AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_aful_mthe_100.orf -o199_aful_mthe_100.ace -a/home/amcguire/alignace/lib/ORF_aful.txt -z/skink1/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RTH00618 16 M.thermo RAG28489 22 Archaeoglobus_fulgidus RTH00964 38 M.thermo RAG28495 21 Archaeoglobus_fulgidus RTH00858 16 M.thermo RTH01010 21 M.thermo RTH01561 41 M.thermo Input sequences: #1 RAG45971 128 Archaeoglobus_fulgidus #2 RAG45930 32 Archaeoglobus_fulgidus #3 RAG50433 95 Archaeoglobus_fulgidus #4 RAG33159 72 Archaeoglobus_fulgidus #5 RAG49679 165 Archaeoglobus_fulgidus #6 RAG48732 101 Archaeoglobus_fulgidus #7 RAG50374 41 Archaeoglobus_fulgidus #8 RAG50371 57 Archaeoglobus_fulgidus #9 RAG32612 62 Archaeoglobus_fulgidus #10 RAG48823 189 Archaeoglobus_fulgidus #11 RAG47824 166 Archaeoglobus_fulgidus #12 RAG10300 21 Archaeoglobus_fulgidus #13 RAG10399 117 Archaeoglobus_fulgidus #14 RAG50247 109 Archaeoglobus_fulgidus #15 RAG11044 30 Archaeoglobus_fulgidus #16 RAG45849 97 Archaeoglobus_fulgidus #17 RAG45848 94 Archaeoglobus_fulgidus #18 RAG11879 223 Archaeoglobus_fulgidus #19 RAG24795 202 Archaeoglobus_fulgidus #20 RAG49671 32 Archaeoglobus_fulgidus #21 RAG50227 57 Archaeoglobus_fulgidus #22 RAG47407 166 Archaeoglobus_fulgidus #23 RAG24310 104 Archaeoglobus_fulgidus #24 RTH01790 170 M.thermo #25 RTH00571 19 M.thermo #26 RTH02039 22 M.thermo #27 RTH00851 46 M.thermo #28 RTH00189 109 M.thermo #29 RTH00952 236 M.thermo #30 RTH01420 17 M.thermo #31 RTH00723 62 M.thermo #32 RTH01329 300 M.thermo #33 RTH01081 40 M.thermo #34 RTH00257 22 M.thermo #35 RTH00179 113 M.thermo #36 RTH00330 34 M.thermo #37 RTH01858 70 M.thermo #38 RTH00707 98 M.thermo #39 RTH01259 73 M.thermo #40 RTH00422 120 M.thermo #41 RTH00483 26 M.thermo #42 RTH01562 52 M.thermo #43 RTH00987 33 M.thermo #44 RTH00617 300 M.thermo Motif number 1 AATTTTTACTCCCGTCCAACAAACTCTG 6 8 0 CCCGTCCACA 0.870649 -94 TTACTTTTTCCCCGGCATTGATTTTCAAAGC 6 37 1 CCCGGCATGA 0.680757 -65 TATATTGCTTCCCGACCCAGCAAAGGCTGCG 9 31 1 CCCGACCAGC 0.829631 -32 AGCGGCTCCTCCCGGCCTGCCAAAAAGACCT 13 96 0 CCCGGCCGCC 0.994742 -22 CGTAGCTCAGCCAGGCAGAGCGACGGGCTTT 19 121 1 CCAGGCAAGC 0.791324 -82 GGGCTTTTAACCCGTCGGTCGCGGGTTCAAA 19 145 1 CCCGTCGTCG 0.938642 -58 GGGTTCAAATCCCGTCGAGCCCGTATTTAAA 19 167 1 CCCGTCGGCC 0.988704 -36 GGCATATTTTCCAGTCCAGCGAAAAAACTTT 28 25 1 CCAGTCCGCG 0.96886 -85 GCTAGGCTATCCCGGCACAGGATGTATCATA 29 57 0 CCCGGCAAGG 0.819297 -180 TTGCGCCTTACCTGGCTAGGCTATCCCGGCA 29 71 0 CCTGGCTGGC 0.807764 -166 CACAAGATTTCCAGTCTTGCGCCTTACCTGG 29 87 0 CCAGTCTGCG 0.859735 -150 GGTTCAAATCCCAGTCCCGGCGTCGGTTAAA 29 135 1 CCAGTCCGGC 0.968045 -102 TTCGCAAACCCCCGTCCCGCGAATTCACTCT 29 200 1 CCCGTCCGCG 0.985964 -37 ATCATGCGGGCCTGTCGAGCCCGCGACTCGG 32 135 1 CCTGTCGGCC 0.91718 -166 GGGTTCAATTCCCGGCCAGGGCGTTTCCTGA 32 164 1 CCCGGCCGGG 0.975953 -137 GGGTTCAATTCCCGTCGGGCCCGCTATCTAA 32 246 1 CCCGTCGGCC 0.988704 -55 CCCTGAGACCCCCGGCAATGGTCATCCCTCC 44 153 1 CCCGGCATGG 0.912392 -148 ******* *** Masking position 4 Map Score: 22.2594 Number of sites scoring better than the average of aligned sites = 239 Number in coding regions = 214 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 2 AGCTTTGGGCAACATTTTTAACTTTTCTGAC 3 23 0 AACTTTTTAA 0.78771 -73 GAAATCCCTCAACATTTAAATACATTCCCCT 3 62 1 AACTTTAAAT 0.908055 -34 TACACCTTTAAACTTTTTGATTTTTACCGGA 4 36 0 AACTTTTGAT 0.834246 -37 TATTAGACAAAACATTTTTAACTAACAACTA 5 23 0 AACTTTTTAA 0.78771 -143 ACGCTTTCGCAAGTTTTTTAAAATAGATTTT 5 110 1 AAGTTTTTAA 0.628493 -56 AACGGAAAAACGTTTTAAATCAGCTGATT 7 9 1 AACTTTTAAA 0.78771 -33 AAGGTTTATATATCCTCCTAA 8 1 1 AAGTTTATAT 0.818275 -57 ATCTGAGCAAAAAATTTAAATTATTGAAGTG 10 101 0 AAATTTAAAT 0.845523 -89 CAGAAGGGGAAACGTTTTAATTCCTCTTATA 11 21 0 AACTTTTAAT 0.900029 -146 AGAACTTCAAAAACTTTATATTCATCTCATC 14 62 1 AAATTTATAT 0.845523 -48 AGTGCTAATAAAGTTTTTGATTTTAGTATTT 16 39 0 AAGTTTTGAT 0.696484 -59 CCCTTATAAGAAAATTTTGATTTCGAATTAA 17 36 0 AAATTTTGAT 0.736105 -59 GAGCACGAAAAAGATTTAAATCCTCACCATC 19 73 1 AAGTTTAAAT 0.818275 -130 TATATAAAAAAAACTTTTAATAAACACTACG 22 96 0 AAATTTTAAT 0.833042 -71 CGCTTTTGGCAAAGTTTAAATGCTTTGTTGT 22 134 1 AAATTTAAAT 0.845523 -33 GGGGGCACATAACCTTTAAATATCCTTACAG 23 57 1 AACTTTAAAT 0.908055 -48 TCACCAGCGGAAAGTTTAAATATGGATACCA 24 13 1 AAATTTAAAT 0.845523 -158 TCCAGCGAAAAAACTTTTTAAGGGGATACCT 28 39 1 AAATTTTTAA 0.672821 -71 ACTCAAGGAAAACCTTTATAAATCTTGAAGG 40 30 1 AACTTTATAA 0.802778 -91 GACAATGCACAAAGTTTATATATAGATTCCA 44 42 0 AAATTTATAT 0.845523 -259 TAATCACTTCAACCTTTATATTATATGAATG 44 233 1 AACTTTATAT 0.908055 -68 *** ******* Masking position 6 Map Score: 19.9225 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 68 Number in noncoding regions = 130 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 3 CACCAACATCGAAAAAAATTATAAGAATTTCT 1 16 1 GAAAAAATAT 0.943187 -113 CGGAGCAAGAGAAAAAAAGGAATAAATTT 4 8 0 GAAAAAAGAA 0.946796 -65 CTCTTGCTCCGGTAAAAATCAAAAAGTTTAAA 4 29 1 GGAAAAATAA 0.883987 -44 AAAGCGTGCTGAGATAAATCATACCTGATATT 5 85 0 GAATAAATAT 0.603141 -81 ATCAATGCCGGGGAAAAAGTAATTTTTACTCC 6 27 0 GGAAAAAGAA 0.914941 -75 TTTTTGCTCAGATAAAAATGCTCACTCTAATA 10 119 1 GAAAAAATCT 0.816743 -71 GATACTACAAGATAAAAAGAACTTCAAAAACT 14 45 1 GAAAAAAGAC 0.845577 -65 TGAAAAATCTGAAAAAAAGTAATACGAGGTGA 16 72 1 GAAAAAAGAA 0.946796 -26 GAAAGCTTAAGGGAAAAATTATAAGATGTGCT 18 177 1 GGAAAAATAT 0.909378 -47 TGTGTGGGGTGATAAAAAGTATTAGCCCAAAT 21 26 0 GAAAAAAGAT 0.959077 -32 TTTGGGCGAGGAGAAAAATAATAGTCTTTCGT 22 67 1 GAAAAAATAT 0.943187 -100 CAGTCCTCCAGATAAAAAGTCACCGTAAAATT 32 275 0 GAAAAAAGCA 0.826911 -26 AATTACCTTAGACAAACAGCATGCCCATTTGC 35 47 1 GAAAACAGAT 0.760755 -67 CATGGCTGAAGGAAAAAATCATTAATTAATGA 38 38 1 GGAAAAATAT 0.909378 -61 GACTTCACCAGAAAAAAATTAATTGGGAGGA 43 10 0 GAAAAAATAA 0.926503 -24 ** ****** ** Masking position 6 Map Score: 15.7496 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 88 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 GAACATCCCCCATTTCTTTTTC 1 117 0 AAATCCCCCA 0.81984 -12 AAGGTTTATATATCCTCCTAATGGATTTA 8 9 1 TAATCCTCCT 0.943173 -49 ACCTATCTCCTCCTTTCTGGTTTT 8 44 0 TACTCCTCCT 0.931759 -14 GGTTTTATCTTATTTCCCCCAAACGTTAAAA 13 34 0 TATTCCCCCA 0.776901 -84 TTTTCAGGATTTCCTCCTCCCTGTAAG 18 7 0 TTCTCCTCCC 0.844044 -217 AGTTTTTCGGCATAGCCCCCTCGACTCTATC 18 98 1 CAAGCCCCCT 0.810332 -126 CAGCACCTTTTTCTGCCCCCTTCTTAGTATC 18 132 0 TTTGCCCCCT 0.892965 -92 GTTGATCCTCCTATTTTTAAAT 19 191 0 TTATCCTCCT 0.928733 -12 TTTAAAGGTTATGTGCCCCCCTTCAATTGAG 23 46 0 ATTGCCCCCC 0.740561 -59 CCGAATATCCTCCTGGTTATTT 26 9 0 AAATCCTCCT 0.918361 -14 TTGTGGAGCTTTGCTCCTCCTGGGTTCAAAT 29 113 1 TTCTCCTCCT 0.914681 -124 TTAACAGCCTCCCGGTGGAAAA 34 10 0 AAAGCCTCCC 0.847627 -13 TTAAATCCTCCTGTAAAAAAGG 36 23 0 TAATCCTCCT 0.943173 -12 TCATTAATTAATGATCCCCCATAAATGTAAA 38 56 1 ATATCCCCCA 0.781328 -43 ATACTGCCCCCTTGCATAGTAT 39 2 1 TATGCCCCCT 0.91398 -72 GCTATTCGCCTCCTTAATCTTTTT 44 287 0 ATCGCCTCCT 0.876813 -14 ** ******** Masking position 6 Map Score: 13.2629 Number of sites scoring better than the average of aligned sites = 622 Number in coding regions = 584 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 5 GCTATATGATGTTCTTTAACCAATATAAGCT 10 169 0 TGTTTTAACC 0.848756 -21 GCAGAGCGACGGGCTTTTAACCCGTCGGTCGC 19 135 1 GGGTTTAACC 0.990837 -68 CGGGCTCGACGGGATTTGAACCCGCGACCGAC 19 158 0 GGGTTGAACC 0.994202 -45 CGCCGGGACTGGGATTTGAACCCAGGAGGAGC 29 125 0 GGGTTGAACC 0.994202 -112 GTGCAACAGGGTTGCTTTAACCGACGCCGGGA 29 149 0 GTTTTTAACC 0.734215 -88 CGCCCTGGCCGGGAATTGAACCCGAGTCGCGG 32 155 0 GGGTTGAACC 0.994158 -146 GCAGAGCGCTTGGCTTTTAACCAAGTGGTCGC 32 214 1 TGGTTTAACC 0.961153 -87 CGGGCCCGACGGGAATTGAACCCGCGACCACT 32 237 0 GGGTTGAACC 0.994158 -64 *** ******* Masking position 9 Map Score: 12.3203 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 8 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 6 CAGGTATGATTTATCTCAGCACGCTTTCGCA 5 90 1 TTATCTCACA 0.884789 -76 TTCATCACCTCTAATAGATATA 5 154 0 TCATCACCCT 0.951917 -12 AAAATCATCACCGCAGCCTTTGCTG 9 48 0 TCATCACCCA 0.97715 -15 GTGAGCATTTTTATCTGAGCAAAAAATTTAA 10 113 0 TTATCTGACA 0.727013 -77 ACTCTAATAATCATCAACTCAACTTAAAGCT 10 142 1 TCATCAACCA 0.788855 -48 TTTTGAAATTTTATCTGCCCATTTCAGAGAA 11 66 1 TTATCTGCCA 0.902665 -101 AACTTTATATTCATCTCATCTCCATCGAACA 14 73 1 TCATCTCACT 0.850534 -37 GTCATCTCACCTTTCTCTTTTT 20 21 0 TCATCTCACT 0.850537 -12 CTAATACTTTTTATCACCCCACACAATTAAG 21 33 1 TTATCACCCA 0.963923 -25 CAGGTTTCTCTTATCTCCACACCAGGTGATC 31 40 1 TTATCTCCCA 0.963923 -23 ACCTTCAGTTCATCAGCACACCTTATAAAT 37 51 0 TCATCAGCCA 0.936879 -20 GGTTTATCCCCGCTATTTATATAG 40 107 0 TTATCCCCCT 0.791924 -14 ATGATCACCTCAAATTTTATTT 42 41 0 TGATCACCCA 0.891309 -12 ******** ** Masking position 3 Map Score: 12.2638 Number of sites scoring better than the average of aligned sites = 448 Number in coding regions = 422 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 7 TAAAAATGTTGCCCAAAGCTCATGAGGCGAAAT 3 34 1 GCCCAGCTCT 0.969829 -62 ACACTGCAGATGCCGACGCTCCTCCGAGTATCA 10 19 1 TGCCGGCTCT 0.816873 -171 ATGGATGAGGGCTCGTAGCTCAGCCAGGCAGAG 19 108 1 GCTCGGCTCG 0.982915 -95 CGGGTTAAAAGCCCGTCGCTCTGCCTGGCTGAG 19 126 0 GCCCGGCTCG 0.998063 -77 GGCCTGTCGAGCCCGCGACTCGGGTTCAATTCC 32 143 1 GCCCGACTCG 0.982913 -158 TTTCCTGAGGGCCCGTAGCTCAGTCTGGCAGAG 32 187 1 GCCCGGCTCG 0.998063 -114 TTGGTTAAAAGCCAAGCGCTCTGCCAGACTGAG 32 205 0 GCCAAGCTCG 0.940098 -96 GCAATGGTCATCCCTCCGCTCAGGGTGCGATAT 44 167 1 TCCCTGCTCG 0.947996 -134 ***** **** * Masking position 10 Map Score: 8.39098 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 88 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 GCTAATGGATGAGGGCTCGTAGCTCAGCCA 19 104 1 GAGGGCTCGT 0.958703 -99 CCCGTCGGTCGCGGGTTCAAATCCCGTCGA 19 155 1 GCGGGTTCAA 0.905477 -48 ATTTTTAAATACGGGCTCGACGGGATTTGA 19 171 0 ACGGGCTCGA 0.935643 -32 TTTGCCAAAAGCGCGCTGGATATATAAAAA 22 117 0 GCGCGCTGGA 0.91859 -50 GGAGGACTGGAAGGGGCATAT 28 2 1 GAGGACTGGA 0.865387 -108 AACCCGAGTCGCGGGCTCGACAGGCCCGCA 32 139 0 GCGGGCTCGA 0.993598 -162 GGCGTTTCCTGAGGGCCCGTAGCTCAGTCT 32 183 1 GAGGGCCCGT 0.90273 -118 CCAAGTGGTCGCGGGTTCAATTCCCGTCGG 32 234 1 GCGGGTTCAA 0.905477 -67 AAATTAGATAGCGGGCCCGACGGGAATTGA 32 250 0 GCGGGCCCGA 0.931383 -51 TTTTTATCTGGAGGACTGAATT 32 289 1 GAGGACTGAA 0.644622 -12 ********** Masking position 3 Map Score: 8.42908 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 146 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 9 GAACATCCCCCATTTCTTTTTCAATTATCAA 1 108 0 CCATCTTTTT 0.899344 -21 GCAGTTACACCTTTAAACTTTTTGATTTTTACC 4 39 0 CTTACTTTTT 0.747945 -34 ATGTGTGAATCGAAGGTCTTTTTGGCAGGCCGG 13 83 1 CGATCTTTTT 0.564881 -35 TTACCCACCTTCACATTTTTTGTTCCTAAA 17 75 0 CCTCATTTTT 0.823687 -20 GCTGTTCGAGCTTTACCCTTTTCGGGAAATCGA 18 59 0 CTTCCTTTTC 0.65428 -165 AAGTACTTCTCCAGCACCTTTTTCTGCCCCCTT 18 141 0 CCGCCTTTTT 0.939164 -83 GTCATCTCACCTTTCTCTTTTTGCAGATTTCA 20 11 0 CCTTCTTTTT 0.961731 -22 TACTATTTAACCGTTCTCTTTTTGGGCGAGGAG 22 47 1 CCTTCTTTTT 0.961731 -120 AATATGGATACCATACAATTTTTAGTACCTATT 24 31 1 CCTAATTTTT 0.516567 -140 AGGTAATTTCCTATATTCTTTTTAATTATATAA 35 22 0 CTTTCTTTTT 0.890179 -92 ACCCACCTCTTCCCTTTTTTACAGGAGGA 36 7 1 CTTCCTTTTT 0.928437 -28 TCATCCCAATCCTAGCCCTTGTTTTTTAACTAT 40 78 1 CCACCTTGTT 0.675965 -43 CACATAAAGACATGGACCTTTTTAATAAATGGT 44 79 1 CAGCCTTTTT 0.602135 -222 CTATTCGCCTCCTTAATCTTTTTTTAATTCCAA 44 277 0 CCTTCTTTTT 0.961731 -24 ** * ******* Masking position 9 Map Score: 5.96293 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 308 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 10 TTTATATACTATCTTGCATTGATAATTGAAA 1 90 1 ACTTGCATTG 0.783013 -39 GACCCAGCAAAGGCTGCGGTGATGATTTT 9 44 1 AGCTGCGGTG 0.976533 -19 GGAGCGTCGGCATCTGCAGTGTACTTTTCG 10 10 0 CTCTGCAGTG 0.815487 -180 TATAAGCTTTAAGTTGAGTTGATGATTATTA 10 146 0 AGTTGAGTTG 0.609042 -44 CGATTCACACATGATGAAGTGTTGGTGCAAG 13 64 0 AGATGAAGTG 0.679103 -54 AAGCTCGAACAGCTTGCAGAGTTTTTCGGCA 18 79 1 ACTTGCAGAG 0.654384 -145 TACCTATTGCAATCTGCGGTGGATCCGCTCA 24 56 1 ATCTGCGGTG 0.954915 -115 TTACTTGCCCAGTCTGCATTGTGGAAATATT 24 121 1 ATCTGCATTG 0.850378 -50 TGATGAAATGATCCTGCAGTGTTGATCTTAA 33 14 0 ACCTGCAGTG 0.968838 -27 TGTAAACAAGAAGCTGCAGTGTGATAGG 38 81 1 AGCTGCAGTG 0.980614 -18 TAAAAAATAAAATTTGAGGTGATCAT 42 37 1 ATTTGAGGTG 0.782215 -16 TATAATATAAAGGTTGAAGTGATTATTACTA 44 227 0 AGTTGAAGTG 0.895595 -74 * ********* Masking position 5 Map Score: 5.54044 Number of sites scoring better than the average of aligned sites = 373 Number in coding regions = 344 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 11 CTCTTCCATCAGAAGCACAGGAAGAGGGCG 1 46 1 AGAAGCACAG 0.94837 -83 TTCAAAATTAAAAAGCACAGACAGAAGGGG 11 43 0 AAAAGCACAG 0.949342 -124 TTCTTATAAGGGATGCACAGTTTAGGAACA 17 55 1 GGATGCACAG 0.966536 -40 GCTGGCCCTAAAATTCACAGGTGATATA 18 206 1 AAATTCACAG 0.823037 -18 CGCAAATCTCGAATGCACCGATAAATATAT 19 21 1 GAATGCACCG 0.943459 -182 CAATGTGAGCGGATCCACCGCAGATTGCAA 24 62 0 GGATCCACCG 0.873443 -109 CTGGGCAAGTAAAACCACAGACCACATCGT 24 103 0 AAAACCACAG 0.887738 -68 CATATACTCAAATGCACAGTAGAGGATCA 38 10 1 AAATGCACAG 0.967808 -89 ********** Masking position 7 Map Score: 4.35906 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 50 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 12 CCTTTCACCAACATCGAAAAAAA 1 3 1 TTTCACCACA 0.934159 -126 ACTTAAAATACCTCTCCACTACTCCCTAAGG 11 103 1 CCTCTCCATA 0.61735 -64 AGATAAAACCTTGCACCAACACTTCATCATG 13 55 1 TTGCACCACA 0.727662 -63 ATATTCATCTCATCTCCATCGAACATATGTT 14 79 1 CATCTCCACG 0.85567 -31 TATTCATAATTTTCTCCAAAATACTAAAATC 16 21 1 TTTCTCCAAA 0.694669 -77 TCCCGAAGTACTTCTCCAGCACCTTTTTCTG 18 148 0 CTTCTCCACA 0.962875 -76 AGATTTAAATCCTCACCATCGCTAATGGATG 19 84 1 CCTCACCACG 0.927712 -119 CCTATCACCAAAAGTTTTTGAGG 22 3 1 TATCACCAAA 0.586471 -164 CCTCACCAGCGGAAAGTTTAA 24 1 1 CCTCACCACG 0.927712 -170 ATGATAGCCCCTACACCACCAGGGCAAGTCT 32 109 0 CTACACCACA 0.888886 -192 GAAGGATAGATTACTCCATCACTCATCCCAA 40 56 1 TTACTCCACA 0.697809 -65 TCGACTTCACCAGAAAAAAATTAAT 43 19 0 CTTCACCAAA 0.887411 -15 CTATCTGGCACATCCCCACCATTTATTAAAA 44 98 0 CATCCCCACA 0.81111 -203 ******** ** Masking position 8 Map Score: 5.7804 Number of sites scoring better than the average of aligned sites = 971 Number in coding regions = 919 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 13 TTCATCACCTCTAATAGATATATTT 5 151 0 CACCTCTAAT 0.875277 -15 CTTACCACCCCGTAGTCCCAGCGGC 11 152 0 CACCCCGTAG 0.871606 -15 TTTCTCACCTCGTATTACTTTTTTT 16 83 0 CACCTCGTAT 0.972395 -15 CTAAACTGTGCATCCCTTATAAGAAAATTT 17 50 0 CATCCCTTAT 0.642319 -45 TTAGGGCCAGCACATCTTATAATTTTTCCC 18 187 0 CACATCTTAT 0.918721 -37 TGGATCCGCTCACATTGTATGCTCTGATAC 24 75 1 CACATTGTAT 0.637372 -96 AACCACAGACCACATCGTATCAGAGCATAC 24 91 0 CACATCGTAT 0.947171 -80 AGTTCATCAGCACACCTTATAAATAATAAT 37 45 0 CACACCTTAT 0.903133 -26 ATGATCACCTCAAATTTTATTTTTT 42 38 0 CACCTCAAAT 0.680819 -15 ********** Masking position 2 Map Score: 1.91384 Number of sites scoring better than the average of aligned sites = 95 Number in coding regions = 86 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 14 TGACAGTTCAATTAATATCAGGTATGATTTATCTCAG 5 72 1 ATATTATAGA 0.719997 -94 GTTTTTTAAAATAGATTTTAACAATAAATAAATATAT 5 122 1 ATATTAAAAA 0.943009 -44 TATCCTCCTAATGGATTTAACGAAAAACCAGAAAGGA 8 21 1 ATATTAAAAA 0.943009 -37 GGGAAGCAATATAAATTTAACTAAGAATGTAAA 9 7 0 ATATTAAAAA 0.943009 -56 GAGTGAGCATTTTTATCTGAGCAAAAAATTTAAATTA 10 109 0 TTATTAAAAA 0.677408 -81 AACTCATAGCATGCATGTCATATAGGAATGGAAAAGT 32 28 1 ATATTATAGA 0.719946 -273 CCCCATTAAACTTATATAATTAAAAAGAATATAGGA 35 10 1 ACATTAAAAA 0.757045 -104 AAGCCTATATATCTCATCAATAAATTTCTCTAT 37 7 1 ATATTAAAAA 0.942999 -64 ATGATCCCCCATAAATGTAAACAAGAAGCTGCAGTGT 38 66 1 ATATTAAAAA 0.943009 -33 CTGTTCTGCTATTTATTTAAATAAGGAGTTATATATA 39 42 0 ATATTAAAGA 0.911998 -32 TATCCCCGCTATTTATATAGTTAAAAAACAAGGGCTA 40 90 0 ATATTGAAAA 0.75705 -31 ** ** * * ** ** Masking position 5 Map Score: 4.94927 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 18 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 15 GCTTCCCGACCCAGCAAAGGCTGCGGTGAT 9 37 1 CCAGCAAAGG 0.986163 -26 ACTTCGATTTCCCGAAAAGGGTAAAGCTCG 18 56 1 CCCGAAAAGG 0.779088 -168 AATTTTAGGGCCAGCACATCTTATAATTTT 18 191 0 CCAGCACATC 0.868376 -33 GCCTTTTCCCCGCAAATCTCGAATGCAC 19 9 1 CCCGCAAATC 0.884299 -194 TCTAAAGATACAAGCAAAGGACAGATATAT 19 45 0 CAAGCAAAGG 0.861647 -158 GGCACCAGCATAGCGATTTGGGCT 21 5 1 CCAGCATAGC 0.850025 -53 TTCGGGTTTATCAGCAAATGCTGAATACAA 28 77 1 TCAGCAAATG 0.726613 -33 CTAGGCTATCCCGGCACAGGATGTATCATA 29 57 0 CCGGCACAGG 0.95173 -180 TTTTTTAGATCCAGCAAATGGGCATGCTGT 35 62 0 CCAGCAAATG 0.968174 -52 CCTGAGACCCCCGGCAATGGTCATCCCTCC 44 154 1 CCGGCAATGG 0.850286 -147 ********** Masking position 6 Map Score: 6.06035 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 194 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