AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -igalR_ecoli_bsub_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 galE 260 UDP-galactose-4-epimerase #2 modF 67 ATP-binding component of molybdate transport system #3 modE 128 molybdate uptake regulatory protein #4 mglA 60 ATP-binding component of methyl-galactoside transport and galactose taxis #5 mglB 279 galactose-binding transport protein; receptor for galactose taxis #6 galS 141 mgl repressor, galactose operon inducer #7 folE 257 GTP cyclohydrolase I #8 galR 300 repressor of galETK operon #9 galP 300 galactose-proton symport of transport system #10 ydjK 300 similar to sugar transporter #11 glvA 300 6-phospho-alpha-glucosidase #12 yfiA 64 similar to hypothetical proteins #13 yfiB 105 similar to ABC transporter (ATP-binding protein) #14 yfiD 154 similar to hypothetical proteins #15 yfiF 93 similar to transcriptional regulator (AraC/XylS family) #16 yfiG 174 similar to metabolite transport protein #17 yhjM 103 similar to transcriptional regulator (LacI family) #18 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #19 yjlC 300 yjlC #20 yjlD 39 similar to NADH dehydrogenase #21 yjmA 197 similar to glucuronate isomerase #22 yjmB 67 similar to Na+:galactoside symporter #23 yjmC 104 similar to malate dehydrogenase #24 yjmE 24 similar to D-mannonate hydrolase #25 yjmG 47 similar to hexuronate transporter #26 yjmH 87 similar to transcriptional regulator (LacI family) #27 ccpA 274 transcriptional regulator (Lacl family) #28 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #29 ytxJ 23 alternate gene name: csb40; similar to general stress protein #30 ytxH 27 alternate gene name: csb40; similar to general stress protein #31 ytxG 161 alternate gene name: csb40; similar to general stress protein #32 murC 249 UDP-N-acetyl muramate-alanine ligase #33 ytpS 159 ytpS #34 ytpP 234 similar to thioredoxin H1 #35 yufN 300 similar to ABC transporter (lipoprotein) #36 yufO 75 similar to ABC transporter (ATP-binding protein) #37 araE 137 permease #38 ywtG 300 similar to metabolite transport protein #39 rbsR 300 transcriptional regulator (LacI family) #40 galK 80 galactokinase #41 ywcC 300 alternate gene name: ipa-33d #42 galE 114 UDP-glucose 4-epimerase #43 yxkA 129 similar to hypothetical proteins #44 iolR 300 transcriptional regulator (DeoR family) #45 iolS 53 alternate gene name: yxbF; myo-inositol catabolism #46 yxcE 261 yxcE #47 yxcC 238 similar to metabolite transport protein Motif number 1 AATAAATTAGTGGAATCGTTTACACAAGAATTTA 1 168 0 TGAACGTACA 0.555451 -93 TAAGATACTGTGAAATCACTCACAGATTGAAAGC 5 13 0 TGAACATACA 0.86948 -267 GTCACAGCAATGGAAACGGTTACAGCCGTTTTGT 6 32 0 TGAACGTACA 0.555451 -110 TACCTTAGTGGGTAAACGCTTACATTCTTTCAGT 8 272 0 GGAACGTACA 0.559655 -29 TCATCACAACTGAAACCGATTACACCAACCACAA 9 22 1 TGAACGTACA 0.502653 -279 TAAATGTTAGTGTAAGCGATTACACTGATGTGAT 9 204 1 TGAACGTACA 0.499969 -97 TCAATCCCTATGGAAGCGATTTCATTTCTCGTTA 10 129 0 TGAACGTTCA 0.551517 -172 TAAATGGAATTGTAAACGTTATCAAGGAGGTCGT 11 274 1 TGAACGTTCA 0.505274 -27 TAATCTTTTTAGAAAGCGGTTACAACAAGGGGTA 16 75 1 AGAACGTACA 0.632436 -100 TCCTAGTTTCTGAAATCGGTAACATGTCAACAAC 17 60 1 TGAACGTACA 0.521734 -44 GAAAATGAAATGTTAACGCTGTCATAAACATAAA 21 76 0 TGTACGTTCA 0.532303 -122 CAAATCAAAATGTTAACGTTAACATTTTGAAATA 21 154 1 TGTACGTACA 0.499176 -44 GTCTTACTTCAGAAAACGATGTCACGGTTTTCCG 35 44 1 AGAACGTTCA 0.890129 -257 AATCTATCTATGTAAACGGTTACATAAACAAGGA 39 268 1 TGAACGTACA 0.499969 -33 ** ** ** * *** Masking position 5 Map Score: 30.823 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 19 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 2 CCTTGTTGTGTTGTTTGCAATTTCTTCATCATACCGTTTATTC 7 19 1 TTTTTTTTTA 0.910887 -239 ATTTGTAATATTTTCATATTATTATTCGGTTTTCACAGTTGTT 9 65 1 TTTCATTTTT 0.71371 -236 GAGATTTGGTTTTTTTACCTTTTTTGTAATCTTAAAGTCTCAC 11 122 0 TTTTTTTTTT 0.94016 -179 GATCCCCCCATTTTCTTTCTATTATATACAATTACAGATTCGA 12 28 0 TTTCATTTTT 0.71371 -37 AGGTCTTTTTTTGTTACAGTTTTATAGTACTTTTATTTCATTT 14 28 1 TTTTTTTTTT 0.94016 -127 ATCTAAAAATTTATTACAAATTTATCCTAGTTTCTGAAATCGG 17 36 1 TTTTTTTTTT 0.94016 -68 TGATTTGTTTTTATTTTACCTTTATATTCCTTTGGGATCAATC 21 118 0 TTTTTTTTTT 0.94016 -80 CAAACACATTTTATTTACAAATTATTTTAAATATTCTTTATAT 23 18 0 TTTTATTTTA 0.82082 -87 CGTGCGGCCTTTTTTTATGCTTTCTCGTTTATTTAGTTATAAA 27 32 1 TTTTTTTTTT 0.94016 -243 ATTTAATTACTTCTCATGAAATTATACACGTTTTTATAGATGA 27 94 0 TTTCATTTTT 0.71371 -181 TAAAGTAGAGTTTTTATAAAATTTTTTGTATTTCAGTATTTCC 28 128 1 TTTTATTTTT 0.875648 -108 ATGGGAAAGCTTATTAAAGGATTTTCTTACATAACGGAGAATA 31 47 1 TTTTATTTTA 0.820829 -115 GTTGTTTATGTTCTTACATGTTTTTTATCGATACTCGTCCATT 34 188 0 TTTTTTTTTA 0.910887 -47 GGTCGAGCCCTTATCCCTTGTTTTTCTTTTATTTTGAAATAAA 36 29 1 TTTCTTTTTT 0.847614 -47 GCAAACAAGATTATTCTATATTTGTACGTACTAATTAAATGTA 37 22 1 TTTTTTTTTA 0.910887 -116 TGGGATGATAGTCTTTTCTGTTTCTCCCCATTTACAGGTCTAA 39 48 1 GTTTTTTTTT 0.724851 -253 ACAATTAGATTTCTTTTGATATTTTTATTGCTAACTTCGGATT 39 216 1 TTTTATTTTA 0.820829 -85 CACCTTTCTGGTTTTTATTTTTTATTCCCCTTATTTCTTCATA 40 41 0 GTTTTTTTTA 0.631529 -40 GTTTAATCGTTTATTAATAGTTTTTTCATATTTTTTAGC 42 7 0 TTTTTTTTTT 0.94016 -108 AACAGGTTACTTTTTGGTCATTTCTTGGTTATATTCTAATCGC 44 61 1 TTTTTTTTTA 0.910887 -240 AACACTACATTTTTTCATTATTTTTATTATATTAATCTTTTAA 44 127 1 TTTTTTTTTT 0.94016 -174 CTTTTGGTTTTTATTATATATTTATGTTACGTAAAGATTCAAG 44 254 1 TTTTTTTTTA 0.910887 -47 TCTATTAACTTTGTTACATATTTTTAGATACTTCATTGGCTCA 47 185 1 TTTTTTTTTT 0.94016 -54 ** ** *** * ** Masking position 12 Map Score: 27.6734 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 56 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 3 TCACATTCCCACGATGAAAACACGCCACCCC 8 215 1 AGATGAAAAC 0.767296 -86 ATCTTAATTCACAATAAAAAATAACCATATT 9 270 1 AAATAAAAAA 0.875306 -31 ATTGGATAAAAACATGAACAACTATTTTCTG 10 194 1 ACATGAACAA 0.804168 -107 AAGGCGGACAAAAATAAAAAATCCCCCTGCC 15 35 0 AAATAAAAAA 0.875306 -59 CCATTTCCTTATAATAAAAAGGGATAGAAAC 18 59 1 AAATAAAAAG 0.636731 -65 TTTTTATCTAAAAATAAACAATTGAATAAGT 19 110 0 AAATAAACAA 0.826306 -191 TGAATATGGCAAGATGAAAAACTGGGTAGTA 19 147 1 AGATGAAAAA 0.779302 -154 CGCTGTCATAAACATAAAAAAAGACATTGCC 21 63 0 ACATAAAAAA 0.860858 -135 ATATAAAGGTAAAATAAAAACAAATCAAAAT 21 134 1 AAATAAAAAC 0.867636 -64 TAAACGAGAAAGCATAAAAAAAGGCCGCACG 27 32 0 ACATAAAAAA 0.860858 -243 GTTTTTATAGATGATGAAAACGTATACTTGG 27 77 0 AGATGAAAAC 0.767296 -198 AATTTGATGAATAATGAAAAATAATGTACAC 27 134 1 AAATGAAAAA 0.873013 -141 CCTTATCTATAGCATAAACACTTTATGTAGA 27 221 0 ACATAAACAC 0.796554 -54 TGATAACTACAAAATAAAAAATGAATGTGCA 28 198 1 AAATAAAAAA 0.875306 -38 GTGCAGGGAAAGGATGAAAAAA 28 224 1 AGATGAAAAA 0.779302 -12 AACATGTAAGAACATAAACAACTGGAGGGAT 34 209 1 ACATAAACAA 0.807429 -26 TATGATCAGAAAAATAAAAAGGTTTAATGGC 38 200 1 AAATAAAAAG 0.636731 -101 TAGATAGATTATCATGAACAATCCGAAGTTA 39 247 0 ACATGAACAA 0.804168 -54 AGGGGAATAAAAAATAAAAACCAGAAAGGTG 40 53 1 AAATAAAAAC 0.867636 -28 CTTATTTATAATAATAAACAATTAAATACTG 41 131 1 AAATAAACAA 0.826306 -170 TAAACACTATATAATGAAAACAGGTCATTTT 42 77 1 AAATGAAAAC 0.865224 -38 CCATAAGTCAATCATAAACACTACATTTTTT 44 111 1 ACATAAACAC 0.796554 -190 TATAATAAAAATAATGAAAAAATGTAGTGTT 44 127 0 AAATGAAAAA 0.873013 -174 ACATAAATATATAATAAAAACCAAAAGTTAA 44 250 0 AAATAAAAAC 0.867636 -51 * ********* Masking position 5 Map Score: 23.699 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 188 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 4 GAGAGGGTGCTAAGGCCGCCTCCGGCAAGG 1 25 0 TAAGGCCGCC 0.661658 -236 TAAGCACAGAAAAGCACTCCCCTTTTGTGC 3 50 1 AAAGCACTCC 0.810942 -79 GTGCTGACAAAATAGCCGCCAGCAAGCAGT 6 90 1 AATAGCCGCC 0.634309 -52 ACCTGAAGCCAAACGCCACCAGCGGTCAAT 8 113 1 AAACGCCACC 0.752691 -188 TCCCACGATGAAAACACGCCACCCCTTGAA 8 221 1 AAAACACGCC 0.829975 -80 ACGGCAAACGAAAACCCTCCCGAAAAGGAG 13 19 0 AAAACCCTCC 0.968692 -87 TTGCCGTCAAAAAGACCGCCATAGTAAAGT 13 42 1 AAAGACCGCC 0.825376 -64 GTAAAAGCCTCCAAACCCCTTT 13 94 0 AAAAGCCTCC 0.972409 -12 GTAAACGCCTCCTAACAAGTTG 15 82 0 AAACGCCTCC 0.941924 -12 TAGCAAACACAAAAAACTCCAATTCGATTA 19 55 0 AAAAAACTCC 0.722777 -246 GAACAATCCAAAAGGCCGCCGTGCGGCCTT 27 13 1 AAAGGCCGCC 0.93612 -262 CCTAAAACCACTCCTTTTACTGGA 27 261 0 AAACCACTCC 0.76557 -14 AAAAAAGCGTCCAGATATCATC 28 3 1 AAAAGCGTCC 0.817854 -233 GCGGCGGCTGAAAAGCCTCCCTTAGCGGCG 32 166 0 AAAAGCCTCC 0.972409 -84 TGGTATACTAAAAACCGTCCCAGAAAACTA 33 119 1 AAAACCGTCC 0.797646 -41 AATAAAAATCCCTCCTTATGTATAT 34 6 1 AAATCCCTCC 0.781839 -229 AAACTGAAGGAAAAACCACCTACCTATTCC 41 71 1 AAAAACCACC 0.680835 -230 GATGTAAACCCTCCTAAAAAATGA 42 101 0 TAAACCCTCC 0.805031 -14 ATAAAAAACTCCTTCTTGAATC 44 289 0 AAAAAACTCC 0.722777 -12 ********** Masking position 2 Map Score: 16.902 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 366 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 AATCGCGCATAAAAAACGGCTAAATTCTTG 1 148 1 AAAAAACGGC 0.977041 -113 GTAACGCTCCAGAAAACGGCTTTAATTGTT 5 138 0 AGAAAACGGC 0.977459 -142 ACATTCGTTAACAAAACGGCTGTAACCGTT 6 22 1 ACAAAACGGC 0.908616 -120 TCTTAATTGCAGATAACAGCGTTTAATCTA 9 127 1 AGATAACAGC 0.742384 -174 CCCCTTGCCGAAATAACGGCAGGGGGATTT 15 18 1 AAATAACGGC 0.888712 -76 CCCTTTCCAAAAAAATCAGCAAACTGCTTA 19 262 1 AAAAATCAGC 0.738768 -39 GAGAAAGCATAAAAAAAGGCCGCACGGCGG 27 28 0 AAAAAAAGGC 0.831724 -247 GGTTTTTTACAAAAAAAAGCGCCAGATGAT 28 27 0 AAAAAAAAGC 0.636412 -209 TTATGATTGAAGAAAACGGGTAAACAGCAG 31 116 1 AGAAAACGGG 0.821797 -46 TGAATAAACGAAAAATCGGATTGGCG 35 285 1 AAAAATCGGA 0.502582 -16 ATTTCTTCATAGAAAACGGCAGATCATATG 40 22 0 AGAAAACGGC 0.977459 -59 GAAGAAAACAGCCTTCTCCAAT 46 3 1 AGAAAACAGC 0.938864 -259 TTATCGCACAAAAAAACAGCCTTCTCCATT 46 30 0 AAAAAACAGC 0.937774 -232 ATTTGTTTTGAAAAAACGGAAACTTTATAG 47 125 0 AAAAAACGGA 0.843366 -114 ********** Masking position 5 Map Score: 12.3135 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 428 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 TGTGACGCCTCCGCCCTGCGTGGGGGCAAA 7 219 0 CCGCCCTGCG 0.93968 -39 ACCTCATAACCTTCCCTTCTTCTTAGCATG 10 163 0 CTTCCCTTCT 0.446089 -138 TCCAGGGCTGCTGCCTTCCTCACATTTCGT 10 235 0 CTGCCTTCCT 0.780336 -66 ATGACGACCTCCTTGATAACGTTTACA 11 284 0 CCTCCTTGAT 0.867998 -17 AGACTGCCCTCCTTTTCGGGAGG 13 4 1 CTGCCCTCCT 0.682262 -102 TTTATCCTCCTTGATAAATGTTATC 14 140 0 CCTCCTTGAT 0.867998 -15 TTATTTTTGTCCGCCTTGTTATGATGAGAG 15 49 1 CCGCCTTGTT 0.851765 -45 CCAATGCATCCCTCCTTCAGCAATACCCCT 16 102 0 CCTCCTTCAG 0.834852 -73 TTGAATCATCCTCCTTTTTAAGTCGGATT 18 105 0 CCTCCTTTTT 0.649783 -19 CGTATATCCTCCGTCCTTTATATCAAT 20 23 0 CCTCCGTCCT 0.873404 -17 GCAAGTGCCTCCTTCCTTTTCAGTTTT 23 88 0 CCTCCTTCCT 0.956213 -17 ATCCAAAAGGCCGCCGTGCGGCCTTTTTTT 27 18 1 CCGCCGTGCG 0.890619 -257 CTCAAACCTCCTTGCTGCAGGATATA 31 146 0 CCTCCTTGCT 0.962072 -16 GGCTGAAAAGCCTCCCTTAGCGGCGTATTT 32 161 0 CCTCCCTTAG 0.565971 -89 TCCGCCCGGAACGCCTTCCGCATCCTTCTC 35 74 1 ACGCCTTCCG 0.523893 -227 CTTCTCTTCCCCGCCTTTCGAAGGAAATAC 35 98 1 CCGCCTTTCG 0.904479 -203 AACAGCTCCTCCTTGTTTATGTAACCG 39 284 0 CCTCCTTGTT 0.83471 -17 ********** Masking position 7 Map Score: 11.8462 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 589 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 7 GCACAGAAAAGCACTCCCCTTTTGTGCGGTCAG 3 53 1 GCACTCCTTT 0.917097 -76 TGCAATCATAGCTATCACATTGTTAAGATACTG 5 37 0 GCTATCCTTT 0.951447 -243 GTCATTTACTGCAATCTCATAACAGGTAGTGAA 6 118 1 GCAATCCTAC 0.61307 -24 CCAAAGGTTTGCAATCTCTTTTTTTGTCTTACT 8 168 1 GCAATCCTTT 0.974431 -133 TACGGGACGAGCTATCTCATGGTATAAATGGAA 11 250 1 GCTATCCTGT 0.741151 -51 CTGCAATCCCCTTGCCGAAATAACG 15 3 1 GCAATCCTTC 0.940564 -91 AAAGACGCGAGAAATCTCGTTGTCTTATAATCT 16 48 1 GAAATCCTTT 0.683174 -127 GGTGTCGGGTGCTCTGCCATTCTTGAAAGAAGG 16 141 1 GCTCTGCTTT 0.598549 -34 AAGTATCGTTTCTATCCCTTTTTATTATAAGGA 18 64 0 TCTATCCTTT 0.765625 -60 GTGCTTTCTGGCAATGTCTTTTTTTATGTTTAT 21 54 1 GCAATGCTTT 0.908801 -144 TCCTTTGGGATCAATCTCTTTTTTGAAAATGAA 21 101 0 TCAATCCTTT 0.863809 -97 TGTAAGATTGGCTTTCCCATTATCATTATCATA 34 102 0 GCTTTCCTTT 0.676252 -133 TCCATCAGCTGCAATGACATTGTCTGTGGGATT 38 261 0 GCAATGCTTT 0.85638 -40 GTGCAATCACCTTTCTGGTTTTTAT 40 66 0 GCAATCCTTC 0.94151 -15 TTTTGCTTTCTCAATCACTTTCTTTCTGAGATA 46 131 0 TCAATCCTTT 0.863809 -131 ****** * ** * Masking position 5 Map Score: 11.061 Number of sites scoring better than the average of aligned sites = 298 Number in coding regions = 263 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 8 TTTTTATCTGAAAAAAGACGCGGTTTCATG 1 80 0 AAAAAAGACG 0.748882 -181 GCTTATGGTATGAAATAACCATAGCATAAC 1 226 0 TGAAATAACC 0.575515 -35 CCGGCAAAAAAAACCTGCGCATCTG 8 6 1 AAAAAAAACC 0.927591 -295 ATTCACAATAAAAAATAACCATATTGGAGG 9 276 1 AAAAATAACC 0.883817 -25 TTATGCACAAAGAAATGACCATTGTTCTTT 10 99 1 AGAAATGACC 0.841734 -202 ACAAAAAAGGTAAAAAAACCAAATCTCTCA 11 138 1 TAAAAAAACC 0.794168 -163 CGTTTGCCGTCAAAAAGACCGCCATAGTAA 13 39 1 CAAAAAGACC 0.672513 -67 AACTGTAACAAAAAAAGACCTCTGTGCAGG 14 19 0 AAAAAAGACC 0.938024 -136 AGAAAGCATAAAAAAAGGCCGCACGGCGGC 27 27 0 AAAAAAGGCC 0.629308 -248 TTAATCGGAAAGAAATAACCTGATACTAAA 32 115 1 AGAAATAACC 0.818231 -135 TAAATCCGCCAAAAAAAACGAATCATGTGA 33 18 1 AAAAAAAACG 0.716239 -142 AAAGATTTCTAAAAAAATCCCACAGACAAT 38 246 1 AAAAAAATCC 0.49225 -55 GGGAATAAAAAATAAAAACCAGAAAGGTGA 40 55 1 AATAAAAACC 0.630932 -26 TTAGCCTATTAAAAATGACCCCTGGGAAAC 41 193 1 AAAAATGACC 0.899877 -108 AACCCTCCTAAAAAATGACCTGTTTTCATT 42 89 0 AAAAATGACC 0.899877 -26 AATATAACCAAGAAATGACCAAAAAGTAAC 44 66 0 AGAAATGACC 0.841734 -235 ATAAATATATAATAAAAACCAAAAGTTAAT 44 249 0 AATAAAAACC 0.630932 -52 GAGAAACCATTAAAAAAACCTTACCCGCGC 47 36 0 TAAAAAAACC 0.794168 -203 ACATTTGTTTTGAAAAAACGGAAACTTTAT 47 127 0 TGAAAAAACG 0.310279 -112 ********** Masking position 5 Map Score: 11.1708 Number of sites scoring better than the average of aligned sites = 272 Number in coding regions = 180 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 9 TGCCCGGTAACGCTCCAGAAAACGGCTTTAAT 5 142 0 CTCCAGAAAA 0.733644 -138 ATCTCAAGCACTACCCTGCATAAGAAAAACCG 5 250 1 CCCCTGCATA 0.724952 -30 GCTATTTTGTCAGCACTGAATACAGGACTTCG 6 74 0 CCACTGAATA 0.768891 -68 ATGACGACCTCCTTGATAACGTTTACAAT 11 282 0 CCCTTGATAA 0.745529 -19 TTTATCCTCCTTGATAAATGTTATCAC 14 138 0 CCCTTGATAA 0.745529 -17 CACTGCTGGTCGGCCCAGAAAAGATTAAGCTA 33 89 0 CCCCAGAAAA 0.976645 -71 TACTAAAAACCGTCCCAGAAAACTATAAGGGA 33 124 1 CCCCAGAAAA 0.976645 -36 CAGTTCTATTCTTCCCTGAATAAGCGTGGTGT 35 130 0 CCCCTGAATA 0.943538 -171 CAAGATATAACCCCCCAGAAAAATTTGGTTCA 35 255 0 CCCCAGAAAA 0.976645 -46 AATGTTTCGGCGACATTGAAAAAAATACAAGT 38 152 1 CCATTGAAAA 0.740648 -149 AAAAGACTATCATCCCAGAAAATGTTTAATTA 39 33 0 CCCCAGAAAA 0.976645 -268 CCCCTTATTTCTTCATAGAAAACGGCAGATCA 40 26 0 CCATAGAAAA 0.767892 -55 GATCTGCCTCCTAGAATAAAATGGATGA 45 36 0 CCCTAGAATA 0.884964 -18 * ********* Masking position 12 Map Score: 9.00819 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 165 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 10 ACCGCGTCTTTTTTCAGATAAAAAGCGCAATCAT 1 86 1 TTTTGATAAA 0.917688 -175 TTATGCGCGATTAAGTGATTATAAAACAGAGGGT 1 126 0 TTAAGATAAA 0.753046 -135 GGTTATGAGGTTATTGGATAAAAACATGAACAAC 10 182 1 TTATGATAAA 0.895477 -119 GTTGGTGAGACTTTAAGATTACAAAAAAGGTAAA 11 118 1 CTTTGATAAA 0.669632 -183 TTGTAATAAATTTTTAGATTATAAAATCATTGGA 17 21 0 TTTTGATAAA 0.918838 -83 CAATTGTTTATTTTTAGATAAAAATAATACTGAA 19 117 1 TTTTGATAAA 0.917688 -184 ATCGATAAAATTTTCTGATAATAACAAATGGAAT 35 171 0 TTTTGATAAA 0.921842 -130 TCGAAAGACATTTTTCGATAAATATTCCTATATT 38 44 1 TTTTGATATA 0.807612 -257 ACCTTTTTATTTTTCTGATCATAAGTTTTCCAAT 38 189 0 TTTTGATAAA 0.921842 -112 CTTATGGGTATTATGCGATTAGAATATAACCAAG 44 84 0 TTATGATAAA 0.895578 -217 TCTTACTTGATTAAAAGATTAATATAATAAAAAT 44 146 0 TTAAGATATA 0.520185 -155 TGTAACAAAGTTAATAGATTAGTACCCATTTCCT 47 169 0 TTAAGATATA 0.520186 -70 **** *** * ** Masking position 8 Map Score: 4.8941 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 20 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 GTGCTAAGGCCGCCTCCGGCAAGGTCAGCA 1 19 0 CGCCTCCGGC 0.979055 -242 TTATGTGCGCCGCCTCACGCACAATAATCA 7 167 1 CGCCTCACGC 0.962032 -91 GCAGGTGTGACGCCTCCGCCCTGCGTGGGG 7 224 0 CGCCTCCGCC 0.974186 -34 TGAAGCCAAACGCCACCAGCGGTCAATCGC 8 116 1 CGCCACCAGC 0.923296 -185 GATGAAAACACGCCACCCCTTGAACCAACG 8 227 1 CGCCACCCCT 0.684743 -74 GAAAGGGTAGTGCCTCTCCCTGTCTCACGC 19 239 0 TGCCTCTCCC 0.779552 -62 TCAAACATACCGCCTCTCCCACTATATTTC 26 15 0 CGCCTCTCCC 0.953393 -73 TAAGTGGTTTTGCCTCAAGCAGTTTGGTAT 34 152 1 TGCCTCAAGC 0.63129 -83 CCGCCCGGAACGCCTTCCGCATCCTTCTCT 35 75 1 CGCCTTCCGC 0.906354 -226 TTGTTGTACTCGCCTCCATCATCGCGCTGG 41 13 0 CGCCTCCATC 0.870112 -288 ********** Masking position 4 Map Score: 5.11445 Number of sites scoring better than the average of aligned sites = 748 Number in coding regions = 713 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 12 AAGACGCGGTTTCATGCCTGCATGCGTCGAA 1 65 0 TCATGCCTGC 0.604713 -196 TTAAAATTCGTTCTTCCATGCCCGGTAACGC 5 161 0 TCTTCCATGC 0.711739 -119 TCATTAACTCTACTGCCCCGCCGAGCATTTA 5 220 1 TCTGCCCCGC 0.885945 -60 TTATCTCAAGCACTACCCTGCATAAGAAAAA 5 248 1 CCTACCCTGC 0.898968 -32 GGTGTGACGCCTCCGCCCTGCGTGGGGGCAA 7 220 0 CCCGCCCTGC 0.897377 -38 AGACTGCCCTCCTTTTCGGGAG 13 2 1 GCTGCCCTCC 0.742112 -104 CATAAGCCAATGCATCCCTCCTTCAGCAATA 16 107 0 TCATCCCTCC 0.872295 -68 TTTTTTCATCCTTTCCCTGCACATTCATTT 28 216 0 CTTTCCCTGC 0.920976 -20 CTCAAGCTCTTCCTTCCCTGC 29 1 0 TCTTCCCTGC 0.977597 -23 TTCATATCCCTCCAGTTGTTTAT 34 222 0 CTATCCCTCC 0.645927 -13 CCGCATCCTTCTCTTCCCCGCCTTTCGAAGG 35 91 1 CCTTCCCCGC 0.949494 -210 GACAGTTCTATTCTTCCCTGAATAAGCGTGG 35 133 0 TCTTCCCTGA 0.711739 -168 GCTCGACCTCCTTATCCCTGCGATTC 36 6 0 CTATCCCTGC 0.8297 -70 TTCCCTGCCCTCCCGAATGTTGA 37 125 0 CCTGCCCTCC 0.945613 -13 GAAATATCTCCTTCACTGCAAGTTATCCA 43 9 1 TCTTCACTGC 0.711739 -121 * ********* Masking position 7 Map Score: 5.71303 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 581 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 13 AAGTGCATGAAAATAATTGAGTTATATCATC 9 158 0 AAATAATGAG 0.536606 -143 AATAAATACCAAATGAACGAGGTTATGCACA 10 77 1 AAATGAAGAG 0.904022 -224 TACGAAAATGAAATAAAAGTACTATAAAACT 14 45 0 AAATAAAGTA 0.69991 -110 TATTATAAGGAAATGGAGGTACACTTTAAAA 18 44 0 AAATGGAGTA 0.665569 -80 TCATTTACAAAAATAAATGTTTACTACCCAG 19 168 0 AAATAAAGTT 0.503631 -133 TTATTTTTGTAAATGATTGTGCATGAATTCA 19 183 1 AAATGATGTG 0.589827 -118 TTTTATAACTAAATAAACGAGAAAGCATAAA 27 45 0 AAATAAAGAG 0.86966 -230 ACAAAATAAAAAATGAATGTGCAGGGAAAGG 28 206 1 AAATGAAGTG 0.892306 -30 GGTATGATCCAAATGGACGAGTATCGATAAA 34 177 1 AAATGGAGAG 0.850598 -58 CTTTATTTCAAAATAAAAGAAAAACAAGGGA 36 42 0 AAATAAAGAA 0.726132 -34 TTTTATTTTGAAATAAAGGAGCGGTCAATCA 36 55 1 AAATAAAGAG 0.86966 -21 AACTTCTTAAAAATGGATGTGGACCGGTTCT 42 47 1 AAATGGAGTG 0.833561 -68 TCCTAGAATAAAATGGATGATAGACTCTCAA 45 25 0 AAATGGAGAT 0.496021 -29 AAATCCGATAAAATAAAGGTAGTTTATCTCA 46 107 1 AAATAAAGTA 0.69991 -155 TCTGACCAGCAAATAAAAGAAGCTGGGTCAG 46 204 0 AAATAAAGAA 0.726132 -58 ******* *** Masking position 3 Map Score: 5.45097 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 115 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 14 TTGCCGGAGGCGGCCTTAGCACCCTCTCCG 1 27 1 CGGCCTTAGC 0.883442 -234 TGAATTACACCAGCCTGCGCAGATGCGCAG 8 25 0 CAGCCTGCGC 0.955766 -276 ACGCCTTCCGCATCCTTCTCTTCCCCGCCT 35 84 1 CATCCTTCTC 0.916858 -217 CAAGATTGGACGGCCTTCTCTTACTTCTCT 44 177 0 CGGCCTTCTC 0.98336 -124 GAAGAAAACAGCCTTCTCCAATGGAGAA 46 9 1 CAGCCTTCTC 0.986164 -253 CACAAAAAAACAGCCTTCTCCATTGGAGAA 46 24 0 CAGCCTTCTC 0.986164 -238 ********** Masking position 6 Map Score: 2.87162 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 47 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 CATTTTGAAAAAGACTGGGGGAAACAGT 10 283 1 AAGATGGGGG 0.757945 -18 TTACAGATTCGAAAATGGGGGAATTTCAT 12 9 0 GAAATGGGGG 0.966225 -56 ATAATAGAAAGAAAATGGGGGGATCTGAT 12 46 1 GAAATGGGGG 0.966225 -19 AGACAATCGAGTAAAAAGGGGTTTGGAGGCT 13 80 1 GTAAAAGGGG 0.762743 -26 TGCCATTCTTGAAAGAAGGGGAAGAAAGCC 16 155 1 GAAAAAGGGG 0.9472 -20 TTAAAAGCGTGAGACAGGGAGAGGCACTACC 19 233 1 GAGAAGGGAG 0.911418 -68 GCAGCTGATGGAGAAAGGGAGTCATCTTT 38 282 1 GAGAAGGGAG 0.911418 -19 TTTCTATGAAGAAATAAGGGGAATAAAAAAT 40 37 1 GAAAAAGGGG 0.9472 -44 **** ****** Masking position 4 Map Score: 1.44635 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 41 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432