGGT 31 26 1 ATAAAAATAA 0.640466 -27 AGTGGCAGAGGAAAAAAATAAAGGGGGAT 32 9 0 GAAAAAATAA 0.414392 -81 AGTTAAAATCACAAACCTTAATATGTGTTGA 36 37 1 ACAAACCTAA 0.807253 -69 ATATGTGTTGATAAACAATTAAAATTCAGTT 36 57 1 ATAAACATTA 0.81978 -49 ******* *** Masking position 5 Map Score: 4.93452 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 86 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 10 TTTAGGGGGCACACCGGATCATTTAATAATTT 6 220 0 ACCGGATCAT 0.931741 -81 CACAACCTCAAGGCCAGATCAGCATGCCCAAA 13 75 0 ACCAGATCAG 0.98673 -189 CTTGAATCATGAACCAGATCAGAATAAGACGG 13 230 0 GCCAGATCAG 0.980407 -34 CCGAGAATAAAGTCAAGCTCAGGTGATGAACC 25 59 1 ACAAGCTCAG 0.917207 -131 TTAAGCCTTCAATCAGGATCAGTCGCCTGATT 25 139 1 ACAGGATCAG 0.96036 -51 TTAATCATCGATCCAAGATCAGCATCACTGAT 26 29 1 ACAAGATCAG 0.972976 -81 CATTTCCGCTGATCCAGATCATACCCTCACGG 28 179 1 GCCAGATCAT 0.931741 -51 * ********* Masking position 11 Map Score: 3.2116 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 23 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 AAATCGAATCCAAGAACCTCTATTTTAATG 1 136 1 CAAGAACCTC 0.948009 -36 CCCTGGAAAACCAGCACCCCTCCAGCGGAA 9 109 0 CCAGCACCCC 0.924363 -87 TATCTCAAACCCTGACCCTCCAGGGGAAAT 9 170 0 CCTGACCCTC 0.969163 -26 TTCAGGGAAACCACAACCTCAAGGCCAGAT 13 88 0 CCACAACCTC 0.966298 -176 TTCCCTGAATCCAGTACCTCAGCGGCGTGT 13 109 1 CCAGTACCTC 0.953318 -155 ATCAGCACAGAATGTACCTCATTGAAGAGG 24 49 1 AATGTACCTC 0.526175 -144 TAAGGGATCTCCTGAACCTCTTCAATGAGG 24 65 0 CCTGAACCTC 0.977847 -128 TAAATCCATACATCACCCTCAGATTAGAAC 25 112 0 CATCACCCTC 0.797339 -78 ACAGAACCCCCAGTGATCAT 25 180 0 ACAGAACCCC 0.928483 -10 TATTCTTCCACACACCCCCACTCAAGGAA 29 10 1 ACACACCCCC 0.803966 -111 ********** Masking position 7 Map Score: 6.94639 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 745 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 ATATTGAAACTTATTTGAGGTGATAG 3 7 1 AAACTTATTT 0.917278 -21 AGTGTGTATTAAACTTATTATTTAAAAATT 6 34 1 AAACTTATTA 0.695708 -267 AGTAATATAAACATTTATTTATATGCTTTC 6 180 0 ACATTTATTT 0.738815 -121 GGTACTTACAATATTTATTTACCATCAGCG 8 164 1 ATATTTATTT 0.82576 -68 ACTTCTATATAAATTTATTTGAGTCCATGT 13 160 0 AAATTTATTT 0.902179 -104 ACACTAATCAAAAATTATTTTATTACTCCT 14 41 0 AAAATTATTT 0.681519 -44 AAATATATTTTTCCCTGGAG 14 75 0 AAATATATTT 0.416574 -10 AAGGGCCCCGGAATTTATTTTCTGCGCGGG 16 39 1 GAATTTATTT 0.681538 -86 GTCCAAGACAATATTTATTAATGGTTACCG 19 59 0 ATATTTATTA 0.496975 -74 CTGGATGTATATACTTATTTATATCATCAC 22 24 1 ATACTTATTT 0.799134 -42 AGAGGTAGAAAAACTTATATCAGTGATGCT 26 49 0 AAACTTATAT 0.543503 -61 GATCACCTCAAATTTTATTTTTTATGGGTT 31 31 0 AATTTTATTT 0.591062 -22 TAATGGCAAAAAATTTATTTTTCTTAATTC 32 43 1 AAATTTATTT 0.902179 -47 ********** Masking position 7 Map Score: 5.9757 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 11 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 TTTCTGTTGCTTAAGCCGTCATAGTAGCCAA 12 12 0 TTAAGCCTCA 0.932278 -43 CTTATACCGGTTGACCCATAAAGGTATCGAA 13 19 1 TTGACCCTAA 0.970478 -245 TGTTCAGATGATGACCCTTAAGGGATCTCCT 24 82 0 ATGACCCTAA 0.872239 -111 ATGTATGGATTTAAGCCTTCAATCAGGATCA 25 129 1 TTAAGCCTCA 0.921086 -61 CCCTTCTGGTTTGACCCTTAACCCGTGAGGG 28 202 0 TTGACCCTAA 0.970162 -28 TCTACAGACCTTAACCCATCCAGATG 30 6 0 TTAACCCTCC 0.910071 -21 CTGGCAATAGTTAACCCATAAAAAATAAAAT 31 19 1 TTAACCCTAA 0.964255 -34 ******* *** Masking position 4 Map Score: 2.82035 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 12 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 14 CTCATAATAAACTCTAGACTGAAAAATAGTG 2 23 0 ACTCTGACTG 0.973085 -29 AAAAAATCAGATTCTATACTGACCGGTGCAG 8 126 0 ATTCTTACTG 0.935911 -106 GTTAACCCTCTAATGGAGTATATTT 14 5 1 ACCCTTAATG 0.817963 -80 TTATCTATTAACTCTTTGCTGTCCAAGACAA 19 78 0 ACTCTTGCTG 0.973085 -55 AATGAGGTACATTCTGTGCTGATTGAAATGG 24 41 0 ATTCTTGCTG 0.892117 -152 CATCACCTTAACTATTGACTGCCAAACCTTA 25 20 0 ACTATGACTG 0.801481 -170 ACACTTTACTGGCAATAGTTA 31 1 1 ACACTTACTG 0.929849 -52 TTCCTCTGCCACTCTGTAATGGCAAAAAATT 32 27 1 ACTCTTAATG 0.935911 -63 ***** ***** Masking position 1 Map Score: 1.93641 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 46 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 GTCCATCCTCCCAGCCATTGAAGAAGTTTC 1 30 1 CCAGCCATTG 0.904117 -142 TTACCAGCCTCAGTCTCCTTATA 6 4 1 CCAGCCTCAG 0.965706 -297 TCCCCTGGGCACAGCCTCTCGCCCATA 8 8 0 ACAGCCTCTC 0.939808 -224 GAATCATGGGCCATCCCCTGGGCACAGCCT 8 21 0 CCATCCCCTG 0.904331 -211 ACCCTCCTTAACAGCCTCTGCAAGTTCCCT 23 116 0 ACAGCCTCTG 0.973685 -20 ACCACCCACTCCTTTTTTTAG 27 2 1 CCACCCACTC 0.875522 -36 TGGGGCCCCCCCAGACTCTGACAAACATGA 28 11 1 CCAGACTCTG 0.946218 -219 ********** Masking position 3 Map Score: 0.935287 Number of sites scoring better than the average of aligned sites = 303 Number in coding regions = 280 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987