AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipurR_ecoli_opreg_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 Motif number 1 ACCTGTTCTGGAAAACGCTTGCGCAGCAAGAAG 1 66 0 GAACGTTGCG 0.998084 -235 AAGATAAAAAGCAATCGTTTTCGTGGGGAAATA 2 220 0 GAACGTTTCG 0.969433 -81 AGAGAGCAAGGAAAACGGTTGCGTGGCTGTGAA 3 32 0 GAACGTTGCG 0.998084 -86 AACAGGTTCGGAAAACGTTTGCGTTTTTTTTGC 8 11 1 GAACGTTGCG 0.998084 -100 TCGTGCAAAGGAAAACGTTTCCGCTTATCCTTT 9 41 1 GAACGTTCCG 0.979169 -65 AAATCGCAAGGTAAACGTTTGCCTTTACACACC 17 242 0 GAACGTTGCC 0.979169 -59 CAGTATAAACGAAAACGTTTGCGTGTGTCTTTA 18 82 0 GAACGTTGCG 0.998084 -52 AACAGAAAAAGAAAACGTTTGCGTAGGGATTTC 21 188 0 GAACGTTGCG 0.998084 -71 TCCTGCAGACGCACACGTTTGCGTATCATATCA 27 45 0 GACCGTTGCG 0.986051 -168 AACAGGGAAAGCAAACGTTTGCGAGACTGCTTT 29 220 0 GAACGTTGCG 0.998084 -78 TATACAGAGCGTAACCGATTGCATCTACCCCTT 31 94 0 GAACGTTGCA 0.969433 -68 TAGCCTGAAGGTAATCGTTTGCGTAAATTCCTT 32 169 1 GAACGTTGCG 0.998084 -132 ATGCGCTGACGAAACCGTTTGCGTGGAAATAAA 36 210 0 GAACGTTGCG 0.998084 -91 TCAGGCAAAAGAGAACGATTGCGTTGGGGACCG 39 197 1 GGACGTTGCG 0.986051 -104 GCATTGTAACGAAAACGTTTGCGCAACGCTCGC 41 179 0 GAACGTTGCG 0.998084 -122 * ** ** ***** Masking position 9 Map Score: 57.3712 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 8 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 GTGTGCCGATGCCTGATGCGACGCTGACGCGTTT 2 19 1 GCCGATCCGC 0.995607 -282 AGGTCCGTAGGCATGATAAAACGCGTCAGCGTCG 2 37 0 GCAGATACGC 0.772647 -264 TGAACCGTAGGTCGGATAAGGCGCTCGCGTCGCA 2 70 1 GTCGATACGC 0.963171 -231 TGAGCATGGTGTCGGATGCGACGCGAGCGCCTTA 2 86 0 GTCGATCCGC 0.987178 -215 ATGCTCAGATGCCTGATGCGACGCTGACGCGTCT 2 113 1 GCCGATCCGC 0.995607 -188 CAGTGGGTAGGCCTGATAAGACGCGTCAGCGTCG 2 131 0 GCCGATACGC 0.987177 -170 TCCTGACCCGCCGCGGCAGCCTGT 10 1 1 TCCGACCCGC 0.971566 -133 TGCGTCAATATCCTGACACAACGCAGCATGTGTC 10 89 0 TCCGACCCGC 0.971566 -45 CCGCATTATAGCCTAATAACGCGCATCTTTCATG 14 154 0 GCCAATACGC 0.856877 -48 GTATTAAAGAGCGCGATGCAACGTCTGGAACAAG 15 44 0 GCGGATCCGT 0.834353 -107 ATTGACCCCTTCCTGACGCTCCGTGTCGTTTTTC 17 177 1 TCCGACCCGT 0.920674 -124 TACGGTCTTGCCTGATGCGACGCTGGCGCGTCT 21 10 1 GCCGATCCGC 0.995607 -249 CCCTGCGTAGGCCTGATAAGACGCGCCAGCGTCG 21 28 0 GCCGATACGC 0.987177 -231 AGAACCGTAGGTCGGATAAGGCGTTTACGCCGCA 21 64 1 GTCGATACGT 0.898821 -195 GGCAATGCGTGTCGGATGCGGCGTAAACGCCTTA 21 80 0 GTCGATCCGT 0.963171 -179 TCGGACGTAGTTCGGATAAGGCGTTCACGCCGCA 27 117 1 TTCGATACGT 0.7077 -96 CGGATGTTTTGTCGGATGCGGCGTGAACGCCTTA 27 133 0 GTCGATCCGT 0.963171 -80 ATATGTACGCTCCGGTTTCTCCGCGCTGTCCATG 34 86 1 TCCGTTCCGC 0.807358 -79 ATAAGGCGGTGCCTAACTCGACGTTTCGCCCGAT 35 248 0 GCCAACCCGT 0.768226 -53 GACTCCACGCTTCAGACGCTACGCCG 44 3 0 TTCGACCCGC 0.920674 -83 *** *** * *** Masking position 12 Map Score: 41.6299 Number of sites scoring better than the average of aligned sites = 1340 Number in coding regions = 835 Number in noncoding regions = 505 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 CGCGTCAGCGTCGCATCAGGCATCGGCACAC 2 19 0 TCCATCAGGC 0.969084 -282 GACGCGAGCGCCTTATCCGACCTACGGTTCA 2 70 0 CCTATCCGAC 0.969321 -231 GGCGCTCGCGTCGCATCCGACACCATGCTCA 2 89 1 TCCATCCGAC 0.975799 -212 CGCGTCAGCGTCGCATCAGGCATCTGAGCAT 2 113 0 TCCATCAGGC 0.969084 -188 CGCTGACGCGTCTTATCAGGCCTACCCACTG 2 134 1 TCTATCAGGC 0.951203 -167 GATGTTGATTTCTCAACCGAAAAGAAATATA 18 46 0 TCCAACCGAA 0.500271 -88 AAATAGTTGCCCTGTCAGACTTGCAGGCAG 19 75 0 CCTGTCAGAC 0.760758 -20 CGCGCCAGCGTCGCATCAGGCAAGACCGTA 21 10 0 TCCATCAGGC 0.969084 -249 CGCTGGCGCGTCTTATCAGGCCTACGCAGGG 21 31 1 TCTATCAGGC 0.951203 -228 GGCGTAAACGCCTTATCCGACCTACGGTTCT 21 64 0 CCTATCCGAC 0.969321 -195 GGCGTTTACGCCGCATCCGACACGCATTGCC 21 83 1 CCCATCCGAC 0.980697 -176 CCATTTTTGCCCCCAACAGACCATGAATGTT 23 75 0 CCCAACAGAC 0.866822 -81 CGTTTGCGTATCATATCAGAAAAAAGGGCCG 27 32 0 TCTATCAGAA 0.753737 -181 GGCGTGAACGCCTTATCCGAACTACGTCCGA 27 117 0 CCTATCCGAA 0.829338 -96 GGCGTTCACGCCGCATCCGACAAAACATCCG 27 136 1 CCCATCCGAC 0.980697 -77 TAACAGCCTATCCTATCAGGCTATTTTATTT 34 14 1 TCTATCAGGC 0.951181 -151 ** ******** Masking position 7 Map Score: 24.4596 Number of sites scoring better than the average of aligned sites = 913 Number in coding regions = 176 Number in noncoding regions = 737 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 4 ACGAATTTCTGGCAAACGGCGGCATTCTGGAGAT 1 194 0 GCAAAGGGGA 0.954867 -107 ATGAATGAGTGCAAAAAGGTGGGGGAAAAATTAT 2 176 0 GAAAAGGGGG 0.99104 -125 GTTTCAAACAGCAAAAAGGGGGAATTTC 2 283 1 GAAAAGGGGA 0.977918 -18 AAGAGAGCAAGGAAAACGGTTGCGTGGCTGTGAA 3 32 0 GAAAAGGTGG 0.911578 -86 ATCCCCTCCAGAACACTGGAGGGGTACTAATTAA 6 32 0 GACACGGGGG 0.877593 -51 TTCCCGGTGTGCAAACCGGGGGCGTATTATGTGC 8 74 0 GAAACGGGGG 0.981427 -37 CAGAAAAAACTGAAAACGGCGGCAACCCGCGAAT 10 35 0 TAAAAGGGGA 0.794779 -99 TCAGTATGAAGGAGTCAGGGGGGAGTATCAAA 11 9 0 GAGTCGGGGA 0.521498 -55 TGAACTGACAGCCAAATGGAGGAGTCAC 11 46 1 GCAAAGGGGG 0.981427 -18 CGGCAATTACTCCAAAAGGGGGCGCTCTCTTTTA 16 80 0 TCAAAGGGGG 0.822094 -134 ATGACAGGGCGTAAAATCGTGGGACACAT 21 240 1 GAAAACGGGA 0.85695 -19 GGTGAGAATAGCAAAAGGGCAGAGCCAGTGGCCC 22 26 0 GAAAAGGAGG 0.85394 -44 TAAAAAAGTGGTCGAACCGCGGAGTTACTTT 23 8 0 GCGAACGGGG 0.722202 -148 TTGCCGCCTTGAAGAAAGGAGGTATAATCCGTCG 29 20 0 GAGAAGGGGA 0.941546 -278 GAAAAGACGTGCAAAAAGGTTGTGTAAAGCAGTC 29 195 1 GAAAAGGTGG 0.911578 -103 AGCATTTTTTGCAAAAAGGGGTAGATGCAATCGG 31 79 1 GAAAAGGGTG 0.906303 -83 GCTTTGTTATGGAATAAGGCGGTGCCTAACTCGA 35 261 0 GAATAGGGGG 0.939996 -40 CCCAAGGGGGGGAAACGGGCGTCATTATAAAGAA 36 247 0 GAAACGGGTA 0.649142 -54 * **** ** ** * Masking position 9 Map Score: 19.6051 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 408 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 CTGAAGATAAAAAGCAATCGTTTTCGTGGG 2 226 0 AAAGCAATCG 0.873098 -75 GAAAGAGAGCAAGGAAAACGGTTGCGTGGC 3 38 0 AAGGAAAACG 0.959136 -80 CGGCAAAAAAAACGCAAACGTTTTCCGAAC 8 16 0 AACGCAAACG 0.934156 -95 TTTTCGTGCAAAGGAAAACGTTTCCGCTTA 9 38 1 AAGGAAAACG 0.959136 -68 AAGGTGTGTAAAGGCAAACGTTTACCTTGC 17 240 1 AAGGCAAACG 0.954461 -61 GCGCAGTATAAACGAAAACGTTTGCGTGTG 18 88 0 AACGAAAACG 0.940786 -46 GATGCGCGGGAAGGAAATCCCTACGCAAAC 21 175 1 AAGGAAATCC 0.662901 -84 TCTAACAGAAAAAGAAAACGTTTGCGTAGG 21 194 0 AAAGAAAACG 0.95077 -65 TGTGCGTCTGCAGGAAAACGCGATTTTAGC 27 63 1 CAGGAAAACG 0.84563 -150 AAAAAAAATCGACGGATTATA 29 2 1 AAAAAAATCG 0.264636 -296 TCTAACAGGGAAAGCAAACGTTTGCGAGAC 29 226 0 AAAGCAAACG 0.945192 -72 ACAAACCTGAAAAGAAATCCGTTTCCGGTT 32 110 1 AAAGAAATCC 0.618037 -191 GCGTAGCCTGAAGGTAATCGTTTGCGTAAA 32 166 1 AAGGTAATCG 0.52029 -135 ATTTTATTTCCACGCAAACGGTTTCGTCAG 36 208 1 CACGCAAACG 0.768043 -93 AGTTCAGGCAAAAGAGAACGATTGCGTTGG 39 194 1 AAAGAGAACG 0.684165 -107 CCCGCATTGTAACGAAAACGTTTGCGCAAC 41 185 0 AACGAAAACG 0.940786 -116 CCTTATAGAAAAAGAAAACCACCGACATCC 45 55 0 AAAGAAAACC 0.802207 -27 AATCCATTTTTAAGCAAACGGTGATTTTGA 46 81 1 TAAGCAAACG 0.596061 -23 ********** Masking position 7 Map Score: 18.2492 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 259 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 6 ACCATTTGGTCCACTTTTTTCTGCTCGTTTT 1 22 1 CCCTTTTTTC 0.802482 -279 TTTTTACACCGATAATTTTTCCCCCACCTTT 2 165 1 GAAATTTTTC 0.442415 -136 GAAATTCCCCCTTTTTGCTGTTTGAAAC 2 283 0 CCCTTTTTGC 0.799192 -18 ATGCTTTAGAGCAATTTTTTGTTAATGATTT 14 86 1 GCATTTTTTG 0.728813 -116 TAAATGACGGGAGATTTTTTCATCACAGTGT 17 66 0 GAATTTTTTC 0.761785 -235 GACGCATAATGCCATTTTTGCCCCCAACAGA 23 86 0 GCATTTTTGC 0.969078 -70 GAATCATCCGGCCCTTTTTTCTGATATGATA 27 24 1 GCCTTTTTTC 0.963403 -189 GCAGGAAAACGCGATTTTAGCGGTAATTCGC 27 72 1 GCATTTTAGC 0.728699 -141 GGGATAGCAAGCATTTTTTGCAAAAAGGGGT 31 70 1 GCTTTTTTGC 0.799381 -92 ACATTGCAGGGCTATTTTTTATAAGATGCAT 32 24 0 GCATTTTTTA 0.644579 -277 GGTTTGTGATGCAAATTTTTCACTTCATCAC 32 86 0 GCAATTTTTC 0.875772 -215 CCGGTTGCAAGCTCTTTATTCTCCAAAGCCT 32 134 1 GCCTTTATTC 0.692544 -167 TTATTCTGTCGCGATTTTTGCATTTTTTAAC 39 106 1 GCATTTTTGC 0.969078 -195 CGCAACGCTCGCGAATTTTTCTCTTTCAATG 41 160 0 GCAATTTTTC 0.888261 -141 CGTATCGTGCGCAATTTTTTCAGAATCGAAA 42 27 1 GCATTTTTTC 0.969472 -59 CAGAGTTACAGCACTTTTTGCACTCAAAAAT 46 35 0 GCCTTTTTGC 0.962614 -69 ** ******** Masking position 6 Map Score: 12.1511 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 565 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 7 AATAATATAAAAAATCCCGCCATTAAGTTGACTTTTAGCGC 1 149 1 AAACGCCTGA 0.952209 -152 CCATATCTCCAGAATGCCGCCGTTTGCCAGAAATTCGTCGG 1 190 1 AAACGCCAGA 0.985109 -111 TTGAAACCCAAAAAATCCGCCGCATTCTATTCATCTGAAGA 2 249 0 AAACGCCATT 0.935509 -52 CGGTTATGCTATAACACCACCCTATATATGACCCGAACTGG 4 108 1 AAACACCTGA 0.830975 -66 GTCACCAGCGATAAACTCGCCAGCAGAAAAAACTGAAAACG 10 51 0 AAACGCCAAA 0.852501 -83 TTTTTTTATCAAAACGTCGCTTTGATAGAGAGTTTTTATCA 12 124 0 AAACGCTAGA 0.777617 -82 AGTTTCGGTGACAACGTCACCTTGTTCCAGACGTTGCATCG 15 24 1 AAACACCAGA 0.942273 -127 CAAGTGTGCCATAATCTCGCGGCCAGGCATACTTGCGAAGA 26 32 0 AAACGCGATA 0.840915 -67 GTCAACGAAAAGAATATTGCCGCCTTGAAGAAAGGAGGTAT 29 29 0 AAATGCCAGA 0.766397 -269 TTTCCCTGTTAGAATTGCGCCGAATTTTATTTTTCTACCGC 29 243 1 AAACGCCATT 0.936008 -55 TACGCTCTGTATAATGCCGCGGCAATATTTATTAACCACTC 31 114 1 AAACGCGTTA 0.61385 -48 CTATTCCTTGAAAAGGTCGCCTGTCTTTTGATCTGCTAAAC 33 29 0 AAACGCCTGA 0.95221 -32 GAACTGACAAATAAAATAGCCTGATAGGATAGGCTGTTAGC 34 12 0 AAAAGCCATA 0.64517 -153 ACTGTCTGCAACAATTACGCCCACTGGGATAGGCTTTAAGT 34 125 1 AAACGCCATA 0.973449 -40 TTGCGTGGAAATAAAATCACCATCGTGAATTAGCAACGCGT 36 184 0 AAACACCATT 0.783036 -117 TAAAAAACCAAAAAATACACCAGTTTCTATACAAAGATGAT 39 68 0 AAACACCATA 0.900462 -233 TTTCGTGGTGATAATTTCACCATGAAAAAGTTGTCAGCCCC 39 250 1 AAACACCAGT 0.86688 -51 TCTTGTTTTTACAAGAGCGCCCTTGTTCAGTCCTCAGTAAC 40 45 0 AAACGCCAGT 0.963493 -76 * ** **** *** Masking position 4 Map Score: 17.2836 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 472 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 GAAAACGCTTGCGCAGCAAGAAGATTGCATGA 1 57 0 GCGCGCAAGA 0.913592 -244 GTGCAAAAAGGTGGGGGAAAAATTATCGGTGT 2 170 0 GTGGGGAAAA 0.724978 -131 ATGCTGATTCGCGCGGGAAATATGGGTATTAT 4 52 0 GCGCGGAAAA 0.976134 -122 GAATTGACCTGCGGCAAAAAAAACGCAAACGT 8 25 0 GCGGAAAAAA 0.673533 -86 CAAACCAGTAGCGCTCGAAGGAGAGGTGA 14 8 0 GCGCCGAAGA 0.952894 -194 CGAAAACTGTGCGGGCCAGGCATGATCCTTTC 15 86 0 GCGGCCAGGA 0.634339 -65 GTGTTGCGGTACGCCGGAAAAACGACACGGAG 17 195 0 ACGCGGAAAA 0.698269 -106 AATAAAAATGGCGCTGAAAAAATATTCAACGC 21 143 0 GCGCGAAAAA 0.921608 -116 TTTTATTGATGCGCGGGAAGGAAATCCCTACG 21 168 1 GCGCGGAAGA 0.977958 -91 CCCCAGGCGCGCGGCGAAAGAAGACTTGTGCC 29 164 0 GCGGGAAAGA 0.935597 -134 CGCGTTACTTGCGGTAGAAAAATAAAATTCGG 29 262 0 GCGGAGAAAA 0.877711 -36 CATTCAAACAGCGGAGGAGACATAAACCCCTC 35 30 1 GCGGGGAGAA 0.936381 -271 AAGCTGGGACGCGCACGACACAGAGAATTAAC 36 57 0 GCGCCGACAA 0.854889 -244 TCGTTACAATGCGGGCGAAAAATAAGGATGCC 41 200 1 GCGGCGAAAA 0.955038 -101 AAATAGATCAGCGGGGAACGCAGGATCGCTGG 43 40 0 GCGGGAACGA 0.821095 -36 **** ***** * Masking position 8 Map Score: 10.6921 Number of sites scoring better than the average of aligned sites = 838 Number in coding regions = 784 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 9 TTTTTTGGGTTTCAAACAGCAAAAAGGGGGAA 2 275 1 TCAAACGCAA 0.63475 -26 TGAAGCACCAATCAAACGGAACAGGATGCAAA 4 151 1 ACAAACGAAC 0.774511 -23 AAAACATCCCTTCAGCCGGAGCATAGAGATTA 9 84 1 TCAGCCGAGC 0.797503 -22 CCCTGACTCCTTCATACTGAAAGTGAACTGAC 11 23 1 TCATACGAAA 0.724933 -41 ATTAAAACATAACAGCCCGAAACTTTGGATAA 23 39 0 ACAGCCGAAA 0.964854 -117 TCGAACCAGGTTCAGACAGAAAGGTCCCTA 23 136 1 TCAGACGAAA 0.944772 -20 CTACGTTGGCTACAGCCTGAAATGTTCCGAGC 24 21 0 TCAGCCGAAA 0.964854 -62 CCAACGTAGTTACAGCCTGAAAGATGACGAGT 24 44 1 TCAGCCGAAA 0.964854 -39 CATCCGACAAAACATCCGGCACACCAGACAGC 27 149 1 ACATCCGCAC 0.639026 -64 CATCCGGCACACCAGACAGCAAAAGATTTTAA 27 161 1 ACAGACGCAA 0.887291 -52 ATTAAAAGCAAGCAGACAGAACCGTTCTGA 28 9 0 ACAGACGAAC 0.939612 -71 ATAAAGAGCTTGCAACCGGAAACGGATTTCTT 32 121 0 TCAACCGAAA 0.858363 -180 CGTGTAAAAAAACAGCCCGAAACC 43 3 0 ACAGCCGAAA 0.964854 -73 ACAAAAAACAGACTGATCGAGGTCATTT 46 7 1 ACAGACGATC 0.623467 -97 * ***** **** Masking position 4 Map Score: 8.66791 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 481 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 10 AAACGTTTTCCTTTGCACGAAAAATAAAGG 9 31 0 CTTTGCACGA 0.914023 -75 GAAGGGATGTTTTTGCCGGACACAAAGGAT 9 67 0 TTTTGCCGGA 0.915841 -39 AAAGCATCCGTATCGCAGGACGCAAACGCA 14 63 0 TATCGCAGGA 0.693224 -139 AAGCGTGGAATTTTGGCCGATCTTGACGAA 17 127 0 TTTTGGCCGA 0.689388 -174 TACCTTGCGATTTTGCAGGAGCTGAAGTTA 17 262 1 TTTTGCAGGA 0.856178 -39 TGCAGGCAGACTTTGCAGGATTTCGGCGGG 19 54 0 CTTTGCAGGA 0.813828 -41 ATCCGACACGCATTGCCCGATGCCGCAAAG 21 97 1 CATTGCCCGA 0.839369 -162 TTTAGCGGTAATTCGCACGAAATTTGTTTG 27 87 1 ATTCGCACGA 0.835286 -126 TACACAACCTTTTTGCACGTCTTTTCCCCA 29 191 0 TTTTGCACGT 0.587618 -107 TTCTCTTCGCCCGACTTCATGTCG 30 5 1 CTTCGCCCGA 0.964831 -64 AGATAATATAAATCGCCCGACATGAAGTCG 30 22 0 AATCGCCCGA 0.713678 -47 TAACTCGACGTTTCGCCCGATGGTTGATAT 35 239 0 TTTCGCCCGA 0.973932 -62 AATCGTTCTCTTTTGCCTGAACTTACCACC 39 187 0 TTTTGCCTGA 0.675883 -114 CATCCTTATTTTTCGCCCGCATTGTAACGA 41 200 0 TTTCGCCCGC 0.84496 -101 TCTGAAAAAATTGCGCACGATACGTCTCAA 42 21 0 TTGCGCACGA 0.734943 -65 ********** Masking position 5 Map Score: 7.76713 Number of sites scoring better than the average of aligned sites = 668 Number in coding regions = 606 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 11 CCGGCACTGTGTGCCGATGCCTG 2 1 1 CCGGCACGTG 0.915611 -300 TGCCTACGGACCTGAACCGTAGGTCGGATAAGG 2 58 1 CCTGAACGGG 0.87272 -243 TTATAGCATAACCGCACGATCGGATCATCACGC 4 89 0 ACCGCACAGG 0.637088 -85 CTATATATGACCCGAACTGGGTTGAAGCACCAA 4 129 1 CCCGAACGTT 0.872006 -45 CACCAATCAAACGGAACAGGATGCAAAA 4 156 1 ACGGAACGTG 0.618916 -18 AAATATTGTCCCCGAAGTGATGGGAAAAGTCTT 12 162 1 CCCGAAGGGG 0.980201 -44 TCATGCCTGGCCCGCACAGTTTTCGGCAGATTC 15 93 1 CCCGCACGTT 0.887573 -58 CAGACCGGCACCCTCAGCGAAGGCA 19 3 0 CCCTCAGGGG 0.8134 -92 TAGAATGCGCCCCGAACAGGATGACAGGGCGTA 21 220 1 CCCGAACGTG 0.98002 -39 GCTTGCTATCCCCGAAGGGCGGGTTACTATCGA 31 49 0 CCCGAAGGGG 0.944026 -113 TGTAGCACGTCCCGAAGGGGCTGACATAAGTCG 35 146 0 CCCGAAGGTG 0.97253 -155 CTGATCCTCTCCCGCAGAAGAGGAATAAAGCCG 37 11 0 CCCGCAGAGG 0.901085 -108 ******* * ** Masking position 6 Map Score: 7.79254 Number of sites scoring better than the average of aligned sites = 636 Number in coding regions = 567 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 12 TTTTGCATCCTGTTCCGTTTGA 4 162 0 TTTGCATCCG 0.888407 -12 ACGCCCCCGGTTTGCACACCGGGAATCCAGG 8 83 1 TTTGCACACG 0.967745 -28 TGCATATGCGTTTGCGTCCTGCGATACGGAT 14 57 1 TTTGCGTCCG 0.938049 -145 ATTACGCATTTTTACACACTGTGATGAAAAA 17 51 1 TTTACACACG 0.906344 -250 GCTTACACTATTTGCGTACTGGCCATTGACC 17 153 1 TTTGCGTACG 0.94847 -148 AAAGAAAACGTTTGCGTAGGGATTTCCTTCC 21 183 0 TTTGCGTAGG 0.81434 -76 GTCCCACGATTTTACGCCCTGTCATCCTGTT 21 234 0 TTTACGCCCG 0.938049 -25 AAAACGTTAATTCACACCCAGGAGTGATAAA 27 191 1 TTCACACCCG 0.577468 -22 GAGACACTTGTTTGCACAGAGGATGGCCC 28 61 1 TTTGCACAGG 0.877299 -19 TTTATACCTTTTTACGCACAGAGTTATCCAC 41 70 1 TTTACGCACG 0.94847 -231 ATTTCTGTATTTTGCCCACGGTAACCACAGT 41 114 1 TTTGCCCACG 0.916462 -187 AACGAAAACGTTTGCGCAACGCTCGCGAATT 41 174 0 TTTGCGCAAG 0.832934 -127 ********* * Masking position 2 Map Score: 7.33819 Number of sites scoring better than the average of aligned sites = 544 Number in coding regions = 505 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 13 GTTTTTATTTCATGCAATCTTCTTGCTGCG 1 48 1 CATGCAATCT 0.762071 -253 AAAACCCGCAACTTTGCTGATTTC 3 5 1 CCCGCAACTT 0.79625 -113 ATCGGATCATCACGCAATGTATGCTGATTC 4 74 0 CACGCAATGT 0.869787 -100 TTTAAATATTCATGAAATCTATAAATTAAA 5 171 1 CATGAAATCT 0.698639 -130 TAGTCCTCGACATGAAATCTGCGTCAATAT 10 112 0 CATGAAATCT 0.698639 -22 CCTACTCCTTCCCGTAACGTCTTTAATACG 12 17 1 CCCGTAACGT 0.642414 -189 CCGCCGAAATCCTGCAAAGTCTGCCTGCAA 19 55 1 CCTGCAAAGT 0.68591 -40 AACATAACAGCCCGAAACTTTGGATAAAAA 23 36 0 CCCGAAACTT 0.738808 -120 TTGGCTACAGCCTGAAATGTTCCGAGCATT 24 18 0 CCTGAAATGT 0.918256 -65 TATCCTTATACCTGAAATCTTCGCAAGTAT 26 15 1 CCTGAAATCT 0.867484 -84 CGGTAATTCGCACGAAATTTGTTTGTCGGA 27 92 1 CACGAAATTT 0.577019 -121 AAAAAATAGCCCTGCAATGTAAATGGTTCT 32 35 1 CCTGCAATGT 0.939467 -266 AGCGATGGTTCCTGAAACGTGCAGTGAATT 37 98 0 CCTGAAACGT 0.891876 -21 TTATTTTTCGCCCGCATTGTAACGAAAACG 41 195 0 CCCGCATTGT 0.649914 -106 ********** Masking position 6 Map Score: 4.87246 Number of sites scoring better than the average of aligned sites = 422 Number in coding regions = 363 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 14 GGCTGCCGCGGCGGGTCAGGA 10 2 0 GCGGGTCAGG 0.982419 -132 GGACTTTTCACAGGGTCTGGTTGCGCAGGT 12 63 0 CAGGGTCTGG 0.861016 -143 TCTCCTTCGAGCGCTACTGGTTTGCTCGTC 14 16 1 GCGCTACTGG 0.573383 -186 CGAAAACTGTGCGGGCCAGGCATGATCCTT 15 88 0 GCGGGCCAGG 0.964616 -63 AAACGACACGGAGCGTCAGGAAGGGGTCAA 17 178 0 GAGCGTCAGG 0.849435 -123 GAGCTGAAGTTAGGGTCTGGAGTGAAATGG 17 280 1 TAGGGTCTGG 0.609272 -21 CGCTGAGGGTGCCGGTCTGGCACCCTGACT 19 17 1 GCCGGTCTGG 0.834483 -78 CAGGATTTCGGCGGGAGTTGCAAGTCAGGG 19 39 0 GCGGGAGTTG 0.582547 -56 TTCTTTCGCCGCGCGCCTGGGGAAAAGACG 29 174 1 GCGCGCCTGG 0.886161 -124 TTCCTCTTCTGCGGGAGAGGATCAGGGTGA 37 19 1 GCGGGAGAGG 0.9582 -100 GGGAGAGGATCAGGGTGAGGAAAATTTATG 37 31 1 CAGGGTGAGG 0.777716 -88 CGAAGAGAGTGAGGGTGAGGCATAAATTTT 37 51 0 GAGGGTGAGG 0.917873 -68 GCGTTGGGGACCGGGAGTGGCTCCGATGCT 39 217 1 CCGGGAGTGG 0.877549 -84 TATAACGACTGCGGTACAGGTCAATAAAGC 45 11 1 GCGGTACAGG 0.825003 -71 ********** Masking position 10 Map Score: 9.21384 Number of sites scoring better than the average of aligned sites = 1173 Number in coding regions = 1111 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 15 TATTTCATGCAATCTTCTTGCTGCGCAAGCG 1 53 1 ATCTTCTTGC 0.714593 -248 AATCAATGCAAATCTGCTTACCGACGAATTT 1 220 0 ATCTGCTTAC 0.947287 -81 TTCCCGCGCGAATCAGCATACATTGCGTGAT 4 65 1 ATCAGCATAC 0.739102 -109 TGTCACCGAAACTCAGCTTGCCCGGC 15 6 0 ATCAGCTTGC 0.966282 -145 TGATAGGGTTAGTCTGCTTGCATCATACAGG 16 35 1 ATCTGCTTGC 0.966282 -179 AATCCTGCAAAGTCTGCCTGCAAGTCTGACA 19 62 1 ATCTGCCTGC 0.870058 -33 AGAACGGTTCTGTCTGCTTGCTTTTAATGCC 28 13 1 TTCTGCTTGC 0.801289 -67 GCATCTCCTGACTCAGCTAACAATAAAATTT 32 278 0 ATCAGCTAAC 0.890557 -23 TTCGCGAAAAACTCAGCTAACGCCCCTAACG 41 233 0 ATCAGCTAAC 0.890557 -68 TTCGCGAAAAATTCAGCTAACGCTCTCTGTA 41 256 1 ATCAGCTAAC 0.890557 -45 * ********* Masking position 3 Map Score: 5.53932 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 65 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555