AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00280_bsub_reg_100.orf -o00280_bsub_100.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 ybgE 208 similar to branched-chain amino acid aminotransferase #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 yheM 284 similar to D-alanine aminotransferase #5 ptsG 238 phosphotransferase system (PTS) glucose-specific enzyme IIABC component #6 ptsH 97 histidine-containing phosphocarrier protein of the phosphotransferase system (PTS) (HPr protein) #7 splA 90 transcriptional regulator #8 splB 77 spore photoproduct lyase #9 ykwC 136 similar to 3-hydroxyisobutyrate dehydrogenase #10 pksF 300 pksF #11 yngG 250 similar to hydroxymethylglutaryl-CoA lyase #12 yqjC 201 similar to hypothetical proteins #13 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #14 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #15 yqiS 124 similar to phosphate butyryltransferase #16 bltD 168 spermine/spermidine acetyltransferase #17 yusL 267 similar to 3-hydroxyacyl-CoA dehydrogenase #18 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #19 ywaA 140 alternate gene name: ipa-0r; similar to branched-chain amino acid aminotransferase #20 yxjD 78 similar to 3-oxoadipate CoA-transferase #21 yxjC 153 similar to hypothetical proteins from B. subtilis #22 iolA 300 methylmalonate-semialdehyde dehydrogenase #23 aldX 142 aldehyde dehydrogenase Motif number 1 TGAAATTAAAGAAAACAGCCAGTTTTATTCTG 1 21 0 GAAAAGCCAG 0.896623 -188 TAAAGCTGCAAAAAGTATACAGCCTTTCCTTT 1 140 0 AAAAATACAG 0.722417 -69 TGCGCAGCAAAAAAACAGCCTGGTCAGCCGGC 2 19 0 AAAAAGCCTG 0.793098 -208 CCAGAAAAAACACGAAAGGGGCAATGGG 3 7 1 AAAACGAAAG 0.825518 -23 ATACAGGAATAAAACTGGAAAGCACATAGAAA 4 110 1 AAAAGGAAAG 0.953778 -175 GGACAAGCTGAAAAACAGAAAGATCAAGAGAT 4 194 0 AAAAAGAAAG 0.975457 -91 ATTGAGGGAAAAAAACGGGAAGTTCATTCTCG 5 69 1 AAAAGGGAAG 0.9079 -170 TCAGACTAGTAAAAAGAGGAGGTCAATTCTT 5 218 1 AAAAAGGAGG 0.894495 -21 GCTTTAAGTTAAAAGGAGAATGATAAAA 6 80 1 AAAAAGAATG 0.895754 -18 TGTACAAAAACCAGACGGCCTCCGGCCT 7 7 1 AAAAAGACGG 0.943091 -84 ACTTATGAAAAAAACCAGACAGGCCGGAGGCC 7 27 0 AAAAAGACAG 0.973762 -64 CGACCAAATCGAAAAGGGCCAGGAGGTAGCCA 11 81 1 GAAAGGCCAG 0.818283 -170 AAAGAAGTCAAAAAAAAGGAAGGCGACTTTGT 11 169 1 AAAAAGGAAG 0.949968 -82 AAACACGCTAAAATATAGACAGATTGTTTAAG 12 134 0 AAATAGACAG 0.808471 -68 ATTCATTTTTAAAAGCATAAAGGAGGGGCTTG 14 51 1 AAAAATAAAG 0.735941 -23 AGGCGGAGTCGAAACAAGAAAGGTGGTAACAG 15 103 1 GAAAAGAAAG 0.951082 -22 GGGATAAGAAAAAAGGAGAATGTAGT 16 153 1 AAAAAGAATG 0.895754 -16 GAATTTGATAAAATGCAGGAAGACAACATTTA 18 30 0 AAATAGGAAG 0.683497 -138 AAATTCATATGAAAAAAGCAGGAGAAA 19 6 0 GAAAAGCAGG 0.805729 -135 TATTCCGATTAAAAAAGGAAAGCTCCTTTTTT 21 30 0 AAAAGGAAAG 0.953778 -124 CGTACATATGGAAAGGGGACGGAAACAGCCGA 21 78 1 GAAAGGACGG 0.808023 -76 TAGGTCCGAGAAAAGAAGAAAGCAAATGAGGG 23 111 1 AAAAAGAAAG 0.975457 -32 **** ****** Masking position 3 Map Score: 25.1577 Number of sites scoring better than the average of aligned sites = 918 Number in coding regions = 737 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 186 Fraction of orfs with sites within 600 bp upstream = 0.0298747 Motif number 2 CCAGAAAAAACACGAAAGGGGCAATGGGC 3 10 1 ACAGAAAGGC 0.795764 -20 TACACAACAAAAAGGCATGAGCAAAATTGGGTG 5 111 0 AAAGCATGGA 0.593184 -128 AAAAAACCAGACAGGCCGGAGGCCGTCTGGTTT 7 18 0 ACAGCCGGGC 0.941234 -73 TTAGTAAAGGAAAAGGATGTGGCATC 8 62 1 AAAGGATGGC 0.935955 -16 AAGTCCACGTCAAAGCCGGCGACCAAATCGAAA 11 62 1 CAAGCCGGGC 0.903447 -189 AAGTCAAAAAAAAGGAAGGCGACTTTGTAAATG 11 173 1 AAAGAAGGGC 0.988515 -78 GCGACTTTGTAAATGAAGGAGACGTACTGCTCG 11 191 1 AAAGAAGGGC 0.988515 -60 ATAACGATAAAAAAGCAGGCGCC 12 1 0 AAAGCAGGGC 0.991417 -201 AGACGTAAGGGAGGATACAATC 13 6 1 TAAGGAGGTC 0.755095 -17 CTTGCATAATAAAAGGCGGAGTCGAAACAAGAA 15 90 1 AAAGGCGGGC 0.98465 -35 CGGCGAGCGTAAAGGGAGATGCCGGTCCGACTC 17 106 0 AAAGGAGAGC 0.859258 -162 TTCATATGAAAAAAGCAGGAGAAA 19 2 0 AAAGCAGGGA 0.920156 -139 GTGTAGAAGAAAACGAAAGGGGCATCAAT 20 60 1 AAAGAAAGGC 0.939774 -19 TCCGATTAAAAAAGGAAAGCTCCTTTTTTCGGA 21 26 0 AAAGAAAGTC 0.705884 -128 CCAAAAAAATAAATGGCGGATGCATATTTACAT 22 167 0 AAAGGCGGTC 0.907969 -134 ATGTGTTTACTAATGAAGGAGGCAATAAGA 22 281 1 TAAGAAGGGC 0.937256 -20 *** ***** * * Masking position 3 Map Score: 16.6714 Number of sites scoring better than the average of aligned sites = 625 Number in coding regions = 524 Number in noncoding regions = 101 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 3 AAACTGGCTGTTTTCTTTAATTTCAGCTTCATCTGA 1 28 1 TTTTTTTTCG 0.680864 -181 AATATCTTTATTTTCTGATATTTTATAAAAAAGCGG 2 75 0 TTTTGTTTTT 0.94618 -152 CTGTAAGCGCTTTTATTAATTTTTCTTTCACATCCG 2 163 0 TTTTTTTTTT 0.93312 -64 CCCATTGCCCCTTTCGTGTTTTTTCTGG 3 3 0 CTTTTTTTTT 0.654342 -27 AAACATCATTTGTTTGGGGATTTTTTATTTTATAAG 9 26 1 TGTTGTTTTT 0.704607 -111 AATTTATCATTTTTCCTTCATTTTCTAGACTACCAT 9 72 0 TTTTTTTTTT 0.93312 -65 CAAGGGATTATTTTAATGATTTTTATAGGTATATTT 10 34 0 TTTTTTTTTT 0.93312 -267 CGCCTTCCTTTTTTTTGACTTCTTTTACGATTCCGC 11 158 0 TTTTGTCTTT 0.690356 -93 TTGATCGTGATTTTGGGAGTTTTTATTCTTTCAACT 12 60 0 TTTTGTTTTT 0.94618 -142 ATCAAAACGCTTTTCATCAGTTTTTGAGACATGATT 12 91 1 TTTTTTTTTG 0.845102 -111 ATAAATGTTGTCTTCCTGCATTTTATCAAATTCCTG 18 29 1 TCTTTTTTTT 0.654342 -139 GCAGATATGAGTTTGTTATTTTTTCTGACAAACCTT 18 73 1 GTTTTTTTTT 0.654342 -95 AAAGCTCCTTTTTTCGGAGCTTTCCTCTACCAT 21 8 0 TTTTGTTTCT 0.87301 -146 ACACTACATTTTTTCATTATTTTTATTATATTAATC 22 43 0 TTTTTTTTTT 0.93312 -258 AACAGGTTACTTTTTGGTCATTTCTTGGTTATATTC 22 110 0 TTTTGTTTCT 0.87301 -191 CGCCATTTATTTTTTTGGTGTTTTTGAAAGCGTTTA 22 182 1 TTTTGTTTTG 0.87301 -119 **** * **** * Masking position 11 Map Score: 12.8589 Number of sites scoring better than the average of aligned sites = 596 Number in coding regions = 431 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 165 Fraction of orfs with sites within 600 bp upstream = 0.0265018 Motif number 4 GGATATATGGGAAGGAGCGGATGTGAAAGAAAAAT 2 146 1 GAAAGCGAGG 0.981112 -81 GAAAAAACACGAAAGGGGCAATGGGC 3 14 1 GAAGGGAAGG 0.958483 -16 TTACTTTTCTCACTAGGCGGAAAGGATATGAGTTG 8 25 0 CACGGCGAAG 0.579909 -53 AAACATCGGTGAATTAGCTGAGGTGCTTT 10 282 1 GAAAGCGAGG 0.981112 -19 CGACCAAATCGAAAAGGGCCAGGAGGTAGCCATTT 11 81 1 GAAGGGCAGG 0.912282 -170 AGCGTGTTTTGAATGGGCGGACAAGCGATATCTAT 12 157 1 GAAGGCGAAG 0.978128 -45 AGGCGGAGTCGAAACAAGAAAGGTGGTAACAG 15 103 1 GAAAAGAAGG 0.646019 -22 AATTCCTGCTGAAAACGCAGATATGAGTTTGTTAT 18 57 1 GAACGCGAAG 0.895804 -111 CCATACCTTACAAAAAGGAGAAACGGA 18 151 1 CAAAGGGAAG 0.824799 -17 AAAGGGGACGGAAACAGCCGATGCGGACAGGTTTT 21 89 1 GAAAGCGAGG 0.981112 -65 CTAGTTCGCGGAAACGGGGGATGTGTGT 21 136 1 GAAGGGGAGG 0.986222 -18 ATATAACCAAGAAATGACCAAAAAGTAACCTGTTG 22 112 1 GAAGACAAAG 0.646019 -189 GTTTACTAATGAAGGAGGCAATAAGA 22 285 1 GAAAGGAAAG 0.885827 -16 *** *** ** * * Masking position 11 Map Score: 9.6301 Number of sites scoring better than the average of aligned sites = 760 Number in coding regions = 674 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 CATAATGCTGTACAGCAGGCAGCTTATGAAGATGCC 4 41 1 TAAGCGAGTA 0.973279 -244 TGTCATGATTTTTAGCTGTAAGGTCAGACTAGTAAA 5 195 1 TTAGCTAGTA 0.974932 -44 TGTGAAGTAATAAAGCTTTAAGTTAAAAGGAGAATG 6 66 1 TAAGCTAGTA 0.934372 -32 AGATGTTTCGTTTAGATTTTAGTTAAAATTTATCAT 9 98 0 TTAGATAGTA 0.812841 -39 GGACACAGATTTGAGCCTGAAGATCAGTTAGTTGAG 10 151 1 TTAGCGAGTA 0.990049 -150 GATCAGTTAGTTGAGCTAGGAGCTGACTCTGTAGAC 10 172 1 TTAGCGAGTA 0.990049 -129 GTCGGGCAACTTAAGCCCGGAGGTGAAGGGAATGGT 17 177 0 TTAGCGAGTA 0.990049 -91 TATCTGCGTTTTCAGCAGGAATTTGATAAAATGCAG 18 44 0 TTAGCGATTA 0.917429 -124 ** *** * ** * * Masking position 11 Map Score: 6.43643 Number of sites scoring better than the average of aligned sites = 54 Number in coding regions = 44 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 TTAATAATACGCCGCTTCACACCTATAAAT 1 112 0 GCCGCTTCAC 0.820617 -97 TTTCACATCCGCTCCTTCCCATATATCCTT 2 144 0 GCTCCTTCCC 0.9486 -83 GCCCATTGCCCCTTTCGTGTTTTTTCT 3 13 0 GCCCCTTTCG 0.982846 -17 GAAAAAATAAACTCCTTTCCGCTATAGATC 4 167 1 ACTCCTTTCC 0.665462 -118 AAAAGCCCTCCCTTTTCGAGATGTCCCT 4 267 0 TCCCTTTTCG 0.870163 -18 GTTTACATTTGCCCTTTTACACAACAAAAA 5 131 0 GCCCTTTTAC 0.758596 -108 CTACCTCCTGGCCCTTTTCGATTTGGTCGC 11 80 0 GCCCTTTTCG 0.964357 -171 TTTCATCCCTGCTTTCGCTAATAGATA 12 185 0 CCTGCTTTCG 0.803951 -17 TCATAATGCAGCTGCTTCCCACGGCTGCTT 17 11 0 GCTGCTTCCC 0.933104 -257 TTTTGACTTGTCCGTTTTCCGCCGCCGTAA 17 72 1 TCCGTTTTCC 0.835128 -196 ATTGATGCCCCTTTCGTTTTCTTCTA 20 63 0 GCCCCTTTCG 0.982846 -16 GCTGTTTCCGTCCCCTTTCCATATGTACGA 21 77 0 TCCCCTTTCC 0.934179 -77 GTCCGCATCGGCTGTTTCCGTCCCCTTTCC 21 87 0 GCTGTTTCCG 0.86819 -67 ACACACATCCCCCGTTTCCGCGAACTAGAA 21 134 0 CCCGTTTCCG 0.832592 -20 ********** Masking position 6 Map Score: 14.3481 Number of sites scoring better than the average of aligned sites = 1112 Number in coding regions = 969 Number in noncoding regions = 143 Number of orfs with sites within 600 bp upstream = 128 Fraction of orfs with sites within 600 bp upstream = 0.0205589 Motif number 7 ATCAAACAGCCAGAATAAAACTGG 1 5 1 AACAGCCAGA 0.929325 -204 AATTAAAGAAAACAGCCAGTTTTATTCTGG 1 20 0 AACAGCCAGT 0.799866 -189 ACCAAACAGCCGGCTGACCAGGCT 2 5 1 AACAGCCGGC 0.984529 -222 GCAGCAAAAAAACAGCCTGGTCAGCCGGCT 2 18 0 AACAGCCTGG 0.883827 -209 CATAATGCTGTACAGCAGGCAGCTTATGAA 4 41 1 TACAGCAGGC 0.965468 -244 ATAACGATAAAAAAGCAGGCGCC 12 4 0 AAAAGCAGGC 0.8796 -198 TATCTGCGTTTTCAGCAGGAATTTGATAAA 18 50 0 TTCAGCAGGA 0.813898 -118 TTCATATGAAAAAAGCAGGAGAAA 19 5 0 AAAAGCAGGA 0.821616 -136 TAAACAATTTAACAGCAGGGAGATTGACC 19 122 1 AACAGCAGGG 0.961219 -19 GATCGCGATTTACAGCCTGACTGGTCTAGT 20 32 1 TACAGCCTGA 0.844007 -47 ATATCCACTTTTCAGCAAGCCAAGAATTAA 22 215 0 TTCAGCAAGC 0.694531 -86 ********** Masking position 4 Map Score: 6.34074 Number of sites scoring better than the average of aligned sites = 1006 Number in coding regions = 927 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 8 TATGCCAATGGAGAGATTGTT 4 2 0 GAGAGATTGT 0.892789 -283 CAGCATTATGTAGAGATTTTATGCCAATGG 4 21 0 TAGAGATTTT 0.785512 -264 CTGACATTTCGACAAATTTTCTATGTGCTT 4 129 0 GACAAATTTT 0.599144 -156 TTGTCGAAATGTCAGATTTTAAGGAAAAAA 4 144 1 GTCAGATTTT 0.742489 -141 CTCGAAAAGGGAGGGCTTTT 4 275 1 GAGGGCTTTT 0.821776 -10 ATCATTTGTTTGGGGATTTTTTATTTTATA 9 30 1 TGGGGATTTT 0.563958 -107 AGCTCAATGCGAGGGATTTTTAACGATAAA 10 240 0 GAGGGATTTT 0.964105 -61 CTAAAATATAGACAGATTGTTTAAGGAGAG 12 129 0 GACAGATTGT 0.877589 -73 TGCCGCTGAAGACGGATTTTTTTTCTCTCG 17 146 1 GACGGATTTT 0.958547 -122 TGACAAGCAGAAGAGATTTTTCACATAATA 18 116 1 AAGAGATTTT 0.674979 -52 AGCCGATGCGGACAGGTTTTTGTAAACGCT 21 104 1 GACAGGTTTT 0.795735 -50 CCAATCATTAGACAGATCTTAGATATATGT 23 22 1 GACAGATCTT 0.781616 -121 AAGCAAATGAGGGGGATTTTACA 23 130 1 GGGGGATTTT 0.902995 -13 ********** Masking position 7 Map Score: 5.44076 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 331 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 9 GAAGCTGAAATTAAAGAAAACAGCCAGTTTT 1 27 0 TTAAGAAAAC 0.632862 -182 GGAGCGGATGTGAAAGAAAAATTAATAAAAG 2 159 1 TGAAGAAAAA 0.937887 -68 ATGTCAGATTTTAAGGAAAAAATAAACTCCT 4 152 1 TTAAGAAAAA 0.91617 -133 GCTGAAAAACAGAAAGATCAAGAGATCTATA 4 189 0 AGAAGATCAA 0.588436 -96 GTAACACGTTATAAGGATAAACTGAATTTAT 5 17 0 ATAAGATAAA 0.857716 -222 CATCAGTGATTGAGGGAAAAAAACGGGAAGT 5 61 1 TGAGGAAAAA 0.721614 -178 AGTTAAAAGGAGAATGATAAAA 6 86 1 AGAAGATAAA 0.892802 -12 GTCTAGAAAATGAAGGAAAAATGATAAATTT 9 78 1 TGAAGAAAAA 0.937887 -59 AGAGAGCGCATTATGGATAAACAGAGAATCT 10 73 1 TTATGATAAA 0.522145 -228 CGAGGGATTTTTAACGATAAATCCTCTAGCA 10 230 0 TTAAGATAAA 0.904152 -71 TCATGTTTCTATAACGATAAAAAAGCAGGCG 12 13 0 ATAAGATAAA 0.857716 -189 AGAGTACAGTTGAAAGAATAAAAACTCCCAA 12 53 1 TGAAGAATAA 0.636222 -149 TATAATAAAAATAATGAAAAAATGTAGTGTT 22 49 1 ATAAGAAAAA 0.874742 -252 **** ****** Masking position 7 Map Score: 6.07133 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 496 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 10 CGCTTACAGATAGAGGCCGTATACACAAAT 2 190 1 TAGAGGCCGT 0.89806 -37 CCAGACAGGCCGGAGGCCGTCTGGTTTTTG 7 15 0 CGGAGGCCGT 0.986356 -76 AGGAGGCAGTTGTCATGACG 11 1 1 AGGAGGCAGT 0.869513 -250 AAGCAGCCGTGGGAAGCAGC 17 1 1 AAGCAGCCGT 0.915547 -267 TGTCCGTTTTCCGCCGCCGTAATGCTGAGT 17 80 1 CCGCCGCCGT 0.940286 -188 AATCCGTCTTCAGCGGCAGTCAGCGCGGCG 17 134 0 CAGCGGCAGT 0.962829 -134 ACAGCAAATACGGCAGCCGTT 20 2 0 CGGCAGCCGT 0.980564 -77 ********** Masking position 10 Map Score: 1.81039 Number of sites scoring better than the average of aligned sites = 388 Number in coding regions = 337 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 11 GGACAGTGATTTACCGCTTTTTTATAAAAT 2 62 1 TTACCGCTTT 0.89726 -165 CCTCTATCTGTAAGCGCTTTTATTAATTTT 2 176 0 TAAGCGCTTT 0.809799 -51 TCCTTTTAACTTAAAGCTTTATTACTTCAC 6 67 0 TTAAAGCTTT 0.750485 -31 AATCACGATCAAAACGCTTTTCATCAGTTT 12 84 1 AAAACGCTTT 0.811244 -118 CAGGTTTTTGTAAACGCTTTCTAGTTCGCG 21 116 1 TAAACGCTTT 0.967329 -38 AGCCAAGAATTAAACGCTTTCAAAAACACC 22 198 0 TAAACGCTTT 0.967329 -103 ********** Masking position 3 Map Score: 1.8723 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 83 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 12 TTCTGCGCAGCAAAAAAACAGCCTGGTCAGC 2 23 0 CAAAAAACAG 0.821838 -204 AATTGTAAGACAAATAAACAATAAGTCAATA 2 107 0 CAAAAAACAA 0.951791 -120 ATTTGTCTTACAATTAAACAAAAGGATATAT 2 123 1 CAATAAACAA 0.75683 -104 ATTGGGTGCGCAAAAGAACGAGAATGAACTT 5 88 0 CAAAGAACGA 0.791878 -151 AAAAAATCCCCAAACAAATGATGTTTGGGGA 9 21 0 CAAAAAATGA 0.926735 -116 AGGCTTCATACAAAAAAATAACAAATTAGCT 17 219 1 CAAAAAATAA 0.938783 -49 AAGCACCCTCCAAAAAAATAAATGTTGTCTT 18 12 1 CAAAAAATAA 0.938783 -156 TAGAATATAACCAAGAAATGACCAAAAAGTA 22 108 1 CCAAAAATGA 0.74718 -193 TCAAAAACACCAAAAAAATAAATGGCGGATG 22 178 0 CAAAAAATAA 0.938783 -123 **** ****** Masking position 7 Map Score: 3.43616 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 162 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 13 AAACAGCCTGGTCAGCCGGCTGTTTGGT 2 9 0 GTCAGCCGGC 0.739673 -218 CATCTTCATAAGCTGCCTGCTGTACAGCAT 4 45 0 AGCTGCCTGC 0.605517 -240 AAAACCAGACGGCCTCCGGCCTGTCTGGTT 7 17 1 GGCCTCCGGC 0.96303 -74 AAATTTATCATTTTTCCTTCATTTTCTAGA 9 79 0 TTTTTCCTTC 0.392275 -58 ACTTTCCACAGGTTTCCTGCCATTTGTATG 11 36 0 GGTTTCCTGC 0.89716 -215 TTTTCGATTTGGTCGCCGGCTTTGACGTGG 11 66 0 GGTCGCCGGC 0.879064 -185 ATTCCAAAATGGCTACCTCCTGGCCCTTTT 11 92 0 GGCTACCTCC 0.655326 -159 GGTCTTCCTCCAAATTATTGA 11 240 0 GTCTTCCTCC 0.86296 -11 GATTGTATCCTCCCTTACGTCT 13 10 0 TGTATCCTCC 0.639871 -13 CTTGTCCGTTTTCCGCCGCCGTAATGCTGA 17 78 1 TTCCGCCGCC 0.765784 -190 AATAAATGTTGTCTTCCTGCATTTTATCAA 18 28 1 GTCTTCCTGC 0.89716 -140 TTTCTCCTGCTTTTTTCATA 19 1 1 TTTCTCCTGC 0.726029 -140 CCGCATCGGCTGTTTCCGTCCCCTTTCCAT 21 85 0 TGTTTCCGTC 0.62461 -69 TATGTAAATATGCATCCGCCATTTATTTTT 22 166 1 TGCATCCGCC 0.820792 -135 TCTTATTGCCTCCTTCATTAGTAAAC 22 285 0 TGCCTCCTTC 0.808506 -16 ********** Masking position 6 Map Score: 5.73657 Number of sites scoring better than the average of aligned sites = 2219 Number in coding regions = 2029 Number in noncoding regions = 190 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 14 ATTATGTGAAAGGTGTGCTGATTAGA 1 193 1 AGGTTTGATT 0.949631 -16 ATCCTTATAACGTGTTACTGATTCGATCAGGCA 5 30 1 CGTGTTGATT 0.902112 -209 CCTGTGAATTCGTTGTCATGATTTTTAGCTGTA 5 182 1 CGTTTTGATT 0.949631 -57 ATGACAAGTACGGTTGTATGATATAATATTGTG 6 37 1 CGGTGTGATA 0.732256 -61 AAAGGATATGAGTTGTAATGATTTCCTTG 8 7 0 AGTTTTGATT 0.905626 -71 TTTCTTATCCCGGTATCCTGATATTGCTAAAAC 16 131 0 CGGTTTGATA 0.921294 -38 CCTTTTTGTAAGGTATGGTGATTTATTATGTGA 18 136 0 AGGTTTGATT 0.949631 -32 GAAAAAATGTAGTGTTTATGATTGACTTATGGG 22 64 1 AGTGTTGATT 0.824273 -237 TATCTAAGATCTGTCTAATGATTGGAGGTGTCT 23 14 0 CTGTTTGATT 0.784082 -129 **** * ***** Masking position 9 Map Score: 1.65674 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 177 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 15 ATCCCGGCCGGACAGTGATTTACCGCTTTTT 2 53 1 GACAGGATTT 0.954049 -174 GAATTAGACGGACACAGATTTGAGCCTGAAG 10 142 1 GACACGATTT 0.826404 -159 TATCTGCAACGATCGGGATTTCCATTTTCAT 11 124 0 GATCGGATTT 0.977444 -127 AAAGCGTTTTGATCGTGATTTTGGGAGTTTT 12 73 0 GATCGGATTT 0.977444 -129 TATTTGCTGTGATCGCGATTTACAGCCTGAC 20 22 1 GATCGGATTT 0.977444 -57 GAAAGCAAATGAGGGGGATTTTACA 23 128 1 GAGGGGATTT 0.904602 -15 ***** ***** Masking position 8 Map Score: 0.482905 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 52 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701