AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00720_bsub_reg_300.orf -o00720_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 yjlC 300 yjlC #2 yjlD 39 similar to NADH dehydrogenase #3 yjmA 197 similar to glucuronate isomerase #4 yjmB 67 similar to Na+:galactoside symporter #5 yjmC 104 similar to malate dehydrogenase #6 ylxM 176 similar to hypothetical proteins #7 rpsP 105 ribosomal protein S16 (BS17) #8 ylqD 121 ylqD #9 rplS 130 ribosomal protein L19 #10 ylqF 142 similar to hypothetical proteins #11 rnh 70 ribonuclease H #12 ylqG 31 ylqG #13 sucC 172 succinyl-CoA synthetase (beta subunit) #14 sucD 28 succinyl-CoA synthetase (alpha subunit) #15 citB 227 aconitate hydratase #16 pps 300 phosphoenolpyruvate synthase #17 sdhA 33 succinate dehydrogenase (flavoprotein subunit) #18 sdhC 292 succinate dehydrogenase (cytochrome b558 subunit) #19 citH 43 malate dehydrogenase #20 citC 163 isocitrate dehydrogenase #21 citZ 300 citrate synthase II #22 ytcI 172 similar to acetate-CoA ligase #23 sspA 226 small acid-soluble spore protein (alpha-type SASP) #24 nifZ 194 NifS protein homolog #25 acsA 160 acetyl-CoA synthetase #26 yukF 300 similar to hypothetical proteins from B. subtilis #27 ald 67 L-alanine dehydrogenase #28 citG 300 fumarate hydratase Motif number 1 AGTCAAAATCCTTTACTCTCTCTGAAAATAG 1 82 0 CTTTCTCTCT 0.390379 -219 AAGGGTAGTGCCTCTCCCTGTCTCACGCTTT 1 236 0 CCTCCCCTGT 0.808227 -65 CAGGGAGAGGCACTACCCTTTCCAAAAAAAT 1 247 1 CACTCCCTTT 0.88237 -54 CGTATATCCTCCGTCCTTTATATCAATTT 2 21 0 CTCCTCCTTT 0.929724 -19 GCAAGTGCCTCCTTCCTTTTCAGTTTTTT 5 86 0 CTCCTCCTTT 0.929724 -19 TTGAGCTCTCCCCTTTGTTAAGTCAA 6 161 0 CTCTCCCTTT 0.961398 -16 GAGGTGCCGGCCCTCTCCCTT 8 1 0 CCCTTCCCTT 0.644173 -121 AGAGGGCCGGCACCTCCCCTTTTTTTACACG 8 16 1 CACCCCCCTT 0.953788 -106 CGCACCAAGCTCCCCGCTTTTAAAACTTTT 8 102 0 CTCCCGCTTT 0.868681 -20 TTTCTCTTCTCCCTTACTGTATGTAT 11 55 0 CTTCCCCTTA 0.83436 -16 TATTTGGTCCCCTGCCTTTCATTCTTTC 14 10 0 CCCCGCCTTT 0.830096 -19 TCTACATCTCCCCTTCAAAAAAAAA 16 286 0 CATCCCCCTT 0.835624 -15 GATAGCCCCTCTCCCTCTAGTAATCTAG 17 16 0 CCTCCCCTCT 0.922554 -18 ATCTGTCTCCCCTCTCTCCTGCGTATA 18 7 1 CTCCCTCTCT 0.91346 -286 TTCTGTAATCCTCCCCCCTGTTTGAGCTATA 18 39 0 CTCCCCCTGT 0.95428 -254 TTTCATTTTACTCCTCCCTCAAAAGGGCGTC 18 180 0 CTCCCCCTCA 0.922672 -113 TGTGCTAAATCTCTTCCCCCACTTCTTTCAA 18 242 0 CTCTCCCCCA 0.665745 -51 TACTTTACCCCCTGTTTGATAAG 18 280 0 CTTTCCCCCT 0.708077 -13 GTCTCTCTTCTCCTTTATGGCTAGT 19 29 0 CTCTCTCCTT 0.751235 -15 GTGGGGATACCCCCACTCCTAAGCCATTATG 22 23 0 CCCCCTCCTA 0.670276 -150 GTGGGGGTATCCCCACTCTTTTTCATTTTTT 22 38 1 CCCCCTCTTT 0.936833 -135 TCCTCACTTTCTCCACCCATTATACATAAAT 22 151 0 CTCCCCCATT 0.884424 -22 CTCCTCACTTTCTCCACCCAT 22 162 0 CTCCCACTTT 0.816958 -11 GCCCAAACATCCCCCTTTGCTGAAGTTG 25 143 0 CATCCCCTTT 0.88237 -18 CTCATCCCCTTCCTTTTATTATGATT 26 285 0 CCCCTCCTTT 0.915579 -16 **** ****** Masking position 8 Map Score: 27.0941 Number of sites scoring better than the average of aligned sites = 785 Number in coding regions = 532 Number in noncoding regions = 253 Number of orfs with sites within 600 bp upstream = 223 Fraction of orfs with sites within 600 bp upstream = 0.0358175 Motif number 2 ATTTTTATCTAAAAATAAACAATTGAATAAGTC 1 109 0 AAAATAAACT 0.594144 -192 TGAATATGGCAAGATGAAAAACTGGGTAGTAAA 1 147 1 AAGAGAAAAT 0.776738 -154 AATCATTTACAAAAATAAATGTTTACTACCCAG 1 168 0 AAAATAAATT 0.789182 -133 CTCTTTTTTGAAAATGAAATGTTAACGCTGTCA 3 86 0 AAAAGAAATT 0.905445 -112 ATATAAAGGTAAAATAAAAACAAATCAAAATGT 3 134 1 AAAAAAAAAA 0.785572 -64 CCGCTTTGACAAGATAAAAACTTGACAGTGTCA 6 93 1 AAGAAAAAAT 0.854629 -84 AACCGTTGTTAAGAAAAAACACTTTACAAACAC 7 28 1 AAGAAAAACT 0.829044 -78 CGGTTCAGCCAAGAAAAAATAAAGACCCGCATT 11 22 0 AAGAAAAATA 0.855518 -49 ATTTCATATTAAAACAAAATCATACATAAGTAA 15 136 0 AAAAAAAATT 0.941809 -92 TCTCCCCTTCAAAAAAAAATATTGACAAGAGCT 16 272 0 AAAAAAAATT 0.941809 -29 ATATATTGATAAAATAAAATTTTTCAATCAACT 18 107 1 AAAAAAAATT 0.94113 -186 AGGGAGGAGTAAAATGAAATTGTCAATAAATCT 18 192 1 AAAAGAAATT 0.90545 -101 TCTTATATAGAAAATAAAATGATTTTTCCTAAC 20 92 0 AAAAAAAATT 0.941809 -72 CTATATAAGAAAAATAAAATGTTTTCTAAATAT 20 115 1 AAAAAAAATT 0.941796 -49 ACAGAATGGAAAAAAAAAATTATAGGTAAACAT 21 49 1 AAAAAAAATT 0.941809 -252 CTCTCCCCCAAAAAGAAAATGCTTACATTTTAC 21 192 0 AAAAAAAATT 0.941809 -109 TTATATGTAAAAAATGAAAAAGAGTGGGGATAC 22 44 0 AAAAGAAAAA 0.684334 -129 AAAAGAGAAAATTGAACACTTTGAA 23 3 1 AAGAAAAATA 0.855518 -224 TAATTAAGGAAAGAAAAAACTGAACCTTTCAGA 26 79 0 AAGAAAAACA 0.698382 -222 GCTGGAAAACAAGAAGAAATTGAACAGCTCATT 28 77 1 AAGAGAAATA 0.77797 -224 ATCTTGAATTAAAATTAAAATCTGCCAAGATCG 28 204 1 AAAATAAAAT 0.639608 -97 CCAAGATCGAAAAATAAAAAGGATTTTTTGTGT 28 228 1 AAAAAAAAAA 0.785572 -73 **** ***** * Masking position 7 Map Score: 23.2278 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 479 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 3 CAGAGAGAGTAAAGGATTTTGACTTATTCAA 1 89 1 AAAGGATTTG 0.673434 -212 TAAACATAAAAAAAGACATTGCCAGAAAGCA 3 55 0 AAAAGAATTG 0.9663 -143 TCATTTTCAAAAAAGAGATTGATCCCAAAGG 3 102 1 AAAAGAATTG 0.966325 -96 AAGAATATTTAAAATAATTTGTAAATAAAAT 5 23 1 AAAATATTTG 0.850712 -82 TAACAATGATAAAAGTGTTTGTAAAGTGTTT 7 44 0 AAAAGTTTTG 0.710425 -62 ATAACGAACGAAAAGAGCTTGTTACCTGTAA 10 13 1 AAAAGACTTG 0.963099 -130 TCTGTATAAAAAAAGAGCTTGTTACAGGTAA 10 34 0 AAAAGACTTG 0.963099 -109 TAGAAGGATTAAAAGATTTTGCATCGAACTG 13 73 1 AAAAGATTTG 0.951076 -100 TAACAAAACTAAAATAGACTGCGCTTTCATT 13 131 0 AAAATAACTG 0.852676 -42 GGAAATTAAGAAAAGAACCTGGTGAAATTTC 16 125 1 AAAAGACCTG 0.947241 -176 GTGCAATATAAAAAGAACCTGGGAAATTTCA 16 147 0 AAAAGACCTG 0.947241 -154 CCCCTTCAAAAAAAAATATTGACAAGAGCTT 16 271 0 AAAAAAATTG 0.635935 -30 GGGAGGAGTAAAATGAAATTGTCAATAAATC 18 193 1 AAATGAATTG 0.672452 -100 TCTTATATAGAAAATAAAATGATTTTTCCTA 20 94 0 AAAATAAATG 0.693475 -70 CTATATAAGAAAAATAAAATGTTTTCTAAAT 20 115 1 AAAATAAATG 0.693475 -49 CTCTCCCCCAAAAAGAAAATGCTTACATTTT 21 194 0 AAAAGAAATG 0.885267 -107 TATCCTTACGGAAAGAGCCTGTATTTATGTA 22 129 1 GAAAGACCTG 0.643524 -44 TAATTATGTTAAAATATTCTGTCAATTAATT 24 28 1 AAAATATCTG 0.796862 -167 GATATTTTGGAAAATTCTTTGTTTGA 27 6 0 AAAATTTTTG 0.4172 -62 CTGGAAAACAAGAAGAAATTGAACAGCTCAT 28 78 1 AGAAGAATTG 0.742619 -223 ****** **** Masking position 10 Map Score: 16.4102 Number of sites scoring better than the average of aligned sites = 650 Number in coding regions = 537 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 4 AAGTCAAAATCCTTTACTCTCTCTGAAAATAGCAAACACA 1 74 0 CTTTTAAAAT 0.907197 -227 CTTATTCAATTGTTTATTTTTAGATAAAAATAATACTGAA 1 111 1 TTTTTAAAAA 0.812444 -190 ACAGCGTTAACATTTCATTTTCAAAAAAGAGATTGATCCC 3 88 1 CTTTTAAAGA 0.814923 -110 TCCTCACCGTCTTTCATTCTATTTCAAAATGTTAACGTTA 3 167 0 CTCTTAAAAT 0.75725 -31 GGCACCTCCCCTTTTTTTACACGCAAAAAAAGGGTAAACT 8 24 1 CTTTCAAAAA 0.872521 -98 ATCACAATTTCATAGCCTATGCAATAAAAT 9 1 0 CTGTTAAAAT 0.68169 -130 AACATTCAAACTTTTACTTTATTAAAAACATAAATTTCAA 13 33 0 CTTTTAAACA 0.920804 -140 ATAAGTCGAACTTATTGTATTTAATAAAAACATTGATATT 15 97 1 CTTTTAAAAA 0.975142 -131 TTCCCAGGTTCTTTTTATATTGCACAAAAACAGACACGGT 16 153 1 CTTTTAAAAA 0.975143 -148 TCTACATCTCCCCTTCAAAAAAAAATATTGACAA 16 277 0 CTTCTAAAAA 0.789613 -24 CTCTCTCCTGCGTATATTATAGCTCAAACAGGGGGGAGGA 18 22 1 CTTTTAAACA 0.921899 -271 ACAGAATGATCCTGTAATTCTTATGAAAAATTAAGCAAGA 18 64 1 CTTTCAAAAA 0.879004 -229 AAAATCATTTTATTTTCTATATAAGAAAAATAAAATGTTT 20 99 1 TTTTTAAAAA 0.75974 -65 TTTTTTCCATTCTGTGATTTCCCCGAAAAAACGCCTTTAT 21 24 0 TTTTTAAAAA 0.81408 -277 GGCCGCTGGTCCTTTTTTATATGTAAAAAATGAAAAAGAG 22 53 0 CTTTTAAAAA 0.974343 -120 ACGAACAAATCTTATTATATGGTAAAAAAATTAGAAGTCA 24 77 1 CTTTTAAAAA 0.975158 -118 TTAAAGAAGGCATGTATTTTTGATAAGAATTGATGGGACG 25 19 0 CTTTTAGAAT 0.643986 -142 GCGTTTTCAACATGGTTTATATTTTAAAAATTGAGAAGAA 25 76 1 CTGTTAAAAA 0.895846 -85 TTATATGAGACATACACTGTCCTGCAAAAAGGCGATTACA 26 162 1 CTCTTAAAAA 0.926083 -139 CACTTCGTATCCTCCGCTTTCATAAAAAAACTTACTCCAT 28 22 0 CTCTTAAAAA 0.926083 -279 CTGCCGTACTCCTTTGATGTATAAGAGACATCATAATGCT 28 123 0 CTTTTAGACA 0.680062 -178 * * * * * ***** Masking position 3 Map Score: 22.9226 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 203 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 5 AGGCACTACCCTTTCCAAAAAAATCAGCAA 1 254 1 CTTTCCAAAA 0.831483 -47 AATGTTAACGCTGTCATAAACATAAAAAAA 3 72 0 CTGTCATAAA 0.816851 -126 GAGCGGATCACTATCCGAAAATTCTTAAGA 4 34 1 CTATCCGAAA 0.81778 -34 GTAGAGTCCCCATTCATAAA 16 1 0 CATTCATAAA 0.841429 -300 AATACAGGCTCTTTCCGTAAGGATATGCCT 22 124 0 CTTTCCGTAA 0.887813 -49 CACATGGCTTCATTCAGAAAAACTTTGGTA 23 170 0 CATTCAGAAA 0.894315 -57 CCTTGTACCGCTTTCATAAAGGAGTAAAAA 24 173 1 CTTTCATAAA 0.955329 -22 CAAAAAAAACCTTTCAGAAAATTTGATGCT 26 38 1 CTTTCAGAAA 0.971514 -263 AAAACTGAACCTTTCAGAAATGGTGCTGTA 26 67 0 CTTTCAGAAA 0.971514 -234 TCAGTTTTTTCTTTCCTTAATTAGTCTTGC 26 89 1 CTTTCCTTAA 0.832285 -212 GTATCCTCCGCTTTCATAAAAAAACTTACT 28 26 0 CTTTCATAAA 0.955329 -275 ********** Masking position 9 Map Score: 10.0069 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 93 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 TTCGATTACCTTCTATATGATAACACTTTTTGA 1 30 0 TTTATTATAA 0.855928 -271 TCAGTATTATTTTTATCTAAAAATAAACAATTG 1 117 0 TTTATTAAAA 0.955653 -184 ATCCTTATTCTTATGCCTTAAAAGCGTGAGACA 1 216 1 TTTGCTAAAA 0.702941 -85 CCGTCTTTCATTCTATTTCAAAATGTTAACGTT 3 168 0 TTTATTAAAA 0.956048 -30 TACAAACACATTTTATTTACAAATTATTTTAAA 5 30 0 TTTATTCAAA 0.737018 -75 TCGGTTATACATGATAAAACCGTTGTT 7 5 1 TTTACTATAA 0.614424 -101 TACCCTTTTTTTGCGTGTAAAAAAAGGGGAGGT 8 27 0 TTCGTTAAAA 0.699994 -95 CATTTTCAAATTCTGTATAAAAAAAGAGCTTGT 10 43 0 TTTGTTAAAA 0.903172 -100 GTCGAACTTATTGTATTTAATAAAAACATTGAT 15 101 1 TTTATTATAA 0.85594 -127 TTTCTCACAATTTCATATTAAAACAAAATCATA 15 145 0 TTCATTAAAA 0.846413 -83 TACGTGCGCTTTCTAGTTAAAAAGTTATAGATA 16 206 1 TTTAGTAAAA 0.763122 -95 TCATTTTATTTTCTATATAAGAAAAATAAAATG 20 103 1 TTTATTAGAA 0.776941 -61 TGGTCCTTTTTTATATGTAAAAAATGAAAAAGA 22 54 0 TTTATTAAAA 0.956427 -119 ACAAATCTTATTATATGGTAAAAAAATTAGAAG 24 81 1 TTTATGAAAA 0.714912 -114 TCAACATGGTTTATATTTTAAAAATTGAGAAGA 25 82 1 TTTATTAAAA 0.954046 -79 ATGATTGTTGTTGTTTGTGAAAATCAACAACAA 26 258 0 TTTTTTAAAA 0.70166 -43 ** *** * **** Masking position 2 Map Score: 9.29397 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 113 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 7 TAGCAAACACAAAAAACTCCAATTCGATTA 1 55 0 AAAAAACTCC 0.830641 -246 AAAAATCCTCCTTAAAATAGG 6 2 1 AAAATCCTCC 0.964017 -175 TCTTGGCCACAAAAACCGGCACAGCGGAAC 9 94 0 AAAAACCGGC 0.937399 -37 AAGAAAAAATAAAGACCCGCATTTCTGCGC 11 15 0 AAAGACCCGC 0.787413 -56 TCTCCAAAATCCCCCTTCAGATCAG 15 213 0 AAAATCCCCC 0.977008 -15 AATAAAAACCTCCCAGTATGTAA 20 151 0 AAAAACCTCC 0.969545 -13 CAAAAACCCGCAAATAAAGGC 21 2 1 AAAAACCCGC 0.951617 -299 GATTTCCCCGAAAAAACGCCTTTATTTGCG 21 19 0 AAAAAACGCC 0.85555 -282 GAAAAAAATCCTCCTAATAATTAT 24 5 1 AAAATCCTCC 0.964017 -190 GCCCAAACATCCCCCTTTGCTGAAG 25 146 0 AACATCCCCC 0.888919 -15 AATTAAAATTAAAATCTGCCAAGATCGAAA 28 210 1 AAAATCTGCC 0.718241 -91 ********** Masking position 2 Map Score: 9.14477 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 217 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 8 TAAACATTTATTTTTGTAAATGATTGTGCATG 1 176 1 TTTTGAAATG 0.911355 -125 TTTGCTGATTTTTTTGGAAAGGGTAGTGCCTC 1 253 0 TTTTGAAAGG 0.978979 -48 AGCAAACTGCTTATAGTAAAGGAGAATTGGAT 1 279 1 TTATGAAAGG 0.960246 -22 ATCAATCTCTTTTTTGAAAATGAAATGTTAAC 3 93 0 TTTTGAAATG 0.911354 -105 GTCTTAAGAATTTTCGGATAGTGATCCGCTCA 4 33 0 TTTTGATAGT 0.770939 -35 ATTTAGCGTATTTTGGAAAAGTTAATCGCCGC 6 65 1 TTTTGAAAGT 0.937584 -112 GTAAACTAAGTTATCGTAAAGGGATTTGACTT 6 136 1 TTATGAAAGG 0.960246 -41 ATGATAAAAGTGTTTGTAAAGTGTTTTTTCTT 7 38 0 TGTTGAAAGT 0.720572 -68 ATTTTATTGCATAGGCTATGAAATT 9 4 1 TTATGATAGG 0.844043 -127 AAGGGGAAATTTATTGAAAAGGAGATGTTATA 21 278 1 TTATGAAAGG 0.960246 -23 TAGCATCAAATTTTCTGAAAGGTTTTTTTTGG 26 37 0 TTTTTAAAGG 0.769674 -264 TAGCTTGATATTTTGGAAAATTCTTTGTTTGA 27 11 0 TTTTGAAATT 0.768306 -57 **** * ***** Masking position 8 Map Score: 10.9136 Number of sites scoring better than the average of aligned sites = 188 Number in coding regions = 149 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 ATGAATTCACAATCCTTATTCTTATGCCTT 1 205 1 AATCCTTATT 0.683565 -96 ATCCAATTCTCCTTTACTATAAGC 1 287 0 AATTCTCCTT 0.81855 -14 AAAAATCCTCCTTAAAATAGGGT 6 4 1 AATCCTCCTT 0.981001 -173 AAATATTCCCCATCCTTCTTTGAAATTTAT 13 14 1 CATCCTTCTT 0.940081 -159 AAAATCTTTTAATCCTTCTAAACATTCAAA 13 63 0 AATCCTTCTA 0.908906 -110 TTCCCATCCTCCTAACTTATGTAA 13 159 0 CATCCTCCTA 0.943333 -14 TCTCCAAAATCCCCCTTCAGATCAGAT 15 211 0 AATCCCCCTT 0.9569 -17 GAAAAAAATCCTCCTAATAATTATGT 24 7 1 AATCCTCCTA 0.958983 -188 GCCCAAACATCCCCCTTTGCTGAAGTT 25 144 0 CATCCCCCTT 0.940504 -17 TGACACAAAAAATCCTTTTTATTTTTCGAT 28 233 0 AATCCTTTTT 0.683567 -68 ********** Masking position 3 Map Score: 8.05313 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 124 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 111 Fraction of orfs with sites within 600 bp upstream = 0.0178285 Motif number 10 ACACTTTTTGAACAAAATTTGAACGTGAAT 1 8 0 AACAAATTGA 0.734078 -293 GTTTTTTCTTAACAACGGTTTTATCATGTATAA 7 15 0 AACACGTTTA 0.948444 -91 GGCACAGCGGAACATCGTTTTCAAGCTTGCAGC 9 74 0 AACACGTTTA 0.948446 -57 GTGACACGAACACCGCCTTTATCTTCAGTAT 10 122 0 AACACGCTTA 0.776012 -21 CTTTATTAAAAACATAAATTTCAAAGAAGGATG 13 24 0 AACAAATTTA 0.936138 -149 TTTAAAGTGTAACCCAATTTTGATGTCTGAACA 20 53 0 AACCAATTTA 0.73408 -111 AACCTCTGTAAACATAGATTTTATAGGCCGCTG 22 85 0 AACAAGTTTA 0.951625 -88 GCTCGAAATCAACAAAGCTTTCAAAGTGTTCAA 23 22 0 AACAAGTTTA 0.951625 -205 AGAATATTTTAACATAATTATTAGGAGGATTTT 24 15 0 AACAAATATA 0.853776 -180 TTGTTATGGTAACATAAATATCATACCTTGTAC 24 148 1 AACAAATATA 0.853776 -47 AGATCATTTGAACAGCATTATGATGTCTCTTAT 28 110 1 AACACATATA 0.845212 -191 **** ** *** * Masking position 2 Map Score: 3.95986 Number of sites scoring better than the average of aligned sites = 102 Number in coding regions = 80 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 11 CTTTTAAAACTTTTACTCGTCCAGGCTTTTCT 8 84 0 TTACTCGTCC 0.800838 -38 TTTCTCTTCTCCCTTACTGTAT 11 59 0 TTTCTTCTCC 0.96696 -12 ATCTGTCTCCCCTCTCTCCTGCG 18 2 1 TTTCTCCCCT 0.810104 -291 GACAATTTCATTTTACTCCTCCCTCAAAAGGG 18 184 0 TTACTCCTCC 0.968802 -109 AAATGTGCTAAATCTCTTCCCCCACTTCTTTC 18 244 0 ATTCTTCCCC 0.745683 -49 GTCTCTCTTCTCCTTTATGGCTA 19 31 0 TTTCTTCTCC 0.96696 -13 GATGCAAGTATTTCTCTCCCCCAAAAAGAAAA 21 206 0 TTTCTCCCCC 0.979931 -95 ATATAACATCTCCTTTTCAATAA 21 288 0 TTACATCTCC 0.786498 -13 GTGTCTCACCTCCTTGTGAGTAT 23 214 0 TTTCACCTCC 0.950159 -13 ATCTGTCTCCTCCTGTATATGTG 27 55 0 TTTCTCCTCC 0.985628 -13 * * ******** Masking position 3 Map Score: 8.45388 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 135 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 12 CGGTTATACATGATAAAACCGTTGTTAAGAAA 7 12 1 TGAAAAACGT 0.939973 -94 ATATTAACAATGATAAAAGTGTTTGTAAAGTG 7 47 0 TGAAAAATGT 0.941092 -59 AAGGGTAAACTGATAGAAGCTTAGGCAAAATA 8 53 1 TGAAGAACTT 0.735001 -69 ATAATAATACTGGAAGAATTGTCTACAGTTCG 13 97 0 TGGAGAATGT 0.870641 -76 GTTCGACTTATGAGAAAAATGTACCGGTAATT 15 76 0 TGAAAAATGT 0.941092 -152 TATGAAATTGTGAGAAAATTGTGATGGAATGT 15 161 1 TGAAAAATGT 0.941092 -67 TGCTTACAATTGAAAGAAGTGGGGGAAGAGAT 18 233 1 TGAAGAATGG 0.870641 -60 AACAATTTCATGAGAGAAACGTTCTATATACA 26 210 0 TGAAGAACGT 0.961297 -91 *** **** *** Masking position 7 Map Score: 2.52646 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 108 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 13 GCTGATTTTTTTGGAAAGGGTAGTGCCTCTC 1 251 0 TGGAAAGGGT 0.773117 -50 TTTTTATGTTTATGACAGCGTTAACATTTCA 3 74 1 TTGACAGCGT 0.745782 -124 GTTTTTATCTTGTCAAAGCGGCGATTAACTT 6 83 0 TTCAAAGCGG 0.827547 -94 GAGTAAAAGTTTTAAAAGCGGGGAGCTTGGT 8 98 1 TTAAAAGCGG 0.764024 -24 AATGATCTGATCTGAAGGGGGATTTTGGAGA 15 207 1 TTGAAGGGGG 0.942993 -21 TTTATGAATGGGGACTCTACGAA 16 3 1 TTGAATGGGG 0.858449 -298 AATATTTTTTTTTGAAGGGGAGATGTAGA 16 282 1 TTGAAGGGGA 0.648779 -19 TTTACAACACTCTTAAAGGGGAAATTTATTG 21 263 1 TTTAAAGGGG 0.78995 -38 AATTGAACACTTTGAAAGCTTTGTTGATTTC 23 20 1 TTGAAAGCTT 0.78737 -207 TTTACTCCTTTATGAAAGCGGTACAAGGTAT 24 170 0 TTGAAAGCGG 0.976242 -25 CATCAAATTTTCTGAAAGGTTTTTTTTGGGA 26 35 0 TTGAAAGGTT 0.811364 -266 CAGCACCATTTCTGAAAGGTTCAGTTTTTTC 26 69 1 TTGAAAGGTT 0.811364 -232 TAAGTTTTTTTATGAAAGCGGAGGATACGAA 28 28 1 TTGAAAGCGG 0.976242 -273 * ********* Masking position 5 Map Score: 7.47486 Number of sites scoring better than the average of aligned sites = 469 Number in coding regions = 377 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 14 ATGCACAATCATTTACAAAAATAAATGTTTAC 1 175 0 ATTTACAAAT 0.669984 -126 CAATATAATATAAAGAATATTTAA 5 3 1 ATATAAAAAA 0.891387 -102 TATAAAGAATATTTAAAATAATTTGTAAATAA 5 19 1 ATTTAAAAAT 0.854212 -86 ACGCTCTCTCATATAACACAATAAAAGAAGCC 15 34 0 ATATAAAAAT 0.918687 -194 AACTTATTGTATTTAATAAAAACATTGATATT 15 105 1 ATTTAAAAAA 0.809686 -123 TTTTTGTGCAATATAAAAAGAACCTGGGAAAT 16 151 0 ATATAAAGAA 0.739876 -150 TCCTAGCAGGATATAATAAAATTATAAGATGG 16 240 0 ATATAAAAAT 0.918584 -61 ATATATATTGATAAAATAAAATTTTTCAATCA 18 105 1 ATAAAAAAAT 0.566779 -188 TTTATTTTCTATATAAGAAAAATAAAATGTTT 20 107 1 ATATAAAAAA 0.891386 -57 TTTTTTTACCATATAATAAGATTTGTTCGTTT 24 75 0 ATATAAAGAT 0.796561 -120 CCATAACAAAATTTAATAGAAAATTACGAAAA 24 125 0 ATTTAAAAAA 0.80976 -70 GAATATGAATATATACTATAATAATTGTGACA 25 113 1 ATATACAAAT 0.796557 -48 ****** * *** Masking position 5 Map Score: 4.79761 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 98 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 15 ********** No masking Map Score: -8.90777e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0