AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00230_aful_reg_300.orf -o00230_aful_300.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 Purged sequences: AF0195 22 A. fulgidus predicted coding region AF0195 Input sequences: #1 AF0194 300 A. fulgidus predicted coding region AF0194 #2 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #3 AF0197 86 acetyl-CoA synthetase (acs-1) #4 AF0204 72 conserved hypothetical protein #5 AF0239 93 xanthine-guanine phosphoribosyltransferase (gptA-1) #6 AF0252 251 CTP synthase (pyrG) #7 AF0288 300 adenylylsulfate 3-phosphotransferase (cysC) #8 AF0481 64 proteasome, subunit beta (psmB) #9 AF0483 101 conserved hypothetical protein #10 AF0484 33 GTP cyclohydrolase II (ribA-1) #11 AF0487 57 penicillin G acylase #12 AF0495 265 A. fulgidus predicted coding region AF0495 #13 AF0496 57 conserved hypothetical transmembrane protein #14 AF0497 132 DNA polymerase B1 (polB) #15 AF0676 72 adenylate kinase (adk) #16 AF0677 165 acetyl-CoA synthetase (acs-3) #17 AF0756 206 exopolyphosphatase (ppx1) #18 AF0764 138 LSU ribosomal protein L7AE (rpl7AE) #19 AF0841 80 adenylosuccinate synthetase (purA) #20 AF0842 65 A. fulgidus predicted coding region AF0842 #21 AF0875_AF0876 326 AF0875: snRNP, putative, AF0876: 5'-nucleotidase (nt5) #22 AF0971 101 conserved hypothetical protein #23 AF1117 62 DNA-directed RNA polymerase, subunit E' (rpoE1) #24 AF1118 111 A. fulgidus predicted coding region AF1118 #25 AF1127 213 LSU ribosomal protein L18E (rpl18E) #26 AF1131 75 DNA-directed RNA polymerase, subunit K (rpoK) #27 AF1157 163 phosphoribosylamine--glycine ligase (purD) #28 AF1215 101 cell division protein, putative #29 AF1232 63 conserved hypothetical protein #30 AF1260 207 phosphoribosylformylglycinamidine synthase I (purQ) #31 AF1261 133 medium-chain acyl-CoA ligase (alkK-4) #32 AF1263 74 iron-sulfur cluster binding protein #33 AF1269 300 A. fulgidus predicted coding region AF1269 #34 AF1270 33 transcriptional regulatory protein, ArsR family #35 AF1319 300 A. fulgidus predicted coding region AF1319 #36 AF1320 24 GMP synthase (guaA-2) #37 AF1342 126 thymidine phosphorylase (deoA-2) #38 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #39 AF1420 216 membrane protein #40 AF1421 49 conserved hypothetical protein #41 AF1422 35 aspartate racemase #42 AF1423 112 conserved hypothetical protein #43 AF1664_AF1665 147 AF1664: ribonucleotide reductase (nrd), AF1665: ornithine cyclodeaminase (arcB) #44 AF1667 158 sulfate adenylyltransferase (sat) #45 AF1693 45 phosphoribosylformylglycinamidine cyclo-ligase (purM) #46 AF1886 32 DNA-directed RNA polymerase, subunit B'' (rpoB2) #47 AF1941 201 conserved hypothetical protein #48 AF2242 61 adenylosuccinate lyase (purB) #49 AF2243 38 3-ketoacyl-CoA thiolase (fadA-3) #50 AF2244 300 acyl-CoA dehydrogenase (acd-11) #51 AF2277 49 DNA polymerase, bacteriophage-type #52 AF2285 104 SSU ribosomal protein S13P (rps13P) #53 AF2287 80 carotenoid biosynthetic gene ERWCRTS, putative #54 AF2289 216 mevalonate kinase (mvk) Motif number 1 AATGAGCAAATTTAAATTCATTATCATCTTAA 3 40 0 TTTAAACATT 0.624376 -47 AAAAAAGCGTTTAAAATGTTTTCGATGCTGAC 5 60 0 TTAAAATTTT 0.936551 -34 TGATAACAGATAAAAAGTTTTTAGAAGTCAAA 7 198 1 TAAAAATTTT 0.715388 -103 TTAAAAATCTTTTTTCTCTATT 8 1 1 TTAAAACTTT 0.890612 -64 AATTTTGGACTAAAAAAATTTTCATAAACAAC 12 30 0 TAAAAATTTT 0.71539 -236 CACACCAAACTTTAAATCCTTTTAAGCATAAT 14 104 1 TTTAAACTTT 0.883856 -29 CAGTTACACCTTTAAACTTTTTGATTTTTACC 15 39 0 TTTAAATTTT 0.932417 -34 TAGTTGTTAGTTAAAAATGTTTTGTCTAATAC 16 23 1 TTAAAAGTTT 0.872228 -143 AAAATCTATTTTAAAAAACTTGCGAAAGCGTG 16 109 0 TTAAAACTTG 0.739313 -57 TTATTTATTGTTAAAATCTATTTTAAAAAACT 16 121 0 TTAAAATATT 0.763267 -45 GGAGTGATATTTTAAATTTTTGTGTATGAAAG 17 45 1 TTTAAATTTG 0.827757 -162 AATCACAAGATTTAAATGGATTAACATCCTAT 18 21 0 TTTAAAGATT 0.582237 -118 CCCGTGCAGTTTTAAAAGTTTTGGTAACACTG 18 68 0 TTTAAATTTT 0.932417 -71 AGCTTCAGGGTTAAAAATGTTTTCGACTTGTG 21 206 1 TTAAAAGTTT 0.872228 -121 ATTTAAATTTTTTCATTTATGAA 22 2 1 TTTAAATTTT 0.932416 -100 AATCTGGCAATATAAAGCTTTTGCAGATACAC 22 65 0 TATAAATTTT 0.701439 -37 ACTTCAATAATTTAAATTTTTTGCTCAGATAA 24 24 1 TTTAAATTTT 0.932416 -88 CATTACGTAATTTAAATCTTTGCCGCATGTTA 25 59 0 TTTAAATTTG 0.827758 -155 AACTCTAAACTTTAAAGACATTCGAAAGCCTT 27 19 1 TTTAAACATT 0.624376 -145 ACGCTTTTTATTTAAACCTTTTTCCCAACTTT 28 61 0 TTTAAATTTT 0.932417 -41 CAGTCCAAGATTAAAATTTATTTAGCCAAACC 35 178 0 TTAAAATATT 0.763265 -123 GTCGTCAGCTTTAAAACCTTTTCAGGTGAGAA 37 22 1 TTAAAATTTT 0.936551 -105 GCTTTGAATGTTAAAAAGTTTGCTGTGCTACC 40 17 0 TTAAAATTTG 0.837176 -33 GAAGTTGAGGTTAAAATTTTTTAGGTTGGGTG 42 23 1 TTAAAATTTT 0.936548 -90 CCTTTAATCATTAAAATATTTTTCGAAACCTT 44 97 1 TTAAAATTTT 0.936551 -62 GAAAAGTCTTTTTAAAAGGTTGCCCATCTGAA 45 13 0 TTTAAAGTTG 0.689686 -33 AATTTATAAGTAAAAAAATTTTACTAAAATAA 47 91 0 TAAAAATTTT 0.71539 -111 TTGTGTTCTATTTAAATCCTTTTTCAATTGTT 50 240 1 TTTAAACTTT 0.883856 -61 TTAAGGCAAATTAAAATAGTTTGCTGATAAGA 51 17 0 TTAAAAGTTT 0.872228 -33 ****** **** Masking position 6 Map Score: 34.6083 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 72 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 2 AGCTTCTGCTCCATCAGCCCAAAGAACCTC 1 64 0 CCATCAGCCC 0.786357 -237 ACTCCTCAAACAACCACCTCCCGTACTCAA 1 225 0 CAACCACCTC 0.895859 -76 ACCACCACCCCTTTTTTATTG 2 121 0 CCACCACCCC 0.944209 -11 TCGTTCTCCTCAACCACTTCAACTTCCAAT 6 133 0 CAACCACTTC 0.414695 -119 TTTCCAGATATAATCTCCTCTTCGTTCTCC 6 154 0 TAATCTCCTC 0.810705 -98 GTTTTGTCATCTCACCCATTTAAACC 7 7 1 TCATCTCACC 0.564233 -294 TTTGCCCCGTTAATCTGCTCCAAACTATAA 12 152 1 TAATCTGCTC 0.483233 -114 TCCCTCTCGCTCATCTGCTCCCATCTCAAT 14 24 0 TCATCTGCTC 0.736069 -109 AAGATACAGCCAATCACACCAAACTTTAAA 14 90 1 CAATCACACC 0.464841 -43 TTCATCACCTCTAATAGATAT 16 155 0 TCATCACCTC 0.953398 -11 TTCACCACCCCCTTTCGTTTT 17 2 1 TCACCACCCC 0.931266 -205 AAATCATCATTCATCGGCTCTTCCCTAATT 18 101 0 TCATCGGCTC 0.545282 -38 GTCATCACCTCCTTCATCAAA 18 128 0 TCATCACCTC 0.953398 -11 CCAACCACCTCATGTTTTATC 20 55 0 CAACCACCTC 0.895859 -11 CCCATCACCGCCTGATTATTT 21 2 1 CCATCACCGC 0.856407 -325 AAAATCATCACCGCAGCCTTTGCT 23 49 0 TCATCACCGC 0.82683 -14 AAACTTGTTTTCATCACATCAACTTAGGGT 35 151 1 TCATCACATC 0.758677 -150 GTCATCTCACCTTTCTCTTTT 46 22 0 TCATCTCACC 0.564233 -11 AAGACCTTCTCCACCGCCTCAGCCTGAGGC 50 62 1 CCACCGCCTC 0.873216 -239 ATGCTTTCAGCAAGCTCCTCCACCTTCACC 50 146 1 CAAGCTCCTC 0.589517 -155 TCCTCCACCTTCACCACTTCAAGTTTTCAA 50 161 1 TCACCACTTC 0.628479 -140 TATCCTGACTCAACCTCCTCTTCGAGGCAG 53 45 0 CAACCTCCTC 0.843035 -36 TCGTAATCCCTCAGCTCCTCCATAATAGCC 54 74 1 TCAGCTCCTC 0.774213 -143 ********** Masking position 3 Map Score: 20.4098 Number of sites scoring better than the average of aligned sites = 1747 Number in coding regions = 1631 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 3 GAAAACTTTAACTTTTTGTCAAAATAA 1 284 0 CTTTATTTTT 0.779001 -17 ACTTTCATTTTTTGCATGAAACG 4 2 1 CTTTCTTTTT 0.865655 -71 CCCTCGAACTTTTTAACTTTTTAGCCAGCTTT 5 23 1 TTTTATTTTT 0.838743 -71 CACTTTGTTTTTGCTTTTTAAAATAGCCC 8 46 0 TTTTTTTTTT 0.868841 -19 AATTTGAAATTATTTAATTTTTATGTTTTGAC 11 25 0 TATTTTTTTT 0.645591 -33 TCTTTATTATTTTGTTGTTGTTTATGAAAATT 12 14 1 TTTGTTTGTT 0.494386 -252 AAATTTATTCCTTTTTTTCTCTTGCTC 15 6 1 TATTCTTTTT 0.72334 -67 ACCTTTAAACTTTTTGATTTTTACCGGAGCAA 15 32 0 TTTTTTTTTT 0.868841 -41 GTATTTGTTTTGTAGTTGTTAGTTAAAAAT 16 9 1 TTTGTTTGTT 0.494386 -157 TCACCACCCCCTTTCGTTTTTTTGGAAGAAAT 17 12 1 CTTTCTTTTT 0.865655 -195 CGGAGTGATATTTTAAATTTTTGTGTATGAAA 17 44 1 TTTTATTTTT 0.838743 -163 GTTTATTTGGTTTGCGATTTTTGGAAAAATGG 19 36 0 TTTGCTTTTT 0.806555 -45 GTATTTAAGCTTTGTTATTTTTACACAGGTAG 27 58 1 TTTGTTTTTT 0.743913 -106 AAGTTTAGGTTTTTCTTTTTTTACTTTTCCCT 30 34 1 TTTTCTTTTT 0.904833 -174 ATTTTCCAACTTTTTTGTTTTTCAGCAGATTA 31 25 1 TTTTTTTTTT 0.868841 -109 GATGGAAGCCCTTGAGCTTTTTGGATTGGGCA 33 122 1 CTTGATTTTT 0.60719 -179 AAAATGGTTATATTTATTTTTTATCCTCAAAA 35 243 1 TATTTTTTTT 0.645591 -58 TCTGAAAGAATATTAACTTTTTCTCGCTATCG 37 91 0 TATTATTTTT 0.588525 -36 CCAAAGCTTTATCTTGTTAGGCGATTAG 41 7 1 CTTTATTGTT 0.542644 -29 AAAATTTTTCTATTCAATTTTTCCTTCAATAG 43 73 1 TATTCTTTTT 0.72334 -75 GTCATCTCACCTTTCTCTTTTTGCAGATTTCA 46 11 0 CTTTCTTTTT 0.865655 -22 ACTCTTTTTTCTTTTTAACGAAAAGG 48 5 1 TTTTTTTTTT 0.868841 -57 TTTAAATCCTTTTTCAATTGTTTAACTTGGCA 50 250 1 TTTTCTTGTT 0.761924 -51 GCACAAAATTCTTTAAGTTTTTCCCGTAGTCT 54 190 1 CTTTATTTTT 0.779001 -27 ***** ***** Masking position 8 Map Score: 20.5571 Number of sites scoring better than the average of aligned sites = 264 Number in coding regions = 129 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 CAGATATAATCTCCTCTTCGTTCTCCTCAA 6 150 0 CTCCTCTTCG 0.892535 -102 ATACTAAGAACTACGCAGCGTACTTTGCTA 12 122 1 CTACGCAGCG 0.773748 -144 TTGTCAAATTCTTCTTTGCGTTCATGTTTT 12 229 1 CTTCTTTGCG 0.580409 -37 TCGATTCTAGCTCCGTTGAGTTCAAAATAA 17 104 0 CTCCGTTGAG 0.626494 -103 AAAATCATCACCGCAGCCTTTGCTGGGT 23 45 0 CACCGCAGCC 0.892387 -18 ATATCAACTACACCTCAGCGTAGTTTTGAC 25 96 0 CACCTCAGCG 0.897132 -118 ATTTGACTTCCTCCTCTGCCAGCTTCCTTA 25 134 0 CTCCTCTGCC 0.97111 -80 TGCAGAACATCAACGCTGCCGACACGGAAA 30 156 1 CAACGCTGCC 0.697332 -52 TGGTGCAGCTCTCCGTCGCCTATATTTTGC 33 202 1 CTCCGTCGCC 0.789942 -99 TTATAAGTTGCACCGTTGCGCAACCAAACA 34 14 1 CACCGTTGCG 0.925337 -20 ATTTTTTGAACTCCTTTGCCTTTTATTTTC 44 18 1 CTCCTTTGCC 0.933975 -141 TAAAAGGTTACTCCTTTTCGTTAAAAAGAA 48 19 0 CTCCTTTTCG 0.777538 -43 CCTTCTCCACCGCCTCAGCCTGAGGCGGAA 50 66 1 CGCCTCAGCC 0.725746 -235 CTGACTCAACCTCCTCTTCGAGGCAGATTT 53 41 0 CTCCTCTTCG 0.892535 -40 TCCTCCCAGCCTCCGCTGCGGGGTCGGAGG 54 108 1 CTCCGCTGCG 0.985726 -109 ********** Masking position 4 Map Score: 11.2377 Number of sites scoring better than the average of aligned sites = 725 Number in coding regions = 685 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 5 TGAATGCTGTTGGAGGTATGAGTAAATAACGATTTCCG 6 46 0 TGAATAAATA 0.4461 -206 GAAGGTTGCCTTAGGGCTATTTTAAAAAGCAAAAACAA 8 33 1 TGTTTAAAAA 0.655968 -32 TCCTTTTTTTCTCTTGCTCCGGTAAAAATCAAAAAGTT 15 19 1 CGTGTAAAAA 0.78134 -54 AGCTTTATATTGCCAGATTTGTTAATTATAAAAA 22 78 1 TGTGTAATTA 0.588761 -24 TAATTTAAATTTTTTGCTCAGATAAAAATGCTCACTCT 24 31 1 TGTGTAAAAA 0.971157 -81 TAATGTTCCTTCCGCGGAAGGCTAAAAACGATTTCGAT 25 16 0 TGAGTAAAAA 0.879306 -198 AAACGGAAAATAATCGATGAGATAAAAAACGGT 27 141 1 TGTGTAAAAA 0.97118 -23 GATCGTCCTGTCTAGGGAAAAGTAAAAAAAGAAAAACC 30 41 0 TGAATAAAAA 0.575598 -167 CGATTAAACTTGATTGATTGGTGAAAAACT 31 114 1 TGTGGAAAAA 0.790783 -20 CACGTCAATCTTCTCCGTAAGGTAAAAA 33 1 0 TCTGTAAAAA 0.687942 -300 TTCTGGATAGTTAACGATGGGGTAAATATTAATATAGA 35 40 1 TGTGTAAATA 0.952405 -261 TCACATCAACTTAGGGTTTGGCTAAATAAATTTTAATC 35 164 1 TGTGTAAATA 0.952405 -137 TAAATTGCAATTCCAGCTAAGTTAAAAATGGTTATATT 35 219 1 TGTGTAAAAA 0.97118 -82 GGTTAAAACTTGTTGGTGAATTAAATAAAGGTAATTT 35 274 0 TGTATAAATA 0.788353 -27 TGGATTTTGCTTGAAGTTGAGGTTAAAATTTTTTAGGT 42 11 1 TGTGTTAAAA 0.706825 -102 TTTTTTAGGTTGGGTGATGCGCTAAATACTTCAAGACA 42 39 1 TGTGTAAATA 0.952405 -74 GATGTTGTTCTGGTTGGGCCGATAAAAATTTACCGCTA 42 84 0 TGGGTAAAAA 0.810372 -29 CAGCCTTATATAAAGGTTTCGAAAAATATTTTAATGAT 44 103 0 TGTGAAAATA 0.602288 -56 CTTCAAGTTTTCAACGGTGCATTAAAAATTGCTCCTCG 50 177 1 TGTATAAAAA 0.862509 -124 * * * * ****** Masking position 15 Map Score: 10.1005 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 61 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 6 GATGGAGCTTCTGCTCCATCAGCCCAAAGAAC 1 67 0 CGCTCCTCAG 0.716799 -234 CTATAATAAGCAGTCCCAGCAAAAAACCATAT 12 176 1 CGTCCCGCAA 0.938391 -90 ATTCTTTCCCTCCAGAATTATCTAA 21 312 0 CTTCCCCCAG 0.79037 -15 ATATTGCTTCCCGACCCAGCAAAGGCTGCGGT 23 32 1 CGACCCGCAA 0.938391 -31 CAAATCTCGGCGGCCCCATCTGCTTTAAGGGG 26 52 1 CGCCCCTCTG 0.841408 -24 AATTATATATCCGCCCCTGCTGACCGAAAACG 27 114 1 CGCCCCGCTG 0.96836 -50 GGAATCAGACCAGCCCCACCAGCTAAAAGAAT 30 88 1 CGCCCCCCAG 0.98318 -120 TAAGCTTTTTCCGTGTCGGCAGCGTTGATGTT 30 161 0 CGTGTCGCAG 0.662409 -47 GTGAGATTTTCCGAGCCCGCAGTTGAATTTGG 39 15 0 CGAGCCGCAG 0.967466 -202 AGTCTTGAAGCGTTGCCAGCAGAATAACTTGA 39 118 0 CTTGCCGCAG 0.79037 -99 AAATTTTTATCGGCCCAACCAGAACAACATCA 42 91 1 CGCCCACCAG 0.794066 -22 GTCGTTGAGCCGGAACCGGCAAAGATAGAGGA 54 41 0 CGAACCGCAA 0.598909 -176 GTCTACACCTCCGACCCCGCAGCGGAGGCTGG 54 113 0 CGACCCGCAG 0.987031 -104 * ***** **** Masking position 10 Map Score: 6.81682 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 295 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 TCCTCAGAAAAGCTTGGTAAGGAGTCTCCA 1 174 0 AGCTTGGTAA 0.721689 -127 GACACCTCAAAGCTGGCTAAAAAGTTAAAA 5 33 0 AGCTGGCTAA 0.870889 -61 GCAAGCTGAGAGCTTGCTGACTACGTAACA 7 98 1 AGCTTGCTGA 0.982033 -203 AAGGATTTAAAGTTTGGTGTGATTGGCTGT 14 95 0 AGTTTGGTGT 0.573546 -38 AACTTGCGAAAGCGTGCTGAGATAAATCAT 16 95 0 AGCGTGCTGA 0.903688 -71 AAGATAAGGAAGCTGGCAGAGGAGGAAGTC 25 130 1 AGCTGGCAGA 0.915708 -84 AAACTTTCAAAGCTGGCAGATCTTTAATT 30 10 0 AGCTGGCAGA 0.915708 -198 GAGGTGAGAGAGCTTGCAATCTGTAATGCT 33 153 0 AGCTTGCAAT 0.68991 -148 AATGTTAAAAAGTTTGCTGTGCTACCAATA 40 13 0 AGTTTGCTGT 0.862218 -37 AATTGAGGATAGCTTGCTGTTCTCAACTAA 47 60 0 AGCTTGCTGT 0.965926 -142 AAGGTGGAGGAGCTTGCTGAAAGCATCTCA 50 142 0 AGCTTGCTGA 0.982033 -159 AAATTAAAATAGTTTGCTGATAAGAAGTTT 51 12 0 AGTTTGCTGA 0.923463 -38 ********** Masking position 1 Map Score: 11.1554 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 414 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 8 AAGCGTTTAAAATGTTTTCGATGCTGACACCT 5 56 0 AAGTTTCGAT 0.812542 -38 AATAGAGAAAAAAGATTTTTAA 8 1 0 AAGTTTTTAA 0.543461 -64 TTCCCTTACAAACGTTTTTGTACTTGAAATAA 9 15 0 AAGTTTTGTA 0.61422 -87 AAATACGTGTAATTATTTTGAACTCAACGGAG 17 92 1 AATTTTTGAA 0.72499 -115 TTGAGTACGAATAGGTTTTGAAAAAATTTCGA 17 152 1 ATGTTTTGAA 0.61422 -55 GGAAGGTAATAACGTTTTCGAAATTTTTTCAA 17 169 0 AAGTTTCGAA 0.952491 -38 CAGGGTTAAAAATGTTTTCGACTTGTGTGCCT 21 211 1 AAGTTTCGAC 0.717717 -116 CTGGCAATATAAAGCTTTTGCAGATACACTCA 22 62 0 AAGTTTTGCA 0.70236 -40 GAAGGCTAAAAACGATTTCGATATGAG 25 6 0 AAGTTTCGAT 0.812536 -208 TACGATTTGTAAGGCTTTCGAATGTCTTTAAA 27 29 0 AAGTTTCGAA 0.952491 -135 CAGCTAAAAGAATTCTTTTCAAATTGATGCCG 30 107 1 AATTTTTCAA 0.372112 -101 TCTCACCTGAAAAGGTTTTAAAGCTGACGACA 37 21 0 AAGTTTTAAA 0.543461 -106 ATATTCTTTCAGAGTTTTTGAAGTTCA 37 110 1 AGGTTTTGAA 0.70236 -17 AGAGGCTAATAAGGTTTTTCATGAGTTTGATA 39 179 0 AAGTTTTCAT 0.505567 -38 GTAGAAAATTTTTTGAACTCCTTTGCC 44 6 1 AATTTTTGAA 0.72499 -153 CGCGGTTTTGAATGTCTTTGAAAATTCGAAAA 44 65 1 AAGCTTTGAA 0.690487 -94 TTAATGATTAAAGGTTTTCGAATTTTCAAAGA 44 79 0 AAGTTTCGAA 0.952491 -80 AGCCTTATATAAAGGTTTCGAAAAATATTTTA 44 108 0 AAGTTTCGAA 0.952491 -51 TCACCCTGCAAACGTTTTTCAAATAATAAAAA 49 13 0 AAGTTTTCAA 0.825466 -26 ** * ******* Masking position 7 Map Score: 10.4582 Number of sites scoring better than the average of aligned sites = 215 Number in coding regions = 176 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 9 TTCTTTGGGCTGATGGAGCAGAAGCTCCATC 1 68 1 TGAGGAGCAG 0.888191 -233 GGTGTTTGAGTACGGGAGGTGGTTGTTTGAG 1 220 1 TACGGAGGTG 0.664037 -81 GTTCGAGGGATTAGGGAGGAT 5 1 0 TTAGGAGGAT 0.818347 -93 GCACGGGGAATTAGGGAAGAGCCGATGAATG 18 93 1 TTAGGAAGAG 0.818347 -46 GATGATTTGATGAAGGAGGTGATGAC 18 123 1 TGAGGAGGTG 0.938427 -16 TAAGGTTCGTTGCAGGAGGAGTTATTTAAAA 21 284 0 TGCGGAGGAG 0.963109 -43 TTTTTACCTTACGGAGAAGATTGACGTGC 33 9 1 TTAGGAGAAG 0.831851 -292 GAAAACAAGTTTTAGGAGGAGTTATCATGGA 35 132 0 TTTGGAGGAG 0.898318 -169 GTTGGCATTTTAAAGGAGGAGGGTATAGAAG 50 102 0 TAAGGAGGAG 0.958307 -199 CTTGAAGTGGTGAAGGTGGAGGAGCTTGCTG 50 153 0 TGAGGTGGAG 0.887373 -148 TATCATGAGTTTAACGAGGAGCAATTTTTAA 50 198 0 TTACGAGGAG 0.86974 -103 ATGGAGGCTATTATGGAGGAGCTGAGGGATT 54 78 0 TTAGGAGGAG 0.984323 -139 *** ******* Masking position 1 Map Score: 7.47026 Number of sites scoring better than the average of aligned sites = 601 Number in coding regions = 566 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 GGGAAAACAGGAAGTTACCGTTTTCC 2 5 1 AAAAGGAAGT 0.906925 -127 TAAATGTTATAAATTGGAGGTGAACT 3 71 1 AAATGGAGGG 0.932804 -16 CAGCATTCATGAAAAGGAAGCTTCTGGAAATC 6 75 1 GAAAGGAAGT 0.879452 -177 CTGCAAGTCGGAATTGGAAGTTGAAGTGGTTG 6 121 1 GAATGGAAGT 0.817018 -131 ATCATAAAAAATAGGATGTTAATCCATTTA 18 9 1 AAAAGGATGT 0.669196 -130 TGTAGTGATAAAACATGAGGTGGTTGG 20 49 1 AAAATGAGGG 0.878702 -17 CGAGTCAGCAAAAAATGAGGCGCCA 25 199 1 AAAATGAGGG 0.878702 -15 ATTTGTAATTAAAAACGAGGATTAATTATATA 27 91 1 AAAACGAGGT 0.730022 -73 GAATCAAAAAAAGAGGAAGGGCTT 38 4 0 AAAAGGAAGG 0.905169 -21 GATTTTGCTTGAAGTTGAGGTTAAAATTTTTT 42 13 1 GAATTGAGGT 0.772141 -100 TACTAAAATAAAAATTGAGGATAGCTTGCTGT 47 70 0 AAATTGAGGT 0.819038 -132 TGGCATTTTAAAGGAGGAGGGTATAGAAGAGC 50 99 0 AAGAGGAGGT 0.852542 -202 TGAAGTGGTGAAGGTGGAGGAGCTTGCTGAAA 50 150 0 AAGTGGAGGG 0.776098 -151 GCACCGTTGAAAACTTGAAGTGGTGAAGGTGG 50 165 0 AAATTGAAGG 0.651056 -136 GCACTTCGAAGAGGAAGATTGACCACCTG 53 8 1 GAAAGGAAGT 0.879452 -73 AATCTGCCTCGAAGAGGAGGTTGAGTCAGGAT 53 42 1 GAAAGGAGGT 0.945462 -39 *** ****** * Masking position 8 Map Score: 8.8961 Number of sites scoring better than the average of aligned sites = 471 Number in coding regions = 429 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 11 TTCATCAAAATTCAGGCTCATGTGAGGCTT 1 143 0 TTCAGGCTCA 0.874695 -158 AAATAACGATTTCCGCCTTAATTTTAAATA 6 31 0 TTCCGCCTTA 0.925315 -221 CAACTTCCAATTCCGACTTGCAGAGAGGAC 6 114 0 TTCCGACTTG 0.885362 -138 TCGTACTCAATTCAGACTCATCTTTAACTC 17 132 0 TTCAGACTCA 0.866067 -75 AAAAAGACTTTTCCGACTTGAATC 45 32 1 TTCCGACTTG 0.885362 -14 GAAGAGCTGTTTCCGCCTCAGGCTGAGGCG 50 76 0 TTCCGCCTCA 0.96239 -225 TCTTTGCCGGTTCCGGCTCAACGACCTCGT 54 48 1 TTCCGGCTCA 0.96239 -169 ********** Masking position 8 Map Score: 1.85177 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 42 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 TTCATGAATGCTGTTGGAGGTATGAGTAAA 6 58 0 CTGTTGGAGG 0.967206 -194 TCTTTTTTCTCTATTGAAGGTTGCCTTAGG 8 18 1 CTATTGAAGG 0.921401 -47 CTGTACTGGTAGAGGGCTGCAAGGA 13 43 0 CTGGTAGAGG 0.831614 -15 ATAAATATATCTATTAGAGGTGATGAA 16 149 1 CTATTAGAGG 0.921401 -17 TTCTCTGTCCCTGTGAGAGGTGAGAGAGCT 33 169 0 CTGTGAGAGG 0.831614 -132 AGAAAATTTCCTGTTAAAGGGTTCTTTTCT 33 281 1 CTGTTAAAGG 0.921384 -20 TCGAGAGCATCTATTGAAGGAAAAATTGAA 43 85 0 CTATTGAAGG 0.921401 -63 GAATAATCCTCAATTGAAGGGGGGCACATA 52 38 1 CAATTGAAGG 0.677504 -67 ********** Masking position 8 Map Score: 2.0562 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 47 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 Motif number 13 GATAGAGAGGTTCTTTGGGCTGATGGAGCAGA 1 58 1 TTCTTTGGTG 0.833799 -243 CATCTGTTTGATTCTTTGGATGAGTTCATTTA 1 95 1 ATTCTTGGTG 0.660122 -206 ATCGTGCTCATTTCGTCAGTTGTTGTTCGGGG 2 36 0 TTTCGTAGTG 0.833799 -96 CATAATTCAATTTTTTAAGATGATAATGAATT 3 26 1 TTTTTTAGTG 0.925904 -61 TTATTTCAGGTTTCTTTAGCTGCCATTGACTC 7 42 1 TTTCTTAGTG 0.935382 -259 CAAACCTGCATTTTTCGAGTTGAAATAGAGTT 9 45 0 TTTTTCAGTG 0.812411 -57 CCCCCTTTCGTTTTTTTGGAAGAAATCGGAGT 17 18 1 TTTTTTGGAG 0.626399 -189 CCTATAAAAGTTTCTTCGGATGGAGGCAATTA 21 80 1 TTTCTTGGTG 0.94372 -247 TGAACCCGAATTTTGCCAGATGCTGAGAGCTT 21 245 0 TTTTGCAGTG 0.60015 -82 TTGAAAAGAATTCTTTTAGCTGGTGGGGCTGG 30 97 0 TTCTTTAGTG 0.812411 -111 GAGGTTAAAATTTTTTAGGTTGGGTGATGCGC 42 29 1 TTTTTTGGTG 0.935382 -84 AATGTCAAGTTTTCTTGAGATGCTGTAAGAAA 43 43 1 TTTCTTAGTG 0.935376 -105 ****** ** ** Masking position 2 Map Score: 3.90079 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 24 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 14 TCAGCAGGTAGCTTCCTCAGAAAAGCTTGGTAAGGAGT 1 179 0 GTCTGAAGCT 0.740374 -122 ATTATTTCGGGATATCACAGAAAAACTTATTTTGACAA 1 258 1 GTTAGAAACT 0.911742 -43 TGCATGAAACGATATCAGCGCAAAGCAAAGTTTAAATC 4 23 1 GTTAGAAGCA 0.969723 -50 CATTTTAAACGCTTTTTTTGTAAAGCCAGC 5 74 1 GTTTGAAGCA 0.943218 -20 ATGACACCTCGGTTTCTTAGGAATGCATCCCCTATATT 7 161 0 GTTTGAAGCT 0.943219 -140 GTCCAAAATTGTTGTAAAGGAAACGCAATTGTATCCAT 12 52 1 GTTAGAAGCA 0.969723 -214 AAAGTTTAAAGGTGTAACTGCAAAGCAATCAC 15 51 1 GTTAGAAGCA 0.969723 -22 GAAAGATTTCGCTGTATTCGAAATACGTGTAATTATTT 17 72 1 GTTTGAAACT 0.842715 -135 TTGGGAAAAAGGTTTAAATAAAAAGCGTATTAAATCTT 28 65 1 GTTAAAAGCT 0.816515 -37 TAGACAGGACGATCTTAGAGAAAGGAATCAGACCAGCC 30 65 1 GTTAGAAGAT 0.696794 -143 TTTAGGAGGAGTTATCATGGAAATACCACTCAGTTCGG 35 115 0 GTTAGAAACA 0.911742 -186 ATTGAAAAAGGATTTAAATAGAACACAATTGTAGTTAT 50 230 0 GTTAAAAACA 0.589376 -71 * * * * * ** ** * Masking position 12 Map Score: 4.6876 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 78 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 AGGTGGTTGTTTGAGGAGTGAAATTATTTCGG 1 236 1 TTGGGGTGAA 0.826804 -65 TCAGTTGTTGTTCGGGGGAAAACGGTAACTTC 2 21 0 TTCGGGAAAA 0.966075 -111 GGAGTTTGATTTCAGGTGTAATAAAAGTATCC 9 76 0 TTCGGGTAAT 0.56781 -26 TTGCTGGAGCTTCAGGGTTAAAAATGTTTTCG 21 199 1 TTCGGTTAAA 0.737509 -128 CCTTAGATAATTCTGGAGGGAAAGAAT 21 310 1 TTCGGGGGAA 0.845403 -17 GTTATATAATTTGTGGAGAAAAGGCTATGAGG 32 46 1 TTGGGGAAAA 0.935769 -29 AGGTAATTTTTTGAGGATAAAAAATAAATATA 35 251 0 TTGGGTAAAA 0.783022 -50 TTAAAACCTTTTCAGGTGAGAATTTTTAAACA 37 32 1 TTCGGGAGAA 0.959007 -95 TTGCTTGAAGTTGAGGTTAAAATTTTTTAGGT 42 17 1 TTGGGTAAAA 0.783022 -96 AGAAGGTCTTTTCCGGCAAAAATCTGCTCCTC 50 40 0 TTCGGAAAAA 0.736112 -261 GGTGTAGAACTTCGGGTGAAAAACGATCTTCA 54 145 1 TTCGGGAAAA 0.966075 -72 AAAAACGATCTTCATGAGAGAATGTTTGCACA 54 163 1 TTCTGGAGAA 0.626842 -54 *** ** ***** Masking position 11 Map Score: 4.97775 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 194 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604