AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_synecho_ctra_100.orf -o199_synecho_ctra_100.ace -a/home/amcguire/genomes/ORF_synecho.txt -z/home/amcguire/genomes/synecho.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RCT00303 21 Chlamydia_trachomatis RCY41239 17 Synechocystis RCT00768 16 Chlamydia_trachomatis RCT00769 20 Chlamydia_trachomatis RCT00490 17 Chlamydia_trachomatis Input sequences: #1 RCY25702 300 Synechocystis #2 RCY23794 104 Synechocystis #3 RCY53156 108 Synechocystis #4 RCY31741 108 Synechocystis #5 RCY09512 82 Synechocystis #6 RCY38222 137 Synechocystis #7 RCY33689 119 Synechocystis #8 RCY05922 107 Synechocystis #9 RCY14231 101 Synechocystis #10 RCY17023 68 Synechocystis #11 RCY34894 39 Synechocystis #12 RCY03648 59 Synechocystis #13 RCY03870 91 Synechocystis #14 RCY00359 106 Synechocystis #15 RCY25341 23 Synechocystis #16 RCY37057 40 Synechocystis #17 RCY34487 29 Synechocystis #18 RCY46798 32 Synechocystis #19 RCY53151 73 Synechocystis #20 RCY50421 39 Synechocystis #21 RCY31267 300 Synechocystis #22 RCY46651 107 Synechocystis #23 RCY25755 109 Synechocystis #24 RCY40141 87 Synechocystis #25 RCY11977 246 Synechocystis #26 RCY00456 110 Synechocystis #27 RCY08095 101 Synechocystis #28 RCY42619 279 Synechocystis #29 RCY36500 280 Synechocystis #30 RCY02337 187 Synechocystis #31 RCY08595 300 Synechocystis #32 RCY07893 147 Synechocystis #33 RCY44389 59 Synechocystis #34 RCY35764 206 Synechocystis #35 RCY36190 150 Synechocystis #36 RCY49047 96 Synechocystis #37 RCY44729 201 Synechocystis #38 RCY16852 164 Synechocystis #39 RCY50281 225 Synechocystis #40 RCY44485 300 Synechocystis #41 RCY17020 157 Synechocystis #42 RCY50817 112 Synechocystis #43 RCY14811 300 Synechocystis #44 RCY17622 25 Synechocystis #45 RCY16281 94 Synechocystis #46 RCY23988 96 Synechocystis #47 RCY23271 201 Synechocystis #48 RCY11277 49 Synechocystis #49 RCY29451 106 Synechocystis #50 RCT00126 206 Chlamydia_trachomatis #51 RCT00300 24 Chlamydia_trachomatis #52 RCT00301 300 Chlamydia_trachomatis #53 RCT00302 31 Chlamydia_trachomatis #54 RCT00304 22 Chlamydia_trachomatis #55 RCT00305 105 Chlamydia_trachomatis #56 RCT00306 300 Chlamydia_trachomatis #57 RCT00307 300 Chlamydia_trachomatis #58 RCT00308 300 Chlamydia_trachomatis #59 RCT00377 292 Chlamydia_trachomatis #60 RCT00418 41 Chlamydia_trachomatis #61 RCT00419 49 Chlamydia_trachomatis #62 RCT00420 300 Chlamydia_trachomatis #63 RCT00441 300 Chlamydia_trachomatis #64 RCT00442 69 Chlamydia_trachomatis #65 RCT00472 300 Chlamydia_trachomatis #66 RCT00481 65 Chlamydia_trachomatis #67 RCT00482 20 Chlamydia_trachomatis #68 RCT00483 21 Chlamydia_trachomatis #69 RCT00484 55 Chlamydia_trachomatis #70 RCT00485 22 Chlamydia_trachomatis #71 RCT00488 21 Chlamydia_trachomatis #72 RCT00489 27 Chlamydia_trachomatis #73 RCT00493 16 Chlamydia_trachomatis #74 RCT00495 32 Chlamydia_trachomatis #75 RCT00497 18 Chlamydia_trachomatis #76 RCT00499 23 Chlamydia_trachomatis #77 RCT00502 300 Chlamydia_trachomatis #78 RCT00596 300 Chlamydia_trachomatis #79 RCT00853 300 Chlamydia_trachomatis #80 RCT00754 23 Chlamydia_trachomatis #81 RCT00767 137 Chlamydia_trachomatis Motif number 1 TCATGGATTATTCGATCGCCACACTT 1 285 1 TTCGATCGCC 0.918851 -16 GCGGGGCAAAGGTGATAGCCA 14 2 0 GGTGATAGCC 0.825271 -105 GTTAATGAATGGCGATAGCGT 16 2 0 GGCGATAGCG 0.720513 -39 TCAGGAGGATGGCGATCGCCTAGGGTCTAA 22 37 1 GGCGATCGCC 0.499945 -71 TTACCAGGGGGGCGATACCCCCAGA 23 6 0 GGCGATACCC 0.94857 -104 CTTCAGCCCCGGCGATCGCCAAGGGGCATT 25 175 1 GGCGATCGCC 0.499945 -72 ACCCCAAGGAGGTGAAACCCGA 25 235 1 GGTGAAACCC 0.601044 -12 CCGCGGTGGGTTTGATCGCCGTTAATTCAC 27 48 1 TTTGATCGCC 0.675909 -54 CTGGATTGCCGGCAATCCCCCCAGTCAATA 28 242 1 GGCAATCCCC 0.859173 -38 GTCCATGGACTGCAATACCCCTCTGACTCT 29 46 0 TGCAATACCC 0.514422 -235 ATTGCTCCCTGGCGATCGCCAATTTTGGCG 30 87 1 GGCGATCGCC 0.499945 -101 CTTGTTTTTGGTCGAACCCCCGGTTAGGAG 34 179 1 GTCGAACCCC 0.907092 -28 TGGTCGTTAGTTCGATCGCCGGAGGTGAGC 37 23 0 TTCGATCGCC 0.918851 -179 CACGGAGGGATTCGAACCCCCGACCCTCAG 39 103 0 TTCGAACCCC 0.788025 -123 AGGAAAAGTATGCGATCGCCATTTAAAAGT 40 251 1 TGCGATCGCC 0.634608 -50 TTTGGGAGAGGTCGAAACCCTTTGCTGAGA 78 254 1 GTCGAAACCC 0.788024 -47 ********** Masking position 5 Map Score: 17.7016 Number of sites scoring better than the average of aligned sites = 6962 Number in coding regions = 6322 Number in noncoding regions = 640 Number of orfs with sites within 600 bp upstream = 411 Fraction of orfs with sites within 600 bp upstream = 0.0660135 Motif number 2 ACCAATCCCTGGAAAGTGGGTGAGCCATGGCAGA 1 92 0 GGAGGGTGAG 0.876181 -209 CACTTTCCAGGGATTGGTGGAGGGGGAACACCGC 1 108 1 GGTGGGAGGG 0.758047 -193 GTGGGCTTACGGGGTGAAGGGAAGCGTTAGAATT 1 237 0 GGGGGGGAAG 0.933812 -64 AAACAGGACAGGGATGGGGGGAAGA 4 2 0 GGAGGGGAAG 0.974868 -107 GCCGGGGAGAGGTTACCAGGGGGGCGATACCCCC 23 14 0 GGTCGGGGGG 0.900154 -96 TTGGGGTTAGGGAAGGCCGGGGAGAGGTTACCAG 23 29 0 GGAGGGGGAG 0.994122 -81 ATACTCGTTAGGGTGGCCGGGGAGCTAGGGGTTA 29 106 0 GGTGGGGGAG 0.980747 -175 TGTAATGTCTGGGGGGAAGTGGAGACCCTTAGGG 31 94 0 GGGGGTGGAG 0.720182 -207 AACTAACCCAGGGAGGCGTGGGGGCAACTCAACC 34 44 0 GGAGTGGGGG 0.965191 -163 TGCAGATCTAGAAAGGTCGGGGAAAACGTATAGA 34 105 1 GAAGGGGGAA 0.760592 -102 TCTTTCCCAAGGGAAAACGGGAGGCCATTAACAA 34 140 0 GGAAGGGAGG 0.715662 -67 CTAGGCTAATGGAAAGTTGGGAAAG 35 2 0 GGAGGGGAAA 0.908056 -149 GGAAAGTGGGGGGGCGGAGATAAA 37 188 0 GGAGGGGGGG 0.995994 -14 GGGGTATAATGGGACGTTTGGGAATTATTAATTA 38 124 1 GGAGTGGGAA 0.827662 -41 CAAGCAGTGTGATATGATGGGGAGTGCTCAATTT 39 173 1 GAAGGGGGAG 0.925806 -53 AATACCCTCTGGGGGGAAGGGGGATATGGATTTA 40 98 0 GGGGGGGGGA 0.958373 -203 ATGTTCAAGGGGTAAGTAGGGAGACTGACAACTA 41 30 0 GGAGGGGAGA 0.935559 -128 GTTGGAATGATTGGGGACAGTCTAGTT 48 33 0 GGAGTGGGGA 0.875927 -17 TGAAGTCTGGGGTTAGTAGGGCAGCCGGTTTTTG 59 195 0 GGTGGGGCAG 0.887155 -98 ATCCTCAAGAGGAAAGGGGAGGGGAAGAAAAATA 65 209 0 GGAGGAGGGG 0.912298 -92 AGTGTAATTAGGCACCGGGGGCGGTCTGTGAAGC 77 246 1 GGACGGGCGG 0.822054 -55 ** * * ****** Masking position 1 Map Score: 23.653 Number of sites scoring better than the average of aligned sites = 887 Number in coding regions = 787 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 112 Fraction of orfs with sites within 600 bp upstream = 0.0179891 Motif number 3 CTGTTGTTAATTTTTTAGGAGTTCAGTTAC 2 57 1 TTTTTTAGGA 0.972949 -48 ATTCCGCTTTATTTTTAGGAGGTCATTAAC 7 97 1 ATTTTTAGGA 0.861923 -23 TCCGATTTTTTTAGGAAAACGCC 15 7 1 TTTTTTAGGA 0.972949 -17 TGTCTATCGGTATTTTAGGAACAAAGCTGG 21 279 1 TATTTTAGGA 0.767043 -22 TTCCCGTTAGTTTTTCAGGAGGATGGCGAT 22 23 1 TTTTTCAGGA 0.850141 -85 AGTTTCAGTATTTTTAAGGATAAACGG 43 284 1 TTTTTAAGGA 0.870949 -17 TACAAGATAGTTTATTAGGATGAT 50 193 1 TTTATTAGGA 0.767043 -14 GTCACCCTTATTTTTTAGAATGTTAACA 53 9 0 TTTTTTAGAA 0.686457 -23 AGATAGAATGTTTTTTAGGTTTTTTTAGGA 58 281 1 TTTTTTAGGT 0.767043 -20 TTTTTTAGGTTTTTTTAGGA 58 291 1 TTTTTTAGGA 0.972949 -10 AGTCAACTTCTTTTTTAGGAAGCAAGGATT 65 146 0 TTTTTTAGGA 0.972949 -155 TAATTTTTAGGAGAGAGTGTT 68 3 1 ATTTTTAGGA 0.861923 -19 TAAGAAGAGTTTTTTTAGCACTGAGAATCT 78 25 1 TTTTTTAGCA 0.764428 -276 GAGGCGATGTTTTTTAAGGAATAAAATAAG 78 159 1 TTTTTAAGGA 0.870949 -142 AATCAGTCTCTTTTTTAAGAGCCCAAGTAA 79 273 1 TTTTTTAAGA 0.670518 -28 ********** Masking position 7 Map Score: 14.1512 Number of sites scoring better than the average of aligned sites = 39 Number in coding regions = 30 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 GGCGCGGTGTTCCCCCTCCACCAATCCCTGGA 1 113 0 TCCCCCCACC 0.982657 -188 ATTCTAACGCTTCCCTTCACCCCGTAAGCCCA 1 238 1 TTCCCCACCC 0.771606 -63 TCTTCCCCCCATCCCTGTCCTGTT 4 3 1 TTCCCCATCC 0.677177 -106 TGTGCTCGAGTTCCCTTCGTCCATCTACTCTC 14 56 1 TTCCCCGTCC 0.693669 -51 CCCTAGGCGATCGCCATCCTCCTGAAAAACTA 22 30 0 TCGCCCCTCC 0.894435 -78 AGGGTCTAATCCTCCTGCCCCCTTAATTGCCT 22 58 1 CCTCCCCCCC 0.92699 -50 TGGTAACCTCTCCCCGGCCTTCCCTAACCCCA 23 30 1 TCCCCCCTTC 0.966928 -80 GCCTTCCCTAACCCCAACCACCGCAAATTTCC 23 46 1 ACCCCCCACC 0.819851 -64 AAATTCTAAATCCCCAACATTCACTCTGCCCA 28 191 1 TCCCCCATTC 0.775303 -89 AACCCCTAGCTCCCCGGCCACCCTAACGAGTA 29 107 1 TCCCCCCACC 0.982657 -174 CCTAAGGGTCTCCACTTCCCCCCAGACATTAC 31 95 1 TCCACCCCCC 0.881922 -206 GTTGAGTTGCCCCCACGCCTCCCTGGGTTAGT 34 45 1 CCCCACCTCC 0.906652 -162 CTATACGTTTTCCCCGACCTTTCTAGATCTGC 34 106 0 TCCCCCCTTT 0.672154 -101 CCAAAGTATGTTCCCGTCCACCGCTACCAATA 37 55 1 TTCCCCCACC 0.89164 -147 GAGTTATTTATCTCCGCCCCCCCACTTTCC 37 182 1 TCTCCCCCCC 0.968043 -20 AATTAATAATTCCCAAACGTCCCATTATACCC 38 125 0 TCCCACGTCC 0.746972 -40 GGGATTCGAACCCCCGACCCTCAGGACCGGAA 39 95 0 CCCCCCCCTC 0.951776 -131 AAATCCATATCCCCCTTCCCCCCAGAGGGTAT 40 99 1 CCCCCCCCCC 0.988042 -202 GAACTAGTTTTCTCAATCCCTCAGCCGCAGAC 57 94 0 TCTCACCCTC 0.578053 -207 CATTCTTACTTCTCAAACCCCCAAGGAATGTT 59 238 0 TCTCACCCCC 0.851522 -55 ATATTTTTCTTCCCCTCCCCTTTCCTCTTGAG 65 208 1 TCCCCCCCTT 0.767548 -93 TGCTGAGAAAGCCCAATCCTCCGGGTCAGCAC 78 276 1 GCCCACCTCC 0.733934 -25 ***** ***** Masking position 8 Map Score: 20.2181 Number of sites scoring better than the average of aligned sites = 1905 Number in coding regions = 1670 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 216 Fraction of orfs with sites within 600 bp upstream = 0.0346932 Motif number 5 AAGTGGGTGAGCCATGGCAGAGGGCAAATA 1 83 0 GCCATGGCAG 0.853679 -218 TCGTGGCCGTGTCATGGCAAATATTAAATT 6 70 0 GTCATGGCAA 0.542491 -68 TTGCAGTGTTGCCAAAGAAAATCAGGC 6 121 1 GCCAAAGAAA 0.618187 -17 AAAAAAGACGGTCAAGGAAGCAGCTTTGTA 8 78 0 GTCAAGGAAG 0.856606 -30 CCCATTAACATCCAAGGAAATTACT 11 25 1 TCCAAGGAAA 0.878509 -15 GAGATTAGGGGGCAAGGCAATTAAGGGGGC 22 74 0 GGCAAGGCAA 0.841905 -34 ATCAAAAGCTGTCAAGGAAGCAAATCCCCA 25 139 0 GTCAAGGAAG 0.856606 -108 TAGTTCAGTTGCCATGGAAGACACTGTTAT 29 198 0 GCCATGGAAG 0.913086 -83 TGTTGCCATGGAAATTTAACTCAG 32 134 0 GCCATGGAAA 0.91471 -14 GCAATAGGCAAGGCAACATTGATACA 34 7 1 GGCAAGGCAA 0.841905 -200 TGTTTGTGCCTCCAAGGAAAAGTATGCGAT 40 237 1 TCCAAGGAAA 0.878509 -64 AGTTCTGATTTCGAAGGAAAAAATTGAGTT 43 82 1 TCGAAGGAAA 0.527411 -219 TCTTCAAGATCCCAAGGAAAGATTTTTATG 49 84 1 CCCAAGGAAA 0.765119 -23 GGAAATAACTGGCAAGGAAAATAGCTCTTT 63 41 0 GGCAAGGAAA 0.905564 -260 TAAAAGAGTTGCGAAGGAAGAGCCCTAAAC 63 247 1 GCGAAGGAAG 0.822409 -54 TAAGTTTTCTTCCAAGGAAGCTCCACTAGT 77 18 1 TCCAAGGAAG 0.87629 -283 ********** Masking position 4 Map Score: 10.6381 Number of sites scoring better than the average of aligned sites = 1262 Number in coding regions = 1157 Number in noncoding regions = 105 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 6 TCCTCTGACTGAGATAGCGTCGGTCAAGCT 3 57 1 GAGATAGCGT 0.968361 -52 CATAGCCTGGGAGAGAGCGATAATAGGTTA 9 34 1 GAGAGAGCGA 0.979996 -68 TTAATGAATGGCGATAGCGT 16 1 0 GCGATAGCGT 0.877316 -40 CCTTGGGAAAGAGAGAGCTTGTTTTTGGTC 34 162 1 GAGAGAGCTT 0.968362 -45 CATCATACAAGAGAGAGCGTTGGACTATTT 43 241 0 GAGAGAGCGT 0.989406 -60 CCGGAAACTCGAGAGAGCGATTATATCGAC 58 183 0 GAGAGAGCGA 0.979996 -118 TAACCTGGCCGAGAGAGCTTCCTTTACCAA 65 259 1 GAGAGAGCTT 0.968362 -42 TAATTTTTAGGAGAGAGTGTT 68 11 1 GAGAGAGTGT 0.901531 -11 CCAATAACTAGAGATAGCTACTCTATAAGA 81 87 0 GAGATAGCTA 0.840303 -51 ********** Masking position 6 Map Score: 9.89596 Number of sites scoring better than the average of aligned sites = 19 Number in coding regions = 13 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 7 TACTAGTTTATTTGCCCTCTGCCATGGCTCACCCACT 1 75 1 TTTTTGCTGG 0.643382 -226 TTATTAATTTGACGGTGGCAAAGGTAAAAAATTA 6 8 1 TTTGGGCAGG 0.981678 -130 GGAGATGGAATTTTCACTTAGTAAAGGCTTGGGGCCT 10 16 0 TTTTAGTAGG 0.591162 -53 TTTAGTCGCGGCTCAGGGTGATTGGTC 13 1 1 TTTGGGCAGG 0.981678 -91 TTATTTACACTTTTATTTAGGTAGAGGGTTACCGTGT 21 245 1 TTTTGGTAGG 0.919539 -56 GGGAGCAATTTTTACCTGGGGCAATGGACAGAAAGGC 30 59 0 TTTGGGCTGG 0.968313 -129 AATCTCTAGGTTTTGCTTGGACAATGGGGTATAATGG 38 99 1 TTTTGACTGG 0.744919 -66 GGTATTGTACTTTTCAAGCGGCCAAGGTTAAGTAGAA 40 126 1 TTTGGGCAGG 0.981678 -175 AATAAATTTTTTTACCTTTGACCATGGGAAGAAAACA 40 190 1 TTTTGACTGG 0.744919 -111 CTGCACCACTTTTGTCTGCGGCTGAGGGATTGAGAAA 57 81 1 TTTGGGCAGG 0.981678 -220 TGCTTCCTCTTTTGTGCTAAGCCCAGGTAGCTCAGTG 57 174 1 TTTTAGCAGG 0.847972 -127 AAGAGCCCCTTTTTCAAGAGGCTCTTGCTTAAGGAAG 59 25 0 TTTGGGCTTG 0.650368 -268 TTCGTATTTCTTTTCTTTAGGTTTAGGGAACCAGC 61 9 0 TTTTGGTAGG 0.919539 -41 GAGGATTATTTTTATGGTTGGTAAAGGAAGCTCTCTC 65 269 0 TTTTGGTAGG 0.919539 -32 *** * *** *** Masking position 3 Map Score: 9.13573 Number of sites scoring better than the average of aligned sites = 365 Number in coding regions = 339 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 8 GACAGTTAAATTTTTTGCTAACAGCTTTTTTGAGCAAA 3 11 1 TTTTTAAATT 0.924315 -98 GCTAGTCATGGTTTTAGCGAATAACAGTGTCTTCCATG 29 178 1 GTTTTAAAGT 0.635064 -103 GACAACAGGTGTTTTGCCAAACTTGTTTGGAGGAGAAT 31 163 0 GTTTTAATTT 0.669261 -138 TAGGAAAGGCTTTTTTTATAAGAACCTTTCGTTCAATA 50 56 0 TTTTTAAATT 0.924315 -151 CGTATAAAATTTTTTCGATAAAAGATTTTAATTAGGAA 50 88 0 TTTTTAAATT 0.924315 -119 AGTTTTTATTTTTTTTCGAAACAGAAGTCGTATAAAAT 50 116 0 TTTTTAAAGT 0.795802 -91 GCTGCTTGTTTTTTTACAAAAGATACTTTCTTAAGAAA 56 83 0 TTTTTAAATT 0.924315 -218 CGTCAAGATTGTTTTGATGAATATTTTTGGCTTTGGAT 56 190 1 GTTTTAAATT 0.845039 -111 TTTCCTTCTGTTTTTTGACAAGTTGTTTGACATTTTCT 58 140 1 TTTTTAATTT 0.819225 -161 TCTTGCAGCTTTTTTTTAAAAAATCCTTCTCCTCTCTT 59 58 1 TTTTTAAATT 0.924315 -235 GTTTTCAAGTTTTTGAACTAACAGTATTCGAAGAAAAC 62 64 1 TTTTGAAATT 0.715986 -237 ATTTAACTCTTTTTTTATTAATTATTTTTAGGGAAGGC 62 117 1 TTTTTAATTT 0.819225 -184 GGGAAGGCTTGTTTTAAGAAAATCTTTTGGAGGAAATG 62 147 1 GTTTTAATTT 0.669261 -154 GGAGGAAATGTTTTTTAATAAAATTGTTATAGAGATCG 62 175 1 TTTTTAAATT 0.924315 -126 CACGAGAGTTTTTTTTTTGAAAAGCATAAGAGTCAGAA 65 110 1 TTTTTAAATA 0.619737 -191 AAATAACAATTTTTGACCTAAGATGCTTATATTACTTT 69 12 1 TTTTGAAATT 0.715986 -44 TGAGATTTTTTAAATAAGAAGAGTTTTTTTAGCA 78 7 1 TTTTTAAAGT 0.795802 -294 GAGGCGATGTTTTTTAAGGAATAAAATAAGGACTGAAC 78 159 1 TTTTTAAATA 0.619737 -142 AAACTGATTATTTTTCAGTAACTTTTTTTCAAAAAGTG 81 31 0 TTTTTAATTT 0.819225 -107 ***** ** * ** Masking position 4 Map Score: 10.3959 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 56 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 TCGAGGTTTGCCATTGACCATGAAGTTTGTAA 1 204 0 CCATTGCCAG 0.980661 -97 TAATTTTTTACCTTTGCCACCGTCAAATTAAT 6 13 0 CCTTTGCACG 0.617119 -125 ATAGGTTGCTCCATTGGCCAACCTATGCTCGT 7 26 0 CCATTGCCAC 0.962884 -94 TGGCTATCACCTTTGCCCCGCAAGCAATGCT 14 10 1 CCTTTGCCCC 0.926031 -97 GCTCGAGTTCCCTTCGTCCATCTACTCTCTGA 14 59 1 CCTTCGCCAC 0.779349 -48 GCGGCAATAACCTTTGGTCAACAGCTTCATAG 21 175 0 CCTTTGTCAC 0.816794 -126 GCCTTTCTGTCCATTGCCCCAGGTAAAAATTG 30 59 1 CCATTGCCCG 0.965927 -129 CCATTATACCCCATTGTCCAAGCAAAACCTAG 38 104 0 CCATTGCCAG 0.980661 -61 TCGAGCTTCCCCATTGGTCTTGGTTTTAAATA 40 18 1 CCATTGTCTG 0.586869 -283 AATTTTTTTACCTTTGACCATGGGAAGAAAAC 40 194 1 CCTTTGCCAG 0.977665 -107 CGGCCAATGACCAGGGGCAGATTTT 45 4 1 CCAATGCCAG 0.843661 -91 GTAATTAATCCCTTTGTTCATGTATGCTAGAT 59 107 1 CCTTTGTCAG 0.897061 -186 AGGTCATATACCATTGCCCATTCGCCGCCTTT 77 138 1 CCATTGCCAT 0.832531 -163 ****** *** * Masking position 2 Map Score: 10.0989 Number of sites scoring better than the average of aligned sites = 682 Number in coding regions = 613 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 10 CAATAAATTTATGGAGTAGGGTTTAAGACAGACC 5 36 0 ATGGTGGTTT 0.717067 -47 CTCCCAGGCTATGGGGAAGGATTTTGGTTACCAT 9 13 0 ATGGAGGTTT 0.810172 -89 GAATTTTCACTTAGTAAAGGCTTGGGGCCTTCAG 10 12 0 TTAGAGGTTG 0.821862 -57 TGAAAGCTTTTTAGTCATGGATTTGGTAACTCCT 26 81 0 TTAGAGGTTT 0.911757 -30 GGACAGGCTTTTGGTAAAGGTTCGACTATGGGAT 29 72 1 TTGGAGGTCG 0.466285 -209 TTGGTGTCAGCTAGTCATGGTTTTAGCGAATAAC 29 169 1 CTAGAGGTTT 0.720665 -112 GACAACTAGCGACGGCTTTGGATATGTTG 31 6 1 CTAGAGGTTT 0.720665 -295 TTTCTTATACTTGGAATAGTTTTTCGGTGGGACA 31 197 0 TTGGTGTTTT 0.578587 -104 CATGATGTAGTTGGTGTTGGGTTGGTTACGGTAA 32 27 1 TTGGTGGTTG 0.830294 -121 GGAACATACTTTGGCTTGGTCGTTAGTTCGATCG 37 35 0 TTGGTGTGTT 0.380063 -167 AGCTTCCCCATTGGTCTTGGTTTTAAATAACTTT 40 21 1 TTGGTGGTTT 0.916366 -280 AAGATTTTAATTAGGAAAGGCTTTTTTTATAAGA 50 71 0 TTAGAGGTTT 0.911757 -136 ATGAATATTTTTGGCTTTGGATTTTCCATCTATT 56 206 1 TTGGTGGTTT 0.916366 -95 GCAACATCTCTTAGAAATGGTGTTTATGCCATAA 59 156 0 TTAGAGGGTT 0.821862 -137 TTAATTATTTTTAGGGAAGGCTTGTTTTAAGAAA 62 134 1 TTAGAGGTTG 0.821862 -167 TGCTGAAGACTTGGCTATGTTTTTTATTTTGACG 63 195 1 TTGGAGTTTT 0.698074 -106 GTTTTCTTGGTTAGAGACGGGGTTTTTAGACAGT 65 173 0 TTAGAGGGTT 0.821862 -128 TTATAGCTAAGGAGTTTGGG 67 3 1 ATAGAGGGTT 0.516246 -18 TTTGCGATTTTTGGTGTGGGATTTCTTAGCGTCA 77 78 1 TTGGTGGTTT 0.916366 -223 **** * ** *** Masking position 2 Map Score: 10.4421 Number of sites scoring better than the average of aligned sites = 792 Number in coding regions = 726 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 11 ATGGCTCACCCACTTTCCAGGGATTGGTGGAGG 1 98 1 CACTCCGGGA 0.778395 -203 TTAATGCTTCCCCTCAGTGGGGAGAGTTAATTT 6 42 1 CCCTGTGGGA 0.869417 -96 AAATCCTTCCCCATAGCCTGGGAGAGAGCGATA 9 23 1 CCATCCGGGA 0.885285 -79 AGTGAAAATTCCATCTCCTGTGAACTTAATTTT 10 35 1 CCATCCGTGA 0.784697 -34 TGACCAATCACCCTGAGCCGCGACTAAA 13 6 0 CCCTGCGCGA 0.944743 -86 AATTTTGTTCCTTCAGCAGTGACGGATAAAAA 20 18 0 CCTTGCGTGA 0.865836 -22 GGCGATCAAACCCACCGCGGGGAGCGAGAATTT 27 35 0 CCCAGCGGGA 0.949986 -67 GCCTAGCCGCCCCTGTCCAGTGAAGGTGTAGCT 35 30 1 CCCTCCGTGA 0.969117 -121 AAGTACAATACCCTCTGGGGGGAAGGGGGATAT 40 105 0 CCCTGGGGGA 0.907986 -196 AGTTCACTGTCCCATGGCGGGGATGTGATGTTC 41 58 0 CCCAGCGGGA 0.949971 -100 TTTCCCTGGTCTGTGAACATTTTCCT 46 4 1 CCCTTCGTGA 0.895401 -93 GTGAATTTTTCCCTGGGCAGTCAGTCTAGGGTG 47 130 1 CCCTGCGTCA 0.895567 -72 TATCCCCTATCCTGTCATTAGTATCAC 50 5 1 CCCTCCGTCA 0.828855 -202 GGGGTACGCGTCCTTAGCAGGGACGTACTTTCG 65 16 1 TCCTGCGGGA 0.861446 -285 GAGGTCGAAACCCTTTGCTGAGAAAGCCCAATC 78 261 1 CCCTGCGAGA 0.920228 -40 TGTTAATCCTCCTTTATCCGGGAAGGCTCTTGT 79 44 1 CCTTTCGGGA 0.677989 -257 **** ** **** Masking position 13 Map Score: 13.3718 Number of sites scoring better than the average of aligned sites = 387 Number in coding regions = 352 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 12 GCCCAGCTTTGTTCCTAAAATACCGATA 21 283 0 CCCGCTTTCA 0.857235 -18 AAATTTCAGACCCTTCATTGTACGATATTTATCGGCC 31 266 0 CCCTCTTTCA 0.905544 -35 TTGGGCTGACCCTTTCATCTTGCGAAAAGAATTCACA 39 18 0 CCTTCTCTCA 0.987291 -208 CTTTTCTTGCCCTATCATCATACAAGAGAGAGCGTTG 43 249 0 CCTTCTCTCA 0.987289 -52 TTCGAAAGTCCCTTTCATTGTTCGGTAAAGTAACAAG 56 255 1 CCTTCTTTCA 0.944899 -46 AGCTGCAGCACCTGTTGTCCTCCGGAAACTCGAGAGA 58 197 0 CCTTTTCTCA 0.847883 -104 AAATCCTTCTCCTCTCTTCTTTCTTAAGAGTAATTAA 59 78 1 CCTTCTCTCA 0.987291 -215 TTCGCTTTTACCTCTCTTCTTGCTGAAGACTTGGCTA 63 175 1 CCTTCTCTCA 0.987291 -126 GAGTCAGAATCCTTGCTTCCTAAAAAAGAAGTTGACT 65 139 1 CCTGCTCTAA 0.777335 -162 GTTATTCTTCTCTTCCTTCTTTA 76 1 0 CTTTCTCTCA 0.847883 -23 AACGGCCATGCCCTCCATCCTGCAAGAGCGATTTCCA 77 202 0 CCCCCTCTCA 0.910288 -99 TAAGCATTGACCTTGCTTCTTCCAATAACTAGAGATA 81 101 0 CCTGCTCTCA 0.979861 -37 *** ** ** * * * Masking position 17 Map Score: 9.2463 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 44 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 GCAGCTTTGTAAGCTTTCCCTAACCGCAGTG 8 58 0 AAGCTTTCCT 0.915085 -50 CGTTTCAATCAAGCTTTGCTTGAGAGACCAC 21 110 0 AAGCTTTCTT 0.818756 -191 GGTAACAGAGTAACTTTGCCTTTCTGTCCAT 30 42 1 TAACTTTCCT 0.545691 -146 TGGCGATCGCATACTTTTCCTTGGAGGCACA 40 241 0 ATACTTTCCT 0.833336 -60 AAAAATACTGAAACTTTTCTTGCCCTATCAT 43 268 0 AAACTTTCTT 0.846664 -33 ATATAGTTACATACATTTCTTGTGATACTAA 50 28 0 ATACATTCTT 0.427951 -179 CTTATAAAAAAAGCCTTTCCTAATTAAAATC 50 72 1 AAGCCTTCCT 0.857642 -135 CCAATACCTTAAACTTGTCCTCCTTAGACTC 58 34 0 AAACTTGCCT 0.640319 -267 ATGTCAAAAGATACTTTTCCTTCTGTTTTTT 58 125 1 ATACTTTCCT 0.833336 -176 CAAGATGCAAAAACATTCCTTGGGGGTTTGA 59 227 1 AAACATTCTT 0.662515 -66 TTCTTAAAACAAGCCTTCCCTAAAAATAATT 62 136 0 AAGCCTTCCT 0.857642 -165 TTTTATTAAAAAACATTTCCTCCAAAAGATT 62 167 0 AAACATTCCT 0.823474 -134 GAAGAGCCCTAAACTTTTCTTATCATCTTCT 63 263 1 AAACTTTCTT 0.846664 -38 AAACTTTACCTAAAAGTTCTA 70 12 0 AAACTTTCCT 0.929183 -11 AATATGCCTTACTTGGGCTCTTAA 79 287 0 ATGCCTTCTT 0.491393 -14 ******* *** Masking position 6 Map Score: 6.61692 Number of sites scoring better than the average of aligned sites = 146 Number in coding regions = 115 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 AGTCATTTGTTTTTGGTTTGTCTAATCAGATT 24 37 1 TTTTTTTGTC 0.932651 -51 TAAAATAAGATTTTTATTTCTCAGCTACGCCC 28 120 1 TTTTTTTCTC 0.726942 -160 CCTCGATATTTTTTATTTTTTCGATCCTGTTG 28 150 1 TTTTTTTTTC 0.896395 -130 TTTAAATAACTTTTGGTTTGTCCAACTGCCCT 40 42 1 TTTTTTTGTC 0.932651 -259 GAAATTGTGCTTTTAATTTTTCCAATGTTGAA 40 160 1 TTTTTTTTTC 0.896395 -141 CAGCCATATCTTTTGATTTTTCACAGTAAGAG 41 124 1 TTTTTTTTTC 0.896395 -34 TCCTCGTGTCTTTTCTTTTTTCTGGCTTGCAT 43 140 0 TTTTTTTTTC 0.896395 -161 GTACACGAGTTTTTATTTTTTTTCGAAACAGA 50 129 0 TTTTTTTTTT 0.522603 -78 TAATTTAACTTTTTCGTTTTTCCCCCTCGTTT 55 51 1 TTTTTTTTTC 0.896395 -55 ACAAATATTTTTTTAATTTGTTTACAAGCAAA 58 68 0 TTTTTTTGTT 0.636643 -233 TGGCTATGTTTTTTATTTTGACGATAAACCTA 63 206 1 TTTTTTTGAC 0.595743 -95 AAGGAGCCGCGTTTTCTTTGTCGTGGAAATCG 77 179 1 GTTTTTTGTC 0.685946 -122 GAATGCTCTTTTGTATTTTGTCAAGCGCGGGG 78 90 1 TTGTTTTGTC 0.685946 -211 **** ****** Masking position 7 Map Score: 6.70827 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 71 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 15 TCACCGTCGGATTTGCTTCCATTGGTGCAT 1 36 1 ATTTGCTTCC 0.827856 -265 AATTTTGTTCCTTCAGCAGTG 20 29 0 ATTTTGTTCC 0.876529 -11 TTTGTTGGGGATTTGCTTCCTTGACAGCTT 25 134 1 ATTTGCTTCC 0.827856 -113 GGGAGCGAGAATTTACTTCCAATCTCCCAC 27 19 0 ATTTACTTCC 0.638091 -83 GGTCTGAAATTTTTTGTTCC 31 291 1 TTTTTGTTCC 0.762723 -10 CGCTCCTAATGTTTTCTTCCCATGGTCAAA 40 206 0 GTTTTCTTCC 0.908087 -95 TTCTTAAGAAATTTTCTTCGGTGATCTTGC 56 64 0 ATTTTCTTCG 0.812873 -237 CTGATAAAATGTTTTCTTCGAATACTGTTA 62 82 0 GTTTTCTTCG 0.755676 -219 TAGTTCATTCTTTTTGTTCGTTTCT 64 55 1 TTTTTGTTCG 0.50157 -15 GAAAACGATATTTTTCTTCCCCTCCCCTTT 65 201 1 TTTTTCTTCC 0.862698 -100 AGCGTTATAAGTTTTCTTCCAAGGAAGCTC 77 11 1 GTTTTCTTCC 0.908087 -290 TTCAGTCCTTATTTTATTCCTTAAAAAACA 78 166 0 ATTTTATTCC 0.576334 -135 AAAAGGGTAAATTTTGTTCCTCTAGTTGTT 79 18 1 ATTTTGTTCC 0.876529 -283 ********** Masking position 4 Map Score: 6.82127 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 183 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 42 Fraction of orfs with sites within 600 bp upstream = 0.0067459