AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_bsub_reg_300.orf -o00640_bsub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/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 ycbA 300 alternate gene name: yzgA; similar to two-component sensor histidine kinase [YcbB] #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 ycgA 300 similar to hypothetical proteins #5 ycgB 115 ycgB #6 amyE 148 alpha-amylase #7 lctE 176 L-lactate dehydrogenase #8 ycnG 106 similar to 4-aminobutyrate aminotransferase #9 ylxM 176 similar to hypothetical proteins #10 rpsP 105 ribosomal protein S16 (BS17) #11 ylqD 121 ylqD #12 rplS 130 ribosomal protein L19 #13 ylqF 142 similar to hypothetical proteins #14 rnh 70 ribonuclease H #15 ylqG 31 ylqG #16 sucC 172 succinyl-CoA synthetase (beta subunit) #17 sucD 28 succinyl-CoA synthetase (alpha subunit) #18 yngG 250 similar to hydroxymethylglutaryl-CoA lyase #19 yngI 43 similar to long-chain acyl-CoA synthetase #20 yngJ 90 similar to butyryl-CoA dehydrogenase #21 ynzE 270 ynzE #22 yngK 135 alternate gene name: yotA; similar to hypothetical proteins #23 yngL 110 yngL #24 ppsD 24 peptide synthetase #25 ppsB 24 peptide synthetase #26 ppsA 300 peptide synthetase #27 yodT 300 similar to adenosylmethionine-8-amino-7-oxononanoate aminotransferase #28 yqjC 201 similar to hypothetical proteins #29 yqjB 51 similar to hypothetical proteins #30 yqjA 70 yqjA #31 yqiY 80 similar to amino acid ABC transporter (permease) #32 yqiX 268 similar to amino acid ABC transporter (binding protein) #33 yqiW 162 similar to hypothetical proteins from B. subtilis #34 mmgA 137 acetyl-CoA acetyltransferase #35 yqiK 78 similar to glycerophosphodiester phosphodiesterase #36 yqiH 300 alternate gene name: yzpA; similar to lipoprotein #37 accB 155 acetyl-CoA carboxylase subunit (biotin carboxyl carrier subunit) #38 spoIIIAC 22 spoIIIAC #39 spoIIIAA 75 spoIIIAA #40 yqhV 144 alternate gene name: yqgE #41 efp 24 elongation factor P #42 yqhS 86 similar to 3-dehydroquinate dehydratase #43 yqhR 226 yqhR #44 yttI 300 similar to acetyl-CoA carboxylase #45 ackA 300 acetate kinase #46 ytcI 172 similar to acetate-CoA ligase #47 sspA 226 small acid-soluble spore protein (alpha-type SASP) #48 nifZ 194 NifS protein homolog #49 acsA 160 acetyl-CoA synthetase #50 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #51 iolA 300 methylmalonate-semialdehyde dehydrogenase #52 aldX 142 aldehyde dehydrogenase Motif number 1 ACCAAACAGCCGGCTGACCAGGCTG 2 5 1 AACAGCCGCT 0.986595 -222 GCAGCAAAAAAACAGCCTGGTCAGCCGGCTG 2 17 0 AACAGCCGGT 0.812601 -210 TGAATAACTCAAAAGCCCGCCGTACAAGCCG 5 25 0 AAAAGCCGCC 0.898539 -91 ATGTTACAATAACAGCCTGCGCTTCTGCAAT 5 55 0 AACAGCCGCG 0.934914 -61 TTCGGAGTCAAAAATCCCTCTTACTTCATTC 6 92 0 AAAATCCTCT 0.717596 -57 GTGAATATCCCCCTGTCGGTATTT 8 93 0 AATATCCCCT 0.760424 -14 AAAAATCCTCCTTAAAATAGGG 9 2 1 AAAATCCCCT 0.969924 -175 CTTGCAGCGGATAAGCCCGCTTAAGCCACAA 12 51 0 ATAAGCCGCT 0.843428 -80 CCGTCATGACAACTGCCTCCT 18 1 0 AACTGCCCCT 0.898015 -250 TGGGAATGATAACATCATCCTTTTTCTTGGA 23 81 1 AACATCACCT 0.760195 -30 ATAACGATAAAAAAGCAGGCGCC 28 3 0 AAAAGCAGCG 0.645101 -199 GGCTGCGTCAAACAGCCTCCTTCTAACAACT 34 20 0 AACAGCCCCT 0.986594 -118 AATGAGGGAAAAAAGCCCGCTAAACAAGCGG 37 12 1 AAAAGCCGCT 0.988168 -144 CAGCAACGCAAAAAGCCCGCTTGTTTAGCGG 37 28 0 AAAAGCCGCT 0.988168 -128 TGGGCACAAAAAAAGCCTGCTCCCATTTGGG 40 32 0 AAAAGCCGCT 0.98816 -113 GGATATGCCTAAAAGCAACCTCTGTAAACAT 46 103 0 AAAAGCACCT 0.903049 -70 GAAAAAAATCCTCCTAATAATTATG 48 5 1 AAAATCCCCT 0.969924 -190 GCCCAAACATCCCCCTTTGCTGAAGT 49 145 0 AACATCCCCT 0.966014 -16 GCATTTTATCAAATTCCTGCTGAAAACGCAG 50 46 1 AAATTCCGCT 0.794148 -122 AAAAGACACCTCCAATCATTA 52 1 1 AAAAGACCCT 0.768584 -142 TGTAAAATCCCCCTCATTTGCTTT 52 129 0 AAAATCCCCT 0.969924 -14 ******* *** Masking position 1 Map Score: 25.9218 Number of sites scoring better than the average of aligned sites = 598 Number in coding regions = 472 Number in noncoding regions = 126 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 2 CCAGTATATATCCGTCTTTTTCAATAAACCG 1 205 0 TCCGTCTTTT 0.770534 -96 GGCTGACCAGGCTGTTTTTTTGCTGCGCAGA 2 22 1 GCTGTTTTTT 0.617055 -205 GCCCATTGCCCCTTTCGTGTTTTTTCTG 3 12 0 GCCCCTTTCT 0.807025 -18 GGTCGTGACATCCCCCTTTGTCACGCGGTCA 4 202 0 TCCCCCTTTT 0.889923 -99 GGCCGGCACCTCCCCTTTTTTTACACGCAAA 11 20 1 TCCCCTTTTT 0.911675 -102 CAGGTAACAAGCTCTTTTCGTTCGTTATCA 13 10 0 GCTCTTTTCT 0.558114 -133 TGTAACAAGCTCTTTTTTTATACAGAATTTG 13 39 1 TCTTTTTTTT 0.825726 -104 AAAGTCGCCTTCCTTTTTTTTGACTTCTTTT 18 168 0 TCCTTTTTTT 0.896067 -83 TCATTGTTCCTCCTTTCTTAATGATAGG 19 26 0 TCCTCCTTTT 0.924743 -18 ATCGTTTCCTCCTTCACATCTTTGTAA 20 74 0 TCCTCCTTCC 0.54753 -17 TCTCTGTCCGTCTTTCTTTTTGTATCAAGAA 23 35 1 TCTTTCTTTT 0.787734 -76 GATAACATCATCCTTTTTCTTGGAGGCTTCT 23 88 1 TCCTTTTTCT 0.836271 -23 ATTTTTCGTTTCTTTTTTTATCAAATTTCCG 26 95 0 TCTTTTTTTT 0.825726 -206 TTGTCATTTTTCTGCTTTTTTCTACATTTTC 26 246 1 TCTGCTTTTT 0.810865 -55 ATCCATACATGCTGTTTTCATCCTTTCTTAT 27 47 0 GCTGTTTTCT 0.488385 -254 TATTGTTGGAGCCGCTTTTATTTGCTAGATG 27 154 1 GCCGCTTTTT 0.842155 -147 TATTAGGAAGGCTCTTTTTATGTGAAAAAGT 27 209 1 GCTCTTTTTT 0.680712 -92 TCGCATGAGCTCTTCCTTCATTGGTCAACCT 29 12 1 TCTTCCTTCT 0.800021 -40 AAGCTCCTCCTTTTTCATTAGGTTG 29 37 0 TCCTCCTTTT 0.924743 -15 CGGCCAGCCTTCTTCTTTTTTATATT 30 6 0 TCTTCTTTTT 0.896067 -65 GCTGGCCGCCTCTTCTTTTTTATTGAAGAAA 30 29 1 TCTTCTTTTT 0.896067 -42 AAAAAGTTGAGCCGCTTTTTT 31 1 0 GCCGCTTTTT 0.842155 -80 AGCCTTTGTCTCCTTTTCTTACAGGAAAA 31 62 0 TCTCCTTTTT 0.85013 -19 GGTTATATAATCCCCTTTTTCTGTAAGCAGT 33 38 1 TCCCCTTTTC 0.631788 -125 TGAAGACCTCTCCTTTTTCATCATCTGTTCT 33 142 0 TCCTTTTTCT 0.836271 -21 GTTTGACGCAGCCTTCTTTTTTCATTCATTC 34 38 1 GCCTTCTTTT 0.82201 -100 GTATGAAATTTCTTTTTTTATAGGTTACTAC 37 119 0 TCTTTTTTTT 0.825726 -37 CAGAGCCTCCTCCTTTCTACCGATTGGC 39 58 0 TCCTCCTTTT 0.924743 -18 GGAACAGACTTCTTTTTTCCTTT 40 3 0 TCTTTTTTCT 0.737322 -142 ATGGGAGCAGGCTTTTTTTGTGCCCAAAAAC 40 37 1 GCTTTTTTTT 0.764174 -108 AGGCCGCTGGTCCTTTTTTATATGTAAAAAA 46 63 0 TCCTTTTTTT 0.896067 -110 GCCCAAACATCCCCCTTTGCTGAAGTTGTC 49 141 0 TCCCCCTTTC 0.573362 -20 TCTTATTGCCTCCTTCATTAGTAAACAC 51 283 0 GCCTCCTTCT 0.832735 -18 TCATTTGCTTTCTTCTTTTCTCGGACCTATT 52 109 0 TCTTCTTTTT 0.896067 -34 ********* * Masking position 7 Map Score: 34.6843 Number of sites scoring better than the average of aligned sites = 1816 Number in coding regions = 1346 Number in noncoding regions = 470 Number of orfs with sites within 600 bp upstream = 516 Fraction of orfs with sites within 600 bp upstream = 0.0828783 Motif number 3 GGCCTCTATCTGTAAGCGCTTTTATTAATT 2 178 0 TGTAAGCGCT 0.970798 -49 TAATTTTAAATGTAAGCGTTAACAAAATTC 6 25 1 TGTAAGCGTT 0.95395 -124 GCTGCAAGCTTGAAAACGATGTTCCGCTGT 12 74 1 TGAAAACGAT 0.638225 -57 TATTATAGAATGAAAGCGCAGTCTATTTTA 16 123 1 TGAAAGCGCA 0.950045 -50 AAATGTAAACGCTTTCCTATCAT 19 4 1 TGTAAACGCT 0.906269 -40 AGACTAGAAATGAAAACGTAAAACACGTCC 21 210 0 TGAAAACGTA 0.775113 -61 AACTAGAAATTGTAAGCGCTGTCTATCTTC 34 102 1 TGTAAGCGCT 0.970798 -36 ACGACAAGGTTGACAGCGCATTCAAAAATA 44 16 0 TGACAGCGCA 0.826048 -285 GAATTGAGGATGACAGCGTTTGACAAAAAA 44 108 1 TGACAGCGTT 0.894197 -193 AACCGCAAATTGTAAGCGTTCATCAATACA 45 86 1 TGTAAGCGTT 0.95395 -215 GACTTCTTATTGTAAGCGTTATCAATACGC 45 146 1 TGTAAGCGTT 0.95395 -155 TTGAACACTTTGAAAGCTTTGTTGATTTCG 47 22 1 TGAAAGCTTT 0.641459 -205 TACTCCTTTATGAAAGCGGTACAAGGTATG 48 169 0 TGAAAGCGGT 0.8999 -26 TAAACCATGTTGAAAACGCTTTATAATTTG 49 65 0 TGAAAACGCT 0.940469 -96 AAATTCCTGCTGAAAACGCAGATATGAGTT 50 56 1 TGAAAACGCA 0.846889 -112 TTGGTGTTTTTGAAAGCGTTTAATTCTTGG 51 196 1 TGAAAGCGTT 0.971303 -105 ********** Masking position 5 Map Score: 20.2548 Number of sites scoring better than the average of aligned sites = 266 Number in coding regions = 189 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 4 CAGCCTGGTCAGCCGGCTGTTTGGT 2 6 0 AGCCGGCTGT 0.939204 -221 GATTGCTGCCCGCCGGCTTGTACGGCGGGC 5 12 1 CGCCGGCTTG 0.948348 -104 CGGCTTGTACGGCGGGCTTTTGAGTTATTC 5 25 1 GGCGGGCTTT 0.975806 -91 ATTGCAGAAGCGCAGGCTGTTATTGTAACA 5 55 1 CGCAGGCTGT 0.867414 -61 TTGTGGCTTAAGCGGGCTTATCCGCTGCAA 12 51 1 AGCGGGCTTA 0.861362 -80 TCGATTTGGTCGCCGGCTTTGACGTGGACT 18 63 0 CGCCGGCTTT 0.981473 -188 GAAATGAGAAGGACGGCTTTCTAAGTCGTC 21 11 1 GGACGGCTTT 0.72652 -260 GGCGCCTGCTTTTTTATCGTTA 28 3 1 CGCCTGCTTT 0.777251 -199 CCGCTTGTTTAGCGGGCTTTTTTCCCTCAT 37 13 0 AGCGGGCTTT 0.979959 -143 CCGCTAAACAAGCGGGCTTTTTGCGTTGCT 37 28 1 AGCGGGCTTT 0.979959 -128 ATCTTACAGGAGCGGACTTGTGAATTCAAC 37 69 0 AGCGGACTTG 0.681951 -87 TATGATGTGAGGCAGACTTTATGACAAGCC 39 16 0 GGCAGACTTT 0.666082 -60 CCCAAATGGGAGCAGGCTTTTTTTGTGCCC 40 32 1 AGCAGGCTTT 0.950283 -113 ********** Masking position 8 Map Score: 11.5281 Number of sites scoring better than the average of aligned sites = 551 Number in coding regions = 489 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 5 TTATAAAATATCAGAAAATAAAGATATTGACTT 2 83 1 TGAAAATAAG 0.940047 -144 GTCAGAATGATAAGAAAATACCGACAGGGGGAT 8 78 1 TGAAAATACG 0.599828 -29 AATCATGCATACTGAAGATAAAGGCGGTGTTCG 13 114 1 AGAAGATAAG 0.824046 -29 GGTTCAGCCAAGAAAAAATAAAGACCCGCATTT 14 21 0 AAAAAATAAG 0.906852 -50 GCTGAATTTTTTAAAAAACAAAGGTGAGATTCA 21 84 1 TAAAAACAAG 0.813994 -187 TCCGAACAGCACAAAAAATAATGTGGCACCTAA 21 242 0 AAAAAATAAG 0.906852 -29 CCATTCTTGATACAAAAAGAAAGACGGACAGAG 23 36 0 TAAAAAGAAG 0.75027 -75 AAAAAAAGAAACGAAAAATAAAGAAATAATACT 26 107 1 AAAAAATAAG 0.906852 -194 TAATACTATATTCAAAAAAAATGTTATAAAAAT 26 133 1 TAAAAAAAAG 0.524138 -168 TTGTTTAAGGAGAGAAAATCATGTCTCAAAAAC 28 110 0 AGAAAATCAG 0.698263 -92 ATATAACCAGAAGGAAAATAAAGGAGCAGTTGT 33 13 0 AGAAAATAAG 0.92223 -150 CATGAATGAATGAAAAAAGAAGGCTGCGTCAAA 34 39 0 TAAAAAGAAG 0.75027 -99 TTCCTGTTGTTAGAAAGATAACGAGCAGATTTG 36 157 0 TAAAGATAAG 0.835631 -144 GTATAGCCCTTTTGAAAATCATGGAACTTGCTC 36 201 1 TGAAAATCAG 0.753685 -100 ATGGAGAATTTGTAAAGACAACGCGAATGCAGG 36 235 0 TAAAGACAAG 0.633471 -66 GCGAGTAAAATTTGAAAATAACGGGTATAATGC 43 136 0 TGAAAATAAG 0.940047 -91 TGACAGCGCATTCAAAAATAATGTT 44 3 0 TAAAAATAAG 0.927916 -298 AGTGAATGTGTCTGAAAATAACGACTTCTTATT 45 124 1 TGAAAATAAG 0.940047 -177 ACAAAATTTAATAGAAAATTACGAAAAACTAGT 48 119 0 AGAAAATTAG 0.458997 -76 AGATTAATATAATAAAAATAATGAAAAAATGTA 51 42 1 AAAAAATAAG 0.906852 -259 CCTTTTCTGTAAGAAAGACAACGGTGAACCATC 52 65 0 AAAAGACAAG 0.566556 -78 * ******** * Masking position 6 Map Score: 11.696 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 214 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 6 TTTTGTATGATTCTGTAGTCTCCATTATACAGTAAT 1 37 0 TTCTCCCATT 0.883917 -264 TACGGCCTCTATCTGTAAGCGCTTTTATTAATTTTT 2 175 0 ATCTCCTTTT 0.886017 -52 GACCTTCCTCCCGCACTTTTACGAATGGCT 5 96 0 TTCCCCTTTT 0.94553 -20 TACTTCATTCTTCCGCTTCCTCCTTTCAAACCGATG 6 66 0 TTCCCCCTTT 0.944457 -83 CTAAGCTTCTATCAGTTTACCCTTTTTTTGCGTGTA 11 41 0 ATCTCCTTTT 0.886017 -81 GTATGCATGATTCATTGTTGTCCTTTATGTATTTTA 13 90 0 TTCTGCCTTT 0.705773 -53 CTAAAATATTCCCCATCCTTCTTTGAAATTTATG 16 9 1 TTCCCTCTTT 0.723403 -164 TTACATCACTTTCACTATTCGCTATTACGGTATTCC 22 92 0 TTCTCCTATT 0.886017 -44 ACAGAGGCCATTCTCTGTCCGTCTTTCTTTTTGTAT 23 24 1 TTCTCTCTTT 0.824851 -87 GCTCAACTTTTTCGTTGAGCCTTTTTATTGAATAGG 31 20 1 TTCTCTTTTT 0.827812 -61 TTCCTTCTGGTTATATAATCCCCTTTTTCTGTAAGC 33 30 1 TTATCCCTTT 0.618094 -133 ATGACTTTGCTTCGCCGTGCACTTTTTTTGGCCTCT 33 75 0 TTCCCCTTTT 0.94553 -88 TGCTAACCATTTCCTTTCACTCTATTGTACAGGAAA 43 39 1 TTCTCCTATT 0.886017 -188 TTTCAAAGTGTTCAATTTTCTCTTTT 47 1 0 TTCTCCTTTT 0.968999 -226 TAACGATAAATTCGCTGAACTCTTTTAAATCAATTT 47 116 1 TTCTCCTTTT 0.968999 -111 ATAGATTCATATCAATATCCACTTTTCAGCAAGCCA 51 223 0 ATCTCCTTTT 0.886017 -78 *** * * ***** Masking position 2 Map Score: 13.2463 Number of sites scoring better than the average of aligned sites = 356 Number in coding regions = 287 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 TTTATGAACAAAAAAGAAACCATCATTGAT 7 45 0 AAAAAGAAAC 0.738958 -132 AAAAGACATCAAAGAGAAACATACCCTGCA 7 147 1 AAAGAGAAAC 0.934292 -30 ATGGTATCAGAAGGAGAAACTACAAA 8 7 0 AAGGAGAAAC 0.969148 -100 ATCATTAAGAAAGGAGGAACAATGA 19 29 1 AAGGAGGAAC 0.832061 -15 AAATAAAATCGAAGAGAAACACGTACAGGA 21 183 1 GAAGAGAAAC 0.951561 -88 TGTAATGGGGGAGAAGAAACAGA 22 123 1 GAGAAGAAAC 0.89627 -13 AATTTGATAAAAAAAGAAACGAAAAATAAA 26 99 1 AAAAAGAAAC 0.738958 -202 ATTGCATAAAAATGAGAAACTGTTTAAAAT 32 189 1 AATGAGAAAC 0.778164 -80 TCTTCTGAATGAGGTGAAACC 34 127 1 GAGGTGAAAC 0.933036 -11 TTTAGGGTTTGAGGTGAAACG 35 68 1 GAGGTGAAAC 0.933036 -11 GACATGCGGTGAAGAGAACCCTTCACAAAA 44 184 1 GAAGAGAACC 0.756004 -117 TACTCACAAGGAGGTGAGACAC 47 215 1 GAGGTGAGAC 0.687268 -12 ACCTTACAAAAAGGAGAAACGGA 50 155 1 AAGGAGAAAC 0.969148 -13 ********** Masking position 2 Map Score: 9.54042 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 174 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 TGTAAGCGCTTTTATTAATTTTTCTTTCACATC 2 165 0 TTTTATTTTT 0.868416 -62 TGACACTCCTTATTTGATTTTTTGAAGACTTAC 6 123 0 TATTATTTTT 0.715506 -26 CCCCATCCTTCTTTGAAATTTATGTTTTTAATA 16 21 1 CTTGATTTAT 0.672939 -152 CACAACATGCTTTAGGACTTTTTTCGTTTATTT 22 19 1 TTTGATTTTT 0.90307 -117 AAACAATACTTTTATCACTTTATATCCGGAAAT 26 69 1 TTTTATTTAT 0.639585 -232 TGATCGTGATTTTGGGAGTTTTTATTCTTTCAA 28 62 0 TTTGATTTTT 0.90307 -140 TTCATATATCCTTGGAAATTTATGCACAAAAAA 32 46 0 CTTGATTTAT 0.672939 -223 AAAGCAAGGCTATGGCAATTTTTTCAGCCTGTC 43 95 0 TATGATTTTT 0.780238 -132 TTTTTATTGACATTTCATTTTTTGGGCACACTT 43 190 1 CATTATTTTT 0.673805 -37 TTACCGAAACTATTGTACTTTTTTTGTCAAACG 44 124 0 TATGATTTTT 0.780238 -177 CAACTTCGTTTTTCGTACTTTTTTCCCGGTGAA 45 249 0 TTTGATTTTT 0.90307 -52 ATCCCCACTCTTTTTCATTTTTTACATATAAAA 46 46 1 TTTTATTTTT 0.868416 -127 CTAGTATTGACTTCTAATTTTTTTACCATATAA 48 91 0 CTTTATTTTT 0.84425 -104 TATTCATATTCTTCTCAATTTTTAAAATATAAA 49 91 0 CTTTATTTTT 0.84425 -70 CAGATATGAGTTTGTTATTTTTTCTGACAAACC 50 74 1 TTTTATTTTT 0.868416 -94 *** * * ***** Masking position 7 Map Score: 8.11847 Number of sites scoring better than the average of aligned sites = 322 Number in coding regions = 231 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 9 AAAAAACACGAAAGGGGCAATGGGC 3 15 1 AAAGGGGAAT 0.701011 -15 AGCCATTCGTAAAAGTGCGGGAGGAAGGTC 5 96 1 AAAAGTGGGG 0.750086 -20 CATCGGTTTGAAAGGAGGAAGCGGAAGAATG 6 66 1 AAAGGAGAAG 0.701494 -83 TTATCTTGTCAAAGCGGCGATTAACTTTTCC 9 79 0 AAAGCGGGAT 0.72854 -98 TTGACTTAACAAAGGGGAGAGCTCAA 9 161 1 AAAGGGGGAG 0.963048 -16 AAGGGAGAGGGCCGGCACCTC 11 1 1 AAGGGAGGGG 0.694567 -121 GCGTGTAAAAAAAGGGGAGGTGCCGGCCCTC 11 17 0 AAAGGGGGGT 0.959568 -105 AAAAGTTTTAAAAGCGGGGAGCTTGGTGCG 11 102 1 AAAGCGGGAG 0.812465 -20 TTTAAAAAACAAAGGTGAGATTCACATGAAT 21 93 1 AAAGGTGGAT 0.822718 -178 CCCGGGCTATAAAAGGGTGATTAACAGAATG 22 63 0 AAAAGGGGAT 0.814821 -73 CTTTTGAAAAGGTGTGTGGAATTG 25 8 1 AAAGGTGGTG 0.464583 -17 TCTATTAGCGAAAGCAGGGATGAAA 28 187 1 AAAGCAGGAT 0.62496 -15 GAAGGAAAATAAAGGAGCAGTTGTAT 33 6 0 AAAGGAGAGT 0.681529 -157 AGATGATGAAAAAGGAGAGGTCTTCA 33 147 1 AAAGGAGGGT 0.936451 -16 AAAATTTGAGAATAGGGTGAGCAAATCGTTT 36 51 0 AATAGGGGAG 0.3142 -250 CAATCGGTAGAAAGGAGGAGGCTCTG 39 60 1 AAAGGAGAGG 0.77551 -16 TCATATAAAAAAATGGGAGGTTGGGAGAGTG 40 122 1 AAATGGGGGT 0.703084 -23 ACCCTCGCGAAAAGGAGAGATTGT 42 73 1 AAAGGAGGAT 0.909292 -14 GCAGCTGCCAAAAAGTGTGAGCTTTTTTATT 43 167 1 AAAAGTGGAG 0.671241 -60 AACCCTTCACAAAAGGGAGGTAATCATTTGT 44 200 1 AAAAGGGGGT 0.866101 -101 TAAAAAATGAAAAAGAGTGGGGATACCCCCA 46 39 0 AAAAGAGGGG 0.866368 -134 AGAAGAAAGCAAATGAGGGGGATTTTACA 52 124 1 AAATGAGGGG 0.703565 -19 ******* *** Masking position 2 Map Score: 16.935 Number of sites scoring better than the average of aligned sites = 653 Number in coding regions = 406 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 279 Fraction of orfs with sites within 600 bp upstream = 0.0448121 Motif number 10 CATCATACCAAAGAGAAGTCAGAATGATAA 8 61 1 AAGAGAAGTC 0.760098 -46 GCGGAATCGTAAAAGAAGTCAAAAAAAAGG 18 158 1 AAAAGAAGTC 0.916075 -93 AAGTCAAAAAAAAGGAAGGCGACTTTGTAA 18 173 1 AAAGGAAGGC 0.961803 -78 GCCTTCCTAATAAGGAAGGCTCTTTTGAAA 27 191 0 TAAGGAAGGC 0.913241 -110 GCCTTCCTTATTAGGAAGGCTCTTTTTATG 27 201 1 TTAGGAAGGC 0.682531 -100 ATAACGATAAAAAAGCAGGCGCC 28 4 0 AAAAGCAGGC 0.847082 -198 AATATAAAAAAGAAGAAGGCTGGCCGCCTC 30 11 1 AGAAGAAGGC 0.867004 -60 AATGAATGAAAAAAGAAGGCTGCGTCAAAC 34 38 0 AAAAGAAGGC 0.974342 -100 TCATACATTTTAAAGAAGCCAATCGGTAGA 39 41 1 TAAAGAAGCC 0.672732 -35 AAAGGAAAAAAGAAGTCTGTTCCCAAA 40 8 1 AAAAGAAGTC 0.916075 -137 GCATGTAGGAAAAGCAAGGCTATGGCAATT 43 108 0 AAAGCAAGGC 0.69435 -119 AACGCTTACAATAAGAAGTCGTTATTTTCA 45 136 0 ATAAGAAGTC 0.690347 -165 TTGGTATTCTTAAAGAAGGCATGTATTTTT 49 38 0 TAAAGAAGGC 0.94074 -123 TAAGAGAAGTAAGAGAAGGCC 51 2 0 AAGAGAAGGC 0.916823 -299 ********** Masking position 7 Map Score: 11.5442 Number of sites scoring better than the average of aligned sites = 508 Number in coding regions = 438 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 11 CACAAATAACAGGAGGTTATGTTG 2 213 1 AGGAGGTTAT 0.522301 -14 CGCGTGACAAAGGGGGATGTCACGACCGCT 4 206 1 AGGGGGATGT 0.828853 -95 TCGGTTTGAAAGGAGGAAGCGGAAGAATGA 6 68 1 AGGAGGAAGC 0.921476 -81 CCCTATTTTAAGGAGGATTTTT 9 3 0 AGGAGGATTT 0.773018 -174 ACCATGGACAAGGAGGCACCTTTTTAAA 15 14 1 AGGAGGCACC 0.839771 -18 TACATAAGTTAGGAGGATGGGAA 16 160 1 AGGAGGATGG 0.791445 -13 AGGAGGCAGTTGTCATGACG 18 1 1 AGGAGGCAGT 0.938851 -250 GAAAAGGGCCAGGAGGTAGCCATTTTGGAA 18 91 1 AGGAGGTAGC 0.724462 -160 TCATTAAGAAAGGAGGAACAATGA 19 30 1 AGGAGGAACA 0.452865 -14 AAAGATGTGAAGGAGGAAACGAT 20 78 1 AGGAGGAAAC 0.721488 -13 TCCAAGAAAAAGGATGATGTTATCATTCCC 23 82 0 AGGATGATGT 0.507999 -29 CTAATGAAAAAGGAGGAGCTT 29 41 1 AGGAGGAGCT 0.654938 -11 AGTTGTTAGAAGGAGGCTGTTTGACGCAGC 34 20 1 AGGAGGCTGT 0.955859 -118 GAATGAAAAAAGAAGGCTGCGTCAAACAGC 34 35 0 AGAAGGCTGC 0.430935 -103 GGTAGAAAGGAGGAGGCTCTG 39 65 1 AGGAGGCTCT 0.908029 -11 CATAATTATTAGGAGGATTTTTTTC 48 6 0 AGGAGGATTT 0.773018 -189 ACTTCAGCAAAGGGGGATGTTTGGGC 49 145 1 AGGGGGATGT 0.828853 -16 TTACTAATGAAGGAGGCAATAAGA 51 287 1 AGGAGGCAAT 0.772174 -14 ********** Masking position 1 Map Score: 11.1835 Number of sites scoring better than the average of aligned sites = 410 Number in coding regions = 266 Number in noncoding regions = 144 Number of orfs with sites within 600 bp upstream = 177 Fraction of orfs with sites within 600 bp upstream = 0.0284292 Motif number 12 GATTACGGTGCCGCTGGCCGGTGAACTGAAATT 1 246 1 CCGCTGCGGG 0.970106 -55 GATGTCACGACCGCTGTTCCGGGAAGCTATCAT 4 221 1 CCGCTGCCGG 0.992984 -80 AAACGATGTTCCGCTGTGCCGGTTTTTGTGGCC 12 87 1 CCGCTGCCGT 0.994177 -44 TGGCCTCTGTCCGCTAATCCGCT 23 1 0 CCGCTACCGT 0.982962 -110 ACAGGAAACACCGCTAAACCTCTAGATTGACAG 43 67 1 CCGCTACCTT 0.951205 -160 ATTTTATAGGCCGCTGGTCCTTTTTTATATGTA 46 68 0 CCGCTGCCTT 0.982962 -105 ****** *** * Masking position 5 Map Score: 2.26411 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 49 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 13 CTTTATTTTCTGATATTTTATAAAAAAGCGGTAAA 2 71 0 TTATATAAAA 0.867044 -156 TAATCGCCGCTTTGACAAGATAAAAACTTGACAGT 9 87 1 TGACATAAAA 0.65464 -90 TCGGTTATACATGATAAAACCGTTGTTAA 10 5 1 TTACATAAAA 0.931231 -101 CAATTTCATAGCCTATGCAATAAAAT 12 2 0 GTATATAAAA 0.641176 -129 ACATTCAAACTTTTACTTTATTAAAAACATAAATT 16 37 0 TTACATTAAA 0.707811 -136 TCTGAGAAACTAGTACTAAATAAAAATAAAATCGA 21 160 1 TTACATAAAA 0.933713 -111 ATGTTTTTTATTGTACTTTAAAAAATATCCGTTAA 26 169 1 TTACAAAAAA 0.791219 -132 GAAAAAAGTTTCCTATTCAATAAAAAGGCTCAACG 31 32 0 TTATATAAAA 0.867044 -49 TGTCTCCTTTTCTTACAGGAAAAAAGTTTCCTATT 31 50 0 TTACAAAAAA 0.791219 -31 TCTCTTCTGATATTACTAGATAAAAATTAAATCGC 32 113 0 TTACATAAAA 0.931231 -156 TTTTTAAAAATAGTATTGCATAAAAATGAGAAACT 32 175 1 TTATATAAAA 0.867044 -94 GTACTTTTAGTAGTAACCTATAAAAAAAGAAATTT 37 110 1 TTAAATAAAA 0.580165 -46 GCAAGCTAGAGCATATCATATAAAAAAATGGGAGG 40 107 1 GTATATAAAA 0.641176 -38 ACAAATCTTATTATATGGTAAAAAAATTAGAAGTC 48 81 1 TTATAAAAAA 0.639841 -114 CTCTTACTTCTCTTACTTGATTAAAAGATTAATAT 51 17 1 TTACATTAAA 0.709827 -284 * *** ****** Masking position 10 Map Score: 5.23215 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 59 Number in noncoding regions = 91 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 14 TACAAAATACGACAAAAACATTTTGAAAAT 1 66 1 GACAAAAACA 0.717554 -235 CTCCCGATTCCCCAAAATAAAAAGCGAGGA 1 153 1 CCCAAAATAA 0.814904 -148 TTTTTTTACACGCAAAAAAAGGGTAAACTG 11 35 1 CGCAAAAAAA 0.613564 -87 GATGCTCTTGGCCACAAAAACCGGCACAGC 12 99 0 GCCACAAAAA 0.648332 -32 TATCGGTTCAGCCAAGAAAAAATAAAGACC 14 28 0 GCCAAGAAAA 0.648332 -43 CGTAAAAGAAGTCAAAAAAAAGGAAGGCGA 18 165 1 GTCAAAAAAA 0.549603 -86 CGTTTCCTGTCCCAAAATCACTTTTTAAAA 21 44 0 CCCAAAATCA 0.693371 -227 AATAAAAACTCCCAAAATCACGATCAAAAC 28 69 1 CCCAAAATCA 0.693371 -133 GAAATTTATGCACAAAAAAACCCGGGCTGC 32 35 0 CACAAAAAAA 0.812815 -234 AAACGAAGAGGCCAAAAAAAGTGCACGGCG 33 69 1 GCCAAAAAAA 0.939346 -94 GAGTGGAGCCGACAAAATAAGTATAATGGA 35 32 1 GACAAAATAA 0.615633 -47 TGTTTTTGGGCACAAAAAAAGCCTGCTCCC 40 39 0 CACAAAAAAA 0.812815 -106 TTTTTTTGTGCCCAAAAACAGAATCTTTCT 40 49 1 CCCAAAAACA 0.874737 -96 GTTAAAGTGTGCCCAAAAAATGAAATGTCA 43 197 0 GCCCAAAAAA 0.648332 -30 GACAGCGTTTGACAAAAAAAGTACAATAGT 44 119 1 GACAAAAAAA 0.831827 -182 GAAGCACCCTCCAAAAAAATAAATGTTGT 50 10 1 TCCAAAAAAA 0.602899 -158 TTTCAAAAACACCAAAAAAATAAATGGCGG 51 181 0 ACCAAAAAAA 0.602899 -120 ********** Masking position 7 Map Score: 6.70369 Number of sites scoring better than the average of aligned sites = 455 Number in coding regions = 361 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 15 TTCAAACCGATGTGAAGACTGGAGAATTTTGTTAAC 6 42 0 TAACTGGAAA 0.911856 -107 CAAGATAGTATATTAACAATGATAAAAGTGTTTGTA 10 52 0 TAAATGATAA 0.599022 -54 GATAGAAGCTTAGGCAAAATAGAAAAGCCTGGACGA 11 64 1 TAAATAGAAA 0.596882 -58 TTTCATTCTATAATAATACTGGAAGAATTGTCTACA 16 102 0 TAACTGGAGA 0.601447 -71 GTTTCTCAGATTCCAATAATGGTAAATGTCCAAACA 21 134 0 TAAATGGTAA 0.808372 -137 TTTCTTTTTGTATCAAGAATGGATAAGGGACACTTG 23 47 1 TAAATGGAAA 0.957411 -64 CCAACAATAATTAATAAAATGAACAAGACAACAATT 27 127 0 TAAATGAAAA 0.888404 -174 GCCGACAAAATAAGTATAATGGAGAAAACTTTAGGG 35 39 1 TAAATGGAAA 0.957411 -40 ATTCTCAAATTTTTTAAAATGAATAAAAAGTTGCTT 36 69 1 TAAATGAAAA 0.888399 -232 CTTTTATCTTTGACCAGAATGGAGAATTTGTAAAGA 36 250 0 TAAATGGAAA 0.957411 -51 CGTGAACATTTTATCATACTGGAAAAGGATTATACA 42 11 0 TAACTGGAAA 0.911856 -76 CTTTTTTATATGTAAAAAATGAAAAAGAGTGGGGAT 46 46 0 TAAATGAAAA 0.888405 -127 ATGGTTTATATTTTAAAAATTGAGAAGAATATGAAT 49 87 1 TAAATTGAAA 0.596871 -74 ATTAATATAATAAAAATAATGAAAAAATGTAGTGTT 51 44 1 TAAATGAAAA 0.888405 -257 * * ****** ** Masking position 8 Map Score: 9.17118 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 47 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295