AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00530_bsub_reg_300.orf -o00530_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 metS 300 methionyl-tRNA synthetase #2 yabD 78 similar to hypothetical proteins #3 yabE 155 similar to hypothetical proteins #4 yabF 144 similar to hypothetical proteins #5 yabG 161 yabG #6 veg 210 veg #7 sspF 159 small acid-soluble spore protein (alpha/beta-type SASP) #8 yabH 147 similar to hypothetical proteins #9 purR 55 transcriptional regulator #10 spoVG 193 spoVG #11 gcaD 192 UDP-N-acetylglucosamine pyrophosphorylase #12 glmS 300 L-glutamine-D-fructose-6-phosphate amidotransferase #13 ybfT 218 similar to glucosamine-6-phosphate isomerase #14 amhX 300 amidohydrolase #15 ycnL 164 ycnL #16 mtlA 172 phosphotransferase system (PTS) mannitol-specific enzyme IIABC component #17 treP 192 phosphotransferase system (PTS) trehalose-specific enzyme IIBC component #18 glvA 300 6-phospho-alpha-glucosidase #19 yfiA 64 similar to hypothetical proteins #20 yjbJ 203 similar to lytic transglycosylase #21 yjbK 124 yjbK #22 ykvY 300 similar to Xaa-Pro dipeptidase #23 ykvZ 281 similar to transcriptional regulator (LacI family) #24 glcT 62 transcriptional antiterminator (BglG family) #25 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #26 mobA 136 molybdopterin-guanine dinucleotide biosynthesis protein A #27 moeB 50 molybdopterin biosynthesis protein #28 yknU 223 similar to ABC transporter (ATP-binding protein) #29 yknW 109 yknW #30 fruR 279 transcriptional regulator (DeoR family) #31 ylbQ 159 similar to pyrimidine-thiamine biosynthesis #32 yllA 70 yllA #33 yllB 125 similar to hypothetical proteins #34 ylxA 69 alternate gene name: yllC; similar to hypothetical proteins #35 ftsL 39 cell-division protein #36 spoVD 116 penicillin-binding protein #37 murE 175 UDP-N-acetylmuramoylananine-D-glutamate-2,6- diaminopimelate ligase #38 mraY 112 phospho-N-acetylmuramoyl-pentapeptide transferase #39 spoVE 60 spoVE #40 murG 122 UDP-N-acetylglucosamine-N-acetylmuramyl- (pentapeptide)pyrophosphoryl-undecaprenol N-acetylglucosamine transferase #41 murB 26 UDP-N-acetylenolpyruvoylglucosamine reductase #42 pksF 300 pksF #43 ypqE 137 similar to phosphotransferase system enzyme II #44 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #45 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #46 yqiS 124 similar to phosphate butyryltransferase #47 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #48 blt 116 multidrug-efflux transporter #49 bltD 168 spermine/spermidine acetyltransferase #50 csn 300 chitosanase #51 levD 189 phosphotransferase system (PTS) fructose-specific enzyme IIA component #52 levR 300 transcriptional regulator (NifA/NtrC family) #53 nagA 181 N-acetylglucosamine-6-phosphate deacetylase #54 yvyH 245 similar to UDP-N-acetylglucosamine 2-epimerase #55 lytD 128 N-acetylglucosaminidase (major autolysin) (CWBP90) #56 pmi 264 mannose-6-phosphate isomerase #57 ywnE 242 similar to cardiolipin synthase #58 murA 33 UDP-N-acetylglucosamine 1-carboxyvinyltransferase #59 ywmB 128 ywmB #60 ywzB 169 ywzB #61 murZ 300 UDP-N-acetylglucosamine 1-carboxyvinyltransferase #62 sacP 300 phosphotransferase system (PTS) sucrose-specific enzyme IIBC component #63 licB 127 phosphotransferase system (PTS) lichenan-specific enzyme IIB component #64 licR 162 transcriptional regulator (antiterminator) #65 yxzF 28 yxzF #66 yxlJ 128 similar to DNA-3-methyladenine glycosidase #67 bglP 300 phosphotransferase system (PTS) beta-glucoside-specific enzyme IIABC component Motif number 1 GTGTTTCGACAAGAAAGGAGTTTTTCACTT 2 59 1 AAGAAAGGAG 0.824279 -20 GGACTCAGCGAAAAAAGGCGCTTTCTCAAG 5 95 1 AAAAAAGGCG 0.912037 -67 ATTGGAAACCAAAAAAGGGCAAAACAAAAA 7 37 0 AAAAAAGGGC 0.793137 -123 TATCACTTCTAAAAAAGGAGTTGTTTCGT 7 141 1 AAAAAAGGAG 0.964686 -19 AATCAGAATTAAAAAAGGACCGCCGGCAAA 11 57 0 AAAAAAGGAC 0.8944 -136 TAAGCGCCCGGAAAAAGGCTTAGTTGACGA 12 76 1 GAAAAAGGCT 0.414407 -225 TCCTAAGATTGTAAAAGGAGACGAAGAAAG 12 270 0 GTAAAAGGAG 0.933187 -31 GCAATCATAAATAAGAGGACATAGGCGTCA 14 73 1 ATAAGAGGAC 0.564197 -228 TACTTTGTTTAAAAAAGGAGAGCATT 21 7 0 AAAAAAGGAG 0.964686 -118 CTTCATCCCGATAAAAGGAGCGGAAATTCC 22 65 1 ATAAAAGGAG 0.947096 -236 TAGAAATAAAAAAGGACTTTGTTCTCG 23 8 1 AAAAAAGGAC 0.8944 -274 TAATGCAGATAAAAAAGGACGATGTCGAGA 23 33 0 AAAAAAGGAC 0.8944 -249 TTTTTGTTGTGTAAAAGGGCAAATGTAAAC 25 131 1 GTAAAAGGGC 0.662202 -108 CAGACTAGTAAAAAGAGGAGGTCAATTCTT 25 219 1 AAAAGAGGAG 0.864343 -20 AATTCGACAAAAATAAGGACAATTGTACGA 30 100 0 AAATAAGGAC 0.384569 -180 GAACGCAAAATTAAAAGGAGGTCATCAGCC 35 19 1 TTAAAAGGAG 0.659933 -21 AAACAAGCCTAAATAAGGAGTGAACGGTCT 36 96 1 AAATAAGGAG 0.668372 -21 TTTAGCGTAAATAAAAGGATACATCCAGCT 37 64 0 ATAAAAGGAT 0.610307 -112 TAATCTGGTTAAAAAAGGCGGTGGCGATA 43 10 0 AAAAAAGGCG 0.912037 -128 AACTTGCATAATAAAAGGCGGAGTCGAAAC 46 88 1 ATAAAAGGCG 0.871711 -37 GTTCAATTGAGTAAAAGGGGAATTCAG 48 100 1 GTAAAAGGGG 0.863439 -17 CCGGGATAAGAAAAAAGGAGAATGTAGT 49 151 1 AAAAAAGGAG 0.964686 -18 AACAGATTTTATAAAAGGGGGGAAAACACC 53 89 1 ATAAAAGGGG 0.89016 -93 CATAGAATAAGAAAGAGGAGAAGGA 55 114 1 GAAAGAGGAG 0.832524 -15 AATTTGTATCAAAAAAGGAGAATTATTCTT 56 49 1 AAAAAAGGAG 0.964686 -216 ACGGGCGTTTGTAAGAGGGGCGCACCGGGA 56 206 1 GTAAGAGGGG 0.595914 -59 TATGAACGCAGAGAAAGGAGTGTAATAG 60 152 1 GAGAAAGGAG 0.785396 -18 TTGCGTAAATGAAAAAGGATCGCTGTGTCC 62 225 1 GAAAAAGGAT 0.650896 -76 TTTTGTTTAAATAAAAGGGGGAGAAATAG 62 282 1 ATAAAAGGGG 0.89016 -19 GTTACCGTTCAAAAAAGGAGGGCCAACCA 66 10 0 AAAAAAGGAG 0.964686 -119 ACAAAAATCGGTAAAAGGAGAGGTCGATTC 66 109 1 GTAAAAGGAG 0.933187 -20 AAAAAAGCTGGTGAAAGGCGGCCACCTTTC 67 246 1 GTGAAAGGCG 0.476527 -55 AGTCCCCCCATAAAAAGGAGGTATACAC 67 283 1 TAAAAAGGAG 0.747551 -18 ********** Masking position 6 Map Score: 40.9174 Number of sites scoring better than the average of aligned sites = 864 Number in coding regions = 597 Number in noncoding regions = 267 Number of orfs with sites within 600 bp upstream = 314 Fraction of orfs with sites within 600 bp upstream = 0.0504337 Motif number 2 ATAAAAGTTCTACATGCTTTCTTCTCCTCATAGG 3 62 1 TCAGTTTTTC 0.902784 -94 TTTCGCTGAGTCCAAGTTTTTTCTTATCATTGAA 5 74 0 TCAGTTTTCT 0.685566 -88 GACGTGCTGTTCCCTGGTTTTTTTATTTTGGATA 8 26 1 TCCGTTTTTT 0.961823 -122 GTGTATCAATTCCACGATTTTTTCTGAAATCCTG 10 134 0 TCAGTTTTTC 0.902784 -60 ATATAAACCCTCCCTGTTTTGTTTGTCGCTGTAA 16 149 0 TCCGTTTTTT 0.961823 -24 TTTCGAACATTTGATGATTTTTTTATTTAATGCA 23 56 0 TGAGTTTTTT 0.803235 -226 GATATGGACGTACCAGATATCTTTTTGTGTTTTT 23 206 0 TCCGTATTTT 0.669262 -76 GAGAATGAACTTCCCGTTTTTTTCCCTCAATCAC 25 66 0 TCCGTTTTTC 0.923289 -173 CCCTGACTAGTTCAGGGTTTCTTTTTATGGGTAA 33 28 1 TCAGTTTTTT 0.951073 -98 GCCGTCGTTATGCAGGCTTTCTTTTTTTATGCCT 36 18 1 TCAGTTTTTT 0.951073 -99 AGTTATCATATTCATGATTTTTTTCCATATGAAA 38 50 0 TCAGTTTTTT 0.951073 -63 TCCTTTTCGCTTGAAGCTTTTTTCAAGTACAATC 48 54 0 TGAGTTTTTC 0.661039 -63 ACCATTTTAATACAGGTTTATTTTTTTCGTTTTA 51 48 1 TCAGTTATTT 0.595319 -142 TGTGCAGCTTTTCAAGCTTTGTTTCAGCCTTTTC 56 85 0 TCAGTTTTTT 0.951073 -180 GTCTTTTCCTGCTTTCTTTCATGATTGAG 62 6 1 TCCGTTTTTT 0.961823 -295 TCCCGGCTGTTTTTTTATAGGTCA 64 1 1 TCCGTGTTTT 0.749946 -162 GATTTTAAAACAGCCGTTTTTTTTGATCTGCTTC 66 59 1 CGCGTTTTTT 0.536847 -70 GGCCGCCTTTCACCAGCTTTTTTTGTATCAAATG 67 235 0 CCCGTTTTTT 0.846612 -66 * ** * *** *** Masking position 8 Map Score: 14.8449 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 148 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 AAACCTATCCTATGAGGAGAAGAAAGCATG 3 74 0 TATGAGGAGA 0.68578 -82 TATTCGGATTTTGGGGGTGAGTTC 9 42 1 TTGGGGGTGA 0.497162 -14 ATATAGGGAAAAGGTGGTGAACTACT 10 178 1 AAGGTGGTGA 0.627138 -16 TCTTCAAACCAAGGGGGTGACTCCTTGAAC 12 171 1 AAGGGGGTGA 0.95525 -130 AAAAAACATGTAGGAGGGGACGATTGAAAG 12 224 1 TAGGAGGGGA 0.880886 -77 TTGCATACAGAATGGGGAGAATGAA 13 6 0 AATGGGGAGA 0.890236 -213 ATAGAAAGAAAATGGGGGGATCTGAT 19 49 1 AATGGGGGGA 0.856229 -16 ACGTTTTCATTAGGAGGTGAAGC 30 267 1 TAGGAGGTGA 0.851725 -13 AGAAACAACAAAGGGGGAGATTTGT 31 6 0 AAGGGGGAGA 0.973976 -154 TTGAAAGAAACAGGAGGAGAAAAGGACA 38 95 1 CAGGAGGAGA 0.850815 -18 AGATTTTATAAAAGGGGGGAAAACACCTCA 53 92 1 AAAGGGGGGA 0.761446 -90 ATAGAATAAGAAAGAGGAGAAGGA 55 115 1 AAAGAGGAGA 0.656504 -14 ACATCAAATAAAGGGGGAGGATTAT 57 6 0 AAGGGGGAGG 0.807617 -237 AACTGGGGATAAGGGGGAGAGATGAAC 59 112 1 AAGGGGGAGA 0.973976 -17 GTTTAAATAAAAGGGGGAGAAATAG 62 286 1 AAGGGGGAGA 0.973976 -15 GGTGCAGGTGCAGGAGGAGACTCTCGCAAT 67 160 1 CAGGAGGAGA 0.850815 -141 TATTCTCTTTTAGGAGGTGATGCAGCATTT 67 210 1 TAGGAGGTGA 0.851725 -91 ACCTCCTTTTTATGGGGGGACTGCTGGATG 67 275 0 TATGGGGGGA 0.784711 -26 ********** Masking position 6 Map Score: 20.0001 Number of sites scoring better than the average of aligned sites = 140 Number in coding regions = 53 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 4 AATTTTGTCGTATATAATCAAATGAAATAAAAAACTTTGGTTC 1 57 0 TTTAAAAAAA 0.89226 -244 AAATGCACTTTGTCTATTATAACGAAAAAAACAGAGGGCGCAA 4 36 0 TTTAAAAACA 0.739707 -109 TATTTCCTCCAAGACAAAATAAAAACTTTTGTA 4 122 0 TTTAAAAAAA 0.89226 -23 TTCGGTAAATTATGTATCATTATGTAAAATAAAAAACCCGCAT 6 37 0 TTTAAAAAAA 0.89226 -174 ACGAAAGTTCCATCTGATTTAACAAAAGATAAAACAGTCACAT 7 74 1 CTTAAAAAAA 0.776406 -86 TTCAGCCCATTATGTATTTATATCCAAAATAAAAAAACCAGGG 8 37 0 TTTAAAAAAA 0.890159 -111 TGACTACCTGTATATACAGGAATACAATATGATTATAAGTTGT 17 123 1 TTTAAAAGAT 0.718672 -70 CATTTTCGAATCTGTAATTGTATATAATAGAAAGAAAATGGGG 19 23 1 TTTAAAAAAA 0.89226 -42 ACATCGTCCTTTTTTATCTGCATTAAATAAAAAAATCATCAAA 23 38 1 TTTAAAAAAA 0.890578 -244 AACGCTACTGCTTGTCTGTTTATTAAAGAGGAATAGCTGTTCA 26 56 0 CTTAAAAGAA 0.848474 -81 TATAAAAGACTTTTTTCATTAAAATAAGAAGAAAATGTCGTAC 30 63 1 TTTAAAAGAA 0.930359 -217 GAACGATGCTCCTCTGAAGGCATAAAAAAAGAAAGCCTGCATA 36 26 0 CTTAAAAGAA 0.848475 -91 ATCAGCATTTTTTCTGCAATAAAAGAATAGGCAGCCCGAA 37 8 0 TTTAAAAGCA 0.848474 -168 ATACAGTTCATATTTTAGCGTAAATAAAAGGATACATCCAGCT 37 64 0 TTTAAAAGAT 0.718672 -112 CCTTGCATTATATATGGATGTACAAAACAGGAAAGGAGCAATA 51 154 1 TTTAAAAGAA 0.930359 -36 ATAAACTAGTTTTATATACTCATAGAATAAGAAAGAGGAGAAG 55 94 1 TTTAAAAGAA 0.930332 -35 TAATTCTCCTTTTTTGATACAAATTAATAAAAACCGTCAATAT 56 31 0 TTTAAAAAAA 0.890578 -234 GCTTTGTACATATGTTGTCATAGGAAAAAGGCAGCTTATACGG 56 167 1 TTTAAAAGCA 0.848474 -98 GCGTTCATACCCTTTCTTATTATATAAGAAGCACAGATAAAGA 60 118 0 CTTAAAAGCA 0.701229 -52 ACATGAGCTTTATTTGCAGAGACAGAATAAAATGACATTTTAT 61 230 1 TTTAAAAAAT 0.613024 -71 * * * * ** * *** Masking position 5 Map Score: 15.5779 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 135 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 5 ATGCCCGAAATGAAAGCTTTATGACCTAATTG 10 59 1 TGAAAGCTTT 0.521197 -135 CAAGGACTGCTGAAAGGGCTGACATAAGCCTT 11 26 1 TGAAAGGGTA 0.715042 -167 GTATAGGGACTGTAAGCGTTTTAACATAGAGT 16 79 1 TGTAAGCGTT 0.922771 -94 CAGACTAGGATGAAAGCGCTATAAAAAAGTGT 17 91 1 TGAAAGCGTT 0.958865 -102 CCAATTCTTATGAAAAGGTTCTTTTGTACGAT 18 58 0 TGAAAAGGTT 0.709876 -243 TAAATGGAATTGTAAACGTTATCAAGGAGGTC 18 274 1 TGTAAACGTT 0.856574 -27 AACTGAAACTTGAAAGCGGGCTTTCCGTATTC 20 108 0 TGAAAGCGGT 0.747229 -96 AAAGGGCAAATGTAAACGGTTAAACTGGAAGA 25 144 1 TGTAAACGTA 0.753774 -95 AATGATTTTCTGTAAGCGTTTATTCTACATAT 28 83 1 TGTAAGCGTA 0.859632 -141 ACAATTTCATTGTAAACGCTATTTTCGGTTTA 30 222 0 TGTAAACGTT 0.856574 -58 CACCTCCTAATGAAAACGTATTCATTTTGAAT 30 254 0 TGAAAACGAT 0.637409 -26 CTACATATATTGTAAACGCTTTATTTAAAAAA 31 34 1 TGTAAACGTT 0.856574 -126 GAAATAACAATGAAAACGCTTAACACAACTGT 51 111 1 TGAAAACGTA 0.856574 -79 AAAAACATATTGAAAAGGGTAAATAGAGAATA 54 55 0 TGAAAAGGTA 0.556385 -191 TCATAAATCATGATAGCGTTTTCGTCAACTAT 62 129 0 TGATAGCGTT 0.638216 -172 TGATTTATGATGAAAGCGTATTCTTAATCTGA 62 151 1 TGAAAGCGAT 0.778618 -150 TGAGTGTTTATGAAAGCGATTTCATAATATGA 63 52 1 TGAAAGCGTT 0.958865 -76 ACACCAAAAATGAAAGCGTTGACATCTCACGA 67 49 1 TGAAAGCGTA 0.922681 -252 ******** * * Masking position 1 Map Score: 14.003 Number of sites scoring better than the average of aligned sites = 305 Number in coding regions = 218 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 6 CGAACCAAAGTTTTTTATTTCATTTGATTA 1 56 1 TTTTTTATTT 0.81608 -245 CGAACAGACTTTTTTTATTTTCATTAAAGA 1 105 1 TTTTTTATTT 0.81608 -196 ACGTGAAACACCTTTTGTTTATCA 2 5 0 CCTTTTGTTT 0.777127 -74 AAGGGCTTTTTGTTTTGCGCACCAC 5 6 1 CTTTTTGTTT 0.85226 -156 GCTATGCGGGTTTTTTATTTTACATAATGA 6 34 1 TTTTTTATTT 0.81608 -177 GGGCAGTGAACCTTTTGTTTACTGCTTTTT 7 12 1 CCTTTTGTTT 0.777127 -148 TTGTTTACTGCTTTTTGTTTTGCCCTTTTT 7 26 1 CTTTTTGTTT 0.85226 -134 GTTCCCTGGTTTTTTTATTTTGGATATAAA 8 34 1 TTTTTTATTT 0.81608 -114 CCGGGATCACTTTTTTATTTACCTTATGCC 10 34 1 TTTTTTATTT 0.81608 -160 AACCAGGAGCCTTTTTATTTTTAAAAAATT 16 11 1 CTTTTTATTT 0.906964 -162 TTTTCTAATGCATTTTATTTCCTGCTCCTC 22 193 0 CATTTTATTT 0.740463 -108 AACAAAGTCCTTTTTTATTTCTA 23 4 0 TTTTTTATTT 0.81608 -278 ATTTGATGATTTTTTTATTTAATGCAGATA 23 52 0 TTTTTTATTT 0.81608 -230 CTGGATGTATCCTTTTATTTACGCTAAAAT 37 66 1 CCTTTTATTT 0.854915 -110 AAACTTATATCATTTTATTTGAATCAAGAA 54 144 1 CATTTTATTT 0.740463 -102 AATAAAATGACATTTTATTTAGCTCCGCAG 61 255 1 CATTTTATTT 0.740463 -46 ATTTTAGGTCTTTTTTGTTTAAATAAAAGG 62 270 1 TTTTTTGTTT 0.724188 -31 TATTTCTCCCCCTTTTATTTAAACAAAAAA 62 280 0 CCTTTTATTT 0.854915 -21 CCTGACGGGTCGTTTTATTTGTTTGTAGGT 67 98 0 CGTTTTATTT 0.625962 -203 ********** Masking position 5 Map Score: 20.0332 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 232 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 7 CTTGAAACCTCCTAATCAGAATG 1 288 0 GAAACCTCCT 0.658144 -13 AAGCTCTTACAAAACCCGCTAGCGTTTTTT 3 12 0 AAAACCCGCT 0.958023 -144 CAGAGGGCGCAAAACCCTCTGAATACATAA 4 18 0 AAAACCCTCT 0.58146 -127 CAGTTGAAAACCTGCATAGGAGAGCT 6 7 1 AAAACCTGCA 0.708112 -204 TGTAAAATAAAAAACCCGCATAGCTCTCCT 6 28 0 AAAACCCGCA 0.796421 -183 ATTTTTTCTGAAATCCTGCTCGTTTTTAAA 10 122 0 AAATCCTGCT 0.766007 -72 CAGAATACGGAAAGCCCGCTTTCAAGTTTC 20 106 1 AAAGCCCGCT 0.931059 -98 TCTTCATCGCCAAGCCCGCTCAGC 20 190 1 CAAGCCCGCT 0.849865 -14 AAGGAAACCCGCTGCACAGCCTA 22 4 1 GAAACCCGCT 0.833331 -297 AAACACCGGTAAAACCTGTTACAATGGAAG 22 242 1 AAAACCTGTT 0.672701 -59 CCTTCTTTCTAAATCCCCTTGATCTGGAAT 23 256 0 AAATCCCCTT 0.322504 -26 CAAACCTGTTCTCCTTATCT 27 41 0 CAAACCTGTT 0.462793 -10 TTCAAAACCTCCTTGAGAATATC 29 97 0 AAAACCTCCT 0.897832 -13 ATAAAAAAAGAAAGCCTGCATAACGACGGC 36 18 0 AAAGCCTGCA 0.589417 -99 AATGTATTTCCAAGCCTCCTGTCTAACATG 40 13 1 CAAGCCTCCT 0.685498 -110 CTTCAGAAAACCCCTTTATCTTTTCA 47 7 1 AAAACCCCTT 0.672986 -146 AAAAACCTCCTTGACTATACG 48 2 1 AAAACCTCCT 0.897832 -115 TATACGCATAAAAGCCAGCTTTGTCAATCT 52 189 1 AAAGCCAGCT 0.652345 -112 AGATTTCTTTAAAACCAGCTTGCACCTGCG 57 75 0 AAAACCAGCT 0.760248 -168 TTACCAGTCACAATCCCGCTTATTCAGATT 62 176 0 CAATCCCGCT 0.688734 -125 GTAAAAGACCCCCTAGAGTTTGAT 63 114 0 AAGACCCCCT 0.563537 -14 GAGAAAAACCTCCTAACTAGTAGA 64 149 0 AAAACCTCCT 0.897832 -14 ********** Masking position 2 Map Score: 14.5856 Number of sites scoring better than the average of aligned sites = 602 Number in coding regions = 446 Number in noncoding regions = 156 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 8 CAAAACCCGCTAGCGTTTTTTG 3 3 0 TAGCGTTTTT 0.655431 -153 TAGGGACTGTAAGCGTTTTAACATAGAGTC 16 82 1 AAGCGTTTTA 0.67531 -91 CACTTTTTTATAGCGCTTTCATCCTAGTCT 17 92 0 TAGCGCTTTC 0.699265 -101 GATTTTCTGTAAGCGTTTATTCTACATATG 28 86 1 AAGCGTTTAT 0.655431 -138 AAACCGAAAATAGCGTTTACAATGAAATTG 30 223 1 TAGCGTTTAC 0.864934 -57 TTTTTAAATAAAGCGTTTACAATATATGTA 31 35 0 AAGCGTTTAC 0.925077 -125 CAGTTGTGTTAAGCGTTTTCATTGTTATTT 51 112 0 AAGCGTTTTC 0.959687 -78 AATAGATAGGAAGCGTTTTCTTTGAAGGGG 56 122 1 AAGCGTTTTC 0.959687 -143 TAAATCATGATAGCGTTTTCGTCAACTATT 62 128 0 TAGCGTTTTC 0.925077 -173 TTTATGATGAAAGCGTATTCTTAATCTGAA 62 154 1 AAGCGTATTC 0.733856 -147 GTGTTTATGAAAGCGATTTCATAATATGAT 63 55 1 AAGCGATTTC 0.751541 -73 CCAAAAATGAAAGCGTTGACATCTCACGAA 67 52 1 AAGCGTTGAC 0.679446 -249 ********** Masking position 2 Map Score: 7.45898 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 136 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 9 TAGAACTTTTATAGAAAAACGCTGTAAGGG 3 44 0 ATAGAAAAAC 0.72851 -112 ATTCAATGATAAGAAAAAACTTGGACTCAG 5 73 1 AAGAAAAAAC 0.645281 -89 TATATCCAAAATAAAAAAACCAGGGAACAG 8 32 0 ATAAAAAAAC 0.839342 -116 AACACAGCCTAAGAAAAAACGTATGACATT 14 112 0 AAGAAAAAAC 0.645281 -189 CCCAATTAAAATGAAGAAACCCATGTGATC 23 162 1 ATGAAGAAAC 0.891803 -120 ATCACTAAACATAAAAAAACCTCATGCATG 30 21 0 ATAAAAAAAC 0.839342 -259 ATACGTTAATATGGAGAAACGTGAAAGATT 30 153 1 ATGGAGAAAC 0.808922 -127 TTTACAATATATGTAGAAACAACAAAGGGG 31 20 0 ATGTAGAAAC 0.44789 -140 GTTTACCCATAAAAAGAAACCCTGAACTAG 33 34 0 AAAAAGAAAC 0.525267 -92 TTTTTTCCATATGAAAAATCTTTTTCAAGC 38 36 0 ATGAAAAATC 0.389042 -77 TCGTTATGTTATAGAGAAACTTAGACTGGG 40 92 1 ATAGAGAAAC 0.72441 -31 AGAGCGCATTATGGATAAACAGAGAATCTT 42 75 1 ATGGATAAAC 0.491947 -226 CTCAGTATACATGAAGAAACTGCCCTATTG 50 247 0 ATGAAGAAAC 0.891803 -54 ACAGGTTCATATGAAAAAACTGTTT 51 6 0 ATGAAAAAAC 0.893777 -184 CCATTTTCTAATAAAAAAACTTAACCTCGA 55 24 0 ATAAAAAAAC 0.839342 -105 GCGCGTGCCGATAAATAAACTAGTTTTATA 55 80 1 ATAAATAAAC 0.539288 -49 AAACTGACCTATAAAAAAACAGCCGGGA 64 9 0 ATAAAAAAAC 0.839342 -154 CTAAAAGAGAATAAAAAAACCTAAATGACA 67 193 0 ATAAAAAAAC 0.839342 -108 ********** Masking position 5 Map Score: 12.6977 Number of sites scoring better than the average of aligned sites = 477 Number in coding regions = 346 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 10 GTATTTCAGGATAATGAAGAGGACACTGAGCT 3 133 1 ATAAGAGAGG 0.689466 -23 AAAGGCTTAGTTGACGAGGATGGAGGTTATCG 12 89 1 TTGAGAGATG 0.560329 -212 TGACAGTTTGATAAGGGCGGTGCTAAATTCGT 13 130 1 ATAAGGGGTG 0.936528 -89 ATAGATCTTAATGAAGAGGGTGTATGA 15 6 0 ATGAGAGGTG 0.971521 -159 GGGCTTGGCGATGAAGAAGGTGCTGATTGCTG 20 175 0 ATGAGAGGTG 0.971521 -29 TTTTATCGGGATGAAGATGGTGGGCTTTTATT 22 49 0 ATGAGAGGTG 0.971521 -252 TGTTAACATCATGAGGGAGATGGTTCGA 26 7 0 ATGAGGGATG 0.900514 -130 AGCTGAAATTATCACGATGGTGCTAGAGGATT 42 210 1 ATCAGAGGTG 0.867691 -91 TTTTAAAAGCATAAAGGAGGGGCTTGA 45 57 1 ATAAGGGGGG 0.849916 -17 TTTTTCGATCATAAGGAAGGTGCCTTTTAA 54 9 0 ATAAGAGGTG 0.94719 -237 GAAACATCAAATAAAGGGGGAGGATTAT 57 7 0 ATAAGGGGAG 0.674919 -236 CTTTTGCCGGATGACGACGATGTCTCTCGAGC 61 86 1 ATGAGAGATG 0.916687 -215 **** ** **** Masking position 4 Map Score: 6.39836 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 107 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 11 CTTATCATTGAATGAAAGGTCCTTCTCTAG 5 56 0 AATGAAAGGT 0.645518 -106 AAATAACCAAAAAGCAAGGACTGCTGAAAG 11 12 1 AAAGCAAGGA 0.693231 -181 ACAAAACGAAACAGAAGGGACTCTGGTATA 15 111 1 ACAGAAGGGA 0.707709 -54 ATGACATTAAAAAGCAGGGTGAGCCTCT 17 9 0 AAAGCAGGGT 0.666727 -184 TGTGTTTTTAGCTGAAAGGAGAAGATCACA 23 185 0 GCTGAAAGGA 0.708989 -97 GGGGATTTAGAAAGAAGGGAATCT 23 268 1 AAAGAAGGGA 0.840292 -14 AATAGTGGTGAATGAAGGGATAACGGTTGA 43 93 1 AATGAAGGGA 0.902199 -45 AAGTCATTTGGATGCAGGGAATGCCCCTGG 49 29 1 GATGCAGGGA 0.910692 -140 ATCCATATATAATGCAAGGATCGTGCCAAC 51 143 0 AATGCAAGGA 0.798471 -47 CTGATATCGGAATGAAGGGTATGCGTACTG 61 56 1 AATGAAGGGT 0.794084 -245 CAGAAAGGATGATGAAGGGATGCGAAATGT 64 98 0 GATGAAGGGA 0.918109 -65 CAGTGAATAGGCAGAAAGGATGATGAAGGG 64 109 0 GCAGAAAGGA 0.581511 -54 CTAACTAGTAGATGCAGGGATTCAGTGAAT 64 131 0 GATGCAGGGA 0.910692 -32 GGGACTGCTGGATGAAAGGTGGCCGCCTTT 67 259 0 GATGAAAGGT 0.688779 -42 ********** Masking position 6 Map Score: 7.30702 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 167 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 59 Fraction of orfs with sites within 600 bp upstream = 0.00947639 Motif number 12 TCTTCTGATTTCAAGGAGACTTCATGAAGT 11 123 0 TCAAGGAGAC 0.908915 -70 TTTCTTCAAACCAAGGGGGTGACTCCTTGA 12 169 1 CCAAGGGGGT 0.817341 -132 TTCTCTTTGTTCAAGGAGTCACCCCCTTGG 12 179 0 TCAAGGAGTC 0.711134 -122 AAGTCAAATTTCAAGGGGACTTTCAATCGT 12 243 0 TCAAGGGGAC 0.903215 -58 TGACACCCCCTCAAAGAGATAGACAAGCAC 13 198 0 TCAAAGAGAT 0.556612 -21 GTAAACGTTATCAAGGAGGTCGTCAT 18 285 1 TCAAGGAGGT 0.962132 -16 GCATTCCAGATCAAGGGGATTTAGAAAGAA 23 254 1 TCAAGGGGAT 0.937107 -28 TTAGATATTCTCAAGGAGGTTTTGAA 29 94 1 TCAAGGAGGT 0.962132 -16 TACCGTATAGTCAAGGAGGTTTTT 48 5 0 TCAAGGAGGT 0.962132 -112 TTCATATTTATCAAGAAGATTGCCATTAGT 57 207 0 TCAAGAAGAT 0.556612 -36 TTGATCAAACTCTAGGGGGTCTTTTAC 63 111 1 TCTAGGGGGT 0.751189 -17 ********** Masking position 4 Map Score: 5.94708 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 69 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 13 GTTCGTGTCGAATTTTGTCGTATATAATCAAA 1 78 0 ATTTTTCGTA 0.779664 -223 TGCGCCCTCTGTTTTTTTCGTTATAATAGACA 4 37 1 GTTTTTCGTT 0.506416 -108 GGTTTCCAATAATTTTAACGAAAGTTCCATCT 7 57 1 ATTTTACGAA 0.903774 -103 CTTTTGCTATGCTTTTAACGAAACTAGAGGTG 26 108 1 GTTTTACGAA 0.840018 -29 AATTGTCCTTATTTTTGTCGAATTTACAGTTT 30 106 1 ATTTTTCGAA 0.872164 -174 AATGCGAGGGATTTTTAACGATAAATCCTCTA 42 233 0 ATTTTACGAT 0.829679 -68 ATACAGGTTTATTTTTTTCGTTTTAAGTGTTT 51 57 1 ATTTTTCGTT 0.647298 -133 TTTAACCATAAATTTTTTCGATCATAAGGAAG 54 22 0 ATTTTTCGAT 0.779664 -224 ATCTGCCCGTATTTTTCACGAAGAATCTGGAT 57 101 1 ATTTTACGAA 0.903774 -142 GAATAGCTCGAGTTTTGACGAAGATTTTTACG 59 56 1 ATTTTACGAA 0.903774 -73 TTTTGACGAAGATTTTTACGTATGGCGCCTCT 59 68 1 GTTTTACGTA 0.73142 -61 TTTCACAATTAATTTTTACGAATTTTTGTCTA 62 67 1 ATTTTACGAA 0.903774 -234 * **** ***** Masking position 6 Map Score: 3.745 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 60 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 14 AGTTTTTTATTTCATTTGATTATATACGAC 1 64 1 TTCATTTGAT 0.593028 -237 AAAGTACAGATTCATTTTATCATATCGAGC 21 31 1 TTCATTTTAT 0.924478 -94 CATTTTCTAATGCATTTTATTTCCTGCTCC 22 195 0 TGCATTTTAT 0.608214 -106 TCACGACGCCTTCATTTTCTAATGCATTTT 22 207 0 TTCATTTTCT 0.753488 -94 CATGGGTTTCTTCATTTTAATTGGGTTATG 23 157 0 TTCATTTTAA 0.511581 -125 ATTTCATAAATTCAGTTTATCCTTATAACG 25 12 1 TTCAGTTTAT 0.608213 -227 AGTTCAGGGTTTCTTTTTATGGGTAAACAG 33 36 1 TTCTTTTTAT 0.648751 -90 GCTCCACAACTTCATTTTACACTGTTTACC 33 57 0 TTCATTTTAC 0.608213 -69 TTAGGCTTGTTTCATTTTATGCCTGAATTT 36 78 0 TTCATTTTAT 0.924478 -39 TTCTAATTCGTTCTTTTTATCATTGAAGTC 37 137 0 TTCTTTTTAT 0.648751 -39 TCAATTTTGCTTCAATTTATAACAACATCT 43 52 0 TTCAATTTAT 0.511576 -86 TTCATTTTCTATAAAGTTAA 49 1 1 TTCATTTTCT 0.753488 -168 ATCTATAAGATTCATTTTTTGTCATTGATT 52 29 1 TTCATTTTTT 0.52844 -272 TCACAATACTTTCATTTTATCACTTTCGGG 53 48 1 TTCATTTTAT 0.924478 -134 TAAAACTTATATCATTTTATTTGAATCAAG 54 142 1 ATCATTTTAT 0.511581 -104 ATAAAGATGATACATTTTATACAGAACGGA 60 95 0 TACATTTTAT 0.511582 -75 TAAATAAAATGTCATTTTATTCTGTCTCTG 61 246 0 GTCATTTTAT 0.608213 -55 ********** Masking position 6 Map Score: 5.4651 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 139 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 15 GGCGTATGTATATATTCTTGATCTTAAAGGCTAAGATG 1 162 1 TTTCTATTAA 0.893349 -139 ATTATTTATATTTATCCTTTATCTATGATACCATCTTA 1 193 0 TTTCTATTGA 0.725752 -108 ATTGTGTAACTATATCCTATTTTTTCAAAAAATATTTT 10 87 1 TTTCATTTAA 0.720657 -107 ATGAAAGATTTGTATCCTTCTTTTATAACAAATTTTCA 13 81 1 TTTCTTTTAA 0.880503 -138 TTATAAGTTGTATATACAAGTTATAAAAACGGATACGG 17 155 1 TTTCATTTAA 0.720657 -38 AGATTTGGTTTTTTTACCTTTTTTGTAATCTTAAAGTC 18 126 0 TTTCTTTTAA 0.880503 -175 ATAAAATGAATCTGTACTTTGTTTAAAAAAGGAGAGCA 21 13 0 TTTCTGTTAA 0.661829 -112 TGACGTGCATTCTGTTCGTTATGTACGATATGAGGTAT 24 32 1 TTTCTATTGA 0.725752 -31 TCTGTAAGCGTTTATTCTACATATGTTACTCCCTATAA 28 91 1 TTTCAATTTA 0.374608 -133 TTTATAGGTATATTTTCATAATATTCAAACTTTTATTT 42 11 0 TTTCTATTAA 0.893349 -290 ACTGAGTCTGTATTTACAATATTTAGAAAGGGGAAGTG 50 271 1 TTTCAATTAA 0.745725 -30 TTAAACAAGCTTTATCCTTAATATTAAAACTTATATCA 54 118 1 TTTCTATTAA 0.893348 -128 ATCATCTTTATCTGTGCTTCTTATATAATAAGAAAGGG 60 114 1 TTTCTTTTAA 0.880503 -56 CCGGCGGGTCTCTGTGCATCTTTTGAAACCTGTACCCC 61 117 1 TTTCTTTTAA 0.880503 -184 GCTTCGCTATTTTCTTCCTGATATTTTACAATGTGTTG 61 160 1 TTTCTATTTA 0.631108 -141 TACGAATTTTTGTCTACATGTTATATCAAACTATTTAA 62 83 1 TTTCTTTTCA 0.558484 -218 * * * * * ** * ** Masking position 12 Map Score: 4.0898 Number of sites scoring better than the average of aligned sites = 141 Number in coding regions = 96 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269