AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -ipurR_bsub_opreg_300.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 guaB 120 inositol-monophosphate dehydrogenase #2 metS 300 methionyl-tRNA synthetase #3 yabD 78 similar to hypothetical proteins #4 yabE 155 similar to hypothetical proteins #5 yabF 144 similar to hypothetical proteins #6 yabG 161 yabG #7 veg 210 veg #8 sspF 159 small acid-soluble spore protein (alpha/beta-type SASP) #9 yabH 147 similar to hypothetical proteins #10 purR 55 transcriptional regulator #11 spoVG 193 spoVG #12 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #13 prs 22 phosphoribosyl pyrophosphate synthetase #14 purT 230 phosphoribosylglycinamide formyltransferase 2 #15 yclB 89 similar to phenylacrylic acid decarboxylase #16 yeaD 300 similar to hypothetical proteins from B. subtilis #17 yebA 196 similar to hypothetical proteins #18 guaA 232 GMP synthetase #19 purE 300 phosphoribosylaminoimidazole carboxylase I #20 purC 72 phosphoribosylaminoimidazole succinocarboxamide synthetase #21 purM 101 phosphoribosylaminoimidazole synthetase #22 yhjM 103 similar to transcriptional regulator (LacI family) #23 yisR 123 alternate gene name: yuxC, yucF; similar to transcriptional regulator (AraC/XylS family) #24 yitV 120 similar to hypothetical proteins #25 yitW 63 similar to hypothetical proteins #26 yitX 54 yitX #27 yitY 57 similar to L-gulonolactone oxydase #28 yitZ 44 similar to multidrug resistance protein #29 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #30 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #31 yjlC 300 yjlC #32 yjlD 39 similar to NADH dehydrogenase #33 yjmA 197 similar to glucuronate isomerase #34 yjmB 67 similar to Na+:galactoside symporter #35 yjmC 104 similar to malate dehydrogenase #36 yjmE 24 similar to D-mannonate hydrolase #37 yjmG 47 similar to hexuronate transporter #38 yjmH 87 similar to transcriptional regulator (LacI family) #39 ileS 300 isoleucyl-tRNA synthetase #40 ylyA 77 alternate gene name: ylmK; similar to hypothetical proteins from B. subtilis #41 lsp 102 signal peptidase II #42 pyrR 273 transcriptional attenuator and uracil phosphoribosyltransferase activity (minor) #43 pyrP 171 uracil permease #44 pyrB 145 aspartate carbamoyltransferase #45 yqhJ 29 similar to glycine dehydrogenase #46 yqhI 300 similar to aminomethyltransferase #47 ccpA 274 transcriptional regulator (Lacl family) #48 aroA 235 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase #49 ytxJ 23 alternate gene name: csb40; similar to general stress protein #50 ytxH 27 alternate gene name: csb40; similar to general stress protein #51 ytxG 161 alternate gene name: csb40; similar to general stress protein #52 murC 249 UDP-N-acetyl muramate-alanine ligase #53 ytpS 159 ytpS #54 ytpP 234 similar to thioredoxin H1 #55 yusH 66 similar to glycine cleavage system protein H #56 yusI 110 similar to arsenate reductase #57 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #58 yusM 300 similar to proline dehydrogenase #59 rbsR 300 transcriptional regulator (LacI family) #60 nrgA 281 ammonium transporter #61 glyA 206 serine hydroxymethyltransferase #62 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #63 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #64 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #65 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #66 ywlB 66 alternate gene name: ipc-28d #67 spoIIR 140 alternate gene name: ipc-27d, csfX #68 purA 205 adenylosuccinate synthetase #69 yycE 120 yycE #70 dnaC 169 replicative DNA helicase Motif number 1 TTTGCGCCCTCTGTTTTTTTCGTTATAATA 5 35 1 CTGTTTTTTT 0.79571 -110 AAGGGCTTTTTGTTTTGCGCAC 6 3 1 GGGCTTTTTG 0.744314 -159 CTTGAGAAAGCGCCTTTTTTCGCTGAGTCC 6 95 0 CGCCTTTTTT 0.916752 -67 GAGAGCTATGCGGGTTTTTTATTTTACATA 7 30 1 CGGGTTTTTT 0.836052 -181 CTTTTGTTTACTGCTTTTTGTTTTGCCCTT 8 23 1 CTGCTTTTTG 0.766221 -137 TTTTTGTTTTGCCCTTTTTTGGTTTCCAAT 8 37 1 GCCCTTTTTT 0.620917 -123 ACGAAACAACTCCTTTTTTAGAAGTGATA 8 141 0 CTCCTTTTTT 0.908573 -19 GTGCTGTTCCCTGGTTTTTTTATTTTGGAT 9 29 1 CTGGTTTTTT 0.821489 -119 TGAAATCCTGCTCGTTTTTAAAATATTTTT 11 114 0 CTCGTTTTTA 0.608692 -80 TTTGCCGGCGGTCCTTTTTTAATTCTGATT 12 57 1 GTCCTTTTTT 0.888457 -136 GCTTTGTCAGCTGGTTTTTGTTTTACGCGT 16 24 1 CTGGTTTTTG 0.570728 -277 TTTATTTTCTGGCTTTTTTATTGCTGTGGG 17 78 1 GGCTTTTTTA 0.539035 -119 GAAACATACAGGCTTTTTTAGTGTCTTTAT 17 141 1 GGCTTTTTTA 0.539035 -56 CATATCTGTCCTCGTTTTTTTCTGTGTCAA 18 185 1 CTCGTTTTTT 0.801239 -48 CTTTTTAAGTCGGATTTTTACAAGAAGTAT 23 91 0 CGGATTTTTA 0.481652 -33 TTGAATCATCCTCCTTTTTAAGTCGGATTT 23 104 0 CTCCTTTTTA 0.793162 -20 GTTCCCTCACTCCTTTTTTCTACAGTATA 25 45 0 CTCCTTTTTT 0.908573 -19 ATGTCAGGCTGTCCTTTTTTGTT 26 4 0 GTCCTTTTTT 0.888457 -51 ATGTGAGGCTGTCCTTTTTTACAGCTGAAA 26 32 1 GTCCTTTTTT 0.888457 -23 CGCGGTCAGCCTGTTTTTTTATGCGGCTGA 29 11 1 CTGTTTTTTT 0.79571 -196 TGGAGTCGTGCTGATTTTTTTTGAGCGGAA 29 70 1 CTGATTTTTT 0.684848 -137 AAGCAGTTTGCTGATTTTTTTGGAAAGGGT 31 261 0 CTGATTTTTT 0.684848 -40 TTCTGGCAATGTCTTTTTTTATGTTTATGA 33 59 1 GTCTTTTTTT 0.732241 -139 TGGGATCAATCTCTTTTTTGAAAATGAAAT 33 99 0 CTCTTTTTTG 0.496409 -99 TGGGATGAGAGGGCTTTTTTTATTTTCTGA 39 258 1 GGGCTTTTTT 0.909715 -43 CGTAAAAGCCGGGCTTTTTTTGTGCCAAGA 40 26 1 GGGCTTTTTT 0.909715 -52 CTTTACTCCAGTGCTTTTTATTGATAAAAT 41 43 1 GTGCTTTTTA 0.778206 -60 TCTGGCAGGAGGGGTTTTTTCTTCTATATG 42 235 1 GGGGTTTTTT 0.803432 -39 ATCTTAGACCGGGGTTTTTTTTCAGCCTTA 44 102 1 GGGGTTTTTT 0.803432 -44 GTGTTTCTCTGTCCTTTTTTGTATGTTTTT 46 249 1 GTCCTTTTTT 0.888457 -52 GCCGCCGTGCGGCCTTTTTTTATGCTTTCT 47 27 1 GGCCTTTTTT 0.898233 -248 TATCATCTGGCGCTTTTTTTTGTAAAAAAC 48 26 1 CGCTTTTTTT 0.790834 -210 CAATGTTCAAGGGTTTTTTACAAAAAAAAG 48 38 0 GGGTTTTTTA 0.571719 -198 AGTGAGATCACTGCTTTTTA 51 1 0 CTGCTTTTTA 0.814043 -161 AGTGATCTCACTGCTTTTTATTTATCTGAT 51 19 1 CTGCTTTTTA 0.814043 -143 TACATAAGGAGGGATTTTTATT 54 3 0 GGGATTTTTA 0.426858 -232 ATGCGCGGAGCTCTTTTTTAAGAAGCACTG 56 28 1 CTCTTTTTTA 0.56833 -83 CCGCTGAAGACGGATTTTTTTTCTCTCGTA 57 148 1 CGGATTTTTT 0.706577 -120 GCCATGAAATGCGCTTTTTTCATCGCGAGC 58 98 1 GCGCTTTTTT 0.651548 -203 AAGGTTTTCACTCTTTTTTTGACAAAGTCT 59 160 0 CTCTTTTTTT 0.773343 -141 GAAGGAGAATGGCATTTTTTGCGATATAAG 60 126 0 GGCATTTTTT 0.628351 -156 TGGACACGCCCCGCTTTTTTAGCCTATGCG 64 43 0 CCGCTTTTTT 0.699961 -36 AGCTGCTCTTGGGGTTTTTTTCATTCGAAA 69 19 1 GGGGTTTTTT 0.803432 -102 TTGTTACCATCTCCTTTTTGCACCATTTTA 69 100 0 CTCCTTTTTG 0.741674 -21 TGTCTGTTTCCTGTTTTTTTCAGTTAGCAG 70 76 0 CTGTTTTTTT 0.79571 -94 ********** Masking position 5 Map Score: 47.8714 Number of sites scoring better than the average of aligned sites = 1698 Number in coding regions = 1212 Number in noncoding regions = 486 Number of orfs with sites within 600 bp upstream = 445 Fraction of orfs with sites within 600 bp upstream = 0.0714745 Motif number 2 AATCTTTAATGAAAATAAAAAAAGTCTGTT 2 107 0 GAAAATAAAA 0.926234 -194 TCCTCCAAGACAAAATAAAAACTTTTGTAT 5 121 0 CAAAATAAAA 0.864779 -24 ATGTGGTGCGCAAAACAAAAAGCCCTT 6 8 0 CAAAACAAAA 0.7796 -154 TATCATTATGTAAAATAAAAAACCCGCATA 7 36 0 TAAAATAAAA 0.800412 -175 CCCATTTTTGTCAAATAAAATTTAAATTAT 7 155 0 TCAAATAAAA 0.50034 -56 ACAAAAAGCAGTAAACAAAAGGTTCACTGC 8 14 0 GTAAACAAAA 0.676556 -146 CAAAAAAGGGCAAAACAAAAAGCAGTAAAC 8 28 0 CAAAACAAAA 0.7796 -132 TATTTATATCCAAAATAAAAAAACCAGGGA 9 36 0 CAAAATAAAA 0.864779 -112 CGGGCATAAGGTAAATAAAAAAGTGATCCC 11 36 0 GTAAATAAAA 0.790876 -158 GAGAAACGCGTAAAACAAAAACCAGCTGAC 16 29 0 TAAAACAAAA 0.689256 -272 AAAAAAGCCAGAAAATAAAATAACAGCAAG 17 67 0 GAAAATAAAA 0.926234 -130 TTTGTTTTCAGAAAATAAAAAATACCCGCT 19 258 0 GAAAATAAAA 0.926234 -43 TTTATTTTCTGAAAACAAAAGCATTAGAAG 19 269 1 GAAAACAAAA 0.874133 -32 AACCCCTTTCGTAAATAAAATCAACGTTTT 23 18 1 GTAAATAAAA 0.790876 -106 AATATAAAGGTAAAATAAAAACAAATCAAA 33 133 1 TAAAATAAAA 0.800412 -65 AAAATAATTTGTAAATAAAATGTGTTTGTA 35 33 1 GTAAATAAAA 0.790876 -72 CATTTTTTCAGAAAATAAAAAAAGCCCTCT 39 265 0 GAAAATAAAA 0.926234 -36 ATGATAACTACAAAATAAAAAATGAATGTG 48 197 1 CAAAATAAAA 0.864779 -39 GCTTGATAATGCAAATAAAATATGATAATG 54 82 1 GCAAATAAAA 0.758179 -153 TTCACTATCTTAAAATAAAAGAAAAGACTG 61 25 0 TAAAATAAAA 0.800412 -182 ********** Masking position 5 Map Score: 22.5566 Number of sites scoring better than the average of aligned sites = 313 Number in coding regions = 218 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 3 ATATGGATATGTTCATCCTGTACTTCAAATGTGAT 9 79 1 GTCATCCTTT 0.635296 -69 GGGATGCCTCCTGTCGGTGTGGTGGTCT 14 4 1 ATCCTCCTTT 0.937234 -227 CTTTGCCCCTCCTATCTGTTCCAAACCAT 14 212 0 GCCCTCCTTT 0.816165 -19 TGTTTTACGCGTTTCTCCCTTTTGTCTTGTATGCC 16 42 1 GTTCTCCCTT 0.753091 -259 GAACAGTACCTCCAATGATTTTATAATCTA 22 6 1 GTCCTCCATT 0.973887 -98 GTTTTAAAGTGTACCTCCATTTCCTTATAATAAAA 23 43 1 GTCCTCCATT 0.973887 -81 GTTCCACCTCTGTGTCTTAAGAATT 34 53 0 GTCCACCTTT 0.738386 -15 GCAAGTGCCTCCTTCCTTTTCAGTTTTTT 35 86 0 GTCCTCCTCT 0.890954 -19 TTTCATTCCTCCACTGCATTTTTTCAGAA 39 282 0 ATCCTCCATT 0.937234 -19 AAACGTTCCTCCAGTTTACGGTTACTTTA 41 84 0 GTCCTCCATC 0.890954 -19 TTTCGGTCAGGTCTCTCCCCTTGCTGTCATTCGCT 46 33 0 GTTCTCCCTT 0.753091 -268 CTAATTCCTCCCCTTTATCAACGGCGCA 46 283 0 ATCCTCCCTT 0.933176 -18 TATTCCTCCTCTTAGTATTTTTTTCT 50 12 0 ATCCTCCTTT 0.937234 -16 AATTGTACCTCCAACAAACGTCTATCTGT 52 231 0 GTCCTCCACC 0.641572 -19 TTCATATCCCTCCAGTTGTTTATGTTCTTA 54 215 0 ATCCTCCATT 0.937234 -20 TTGAATCCCTCCATTTTTTACAGCACTAC 55 48 0 ATCCTCCATT 0.937234 -19 TATCCATTGTGATCCTCCTTTGGTTTCTGTTCATT 58 210 1 GACCTCCTTT 0.749717 -91 CTTTCATTCCTCCCTTATGTTTTATTGCAT 70 6 1 ATCCTCCCTT 0.933176 -164 ** ****** * * Masking position 8 Map Score: 17.632 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 65 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 4 AAAAGTGATCCCGGCTCTCCCAGAATCACT 11 18 0 CCGGCTCTCC 0.980949 -176 AAGCCTTTTGCCGGCGGTCCTTTTTTAATT 12 51 1 CCGGCGGTCC 0.940703 -142 CCGTTACGCCCAGCCTGTCCCCCGCATGCA 16 140 0 CAGCCTGTCC 0.986361 -161 CCTCACATGTCAGGCTGTCCTTTTTTGTT 26 10 0 CAGGCTGTCC 0.990727 -45 CCTGACATGTGAGGCTGTCCTTTTTTACAG 26 26 1 GAGGCTGTCC 0.932589 -29 CATAAAAAAACAGGCTGACCGCG 29 4 0 CAGGCTGACC 0.93763 -203 ATCAAACATACCGCCTCTCCCACTATATTT 38 16 0 CCGCCTCTCC 0.972109 -72 TTATCCTTCTCAGCCTCTCTGGACTGTTTT 42 150 0 CAGCCTCTCT 0.810493 -124 ATTGACCGCGCAGCCTGTCCGCTCTTTGAT 62 95 0 CAGCCTGTCC 0.986361 -62 ACGTTTATCCCAGGCTCTCCTTGTCCATAA 67 80 1 CAGGCTCTCC 0.986361 -61 ********** Masking position 5 Map Score: 13.5527 Number of sites scoring better than the average of aligned sites = 126 Number in coding regions = 116 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 TAGTAAATCCCCCTCTTTTCGGCAAAATATT 1 100 0 CCCTCTTTCG 0.715057 -21 GCACTTATCGCCGCTCTCGTCCTTTGGGCGGG 2 246 1 CCCTCTCTCC 0.963379 -55 GTGAAAAACTCCTTTCTTGTCGAAACACAAAA 3 55 0 CCTTCTTTCG 0.640969 -24 AGTTCTACATGCTTTCTTCTCCTCATAGGATA 4 67 1 GCTTCTTTCC 0.882767 -89 CTTTCTCAAGGCTCTTTCTTTCATGATGAGGC 6 115 1 GCCTTTCTTC 0.3869 -47 CAACACGAGCCCATTTTTGTCAAATAAAATTT 7 162 0 CCTTTTTTCA 0.496189 -49 CTTTGCCCCTCCTATCTGTTCCAAACC 14 214 0 CCCTCCTTCT 0.528727 -17 TGTATCCGCTCCGTTCTTTTCAGGCTTCAGGC 16 90 1 CCTTCTTTCA 0.849644 -211 GGAAATGGCAGCTCTCTTCTCAGCGTAACCGT 16 166 0 GCCTCTTTCA 0.837943 -135 AGTTCGGCTGCCTTTCTCTTTCTGCCCTCGTT 21 39 1 CCTTCTCTTC 0.798267 -63 AAGGGTAGTGCCTCTCCCTGTCTCACGCTTTT 31 235 0 CCCTCCCGTC 0.656052 -66 ATTGCCAAAAGCATTCCTTTCCGAGTGCTTTC 33 30 1 GCTTCCTTCC 0.901791 -168 CGCGAGATAAGCTTTCTCGTCCCTTATGGGAT 39 232 1 GCTTCTCTCC 0.924144 -69 AATAAAAAAAGCCCTCTCATCCCATAAGGGAC 39 250 0 GCCTCTCTCC 0.944827 -51 GTTCTTTCCCCTCTCTTTTCAACTTAAGGCT 44 125 0 CCCTCTTTCA 0.888183 -21 CCTAAAACCACTCCTTTTACTGGATACAC 47 256 0 CCCTCCTTTA 0.671915 -19 TTTTTTCATCCTTTCCCTGCACATTCATTTT 48 215 0 CCTTCCCGCA 0.758172 -21 GACTCAAGCTCTTCCTTCCCTGC 49 5 0 GCCTTCCTCC 0.784462 -19 CCTTTAATAAGCTTTCCCATCAGATAAATAAA 51 35 0 GCTTCCCTCA 0.878896 -127 TGCTGTTTACCCGTTTTCTTCAATCATAAACA 51 113 0 CCTTTTCTCA 0.614409 -49 TGTAAGATTGGCTTTCCCATTATCATTATCAT 54 103 0 GCTTCCCTTA 0.605439 -132 TTTGACTTGTCCGTTTTCCGCCGCCGTAATGC 57 73 1 CCTTTTCGCC 0.478424 -195 TTCTCTCGTACCATTCCCTTCACCTCCGGGCT 57 168 1 CCTTCCCTCA 0.917687 -100 GCCATGAAATGCGCTTTTTTCATCGCGAGCAA 58 98 1 GCCTTTTTCA 0.47401 -203 GCAAAAAATGCCATTCTCCTTCCTTTCCATCC 60 134 1 CCTTCTCTTC 0.798267 -148 CAGCGAGATCCTCTCCTATCCGTATCCTGTT 61 186 0 CCCTCCTTCC 0.951988 -21 TTTATCCCAGGCTCTCCTTGTCCATAATAGGG 67 83 1 GCCTCCTGTC 0.434212 -58 CGGTCCCCACCGTTCCTCTCCGTGCTTTGTT 67 120 0 CCTTCCTTCC 0.933801 -21 ** ***** *** Masking position 5 Map Score: 16.2947 Number of sites scoring better than the average of aligned sites = 1140 Number in coding regions = 944 Number in noncoding regions = 196 Number of orfs with sites within 600 bp upstream = 194 Fraction of orfs with sites within 600 bp upstream = 0.0311597 Motif number 6 CATGTAGAACTTTTATAGAAAAACGCTGTAA 4 47 0 TTTTATGAAA 0.881398 -109 CTATATCCTATTTTTTCAAAAAATATTTTAA 11 96 1 TTTTTTAAAA 0.821026 -98 ATTCCACGATTTTTTCTGAAATCCTGCTCGT 11 129 0 TTTTTCGAAA 0.847648 -65 AAAAATAAATTTTTATTAAAAAAGATAAAAT 14 164 0 TTTTATAAAA 0.761963 -67 TAAAAATTTATTTTTCAAATATTTCAGTTAT 14 180 1 TTTTTCAATA 0.610988 -51 CGCTTGACAGTTTTACTGAAACGAAACATAC 17 119 1 TTTTACGAAA 0.859117 -78 TTTTTTTTCGATATAAAGGCATA 30 3 1 TTTTTTGATA 0.7387 -68 GTTTGCTGATTTTTTTGGAAAGGGTAGTGCC 31 255 0 TTTTTTGAAA 0.872723 -46 GATCAATCTCTTTTTTGAAAATGAAATGTTA 33 95 0 TTTTTTAAAA 0.821026 -103 GTATGCTTGCTTTTTCTAAAAGGGTGGTACC 39 202 1 TTTTTCAAAA 0.722472 -99 TCCACTGCATTTTTTCAGAAAATAAAAAAAG 39 271 0 TTTTTCGAAA 0.847768 -30 CTCCAGTGCTTTTTATTGATAAAATGCATAA 41 48 1 TTTTATGATA 0.756153 -55 TTCAAGGGTTTTTTACAAAAAAAAGCGCCAG 48 32 0 TTTTACAAAA 0.740984 -204 ATACAAAAAATTTTATAAAAACTCTACTTTA 48 128 0 TTTTATAAAA 0.767362 -108 CTTACATGTTTTTTATCGATACTCGTCCATT 54 188 0 TTTTATGATA 0.75617 -47 TGTAAATTTTTTTTGAAAAGTGTGGTAT 55 8 1 TTTTTTGAAA 0.871358 -59 AAATATTAAGTTTTATTAAAATTGTTTCAAA 59 100 0 TTTTATAAAA 0.761963 -201 GAATAGTTTCTTTTATAGATACAAAGTCTTA 60 99 1 TTTTATGATA 0.756154 -183 TAATATTCGTTTTTACCAATAAAAATTTAGA 61 89 1 TTTTACAATA 0.6336 -118 AAAATTTAGATTTTTTAAAAATAATCTTTTA 61 110 1 TTTTTTAAAA 0.755494 -97 TTTTGCACCATTTTATTAAAACGCTTTCAAT 69 84 0 TTTTATAAAA 0.761963 -37 ****** **** Masking position 4 Map Score: 17.0682 Number of sites scoring better than the average of aligned sites = 687 Number in coding regions = 435 Number in noncoding regions = 252 Number of orfs with sites within 600 bp upstream = 230 Fraction of orfs with sites within 600 bp upstream = 0.0369419 Motif number 7 TCCTGCTCGTTTTTAAAATATTTTTTGAAAAAATA 11 104 0 TTTTATTTTT 0.6998 -90 TGTAGCATGATTTTGGGGGATTTCTTGTATGATGT 14 48 1 TTTTGGTTTT 0.852311 -183 TGTTATTTTATTTTCTGGCTTTTTTATTGCTGTGG 17 72 1 TTTTGCTTTT 0.873143 -125 ATACAGGCTTTTTTAGTGTCTTTATCGGCTTGACG 17 146 1 TTTTGTTTTT 0.863851 -51 CAGTGTAGCTTTTTACCATCTTTATTGTCTACATG 24 56 1 TTTTATTTTT 0.6998 -65 ATGTCAGCCATTTTAATTTGTTTTTCCCCA 28 6 0 TTTTTTTTTT 0.834312 -39 ATATTTAATATTTTTATTCATTTATAAATTTTCTG 29 111 0 TTTTTCTTTT 0.845259 -96 TAAAAATGAATTTTTATGCCTTTATATCGAAAAAA 30 13 0 TTTTGCTTTT 0.873143 -58 TGGCAATGTCTTTTTTTATGTTTATGACAGCGTTA 33 62 1 TTTTATTTTT 0.6998 -136 AACGTTAACATTTTGATTTGTTTTTATTTTACCTT 33 139 0 TTTTTTTTTT 0.834312 -59 TGCCGAATACTTTTTGGGCCTTTGTTGTGCACCTC 43 48 0 TTTTGCTTTT 0.873143 -124 CTCTGTCCTTTTTTGTATGTTTTTTAGCTGCGCCG 46 255 1 TTTTTGTTTT 0.820787 -46 CGTGCGGCCTTTTTTTATGCTTTCTCGTTTATTTA 47 32 1 TTTTTGTTTT 0.820787 -243 TAGCGGCGTATTTTATATGTTTTGTTATGTTTAGT 52 139 0 TTTTTGTTTT 0.820787 -111 GATTCGTTTTTTTTGGCGGATTTATGGGAGT 53 7 0 TTTTGGTTTT 0.852311 -153 AAATTTAAGGTTTTCACTCTTTTTTTGACAAAGTC 59 161 0 TTTTTCTTTT 0.845259 -140 ATTAGATTTCTTTTGATATTTTTATTGCTAACTTC 59 219 1 TTTTATTTTT 0.6998 -82 TTCACCCCGTTTTTGCGTTCTTTCTTCCAATCTAT 66 39 0 TTTTTTTTTT 0.834312 -28 CTCCCTTATGTTTTATTGCATTTTTCCCGCCTTGT 70 20 1 TTTTGCTTTT 0.873143 -150 AACAGACAATTTTTCTATTTTTTTTCTGTAGAAAT 70 98 1 TTTTTTTTTT 0.834312 -72 **** ** *** * Masking position 11 Map Score: 20.7618 Number of sites scoring better than the average of aligned sites = 833 Number in coding regions = 625 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 222 Fraction of orfs with sites within 600 bp upstream = 0.0356569 Motif number 8 TCCTATGCAGGTTTTCAACTG 7 1 0 GTTTTCACTG 0.60901 -210 TTAATTCTGATTTTTCAAACTTAGTTGCACT 12 75 1 TTTTTCAACT 0.451569 -118 TTAATAGATATTTTTCATATGGATATATCAG 15 56 1 TTTTTCAATG 0.564685 -34 TCAGGGCGGCTTTGTCAGCTGGTTTTTGTTT 16 16 1 TTTGTCACTG 0.665301 -285 TCCTTTCAGCTGTAAAAAAGGA 26 43 0 CCTTTCACTG 0.746635 -12 TGCGGTGCCGCATTTCAGCCGCATAAAAAAA 29 24 0 CATTTCACCG 0.597413 -183 TACTACCCAGTTTTTCATCTTGCCATATTCA 31 147 0 TTTTTCACTT 0.742176 -154 TTTCAACCGTTTTTTCATCTGAATTTATGAA 39 17 0 TTTTTCACTG 0.900728 -284 CATGACTGTCCCTTTCAACCGTTTTTTCATC 39 29 0 CCTTTCACCG 0.854984 -272 AAAGAAACCCTCTGTCAACCGTTTTTTCTGA 42 85 0 TCTGTCACCG 0.591245 -189 ACCGGGGTTTTTTTTCAGCCTTAAGTTGAAA 44 109 1 TTTTTCACCT 0.852054 -37 TTTCCCCTCTCTTTTCAACTTAAGGCTGAAA 44 121 0 CTTTTCACTT 0.719928 -25 TTTTTTCATCCTTTCCCTGCAC 48 224 0 TTTTTCACCT 0.852054 -12 CTAAGGGAGGCTTTTCAGCCGCCGCGGTCGC 52 171 1 CTTTTCACCG 0.941894 -79 GGCTTAGCGGCTTTTCACATGATTCGTTTTT 53 31 0 CTTTTCAATG 0.536678 -129 TTGCTAGATTTTTTTCACCCTGCACGTTTAT 67 57 1 TTTTTCACCT 0.852054 -84 TCTTGGGGTTTTTTTCATTCGAAAGATGGAA 69 25 1 TTTTTCATCG 0.506693 -96 ACGCTTTCAATTTTTCATCCGCTGAGCGAAC 69 64 0 TTTTTCACCG 0.947789 -57 ******* *** Masking position 5 Map Score: 8.54366 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 677 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 9 ATATAGGGAAAAGGTGGTGAACTACT 11 178 1 AAGGGTGAAC 0.976501 -16 AAAGCATTAGAAGGTGGGGAACAGA 19 286 1 AAGGGGGAAC 0.963 -15 TGGTTATCCTAAGGAGGGGCACATT 24 106 1 AAGGGGGCAC 0.972166 -15 CACAAAGACCAAGAGGGTGAACTTGTT 29 190 1 AAAGGTGAAC 0.864901 -17 CGAAAGCGGTGCAACAGAAACTGA 37 3 1 AAGGGTGCAA 0.895739 -45 TGAGCATCGTAACGTGATGAACGTCCTAACCT 39 158 0 AAGGATGAAC 0.864901 -143 GAGAGGTTGCAAAGAGGTGCACAACAAAGGCC 43 35 1 AAGGGTGCAC 0.982384 -137 AGAACGCAAAAACGGGGTGAACGG 66 53 1 AAGGGTGAAC 0.976501 -14 GAAACAAAGCACGGAGAGGAACGGTGGGGACC 67 118 1 ACGGAGGAAC 0.606131 -23 TGAAAGGTTAACGGAGGTGCACGGAC 68 190 1 ACGGGTGCAC 0.955363 -16 GCGTTTTAATAAAATGGTGCAAAAAGGAGATG 69 91 1 AAAGGTGCAA 0.569629 -30 ** * ******* Masking position 11 Map Score: 7.26981 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 61 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 10 GCCGCTCTCGTCCTTTGGGCGGGAGCTTTTT 2 255 1 TCCTTTGGCG 0.64392 -46 TTGAGAAAGCGCCTTTTTTCGCTGAGTCCAA 6 93 0 GCCTTTTTCG 0.642681 -69 GCTGACATAAGCCTTTTGCCGGCGGTCCTTT 12 43 1 GCCTTTTCCG 0.868305 -150 GGGATGCCTCCTGTCGGTGTGGTGGT 14 6 1 GCCTCCTTCG 0.716361 -225 GGAAAAACGAGCCGTTTGGCGCGGCCTCCGT 16 258 0 GCCGTTTGCG 0.950843 -43 CTTTGGCAAGGCCGTTTGCCGGAGTCAGGCC 18 138 0 GCCGTTTCCG 0.933167 -95 CGGATAGTGATCCGCTCAGCGATACTGAGCG 34 20 0 TCCGCTCGCG 0.847736 -48 AATTTGAAGCGCCGCTTCCCGAGGATATGGC 42 37 1 GCCGCTTCCG 0.967286 -237 GTCTTTGTATGCCTCTTTGCGTAAAAAAGCA 43 84 1 GCCTCTTGCG 0.950843 -88 AATCCAAAAGGCCGCCGTGCGGCCTTTTTTT 47 17 1 GCCGCCGGCG 0.938213 -258 TTTTGACTTGTCCGTTTTCCGCCGCCGTAAT 57 72 1 TCCGTTTCCG 0.831782 -196 AATCTCAAATGCCGCCTTCCGTTATTTCGAC 58 170 0 GCCGCCTCCG 0.951471 -131 CTGCTTTTCCTCCCAGCGTGTGTGATGC 62 139 0 TCCTCCCGCG 0.635471 -18 CAATTTTTCATCCGCTGAGCGAACGTCATTT 69 57 0 TCCGCTGGCG 0.890228 -64 ******* *** Masking position 3 Map Score: 10.5167 Number of sites scoring better than the average of aligned sites = 501 Number in coding regions = 474 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 11 AACTCTTTCCCGCTTCCTTGACATGCTCTTGGCT 1 48 1 CGCTCCTTAT 0.94241 -73 AAGAAAGCGCCTCCTTATCATACCTTTTAGG 15 8 1 CGCTCCTTAT 0.94241 -82 TCTGTTCCCCACCTTCTAATGCTTTTGTTT 19 281 0 CCCACCTTAT 0.895952 -20 ATTTTCCCTTCCTTAAAAAAGTTGTTGAC 22 85 0 CCCTCCTTAA 0.906078 -19 AATGTGCCCCTCCTTAGGATAACCATAATC 24 101 0 CCCTCCTTAT 0.983922 -20 CGTATATCCTCCGTCCTTTATATCAATTTGAAT 32 17 0 TCCTCCTTAT 0.963121 -23 GCAAGTGCCTCCTTCCTTTTCAGTTTTTTGGGC 35 82 0 TCCTCCTTAG 0.859192 -23 CTAATTCCCTTCCTTATCATACCGGCTGCG 38 68 0 CCCTCCTTAT 0.983922 -20 AATGCCATTCTCCTTCCTTTCCATCCCTCGATAA 60 140 1 TCCTCCTTAT 0.963121 -142 CGTCATTTCTTCCATCTTTCGAATGAAAAAAACC 69 31 0 TCCTCTTTAT 0.695278 -90 *** ***** ** Masking position 8 Map Score: 6.15406 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 30 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 12 ATTTTGCCGAAAAGAGGGGGATTTACTA 1 103 1 AAGAGGGGGA 0.812639 -18 AACGAAAAAAACAGAGGGCGCAAAACCCTCT 5 28 0 ACGAGGGCGC 0.927626 -117 TTAAATCGAGACGGAGGCCGCGCCAAACGGC 16 248 1 ACGAGGCCGC 0.940709 -53 GAATTTTCAAACTGCGGCGGCTTAGAAGAAG 20 26 0 ACGCGGCGGC 0.984655 -47 TTCTTAAGACACAGAGGTGGAAC 34 55 1 ACGAGGTGGA 0.894491 -13 TCAATTTGCGACCGCGGCGGCTGAAAAGCCT 52 178 0 ACGCGGCGGC 0.983087 -72 CGATTATTTTATTGAGGGGGAAGAAG 56 95 1 ATGAGGGGGA 0.812639 -16 ACTCAGCATTACGGCGGCGGAAAACGGACAA 57 79 0 ACGCGGCGGA 0.983007 -189 CAAGAACTCGACCGCGTCGGACACATGCATC 58 39 0 ACGCGTCGGA 0.837115 -262 CAAATAATACACTGAGGGGGATGT 60 4 0 ACGAGGGGGA 0.977897 -278 ** ******** Masking position 1 Map Score: 7.0539 Number of sites scoring better than the average of aligned sites = 125 Number in coding regions = 109 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 13 TTACACGTGAAACACCTTTTGTTTATCA 3 8 0 AACACTTTTG 0.962977 -71 CAATTCGTCGAACACCTTTTGTGTTTCGACA 3 39 1 AACACTTTTG 0.962977 -40 CGTGTCTAACCCCTTTCGTAAATAAAAT 23 8 1 AACCCTTTCG 0.748143 -116 TCTATATGATAACACTTTTTGAACAAAATTT 31 21 0 AACACTTTTG 0.962977 -280 AACCCCTACAAACACATTTTATTTACAAATT 35 38 0 AACACTTTTA 0.718301 -67 AGACCTGCCGAATACTTTTTGGGCCTTTGTT 43 57 0 AATACTTTTG 0.7183 -115 CTATAGCATAAACACTTTATGTAGAGAAATG 47 215 0 AACACTTATG 0.803931 -60 AGGTTATTTTAACACAGTTTGTTTTAAAAAC 56 64 0 AACACGTTTG 0.858695 -47 CAGATGTTCTAACCCTTTTTGGACACGCATA 64 18 1 AACCCTTTTG 0.927081 -61 ***** ***** Masking position 8 Map Score: 2.94254 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 24 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 ATTAAAAATCTTTAATGAAAATAAAAAAAGT 2 112 0 TTAATGAAAA 0.492936 -189 CTTTGTCTATTATAACGAAAAAAACAGAGGG 5 41 0 TAAACGAAAA 0.609387 -104 TTTCTTATCATTGAATGAAAGGTCCTTCTCT 6 58 0 TTAATGAAAG 0.87495 -104 TTCCAATAATTTTAACGAAAGTTCCATCTGA 8 60 1 TTAACGAAAG 0.928611 -100 TTCCATCTGATTTAACAAAAGATAAAACAGT 8 81 1 TTAACAAAAG 0.622044 -79 TTTTAAATTCTTAAACGAAAGCAGACAAATA 14 113 0 TTAACGAAAG 0.928611 -118 CATTTTGAAATAGAATGAAAGACGGTGAGGA 33 176 1 TAAATGAAAG 0.857947 -22 TGACATCCTTTAGAACGAAAGGAAAAATCTT 40 57 1 TAAACGAAAG 0.918223 -21 TGAGTCATCCTAAAATGAAAGTCAACAATCA 43 138 1 TAAATGAAAG 0.857947 -34 AACCTTTTAATGAAAGTCCAGAGAGG 44 6 1 TTAATGAAAG 0.87495 -140 GTACACGATGTTAAACGAAACGAGCTTGATA 54 59 1 TTAACGAAAC 0.603028 -176 TTCACTATCTTAAAATAAAAGAAAAGACTGG 61 24 0 TAAATAAAAG 0.433158 -183 AAAACGCTTATAAAACGAATGGAAGCGAACG 68 68 1 TAAACGAATG 0.544398 -138 ** ******** Masking position 5 Map Score: 4.67895 Number of sites scoring better than the average of aligned sites = 156 Number in coding regions = 96 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 15 GGCCTTGTATCCGCTCCGTTCTTTTCAGGCTTC 16 85 1 CCGCTCGCTT 0.959525 -216 CACCTAATCTCCTCTAAGTTTTTTGACACAGAA 18 204 0 CCTCTAGTTT 0.859809 -29 TAAAAAATACCCGCTCTGCATTGCACTTATGAG 19 240 0 CCGCTCGTTG 0.9324 -61 ACAAGTTCACCCTCTTGGTCTTTGTGAAATTAT 29 183 0 CCTCTTGTTT 0.859809 -24 GTCCTCACCGTCTTTCATTCTATTT 33 183 0 CCTCACGTTT 0.717782 -15 CAAAGTGTCCGCTCAGTATCGCTGAGCGGAT 34 9 1 CCGCTCGTCG 0.651738 -59 TCCTTCTCAGCCTCTCTGGACTGTTTTAAAGAA 42 144 0 CCTCTCGCTG 0.969891 -130 TCCTAAAACCCCTCTATGCTCTGGCAGGAGGGG 42 216 1 CCTCTAGCTG 0.876711 -58 CTCTTTGCAACCTCTCTGGATTGCTTAAAAAGG 43 18 0 CCTCTCGTTG 0.958016 -154 TATAAAAAAACCTCTTTGCTTTTTTACGCAAAG 43 98 0 CCTCTTGTTT 0.859809 -74 CCCTTCCAAGCCTCTCTGGACTTTCATTAAAAG 44 14 0 CCTCTCGCTT 0.975137 -132 TATTCCTCCTCTTAGTATTTTTTTCTC 50 8 0 CCTCTTGTTT 0.859809 -20 ATGTGAAAAGCCGCTAAGCCCTTGTTTAGCGGC 53 42 1 CCGCTAGCTT 0.839571 -118 GACCGCGCAGCCTGTCCGCTCTTTGATTCACAC 62 89 0 CCTGTCGCTT 0.766851 -68 CCCCACCGTTCCTCTCCGTGCTTTGTTTCTAGC 67 114 0 CCTCTCGCTT 0.975137 -27 ****** * *** Masking position 8 Map Score: 15.7029 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 86 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