AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i294_mixed1_aquae_reg_100.orf -o294_aquae_100.ace -a/home/amcguire/genomes/ORF_aquae.txt -z/home/amcguire/genomes/aquae.fna -g0.44 -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 = 0.44 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RAA01117 16 Aquifex_aeolicus RAA01268 16 Aquifex_aeolicus RAA00291 18 Aquifex_aeolicus RAA01569 24 Aquifex_aeolicus RAA00301 25 Aquifex_aeolicus RAA00343 36 Aquifex_aeolicus RAA01155 17 Aquifex_aeolicus Input sequences: #1 RAA01012 41 Aquifex_aeolicus #2 RAA01257 174 Aquifex_aeolicus #3 RAA01258 57 Aquifex_aeolicus #4 RAA01264 77 Aquifex_aeolicus #5 RAA01265 27 Aquifex_aeolicus #6 RAA01266 42 Aquifex_aeolicus #7 RAA01362 126 Aquifex_aeolicus #8 RAA01371 29 Aquifex_aeolicus #9 RAA01459 211 Aquifex_aeolicus #10 RAA01460 33 Aquifex_aeolicus #11 RAA01499 76 Aquifex_aeolicus #12 RAA01500 110 Aquifex_aeolicus #13 RAA00451 300 Aquifex_aeolicus #14 RAA00455 72 Aquifex_aeolicus #15 RAA00466 48 Aquifex_aeolicus #16 RAA00049 45 Aquifex_aeolicus #17 RAA00179 62 Aquifex_aeolicus #18 RAA00181 41 Aquifex_aeolicus #19 RAA00197 66 Aquifex_aeolicus #20 RAA00199 271 Aquifex_aeolicus #21 RAA00232 68 Aquifex_aeolicus #22 RAA00236 96 Aquifex_aeolicus #23 RAA00237 37 Aquifex_aeolicus #24 RAA00669 250 Aquifex_aeolicus #25 RAA00757 300 Aquifex_aeolicus #26 RAA01104 62 Aquifex_aeolicus #27 RAA01105 38 Aquifex_aeolicus #28 RAA01116 91 Aquifex_aeolicus #29 RAA01118 74 Aquifex_aeolicus Motif number 1 CAGGATGAAGCTTCCTCCTCTG 1 2 0 CTTCTCCTCT 0.973082 -40 CATTTTCCTTTACCTCTATTTATATCT 4 61 0 CCTTACCTCT 0.90204 -17 TTCCCCTTCTCTCTCCTTTTAAAACCTTT 6 9 1 CTCCTCCTTT 0.939292 -34 TTTATACAATCCTTCTCCTGTCCCACCATGC 7 24 1 CCTCTCCTGT 0.733373 -103 TCAAATTTAACTTTTTCCTCAAAATCT 9 7 0 CTTTTCCTCA 0.626538 -205 TCCTTTTTAATCTCTTCCTCTTTAAAGAGTT 9 61 0 TCTTTCCTCT 0.753491 -151 CAAGGGGTATCGTCTTCCTTTCCTTTTTAAT 9 81 0 CGTTTCCTTT 0.857836 -131 TTAAGAAGAACTTTTACCTGCTTGGTCAAAA 9 163 1 CTTTACCTGC 0.699757 -49 TCCCTGCTCCTTTAAATAGGTGT 10 21 0 CCTCTCCTTT 0.916775 -13 CTTTATACCTTTTTATAATCTT 15 2 1 TTTTACCTTT 0.881394 -47 GGCTTTTACCTCTTTGTAGAGTT 16 33 0 CTTTACCTCT 0.962977 -13 TACCGAAATCTTTATTCCTTTTAGTGATTTT 20 61 1 TTTTTCCTTT 0.881394 -211 GGTATTTTATTTCTCACCTTTAGTTTTATTG 20 146 1 TTCCACCTTT 0.837027 -126 GTTTTATTGACTTATTACTTTGCCGATCCAC 20 168 1 CTTTTACTTT 0.727154 -104 AAGAATTTAGTTCCCACCTTTTGTAGGCAAA 20 234 0 TTCCACCTTT 0.837027 -38 GTCTCTTACCTCTCTCAGTTTTT 22 84 0 CTCTACCTCT 0.928232 -13 GCCCCTTTTTCCTTCTTTCCTTTAT 23 5 1 CTTTTCCTTC 0.903231 -33 GCCCGCAAAGTGCCTACCTCTACGGCTCGGT 24 38 0 TGCTACCTCT 0.536437 -213 AAAAAGTATACTTACTCCTTTCCCAAAACCT 24 108 0 CTTCTCCTTT 0.968862 -143 AAGTATACTTTTTCTTACTTTCCACTTTTGT 24 126 1 TTTTTACTTT 0.469399 -125 TGCTTTAGCTCTTTCAACTTTCAACTCCACA 25 157 0 CTTCAACTTT 0.787419 -144 GCATTTTCCACTTTCAACTCCACACGGTACA 25 215 0 CTTCAACTCC 0.642125 -86 GGAACCTCAGCTTTTTCCTTTTTGTTTTTGC 25 247 0 CTTTTCCTTT 0.957241 -54 TTTCCACCTCCTTCTTTTTGT 27 1 1 TTTCACCTCC 0.833421 -38 ACTTCACACCTCCTTGGGTTTTG 28 79 0 TTCCACCTCC 0.713294 -13 CTCAGAAAGTCGTGCACCTTTAAGTCTTTAA 29 40 1 CGTCACCTTT 0.893465 -35 *** ******* Masking position 9 Map Score: 27.8497 Number of sites scoring better than the average of aligned sites = 2306 Number in coding regions = 2125 Number in noncoding regions = 181 Number of orfs with sites within 600 bp upstream = 172 Fraction of orfs with sites within 600 bp upstream = 0.0276261 Motif number 2 GCTCCAAGCTTCTTTATAACAGCTGTGGAA 2 120 0 TCTTTATAAC 0.650124 -55 CTTTTGGCGGGCTTTAAAAATAAAAAAAAT 4 25 1 GCTTTAAAAA 0.741027 -53 CCTTCTCTCTCCTTTTAAAACCTTTTGAGG 6 15 1 CCTTTTAAAA 0.818135 -28 TTAATCTCTTCCTCTTTAAAGAGTTCCTTG 9 56 0 CCTCTTTAAA 0.790844 -156 GTCTTCCTTTCCTTTTTAATCTCTTCCTCT 9 71 0 CCTTTTTAAT 0.911389 -141 ACTTTAAACACCTATTTAAAGGAGCAGGGA 10 14 1 CCTATTTAAA 0.718401 -20 ATTGAGTATGCCTTTATAAAATTTTTACCC 13 27 0 CCTTTATAAA 0.980057 -274 CTAAAAAAACGCTTTATAAATAACTTATTA 13 113 0 GCTTTATAAA 0.952842 -188 AATATTATGACCTTTATCAAAGTAAATCAA 14 45 0 CCTTTATCAA 0.943524 -28 CTTTATACCTTTTTATAATCTTTAAGT 15 8 1 CCTTTTTATA 0.706208 -41 TACAATTTGTTCTTTATAATAAATCCTTCA 19 22 0 TCTTTATAAT 0.804889 -45 GTGTTATATATCTTTATAATGTCTTT 22 7 0 TCTTTATAAT 0.804889 -90 AAAAACCTAAGCTTTTTCAAGGCTATGACA 22 43 0 GCTTTTTCAA 0.816176 -54 TTCCTTCTTTCCTTTATAATACTTTCCTT 23 19 1 CCTTTATAAT 0.940875 -19 CAAGGGGAAGCCTTTTTAAAAGCCCGCAAA 24 60 0 CCTTTTTAAA 0.969478 -191 CTTGAGTATACCTTTATAAAATTTCCAT 25 9 0 CCTTTATAAA 0.980057 -292 AAAAAATAACGCTTTATCAATAACTTATTA 25 95 0 GCTTTATCAA 0.872928 -206 AACTTAATTTTCTTTATAAAGAATATATCA 26 25 0 TCTTTATAAA 0.927193 -38 ********** Masking position 5 Map Score: 21.5321 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 376 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 3 GTTAAATTTGAAAACCTCGGAGAATTTTTCAA 9 27 1 AAAACCTCGG 0.954588 -185 TCCGCGGGCTAAAACCGCGTATCTATGATACG 12 31 1 AAAACCGCTT 0.885358 -80 TCAATTTTGCAGAACCTCGGGTTAGCGGAAAT 13 52 1 AGAACCTCGT 0.985898 -249 ATGAGAAAGAAAAACCTCTTATTTACTTAGGG 13 233 0 AAAACCTCTT 0.976194 -68 GTTTAAGAATAAAACTTCTTTTTAGGAGGTTA 17 15 0 AAAACTTCTT 0.76366 -48 GTTGAATAAAAAACCTACGGTATTAAGTTTA 17 42 0 AAAACCTAGT 0.945044 -21 TGAGAAATAAAATACCTCATTTTCTCCCAAAG 20 130 0 AATACCTCTT 0.838989 -142 TAAAATAAAAAAAACCTAAGCTTTTTCAAGGC 22 50 0 AAAACCTAGT 0.945044 -47 TCAAGTTTGCAGAACCTCGGGTTAGCGGAAAT 25 34 1 AGAACCTCGT 0.985898 -267 CGGTACATTAGGAACCTCAGCTTTTTCCTTTT 25 256 0 GGAACCTCGT 0.929407 -45 AAAAACCTCCGTTTACTAAACTT 26 50 0 AAAACCTCGT 0.991121 -13 ******** * * Masking position 4 Map Score: 13.9875 Number of sites scoring better than the average of aligned sites = 151 Number in coding regions = 134 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 4 TATAGAAGGGGGCAAGAGCCCCCATGTATG 3 16 0 GGCAAGAGCC 0.966124 -42 CCAAAAGGCGGGCAAAAGACA 4 2 0 GGCAAAAGAC 0.967884 -76 TAAATCCGCGGGCTAAAACCGCGTATCTAT 12 27 1 GGCTAAAACC 0.810528 -84 TCATTATTAGGGCGTAACCCTGCACGCCTG 13 146 0 GGCGTAACCC 0.892477 -155 TCTACAAAGAGGTAAAAGCC 16 36 1 GGTAAAAGCC 0.941201 -10 GGATACTTCAGGGGAAAGCCCGTGGCAGTC 18 22 1 GGGGAAAGCC 0.962714 -20 CTCTAGATATGGCAAAACACAAGAACAAAA 20 88 0 GGCAAAACAC 0.960555 -184 AACTGAGAGAGGTAAGAGAC 22 87 1 GGTAAGAGAC 0.695134 -10 TAAATATCAAGGCGAAAAACAGGTATAGCA 24 171 1 GGCGAAAAAC 0.899159 -80 CCCCGAAGCTGGGGCAACCCAAGCGGGGAA 28 33 0 GGGGCAACCC 0.81521 -59 GGGGAAGGGTGGCAAAACCCAAGGAGGTGT 28 67 1 GGCAAAACCC 0.984485 -25 ********** Masking position 7 Map Score: 10.3148 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 176 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TGTCATTAAAAAAGTAAATTTTAAATT 8 13 1 AGTAAATTTA 0.869424 -17 GGGAATACAAAAGGGGAATTTTTAAGAAGAACTT 9 142 1 AGGGAATTTA 0.716332 -70 ACCTCGGGTTAGCGGAAATTAACATTCGTTTCAT 13 65 1 AGGAAATTAA 0.976401 -236 GACCTTTATCAAAGTAAATCAACACTTACTTATC 14 33 0 AGTAAATCAA 0.762753 -40 GTTCCACAAAAGTGGAAAGTAAGAAAAAGTATAC 24 128 0 AGGAAAGTAA 0.886256 -123 CTTTTGTGGAACAGGAAATTATAAATATCAAGGC 24 150 1 AGGAAATTAA 0.976401 -101 ACCTCGGGTTAGCGGAAATTAACATTCGTTTCGT 25 47 1 AGGAAATTAA 0.976401 -254 TCAACTCCACACGGTACATTAGAAACCCTGTGTG 25 134 0 AGTACATTAA 0.912815 -167 TCAACTCCACACGGTACATTAGAAACTCATAACC 25 199 0 AGTACATTAA 0.912815 -102 ATACATCCACACGGTACATTAGGAACCTCAGCTT 25 265 0 AGTACATTAA 0.912815 -36 CCAAAAGGAAAATATGATATATTCTTT 26 4 1 AGGAAAATAA 0.840181 -59 AGTGGAAATTTTAACTCAGTATGA 29 1 1 AGGAAATTTA 0.936346 -74 * ******** * Masking position 8 Map Score: 10.5518 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 43 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 6 CTACCCCTACGACCCCGAAGTTTACAACGG 2 75 1 GACCCCGAAG 0.928125 -100 ATATACTCTATAACCTGAAGGAGGTTAGCA 7 106 1 TAACCTGAAG 0.925241 -21 TAATTTCCGCTAACCCGAGGTTCTGCAAAA 13 56 0 TAACCCGAGG 0.969044 -245 CCACGGGCTTTCCCCTGAAGTATCCAAAAC 18 17 0 TCCCCTGAAG 0.898199 -25 TAATTTCCGCTAACCCGAGGTTCTGCAAAC 25 38 0 TAACCCGAGG 0.969044 -263 GTTTCTAATGTACCGTGTGGAGTTGAAAGT 25 142 1 TACCGTGTGG 0.952507 -159 GTTTCTAATGTACCGTGTGGAGTTGAAAGT 25 207 1 TACCGTGTGG 0.952507 -94 GTTCCTAATGTACCGTGTGGATGTATATTC 25 273 1 TACCGTGTGG 0.952507 -28 CCTTCCCCATCACCCCGAAGCTGGGGCAAC 28 45 0 CACCCCGAAG 0.928124 -47 ********** Masking position 4 Map Score: 6.53047 Number of sites scoring better than the average of aligned sites = 195 Number in coding regions = 150 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 7 AGCTTCATCCTGAAAATGTTAAAATAGCGTT 1 21 1 TGAAAATGTA 0.64717 -21 TGCCACACCTGGAAGATGATAGCTGACGACT 2 46 1 GGAAGATGTA 0.91556 -129 TAACAGCTGTGGAAGCTGCTGGTCTTTGTCC 2 103 0 GGAAGCTGTG 0.854537 -72 AGATTTTGAGGAAAAAGTTAAATTTGAAAA 9 10 1 GGAAAAAGTA 0.929585 -202 AAAAAGGAAAGGAAGACGATACCCCTTGAGA 9 84 1 GGAAGACGTA 0.742262 -128 TTTTGCGGGAGGAAAGTGTGAACTATCCCGC 11 12 0 GGAAAGTGGA 0.854215 -65 TAGCTTTGGGAGAAAATGAGGTATTTTATTT 20 127 1 AGAAAATGGG 0.691612 -145 GATATATTAGAGAAACAGGTACTCAGCTCAT 21 26 0 AGAAACAGTA 0.502171 -43 AAGGAAAGAAGGAAAAAGGGGC 23 2 0 GGAAAAAGGG 0.918465 -36 TGTCATTATAGCAAAAAGTTACTCAGATTGC 24 222 0 GCAAAAAGTA 0.525415 -29 AGTTGAAAGTTGAAAGAGCTAAAGCAACCGC 25 162 1 TGAAAGAGTA 0.5739 -139 AGTTGAAAGTGGAAAATGCTGCAAAAACAAA 25 227 1 GGAAAATGTG 0.949074 -74 AAAACAAAAAGGAAAAAGCTGAGGTTCCTAA 25 250 1 GGAAAAAGTG 0.949074 -51 ATAAACAAAAAGAAGGAGGTGGAAA 27 5 0 AGAAGGAGTG 0.691135 -34 ACCCAAGCGGGGAAGGTGCGGTTTAAAGAAA 28 16 0 GGAAGGTGGG 0.871692 -76 ******** ** Masking position 4 Map Score: 8.08555 Number of sites scoring better than the average of aligned sites = 810 Number in coding regions = 753 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 8 GGGGCAAGAGCCCCCATGTATGTGTGT 3 7 0 CCCCCATTAT 0.7938 -51 GGGGCTCTTGCCCCCTTCTATAAATCCTTTT 3 24 1 CCCCCTTTAT 0.968049 -34 TGTCTTTTGCCCGCCTTTTGGCGGGCTTTAA 4 11 1 CCGCCTTTGG 0.793901 -67 TTCCCCTTCTCTCTCCTTTTAA 6 2 1 TCCCCTTTCT 0.972603 -41 TCTTAAAAATTCCCCTTTTGTATTCCCTGCT 9 138 0 TCCCCTTTGT 0.982981 -74 ACCTCCGCTTATCTTTTCTAATTA 11 63 0 TCCGCTTTCT 0.915348 -14 ACTTTGCCGATCCACTTGTCTTTCCGTTAAT 20 184 1 TCCACTTTCT 0.874852 -88 AATTTAGTTCCCACCTTTTGTAGGCAAAATA 20 231 0 CCACCTTTGT 0.871329 -41 TAAAAAGGCTTCCCCTTGTAGGCTTTTCTTC 24 72 1 TCCCCTTTAG 0.896533 -179 TTTCTTACTTTCCACTTTTGTGGAACAGGAA 24 136 1 TCCACTTTGT 0.919181 -115 CCGCACCTTCCCCGCTTGGGTTGCCCCAGCT 28 26 1 CCCGCTTGGT 0.816369 -66 ******* *** Masking position 7 Map Score: 7.41377 Number of sites scoring better than the average of aligned sites = 198 Number in coding regions = 180 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 9 ATTTTAACATTTTCAGGATGAAGCTTCCTC 1 16 0 TTTCAGGATG 0.603875 -26 CTATAAATCCTTTTAGGAGGGAAAATA 3 41 1 TTTTAGGAGG 0.923813 -17 TTCAATAAATTTAAGGGAGGTGTGCT 5 12 1 TTAAGGGAGG 0.922756 -16 TTAAAACCTTTTGAGGGAGCGGTA 6 29 1 TTGAGGGAGC 0.873723 -14 ACTCTATAACCTGAAGGAGGTTAGCAA 7 110 1 CTGAAGGAGG 0.935929 -17 CAAGGAACTCTTTAAAGAGGAAGAGATTAA 9 56 1 TTTAAAGAGG 0.772116 -156 AAACACCTATTTAAAGGAGCAGGGA 10 19 1 TTAAAGGAGC 0.592977 -15 AAGGGAACTTTTGCGGGAGGAAAGTGTGAA 11 21 0 TTGCGGGAGG 0.970642 -56 TAAAACTTCTTTTTAGGAGGTTAGCGT 17 8 0 TTTTAGGAGG 0.923813 -55 ATAATAAATCCTTCAGGAGGTCACGC 19 7 0 CTTCAGGAGG 0.943185 -60 AAGATAATAATGTCGGGAGGTAGGTT 19 51 1 TGTCGGGAGG 0.854284 -16 GTATCGGTAGCTTTGGGAGAAAATGAGGTA 20 120 1 CTTTGGGAGA 0.480737 -152 TTATAAAAAACTGAGAGAGGTAAGAGAC 22 79 1 CTGAGAGAGG 0.747857 -18 TTGCTATATTTTTAGTGAGGGGCTATGCTA 24 196 0 TTTAGTGAGG 0.755113 -55 ********** Masking position 8 Map Score: 8.88444 Number of sites scoring better than the average of aligned sites = 588 Number in coding regions = 500 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 10 AGCACACCTCCCTTAAATTTATTGAAA 5 5 0 CTAATTTATT 0.784389 -23 CCCATCAAATTAATTTATACAATCC 7 3 1 CTAATTAATT 0.908526 -124 GTCAAAACGCCATCACATTAATAAATCTCTCTT 9 187 1 CTAATTAATA 0.964477 -25 TTTCTCATTTCATAAACTTAATAAATAAACACT 13 257 1 CTACTTAATA 0.938412 -44 TAAACACTCACTTATAATTAATATTTCCT 13 282 1 CTTATTAATA 0.829523 -19 TGATAAAGGTCATAATATTAATATCAA 14 56 1 CTAATTAATA 0.964459 -17 AAGTTTTATTCTTAAACTTAATACCGTAGGTTT 17 30 1 CTACTTAATA 0.938914 -33 TGTTTTTCGCCTTGATATTTATAATTTCCTGTT 24 159 0 CTAATTTATA 0.908594 -92 * * * ******* Masking position 11 Map Score: 4.17244 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 6 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 11 AGTTTACAACGGACAAAGACCAGCAGCTTC 2 93 1 GGACAAAGAC 0.939307 -82 TATGATACGGGGACAGAAGCCGCCTGTGTA 12 54 1 GGACAGAAGC 0.941564 -57 AAAAAACTGCTTACACAGGCGGCTTCTGTC 12 65 0 TTACACAGGC 0.880366 -46 GCGTTTTTTTAGACACAGGCGTGCAGGGTT 13 131 1 AGACACAGGC 0.957362 -170 TTCAAGGCTATGACAAAAACAGTGTTATAT 22 28 0 TGACAAAAAC 0.826554 -69 TTTGCTATAATGACAAAAGCATA 24 238 1 TGACAAAAGC 0.945856 -13 GTTATTTTTTGGACACAGGCACACAGGGTT 25 115 1 GGACACAGGC 0.988915 -186 ********** Masking position 5 Map Score: 2.64037 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 47 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 12 TCTTAATCGAAGAGTTTAATCTAAAATGTTGACCGT 7 71 0 AAGTTTTAAA 0.954967 -56 TTTTGAGGAAAAAGTTAAATTTGAAAACCTCGGAGA 9 14 1 AAGTTTTAAA 0.954967 -198 TCCTCTTTAAAGAGTTCCTTGAAAAATTCTCCGAGG 9 41 0 AAGTTTAAAA 0.925943 -171 CAAGCAGGTAAAAGTTCTTCTTAAAAATTCCCCTTT 9 151 0 AAGTTCTAAA 0.815581 -61 AGAAGTCTAATAAGTTATTTATAAAGCGTTTTTTTA 13 106 1 TAGTTTTAAG 0.770674 -195 ACCTCTTTGTAGAGTTAAGTATTAAATTTAATTTAA 16 13 0 AAGTTTTAAA 0.954967 -33 CCTACGGTATTAAGTTTAAGAATAAAACTTCTTTTT 17 24 0 TAGTTGAAAA 0.686937 -39 AAAAGTTGATTTAAAAAAAGAATTTAG 20 255 0 AAGTTTAAAA 0.925943 -17 AAACAGGTACTCAGCTCATTGTAAAATTTTGATA 21 9 0 TAGCTTTAAA 0.788206 -60 CTTACCTCTCTCAGTTTTTTATAAAATAAAAAAAAC 22 67 0 TAGTTTTAAA 0.946936 -30 TAACTCAGTATGAGATTCCTCAGAAAGTCGTGCACC 29 22 1 TAGATTAAAA 0.596852 -53 * **** * * *** Masking position 3 Map Score: 3.54142 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 60 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 13 CCTTCTCTCTCCTTTTAAAACCTTTTGAGGGAGCG 6 15 1 CTTAACCTTT 0.837984 -28 GTTGACCGTGAGTGTCATAGCCTTCGCATGGTGGG 7 45 0 ATTATCCTTC 0.703085 -82 TCTTCCTTTCCTTTTTAATCTCTTCCTCTTTAAAG 9 65 0 CTTAATCTTC 0.685782 -147 AAAAAAACGCTTTATAAATAACTTATTAGACTTCT 13 106 0 TTTAAACTTA 0.681791 -195 GAAAGAAAAACCTCTTATTTACTTAGGGCATTTCA 13 226 0 CTTATACTTA 0.953531 -75 TTTTCTTTCTCATTTCATAAACTTAATAAATAAAC 13 252 1 CTTATACTTA 0.953531 -49 GAAATTCTTATATCCTTATAATGATAAG 14 4 1 ATTATCCTTA 0.872328 -69 TTGATATTAATATTATGACCTTTATCAAAGTAA 14 50 0 ATTATCCTTT 0.686871 -23 CTTTATACCTTTTTATAATCTTTAAGTATGTAC 15 9 1 CTTATTCTTT 0.748932 -40 AACGACACTTCTTGTTATCTTCTTACCGAAATCTT 20 38 1 CTTATTCTTA 0.902831 -234 TCTCACCTTTAGTTTTATTGACTTATTACTTTGCC 20 157 1 ATTATACTTA 0.855036 -115 ACGTCCCCAACTTCTGAAGCCCTTACCGAGCCGTA 24 14 1 CTTAACCTTA 0.941556 -237 AAAATAACGCTTTATCAATAACTTATTAGACACCT 25 88 0 TTTAAACTTA 0.681791 -213 AAAAACCTCCGTTTACTAAACTTAATTTTCTTTA 26 39 0 CTTCTACTTA 0.735737 -24 TTAAGATAAACATATTAAAGACTTAAAGGTGCACG 29 50 0 CTTAAACTTA 0.93292 -25 * * * ** ***** Masking position 5 Map Score: 8.90493 Number of sites scoring better than the average of aligned sites = 165 Number in coding regions = 149 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 14 TTCCCTCCTAAAAGGATTTATAGAAGGGGG 3 34 0 AAAGGATTTA 0.94279 -24 CGCTCCCTCAAAAGGTTTTAAAAGGAGAGA 6 20 0 AAAGGTTTTA 0.911275 -23 CTTATCATTATAAGGATATAAGAATTTC 14 9 0 TAAGGATATA 0.773825 -64 TTACTTTGATAAAGGTCATAATATTAATAT 14 50 1 AAAGGTCATA 0.731777 -23 GTACATACTTAAAGATTATAAAAAGGTATA 15 14 0 AAAGATTATA 0.800614 -35 GTGACCTCCTGAAGGATTTATTATAAAGAA 19 13 1 GAAGGATTTA 0.835278 -54 TGATTTAAAAAAAGAATTTAGTTCCCACCT 20 246 0 AAAGAATTTA 0.865609 -26 TTTTCTTTATAAAGAATATATCATATTTTC 26 18 0 AAAGAATATA 0.865624 -45 ********** Masking position 3 Map Score: 1.42712 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 188 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 15 TGTCTTTTGCCCGCCTTTTGGCGGGC 4 7 1 TTGCCCGCCT 0.645718 -71 TTTATTTTTAAAGCCCGCCAAAAGGCGGGC 4 19 0 AAGCCCGCCA 0.972976 -59 TACGCGGTTTTAGCCCGCGGATTTACTATA 12 22 0 TAGCCCGCGG 0.989921 -89 TAATTTCCGCTAACCCGAGGTTCTGCAAAA 13 56 0 TAACCCGAGG 0.880447 -245 GAAGTATCCAAAACCCGCAA 18 1 0 AAACCCGCAA 0.839725 -41 CTTCAGGGGAAAGCCCGTGGCAGTC 18 27 1 AAGCCCGTGG 0.940118 -15 TTACGCCTATAAGCACGCCGTAAAATTCT 20 10 0 AAGCACGCCG 0.900337 -262 GCCTTTTTAAAAGCCCGCAAAGTGCCTACC 24 51 0 AAGCCCGCAA 0.941082 -200 TAATTTCCGCTAACCCGAGGTTCTGCAAAC 25 38 0 TAACCCGAGG 0.880447 -263 ********** Masking position 6 Map Score: 4.43629 Number of sites scoring better than the average of aligned sites = 109 Number in coding regions = 99 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678