AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ilexA_ecoli_bsub_100.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 uvrB 300 DNA repair; excision nuclease subunit B #4 dinG 119 probably ATP-dependent helicase #5 ybiB 27 putative enzyme #6 ftsK 134 cell division protein #7 sulA 218 suppressor of lon; inhibits cell division and ftsZ ring formation #8 dinI 73 damage-inducible protein I #9 pyrC 105 dihydro-orotase #10 umuD 300 SOS mutagenesis; error-prone repair; processed to UmuD'; forms complex with UmuC #11 b1741 229 putative excinuclease subunit #12 ruvA 175 Holliday junction helicase subunit B; branch migration; repair #13 yfjB 122 orf, hypothetical protein #14 recN 85 protein used in recombination and DNA repair #15 recA 79 DNA strand exchange and renaturation, DNA-dependent ATPase, DNA- and ATP-dependent coprotease #16 ygaD 144 orf, hypothetical protein #17 dinD 208 DNA-damage-inducible protein #18 dapF 300 diaminopimelate epimerase #19 uvrD 83 DNA-dependent ATPase I and helicase II #20 lexA 109 regulator for SOS(lexA) regulon #21 uvrA 253 excision nuclease subunit A #22 yjiW 170 orf, hypothetical protein #23 yerE 264 similar to hypothetical proteins #24 yerF 61 similar to ATP-dependent DNA helicase #25 spoIIIE 300 DNA translocase #26 recA 172 multifunctional SOS repair regulator #27 lexA 149 transcriptional regulator #28 dinG 125 ATP-dependent helicase #29 yqjW 165 similar to ATP/GTP-binding protein #30 recN 36 recN #31 ahrC 134 transcriptional regulator #32 ruvB 250 Holliday junction DNA helicase #33 ruvA 138 Holliday junction DNA helicase #34 ytpS 159 ytpS #35 uvrB 185 excinuclease ABC (subunit B) Motif number 1 TGACTGTATAAAACCACAGCCAATCAAAC 1 4 1 CTGTATACAG 0.986381 -71 ACAAATTATACTGGATAAAAAAACAGTTCATCACCA 3 209 0 CTGGATACAG 0.717511 -92 ACCTGAAATACTGTATAAACAGCCAATATTGTGGCA 4 88 0 CTGTATACAA 0.928631 -32 AGTACTGTTGCTGTATGGATTAACAGGAGTGTAATC 6 41 0 CTGTATACAG 0.995135 -94 CTGTGAGTTACTGTATGGATGTACAGTACATCCAGT 7 179 0 CTGTATACAG 0.737187 -40 GTTATTTTACCTGTATAAATAACCAGTATATTCAAC 8 37 1 CTGTATACAG 0.856404 -37 GAACAGACTACTGTATATAAAAACAGTATAACTTCA 10 264 1 CTGTATACAG 0.547848 -37 GCCTGTTACACTGGATAGATAACCAGCATTCGGAGT 11 199 1 CTGGATACAG 0.964493 -31 TAAAAAAATGCTGGATAGATATCCAGCGAAGGATGA 12 109 0 CTGGATACAG 0.611926 -67 AGCCTCTTTACTGTATATAAAACCAGTTTATACTGT 14 20 1 CTGTATACAG 0.625409 -66 CCAGTTTATACTGTACACAATAACAGTAATGGTTTT 14 42 1 CTGTACACAG 0.966768 -44 AGTCGTTTTCCTGTATGAAAAACCATTACTGTTATT 14 60 0 CTGTATACAT 0.928631 -26 AGCAATTATACTGTATGCTCATACAGTA 15 3 0 CTGTATTCAG 0.535769 -77 AAATCTGTAACTGTATTTATATACAGTTGTGAGTAT 17 160 0 CTGTATACAG 0.499994 -49 TCAGCAAATCTGTATATATACCCAGCTTTTTGGCG 19 10 1 CTGTATACAG 0.625409 -74 TCGCCTTTTGCTGTATATACTCACAGCATAACTGTA 20 65 1 CTGTATACAG 0.929428 -45 CACAGCATAACTGTATATACACCCAGGGGGCGGA 20 86 1 CTGTATACAG 0.625409 -24 CATTCCAATACTGTATATTCATTCAGGTCAATTTGT 21 153 1 CTGTATTCAG 0.533533 -101 CGCTAAATACCTGTATATATCATCAGTAAATATGGG 22 135 0 CTGTATACAG 0.99505 -36 ****** * *** Masking position 2 Map Score: 70.3668 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 1 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 2 GTAGCCGCATCCGGTATGTAACGCC 2 6 1 CGCATCCGGT 0.925192 -279 GCGTCAGCGTCGCATCAGGCGTTACATACC 2 23 0 CGCATCAGGC 0.99039 -262 GCTGACGCGTCTTATCTGGCCTACACGCTG 2 45 1 CTTATCTGGC 0.829988 -240 ATGCGCTTTGCTTATCCGGCCTACAAAATC 2 76 0 CTTATCCGGC 0.988543 -209 ATAAGCAAAGCGCATCCGGCATTCAACGCC 2 91 1 CGCATCCGGC 0.996946 -194 GCGCCAGCGTCGCATCAGGCGTTGAATGCC 2 108 0 CGCATCAGGC 0.99039 -177 GCTGGCGCGTCTTATCAGGCCTACGCGCTG 2 130 1 CTTATCAGGC 0.964592 -155 ATGCGCTTTGCTTATCCGGCCTACAAAATC 2 161 0 CTTATCCGGC 0.988543 -124 ATAAGCAAAGCGCATCCGGCATTCAACGCC 2 176 1 CGCATCCGGC 0.996946 -109 GCGCCAGCGTCGCATCAGGCGTTGAATGCC 2 193 0 CGCATCAGGC 0.99039 -92 GCTGGCGCGTCTTATCAGGCCTACACGCTG 2 215 1 CTTATCAGGC 0.964592 -70 ATGCGCTTTGCTTATCCGGCCTACAAAATC 2 246 0 CTTATCCGGC 0.988543 -39 ATAAGCAAAGCGCATCCGGCACGAAGGAGT 2 261 1 CGCATCCGGC 0.996946 -24 GCTTATCCTTTGTGTCCGGCAAAAACATCC 9 63 1 TGTGTCCGGC 0.824127 -43 AAGACATTGACGCATCCCGCCCGGCTAACT 10 22 0 CGCATCCCGC 0.973856 -279 GGCGACGACGCTCATCCAGCAGAAATGAAA 10 138 0 CTCATCCAGC 0.874434 -163 GCGTTCACGCCGCATCCGGCGTGAACAAAT 11 46 0 CGCATCCGGC 0.996946 -184 ACGTGCTACGCCTGTCAGGCCTATTCGACT 11 119 0 CCTGTCAGGC 0.805038 -111 CTTTTTTAATCGCTTCCCGCCTGTTACACT 11 181 1 CGCTTCCCGC 0.738153 -49 AAAGTGCTATCTTGTCCGGCATAAATTTTT 16 108 1 CTTGTCCGGC 0.97149 -37 CAGACCGCAGCCCGTCAGGCTGAAGAGAGT 18 110 0 CCCGTCAGGC 0.888463 -191 CGCGATCGTTTTTATCCGGCACCGTGGATT 18 213 0 TTTATCCGGC 0.858163 -88 ********** Masking position 5 Map Score: 59.555 Number of sites scoring better than the average of aligned sites = 1191 Number in coding regions = 534 Number in noncoding regions = 657 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 3 GTTTGATTGGCTGTGGTTTTATACAGTCA 1 6 0 CTGTTTATAC 0.984688 -69 AGCGTCGCATCAGGCGTTACATACCGGATGCGGC 2 14 0 CAGGTCATAC 0.832224 -271 TGGTGATGAACTGTTTTTTTATCCAGTATAATTT 3 209 1 CTGTTTATCC 0.940143 -92 TGCCACAATATTGGCTGTTTATACAGTATTTCAG 4 88 1 TTGGTTATAC 0.865009 -32 GATTACACTCCTGTTAATCCATACAGCAACAGTA 6 41 1 CTGTTCATAC 0.972581 -94 ACTGGATGTACTGTACATCCATACAGTAACTCAC 7 179 1 CTGTTCATAC 0.97258 -40 GTTGAATATACTGGTTATTTATACAGGTAAAATA 8 39 0 CTGGTTATAC 0.988617 -35 TGAAGTTATACTGTTTTTATATACAGTAGTCTGT 10 266 0 CTGTTTATAC 0.984688 -35 ACTCCGAATGCTGGTTATCTATCCAGTGTAACAG 11 201 0 CTGGTTATCC 0.954981 -29 TCATCCTTCGCTGGATATCTATCCAGCATTTTTT 12 109 1 CTGGTTATCC 0.954981 -67 ACAGTATAAACTGGTTTTATATACAGTAAAGAGG 14 22 0 CTGGTTATAC 0.988617 -64 AAAACCATTACTGTTATTGTGTACAGTATAAACT 14 44 0 CTGTTTGTAC 0.9115 -42 AATAACAGTAATGGTTTTTCATACAGGAAAACGA 14 60 1 ATGGTCATAC 0.835108 -26 TACTGTATGAGCATACAGTATAATTG 15 3 1 CTGTACATAC 0.785991 -77 AAATCTGTAACTGTATTTATATACAGTTGTGAGT 17 162 0 CTGTTTATAC 0.984688 -47 CGCCAAAAAGCTGGGTATATATACAGATTTGCTG 19 12 0 CTGGTTATAC 0.988617 -72 TACAGTTATGCTGTGAGTATATACAGCAAAAGGC 20 67 0 CTGTTTATAC 0.984688 -43 TCCGCCCCCTGGGTGTATATACAGTTATGCTG 20 88 0 CTGGTTATAC 0.988617 -22 ACAAATTGACCTGAATGAATATACAGTATTGGAA 21 155 0 CTGAATATAC 0.555453 -99 CCCATATTTACTGATGATATATACAGGTATTTAG 22 135 1 CTGATTATAC 0.923474 -36 GCGTTAAAAAATGTAAGTTCATACATAATGAAGA 25 262 0 ATGTTCATAC 0.789469 -39 ACAGAAACGTTTGTTCGTATATACTGAAATTATA 27 42 0 TTGTTTATAC 0.825921 -108 ACGCTGGATCATGTTCTTCTGTACGGGCCGCCCG 32 174 1 ATGTTTGTAC 0.521263 -77 GTTTTAAAAGCAGGTTTTTTATACACAAAAACAG 35 52 1 CAGGTTATAC 0.899929 -134 **** * ***** Masking position 12 Map Score: 46.2716 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 77 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 4 TATAAAACCACAGCCAATCAAACGAAACCAGGC 1 17 1 CAGCCCAAAC 0.780214 -58 CTTTGCTTATCCGGCCTACAAAATCGCAGCGTG 2 68 0 CCGGCCAAAA 0.988993 -217 CTTTGCTTATCCGGCCTACAAAATCGCAGCGCG 2 153 0 CCGGCCAAAA 0.988993 -132 CTTTGCTTATCCGGCCTACAAAATCGCAGCGTG 2 238 0 CCGGCCAAAA 0.988993 -47 AAATTACATACCTGCCCGCCCAACTCCTTCAGG 3 269 1 CCTGCCCCAA 0.643695 -32 TCCTTTGTGTCCGGCAAAAACATCCCTTCAGCC 9 68 1 CCGGCAACAT 0.672246 -38 TTGACGCATCCCGCCCGGCTAACTATGAATTAG 10 13 0 CCGCCCTAAC 0.78207 -288 AAAATATCACCCGGCTAAAAAATAGAATAGAAG 10 107 0 CCGGCAAAAT 0.823857 -194 CACGCCGCATCCGGCGTGAACAAATTACTCTTT 11 38 0 CCGGCAACAA 0.935408 -192 TAATCGCTTCCCGCCTGTTACACTGGATAGATA 11 187 1 CCGCCTACAC 0.866914 -43 TTTTCTGAATCCTCCTCGTAAAATTGCAACGCC 16 57 1 CCTCCTAAAA 0.811035 -88 TCTTACTTTTCCGCCTTCACAAATGCCGCCACT 17 25 1 CCGCCACAAA 0.894324 -184 TTCACAAATGCCGCCACTCAAACAGAGCGGCAT 17 40 1 CCGCCCAAAC 0.982344 -169 AAATCTGGAGCAGGCACGCAAAACAGAATTGAA 17 90 0 CAGGCCAAAA 0.851474 -119 CTATTTCCCGCCTGCAGATAAAAACGCACCGCC 18 151 1 CCTGCTAAAA 0.811035 -150 AAACGCACCGCCGCCGACCAAACCGGTAGAGAC 18 172 1 CCGCCCAAAC 0.982344 -129 AGCGCAACGCCCTCCGCCAAAAAGCTGGGTATA 19 27 0 CCTCCAAAAA 0.855252 -57 TGGCACCGCCGCGTAAAAATAGGTTGGG 19 66 0 CCGCCTAAAA 0.959982 -18 GACCTCGGTTCCGGGAAACAAACCTGGCCAGAC 21 94 1 CCGGGCAAAC 0.7406 -160 CATGGTGCTACCGGCGATCACAAACGGTTAATT 21 194 0 CCGGCCACAA 0.975249 -60 TAGCACCATGCCACCGGGCAAAAAAGCGTTTAA 21 217 1 CCACCCAAAA 0.798631 -37 ATTTGTTCACCCGCCTATACAAAACATACGTTC 24 38 0 CCGCCACAAA 0.894324 -24 TCCCATAAATCCGCCAAAAAAAACGAATCATGT 34 13 1 CCGCCAAAAA 0.970609 -147 GTATAAAAAACCTGCTTTTAAAACGTAAAAGCA 35 43 0 CCTGCTAAAA 0.811035 -143 ***** ***** Masking position 12 Map Score: 34.6471 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 749 Number in noncoding regions = 185 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 5 AGCGTCGCATCAGGCGTTACATACCGGATGC 2 17 0 CAGGCTTACA 0.50828 -268 CGCGTCTTATCTGGCCTACACGCTGCGATTT 2 50 1 CTGGCTACAC 0.845818 -235 CTTTGCTTATCCGGCCTACAAAATCGCAGCG 2 70 0 CCGGCTACAA 0.976141 -215 CAAAGCGCATCCGGCATTCAACGCCTGATGC 2 96 1 CCGGCTTCAA 0.960467 -189 CTTTGCTTATCCGGCCTACAAAATCGCAGCG 2 155 0 CCGGCTACAA 0.976141 -130 CAAAGCGCATCCGGCATTCAACGCCTGATGC 2 181 1 CCGGCTTCAA 0.960467 -104 CGCGTCTTATCAGGCCTACACGCTGCGATTT 2 220 1 CAGGCTACAC 0.877198 -65 CTTTGCTTATCCGGCCTACAAAATCGCAGCG 2 240 0 CCGGCTACAA 0.976141 -45 AGATAAAACTCCGGCCTTACCGGGTTATCCC 3 117 0 CCGGCTTACC 0.856475 -184 TCCTTTGTGTCCGGCAAAAACATCCCTTCAG 9 68 1 CCGGCAAAAC 0.936614 -38 CGCATCCCGCCCGGCTAACTATGAATTAGAT 10 11 0 CCGGCAACTA 0.642608 -290 AAAATATCACCCGGCTAAAAAATAGAATAGA 10 109 0 CCGGCAAAAA 0.936379 -192 AATACTGATTCAGGCTATCAATATTTGTCGC 10 220 0 CAGGCATCAA 0.710444 -81 TATTGATCTGCTGGCAAGAACAGACTACTGT 10 247 1 CTGGCAGAAC 0.454859 -54 CACGCCGCATCCGGCGTGAACAAATTACTCT 11 40 0 CCGGCTGAAC 0.914954 -190 AGTAAAGAGGCTGGCGTAAAA 14 1 0 CTGGCTAAAA 0.771947 -85 CCGGTATTACCCGGCATGACAGGAGTAAAA 15 60 1 CCGGCTGACA 0.808872 -20 GCTATCTTGTCCGGCATAAATTTTTGACTGA 16 113 1 CCGGCTAAAT 0.713836 -32 ATGAACTTTACAGGCAATCCATAATGAAAAA 18 51 1 CAGGCATCCA 0.492127 -250 ATCCACGGTGCCGGATAAAAACGATCGCGCC 18 214 1 CCGGAAAAAA 0.507897 -87 CATGGTGCTACCGGCGATCACAAACGGTTAA 21 196 0 CCGGCATCAC 0.934056 -58 TCACCTTTCCCGGATTAAACGCTTTTTTGC 21 234 0 CCGGATAAAC 0.640845 -20 ***** ***** Masking position 4 Map Score: 27.8487 Number of sites scoring better than the average of aligned sites = 1107 Number in coding regions = 783 Number in noncoding regions = 324 Number of orfs with sites within 600 bp upstream = 127 Fraction of orfs with sites within 600 bp upstream = 0.0203983 Motif number 6 GAATGCCGGATGCGCTTTGCTTATCCGGCCTA 2 83 0 TCGCTTTCTT 0.975513 -202 GAATGCCGGATGCGCTTTGCTTATCCGGCCTA 2 168 0 TCGCTTTCTT 0.975513 -117 TCGTGCCGGATGCGCTTTGCTTATCCGGCCTA 2 253 0 TCGCTTTCTT 0.975513 -32 CGAGGGCGCATTCGCGCCCTTTATTTTTCGTG 9 14 1 TCGCGCCTTT 0.523786 -92 GAATTTCTCCGCGTTTTTTTCGCATTCAT 13 8 1 TCGCGTTTTT 0.828206 -115 GAGGGGGGCGTGAGCTTCCCTCTGGCTAATCA 16 21 1 TAGCTTCCTC 0.712463 -124 CTCTGGCTAATCAGCTTTTTTCTGAATCCTCC 16 40 1 TAGCTTTTTC 0.669422 -105 TTCATCGCTTTCTGCTTTCTATCATCGCAGGA 18 24 0 TTGCTTTTAT 0.674387 -277 GTCTGAAAGGTCCGCTCTATTTCCCGCCTGCA 18 135 1 TCGCTCTTTT 0.881347 -166 ACCTTTCCGGTGCGCTTTTTATTATTTCACGC 22 28 1 TCGCTTTTAT 0.867165 -143 GGTACTGCCATATGCTCTCTTTTTTTATGAAA 23 124 1 TTGCTCTTTT 0.702079 -141 TTTGCTCATGTGCGCTTGTCTCTTGGTTCTGT 25 13 0 TCGCTTGCTC 0.803973 -288 TTGAATGACTTCCGCTTCATTCCCTTTCATTT 25 75 0 TCGCTTCTTC 0.929724 -226 CGAATATGCGTTCGCTTTTTTCTTGGCAAATC 26 97 1 TCGCTTTTTC 0.945756 -76 CTCCTATCCTTATGCTTCGCTTTTATTCTACT 29 18 1 TTGCTTCCTT 0.905573 -148 AGAACTTATGTTCGCTTTTCATTATATGCGAA 29 130 0 TCGCTTTCAT 0.913249 -36 TTCCGGTACATCTGCTTTTTTTTCTTTTAACG 31 13 0 TTGCTTTTTT 0.886847 -122 TTCATGGTTGTCTGCTTCACTTGAGACGAGCC 32 31 0 TTGCTTCCTT 0.905573 -220 TTAACATATGTTCGCTTCTCTCTCATTCTTTC 33 53 0 TCGCTTCCTC 0.955225 -86 TTTTAGTGATTTTGCTTTCCATTGTGTTACTA 35 121 1 TTGCTTTCAT 0.769579 -65 * ****** *** Masking position 1 Map Score: 17.8953 Number of sites scoring better than the average of aligned sites = 414 Number in coding regions = 328 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 7 ATACTCAAGCCTGGTTTTTTGATGGATTTT 1 51 1 CTGGTTTTTT 0.834749 -24 CCCAAAGCAACGGCTTTTTTAACATTTGTC 3 89 0 CGGCTTTTTT 0.890188 -212 TGGTGATGAACTGTTTTTTTATCCAGTATA 3 209 1 CTGTTTTTTT 0.683115 -92 GCATAGGCTGCTGATTTTTCGTTCTCTTAT 10 189 0 CTGATTTTTC 0.749496 -112 GAATTTCTCCGCGTTTTTTTCGCATTCAT 13 10 1 CGCGTTTTTT 0.829426 -113 TCTGGCTAATCAGCTTTTTTCTGAATCCTC 16 41 1 CAGCTTTTTT 0.881975 -104 GTGCCTGCTCCAGATTTTGCGATGTTTTTT 17 106 1 CAGATTTTGC 0.702342 -103 GTGCCTTAAACACGTTTTTCATTATGGATT 18 66 0 CACGTTTTTC 0.834701 -235 GTTCCAAAATCGCCTTTTGCTGTATATACT 20 56 1 CGCCTTTTGC 0.79757 -54 GGCAGGAGCACACATTTTTCACCAGATTCC 23 74 0 CACATTTTTC 0.726399 -191 GCCATATGCTCTCTTTTTTTATGAAAAAAG 23 130 1 CTCTTTTTTT 0.600316 -135 AGAATCAAAACACCTTTTTCAGTGAATAAC 23 158 1 CACCTTTTTC 0.854343 -107 ACGAGATTAACGGCTTTTTCCGTTTTTCCG 23 186 1 CGGCTTTTTC 0.901305 -79 CGTTTAATTTCAGCTTTTGTCCCGGTGAAA 25 147 0 CAGCTTTTGT 0.822295 -154 CGTTTACAGGCTCGTTTTTTCTGTAGGATT 25 225 0 CTCGTTTTTT 0.778738 -76 AACGCATATTCGGATTTTTTCTTGGCGTGA 26 79 0 CGGATTTTTT 0.785838 -94 AATATGCGTTCGCTTTTTTCTTGGCAAATC 26 99 1 CGCTTTTTTC 0.700393 -74 AAAAGTGTAACACGTTTTGTACGGAAATGG 28 75 0 CACGTTTTGT 0.735143 -51 TCCGGTACATCTGCTTTTTTTTCTTTTAAC 31 14 0 CTGCTTTTTT 0.854386 -121 TATACTGTGCCAGATTTTGCGGCCTCAGGC 32 79 0 CAGATTTTGC 0.702342 -172 GTTTTAAAAGCAGGTTTTTTATACACAAAA 35 52 1 CAGGTTTTTT 0.865473 -134 TTATTTCCAGCTGTTTTTGTGTATAAAAAA 35 66 0 CTGTTTTTGT 0.571709 -120 ********** Masking position 5 Map Score: 19.3988 Number of sites scoring better than the average of aligned sites = 1274 Number in coding regions = 1060 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 212 Fraction of orfs with sites within 600 bp upstream = 0.0340508 Motif number 8 AGATAAGACGCGTCAGCGTCGCATCAGGCGTT 2 30 0 CGCAGCGCGC 0.994265 -255 AGGCGTTGAATGCCGGATGCGCTTTGCTTATC 2 90 0 TGCGGATCGC 0.893938 -195 TGATAAGACGCGCCAGCGTCGCATCAGGCGTT 2 115 0 CGCAGCGCGC 0.994265 -170 AGGCGTTGAATGCCGGATGCGCTTTGCTTATC 2 175 0 TGCGGATCGC 0.893938 -110 TGATAAGACGCGCCAGCGTCGCATCAGGCGTT 2 200 0 CGCAGCGCGC 0.994265 -85 GACTCCTTCGTGCCGGATGCGCTTTGCTTATC 2 260 0 TGCGGATCGC 0.893938 -25 CGTGGCCTTCTGGCGACGACGCTCATCCAGCA 10 147 0 TGCGACGCGC 0.957481 -154 TCGAATAAGGCGTTCACGCCGCATCCGGCGTG 11 53 0 CGTCACGCGC 0.703846 -177 GCATTCATCTCGCTAACTTCGCTTATTATGGG 13 32 1 CGTAACTCGC 0.698761 -91 AGGAAGATGGTGTTGGCGTTGCAATTTTACGA 16 72 0 TGTGGCGTGC 0.773017 -73 CCGGTTTGGTCGGCGGCGGTGCGTTTTTATCT 18 166 0 CGCGGCGTGC 0.965302 -135 CCGACCAAACCGGTAGAGACGCAAACGCAATC 18 185 1 CGTAGAGCGC 0.928156 -116 GATGGACCATCGCCAGTGGCGCGATCGTTTTT 18 230 0 CGCAGTGCGC 0.938069 -71 TGGCACCGCCGCGTAAAAATAG 19 72 0 TGCACCGCGC 0.90531 -12 ** ***** *** Masking position 12 Map Score: 17.0006 Number of sites scoring better than the average of aligned sites = 1937 Number in coding regions = 1763 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 9 GTTACAGGCTTTTCCTGCCCGATGCTAAAACG 6 99 0 TTTCCTGCGA 0.735838 -36 TAATTTATGTTTTCCCGTCACCAACGACAAAA 7 105 1 TTTCCCGCCC 0.942247 -114 TTTTCCGAGGTCCTTGTTGCGA 13 111 0 TTTTCCGGTC 0.846069 -12 AGTCGTTTTCCTGTATGAAAAACCATTA 14 68 0 TTTCCTGAGA 0.634472 -18 TAATCAGCTTTTTTCTGAATCCTCCTCGTAAA 16 47 1 TTTTCTGACC 0.902082 -98 CAATTCTTACTTTTCCGCCTTCACAAATGCCG 17 21 1 TTTTCCGCTC 0.883916 -188 GTCCGCTCTATTTCCCGCCTGCAGATAAAAAC 18 144 1 TTTCCCGCGC 0.902094 -157 GCGATCGTTTTTATCCGGCACCGTGGATTGCG 18 210 0 TTATCCGCCC 0.606041 -91 GCCAGGTTTGTTTCCCGGAACCGAGGTCACAA 21 90 0 TTTCCCGACC 0.910413 -164 TCACCTTTCCCGGATTAAACGCTTTTT 21 237 0 TTTCCCGATA 0.612751 -17 ACATTATTTTCTGGCGCACCTTTCCGGT 22 7 1 TTTTCTGCCA 0.866674 -164 CTTTTTCCGTTTTTCCGCGCTATGTGAATTTG 23 199 1 TTTTCCGGTA 0.707315 -66 ATCCAATGCATTTTCTGCATCCGGACATTTCA 25 120 1 TTTTCTGACC 0.902082 -181 CAGGCTCGTTTTTTCTGTAGGATTCCCCTATT 25 217 0 TTTTCTGAGA 0.695823 -84 TTGGATCATATTTTCTGTCAGACAAGAATCAT 29 74 1 TTTTCTGCGA 0.785916 -92 ATTATTCCTTTTTTCTGCATTCATGTACAATG 31 57 1 TTTTCTGATC 0.765398 -78 CAAGCGTTGTTTTTCCGAGTCCGGGCGGCCCG 32 197 0 TTTTCCGGCC 0.939469 -54 TAGCTTAATCTTTTCTGGGCCGACCAGCAGTG 34 89 1 TTTTCTGGCG 0.696378 -71 TCCCTTATAGTTTTCTGGGACGGTTTTTAGTA 34 124 0 TTTTCTGGCG 0.696378 -36 ******* * ** Masking position 2 Map Score: 14.1221 Number of sites scoring better than the average of aligned sites = 858 Number in coding regions = 788 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 10 AGGCCAGATAAGACGCGTCAGCGTCGCATCAGGC 2 33 0 AACGCGTAGT 0.918728 -252 AGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC 2 118 0 AACGCGCAGT 0.991392 -167 AGGCCTGATAAGACGCGCCAGCGTCGCATCAGGC 2 203 0 AACGCGCAGT 0.991392 -82 CCCGATGCTAAAACGGACAACAGTACCAGGTTAC 6 80 0 AACGGACAGT 0.903192 -55 GACACAAAGGATAAGCGGAAACGTTTTCCTTTGC 9 45 0 AAAGCGGAGT 0.763196 -61 CTTTGATTCATTACGCAGGAGCGTCAT 12 159 1 TACGCAGAGT 0.862784 -17 AGAACGTGAGATACTCACAACTGTATATAAATAC 17 150 1 AACTCACAGT 0.837916 -59 GAATAAGTGTAAACGCGCGATTGTACCATTACCA 21 39 1 AACGCGCAGT 0.990342 -215 TTACATTTTTTAACGCAGTAAGGTGATGAGT 25 280 1 TACGCAGAGT 0.862784 -21 ATTTCAGTATATACGAACAAACGTTTCTGTCAAT 27 46 1 AACGAACAGT 0.917356 -104 GCATCTATAAACACGCGCAAATTTTCTTTTACCT 32 121 0 AACGCGCATT 0.892112 -130 ATCACTAAAAATACGAACTAAAGTTCGGTGGTTT 35 97 0 AACGAACAGT 0.917356 -89 * ****** * ** Masking position 10 Map Score: 9.16851 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 265 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 11 TCAGGCGTTACATACCGGATGCGGCTAC 2 5 0 CATCGGGCGG 0.920971 -280 TCTTATCTGGCCTACACGCTGCGATTTTGTAGGC 2 54 1 CCTCCGGCGA 0.99553 -231 TCTTATCAGGCCTACGCGCTGCGATTTTGTAGGC 2 139 1 CCTCCGGCGA 0.99553 -146 TCTTATCAGGCCTACACGCTGCGATTTTGTAGGC 2 224 1 CCTCCGGCGA 0.99553 -61 TTGACTCCTTCGTGCCGGATGCGCTTTGCTTATC 2 260 0 CGTCGGGCGC 0.947441 -25 CCGCCCAACTCCTTCAGGTAGCGACTC 3 284 1 CCTCGGGCGA 0.995531 -17 ACAGGCTTTTCCTGCCCGATGCTAAAACGGACAA 6 94 0 CCTCCGGCTA 0.95114 -41 GCTCACGTGGCCTTCTGGCGACGACGCTCATCCA 10 150 0 CCTCGGACGA 0.951134 -151 TCCAGTGTAACAGGCGGGAAGCGATTAAAAAAGA 11 180 0 CAGCGGGCGA 0.901479 -50 TTCTGGCGCACCTTTCCGGTGCGCTTTTTATTAT 22 19 1 CCTTCGGCGC 0.904895 -152 *** * ** **** Masking position 12 Map Score: 12.5341 Number of sites scoring better than the average of aligned sites = 217 Number in coding regions = 196 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 GCATCCGGTATGTAACGCCTGATGCGACGCT 2 17 1 TGTACGCCTG 0.968169 -268 GCATCCGGCATTCAACGCCTGATGCGACGCT 2 102 1 TTCACGCCTG 0.98997 -183 GCATCCGGCATTCAACGCCTGATGCGACGCT 2 187 1 TTCACGCCTG 0.98997 -98 CGTATTTTGATTACACTCCTGTTAATCCATA 6 33 1 TTAACTCCTG 0.861084 -102 GTCAGGCCTATTCGACTCCTGCAATGTATTG 11 105 0 TTCACTCCTG 0.970013 -125 CCGTCTGACGTGCTACGCCTGTCAGGCCTAT 11 125 0 TGCACGCCTG 0.979693 -105 TTTTACGCCAGCCTCTTTACT 14 1 1 TTTACGCCAG 0.907488 -85 TTTTACTCCTGTCATGCCGGG 15 69 0 TTTACTCCTG 0.953258 -11 GTCCGCTCTATTTCCCGCCTGCAGATAAAAA 18 144 1 TTTCCGCCTG 0.935644 -157 *** ******* Masking position 1 Map Score: 11.2603 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 126 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 TTAAAATCATAACATAAAAGAATGATTCACAT 7 21 1 ACTAAAAGAA 0.956196 -198 ACGTGAGCACAAGATAAGAGAACGAAAAATCA 10 176 1 AGTAAGAGAA 0.819898 -125 ATAATGCTGTATGATAAAAAAATGCTGGATAG 12 127 0 AGTAAAAAAA 0.65602 -49 CTCTTTTTTTATGAAAAAAGAATCAAAACACC 23 140 1 AGAAAAAGAA 0.754394 -125 GCTGAAATTAAACGTATAAGAATCCAACCCTT 25 163 1 ACTATAAGAA 0.754392 -138 TACTCTCAAAATCTTAAAAGAAAACCCCCGAT 28 27 0 ACTAAAAGAA 0.956117 -99 GACGTTAAAAGAAAAAAAAGCAG 31 2 1 AGTAAAAGAA 0.956196 -133 AGAATCATATAACATAAAAGAACAGATAAGCT 31 94 1 ACTAAAAGAA 0.956196 -41 CGGGCAGCATAAGGTAAAAGAAAATTTGCGCG 32 110 1 AGTAAAAGAA 0.956196 -141 CTGCTTTTAAAACGTAAAAGCAGGTATTCAGT 35 33 0 ACTAAAAGCA 0.819898 -153 * * ******** Masking position 6 Map Score: 5.57079 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 20 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 14 TCTTATCTGGCCTACACGCTGCGATTTTGTA 2 54 1 CCTACCGCTG 0.975587 -231 TCTTATCAGGCCTACGCGCTGCGATTTTGTA 2 139 1 CCTACCGCTG 0.975587 -146 TCTTATCAGGCCTACACGCTGCGATTTTGTA 2 224 1 CCTACCGCTG 0.975587 -61 GTTGACTCCTTCGTGCCGGATGCGCTTT 2 267 0 CCTTCTGCCG 0.945346 -18 AAATTACATACCTGCCCGCCCAACTCCTTCA 3 269 1 CCTGCCGCCC 0.977345 -32 ACAGGCTTTTCCTGCCCGATGCTAAAACGGA 6 97 0 CCTGCCGATG 0.878209 -38 CACGAGGGCGCATTCGCGCCCTTTATTTTTC 9 12 1 CATTCCGCCC 0.752305 -94 AAGAGTAATTTGTTCACGCCGGATGCGGCGT 11 39 1 TGTTCCGCCG 0.709396 -191 TCGAATAAGGCGTTCACGCCGCATCCGGCGT 11 54 0 CGTTCCGCCG 0.968732 -176 TTCTGTTTTGCGTGCCTGCTCCAGATTTTGC 17 95 1 CGTGCTGCTC 0.779394 -114 TATGGCAGTACCTGCATGGTGAGTCCTGTAT 23 105 0 CCTGCTGGTG 0.725824 -160 ***** ***** Masking position 3 Map Score: 5.31579 Number of sites scoring better than the average of aligned sites = 1361 Number in coding regions = 1209 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 15 CCAGGCTTGAGTATAGCCTGGTTTCGTTTG 1 35 0 GTATAGCCTG 0.517973 -40 CATCCGGTATGTAACGCCTGATGCGACGCT 2 18 1 GTAACGCCTG 0.90774 -267 CATCCGGCATTCAACGCCTGATGCGACGCT 2 103 1 TCAACGCCTG 0.948484 -182 CATCCGGCATTCAACGCCTGATGCGACGCT 2 188 1 TCAACGCCTG 0.948484 -97 CACTGAACAGGCATCTCTTGCCATAAAACT 3 44 1 GCATCTCTTG 0.51143 -257 TGGATGAGCGTCGTCGCCAGAAGGCCACGT 10 150 1 TCGTCGCCAG 0.646935 -151 TCAGGCCTATTCGACTCCTGCAATGTATTG 11 105 0 TCGACTCCTG 0.914744 -125 CGTCTGACGTGCTACGCCTGTCAGGCCTAT 11 125 0 GCTACGCCTG 0.947245 -105 TTTTACTCCTGTCATGCCGGG 15 69 0 TTTACTCCTG 0.598917 -11 CTTTTACGTCTTCTCCTGCGATGATAGA 18 9 1 TCTTCTCCTG 0.81766 -292 GTTCGTGTCTCCTGAAAAAAATCG 21 5 1 GTGTCTCCTG 0.831914 -249 CAGTGATAGAGCAAAGCCTGAGGCCGCAAA 32 64 1 GCAAAGCCTG 0.812411 -187 ACATGATCCAGCGTCTCCTGTCTCATTTTC 32 158 0 GCGTCTCCTG 0.94511 -93 ********** Masking position 7 Map Score: 7.95317 Number of sites scoring better than the average of aligned sites = 1993 Number in coding regions = 1891 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949