AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_aquae_reg_100.orf -o00230_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: purE 24 phosphoribosylaminoimidazole carboxylase Input sequences: #1 rpmJ 60 ribosomal protein L36 #2 secY 44 preprotein translocase SecY #3 nrdA 85 ribonucleotide reductase alpha chain #4 rpsO 58 ribosomal protein S15 #5 aldH2 300 aldehyde dehydrogenase #6 guaA 45 GMP synthase #7 purK 300 phosphoribosyl aminoimidazole carboxylase #8 mtfB 300 mannosyltransferase B #9 spsK 63 spore coat polysaccharide biosynthesis protein SpsK #10 bcpC 229 phosphonopyruvate decarboxylase #11 purB 41 adenylosuccinate lyase #12 aq_598 99 putative protein #13 purD 35 phosphoribosylamine-glycine ligase #14 aq_765 33 putative protein #15 spoT 37 (p)ppGpp 3-pyrophosphohydrolase #16 dnaQ 230 DNA polymerase III epsilon subunit #17 cysD 89 sulfate adenylyltransferase #18 aq_1104 45 putative protein #19 aq_1173 115 hypothetical protein #20 purF 27 amidophosphoribosyltransferase #21 purA 28 adenylosuccinate synthetase #22 aq_1292 68 hypothetical protein #23 htrA 28 periplasmic serine protease #24 rpoD 38 RNA polymerase sigma factor RpoD #25 dnaG 66 DNA primase #26 nrdF 105 ribonucleotide reductase beta chain #27 mutL 32 DNA mismatch repair protein MutL #28 atpF1 33 ATP synthase F0 subunit b #29 aq_1625 300 hypothetical protein #30 purL 52 phosphoribosylformylglycinamidine synthase II #31 dnaX 178 DNA polymerase III gamma subunit #32 aq_1873 300 putative protein #33 rplM 45 ribosomal protein L13 #34 dnaN 24 DNA polymerase III beta chain #35 rpoB 212 RNA polymerase beta subunit #36 guaB 300 inosine monophosphate dehydrogenase #37 hemN 300 oxygen-independent coproporphyrinogen II Motif number 1 AAGTTCTCTCGGAGGTAGAAGA 2 3 0 GGAGGTAGAA 0.937862 -42 TTTCTTGAAGAGAGGTAGAATTCTCAAATC 3 66 1 AGAGGTAGAA 0.835796 -20 ATGAATAAAGGGAGGTGAAACC 6 3 0 GGAGGTGAAA 0.967473 -43 TGTACCGTGTGGAGTTGAAACCTTGCTTTA 7 51 1 GGAGTTGAAA 0.887293 -250 TGTACCGTGTGGAGTTGAAACCTCTTGATA 7 125 1 GGAGTTGAAA 0.887293 -176 GTACCGTAGTGGAGTTGAAACTTCGGTGAT 7 197 1 GGAGTTGAAA 0.887293 -104 GTGGAAGGAGAAAGTGGTGTATG 8 4 1 GAAGGAGAAA 0.942674 -297 ACCATCGCTCGAAGGTTGAAAAGAAGCTCT 8 52 0 GAAGGTTGAA 0.656153 -249 GCATGTGTTTAAAGTTGGGATAATGATCAT 8 128 1 AAAGTTGGGA 0.423483 -173 TAGAACTCAAAAAGGTGGAGGAACTTCTCT 10 133 1 AAAGGTGGAG 0.808584 -97 TTGAGAGAAAGGAGGTAGAGAAGTTCCTCC 10 149 0 GGAGGTAGAG 0.912844 -81 GGCGAGGGAGGAAGTAGGGGAAATCCTTAG 10 185 1 GAAGTAGGGG 0.588299 -45 GAAGGGAGGGAAAGGAAAGAAGGGA 11 6 0 AAAGGAAAGA 0.552828 -36 ATCAAACGTGAGAGTAGGAAAAGTTGTTGA 16 131 1 AGAGTAGGAA 0.722582 -100 CAATTCTTATAGAGGTAAAGGAAGATCTAG 17 29 1 AGAGGTAAAG 0.772915 -61 TATCCGATGAAGAGGAGAAAAAAGAAGTT 17 71 1 AGAGGAGAAA 0.904607 -19 AACTCTACAAAGAGGTAAAAGCC 18 4 0 AGAGGTAAAA 0.830648 -42 AATCCTAACAGGAGGTGGAAGGATGGGCGA 19 17 1 GGAGGTGGAA 0.968619 -99 TTTAGAGTTAGGAGGTAAGAGA 24 27 1 GGAGGTAAGA 0.868952 -12 CAGGAATTTGGAAGTAGAAAATTCATGAAA 26 28 0 GAAGTAGAAA 0.813169 -78 ATTGTTTAGCGGAGGAGAAGA 28 23 1 GGAGGAGAAG 0.951251 -11 AAAAAGAGGGGAAGGAAAAGATTA 29 5 0 GAAGGAAAAG 0.848021 -296 CGAAGTCAGAGAAGTAGAAGAAGAGTGCCC 29 248 1 GAAGTAGAAG 0.751262 -53 TTTACTTACCGAAGGAGGAAGCGA 30 5 0 GAAGGAGGAA 0.944644 -48 TTACTAACCAGGAGGTGTAAA 31 2 0 GGAGGTGTAA 0.635901 -177 AAAGTCCGCCGAAGGTAGGATTACTTACTA 32 34 0 GAAGGTAGGA 0.800957 -267 CGTTCACCGTAAAGTAGAAGAAGGATATAT 32 85 0 AAAGTAGAAG 0.504595 -216 ACGAACTGAGGGAGGTTAAAGTAATCAGAA 32 112 1 GGAGGTTAAA 0.758713 -189 AAACCATTAAAAAGTTAGAAAATAAATAGG 32 271 1 AAAGTTAGAA 0.440667 -30 GTGTAAAGGAAAAGGAAAAGAAGGAG 35 7 0 AAAGGAAAAG 0.652986 -206 CTTTTGCTCAGGAGGCAGGAACGCTCTGTA 35 36 1 GGAGGCAGGA 0.573166 -177 GTTTCTTAAAGAAGGCGGAATGAAGCAATA 35 171 0 GAAGGCGGAA 0.778887 -42 GAAACATAAAAGAGGAGAGGTATAAAA 35 196 1 AGAGGAGAGG 0.750006 -17 AAAGGAAAAAGGAGGAAAGGATTTTTACTG 36 255 0 GGAGGAAAGG 0.813086 -46 TCAAAGGTTAAAAGGAAAAAGGAGGAAAGG 36 265 0 AAAGGAAAAA 0.730581 -36 GCCTCTGGCGAAGGATAAATTGGATCTCT 37 10 1 GAAGGATAAA 0.634828 -291 CCTCAGGAAAGAAGTAAAAATAGATGATAA 37 237 1 GAAGTAAAAA 0.680333 -64 ********** Masking position 3 Map Score: 38.2875 Number of sites scoring better than the average of aligned sites = 2803 Number in coding regions = 2486 Number in noncoding regions = 317 Number of orfs with sites within 600 bp upstream = 258 Fraction of orfs with sites within 600 bp upstream = 0.0414391 Motif number 2 TCAAAATACGGTTCCTAATGTACCGTGTGGAGT 7 33 1 GTTCCTTGAC 0.975526 -268 ATAAAGCAAGGTTTCAACTCCACACGGTACATT 7 49 0 GTTTCATCAC 0.940499 -252 TTCATAGTTTGTTCCTAATGTACCGTGTGGAGT 7 107 1 GTTCCTTGAC 0.975526 -194 CTATCAAGAGGTTTCAACTCCACACGGTACATT 7 123 0 GTTTCATCAC 0.940499 -178 CGATTCTTTTGTTCCTAATGTACCGTAGTGGAG 7 178 1 GTTCCTTGAC 0.975526 -123 TATCACCGAAGTTTCAACTCCACTACGGTACAT 7 195 0 GTTTCATCAC 0.940499 -106 AAAGAAATCAGTTTCTAATGTACCGTGTGGATA 7 245 1 GTTTCTTGAC 0.97503 -56 CTTATTGAGAGCTTCTTTTCAACCTTCGAGCGA 8 45 1 GCTTCTTCAC 0.944635 -256 GACCTGATTATTTTCTCGTCCACATCAACTCCA 8 194 0 TTTTCTTCAC 0.863199 -107 CCGATATCATGCTCCTTTGGGACTTGGACTTGC 9 15 1 GCTCCTGGAC 0.734651 -49 TTGTAGAAAAGTACCTCATCAACCCGTTAATAG 16 196 1 GTACCTTCAC 0.905153 -35 GCCGTACAGGTTTCCTGGTCAACCATGGTCTTT 29 83 0 TTTCCTTCAC 0.920219 -218 TCAAAAGAATGTTCCTTTTCGGCTTTTCTGATT 32 134 0 GTTCCTTCGC 0.93581 -167 AAGCCCTAAAGGTTCTATTGCACACTGAAAAAA 32 193 1 GGTTCTTGAC 0.861974 -108 TTGTTGCAGAGTTCCTCGTCAACTTCCTTAATT 36 35 0 GTTCCTTCAC 0.990709 -266 ****** ** ** Masking position 5 Map Score: 22.137 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 52 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 3 TGCAAGTCCAAGTCCCAAAGGAGCATGATATC 9 17 0 ATCCCAAAGA 0.747862 -47 CTTAAGAGAAAGTCCCTAAGGATTTCCCCTAC 10 198 0 ATCCCTAAGA 0.949534 -32 TTTAATATAAATTCCTTAAAGGGGATTAGAA 15 10 0 ATCCTTAAGG 0.949534 -28 CTCAACGGCTCTGCCCTGAGGGTCCAGAAGCC 16 70 0 CGCCCTGAGG 0.92479 -161 TTGGTTTACCTCCTGAAGGGTGGAGTGTTG 26 86 0 CTCCTGAAGG 0.886544 -20 GCTGGATGATAGTCCCGGAAGGACTGGAAGAC 29 217 1 ATCCCGGAGG 0.951599 -84 GAACTCCCCCAGGCCCGAAAGGGAGCAAGGGT 31 102 1 AGCCCGAAGG 0.975425 -77 AACTCTCTCAAAGCCCTAAAGGTTCTATTGCA 32 183 1 AGCCCTAAGG 0.979695 -118 AAGCTAAATCCATCCTTGATGAAACCATTAAA 32 250 1 CTCCTTGAGA 0.655818 -51 TCCTTTTTCAATTCCCTAACCGGTAAGAAGAT 35 83 0 ATCCCTAACG 0.822135 -130 CCTTAAGAATAAGCCCGAAAGAATTAAGGAAG 36 14 1 AGCCCGAAGA 0.94038 -287 CTCGCTCAGTACGCCTTAATGGGTCCTTACGA 36 84 1 AGCCTTAAGG 0.950428 -217 TGTTCCTTTAAGTCCTTAATGAGTGTGTCAAT 36 222 0 ATCCTTAAGA 0.882031 -79 * ******* ** Masking position 9 Map Score: 11.3366 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 236 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 4 AATTTTCTTGAAGAGAGGTAGAATTCTCAA 3 63 1 AAGAGAGGTA 0.725849 -23 CAATTCTAAGAAAAGACGGAGGTATATGGG 4 36 1 AAAAGACGGA 0.941343 -23 GCACCGTTTTAATAGACGGAAATCCTGTGA 5 64 1 AATAGACGGA 0.594999 -237 CGAACCCTTCAAAAGAGGAAATAGTAAGTG 5 265 1 AAAAGAGGAA 0.899683 -36 GGAGGGAAAGGAAAGAAGGGA 11 2 0 GAAAGAAGGG 0.914537 -40 TAATAATGCCGAAAGAGGGGCTTCTGGACC 16 52 1 GAAAGAGGGG 0.964195 -179 AAAATTCATGAAAAGAGGTGTTATAATAAC 26 11 0 AAAAGAGGTG 0.904167 -95 ATTTAAGGAAAAGAGAGGGA 27 1 0 AAGAGAGGGA 0.902066 -32 AGATTTATGAAAAAGAGGGGAAGGAAAAGA 29 14 0 AAAAGAGGGG 0.970434 -287 ACAAGAACAGGGGAGACGGAATAGCGGATG 29 151 1 GGGAGACGGA 0.752883 -150 AGTGTGACATAAAAGACGAGGAAGATCACT 29 187 1 AAAAGACGAG 0.880469 -114 CGGAAGGACTGGAAGACGAAGTCAGAGAAG 29 232 1 GGAAGACGAA 0.747885 -69 TCAGAGAAGTAGAAGAAGAGTGCCCCAGCG 29 253 1 AGAAGAAGAG 0.746106 -48 ACCGTAAAGTAGAAGAAGGATATATAAAGA 32 80 0 AGAAGAAGGA 0.864909 -221 CTTTAAACTCGGAAGAGGTGAATGGG 33 30 1 GGAAGAGGTG 0.831212 -16 AAGGAAAAGGAAAAGAAGGAG 35 2 0 AAAAGAAGGA 0.909612 -211 TAAGAAACATAAAAGAGGAGAGGTATAAAA 35 193 1 AAAAGAGGAG 0.920785 -20 AAAGCCTCAGGAAAGAAGTAAAAATAGATG 37 233 1 GAAAGAAGTA 0.703549 -68 ********** Masking position 6 Map Score: 16.652 Number of sites scoring better than the average of aligned sites = 817 Number in coding regions = 758 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 5 TTAAAAGATTTTAATATAATAAAGTTCTCTCGGAG 2 19 0 TTAATAAAAT 0.825936 -26 GGACTTTCTCTTAAGATAAATACTT 10 215 1 TTAATAATAT 0.849366 -15 GTTAAACTTATTATATAAGTGGTAAG 13 20 0 TTAATTATAT 0.933993 -16 GGAAAAAAGTTTAACTTTAAAATTTAGACTT 14 7 0 TTAATTAAAT 0.922557 -27 TCGGATATAATTAAGCTAACTAGATCTTCCTTTAC 17 43 0 TTAATAATAT 0.849366 -47 AGTTAAATTAAATTTAATACTTAACTCTACAA 18 24 0 TTAATTATAT 0.93402 -22 TTAACTTTAATAAATTTTTAGAGTT 24 1 1 TTAATTATAT 0.93402 -38 AGTTTTTATTTTAACCTTATAATTTTACTTACCGA 30 23 0 TTAATTAAAT 0.922557 -30 TTCACGAGGTTTATATTTATTAATTAGCCCTGCGG 31 56 1 TTATTTATAT 0.778389 -123 TGTTATAATTACAATCTTGCTTTAAAC 33 3 1 TTATTTAAAT 0.747184 -43 CTTTTTTGGTTTAAATTTAAAAGATCAGTTAATGG 35 130 1 TTAATTAAAT 0.922556 -83 **** *** ** * Masking position 9 Map Score: 7.70645 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 23 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 AAATCACCCAGAGGGTTATAAATTCCATGCT 8 256 0 GAGGTTATAA 0.962976 -45 ACATATGGAGGATTTTGAAAAAATTCTC 10 8 1 GAGGTTTTGA 0.962255 -222 TTAAGGGAAGGAGGTTTTTATGAAGCTCGTA 16 14 1 GAGGTTTTAT 0.904958 -217 CCCGTTAATAGAGGATTACGAGA 16 218 1 GAGGTTACGA 0.935218 -13 TAGAGTTCCCGAGGTTTACAAGAACAGGGGA 29 134 1 GAGGTTACAA 0.93642 -167 GAAATTTCACGAGGTTTATATTTATTAATTA 31 51 1 GAGGTTATAT 0.904958 -128 CGTACTGAGCGAGGATTTTGATTCCGTACTT 36 66 0 GAGGTTTTGA 0.962255 -235 CTTCTTTCCTGAGGCTTTTAATTGTTTATTT 37 220 0 GAGGTTTTAA 0.962976 -81 **** ****** Masking position 2 Map Score: 7.2393 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 100 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 GGAACCGCATATTCCCTTACCGCATCCGAA 5 33 0 ATTCCCTTAC 0.876023 -268 TTTCATTCCGCTTCCTTGACTGGGTACTGA 5 101 0 CTTCCTTGAC 0.871281 -200 ACCTGCCCTACTACCTTTGCAGGGACATAC 10 67 1 CTACCTTTGC 0.897751 -163 TCCCTAAGGATTTCCCCTACTTCCTCCCTC 10 188 0 TTTCCCCTAC 0.853863 -42 TCCCTTCTTTCCTTTCCCTCCCTTCTG 11 8 1 TTTCCTTTCC 0.872852 -34 TAAAAACCTCCTTCCCTTAAATT 16 4 0 CTTCCCTTAA 0.863874 -227 GGCATTATTATTACCCTTACGAGCTTCATA 16 32 0 TTACCCTTAC 0.923668 -199 TTAAAGCCGTTTTCCTTTAACATCTCCTCA 16 98 0 TTTCCTTTAA 0.803239 -133 CTAACTAGATCTTCCTTTACCTCTATAAGA 17 33 0 CTTCCTTTAC 0.975266 -57 GACGGCGGGCTTACCCTTGCTCCCTTTCGG 31 116 0 TTACCCTTGC 0.883436 -63 GAGTTTATTACTTCCTTTGCGTCAAAAGAA 32 158 0 CTTCCTTTGC 0.961083 -143 TTCTTTTCCTTTTCCTTTACACTTTTGCTC 35 15 1 TTTCCTTTAC 0.967085 -198 ********** Masking position 2 Map Score: 7.90119 Number of sites scoring better than the average of aligned sites = 800 Number in coding regions = 744 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 8 TCAACTCCACACGGTACATTAGGAACCGTA 7 39 0 ACGGTACATT 0.98705 -262 TCAACTCCACACGGTACATTAGGAACAAAC 7 113 0 ACGGTACATT 0.98705 -188 CAACTCCACTACGGTACATTAGGAACAAAA 7 184 0 ACGGTACATT 0.98705 -117 TTTTATCCACACGGTACATTAGAAACTGAT 7 251 0 ACGGTACATT 0.98705 -50 AAAAGCCGAAAAGGAACATTCTTTTGACGC 32 140 1 AAGGAACATT 0.840408 -161 ********** Masking position 6 Map Score: 7.03797 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 2 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 AAATGCTGTCTTATGAATAATTTTCGCCCGGCTATGA 3 12 1 TAAATTTTCC 0.89485 -74 TGAAGACATAGAAAGAATACTATTCTCTGATAAAGCA 7 74 0 GAAATTATCC 0.954275 -227 TAAACACAAATAATCATTTTTATCCACACGGTACATT 7 261 0 TAATTTATCC 0.81697 -40 TTCTAAAGAATTTTAAACACAAATAATCAT 7 281 0 TAAATTAACC 0.81697 -20 ACCCAGAGGGTTATAAATTCCATGCTCTGTCCAATAA 8 245 0 TAAATCATCC 0.86869 -56 TTCCCTCCCTTCTGATATCCTATTCCCT 11 24 1 TTTATTATCC 0.713518 -18 CTCCCACGATTAAAAATTTTATCCCTTTCGGTTAAT 12 10 1 TAAATTATCT 0.840442 -90 TATAGATTTTTTAAAAATAGTATTCACTAACCATTCT 12 68 0 TAAATTATCC 0.978425 -32 GATTTTCTATTGTATACTCAATTCTTATA 17 3 1 TTTATTATCC 0.713519 -87 AAGGCGGAATGAAGCAATAATATCCCCATTAACTGAT 35 153 0 GAAATTATCC 0.954267 -60 AGGAACAGCAGTAAAAATCCTTTCCTCCTTTTTCCTT 36 247 1 GAAATTTTCC 0.796574 -54 ATTAAAGCAATAATAAATCCTATCCCCAGTATAGAGA 37 37 0 TAAATTATCC 0.978425 -264 TGAAAAGGCATTACTAATTGTATACCTTGCTCTTTTC 37 142 1 TAAATTATCT 0.840442 -159 ATTAAGTTTTTCACCTATATTATTCTCATA 37 281 1 TATATTATCC 0.929935 -20 * * *** *** * * Masking position 8 Map Score: 9.73569 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 21 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 TAACCTAAGTCCTTGCCTTTTTCAACT 1 7 0 CCTTGCCTTT 0.956894 -54 GAAGTTCAATCCATGCCCTTTTAACAGGGTG 5 165 0 CCATGCCCTT 0.982135 -136 GGAGTTGAAACCTTGCTTTATCAGAGAATAG 7 61 1 CCTTGCTTTT 0.945183 -240 CCTTATGTTACCAAGCCTTTTGCTCACTACA 8 92 0 CCAAGCCTTT 0.739606 -209 GTTATAAATTCCATGCTCTGTCCAATAAATC 8 242 0 CCATGCTCTT 0.977118 -59 TAATCTTTTCCTTCCCCTCTTTTTCATAAA 29 10 1 CCTTCCCCTT 0.907761 -291 TCCTGGTCAACCATGGTCTTTAATTTTGCCA 29 73 0 CCATGGTCTT 0.8612 -228 GCGGGCTTACCCTTGCTCCCTTTCGGGCCTG 31 111 0 CCTTGCTCCT 0.924767 -68 TAATTGTATACCTTGCTCTTTTCATATTTAT 37 156 1 CCTTGCTCTT 0.981347 -145 ********* * Masking position 11 Map Score: 7.224 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 77 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 AAGCGGAATGAAAAGAAATAATAACCATCGA 5 118 1 AAAAAAATAA 0.795844 -183 ATGAAGACATAGAAAGAATACTATTCTCTGA 7 81 0 AGAAGAATAC 0.742797 -220 GAATACGCGGAAAACAGATACTATCAAGAGG 7 145 0 AAAAAGATAC 0.867422 -156 CATTTTTCACAAAAGAAATCAGTTTCTAATG 7 234 1 AAAAAAATCA 0.493252 -67 ACTTTCTCTTAAGATAAATACTT 10 217 1 AAGAAAATAC 0.681672 -13 TTTTGATTATAGAATAGATAAAA 23 3 0 AGAAAGATAA 0.49375 -26 TGTGTCAAGCTGAAGAAATACCTGTAAAATC 25 16 0 TGAAAAATAC 0.651208 -51 GATCAGAAATAAAATAAATTCTTTTGAGTG 25 47 1 AAAAAAATTC 0.62218 -20 TGTTGCCCCGAAAATAAATCCTAAATCCTTC 26 60 0 AAAAAAATCC 0.817907 -46 CCTCCTTTGAAAAAGAAAAAAGATTTATGAA 29 33 0 AAAAAAAAAA 0.370344 -268 TTATAAGGTTAAAATAAAAACTCTAAA 30 36 1 AAAAAAAAAC 0.73076 -17 GCAGGGTCCTAAAACAAATACCCTCCAGAGG 31 152 1 AAAAAAATAC 0.947337 -27 GGATATATAAAGAATAAATACAAAGGCTAAA 32 62 0 AGAAAAATAC 0.925229 -239 TATTGCACACTGAAAAAATACTCAAAGAGGA 32 208 1 TGAAAAATAC 0.651208 -93 AAAAAGTTAGAAAATAAATAGGAGGGGCTTG 32 279 1 AAAAAAATAG 0.637165 -22 AGGGAATTGAAAAAGGAATACTTGACAGTGT 35 98 1 AAAAGAATAC 0.80763 -115 GTGCAACACCAAAAAAGATACTTATTAAAGC 37 66 0 AAAAAGATAC 0.867422 -235 **** ****** Masking position 4 Map Score: 6.88408 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 178 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 GTTGAAAAAGGCAAGGACTTAGGTTATACTAAG 1 12 1 GCAAGTTAGG 0.848785 -49 GACGAAGTTCGGATGCGGTAAGGGAATATGCGG 5 26 1 GGATGTAAGG 0.966308 -275 CTTCAAAAGAGGAAATAGTAAGTGTCATGTCTT 5 271 1 GGAAATAAGT 0.711909 -30 ATATATAGATGGATGAATAAAGGGAGGTGAAAC 6 12 0 GGATGAAAGG 0.854182 -34 GTGGAAGGAGAAAGTGGTGTATGGC 8 3 1 GGAAGAAAGT 0.660663 -298 AGGAAGTAGGGGAAATCCTTAGGGACTTTCTCT 10 193 1 GGAAATTAGG 0.881447 -37 AGGGAATAGGATATCAGAAGGGAGGGAAAGG 11 21 0 GGATAGAAGG 0.560704 -21 AAATTCCTGTGGAAGGATTTAGGATTTATTTTC 26 49 1 GGAAGTTAGG 0.966308 -57 CGGATAAGGAAAATTTAAGGAAAAGAGAGG 27 13 0 GGAAATAAGG 0.946767 -20 TTGACGCAAAGGAAGTAATAAACTCTCTCAAAG 32 163 1 GGAAGTAAAC 0.473004 -138 GTTTCATCAAGGATGGATTTAGCTTTCTCCACA 32 242 0 GGATGTTAGC 0.720419 -59 GAATAAGCCCGAAAGAATTAAGGAAGTTGACGA 36 20 1 GAAAGTAAGG 0.831158 -281 ACAACGTTCAGGAAGTCGTAAGGACCCATTAAG 36 98 0 GGAAGTAAGG 0.985634 -203 TTGTTTATTTGCAAGAAATAAGGCAGCCCCACC 37 197 0 GCAAGTAAGG 0.930686 -104 ***** ***** Masking position 3 Map Score: 9.75548 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 425 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 CCGCACTGGGGAACCTGAAGTTCAATCCAT 5 182 0 GAACCTGAAG 0.779012 -119 ACCGTATTTTGAAGTTGACGATAACTTCAA 7 15 0 GAAGTTGACG 0.884187 -286 TGTACCGTGTGGAGTTGAAACCTTGCTTTA 7 51 1 GGAGTTGAAA 0.90953 -250 TGTACCGTGTGGAGTTGAAACCTCTTGATA 7 125 1 GGAGTTGAAA 0.90953 -176 GTACCGTAGTGGAGTTGAAACTTCGGTGAT 7 197 1 GGAGTTGAAA 0.90953 -104 TGGCTGTGGTGGAGTTGATGTGGACGAGAA 8 185 1 GGAGTTGATG 0.817912 -116 TTTGGGACTTGGACTTGCAGTGGTGTAACT 9 30 1 GGACTTGCAG 0.849785 -34 AATTCTCCTGGAACTTGAAAATGATAACGT 10 32 1 GAACTTGAAA 0.862346 -198 AAAAGTTGTTGAACTCGAAGTTTCAGAAGA 16 149 1 GAACTCGAAG 0.893335 -82 AGTCCCGGAAGGACTGGAAGACGAAGTCAG 29 227 1 GGACTGGAAG 0.879565 -74 CGAAGTCAGAGAAGTAGAAGAAGAGTGCCC 29 248 1 GAAGTAGAAG 0.754331 -53 TATCGTTGAAGAACTCGAAGA 29 290 1 GAACTCGAAG 0.893335 -11 AAGAATTAAGGAAGTTGACGAGGAACTCTG 36 32 1 GAAGTTGACG 0.884187 -269 CACTCATTAAGGACTTAAAGGAACAGCAGT 36 229 1 GGACTTAAAG 0.702441 -72 ********** Masking position 3 Map Score: 11.7273 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 403 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 14 AGAGAGGTAGAATTCTCAAATC 3 74 1 AATTCTCAAA 0.887961 -12 GCTCACTACATACTCTCCAAACCATCGCTC 8 72 0 TACTCTCCAA 0.722142 -229 TTTTCTATTGTATACTCAATTCTTATAGAG 17 13 1 TATACTCAAT 0.627174 -77 TTAATACCCGTATTCTCAAAGCTTCTTCCC 19 87 1 TATTCTCAAA 0.945954 -29 TTATCTATTCTATAATCAAAAGTATT 23 13 1 TATAATCAAA 0.67391 -16 ACACTGAAAAAATACTCAAAGAGGAAAGTG 32 214 1 AATACTCAAA 0.844077 -87 TTGTTATACTAATTCTCCAA 34 15 1 AATTCTCCAA 0.849464 -10 ACAACGACACTATACTCAAAATGGCAATTG 36 142 1 TATACTCAAA 0.922811 -159 ATGATAACTCTATTATCCAATATTAAGTTT 37 260 1 TATTATCCAA 0.682976 -41 TCACCTATATTATTCTCATA 37 291 1 TATTCTCATA 0.71121 -10 ********** Masking position 6 Map Score: 2.18523 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 80 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 TTGAGACTTACCGGGACGAAGTTCGGATGCG 5 12 1 CCGGGAGAAG 0.90727 -289 AAGTTCGGATGCGGTAAGGGAATATGCGGTT 5 30 1 GCGGTAGGGA 0.834954 -271 AGTCAAGGAAGCGGAATGAAAAGAAATAATA 5 110 1 GCGGAAGAAA 0.942587 -191 GTGGAAGGAGAAAGTGGTGTA 8 1 1 GTGGAAGAGA 0.851729 -300 ATGAGGTCAGGTGGTATGAGAGATGGCTGTG 8 162 1 GTGGTAGAGA 0.80668 -139 ACCCTATGGCGAGGGAGGAAGTAGGGGAAAT 10 178 1 GAGGGAGAAG 0.909263 -52 TATTATATAAGTGGTAAGGAGTTTACG 13 7 0 GTGGTAGGAG 0.798518 -29 TAATAATAATGCCGAAAGAGGGGCTTCTGGA 16 49 1 GCCGAAGAGG 0.786153 -182 CTAACAGGAGGTGGAAGGATGGGCGACGTAA 19 21 1 GTGGAAGATG 0.662531 -95 GGCTTAAGCGGGAAGAAGCTTTGAGAAT 19 98 0 GCGGGAGAAG 0.975877 -18 TTAGAGTTAGGAGGTAAGAGA 24 28 1 GAGGTAGAGA 0.762165 -11 ATGAAAAAGAGGGGAAGGAAAAGATTA 29 7 0 GGGGAAGAAA 0.704621 -294 TAGCCCTGCGGCGGGACAGGGTGAACTCCCC 31 80 1 GCGGGAAGGG 0.475638 -99 AATTCCCTAACCGGTAAGAAGATTAATGTTT 35 75 0 CCGGTAGAAG 0.883715 -138 CTTAAAGAAGGCGGAATGAAGCAATAATATC 35 166 0 GCGGAAGAAG 0.977405 -47 TTAAAAGCCTCAGGAAAGAAGTAAAAATAGA 37 230 1 CAGGAAGAAG 0.721563 -71 ****** **** Masking position 6 Map Score: 9.89938 Number of sites scoring better than the average of aligned sites = 489 Number in coding regions = 454 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974