AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_ctra_reg_300.orf -o00240_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: rs11 21 S11 Ribosomal Protein Input sequences: #1 dcd 87 Deoxycytidine triphosphate deaminase family protein #2 dnaN 129 DNA Pol III (beta chain) #3 trxB 244 Thioredoxin Reductase #4 kdsB 300 CMP-2-keto-3-deoxyoctulosonic acid synthetase #5 CT191 146 hypothetical protein #6 CT192 26 hypothetical protein #7 tgt 126 Queuine tRNA Ribosyl Transferase #8 mgtE 300 Mg++ Transporter (CBS Domain) #9 CT260 300 hypothetical protein #10 dut 36 dUTP Nucleotidohydrolase #11 accD 71 AcCoA Carboxylase/Transferase Beta #12 sodM 131 Superoxide Dismutase (Mn) #13 yhxB 151 Phosphomannomutase #14 CT296 108 hypothetical protein #15 rpoC 24 RNA Polymerase Beta' #16 rpoB 300 RNA Polymerase Beta #17 tpiS 196 Triosephosphate Isomerase #18 CT330 208 hypothetical protein #19 pykF 96 Pyruvate Kinase #20 uvrA 22 Excinuclease ABC Subunit A #21 dnaX_2 217 DNA Pol III Gamma and Tau #22 yaeS 300 YaeS family #23 CT460 300 SWIB (YM74) complex protein #24 yaeI 57 phosphohydrolase #25 sohB 102 Protease #26 CT495 211 ADP/ATP Translocase #27 pgsA_1 300 CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase #28 ndk 159 Nucleoside-2-P Kinase #29 ruvC 107 Crossover Junction Endonuclease #30 CT503 286 hypothetical protein #31 gapA 43 Glyceraldehyde-3-P Dehydrogenase #32 rs13 55 S13 Ribosomal Protein #33 secY 22 Translocase #34 rl18 21 L18 Ribosomal Protein #35 rl6 27 L6 Ribosomal Protein #36 rl16 32 L16 Ribosomal Protein #37 rl2 23 L2 Ribosomal Protein #38 rl3 300 L3 Ribosomal Protein #39 CT538 300 hypothetical protein #40 uhpC 300 Hexosphosphate Transport #41 nrdA 300 Ribonucleoside Reductase, Large Chain #42 nrdB 37 Ribonucleoside Reductase, Small Chain #43 pnp 28 Polyribonucleotide Nucleotidyltransferase #44 rs15 156 S15 Ribosomal Protein Motif number 1 GAAACTAGTGAAACTTTTTTTAATAAAGAGA 3 112 0 AAATTTTTTT 0.797672 -133 ACTGTATAAGAAGTTTTGCTTCTTAGGTGGG 4 260 1 AAGTTTGCTT 0.859231 -41 TCCGAAGACAAAGGTTTTCTTCGGGCTTTTT 7 19 1 AAGTTTTCTT 0.945178 -108 TTTGCACTGTAAGCTTCGTTTCTTCTG 8 7 0 AAGTTCGTTT 0.578202 -294 AGGTATAGCAAAGATTTTTTTAAAAAAGAAA 9 53 1 AAGTTTTTTT 0.907424 -248 TATACAGATAAAAGTTTGCTTTCTTTTTTAA 9 72 0 AAATTTGCTT 0.710523 -229 CTCTTTACACAAACTTTTTTTGAAAAAGAAA 9 120 0 AAATTTTTTT 0.797672 -181 TTCTGATCGGAAGGTTGTCTT 13 141 1 AAGTTGTCTT 0.78065 -11 ACGTCTTTAGAAGCTTCTCTTGCCTTGTATG 18 87 1 AAGTTCTCTT 0.871928 -122 AAACCCATTCATAGTTTTCTTCATCAAGAAT 21 175 1 ATATTTTCTT 0.607453 -43 TTTATATTTGAAGTTTTGTTTTGATGGTTGC 22 31 0 AAGTTTGTTT 0.776337 -270 TTCAAATATAAAAATTTTTATTTTGCTGATG 22 50 1 AAATTTTTAT 0.468077 -251 AGACTTGGCTATGTTTTTTATTTTGACGATA 23 201 1 ATGTTTTTAT 0.328154 -100 GAAGAGCCCTAAACTTTTCTTATCATCTTCT 23 263 1 AAATTTTCTT 0.873936 -38 TTTTTATTTAAAAATTCTTTTTATAATCCCC 25 57 1 AAATTCTTTT 0.608916 -46 GCATAATTACAAGATTTTTATGAAATCCAGG 26 82 0 AAGTTTTTAT 0.686353 -130 GTTGATTCGGAAGCTTGTCTTGAAAATTCTT 27 277 0 AAGTTGTCTT 0.780636 -24 GAGCTAAGTTATAGTTTTCTTACAATTGTGT 28 49 1 ATATTTTCTT 0.607453 -111 AGAAATGATTTTCTTGCTCGACATA 39 5 1 ATGTTTTCTT 0.79373 -296 CTCGACATAGAAGTTTTTCATTTGAATTCAA 39 27 1 AAGTTTTCAT 0.793739 -274 CTGCGATGAAAAATTTCTTTTCGAGAGCAAA 41 61 0 AAATTCTTTT 0.608924 -240 CCCGATAAAAAAGGTTTTCTTGAATTAAGAA 44 25 1 AAGTTTTCTT 0.945178 -132 CTAGAGTAAGAAGTTTTTTTTCTCTGTGCAG 44 130 0 AAGTTTTTTT 0.907444 -27 *** ******* Masking position 6 Map Score: 18.2386 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 323 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 2 ACCTCTTAAAAACTAAGGAGAGTATAGCAAAAAGGG 2 17 1 AAGGAGAGTA 0.762978 -113 TCGAATATAGGAACGAAGAGAGCCTATGAGAAGGCT 4 59 0 GGAGAGAGTA 0.94533 -242 ATCATTCTAAAGAGAGAGGGAGAAAAGACATAGTGA 7 50 0 AAAGGGAGAA 0.641409 -77 AAAAAAGTTTGTGTAAAGAGGGTCTATCTCCAAAAG 9 131 1 GAAGAGGGTA 0.966795 -170 TGATGGGAGGGGGGGGGGGGAGAATAAAAATTTCTT 9 175 0 GGGGGGAGTA 0.864645 -126 AGTACGGCTTATTAAAAGGGAGGCAACTTTTGATAC 9 260 0 AAAGGGAGAA 0.641409 -41 CACAGTAGCTGGGCACAGAGGGGTTCCCGGTACGTC 16 11 1 GAAGAGGGTC 0.897483 -290 GGATGGACAAGTGTATAGAGAGTATCTAGCGTCTCT 16 151 1 GAAGAGAGTC 0.925397 -150 TTCCAGCTAGGACAAAACAGAGCCTATCCAATGCAG 16 185 0 GAACAGAGTA 0.832407 -116 CCTGTTTAGAGATCACAGAGAGACTAAATAGGGAAA 16 236 1 GAAGAGAGTA 0.976334 -65 TCTAACTTCGTAAAAGAGAGAGTATATTTTTTATAG 21 88 0 TAAGAGAGTA 0.80454 -130 CAAGTCTTCAGCAAGAAGAGAGGTAAAAGCGAATTA 23 172 0 GGAGAGAGAA 0.820447 -129 AAAACGGTACTAAAACAGGGGGATTATAAAAAGAAT 25 70 0 TAAGGGGGTA 0.719132 -33 GTAAAGAAACGGAAAGAGAGGGATTCGAACCCTCGG 27 103 0 GAAGAGGGTC 0.897483 -198 CACTCCAAAAGCAAGCAGAGAGTTTAGCTATGTTTC 27 204 0 GGAGAGAGTA 0.94533 -97 CTATGGCACAGGAGAAAGAGAGGCAAAAAGGAGAAT 28 132 1 GAAGAGAGAA 0.915978 -28 CCTACCCCTAGAGCATGGGGAGGTTAGGCCTGTTTT 39 131 1 GAGGGGAGTA 0.938425 -170 TATTGTGGATGGATAAGCGGAGAGTAAGGTGTGTCA 40 32 0 GAGCGGAGTA 0.647251 -269 CGTTTGCTGTGTAAAGAGAGGGAGTAGGGGTGAGGA 40 75 0 GAAGAGGGTA 0.966795 -226 CGTTTTTTTGACGGATAGGGGGACTAGAGGCGTCTT 41 245 1 AAAGGGGGTA 0.826905 -56 * * ****** ** Masking position 10 Map Score: 17.6748 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 138 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 3 TTTTATCTCTTTTTTTTCTAACTAAAGTCTTTTC 1 29 1 TTTTTTCAAA 0.713425 -59 AACTAAAGTCTTTTCCTAGAAATATAGATAACAA 1 48 1 TTTTCTAAAA 0.653593 -40 GGCATACGGTTCTTTCAAGAAGAAGCCCTTTTTG 2 44 0 TCTTTAAAAA 0.766005 -86 TAGTGAAACTTTTTTTAATAAAGAGATGCATCTT 3 104 0 TTTTTAAAAA 0.82669 -141 TATTTGATTATTTTTCACGAATGAAACGCGGGAG 4 98 0 TTTTTACAAA 0.767001 -203 AATTTTATTATTTTTTTAGAATTCGCTTAGATAA 7 91 1 TTTTTTAAAC 0.797205 -36 ATTAAGAGACTTTTTTACGAAAACGACAAAAAGT 8 121 0 TTTTTACAAC 0.729615 -180 CTTTTAAGAGTCTTTATATAAAGAACGGAGAAGG 8 215 1 TCTTTTAAAA 0.458946 -86 TAGCAAAGATTTTTTTAAAAAAGAAAGCAAACTT 9 58 1 TTTTTAAAAA 0.82669 -243 ACACAAACTTTTTTTGAAAAAGAAACAGATTAAC 9 111 0 TTTTTAAAAA 0.862638 -190 ATTGTAATTTTTTTTAACCAATCAATAATAAAA 11 10 0 TTTTTACAAA 0.767018 -62 CAGGCTTCTGTTTTTGTAAAAAACTTGCTTAACT 13 44 0 TTTTTTAAAC 0.749161 -108 AACTATTTTTTAAGAATACAAAATCTTGA 14 6 1 TTTTTAAAAC 0.838649 -103 TTGATCAGCCTCTTCATACAAGGCAAGAGAAGCT 18 98 0 TCTTCTAAAC 0.446323 -111 GGAAAATAGCTCTTTGAAAAAGAAGAGTTTAAAG 23 22 0 TCTTTAAAAA 0.766005 -279 ATAAAAAGAATTTTTAAATAAAAATTAAAAGACC 25 47 0 TTTTTAAAAA 0.797986 -56 ATTTAAAAATTCTTTTTATAATCCCCCTGTTTTA 25 62 1 TCTTTTAAAC 0.671164 -41 GTAGTCAGTGTTTTCGAAAAATTAGCATCA 31 7 0 TTTTCAAAAA 0.714637 -37 GCGTTATAAGTTTTCTTCCAAGGAAGCTCCACTA 38 12 1 TTTTCTCAAA 0.49579 -289 GCTCATTACGTTTTTCAATAAGACTTTGAATTCA 39 49 0 TTTTTAAAAC 0.838649 -252 CCTGTTTTGCTTTTTGTAAAAATACTTTTGCAAG 39 159 1 TTTTTTAAAA 0.764675 -142 ***** ** ** * Masking position 4 Map Score: 17.6189 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 202 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 4 GATTATTATCAATGACAAAGGAAGAATCCTTTTA 2 88 0 AATGAGGAAG 0.531745 -42 TGAGATTTTCAAGGATATCGGAGGGGG 3 228 1 AAGGCGGAGG 0.972402 -17 ACTCTTGTTTAAGAGTCTCGGAAGACTTTTTGTC 8 97 1 AAGACGGAAG 0.966135 -204 TCTTTATATAAAGAACGGAGAAGGGCGTGAAAGA 8 225 1 AAGAAGAAGG 0.901977 -76 AAGATTTCCGGAAGTTAGCGCAAC 8 287 0 AAGACGGAAG 0.966135 -14 TCAATCGCTTAAGATTCTCGGAGGTATAGCAAAG 9 32 1 AAGACGGAGG 0.984382 -269 AAGATCATAGGAGGCTCTTCAAAA 10 1 1 AAGAAGGAGG 0.953115 -36 TATTTAGGCGAATAAACTCGAAAGTACTATAGAC 14 78 0 AATACGAAAG 0.740304 -31 TAAGGCATAAAAGAGTTGCGAAGGAAGAGCCCTA 23 240 1 AAGACGAAGG 0.966135 -61 GTGCCCAAAGAAAAGAGGAGGCGGAGTGATC 26 8 1 AAGAAGGAGG 0.953115 -204 GTACCCCTTAAAGGGTACCGAGGGTTCGAATCCC 27 86 1 AAGGCGAGGG 0.732473 -215 CATTTTCAGAAATACCTGCGAAAGGATCCCTGAT 28 13 0 AATACGAAAG 0.740304 -147 **** ****** Masking position 2 Map Score: 8.76811 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 59 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 5 AGAACCCGACCATCCTAACAAGGAGATCGTTA 4 184 0 CTCCTACAAG 0.635033 -117 GCAAGCACACCTTCCTTCGCAGAAGGCTCAGG 5 107 0 CTCCTTGCAG 0.96084 -40 ATTTATCAACCGTCTATGGAAA 9 1 0 CTCTATGAAA 0.471242 -300 AAAACCATCCTCTTTACAAAAAATTGAGCA 11 52 0 CTCTTTCAAA 0.768669 -20 AAAAATAAGCCTTCCTTGCAAGAAATCGAGTA 17 122 1 CTCCTTCAAG 0.944448 -75 GTGGAAAAAATCTCTTTTGAAGACGCTATGAA 18 15 1 TTCTTTGAAG 0.507067 -194 CAACCAACCACGTCTTTAGAAGCTTCTCTTGC 18 78 1 CTCTTTGAAG 0.902755 -131 ACTTTAAACTCTTCTTTTTCAAAGAGCTATTT 23 21 1 CTCTTTTCAA 0.426771 -280 AAAGAGCTATTTTCCTTGCCAGTTATTTCCAC 23 41 1 TTCCTTCCAG 0.626362 -260 GTTTAGGGCTCTTCCTTCGCAACTCTTTTATG 23 245 0 CTCCTTGCAA 0.930943 -56 AAGGGGTACGCGTCCTTAGCAGGGACGTACTT 27 63 0 CTCCTTGCAG 0.960953 -238 CGAGTCATCTCTTCCATAGAAACGAAATGAGG 28 90 0 CTCCATGAAA 0.647123 -70 ACTAGTGGAGCTTCCTTGGAAGAAAACTTATA 38 16 0 CTCCTTGAAG 0.733461 -285 CCTACTCTCACTTCCTTGCAAAAGTATTTTTA 39 175 0 CTCCTTCAAA 0.911728 -126 TAATCACCAGCCTCCTTCTAAAGGGAAGCCTT 39 230 0 CTCCTTTAAA 0.739459 -71 * ***** **** Masking position 11 Map Score: 9.11134 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 156 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 6 TTCGCTTAGATAAAGGAGTGGATTT 7 112 1 TAAAGGGTGG 0.900312 -15 TACGGCTTATTAAAAGGGAGGCAACTTTTGA 9 263 0 TAAAAGGAGG 0.715033 -38 CAATTTTTTGTAAAGAGGATGGTTTT 11 56 1 TAAAGAGATG 0.888171 -16 CATCAGTACGTAAAGATGTGGATAGCTCTTG 12 11 1 TAAAGAGTGG 0.966201 -121 GAGAAGCTTCTAAAGACGTGGTTGGTTGATT 18 75 0 TAAAGAGTGG 0.966201 -134 AGCTCTTTGAAAAAGAAGAGTTTAAAGTTGG 23 18 0 AAAAGAGAGT 0.703628 -283 GACTCCTAGTTAAAGAAGATGATAAGAAAAG 23 276 0 TAAAGAGATG 0.888171 -25 TTCCTCATCTTAAAGACGAGGAACACGTGAG 24 23 0 TAAAGAGAGG 0.985587 -35 GTGCCCAAAGAAAAGAGGAGGCGGAGTGATC 26 11 1 AAAAGAGAGG 0.975001 -201 GAACTTCTTGTAAAGCTGTGGCGAGGACTCT 30 79 1 TAAAGCGTGG 0.830721 -208 ATCTGAGCAAAAACGACGAGGACCCTAAAGA 30 107 0 AAACGAGAGG 0.850509 -180 CTTTTTGATTTATAGATGAGGAGAGCTATTT 30 247 1 TATAGAGAGG 0.870639 -40 CAAATTAAAAGATTAGGACGGTAACGA 35 7 1 AAAAGATAGG 0.703628 -21 GACTGATAGCAAAAAACGAGGTCTTAGAAGC 40 203 1 AAAAAAGAGG 0.819164 -98 ****** **** Masking position 2 Map Score: 8.45103 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 125 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 7 ATGAAACGCGGGAGGTGTCGAATATAGGAACGAAGAGAG 4 73 0 GAGGGTCGTA 0.918645 -228 ACCTTCCTTCGCAGAAGGCTCAGGAAGAAGGCTCTTATA 5 92 0 GAGAGGCTGA 0.753551 -55 CTGTTTGATGGGAGGGGGGGGGGGGAGAATAAAAATTTC 9 177 0 GAGGGGGGGA 0.909188 -124 AAGATCATAGGAGGCTCTTCAAAAAGAGGGCCTTC 10 7 1 AAGGGGCTTA 0.958305 -30 AGAAAATAGAGAAGGTGGCGAGGATAGTAACCTTATTTT 12 92 1 GAGGGGCGGA 0.98949 -40 GCTAGTAGGAAGAGGTGGCGACTCTGGTAGAGGGTTCTT 22 174 0 AAGGGGCGTA 0.980686 -127 CCCAAAGAAAAGAGGAGGCGGAGTGATCAAGAACTTGAA 26 14 1 AAGGGGCGGA 0.983283 -198 CATAGAAACGAAATGAGGCTGATTTTCAACACAATTGTA 28 69 0 AATGGGCTTA 0.76153 -91 TAAAGCAAACAAAGGCGGCGAATGGGCAATGGTATATGA 38 141 0 AAGGGGCGTA 0.980686 -160 CTTCCCTTTAGAAGGAGGCTGGTGATTAAAAGAAGAATC 39 234 1 GAGGGGCTTA 0.973536 -67 GTAGGGGTGAGGATGCGGCGTATTGTGGATGGATAAGCG 40 49 0 GATGGGCGTA 0.918645 -252 TAGGGGGACTAGAGGCGTCTTTGCTTCAAAATAGAGAAT 41 260 1 AAGGGTCTGA 0.787199 -41 * *** **** * * Masking position 3 Map Score: 9.78049 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 43 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 AAGAAGCCCTTTTTGCTATACTCTCCTTAGTTTTTAAGAGG 2 18 0 TCTTTCTTAT 0.704566 -112 ATGGTACTTGCTGATTAGGATTATTATCAATG 2 108 0 TCTGGATGAT 0.827377 -22 TTAAAAAAAGTTTCACTAGTTTCTGTGTAATTTTAGTTTTA 3 120 1 TCTGTCTGAT 0.969352 -125 GTGTATAGAGAGTATCTAGCGTCTCTGCATTGGATAGGCTC 16 161 1 ACTGTCTGAT 0.923089 -140 AATCTTCTTGTCTTACTTTTTTCTGTGAATTTGCTTAAATA 17 34 0 TCTTTCTGAT 0.909929 -163 TGAGTAGAATATCTTCTAGAATATCCGAAATGAAAGAAGCC 19 45 0 ACTGTATGAT 0.564052 -52 TATTCCTTGGATTAGCTAGATGCTGTTAAATTATGAGACAG 21 47 1 ACTGGCTTAT 0.800489 -171 ATGGGTTTCATTAATCTTTTTGCTGATTAGTTTACGCATTT 21 142 0 TCTTGCTTAT 0.770991 -76 ACTAGCGATATGGGGATGGTTTCTTAGAAATGAGGGGGATA 22 207 1 TATGTCTGAT 0.641544 -94 TGGCTGGAGATTTGGCTGTTCTCTGAGAATTATAGGGATCC 22 249 0 TCTTTCTGAT 0.909929 -52 AATTTGGGATAATTACTGGATGCTTGGCAATGCATAATTAC 26 103 0 ACTGGCTGAT 0.943318 -109 ATATGTGTCATTGCGCTGGAGGCTAAGAATTTTCAAGACAA 27 253 1 TCTGGCTGAT 0.978095 -48 GCCTTTCTTAACACTCGCGTCTTGTCATTTTCTATATTT 29 79 0 TCTGTCTTAT 0.881895 -29 ACACAAGAGATTTTTCTTGACGCTAAGAAATCCCACACCAA 38 88 0 TCTGGCTGAT 0.97809 -213 TAAGAAGTTTTTTTTCTCTGTGCAGAGAAATATAAGATGTC 44 114 0 TCTTGCAGAT 0.566262 -43 * ** * *** * * * Masking position 19 Map Score: 8.97727 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 58 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 TAAGGAGAGTATAGCAAAAAGGGCTTCTTCT 2 30 1 ATAGAAAAAG 0.843229 -100 CGCAGAAGGCTCAGGAAGAAGGCTCTTATAC 5 91 0 TCAGAAGAAG 0.865581 -56 GAAAAGACATAGTGAAAAAAGCCCGAAGAAA 7 34 0 AGTGAAAAAG 0.76477 -93 ACCTTTTTATACAGATAAAAGTTTGCTTTCT 9 79 0 ACAGTAAAAG 0.848001 -222 TCTCCAAAAGATAGGAAGAAGAAATTTTTAT 9 157 1 ATAGAAGAAG 0.797963 -144 AAGCAAATTCACAGAAAAAAGTAAGACAAGA 17 39 1 ACAGAAAAAG 0.964683 -158 CGTAAACTAATCAGCAAAAAGATTAATGAAA 21 147 1 TCAGAAAAAG 0.89764 -71 CAGCAAGAAGAGAGGTAAAAGCGAATTAGAA 23 169 0 AGAGTAAAAG 0.76477 -132 AGCCAAGTCTTCAGCAAGAAGAGAGGTAAAA 23 180 0 TCAGAAGAAG 0.865581 -121 GTGCTATGGCACAGGAGAAAGAGAGGCAAAA 28 129 1 ACAGAGAAAG 0.811614 -31 CTCAAGAACCAGAGAAAAAAGATGTGCTCAG 30 206 0 AGAGAAAAAG 0.940892 -81 CCATTAAGCAACTGAAAAAAGTAAGGATAAG 39 279 1 ACTGAAAAAG 0.848001 -22 CTTTTGCTAGAGTAAGAAGTTTTTTTTCT 44 138 0 AGAGAAGAAG 0.921189 -19 **** ****** Masking position 9 Map Score: 8.77313 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 89 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 10 ACTCTTTTTGACTTTGTAGTTTTTAGGAGAACA 3 18 0 ACTTTGTTTT 0.848657 -227 TGCAAGGGAAATCTTGCCTTTTTTAAGGTGAAT 3 60 0 ATCTTGTTTT 0.752738 -185 TTCACTAGTTTCTGTGTAATTTTAGTTTTAGAT 3 131 1 TCTGTGTTTT 0.593184 -114 GGACTGTCAATCCTTGAGATTTTCAAGGATATC 3 214 1 TCCTTGTTTT 0.927189 -31 TTCTAGTAAATCCTTGGATTCTTAAAATGGGTA 5 20 0 TCCTTGTCTT 0.736133 -127 TAGCGCTAATACTTTGACTTTTTTAGTTCGCAA 5 55 1 ACTTTGTTTT 0.848657 -92 ACAAAGGTTTTCTTCGGGCTTTTTTCACTATGT 7 26 1 TCTTCGTTTT 0.740121 -101 CTCGGAAGACTTTTTGTCGTTTTCGTAAAAAAG 8 113 1 TTTTTGTTTT 0.878117 -188 AGCAATAATTTTATTGTAATTTTTTTTAACCAA 11 23 0 TTATTGTTTT 0.617477 -49 TTCTTTGGATTTTTGTGCCTATCC 13 2 1 TCTTTGTTTT 0.92857 -150 GACTCTCAAGATTTTGTATTCTTAAAAAATAGT 14 12 0 ATTTTGTCTT 0.405059 -97 AAAATTTTTATATTTGAAGTTTTGTTTTGATGG 22 35 0 TATTTGTTTT 0.531779 -266 TAACACTCGCGTCTTGTCATTTTCTATATTTGT 29 77 0 GTCTTGTTTT 0.526769 -31 GAAGTTCATTGCTTTTTTTTAGAACTTT 30 6 1 TCATTGTTTT 0.744418 -281 CTCTTTAGGGTCCTCGTCGTTTTTGCTCAGATG 30 106 1 TCCTCGTTTT 0.736133 -181 TCAGGCTTTGTTTTTGCGATTTTTGGTGTGGGA 38 66 1 TTTTTGTTTT 0.878117 -235 ACATCTAGCTTTTTTGTGCTTTTT 41 2 0 TTTTTGTTTT 0.878117 -299 CGTTCACAATATCTTGGGTTTTTAGGGGCTCGC 41 157 1 ATCTTGTTTT 0.752738 -144 ****** **** Masking position 10 Map Score: 7.89062 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 122 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 11 AGTTCTAGTAAATCCTTGGATTCTTAAAAT 5 25 0 AATCCTTGGA 0.77486 -122 AAAAATAAGCCTTCCTTGCAAGAAATCGAG 17 122 1 CTTCCTTGCA 0.948879 -75 ACGCTTGCCTATTCCTTGGATTAGCTAGAT 21 38 1 ATTCCTTGGA 0.950508 -180 AAAACGATTTATTCCTCGGACTATTACGCA 23 141 0 ATTCCTCGGA 0.915791 -160 CGGTATTCTAGTTCCCTGGATTTCATAAAA 26 68 1 GTTCCCTGGA 0.846308 -144 AGAGTGCGAGGTTCCTCGCATCACAAAAAT 26 149 1 GTTCCTCGCA 0.878284 -63 ACTAGTGGAGCTTCCTTGGAAGAAAACTTA 38 18 0 CTTCCTTGGA 0.967947 -283 CCTACTCTCACTTCCTTGCAAAAGTATTTT 39 177 0 CTTCCTTGCA 0.948879 -124 ********** Masking position 10 Map Score: 3.84235 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 28 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 12 ATACGGTTCTTTCAAGAAGAAGCCCTTTTT 2 45 0 TTCAAGAAGA 0.667844 -85 GAAGAATCCTTTTAAGGAGAGAGGGGCATA 2 72 0 TTTAAGGAGA 0.881754 -58 ACTTTGTAGTTTTTAGGAGAACATCATTAA 3 11 0 TTTTAGGAGA 0.96406 -234 GAAGGCCCTCTTTTTGAAGAGCCTCCTATG 10 16 0 TTTTTGAAGA 0.726126 -21 AGTCTTAAAGTCTTAGGAGAGCTCGC 16 285 1 TCTTAGGAGA 0.84828 -16 ATTTCGGATATTCTAGAAGATATTCTACTC 19 55 1 TTCTAGAAGA 0.878537 -42 TAAAATAGATTTTTAGAAGAACTGGTTTCT 22 83 1 TTTTAGAAGA 0.943841 -218 TAGTAAAGCCTTTTGGGAGATTCCTGATTT 29 11 1 TTTTGGGAGA 0.862403 -97 GCTTAATAGCTTTTAGAAGACAATACGTTT 40 106 0 TTTTAGAAGA 0.943841 -195 CCCATTTCGTTTTTAGGACAACTCC 43 14 1 TTTTAGGACA 0.776468 -15 ********** Masking position 8 Map Score: 3.51979 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 90 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 13 TTGATAATCTAGAGGGATCTATCTAGCTAGCCTGTAG 12 57 1 AAGGATTCGC 0.898354 -75 TTCTCAGAGAACAGCCAAATCTCCAGCCACTATAGAA 22 261 1 AAGCATTCGC 0.98556 -40 TCTTTTTCAAAGAGCTATTTTCCTTGCCAGTTATTTC 23 33 1 AAGCATCCGC 0.979837 -268 AATAAAAAACATAGCCAAGTCTTCAGCAAGAAGAGAG 23 186 0 AAGCATTTGC 0.921869 -115 ATTTCAACAGAGTGCGAGGTTCCTCGCATCACAAAAA 26 141 1 ATGCATCCGC 0.872417 -71 AGCAGAGAGTTTAGCTATGTTTCCCGCCATTTCCCCC 27 190 0 TAGCATTCGC 0.955691 -111 AGTAAAACCTAGAACGATTTTTCAGGCTTTGTTTTTG 38 45 1 AAACATTCGC 0.856387 -256 AATTACACTTTTAGCAAACGGCCATGCCCTCCATCCT 38 218 0 TAGCAGCCGC 0.762054 -83 TTTCTTTTCGAGAGCAAACTTTTAAGCATGATGTCCT 41 42 0 AAGCATTTGC 0.921869 -259 TATATAGAAGCTAGCAACGTTTCCTGCAATTGAAAAA 41 101 0 CAGCATTCGC 0.947722 -200 * *** * * ** ** Masking position 7 Map Score: 2.41314 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 36 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 14 ATGACAAAGGAAGAATCCTTTTAAGGAGAGAGG 2 78 0 AAGAACCTTA 0.743932 -52 CTCAAGGATTGACAGTCCTTTCCATGGGGATGT 3 199 0 GACAGCCTTC 0.847333 -46 CAACAAGTATAAGAGCCTTCTTCCTGAGCCTTC 5 85 1 AAGAGCTTCC 0.702378 -62 ACTCTTAAACAAGAGTCCTTCACTATAAAAAGA 8 80 0 AAGAGCCTTC 0.978811 -221 TCCGAAATGAAAGAAGCCTTCAACTATACAAAA 19 30 0 AAGAACCTTA 0.743928 -67 TCTGAGTTCTAAGAACCCTCTACCAGAGTCGCC 22 164 1 AAGAACCTCC 0.937059 -137 CCTCATTTCTAAGAAACCATCCCCATATCGCTA 22 209 0 AAGAACCATC 0.707764 -92 GTTGCGAAGGAAGAGCCCTAAACTTTTCTTATC 23 254 1 AAGAGCCTAC 0.935888 -47 GAGGACCCTAAAGAGTCCTCGCCACAGCTTTAC 30 88 0 AAGAGCCTCC 0.970493 -199 CAAAAAGCAAAACAGGCCTAACCTCCCCATGCT 39 142 0 AACAGCCTAC 0.758297 -159 TCCTTCTAAAGGGAAGCCTTTCCGCCCATATCC 39 217 0 GGGAACCTTC 0.667025 -84 AAACGGTAGAGAGAGCCCTTATCTTATACTTAA 41 217 0 GAGAGCCTTC 0.96272 -84 ***** **** * Masking position 4 Map Score: 2.2277 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 102 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 15 TCCATGGGGATGTTTAGATGGAATATTTATA 3 181 0 TGTTTGATGG 0.959932 -64 ACGATCTCCTTGTTAGGATGGTCGGGTTCTG 4 186 1 TGTTAGATGG 0.959932 -115 AAAAAGTTTGTGTAAAGAGGGTCTATCTCCA 9 132 1 TGTAAGAGGG 0.742868 -169 TAACCTTATTTTTTAGGATGGCT 12 119 1 TTTTAGATGG 0.845672 -13 TTTGAAGTTTTGTTTTGATGGTTGCGGTTTA 22 25 0 TGTTTGATGG 0.959932 -276 TTGGGCCGGTTGTTTCGTTGGAAAGATGACT 27 22 1 TGTTTGTTGG 0.811084 -279 TCTCTACCGTTTTTTTGACGGATAGGGGGAC 41 238 1 TTTTTGACGG 0.66707 -63 CTTTGTAGTATGTTATGAGGGGTTTTTGATT 44 74 0 TGTTAGAGGG 0.941593 -83 ***** ***** Masking position 3 Map Score: 1.40187 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 15 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