AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00260_bsub_reg_300.orf -o00260_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 serS 300 seryl-tRNA synthetase #2 purT 230 phosphoribosylglycinamide formyltransferase 2 #3 mpr 143 extracellular metalloprotease #4 ybfK 165 similar to carboxylesterase #5 pssA 195 phosphatidylserine synthase #6 serC 146 phosphoserine aminotransferase #7 hit 300 Hit-like protein #8 yjcI 300 similar to cystathionine gamma-synthase #9 yjlC 300 yjlC #10 yjlD 39 similar to NADH dehydrogenase #11 yjmA 197 similar to glucuronate isomerase #12 yjmB 67 similar to Na+:galactoside symporter #13 yjmC 104 similar to malate dehydrogenase #14 pdhA 300 pyruvate dehydrogenase (E1 alpha subunit) #15 pdhC 114 pyruvate dehydrogenase (dihydrolipoamide acetyltransferase E2 subunit) #16 yloU 276 similar to alkaline-shock protein #17 yloW 138 similar to phosphoglycerate dehydrogenase #18 ylpA 25 similar to L-serine dehydratase #19 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #20 nusA 34 nusA #21 truB 81 tRNA pseudouridine 55 synthase #22 rpsO 156 ribosomal protein S15 (BS18) #23 pnpA 172 polynucleotide phosphorylase (PNPase) #24 ylxY 117 alternate gene name: ymxI; similar to deacetylase #25 ymxG 39 similar to processing protease #26 ymxH 77 similar to hypothetical proteins #27 spoVFA 185 dipicolinate synthase subunit A #28 asd 125 aspartate-semialdehyde dehydrogenase #29 dapG 91 aspartokinase I (alpha and beta subunits) #30 pgsA 300 phosphatidylglycerophosphate synthase #31 recA 172 multifunctional SOS repair regulator #32 pbpX 167 penicillin-binding protein #33 ymdA 276 similar to hypothetical proteins #34 ymdB 68 similar to hypothetical proteins #35 spoVS 199 spoVS #36 tdh 265 threonine 3-dehydrogenase #37 yoaD 300 similar to phosphoglycerate dehydrogenase #38 ilvA 248 threonine dehydratase #39 serA 226 phosphoglycerate dehydrogenase #40 yqjR 75 similar to D-serine dehydratase #41 yqjP 300 yqjP #42 yqiS 124 similar to phosphate butyryltransferase #43 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #44 yqhJ 29 similar to glycine dehydrogenase #45 yqhI 300 similar to aminomethyltransferase #46 glyQ 296 glycyl-tRNA synthetase (alpha subunit) #47 yqxN 300 alternate gene name: yqfI; similar to hypothetical proteins #48 yrhA 64 similar to cysteine synthase #49 yrrT 192 yrrT #50 lysC 175 aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408) #51 ask 94 ask #52 uvrC 135 excinuclease ABC (subunit C) #53 trxA 300 thioredoxin #54 thrS 300 threonyl-tRNA synthetase #55 gbsA 198 glycine betaine aldehyde dehydrogenase #56 yugK 103 similar to NADH-dependent butanol dehydrogenase #57 yugJ 229 similar to NADH-dependent butanol dehydrogenase #58 hom 200 homoserine dehydrogenase #59 yutH 152 yutH #60 glyA 206 serine hydroxymethyltransferase #61 ywlF 156 alternate gene name: ipc-32d; similar to ribose 5-phosphate epimerase (pentose phosphate) #62 ywlE 75 alternate gene name: ipc-31d; similar to protein-tyrosine-phosphatase #63 ywlD 78 alternate gene name: ipc-30d; similar to hypothetical proteins #64 ywlC 156 alternate gene name: ipc-29d; similar to hypothetical proteins #65 ywlB 66 alternate gene name: ipc-28d #66 spoIIR 140 alternate gene name: ipc-27d, csfX #67 thrZ 300 threonyl-tRNA synthetase Motif number 1 GCGAAACACTCCTTTTTTTATTGATTTATCGA 1 279 0 CTTTTTTTTT 0.562081 -22 AAATAACGGTCTGCTTTCTCTATTCCTAAACAGC 2 84 0 CTTTTCTTTT 0.479743 -147 TGGGACAAGGCCTGTTTTTTTCTTTCTCCGTAAA 3 31 1 CCTTTTTTTT 0.813385 -113 TTTAAGGGAACTGCCTTTTTTATTTATTGCAGGA 4 24 1 CTCTTTTTTT 0.697631 -142 AAAAGGGGCGTTATCCTTTATATCAATCAAACCC 4 125 1 TTCCTTTTTC 0.600381 -41 CTTCTTCTTTTTCCTCCGGGTTTGAT 4 150 0 TCCTTTTCTC 0.388937 -16 TATGATCTCTCCCTGTTTTCCACGTTAAT 6 128 0 TCTCCCTTTT 0.786187 -19 TCATATAAGCTCTTCCTCTGCATTCAGGGTGAAC 7 188 1 TCCCTCTCTT 0.638836 -113 GCCGTTCATCCTGTTTTCTATTTTCTGCATTTCT 7 226 1 CTTTTCTTTT 0.479743 -75 GGGTTTAACGCTTCTTCTTATCTTCCAAGCATAA 8 224 0 CTTTCTTTTT 0.518209 -77 AAGGGTAGTGCCTCTCCCTGTCTCACGCTTTTAA 9 233 0 CCTCCCTTTC 0.686715 -68 CGTATATCCTCCGTCCTTTATATCAATTTGAATC 10 16 0 CCCCTTTTTC 0.867458 -24 TCTGGCAATGTCTTTTTTTATGTTTATGACAGCG 11 60 1 TCTTTTTTTT 0.772606 -138 TCCTTTGGGATCAATCTCTTTTTTGAAAATGAAA 11 100 0 TCTCTCTTTT 0.814396 -98 TTGTTTTTATTTTACCTTTATATTCCTTTGGGAT 11 123 0 TTCCTTTTTT 0.76376 -75 GTTCCACCTCTGTGTCTTAAGAATTT 12 52 0 TCCCTCTTTC 0.785652 -16 CTAAGTCACCTCTTCCTTTCTTTTAAACAGTCAT 14 276 0 TCCCTTTTTT 0.916518 -25 AAGGGCAATTTGCCCTTCTATTCTTATGTCTG 17 9 1 TTCCCTTTTT 0.730402 -130 GCGGGTTTCCCCACTCTTTGCCTCGGTAATCGTT 19 144 0 CCTCTTTCTC 0.449495 -157 CGATATACGCCTATCCTCTCTTTTT 21 2 0 CTCCTCTTTT 0.748718 -80 CGTATATCGTCTGTCCTCTTTCTTCGTTTATAAG 21 27 1 CTCCTCTTTT 0.748718 -55 TTGCCTTTCACTCCTTCTTTTGAGTTTTTTT 21 61 0 TCTCCTTTTT 0.836549 -21 CGGGAGGATTCCCGCTTTTTTATCGTATTAAAGC 23 21 1 CCCTTTTTTC 0.784525 -152 CCTGGGAGACCCGGCTTCTTTATTTTGAAGCTTT 24 29 1 CCCTTCTTTT 0.849144 -89 AACCTTACCGTTGATTTTTATTTTCAGATTAGGT 30 147 0 TTTTTTTTTT 0.500136 -154 AGATGACTTTTCTTCCTTTTTATTTACAATCTTT 30 225 0 TCCCTTTTTT 0.916518 -76 CGAATATGCGTTCGCTTTTTTCTTGGCAAATCCC 31 97 1 TTCTTTTTTT 0.642671 -76 TCTATTTTTTCCTCCTTTATGTTACCACTACAT 31 150 0 TCCCTTTTTT 0.916518 -23 TTGCTATATTCCTGCTTTTCTTTTTAATATTTTT 35 32 0 CCCTTTTTTT 0.886812 -168 CAGATTGATGTCAATCTCTTTTTTTCAGAATTGA 37 49 0 TCTCTCTTTT 0.814396 -252 TATTTTACGATCATCTTTTTTCTTGGCTCTGCAG 38 75 1 TCCTTTTTTT 0.859304 -174 GTACAGATTCCTTTCTTGTTTTAAATCCCTAT 38 227 0 TCTTCTTTTT 0.740072 -22 CCTTTCGCTCCTTGTCTTCATTCATTAT 41 283 0 TCTCCTTTTT 0.836549 -18 CTTTATCTTTTCATTTCCTTTATTGTCCAGCGGA 43 24 1 TCTTCCTTTT 0.67165 -129 GTGTTGTCTCCTCTCTCCAAGAAAAAA 44 13 0 TTCTCCTTTC 0.334744 -17 CTAATTCCTCCCCTTTATCAACGGCGCAG 45 282 0 TCCCCCTTTC 0.754391 -19 GAACAAAATCCCAGCCTCTTTTTTAAAATTGCTC 46 148 0 CCCCTCTTTT 0.910057 -149 CGGGAGAACTCTCGTCCCTATGTTTGCGGCTGGC 46 203 1 CTTCCCTTTT 0.581422 -94 TTCAAGCACCTCCACTTTTCTTTCATAAGTTGAC 46 273 0 TCCTTTTTTC 0.739461 -24 ACTCCAAATTCTTACCTTTATCTTGACCAGATGT 47 58 0 CTCCTTTTTT 0.805726 -243 ATTCCTCTCATTGCTTTTTTTATTGTGGACAAAG 50 103 1 TTTTTTTTTT 0.500136 -73 GTATTACCACCCTTTACATTTTGGTTCGTG 50 156 0 CCCCTTTCTT 0.759523 -20 GATTGAGGGATCGCTTTTTTTATTCGCCAATTGT 52 42 1 TCTTTTTTTT 0.772606 -94 ATGTTACCCTTCCTTATGTTTAATCCTTTA 52 116 0 CCTCCTTTTT 0.867823 -20 GAATCGTGGTTCCACCCTTTTTTCCGCAAAGCCA 54 210 0 TCCCCTTTTC 0.810437 -91 CTTTGTCACTCCTTTTTTTGCATATAAAA 54 282 0 TCTCCTTTTT 0.836549 -19 ACTGACCCTCTTTTCCTTTAGAAAATTAA 55 6 1 CCCTTTTCTT 0.637294 -193 AAGTCCCATTTTGATTTTTCTTTTTGACTTTTCC 55 86 0 TTTTTTTTTT 0.500136 -113 CGTTTGGCTGCTTCCCTTTTTCTTTTTTGTCAAC 56 27 1 CTCCTTTTTT 0.805726 -77 ATTATATAAGCCCGCTCCTGTTTTGACAAGACAT 58 100 0 CCCTCCTTTT 0.825081 -101 AAAAACTCCACCTTTCTTTTGATTGTCCTC 58 181 0 TCCCTTTTTT 0.916518 -20 GCATAGCCAGTCTTTTCTTTTATTTTAAGATAGT 60 18 1 TCTTCTTTTT 0.740072 -189 TATCCGTATCCTGTTCTTTGTTTTTACCATCACT 60 167 0 CTTCTTTTTT 0.697631 -40 AACGGCGACTTCGTTTCTTTTATTGGTATA 62 7 0 TCTTCTTTTT 0.740072 -69 AACGAAGTCGCCGTTTCTTTTTTCTTCATATATA 62 26 1 CCTTCTTTTC 0.629264 -50 GTCAGTCACCCCTTATTTTTCTCTATTAT 62 57 0 TCCCCTTTTT 0.901961 -19 CACATACTTATCCACTTCTTTATTAGCGTTGTCC 64 23 1 TCCTTCTTTT 0.814396 -134 CCGTTCACCCCGTTTTTGCGTTCTTTCTTCCA 65 45 0 CCTTTTTCTT 0.494302 -22 GAAGCTCTCACCTTTCCTTCCCTCTCTGAAAACC 67 71 0 CCTCCTTCTC 0.406258 -230 ** ***** * ** Masking position 9 Map Score: 43.4642 Number of sites scoring better than the average of aligned sites = 2681 Number in coding regions = 2004 Number in noncoding regions = 677 Number of orfs with sites within 600 bp upstream = 633 Fraction of orfs with sites within 600 bp upstream = 0.10167 Motif number 2 CTTTGCCCCTCCTATCTGTTCCAA 2 217 0 GCCCCTCCTA 0.662289 -14 TTTGTCATCTCCCTCCTTTAGTGTCAAC 3 126 0 CTCCCTCCTT 0.854256 -18 GAGGGTTCCTCCTTATGAAATTGT 7 287 0 GTTCCTCCTT 0.946181 -14 GCAAGTGCCTCCTTCCTTTTCAGT 13 91 0 GTGCCTCCTT 0.895837 -14 ACTAGTTCCTCCTTCGAATGCATA 16 263 0 GTTCCTCCTT 0.946181 -14 GCGCTGTAACGCGCCCGCTTGCCATTTTAT 17 58 1 GCGCCCGCTT 0.791998 -81 GCTATTCCTCCTTATGAACCAGA 17 126 0 ATTCCTCCTT 0.795123 -13 AACTGGCTCCTCCTGACCCTTTTCG 18 11 0 GCTCCTCCTG 0.746075 -15 GTTCTTCCTCCTTGTGCTGTCGA 19 288 0 CTTCCTCCTT 0.951205 -13 TTAACGGTCTCCCCCCTTAAAACATTTG 20 17 0 CTCCCCCCTT 0.789709 -18 AAGCGGGAATCCTCCCGCTTTTTACGA 23 8 0 CCTCCCGCTT 0.896163 -165 AAGCGGGAGGATTCCCGCTTTTTTATCGTA 23 18 1 ATTCCCGCTT 0.495675 -155 AAGGTAGAACCCGCCTGCTTTTGAAAAGCT 24 57 0 CCGCCTGCTT 0.868243 -61 TCTACCTTGTCCTTCTCCTTCATAATGTGA 24 79 1 CCTTCTCCTT 0.530769 -39 ATTTGTTCCTCCTATTCAAAGACA 25 26 0 GTTCCTCCTA 0.78862 -14 TCTATTTTTTCCTCCTTTATGTTACCA 31 156 0 TTTCCTCCTT 0.795123 -17 GAGTTGCTATATTCCTGCTTTTCTTTTTAA 35 39 0 ATTCCTGCTT 0.605374 -161 TTCTGCTCCCCCTTAGTTTTACAA 35 186 0 GCTCCCCCTT 0.951671 -14 CGTTAGATTTCCTCCTAAATTGACAAA 39 210 0 TTTCCTCCTA 0.45163 -17 CCTCTTGGCCGCTCCTGCTTGAGGAAGGTG 47 276 1 GCTCCTGCTT 0.923947 -25 ATATGTCCTCCTCCTTAATAGAGGTT 48 49 0 CCTCCTCCTT 0.971493 -16 TATAAAAACCCCGCCCCCTATGAAAGGGAC 54 259 0 CCGCCCCCTA 0.693877 -42 GTTTTGCAACCTCCTCCATGAATTATTAA 57 10 1 CCTCCTCCAT 0.647446 -220 GACATCTCCTCCTTAGATTTTTTA 57 216 0 TCTCCTCCTT 0.871545 -14 GTGATGCGGCCCGCCCGCTTTATTGACCGC 61 116 0 CCGCCCGCTT 0.808501 -41 ********** Masking position 5 Map Score: 21.2546 Number of sites scoring better than the average of aligned sites = 583 Number in coding regions = 326 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 316 Fraction of orfs with sites within 600 bp upstream = 0.0507549 Motif number 3 TAATTTTATCTTTTTTAATAAAAATTTATTTTTC 2 162 1 TTTTATAAAA 0.865337 -69 TCCTCCGGGTTTGATTGATATAAAGGATAACGCC 4 131 0 TTATATAAAA 0.76524 -35 GTTATCATGCTTATTGGAGAAAAATTTTTCCTGT 5 107 1 TTTTAGAAAA 0.836671 -89 AAAAATTCAGTTTTTTGATAAAAAATTAGAATTA 6 66 0 TTTTATAAAA 0.931687 -81 CAATTGTTTATTTTTAGATAAAAATAATACTGAA 9 117 1 TTTTATAAAA 0.754915 -184 GTGCATTCCTTTTATACATACAAACTTAGGGTAC 14 237 0 TTATATAAAA 0.760273 -64 TCTTTTGAGTTTTTTTCTTATAAACGAAGAAAGA 21 43 0 TTTTTTAAAA 0.818377 -39 AAAGATGCGCTTTTTCCATATAAAAAAACATCGG 27 72 0 TTTTATAAAA 0.916355 -114 ATGAACTTGGTTGTTGCTTAAAAAGTGTCGGCAT 33 234 0 TTTTTTAAAA 0.819453 -43 GAACATATGGTTATTTTATAAAAATATTAAAAAG 35 13 1 TTTTATAAAA 0.93301 -187 AATCTGAGTCTTCTTTATGATAAACGTATTCTTC 37 77 1 TTTTTGAAAA 0.606703 -224 ATTTTTTTAATTATTAAATAAAAATAATTGTCTT 38 158 1 TTTTATAAAA 0.875583 -91 GGTGTGCAAATTTTTTCATACAAAGGGGTATCGG 43 128 1 TTTTATAAAA 0.937681 -25 ATAGAGGTTGTTTTTAGAGAAAAACGGAGGAGAA 48 24 0 TTTTAGAAAA 0.677576 -41 TCACGCTATTTTAATGCTTACAAATTATTTTTTC 53 222 0 TTATTTAAAA 0.495426 -79 GTCACTCCTTTTTTTGCATATAAAAACCCCGCCC 54 273 0 TTTTATAAAA 0.936469 -28 TAAATAAAGTTTGTTAAATAAAAATTTAATGTTT 55 159 0 TTTTATAAAA 0.875583 -40 TCCTTATTCATTGTTGTATATAAAAAAACACACC 67 267 0 TTTTATAAAA 0.936761 -34 ** ** *** *** Masking position 5 Map Score: 21.4234 Number of sites scoring better than the average of aligned sites = 135 Number in coding regions = 68 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 4 ACTGAAATATTTGAAAAATAAATTTTTATTAA 2 176 0 TTGAAATAAA 0.85408 -55 TTGTTACCTTTTGAAAAATGAATGCCAATCTT 5 24 0 TTGAAATGAA 0.923111 -172 CACCTTCCCTTTTCAAAATAAAAACCCCTTCT 8 271 0 TTTAAATAAA 0.78448 -30 CAATCTCTTTTTTGAAAATGAAATGTTAACGC 11 91 0 TTTAAATGAA 0.881883 -107 TGCCTGGTCTTTTCATAATGGAAACCATATAG 16 214 1 TTTAAATGGA 0.650873 -63 TATGCAAATATTTTAGAATAAAATTTGCGTGC 22 19 0 TTTAAATAAA 0.78448 -138 TTTCCGACACATTTACAATGAAGTTGTAACAT 33 97 1 ATTAAATGAA 0.64995 -180 TCCCCCTTAGTTTTACAATGGATAAGTGAGTG 35 172 0 TTTAAATGGA 0.650873 -28 AGTATGTAATTTTCAGAATGAAGAATACGTTT 37 98 0 TTTAAATGAA 0.881883 -203 TTGTCCGCCATTGCATAATGAACAACAAACTA 41 170 0 TTGAAATGAA 0.923111 -131 AAGCTAAAATATGAATAATGAATGAAGACAAG 41 269 1 ATGAAATGAA 0.749101 -32 TTTGCAGAATAAACGCAAACATC 42 2 1 TTGAAATAAA 0.85408 -123 GGCATGGAACTTGCATAATAAAAGGCGGAGTC 42 81 1 TTGAAATAAA 0.85408 -44 GAAACACCTCATGTAAAATGAAGGTTCTCTGT 45 224 0 ATGAAATGAA 0.749101 -77 CTGCAACATATTTAATAATAAATGATCATATA 46 28 0 TTTAAATAAA 0.783451 -269 TCCCAGCACCTTGCAAAATAAAACCATCTGGT 57 130 1 TTGAAATAAA 0.85408 -100 *** * ****** Masking position 7 Map Score: 10.6715 Number of sites scoring better than the average of aligned sites = 193 Number in coding regions = 127 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 5 GATGAGGGCTCTTTTTATTTTCGATAAATCAA 1 259 1 CTTTTATTTC 0.651408 -42 GAATGCCAATCTTTTCATGTTCCTTA 5 5 0 CTTTCATTTC 0.945679 -191 AGTTTTTCATCTTGCCATATTCAGTATTATTT 9 138 0 CTTGCATTTC 0.960901 -163 ACAGCGTTAACATTTCATTTTCAAAAAAGAGA 11 88 1 CATTCATTTC 0.614452 -110 AATGTATTCGCTTTACATTTTCATCAA 14 6 0 CTTTCATTTC 0.945679 -295 AGAAAATTCACTTGACATCTTGCGGAAACAGC 16 144 1 CTTGCATTTG 0.84081 -133 AACGCGCCCGCTTGCCATTTTATATCTGATCA 17 65 1 CTTGCATTTA 0.830302 -74 AGAATTTTGTCTCGACATGTTCATCGTTTACT 19 196 1 CTCGCATTTC 0.769292 -105 ACTTGTCAAGCTTGCCATCTTAACGTTTGCAG 33 64 0 CTTGCATTTA 0.830302 -213 TTGAAAAATTCTTGTTATATTCGGATTGTACC 36 232 0 CTTGTATTTC 0.725123 -34 ATATGAATCTCTTTCCATCTTCGGAAAGAGAT 37 272 1 CTTTCATTTC 0.945679 -29 ACCCCTTTATCTTTTCATTTCCTTTATTGTCC 43 20 1 CTTTCATTCC 0.823745 -133 TTCTTCGGGTCTTTCCATGTTCTCTTTTTCCA 47 201 0 CTTTCATTTC 0.945679 -100 TATTACCACCCTTTACATTTTGGTTCGTGCGG 50 153 0 CTTTCATTTG 0.789097 -23 AATAAAGAATCTTGTCATATCAATGCGTTAAG 58 39 1 CTTGCATTCA 0.567756 -162 **** *** *** Masking position 7 Map Score: 11.7529 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 91 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 AAAAACGCTTGCTGGATTTAGCACCTTGGCGCTT 8 191 0 GCTGGTACAC 0.908847 -110 GCTCAGTATCGCTGAGCGGATCACTATCCGAAAA 12 21 1 GCTGAGACAC 0.743649 -47 GGCAATAATCGCTGGCCGTACCTCTACATATACT 16 184 0 GCTGGGACTC 0.959353 -93 ATACAAAAGAGCGGGTTTCCCCACTCTTTGCCTC 19 154 0 GCGGGTCCAC 0.92934 -147 CGATAAAAAAGCGGGAATCCTCCCGCTTTTTACG 23 12 0 GCGGGTCCCC 0.807375 -161 GCTAGCGCTTGCTGGAATTGGCACAATAATGTTG 37 180 0 GCTGGTGCAC 0.675256 -121 CTACAAACAAGCGGGCCGCAACACCTTTCAGCCG 41 66 1 GCGGGGACAC 0.952734 -235 CTCTCCCCTTGCTGTCATTCGCTCATATTTTCAT 45 22 0 GCTGTTCCTC 0.533808 -279 GGAGCAAACTGCGGAGTGAATCTCTCAGGCAAAA 45 90 1 GCGGAGACTC 0.843582 -211 AAGAACTCTTGCTCGACGCAACTCTGGAGAGTGT 45 122 1 GCTCGGACTC 0.64906 -179 GGGTGGAACCGCGGGAGAACTCTCGTCCCTATGT 46 192 1 GCGGGACCTC 0.864023 -105 AACAGTAATGGCTGACGGGAACTCCCGTTACAGA 54 151 1 GCTGAGACTC 0.810609 -150 CACGGCACCTGCGGCTCTAAGCTCTGTAACGGGA 54 173 0 GCGGCTACTC 0.663435 -128 TATGAGGGAAGCTGGCCTGCCCTCGCTTATATCA 57 89 1 GCTGGTCCTC 0.940893 -141 AATAAAGCGGGCGGGCCGCATCACACACGCTGGG 61 122 1 GCGGGGACAC 0.952734 -35 ATATTCCTAAGCTGGGAAGCTCTCACCTTTCCTT 67 86 0 GCTGGACCTC 0.834518 -215 ***** * * *** Masking position 12 Map Score: 9.35138 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 198 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 GTGTAACCAAACCTCCAATTGTAAAACCAT 5 175 0 ACCTCCAATT 0.925723 -21 AAGGGCCAGTCCCTCCACCTCTCACGATAA 8 126 0 CCCTCCACCT 0.955388 -175 AAACACAAAAAACTCCAATTCGATTACCTT 9 51 0 AACTCCAATT 0.800788 -250 CCTGTTTCACCTCCAAATCATATTTAGC 22 139 0 ACCTCCAAAT 0.925723 -18 TGTTTTCACTCCAAATTATTCGGACG 29 76 0 CACTCCAAAT 0.823215 -16 AAAGCCCCTCCAATTTCATACTCGG 30 286 0 CCCTCCAATT 0.935221 -15 TAGGGCCAGTCCCTCCACCTCTCTGGATAG 37 139 0 CCCTCCACCT 0.955388 -162 TTCAAGCACCTCCACTTTTCTTTCATA 46 280 0 ACCTCCACTT 0.920983 -17 AGCTTACCTAAACTCCAAATTCTTACCTTT 47 73 0 AACTCCAAAT 0.800791 -228 GTCTTGACCCTCCAGCTTTCACAAGTC 49 8 1 CCCTCCAGCT 0.858802 -185 AGTAAAACCTCCAAATGATGCTGGTA 56 88 0 ACCTCCAAAT 0.925723 -16 AAAAACTCCACCTTTCTTTTGAT 58 188 0 AACTCCACCT 0.856382 -13 ********** Masking position 7 Map Score: 8.48509 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 44 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 8 GAATTTGAATGCTGCTTTTTTTGGGAGCATT 5 72 1 GCTGCTTTTT 0.885859 -124 CAAGCCGGTTGCTGAGGTTTCTAAGGGCCAG 8 147 0 GCTGAGTTTC 0.491006 -154 TAAGCAGTTTGCTGATTTTTTTGGAAAGGGT 9 261 0 GCTGATTTTT 0.773364 -40 ATACTATAGCGCTGCTGTTTCCGCAAGATGT 16 158 0 GCTGCTTTTC 0.787582 -119 GCGATTATTGCCTGGTCTTTTCATAATGGAA 16 206 1 CCTGGTTTTT 0.649059 -71 AGTGGGGAAACCCGCTCTTTTGTATTGAACA 19 163 1 CCCGCTTTTT 0.949766 -138 CTTTTTAGCCCCTGCTCTTTTGAAGCAGGGT 19 226 1 CCTGCTTTTT 0.895894 -75 CGGGAATCCTCCCGCTTTTTACGA 23 4 0 CCCGCTTTTA 0.633808 -169 CGGGAGGATTCCCGCTTTTTTATCGTATTAA 23 21 1 CCCGCTTTTT 0.949766 -152 GGCTCCGGCAGCCGATGTTTCAGATGTTTTC 27 43 0 GCCGATTTTC 0.781735 -143 GGCTGCCGGAGCCGATGTTTTTTTATATGGA 27 61 1 GCCGATTTTT 0.882313 -125 ATACAAAAAAGCTGAGTTTTTCACTCAGCCT 32 39 0 GCTGAGTTTT 0.668793 -129 TGGAAGGTAGCCCGCTATTTTTGAAAAGCAT 35 89 1 CCCGCTTTTT 0.949766 -111 CAATAATGTTGCCGAGGTTTCATAGGGCCAG 37 160 0 GCCGAGTTTC 0.679425 -141 GGTGTTGCGGCCCGCTTGTTTGTAGAACCTG 41 60 0 CCCGCTGTTT 0.667206 -241 GCGCCTGTATCCCGAGGTTTTCGGTCAGGTC 45 55 0 CCCGAGTTTT 0.831056 -246 TAAAAAAGAGGCTGGGATTTTGTTCTCAGCA 46 157 1 GCTGGGTTTT 0.496734 -140 ATGCGGCCCGCCCGCTTTATTGACCGCGCAG 61 112 0 CCCGCTTATT 0.574956 -45 TTGGACACGCCCCGCTTTTTTAGCCTATGCG 63 43 0 CCCGCTTTTT 0.949766 -36 ****** **** Masking position 10 Map Score: 13.1953 Number of sites scoring better than the average of aligned sites = 704 Number in coding regions = 602 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 9 GCGAAACACTCCTTTTTTTATTGATT 1 285 0 GAAACACTTT 0.780478 -16 GAGAAAGAAAAAAACAGGCCTTGTCCCATGACAA 3 25 0 AAAACACTTT 0.957519 -119 TCCTCCTAAGAAAACATGATTTCTCTGATACATT 31 27 1 AAAACAATTT 0.597487 -146 AGTGTTCATTAGAACAATCATTATTAGATGTTGC 35 142 0 AGAACACTTT 0.943024 -58 CAATAAATGAAAAACAACCTGTTTGCATTACGCA 36 38 0 AAAACACGTT 0.794648 -228 CTTTTGGTTGAAAACACCCTTTATTTTACGATCA 38 54 1 AAAACACTTT 0.957519 -195 TTGCAGAATGAGAACAAACCTTTTTGAAAAAGCT 41 214 0 AGAACACTTT 0.942908 -87 GCCAGGACAGAGAACCTTCATTTTACATGAGGTG 45 218 1 AGAACCCTTT 0.722955 -83 TTTTTCTCTAAAAACAACCTCTATTAAGGAGGAG 48 34 1 AAAACACCTT 0.794651 -31 ACCATAGAGAAAAACAAACGTTCGTGTTAAACTG 52 78 1 AAAACACTTG 0.780352 -58 GTCCTGTAATAAAACAAGCGTTATCCACAAATTG 64 58 0 AAAACACTTT 0.957241 -99 TTACACGCGTAAAACAATCGTTTTATTGTTGTGA 64 114 1 AAAACACTTT 0.949201 -43 TTTAGAACACTCCTTATTCATTGTTGT 67 284 0 AGAACACTTT 0.943024 -17 ****** * ** * Masking position 4 Map Score: 7.05878 Number of sites scoring better than the average of aligned sites = 80 Number in coding regions = 55 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 10 TTTCTAAGGGCCAGTCCCTCCACCTCTCACG 8 130 0 CCAGTCCTCC 0.95895 -171 TTAACGGTCTCCCCCCTTAAAACA 20 21 0 ACGGTCCCCC 0.921124 -14 TTGCCTTTCACTCCTTCTTTTGAG 21 68 0 CCTTTCCTCC 0.882832 -14 GTTCTGTCCCCCCCTCACCTCAC 24 105 0 TCTGTCCCCC 0.913419 -13 GTCTGTCACCCCCTTGTACTAT 26 66 0 TCTGTCCCCC 0.913419 -12 TTTCATAGGGCCAGTCCCTCCACCTCTCTGG 37 143 0 CCAGTCCTCC 0.95895 -158 CCTTTCGCTCCTTGTCTTCAT 41 290 0 CCTTTCCTCC 0.882832 -11 GGTTTTCGGTCAGGTCTCTCCCCTTGCTGTC 45 40 0 CAGGTCCTCC 0.726676 -261 ACGGAGGAGAACGTTCTCCCCGTT 48 4 0 ACGTTCCCCC 0.790211 -61 GTCAGTCACCCCTTATTTTTCT 62 64 0 TCAGTCCCCC 0.913419 -12 CCGTTCACCCCGTTTTTGCGT 65 56 0 CCGTTCCCCC 0.95032 -11 CACGTTTATCCCAGGCTCTCCTTGTCCATAA 66 79 1 CCAGGCCTCC 0.800412 -62 ****** **** Masking position 6 Map Score: 9.57658 Number of sites scoring better than the average of aligned sites = 113 Number in coding regions = 76 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 GAAGCGTTAAACCCCTTCTTCTTATGAAGAA 8 244 1 ACCCTTCTTC 0.97123 -57 CAAAATAAAAACCCCTTCTTCATAAGAAGAA 8 259 0 ACCCTTCTTC 0.97123 -42 TTGCCTTTCACTCCTTCTTTTGAGTTTTTT 21 62 0 ACCCTTCTTT 0.746795 -20 CTGTAAAACTCCTTCCGCCAATCAGCTT 28 108 0 ACCCTTCCGC 0.922917 -18 CAGGCTGATAGCGCCTTACTCTCTTCTATTC 29 32 0 GCCCTTACTC 0.89487 -60 TCCGCAGTTTGCTCCTTCGGCGCCTGTATCC 45 74 0 GCCCTTCGGC 0.828736 -227 TTCCGCACCTTCCTCAAGCAGGAGC 47 286 0 GCCCTTCCTC 0.967916 -15 ACTTTTTCTTGCGCCTTCTTCGGATTAAAAT 59 65 1 GCCCTTCTTC 0.973386 -88 TTCTGACCAAACTCCTTATTCACAACAATAA 64 136 0 ACCCTTATTC 0.90499 -21 TTTAGAACACTCCTTATTCATTGTTGTAT 67 282 0 ACCCTTATTC 0.90499 -19 ** ******** Masking position 6 Map Score: 6.57179 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 113 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 12 GCTCTCTTAGAAAGAGAGGCTCCCTACTAGTTCCT 1 56 0 AAAGAGGCCT 0.962714 -245 TATCGAAAATAAAAAGAGCCCTCATCCCCATAAAG 1 250 0 AAAAAGGCCT 0.969125 -51 AATTTTGTTCAAAAAGTGTTATCATATAGAAGGTA 9 22 1 AAAAAGGTCT 0.920207 -279 ACATAAGCGCAAAAAGTGCCATCGTAATATTAGAG 19 23 1 AAAAAGGCCT 0.969125 -278 TCCTTCTTTTAAAGAGCTGCCACTTCATCGCGCAC 30 38 0 AAAGAGTCCT 0.649469 -263 CTCGATCCGAAAAAAGTGATGGCACAAACCATAAA 30 193 1 AAAAAGGTCC 0.799872 -108 TTTGCCAAGAAAAAAGCGAACGCATATTCGGATTT 31 92 0 AAAAAGGACT 0.778034 -81 GTTGTTGCTTAAAAAGTGTCGGCATGTACATTGTC 33 224 0 AAAAAGGCCT 0.969125 -53 CATATTCTCAAAAGAGTGTCAACGTGTATTGACGC 39 155 0 AAAGAGGCCT 0.962718 -72 TCAAGAGAAGAAAACGTGGTAACATAGGGTTGTGC 43 70 1 AAAACGGTCT 0.664401 -83 TGGCGAATAAAAAAAGCGATCCCTCAATCGGAATC 52 36 0 AAAAAGGTCC 0.799872 -100 AAAACCTGAAAAAGAGCGCCGGCATG 53 2 0 AAAGAGGCCT 0.962718 -299 ****** * * * * Masking position 3 Map Score: 7.55657 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 42 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 CATCAATTCAGTGAAGAGAAATGGTTTGAG 7 37 0 GTGAAGAGAA 0.733866 -264 AAGAGCTTATATGAAGAAAATGTGTTATGC 7 172 0 ATGAAGAAAA 0.817718 -129 GGTTCGGCACACGAAGAAAAAAGTGTTGAA 8 41 1 ACGAAGAAAA 0.787245 -260 TTGAAAATCAGCGATGAAAACGATTGACGG 14 40 1 GCGATGAAAA 0.552627 -261 GTAAATAAAAAGGAAGAAAAGTCATCTTAA 30 232 1 AGGAAGAAAA 0.829357 -69 ATACTCGGACGTGAAGAAAAGTCATCTGGT 30 264 0 GTGAAGAAAA 0.904762 -37 GGTAACATAAAGGAGGAAAAAATAGA 31 157 1 AGGAGGAAAA 0.832004 -16 AATTTATTTTGGGAGGAAAAAATGA 32 153 1 GGGAGGAAAA 0.912952 -15 ATTTTGTCAAGAGAAGAAAACGTGGTAACA 43 64 1 GAGAAGAAAA 0.663556 -89 GTTCGTGCGGGTGAGGAGAAAGAGCGCTTT 50 133 0 GTGAGGAGAA 0.737526 -43 TTAACGAAACATGAGGAAAAGTCAAAAAGA 55 72 1 ATGAGGAAAA 0.820507 -127 CACACACGCTGGGAGGAAAAGCAG 61 143 1 GGGAGGAAAA 0.912952 -14 TCTATTATATATGAAGAAAAAAGAAACGGC 62 35 0 ATGAAGAAAA 0.817718 -41 TTGAATACATGCGAAGAAAAGGACATGAAT 67 32 1 GCGAAGAAAA 0.886826 -269 ********** Masking position 4 Map Score: 8.25828 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 211 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 14 TGATTTGTTTTCAATCAGGGTGGCAACGCG 1 207 1 TCAATCAGGG 0.702681 -94 CATTAACGTGGAAAACAGGGAGAGATCATA 6 127 1 GAAAACAGGG 0.751854 -20 AAAAAAATCAGCAAACTGCTTATAGTAAAG 9 270 1 GCAAACTGCT 0.789075 -31 AAAGGTTTTGGCAAACTGGGGATCGGCTAA 14 175 1 GCAAACTGGG 0.938713 -126 GCAAATCCCTTCAAACAGGGTATAGTATAT 31 122 1 TCAAACAGGG 0.90499 -51 TTTGCATTACGCAAACAGGTTGAGAATGCT 36 21 0 GCAAACAGGT 0.96018 -245 TTTGCGTAATGCAAACAGGTTGTTTTTCAT 36 36 1 GCAAACAGGT 0.96018 -230 CGCCGAAGGAGCAAACTGCGGAGTGAATCT 45 83 1 GCAAACTGCG 0.856442 -218 ACGTATTTTCTCAAACAGGAAATGTTGATA 47 150 1 TCAAACAGGA 0.595725 -151 CACATGTAAAGCAATCAGCTCTCACCGATC 57 167 0 GCAATCAGCT 0.699733 -63 CAGAAAATCTGCAAACAGGTCATTTGCAAA 61 16 1 GCAAACAGGT 0.96018 -141 ********** Masking position 4 Map Score: 5.32127 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 149 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 15 CGAGAGCTCTCGCGTTGCCACCCTGATTGAAAA 1 214 0 CGGTCCACCC 0.994528 -87 GGATGAACGGCGAGCGTTCACCCTGAATGCAGA 7 204 0 CGGGTCACCC 0.861971 -97 TACAAAAGAGCGGGTTTCCCCACTCTTTGCCTC 19 154 0 CGGTCCCCAC 0.881248 -147 GATAAAAAAGCGGGAATCCTCCCGCTTTTTACG 23 12 0 CGGACCTCCC 0.942575 -161 TCAAAAATAGCGGGCTACCTTCCATTTTTACTA 35 80 0 CGGTCCTTCC 0.898261 -120 AGAGTTCTCCCGCGGTTCCACCCTAGTTGCTGA 46 182 0 CGGTCCACCC 0.994528 -115 TAAACGGAATCGTGGTTCCACCCTTTTTTCCGC 54 217 0 CGGTCCACCC 0.994528 -84 GTGATTAACCCGTGGTTCCACCCAAGTTCCCGA 67 210 0 CGGTCCACCC 0.994528 -91 ** * * ****** Masking position 9 Map Score: 6.91034 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 8 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911