AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00240_tpal_reg_100.orf -o00240_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0002 242 DNA polymerase III, subunit beta (dnaN) #2 TP0053 170 ribonucleoside-diphosphate reductase, subunit beta (nrdB) #3 TP0104 246 5'-nucleotidase (ushA) #4 TP0105 166 DNA polymerase I (polA) #5 TP0207 187 ribosomal protein L15 (rplO) #6 TP0241 262 DNA-directed RNA polymerase, beta subunit (rpoB) #7 TP0274 88 deoxycytidylate deaminase, putative #8 TP0276 172 conserved hypothetical protein #9 TP0342 120 cytidylate kinase (cmk) #10 TP0354 262 thymidylate kinase (tmk) #11 TP0445 135 4-methyl-5(b-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme (thiJ) #12 TP0446 41 gcpE protein (gcpE) #13 TP0448 57 uracil phosphoribosyltransferase, putative #14 TP0524 135 ATP-dependent protease LA (lon-2) #15 TP0642 140 phosphomannomutase (manB) #16 TP0667 230 uridine kinase (udk) #17 TP0669 153 DNA polymerase III, subunit alpha (dnaE) #18 TP0734 81 purine nucleoside phosphorylase (deoD) #19 TP0736 233 hydrogenase, gamma chain (hydG) #20 TP0814 222 thioredoxin reductase (trxB) #21 TP0824 300 transketolase B (tktB) #22 TP0886 147 polyribonucleotide nucleotidyltransferase (pnp) #23 TP1005 58 DNA polymerase III, subunits gamma and tau (dnaH) #24 TP1006 108 DNA gyrase, subunit B (gyrB) #25 TP1008 126 ribonucleoside-diphosphate reductase, subunit alpha (nrdA) #26 TP1010 125 nucleoside-diphosphate kinase (ndk) #27 TP1027 121 uridine phosphorylase (udp) Motif number 1 GTCCGCTCGATGTGTTCCGTGCCCGCACGGTAC 3 202 0 TGTTCCGTCC 0.718487 -45 TGCAGCACCCTTCTTTCCGCTCCTAACGTGGCA 4 98 0 TTCTCCGCCC 0.835345 -69 TCCTCACCAGCGTTATACGCACCCTCTTTGTCA 5 14 0 CGTTACGCCC 0.874113 -174 AACCGTCCGACGCACCGGCTCCCTCTGACCGAT 5 52 0 CGCCGGCTCC 0.711568 -136 AACCTAACTCCTCCACCCGCACCAGGTGCGAAA 5 164 0 CTCCCCGCCC 0.967598 -24 TTTTTTTGCATGCGTCCGGCGCGTCGTTGTGTG 6 19 1 TGCCCGGCCG 0.907458 -244 TACTCAAAAGCGCGACGCCCTCCCACACGAAAG 6 63 0 CGCCGCCCCC 0.980558 -200 ACAGGGGAGACGCCGTCCCCTCCACTCAAGTGA 6 166 0 CGCTCCCCCC 0.983891 -97 GCACTCCCCCCTCAAGCTGCACCG 6 249 0 CACCCCCCCA 0.692889 -14 CCCGCCAGAGTGTGCTGCGCACCGCAGCACAAG 7 27 1 TGTTGCGCCC 0.857986 -62 ACGTCCAGTTCGCTACGCGTGCGCCCTTGTTAT 8 11 1 CGCCGCGTCG 0.977726 -162 CCAGACTGTGCGTGCTCGGCGCCGCACTACTTT 8 110 1 CGTTCGGCCC 0.88589 -63 CCACCAGATCCACAGCCGGCACCACCACCATGT 9 32 0 CACCCGGCCC 0.899841 -89 GCACCCCTCCGCACTCCGCTCTTTGCATCACC 9 99 0 CGCTCCGCCT 0.899295 -22 CGGACCAATACATTGTCCCCACGGCGCAAAACT 10 29 0 CATTCCCCCG 0.79909 -234 AAAGTTCCTGCACAATCCGTGCGCGCCTCATTC 10 102 0 CACTCCGTCG 0.916687 -161 ACCAAACCGTCGTCCCGCGTACCAAAGTTCCTG 10 125 0 CGTCGCGTCC 0.900574 -138 GAGGAGAAAGTGCAACGCGCACGTGTACACCGC 10 187 0 TGCCGCGCCG 0.975675 -76 GTGCTGCGCTCGCGGGGCGCACGGCTAGTACGT 11 29 1 CGCGGCGCCG 0.533657 -107 TACGGATAATCGTCCTCCGTTCAAAAGCGACGT 11 58 0 CGTTCCGTCA 0.5946 -78 CGCAACACCCCCGTACCTGTTCT 11 123 0 CGCCACCCCG 0.944483 -13 CTGGCTGCCGCGCAGCACGCTCGTCCCTCTGAT 12 11 0 CGCCACGCCG 0.978919 -31 CCCCAATTCACGTTCCTCGCGCGTGTGCTATAC 13 21 0 CGTCTCGCCG 0.738449 -37 CTGCGCGGTATACTGCGCCCCCGCAGGTCGTGC 14 44 0 TACCGCCCCG 0.749659 -92 GCCCCTAGGCCACGTCCCGTACGCTTGACACTG 16 151 1 CACCCCGTCG 0.937648 -80 CGTCACTCCCTCCCTTCGTGGGGCCTAG 18 64 0 CTCTCCCTCG 0.717634 -18 TCAAGCAAAACGCCATCGGCGCCGAGAAGGGTC 19 44 0 CGCTCGGCCC 0.970141 -190 TGAGAAAAGCAGCGGTCGGCGCGTTAGTTGCCT 19 114 1 AGCTCGGCCG 0.53968 -120 TGATTATTCCTGCCGTGCGTGCGCCTGTCATTC 20 93 0 TGCTGCGTCG 0.884124 -130 AGGTGGGTGACGCTTTACCCACGGACCTGATTT 21 30 0 CGCTACCCCG 0.925582 -271 CTTCCGAGCCTGTGCTACGCACGAGTATACCTT 21 86 1 TGTTACGCCG 0.670663 -215 AACAGGTAGTCTCGGCCCGTGCGCCTTCTGTTC 21 259 1 CTCCCCGTCG 0.895207 -42 GGGGAAGTTTCGCAGTGCGTGCCGCCGAGGGGT 22 22 1 CGCTGCGTCC 0.962763 -126 CAGAATGTATCGCAGGCCGCACCAAGCCCTGGC 22 111 0 CGCGCCGCCC 0.972997 -37 AAGTCTATAGTGCGCTCGTCTGTGTGAG 24 6 1 TATTGCGCCG 0.606907 -103 ACGGGGGTGTTTTCTTCCGCGCGTCTCTGTGGG 25 12 1 TTTTCCGCCG 0.62035 -115 TCGTTCTTTACGCTTCCCCCACAGAGACGCGCG 25 29 0 CGCCCCCCCA 0.917736 -98 CTAGCTAATACACGTGGCGCGCCAGCGTACCCA 26 89 0 CACGGCGCCC 0.847539 -37 *** ***** ** Masking position 12 Map Score: 54.6998 Number of sites scoring better than the average of aligned sites = 3220 Number in coding regions = 2952 Number in noncoding regions = 268 Number of orfs with sites within 600 bp upstream = 180 Fraction of orfs with sites within 600 bp upstream = 0.028911 Motif number 2 TCGTATCTGCAGGAAAGCAAGAAGGATGGCGA 3 27 1 AGGAAGCAGA 0.495901 -220 GAAAGCAAGAAGGATGGCGAGAACATACAGTT 3 39 1 AGGAGGCGGA 0.917542 -208 GTTCCGTGCCCGCACGGTACGGAACCTAGACC 3 190 0 CGCAGGTAGG 0.750149 -57 ACGTTAGGAGCGGAAAGAAGGGTGCTGCACAT 4 102 1 CGGAAGAAGG 0.8915 -65 GGAGTACGATCGGTCAGAGGGAGCCGGTGCGT 5 44 1 CGGTAGAGGA 0.615087 -144 GCCGGTGCGTCGGACGGTTCGGTCTTTGGGTT 5 66 1 CGGAGGTTGG 0.764525 -122 TGCCGTCTTGGGGATGGTGCGAGCTGTTTCGC 5 138 1 GGGAGGTGGA 0.969493 -50 CCTTTCGTGTGGGAGGGCGTCGCGCTTTTGAG 6 62 1 GGGAGGCGCG 0.786084 -201 CTCACTTGAGTGGAGGGGACGGCGTCTCCCCT 6 165 1 TGGAGGGAGG 0.601824 -98 CCGACAGTTGGTGATGGAGCGAAGATATTTTC 10 59 1 GTGAGGAGGA 0.892453 -204 AAGATATTTTCGCAAGGAGGGAGAATGAGGCG 10 80 1 CGCAGGAGGA 0.9687 -183 CTAGTATCCAGGCAAGGGACGAAAAGTCAATG 14 107 0 GGCAGGGAGA 0.852088 -29 ACGGCACCACAGGATAGAGGGGCATTGTAATG 15 83 0 AGGAAGAGGG 0.79209 -58 GAAATTATTCGGGACGGAGGGATTTGAACCCT 16 89 1 GGGAGGAGGA 0.989103 -142 ATAGCTCACCCGGATAGAGCGACTGCCTT 17 8 0 CGGAAGAGGA 0.967378 -146 GCCCCACGAAGGGAGGGAGTGACG 18 68 1 GGGAGGAGGA 0.989103 -14 ACCAAACTCTCGGAGGGATGGATGATAGTACA 19 196 0 CGGAGGATGA 0.923151 -38 TACAAACCAAGGGAAAGGAAGGGCCTAACCGC 20 58 1 GGGAAGGAGG 0.809926 -165 GACAGGCGCACGCACGGCAGGAATAATCAATT 20 97 1 CGCAGGCAGA 0.860511 -126 AGCACAGGCTCGGAAGGAGCGAGTTTACTGAA 21 70 0 CGGAGGAGGA 0.991762 -231 GAACAGAAGGCGCACGGGCCGAGACTACCTGT 21 260 0 CGCAGGGCGA 0.640979 -41 GTGGTGCCGTCTGACAGGGGGAAGGATCA 23 40 1 CTGAAGGGGA 0.650954 -19 AATCCGCGTTCGGACGGAGAGATAT 25 112 1 CGGAGGAGGA 0.991762 -15 TCACCATACGGTGAAGGAAGGGTAAAAAGAGA 26 23 1 GTGAGGAAGG 0.696903 -103 CCGACCACGGGGGACGGTGACAGGTAGTTCTC 27 48 0 GGGAGGTGCA 0.750071 -74 **** **** ** Masking position 7 Map Score: 25.3989 Number of sites scoring better than the average of aligned sites = 576 Number in coding regions = 473 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 3 AATGTCTGTCTGCAGGGCTCTGTGTCTTGTG 2 72 0 TGCGGGCTCT 0.529353 -99 GACATTTTTACGCCCGCCGCAATTGAGAATT 2 97 1 CGCCGCCGCA 0.989314 -74 TCCTCACCAGCGTTATACGCACCCTCTTTGT 5 16 0 CGTATACGCA 0.470706 -172 TCTGACCGATCGTACTCCTCACCAGCGTTAT 5 31 0 CGTCTCCTCA 0.845016 -157 AAGACCGAACCGTCCGACGCACCGGCTCCCT 5 61 0 CGTCGACGCA 0.946321 -127 CACAACGACGCGCCGGACGCATGCAAAAAAA 6 19 0 CGCGGACGCA 0.972965 -244 TAGAAGCCCACGCTCTACTCAAAAGCGCGAC 6 80 0 CGCCTACTCA 0.919639 -183 GGTTGGGTCGCGTTCTCCTCACTTGAGTGGA 6 148 1 CGTCTCCTCA 0.845018 -115 GCCCTTGTGCTGCGGTGCGCAGCACACTCTG 7 32 0 TGCGTGCGCA 0.533039 -57 AGACTGTGCGTGCTCGGCGCCGCACTACTTT 8 112 1 TGCCGGCGCC 0.771171 -61 GCACCCCTCCGCACTCCGCTCTTTGCATCA 9 101 0 CGCCTCCGCT 0.962922 -20 ATACATTGTCCCCACGGCGCAAAACTGTTAC 10 24 0 CCCCGGCGCA 0.840771 -239 GCACAATCCGTGCGCGCCTCATTCTCCCTCC 10 95 0 TGCCGCCTCA 0.847329 -168 GTTTGGTTTTTGCGGTACGCTGTCTTATTCT 10 151 1 TGCGTACGCT 0.745446 -112 GTGCTGCGCTCGCGGGGCGCACGGCTAGTAC 11 29 1 CGCGGGCGCA 0.930445 -107 GAGGGACGAGCGTGCTGCGCGGCAGCCAGAG 12 15 1 CGTCTGCGCG 0.750246 -27 GGGAAGGTGCTGCTCTGTGCAATGCTCACAA 15 53 0 TGCCTGTGCA 0.625876 -88 GCTATGATCCCGTGGTACGCTGCGAGCAAAA 17 35 1 CGTGTACGCT 0.74696 -119 CGCGCGTGTACGCTCAGCGCATGCAGCACCC 18 12 0 CGCCAGCGCA 0.919397 -70 AGGTTTTGCGTGCAGTCCTCATTCAAGCAAA 19 68 0 TGCGTCCTCA 0.766009 -166 GCAACTAACGCGCCGACCGCTGCTTTTCTCA 19 114 0 CGCGACCGCT 0.720769 -120 CTTCCGAGCCTGTGCTACGCACGAGTATACC 21 86 1 TGTCTACGCA 0.832411 -215 CTCGGCGGCACGCACTGCGAAACTTCCCCAT 22 20 0 CGCCTGCGAA 0.772576 -128 AACGGACAACCGTCCTATGCACAACCCCTCG 22 47 0 CGTCTATGCA 0.506706 -101 CAGAATGTATCGCAGGCCGCACCAAGCCCTG 22 113 0 CGCGGCCGCA 0.980771 -35 *** ******* Masking position 10 Map Score: 28.6541 Number of sites scoring better than the average of aligned sites = 1839 Number in coding regions = 1702 Number in noncoding regions = 137 Number of orfs with sites within 600 bp upstream = 113 Fraction of orfs with sites within 600 bp upstream = 0.0181497 Motif number 4 TTCTTCACAAGCTTGTGTGCGGTTTTTGTTTG 1 118 1 GTTGTGTGGG 0.925613 -125 GATTTCCTACGTCTCTGTTAGGTTTCCCCAAA 2 15 1 GCTCTGTTGG 0.635135 -156 AAGTATACTACCCTGTGCCCGCACTCAGGAGG 2 139 1 CCTGTGCCGC 0.875756 -32 CGATTCTGCGAGCAAATCGTATC 3 2 1 GTTCTGCGGC 0.948308 -245 GAGCGGACGCGTCTGTTCGTGGAGGATATT 3 227 1 GCTGTTCGGG 0.784741 -20 GTCAGAGGGAGCCGGTGCGTCGGACGGTTCGG 5 56 1 GCGGTGCGCG 0.858418 -132 CCGTCTTGGGGATGGTGCGAGCTGTTTCGCAC 5 140 1 GTGGTGCGGC 0.964542 -48 CGTCCGGCGCGTCGTTGTGTGCCTCTGACACC 6 31 1 GCGTTGTGGC 0.869783 -232 ACGGCGTCTCCCCTGTGTGGGGAGTATTACGG 6 183 1 CCTGTGTGGG 0.899585 -80 CACTCACCAAGTCTTTGCAAGGGGTATAACAA 8 37 0 GCTTTGCAGG 0.804812 -136 ATGGGAGCCAGACTGTGCGTGCTCGGCGCCGC 8 103 1 GCTGTGCGGC 0.992007 -70 CCAACATGGTGGTGGTGCCGGCTGTGGATCTG 9 29 1 GTGGTGCCGC 0.850894 -92 ATTATCCGTAGTCTGTGTGCGCGGGGTTGCAC 11 81 1 GCTGTGTGGC 0.975028 -55 GAGGGACGAGCGTGCTGCGCGGCAGCCAGAGG 12 15 1 CTGCTGCGGG 0.710637 -27 AAGACATGCACTTTTTGTGAGCATTGCACAGA 15 39 1 CTTTTGTGGC 0.537701 -102 CCCTTGCAGGGTTTTTGCTCGCAGCGTACCAC 17 46 0 GTTTTGCTGC 0.646111 -108 CGGGTGCTGCATGCGCTGAGCGTA 18 3 1 GTGCTGCAGC 0.588395 -79 TTTCCTGGCAGGTTTTGCGTGCAGTCCTCATT 19 76 0 GTTTTGCGGC 0.931835 -158 CTCCTTCCGAGCCTGTGCTACGCACGAGTATA 21 83 1 GCTGTGCTCG 0.581211 -218 GGGCTTTGCATGGGGAAGTTTCG 22 2 1 GCTTTGCAGG 0.804812 -146 GGGGAAGTTTCGCAGTGCGTGCCGCCGAGGGG 22 22 1 CCAGTGCGGC 0.717538 -126 CTTCGCAGGTGGCTGTGCCAGGGCTTGGTGCG 22 95 1 GCTGTGCCGG 0.956724 -53 TAGTGCGCTCGTCTGTGTGAGCAGCAAGAGTA 24 18 1 GCTGTGTGGC 0.975028 -91 TCTTCCGCGCGTCTCTGTGGGGGAAGCGTAAA 25 24 1 GCTCTGTGGG 0.928744 -103 * ******* ** Masking position 6 Map Score: 29.5731 Number of sites scoring better than the average of aligned sites = 1141 Number in coding regions = 1033 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 5 GGTTTCCCCAAACCTACCCACAAAACAGGG 2 35 1 AACCTACCCA 0.816485 -136 GATGAAACCTCCTCCTGAGTGCGGG 2 156 0 AACCTCCTCC 0.874316 -15 CTGACCGATCGTACTCCTCACCAGCGTTAT 5 31 0 GTACTCCTCA 0.636051 -157 CATTGAATGCAACTTCCTCAAACCCAAAGA 5 88 0 AACTTCCTCA 0.562005 -100 AACAGCTCGCACCATCCCCAAGACGGCAGG 5 136 0 ACCATCCCCA 0.647462 -52 TAACTCCTCCACCCGCACCAGGTGCGAAAC 5 163 0 ACCCGCACCA 0.489249 -25 CTCTACCGTAATACTCCCCACACAGGGGAG 6 190 0 ATACTCCCCA 0.920594 -73 GCACTCCCCCCTCAAGCTGC 6 253 0 GCACTCCCCC 0.87988 -10 GCGATGTTTAAACTCACCCGCCAGAGTGT 7 10 1 AAACTCACCC 0.694389 -79 GATAAGGGCCACACTCACCAAGTCTTTGCA 8 50 0 ACACTCACCA 0.777792 -123 ATAAACTCCTCATCCCCCAATT 13 46 0 AAACTCCTCA 0.921576 -12 GTAAACCTCCCCGACACGTATAT 19 4 1 AACCTCCCCG 0.878775 -230 TTACTAGAATGACCTCCCTACAAACCAAGG 20 40 1 GACCTCCCTA 0.569484 -183 AGCGTAGCGGAAACTACCCAAATGGTCAAG 21 116 0 AAACTACCCA 0.770429 -185 GGGCACGTAGAAACTCCTCAGGAATCCAAG 21 154 0 AAACTCCTCA 0.921576 -147 GACGAAAACGCCTCATGTCGAACAG 21 286 0 AAACGCCTCA 0.708089 -15 CGCACTGCGAAACTTCCCCATGCAAAGCCC 22 11 0 AACTTCCCCA 0.824806 -137 GCGCGGAAGAAAACACCCCCGTG 25 4 0 AAACACCCCC 0.593002 -123 CTTTATGCAAGTCCTCCCCACACTTTCTCT 26 50 0 GTCCTCCCCA 0.894749 -76 AAGGTGCACAGCACTCCCCAGTCACGAAGA 27 83 0 GCACTCCCCA 0.942543 -39 ********** Masking position 9 Map Score: 14.9851 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 417 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 6 AAAGAAGGGTGCTGCACATAACCTTATCTTTGC 4 115 1 GTGCACATCC 0.958199 -52 CGAACCGTCCGACGCACCGGCTCCCTCTGACCG 5 54 0 GCGCACCGTC 0.960482 -134 TGTGGTATAGGGAGCACCGTGTCGGTTCGGTGC 6 222 1 GAGCACCGTC 0.976364 -41 CCCCCCTCAAGCTGCACCGAACCGACACGGTGC 6 235 0 GTGCACCGCC 0.992813 -28 TTCCCTTAAAGATGCACATGCCCTTGTGCTGCG 7 49 0 GTGCACATCC 0.9582 -40 ACACGTGCGCGTTGCACTTTCTCCTCGGGTGTA 10 194 1 GTGCACTTTC 0.929171 -69 GGGTGTACATGCTGCACTGTTTTTAGAGGAAAG 10 220 1 GTGCACTGTT 0.899767 -43 TGTGCGCGGGGTTGCACTGTTGCTGTAAGAACA 11 96 1 GTGCACTGGC 0.925828 -40 ATTGCACAGAGCAGCACCTTCCCATTACAATGC 15 61 1 GAGCACCTCC 0.9472 -80 CTGCTTATCGGGTGCACCGTTTTTTGTTATA 17 133 1 GTGCACCGTT 0.958278 -21 ATACTCGTGCGTAGCACAGGCTCGGAAGGAGCG 21 81 0 GAGCACAGTC 0.95474 -220 TTAAGCGTAAGGTGCACAGCACTCCCCAGTCAC 27 88 0 GTGCACAGCT 0.939767 -34 * ******* ** Masking position 6 Map Score: 14.6334 Number of sites scoring better than the average of aligned sites = 169 Number in coding regions = 151 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 7 TAAAAATGCGCGTAACTCGCGGAATATACAA 3 74 0 CGTACTCGCG 0.874765 -173 GTCTAGGTTCCGTACCGTGCGGGCACGGAAC 3 191 1 CGTCCGTGCG 0.773867 -56 CGAGCTGTTTCGCACCTGGTGCGGGTGGAGG 5 157 1 CGCCCTGGTG 0.554477 -31 TTTTTGCATGCGTCCGGCGCGTCGTTGTGTG 6 21 1 CGTCGGCGCG 0.658321 -242 ACGTCCAGTTCGCTACGCGTGCGCCCTTGTT 8 11 1 CGCACGCGTG 0.913366 -162 ACCAAACCGTCGTCCCGCGTACCAAAGTTCC 10 127 0 CGTCCGCGTA 0.910524 -136 ACTAGCCGTGCGCCCCGCGAGCGCAGCACTA 11 27 0 CGCCCGCGAG 0.916783 -109 GAGGGACGAGCGTGCTGCGCGGCAGCCAGAG 12 15 1 CGTCTGCGCG 0.69952 -27 CCCCAATTCACGTTCCTCGCGCGTGTGCTAT 13 23 0 CGTCCTCGCG 0.98071 -35 CCCTAGGCCACGTCCCGTACGCTTGACACTG 16 153 1 CGTCCGTACG 0.684049 -78 TTGCTCGCAGCGTACCACGGGATCATAGCTC 17 33 0 CGTCCACGGG 0.81513 -121 CGCGCGTGTACGCTCAGCGCATGCAGCACCC 18 12 0 CGCCAGCGCA 0.51608 -70 AGAAAAGCAGCGGTCGGCGCGTTAGTTGCCT 19 116 1 CGGCGGCGCG 0.905131 -118 ATTGATTATTCCTGCCGTGCGTGCGCCTGTC 20 97 0 CCTCCGTGCG 0.748141 -126 TTGACTAATCAGTTACGCGTGCATACACTCT 20 198 1 AGTACGCGTG 0.405998 -25 GGAGTTTCTACGTGCCCTGCGGAAAGAAAAG 21 167 1 CGTCCCTGCG 0.924004 -134 CAGGTAGTCTCGGCCCGTGCGCCTTCTGTTC 21 261 1 CGGCCGTGCG 0.932308 -40 GGTACGCTGGCGCGCCACGTGTATTAGCTAG 26 91 1 CGCCCACGTG 0.904118 -35 TACCTGTCACCGTCCCCCGTGGTCGGGATTC 27 54 1 CGTCCCCGTG 0.956882 -68 *** ******* Masking position 9 Map Score: 22.7594 Number of sites scoring better than the average of aligned sites = 845 Number in coding regions = 778 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 GGCGTAGACACTGAATTCGAT 1 1 1 GGCGTAACAC 0.849172 -242 GGTTTCCCCAAACCTACCCACAAAACAGGGA 2 35 1 AACCTACCAC 0.387686 -136 CAAGTATACTACCCTGTGCCCGCACTCAGGA 2 138 1 ACCCTGGCCC 0.70737 -33 CTCGATGTGTTCCGTGCCCGCACGGTACGGA 3 199 0 TCCGTGCCGC 0.726788 -48 GGAGAACGCGACCCAACCCGCATGCCAAAAT 6 135 0 ACCCAACCGC 0.827227 -128 TGGAGGGGACGGCGTCTCCCCTGTGTGGGGA 6 175 1 GGCGTCCCCC 0.850904 -88 GTAGTGCGGCGCCGAGCACGCACAGTCTGGC 8 109 0 GCCGAGACGC 0.823191 -64 AACTTCTCTCACCGTAAACCCTATACATATC 8 145 0 ACCGTAACCC 0.90512 -28 CCACCATGTTGGCGAAACCGCAACCGAACT 9 10 0 GGCGAACCGC 0.939589 -111 CAAAACTGTTACCGTAGGCGCGACT 10 5 0 ACCGTAGCGC 0.912366 -258 CGACGTACTAGCCGTGCGCCCCGCGAGCGCA 11 33 0 GCCGTGGCCC 0.899622 -103 CAAACCGGGTGCCCTAGCCCCTAGGCCACGT 16 135 1 GCCCTACCCC 0.958197 -96 GCATGCGCTGAGCGTACACGCGCGAGGTTAC 18 19 1 AGCGTAACGC 0.917224 -63 CCCTTCGTGGGGCCTAGACCCACACGTTTCG 18 50 0 GGCCTAACCC 0.904786 -32 GGAAAGGAAGGGCCTAACCGCTGAGAATGAC 20 69 1 GGCCTACCGC 0.963754 -154 GACGAAAACGCCTCATGTCGA 21 290 0 GACGAAACGC 0.591717 -11 GTGGCGCGCCAGCGTACCCACCATTCTTTCT 26 78 0 AGCGTACCAC 0.853213 -48 ****** **** Masking position 3 Map Score: 9.83594 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 420 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 9 AAACCTCCTCCTGAGTGCGGGCACAGGGTA 2 147 0 CTGAGTGCGG 0.936463 -24 GGAGAAAGACGGGAGTCCTGCCGTCTTGGG 5 120 1 GGGAGTCCTG 0.934834 -68 CAAAGACTTGGTGAGTGTGGCCCTTATCAG 8 52 1 GTGAGTGTGG 0.90502 -121 CATATCTGAAAGTAGTGCGGCGCCGAGCAC 8 121 0 AGTAGTGCGG 0.764518 -52 ATGCAAAGAGCGGAGTGCGGAGGGGTGC 9 103 1 CGGAGTGCGG 0.978247 -18 TCTATCCTAAGGTAGTGCTGCGCTCGCGGG 11 15 1 GGTAGTGCTG 0.95108 -121 GAACAGGTACGGGGGTGTTGCG 11 124 1 GGGGGTGTTG 0.840668 -12 GTATTTCCATGTGAGTGGTGCCGTCTGACA 23 26 1 GTGAGTGGTG 0.861509 -33 TTCGTGACTGGGGAGTGCTGTGCACCTTAC 27 85 1 GGGAGTGCTG 0.989973 -37 ********** Masking position 6 Map Score: 5.52847 Number of sites scoring better than the average of aligned sites = 180 Number in coding regions = 161 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 10 AACCGCACACAAGCTTGTGAAGAAAGTATATTTT 1 108 0 AGCTGAAGAA 0.979836 -135 CTTACATTAGAGGCCTGTAAAGAACTACGTTCTT 4 21 1 AGCTGAAGAA 0.979836 -146 CAGATTGGCACAGCCTGTAAAGAACGTAGTTCTT 4 40 0 CGCTGAAGAA 0.975659 -127 GACGCGCCGGACGCATGCAAAAAAAACCAGACA 6 10 0 AGCTGAAAAA 0.905382 -253 TGCCGAGAACAAGTATGAAAAGAAATAGAAGCCC 6 102 0 AGTTGAAGAA 0.96114 -161 ACGCTTGACACTGTGTGTTAAGAATGGATAGGCT 16 171 1 CGTTGAAGAA 0.953273 -60 GCGCAAGAAGAAGCTTCGCAAGAATCGGCACAAG 21 225 1 AGCTCAAGAA 0.961602 -76 ACGTTTCCTAAGAACAGAATGTAT 22 134 0 AGTTCAAGAA 0.927253 -14 TATTGCCTTTCTGTGTCTTAAAAAGGTGAATGTG 24 48 1 CGTTCAAAAA 0.674296 -61 * ** ** ***** Masking position 6 Map Score: 6.69686 Number of sites scoring better than the average of aligned sites = 30 Number in coding regions = 22 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 11 CATTTTTATGGCCGAGTGGTTAGCATTACTTCT 3 97 1 GCCGAGTTAG 0.947645 -150 TTCATGTGTCTCCGATACGGTGTGGTCTAGGTT 3 167 1 TCCGACGTGT 0.639371 -80 TGGTGGTGGTGCCGGCTGTGGATCTGGTGGATA 9 35 1 GCCGGGGGAT 0.845526 -86 GATGCAAAGAGCGGAGTGCGGAGGGGTGC 9 102 1 GCGGAGGGAG 0.713275 -19 AATGTATTGGTCCGACAGTTGGTGATGGAGCGA 10 48 1 TCCGAGTGGT 0.930517 -215 TGGTACGCGGGACGACGGTTTGGTTTTTGCGGT 10 134 1 GACGAGTTGG 0.615372 -129 GTGCTGTAGCTCCGACTGCTTATCGGGTGCACC 17 118 1 TCCGAGTTAT 0.907368 -36 CCTTCTCGGCGCCGATGGCGTTTTGCTTGAATG 19 47 1 GCCGAGGTTT 0.87609 -187 CAACTAACGCGCCGACCGCTGCTTTTCTCATCA 19 111 0 GCCGAGTGCT 0.885438 -123 CATCCATCCCTCCGAGAGTTTGGTCGAAGGAGG 19 204 1 TCCGAGTTGG 0.906125 -30 GCCGAGAGTGTATGCACGCGTAA 20 210 0 GCCGAGGTAT 0.971475 -13 AGTGCGTGCCGCCGAGGGGTTGTGCATAGGACG 22 35 1 GCCGAGTTGT 0.970657 -113 TATCTCTCCGTCCGAACGCGGATTATGGGCCAA 25 103 0 TCCGAGGGAT 0.932389 -24 ***** * **** Masking position 4 Map Score: 4.93667 Number of sites scoring better than the average of aligned sites = 173 Number in coding regions = 154 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 ACACAAGCTTGTGAAGAAAGTATATTTTTT 1 106 0 GTGAAGAAAG 0.960054 -137 TTAGAGGCCTGTAAAGAACTACGTTCTTTA 4 27 1 GTAAAGAACT 0.653962 -140 GGCACAGCCTGTAAAGAACGTAGTTCTTTA 4 38 0 GTAAAGAACG 0.904694 -129 GCATTCAATGGTGGAGAAAGACGGGAGTCC 5 108 1 GTGGAGAAAG 0.946374 -80 GAACAAGTATGAAAAGAAATAGAAGCCCAC 6 100 0 GAAAAGAAAT 0.543686 -163 CCACTCAAGTGAGGAGAACGCGACCCAACC 6 148 0 GAGGAGAACG 0.857126 -115 ATGTACACCCGAGGAGAAAGTGCAACGCGC 10 200 0 GAGGAGAAAG 0.890948 -63 TATGTATTGCCTGAAGAAATTATTCGGGAC 16 74 1 CTGAAGAAAT 0.532761 -157 TGCGACAGAGCTGAAGAAAGGCTTTTCTTT 19 149 1 CTGAAGAAAG 0.851351 -85 TGGGGGAAGCGTAAAGAACGAGTCTAGGAG 25 41 1 GTAAAGAACG 0.904694 -86 TCACCATACGGTGAAGGAAGGGTAAAAAGA 26 23 1 GTGAAGGAAG 0.791261 -103 GGAAGGGTAAAAAGAGAAAGTGTGGGGAGG 26 38 1 AAAGAGAAAG 0.403703 -88 GAGGACTTGCATAAAGAAAGAATGGTGGGT 26 64 1 ATAAAGAAAG 0.665729 -62 ********** Masking position 5 Map Score: 6.7545 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 199 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 13 CCGATACGGTGTGGTCTAGGTTCCGTACCGT 3 178 1 GTGGTTAGGT 0.976335 -69 GGTAGAGCGTGTGGTATAGGGAGCACCGTGT 6 213 1 GTGGTTAGGG 0.993936 -50 GTGGTGTAGGGTATAGCACAC 13 1 1 GTGGTTAGGG 0.993936 -57 CGTACGGGACGTGGCCTAGGGGCTAGGGCAC 16 143 0 GTGGCTAGGG 0.989707 -88 ***** ***** Masking position 7 Map Score: 1.94402 Number of sites scoring better than the average of aligned sites = 3 Number in coding regions = 1 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 TACTCACGAATATCCCCCTTTTTTTAGAGA 1 77 1 TATCCCCCTT 0.956279 -166 AGTTAGTTTCCTCCTTATTAATCTTA 1 227 0 TTTCCTCCTT 0.83341 -16 CCTAACGTGGCATACCCTTTGTCTTTCCCG 4 80 0 CATACCCTTT 0.788881 -87 TTGACCGTGGTATACTCCTTGCACCTT 4 150 1 TATACTCCTT 0.836171 -17 GCGCCCTTGTTATACCCCTTGCAAAGACTT 8 31 1 TATACCCCTT 0.957109 -142 ACTTTCTCTTTTTACCCTTCCTTCACCGTA 26 29 0 TTTACCCTTC 0.788881 -97 CGAGGCATCTTTTACCCTTTTTTCATAGAC 27 11 0 TTTACCCTTT 0.933636 -111 GTGTTTCCCCTTTAAGCGTAAGG 27 109 0 TTTCCCCTTT 0.932385 -13 ********** Masking position 3 Map Score: 1.7459 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 30 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 ATTCTGCGAGCAAATCGTATCTGCAGGAAAGCAA 3 13 1 CAAATGTCGC 0.736021 -234 ATTACTTCTACAGGTTTTTTATGCAATTTTATAT 3 121 1 CAGGTTTAGC 0.9236 -126 CCCGGAAAAGCAGATTGGCACAGCCTGTAAAGAA 4 50 0 CAGATGGCGC 0.960743 -117 TGGCCCTTATCAGGTCGGTCCCGCTGCCCAGGCT 8 69 1 CAGGTGGCGC 0.990741 -104 TGCGCCCCCGCAGGTCGTGCAAGACGTTTACTAG 14 30 0 CAGGTGTAGA 0.855118 -106 TGTTTCCTGGCAGGTTTTGCGTGCAGTCCTCATT 19 76 0 CAGGTTTGGC 0.876409 -158 TGAATGCGTACAGGTGGGTGACGCTTTACCCACG 21 40 0 CAGGTGGAGC 0.981063 -261 GGCACAAGAACAGGTAGTCTCGGCCCGTGCGCCT 21 251 1 CAGGTGTCGC 0.990922 -50 ***** ** * ** Masking position 2 Map Score: 2.05602 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 87 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493