AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i199_trans1_pyro_reg_100.orf -o199_pyro_100.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 RPH01507 26 Pyrococcus_OT3 #13 RPH01510 101 Pyrococcus_OT3 #14 RPH01565 300 Pyrococcus_OT3 #15 RPH01566 76 Pyrococcus_OT3 #16 RPH01626 35 Pyrococcus_OT3 #17 RPH01636 139 Pyrococcus_OT3 #18 RPH01746 82 Pyrococcus_OT3 #19 RPH01748 300 Pyrococcus_OT3 #20 RPH01754 99 Pyrococcus_OT3 #21 RPH01755 65 Pyrococcus_OT3 #22 RPH01756 40 Pyrococcus_OT3 #23 RPH01041 42 Pyrococcus_OT3 Motif number 1 CTCCTACCCCCACAACTTGATGGTTATT 1 34 0 CCCCACAATT 0.924878 -18 AAACTTTGATCCTCAAGAATTGGAGATGAGG 6 105 0 CCTCAAGATT 0.983802 -74 AGGTAAAGTTCCTCCCGAAGAAGTTGTTAGA 7 142 0 CCTCCCGAGA 0.818238 -159 CTCGCAACCTCCCGAGATTTATTAAGGA 8 8 1 CCTCCCGAAT 0.849386 -41 TTAAATCACCCCAAGAATTAAAGAAAAGG 9 18 0 CCCCAAGATT 0.971206 -19 GTTCAACCCCCTAAGAGTTTAAGAGGAGG 10 9 1 CCCTAAGATT 0.783574 -273 CACCGCTGAGCCTTAAGAATTAGTTAAATTT 10 118 1 CCTTAAGATT 0.86701 -164 TAAAAGATCTCCTCAAAAGTAGGGTTAGGCA 10 240 1 CCTCAAAATA 0.896542 -42 CTTGAATCACCTCCAAATTTTTGCCTAACC 10 262 0 CCTCCAAATT 0.973897 -20 GAGAATTGCCCCCCAAAAGTTTTTTAAGATG 11 223 0 CCCCAAAATT 0.942673 -22 TTCCTCCAAAATGGGAAAATGAA 12 14 0 CCTCCAAATG 0.921798 -13 TTTATCCCCCTCCAGATTGAGTGAAATTC 13 83 0 CCTCCAGATG 0.960283 -19 GTTCTATAATCCTCACAATTTGTTAAAATCC 14 162 0 CCTCACAATT 0.95684 -139 ACCTCCTCGCCTCCAGAAGTGTTTGTTGAT 15 57 0 CCTCCAGAGT 0.953582 -20 TGGAATCCCTCCTAAAAACTTAAGAAATAAA 22 17 0 CCTAAAAATT 0.643167 -24 CTCCATCACACCTCCCGATTAGCTTTATGGG 23 22 0 CCTCCCGATA 0.943723 -21 ******** ** Masking position 8 Map Score: 19.8855 Number of sites scoring better than the average of aligned sites = 294 Number in coding regions = 262 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 2 GGTTATTTAATTTAAAAATTTTAAGAAAAG 1 11 0 TTTAAAAATT 0.940157 -41 CTTTTTCAAATTAAAAACTTTTCCCTCATC 6 82 1 TTAAAAACTT 0.951913 -97 CTAGTTTAGATTAAAAACCTTGGTTTGACT 6 145 0 TTAAAAACCT 0.831733 -34 ATTTAAAAATCAAGTGTTAAT 8 38 0 TTTAAAAATC 0.665814 -11 AGGAGGTATATTTTAAAATTGATTTAGGAG 10 34 1 TTTTAAAATT 0.573425 -248 AAGGGAGGAGTTTAAAAATTTAACTAATTC 10 134 0 TTTAAAAATT 0.940157 -148 GAGGAGATCTTTTAAAACTTTCGGATCTCG 10 224 0 TTTAAAACTT 0.951913 -58 GATGTTCATCTTAAAAAACTTTTGGGGGGC 11 217 1 TTAAAAAACT 0.796864 -28 AAGCTGGATTTTAACAAATTGTGAGGATTA 14 157 1 TTAACAAATT 0.665814 -144 TCTTAAAGCATTTAAGAATTTTTCTGGAGT 14 191 0 TTTAAGAATT 0.665814 -110 AAATAACTTTTTAAAATCTTTTAAGCAATT 14 247 1 TTAAAATCTT 0.761652 -54 TTGATAATTCTTAAAAAATTTTTGCAAAAG 17 27 0 TTAAAAAATT 0.940157 -113 TCGAAAGCCTTTTAAATCTTTTATAAAAAC 17 76 1 TTTAAATCTT 0.761652 -64 GAAGAAGAAGTTAAAAACTTAGCTAAATTG 19 135 0 TTAAAAACTT 0.951913 -166 TTCTTGGCTATTTAAAAATTGCTTTAGAGG 20 34 1 TTTAAAAATT 0.940157 -66 GGAATCCCTCCTAAAAACTTAAGAAATAAA 22 17 0 CTAAAAACTT 0.715137 -24 ********** Masking position 2 Map Score: 16.8191 Number of sites scoring better than the average of aligned sites = 133 Number in coding regions = 79 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 3 TTATATATTTCCTCTCTTCAAATTCTCTCCT 2 15 1 CCTCTCTTCA 0.785473 -53 ACTCCAACCCTCCCTATCATTGAAGTTAA 2 49 0 CCTCCCTATA 0.856392 -19 ATTCCTTCCCCTTTCCCACTTTTAG 6 5 1 CTTCCCCTTC 0.900908 -174 AAAACTTTTCCCTCATCTCCAATTCTTGAGG 6 95 1 CCTCATCTCA 0.768014 -84 CTAACGACATCCTCCTTTTTCACTCCCATCT 7 68 1 CCTCCTTTTC 0.97881 -233 TTTCTTCCCTTTTCTTTAATTCTT 9 4 1 CTTCCCTTTC 0.946527 -33 TTAAAATATACCTCCTCTTAAACTCTTAGGG 10 19 0 CCTCCTCTTA 0.963728 -263 TTTTTAAACTCCTCCCTTAACTTCAAACAGG 10 146 1 CCTCCCTTAC 0.884783 -136 CTGAAGGAAGCCTCATTTTCCCTGTTTGAAG 10 166 0 CCTCATTTTC 0.884892 -116 TTTGCCTAACCCTACTTTTGAGGAGATCTTT 10 242 0 CCTACTTTTA 0.828222 -40 CATCTACACTCCGCCTTTTGATTCTGATATA 11 187 0 CCGCCTTTTA 0.860295 -58 CTCTTCATTTTCCCATTTTGGAG 12 3 1 CTTCATTTTC 0.672393 -24 CCTCCTTTTCTTCCCTTCAATTTACAATAA 15 10 1 CTTCCCTTCA 0.936874 -67 ACCTCCTCGCCTCCAGAAGTGTTTG 15 62 0 CCTCGCCTCA 0.735957 -15 GCTTTATAACCCTACTTTTTAAGTAAACCCG 18 38 1 CCTACTTTTA 0.828222 -45 TCAAGCTTAACTTCCCTTCCACACTTCGCAC 19 15 0 CTTCCCTTCA 0.936874 -286 TCATACCCCCTCCTTTTGAATTCTATCTC 21 47 0 CCTCCTTTTA 0.981035 -19 ********* * Masking position 1 Map Score: 16.8011 Number of sites scoring better than the average of aligned sites = 934 Number in coding regions = 844 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 4 TCTAAAAGTGGGAAAGGGGAAGGAAT 6 7 0 GGAAAGGGGA 0.811439 -172 AAAATTTTATGGAAACCGGAAACTTT 7 7 0 GGAAACCGGA 0.898487 -294 TTACTGCGAAGAGAACGCGCCTAACTTTGT 7 177 1 GAGAACGCGC 0.879359 -124 TCATTAGCTTGGGCACGGGAATCACCCTTA 7 237 1 GGGCACGGGA 0.968527 -64 TCCTTCGGCGGGAAACCCGCCAAACTGAAG 10 191 0 GGAAACCCGC 0.876922 -91 TGAGCCACCGGGGCACCGCCGAAGATTCTT 11 48 0 GGGCACCGCC 0.90104 -197 CAGCCTGGTAGAGCGGCCGCTTGGTAAGCG 11 76 1 GAGCGGCCGC 0.767273 -169 GCGGCCGCTTGGTAAGCGGCAGGTCCCGGG 11 88 1 GGTAAGCGGC 0.776893 -157 GCCGGGCTTTGAACCCGGGACCTGCCGCTT 11 101 0 GAACCCGGGA 0.826099 -144 TATTAGAATGGAGCCCCGGCCGGGCTTTGA 11 119 0 GAGCCCCGGC 0.975129 -126 CCTGGTAGGGCGCGGGCCTTGAGAGCC 13 8 1 GGGCGCGGGC 0.973431 -94 ACGGGGATTTGAACCCCGGCGGGCAAACGC 13 43 0 GAACCCCGGC 0.93969 -59 TTCTGGCGCCGGGACGGGGATTTGAACCCC 13 56 0 GGGACGGGGA 0.89908 -46 ATTAAATTATGAGAAGAGGCAATTGACAGA 14 117 1 GAGAAGAGGC 0.651934 -184 ********** Masking position 1 Map Score: 8.31129 Number of sites scoring better than the average of aligned sites = 341 Number in coding regions = 285 Number in noncoding regions = 56 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 5 TATTTAATTTAAAAATTTTAAGAAAAG 1 8 0 AAAAATTTTA 0.750037 -44 GAGATGAGGGAAAAGTTTTTAATTTGAAAA 6 84 0 AAAAGTTTTT 0.615406 -95 TTGAAGATGGAAAAATTTTATGGAAACCGG 7 18 0 AAAAATTTTA 0.750037 -283 GCCGAGATCCGAAAGTTTTAAAAGATCTCC 10 222 1 GAAAGTTTTA 0.896411 -60 TATTACTTGCGAAAGATTTATTAGAATGGA 11 137 0 GAAAGATTTA 0.800379 -108 ATTGCCCCCCAAAAGTTTTTTAAGATGAAC 11 220 0 AAAAGTTTTT 0.615406 -25 AAAGATTTTAAAAAGTTATTTGATGAAGAA 14 238 0 AAAAGTTATT 0.688788 -63 TGAATTGCTTAAAAGATTTTAAAAAGTTAT 14 249 0 AAAAGATTTT 0.81215 -52 TGGCTTTTGCAAAAATTTTTTAAGAATTAT 17 24 1 AAAAATTTTT 0.485213 -116 GTGTTTTTATAAAAGATTTAAAAGGCTTTC 17 78 0 AAAAGATTTA 0.909123 -62 TAATCCCAGGAAAAGCTTTATAACCCTACT 18 24 1 AAAAGCTTTA 0.752098 -59 ********** Masking position 4 Map Score: 9.90328 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 108 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 6 GTTAATCTAGGAGAGAATTTGAAGAGAGGAA 2 23 0 GAGGAATTTG 0.972179 -45 CCAAATTAGCGAGGGATTAAGTCGATGATAA 6 45 0 GAGGATTAAG 0.802398 -134 CAGGAGATGGGAGTGAAAAAGGAGGATGTCG 7 72 0 GAGGAAAAAG 0.936348 -229 TAACTTCAAACAGGGAAAATGAGGCTTCCTT 10 163 1 CAGGAAAATG 0.859069 -119 TCAAAAGGCGGAGTGTAGATGATGTTCATCT 11 197 1 GAGGTAGATG 0.798678 -48 CCTCCAGATTGAGTGAAATTCTGGCGCCGGG 13 73 0 GAGGAAATTC 0.907793 -29 AGAGGCAATTGACAGAATTTGCCAAAAAGCT 14 131 1 GACGAATTTG 0.787959 -170 GTTGCCCTCCGAGAGATTTTCTTAGACCAAA 17 118 0 GAGGATTTTC 0.731014 -22 ACAGTATGGACAGCGAAGATCTCTAGTCGTT 19 52 0 CAGGAAGATC 0.718717 -249 TAGTAAGATAGAGAGAATTAGGAATCACTCT 19 251 0 GAGGAATTAG 0.947709 -50 TATCTTACTAGAGGGAAAAAGACTATCCAGG 19 272 1 GAGGAAAAAG 0.936348 -29 CTAACTATTCGAGGGAAGTTGA 20 88 1 GAGGAAGTTG 0.971632 -12 *** ******* Masking position 2 Map Score: 7.12904 Number of sites scoring better than the average of aligned sites = 346 Number in coding regions = 323 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 7 AATTTTTAAATTAAATAACCATCAAGTTGTGGGG 1 21 1 TTAAACCATA 0.823098 -31 TCTCCCATCATTTGACAACCCTTATAAATCCTTA 5 39 0 TTAAACCCTA 0.959397 -35 TAAGACTATTTTTGAGAAACTTCAGGAGATGGGA 7 91 0 TTAAAACTTA 0.778042 -210 TTAAATCACCCCAAGAATTAAAGA 9 23 0 TTACACCCCA 0.977672 -14 CTTGAATCACCTCCAAATTTTTGCC 10 267 0 TTACACCTCA 0.925157 -15 TCAACGAAATTTGTAACAACTTAAATGAGAAACC 14 60 1 TTACAACTTA 0.848723 -241 TTTTCTGGAGTTCTATAATCCTCACAATTTGTTA 14 168 0 TTAAATCCTA 0.753992 -133 CTCCATCACCCCTACTTTCGGCTC 14 287 0 CTACACCCCA 0.88264 -14 TTTAAATCTTTTATAAAAACACCACAACAGTCTT 17 86 1 TTAAAACACA 0.739164 -54 ACCCTACTTTTTAAGTAAACCCGAGCAAGCTTAT 18 46 1 TTGAAACCCA 0.711847 -37 TTCCACCACCCTGATAAGCTTGCT 18 69 0 TTACACCCTA 0.97424 -14 ACGTTAAATTTTAGAGCAACCTAACTATTCGAGG 20 68 1 TTACAACCTA 0.952043 -32 ** * ****** * Masking position 8 Map Score: 5.75068 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 175 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 8 AATTTGGGAACGACTTTTTCAAATTAAAAAC 6 69 1 CGACTTTTCA 0.881385 -110 TAACGACATCCTCCTTTTTCACTCCCATCTC 7 69 1 CTCCTTTTCA 0.942903 -232 TAAAATATACCTCCTCTTAAACTCTTAGGGG 10 18 0 CTCCTCTTAA 0.942903 -264 TTGCCTAACCCTACTTTTGAGGAGATCTTTT 10 241 0 CTACTTTTAG 0.716866 -41 ATCTACACTCCGCCTTTTGATTCTGATATAT 11 186 0 CGCCTTTTAT 0.906147 -59 TAATTTAATAAGCCTTTTTAAGTTCTGTTTT 14 95 0 AGCCTTTTAA 0.913702 -206 TTTGAGAACTCGCCTCTTAAAGCATTTAAGA 14 204 0 CGCCTCTTAA 0.963417 -97 AACCTTCGAAAGCCTTTTAAATCTTTTATAA 17 71 1 AGCCTTTTAA 0.913702 -69 CTTTATAACCCTACTTTTTAAGTAAACCCGA 18 39 1 CTACTTTTAA 0.915516 -44 TCATACCCCCTCCTTTTGAATTCTATCTCA 21 46 0 CTCCTTTTAA 0.974623 -20 ******** ** Masking position 5 Map Score: 8.60125 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 104 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 9 GAAATTTCCCTAAATTCGGTGAAAAGGT 3 12 1 TAATTCGTGA 0.937863 -18 TAGCGAGGGATTAAGTCGATGATAACTCACTA 6 38 0 TAAGTCGTGA 0.974755 -141 CCTTATTATTTTTATGCGTTGAAATATAAATC 7 262 1 TTATGCGTGA 0.950476 -39 GGAGAATTCGTCAAGGCGATGAGGAGATCGGT 10 60 1 TAAGGCGTGA 0.973093 -222 ATATATCATCTGTATTCGAAGAATCTTCGGCG 11 30 1 TTATTCGAGA 0.829019 -215 CAAACACTTCTGGAGGCGAGGAGGT 15 62 1 TGAGGCGGGA 0.937261 -15 AGCGAAGATCTCTAGTCGTTGATAAATCAAGC 19 40 0 TTAGTCGTGA 0.980319 -261 TATAAAGCCATGTAGTCGAGGATGTTTCTTGA 21 17 1 TTAGTCGGGA 0.971292 -49 * ****** *** Masking position 4 Map Score: 5.35172 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 10 GGTTAATAAGGATTTATAAGGGTTGTCAAA 5 33 1 GATTTATAAG 0.957663 -41 TTTATGCGTTGAAATATAAATCCTTGATGG 7 272 1 GAAATATAAA 0.640985 -29 AACCTCCCGAGATTTATTAAGGATTAACAC 8 16 1 GATTTATTAA 0.838521 -33 ATTAACACTTGATTTTTAAAT 8 38 1 GATTTTTAAA 0.66621 -11 GAATACAGATGATATATAAGGTTTTCGGTA 11 17 0 GATATATAAG 0.911046 -228 ACTTGCGAAAGATTTATTAGAATGGAGCCC 11 133 0 GATTTATTAG 0.892252 -112 TTTTGATTCTGATATATAAGCTTTACTCTG 11 173 0 GATATATAAG 0.911046 -72 AATTTTTTAAGAATTATCAATCTTCGAGGG 17 37 1 GAATTATCAA 0.690671 -103 TTTTATAAAAGATTTAAAAGGCTTTCGAAG 17 74 0 GATTTAAAAG 0.760928 -66 AGTTAAGCTTGATTTATCAACGACTAGAGA 19 34 1 GATTTATCAA 0.889286 -267 ********** Masking position 5 Map Score: 4.87973 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 56 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 AGAAATTTCCCTAAATTCGG 3 1 1 AGAAATTTCC 0.812488 -29 TTTCAAATTAAAAACTTTTCCCTCATCTCC 6 85 1 AAAACTTTTC 0.778429 -94 CAGAGAACTTTTCGCTAGTTTAG 6 166 0 AGAACTTTTC 0.946818 -13 CGGTTTCCATAAAATTTTTCCATCTTCAAT 7 19 1 AAAATTTTTC 0.689044 -282 TACTGCGAAGAGAACGCGCCTAACTTTGTT 7 178 1 AGAACGCGCC 0.850786 -123 TTGATTTAGGAGAATTCGTCAAGGCGATGA 10 52 1 AGAATTCGTC 0.922784 -230 GGCAATTGACAGAATTTGCCAAAAAGCTGG 14 134 1 AGAATTTGCC 0.949114 -167 AAAGCATTTAAGAATTTTTCTGGAGTTCTA 14 187 0 AGAATTTTTC 0.918372 -114 GAAAAATTTGAGAACTCGCCTCTTAAAGCA 14 211 0 AGAACTCGCC 0.960636 -90 ********** Masking position 4 Map Score: 3.44161 Number of sites scoring better than the average of aligned sites = 205 Number in coding regions = 187 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 12 GAAGGAAGCCTCATTTTCCCTGTTTGAAGT 10 165 0 TCATTTTCCC 0.974572 -117 CTCTTCATTTTCCCATTTTGGAGG 12 5 1 TCATTTTCCC 0.974572 -22 CCTCCTTTTCTTCCCTTCAATTTAC 15 6 1 TTTTCTTCCC 0.916067 -71 TAAATCAAGCTTAACTTCCCTTCCACACTT 19 20 0 TTAACTTCCC 0.916067 -281 TCCTGGATAGTCTTTTTCCCTCTAGTAAGA 19 274 0 TCTTTTTCCC 0.953578 -27 TCAACTTCCCTCGAATAGTT 20 90 0 TCAACTTCCC 0.96997 -10 ********** Masking position 6 Map Score: 5.3946 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 67 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 13 AAAATAATAAGGGTGATTCCCGTGCCCAAG 7 244 0 GGGTGATTCC 0.964482 -57 CTTCAGTTTGGCGGGTTTCCCGCCGAAGGA 10 191 1 GCGGGTTTCC 0.958138 -91 TCCCCATGTTTAATGATTCCAAACAATCTT 14 24 0 TAATGATTCC 0.75912 -277 AAAGGCTTTCGAAGGTTTCCACCCTCGAAG 17 58 0 GAAGGTTTCC 0.944955 -82 GATCTGGAGAGAGTGATTCCTAATTCTCTC 19 242 1 GAGTGATTCC 0.983683 -59 AAGTTTTTAGGAGGGATTCCAGGA 22 27 1 GAGGGATTCC 0.989561 -14 ********** Masking position 7 Map Score: 2.85622 Number of sites scoring better than the average of aligned sites = 59 Number in coding regions = 56 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 14 AATTTTATGGAAACCGGAAACTTT 7 4 0 AACCGGAAAC 0.974546 -297 TGTGAGTACCGAAAACCTTATATATC 11 6 1 GACCGAAAAC 0.974546 -239 CTTAAATGAGAAACCAAAAACAGAACTTAAA 14 79 1 AACCAAAAAC 0.974174 -222 AGATTTTCTTAGACCAAAGACTGTTGTGGTG 17 105 0 AACCAAAGAC 0.944422 -35 CTCTGACACCGAAAACTCTATTTTTC 20 6 1 AACCGAAAAC 0.988371 -94 * ********* Masking position 8 Map Score: 0.707634 Number of sites scoring better than the average of aligned sites = 11 Number in coding regions = 9 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 15 CCGGGCTTTGAACCCGGGACCTGCCGCTTA 11 100 0 AACCCGGGAC 0.825574 -145 ATTAGAATGGAGCCCCGGCCGGGCTTTGAA 11 118 0 AGCCCCGGCC 0.979585 -127 GGGCTCTCAAGGCCCGCGCCCTACCAGG 13 9 0 GGCCCGCGCC 0.702443 -93 CGGGGATTTGAACCCCGGCGGGCAAACGCC 13 42 0 AACCCCGGCG 0.945203 -60 CGGGGTTCAAATCCCCGTCCCGGCGCCAGA 13 55 1 ATCCCCGTCC 0.966022 -47 TTTATCCCCCTCCAGATTGAGTG 13 89 0 ATCCCCCTCC 0.94593 -13 ATCCTCTACAAGCCTAGGCCAAAGATACCG 19 92 1 AGCCTAGGCC 0.723037 -209 TCATACCCCCTCCTTTTGAATTC 21 53 0 TACCCCCTCC 0.838822 -13 ********** Masking position 4 Map Score: 1.62969 Number of sites scoring better than the average of aligned sites = 176 Number in coding regions = 129 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282