AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ilexA_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 polB 74 DNA polymerase II #2 araD 284 L-ribulose-5-phosphate 4-epimerase #3 araB 300 L-ribulokinase #4 uvrB 300 DNA repair; excision nuclease subunit B #5 dinG 119 probably ATP-dependent helicase #6 ybiB 27 putative enzyme #7 lrp 300 regulator for leucine (or lrp) regulon and high-affinity branched-chain amino acid transport system #8 ftsK 134 cell division protein #9 sulA 218 suppressor of lon; inhibits cell division and ftsZ ring formation #10 dinI 73 damage-inducible protein I #11 pyrC 105 dihydro-orotase #12 yceB 133 orf, hypothetical protein #13 grxB 63 glutaredoxin 2 #14 yceL 205 orf, hypothetical protein #15 umuD 300 SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC #16 nadE 201 NAD synthetase, prefers NH3 over glutamine #17 b1741 229 putative excinuclease subunit #18 ruvA 175 Holliday junction helicase subunit B; branch migration; repair #19 yfjB 122 orf, hypothetical protein #20 recN 85 protein used in recombination and DNA repair #21 recA 79 DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease #22 ygaD 144 orf, hypothetical protein #23 mltB 255 membrane-bound lytic murein transglycosylase B #24 yicC 126 putative alpha helix protein #25 dinD 208 DNA-damage-inducible protein #26 dapF 300 diaminopimelate epimerase #27 uvrD 83 DNA-dependent ATPase I and helicase II #28 dgkA 110 diacylglycerol kinase #29 lexA 109 regulator for SOS(lexA) regulon #30 uvrA 253 excision nuclease subunit A #31 yjiW 170 orf, hypothetical protein #32 hsdM 200 host modification; DNA methylase M #33 hsdR 133 host restriction; endonuclease R #34 yerE 264 similar to hypothetical proteins #35 yerF 61 similar to ATP-dependent DNA helicase #36 spoIIIE 300 DNA translocase #37 pgsA 300 phosphatidylglycerophosphate synthase #38 recA 172 multifunctional SOS repair regulator #39 lexA 149 transcriptional regulator #40 dinG 125 ATP-dependent helicase #41 panB 245 ketopantoate hydroxymethyltransferase #42 ypjH 31 alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein #43 ypjD 300 alternate gene name: jojD #44 yqjW 165 similar to ATP/GTP-binding protein #45 recN 36 recN #46 ahrC 134 transcriptional regulator #47 yqiE 246 similar to hypothetical proteins #48 yqiC 85 similar to exodeoxyribonuclease VII (small subunit) #49 yqiB 137 similar to exodeoxyribonuclease VII (large subunit) #50 yqhZ 263 similar to transcription termination #51 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #52 spoIIIAC 22 spoIIIAC #53 spoIIIAA 75 spoIIIAA #54 yqhV 144 alternate gene name: yqgE #55 efp 24 elongation factor P #56 yqhS 86 similar to 3-dehydroquinate dehydratase #57 yqhR 226 yqhR #58 ruvB 250 Holliday junction DNA helicase #59 ruvA 138 Holliday junction DNA helicase #60 bofC 47 bofC #61 csbX 70 alpha-ketoglutarate permease #62 yrbE 237 similar to opine catabolism #63 ytpS 159 ytpS #64 ytpP 234 similar to thioredoxin H1 #65 uvrB 185 excinuclease ABC (subunit B) #66 csbA 300 putative membrane protein Motif number 1 GTTTGATTGGCTGTGGTTTTATACAGTCA 1 4 0 CTGTTATCAG 0.994259 -71 TGGTGATGAACTGTTTTTTTATCCAGTATAATTTGT 4 209 1 CTGTTATCAG 0.987615 -92 TGCCACAATATTGGCTGTTTATACAGTATTTCAGGT 5 88 1 TTGTTATCAG 0.884832 -32 GATTACACTCCTGTTAATCCATACAGCAACAGTACT 8 41 1 CTGTCATCAG 0.989111 -94 ACTGGATGTACTGTACATCCATACAGTAACTCACAG 9 179 1 CTGTCATCAG 0.723954 -40 GTTGAATATACTGGTTATTTATACAGGTAAAATAAC 10 37 0 CTGTTATCAG 0.793224 -37 TGAAGTTATACTGTTTTTATATACAGTAGTCTGTTC 15 264 0 CTGTTATCAG 0.945415 -37 ACTCCGAATGCTGGTTATCTATCCAGTGTAACAGGC 17 199 0 CTGTTATCAG 0.952764 -31 TCATCCTTCGCTGGATATCTATCCAGCATTTTTTTA 18 109 1 CTGTTATCAG 0.56939 -67 ACAGTATAAACTGGTTTTATATACAGTAAAGAGGCT 20 20 0 CTGTTATCAG 0.945415 -66 AAAACCATTACTGTTATTGTGTACAGTATAAACTGG 20 42 0 CTGTTGTCAG 0.971813 -44 AATAACAGTAATGGTTTTTCATACAGGAAAACGACT 20 60 1 ATGTCATCAG 0.81182 -26 TACTGTATGAGCATACAGTATAATTGCT 21 3 1 CTGACATCAG 0.580522 -77 AAATCTGTAACTGTATTTATATACAGTTGTGAGTAT 25 160 0 CTGTTATCAG 0.559208 -49 CGCCAAAAAGCTGGGTATATATACAGATTTGCTGA 27 10 0 CTGTTATCAG 0.575918 -74 CGATAAATCTCTGGTTTATTGTGCAGTTTATGGTTC 29 24 1 CTGATGTCAG 0.807636 -86 TACAGTTATGCTGTGAGTATATACAGCAAAAGGCGA 29 65 0 CTGTTATCAG 0.970463 -45 TCCGCCCCCTGGGTGTATATACAGTTATGCTGTG 29 86 0 CTGTTATCAG 0.622751 -24 CATTCCAATACTGTATATTCATTCAGGTCAATTTGT 30 153 1 CTGTCATCAG 0.5082 -101 CCCATATTTACTGATGATATATACAGGTATTTAGCG 31 135 1 CTGTTATCAG 0.952764 -36 *** * *** *** Masking position 12 Map Score: 59.8744 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 17 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 2 GGCGTTACATACCGGATGCGGCTAC 2 6 0 ACCGGATGCG 0.885537 -279 GGTATGTAACGCCTGATGCGACGCTGACGC 2 23 1 GCCTGATGCG 0.985786 -262 CAGCGTGTAGGCCAGATAAGACGCGTCAGC 2 45 0 GCCAGATAAG 0.797001 -240 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 2 76 1 GCCGGATAAG 0.984732 -209 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 2 91 0 GCCGGATGCG 0.995126 -194 GGCATTCAACGCCTGATGCGACGCTGGCGC 2 108 1 GCCTGATGCG 0.985786 -177 CAGCGCGTAGGCCTGATAAGACGCGCCAGC 2 130 0 GCCTGATAAG 0.956348 -155 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 2 161 1 GCCGGATAAG 0.984732 -124 GGCGTTGAATGCCGGATGCGCTTTGCTTAT 2 176 0 GCCGGATGCG 0.995126 -109 GGCATTCAACGCCTGATGCGACGCTGGCGC 2 193 1 GCCTGATGCG 0.985786 -92 CAGCGTGTAGGCCTGATAAGACGCGCCAGC 2 215 0 GCCTGATAAG 0.956348 -70 GATTTTGTAGGCCGGATAAGCAAAGCGCAT 2 246 1 GCCGGATAAG 0.984732 -39 ACTCCTTCGTGCCGGATGCGCTTTGCTTAT 2 261 0 GCCGGATGCG 0.995126 -24 GGATGTTTTTGCCGGACACAAAGGATAAGC 11 63 0 GCCGGACACA 0.768067 -43 AGTTAGCCGGGCGGGATGCGTCAATGTCTT 15 22 1 GCGGGATGCG 0.92328 -279 TTTCATTTCTGCTGGATGAGCGTCGTCGCC 15 138 1 GCTGGATGAG 0.805465 -163 ATTTGTTCACGCCGGATGCGGCGTGAACGC 17 46 1 GCCGGATGCG 0.995126 -184 AGTCGAATAGGCCTGACAGGCGTAGCACGT 17 119 1 GCCTGACAGG 0.75842 -111 AAAAATTTATGCCGGACAAGATAGCACTTT 22 108 0 GCCGGACAAG 0.96013 -37 GGTAGTCACTGCCCGATACGGACTTTACAT 23 168 0 GCCCGATACG 0.919429 -88 ACTCTCTTCAGCCTGACGGGCTGCGGTCTG 26 110 1 GCCTGACGGG 0.835197 -191 AATCCACGGTGCCGGATAAAAACGATCGCG 26 213 1 GCCGGATAAA 0.818935 -88 ********** Masking position 6 Map Score: 47.1896 Number of sites scoring better than the average of aligned sites = 1093 Number in coding regions = 440 Number in noncoding regions = 653 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 3 CTGGCCTACACGCTGCGATTTTGTAGGCCGGATA 2 60 1 CGCGCTTTTT 0.963133 -225 CAGGCCTACGCGCTGCGATTTTGTAGGCCGGATA 2 145 1 CGCGCTTTTT 0.963133 -140 CAGGCCTACACGCTGCGATTTTGTAGGCCGGATA 2 230 1 CGCGCTTTTT 0.963133 -55 CAAATAATCAATGTGGACTTTTCTGCCGTGATTA 3 153 0 ATGGGTTTTT 0.73298 -148 AACCCGGTAAGGCCGGAGTTTTATCTCGCCACAG 4 122 1 GGCGGTTTTT 0.869796 -179 CCTCTGAAAGCGGAGCCGTTTCGTTCACGGGCTT 16 71 0 CGGGCTTTCT 0.823757 -131 ATAAATTATACTGTGCCATTTTTCAGTTCATCGA 18 56 1 CTGGCTTTTC 0.544714 -120 GAATTTCTCCGCGTTTTTTTCGCATTCATC 19 7 1 CTCGCTTTTT 0.896607 -116 CCTCTGGCTAATCAGCTTTTTTCTGAATCCTCCT 22 39 1 ATCGCTTTTT 0.892196 -106 ACTCAAACAGAGCGGCATTTTTCTTCCCCGCAAC 25 55 1 AGCGCTTTTT 0.961438 -154 TGGTCGGCGGCGGTGCGTTTTTATCTGCAGGCGG 26 158 0 CGGGCTTTTT 0.921645 -143 TTCTATTTTTAGCTGGACTTTCCCCATATTTACT 31 113 1 AGCGGTTTCC 0.691013 -58 GTATATTACCCTCGGCAATTTCTTCTTCTGCGGC 32 137 1 CTCGCTTTCT 0.775073 -64 CCCCCGATAAAGGGGGCTTTTCTT 40 1 0 AGGGGTTTCT 0.766686 -125 AGCCCCCTTTATCGGGGGTTTTCTTTTAAGATTT 40 17 1 ATCGGTTTTT 0.85909 -109 AGAGGAGATGATCTGCCGTTTTCTTCTGCAAGCC 41 202 0 ATCGCTTTTT 0.892196 -44 TTTTAATCGGAGCGGCAATTTTTTCATTTGGCTT 43 101 0 AGCGCTTTTT 0.961438 -200 ATTCCGGTACATCTGCTTTTTTTTCTTTTAACGT 46 12 0 ATCGCTTTTT 0.892196 -123 CCTAAAGCCAGGGCGGGTTTTCTTTAGTTATGGT 49 83 1 GGGGGTTTCT 0.544457 -55 CCGCTTGTTTAGCGGGCTTTTTTCCCTCATTC 51 9 0 AGCGGTTTTC 0.849125 -147 CCGCTAAACAAGCGGGCTTTTTGCGTTGCTGTCA 51 28 1 AGCGGTTTTC 0.849125 -128 CCCAAATGGGAGCAGGCTTTTTTTGTGCCCAAAA 54 32 1 AGCGGTTTTT 0.948365 -113 GCCAAAAAGTGTGAGCTTTTTTATTGACATTTCA 57 173 1 GTGGCTTTTT 0.575426 -54 ACGTTTTAAAAGCAGGTTTTTTATACACAAAAAC 65 50 1 AGCGGTTTTT 0.948365 -136 AACTAAAGTTCGGTGGTTTTTTATTTCCAGCTGT 65 82 0 CGGGGTTTTT 0.896534 -104 TGTTCTAATCAGCGGCACTTTTTTTATTACATCA 66 111 0 AGCGCTTTTT 0.961438 -190 *** ** **** * Masking position 9 Map Score: 33.069 Number of sites scoring better than the average of aligned sites = 576 Number in coding regions = 452 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 4 ACGCTGCGATTTTGTAGGCCGGATAAGCAAAG 2 69 1 TTTGAGCCGG 0.980728 -216 CGCATCAGGCGTTGAATGCCGGATGCGCTTTG 2 96 0 GTTGAGCCGG 0.932047 -189 GCGCTGCGATTTTGTAGGCCGGATAAGCAAAG 2 154 1 TTTGAGCCGG 0.980728 -131 CGCATCAGGCGTTGAATGCCGGATGCGCTTTG 2 181 0 GTTGAGCCGG 0.932047 -104 ACGCTGCGATTTTGTAGGCCGGATAAGCAAAG 2 239 1 TTTGAGCCGG 0.980728 -46 GCTGAAGGGATGTTTTTGCCGGACACAAAGGA 11 68 0 TGTTTGCCGG 0.873887 -38 TTCTATTCTATTTTTTAGCCGGGTGATATTTT 15 108 1 TTTTTGCCGG 0.955975 -193 AAGAGTAATTTGTTCACGCCGGATGCGGCGTG 17 39 1 TGTTAGCCGG 0.89382 -191 AGCCACATTTGTTTCAAGCCGGAGATTTCAAT 24 11 0 GTTTAGCCGG 0.876698 -116 GTGGCGGCATTTGTGAAGGCGGAAAAGTAAGA 25 25 0 TTGTAGGCGG 0.770932 -184 TGCCGCTCTGTTTGAGTGGCGGCATTTGTGAA 25 40 0 TTTGGGGCGG 0.883854 -169 TCTCTACCGGTTTGGTCGGCGGCGGTGCGTTT 26 172 0 TTTGTGGCGG 0.951987 -129 CGCGTAAAAATAGGTTGGGCGGAGAAGCGCAA 27 53 0 TAGGTGGCGG 0.520289 -31 TCTGGCCAGGTTTGTTTCCCGGAACCGAGGTC 30 94 0 TTTGTCCCGG 0.819615 -160 ATTAACCGTTTGTGATCGCCGGTAGCACCATG 30 195 1 TGTGTGCCGG 0.930398 -59 GATTAAACGCTTTTTTGCCCGGTGGCATGGTG 30 220 0 TTTTTCCCGG 0.70197 -34 AACGTATGTTTTGTATAGGCGGGTGAACAAAT 35 39 1 TTGTTGGCGG 0.734774 -23 ATACATGTCTTTTGCATGCCGAGCTGACAATA 47 187 0 TTTGAGCCGA 0.658491 -60 ATCGTGCTCATATTCAAGGCGGGTAAACATTT 49 34 0 TATTAGGCGG 0.717035 -104 GAAACTCGGCTATGTAAGCCGGCTTTCTTCAT 50 81 0 TATGAGCCGG 0.911718 -183 CATGATTCGTTTTTTTTGGCGGATTTATGGGA 63 13 0 TTTTTGGCGG 0.911334 -147 CATATTTGCATTTTGGTGCCGGTCAAAACTTA 66 159 0 TTTTGGCCGG 0.892865 -142 **** * ***** Masking position 10 Map Score: 26.8903 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 408 Number in noncoding regions = 175 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 5 GGCCGGATAAGCAAAGCGCATCCGGCATTC 2 85 1 GCAAAGCGCA 0.966368 -200 GGCCGGATAAGCAAAGCGCATCCGGCATTC 2 170 1 GCAAAGCGCA 0.966368 -115 GGCCGGATAAGCAAAGCGCATCCGGCACGA 2 255 1 GCAAAGCGCA 0.966368 -30 AGGTTGGGCGGAGAAGCGCAACGCCCTCCG 27 44 0 GAGAAGCGCA 0.951752 -40 CACAACATAGTAAAAGCGCTATTGGTAATG 30 65 0 TAAAAGCGCT 0.639236 -189 GTGAAATAATAAAAAGCGCACCGGAAAGGT 31 28 0 AAAAAGCGCA 0.896645 -143 AGAACCAAGAGACAAGCGCACATGAGCAAA 36 15 1 GACAAGCGCA 0.914668 -286 TTTGCCAAGAAAAAAGCGAACGCATATTCG 38 97 0 AAAAAGCGAA 0.69221 -76 GGCTGATGTGGAAAAGGGCATAAAGCAAAA 43 15 1 GAAAAGGGCA 0.849245 -286 TTTAGTAGAATAAAAGCGAAGCATAAGGAT 44 23 0 TAAAAGCGAA 0.69221 -143 CGCATATAATGAAAAGCGAACATAAGTTCT 44 132 1 GAAAAGCGAA 0.941815 -34 AAATGAAAAGGAAAAGCGCGTTTGTCTTTT 47 143 1 GAAAAGCGCG 0.914668 -104 AAGAATGAGAGAGAAGCGAACATATGTTAA 59 55 1 GAGAAGCGAA 0.836436 -84 TTCCATTCTTGAAAAGCGCTTACAAATGGG 62 164 1 GAAAAGCGCT 0.927288 -74 ********** Masking position 5 Map Score: 12.8608 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 319 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 AACGCCTGATGCGACGCTGACGCGTCTTATCTG 2 30 1 GCGCGCACGC 0.993447 -255 CTACAAAATCGCAGCGTGTAGGCCAGATAAGAC 2 53 0 GCACGTAGGC 0.914639 -232 AACGCCTGATGCGACGCTGGCGCGTCTTATCAG 2 115 1 GCGCGCGCGC 0.987195 -170 CTACAAAATCGCAGCGCGTAGGCCTGATAAGAC 2 138 0 GCACGCAGGC 0.970777 -147 AACGCCTGATGCGACGCTGGCGCGTCTTATCAG 2 200 1 GCGCGCGCGC 0.987195 -85 CTACAAAATCGCAGCGTGTAGGCCTGATAAGAC 2 223 0 GCACGTAGGC 0.914639 -62 ATGATTGACAGCGGAGTTTACGCTGTATCAGAA 4 170 1 GCGAGTACGC 0.954127 -131 CACGCCGGATGCGGCGTGAACGCCTTATTCGAC 17 53 1 GCGCGTACGC 0.989593 -177 ATTAGCCAGAGGGAAGCTCACGCCCCCCTCTTG 22 18 0 GGGAGCACGC 0.884383 -127 TCGTAAAATTGCAACGCCAACACCATCTTCCTG 22 72 1 GCACGCACAC 0.872885 -73 CAAACCGGTAGAGACGCAAACGCAATCCACGGT 26 190 1 GAGCGCACGC 0.958981 -111 GGGTGAACGAGCGCAGCCAACGCAGAGGCAGCC 32 33 0 GCGAGCACGC 0.940774 -168 *** *** **** Masking position 13 Map Score: 15.5601 Number of sites scoring better than the average of aligned sites = 842 Number in coding regions = 552 Number in noncoding regions = 290 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 7 AATAGCCCCCTGTTGAATATACTGGTTA 10 56 0 CCCCCTTGAT 0.57836 -18 GTGACTCCTCCATTTGGCTGTCAGTTCAC 13 45 0 CCTCCTTGCT 0.79818 -19 ATTCCGTCCTCTTGTTTATCAGCGTGT 16 5 1 CGTCCTTGTT 0.908313 -197 TGTCATCGACCCGCCTCTTTTTTAATCGCTTCC 17 165 1 CCGCCTTTTT 0.906181 -65 CTCTCAGCCTCCCTTTTTATGTAACCATTT 34 8 1 CCTCCTTTAT 0.858293 -257 GTCATACGTTCCTCCATTCGTTTGTTACCATTT 34 242 0 CCTCCTCGTT 0.758201 -23 ATTTGAATGACTTCCGCTTCATTCCCTTTCATT 36 76 0 CTTCCTTCTT 0.573071 -225 GATGACTTTTCTTCCTTTTTATTTACAATCTTT 37 225 0 CTTCCTTTTT 0.777651 -76 AAAGCCCCTCCAATTTCATACTCGGACGT 37 282 0 CCTCCTTTAT 0.858293 -19 TCTATTTTTTCCTCCTTTATGTTACCACTACAT 38 150 0 CCTCCTATTT 0.542275 -23 AGGAGATGATCTGCCGTTTTCTTCTGCAAGCCA 41 201 0 CTGCCTTTTT 0.659217 -45 GTTTTCTCCTCCTCATGTTTAGAGGAGATG 41 226 0 CCTCCATGTT 0.849344 -20 AAAGGGCCGCCCTCCCCTTGGTTTCGTGTTAAG 50 15 0 CCTCCTTGTT 0.96893 -249 AAGGGGAGGGCGGCCCTTTGGTTTTTTTACACG 50 29 1 CGGCCTTGTT 0.845663 -235 ACTCTCCCAACCTCCCATTTTTTTATATGATAT 54 119 0 CCTCCTTTTT 0.945838 -26 ATTATCAACCTGCCTATTTCTTTAGGATTGCT 57 10 1 CTGCCTTTTT 0.659217 -217 AATAAAAATCCCTCCTTATGTATATCCATCTGT 64 11 1 CCTCCATGAT 0.661627 -224 TATCGATACTCGTCCATTTGGATCATACCAAAC 64 173 0 CGTCCTTGAT 0.774569 -62 TTCATATCCCTCCAGTTGTTTATGTTCTTAC 64 214 0 CCTCCTTGTT 0.96893 -21 AAAAATAAGCCTCCGTTTCTTTAACGAAATCT 65 164 0 CCTCCTTCTT 0.87017 -22 AGTACCAGTACGGCCGCATTTTTCAGGATAATA 66 33 0 CGGCCATTTT 0.356776 -268 ***** *** ** Masking position 13 Map Score: 15.2371 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 128 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 GAATGCTTTTAATAAGCGGGGTTACCGGTT 3 71 0 AATAAGCGGG 0.796383 -230 AAAAAACTGAAAACGGCGGCAACCCGCGAA 12 36 0 AAACGGCGGC 0.929839 -98 GCGATTAAAAAAGAGGCGGGTCGATGACAA 17 164 0 AAGAGGCGGG 0.945725 -66 TATCCAGTGTAACAGGCGGGAAGCGATTAA 17 186 0 AACAGGCGGG 0.880278 -44 ATATACAGTAAAGAGGCTGGCGTAAAA 20 8 0 AAGAGGCTGG 0.891637 -78 GCCCTCCGCCAAAAAGCTGGGTATATATAC 27 22 0 AAAAAGCTGG 0.80936 -62 TCCGTAAATTAAGCAGCGGCCCAAATTCAT 32 174 0 AAGCAGCGGC 0.945622 -27 ACGAGCCTGTAAACGGCTGCTTTCTTCATT 36 240 1 AAACGGCTGC 0.862225 -61 TCCTAATTTGAAGCGGCTGCACGAGGGTAT 47 87 1 AAGCGGCTGC 0.908926 -160 TAGGAGCCTGAAGAAGCGGGTATCGTGCTC 49 57 0 AAGAAGCGGG 0.9348 -81 AAGCCCGCTAAACAAGCGGGCTTTTTGCGT 51 24 1 AACAAGCGGG 0.858154 -132 ATTTTCCTATAAACAGCTGCATAAAATAGA 62 29 0 AAACAGCTGC 0.837382 -209 TTATACACAAAAACAGCTGGAAATAAAAAA 65 70 1 AAACAGCTGG 0.87201 -116 CCGCTGTTCTAATCAGCGGCACTTTTTTTA 66 119 0 AATCAGCGGC 0.825902 -182 ********** Masking position 2 Map Score: 11.5467 Number of sites scoring better than the average of aligned sites = 659 Number in coding regions = 619 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 GGGGTAATGGTTTTTCTGTTTCTGGAAAGCGGC 5 41 0 TTTTCTTTCT 0.611548 -79 TATTGTGGCATTTTTCGGTTTTCAGGGGTAATG 5 65 0 TTTTCTTTTC 0.815402 -55 GCGAATGCTTCTATTCTATTTTTTAGCCGGGTG 15 100 1 CTTTCTTTTT 0.770646 -201 CTGGAATACATTGGGCGCTTTTTCAAGCCCGTG 16 47 1 TTGGCTTTTT 0.787337 -155 ATAAATTATACTGTGCCATTTTTCAGTTCATCG 18 56 1 CTTGCTTTTT 0.689105 -120 CGCACCTTTCCGGTGCGCTTTTTATTATTTCAC 31 25 1 CGTGCTTTTT 0.466775 -146 ATTGCCCATTTTATTCTATTTTTAGCTGGACTT 31 100 1 TTTTCTTTTT 0.894824 -71 TTCTAACGTGTTCGTCTATTTTTGTAGTGCTAT 33 52 0 TTGTCTTTTT 0.848768 -82 AAAGGTGTTTTGATTCTTTTTTCATAAAAAAAG 34 142 0 TGTTCTTTTC 0.635634 -123 GATTAACGGCTTTTTCCGTTTTTCCGCGCTATG 34 190 1 TTTTCTTTTT 0.894824 -75 TTTTATAGGTTTCGTCTTTTTTCAGCGTTCCTT 37 68 0 TTGTCTTTTC 0.744497 -233 ACGAGAAGGATTCTTCACTTTCTAAAGTTCGGC 41 151 0 TTTTCTTTCT 0.611548 -95 CACTTTTGCTTTATGCCCTTTTCCACATCAGCC 43 15 0 TTTGCTTTTC 0.744497 -286 TAGGGCGCTATTATTCCTTTTTTCTGCATTCAT 46 48 1 TTTTCTTTTT 0.894824 -87 CGCGCTTTTCCTTTTCATTTTTCATATAAACTG 47 130 0 CTTTCTTTTC 0.635634 -117 GAAAAGCGCGTTTGTCTTTTTTTATGTCTGAGA 47 153 1 TTGTCTTTTT 0.848768 -94 TCAAATGTCATGTTTCATTTTTTTTCACGTCTG 48 11 0 TGTTCTTTTT 0.770646 -75 TCTATAAGACTTTGGCTGTTTTTATGGTACAAT 59 89 1 TTGGCTTTTT 0.787337 -50 TACACTAGAATTAGGCTCTTTTTCCTGAACAGT 62 64 0 TTGGCTTTTT 0.787337 -174 GCTTTTCACATGATTCGTTTTTTTTGGCGGATT 63 20 0 TGTTCTTTTT 0.770646 -140 GATTGTCCGATTCTTCATTTTTTACTATAATCA 66 245 1 TTTTCTTTTT 0.894824 -56 ** *** ***** Masking position 9 Map Score: 16.1289 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 127 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 10 CCTACAAAATCGCAGCGTGTAGGCCAGATAAGA 2 54 0 CGCGCGGTAG 0.988717 -231 CCTACAAAATCGCAGCGCGTAGGCCTGATAAGA 2 139 0 CGCGCGGTAG 0.988717 -146 CCTACAAAATCGCAGCGTGTAGGCCTGATAAGA 2 224 0 CGCGCGGTAG 0.988717 -61 CCAGGCATTGCGCGCCGTGAATCTTCATGATTT 7 192 1 CGCCCGGAAC 0.92698 -109 TACAGGCTGCCGCGGCGGGTCAGGA 12 3 0 CGCGCGGTCG 0.937666 -131 TCACGCCGGATGCGGCGTGAACGCCTTATTCGA 17 52 1 TGCGCGGAAG 0.935349 -178 TAAAGCATCACGCCCCGCACAAGGAAGCGGTAG 23 193 0 CGCCCGACAG 0.881229 -63 TGGCACCGCCGCGTAAAAATAGGTTGGGC 27 65 0 CGCGCGAAAA 0.804606 -19 GTTTGCGTAGCGCCGCGCGAAACATGAGCGGAT 28 26 0 CGCGCGGAAC 0.961261 -85 TAATAAAAAGCGCACCGGAAAGGTGCGCCAGAA 31 19 0 CGCCCGAAAG 0.96018 -152 AGTTGATATCCGCACCGGATATGCACCTAATCT 37 123 1 CGCCCGATAG 0.953033 -178 TGTTTATAGATGCGGCGAAAATGAGACAGGAGA 58 142 1 TGCGCGAAAG 0.867527 -109 *** *** *** * Masking position 6 Map Score: 12.4922 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 366 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 11 ATACTGTTTTTTTTCTTCCTCGAATGTTTT 7 33 0 TTTTCTTCCT 0.791214 -268 CAAAATGCCATTTTCTGCATTATTCACATA 14 92 1 TTTTCTGCAT 0.877559 -114 TTTCTATTCTGCATTGCCGCTAAG 14 192 0 TATTCTGCAT 0.731995 -14 ACCTCGCAAGTTTTCTTCATCCTTCGCTGG 18 93 1 TTTTCTTCAT 0.912428 -83 AGAGCGGCATTTTTCTTCCCCGCAACATTC 25 63 1 TTTTCTTCCC 0.579536 -146 ATCCAATGCATTTTCTGCATCCGGACATTT 36 120 1 TTTTCTGCAT 0.877559 -181 TAAACGGCTGCTTTCTTCATTATGTATGAA 36 249 1 CTTTCTTCAT 0.766993 -52 TTAAGATGACTTTTCTTCCTTTTTATTTAC 37 232 0 TTTTCTTCCT 0.791214 -69 ACCAGATGACTTTTCTTCACGTCCGAGTAT 37 264 1 TTTTCTTCAC 0.791214 -37 CAACGAGAAGGATTCTTCACTTTCTAAAGT 41 156 0 GATTCTTCAC 0.46607 -90 TCAGCCAGATTGTTCTGCATATTGAAATGA 43 68 1 TGTTCTGCAT 0.693659 -233 ATTATTCCTTTTTTCTGCATTCATGTACAA 46 57 1 TTTTCTGCAT 0.877559 -78 TGTAAGCCGGCTTTCTTCATGCTTTGAAAT 50 71 0 CTTTCTTCAT 0.766993 -193 ACATAGCCGAGTTTCTTCATGAACGTGAAA 50 98 1 GTTTCTTCAT 0.862974 -166 CCTCTTTGACTGTTCTTCATTGTACCATAA 59 110 0 TGTTCTTCAT 0.766993 -29 ACGATTGTCCGATTCTTCATTTTTTACTAT 66 243 1 GATTCTTCAT 0.705881 -58 CCTCCTCAGGGATTCTTCATCTGATCTGAT 66 274 0 GATTCTTCAT 0.705881 -27 ********** Masking position 6 Map Score: 12.3109 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 182 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 12 AGCGCATCCGGCATTCAACGCCTGATGCGACGCT 2 99 1 GCACAACCTG 0.971777 -186 AGCGCATCCGGCATTCAACGCCTGATGCGACGCT 2 184 1 GCACAACCTG 0.971777 -101 GGTTGGGTTAGCGAGAAGAGCCAGTAAAAGACGC 3 41 0 GCGAAGCCAG 0.847086 -260 TATAATCACGGCAGAAAAGTCCACATTGATTATT 3 151 1 GCAAAACCAC 0.718067 -150 CAGTTTTATGGCAAGAGATGCCTGTTCAGTGACT 4 41 0 GCAAGACCTG 0.826665 -260 AAGATTCACGGCGCGCAATGCCTGGGTCTACGGT 7 183 0 GCGCAACCTG 0.950303 -118 TTAGCATCGGGCAGGAAAAGCCTGTAACCTGGAG 8 103 1 GCAAAACCTG 0.972338 -32 CATGAAATCTGCGTCAATATCCTGACACAACGCA 12 98 0 GCGAATCCTG 0.693345 -36 CTATACCTGCGCAACCAGACCCTGTGAAAAGTCC 14 59 1 GCACAGCCTG 0.954155 -147 ATCAATCTTCGCAACAAGGACCTCGGAAAA 19 103 1 GCAAAGCCTC 0.766303 -20 ACCATAAACTGCACAATAAACCAGAGATTTATCG 29 24 0 GCAATACCAG 0.601711 -86 ATCCGCACCGCGCTAAATACCTGTATATATCAT 31 148 0 GCGAAACCTG 0.951268 -23 ACTTCATCGCGCACTCAAATCCAGGAGCTGTCTG 37 18 0 GCACAACCAG 0.941745 -283 GTTTTTGGGCACAAAAAAAGCCTGCTCCCATTTG 54 34 0 ACAAAACCTG 0.650098 -111 CTGTTTTTGTGTATAAAAAACCTGCTTTTAAAAC 65 52 0 GTAAAACCTG 0.650098 -134 AAGAAAATAGGCATACAGTACCAGTACGGCCGCA 66 48 0 GCACAGCCAG 0.907162 -253 *** *** **** Masking position 11 Map Score: 12.5045 Number of sites scoring better than the average of aligned sites = 698 Number in coding regions = 632 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 13 GAGTCGCTACCTGAAGGAGTTGGGCGG 4 284 0 GCCCTGAAGG 0.95979 -17 ATCTCTATGCTCCGGCTGAAGGGATGTTTTTG 11 82 0 TCGCTGAAGG 0.953614 -24 AATAATCTGCCTGAAGTTATACTGTTT 15 284 0 TCCCTGAAGT 0.770594 -17 ACAAGCGACAGCGGGCTGAATGGTGGTTAAAA 16 119 0 GCGCTGAATG 0.958452 -83 AGCGAAGTTAGCGAGATGAATGCGAAAAAAAC 19 23 0 GCGATGAATG 0.807033 -100 CCGCAGCCCGTCAGGCTGAAGAGAGTAAGTAA 26 104 0 TCGCTGAAGA 0.668372 -197 CAACGCAGAGGCAGCCTGAAGGATGAAGTGTA 32 17 0 GCCCTGAAGG 0.959791 -184 CCGCCTTGATGCAACCTGAATGATTTTGTGTA 32 108 1 GCCCTGAATG 0.90463 -93 TTCTTCTGCGGCTCGATGAATTTGGGCCGCTG 32 159 1 GCGATGAATT 0.624332 -42 GGATTTGAGTGCGCGATGAAGTGGCAGCTCTT 37 30 1 GCGATGAAGT 0.807033 -271 TGCAGAACAATCTGGCTGAGGGCGGTTTTACA 43 55 0 TCGCTGAGGG 0.749932 -246 TTGCAGAAATTCATGCTGAAAGTGAGTTGATC 47 221 1 TCGCTGAAAG 0.668372 -26 ATATGCTCTAGCTTGCTGAAGTAGTCTTGTCA 54 91 0 GCGCTGAAGT 0.958451 -54 ATGTACCCAAGCTTGCTGAATTGTAATCCTGT 61 15 0 GCGCTGAATT 0.901641 -56 ** ******** Masking position 9 Map Score: 9.95673 Number of sites scoring better than the average of aligned sites = 514 Number in coding regions = 492 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 GATAAGACGCGTCAGCGTCGCATCAGGCGTT 2 30 0 GCAGCGTCGC 0.975327 -255 GATAAGACGCGCCAGCGTCGCATCAGGCGTT 2 115 0 GCAGCGTCGC 0.975327 -170 GATAAGACGCGCCAGCGTCGCATCAGGCGTT 2 200 0 GCAGCGTCGC 0.975327 -85 AACTCCTTCAGGTAGCGACTC 4 290 1 GTAGCGACTC 0.792787 -11 TATCGTGACGGGTAGCGACTCTGAACAGTGA 7 230 1 GTAGCGACTC 0.792787 -71 GTTGTGTCAGGATATTGACGCAGATTTCATG 12 101 1 GTATTGACGC 0.809719 -33 TAGAAATAAAGACATTGACGCATCCCGCCCG 15 29 0 GCATTGACGC 0.923173 -272 TGTAACCTTTGTCATCGACCCGCCTCTTTTT 17 156 1 GCATCGACCC 0.762795 -74 AAGGATTATAGCCATCGATGCCTTGTCAGGA 24 76 0 GCATCGATGC 0.647975 -51 CGACCAAACCGGTAGAGACGCAAACGCAATC 26 186 1 GTAGAGACGC 0.747759 -115 ATGGACCATCGCCAGTGGCGCGATCGTTTTT 26 230 0 GCAGTGGCGC 0.87618 -71 ACGGTACACTGATATTGACGCTCATAATGTA 28 76 1 GTATTGACGC 0.809719 -35 ACTTCCATTGGGCAGTATCGCCTGCGAACTG 41 42 1 GCAGTATCGC 0.645945 -204 ACTCTAATATGACAGCAACGCAAAAAGCCCG 51 40 0 GCAGCAACGC 0.908403 -116 * ********* Masking position 4 Map Score: 9.04526 Number of sites scoring better than the average of aligned sites = 1077 Number in coding regions = 943 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 15 GGTTTATGATAGAACGTATGTTTTGTATAGGC 35 27 1 AGAACTAGTT 0.732817 -35 AAGAAAAAAGCGAACGCATATTCGGATTTTTT 38 89 0 CGAACCAATT 0.700582 -84 TATAAAAATGCGAACAAACATTCCTGTTGGAG 39 14 0 CGAACAAATT 0.799555 -136 TCAGTATATACGAACAAACGTTTCTGTCAATT 39 49 1 CGAACAAGTT 0.945769 -101 ATTGTTTTTTCGAACCTATGTTTGTACTGTAA 39 78 1 CGAACTAGTT 0.96549 -72 CAGTATAAAACGAACATACTTTCGCATATAAT 44 110 1 CGAACTATTT 0.783968 -56 TAATGAAAAGCGAACATAAGTTCTTTTTAGAG 44 138 1 CGAACTAGTT 0.96549 -28 GAGAGAGAAGCGAACATATGTTAACTTTTCTA 59 61 1 CGAACTAGTT 0.96549 -78 ACTAAAAATACGAACTAAAGTTCGGTGGTTTT 65 96 0 CGAACAAGTT 0.945769 -90 ***** ** *** Masking position 8 Map Score: 4.60806 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 19 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185