AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i259_tpal_bbur_300.orf -o259_tpal_bbur_300.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/synecho.fna -g0.40 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RBB00437 22 3615 RBB00453 18 3615 RBB00448 23 3615 RBB00447 33 3615 RBB00792 20 3615 Input sequences: #1 RTP01136 83 AE000520 #2 RTP01045 27 AE000520 #3 RTP00239 45 AE000520 #4 RTP00117 32 AE000520 #5 RTP00119 147 AE000520 #6 RTP00120 84 AE000520 #7 RTP00121 55 AE000520 #8 RTP00124 116 AE000520 #9 RTP00126 47 AE000520 #10 RTP00129 27 AE000520 #11 RTP00531 65 AE000520 #12 RTP00530 55 AE000520 #13 RTP00526 34 AE000520 #14 RTP00978 18 AE000520 #15 RTP00518 21 AE000520 #16 RTP00514 57 AE000520 #17 RTP00513 70 AE000520 #18 RTP00512 75 AE000520 #19 RTP00725 75 AE000520 #20 RTP00726 85 AE000520 #21 RTP00727 110 AE000520 #22 RTP00730 24 AE000520 #23 RTP00731 46 AE000520 #24 RTP01206 21 AE000520 #25 RTP00735 155 AE000520 #26 RTP00736 87 AE000520 #27 RBB00465 45 3615 #28 RBB00464 37 3615 #29 RBB00463 48 3615 #30 RBB00459 22 3615 #31 RBB00440 35 3615 #32 RBB00433 30 3615 #33 RBB00432 92 3615 #34 RBB00430 43 3615 #35 RBB00429 50 3615 #36 RBB00737 178 3615 Motif number 1 CCCCGAGGCAGCCGTGTCTGT 4 22 0 CCCGAGGCAG 0.931112 -11 AATCCCCCAGGCCGGGGCAGGCCTTTACGC 5 114 0 GCCGGGGCAG 0.993802 -34 AGACAGGGGGGTGGGGGCGCG 6 2 1 GACAGGGGGG 0.935257 -83 TTCTCAGTGCGCAGAGGGAGTTTTGTATCG 6 44 1 GCAGAGGGAG 0.8342 -41 AGCGCGCGGCGCACGGGGCGATACAAAACT 6 62 0 GCACGGGGCG 0.949023 -23 CCGGGCAGAGGGCGGGGTAGTCGCGCGCTT 7 18 0 GGCGGGGTAG 0.818317 -38 TCGTGGTGTCCCCCGGGCAGAGGGCGGGGT 7 30 0 CCCCGGGCAG 0.983837 -26 AGGTAGGATTCCACGCGCAGCCCTGCAACC 8 19 0 CCACGCGCAG 0.905909 -98 TCTTATCCTTGCCGGCGCAGGCTC 8 103 1 GCCGGCGCAG 0.992147 -14 CGACCACGGGGGACGGTGACA 9 2 1 GACCACGGGG 0.898435 -46 CCAGTTCCCCAGGGAGATGCACCCTG 10 12 0 CCCCAGGGAG 0.90476 -16 GTCGGATGCAGACGGCACAGGCACATGCGG 11 11 0 GACGGCACAG 0.722735 -55 AGCGTCACGCGACGGGTCGGATGCAGACGG 11 26 0 GACGGGTCGG 0.759038 -40 GTAGAGCTCGGACAGCGGAGGCCTTCTTGT 17 12 0 GACAGCGGAG 0.922802 -59 CTCCAAAGATCACCGGGCCGGT 19 64 1 CACCGGGCCG 0.962905 -12 GCACGTTCGCGGCCGCGCGGTTTTTGTTAT 20 24 1 GGCCGCGCGG 0.964155 -62 ATGCGCCGGGCGGTGTTGCCGTT 20 73 0 CGCCGGGCGG 0.935598 -13 CGACATAGATGACAACGCCGTGTACGTCTT 21 74 1 GACAACGCCG 0.718982 -37 CCAGCCAGGCGAGTTCTTGCTCA 23 4 1 GCCAGGCGAG 0.822077 -43 GCATTGTTTCGAAGGGCGCGTGCGTGTACG 25 16 1 GAAGGGCGCG 0.626527 -140 CTCCCGTTCTTCCGGCGCCGTTGCTGGTGT 25 76 0 TCCGGCGCCG 0.828838 -80 TAAAACGGTTGAAGGCGTCGTGGTCCCTCC 25 102 0 GAAGGCGTCG 0.537746 -54 AATGCCCTGAGCACGGGCGGCAGCCCCGTG 26 34 1 GCACGGGCGG 0.965565 -54 GTCTCCTGAACCCCACGGGGCTGCCGCCCG 26 47 0 CCCCACGGGG 0.646442 -41 GGGTTCAGGAGACGGCCGAGTCTTTGAACT 26 64 1 GACGGCCGAG 0.888884 -24 ********** Masking position 10 Map Score: 31.8331 Number of sites scoring better than the average of aligned sites = 6357 Number in coding regions = 1880 Number in noncoding regions = 4477 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 2 AAAAGTTTAATGGGGTGTCCAGAAAGTTCG 1 40 1 TGGGGTGTCC 0.778926 -44 CGTGTCTGTATACGCTGCGC 4 1 0 TACGCTGCGC 0.902647 -32 CGTAAAGGCCTGCCCCGGCCTGGGGGATTC 5 115 1 TGCCCCGGCC 0.967819 -33 ACAGGGGGGTGGGGGCGCGCTATACTTGCA 6 13 1 GGGGGCGCGC 0.925369 -72 TATCGCCCCGTGCGCCGCGCGCTGCA 6 69 1 TGCGCCGCGC 0.995112 -16 AGCGCGCGACTACCCCGCCCTCTGCCCGGG 7 19 1 TACCCCGCCC 0.926604 -37 GCTCGTGGTGTCCCCCGGGCAGAGGGCGGG 7 32 0 TCCCCCGGGC 0.959819 -24 TTTCGGTTGCAGGGCTGCGCGTGGAATCCT 8 15 1 AGGGCTGCGC 0.710426 -102 CAAACGGCCTGACGCTGCGCCTCATTGAGC 8 55 0 GACGCTGCGC 0.827997 -62 GAGCCTGCGCCGGCAAGGATAAGAA 8 102 0 TGCGCCGGCA 0.849386 -15 CCTGTCACCGTCCCCCGTGGTCG 9 4 0 TCCCCCGTGG 0.716679 -44 GATGCCTCGCCAAAAAGAGAAC 9 36 0 TGCCTCGCCA 0.386202 -12 GCTGGCGCGTGCCGGTTGCCGA 12 3 1 TGGCGCGTGC 0.900107 -53 CAAGAAGGCCTCCGCTGTCCGAGCTCTACC 17 13 1 TCCGCTGTCC 0.882089 -58 CCATTGCGGTGGCCATCGCGTGGT 18 5 1 TGCGGTGGCC 0.903037 -71 GCGCACGTTCGCGGCCGCGCGGTTTTTGTT 20 22 1 GCGGCCGCGC 0.961226 -64 ATGCGCCGGGCGGTGTTGCCG 20 75 0 TGCGCCGGGC 0.990448 -11 TCTTTGGGTCGTGCCTGCAGCGAA 21 5 1 TGGGTCGTGC 0.796812 -106 TTGTTTCGAAGGGCGCGTGCGTGTACGCCT 25 19 1 GGGCGCGTGC 0.759162 -137 CTCCCGTTCTTCCGGCGCCGTTGCTGGTGT 25 76 0 TCCGGCGCCG 0.778129 -80 AGAGTTTGAATGCCCTGAGCACGGGCGGCA 26 26 1 TGCCCTGAGC 0.732721 -62 ACCCCACGGGGCTGCCGCCCGTGCTCAGGG 26 38 0 GCTGCCGCCC 0.66245 -50 ********** Masking position 7 Map Score: 25.0831 Number of sites scoring better than the average of aligned sites = 2541 Number in coding regions = 774 Number in noncoding regions = 1767 Number of orfs with sites within 600 bp upstream = 61 Fraction of orfs with sites within 600 bp upstream = 0.00979762 Motif number 3 CCGAACTGCTTTATTAACTTTGCGCAGCTGT 5 12 0 TTATTAATTT 0.835173 -136 ATTCAACCTCTTAATAATTTAAGTTTTAATA 27 24 0 TTAATAATTA 0.790559 -22 TTTAAAATTCTTTTAAATTTA 28 1 0 TTTTAAATTA 0.735626 -37 TTTAAAAGAATTTTAAATTTAAAGGAATTTT 28 15 1 TTTTAAATTA 0.735626 -23 GTAATTCTTTTTAACTTTAAAAAAGAAA 29 8 1 TTTTTAATTT 0.940414 -41 AGGGTGTTTTTTATAAATTTATAACTTGTT 33 10 1 TTTATAATTT 0.931617 -83 GTTAAAATATTTAATATATTTTTTGCTAAAA 33 38 1 TTAATATTTT 0.608614 -55 ATTTTATACCTTTAAATCTGTTT 34 31 0 TTTATACTTT 0.739662 -13 TATAGCTCTTTTTTTAAATTACTCATGTAAG 36 29 1 TTTTTAATTA 0.931616 -150 TTGTGGCTAATTTTTAAATTAGCTGCCTTAC 36 55 0 TTTTTAATTA 0.931616 -124 TACAACTTATTTTATAATTTTAATTATTAAG 36 95 1 TTTATAATTT 0.931617 -84 TTTGTCTAGGTTTTTATCTTAATAATTAAAA 36 112 0 TTTTTATTTA 0.828873 -67 TTTGCTTAATTTTATATTTTTTTGTCTAGGT 36 132 0 TTTATATTTT 0.828873 -47 ******* *** Masking position 6 Map Score: 9.92664 Number of sites scoring better than the average of aligned sites = 112 Number in coding regions = 26 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AGACACTCAGCCAGATACGGAGTGA 2 2 0 CCAGACGATG 0.879714 -26 AAGCAACGCTCCACTGCTACAACGCGTACCTGAC 5 56 0 CCACCTCACG 0.79869 -92 AGCGTAAAGGCCTGCCCCGGCCTGGGGGATTCAA 5 113 1 CCTGCCGCTG 0.979742 -35 GTATAGCGCGCCCCCACCCCCCTGTCT 6 4 0 CCCCCCCCTG 0.902815 -81 ACTACCCCGCCCTCTGCCCGGGGGACACCACGAG 7 27 1 CCTCCCGGGG 0.954881 -29 ACGGCCTGACGCTGCGCCTCATTGAGCGCGCTCA 8 48 0 GCTGCCCATG 0.911031 -69 GAGCCTGCGCCGGCAAGGATAAGAAGC 8 100 0 CCTGCCGCAG 0.90928 -17 CCAGTTCCCCAGGGAGATGCACCC 10 14 0 CCAGCCCAGG 0.985597 -14 TCTTCTGACTCCTCCTCTGGAGCGTCACGCGACG 11 42 0 CCTCCTGACG 0.890955 -24 GCCTGTCCCCAACTGCCACGCACAC 13 2 1 CCTGCCAATG 0.96007 -33 TCCCCAACTGCCACGCACACAATGCTCGG 13 16 1 CCACACCATG 0.881753 -19 CTTTGGAGAGCCTGGGACAAACGGTCAGCACTCG 19 38 0 CCTGACAAGG 0.842938 -38 TCGGTGAGCACCTCGACCAGAACGGCAACACCGC 20 53 1 CCTCCCGACG 0.987032 -33 TCAGAAACGCCCTCCTCCTCAAGGAG 23 31 1 CCTCCCCAGG 0.992971 -16 TCGGCCGTCTCCTGAACCCCACGGGGCTGCCGCC 26 49 0 CCTGCCCAGG 0.993934 -39 **** ** ** ** Masking position 2 Map Score: 17.9051 Number of sites scoring better than the average of aligned sites = 1757 Number in coding regions = 492 Number in noncoding regions = 1265 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 5 CATGAGGGGTGCCTTTTTTAACG 1 3 1 TGAGGGTGCC 0.966715 -81 AAAAGTTTAATGGGGTGTCCAGAAAGTTCGA 1 40 1 TGGGGTTCCA 0.827084 -44 TGCCCCGGCCTGGGGGATTCAAAATCAACGG 5 125 1 TGGGGGTTCA 0.863789 -23 CGCAGCGTCAGGCCGTTTGCCATTATGGCAG 8 66 1 GGCCGTTGCC 0.969081 -51 AAGGATAAGAAGCGGGCTGCCATAATGGCAA 8 82 0 AGCGGGTGCC 0.971035 -35 CATGTGCCTGTGCCGTCTGCATCCGACCCGT 11 14 1 TGCCGTTGCA 0.953123 -52 GCTGGCGCGTGCCGGTTGCCGATGAGCCCT 12 10 1 TGCCGGTGCC 0.992166 -46 CCAGCGTTCTTGGGGTATGCATACTAAGCAA 16 26 1 TGGGGTTGCA 0.97049 -32 ACCCGCCAATGCGGATTGCCCCATTTGTTT 25 136 0 TGCGGATGCC 0.966351 -20 CCCTGAGCACGGGCGGCAGCCCCGTGGGGTT 26 38 1 GGGCGGAGCC 0.875448 -50 ****** **** Masking position 10 Map Score: 8.7672 Number of sites scoring better than the average of aligned sites = 557 Number in coding regions = 141 Number in noncoding regions = 416 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 AGTTCGGGTCCTTGCCAATGGTCAGGTACG 5 36 1 CTTGCCAATG 0.858151 -112 TTTGAAGCAACGCTCCACTGCTACAACGCG 5 64 0 CGCTCCACTG 0.870685 -84 AGCGTAAAGGCCTGCCCCGGCCTGGGGGAT 5 113 1 CCTGCCCCGG 0.929216 -35 CACGCGCAGCCCTGCAACCGAAAACTG 8 8 0 CCTGCAACCG 0.958307 -109 AAGAGAACTACCTGTCACCGTCCCCCGTGG 9 14 0 CCTGTCACCG 0.921608 -34 TCCCTCCAACGGCGTACATAT 18 65 0 CCCTCCAACG 0.974472 -11 TTGTCCCAGGCTCTCCAAAGATCACCGGGC 19 52 1 CTCTCCAAAG 0.74633 -24 CCGTGTACGTCTTTCCACAGATATACACCG 21 91 1 CTTTCCACAG 0.895415 -20 CGTGTACACACCTTCCCCCGAAACACAGGC 25 45 0 CCTTCCCCCG 0.977089 -111 GACCACGACGCCTTCAACCGTTTTAGGCAA 25 107 1 CCTTCAACCG 0.944786 -49 ACCCGCCAATGCGGATTGCCC 25 145 0 CCCGCCAATG 0.952509 -11 ********** Masking position 1 Map Score: 8.39417 Number of sites scoring better than the average of aligned sites = 1489 Number in coding regions = 459 Number in noncoding regions = 1030 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 GAAAACAAATTGCGCACGTTC 20 2 1 AAAACAAATT 0.884364 -84 CGTTTTAGGCAAAACAAATGGGGCAATCCG 25 125 1 AAAACAAATG 0.701779 -31 TTTAATAAATAAAACAACTA 27 1 0 AAAACAACTA 0.753947 -45 TAAATTTAAAAGAATTTTAAATTTAAA 28 8 1 AAAAGAATTT 0.934032 -30 TTTTAAATTTAAAGGAATTTTAA 28 25 1 AAAGGAATTT 0.727278 -13 TTTAAAGTTAAAAAGAATTAC 29 2 0 AAAAGAATTA 0.906303 -47 TTAACTTTAAAAAAGAAATTAATGGGAGGA 29 21 1 AAAAGAAATT 0.865089 -28 ATACTAAAAAAACAATCTTAGA 30 5 0 AAAACAATCT 0.760805 -18 AAATCTGTTTATAACAATTTGATTAATTTG 34 11 0 ATAACAATTT 0.870592 -33 AATAAGAATTATAATGAAAAA 35 2 1 ATAAGAATTA 0.793934 -49 ATAACAATTAATTGGCCTGT 36 169 0 ATAACAATTA 0.821274 -10 ********** Masking position 6 Map Score: 4.44808 Number of sites scoring better than the average of aligned sites = 360 Number in coding regions = 113 Number in noncoding regions = 247 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 AGAAAAGCTTGAGCGCAAGTTCCTCGAACT 1 64 0 GAGCGCAAGT 0.957867 -20 CACAGCTGCGCAAAGTTAATAAAGC 5 6 1 CTGCGCAAAG 0.961738 -142 TGGGTTTTTTGAGCGTAAAGGCCTGCCCCG 5 102 1 GAGCGTAAAG 0.92877 -46 GCAATTCTCAGTGCGCAGAGGGAGTTTTGT 6 40 1 GTGCGCAGAG 0.988773 -45 GAGCGCAAAGCGCGCGACTA 7 1 1 GAGCGCAAAG 0.99015 -55 GGCCGCGAACGTGCGCAATTTGTTTTC 20 8 0 GTGCGCAATT 0.915634 -78 GCTGCCGCCCGTGCTCAGGGCATTCAAACT 26 28 0 GTGCTCAGGG 0.904505 -60 ********** Masking position 7 Map Score: 4.54103 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 30 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 AGTGGAGCGTTGCTTCAAAAGACGCTTTGGG 5 75 1 TGCTTCAAAG 0.965291 -73 CGTCGCGTGACGCTCCAGAGGAGGAGTCAGA 11 42 1 CGCTCCAGAG 0.816312 -24 CGCTGGATGATGTTGCGAAGG 16 1 0 TGTTGCGAAG 0.964621 -57 AGCTCTACCGTGCTTCAGATGAGCCCTTTTC 17 34 1 TGCTTCAGAG 0.958238 -37 AGAATCGTCTTGTTCCAAATGAACCACGCGA 18 26 0 TGTTCCAAAG 0.935605 -50 TGTTCCTTGATGCAAATGTTGGTAGAAC 19 8 1 TGATGCAAAG 0.86554 -68 GGGTCGTGCCTGCAGCGAAAGTAAGAAGTGA 21 16 1 TGCAGCGAAG 0.872087 -95 TACCAGCATTGTTTCGAAGGGCGCGTGCGT 25 10 1 TGTTTCGAAG 0.957561 -146 TGTACGCCTGTGTTTCGGGGGAAGGTGTGTA 25 40 1 TGTTTCGGGG 0.813132 -116 ********* * Masking position 6 Map Score: 3.03676 Number of sites scoring better than the average of aligned sites = 132 Number in coding regions = 42 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 10 AGTTAATAAAGCAGTTCGGGTCCTTGCCAA 5 24 1 GCAGTTCGGG 0.955769 -124 CAGGCCGTTTGCCATTATGGCAGCCCGCTT 8 74 1 GCCATTATGG 0.797728 -43 GACGGCACAGGCACATGCGG 11 1 0 GCACATGCGG 0.896368 -65 TTGCACGAGAGCCCATAGGGCTCATCGGCA 12 27 0 GCCCATAGGG 0.903332 -29 TGTGTGCGTGGCAGTTGGGGACAGGC 13 7 0 GCAGTTGGGG 0.980848 -28 AAATATGTACGCCGTTGGAGGGA 18 63 1 GCCGTTGGAG 0.945983 -13 GGGCGGTGTTGCCGTTCTGGTCGAGGTGCT 20 59 0 GCCGTTCTGG 0.957042 -27 TTCTTCCGGCGCCGTTGCTGGTGTACGTGT 25 70 0 GCCGTTGCTG 0.930237 -86 ACCCGCCAATGCGGATTGCCCCAT 25 142 0 GCCAATGCGG 0.944696 -14 ********** Masking position 6 Map Score: 5.88774 Number of sites scoring better than the average of aligned sites = 1187 Number in coding regions = 351 Number in noncoding regions = 836 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 TTCGGTTGCAGGGCTGCGCGTGGAATCCTA 8 16 1 GGGCTGCGCG 0.967577 -101 AGAGCCCATAGGGCTCATCGGCAACCGGCA 12 20 0 GGGCTCATCG 0.990191 -36 GAAAAGAAAAGGGCTCATCTGAAGCACGGT 17 40 0 GGGCTCATCT 0.939821 -31 GGTAGAACGAGTGCTGACCGTTTGTCCCAG 19 31 1 GTGCTGACCG 0.981098 -45 TCTGGTCGAGGTGCTCACCGATAACAAAAA 20 44 0 GTGCTCACCG 0.99003 -42 GCTGCCGCCCGTGCTCAGGGCATTCAAACT 26 28 0 GTGCTCAGGG 0.957929 -60 ********** Masking position 5 Map Score: 4.12398 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 36 Number in noncoding regions = 67 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 12 CGAGGAACTTGCGCTCAAGCTTTTCT 1 68 1 GCGCTCAAGC 0.964691 -16 AATTCTCAGTGCGCAGAGGGAGTTTTGTAT 6 42 1 GCGCAGAGGG 0.861355 -43 GCAGCGCGCGGCGCACGGGGCGATACAAAA 6 64 0 GCGCACGGGG 0.988231 -21 CTACCTGAGCGCGCTCAATGAGGCGCAGCG 8 43 1 GCGCTCAATG 0.918259 -74 AGCCCTATGGGCTCTCGTGCAATGCAGTAG 12 35 1 GCTCTCGTGC 0.857311 -21 CAACTGCCACGCACACAATGCTCGG 13 20 1 GCACACAATG 0.759939 -15 CAAACGGTCAGCACTCGTTCTACCAACATT 19 25 0 GCACTCGTTC 0.860402 -51 AAAACAAATTGCGCACGTTCGCGGCCGCGC 20 12 1 GCGCACGTTC 0.970984 -74 TGAATGCCCTGAGCACGGGCGGCAGCCCCG 26 32 1 GAGCACGGGC 0.910603 -56 ********** Masking position 4 Map Score: 3.25872 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 68 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 AACGAGACGTATTGCTTAGTATGCATACC 16 39 0 TATTGCTTAG 0.869106 -19 GCGTACATATTTTTTCCTAGAATCGTCTTG 18 45 0 TTTTTCCTAG 0.833606 -31 TCCTGAGTGATTTTGCTTTACCGACATAGA 21 53 1 TTTTGCTTTA 0.845995 -58 GCCCCATTTGTTTTGCCTAAAACGGTTGAA 25 119 0 TTTTGCCTAA 0.968993 -37 TTAATATATTTTTTGCTAAAATCAATATAT 33 48 1 TTTTGCTAAA 0.83243 -45 TTTTATATTTTTTTGTCTAGGTTTTTATCT 36 124 0 TTTTGTCTAG 0.833606 -55 CCTGTTGTGTTTTTGCTTAATTTTATATTT 36 144 0 TTTTGCTTAA 0.962933 -35 ********** Masking position 4 Map Score: 0.905798 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 82 Number in noncoding regions = 187 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 AACGGCAAACAAAAGTTTAATGGGGTGTCC 1 30 1 AAAAGTTTAA 0.743451 -54 AGAAAAGCTTGAGCGCAAGTTC 1 72 0 AAAAGCTTGA 0.940215 -12 GTTTTGCCTAAAACGGTTGAAGGCGTCGTG 25 110 0 AAACGGTTGA 0.939144 -46 CAGTTTTTTGAAGAGTTTGAATGCCCTGAG 26 15 1 AAGAGTTTGA 0.939503 -73 TTAAATTATTAAGAGGTTGAATT 27 33 1 AAGAGGTTGA 0.972215 -13 AAAAGGGTGATTTATCAGCT 33 83 0 AAAAGGGTGA 0.939144 -10 ********** Masking position 8 Map Score: 0.849132 Number of sites scoring better than the average of aligned sites = 142 Number in coding regions = 47 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 ********** No masking Map Score: 6.63809e-14 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