AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00620_aful_reg_300.orf -o00620_aful_300.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/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 Input sequences: #1 AF0194 300 A. fulgidus predicted coding region AF0194 #2 AF0195 22 A. fulgidus predicted coding region AF0195 #3 AF0196 131 medium-chain acyl-CoA ligase (alkK-1) #4 AF0197 86 acetyl-CoA synthetase (acs-1) #5 AF0219 180 2-isopropylmalate synthase (leuA-2) #6 AF0366 218 acetyl-CoA synthetase (acs-2) #7 AF0396 154 A. fulgidus predicted coding region AF0396 #8 AF0677 165 acetyl-CoA synthetase (acs-3) #9 AF0710 88 phosphoenolpyruvate synthase (ppsA) #10 AF0818 102 acylphosphatase (acyP) #11 AF0957 53 2-isopropylmalate synthase (leuA-1) #12 AF0971 101 conserved hypothetical protein #13 AF0973 108 bile acid-inducible operon protein F (baiF-1) #14 AF1215 101 cell division protein, putative #15 AF1252 194 oxaloacetate decarboxylase, subunit alpha (oadA) #16 AF1287 300 acetyl-CoA synthetase (acs-6) #17 AF1446 63 A. fulgidus predicted coding region AF1446 #18 AF1448 114 transcriptional regulatory protein, AsnC family #19 AF1449 33 pyruvate formate-lyase 2 (pflD) #20 AF1695 50 thiamine biosynthesis protein (apbA) #21 AF1696 28 small multidrug export protein (qacE) #22 AF1697 49 conserved hypothetical protein #23 AF1699 102 pyruvate ferredoxin oxidoreductase, subunit gamma (porG) #24 AF2086 41 protease inhibitor, putative #25 AF2089 111 conserved hypothetical protein #26 AF2389-C 300 acetyl-CoA synthetase, putative Motif number 1 TTTCAAAGCTTTTCTTGAGGTT 2 2 1 TTCAAATTTT 0.892719 -21 TATGAGTATTCATAAATACTTTATCATCATAA 3 76 0 CATAAACTTT 0.748818 -56 AGCCACCGATTTAAAAACCTTTTTTCAAATAG 5 27 1 TTAAAACTTT 0.961905 -154 TTTGCGAAAATTAAAACACTTTTGCGCAAATT 6 96 0 TTAAAACTTT 0.961905 -123 AGTTGTTAGTTAAAAATGTTTTGTCTAATACT 8 24 1 TAAAAATTTT 0.887236 -142 AAAATCTATTTTAAAAAACTTGCGAAAGCGTG 8 109 0 TTAAAACTTG 0.687253 -57 TGCCAAAGCCTTAAAAAATTTTAGGTGGAGCG 9 46 0 TTAAAATTTT 0.923646 -43 AACGAGTGGGTAAAAAAACTTTGGCCTTCCAG 11 20 0 TAAAAACTTT 0.94262 -34 ATTTAAATTTTTTCATTTATGAA 12 2 1 TTTAAATTTT 0.861126 -100 AATCTGGCAATATAAAGCTTTTGCAGATACAC 12 65 0 TATAAATTTT 0.801358 -37 ACGCTTTTTATTTAAACCTTTTTCCCAACTTT 14 61 0 TTTAAATTTT 0.861126 -41 ACGCTAAGATTTAATACGCTTTTTATTTAAAC 14 76 0 TTAATACTTT 0.879847 -26 GCCATCAACCTAAATAAACTTTCCTGAAGAAC 15 33 1 TAAATACTTT 0.826514 -162 TGATGGGAAATACAAAAATTTTTTGTTTTTAA 15 97 0 TACAAATTTT 0.844086 -98 GGACATTGAACACATAGACTTTGTGAGAGACA 16 28 0 CACATACTTT 0.537085 -273 GTTCTGAAAACTTAAAACTTTTCATTTAATTC 16 209 1 CTTAAATTTT 0.687036 -92 ATTTTTCCCTCTTAAAAACTTTCACCAGTACA 17 17 0 CTTAAACTTT 0.820861 -47 AAGCAGCAGGTTAATATTCTTTGTGCAGACTT 20 21 1 TTAATACTTT 0.879847 -30 GAATCGGCATTTAAAATATTTTTTTAGCTTTC 23 31 1 TTAAAATTTT 0.92364 -72 TTTTTTAGCTTTCAAAACCTTTTCCGTTAATT 23 50 1 TTCAAACTTT 0.945562 -53 AACTTTATGATTAAAAAGCTTTGGTTTT 24 7 0 TTAAAACTTT 0.961905 -35 ATTTCAAGTTTAAAAACGCTTTTCAAAAGGTT 25 78 0 TAAAAACTTT 0.94262 -34 CGCCTCCTCCTACATAACTTTTGCGGTTTTTG 26 80 1 TACATATTTT 0.610899 -221 ****** **** Masking position 10 Map Score: 27.5771 Number of sites scoring better than the average of aligned sites = 282 Number in coding regions = 151 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 2 CTTAACGTAATTGTACCAATAAATGAACTCATCCAAA 1 109 0 TTTATAATAA 0.946452 -192 GAAAAACTTATTTTGACAAAAAGTTAAAGTTTTC 1 277 1 TTTAAAATAA 0.892453 -24 CATAAATACTTTATCATCATAAATAAACAAATCGTGC 3 61 0 TTTATAATAA 0.94644 -71 TGCTCACACTTTGAGCATAATTCAATTTTTTAAGA 4 9 1 CTTATAATAA 0.857321 -78 TTTATAACATTTAATGAGCAAATTTAAATTCATTATC 4 47 0 TTACAAATAA 0.651716 -40 AGATAACAATTTATCGAAATAAATAAAATTCTCGGCA 5 122 0 TTTATAATAA 0.946452 -59 AAAATGAAAATTTTTGCGAAAATTAAAACACTTTTGC 6 103 0 TTTAAAATAA 0.892454 -116 AAATTTTTCTTTAAGATAAAAACTTAAAACTAATTTG 7 56 1 TTAAAAATAA 0.71248 -99 AATGTTTTGTCTAATACTCTAATTGAATAAAAGTTGA 8 38 1 CTACTAATAA 0.575366 -128 TTAAAATAGATTTTAACAATAAATAAATATATCTATT 8 127 1 TTTATAATAA 0.946452 -39 TGTATGAATATTTTCGAACGAATTGAAATCATATAAA 10 35 0 TTTCGAATAA 0.806974 -68 TCAACATTAGTTGTGTTCATAAATGAAAAAATTTAAA 12 12 0 TTTATAATAA 0.945715 -90 GATACACTCATTTTAAATATCAATCAACATTAGTTGT 12 35 0 TTTATCATAA 0.664713 -67 TCATATGTCATTGTTCTGAAAACTTAAAACTTTTCAT 16 197 1 TTTAAAATAA 0.892453 -104 TATTTAAGAATTTTGATTCGAATTGAATTAAATGAAA 16 228 0 TTTCGAATAA 0.806798 -73 AATGACAGTCTTTTCTTTGTAATTGAAGTAGCTGTCT 18 12 1 TTTGTAATAA 0.822983 -103 GATTGTAACACTTTCATTGTAAATAAAGTTTACCTTA 18 83 0 CTTGTAATAA 0.654968 -32 CCTTAAAAACCTAATTAAAAAAGATTACG 19 15 0 TTACTAATAA 0.7993 -19 ** * **** * ** Masking position 14 Map Score: 16.8284 Number of sites scoring better than the average of aligned sites = 70 Number in coding regions = 39 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 3 TCTTTGGGCTGATGGAGCAGAAGCTCCATCT 1 69 1 GATGGAGCGA 0.938026 -232 AATGTTATAAATTGGAGGTGAACT 4 73 1 ATTGGAGGGA 0.851993 -14 ACAGTAGCAGTGCGGAGGGGATAGG 7 5 0 TGCGGAGGGA 0.856631 -150 AAATATATCTATTAGAGGTGATGAA 8 151 1 ATTAGAGGGA 0.470012 -15 AAAAATTTTAGGTGGAGCGGAATCGCAAGCG 9 34 0 GGTGGAGCGA 0.988708 -55 GGCAAACTCAGAACGAGGTGAGTAA 9 74 1 GAACGAGGGA 0.816241 -15 TATTGAGTAGTGTGGAGGAGTAT 13 96 1 TGTGGAGGGT 0.827553 -13 CGGTCAAGCTGAGGCGTTGCTG 14 2 1 GGTCAAGCGA 0.649128 -100 TTACTTCGAAGGTGGAGCAGA 17 53 1 GGTGGAGCGA 0.988708 -11 ATCATAAAGTTTAGGAGGAGAAGG 24 28 1 TTAGGAGGGA 0.840527 -14 AAGTTATGTAGGAGGAGGCGTAAGCCTCCTC 26 69 0 GGAGGAGGGT 0.932845 -232 GATTAAGGGAGTTAGAGGGGAGATTAGGATT 26 187 1 GTTAGAGGGA 0.851993 -114 ACCAGCCGTCGGACGAGCTGAAGGAGGAGCT 26 270 1 GGACGAGCGA 0.951029 -31 ACGAGCTGAAGGAGGAGCTGAGAGAGCAT 26 282 1 GGAGGAGCGA 0.98244 -19 ******** ** Masking position 6 Map Score: 13.9259 Number of sites scoring better than the average of aligned sites = 1527 Number in coding regions = 1457 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 AAATTCATTATCATCTTAAAAAATTGAATTAT 4 27 0 TACTTAAAAA 0.552845 -60 GCTAAAGCCACCGATTTAAAAACCTTTTTTCA 5 22 1 CGTTTAAAAA 0.855549 -159 TCTTGCAGTTCTATTTGAAAAAAGGTTTTTAA 5 37 0 CATTGAAAAA 0.747274 -144 AATTAATCAGCGATATTAAAAAGGAACA 6 7 0 CAATTAAAAA 0.927563 -212 ATTCAAGCTACAAACTTAAAAAGCAAATTAGT 7 84 0 CACTTAAAAA 0.953075 -71 TTGTTAAAATCTATTTTAAAAAACTTGCGAAA 8 114 0 CATTTAAAAA 0.94936 -52 TTTTCGATTTCAAACTTTAAAAAATTGTAGAA 13 14 0 CACTTTAAAA 0.792159 -95 TCGATAAAGGCAAGTTTAAAAACAGCAACGCC 14 23 0 CATTTAAAAA 0.94936 -79 GAGGTGCAAGCAATATTAAAAACAAAAAATTT 15 82 1 CAATTAAAAA 0.927563 -113 TGAGACATGGCAAAAGTAAAAATTGTTGACTT 15 133 1 CAAGTAAAAA 0.651316 -62 TTGGATTTTTCCCTCTTAAAAACTTTCACCAG 17 21 0 CCCTTAAAAA 0.777121 -43 CCTTAAAAACCTAATTAAAAAAGATTACGATT 19 12 0 CATTAAAAAA 0.666112 -22 CAACCAGAATCGGCATTTAAAATATTTTTTTA 23 25 1 CGATTTAAAA 0.431542 -78 ATTTCGATTTCAAGTTTAAAAACGCTTTTCAA 25 84 0 CATTTAAAAA 0.94936 -28 * * ******** Masking position 9 Map Score: 11.7071 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 36 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459 Motif number 5 TACCTGCTGAAAGGGTGTTTGAGTACGGGAG 1 207 1 AAGGGTGTTG 0.981939 -94 GTGTTTGAGTACGGGAGGTGGTTGTTTGAGG 1 221 1 ACGGGAGGTG 0.986274 -80 TCAATAAAAAAGGGGTGGTGGT 3 120 1 AGGGGTGGTG 0.974691 -12 AAATGTAGGTAAGGGAGGTTGTT 16 288 1 AAGGGAGGTG 0.99377 -13 AATTACTTTTAAGGGAGTTGG 25 1 0 AAGGGAGTTG 0.990238 -111 TTTGGTGATTAAGGGAGTTAGAGGGGAGATT 26 181 1 AAGGGAGTTG 0.990238 -120 ********* * Masking position 9 Map Score: 7.85077 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 60 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 6 CATCTTAAAAAATTGAATTATGCTCAAAGTGT 4 16 0 ATTGAATTTG 0.843492 -71 TGTTGCAATTACTTGGATTTTACGTATTCTTG 5 64 0 ATTGGATTTA 0.835726 -117 AAGAATACGTATTTGATTTGTAGCAGTTGCCG 5 95 1 ATTGATTTTA 0.504875 -86 ACCAAAAATAGGTTAAATTATTGATATTTAAC 6 161 0 GTTAAATTTT 0.822671 -58 CACTGACGATATTTAAATTTTTCTTTAAGATA 7 42 1 ATTAAATTTT 0.713909 -113 TAAGTTTGTAGCTTGAATTTTTCTGTACGTCG 7 98 1 GTTGAATTTT 0.958852 -57 CGGTATATAAGTTTGAATTCTTTTGTATGAAT 10 63 0 GTTGAATTTT 0.958852 -40 ATTTAAATTTTTTCATTTATGA 12 1 1 ATTAAATTTT 0.713909 -101 CCTTCGAAGTAATTGGATTTTTCCCTCTTAAA 17 33 0 ATTGGATTTT 0.92739 -31 GGTTGGATTGTAACACTTTCAT 18 103 0 GTTGGATTTA 0.90438 -12 TGCCGATTCTGGTTGAATTCTGATTCAAC 23 8 0 GTTGAATTTG 0.909253 -95 TGCGGTTTTTGATTGGTTTATTTCGGCTGGAG 26 101 1 GTTGGTTTTT 0.829054 -200 TTGATGGGAGGGTTGGATTGTTTGTAGTTTGG 26 154 1 GTTGGATTTT 0.959588 -147 * ******* ** Masking position 8 Map Score: 10.0257 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 40 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 CTTAACGTAATTGTACCAATAAATGAACTCATC 1 113 0 TTTAAATAAA 0.900371 -188 CTTTAACTTTTTGTCAAAATAAGTTTTTCTGTG 1 273 0 TTTCAATAAG 0.808529 -28 CATAAATACTTTATCATCATAAATAAACAAATC 3 65 0 TTTCCATAAA 0.966095 -67 TTTAAATTCATTATCATCTTAAAAAATTGAATT 4 29 0 TTTCCTTAAA 0.783573 -58 AGATAACAATTTATCGAAATAAATAAAATTCTC 5 126 0 TTTCAATAAA 0.960933 -55 TTAAAATAGATTTTAACAATAAATAAATATATC 8 127 1 TTTAAATAAA 0.900363 -39 TCAACATTAGTTGTGTTCATAAATGAAAAAATT 12 16 0 TTTGCATAAA 0.825045 -86 TAAACTTTTGGTTTCGTAATAAA 22 1 0 GTTCAATAAA 0.808527 -49 GGTTCTGCAGTTTTCCCAATAAACTTTTGGTTT 22 20 0 TTTCAATAAA 0.960932 -30 CTGAGGATGCTTAAAAGAATAAAAAATTAACGG 23 73 0 TTAAAATAAA 0.511418 -30 AACCAAAGCTTTTTAATCATAAAGTTTAGGAGG 24 13 1 TTTACATAAA 0.912798 -29 CCTTCTCCTCCTAAACTTTATGATT 24 27 0 TTTCCCTAAA 0.842916 -15 ** ** ****** Masking position 11 Map Score: 5.39047 Number of sites scoring better than the average of aligned sites = 34 Number in coding regions = 24 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 AAGAATCAAACAGATGGAGCTTCTGCTCCATC 1 79 0 CGATGGGCTT 0.956032 -222 CCAAGCTTTTCTGAGGAAGCTACCTGCTGAAA 1 187 1 CGAGGAGCTA 0.93683 -114 TATGATTTATCTCAGCACGCTTTCGCAAGTTT 8 94 1 CCAGCAGCTT 0.966974 -72 TTTTGTATTTCCCATCAGGCTTGAGACATGGC 15 112 1 CCATCAGCTT 0.919645 -83 CCTGCTGAGCGTTCTTCTTGTGTCAG 21 5 1 CGAGCGTCTT 0.861462 -24 CTCTTAACTGAGGATGCTTAAAAGAATAA 23 84 0 CGAGGAGCTT 0.988061 -19 TGAAACAATGCAGATCCCGCTTGCAGTCGACC 26 33 0 CGATCCGCTT 0.921835 -268 TTGTTTCACCCAGAGGAGGCTTACGCCTCCTC 26 57 1 CGAGGAGCTT 0.98806 -244 * ***** **** Masking position 4 Map Score: 4.58258 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 70 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 9 CACAAACGAATGGGAAGATAGAGAGGTTCTTT 1 42 1 TGGAAGTAGA 0.555443 -259 TTTCGATAAATTGTTATCTAAGGCACCGAAAA 5 140 1 TTGTATTAAG 0.711874 -41 GGTTAAATTATTGATATTTAACTTTATTTGGG 6 151 0 TTGTATTAAC 0.573036 -68 AGTGGCAATATTGCAATATAAATTTTCCGACG 7 125 0 TTGAATTAAA 0.937244 -30 TGTTTTGTAGTTGTTAGTTAAAAATGTTTTGT 8 16 1 TTGTAGTAAA 0.878996 -150 CTAATGTTGATTGATATTTAAAATGAGTGTAT 12 39 1 TTGTATTAAA 0.872139 -63 TTAACAAATCTGGCAATATAAAGCTTTTGCAG 12 71 0 TGGAATTAAA 0.885983 -31 TTTTTAAAGTTTGAAATCGAAAAACTTATACA 13 23 1 TTGAATGAAA 0.918579 -86 AAGGAAAGAATGGGAAGAGAAATGTCTCAAAC 16 142 0 TGGAAGGAAA 0.853304 -159 AGTCTTTTCTTTGTAATTGAAGTAGCTGTCTT 18 18 1 TTGAATGAAG 0.7967 -97 CAACGTCAGTTTATAAGGTAAACTTTATTTAC 18 70 1 TTAAAGTAAA 0.50825 -45 GGAAAAGGTTTTGAAAGCTAAAAAAATATTTT 23 43 0 TTGAAGTAAA 0.940086 -60 GTTTTTAAACTTGAAATCGAAATCCGGCT 25 93 1 TTGAATGAAA 0.918579 -19 *** *** **** Masking position 6 Map Score: 4.73802 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 69 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 10 CAAACAACCACCTCCCGTACTCAAACACCC 1 219 0 CCTCCCGTAC 0.968523 -82 CTAAACTCCCCCCTTAAAGTCCGTCAT 6 202 0 CCCCCCTTAA 0.967871 -17 AACAACCTCCCTTACCTACATTTTT 16 286 0 CCTCCCTTAC 0.985571 -15 CCAACTCCCTTAAAAGTAATTAC 25 4 1 ACTCCCTTAA 0.965325 -108 ACAATCCAACCCTCCCATCAAAAGAGACAT 26 145 0 CCTCCCATCA 0.901539 -156 CTCCCCTCTAACTCCCTTAATCACCAAACT 26 179 0 ACTCCCTTAA 0.965325 -122 ********** Masking position 8 Map Score: 3.30885 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 43 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 11 CTGCTTAATATATCGCTTGCGATTCCGCTC 9 21 1 TATCGCTTGC 0.940418 -68 CAAACTTATATACCGCAGGCAAAAGGTGGG 10 80 1 TACCGCAGGC 0.931819 -23 AAATTATTAATACTGCATGGAGGGATTGTA 13 68 1 TACTGCATGG 0.876083 -41 TTGTTTTTAATATTGCTTGCACCTCAAAAG 15 77 0 TATTGCTTGC 0.928928 -118 GGACACCAGTCCCTGCTTGCCACAAGA 15 178 1 CCCTGCTTGC 0.908257 -17 TCTTTATCCATACTGCATGCTCTCCAACGT 18 46 1 TACTGCATGC 0.973531 -69 ACAATGCAGATCCCGCTTGCAGTCGACCCA 26 31 0 TCCCGCTTGC 0.974956 -270 ********** Masking position 5 Map Score: 2.19335 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 93 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 12 GTAAGGCACATTCTTGCGAGAGTGA 1 3 1 AAGCAATCTT 0.778407 -298 TTTTGACAAAAAGTTAAAGTTTTC 1 287 1 AAGTAATTTT 0.726779 -14 GGAAAACAGGAAGTTACCGTTTTCCCCCGAACA 3 12 1 AAGTACTTTT 0.891983 -120 TTTAAGGCTAAAGCCACCGATTTAAAAACCTTT 5 16 1 AAGCACATTT 0.962303 -165 TTCGGTGCCTTAGATAACAATTTATCGAAATAA 5 137 0 TAGTACATTT 0.648839 -44 ATTTTTCTTTAAGATAAAAACTTAAAACTAATT 7 58 1 AAGTAAACTT 0.794686 -97 AGAAAAATTCAAGCTACAAACTTAAAAAGCAAA 7 89 0 AAGTAAACTT 0.807838 -66 TCTAAGAGTTAAGTCAACAATTTTTACTTTTGC 15 142 0 AAGCACATTT 0.962185 -53 AGTATGGATAAAGACAGCTACTTCAATTACAAA 18 27 0 AAGCACACTT 0.954352 -88 CTAATTAAAAAAGATTACGATTT 19 1 0 AAGTTCATTT 0.64787 -33 TAATAGTTATAAGGCAACCTTTTGAAAAGCGTT 25 63 1 AAGCACTTTT 0.929787 -49 GAGGATGACGAAGGCAACTATATAAGGTGCTTA 26 227 0 AAGCACATAT 0.747306 -74 *** ** * **** Masking position 2 Map Score: 6.81482 Number of sites scoring better than the average of aligned sites = 67 Number in coding regions = 52 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 13 TGAGGAGTGAAATTATTTCGGGATATCACA 1 247 1 AATTATTTCG 0.961752 -54 TTTATTGAATAATAATTTCGTATGAGTATT 3 98 0 AATAATTTCG 0.919263 -34 TTCTTGTTGCAATTACTTGGATTTTACGTA 5 70 0 AATTACTTGG 0.743006 -111 CGAGAATTTTATTTATTTCGATAAATTGTT 5 125 1 ATTTATTTCG 0.779647 -56 TAAAAATGAAAATTTTTGCGAAAATTAAAA 6 112 0 AATTTTTGCG 0.781749 -107 CTTTTGTATGAATATTTTCGAACGAATTGA 10 46 0 AATATTTTCG 0.886067 -57 ATTTAAATTTTTTCATTTATGAACA 12 6 1 AATTTTTTCA 0.60009 -96 TCAAATGTATAAGTTTTTCGATTTCAAACT 13 30 0 AAGTTTTTCG 0.781749 -79 ATGCAGTATTAATAATTTGGTAATTTTCAA 13 56 0 AATAATTTGG 0.752756 -53 GGAAAAATCCAATTACTTCGAAGGTGGAGC 17 41 1 AATTACTTCG 0.915341 -23 ********** Masking position 7 Map Score: 2.46225 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 93 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 14 AATATCGTCAGTGAGAGGCACAGTAGCAGTG 7 24 0 GTGGAGGCAC 0.961761 -131 TTCCCATCAGGCTTGAGACATGGCAAAAGTA 15 120 1 GCTGAGACAT 0.956069 -75 CATAGACTTTGTGAGAGACATCGGCTATCCG 16 17 0 GTGGAGACAT 0.981175 -284 GAGAAGAAAAGTTCGAGACACTATCCGGCAT 16 87 0 GTTGAGACAC 0.981115 -214 TGCAACCACGGTTTGAGACATTTCTCTTCCC 16 132 1 GTTGAGACAT 0.979715 -169 *** ******* Masking position 6 Map Score: 0.538231 Number of sites scoring better than the average of aligned sites = 17 Number in coding regions = 14 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 15 GGGAAAACAGGAAGTTACCG 3 1 1 GGGAAAACAG 0.986918 -131 TGTTGTTCGGGGGAAAACGGTAACTTCCTG 3 18 0 GGGAAAACGG 0.991503 -114 TTGCAAAGTTGGGAAAAAGGTTTAAATAAA 14 57 1 GGGAAAAAGG 0.957195 -45 AAAGTTTATTGGGAAAACTGCAGAACCTTA 22 26 1 GGGAAAACTG 0.97716 -24 TCCTCAGGAAGGGATACCAGCCGTCGGACG 26 255 1 GGGATACCAG 0.911735 -46 ********** Masking position 6 Map Score: 2.49853 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 28 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185