AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00440_bsub_reg_300.orf -o00440_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 yclB 89 similar to phenylacrylic acid decarboxylase #6 yerQ 300 similar to hypothetical proteins #7 yefA 255 alternate gene name: yerS; similar to RNA methyltransferase #8 patA 300 aminotransferase #9 gerCA 162 heptaprenyl diphosphate synthase component I #10 mtrB 21 tryptophan operon RNA-binding attenuation protein (TRAP) #11 mtrA 187 GTP cyclohydrolase I #12 hbs 300 non-specific DNA-binding protein HBsu #13 yqeT 24 similar to ribosomal protein L11 methyltransferase #14 dnaJ 199 heat-shock protein #15 dnaK 23 class I heat-shock protein (chaperonin) #16 grpE 71 heat-shock protein #17 hrcA 119 transcriptional regulator #18 hemN 52 coproporphyrinogen III oxidase #19 lepA 133 GTP-binding protein #20 spoIIP 62 spoIIP #21 gpr 203 spore protease #22 patB 80 aminotransferase #23 ywnE 242 similar to cardiolipin synthase Motif number 1 GAAAGTCTTGATTTAAAAGGATTTTTAGTAGGAT 1 23 0 ATAAAGGATT 0.830862 -278 TGATAAACAAAAGGTGTTTCACGTGTAA 2 5 1 AAAAAGGTTT 0.960326 -74 TCTTGTCGAAACACAAAAGGTGTTCGACGAATTG 2 39 0 AAAAAGGTTT 0.960326 -40 TTGTGTTTCGACAAGAAAGGAGTTTTTCACTT 2 57 1 AAAAAGGATT 0.830862 -22 TCTTCTCCTCATAGGATAGGTTTGTCGACAAGTC 3 81 1 AAATAGGTTG 0.56786 -75 ATACTTATGTATTCAGAGGGTTTTGCGCCCTCTG 4 14 1 ATGAGGGTTT 0.864788 -131 TTTCATGAATATACAAAAGTTTTTATTTTGTCTT 4 111 1 AAAAAGTTTT 0.752052 -34 TATAATTAATACCTAAAAGGTATGATAAGGAGGC 5 19 0 ACAAAGGTTG 0.792976 -71 CCTGACAACGAATGCGAGGGTTTTTCAACAAGCT 6 22 0 ATGAGGGTTT 0.864788 -279 CCCTTCCTAGACTACAAGGGTTTTCAATCAAGCT 6 106 1 ATAAGGGTTT 0.934741 -195 CTCATAGTATAATTAAAGGTTGTTAGTGTAAAAA 6 243 1 ATAAGGTTTT 0.642196 -58 CCCTTCCTAGACTTCAAAGGTTTTCAATCACGCT 7 90 0 ATAAAGGTTT 0.960326 -166 CCTGACAACGAATGCGAAGGTTTGCCTACACGCT 7 174 1 ATGAAGGTTG 0.891319 -82 AGCCATAATCAAAATGAAGGTCTTCGTGCCAAAT 8 71 0 AAGAAGGTTT 0.915314 -230 TTTTTTTCTGAAAAGAAAGGTATGTTTAGAAAAA 8 179 1 AAAAAGGTTG 0.948365 -122 TTCTGTGAAGAAATAAAGTGTATGTAAGCTAGAT 11 34 0 AAAAGTGTTG 0.472338 -154 GCTAGAATCGAAATTAAATGTATTCATTGGTGGA 11 153 1 AAAAATGTTT 0.665951 -35 TTTATATTGCAATCTAAAGGTGTGTTTGATAGAA 21 87 0 ATAAAGGTTG 0.948365 -117 TTGCAATATAAATGTAAAGTATTTTTCATTGAAG 21 109 1 ATAAAGTATT 0.381014 -95 * * ****** ** Masking position 13 Map Score: 16.2674 Number of sites scoring better than the average of aligned sites = 567 Number in coding regions = 420 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 159 Fraction of orfs with sites within 600 bp upstream = 0.0255381 Motif number 2 TATATGAATATTATTTATATTTATCCTTTATCTATGATA 1 201 0 TATTTTCCTT 0.885401 -100 TTTTGTATATTCATGAAACTTTTTCTTATATCGAGCGTC 4 90 0 TATTTTCTTT 0.952673 -55 ATTATAGATTTAATAGATATTTTTCATATGGATATATCA 5 47 1 TATTTTCATT 0.940498 -43 CTGATTCTTGTTTTGAGCTTTTGTCATCCTTAACATTCT 6 143 0 TGTTTTCATC 0.949012 -158 ACAGTTTTCGTTTTAGGATTTTGTCATCTTTTCAGCGTG 7 57 1 TGTTTTCATT 0.957782 -199 TTGGCTTGAATAGGCCAAGTTTTTCTTTCGCTTAAAACT 7 213 1 TATTTTCTTC 0.942908 -43 CCTTAACAAATATAATGAGTTTATCCTATTTTACCACTA 8 263 0 TGTTTTCCTT 0.917282 -38 TCTTAATCTATGTATGAGTTTTATCTTTTCATTCGCTTA 9 100 0 TATTTTCTTT 0.952675 -63 AAAGCCCCTTTCTAAGGGGCTTTTCATATTTCAAGAGCA 11 67 1 TGCTTTCATT 0.742072 -121 GAATATTCCTTTTTTTCCTTTTTTCATCC 12 1 0 TCTTTTCATC 0.730051 -300 AAAAAGCCGTTTAATTGTCTTTCTCTTACTTGCTCTCAT 12 181 1 TGTTTTCTTC 0.959522 -120 AAGTCAGGCATCTCTTGGCTTTGACTTTTTTTCTTGCCC 14 92 1 TGTTTACTTT 0.686188 -108 CTCGCTTCACTCTCCCGAATTTCTCACATAAATTAGATT 14 171 0 TGTTTTCACT 0.717883 -29 GGGTGAGTTATAATTGACATTTTTCTTGTGGTTTGATAC 17 37 1 TATTTTCTTT 0.952675 -83 CTATCATATCTGGGTTGCTTTTCTCTTTCACGTAC 19 7 0 TGTTTTCTTC 0.959522 -127 CCAGATATGATAGGGAACTTTTCTCTTTCTTGTTTTACA 19 33 1 TATTTTCTTC 0.942908 -101 AAAGTATTTTTCATTGAAGGTTCTCTTTTTAGCATGATT 21 124 1 TAGTTTCTTT 0.824507 -80 TGTTTCAAGCTTCACGAACGTTATCATATGTGTTTATTT 23 33 1 TAGTTTCATT 0.786732 -210 * * *** **** * Masking position 11 Map Score: 15.9615 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 396 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 3 CTGAGGCTTTCAGCTTGTTGAAAAACCCT 6 9 1 TTCAGCTGTT 0.974119 -292 TTAACATTCTTTCAGCTTGATTGAAAACCCT 6 122 0 TTCAGCTGAT 0.981997 -179 TTGTCATCTTTTCAGCGTGATTGAAAACCTT 7 77 1 TTCAGCTGAT 0.979136 -179 CAAGCCAAGTTTCAGCGTGTAGGCAAACCTT 7 190 0 TTCAGCTGTA 0.824527 -66 CACGAAGACCTTCATTTTGATTATGGCTATT 8 77 1 TTCATTTGAT 0.820836 -224 TGACAGGGCATTCACTTTGCTTTTAGCGGGG 11 115 1 TTCACTTGCT 0.848634 -73 ACAGAAATTCTTCACTTTGTTGGACAAACAT 12 128 1 TTCACTTGTT 0.925624 -173 TTCTTCACAGTTCAGTCTGATTCTAAACCTG 12 232 0 TTCAGTTGAT 0.969466 -69 AAAGGATACATTCAGTTCGTTTATTATCATT 12 262 0 TTCAGTCGTT 0.840835 -39 AGGTTCTCTTTTTAGCATGATTTATTCAGCA 21 141 1 TTTAGCTGAT 0.812816 -63 TCTTCTAAGCTTCACTATGATAAGATAGAAC 22 34 0 TTCACTTGAT 0.947232 -47 ****** **** Masking position 4 Map Score: 9.58757 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 249 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 4 AATGTCAAAAAGCTCCCGCCCAAAGGACGA 1 262 0 AGCTCCCGCC 0.714243 -39 TCTACATGCTTTCTTCTCCTCATAGGATAG 3 70 1 TTCTTCTCCT 0.676433 -86 CAGAGGGTTTTGCGCCCTCTGTTTTTTTCG 4 27 1 TGCGCCCTCT 0.847009 -118 AAGAAAGCGCCTCCTTATCATACCT 5 6 1 AGCGCCTCCT 0.874433 -84 TCCGCTCCAATGCTCCCCCTTCCTAGACTA 6 90 1 TGCTCCCCCT 0.983144 -211 TGTGCTCCGATGCTCGCCCTTCCTAGACTT 7 110 0 TGCTCGCCCT 0.820445 -146 ATTGGCTGTATCCTCCCGCTGTTTGCGAGC 9 40 0 TCCTCCCGCT 0.939384 -123 TTATAGCACCCTCTATCTTTA 10 8 0 AGCACCCTCT 0.773884 -14 GCCTTTCACCTCCTCCCAAAAGGA 12 287 0 TTCACCTCCT 0.940863 -14 TTGAATAACCTCCTGCTATGTAA 15 7 0 ACCTCCTGCT 0.811536 -17 GCAGCACCTGTCCTTCTCCTTACACTTTGA 16 38 1 TCCTTCTCCT 0.729105 -34 TGTGTTCACCTCCCTCAAAGTGTA 16 58 0 TTCACCTCCC 0.810287 -14 CGGATTCACCTTCTTTACAGAAAG 18 39 0 TTCACCTTCT 0.778376 -14 GTGTTTCACCTCCTAAGATACAAC 21 5 1 TTCACCTCCT 0.940863 -199 ATAATCCTCCCCCTTTATTTGATG 23 5 1 TCCTCCCCCT 0.971421 -238 AAAACCAGCTTGCACCTGCGTTAAAATAAA 23 65 0 TGCACCTGCG 0.700384 -178 ********** Masking position 3 Map Score: 11.3494 Number of sites scoring better than the average of aligned sites = 943 Number in coding regions = 713 Number in noncoding regions = 230 Number of orfs with sites within 600 bp upstream = 233 Fraction of orfs with sites within 600 bp upstream = 0.0374237 Motif number 5 AAAACCCTCGCATTCGTTGTCAGGTCTGCG 6 32 1 CATTCGTTGT 0.855389 -269 ACGAATTCAACATTCGCTGTGCTCCGATGC 7 127 0 CATTCGCTGT 0.974616 -129 CAAACCTTCGCATTCGTTGTCAGGCCTGTG 7 168 0 CATTCGTTGT 0.855389 -88 CCAAGTTTTTCTTTCGCTTAAAACTAGAGG 7 227 1 CTTTCGCTTA 0.812027 -29 CCTATTTTACCACTAGCTGATCATTTGTCA 8 248 0 CACTAGCTGA 0.849104 -53 TGTTTGCGAGCATTTGCTTTTAACAGCGGG 9 21 0 CATTTGCTTT 0.849258 -142 TTTATCTTTTCATTCGCTTACGCAGGTATC 9 90 0 CATTCGCTTA 0.971428 -73 CCTGACAGGGCATTCACTTTGCTTTTAGCG 11 113 1 CATTCACTTT 0.692717 -75 ATAGAATTAGCACTCGCTTATTGAGAGTGC 17 83 1 CACTCGCTTA 0.955145 -37 ACGCAAAATACACTAGCTTAGATTATATCA 19 92 0 CACTAGCTTA 0.807437 -42 ATATTGTTGCCATTTGCTGAATAAATCATG 21 156 0 CATTTGCTGA 0.899843 -48 ********** Masking position 4 Map Score: 8.69437 Number of sites scoring better than the average of aligned sites = 400 Number in coding regions = 370 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 ACCAAAGTTTTTTATTTCATTTGATTATAT 1 59 1 TTTATTTCAT 0.688819 -242 ACGAACAGACTTTTTTTATTTTCATTAAAG 1 104 1 TTTTTTTATT 0.825043 -197 GCGCCCTCTGTTTTTTTCGTTATAATAGAC 4 38 1 TTTTTTTCGT 0.878721 -107 GGTTGTCTTCTTTTTTTCTGAAAAGAAAGG 8 169 1 TTTTTTTCTG 0.951035 -132 AGCCAATTCTTTTTTTTATGCTATAATGAT 9 63 1 TTTTTTTATG 0.770515 -100 CAAATTCACATTTATTTCTTAATCTATGTA 9 125 0 TTTATTTCTT 0.925105 -38 TTACATACACTTTATTTCTTCACAGAAAAG 11 41 1 TTTATTTCTT 0.925105 -147 CGAATATTCCTTTTTTTCCTTTTTTCATCC 12 11 0 TTTTTTTCCT 0.878721 -290 CTTGCTCTCATTTTTTTCTGAGACAGGTTT 12 209 1 TTTTTTTCTG 0.951035 -92 TGGCTTTGACTTTTTTTCTTGCCCGGGATA 14 107 1 TTTTTTTCTT 0.964638 -93 ********** Masking position 5 Map Score: 7.4628 Number of sites scoring better than the average of aligned sites = 472 Number in coding regions = 351 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 7 AAAAACTCCTTTCTTGTCGAAACACAAAAG 2 54 0 TTCTTGTCGA 0.646464 -25 GGATTTTGTCATCTTTTCAGCGTGATTGAA 7 72 1 ATCTTTTCAG 0.707402 -184 GAGGATGCTCTTCTTGAAGGTCAGCTGATT 8 33 0 TTCTTGAAGG 0.614006 -268 AAACATACCTTTCTTTTCAGAAAAAAAGAA 8 176 0 TTCTTTTCAG 0.93741 -125 TACACTTTATTTCTTCACAGAAAAGCCCCT 11 46 1 TTCTTCACAG 0.940091 -142 GAGCATGGGCTTCCTGACAGGGCATTCACT 11 101 1 TTCCTGACAG 0.665553 -87 TTATTATCATTTCTTCACAGTTCAGTCTGA 12 243 0 TTCTTCACAG 0.940091 -58 GTTCTTTTTAGTGTCAGCCCC 14 2 1 TTCTTTTTAG 0.67542 -198 ATGAAATGTGTTCTTTTCGGTCAGCTCCGG 14 36 0 TTCTTTTCGG 0.854154 -164 CGGATTCACCTTCTTTACAGAAAGAAGCCG 18 33 0 TTCTTTACAG 0.950186 -20 TTTACATTGAATCTTTACAATCCTATTGAT 19 66 1 ATCTTTACAA 0.538878 -68 AGGTTAAATCTTCTTCACAATAGAACAAAT 21 53 1 TTCTTCACAA 0.856229 -151 TGTATGTTTATTCTTCTAAGCTTCACTATG 22 46 0 TTCTTCTAAG 0.761566 -35 ACGGGCAGATTTCTTTAAAACCAGCTTGCA 23 81 0 TTCTTTAAAA 0.65238 -162 CCGCTCTTTATTCTTTTAAAATGTGAGTGT 23 135 1 TTCTTTTAAA 0.595723 -108 AATGGCAATCTTCTTGATAAATATGAATGA 23 210 1 TTCTTGATAA 0.452795 -33 ********** Masking position 5 Map Score: 9.6378 Number of sites scoring better than the average of aligned sites = 801 Number in coding regions = 678 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 8 CACCGACGCGCAGACCTGACAACGAATGCG 6 40 0 CAGACCTGAC 0.948543 -261 GTCTGCGCGTCGGTGCTCACGAATTCTACA 6 55 1 CGGTGCTCAC 0.981994 -246 GCCTGTGCTTCGGTGCTCACGAATTCAACA 7 145 0 CGGTGCTCAC 0.981994 -111 CACCGAAGCACAGGCCTGACAACGAATGCG 7 160 1 CAGGCCTGAC 0.966117 -96 GCTCCGGAAGCGGGGCTGACACTAAAAAGA 14 13 0 CGGGGCTGAC 0.993844 -187 GCCCCGCTTCCGGAGCTGACCGAAAAGAAC 14 27 1 CGGAGCTGAC 0.990506 -173 ********** Masking position 7 Map Score: 6.1765 Number of sites scoring better than the average of aligned sites = 81 Number in coding regions = 68 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 9 ATTTTGTCGTATATAATCAAATGAAATAAAAAAC 1 65 0 ATATAAATGA 0.933447 -236 AATATAAATAATATTCATATATGATTTGCACTTA 1 219 1 ATATTAATGA 0.880343 -82 CATACTCCTGATATATCCATATGAAAAATATCTA 5 60 0 ATATAAATGA 0.933437 -30 CATATAAACAATAATAGAACATGATACAATAAAG 8 121 1 ATAATAATGA 0.933447 -180 CTTGCCCGGGATAAAAGGAATTGAAAAATCATAA 14 124 1 ATAAAATTGA 0.808245 -76 TTGAAAAATCATAATTCAAAATGATACAATCTAA 14 144 1 ATAATAATGA 0.933447 -56 GCTTAGAAGAATAAACATACATGAGGGGGTAACA 22 55 1 ATAAAAATGA 0.963948 -26 CTGCGTTAAAATAAACACATATGATAACGTTCGT 23 46 0 ATAAAAATGA 0.963948 -197 AATCTTCTTGATAAATATGAATGAGCGGGGTTAC 23 216 1 ATAAAGATGA 0.862013 -27 ***** * **** Masking position 3 Map Score: 5.278 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 51 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 10 TTGCACTTATCGCCGCTCTCGTCCTTTGGG 1 244 1 CGCCGCTCTC 0.971592 -57 GCTGGCTGTCCCCGCTGTTAAAAGCAAAT 9 10 1 CCCCGCTGTT 0.986213 -153 GGCTGTATCCTCCCGCTGTTTGCGAGCATT 9 37 0 TCCCGCTGTT 0.875203 -126 TTAGTGTCAGCCCCGCTTCCGGAGCTGACC 14 18 1 CCCCGCTTCC 0.859845 -182 CATCATCACCTCTGTTAGCACTCTCA 17 104 0 CACCTCTGTT 0.703239 -16 AAGCCGCCGCAGTCTTGTACTGCG 18 5 1 CGCCGCAGTC 0.87626 -48 CACCGCTTATAATAAAATTT 22 1 1 CACCGCTTAT 0.749382 -80 GAATCTGGATCGCCGCTCTTTATTCTTTTA 23 123 1 CGCCGCTCTT 0.976451 -120 TTTGTAACCCCGCTCATTCATATTTAT 23 226 0 CCCCGCTCAT 0.952241 -17 ********** Masking position 6 Map Score: 4.45901 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 549 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 11 GTCGAACACCTTTTGTGTTTCGACAAGAAA 2 45 1 TTTTGTGTTT 0.695156 -34 ACAAAGTGCATTTTCTGCTTATTAGACGCT 4 66 1 TTTTCTGCTT 0.857547 -79 CTGAGGCTTTCAGCTTGTTGAAAAAC 6 7 1 CTTTCAGCTT 0.868458 -294 CCTTAACATTCTTTCAGCTTGATTGAAAAC 6 125 0 CTTTCAGCTT 0.868458 -176 CTGATTCTTGTTTTGAGCTTTTGTCATCCT 6 152 0 TTTTGAGCTT 0.970317 -149 CAAGAATCAGTTTTGAGCTTTTGTGCGTTT 6 172 1 TTTTGAGCTT 0.970317 -129 TTTTGAGCTTTTGTGCGTTTTCACCTGTAA 6 182 1 TTGTGCGTTT 0.517261 -119 TTTGTCAACATTCTGAGCTTGGCTTACCAA 7 19 0 TTCTGAGCTT 0.926178 -237 TTTTGTCATCTTTTCAGCGTGATTGAAAAC 7 75 1 TTTTCAGCGT 0.765823 -181 CAATGAAGTTTTTGGCGCTTTTTTTGGGTG 17 12 1 TTTGGCGCTT 0.799823 -108 AGCTAGTGTATTTTGCGTTTAATAGTAGGA 19 104 1 TTTTGCGTTT 0.83708 -30 ATGTTTATTCTTCTAAGCTTCACTATGATA 22 43 0 TTCTAAGCTT 0.583509 -38 ********** Masking position 2 Map Score: 4.10436 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 642 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 12 CTTGAAACCTCCTAATCAGAATGTCAA 1 284 0 CCTCCTAATC 0.954765 -17 TATTTCCTCCAAGACAAAATAAAAA 4 130 0 CCTCCAAGAC 0.894614 -15 AAGAAAGCGCCTCCTTATCATACCTTTTA 5 10 1 CCTCCTTATC 0.954765 -80 AATGCTCCCCCTTCCTAGACTACAAGGGTT 6 98 1 CTTCCTAGAC 0.917725 -203 GAGCTTTTGTCATCCTTAACATTCTTTCAG 6 138 0 CATCCTTAAC 0.839698 -163 GATGCTCGCCCTTCCTAGACTTCAAAGGTT 7 102 0 CTTCCTAGAC 0.917725 -154 AGAAGAGCATCCTCCGTATCTGATTTGGCA 8 49 1 CCTCCGTATC 0.866569 -252 ACAGGGGCCTCCTTCACATTAAGTACC 21 187 0 CCTCCTTCAC 0.938474 -17 ********** Masking position 3 Map Score: 2.97126 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 84 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 13 GTTGTCAGGTCTGCGCGTCGGTGCTCACGAAT 6 47 1 CTGGCGTCGT 0.987908 -254 TGTCAACATTCTGAGCTTGGCTTACCAAGCCA 7 15 0 CTGGCTTGGT 0.980955 -241 TCAACATTCGCTGTGCTCCGATGCTCGCCCTT 7 119 0 CTGGCTCCGT 0.987908 -137 GTTGTCAGGCCTGTGCTTCGGTGCTCACGAAT 7 151 0 CTGGCTTCGT 0.994516 -105 AGGACAGGTGCTGCCCTTCGATAAAATTTGCC 16 20 0 CTGCCTTCGT 0.980955 -52 *** ****** * Masking position 2 Map Score: 2.05359 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 11 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 14 ACAAGCTCTTACAAAACCCGCTAGCGTTTTTT 3 12 0 AAAAACCGCT 0.782344 -144 AACGAAAAAAACAGAGGGCGCAAAACCCTCTG 4 27 0 AAGAGGCGCA 0.750241 -118 TCGTTATAATAGACAAAGTGCATTTTCTGCTT 4 54 1 AACAAGTGCA 0.820048 -91 AAAAATCGCAACAAAATGTACATAATCTTACA 6 207 0 AAAAAGTACA 0.605802 -94 ACTATGAGTTAAAAAAATCGCAACAAAATGTA 6 219 0 AAAAATCGCA 0.935486 -82 GTATGTTTAGAAAAAAGGCGCATACAATCGAA 8 198 1 AAAAAGCGCA 0.973751 -103 CGGCTTTTTAAGAAAAACTGCACTCTGAGGAA 12 158 0 AAAAACTGCA 0.923007 -143 CTGCCCTTCGATAAAATTTGCCAAAATTCCC 16 10 0 AAAAATTGCC 0.766255 -62 TAACTCACCCAAAAAAAGCGCCAAAAACTTCA 17 15 0 AAAAAGCGCC 0.941006 -105 TTCTTTACAGAAAGAAGCCGCAGTACAAGACT 18 21 0 AAGAACCGCA 0.907442 -32 ACCGCTTATAATAAAATTTGCAGTTCTATCTT 22 12 1 AAAAATTGCA 0.884044 -69 * **** ***** Masking position 5 Map Score: 2.51565 Number of sites scoring better than the average of aligned sites = 509 Number in coding regions = 392 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 110 Fraction of orfs with sites within 600 bp upstream = 0.0176678 Motif number 15 GGATTTTTAGTAGGATAATAGCTTTATT 1 6 0 TAGATTAGCT 0.79038 -295 TCTTAAAGGCTAAGATGGTATCATAGATAAAGG 1 183 1 TAGATTATCA 0.928011 -118 ATACAAAAGTTTTTATTTTGTCTTGGAGGAAAT 4 121 1 TTTATTGTCT 0.56251 -24 AAAACTGTTTTAGGATTTTGTCAACATTCTGAG 7 32 0 TAGATTGTCA 0.913833 -224 GTTTTCGTTTTAGGATTTTGTCATCTTTTCAGC 7 60 1 TAGATTGTCA 0.913833 -196 AGACCTTCATTTTGATTATGGCTATTAATGAAA 8 82 1 TTGATTGGCT 0.810253 -219 CTTACGCAGGTATCATTATAGCATAAAAAAAAG 9 71 0 TACATTAGCA 0.606392 -92 TACATTTAATTTCGATTCTAGCACATATGCCCC 11 142 0 TTGATTAGCA 0.935895 -46 CTCACATAAATTAGATTGTATCATTTTGAATTA 14 155 0 TTGATTATCA 0.946656 -45 ATACACTAGCTTAGATTATATCAATAGGATTGT 19 82 0 TTGATTATCA 0.946556 -52 ATAGAACAAATTGTATTCTATCAAACACACCTT 21 72 1 TTTATTATCA 0.814677 -132 AAATTTGCAGTTCTATCTTATCATAGTGAAGCT 22 25 1 TTTATTATCA 0.81463 -56 ** *** ***** Masking position 5 Map Score: 6.082 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 113 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467