AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ipurR_ecoli_hinf_100.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 pyrD 110 dihydro-orotate dehydrogenase #5 pyrC 105 dihydro-orotase #6 ycfC 35 orf, hypothetical protein #7 ymfC 201 orf, hypothetical protein #8 prsA 150 phosphoribosylpyrophosphate synthetase #9 purR 300 transcriptional repressor for pur regulon, glyA, glnB, prsA, speA #10 purT 133 phosphoribosylglycinamide formyltransferase 2 #11 ubiX 94 3-octaprenyl-4-hydroxybenzoate carboxy-lyase #12 purF 36 amidophosphoribosyltransferase = PRPP amidotransferase #13 cvpA 258 membrane protein required for colicin V production #14 purC 212 phosphoribosylaminoimidazole-succinocarboxamide synthetase = SAICAR synthetase #15 purM 297 phosphoribosylaminoimidazole synthetase = AIR synthetase #16 guaA 68 GMP synthetase (glutamine-hydrolyzing) #17 guaB 161 IMP dehydrogenase #18 glyA 300 serine hydroxymethyltransferase #19 glnB 60 regulatory protein P-II for glutamine synthetase #20 yfhG 164 putative alpha helix protein #21 purL 300 phosphoribosylformyl-glycineamide synthetase = FGAM synthetase #22 gcvP 118 glycine decarboxylase, P protein of glycine cleavage system #23 gcvH 23 in glycine cleavage complex, carrier of aminomethyl moiety via covalently bound lipoyl cofactor #24 gcvT 300 aminomethyltransferase (T protein; tetrahydrofolate-dependent) of glycine cleavage system #25 yqgB 120 orf, hypothetical protein #26 purH 300 phosphoribosylaminoimidazolecarboxamideformyltransferase = AICAR formyltransferase; IMP cyclohydrolase #27 purA 103 adenylosuccinate synthetase #28 HI0221 129 inosine-5'-monophosphate dehydrogenase (guaB) #29 HI0222 109 GMP synthase (guaA) #30 HI0329 37 conserved hypothetical protein #31 HI0330 98 opacity associated protein (oapA) #32 HI0331 59 opacity associated protein (oapB) #33 HI0334 77 GTP pyrophosphokinase (relA) #34 HI0336 82 molybdopeterin biosynthesis protein (mog) #35 HI0501 167 high affinity ribose transport protein (rbsD) #36 HI0505 97 ribokinase (rbsK) #37 HI0506 27 rbs repressor (rbsR) #38 HI0638 128 conserved hypothetical protein #39 HI0639 22 adenylosuccinate lyase (purB) #40 HI0752 300 phosphoribosylformylglycinamidine synthase (purL) #41 HI0842 197 H. influenzae predicted coding region HI0842 #42 HI0887 187 phosphoribosylaminoimidazolecarboxamide formyltransferase (purH) #43 HI0888 95 phosphoribosylamine--glycine ligase (purD) #44 HI0889 123 serine hydroxymethyltransferase (serine methylase) (glyA) #45 HI1205 214 conserved hypothetical protein #46 HI1206 86 colicin V production protein (cvpA) #47 HI1401 229 dihydroorotate dehydrogenase (pyrD) #48 HI1429 179 phosphoribosylaminoimidazole synthetase (purM) #49 HI1603 207 conserved hypothetical protein #50 HI1604 24 phosphate permease, putative #51 HI1605 65 conserved hypothetical protein #52 HI1607 62 hemM protein (hemM) #53 HI1615 160 phosphoribosylaminoimidazole carboxylase, catalytic subunit (purE) #54 HI1616 69 phosphoribosylaminoimidazole carboxylase, ATPase subunit (purK) #55 HI1633 128 adenylosuccinate synthetase (purA) #56 HI1635 274 purine nucleotide synthesis repressor (purR) #57 HI1726 124 phosphoribosylaminoimidazole-succinocarboxamide synthase (purC) Motif number 1 ACCTGTTCTGGAAAACGCTTGCGCAGCAAGAA 1 67 0 GAAACGTTGC 0.930857 -234 ATTTCCCCACGAAAACGATTGCTTTTTATCTT 2 221 1 GAAACGTTGC 0.800385 -80 AGAGAGCAAGGAAAACGGTTGCGTGGCTGTGA 3 33 0 GAAACGTTGC 0.678107 -85 AACAGGTTCGGAAAACGTTTGCGTTTTTTTTG 4 11 1 GAAACGTTGC 0.548459 -100 TCGTGCAAAGGAAAACGTTTCCGCTTATCCTT 5 41 1 GAAACGTTCC 0.542742 -65 AAATCGCAAGGTAAACGTTTGCCTTTACACAC 9 243 0 GAAACGTTGC 0.548459 -58 CAGTATAAACGAAAACGTTTGCGTGTGTCTTT 10 83 0 GAAACGTTGC 0.548459 -51 AACAGAAAAAGAAAACGTTTGCGTAGGGATTT 13 189 0 GAAACGTTGC 0.548459 -70 GATATGATACGCAAACGTGTGCGTCTGCAGGA 14 46 1 GAAACGGTGC 0.527497 -167 AAGCAGTCTCGCAAACGTTTGCTTTCCCTGTT 15 221 1 GAAACGTTGC 0.499998 -77 TATACAGAGCGTAACCGATTGCATCTACCCCT 17 95 0 GAACCGTTGC 0.793673 -67 TAGCCTGAAGGTAATCGTTTGCGTAAATTCCT 18 169 1 GAATCGTTGC 0.538979 -132 ATGCGCTGACGAAACCGTTTGCGTGGAAATAA 21 211 0 GAACCGTTGC 0.545404 -90 TCAGGCAAAAGAGAACGATTGCGTTGGGGACC 24 197 1 GGAACGTTGC 0.973272 -104 GCATTGTAACGAAAACGTTTGCGCAACGCTCG 26 180 0 GAAACGTTGC 0.548459 -121 TAAATATCAGGAAAACGTTTCCGTTAAATATA 38 104 0 GAAACGTTCC 0.542742 -25 CTATATTTAAGCAAACGTTTGCGTTATAATTC 42 126 1 GAAACGTTGC 0.499998 -62 AAGCCAAAAAGAAAACGTTTGCGTAAA 46 6 0 GAAACGTTGC 0.548459 -81 TAACAATATCGCAAACGTTTGCTTGATGATAT 48 119 1 GAAACGTTGC 0.499998 -61 AAGCCATTTAGCAAACGTTTGCCTGATATATG 53 87 1 GAAACGTTGC 0.499998 -74 TTAAAAAATAGCAAACGTTTGCTTTATTTGAT 57 97 1 GAAACGTTGC 0.499998 -28 * ***** **** Masking position 10 Map Score: 91.1442 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 CGTAAGTGTGAAAGTTCGGCGAAACCACGA 25 92 0 AAAGTTCGGC 0.852126 -29 TTGAGTGCAAAAAGTGCTGTAACTCTGAAA 27 39 1 AAAGTGCTGT 0.941052 -65 TTTGCTGTTTAAAGTGCGGTTGGTTTTTGC 29 37 1 AAAGTGCGGT 0.997083 -73 GAGAAGCTCAAAAGTGCGGCGAAAAAATTA 31 29 0 AAAGTGCGGC 0.991467 -70 CCCTCCAAAAGTGCGGTAAGTTTTTAC 34 8 1 AAAGTGCGGT 0.997083 -75 GGATAAATCAAAAATGCGGTAAAAACTTAC 34 26 0 AAAATGCGGT 0.944292 -57 ATAATTTCTTAAAGTGCGGTAAAAATACGA 42 84 0 AAAGTGCGGT 0.997083 -104 TAATTTAAAAAAAGTACGGCTATTTTTTAC 43 55 0 AAAGTACGGC 0.852126 -41 TAGCGTATGATAAGTGCGGTCAATTTTTGA 45 186 1 TAAGTGCGGT 0.96278 -29 CCTTACCTTTAAAGTGCGGTGAAAATTGAC 47 169 1 AAAGTGCGGT 0.997083 -61 TTACTGTAAGAAAGTGCGGTCAATTTTCAC 47 187 0 AAAGTGCGGT 0.997083 -43 ATCTCAATAAAAAGTGCGGTTAATTTTAAC 51 14 1 AAAGTGCGGT 0.997083 -52 CATCACAACAAAAGTGCGGTTAAAATTAAC 51 32 0 AAAGTGCGGT 0.997083 -34 CCGCACTTTAAAAGTGCGGTCAGATCTAAA 54 18 0 AAAGTGCGGT 0.997083 -52 CCGCACTTTTAAAGTGCGGTTGTTTTTTTC 54 29 1 AAAGTGCGGT 0.997083 -41 ATTTAAACCTAAAGTGCGGTGAAAAATCAC 55 12 1 AAAGTGCGGT 0.997083 -117 TATAAAAGAAAAAGTGTGGTGATTTTTCAC 55 30 0 AAAGTGTGGT 0.941054 -99 TGTAGAAACAAAACTGCGGTGATAATAAAA 56 18 1 AAACTGCGGT 0.96172 -257 ********** Masking position 5 Map Score: 60.6637 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 GTGTGCCGATGCCTGATGCGACGCTGACGCGTT 2 19 1 GCTGATGGCG 0.997182 -282 TGAACCGTAGGTCGGATAAGGCGCTCGCGTCGC 2 70 1 GCGGATAGCG 0.996114 -231 TGAGCATGGTGTCGGATGCGACGCGAGCGCCTT 2 87 0 GCGGATGGCG 0.998237 -214 ATGCTCAGATGCCTGATGCGACGCTGACGCGTC 2 113 1 GCTGATGGCG 0.997182 -188 CAGTGGGTAGGCCTGATAAGACGCGTCAGCGTC 2 132 0 GCTGATAGCG 0.993795 -169 TACGGTCTTGCCTGATGCGACGCTGGCGCGTC 13 10 1 GCTGATGGCG 0.997182 -249 CCCTGCGTAGGCCTGATAAGACGCGCCAGCGTC 13 29 0 GCTGATAGCG 0.993795 -230 AGAACCGTAGGTCGGATAAGGCGTTTACGCCGC 13 64 1 GCGGATAGCG 0.996114 -195 GGCAATGCGTGTCGGATGCGGCGTAAACGCCTT 13 81 0 GCGGATGGCG 0.998237 -178 TCGGACGTAGTTCGGATAAGGCGTTCACGCCGC 14 117 1 TCGGATAGCG 0.948432 -96 CGGATGTTTTGTCGGATGCGGCGTGAACGCCTT 14 134 0 GCGGATGGCG 0.998237 -79 ATCTTTTGCTGTCTGGTGTGCCGGATGTTTTGT 14 155 0 GCTGGTGGCG 0.983802 -58 * ****** * ** Masking position 7 Map Score: 37.0344 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 4 TAACCTGTTCTGGAAAACGCTTGCGCAGCAA 1 70 0 TGAAAACGCT 0.373904 -231 ATATTTCCCCACGAAAACGATTGCTTTTTAT 2 219 1 AGAAAACGAT 0.872933 -82 AAAGAGAGCAAGGAAAACGGTTGCGTGGCTG 3 36 0 AGAAAACGGT 0.939316 -82 GGCAAAAAAAACGCAAACGTTTTCCGAACCT 4 14 0 AGCAAACGTT 0.98812 -97 TTTCGTGCAAAGGAAAACGTTTCCGCTTATC 5 39 1 AGAAAACGTT 0.980945 -67 AGGTGTGTAAAGGCAAACGTTTACCTTGCGA 9 241 1 AGCAAACGTT 0.98812 -60 CGCAGTATAAACGAAAACGTTTGCGTGTGTC 10 86 0 AGAAAACGTT 0.980945 -48 CTAACAGAAAAAGAAAACGTTTGCGTAGGGA 13 192 0 AGAAAACGTT 0.980945 -67 CTGATATGATACGCAAACGTGTGCGTCTGCA 14 44 1 AGCAAACGTG 0.953083 -169 GTGCGTCTGCAGGAAAACGCGATTTTAGCGG 14 64 1 AGAAAACGCG 0.721867 -149 CTAACAGGGAAAGCAAACGTTTGCGAGACTG 15 224 0 AGCAAACGTT 0.98812 -74 AAAGGAATTTACGCAAACGATTACCTTCAGG 18 172 0 AGCAAACGAT 0.917352 -129 TTTTATTTCCACGCAAACGGTTTCGTCAGCG 21 209 1 AGCAAACGGT 0.961551 -92 CCGGTCCCCAACGCAATCGTTCTCTTTTGCC 24 200 0 AGCAATCGTT 0.823767 -101 TAATTTCACCATGAAAAAGTTGTCAGCCCCG 24 261 1 AGAAAAAGTT 0.766605 -40 CCGCATTGTAACGAAAACGTTTGCGCAACGC 26 183 0 AGAAAACGTT 0.980945 -118 ATCCATTTTTAAGCAAACGGTGATTTTGAAA 27 82 1 AGCAAACGGT 0.961551 -22 AGTAAATATCAGGAAAACGTTTCCGTTAAAT 38 107 0 AGAAAACGTT 0.980945 -22 TTCTATATTTAAGCAAACGTTTGCGTTATAA 42 124 1 AGCAAACGTT 0.98812 -64 TAAAGCCAAAAAGAAAACGTTTGCGTAAA 46 9 0 AGAAAACGTT 0.980945 -78 TTATATCATCAAGCAAACGTTTGCGATATTG 48 122 0 AGCAAACGTT 0.98812 -58 TACATATATCAGGCAAACGTTTGCTAAATGG 53 90 0 AGCAAACGTT 0.98812 -71 AATGATATAAAAGAAAAAGTGTGGTGATTTT 55 34 0 AGAAAAAGTG 0.44513 -95 AAATCAAATAAAGCAAACGTTTGCTATTTTT 57 100 0 AGCAAACGTT 0.98812 -25 * ********* Masking position 6 Map Score: 60.3435 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 43 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 TGAAACCCAAAAAATCCGCCGCATTCTATTCA 2 257 0 AAAACGCCGC 0.973314 -44 ATTCCATCCGAAAACTAACCTTTACCCTGGCA 15 136 1 AAAATACCTT 0.726164 -162 GTAGAAAAATAAAATTCGGCGCAATTCTAACA 15 249 0 AAAATGGCGC 0.885776 -49 AGTGGTTAATAAATATTGCCGCGGCATTATAC 17 122 0 AAATTGCCGC 0.812683 -40 TTTTGCACTCAAAAATGACCTCGATCAGTCTG 27 19 0 AAAATACCTC 0.914875 -85 AAACTTTGCAAAAACCAACCGCACTTTAAACA 29 42 0 AAAACACCGC 0.978 -68 AAATGCGGTAAAAACTTACCGCACTTTTGGAG 34 13 0 AAAATACCGC 0.985891 -70 AAACACCCTAAAAATTCACCGCACT 37 4 0 AAAATACCGC 0.985891 -24 ATTGCAGGTAAAAAATAGCCGTACTTTTTTTA 43 48 1 AAAATGCCGT 0.933973 -48 AAACACCTCAAAAATTGACCGCACTTATCATA 45 191 0 AAAATACCGC 0.985891 -24 TCTCTCAATGAAAAACGGCCGTTTAAAACGAC 46 58 0 AAAACGCCGT 0.899993 -29 CCATAAAAATAAAACTAGCCGTTTTTTATACA 47 29 1 AAAATGCCGT 0.933973 -201 AAAATATTGTAAAATTAAGCTCTACACGATCA 47 78 0 AAAATAGCTC 0.592467 -152 AAGTGCGGTGAAAATTGACCGCACTTTCTTAC 47 180 1 AAAATACCGC 0.985891 -50 AAGTGCGGTTAAAATTAACCGCACTTTTTATT 51 19 0 AAAATACCGC 0.985891 -47 AATTTACGAAAAAAACAACCGCACTTTAAAAG 54 34 0 AAAACACCGC 0.978 -36 AAGTGCGGTGAAAAATCACCACACTTTTTCTT 55 23 1 AAAATACCAC 0.882359 -106 CAGACATACTAAAAACAACCATAATCATTGCA 56 91 1 AAAACACCAT 0.540738 -184 **** * ***** Masking position 3 Map Score: 27.1995 Number of sites scoring better than the average of aligned sites = 258 Number in coding regions = 224 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 6 GATGCCTGATGCGACGCTGACGCGTTTTATCAT 2 26 1 GCGACGCCGC 0.99241 -275 GGTGTCGGATGCGACGCGAGCGCCTTATCCGAC 2 80 0 GCGACGCCGC 0.997101 -221 GATGCCTGATGCGACGCTGACGCGTCTTATCAG 2 120 1 GCGACGCCGC 0.99241 -181 TCACGAGGGCGCATTCGCGCCCTTTATT 5 6 1 AGGGCGCCGC 0.976201 -100 TCCGTATCGCAGGACGCAAACGCATATGCAACG 7 54 0 AGGACGCCGC 0.972536 -148 CTTGCCTGATGCGACGCTGGCGCGTCTTATCAG 13 17 1 GCGACGCCGC 0.99241 -242 CGTGTCGGATGCGGCGTAAACGCCTTATCCGAC 13 74 0 GCGGCGTCGC 0.984065 -185 CATCCTGTTCGGGGCGCATTCTAACAGAAAAAG 13 210 0 GGGGCGCCTA 0.90055 -49 TTTGTCGGATGCGGCGTGAACGCCTTATCCGAA 14 127 0 GCGGCGTCGC 0.984065 -86 TTTTCAAGCTGGGACGCGCACGACACAGAGAAT 21 61 0 GGGACGCCGA 0.982536 -240 AAACGTTTGCGCAACGCTCGCGAATTTTTCTCT 26 167 0 GCAACGCCGA 0.848313 -134 AAAAGAAAAAGGGGCGATTACTCGCCCAAAAAA 32 11 0 GGGGCGACTC 0.781841 -49 ******* *** Masking position 5 Map Score: 19.9886 Number of sites scoring better than the average of aligned sites = 701 Number in coding regions = 409 Number in noncoding regions = 292 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 7 TGCATGAAATAAAAACGAGCAGAAAAAAGTGGACCAA 1 27 0 AAAGCAAAAA 0.897069 -274 AATGAGTGCAAAAAGGTGGGGGAAAAATTATCGGTGT 2 170 0 AAAGGAAAAA 0.94514 -131 CATTGGTGGAAAGAATCTGCCGAAAACTGTGCGGGCC 8 101 0 AAAGCAAAAC 0.774874 -50 TTGTGTGGTAATAAAAAAGGAGAAAACTTGAT 9 6 0 ATAGGAAAAC 0.70006 -295 AGATTTTTTCATCACAGTGTGTAAAAATGCGTAATAT 9 49 0 ATAGTAAAAA 0.620559 -252 ACCGAAAAGAAATATACTGTATAAAATCACAGTTATT 10 25 0 AAAGTAAAAT 0.73956 -109 CGCATCAATAAAAATGGCGCTGAAAAAATATTCAACG 13 144 0 AAAGCAAAAA 0.897069 -115 CCCGAACAGGATGACAGGGCGTAAAATCGTGGGACAC 13 230 1 ATAGCAAAAT 0.64037 -29 GATTGTGGATAACTCTGTGCGTAAAAAGGTATAAAGC 26 68 0 AATGCAAAAA 0.863673 -233 CGTTTTCGTTACAATGCGGGCGAAAAATAAGGATGCC 26 195 1 ACAGGAAAAA 0.807981 -106 GCGTTAGCTGAATTTTTCGCGAAAAACTCAGCTAACG 26 242 0 AATGCAAAAC 0.714451 -59 GATCGAGGTCATTTTTGAGTGCAAAAAGTGCTGTAAC 27 25 1 ATTGTAAAAA 0.543117 -79 TCTCGCTAATAAGTTGAAGTTAAAAAATATTGCGACG 28 95 0 AATGTAAAAA 0.776072 -35 TGAGAAGCTCAAAAGTGCGGCGAAAAAATTATGTGTA 31 23 0 AAAGGAAAAA 0.94514 -76 TGGATAAATCAAAAATGCGGTAAAAACTTACCGCACT 34 20 0 AAAGGAAAAC 0.871861 -63 AAAAAATATAACAATACAGGATAAAATA 36 80 1 ACAGGAAAAT 0.714793 -18 GTTCGAGTTCAAAAGCTAGGTTAAAAATGCTATATTT 38 74 1 AAAGGAAAAA 0.94514 -55 TCCTTAAATTAATTAAAAGTATAAAAATTTCCGAGTT 40 45 1 AATGTAAAAA 0.776072 -256 GAGTATAAAGACTTAAGGGCAAAAAATCCATTCTTTT 41 24 0 ACTGCAAAAT 0.479602 -174 AACTCCGTAAAAAAGAAAGGATAAAAAGACGAGAATG 41 168 0 AAAGGAAAAA 0.94514 -30 AAATGTGGGCAAAAATAAGGATAAAATTATGAAACTA 42 19 0 AAAGGAAAAT 0.911201 -169 AAATACGATAAATTTCAGGCATAAAAAAGCCCACATA 42 55 0 AATGCAAAAA 0.863673 -133 TTTTCCTTTCATTAAATAGTTAAAAATAAGCGATGAG 42 157 0 ATAGTAAAAT 0.493438 -31 AAAGAGGGGGAATTGCAGGTAAAAAATAGCCGTACTT 43 37 1 AATGTAAAAT 0.673652 -59 AAATAAGCTCAAGATTTAGGAGAAAAA 48 1 0 AAAGGAAAAA 0.94514 -179 AAGCGAGAAAATTTGAAAGGTAAAAAA 49 1 0 ATTGGAAAAA 0.811178 -207 ATTTACTCCAAATTAAGGGGTTAAAAATTCGTGCGCA 49 176 0 AATGGAAAAA 0.926056 -32 ACATCACAACAAAAGTGCGGTTAAAATTAACCGCACT 51 26 0 AAAGGAAAAT 0.911201 -40 TTTTGTTGTGATGTTTAAGGGGAAAAA 51 49 1 ATTGGAAAAA 0.811178 -17 ATACCATTGCAACTTTAAGGATAAAATTTTATCCTAA 53 40 0 AATGGAAAAT 0.881785 -121 ATGTTAGGGGAAGTATAGGGGGAAAATGTTTATTATT 57 38 0 AATGGAAAAT 0.881786 -87 ** * ** ***** Masking position 13 Map Score: 32.3983 Number of sites scoring better than the average of aligned sites = 454 Number in coding regions = 337 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 8 TCCAGAGAATATTCACTCACTTTATTTGCATAT 1 271 0 ATTCCCCTTT 0.947358 -30 GAAATTCCCCCTTTTTGCTGTTTGAA 2 285 0 ATTCCCTTTT 0.938392 -16 ACGAGGGCGCATTCGCGCCCTTTATTTTTCGTG 5 13 1 ATTCCCCTTT 0.947358 -93 CCAGACGTTGCATCGCGCTCTTTAATACACCGC 8 50 1 CATCCCCTTT 0.93719 -101 ATCAAGTTTTCTCCTTTTTTATTACCACAC 9 8 1 TTTCCTTTTT 0.505537 -293 CAAAAAGTGATATTACGCATTTTTACACACTGT 9 40 1 TATTCCTTTT 0.531004 -261 TTTTTCACTTCATCACATTCTTTCTGAAAAACA 18 69 0 CATCCTCTTT 0.773868 -232 TTTTCAAACCATCTCTCATTTTTAGGATATTT 30 16 0 CATCCCTTTT 0.926628 -22 TTGGGCGAGTAATCGCCCCTTTTTCTTTTTAAG 32 15 1 AATCCCTTTT 0.944034 -45 ACAGACGTAAAATTACACACTTTCATAAACTCG 40 76 0 AATTCCCTTT 0.820493 -225 ATTAATATACATTCTCGTCTTTTTATCCTTTCT 41 159 1 ATTCCTTTTT 0.777454 -39 TTATAATTCTCATCGCTTATTTTTAACTATTTA 42 149 1 CATCCTTTTT 0.743361 -39 TTTATCTAACTATCCCCCTCTTTACAAAAGAGG 43 11 1 TATCCCCTTT 0.853641 -85 TTTACCTGCAATTCCCCCTCTTTTGTAAAGAGG 43 27 0 ATTCCCCTTT 0.947358 -69 TACCTTTCAAATTTTCTCGCTTTTAAAGCGAAA 49 16 1 ATTTCCCTTT 0.804972 -192 CAGCCGTTTACTTTACTCTTTTTCGGCTTTAAT 55 68 0 CTTTCCTTTT 0.723419 -61 AATTTCCGCCTTTTATTCGGTTAA 55 115 0 ATTTCCTTTT 0.777454 -14 GCATAACCAAAATCGCTCATTTTGTTCTCCTCA 56 120 1 AATCCCTTTT 0.944034 -155 AATACGAAAAAATCACTTCTTTTTATAAAAAAT 56 184 1 AATCCTTTTT 0.794606 -91 **** * * **** Masking position 3 Map Score: 16.3755 Number of sites scoring better than the average of aligned sites = 394 Number in coding regions = 329 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 9 GGGAAATATATTTTTTATATGAATGAGTGCAAA 2 195 0 TTTTTTATAA 0.354597 -106 AACGTTTTCCTTTGCACGAAAAATAAAGGGCGC 5 27 0 TTTGCAAAAA 0.802105 -79 ATAGCAAGCATTTTTTGCAAAAAGGGGTAGATG 17 73 1 TTTTTTAAAA 0.54824 -89 TCTTTGGTGTTTTTCAGAAAGAATGTGATGAAG 18 62 1 TTTTCAAAAA 0.879526 -239 ATTTTTGCATTTTTTAACCATAAGCTAATGTGA 24 119 1 TTTTTACAAA 0.821389 -182 TACAGCACTTTTTGCACTCAAAAATGACCTCGA 27 27 0 TTTGCACAAA 0.69154 -77 TAAAATTTCGTTTTCAAAATAAAGTGAAATCTG 28 54 1 TTTTCAATAA 0.71724 -76 ATACTCCCTATTTTCAAAAAAAAGATTTTGTAA 40 246 0 TTTTCAAAAA 0.853445 -55 TTAATAACATTTTTCAGTCTTAAACTGAGGCGT 41 61 0 TTTTCACTAA 0.584407 -137 AACTCACGGATTTTCATTAATAACATTTTTCAG 41 77 0 TTTTCAAAAA 0.877709 -121 TTTAATTAAATTTTTATCCATAAACAGTTAAAC 44 68 1 TTTTTACAAA 0.821389 -56 AATTAAACTATTTTTACTAAAAATAGACTTAAA 45 152 1 TTTTTAAAAA 0.49424 -63 AACTAGCCGTTTTTTATACATAATTAAAATGTA 47 41 1 TTTTTACAAA 0.820969 -189 CTTGAGCTTATTTGTACTATTAAAGTAGTACAA 48 25 1 TTTGTAATAA 0.614682 -155 TTTAATGACATTTTTAAAATTAAAATGAAATTG 48 76 0 TTTTTAATAA 0.74221 -104 TTCAAAAAAATTTGTAAGAAAAAAGGTTTATCT 49 111 0 TTTGTAAAAA 0.818972 -97 TTCTTACAAATTTTTTTGAAAAATTTTAACTAT 49 124 1 TTTTTTAAAA 0.54824 -84 CGCACTTTGTAGAAACAAAACTGCGGTG 56 6 1 TTTGTAAAAA 0.82103 -269 AAATCACTTCTTTTTATAAAAAATTTGCAATAA 56 193 1 TTTTTAAAAA 0.567946 -82 CGTTTGCTATTTTTTAAAAAGAAATAAAAATCC 57 81 0 TTTTTAAAAA 0.872062 -44 ****** ** ** Masking position 3 Map Score: 13.5236 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 94 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 10 ACCATTTGGTCCACTTTTTTCTGCTCGTTTTT 1 22 1 CACTTTTTCT 0.783758 -279 ATTTTTCCCCCACCTTTTTGCACTCATTCATA 2 179 1 CCCTTTTTCA 0.980505 -122 GAAATTCCCCCTTTTTGCTGTTTGAAACC 2 282 0 CCCTTTTTCT 0.984629 -19 GTGACAACGTCACCTTGTTCCAGACGTTGCAT 8 31 1 CCCTTGTTCA 0.926246 -120 ATCAAGTTTTCTCCTTTTTTATTACCACACAA 9 11 1 CCCTTTTTAT 0.881513 -290 AGTGATATTACGCATTTTTACACACTGTGATG 9 45 1 CCATTTTTCA 0.726662 -256 ACGTCTTTTTCCTCGTTAAGCCA 12 24 0 CTCTTTTTCT 0.783758 -13 GAATCATCCGGCCCTTTTTTCTGATATGATAC 14 24 1 GCCTTTTTCT 0.852488 -189 CGGATTATACCTCCTTTCTTCAAGGCGGCAAT 15 23 1 CCCTTTCTCA 0.864468 -275 TGCTTTACACAACCTTTTTGCACGTCTTTTCC 15 194 0 ACCTTTTTCA 0.843717 -104 ATTGCATCTACCCCTTTTTGCAAAAAATGCTT 17 78 0 CCCTTTTTCA 0.980505 -84 CGAGTAATCGCCCCTTTTTCTTTTTAAGTTCT 32 20 1 CCCTTTTTTT 0.881513 -40 AATACCCCCTTGTTGATGAAGAGCAAG 33 61 0 CCCTTGTTAT 0.650067 -17 CTAAAAGCTCCTTTTTGTTATCGAAACGT 35 149 0 CCCTTTTTTT 0.881513 -19 TCTAACTATCCCCCTCTTTACAAAAGAGGGGG 43 15 1 CCCTCTTTCA 0.864468 -81 GTCGAAGATAAACCTTTTTTCTTACAAATTTT 49 106 1 ACCTTTTTCT 0.873028 -102 * ******* ** Masking position 5 Map Score: 10.4473 Number of sites scoring better than the average of aligned sites = 329 Number in coding regions = 264 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 11 CAACTTAATGGCGGGATTTTTTATATTATT 1 149 0 GCGGGATTTT 0.755749 -152 CTGGCAAACGGCGGCATTCTGGAGATATGG 1 190 0 GCGGCATTCT 0.971703 -111 CAAAAAATCCGCCGCATTCTATTCATCTGA 2 252 0 GCCGCATTCT 0.962899 -49 ATTATGAATTGCCGCATTATAGCCTAATAA 7 169 0 GCCGCATTAT 0.942405 -33 TATTTTTTCAGCGCCATTTTTATTGATGCG 13 151 1 GCGCCATTTT 0.755749 -108 TCCTGTTCGGGGCGCATTCTAACAGAAAAA 13 211 0 GGCGCATTCT 0.700735 -48 TTTCTTCAAGGCGGCAATATTCTTTTCGTT 15 37 1 GCGGCAATAT 0.697325 -261 TTAGAATTGCGCCGAATTTTATTTTTCTAC 15 251 1 GCCGAATTTT 0.612079 -47 AAATATTGCCGCGGCATTATACAGAGCGTA 17 114 0 GCGGCATTAT 0.955849 -48 TATCTGTTCATCGGCATTCTGG 21 3 0 TCGGCATTCT 0.693418 -298 TCATAAATGAGCGGCATTTTGCGTAAACCT 21 119 1 GCGGCATTTT 0.969415 -182 GGGGAAACGGGCGTCATTATAAAGAATCTG 21 243 0 GCGTCATTAT 0.58779 -58 TAATTTTTTCGCCGCACTTTTGAGCTTCTC 31 29 1 GCCGCACTTT 0.790722 -70 GTAAGTTTTTACCGCATTTTTGATTTATCC 34 26 1 ACCGCATTTT 0.612079 -57 ********** Masking position 6 Map Score: 8.72729 Number of sites scoring better than the average of aligned sites = 425 Number in coding regions = 386 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 GAATGCCGCCGTTTGCCAGAAATTCGTCGG 1 201 1 GTTTGCCAGA 0.692184 -100 GACCTGAACCGTAGGTCGGATAAGGCGCTC 2 66 1 GTAGGTCGGA 0.925454 -235 AAAACAGTGGGTAGGCCTGATAAGACGCGT 2 139 0 GTAGGCCTGA 0.914639 -162 GAAGGGATGTTTTTGCCGGACACAAAGGAT 5 67 0 TTTTGCCGGA 0.883983 -39 AAGTGTTGCGGTACGCCGGAAAAACGACAC 9 199 0 GTACGCCGGA 0.823733 -102 CTACCCCTGCGTAGGCCTGATAAGACGCGC 13 36 0 GTAGGCCTGA 0.914639 -223 GGGTAGAACCGTAGGTCGGATAAGGCGTTT 13 60 1 GTAGGTCGGA 0.925454 -199 CACGAAATTTGTTTGTCGGACGTAGTTCGG 14 102 1 GTTTGTCGGA 0.926189 -111 TTTGTCGGACGTAGTTCGGATAAGGCGTTC 14 113 1 GTAGTTCGGA 0.536418 -100 GTGCCGGATGTTTTGTCGGATGCGGCGTGA 14 141 0 TTTTGTCGGA 0.770121 -72 TTGCTGTCTGGTGTGCCGGATGTTTTGTCG 14 153 0 GTGTGCCGGA 0.856152 -60 AATCGTTCTCTTTTGCCTGAACTTACCACC 24 187 0 TTTTGCCTGA 0.74305 -114 TGAATGTAAATTTGGTCGGAGAATTTTTTA 35 30 1 TTTGGTCGGA 0.808477 -138 TAACGGAAACGTTTTCCTGATATTTACTA 38 110 1 GTTTTCCTGA 0.50238 -19 GTGGGCTTTTTTATGCCTGAAATTTATCGT 42 58 1 TTATGCCTGA 0.69424 -130 TAAAGGTAAGGTTGGTCGTATTCTACGAGG 47 150 0 GTTGGTCGTA 0.439498 -80 TTTAGCAAACGTTTGCCTGATATATGTAAG 53 93 1 GTTTGCCTGA 0.91548 -68 ********** Masking position 2 Map Score: 12.9601 Number of sites scoring better than the average of aligned sites = 1291 Number in coding regions = 790 Number in noncoding regions = 501 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 13 AAGATTGCATGAAATAAAAACGAGCAGAAA 1 39 0 GAAATAAAAA 0.735367 -262 CGGAAAGAGAGCAAGGAAAACGGTTGCGTG 3 40 0 GCAAGGAAAA 0.751455 -78 TTTTTGTGTGGTAATAAAAAAGGAGAAAAC 9 16 0 GTAATAAAAA 0.792766 -285 TTTACACACTGTGATGAAAAAATCTCCCGT 9 61 1 GTGATGAAAA 0.78215 -240 GAGGATCAGGGTGAGGAAAATTTATGCCTC 22 35 1 GTGAGGAAAA 0.851774 -84 CGCCCGCATTGTAACGAAAACGTTTGCGCA 26 187 0 GTAACGAAAA 0.686358 -114 CCATTGTGTAGAAAGAAAAAATATAACAAT 36 65 1 GAAAGAAAAA 0.816434 -33 ACTATTTAATGAAAGGAAAATACA 42 174 1 GAAAGGAAAA 0.89211 -14 TTTCATTTAAGTGATGAAAATTTAGGAATG 44 34 1 GTGATGAAAA 0.78215 -90 AAATTCATCGGTAAGGAAAAAATACAAACT 45 104 1 GTAAGGAAAA 0.919245 -111 TCGATCAATTGAAATAAAAATTGGGCAGAT 48 152 0 GAAATAAAAA 0.735367 -28 AAAAAAATTTGTAAGAAAAAAGGTTTATCT 49 111 0 GTAAGAAAAA 0.859607 -97 TTTTTAAAAAGAAATAAAAATCCTCTGAAA 57 74 0 GAAATAAAAA 0.735367 -51 ********** Masking position 4 Map Score: 6.04435 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 107 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 14 AAATTCCCCCTTTTTGCTGTTTGAAACCCA 2 280 0 TTTTTGCTGT 0.780146 -21 CGTAATATCACTTTTTGTGTGGTAATAAAA 9 27 0 CTTTTTGTGT 0.712981 -274 TACCGCAACACTTTTGTTGTGCGTAAGGTG 9 216 1 CTTTTGTTGT 0.902817 -85 CAAACGTTTTCTTTTTCTGTTAGAATGCGC 13 200 1 CTTTTTCTGT 0.875331 -59 GTTTTAAAATCTTTTGCTGTCTGGTGTGCC 14 166 0 CTTTTGCTGT 0.975971 -47 GTCTTCTAAGCTTTCGGTGTACCCAAGGGG 21 272 0 CTTTCGGTGT 0.770505 -29 ATAAAGCGGGCTTTTGCTGGGGAATGCAGC 26 45 0 CTTTTGCTGG 0.945841 -256 TTTAGCCTGCCTTTTGCTGTTTAAAGTGCG 29 25 1 CTTTTGCTGT 0.975971 -85 ATTGGGTTATCTTTGGCTGGCTGTTCATAA 40 139 1 CTTTGGCTGG 0.803164 -162 TTTAACCGCACTTTTGTTGTGATGTTTAAG 51 38 1 CTTTTGTTGT 0.902817 -28 ********** Masking position 4 Map Score: 5.91515 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 139 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 15 AAATAATATAAAAAATCCCGCCATTAAGTTGACT 1 148 1 AAAAATCCAT 0.522284 -153 ATCATTAACAAAAAATTGCTCTAAAGCATCCGTA 7 81 0 AAAAATCTAA 0.814074 -121 GCGCATCAATAAAAATGGCGCTGAAAAAATATTC 13 148 0 AAAAATCTGA 0.681723 -111 TATAAAGGCCAAAAATTTTATTGTTAGCTGAGTC 18 266 1 AAAAATTTGT 0.359125 -35 TAAAAAACCAAAAAATACACCAGTTTCTATACAA 24 75 0 AAAAATCAGT 0.648204 -226 GTTTTTCGCGAAAAATTCAGCTAACGCTCTCTGT 26 252 1 AAAAATCTAA 0.814074 -49 TGGATAAATCAAAAATGCGGTAAAAACTTACCGC 34 23 0 AAAAATTAAA 0.699523 -60 TGTAGAAAGAAAAAATATAACAATACAGGATAAA 36 71 1 AAAAATCAAT 0.790204 -27 ATTATCAAACAAAAATACTTCAATTGGGTTATCT 40 117 1 AAAAATCAAT 0.790204 -184 ACAACCGCTAAAAAATCAATCAATTACTTTATCT 40 191 0 AAAAATCAAT 0.790204 -110 TTTAAGACTGAAAAATGTTATTAATGAAAATCCG 41 70 1 AAAAATTTAA 0.637772 -128 AAAGTGCGGTAAAAATACGATAAATTTCAGGCAT 42 70 0 AAAAATTAAA 0.699523 -118 GTTTATGGATAAAAATTTAATTAAAATTTCATTC 44 59 0 AAAAATTTAA 0.637772 -65 AGATGGTTTGAAAAATCAGACATAGAATACACCT 45 55 1 AAAAATCATA 0.304654 -160 TAATTTTTCAAAAAATACGATAAAGTTTGTATTT 45 123 0 AAAAATTAAA 0.699523 -92 GTATTTTTTGAAAAATTAAACTATTTTTACTAAA 45 139 1 AAAAATCTAT 0.740166 -76 TATTTTTACTAAAAATAGACTTAAAATAGCGTAT 45 160 1 AAAAATTTAA 0.637772 -55 GCTATTCTACAAAAATAAAGCCAAAAAGAAAACG 46 21 0 AAAAATCCAA 0.626929 -66 TAAAAAATCTCTCAATGAAAAACGGC 46 71 0 AAAAATCAAT 0.790204 -16 TTTTAATTTTAAAAATGTCATTAAATGAATTAAT 48 84 1 AAAAATTTAA 0.637772 -96 CAATTGAAATAAAAATTGGGCAGATTATATCATC 48 143 0 AAAAATCAGA 0.739047 -37 AACTATCAACAAAAATCGGGTAATATGCGCACGA 49 151 1 AAAAATTAAT 0.602324 -57 TCTCCTCATAAAAAATAACGCAGACATTCTAGCA 56 145 1 AAAAATCAGA 0.739047 -130 ****** **** Masking position 6 Map Score: 16.4539 Number of sites scoring better than the average of aligned sites = 204 Number in coding regions = 127 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011