AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i02010_ctra_reg_300.orf -o02010_ctra_300.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ytgA 300 Solute Protein Binding Family #2 glnP 206 ABC Amino Acid Transporter Permease #3 oppA_2 194 Oligopeptide binding protein permease #4 CT196 223 hypothetical protein #5 gcp_1 75 O-Sialoglycoprotein Endopeptidase #6 oppB_1 158 Oligopeptide Permease #7 oppC_1 31 Oligopeptide Permease #8 artJ 68 Arginine Binding Protein #9 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #10 CT382.1 182 hypothetical protein #11 yebL 300 Solute-binding protein #12 oppA_4 250 oligopeptide Binding Lipoprotein #13 CT480.1 192 hypothetical protein #14 CT481 161 hypothetical protein #15 CT482 300 hypothetical protein #16 fliY 45 Glutamine Binding Protein #17 CT488 88 hypothetical protein #18 glgC 192 Glucose-1-P Adenyltransferase #19 dppD 160 ABC Transport ATPase Motif number 1 ACGCGCTAGATTTTCCTTTTGGTTGAGGATATA 1 54 1 TTTTCTTTTT 0.923798 -247 GTACACGAGTTTTTATTTTTTTTCGAAACAGAA 2 67 1 TTTTTTTTTT 0.871607 -140 ATTGTTAAGGTTTTTCTTTTTTTTATTGGTAAC 3 64 1 TTTTCTTTTT 0.923798 -131 CTTCTAAAAATTTTACTTTTACAAAGTTGAAGC 4 23 1 TTTTCTTTTA 0.964348 -201 GCAAAGGCCTTTTATGTTTTCAACTTGTTATCT 6 98 1 TTTAGTTTTA 0.644459 -61 ATTCTTATTTTTTTTAAGAATCATG 8 3 1 TCTTTTTTTT 0.634992 -66 TTAACAAAAGTTTTTCTTTGTCTTCAATGAATT 10 57 1 TTTTCTTTGT 0.756495 -126 TTGAATTTAATTTTATTTTTTAAGATCTATTTG 10 118 1 TTTTTTTTTA 0.938067 -65 GATCTATTTGTTTTAGTTTTATAATAGAAACTA 10 141 1 TTTTGTTTTA 0.917506 -42 GAAAGAATATTCTTAGTTTTTTAAGATTTTATC 11 60 1 TCTTGTTTTA 0.740273 -241 TTCGTACAATTTTTGCTTTTTCTTTAAAAAACT 11 103 1 TTTTCTTTTT 0.923798 -198 CAACTCTCTTTTTTTTTCTTAAAAGATTCTCTA 12 37 1 TTTTTTCTTA 0.842825 -214 AAGAAAAGCTTTTTCCTCTTACAAACAAGATGA 12 120 0 TTTTCTCTTA 0.905447 -131 AGGAAAAAGCTTTTCTTTTGCTATAATTCGCTA 12 136 1 TTTTTTTTGA 0.795146 -115 AGGGGTATGCTCTTTTTCTTCAAGAACTCGCTC 14 74 0 TCTTTTCTTA 0.578802 -88 GTGAAGGACTGTTTGCTTTTATAGGGTGCGTAA 15 274 1 GTTTCTTTTA 0.701847 -27 TGGATAAAAATTTTTCTCTTGAAT 16 32 1 TTTTCTCTTA 0.905447 -14 AGAGTGGATTTTTCTTTTCGAGCTGTTGACA 17 9 1 TTTTCTTTTA 0.964348 -80 GCCAACCACTTTTACCTTTGTCAACAGCTCGAA 17 27 0 TTTACTTTGA 0.530445 -62 ATTAGATAATTTTTATTTTTCAAACATCTAAAA 18 70 1 TTTTTTTTTA 0.938067 -123 AATAAATCGATTTTATTTTTAGATGTTTGAAAA 18 86 0 TTTTTTTTTA 0.938067 -107 TTTTTAATAATTTATTTTTTAAAATTATTTTTT 18 154 1 TTTATTTTTA 0.71169 -39 GAACCAAAATTTTTTGTTTTTTTCTAAGATTTT 19 96 1 TTTTGTTTTT 0.832911 -65 **** ***** * Masking position 7 Map Score: 27.0325 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 332 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 Motif number 2 CACATGGGATCATAAGAAAAACTCTATTTTAAAGG 1 166 0 CTAAAAATCT 0.974352 -135 TAAAATCTTTTATCGAAAAAATTTTATACGACTTC 2 97 0 TTAAAAATTT 0.693131 -110 ACGAAAGGTTCTTATAAAAAAAGCCTTTCCTAATT 2 131 0 CTAAAAAGCC 0.980468 -76 TCACCCCCTTTATGAAAAAAATGCCCAGTATCCTA 3 14 1 TTAAAAAGCC 0.941287 -181 TTAATTCTAACCTTCTAAAAATTTTACTTTTACAA 4 12 1 CTAAAAATTT 0.876117 -212 ATTTCATTTCTTTTGCAAAAACTCTCTACTTTAAA 4 176 1 TTAAAAATCT 0.923857 -48 TTACTCCGTGCGTAGAAAAGATTCTCTCTTTAAAA 6 20 1 CTAAAGATCT 0.809926 -139 AAGATTTTTCAATGAAAAAAACGCCCTCTTCTCTT 9 36 0 ATAAAAAGCC 0.909038 -101 AAGCAAAAATTGTACGAAAAAAGCTGGAGATAAAA 11 86 0 TTAAAAAGCT 0.951317 -215 TGAACCCCATATTACTAAAAAATTTATATGTGAAT 11 170 1 ATAAAAATTT 0.584714 -131 TCGTTGAAAACGCACCAAAAAGTCTCAAGACAGGT 12 210 0 CCAAAAATCT 0.828112 -41 TACTTTCTCTCCTCGAAAAAATGCTATAGAAAAGA 13 121 0 CTAAAAAGCT 0.983919 -72 AGGAGCTATGCATAGCAAAAATTCCAAA 14 4 0 CTAAAAATCC 0.968913 -158 AGAGAAGATCCTTCTTAAAAAGGCCTACATCCAAA 15 99 1 CTAAAAAGCC 0.980468 -202 ATTCAAGAGAAAAATTTTTATCCACCCA 16 28 0 CAAAAAATTT 0.51622 -18 TAAAAAATAAATTATTAAAAAAGCCAGACAAACAA 18 140 0 ATAAAAAGCC 0.909038 -53 TTCTCAAAGACAATTAAAAAAGGCTTAT 19 4 0 CAAAAAAGCT 0.902263 -157 TTTAATTGTCTTTGAGAAAAATGCTCCCAAAATAT 19 21 1 TTAAAAAGCT 0.951317 -140 * * ***** *** Masking position 8 Map Score: 18.2686 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 222 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 Motif number 3 CATTAAACGTTCTCTTCTCTTCAAGAGAAGAG 9 14 1 TCTTTCTTTC 0.95576 -123 TCTTTCTATTTCTTTTCTCTTCCCTGTGTGTA 9 67 1 TCTTTCTTTC 0.95576 -70 TTTCCTTGTTTCTTCTCTTAACTCATGAACAG 9 106 0 TCTCTCTAAC 0.892192 -31 GAATATTCTTTCTACTGTCTTTTTGCCGGCGA 11 40 0 TCTCTGTTTT 0.860022 -261 CTAAAGCTTCTCTGCTCTGAACCCCATATTAC 11 153 1 TCTCTCTAAC 0.892192 -148 AGTTGAAAATTCAACTCTCTTTTAGAAAAAA 12 10 0 TCACTCTTTT 0.908675 -241 AGTTGAATTTTCAACTCTCTTTTTTTTTCTTA 12 26 1 TCACTCTTTT 0.908675 -225 GCGTTGTCTCCTCTATTCGTTGAAAACG 12 233 0 TCTCTCTTTC 0.985432 -18 CAAGGATCTATTCTGATCGACAACTATC 13 7 1 TCTTTCTATC 0.891692 -186 TAGGTCCGCTTCTATTCTTTTCTATAGCATTT 13 106 1 TCTTTCTTTC 0.95576 -87 AAGAACTCGCTCTGCTGTTTCCATAGAACAGA 14 54 0 TCTCTGTTCC 0.795602 -108 ATAGTAGGGGTATGCTCTTTTTCTTCAAGAAC 14 80 0 TATCTCTTTT 0.676771 -82 TTAAGAAGGATCTTCTCTGTTTACAAAGACGA 15 85 0 TCTCTCTTTT 0.973687 -216 GATAGAAGAATCAGCTCTTTATTTTGCCAACC 17 53 0 TCACTCTTAT 0.761587 -36 AGATAAGAACTCTTTTCTGACTCGCCT 18 6 0 TCTTTCTACT 0.60951 -187 *** **** *** Masking position 6 Map Score: 14.3213 Number of sites scoring better than the average of aligned sites = 252 Number in coding regions = 251 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 4 CATTCTGTTAAAAGTATCTTTGCGATAAGC 1 91 1 AAAGTATCTT 0.763274 -210 TTGCGATAAGCGAGGTTCTTTTTTTGGAGG 1 110 1 CGAGGTTCTT 0.900328 -191 TTTTGTCCTTAGGGGATCGTATACTTTTTC 1 245 1 AGGGGATCGT 0.828797 -56 TCGATTATCTGGAGGCTCTT 1 291 1 GGAGGCTCTT 0.905591 -10 ATATTGAACGAAAGGTTCTTATAAAAAAAG 2 143 0 AAAGGTTCTT 0.909651 -64 TTTTGGAAGGAGAGGATCGTATCATGAGAT 5 29 0 AGAGGATCGT 0.970749 -47 CATTTTAAAGAGAGAATCTTTTCTACGCAC 6 27 0 AGAGAATCTT 0.901227 -132 AAAATGATTGCGAGGCTCTTAAAAGCA 10 8 0 CGAGGCTCTT 0.93321 -175 GAGCTGGTATAGAGAATCTTTTAAGAAAAA 12 49 0 AGAGAATCTT 0.901227 -202 CAAGGATCTATTCTGATCGA 13 1 1 CAAGGATCTA 0.824997 -192 TAGGCAAGGAAAAGGATCGTTTCTGGATAG 13 34 0 AAAGGATCGT 0.953873 -159 GGGAATTGCAAAAGGATCTTCTGGGTAAAT 14 131 0 AAAGGATCTT 0.97823 -31 TTCGATGTACAAAGGATCTAGGGTGGTTTC 15 24 1 AAAGGATCTA 0.893984 -277 GCCTTTTTAAGAAGGATCTTCTCTGTTTAC 15 93 0 GAAGGATCTT 0.945196 -208 ********** Masking position 7 Map Score: 13.7784 Number of sites scoring better than the average of aligned sites = 226 Number in coding regions = 226 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 Motif number 5 GACAATTCTAAATAATTTTAACAACTAA 1 9 0 AATAATTTTA 0.50838 -292 CTTTTATCGAAAAAATTTTATACGACTTCT 2 96 0 AAAAATTTTA 0.51304 -111 TTTTTCGATAAAAGATTTTAATTAGGAAAG 2 112 1 AAAGATTTTA 0.800707 -95 TTTAATTAGGAAAGGCTTTTTTTATAAGAA 2 128 1 AAAGGCTTTT 0.56655 -79 GAATAATTGTTAAGGTTTTTCTTTTTTTTA 3 59 1 TAAGGTTTTT 0.740045 -136 GTAACAGAAAAACAGTTTTGGCTTTTTGCT 3 92 1 AACAGTTTTG 0.636969 -103 GGCTTTTTGCTATGGTTTTTTGTACAATCC 3 111 1 TATGGTTTTT 0.469183 -84 CTAACCTTCTAAAAATTTTACTTTTACAAA 4 18 1 AAAAATTTTA 0.51304 -206 TTAGAAATAAAACGGTTTTTTTAATTAGTA 4 87 0 AACGGTTTTT 0.826429 -137 AAAGGTTTTAAAGTCCAAAT 4 214 0 AAAGGTTTTA 0.865862 -10 AAAGAAATAGAAAGATTTTTCAATGAAAAA 9 52 0 AAAGATTTTT 0.801119 -85 GGTATAGCGAAAAAATTTTAACAAAAGTTT 10 40 1 AAAAATTTTA 0.51304 -143 AAATTTTAACAAAAGTTTTTCTTTGTCTTC 10 52 1 AAAAGTTTTT 0.620273 -131 CAATGAATTTAATGGTTTTAAATTAAATTG 10 81 1 AATGGTTTTA 0.66623 -102 CTTAGTTTTTTAAGATTTTATCTCCAGCTT 11 71 1 TAAGATTTTA 0.609363 -230 GCTTTTTTCGTACAATTTTTGCTTTTTCTT 11 97 1 TACAATTTTT 0.463794 -204 CGGGGTGAGGAACAGTTTTTTAAAGAAAAA 11 119 0 AACAGTTTTT 0.784783 -182 TGTAAGAGGAAAAAGCTTTTCTTTTGCTAT 12 130 1 AAAAGCTTTT 0.384528 -121 GTGGGTGGATAAAAATTTTTCTCTTGAAT 16 27 1 AAAAATTTTT 0.482508 -19 ATGCAATAATTACAGTTTTGTTTGTCTGGC 18 123 1 TACAGTTTTG 0.390152 -70 CACCATAAAAAATAATTTTAAAAAATAAAT 18 163 0 AATAATTTTA 0.50838 -30 GAAAAAAACAAAAAATTTTGGTTCTTAGTA 19 90 0 AAAAATTTTG 0.623244 -71 TGTTTTTTTCTAAGATTTTTCACGCTCGAG 19 110 1 TAAGATTTTT 0.636084 -51 ********** Masking position 7 Map Score: 18.0838 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 365 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 Motif number 6 ATCGCAAAGATACTTTTAACAGAATGAATTTA 1 85 0 TACTTTAAAG 0.615469 -216 TACGATCCTCTCCTTCCAAAATGTTTCCCTCT 5 38 1 TCCTTCAAAT 0.925217 -38 AGTAGATTCCTTTGTATATTGTATTGCGA 6 140 0 TCCTTTTAAT 0.936318 -19 TGCTTTTAAGAGCCTCGCAATC 10 1 1 TGCTTTAAAG 0.703448 -182 CTATACCAGCTCCTTCCTAAATATTTTTTGAA 12 67 1 TCCTTCTAAT 0.944543 -184 CCGCTTCTATTCTTTTCTATAGCATTTTTTCG 13 111 1 TCTTTTTAAG 0.667388 -82 CGACGTCTCCTTTTAATAGGTAGATTTCA 13 174 0 TCCTTTAAAG 0.953081 -19 CCACCCTAGATCCTTTGTACATCGAACGAAAA 15 18 0 TCCTTTTAAT 0.936318 -283 ACAGAGAAGATCCTTCTTAAAAAGGCCTACAT 15 97 1 TCCTTCTAAA 0.80776 -204 CGGACCCATGCCCTTTATAGAGATAAGAACTC 18 26 0 CCCTTTTAAG 0.906394 -167 AAAATATACCTCCTTCATATATATATTTGCAA 19 49 1 TCCTTCTAAT 0.944543 -112 GCTCGAGGTCCCCTTCAAATAGTAGGAGATAC 19 133 1 CCCTTCAAAG 0.890723 -28 ****** ** ** Masking position 9 Map Score: 7.26121 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 103 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 Motif number 7 GCGAGGTTCTTTTTTTGGAGGGGGAGCTCCT 1 119 1 TTTTTTGGAG 0.937133 -182 AGTTTTTATTTTTTTTCGAAACAGAAGTCGT 2 74 1 TTTTTTCGAA 0.863012 -133 TCGTATAAAATTTTTTCGATAAAAGATTTTA 2 101 1 TTTTTTCGAA 0.863012 -106 AGGAAAGGCTTTTTTTATAAGAACCTTTCGT 2 135 1 TTTTTTATAG 0.573787 -72 CAGTTTTGGCTTTTTGCTATGGTTTTTTGTA 3 104 1 TTTTTGCTAG 0.76928 -91 TTTGCTATGGTTTTTTGTACAATCCCCTGGC 3 116 1 TTTTTTGTAA 0.823463 -79 AAAAACCGTTTTATTTCTAAGTCGACTAATC 4 97 1 TTATTTCTAG 0.593817 -127 AAAGAGAGAATCTTTTCTACGCACGGAGTAA 6 20 0 TCTTTTCTAG 0.644352 -139 ATTCTTATTTTTTTTAAGAATCATGTTG 8 8 1 TTTTTTTTAG 0.573787 -61 TTTGTTAAAATTTTTTCGCTATACCGCAAAA 10 34 0 TTTTTTCGCA 0.654487 -149 GATAGCCGAGTTGTTTGGAGAGTAGTAGTTT 11 11 0 TTGTTTGGAA 0.693341 -290 AAGAATGAAATTGTTTGGAAGACAAGCCATT 11 225 1 TTGTTTGGAG 0.869387 -76 TTTTTTCTAAAAGAGAGTTGA 12 1 1 TTTTTTCTAA 0.85302 -250 GTCGATCATCTTGTTTGTAAGAGGAAAAAGC 12 115 1 TTGTTTGTAG 0.859784 -136 TTCTATAGCATTTTTTCGAGGAGAGAAAGTA 13 125 1 TTTTTTCGAG 0.948841 -68 TTTGGAATTTTTGCTATGCATAGCTCCT 14 8 1 TTTTTGCTAG 0.76928 -154 CAATGGTTGTTATTTTGGATGTAGGCCTTTT 15 116 0 TATTTTGGAG 0.516091 -185 CATGGGTCCGTTTTTTGTCAAAATTAGATAA 18 48 1 TTTTTTGTCA 0.583772 -145 AATTACAGTTTTGTTTGTCTGGCTTTTTTAA 18 130 1 TTGTTTGTCG 0.648347 -63 AATTTTTTGTTTTTTTCTAAGATTTTTCACG 19 103 1 TTTTTTCTAG 0.944708 -58 ********* * Masking position 5 Map Score: 18.0107 Number of sites scoring better than the average of aligned sites = 235 Number in coding regions = 235 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 Motif number 8 AGAGTTTCAGCAAACAATCAAATAA 3 180 0 GTTTCAGAAC 0.922856 -15 AACTAGTTGGGTTTTATTAAACCAGCGGTTGA 4 136 0 GTTTTATAAC 0.685383 -88 GAGTTTGTTTTAGAAATCCTTTATTAAA 7 14 0 GTTTTAGAAC 0.949116 -18 GAGCAGAGAAGCTTTAGAAAACGGGGTGAGGA 11 138 0 GCTTTAGAAC 0.791477 -163 GAGAAAGCAAGCTTTAGGAATCGTCTTTGTAA 15 65 1 GCTTTAGAAC 0.974632 -236 CAGTTCCAATGCATTAGAAAACCCTGAGACAC 15 242 0 GCATTAGAAC 0.928693 -59 ******* ** * Masking position 6 Map Score: 2.09903 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 28 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 Motif number 9 AAAGGATACAAGCCTCCTGTAAGGAGCTCCCCCT 1 137 0 ACTCTGTAGG 0.813106 -164 AAGAGCCTCCAGATAATCGATACGGGG 1 284 0 ACTCAGAAAT 0.742457 -17 ATTTCTTGTGATACTAATGACAGGATAGGGGATA 2 183 1 ACTATGAAGG 0.929552 -24 AATGCCCAGTATCCTATAGAGAGGTTGAATAATT 3 33 1 ACTAAGAAGG 0.966775 -162 CTTGATTAACAATCTCATGATACGATCCTCTCCT 5 18 1 ACTCTGAACG 0.958942 -58 ATAATTTAACACTCTCTAGACAAGACCTCTCCGC 6 56 0 ACTCAGAAAG 0.967069 -103 CGCACCAAAAAGTCTCAAGACAGGTCTAGAATAC 12 201 0 ACTCAGAAGG 0.98431 -50 CTGATCGACAACTATCCAGAAACGATCCTTTTCC 13 23 1 AATCAGAACG 0.81943 -170 CCTCGAAAAAATGCTATAGAAAAGAATAGAAGCG 13 112 0 ACTAAGAAAG 0.933815 -81 GAAGATAACCAACCTATAGAGACGGTTTTGCACT 15 207 1 ACTAAGAACG 0.956866 -94 * *** *** *** Masking position 5 Map Score: 6.6553 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 44 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 Motif number 10 CGATAAGCGAGGTTCTTTTTTTGGAGGGGG 1 113 1 GGTTCTTTTT 0.855179 -188 TAGAAATATCGGTTGGTTTTTGTCCTTAGG 1 228 1 GGTTGGTTTT 0.971958 -73 ATTATAACTAGTTGGGTTTTATTAAACCAG 4 143 0 GTTGGGTTTT 0.788457 -81 ATAGAATAATGGTTCGTTGTTAATATTTTA 11 274 1 GGTTCGTTGT 0.943331 -27 GAGACTTTTTGGTGCGTTTTCAACGAATAG 12 219 1 GGTGCGTTTT 0.974188 -32 CGTCTCTATAGGTTGGTTATCTTCTCGATA 15 201 0 GGTTGGTTAT 0.895297 -100 AAAGGGCATGGGTCCGTTTTTTGTCAAAAT 18 42 1 GGTCCGTTTT 0.953507 -151 ********** Masking position 7 Map Score: 2.25586 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 24 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 Motif number 11 TGATCCCATGTGGCGATAGGCCGGGTCTAGCG 1 189 1 TGGCGTAGCC 0.9928 -112 TTTCTACTATCGGCGCTAGACCCGGCCTATCG 1 202 0 CGGCGTAGCC 0.993457 -99 AGAATCATGTTGGGTATAGTCCCTGCCGTTAG 8 27 1 TGGGTTAGCC 0.946702 -42 GTATAGTCCCTGCCGTTAGACCATTGAGTCGG 8 40 1 TGCCGTAGCC 0.977043 -29 GTCTTTTTGCCGGCGATAGCCGAGTTGTTTGG 11 24 0 CGGCGTAGCG 0.712059 -277 GTTGTTATTTTGGATGTAGGCCTTTTTAAGAA 15 110 0 TGGATTAGCC 0.92318 -191 ***** *** ** Masking position 7 Map Score: 1.87723 Number of sites scoring better than the average of aligned sites = 7 Number in coding regions = 7 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 Motif number 12 TTGGAGGGGGAGCTCCTTACAGGAGGCTTG 1 133 1 AGCTCCTTAC 0.955347 -168 TGATACGATCCTCTCCTTCCAAAATGTTTC 5 35 1 CTCTCCTTCC 0.92679 -41 TCTCTATACCAGCTCCTTCCTAAATATTTT 12 64 1 AGCTCCTTCC 0.991123 -187 TGCTATGCATAGCTCCTCCCCCATTTCTGA 14 22 1 AGCTCCTCCC 0.980506 -140 CCCAAAATATACCTCCTTCATATATATATT 19 46 1 ACCTCCTTCA 0.888656 -115 ********** Masking position 4 Map Score: 0.192996 Number of sites scoring better than the average of aligned sites = 44 Number in coding regions = 44 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 Motif number 13 TAAGCCGACAATACTTTTGGAGGCCATATAA 2 33 1 ATACTTTGGA 0.74441 -174 TGTAAAAGTAAAATTTTTAGAAGGTTAGAAT 4 15 0 AAATTTTAGA 0.744917 -209 CCAGCGGTTGATATTTCTTGATTAGTCGACT 4 116 0 ATATTTCTGA 0.729585 -108 ATTTAATTTTATTTTTTAAGATCTATTTGTT 10 122 1 ATTTTTTAGA 0.765902 -61 TTCGTTGTTAATATTTTAAGATAAT 11 286 1 ATATTTTAGA 0.954032 -15 GGTATAGAGAATCTTTTAAGAAAAAAAAAGA 12 43 0 ATCTTTTAGA 0.829033 -208 TCCTTCCTAAATATTTTTTGAAATATTTCTT 12 77 1 ATATTTTTGA 0.928249 -174 TTCCTTGCCTATATTTTCTGATTTTCTTAAA 13 53 1 ATATTTTTGA 0.928249 -140 TAAATCGATTTTATTTTTAGATGTTTGAAAA 18 86 0 TTATTTTAGA 0.744917 -107 TGAAGGAGGTATATTTTGGGAGCATTTTTCT 19 35 0 ATATTTTGGA 0.933181 -126 ******* *** Masking position 6 Map Score: 3.26772 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 32 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 Motif number 14 ********** No masking Map Score: 1.4327e-11 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 Motif number 15 ********** No masking Map Score: 1.4327e-11 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