AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -inarP_bsub_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 nasF 60 uroporphyrin-III C-methyltransferase #2 nasE 31 assimilatory nitrite reductase (subunit) #3 nasD 121 assimilatory nitrite reductase (subunit) #4 nasB 179 assimilatory nitrate reductase (electron transfer subunit) #5 cysH 300 phosphoadenosine phosphosulfate #6 ylnB 48 similar to sulfate adenylyltransferase #7 ylnD 98 similar to uroporphyrin-III C-methyltransferase #8 citB 227 aconitate hydratase #9 yneN 71 similar to thiol:disulfide interchange protein #10 resC 135 essential protein similar to cytochrome c biogenesis protein #11 resA 131 essential protein similar to cytochrome c biogenesis protein #12 ypuL 91 similar to hypothetical proteins #13 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #14 ypuI 54 similar to hypothetical proteins from B. subtilis #15 ypuG 280 similar to hypothetical proteins #16 spoIIIAC 22 spoIIIAC #17 spoIIIAA 75 spoIIIAA #18 yqhV 144 alternate gene name: yqgE #19 efp 24 elongation factor P #20 yqhS 86 similar to 3-dehydroquinate dehydratase #21 yqhR 226 yqhR #22 gerBA 264 gerBA #23 ywcJ 300 alternate gene name: ipa-48r; similar to nitrite transporter Motif number 1 GTATCTTAAATATTCCTTTTTGCTGTGCTA 3 65 1 TATTCCTTTT 0.746507 -57 AAGATTCCCCTTTCTAGACCCTCA 4 5 1 TTCCCCTTTC 0.877025 -175 CTCGTAAGTTTTCTCCTATTAAAAATTATG 4 137 0 TTCTCCTATT 0.768949 -43 GCTGTTCCTGTCTTTCTTTCCGCCGGATTG 5 156 1 TCTTTCTTTC 0.800915 -145 TTCTTCTTTCCTCCTTTCGGAGACAAAC 5 283 0 TCCTCCTTTC 0.984747 -18 AAATGCCTTCTCTTCCTATTGATTCA 9 7 0 TCTTCCTATT 0.933655 -65 TTTCGCTTTCTCTTCTTTTTATGACACAAT 9 34 1 TCTTCTTTTT 0.808158 -38 CCATGACATCACTCCCTTTTCGC 10 4 0 ACTCCCTTTT 0.683544 -132 ATTTCACATTTCTTACTTTTTGAAGGTTAT 11 62 0 TCTTACTTTT 0.830721 -70 TGCCCCCTTCCCCCTATTGCAGATCCAT 11 114 0 TCCCCCTATT 0.911159 -18 TCAAGTATTATCTTACTTTTTTCAACCTTA 12 62 0 TCTTACTTTT 0.830721 -30 CGTTTACTCTCCCTTTTTCAGGGAGAG 13 8 1 TCTCCCTTTT 0.973535 -115 GATAGCTTCTTCCTTATATCTTATGAT 14 38 0 TCTTCCTTAT 0.787331 -17 GGTGCTTCCTCCTTTAATGTGCTTTT 15 7 1 TCCTCCTTTA 0.927078 -274 GGGCGTTCTTTTTTCCTTTTATCCCTTCTA 15 46 0 TTTTCCTTTT 0.922702 -235 TTGCTTCTGGTTTTCCTTTCTAAGAAGCAC 15 84 0 TTTTCCTTTC 0.907284 -197 CAGAGCCTCCTCCTTTCTACCGATTGG 17 59 0 TCCTCCTTTC 0.984747 -17 AAAAACAGAATCTTTCTTTTATACGGAAAT 18 62 1 TCTTTCTTTT 0.830721 -83 GTTTAATGTCCTCCTATATTCCAA 19 7 0 TCCTCCTATA 0.739421 -18 ACAATCTCTCCTTTTCGCGAGGGTTT 20 71 0 TCTCCTTTTC 0.668313 -16 ATAAGAATAATTCTCCTTTTTTGATACAAA 22 205 1 TTCTCCTTTT 0.937149 -60 TATTTCTCCCCCTTTTATTTAAACAA 23 7 1 TCCCCCTTTT 0.978701 -294 TGTCTTTTCCTGCTTTCTTTCATGATT 23 284 0 TCCTGCTTTC 0.808566 -17 ********** Masking position 7 Map Score: 29.1336 Number of sites scoring better than the average of aligned sites = 1327 Number in coding regions = 835 Number in noncoding regions = 492 Number of orfs with sites within 600 bp upstream = 568 Fraction of orfs with sites within 600 bp upstream = 0.0912303 Motif number 2 TATACAGATAGCCTTTTTACCTCTTAAAATA 5 195 0 GCCTTTTTCC 0.938712 -106 ATGATCTGCTGCGTTCTTCTCAGATGCCGGA 7 13 1 GCGTTCTTTC 0.945872 -86 AAAGCGAAATGCCTTCTCTTCCTATTGATTC 9 12 0 GCCTTCTCTC 0.973153 -60 AAGGCATTTCGCTTTCTCTTCTTTTTATGAC 9 28 1 GCTTTCTCTC 0.951213 -44 GTTTGGCCTGCCCTTTTTATCTTTATTCCCG 10 113 0 CCCTTTTTTC 0.81378 -23 AATTTAGAAAGCGTTTTTACCGTGATCCGCC 11 27 0 GCGTTTTTCC 0.929509 -105 AAACGGCGTTTTTTTTAGATTTGGCA 12 6 1 GCGTTTTTTT 0.942976 -86 AATGAATCGCGCTTTTTCATCATCATAAGAT 14 17 1 GCTTTTTCTC 0.970544 -38 GATAGCTTCTTCCTTATATCTTATG 14 40 0 GCTTCTTCTT 0.801668 -15 TAGAGGCCGGGCGTTCTTTTTTCCTTTTATC 15 53 0 GCGTTCTTTT 0.907282 -228 AGAAGCAAAGGCTTTTTCTCCCGCTTCTGCG 15 106 1 GCTTTTTCCC 0.936356 -175 CAGAGCCTCCTCCTTTCTACCGATT 17 61 0 GCCTCCTCTT 0.816405 -15 TTATCAACCTGCCTATTTCTTTAGGATTGCT 21 12 1 GCCTATTTTT 0.606725 -215 AAAAGTGTGAGCTTTTTTATTGACATTTCAT 21 177 1 GCTTTTTTTT 0.911752 -50 CGTATAAGCTGCCTTTTTCCTATGACAACAT 22 77 1 GCCTTTTTCT 0.895581 -188 TAGATAGGAAGCGTTTTCTTTGAAGGGGTAA 22 131 0 GCGTTTTCTT 0.967246 -134 CTTTGTTTCAGCCTTTTCCTCGATAAGAATA 22 183 1 GCCTTTTCTC 0.983937 -82 ACACAGCGATCCTTTTTCATTTACGCAAATT 23 68 1 CCTTTTTCTT 0.701543 -233 AATCATGATAGCGTTTTCGTCAACTATTTTT 23 165 1 GCGTTTTCTC 0.98139 -136 ******** ** Masking position 7 Map Score: 26.7066 Number of sites scoring better than the average of aligned sites = 1198 Number in coding regions = 1046 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 3 CCTTATCAAATGTTTTTTCCAGCGTAGCAC 3 89 0 TGTTTTTTCC 0.930941 -33 AACTTACACATGTCTTTTCCAGAAAATAAT 4 70 0 TGTCTTTTCC 0.967338 -110 GAAGCTCGTAAGTTTTCTCCTATTAAAAAT 4 141 0 AGTTTTCTCC 0.85896 -39 GTTTGTAAGGTGCTACTTCCAGCAAAATGA 5 98 1 TGCTACTTCC 0.780357 -203 TTCTGCCGGTTGTCTTTTCCCATGTAATGT 5 242 0 TGTCTTTTCC 0.967338 -59 TTCTTCTTTCCTCCTTTCGGAGAC 5 287 0 TCTTTCCTCC 0.693276 -14 GAAAGCGAAATGCCTTCTCTTCCTATTGAT 9 14 0 TGCCTTCTCT 0.644357 -58 ATGCCACCTCCGCAGCACATT 9 61 0 TGCCACCTCC 0.881497 -11 GATAGCTTCTTCCTTATATCTTA 14 42 0 AGCTTCTTCC 0.892468 -13 GGTGCTTCCTCCTTTAATGTGC 15 3 1 TGCTTCCTCC 0.943449 -278 GGCCGGGCGTTCTTTTTTCCTTTTATCCCT 15 50 0 TCTTTTTTCC 0.726484 -231 CAGAGCCTCCTCCTTTCTACCGA 17 63 0 AGCCTCCTCC 0.945583 -13 GGAACAGACTTCTTTTTTCCTTT 18 4 0 TCTTTTTTCC 0.726484 -141 GGAAAAAAGAAGTCTGTTCCCAAATGGGAG 18 14 1 AGTCTGTTCC 0.816037 -131 GCACAAAAAAAGCCTGCTCCCATTTGGGAA 18 30 0 AGCCTGCTCC 0.860098 -115 GAAGTAGTCTTGTCATTTCCGTATAAAAGA 18 76 0 TGTCATTTCC 0.857357 -69 CCGTATAAGCTGCCTTTTTCCTATGACAAC 22 76 1 TGCCTTTTTC 0.655318 -189 GCTTTGTTTCAGCCTTTTCCTCGATAAGAA 22 182 1 AGCCTTTTCC 0.953314 -83 TGTCTTTTCCTGCTTTCTTT 23 291 0 TGTCTTTTCC 0.967338 -10 ********** Masking position 8 Map Score: 25.0596 Number of sites scoring better than the average of aligned sites = 1443 Number in coding regions = 1302 Number in noncoding regions = 141 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 4 CCTCCTCAATGATAGTTTTTGTCA 2 5 0 GATAGTTTTT 0.892211 -27 AAAGACATGTGTAAGTTTTTGTGACACGTT 4 83 1 GTAAGTTTTT 0.71673 -97 CCGCCGGATTGAAAGTTTTTTATTTTAAGA 5 175 1 GAAAGTTTTT 0.910525 -126 CTGATATACAGATAGCCTTTTTACCTCTTA 5 200 0 GATAGCCTTT 0.87206 -101 GTGAAATTTAGAAAGCGTTTTTACCGTGAT 11 32 0 GAAAGCGTTT 0.966986 -100 CTTTTTCAGGGAGAGTTTTTTTATGTTTGC 13 23 1 GAGAGTTTTT 0.909055 -100 GATAGCTTCTTCCTTATATC 14 45 0 GATAGCTTCT 0.82851 -10 AGTATTGGACGAGAGCTTTTTGGTGGCTTA 15 203 1 GAGAGCTTTT 0.96844 -78 GCCAAAAAGTGTGAGCTTTTTTATTGACAT 21 173 1 GTGAGCTTTT 0.884887 -54 ATAATAGATAGGAAGCGTTTTCTTTGAAGG 22 136 0 GGAAGCGTTT 0.860416 -129 GATTTATGATGAAAGCGTATTCTTAATCTG 23 139 0 GAAAGCGTAT 0.789731 -162 CATAAATCATGATAGCGTTTTCGTCAACTA 23 161 1 GATAGCGTTT 0.959994 -140 ********** Masking position 4 Map Score: 10.1792 Number of sites scoring better than the average of aligned sites = 426 Number in coding regions = 346 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 5 ACTAGAAAAGTGATCCGGTCTTTTGA 1 7 0 TGATCCGGTC 0.913292 -54 CAGATGATCCGCTCCTTATCAAAT 3 108 0 TGATCCGCTC 0.961482 -14 ATATGATCTGCTGCGTTCTTCTCAGATG 7 9 1 TGCTGCGTTC 0.852038 -90 CATTATCACCTCAATCATAATA 8 3 1 TTATCACCTC 0.707985 -225 TGCCCCCTTCCCCCTATTGC 11 122 0 TGCCCCCTTC 0.946893 -10 GTTTGCTCACGTCCTTGTGGTGG 13 110 0 TGCTCACGTC 0.841172 -13 TTTTTTCCTTTTATCCCTTCTATGGTACAC 15 38 0 TTATCCCTTC 0.889012 -243 TTTCTCCCGCTTCTGCGCTCCGAGCAAACA 15 120 1 TTCTGCGCTC 0.806077 -161 TTTATTTTTGCTCCCCTCACGT 16 5 0 TGCTCCCCTC 0.987874 -18 ATTTTCCCGGTGCGCCCCTCTTACAAACGC 22 46 1 TGCGCCCCTC 0.950087 -219 CATCTTTTCATTACCCCTTCAAAGAAAACG 22 121 1 TTACCCCTTC 0.774985 -144 ********** Masking position 9 Map Score: 7.10989 Number of sites scoring better than the average of aligned sites = 434 Number in coding regions = 377 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 6 TTCATAAAATTTTTAGAACTTTTCGTATATTTTGTTACA 3 15 1 TTTTATTCGA 0.873106 -107 ACCCTCATTATTTTACATTTTCTGAATCAAGGATATAGG 4 28 1 TTTTATTGAA 0.907858 -152 AGTTTTCTCCTATTAAAAATTATGTCACAATGCATTGTT 4 122 0 TATTATTGTA 0.734452 -58 GGATTGAAAGTTTTTTATTTTAAGAGGTAAAAAGGCTAT 5 180 1 TTTTATTGAA 0.907915 -121 ATCTGAGTAATTTTATAAGTTAACTAGGAGGAGATGGAT 6 17 1 TTTTATTCTA 0.962921 -32 ATTTCTTACTTTTTGAAGGTTATGTGAAATTTAGAAAGC 11 46 0 TTTTATTGTA 0.956088 -86 TATCTTACTTTTTTCAACCTTAACAAACAAGCTTTTTCA 12 45 0 TTTTATTCAA 0.921625 -47 CAGGGAGAGTTTTTTTATGTTTGCTTCCAGAAATATAAT 13 29 1 TTTTATTCTA 0.962921 -94 ACCTCTTGTGTTTTGAATATTCTGTACAAACTCCTTCAA 15 149 1 TTTTATTGTA 0.955978 -132 CATCTCACCATTTTCAAGTATCACTCTCATTGCCGGAAA 15 252 0 TTTTAATCTA 0.767428 -29 ATACCCGTTATTTTCAAATTTTACTCGCAGCTGCCAAAA 21 141 1 TTTTATTCTA 0.962921 -86 **** * ** ** * Masking position 7 Map Score: 7.96611 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 81 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 7 TTCCGTCACTGTAAAAAATGAAGGACCACT 1 34 0 GTAAAAAATG 0.940206 -27 TCAGAAAATGTAAAATAATGAGGGTCTAGA 4 23 0 TAAAATAATG 0.433402 -157 GTCTTTTCCAGAAAATAATGGTCCTATATC 4 59 0 GAAAATAATG 0.746879 -121 TTTTCTCCTATTAAAAATTATGTCACAATG 4 129 0 TTAAAAATTA 0.445182 -51 AGCGTAAACAGTAAAAATTACCGGTACATT 8 61 1 GTAAAAATTA 0.755813 -167 TTCGACTTATGAGAAAAATGTACCGGTAAT 8 77 0 GAGAAAAATG 0.820279 -151 ATGAAATTGTGAGAAAATTGTGATGGAATG 8 162 1 GAGAAAATTG 0.776071 -66 CCTTCAAAAAGTAAGAAATGTGAAATGAAC 11 66 1 GTAAGAAATG 0.696394 -66 GCATATCATATAAAAAAATGGGAGGTTGGG 18 117 1 TAAAAAAATG 0.803005 -28 GGTTTCTCATGTAAAAAATGTTCACTTCTC 20 46 0 GTAAAAAATG 0.940206 -41 TTGACAGGCTGAAAAAATTGCCATAGCCTT 21 93 1 GAAAAAATTG 0.922719 -134 GCAGCTGCGAGTAAAATTTGAAAATAACGG 21 145 0 GTAAAATTTG 0.54026 -82 ACTATTTAACTAAAAAAATAGTTGACGAAA 23 179 0 TAAAAAAATA 0.513788 -122 ACAAAAATTCGTAAAAATTAATTGTGAAAT 23 225 1 GTAAAAATTA 0.755813 -76 ********** Masking position 4 Map Score: 6.35422 Number of sites scoring better than the average of aligned sites = 1196 Number in coding regions = 1003 Number in noncoding regions = 193 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 8 TTAACAATGCATTGTGACATAATTTTTAATA 4 120 1 ATTGTGCATA 0.979638 -60 TAGAATTGTGCTAAAATTTACTACA 5 5 1 ATTGTGTAAA 0.90299 -296 GGCTTCTTTTATTGTGTTATATGAGAGAGCG 8 34 1 ATTGTGTATA 0.955351 -194 TTAATATGAAATTGTGAGAAAATTGTGATGG 8 157 1 ATTGTGGAAA 0.886646 -71 TCCGCAGCACATTGTGTCATAAAAAGAAGAG 9 43 0 ATTGTGCATA 0.979677 -29 GTAAAAATTAATTGTGAAATACTTCACAATA 23 235 1 ATTGTGAATA 0.923862 -66 ACTTCACAATATCGTGCCATACTATGCTCAA 23 255 1 ATCGTGCATA 0.936846 -46 ****** **** Masking position 9 Map Score: 4.31139 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 37 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 9 GACCGGATCACTTTTCTAGTGGTCCTTCATT 1 17 1 CTTTTTAGTG 0.960049 -44 AATATGGCTTCTTTTATTGTGTTATATGAGA 8 29 1 CTTTTTTGTG 0.972362 -199 CTTTATGCGGCCTTTCTTGTGTATTTAATCG 10 54 1 CCTTTTTGTG 0.945046 -82 TTTACTCTCCCTTTTTCAGGGAGAGTTTTTT 13 13 1 CTTTTCAGGG 0.858815 -110 GGTGCTTCCTCCTTTAATGTGCTTTTAGTGT 15 11 1 CCTTTATGTG 0.730518 -270 TGGGAGCAGGCTTTTTTTGTGCCCAAAAACA 18 38 1 CTTTTTTGTG 0.972362 -107 AAGAAAGATTCTGTTTTTGGGCACAAAAAAA 18 49 0 CTGTTTTGGG 0.888257 -96 CAGAATCTTTCTTTTATACGGAAATGACAAG 18 67 1 CTTTTTACGG 0.790912 -78 AAAGTGTGAGCTTTTTTATTGACATTTCATT 21 178 1 CTTTTTATTG 0.702014 -49 ATTGACATTTCATTTTTTGGGCACACTTTAA 21 195 1 CATTTTTGGG 0.872298 -32 ***** ***** Masking position 5 Map Score: 4.35298 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 206 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 10 GCTGTGCTACGCTGGAAAAAACATTTGATAAG 3 86 1 GCTGGAAAAC 0.90168 -36 ATGCCGGAATGCAAGCGAGAACATCATCACAG 7 36 1 GCAAGCAGAC 0.98318 -63 GATAAAAAGGGCAGGCCAAACCG 10 123 1 GCAGGCAAAC 0.990992 -13 GACTACTTCAGCAAGCTAGAGCATATCATATA 18 97 1 GCAAGCAGAC 0.983177 -48 GACTGGTAAAGCAGGCAAGACCTAAAATTTGC 23 92 0 GCAGGCAGAC 0.994252 -209 ATGAAAGAAAGCAGGAAAAGACA 23 288 1 GCAGGAAAGC 0.931471 -13 ****** *** * Masking position 8 Map Score: 2.55974 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 90 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 11 TTAAATATTCCTTTTTGCTGTGCTACGCTGG 3 70 1 CTTTTGCTGT 0.733618 -52 ACAAACTATGCAGGTTGCCGGGCTTCATAGG 5 73 0 CAGTTGCCGG 0.938388 -228 AAATGGAATTCATTTTGCTGGAAGTAGCACC 5 106 0 CATTTGCTGG 0.953721 -195 TCCTGTCTTTCTTTCCGCCGGATTGAAAGTT 5 161 1 CTTCCGCCGG 0.899511 -140 CAAACAGTAGCTTTCTGCCGGTTGTCTTTTC 5 253 0 CTTCTGCCGG 0.979378 -48 ACATTTCTTACTTTTTGAAGGTTATGTGAAA 11 56 0 CTTTTGAAGG 0.731464 -76 TGGACGAGAGCTTTTTGGTGGCTTATACTAT 15 208 1 CTTTTGGTGG 0.914134 -73 AAGTATCACTCTCATTGCCGGAAAAACTGGC 15 245 0 CTCTTGCCGG 0.962734 -36 AAAGCTCACACTTTTTGGCAGCTGCGAGTAA 21 161 0 CTTTTGGCAG 0.748291 -66 AACTGATCATCATTTTCCCGGTGCGCCCCTC 22 35 1 CATTTCCCGG 0.895061 -230 CCTTCTTAAACATATTGACGGTTTTTATTAA 22 235 0 CATTTGACGG 0.934989 -30 *** ******* Masking position 1 Map Score: 4.75385 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 621 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 TCGCTTGCATTCCGGCATCTGAGAAGAACGC 7 23 0 TCCGGCTCTG 0.960084 -76 TCTCCAAAATCCCCCTTCAGATCAGATCAT 8 208 0 TCCCCCTCAG 0.951866 -20 TTATCTTTATTCCCGCGTATGGCCCCGCCGA 10 97 0 TCCCGCTATG 0.98231 -39 TGCCCCCTTCCCCCTATTGCAGATCCATT 11 113 0 TCCCCCATTG 0.897718 -19 AGGCTTTTTCTCCCGCTTCTGCGCTCCGAGC 15 114 1 TCCCGCTCTG 0.992071 -167 TATTTCTCCCCCTTTTATTTAAACAAA 23 7 1 TCCCCCTTTA 0.867378 -294 CCAGTCACAATCCCGCTTATTCAGATTAAGA 23 118 1 TCCCGCTATT 0.89573 -183 ****** **** Masking position 1 Map Score: 1.99471 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 121 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 TCAAAAGACCGGATCACTTTTCTAGTGGT 1 9 1 CCGGATCACT 0.948961 -52 GTTTTTTCCAGCGTAGCACAGCAAAAAGGAA 3 77 0 GCGTAGCACG 0.877943 -45 TTGATAAGGAGCGGATCATCTG 3 110 1 GCGGATCATT 0.967398 -12 ACCTCCTTTGGCGAAGCTCGTAAGTTTTCTC 4 152 0 GCGAAGCTCT 0.869506 -28 ATCAGCAGCCGCGAATCACATTACATGGGAA 5 225 1 GCGAATCACT 0.971153 -76 GAAGAACGCAGCAGATCATAT 7 1 0 GCAGATCATT 0.836857 -98 CATCATCACAGCGAATCTTCTGGAAGAACTC 7 57 1 GCGAATCTTT 0.799749 -42 ATGCCACCTCCGCAGCACATTGTGTCATAA 9 52 0 CCGCAGCACT 0.789904 -20 CAGAGCACTGGCGGATCACGGTAAAAACGCT 11 18 1 GCGGATCACG 0.967635 -114 GCAAGCTAGAGCATATCATATAAAAAAATGG 18 107 1 GCATATCATT 0.634141 -38 ********* * Masking position 5 Map Score: 2.33397 Number of sites scoring better than the average of aligned sites = 493 Number in coding regions = 453 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 GTGATTCGCGGCTGCTGATATACAGATAGC 5 214 0 GCTGCTGATA 0.910734 -87 TTGCATTCCGGCATCTGAGAAGAACGCAGC 7 20 0 GCATCTGAGA 0.975803 -79 AATGTAATGTTCATCTGAGAATGATCTGAT 8 188 1 TCATCTGAGA 0.839506 -40 GGCCTCTAGTGCTTCTTAGAAAGGAAAACC 15 76 1 GCTTCTTAGA 0.89416 -205 TTTTTCTCCCGCTTCTGCGCTCCGAGCAAA 15 118 1 GCTTCTGCGC 0.865091 -163 ACACTTTTTGGCAGCTGCGAGTAAAATTTG 21 155 0 GCAGCTGCGA 0.970388 -72 TAGGAAAAAGGCAGCTTATACGGGCGTTTG 22 69 0 GCAGCTTATA 0.783738 -196 ********** Masking position 6 Map Score: 0.0442507 Number of sites scoring better than the average of aligned sites = 409 Number in coding regions = 389 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 15 TTTTCGTATATTTTGTTACATTTTATAACATGTAT 3 34 1 TTTGACATTA 0.978458 -88 AAAGGAATATTTAAGATACATGTTATAAAATGTAA 3 49 0 TTAGACATTA 0.890586 -73 ATGTGTAAGTTTTTGTGACACGTTTAATGCGTTAA 4 89 1 TTTGACATTT 0.94327 -91 CCTGCTCCCATTTGGGAACAGACTTCTTTTTTCCT 18 13 0 TTTGACACTT 0.815375 -132 TGTGAGCTTTTTTATTGACATTTCATTTTTTGGGC 21 182 1 TTTTACATCA 0.733992 -45 CATTTCATTTTTTGGGCACACTTTAACTGGAGGTG 21 200 1 TTTGACATTA 0.978458 -27 AATTCTCCTTTTTTGATACAAATTAATAAAAACCG 22 213 1 TTTGACATTA 0.978458 -52 TTTACGAATTTTTGTCTACATGTTATATCAAACTA 23 205 0 TTTTACATTA 0.912194 -96 *** * *** *** Masking position 8 Map Score: 1.7727 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 27 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925