AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_mpneu_reg_300.orf -o00230_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: B01_orf299V 32 trsB; TrsB protein. F11_orf358a 21 pdhA; pyruvate dehydrogenase E1 component, alpha subunit. Input sequences: #1 D09_orf127a 167 hypothetical protein. #2 D09_orf238 55 deoD; purine nucleoside phosphorylase (inosine phosphorylase) (PNP). #3 D09_orf450 287 ffh; signal recognition particle protein (fifty-four homolog). #4 D09_orf560L 300 potA; spermidine/putrescine transport ATP-binding protein potA #5 B01_orf1443 123 polC1, dnaE1; putative DNA polymerase III, alpha chain 1. #6 B01_orf108 223 hypothetical protein. #7 D12_orf390o 45 dnaJ; dnaJ protein. [SP:DNAJ_MYCPN] #8 D12_orf623 133 pmd1; transport ATP-binding protein. #9 MPNtRNA-Ala 44 tRNA-Ala. #10 D12_orf212 101 dnaE; [EC:2.7.7.-] [SP:PRIM_MYCPN] #11 D12_orf257 300 hypothetical protein. #12 K05_orf650 101 gyrB; DNA gyrase subunit B. [EC:5.99.1.3] [SP:GYRB_MYCPN] #13 K05_orf380 300 dnaN; DNA polymerase III, beta chain. [EC:2.7.7.7] [SP:DP3B_MYCPN] #14 K05_orf175 180 hpt; hypoxanthine-guanine phosphoribosyltransferase (HGPRT) #15 K05_orf709 300 ftsH; cell division protein ftsH homolog. [EC:3.4.24.-] #16 C12_orf681 30 dnaX; DNA polymerase III subunits gamma and tau. [EC:2.7.7.7] #17 C12_orf132 300 rpsI; 30S ribosomal protein S9. [SP:RS9_MYCPN] #18 F04_orf1290 161 rpoC; DNA-directed RNA polymerase beta' chain (transcriptase beta' #19 F04_orf120 300 hypothetical protein. #20 F11_orf733 255 spoT; probable guanosine-3',5'-bis(diphosphate) 3'- #21 F11_orf887 166 hypothetical protein. #22 F11_orf133 67 apt; adenine phosphoribosyltransferase (APRT). [EC:2.4.2.7] #23 F11_orf327 300 pdhB; pyruvate dehydrogenase E1 component, beta subunit. #24 A19_orf872 300 polC2, dnaE2; putative DNA polymerase III, alpha chain 2. #25 F10_orf721 23 nrdE; ribonucleoside-diphosphate reductase alpha chain #26 F10_orf328 300 thyA; thymidylate synthase. [EC:2.1.1.45] [SP:TYSY_MYCPN] #27 H10_orf149 206 hypothetical protein. #28 H10_orf220L 48 hypothetical protein. #29 H10_orf206 38 hypothetical protein. #30 H10_orf145L 138 hypothetical protein. #31 H10_orf187V 89 hsdS1B; #32 A65_orf787o 300 hypothetical protein. #33 K04_orf726 273 vacB; vacB protein homolog. [SP:VACB_MYCPN] #34 G07_orf479 197 hypothetical protein. #35 G07_orf240 24 ung; uracil-DNA glycosylase. [EC:3.2.2.-] [SP:UNG_MYCPN] #36 G07_orf417 300 hypothetical protein. #37 VXpSPT7_orf108 93 rpsJ; 30S ribosomal protein S10. [SP:RS10_MYCPN] #38 VXpSPT7_orf112 246 hypothetical protein. #39 VXpSPT7_orf320 121 hypothetical protein. #40 VXpSPT7_orf445 153 hypothetical protein. #41 VXpSPT7_orf424 25 hlyC; #42 VXpSPT7_orf617 280 infB; initiation factor IF-2. [SP:IF2_MYCPN] Motif number 1 CTATACGTAGAAATAATAAAAAAATAAATAATTAAAG 2 15 0 AAAAAAAAAA 0.709591 -41 CTAAAGCACCATTTTTTAAAAAGAAAACACCACCAGT 3 17 1 ATAAAAAGAA 0.933506 -271 CAAGAAAACCAAAATTAAAAAAGTAAAGGAAGCAGGG 3 96 1 ATAAAAAGAA 0.933506 -192 AAGGACACTAAAACAGCAAACAGGTAAGGGTGTTTTT 3 170 0 AAAAACAGAA 0.883766 -118 CAAATTCCTTAAGCTGCAAAAAGATAAAAAAGCAAGG 3 256 1 ATAAAAAGAA 0.933506 -32 GGAATCTTTTAACAAGAAAAAAGAGAAGTTGTAGGCT 4 32 0 AAAAAAAGAA 0.920359 -269 TTCAAAATTTAGTCCAAAAACAGTCAAATTTTTAGCA 4 127 1 ACAAACAGAA 0.916058 -174 ATTGACCAGAATTTCAAAAACTGCCAATAAAATTGCT 11 143 0 ACAAACTGAA 0.789186 -158 AATCAAATAAACAAAACAAAAAGCAAAAAAACTATAA 13 267 1 AAAAAAAGAA 0.920359 -34 CTAGGAGCTGATCGACAAAACTAGCAAAC 15 282 1 AAAAACTAAA 0.355446 -19 TGATCTAGCAAAATTAGAATAAGTTAACTTTGAAGTT 18 34 0 ATAATAAGAA 0.647389 -128 CTTAGTTTTCACTGTTCAAACAATTAAAAAAGCACCA 18 95 1 ATAAACAAAA 0.661357 -67 CCTTGGACTTATGGTTTAAAAAATAAACAGTGGTGGT 20 76 1 ATAAAAAAAA 0.748005 -180 AATTCCAAACAGGCCCAAAAAAGCTAAGACCAGGATA 20 176 1 ACAAAAAGAA 0.943139 -80 ACAGTTTTTAAGATAATAAACAGTGAAACAGAAACTC 21 128 0 AAAAACAGAA 0.883766 -39 CTGTGGTTGCAAAACCGAAACAGCTAACTGCAGTAAA 23 136 0 ACAAACAGAA 0.916058 -165 ATACATGTCAAAGGATAAAAAAAATAAGGTTGAACAG 24 79 1 AAAAAAAAAA 0.709591 -222 TGCCATAAGACAAAAAATACAAAAAGCATTCAG 26 7 1 ACAAAATAAA 0.546079 -294 TGATGAGCTTAATTTTAAAAATGTAAAATAACGGCC 29 13 1 ATAAAATGAA 0.828054 -26 AAGAAGACATAAAATCGAAACTATTAAAAACAAATTT 32 201 0 ATAAACTAAA 0.401172 -100 TGAAAAACTAACCCTAAAATAAGAAAAAGCACTACTA 33 224 0 ATAATAAGAA 0.647389 -50 GTTAGATTTTAAAGCGCAAAATGAAAAACTAACCCTA 33 245 0 ACAAAATGAA 0.850519 -29 CATAAGAAAAATAATGAAAAATGCTAAAGCTTTGTTT 34 43 0 ATAAAATGAA 0.828054 -155 GGAAAAAGCCACTGCCCAAAAAGTCAAATAAGCGTGC 36 113 0 ACAAAAAGAA 0.943139 -188 GCGGCAAACTAGTTTGGAAAAAGATAAGGAATTAGTC 38 196 1 ATAAAAAGAA 0.933506 -51 TATTTTTAAAAATTCAAAATAAGCAAATATAATTAAA 39 76 1 ACAATAAGAA 0.684463 -46 GAAATTGCTGATTAAACAAAAAGCTAAATTATTTACC 40 13 0 AAAAAAAGAA 0.920359 -141 AATTTCCTTTATATATAAAAAAGGTAATACAACGATA 40 44 1 AAAAAAAGAA 0.920359 -110 * * ****** ** Masking position 9 Map Score: 29.5956 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 113 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 2 CAGCAAACAGGTAAGGGTGTTTTTTTACCTTTGCTTTAAT 3 154 0 GTTTTTTACT 0.729178 -134 TGATTGCAATTTTGTGAGATTTTTTGAACAGTTTTTGCAG 4 173 0 TTTTTTTACA 0.963077 -128 CGATCAAAGCGTGGTGCACTTTTTTGATCACGGTTAAAGA 5 64 1 GTTTTTTACA 0.923448 -60 TGACACTAGTTTAAACGAGTTAATTAACCACCGCTTGTTC 6 21 0 TTTTATTACA 0.877641 -203 AAACAACTAATTTTCTTCATTGTTTAACCATCTTGGTATT 13 51 0 TTTTTTTACA 0.963077 -250 TTATACTTAATTATAGTTATTTTATTAACAAAATTAGTGA 13 203 1 TTTTTATACA 0.802038 -98 TTAAGATGATTTTTTTGTGCTTTTTTACCAGGGAAACCAA 14 113 1 TTCTTTTACA 0.684801 -68 GCAATAAAGTTTTGCGGGGTTTTATCAACATCGTTGAGGG 15 164 1 TTTTTATACA 0.802038 -137 TATCTTTGATTTTGAAACGTTTAATCAACACAGTAAAACT 17 208 1 TTTTAATACA 0.526986 -93 CTAGCTGGTGCTTTTTTAATTGTTTGAACAGTGAAAACTA 18 97 0 CTTTTTTACA 0.734458 -65 GGCGTTTTTCTTTGTGAATTTTTTTAAACAAACTGGGTTC 19 32 1 TTTTTTTACA 0.963077 -269 TTTACGACATTACGCCAATTTTTTTAAACAGTGAATTGTT 21 30 0 TATTTTTACA 0.615894 -137 TTAGAATAATTGCACCTAGTTTTTTTAACTAAAAGTTGAG 23 223 0 TGTTTTTACT 0.493974 -78 CAAAGGTGTTTTCCAATTCTTTTTTCAACTCTTCTAGTTT 24 197 0 TTTTTTTACT 0.853413 -104 TAACCACCGGTTTGAATAGTTAATTGAGCTGCTAAAACGG 26 55 1 TTTTATTACT 0.615523 -246 TTACAAGCGGTTATTAACATTGTTTTAACAGGTTATTAAC 26 187 1 TTTTTTTACA 0.963077 -114 ATTAAACATTTTTAAGGTTTTGTTTTAACCTGAAATTATT 31 36 0 TTTTTTTACC 0.723959 -54 CAGTAACAATTTAATTTCTTTCATTAAACATTTTTAAGGT 31 58 0 TTTTATTACA 0.877641 -32 ATAGTTTCGATTTTATGTCTTCTTTAATCACTGAATTTTT 32 214 1 TTTTTTTACA 0.963077 -87 TGTTTGTAATGGCAATCCTTTGTTTAATCATCGGTTTATT 33 65 1 GGTTTTTACA 0.669166 -209 TTTTGGTAAAGTTTTGTCTTTAATTCAACAAACAAAGCTT 34 14 1 GTTTATTACA 0.768366 -184 AGCGGACAACGTTGCTAGTTTGTTTGAACAGTTTCAGCTA 36 178 1 GTTTTTTACA 0.923448 -123 TTTTTTGCTGTTAGTAAGTTTCTTTTAACAATTAAATGGG 38 57 1 TTTTTTTACA 0.963077 -190 AGGTAAATAATTTAGCTTTTTGTTTAATCAGCAATTTCCT 40 12 1 TTTTTTTACA 0.963077 -142 ** ** *** * ** Masking position 11 Map Score: 25.6692 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 49 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 TTTGTTTGCCAAGACTGTTTAAGTAGGAACTA 1 113 0 AAGACGTTAA 0.623658 -55 ATTTAGTCCAAAAACAGTCAAATTTTTAGCAC 4 133 1 AAAACGTCAA 0.81399 -168 TTTAACTGCAAAAACTGTTCAAAAAATCTCAC 4 168 1 AAAACGTTAA 0.896858 -133 ATCAAAGCAGTTTTATAATTAACAC 7 4 1 AAAGCGTTTA 0.603625 -42 CTTTAATTATAAGACCGCTTAAAAACTAGCTT 8 100 0 AAGACGCTAA 0.77738 -34 CAGAATTTCAAAAACTGCCAATAAAATTGCTA 11 142 0 AAAACGCCAT 0.659238 -159 GTTAGAATAAAAACCAGTCAAATCACCCAACA 14 22 0 AAACCGTCAA 0.78191 -159 CACTGCTGCAAAACCAGCCAAAGTTAGAAAGG 14 78 1 AAACCGCCAA 0.883107 -103 CGCACTTGCAAAAGCAGCTCAACCACTTGCAA 15 241 0 AAAGCGCTAA 0.919001 -60 ATTAACAAAACTGCTTATTATTCTAATT 16 7 1 AAAACGCTAT 0.793564 -24 ATTCACAAAGAAAAACGCCGAAAAGAAATTTT 19 19 0 AAAAAGCCAA 0.640487 -282 AAATAATTCCAAACAGGCCCAAAAAAGCTAAG 20 172 1 AAACAGCCAA 0.59343 -84 CAGTCAAAGGAAACCCGCTTTTTCAGTCCCAC 20 231 1 AAACCGCTTT 0.471113 -25 TATTATCTTAAAAACTGTTAAAAGCGTTTC 21 147 1 AAAACGTTAA 0.896858 -20 TGCAAATAAAAAACCAGTCTTACGACTGGCTT 23 35 1 AAACCGTCTA 0.503482 -266 AAGACACTAAAAAGCCGTTTTAGCAGCTCAAT 26 77 0 AAAGCGTTTA 0.603618 -224 TTGCAGTGTTAAAACCGCTTTAAAGCTTATAA 26 257 1 AAAACGCTTA 0.838247 -44 ATTTCTAGCGAAACCCGTTTAAACTTTTTTAA 27 52 0 AAACCGTTAA 0.876908 -155 AGGTGGTGAAAAACCTGCTGATTTTAGTAAGA 30 58 1 AAACCGCTAT 0.759004 -81 ACAAAACCTTAAAAATGTTTAATGAAAGAAAT 31 53 1 AAAAAGTTAA 0.626858 -37 AATAAAGATTAAACAAGTTTAATTCCTAAAAA 32 249 0 AAACAGTTAA 0.579189 -52 AAAAATAATGAAAAATGCTAAAGCTTTGTTTG 34 42 0 AAAAAGCTAA 0.779735 -156 AAAGAACTGCAAAGCTGCTTAAACTGTCTTTG 34 141 1 AAAGCGCTAA 0.919001 -57 AAAGGAAATAAAAGCTGCTAATGACATTTTCC 36 46 1 AAAGCGCTAT 0.704172 -255 TACTAACAGCAAAAAAGCTCCAAGCTAAAAGC 38 41 0 AAAAAGCTCA 0.361823 -206 TTAGTTTCCAAAAACGGTTTTAAATTAGAGGC 39 43 1 AAAACGTTTA 0.710927 -79 ATTCAGATAAAAGACGGTTTAATTATATTTGC 39 98 0 AAGACGTTAA 0.623658 -24 TAATTTGCAGAAAACAGCTAAACCATTGTTTC 40 102 1 AAAACGCTAA 0.948248 -52 CTCCAGTTTTAAAGCAGCTACACTTAAATAAT 42 159 0 AAAGCGCTCA 0.645031 -122 GCACTGTTACAAAAACGCTTAAAGGTAAGCTG 42 206 1 AAAAAGCTAA 0.779735 -75 ***** *** ** Masking position 2 Map Score: 27.8952 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 285 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 4 ACCAAAAAACCAAGCACCTCGATTCCTTTTAA 1 16 0 CAAGCACTCA 0.696585 -152 ATAAGTATTGCAAGCACTGCAACCAAAAAACC 1 37 0 CAAGCACGCA 0.96334 -131 TTTTAAAAAGAAAACACCACCAGTACCACCAA 3 30 1 AAAACACACA 0.916435 -258 TGCAAATGTCAAAGCACAACCAGCACTACGAC 6 87 1 AAAGCACACA 0.961453 -137 TAAAGTGATCAAAGCACCGCAATGTTAGCCCA 6 147 0 AAAGCACGCA 0.980829 -77 TTAGCTTGACAAAAAACAACAACTTAAGAG 9 9 0 AAAAAACACA 0.627803 -36 ACCAGAATTTCAAAAACTGCCAATAAAATTGC 11 144 0 CAAAAACGCA 0.639906 -157 CCCTGGTAAAAAAGCACAAAAAAATCATCTTA 14 114 0 AAAGCACAAA 0.713355 -67 CGATGTTGATAAAACCCCGCAAAACTTTATTG 15 165 0 AAAACCCGCA 0.7281 -136 TGAGGGTGGTAAAACACTGAAAGCTATAGGTG 15 198 1 AAAACACGAA 0.691778 -103 GTTACGATAAAAAACACTACCAGCTTGGGCTC 17 17 1 AAAACACACA 0.916435 -284 CTACCCAGAAAAAGGACGGCAATGGCAGCGGT 20 23 0 AAAGGACGCA 0.821931 -233 AAAATAAGAAAAAGCACTACTAAAATAAACAT 33 214 0 AAAGCACACA 0.961453 -60 CTCAAACAGAAAAGCACAGCGAGCAGTCTTTT 34 98 1 AAAGCACGCA 0.980829 -100 TTTACAATGTAAAGAACTGCAAAGCTGCTTAA 34 131 1 AAAGAACGCA 0.887248 -67 GGATTTAGCGCAAACACTACCAGGTCGGGGGT 42 127 1 CAAACACACA 0.849233 -154 GAAAAACTTTAAAGCACTGTTACAAAAACGCT 42 193 1 AAAGCACGTA 0.743251 -88 ******* ** * Masking position 3 Map Score: 18.0319 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 96 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 5 AAATACCGTTTTTTCTTTAAAAATTAAGTAG 4 275 1 TTTCTTTAAA 0.87819 -26 CTTGATGTTGTTTTGTTTGAAGTCTCTTTAC 11 92 1 TTTGTTTGAA 0.659105 -209 TTGAAGTCTCTTTACTTTAAATTGCAAAAAT 11 108 1 TTTCTTTAAA 0.878114 -193 TTAATCTCCTTTAAGTTTAAAGATTAAGTGG 17 247 1 TTAGTTTAAA 0.846932 -54 TTAGAATAAGTTAACTTTGAAGTTGCAGTAC 18 27 0 TTACTTTGAA 0.813759 -135 TTGCATTACTTTTGCTTTAAATCTAAAAT 23 9 0 TTTCTTTAAA 0.87819 -292 TGATTTAGAGTTAGCTTTAAAAAAGTTTAAA 27 36 1 TTACTTTAAA 0.904715 -171 CTTGATGAGCTTAATTTTAAAAATGTAAAAT 29 11 1 TTATTTTAAA 0.728187 -28 TGTTATAGTTTTTGGTTTGAAATTTTGATTT 32 118 0 TTTGTTTGAA 0.659105 -183 TTAATGTGTGTTAATTTTAAACTAATGCT 33 9 0 TTATTTTAAA 0.728187 -265 AATTAGAGGCTTATTTTTAAAAATTCAAAAT 39 65 1 TTATTTTAAA 0.728189 -57 ATGGCATTAACTTTAAATTGTTTGCCA 40 137 0 TTACTTTAAA 0.904712 -17 AAGTTAAATTAGGTTTAAATTTTAT 41 7 0 TTAGTTTAAA 0.846934 -19 CGCTTTCCCTTTCCTTTAAACAAGCAATAA 42 261 0 TTTCTTTAAA 0.87819 -20 *** ******* Masking position 10 Map Score: 12.2946 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 95 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 6 AGGGGATACCAATCTTTGGGATAAGATTAAA 3 129 1 AATCTTTGGA 0.780263 -159 AAAACAGTCAAATTTTTAGCACAAATTTAAC 4 143 1 AATTTTTAGA 0.878579 -158 TCAATCTTTAATATAACCTTATT 5 111 0 AATCTTTAAA 0.840156 -13 CACCCAAATAAATTTTTAAGAGTATTTAGAA 11 49 0 AATTTTTAAA 0.741959 -252 AAATTGCAAAAATTTTTAGCAATTTTATTGG 11 126 1 AATTTTTAGA 0.878579 -175 GCCATTTTGCAAGTTTTAGTACCTTTAGTAA 19 178 0 AAGTTTTAGA 0.813908 -123 GGATAATTCCAATCTTTAAGAGCCAGTCAAA 20 208 1 AATCTTTAAA 0.840156 -48 GAACTGCGCAAATCTTTATTAAAATTAGCTG 24 28 1 AATCTTTATA 0.69573 -273 AAAGCTTATAAAGCTTTAAAAAAAGGCGTTT 26 278 1 AAGCTTTAAA 0.760597 -23 TTTTAACTTCAATCTTTGGCA 27 1 0 AATCTTTGGA 0.780263 -206 ATAGCTCAAAAAGTTTTAGTAGGTGGTGAAA 30 38 1 AAGTTTTAGA 0.813908 -101 TTAATCACTGAATTTTTAGGAATTAAACTTG 32 237 1 AATTTTTAGA 0.878579 -64 AAACTTGTTTAATCTTTATTAAGATTTCTCC 32 261 1 AATCTTTATA 0.69573 -40 TCAACAAACAAAGCTTTAGCATTTTTCATTA 34 38 1 AAGCTTTAGA 0.888828 -160 GCTTATTTTGAATTTTTAAAAATAAGCCTCT 39 69 0 AATTTTTAAA 0.741959 -53 ********* * Masking position 2 Map Score: 11.7759 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 35 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 AACTCAAGAAAACCAAAATTAAAAAAGTAAA 3 92 1 AACCAAAATA 0.873914 -196 GATAAGATTAAAGCAAAGGTAAAAAAACACC 3 148 1 AAGCAAAGTA 0.734537 -140 CTAAATTTTGAACCAAAATAAAGACCACTTT 4 108 0 AACCAAAAAA 0.615859 -193 GTTTTTTGTCAAGCTAAACAAAAAACGCCTA 9 24 1 AAGCTAAAAA 0.575738 -21 ATAACAATCAAAGCAAAAATACCAGCAGTTG 10 11 1 AAGCAAAATA 0.956177 -91 TAAAAGCCATAAGCAAAATTTATGGCGAATC 12 45 0 AAGCAAAATT 0.636689 -57 CCAGAAATAAAAGCCAAATTAATCTATAATT 13 166 1 AAGCCAAATA 0.863635 -135 ACAAAACAAAAAGCAAAAAAACTATAAAAAG 13 277 1 AAGCAAAAAA 0.834625 -24 ACCAATGATCTAGCAAAATTAGAATAAGTTA 18 45 0 TAGCAAAATA 0.834625 -117 GGTTCAAATTTAGCAAAAATATCAAAGTCAC 19 67 1 TAGCAAAATA 0.834625 -234 AGCTTATAACTACCAAAAATAATTCCAAACA 20 156 1 TACCAAAATA 0.615859 -100 TAATATTTTCACGCCAAACTAAGTTTAGTTA 22 33 1 ACGCCAAATA 0.697289 -35 TTTAGATTTAAAGCAAAAGTAATGCAAATAA 23 13 1 AAGCAAAATA 0.956177 -288 TGAAAAACTAACCCTAAAATAAGAAAAAGCA 33 230 0 ACCCTAAATA 0.403997 -44 AATTCAAAATAAGCAAATATAATTAAACCGT 39 86 1 AAGCAAATTA 0.651195 -36 ATTAAACAAAAAGCTAAATTATTTACCTT 40 9 0 AAGCTAAATA 0.854372 -145 ATTTTACAAGACGCAAAAGTAGCGGCTTAGC 42 77 0 ACGCAAAATA 0.888091 -204 ******** ** Masking position 6 Map Score: 9.68945 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 94 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 GAGTATTTAGAAACATAAGCGATGTATTTA 11 31 0 AAACATAAGC 0.770536 -270 TACCACATTAAAAATTAAGCGATT 12 5 0 AAAATTAAGC 0.799807 -97 TAAATTAGAATAATAAGCAGTTTTGTTA 16 13 0 AATAATAAGC 0.862636 -18 TTATTACGTCAATAATAAGCACTGTCCTTG 19 213 1 AATAATAAGC 0.862636 -88 TTATGGTTTAAAAAATAAACAGTGGTGGTA 20 84 1 AAAAATAAAC 0.563011 -172 AAATGCTGCCAAAAATAAGGCGAAATTTCT 23 88 0 AAAAATAAGG 0.899177 -213 AAAGGATAAAAAAAATAAGGTTGAACAGCT 24 88 1 AAAAATAAGG 0.899177 -213 TTAACACTGCAAAAATGAGCTAATGGAGCC 26 239 0 AAAAATGAGC 0.755214 -62 TTACATTTTTAAAATTAAGCTCATCAAG 29 9 0 AAAATTAAGC 0.799807 -30 ATTATGGGAAAATAATAAGGCCTGCAAGCG 38 169 1 AATAATAAGG 0.741148 -78 TAGTTTGGAAAAAGATAAGGAATTAGTCAG 38 205 1 AAAGATAAGG 0.6049 -42 TTGAATTTTTAAAAATAAGCCTCTAATTTA 39 63 0 AAAAATAAGC 0.951364 -59 TTTAAAAATTCAAAATAAGCAAATATAATT 39 80 1 CAAAATAAGC 0.755214 -42 ********** Masking position 8 Map Score: 7.67144 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 44 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 9 AAGCTCCTAAAGCACCATTTTTTAAAAAGAAAA 3 8 1 TAAACCTTTT 0.763791 -280 TTTGTTAATTCCCCTTCTTTTAGCCTACAA 4 5 1 TTAACCTCTT 0.87292 -296 TTGAACCAAAATAAAGACCACTTTTAAGACATAAAA 4 96 0 ATAACCTTTA 0.721098 -205 AATTGCTACAATAAATACCGTTTTTTCTTTAAAAAT 4 263 1 ATAACCTTTT 0.697826 -38 AACGAGTTAATTAACCACCGCTTGTTCGGTAACGAA 6 12 0 TTAACCTTTT 0.908973 -212 TAGCTCTAACTTAATATCCCTTTAATACCAAGATGG 13 28 1 TTAACCTTAT 0.859384 -273 TGTTGTTAGAATAAAAACCAGTCAAATCACCCAACA 14 22 0 ATAACCTCAA 0.521405 -159 AAAAATCATCTTAATTACCTTTCTAACTTTGGCTGG 14 91 0 TTAACCTCAA 0.824868 -90 ATTCCAATCTTTAAGAGCCAGTCAAAGGAAACCCGC 20 213 1 TTAACCTCAA 0.824868 -43 GTAATGCAAATAAAAAACCAGTCTTACGACTGGCTT 23 31 1 TAAACCTCTA 0.713625 -270 CGTTTATCTCTTAACCACCGGTTTGAATAGTTAATT 26 44 1 TTAACCTTGA 0.678127 -257 TAAAACAATGTTAATAACCGCTTGTAAGCCCCCAAA 26 178 0 TTAACCTTTA 0.917948 -123 TAAAACAATGTTAATAACCTGTTAAAACAATGTTAA 26 200 0 TTAACCTTAA 0.872563 -101 TTAAACGCCTTTTTTTAAAGCTTTAT 26 285 0 TTAACCTTTT 0.908916 -16 ACGAAGTTTATAAATATCCAATTCTTTCTAACAGCA 30 96 1 TAAACCTTTT 0.763792 -43 CTCATTGATTTTAATCTCCAGTTTTTTCTCATTTAA 32 156 1 TTAACCTTTT 0.908972 -145 TGTGTCACTTTAAAAGACCCATTTAATTGTTAAAAG 38 78 0 TAAACCTTAA 0.68823 -169 **** ** ** ** Masking position 12 Map Score: 10.3169 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 53 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 10 GAAGCTTAAAAGGAATCGAGGT 1 3 1 AGCTTAAAAG 0.823101 -165 ATTATAAGACCGCTTAAAAACTAGCTTTGG 8 97 0 CGCTTAAAAA 0.960163 -37 TTTCTAAATACTCTTAAAAATTTATTTGGG 11 48 1 CTCTTAAAAA 0.800437 -253 CTTTGACTGGCTCTTAAAGATTGGAATTAT 20 210 0 CTCTTAAAGA 0.518496 -46 GTCATTAAATCGCTTAATAGCTCGATCAAG 21 92 1 CGCTTAATAG 0.571481 -75 ACTGTTTATTATCTTAAAAACTGTTAAAAG 21 141 1 ATCTTAAAAA 0.561616 -26 TAGCTTAGTCCGCTCAAAAAGGTCTACTGG 24 122 0 CGCTCAAAAA 0.866138 -179 GTCTTATAAGCGCTTAGAAAGCCTTTTCTG 26 104 1 CGCTTAGAAA 0.765818 -197 GTGTTAAAACCGCTTTAAAGCTTATAAAGC 26 262 1 CGCTTTAAAG 0.847369 -39 AAGCTTATAAAGCTTTAAAAAAAGGCGTTT 26 279 1 AGCTTTAAAA 0.745772 -22 ATTTAGAGTTAGCTTTAAAAAAGTTTAAAC 27 38 1 AGCTTTAAAA 0.745772 -169 AACGCGCTTGCGCTTAAAAAATCGCT 28 33 1 CGCTTAAAAA 0.960163 -16 TGGGAGAAATAGCTCAAAAAGTTTTAGTAG 30 30 1 AGCTCAAAAA 0.673899 -109 TTTCATTTTGCGCTTTAAAATCTAACAG 33 256 1 CGCTTTAAAA 0.901815 -18 GTTACAAAAACGCTTAAAGGTAAGCTGTTC 42 211 1 CGCTTAAAGG 0.796375 -70 ********** Masking position 4 Map Score: 8.95957 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 112 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 11 GTATTGCAAGCACTGCAACCAAAAAACCAAG 1 34 0 CACTGCACCA 0.869285 -134 AAAACACCACCAGTACCACCAAAGAATCCTG 3 40 1 CAGTACACCA 0.93927 -248 CTGTGGTAACCAGCACTACCCCAGAACTCAA 3 68 1 CAGCACACCC 0.722261 -220 CCCCAGAACTCAAGAAAACCAAAATTAAAAA 3 86 1 CAAGAAACCA 0.722103 -202 GCACAACCAGCACTACGACCAGTGACGAGTT 6 100 1 CACTACACCA 0.93927 -124 CGAATCCAAACAATTATACCACATTAAAAAT 12 20 0 CAATTAACCA 0.668689 -82 GCTTTTTTACCAGGGAAACCAACACACTAAA 14 131 1 CAGGGAACCA 0.773196 -50 CTTGCAAAAGCAGCTCAACCACTTGCAACCC 15 238 0 CAGCTCACCA 0.860914 -63 TCAACGGTTCCACTACCACCACTGTTTATTT 20 96 0 CACTACACCA 0.93927 -160 AGCACAGCGTCACGAATACCACCTTCGAAAA 27 93 1 CACGAAACCA 0.887998 -114 GCACTAAAACCCAAAATTTGGA 32 289 0 CACTAAACCC 0.721236 -12 GCAAGTCCGCCAGTAGAACCATGGTTGGATA 33 107 0 CAGTAGACCA 0.719084 -167 GGAATTGTTTCAAGTACACCAGTCAA 36 6 0 CAAGTAACCA 0.624115 -295 TCGGTGTATCCACTTCGACCAAAGCCTTAAG 37 25 0 CACTTCACCA 0.908112 -69 TTGCAGAAAACAGCTAAACCATTGTTTCACC 40 106 1 CAGCTAACCA 0.794114 -48 ****** **** Masking position 8 Map Score: 6.898 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 175 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 12 TGTGAGATTTTTTGAACAGTTTTTGCAGTTA 4 170 0 TTTAACAGTT 0.921527 -131 ACGGTATTTATTGTAGCAATTTTTGACCCCG 4 253 0 TTGAGCAATT 0.69905 -48 TTGCAAAAATTTTTAGCAATTTTATTGGCAG 11 129 1 TTTAGCAATT 0.784994 -172 TTGGCTGGTTTTGCAGCAGTGGGTGTATTAG 14 68 0 TTGAGCAGTG 0.828627 -113 GTTTGTATCAATTTTTCGGTGTG 15 3 1 TTGATCAATT 0.313843 -298 TTTTTAATTGTTTGAACAGTGAAAACTAAGT 18 94 0 TTTAACAGTG 0.857785 -68 CGCCAATTTTTTTAAACAGTGAATTGTTTGA 21 27 0 TTTAACAGTG 0.857785 -140 GAAACGCTTTTAACAGTTTTTAAGATAA 21 149 0 TTTAACAGTT 0.921527 -18 TTAATAAAGATTTGCGCAGTTCTCAGAGATT 24 19 0 TTTCGCAGTT 0.624019 -282 TAAAAAGCCGTTTTAGCAGCTCAATTAACTA 26 71 0 TTTAGCAGCT 0.775454 -230 ATTAACATTGTTTTAACAGGTTATTAACATT 26 199 1 TTTAACAGGT 0.598272 -102 GCAAAGACAGTTTAAGCAGCTTTGCAGTTCT 34 143 0 TTTAGCAGCT 0.775454 -55 ACTGGTGTACTTGAAACAATTCCCCAACTGC 36 14 1 TTGAACAATT 0.648312 -287 TGCTAGTTTGTTTGAACAGTTTCAGCTAGCA 36 190 1 TTTAACAGTT 0.921527 -111 TGTCATGCGTTTTAATCAGTTTGACTTCAAA 36 239 0 TTTATCAGTT 0.744489 -62 AGTAAGTTTCTTTTAACAATTAAATGGGTCT 38 69 1 TTTAACAATT 0.743428 -178 GCTTTTAGCAGTCACAATTGAAC 38 234 0 TTTAGCAGTC 0.683394 -13 TTAAGCGTTTTTGTAACAGTGCTTTAAAGTT 42 197 0 TTGAACAGTG 0.793274 -84 *** ******* Masking position 2 Map Score: 11.0197 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 135 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 GAATCGAGGTGCTTGGTTTTTTGGTTGCAGT 1 23 1 GCTTGGTTTT 0.661915 -145 AAGAAGATTATCTTTGTTTGCCAAGACTGTT 1 126 0 TCTTTGTTGC 0.861004 -42 TGGTATTTTTGCTTTGATTGTTAT 10 4 0 GCTTTGTTGT 0.829177 -98 GATTAATTTGGCTTTTATTTCTGGATGCCTA 13 159 0 GCTTTTTTTC 0.665725 -142 GGTAATCACATCCTTGTTTTCTTCTAACAAC 15 55 1 TCCTTGTTTC 0.73114 -246 AGTTAGCACAGCATTGGTTTCACAACCCAAC 15 109 1 GCATTGTTTC 0.883809 -192 ATCGCAAATATCTTTGATTTTGAAACGTTTA 17 200 1 TCTTTGTTTT 0.907845 -101 TTTTGCTAGATCATTGGTTTCATTCACAGTT 18 58 1 TCATTGTTTC 0.857887 -104 ATTATCCTGGTCTTAGCTTTTTTGGGCCTGT 20 184 0 TCTTAGTTTT 0.511801 -72 ACGTTCCAACTCTTTGATTTCACGTTTAATT 24 256 0 TCTTTGTTTC 0.940621 -45 TAACTCTAAATCATCGTTTTTAACTTCAATC 27 18 0 TCATCGTTTT 0.521459 -189 CACACCAAGCTCATTGATTTTAATCTCCAGT 32 147 1 TCATTGTTTT 0.789656 -154 TGGCGGACTTGCTTCGCTTTCAGGTCAAGAT 33 126 1 GCTTCGTTTC 0.852807 -148 AATTCCGCGGTCTTTGGTTTTGCGAAAAATT 33 162 0 TCTTTGTTTT 0.907845 -112 AAATGCTAAAGCTTTGTTTGTTGAATTAAAG 34 31 0 GCTTTGTTGT 0.829177 -167 GTCATTAGCAGCTTTTATTTCCTTTTGCAGT 36 40 0 GCTTTTTTTC 0.665725 -261 ****** **** Masking position 4 Map Score: 5.9274 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 123 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 14 GAAACTAGCTTTATCTATACGT 2 44 0 AACTAGCTTT 0.723359 -12 AAAACACCCTTACCTGTTTGCTGTTTTAGT 3 171 1 TACCTGTTTG 0.455267 -117 GCGAACCTTGCTTTTTTATCTTTT 3 274 0 ACCTTGCTTT 0.757075 -14 AGAAAATTTATCCCAGTTTTAGGGGGCAAG 4 223 1 TCCCAGTTTT 0.724314 -78 GCAATTTTTGACCCCGCTTGCCCCCTAAAA 4 239 0 ACCCCGCTTG 0.868829 -62 AAAAAAGTGCACCACGCTTTGATCGAAAAC 5 59 0 ACCACGCTTT 0.545543 -65 TGCGGTCTGCACCTTGTTTGATGACACTAG 6 52 0 ACCTTGTTTG 0.594455 -172 ACCGCTTAAAAACTAGCTTTGGCTAAATTA 8 89 0 AACTAGCTTT 0.723359 -45 AAAAACTACTTGCTTTAATTATAAGA 8 118 0 TACTTGCTTT 0.524558 -16 GGTAATCACATCCTTGTTTTCTTCTAACAA 15 55 1 TCCTTGTTTT 0.476477 -246 TAAAAAACACTACCAGCTTGGGCTCCATCA 17 24 1 TACCAGCTTG 0.795058 -277 CTAAATTTGAACCCAGTTTGTTTAAAAAAA 19 50 0 ACCCAGTTTG 0.808847 -251 AGTCAAAGGAAACCCGCTTTTTCAGTCCCA 20 232 1 AACCCGCTTT 0.717951 -24 GAATAATTGCACCTAGTTTTTTTAACTAAA 23 230 0 ACCTAGTTTT 0.683242 -71 TGTGCCATTTTCCTAGCTTGAGCCTAAAAT 26 132 1 TCCTAGCTTG 0.837288 -169 ACTAGCACCTTACCAGTTTTAT 27 195 1 TACCAGTTTT 0.551538 -12 GAGCTATTTCTCCCAGCTTGTAATATTTAT 30 15 0 TCCCAGCTTG 0.89233 -124 TTGAATTGCGTCCATGCTTTAATGTGTGTT 33 28 0 TCCATGCTTT 0.455926 -246 GCAACTCTAAAACAAGCTTGCAAAGACAGT 34 163 0 AACAAGCTTG 0.531034 -35 AAAAGTAGTAACCCCGCTTTTTGGCGATCT 38 117 0 ACCCCGCTTT 0.84467 -130 GCAAGCGGCAAACTAGTTTGGAAAAAGATA 38 192 1 AACTAGTTTG 0.551538 -55 ********** Masking position 8 Map Score: 11.7871 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 152 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 TGTTTGCTGTTTTAGTGTCCTTTATTCTTTT 3 185 1 TTTAGTGTCT 0.517778 -103 AAAAATTTATTTGGGTGACTTGGATCGCTCT 11 63 1 TTGGGTGATT 0.810252 -238 TTGTTGTTTGTTGGGTGATTTGACTGGTTTT 14 14 1 TTGGGTGATT 0.810252 -167 TTTTGCAGCAGTGGGTGTATTAGTTACCCTT 14 60 0 GTGGGTGTTT 0.796186 -121 TATGCGATGGTTTAGTGTGTTGGTTTCCCTG 14 141 0 TTTAGTGTTT 0.787196 -40 GTATCAATTTTTCGGTGTGTTTAACAAGGGT 15 15 1 TTCGGTGTTT 0.948377 -286 ACCTATAGCTTTCAGTGTTTTACCACCCTCA 15 198 0 TTCAGTGTTT 0.826462 -103 AAAATTTCTTTTCGGCGTTTTTCTTTGTGAA 19 19 1 TTCGGCGTTT 0.72825 -282 AAGCACTGTCCTTGGTGTTTTCCACCATATC 19 229 1 CTTGGTGTTT 0.81845 -72 AATGATTTGTTTGGGTGTTTT 19 290 1 TTGGGTGTTT 0.957905 -11 CATTTAAAACTTGGGTGTCCTCTAGCTTAGT 24 143 0 TTGGGTGTCT 0.86851 -158 AAAACGGCTTTTTAGTGTCTTATAAGCGCTT 26 88 1 TTTAGTGTTT 0.787196 -213 AATCAATGAGCTTGGTGTGTTATAGTTTTTG 32 135 0 CTTGGTGTTT 0.81845 -166 GACTACGCTTTTCGGTGTATCCACTTCGACC 37 36 0 TTCGGTGTTC 0.72825 -58 ******** ** Masking position 2 Map Score: 6.30058 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 43 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548