AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -ilexA_ecoli_hinf_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 HI0070 143 DNA repair protein (recN) #35 HI0072 63 conserved hypothetical protein #36 HI0249 153 excinuclease ABC, subunit A (uvrA) #37 HI0313 62 Holliday junction DNA helicase (ruvA) #38 HI0314 46 crossover junction endodeoxyribonuclease (ruvC) #39 HI0315 159 conserved hypothetical protein #40 HI0316 21 datP pyrophosphohydrolase (ntpA) #41 HI0317 218 aspartyl-tRNA synthetase (aspS) #42 HI0600 300 recA protein (recA) #43 HI0749 248 lexA repressor (lexA) #44 HI1188 300 DNA helicase II (uvrD) #45 HI1247 300 excinuclease ABC, subunit B (uvrB) #46 HI1593 34 H. influenzae predicted coding region HI1593 #47 HI1596 58 leucine responsive regulatory protein (lrp) #48 HI1597 84 DNA repair protein (radA) #49 HI1598 300 conserved hypothetical protein Motif number 1 GTTTGATTGGCTGTGGTTTTATACAGTCA 1 4 0 CTGTATACAG 0.987484 -71 TGGTGATGAACTGTTTTTTTATCCAGTATAATTTGT 4 209 1 CTGTATCCAG 0.518545 -92 TGCCACAATATTGGCTGTTTATACAGTATTTCAGGT 5 88 1 TTGTATACAG 0.936087 -32 GATTACACTCCTGTTAATCCATACAGCAACAGTACT 8 41 1 CTGTATACAG 0.969914 -94 ACTGGATGTACTGTACATCCATACAGTAACTCACAG 9 179 1 CTGTATACAG 0.864171 -40 GTTGAATATACTGGTTATTTATACAGGTAAAATAAC 10 37 0 CTGTATACAG 0.537595 -37 TGAAGTTATACTGTTTTTATATACAGTAGTCTGTTC 15 264 0 CTGTATACAG 0.504616 -37 ACTCCGAATGCTGGTTATCTATCCAGTGTAACAGGC 17 199 0 CTGTATCCAG 0.809521 -31 TCATCCTTCGCTGGATATCTATCCAGCATTTTTTTA 18 109 1 CTGTATCCAG 0.632496 -67 ACAGTATAAACTGGTTTTATATACAGTAAAGAGGCT 20 20 0 CTGTATACAG 0.509851 -66 AAAACCATTACTGTTATTGTGTACAGTATAAACTGG 20 42 0 CTGTGTACAG 0.907359 -44 AATAACAGTAATGGTTTTTCATACAGGAAAACGACT 20 60 1 ATGTATACAG 0.82705 -26 TACTGTATGAGCATACAGTATAATTGCT 21 3 1 CTGAATACAG 0.575282 -77 ATACTCACAACTGTATATAAATACAGTTACAGATTT 25 160 1 CTGTATACAG 0.499986 -49 CGCCAAAAAGCTGGGTATATATACAGATTTGCTGA 27 10 0 CTGTATACAG 0.639075 -74 GAACCATAAACTGCACAATAAACCAGAGATTTATCG 29 24 0 CTGAAACCAG 0.815379 -86 TACAGTTATGCTGTGAGTATATACAGCAAAAGGCGA 29 65 0 CTGTATACAG 0.90161 -45 TCCGCCCCCTGGGTGTATATACAGTTATGCTGTG 29 86 0 CTGTATACAG 0.639075 -24 ACAAATTGACCTGAATGAATATACAGTATTGGAATG 30 153 0 CTGAATACAG 0.572391 -101 CCCATATTTACTGATGATATATACAGGTATTTAGCG 31 135 1 CTGTATACAG 0.988347 -36 TATGATATAACTGACTTAATTTACAGTAAAGGATTT 34 91 0 CTGATTACAG 0.687895 -53 ATTTTAATATCTGTGCAAATATCCAGTTAAAATATA 36 76 0 CTGAATCCAG 0.841899 -78 TAAAATAAAACTGGACGAACATCCAG 37 1 0 CTGAATCCAG 0.52168 -62 TTTTCTTGACCTGTACATCAATACAGATATAATCAC 42 243 1 CTGTATACAG 0.864171 -58 TCACAAAAATTTGAACATTCAAACAGGATTTTAATT 42 275 1 TTGTAAACAG 0.767948 -26 ACACAGATAACTGGTATTGTATACAGATTGTGTAAA 43 211 0 CTGTATACAG 0.98136 -38 TACCAGTTATCTGTGTTTAAAAACAGGA 43 231 1 CTGTAAACAG 0.576255 -18 ACTATAATAACTGTAAATTTAAACAGATTAAAGATA 44 271 1 CTGTAAACAG 0.575027 -30 TTCTATTGTATTGTATATTTAACCAGTTAATTTAA 49 276 1 TTGTAACCAG 0.521645 -25 *** * ****** Masking position 2 Map Score: 93.1925 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 15 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 2 GTAGCCGCATCCGGTATGTAACGCC 2 6 1 CGCATCCGGT 0.861217 -279 GCGTCAGCGTCGCATCAGGCGTTACATACC 2 23 0 CGCATCAGGC 0.982341 -262 GCTGACGCGTCTTATCTGGCCTACACGCTG 2 45 1 CTTATCTGGC 0.758989 -240 ATGCGCTTTGCTTATCCGGCCTACAAAATC 2 76 0 CTTATCCGGC 0.981037 -209 ATAAGCAAAGCGCATCCGGCATTCAACGCC 2 91 1 CGCATCCGGC 0.993931 -194 GCGCCAGCGTCGCATCAGGCGTTGAATGCC 2 108 0 CGCATCAGGC 0.982341 -177 GCTGGCGCGTCTTATCAGGCCTACGCGCTG 2 130 1 CTTATCAGGC 0.946158 -155 ATGCGCTTTGCTTATCCGGCCTACAAAATC 2 161 0 CTTATCCGGC 0.981037 -124 ATAAGCAAAGCGCATCCGGCATTCAACGCC 2 176 1 CGCATCCGGC 0.993931 -109 GCGCCAGCGTCGCATCAGGCGTTGAATGCC 2 193 0 CGCATCAGGC 0.982341 -92 GCTGGCGCGTCTTATCAGGCCTACACGCTG 2 215 1 CTTATCAGGC 0.946158 -70 ATGCGCTTTGCTTATCCGGCCTACAAAATC 2 246 0 CTTATCCGGC 0.981037 -39 ATAAGCAAAGCGCATCCGGCACGAAGGAGT 2 261 1 CGCATCCGGC 0.993931 -24 GCTTATCCTTTGTGTCCGGCAAAAACATCC 11 63 1 TGTGTCCGGC 0.726496 -43 AAGACATTGACGCATCCCGCCCGGCTAACT 15 22 0 CGCATCCCGC 0.906128 -279 GGCGACGACGCTCATCCAGCAGAAATGAAA 15 138 0 CTCATCCAGC 0.768578 -163 GCGTTCACGCCGCATCCGGCGTGAACAAAT 17 46 0 CGCATCCGGC 0.993931 -184 ACGTGCTACGCCTGTCAGGCCTATTCGACT 17 119 0 CCTGTCAGGC 0.715759 -111 AAAGTGCTATCTTGTCCGGCATAAATTTTT 22 108 1 CTTGTCCGGC 0.950777 -37 ATGTAAAGTCCGTATCGGGCAGTGACTACC 23 168 1 CGTATCGGGC 0.901508 -88 CAGACCGCAGCCCGTCAGGCTGAAGAGAGT 26 110 0 CCCGTCAGGC 0.802565 -191 CGCGATCGTTTTTATCCGGCACCGTGGATT 26 213 0 TTTATCCGGC 0.783916 -88 ********** Masking position 5 Map Score: 53.885 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 TGACTGTATAAAACCACAGCCAATCAA 1 4 1 CTGTATAAAC 0.975002 -71 TAGCCGCATCCGGTATGTAACGCCTGATGCGACG 2 12 1 CGGTATGACC 0.682608 -273 ACAAATTATACTGGATAAAAAAACAGTTCATCAC 4 211 0 CTGGATAAAC 0.946432 -90 ACCTGAAATACTGTATAAACAGCCAATATTGTGG 5 90 0 CTGTATAACC 0.980313 -30 AGTACTGTTGCTGTATGGATTAACAGGAGTGTAA 8 43 0 CTGTATGAAC 0.959532 -92 CTGTGAGTTACTGTATGGATGTACAGTACATCCA 9 181 0 CTGTATGAAC 0.959532 -38 GTTATTTTACCTGTATAAATAACCAGTATATTCA 10 37 1 CTGTATAACC 0.980313 -37 GAACAGACTACTGTATATAAAAACAGTATAACTT 15 264 1 CTGTATAAAC 0.975016 -37 GCCTGTTACACTGGATAGATAACCAGCATTCGGA 17 199 1 CTGGATAACC 0.957522 -31 TAAAAAAATGCTGGATAGATATCCAGCGAAGGAT 18 111 0 CTGGATAACC 0.957522 -65 AGCCTCTTTACTGTATATAAAACCAGTTTATACT 20 20 1 CTGTATAACC 0.980313 -66 CCAGTTTATACTGTACACAATAACAGTAATGGTT 20 42 1 CTGTACAAAC 0.735081 -44 AGTCGTTTTCCTGTATGAAAAACCATTACTGTTA 20 62 0 CTGTATGACC 0.968001 -24 AGCAATTATACTGTATGCTCATACAGTA 21 5 0 CTGTATGTAC 0.807831 -75 ATACTCACAACTGTATATAAATACAGTTACAGAT 25 160 1 CTGTATAAAC 0.975016 -49 TCAGCAAATCTGTATATATACCCAGCTTTTTGG 27 10 1 CTGTATAACC 0.98019 -74 TCGCCTTTTGCTGTATATACTCACAGCATAACTG 29 65 1 CTGTATAAAC 0.975018 -45 CACAGCATAACTGTATATACACCCAGGGGGCGGA 29 86 1 CTGTATAACC 0.980312 -24 CATTCCAATACTGTATATTCATTCAGGTCAATTT 30 153 1 CTGTATATTC 0.615466 -101 CGCTAAATACCTGTATATATCATCAGTAAATATG 31 137 0 CTGTATAATC 0.900276 -34 TATATTTTAACTGGATATTTGCACAGATATTAAA 36 76 1 CTGGATATAC 0.758011 -78 CTGGATGTTCGTCCAGTTTTATTT 37 1 1 CTGGATGTCC 0.708278 -62 GTGATTATATCTGTATTGATGTACAGGTCAAGAA 42 245 0 CTGTATTAAC 0.8236 -56 AATTAAAATCCTGTTTGAATGTTCAAATTTTTGT 42 277 0 CTGTTTGATC 0.492992 -24 TTTACACAATCTGTATACAATACCAGTTATCTGT 43 211 1 CTGTATAACC 0.980313 -38 TCCTGTTTTTAAACACAGATAACTGG 43 233 0 CTGTTTTAAC 0.452744 -16 TATCTTTAATCTGTTTAAATTTACAGTTATTATA 44 273 0 CTGTTTAAAC 0.873731 -28 TTAAATTAACTGGTTAAATATACAATACAATAG 49 278 0 CTGGTTAAAC 0.75801 -23 ******* * ** Masking position 3 Map Score: 54.0247 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 50 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 4 CGCGTCTTATCTGGCCTACACGCTGCGATTT 2 50 1 CTGGCTACAC 0.808276 -235 CTTTGCTTATCCGGCCTACAAAATCGCAGCG 2 70 0 CCGGCTACAA 0.960542 -215 CAAAGCGCATCCGGCATTCAACGCCTGATGC 2 96 1 CCGGCTTCAA 0.894103 -189 CTTTGCTTATCCGGCCTACAAAATCGCAGCG 2 155 0 CCGGCTACAA 0.960542 -130 CAAAGCGCATCCGGCATTCAACGCCTGATGC 2 181 1 CCGGCTTCAA 0.894103 -104 CGCGTCTTATCAGGCCTACACGCTGCGATTT 2 220 1 CAGGCTACAC 0.561668 -65 CTTTGCTTATCCGGCCTACAAAATCGCAGCG 2 240 0 CCGGCTACAA 0.960542 -45 AGATAAAACTCCGGCCTTACCGGGTTATCCC 4 117 0 CCGGCTTACC 0.559436 -184 TCCTTTGTGTCCGGCAAAAACATCCCTTCAG 11 68 1 CCGGCAAAAC 0.939196 -38 AAAATATCACCCGGCTAAAAAATAGAATAGA 15 109 0 CCGGCAAAAA 0.928329 -192 TATTGATCTGCTGGCAAGAACAGACTACTGT 15 247 1 CTGGCAGAAC 0.632189 -54 GTTTCGTTCACGGGCTTGAAAAAGCGCCCAA 16 57 0 CGGGCTGAAA 0.793317 -145 CACGCCGCATCCGGCGTGAACAAATTACTCT 17 40 0 CCGGCTGAAC 0.952087 -190 AGTAAAGAGGCTGGCGTAAAA 20 1 0 CTGGCTAAAA 0.75951 -85 CCGGTATTACCCGGCATGACAGGAGTAAAA 21 60 1 CCGGCTGACA 0.701711 -20 GCTATCTTGTCCGGCATAAATTTTTGACTGA 22 113 1 CCGGCTAAAT 0.650445 -32 ATTGAAATCTCCGGCTTGAAACAAATGTGGC 24 11 1 CCGGCTGAAA 0.943385 -116 TTGAATGTTGCGGGGAAGAAAAATGCCGCTC 25 64 0 CGGGGAGAAA 0.474693 -145 TCTCAGTGTGCTGGGCAAAAAAACATCGCAA 25 122 0 CTGGGAAAAA 0.426448 -87 ATCCACGGTGCCGGATAAAAACGATCGCGCC 26 214 1 CCGGAAAAAA 0.502033 -87 GACCTCGGTTCCGGGAAACAAACCTGGCCAG 30 94 1 CCGGGAACAA 0.851437 -160 CATGGTGCTACCGGCGATCACAAACGGTTAA 30 196 0 CCGGCATCAC 0.85708 -58 CACCATGCCACCGGGCAAAAAAGCGTTTAAT 30 220 1 CCGGGAAAAA 0.836597 -34 TCACCTTTCCCGGATTAAACGCTTTTTTGC 30 234 0 CCGGATAAAC 0.668712 -20 AAGTACGTGACCGGGGTGAACGAGCGCAGCC 32 48 0 CCGGGTGAAC 0.887063 -153 TGTACGCTCCCGGGGATTCACTCACTTGCCG 32 80 1 CGGGGTTCAC 0.478279 -121 CCACTCCCAACGGGGTAACACTTTTACTAAC 39 65 1 CGGGGAACAC 0.611544 -95 ***** ***** Masking position 4 Map Score: 27.6864 Number of sites scoring better than the average of aligned sites = 1193 Number in coding regions = 932 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 5 GCTTATCCGGCCTACAAAATCGCAGCGTGTAGGCCA 2 61 0 CCTACGCAGC 0.995592 -224 AGCGCGTAGGCCTGATAAGACGCGCCAGCGTCGCAT 2 123 0 CCTACGCGCC 0.976341 -162 GCTTATCCGGCCTACAAAATCGCAGCGCGTAGGCCT 2 146 0 CCTACGCAGC 0.995592 -139 AGCGTGTAGGCCTGATAAGACGCGCCAGCGTCGCAT 2 208 0 CCTACGCGCC 0.976341 -77 GCTTATCCGGCCTACAAAATCGCAGCGTGTAGGCCT 2 231 0 CCTACGCAGC 0.995592 -54 TCCTGACCCGCCGCGGCAGCCTGTATT 12 2 1 CCTCCGCGGC 0.973159 -132 GCGTCAATATCCTGACACAACGCAGCATGTGTCACC 12 86 0 CCTACGCAGC 0.995649 -48 AGATAAGAGAACGAAAAATCAGCAGCCTATGCAGCG 15 187 1 ACGAAGCAGC 0.728487 -114 ATACAGGAATCCTCTGAAAGCGGAGCCGTTTCGTTC 16 79 0 CCTACGGAGC 0.950486 -123 CGCCGGAAGTCCGTATAATGCGCAGCCACATTTGTT 24 30 0 CCGACGCAGC 0.989783 -97 AAATGCCGCCACTCAAACAGAGCGGCATTTTTCTTC 25 45 1 ACTAAGCGGC 0.87316 -164 ATAGAGCGGACCTTTCAGACCGCAGCCCGTCAGGCT 26 119 0 CCTACGCAGC 0.995654 -182 TTACTCCAATCACGCGGGTACAGAAACT 26 283 0 ACTACGCGGG 0.776222 -18 CTCCGCCCAACCTATTTTTACGCGGCGGTGCCA 27 61 1 CCTTCGCGGC 0.960726 -23 TGTGAGTTCCGTAAATTAAGCAGCGGCCCAAATT 32 177 0 CCGAAGCAGC 0.941595 -24 *** * ****** Masking position 12 Map Score: 27.0716 Number of sites scoring better than the average of aligned sites = 229 Number in coding regions = 196 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 6 TTAACAGGAGTGTAATCAAAATACGCCGATTTT 8 25 0 TAATAAAATA 0.773124 -110 AAAGCGACGTTTTGATAAAAAAATATTGTCCCC 14 142 1 TGATAAAAAA 0.85505 -64 ACAGGCGGGAAGCGATTAAAAAAGAGGCGGGTC 17 172 0 AGATAAAAAA 0.657598 -58 TGAATATGTAATATTAAAATATTTGCTTCCA 18 9 1 TTATAAAATA 0.641247 -167 GATAATGCTGTATGATAAAAAAATGCTGGATAG 18 127 0 TGATAAAAAA 0.855048 -49 TCTTTCATTTTGCGATCAAAATAACACTTTTAA 23 78 0 TGATAAAATA 0.914828 -178 ATTCAAACTTTCAAATTAAAATATTTATCTTTC 23 105 0 TAATAAAATA 0.773124 -151 GGTAAAAATTTTCGATTGAAATAGATTTGACAA 34 47 1 TGATGAAATA 0.665275 -97 ATATTTGCACAGATATTAAAATATGCGATAATG 36 90 1 ATATAAAATA 0.367877 -64 AATTCTTCCGAATGATAAAAAAATTAACGCATA 37 40 0 AGATAAAAAA 0.657598 -23 TCAAGATCAATAAGATCAAAACAGAAGGAAATA 39 135 1 TGATAAAACA 0.610414 -25 TGCCGCTTGTTGAGATTAAATTACGTTAAGGAT 41 17 0 TGATAAATTA 0.409261 -202 ATGCTGACAAATCAATCAAAAAAGCAAAGAAAA 41 111 0 AAATAAAAAA 0.378617 -108 AACCAATCGTTTAGATAAAAATAAATTTTAAAT 42 113 0 TGATAAAATA 0.914828 -188 AAATATTTATATTAATAAAAAAATATGGGGTAT 42 212 0 AAATAAAAAA 0.378617 -89 TGTTTATAAATAGTATAAAAATAGCTTTCAAAG 44 119 1 TTATAAAATA 0.641259 -182 ATGCTGAGTAAGATGAAAATATTCATATTTT 49 9 1 TGATAAAATA 0.914828 -292 TTAAAATAAGTAAGATGAAAATATGAATATTTT 49 26 0 TGATAAAATA 0.914828 -275 ATTGCGACTTTTAAATAAAAAAATAATCCGAAA 49 165 0 TAATAAAAAA 0.651756 -136 TTTTATTTATTGTGATTAAAATATTGCGACTTT 49 187 0 TGATAAAATA 0.914828 -114 AAATATACAATACAATAGAAATAAATCAAGATT 49 263 0 TAATGAAATA 0.386717 -38 * *** ****** Masking position 6 Map Score: 14.0663 Number of sites scoring better than the average of aligned sites = 138 Number in coding regions = 84 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 7 AACGCCTGATGCGACGCTGACGCGTCTTATC 2 30 1 GCGACGCTGC 0.980669 -255 AACGCCTGATGCGACGCTGGCGCGTCTTATC 2 115 1 GCGACGCTGC 0.980669 -170 AACGCCTGATGCGACGCTGGCGCGTCTTATC 2 200 1 GCGACGCTGC 0.980669 -85 GAGTCGCTACCTGAAGGAGTT 4 290 0 GAGTCGCTAC 0.898801 -11 TCACTGTTCAGAGTCGCTACCCGTCACGATA 7 230 0 GAGTCGCTAC 0.898801 -71 CATGAAATCTGCGTCAATATCCTGACACAAC 12 101 0 GCGTCAATAC 0.905547 -33 CGGGCGGGATGCGTCAATGTCTTTATTTCTA 15 29 1 GCGTCAATGC 0.954916 -272 AAAAAGAGGCGGGTCGATGACAAAGGTTACA 17 156 0 GGGTCGATGC 0.881867 -74 TCCTGACAAGGCATCGATGGCTATAATCCTT 24 76 1 GCATCGATGC 0.805315 -51 GATTGCGTTTGCGTCTCTACCGGTTTGGTCG 26 186 0 GCGTCTCTAC 0.865551 -115 AAAAACGATCGCGCCACTGGCGATGGTCCAT 26 230 1 GCGCCACTGC 0.916198 -71 TACATTATGAGCGTCAATATCAGTGTACCGT 28 76 0 GCGTCAATAC 0.905547 -35 ********* * Masking position 8 Map Score: 10.0167 Number of sites scoring better than the average of aligned sites = 815 Number in coding regions = 721 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 8 GAATGCCGGATGCGCTTTGCTTATCCGGCCTAC 2 82 0 TGCGTGCTTA 0.945767 -203 GAATGCCGGATGCGCTTTGCTTATCCGGCCTAC 2 167 0 TGCGTGCTTA 0.945767 -118 TCGTGCCGGATGCGCTTTGCTTATCCGGCCTAC 2 252 0 TGCGTGCTTA 0.945767 -33 TCAGGTAGGATCCGCTAATCTTATGGATAAAAA 3 217 0 TCCGTTCTTA 0.672792 -84 TGGTGGTTATTGCGAGCCGCTTTCCAGAAACAG 5 26 1 TGCGGGCTTT 0.962141 -94 CGACAAAATTTGCGAGGCTCTTTCCGAAAATAG 9 129 1 TGCGGTCTTT 0.925316 -90 GAATTTCTCCGCGTTTTTTTCGCATTCATC 19 8 1 TCCGGTTTTT 0.532108 -115 CCTTGTGCGGGGCGTGATGCTTTACCATACTTG 23 202 1 GGCGGGCTTT 0.93888 -54 CTCCAGATTTTGCGATGTTTTTTTGCCCAGCAC 25 113 1 TGCGTTTTTT 0.894373 -96 TTTGGTCGGCGGCGGTGCGTTTTTATCTGCAGG 26 161 0 GGCGTGTTTT 0.913029 -140 TTTGGCGGAGGGCGTTGCGCTTCTCCGCCCAAC 27 39 1 GGCGTGCTTC 0.826041 -45 GGCGCACCTTTCCGGTGCGCTTTTTATTATTTC 31 23 1 TCCGTGCTTT 0.917133 -148 TTTTATTCTATGCGTTAATTTTTTTATCATTCG 37 32 1 TGCGTTTTTT 0.894373 -31 TTATGGTGATAGCGGTTCTCTTTTGGGAAAAGC 39 27 1 AGCGTTCTTT 0.720988 -133 AAAGTGCGGTCGGTTTTTTGATAGTTT 45 284 0 TGCGTGTTTT 0.945558 -17 ATTTTCAGTAGGCGATGATTTTT 47 1 0 GGCGTTTTTT 0.836549 -58 **** * ***** Masking position 11 Map Score: 10.618 Number of sites scoring better than the average of aligned sites = 554 Number in coding regions = 426 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 104 Fraction of orfs with sites within 600 bp upstream = 0.0167041 Motif number 9 TTTGCTTATCCGGCCTACAAAATCGCAGCGT 2 69 0 CGGCTACAAA 0.837084 -216 TTTGCTTATCCGGCCTACAAAATCGCAGCGC 2 154 0 CGGCTACAAA 0.837084 -131 TTTGCTTATCCGGCCTACAAAATCGCAGCGT 2 239 0 CGGCTACAAA 0.837084 -46 CAAAGTGTGACGCCGTGCAAATAATCAATGT 3 173 0 CGCCTGCAAA 0.958806 -128 TTCTGGAAAGCGGCTCGCAATAACCACCAAC 5 24 0 CGGCCGCAAT 0.974049 -96 TGAAGATTCACGGCGCGCAATGCCTGGGTCT 7 188 0 CGGCCGCAAT 0.974049 -113 TTTCGGAAAGAGCCTCGCAAATTTTGTCGTT 9 127 0 AGCCCGCAAA 0.958806 -92 TAAAGCATCACGCCCCGCACAAGGAAGCGGT 23 195 0 CGCCCGCACA 0.963047 -61 TCACAAATGCCGCCACTCAAACAGAGCGGCA 25 41 1 CGCCCTCAAA 0.93258 -168 AATCTGGAGCAGGCACGCAAAACAGAATTGA 25 91 0 AGGCCGCAAA 0.958806 -118 AACGTGTTTAAGGCACTCACTGTATTACTTA 26 80 1 AGGCCTCACT 0.303191 -221 TGGCACCGCCGCGTAAAAATAGGTTGG 27 67 0 CGCCCGTAAA 0.845331 -17 GTTTGCGTAGCGCCGCGCGAAACATGAGCGG 28 28 0 CGCCCGCGAA 0.929065 -83 CTTGTAGGTAAGCCTCGCAATGATATTAACT 35 38 1 AGCCCGCAAT 0.906805 -26 **** ****** Masking position 4 Map Score: 11.2637 Number of sites scoring better than the average of aligned sites = 707 Number in coding regions = 639 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 10 AAAATTCCTTTTAAAATCATAAC 9 1 1 AAAATCTTTA 0.774319 -218 CGTTAATGTGAATCATTCTTTTATGTTATGATT 9 25 0 AATCACTTTA 0.817055 -194 TGTCCGGCAAAAACATCCCTTCAGCCGGAGCAT 11 75 1 AAACACTTCA 0.673525 -31 TGAAAAGTCCAAAATGCCATTTTCTGCATTATT 14 83 1 AAAATCTTTT 0.423639 -123 GGCGTGAACAAATTACTCTTTTTCGCACAATCC 17 26 0 AATTACTTTT 0.625158 -204 TTATAGGTCGAATAAGGCGTTCACGCCGCATCC 17 59 0 AATAACTTCA 0.683857 -171 TTGCGATCAAAATAACACTTTTAAATCTTTCAA 23 69 0 AATAACTTTA 0.844806 -187 GCGGGTACAGAAACTGACTTTTAGTAATTCACC 26 265 0 AAACTCTTTA 0.737787 -36 TTATGGTTCCAAAATCGCCTTTTGCTGTATATA 29 51 1 AAAATCTTTT 0.604967 -59 TGTCTCCTGAAAAAAATCGTTCTGAATAAGTGT 30 16 1 AAAAACTTCT 0.532978 -238 GTAATGGTACAATCGCGCGTTTACACTTATTCA 30 38 0 AATCGCTTTA 0.602905 -216 TACCATTACCAATAGCGCTTTTACTATGTTGTG 30 62 1 AATAGCTTTA 0.649195 -192 GCCACCGGGCAAAAAAGCGTTTAATCCGGGAAA 30 226 1 AAAAACTTTA 0.863534 -28 TCATTCCAGAAATTGCCCATTTTATTCTATTTT 31 89 1 AATTGCTTTT 0.36183 -82 AAAATACTGTAAAAAATCCTTTACTGTAAATTA 34 78 1 AAAAACTTTA 0.863466 -66 AATGATCGCAAAATTTACATTTATTTCATACTT 36 119 1 AAATTCTTTA 0.698674 -35 TGGGTAATTAAATTACCCATTTATTGCATCA 38 9 0 AATTACTTTA 0.786087 -38 TGGGTAATTTAATTACCCATTTTTTATAGAAAT 38 23 1 AATTACTTTT 0.625159 -24 ATCTTGATTTAATTAAACGTTTTGACCTAGGCT 39 109 0 AATTACTTTT 0.62516 -51 GATATGGCACAAAAAAGCCTTTATTTTGAATAT 41 71 1 AAAAACTTTA 0.863466 -148 TTGTCAGCATAAATAACCTTTTTATCTCTCTTG 41 134 1 AAATACTTTT 0.65956 -85 CTGGCTCACAAATCTGACATTTATATTTAGGTG 42 73 0 AATCTCTTTA 0.707953 -228 TACTATTTATAAACAAACTTTTAATTCGTTTAC 44 101 0 AAACACTTTA 0.838492 -200 AAATAGTATAAAAATAGCTTTCAAAGCATATGG 44 126 1 AAAATCTTCA 0.577141 -175 TATTCTACAGAATTTTCCTTTCATTTTCAGTAG 47 23 0 AATTTCTTCA 0.442149 -36 CACAATAAATAAAAATTCATTTATAGCTATTTA 49 206 1 AAAAACTTTA 0.863423 -95 ***** * **** Masking position 10 Map Score: 10.2745 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 204 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 89 Fraction of orfs with sites within 600 bp upstream = 0.0142949 Motif number 11 AGCGTCGCATCAGGCGTTACATACCGGATGC 2 17 0 CAGGCGTACA 0.951974 -268 AGCGTCGCATCAGGCGTTGAATGCCGGATGC 2 102 0 CAGGCGTGAA 0.976232 -183 AGCGTCGCATCAGGCGTTGAATGCCGGATGC 2 187 0 CAGGCGTGAA 0.976232 -98 AACATCCCTTCAGCCGGAGCATAGAGATTA 11 86 1 CAGCCGGGCA 0.738814 -20 CAATACATTGCAGGAGTCGAATAGGCCTGAC 17 105 1 CAGGAGTGAA 0.850897 -125 ATAGGCCTGACAGGCGTAGCACGTCAGACGG 17 125 1 CAGGCGTGCA 0.958267 -105 TCCAGTGTAACAGGCGGGAAGCGATTAAAAA 17 183 0 CAGGCGGAAG 0.934361 -47 AGTAAAGAGGCTGGCGTAAAA 20 1 0 CTGGCGTAAA 0.804186 -85 CCCGGCATGACAGGAGTAAAA 21 69 1 CAGGAGTAAA 0.831264 -11 GGCATTTGTGAAGGCGGAAAAGTAAGAATTG 25 21 0 AAGGCGGAAA 0.850897 -188 TTTTTATCTGCAGGCGGGAAATAGAGCGGAC 26 144 0 CAGGCGGAAA 0.976232 -157 AGGTTGCATCAAGGCGGCAAGTGAGTGAATC 32 94 0 AAGGCGGAAG 0.664182 -107 ******* *** Masking position 6 Map Score: 9.11385 Number of sites scoring better than the average of aligned sites = 930 Number in coding regions = 858 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 12 CACCAACGACAAAATTTGCGAGGCTCTTTCC 9 123 1 AAATTTGCGA 0.968326 -96 AAGGATGAAGAAAACTTGCGAGGTGTCTCGA 18 86 0 AAACTTGCGA 0.877191 -90 TGCCTGCTCCAGATTTTGCGATGTTTTTTTG 25 107 1 AGATTTGCGA 0.929304 -102 GATTATGGTAAAAATTTTCGATTGAAATAGA 34 41 1 AAATTTTCGA 0.727588 -103 CACAGATATTAAAATATGCGATAATGATCGC 36 97 1 AAATATGCGA 0.811379 -57 AAATAAATGTAAATTTTGCGATCATTATCGC 36 114 0 AAATTTGCGA 0.968326 -40 CTAATTTAGAAAATTTGGCGACAAAATGTGA 43 145 1 AAATTGGCGA 0.877191 -104 TAACTTTTTAAAATTTTGCGGATCCCTTGTT 45 44 1 AAATTTGCGG 0.864417 -257 AGTTTTACACAGACTTAGCGATGTCAAGAGG 45 197 0 AGATTAGCGA 0.674501 -104 ATTGTGATTAAAATATTGCGACTTTTAAATA 49 181 0 AAAATTGCGA 0.828157 -120 *** ******* Masking position 3 Map Score: 4.17762 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 47 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 TCTTATCTGGCCTACACGCTGCGATTTTGTA 2 54 1 CCTACAGCTG 0.976977 -231 TCTTATCAGGCCTACGCGCTGCGATTTTGTA 2 139 1 CCTACGGCTG 0.960047 -146 TCTTATCAGGCCTACACGCTGCGATTTTGTA 2 224 1 CCTACAGCTG 0.976977 -61 GTTGACTCCTTCGTGCCGGATGCGCTTT 2 267 0 CCTTCGGCCG 0.956196 -18 CCCCCTGACTCCTTCATACTGAAAGTGAACT 13 21 1 CCTTCAACTG 0.883746 -43 TCGAATAAGGCGTTCACGCCGCATCCGGCGT 17 54 0 CGTTCAGCCG 0.8645 -176 AGACCGCAGCCCGTCAGGCTGAAGAGAGTAA 26 108 0 CCGTCAGCTG 0.947585 -193 TACACTTCATCCTTCAGGCTGCCTCTGCGTT 32 17 1 CCTTCAGCTG 0.985523 -184 ****** **** Masking position 5 Map Score: 6.45322 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 86 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 TTAAAAAAGCCGTTGCTTTGGGGATAACCCGG 4 97 1 CTGCTTTGGG 0.861784 -204 GTGAGAAGACCGTTGCCTTGTGGCAGCTATCG 7 153 0 CTGCCTTGTG 0.960738 -148 AAATCGTAGCTTCCTGTTGTCATTAG 10 5 1 CTGCTTCCTG 0.946118 -69 CTTGTGCTCACGTGGCCTTCTGGCGACGACGC 15 157 0 CTGCCTTCTG 0.983048 -144 CTGTAAAGTTCATCGCTTTCTGCTTTCTATCA 26 32 0 CTGCTTTCTG 0.979601 -269 CTCATCTTAGCTTTCTGTACCTTTCCG 33 117 0 CTGCTTTCTG 0.979601 -17 AAAAATCATCGCCTACTGAAAATGAAAG 47 7 1 CTGCCTACTG 0.934669 -52 * * ******** Masking position 8 Map Score: 1.89609 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 40 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 GAATGCCGGATGCGCTTTGCTTATCCGGCC 2 85 0 TGCGCTTTGC 0.971668 -200 GAATGCCGGATGCGCTTTGCTTATCCGGCC 2 170 0 TGCGCTTTGC 0.971668 -115 TCGTGCCGGATGCGCTTTGCTTATCCGGCC 2 255 0 TGCGCTTTGC 0.971668 -30 GAAGATGGTGTTGGCGTTGCAATTTTACGA 22 72 0 TTGGCGTTGC 0.813449 -73 TTTTTGGCGGAGGGCGTTGCGCTTCTCCGC 27 37 1 AGGGCGTTGC 0.937914 -47 ACAGGTATTTAGCGCGGTGCGGAT 31 157 1 AGCGCGGTGC 0.913556 -14 ********** Masking position 8 Map Score: 1.24395 Number of sites scoring better than the average of aligned sites = 199 Number in coding regions = 179 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295