AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i210_synecho_ctra_300.orf -o210_synecho_ctra_300.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 Input sequences: #1 RCY46971 127 Synechocystis #2 RCY52434 262 Synechocystis #3 RCY14336 151 Synechocystis #4 RCY52311 104 Synechocystis #5 RCY11783 300 Synechocystis #6 RCY30106 164 Synechocystis #7 RCY08201 100 Synechocystis #8 RCY53401 171 Synechocystis #9 RCY46834 124 Synechocystis #10 RCY13164 111 Synechocystis #11 RCY00205 96 Synechocystis #12 RCY15170 266 Synechocystis #13 RCY30644 193 Synechocystis #14 RCY15530 257 Synechocystis #15 RCY50074 106 Synechocystis #16 RCY01064 148 Synechocystis #17 RCY25844 58 Synechocystis #18 RCY07234 110 Synechocystis #19 RCY40897 73 Synechocystis #20 RCY05266 273 Synechocystis #21 RCY32230 204 Synechocystis #22 RCY20293 90 Synechocystis #23 RCY09345 70 Synechocystis #24 RCY43126 111 Synechocystis #25 RCT00092 37 Chlamydia_trachomatis #26 RCT00095 117 Chlamydia_trachomatis #27 RCT00096 300 Chlamydia_trachomatis #28 RCT00805 28 Chlamydia_trachomatis #29 RCT00806 252 Chlamydia_trachomatis Motif number 1 AAAGGTTGATCACCGGGGAAATGGGCCTTGTC 1 27 0 CCGGGGAAAT 0.666525 -101 CAAGGGGAAGGGATGGGGGAATTTTGCATAAA 2 210 0 GAGGGGGAAT 0.953284 -53 TTGATGAATTGCCAAGGGGAAGGGATGGGGGA 2 222 0 GCAGGGGAAG 0.97481 -41 ACCACCTACGGGTATGGGAAAAGACCGGAATG 3 83 0 GTTGGGAAAA 0.677119 -69 GATACTAGGGGGATGGGGAAAGAAATCGACTG 3 130 0 GAGGGGAAAG 0.921852 -22 GATTAATGGGGGAGTGGGGAGATTAGGTCGGA 4 19 1 GATGGGGAGA 0.785578 -86 GATTGGGGCAGACCGCACCGTT 4 93 0 GTGGGGCAGA 0.922164 -12 CCATGGTGATGGATAGGGAAAGGGTTTATGGC 5 58 0 GAAGGGAAAG 0.886927 -243 TGGATCATTAGTCAGGGGGACAGTGG 5 285 1 GCGGGGGACA 0.896505 -16 AACCAAAGACGTTGGGGGGCAAATCATTCCAG 6 24 0 GTGGGGGCAA 0.903749 -141 TTTCCATCACGAAAAGGGAAAGTTATCGACAA 6 54 0 GAAGGGAAAG 0.886927 -111 GGCAGAGTCAGCCCAGGGGACAAAAACTTCCT 7 62 0 GCAGGGGACA 0.852071 -39 AGAAAAGGGGAAAATTCCCAATA 8 159 0 GAAGGGGAAA 0.950977 -13 AATCCTCAGCCCTGGGGGGAAACTGTCC 9 107 1 CTGGGGGAAA 0.818038 -18 AGGGTATTTAGCCTGGGGCAGTATGGGGCAAC 10 48 1 GCGGGGCAGT 0.936204 -64 AGCCAGAGTACCCTAGGGGAGAGCGAGTAAAT 12 107 0 CCAGGGGAGA 0.768489 -160 GGGTACTCTGGCTTTGGGAAAGGGTAAATGGG 12 126 1 GTTGGGAAAG 0.7026 -141 AAGGGCGATCGCCGTGGGCCGGCCTTGGCTTG 13 87 0 GCTGGGCCGG 0.60372 -107 AGTGGCTTGGGGCAGAATTGTGCATA 13 178 0 GTGGGGCAGA 0.922164 -16 TGGCGATCGGGGCAAGCTCAAGCCGA 14 5 1 GTGGGGCAAG 0.955126 -253 CCACGACTGTGGATGGGGGAAGCAACCATCTG 14 72 1 GAGGGGGAAG 0.970471 -186 ATTTAAGCTAGTCGAGGGCAGTTAGACCCCTC 15 17 0 GCAGGGCAGT 0.907047 -90 AAAACTAATCGGTCAGGGCAAAAAAATCGTTA 16 105 0 GTAGGGCAAA 0.926272 -44 CACAGGACGAGGATGGGGCCATTAGAGCACAG 20 43 1 GAGGGGCCAT 0.809651 -231 GTGGAACTTTGACCGGGGGAATAGAGTTTAAT 20 173 1 GCGGGGGAAT 0.973072 -101 GAGAAGGATGGCCCAGGGCCATGTTCTGCTAG 21 116 1 GCAGGGCCAT 0.833571 -89 CCAATGGCTAGGCGAGGGAAATATTACCAGGG 22 19 0 GCAGGGAAAT 0.896099 -72 CTAGCCATTGGTAGAGGGGAATGCCAAAATGA 22 40 1 GAAGGGGAAT 0.931361 -51 CCTAACCATAGGGGAAACCGTCTACCG 23 6 1 CAAGGGGAAA 0.749333 -65 AATTGCTGGAGTTAAGGGGCGGCCACCAAAAA 24 82 0 GTAGGGGCGG 0.815172 -30 TCCTCTTATGGGTAAGGGAAAAAAAGCAAAAA 26 90 0 GTAGGGAAAA 0.874416 -28 * * ******** Masking position 6 Map Score: 39.4359 Number of sites scoring better than the average of aligned sites = 4027 Number in coding regions = 3560 Number in noncoding regions = 467 Number of orfs with sites within 600 bp upstream = 461 Fraction of orfs with sites within 600 bp upstream = 0.0740443 Motif number 2 GACACCCGGTGGACAAGGCCCATTTCCCCGGT 1 16 1 GGCAAGCCCA 0.778988 -112 GGAATCGAACGGGAAAAGCTCCTCGGGTTAGA 2 176 0 GGAAAGCTCC 0.596356 -87 TACGGGTATGGGAAAAGACCGGAATGCCAAAA 3 77 0 GGAAAACCGG 0.869532 -75 GCTTTCTTGGGGACAATGCCCCTGGAAAAAGC 5 188 1 GGCAAGCCCC 0.934331 -113 AGCAAAGCCAGGCAGAGTCAGCCCAGGGGACA 7 72 0 GGAGATCAGC 0.893234 -29 AGAAAAGGGGAAAATTCCCAATAACAACAA 8 152 0 GGAAATCCCA 0.78183 -20 GGGCAGTATGGGGCAACTCAGGCTAAACTACA 10 63 1 GGCAATCAGG 0.952138 -49 TCGGTAAAATGGCAAAGTCAGCATTTTCGCTT 12 52 0 GGAAATCAGC 0.963259 -215 CCGTTGTTCCGGAAAATTCAGCAGGTTGATAG 13 14 1 GGAAATCAGC 0.963237 -180 GAGCAGATCAAGCCAAGGCCGGCCCACGGCGA 13 79 1 AGCAAGCCGG 0.694839 -115 AGGAAAACGGGGTAAAATCAGCAAGTATTCCT 13 147 1 GGAAATCAGC 0.963249 -47 CGTCAACGATGGGAGAATTCGGCTTGAGCTTG 14 23 0 GGAGATTCGG 0.579587 -235 CATCGTTGACGGCAAAGGCAGATCTAAACCAC 14 44 1 GGAAAGCAGA 0.893809 -214 AACTGCTCCGGGAAATTTCAGGTAAATCACGC 14 138 1 GGAATTCAGG 0.652263 -120 GTGACGATTTGTAAAAATCCGCCCAATTTTTA 14 216 1 GTAAATCCGC 0.698365 -42 GGTTAGGGTTGGCCAAGTCCGCTCCCCAGTGT 18 43 0 GGCAATCCGC 0.975491 -68 TGGGGCCGATGGGAGAAGCCGGAGGAGAAGGA 21 92 1 GGAGAGCCGG 0.955936 -113 TCTTTTCAACGGCCAAAGCAGGCGATCGCCAA 24 35 1 GGCAAGCAGG 0.962664 -77 TGTCGTTTGCGGAAAAAGTCGGGTTGGTTATA 27 30 0 GGAAAGTCGG 0.848468 -271 ** *** ***** Masking position 6 Map Score: 17.0155 Number of sites scoring better than the average of aligned sites = 1933 Number in coding regions = 1782 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 169 Fraction of orfs with sites within 600 bp upstream = 0.0271442 Motif number 3 TACCCGACACCCGGTGGACAAGGCCCATTT 1 10 1 CCCGGGGACA 0.853012 -118 CATTGACGAACCCTGGGCCGACCAAAGGTTG 1 51 0 CCCTGGCCGA 0.992687 -77 TCGGGTTAGAATCTGGGGAGATTGATGGGGC 2 155 0 ATCTGGGAGA 0.503849 -108 TGCGTATCTACTCTGCGTCCAGTTTAGCAAA 4 63 0 CTCTGGTCCA 0.607338 -42 TCTCACCACTCCCTGAGGCGCTGCCATAAAC 5 36 1 CCCTGGGCGC 0.983384 -265 ACCATGGATGCCCTCTGCCGAAACTTACCCA 5 83 1 CCCTCGCCGA 0.942338 -218 TGGAAAGGAGCCCTCCGGCAAACGTGATATA 6 80 1 CCCTCGGCAA 0.846377 -85 AGTCTCTGTGGAAAAAACCTAGGC 6 151 0 CTCTGGGAAA 0.850226 -14 AGTTTTTGTCCCCTGGGCTGACTCTGCCTGG 7 66 1 CCCTGGCTGA 0.906887 -35 TAATCCTCAGCCCTGGGGGGAAACTGTCC 9 106 1 CCCTGGGGGA 0.951744 -19 CCTGAAATTTCCCGGAGCAGTTATCCTGAGA 14 129 0 CCCGGGCAGT 0.71325 -129 GACGTTCAACCCCTGAGGCAATCCAGTGGGG 14 169 0 CCCTGGGCAA 0.978615 -89 AAGTTCCGTGGCCTGGGTCGATCAAACTTTT 15 73 1 GCCTGGTCGA 0.738571 -34 TCTCTTGCTACACTGGGGAGCGGACTTGGCC 18 34 1 CACTGGGAGC 0.603835 -77 TCCCGACAACCCTGAGCCGACAATTATGCA 20 10 1 CCCTGGCCGA 0.992687 -264 AAACCTCCAGCTCTGCGCCCAAATATGCTCC 20 139 1 CTCTGGCCCA 0.89947 -135 AAATATGCTCCTCTGTGGAACTTTGACCGGG 20 159 1 CTCTGGGAAC 0.64432 -115 GATGGGAGAAGCCGGAGGAGAAGGATGGCCC 21 99 1 GCCGGGGAGA 0.74286 -106 CAGAACATGGCCCTGGGCCATCCTTCTCCTC 21 113 0 CCCTGGCCAT 0.825893 -92 CTTAGCAGTTCCCTTTGGCGATCGCCTGCTT 24 50 0 CCCTTGGCGA 0.891141 -62 AGTTTTTTTTCTCTGTGCAGAGAAATATAAG 29 146 0 CTCTGGCAGA 0.943942 -107 ***** ***** Masking position 7 Map Score: 22.3787 Number of sites scoring better than the average of aligned sites = 1650 Number in coding regions = 1536 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863 Motif number 4 CTTGTCCACCGGGTGTCGGGTA 1 2 0 GGGTGCGGGT 0.755455 -126 AGGGCGATGGAAAAAGGGTTTG 2 2 1 GGGCGTGGAA 0.94606 -261 AATGTCAGGCGGCGTTTGGGTACGCAGTCTC 2 49 1 GGCGTTGGGT 0.708901 -214 GAGCAGGGGGATGTTTTCCTTGATGA 2 247 0 GGGGGTGTTT 0.776168 -16 GATACTAGGGGGATGGGGAAAGAAATCG 3 134 0 GGGGGTGGGG 0.935246 -18 AGGGCATCCATGGTGATGGATAGGGAAAGGG 5 66 0 TGGTGTGGAT 0.601322 -235 TAACGATAACTGCCGCTGGGTAAGTTTCGGC 5 99 0 TGCCGTGGGT 0.934673 -202 TGCAATCCAATGCCGATGATAACGCGAGGGC 8 95 0 TGCCGTGATA 0.375114 -77 TTAACGAAGATGGCGGTGGGTTTCTGTGGCC 9 29 1 TGGCGTGGGT 0.976677 -96 TAGGGTACTCTGGCTTTGGGAAAGGGTAAAT 12 124 1 TGGCTTGGGA 0.659342 -143 ATTTTTCGAGGGCGGCGGGTTTAAGACCGG 16 10 1 GGGCGCGGGT 0.95696 -139 TCCTAGAAGGGGGGGTTGAGAAATTTTGGAG 16 73 0 GGGGGTGAGA 0.910097 -76 TTGTAATGATGAGCGATGGGTGGTGATACGA 20 101 0 GAGCGTGGGT 0.826599 -173 TACGGGCGATAGGCGCTGGTTTCGTCCTGCT 20 253 0 AGGCGTGGTT 0.740134 -21 CTAGTTCAAGGGGGGCTGGTTTATCTTTTGG 21 28 1 GGGGGTGGTT 0.972032 -177 GTTTATCTTTTGGGGATGGTAACAGATTTCC 21 46 1 TGGGGTGGTA 0.883523 -159 TAACTGTTGGGGCCGATGGGAGAAGCCGGAG 21 85 1 GGCCGTGGGA 0.958535 -120 CGCCTGCTTTGGCCGTTGAAAAGAGTTGTTG 24 28 0 GGCCGTGAAA 0.527319 -84 GGATATCGGAGGGGGATGAATGTCGTTTGCG 27 51 0 GGGGGTGAAT 0.815472 -250 GTCCTTTCCATGGGGATGTTTAGATGGAATA 27 104 1 TGGGGTGTTT 0.560343 -197 ***** ***** Masking position 8 Map Score: 15.372 Number of sites scoring better than the average of aligned sites = 2393 Number in coding regions = 2216 Number in noncoding regions = 177 Number of orfs with sites within 600 bp upstream = 193 Fraction of orfs with sites within 600 bp upstream = 0.030999 Motif number 5 CGTCAATGGTGTTAGGATCTGCTGAGAAGAAGA 1 74 1 GTAGTCTGCT 0.886627 -54 GCCTTTGCTTACCGAGGTTTGCCCTAGCTGTCA 2 103 1 ACGGTTTGCC 0.858171 -160 TGCCCTAGCTGTCAGGGTTTGCCCATGTATCTA 2 122 1 GCAGTTTGCC 0.981052 -141 GATACGCAACGGTGCGGTCTGCCCCAATC 4 86 1 GTGGTCTGCC 0.976638 -19 CATCACCATGGATGCCCTCTGCCGAAACTTACC 5 79 1 GTGCTCTGCC 0.766085 -222 ATTTGAATCTGGAATGATTTGCCCCCCAACGTC 6 16 1 GAAGTTTGCC 0.836932 -149 GGCTGACTCTGCCTGGCTTTGCTTAAATCT 7 81 1 GCTGTTTGCT 0.869945 -20 TTTATTTAGTGCCAAGTTTTGGCCGGGAAACTA 8 47 1 GCAGTTTGGC 0.888167 -125 GGCCGGCCTTGGCTTGATCTGCTCTGGCAGGCC 13 70 0 GCTGTCTGCT 0.893942 -124 CACAGTCGTGGTTTAGATCTGCCTTTGCCGTCA 14 50 0 GTTGTCTGCC 0.955112 -208 AATCCAGTGGGGCGTGATTTACCTGAAATTTCC 14 148 0 GCGGTTTACC 0.774344 -110 CACCCACAAGGTTAGGGTTGGCCAAGTCCGCTC 18 51 0 GTAGTTGGCC 0.877322 -60 GGAGGATTTAAATTAGTTTTGCCTGATCGTATC 20 75 1 ATTGTTTGCC 0.627541 -199 AACTGAGAAAGTTGTGCTCGGGCCTCTCACAAG 20 208 0 GTGGTCGGGC 0.617009 -66 ATGGCCCAGGGCCATGTTCTGCTAGATTAGCCG 21 123 1 GCAGTCTGCT 0.934617 -82 CCTTAAAAAAGGCAAGATTTCCCTTGCACTACA 27 224 0 GCAGTTTCCC 0.814256 -77 * ** * ****** Masking position 8 Map Score: 9.77751 Number of sites scoring better than the average of aligned sites = 782 Number in coding regions = 689 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 6 AGGGCGATGGAAAAAGGGTTTG 2 3 1 GGCGATGGAA 0.783043 -260 GGTAAGCAAAGGCCACAGATCAAGCATAAT 2 86 0 GGCCACAGAT 0.862441 -177 TAGGTCGGATGGCCACGAAGATTTGCTAAA 4 42 1 GGCCACGAAG 0.886249 -63 AGTAAGAGATTGCAACGAAATTTATCGCCC 6 110 1 TGCAACGAAA 0.558854 -55 AGTCAGCCCAGGGGACAAAAACTTCCTGAA 7 59 0 GGGGACAAAA 0.700968 -42 AGGCATAGTCGGCCACAGAAACCCACCGCC 9 40 0 GGCCACAGAA 0.980136 -85 TCCCTGGTACGGGAACGGAAAGGGCTAAAA 11 19 0 GGGAACGGAA 0.858622 -78 AATGGTGTGGGGCCATAGAATGAAGGCAAT 12 222 1 GGCCATAGAA 0.883745 -45 GATCGACCCAGGCCACGGAACTTAGTGAAT 15 66 0 GGCCACGGAA 0.985123 -41 AATCGGTCAGGGCAAAAAAATCGTTATTCC 16 101 0 GGCAAAAAAA 0.534761 -48 CCTGCTCCTCGGCAACAAAAAAGTCCGAGC 17 36 0 GGCAACAAAA 0.92936 -23 GTTAAGGGGCGGCCACCAAAAACCTTAGCA 24 74 0 GGCCACCAAA 0.904635 -38 ********** Masking position 5 Map Score: 5.249 Number of sites scoring better than the average of aligned sites = 818 Number in coding regions = 756 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 76 Fraction of orfs with sites within 600 bp upstream = 0.0122069 Motif number 7 AACGGGAAAAGCTCCTCGGGTTAGAATCTG 2 171 0 GCTCCTCGGG 0.963895 -92 GCAGGCCATTGCTCAACTGACCGCTCCATG 3 21 0 GCTCAACTGA 0.660942 -131 ACGAAGATTTGCTAAACTGGACGCAGAGTA 4 56 1 GCTAAACTGG 0.928612 -49 TCTCCCCTAGGGTACTCTGGCTTTGGGAAA 12 117 1 GGTACTCTGG 0.858223 -150 GGTAAATCACGCCCCACTGGATTGCCTCAG 14 158 1 GCCCCACTGG 0.899474 -100 GGGAGTTTGGGCTAATCTGTCCAGGCTCGG 17 12 1 GCTAATCTGT 0.789475 -47 AGACCTGCTCCTCGGCAACAAAAAAG 17 43 0 GCTCCTCGGC 0.815451 -16 TAGGTCTCTTGCTACACTGGGGAGCGGACT 18 30 1 GCTACACTGG 0.972531 -81 GCCCAAATATGCTCCTCTGTGGAACTTTGA 20 155 1 GCTCCTCTGT 0.931961 -119 TCGCACCTCGGCTAATCTAGCAGAACATGG 21 134 0 GCTAATCTAG 0.600087 -71 TCTAGCTACCCTGGTAATATTTCC 22 5 1 GCTACCCTGG 0.941001 -86 ********** Masking position 7 Map Score: 5.09568 Number of sites scoring better than the average of aligned sites = 503 Number in coding regions = 434 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 8 GGGGACAATGCCCCTGGAAAAAGCTAGTGCTCT 5 196 1 CCCCTGAAAG 0.90302 -105 TGTTTTGAAAGCCCTTTAATATTGTCGGAGCTT 8 15 1 GCCCTTAAAT 0.729334 -157 TTGCCGACAGGCCCTCGCGTTATCATCGGCATT 8 85 1 GCCCTGCGTT 0.853464 -87 TACTCGCTCTCCCCTAGGGTACTCTGGCTTTGG 12 110 1 CCCCTGGGAT 0.854251 -157 AGACGATTATCCCTTGGAATTATACTGGCCTGC 13 44 1 CCCTTGAATT 0.922659 -150 ACGTCCGCTACCCTTAGAACTGTGACGATTTGT 14 195 1 CCCTTGAATT 0.922659 -63 TAAACCCGCCGCCCTCGAAAAAT 16 1 0 GCCCTGAAAT 0.950965 -148 TCTCAACCCCCCCTTCTAGGAATAACGATTTTT 16 83 1 CCCTTTAGAT 0.582421 -66 CCTAAAATTAGCCTTCGAGGTGTGCCATATCAA 19 17 1 GCCTTGAGTT 0.908887 -57 TAAACCAGCCCCCCTTGAACTAGCTTTTTCCTA 21 18 0 CCCCTGAATG 0.927634 -187 ACAGTTAAGACCCCTGGAAATCTGTTACCATCC 21 59 0 CCCCTGAATT 0.973675 -146 ACGGAGCAGAGCCCTAGAGCTCTGCTCTTATGT 26 46 0 GCCCTGAGTT 0.968679 -72 ***** *** * * Masking position 5 Map Score: 6.42736 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 380 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 9 GGAATCGAACGGGAAAAGCTCCTCGGGTTA 2 178 0 GGGAAAAGCT 0.729368 -85 TGATGGATAGGGAAAGGGTTTATGGCAGCG 5 54 0 GGAAAGGGTT 0.936201 -247 CAATGCCCCTGGAAAAAGCTAGTGCTCTGT 5 201 1 GGAAAAAGCT 0.928176 -100 GGAAGCAGCAGGAAAAAGTACACTGCCTCA 10 11 1 GGAAAAAGTA 0.826404 -101 GTACGGGAACGGAAAGGGCTAAAATTTGTT 11 13 0 GGAAAGGGCT 0.959162 -84 TCTGGCTTTGGGAAAGGGTAAATGGGGTTA 12 132 1 GGAAAGGGTA 0.896395 -135 CATCGTTGACGGCAAAGGCAGATCTAAACC 14 44 1 GGCAAAGGCA 0.778296 -214 GATAAAGGGTGGAAAAGTTTGATCGACCCA 15 86 0 GGAAAAGTTT 0.584283 -21 GGGTAAAGGTAATTAAACTTA 19 63 0 GGTAAAGGTA 0.596749 -11 AAAAGTTTAGGAAAAAGCTAGTTCAAGGG 21 10 1 GGAAAAAGCT 0.928176 -195 TGTCGTTTGCGGAAAAAGTCGGGTTGGTTA 27 32 0 GGAAAAAGTC 0.681987 -269 ACATCCCCATGGAAAGGACTGTCAATCCTT 27 93 0 GGAAAGGACT 0.649198 -208 ********** Masking position 5 Map Score: 5.74806 Number of sites scoring better than the average of aligned sites = 736 Number in coding regions = 662 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 10 GGTTCGTCAATGGTGTTAGGATCTGCTGAG 1 70 1 TGGTGTTAGG 0.75757 -58 GATACTAGGGGGATGGGGAAAGAAATC 3 135 0 GGGGGATGGG 0.760293 -17 TGATTAATGGGGGAGTGGGGAGATTAGGTC 4 18 1 GGGAGTGGGG 0.748745 -87 CCTCAGGGAGTGGTGAGAAGACGGGCTTCT 5 24 0 TGGTGAGAAG 0.756777 -277 CTGAAGCTCACGGTGAGAGGAGCAAAAAAC 7 34 0 CGGTGAGAGG 0.910167 -67 CACTGCCTCAGGATGAGAGGGTATTTAGCC 10 31 1 GGATGAGAGG 0.790515 -81 TTTAACGCAATGGTGTGGGGCCATAGAATG 12 214 1 TGGTGTGGGG 0.967931 -53 AGAGGAAGAATTGTGTGAGGAAAATTTTCA 14 102 0 TTGTGTGAGG 0.87885 -156 GGTTGGGAGGGGTCTAACTGCC 15 3 1 TTGGGAGGGG 0.921605 -104 CTTGCTACACTGGGGAGCGGACTTGGCCAA 18 37 1 TGGGGAGCGG 0.893129 -74 TTTAATAGTCTTGTGAGAGGCCCGAGCACA 20 199 1 TTGTGAGAGG 0.933274 -75 TTGTAGTATGTTATGAGGGGTTTTTGATTT 29 100 0 TTATGAGGGG 0.72283 -153 ********** Masking position 5 Map Score: 5.64491 Number of sites scoring better than the average of aligned sites = 1160 Number in coding regions = 1054 Number in noncoding regions = 106 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 11 CCCCTGACTAATGATCCATAAATTTAATAAGTGACAA 5 266 0 ATACAAAAAA 0.896994 -35 GAGAGGAGCAAAAAACGATAATACCAAACTGCGATCT 7 13 0 AAACAAATAA 0.831605 -88 GAAAATTCCCAATAACAACAAAATTAAGCTGGGGGAG 8 136 0 AAACAAAAAA 0.964983 -36 CAAAACAGCCAAAAACGAGAAAACGAAGAAGGCATAG 9 62 0 AAACAAAAAA 0.964983 -63 TAAACCCAACATTACCTACAAACTTCAACAAAAAACA 12 14 0 ATACAAAACA 0.809763 -253 CAACACTGCAAATAGCAAAAAATAGCAAAACAGTT 23 46 1 AAACAAAACA 0.930892 -25 GTAAGGGAAAAAAAGCAAAAAAAATAATGCTAACGGA 26 74 0 AAACAAAAAA 0.964983 -44 TTCGACACACAAAATCTAAAACTAAAATTACACAGAA 27 145 1 AAACAAACAA 0.879798 -156 ATGTTCTCCTAAAAACTACAAAGTCAAAAAGAGTAGT 27 268 0 AAACAAAAAA 0.964983 -33 ** * * * *** ** Masking position 8 Map Score: 3.36977 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 38 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 CCACAGATCAAGCATAATCGAGGAGAGACT 2 74 0 AGCATAATCG 0.583953 -189 GACCGCTCCATGGAGAATTGGT 3 3 0 TGGAGAATTG 0.861781 -149 AAACGAAGAAGGCATAGTCGGCCACAGAAA 9 49 0 GGCATAGTCG 0.729452 -76 CCGAAAATCCGAGAGAATCGGTAAAATGGC 12 71 0 GAGAGAATCG 0.726602 -196 ATAATTCCAAGGGATAATCGTCTATCAACC 13 37 0 GGGATAATCG 0.946621 -157 AGTGGCTTGGGGCAGAATTGTGCATAGGAA 13 174 0 GGCAGAATTG 0.966797 -20 CGTCAACGATGGGAGAATTCGGCTTGAGCT 14 25 0 GGGAGAATTC 0.808133 -233 TATCCTGAGAGGAAGAATTGTGTGAGGAAA 14 109 0 GGAAGAATTG 0.848015 -149 GTCCTGTGATTGCATAATTGTCGGCTCAGG 20 21 0 TGCATAATTG 0.725764 -253 AGGGGGAGAATTGCTGGAGTTAA 24 99 0 GGGAGAATTG 0.973022 -13 AAACCTCTTAGGTATAATTGGTCATTACGG 29 206 1 GGTATAATTG 0.74578 -47 ********** Masking position 6 Map Score: 3.88834 Number of sites scoring better than the average of aligned sites = 432 Number in coding regions = 368 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 13 TCGCTTTTCAAACCCTTTTTCCATCGCCCT 2 10 0 ACCCTTTTTC 0.91315 -253 AGCAACTAGAAGCCCGTCTTCTCACCACTCC 5 17 1 ACCCGTCTTC 0.974077 -284 ATTAGGAGTAAAACCATTTACTATTTCGGCT 5 136 1 AACCATTTAC 0.804299 -165 GTGGCCGACTATGCCTTCTTCGTTTTCTCGT 9 54 1 AGCCTTCTTC 0.792695 -71 AGGCCGGATAACCCCATTTACCCTTTCCCAA 12 139 0 ACCCATTTAC 0.937755 -128 CCGTTTTCCTAGCCCATCTACTGCGGTTTTA 13 126 0 ACCCATCTAC 0.959834 -68 TGCTGATTTTACCCCGTTTTCCTAGCCCATC 13 139 0 ACCCGTTTTC 0.959497 -55 ACCATAGGGGAAACCGTCTACCGCAAGTTGT 23 15 1 AACCGTCTAC 0.911114 -56 * ********* Masking position 1 Map Score: 2.09994 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 114 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 14 AAGGAAAACATCCCCCTGCTC 2 252 1 TCCCCCTGCT 0.984295 -11 AAAGTCCGGCTCCCCCAGCTTAATTTTGTT 8 127 1 TCCCCCAGCT 0.945716 -45 GTGTACTTTTTCCTGCTGCTTCC 10 4 0 TCCTGCTGCT 0.942933 -108 AGACCTGCTCCTCGGCAACAAA 17 47 0 ACCTGCTCCT 0.774646 -12 AATGGCCCCATCCTCGTCCTGTGATTGCAT 20 36 0 TCCTCGTCCT 0.903209 -238 ATTTAAATCCTCCCTGTGCTCTAATGGCCC 20 58 0 TCCCTGTGCT 0.830364 -216 AATCTCATAAACCTCCAGCTCTGCGCCCAA 20 131 1 ACCTCCAGCT 0.763042 -143 GGCGCTGGTTTCGTCCTGCTGTCATTGGGG 20 243 0 TCGTCCTGCT 0.845059 -31 CCCTGGGCCATCCTTCTCCTCCGGCTTCTC 21 104 0 TCCTTCTCCT 0.927713 -101 TGGTAATATTTCCCTCGCCTAGCCATTGGT 22 22 1 TCCCTCGCCT 0.800954 -69 ACGACATTCATCCCCCTCCGATATCCTTGA 27 56 1 TCCCCCTCCG 0.908225 -245 ********** Masking position 2 Map Score: 5.70674 Number of sites scoring better than the average of aligned sites = 613 Number in coding regions = 539 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 15 GGATGGGGAAAGAAATCGACTGAACAGACTATTT 3 118 0 AAATCCTGAA 0.960515 -34 CCCAGGGGACAAAAACTTCCTGAAGCTCACGGTG 7 49 0 AAACTCTGAA 0.917609 -52 ATAATCGTCTATCAACCTGCTGAATTTTCCGGAA 13 20 0 AAACCCTGAA 0.986289 -174 GGATGGGGGAAGCAACCATCTGAAAATTTTCCTC 14 82 1 AAACCCTGAA 0.9863 -176 GGTGTGCCATATCAATCACCTGAATTATTAAGTT 19 35 1 AAATCCTGAA 0.960513 -39 CAAAAAGACAATCCTTCTGAACTCCACTATC 25 8 1 AATCCCTGAA 0.946697 -30 * **** ***** Masking position 4 Map Score: 1.68823 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 3 Number in noncoding regions = 1 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234