AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00600_ecoli_reg_300.orf -o00600_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.51 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 caiA 30 probable carnitine operon oxidoreductase #2 caiT 300 probable carnitine transporter #3 yabB 300 orf, hypothetical protein #4 lacZ 122 beta-D-galactosidase #5 lacI 76 transcriptional repressor of the lac operon #6 mhpR 76 transcriptional regulator for mhp operon #7 ybjU 36 putative arylsulfatase #8 poxB 132 pyruvate oxidase #9 ybjW 137 putative prismane #10 ybjE 300 putative surface protein #11 gatZ 28 putative tagatose 6-phosphate kinase 1 #12 gatY 197 tagatose-bisphosphate aldolase 1 #13 BIME96 27 BIME #14 b2097 184 orf, hypothetical protein #15 lgt 150 phosphatidylglycerol-prolipoprotein diacylglyceryl transferase; a major membrane phospholipid #16 ygdP 300 putative invasion protein #17 ebgR 218 regulator of ebg operon #18 ebgA 147 evolved beta-D-galactosidase, alpha subunit; cryptic gene #19 agaZ 248 putative tagatose 6-phosphate kinase 2 #20 BIME157 76 BIME #21 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #22 yiaK 200 putative dehydrogenase #23 yiaM 117 orf, hypothetical protein #24 rfaS 36 lipopolysaccharide core biosynthesis #25 rfaQ 300 lipopolysaccharide core biosynthesis #26 trxA 76 thioredoxin 1 #27 rhoL 140 rho operon leader peptide #28 rho 84 transcription termination factor Rho; polarity suppressor #29 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #30 wecD 106 orf, hypothetical protein #31 yifM_2 241 orf, conceptual translation in SwissProt is fused with b4404 #32 aslA 300 arylsulfatase #33 melA 282 alpha-galactosidase #34 sgaT 291 orf, hypothetical protein Motif number 1 TTTGCGTTCCCGTTTGTTTTATTTTTGTTAACATT 2 244 0 CTTTTTATTT 0.799007 -57 AGCAGTAGAGTATTCGTTTTCATTTAAAGATATTC 10 219 0 TTTTTTCTTT 0.882406 -82 GCTCCTTATGCATAACATTTCCTTTTAATTGCAAC 10 251 1 CTATTTCTTT 0.865504 -50 ATCGGGAGGCCGTTTTTTTGCCTTTCACTCCTCGA 12 79 1 CTTTTGCTTT 0.905103 -119 ATCCTGTCGTTTGTTTTCGATTTCAAAATATA 12 176 0 CTTTTTCATT 0.873175 -22 GTAAAACTTTCGTTTCATTTCGTTTTGCCTATTAA 19 24 1 CTTTTTCTTT 0.986878 -225 CAGTGACTTTCATTATGTTTCTTTTGTGAATCAGA 19 119 1 CTTTTTCTTT 0.986878 -130 ATCAGAAAACCATTATCTTTCGTTTTATTTTTATC 19 153 1 CTTTTTCTTT 0.986878 -96 ATTAATCTTTCGTTTTGTTTCAGTTGATACTGCGT 19 196 0 CTTTTTCGTT 0.910748 -53 TAAGGCCTTTCTTTTTCTTTCGTTTTGATCTGTGC 20 46 1 CTTTTTCTTT 0.986878 -31 ATCCCTTTTGCTTCCTTTATCTTTTCTT 21 4 1 CTTCTTCTTT 0.916464 -188 TCACAAATTTCGTTTTATTTCTTTTTTCTCCATTG 21 46 1 CTTTTTCTTT 0.986878 -146 CTCCATTGAACTTTCAGTTTCTTTTCTATAGATTT 21 73 1 CTTTTTCTTT 0.986878 -119 CTTTCACTTGCCTTTCGTTTCATTTCACTTGGTGA 21 124 0 CTTTTTCTTT 0.986878 -68 GCTCTCCTGATTTTCCAATTCATTTTCTGGATAAA 32 159 1 TTTATTCTTT 0.565656 -142 AACAATTATCCATTTAAATTCATTTAGTTAATTGA 34 165 0 CTTATTCTTT 0.928837 -127 * ** **** *** Masking position 9 Map Score: 26.2092 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 15 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 2 TCATTAGGCACCCCAGGCTTTACACTTTATGCTTC 4 41 1 CCCCGGCTTC 0.947908 -82 ACACTTTATGCTTCCGGCTCGTATGTTGTGTGGAA 4 62 1 CTTCGGCTCG 0.891009 -61 CCCCCTGCACCCCCGGGCTCTGGCGAACAAAATCG 10 12 1 CCCCGGCTCG 0.91906 -289 TGTTACCTCGCGCCCGACCCGGTAGCCGTAAGGGA 10 71 0 CGCCGACCCG 0.871802 -230 ATGTGGGCTGCCCCGGCCTTCAGGGAACGCCTCGG 10 137 1 CCCCGCCTTG 0.91446 -164 ATGAACTTGACGTCGGGCGTTGTCGCTTTCACTTG 21 149 0 CGTCGGCGTG 0.957703 -43 CAATAACATTACCCAGGCGTTCTGGCGTAGACGAT 23 18 0 ACCCGGCGTG 0.89548 -100 CACGCTACCGCCCCAGGCTCAACAGCTACCTGAAT 25 193 0 CCCCGGCTCG 0.995028 -108 AAAAACTGGACGCCCGGCGTGAGTCATGCTAACTT 27 41 1 CGCCGGCGTC 0.940939 -100 CCGCTCCTGACGCCAGACGCGTTAGCGCCGTGGTC 30 78 1 CGCCGACGCG 0.953201 -29 CCCACTACGTCGCCTGGCGCAAAAGCGAGTCGGCT 31 164 1 CGCCGGCGCG 0.99427 -78 TTCAATCCTACCTCTGGCGCAGTTGATATGTAAGG 32 121 0 CCTCGGCGCG 0.98488 -180 CTCGGAGAGTCCCCTCGCCCCTCTGGGAAGAGGGT 33 88 0 CCCCCGCCCG 0.89145 -195 CTGCAGAAAACCTCCGGCTTCCAGGTTGAGCATTC 33 212 0 CCTCGGCTTG 0.962782 -71 GCAGATCTCCTGGCTTGCTTGAATAACTTCA 33 262 0 CTCCGGCTTG 0.949864 -21 **** ***** * Masking position 8 Map Score: 21.4992 Number of sites scoring better than the average of aligned sites = 640 Number in coding regions = 606 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 3 GGGTGAATAGAGGGCGTTTTTTCGTTAATT 2 116 0 AGGGCGTTTT 0.894945 -185 TGCGACGCGAGCGGCATTTTAGGACATATC 3 17 0 GCGGCATTTT 0.893556 -284 GCACCGCGCAGCGGCGATTTTGTTCGCCAG 10 31 0 GCGGCGATTT 0.954605 -270 GTGGGCTGAGGGCGCGTTTTACAGGGATGT 10 103 0 GGCGCGTTTT 0.953505 -198 AGGGAACGCCTCGGCGATTTTGACGCCACC 10 158 1 TCGGCGATTT 0.726824 -143 GGATGTTTTTTCAGCGTTTTCTGTTGGCTC 14 129 0 TCAGCGTTTT 0.817483 -56 GGTCGTTACGGGCGAGTTTTTCCATCTTTT 14 159 0 GGCGAGTTTT 0.687627 -26 ACGTAAACACGTGGCGTTTTTGGCATAAGA 29 16 0 GTGGCGTTTT 0.939024 -224 ACGTGTTTACGTGGCGTTTTGCTTTTATAT 29 34 1 GTGGCGTTTT 0.939024 -206 CCGTCAGCAGCGTTTTTTCTTCCACG 31 7 1 GCAGCGTTTT 0.972527 -235 TTTGCCACCCGCGGCGATTTGAGCTTTTTT 31 204 1 GCGGCGATTT 0.954605 -38 CTTTGGGTGCGTTTTGGCAAAAAAG 31 227 0 GGTGCGTTTT 0.88261 -15 GAAAATCAGGAGAGCGTTTTCAATCCTACC 32 144 0 AGAGCGTTTT 0.794068 -157 ACATGAAACCGGAGCATTTTGC 32 289 1 GGAGCATTTT 0.76588 -12 TACCTGAAAAGCAGAGTTTTCGGCCTCATG 33 126 0 GCAGAGTTTT 0.791658 -157 ********** Masking position 8 Map Score: 15.2137 Number of sites scoring better than the average of aligned sites = 1076 Number in coding regions = 981 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 4 AATAAATATTCGTTTTCACAGTGGAATTAACTC 2 278 1 CTTTTCAGAA 0.975579 -23 AAATGACTCACTATTTTCCACAGCAAATATAAAGTG 3 53 0 CATTTCAGAA 0.980086 -248 CTTTGCCCCACAATTTCCCACTGAAAGGAGTTTACG 3 252 0 CATTTCAGAA 0.980086 -49 GAGCGGATAACAATTTCACACAGGAAACAGCT 4 101 1 CATTTCAGAA 0.980086 -22 CGCACCTGCCATTTAACAAGGAAAAAAC 11 9 1 CATTTCAGAA 0.980086 -20 TTAGCGCGGTCAAGTTTTCACCGCAAAGGTATTTAA 14 75 0 CAGTTCAGAA 0.960091 -110 ATATCGATCACTTTTTAACAAGGCAATCTGATTGAT 22 105 0 CTTTTCAGAA 0.975579 -96 AATGCATGCTCTCAGAGAAAATTATTAGCA 29 220 0 CTGCTCAGAA 0.820217 -20 CATTTTTTGACTTTTTGCCAGGGAAGTTGTTGTTGA 34 94 1 CTTTTCAGAG 0.903228 -198 * **** ** * ** Masking position 10 Map Score: 7.31884 Number of sites scoring better than the average of aligned sites = 38 Number in coding regions = 27 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 5 TTTTGTTTCGGGTGAATAGAGGGCGTTTTTTCGT 2 121 0 GGTGAGGGGC 0.961047 -180 GGGAAATTGTGGGGCAAAGTGGGAATAAGGGGTG 3 269 1 GGGGAGGGGA 0.988798 -32 GTGGGAATAAGGGGTGAGGCTGGC 3 287 1 GGGGGGTGGC 0.973095 -14 TCTGACGGAGGGGGAAGGGATGGGAGAGAAAGGA 8 64 0 GGGGAGTGGG 0.922224 -69 CCAGAGCCCGGGGGTGCAGGGGGC 10 1 0 GGGGGGGGGC 0.989944 -300 CCCACATGGATGTGGGCTGAGGGCGCGTTTTACA 10 110 0 TGTGGGGGGC 0.849347 -191 GTTATAAACAGAGGAAGGGGTGGATAGCCGTTTT 16 153 0 GAGGAGTGGA 0.681118 -148 AGGCTAAAAATGGAGAATGCAGGCGTGATCACAT 17 71 1 TGGAAGAGGC 0.68741 -148 CTTGCGTCAATGGGCAAGGTGGGCTTGCATTTGC 19 73 0 TGGGAGGGGC 0.988798 -176 AGGCCTTACGGGGGAAGTGAAGGCCCAATAAAGG 20 20 0 GGGGAGAGGC 0.974618 -57 TAAGATAAAACGGGAAGCGTTGGAAATTACAAGA 27 116 0 CGGGAGTGGA 0.842946 -25 CTCGCCCCTCTGGGAAGAGGGTGAAAACCGTGCT 33 76 0 TGGGAGGTGA 0.724635 -207 TAATTCCACATGGATAGAGTGGGATTCACACAAC 34 202 0 TGGAAGGGGA 0.834848 -90 **** * * **** Masking position 9 Map Score: 10.2697 Number of sites scoring better than the average of aligned sites = 428 Number in coding regions = 390 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 AAACTGATTATTAATCAAAATTAACGAAAAAAC 2 98 1 TTAATCAAAA 0.937988 -203 GTCCACGAGGTTAATAATAATTATATTAAATGT 2 216 1 TTAATAAAAA 0.813009 -85 GGCATTTCCCGTCATAATAAGGACATGCC 7 18 1 GTCATAAAAA 0.691036 -19 GTTGGCTCGATTCATCAGAAAAAATGTTAGCGC 14 104 0 TTCATCAAAA 0.939066 -81 CGACGTCAAGTTCATCAGACTAAGGATTGAGTT 21 169 1 TTCATCAACA 0.829443 -23 AAAATATACTTTAATCATAAAAATCAAATAGAT 25 83 0 TTAATCAAAA 0.937986 -218 TCTGGTTAAGTTAAGCAGAAAAAAGCACGCTAC 25 220 0 TTAAGCAAAA 0.704643 -81 AATTTTATCATTCATAATAAGTATGTGTAGG 32 9 0 TTCATAAAAA 0.815854 -292 ATTCATTCAATTAATAACACATATATTAATTGC 32 39 1 TTAATAAACA 0.578703 -262 CCGGTTTCATGTCATCAAAATGATGACGTAATT 32 268 0 GTCATCAAAA 0.886119 -33 AGTGTCAGGATTAATCAAAACCAATCACATATT 34 39 0 TTAATCAAAA 0.937988 -253 CGCGTCACATTTAATCATAAATAATCTTGTTGT 34 245 1 TTAATCAAAA 0.937988 -47 ATTTTCAAAAGTAATCACAACAAGATTATTTAT 34 261 0 GTAATCAAAA 0.884205 -31 ******* ** * Masking position 7 Map Score: 8.50585 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 59 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 7 ATGTTTACGGCTAATATCAGCGTTGTTTATTTTACGTCCA 3 156 0 CAACGCGGAT 0.97848 -145 TCGTTGCGCGCACAGTACAGCGCAACTTATTTTGTTAAAA 6 39 1 CATCGCGAAT 0.975765 -38 ATCAATCTCCCTTAAAGTTGCATGAAAAATCCCTTTTATC 9 53 1 CAATGCAAAT 0.635885 -85 TTTGGAGCGCCTGAAACCTGCGGCGCGCATTTCAATCGCT 15 82 1 CAACGCGGAT 0.97848 -69 TAAACGGCAGCACTGTCCGGCAAAAACGATTGCCGGACAG 18 24 0 CTTCGCAAAT 0.728983 -124 CTCTCCAGTTCAGATTACTGCGATATTAATCTTTCGTTTT 19 215 0 CATCGCGAAT 0.97574 -34 TCATTCGGGTCGGATTGCTGCGAAAGAAATGATACACTAG 25 127 1 CATCGCGAAT 0.975762 -174 CCGTAAACAGGCATGGATGATCCTGCCATAC 28 2 1 CAAAGCAGAT 0.805173 -83 TATCTGTAATCTTAATGCCGCGCTGGCGATGTTAGGAAAA 29 61 1 CATCGCGGAT 0.981828 -179 GCCGTTAAAACTAAAAACAGCATCAATAATCAACGCGATA 32 70 1 CAACGCAAAT 0.946845 -231 AAAATGATGACGTAATTAAGCATTGATAATTGAGATCCCT 32 245 0 CATAGCAGAT 0.830825 -56 * * * * *** * ** Masking position 19 Map Score: 6.1113 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 176 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 8 TAAGCTGTATTCTGTGATTGGTATCACATT 2 154 0 TCTGTGATTG 0.827389 -147 TCGTATGTTGTGTGGAATTGTGAGCGGATA 4 80 1 TGTGGAATTG 0.96171 -43 CTGTTTCCTGTGTGAAATTGTTATCCGCTC 4 101 0 TGTGAAATTG 0.863418 -22 GATGGTAGTTTGTGTAATTGCTGGGGAGTT 18 125 0 TGTGTAATTG 0.968203 -23 GCGACTCTTTTGTGTGATTGTCTGGTTAAG 25 243 0 TGTGTGATTG 0.970579 -58 CCAGCCACAGTGTGGGATTGAACTGACCGT 31 34 0 TGTGGGATTG 0.964553 -208 GCGAGTCGGCTGTGTATTTGCCACCCGCGG 31 188 1 TGTGTATTTG 0.81077 -54 TTCGAATCAATATGTGATTGGTTTTGATTA 34 31 1 TATGTGATTG 0.763824 -261 TTTAATGGAATGTGTAATTCAATTAACTAA 34 147 1 TGTGTAATTC 0.815646 -145 ACTCTATCCATGTGGAATTATTTGCGGGTC 34 216 1 TGTGGAATTA 0.711172 -76 ********** Masking position 3 Map Score: 5.73785 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 55 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 9 CAGTTTGCGACGCGAGCGGCATTTTAGGACAT 3 20 0 CGAGCGGCAT 0.726699 -281 AATCCCTCATCGTCATCACCGTTTTAAAATGA 3 83 0 CGATCACCGT 0.841439 -218 AGGGATAAGTCGAGGGCACCGCGCAGCGGCGA 10 44 0 CGGGCACCGC 0.939796 -257 GTTTTTATGCCGGATGCGGTGTAAACATACGT 12 22 0 CGTGCGGTGT 0.738646 -176 TCAGAAAAAATGTTAGCGCGGTCAAGTTTTCA 14 91 0 TGAGCGCGGT 0.878625 -94 CGAAAATAAACGGCAGCACTGTCCGGCAAAAA 18 38 0 CGAGCACTGT 0.957865 -110 ATTTCATGTTCGGGTGCCCCGTCGCTAAAAAC 27 15 1 CGTGCCCCGT 0.860159 -126 TTCCTAACATCGCCAGCGCGGCATTAAGATTA 29 67 0 CGAGCGCGGC 0.966536 -173 GTAATGCGCACGATGGCGCTGTTAACACCAAA 30 36 0 CGGGCGCTGT 0.933176 -71 CGCATTACGTCTGAAGCACCGCTCCTGACGCC 30 60 1 CTAGCACCGC 0.728185 -47 ACGCCAGACGCGTTAGCGCCGTGGTCACGG 30 87 1 CGAGCGCCGT 0.992305 -20 CCGTCAGCAGCGTTTTTTCTTCC 31 2 1 CGAGCAGCGT 0.961865 -240 TGACTGCGAGTGGGAGCACGGTTTTCACCCTC 33 62 1 TGAGCACGGT 0.818931 -221 ** ******** Masking position 7 Map Score: 5.61592 Number of sites scoring better than the average of aligned sites = 1473 Number in coding regions = 1392 Number in noncoding regions = 81 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701 Motif number 10 AGTGGGAAATTGTGGGGCAAAGTGGGAATA 3 266 1 TGTGGGGCAA 0.67444 -35 AAAGGAATATCATCGGGCATAAGGCGA 8 8 0 CATCGGGCAT 0.951962 -125 ATATTCCTTTCATCGGGCTATTTAACCGTT 8 28 1 CATCGGGCTA 0.91224 -105 GTTTACACCGCATCCGGCATAAAAACACGC 12 28 1 CATCCGGCAT 0.951961 -170 CTTTTAACGGTATCCGGCAACCAGCCAGGT 15 29 1 TATCCGGCAA 0.925324 -122 AAAATGTCTATATCGGGCTTATTCAGAATG 16 60 1 TATCGGGCTT 0.866992 -241 CCTTACACACTGTCCGGCAATCGTTTTTGC 18 15 1 TGTCCGGCAA 0.941153 -133 ACGGCAGCACTGTCCGGCAAAAACGATTGC 18 31 0 TGTCCGGCAA 0.941153 -117 ATGAACTTGACGTCGGGCGTTGTCGCTTTC 21 154 0 CGTCGGGCGT 0.88701 -38 CTGCAGAAAACCTCCGGCTTCCAGGTTGAG 33 217 0 CCTCCGGCTT 0.791702 -66 ********** Masking position 3 Map Score: 4.44523 Number of sites scoring better than the average of aligned sites = 814 Number in coding regions = 514 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 11 CGGGCGCTATCATGCCATACCGCGAAAGGT 5 30 0 CATGCCATAC 0.868281 -47 CGCACCTGCCATTTAACAAGGAAA 11 5 1 CCTGCCATTT 0.77468 -24 CCTTACATTACCTGTCATGAAGGAATTAAA 14 13 0 CCTGTCATGA 0.817416 -172 CATGGATGATCCTGCCATACCATTCACAAC 28 22 1 CCTGCCATAC 0.983342 -63 ATATAATAAACCTGCCTTACATATCAACTG 32 107 1 CCTGCCTTAC 0.955772 -194 CTCCCTCACTCCTGCCATAATTCTGATATT 33 30 0 CCTGCCATAA 0.966195 -253 TGCAGATTCGCCTGCCATGATGAAGTTATT 33 242 1 CCTGCCATGA 0.971843 -41 GCAGATCTCCTGGCTTGCTTGAATAACT 33 265 0 CCTGGCTTGC 0.833803 -18 ********** Masking position 3 Map Score: 3.1849 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 167 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 AAAATGCCGCTCGCGTCGCAAACTGACACT 3 27 1 TCGCGTCGCA 0.914271 -274 TAACGTTAATTTGCTTCGCACGTTGGACGT 3 133 1 TTGCTTCGCA 0.89471 -168 CTCACATTAATTGCGTTGCGC 4 2 0 TTGCGTTGCG 0.699573 -121 GGACAAAATGTCGTTGCGCGCACAGTACAG 6 29 1 TCGTTGCGCG 0.696364 -48 AACAAAATCGCCGCTGCGCGGTGCCCTCGA 10 37 1 CCGCTGCGCG 0.964565 -264 CGCCTGAAACCTGCGGCGCGCATTTCAATC 15 89 1 CTGCGGCGCG 0.949924 -62 ACCGCTGCACAGATCAAAACG 20 66 0 CCGCTGCACA 0.882694 -11 ATAATTCAGGTTGCTGCACATGCGACTTGA 23 67 1 TTGCTGCACA 0.857055 -51 CAGCTTACTATTGCTTTACGAAAGCGTATC 26 26 1 TTGCTTTACG 0.566938 -51 AGATTTACTGCTGCTTCACGCAGGATCTGA 33 174 1 CTGCTTCACG 0.88823 -109 TATTTGCGGGTCGCGTCACATTTAATCATA 34 234 1 TCGCGTCACA 0.848649 -58 ********** Masking position 9 Map Score: 2.888 Number of sites scoring better than the average of aligned sites = 2575 Number in coding regions = 2449 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 118 Fraction of orfs with sites within 600 bp upstream = 0.0189528 Motif number 13 GTAAACATCGGGTTTTTTACCTCGGTATGCC 3 188 1 GTTTTTTACC 0.922224 -113 AAGTGCGCGTGTTTTTATGCCGGATGCGGTG 12 33 0 GTTTTATGCC 0.895605 -165 TCGGGAGGCCGTTTTTTTGCCTTTCACTCCT 12 80 1 GTTTTTTGCC 0.979539 -118 TTTTTTGATCGCTTTTTTGGCTTAAAATTTC 22 165 0 GTTTTTTGGC 0.9491 -36 ATAGTAAGCTGATATTCTACCACACT 26 6 0 GTATTCTACC 0.517557 -71 TAAACACGTGGCGTTTTTGGCATAAGACAAA 29 12 0 GGTTTTTGGC 0.795445 -228 AGCCCAGCCAGTTTTTCTGGCATATCTGGGG 31 85 1 GTTTTCTGGC 0.929954 -157 TGAGATATAAGCTTTTTTACCCACTACGTCG 31 145 1 GTTTTTTACC 0.922227 -97 GGCGATTTGAGCTTTTTTGCCAAAACGCACC 31 216 1 GTTTTTTGCC 0.979538 -26 GGAAGCCGGAGGTTTTCTGCAGATTCGCCTG 33 225 1 GTTTTCTGCA 0.728681 -58 ACCATTTTTTGACTTTTTGCCAGGGAAGTTG 34 92 1 GCTTTTTGCC 0.908956 -200 * ********* Masking position 6 Map Score: 8.45249 Number of sites scoring better than the average of aligned sites = 337 Number in coding regions = 299 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 14 ATTTCCCACTGAAAGGAGTTTACGGAGCTG 3 246 0 GAAAGGAGTT 0.95307 -55 AAAGTTTTACGAAAGGACTTACT 19 4 0 GAAAGGACTT 0.9673 -245 TTGCTTAATAGAAAGGCGTTAATAGGCAAA 19 47 0 GAAAGGCGTT 0.956375 -202 GAAAGAAAAAGAAAGGCCTTACGGGGGAAG 20 37 0 GAAAGGCCTT 0.969635 -40 GGTGGGTTTGGAACGGACTTTCCCTTCTGA 29 165 1 GAACGGACTT 0.930196 -75 ********** Masking position 3 Map Score: 1.41443 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 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 15 GCAAAAAGAAATTTTCAATATTGTTTTATGG 2 15 1 ATTTCAATAT 0.916563 -286 ATAACATCTGACTTTCAATATTGGTGATCCA 2 43 0 ATTTCAATAT 0.924197 -258 ATTTTTGTTAACATTTAATATAATTATTATT 2 228 0 AATTTAATAT 0.630373 -73 TTTTAAAGTTATATTTAATATACATGTTTAA 9 114 0 AATTTAATAT 0.542869 -24 AAAAACAAATAATTTCATTATATTTTGAAAT 12 158 1 ATTTCATTAT 0.884152 -40 ACATTTTAAAATATTCATTATCAGTCAATGC 16 36 0 AATTCATTAT 0.819241 -265 CGTTTCAGTGACTTTCATTATGTTTCTTTTG 19 114 1 ATTTCATTAT 0.884152 -135 TTTGGCTTAAAATTTCAATATGCGAAACTTG 22 150 0 ATTTCAATAT 0.924197 -51 * ********* Masking position 7 Map Score: 1.38333 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 36 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467