AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_tpal_bbur_300.orf -o199_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: RTP00282 17 AE000520 RBB00253 17 3615 RBB00627 28 3615 RBB00621 17 3615 RBB00260 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 RTP01071 100 AE000520 #13 RTP01112 99 AE000520 #14 RTP00264 30 AE000520 #15 RTP01113 234 AE000520 #16 RTP01114 149 AE000520 #17 RTP00261 106 AE000520 #18 RTP00258 108 AE000520 #19 RTP00257 262 AE000520 #20 RTP00255 102 AE000520 #21 RTP00254 21 AE000520 #22 RTP00816 164 AE000520 #23 RTP00038 23 AE000520 #24 RTP01010 107 AE000520 #25 RTP00035 36 AE000520 #26 RTP01003 103 AE000520 #27 RTP01001 90 AE000520 #28 RTP01158 249 AE000520 #29 RTP00025 300 AE000520 #30 RTP00480 300 AE000520 #31 RTP00479 210 AE000520 #32 RTP00609 300 AE000520 #33 RTP00625 123 AE000520 #34 RTP00626 92 AE000520 #35 RBB00724 96 3615 #36 RBB00626 79 3615 #37 RBB00624 136 3615 #38 RBB00618 139 3615 #39 RBB00617 173 3615 #40 RBB00570 114 3615 #41 RBB00359 24 3615 #42 RBB00358 67 3615 #43 RBB00356 82 3615 #44 RBB00355 70 3615 #45 RBB00352 51 3615 #46 RBB00351 23 3615 #47 RBB00808 108 3615 #48 RBB00809 173 3615 #49 RBB00349 300 3615 #50 RBB00336 248 3615 #51 RBB00335 32 3615 #52 RBB00333 36 3615 #53 RBB00278 300 3615 #54 RBB00277 50 3615 #55 RBB00276 35 3615 #56 RBB00273 21 3615 #57 RBB00266 21 3615 #58 RBB00261 16 3615 #59 RBB00250 21 3615 #60 RBB00214 283 3615 #61 RBB00144 165 3615 #62 RBB00143 121 3615 Motif number 1 CCGCCCGTACGAAAAAGTACC 1 95 0 CCCCCGTACG 0.670284 -11 CGCAGAACACGCTCGCGCACGGAAGTGCGTT 3 50 0 GCCGCGCACG 0.852574 -92 AATACCACCACCTGCCGCGCGTACGCATACG 4 57 1 CCGCCGCGCG 0.940587 -113 ACGGACACTGCAACGTGCACACGTACTCCAT 4 118 1 CACGTGCACA 0.810152 -52 GGAAGACTTTCAGCGAGCGCAGCATATGATG 4 146 0 CACGAGCGCA 0.822922 -24 CACCCCACGCCAACGCGCACGACCTGCCTTC 5 40 1 CACGCGCACG 0.927608 -108 TTTCTTCATGCACCCTGTGCCAAGTATCACT 7 43 1 CACCTGTGCC 0.482711 -21 ACATAGTCCGCGTGCCCAGGACAATCAA 8 8 1 CCCGTGCCCA 0.590139 -64 GCACCGCGCACAACCAGCGCGGGATCCAAGC 9 20 1 CACCAGCGCG 0.954623 -27 AGAGCATTTTCCGCCAGCGCCTACCCTTCCG 11 69 1 CCCCAGCGCC 0.903741 -119 TCCGTGGGTACACCCTGCGCG 13 1 0 CACCTGCGCG 0.984825 -99 CGCATCAAAACACCGCGCGAGTTTTTTCAAC 15 146 1 CACGCGCGAG 0.691728 -89 TACTGAGCAGGCAGCTGCGCGTACGCACCAG 16 51 1 GCGCTGCGCG 0.781245 -99 TACGCACCAGCAACCTGCGCGACAAGGTGAA 16 72 1 CACCTGCGCG 0.984841 -78 GTGCAGCGTACCACCTGCACCATGACAACCA 17 59 1 CCCCTGCACC 0.896065 -48 AACTCATTGGGCTCCTGCACGTCGGAGAATT 19 46 1 GCCCTGCACG 0.897105 -217 TCCCGAGCATGCACGCGCGCAGTTTTTTTTG 19 162 0 GCCGCGCGCA 0.889997 -101 TTCCACAAAACCGCCGGCGCAGGATCCGAAA 26 28 1 CCCCGGCGCA 0.921499 -76 AGAGCTGTTGCACCCGGCGCAG 26 92 1 CACCGGCGCA 0.878867 -12 CCTCGTTTTACCACCAGCACATTCGCGTAGG 27 23 1 CCCCAGCACA 0.808072 -68 CCTGATGCCTCAGCCTACGCGAATGTGCTGG 27 36 0 CACCTACGCG 0.649175 -55 GCCAGCGCATGGACGCGCGCG 31 1 0 GGCGCGCGCG 0.619917 -210 AAGAGGAGCGCCGCCTGCGACGTAAGACCGA 31 40 0 CCCCTGCGAC 0.601554 -171 ATCGCCTGCGCACGCGTACCTT 32 2 1 TCCCTGCGCA 0.612728 -299 GGTACGTGCACATCCTGCGCGACACCATCGC 32 192 0 CACCTGCGCG 0.984836 -109 AGCGCTGTGGCAGCCTGCACGGGGCGCTGAA 32 275 1 CACCTGCACG 0.950782 -26 CGTTCGCACTCCGCGCGCGCACTGAATT 33 8 0 CCCGCGCGCA 0.96667 -116 TGGTTGAAGCGAACGCGCGCGAGTTTGTTTC 34 50 1 GACGCGCGCG 0.923201 -43 TAAGACATAACAAGCCGCACATCATAACGAC 43 46 0 CAGCCGCACA 0.550097 -37 ** ******** Masking position 7 Map Score: 37.5355 Number of sites scoring better than the average of aligned sites = 435 Number in coding regions = 135 Number in noncoding regions = 300 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 2 AAATCGAGCACAAGGCCGTGCTTCCGCCGATCCTCAGG 3 97 0 CAGCTCCCCC 0.989566 -45 ATAGCCATACCACGAACTGTCGGCCGCACCCCACGCCA 5 14 1 CAGCGCCCCA 0.992529 -134 CGCCAACGCGCACGACCTGCCTTCCCCAAAGCCGTGTT 5 47 1 CAGCGCCCCA 0.992529 -101 GCCTCTCAGGCACCGCGCACAACCAGCGCGGGAT 9 7 1 CAGCGGCACC 0.955416 -40 CTTGCTGGTTCAAGTCCAGTCCGCCGCAAAGGCCCCGC 12 33 1 CAGCGCCCCA 0.992529 -68 GGGCGTGTACGCCGCTCCTCTGCTCCGCAAA 12 80 0 CGGCCGCCCT 0.669972 -21 CATCGCCTGGTACGCACCGCCCGCATCCAACAACACGA 15 89 1 TAGCGCCACC 0.829982 -146 CATCCAACAACACGATCTGCGACACGCTCGGCAACGCA 15 112 1 CAGCGGACCT 0.866482 -123 GGAAGCCGCACTGGTACTTAGTTACACCACAAGTGCAG 17 27 1 CTGCTGACCC 0.605191 -80 AGTTACACCACAAGTGCAGCGTACCACCTGCACCATGA 17 46 1 CAGCGGCCCC 0.992444 -61 ACTCAACGCTCATGCGCATTCCTACACCTGTTATTTTT 18 17 1 CAGCTCACCC 0.962756 -92 CACCCTCGCACGTGAACTGGCATCCACAGGCAATGCAA 24 26 1 CGGCGCCCCA 0.985557 -82 TACGCAAAAGCGTGGTCTTTCCGCAGCCTGAAGGACCG 30 37 1 CGGCTCCACC 0.88825 -264 CGCATCCTTTCACGGTCTGTCGCACTCCTTCTCATTGC 30 172 1 CAGCGCACCC 0.990545 -129 ATCTGTCCAGCAAGGACACACGGACGCCTTGCGTACCC 30 260 0 CAGCCCACCC 0.945636 -41 CGCGCGCGTCCATGCGCTGGCTTCCGATTTCGGTCTTA 31 11 1 CAGCGCCCAT 0.744625 -200 TTGGCGCGGTTACGACCGGTCACCCTCAGTATTCATCC 31 147 1 TAGCGCCCCA 0.911821 -64 TCTTTATTTCCGCGCTCATTCCAAACCCCCAAAGGTAC 32 26 0 CGGCTCAACC 0.684179 -275 GATTCAGCGCCCCGTGCAGGCTGCCACAGCGCTGCATA 32 270 0 CCGCGCCCCA 0.950932 -31 CTCAATCGGACTTGAACCGACGACCCCCACCTTACCAT 48 115 0 CTGCGCCCCC 0.98523 -59 ** * * * * ** ** Masking position 7 Map Score: 27.182 Number of sites scoring better than the average of aligned sites = 309 Number in coding regions = 104 Number in noncoding regions = 205 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 3 TATTTTAGATGCGTATGCGTACGCGCGGCAGGTG 4 65 0 GGATGCGAGC 0.962681 -105 CTCCTGATATCTGCATGAGCACGGACGGCAGTTT 11 26 1 CGATGAGAGG 0.740029 -162 GGAAACAACACCGGAAGGGTAGGCGCTGGCGGAA 11 77 0 CGAAGGGAGC 0.889152 -111 AAGAAGTGTTCTGTATGCGAATGGTAGTTGAGCA 11 161 0 CGATGCGAGG 0.945788 -27 TTGCCATGCGCAGTGAGCGCAGGCCAGTGTTCGG 13 33 0 CGGAGCGAGC 0.992011 -67 TGAGTTTGTCCAGAATGAGGACGGTTCTGCGCGG 15 50 0 CGATGAGAGG 0.740029 -185 CTACTTTTAGCATACTGAGCAGGCAGCTGCGCGT 16 39 1 CTCTGAGAGC 0.697519 -111 CGCGCAGGTTGCTGGTGCGTACGCGCAGCTGCCT 16 59 0 GTGTGCGAGC 0.892195 -91 TTTTTGAACACTGCAAGCGCAAGCGGCTCTGATA 20 65 0 CGAAGCGAGC 0.99092 -38 CCGAGTCAGCGAAGGCATTCCACAAA 26 3 1 GGCAGCGAGC 0.961126 -101 ACCGCCGGCGCAGGATCCGAAAGCACAAACCGGT 26 37 1 CGATCCGAGC 0.95146 -67 CACTGATTTTCTTCCAGCGTAAGCTCAGACGCCG 28 83 1 CTCAGCGAGC 0.939408 -167 TAAGTCAAAGCTTGGTGCGAATGCT 29 2 0 CTGTGCGAGC 0.960399 -299 AACGGCGAGGCAGTGACCGTATGCTTTTGAGACC 30 122 1 CGGACCGAGC 0.960732 -179 CGACGTAAGACCGAAATCGGAAGCCAGCGCATGG 31 20 0 CGAATCGAGC 0.905154 -191 CCCCAAAGGTACGCGTGCGCAGGCGAT 32 4 0 AGGTGCGAGC 0.856797 -297 GTTGGTATATGCGGCACCGCATGCACACTTCCTA 32 104 1 GGCACCGAGC 0.829686 -197 GCTGCATATCCTAAAAGCGGaAGCACAAGACTGA 32 244 0 CAAAGCGaGC 0.852254 -57 AGTGCGCGCGCGGAGTGCGAACGCGATTACCAGT 33 16 1 CGGTGCGAGC 0.991243 -108 TACAGACTTGGTTGAAGCGAACGCGCGCGAGTTT 34 42 1 GTAAGCGAGC 0.888751 -51 TTTCATTTCACAGTGATAGCATGCACTCAAAAAT 44 30 0 CGGATAGAGC 0.639218 -41 * * ***** * ** Masking position 11 Map Score: 24.4055 Number of sites scoring better than the average of aligned sites = 255 Number in coding regions = 81 Number in noncoding regions = 174 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AGAAATTGGAGAGTATTTAAACACACGTGGAGG 11 127 0 GATTTTAACA 0.668672 -61 ATTTAACCTGAATTATTTAATAAACAAGCTAAA 37 27 0 AATTTTATAA 0.682595 -110 ATTACTCCTAAAGTCTTAATAAACTTATTGAAT 37 113 0 AATTTAAAAA 0.9018 -24 TCAACAATAAAAATTTTTATAATATACAAAATG 38 34 0 AATTTTAAAT 0.536936 -106 CCGTTTTATCACTTATTTATAAAAAATATATAA 39 21 1 ACTTTTAAAA 0.903227 -153 CCTATAAATTACATTTTTAAAAAACTTCGTGTA 40 19 1 ACTTTTAAAA 0.903227 -96 CTTTTCTTGAAACTATTAATAAAATGGTAGCAA 42 31 0 AATTTAAAAA 0.9018 -37 TATCTTAGTTGATTGTTTAGAAAAAAACAAGTA 48 26 0 GATTTTAAAA 0.836337 -148 TTAATTTAATACCTATTTAAAAAGCAATCGTCT 49 14 0 ACTTTTAAAA 0.903227 -287 ACCAATGTAAAAATATTAAAACAACAAAACTAA 49 169 0 AATTTAAACA 0.783868 -132 AAAGTTGTCAAAATTTTTATAAATACTAACTTA 49 225 0 AATTTTAAAA 0.947305 -76 ATAAACAAAAACCTTTTTATAAACCTATGTCTT 50 104 1 ACTTTTAAAA 0.903227 -145 AATAGGCAATACTTATTTATAAAGAGAAGAATT 50 210 1 ACTTTTAAAA 0.903227 -39 TTAAAATAACAAATATTTAAACAGGAGTATAT 52 15 1 AATTTTAACA 0.87654 -22 GAAAAGCACAAAATATTAAAAAATAAAGCT 53 8 0 AATTTAAAAA 0.9018 -293 AAGCTATTAAAATTTTTTAGAAAAACACGTAGT 53 151 1 AATTTTAAAA 0.947305 -150 TAAAAAAATCAATTTTTTAGAAATTGACCCGCA 53 183 0 AATTTTAAAA 0.947305 -118 CTCTTTAAAAAATTTTTAACAAATTTATTCTTA 53 252 0 AATTTAAAAA 0.9018 -49 TTAAACTTCCAAATATTTAATAATATAAAACGA 60 173 1 AATTTTATAA 0.682595 -111 ATATAAGATAGATTTTTAAAAAAAAATTTTGTA 60 205 1 GATTTAAAAA 0.723023 -79 TTACAATTTAAAATGTTAACACAACTTTATTAT 61 43 0 AATTTAAACA 0.783868 -123 ** * **** *** Masking position 7 Map Score: 19.9129 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 37 Number in noncoding regions = 109 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 5 ATGTATGCAGGGCTCGCCGGTGTGTTGCTAGC 1 59 1 GGCCGCGGTG 0.984281 -47 GTATGCGTACGCGCGGCAGGTGGTGGTATTTG 4 55 0 GCGGGCGGTG 0.843939 -115 CGCGTCTGGTGCATCGCAGGTGCTATGCCACT 5 115 0 GCACGCGGTG 0.981025 -33 TTTCATGGAAGAGATGCAGTTGGACGAGCACT 10 22 0 GAGTGCGTTG 0.525459 -34 AGTGCCGTAAGGCTTGCTGGTTCAAGTCCAGT 12 21 1 GGCTGCGGTT 0.623449 -80 CGCAAACCCTGGCCCGCGGGGCCTTTGCGGCG 12 54 0 GGCCGCGGGC 0.565129 -47 TGTGGAGAATGACGCGCAGTTGAAAAAACTCG 15 163 0 GACCGCGTTG 0.852326 -72 GCTTGTTCACCGCAGGGGAAGCCGCACT 17 7 1 TCACGCGGGG 0.83314 -100 GGGAGTGGATGGCACGCTTTGGTTTACAGAAC 19 189 1 GGCCGCTTGG 0.924622 -74 CGTGCACCGCGTGGTGCACCA 21 4 1 GCACGCTGGT 0.603637 -18 CTTCCACCTTGCATTGCCTGTGGATGCCAGTT 24 40 0 GCATGCTGTG 0.847356 -68 CGGCGTGACGGGCTTGCAGTGGAACCTGATGC 27 59 0 GGCTGCGTGG 0.929558 -32 CCACATCACTGGGCTGCCGGGGCTTTTGATGC 28 23 0 GGGTGCGGGG 0.940905 -227 TTGTTTCTGTTCGACGCTGGGGAAGGTACCCA 28 127 0 TCGCGCGGGG 0.85433 -123 GGTAGCTTTGGCCGTGCGTGTGTTCCTTCAGG 29 222 0 GCCTGCTGTG 0.91914 -79 TACGGTCACTGCCTCGCCGTTGACCGTGCCAC 30 111 0 GCCCGCGTTG 0.98027 -190 GTTCTGTCAAGGCTCGCGGTTGGGGTACGCAA 30 238 1 GGCCGCGTTG 0.967004 -63 GAAAAGAGGAGCGCCGCCTGCGACGTAAGACC 31 42 0 GCGCGCTGCG 0.76465 -169 CGACATGTCCGCAACGCATTGGCGCGGTTACG 31 129 1 GCACGCTTGG 0.90823 -82 TTTAGGATATGCAGCGCTGTGGCAGCCTGCAC 32 263 1 GCACGCGTGG 0.969805 -38 TTTATATTAGGCATTGCCTTTGGGGCACTTAC 33 56 1 GCATGCTTTG 0.722112 -68 *** *** **** Masking position 6 Map Score: 16.5476 Number of sites scoring better than the average of aligned sites = 1071 Number in coding regions = 280 Number in noncoding regions = 791 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TGCAGTGTTCAAAAATAAGGGTGAGACGT 20 84 1 AAAAATAATA 0.841453 -19 GCCACACCCTAAAATAAACGCTTCAAGATTCATATG 28 219 1 AAAATAAATA 0.86314 -31 TGGAACGCCGAAAAAAAAGATTAACAGCCTCTTTAT 32 57 0 AAAAAAAATA 0.918727 -244 TGCCTAATATAAAAAAAAGACTGGTAATCGCGTTCG 33 33 0 AAAAAAAATA 0.918727 -91 TTATTTAATAAAAATAAACTATTTAACCTGAATTAT 37 44 0 AAAATAAATA 0.86314 -93 TTTTTTTTTGCAAAAAAAGCTTTATAATAAAATAGT 39 146 1 CAAAAAAATA 0.605328 -28 AATGTAAACAAAAAATAATGCTTTTATTCTTAAAAA 40 73 1 AAAAATAATA 0.841368 -42 TTTTATTCTTAAAAAGAATAATTGAAATGAT 40 94 1 AAAAAGAATA 0.659931 -21 CATGCACTCAAAAATTAAGACTAACACTGTCATG 44 9 0 AAAATTAATA 0.747539 -62 GAAAATTAAATTTAGTACTTGTTTTTT 48 2 1 AAAATTAATA 0.747539 -172 AAAAACGTTGAAAAATAATCTTATAATGACCTATAA 49 53 0 AAAAATAATA 0.841453 -248 AACTCCAATATAAAAAAATAGTAAAAATCATTTCAT 49 108 0 TAAAAAAATA 0.645991 -193 ATTTTTTTTGAAAAAAAATTGTAAAATTAATATAAG 50 149 0 AAAAAAAATA 0.918727 -100 ATTTTTTTTCAAAAAAAATATTCTTACCTAAGAGAT 50 166 1 AAAAAAAATA 0.918717 -83 GTTAATTCACTAAATAAAAAGTTTTAATCAATAAAA 60 45 1 TAAATAAATA 0.504478 -239 ATAGATTTTTAAAAAAAAATTTTGTAAAATTACTAA 60 212 1 AAAAAAAATA 0.918717 -72 TCACATATTAAAAATAAAGCATAGCAGGGATAGGAC 61 136 0 AAAATAAATA 0.86314 -30 ******** * * Masking position 8 Map Score: 13.9807 Number of sites scoring better than the average of aligned sites = 114 Number in coding regions = 34 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 7 TCTTGCAGGAATGGTAGGGGGAGGACTGTGGGGT 2 72 1 AGAGGGGGGG 0.945274 -45 CAGTGAAAATAGGACAGGGAGCGGGGCATTTATA 4 15 0 AGAGGGAGGG 0.963031 -155 ATGCGTACGCGCGGCAGGTGGTGGTATTTGTACC 4 51 0 GGAGGTGGGG 0.525496 -119 ATTTAAACACACGTGGAGGAATGCACGCTTCTAA 11 112 0 AGGAGGAAGC 0.723022 -76 AGGGTTTGCGGAGCAGAGGAGCGGCGTACACGCC 12 76 1 GGGAGGAGGG 0.969941 -25 GGAAAGAGGAGAGGTTTAAAGCGC 17 93 0 GAGAGGAGGG 0.895997 -14 ATTGTCTTCAAGAGAGAGGTGAGGAAACAGCGCA 19 97 0 AAGAGGTGGG 0.800828 -166 GCGCGCGTGCATGCTCGGGAGTGGATGGCACGCT 19 173 1 AGCGGGAGGG 0.858884 -90 TTGAACAAATAAAGAAAGGGGGGCCCGTTACCGT 22 109 0 AAAAGGGGGC 0.852831 -56 ATGCGTGATGGAGACAAGGAGCGCTATAACGGTA 29 157 0 GGAAGGAGGC 0.957478 -144 GGCCTCCGCAATGAGAAGGAGTGCGACAGACCGT 30 183 0 AGAAGGAGGC 0.970356 -118 TCCGAGGGATGAAAAGAGGAGCGCCGCCTGCGAC 31 50 0 GAGAGGAGGC 0.906253 -161 TAGCCTTTTTAGGGTGGGGGGAGCGCTATACAGA 34 14 1 AGGGGGGGGC 0.968912 -79 TAATAGTTTCAAGAAAAGGAGAGCGTTGATAA 42 46 1 AGAAGGAGGC 0.970356 -22 GAGCACCACCATGGTAAGGTGGGGGTCGTCGGTT 48 105 1 AGAAGGTGGG 0.903527 -69 ACAACTTTTTAAATTGAGGTGTGCATTTTATTAT 49 250 1 AAGAGGTGGC 0.818568 -51 AAATTGTAAGACGCAGGGTAGAGCAGTTGGTAGC 61 67 1 AGGGGTAGGC 0.814161 -99 * * ****** ** Masking position 8 Map Score: 12.2904 Number of sites scoring better than the average of aligned sites = 585 Number in coding regions = 149 Number in noncoding regions = 436 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GAGGATCGGCGGAAGCACGGCCTTGTGCTCGAT 3 100 1 GGAAGCCGCT 0.688389 -42 CTCTGGGGAGGCGCGTCTGGTGCATCGCA 5 129 0 GGAGGCCGCG 0.832644 -19 AGGCGCTGGCGGAAAATGCTCTGCGGCCCAAAA 11 58 0 GGAAAAGCCG 0.899624 -130 CGCTTCTAAGGGAAACAACACCGGAAGGGTAGG 11 88 0 GGAAACACCG 0.959232 -100 ACGGTCTGACGGAAACGGCGCCGGTAATTGCCA 13 61 0 GGAAACGCCG 0.978143 -39 TCACCGCAGGGGAAGCCGCACTGGTACTTAGTT 17 17 1 GGAAGCGCCG 0.979817 -90 AGAGAGGTGAGGAAACAGCGCAAAATCTTGGCA 19 86 0 GGAAACGCCA 0.702861 -177 TGAGTCCCTGGGAAACTAATCCGTAGCCTATAT 19 129 0 GGAAACAACG 0.896314 -134 AGACACGATCGGTAACCACGCTGTCCCATGGGG 19 225 1 GGTAACACCG 0.883978 -38 TGTCCCATGGGGAAAAGCAACGGGTGG 19 246 1 GGAAAACACG 0.767053 -17 TGGAACACAAGGTATCAGAGCCGCTTGCGCTTG 20 53 1 GGTATCGACG 0.569153 -50 GGTAAAACGAGGAAACGAGGCTGA 27 2 0 GGAAACAGCG 0.952955 -89 AGCTTACGCTGGAAGAAAATCAGTGCCATTTTC 28 75 0 GGAAGAAACG 0.652546 -175 CACGCGATGCGGAATCTGGACGGCACTGACAAT 29 35 0 GGAATCGGCG 0.905297 -266 CGATTCTCGGGGAAACCCCACTGTCGAAGTGGA 29 270 0 GGAAACCCCG 0.978143 -31 TAGTTCCAACGGTAGAACGACAGTCTCCAAAAC 47 26 1 GGTAGACGCG 0.73049 -83 TAGAGCAGTTGGTAGCTCGTCGGGCTCATAACC 61 85 1 GGTAGCCGCG 0.931194 -81 ****** ** * * Masking position 2 Map Score: 12.002 Number of sites scoring better than the average of aligned sites = 564 Number in coding regions = 181 Number in noncoding regions = 383 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 ACACCACGCAGAACACGCTCGCGCACGGAA 3 57 0 GAACACGCTC 0.978643 -85 CCGCATCCAACAACACGATCTGCGACACGC 15 109 1 CAACACGATC 0.904984 -126 ACACGATCTGCGACACGCTCGGCAACGCAT 15 121 1 CGACACGCTC 0.972944 -114 ATCTGCACAAGATCACGCTC 15 225 1 GATCACGCTC 0.947912 -10 CAAAACGAGTGAACACGCTTCGGGAATAGT 22 48 1 GAACACGCTT 0.876013 -117 TGCAGAATAGGAACACCCTCGCACGTGAAC 24 13 1 GAACACCCTC 0.974653 -95 TTGGAACTGTCAACACGCTCATTGCTGATA 29 109 0 CAACACGCTC 0.974653 -192 ACGGCCTTGAGAACACCCTTACCGTTATAG 29 138 1 GAACACCCTT 0.855575 -163 AAGGATGCGCCGTCACCATCGACCAGGTCT 30 151 0 CGTCACCATC 0.748421 -150 GGTTACGACCGGTCACCCTCAGTATTCATC 31 154 1 GGTCACCCTC 0.934742 -57 ACATCCTGCGCGACACCATCGCATGCATTT 32 184 0 CGACACCATC 0.881918 -117 ********** Masking position 5 Map Score: 11.3232 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 14 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 10 AGGTCGTGCGCGTTGGCGTGGGGTGCGGCCG 5 34 0 CGTTGCGTGG 0.923674 -114 TTTGGAGTAACGGTTAGGCGGTGTACG 6 7 0 CGGTTGGCGG 0.960483 -48 ATTAAGCAGGCGGTGACGCAGCTTTTTGGAG 6 31 0 CGGTGCGCAG 0.96746 -24 GGCCAGTGTTCGGTTCCGTGGGTACACCCTG 13 15 0 CGGTTCGTGG 0.950423 -85 TGCAGATTCTCGGTGCGGTAGAGGCACGCAC 15 201 0 CGGTGGGTAG 0.904289 -34 AAAATCTAGTCGGTTGCGCGACAACATCTGT 18 60 0 CGGTTCGCGA 0.684563 -49 TTTTGCAAGTCGGTGGAGTAGGAGTAAATGG 22 22 0 CGGTGAGTAG 0.593767 -143 CCTGCGCCGGCGGTTTTGTGGAATGCCTTCG 26 20 0 CGGTTTGTGG 0.860789 -84 AAGCACAAACCGGTTACGTGTCGCAACATCT 26 57 1 CGGTTCGTGT 0.732677 -47 CCCGGCAGCCCAGTGATGTGGTCTGCATGGG 28 34 1 CAGTGTGTGG 0.630228 -216 ACCCAAGTGTCGTTGCGGCGTCTGAGCTTAC 28 101 0 CGTTGGGCGT 0.686869 -149 GTTTATTTTAGGGTGTGGCGGCATGGTGCCA 28 207 0 GGGTGGGCGG 0.841356 -43 CGAATGTGAACGGTGGCACGGTCAACGGCGA 30 99 1 CGGTGCACGG 0.848739 -202 GCACGGTCAACGGCGAGGCAGTGACCGTATG 30 114 1 CGGCGGGCAG 0.679488 -187 TTGCGGAGGCCGATGGTGCGGTATTTGGGTA 30 206 1 CGATGTGCGG 0.70358 -95 GTCCGCAACGCATTGGCGCGGTTACGACCGG 31 135 1 CATTGCGCGG 0.679209 -76 AGTGTGCATGCGGTGCCGCATATACCAACAT 32 102 0 CGGTGCGCAT 0.810052 -199 TATTTTTCAACGTTTTTGTGGTCATAATTGT 49 72 1 CGTTTTGTGG 0.553246 -229 ***** ***** Masking position 4 Map Score: 10.0839 Number of sites scoring better than the average of aligned sites = 1135 Number in coding regions = 351 Number in noncoding regions = 784 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 11 CCGCCACACCCTAAAATAAACGCTTCAAGA 28 217 1 CTAAAATAAA 0.545113 -33 GTTTATTTAATAAAAATAAACTATTTAACC 37 52 0 TAAAAATAAA 0.739195 -85 AAAAAAAGCTTTATAATAAAATAGTGT 39 157 1 TTATAATAAA 0.845314 -17 TTATTCTTTTTAAGAATAAAAGCATTATTT 40 85 0 TAAGAATAAA 0.773892 -30 TTTACCCTTCTTATAATAAAA 46 2 0 TTATAATAAA 0.845314 -22 TTATAATGACCTATAATAAATGTTAATTTA 49 39 0 CTATAATAAA 0.697931 -262 TGCAAATAAATTAAAATAAACAAAAACCTT 50 89 1 TTAAAATAAA 0.739194 -160 AACCTATGTCTTATAATAAAATTACTTATA 50 125 1 TTATAATAAA 0.845314 -124 TATTGCCTATTTATAATAAATCTCTTAGGT 50 191 0 TTATAATAAA 0.845314 -58 TTTAACAAGAATAAAATGGGAAAAA 51 6 1 CAAGAATAAA 0.591356 -27 CTTATTTTAATAAGAATAAATTTGTTAAAA 53 242 1 TAAGAATAAA 0.773892 -59 CTTAGGAGTATAATAATAAAGTAAGAGTTA 60 19 1 TAATAATAAA 0.845314 -265 TTAAATTAATAATAAACAAATAATTG 61 7 1 TAATAATAAA 0.845314 -159 TAATTGACACTCATAATAAAGTTGTGTTAA 61 31 1 TCATAATAAA 0.592079 -135 CCTCACATATTAAAAATAAAGCATAGCAGG 61 144 0 TAAAAATAAA 0.739195 -22 ********** Masking position 5 Map Score: 11.4267 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 11 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 12 CTGCAAGAACCGCCGCAGGAATGGTAAAGAA 2 49 0 CGCGCAGGAA 0.893723 -68 CTGCGGCGGTTCTTGCAGGAATGGTAGGGGG 2 62 1 TCTGCAGGAA 0.771736 -55 GTAACTGACACCACGCAGAACACGCTCGCGC 3 63 0 CCCGCAGAAC 0.956322 -79 GCCTCTCAGGCACCGCGCACAA 9 2 1 CCCTCAGGCA 0.615303 -45 CTCTCAGGCACCGCGCACAACCAGCGCGGGA 9 13 1 CCCGCACAAC 0.63171 -34 GCCGCAAAGGCCCCGCGGGCCAGGGTTTGCG 12 55 1 CCCGCGGGCC 0.859125 -46 AAGAGCACTTCCGCGCAGAACCGTCCTCATT 15 40 1 CCCGCAGAAC 0.956322 -195 ACAAAACCGCCGGCGCAGGATCCGAAAGCAC 26 32 1 CGCGCAGGAT 0.792004 -72 GCCCGTCACGCCGTGCAGAAAGA 27 78 1 CCTGCAGAAA 0.907878 -13 TCAGTCACACCCATGCAGACCACATCACTGG 28 43 0 CCTGCAGACC 0.883199 -207 gGGTAGACGCCCCTGAAGGAACACACGCACG 29 211 1 CCTGAAGGAA 0.641716 -90 GTCCGTGTGTCCTTGCTGGACAGATTACCGC 30 273 1 CCTGCTGGAC 0.890411 -28 TGCGATGGTGTCGCGCAGGATGTGCACGTAC 32 191 1 TCCGCAGGAT 0.711123 -110 ATTCAGCGCCCCGTGCAGGCTGCCACAGCGC 32 276 0 CCTGCAGGCT 0.894968 -25 AAAACCCTGCTGGAAGCCGTTCATA 33 109 0 CCTGCTGGAA 0.85467 -15 TCGTTCTCCGTGCAGGAACGAGGAAACA 34 75 0 CCTGCAGGAA 0.971334 -18 ** ******** Masking position 6 Map Score: 10.3768 Number of sites scoring better than the average of aligned sites = 488 Number in coding regions = 121 Number in noncoding regions = 367 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 CGTTGTATCTCGCACCCGTCAAGCAGAATCTG 3 22 0 CGCACCCGCA 0.974558 -120 AACTGTCGGCCGCACCCCACGCCAACGCGCAC 5 28 1 CGCACCCCCC 0.991969 -120 GCACCTGCGATGCACCAGACGCGCCTCCCCAG 5 124 1 TGCACCAGCC 0.755846 -24 TCCGTCAGACCGTACCCCTCAAGCACTCT 13 81 1 CGTACCCCCA 0.868499 -19 GCGGGCGGTGCGTACCAGGCGATGAAGGATGA 15 81 0 CGTACCAGCA 0.654322 -154 ACGCACCGCCCGCATCCAACAACACGATCTGC 15 100 1 CGCATCCACA 0.617746 -135 GCTGCGCGTACGCACCAGCAACCTGCGCGACA 16 64 1 CGCACCAGAC 0.918243 -86 GATGTTGTCGCGCAACCGACTAGATTTTTTCT 18 63 1 CGCAACCGCA 0.669388 -46 AACTGCACGTACCAATCTCCCAC 23 8 1 CGTACCAACC 0.762424 -16 CAAGAGCTGTTGCACCCGGCGCAG 26 90 1 TGCACCCGCC 0.926181 -14 AGCATTCGCACCAAGCTTTGACTTATTG 29 7 1 CGCACCAACT 0.513484 -294 CCTGGTTGAGCGCATCCATACCTTCGAGCGTA 29 79 1 CGCATCCAAC 0.657582 -222 GGACGCCTTGCGTACCCCAACCGCGAGCCTTG 30 245 0 CGTACCCCAC 0.886984 -56 ATCGCCTGCGCACGCGTACCTTTGGGGGTT 32 9 1 CGCACGCGAC 0.769884 -292 TTTCCCATACCGCACCCATAACTGATCCGAAG 32 155 0 CGCACCCAAC 0.953712 -146 TAATCGCGTTCGCACTCCGCGCGCGCACTGAA 33 13 0 CGCACTCCCC 0.859661 -111 GTCTGTATAGCGCTCCCCCCACCCTAAAAAGG 34 17 0 CGCTCCCCCC 0.903361 -76 AGGAGGGATTCGAACCCCCAGCATACAGTTTT 47 54 0 CGAACCCCAC 0.704618 -55 ******** * * Masking position 2 Map Score: 12.3532 Number of sites scoring better than the average of aligned sites = 468 Number in coding regions = 128 Number in noncoding regions = 340 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 14 AGGCAATGCCTAATATAAAAAAAAGACTGG 33 45 0 TAATATAAAA 0.873993 -79 TATATTAGTATAATATAAAATATATAAATA 35 52 0 TAATATAAAA 0.873993 -45 TAAAATGTTATAATTTTAAA 37 1 0 TAATTTTAAA 0.380137 -136 ATACAATAGATCATATAAAAACTAAGTTTA 37 77 0 TCATATAAAA 0.633957 -60 CAATTTCTTATAATGTAAACAAAAAATAAT 40 62 1 TAATGTAAAC 0.665734 -53 AAAGGTGGGTTAATATTAAAT 41 14 1 TAATATTAAA 0.633015 -11 CATAAAACTCCAATATAAAAAAATAGTAAA 49 119 0 CAATATAAAA 0.83853 -182 ACATTAACACCAATGTAAAAATATTAAAAC 49 180 0 CAATGTAAAA 0.792242 -121 ACATTGGTGTTAATGTAAAATGTGGTGATG 49 194 1 TAATGTAAAA 0.835882 -107 ATGCACACCTCAATTTAAAAAGTTGTCAAA 49 246 0 CAATTTAAAA 0.648669 -55 GAGTATTTTACAATATAAACTACACATAAT 49 279 0 CAATATAAAC 0.670045 -22 CATTAAAAATTAATATAAACTTTACATTAA 53 46 0 TAATATAAAC 0.730625 -255 CTGTCAAATTTCATATAAAATAGTTTAAAC 60 149 1 TCATATAAAA 0.633957 -135 AAATATTTAATAATATAAAACGATATAAGA 60 183 1 TAATATAAAA 0.873993 -101 CTGCGTCTTACAATTTAAAATGTTAACACA 61 53 0 CAATTTAAAA 0.648669 -113 ATATTAGCAGTAATGTTAAATTTTATCATT 62 65 0 TAATGTTAAA 0.55881 -57 ********** Masking position 6 Map Score: 7.28964 Number of sites scoring better than the average of aligned sites = 71 Number in coding regions = 19 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 15 GTCGGTGTCCTTTGGCATGAGCACCTTTCTTTCTTT 2 19 1 TGGAGCACCT 0.977167 -98 CAGCAAGCCTTACGGCACTAGCACCTCGA 12 4 0 TGGAGCACCT 0.977174 -97 TACGAACGGCTCAGGGAGCACCCCCACTACGTGGTG 20 12 1 TGGACCCCCA 0.977789 -91 GCAACGACACTTGGGTACCTTCCCCAGCGTCGAACA 28 116 1 TGGATCCCCA 0.870554 -134 CAGATGCCGATGGGGTAATGGCACCATGCCGCCACA 28 189 1 TGGAGCACCA 0.973809 -61 CCTCGAACTCTCgGGTAGACGCCCCTGAAGGAACAC 29 199 1 TGGAGCCCCT 0.990824 -102 TCATCGATTCTCGGGGAAACCCCACTGTCGAAGTGG 29 271 0 TGGACCCACT 0.836446 -30 GGATGACAATTAAGGTAAGTGCCCCAAAGGCAATGC 33 66 0 TGGAGCCCCA 0.988529 -58 * ** * ****** Masking position 7 Map Score: 4.68942 Number of sites scoring better than the average of aligned sites = 97 Number in coding regions = 40 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467