AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_ecoli_reg_300.orf -o00310_ecoli_300.ace -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.51 -x5 -e Parameter values: expect = 5 ncols = 10 npass = 1000 maxnpass = 100 nruns = 1000 maxnruns = 100 repeat = 15 maxreps = 3 nread = 500 ncycles = 1 fragment = 1 psfact = 0.1 gcback = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: caiA 30 probable carnitine operon oxidoreductase Input sequences: #1 caiC 58 probable crotonobetaine/carnitine-CoA ligase #2 caiB 35 l-carnitine dehydratase #3 caiT 300 probable carnitine transporter #4 rpsB 300 30S ribosomal subunit protein S2 #5 tsf 257 protein chain elongation factor EF-Ts #6 pyrH 146 uridylate kinase #7 frr 291 ribosome releasing factor #8 yaeM 91 putative ATP-binding component of a transport system #9 yaeS 185 orf, hypothetical protein #10 cdsA 120 CDP-diglyceride synthetase #11 yaeT 29 orf, hypothetical protein #12 hlpA 121 histone-like protein, located in outer membrane or nucleoid #13 fabZ 104 (3R)-hydroxymyristol acyl carrier protein dehydratase #14 dnaE 36 DNA polymerase III, alpha subunit #15 ldcC 98 lysine decarboxylase 2, constitutive #16 ybcR 300 orf, hypothetical protein #17 entC 300 isochorismate hydroxymutase 2, enterochelin biosynthesis #18 lipB 166 protein of lipoate biosynthesis #19 ybeD 109 orf, hypothetical protein #20 dacA 138 D-alanyl-D-alanine carboxypeptidase, fraction A; penicillin-binding protein 5 #21 mrdA 30 cell elongation, e phase; peptidoglycan synthetase; penicillin-binding protein 2 #22 ybeB 300 orf, hypothetical protein #23 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #24 ybeX 89 putative transport protein #25 ybeZ 113 putative ATP-binding protein in pho regulon #26 yleA 145 orf, hypothetical protein #27 sdhC 300 succinate dehydrogenase, cytochrome b556 #28 ybjU 36 putative arylsulfatase #29 poxB 132 pyruvate oxidase #30 ybjW 137 putative prismane #31 ybjE 300 putative surface protein #32 dmsA 300 anaerobic dimethyl sulfoxide reductase subunit A #33 htrB 224 heat shock protein #34 sohB 219 putative protease #35 ycjL 121 probable amidotransferase subunit #36 ycjC 26 orf, hypothetical protein #37 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #38 ydbO 284 orf, hypothetical protein #39 ydcH 72 orf, hypothetical protein #40 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #41 rspA 205 starvation sensing protein #42 b1582 134 orf, hypothetical protein #43 sppA 160 protease IV, a signal peptide peptidase #44 msbB 119 suppressor of htrB, heat shock protein #45 yebA 78 orf, hypothetical protein #46 yebL 24 putative adhesin #47 wcaA 34 putative regulator #48 BIME92 24 BIME #49 wza 300 putative polysaccharide export protein #50 b2074 300 putative membrane protein #51 b2080 151 orf, hypothetical protein #52 yegQ 146 orf, hypothetical protein #53 gatD 47 galactitol-1-phosphate dehydrogenase #54 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #55 gatZ 28 putative tagatose 6-phosphate kinase 1 #56 gatY 197 tagatose-bisphosphate aldolase 1 #57 BIME96 27 BIME #58 b2097 184 orf, hypothetical protein #59 atoS 214 sensor protein AtoS for response regulator AtoC #60 atoD 195 acetyl-CoA:acetoacetyl-CoA transferase alpha subunit #61 atoB 30 acetyl-CoA acetyltransferase #62 pdxB 98 erythronate-4-phosphate dehyrogenase #63 glyA 300 serine hydroxymethyltransferase #64 yqeF 251 putative acyltransferase #65 agaZ 248 putative tagatose 6-phosphate kinase 2 #66 BIME157 76 BIME #67 agaS 191 putative tagatose-6-phosphate aldose/ketose isomerase #68 yhbU 208 putative collagenase #69 yiaK 200 putative dehydrogenase #70 yiaM 117 orf, hypothetical protein #71 trxA 76 thioredoxin 1 #72 rhoL 140 rho operon leader peptide #73 rho 84 transcription termination factor Rho; polarity suppressor #74 rfe 239 UDP-GlcNAc:undecaprenylphosphate GlcNAc-1-phosphate transferase; synthesis of enterobacterial common antigen (ECA) #75 fadB 189 4-enzyme protein: 3-hydroxyacyl-CoA dehydrogenase; 3-hydroxybutyryl-CoA epimerase; delta(3)-cis-delta(2)-trans-enoyl-CoA isomerase; enoyl-CoA hydratase #76 pepE 211 peptidase E, a dipeptidase where amino-terminal residue is aspartate #77 cadA 79 lysine decarboxylase 1 #78 cadB 300 transport of lysine/cadaverine #79 ampC 62 beta-lactamase; penicillin resistance #80 frdA 294 fumarate reductase, anaerobic, flavoprotein subunit #81 hfq 85 host factor I for bacteriophage Q beta replication, a growth-related protein #82 hflX 75 GTP - binding subunit of protease specific for phage lambda cII repressor #83 hflK 85 protease specific for phage lambda cII repressor #84 sgaT 291 orf, hypothetical protein #85 yjfG 175 putative ligase #86 lplA 27 lipoate-protein ligase A #87 smp 105 orf, hypothetical protein Motif number 1 ACGCGTGGCGTCAGTCGGCTTGCCT 1 2 1 CGCGGGCCGT 0.761584 -57 GTTTGTTATTGGGCGGGCGCTAGTCAGGCAAGCC 1 27 0 GGGCGGCTGT 0.847574 -32 ATCGGAAGTCCGGCGCGCTTTATACCACAAATAC 4 127 0 CGGCCGCTTA 0.555693 -174 TGCAGAAAGGCGGCAAGCTCGAGAATTCCCGGGA 5 45 1 CGGCAGCGGA 0.655735 -213 CCTTGCGGATCGGCTGGCGGCGTTTTGCTTTTTA 8 44 1 CGGCGGCCTT 0.919845 -48 GCGAACCCCACCGGCGGCAACAGAAACAACGCCG 10 75 0 CCGGGGCCGA 0.782115 -46 TTCTTTGCGTGGCCCGGCGATCTTATATTGATCG 12 58 0 GGCCGGCTTT 0.57638 -64 CTTACGATTGCGGCAGGCCGTGTTATTATTGTCG 13 53 1 CGGCGGCTTT 0.940208 -52 AAGGGTCACTTCGGTGGCCCTTTTTTATCGCCAC 15 29 1 TCGGGGCTTT 0.323993 -70 AATGCACTACCGGCAGGCATCTGACTTTCCGCGT 20 63 0 CGGCGGCCGA 0.972237 -76 TTTGCCAGGCATTTGACTGGCAGACG 24 3 1 TGCCGGCTGA 0.849722 -87 CCCACCGGAACGGCAGGCCTGAGAA 25 2 0 CGGCGGCGGA 0.963591 -112 GTTACAACGCTGGGTGGCTCGGGATTGCAGGGTG 27 101 0 TGGGGGCGGA 0.772772 -200 TGCCAGGCCGCCGATCGCTGTCGT 32 287 0 TGCCGGCCGA 0.797475 -14 AAGCGCAATGCGCCCGGCAATCTATACACAAAAT 37 34 1 CGCCGGCTTA 0.921515 -241 AAAAGCCGCCTGGCTGGCGGCTTAGGAAAGT 40 8 0 TGGCGGCCTA 0.8654 -55 CACGCTACCGCCCCTGGCTTTTTAGCTACCAATA 49 99 0 CCCCGGCTTA 0.735103 -202 TTGATTTCATCCGCAGGCTATTGACAGAATAATT 49 158 0 CCGCGGCTGA 0.918969 -143 GATTGTCAATCCGCAGGCTTTGTAGTCTGCGATC 50 27 0 CCGCGGCTTA 0.875038 -274 CTCTCCGCCCTGGCAGGCATCAGAAAATCGCTCA 51 100 1 TGGCGGCCGA 0.912379 -52 CAACAACCCACGCCCGGCATCGTAA 52 2 0 CGCCGGCCTA 0.895493 -145 TGTAGCGCTGTGGGGGGCTCTGGTAAAGCGCCGG 52 40 0 TGGGGGCTGT 0.766584 -107 CCCACTTTAAGGGCGGGCATTGTAGCGCTGTGGG 52 60 0 GGGCGGCTTA 0.866114 -87 GCTTCCCTATCGGGAGGCCGTTTTTTTGCCTTTC 56 71 1 CGGGGGCTTT 0.872118 -127 CTTCAGGCTACGCAAGGCTTTGGAGAATAAAGAG 63 145 0 CGCAGGCTGA 0.559576 -156 TTAAACAAAATGGAGGGCAATTTACCATAAACCA 64 34 1 TGGAGGCTTA 0.370525 -218 AAAAACTGGACGCCCGGCGTGAGTCATGCTAACT 72 41 1 CGCCGGCGGT 0.847719 -100 TAAGATAAAACGGGAAGCGTTGGAAATTACAAGA 72 116 0 CGGGAGCTGA 0.599624 -25 TCTTAATGCCGCGCTGGCGATGTTAGGAAAATTC 74 70 1 GCGCGGCTTT 0.447963 -170 TAAGAAATCACGGGAGGCATGCTACCACTGCGAA 76 173 0 CGGGGGCGTA 0.876353 -39 GGCCCGCCTATGGCGGGCCGTTTTGTATGGAAAC 79 31 1 TGGCGGCTTT 0.82381 -32 TTTTTTTACACGGGGAGCCAGCGATCCTGCGTTC 82 23 1 CGGGAGCGGA 0.452188 -53 **** *** * ** Masking position 7 Map Score: 31.679 Number of sites scoring better than the average of aligned sites = 2454 Number in coding regions = 2328 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 2 GGTGAATAGAGGGCGTTTTTTCGTTAATTT 3 115 0 GGGCGTTTTT 0.979155 -186 ATCTACTGAGCGGCGTTTTTGTCGTTCAAG 8 14 0 CGGCGTTTTT 0.983177 -78 GATCGGCTGGCGGCGTTTTGCTTTTTATTC 8 51 1 CGGCGTTTTG 0.946158 -41 TGGTTTTACACGGCTTTTTTTTGTATAGGC 9 119 1 CGGCTTTTTT 0.935151 -67 GTCGTCATCGCGGCGTTGTTTCTGTTGCCG 10 65 1 CGGCGTTGTT 0.923454 -56 GCCAGAAGGCGGGAGTTTTTTACTGATGCT 19 53 0 GGGAGTTTTT 0.662769 -57 TGATTAACGACGGCGTTTTGATTAACTAAC 24 50 1 CGGCGTTTTG 0.946158 -40 CCGTTCCGGTGGGCCTTGTTTTTTCTCTCT 25 23 1 GGGCCTTGTT 0.616845 -91 AACAGCATGTGGGCGTTATTC 27 290 1 GGGCGTTATT 0.780454 -11 CACCGCGCAGCGGCGATTTTGTTCGCCAGA 31 30 0 CGGCGATTTT 0.922244 -271 GGGAACGCCTCGGCGATTTTGACGCCACCA 31 159 1 CGGCGATTTT 0.922244 -142 GCGCCTGCGGGCGCTTTTTTTGTCTCCC 32 9 1 GGGCGCTTTT 0.848295 -292 GCCAGCCAGGCGGCTTTTTTAACAACTGCA 40 24 1 CGGCTTTTTT 0.935151 -39 GTGATCACTCCGGCTTTTTTCGATCTTTAT 41 119 1 CGGCTTTTTT 0.935151 -87 CAGTCAGTACCGGCTTTTTTTATTTGGTGC 44 36 1 CGGCTTTTTT 0.935151 -84 CCTATCGGGAGGCCGTTTTTTTGCCTTTCA 56 76 1 GGCCGTTTTT 0.744432 -122 TTACATTGCAGGGCTATTTTTTATAAGATG 63 27 0 GGGCTATTTT 0.701683 -274 CGTAAACACGTGGCGTTTTTGGCATAAGAC 74 15 0 TGGCGTTTTT 0.890353 -225 CGTGTTTACGTGGCGTTTTGCTTTTATATC 74 35 1 TGGCGTTTTG 0.709434 -205 GTGTTGGGAGGGGCCTTTTTTACCTGGAGA 77 53 1 GGGCCTTTTT 0.886352 -27 ********** Masking position 7 Map Score: 22.3368 Number of sites scoring better than the average of aligned sites = 702 Number in coding regions = 586 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 3 CAGTCGGCTTGCCTGACTAGCGCCCGCCCAATAACAAAC 1 22 1 GCCATACGCC 0.811517 -37 CGCCGCAGATGCGTTATCTTCGCTCGCTCATCCCGGTCA 5 94 0 GCGACTCGCC 0.981482 -164 TTACGCCCCCGCGATACTTACGCGGAATCTTACCCTTAT 7 27 0 GCGATTCGCC 0.964883 -265 CGTGAGGATGGCGAGCACTGCCCGGGGCCAAAATGGCAA 7 141 1 GCGCCTCCCC 0.967162 -151 TTTCGAAAGTGGGCTATCATCCCACCCCGCGCCGCAGAT 22 73 0 GGGACACCCG 0.843382 -228 ACCAGTATGAGCGTTATCAGCCCTTAGGGGTAAAAATCC 26 49 0 GCGACACCCG 0.908987 -97 GATCCCTGCCGCCAAAATTGCGCTAAATCAATCTCCCTT 30 27 1 GCCATTCGCC 0.886871 -111 CCTGTAAAACGCGCCCTCAGCCCACATCCATGTGGGCTG 31 108 1 GCGCCACCCC 0.941777 -193 GATGTTGGTGGCGTCAAAATCGCCGAGGCGTTCCCTGAA 31 155 0 GCGAAACGCC 0.657225 -146 ATTTACAAGCGCGGCAATTTCGCCCAGTCTTCAGCCACA 33 125 1 GCGATTCGCC 0.964883 -100 TCAGCCTGGGGCGATAACACCGCAAAATGGATACTTTGT 34 98 1 GCGACACGCG 0.928201 -122 ATAGATTGCCGGGCGCATTGCGCTTACCCGGCTTACAGA 37 20 0 GGGCTTCGCC 0.914201 -255 TGCCTTGGCTGCGTTCGCTCCCCCGAATCACTTACCTGA 37 117 0 GCGCCTCCCC 0.967162 -158 ATACGGCCCGGGGATCTCTGCGCCCTGACGTTCACAAAC 37 211 1 GGGCCTCGCC 0.953607 -64 TAGTGTAGCGGCGCAACTTGCCCCGCACCAAATAAAAAA 44 51 0 GCGATTCCCC 0.955009 -69 TACCAGGGCGGGGGAAACCCCGCTCTACCCTCACTCCTG 50 81 0 GGGACCCGCC 0.917865 -220 CCCTTAAAGTGGGGGCACTCCCCTAACCGCTTCATCAGG 52 81 1 GGGCCTCCCG 0.875811 -66 ATTGTTAAGGGGGATAACCTCCCCCTCAGGTAAAAA 53 8 0 GGGACCCCCG 0.793136 -40 ATTTCAAAGGGGCGAAGCTCCGCCTCAGGTGACCGATGG 59 52 1 GGCACTCGCG 0.783604 -163 GGACAAGTGTGCCATAATCTCGCGGCCAGGCATACTTGC 62 37 0 GCCATCCGCG 0.576525 -62 GGTTAAGTATGGGAGATTAACGCCCTATCTACCCCTCTA 64 68 1 GGGATACGCC 0.890544 -184 GCAAATGCAAGCCCACCTTGCCCATTGACGCAAGCTACT 65 73 1 GCCCTTCCCC 0.813298 -176 GTAGCCTCATGCGTTATTTTCCCTGCTTCGAACGATTTT 87 23 0 GCGATTCCCC 0.955009 -83 *** * ** *** * Masking position 11 Map Score: 27.5486 Number of sites scoring better than the average of aligned sites = 1189 Number in coding regions = 1116 Number in noncoding regions = 73 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 TCAGTCGGCTTGCCTGACTAGCGCCCGCCCAATAACA 1 21 1 TGCCGATCCG 0.540519 -38 AACGAAAAAACGCCCTCTATTCACCCGAAACAAAAAT 3 120 1 CGCCTCACCG 0.757084 -181 TCGAGCTTGCCGCCTTTCTGCAACTCGAACTATTTTG 5 30 0 CGCCTTTCCG 0.921688 -228 AAGGGCTCTCCCCCTTCATATTTCGCGCCGCAGATGC 5 121 0 CCCCTCTCCG 0.687711 -137 GAAGGGGGAGAGCCCTTATAGACCAGGTAGTACACGT 5 141 1 AGCCTTTCGG 0.735388 -117 CTATTTTATTTGCCATTTTGGCCCCGGGCAGTGCTCG 7 152 0 TGCCTTTCGG 0.970131 -140 ACAAATAGCGCGACTCTCTGTAGCCGGATTATCC 9 8 0 CGACCTTCGG 0.627314 -178 CGGTGGGGTTCGCCATTGTAACGCTGGTGGTCTGC 10 96 1 CGCCTTTCGG 0.976806 -25 TCCACGGAGATGCCGTTTTGTATCAGGATAAAATTCT 18 94 1 TGCCTTTCGG 0.970131 -73 AGTAAAAAACTCCCGCCTTCTGGCGGGAGTTGCTATT 19 59 1 TCCCCCTCGG 0.633423 -51 ACAAAATTGATGACCTCAAAGGTCAGGACATCATCGC 22 237 1 TGACTCACGG 0.546898 -64 AGGACATCATCGCCTTAGACGTTCAGGGCAAATCCAG 22 261 1 CGCCTAACGG 0.826631 -40 CAGCCTATACTGCCGCCAGGTCTCCGGAACACCCTGC 27 72 1 TGCCCCGCGG 0.604931 -229 TTAACCTCTGTGCCCGTAGTCCCCAGGGAATAATAAG 27 253 1 TGCCGTGCGG 0.843425 -48 GCATGAAAAATCCCTTTTATCCCCGCGTTAAGCGTCT 30 72 1 TCCCTTACCG 0.5961 -66 CCTCGACTTATCCCTTACGGCTACCGGGTCGGGCGCG 31 61 1 TCCCTAGCGG 0.438205 -240 TACTCCTCAACGACGTTGTCTGTCGCGCTGCCAGTGT 34 14 1 CGACTTTCCG 0.622833 -206 CTGATTGAAATGCCCTTCTGTTTCAGGCATAAAGCCC 34 65 0 TGCCTTTCGG 0.970131 -155 ACGCTTTGGCTCACAGTTTACAACAGGCATGTTAAGC 34 171 0 TCACGTTCGG 0.460366 -49 CCGGGCCGTATGCCCGTTTATTTCTGGCGACATTCTT 37 185 0 TGCCGTTCGG 0.947132 -90 CTACAATGCCCGCCCTTAAAGTGGGGGCACTCCCCTA 52 69 1 CGCCTTAGGG 0.466751 -78 GGGAGGTTATCCCCCTTAACAATCAGGAGTTTTT 53 24 1 CCCCTTACGG 0.872954 -24 TGGAAAAACTCGCCCGTAACGACCAGGATT 58 165 1 CGCCGTACGG 0.917845 -20 TTATACTGTTCGCCGTTGTCCAACAGGACCGCCTATA 63 233 1 CGCCTTTCGG 0.976848 -68 GGCGTTAATCTCCCATACTTAACCTGGTTTATGGTAA 64 55 0 TCCCTATCGG 0.72177 -197 AACTAAAGGTTGACTTTATTTCACCGGATACGCTTTC 71 45 0 TGACTTTCGG 0.820087 -32 TTGCATAACATGCCAGCAAATTCCAGGAATTTTCCTA 74 93 0 TGCCGCACGG 0.825902 -147 CGCATCGCCAATGTAAATCCGGCCCGCCTATG 79 6 1 CGCCATTCGG 0.751164 -57 **** ** * * ** Masking position 4 Map Score: 19.8722 Number of sites scoring better than the average of aligned sites = 1948 Number in coding regions = 1831 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 AATATTGAAAATTTCTTTTTGCTACG 3 7 0 ATTTCTTTTT 0.691899 -294 CGTGTTATTATTGTCGTTTCTTATATTTTG 13 71 1 TTGTCGTTTC 0.554094 -34 GCATCAGGGATTTTCGTTTTCATAATGGCT 32 217 0 TTTTCGTTTT 0.897126 -84 CCGCCGATCGCTGTCGTTTTTACCAAACCA 32 274 0 CTGTCGTTTT 0.875049 -27 TAGCAGTGGGTTTTCATTTTTGCAAACTCA 35 36 0 TTTTCATTTT 0.592057 -86 AAAGCGAGGATTTTCGTTTTTCAGACGGGA 39 53 0 TTTTCGTTTT 0.897126 -20 AATTTTCATATTGTCGTTTTTGTGATCGTT 56 116 1 TTGTCGTTTT 0.735651 -82 CCGGAAACGGATTTCTTTTCAGGTTTGTGA 63 108 0 ATTTCTTTTC 0.500688 -193 TTTCGTAAAACTTTCGTTTCATTTCGTTTT 65 20 1 CTTTCGTTTC 0.907401 -229 CTTTCGTTTCATTTCGTTTTGCCTATTAAC 65 30 1 ATTTCGTTTT 0.911995 -219 AAACCATTATCTTTCGTTTTATTTTTATCT 65 159 1 CTTTCGTTTT 0.956419 -90 CGATATTAATCTTTCGTTTTGTTTCAGTTG 65 205 0 CTTTCGTTTT 0.956419 -44 CCCGTAAGGCCTTTCTTTTTCTTTCGTTTT 66 42 1 CTTTCTTTTT 0.826258 -35 CTTTCTTTTTCTTTCGTTTTGATCTGTGCA 66 52 1 CTTTCGTTTT 0.956419 -25 ACGATCACAAATTTCGTTTTATTTCTTTTT 67 42 1 ATTTCGTTTT 0.911995 -150 ATTTCGTTTTATTTCTTTTTTCTCCATTGA 67 52 1 ATTTCTTTTT 0.691899 -140 TTTCACTTGCCTTTCGTTTCATTTCACTTG 67 128 0 CTTTCGTTTC 0.907401 -64 GAGGCTCCTCCTTTCATTTTGTCCCATGTG 77 26 1 CTTTCATTTT 0.785051 -54 TCTTCTCCTAATTTCATTTTTGAATTTGGA 78 279 0 ATTTCATTTT 0.63298 -22 ********** Masking position 4 Map Score: 16.4226 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 91 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TCAGGCAAGCCGACTGACGCCACGCGT 1 7 0 CGACGACGCC 0.509326 -52 AAAAAGGAGCCGCCTGAGGGCGGCTTCTTTT 6 16 1 CGCCGAGGGC 0.980019 -131 TTTCTGTTGCCGCCGGTGGGGTTCGCCATTG 10 83 1 CGCCGTGGGG 0.754198 -38 TGGAAAAACCCGCTCGACGGCGGGTTTAAGC 16 162 0 CGCTGACGGC 0.544383 -139 AATTCTTGTCCGCCAGCTCGGTCTTCAGCCT 18 125 1 CGCCGCTCGG 0.734288 -42 TAGCAACTCCCGCCAGAAGGCGGGAGTTTTT 19 63 0 CGCCGAAGGC 0.934527 -47 AATTACGTTACGCCGGAGCTGAC 19 97 1 CGCCGAGCTG 0.822718 -13 AGACTTTTTCCGCCAGACACGACTTTGTAGA 22 16 1 CGCCGACACG 0.802891 -285 AAACAAGGCCCACCGGAACGGCAGGCCTGAG 25 13 0 CACCGAACGG 0.569775 -101 AGGGATCTACCGCCAGAGAGGTA 30 3 0 CGCCGAGAGG 0.921616 -135 CGATTTTGTTCGCCAGAGCCCGGGGGTGCAG 31 16 0 CGCCGAGCCC 0.96673 -285 TGTTACCTCGCGCCCGACCCGGTAGCCGTAA 31 75 0 CGCCGACCCG 0.94522 -226 GCGCCTGCGGGCGCTTTTTTTG 32 2 1 CGCCGCGGGC 0.955586 -299 TTTCCCATCTCGCAGGAACCGTACACC 33 7 0 CGCAGAACCG 0.427837 -218 CGCATTTTTTCGCCCGCAACCAAAATTTGTG 33 160 0 CGCCGCAACC 0.466631 -65 TTTCCTAAGCCGCCAGCCAGGCGGCTTTTTT 40 13 1 CGCCGCCAGG 0.768142 -50 AACGCCAGGGCGACAGAGCGGGCTATCTGTT 45 30 0 CGACGAGCGG 0.752526 -49 TCTGGTAAAGCGCCGGACGCCAACAACCCAC 52 25 0 CGCCGACGCC 0.944445 -122 CTCCATCGGTCACCTGAGGCGGAGCTTCGCC 59 62 0 CACCGAGGCG 0.670515 -153 AAAGCGACAACGCCCGACGTCAAGTTCATCA 67 155 1 CGCCGACGTC 0.746137 -37 TAATCGTCTACGCCAGAACGCCTGGGTAATG 70 16 1 CGCCGAACGC 0.940027 -102 TTCCTAACATCGCCAGCGCGGCATTAAGATT 74 68 0 CGCCGCGCGG 0.956219 -172 TTTTTTAGTGCGCAAGAGGGCTAAATTATCA 80 127 0 CGCAGAGGGC 0.824516 -168 CAGCGGGGAACGCAGGATCGCTGGCTCCCCG 82 33 0 CGCAGATCGC 0.394973 -43 TGGCGCGATTCACCTGAGCGCAACATTGAGA 85 68 0 CACCGAGCGC 0.831284 -108 **** ****** Masking position 6 Map Score: 24.4192 Number of sites scoring better than the average of aligned sites = 2765 Number in coding regions = 2618 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 7 CTCACCCTAACCCTCTCCCCAAAGGGG 17 8 0 CCCTCTCCCC 0.96371 -293 CTGGCTGTTCCCCTCACCCTAACCCTCTCC 17 20 0 CCCTCACCCT 0.962223 -281 CGAACATTAACCCTCACCCCAGCCCTCACC 17 58 1 CCCTCACCCC 0.978974 -243 CTCACCCCAGCCCTCACCCTGGAAGGGAGA 17 70 1 CCCTCACCCT 0.962223 -231 CCGTTCTGCCCCCTCTCCCTTCCAGGGTGA 17 83 0 CCCTCTCCCT 0.935598 -218 CGGGTAACTCCCCTCTCCTCGCTGTGATAT 18 39 1 CCCTCTCCTC 0.86804 -128 ATATACTTTTCCCCCACTTTTACTCATTCT 18 65 1 CCCCCACTTT 0.507795 -102 CCCATCCCTTCCCCCTCCGTCAGATGAACT 29 74 1 CCCCCTCCGT 0.85924 -59 GTAAAACGCGCCCTCAGCCCACATCCATGT 31 111 1 CCCTCAGCCC 0.796112 -190 ATTTTTCACACCCTCTCAGCATGCAGTCGT 49 54 0 CCCTCTCAGC 0.653698 -247 CCCCGCTCTACCCTCACTCCTGAAAGTATG 50 73 0 CCCTCACTCC 0.902626 -228 AGCGGGGTTTCCCCCGCCCTGGTAGTCTTA 50 96 1 CCCCCGCCCT 0.81353 -205 TTACCAGAGCCCCCCACAGCGCTACAATGC 52 48 1 CCCCCACAGC 0.731059 -99 TAGGGGAGTGCCCCCACTTTAAGGGCGGGC 52 76 0 CCCCCACTTT 0.507795 -71 GGGGGCACTCCCCTAACCGCTTCATCAGGT 52 91 1 CCCTAACCGC 0.574072 -56 ********** Masking position 3 Map Score: 12.49 Number of sites scoring better than the average of aligned sites = 286 Number in coding regions = 159 Number in noncoding regions = 127 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 8 ATAATTGTTGGCGCTGTGTACAGCATCAGACGTC 4 80 0 GCGGTACAGC 0.760903 -221 CATCTGCGGCGCGAAATATGAAGGGGGAGAGCCC 5 122 1 GCGATGAAGG 0.451975 -136 TGGTAGTGTAGCGATGACTTTAGGCGATCAATAT 12 34 1 GCGGTTTAGG 0.7324 -88 CCCATTTGCACCGGAGGGTGCAGTTCTTTGCGTG 12 81 0 CCGGTGCAGT 0.553243 -41 TCCCGAAATCGCCTCTGGTTCAGGTATACTGACA 22 131 1 GCCTTTCAGG 0.714998 -170 CGAAATAGTAGCCAGGAATGCAGGGCGCATAGTG 26 109 0 GCCGTGCAGG 0.943737 -37 GAAGGAAATCCCGACGTCTCCAGGTAACAGAAAG 27 219 1 CCGGTCCAGG 0.835983 -82 TTCGCCAGAGCCCGGGGGTGCAGGGGGC 31 5 0 CCCGTGCAGG 0.894718 -296 TGGGCTGAGGGCGCGTTTTACAGGGATGTTACCT 31 98 0 GCGTTACAGG 0.696082 -203 ATGTGGGCTGCCCCGGCCTTCAGGGAACGCCTCG 31 137 1 CCCGTTCAGG 0.904924 -164 CGGCAATTTCGCCCAGTCTTCAGCCACAAATTTT 33 136 1 GCCGTTCAGC 0.777077 -89 TAGCTCAGTTGCGTAGATTTCATGCATCACGACA 41 162 1 GCGGTTCATG 0.699722 -44 AGGAGGTAAGCCGACGATTTCAGCGGGACGCTGA 50 228 0 CCGGTTCAGC 0.846381 -73 GTAGCGCGAGGCTTTCAGGGTTGTACGAA 59 6 1 GCGGTTCAGG 0.983221 -209 AGGCATACTTGCGAAGATTTCAGGTATAAGGATA 62 15 0 GCGGTTCAGG 0.98322 -84 CCAAAGCCTTGCGTAGCCTGAAGGTAATCGTTTG 63 156 1 GCGGTGAAGG 0.860631 -145 CGTTTTGATAGCGCAACCTTCAGGAAAAATT 68 188 1 GCGATTCAGG 0.886697 -21 GTGCTAAGATGCGGAGACTTAAGGTCAAAAAAAC 75 24 0 GCGGTTAAGG 0.873654 -166 ACGGTATATTCCGTTTTTTACAGGAGAATTT 76 8 0 CCGTTACAGG 0.537147 -204 CGTTCGCAGACCGTAACTTTCAGGTACTTACCCT 80 229 1 CCGATTCAGG 0.798542 -66 AAATAGATCAGCGGGGAACGCAGGATCGCTGGCT 82 38 0 GCGGCGCAGG 0.83338 -38 *** * ****** Masking position 12 Map Score: 17.3211 Number of sites scoring better than the average of aligned sites = 998 Number in coding regions = 938 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 9 CCTTCATATTTCGCGCCGCAGATGCGTTATC 5 115 0 TCGCGCGCAG 0.919299 -143 TTGGTCACGGCCAGCGCGCAGCAACCGGAGC 7 99 1 CCAGCCGCAG 0.96699 -193 AGTGGTTACTTCGTCACACAGCTTAAACCCG 16 142 1 TCGTCCACAG 0.411006 -159 AACCCCACCTCGCAGACAAAGCGGG 16 286 0 CCACCCGCAG 0.972172 -15 TCATCCCACCCCGCGCCGCAGATTGCATCGC 22 65 0 CCGCGCGCAG 0.9664 -236 AGGAAATTATTCACGCCACAGGAAAAAGGCG 25 80 0 TCACGCACAG 0.636475 -34 TAAGTCGAGGGCACCGCGCAGCGGCGATTTT 31 40 0 GCACCCGCAG 0.803154 -261 TGCCAGGCCGCCGATCGCTGTCG 32 288 0 CCAGGCGCCG 0.821957 -13 TTTTACTTTCCCATCTCGCAGGAACCGTACA 33 13 0 CCATCCGCAG 0.937146 -212 GCATGTTAAGCCGTCTCGCAGAGATGTTATT 34 151 0 CCGTCCGCAG 0.94175 -69 TTTGTGAACGTCAGGGCGCAGAGATCCCCGG 37 218 0 TCAGGCGCAG 0.898175 -57 CCATTCGCAGCCGGTACGCAGTCAGTACCGG 44 18 1 CCGGTCGCAG 0.879055 -102 CTGATGCCTGCCAGGGCGGAGAGATAATGTC 51 92 0 CCAGGCGGAG 0.740496 -60 TTTTATCTCACCATGACGCAGTATCAACTGA 65 181 1 CCATGCGCAG 0.945386 -68 ACCGCTGCACAGATCAAAACGA 66 65 0 CCGCTCACAG 0.59058 -12 ***** ***** Masking position 7 Map Score: 11.1225 Number of sites scoring better than the average of aligned sites = 819 Number in coding regions = 775 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 10 TTATATTAAATGTTAACAAAAATAAAACAA 3 236 1 TGTTAACAAA 0.686513 -65 TGAAGCCCTACGCTAACAAATAGCGCGACT 9 30 0 CGCTAACAAA 0.693355 -156 CAAACCGTGGCGATAAAAAAGGGCCACCGA 15 39 0 CGATAAAAAA 0.715 -60 CTGTAAATGACGTTAACAAAGTCACGCGGA 20 40 1 CGTTAACAAA 0.860799 -99 TCAATTTTGTCGATAACAAAATCCTGGAGT 22 217 0 CGATAACAAA 0.906346 -84 CAGTATAGGCTGTTCACAAAATCATTACAA 27 54 0 TGTTCACAAA 0.726888 -247 TGCGCCCTGACGTTCACAAACTGCATATAT 37 229 1 CGTTCACAAA 0.882567 -46 TCCATGCAGTTGTTAAAAAAGCCGCCTGGC 40 28 0 TGTTAAAAAA 0.362126 -35 AAAGCCGGAGTGATCACAAAAAAAGGCGTA 41 106 0 TGATCACAAA 0.806396 -100 ATCGAGATAACGATCACAAAAACGACAATA 56 124 0 CGATCACAAA 0.921639 -74 ATTTTGAAATCGAAAACAAACGACAGGAT 56 179 1 CGAAAACAAA 0.487833 -19 TTTCTTTCAACGATCACAAATTTCGTTTTA 67 33 1 CGATCACAAA 0.921639 -159 GCCAAAAAAGCGATCAAAAAAACAAGGAAG 69 175 1 CGATCAAAAA 0.753026 -26 ACCTTTGGGTTGATAAAAAATAGTCATGAG 76 42 1 TGATAAAAAA 0.470464 -170 ********** Masking position 6 Map Score: 5.52341 Number of sites scoring better than the average of aligned sites = 171 Number in coding regions = 139 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 TTCGTATACACAGACTGGACGGAAGCGACAAT 4 165 1 CAGACTGACG 0.8353 -136 TTGTCTCAGTCAGACCAGACAGTCACACACAG 7 251 0 CAGACCAACG 0.94054 -41 CCCCACCTCGCAGACAAAGCGGGTGTAAATTG 16 277 0 CAGACAAGCG 0.918947 -24 GTGAGGGGAACAGCCAGCACTGGTGCGAACAT 17 33 1 CAGCCAGACG 0.928667 -268 ATTTTGTGAACAGCCTATACTGCCGCCAGGTC 27 62 1 CAGCCTAACG 0.909869 -239 AAGGCCGGGGCAGCCCACATGGATGTGGGCTG 31 125 0 CAGCCCAATG 0.700933 -176 CTCACCTCAGCAGCCAATACCGCATCAGGGAT 32 236 0 CAGCCAAACG 0.962977 -65 GGCAGCGCGACAGACAACGTCGTTGAGGAGTA 34 14 0 CAGACAAGTG 0.589244 -206 GGAGCGAACGCAGCCAAGGCAGAGGCGGCTTG 37 135 1 CAGCCAAGCG 0.925412 -140 AGCCGGTACGCAGTCAGTACCGGCTTTTTTTA 44 26 1 CAGTCAGACG 0.670149 -94 ATTTCCTGACCAGACCAAACTGGCGATAAGAT 78 225 0 CAGACCAACG 0.940771 -76 GTCTGGTTTCCATACAAAACGGCCCGCCATAG 79 38 0 CATACAAACG 0.596661 -25 ACTTATCCATCAGACTATACTGTTGTACCTAT 80 179 1 CAGACTAACG 0.909755 -116 ******* ** * Masking position 2 Map Score: 6.89702 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 276 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 GTGGCACGTTTGGCGAAATTCAGAATGATT 4 24 0 TGGCGAAATT 0.816457 -277 GAATTAATACTAGCGACATTGTACGTCGCT 6 95 0 TAGCGACATT 0.9011 -52 AAAGCCGATTCGGCGACAATTGTCCCGAAA 22 109 1 CGGCGACAAT 0.801682 -192 CGTTTATTTCTGGCGACATTCTTTATATAC 37 178 0 TGGCGACATT 0.975511 -97 TAAATGTGCATGGCGACATTGCTATTAATA 49 241 1 TGGCGACATT 0.975511 -60 TTTTAGCGACATTATTTTGTTAG 51 4 1 TAGCGACATT 0.9011 -148 AGACCAGATCCGGCAACATTATCCCACGCA 51 49 1 CGGCAACATT 0.837646 -103 CCATTGCTTCTGGCAACATTAAGTCTCAAA 87 69 1 TGGCAACATT 0.9011 -37 ********** Masking position 6 Map Score: 3.76504 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 105 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 13 TCATGCGCTACATAAATTTTTCAGGAGCAAATA 2 13 1 CATAATTCAG 0.842688 -23 TAGCAATATGCTTTAAGTTTACAGGATTTTTACC 26 26 1 CTTTATTCAG 0.911595 -120 AATCAATCTCCCTTAAAGTTGCATGAAAAATCCC 30 52 1 CCTTATTCAT 0.6189 -86 CTTTACTCGTCCTTCCGCTTTCAGTA 31 285 1 CCTTCTTCAG 0.867274 -16 TACACAAAATCATTCAAGTTGCATCAAGGCGGCA 37 58 1 CATTATTCAT 0.768645 -217 GTCATCACCTTTACGATTCCAGTTTTCGTGAA 38 263 0 CTTTCTTCAG 0.858215 -22 TCGCCATGCACATTTACCTTGCAGTTAATTGAAT 49 223 0 CATTATTCAG 0.959859 -78 TCGGGAGGGGCTTTCCCGTTTCAGCGTCCCGCTG 50 208 1 CTTTCTTCAG 0.858217 -93 ACCAAAGAACCATTTACATTGCAGGGCTATTTTT 63 36 0 CATTATTCAG 0.959859 -265 CTTTTTTCTCCATTGAACTTTCAGTTTCTTTTCT 67 66 1 CATTATTCAG 0.959858 -126 GCCAGCGCGGCATTAAGATTACAGATATAAAAGC 74 54 0 CATTATTCAG 0.959756 -186 CGCTTTACTCCATAAACATTGCAGGGAAAGTTTT 85 11 0 CATAATTCAG 0.842705 -165 **** * ** *** Masking position 13 Map Score: 5.19324 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 56 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 GAAAAAGGGGGCCATATGCAGGCCCCCTAACCAAA 5 177 0 GCAAGCACCC 0.985089 -81 GCGATACTTCAGCAAAAGCGACCCCCA 10 3 0 ACAAGCGCCC 0.978427 -118 TGTAACCACAACCAGATGCAACCCCGAGTTGCAGA 17 169 1 ACAAGCACCC 0.98538 -132 GCCCTACTATAGCAAATGCACTACCGGCAGGCATC 20 76 0 ACAAGCAACC 0.882718 -63 GTATTCTGGAAACATACGCACTCCCTGTTA 39 6 0 ACAAGCACCC 0.98538 -67 GGTGCTCTTAGTCATAAGCTTCCCCGCTTACTAAG 50 122 0 GCAAGCTCCC 0.94219 -179 CTTTCTATTAAGCAAATGCAAGCCCACCTTGCCCA 65 62 1 ACAAGCACCC 0.98538 -187 AAAACGGCCCGCCATAGGCGGGCCGGATTTACATT 79 20 0 GCAAGCGCCG 0.880348 -43 * ** * *** *** Masking position 6 Map Score: 3.34678 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 35 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 ATTTATTTTGCGTTCCCGTTTGTTTTATTTT 3 254 0 CGTCCCGTTT 0.776125 -47 CTCGCTTCTCCGTTACCCGGCTCCT 18 5 1 CTTTCCGTTA 0.651608 -162 GCGCATTGCGCTTACCCGGCTTACAGAACAA 37 16 0 CTTCCCGGCT 0.811238 -259 GCTTTTCCAGTTTCGGATAAGG 44 108 0 CTTTCCAGTT 0.68588 -12 TAGTCATAAGCTTCCCCGCTTACTAAGACTA 50 118 0 CTTCCCGCTT 0.784367 -183 TCGGGAGGGGCTTTCCCGTTTCAGCGTCCCG 50 208 1 CTTCCCGTTT 0.861134 -93 ATCCACTAGTCTTGTCCGGTATATGACGATT 59 188 0 CTTTCCGGTA 0.883049 -27 TTATGGCACACTTGTCCGGTTAACTCTCGTC 62 59 1 CTTTCCGGTT 0.968184 -40 AAACGGATTTCTTTTCAGGTTTGTGATGCAA 63 103 0 CTTTCAGGTT 0.68588 -198 AAAAGAAATCCGTTTCCGGTTGCAAGCTCTT 63 119 1 CGTTCCGGTT 0.944483 -182 TTTACGAAAGCGTATCCGGTGAAATAAAGTC 71 40 1 CGTTCCGGTG 0.780119 -37 TACTTCTCCGGTTAGTAAGAAAT 76 199 0 CTTTCCGGTT 0.968184 -13 *** ******* Masking position 3 Map Score: 3.25908 Number of sites scoring better than the average of aligned sites = 209 Number in coding regions = 177 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974