AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipurR_ecoli_hinf_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 carA 300 carbamoyl-phosphate synthetase, glutamine (small) subunit #2 codB 300 cytosine permease/transport #3 purE 117 phosphoribosylaminoimidazole carboxylase = AIR carboxylase, catalytic subunit #4 ppiB 173 peptidyl-prolyl cis-trans isomerase B (rotamase B) #5 ycbQ 300 putative fimbrial-like protein #6 ycbR 82 putative chaperone #7 ycbS 24 putative outer membrane protein #8 pyrD 110 dihydro-orotate dehydrogenase #9 pyrC 105 dihydro-orotase #10 yceB 133 orf, hypothetical protein #11 grxB 63 glutaredoxin 2 #12 yceL 205 orf, hypothetical protein #13 ycfC 35 orf, hypothetical protein #14 ymfC 201 orf, hypothetical protein #15 prsA 150 phosphoribosylpyrophosphate synthetase #16 hemM 213 an enzyme in main pathway of synthesis of 5-aminolevulinate, possibly glutamyl-tRNA dehydrogenase #17 purR 300 transcriptional repressor for pur regulon, glyA, glnB, prsA, speA #18 purT 133 phosphoribosylglycinamide formyltransferase 2 #19 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #20 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #21 cvpA 258 membrane protein required for colicin V production #22 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #23 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #24 dedA 82 orf, hypothetical protein #25 usg 65 putative PTS system enzyme II A component #26 pdxB 98 erythronate-4-phosphate dehyrogenase #27 purC 212 phosphoribosylaminoimidazole-succinocarboxamide synthetase = SAICAR synthetase #28 dapA 79 dihydrodipicolinate synthase #29 purM 297 phosphoribosylaminoimidazole synthetase = AIR synthetase #30 guaA 68 GMP synthetase (glutamine-hydrolyzing) #31 guaB 161 IMP dehydrogenase #32 glyA 300 serine hydroxymethyltransferase #33 glnB 60 regulatory protein P-II for glutamine synthetase #34 yfhG 164 putative alpha helix protein #35 yfhK 300 putative 2-component sensor protein #36 purL 300 phosphoribosylformyl-glycineamide synthetase = FGAM synthetase #37 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #38 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #39 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #40 yqgB 120 orf, hypothetical protein #41 purH 300 phosphoribosylaminoimidazolecarboxamideformyltransferase = AICAR formyltransferase; IMP cyclohydrolase #42 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #43 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #44 hflK 85 protease specific for phage lambda cII repressor #45 yjeT 81 orf, hypothetical protein #46 purA 103 adenylosuccinate synthetase #47 HI0221 129 inosine-5'-monophosphate dehydrogenase (guaB) #48 HI0221.1 109 H. influenzae predicted coding region HI0221.1 #49 HI0222 109 GMP synthase (guaA) #50 HI0329 37 conserved hypothetical protein #51 HI0330 98 opacity associated protein (oapA) #52 HI0331 59 opacity associated protein (oapB) #53 HI0334 77 GTP pyrophosphokinase (relA) #54 HI0336 82 molybdopeterin biosynthesis protein (mog) #55 HI0500 300 conserved hypothetical protein #56 HI0501 167 high affinity ribose transport protein (rbsD) #57 HI0505 97 ribokinase (rbsK) #58 HI0506 27 rbs repressor (rbsR) #59 HI0638 128 conserved hypothetical protein #60 HI0639 22 adenylosuccinate lyase (purB) #61 HI0752 300 phosphoribosylformylglycinamidine synthase (purL) #62 HI0840 116 conserved hypothetical protein #63 HI0842 197 H. influenzae predicted coding region HI0842 #64 HI0885 191 thiol:disulfide interchange protein (dsbD) #65 HI0886 111 H. influenzae predicted coding region HI0886 #66 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #67 HI0888 95 phosphoribosylamine--glycine ligase (purD) #68 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #69 HI1205 214 conserved hypothetical protein #70 HI1206 86 colicin V production protein (cvpA) #71 HI1401 229 dihydroorotate dehydrogenase (pyrD) #72 HI1402 32 H. influenzae predicted coding region HI1402 #73 HI1403 32 H. influenzae predicted coding region HI1403 #74 HI1404 300 H. influenzae predicted coding region HI1404 #75 HI1429 179 phosphoribosylaminoimidazole synthetase (purM) #76 HI1603 207 conserved hypothetical protein #77 HI1604 24 phosphate permease, putative #78 HI1605 65 conserved hypothetical protein #79 HI1607 62 hemM protein (hemM) #80 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #81 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #82 HI1632 300 H. influenzae predicted coding region HI1632 #83 HI1633 128 adenylosuccinate synthetase (purA) #84 HI1635 274 purine nucleotide synthesis repressor (purR) #85 HI1723 135 conserved hypothetical protein #86 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) Motif number 1 TTCTTGCTGCGCAAGCGTTTTCCAGAACAGGT 1 67 1 GCAACGTTTC 0.746625 -234 AAGATAAAAAGCAATCGTTTTCGTGGGGAAAT 2 221 0 GCAACGTTTC 0.593568 -80 TCACAGCCACGCAACCGTTTTCCTTGCTCTCT 3 33 1 GCAACGTTTC 0.567039 -85 CAAAAAAAACGCAAACGTTTTCCGAACCTGTT 8 11 0 GCAACGTTTC 0.506899 -100 TCGTGCAAAGGAAAACGTTTCCGCTTATCCTT 9 41 1 GAAACGTTTC 0.560571 -65 GTGTGTAAAGGCAAACGTTTACCTTGCGATTT 17 243 1 GCAACGTTTC 0.571312 -58 AAAGACACACGCAAACGTTTTCGTTTATACTG 18 83 1 GCAACGTTTC 0.506899 -51 AAATCCCTACGCAAACGTTTTCTTTTTCTGTT 21 189 1 GCAACGTTTC 0.506899 -70 TCCTGCAGACGCACACGTTTGCGTATCATATC 27 46 0 GCACCGTTTC 0.541555 -167 AAGCAGTCTCGCAAACGTTTGCTTTCCCTGTT 29 221 1 GCAACGTTTC 0.499994 -77 AGGGGTAGATGCAATCGGTTACGCTCTGTATA 31 95 1 GCAACGGTTC 0.828873 -67 AGGAATTTACGCAAACGATTACCTTCAGGCTA 32 169 0 GCAACGATTC 0.553076 -132 ATGCGCTGACGAAACCGTTTGCGTGGAAATAA 36 211 0 GAAACGTTTC 0.500314 -90 GGTCCCCAACGCAATCGTTCTCTTTTGCCTGA 39 197 0 GCAACGTTCC 0.936068 -104 CGAGCGTTGCGCAAACGTTTTCGTTACAATGC 41 180 1 GCAACGTTTC 0.506899 -121 TAAATATCAGGAAAACGTTTCCGTTAAATATA 59 104 0 GAAACGTTTC 0.560571 -25 CTATATTTAAGCAAACGTTTGCGTTATAATTC 66 126 1 GCAACGTTTC 0.499994 -62 TTTACGCAAACGTTTTCTTTTTGGCTT 70 6 1 GCAACGTTTC 0.506899 -81 TAACAATATCGCAAACGTTTGCTTGATGATAT 75 119 1 GCAACGTTTC 0.499994 -61 AAGCCATTTAGCAAACGTTTGCCTGATATATG 80 87 1 GCAACGTTTC 0.499994 -74 TTAAAAAATAGCAAACGTTTGCTTTATTTGAT 86 97 1 GCAACGTTTC 0.499994 -28 **** ***** * Masking position 9 Map Score: 82.3214 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 6 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 2 TTTCAGAGTTACAGCACTTTTTGCACTCAA 46 39 0 ACAGCACTTT 0.917731 -65 GCAAAAACCAACCGCACTTTAAACAGCAAA 48 37 0 ACCGCACTTT 0.996263 -73 GCAAAAACCAACCGCACTTTAAACAGCAAA 49 37 0 ACCGCACTTT 0.996263 -73 TAATTTTTTCGCCGCACTTTTGAGCTTCTC 51 29 1 GCCGCACTTT 0.964039 -70 GTAAAAACTTACCGCACTTTTGGAGGG 54 8 0 ACCGCACTTT 0.996263 -75 GTAAGTTTTTACCGCATTTTTGATTTATCC 54 26 1 ACCGCATTTT 0.921683 -57 TGAAAAATTGACCGCACTTTCTCAAGAATT 55 193 1 ACCGCACTTT 0.996263 -108 GCAAATTATAACCGCACTTTTTCAGCAAGA 62 27 1 ACCGCACTTT 0.996263 -90 GTAAAAAATCACCGCACTTTTTTATTGTTA 64 78 0 ACCGCACTTT 0.996263 -114 TCGTATTTTTACCGCACTTTAAGAAATTAT 66 84 1 ACCGCACTTT 0.996263 -104 TCAAAAATTGACCGCACTTATCATACGCTA 69 186 0 ACCGCACTTA 0.94761 -29 GTCAATTTTCACCGCACTTTAAAGGTAAGG 71 169 0 ACCGCACTTT 0.996263 -61 GTGAAAATTGACCGCACTTTCTTACAGTAA 71 187 1 ACCGCACTTT 0.996263 -43 GTTAAAATTAACCGCACTTTTTATTGAGAT 78 14 0 ACCGCACTTT 0.996263 -52 GTTAATTTTAACCGCACTTTTGTTGTGATG 78 32 1 ACCGCACTTT 0.996263 -34 TTTAGATCTGACCGCACTTTTAAAGTGCGG 81 18 1 ACCGCACTTT 0.996263 -52 GAAAAAAACAACCGCACTTTAAAAGTGCGG 81 29 0 ACCGCACTTT 0.996263 -41 GTGATTTTTCACCGCACTTTAGGTTTAAAT 83 12 0 ACCGCACTTT 0.996263 -117 GTGAAAAATCACCACACTTTTTCTTTTATA 83 30 1 ACCACACTTT 0.917731 -99 TTTTATTATCACCGCAGTTTTGTTTCTACA 84 18 0 ACCGCAGTTT 0.945777 -257 ********** Masking position 8 Map Score: 79.2966 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 3 AAAATAATATAAAAAATCCCGCCATTAAGTTGAC 1 147 1 AAAACCGCCA 0.92461 -154 TGAAACCCAAAAAATCCGCCGCATTCTATTCATC 2 255 0 AAAACCGCAT 0.87793 -46 TAAGATCAATAAAAGAGAGCGCCCCCTTTTGGAG 16 71 1 AAAAGCGCCC 0.890254 -143 CTGTGATGAAAAAATCTCCCGTCATTTATAATGA 17 69 1 AAAACCGTCA 0.475024 -232 CGCATCCGACAAAACATCCGGCACACCAGACAGC 27 147 1 AAAACGGCAC 0.886068 -66 GTAGAAAAATAAAATTCGGCGCAATTCTAACAGG 29 247 0 AAAAGCGCAA 0.845523 -51 TTCGATTCTGAAAAAATTGCGCACGATACGTCTC 42 23 0 AAAAGCGCAC 0.958182 -63 CCCGTGTAAAAAAACAGCCCGAAACC 43 3 0 AAAACCGAAA 0.718774 -73 AAACTTTGCAAAAACCAACCGCACTTTAAACAGC 48 40 0 AAAACCGCAC 0.993152 -70 AAACTTTGCAAAAACCAACCGCACTTTAAACAGC 49 40 0 AAAACCGCAC 0.993152 -70 AAATGCGGTAAAAACTTACCGCACTTTTGGAGGG 54 11 0 AAAACCGCAC 0.993152 -72 ATTTGACTGAAAAATTGACCGCACTTTCTCAAGA 55 186 1 AAAACCGCAC 0.993152 -115 GATAGGATAAAAAATTCTCCGACCAAATTTACAT 56 33 0 AAAACCGACC 0.791141 -135 AAACACCCTAAAAATTCACCGCACT 58 2 0 AAAACCGCAC 0.993152 -26 CTTTGAAAAATTTGCCGCAAATTATAACCG 62 7 1 AAAACCGCAA 0.971943 -110 AAATCAGGTAAAAAATCACCGCACTTTTTTATTG 64 81 0 AAAACCGCAC 0.993152 -111 ATTGCAGGTAAAAAATAGCCGTACTTTTTTTAAA 67 48 1 AAAACCGTAC 0.914526 -48 AAACACCTCAAAAATTGACCGCACTTATCATACG 69 189 0 AAAACCGCAC 0.993152 -26 AAGTGCGGTGAAAATTGACCGCACTTTCTTACAG 71 180 1 AAAACCGCAC 0.993152 -50 AAGTGCGGTTAAAATTAACCGCACTTTTTATTGA 78 17 0 AAAACCGCAC 0.993152 -49 AATTTACGAAAAAAACAACCGCACTTTAAAAGTG 81 32 0 AAAACCGCAC 0.993152 -38 AAATTAGCATAATACGCCCCGCAAAGCCGATATG 82 17 0 AATACCGCAA 0.670416 -284 AAGTGCGGTGAAAAATCACCACACTTTTTCTTTT 83 23 1 AAAACCACAC 0.839932 -106 **** ****** Masking position 4 Map Score: 51.0819 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 132 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 4 GTGTTATAGCATAACCGCACGATCGGATCA 4 95 0 ATAACCGCAC 0.947353 -79 CTCCTTTTTTATTACCACACAAAAAGTGAT 17 21 1 ATTACCACAC 0.544423 -280 AGGTTCACAATTCACTGCACGTTTCAGGAA 37 90 1 TTCACTGCAC 0.644733 -29 GACAACAGGGATCACCGCATAACAAATATG 44 56 1 ATCACCGCAT 0.701936 -30 TTTGCAAAAACCAACCGCACTTTAAACAGC 48 40 0 CCAACCGCAC 0.810523 -70 TTTGCAAAAACCAACCGCACTTTAAACAGC 49 40 0 CCAACCGCAC 0.810523 -70 ACATAATTTTTTCGCCGCACTTTTGAGCTT 51 26 1 TTCGCCGCAC 0.813671 -73 GCGGTAAAAACTTACCGCACTTTTGGAGGG 54 11 0 CTTACCGCAC 0.930165 -72 GCGGTAAGTTTTTACCGCATTTTTGATTTA 54 23 1 TTTACCGCAT 0.552658 -60 GACTGAAAAATTGACCGCACTTTCTCAAGA 55 190 1 TTGACCGCAC 0.961432 -111 ACCCTAAAAATTCACCGCACT 58 2 0 TTCACCGCAC 0.982039 -26 GCCGCAAATTATAACCGCACTTTTTCAGCA 62 24 1 ATAACCGCAC 0.947353 -93 CAGGTAAAAAATCACCGCACTTTTTTATTG 64 81 0 ATCACCGCAC 0.973622 -111 TTATCGTATTTTTACCGCACTTTAAGAAAT 66 81 1 TTTACCGCAC 0.950891 -107 ACCTCAAAAATTGACCGCACTTATCATACG 69 189 0 TTGACCGCAC 0.961432 -26 GCGGTCAATTTTCACCGCACTTTAAAGGTA 71 172 0 TTCACCGCAC 0.982039 -58 GCGGTGAAAATTGACCGCACTTTCTTACAG 71 184 1 TTGACCGCAC 0.961432 -46 AGTTACTTATCTTACCACACTAGGAAATAT 76 58 1 CTTACCACAC 0.549088 -150 GCGGTTAAAATTAACCGCACTTTTTATTGA 78 17 0 TTAACCGCAC 0.963841 -49 GCGGTTAATTTTAACCGCACTTTTGTTGTG 78 29 1 TTAACCGCAC 0.963841 -37 ATCTTTAGATCTGACCGCACTTTTAAAGTG 81 15 1 CTGACCGCAC 0.944898 -55 TACGAAAAAAACAACCGCACTTTAAAAGTG 81 32 0 ACAACCGCAC 0.807615 -38 GTGGTGATTTTTCACCGCACTTTAGGTTTA 83 15 0 TTCACCGCAC 0.982039 -114 GCGGTGAAAAATCACCACACTTTTTCTTTT 83 27 1 ATCACCACAC 0.7714 -102 ACTTTTTATTATCACCGCAGTTTTGTTTCT 84 21 0 ATCACCGCAG 0.664361 -254 ********** Masking position 9 Map Score: 44.2199 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 212 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 TGAAGATAAAAAGCAATCGTTTTCGTGGGG 2 225 0 AAGCAATCGT 0.638612 -76 TTTCACAGCCACGCAACCGTTTTCCTTGCT 3 31 1 ACGCAACCGT 0.964778 -87 GGCAAAAAAAACGCAAACGTTTTCCGAACC 8 15 0 ACGCAAACGT 0.992061 -96 TTTCGTGCAAAGGAAAACGTTTCCGCTTAT 9 39 1 AGGAAAACGT 0.813354 -67 GTATCGCAGGACGCAAACGCATATGCAACG 14 54 0 ACGCAAACGC 0.929874 -148 AGGTGTGTAAAGGCAAACGTTTACCTTGCG 17 241 1 AGGCAAACGT 0.973632 -60 ATAAAGACACACGCAAACGTTTTCGTTTAT 18 81 1 ACGCAAACGT 0.992061 -53 GGAAATCCCTACGCAAACGTTTTCTTTTTC 21 187 1 ACGCAAACGT 0.992061 -72 CTGATATGATACGCAAACGTGTGCGTCTGC 27 44 1 ACGCAAACGT 0.992061 -169 TAAAGCAGTCTCGCAAACGTTTGCTTTCCC 29 219 1 TCGCAAACGT 0.943464 -79 AAAGGAATTTACGCAAACGATTACCTTCAG 32 173 0 ACGCAAACGA 0.899465 -128 TGATGCGCTGACGAAACCGTTTGCGTGGAA 36 215 0 ACGAAACCGT 0.763735 -86 CCGGTCCCCAACGCAATCGTTCTCTTTTGC 39 201 0 ACGCAATCGT 0.946494 -100 CGCGAGCGTTGCGCAAACGTTTTCGTTACA 41 178 1 GCGCAAACGT 0.933449 -123 AGTAAATATCAGGAAAACGTTTCCGTTAAA 59 108 0 AGGAAAACGT 0.813354 -21 GAGAATTATAACGCAAACGTTTGCTTAAAT 66 130 0 ACGCAAACGT 0.992061 -58 TTTACGCAAACGTTTTCTTTTTG 70 4 1 ACGCAAACGT 0.992061 -83 TTTAACAATATCGCAAACGTTTGCTTGATG 75 117 1 TCGCAAACGT 0.943464 -63 TACATATATCAGGCAAACGTTTGCTAAATG 80 91 0 AGGCAAACGT 0.973632 -70 AAATCAAATAAAGCAAACGTTTGCTATTTT 86 101 0 AAGCAAACGT 0.925799 -24 ********** Masking position 5 Map Score: 45.5327 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 37 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 6 AACGCGTCAGCGTCGCATCAGGCATCGGCACAC 2 19 0 CGCCATCAGC 0.995036 -282 GCGACGCGAGCGCCTTATCCGACCTACGGTTCA 2 70 0 CGCTATCCGC 0.993161 -231 AAGGCGCTCGCGTCGCATCCGACACCATGCTCA 2 87 1 CGCCATCCGC 0.996893 -214 GACGCGTCAGCGTCGCATCAGGCATCTGAGCAT 2 113 0 CGCCATCAGC 0.995036 -188 GACGCTGACGCGTCTTATCAGGCCTACCCACTG 2 132 1 CGCTATCAGC 0.989098 -169 GACGCGCCAGCGTCGCATCAGGCAAGACCGTA 21 10 0 CGCCATCAGC 0.995036 -249 GACGCTGGCGCGTCTTATCAGGCCTACGCAGGG 21 29 1 CGCTATCAGC 0.989098 -230 GCGGCGTAAACGCCTTATCCGACCTACGGTTCT 21 64 0 CGCTATCCGC 0.993161 -195 AAGGCGTTTACGCCGCATCCGACACGCATTGCC 21 81 1 CGCCATCCGC 0.996893 -178 GCGGCGTGAACGCCTTATCCGAACTACGTCCGA 27 117 0 CGCTATCCGA 0.912428 -96 AAGGCGTTCACGCCGCATCCGACAAAACATCCG 27 134 1 CGCCATCCGC 0.996893 -79 ACAAAACATCCGGCACACCAGACAGCAAAAGAT 27 155 1 CGCCACCAGC 0.971758 -58 ** * ****** * Masking position 7 Map Score: 32.397 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 84 Number in noncoding regions = 563 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 7 TTCTGGAAAACGCTTGCGCAGCAAGAAGATTG 1 62 0 CGCGCGCAGC 0.967828 -239 TGATAAAACGCGTCAGCGTCGCATCAGGCATC 2 26 0 CGTGCGTCGC 0.993041 -275 TCGGATAAGGCGCTCGCGTCGCATCCGACACC 2 81 1 CGCGCGTCGC 0.992897 -220 TGATAAGACGCGTCAGCGTCGCATCAGGCATC 2 120 0 CGTGCGTCGC 0.993041 -181 GTTGCATATGCGTTTGCGTCCTGCGATACGGA 14 55 1 CGTGCGTCCT 0.76852 -147 TGATAAGACGCGCCAGCGTCGCATCAGGCAAG 21 17 0 CGCGCGTCGC 0.992897 -242 TCGGATAAGGCGTTTACGCCGCATCCGACACG 21 75 1 CGTACGCCGC 0.914236 -184 AAAAAGAAAACGTTTGCGTAGGGATTTCCTTC 21 184 0 CGTGCGTAGG 0.774762 -75 CAGACGCACACGTTTGCGTATCATATCAGAAA 27 41 0 CGTGCGTATC 0.850725 -172 TCGGATAAGGCGTTCACGCCGCATCCGACAAA 27 128 1 CGTACGCCGC 0.914236 -85 GTCTCGCAAACGTTTGCTTTCCCTGTTAGAAT 29 226 1 CGTGCTTTCC 0.563769 -72 TTCTCTGTGTCGTGCGCGTCCCAGCTTGAAAA 36 62 1 CGTGCGTCCC 0.980802 -239 AGCCATTGGCGGCACGCGTTGCTAATTCACGA 36 171 1 GGCGCGTTGC 0.707359 -130 CAAACGGTTTCGTCAGCGCATCAGATTCTTTA 36 222 1 CGTGCGCATC 0.810134 -79 GAGAAAAATTCGCGAGCGTTGCGCAAACGTTT 41 168 1 CGCGCGTTGC 0.96861 -133 AACGCAGGATCGCTGGCTCCCCGTGTAAAAAA 43 24 0 CGCGCTCCCC 0.811097 -52 *** ******* Masking position 7 Map Score: 14.7425 Number of sites scoring better than the average of aligned sites = 989 Number in coding regions = 847 Number in noncoding regions = 142 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 8 AAGAAATCCGTTTCCGGTTGCAAGCTCTTTATTCTCCAAA 32 121 1 TTTCTTATTT 0.803755 -180 GAGTAAACCTTTCACTATTATTACGTTTTTTCAAGCTGGG 36 81 0 TTCCTTATTT 0.5247 -220 GTGTAAGCGGTTCATATTATTTAAAACTTTGCAAAAACCA 48 57 0 TTCTTAATTT 0.754299 -53 GTGTAAGCGGTTCATATTATTTAAAACTTTGCAAAAACCA 49 57 0 TTCTTAATTT 0.754299 -53 TAATCGCCCCTTTTTCTTTTTAAGTTCTTTTCTCAAGGTA 52 24 1 TTTTTTATTT 0.868668 -36 ATTTTTCCTTATTTTTATAAATGATTTTGACGTGATT 54 56 0 CTTTTTATTT 0.640647 -27 ACTTTAATTGTTTGTTGTTCAAACTGGTTTTTAATGCTAC 55 66 0 TTTTTTATTT 0.868668 -235 CGGAGAATTTTTTATCCTATCTAGAAATTTTGTGATCAAT 56 46 1 TTTTTAATTT 0.919289 -122 GTTATCTATATTTGTCTTATCGAAACGTTTCGATAACAAA 56 125 1 TTTTTAATTT 0.919289 -43 CTCGGAAATTTTTATACTTTTAATTAATTTAAGGACATAA 61 40 0 TTTTTTATTT 0.868668 -261 GGGTATAAGCTTTGTATTACAAAATCTTTTTTTTGAAAAT 61 230 1 TTTTTAATTT 0.919289 -71 AACTCACGGATTTTCATTAATAACATTTTTCAGTCTTAAA 63 70 0 TTTCTAATTT 0.87582 -128 TTATTTTTTACTTTTGGTAAAAAGTATTTTTCAATTTTAA 65 11 1 CTTTTAATTT 0.754299 -101 AGTTTGTATTTTTTCCTTACCGATGAATTTATTTTATTCA 69 94 0 TTTCTAATTT 0.87582 -121 TAAACGGCCGTTTTTCATTGAGAGATTTTTTA 70 65 1 TTTTTTATTT 0.868668 -22 TTTACAATATTTTCCATTAATTATTTCTTTATTATTTGCA 71 97 1 TTTCTAATTT 0.87582 -133 AGATAAACCTTTTTTCTTACAAATTTTTTTGAAAAATTTT 76 111 1 TTTTTAATTT 0.919289 -97 AGGATAAAATTTTATCCTAAGCACAATTTTTATAAGAATA 80 20 0 TTTTTAATTT 0.919289 -141 TAAAATTACTTTTTTTGTAAAAAAGTATTTGACGAGGATC 82 55 0 TTTTTAATTT 0.919289 -246 GAAAAAATCACTTCTTTTTATAAAAAATTTGCAATAAAGA 84 189 1 CTTTTTATTT 0.640647 -86 TCAACAAACCTTTATAATAGGAAAAATTTTTAGGGATTTA 84 240 1 TTTTTAATTT 0.919289 -35 ATTTACTAAATTTCCAATAATAAACATTTTCCCCCTATAC 86 23 1 TTTCTAATTT 0.87582 -102 *** * ** * *** Masking position 8 Map Score: 18.9122 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 48 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 9 TATGAATGAGTGCAAAAAGGTGGGGGAAAA 2 181 0 TGCAAAAAGG 0.934319 -120 GGTTTCAAACAGCAAAAAGGGGGAATTTC 2 282 1 AGCAAAAAGG 0.968482 -19 GCGAGTTCGGACCAAAAGGGAATTGACCTG 8 46 0 ACCAAAAGGG 0.901223 -65 CGGCAATTACTCCAAAAGGGGGCGCTCTCT 16 84 0 TCCAAAAGGG 0.808569 -130 CGGTGAGAATAGCAAAAGGGCAGAGCCAGT 22 31 0 AGCAAAAGGG 0.976987 -39 GTATCATATCAGAAAAAAGGGCCGGATGAT 27 26 0 AGAAAAAAGG 0.859501 -187 GGAAAAGACGTGCAAAAAGGTTGTGTAAAG 29 194 1 TGCAAAAAGG 0.934319 -104 AAGCATTTTTTGCAAAAAGGGGTAGATGCA 31 78 1 TGCAAAAAGG 0.934319 -84 CACTTTAAACAGCAAAAGGCAGGCTAAAGC 48 23 0 AGCAAAAGGC 0.892571 -87 CACTTTAAACAGCAAAAGGCAGGCTAAAGC 49 23 0 AGCAAAAGGC 0.892571 -87 GAACTTAAAAAGAAAAAGGGGCGATTACTC 52 21 0 AGAAAAAGGG 0.894201 -39 ACGTTTCGATAACAAAAAGGAGCTTTTAG 56 149 1 AACAAAAAGG 0.707698 -19 AAAATTTGTAAGAAAAAAGGTTTATCTTCG 76 108 0 AGAAAAAAGG 0.859501 -100 ********** Masking position 5 Map Score: 12.0784 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 118 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 10 AAGTCAACTTAATGGCGGGATTTTTTATATTA 1 151 0 AAGGCGGATT 0.96932 -150 ATTTCTGGCAAACGGCGGCATTCTGGAGATAT 1 192 0 AAGGCGGATT 0.968691 -109 CAAACAGCAAAAAGGGGGAATTTC 2 287 1 AAGGGGGATT 0.948654 -14 ACGAAAAATAAAGGGCGCGAATGCGCCCTCGT 9 13 0 AAGGCGCAAT 0.854561 -93 AAAAACTGAAAACGGCGGCAACCCGCGAATAC 10 33 0 AAGGCGGAAC 0.904725 -101 AAATACAGGGCTGGAATCATCCGGCCC 27 6 1 CAGGCTGAAT 0.636177 -207 CTCCTTTCTTCAAGGCGGCAATATTCTTTTCG 29 33 1 CAGGCGGAAT 0.937714 -265 GCGTGCCGCCAATGGCTGTAATAAGTTGCCAT 36 156 0 AAGGCTGAAT 0.791654 -145 GGTGTACCCAAGGGGGGGAAACGGGCGTCATT 36 255 0 AGGGGGGAAC 0.608863 -46 TTAAAAAGAAAAAGGGGCGATTACTCGCCCAA 52 15 0 AAGGGGCATT 0.768459 -45 TCTTCATCAACAAGGGGGTATT 53 66 1 CAGGGGGATT 0.894763 -12 TCTTTACAAAAGAGGGGGAATTGCAGGTAAAA 67 29 1 AGGGGGGATT 0.842838 -67 TAACCGAATAAAAGGCGGAAATT 83 116 1 AAGGCGGAAT 0.970339 -13 GTTATTAGATAATGGCGGGATTGAAATTTTAG 85 97 1 AAGGCGGATT 0.96932 -39 ** ***** *** Masking position 10 Map Score: 9.95374 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 274 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 TTTACAGGCATTAAGCGACAAAAAGATCATCTAACC 1 96 0 TTAAAAAAGA 0.697648 -205 GAGATGTGGCTTAACGAGGAAAAAGACGT 20 18 1 TTAAAAAAGA 0.697648 -19 ACACAGAGAATTAACTAATTGAAAAAATTAAAGATT 36 36 0 TTAAGAAAAA 0.780014 -265 TAAGACAATATTAAGAGCTAAAAAAATGTCAAAAA 39 10 0 TTAAAAAAAA 0.84696 -291 TTCATATTATTTAAAACTTTGCAAAAACCAACCGCA 48 51 0 TTAAGCAAAA 0.647998 -59 TTCATATTATTTAAAACTTTGCAAAAACCAACCGCA 49 51 0 TTAAGCAAAA 0.647998 -59 CTTATTTATATTAATTAGCCACAAAATTGAGAAGCT 51 51 0 TTAAACAAAA 0.741822 -48 CTTAAATTAATTAAAAGTATAAAAATTTCCGAGTTT 61 47 1 TTAAAAAAAT 0.726539 -254 AATGTTAAAAATAAAAAAAATTTGGCTTAT 62 97 0 TTAAAAAAAA 0.84696 -20 ATATAATTTCTTAAAGTGCGGTAAAAATACGATAAA 66 80 0 TTAAGTAAAA 0.483733 -108 AAACGTTTGCTTAAATATAGAAAAGATTAAATATAA 66 110 0 TTAAAAAAGA 0.697648 -78 TTTCCTTTCATTAAATAGTTAAAAATAAGCGATGAG 66 157 0 TTAAAAAAAT 0.726539 -31 TAAAAATAGTTTAATTTTTCAAAAAATACGATAAAG 69 132 0 TTAAAAAAAA 0.84696 -83 TTAATACATTTTAATTATGTATAAAAAACGGCTAGT 71 42 0 TTAAATAAAA 0.593901 -188 ATTTGTACTATTAAAGTAGTACAAATAAATTTTGAT 75 34 1 TTAAACAAAT 0.579723 -146 ACTTTTCGCTTTAAAAGCGAGAAAATTTGAAAGGTA 76 16 0 TTAAGAAAAT 0.629932 -192 TTGAAAAATTTTAACTATCAACAAAAATCGGGTAAT 76 139 1 TTAAACAAAA 0.741822 -69 TTACTCCAAATTAAGGGGTTAAAAATTCGTGCGCAT 76 175 0 TTAAAAAAAT 0.726539 -33 ATATTTCTCGTTAAATTTACGAAAAAAACAACCGCA 81 43 0 TTAAGAAAAA 0.780014 -27 TATAAGTTGTTTAAATGAATAAAAAATAAGTGATAT 82 119 0 TTAAAAAAAA 0.84696 -182 CAAATAAATTTTAATTACAATAAATGAACGCATAA 82 206 0 TTAAATAAAT 0.412483 -95 ATCATTGAGATTAAAGCCGAAAAAGAGTAAAGTAAA 83 59 1 TTAAAAAAGA 0.697648 -70 GTTGGTTTGATTAAAAGATTGAAAGTGCAAGCCCCA 84 49 1 TTAAGAAAGT 0.415103 -226 ATATTTAAATCCCTAAAAATTTTTCCTATT 84 255 0 TTAAAAAAAT 0.726539 -20 TTGCTATTTTTTAAAAAGAAATAAAAATCCTCTGAA 86 75 0 TTAAATAAAA 0.593901 -50 **** ****** Masking position 2 Map Score: 15.8572 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 93 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 12 GTGCAAAAAGGTGGGGGAAAAATTATCGGTGTA 2 169 0 GGGGAAAAAT 0.911116 -132 GAATTGACCTGCGGCAAAAAAAACGCAAACGTT 8 24 0 GGGAAAAAAA 0.803084 -87 TTTACACACTGTGATGAAAAAATCTCCCGTCAT 17 61 1 GGAAAAAAAT 0.600767 -240 AATAAAAATGGCGCTGAAAAAATATTCAACGCC 21 142 0 GGCAAAAAAT 0.804095 -117 CGCGTTACTTGCGGTAGAAAAATAAAATTCGGC 29 261 0 GGGGAAAAAT 0.911116 -37 CTCGACCAGAGTGGTTAATAAATATTGCCGCGG 31 130 0 GGGAATAAAT 0.687395 -32 AGAATGTGATGAAGTGAAAAATTTGCATCACAA 32 81 1 GAGAAAAATT 0.553148 -220 ACCGCCTATAAAGGCCAAAAATTTTATTGTTAG 32 260 1 AGGAAAAATT 0.644252 -41 AACCGTTTGCGTGGAAATAAAATCACCATCGTG 36 198 0 GGGATAAAAT 0.687395 -103 ACAATATTAAGAGCTAAAAAAATGTCAAAAA 39 9 0 GGCAAAAAAT 0.804095 -292 ACATTAGCTTATGGTTAAAAAATGCAAAAATCG 39 117 0 AGGAAAAAAT 0.84762 -184 TCGTTACAATGCGGGCGAAAAATAAGGATGCCC 41 200 1 GGGGAAAAAT 0.911116 -101 CTAATAAGTTGAAGTTAAAAAATATTGCGACGA 47 94 0 GAGAAAAAAT 0.791763 -36 GCTCAAAAGTGCGGCGAAAAAATTATGTGTATT 51 21 0 GGGAAAAAAT 0.971503 -78 AATTTCTAGATAGGATAAAAAATTCTCCGACCA 56 42 0 TGGAAAAAAT 0.628349 -126 ATAAAGACTTAAGGGCAAAAAATCCATTCTTTT 63 24 0 AGGAAAAAAT 0.84762 -174 CCACATAAATGTGGGCAAAAATAAGGATAAAAT 66 29 0 GGGAAAAATA 0.570403 -159 AGGGGGAATTGCAGGTAAAAAATAGCCGTACTT 67 41 1 GAGAAAAAAT 0.791763 -55 TTAACTGTTTATGGATAAAAATTTAATTAAAAT 68 66 0 AGGAAAAATT 0.644252 -58 CGTATTCTACGAGGAACAAAAATGATGTGCAAA 71 131 0 GGGCAAAAAT 0.792699 -99 TCCAAATTAAGGGGTTAAAAATTCGTGCGCATA 76 174 0 GGGAAAAATT 0.91735 -34 * ** ******* Masking position 10 Map Score: 10.7751 Number of sites scoring better than the average of aligned sites = 415 Number in coding regions = 335 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 13 TTGTGTATCTTTTTCTGAAAATAAACTAAAG 5 59 1 TTTCTGAAAA 0.772706 -242 ATAGCAAGCATTTTTTGCAAAAAGGGGTAGA 31 73 1 TTTTTGCAAA 0.630061 -89 TGAACCTTTCGATTCTGAAAAAATTGCGCAC 42 33 0 GTTCTGAAAA 0.677515 -53 AGCAAACGGTGATTTTGAAAA 46 93 1 GTTTTGAAAA 0.820333 -11 TTATGGCAAATAGTATGAAAATCATAGCATA 47 18 1 TGTATGAAAA 0.482549 -112 GATTTCACTTTATTTTGAAAACGAAATTTTA 47 54 0 TTTTTGAAAA 0.921091 -76 AAATGAGAGATGGTTTGAAAA 50 27 1 TGTTTGAAAA 0.820333 -11 TTTAGATGGTTCTGAAAATAAGCTCATT 61 8 1 GTTCTGAAAA 0.677515 -293 ACAAAATCTTTTTTTTGAAAATAGGGAGTAT 61 248 1 TTTTTGAAAA 0.920011 -53 ATTATGATAATGTTATGAAAAACTCACGGAT 63 99 0 TTTATGAAAA 0.704545 -99 CAATTCCCCCTCTTTTGTAAAGAGGGGGATA 67 21 0 TTTTTGTAAA 0.669579 -75 TCATCTAAGATGGTTTGAAAAATCAGACATA 69 48 1 TGTTTGAAAA 0.820333 -167 CTTTATCGTATTTTTTGAAAAATTAAACTAT 69 132 1 TTTTTGAAAA 0.920011 -83 TCTTACAAATTTTTTTGAAAAATTTTAACTA 76 125 1 TTTTTGAAAA 0.920011 -83 TAAAATTACTTTTTTTGTAAAAAAGTATTTG 82 64 0 TTTTTGTAAA 0.669565 -237 TTTATCTCACTTTTTTGAAAAAACTTTACGA 85 12 1 TTTTTGAAAA 0.920011 -124 * ********* Masking position 6 Map Score: 11.1241 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 34 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 CTGACTCCTTCATACTGAAAGTGAACTGAC 11 25 1 CATACTGAAA 0.661405 -39 TAAAACATAACAGCCCGAAACTTTGGATAA 23 39 0 CAGCCCGAAA 0.945736 -117 GAACCAGGTTCAGACAGAAAGGTCCCTA 23 138 1 CAGACAGAAA 0.80027 -18 ACGTTGGCTACAGCCTGAAATGTTCCGAGC 24 21 0 CAGCCTGAAA 0.972719 -62 AACGTAGTTACAGCCTGAAAGATGACGAGT 24 46 1 CAGCCTGAAA 0.972719 -37 ATTCACCAGACTTAAAGCCTATCCCA 34 149 0 CAGACTTAAA 0.661405 -16 GTGCGCGTCCCAGCTTGAAAAAACGTAATA 36 73 1 CAGCTTGAAA 0.756991 -228 TGTAAAAAAACAGCCCGAAACC 43 3 0 CAGCCCGAAA 0.945736 -73 AATTAAAGTACAGACTGAAAATCAAGGACT 55 97 1 CAGACTGAAA 0.957189 -204 GCCTCAGTTTAAGACTGAAAAATGTTATTA 63 63 1 AAGACTGAAA 0.661405 -135 ********** Masking position 8 Map Score: 6.11231 Number of sites scoring better than the average of aligned sites = 223 Number in coding regions = 202 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 15 TGCCGGACACAAAGGATAAGCGGAAACGTTTTC 9 51 0 AAGTAAGCGG 0.982799 -55 AGTGATGGGAAAAGTCTTAGCGGCAATGCAGAA 12 177 1 AAGTTAGCGG 0.947521 -29 CAGTACGCAAATAGTGTAAGCGTGGAATTTTGG 17 141 0 AAGTAAGCGT 0.848513 -160 AAATAGCCTGATAGGATAGGCTGTTAGCA 34 7 0 AAGTAGGCTG 0.84614 -158 CTTGTCCTCATTGAATAAGCGGGGCTGACAAC 39 279 0 ATGTAAGCGG 0.900069 -22 ACTATTACAGAGAGCGTTAGCTGAATTTTTCGC 41 259 0 AAGTTAGCTG 0.780475 -42 CTTATTATTGATAGTGTAAGCGGTTCATATTAT 48 77 0 AAGTAAGCGG 0.982799 -33 CTTATTATTGATAGTGTAAGCGGTTCATATTAT 49 77 0 AAGTAAGCGG 0.982799 -33 TTTAGCCAAAAAAGACTAGGCGGTGTGAATGGT 74 108 1 AAGTAGGCGG 0.965431 -193 * ** ******* Masking position 7 Map Score: 5.4262 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 12 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701