AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_ctra_reg_300.orf -o00620_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 araD 83 Ribulose-P Epimerase #2 dhnA 300 Predicted 1,6-Fructose biphosphate aldolase (dehydrin family) #3 ydaO 153 PP-Loop Superfamily ATPase #4 surE 100 SurE-like Acid Phosphatase #5 ubiA 111 4-hydroxybenzoate octaphenyltransferase #6 pdhA 221 Pyruvate Dehydrogenase Alpha #7 accA 132 AcCoA Carboxylase/Transferase Alpha #8 CT266 117 hypothetical protein #9 himD 219 Integration Host Factor Alpha #10 murE 300 UDP-N-acetylmuramoylalanylglutamyl DAP Ligase #11 accD 71 AcCoA Carboxylase/Transferase Beta #12 sodM 131 Superoxide Dismutase (Mn) #13 yhxB 151 Phosphomannomutase #14 CT296 108 hypothetical protein #15 tpiS 196 Triosephosphate Isomerase #16 CT330 208 hypothetical protein #17 pykF 96 Pyruvate Kinase #18 mdhC 190 Malate Dehyrogenase #19 ltuA 114 hypothetical protein #20 pgi 112 Glucose-6-P Isomerase #21 phnP 28 predicted metal dependent hydrolase (histidinic triad) #22 artJ 68 Arginine Binding Protein #23 aroG 136 phospho-2-dehydro-3-deoxyheptonate aldolase #24 CT382.1 182 hypothetical protein #25 sucB_2 245 Dihydrolipoamide Succinyltransferase #26 ribC 300 Riboflavin Synthase #27 CT552 300 hypothetical protein #28 fmu 124 RNA Methyltransferase #29 brnQ 149 Amino Acid (Branched) Transport #30 CT555 174 SWI/SNF family helicase #31 CT556 177 hypothetical protein #32 lpdA 208 Lipoamide Dehydrogenase Motif number 1 GAGTCTTTCATTTTCTTTACCTCACCTTCTCA 2 102 1 TTTTCTTCCT 0.763324 -199 GTCTATAAATCTTTCTTAGCATGCAAACATTT 2 194 0 CTTTCTTCAT 0.608018 -107 TCTTCTTCCCTTTTCCCGGCTT 8 1 1 TCTTCTTCTT 0.912204 -117 GATTCAAGACTTTTTTTATCTTTTCCATGAAC 9 112 0 TTTTTTTCTT 0.747433 -108 ATTATGAAATTGCTCTTTTCTTTATTATTAGT 10 76 0 TGCTCTTCTT 0.886945 -225 AAAAGACGAGTTCTCTTGTCTTTGCTCTTTCT 10 171 1 TTCTCTTCTT 0.983 -130 GATATGCTAATCTTCTTGTCTTACTTTTTTCT 15 51 0 TCTTCTTCTT 0.912204 -146 CTTTAGAAGCTTCTCTTGCCTTGTATGAAGAG 16 91 1 TTCTCTTCTT 0.983 -118 AGGTACTTGATTCTTTTATCATCCAAACGTAT 18 91 1 TTCTTTTCAT 0.702282 -100 AAGCCACCCTCTCTTTACTTTTACAAAACG 18 171 0 CTCTCTTCTT 0.967763 -20 GAGACCTTCTTTCTTTTTACTTGTACTATCTT 20 62 0 TTCTTTTCTT 0.920782 -51 TCATTAAACGTTCTCTTCTCTTCAAGAGAAGA 23 13 1 TTCTCTTCTT 0.983 -124 GAAAAAAACGCCCTCTTCTCTTGAAGAGAAGA 23 26 0 CCCTCTTCTT 0.954929 -111 ATCTTTCTATTTCTTTTCTCTTCCCTGTGTGT 23 66 1 TTCTTTTCTT 0.920782 -71 TCCTTGTTTCTTCTCTTAACTCATGAACAGCA 23 104 0 TTCTCTTCTC 0.958046 -33 CAGTTGATAATCTTCTTCTCATATTGAGTTAA 25 184 1 TCTTCTTCAT 0.678309 -62 TAACCCTTTTTTCTCTTAACTCTCTATCTAAG 27 159 1 TTCTCTTCTC 0.958046 -142 TTCCTTTTCGCTTCCATCATCTC 28 2 1 TCCTTTTCTT 0.891344 -123 AAGAGCATCCCTCTCTTGGCTCGAAGGACCGT 28 101 1 CTCTCTTCTC 0.922215 -24 TCTGAAGGACCTCTCTTTTCCTTTCCTAGAAA 32 102 1 CTCTCTTCCT 0.868017 -107 GGAAGGAGAATCCTCTTCCCTCAGATAATCAT 32 139 1 TCCTCTTCTC 0.941578 -70 ******* *** Masking position 6 Map Score: 29.2519 Number of sites scoring better than the average of aligned sites = 170 Number in coding regions = 170 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 GCTTCTTTACAAAGCCCTTTTCTGTGCAAAAGA 3 13 0 AAAGTTTTCT 0.939658 -141 CTTAGAAAGAAAAGAGCTTCTTTACAAAGCCCT 3 28 0 AAAGTTCTTT 0.771564 -126 AACGAACTTCAACGTACTTTTTTCAGCAAGAAA 5 26 1 AACGTTTTTT 0.837936 -86 TTGTAATCAGAAGGAGCTTTTCTTGCTGAAAAA 5 44 0 AAGGTTTTCT 0.890131 -68 GTAGTGCCGAAAAGTTTTTTTTTGTAGCATAGA 6 48 1 AAAGTTTTTT 0.958786 -174 AAATTTCCTCAAGATTATTTTTTGCCATTGGAC 8 80 1 AAGATTTTTT 0.687783 -38 TCTCACAAACAAAACATTTCTTTGCTCCATATA 10 112 1 AAAATTCTTT 0.665074 -189 AGCGTCTTCAAAAGAGATTTTTTCCACGTTT 16 9 0 AAAGTTTTTT 0.908917 -200 ACGGCTAGGCAAAGTTTTTTTGTTTGCAGAGTT 19 27 1 AAAGTTTTGT 0.846965 -88 CTTCTCTCTTAAAATCGTTTTTTTAGGGGCTTT 19 92 1 AAAATTTTTT 0.808668 -23 ATGTGATACGAGAGACCTTCTTTCTTTTTACTT 20 72 0 AGAGTTCTTT 0.763929 -41 TCAAGAGAAGAGGGCGTTTTTTTCATTGAAAAA 23 34 1 AGGGTTTTTT 0.813395 -103 AATTTTAACAAAAGTTTTTCTTTGTCTTCAATG 24 53 1 AAAGTTCTTT 0.957127 -130 TCTTTTAACGAAGAGGGTTTTCTCTCTTCGTTT 25 14 1 AAGATTTTCT 0.592371 -232 TAAACCCTCAAAAGGCATTTTTTATCTGTAAAA 25 149 1 AAAGTTTTTT 0.958786 -97 ACCTTTCTAAGAAGAGGTTCTTTTCAACACAAG 26 121 0 GAAGTTCTTT 0.68083 -180 CTCTTCTTAGAAAGGTTTTCTCTACGGGCGGTC 26 138 1 AAAGTTCTCT 0.941042 -163 CTCGTGCGACAAAAACTTTTTCTAACCCTTTTT 27 137 1 AAAATTTTCT 0.722719 -164 AGAAATCTTTAGCGGACTTTTTTTCCGCTTTTT 27 189 1 AGCGTTTTTT 0.647475 -112 GGACAGGAAAAAAGACTTTCTCTAACAACCAGG 27 232 0 AAAGTTCTCT 0.853657 -69 TATTCTTTCCAAAGAACTTCTGTGACTTGGGAA 29 84 1 AAAGTTCTGT 0.670647 -66 TGAATAAGTAAGGGATGTTCTTTTGCCCGGAAA 30 47 1 AGGGTTCTTT 0.818023 -128 GGTGTCTTCTAAAGGCGTTTTTTGGGTTGCTTT 30 77 0 AAAGTTTTTT 0.958786 -98 **** ****** Masking position 8 Map Score: 25.149 Number of sites scoring better than the average of aligned sites = 319 Number in coding regions = 318 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 3 AGAAGCTCTTTTCTTTCTAAGACTTACCTGGA 3 40 1 TTTTTTAAGA 0.966059 -114 ATTTTTCTTATTATTTTAAAAAGATCTAATAG 4 61 1 TTTTTAAAAA 0.519584 -40 TTCAAAAGATTTATTTGAAAGACATTCTAGAA 6 169 1 TTTTTAAAGA 0.853225 -53 TTTCTTTTTAAGAGAAATTAAAA 7 2 1 TTTTTTAAGA 0.966059 -131 AAAATAACTCTTTTTTATAAGAAGGGAGCGTG 7 106 1 TTTTTTAAGA 0.96568 -27 AAGAAATGTTTTGTTTGTGAGATGTAATTATG 10 102 0 TTTTTTGAGA 0.861795 -199 AAGAGTTACTTTTTTTGTGAAAGAGTAAAAAG 10 144 1 TTTTTTGAAA 0.537175 -157 GTTAAGCAAGTTTTTTACAAAAACAGAAGCCT 13 45 1 TTTTTCAAAA 0.783846 -107 AACTATTTTTTAAGAATACAAAATC 14 4 1 TATTTTAAGA 0.860211 -105 AAAATAAGCCTTCCTTGCAAGAAATCGAGTAT 15 123 1 TTCTTCAAGA 0.823592 -74 CCTGTGCATGTATTTTGTAAGATAGATCAAAG 15 159 0 TATTTTAAGA 0.860211 -38 ATTCTTATTTTTTTTAAGAATCATGTTGG 22 8 1 TTTTTTAAGA 0.966053 -61 AAACGTTCTCTTCTCTTCAAGAGAAGAGGGCG 23 18 1 TTTCTCAAGA 0.705041 -119 AATTTAATTTTATTTTTTAAGATCTATTTGTT 24 121 1 TATTTTAAGA 0.860211 -62 TTGTGGTGATTTTTTTTCAAAAGTCGCCTAAT 26 33 1 TTTTTCAAAA 0.798417 -268 TTTTTTCCGCTTTTTTCTAAGATTTCCTGGTT 27 207 1 TTTTTTAAGA 0.966053 -94 ATGATAATTTTTACTTATAAGAGGGCATATCA 29 120 0 TTCTTTAAGA 0.861794 -30 CAACATCCCCTTGTTTGCAAGACGATACCCCT 31 88 0 TTTTTCAAGA 0.955178 -90 ** *** ***** Masking position 6 Map Score: 20.6943 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 109 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 4 TATGGGATTATAGGTGTAAAAGATCTTGTATTGTA 5 72 0 TGGGAAAGAC 0.956247 -40 GAGTCAGGCTTCAGCGTAAGCAAGCTTGACTCTAA 8 47 1 TAGGAAGAAC 0.655404 -71 AGACGTCCAATGGCAAAAAATAATCTTGAGGAAAT 8 82 0 TGCAAAAAAC 0.732702 -36 CCACTTTAACTAGGAGGCAACAAGCTACC 9 201 1 TGGGCAAAAC 0.875211 -19 GAAAGTGGGATAGGCACAAAAATCCAAAGAA 13 7 0 TGGAAAAATC 0.619033 -145 CGGGTTTTTATAGGCGGAAATAATCTTAAAGTCTA 14 48 1 TGGGAAAAAC 0.981022 -61 CTCACTTATTTAGGCGAATAAACTCGAAAGTACTA 14 83 0 TGGGATAACC 0.669698 -26 GTAAAAGCTTTTGGCAAAAAAAAGCTCATCTATTT 18 46 0 TGGAAAAAAC 0.942888 -145 GGATCTATCGTAGGAAAAAGCAACCTCGTGCGACA 27 113 1 TGGAAAGAAC 0.908918 -188 TCTTCCCCAATAGGAGAAAGCAACCGTGTAGCTGC 28 58 1 TGGGAAGAAC 0.968987 -67 TGGGTTGCTTTCCGGGCAAAAGAACATCCCTTACT 30 53 0 TCGGAAAGAC 0.663504 -122 GCGCATGACCTAGGCAGAAAGGAACGAGTGTTTAG 30 119 0 TGGAAAAGAC 0.874691 -56 TTATAGTTCCTAGGAGGAAAAAATCAAGGTAATAC 31 47 0 TGGGAAAAAC 0.981022 -131 GACATACAGATGGCAGTATGGAAGCCATAAAAAGG 31 126 1 TGCGATGAAC 0.582449 -52 GTTGTACATCTGGGTGGATAAAATCTCAATGAGGA 32 51 0 TGGGATAAAC 0.932882 -158 * ** * *** ** * Masking position 1 Map Score: 10.1223 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 67 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 CTATTTTCTCTTTTTAATTTTTATTCTGCACACAT 2 13 1 TTTTATTATT 0.573978 -288 TGACGGAGAGTGTGTTGCGCTTTTTTGGGTTTTCA 2 249 1 TGTTTTTTTT 0.612415 -52 TAATACTTGGTTTATTTTTCTTATTATTTTAAAAA 4 48 1 TTTTTTTATT 0.741579 -53 ACCAACTTCATCTCTATCCATTTTTCTGGGTAGTG 6 19 1 TCTTATTTTT 0.577209 -203 AAATAGTTGGTTTTTGGTTGTTTTTGATTATTGTT 7 65 1 TTTTGTTTTT 0.859318 -68 GATTCAAGACTTTTTTTATCTTTTCCATGAACGCA 9 109 0 TTTTTTTTTC 0.744107 -111 GAGCAATAATTTTATTGTAATTTTTTTTAACCAAT 11 22 0 TTTTTTTTTT 0.929939 -50 AAGGCTTATTTTTATATGATTTATTTTCTATTGCT 15 100 0 TTTTATTATT 0.573978 -97 ATTCTTATTTTTTTTAAGAATCATG 22 1 1 ATTTTTTTTT 0.487086 -68 TTGAAAAATCTTTCTATTTCTTTTCTCTTCCCTGT 23 59 1 TTTTATTTTC 0.577209 -78 TAGATTTGTTTTCCTTGTTTCTTCTCTTA 23 118 0 TTTTTTTGTT 0.627322 -19 AAGAAAAACTTTTGTTAAAATTTTTTCGCTATACC 24 40 0 TTTTTTTTTT 0.929939 -143 TTCATTTGAATTTAATTTTATTTTTTAAGATCTAT 24 113 1 TTTATTTTTT 0.487086 -70 TTAAGATCTATTTGTTTTAGTTTTATAATAGAAAC 24 137 1 TTTTTTTTTA 0.515995 -46 TTGATTGTGATTTGTGGTGATTTTTTTTCAAAAGT 26 22 1 TTTTGTTTTT 0.859318 -279 ACAAAAACTTTTTCTAACCCTTTTTTCTCTTAACT 27 145 1 TTTTATTTTT 0.861721 -156 TTAGCGGACTTTTTTTCCGCTTTTTTCTAAGATTT 27 197 1 TTTTTTTTTT 0.929939 -104 TGATTGACCTTTTATTCTTCTTTTTACGTATTACC 31 20 1 TTTTTTTTTT 0.929939 -158 TCTTTAACAGTCTTTGGGCCTTTTTATGGCTTCCA 31 144 0 TCTTGTTTTT 0.572316 -34 *** ** ***** Masking position 11 Map Score: 7.55203 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 173 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 AGTGTATGTGCGTCATCTCTACAGAAGGAA 1 64 1 CTCATCTTAC 0.98873 -20 TTAAAATTTCCCTCATGTTTACACTACAATGT 3 90 1 CTCATGTTAC 0.944028 -64 TTCAAACCAACTTCATCTCTATCCATTTTTCT 6 14 1 CTCATCTTAT 0.919222 -208 AAAACCATCCTCTTTACAAAAAATTGA 11 55 0 CTCCTCTTAC 0.964279 -17 CAAGAGCTATCCACATCTTTACGTACTGATG 12 10 0 CACATCTTAC 0.947954 -122 TGAAAGAAGCCTTCAACTATACAAAATATTTA 17 24 0 CTCAACTTAC 0.947954 -73 TTTTCGCTTCCATCATCTCTACATTTTGCTCG 28 15 1 CTCATCTTAC 0.98873 -110 * ****** *** Masking position 11 Map Score: 4.35432 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 12 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 TATTTTCTCTTTTTAATTTTTATTCTGCACAC 2 14 1 TTTTATTTTA 0.467474 -287 CACCAAGGTTATTTTAATATAACTGATCTTTA 2 52 1 ATTTAATTAA 0.4572 -249 AAAGAAGCTCTTTTCTTTCTAAGACTTACCTG 3 38 1 TTTTTTTTAA 0.728447 -116 TTAATACAAATTTTTATTTAAATCTAGGAAAG 4 13 0 TTTTATTAAA 0.854431 -88 TTTATTTTTCTTATTATTTTAAAAAGATCTAA 4 58 1 TTATATTTAA 0.46741 -43 AATTCAAAAGATTTATTTGAAAGACATTCTAG 6 167 1 ATTTTTTAAA 0.412849 -55 AAAACCAACTATTTGATTATAATGACCTTTGT 7 47 0 ATTTATTTAA 0.855952 -86 TTGATTATTGTTTGTATTAAAATAACTCTTTT 7 88 1 TTTGATTAAA 0.383454 -45 TTGAGCAATAATTTTATTGTAATTTTTTTTAA 11 27 0 ATTTATTTAA 0.856049 -45 GTTTGCAGAGTTTTTATTTTAAATATGTTATA 19 48 1 TTTTATTTAA 0.920519 -67 GAGGGCGTTTTTTTCATTGAAAAATCTTTCTA 23 43 1 TTTTATTAAA 0.846061 -94 AATGAAAACAATTTAATTTAAAACCATTAAAT 24 87 0 ATTTATTAAA 0.751567 -96 AATTGTTTTCATTTGAATTTAATTTTATTTTT 24 106 1 ATTTAATTAA 0.457213 -77 AACACAATAGTTTCTATTATAAAACTAAAACA 24 149 0 TTTCATTTAA 0.575716 -34 TTTGTGGTGATTTTTTTTCAAAAGTCGCCTAA 26 32 1 TTTTTTTAAA 0.578091 -269 GATACCACGGTTTTTATTTTAATGGATAAAAT 26 82 1 TTTTATTTAA 0.920519 -219 TATAATTATTTTTTGATTATAAGTAACCGCTG 26 177 1 TTTTATTTAA 0.913746 -124 AAATGATAATTTTTACTTATAAGAGGGCATAT 29 122 0 TTTTCTTTAA 0.606422 -28 **** *** *** Masking position 8 Map Score: 5.87373 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 99 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 GATTTTTCCCCGTTCTAAAGATCAGTTATAT 2 68 0 CGTTCAAAGA 0.505894 -233 TCCAGGTAAGTCTTAGAAAGAAAAGAGCTTC 3 41 0 TCTTAAAAGA 0.81661 -113 TTTTAATTTCTCTTAAAAAGAAA 7 3 0 TCTTAAAAGA 0.81661 -130 GACCTTTAAGTGCTCGAAAGGATATTCGTAG 9 36 1 TGCTCAAAGG 0.819245 -184 TTTCATAGCGTCTTCAAAAGAGATTTTTTCC 16 17 0 TCTTCAAAGA 0.935541 -192 GTCTATGATCTCTTCCAAACGTTTCATAGCG 16 38 0 TCTTCAAACG 0.832591 -171 GGCAAGAGAAGCTTCTAAAGACGTGGTTGGT 16 80 0 GCTTCAAAGA 0.712722 -129 GATTCTTTTATCATCCAAACGTATGTTGGGA 18 99 1 TCATCAAACG 0.552859 -92 GTATCACATTTCCTCAAAAGGAGAATC 20 96 1 TCCTCAAAGG 0.967031 -17 CGTTCTCTTCTCTTCAAGAGAAGAGGGCGTT 23 21 1 TCTTCAGAGA 0.666186 -116 TGTTATTAAACCCTCAAAAGGCATTTTTTAT 25 143 1 CCCTCAAAGG 0.92539 -103 AAGAACCTCTTCTTAGAAAGGTTTTCTCTAC 26 132 1 TCTTAAAAGG 0.90183 -169 GGAAAAAAAGTCCGCTAAAGATTTCTTAGAT 27 184 0 TCCGCAAAGA 0.644851 -117 TAGATAGGTGTCTTCTAAAGGCGTTTTTTGG 30 85 0 TCTTCAAAGG 0.967886 -90 AGTATGGAAGCCATAAAAAGGCCCAAAGACT 31 140 1 CCATAAAAGG 0.496223 -38 TCTTTTCCTTTCCTAGAAAGGCTTGGAAGGA 32 115 1 TCCTAAAAGG 0.895158 -94 ***** ***** Masking position 7 Map Score: 9.4914 Number of sites scoring better than the average of aligned sites = 312 Number in coding regions = 310 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 TCCGGTTACTTTTCCGCGCCGGCCTTGCAT 6 126 1 TTTCCGCGCC 0.816533 -96 TTATTATTAGTTTCCTCTCCCGCTTTCCTT 10 57 0 TTTCCTCTCC 0.978065 -244 ATAAGGTTACTATCCTCGCCACCTTCTCTA 12 98 0 TATCCTCGCC 0.818929 -34 TTTCTATTTCTTTTCTCTTCCCTGTGTGTA 23 69 1 TTTTCTCTTC 0.912356 -68 ACGAAGAGGGTTTTCTCTCTTCGTTTTCTT 25 21 1 TTTTCTCTCT 0.680078 -225 CTTAGAAAGGTTTTCTCTACGGGCGGTCTC 26 143 1 TTTTCTCTAC 0.759846 -158 GAAAGTCTTTTTTCCTGTCCCGTTCTTTCT 27 245 1 TTTCCTGTCC 0.838899 -56 TTCCTTTTCGCTTCCATCATCTCT 28 5 1 TTTTCGCTTC 0.766832 -120 CTCGATAGTTTATTCTCTTCCCCAATAGGA 28 43 1 TATTCTCTTC 0.769693 -82 ATTCATCCTTTATTCTTTCCAAAGAACTTC 29 74 1 TATTCTTTCC 0.590104 -76 CGTTCCTATTTTTTCTCTCCTGCTACCACT 32 19 1 TTTTCTCTCC 0.969947 -190 GGACCTCTCTTTTCCTTTCCTAGAAAGGCT 32 108 1 TTTCCTTTCC 0.861022 -101 AACATTTCCTCTTCAATGAGTGTT 32 195 0 TTTCCTCTTC 0.934989 -14 ********** Masking position 3 Map Score: 10.0169 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 10 ATCTTTCCTGGAGTCTTTAGTTAAGATCTT 2 134 0 GAGTCTTTAG 0.900643 -167 CTCTGACGGAGAGTGTGTTGCGCTTTTTTG 2 246 1 GAGTGTGTTG 0.906049 -55 GCTTTGGGATGAGTGTGCAGCCTGGCATAA 10 29 1 GAGTGTGCAG 0.963376 -272 GAGCGTGGATGAGTGTTTCGTTCTGATCGG 13 121 1 GAGTGTTTCG 0.945178 -31 GCCTTCAGGTGAGTGTACAGATTTTCATGT 25 116 1 GAGTGTACAG 0.906049 -130 AGAAAGGAACGAGTGTTTAGGAGTAGATAG 30 109 0 GAGTGTTTAG 0.979232 -66 CCTCTTCAATGAGTGTTTAGGATTGCAACG 32 182 0 GAGTGTTTAG 0.979232 -27 ********** Masking position 2 Map Score: 4.06767 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 11 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 11 TTTCTTTACCTCACCTTCTCAAAGATCTTA 2 113 1 TCACCTTCTC 0.842032 -188 TTGTTAAAGCCCTCCCTCCCCCGGA 9 6 0 CCTCCCTCCC 0.960954 -214 CACTCAACCGAAACCTTCTCCACTACGAAT 9 59 0 AAACCTTCTC 0.770673 -161 ACTATCCTCGCCACCTTCTCTATTTTCTAC 12 90 0 CCACCTTCTC 0.976244 -42 AAGACAACCTTCCGATCAGAACGA 13 138 0 CAACCTTCCG 0.807805 -14 AAGCCACCCTCTCTTTACTTTTA 18 178 0 CCACCCTCTC 0.975775 -13 CTTTAAAGAGCATCCCTCTCTTGGCTCGAA 28 96 1 CATCCCTCTC 0.940582 -29 GAGGGCATATCATCCTTCCCAAGTCACAGA 29 102 0 CATCCTTCCC 0.940582 -48 ********** Masking position 7 Map Score: 3.34189 Number of sites scoring better than the average of aligned sites = 72 Number in coding regions = 72 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 GTACGTTGAAGTTCGTTTCAACGTACAGATAA 5 11 0 GTTCGTTTAC 0.817103 -101 TAGAGATGAAGTTGGTTTGAAGTT 6 3 0 GTTGGTTTAG 0.918768 -219 TAATCAAATAGTTGGTTTTTGGTTGTTTTTGA 7 60 1 GTTGGTTTTG 0.933041 -73 TGCTTAAATAGTTGGTTTTAGCCCCTTTGTTA 15 12 0 GTTGGTTTAC 0.943532 -185 TAAAGACGTGGTTGGTTGATTCATAAGGTCTA 16 64 0 GTTGGTTGTC 0.811077 -145 AAAAGAATTCGTTGCTTTAAAGTAGGGAGGAT 27 22 0 GTTGCTTTAG 0.918768 -279 GTCGCACGAGGTTGCTTTTTCCTACGATAGAT 27 115 0 GTTGCTTTTC 0.953674 -186 CAGCTACACGGTTGCTTTCTCCTATTGGGGAA 28 60 0 GTTGCTTTTC 0.953674 -65 CGTTTTTTGGGTTGCTTTCCGGGCAAAAGAAC 30 63 0 GTTGCTTTCG 0.835935 -112 CTAAACACTCGTTCCTTTCTGCCTAGGTCATG 30 119 1 GTTCCTTTTC 0.846264 -56 ******** * * Masking position 6 Map Score: 5.47948 Number of sites scoring better than the average of aligned sites = 27 Number in coding regions = 27 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 AAGGTCTTGTTAAAGCCCTCCCTCCCCCGG 9 12 0 TAAAGCCCTC 0.966284 -208 GAAAGCTTTTTGAAGCCCTTGTGTGCGTGT 10 267 1 TGAAGCCCTT 0.712916 -34 TCATATAAAAATAAGCCTTCCTTGCAAGAA 15 116 1 ATAAGCCTTC 0.878597 -81 CCGAAATGAAAGAAGCCTTCAACTATACAA 17 32 0 AGAAGCCTTC 0.876445 -65 TCAATGAAAAAAACGCCCTCTTCTCTTGAA 23 33 0 AAACGCCCTC 0.796771 -104 CTGAAGGCGGTTAAGCACTCCCTATGTTAC 25 94 0 TTAAGCACTC 0.716997 -152 TTTCATGTTATTAAACCCTCAAAAGGCATT 25 138 1 TTAAACCCTC 0.830679 -108 AACAGAATACTAAAGCCTTCGAGTTCAGAA 25 214 1 TAAAGCCTTC 0.889945 -32 AGATACACGAAAAAGCCCTCTCCGGATCTG 26 220 0 AAAAGCCCTC 0.954167 -81 AATCTTGATCTTAAACCATCAGTGCAGGTA 29 11 1 TTAAACCATC 0.491365 -139 GGGAAGGATGATATGCCCTCTTATAAGTAA 29 112 1 ATATGCCCTC 0.765202 -38 CGCAATTGTTTGAAGCCATCCCTTACTGAA 30 21 1 TGAAGCCATC 0.872043 -154 ********** Masking position 3 Map Score: 4.96237 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 115 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 CATACACTTCAATCTTGTGGTCAAAAATTT 1 42 0 AATCTTGTGG 0.870221 -42 AAAGATCGTTTATCTTGAGGTTTTCTCCTA 2 158 1 TATCTTGAGG 0.930744 -143 GGCAAAAAATAATCTTGAGGAAATTTAGAG 8 76 0 AATCTTGAGG 0.977029 -42 TTTTATTGATAATCTAGAGGGATCTATCTA 12 52 1 AATCTAGAGG 0.870179 -80 AAGAATACAAAATCTTGAGAGTCAATCGGG 14 22 1 AATCTTGAGA 0.934939 -87 AAAACCGTGGTATCTTGAGCGTCCTGCAGA 26 66 0 TATCTTGAGC 0.91097 -235 ACTTTTTAGCAATCTTGAAAAACTAGATAC 26 244 0 AATCTTGAAA 0.616118 -57 CTATCTAAGAAATCTTTAGCGGACTTTTTT 27 182 1 AATCTTTAGC 0.760465 -119 AATCTTGATCTTAAACCATC 29 1 1 AATCTTGATC 0.783339 -149 ********** Masking position 5 Map Score: 2.79136 Number of sites scoring better than the average of aligned sites = 40 Number in coding regions = 40 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 AGTCTTTAGTTAAGATCTTTGAGAAGGTGA 2 123 0 TAAGATCTTT 0.753314 -178 GATTACAATACAAGATCTTTTACACCTATA 5 69 1 CAAGATCTTT 0.929422 -43 AGGGCTTTAACAAGACCTTTAAGTGCTCGA 9 23 1 CAAGACCTTT 0.946206 -197 CCTTTGGATTCAAGACTTTTTTTATCTTTT 9 120 0 CAAGACTTTT 0.664615 -100 TATTCACTGTCAAGAGCTATCCACATCTTT 12 22 0 CAAGAGCTAT 0.914737 -110 TTAGCATATCCAAGAGATTTATATCAAAGC 15 73 1 CAAGAGATTT 0.791306 -124 TTTTTTTTGCCAAAAGCTTTTACTAAGGAA 18 58 1 CAAAAGCTTT 0.768954 -133 TTTTATTTTTTAAGATCTATTTGTTTTAGT 24 128 1 TAAGATCTAT 0.505455 -55 CGTTCTTTCTCAAGAGCTTTTGTTCGGATT 27 265 1 CAAGAGCTTT 0.970926 -36 ********** Masking position 5 Map Score: 2.97658 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 66 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