AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_pyro_reg_100.orf -o00230_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 PH0021 214 611aa long hypothetical protein #2 PH0112 300 855aa long hypothetical replication factor C subunit #3 PH0124 300 437aa long hypothetical protein #4 PH0239_PH0240 56 PH0239: 238aa long hypothetical phosphoribosylaminoimidazole-succinocarboxamide synthase, PH0240: 449aa long hypothetical amidophosphoribosyltransferase #5 PH0307 112 486aa long hypothetical inosine-5'-monophosphate dehydrogenase #6 PH0316 300 334aa long hypothetical phosphoribosylformylglycinamide cyclo-ligase #7 PH0320 88 177aa long hypothetical phosphoribosylaminoimidazole carboxylase catalytic subunit #8 PH0322_PH0323 157 PH0322: 219aa long hypothetical protein, PH0323: 438aa long hypothetical phosphoribosylamide--glycine ligase #9 PH0437 263 367aa long hypothetical protein #10 PH0438 58 339aa long hypothetical adenylosuccinate synthetase #11 PH0698 216 160aa long hypothetical nucleoside-diphosphate kinase #12 PH1014 60 181aa long hypothetical 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #13 PH1348 131 333aa long hypothetical protein #14 PHS044 244 82aa long hypothetical DNA-directed RNA polymerase subunit Hprotein #15 PH1598 94 503aa long hypothetical pyrimidine-nucleoside phosphorylase #16 PH1637 26 261aa long hypothetical DNA-directed RNA polymerase subunit D #17 PH1753 77 196aa long hypothetical adenylate kinase #18 PH1754 33 468aa long hypothetical preprotein translocase secY subunit #19 PH1907 96 178aa long hypothetical inorganic pyrophosphatase #20 PH1908 40 188aa long hypothetical DNA-directed RNA polymerase subunit E #21 PH1922 46 118aa long hypothetical protein #22 PH1953 110 705aa long hypothetical phosphoribosylformylglycinamidine synthase II #23 PH1955 299 227aa long hypothetical phosphoribosylformylglycinamidine synthase I Motif number 1 GATATTTTTCATTTTTTGGACATGCATTTGTCAAATAAA 3 118 1 ATTTTAATTT 0.969911 -183 TACTTTTAAGATTTTTTAGACATATATCTGGCAAAAG 4 9 0 ATTTTAATTT 0.969911 -48 ATGGGAAGGTAAAATTTAAATATACATTTTTACACAATC 5 22 0 AATTTAATTT 0.966782 -91 TATAAGTAGTAATATTTATATATTCCCATATTTTATTTT 6 25 0 AATTTAATCT 0.928559 -276 TTTTCGTAGGATTTTTTATTTATAATTATTAAAATCCGA 6 87 1 ATTTTTATTT 0.697535 -214 TCTACACTACATAATATAAAAATGATTGTTTGTGTTCTT 6 167 0 AATATAATTT 0.675594 -134 TATCTCACCTAGAATTGATAAATTTATGTGTACTTAAAA 6 272 0 AATTGAATTT 0.755298 -29 AGTTTCTTCGAATATTTCTACATATATGTG 7 2 0 AATTTAATTT 0.966786 -87 ATTCGAAGAAACTTTTTAAATATTGACATTAAATTGCTA 7 28 1 ATTTTAATCT 0.935038 -61 TTAATACCTTATAATTTTGACTTAAATATGGTGATATAA 8 12 0 AATTTATTTT 0.675172 -146 AAACTGATTTATATTTTCAAAATGTATCTTTAACCAGGT 8 120 1 ATTTTAATTT 0.969911 -38 TAAAAATTGGCAATTTTTAAGATTTATTTTACCATATTC 13 81 0 CTTTTAATTT 0.911399 -51 TAAAAATTGCCAATTTTTAACATGAACATGGTGATATCA 13 101 1 CTTTTAATCT 0.821211 -31 GCCCCCCAAAAGTTTTTTAAGATGAACATCATCTACACT 14 208 0 ATTTTAATCT 0.935038 -37 ACAACCCTGAAAGTGTTTAAAATTATTATCCTTCAGAAT 17 32 0 ATGTTAATTT 0.773647 -46 TAAAAATTTTAAATTTTTAAGATTTATTTTGACAAAGAA 22 52 0 ATTTTAATTT 0.96991 -59 TTAAAAATTTAAAATTTTTACATTTTTCTGGCAAATAAG 22 71 1 AATTTAATTT 0.966786 -40 ATTTAAAAGGATTATTTTAACATTTTTATGTTAA 23 6 0 AATTTAATTT 0.966786 -294 TTTTAAATTTCCAATTTTTACATCTTTTTGGTAATGGAA 23 37 1 CATTTAATTT 0.902807 -263 * **** * ** * * Masking position 13 Map Score: 22.607 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 32 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 2 TGAATTCCAGAACCTTTGAGAGGTAAGCTGGAT 2 20 0 ATTTGAGAGG 0.951254 -281 AAAGGATAAAAACTGTTGAGGTGAGAATTAGGT 3 154 1 AGTTGAGGTG 0.849207 -147 TTTTTTATGAACTAATTGAGGGGTATAAAAAAC 5 71 0 AATTGAGGGG 0.952521 -42 TCTTCACCTAATATTTTGAGGAGATCCCTGGTA 9 35 0 ATTTGAGGAG 0.967898 -229 TATTAGGTGAAGAGTTTGAGAAGAGAATTAAGG 9 55 1 ATTTGAGAAG 0.898378 -209 CTCCAATCGAAAAGTATGAGGAGTATTATGTGA 9 91 1 ATATGAGGAG 0.683257 -173 CAATAATCTTAGCGTTAGAGGTGGTCTTTATCT 11 22 1 ATTAGAGGTG 0.899736 -195 CCCCTGTGCCACCTATAAAGGAGGTAGTTCTGA 11 80 0 AATAAAGGAG 0.419139 -137 GAACAAAGGGAGTCTTTGAGGGTAGGGGTAATC 11 112 0 ATTTGAGGGT 0.746178 -105 AACTTACTTAAACCTTCAAGGGGAAGATAATAG 11 192 1 ATTCAAGGGG 0.756212 -25 GCAACTTTATAAACATTGAGAAGGTTTACTGAA 12 26 1 AATTGAGAAG 0.726971 -35 CATCTTAAAAAACTTTTGGGGGGCAATTCTCC 14 223 1 ATTTGGGGGG 0.980599 -22 TAGAAACTGGACACTTTAAGATGATCGATATTT 15 28 1 ATTTAAGATG 0.817241 -67 CGCATTAATTAAGTATTGAGGTGTTGAAAGA 15 74 1 AATTGAGGTG 0.925933 -21 TCAGGGTTGTAAGATTAGGGGTGAAGA 17 61 1 ATTAGGGGTG 0.871944 -17 CCTAAAAAATAAATTTTAGGAGG 18 1 0 ATTTAGGAGG 0.844883 -33 CCTAAAATTTATTTTTTAGGGTGTTGAGTC 18 14 1 ATTTAGGGTG 0.920481 -20 TTATTTCTTAAGTTTTTAGGAGGGATTCCAGGA 20 18 1 ATTTAGGAGG 0.844883 -23 TTCAGTTGATAGGATTTAGGGTGAGTGATTGAC 22 17 1 ATTTAGGGTG 0.920481 -94 * ********* Masking position 1 Map Score: 15.6708 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 397 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 90 Fraction of orfs with sites within 600 bp upstream = 0.0144555 Motif number 3 AAAATATAACTGCAATTTTTAGAATTTTGACTAAATATT 1 86 1 TTTTATTTTG 0.938707 -129 ACTTTCACCTCTTGGATATTTTGTCCAACTTGG 1 192 0 TTTGATTTTG 0.792708 -23 TCCTACTTTCTCCTTCCCTTCTCATTTTTATATAGAACC 2 185 0 TCTTATTTTT 0.962651 -116 GAAGATTATATGAGATATTTTTCATTTTTTGGACATGCA 3 105 1 TTTTATTTTT 0.953391 -196 GTAAAAATCATAATACTTTTAAGATTTTTTAGACATATA 4 22 0 TTTTATTTTT 0.953391 -35 ATAAATCTTTTTCTTTTCGTAGGATTTTTTATTTATAAT 6 74 1 TCGTATTTTT 0.765735 -227 TTTTGTTCACTCTTTTACTTTGGCTTTTTTCGTTTGAAT 6 130 0 TCTTCTTTTT 0.865516 -171 ACAAAAACCATTAATACCTTATAATTTTGACTTAAATAT 8 22 0 TCTTATTTTG 0.950733 -136 AGGGGTACCTTAAAATGCTTACCCTTTTGACAGGG 10 7 0 TCTTCTTTTG 0.82813 -52 AAAATAAATCTTAAAAATTGCCAATTTTTAACATGAACA 13 90 1 TTTGATTTTT 0.83627 -42 CTCTTCATTTTCCCATTTTGGAGGAA 16 2 1 TTTTATTTTG 0.938707 -25 TGTTTAAAATTATTATCCTTCAGAATTTTAATAAAAAGG 17 19 0 TCTTAATTTT 0.806227 -59 TACATGGCTTTATAATACTTTTAAATTTTTAGCTCTTCC 19 23 0 TCTTAATTTT 0.806227 -74 AAAATAAATCTTAAAAATTTAAAATTTTTACATTTTTCT 22 61 1 TTTTATTTTT 0.953391 -50 AAATTTAAAAGGATTATTTTAACATTTTTATGTTAA 23 8 0 GTTTATTTTT 0.721765 -292 AAAATAATCCTTTTAAATTTCCAATTTTTACATCTTTTT 23 27 1 TTTTATTTTT 0.953391 -273 * *** ****** Masking position 16 Map Score: 12.7319 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 52 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 4 TTTCCTACTTTCTCCTTCCCTTCTCATTTTTA 2 194 0 TTCCTTCCCT 0.848214 -107 AGAAGCTACATAATTTTCCAGGAGAAGCAGGG 3 69 0 TATTTTCCAG 0.696845 -232 ATATCTCATATAATCTTCCAATAGAAGCTACA 3 91 0 TATCTTCCAT 0.955419 -210 GAGAATTAGGTTGCTTTCCAATGGTTCCAATG 3 176 1 TGCTTTCCAT 0.835479 -125 AATTTGACAATAACGTTCCAATTTCAAAAGCT 3 220 1 TACGTTCCAT 0.901012 -81 TATTTAAATTTTACCTTCCCATAGGTCGACAA 5 39 1 TACCTTCCCT 0.979694 -74 AGGTACCCCTTTACTTACCCTTTGGTAAGGAG 10 36 1 TACTTACCCT 0.762347 -23 AGTAAGTTCCTAACCTTCCATAATAAGAATAC 11 168 0 TACCTTCCAA 0.845775 -49 CCCTATTATCTTCCCCTTGAAGGTTTA 11 200 0 TATCTTCCCT 0.956214 -17 CTCTTCATTTTCCCATTTTGGAGGAA 16 5 1 TATTTTCCCT 0.931714 -22 ATAATCCTTTTAAATTTCCAATTTTTACATCT 23 30 1 TAATTTCCAT 0.767623 -270 ACCTTCCACTTCATTTTCCATTACCAAAAAGA 23 59 0 TATTTTCCAT 0.930507 -241 ACGAGAACCCTAACCTTCCACTTCATTTTCCA 23 71 0 TACCTTCCAT 0.979316 -229 * ******** * Masking position 6 Map Score: 10.4436 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 156 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 5 TTAGTCAAAATTCTAAAAATTGCAGTTATA 1 90 0 TTCTAAAAAT 0.530838 -125 ATGCCATAAATCCTAAAAGCCTTGAATCTG 1 156 1 TCCTAAAAGC 0.760762 -59 TCTCCAGCCCACCTAAACACTTCTAATATG 2 243 0 ACCTAAACAC 0.544676 -58 CAAATGCATGTCCAAAAAATGAAAAATATC 3 118 0 TCCAAAAAAT 0.620108 -183 GTCTAAAAAATCTTAAAAGTATTATGATTT 4 27 1 TCTTAAAAGT 0.713988 -30 ATTTATGTGTACTTAAAAACGTTGGTTTTA 6 260 0 ACTTAAAAAC 0.842034 -41 TATAATTTTGACTTAAATATGGTGATATAA 8 12 0 ACTTAAATAT 0.388034 -146 ACCAGGGATCTCCTCAAAATATTAGGTGAA 9 36 1 TCCTCAAAAT 0.719027 -228 GTAAAGGGGTACCTTAAAATGCTTACCCTT 10 20 0 ACCTTAAAAT 0.559137 -39 TTCAATGAGAACTTAAAAACCAAGCTATTC 13 25 1 ACTTAAAAAC 0.842034 -107 GTAAAATAAATCTTAAAAATTGCCAATTTT 13 88 1 TCTTAAAAAT 0.919368 -44 ACCATGTTCATGTTAAAAATTGGCAATTTT 13 103 0 TGTTAAAAAT 0.606694 -29 ATGATGTTCATCTTAAAAAACTTTTGGGGG 14 215 1 TCTTAAAAAA 0.52882 -30 GCGAAGAGAAACCTAAAAATATCGATCATC 15 47 0 ACCTAAAAAT 0.943703 -48 CCTCCTAAAATTTATTTTTTAG 18 3 1 TCCTAAAATT 0.646953 -31 AAGTGGGAAGAGCTAAAAATTTAAAAGTAT 19 18 1 AGCTAAAAAT 0.693961 -79 CTGGAATCCCTCCTAAAAACTTAAGAAATA 20 19 0 TCCTAAAAAC 0.935547 -22 TCAAAATAAATCTTAAAAATTTAAAATTTT 22 59 1 TCTTAAAAAT 0.919368 -52 TTAACATAAAAATGTTAAAATAA 23 4 1 ACATAAAAAT 0.569117 -296 ********** Masking position 6 Map Score: 8.76575 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 213 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 88 Fraction of orfs with sites within 600 bp upstream = 0.0141343 Motif number 6 TAGGGCCAAGGAAAAGCTAATACTAATAGCA 2 87 1 GAAAGCTAAT 0.863169 -214 CGAAGGATTTGGAAACCTTCGAGATACTAAG 2 143 1 GAAACCTTCG 0.936779 -158 TCTTCATGTCGTAAAGCTTCTTAGGCGCTTC 9 143 0 GAAAGCTTCT 0.973414 -121 GCTATTGAGAGCAAACCTTATATTATATACC 9 216 1 GAAACCTTAT 0.975554 -48 ACCAATTTCAGTAAACCTTCTCAATGTTTAT 12 34 0 GAAACCTTCT 0.97963 -27 TGTGAGTACCGAAAACCTTATATATCATCTG 14 11 1 GAAACCTTAT 0.975554 -234 TAAGCACAGAGTAAAGCTTATATATCAGAAT 14 167 1 GAAAGCTTAT 0.968082 -78 * ********* Masking position 5 Map Score: 6.61741 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 58 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 ATATAAAAATGAGAAGGGAAGGAGAAAGTA 2 191 1 GAGAAGGGAA 0.922977 -110 AAAAACTGTTGAGGTGAGAATTAGGTTGCT 3 161 1 GAGGTGAGAA 0.905604 -140 AAAGGGTGAGGAGGAGAGGAAG 5 101 1 GAGGAGAGGA 0.9616 -12 TATGTCGATAAGAAGAGAAATCTCTACCA 9 10 1 AAGAAGAGAA 0.898826 -254 TGAAGAGTTTGAGAAGAGAATTAAGGAGAC 9 62 1 GAGAAGAGAA 0.978316 -202 GTGAAGGCTAGAGAAGCGGAGTGGAAGCGC 9 120 1 GAGAAGCGGA 0.908124 -144 CTTAATTAATGCGAAGAGAAACCTAAAAAT 15 57 0 GCGAAGAGAA 0.913353 -38 AACCAAAATTGAGTAGAGAAAAAGCAAGTA 21 27 0 GAGTAGAGAA 0.95152 -20 CTTGGGTATAAAGTTGAGGATCTAAGGGTG 23 164 1 AAGTTGAGGA 0.501836 -136 ********** Masking position 10 Map Score: 6.30829 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 273 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ACTTGGAGATAGCAGATTCAAGGCTTTTAGGAT 1 165 0 AGAGTTCAGG 0.832943 -50 CGTCGCCGGTAGTAGGGCCAAGGAAAAGCTAAT 2 75 1 AGAGGCCAGG 0.955291 -226 TTAAATTGCTAGGGTATCCCAGGGATAGCTAGA 7 56 1 AGGTTCCCGG 0.944075 -33 TAATATTTTGAGGAGATCCCTGGTAGAGATTTC 9 27 0 AGAGTCCCGG 0.989616 -237 AAGAATCTTCGGCGGTGCCCCGGTGGCTCAGCC 14 48 1 GGGGGCCCGG 0.993162 -197 CTTGGTAAGCGGCAGGTCCCGGGTTCAAAGCCC 14 95 1 GGAGTCCCGG 0.989408 -150 GATTTATTAGAATGGAGCCCCGGCCGGGCTTTG 14 120 0 AAGGGCCCGG 0.971338 -125 AAGTTTTTAGGAGGGATTCCAGGA 20 27 1 GAGGTTCCGG 0.885735 -14 ** ** **** ** Masking position 9 Map Score: 4.04107 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 123 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 9 ACTTTCTCCTTCCCTTCTCATTTTTATATA 2 190 0 TCCCTTCTCA 0.971718 -111 GCAACCTAATTCTCACCTCAACAGTTTTTA 3 160 0 TCTCACCTCA 0.897833 -141 GGTAGAGATTTCTCTTCTTATCGACATA 9 9 0 TCTCTTCTTA 0.887626 -255 TCTCCTTAATTCTCTTCTCAAACTCTTCAC 9 61 0 TCTCTTCTCA 0.980791 -203 TTTTTAGGTTTCTCTTCGCATTAATTAAGT 15 58 1 TCTCTTCGCA 0.940158 -37 TCCTGGAATCCCTCCTAAAAACTTAAGA 20 23 0 TCCCTCCTAA 0.815038 -18 ACTTGCTTTTTCTCTACTCAATTTTGGTT 21 28 1 TCTCTACTCA 0.939463 -19 ********** Masking position 10 Map Score: 3.7933 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 81 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 TTTATGGCATGAGGGCTTGAGAATTGGATA 1 136 0 GAGGGCTTGA 0.956862 -79 CCTTTGAGAGGTAAGCTGGATCGCTGGATG 2 11 0 GTAAGCTGGA 0.926993 -290 ATCCTTCGCAGAAAGCGTGAACAAATTCTT 2 121 0 GAAAGCGTGA 0.79944 -180 AAGTGTTTAGGTGGGCTGGAGAGTAAGGCT 2 251 1 GTGGGCTGGA 0.956028 -50 CACAATCATAGAAGGCTGGACTATATTCTA 6 202 0 GAAGGCTGGA 0.983682 -99 GTATCCCAGGGATAGCTAGAAATCTCAAAT 7 69 1 GATAGCTAGA 0.79746 -20 AGTATTATGTGAAGGCTAGAGAAGCGGAGT 9 112 1 GAAGGCTAGA 0.963971 -152 ********** Masking position 10 Map Score: 2.30775 Number of sites scoring better than the average of aligned sites = 130 Number in coding regions = 121 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 CAATTAGTTCATAAAAAAGGGTGAGGAGGAGAGG 5 86 1 ATAAAAGTGA 0.9573 -27 ATCCTACGAAAAGAAAAAGATTTATTAACTCAAT 6 65 0 AAAAAAGTTA 0.816964 -236 AAAAAAGCCAAAGTAAAAGAGTGAACAAAAGAAC 6 139 1 AAAAAAGTGA 0.9573 -162 GGAGACTCCAATCGAAAAGTATGAGGAGTATTAT 9 86 1 ATAAAAGTGA 0.9573 -178 AAATCCCTGCAATGAATAGAATGGCTATTGAGAG 9 193 1 AAAATAGTGG 0.659403 -71 TAGTTCTGATAAAGAAAAGCATAAGTAAACCAGG 11 55 0 AAAAAAGTAA 0.63853 -162 TTAAGTTCTCATTGAAATGTTGGAACGGGG 13 7 0 ATAAATGGGA 0.618359 -125 TAGTTTTAGCATCGAATAGCTTGGTTTTTAAGTT 13 34 0 ATAATAGTGG 0.659403 -98 TATATATCAGAATCAAAAGGCGGAGTGTAGATGA 14 185 1 AAAAAAGGGA 0.942734 -60 TCAGAATTTTAATAAAAAGGAAGAAAAT 17 5 0 AAAAAAGAGA 0.759302 -73 GAAGAAAAAGTGGGAAGAGCTAAAA 19 2 1 AAAAAAGGGA 0.942734 -95 AGAGCTAAAAATTTAAAAGTATTATAAAGCCATG 19 26 1 ATAAAAGTTA 0.816964 -71 TTGAGATAGAATTCAAAAGGAGGGGGTATGA 19 76 1 ATAAAAGGGG 0.883393 -21 AAAATTGGAAATTTAAAAGGATTATTTTAACATT 23 21 0 ATAAAAGTTA 0.816964 -279 ** ***** *** Masking position 6 Map Score: 9.46712 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 179 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 12 TTTTATATAGAACCTCTTCCATGGCCTTAGTA 2 167 0 AACCTCTCCT 0.806613 -134 AAGTTTTTTATACCCCTCAATTAGTTCATAAA 5 69 1 TACCCCTAAT 0.943427 -44 GGAAGCACTAAATCCCTGCAATGAATAGAATG 9 184 1 AATCCCTCAT 0.897075 -80 CATTTTAAGGTACCCCTTTACTTACCCTTTGG 10 29 1 TACCCCTTAT 0.904372 -30 CACAGGGGATTACCCCTACCCTCAAAGACTCC 11 105 1 TACCCCTCCT 0.983585 -112 ATAATAAGAATACCCCTCCAGTAAAGATCCCG 11 149 0 TACCCCTCAT 0.983905 -68 TCATACCCCCTCCTTTTGAATTCTA 19 82 0 TACCCCCCCT 0.940881 -15 ATTGTTAGCTAATCCCTTAATTCATACTTGGG 23 262 1 AATCCCTAAT 0.703936 -38 ******* ** * Masking position 2 Map Score: 1.89756 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 94 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 13 AAGCGAAAAGTTGAACAAAATATCAA 1 4 0 TGACAAATAT 0.955035 -211 TGTACATAAGACGGATACATTATTATCAAATAG 1 54 0 AGATAATTAT 0.655244 -161 TATCCGTCTTATGTACAAAATATAACTGCAATT 1 70 1 AGACAAATAT 0.905813 -145 GGCTTGAGAATTGGATAAAATATCCAATAATAT 1 120 0 TGATAAATAT 0.967565 -95 TATCTCCAAGTTGGACAAAATATCCAAGAGGTG 1 187 1 TGACAAATAT 0.955035 -28 ATTAGTCACTTAAAATAAAATATGGGAATATAT 6 14 1 TAATAAATAT 0.7227 -287 TTATATTATGTAGTGTAGAATATAGTCCAGCCT 6 187 1 TGGTAAATAT 0.861516 -114 GTAATTTACATGGTATATAATATAAGGTTTGCT 9 225 0 TGATAAATAT 0.967565 -39 ACTAAGTATTTTGCATAGAATATGGTAAAATAA 13 64 1 TGATAAATAT 0.967565 -68 GAGAAAAAGCAAGTATATAAAATTAAGGTTC 21 9 0 AGATAAAAAT 0.655244 -38 * * *** ***** Masking position 7 Map Score: 5.1093 Number of sites scoring better than the average of aligned sites = 22 Number in coding regions = 12 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 Motif number 14 GCGATTAGTGTTATATTTCCA 3 290 1 TTATATTCCA 0.962372 -11 AAAAGTATTATGATTTTTACATAAAC 4 41 1 TGATTTTACA 0.638505 -16 AGTAATATTTATATATTCCCATATTTTATTT 6 26 0 ATATATTCCA 0.764696 -275 TTTATATCACCATATTTAAGTC 8 2 1 TTATATCCCA 0.898623 -156 CAAAACTGATTTATATTTTCAAAATGTATCT 8 118 1 TTATATTTCA 0.714859 -40 TTTTTAAGATTTATTTTACCATATTCTATGC 13 76 0 TTATTTTCCA 0.948925 -56 TCTGATATCACCATGTTCATGTT 13 119 0 TGATATCCCA 0.772814 -13 CTCTTCATTTTCCCATTTTGGAGGA 16 5 1 TCATTTTCCA 0.794856 -22 TTTTTAAGATTTATTTTGACAAAGAAATGTC 22 47 0 TTATTTTACA 0.821497 -64 TTTAAAAGGATTATTTTAACATTTTTATGTT 23 13 0 TTATTTTACA 0.821497 -287 AATAATCCTTTTAAATTTCCAATTTTTACAT 23 29 1 TTAAATTCCA 0.747633 -271 TTTTCGATGGTATATTCCCAAGTATGAATT 23 280 0 GTATATTCCA 0.82808 -20 ******* *** Masking position 3 Map Score: 5.30246 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 108 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 ACTTTCATCTATTTGATAATAATGTATCCGT 1 46 1 ATTTGAAATA 0.756171 -169 ATTTTGTCCAACTTGGAGATAGCAGATTCAA 1 177 0 ACTTGGGATA 0.940063 -38 CCTATGGAAAATTTGACAATAACGTTCCAAT 3 211 1 ATTTGAAATA 0.756168 -90 TTAAAATAAAATATGGGAATATATAAATATT 6 23 1 ATATGGAATA 0.920998 -278 TTTGACTTAAATATGGTGATATAAA 8 5 0 ATATGGGATA 0.937535 -153 AAGCTTTACGACATGAAGATACCGTACTGGG 9 155 1 ACATGAGATA 0.863629 -109 TTTGCATAGAATATGGTAAAATAAATCTTAA 13 73 1 ATATGGAAAA 0.647611 -59 TTTAACATGAACATGGTGATATCAGA 13 116 1 ACATGGGATA 0.950795 -16 CTTAATTCATACTTGGGAATATACCATCGAA 23 277 1 ACTTGGAATA 0.924141 -23 ****** **** Masking position 4 Map Score: 4.22117 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 67 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357