AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -icpxR6_bsub_opreg_300.orf -g0.435 -x5 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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 ybcO 300 ybcO #10 ybcP 66 ybcP #11 ybcQ 43 similar to hypothetical proteins #12 ybdB 64 similar to ABC transporter (permease) #13 ybdD 46 ybdD #14 ybdE 105 similar to hypothetical proteins #15 yczA 300 yczA #16 ycbL 96 similar to two-component response regulator [YcbM] #17 yclJ 212 similar to two-component response regulator [YclK] #18 yerE 264 similar to hypothetical proteins #19 yerF 61 similar to ATP-dependent DNA helicase #20 yerG 23 similar to DNA ligase #21 yerI 161 yerI #22 htrA 168 serine protease Do (heat-shock protein) #23 ykoG 300 similar to two-component response regulator [YkoH] #24 resD 80 two-component response regulator #25 resC 135 essential protein similar to cytochrome c biogenesis protein #26 resA 131 essential protein similar to cytochrome c biogenesis protein #27 ypuL 91 similar to hypothetical proteins #28 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #29 ypuI 54 similar to hypothetical proteins from B. subtilis #30 ypuG 280 similar to hypothetical proteins #31 ppiB 253 peptidyl-prolyl isomerase #32 yrkP 267 similar to two-component response regulator [YrkQ] #33 phoP 211 two-component response regulator #34 citH 43 malate dehydrogenase #35 citC 163 isocitrate dehydrogenase #36 citZ 300 citrate synthase II #37 yvqA 277 similar to two-component response regulator [YvqB] #38 yvrI 300 yvrI #39 yyxA 68 alternate gene name: yycK; similar to serine protease Do #40 yycJ 21 yycJ #41 yycF 300 similar to two-component response regulator [YycG] Motif number 1 AAGCCGATTTTTTTCATTTTTAGACAACATT 1 138 1 TTTTATTTTT 0.639326 -163 TTCGCTTTCTTTCTAAAAAAACTG 6 4 1 GCTTCTTTCT 0.800862 -191 AGTTTCTCTACTTTACTTTTTACAAACATTC 6 153 0 CTTTCTTTTT 0.774917 -42 CTTGTCAGCTTTTCTATTTTTAAAGGGTTAA 9 137 1 TTTCATTTTT 0.626302 -164 GTAAACCTCCTCTCAATTTTTGCATAGAGTC 9 278 0 TCTCATTTTT 0.822683 -23 TTGATATCCTCCTTTCTAACTCATCTG 15 284 0 TCCTCTTTCT 0.701508 -17 CTCTCAGCCTCCCTTTTTATGTAACCAT 18 8 1 CCTCCTTTTT 0.900113 -257 ACTGCCATATGCTCTCTTTTTTTATGAAAAA 18 127 1 GCTCCTTTTT 0.883117 -138 GTACCGTTTTCCGCACTTTTTCACAATTTCC 22 42 1 CCGCCTTTTT 0.838838 -127 TCCCATAATCTTTTCATTTTTATCCCACAGT 22 70 1 TTTTATTTTT 0.639326 -99 CGGTTTGGCCTGCCCTTTTTATCTTTATTC 25 116 0 CTGCCTTTTT 0.652797 -20 ATTTCACATTTCTTACTTTTTGAAGGTTATG 26 61 0 TCTTCTTTTT 0.947979 -71 TCAAGTATTATCTTACTTTTTTCAACCTTAA 27 61 0 TCTTCTTTTT 0.947979 -31 CGTTTACTCTCCCTTTTTCAGGGAGAGT 28 8 1 TCTCCTTTTT 0.945144 -115 GTTTAATGAATCGCGCTTTTTCATCATCATA 29 13 1 TCGCCTTTTT 0.90869 -42 TAGAGGCCGGGCGTTCTTTTTTCCTTTTATC 30 53 0 GCGTCTTTTT 0.821928 -228 TTGCTTCTGGTTTTCCTTTCTAAGAAGCACT 30 83 0 TTTTCTTTCT 0.76813 -198 TCAGGTTTCATTTTTATTTTTTAGTAAAGCT 31 118 1 TTTTATTTTT 0.639326 -136 TTGTATGCCTACTTTCTTTATTTTAAT 31 237 0 GCCTCTTTCT 0.507536 -17 ATGATTCTTGTTGTTATTTCTCGTGTGTCCT 32 233 0 TTGTATTTCT 0.340048 -35 AGCAAGCCTTTCTCTCTTTTTA 33 2 0 TCTCCTTTTT 0.945144 -210 TAATACAGCCTTTCTCTTTTTACTATAAATG 33 33 1 TTTCCTTTTT 0.861568 -179 ATCATAAACGTCTTTATTTCTTTTAAAAATG 33 72 1 TCTTATTTCT 0.71178 -140 AATACTTGCATCGTGCTTTTTAAGTAAGCCT 36 226 1 TCGTCTTTTT 0.913236 -75 TACATCTTCCTCGCTCTTTTTCTCTTCCTTT 37 132 1 TCGCCTTTTT 0.90869 -146 GCTCTTTTTCTCTTCCTTTCTTCCCTTAACC 37 144 1 TCTTCTTTCT 0.90168 -134 TCACATATTCTTTTCATTTTTATCCCACAAT 37 190 0 TTTTATTTTT 0.639326 -88 GAAAATACCTCCCTTCTTTTTCTGCAGTCAT 38 158 1 CCCTCTTTTT 0.709507 -143 GAAAGTAGTAGTTTACTTTTTTTTGCTTTCC 38 254 1 GTTTCTTTTT 0.742707 -47 TTTTTCTAAACCTTTATTTTTTTTATCTTTT 41 168 1 CCTTATTTTT 0.719614 -133 **** ****** Masking position 7 Map Score: 28.2994 Number of sites scoring better than the average of aligned sites = 1729 Number in coding regions = 1299 Number in noncoding regions = 430 Number of orfs with sites within 600 bp upstream = 432 Fraction of orfs with sites within 600 bp upstream = 0.0693864 Motif number 2 ACCGCCGTGAAAGGGCGGTGTCTTAACCGCTTGA 1 50 0 AAGGGTTCTT 0.870675 -251 TTGTCGAAGTAAGGGGGATTTTGTATATTATCCT 9 201 0 AAGGGTTTGT 0.879218 -100 ATTTTCTCTTAAGGGGGATTTTAT 10 53 1 AAGGGTTTAT 0.959444 -14 CTTCAGTCAAAAAGGCGTTTTGTAAGTCAAGGTC 12 30 1 AAGGGTTGTA 0.815847 -35 TAAAACGAGGAGAGGGGCTCTTTT 13 33 1 AGGGGTTTTT 0.953718 -14 CTTTGCATAGGACGGGGGTTTTTTGTGTTTCTTA 15 208 1 GAGGGTTTTT 0.830335 -93 GACGCGCCCCAGAGGCGGTCTTATCAATAAAAAT 17 31 0 AGGGGTTTAT 0.913522 -182 TTCTGTTTAAAATGGTGCTATTATATAAAAAAGC 17 167 1 AAGGGTTTAT 0.959444 -46 ATTCACTGAAAAAGGTGTTTTGATTCTTTTTTCA 18 151 0 AAGGGTTGAT 0.937698 -114 ACACAAATCAAGGGGAGGTATGTTGATGCTGGAA 21 95 1 AGGGGTTGTT 0.929134 -67 AGGTTGACCGAATGGTGTATTTTTTTGTGCGCTT 23 75 0 AAGGGATTTT 0.928534 -226 GGAAAGCACTAGGGGTGCTGTTTTGGCTGAGATA 23 176 0 AGGGGTTTTT 0.953721 -125 AAACGGCGTTTTTTTTAGATTTGGC 27 2 1 AAGGGTTTTT 0.978792 -90 GATAAATGGGAAAGGAGTATTGAT 32 1 0 AAGGGATGAT 0.809054 -267 AAATGATGTAAAAGGCGAATTGTCGGAATGTCCT 33 98 1 AAGGGATGTC 0.658607 -114 ACCCGCAAATAAAGGCGTTTTTTCGGGGAAATCA 36 16 1 AAGGGTTTTC 0.915048 -285 CAACACTCTTAAAGGGGAAATTTATTGAAAAGGA 36 267 1 AAGGGATTTA 0.662203 -34 AATTTATTGAAAAGGAGATGTTATAT 36 285 1 AAGGGTTTAT 0.959444 -16 GCAGAAAAAGAAGGGAGGTATTTTCCTATGGATC 38 149 0 AAGGGTTTTT 0.978792 -152 ** ** * * **** Masking position 11 Map Score: 24.2801 Number of sites scoring better than the average of aligned sites = 236 Number in coding regions = 166 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 3 AATGTCCTCCTCACAATGAGCAGGT 4 89 0 CCTCCTCACA 0.713843 -15 TCCTTACCTCCTCCCACAGTAAGCAC 5 82 0 CCTCCTCCCA 0.928664 -16 TACTAAACCTCCTATACACTTCCTACG 7 69 0 CCTCCTATAC 0.514414 -17 ACCTGCTTTCAGCCCCTTTTC 8 36 0 CCTGCTTTCA 0.892548 -11 AAGTAAACCTCCTCTCAATTTTTGCAT 9 284 0 CCTCCTCTCA 0.970556 -17 ATGTTTCGATACTCCTCTCTTGGTAACGGG 15 110 0 ACTCCTCTCT 0.5835 -191 TTGGCCGTCACCTCCTTTAAGAAACACAAA 15 229 0 CCTCCTTTAA 0.922699 -72 TTGATATCCTCCTTTCTAACTCATCTG 15 284 0 CCTCCTTTCT 0.935996 -17 CTGCTTCTTCCTTTCCTCTTCAA 20 8 0 CTTCCTTTCC 0.695839 -16 ATTTGACCATCCTCTCCCGTCCCTATA 23 284 0 CATCCTCTCC 0.792237 -17 GTTTTCCCCCTGCTTTCCTTCTGTTACT 24 63 0 CCTGCTTTCC 0.896004 -18 TGCCCCCTTCCCCCTATTGCAG 26 120 0 CCCCCTTCCC 0.650956 -12 GGTGCTTCCTCCTTTAATGTGCTTTTA 30 8 1 CCTCCTTTAA 0.922699 -273 TTCTGTACAAACTCCTTCAAAACAGGATAT 30 168 1 ACTCCTTCAA 0.406387 -113 AGCAGTTTGACCTCCTTCAATTTCACAAGC 31 11 1 CCTCCTTCAA 0.824995 -243 ATCAATACTCCTTTCCCATTTATCAC 32 7 1 ACTCCTTTCC 0.882723 -261 GTCGGAATGTCCTGCTTTCGCTAAAATAAA 33 119 1 CCTGCTTTCG 0.587793 -93 GTTCTTACACTCCTTTAACGGTTATTCA 37 9 1 ACTCCTTTAA 0.634162 -269 GGCTCTTCACATCCTTTCAACGTCATTAT 37 259 0 CATCCTTTCA 0.847862 -19 TAGGAAAATACCTCCCTTCTTTTTCTGCAG 38 155 1 CCTCCCTTCT 0.720109 -146 ATTCCATCCTTTCCAAGAACGTTA 39 55 0 CATCCTTTCC 0.852517 -14 TTTATTGAAACCTCCCCTCACCGGAGTGCG 41 64 0 CCTCCCCTCA 0.852924 -237 ********** Masking position 5 Map Score: 18.5989 Number of sites scoring better than the average of aligned sites = 656 Number in coding regions = 357 Number in noncoding regions = 299 Number of orfs with sites within 600 bp upstream = 308 Fraction of orfs with sites within 600 bp upstream = 0.04947 Motif number 4 GCGGTTAAGACACCGCCCTTTCACGGCGGTAAC 1 54 1 CACCCTTTCA 0.726607 -247 TAAACCTCCTCTCAATTTTTGCATAGAGTCTAT 9 275 0 CTCATTTGCA 0.747771 -26 TTATAAAACACACACGTTTTTCAATTACAATAA 16 14 1 CACATTTTCA 0.979833 -83 ATAGATTGTTCATATTTTTTTCATACCTTTGGA 17 89 0 CATATTTTCA 0.923005 -124 TCGGCAGGAGCACACATTTTTCACCAGATTCCT 18 73 0 CACATTTTCA 0.979833 -192 AAAGAATCAAAACACCTTTTTCAGTGAATAACG 18 156 1 AACATTTTCA 0.900444 -109 TGATTGTTTTCACACGATTTCCAGCATCAACAT 21 114 0 CACATTTCCA 0.852587 -48 CGACTCAGTCCTTTCATATACAATAT 22 4 1 CTCACTTTCA 0.861467 -165 CACAATTTCCCATAATCTTTTCATTTTTATCCC 22 63 1 CATATTTTCA 0.923005 -106 AAACAACGAAATCATTTTTTTCATATAGGGACG 23 261 1 ATCATTTTCA 0.822575 -40 CAAGTATTATCTTACTTTTTTCAACCTTAACAA 27 58 0 CTTATTTTCA 0.86004 -34 CATCTCACCATTTTCAAGTATCACTC 30 265 0 CTCATTTTCA 0.961396 -16 CATTGTAAGGCTCAAGTTTTTCAGATCCGCACT 32 47 0 CTCATTTTCA 0.961396 -221 TGATGCTCGCCACAAATTTGTCACATTTTCTAA 32 131 0 CACATTGTCA 0.84495 -137 ATATAACATCTCCTTTTCAATAAATTTCC 36 282 0 CATCTTTTCA 0.724236 -19 CATAATTTCACATATTCTTTTCATTTTTATCCC 37 195 0 CATATTTTCA 0.923005 -83 TTAGAAAAAAAACACATGTTTCACCTTTATCGC 41 144 0 AACAGTTTCA 0.693101 -157 TCATCTATATAACATTCGTTTCATCACTTATGG 41 244 0 AACAGTTTCA 0.693101 -57 **** ****** Masking position 9 Map Score: 16.4156 Number of sites scoring better than the average of aligned sites = 364 Number in coding regions = 301 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 5 CGGAAATTCTTTTCATAAACGAATATCAAG 1 170 1 TTTCATAAAC 0.959385 -131 AGCCAATCATTTACATAAAAAAACTGCCAG 6 45 0 TTACATAAAA 0.735991 -150 ACGCGGTTTCTTTCATAAATCAATTCCAGC 7 42 0 TTTCATAAAT 0.823256 -44 TTAGTTTTTATTTCATCAACTAGAAATAGA 17 117 0 TTTCATCAAC 0.788635 -96 GTGGAAATGGTTACATAAAAAGGGAGGCTG 18 15 0 TTACATAAAA 0.735991 -250 TTGATTCTTTTTTCATAAAAAAAGAGAGCA 18 136 0 TTTCATAAAA 0.894037 -129 ACATACGTTCTATCATAAACCAAATCCGTA 19 18 0 TATCATAAAC 0.937969 -44 CTGTTAATTGTAACATAAAAACCCTTGTGC 21 34 0 TAACATAAAA 0.640749 -128 GACTCAGTCCTTTCATATACAATATGAAGT 22 12 1 TTTCATATAC 0.715756 -157 GACTTGAGTTTATCATAAACAAAAACTGTG 22 95 0 TATCATAAAC 0.937969 -74 GAGCATCAGCTTTCATAAATTGGTAAGATT 32 156 1 TTTCATAAAT 0.823256 -112 ATGAAAGCGCTATCATAAACGTCTTTATTT 33 61 1 TATCATAAAC 0.937969 -151 CCCTTAACCATATCATAAACAAACATTGTG 37 166 1 TATCATAAAC 0.937969 -112 ********** Masking position 5 Map Score: 10.8657 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 129 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 6 ATCGGCTTCTGCAAGAGAAACCGATTTGTT 1 116 0 GCAAGAGAAA 0.726405 -185 CTTGGTAACGGGGAGAGAAACCCGGCATCG 15 92 0 GGGAGAGAAA 0.880851 -209 AATTCACATAGCGCGGAAAAACGGAAAAAG 18 199 0 GCGCGGAAAA 0.942657 -66 TTGTGAAAAAGTGCGGAAAACGGTACACTT 22 38 0 GTGCGGAAAA 0.857949 -131 CTGAGATAAAGCGCGGAAGAAACGCGCTTT 23 154 0 GCGCGGAAGA 0.924858 -147 TTTCATATAGGGACGGGAGAGGATGGTCAA 23 279 1 GGACGGGAGA 0.787393 -22 GCGCAGAAGCGGGAGAAAAAGCCTTTGCTT 30 108 0 GGGAGAAAAA 0.821349 -173 TTTTAGTAAAGCTCGGGAGATTCGTTTTCC 31 136 1 GCTCGGGAGA 0.733323 -118 GAATCATGAGGTGAGAGAGAC 32 257 1 GTGAGAGAGA 0.738033 -11 GCAAGGAAAAAGCCTAAAAC 34 1 1 GCAAGGAAAA 0.813099 -43 TAAATTGAATGTTAGGAAAAATCATTTTAT 35 82 1 GTTAGGAAAA 0.461398 -82 TTCTTTTTGGGGGAGAGAAATACTTGCATC 36 208 1 GGGAGAGAAA 0.880851 -93 GAGAAAAAGAGCGAGGAAGATGTAGGATGA 37 126 0 GCGAGGAAGA 0.926279 -152 AGGGAAGAAAGGAAGAGAAAAAGAGCGAGG 37 140 0 GGAAGAGAAA 0.657123 -138 ATTGCAATCAGCGCGGGAAACCCCAAATTG 38 85 1 GCGCGGGAAA 0.963549 -216 ATGTATGTAAGTGAGGAAAACCGATAAAAC 38 187 1 GTGAGGAAAA 0.860445 -114 ********** Masking position 8 Map Score: 11.5867 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 397 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 7 AAATCGGTTTCTCTTGCAGAAGCCGATTTTT 1 119 1 CTTTGCAGAA 0.876671 -182 AATCAAATTTCTTCTGGCGAAGATGGGAATA 2 23 1 CTCTGGCGAA 0.979947 -62 ATTCATTCCTCCTGGAGAATACGAGGATT 2 66 0 CTCTGGAGAA 0.941232 -19 CGATCCTCCCCTGATGCCGAATGGGCTTCTG 15 35 1 CTATGCCGAA 0.924811 -266 AAAATGTGTGCTCCTGCCGATACAGGACTCA 18 86 1 CTCTGCCGAT 0.980293 -179 AATATTTTCACTTCTGCCGAAACACAAATCA 21 74 1 CTCTGCCGAA 0.989564 -88 CCCCTTCCCCCTATTGCAGATCCATTCAATT 26 108 0 CTTTGCAGAT 0.78853 -24 AATAGATAAACAACTGGCGATAAAGGTGAAA 41 128 1 CACTGGCGAT 0.80163 -173 TTTGATTTTCCTCCTGCCGAATGACTTCATT 41 277 0 CTCTGCCGAA 0.989564 -24 ** ******** Masking position 5 Map Score: 7.75232 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 122 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 AATATCTTTAAAATACCTGCTCATTGTGAG 4 75 1 AAATACCTGC 0.82314 -29 TTTCTTTCTAAAAAAACTGCCGGCTGACGC 6 16 1 AAAAAACTGC 0.918602 -179 CATTTACATAAAAAAACTGCCAGCGTCAGC 6 38 0 AAAAAACTGC 0.918602 -157 TGATTTATGAAAGAAACCGCGTAGGAAGTG 7 50 1 AAGAAACCGC 0.710753 -36 TTCTCAAATTAAAAACCCGCTAAAGAGC 8 9 0 AAAAACCCGC 0.977291 -38 GATAATATACAAAATCCCCCTTACTTCGAC 9 203 1 AAAATCCCCC 0.834185 -98 ATAAAATCCCCCTTAAGAGAAA 10 55 0 AAAATCCCCC 0.834185 -12 AAGAAACACAAAAAACCCCCGTCCTATGCA 15 211 0 AAAAACCCCC 0.966652 -90 TTGGTAAAATAAAAAACTGCATATCCTAAG 23 21 1 AAAAAACTGC 0.918602 -280 GCCAAATCTAAAAAAAACGCCGTTT 27 6 0 AAAAAAACGC 0.50611 -86 AATAAAAACCTCCCAGTATGTAA 35 151 0 AAAAACCTCC 0.947542 -13 CAAAAACCCGCAAATAAAGGC 36 2 1 AAAAACCCGC 0.977291 -299 GATTTCCCCGAAAAAACGCCTTTATTTGCG 36 19 0 AAAAAACGCC 0.66876 -282 CTTCCTCTATAAAAACCTGATCCATAGGAA 38 131 1 AAAAACCTGA 0.602759 -170 ATCCATAGGAAAATACCTCCCTTCTTTTTC 38 150 1 AAATACCTCC 0.758154 -151 ********** Masking position 2 Map Score: 15.0539 Number of sites scoring better than the average of aligned sites = 661 Number in coding regions = 469 Number in noncoding regions = 192 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 9 ACAAGAAAATATTCAAAACATAAGTGGAAAATTA 9 71 1 ACAAACATAG 0.884057 -230 TTTTTATAAAACACACACGTTTTTCAATT 16 6 1 AAAAACACAG 0.974329 -91 TTACAAAATCAAAAAACACACACGTAATTACACT 16 46 0 AAAAACACAG 0.974329 -51 GTCCAAAGGTATGAAAAAAATATGAACAATCTAT 17 88 1 AAAAAAATAG 0.649281 -125 TCACCCGCCTATACAAAACATACGTTCTATCATA 19 31 0 ACAAACATAG 0.884057 -31 TTTTTATTTTACCAAAAAAACAGGA 23 2 0 AAAAAAACAG 0.867746 -299 TGGGACAGCGATTAAATACACAAGAAAGGCCGCA 25 59 0 AAAAACACAG 0.974329 -77 TGTACAGAATATTCAAAACACAAGAGGTGTTTGC 30 143 0 ACAAACACAG 0.964316 -138 AACGATATATAGTAAGGACACACGAGAAATAACA 32 219 1 AAAGACACAG 0.887833 -49 AAAGGTTTAGAAAAAAAACACATGTTTCACCTTT 41 149 0 AAAAACACAG 0.974329 -152 * *** ***** * Masking position 8 Map Score: 8.87125 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 23 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 10 ATTTCCGGAATGTTGTCTAAAAATGAAAAAA 1 146 0 TGTTTCTAAA 0.809752 -155 ACAGATAGGATTTTGTCAAAAGAAGGTAACA 1 229 0 TTTTTCAAAA 0.76788 -72 TTTCAGCCCCTTTTCTCAAATTAAAAACCCG 8 20 0 TTTTTCAAAT 0.677297 -27 CGGTCCATTATGTTATAAAAATTCTGATGCC 9 16 0 TGTTTAAAAA 0.828186 -285 AATATTTTCTTGTTCTATAAACAAAACGTCA 9 53 0 TGTTTATAAA 0.755023 -248 AACGTGTGTGTTTTATAAAAA 16 1 0 TTTTTAAAAA 0.821762 -96 TTTGATGCTTTTTTATATAATAGCACCATTT 17 176 0 TTTTTATAAT 0.49265 -37 GTTACTTTCATTTTATCAAATCGTGAGAAAG 24 38 0 TTTTTCAAAT 0.677297 -43 ATTTGTCACATTTTCTAAAAAAAATGATGAC 32 118 0 TTTTTAAAAA 0.821762 -150 AAAAATAAAATGTTTTCTAAATATGAATTAC 35 124 1 TGTTTCTAAA 0.80977 -40 CCTTTAAGAGTGTTGTAAAAACATGAGGCTT 36 251 0 TGTTTAAAAA 0.825361 -50 TAAAGTTATCTTTTTTAAAAAAAGTTGACCA 41 90 1 TTTTTAAAAA 0.752406 -211 AACATGTGTTTTTTTTCTAAACCTTTATTTT 41 157 1 TTTTTCTAAA 0.804843 -144 **** ****** Masking position 9 Map Score: 6.86139 Number of sites scoring better than the average of aligned sites = 451 Number in coding regions = 293 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 11 CGAATATAACAGGTGGGAGATGAGAGGA 1 283 1 AGAGTGAGAG 0.984983 -18 CATTTGAGAATAGGGAGTTGAGCGTATTTGCTTA 10 9 1 AGAGTGAGCG 0.988297 -58 TTTTTCAGTGAATAACGAGATTAACGGCTTTTTCCG 18 172 1 AGAGTTAACG 0.808194 -93 GAGTGATGTCATGGCAGAGCTGAGCGGAAATTTTCT 25 20 1 AGAGTGAGCG 0.988297 -116 AAAAAGTAAGAAATGTGAAATGAACGTGCAATGATA 26 71 1 AGAATGAACG 0.894331 -61 AAGTAAGATAATACTTGAGGTGAAAGAC 27 74 1 AGAGTGAAAG 0.970917 -18 TAACAACAAGAATCATGAGGTGAGAGAGAC 32 248 1 AGAGTGAGAG 0.984983 -20 AAAACTAGCCATAAAGGAGAAGAGAGAC 34 26 1 AGAGAGAGAG 0.911816 -18 AATAGAACTAATGACAGAACTGAAAGATCATGCAA 38 10 0 AGAATGAAAG 0.867967 -291 * *** ****** Masking position 8 Map Score: 4.8245 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 58 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 TCAGATTCATATATTCCCATCTTCGCCAGA 2 35 0 ATATTCCCAT 0.76747 -50 ACATTATAACAAATTCACATAGCGCGGAAA 18 210 0 AAATTCACAT 0.796845 -55 AAGTGAAAATATTTTCCCTTTTCCTGTTAA 21 57 0 ATTTTCCCTT 0.787129 -105 AAGGGAAAATATTTTCACTTCTGCCGAAAC 21 67 1 ATTTTCACTT 0.761453 -95 ACTTTTTCACAATTTCCCATAATCTTTTCA 22 56 1 AATTTCCCAT 0.92743 -113 CCGTTTCTCTATTTTCACATGTCTATTTAT 22 139 0 ATTTTCACAT 0.889059 -30 CTATGACTGCATATTCCCTTAGGATATGCA 23 38 0 ATATTCCCTT 0.567969 -263 ACGCTTTCTAAATTTCACATAACCTTCAAA 26 44 1 AATTTCACAT 0.91689 -88 ATTGCACGTTCATTTCACATTTCTTACTTT 26 73 0 CATTTCACAT 0.654448 -59 GACCTCCTTCAATTTCACAAGCAGCTGGAT 31 19 1 AATTTCACAA 0.560988 -235 CTTTTCAATAAATTTCCCCTTTAAGAGTGT 36 269 0 AATTTCCCCT 0.749118 -32 CAATTTTCATAATTTCACATATTCTTTTCA 37 205 0 AATTTCACAT 0.91689 -73 ********** Masking position 5 Map Score: 5.18906 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 137 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 13 TTATGTTTTGAATATTTTCTTGTTCTATAAACA 9 61 0 AATTTTTTGT 0.808795 -240 TATCATTTCTTTTTTATGGCTTCA 12 2 1 AATTTCTTTT 0.907677 -63 ATTTCCCATAATCTTTTCATTTTTATCCCACAG 22 67 1 ATTTTCTTTT 0.667558 -102 TAGGATATGCAGTTTTTTATTTTACCAAAAAAA 23 16 0 ATTTTTTTTT 0.732237 -285 CTTTCCGTATACAATTTTTTATTTTAACATCAT 23 204 1 AATTTTTATT 0.5876 -97 TATGAAAAAAATGATTTCGTTGTTTACAAAATG 23 253 0 AATTTCTTGT 0.756459 -48 ATGAAGAGTCATCATTTTTTTTAGAAAATGTGA 32 111 1 AATTTTTTTA 0.587601 -157 AACATGTTTCATGATTTTATTTTAGCGAAAGCA 33 131 0 AATTTTTTTT 0.930503 -81 GTTAGGAAAAATCATTTTATTTTCTATATAAGA 35 92 1 AATTTTTTTT 0.930503 -72 ATATTTAGAAAACATTTTATTTTTCTTATATAG 35 115 0 AATTTTTTTT 0.930497 -49 ATGTTTACCTATAATTTTTTTTTTCCATTCTGT 36 49 0 AATTTTTTTT 0.930503 -252 GTAAAATGTAAGCATTTTCTTTTTGGGGGAGAG 36 192 1 AATTTTTTTT 0.930503 -109 ATATAACATCTCCTTTTCAATAAATTT 36 284 0 AATCTCTTTT 0.607947 -17 * ***** **** Masking position 1 Map Score: 5.49459 Number of sites scoring better than the average of aligned sites = 181 Number in coding regions = 136 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 14 AAGCAAAGAAGAAGCATAGGCTCTGCAGTTTG 4 17 0 GAAGAAGGCT 0.956775 -87 GAGGAGTATCGAAACATAGGTTTTCTGTACTT 15 123 1 GAAAAAGGTT 0.813608 -178 AGGAAAACCAGAAGCAAAGGCTTTTTCTCCCG 30 97 1 GAAGAAGGCT 0.956775 -184 CTCATTGCCGGAAAAACTGGCTACCCTATAGT 30 234 0 GAAAATGGCT 0.860375 -47 CCGCGACAAGGAGAGACAGGCTATAACCTATA 31 188 1 GAGAAAGGCT 0.980516 -66 TAAAAAGAGAGAAAGGCTTGCTTAATAC 33 7 1 GAGAAAGGCT 0.980516 -205 TTATAGTAAAAAGAGAAAGGCTGTATTAAGCA 33 29 0 AAGAAAGGCT 0.831467 -183 ACATAAAATAGAGAAATAGGATGTCGGGGAAT 33 170 1 GAGAAAGGAT 0.848936 -42 TTTGATGTCTGAACAAGAGGCTAACCTCATTG 35 36 0 GAACAAGGCT 0.92324 -128 **** * ***** Masking position 6 Map Score: 4.44181 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 89 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 15 GATCCCCTCCGCCGCTACCATAT 1 4 1 CCCCTCCGCC 0.665476 -297 ATTCCATTGGCCCCTTTACCAAGCTGTTTA 3 68 0 CCCCTTTACC 0.808965 -21 TCCTTACCTCCTCCCACAGTAAGCA 5 83 0 ACCTCCTCCC 0.492568 -15 CTGCTTTCAGCCCCTTTTCTCAAATTAAAA 8 25 0 CCCCTTTTCT 0.53273 -22 TATACAAAATCCCCCTTACTTCGACAATTG 9 208 1 CCCCCTTACT 0.807303 -93 AAAAGAGCCCCTCTCCTCGTTTTAAAA 13 30 0 CCCCTCTCCT 0.926555 -17 GGGTTTCTCTCCCCGTTACCAAGAGAGGAG 15 99 1 CCCCGTTACC 0.443661 -202 TACCGCGAGACCCTCGTCCTTTGCATAGGA 15 190 1 CCCTCGTCCT 0.87631 -111 ACACAAAAAACCCCCGTCCTATGCAAAGGA 15 206 0 CCCCCGTCCT 0.948313 -95 CTGGGGCGCGTCCCCTTGCTGATAAATTAA 17 53 1 TCCCCTTGCT 0.767464 -160 TTCACCAGATTCCTTCTGCTATTGTTTGGA 18 57 0 TCCTTCTGCT 0.487339 -208 TAGAAAACCCTTGTGCCATATTGGCAC 21 8 1 CCCTTGTGCC 0.889324 -154 AACATAAAAACCCTTGTGCCAATATGGCAC 21 23 0 CCCTTGTGCC 0.889324 -139 AAAATATTTTCCCTTTTCCTGTTAATTGTA 21 52 0 CCCTTTTCCT 0.817872 -110 AAAACAGCACCCCTAGTGCTTTCCGTATAC 23 186 1 CCCTAGTGCT 0.409872 -115 TGACCATCCTCTCCCGTCCCTATATGAAAA 23 278 0 CTCCCGTCCC 0.665536 -23 GTTTTCCCCCTGCTTTCCTTCTGT 24 67 0 TCCCCCTGCT 0.781673 -14 TGCCCCCTTCCCCCTATTGCAG 26 120 0 CCCCCTTCCC 0.961334 -12 ATCAATACTCCTTTCCCATTTATCACG 32 8 1 CTCCTTTCCC 0.557771 -260 TGGAACTAAAACCCTTTGCTTTTGAAAGAA 36 155 0 ACCCTTTGCT 0.548796 -146 ATTTTGATTTTCCTCCTGCCGAATGACTTC 41 280 0 TCCTCCTGCC 0.670216 -21 ********** Masking position 3 Map Score: 10.2849 Number of sites scoring better than the average of aligned sites = 739 Number in coding regions = 570 Number in noncoding regions = 169 Number of orfs with sites within 600 bp upstream = 152 Fraction of orfs with sites within 600 bp upstream = 0.0244137