AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_aquae_reg_300.orf -o00230_aquae_300.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 aq_935 49 putative protein #18 cysD 89 sulfate adenylyltransferase #19 aq_1104 45 putative protein #20 carB1 300 carbamoyl-phosphate synthase large subunit #21 aq_1173 115 hypothetical protein #22 purF 27 amidophosphoribosyltransferase #23 purA 28 adenylosuccinate synthetase #24 aq_1292 68 hypothetical protein #25 htrA 28 periplasmic serine protease #26 rpoD 38 RNA polymerase sigma factor RpoD #27 dnaG 66 DNA primase #28 nrdF 105 ribonucleotide reductase beta chain #29 aq_1510 113 putative protein #30 mutL 32 DNA mismatch repair protein MutL #31 atpF1 33 ATP synthase F0 subunit b #32 aq_1625 300 hypothetical protein #33 purL 52 phosphoribosylformylglycinamidine synthase II #34 dnaX 178 DNA polymerase III gamma subunit #35 aq_1873 300 putative protein #36 rplM 45 ribosomal protein L13 #37 dnaN 24 DNA polymerase III beta chain #38 nusG 300 transcription antitermination protein NusG #39 rpoB 212 RNA polymerase beta subunit #40 guaB 300 inosine monophosphate dehydrogenase #41 hemN 300 oxygen-independent coproporphyrinogen II Motif number 1 TCTTCTACCTCCGAGAGAACTT 2 3 1 TTCTACCTCC 0.937077 -42 GATTTGAGAATTCTACCTCTCTTCAAGAAA 3 66 0 TTCTACCTCT 0.868007 -20 TGACACTTACTATTTCCTCTTTTGAAGGGT 5 268 0 TATTTCCTCT 0.636647 -33 GGTTTCACCTCCCTTTATTCAT 6 3 1 TTTCACCTCC 0.96321 -43 TAAAGCAAGGTTTCAACTCCACACGGTACA 7 51 0 TTTCAACTCC 0.812454 -250 TATCAAGAGGTTTCAACTCCACACGGTACA 7 125 0 TTTCAACTCC 0.812454 -176 ATCACCGAAGTTTCAACTCCACTACGGTAC 7 197 0 TTTCAACTCC 0.812454 -104 CATACACCACTTTCTCCTTCCAC 8 4 0 TTTCTCCTTC 0.926215 -297 AGAGCTTCTTTTCAACCTTCGAGCGATGGT 8 52 1 TTCAACCTTC 0.548721 -249 TTCTCGTCCACATCAACTCCACCACAGCCA 8 185 0 CATCAACTCC 0.343383 -116 GCACCTGCCCTACTACCTTTGCAGGGACAT 10 65 1 TACTACCTTT 0.375457 -165 AGAGAAGTTCCTCCACCTTTTTGAGTTCTA 10 133 0 CTCCACCTTT 0.71522 -97 GGAGGAACTTCTCTACCTCCTTTCTCTCAA 10 149 1 CTCTACCTCC 0.896737 -81 GGATTTCCCCTACTTCCTCCCTCGCCATAG 10 181 0 TACTTCCTCC 0.769989 -49 TCCCTTCTTTCCTTTCCCTCCCTTC 11 6 1 TCTTTCCTTT 0.516663 -36 CGTTAAAGCCGTTTTCCTTTAACATCTCCT 16 100 0 GTTTTCCTTT 0.449342 -131 TCAACAACTTTTCCTACTCTCACGTTTGAT 16 131 0 TTCCTACTCT 0.636673 -100 GACCTCCTCCTGAAGATTAC 17 1 1 GACCTCCTCC 0.520177 -49 CTAGATCTTCCTTTACCTCTATAAGAATTG 18 29 0 CTTTACCTCT 0.819665 -61 AACTTCTTTTTTCTCCTCTTCATCGGATA 18 71 0 TTTCTCCTCT 0.926215 -19 GGCTTTTACCTCTTTGTAGAGTT 19 4 1 TTTTACCTCT 0.886295 -42 CTTCACAGCCTTCTTCCTTCACAACATCGT 20 63 0 TTCTTCCTTC 0.877156 -238 GATTATACTTATTCTCCTCCGTACTCCACG 20 274 0 ATTCTCCTCC 0.677142 -27 TCGCCCATCCTTCCACCTCCTGTTAGGATT 21 17 0 TTCCACCTCC 0.956688 -99 TCTCTTACCTCCTAACTCTAAA 26 27 0 TCTTACCTCC 0.83468 -12 TTTCATGAATTTTCTACTTCCAAATTCCTG 28 28 1 TTTCTACTTC 0.675014 -78 TTGGTTTACCTCCTGAAGGGTGG 28 93 0 GTTTACCTCC 0.793992 -13 CGCTCTCCTCCGAAAGTAGAG 29 2 1 GCTCTCCTCC 0.639683 -112 ACTTAAAGATTTTACCTCTAGAGATTTAT 29 95 0 TTTTACCTCT 0.886295 -19 TCTTCTCCTCCGCTAAACAAT 31 23 0 CTTCTCCTCC 0.943106 -11 TAATCTTTTCCTTCCCCTCTTTTT 32 5 1 CTTTTCCTTC 0.831514 -296 GGGCACTCTTCTTCTACTTCTCTGACTTCG 32 248 0 CTTCTACTTC 0.547749 -53 TCGCTTCCTCCTTCGGTAAGTAAA 33 5 1 TTCCTCCTTC 0.913723 -48 TTTACACCTCCTGGTTAGTAA 34 2 1 TTACACCTCC 0.522767 -177 TTATTACCTCTGGAGGGTATT 34 168 0 TATTACCTCT 0.617399 -11 TAGTAAGTAATCCTACCTTCGGCGGACTTT 35 34 1 TCCTACCTTC 0.65289 -267 ATATATCCTTCTTCTACTTTACGGTGAACG 35 85 1 CTTCTACTTT 0.348459 -216 TTCTGATTACTTTAACCTCCCTCAGTTCGT 35 112 0 TTTAACCTCC 0.765469 -189 GAGAGTTTATTACTTCCTTTGCGTCAAAAG 35 160 0 TACTTCCTTT 0.394949 -141 CCTATTTATTTTCTAACTTTTTAATGGTTT 35 271 0 TTCTAACTTT 0.324546 -30 CCCATTCACCTCTTCCGAGTTTA 36 33 0 ATTCACCTCT 0.460321 -13 AATTATATCCTTCATCCTTTCCTTGAGAGG 38 275 1 TTCATCCTTT 0.368285 -26 CTCCTTCTTTTCCTTTTCCTTTACAC 39 7 1 CTTTTCCTTT 0.685463 -206 TTTTATACCTCTCCTCTTTTATGTTTC 39 196 0 CCTCTCCTCT 0.676757 -17 CAGTAAAAATCCTTTCCTCCTTTTTCCTTT 40 255 1 CCTTTCCTCC 0.761717 -46 CCTTTCCTCCTTTTTCCTTTTAACCTTTGA 40 265 1 TTTTTCCTTT 0.788909 -36 AGAGATCCAATTTATCCTTCGCCAGAGGC 41 10 0 TTTATCCTTC 0.61012 -291 TTATCATCTATTTTTACTTCTTTCCTGAGG 41 237 0 TTTTTACTTC 0.583402 -64 ********** Masking position 8 Map Score: 38.1603 Number of sites scoring better than the average of aligned sites = 3377 Number in coding regions = 3015 Number in noncoding regions = 362 Number of orfs with sites within 600 bp upstream = 288 Fraction of orfs with sites within 600 bp upstream = 0.0462576 Motif number 2 ATATCATGCTCCTTTGGGACTTGGACTTGCAG 9 18 1 CCTTTGGACT 0.86473 -46 TTCTAATCCCCTTTAAGGAATTTATATTAAA 15 10 1 CCTTTAGGAT 0.970651 -28 CCTTCCACCTCCTGTTAGGATTTACTAA 21 7 0 CCTGTAGGAT 0.905659 -109 GACCAGGAAACCTGTACGGCTTGCGAGCTGTG 32 96 1 CCTGTCGGCT 0.908568 -205 GTCTTCCAGTCCTTCCGGGACTATCATCCAGC 32 217 0 CCTTCGGGAT 0.848223 -84 ACCCTTGCTCCCTTTCGGGCCTGGGGGAGTTC 34 102 0 CCTTTGGGCT 0.987824 -77 AAAGAATGTTCCTTTTCGGCTTTTCTGATTAC 35 132 0 CCTTTCGGCT 0.971619 -169 TGCAATAGAACCTTTAGGGCTTTGAGAGAGTT 35 183 0 CCTTTGGGCT 0.987824 -118 CACACTTTCCTCTTTGAGTATTTTTTCAGTGT 35 214 0 TCTTTAGTAT 0.433345 -87 ATCTCTTACGCCTTTGAGGAATTCTTTTAATT 38 124 0 CCTTTAGGAT 0.970651 -177 CTTCCTTAATTCTTTCGGGCTTATTCTTAAGG 40 14 0 TCTTTGGGCT 0.904058 -287 TCGTAAGGACCCATTAAGGCGTACTGAGCGAG 40 84 0 CCATTAGGCT 0.87331 -217 TACTGCTGTTCCTTTAAGTCCTTAATGAGTGT 40 228 0 CCTTTAGTCT 0.933082 -73 TTCCTTTTAACCTTTGAGTAATATAATATTTT 40 278 1 CCTTTAGTAT 0.86815 -23 ***** **** * Masking position 12 Map Score: 16.053 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 153 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 3 GGTTTCAACTCCACACGGTACATTAGGAACCGTATTTTG 7 34 0 CAGGCAAGAA 0.992781 -267 GGTTTCAACTCCACACGGTACATTAGGAACAAACTATGA 7 108 0 CAGGCAAGAA 0.992781 -193 GTTTCAACTCCACTACGGTACATTAGGAACAAAAGAATC 7 179 0 CAGGCAAGAA 0.992781 -122 TCATTTTTATCCACACGGTACATTAGAAACTGATTTCTT 7 246 0 CAGGCAAGAA 0.992781 -55 CAAACCATCGCTCGAAGGTTGAAAAGAAGCTCTCAATAA 8 46 0 CAGGGAAGAG 0.860554 -255 TTTCTCTCAACCCTATGGCGAGGGAGGAAGTAGGGGAAA 10 169 1 CAGGAGAGAA 0.870013 -61 AATAGGATATCAGAAGGGAGGGAAAGGAAAGAAGGGA 11 9 0 CAGGGGAGAA 0.911917 -33 ACGGCTCTGCCCTGAGGGTCCAGAAGCCCCTCTTTCGGC 16 59 0 CAGGCAAGCC 0.937721 -172 AGTTGTTGAACTCGAAGTTTCAGAAGACACCGATCTCAG 16 152 1 CAGTCAAGCA 0.757119 -79 CCCCCAGGCCCGAAAGGGAGCAAGGGTAAGCCCGCCGTC 34 107 1 CAGGCAGGAA 0.9775 -72 GAACTAAACTCCAGAGGAACCATAAGGACACTCACGATG 40 171 1 CAGACAAGAC 0.773735 -130 TCATTAAGGACTTAAAGGAACAGCAGTAAAAATCCTTTC 40 232 1 CAGGCAAGAA 0.992781 -69 TATTATATTACTCAAAGGTTAAAAGGAAAAAGGAGGAAA 40 267 0 CAGGAAGGAA 0.870013 -34 * * ** ** ** ** Masking position 5 Map Score: 14.998 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 63 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 4 ACTCCACACGGTACATTAGGAACCGTATTTTGA 7 33 0 GTCAAGGAAC 0.972121 -268 AATGTACCGTGTGGAGTTGAAACCTTGCTTTAT 7 49 1 GTGATGAAAC 0.911221 -252 ACTCCACACGGTACATTAGGAACAAACTATGAA 7 107 0 GTCAAGGAAC 0.972121 -194 AATGTACCGTGTGGAGTTGAAACCTCTTGATAG 7 123 1 GTGATGAAAC 0.911221 -178 CTCCACTACGGTACATTAGGAACAAAAGAATCG 7 178 0 GTCAAGGAAC 0.972121 -123 ATGTACCGTAGTGGAGTTGAAACTTCGGTGATA 7 195 1 GTGATGAAAC 0.911221 -106 TATCCACACGGTACATTAGAAACTGATTTCTTT 7 245 0 GTCAAGAAAC 0.962347 -56 TCGCTCGAAGGTTGAAAAGAAGCTCTCAATAAG 8 45 0 GTGAAGAAGC 0.917216 -256 TGGAGTTGATGTGGACGAGAAAATAATCAGGTC 8 194 1 GTGAAGAAAA 0.80382 -107 GCAAGTCCAAGTCCCAAAGGAGCATGATATCGG 9 15 0 GTCCAGGAGC 0.646014 -49 CTATTAACGGGTTGATGAGGTACTTTTCTACAA 16 196 0 GTGAAGGTAC 0.863048 -35 AAAGACCATGGTTGACCAGGAAACCTGTACGGC 32 83 1 GTGAAGGAAA 0.882213 -218 AATCAGAAAAGCCGAAAAGGAACATTCTTTTGA 35 134 1 GCGAAGGAAC 0.904463 -167 TTTTTTCAGTGTGCAATAGAACCTTTAGGGCTT 35 193 0 GTCAAGAACC 0.802185 -108 AATTAAGGAAGTTGACGAGGAACTCTGCAACAA 40 35 1 GTGAAGGAAC 0.985825 -266 ** ** ****** Masking position 9 Map Score: 19.6095 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 5 ACTCCTTACCACTTATATAATAAGTTTAAC 13 16 1 ATATTAATAA 0.937283 -20 AAGTCTAAATTTTAAAGTTAAACTTTTTTCC 14 3 1 GTATTAATAA 0.900331 -31 GGAGGTTTTTATGAAGCTCGTAAGGGTAATAATAATGCC 16 23 1 AAATTAATAA 0.894999 -208 TTTGCAGTTTAACTATTTTTTAAAAGTAATCTTCAGGAG 17 17 0 ATATTAATAA 0.937283 -33 CTCTTTGTAGAGTTAAGTATTAAATTTAATTTAACT 19 20 1 ATATTAATAA 0.937283 -26 TCCTAACTCTAAAAATTTATTAAAGTTAA 26 1 0 AAATTAATAA 0.894991 -38 TCCTTCGGTAAGTAAAATTATAAGGTTAAAATAAAAACT 33 19 1 AAATTAATAA 0.894999 -34 CCCGCCGCAGGGCTAATTAATAAATATAAACCTCGTGAA 34 56 0 GTATTAATAA 0.900328 -123 GATATATAAAGAATAAATACAAAGGCTAAAAGTCCGCCG 35 53 0 GTATAAATAA 0.708364 -248 CCGAGTTTAAAGCAAGATTGTAATTATAACA 36 3 0 AAATTAATAA 0.894999 -43 TATAGCAAGGGAAAATATTATAACACTAATCGTAGCCTT 38 198 0 GAATTAATAA 0.837455 -103 AACGCTCTGTACGTAAATGGAAACATTAATCTTCTTACC 39 55 1 ATATAAATAA 0.800734 -158 ATCCCCATTAACTGATCTTTTAAATTTAAACCAAAAAAG 39 130 0 AGATTAATAA 0.757085 -83 AAAGAAGTAAAAATAGATGATAACTCTATTATCCAATAT 41 244 1 ATATTAATAT 0.577718 -57 TATGAGAATAATATAGGTGAAAAACTTAATATTGGATAA 41 272 0 ATATAAATAA 0.800734 -29 * ** * *** *** Masking position 12 Map Score: 11.3037 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 36 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 AGCATGGAATTTATAACCCTCTGGGTGATTTTTA 8 256 1 TTAAACCTCG 0.983555 -45 GAGAATTTTTTCAAAATCCTCCATATGT 10 5 0 TCAAACCTCT 0.963903 -225 TACGAGCTTCATAAAAACCTCCTTCCCTTAAATT 16 11 0 ATAAACCTCT 0.912475 -220 TCTCGTAATCCTCTATTAACGGGTTG 16 215 0 TCGAACCTCT 0.919883 -16 TAACACCCGGTTACAAACCTCAGTATCCGTACGT 20 99 1 TTAAACCTCT 0.974029 -202 TTGATTTTTGTTATAAATCTCTAGAGGTAAAATC 29 83 1 TTAAATCTCG 0.839363 -31 TCCCCTGTTCTTGTAAACCTCGGGAACTCTATCG 32 131 0 TTGAACCTCG 0.96257 -170 TAATTAATAAATATAAACCTCGTGAAATTTCCTG 34 48 0 ATAAACCTCG 0.943263 -131 AAGTACGGAATCAAAATCCTCGCTCAGTACGCCT 40 66 1 TCAAACCTCT 0.963903 -235 AAATAAACAATTAAAAGCCTCAGGAAAGAAGTAA 41 220 1 TTAAACCTCG 0.983555 -81 *** ** **** * Masking position 6 Map Score: 9.13179 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 77 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 7 GTTGAAAAAGGCAAGGACTTAGGTTATACTAAG 1 12 1 GCAAGTTAGG 0.877759 -49 GACGAAGTTCGGATGCGGTAAGGGAATATGCGG 5 26 1 GGATGTAAGG 0.961414 -275 CTTCAAAAGAGGAAATAGTAAGTGTCATGTCTT 5 271 1 GGAAATAAGT 0.775005 -30 ATATATAGATGGATGAATAAAGGGAGGTGAAAC 6 12 0 GGATGAAAGG 0.879401 -34 GTGGAAGGAGAAAGTGGTGTATGGC 8 3 1 GGAAGAAAGT 0.776091 -298 AGGAAGTAGGGGAAATCCTTAGGGACTTTCTCT 10 193 1 GGAAATTAGG 0.906693 -37 AGGGAATAGGATATCAGAAGGGAGGGAAAGG 11 21 0 GGATAGAAGG 0.695994 -21 AAATTCCTGTGGAAGGATTTAGGATTTATTTTC 28 49 1 GGAAGTTAGG 0.97094 -57 CGGATAAGGAAAATTTAAGGAAAAGAGAGG 30 13 0 GGAAATAAGG 0.953911 -20 GTTTCATCAAGGATGGATTTAGCTTTCTCCACA 35 242 0 GGATGTTAGC 0.533139 -59 TAAAAAGTTAGAAAATAAATAGGAGGGGCTTGA 35 278 1 GAAAAATAGG 0.424373 -23 TATACCTCTGGAAAGTTTTAAGTGGCGGGGCTG 38 77 0 GAAAGTAAGT 0.754313 -224 CCCTCTCAAGGAAAGGATGAAGGATATAATTTT 38 273 0 GAAAGGAAGG 0.853551 -28 GAATAAGCCCGAAAGAATTAAGGAAGTTGACGA 40 20 1 GAAAGTAAGG 0.948581 -281 ACAACGTTCAGGAAGTCGTAAGGACCCATTAAG 40 98 0 GGAAGTAAGG 0.986143 -203 TTGTTTATTTGCAAGAAATAAGGCAGCCCCACC 41 197 0 GCAAGTAAGG 0.938629 -104 ***** ***** Masking position 3 Map Score: 11.3541 Number of sites scoring better than the average of aligned sites = 521 Number in coding regions = 492 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 CAACTCCACACGGTACATTAGGAACCGTAT 7 38 0 CGGTACATTA 0.988848 -263 CAACTCCACACGGTACATTAGGAACAAACT 7 112 0 CGGTACATTA 0.988848 -189 AACTCCACTACGGTACATTAGGAACAAAAG 7 183 0 CGGTACATTA 0.988848 -118 TTTATCCACACGGTACATTAGAAACTGATT 7 250 0 CGGTACATTA 0.988848 -51 ********** Masking position 5 Map Score: 6.14449 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 ACGTAAGGCACCTGCCCTACTACCTTTGCAG 10 58 1 CCTGCCCTCT 0.786761 -172 AGGAGGTAGAGAAGTTCCTCCACCTTTTTGA 10 139 0 GAAGTTCCCC 0.387408 -91 TCCCCTACTTCCTCCCTCGCCATAGGGTTGA 10 175 0 CCTCCCTCCC 0.697702 -55 TCCCTTCTTTCCTTTCCCTCCCTTCTGATAT 11 11 1 CCTTTCCCCC 0.870253 -31 TGAGGGTCCAGAAGCCCCTCTTTCGGCATTA 16 55 0 GAAGCCCCCT 0.857799 -176 TAATCTTTTCCTTCCCCTCTTTTTCATAAA 32 10 1 CCTTCCCCCT 0.821127 -291 ACTTCGTCTTCCAGTCCTTCCGGGACTATCA 32 223 0 CCAGTCCTCC 0.881253 -78 GGGAGTTCACCCTGTCCCGCCGCAGGGCTAA 34 79 0 CCTGTCCCCC 0.974874 -100 TCAAGCCCCTCCTATTTATTTT 35 289 0 CAAGCCCCCC 0.981622 -12 GGGAGGACTCGAACCCCCACCCACGGGATTT 38 47 0 GAACCCCCCC 0.87962 -254 TCGAGTCCTCCCAGCCCCGCCACTTAAAACT 38 66 1 CCAGCCCCCC 0.993998 -235 AAGAAATAAGGCAGCCCCACCTAATACTACA 41 187 0 GCAGCCCCCC 0.988334 -114 ******** ** Masking position 10 Map Score: 8.53991 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 148 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 10 TTCGGATTTTTACTCAGAAGTGCATAGGCTTC 5 237 0 TCTCAGAAGG 0.88181 -64 GGGAGCGTAGAACTCAAAAAGGTGGAGGAACT 10 126 1 ACTCAAAAAG 0.836595 -104 TAATATAAATTCCTTAAAGGGGATTAGAA 15 8 0 TCTTAAAGGG 0.906235 -30 TTCTATCTTCTTCTCAAAAAGGTCTCCGTCTC 20 153 0 TCTCAAAAAG 0.958072 -148 CCACCCGAAATACTCAAAAAAGACATTAAAGA 20 188 1 TCTCAAAAAG 0.958072 -113 TCTTTTTTCTTTTTCAAAGGAGGTCTGAGCCA 32 41 1 TTTCAAAGGG 0.833089 -260 ACTGAAAAAATACTCAAAGAGGAAAGTGTGGA 35 216 1 TCTCAAAGAG 0.973386 -85 TTAAAAGAATTCCTCAAAGGCGTAAGAGATGA 38 126 1 TCTCAAAGGG 0.985828 -175 GTAAGAGATGAACTCAAAAGGGTAGTTTGGCC 38 147 1 ACTCAAAAGG 0.90687 -154 TCTTTTATGTTTCTTAAAGAAGGCGGAATGAA 39 177 0 TCTTAAAGAG 0.835569 -36 AACGACACTATACTCAAAATGGCAATTGAACT 40 144 1 TCTCAAAATG 0.849337 -157 AATATTATATTACTCAAAGGTTAAAAGGAAAA 40 276 0 TCTCAAAGGT 0.833088 -25 * ******** * Masking position 6 Map Score: 9.41667 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 155 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 TCAATTCTAAGAAAAGACGGAGGTATATGG 4 35 1 GAAAAGACGG 0.854181 -24 GTGGAAGGAGAAAGTGGTGTA 8 2 1 TGGAAGGAGA 0.578568 -299 CTCGAAGGTTGAAAAGAAGCTCTCAATAAG 8 45 0 GAAAAGAAGC 0.711154 -256 GGGAGGGAAAGGAAAGAAGGGA 11 3 0 GGAAAGAAGG 0.936825 -39 AATTTAAGGGAAGGAGGTTTTTATGAA 16 8 1 GGGAAGGAGG 0.903844 -223 GATGTTGTGAAGGAAGAAGGCTGTGAAGTT 20 65 1 AGGAAGAAGG 0.738634 -236 AGACCTTTTTGAGAAGAAGATAGAAATACC 20 160 1 GAGAAGAAGA 0.935789 -141 AAGAAGCTTTGAGAATACGGGTATTAACGC 21 84 0 GAGAATACGG 0.441854 -32 GGCTTAAGCGGGAAGAAGCTTTGAGAATA 21 97 0 GGGAAGAAGC 0.919827 -19 TTGTTTAGCGGAGGAGAAGA 31 24 1 GAGGAGAAGA 0.761495 -10 TACAAGAACAGGGGAGACGGAATAGCGGAT 32 150 1 GGGGAGACGG 0.856738 -151 AAGTGTGACATAAAAGACGAGGAAGATCAC 32 186 1 TAAAAGACGA 0.461075 -115 CCGGAAGGACTGGAAGACGAAGTCAGAGAA 32 231 1 TGGAAGACGA 0.799471 -70 GTCAGAGAAGTAGAAGAAGAGTGCCCCAGC 32 252 1 TAGAAGAAGA 0.79554 -49 CACCGTAAAGTAGAAGAAGGATATATAAAG 35 81 0 TAGAAGAAGG 0.876735 -220 AAAGGAAAAGGAAAAGAAGGAG 39 3 0 GAAAAGAAGG 0.902032 -210 TTCCCTAACCGGTAAGAAGATTAATGTTTC 39 74 0 GGTAAGAAGA 0.627441 -139 AAAAGCCTCAGGAAAGAAGTAAAAATAGAT 41 232 1 GGAAAGAAGT 0.592461 -69 ********** Masking position 5 Map Score: 11.0335 Number of sites scoring better than the average of aligned sites = 872 Number in coding regions = 828 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 12 TTATTATATTAAAATCTTTTAAC 2 32 1 AAAATCTTTT 0.709463 -13 AAATTCCTTATAATATTTAT 4 1 1 AAATTCCTTA 0.931454 -58 TTTGTGTTTAAAATTCTTTAGAA 7 288 1 AAATTCTTTA 0.860156 -13 CGTAAACTCCTTACCACTTATAT 13 4 1 AAACTCCTTA 0.760475 -32 AGTTTAATATAAATTCCTTAAAGGGGATTA 15 14 0 AAATTCCTTA 0.931454 -24 AACTTCTTTTTTCTCCTCTT 18 80 0 AACTTCTTTT 0.680686 -10 CAAAGGTTACAAATTCCTTTATTTCTTTAA 20 213 0 AAATTCCTTT 0.931449 -88 GAAATAAAATAAATTCTTTTGAGTG 27 52 1 AAATTCTTTT 0.860109 -15 TTCTACTTCCAAATTCCTGTGGAAGGATTT 28 39 1 AAATTCCTGT 0.69995 -67 CTCTAGAGGTAAAATCTTTAAGT 29 101 1 AAAATCTTTA 0.710127 -13 GTTCCTCGTCAACTTCCTTAATTCTTTCGG 40 28 0 AACTTCCTTA 0.824853 -273 AACAGCAGTAAAAATCCTTTCCTCCTTTTT 40 250 1 AAAATCCTTT 0.843981 -51 ********** Masking position 2 Map Score: 8.98207 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 151 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 ACAAATAATCATTTTTATCCACACGGTACA 7 263 0 ATTTTTATCC 0.54483 -38 CACGATTAAAAATTTTATCCCTTTCGGTTA 12 15 1 AATTTTATCC 0.904035 -85 TTAAAGTTAAACTTTTTTCCTG 14 22 1 ACTTTTTTCC 0.7381 -12 TAGTTAGCTTAATTATATCCGATGAAGAGG 18 56 1 AATTATATCC 0.831697 -34 AGTAGAGTGTAATTTTATTCATTTTGAAGA 29 25 1 AATTTTATTC 0.382902 -89 TAATCTTTTCCTTCCCCTCTT 32 2 1 AATCTTTTCC 0.883787 -299 TTAGTGTTATAATATTTTCCCTTGCTATAG 38 208 1 AATATTTTCC 0.719864 -93 CTTTTACTAAAATTATATCCTTCATCCTTT 38 265 1 AATTATATCC 0.831697 -36 TTATATCCTTCATCCTTTCCTTGAGAGGGA 38 277 1 CATCCTTTCC 0.565126 -24 GGAATGAAGCAATAATATCCCCATTAACTG 39 155 0 AATAATATCC 0.609618 -58 CAGCAGTAAAAATCCTTTCCTCCTTTTTCC 40 252 1 AATCCTTTCC 0.891765 -49 AGCAATAATAAATCCTATCCCCAGTATAGA 41 39 0 AATCCTATCC 0.905168 -262 ATCTATTTTTACTTCTTTCCTGAGGCTTTT 41 232 0 ACTTCTTTCC 0.753289 -69 ********** Masking position 6 Map Score: 2.42879 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 180 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 GAGCTGTCAGTACCCAGTCAAGGAAGCGGAAT 5 95 1 TACCCAGCAG 0.459719 -206 AGTGCGGATACTGCCAGCCCGGACAAATAGTG 5 205 1 CTGCCAGCCG 0.937738 -96 CTGTTATGATCTCCCTGACCTGATTATTTTCT 8 211 0 CTCCCTGCCG 0.993517 -90 CCCCTACTTCCTCCCTCGCCATAGGGTTGAGA 10 173 0 CTCCCTCCCT 0.861556 -57 TCAAAAAGGTCTCCGTCTCCAGTTTTGTAAAC 20 140 0 CTCCGTCCCG 0.910929 -161 TGGGGGAGTTCACCCTGTCCCGCCGCAGGGCT 34 81 0 CACCCTGCCG 0.977065 -98 AGGGTGAACTCCCCCAGGCCCGAAAGGGAGCA 34 97 1 CCCCCAGCCG 0.967879 -82 GAGCGCGGGACTCCAAATCCCGTGGGTGGGGG 38 33 1 CTCCAAACCG 0.720451 -268 GGTTCGAGTCCTCCCAGCCCCGCCACTTAAAA 38 63 1 CTCCCAGCCG 0.992306 -238 AGGCTCCCTCTCAAGGAAAGGATGA 38 286 0 CTCCCTCCAG 0.924057 -15 CCTTTTTCAATTCCCTAACCGGTAAGAAGATT 39 82 0 TTCCCTACCG 0.843758 -131 ******* ** * Masking position 4 Map Score: 7.3332 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 95 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 TTCTTTTGTGAAAAATGCTCCTTTATCACCG 7 220 0 AAAAATCTCC 0.943147 -81 TTTGCTCACTACATACTCTCCAAACCATCGC 8 74 0 ACATACCTCC 0.927519 -227 AGAATTTTTTCAAAATCCTCCATATGT 10 7 0 CAAAATCTCC 0.775766 -223 AGGATTTTGAAAAAATTCTCCTGGAACTTGA 10 19 1 AAAAATCTCC 0.943147 -211 CTTTGCAGGGACATACTCTCCGAGGTCAAGT 10 81 1 ACATACCTCC 0.927519 -149 GAAAGATTATACTTATTCTCCTCCGTACTCC 20 277 0 ACTTATCTCC 0.833224 -24 TAACAAGTTTAAATATACACCTTTT 22 5 0 AAATATCACC 0.700082 -23 GTCCTAAAACAAATACCCTCCAGAGGTAATA 34 157 1 AAATACCTCC 0.921945 -22 TGCACACTGAAAAAATACTCAAAGAGGAAAG 35 211 1 AAAAATCTCA 0.591728 -90 AGTTTGTTATACTAATTCTCCAA 37 12 1 ACTAATCTCC 0.833224 -13 ****** **** Masking position 5 Map Score: 3.41667 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 58 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678