AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_aful_reg_100.orf -o00230_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #2 AF0197 86 acetyl-CoA synthetase (acs-1) #3 AF0204 72 conserved hypothetical protein #4 AF0239 93 xanthine-guanine phosphoribosyltransferase (gptA-1) #5 AF0252 251 CTP synthase (pyrG) #6 AF0288 300 adenylylsulfate 3-phosphotransferase (cysC) #7 AF0497 132 DNA polymerase B1 (polB) #8 AF0676 72 adenylate kinase (adk) #9 AF0677 165 acetyl-CoA synthetase (acs-3) #10 AF0756 206 exopolyphosphatase (ppx1) #11 AF0764 138 LSU ribosomal protein L7AE (rpl7AE) #12 AF0841 80 adenylosuccinate synthetase (purA) #13 AF0842 65 A. fulgidus predicted coding region AF0842 #14 AF0875_AF0876 326 AF0875: snRNP, putative, AF0876: 5'-nucleotidase (nt5) #15 AF0971 101 conserved hypothetical protein #16 AF1117 62 DNA-directed RNA polymerase, subunit E' (rpoE1) #17 AF1118 111 A. fulgidus predicted coding region AF1118 #18 AF1127 213 LSU ribosomal protein L18E (rpl18E) #19 AF1131 75 DNA-directed RNA polymerase, subunit K (rpoK) #20 AF1157 163 phosphoribosylamine--glycine ligase (purD) #21 AF1215 101 cell division protein, putative #22 AF1232 63 conserved hypothetical protein #23 AF1260 207 phosphoribosylformylglycinamidine synthase I (purQ) #24 AF1269 300 A. fulgidus predicted coding region AF1269 #25 AF1270 33 transcriptional regulatory protein, ArsR family #26 AF1319 300 A. fulgidus predicted coding region AF1319 #27 AF1320 24 GMP synthase (guaA-2) #28 AF1342 126 thymidine phosphorylase (deoA-2) #29 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #30 AF1420 216 membrane protein #31 AF1664 147 ribonucleotide reductase (nrd) #32 AF1667 158 sulfate adenylyltransferase (sat) #33 AF1693 45 phosphoribosylformylglycinamidine cyclo-ligase (purM) #34 AF1886 32 DNA-directed RNA polymerase, subunit B'' (rpoB2) #35 AF1941 201 conserved hypothetical protein #36 AF2242 61 adenylosuccinate lyase (purB) #37 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #38 AF2244 300 acyl-CoA dehydrogenase (acd-11) #39 AF2277 49 DNA polymerase, bacteriophage-type #40 AF2285 104 SSU ribosomal protein S13P (rps13P) Motif number 1 AATGAGCAAATTTAAATTCATTATCATCTTAA 2 40 0 TTTAAACATT 0.546239 -47 CCCTCGAACTTTTTAACTTTTTAGCCAGCTTT 4 23 1 TTTTAATTTT 0.811931 -71 AAAAAAGCGTTTAAAATGTTTTCGATGCTGAC 4 60 0 TTAAAATTTT 0.930332 -34 GTTTGACTTCTAAAAACTTTTTATCTGTTATC 6 199 0 TAAAAATTTT 0.881459 -102 CACACCAAACTTTAAATCCTTTTAAGCATAAT 7 104 1 TTTAAACTTT 0.856417 -29 CAGTTACACCTTTAAACTTTTTGATTTTTACC 8 39 0 TTTAAATTTT 0.934884 -34 AGTTGTTAGTTAAAAATGTTTTGTCTAATACT 9 24 1 TAAAAATTTT 0.881459 -142 TTATTTATTGTTAAAATCTATTTTAAAAAACT 9 121 0 TTAAAATATT 0.729374 -45 CGGAGTGATATTTTAAATTTTTGTGTATGAAA 10 44 1 TTTTAATTTT 0.811931 -163 GATGGGAAGGTAATAACGTTTTCGAAATTTTT 10 173 0 TAATAATTTT 0.690986 -34 CCCGTGCAGTTTTAAAAGTTTTGGTAACACTG 11 68 0 TTTAAATTTT 0.934884 -71 GCTTCAGGGTTAAAAATGTTTTCGACTTGTGT 14 207 1 TAAAAATTTT 0.881459 -120 ATTTAAATTTTTTCATTTATGAA 15 2 1 TTTAAATTTT 0.934882 -100 AATCTGGCAATATAAAGCTTTTGCAGATACAC 15 65 0 TATAAATTTT 0.888828 -37 ACTTCAATAATTTAAATTTTTTGCTCAGATAA 17 24 1 TTTAAATTTT 0.934882 -88 AACTCTAAACTTTAAAGACATTCGAAAGCCTT 20 19 1 TTTAAACATT 0.546239 -145 TAAATACGATTTGTAAGGCTTTCGAATGTCTT 20 33 0 TTGTAACTTT 0.461449 -131 ACGCTTTTTATTTAAACCTTTTTCCCAACTTT 21 61 0 TTTAAATTTT 0.934884 -41 AACCGCAATCTTTTAAGCTTTTTCCGTGTCGG 23 174 0 TTTTAATTTT 0.811931 -34 CAGTCCAAGATTAAAATTTATTTAGCCAAACC 26 178 0 TTAAAATATT 0.729368 -123 GTCGTCAGCTTTAAAACCTTTTCAGGTGAGAA 28 22 1 TTAAAATTTT 0.930332 -105 TCTGAAAGAATATTAACTTTTTCTCGCTATCG 28 91 0 TATTAATTTT 0.706237 -36 AACAAGAGGCTAATAAGGTTTTTCATGAGTTT 30 183 0 TAATAATTTT 0.690986 -34 TCCTGTCTTCTTGAAAAGTATTAAAGTTAATG 31 15 1 TTGAAATATT 0.580586 -133 AAAAATTGAATAGAAAAATTTTTCTTACAGCA 31 63 0 TAGAAATTTT 0.792508 -85 GTAGAAAATTTTTTGAACTCCTT 32 2 1 TAGAAATTTT 0.792508 -157 CCTTTAATCATTAAAATATTTTTCGAAACCTT 32 97 1 TTAAAATTTT 0.930332 -62 GGCAACCTTTTAAAAAGACTTTTCCGACTTGA 33 21 1 TAAAAACTTT 0.755465 -25 AATTTATAAGTAAAAAAATTTTACTAAAATAA 35 91 0 TAAAAATTTT 0.881465 -111 TTGTGTTCTATTTAAATCCTTTTTCAATTGTT 38 240 1 TTTAAACTTT 0.856417 -61 TTAAGGCAAATTAAAATAGTTTGCTGATAAGA 39 17 0 TTAAAAGTTT 0.516099 -33 ****** **** Masking position 6 Map Score: 35.4208 Number of sites scoring better than the average of aligned sites = 325 Number in coding regions = 120 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 2 TTCAATAAAAAAGGGGTGGTGGT 1 119 1 AAGGGTGGTG 0.96824 -13 CGTAATCGAAAGAAGGTGATGTAG 6 287 1 AGAGGTGATG 0.967618 -14 ATATATCTATTAGAGGTGATGAA 9 153 1 TAGGGTGATG 0.857647 -13 AAAAAACGAAAGGGGGTGGTGAA 10 3 0 AGGGGTGGTG 0.99083 -204 GATTTGATGAAGGAGGTGATGAC 11 126 1 AGGGGTGATG 0.993453 -13 GAAAATAATCAGGCGGTGATGGG 14 3 0 AGGGGTGATG 0.993453 -324 GCCCTTAAGTTGGTGAAGGAAAAA 27 7 0 AGTGGTGAAG 0.884702 -18 CCTCAGGCTGAGGCGGTGGAGAAGGTCTTTT 38 60 0 AGGGGTGGAG 0.97997 -241 TGAAAACTTGAAGTGGTGAAGGTGGAGGAGC 38 159 0 AAGGGTGAAG 0.950951 -142 GCTTCCTCTTAGACGGTGATGTT 40 92 1 AGAGGTGATG 0.967618 -13 *** ******* Masking position 7 Map Score: 16.6504 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 155 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 3 TTTTAACTTTTTAGCCAGCTTTGAGGTGTC 4 33 1 TTAGCCAGCT 0.880291 -61 TGTTACGTAGTCAGCAAGCTCTCAGCTTGC 6 98 0 TCAGCAAGCT 0.965557 -203 AGCGAGAGGGACTGCAAGATCACATTATCT 7 43 1 ACTGCAAGAT 0.788175 -90 ATGATTTATCTCAGCACGCTTTCGCAAGTT 9 95 1 TCAGCACGCT 0.882707 -71 GAACCCGAATTTTGCCAGATGCTGAGAGCT 14 246 0 TTTGCCAGAT 0.719204 -81 AAAGCTTTATATTGCCAGATTTGTTAATTA 15 76 1 ATTGCCAGAT 0.493942 -26 GACTTCCTCCTCTGCCAGCTTCCTTATCTT 18 130 0 TCTGCCAGCT 0.971405 -84 TTTTCCCAACTTTGCAATCTCGATAAAGGC 21 44 0 TTTGCAATCT 0.705444 -58 AATTAAAGATCTGCCAGCTTTGAAAGTTT 23 10 1 TCTGCCAGCT 0.971405 -198 GCGTTGATGTTCTGCACTCTTTAGTGCTAG 23 142 0 TCTGCACTCT 0.668111 -66 AGCATTACAGATTGCAAGCTCTCTCACCTC 24 153 1 ATTGCAAGCT 0.834274 -148 GGATTCGTTTTCTGCAATATCTCAATATCA 30 154 1 TCTGCAATAT 0.639015 -63 TTAGTTGAGAACAGCAAGCTATCCTCAATT 35 60 1 ACAGCAAGCT 0.914404 -142 TGAGATGCTTTCAGCAAGCTCCTCCACCTT 38 142 1 TCAGCAAGCT 0.965557 -159 AAACTTCTTATCAGCAAACTATTTTAATTT 39 12 1 TCAGCAAACT 0.667932 -38 ********** Masking position 10 Map Score: 14.4943 Number of sites scoring better than the average of aligned sites = 744 Number in coding regions = 704 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 4 TCGGAATTGGAAGTTGAAGTGGTTGAGGAGA 5 128 1 AAGTGAAGTG 0.92139 -124 GTAGTGATAAAACATGAGGTGGTTGG 13 50 1 AACTGAGGTG 0.967341 -16 GACCCAGCAAAGGCTGCGGTGATGATTTT 16 44 1 AGGTGCGGTG 0.833686 -19 TATAAGCTTTAAGTTGAGTTGATGATTATTA 17 68 0 AAGTGAGTTG 0.86923 -44 GGTCAAAACTACGCTGAGGTGTAGTTGATAT 18 95 1 ACGTGAGGTG 0.940711 -119 GAGTCAGCAAAAAATGAGGCGCCA 18 200 1 AAATGAGGCG 0.806565 -14 CGGTCAAGCTGAGGCGTTGCTGTTTT 21 6 1 AAGTGAGGCG 0.977028 -96 GCCAAACCCTAAGTTGATGTGATGAAAACAA 26 155 0 AAGTGATGTG 0.869229 -146 CAAAAAGAGAAAGGTGAGATGAC 34 20 1 AAGTGAGATG 0.92139 -13 TTTCCGCCTCAGGCTGAGGCGGTGGAGAAGG 38 66 0 AGGTGAGGCG 0.942276 -235 CCAACAGCATAACTTGAGATGCTTTCAGCAA 38 128 1 AACTGAGATG 0.820315 -173 CACCGTTGAAAACTTGAAGTGGTGAAGGTGG 38 165 0 AACTGAAGTG 0.820294 -136 *** ******* Masking position 1 Map Score: 9.25396 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 276 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 5 TGGTAGGCTTTTTTGCGGTATTTAAAATTAAGGCGGA 5 13 1 TTTTTTAAAA 0.743029 -239 CACCACCCCCTTTCGTTTTTTTGGAAGAAATCGGAGT 10 13 1 TTTTTTGAAG 0.9337 -194 GTATGAAAGATTTCGCTGTATTCGAAATACGTGTAAT 10 68 1 TTTTTTGAAA 0.972674 -139 CCCGTGCAGTTTTAAAAGTTTTGGTAACACTGATATG 11 63 0 TTTTTTGTAA 0.900557 -76 GTTTATTTGGTTTGCGATTTTTGGAAAAATGGTAGGT 12 31 0 TTTTTTGAAA 0.972931 -50 TACATTTTACTTTAGTGTTGTTAGTAACTTCTCGTTA 13 16 0 TTTTTTGTAA 0.901065 -50 AACTCTAAACTTTAAAGACATTCGAAAGCCTTACAAA 20 19 1 TTTCTTGAAA 0.873127 -145 GTTAATATTCTTTCAGAGTTTTTGAAGTTCA 28 106 1 TTTTTTGAAG 0.932949 -21 ACCGCGCAATTTTCAAACTCTTCGAAAATAAAAGGCA 32 34 0 TTTTTTGAAA 0.641607 -125 ATTGCGCGGTTTTGAATGTCTTTGAAAATTCGAAAAC 32 61 1 TTTTTTGAAA 0.972931 -98 ATTTTTTATTATTTGAAAAACGTTTGCA 37 2 1 TTTTTTGAAA 0.97117 -37 *** * ** **** Masking position 16 Map Score: 10.4458 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 6 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 AACACTGACAGTCCTTCGCAGGGGTTTATTTGG 12 58 0 TATCTCGAGG 0.962486 -23 GATTCCCTATAAAAGTTTCTTCGGATGGAGGCAATTAA 14 75 1 AATCTCGAGG 0.910868 -252 GAAATCGTTTTTAGCCTTCCGCGGAAGGAACATTAAAA 18 19 1 TATCGCGAGG 0.987001 -195 CCTGGTGATCCTGCGGCGTTCGGGACGCCGTGA 19 6 1 TATCGCGTGG 0.967993 -70 CAGTGAACCTACAGCGAAAGGTATATATAAT 22 43 0 TATCGCGAGG 0.987001 -21 CTCGGGCACGTCAATCTTCTCCGTAAGGTAAAAA 24 7 0 TATCCCGAGG 0.989479 -294 ATGTGCTAGTTTATGGTGCTCTGTACGGTCTGAATAAA 24 64 1 TATCCTGAGG 0.935439 -237 TCCGTCGCCTATATTTTGCAGCGCAAAGTATAAATCTC 24 213 1 AATCGCGAAG 0.747788 -88 TAAATCTCCTTGACGATCCTCTGGTTGGGATAGACAGT 24 243 1 TATCCTGTGG 0.852318 -58 CCGTTATAAGTTGCACCGTTGCGCAACCAAACA 25 6 1 AATCCCGTCG 0.7996 -28 TCATACACTATCATCATACACCGAATCGCTTGATTTTT 35 150 1 TATCCCGACG 0.961758 -52 * * * * *** * ** Masking position 3 Map Score: 7.57648 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 24 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 7 ATATTGCTTCCCGACCCAGCAAAGGCTGCG 16 32 1 CCGACCCAGC 0.945755 -31 CATATCAACTACACCTCAGCGTAGTTTTGA 18 97 0 ACACCTCAGC 0.874708 -117 GATTTGACTTCCTCCTCTGCCAGCTTCCTT 18 135 0 CCTCCTCTGC 0.950066 -79 ATCTCGGCGGCCCCATCTGCTTTAAGGGGT 19 55 1 CCCCATCTGC 0.9223 -21 AATTATATATCCGCCCCTGCTGACCGAAAA 20 114 1 CCGCCCCTGC 0.989829 -50 AAAAACAGCAACGCCTCAGCTTGACCG 21 8 0 ACGCCTCAGC 0.973285 -94 ATCAGACCAGCCCCACCAGCTAAAAGAATT 23 91 1 CCCCACCAGC 0.949148 -117 ACCTTCTCCACCGCCTCAGCCTGAGGCGGA 38 65 1 CCGCCTCAGC 0.993761 -236 ********** Masking position 7 Map Score: 6.01323 Number of sites scoring better than the average of aligned sites = 254 Number in coding regions = 239 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 8 GCATAATTCAATTTTTTAAGATGATAATGAA 2 25 1 ATTTTTTAAA 0.919034 -62 TCATAACGTTATTTTTTAATACTCTATGGAA 6 247 1 ATTTTTTAAA 0.919034 -54 TAGACAAAACATTTTTAACTAACAACTACAA 9 20 0 ATTTTTAACA 0.726182 -146 GCTTTCGCAAGTTTTTTAAAATAGATTTTAA 9 112 1 GTTTTTTAAA 0.797316 -54 CGTTTTCGAAATTTTTTCAAAACCTATTCGT 10 158 0 ATTTTTTCAA 0.79732 -49 TTAACATCCTATTTTTTATGAT 11 2 0 ATTTTTTATA 0.818881 -137 GTTCAGCGATATTTTTAAATAACTCCTCCTG 14 272 1 ATTTTTAAAA 0.919029 -55 AAGCTTTGTTATTTTTACACAGGTAGAATTT 20 64 1 ATTTTTACAA 0.79732 -100 ATTAATCCTCGTTTTTAATTACAAATTCTAC 20 86 0 GTTTTTAATA 0.610429 -78 TCAGGTGAGAATTTTTAAACATAAACAACAT 28 43 1 ATTTTTAAAA 0.919029 -84 GAATCGCTTGATTTTTAAAGAGCATGAGCAA 35 172 1 ATTTTTAAAA 0.919029 -30 ATTTTTTATTATTTGAAAAAC 37 1 1 ATTTTTTATA 0.818881 -38 ********* * Masking position 11 Map Score: 5.29554 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 18 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 9 TTTCCAGATATAATCTCCTCTTCGTTCTCC 5 154 0 TAATCTCCTC 0.702968 -98 GTTTTGTCATCTCACCCATTTAAACC 6 7 1 TCATCTCACC 0.905117 -294 TCCCTCTCGCTCATCTGCTCCCATCTCAAT 7 24 0 TCATCTGCTC 0.925096 -109 CAGGTATGATTTATCTCAGCACGCTTTCGC 9 90 1 TTATCTCAGC 0.718057 -76 TTCATCACCTCTAATAGATAT 9 155 0 TCATCACCTC 0.972923 -11 TTCACCACCCCCTTTCGTTTT 10 2 1 TCACCACCCC 0.727695 -205 AAATCATCATTCATCGGCTCTTCCCTAATT 11 101 0 TCATCGGCTC 0.841533 -38 ATCACCTCCTTCATCAAATCATCATTCATC 11 116 0 TCATCAAATC 0.625595 -23 GTCATCACCTCCTTCATCAAA 11 128 0 TCATCACCTC 0.972923 -11 CCCATCACCGCCTGATTATTT 14 2 1 CCATCACCGC 0.727695 -325 AAAATCATCACCGCAGCCTTTGCT 16 49 0 TCATCACCGC 0.959718 -14 GTGAGCATTTTTATCTGAGCAAAAAATTTA 17 36 0 TTATCTGAGC 0.466781 -76 ACTCTAATAATCATCAACTCAACTTAAAGC 17 64 1 TCATCAACTC 0.806697 -48 ACCGTTTTTTATCTCATCGATTATTTTC 20 146 0 TTATCTCATC 0.793427 -18 TCTTTTGTGGTTATCTGCTCGGGCACGTCA 24 32 0 TTATCTGCTC 0.767299 -269 AAACTTGTTTTCATCACATCAACTTAGGGT 26 151 1 TCATCACATC 0.935007 -150 GTCATCTCACCTTTCTCTTTT 34 22 0 TCATCTCACC 0.905117 -11 GAGTAACCTTTTATCGCCCCCTGTTAACTT 36 36 1 TTATCGCCCC 0.732268 -26 ********** Masking position 3 Map Score: 14.7498 Number of sites scoring better than the average of aligned sites = 977 Number in coding regions = 905 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 10 AAATGTTTTCGATGCTGACACCTCAAAGCTGGCTAA 4 43 0 GATGGCATAA 0.945821 -51 AGTTTCTTCGGATGGAGGCAATTAAAAACCAATGTG 14 88 1 GATGGCATAA 0.945821 -239 AATTTTGCCAGATGCTGAGAGCTTAAAGGCACACAA 14 233 0 GATGGGATAA 0.649921 -94 CCTTAAAGCAGATGGGGCCGCCGAGATTTGAACTCG 19 46 0 GATGGCGGGA 0.681543 -30 GAACATCAACGCTGCCGACACGGAAAAAGCTTAAAA 23 160 1 GCTGGCAGAA 0.978034 -48 TTAATCTTGGACTGGAGTCTTATTAAATTGCAATTC 26 196 1 ACTGGCTTAA 0.676419 -105 AGGTTTTAAAGCTGACGACAATTTAACATC 28 5 0 GCTGGCATAA 0.981859 -122 TCCAAATTCAACTGCGGGCTCGGAAAATCTCACGAT 30 14 1 ACTGGCTGAA 0.632313 -203 AAGTTATTCTGCTGGCAACGCTTCAAGACTTCGTGG 30 120 1 GCTGACGTAA 0.763789 -97 TTTACCCGCCGCTGTGGGCATTGCGAGGAGCAGATT 38 16 1 GCTGGCAGGA 0.939141 -285 CTCAAGTTATGCTGTTGGCATTTTAAAGGAGGAGGG 38 110 0 GCTGGCATAA 0.981859 -191 GGAGGAGCTTGCTGAAAGCATCTCAAGTTATGCTGT 38 131 0 GCTGACATAA 0.88263 -170 **** * ** * ** Masking position 16 Map Score: 5.173 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 147 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 ATCGTTTCATGCAAAAAATGAAAGT 3 4 0 GCAAAAATAA 0.836235 -69 TCAGCGCAAAGCAAAGTTTAAATCCTCAACAA 3 37 1 GCAAGTTTAA 0.838796 -36 CTCTTGCTCCGGTAAAAATCAAAAAGTTTAAA 8 29 1 GGAAAAATAA 0.85896 -44 GTTCATAAATGAAAAAATTTAAAT 15 3 0 GAAAAATTAA 0.572615 -99 TTAACATGCGGCAAAGATTTAAATTACGTAAT 18 58 1 GCAAGATTAA 0.909358 -156 TCTCGATAAAGGCAAGTTTAAAAACAGCAACG 21 25 0 GGAAGTTTAA 0.861225 -77 CTCAACGCTAAGATTTAATACGCTTTTT 21 84 0 GCAAGATTAA 0.909358 -18 GTCCTGTCTAGGGAAAAGTAAAAAAAGAAAAA 23 43 0 GGAAAAGTAA 0.732872 -165 ATTTTGCAGCGCAAAGTATAAATCTCCTTGAC 24 225 1 GCAAGTATAA 0.754173 -76 TTAACGATGGGGTAAATATTAATATAGAATTC 26 50 1 GGAAATATAA 0.75954 -251 ATCTATTGAAGGAAAAATTGAATAGAAAAATT 31 75 0 GGAAAATTAA 0.911733 -73 TGTTTAACTTGGCAAAATTTAAATAATCACAA 38 268 1 GGAAAATTAA 0.911733 -33 ** ****** ** Masking position 5 Map Score: 4.96567 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 54 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 TGCTGACACCTCAAAGCTGGCTAAAAAGTT 4 37 0 TCAAAGCTGG 0.832901 -57 TATTTTGAACTCAACGGAGCTAGAATCGAG 10 105 1 TCAACGGAGC 0.902394 -102 AAAATCATCACCGCAGCCTTTGCTGGG 16 46 0 TCACCGCAGC 0.812823 -17 TTTAAAAACAGCAACGCCTCAGCTTGACCG 21 11 0 GCAACGCCTC 0.778996 -91 ACCTAAACTTTCAAAGCTGGCAGATCTTTA 23 14 0 TCAAAGCTGG 0.832901 -194 GTGCAGAACATCAACGCTGCCGACACGGAA 23 155 1 TCAACGCTGC 0.984145 -53 GTTTGGTTGCGCAACGGTGCAACTTATAAC 25 13 0 GCAACGGTGC 0.792684 -21 TCACTCAGCTTCAAAGCTTCCCGGATAGTC 30 56 1 TCAAAGCTTC 0.840245 -161 TATTCTGCTGGCAACGCTTCAAGACTTCGT 30 124 1 GCAACGCTTC 0.929217 -93 CTTCAAGTTTTCAACGGTGCATTAAAAATT 38 177 1 TCAACGGTGC 0.961264 -124 ********** Masking position 3 Map Score: 5.96296 Number of sites scoring better than the average of aligned sites = 358 Number in coding regions = 346 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 13 GCATAATTCAATTTTTTAAGATGATAATGA 2 25 1 ATTTTTTAAG 0.873882 -62 TCATAACGTTATTTTTTAATACTCTATGGA 6 247 1 ATTTTTTAAT 0.710453 -54 TAGACAAAACATTTTTAACTAACAACTACA 9 21 0 ATTTTTAACT 0.659248 -145 TTAACATCCTATTTTTTATGAT 11 3 0 ATTTTTTATG 0.798063 -136 AGTCGAAAACATTTTTAACCCTGAAGCTCC 14 204 0 ATTTTTAACC 0.65475 -123 GTTCAGCGATATTTTTAAATAACTCCTCCT 14 272 1 ATTTTTAAAT 0.774918 -55 CCGCATGTTAATTTTTAATGTTCCTTCCGC 18 39 0 ATTTTTAATG 0.847884 -175 ATCAACCGCAATCTTTTAAGCTTTTTCCGT 23 179 0 ATCTTTTAAG 0.467726 -29 AAATATAACCATTTTTAACTTAGCTGGAAT 26 228 0 ATTTTTAACT 0.659248 -73 GGTTATATTTATTTTTTATCCTCAAAAAAT 26 248 1 ATTTTTTATC 0.578382 -53 AATAAAGGTAATTTTTTGAGGATAAAAAAT 26 258 0 ATTTTTTGAG 0.452011 -43 TCAGGTGAGAATTTTTAAACATAAACAACA 28 43 1 ATTTTTAAAC 0.772312 -84 AGGTTTTCGAATTTTCAAAGACATTCAAAA 32 70 0 ATTTTCAAAG 0.537747 -89 GAATCGCTTGATTTTTAAAGAGCATGAGCA 35 172 1 ATTTTTAAAG 0.907154 -30 ATTTTTTATTATTTGAAAAA 37 1 1 ATTTTTTATT 0.583257 -38 ACGAGGAGCAATTTTTAATGCACCGTTGAA 38 186 0 ATTTTTAATG 0.847884 -115 GCCTGTAAGGATATTTAAAGGTTATGTGCC 40 60 0 ATATTTAAAG 0.455399 -45 ********** Masking position 5 Map Score: 4.52547 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 76 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 14 ATTATTATTCAATAAAAAAGGGGTGGTGGT 1 112 1 ATAAAAAGGG 0.913341 -20 GCTGGCTTTACAAAAAAAGCGTTTAAAATGTT 4 72 0 AAAAAAAGGT 0.730549 -22 CTTGCTGACTACGTAACACGCGGAGTGTTGATA 6 110 1 AGTAACAGGG 0.915881 -191 AAATGTAGTGATAAAACATGAGGTGGTTGG 13 46 1 AAAAACAGGG 0.924734 -20 TGTTGCTGAAAATAATCAGGCGGTGATGGG 14 8 0 ATAATCAGGG 0.760417 -319 GTTGATTGATATTTAAAATGAGTGTATCTGCAA 15 44 1 ATTAAAAGGT 0.830951 -58 GAACATTAAAAATTAACATGCGGCAAAGATTTA 18 46 1 ATTAACAGGG 0.957035 -168 AGAATTTGTAATTAAAAACGAGGATTAATTATA 20 88 1 ATAAAAAGGG 0.913341 -76 AAAAAGGTTTAAATAAAAAGCGTATTAAATCTT 21 70 1 AATAAAAGGT 0.78121 -32 ACGCAAATAAATAACAAGAGGCTAATAAGGT 30 196 0 AATAACAGGG 0.941794 -21 TTTCGTTAAAAAGAAAAAAGAGT 36 1 0 AGAAAAAGGT 0.645946 -61 GAAGCGAAGTTAACAGGGGGCGATAAAAGG 36 42 0 ATTAACAGGG 0.957035 -20 TGCTGTTGGCATTTTAAAGGAGGAGGGTATAGA 38 104 0 ATTTAAAGGG 0.577366 -197 AATTGTAGTTATATATCATGAGTTTAACGAGGA 38 209 0 AATATCAGGT 0.518133 -92 * ****** * ** Masking position 8 Map Score: 7.17934 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 41 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 15 CAATTCCGACTTGCAGAGAGGACACGCGAG 5 107 0 TTGCAGAGAG 0.808246 -145 GTGATTGCTTTGCAGTTACACCTTTAAAC 8 54 0 TTGCAGTTAC 0.709508 -19 GCAAAGATTGTTGCTGAAAATAATCAGGCG 14 19 0 TTGCTGAAAA 0.869393 -308 TATAAAGCTTTTGCAGATACACTCATTTTA 15 57 0 TTGCAGATAC 0.931643 -45 TAATATGGAATTGCTGATACCTTTATCGTT 26 11 1 TTGCTGATAC 0.931643 -290 TATTGAGATATTGCAGAAAACGAATCCACG 30 151 0 TTGCAGAAAA 0.869393 -66 GTGGAGGAGCTTGCTGAAAGCATCTCAAGT 38 139 0 TTGCTGAAAG 0.877837 -162 TTAAAATAGTTTGCTGATAAGAAGTTTT 39 9 0 TTGCTGATAA 0.896561 -41 ********** Masking position 9 Map Score: 2.12651 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 64 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678