AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00330_mpneu_reg_300.orf -o00330_mpneu_300.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: F11_orf358a 21 pdhA; pyruvate dehydrogenase E1 component, alpha subunit. Input sequences: #1 D12_orf390o 45 dnaJ; dnaJ protein. [SP:DNAJ_MYCPN] #2 D12_orf623 133 pmd1; transport ATP-binding protein. #3 MPNtRNA-Ala 44 tRNA-Ala. #4 D12_orf212 101 dnaE; [EC:2.7.7.-] [SP:PRIM_MYCPN] #5 D12_orf257 300 hypothetical protein. #6 H03_orf612 27 gidA; glucose inhibited division protein. [SP:GIDA_MYCPN] #7 H03_orf537 42 argS; arginyl-tRNA synthetase (arginine--tRNA ligase) (argRS). #8 G12_orf326 54 hypothetical protein. #9 G12_orf218 60 hypothetical protein. #10 G12_orf122 37 rplL; 50S ribosomal protein L7/L12. [SP:RL7_MYCPN] #11 G12_orf161 117 rplJ; 50S ribosomal protein L10. [SP:RL10_MYCPN] #12 G12_orf140b 300 hypothetical protein. #13 F11_orf483 281 proS; prolyl-tRNA synthetase (proline--tRNA ligase) (proRS). #14 F11_orf160 94 greA; transcription elongation factor greA (transcript cleavage #15 MPNtRNA-Gln02 43 mptrna; tRNA-Gln. #16 MPNtRNA-Gly01 222 tRNA-Gly. #17 F11_orf582 61 hypothetical protein. #18 F11_orf733 255 spoT; probable guanosine-3',5'-bis(diphosphate) 3'- #19 F11_orf887 166 hypothetical protein. #20 F11_orf133 67 apt; adenine phosphoribosyltransferase (APRT). [EC:2.4.2.7] #21 F11_orf327 300 pdhB; pyruvate dehydrogenase E1 component, beta subunit. #22 H10_orf273o 247 argI; ornithine carbamoyltransferase, catabolic (OTCase). #23 H10_orf238 110 arcA; arginine deiminase. [EC:3.5.3.6] [SP:ARCA_MYCPN] #24 MPNtRNA-Ser04 40 mptgc; tRNA-Ser. #25 MPNtRNA-Met02 38 mptgc; tRNA-Met. #26 MPNtRNA-Pro 51 mptgc; tRNA-Pro. #27 MPNtRNA-Cys 122 mptgc; tRNA-Cys. #28 H10_orf149 206 hypothetical protein. #29 H10_orf220L 48 hypothetical protein. #30 H10_orf206 38 hypothetical protein. #31 H10_orf145L 138 hypothetical protein. #32 H10_orf187V 89 hsdS1B; #33 A65_orf787o 300 hypothetical protein. Motif number 1 CTCTTAAGTTGTTGTTTTTTGTCAAGCTAAACAAAAAACGC 3 9 1 TTTTTATAAA 0.956201 -36 TTAAAGGCATTTAAGAGATGTAAATACATCGCTT 5 2 1 TTTTAATAAA 0.733633 -299 CAATAAAATTGCTAAAAATTTTTGCAATTTAAAGTAAAGAGAC 5 113 0 GTTTTATAAA 0.966604 -188 ATTGAGTAAAGACATAATTTTTCCTTCACTAAATAAATTGACC 5 173 0 GTTTTCTAAA 0.87845 -128 TGGCAACAAAGTTGCACGTTTTAGTTTTCTAAACCTTGAGCAG 5 251 1 GTTTTTTAAA 0.897091 -50 AATGGCAATATAAACCGATTTATCACAGATAAAACAGGTTTTA 8 18 0 TTTTAATAAA 0.733638 -37 ATGATAATCCTCGATAACTTTTTTAAAGTTAAAAACTCGTTAT 11 56 0 TTTTTATAAA 0.956201 -62 GTCCTCATTTTTTCTCTAATAACTGTCAATGAG 12 1 1 GTTTTTTAAC 0.629792 -300 ATTTGACTACGTTTCTTTTTTTGAACAGGTAAATAATTCAAAA 12 204 0 GTTTTATAAA 0.966066 -97 ACTGTTTTAGTTCTGCAATTTTAAACTATTAAAAAAG 16 5 0 TTTTTTTAAA 0.86725 -218 TGGGCCTGTTTGGAATTATTTTTGGTAGTTATAAGCTTCTAAA 18 150 0 TTTTTATATA 0.596949 -106 GAAACGCTTTTAACAGTTTTTAAGATAATAAACAGTGAAACA 19 135 0 TTTTTTTAAA 0.86784 -32 TAGAATAATTGCACCTAGTTTTTTTAACTAAAAGTTGAGAAGG 21 219 0 GTTTTAAAAA 0.662565 -82 TTAAGTTAATTGGCATAAATTTGTATAAGTAAATAAAGAAAAA 22 11 0 TATTTATAAA 0.733639 -237 CGGGTACGGGTAGAATCTTTTTGGAACAGTAAAACAATGTTCT 22 181 0 TTTTTCTAAA 0.844993 -67 AGCGAAACCCGTTTAAACTTTTTTAAAGCTAACTCTAAATCAT 28 35 0 GTTTTATAAC 0.849581 -172 CTTGATGAGCTTAATTTTAAAAATGTAAAATAACGGCC 30 7 1 GTTTTATAAA 0.966601 -32 ATTGAAATTTGACGTCACATTTAAAAAACTAAATCAATTTATT 33 73 0 GATTTATAAA 0.785014 -228 TTGATTTTAATCTCCAGTTTTTTCTCATTTAAAAAGGATCAAA 33 160 1 TTTTTATAAA 0.956201 -141 TCTTCTTTAATCACTGAATTTTTAGGAATTAAACTTGTTTAAT 33 231 1 TTTTTATAAA 0.956201 -70 * **** * **** Masking position 11 Map Score: 18.4874 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 67 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 2 CAACTGAGCTATACTTCCAGGCAAAATCTTCGTAC 2 33 1 AATCCACAAA 0.752974 -101 ATAACAATCAAAGCAAAAATACCAGCAG 4 4 1 AATAAAAAAA 0.911819 -98 TAAAGTAAAGAGACTTCAAACAAAACAACATCAAG 5 92 0 AATCAAAAAA 0.959213 -209 AGAATTTCAAAAACTGCCAATAAAATTGCTAAAAA 5 138 0 AATCCAAAAA 0.845887 -163 GTTGGTTTAAGAATTACAATTTAAACGATATTAAA 7 12 0 GATCAATAAA 0.690865 -31 TTAACCTGCAATAAACCAAAGAAAATAACGAGTTT 11 32 1 AAACAAAAAA 0.844716 -86 GAACAGGTAAATAATTCAAAAAACACAGGCGTTAA 12 190 0 AATCAAAACA 0.736815 -111 AAAAAGAAACGTAGTCAAATAAAAAAGTTTGGCGC 12 227 1 GATAAAAAAA 0.902282 -74 CTGTTAGGTCAAATTGCAAATAAAATTTTGCATTT 13 73 0 AATCAAAAAA 0.959213 -209 GACAATTCTGGCATTAAAAGTAAAAGACGGATTCG 13 153 1 GATAAAAAAA 0.902282 -129 ATTTTAGATTTAAAGCAAAAGTAATGCAAA 21 6 1 AATAAAAAAA 0.911819 -295 TAAAGCAAAAGTAATGCAAATAAAAAACCAGTCTT 21 21 1 GATCAAAAAA 0.954547 -280 ATTTGTATAAGTAAATAAAGAAAAA 22 1 0 GAAAAAAAAA 0.6811 -247 CAAAAGCCCAAGAAAAAAAGGCAAAGTGAACTTGA 23 36 0 AAAAAACAAA 0.570495 -75 ATGTGACGTCAAATTTCAATAAAAATCAAAATTTC 33 96 1 AATCAAAAAA 0.959213 -205 ATAAAAATCAAAATTTCAAACCAAAAACTATAACA 33 114 1 AATCAACAAA 0.928879 -187 GCACTAAAACCCAAAATTTGGAGAA 33 286 0 GATAAACAAA 0.83681 -15 * * * *** **** Masking position 9 Map Score: 13.0507 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 60 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 3 AGACCGCTTAAAAACTAGCTTTGGCTAAATTA 2 89 0 AAAACTGCTT 0.679422 -45 AGTGAAGGAAAAATTATGTCTTTACTCAATAT 5 186 1 AAATTAGTTT 0.832004 -115 ACGAAGTTAAAACCTGTTTTATCTGTGATA 8 9 1 AAAACCGTTT 0.504602 -46 AAGTTAAATTAAATCTACTTTTTTTTCCCAAT 13 30 1 AAATCTCTTT 0.796573 -252 ATTGCAAATAAAATTTTGCATTTTTTTGGCAA 13 64 0 AAATTTGCTT 0.913657 -218 TTTTTGTAAAATATCTTTTGCTGGTTATT 14 76 0 AAAATACTTT 0.523888 -19 GTGTTCAATTAAATTTCCCGTTGTCGTTGAGG 16 74 0 AAATTTCCTT 0.832386 -149 GTAATCGCCAAAAATTTCTCTTTTTTTGGTAC 16 178 0 AAAATTCTTT 0.725001 -45 ATGCAAATAAAAAACCAGTCTTACGACTGGCT 21 34 1 AAAACCGTTT 0.731806 -267 AAATTTCTCTAAATTTCGTTTTAGATAAAAAG 21 64 0 AAATTTGTTT 0.921984 -237 AAATTTAGAGAAATTTCGCCTTATTTTTGGCA 21 80 1 AAATTTGCTT 0.913659 -221 ACTACTGCTCAAATTAACTATTTAATTGACCT 22 86 1 AAATTACTTT 0.699232 -162 TCGCAGGTTCAAATCCTGTCTTCCCGACCATA 26 24 1 AAATCCGTTT 0.877846 -28 GTTTCGCTAGAAATTCGCCGTTTAGCACAGCG 28 70 1 AAATTCCCTT 0.803102 -137 TGGGAACAGAAAATCAGGCTTTCAACACAGAA 33 18 1 AAATCAGCTT 0.755788 -283 AGGAAAACGAAAATTCTGTGTTGAAAGCCTGA 33 31 0 AAATTCGTTT 0.906786 -270 TTTTGGTTTGAAATTTTGATTTTTATTGAAAT 33 108 0 AAATTTGATT 0.574952 -193 AAAAAGGATCAAAATTTGTTTTTAATAGTTTC 33 190 1 AAAATTGTTT 0.82826 -111 AGATTTCTCCAAATTTTGGGTTTTAGTGC 33 282 1 AAATTTGGTT 0.670437 -19 ****** ** ** Masking position 11 Map Score: 11.8565 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 91 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 ATCAAAGCAGTTTTATAATTAACACTCGAAT 1 11 1 TTTTAAATTA 0.813829 -35 TTTTAAGCGGTCTTATAATTAAAGCAAGTAG 2 108 1 TCTTAAATTA 0.597761 -26 AGGGCGTTGGTTTAAGAATTACAATTTAAAC 7 21 0 TTTAAAATTA 0.568335 -22 TTTTATATTTACTTATTAATT 10 27 0 TTTTAATTTA 0.895047 -11 AATAACGAGTTTTTAACTTTAAAAAAGTTAT 11 55 1 TTTTACTTTA 0.938978 -63 ATGATTAAGGTCTTATCATTACTTACACCAA 12 127 0 TCTTACATTA 0.728366 -174 AGTAGATTTAATTTAACTTTAAACACAATTT 13 18 0 ATTTACTTTA 0.685471 -264 CGAATCCGTCTTTTACTTTTAATGCCAGAAT 13 157 0 TTTTATTTTA 0.573446 -125 CGGATTCGTTTTTTAGCTTTAGGAATTATTA 13 180 1 TTTTACTTTA 0.938978 -102 TTCTTCTCTATTTTAGATTTAGTAATCCCTA 16 123 1 TTTTAATTTA 0.895047 -100 ATTATCCTGGTCTTAGCTTTTTTGGGCCTGT 18 184 0 TCTTACTTTT 0.425581 -72 ATTTTAGATTTAAAGCAAAAGT 21 2 1 TTTTAATTTA 0.895047 -299 TTGACTCTGCTTTAAACTTTACTACTGCTCA 22 66 1 TTTAACTTTA 0.822524 -182 AAATCATCGTTTTTAACTTCAATCTTTGGCA 28 11 0 TTTTACTTCA 0.633156 -196 GCGAAACCCGTTTAAACTTTTTTAAAGCTAA 28 46 0 TTTAACTTTT 0.39628 -161 AACCAACAATTTAAAATTACCTAACGCGC 29 9 1 ATTTAAATTA 0.382382 -40 TATTTTACATTTTTAAAATTAAGCTCATCAA 30 12 0 TTTTAAATTA 0.813829 -27 ATTAAACTTGTTTAATCTTTATTAAGATTTC 33 258 1 TTTAACTTTA 0.822524 -43 ***** ***** Masking position 3 Map Score: 11.2002 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 77 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 5 CCTACAGCTGTCGAAACAGCAGCCACAATATATGAAG 12 52 0 TGCGCAGCCA 0.875438 -249 TATTTGCAATTTGACCTAACAGCACTAGTTAAAGCTA 13 86 1 TGTACAGCTA 0.956105 -196 ACAAATAAAATGGTGATTACAGCAATTACAAGAATCA 13 214 0 TGTACAGCTT 0.97365 -68 TTCAGTATTGTTACCGCTGCCATTGCCGTCCTTT 18 8 1 TGCGCTGCTT 0.948219 -248 AATTTCGCCTTATTTTTGGCAGCATTTGCAACCGCCA 21 91 1 TTTGCAGCTT 0.884253 -210 ACCGCCACAGTTGCATTTACTGCAGTTAGCTGTTTCG 21 121 1 TGTACTGCTT 0.956115 -180 TGTTTCGGTTTTGCAACCACAGCATTTCTTGTCTTCC 21 151 1 TGCACAGCTT 0.958581 -150 ATGTGCAACTTGGTATTTACTGCGTTTTAAATCAATG 22 121 0 TGTACTGCTT 0.956115 -127 CGTTGTGCCTTTGAAGTGGCTGCCTTTGACTTGGGT 22 222 1 TGTGCTGCTT 0.966928 -26 ACTGACGATATGGAGGTTGCAGCTCCAGGCCTTGAAT 27 68 0 TGTGCAGCCA 0.918067 -55 AATATCCAATTCTTTCTAACAGCAGTAAAGCTGAGGA 31 108 1 TTTACAGCTA 0.770455 -31 * * * ***** ** Masking position 1 Map Score: 6.42585 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 57 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 CCAAAGCTAGTTTTTAAGCGGTCTTATAAT 2 97 1 TTTTTAAGCG 0.678506 -37 TTGGTATTTTTATTTTGGCGCTTACTAGTT 4 60 1 TATTTTGGCG 0.922067 -42 AATTGCAAAAATTTTTAGCAATTTTATTGG 5 127 1 ATTTTTAGCA 0.839879 -174 TTAGGTTTTTTCGCGATTCACAGTA 9 6 1 TTTTTTCGCG 0.804394 -55 TCAAATAAAAAAGTTTGGCGCTTTAAATTC 12 241 1 AAGTTTGGCG 0.831158 -60 AATTTTGCATTTTTTTGGCAAATATTGGGA 13 55 0 TTTTTTGGCA 0.90928 -227 AACGAAAGACAATTCTGGCATTAAAAGTAA 13 146 1 AATTCTGGCA 0.615635 -136 AAAAAGAGAAATTTTTGGCGATTACGTTAT 16 185 1 ATTTTTGGCG 0.973872 -38 TAACTAAACTTAGTTTGGCGTGAAAATATT 20 34 0 TAGTTTGGCG 0.788938 -34 ATTTCGCCTTATTTTTGGCAGCATTTGCAA 21 92 1 ATTTTTGGCA 0.929576 -209 ACTCTAATTAATTTTTAGCGC 27 2 0 ATTTTTAGCG 0.936755 -121 TTTAACTTCAATCTTTGGCA 28 1 0 ATCTTTGGCA 0.693815 -206 TAAACGGCGAATTTCTAGCGAAACCCGTTT 28 64 0 ATTTCTAGCG 0.811294 -143 AGCGATTTTTTAAGCGCAAGCGCGTT 29 33 0 TTTTTAAGCG 0.678506 -16 ********** Masking position 4 Map Score: 7.65135 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 118 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 7 CAGCTGTCGAAACAGCAGCCACAATATATGA 12 54 0 AACGCAGCCA 0.962819 -247 TCAAAAAAAGAAACGTAGTCAAATAAAAAAG 12 223 1 AAAGTAGTCA 0.668191 -78 TGATTCTTGTAATTGCTGTAATCACCATTTT 13 214 1 AATGCTGTAA 0.641618 -68 TCAGTATTGTTACCGCTGCCATTGCCGTCCT 18 12 1 TACGCTGCCA 0.744202 -244 TGGCGGTTGCAAATGCTGCCAAAAATAAGGC 21 97 0 AAAGCTGCCA 0.915418 -204 CGAAACAGCTAACTGCAGTAAATGCAACTGT 21 127 0 AACGCAGTAA 0.953775 -174 CATTGATTTAAAACGCAGTAAATACCAAGTT 22 121 1 AAAGCAGTAA 0.950112 -127 ACCCAAGTCAAAGGCAGCCACTTCAAAGGC 22 228 0 AAAGCAGCCA 0.959842 -20 GTGTAACAATTAAAGCAGTAAGCTTAGCCTT 23 78 1 TAAGCAGTAA 0.82534 -33 TGCGCAGAAGAAACGCCGTAAGTTTCGTAAT 28 153 1 AAAGCCGTAA 0.83494 -54 AATTCTTTCTAACAGCAGTAAAGCTGAGGAA 31 115 1 AACGCAGTAA 0.953775 -24 *** ******* Masking position 2 Map Score: 5.43757 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 44 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TTTGGCTAAATTAATATAATTATGAAGCGAA 2 71 0 TAATATAATT 0.657747 -63 AATACTCTTAAAAATTTATTTGGGTGACTTG 5 54 1 AAATTTATTT 0.589992 -247 GAAATTCTGGTCAATTTATTTAGTGAAGGAA 5 165 1 TAATTTATTT 0.875705 -136 ATGTCTTTACTCAATATATTTATTAGATCAA 5 201 1 TAATATATTT 0.858789 -100 TTTGCAAGGTTAAATATAATTTAAGTA 6 7 0 TAATATAATT 0.657747 -21 ATTTAATATCGTTTAAATTGTAA 7 3 1 TAATATCGTT 0.806813 -40 TTTAATTTAGTTATGTTATTAT 11 2 1 TAATTTAGTT 0.868228 -116 TTTTTGTAAAATATCTTTTGCTGGTTAT 14 77 0 AAATATCTTT 0.477011 -18 AGGCTTAAGGTTAATATATTTAACCAAACGG 17 26 1 TAATATATTT 0.858789 -36 CACGCCAAACTAAGTTTAGTTAAGTGCGGTA 20 42 1 TAGTTTAGTT 0.509616 -26 GAAATTTCTCTAAATTTCGTTTTAGATAAAA 21 66 0 TAATTTCGTT 0.828714 -235 CAGTAACAATTTAATTTCTTTCATTAAACAT 32 67 0 TAATTTCTTT 0.838015 -23 AAAAACTAAATCAATTTATTTATTGGGAGCA 33 62 0 TAATTTATTT 0.875705 -239 * ********* Masking position 3 Map Score: 5.1479 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 44 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 GTTGCCAGCAAGGATCAACATCATCGTTGAT 5 227 0 AGGATCACAT 0.842174 -74 CAGATAAAACAGGTTTTAACTTCGT 8 5 0 AGGTTTAACT 0.781519 -50 AGCAATTACAAGAATCAAAATAATAATTCCT 13 200 0 AGAATCAAAT 0.887167 -82 CCCGAGGATCGAACTCGGGACCCTT 15 5 1 AGGATCAACT 0.980927 -39 TTTTCTGGGTAGGATCTAACTCCTTGTTAGC 18 43 1 AGGATCAACT 0.980927 -213 GGCTGGAGTGAGATTCGAACT 25 1 0 AGATTCAACT 0.926092 -38 GGTGCCTGTCAGATTCGAACTGACGATATGG 27 92 0 AGATTCAACT 0.926092 -31 TCATTTAAAAAGGATCAAAATTTGTTTTTAA 33 184 1 AGGATCAAAT 0.952634 -117 ****** **** Masking position 8 Map Score: 3.98257 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 = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 10 GTGTTCAACGGTTCCACTACCACCACTGTTT 18 100 0 GTTCACTACC 0.869166 -156 GAAACCCGCTTTTTCAGTCCCACTGG 18 240 1 TTTCAGTCCC 0.841634 -16 TAAATACCAAGTTGCACATCCAGAACCGTCC 22 139 1 GTTCACATCC 0.793808 -109 AGAACATTGTTTTACTGTTCCAAAAAGATTC 22 181 1 TTTCTGTTCC 0.886628 -67 TGCTTTAATTGTTACACGTCCACACAAAAGC 23 64 0 GTTCACGTCC 0.850879 -47 CCTCGCGTGCTTTTCAGCACC 24 1 0 TTTCAGCACC 0.934928 -40 CGATATGGAGGTTGCAGCTCCAGGCCTTGAA 27 69 0 GTTCAGCTCC 0.967291 -54 ATCAGCAGGTTTTTCACCACCTACTAAAACT 31 49 0 TTTCACCACC 0.906782 -90 GAAAGCCTGATTTTCTGTTCCCATCAATTT 33 10 0 TTTCTGTTCC 0.88663 -291 GAATTTTCGTTTTCCTGCTCCCAATAAATAA 33 47 1 TTTCTGCTCC 0.925399 -254 *** ******* Masking position 3 Map Score: 3.5699 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 26 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 11 TCGACAGCTGTAGGTATTATTCTCTACTTT 12 75 1 TAGGTATTAT 0.804256 -226 GCCTGTGTTTTTTGAATTATTTACCTGTTC 12 195 1 TTTGAATTAT 0.769724 -106 TTTTTAGCTTTAGGAATTATTATTTTGATT 13 189 1 TAGGAATTAT 0.951902 -93 GTTAGCGTCCTTGGACTTATGGTTTAAAAA 18 68 1 TTGGACTTAT 0.88801 -188 TTGGGCCTGTTTGGAATTATTTTTGGTAGT 18 164 0 TTGGAATTAT 0.962645 -92 CTCTTAAAGATTGGAATTATCCTGGTCTTA 18 200 0 TTGGAATTAT 0.962645 -56 ACTGAATTTTTAGGAATTAAACTTGTTTAA 33 243 1 TAGGAATTAA 0.804256 -58 ********** Masking position 9 Map Score: 2.81666 Number of sites scoring better than the average of aligned sites = 8 Number in coding regions = 4 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 12 AAAAGTAAAAGACGGATTCGTTTTTTAGCT 13 168 1 GACGGATTCG 0.972486 -114 GAGACTGAGGGATTCGAACCCTCGCG 24 25 0 GAGGGATTCG 0.980946 -16 GGTGGCTGGAGTGAGATTCGAACT 25 5 0 GTGAGATTCG 0.970363 -34 GGAGGTGCCTGTCAGATTCGAACTGACGAT 27 96 0 GTCAGATTCG 0.957406 -27 CTTTTCGAAGGTGGTATTCGTGACGCTGTG 28 95 0 GTGGTATTCG 0.933934 -112 ********** Masking position 6 Map Score: 1.21347 Number of sites scoring better than the average of aligned sites = 10 Number in coding regions = 1 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 13 TTGTCAAGCTAAACAAAAAACGCCTA 3 29 1 AAAAACGCCT 0.87879 -16 AGTCAAATAAAAAAGTTTGGCGCTTTAAATTCTCC 12 239 1 AAATTCGCTT 0.748109 -62 TCTGTCATCCAACAAGCAGTAGCTTTAACTAGTGC 13 107 0 AACCAAGCTT 0.825705 -175 ATAAGCTTCTAAACGACAGTCGCTTAGGGGTAGTG 18 128 0 AAACACGCTT 0.967081 -128 AGAGCCAGTCAAAGGAAACCCGCTTTTTCAGTCCC 18 226 1 AAAAACGCTT 0.968768 -30 AGTGAAACAGAAACTCCAAGCGCTTGATCGAGCTA 19 109 0 AAACACGCTT 0.979584 -58 ACCACCTTCGAAAAGGAATGCGCTTGCGTGAAAAG 28 110 1 AAAAACGCTT 0.968609 -97 AAAATTACCTAACGCGCTTGCGCTTAAAAAATCGC 29 23 1 AACCTCGCTT 0.883746 -26 ACTGGAGATTAAAATCAATGAGCTTGGTGTGTTAT 33 143 0 AAAAAAGCTT 0.859333 -158 *** ** ***** Masking position 2 Map Score: 2.13646 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 40 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 TTAACACTCGAATGATTAAAGTGATAA 1 29 1 AATGATTAAG 0.965777 -17 TAATAAATATATTGAGTAAAGACATAATTTT 5 195 0 ATTGAGTAAG 0.741189 -106 CAAAAAAGACAATGATTAAGGTCTTATCATT 12 138 0 AATGATTAAG 0.965778 -163 TATCTAAATGAATGTGTAAGGAGAATTTAAA 12 262 0 AATGTGTAAG 0.893422 -39 TTTGGAAAGAAATGAATAACGTAATCGCCAA 16 199 0 AATGAATAAG 0.854199 -24 GAGCAGTAGTAAAGTTTAAAGCAGAGTCAAG 22 65 0 AAAGTTTAAG 0.70003 -183 CAGCCACCAAAATCATTAAGGA 25 27 1 AATCATTAAG 0.803939 -12 AAACCTTAAAAATGTTTAATGAAAGAAATTA 32 56 1 AATGTTTAAG 0.936723 -34 CTAAAAATTCAGTGATTAAAGAAGACATAAA 33 225 0 AGTGATTAAG 0.882292 -76 ********* * Masking position 7 Map Score: 2.71574 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 16 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 AAAAACTACTTGCTTTAATTATAAGACCG 2 115 0 TTGCTTTAAT 0.770129 -19 TGAAGTCTCTTTACTTTAAATTGCAAAAAT 5 109 1 TTACTTTAAA 0.780854 -192 AACGAGTTTTTAACTTTAAAAAAGTTATCG 11 58 1 TAACTTTAAA 0.909273 -60 TTTTTTGTACTAGCTTCAATCATCATTATT 12 162 1 TAGCTTCAAT 0.802052 -139 AGATTTAATTTAACTTTAAACACAATTTCT 13 16 0 TAACTTTAAA 0.909273 -266 CAACAAGCAGTAGCTTTAACTAGTGCTGTT 13 103 0 TAGCTTTAAC 0.809342 -179 AAGAACACTATATCTTTAATAGGTGTTCAA 16 98 0 TATCTTTAAT 0.719936 -125 CACTGTTTATTATCTTAAAAACTGTTAAAA 19 140 1 TATCTTAAAA 0.547912 -27 TGCATTACTTTTGCTTTAAATCTAAAAT 21 9 0 TTGCTTTAAA 0.850349 -292 TTATGCCAATTAACTTAAAAGGTCGTAGCC 22 36 1 TAACTTAAAA 0.735864 -212 TCATCGTTTTTAACTTCAATCTTTGGCA 28 9 0 TAACTTCAAT 0.717578 -198 GATTTAGAGTTAGCTTTAAAAAAGTTTAAA 28 37 1 TAGCTTTAAA 0.941115 -170 ********** Masking position 8 Map Score: 5.21152 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 148 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911