AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_bsub_reg_100.orf -o00340_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 yabF 144 similar to hypothetical proteins #2 ycbC 226 similar to 5-dehydro-4-deoxyglucarate dehydratase #3 ycbD 29 similar to aldehyde dehydrogenase #4 amhX 300 amidohydrolase #5 yefA 255 alternate gene name: yerS; similar to RNA methyltransferase #6 patA 300 aminotransferase #7 pksF 300 pksF #8 xpt 300 xanthine phosphoribosyltransferase #9 trpE 215 anthranilate synthase #10 gerCA 162 heptaprenyl diphosphate synthase component I #11 bfmBB 22 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) #12 bfmBAA 73 branched-chain alpha-keto acid dehydrogenase E1 (2-oxoisovalerate dehydrogenase alpha subunit) #13 yqiS 124 similar to phosphate butyryltransferase #14 yqeT 24 similar to ribosomal protein L11 methyltransferase #15 dnaJ 199 heat-shock protein #16 bltD 168 spermine/spermidine acetyltransferase #17 hisS 300 histidyl-tRNA synthetase #18 patB 80 aminotransferase #19 hisZ 250 histidyl-tRNA synthetase #20 ywdH 167 alternate gene name: ipa-58r; similar to aldehyde dehydrogenase #21 hutH 112 histidase #22 aldX 142 aldehyde dehydrogenase Motif number 1 GCAAAACCCTCTGAATACATAAGTATATA 1 6 0 CTGAATAAAT 0.734997 -139 GTCTAATAAGCAGAAAATGCACTTTGTCTATTAT 1 59 0 CAGAAAAGAT 0.906785 -86 AAAAAGTTTCATGAATATACAAAAGTTTTTATTT 1 105 1 ATGAATAAAA 0.585593 -40 TATAAAATATCAGAAAATAAAGATATTGACTTAT 2 84 1 CAGAAAAAAT 0.931153 -143 CCAGAAAAAACACGAAAGGGGCAAT 3 2 1 CAGAAAAAAA 0.93639 -28 AACACAGCCTAAGAAAAAACGTATGACATTTAAA 4 108 0 AAGAAAAAGT 0.786954 -193 TTCAATCACGCTGAAAAGATGACAAAATCCTAAA 5 68 0 CTGAAAAAGA 0.887528 -188 ACTTACCTGAATATGAAGAAAGAATCAGCT 6 7 1 CTGAATAGAA 0.684669 -294 TTCTTTTTTTCTGAAAAGAAAGGTATGTTTAGAA 6 176 1 CTGAAAAAAT 0.925519 -125 TTTGAATATTATGAAAATATACCTATAAAAATCA 7 20 1 ATGAAAAAAT 0.853302 -281 CTTGCATAGGCTGAAAATAAAAATTCCCGAACTT 8 64 0 CTGAAAAAAT 0.925519 -237 GCGTAAGCGAATGAAAAGATAAAACTCATACATA 10 97 1 ATGAAAAAAA 0.863593 -66 TTTGCAGAATAAACGCAAACATCTGCAC 13 5 1 CAGAATAAGA 0.657185 -120 TATCCCGGGCAAGAAAAAAAGTCAAAGCCAAGAG 15 103 0 AAGAAAAAGA 0.800813 -97 TAGGCACAATAAGAAAAGGTACTTAATTTGATAG 16 60 1 AAGAAAAGAT 0.819937 -109 ATACCGGGATAAGAAAAAAGGAGAATGTAGT 16 148 1 AAGAAAAAGA 0.800813 -21 ATCGTTAATGATGAAAATGAAAAAAACTCCCGCC 17 237 0 ATGAAAAGAA 0.819937 -64 CAAATTCCTGCTGAAAACGCAGATATGAGTTTGT 20 55 1 CTGAAAAGAT 0.899373 -113 CAAGGTTTGTCAGAAAAAATAACAAACTCATATC 20 76 0 CAGAAAAAAA 0.93639 -92 GGGGCTATGCGTGAAAACAGAAGTTCACAGCATA 21 37 1 GTGAAAAAAT 0.690637 -76 TACCAAAGTAAAGAAAAAGGAGTTGGGCTT 21 93 1 AAGAAAAGAT 0.819937 -20 GTCTTTCTTACAGAAAAGGTACCACCTTATAATA 22 79 1 CAGAAAAGAA 0.913704 -64 TAATAGGTCCGAGAAAAGAAGAAAGCAAATGAGG 22 108 1 GAGAAAAAGA 0.606768 -35 ******* * * * Masking position 7 Map Score: 22.6171 Number of sites scoring better than the average of aligned sites = 1214 Number in coding regions = 1013 Number in noncoding regions = 201 Number of orfs with sites within 600 bp upstream = 214 Fraction of orfs with sites within 600 bp upstream = 0.034372 Motif number 2 GGGCGCAAAACCCTCTGAATACATAAGTAT 1 14 0 CCCTCTGAAT 0.8067 -131 GGGTTTTGCGCCCTCTGTTTTTTTCGTTAT 1 31 1 CCCTCTGTTT 0.76618 -114 GCCTGGTCAGCCGGCTGTTTGGT 2 4 0 CCGGCTGTTT 0.934853 -223 GCCGGCTGACCAGGCTGTTTTTTTGCTGCG 2 19 1 CAGGCTGTTT 0.874936 -208 TCGATCCATCCCCTCTGTTTGAAAATATTA 4 165 1 CCCTCTGTTT 0.76618 -136 AACAGGAAGATAGGCTGTATATAATATAGC 4 220 0 TAGGCTGTAT 0.578132 -81 GGTTTTCAATCACGCTGAAAAGATGACAAA 5 76 0 CACGCTGAAA 0.943969 -180 GGTTTGCCTACACGCTGAAACTTGGCTTGA 5 192 1 CACGCTGAAA 0.943969 -64 AACTGATCTTCAGGCTCAAATCTGTGTCCG 7 150 0 CAGGCTCAAA 0.63654 -151 ATCTCTTGCATAGGCTGAAAATAAAAATTC 8 72 0 TAGGCTGAAA 0.635748 -229 AAAAGCATTGCCCGCTCAAATAAAGAGCAA 8 254 0 CCCGCTCAAA 0.842106 -47 GCTGGCTGTCCCCGCTGTTAAAAGCAAATG 10 11 1 CCCGCTGTTA 0.964455 -152 GCTGTATCCTCCCGCTGTTTGCGAGCATTT 10 36 0 CCCGCTGTTT 0.955166 -127 GAACCCGCCCCAGGCTGAAAGCGGATCCCA 17 37 1 CAGGCTGAAA 0.919013 -264 CCCGAGCACCTCCGCTGTTATCTTATGAAG 19 228 0 TCCGCTGTTA 0.8067 -23 TTATCAAATTCCTGCTGAAAACGCAGATAT 20 51 1 CCTGCTGAAA 0.751192 -117 ********** Masking position 6 Map Score: 13.7057 Number of sites scoring better than the average of aligned sites = 1946 Number in coding regions = 1815 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 3 AAGGTGACAAATGATCAGCTAGTGGTAAAATA 6 244 1 ATGATAGCAG 0.841038 -57 AAATAATCCCTTGAGGAGAGAGCGCATTATGG 7 57 1 TTGAGAGAAG 0.817522 -244 TTTGAGCCTGAAGATCAGTTAGTTGAGCTAGG 7 160 1 AAGATAGTAG 0.790384 -141 GGCAAGGAGAATGAGAAGATGGCATGAGAGGA 9 178 0 ATGAGAGAGG 0.968665 -38 TCTCCTTGCCATAAGGAGTGAGAGCA 9 200 1 ATAAGAGTAG 0.828181 -16 TTATTGGATGAGGAGTTGGTAGTT 14 8 1 ATGAGAGTGG 0.941292 -17 ATCTGATTCAATGATTAGAAAGTCAAAGTCAG 15 67 1 ATGATAGAAG 0.957707 -133 GTCAGATTGCATGATTAGAGAGGAACCCGCCC 17 15 1 ATGATAGAAG 0.957707 -286 AAGCTTCACTATGATAAGATAGAACTGCAAAT 18 27 0 ATGATAGAAG 0.957707 -54 TTTTTTCATAATGAGGAGAAGGATATTTGAAC 19 103 1 ATGAGAGAGG 0.968665 -148 AAAGTAAAGAAAAAGGAGTTGGGCTT 21 97 1 AAAAGAGTGG 0.531903 -16 GACACCTCCAATCATTAGACAGATCTTAGATA 22 15 1 ATCATAGAAG 0.745692 -128 TAGGTCCGAGAAAAGAAGAAAGCAAATGAGGG 22 111 1 AAAAGAGAAG 0.748974 -32 ***** *** ** Masking position 7 Map Score: 9.81849 Number of sites scoring better than the average of aligned sites = 228 Number in coding regions = 173 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 4 CATAGGCGTCAGGCATTTTAAATGTCATACGT 4 92 1 AGGCATTTTA 0.742529 -209 AAACTGTTTTAGGATTTTGTCAACATTCTGAG 5 32 0 AGGATTTTGA 0.94236 -224 TTTTCGTTTTAGGATTTTGTCATCTTTTCAGC 5 61 1 AGGATTTTGA 0.94236 -195 ATGGCTATTAATGAAATTGGCACATATAAACA 6 99 1 ATGAAATTGA 0.5942 -202 GATTATTTTAATGATTTTTATAGGTATATTTT 7 33 0 ATGATTTTTA 0.896157 -268 GCTCAATGCGAGGGATTTTTAACGATAAATCC 7 237 0 AGGGATTTTA 0.610451 -64 TGAGCGGGCAATGCTTTTTTTATTCTCATAAC 8 266 1 ATGCTTTTTA 0.74943 -35 ATTTTGAATTATGATTTTTCAATTCCTTTTAT 15 134 0 ATGATTTTTA 0.896157 -66 TACATTATTCATGATTTTTTCATAATGAGGAG 19 89 1 ATGATTTTTA 0.896157 -162 AATGAGGAGAAGGATATTTGAACTAAAAATAT 19 112 1 AGGATATTTA 0.837423 -139 AACTTCAGTAAGGATATTTTTAGTTCAAATAT 19 125 0 AGGATATTTA 0.837423 -126 CGTTTTCAGCAGGAATTTGATAAAATGCAGGA 20 42 0 AGGAATTTGA 0.894509 -126 AAACGCAGATATGAGTTTGTTATTTTTTCTGA 20 69 1 ATGAGTTTGA 0.67263 -99 ********* * Masking position 1 Map Score: 5.92185 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 283 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 5 ACAAAAGGATATATGGGAAGGAGCGGATGTGAA 2 140 1 ATAGAAGGAG 0.807306 -87 CCGTATACACAAATAACAGGAGGTTATGTTG 2 206 1 AAAAAGGAGG 0.559377 -21 AAATTCATTCTGATAGAAGGAGGTATTTCTTAC 4 277 1 TGAAAGGAGG 0.745532 -24 CTTTCTTTTCAGAAAAAAAGAAGACAACCAGCG 6 165 0 AGAAAAGAAG 0.817318 -136 ATTTATTACAATATAATAGGAACACTCATATAA 8 117 1 ATAAAGGAAC 0.53896 -184 CTCTCACTCCTTATGGCAAGGAGAATGAGAAGA 9 191 0 TTAGAAGGAG 0.625667 -25 AGACGTAAGGGAGGATACAATC 11 1 1 AGAGAGGGAG 0.930932 -22 TTTTAAAAGCATAAAGGAGGGGCTTGA 12 57 1 ATAAAGGGGC 0.751431 -17 AATTTATGTGAGAAATTCGGGAGAGTGAAGCGA 15 176 1 AGAACGGGAG 0.860743 -24 CTACTATACATGATAGTAGGGACGAGAGTTATA 17 203 0 TGAAAGGGAC 0.702716 -98 TTTATAAGGAATACATAAGGAGGTCTACCT 17 281 1 ATAAAGGAGG 0.820369 -20 AAGAATAAACATACATGAGGGGGTAACAGA 18 61 1 ATAAAGGGGG 0.935043 -20 CAAATCAAATAGAGAACAAGGAGATAAAG 19 7 0 AGAAAAGGAG 0.933783 -244 CTTGCGCGATTGACAAGCAGAAGAGATTTTTCA 20 106 1 TGAACAGAAG 0.281108 -62 TCACCATACCTTACAAAAAGGAGAAACGGA 20 148 1 TTAAAAGGAG 0.777712 -20 CATAGATCTTAGACGATAGGGGGCTATGCGTGA 21 18 1 AGAGAGGGGG 0.917069 -95 TAAAGCGCCCATACAAAAAGGAGCTATGCTGTG 21 62 0 ATAAAAGGAG 0.897643 -51 TTACCAAAGTAAAGAAAAAGGAGTTGGGCTT 21 92 1 AAAAAAGGAG 0.709116 -21 *** * ****** Masking position 3 Map Score: 9.40488 Number of sites scoring better than the average of aligned sites = 786 Number in coding regions = 486 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 327 Fraction of orfs with sites within 600 bp upstream = 0.0525217 Motif number 6 TCGAGCGTCTAATAAGCAGAAAATGCACTTTG 1 67 0 AAAAGCAGAA 0.886335 -78 CTTACAATTAAACAAAAGGATATATGGGAAGG 2 129 1 AAAAAAGGAA 0.518598 -98 AGCAATCATAAATAAGAGGACATAGGCGTCAG 4 72 1 AAAAGAGGAA 0.902678 -229 TTTATATTGAAACAGGAAGATAGGCTGTATAT 4 228 0 AAAGGAAGAA 0.822396 -73 ACTTACCTGAATATGAAGAAAGAATCAGCTG 6 10 1 AAATGAAGAA 0.757532 -291 CTTTTCAGAAAAAAAGAAGACAACCAGCGATT 6 162 0 AAAAGAAGAA 0.96706 -139 TATATCAGTTAAAAAGGTGACAAATGATCAGC 6 231 1 AAAAGGTGAA 0.824503 -70 TGCCCGCTCAAATAAAGAGCAAGCAATGCTGA 8 244 0 AAAAAGAGCA 0.577603 -57 CGGGATAAGAAAAAAGGAGAATGTAGT 16 152 1 AAAAGGAGAT 0.799686 -17 TCAAATAGAGAACAAGGAGATAAAG 19 4 0 AAAAGGAGAA 0.975939 -247 CGCGATTGACAAGCAGAAGAGATTTTTCACAT 20 110 1 AACAGAAGAA 0.8107 -58 CATACCTTACAAAAAGGAGAAACGGA 20 152 1 AAAAGGAGAA 0.975939 -16 GCGCCCATACAAAAAGGAGCTATGCTGTGAAC 21 59 0 AAAAGGAGCA 0.921713 -54 ATAGGTCCGAGAAAAGAAGAAAGCAAATGAGG 22 110 1 GAAAGAAGAA 0.8107 -33 ** ******* * Masking position 2 Map Score: 8.28871 Number of sites scoring better than the average of aligned sites = 603 Number in coding regions = 497 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 7 TTGGCTTGGTAAGCCAAGCTCAGAATGTTGACAA 5 14 1 AAGAGCTAGA 0.980315 -242 GAAGATCAGTTAGTTGAGCTAGGAGCTGACTCTG 7 169 1 TAGAGCTGGA 0.971407 -132 TACGATAAGAACAGCTTAGAAATACACAAG 9 7 1 AAGAGCTAGA 0.980315 -209 AGTTAGAGAATAGGGTAGCAGAGAATGAGTTTAG 9 70 1 TAGAGCAAGA 0.958199 -146 AGAATGAGTTTAGTTGAGCTGAGACATTATGTTT 9 91 1 TAGAGCTAGA 0.989352 -125 TATCTTATCATAGTGAAGCTTAGAAGAATAAACA 18 38 1 TAGAGCTAGA 0.989352 -43 *** **** *** Masking position 7 Map Score: 3.74548 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 5 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 8 TGACTTATTGTTTATTTGTCTTACAATTAAACA 2 110 1 TTTATTTCTA 0.720519 -117 TTATGATTGCTTTCATTTGCGCAATCGCTTCAT 4 50 0 TTTCATGCGA 0.687443 -251 TCATACGTTTTTTCTTAGGCTGTGTTTCGGCTG 4 116 1 TTTCTTGCTT 0.890535 -185 AGGCCAAGTTTTTCTTTCGCTTAAAACTAGAGG 5 224 1 TTTCTTGCTA 0.955254 -32 TTCTAATCTCTTGCATAGGCTGAAAATAAAAAT 8 74 0 TTGCATGCTA 0.813146 -227 GATATCAGCATTGCTTGCTCTTTATTTGAGCGG 8 240 1 TTGCTTTCTT 0.544367 -61 GGGCAATGCTTTTTTTATTCTCATAACGGAGGT 8 271 1 TTTTTTTCTA 0.720519 -30 TTATATAGTATTTTATCCTCTCATGCCATCTTC 9 163 1 TTTTATTCTA 0.661887 -53 GCCAATTCTTTTTTTTATGCTATAATGATACCT 10 64 1 TTTTTTGCTT 0.642333 -99 AGTTTTATCTTTTCATTCGCTTACGCAGGTATC 10 90 0 TTTCATGCTA 0.941895 -73 TTCACATTTATTTCTTAATCTATGTATGAGTTT 10 118 0 TTTCTTTCTT 0.816529 -45 AAAGAACACATTTCATAATCTGATTCAATGATT 15 50 1 TTTCATTCTA 0.89866 -150 CTCATGTATGTTTATTCTTCTAAGCTTCACTAT 18 47 0 TTTATTTCTA 0.720519 -34 ATTTTCATTCTTTCATCTGCTAACATATTATCA 19 165 1 TTTCATGCTA 0.941895 -86 TTCCGAATCCTTTAGTTCGCTAATATGATAATA 19 190 0 TTTAGTGCTA 0.524056 -61 ****** *** * Masking position 6 Map Score: 7.07041 Number of sites scoring better than the average of aligned sites = 540 Number in coding regions = 485 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 9 AAATTAATAAAAGCGCTTACAGATAGAGGCCG 2 177 1 AAGGCTACAG 0.772195 -50 TTTAGAAAAAAGGCGCATACAATCGAAATATA 6 203 1 AGGGCAACAA 0.846923 -98 ATATCAGTTAAAAAGGTGACAAATGATCAGCT 6 232 1 AAAGGTACAA 0.535676 -69 TTCCTGAATTAGACGGACACAGATTTGAGCCT 7 137 1 AGAGGAACAG 0.959435 -164 TTCTCATAACGGAGGTAGACAGG 8 288 1 GGAGTAACAG 0.793891 -13 CGCAAACAGCGGGAGGATACAGCCAATTCTTT 10 43 1 GGGGGAACAG 0.975285 -120 AGACGTAAGGGAGGATACAATC 11 9 1 GGGGGAACAA 0.917589 -14 GAAACAAGAAAGGTGGTAACAG 13 113 1 AGGGGTACAG 0.982277 -12 AACATACATGAGGGGGTAACAGA 18 68 1 AGGGGTACAG 0.982277 -13 GCGTGAAAACAGAAGTTCACAGCATAGCTCCT 21 45 1 AGAGTTACAG 0.843989 -68 *** *** **** Masking position 9 Map Score: 3.89293 Number of sites scoring better than the average of aligned sites = 291 Number in coding regions = 221 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 10 AGAAGGTAAAAATTCATTCTGATAGAAGGA 4 268 1 AATTCATTCT 0.771538 -33 GGTAAGAAATACCTCCTTCTATCAGAATGA 4 281 0 ACCTCCTTCT 0.950037 -20 AAATAGGATAAACTCATTATATTTGTTAAG 6 271 1 AACTCATTAT 0.918339 -30 TCTCTAACTCAACTCATTCTAATTGCTTTA 9 49 0 AACTCATTCT 0.928709 -167 AGCTCAACTAAACTCATTCTCTGCTACCCT 9 81 0 AACTCATTCT 0.928709 -135 TGCTCTCACTCCTTATGGCAAGGAGA 9 200 0 CACTCCTTAT 0.740021 -16 AACTACCAACTCCTCATCCAATAA 14 8 0 AACTCCTCAT 0.724716 -17 ATGATTTTTCAATTCCTTTTATCCCGGGCA 15 126 0 AATTCCTTTT 0.596518 -74 ACTACATTCTCCTTTTTTCT 16 159 0 ACTACATTCT 0.473392 -10 AGGTAGACCTCCTTATGTATTCCTTA 17 285 0 ACCTCCTTAT 0.942578 -16 ACGTACCTTTAATACATTATTCATGATTTT 19 77 1 AATACATTAT 0.460393 -174 AATATCCTTCTCCTCATTATGAAAAAATCA 19 100 0 TCCTCATTAT 0.521188 -151 AAGCCCAACTCCTTTTTCTTTACTTT 21 97 0 AACTCCTTTT 0.850813 -16 CAGAAAAGGTACCACCTTATAATAGGTCCG 22 89 1 ACCACCTTAT 0.827704 -54 ********** Masking position 7 Map Score: 5.96016 Number of sites scoring better than the average of aligned sites = 399 Number in coding regions = 263 Number in noncoding regions = 136 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 11 CGGCCGGGATTCTGCGCAGCAAAAAAACAGCCTGGTC 2 26 0 TCTGCAAAAA 0.756283 -201 ATCTTTATTTTCTGATATTTTATAAAAAAGCGGTAAA 2 71 0 TCTGATAAAA 0.698653 -156 ATGGGAAGGAGCGGATGTGAAAGAAAAATTAATAAAA 2 152 1 GCGGAAAAAA 0.962308 -75 TATTAATTATTCTGAATAGTAGCAATATGTGCTATAT 4 190 1 TCTGAAGAAA 0.863465 -111 GAAAGAATCAGCTGACCTTCAAGAAGAGCATCCTCCG 6 28 1 GCTGAAAAAA 0.98519 -273 AGCAAGCAATGCTGATATCACAAAAAACCGTACACGT 8 222 0 GCTGACAAAA 0.932764 -79 ATAATAAAAGGCGGAGTCGAAACAAGAAAGGTGGTAA 13 95 1 GCGGAAAAAA 0.962308 -30 CGGAAGCGGGGCTGACACTAAAAAGAAC 15 2 0 GCTGAAAAGA 0.926076 -198 CGCTTCCGGAGCTGACCGAAAAGAACACATTTCATAA 15 31 1 GCTGAAAAAA 0.98519 -169 TATAGTATAAGCTGAGTTTTAGCAATATCAGGATACC 16 116 1 GCTGAAGAAA 0.962308 -53 GATCGTTAATGATGAAAATGAAAAAAACTCCCGCCCC 17 235 0 GATGAAAAAA 0.839782 -66 ***** ** ** * Masking position 14 Map Score: 4.61689 Number of sites scoring better than the average of aligned sites = 543 Number in coding regions = 482 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 12 CGCATTCGTTGTCAGGCCTGTGCTTCGGTG 5 160 0 GTCAGGCCTG 0.921934 -96 TGTCTACAGAGTCAGCTCCTAGCTCAACTA 7 179 0 GTCAGCTCCT 0.970596 -122 TCGTGATAATTTCAGCTCTGTCTACAGAGT 7 197 0 TTCAGCTCTG 0.90576 -104 CAAGTTCCATGCCAGCTCTTAAGGGTGCTG 13 64 0 GCCAGCTCTT 0.884739 -61 TCTTTTTAGTGTCAGCCCCGCTTCCGGAGC 15 13 1 GTCAGCCCCG 0.987803 -187 GTTCTTTTCGGTCAGCTCCGGAAGCGGGGC 15 27 0 GTCAGCTCCG 0.989867 -173 ********** Masking position 4 Map Score: 2.32355 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 166 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 TTTTCAAACAGAGGGGATGGATCGAAATAT 4 160 0 GAGGGGATGG 0.794511 -141 CTTAAAACTAGAGGTGATTATAG 5 243 1 GAGGTGATTA 0.702841 -13 TATATTTGTTAAGGTGATGAATT 6 288 1 AAGGTGATGA 0.549326 -13 CAATATTTGCGAGGTGCTTCCTGAATTAGA 7 120 1 GAGGTGCTTC 0.908318 -181 TGAATTAGCTGAGGTGCTTT 7 291 1 GAGGTGCTTT 0.909972 -10 TTCGTATTTCAAGGGGATTCGATATAAAAG 8 11 0 AAGGGGATTC 0.797181 -290 TTTGGGGACAAGGGTGATATTT 10 151 1 AGGGTGATAT 0.558924 -12 AAGCATAAAGGAGGGGCTTGA 12 63 1 GAGGGGCTTG 0.909875 -11 CCAGCTCTTAAGGGTGCTGTCATACCAGGT 13 53 0 AGGGTGCTGT 0.841472 -72 GATAACAGCGGAGGTGCTCGGGTTG 19 236 1 GAGGTGCTCG 0.72463 -15 ATTTTTTTGGAGGGTGCTTC 20 1 0 AGGGTGCTTC 0.879623 -167 CTTAGACGATAGGGGGCTATGCGTGAAAAC 21 25 1 AGGGGGCTAT 0.705935 -88 AAAGCAAATGAGGGGGATTTTACA 22 129 1 AGGGGGATTT 0.803389 -14 ********** Masking position 8 Map Score: 2.77759 Number of sites scoring better than the average of aligned sites = 614 Number in coding regions = 462 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 119 Fraction of orfs with sites within 600 bp upstream = 0.0191134 Motif number 14 TTGGCTTACCAAGCCAAGTT 5 1 0 AAGCCAAGTT 0.984243 -255 TTGGCTTGGTAAGCCAAGCTCAGAATGTTG 5 14 1 AAGCCAAGCT 0.973433 -242 TGGCCTATTCAAGCCAAGTTTCAGCGTGTA 5 200 0 AAGCCAAGTT 0.984243 -56 TGGCTTGAATAGGCCAAGTTTTTCTTTCGC 5 214 1 AGGCCAAGTT 0.965682 -42 AAAAAAGTCAAAGCCAAGAGATGCCTGACT 15 93 0 AAGCCAAGAG 0.917605 -107 ********** Masking position 6 Map Score: 2.9116 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 28 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 15 ATCACTGTCCGGCCGGGATTCTGCGCAGCAAAAAAAC 2 35 0 GGGATCTCGA 0.817523 -192 TTTTCAGCGTGATTGAAAACCTTTGAAGTCTAGGAAG 5 85 1 GGAAACTTGA 0.784974 -171 GTTTCAGCGTGTAGGCAAACCTTCGCATTCGTTGTCA 5 176 0 GGAAACTCGA 0.963336 -80 TCAGAAAAAAAGAAGACAACCAGCGATTTGATTGTCT 6 153 0 AGCAACACGT 0.723211 -148 ATTATGGATAAACAGAGAATCTTTGAAGTATTAATCA 7 82 1 AGGAACTTGA 0.688959 -219 GAGCTATCCGGGGTGAAAAACATCGGTGAATTAGCTG 7 265 1 GGAAACACGT 0.949393 -36 AGCAATTGGAGAAGCTGCGCTTGCCGCAGAT 12 5 1 AGGAACTCGT 0.956357 -69 TCACGCGTTCAGCAGGAAACCTCCGGAGTGTTGTTTC 17 80 0 AGAAACTCGA 0.922438 -221 ATTAGGCAGTGAACGTGAACCTGCGTTAAAGGATCGA 17 125 1 GGGAACTCGT 0.979814 -176 GCAGATGAAAGAATGAAAATCAACGCTTAACTTCAGT 19 148 0 GGAAACACGT 0.949393 -103 CAACCCGAGCACCTCCGCTGTTATCTTAT 19 232 0 AGGCACTCGT 0.789313 -19 TACCTTTTCTGTAAGAAAGACAACGGTGAACCATCTA 22 63 0 GGAAGCACGT 0.77939 -80 * * *** ** ** * Masking position 11 Map Score: 3.21868 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 262 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665