AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_pyro_reg_300.orf -o199_pyro_300.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -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 = 0.42 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: RPH01425 17 Pyrococcus_OT3 Input sequences: #1 RPH01036 51 Pyrococcus_OT3 #2 RPH01035 67 Pyrococcus_OT3 #3 RPH01034 29 Pyrococcus_OT3 #4 RPH01033 49 Pyrococcus_OT3 #5 RPH01032 73 Pyrococcus_OT3 #6 RPH00918 178 Pyrococcus_OT3 #7 RPH00045 300 Pyrococcus_OT3 #8 RPH01140 48 Pyrococcus_OT3 #9 RPH01365 36 Pyrococcus_OT3 #10 RPH01366 281 Pyrococcus_OT3 #11 RPH01426 244 Pyrococcus_OT3 #12 RPH01427 286 Pyrococcus_OT3 #13 RPH01428 22 Pyrococcus_OT3 #14 RPH01431 27 Pyrococcus_OT3 #15 RPH01432 156 Pyrococcus_OT3 #16 RPH01507 26 Pyrococcus_OT3 #17 RPH01510 101 Pyrococcus_OT3 #18 RPH01511 63 Pyrococcus_OT3 #19 RPH01565 300 Pyrococcus_OT3 #20 RPH01566 76 Pyrococcus_OT3 #21 RPH01626 35 Pyrococcus_OT3 #22 RPH01636 139 Pyrococcus_OT3 #23 RPH01637 124 Pyrococcus_OT3 #24 RPH01638 57 Pyrococcus_OT3 #25 RPH01639 300 Pyrococcus_OT3 #26 RPH01746 82 Pyrococcus_OT3 #27 RPH01748 300 Pyrococcus_OT3 #28 RPH01754 99 Pyrococcus_OT3 #29 RPH01755 65 Pyrococcus_OT3 #30 RPH01756 40 Pyrococcus_OT3 #31 RPH01041 42 Pyrococcus_OT3 Motif number 1 TTTTCCCTCATCTCCAATTCTTGAGGATCAAAGTTTAC 6 100 1 TAATCTTGGT 0.9363 -79 ATATTGAAGATGGAAAAATTTTATGGAAACCGGAAACT 7 13 0 TAATTTTGGA 0.864299 -288 GCTGATGCTCTAACAACTTCTTCGGGAGGAACTTTACC 7 134 1 TACTCTTGGG 0.955 -167 TCTTCCCTTTTCTTTAATTCTTGGGGTGATTTAA 9 13 1 TAATCTTGGG 0.990367 -24 ATATACCTCCTCTTAAACTCTTAGGGGGTTGAAC 10 7 0 TAATCTTGGG 0.990367 -275 TTTAAAAATTTAACTAATTCTTAAGGCTCAGCGGTGAC 10 116 0 TAATCTTGGT 0.9363 -166 AAATGAGGCTTCCTTCAGTTTGGCGGGTTTCCCGCCGA 10 179 1 TCATTTGGGT 0.769765 -103 AGTAGGGTTAGGCAAAAATTTGGAGGTGATTCAAG 10 257 1 GAATTTGGGG 0.84741 -25 ATGTTCATCTTAAAAAACTTTTGGGGGGCAATTCTCC 11 218 1 TAATTTTGGG 0.984576 -27 AGGAAGTTAGTATATAAATCTTTCGGAGAAAAATACAT 12 29 0 TAATCTTGGG 0.990367 -258 AGAGGTTTACTACACAAAATTGGTGGGGCCGCCGGGAT 12 221 0 TAAATTGGGG 0.789335 -66 ATTTTTCCTTTTTGTGGGGGTGAAACC 14 2 1 TCCTTTTGGG 0.854733 -26 CTCTTCATTTTCCCATTTTGGAGGAA 16 9 1 TCATTTGGGA 0.699996 -18 CGCCAGAATTTCACTCAATCTGGAGGGGGATAAA 17 78 1 TCATCTGGGG 0.974136 -24 TACGTCAAGCTTTTTAACTATTTTGGAGCTTGATGTTT 18 33 1 TAATATTGGG 0.899822 -31 CTTAAAGCATTTAAGAATTTTTCTGGAGTTCTATAATC 19 182 0 TAATTTTGGG 0.984576 -119 GTCTTTGGTCTAAGAAAATCTCTCGGAGGGCAACA 22 115 1 TAATCTCGGG 0.941913 -25 ACCCCACAAATAACAAAATCTGGAGGTG 25 1 0 TAATCTGGGG 0.988283 -300 TTCGCTTTATTTCTTAAGTTTTTAGGAGGGATTCCAGG 30 12 1 TAATTTTGGG 0.984576 -29 * ** **** ** * Masking position 11 Map Score: 29.8184 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 73 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 2 GGCTGAGCCACCGGGGCACCGCCGAAGATT 11 51 0 CCGGGGCACC 0.992384 -194 AGCGGCAGGTCCCGGGTTCAAAGCCCGGCC 11 102 1 CCCGGGTTCA 0.985723 -143 CAAAGCCCGGCCGGGGCTCCATTCTAATAA 11 120 1 CCGGGGCTCC 0.9981 -125 GGCTAGGCTACCGGGGCACCGAGAGATGGA 12 69 0 CCGGGGCACC 0.992384 -218 ATCCCCAGGTCGCGGGTTCAAATCCCGCCC 12 120 1 CGCGGGTTCA 0.919529 -167 CAAATCCCGCCCGGGGCTCCAGCGGGGCCG 12 138 1 CCGGGGCTCC 0.9981 -149 GAACCCGGGTCACGGGCTCCCAAAGCCCGC 12 189 0 CACGGGCTCC 0.992016 -98 GAGCCCGTGACCCGGGTTCAAATCCCGGCG 12 200 1 CCCGGGTTCA 0.985723 -87 GGCAAACGCCCACGGGCTCTCAAGGCCCGC 17 22 0 CACGGGCTCT 0.941575 -80 CGTTTGCCCGCCGGGGTTCAAATCCCCGTC 17 44 1 CCGGGGTTCA 0.988002 -58 AAAGACTATCCAGGAGCTCCTT 27 289 1 CAGGAGCTCC 0.921111 -12 ********** Masking position 9 Map Score: 25.3225 Number of sites scoring better than the average of aligned sites = 41 Number in coding regions = 26 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 3 CTTTTCTTAAAATTTTTAAATTAAATAAC 1 9 1 AAATTTTTAA 0.941999 -43 AGATGAGGGAAAAGTTTTTAATTTGAAAAAG 6 82 0 AAATTTTTAA 0.941999 -97 AAGTCAAACCAAGGTTTTTAATCTAAACTAG 6 144 1 AAGTTTTTAA 0.958866 -35 AGAATTAGTTAAATTTTTAAACTCCTCCCTT 10 133 1 AAATTTTAAA 0.875089 -149 CCGAGATCCGAAAGTTTTAAAAGATCTCCTC 10 223 1 AAATTTTAAA 0.875089 -59 TGCCCCCCAAAAGTTTTTTAAGATGAACATC 11 217 0 AAGTTTTTAA 0.958866 -28 GAGATCATGGAAACATTTTAATATCAATGAA 15 52 0 AAAATTTTAA 0.710185 -105 CTTTTACGTCAAGCTTTTTAACTATTTTGGA 18 29 1 AAGTTTTTAA 0.958866 -35 AACTCCAGAAAAATTCTTAAATGCTTTAAGA 19 190 1 AAATCTTAAA 0.718156 -111 AATTGCTTAAAAGATTTTAAAAAGTTATTTG 19 246 0 AAGTTTTAAA 0.909545 -55 AATTTACAATAAACTCTTTAAACTACGGATC 20 29 1 AAATCTTTAA 0.855221 -48 GCTTTTGCAAAAATTTTTTAAGAATTATCAA 22 26 1 AAATTTTTAA 0.941999 -114 GTTTTTATAAAAGATTTAAAAGGCTTTCGAA 22 75 0 AAGTTTAAAA 0.699325 -65 AAAATTTTTGAAGGTCTTTAATTCCTTTTCT 25 264 0 AAGTCTTTAA 0.894497 -37 ATCCCAGGAAAAGCTTTATAACCCTACTTTT 26 26 1 AAGTTTATAA 0.843553 -57 GCAATTTAGCTAAGTTTTTAACTTCTTCTTC 27 134 1 TAATTTTTAA 0.56606 -167 AAGTATTATAAAGCCATGTAG 29 1 1 AAGATTATAA 0.448594 -65 *** ******* Masking position 7 Map Score: 21.1691 Number of sites scoring better than the average of aligned sites = 155 Number in coding regions = 98 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 4 TCCTTAATAAATCTCGGGAGGTTGCGAG 8 8 0 ACTCGGGAGG 0.771109 -41 CTTCGGCGGTGCCCCGGTGGCTCAGCCTGGT 11 54 1 GCCCGGTGGC 0.948794 -191 CCGGGCTTTGAACCCGGGACCTGCCGCTTAC 11 99 0 ACCCGGGACC 0.983471 -146 CCGGGTTCAAAGCCCGGCCGGGGCTCCATTC 11 113 1 ACCCGGCCGG 0.967592 -132 ATCTCTCGGTGCCCCGGTAGCCTAGCCTGGT 12 72 1 GCCCGGTAGC 0.959224 -215 CCGGTAGCCTAGCCTGGTGGGGCGGGGGACT 12 85 1 ACCTGGTGGG 0.777648 -202 GCGGGATTTGAACCCGCGACCTGGGGATTAC 12 117 0 ACCCGCGACC 0.949081 -170 CCCCGCTGGAGCCCCGGGCGGGATTTGAACC 12 134 0 GCCCGGGCGG 0.978376 -153 AGCTTGGCCCATCCTGCGGGCTTTGGGAGCC 12 174 1 ACCTGCGGGC 0.896675 -113 GGGCTTTGGGAGCCCGTGACCCGGGTTCAAA 12 191 1 ACCCGTGACC 0.89215 -96 CCGGGTTCAAATCCCGGCGGCCCCACCAATT 12 211 1 ACCCGGCGGC 0.992476 -76 GGGCTCTCAAGGCCCGCGCCCTACCAGG 17 8 0 GCCCGCGCCC 0.937292 -94 GGGCCTTGAGAGCCCGTGGGCGTTTGCCCGC 17 24 1 ACCCGTGGGC 0.972534 -78 GGGGATTTGAACCCCGGCGGGCAAACGCCCA 17 40 0 ACCCGGCGGG 0.985334 -62 TCAAATCCCCGTCCCGGCGCCAGAATTTCAC 17 61 1 GCCCGGCGCC 0.981579 -41 * ********* Masking position 6 Map Score: 21.3154 Number of sites scoring better than the average of aligned sites = 115 Number in coding regions = 59 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 5 ACTCCAACCCTCCCTATCATTGAAGTTAA 2 49 0 CCTCCCTATA 0.741435 -19 ATTCCTTCCCCTTTCCCACTTTTAG 6 5 1 CTTCCCCTTC 0.807835 -174 CTAACGACATCCTCCTTTTTCACTCCCATCT 7 68 1 CCTCCTTTTC 0.99097 -233 TTTCTTCCCTTTTCTTTAATTCTT 9 4 1 CTTCCCTTTC 0.939974 -33 TTAAAATATACCTCCTCTTAAACTCTTAGGG 10 19 0 CCTCCTCTTA 0.932939 -263 TTTTTAAACTCCTCCCTTAACTTCAAACAGG 10 146 1 CCTCCCTTAC 0.858607 -136 CTGAAGGAAGCCTCATTTTCCCTGTTTGAAG 10 166 0 CCTCATTTTC 0.948089 -116 TTTGCCTAACCCTACTTTTGAGGAGATCTTT 10 242 0 CCTACTTTTA 0.896097 -40 CATCTACACTCCGCCTTTTGATTCTGATATA 11 187 0 CCGCCTTTTA 0.875485 -58 TATTTACCTAATTTTCCTATGTATTTT 12 7 1 CCTAATTTTC 0.752447 -280 TATATACTAACTTCCTTTTCCATCTCTCGGT 12 51 1 CTTCCTTTTC 0.962835 -236 CTCTTCATTTTCCCATTTTGGAG 16 3 1 CTTCATTTTC 0.81173 -24 CCTCCTTTTCTTCCCTTCAAT 20 1 1 CCTCCTTTTT 0.914955 -76 GCTTTATAACCCTACTTTTTAAGTAAACCCG 26 38 1 CCTACTTTTA 0.896097 -45 TCATACCCCCTCCTTTTGAATTCTATCTC 29 47 0 CCTCCTTTTA 0.981068 -19 ********* * Masking position 1 Map Score: 16.6528 Number of sites scoring better than the average of aligned sites = 499 Number in coding regions = 451 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 6 AATTGGAGATGAGGGAAAAGTTTTTAATTTG 6 88 0 GAGGAAAAGT 0.943642 -91 TAATCTAAACTAGCGAAAAGTTCTCTG 6 162 1 TAGGAAAAGT 0.812754 -17 TGATATTGAAGATGGAAAAATTTTATGGAAA 7 22 0 GATGAAAAAT 0.731318 -279 CAGGAGATGGGAGTGAAAAAGGAGGATGTCG 7 72 0 GAGGAAAAAG 0.943642 -229 CCCCAAGAATTAAAGAAAAGGGAAGAAA 9 8 0 TAAGAAAAGG 0.894983 -29 TTATATATCAGAATCAAAAGGCGGAGTGTAG 11 184 1 GAACAAAAGG 0.762428 -61 GGCACCGAGAGATGGAAAAGGAAGTTAGTAT 12 54 0 GATGAAAAGG 0.975905 -233 TAAATTGAAGGGAAGAAAAGGAGG 20 4 0 GGAGAAAAGG 0.827453 -73 TTTTATAAAAGATTTAAAAGGCTTTCGAAGG 22 73 0 GATTAAAAGG 0.727349 -67 ATGTAATGAAGATAGAAAAGGTAGTAAAATT 23 12 0 GATGAAAAGG 0.975905 -113 ATTTAAATCTTATTGAAAAATGTTGGGTAAG 23 67 0 TATGAAAAAT 0.413698 -58 AGTTCATTCATAGAGAAAAGGAATTAAAGAC 25 251 1 TAGGAAAAGG 0.943642 -50 AGGCCTACTAGAAGGACAAGGAGTTTTGGTC 27 209 1 GAAGACAAGG 0.827453 -92 TATCTTACTAGAGGGAAAAAGACTATCCAGG 27 272 1 GAGGAAAAAG 0.943642 -29 *** ******* Masking position 6 Map Score: 12.2976 Number of sites scoring better than the average of aligned sites = 519 Number in coding regions = 476 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 CTCCTACCCCCACAACTTGATG 1 40 0 CTCCTCCCCA 0.758928 -12 ATTCCTTCCCCTTTCCCACTTTTAGAAT 6 7 1 TCCCCTCCCA 0.903714 -172 AAAAACTTTTCCCTCATCTCCAATTCTTGAGG 6 94 1 CCCTCCTCCA 0.922347 -85 TCCTTTTTCACTCCCATCTCCTGAAGTTTCTC 7 80 1 CTCCCCTCCT 0.669006 -221 ATAAGGGTGATTCCCGTGCCCAAGCTAATGAG 7 236 0 TTCCCGCCCA 0.909655 -65 GGATTACAAGTCCCCCGCCCCACCAGGCTAGG 12 92 0 TCCCCCCCCA 0.992413 -195 GGTTTCACCCCCACAAAAAGGAAAA 14 13 0 TTCACCCACA 0.752418 -15 CTTCTCACCTCCACCTTAAGTAA 15 144 0 TTCTCCTCCA 0.944537 -13 TTTATCCCCCTCCAGATTGAGTGAAA 17 86 0 TCCCCCCAGA 0.785893 -16 ACCTCCTCGCCTCCAGAAGTGTTTG 20 62 0 TCCTCCTCCA 0.959231 -15 ATTCTCTCCCCCAAATAAAATTT 25 288 0 TTCTCCCCCA 0.977198 -13 CAAGCTTAACTTCCCTTCCACACTTCGCACAT 27 13 0 TTCCCCCACA 0.964558 -288 TCAAGAAACATCCTCGACTACATGGCTTTATA 29 17 0 TCCTCCTACA 0.871186 -49 ***** ***** Masking position 3 Map Score: 11.5352 Number of sites scoring better than the average of aligned sites = 345 Number in coding regions = 297 Number in noncoding regions = 48 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 8 AAATTTATATATTTCCTCTCTTCAA 2 6 1 TATATATTTC 0.402894 -62 TTTGACAACCCTTATAAATCCTTATTAACC 5 33 0 CTTATAAATC 0.891342 -41 CCATCAAGGATTTATATTTCAACGCATAAA 7 272 0 TTTATATTTC 0.767692 -29 GTGTTAATCCTTAATAAATCTCGGGAGGTT 8 16 0 TTAATAAATC 0.75642 -33 ATTTAAAAATCAAGTGTTAAT 8 38 0 TTTAAAAATC 0.543137 -11 TACCGAAAACCTTATATATCATCTGTATTC 11 17 1 CTTATATATC 0.839775 -228 GGGCTCCATTCTAATAAATCTTTCGCAAGT 11 133 1 CTAATAAATC 0.695151 -112 CAGAGTAAAGCTTATATATCAGAATCAAAA 11 173 1 CTTATATATC 0.839775 -72 AGGAAGTTAGTATATAAATCTTTCGGAGAA 12 37 0 TATATAAATC 0.695269 -250 CCCTCGAAGATTGATAATTCTTAAAAAATT 22 37 0 TTGATAATTC 0.764106 -103 TTCCGAAAAGTTTATATATCTCTATTTTCA 25 56 0 TTTATATATC 0.877112 -245 TTTATTCACATTGATAATTCAACATGGTTA 25 103 1 TTGATAATTC 0.764106 -198 TCTCTAGTCGTTGATAAATCAAGCTTAACT 27 34 0 TTGATAAATC 0.874952 -267 ********** Masking position 6 Map Score: 6.7204 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 54 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 9 CCCTCCCTATCATTGAAGTTAATCTAGGAGAGAA 2 37 0 CTGAAGTATC 0.852334 -31 TTTACTTGGACATCAAAGATAAACTATGTGAAAG 4 24 1 CTAAAGAAAC 0.961094 -26 AAAGTTTACACTTCAAAGTCAAACCAAGGTTTTT 6 129 1 CTAAAGTAAC 0.979206 -50 CCATCACCGCCATTAAAGTTCAACGTTCCACTAT 15 14 1 CTAAAGTAAC 0.979201 -143 TATCAATGAACCTAATAGTGGAACGTTGAACTTT 15 28 0 CTATAGTAAC 0.961098 -129 AAAAGCTTGACGTAAAAGTTAAACTGAGGTGAGT 18 13 0 CTAAAGTAAC 0.979208 -51 TTTGTAACAACTTAAATGAGAAACCAAAAACAGA 19 69 1 CTAATGAAAC 0.795696 -232 CCTCTGTCCTCGTAATAGACTATCGAATTCATTT 24 32 0 CTATAGAATC 0.871766 -26 TCGTTATTAGCATCATAGTTAATCCCTTTAATGT 27 167 0 CTATAGTATC 0.928362 -134 * * ***** *** Masking position 3 Map Score: 6.26399 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 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 10 TCTTCAAATTCTCTCCTAGATTAACTTCAATGAT 2 29 1 CTCCTAGTTA 0.925143 -39 CACCACCTATCTCCCATCATTTGACAACCCTTAT 5 48 0 CTCCTCATTA 0.978545 -26 CCTTGACGAATTCTCCTAAATCAATTTTAAAATA 10 42 0 TTCCTAATCA 0.828497 -240 TTTTAAACTCCTCCCTTAACTTCAAACAGGGAAA 10 147 1 CTCCTAATTA 0.978961 -135 ATACTCACCTCAGTTTAACTTTTACGT 18 4 1 CTCCTCATTA 0.978544 -60 CAATTGCCTCTTCTCATAATTTAATAAGCCTTTT 19 108 0 TTCCTAATTA 0.947884 -193 CTACTTTCGGCTCGCCTAACGTGAATTGCTTAAA 19 266 0 CTCCTAAGTA 0.925143 -35 CCTCCTTTTCTTCCCTTCAATTTACAATAAACTC 20 11 1 TTCCTCATTA 0.946887 -66 *** * *** ** * Masking position 14 Map Score: 3.18375 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 11 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 11 CTTTTCTTAAAATTTTTAAATTA 1 1 1 CTTTCTTAAT 0.569432 -51 TTATATATTTCCTCTCTTCAAATTCTCTCCTAG 2 15 1 CTCTCTTAAT 0.934163 -53 TTTTCACTCCCATCTCCTGAAGTTTCTCAAAAA 7 84 1 CTCTCCTAAT 0.926849 -217 TTTCTTCCCTTTTCTTTAATTCTTGGGGTGA 9 9 1 CTTTCTTAAT 0.569432 -28 TAAAATATACCTCCTCTTAAACTCTTAGGGGGT 10 16 0 CCCTCTTAAT 0.976221 -266 GCCTTGACGAATTCTCCTAAATCAATTTTAAAA 10 44 0 ATCTCCTAAC 0.634699 -238 CTTGAATCACCTCCAAATTTTTGCCTAACC 10 262 0 CCCTCCAATT 0.641726 -20 TTGTGTAGTAAACCTCTTAAACTATGTACTAAT 12 242 1 ACCTCTTAAT 0.916394 -45 CTTCTCACCTCCACCTTAAGTAAGTCAAGAC 15 136 0 CCCACCTAAT 0.758271 -21 TAATTTAATAAGCCTTTTTAAGTTCTGTTTTTG 19 93 0 ACCTTTTAAT 0.610448 -208 TTTGAGAACTCGCCTCTTAAAGCATTTAAGAAT 19 202 0 CCCTCTTAAC 0.954724 -99 CCTCCTTTTCTTCCCTTCAATTTACAATAAAC 20 10 1 CTCCCTTAAT 0.642784 -67 ACCTCCTCGCCTCCAGAAGTGTTTGTTGAT 20 57 0 CCCTCCAAAT 0.922308 -20 AACCTTCGAAAGCCTTTTAAATCTTTTATAAAA 22 71 1 ACCTTTTAAC 0.445944 -69 CACCTCCAGATTTTGTTATTTGT 25 1 1 CCCTCCAATT 0.641726 -300 TGGTAGTAAAATCCTCTACAAGCCTAGGCCAAA 27 82 1 ACCTCTAAAC 0.645768 -219 TCATACCCCCTCCTTTTGAATTCTATCTCAAG 29 44 0 CCCTTTTAAT 0.854429 -22 * ****** ** * Masking position 10 Map Score: 8.19641 Number of sites scoring better than the average of aligned sites = 795 Number in coding regions = 716 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 12 TATCATCGACTTAATCCCTCGCTAATTTGG 6 46 1 TTAATCCCTC 0.857196 -133 AGTGTAAACTTTGATCCTCAAGAATTGGAG 6 111 0 TTGATCCTCA 0.862206 -68 AAATCAAGTGTTAATCCTTAATAAATCTCG 8 23 0 TTAATCCTTA 0.869232 -26 CGGGGGACTTGTAATCCCCAGGTCGCGGGT 12 107 1 GTAATCCCCA 0.897726 -180 TTTATCCCCCTCCAGATTGA 17 92 0 TTTATCCCCC 0.870511 -10 TTCGTTGAACTTTATCCCCATGTTTAATGA 19 38 0 TTTATCCCCA 0.922311 -263 CTGGAGTTCTATAATCCTCACAATTTGTTA 19 168 0 ATAATCCTCA 0.787855 -133 CACTTTGTAATTAATCCTCATGTAATGAAG 23 32 0 TTAATCCTCA 0.959281 -93 AGCATCATAGTTAATCCCTTTAATGTTAGA 27 163 0 TTAATCCCTT 0.795107 -138 AAATTTAACGTTAATCCTCTAAAGCAATTT 28 49 0 TTAATCCTCT 0.896097 -51 ********** Masking position 5 Map Score: 5.29788 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 165 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 13 AGAAATTTCCCTAAATTCGGTGAAAA 3 4 1 AATTTCTAAT 0.961111 -26 CGCCTTGACGAATTCTCCTAAATCAATTTTAAA 10 45 0 AATTCCTAAT 0.852435 -237 GGAGTTTAAAAATTTAACTAATTCTTAAGGCTC 10 125 0 AATTTCTAAT 0.960522 -157 TATTTACCTAATTTTCCTATGTATTTTTCTCC 12 10 1 AATTTCTATT 0.836965 -277 CCGGCGCCAGAATTTCACTCAATCTGGAGGGGG 17 74 1 AATTTCTCAT 0.933344 -28 CGAGTTCTCAAATTTTTCTTCATCAAATAACTT 19 223 1 AATTTCTTCT 0.744052 -78 CAATTTTACTACCTTTTCTATCTT 23 2 1 AATTTCTACT 0.93334 -123 TAATTATTTCAAGTTGCCTCAATTCAGCTAAGC 25 165 0 AAGTTCTCAT 0.765883 -136 GGGTTAAGGCAATTTAGCTAAGTTTTTAACTTC 27 126 1 AATTTCTAAT 0.961111 -175 ***** **** * Masking position 9 Map Score: 2.80359 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 27 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 14 TGTGAGTACCGAAAACCTTATATATCATCTG 11 7 1 TCCGAACCTT 0.96084 -238 TGACAGAATTTGCCAAAAAGCTGGATTTTAACAAA 19 140 1 TCCAAAGCTA 0.934523 -161 TGGTTCTCTGTGCCTAAATGCTATTAGGTGATATG 23 99 1 TCCTAAGCTT 0.95157 -26 AAGGCTCAAATTCCGAAAAGTTTATATATCTCTAT 25 61 0 TCCGAAGTTT 0.748714 -240 GTGAATAAATTACCAGAAGGCTCAAATTCCGAAAA 25 77 0 TCCAAAGCTA 0.934523 -224 TTCCACCACCCTGATAAGCTTGCTC 26 68 0 TCCACACCTT 0.894952 -15 TTAGCTAAATTGCCTTAACCCTTCTCGGTATCTTT 27 112 0 TCCTAACCTT 0.940697 -189 AATAACGACTTCCCATAGGCCTACTAGAAGGACAA 27 193 1 TCCAAGCCTT 0.894952 -108 TTTACGCGTATCCCATAAAGCTAATCGGGAGGTGT 31 11 1 TCCAAAGCTT 0.978339 -32 * *** ** *** * Masking position 12 Map Score: 2.17383 Number of sites scoring better than the average of aligned sites = 62 Number in coding regions = 51 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 15 CTCCTACCCCCACAACTTGATGGTTATT 1 34 0 CCCCACAATT 0.986556 -18 TTAAATCACCCCAAGAATTAAAGAAAAGGG 9 17 0 CCCAAGAATA 0.669959 -20 TAAAAGATCTCCTCAAAAGTAGGGTTAGGCA 10 240 1 CCTCAAAATA 0.657734 -42 GAGAATTGCCCCCCAAAAGTTTTTTAAGATG 11 223 0 CCCCAAAATT 0.943771 -22 ATCCCGGCGGCCCCACCAATTTTGTGTAGTA 12 221 1 CCCCACCATT 0.926457 -66 GGTTTCACCCCCACAAAAAGGAAAAAT 14 9 0 CCCCACAAAA 0.815101 -19 CCCGTCCCGGCGCCAGAATTTCACTCAATCT 17 68 1 CGCCAGAATT 0.91435 -34 GTTCTATAATCCTCACAATTTGTTAAAATCC 19 162 0 CCTCACAATT 0.941858 -139 ATTGCAAATACCCCACAAATAACAAAATCTG 25 17 0 CCCCACAATA 0.974398 -284 TTCAGCTAAGCCCCAGAAATTTCACGCTGTT 25 145 0 CCCCAGAATT 0.980265 -156 TGAAATAATTACTCACAAATTAAGTATAAGT 25 187 1 ACTCACAATT 0.537536 -114 GGTTTAAGATCGCGAGAAGTTCATTCATAGA 25 234 1 CGCGAGAATT 0.554901 -67 ******** ** Masking position 5 Map Score: 8.48583 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 144 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419