AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_bsub_mtub_300.orf -o060_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 ylxS 300 alternate gene name: ymxA; similar to hypothetical proteins #2 nusA 34 nusA #3 truB 81 tRNA pseudouridine 55 synthase #4 rpsO 156 ribosomal protein S15 (BS18) #5 pnpA 172 polynucleotide phosphorylase (PNPase) #6 ylxY 117 alternate gene name: ymxI; similar to deacetylase #7 ymxG 39 similar to processing protease #8 ymxH 77 similar to hypothetical proteins #9 spoVFA 185 dipicolinate synthase subunit A #10 asd 125 aspartate-semialdehyde dehydrogenase #11 dapG 91 aspartokinase I (alpha and beta subunits) #12 dapA 30 dihydrodipicolinate synthase #13 ypjD 300 alternate gene name: jojD #14 lysC 175 aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408) #15 ask 94 ask #16 uvrC 135 excinuclease ABC (subunit C) #17 trxA 300 thioredoxin #18 dapA 68 dapA #19 Rv2754c 243 hypothetical protein Rv2754c #20 hsdM 86 hsdM #21 Rv2758c 25 hypothetical protein Rv2758c #22 Rv2762c 73 hypothetical protein Rv2762c #23 dfrA 70 dfrA #24 thyA 164 thyA #25 Rv2774c 152 hypothetical protein Rv2774c #26 ask 256 ask Motif number 1 ATAAAAGGAGCCTGGGAGACCCGGCTTCTTTAT 6 19 1 CGGGGACCCG 0.590222 -99 TGAAACATCGGCTGCCGGAGCCGATGTTTTTTT 9 52 1 GGCCGAGCCG 0.976055 -134 CCGCTGCTTACATGCCAGAGCGATTCCGATTGA 16 15 1 CGCCGAGCGA 0.948413 -121 CATGCCGGCGCTCTTTTTCAGGT 17 1 1 CGCCGCGCTC 0.980016 -300 TTTACCATGCCCTGCCGGAGCTGTTTTAAAACC 17 31 0 CGCCGAGCTG 0.925664 -270 CTTTATCCCGGCCGCGAGCGCGCGTGTTTGTCC 18 25 0 GGCGGCGCGC 0.961149 -44 TTCAACTCTGGGAGCCAGCGCCAACGCGGACGC 19 47 1 GGCCGCGCCA 0.982802 -197 GTCGAGGTGACTGGCCAGTGCCACGTAGAGGGC 19 123 0 CGCCGTGCCA 0.818148 -121 GGCCAGTCACCTCGACATCCCCCTGCTGACCGC 19 140 1 CGACTCCCCC 0.660277 -104 ACCGCGGACCCGCGTCTGCGCCGGGAGCCCGGG 19 168 1 CGTCGCGCCG 0.980727 -76 CTCGGTGTGGCAGGTCAGCCCGGGCTCCCGGCG 19 186 0 CGTCGCCCGG 0.613947 -58 TCGTCTAGTTGCGGCCGGCGCTAAGGTGAGCGC 19 220 1 GGCCGCGCTA 0.897442 -24 GCCCACCACGCCCGGCATCGCCGCGGCGCATCG 20 47 1 CGGCTCGCCG 0.986026 -40 CCCACTGCATCGTCGCGGCGCGCGCTC 22 57 1 CCGCGCGCGC 0.854659 -17 CGACTTCATTGTCGTCGGCGCGCC 23 2 0 GGTCGCGCGC 0.971199 -69 CGGCTTGAAGGCTGTCCGAGCCGACTTCATTGT 23 23 0 GGTCGAGCCG 0.907417 -48 ACTCGCTGTGCCCGGCTTCGCCGCGCTTGCGAT 24 58 1 CGGCTCGCCG 0.986026 -107 CTTCGCCGCGCTTGCGATCGCCCGCTGGGTTTG 24 73 1 CGCGTCGCCC 0.947663 -92 GAGTCGCTGCGGCGGCTTCGCCGCGCTTGCGAT 24 115 1 GGGCTCGCCG 0.973094 -50 CTTCGCCGCGCTTGCGATCGCCGCTAGGCTGAC 24 130 1 CGCGTCGCCG 0.960028 -35 GCGATCGCCGCTAGGCTGACCGCGTGTCAATC 24 143 1 CGGCGACCGC 0.835616 -22 CGCTGACCGCCGCGACTGCGCCCACGACCTATC 25 116 0 CGACGCGCCC 0.970638 -37 CGCAGTCGCGGCGGTCAGCGCGTAGTTGTTTGG 25 129 1 GGTCGCGCGT 0.739898 -24 AACCTCAGACCGGCGCATCGCGAACGTCCCGCG 26 38 1 CCGCTCGCGA 0.74517 -219 TCCAGACCGGCTTCCCGTCGCGGGACGTTCGCG 26 56 0 CCCCTCGCGG 0.953218 -201 GTCTGGATCAGACCCCGTCGCGGCGTCCGAGGA 26 82 1 GCCCTCGCGG 0.911458 -175 AGAGTCAGCGCAGGCCGGCGCGCCCCCTATTCT 26 199 1 CGCCGCGCGC 0.99089 -58 * *** ****** Masking position 11 Map Score: 43.5052 Number of sites scoring better than the average of aligned sites = 1473 Number in coding regions = 1396 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 2 CTTGGCAATCCGAAGTCACCGACGGTTGCT 4 98 1 CGAAGTCACC 0.447047 -59 TTCAAAATAAAGAAGCCGGGTCTCCCAGGC 6 28 0 AGAAGCCGGG 0.447337 -90 GCTTTTCAAAAGCAGGCGGGTTCTACCTTG 6 58 1 AGCAGGCGGG 0.900844 -60 AAAACATCGGCTCCGGCAGCCGATGTTTCA 9 52 0 CTCCGGCAGC 0.857669 -134 TGAAAAAGAGCGCCGGCATG 17 1 0 CGCCGGCATG 0.703176 -300 TTTAAAACAGCTCCGGCAGGGCATGGTAAA 17 34 1 CTCCGGCAGG 0.897103 -267 CACGCGCGCTCGCGGCCGGGATAAAGCGCC 18 32 1 CGCGGCCGGG 0.793542 -37 TGGGAGCCAGCGCCAACGCGGACGCTCGAC 19 55 1 CGCCAACGCG 0.801298 -189 GACGCGGGTCCGCGGTCAGCAGGGGGATGT 19 154 0 CGCGGTCAGC 0.860688 -90 GGGCTCCCGGCGCAGACGCGGGTCCGCGGT 19 168 0 CGCAGACGCG 0.973839 -76 CTCACCTTAGCGCCGGCCGCAACTAGACGA 19 220 0 CGCCGGCCGC 0.96449 -24 TGCGCCGCGGCGATGCCGGGCGTGGTGGGC 20 47 0 CGATGCCGGG 0.714216 -40 ACGGATGTATCTCAGGCGGGGC 21 3 0 CTCAGGCGGG 0.967213 -23 CTTCGTCCCCCGCAAGCGGGTGGTACCCCC 22 30 1 CGCAAGCGGG 0.948481 -44 GGCGCGCCGACGACAATGAAGTCG 23 5 1 CGCCGACGAC 0.682243 -66 ATGAAGTCGGCTCGGACAGCCTTCAAGCCG 23 26 1 CTCGGACAGC 0.656649 -45 GCAAGCGCGGCGAAGCCGGGCACAGCGAGT 24 58 0 CGAAGCCGGG 0.935044 -107 AGCGGGCGATCGCAAGCGCGGCGAAGCCGG 24 69 0 CGCAAGCGCG 0.911888 -96 GCAAGCGCGGCGAAGCCGCCGCAGCGACTC 24 115 0 CGAAGCCGCC 0.849605 -50 TAGCGGCGATCGCAAGCGCGGCGAAGCCGC 24 126 0 CGCAAGCGCG 0.911888 -39 GATTGACACGCGGTCAGCCTAGCGGCGA 24 147 0 CGCGGTCAGC 0.860688 -18 CGCCGCCACCTTCGGGAAAT 25 1 1 CGCCGCCACC 0.91924 -152 AGGTCGTGGGCGCAGTCGCGGCGGTCAGCG 25 119 1 CGCAGTCGCG 0.934043 -34 AACAACTACGCGCTGACCGCCGCGACTGCG 25 129 0 CGCTGACCGC 0.701635 -24 GAGAAGGAACCTCAGACCGGCGCATCGCGA 26 31 1 CTCAGACCGG 0.781562 -226 GGTGCTCCTCCTCGGACGCCGCGACGGGGT 26 93 0 CTCGGACGCC 0.763873 -164 GCAGAGTCAGCGCAGGCCGGCGCGCCCCCT 26 197 1 CGCAGGCCGG 0.978064 -60 ********** Masking position 7 Map Score: 31.8813 Number of sites scoring better than the average of aligned sites = 2445 Number in coding regions = 2287 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 97 Fraction of orfs with sites within 600 bp upstream = 0.0155798 Motif number 3 GAGACAAAATTCTCCTGTTCAATACAAAAGA 1 178 0 TCTCCTGTCA 0.885136 -123 GATCTCATATTCGTCTCGTCACTCTGCATAA 1 259 0 TCGTCTCTCA 0.719832 -42 TTAACGGTCTCCCCCCTTAAAACATTTGTA 2 15 0 TCCCCCCTAA 0.667785 -20 AATTACGAACTCCTCTCTTCGTTGTGTGAAA 5 150 0 TCCTCTCTCG 0.935773 -23 GTTCTGTCCCCCCCTCACCTCACATTA 6 101 0 TCCCCCCTCA 0.974378 -17 GTCTGTCACCCCCTTGTACTATGTAT 8 62 0 TCACCCCTTG 0.782563 -16 TAGTTGTTAAGCTCCCCTTCATCTTATGATC 9 129 0 GCTCCCCTCA 0.961152 -57 CGCCTTACTCTCTTCTATTCGTCTTTAGAAA 11 21 0 TCTTCTATCG 0.664397 -71 TTTATTCACCTCATCATGATTCAATC 12 15 0 TCACCTCTCA 0.958532 -16 ATGAGAGTATTCCTCTCATTGCTTTTTTTAT 14 95 1 TCCTCTCTTG 0.575911 -81 CTCTTTCTCCTCACCCGCACGAACCAAAATG 14 139 1 TCACCCGACG 0.563016 -37 TAAGATCACATCTCCTCTTCACTGTCATGTA 17 65 0 TCTCCTCTCA 0.980365 -236 TAGTATAGCATCTCCCATTCGTTCACGCTAT 17 247 0 TCTCCCATCG 0.892728 -54 CACTGGCCAGTCACCTCGACATCCCCCTGCT 19 136 1 TCACCTCACA 0.833261 -108 TGGTGGGCCAGCTCCTCGACAACACGAAGGT 20 24 0 GCTCCTCACA 0.837584 -63 GCGCCGCTTCTCCTCATCGCTTCGTCCCC 22 9 1 TCTCCTCTCG 0.987717 -65 ATCCAGACCGGCTTCCCGTCGCGGGACGTTC 26 59 0 GCTTCCCTCG 0.90768 -198 TGCAGCGGGTGCTCCTCCTCGGACGCCGCGA 26 99 0 GCTCCTCTCG 0.97463 -158 ******* *** Masking position 5 Map Score: 16.2891 Number of sites scoring better than the average of aligned sites = 623 Number in coding regions = 488 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 122 Fraction of orfs with sites within 600 bp upstream = 0.0195952 Motif number 4 TCGTAAAAAGCGGGAGGATTCC 5 3 1 GTAAAAAGCG 0.699346 -170 TTTTTTATATGGAAAAAGCGCATCTTTTAT 9 79 1 GGAAAAAGCG 0.948412 -107 TTTTTATTGTGGACAAAGCGCTCTTTCTCC 14 119 1 GGACAAAGCG 0.984884 -57 GTGCGGGTGAGGAGAAAGAGCGCTTTGTCC 14 129 0 GGAGAAAGAG 0.798026 -47 GCTCTGGCATGTAAGCAGCGGAAAA 16 6 0 GTAAGCAGCG 0.853013 -130 CTCGCGGCCGGGATAAAGCGCCAGGTAACC 18 40 1 GGATAAAGCG 0.879169 -29 TTCAACTCTGGGAGCCAGCGCCAACGCGGA 19 47 1 GGAGCCAGCG 0.954324 -197 CGACGGGCGTGGACCCTGCGGCACAACTTC 19 81 1 GGACCCTGCG 0.888207 -163 CGCTTGCGGGGGACGAAGCGATGAGGAGAA 22 18 0 GGACGAAGCG 0.988693 -56 CGGCGAAGCCGGGCACAGCGAGTCGACGGG 24 51 0 GGGCACAGCG 0.950263 -114 GCTCCTCCTCGGACGCCGCGACGGGGTCTG 26 90 0 GGACGCCGCG 0.965406 -167 CCCACACGGTGGACGCAGAGTCAACGTGTA 26 142 0 GGACGCAGAG 0.970027 -115 TTCCCGTGGTGGACGCAGAGTCAGCGCAGG 26 183 1 GGACGCAGAG 0.970027 -74 ********** Masking position 8 Map Score: 17.5575 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 435 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 5 GGCGGCGTGTCGCTGGACAAAC 18 3 1 CGGCGTGTCG 0.929132 -66 ACAACACGAAGGTCGCATCGGGCGAA 20 7 0 GGTCGCATCG 0.941243 -80 GGCATCGCCGCGGCGCATCGATAGGAAGGA 20 60 1 CGGCGCATCG 0.967754 -27 CCCACTGCATCGTCGCGGCGCGCGCTC 22 57 1 CGTCGCGGCG 0.834935 -17 ACTTCATTGTCGTCGGCGCGCC 23 3 0 CGTCGGCGCG 0.903585 -68 GGTGTATTCCCGTCGACTCGCTGTGCCCGG 24 43 1 CGTCGACTCG 0.917928 -122 ATCGCAAGCGCGGCGAAGCCGGGCACAGCG 24 61 0 CGGCGAAGCC 0.899318 -104 GTTTGTTTGGCGGCGAGTCGCTGCGGCGGC 24 101 1 CGGCGAGTCG 0.964501 -64 ATCGCAAGCGCGGCGAAGCCGCCGCAGCGA 24 118 0 CGGCGAAGCC 0.899318 -47 ATTTCCCGAAGGTGGCGGCG 25 1 0 GGTGGCGGCG 0.846261 -152 TCGTGGGCGCAGTCGCGGCGGTCAGCGCGT 25 122 1 AGTCGCGGCG 0.940141 -31 AACCTCAGACCGGCGCATCGCGAACGTCCC 26 38 1 CGGCGCATCG 0.967754 -219 GATCAGACCCCGTCGCGGCGTCCGAGGAGG 26 87 1 CGTCGCGGCG 0.834935 -170 CCAGAATAGGGGGCGCGCCGGCCTGCGCTG 26 204 0 GGGCGCGCCG 0.5073 -53 ********** Masking position 9 Map Score: 24.4141 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 257 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 6 GTGGGGAAACCCGCTCTTTTGTATTGAACA 1 164 1 CCGCTCTTTT 0.983801 -137 TTTTTAGCCCCTGCTCTTTTGAAGCAGGGT 1 227 1 CTGCTCTTTT 0.962346 -74 ATACGCCTATCCTCTCTTTTT 3 2 0 CCTCTCTTTT 0.940276 -80 TATCGTCTGTCCTCTTTCTTCGTTTATAAG 3 31 1 CCTCTTTCTT 0.837091 -51 GGGAATCCTCCCGCTTTTTACGA 5 4 0 CCGCTTTTTA 0.688401 -169 GGGAGGATTCCCGCTTTTTTATCGTATTAA 5 22 1 CCGCTTTTTT 0.960212 -151 CAATTACGAACTCCTCTCTTCGTTGTGTGA 5 152 0 CTCCTCTCTT 0.710259 -21 TCTTTAGAAAATTCTCTCTT 11 1 0 ATTCTCTCTT 0.545713 -91 CGCTATCAGCCTGCTCTCTTCTGTTACGTC 11 50 1 CTGCTCTCTT 0.954527 -42 ATTCCTCTCATTGCTTTTTTTATTGTGGAC 14 103 1 TTGCTTTTTT 0.610079 -73 GAAGTTCGCACCTCTATCTTCACCATATAA 15 44 0 CCTCTATCTT 0.690914 -51 GATTGAGGGATCGCTTTTTTTATTCGCCAA 16 42 1 TCGCTTTTTT 0.788043 -94 CATGCCGGCGCTCTTTTTCAGGTTTTA 17 8 1 GCGCTCTTTT 0.887184 -293 TGAATGGGATATGCTCTTTTTTTAAAACAC 17 158 0 ATGCTCTTTT 0.84944 -143 CCATTCGTTCACGCTATTTTAATGCTTACA 17 234 0 ACGCTATTTT 0.698576 -67 ********** Masking position 5 Map Score: 12.211 Number of sites scoring better than the average of aligned sites = 1319 Number in coding regions = 1087 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 205 Fraction of orfs with sites within 600 bp upstream = 0.0329264 Motif number 7 CTTTCTTCGTTTATAAGAAAAAAACTCAAAAGA 3 44 1 TTAAAAAAAA 0.858775 -38 ACGAAAACTATCATACTAAAAATCGTGCCTATA 4 49 0 TCAAAAAAAT 0.804178 -108 TTGAAAAGCTTCAAAATAAAGAAGCCGGGTCTC 6 34 0 TCAAAAAGAA 0.7571 -84 TGCGCTTTTTCCATATAAAAAAACATCGGCTCC 9 68 0 CCAAAAAAAA 0.969212 -118 AAAATCTTTCCCAAACTAAAAAATTCGGTCATC 10 19 1 CCAAAAAAAA 0.969212 -107 ATGAACCAAGCCAAATGAAAAAATTGCCGCTCC 13 94 1 CCAAAAAAAA 0.969212 -207 GCCGCTCCGATTAAAATAAAAAATATGTTTTTT 13 119 1 TTAAAAAAAA 0.858775 -182 CTTGGAGAAATTAGATTAAAAAACATATTTTTT 13 136 0 TTAAAAAAAA 0.858775 -165 AGCGCTTTGTCCACAATAAAAAAAGCAATGAGA 14 108 0 CCAAAAAAAA 0.969212 -68 CAATTGTGAACCATAGAGAAAAACAAACGTTCG 16 69 1 CCAAGAAAAA 0.855664 -67 ATGGGAGATGCTATACTAAAAATCATCATTTCA 17 260 1 CTAAAAAAAT 0.741582 -41 *** * ****** Masking position 5 Map Score: 8.69776 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 174 Number in noncoding regions = 82 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 8 GCTTAGGTATGAAGGTAAGCGTATATCCATT 1 70 1 GAAGGTAACG 0.937754 -231 ATGTTTTAAGGGGGGAGACCGTTAA 2 20 1 GGGGGAGACG 0.765047 -15 CTCACATTATGAAGGAGAAGGACAAGGTAGA 6 79 0 GAAGGAGAGG 0.983114 -39 CTTCATAATGTGAGGTGAGGGGGGGACAGAA 6 96 1 TGAGGTGAGG 0.935285 -22 CTTTTGATCATAAGATGAAGGGGAGCTTAAC 9 124 1 TAAGATGAGG 0.782223 -62 TATATACAAAGAAGGTGAACGTTTAGA 9 169 1 GAAGGTGACG 0.979039 -17 CTATCTAATGGAAGGAAAAGGGGTTTTGTGT 13 173 0 GAAGGAAAGG 0.949441 -128 TTCGTGCGGGTGAGGAGAAAGAGCGCTTTGT 14 131 0 TGAGGAGAAG 0.539665 -45 GTTATATGGTGAAGATAGAGGTGCGAACTTC 15 43 1 GAAGATAGGG 0.554533 -52 CGGCCGGCGCTAAGGTGAGCGCC 19 231 1 TAAGGTGACG 0.937754 -13 GCATCGATAGGAAGGAAACGGGA 20 74 1 GAAGGAAAGG 0.949441 -13 TCGATTTCCCGAAGGTGGCGGCG 25 3 0 GAAGGTGGGG 0.965251 -150 ******** ** Masking position 4 Map Score: 7.98365 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 503 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 9 GCATAAAAACCCTGCTTCAAAAGAGCAGGG 1 235 0 CCTGCTTCAA 0.879705 -66 CCTGTTTCACCTCCAAATCA 4 147 0 CCTGTTTCAC 0.918836 -10 GTTCTGTCCCCCCCTCACCTCACATTAT 6 100 0 CCCCCCTCAC 0.848213 -18 AAAGGAAAGCCTGCCCCATAATGGAGCAG 8 10 1 CCTGCCCCAT 0.92777 -68 TTAAAAAATGCCTGCTCCATTATGGGGCAG 8 21 0 CCTGCTCCAT 0.939658 -57 TTCTTTAGAGCCCGCTTCACAGTCAATTGG 9 16 0 CCCGCTTCAC 0.979004 -170 TGCTTTATGCCCTTTTCCACATCAGCCCCT 13 12 0 CCTTTTCCAC 0.572691 -289 GGGCGTGGACCCTGCGGCACAACTTCACGT 19 85 1 CCTGCGGCAC 0.94352 -159 CCCGGGCTGACCTGCCACACCGAGTTCGTC 19 195 1 CCTGCCACAC 0.942588 -49 AGGAGGAGCACCCGCTGCACATGAAGCACT 26 111 1 CCCGCTGCAC 0.974783 -146 ********** Masking position 9 Map Score: 5.88906 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 283 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 ATACAAAAGAGCGGGTTTCCCCACTCTTTGCC 1 156 0 GCGGTTTCCC 0.961381 -145 AATGTTTTAAGGGGGGAGACCGTTAA 2 19 1 GGGGGAGCCG 0.83151 -16 CGTAAAAAGCGGGAGGATTCCCGCTTTTTTAT 5 12 1 GGGGGATCCC 0.975834 -161 ATCTGGCTGAGGGCGGTTTTACAGGTATTACA 13 46 0 GGGGGTTTAC 0.897149 -255 AAAATGTAAAGGGTGGTAATAC 14 164 1 GGGGGTATAC 0.761525 -12 CCGCGAGCGCGCGTGTTTGTCCAGCGACACGC 18 15 0 GCGGTTTTCC 0.901482 -54 GACGCTCGACGGGCGTGGACCCTGCGGCACAA 19 75 1 GGGGTGGCCC 0.924142 -169 GCGATGCCGGGCGTGGTGGGCCAGCTCCTCGA 20 36 0 GCGGGTGGCC 0.907972 -51 CCCCGCAAGCGGGTGGTACCCCCACTGCATCG 22 37 1 GGGGGTACCC 0.975152 -37 GCGCGGATCTGGGTGTATTCCCGTCGACTCGC 24 32 1 GGGGTATCCC 0.937256 -133 TCCTGATATTGCTGGGTTTCACATGAGCACCT 25 52 1 GCTGGTTCAC 0.627925 -101 GGTAGTTGCTCCGGGATGGTGA 26 1 1 GGTGTTGTCC 0.72917 -256 *** **** *** Masking position 5 Map Score: 4.85259 Number of sites scoring better than the average of aligned sites = 256 Number in coding regions = 186 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 AAAAAGAGAGGATAGGCGTATATCGTCT 3 8 1 GAGATAGGCG 0.978263 -74 TCATTTCGTTCATAATAGGAGTAATTGATTA 5 119 1 CAAATAGGAG 0.834603 -54 TTCACACAACGAAGAGAGGAGTTCGTAATTG 5 151 1 GAGAGAGGAG 0.896338 -22 ATTCAATGAAGCTGATTGGCGGAAGGAGTTT 10 100 1 GCGATTGGCG 0.877031 -26 GGTTTTGTGTGATGCTTGGAGAAATTAGATT 13 152 0 GAGCTTGGAG 0.879174 -149 CATGTAAGAGGATGATAGGAGGTTTCGTTCA 13 280 1 GAGATAGGAG 0.978685 -21 GTTATATGGTGAAGATAGAGGTGCGAACTTC 15 43 1 GAGATAGAGG 0.78003 -52 CTCTATGGTTCACAATTGGCGAATAAAAAAA 16 56 0 CAAATTGGCG 0.806283 -80 CCATTTTAATGATTATTGGGGCAATTGTAGT 17 105 1 GATATTGGGG 0.808766 -196 GAGACAGGTCCAGAATAGGGGGCGCGCCGGC 26 212 0 CAAATAGGGG 0.831821 -45 CCTTTCCGGGGAAGATTGGAGACAGGTCCAG 26 230 0 GAGATTGGAG 0.974772 -27 ** ******** Masking position 8 Map Score: 5.16696 Number of sites scoring better than the average of aligned sites = 268 Number in coding regions = 223 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 12 AGCAGGGGCTAAAAAGTAAACGATGAACAT 1 212 0 AAAAAGTAAA 0.797357 -89 ATGAAAACATAAAAGGAGCCTGG 6 4 1 AAAACATAAA 0.760573 -114 ATGGTAAAATAAAACGTAAAATCATAGTCA 10 65 1 AAAACGTAAA 0.953561 -61 CGCACGAACCAAAATGTAAAGGGTGGTAAT 14 154 1 AAAATGTAAA 0.874031 -22 TAAAATGTGAACTAATTTCAT 15 2 1 AAAATGTGAA 0.893377 -93 GAGCTGTTTTAAAACCTGAAAAAGAGCGCC 17 17 0 AAAACCTGAA 0.850424 -284 AGGGCGTCGTAAAACGTGAAGTTGTGCCGC 19 98 0 AAAACGTGAA 0.961235 -146 ********** Masking position 4 Map Score: 2.04014 Number of sites scoring better than the average of aligned sites = 101 Number in coding regions = 73 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 13 CCATAGAATATGCGGGTGATGACCGAATTTT 10 38 0 TGCGGTGATG 0.822596 -88 TTTTGGTTCGTGCGGGTGAGGAGAAAGAGCG 14 137 0 TGCGGTGAGG 0.872974 -39 TTCGTCTAGTTGCGGCCGGCGCTAAGGTGAG 19 219 1 TGCGGCGGCG 0.915672 -25 ACCACCCGCTTGCGGGGGACGAAGCGATGAG 22 23 0 TGCGGGGACG 0.992014 -51 ACTGCATCGTCGCGGCGCGCGCTC 22 60 1 CGCGGGCGCG 0.891999 -14 CAAGGAGTGACGCGTGTGACG 23 60 1 CGCGTTGACG 0.919222 -11 TGAGCACCTTCGCTGCTGACGCCTCGGATCA 25 75 1 CGCTGTGACG 0.919222 -78 TGGGCGCAGTCGCGGCGGTCAGCGCGTAGTT 25 125 1 CGCGGGGTCA 0.826973 -28 CAGACCCCGTCGCGGCGTCCGAGGAGGAGCA 26 90 1 CGCGGGTCCG 0.887045 -167 GAGTAGCCCACACGGTGGACGCAGAGTCAAC 26 147 0 CACGGGGACG 0.963852 -110 CGCACATTCCCGTGGTGGACGCAGAGTCAGC 26 177 1 CGTGGGGACG 0.963639 -80 ***** ***** Masking position 3 Map Score: 6.20028 Number of sites scoring better than the average of aligned sites = 405 Number in coding regions = 375 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 14 GACGAATATGAGATCGACAGCACAAGGAGGA 1 275 1 AGATCGCAGC 0.699832 -26 CATATTGAAATGAACCAAGCCAAATGAAAAA 13 85 1 TGAACCAGCC 0.930984 -216 TGAACGAAACCTCCTATCATC 13 290 0 TGAACGAACC 0.876029 -11 GCAATTGTAGTGATCGGGGCCATTATCAGAT 17 125 1 TGATCGGGCC 0.963288 -176 TATTTTTTCCTGATCACAGCCGGTTTACTCA 17 200 0 TGATCAAGCC 0.83112 -101 ACCTGGCGCTTTATCCCGGCCGCGAGCGCGC 18 35 0 TTATCCGGCC 0.691882 -34 CTCCCAGAGTTGAACCCCACCAAATCTGTTG 19 30 0 TGAACCCACC 0.874241 -214 GAATACACCCAGATCCGCGCCACAGGAGTAC 24 21 0 AGATCCCGCC 0.896901 -144 ACCCAGCGGGCGATCGCAAGCGCGGCGAAGC 24 72 0 CGATCGAAGC 0.813857 -93 AGCCTAGCGGCGATCGCAAGCGCGGCGAAGC 24 129 0 CGATCGAAGC 0.813857 -36 TAGGCTTTAATGATCCGAGGCGTCAGCAGCG 25 85 0 TGATCCAGGC 0.951006 -68 CGACGGGGTCTGATCCAGACCGGCTTCCCGT 26 71 0 TGATCCGACC 0.951345 -186 ****** **** Masking position 3 Map Score: 4.38536 Number of sites scoring better than the average of aligned sites = 466 Number in coding regions = 447 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 15 GTTCTGTCCCCCCCTCACCTCA 6 106 0 TCTGTCCCCC 0.917323 -12 GAAAGAGCGCTTTGTCCACAATAAAAAAAG 14 116 0 TTTGTCCACA 0.825874 -60 AGCGCGCGTGTTTGTCCAGCGACACGCCGC 18 12 0 TTTGTCCAGC 0.939192 -57 TCCTCATCGCTTCGTCCCCCGCAAGCGGGT 22 21 1 TTCGTCCCCC 0.980723 -53 AATATCAGGATTCGTGCAGCCAAACCGATC 25 32 0 TTCGTGCAGC 0.859806 -121 ACGTTGACTCTGCGTCCACCGTGTGGGCTA 26 145 1 TGCGTCCACC 0.984284 -112 GCGCTGACTCTGCGTCCACCACGGGAATGT 26 180 0 TGCGTCCACC 0.984284 -77 ********** Masking position 5 Map Score: 3.17447 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 75 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911