AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00970_aful_reg_300.orf -o00970_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0260 30 glutamyl-tRNA synthetase (gltX) #2 AF0409 74 aspartate aminotransferase (aspB-4) #3 AF0410 56 signal-transducing histidine kinase, putative #4 AF0411 30 cysteinyl-tRNA synthetase (cysS) #5 AF0546 300 nitrate reductase, gamma subunit (narI) #6 AF0548 59 threonyl-tRNA synthetase (thrS) #7 AF0633 173 isoleucyl-tRNA synthetase (ileS) #8 AF0776 135 tyrosyl-tRNA synthetase (tyrS) #9 AF0894 300 arginyl-tRNA synthetase (argS) #10 AF0916 59 glycyl-tRNA synthetase (glyS) #11 AF0919 30 conserved hypothetical protein #12 AF0920 36 aspartyl-tRNA synthetase (aspS) #13 AF1216 101 lysyl-tRNA synthetase (lysS) #14 AF1424 112 phenylalanyl-tRNA synthetase, subunit beta (pheT) #15 AF1446 63 A. fulgidus predicted coding region AF1446 #16 AF1448 114 transcriptional regulatory protein, AsnC family #17 AF1449 33 pyruvate formate-lyase 2 (pflD) #18 AF1451 88 thermosome, subunit beta (thsB) #19 AF1452 117 signal-transducing histidine kinase #20 AF1453 37 methionyl-tRNA synthetase (metS) #21 AF1609 59 prolyl-tRNA synthetase (proS) #22 AF1642 50 histidyl-tRNA synthetase (hisS) #23 AF1694 50 tryptophanyl-tRNA synthetase (trpS) #24 AF1955 68 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #25 AF2035 23 seryl-tRNA synthetase (serS) #26 AF2036 62 cytochrome C oxidase folding protein (coxD) #27 AF2037 54 translation initiation factor eIF-2B, subunit delta (eif2BD) #28 AF2224 38 valyl-tRNA synthetase (valS) #29 AF2225 64 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase (hpcE-2) #30 AF2253 78 molybdopterin-guanine dinucleotide biosynthesis protein B (mobB) #31 AF2254 207 ATP-dependent RNA helicase, DEAD-family (deaD) #32 AF2255 53 alanyl-tRNA synthetase (alaS) #33 AF2421 58 leucyl-tRNA synthetase (leuS) #34 AF2425 85 methanol dehydrogenase regulatory protein (moxR) Motif number 1 TTTTGAATTATTTAAAATTTTCTCAAGTTTT 5 26 1 TTAAAATTTT 0.744935 -275 ATATTGAAATTGCAAACATTTGATTTGACCT 5 122 0 TGAAACATTT 0.861158 -179 ATCTTATCTTTGGAAAACTTTATAA 5 286 1 TGAAAACTTT 0.861158 -15 TTTAATTGCTTAGAAAAATTTATTACTCCTC 6 23 1 TAAAAAATTT 0.829876 -37 TAAATATATTTTCAAGCCTTTGCAACCTTTT 8 35 1 TTAAGCCTTT 0.952546 -101 TTGGAGGGCTTTTAAACATTTAAACAACTTT 8 89 1 TTAAACATTT 0.936183 -47 ACGCTTTTTATTTAAACCTTTTTCCCAACTT 13 30 1 TTAAACCTTT 0.963231 -72 AAGGCCTGTCTTGAAGTATTTAGCGCATCAC 14 51 1 TTAAGTATTT 0.691152 -62 TCACCCAACCTAAAAAATTTTAACCTCAACT 14 78 1 TAAAAATTTT 0.634277 -35 TTTTTCCCTCTTAAAAACTTTCACCAGTACA 15 17 0 TTAAAACTTT 0.936183 -47 GAATTTAAATTGCAAGCATTTGTTA 18 5 0 TGAAGCATTT 0.826163 -84 GGTATTTCTATATAAGCTTTTCTATCACGAA 18 33 0 TAAAGCTTTT 0.703539 -56 TCTTTGTAAATAAAAGCATTTGGCCGATTAT 19 84 0 TAAAGCATTT 0.869705 -34 CCATTTTGTATAAAAAACTTTCGTGTCAGCC 21 25 1 TAAAAACTTT 0.897027 -35 TCGCTCAACTCTAAAACCTTTTAAACACCCT 22 15 1 CTAAACCTTT 0.704741 -36 AAGAAACACTTTAAAACATTTCTACTACTCA 24 44 1 TTAAACATTT 0.936183 -25 TTTTCAAAGGTTAAAGAATTTTAACCTGAAG 27 24 0 TTAAGAATTT 0.862907 -31 GAGATAACTCTTAAAACCTTTGCCTTCTTAC 29 18 0 TTAAACCTTT 0.963231 -47 TGCGGAGAGGTTTAAATCTTTTGAGATTAAA 30 23 1 TTAAATCTTT 0.839113 -56 ATTTTAACTTTACAAAACTTTCACCATGAAA 31 18 0 TAAAAACTTT 0.897027 -190 CTGAAGGGTATATAAGTCTTTGTTTGAATCC 31 142 0 TAAAGTCTTT 0.703539 -66 ATAAATGGGATTAAAAAATTTGGCGTTTGGC 33 26 0 TTAAAAATTT 0.891477 -33 ** ******** Masking position 9 Map Score: 27.5424 Number of sites scoring better than the average of aligned sites = 238 Number in coding regions = 152 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 117 Fraction of orfs with sites within 600 bp upstream = 0.0187922 Motif number 2 GAAACCTGAACAGCCGGTGGATTAAAAAAG 7 154 0 CCGGCCGGGG 0.999304 -20 CGAGGGGAGGCCTGTCAAGCGGGCGGCAGCGGTTCC 9 27 1 CCGGCGGGGG 0.999129 -274 GAGTCCTCGTCCCGGAGGGCCGGCGGTTATGGCCGG 9 73 1 CCGGCCGGGG 0.998954 -228 GCGGTTATGGCCGGGCTGCCCGGAGGGGCTGTCCGC 9 95 1 CCGCCCGGGG 0.995727 -206 GGGCTGTCCGCCATATTAGCCGGGGGGAACGGCCCA 9 120 1 CCTGCCGGGG 0.991405 -181 ACGGCCCAGGCCCGGAAGGGAGCAGGCTAACCCCGG 9 148 1 CCGGGAGCGG 0.924619 -153 GCAGGCTAACCCCGGACGACCGGCGCTTCCGGGGGT 9 169 1 CCGACCGGGC 0.979703 -132 ACCGGCGCTTCCGGGGGTGCGGGGAGGAGGTGCCTG 9 187 1 CCGGCGGGAG 0.994256 -114 CTCGGGTCGACCTGCCTTACGGGCGGCTTGAAGCCC 9 223 0 CCGACGGGGG 0.980941 -78 AGAATTTTAACCTGAAGCAGAGGTGGGAAC 27 5 0 CCGAGAGGGG 0.96201 -50 ACAATCCCGTCATGCGGAGAGGTTTAAATCT 30 6 1 CCGGCGGAAG 0.940875 -73 ** * ***** ** Masking position 2 Map Score: 24.4423 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 56 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 TTTGCTGTTCAGTTAAATAAAAA 3 4 0 AGTTAAATAA 0.731031 -53 AACGGTCATGGGTTTAAAAATT 4 3 0 GGTTTAAAAA 0.866365 -28 TTAATAATTAAGATAAAAAATTTAATTTTT 5 56 1 AGATAAAAAA 0.78521 -245 AATAGCTAATAGTCTAAAAAGGTCAAATCA 5 103 1 AGTCTAAAAA 0.606236 -198 AAAAAACGAAAATTTAATAATTTAAAGTCT 5 217 1 AATTTAATAA 0.548348 -84 GCATAATAATAATTTAAAAAAAGCATTAAT 5 247 0 AATTTAAAAA 0.889461 -54 TTTTCTAAGCAATTAAAAAAGAAAAAAGT 6 10 0 AATTAAAAAA 0.908953 -50 ACAGCCGGTGGATTAAAAAAGTTATCAGCT 7 145 0 GATTAAAAAA 0.816776 -29 AATTGAAGTTAGTTTAAGAAGTATAAATAT 8 12 1 AGTTTAAGAA 0.772135 -124 CATTTAAACAACTTTAAAAACAGCCTGGGT 8 105 1 ACTTTAAAAA 0.77578 -31 TTTTCAGTTAAATTGAAAAATCCTCCAGCC 9 270 1 AATTGAAAAA 0.652784 -31 GGCTAAACTTAAAAAACTGCCTGAAG 12 7 1 ACTTAAAAAA 0.811059 -30 GATAAAGGCAAGTTTAAAAACAGCAACGCC 13 70 1 AGTTTAAAAA 0.935562 -32 TTAAAAACCTAATTAAAAAAGATTACGATT 17 12 0 AATTAAAAAA 0.908953 -22 ACCAAAACAAAAATTAAAAA 19 1 0 AAATTAAAAA 0.620207 -117 TAGATAAAAAATTGGGCTGAC 21 49 0 AGATAAAAAA 0.78521 -11 TTTTTTCAAAGGTTAAAGAATTTTAACCTG 27 27 0 GGTTAAAGAA 0.652445 -28 ATTAAACAAAAGTTAAAAAACTTCCTGGGT 30 48 1 AGTTAAAAAA 0.947406 -31 TAATAAATGGGATTAAAAAATTTGGCGTTT 33 29 0 GATTAAAAAA 0.816776 -30 ********** Masking position 6 Map Score: 19.5964 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 67 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 4 GAAACCTGAACAGCCGGTGGATTAAAAAAG 7 154 0 GACGCCGGGG 0.980751 -20 ACGCGGGGGCCGAAGCCGAGGGGAG 9 3 1 GGGGGCCGAG 0.973317 -298 GAGGCCTGTCAAGCGGGCGGCAGCGGTTCCAGG 9 33 1 AGCGGCGGAG 0.917732 -268 CGAGGACTCTGCGGTGCCTGGAACCGCTGCCGC 9 49 0 GGGGCCTGAA 0.905099 -252 TCCTCGTCCCGGAGGGCCGGCGGTTATGGCCGG 9 76 1 GAGGCCGGGG 0.983528 -225 GGTTATGGCCGGGCTGCCCGGAGGGGCTGTCCG 9 97 1 GGCGCCCGAG 0.987074 -204 CGCACCCCCGGAAGCGCCGGTCGTCCGGGGTTA 9 175 0 GAGGCCGGCG 0.957078 -126 GGCGCTTCCGGGGGTGCGGGGAGGAGGTGCCTG 9 190 1 GGGGCGGGAG 0.963858 -111 GTGCGGGGAGGAGGTGCCTGGGGCTTCAAGCCG 9 203 1 GGGGCCTGGG 0.987515 -98 CCTGCCTTACGGGCGGCTTGAAGCCCCAGGCAC 9 216 0 GGCGCTTGAG 0.906353 -85 CGGTCAGAATTGGCTGGAGGATTTTTCAA 9 282 0 GATGGCTGAG 0.772583 -19 TAAACTTAAAAAACTGCCTGAAGGTGTAAGAGC 12 14 1 AACGCCTGAG 0.889613 -23 AACTGACGTTGGAGAGCATGCAGTATGGATAAA 16 48 0 GAGGCATGAG 0.841486 -67 TAAAGCGTATTTGCTGGCGGCAGTTTTTTGGAA 19 37 1 TGCGGCGGAG 0.858474 -81 * ** ***** ** Masking position 6 Map Score: 13.3956 Number of sites scoring better than the average of aligned sites = 573 Number in coding regions = 541 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 GGCCCACCTGGGAAGTTGAGAAATATAAAG 1 11 0 GGAAGTTGAG 0.947638 -20 GTAAATATCAGAAGCTTGAGGTTCTTGC 2 9 0 GAAGCTTGAG 0.929223 -66 TTAAAAGGTATGAGATAGAGACTTAAGGCG 5 157 1 TGAGATAGAG 0.741339 -144 GGAGGGAGAGTGAGGGAAGG 7 1 1 GGAGGGAGAG 0.964314 -173 GCAAAAATTAGGAGGGATAGTAGGCTGAAA 7 64 0 GGAGGGATAG 0.856431 -110 GGATTTTGCTTGAAGTTGAGGTTAAAATTT 14 92 0 TGAAGTTGAG 0.715465 -21 CAATTACTTCGAAGGTGGAGCAGA 15 50 1 GAAGGTGGAG 0.907887 -14 CACCCTTGCCGAAGCTTGAGC 22 40 1 GAAGCTTGAG 0.929223 -11 ATAGAAAATTTAGTTTGAGGGCA 26 50 0 GAAAATTTAG 0.435578 -13 GGAGAGAGTCGAAGATTGAGGGATTCAAAC 31 122 1 GAAGATTGAG 0.940605 -86 CCAAGCGTTGGGAGATAGAGTGGAACGTTG 31 173 1 GGAGATAGAG 0.953764 -35 AAGAATGGTAGGAGGGTTAGAGCTATGGGA 34 43 0 GGAGGGTTAG 0.910051 -43 ********** Masking position 3 Map Score: 8.26058 Number of sites scoring better than the average of aligned sites = 2131 Number in coding regions = 2037 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 AATTTTTAAACCCATGACCGTT 4 3 1 TTTTTAAACC 0.508737 -28 TATCTCATACCTTTTAAACCGATATTGAAA 5 144 0 CTTTTAAACC 0.951478 -157 TTTTTAATTGCTTAGAAAAATTTATTACTC 6 21 1 CTTAGAAAAA 0.477295 -39 ATTTTCAAGCCTTTGCAACCTTTTTCATCA 8 42 1 CTTTGCAACC 0.699485 -94 CTTTGGAGGGCTTTTAAACATTTAAACAAC 8 87 1 CTTTTAAACA 0.881481 -49 ATTTAAACAACTTTAAAAACAGCCTGGGTT 8 106 1 CTTTAAAAAC 0.87418 -30 GGCTAAACTTAAAAAACTGCCTGAAGG 12 8 1 CTTAAAAAAC 0.651429 -29 GCTCTTACACCTTCAGGCAGT 12 26 0 CTCTTACACC 0.650776 -11 GGATTTTTCCCTCTTAAAAACTTTCACCAG 15 21 0 CTCTTAAAAA 0.730971 -43 CCTTAAAAACCTAATTAAAAA 17 23 0 CTTAAAAACC 0.793106 -11 ATTCGCTCAACTCTAAAACCTTTTAAACAC 22 13 1 CTCTAAAACC 0.914339 -38 TGAAGAAACACTTTAAAACATTTCTACTAC 24 42 1 CTTTAAAACA 0.84401 -27 ATTCTTTAACCTTTGAAAAAATTGAACAC 27 36 1 CTTTGAAAAA 0.771605 -19 TCTGAGATAACTCTTAAAACCTTTGCCTTC 29 22 0 CTCTTAAAAC 0.877471 -43 AACCTCTGAAAACCCAGGAAGTT 30 66 0 CTCTGAAAAC 0.870118 -13 GCAAATTAAACTTCTAAACATGTCTGAACG 31 87 0 CTTCTAAACA 0.540195 -121 ********** Masking position 8 Map Score: 11.138 Number of sites scoring better than the average of aligned sites = 418 Number in coding regions = 367 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 GCTTTCGAATATATCAACTTTTACCCGAATA 2 41 0 ATATAACTTT 0.857255 -34 TGGACGATGAATATAAACTTTGCTGTTCAGT 3 21 0 ATATAACTTT 0.857255 -36 CTTTTGAATTATTTAAAATTTTCTCAAGTTT 5 25 1 ATTTAAATTT 0.623942 -276 CAAACATTTGATTTGACCTTTTTAGACTATT 5 110 0 ATTTACCTTT 0.876599 -191 AAATTTAATAATTTAAAGTCTATTAATGCTT 5 226 1 ATTTAAGTCT 0.706604 -75 TTATAAAGTTTTCCAAAGATA 5 290 0 TTATAAGTTT 0.68918 -11 TTTACATGACAATTAAAGTTTAATACCTTCC 7 25 0 AATTAAGTTT 0.825258 -149 TTCAGGCAGTTTTTTAAGTTTAGCC 12 5 0 TTTTAAGTTT 0.825258 -32 TACGCTTTTTATTTAAACCTTTTTCCCAACT 13 29 1 ATTTAACCTT 0.618637 -73 CTTTCATTGTAAATAAAGTTTACCTTATAAA 16 79 0 AAATAAGTTT 0.689179 -36 TGCGAGGGGTAAATAACGTTTTAC 20 4 0 AAATACGTTT 0.551843 -34 AAAAAGTTATATTTCAAGTTTCTGTGAGGTG 28 13 1 ATTTAAGTTT 0.949977 -26 CCCAGGAAGTTTTTTAACTTTTGTTTAATCT 30 46 0 TTTTAACTTT 0.760824 -33 CCACTCCTTAATTTTAACTTTACAAAACTTT 31 28 0 ATTTAACTTT 0.927491 -180 GGATTAAAAAATTTGGCGTTTGGCCTGATTG 33 19 0 ATTTGCGTTT 0.572188 -40 GCAATCTGCTATTTGACGTTTCCCATAGCTC 34 23 1 ATTTACGTTT 0.913393 -63 **** ****** Masking position 4 Map Score: 11.1237 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 71 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 8 CGGGGGCCGAAGCCGAGGGGAGGCCTGTCA 9 14 1 AGCCGAGGGG 0.980428 -287 TGGCCGGGCTGCCCGGAGGGGCTGTCCGCC 9 102 1 GCCCGGAGGG 0.938019 -199 CCGCCATATTAGCCGGGGGGAACGGCCCAG 9 127 1 AGCCGGGGGG 0.98189 -174 TCCCTTCCGGGCCTGGGCCGTTCCCCCCGG 9 139 0 GCCTGGGCCG 0.898077 -162 GGGAGGAGGTGCCTGGGGCTTCAAGCCGCC 9 208 1 GCCTGGGGCT 0.855871 -93 AGGCAGGTCGACCCGAGGCGTGCCCACCTT 9 242 1 ACCCGAGGCG 0.980428 -59 CGGTCAAGCTGAGGCGTTGCTGTTTT 13 86 0 AGCTGAGGCG 0.975199 -16 TTTAACCTGAAGCAGAGGTGGGAAC 27 6 0 AGCAGAGGTG 0.766532 -49 GAAGTTCTACGCCTGAGGTGATATC 29 50 1 GCCTGAGGTG 0.955001 -15 CCCAACGCTTGGCTGAAGGGTATATAAGTC 31 155 0 GGCTGAAGGG 0.91566 -53 ********** Masking position 3 Map Score: 8.19275 Number of sites scoring better than the average of aligned sites = 539 Number in coding regions = 506 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 9 TATTTAACTGAACAGCAAAGTTTATATTCA 3 15 1 AACAGCAAAG 0.973884 -42 AGGCGAAAAAAACAGCAATTTAGGTTATGA 5 182 1 AACAGCAATT 0.903653 -119 CAAGTTTAAAAACAGCAACGCCTCAGCTTG 13 78 1 AACAGCAACG 0.993296 -24 TTTATCGATTAACAGCAACCATCG 26 5 0 AACAGCAACC 0.982228 -58 CAGAGAACAGAACAGCAACGTTCCACTCTA 31 188 0 AACAGCAACG 0.993296 -20 ********** Masking position 4 Map Score: 4.87157 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 17 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 CATGTATATAAAAAATAAAAATTAAATTTTTTA 5 69 0 AAAAAAAAAT 0.721126 -232 ATGAGCTATAAAAAACGAAAATTTAATAATTTA 5 208 1 AAAAAAAAAT 0.721126 -93 TAAAGTTTTCCAAAGATAAGATTCATCTTTAGC 5 275 0 CAAAGAAGAT 0.954922 -26 AAGCAATTAAAAAAGAAAAAAGT 6 1 0 AAAAGAAAAT 0.928512 -59 GAAAAAGCGACAAATGGAGGAGTAA 6 45 0 AAAAGACAAT 0.671979 -15 GGTTGTTCGACAGAGGAAAGAATAAAT 11 5 0 CAGAGAAGAT 0.870004 -26 CTCAACGCTAAGATTTAATACGCTT 13 3 1 CAACGAAGAT 0.769647 -99 GAAAGTTTTTAAGAGGGAAAAATCCAATTACTT 15 26 1 AAGAGAAAAT 0.804053 -38 ACTTCAATTACAAAGAAAAGACTGTCATTA 16 8 0 CAAAGAAGAT 0.954922 -107 TACAGGTAACCAAAACAAAAATTAAAAA 19 6 0 CAAAAAAAAT 0.805401 -112 GAGATTAAACAAAAGTTAAAAAACTTCCTGGGT 30 45 1 AAAAGAAAAA 0.726238 -34 GAAAGTTTTGTAAAGTTAAAATTAAGGAGTGGA 31 27 1 TAAAGAAAAT 0.729473 -181 TCGAAATAAGCAAAGGCAAGAGATATAAACATC 32 13 1 CAAAGAAGAA 0.812264 -41 ***** **** * Masking position 8 Map Score: 6.6601 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 116 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 11 TAGCTATTGCATGTATATAAAAAATAAAAATT 5 79 0 ATGTATTAAA 0.732831 -222 AATCAAATGTTTGCAATTTCAATATCGGTTTA 5 128 1 TTGCAATCAA 0.75619 -173 AAATTTTTCTAAGCAATTAAAAAAGAAAAAAG 6 12 0 AAGCAATAAA 0.706003 -48 GTATATGCTTTTGCATGTCAAAATTCCGGAAA 7 109 1 TTGCATTAAA 0.927311 -65 GCAGTGCAGAATGCAACTTAAAAGGTTATCTT 10 38 0 ATGCAATAAA 0.949759 -22 AGTCTTTTCTTTGTAATTGAAGTAGCTGTCTT 16 18 1 TTGTAATAAG 0.831567 -97 AACACTTTCATTGTAAATAAAGTTTACCTTAT 16 82 0 TTGTAATAAG 0.834634 -33 TAACAAATGCTTGCAATTTAAATTCGTGATAG 18 11 1 TTGCAATAAA 0.96715 -78 TTGGAATGGATTGCATCTGAATAATCGGCCAA 19 64 1 TTGCATTAAT 0.666701 -54 TTGCCTATCTTTGTAAATAAAAGCATTTGGCC 19 90 0 TTGTAATAAA 0.90836 -28 TCTCTCCGAGATGCAAATTAAACTTCTAAACA 31 97 0 ATGCAATAAA 0.949612 -111 ****** * *** Masking position 5 Map Score: 5.86129 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 48 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 CTAATTTTTGCTGCCCCACCATGATGGTAT 7 83 1 CTGCCCCACC 0.974745 -91 CCCTCGGCTTCGGCCCCCGCGT 9 3 0 CGGCCCCCGC 0.855855 -298 GCCCGCTTGACAGGCCTCCCCTCGGCTTCG 9 21 0 CAGGCCTCCC 0.869867 -280 GCCATAACCGCCGGCCCTCCGGGACGAGGA 9 76 0 CCGGCCCTCC 0.944635 -225 CCCCTCCGGGCAGCCCGGCCATAACCGCCG 9 93 0 CAGCCCGGCC 0.89506 -208 ATATGGCGGACAGCCCCTCCGGGCAGCCCG 9 106 0 CAGCCCCTCC 0.979482 -195 CGGAAGGGAGCAGGCTAACCCCGGACGACC 9 160 1 CAGGCTAACC 0.813843 -141 GGGCACGCCTCGGGTCGACCTGCCTTACGG 9 237 0 CGGGTCGACC 0.836414 -64 CGACCCGAGGCGTGCCCACCTTTTCAGTTA 9 250 1 CGTGCCCACC 0.943777 -51 AAATTTTTATCGGCCCAACCAGAACAACAT 14 13 0 CGGCCCAACC 0.969905 -100 TCTGCTCCACCTTCGAAGTAA 15 53 0 CTGCTCCACC 0.830028 -11 ATCCATACTGCATGCTCTCCAACGTCAGTT 16 51 1 CATGCTCTCC 0.470248 -64 TTTGGTCAATCAGGCCAAACGCCAAATTTT 33 13 1 CAGGCCAAAC 0.712582 -46 ********** Masking position 1 Map Score: 7.5884 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 375 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 13 TGGGAAGTTGAGAAATATAAAG 1 2 0 AGAATATAAA 0.924551 -29 ATTTAGGTTATGAGCTATAAAAAACGAAAAT 5 199 1 TGAGTATAAA 0.84453 -102 AGTTAGTTTAAGAAGTATAAATATATTTTCA 8 18 1 AGAATATAAA 0.924551 -118 AAGTTGGGAAAAAGGTTTAAATAAAAAGCGT 13 30 0 AAAGTTTAAA 0.538352 -72 GTGTTTCTTCAGAGATATTAAACAATTAATT 24 22 0 AGAGTATTAA 0.73331 -47 CAAAGGTTAAAGAATTTTAACCTGAAGCAGA 27 20 0 AGAATTTAAC 0.803586 -35 CACAGAAACTTGAAATATAACTTTTTGC 28 8 0 TGAATATAAC 0.624771 -31 CGTCATGCGGAGAGGTTTAAATCTTTTGAGA 30 18 1 AGAGTTTAAA 0.930303 -61 AGACATGTTTAGAAGTTTAATTTGCATCTCG 31 92 1 AGAATTTAAT 0.599994 -116 AGCAAAGGCAAGAGATATAAACATCCAATGC 32 21 1 AGAGTATAAA 0.951318 -33 **** ****** Masking position 6 Map Score: 2.72412 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 73 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 GATTAAAAAAGTTATCAGCTTTCCTTTCCGG 7 134 0 GTATCAGCTT 0.80431 -40 GACCCGAGGCGTGCCCACCTTTTCAGTTAAA 9 251 1 GTCCCACCTT 0.956993 -50 TTCACATCACCTCCTATTGCAGA 18 76 0 CAATCACCTC 0.869916 -13 CTAACCACCTCAATTAATTGT 24 1 1 CTACCACCTC 0.966638 -68 AACATTTCTACTACTCAGCTT 24 58 1 CTCTCAGCTT 0.753129 -11 GTTCCCACCTCTGCTTCAGGT 27 1 1 GTCCCACCTC 0.982737 -54 GTGTCCACCTCACAGAAACTT 28 28 0 GTTCCACCTC 0.93476 -11 GATATCACCTCAGGCGTAGAA 29 54 0 GAATCACCTC 0.915814 -11 ** ******** Masking position 7 Map Score: 1.67387 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 245 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 15 CCTGGGGCTTCAAGCCGCCCGTAAGGCAGG 9 219 1 CAAGCCGCCC 0.963926 -82 GAAAGTGTTACAATCCAACC 16 105 1 CAATCCAACC 0.961135 -10 ATAGAAATACCAATCCACCAATTTCTGCAA 18 53 1 CAATCCACCA 0.943629 -36 TATTCAGATGCAATCCATTCCAAAAAACTG 19 57 0 CAATCCATTC 0.922404 -61 AGAACACAATCAATCCATTTTGTATA 21 7 1 CAATCAATCC 0.849765 -53 ACAAGCCACCCTAACTTATCC 25 2 1 CAAGCCACCC 0.988616 -22 CAAATCGGGCGAATCCACTCCTTAATTTTA 31 43 0 GAATCCACTC 0.871199 -165 ********** Masking position 3 Map Score: 2.65781 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 156 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678