AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_aful_reg_300.orf -o02010_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: AF1404 29 transcriptional regulatory protein, AsnC family Input sequences: #1 AF0088 300 thiamine biosynthesis protein, putative #2 AF0094 300 conserved hypothetical protein #3 AF0231 232 glutamine ABC transporter, periplasmic glutamine-binding protein (glnH) #4 AF0232 39 glutamine ABC transporter, permease protein (glnP) #5 AF0433 122 conserved hypothetical protein #6 AF0438 79 3-ketoacyl-CoA thiolase (acaB-8) #7 AF0439 82 transcriptional regulatory protein, AsnC family #8 AF0442 300 succinoglycan biosynthesis regulator (exsB) #9 AF0641 51 ISA1214-3, ISORF2 #10 AF0680 145 glutamine ABC transporter, ATP-binding protein (glnQ) #11 AF0825 148 branched-chain amino acid ABC transporter, permease protein (braD-2) #12 AF0827 285 branched-chain amino acid ABC transporter, periplasmic binding protein (braC-2) #13 AF0887 128 ribose ABC transporter, ATP-binding protein (rbsA-1) #14 AF0968 205 3-ketoacyl-CoA thiolase (acaB-10) #15 AF0970 101 A. fulgidus predicted coding region AF0970 #16 AF0982 300 osmoprotection protein (proX) #17 AF0986 30 phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (hisA-2) #18 AF0987 109 conserved hypothetical protein #19 AF1006 300 ABC transporter, ATP-binding protein #20 AF1127 213 LSU ribosomal protein L18E (rpl18E) #21 AF1131 75 DNA-directed RNA polymerase, subunit K (rpoK) #22 AF1132 108 enolase (eno) #23 AF1134 74 A. fulgidus predicted coding region AF1134 #24 AF1135 99 A. fulgidus predicted coding region AF1135 #25 AF1136 103 ABC transporter, ATP-binding protein #26 AF1299 300 transcription initiation factor IIB #27 AF1300 85 ABC transporter, ATP-binding protein #28 AF1302 44 conserved hypothetical protein #29 AF1356 96 phosphate ABC transporter, periplasmic phosphate-binding protein (phoX) #30 AF1391_AF1392 50 AF1391: branched-chain amino acid ABC transporter, periplasmic binding protein (braC-4), AF1392: branched-chain amino acid ABC transporter, permease protein (braD-4) #31 AF1405 32 conserved hypothetical protein #32 AF1406 92 A. fulgidus predicted coding region AF1406 #33 AF1409 88 modification methylase, type III R/M system #34 AF1410 284 ISA0963-5, putative transposase #35 AF1411 140 A. fulgidus predicted coding region AF1411 #36 AF1413 104 surface layer protein B (slgB-2) #37 AF1415 203 chloride channel, putative #38 AF1418 49 glycerol-3-phosphate cytidyltransferase (taqD) #39 AF1419 24 ribose-phosphate pyrophosphokinase (prsA-2) #40 AF1420 216 membrane protein #41 AF1421 49 conserved hypothetical protein #42 AF1422 35 aspartate racemase #43 AF1423 112 conserved hypothetical protein #44 AF1608 59 spermidine/putrescine ABC transporter, ATP-binding protein (potA) #45 AF1767_AF1768 311 AF1767: dipeptide ABC transporter, dipeptide-binding protein (dppA), AF1768: dipeptide ABC transporter, permease protein (dppB) #46 AF1984 45 iron-dependent repressor (troR) Motif number 1 ATTTTCGAAAACAAAAATTTTATAATACGCATG 2 148 1 AAAATTTTAT 0.727836 -153 GCGACACTTCACAAAAGTTAAATATCCGATATG 2 271 1 AAAATTAAAT 0.638628 -30 TCAAAAATTGGAAAAGCTTAAATACATGCTGCT 3 165 0 GAAATTAAAT 0.849254 -68 TTTATCTATCGAAAATTTTTTAAGTTTTAAAAA 3 198 1 GAAATTTTAA 0.851851 -35 CAAAAAAATTTTTTATATCCCTCCTT 4 4 1 AAAATTTTAT 0.751469 -36 ATTTATGAGAAGAAAAATTGAAAGAAAA 5 6 0 AAAATTGAAA 0.464074 -117 CATATTTCACGAAAACATTAAATATTACACGAC 6 46 1 GAAATTAAAT 0.849254 -34 AATGGCAAACATAAAATTTTTATATTTTTAGTT 7 48 1 AAAATTTTAT 0.469189 -35 ACGCACGAGAAAAAAGATTTTATATAACAAACC 10 110 1 AAAATTTTAT 0.751469 -36 GAAAAAAACCAAAAAGGTTTTATACTTTTGCAA 11 114 1 AAAATTTTAT 0.751469 -35 CGCAAAAAAGGAAAAGCTTATATGTAATAATGT 12 242 1 GAAATTATAT 0.839743 -44 ATCTAAACGCGTAAAAATTGAATATATCAAGTA 14 105 1 GAAATTGAAT 0.822519 -101 GTTCATAAATGAAAAAATTTAAAT 15 88 1 GAAATTTAAA 0.860762 -14 CAATTAGAGAGCAAAATTTTAAAAGATGAAGAA 16 93 0 GAAATTTAAA 0.860762 -208 TCCGAACCTCAAAAAGCTTTTATAAGGGATTTA 16 252 1 AAAATTTTAT 0.751469 -49 GGAGTGGGAAGAAAAGGTTAAAAAA 17 3 0 GAAATTAAAA 0.770403 -28 AACTATTTTGAAAAACTTTTTATTGATAAATCA 18 25 0 AAAATTTTAT 0.751469 -85 TTAACATGCGGCAAAGATTTAAATTACGTAATG 20 58 1 GAAATTTAAA 0.860762 -156 CGTGGCTACCGAAAAGTTTAAATACTCTGCCGA 26 27 1 GAAATTAAAT 0.849254 -274 ATACTCTGCCGAAAACCTTATATACTGCATGAG 26 48 1 GAAATTATAT 0.839743 -253 CATATAGTTAGTAAATGTTGTATATACCATCCC 29 52 0 GAAATTGTAT 0.811696 -45 CCGAGCTTTAGTAAAGTTTTAAAATTTTAACGT 30 16 1 GAAATTTAAA 0.860762 -35 CTAAAGCTTCGTAAAGCTTTAAATCCATTTTGC 35 54 1 GAAATTTAAA 0.860762 -87 TTGTTAAATAGGAAAATTTATATTGATTAAAGT 36 34 1 GAAATTATAT 0.839737 -71 GAGCAAAGAAGTAAACTTTGAAAGTTGGGCTGA 37 35 0 GAAATTGAAA 0.734071 -169 TGGTAGCACAGCAAACTTTTTAACATTCAAAGC 41 16 1 GAAATTTTAA 0.851851 -34 AGTGTATCTGGCAAAAATTTAATGGGCTAATCT 45 250 0 GAAATTTAAT 0.912114 -62 * *** ****** Masking position 8 Map Score: 34.3072 Number of sites scoring better than the average of aligned sites = 218 Number in coding regions = 74 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 2 CATTACAGTGGGAGCGGCGGTGGGCGGCTGACC 1 30 1 GGGGGGGTGG 0.99054 -271 CCCCCCACCCGCTGTGGCGGAAGGCCCCTGAGA 1 77 1 GCGGGGGAAG 0.994331 -224 CCCCTGAGAAGGGGCGGAGGAGGAACAGAAACG 1 101 1 GGGGGGGAGG 0.99054 -200 CGTTGCACCCGGCGGGGAGGAGGCCGTTTCATC 1 187 0 GGGGGGGAGG 0.99054 -114 AAAAACTTTGGGAGTGGCGGTAGTAAGCCCCCT 1 254 0 GGGGGGGTAG 0.993246 -47 GCTACACCATGCATTGGAGGAAGGTTTAGCAGC 3 138 1 GCTGGGGAAG 0.974823 -95 ATTTTTCATCTGAGCGGGGGTTGCCGAGCGGAC 8 206 0 TGGGGGGTTG 0.769287 -95 CGACCTTCAGGCTGAGGTGATAGCCTTTGGAAA 13 95 1 GCGGGGATAG 0.926388 -34 AAGGAAGCTGGCAGAGGAGGAAGTCAAATCCAA 20 135 1 GCGGGGGAAG 0.994331 -79 TGAAGTCGTTGCTGGGGAGGTTGTTGCGAAGGC 22 85 1 GCGGGGGTTG 0.982277 -24 CTTAACTAAAGCGTAGGGGGAAGATACTGGCCC 26 226 0 GCTGGGGAAG 0.974823 -75 GCTCAAAAATGAATGGGTGGTAGGATAATAAGA 33 52 1 GATGGGGTAG 0.833946 -37 ** * ** ***** Masking position 7 Map Score: 21.4216 Number of sites scoring better than the average of aligned sites = 398 Number in coding regions = 374 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 3 AGTTTAATAAATTTTGTTTTTGTAATTAAAA 2 45 0 ATTTGTTTTT 0.760656 -256 TATTATAAAATTTTTGTTTTCGAAAATATAT 2 144 0 TTTTGTTTTC 0.904169 -157 CTTTTCCAATTTTTGATTTATCTATCGAAAA 3 182 1 TTTTATTTAT 0.75565 -51 AAGATTAAAATTTTGGTTTTTGGTGTTACCA 5 59 0 TTTTGTTTTT 0.9676 -64 ATTTTTATATTTTTAGTTTACTTTCATACT 7 63 1 TTTTGTTTAC 0.751805 -20 TATAAAACCTTTTTGGTTTTTTTCCAATTAA 11 107 0 TTTTGTTTTT 0.9676 -42 ACATATAAGCTTTTCCTTTTTTGCGTAGTTT 12 236 0 TTTTCTTTTT 0.812708 -50 ATTTTTATTTTTATATTTTTGT 14 2 1 TTTTATTTTT 0.905949 -204 TATTTTTATATTTTTGTTTTTAACACGCTGT 14 16 1 TTTTGTTTTT 0.9676 -190 ATTTAAATTTTTTCATTTATGAACACAACT 15 82 0 TTTTATTTAT 0.75565 -20 ATTTTGTGAGTTTTAGTTTTTCACTGACTAT 19 134 0 TTTTGTTTTT 0.9676 -167 TAATGTTTGATTTTTATTTTTAATATAGTTT 34 241 1 TTTTATTTTT 0.905949 -44 TTTTTGTTTTTTATTTCATAA 37 1 1 TTTTGTTTTT 0.9676 -203 **** ****** Masking position 7 Map Score: 12.6841 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 23 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 ATCTGGCAATATAAAGCTTTTGCAGATACA 15 27 1 ATAAAGCTTT 0.756732 -75 CTACCTCCGGACAAAGCTATTTATAAGTGA 18 75 1 ACAAAGCTAT 0.636247 -35 GTCCTCAATTATCAAGCTACCACC 22 5 0 ATCAAGCTAC 0.806065 -104 ATTCTCCCCTACCAAGCTCCAGC 25 91 1 ACCAAGCTCC 0.923771 -13 TTTAGCGAACCTCAAGCTTTCTTTTGGCAT 27 23 1 CTCAAGCTTT 0.890877 -63 TAAGAGAAAGCTCAAGCTCCTGAGATATAG 32 57 1 CTCAAGCTCC 0.941036 -36 GGAGAAGCTGCTCAAGCTCCTGTAGGTCCT 34 180 0 CTCAAGCTCC 0.941036 -105 TGTCCAAGCTCTCAAGCTCCTGGAGAAGCT 34 201 0 CTCAAGCTCC 0.941036 -84 CTGAAGTATCCTAAAGCTTCGTAAAGCTTT 35 44 1 CTAAAGCTTC 0.932168 -97 CAAAATGGATTTAAAGCTTTACGAAGCTTT 35 56 0 TTAAAGCTTT 0.532443 -85 AATTGGCGAAACCAAGCTACGGGCTATTTT 36 69 1 ACCAAGCTAC 0.854386 -36 CTTCTTTGCTCCAAAGCTTCAATTGACACC 37 57 1 CCAAAGCTTC 0.95098 -147 ATTGATAAATACAAAGCTTTATCCTCCTAC 37 89 1 ACAAAGCTTT 0.814516 -115 TCACTCAGCTTCAAAGCTTCCCGGATAGTC 40 56 1 TCAAAGCTTC 0.792533 -161 CCAAAGCTTTATCTTGTTAG 42 1 1 CCAAAGCTTT 0.890877 -35 ********** Masking position 5 Map Score: 12.214 Number of sites scoring better than the average of aligned sites = 513 Number in coding regions = 489 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 5 ACATTTAAAGTCGAATTTTTAATTACAAAA 2 29 1 TCGAATTTTT 0.850647 -272 TCGGAGCCAACCGAATTGTTCAGAAAGTCC 2 88 0 CCGAATTGTT 0.895565 -213 TCGATTAATTCCGAATTGTTCGGAGCCAAC 2 107 0 CCGAATTGTT 0.895565 -194 TCGGAATTAATCGAATTTTTAATATATTTT 2 123 1 TCGAATTTTT 0.850647 -178 TTTAAGCTTTTCCAATTTTTGATTTATCTA 3 176 1 TCCAATTTTT 0.820709 -57 GAGGGCTCACAATTTTTAAAACTTAAA 3 216 0 CACAATTTTT 0.820703 -17 CTGCCATTAGCACAGTTGTTAGTAACACCA 5 94 1 CACAGTTGTT 0.569306 -29 AAATCCTATGCAGAATTTTTCATCTGAGCG 8 223 0 CAGAATTTTT 0.850647 -78 TCCATGCTGCCAGAGTTTGTAATTCACCTC 12 126 1 CAGAGTTTGT 0.621881 -160 TCCGCCTGTACCGAATTTGTTCCAATTAAT 14 137 0 CCGAATTTGT 0.895575 -69 TTTATATTGCCAGATTTGTTAATTATAAAA 15 12 0 CAGATTTGTT 0.443304 -90 ACATAATCTCCCGAGTTTGTGTTAAAATGA 19 25 1 CCGAGTTTGT 0.838291 -276 GCTATTTCCCATTTTTTCTCAGCTTCC 25 8 1 CCCATTTTTT 0.808529 -96 CCACAAGCATTCCAGTTTTTGACATATGCT 26 107 0 TCCAGTTTTT 0.734535 -194 TGTCTGTTTTCACAATTTTTGGGGAAAAAT 32 26 1 CACAATTTTT 0.820703 -67 AATTGCCATTTCGAATTTTTGTGCTGCCAG 37 121 0 TCGAATTTTT 0.850647 -83 TTCGTGTCAGCCCAATTTTTTATCTA 44 7 0 CCCAATTTTT 0.93518 -53 ACACAATCAATCCATTTTGTATAAAAAACT 44 37 0 TCCATTTTGT 0.390251 -23 ********** Masking position 6 Map Score: 12.0458 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 138 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 6 AAAAATTTGTGGAGGGTTCAAAAAACTTTGGGA 1 274 0 GGGGTCAAAA 0.952791 -27 CTTAAAAAAAGGAGGGATATAAAAAATTTTTTT 4 12 0 GGGGTATAAA 0.753493 -28 CGTTGAGTTTGGGAGGTTCAAGAAGCATGTCCA 8 98 0 GGGGTCAAGA 0.732504 -203 AGCTAAATACAGTACGCTAAAAACAGCGTGTTA 14 36 0 AGCGTAAAAA 0.806317 -170 GAGTGGGAAGAAAAGGTTAAAAAA 17 2 0 AAGGTAAAAA 0.393859 -29 TTCCTTCCGCGGAAGGCTAAAAACGATTTCGAT 20 16 0 GGGGTAAAAA 0.970922 -198 TTCCGCGGAAGGAACATTAAAAATTAACATGCG 20 35 1 GGCATAAAAA 0.686962 -179 ATTACGTAATGTAACGGTCAAAACTACGCTGAG 20 80 1 GTCGTCAAAA 0.627156 -134 TTTGGCGTAAGGTAAGTTAAAAAG 24 2 0 GGAGTAAAAA 0.884221 -98 GAAAGCTTGAGGTTCGCTAAAAAAGAGAGAAAG 27 11 0 GGCGTAAAAA 0.974864 -75 ACACGAAACCGATACGCTCAAAAATGAATGGGT 33 37 1 GACGTCAAAA 0.809529 -52 ATGAATGGGTGGTAGGATAATAAGACTAAAGAC 33 60 1 GGGGTAATAA 0.753493 -29 GGATACTTCAGAACAGTTAAAAATCGTAGGAGG 35 22 0 GAAGTAAAAA 0.58064 -119 TGTTCTGGTTGGGCCGATAAAAATTTACCGCTA 43 84 0 GGCGTAAAAA 0.974864 -29 GCTCCCAGCCGGAGCGATAAAAAGATTAGCCCA 45 228 1 GGCGTAAAAA 0.974864 -84 ** ** ****** Masking position 13 Map Score: 9.67735 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 69 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 7 TTTTTGTTTTCGAAAATATATTAAAAATTCG 2 134 0 CGAAAATTAT 0.473984 -167 GTTTATGCTCTAAAAATATAAGAG 3 4 0 TAAAAATTAA 0.731352 -229 TTTATGAGAAGAAAAATTGAAAGAAAA 5 7 0 GAAAAATGAA 0.634314 -116 GAAAGTAAACTAAAAATATAAAAATTTTATG 7 57 0 TAAAAATTAA 0.731352 -26 ACTCCATGAGGAAAAATTTCACTTTCTATGA 11 53 1 GAAAAATTCA 0.771502 -96 GTGTTAAAAACAAAAATATAAAAATAAAAAT 14 11 0 CAAAAATTAA 0.810632 -195 GAGAGCAAATGAAAAATCTAAACGCGTAAAA 14 90 1 GAAAAATTAA 0.942389 -116 GGCACATTACGTAAAATTTAAGTATTAACGA 14 184 1 GTAAAATTAA 0.654474 -22 TTCATAAATGAAAAAATTTAAAT 15 89 1 AAAAAATTAA 0.518626 -13 CAGGTGACAAGGAAAATGTAATTGTAAAATT 16 203 1 GGAAAATTAA 0.944342 -98 TTGATTTAATGGAAAATTTAATTTAATAAAT 19 279 0 GGAAAATTAA 0.944322 -22 GCTTGGTAGGGGAGAATATAAATGTTACCAA 25 77 0 GGAGAATTAA 0.64275 -27 CGTGGCTACCGAAAAGTTTAAATACTCTGCC 26 27 1 GAAAAGTTAA 0.634313 -274 ATACCATCGTGAAAATCTAAATATTTATGC 29 10 1 TGAAAATTAA 0.738388 -87 AATTTTTGGGGAAAAATTTAAGAGAAAGCTC 32 39 1 GAAAAATTAA 0.942388 -54 TTGTTAAATAGGAAAATTTATATTGATTAAA 36 34 1 GGAAAATTAT 0.774937 -71 GAATCTGAAAGAAAAATATATCATCACTCCC 37 167 1 GAAAAATTAT 0.768504 -37 CTGCGGGCTCGGAAAATCTCACGATACTCTG 40 25 1 GGAAAATTCA 0.777878 -192 GTGTATCTGGCAAAAATTTAATGGGCTAATC 45 251 0 CAAAAATTAA 0.81063 -61 ******* *** Masking position 7 Map Score: 12.2795 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 12 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 8 CCTTTCGGTCAGCCGCCCACCGCCGCTCCCAC 1 37 0 AGCCCCCCCG 0.957323 -264 AGGAGGAAAGTCCCCCCACCCGCTGTGGCGGA 1 66 1 TCCCCCACCG 0.981501 -235 ATCATCGCATTTCCCCGCACCGGTCTCGTTTC 1 128 0 TTCCCGCCCG 0.91416 -173 AAGGATGAGGTCACCCGCTCCGGATGAAACGG 1 165 1 TCACCGCCCG 0.956172 -136 TGAAACGGCCTCCTCCCCGCCGGGTGCAACGC 1 189 1 TCCTCCCCCG 0.964491 -112 AGGGTTCGAATCCCTCCCCCCGCATTTAGTTC 8 135 0 TCCCCCCCCG 0.99337 -166 CCGCTCGGCAACCCCCGCTCAGATGAAAAATT 8 208 1 ACCCCGCCAG 0.894888 -93 AAACCATCAATCCCTACCTCCGGACAAAGCTA 18 62 1 TCCCACCCCG 0.901185 -48 CATTTTTTGCTGACTCGCTCAGCAGTACATCG 20 184 0 TGACCGCCAG 0.840523 -30 ACCCCTCAAGTTACTCCAACAGAGCAGCAAAC 34 116 1 TTACCCACAG 0.605337 -169 CGAATTTTTGTGCTGCCAGCAGTAGGAGGATA 37 108 0 TGCTCCACAG 0.69914 -96 AAATATATCATCACTCCCCCAGCAAAAACGAA 37 180 1 TCACCCCCAG 0.961618 -24 AGTCTATTTCACACTCCATCAGGGCTATTCGT 40 82 1 ACACCCACAG 0.721965 -135 ATGAATCTTATGCTCCCAGCCGGAGCGATAAA 45 217 1 TGCTCCACCG 0.831113 -95 **** *** *** Masking position 10 Map Score: 12.8695 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 313 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 9 AAAATTTGTGGAGGGTTCAAAAAACTTTGGG 1 275 0 GAGGGTTAAA 0.875888 -26 GAGGGCTCACAATTTTTAAAA 3 222 0 GAGGGCTACA 0.716535 -11 GTAGGGGTTCGAGGGTTCGAATCCCTCCCCC 8 147 0 GAGGGTTGAA 0.930665 -154 AGTTGATCTCGAAGTTAGAAAGCAATACGTG 12 96 0 GAAGTTAAAA 0.621456 -190 TCCTTCCGCGGAAGGCTAAAAACGATTTCGA 20 17 0 GAAGGCTAAA 0.875888 -197 ATTCCGCACCGAAGTCATAAAAAGCCTGAAG 27 51 1 GAAGTCAAAA 0.757427 -35 TATAGTACTGGAGGGTATGAA 32 82 1 GAGGGTAGAA 0.91867 -11 TGAGCCATGAGGTCAAGAATTGCATTTGT 34 9 1 GAGGTCAGAA 0.91867 -276 ACGAATCCACGAAGTCTTGAAGCGTTGCCAG 40 131 0 GAAGTCTGAA 0.875888 -86 GCACTTCTGAGAAGGCTCGAAAACGATAGTG 45 71 1 GAAGGCTGAA 0.930665 -241 ATTCATTGGAGAGGTTACGAAACTAATCATG 45 192 0 GAGGTTAGAA 0.855884 -120 ******* *** Masking position 2 Map Score: 2.95938 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 363 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 TATAAAATTTTTGTTTTCGAAAATATATTA 2 142 0 TTGTTTTCGA 0.808703 -159 GTTTACAAACTCGTTTTGGAAAGGCTGGAA 2 204 0 TCGTTTTGGA 0.929241 -97 AAGGCTAAAAACGATTTCGATATGAG 20 7 0 ACGATTTCGA 0.77993 -207 CACTACAGAGTCGTTTTCGACAGCAGGGGA 22 38 1 TCGTTTTCGA 0.976425 -71 GTCGATTTGGGCTATCTGGAC 28 34 0 TCGATTTGGG 0.850364 -11 CGTATCGGTTTCGTGTTCGAGATGTGATAT 33 23 0 TCGTGTTCGA 0.908868 -66 CTTCGTGGATTCGTTTTCTGCAATATCTCA 40 148 1 TCGTTTTCTG 0.777152 -69 TTTTTCACTATCGTTTTCGAGCCTTCTCAG 45 77 0 TCGTTTTCGA 0.976425 -235 AAGAACCATGTCGATTTCGGGAGAAATAAT 45 105 1 TCGATTTCGG 0.948143 -207 ********** Masking position 6 Map Score: 4.54192 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 117 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 GCTCAGTCTAATGCCGCCGGAACAGAAGGGG 1 228 1 ATGCCGCCGA 0.895905 -73 TTACTTGGACATGCTTCTTGAACCTCCCAAA 8 93 1 ATGCTTCTGA 0.67904 -208 GATCAACTCCATGCTGCCAGAGTTTGTAATT 12 119 1 ATGCTGCCGA 0.946258 -167 TAAAAAGCTTACGCTGCATGAGATGTAGTGT 19 102 1 ACGCTGCAGA 0.975628 -199 GGCGTCCCGAACGCCGCAGGATCACCAGG 21 9 0 ACGCCGCAGA 0.95138 -67 AAAACCTTATATACTGCATGAGCAGGTTGCG 26 59 1 ATACTGCAGA 0.859605 -242 TCTGCTGGCAACGCTTCAAGACTTCGTGGAT 40 127 1 ACGCTTCAGA 0.929178 -90 GATGCGCTAAATACTTCAAGACAGGCCTTTT 43 54 1 ATACTTCAGA 0.667407 -59 TATTTAACGGACGCTGCAACACGGAGC 46 7 0 ACGCTGCACA 0.853298 -39 ******** ** Masking position 1 Map Score: 2.31051 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 133 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 CGGAGGAGGAACAGAAACGAGACCGGTGCGG 1 115 1 ACAGAAACGG 0.845374 -186 CCAGATTTAGAGAGTAACGAGGTTCTTTAAA 12 17 0 AGAGTAACGG 0.96047 -269 TATAGTTTGAAGAGAATCGTGAATTGTTGAA 12 181 1 AGAGAATCGG 0.93451 -105 TGCTGCAGAAACTGTATCGTGATATCTGTTG 13 28 0 ACTGTATCGG 0.897653 -101 TACATCGATGAGAGTAACGAGGTTTGGATTT 20 160 0 AGAGTAACGG 0.96047 -54 GCTGAGTGACAGAGTATCGTGAGATTTTCCG 40 34 0 AGAGTATCGG 0.974987 -183 CAGTATCTTGAGTGTATCTGGCAAAAATTTA 45 262 0 AGTGTATCTG 0.765463 -50 ATGATATATAACAGTATCTTGAGTGTATCTG 45 273 0 ACAGTATCTG 0.845672 -39 ********* * Masking position 6 Map Score: 3.18293 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 15 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 AAACCTAAAATAAAATCCAAACACCCTGGTTT 3 104 1 TAAATCCAAC 0.903927 -129 TGCGTACTAATCAATACAAAGCATACGAAGTG 10 83 0 TCAAACAAAC 0.403582 -63 ATAACAAACCTAAACTTCAAGCG 10 133 1 TAAATTCAAC 0.835008 -13 AACTTCGAGATCAACTCCATGCTGCCAGAGTT 12 111 1 TCAATCCATC 0.727552 -175 TAGAGAGAGGTGAATTACAAACTCTGGCAGCA 12 130 0 TGAATACAAC 0.691104 -156 ACACTCATTTTAAATATCAATCAACATTAGTT 15 54 1 TAAAATCAAC 0.658539 -48 AAATAAATTACCAAATCCAATCAATTAACCGA 19 233 1 CCAATCCAAC 0.798301 -68 GAGGAGGAAGTCAAATCCAAACCTCGTTACTC 20 148 1 TCAATCCAAC 0.966855 -66 ATAAAAAGCCTGAAGTCCAATCTGCCTTG 27 67 1 TGAATCCAAC 0.919107 -19 ATATTAAAAATAAAAATCAAACATTAAACTCA 34 235 0 TAAAATCAAC 0.658539 -50 TTTCGCCAATTCAACTTTAATCAATATAAATT 36 48 0 TCAATTTAAC 0.488523 -57 ACCCTTTTCTTCATCTCCAATCCAAATTCAGG 38 27 0 TCATTCCAAC 0.727552 -23 CTGCAATATCTCAATATCAAACTCATGAAAAA 40 165 1 TCAAATCAAC 0.856721 -52 AATTTTAACCTCAACTTCAAGCAAAATCCA 43 9 0 TCAATTCAAC 0.940086 -104 GTGCATCTGATGAAATACAATCTTCAGGCGAT 45 25 0 TGAATACAAC 0.691104 -287 **** ***** * Masking position 9 Map Score: 5.2601 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 239 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 14 GTTCACGTATTGCTTTCTAACTTCGAGATCA 12 93 1 TGCTTTCTAC 0.649316 -193 AAACCTCATTACCTTCCTAATAACTCCCGAT 16 19 0 ACCTTCCTAT 0.792375 -282 CATGTTTGTTAGCTTTCTCACGTGGCAATCT 16 161 0 AGCTTTCTAC 0.929373 -140 ATGCAGCGTAAGCTTTTTAATATCAAAACTT 19 90 0 AGCTTTTTAT 0.617543 -211 CTCCTCTGCCAGCTTCCTTATCTTGCTCATA 20 123 0 AGCTTCCTAT 0.967184 -91 ATTTTTTCTCAGCTTCCTAATTGTCATCATA 25 21 1 AGCTTCCTAT 0.967184 -83 TTCGTCAGCTTCCTCACGTGGCTACCG 26 7 1 AGCTTCCTAC 0.954514 -294 GCGAACCTCAAGCTTTCTTTTGGCATTCCGC 27 27 1 AGCTTTCTTT 0.837066 -59 CAGGAGCTTGAGCTTTCTCTTAAATTTTTCC 32 48 0 AGCTTTCTTT 0.837066 -45 TAAGAACGAAAGTTTCCTTATAAATTCCGAA 35 103 1 AGTTTCCTAT 0.720275 -38 ******** ** Masking position 5 Map Score: 4.30686 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 210 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 TGTAAATCTTCTTTTCGTCATCAGAGATATC 8 60 1 CTTTTCTCAT 0.849189 -241 GAAAGTGAAATTTTTCCTCATGGAGTTTCAC 11 48 0 TTTTTCTCAT 0.920125 -101 ACCTTTTTGGTTTTTTTCCAATTAATAGCAT 11 101 0 TTTTTTCCAA 0.584775 -48 TTTTTCACCATTTGTGATTTT 12 275 0 TTTTTCCCAT 0.957686 -11 ATAAGTGGGGTTTTTCTTCATCTTTTAAAAT 16 80 1 TTTTTCTCAT 0.920125 -221 TTCTCTTAAATTTTTCCCCAAAAATTGTGAA 32 34 0 TTTTTCCCAA 0.877331 -59 CTTTTTTTGCCATTATAACATTA 36 3 1 TTTTTTCCAT 0.816738 -102 GACCCTTTTCTTCATCTCCAATCCA 38 35 0 CTTTTCTCAT 0.849189 -15 GACATGGTTCTTTTTCACTATCGTTTTCGAG 45 86 0 TTTTTCCTAT 0.689324 -226 ****** **** Masking position 5 Map Score: 1.93682 Number of sites scoring better than the average of aligned sites = 128 Number in coding regions = 115 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863