AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_bsub_reg_300.orf -o00340_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 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #6 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #7 ycbD 29 similar to aldehyde dehydrogenase #8 amhX 300 amidohydrolase #9 yerQ 300 similar to hypothetical proteins #10 yefA 255 alternate gene name: yerS; similar to RNA methyltransferase #11 patA 300 aminotransferase #12 pksF 300 pksF #13 xpt 300 xanthine phosphoribosyltransferase #14 trpE 215 anthranilate synthase #15 aroB 61 3-dehydroquinate synthase #16 aroF 69 chorismate synthase #17 cheR 236 methyl-accepting chemotaxis proteins (MCPs) methyltransferase #18 ndk 115 nucleoside diphosphate kinase #19 gerCA 162 heptaprenyl diphosphate synthase component I #20 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #21 mtrA 187 GTP cyclohydrolase I #22 hbs 300 non-specific DNA-binding protein HBsu #23 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #24 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #25 yqiS 124 similar to phosphate butyryltransferase #26 yqiR 152 similar to transcriptional regulator (sigma-L-dependent) #27 yqeT 24 similar to ribosomal protein L11 methyltransferase #28 dnaJ 199 heat-shock protein #29 dnaK 23 class I heat-shock protein (chaperonin) #30 grpE 71 heat-shock protein #31 hrcA 119 transcriptional regulator #32 hemN 52 coproporphyrinogen III oxidase #33 lepA 133 GTP-binding protein #34 spoIIP 62 spoIIP #35 gpr 203 spore protease #36 blt 116 multidrug-efflux transporter #37 bltD 168 spermine/spermidine acetyltransferase #38 hisS 300 histidyl-tRNA synthetase #39 patB 80 aminotransferase #40 hisZ 250 histidyl-tRNA synthetase #41 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #42 hutP 300 transcriptional regulator #43 hutH 112 histidase #44 aldX 142 aldehyde dehydrogenase Motif number 1 AAAATCTTTAATGAAAATAAAAAAAGTCTGTTCGT 1 104 0 ATGAAAATAA 0.676018 -197 TATTTCCTCCAAGACAAAATAAAAACTTTTGTATA 4 120 0 AAGACAAAAA 0.869571 -25 TATAAAATATCAGAAAATAAAGATATTGACTTATT 6 84 1 CAGAAAATAA 0.649468 -143 GTTTAATTGTAAGACAAATAAACAATAAGTCAATA 6 107 0 AAGACAAATA 0.541709 -120 GCGGATGTGAAAGAAAAATTAATAAAAGCGCTTAC 6 162 1 AAGAAAAATA 0.764916 -65 CCAGAAAAAACACGAAAGGGGCAATG 7 2 1 CAGAAAAAAA 0.93407 -28 AACACAGCCTAAGAAAAAACGTATGACATTTAAAA 8 107 0 AAGAAAAAAG 0.566117 -194 TTCAATCAAGCTGAAAGAATGTTAAGGATGACAAA 9 128 1 CTGAAAGAAA 0.733343 -173 AATGTTAAGGATGACAAAAGCTCAAAACAAGAATC 9 145 1 ATGACAAAAA 0.852857 -156 GCTCAGAATGTTGACAAAATCCTAAAACAGTTTTC 10 31 1 TTGACAAAAA 0.525689 -225 CGCTGAAAAGATGACAAAATCCTAAAACGAAAACT 10 59 0 ATGACAAAAA 0.852857 -197 CCTTTCTTTTCAGAAAAAAAGAAGACAACCAGCGA 11 164 0 CAGAAAAAAA 0.93407 -137 AAGGTATGTTTAGAAAAAAGGCGCATACAATCGAA 11 195 1 TAGAAAAAAA 0.77824 -106 TTTGAATATTATGAAAATATACCTATAAAAATCAT 12 20 1 ATGAAAATAA 0.676018 -281 CTTTTTGCTGAAAAATATGTTATAGTAGTCTT 16 8 1 CTGAAAAATA 0.685898 -62 TACATAGATTAAGAAATAAATGTGAATTTGGGGAC 19 125 1 AAGAAATAAA 0.645231 -38 CTTTTCTGTGAAGAAATAAAGTGTATGTAAGCTAG 21 36 0 AAGAAATAAA 0.645231 -152 GGATGAAAAAAGGAAAAAAAGGAATAT 22 3 1 ATGAAAAAAA 0.941021 -298 AAACCTGTCTCAGAAAAAAATGAGAGCAAGTAAGA 22 204 0 CAGAAAAAAA 0.93407 -97 ACCCCTTTGTATGAAAAAATTTGCACACCTATTTA 26 122 0 ATGAAAAAAA 0.941021 -31 TATCCCGGGCAAGAAAAAAAGTCAAAGCCAAGAGA 28 102 0 AAGAAAAAAA 0.948327 -98 ACCTTCTTTACAGAAAGAAGCCGCAGTACAAGACT 32 21 0 CAGAAAGAAA 0.75981 -32 AGAACCTTCAATGAAAAATACTTTACATTTATATT 35 113 0 ATGAAAAATA 0.738818 -91 TTGATTGTACTTGAAAAAAGCTTCAAGCGAAAAGG 36 52 1 TTGAAAAAAA 0.753144 -65 ATACCGGGATAAGAAAAAAGGAGAATGTAGT 37 148 1 AAGAAAAAAA 0.948328 -21 TCTCCTCATTATGAAAAAATCATGAATAATGTATT 40 87 0 ATGAAAAAAA 0.941021 -164 ATGTTAGCAGATGAAAGAATGAAAATCAACGCTTA 40 156 0 ATGAAAGAAA 0.780823 -95 CAAGGTTTGTCAGAAAAAATAACAAACTCATATCT 41 75 0 CAGAAAAAAA 0.93407 -93 ********* * Masking position 6 Map Score: 22.608 Number of sites scoring better than the average of aligned sites = 748 Number in coding regions = 566 Number in noncoding regions = 182 Number of orfs with sites within 600 bp upstream = 204 Fraction of orfs with sites within 600 bp upstream = 0.0327658 Motif number 2 GTCTTGATTTAAAAGGATTTTTAGTAGGATA 1 22 0 AAAAGGTTTT 0.719406 -279 GTCCTTTGGGCGGGAGCTTTTTGACATTCTG 1 264 1 CGGGAGTTTT 0.825894 -37 TTCGACAAGAAAGGAGTTTTTCACTT 2 63 1 AAGGAGTTTT 0.727386 -16 CTTATGTATTCAGAGGGTTTTGCGCCCTCTG 4 17 1 CAGAGGTTTT 0.906612 -128 CATGAATATACAAAAGTTTTTATTTTGTCTT 4 114 1 CAAAAGTTTT 0.411157 -31 TTCTGATAGAAGGAGGTATTTCTTACC 8 284 1 AGGAGGATTT 0.641817 -17 ACAACGAATGCGAGGGTTTTTCAACAAGCTG 9 21 0 CGAGGGTTTT 0.935273 -280 TCCTAGACTACAAGGGTTTTCAATCAAGCTG 9 110 1 CAAGGGTTTC 0.904711 -191 TCCTAGACTTCAAAGGTTTTCAATCACGCTG 10 89 0 CAAAGGTTTC 0.749856 -167 TAGCTCAATGCGAGGGATTTTTAACGATAAA 12 240 0 CGAGGGTTTT 0.935273 -61 ATTCGTATTTCAAGGGGATTCGATATAAAAG 13 11 0 CAAGGGATTC 0.755564 -290 AGAAAACTGTCGAGGGAATTTTA 15 49 1 CGAGGGATTT 0.824694 -13 GCCCCTTAGAAAGGGGCTTTTCTGTGAAGAA 21 56 0 AAGGGGTTTT 0.945537 -132 GCCCCTTTCTAAGGGGCTTTTCATATTTCAA 21 70 1 AAGGGGTTTT 0.945537 -118 TGAAAAGATAAAGGGGTTTTCTGAAG 26 6 0 AAGGGGTTTC 0.919703 -147 CGTATAGTCAAGGAGGTTTTT 36 1 0 AGGAGGTTTT 0.846244 -116 AATTGAGTAAAAGGGGAATTCAG 36 104 1 AAGGGGATTC 0.788537 -13 TGTGCCTAACCAGGGGCATTCCCTGCATCCA 37 37 0 CAGGGGATTC 0.86848 -132 ATAGTAGGGGCGGGAGTTTTTTTCATTTTCA 38 229 1 CGGGAGTTTT 0.825894 -72 AGCAGAAGTCAAAAGGTTTTTTTATAGTCTT 42 224 0 AAAAGGTTTT 0.717066 -77 AAAGCAAATGAGGGGGATTTTACA 44 129 1 AGGGGGTTTT 0.945745 -14 ****** **** Masking position 9 Map Score: 19.358 Number of sites scoring better than the average of aligned sites = 643 Number in coding regions = 434 Number in noncoding regions = 209 Number of orfs with sites within 600 bp upstream = 147 Fraction of orfs with sites within 600 bp upstream = 0.0236107 Motif number 3 CCTATCCTATGAGGAGAAGAAAGCATGTAGA 3 70 0 GAGGGAAGAA 0.975763 -86 ATTCTTCATTGAGGGGATAAAATTTCAGTTC 5 268 0 GAGGGATAAA 0.872615 -33 TTTTCAAACAGAGGGGATGGATCGAAATATG 8 159 0 GAGGGATGGA 0.935679 -142 GTAGTCTAGGAAGGGGGAGCATTGGAGCGGA 9 90 0 AAGGGGAGCA 0.78328 -211 TATATTTGTTAAGGTGATGAATT 11 288 1 AAGGGATGAA 0.923061 -13 TGAGCTATCCGGGGTGAAAAACATCGGTGAA 12 264 1 GGGGGAAAAA 0.867234 -37 AATGCGATGAAGGGAGAAGAAGTC 16 56 1 AGGGGAAGAA 0.919615 -14 TAATCAATCCGGGGCGGAGAAATTTCTTAAT 18 22 0 GGGGGGAGAA 0.95757 -94 ACATAATGATGGGGTGGAGAAT 18 104 1 GGGGGGAGAA 0.95757 -12 ATCCTTTTGGGAGGAGGTGAAAGGC 22 286 1 GAGGGGTGAA 0.959461 -15 CTCAAAGTGTAAGGAGAAGGACAGGTGCTGC 30 38 0 AAGGGAAGGA 0.875491 -34 TTACACTTTGAGGGAGGTGAACACA 30 57 1 AGGGGGTGAA 0.870555 -15 AGTGCTAACAGAGGTGATGATG 31 108 1 GAGGGATGAT 0.730079 -12 TGTATCTTAGGAGGTGAAACAC 35 2 0 GAGGGAAACA 0.73378 -202 AATAGAGAACAAGGAGATAAAG 40 2 0 AAGGGATAAA 0.722211 -249 TTTTCATAATGAGGAGAAGGATATTTGAACT 40 105 1 GAGGGAAGGA 0.948789 -146 **** ****** Masking position 6 Map Score: 14.8432 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 361 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 130 Fraction of orfs with sites within 600 bp upstream = 0.0208802 Motif number 4 GGTTTTTCAACAAGCTGAAAGCCTCAG 9 7 0 CAGCTGAAAG 0.982327 -294 GGTTTTCAATCAAGCTGAAAGAATGTTAAGG 9 124 1 CAGCTGAAAG 0.982327 -177 GGTTTTCAATCACGCTGAAAAGATGACAAAA 10 75 0 CAGCTGAAAA 0.97201 -181 GGTTTGCCTACACGCTGAAACTTGGCTTGAA 10 192 1 CAGCTGAAAC 0.914424 -64 ATCTCTTGCATAGGCTGAAAATAAAAATTCC 13 71 0 TAGCTGAAAA 0.814602 -230 CGATCTAAAATCAGCTGAAAAGCTGATTTTT 17 141 1 TCGCTGAAAA 0.817428 -96 GCACATATGCCCCGCTAAAAGCAAAGTGAAT 21 124 0 CCGCTAAAAG 0.918541 -64 CCTTTATTGTCCAGCGGAAAAAATATTTTGT 26 40 1 CCGCGGAAAA 0.917896 -113 CTGAATAAATCATGCTAAAAAGAGAACCTTC 35 139 0 CAGCTAAAAA 0.873637 -65 AAAAAAGCTTCAAGCGAAAAGGATAGGTAAA 36 65 1 CAGCGAAAAG 0.77758 -52 GAACCCGCCCCAGGCTGAAAGCGGATCCCAT 38 37 1 CAGCTGAAAG 0.982327 -264 CCGGAGGTTTCCTGCTGAACGCGTGAATAAC 38 91 1 CCGCTGAACG 0.899327 -210 TTATCAAATTCCTGCTGAAAACGCAGATATG 41 51 1 CCGCTGAAAA 0.972517 -117 ** ******** Masking position 8 Map Score: 15.8053 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 380 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 5 TGATAAACAAAAGGTGTTTCACGT 2 5 1 AAACAAAAGG 0.827648 -74 TCTTGTCGAAACACAAAAGGTGTTCGACGA 2 43 0 ACACAAAAGG 0.845296 -36 TTGTGTTTCGACAAGAAAGGAGTTTTTCAC 2 57 1 ACAAGAAAGG 0.952356 -22 AAAATATCAGAAAATAAAGATATTGACTTA 6 87 1 AAAATAAAGA 0.713575 -140 TCTTACAATTAAACAAAAGGATATATGGGA 6 128 1 AAACAAAAGG 0.827648 -99 CCAGAAAAAACACGAAAGGGGCAATGGGC 7 10 1 ACACGAAAGG 0.932204 -20 CTCTAGTTTTAAGCGAAAGAAAAACTTGGC 10 226 0 AAGCGAAAGA 0.731833 -30 AGAACATGATACAATAAAGACAATCAAATC 11 136 1 ACAATAAAGA 0.739224 -165 TTTTTTTCTGAAAAGAAAGGTATGTTTAGA 11 179 1 AAAAGAAAGG 0.946142 -122 AAATAAACCCAAAAGAAAGACTTCTTTTGG 14 132 0 AAAAGAAAGA 0.885374 -84 ATTATAGCATAAAAAAAAGAATTGGCTGTA 19 60 0 AAAAAAAAGA 0.754261 -103 GAGAGCAAGTAAGAGAAAGACAATTAAACG 22 188 0 AAGAGAAAGA 0.798681 -113 CGGAGTCGAAACAAGAAAGGTGGTAACAG 25 106 1 ACAAGAAAGG 0.952356 -19 AGGAAATGAAAAGATAAAGGGGTTTTCTGA 26 13 0 AAGATAAAGG 0.744265 -140 TTTCCGCTGGACAATAAAGGAAATGAAAAG 26 30 0 ACAATAAAGG 0.865722 -123 TCAATGTAAAACAAGAAAGAGAAAAGTTCC 33 46 0 ACAAGAAAGA 0.897841 -88 TACCAAAGTAAAGAAAAAGGAGTTGGGCTT 43 93 1 AAGAAAAAGG 0.781924 -20 ********** Masking position 6 Map Score: 14.701 Number of sites scoring better than the average of aligned sites = 491 Number in coding regions = 353 Number in noncoding regions = 138 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 6 ATAACGAAAAAAACAGAGGGCGCAAAACCC 4 31 0 AAACAGAGGG 0.940529 -114 TCCCCAAAATAAAAAGCGAGGATGTGATCA 5 161 1 AAAAAGCGAG 0.825348 -140 CGGTTTATTGAAAAAGACGGATATATACTG 5 205 1 AAAAAGACGG 0.87986 -96 ACCAAACAGCCGGCTGACCAGGC 6 4 1 AAACAGCCGG 0.971642 -223 CGCAGCAAAAAAACAGCCTGGTCAGCCGGC 6 19 0 AAACAGCCTG 0.749592 -208 ATATTTTATAAAAAAGCGGTAAATCACTGT 6 64 0 AAAAAGCGGT 0.860206 -163 TAATATTTTCAAACAGAGGGGATGGATCGA 8 165 0 AAACAGAGGG 0.940529 -136 ATACTAGGACAAAAAGACAGCGAGACTGGG 17 208 1 AAAAAGACAG 0.617839 -29 CATTTGCTTTTAACAGCGGGGACAGCCAGC 19 11 0 TAACAGCGGG 0.890454 -152 AAATGCTCGCAAACAGCGGGAGGATACAGC 19 36 1 AAACAGCGGG 0.975489 -127 TAACACATATAAAAAGCCATATCAAGCATT 22 90 0 AAAAAGCCAT 0.539052 -211 AGTTTTTCTTAAAAAGCCGTTTAATTGTCT 22 171 1 AAAAAGCCGT 0.841208 -130 TTGAGAGTGCTAACAGAGGTGATGATG 31 103 1 TAACAGAGGT 0.481457 -17 ********** Masking position 5 Map Score: 8.74299 Number of sites scoring better than the average of aligned sites = 1207 Number in coding regions = 1062 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 136 Fraction of orfs with sites within 600 bp upstream = 0.0218439 Motif number 7 CTTGAAACCTCCTAATCAGAATGTCAAA 1 283 0 ACCTCCTTCA 0.865929 -18 ATTTATAAAAACCTCATGTTCTGGGTCAAAAG 5 106 1 ACCTCATTCT 0.939976 -195 CAACATAACCTCCTGTTATTTGTGTATAC 6 208 0 ACCTCCTTAT 0.968375 -19 GGTAAGAAATACCTCCTTCTATCAGAATGAAT 8 279 0 ACCTCCTTAT 0.968375 -22 CGATTTTTTTAACTCATAGTATAATTAAAGGT 9 231 1 AACTCATTAT 0.80452 -70 AAATAGGATAAACTCATTATATTTGTTAAGGT 11 271 1 AACTCATTAT 0.80452 -30 TCTCTAACTCAACTCATTCTAATTGCTTTATA 14 47 0 AACTCATTAA 0.416665 -169 AGCTCAACTAAACTCATTCTCTGCTACCCTAT 14 79 0 AACTCATTCT 0.833385 -137 TTGAATAACCTCCTGCTATGTAA 29 5 0 ACCTCCTTAT 0.968375 -19 AATCTATCACTCCTACTATTAAACGCAAA 33 115 0 CACTCCTTAT 0.739497 -19 GTGTTTCACCTCCTAAGATACAACCTGTA 35 8 1 ACCTCCTGAT 0.898865 -196 AAAAACCTCCTTGACTATACGGTAAC 36 5 1 ACCTCCTACT 0.798399 -112 AGGTAGACCTCCTTATGTATTCCTTATA 38 283 0 ACCTCCTTGT 0.877364 -18 AGCGGCGCTTGCCTCCTTGTCTGGATATCGTG 42 125 1 GCCTCCTTCT 0.854432 -176 TGTAAAATCCCCCTCATTTGCTTTCTTCTTTT 44 121 0 CCCTCATGCT 0.568872 -22 ******* *** Masking position 7 Map Score: 7.52102 Number of sites scoring better than the average of aligned sites = 240 Number in coding regions = 117 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 8 AAGTCTTTCTTCCGTTTCTCAGTGTATTTC 3 110 1 TCCGTTTCTC 0.918536 -46 TTCGCTCCGCTCCAATGCTCCCCCTTCCTA 9 85 1 TCCAATGCTC 0.969089 -216 TTCGCTGTGCTCCGATGCTCGCCCTTCCTA 10 115 0 TCCGATGCTC 0.980118 -141 CACGTGCGGTTCCATTGCTCACCCATAGTC 13 197 0 TCCATTGCTC 0.969089 -104 CTGTCAGGAAGCCCATGCTCTTGAAATATG 21 91 0 GCCCATGCTC 0.899885 -97 AAAGCGTCAATCCCTTGCTCGTCAAGGATT 22 58 0 TCCCTTGCTC 0.9713 -243 TTATAAAATATCCAATGATCGTTAATGATG 38 258 0 TCCAATGATC 0.777822 -43 TCCGTTTCTCCTTTTTGTAA 41 158 0 TCCGTTTCTC 0.918536 -10 ********** Masking position 6 Map Score: 4.81794 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 56 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 GCCGGCACAATATATGAAGCGATTGCGCAAATGAAAGCA 8 37 1 TTTAGTGCCA 0.781642 -264 GCGGAGCGAATGTAGAATTCGTGAGCACCGACGCGCAGA 9 56 0 TTGTGAGCCC 0.934566 -245 ACCTTTGAAGTCTAGGAAGGGCGAGCATCGGAGCACAGC 10 103 1 TTGAGAGCTC 0.670191 -153 GCACAGCGAATGTTGAATTCGTGAGCACCGAAGCACAGG 10 135 1 TTGTGAGCCC 0.934566 -121 TTAACTGATATATTTCGATTGTATGCGCCTTTTTTCTAA 11 204 0 TTTAGTGCCC 0.965861 -97 ATTTCAGCTCTGTCTACAGAGTCAGCTCCTAGCTCAACT 12 180 0 TTTAGAGCCC 0.9839 -121 TGTTTCGGTATACCTGGTATGACAGCACCCTTAAGAGCT 25 42 1 TCTTGAGCCC 0.829261 -83 GTTCTTTTTAGTGTCAGCCCCGCTTCCGGAG 28 3 1 TTTAGAGCCC 0.9839 -197 TATGAAATGTGTTCTTTTCGGTCAGCTCCGGAAGCGGGG 28 28 0 GTTTGAGCCC 0.816928 -172 TTTGGCAAATTTTATCGAAGGGCAGCACCTGTCCTTCTC 30 17 1 TTTAGAGCCC 0.9839 -55 TTAAGTCATTTGGATGCAGGGAATGCCCCTGGTTAGGCA 37 27 1 TGTAGTGCCC 0.829261 -142 GCAGAACAGGTTTTTTCAGCGATTGCACACGATATCCAG 42 145 0 TTTAGTGCCA 0.781642 -156 TGTGAACTTCTGTTTTCACGCATAGCCCCCTATCGTCTA 43 27 0 TTTACAGCCC 0.856444 -86 * * * * * *** ** Masking position 16 Map Score: 6.9379 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 149 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 10 AATTTTAATTATTCTTTTTCAGGGCGTATGTAT 1 140 1 ATCTTTCAGG 0.956842 -161 TCCGTTTCTCAGTGTATTTCAGGATAATGAAGA 3 120 1 ATGTTTCAGG 0.74165 -36 AAAAGCGGTAAATCACTGTCCGGCCGGGATTCT 6 50 0 ATCTGTCCGG 0.923883 -177 AAACCCTCGCATTCGTTGTCAGGTCTGCGCGTC 9 33 1 ATCTGTCAGG 0.981115 -268 AAACCTTCGCATTCGTTGTCAGGCCTGTGCTTC 10 164 0 ATCTGTCAGG 0.981115 -92 CTGATTCTTTCTTCATATTCAGGTAAGT 11 6 0 CTCATTCAGG 0.877221 -295 AATCTGTGTCCGTCTAATTCAGGAAGCACCTCG 12 129 0 CTCATTCAGG 0.877247 -172 AGCAAAGTGAATGCCCTGTCAGGAAGCCCATGC 21 103 0 AGCTGTCAGG 0.9155 -85 ATGATTAGAAAGTCAAAGTCAGGCATCTCTTGG 28 77 1 ATCAGTCAGG 0.95921 -123 GCGGCGCTTGCCTCCTTGTCTGGATATCGTGTG 42 126 1 CTCTGTCTGG 0.853609 -175 * ** ******* Masking position 9 Map Score: 4.77093 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 90 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 11 CAATATAAATAAAGTAAAGAAGGTAAAAATT 8 251 1 AAGTAAAGAA 0.838715 -50 ACTTACCTGAATATGAAGAAAGAATCAGCT 11 10 1 ATATGAAGAA 0.698664 -291 CATTAGAGAAAATGTGGAGAATATGAGAAAA 15 24 1 ATGTGGAGAA 0.847264 -38 AAGGGGCTTTTCTGTGAAGAAATAAAGTGTA 21 46 0 TTGTGAAGAA 0.878641 -142 TTTGTCCAACAAAGTGAAGAATTTCTGTATG 22 125 0 AAGTGAAGAA 0.919926 -176 ATCAGACTGAACTGTGAAGAAATGATAATAA 22 242 1 ATGTGAAGAA 0.969982 -59 GCGGCTTCTTTCTGTAAAGAAGGTGAATCCG 32 32 1 TTGTAAAGAA 0.766199 -21 TATCAATAGGATTGTAAAGATTCAATGTAAA 33 66 0 ATGTAAAGAT 0.628825 -68 AATTTGTTCTATTGTGAAGAAGATTTAACCT 35 53 0 ATGTGAAGAA 0.969982 -151 TTGCAATATAAATGTAAAGTATTTTTCATTG 35 109 1 ATGTAAAGTA 0.650162 -95 ATAGGTACTTAATGTGAAGGAGGCCCCTGT 35 184 1 ATGTGAAGGA 0.858862 -20 GCGCTTTACCAAAGTAAAGAAAAAGGAGTTG 43 87 1 AAGTAAAGAA 0.838715 -26 * ********* Masking position 8 Map Score: 4.28911 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 164 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 12 TCAGAATGTCAAAAAGCTCCCGCCCAAAGG 1 266 0 AAAAAGCTCC 0.752661 -35 AAGTGAAAAACTCCTTTCTTGTCG 2 65 0 GAAAAACTCC 0.845673 -14 CAAAAAACGCTAGCGGGTTTT 3 2 1 AAAAAACGCT 0.833842 -154 AACTTTTATAGAAAAACGCTGTAAGGGACA 3 41 0 GAAAAACGCT 0.889742 -115 GAAAAATTAATAAAAGCGCTTACAGATAGA 6 174 1 TAAAAGCGCT 0.413981 -53 TCAGCTTGTTGAAAAACCCTCGCATTCGTT 9 20 1 GAAAAACCCT 0.697012 -281 AGCCGGCAACATATAACGCCGCCGGTTTTT 17 33 1 ATATAACGCC 0.478723 -204 TTTCTTCACAGAAAAGCCCCTTTCTAAGGG 21 55 1 GAAAAGCCCC 0.884982 -133 CTTGAAATATGAAAAGCCCCTTAGAAAGGG 21 72 0 GAAAAGCCCC 0.884982 -116 AGTAACACATATAAAAAGCCATATCAAGCA 22 92 0 ATAAAAAGCC 0.361967 -209 ACTCACCCAAAAAAAGCGCCAAAAACTTCA 31 15 0 AAAAAGCGCC 0.943772 -105 GATTGTACTTGAAAAAAGCTTCAAGCGAAA 36 54 1 GAAAAAAGCT 0.42927 -63 CTGAACGCGTGAATAACGCCATTAGGCAGT 38 105 1 GAATAACGCC 0.820158 -196 ATGAAAATGAAAAAAACTCCCGCCCCTACT 38 231 0 AAAAAACTCC 0.773128 -70 GCATCATCTTAAAAAACGCC 42 1 0 AAAAAACGCC 0.949486 -300 CTGGCTCTTTATAAAACGCCTTGCGAAAAA 42 62 1 ATAAAACGCC 0.85889 -239 CTTTACTTTGGTAAAGCGCCCATACAAAAA 43 76 0 GTAAAGCGCC 0.897329 -37 ********** Masking position 5 Map Score: 11.022 Number of sites scoring better than the average of aligned sites = 1053 Number in coding regions = 916 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 13 ATACAAAAGTTTTTATTTTGTCTTGGAGGAAAT 4 121 1 TTTATTTTCT 0.545381 -24 TGAACTGAAATTTTATCCCCTCAATGAAGAATT 5 267 1 TTTATCCTCA 0.571039 -34 AAAACTGTTTTAGGATTTTGTCAACATTCTGAG 10 32 0 TAGATTTTCA 0.650209 -224 GTTTTCGTTTTAGGATTTTGTCATCTTTTCAGC 10 60 1 TAGATTTTCA 0.650209 -196 ATTTGATTGTCTTTATTGTATCATGTTCTATTA 11 132 0 CTTATTTTCA 0.777818 -169 TTATATAGTATTTTATCCTCTCATGCCATCTTC 14 163 1 TTTATCTTCA 0.913021 -53 TATCAGGAAATTGTATTGTTTCAATAAAAAAAT 17 166 0 TTTATTTTCA 0.933423 -71 TATGTATGAGTTTTATCTTTTCATTCGCTTACG 19 98 0 TTTATCTTCA 0.913021 -65 TACATTTAATTTCGATTCTAGCACATATGCCCC 21 142 0 TTGATTTGCA 0.741956 -46 CAGAAAACCCCTTTATCTTTTCATTTCCTTTAT 26 14 1 CTTATCTTCA 0.72384 -139 CTCACATAAATTAGATTGTATCATTTTGAATTA 28 155 0 TTGATTTTCA 0.920096 -45 ATACACTAGCTTAGATTATATCAATAGGATTGT 33 82 0 TTGATTTTCA 0.920007 -52 ATAGAACAAATTGTATTCTATCAAACACACCTT 35 72 1 TTTATTTTCA 0.933423 -132 AAATTTGCAGTTCTATCTTATCATAGTGAAGCT 39 25 1 TTTATCTTCA 0.913021 -56 TCTATTTGATTTGTATTATAGCATGCCAAACAT 40 27 1 TTTATTTGCA 0.777816 -224 AAGCGTTGATTTTCATTCTTTCATCTGCTAACA 40 157 1 TTCATTTTCA 0.725297 -94 ** **** * *** Masking position 6 Map Score: 7.88451 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 110 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 14 AAAAGCTCAAAACTGATTCTTGTTTTGAGCT 9 163 0 AACTGATTTT 0.897636 -138 CTTGAAGGTCAGCTGATTCTTTCTTCATATT 11 20 0 AGCTGATTTT 0.96983 -281 TTTTACCACTAGCTGATCATTTGTCACCTTT 11 243 0 AGCTGATCTT 0.908182 -58 TCAGCTTTTCAGCTGATTTTAGATCGTTGGG 17 136 0 AGCTGATTTA 0.869683 -101 TCAGCTGAAAAGCTGATTTTTTTATTGAAAC 17 151 1 AGCTGATTTT 0.96983 -86 ATATAGTATAAGCTGAGTTTTAGCAATATCA 37 115 1 AGCTGAGTTT 0.955813 -54 GATAACTATTAACTGAGTATTATATTAATTG 42 262 0 AACTGAGTTT 0.85509 -39 ******** ** Masking position 6 Map Score: 1.52291 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 50 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 CCCAAAGGACGAGAGCGGCGATAAGTGCAA 1 244 0 GAGAGCGGCG 0.904662 -57 CAGTTCACCGGCCAGCGGCACCGTAATCAG 5 244 0 GCCAGCGGCA 0.970008 -57 CAGAACAAAAACCGGCGGCGTTATATGTTG 17 39 0 ACCGGCGGCG 0.94572 -198 ATTTGCTTTTAACAGCGGGGACAGCCAGC 19 10 0 AACAGCGGGG 0.941827 -153 AATGCTCGCAAACAGCGGGAGGATACAGCC 19 37 1 AACAGCGGGA 0.856081 -126 TGGCTTTGCCATCTGCGGCAAGCGCAGCTT 24 22 0 ATCTGCGGCA 0.676499 -52 CGCAGTACAAGACTGCGGCGGCTT 32 5 0 GACTGCGGCG 0.973539 -48 ATTGTGCCTAACCAGGGGCATTCCCTGCAT 37 40 0 ACCAGGGGCA 0.851704 -129 TCCGCTTTCAGCCTGGGGCGGGTTCCTCTC 38 32 0 GCCTGGGGCG 0.904753 -269 TTCATAAGATAACAGCGGAGGTGCTCGGGT 40 229 1 AACAGCGGAG 0.85582 -22 TTGAGAGTTAGACAGCGGCGCTTGCCTCCT 42 112 1 GACAGCGGCG 0.987842 -189 ********** Masking position 5 Map Score: 6.07212 Number of sites scoring better than the average of aligned sites = 624 Number in coding regions = 580 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344