AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00040_ecoli_reg_100.orf -o00040_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/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 BIME6 21 BIME #2 araB 300 L-ribulokinase #3 ybaC 151 putative lipase (EC 3.1.1.-) #4 galU 201 glucose-1-phosphate uridylyltransferase #5 uxaB 226 altronate oxidoreductase #6 eda 36 2-keto-3-deoxygluconate 6-phosphate aldolase and 2-keto-4-hydroxyglutarate aldolase #7 edd 234 6-phosphogluconate dehydratase #8 ugd 248 UDP-glucose 6-dehydrogenase #9 galF 174 homolog of Salmonella UTP--glucose-1-P uridyltransferase, probably a UDP-gal transferase #10 araE 300 low-affinity L-arabinose transport system proton symport protein #11 kduD 29 2-deoxy-D-gluconate 3-dehydrogenase #12 kduI 286 homolog of pectin degrading enzyme 5-keto 4-deoxyuronate isomerase #13 uxaC 300 uronate isomerase #14 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #15 agaC 38 PTS system N-acetylgalactosamine-specific IIC component 1 #16 dam 106 DNA adenine methylase #17 xylB 71 xylulokinase #18 xylA 300 D-xylose isomerase #19 yiaM 117 orf, hypothetical protein #20 rhaD 85 rhamnulose-phosphate aldolase #21 rhaB 287 rhamnulokinase #22 uxuA 300 mannonate hydrolase #23 uxuB 80 D-mannonate oxidoreductase Motif number 1 GCCAGTTTCAATATCAGCAGGCGGGATCGCAT 3 80 1 ATTCAGCGGC 0.716963 -72 ATTCAGGGTAATTGATGCTGGCGAAAAAAATC 9 109 1 ATGATGCGGC 0.956274 -66 CTATGTCTTACTCTCTGCTGGCAGGAAAAA 10 281 1 CTTCTGCGGC 0.972225 -20 TTACCGATAAATATCTGCCGTCATTAATCTGT 12 26 1 ATTCTGCGTC 0.949697 -261 GACAAGTTATCTTTCTGCCGTCGCAAATCATA 13 36 0 CTTCTGCGTC 0.967967 -265 CAGTACTGGCCTTGCTGTCGTCAGGTAATGTC 13 118 0 CTGCTGTGTC 0.935204 -183 AGTGGTAAATCTCGCTGCAGGCCGCGCCAGTA 13 145 0 CTGCTGCGGC 0.99087 -156 GCCTGAAGCGCTGGATGCTGTCGGAGCTTTCT 16 51 1 CTGATGCGTC 0.967967 -56 GCCGCGGGTGATGGATGATGTCGTAATATTGG 18 256 0 ATGATGAGTC 0.622561 -45 ACTGGCCTCCTGATGTCGTCAACACGGCGA 21 9 1 CCGATGTGTC 0.617355 -279 ATGCAACGCCACGGCTGCGGTCTGGTTGTTCA 22 206 1 ACGCTGCGTC 0.953021 -95 ATCCACCGGCATGGCTGCGCGCCGTGCCGGTT 23 12 1 ATGCTGCCGC 0.878208 -69 ** ***** *** Masking position 12 Map Score: 10.4055 Number of sites scoring better than the average of aligned sites = 1118 Number in coding regions = 1068 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 2 CAGGCGGGATCGCATTTTCATGGCAGTGGTT 3 97 1 CCATTTTCAT 0.887988 -55 GCTAACTCGCCTCCTTTTCAGAACTTAGCCC 4 103 1 CCCTTTTCAG 0.958002 -99 CGAGGAAAAACGCCTTTTCCTGGATCATAAA 5 57 0 CCCTTTTCCT 0.972918 -170 GCTCTGACAACTCAATTTCAGGAGCCTTT 7 216 1 CCAATTTCAG 0.853986 -19 CTCTGCATTTCCTCCTTACCGAT 12 3 1 CGCATTTCCT 0.881498 -284 GTTTAGTTATCTCCTTTTCCATTAAGGCACT 14 62 0 CCCTTTTCCA 0.849924 -105 TAACTAATTACACCTTCTCCGGCTGTGGAGA 16 80 0 CCCTTCTCCG 0.920416 -27 CGAGGAATTACCCAGTTTCATCATTCCATTT 18 144 1 CCAGTTTCAT 0.678006 -157 ATATTGGGCACTCCCTTTCAGTTGCTCAATT 18 232 0 CCCCTTTCAG 0.858333 -69 TGCGCGCGAGCGCCTTATCCGGCCTACGGGT 20 26 1 CCCTTATCCG 0.809163 -60 GTGATGCTCACCGCATTTCCTGAAAATTCAC 21 123 0 CGCATTTCCT 0.881507 -165 TTGCCAATGGCCCATTTTCCTGTCAGTAACG 21 205 1 CCATTTTCCT 0.927126 -83 TGTGATCCTGCTGAATTTCATTACGACCAGT 21 265 0 CGAATTTCAT 0.621151 -23 AGAACTTATACGCCATCTCATCCGATGCAAC 22 182 1 CCCATCTCAT 0.837065 -119 * ********* Masking position 6 Map Score: 8.98239 Number of sites scoring better than the average of aligned sites = 663 Number in coding regions = 424 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 3 AAAGACGCAGTGACGGCAATGTCTGATGCAA 2 18 0 TGACGCAATG 0.969238 -283 ACCAAAGCCATGACAAAAACGCGTAACAAAA 2 115 1 TGACAAAACG 0.85214 -186 ACGCGCGATTTGAATGCAATGTGTTCTACCA 5 25 1 TGAAGCAATG 0.91171 -202 TTTATTACACTGACTGAAACGTTTTTGCCCT 7 120 1 TGACGAAACG 0.983274 -115 AGAGGATTTATGACTGAAACGCCTGTAACCG 7 159 0 TGACGAAACG 0.983274 -76 ATAAATCCTCTGAATGAAACGCGTTGTGAAT 7 179 1 TGAAGAAACG 0.950658 -56 TGTTCGATGGTCAACGCAACGAAAAACAATT 8 147 0 TCAAGCAACG 0.846157 -102 CATTACCTGACGACAGCAAGGCCAGTACTGG 13 120 1 CGACGCAAGG 0.91927 -181 CTTCAAAGAGTGACGGCAAGGAAGAAGGAAC 23 41 0 TGACGCAAGG 0.979894 -40 **** ****** Masking position 8 Map Score: 6.88941 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 402 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 ACTGTGAATCATGATGTTTTTAGCATCCTGATAAGAGCT 8 197 0 ATGATGTTCT 0.866186 -52 ATGTCGTTATGTGATGGATATTCCAATTTTCAAATTAAG 10 169 0 GTGATGTTCT 0.989048 -132 TCCCACATTTGTGATGGCTCTCACCTTTTAAAGTTGTAT 13 68 0 GTGATGTTCT 0.989048 -233 CACTTTGAGAGTAATTTTTTTAACTACGTTTATTGATCT 13 173 1 GTAATTTTCT 0.836372 -128 GGAAATTGGTGTGATAACTTTGTCAGCATCGCACCATAA 13 238 1 GTGATATTCT 0.909783 -63 CGATATTGTAGTGATGTATTTATTAAGGTTTAGTTATCT 14 81 0 GTGATGTTTT 0.866303 -86 ATAAAAATCTGTAATTGTTTTCCCCTGTTTAGTTGCTAA 18 17 0 GTAATTTTCT 0.836372 -284 CCTGGGTAATGTTATTGCTCTAACTATATTAATAATTCA 19 36 1 GTTATTTTCT 0.743504 -82 ACCTGACCTCGTGATTACTATTTCGCCGTGTTGACGACA 21 24 0 GTGATTTTCT 0.970742 -264 AAAGATGAACGTGATGATGTTCACAATTTGCTGAATTGT 21 160 0 GTGATGGTCT 0.969038 -128 AACCATTGTTGCGATGAATGTCACATCCTCTGATCAATA 22 34 1 GCGATGTTCT 0.939401 -267 TGAAATTCTTGTGATGTGGTTAACCAATTTCAGAATTCG 22 119 1 GTGATGGTCT 0.969038 -182 ****** * * * * Masking position 4 Map Score: 9.90731 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 132 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 AATGTGGACTTTTCTGCCGTGATTATAGAC 2 148 0 TTTCTGCCGT 0.970227 -153 TTATCGCAACTCTCTACTGTTTCTCCATAC 2 256 1 TCTCTACTGT 0.836734 -45 TTATGAATTTTATCTGCTGTAAAATTAGGT 10 113 1 TATCTGCTGT 0.946423 -188 TTAATCCATATTTATGCTGTTTCCGACCTG 10 219 1 TTTATGCTGT 0.766527 -82 TATGTCTTACTCTCTGCTGGCAGGAAAAA 10 282 1 TCTCTGCTGG 0.924324 -19 TACCGATAAATATCTGCCGTCATTAATCTG 12 27 1 TATCTGCCGT 0.957881 -260 ACAAGTTATCTTTCTGCCGTCGCAAATCAT 13 37 0 TTTCTGCCGT 0.970227 -264 GTTCCGCGTCTCTTTGCTGTGGAACCCACT 22 262 1 TCTTTGCTGT 0.922822 -39 GGTTCCTTCTTCCTTGCCGTCACTCTTTGA 23 40 1 TCCTTGCCGT 0.782454 -41 ********** Masking position 5 Map Score: 5.55935 Number of sites scoring better than the average of aligned sites = 338 Number in coding regions = 303 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 6 GAGTTGCGATAAAAAGCGTCAGGTAGGATC 2 238 0 AAAAAGCGTC 0.908418 -63 TTTAATCGAGGAAAAACGCCTTTTCCTGGA 5 64 0 GAAAAACGCC 0.943268 -163 TCAGTGTAATAAAAAAAGCCTCGTGGGTGA 7 103 0 AAAAAAAGCC 0.948076 -132 ATATTTGGCAAAAAAAAGCCCGGTGCAATA 8 48 0 AAAAAAAGCC 0.948076 -201 TCGTTCCTTAAAAAAATGCCCGGTATCGCT 17 47 0 AAAAAATGCC 0.91193 -25 AAAACCACGTAAAAAACGTCGATTTTTCAA 21 85 1 AAAAAACGTC 0.936471 -203 CGACCAGTCTAAAAAGCGCCTGAATTCGCG 21 243 0 AAAAAGCGCC 0.973234 -45 ********** Masking position 5 Map Score: 4.96662 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 130 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 7 TCATAAAACTGCTCATTAATCATCAGGAGT 5 117 1 GCTCATTAAT 0.679694 -110 TAAAATGGTTGCTGAATTATAGCTTGTTCG 9 140 0 GCTGAATTAT 0.958675 -35 AATTCATAAAGTTCATTAATTGATAATTAA 10 92 0 GTTCATTAAT 0.612591 -209 TTCAAATTAAGTTGAATTATTGAGATTATT 10 150 0 GTTGAATTAT 0.945315 -151 TCATTAATCTGTTGAATAATGATGGCTGGC 12 46 1 GTTGAATAAT 0.910652 -241 TCACCATAAAGTTGAATAATATAATTTTTT 14 137 0 GTTGAATAAT 0.910652 -30 TGGTTTATTTCTTGATTTATGACCGAGATC 18 73 1 CTTGATTTAT 0.728401 -228 CCTTTCAGTTGCTCAATTATGTTATTTCAC 18 220 0 GCTCAATTAT 0.900356 -81 TGTGCAGCAACCTGAATTATTAATATAGTT 19 57 0 CCTGAATTAT 0.900356 -61 GCACATGCGACTTGAATTATGACAGACATA 19 82 1 CTTGAATTAT 0.870686 -36 TTCACAATTTGCTGAATTGTGGTGATGTGA 21 150 0 GCTGAATTGT 0.813735 -138 ********** Masking position 5 Map Score: 5.44273 Number of sites scoring better than the average of aligned sites = 276 Number in coding regions = 231 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 AATTCAGCAACCATTTTACAGGTGGATGAAA 9 152 1 CCATTTTCAG 0.959838 -23 GATGGATATTCCAATTTTCAAATTAAGTTGA 10 165 0 CCAATTTCAA 0.923502 -136 ATCGGCAATTTGCATTCCGTCGACT 13 5 1 GCAATTTCAT 0.78619 -296 AGTTATCACACCAATTTCCAGAGTCCGAAGA 13 226 0 CCAATTTCAG 0.981406 -75 CCGACAACACCGAATTTACAGGAACACAGAA 20 64 1 CGAATTTCAG 0.959045 -22 TAAAAAACGTCGATTTTTCAAGATACAGCGT 21 94 1 CGATTTTCAA 0.708051 -194 AGATACAGCGTGAATTTTCAGGAAATGCGGT 21 114 1 TGAATTTCAG 0.723373 -174 TGCCAATGGCCCATTTTCCTGTCAGTAACGA 21 206 1 CCATTTTCTG 0.770791 -82 CAATGGTTGACCAATTTACATAACATATCGC 22 11 0 CCAATTTCAT 0.923502 -290 ACCCTTTGCTGCAATTTGCAGCAACAACCAT 22 83 1 GCAATTTCAG 0.941439 -218 ******* *** Masking position 6 Map Score: 5.98151 Number of sites scoring better than the average of aligned sites = 210 Number in coding regions = 183 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 9 TACTGGCTCTTCTCGCTAACCCAACCGGTA 2 49 1 TCTCGCTAAC 0.781001 -252 ACTGGCTGCGTCTCGCGCGCTCCCGTCAGA 3 56 0 TCTCGCGCGC 0.963791 -96 TCTTAATTATGCTAACTCGCCTCCTTTTCA 4 93 1 GCTAACTCGC 0.932515 -109 CGTTTATTGATCTAACTCACGAAAATATCT 13 199 1 TCTAACTCAC 0.786786 -102 CCATAAGCAAGCTAGCTCACTCGTTGAGAG 13 271 1 GCTAGCTCAC 0.957483 -30 ACAAGTGTGCGCTCGCTCGCAAAATAAAAT 18 171 0 GCTCGCTCGC 0.843452 -130 CGGATAAGGCGCTCGCGCGCATCCACGGCA 20 17 0 GCTCGCGCGC 0.756881 -69 ********** Masking position 3 Map Score: 4.35745 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 181 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 10 TTTTAATAAGCGGGGTTACCGGTTGGGTTAGCGAGA 2 59 0 CGTTCCGTGG 0.941531 -242 TTTGGTCCCGCTTTGTTACAGAATGCTTTTAATAAG 2 85 0 CGTTCAGAGC 0.819191 -216 CAAATTTAGCCCGCGTTATCGTTTGC 4 1 0 CGTTTCGTGC 0.992612 -201 CAGAGTTTTCTCTCGCCTGATTACAA 6 21 0 CGTTTCTTGC 0.968486 -16 TGTTACGCCGCTTCGTTGTGGATTGCAGTAGCATTG 9 52 0 CGTTTGGTGC 0.956967 -123 TCAAGGTTATCTCCCGCAATGGTTTAT 16 2 1 CGTTTCTCGC 0.904363 -105 AGTCCGTTGGCCCGGTTATCGGTAGCGATACCGGGC 17 24 1 CGTTTCGTGC 0.992612 -48 CCTGTAAATTCGGTGTTGTCGGATGCACGACCCGTA 20 50 0 CGTTTCGAGC 0.980075 -36 TTCATCTTTCCCTGGTTGCCAATGGCCCATTTTCCT 21 190 1 CGTTCCATGC 0.93496 -98 * *** *** * ** Masking position 7 Map Score: 5.07986 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 216 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 11 TTTGCTATGCCATAGCATTTTTATCCATAAGATTAGC 2 200 1 CACATTTATA 0.763645 -101 GCTAAATTTGCATTACCTGCTAATGTCGGCTGGTGGT 4 27 1 CACCTGTATC 0.87837 -175 AAAACACGAACAGTCCAGGAGAATTTAA 4 184 1 CACAGGGATA 0.919846 -18 CTGTTTTGATCAACTCCTGATGATTAATGAGCAGTTT 5 122 0 CACCTGTATA 0.974586 -105 ATTGAGTTGTCAGAGCAGGATGATTCACAACGCGTTT 7 195 0 CACAGGTATA 0.982151 -40 ATTCAGTAATCAATTCAGGGTAATTGATGCTGGCGAA 9 97 1 CACAGGTATA 0.982152 -78 GACCCTGCCGCATGGCAGGGTTTTTTATACCTGTAGA 10 17 1 CACAGGTTTA 0.874874 -284 CATCATAATCCATATCATGGTTATGAAATAATCCATA 10 55 1 CACATGTATA 0.976193 -246 TCACCCGCGGCATTACCTGATTATGGAGTTCAAT 18 277 1 CACCTGTATA 0.974586 -24 ATGCTCACCGCATTTCCTGAAAATTCACGCTGTATCT 21 114 0 CACCTGAATA 0.84365 -174 CTGCAAATTGCAGCAAAGGGTAATCGATGGTTATTGA 22 67 0 CAAAGGTATA 0.812588 -234 ** **** * ** * Masking position 2 Map Score: 6.07081 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 89 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 12 GTAGCCGCATCCGGTATGTAA 1 5 1 CCGCATCCGG 0.905999 -17 CAAAGCGGGACCAAAGCCATGACAAAAACG 2 106 1 CCAAAGCCAT 0.513751 -195 AGCGCGCGAGACGCAGCCAGTTTCAATATC 3 65 1 ACGCAGCCAG 0.849475 -87 GTTTCAATATCAGCAGGCGGGATCGCATTT 3 84 1 CAGCAGGCGG 0.70781 -68 TTGTAAGGAACCACTGCCATGAAAATGCGA 3 106 0 CCACTGCCAT 0.630767 -46 AGCTATAATTCAGCAACCATTTTACAGGTG 9 146 1 CAGCAACCAT 0.912862 -29 CAGGCAACTCCCGCAACGATAAACCATTGC 16 26 0 CCGCAACGAT 0.666838 -81 AAAGCTCCGACAGCATCCAGCGCTTCAGGC 16 51 0 CAGCATCCAG 0.879659 -56 GGAGCTTTCTCCACAGCCGGAGAAGGTGTA 16 73 1 CCACAGCCGG 0.953383 -34 GTCGCATGTGCAGCAACCTGAATTATTAAT 19 63 0 CAGCAACCTG 0.702783 -55 CAATTTGCAGCAACAACCATGAGAGTGAAA 22 94 1 CAACAACCAT 0.787684 -207 AACAACCAGACCGCAGCCGTGGCGTTGCAT 22 206 0 CCGCAGCCGT 0.972941 -95 GTATCCGGATGAACAACCAGACCGCAGCCG 22 217 0 GAACAACCAG 0.538151 -84 CCGGCACGGCGCGCAGCCATGCCGGTGGAT 23 12 0 GCGCAGCCAT 0.905591 -69 ********** Masking position 5 Map Score: 4.92427 Number of sites scoring better than the average of aligned sites = 4297 Number in coding regions = 3972 Number in noncoding regions = 325 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 13 CGAGGCTTTTTTTATTACACTGACTGAAACGTT 7 110 1 TTATACCTGA 0.83661 -125 AAACGCGTTGTGAATCATCCTGCTCTGACAACT 7 195 1 TAATATCTGC 0.79117 -40 TCTTATAGACTAAATTTCACTGCTTAATATTAA 8 77 1 TAATTCCTGC 0.95154 -172 TTCGCCAGCATCAATTACCCTGAATTGATTACT 9 101 0 TAATACCTGA 0.8823 -74 TTTTATGACCCTGCCGCATGGCAG 10 2 1 TTATACCTGC 0.967341 -299 TCTACAGGTATAAAAAACCCTGCCATGCGGCAG 10 21 0 TAAAACCTGC 0.931988 -280 TTTCACTATGTCTTACTCTCTGCTGGCAGGAAA 10 276 1 TTTATCCTGC 0.657427 -25 GACATATTCGTGATCGACACTGCACTTTTTTTA 12 121 1 TATCACCTGC 0.839105 -166 CTCAAAGTGGTAAATCTCGCTGCAGGCCGCGCC 13 149 0 TAATTCCTGC 0.95154 -152 TCAATTATGTTATTTCACACTGCTATTGAGATA 18 205 0 TTTTACCTGC 0.930613 -96 * *** ** **** Masking position 11 Map Score: 2.97245 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 205 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 14 GTAGAACAATTTTTACACTTTCAGGCCTCGTG 7 66 1 TTTTCCTTTC 0.92772 -169 ACTGAAACGTTTTTGCCCTATGAGCTCCGGTT 7 132 1 TTTTCCTATG 0.949904 -103 AGCTAAAAGTTTTAACGCTACGTTGTTCGATG 8 169 0 TTTACCTACG 0.789602 -80 GTTCACGTATTTTTTCACTATGTCTTACTCTC 10 264 1 TTTTCCTATG 0.949904 -37 AACGAAACAGTGTTTCACTATCGTTTTCTATT 12 235 1 TGTTCCTATC 0.728019 -52 TGCAGCGAGATTTACCACTTTGAGAGTAATTT 13 158 1 TTTACCTTTG 0.840534 -143 GAGAGTAATTTTTTTAACTACGTTTATTGATC 13 179 1 TTTTACTACG 0.700049 -122 CAATTACAGATTTTTATCTTTCGATTACGATT 18 39 1 TTTTACTTTC 0.689326 -262 ACTTATTGCATTTTTCTCTTCGAGGAATTACC 18 124 1 TTTTCCTTCG 0.931038 -177 GATTTTTCCTCTTTCACATAGTGGG 22 286 0 TTTTCCTTTC 0.92772 -15 **** * ***** Masking position 9 Map Score: 3.10591 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 231 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 15 CGCTTATTAAAAGCATTCTGTAACAAAGCG 2 83 1 AAGCATTCTG 0.820377 -218 TTACACTTTCAGGCCTCGTGCGGATTCACC 7 78 1 AGGCCTCGTG 0.947558 -157 GTAATAAAAAAAGCCTCGTGGGTGAATCCG 7 98 0 AAGCCTCGTG 0.937353 -137 TCTGAATGAAACGCGTTGTGAATCATCCTG 7 187 1 ACGCGTTGTG 0.854452 -48 AAAGGCTCCTGAAATTGAGTT 7 224 0 AAGGCTCCTG 0.907379 -11 ATGATGTTTTTAGCATCCTGATAAGAGCTA 8 196 0 TAGCATCCTG 0.748357 -53 AACATTACCCAGGCGTTCTGGCGTAGACGA 19 19 0 AGGCGTTCTG 0.896617 -99 TATCCGGCCTACGGGTCGTGCATCCGACAA 20 41 1 ACGGGTCGTG 0.85922 -45 ACTGGCCTCCTGATGTCGTCAA 21 3 1 TGGCCTCCTG 0.881237 -285 CTCTTTGAAGACGGATTCTGGAGTTTACG 23 62 1 ACGGATTCTG 0.709896 -19 ********** Masking position 6 Map Score: 2.38999 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 347 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 60 Fraction of orfs with sites within 600 bp upstream = 0.00963701