AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00252_ecoli_reg_300.orf -o00252_ecoli_300.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 Purged sequences: BIME145 77 BIME Input sequences: #1 panD 273 aspartate 1-decarboxylase #2 pepD 260 aminoacyl-histidine dipeptidase (peptidase D) #3 asnB 247 asparagine synthetase B #4 BIME40 115 BIME #5 nagD 47 N-acetylglucosamine metabolism #6 nagA 59 N-acetylglucosamine-6-phosphate deacetylase #7 nagB 300 glucosamine-6-phosphate deaminase #8 aspC 184 aspartate aminotransferase #9 ompF 300 outer membrane protein 1a (Ia;b;F) #10 asnS 168 asparagine tRNA synthetase #11 pncB 265 nicotinate phosphoribosyltransferase #12 ycfC 35 orf, hypothetical protein #13 ymfC 201 orf, hypothetical protein #14 dadA 300 D-amino acid dehydrogenase subunit #15 ycjL 121 probable amidotransferase subunit #16 ycjC 26 orf, hypothetical protein #17 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #18 goaG 37 4-aminobutyrate aminotransferase #19 gadB 300 glutamate decarboxylase isozyme #20 sppA 160 protease IV, a signal peptide peptidase #21 ansA 166 cytoplasmic L-asparaginase I #22 aspS 276 aspartate tRNA synthetase #23 nadB 300 quinolinate synthetase, B protein #24 b2654 300 orf, hypothetical protein #25 b2657 171 putative enzyme #26 b2658 138 orf, hypothetical protein #27 b2659 230 orf, hypothetical protein #28 gabD 22 succinate-semialdehyde dehydrogenase, NADP-dependent activity #29 alaS 128 alanyl-tRNA synthetase #30 oraA 68 regulator, OraA protein #31 recA 79 DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease #32 ygaD 144 orf, hypothetical protein #33 mltB 255 membrane-bound lytic murein transglycosylase B #34 ansB 175 periplasmic L-asparaginase II #35 yggN 71 orf, hypothetical protein #36 yggH 160 orf, hypothetical protein #37 argG 300 argininosuccinate synthetase #38 gadA 210 glutamate decarboxylase isozyme #39 yhjA 300 putative cytochrome C peroxidase (EC 1.11.1) #40 asnA 151 asparagine synthetase A #41 argC 153 N-acetyl-gamma-glutamylphosphate reductase #42 argH 60 argininosuccinate lyase #43 dnaB 82 replicative DNA helicase; part of primosome #44 alr 52 alanine racemase 1 #45 aspA 300 aspartate ammonia-lyase (aspartase) #46 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #47 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #48 hflK 85 protease specific for phage lambda cII repressor #49 yjeT 81 orf, hypothetical protein #50 purA 103 adenylosuccinate synthetase Motif number 1 AGCCACACGGAAGACAGGGAAG 1 2 0 AAGACAGGGA 0.803873 -272 TGCTTCGTTAACGACAGGGTAGAAAGGTAGA 1 249 1 ACGACAGGGA 0.856341 -25 ACTTTATCCCGCGTCAGGGAGAGGCAGTGCG 2 134 0 GCGTCAGGGG 0.921313 -127 AAATGCCGAAAAAACAGGACTTTGGTCCTGT 8 28 1 AAAACAGGAT 0.710154 -157 CGCGATTTACGCAACAGGAATAGACTGAACA 11 43 0 GCAACAGGAT 0.838246 -223 TATTGCCGCAGAGTCAGGGAGATGTGAGCCA 14 176 1 GAGTCAGGGG 0.889513 -125 CAGTTTGTGAACGTCAGGGCGCAGAGATCCC 17 221 0 ACGTCAGGGG 0.889513 -54 TGATAGACGTGAAACAGGAGTCATA 17 260 1 GAAACAGGAT 0.78086 -15 AATAAATATCACGACAGGAGTTAATCAA 20 8 0 ACGACAGGAT 0.864192 -153 GTATATACGTGAGGCAGGGGGAGCGCACCTG 21 113 0 GAGGCAGGGG 0.943271 -54 GGTCACCTGCGCAGCAGGGGGCATCCGCCGG 22 234 1 GCAGCAGGGG 0.931231 -43 ATATATAGATAAAGCAGGAATATGGAGCGCA 26 64 1 AAAGCAGGAT 0.57639 -75 AAGGCAAAGTGAGACAGGAAATGAATAACTA 27 153 0 GAGACAGGAA 0.769477 -78 CCTTTGAAAACAGGATGTAGCG 28 7 1 AAAACAGGAG 0.865873 -16 CAGCACAGCGACGGCAGGGTGTAAACCGGAA 36 46 1 ACGGCAGGGG 0.943271 -115 TCTTTTATCGGAGACAGGAAGAGTTTAGTGT 37 188 0 GAGACAGGAG 0.943714 -113 GCCATCATAAAAAACAGGGAGATACGCTTTT 39 203 0 AAAACAGGGG 0.920182 -98 TTAATCATAAGCAACAGGACGCAGGAGTATA 40 127 1 GCAACAGGAG 0.931761 -25 GCGTCGAAAGACAACAGGGATCACCGCATAA 48 47 1 ACAACAGGGT 0.864192 -39 ********* * Masking position 6 Map Score: 16.3559 Number of sites scoring better than the average of aligned sites = 646 Number in coding regions = 567 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 2 GCCAACCACGTCCGCAGACGTGGTTGCTAT 4 9 0 TCCGCGCGTG 0.874162 -107 AACCTGGATTTGCGCAGACAGGCGTCAATCCG 7 223 0 TGCGCGCAGG 0.871797 -78 AGATGCCTAATCCGCCAACGGCTTACATTTTA 7 263 1 TCCGCACGGC 0.970599 -38 AAAAACAGCCTGCGTTTTCATCAGTAATAGTT 8 95 1 TGCGTTCATC 0.645261 -90 AGAAGGGAAGTCCGCTATCAGGGTAACGGGAG 8 141 0 TCCGCACAGG 0.934722 -44 CGCAGTAGCGTCCTCGTACAGGAGCGTTTAGT 11 239 0 TCCTCTCAGG 0.779406 -27 ACGTTGCATATGCGTTTGCGTCCTGCGATACG 13 53 1 TGCGTTCGTC 0.702161 -149 AATTTGTCGTTCCGCCATCGGCTAATCGCATT 22 16 0 TCCGCACGGC 0.973231 -261 GCAGGGGGCATCCGCCGGCAGCTAAGTTAAGG 22 247 1 TCCGCGCAGC 0.963376 -30 TAGATAATGATCCGTCTACAGCATGACAAACA 23 30 0 TCCGTTCAGC 0.899437 -271 CACCACCTAATCCTCCACCAGCCAGTAACTTC 23 154 1 TCCTCACAGC 0.87434 -147 CTCGCCGCCCTGCGTCAGCGTGTTTAGCAACT 23 193 1 TGCGTACGTG 0.544862 -108 TTTTTATGTTTCCGTATACATCATATTACTCT 24 259 1 TCCGTTCATC 0.781759 -42 GACTACCGCTTCCTTGTGCGGGGCGTGATGCT 33 191 1 TCCTTTCGGG 0.592309 -65 GCCGGAAAGCTGCGCCTCCGGCCAACAAAAC 42 10 0 TGCGCTCGGC 0.948871 -51 CAAAAATAGTTGCGCAAACATCTTGAAATTTT 45 105 0 TGCGCACATC 0.851485 -196 ACGGTAGAAATCCTCAAGCAGCATATGATCTC 45 216 1 TCCTCACAGC 0.874339 -85 TGGAGTCATATCCTCTGGCGTCGAAAGACAAC 48 30 1 TCCTCGCGTC 0.77152 -56 ***** * **** Masking position 1 Map Score: 13.9957 Number of sites scoring better than the average of aligned sites = 2788 Number in coding regions = 2512 Number in noncoding regions = 276 Number of orfs with sites within 600 bp upstream = 157 Fraction of orfs with sites within 600 bp upstream = 0.0252168 Motif number 3 ATCGATAATTTTTAGCGGGTTTTATTGAATGTTTATAT 3 52 0 TGCTTTATTA 0.795757 -196 CACAGTGCTGCTTTGCGGCATTTTTTTAAACAAGCAAA 3 182 1 CGCTTTTTTA 0.880822 -66 GCTCCTTGCTCAGGGCAATATTTTTTAAAATCGGGGGT 6 28 1 CGCTTTTTTA 0.880822 -32 CAGGCGTCAATCCGACCTGATTTTTTGAATGATAAAAT 7 199 0 TACTTTTTTA 0.483614 -102 AAACAGGACTTTGGTCCTGTTTTTTTTATACCTTCCAG 8 39 1 TTCTTTTTTA 0.839383 -146 CAGGGAGCTAATCGGCTCCCTTTTTTTACCTTTAATTC 10 17 1 AGCTTTTTTA 0.781586 -152 AAATAACCTTTAGCATCTTTTATAGAGTCTGGTGTT 11 9 1 TGCTTTATAA 0.544454 -257 CAAACGCCTTTATTGCTACATTTTTATAACATACACCG 11 102 1 TGCTTTTTAA 0.835456 -164 GAGTATACCTTGTTTCGCAATTTATTGAACCCCGATCA 11 175 0 TTCTTTATTA 0.5516 -91 ACGGATGCTTTAGAGCAATTTTTTGTTAATGATTTGTA 13 82 1 TGCTTTTGTA 0.860721 -120 AATGACCTTTATGTTCAATATTTTTTCAATCTAGCAGT 15 59 0 ATCTTTTTTA 0.530485 -63 ACTTTATCGATAAATCCTACTTTTTTAATGCGATCCAA 19 254 1 TTCTTTTTTA 0.839383 -47 TTTCCAGTATAATAGCCGCCTTTTTTCATTCAGTTGTG 22 173 1 AGCTTTTTTA 0.781586 -104 TGCTGATAGGTAGAGCAACCTTTATTAAG 26 2 0 TGCTTTATTA 0.795756 -137 TGCTATCTTGTCCGGCATAAATTTTTGACTGACAGAGG 32 112 1 TGCATTTTTA 0.504335 -33 TTATGCCGTTTAATTCTTCGTTTTGTTACCTGCCTCTA 34 41 1 TTCTTTTGTA 0.661156 -135 TTATAGTGATCCACGCCACATTTTGTCAACGTTTATTG 37 57 1 CGCTTTTGTA 0.734004 -244 AAAACAACACCAAATCGGTATTTTTATAAATTCCATTG 39 43 0 CTCTTTTTAA 0.417194 -258 TTCATTCTATTTTAGCCTTCTTTTTTAATGAATCAAAA 40 36 1 TGCTTTTTTA 0.943026 -116 AACTCTGTTTCCTTATTTTGAAATTCAATGCCG 42 38 0 TTCTTTTGAA 0.374434 -23 TTGAGACGTATCGTGCGCAATTTTTTCAGAATCGAAAG 46 21 1 TGCTTTTTTA 0.943026 -65 GGTTTCGGGCTGTTTTTTTACACGGGGAGCCA 47 5 1 TGCTTTTTAA 0.835456 -71 * ** ****** * Masking position 12 Map Score: 13.6718 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 192 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 4 CAAAAATCGGGCAATACTGCGTGAGAATTTC 1 200 1 GCAATCTGCG 0.896463 -74 CGAGATTATAGAGATCTGGCGCACTAAAAAC 2 73 1 GAGATTGGCG 0.878609 -188 CACTTTGTCAGCAATTTGGCCCCCGTAAAAT 3 23 1 GCAATTGGCC 0.960395 -225 CTGTGCGCAAGCGATTTGGCGGTGAAAAAAT 3 156 0 GCGATTGGCG 0.958007 -92 AGCGCATCAGGCAGTTTGGCGTTTGTCATCA 4 43 0 GCAGTTGGCG 0.842677 -73 ACCTTCCAGAGCAATCTCACGTCTTGCAAAA 8 68 1 GCAATTCACG 0.780078 -117 CGTCTCTATGGAAATATGACGGTGTTCACAA 9 58 1 GAAATTGACG 0.839647 -243 TGACTCTGCGGCAATATGGCGTCTTTAGTAT 14 161 0 GCAATTGGCG 0.979489 -140 CCGGGTAAGCGCAATGCGCCCGGCAATCTAT 17 28 1 GCAATCGCCC 0.551963 -247 TATTTATCGTGAGATATTACGCGAATAATAT 19 178 0 GAGATTTACG 0.487021 -123 CACCTTTATAGCAAACTGGCGTAGAGTCTGA 22 74 1 GCAAATGGCG 0.871191 -203 TATTATACTGGAAATTCTGCCGCACCGTAAG 22 156 0 GAAATCTGCC 0.582446 -121 TGGCTTCACTGCAAAATGACCGTTAGTAAAC 27 58 0 GCAAATGACC 0.54275 -173 TCAAGCTAACGAAATATCGCCACCAGCTCCA 29 95 0 GAAATTCGCC 0.623128 -34 TGTTGGCGTTGCAATTTTACGAGGAGGATTC 32 63 0 GCAATTTACG 0.862334 -82 CTCTGTATGGGAAATTTGACGTTAAACAATT 34 113 0 GAAATTGACG 0.839647 -63 TCGCTGTGCTGCAATCTTGCCCCCAACAACA 36 26 0 GCAATTTGCC 0.901992 -135 CGGGGAGCCAGCGATCCTGCGTTCCCCGCTG 47 33 1 GCGATCTGCG 0.805311 -43 ***** ***** Masking position 10 Map Score: 10.0767 Number of sites scoring better than the average of aligned sites = 1212 Number in coding regions = 1127 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 5 GCGGTGAAAAAATAAAAAACGTAATGGTGA 3 139 0 AATAAAAAAC 0.640358 -109 TTTGCAGCAAAATAAAAATACGGCTTGAAA 7 12 0 AATAAAAATA 0.728276 -289 AAGTTCTGTCAATAAAAATTTACGGAACTA 9 231 0 AATAAAAATT 0.625568 -70 TGGCAGGTGTCATAAAAAAAACCATGAGGG 9 272 1 CATAAAAAAA 0.81191 -29 GCCAGCTCACCATAAAAAAGCCGCATGTTG 14 203 1 CATAAAAAAG 0.8475 -98 ACAGAATGCGCATAAAAATAACAGCATAAA 19 96 1 CATAAAAATA 0.864294 -205 TGCCCGAACTCATAAAAATTAACAAAATTT 22 43 0 CATAAAAATT 0.798794 -234 CTTTTCACTCCATAAAAATAAACTTCGTAT 24 45 1 CATAAAAATA 0.864294 -256 TATACGGAAACATAAAAATGTTTAATTGTT 24 247 0 CATAAAAATG 0.891298 -54 AATTAAACGGCATAAAAAAGTATTATGCCG 34 26 0 CATAAAAAAG 0.8475 -150 ATTTATTTTGCATAAAAATTCAGTGAGAGC 37 236 1 CATAAAAATT 0.798794 -65 TTATTATCGTAATAAAAATCGCCCAAACAT 38 34 0 AATAAAAATC 0.724296 -177 ATTTGAAGGCAATAAAAAAGTAGGATTTAT 38 173 0 AATAAAAAAG 0.700483 -38 ACAAAGCCATCATAAAAAACAGGGAGATAC 39 209 0 CATAAAAAAC 0.808833 -92 AGTATTTATGAATAAAAATACACTAACGTT 41 52 1 AATAAAAATA 0.728276 -102 ********** Masking position 5 Map Score: 8.57792 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 114 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 6 AGGCGCGCTATCGTCAGCCACCTCTTTATTG 1 57 1 TCTCAGCCAC 0.832032 -217 ACTTTATCCCGCGTCAGGGAGAGGCAGTGCG 2 134 0 GCTCAGGGAG 0.875486 -127 TAAGCGTAGCGCATCAGGCAGTTTGGCGTTT 4 50 0 GCTCAGGCAG 0.932174 -66 TCTTTATGTGTCTGCAGGCATCTTTCCATTC 9 183 0 TCGCAGGCAT 0.939204 -118 TATCATCAGGGAGCTAATCGGCT 10 3 1 TCTCAGGGAG 0.963224 -166 ACAATAAACATCTTCAGGAACTGCTGGAGTA 11 208 0 TCTCAGGAAC 0.880812 -58 CCGGTACTTGTCAGCAGGAATTGCGGACTGT 20 74 0 TCGCAGGAAT 0.792818 -87 GCAGGGGGCATCCGCCGGCAGCTAAGTTAAG 22 247 1 TCGCCGGCAG 0.850859 -30 GTTGGGTTACTCTTCAGGCAGTTAAATGGGC 23 110 0 TCTCAGGCAG 0.980841 -191 GATAGCACTTTCGTCAGGAAGATGGTGTTGG 32 88 0 TCTCAGGAAG 0.926908 -57 ACCGGAACTTTCCGCAGCCACGGCCTTATCA 36 70 1 TCGCAGCCAC 0.802701 -91 GGACGTAAAATCTGCAGGCATTATAGTGATC 37 37 1 TCGCAGGCAT 0.939204 -264 CCAGAACGTATCGTCAGGGTCTGCTTCATAT 43 18 1 TCTCAGGGTC 0.582856 -65 ACGGTAGAAATCCTCAAGCAGCATATGATCT 45 216 1 TCTCAAGCAG 0.743375 -85 AGCCACCGCATCCTCAGGGATGTCGGTGGTT 49 38 1 TCTCAGGGAT 0.905862 -44 ** ******** Masking position 5 Map Score: 12.4594 Number of sites scoring better than the average of aligned sites = 604 Number in coding regions = 547 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 51 Fraction of orfs with sites within 600 bp upstream = 0.00819146 Motif number 7 TGAAAACGCAGGCTGTTTTTGCAAGACGTG 8 85 0 GGCTGTTTTT 0.905839 -100 CAATCTAGCAGTGGGTTTTCATTTTTGCAA 15 41 0 GTGGGTTTTC 0.510699 -81 ATATTTTAAGGTCTGATTTTTACGTGATAA 19 56 1 GTCTGATTTT 0.899108 -245 CTGGCGTAGAGTCTGATTTCAGGCCCGATA 22 89 1 GTCTGATTTC 0.755412 -188 TCCGTAACGCATCTGTTTTTGTTTGTCATG 23 11 1 ATCTGTTTTT 0.642665 -290 GCAAATGCTGGCCTGATTTTTCTTGAGGGA 35 47 1 GCCTGATTTT 0.650165 -25 GAAGAGTTTAGTGTGTTTTTTGTAAAATAA 37 172 0 GTGTGTTTTT 0.843432 -129 CGATAATAAAGTCTGTTTTTAATATTATCA 38 55 1 GTCTGTTTTT 0.961635 -156 TTGCATGTGTGTCGGTTTTTGTTGCTTAAT 40 102 1 GTCGGTTTTT 0.93339 -50 CACTTTAAGTGTCGGTTTTTACCCCTTAAT 45 177 0 GTCGGTTTTT 0.93339 -124 GGTTTCGGGCTGTTTTTTTACACGGGG 47 8 1 GGCTGTTTTT 0.905839 -68 ACCTCGATCAGTCTGTTTTTTGT 50 4 0 GTCTGTTTTT 0.961635 -100 ********** Masking position 7 Map Score: 9.0861 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 120 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 8 AACAATCTGATTACAGAACATCGGCAGTAC 7 44 0 TTACAGAACA 0.957779 -257 CTTACCCGGCTTACAGAACAAAAAGA 17 7 0 TTACAGAACA 0.957779 -268 GTGGATTTTGTTACAGCACAGTCCGCAATT 20 57 1 TTACAGCACA 0.956962 -104 GGAGTTAACATTAGAGAACAGATTATCTGG 27 107 0 TTAGAGAACA 0.789674 -124 GGGGGCAAGATTGCAGCACAGCGACGGCAG 36 33 1 TTGCAGCACA 0.890473 -128 TAATGCCCGTTTTCAGAACACTTTCACAAG 36 128 1 TTTCAGAACA 0.907991 -33 TGTTTTTCATTTTCAGAACATTCAATCCTG 39 75 1 TTTCAGAACA 0.907991 -226 TTTTTCAGAGTTACAGCACTTTTTGCACTC 50 41 0 TTACAGCACT 0.799386 -63 ********** Masking position 5 Map Score: 4.42173 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 37 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 AATTTTTAGCGGGTTTTATTGAATGTTTATA 3 53 0 GGGTTTTTTG 0.77135 -195 CTGCTTTGCGGCATTTTTTTAAACAAGCAAA 3 189 1 GCATTTTTTA 0.787452 -59 TTACCCTCATGGTTTTTTTTATGACACCTGC 9 274 0 GGTTTTTTTA 0.841107 -27 AATAACATTAGGATTTTGTTATTTAAACACG 19 205 1 GGATTTTTTA 0.962261 -96 ACACGAGAGTGGATTTTGTTACAGCACAGTC 20 49 1 GGATTTTTTA 0.962261 -112 TCTTCTGGATGGATTTGTTTACGTTCTTTTG 25 51 0 GGATTTGTTA 0.856268 -121 TTTCTGCTTAGGATTTTGTTATTTAAATTAA 38 115 1 GGATTTTTTA 0.962261 -96 AGGATTTTCTTATGCGGATTGA 40 2 1 GGATTTTTTA 0.962261 -150 TACGGCTGGTGGGTTTTATTACGCTCAACGT 41 77 0 GGGTTTTTTA 0.935228 -77 ******* *** Masking position 6 Map Score: 5.40876 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 24 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 TAAGTGATTCGGGGGAGCGAACGCAGCCAA 17 122 1 GGGGGAGCGA 0.971542 -153 TGAACGTCAGGGCGCAGAGATCCCCGGGCC 17 215 0 GGCGCAGAGA 0.875708 -60 ACGTGAGGCAGGGGGAGCGCACCTGATACT 21 108 0 GGGGGAGCGC 0.865396 -59 GCTGACGCAGGGCGGCGAGAAAAAGAGAAG 23 182 0 GGCGGCGAGA 0.918744 -119 CCGTTTTATCGGGGCAGATATAACATTAAA 27 11 0 GGGGCAGATA 0.87986 -220 CCGATAAAACGGGGCAGATAATATGTTTAG 27 29 1 GGGGCAGATA 0.87986 -202 CAACAGGTTAGGGGGAGTTAACATTAGAGA 27 120 0 GGGGGAGTTA 0.910718 -111 TTTACAAGAGGGGGGCGTGAGCTTCCCTCT 32 14 1 GGGGGCGTGA 0.974691 -131 AAGTCCGTATCGGGCAGTGACTACCGCTTC 33 173 1 CGGGCAGTGA 0.851162 -83 CTTCCTTGTGCGGGGCGTGATGCTTTACCA 33 199 1 CGGGGCGTGA 0.901743 -57 CACTGTTGTTGGGGGCAAGATTGCAGCACA 36 23 1 GGGGGCAAGA 0.788962 -138 ********** Masking position 4 Map Score: 5.34555 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 125 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 11 CCTGCAATACTGTTTTGCGGGTGATCGACA 2 229 1 TGTTTTGCGG 0.890522 -32 CGCACAGTGCTGCTTTGCGGCATTTTTTTA 3 180 1 TGCTTTGCGG 0.789176 -68 GCCGTATTTTTATTTTGCTGCAAATTGTAC 7 18 1 TATTTTGCTG 0.546838 -283 CTGAACGGAATTTTATGCTGGATAAAAAGG 14 117 1 TTTTATGCTG 0.789858 -184 TGGTAAGGTGTTTTATGCTGTTATTTTTAT 19 107 0 TTTTATGCTG 0.789858 -194 GCGCACCTGATACTATGCGGATAAGGAAAT 21 92 0 TACTATGCGG 0.766892 -75 TGTTTTTGTTTGTCATGCTGTAGACGGATC 23 24 1 TGTCATGCTG 0.794521 -277 CATAGCATCATGTTGTGCGGATAAACACCT 23 245 0 TGTTGTGCGG 0.826732 -56 CACAACATGATGCTATGCTGACCAAACCAT 23 258 1 TGCTATGCTG 0.859753 -43 TTTTACTCCTGTCATGCCGGGTAATACCG 31 61 0 TGTCATGCCG 0.791233 -19 CATAAAAAAGTATTATGCCGTCTTAAAATA 34 16 0 TATTATGCCG 0.786515 -160 CATAATACTTTTTTATGCCGTTTAATTCTT 34 29 1 TTTTATGCCG 0.786515 -147 AGGATTTTCTTATGCGGATTGATGATT 40 8 1 TCTTATGCGG 0.807448 -144 GCTCCATATTTGTTATGCGGTGATCCCTGT 48 60 0 TGTTATGCGG 0.96203 -26 ********** Masking position 6 Map Score: 7.85757 Number of sites scoring better than the average of aligned sites = 168 Number in coding regions = 135 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 12 CAATTCGTTACAGGCGATACATGGCACGCT 1 115 1 CAGGCGATAC 0.918492 -159 GTTAACGAAGCAGGCGATGCCTGCTTTGAG 1 231 0 CAGGCGATGC 0.947286 -43 CAATATATTGCAGGAGCTGCGTAGGCCTGA 4 81 0 CAGGAGCTGC 0.925021 -35 AAAAAATTCTCCGGCGACGCGGTTTTTAAC 14 46 0 CCGGCGACGC 0.96154 -255 GGGCGTTCAGCAGGAGATACTAAAGACGCC 14 145 1 CAGGAGATAC 0.940571 -156 CGTGATAATTCAGGAGACACAGAATGCGCA 19 78 1 CAGGAGACAC 0.953219 -223 AGCAAAAGGGCCGCAGATGCGACCCTTGTG 30 26 0 CCGCAGATGC 0.87969 -43 CCGGAACTTTCCGCAGCCACGGCCTTATCA 36 71 1 CCGCAGCCAC 0.742627 -90 GTTTTGTTGGCCGGAGGCGCAGCTTTCCGG 42 11 1 CCGGAGGCGC 0.903367 -50 GCTGCTATTACAGGAGAAACCTTTGCGCTG 45 12 0 CAGGAGAAAC 0.796108 -289 ********** Masking position 1 Map Score: 3.80873 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 473 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 13 AACCTTCTCCGTTAACCTGGTATTTGTTGCTT 3 226 0 CTTACCGGTA 0.934575 -22 GTAAATCTCCCGTTACCCTGATAGCGGACTTCC 8 135 1 CTTACCGATA 0.801212 -50 GAAACCAAATCTTTATCTTTGTAGCACTTTCAC 9 131 1 CTTACTTGTA 0.948765 -170 CTGAACATCGCATTATCTGTGTAGAAATGCCCA 23 82 1 CTTACTTGTA 0.948765 -219 CATATTCCTGCTTTATCTATATATAATGCGTGG 26 55 0 CTTACTTATA 0.839357 -84 TGTTACCTGCCTCTAACTTTGTAGATCTCCAAA 34 64 1 CCTACTTGTA 0.794318 -112 ACGCATTATCCCTTAGCTCTGTATGGGAAATTT 34 127 0 CTTACTTGTA 0.948765 -49 ATATGCCATTCCTGATCTGGGTAATAGGCACAG 39 122 1 CTGACTGGTA 0.807099 -179 TCGACCCATTCTTTATCTCGGTAACTCCATTCA 43 58 1 CTTACTGGTA 0.952522 -25 TCATTATCCTTATAGAAAAAGAAA 49 68 0 CTTACCTATA 0.788144 -14 * *** ** **** Masking position 5 Map Score: 3.99419 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 23 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 GCACGCTTCGGCGCGGTACGCAAACTGCTGACG 1 138 1 GCGCTCGCAA 0.976789 -136 CGGTACGCAAACTGCTGACGCAAATGCCGTCAG 1 151 1 ACTGGCGCAA 0.725942 -123 CCGCAAAGCAGCACTGTGCGCAAGCGATTTGGC 3 167 0 GCACTCGCAA 0.953221 -81 CGGATTGACGCCTGTCTGCGCAAATCCAGGTTA 7 223 1 CCTGTCGCAA 0.799297 -78 GAAAACGCAGGCTGTTTTTGCAAGACGTGAGAT 8 81 0 GCTGTTGCAA 0.662918 -104 AATCAGACAAGCAGAATTCGCAAATGCAGCGAA 10 63 0 GCAGTCGCAA 0.944707 -106 TCTGCATAGCGCGATTTACGCAACAGGAATAGA 11 50 0 GCGATCGCAA 0.845177 -216 AGCATCCGTATCGCAGGACGCAAACGCATATGC 13 58 0 TCGCGCGCAA 0.69757 -144 TTTTGTTACAGCACAGTCCGCAATTCCTGCTGA 20 62 1 GCACTCGCAA 0.953221 -99 ATTCAATCCTGCTCTCGCCGCAATCATGATATG 39 94 1 GCTCGCGCAA 0.94812 -207 TATAAGCTAAACGCGATTCGCAACCCATTCAGG 45 58 0 ACGCTCGCAA 0.87916 -243 AAAATTTCAAGATGTTTGCGCAACTATTTTTGG 45 105 1 GATGTCGCAA 0.662918 -196 **** * ***** Masking position 12 Map Score: 3.39152 Number of sites scoring better than the average of aligned sites = 362 Number in coding regions = 335 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 15 CGTAAAATATAAACATTCAATAAAACCCGC 3 46 1 AAACATTCAA 0.93245 -202 AAACTTATTTTATCATTCAAAAAATCAGGT 7 193 1 TATCATTCAA 0.620423 -108 CTATACACAAAATCATTCAAGTTGCATCAA 17 55 1 AATCATTCAA 0.920737 -220 AACACTTTTAAATCTTTCAATCTGATTAGA 33 59 0 AATCTTTCAA 0.822283 -197 CCTTTTATTCAAACTTTCAAATTAAAATAT 33 114 0 AAACTTTCAA 0.846113 -142 TTCATTTTCAGAACATTCAATCCTGCTCTC 39 80 1 GAACATTCAA 0.742186 -221 ACATGAATATAAACTATCAATAAGATAGCC 39 154 0 AAACTATCAA 0.577031 -147 TTTTGATAGGAATCAATCAATTACATGAAT 39 176 0 AATCAATCAA 0.742416 -125 CACATGCAATAATCATTCAATAAAAAGCCT 40 81 0 AATCATTCAA 0.920737 -71 GTTAAACGTAAAACATTCACCTTACGGCTG 41 100 0 AAACATTCAC 0.722187 -54 GTCGGTCGAAAAACATTCGAAACCACATAT 45 276 1 AAACATTCGA 0.722187 -25 ********** Masking position 2 Map Score: 2.06994 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 29 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604