AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_ecoli_reg_100.orf -o00300_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 thrL 189 thr operon leader peptide #2 thrA 81 aspartokinase I, homoserine dehydrogenase I #3 dapB 166 dihydrodipicolinate reductase #4 yabB 300 orf, hypothetical protein #5 dapD 30 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase #6 glnD 61 protein PII; uridylyltransferase acts on regulator of glnA #7 map 300 methionine aminopeptidase #8 hlpA 121 histone-like protein, located in outer membrane or nucleoid #9 ybdL 108 putative aminotransferase #10 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #11 ybeX 89 putative transport protein #12 ybeZ 113 putative ATP-binding protein in pho regulon #13 htrB 224 heat shock protein #14 ydcH 72 orf, hypothetical protein #15 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #16 malX 174 PTS system, maltose and glucose-specific II ABC #17 cstC 300 acetylornithine delta-aminotransferase #18 msbB 119 suppressor of htrB, heat shock protein #19 wcaA 34 putative regulator #20 BIME92 24 BIME #21 wza 300 putative polysaccharide export protein #22 yffB 300 orf, hypothetical protein #23 dapA 79 dihydrodipicolinate synthase #24 lysA 121 diaminopimelate decarboxylase #25 prfB 90 peptide chain release factor RF-2 #26 dsbC 24 protein disulfide isomerase II #27 xerD 111 site-specific recombinase #28 asd 192 aspartate-semialdehyde dehydrogenase #29 dapF 300 diaminopimelate epimerase #30 metB 276 cystathionine gamma-synthase #31 lysC 300 aspartokinase III, lysine sensitive #32 lysU 236 lysine tRNA synthetase, inducible; heat shock protein #33 yjeA 294 putative lysyl-tRNA synthetase Motif number 1 TGTCAGGTGCGGGCTTTTTTCTGTGTTTCC 2 19 0 GGGCTTTTTT 0.973385 -63 CTGACAGTGCGGGCTTTTTTTTTCGACCAA 2 43 1 GGGCTTTTTT 0.973385 -39 TTCTAATTATCAGCGTTTTTGGCTGGCGGC 3 88 1 CAGCGTTTTT 0.837428 -79 ATGACGATGAGGGATTTTTTCTTACAGCTA 4 99 1 GGGATTTTTT 0.674204 -202 CGGCTAATATCAGCGTTGTTTATTTTACGT 4 159 0 CAGCGTTGTT 0.562596 -142 CCGTAAACATCGGGTTTTTTACCTCGGTAT 4 186 1 CGGGTTTTTT 0.834686 -115 CGGCGAATGCCGGCTTTTTTAATGCGATAA 6 19 1 CGGCTTTTTT 0.983662 -43 TGATTAACGACGGCGTTTTGATTAACTAAC 11 50 1 CGGCGTTTTG 0.928951 -40 GCCAGCCAGGCGGCTTTTTTAACAACTGCA 15 24 1 CGGCTTTTTT 0.983662 -39 CAGTCAGTACCGGCTTTTTTTATTTGGTGC 18 36 1 CGGCTTTTTT 0.983662 -84 CTCCAGATAAGTGCTTTTTTATGATTACGC 24 96 0 GTGCTTTTTT 0.928326 -26 GCGACTTATCCTGCTTTGTTAGCACGCAGA 28 43 0 CTGCTTTGTT 0.84187 -150 GCGACTTTGGCTGCTTTTTGTATGGTGAAA 28 111 1 CTGCTTTTTG 0.892906 -82 GTCGGCGGCGGTGCGTTTTTATCTGCAGGC 29 160 0 GTGCGTTTTT 0.877942 -141 ATAATTTTAACGGCTATTTGGGATTTGCTC 30 149 1 CGGCTATTTG 0.668269 -128 CCATCAGATCGTGCTTTTTTTAGTCACTGC 33 216 1 GTGCTTTTTT 0.928326 -79 ********** Masking position 7 Map Score: 20.9149 Number of sites scoring better than the average of aligned sites = 657 Number in coding regions = 503 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 134 Fraction of orfs with sites within 600 bp upstream = 0.0215226 Motif number 2 AAAAAAAGCCCGCACTGTCAGGTGCGGGCTTTTTT 2 29 0 CGCCTTGGGC 0.774522 -53 ACCAGCGCATCGCTACGCCGCCAGCCAAAAACGCT 3 99 0 CGCACCCCGC 0.993893 -68 AGTGTCAGTTTGCGACGCGAGCGGCATTTTAGGAC 4 22 0 TGCACCGCGC 0.98091 -279 TTCTGAATTTCGCCAAACGTGCCACTGAAGGTTTT 7 191 0 CGCAACGCAC 0.664881 -110 CTAAAGTCATCGCTACACTACCACTACATTCCTTT 8 22 0 CGCACCCCCT 0.79228 -100 CGCAAAGAACTGCACCCTCCGGTGCAAATGGGATG 8 83 1 TGCCCTGGGC 0.814663 -39 CCATCTTTATTGCAATGCTTGCGCCTTTTTCCTGT 12 59 1 TGCATCGCCC 0.801096 -55 TTTCCTAAGCCGCCAGCCAGGCGGCTTTTTTAACA 15 13 1 CGCAGCGCGC 0.964313 -50 AGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAA 18 54 0 CGCACTCCGC 0.976434 -66 CAAGTTGCGCCGCTACACTATCACCAGATTGATTT 18 70 1 CGCACCTCCC 0.802895 -50 AAAGCGATTCTGATACACTAGCCGCAAAAGCCACA 27 33 0 TGAACCGCGC 0.671422 -79 CCATCAGTAATGCGACTTATCCTGCTTTGTTAGCA 28 49 0 TGCACTCCGC 0.92899 -144 TAATTTCACTTGCGACTTTGGCTGCTTTTTGTATG 28 100 1 TGCACTGCGC 0.92899 -93 CTGAAAGGTCCGCTCTATTTCCCGCCTGCAGATAA 29 137 1 CGCCTTCCGC 0.925667 -164 CAGATAAAAACGCACCGCCGCCGACCAAACCGGTA 29 165 1 CGCCCCCCAC 0.97543 -136 GAGACGCAAACGCAATCCACGGTGCCGGATAAAAA 29 200 1 CGCATCGGGC 0.917194 -101 TAAAAACGATCGCGCCACTGGCGATGGTCCATCCC 29 229 1 CGCCCCGCAT 0.745483 -72 ACTTGGGCAACGCGCCTCTTCTGGCCTGCGCTAGC 31 16 0 CGCCCCCTGC 0.948655 -285 ACTTGCGAAACGCCCGACTGCGAACGCTTCTGGTG 31 165 0 CGCCGCCGAC 0.645167 -136 CACCCAGAAGTGCTCCACCACTTGCGAAACGCCCG 31 184 0 TGCCCCCTGC 0.853666 -117 AGCGAAGTATCGCTCTGCGCCCACCCGTCTTCCGC 31 227 1 CGCCTCCCCC 0.939531 -74 *** ** * ** ** Masking position 2 Map Score: 18.8494 Number of sites scoring better than the average of aligned sites = 4457 Number in coding regions = 4144 Number in noncoding regions = 313 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 3 AGCTTTTCATTCTGACTGCAACGGGCAATATG 1 9 1 ATTCACGCAC 0.870759 -181 TGACTCACTATTTTCCACAGCAAATATAAAGTGT 4 52 0 TTTTACGCAA 0.879202 -249 CGATGAGGGATTTTTTCTTACAGCTATTCATAAC 4 103 1 TTTTCTACAC 0.415461 -198 TTTGCCAGGCATTTGACTGGCAGACGTCCCCGCC 11 11 1 ATTTCTGCAA 0.795332 -79 TTGTCGCATTTTTTCGCCCGCAACCAAAATTTGT 13 161 0 TTTTCCGCAC 0.967608 -64 AACCATATGCATTTAAAGTGCATATAAAGTGAAT 17 130 0 ATTTAGGCAA 0.648433 -171 TGCAATCTACATTTACAGCGCAAACATTACTTAT 17 235 1 ATTTAGGCAA 0.648433 -66 TAGCGGCGCAACTTGCCCCGCACCAAATAAAAAA 18 51 0 ACTTCCGCAC 0.83376 -69 TTGAATAAAAATTTAACTGGCATCAGTCCTAAAA 21 195 0 ATTTCTGCAC 0.875182 -106 ATTTCGAGATATTCATACGGCATCTAATACTGAT 22 84 1 ATTCACGCAC 0.870759 -217 GGGTGAAAACATTTTGCCTGCAAATGATTATCAG 22 235 0 ATTTCCGCAA 0.958932 -66 AGACCGGCACATTTATACAGCACACATCTTTGCA 28 155 1 ATTTACGCAA 0.91124 -38 AAGCGTTTTTTTCCTGCAAAGATGTGTGCT 28 173 0 TTTTCCGCAA 0.943036 -20 AGAGCGGACCTTTCAGACCGCAGCCCGTCAGGCT 29 119 0 TTTCACGCAC 0.8269 -182 GCGCGATCGTTTTTATCCGGCACCGTGGATTGCG 29 210 0 TTTTCCGCAC 0.967608 -91 GGTGCCTGACATTTCACCGACAAAGCCCAGGGAA 30 244 1 ATTTCCACAA 0.769492 -33 TCCAGATTGTTTTTATCCCACAGCCACGTACTTC 33 19 1 TTTTCCACAC 0.810272 -276 **** ** *** * Masking position 3 Map Score: 13.789 Number of sites scoring better than the average of aligned sites = 1209 Number in coding regions = 1124 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 GCGCTGGTTACTCTGAAAACGGTCTATGCAA 3 126 1 CCTGAAAACG 0.758839 -41 GATGAAGCCGGCGAATGCCGGCTTTTT 6 7 1 GCGGCGAATG 0.928903 -55 CTGCACCCTCCGGTGCAAATGGGATGGTAAG 8 92 1 CGTGCAAATG 0.898366 -30 TAACAGGGAGTGCGTATGTTTCCAGAAT 14 8 1 GGTGCGTATG 0.767169 -65 GTAATGTTTGCGCTGTAAATGTAGATTGCAG 17 234 0 CCTGTAAATG 0.711554 -67 ACTGCGTACCGGCTGCGAATGGATGTTAA 18 9 0 GCTGCGAATG 0.988072 -111 GGGGCGGTGCGAATGCAGGCGTCG 20 10 0 CGTGCGAATG 0.942638 -15 TCTGTCAATAGCCTGCGGATGAAATCAATTT 21 164 1 GCTGCGGATG 0.96634 -137 AAAACATTTTGCCTGCAAATGATTATCAGGA 22 233 0 GCTGCAAATG 0.978049 -68 CGAAACGCCCGACTGCGAACGCTTCTGGTGA 31 164 0 GCTGCGAACG 0.976645 -137 CTTGTGCCAAGGCTGAAAATGGATCCCCTGA 31 268 1 GCTGAAAATG 0.907715 -33 GAAAGTTACGGTCTGCGAACGCTATTCCACT 33 66 1 GCTGCGAACG 0.976645 -229 GCTAAATTATCACTGAAGATGATTAATTTAA 33 177 1 CCTGAAGATG 0.683565 -118 * ********* Masking position 9 Map Score: 11.7311 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 310 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 AGCGTTTTTGGCTGGCGGCGTAGCGATGCG 3 99 1 GCTGGCGGCG 0.980497 -68 GTCGTTAATCACCAACGGCGGGGACGTCTG 11 31 0 ACCAACGGCG 0.865336 -59 GTTGGTGATTAACGACGGCGTTTTGATTAA 11 45 1 AACGACGGCG 0.886678 -45 AAGCCGCCTGGCTGGCGGCTTAGGAAAGT 15 10 0 GCTGGCGGCT 0.782947 -53 CTGACTGCGTACCGGCTGCGAATGGATGTT 18 13 0 ACCGGCTGCG 0.984735 -107 AAAAGCCGGTACTGACTGCGTACCGGCTGC 18 24 0 ACTGACTGCG 0.945355 -96 CTTCAGCCTGACGGGCTGCGGTCTGAAAGG 29 115 1 ACGGGCTGCG 0.958109 -186 TACCGGTTTGGTCGGCGGCGGTGCGTTTTT 29 170 0 GTCGGCGGCG 0.911441 -131 GTGTAATGCACCTGTCGGCGTGATAATGCA 30 118 1 CCTGTCGGCG 0.932039 -159 TTGCGAAACGCCCGACTGCGAACGCTTCTG 31 168 0 CCCGACTGCG 0.970955 -133 CCTGAAAGTTACGGTCTGCGAACGCTATTC 33 63 1 ACGGTCTGCG 0.861865 -232 CTACTCGCAACGCGACGGCGAGACAAATTT 33 270 0 CGCGACGGCG 0.905256 -25 ********** Masking position 6 Map Score: 8.95394 Number of sites scoring better than the average of aligned sites = 2334 Number in coding regions = 2266 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 6 GCTGTGGAAAATAGTGAGTCATTTTAAAACGGTGAT 4 65 1 ATTATCATTA 0.91601 -236 TAACATTGCGTTTTTTATTCTTTTTATTCACCCACA 17 84 1 TTTATCTTTA 0.880495 -217 TGCCAGTTAAATTTTTATTCAATTAACTGCAAGGTA 21 207 1 ATTATCATTA 0.91601 -94 ATTTATGAGAATAAATACTCATTTAAGGGTGAAAAC 22 259 0 ATAATCATTA 0.580846 -42 TAAATCGATATTTTTTATTCTTTTTATGATGTGGCG 24 63 1 TTTATCTTTA 0.880495 -59 TGCGCCCCTTATGGTCACTCATTTGATCCATTATGC 27 85 0 ATTATCATTA 0.91601 -27 ACTCACTGTATTACTTACTCTCTTCAGCCTGACGGG 29 94 1 TTTATCTTTA 0.880495 -207 CTTAATCCTCTTCGTCAATAAATTGAGACCAGACCA 30 17 1 TTTATAATTA 0.740242 -260 CAAATCGAGATTAATAAGTCATTTAAACCATTTTGA 32 65 1 TTTATCATTA 0.948698 -172 GCCTCGACTATTAGTAACTCAGTTTATCTTATCGAA 32 142 0 TTTATCATTA 0.948712 -95 ATCTGATGGTTTAGTAATTAAATTAATCATCTTCAG 33 189 0 TTTATAATTA 0.740239 -106 ** * * *** ** * Masking position 7 Map Score: 5.05213 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 35 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 7 GGATGTTGTGTACTCTGTAATTTTTAT 1 173 0 TGTGTACCTG 0.957158 -17 GGCTTTTTTCTGTGTTTCCTGTACGCG 2 7 0 TGTGTTTCTG 0.836336 -75 AGCGATGCGCTGGTTACTCTGAAAACGGTCT 3 120 1 TGGTTACCTG 0.745009 -47 TGTGTTTACTGATATGAAAAG 5 1 1 TGTGTTTCTG 0.836336 -30 CACCAATAATTGTTGGCGCTGTGTACAGCAT 7 136 1 TGTTGGCCTG 0.939065 -165 TAATAAGTAATGTTTGCGCTGTAAATGTAGA 17 240 0 TGTTTGCCTG 0.972856 -61 TTGAGACACTTGTTTGCACAGAGGATGGCCC 23 59 1 TGTTTGCCAG 0.834523 -21 CCACATCAACTGTGTGGTCTGGTCTCAATTT 30 36 0 TGTGTGGCTG 0.916583 -241 ACACAGTTGATGTGGGTACTGACCGTAAACC 30 52 1 TGTGGGTCTG 0.889558 -225 ATTAACACAATGTTTACTCTGGTGCCTGACA 30 224 1 TGTTTACCTG 0.933377 -53 ******* *** Masking position 1 Map Score: 4.10023 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 245 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 8 TGCGACGCGAGCGGCATTTTAGGACATATCTTC 4 14 0 GCGGCTTTGG 0.987914 -287 CACCCCGGAATATGTGCCGATACGTGT 7 5 1 CCGGATATGC 0.749248 -296 TCACCGGCCTATAAGGAAATTATTCA 12 98 0 CCGGCTATGG 0.963336 -16 ATTTACAAGCGCGGCAATTTCGCCCAGTCTTCA 13 125 1 GCGGCATTGC 0.941907 -100 CAGTTAGCCTCCGCCGTTTATGCACTTTTATCA 17 185 1 CCGCCTTTGC 0.956629 -116 GGTTGTTCTCCCGGCTTATGAGCTGGTTTGCTT 19 11 0 CCGGCTATGC 0.957573 -24 GCTACCGCCCCTGGCTTTTTAGCTACCAATACA 21 97 0 CTGGCTTTGC 0.933455 -204 ATAATTCAGACTGGTCTTTCAGGCATCCAGACA 21 131 0 CTGGTTTTGG 0.562137 -170 CGATTCTGCTGTGGCTTTTGCGGCTAGTGTATC 27 24 1 GTGGCTTTGG 0.942098 -88 TTGCGCCCCTTATGGTCACTCATTT 27 97 0 GCGCCCTTGG 0.90769 -15 GATAATTGCCGCGGACTTTCTGCGTGCTAACAA 28 25 1 GCGGATTTGC 0.906365 -168 TATAATTTTAACGGCTATTTGGGATTTGCTCAA 30 148 1 ACGGCATTGG 0.724816 -129 CTTGGGCAACGCGCCTCTTCTGGCCTGCGCTAG 31 17 0 GCGCCCTTGG 0.907658 -284 ***** *** ** Masking position 9 Map Score: 6.93362 Number of sites scoring better than the average of aligned sites = 1001 Number in coding regions = 908 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 9 TCCCATTTGCACCGGAGGGTGCAGTTCTTT 8 86 0 ACCGGAGGGT 0.889046 -36 GCCCACCGGAACGGCAGGCCTGAGAA 12 7 0 ACGGCAGGCC 0.974116 -107 GGCCTGCCGTTCCGGTGGGCCTTGTTTTTT 12 17 1 TCCGGTGGGC 0.897973 -97 ATTGATTTCATCCGCAGGCTATTGACAGAA 21 163 0 TCCGCAGGCT 0.802999 -138 ACAAATCATCACCGCAGGACCATAGTATTT 22 37 0 ACCGCAGGAC 0.92919 -264 GACCTTTCAGACCGCAGCCCGTCAGGCTGA 29 117 0 ACCGCAGCCC 0.916553 -184 CCTGCGCTAGCGCAGGCCAGAAGAGGCG 31 9 1 AGCGCAGGCC 0.957773 -292 AGGTGATTGAACGGCTGGCCACGTTCATCA 31 104 1 ACGGCTGGCC 0.962555 -197 AGAGCGGAAGACGGGTGGGCGCAGAGCGAT 31 235 0 ACGGGTGGGC 0.933543 -66 GGAATCAAACAGCGGTGGGCAGTGACTAAA 33 234 0 AGCGGTGGGC 0.894362 -61 ********** Masking position 4 Map Score: 6.39688 Number of sites scoring better than the average of aligned sites = 711 Number in coding regions = 659 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 TCTGAACTGGTTACCTGCCGTGAGTAAATTAA 1 82 1 TTCCTGCGTG 0.863928 -108 ATTCTGAATTTCGCCAAACGTGCCACTGAAGG 7 195 0 TCCCAACGTG 0.842342 -106 CCGTCGTTAATCACCAACGGCGGGGACGTCTG 11 31 0 TCCCAAGGCG 0.941727 -59 CTTGCGCCTTTTTCCTGTGGCGTGAATAATTT 12 76 1 TTCCTGGGCG 0.950505 -38 TTTTACGTCTTCTCCTGCGATGATAGAAAGCA 29 12 1 TCCCTGGATG 0.963247 -289 GGATGGACCATCGCCAGTGGCGCGATCGTTTT 29 231 0 TCCCAGGGCG 0.990557 -70 TTTTAGTAATTCACCTGGGATGGACCATCGCC 29 248 0 TCCCTGGATG 0.963247 -53 AGGGGCTGAATCCCCTGGGTTGTCACCAGAAG 31 142 1 TCCCTGGTTG 0.91207 -159 CCCTGGGTTGTCACCAGAAGCGTTCGCAGTCG 31 154 1 TCCCAGAGCG 0.921346 -147 GTCGGGCGTTTCGCAAGTGGTGGAGCACTTCT 31 182 1 TCCAAGGGTG 0.860316 -119 TGAAAATGGATCCCCTGACACGAGGTAGTT 31 281 1 TCCCTGCACG 0.939776 -20 ** **** **** Masking position 1 Map Score: 6.9513 Number of sites scoring better than the average of aligned sites = 946 Number in coding regions = 885 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 11 GGTTAAAGTATTTAGTGACCTAAGTCAATAAA 1 117 0 TTTATGACCA 0.908145 -73 TGCCGGCTTTTTTAATGCGATAATTTAATCTT 6 26 1 TTTATGCGAA 0.92274 -36 ACAAATAATTTTTAATGCGCAAATGTAGCGTA 13 92 0 TTTATGCGCA 0.981209 -133 TTTATCAAATTTTAGTGAGGCATAAATCACAT 16 93 0 TTTATGAGGA 0.887438 -82 TTTACTGGAAATTACTGCGCCATTCTGAC 17 8 0 ATTATGCGCA 0.880202 -293 GCAATCTACATTTACAGCGCAAACATTACTTA 17 236 1 TTTAAGCGCA 0.880202 -65 TCTGCTTGCTTTTAATGCCATACCAAACGTAC 23 25 1 TTTATGCCAA 0.841243 -55 TCTGATTTCTTTTATTGAGCTAGTCAAAATGC 25 67 0 TTTATGAGCA 0.957052 -24 CTGGTCTCAATTTATTGACGAAGAGGATTAAG 30 17 0 TTTATGACGA 0.777673 -260 GATCGATTTTTTTAGTGCGCAAGAGGGCTAAA 33 151 1 TTTATGCGCA 0.981209 -144 **** ***** * Masking position 4 Map Score: 5.88571 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 94 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 TATGCCTTGTGACTGGCTTGACAAGCTTTT 4 213 1 GACTGGCTTG 0.91422 -88 CGTATACACAGACTGGACGGAAGCGACAAT 7 58 0 GACTGGACGG 0.807837 -243 GCAGTTCTTTGCGTGGCCCGGCGATCTTAT 8 66 0 GCGTGGCCCG 0.82876 -56 TAAAAAAGCCGCCTGGCTGGCGGCTTAGGA 15 15 0 GCCTGGCTGG 0.9848 -48 TTTAACAACTGCATGGATTGACTGGAGATA 15 41 1 GCATGGATTG 0.739215 -22 GCACTTTTATCACTGGCTGGCACGAACCCT 17 206 1 CACTGGCTGG 0.879766 -95 ACGCTACCGCCCCTGGCTTTTTAGCTACCA 21 102 0 CCCTGGCTTT 0.639282 -199 AGGGGCGGTAGCGTGTCTGGATGCCTGAAA 21 118 1 GCGTGTCTGG 0.839896 -183 ATAAAAAAGAGCGTGGATTGGGTACAATCC 25 24 1 GCGTGGATTG 0.936678 -67 TTATCCGGCACCGTGGATTGCGTTTGCGTC 29 202 0 CCGTGGATTG 0.883223 -99 TCACGGTAACGCCTGTACGGTAAACTATGC 30 84 0 GCCTGTACGG 0.725722 -193 GGGCTGAATCCCCTGGGTTGTCACCAGAAG 31 144 1 CCCTGGGTTG 0.826039 -157 ********** Masking position 4 Map Score: 2.23065 Number of sites scoring better than the average of aligned sites = 1873 Number in coding regions = 1804 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 13 CACTGATATCCCTCCCTGTTTATCATTAAT 3 58 1 CCTCCCTGTT 0.93273 -109 AAACATACGCACTCCCTGTTA 14 2 0 ACTCCCTGTT 0.974307 -71 CAGATGACCTACTCCCTGATTATGTGACAG 16 12 1 ACTCCCTGAT 0.986063 -163 TTTGGTTATAACTCCTTGATTTCCAGTTAG 17 162 1 ACTCCTTGAT 0.916286 -139 ATAATGTTATATTTCCTGATAATCATTTGC 22 220 1 ATTTCCTGAT 0.787165 -81 AACTCAAATTCCCTGATAATTGCCGCG 28 8 1 ATTCCCTGAT 0.959851 -185 ********** Masking position 7 Map Score: 1.56203 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 42 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 14 TATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTG 1 39 1 TTGGTTAAAA 0.817316 -151 CCTCGTTACCTTTGGTCGAAAAAAAAAGCCCGCA 2 50 0 TTGGCGAAAA 0.957347 -32 AACCAAAATTTGTGGCTGAAGACTGGGCGAAATT 13 140 0 TTGGTGAAAT 0.877747 -85 AAATTTTGGTTGCGGGCGAAAAAATGCGACAATA 13 163 1 TCGGCGAAAA 0.89242 -62 ACGTTTGCGATGTGGGTGAATAAAAAGAATAAAA 17 96 0 TTGGTGAAAA 0.975647 -205 AATACTCATTTAAGGGTGAAAACATTTTGCCTGC 22 248 0 TAGGTGAAAA 0.945738 -53 CCGCAGCCCGTCAGGCTGAAGAGAGTAAGTAATA 29 102 0 TAGGTGAAAA 0.945738 -199 GTGGAGCACTTCTGGGTGAAAATAGTAGCGAAGT 31 201 1 TTGGTGAAAA 0.975647 -100 * *** **** * * Masking position 9 Map Score: 2.67267 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 61 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 15 TCCTAAAATGCCGCTCGCGTCGCAAACTGAC 4 23 1 CCGCTCGCTC 0.964118 -278 TATCTTATACCCGCTATTATCGTTGCGTAAT 16 64 1 CCGCTATTTC 0.903657 -111 CCGTAATAACCCTTTCTCATCAACGACTGCA 21 32 1 CCTTTCTCTC 0.792845 -269 GGGTACAATCCCGCTCTTATCACCGCATTTT 25 43 1 CCGCTCTTTC 0.98636 -48 AAATCTTCCCGTTCTTTTCAGACA 26 6 0 CCGTTCTTTC 0.960683 -19 TATAAATGTGCCGGTCTCCTCTTGGCACATC 28 141 0 CCGGTCTCTC 0.961241 -52 CACCCGTCTTCCGCTCTTCCCTTGTGCCAAG 31 248 1 CCGCTCTTCC 0.95699 -53 ******** ** Masking position 5 Map Score: 1.64202 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 106 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987