AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00500_ecoli_reg_100.orf -o00500_ecoli_100.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/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 Input sequences: #1 yacA 155 orf, hypothetical protein #2 secA 61 preprotein translocase; secretion protein #3 mutT 59 7,8-dihydro-8-oxoguanine-triphosphatase, prefers dGTP, causes AT-GC transversions #4 yadI 104 putative PTS enzyme II B component #5 yagG 226 putative permease #6 malZ 155 maltodextrin glucosidase #7 nagE 300 PTS system, N-acetylglucosamine-specific enzyme IIABC #8 seqA 184 negative modulator of initiation of replication #9 pgm 25 phosphoglucomutase #10 hrsA 108 protein modification enzyme, induction of ompC #11 helD 122 DNA helicase IV #12 ptsG 294 PTS system, glucose-specific IIBC component #13 treA 300 trehalase, periplasmic #14 galU 201 glucose-1-phosphate uridylyltransferase #15 ycjM 185 putative polysaccharide hydrolase #16 ycjQ 30 putative oxidoreductase #17 uidA 300 beta-D-glucuronidase #18 malX 174 PTS system, maltose and glucose-specific II ABC #19 rnt 102 RNase T, degrades tRNA #20 lhr 92 member of ATP-dependent helicase superfamily II #21 celC 50 PEP-dependent phosphotransferase enzyme III for cellobiose, arbutin, and salicin #22 celB 84 PEP-dependent phosphotransferase enzyme II for cellobiose, arbutin, and salicin #23 celA 298 PEP-dependent phosphotransferase enzyme IV for cellobiose, arbutin, and salicin #24 manX 300 PTS enzyme IIAB, mannose-specific #25 ntpA 117 dATP pyrophosphohydrolase #26 otsB 166 trehalose-6-phosphate phophatase, biosynthetic #27 fliD 265 flagellar biosynthesis; filament capping protein; enables filament assembly #28 fliS 24 flagellar biosynthesis; repressor of class 3a and 3b operons (RflA activity) #29 amyA 77 cytoplasmic alpha-amylase #30 ugd 248 UDP-glucose 6-dehydrogenase #31 galF 174 homolog of Salmonella UTP--glucose-1-P uridyltransferase, probably a UDP-gal transferase #32 gatB 30 galactitol-specific enzyme IIB of phosphotransferase system #33 gatZ 28 putative tagatose 6-phosphate kinase 1 #34 gatY 197 tagatose-bisphosphate aldolase 1 #35 bglX 195 beta-D-glucoside glucohydrolase, periplasmic #36 fruB 300 PTS system, fructose-specific IIA/fpr component #37 glk 203 glucokinase #38 ptsH 300 PTS system protein HPr #39 ptsI 44 PEP-protein phosphotransferase system enzyme I #40 crr 40 PTS system, glucose-specific IIA component #41 srlA 255 PTS system, glucitol/sorbitol-specific IIC component, one of two #42 ascF 256 PTS system enzyme II ABC (asc), cryptic, transports specific beta-glucosides #43 cmtA 27 PTS system, mannitol-specific enzyme II component, cryptic #44 cmtB 300 PTS system, mannitol-specific enzyme II component, cryptic #45 agaZ 248 putative tagatose 6-phosphate kinase 2 #46 agaB 166 PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 1 (EIIB-AGA) #47 ptsN 117 phosphotransferase system enzyme IIA, regulates N metabolism #48 malP 300 maltodextrin phosphorylase #49 glgB 272 1,4-alpha-glucan branching enzyme #50 yhhN 140 putative enzyme #51 zntA 73 zinc-transporting ATPase #52 treF 300 cytoplasmic trehalase #53 malS 300 alpha-amylase #54 mtlA 300 PTS system, mannitol-specific enzyme IIABC components #55 gmk 251 guanylate kinase #56 rpoZ 54 RNA polymerase, omega subunit #57 glvB 24 PTS system, arbutin-like IIB component #58 glvC 34 PTS system, arbutin-like IIC component #59 bglF 133 PTS system beta-glucosides, enzyme II, cryptic #60 rep 174 rep helicase, a single-stranded DNA dependent ATPase #61 dapF 300 diaminopimelate epimerase #62 uvrD 83 DNA-dependent ATPase I and helicase II #63 recQ 126 ATP-dependent DNA helicase #64 frvA 300 PTS system, fructose-specific IIA component #65 frwC 300 PTS system, fructose-like enzyme II component #66 pflD 50 formate acetyltransferase 2 #67 pgi 300 glucosephosphate isomerase #68 dnaB 82 replicative DNA helicase; part of primosome #69 sgaT 291 orf, hypothetical protein #70 treC 49 trehalase 6-P hydrolase #71 treB 118 PTS system enzyme II, trehalose specific #72 mgtA 300 Mg2+ transport ATPase, P-type 1 #73 sgcA 130 putative PTS system enzyme II A component Motif number 1 AATTCCCCTGTGATGAAAATCTGATCACCTTGCCATA 6 129 0 TGTGATCGTA 0.812948 -27 GCGTGTCTTTTGTGAGTTTTGTCACCAAATATCGTTATT 7 125 0 TGTGATCCAA 0.971887 -176 TATGTGATCAATTTCACTTGATTGAAATTAT 10 88 0 TGTGATCCTA 0.963161 -21 TTTAACTACCTGTTATATTTTTCACCAATTTATGATGAT 13 52 1 TGTTATCCAT 0.496667 -249 ATACCCACAGCGTGATATAGATCGCATTAATCTTTAAAA 17 120 0 CGTGATCCTA 0.70433 -181 CGTTGCGTAATGTGATTTATGCCTCACTAAAATTTGATA 18 84 1 TGTGACCCCA 0.595087 -91 AATTATTTTATGTGATGAAGATCCGTAATTTAACTTTCG 24 135 0 TGTGATCGAT 0.689758 -166 GTATAGACAGTGTGACGGGGGTCGCCATTTGCAACGAAG 26 77 0 TGTGATCCAT 0.930432 -90 TTGTCGTTTTTGTGATCGTTATCTCGATATTTAAAAACA 34 126 1 TGTGATCCAA 0.971887 -72 GATTTAAAAGTGTTATTTTGATCGCAAAATGAAAGATAA 41 163 0 TGTTATCCAA 0.718354 -93 TTTTTATATTTGTGAAACCGGTCACCTGAATATTTTTCC 42 80 0 TGTGATCCTA 0.963161 -177 TTCATGATTTTGTGAAACCGGTTTCTTAATTCCGTTTCA 42 157 1 TGTGATTCTA 0.509741 -100 ATATCAATTATGTAATATGCATCACGATATGCGGTATTG 44 114 1 TGTAATCCAA 0.591239 -187 ATGTTTCTTTTGTGAATCAGATCAGAAAACCATTATCTT 45 133 1 TGTGATCGAA 0.85178 -116 AGCAAGGAAATGTGATCTCAACCACTTAAAGCTAGTGCA 48 160 0 TGTGACCCTA 0.875732 -141 TCGCAGAAAATGTGGGGGTTATCGCAAAATTCAGCCGTT 53 152 1 TGTGGTCCAA 0.758616 -149 GGCATTTAAATGTGAGTAGTGTCACATTTTTGTTTTGAT 54 22 0 TGTGATCCTT 0.910033 -279 ACAAGCGTTTTGTGATGAACGTCACGTCAATTACCTCTC 54 98 1 TGTGATCCTA 0.963157 -203 CGGCCTTTTGTGTGATATCAATCACATAAATATAGGGGG 54 139 0 TGTGATCCTA 0.963162 -162 CGGCCTGCCATGTGACAAATCTGCCAAAAGCTGGACAAA 65 54 1 TGTGATGCAA 0.670791 -247 AACAGCGTCTTGTGAGACGCGTCGCAAATTGACGGTTAC 65 99 0 TGTGATCCAT 0.930433 -202 TATGATTAAATGTGACGCGACCCGCAAATAATTCCACAT 69 225 0 TGTGACCCAT 0.782842 -67 ***** ** * * * Masking position 3 Map Score: 20.0685 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 41 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 2 ACAGCGTTCGCACCGTTTTTTATAGCTCTTA 1 98 0 CACCTTTTTT 0.834953 -58 CAGGATTCTGCGCCTTTTTTATAGGTTTAAG 3 36 1 CGCCTTTTTA 0.747236 -24 GGCATCTAAGCGCCCTTTATTTATTACACAG 12 195 0 CGCCTTTATT 0.891366 -100 CACTCTATTTCGCCGTTATTTATCCCTTTAA 13 152 1 CGCCTTATTT 0.747236 -149 GGCGCTTATGCGCCGTTTTTTTTTCTGTCAC 15 28 1 CGCCTTTTTT 0.980525 -158 CCGGCCATTGCGCCGGTTTTTTTTGGCCTGA 23 45 1 CGCCGTTTTT 0.946877 -254 CCCTGCGTTTCGCGATTTATTTTAGATATCG 24 178 0 CGCGTTTATT 0.712422 -123 TTTCAAAAACAGCCATTTTTTGTTAGTCGCC 27 121 1 AGCCTTTTTT 0.843852 -145 TATTGCACCGGGCTTTTTTTTGCCAAATATC 30 48 1 GGCTTTTTTT 0.593521 -201 TAGCAAAGTGCGCGTGTTTTTATGCCGGATG 34 38 0 CGCGGTTTTT 0.843297 -160 CCTATCGGGAGGCCGTTTTTTTGCCTTTCAC 34 76 1 GGCCTTTTTT 0.969003 -122 AAGCCAGGTTGGCGCTTTTTTTCTCATAGAG 36 245 1 GGCGTTTTTT 0.904201 -56 GTATTGTTAGCGCCAGTTTTTAACAGACGCG 38 211 0 CGCCGTTTTT 0.946877 -90 GGTGCTTCGGCGACCTTTTTTATTACCTTGA 44 17 1 CGACTTTTTT 0.770848 -284 AATACGCAACGGCCATTTTTTGCACTTAGAT 48 80 1 GGCCTTTTTT 0.969003 -221 CGCAAAATTCAGCCGTTTTTTGCGCGAGATC 53 174 1 AGCCTTTTTT 0.843852 -127 GCTGGAAGCCCGAGGTTTTTTGTTAATGTGG 54 246 0 CGAGTTTTTT 0.503877 -55 ATTCACGTCAGGCCGTTTTTTTCAGGTTTTT 59 76 1 GGCCTTTTTT 0.969003 -58 CTGAAAATAGCGCCTGTTTTTATTTCAGGCA 63 100 1 CGCCGTTTTT 0.946877 -27 TCCAGTAAATGGCCTTTTTATCCACTGTTTG 65 206 1 GGCCTTTTAT 0.647343 -95 CCGCCCCGCTCACCCTTTATTTATAAATGTA 67 90 0 CACCTTTATT 0.451895 -211 GGAAGGCAATGACCATTTTTTGACTTTTTGC 69 81 1 GACCTTTTTT 0.758524 -211 TATTATTTGCGGCGCTTTTTTCACTTACCGG 72 79 1 GGCGTTTTTT 0.904201 -222 **** ****** Masking position 7 Map Score: 22.7761 Number of sites scoring better than the average of aligned sites = 773 Number in coding regions = 635 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 3 ACTGGTTCACCTGGCCGGAGAGAGTGCCAGATTTGCC 1 42 0 CGCGGAGAGC 0.916285 -114 TGGATTTGCGCAGACAGGCGTCAATCCGACCTGATTT 7 39 1 CGCGGCGAAC 0.993621 -262 AGCGTCAAGCCTGGCTTGCAGAAAAACTCGGAATAAA 8 88 0 CGCTGCAAAC 0.925052 -97 TCTCCTGCCGGGCGTGAACTCATCGCGCCCG 19 5 1 CGCGGCGAAC 0.993621 -98 GGCGATTGAGCCGACGGGTGGAAACCCAATACGTAAT 27 40 0 CGCGGTGAAC 0.973526 -226 GATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCT 41 216 1 CGTGGTAAAC 0.645014 -40 TTTTAGGGTACCGTCCGGCGGTAAAAATAAAATACTC 44 256 0 CGCGGCGAAA 0.885389 -45 GCATGGCGGTCTGTTGTGCGGCACAACGGGCCATTTG 47 32 1 CGTTGCGACC 0.824747 -86 TTCGCTCCGCCTGGTGGGCGACAAAGCGTGCGGTGGA 52 217 0 CGTGGCGAAC 0.981764 -84 GTTAACGATTCAGATTGGCGCTAAATCGCAGAAAATG 53 127 1 CGTGGCGAAC 0.981764 -174 CGGGATCCAGTTTTGCGGTAAAAC 57 1 0 CGTTGCGAAC 0.967572 -24 TTGCCCTCTACCGCTTTGCGGCAAAACTCCAAAAAAA 59 104 0 CGTTGCGAAC 0.967572 -30 TTTTTATCTGCAGGCGGGAAATAGAGCGGACCTTTCA 61 138 0 CGCGGAAAGC 0.61011 -163 CGGCAACGGCCTGCCATGTGACAAATCTGCCAAAAGC 65 48 1 CGCTGTGAAC 0.953228 -253 AAGCTGCTCCCGGGCTTGCGAAAGCCCATGTCCATAT 65 274 0 CGCTGCGAGC 0.979568 -27 TTGGAGGAGCCAGTCCTGTGATAACACCT 67 3 0 CGCTGTGAAC 0.953228 -298 CGCGCCTCTTCTGGCCTGCGCTAGCGCAGGTAGTACA 67 57 1 CGCTGCGAGC 0.979568 -244 * * * **** ** * Masking position 13 Map Score: 24.6923 Number of sites scoring better than the average of aligned sites = 531 Number in coding regions = 508 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 4 AAATCTCAAACGCCCCGCGTTGCGGAGTTAATAAA 2 33 0 CCGCGTGCGG 0.908261 -29 TTTTAAGAGATAAAACCGTCTGCGGAATATTTCCC 5 14 1 TCCGTTGCGG 0.968963 -213 TCAAAAACAACAAAGCCGTCTGCGGGAAATATTCC 5 37 0 CCCGTTGCGG 0.990695 -190 GTATATGAATAAATCCCGGCAGCGGATAGCGTCAA 8 117 0 ACCGGAGCGG 0.7583 -68 AGAACTTAGCCCCTTCGGGGTGCTGATATACTGGG 14 122 1 CCGGGTGCTG 0.65658 -80 ACATTAGAAGCGTAGCCGTAATCGGATTATTCGCG 29 31 0 CCCGTATCGG 0.709864 -47 GCGCGTGTTTTTATGCCGGATGCGGTGTAAACATA 34 25 0 TCCGGTGCGG 0.964932 -173 GTTCTATTCCTTATGCGGGGTCAGATAC 37 4 1 CCCTTTGCGG 0.942451 -200 TTTGGTTCAATTCTTCCTTTAGCGGCATAATGTTT 38 110 1 TCCTTAGCGG 0.725061 -191 CAGTGACTACCGCTTCCTTGTGCGGGGCGTGATGC 41 55 0 CCCTTTGCGG 0.942451 -201 ACGCAGTGTACTGCACCGTTTGCCGATTGTCCTTG 42 34 1 CCCGTTGCCG 0.88042 -223 ATTACCTTGATATGTCCGTTTGCGGACAAGCAATA 44 38 1 TCCGTTGCGG 0.968963 -263 ATGTAATATGCATCACGATATGCGGTATTGACATT 44 123 1 CCGATTGCGG 0.73872 -178 CCAAACAAAACTCATCCCTGAGCGGTAAGTCCACA 53 226 0 CCCCTAGCGG 0.93395 -75 AACTTGCCCTCTACCGCTTTGCGGCAAAACTCCA 59 110 0 TCGCTTGCGG 0.767098 -24 ACATCCGCAGCCAACCGGTTAGCGGCTTACACGCG 60 88 1 CCGGTAGCGG 0.962277 -87 CTCTCTTCAGCCTGACGGGCTGCGGTCTGAAAGGT 61 111 1 CCGGGTGCGG 0.976154 -190 TGGGCTTTCGCAAGCCCGGGAGCAGCTT 65 283 1 CCCGGAGCAG 0.706512 -18 GTGATGGTTTTAGTGCCGTTAGCGTAATGTTGAGT 67 210 0 TCCGTAGCGT 0.571651 -91 CTTTTCACGGCGTTACCGGATGCGTAAGGCCGTGA 72 177 1 CCCGGTGCGT 0.87958 -124 * **** ***** Masking position 6 Map Score: 19.3434 Number of sites scoring better than the average of aligned sites = 1171 Number in coding regions = 944 Number in noncoding regions = 227 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 5 CAAATTGGCACTGAATTATTTTACTCTGTGT 12 170 1 CTGAATTATT 0.761336 -125 TAGCCCTTATCTGAATCGATTCGATTGTGGA 24 220 1 CTGAATCGTT 0.967943 -81 TAAAGAAAATCTGAATTGTTTTTCGTTGCGT 30 134 1 CTGAATTGTT 0.936389 -115 GAATTGATTACTGAATTACTTGTGATGTTAC 31 82 0 CTGAATTATT 0.761336 -93 ATCAATTACCCTGAATTGATTACTGAATTAC 31 94 0 CTGAATTGTT 0.936389 -81 TATTCACTCGCTGAATTGTTATACAAGGCGC 35 55 0 CTGAATTGTA 0.873597 -141 CAAGATCGCGCTGAAACGTTTCAAGAAAGCA 36 203 0 CTGAAACGTT 0.913583 -98 CTCATAGAGGCTGAATCGTTTCAATTCAGCA 36 267 1 CTGAATCGTT 0.967943 -34 GCAATTGGTGCTGAAACGATAAAGTAATTGT 37 71 1 CTGAAACGTA 0.832311 -133 TTGGCTTTTCCTGTAACGATTAATTTCGCGC 38 60 0 CTGTAACGTT 0.724446 -241 AAAGCCAAAGCTGAATCGATTTTATGATTTG 38 83 1 CTGAATCGTT 0.967943 -218 CGACTTTAGCCTGTATTGTTAGCGCCAGTTT 38 223 0 CTGTATTGTA 0.63218 -78 TAGCGCCAATCTGAATCGTTAACACGTGACA 53 119 0 CTGAATCGTA 0.934108 -182 AAATCTGGCACTGAATCGGTTAACTGTCCAG 54 182 0 CTGAATCGTT 0.967943 -119 AAGGCACTCACTGTATTACTTACTCTCTTCA 61 89 1 CTGTATTATT 0.442369 -212 TCCGCACTGTCTGAAACAGTACAGAAATGTC 72 270 0 CTGAAACATA 0.518209 -31 ******** ** Masking position 5 Map Score: 15.6215 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 135 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 AAGCACTTTTCCGCACAACTTATCTTCATTC 1 135 1 CCGCCAACTT 0.783368 -21 TGCAGCCCTGTGGCACAATGGTCAACATAATAC 8 45 0 TGGCCAATGC 0.887433 -140 TGGTTATTCACCGCCCAATTTTCGGCGGTGAAC 12 55 0 CCGCCAATTC 0.971038 -240 TTTTATCTTCTCGCGCAATTTACTGAATCCAGA 18 128 1 TCGCCAATTC 0.892156 -47 CAAAAAAAACCGGCGCAATGGCCGGTTTCCGTT 23 37 0 CGGCCAATGC 0.969652 -262 TTCCACCCGTCGGCTCAATCGCCGTCAACCCTG 27 54 1 CGGCCAATGC 0.969652 -212 AAAAAAAGCCCGGTGCAATATACGCCGGGCCTC 30 35 0 CGGTCAATTC 0.645262 -214 GTTTGATGTGCTGCACAATTTTTTGCCATTTTT 36 120 0 CTGCCAATTT 0.848316 -181 CCACGAGATGCGGCCCAATTTACTGCTTAGGAG 40 12 1 CGGCCAATTC 0.974965 -29 CCGATTGTCCTTGCACAATCGGCGGGAAAAATA 42 56 1 TTGCCAATGC 0.781108 -201 ACCGGTTTCCCTGCTCAATTGCTTTCATTAAAC 44 218 1 CTGCCAATGT 0.821056 -83 GTCTGTTGTGCGGCACAACGGGCCATTTGTACG 47 40 1 CGGCCAACGC 0.915696 -78 AGGTGTATTGCTCAATCTTCGAACGGGGGG 60 155 0 TTGCCAATTC 0.813067 -20 TCTGAAAGGTCCGCTCTATTTCCCGCCTGCAGA 61 136 1 CCGCCTATTC 0.717301 -165 TTGCGCTTCTCCGCCCAACCTATTTTTACGCGG 62 53 1 CCGCCAACTT 0.783368 -31 TTGCCCAATGTGCCAGAGATGCC 64 1 1 TTGCCAATTC 0.813067 -300 GAGATGCCTCCGGCACAATATTTTAAATTTCGA 64 26 1 CGGCCAATTT 0.925124 -275 TTAAATTTTTCCGCGCAATATATTCTGCAGCCA 71 67 1 CCGCCAATTT 0.914067 -52 **** **** * * Masking position 8 Map Score: 17.7387 Number of sites scoring better than the average of aligned sites = 351 Number in coding regions = 328 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 7 CTTAGATGCCCTGTACACGGCGAGGCTCTCCC 12 216 1 CTTACAGGCG 0.947691 -79 CGGCCAGTTTCTTTACAAGGAGTTTTAA 16 13 1 CTTACAGGAG 0.766603 -18 CCAGATTGTTCTCTACGAGGAGTCGTTTT 18 156 1 CTTACGGGAG 0.900432 -19 CCGGTATTCGTTTTACGTGTCGAAAGATAAAA 27 235 1 TTTACGGTCG 0.773951 -31 ATCTGAATTGTTTTTCGTTGCGTTGACCATCG 30 142 1 TTTTCGTGCG 0.747184 -107 AATATGAAAATTATTCGAGGAGTGAAAGGCAA 34 96 0 TTTTCGGGAG 0.897981 -102 CGCTGAATTGTTATACAAGGCGCTATTCTAGT 35 46 0 TTTACAGGCG 0.952196 -150 GGCATTTTGACTATTCGTGGCGCTTTTGATTT 36 11 0 CTTTCGGGCG 0.977853 -290 TACCGCTTCCTTGTGCGGGGCGTGATGCTTTA 41 51 0 TTTGCGGGCG 0.937262 -205 TACGAGCTTATTATACACGGCGCGGCCATGTG 55 191 0 TTTACAGGCG 0.952196 -61 CCCAACCTATTTTTACGCGGCGGTGCCA 62 66 1 TTTACGGGCG 0.982532 -18 TTTTCTTCGGGGCGCAATTGCGCC 70 3 1 TTTTCGGGCG 0.979819 -47 ATTCTCCTTATTATTTGCGGCGCTTTTTTCAC 72 71 1 TTTTTGGGCG 0.747184 -230 GTAAGCCCGTCTTTTCACGGCGTTACCGGATG 72 167 1 CTTTCAGGCG 0.939899 -134 ** **** **** Masking position 4 Map Score: 12.9765 Number of sites scoring better than the average of aligned sites = 227 Number in coding regions = 204 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 8 GTATAAAATTCGACTGGCAAATCTGGCACTCTCTCC 1 27 1 CGTGGCAAGG 0.992875 -129 TACGTTCTCACGCGTGGCAAGGGGGGAGAGCCTCGC 12 235 0 CGTGGCAAGG 0.992875 -60 ACCGTTATGGCGGTTGGCTATGGTGGGAAAAAACGC 26 33 0 CGTGGCTAGG 0.941662 -134 ACGTAATCAACGACTTGCAATATAGGATAACGAATC 27 11 0 CGTTGCAAGG 0.916531 -255 TTCGCTGCCACGTCGGGCAACAAAGGAAGAAAAATC 35 167 1 CGGGGCAAGG 0.988672 -29 ACAGATTCAACCAGGGGCAAGTATGGTAAAGCATCA 41 25 1 CCGGGCAAGG 0.954128 -231 TAGCTTGCGTCAATGGGCAAGGTGGGCTTGCATTTG 45 74 0 CAGGGCAAGG 0.884068 -175 AAAGCAAAGCCGAGTGGCAAAAACGGAGTCTGCGAG 55 49 1 CGTGGCAAGG 0.992875 -203 TTGCAGTGAATGACAGGCAAATGCGGAAGCAGCTAC 55 109 1 TGAGGCAAGG 0.75323 -143 AACGGTTGAGTGGTTGGCAAATCTGGAATCCAGCAT 63 13 1 TGTGGCAAGG 0.950891 -114 GTTCTTCTCCCGCTCGCAAGGGCGGGTTCGCTTTC 66 10 1 CCTCGCAAGG 0.795009 -41 GTGAGCGGGGCGGTTGTCAACGATGGGGTCATGCGG 67 108 1 CGTGTCAAGG 0.909084 -193 ** ****** ** Masking position 10 Map Score: 12.5613 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 131 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 ATCTGGCACTCTCTCCGGCCAGGTGAACCA 1 47 1 CTCTCCGGCC 0.909005 -109 AGGCGCAGAATCCTGCGCCTTTTACTTCAA 3 21 0 TCCTGCGCCT 0.803186 -39 AGGCGCAGGATTCTGCGCCTTTTTTATAGG 3 31 1 TTCTGCGCCT 0.865129 -29 GTCAAAACTCCTCTCCCCCAAATCCAGAGG 4 24 0 CTCTCCCCCA 0.889262 -81 GCCCCCGTCCTCCTCCCCCAAATATCCTTC 6 73 1 TCCTCCCCCA 0.760087 -83 AACGTGGTTATTCACCGCCCAATTTTCGGC 12 62 0 TTCACCGCCC 0.695807 -233 CACGGCGAGGCTCTCCCCCCTTGCCACGCG 12 231 1 CTCTCCCCCC 0.970077 -64 CCGGTTCTCCTCCTTCTCTTTTCT 26 153 0 TTCTCCTCCT 0.52463 -14 ATACTCTTTTCTCTGCCCCTTATTCCCGCT 27 155 1 CTCTGCCCCT 0.919804 -111 GGTAGTCATTCGCTCCGCCTGGTGGGCGAC 52 232 0 CGCTCCGCCT 0.845406 -69 TCAATTACCTCTCTACCCCCTATATTTATG 54 124 1 CTCTACCCCC 0.790149 -177 GTCCGGCTACCTCTGCCGCCACATTAACAA 54 228 1 CTCTGCCGCC 0.849049 -73 AACTTGCCCTCTACCGCTTTGCGGCAAA 59 116 0 CTCTACCGCT 0.472665 -18 TCTGCTACAATCCTCCCCCCGTTCGAAGAT 60 141 1 TCCTCCCCCC 0.927484 -34 AAGCGCAACGCCCTCCGCCAAAAAGCTGGG 62 31 0 CCCTCCGCCA 0.82167 -53 GGCGTTGCGCTTCTCCGCCCAACCTATTTT 62 49 1 TTCTCCGCCC 0.947728 -35 AGGCGCTATTTTCAGCGCCTGCGCGAGAAA 63 85 0 TTCAGCGCCT 0.447286 -42 ATCCACTGTTTGCTCCGCCTGCGATTGCCT 65 225 1 TGCTCCGCCT 0.77227 -76 GTTCTTCTCCCGCTCGCAAGGGCG 66 5 1 TTCTCCCGCT 0.827159 -46 CTTCTGCGATCCCTGCCGCCTTCGTCAAAA 73 56 1 CCCTGCCGCC 0.781585 -75 ********** Masking position 6 Map Score: 12.6485 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 372 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 10 GAGGAGGACGGGGGCGGATAACTTTCGGAATAGCCG 6 52 0 GGGGTACTTC 0.65771 -104 ACGTTTTTTTGGGCTGGAGCACGTTTTCTCTGACGG 11 56 1 GGGGGCCTTT 0.976763 -67 CAGATCATTGGAGAAGTTGCACATTTTGACAAAACA 12 109 0 GGGTGCCTTT 0.923563 -186 ATTTTCTGCGGAGTAGTCTCTCGTTTC 15 169 1 GGGTTCCTTT 0.947977 -17 TACCGATTTGGTGTTGTTTTTCATTTTCAGAACATT 52 122 0 GGGTTTCTTT 0.545498 -179 GACAAAGCGTGCGGTGGATCACGTTTATTAACCTGT 52 199 0 GGGGTCCTTT 0.98447 -102 ATTTAAATGTGAGTAGTGTCACATTTTTGTTTTGAT 54 22 0 GGGTTCCTTT 0.947977 -279 GGTTTGGTCGGCGGCGGTGCGTTTTTATCTGCAGGC 61 160 0 GGGGGCTTTT 0.734653 -141 CGCAAGTTATGAGGCGGATCGCATTTTTGTACTGAT 65 160 1 GGGGTCCTTT 0.984469 -141 CCGCTCGCAAGGGCGGGTTCGCTTTCCCACAGGAGT 66 20 1 GGGGTCCTTC 0.966857 -31 AATTATTTGCGGGTCGCGTCACATTTAATCATAAAT 69 231 1 GGGCTCCTTT 0.891407 -61 TCCTGCGAATGCGAGGGGGCGCAATTGCGCCCCGAA 70 16 0 GGGGGCCATT 0.80534 -34 GCTGCGTTTCGGGAACGTTCCCGTTTTTAAATTTTT 71 41 1 GGCGTCCTTT 0.851176 -78 CGAGGGAGAGGCGTGGGATCAGGTTCCATATAACCT 72 110 0 GGGGTCGTTC 0.740116 -191 * * ** ** * *** Masking position 15 Map Score: 10.0972 Number of sites scoring better than the average of aligned sites = 98 Number in coding regions = 76 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 TTCTGCAAGCCAGGCTTGACGCTATCCGCTG 8 102 1 CAGGCTTGCG 0.896519 -83 AGTAAAGATGCGGGCGCGATGAGTTCACGCC 19 21 0 CGGGCGCGTG 0.973674 -82 CAATAAAATTGAGGCCCGGCGTATATTGCAC 30 25 1 GAGGCCCGCG 0.876382 -224 CAGTTTTTAACAGACGCGACGCACGAAGAGC 38 198 0 CAGACGCGCG 0.895313 -103 TTCCTTGTGCGGGGCGTGATGCTTTACCATA 41 46 0 GGGGCGTGTG 0.91386 -210 AGCAATAGATAAGGCGTGTTGTAGATCACAA 44 66 1 AAGGCGTGTG 0.690892 -235 AACAGTGGAACAGGCTCGGAGCATTAACCGT 47 70 0 CAGGCTCGAG 0.856062 -48 GCTAGTTTGCCAGGCTCGATGTTGACCTTCC 48 240 0 CAGGCTCGTG 0.942016 -61 CATTAAATCTGGGGCGCGATGCCGCCCCTGT 49 19 1 GGGGCGCGTG 0.963896 -254 TACCCGGGCTTGCAGGCAAAAAAGA 58 20 0 CGGGCTTGAG 0.634426 -15 AGCGTCTTGTGAGACGCGTCGCAAATTGACG 65 104 0 GAGACGCGCG 0.860595 -197 CAGGCCAGAAGAGGCGCGTTGCCCAAGTAAC 67 44 0 GAGGCGCGTG 0.973232 -257 GAAATGTCTTCAGGCGTGGCGAAGCCTTACC 72 247 0 CAGGCGTGCG 0.964107 -54 ******** ** Masking position 5 Map Score: 8.34153 Number of sites scoring better than the average of aligned sites = 912 Number in coding regions = 881 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 CACGATTACCCGTACCGGCATCGA 21 5 0 CGTACCGGCA 0.936845 -46 CCTCTCTTTTCTTACCGGCACGATTACCCG 21 23 0 CTTACCGGCA 0.9681 -28 TGTTTCATGATTTACCGGGAGTTAAATAGA 49 78 1 TTTACCGGGA 0.812511 -195 TATTCACAGCCTTACCTGAAGTGAGGACGA 49 145 1 CTTACCTGAA 0.87817 -128 GGAAATATAACTTACCGGGAGATGTAATAT 64 74 0 CTTACCGGGA 0.977879 -227 AACAGAAAACCGTACCGGGA 65 1 0 CGTACCGGGA 0.955767 -300 GCTTTTTTCACTTACCGGAGGTTATATGGA 72 92 1 CTTACCGGAG 0.895318 -209 AAAAGACGGGCTTACCGGAAAAGTTTTAAT 72 152 0 CTTACCGGAA 0.973408 -149 GTGGCGAAGCCTTACCTGAAGGTAATAAAG 72 233 0 CTTACCTGAA 0.87817 -68 ********** Masking position 4 Map Score: 6.38317 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 123 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 ATGAAGATAAGTTGTGCGGAAAAGTGCTTAAGA 1 131 0 GTTTGCGGAA 0.757846 -25 GAGATAAAACCGTCTGCGGAATATTTCCCGCAG 5 20 1 CGTTGCGGTA 0.930859 -207 ACAACAAAGCCGTCTGCGGGAAATATTCCGCAG 5 33 0 CGTTGCGGAA 0.923178 -194 GGGAGGAGGACGGGGGCGGATAACTTTCGGAAT 6 57 0 CGGGGCGGAA 0.786833 -99 GAATAAATCCCGGCAGCGGATAGCGTCAAGCCT 8 113 0 CGGAGCGGAG 0.775022 -72 AGCAGGTTAAGGCTTGCGGAGTGTCTGGCTGAC 23 250 1 GGCTGCGGTG 0.721226 -49 GTTTTTATGCCGGATGCGGTGTAAACATACGTG 34 21 0 CGGTGCGGTA 0.881606 -177 ATTATTTTGACTTTAGCGGAGCAGTTGAAGA 37 183 1 CTTAGCGGCA 0.777158 -21 TCAATTCTTCCTTTAGCGGCATAATGTTTAATG 38 116 1 CTTAGCGGTA 0.762745 -185 ACGTACGAAACGTCAGCGGTCAACACCCGCCAG 38 149 1 CGTAGCGGAA 0.87709 -152 CTACCGCTTCCTTGTGCGGGGCGTGATGCTTTA 41 51 0 CTTTGCGGCG 0.836759 -205 TTGATATGTCCGTTTGCGGACAAGCAATAGATA 44 44 1 CGTTGCGGAA 0.923178 -257 AAATAAAATACTCGTGCGGTTTAATGAAAGCAA 44 236 0 CTCTGCGGTA 0.647946 -65 ATGGCGGTCTGTTGTGCGGCACAACGGGCCATT 47 34 1 GTTTGCGGCA 0.79182 -84 GTTATTTTTTCGTAAGCGGAATGCCTACGGTCT 50 101 0 CGTAGCGGTG 0.874653 -40 CGGGATCCAGTTTTGCGGTAAAAC 57 3 0 GTTTGCGGAA 0.757846 -22 GCAGCCAACCGGTTAGCGGCTTACACGCGGTCA 60 94 1 GGTAGCGGTA 0.838128 -81 TCAGCCTGACGGGCTGCGGTCTGAAAGGTCCGC 61 117 1 GGGTGCGGTG 0.808031 -184 CCGGTTTGGTCGGCGGCGGTGCGTTTTTATCTG 61 165 0 CGGGGCGGCG 0.796558 -136 GTAAAAATAGGTTGGGCGGAGAAGCGCAACGCC 62 49 0 GTTGGCGGAA 0.634772 -35 ACAAGACGCTGTTTTGCGGCATGCTTCCGGTTT 65 125 1 GTTTGCGGTG 0.753709 -176 AATAGGCAATCGCAGGCGGAGCAAACAGTGGAT 65 225 0 CGCGGCGGCA 0.733851 -76 ATAAATAAAGGGTGAGCGGGGCGGTTGTCAACG 67 97 1 GGTAGCGGCG 0.830576 -204 *** ***** ** Masking position 7 Map Score: 18.6584 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 1109 Number in noncoding regions = 262 Number of orfs with sites within 600 bp upstream = 132 Fraction of orfs with sites within 600 bp upstream = 0.0212014 Motif number 14 ATGGTCATATCTTATTTCCGAATTACGTTA 5 128 0 CTTATTTCCG 0.57999 -99 CGCCCCCGTCCTCCTCCCCCAAATATCCTT 6 72 1 CTCCTCCCCC 0.737606 -84 CTTATTCCCCCTACGAGAAC 7 291 0 CTTATTCCCC 0.879012 -10 TTTTATTTATCTTATACCCGCTATTATCGT 18 57 1 CTTATACCCG 0.727581 -118 TAACGCTATTCCCCGTGAATATCAT 20 78 0 CTATTCCCCG 0.69833 -15 TTCTCTGCCCCTTATTCCCGCTATTAAAAA 27 163 1 CTTATTCCCG 0.927875 -103 CATAACTCAACTCATTCCCCTCGCTATCCT 41 106 1 CTCATTCCCC 0.893799 -150 CATTTCCTTGCTCATCCCCGCAACTCCTCC 48 187 1 CTCATCCCCG 0.969286 -114 TCCTCCCTGCCTAATCCCCCGCAGGATGAG 48 211 1 CTAATCCCCC 0.874477 -90 GCAGGGTATGCTTATTTCCGCATTTTCCGA 50 23 0 CTTATTTCCG 0.57999 -118 CCAAACAAAACTCATCCCTGAGCGGTAAGT 53 231 0 CTCATCCCTG 0.641021 -70 GCAATAAGGACTCATCCGCC 53 291 1 CTCATCCGCC 0.599141 -10 AAGGTCCGCTCTATTTCCCGCCTGCAGATA 61 141 1 CTATTTCCCG 0.522243 -160 AAGCGCTCTGCTTATCCCCATC 73 3 0 CTTATCCCCA 0.704159 -128 AAGCAGAGCGCTTATCCCCGGCAAAGAGCA 73 20 1 CTTATCCCCG 0.964594 -111 ********** Masking position 5 Map Score: 6.49473 Number of sites scoring better than the average of aligned sites = 182 Number in coding regions = 155 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 15 ATAAAATTCAAAAAAAAACGACTGGTTCACCT 1 67 0 AAAAAAAGAC 0.644973 -89 GTTGCGGAGTTAATAAAATGAAGTAAAGGTTT 2 18 0 TAAAAAAGAA 0.55071 -44 AGAGAAATGGAAATAAAAAGAACTGACACCGC 17 181 0 AAAAAAAGAA 0.930505 -120 GGTATAAGATAAATAAAAGGTAAAACGTTTTA 18 43 0 AAAAAAAGTA 0.55071 -132 ACGTGTCGAAAGATAAAAGGAAATCGC 27 249 1 AGAAAAAGAA 0.795355 -17 GATGCTGGCGAAAAAAATCGAACAAGCTATAA 31 122 1 AAAAAATGAA 0.55071 -53 TTCGATTTCAAAATATAATGAAATTATTTGTT 34 161 0 AAAATAAGAA 0.836132 -37 CATGATGGAGAGAGAAAAAGAATGCTCAGTTT 35 105 0 AGAAAAAGAA 0.795355 -91 TTTCACAAATATAAAAAATGAACAATTCACTC 42 102 1 ATAAAAAGAA 0.587608 -155 AGGCAAAACGAAATGAAACGAAAGTTTTACGA 45 22 0 AAAGAAAGAA 0.644973 -227 TTCACAAAAGAAACATAATGAAAGTCACTGAA 45 117 0 AAAATAAGAA 0.836132 -132 GGTGAGATAAAAATAAAACGAAAGATAATGGT 45 161 0 AAAAAAAGAA 0.930505 -88 GTATCAACTGAAACAAAACGAAAGATTAATAT 45 201 1 AAAAAAAGAA 0.930505 -48 CCGCTTACGAAAAAATAACGAATTCAAGGAAC 50 115 1 AAAATAAGAA 0.836132 -26 AGTAAATCACAAAAATAATGAATAACCCATTA 64 117 1 AAAATAAGAA 0.836132 -184 *** **** *** Masking position 7 Map Score: 4.44258 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 60 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542