AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_tpal_bbur_100.orf -o199_tpal_bbur_100.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: RTP00282 17 AE000520 RBB00627 28 3615 RBB00621 17 3615 RBB00260 17 3615 RBB00253 17 3615 RBB00334 24 3615 Input sequences: #1 RTP00386 105 AE000520 #2 RTP01082 116 AE000520 #3 RTP01072 141 AE000520 #4 RTP01088 169 AE000520 #5 RTP00306 147 AE000520 #6 RTP00305 54 AE000520 #7 RTP00304 63 AE000520 #8 RTP00303 71 AE000520 #9 RTP00302 46 AE000520 #10 RTP00299 55 AE000520 #11 RTP00286 187 AE000520 #12 RTP01113 234 AE000520 #13 RTP01114 149 AE000520 #14 RTP00261 106 AE000520 #15 RTP00258 108 AE000520 #16 RTP00257 262 AE000520 #17 RTP00255 102 AE000520 #18 RTP00254 21 AE000520 #19 RTP00816 164 AE000520 #20 RTP00038 23 AE000520 #21 RTP01010 107 AE000520 #22 RTP00479 210 AE000520 #23 RTP00609 300 AE000520 #24 RTP00625 123 AE000520 #25 RBB00724 96 3615 #26 RBB00626 79 3615 #27 RBB00624 136 3615 #28 RBB00618 139 3615 #29 RBB00570 114 3615 #30 RBB00359 24 3615 #31 RBB00358 67 3615 #32 RBB00356 82 3615 #33 RBB00355 70 3615 #34 RBB00352 51 3615 #35 RBB00351 23 3615 #36 RBB00808 108 3615 #37 RBB00809 173 3615 #38 RBB00336 248 3615 #39 RBB00335 32 3615 #40 RBB00333 36 3615 #41 RBB00278 300 3615 #42 RBB00277 50 3615 #43 RBB00276 35 3615 #44 RBB00273 21 3615 #45 RBB00266 21 3615 #46 RBB00261 16 3615 #47 RBB00250 21 3615 #48 RBB00214 283 3615 #49 RBB00144 165 3615 Motif number 1 CAACACACCGGCGAGCCCTGCATACATACCCGA 1 53 0 GCGGCCCGCT 0.894391 -53 TGCAGGAATGGTAGGGGGAGGACTGTGGGGTTT 2 75 1 GTAGGGGGGC 0.547561 -42 GAGGATCGGCGGAAGCACGGCCTTGTGCTCGAT 3 100 1 GGAGCACGCT 0.525739 -42 AAATAGGACAGGGAGCGGGGCATTTATATCGG 4 10 0 GGGGCGGGCT 0.924196 -160 ATGCGTATGCGTACGCGCGGCAGGTGGTGGTAT 4 58 0 GTAGCGCGCG 0.979234 -112 AAGACTTTCAGCGAGCGCAGCATATGATGGAGT 4 142 0 GCGGCGCGCT 0.987944 -28 GTGCGCGTTGGCGTGGGGTGCGGCCGACAGTTC 5 27 0 GCGGGGGGCG 0.979321 -121 CTCTGGGGAGGCGCGTCTGGTGCATCGCA 5 129 0 GGAGCGCTCG 0.730126 -19 CAGATTAAGCAGGCGGTGACGCAGCTTTTTG 6 34 0 GCAGCGGGAG 0.948499 -21 ACATAGTCCGCGTGCCCAGGACAATCAATATG 8 10 1 GCGGCCCGGC 0.744525 -62 CGCGCTGGTTGTGCGCGGTGCCTGAGAGGC 9 8 0 GTGGCGGGCT 0.925535 -39 ATCTGCATGAGCACGGACGGCAGTTTTTGGGCC 11 34 1 GCAGGACGCG 0.811796 -154 CACCGGAAGGGTAGGCGCTGGCGGAAAATGCTC 11 70 0 GTAGCGCGGG 0.951749 -118 GTTGTTGGATGCGGGCGGTGCGTACCAGGCGAT 12 90 0 GCGGCGGGCT 0.985818 -145 TTGCTGGTGCGTACGCGCAGCTGCCTGCTCAGT 13 52 0 GTAGCGCGCG 0.979235 -98 CTTGTTCACCGCAGGGGAAGCCGCACTGGTACT 14 12 1 GCAGGGAGCG 0.87389 -95 CTGCGCGCGTGCATGCTCGGGAGTGGATGGCAC 16 171 1 GCAGCTCGGG 0.80685 -92 CACTGCAAGCGCAAGCGGCTCTGATACCTTGTG 17 58 0 GCAGCGGTCG 0.929013 -45 TGGTGCACCACGCGGTGCACG 18 2 0 CCAGCGGGCC 0.856441 -20 CGCGCGCGTCCATGCGCTGGCTTCCGATTTCG 22 10 1 CCAGCGCGGT 0.781778 -201 GTCTTACGTCGCAGGCGGCGCTCCTCTTTTCAT 22 43 1 GCAGCGGGCC 0.985076 -168 CCAAAGGTACGCGTGCGCAGGCGAT 23 3 0 GCGGCGCGGG 0.989637 -298 TAGGAAGTGTGCATGCGGTGCCGCATATACCAA 23 105 0 GCAGCGGGCG 0.995548 -196 TATGGGAAATGCATGCGATGGTGTCGCGCAGGA 23 178 1 GCAGCGAGGG 0.922081 -123 GTGGCAGCCTGCACGGGGCGCTGAATCTGT 23 281 1 GCAGGGGGCG 0.981997 -20 AATTCAGTGCGCGCGCGGAGTGCGAACGCGA 24 9 1 GCGGCGCGAT 0.870959 -115 *** **** ** * Masking position 5 Map Score: 42.4199 Number of sites scoring better than the average of aligned sites = 371 Number in coding regions = 105 Number in noncoding regions = 266 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 2 GTGTCCTTTGGCATGAGCACCTTTCTTTCT 2 23 1 GCATGAGCAC 0.719025 -94 CCCCTGGTATCAAACCCCACAGTCCTCCCC 2 89 0 CAAACCCCAC 0.20728 -28 CGCAGAACACGCTCGCGCACGGAAGTGCGT 3 51 0 GCTCGCGCAC 0.948055 -91 AATACCACCACCTGCCGCGCGTACGCATAC 4 57 1 CCTGCCGCGC 0.799651 -113 ACGGACACTGCAACGTGCACACGTACTCCA 4 118 1 CAACGTGCAC 0.860618 -52 CACCCCACGCCAACGCGCACGACCTGCCTT 5 40 1 CAACGCGCAC 0.935153 -108 ATTGTCCTGGGCACGCGGACTATGT 8 6 0 GCACGCGGAC 0.555305 -66 ATCCCGCGCTGGTTGTGCGCGGTGCCTGAG 9 15 0 GGTTGTGCGC 0.525427 -32 AATGCGCTTGGATCCCGCGCTGGTTGTGCG 9 26 0 GATCCCGCGC 0.940344 -21 AGATGCAGTTGGACGAGCACTCCTAcTTCG 10 13 0 GGACGAGCAC 0.87189 -43 CCTGATATCTGCATGAGCACGGACGGCAGT 11 28 1 GCATGAGCAC 0.719025 -160 AGAGCATTTTCCGCCAGCGCCTACCCTTCC 11 69 1 CCGCCAGCGC 0.681169 -119 GAATGAGGACGGTTCTGCGCGGAAGTGCTC 12 42 0 GGTTCTGCGC 0.595403 -193 ACCGCACCGAGAATCTGCACAAGATCACGC 12 213 1 GAATCTGCAC 0.754796 -22 TACTGAGCAGGCAGCTGCGCGTACGCACCA 13 51 1 GCAGCTGCGC 0.837997 -99 TACGCACCAGCAACCTGCGCGACAAGGTGA 13 72 1 CAACCTGCGC 0.887849 -78 CACCGCAGGGGAAGCCGCACTGGTACTTAG 14 18 1 GAAGCCGCAC 0.892799 -89 GTGCAGCGTACCACCTGCACCATGACAACC 14 59 1 CCACCTGCAC 0.92505 -48 AACTCATTGGGCTCCTGCACGTCGGAGAAT 16 46 1 GCTCCTGCAC 0.913221 -217 GAGAGGTGAGGAAACAGCGCAAAATCTTGG 16 88 0 GAAACAGCGC 0.562619 -175 TCCCGAGCATGCACGCGCGCAGTTTTTTTT 16 163 0 GCACGCGCGC 0.833666 -100 GGCTCAGGGAGCACCCCCACTACGTGGTGC 17 19 1 GCACCCCCAC 0.821078 -84 CGTGCACCGCGTGGTGCACCA 18 10 1 CGTGGTGCAC 0.452838 -12 GCCAGCGCATGGACGCGCGCG 22 2 0 GGACGCGCGC 0.951558 -209 ATCGCCTGCGCACGCGTACCTTTGGGGGT 23 10 1 GCACGCGTAC 0.452199 -291 TGGGGGTTTGGAATGAGCGCGGAAATAAAG 23 33 1 GAATGAGCGC 0.621414 -268 ATGCATTTCCCATACCGCACCCATAACTGA 23 162 0 CATACCGCAC 0.583401 -139 GGTACGTGCACATCCTGCGCGACACCATCG 23 193 0 CATCCTGCGC 0.807752 -108 AGCGCTGTGGCAGCCTGCACGGGGCGCTGA 23 275 1 CAGCCTGCAC 0.667162 -26 ACAGATTCAGCGCCCCGTGCAGG 23 288 0 GATTCAGCGC 0.536588 -13 TTCGCACTCCGCGCGCGCACTGAATT 24 7 0 GCGCGCGCAC 0.810222 -117 TAAGACATAACAAGCCGCACATCATAACGA 32 47 0 CAAGCCGCAC 0.838293 -36 TAGCTCAGTTGGTAGAGCACCACCATGGTA 37 91 1 GGTAGAGCAC 0.332098 -83 CTTGAACCGACGACCCCCACCTTACCATGG 37 113 0 CGACCCCCAC 0.63948 -61 TTTTAGAAATTGACCCGCACTACGTGTTTT 41 172 0 TGACCCGCAC 0.521427 -129 ********** Masking position 10 Map Score: 24.087 Number of sites scoring better than the average of aligned sites = 1259 Number in coding regions = 326 Number in noncoding regions = 933 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 TACCCACTAATTTAACAAAATTTTACATTTAAAT 26 29 0 TTTAAAAATT 0.803881 -51 TAAGTGATTCTTTAATAAGAGGTTATGTT 26 61 1 TTTAAAAATT 0.803881 -19 ACTAAGTTTATTTAATAAAAATAAACTATTTAAC 27 53 0 TTTAAAAAAA 0.769309 -84 ATTCAATAAGTTTATTAAGACTTTAGGAGTAATT 27 113 1 TTTATAAATT 0.832762 -24 GAGACTAATTTTTTTCAACAATAAAAATTTTTAT 28 47 0 TTTTTAAAAA 0.7693 -93 TACACGAAGTTTTTTAAAAATGTAATTTATAGGG 29 18 0 TTTTTAAATA 0.858597 -97 TTGCTACCATTTTATTAATAGTTTCAAGAAAAGG 31 31 1 TTTATAAATT 0.832762 -37 AAAAGACTCCTTTTTTAAGACATAACAAGCCGCA 32 58 0 TTTTTAAATA 0.858597 -25 TAATATGCATTTTAAAAAGATCAA 38 1 0 TTTAAAAAAA 0.769309 -248 AAGACATAGGTTTATAAAAAGGTTTTTGTTTATT 38 103 0 TTTATAAATT 0.832762 -146 TTTACAATTTTTTTTCAAAAAAAATATTCTTACC 38 160 1 TTTTTAAAAA 0.768712 -89 AATTCTTCTCTTTATAAATAAGTATTGCCTATTT 38 209 0 TTTATAAATA 0.880617 -40 TTTAACAAGAATAAAATGGGAAAA 39 1 1 TTTAAAAAAA 0.769309 -32 AGCTTTATTTTTTAATATTTTGTGCTTTTCT 41 8 1 TTTTTAAATT 0.803881 -293 ATTCTACACATTTTACAAAATATAGTCAATACGC 41 113 0 TTTTAAAATA 0.833284 -188 ATTTTCTTATTTTAATAAGAATAAATTTGTTAAA 41 237 1 TTTAAAAAAA 0.769309 -64 TGTTAAAAATTTTTTAAAGAGATTAAATGTAAGT 41 264 1 TTTTTAAATT 0.803881 -37 CTTCCAAATATTTAATAATATAAAACGATATAAG 48 178 1 TTTAAAAAAA 0.769298 -106 ACAAAATTTTTTTTTAAAAATCTATCTTATATCG 48 203 0 TTTTTAAATA 0.858597 -81 ATCTTAGTAATTTTACAAAATTTTTTTTTAAAAA 48 217 0 TTTTAAAATT 0.771383 -67 ***** ** * ** Masking position 3 Map Score: 17.1418 Number of sites scoring better than the average of aligned sites = 150 Number in coding regions = 42 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 4 GGTTAAATAGTTTATTTTTATTAAATAAACTT 27 52 1 TTTATTTTAT 0.938768 -85 TTACATTTTGTATATTATAAAAATTTTTATTG 28 31 1 TATATTTAAA 0.424258 -109 TATAAAAATTTTTATTGTTGAAAAAAATTAGT 28 46 1 TTTATTTTGA 0.652693 -94 AAATAATGCTTTTATTCTTAAAAAGAATAATT 29 85 1 TTTATTTTAA 0.900872 -30 TTGCTACCATTTTATTAATAGTTTCAAGAAAA 31 31 1 TTTATTATAT 0.536982 -37 ACAACTTTGATATATTTTTAATTTT 32 4 0 TATATTTTAT 0.756773 -79 TTTTATTATAAGAAGGGTAAATT 35 2 1 TTTATTTAAA 0.784114 -22 ATTGAGGGCTTTTATTGGTAGTTAGGAGTTTT 37 147 1 TTTATTGTAT 0.632307 -27 AAGGTTTTTGTTTATTTTAATTTATTTGCAGC 38 87 0 TTTATTTAAT 0.859481 -162 TATAAGTAATTTTATTATAAGACATAGGTTTA 38 123 0 TTTATTTAAA 0.784114 -126 ACCTAAGAGATTTATTATAAATAGGCAATACT 38 191 1 TTTATTTAAT 0.859479 -58 TTTTTCCCATTTTATTCTTGTTAAA 39 4 0 TTTATTTTGT 0.75989 -29 AAAGTTTATATTAATTTTTAATGCTATTATAT 41 53 1 TTAATTTTAT 0.523106 -248 TTTTAACAAATTTATTCTTATTAAAATAAGAA 41 240 0 TTTATTTTAT 0.938768 -61 TAACTCTTACTTTATTATTATACTCCTAAGAT 48 17 0 TTTATTTTAA 0.899019 -267 TATATCGTTTTATATTATTAAATATTTGGAAG 48 178 0 TATATTTTAA 0.641852 -106 CAATTATTTGTTTATTATTAATTTAA 49 5 0 TTTATTTTAT 0.938602 -161 TTAACACAACTTTATTATGAGTGTCAATTATT 49 29 0 TTTATTTGAT 0.691021 -137 CCTGCTATGCTTTATTTTTAATATGTGAGGAA 49 144 1 TTTATTTTAT 0.938766 -22 ****** *** * Masking position 6 Map Score: 14.4187 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 23 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 5 TTACCATTCCTGCGGCGGTTCTTGCAGGAATGGTAGGGG 2 53 1 TGCGGTCAGA 0.476167 -64 ACTGACACCACGCAGAACACGCTCGCGCACGGAAGTGCG 3 52 0 CGCAGCGCGA 0.987834 -90 GTGTGCACGTTGCAGTGTCCGTTTCCGCTCTCTTCCGAT 4 101 0 TGCAGCCCGT 0.950273 -69 TTTCAGCGAGCGCAGCATATGATGGAGTACGTGTGCACG 4 131 0 CGCAGTGAGA 0.910598 -39 GCACAACCAGCGCGGGATCCAAGCGCATTG 9 27 1 CGCGGCGCAT 0.916431 -20 TCCGTGCTCATGCAGATATCAGGAGAAATATTGCGGTAG 11 12 0 TGCAGCGAAT 0.734444 -176 AAAAAACTCGCGCGGTGTTTTGATGCGTTGCCGAGCGTG 12 134 0 CGCGGTGCGT 0.970961 -101 CGTGATCTTGTGCAGATTCTCGGTGCGGTAGAGGCACGC 12 203 0 TGCAGTGCGT 0.959697 -32 GGTGCGTACGCGCAGCTGCCTGCTCAGTATGCTAAAAGT 13 41 0 CGCAGCCAGA 0.891294 -109 CACCTTGTCGCGCAGGTTGCTGGTGCGTACGCGCAGCTG 13 62 0 CGCAGCGCGA 0.987837 -88 TTCTCCGACGTGCAGGAGCCCAATGAGTTACGTTTGTTC 16 36 0 TGCAGCGAGT 0.959697 -227 ACGACATGTCCGCAACGCATTGGCGCGGTTACGACCGGT 22 128 1 CGCAATGCGT 0.754276 -83 CAGCGCCCCGTGCAGGCTGCCACAGCGCTGCATATCCTA 23 265 0 TGCAGCGCGT 0.985344 -36 TCAGTGCGCGCGCGGAGTGCGAACGCGATTACCAGTCTT 24 14 1 CGCGGCGCGT 0.98952 -110 ***** * *** * Masking position 3 Map Score: 13.4323 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 52 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 6 ATACCACGAACTGTCGGCCGCACCCCACGCCAA 5 20 1 CGTGGCGCAC 0.862094 -128 GAGGCGCGTCTGGTGCATCGCAGGTGCTATGCC 5 118 0 TGTCACGCAG 0.924198 -30 GATCCCGCGCTGGTTGTGCGCGGTGCCTGAGAG 9 13 0 TGTGTCGCGG 0.927309 -34 GGACGGCAGTTTTTGGGCCGCAGAGCATTTTCC 11 48 1 TTTGGCGCAG 0.931956 -140 AGAATGAGGACGGTTCTGCGCGGAAGTGCTCTT 12 40 0 CGTCTCGCGG 0.811358 -195 GCAGATCGTGTTGTTGGATGCGGGCGGTGCGTA 12 99 0 TGTGGTGCGG 0.943329 -136 GCTTGTTCACCGCAGGGGAAGCCGC 14 3 1 TGTCACGCAG 0.924198 -104 ATGGTGCAGGTGGTACGCTGCACTTGTGGTGTA 14 49 0 TGTCGTGCAC 0.819341 -58 AGAAAAAATCTAGTCGGTTGCGCGACAACATCT 15 62 0 TGTGGTGCGC 0.825945 -47 CCCCACTACGTGGTGCGACGTGGAACACAAGGT 17 33 1 TGTCGCGTGG 0.866522 -70 CCGATTTCGGTCTTACGTCGCAGGCGGCGCTCC 22 34 1 TTTCGCGCAG 0.94086 -177 TCAAAGACAATATTTGGACGCAGAAAGGGTCCG 22 80 0 TTTGGCGCAG 0.931956 -131 AACGAAATTATAGTCCGTCGCGGCTTTATCGTA 22 186 1 TGTCGCGCGG 0.99071 -25 ACATTTTAAATTGTAAGACGCAGGGTAGAGCAG 49 60 1 TGTAGCGCAG 0.9074 -106 * ** ** ***** Masking position 4 Map Score: 12.8083 Number of sites scoring better than the average of aligned sites = 152 Number in coding regions = 48 Number in noncoding regions = 104 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 CTTCCGTGCGCGAGCGTGTTCTGCGTGGTG 3 56 1 CGAGCGTGTT 0.98451 -86 AGCGTGTCGCAGATCGTGTTGTTGGATGCG 12 110 0 AGATCGTGTT 0.862131 -125 GATGCGTTGCCGAGCGTGTCGCAGATCGTG 12 122 0 CGAGCGTGTC 0.990093 -113 GCGTGGTTACCGATCGTGTCTCCATGTTCT 16 216 0 CGATCGTGTC 0.98451 -47 AGTTCACGTGCGAGGGTGTTCCTATTCTGC 21 14 0 CGAGGGTGTT 0.970778 -94 GAAATGCATGCGATGGTGTCGCGCAGGATG 23 183 1 CGATGGTGTC 0.970778 -118 ********** Masking position 7 Map Score: 4.89699 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 2 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 8 GGCGGCGTGTGATGCTTGCAACGAGCATTT 1 24 1 GATGCTTGCA 0.771627 -82 TTCCTGCGGCGGTTCTTGCAGGAATGGTAG 2 59 1 GGTTCTTGCA 0.726353 -58 GTTTCCCTTAGAAGCGTGCATTCCTCCACG 11 105 1 GAAGCGTGCA 0.73009 -83 GGATGCGGGCGGTGCGTACCAGGCGATGAA 12 87 0 GGTGCGTACC 0.801464 -148 CCACAATTACGGTGCGTGCCTCTACCGCAC 12 190 1 GGTGCGTGCC 0.980486 -45 GCAGGTTGCTGGTGCGTACGCGCAGCTGCC 13 60 0 GGTGCGTACG 0.858659 -90 GTGGGAGATTGGTACGTGCAGTT 20 4 0 GGTACGTGCA 0.966603 -20 AAAACCAGTGGGTACGTGCACATCCTGCGC 23 203 0 GGTACGTGCA 0.966603 -98 TGACAATTAAGGTAAGTGCCCCAAAGGCAA 24 69 0 GGTAAGTGCC 0.732689 -55 ********** Masking position 7 Map Score: 4.12761 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 20 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 9 GACGCAGCTTTTTGGAGTAACGGTTAGGCG 6 18 0 TTTGGAGTAA 0.764453 -37 CATGCAGATATCAGGAGAAATATTGCGGTA 11 13 0 TCAGGAGAAA 0.764219 -175 TAAAAGTAGCTCAGGAGTCTTTGAAATTAC 13 18 0 TCAGGAGTCT 0.776705 -132 TATTAAGACTTTAGGAGTAATT 27 125 1 TTAGGAGTAA 0.901267 -12 CGATAGACCATAAGGAGTTTTAGTA 28 125 1 TAAGGAGTTT 0.795362 -15 TGAAAATATATAAGGAGTTAAT 33 59 1 TAAGGAGTTA 0.738445 -12 GTTACTACCATAAGGAGATTAT 34 40 1 TAAGGAGATT 0.738445 -12 AGCATACAGTTTTGGAGACTGTCGTTCTAC 36 37 0 TTTGGAGACT 0.647614 -72 TTATTGGTAGTTAGGAGTTTTGTTAT 37 158 1 TTAGGAGTTT 0.895655 -16 TCTCTAAAGTTTAGGAGAATAAA 42 38 1 TTAGGAGAAT 0.901268 -13 TGGTTTTGGAGAAAAATAAAT 44 5 1 TTTGGAGAAA 0.70216 -17 ATAATTATCTTAGGAGTATAATAATAAAG 48 10 1 TTAGGAGTAT 0.92629 -274 ********** Masking position 6 Map Score: 4.08982 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 31 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 10 CCCCAAAGGCAATGCCTAATATAAAAAAAAGACTGGT 24 44 0 AATATATAAA 0.910383 -80 AAAACAATTTAATTTAATAATTACAAACTGTGCTTAT 25 18 1 AATAATTAAA 0.706198 -79 ATATTAGTATAATATAAAATATATAAATAAGCACAGT 25 44 0 AATATATAAA 0.910383 -53 AACAAGCTAAAATGTTATAATTTTAAA 27 1 0 AATAATTAAA 0.706198 -136 TATACAATACAATAGATCATATAAAAACTAAGTTTAT 27 76 0 AATATATAAA 0.910383 -61 AAATTTTTATAATATACAAAATGTAACTGAAAAATAA 28 20 0 AATAAATAAC 0.649882 -120 AAAATTAAAAATATATCAAAGTTGTTATT 32 3 1 AATATATCAA 0.615718 -80 ACCCTTAAAATAACAAATATTTAAACAGGAGTATA 40 9 1 AATATATAAA 0.910383 -28 AGCTACAAATAATCAAAAAAATAAAAAAATCAATTTT 41 200 0 AATAAATAAA 0.921683 -101 TAAAATACCTCAAATTCATATACTTAAAAT 43 16 0 AATAAATATA 0.556025 -20 AGTAAGAGTTAATTCACTAAATAAAAAGTTTTAATCA 48 38 1 AATAAATAAA 0.921683 -246 AAAAAGTTTTAATCAATAAAATCAAAATCTACTAAAT 48 60 1 AATAAATAAA 0.921682 -224 TTAAATTAATAATAAACAAATAATTGACAC 49 4 1 AATATAAAAA 0.519475 -162 *** **** *** Masking position 9 Map Score: 4.18216 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 22 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 11 GTACTCCATCATATGCTGCGCTCGCTGAAA 4 140 1 ATATGCTGCG 0.616876 -30 CGTTACTCCAAAAAGCTGCGTCACCGCCTG 6 26 1 AAAAGCTGCG 0.845222 -29 TGAGCAAAGAAATTGGAGAGTATTTAAACA 11 137 0 AATTGGAGAG 0.580655 -51 GTTACACCACAAGTGCAGCGTACCACCTGC 14 47 1 AAGTGCAGCG 0.949036 -60 GGAAAGAGGAGAGGTTTAAAGCG 14 94 0 AAGAGGAGAG 0.822366 -13 TCCCATGGGGAAAAGCAACGGGTGG 16 248 1 AAAAGCAACG 0.772245 -15 GAGTAGGAGTAAATGGAGCGTCGTATC 19 8 0 AAATGGAGCG 0.968937 -157 GAGGGATGAAAAGAGGAGCGCCGCCTGCGA 22 51 0 AAGAGGAGCG 0.949212 -160 GAAGATAACCAAATGGAACGCTAGGAAGTG 23 129 0 AAATGGAACG 0.827752 -172 CGCTTTTAGGATATGCAGCGCTGTGGCAGC 23 259 1 ATATGCAGCG 0.866476 -42 TAGTTTCAAGAAAAGGAGAGCGTTGATAA 31 49 1 AAAAGGAGAG 0.866705 -19 ********** Masking position 1 Map Score: 3.86629 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 50 Number in noncoding regions = 152 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 12 AATTATTAAATTAAATTGTTTTTGAATTT 25 8 0 TTAAATTTTT 0.83561 -89 TTGTATATTATAAAAATTTTTATTGTTGAAAA 28 38 1 TAAAATTTTA 0.486497 -102 TAATTCCCTATAAAACTCTTTATTATCTTAGT 37 50 0 TAAAATTTTA 0.831859 -124 GTCAATACGCTTAAACTTTTAAACTCAATTCA 41 91 0 TTAAATTTAA 0.707809 -210 TTTAAAGCTATTAAAATTTTTTAGAAAAACAC 41 147 1 TTAAATTTTT 0.785445 -154 ATAAATTTGTTAAAAATTTTTTAAAGAGATTA 41 257 1 TAAAATTTTT 0.688501 -44 TAATATATCCTTAAAGTCTTAAC 42 2 0 TTAAATTTAA 0.768884 -49 TTTTATTGATTAAAACTTTTTATTTAGTGAAT 48 49 0 TAAAATTTTA 0.740016 -235 ATTTGGAAGTTTAAACTATTTTATATGAAATT 48 155 0 TTAAATTTTT 0.83561 -129 GTCTTACAATTTAAAATGTTAACACAACTTTA 49 47 0 TTAAATTTAA 0.707809 -119 ***** * **** Masking position 7 Map Score: 3.06671 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 24 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 13 GGTACAAATACCACCACCTGCCGCGCGTAC 4 51 1 CCACCACCTG 0.99114 -119 CATAGCCATACCACGAACTGTCGGCCGCAC 5 13 1 CCACGAACTG 0.895818 -135 ACGCCAACGCGCACGACCTGCCTTCCCCAA 5 46 1 GCACGACCTG 0.851399 -102 TAGGAGTGCTCGTCCAACTGCATCTCTTCC 10 18 1 CGTCCAACTG 0.778814 -38 AGCGTGCATTCCTCCACGTGTGTTTAAATA 11 117 1 CCTCCACGTG 0.934105 -71 CAAGTGCAGCGTACCACCTGCACCATGACA 14 56 1 GTACCACCTG 0.898305 -51 CATGCGCATTCCTACACCTGTTATTTTTAC 15 27 1 CCTACACCTG 0.825561 -82 GGGAGCACCCCCACTACGTGGTGCGACGTG 17 25 1 CCACTACGTG 0.677475 -78 CTTAATACGTCTTCCACCTTGCATTGCCTG 21 52 0 CTTCCACCTT 0.771009 -56 TGGTGGTGCTCTACCAACTGAGCTATAAGG 37 86 0 CTACCAACTG 0.929858 -88 GAACCGACGACCCCCACCTTACCATGGTGG 37 110 0 CCCCCACCTT 0.805006 -64 GCCCGACGAGCTACCAACTGCTCTACCCTG 49 80 0 CTACCAACTG 0.929858 -86 ********** Masking position 6 Map Score: 4.6039 Number of sites scoring better than the average of aligned sites = 1067 Number in coding regions = 319 Number in noncoding regions = 748 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 14 AACCGCCGCAGGAATGGTAAAGAAAGAAAG 2 43 0 GGAATGGTAA 0.911 -74 GGTTCTTGCAGGAATGGTAGGGGGAGGACT 2 69 1 GGAATGGTAG 0.974041 -48 AAACAACACCGGAAGGGTAGGCGCTGGCGG 11 79 0 GGAAGGGTAG 0.978407 -109 GTTCTGTATGCGAATGGTAGTTGAGCAAAG 11 158 0 CGAATGGTAG 0.951485 -30 AATAAAGAGCGGCATGATAGAACCACGGGA 19 141 1 GGCATGATAG 0.766087 -24 TTTTATTATAAGAAGGGTAAATT 35 11 1 AGAAGGGTAA 0.703145 -13 AATTGTAAGACGCAGGGTAGAGCAGTTGGT 49 68 1 CGCAGGGTAG 0.940957 -98 ********** Masking position 4 Map Score: 1.51163 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 20 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 15 ********** No masking Map Score: 8.98369e-12 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