AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_mjan_pyro_300.orf -o056_mjan_pyro_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.37 -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 = 0.37 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RMJ04589 300 M_jannaschii_chromosome #2 RMJ13440 183 M_jannaschii_chromosome #3 RMJ13199 103 M_jannaschii_chromosome #4 RMJ06792 300 M_jannaschii_chromosome #5 RMJ13997 135 M_jannaschii_chromosome #6 RMJ11052 103 M_jannaschii_chromosome #7 RMJ05932 226 M_jannaschii_chromosome #8 RMJ04294 123 M_jannaschii_chromosome #9 RMJ00594 184 M_jannaschii_chromosome #10 RMJ00596 205 M_jannaschii_chromosome #11 RMJ11884 235 M_jannaschii_chromosome #12 RPH01583 215 Pyrococcus_OT3 #13 RPH01584 238 Pyrococcus_OT3 Motif number 1 TACGAAAAACTATGAAAATTTTCTTTTAATC 1 31 0 TATAAAATTT 0.961183 -270 TAAATTTAGTTATGAAAAATTGAACACCCTC 1 69 1 TATAAAAATT 0.961183 -232 TTAATTAACAAAAGAAAAATTAAGCCTTGTC 1 168 1 AAAAAAAATT 0.779432 -133 AAAATATGCAAATCAAAAATTTCAGGTATCA 1 210 1 AATAAAAATT 0.948162 -91 TAAGATTAGTAATTAAATATTAAATACCAAC 2 47 1 AATAAATATT 0.922459 -137 AAAAGTTTGATATAAAAAAGTGTTGGTATTT 2 68 0 TATAAAAAGT 0.937668 -116 AAATCCTTAGTATAAAAATTTTTATATATGA 2 117 1 TATAAAATTT 0.961183 -67 GTGTAAGTGATATAAAAAAGTTTATAAAAAA 4 119 0 TATAAAAAGT 0.937668 -182 ATAAACTTATTATTAAACTTTGAACGCCTTC 4 217 0 TATAAACTTT 0.860782 -84 GATGGGATGTTATAAAAATTTTACCTAATCA 5 79 0 TATAAAATTT 0.961183 -57 AATAACAGAAAATTAAAAAGTTTTGGTGGGA 5 113 1 AATAAAAAGT 0.917443 -23 ATTATCCCTCAATTAAATTTTAGATAAAGAT 6 17 1 AATAAATTTT 0.922481 -87 GAAAAAGATATATTAAATATTTTTGCTTTGT 6 58 1 TATAAATATT 0.941554 -46 ATTATAACTAAAATAAAAAGTAAGTGAATAA 8 73 0 AAAAAAAAGT 0.682223 -51 TAGTTTTAAATATAAAAATTTGTATATTTAA 9 27 0 TATAAAATTT 0.961183 -158 TTAAAACTAATATAAAATTTTAAATTTTTAA 9 49 1 TATAAATTTT 0.941555 -136 CATTCAACTATATAAAAATTTCTACTGTATT 9 92 0 TATAAAATTT 0.961183 -93 TAGTTTAAAGTATTAAAAATTTTATTATGGC 9 159 1 TATAAAAATT 0.961183 -26 ATTATCCTAAAATTAAATAGTATGGTGAAAT 10 13 0 AATAAATAGT 0.878493 -193 CTTCAAAATTAATTAAAGTTTATTAATAAAT 11 97 1 AATAAAGTTT 0.712798 -139 TAAAGTTTATTAATAAATATTTGACAATAAA 11 110 1 TAAAAATATT 0.756823 -126 AAAGACACTATATAAAAAAGTTTTTGGTGCT 11 202 1 TATAAAAAGT 0.937668 -34 AAGATTTTCGAAAAAAATTGTGAACATTATA 12 60 0 AAAAAATTGT 0.582766 -156 TGGATTATCGAATAAAATTTTAAGATCTTAA 12 121 0 AATAAATTTT 0.922483 -95 AACCTAGGTATATAAAATTTTCGAGAAATAT 12 154 0 TATAAATTTT 0.941555 -62 TAAAAAACTAAATCAAACTTTCAATC 13 6 0 AATAAACTTT 0.820388 -233 *** ******* Masking position 11 Map Score: 39.2667 Number of sites scoring better than the average of aligned sites = 1036 Number in coding regions = 648 Number in noncoding regions = 388 Number of orfs with sites within 600 bp upstream = 324 Fraction of orfs with sites within 600 bp upstream = 0.0520398 Motif number 2 TACGAAAAACTATGAAAATTTTCTTTTAAT 1 32 0 TATGAAAATT 0.748262 -269 TAAATTTAGTTATGAAAAATTGAACACCCT 1 69 1 TATGAAAAAT 0.838899 -232 TGTCATATCCTATCAAAAATATGCAAATCA 1 195 1 TATCAAAAAT 0.838899 -106 AAAATATGCAAATCAAAAATTTCAGGTATC 1 210 1 AATCAAAAAT 0.736889 -91 ATTTAAAAATAATAAAATAGATATTTAGTA 1 262 0 AATAAAATAG 0.826809 -39 TAAATCTTACTATAAAAAGGATTG 1 287 1 TATAAAAAGG 0.79272 -14 AAAGACTAAAAATAAAAAATAGAATTAAAG 2 18 0 AATAAAAAAT 0.931355 -166 TAAGATTAGTAATTAAATATTAAATACCAA 2 47 1 AATTAAATAT 0.715488 -137 AAAAGTTTGATATAAAAAAGTGTTGGTATT 2 69 0 TATAAAAAAG 0.945819 -115 AAATCCTTAGTATAAAAATTTTTATATATG 2 117 1 TATAAAAATT 0.935063 -67 CGCTTTTGTCCATAAAAAATAATAACAAAA 3 29 1 CATAAAAAAT 0.738871 -75 TAAAAAAGTTTATAAAAAATCTTTCATGAA 4 108 0 TATAAAAAAT 0.96187 -193 GTGTAAGTGATATAAAAAAGTTTATAAAAA 4 120 0 TATAAAAAAG 0.945819 -181 GATGGGATGTTATAAAAATTTTACCTAATC 5 80 0 TATAAAAATT 0.935063 -56 AATAACAGAAAATTAAAAAGTTTTGGTGGG 5 113 1 AATTAAAAAG 0.773885 -23 ATTATCCCTCAATTAAATTTTAGATAAAGA 6 17 1 AATTAAATTT 0.589401 -87 GAAAAAGATATATTAAATATTTTTGCTTTG 6 58 1 TATTAAATAT 0.823811 -46 TTATAACTAAAATAAAAAGTAAGTGAATAA 8 73 0 AATAAAAAGT 0.748262 -51 TAGTTTTAAATATAAAAATTTGTATATTTA 9 28 0 TATAAAAATT 0.935063 -157 TTAAAACTAATATAAAATTTTAAATTTTTA 9 49 1 TATAAAATTT 0.879832 -136 CATTCAACTATATAAAAATTTCTACTGTAT 9 93 0 TATAAAAATT 0.935063 -92 TAGTTTAAAGTATTAAAAATTTTATTATGG 9 159 1 TATTAAAAAT 0.90192 -26 ATTATCCTAAAATTAAATAGTATGGTGAAA 10 14 0 AATTAAATAG 0.635069 -192 AAAGACACTATATAAAAAAGTTTTTGGTGC 11 202 1 TATAAAAAAG 0.945819 -34 TTGTGAACATTATAAAATAGGAGTACAATA 12 44 0 TATAAAATAG 0.898746 -172 TGGATTATCGAATAAAATTTTAAGATCTTA 12 122 0 AATAAAATTT 0.797485 -94 AACCTAGGTATATAAAATTTTCGAGAAATA 12 155 0 TATAAAATTT 0.879832 -61 ********** Masking position 5 Map Score: 31.4701 Number of sites scoring better than the average of aligned sites = 1351 Number in coding regions = 894 Number in noncoding regions = 457 Number of orfs with sites within 600 bp upstream = 377 Fraction of orfs with sites within 600 bp upstream = 0.0605525 Motif number 3 CAACTTTACGAAAAACTATGAAAATTTTCTTTTA 1 34 0 AAACTAGAAA 0.50712 -267 TTATCTTTAGAATATTTGCAAAAACCAATAATTT 1 125 1 AAATTGAAAA 0.679636 -176 TTTTTATAGTAAGATTTAAAAATAATAAAATAGA 1 271 0 AAATTAAAAA 0.852983 -30 TTAGCATTTGAAGAACTTTAAAAAGTTTGATATA 2 85 0 AAACTTAAAA 0.86201 -99 TAAAATTGAAATCATATATAAAAATTTTTATACT 2 125 0 ATAATAAAAA 0.497768 -59 AGTGATATAAAAAAGTTTATAAAAAATCTTTCAT 4 111 0 AAATTTTAAA 0.623173 -190 TATTATCTCAATAAGTTTTGAAAGGCACTATACT 4 156 0 ATATTTGAAG 0.76373 -145 TAATAAGTTTATTAATTTTGAAAGGCACTATATA 4 236 1 ATATTTGAAG 0.76373 -65 ACTTTAATCTATCATTTTGAAAGGTTAAGTTATA 5 27 1 ATATTTAAAG 0.823668 -109 TTAGATAAAGATAATTATAAAAGAAAAAGATATA 6 36 1 ATATATAAAA 0.583056 -68 TATTGATAAAAATAAATTCAAAAAGGAGCTTGAA 7 76 1 AAAATTAAAA 0.864375 -151 GTAGATGTTGAAAAAATTGAAAAAGAATGTGAAG 7 166 1 AAAATTAAAA 0.864375 -61 AAAGAATGTGAAGAATTTAGAAAAAAATTCAAAT 7 187 1 AAATTTGAAA 0.944037 -40 ATCTACATTAATCATATTCAAAAGGTGAAATA 8 102 1 ATAATTAAAG 0.549804 -22 AAAATTTTATATTAGTTTTAAATATAAAAATTTG 9 36 0 ATATTTAAAA 0.940924 -149 TATATTGCTTAAAAATTTAAAATTTTATATTAGT 9 54 0 AAATTTAAAT 0.578051 -131 ATTTATAGAAATAATTTTAAAGTATTTATTAGGT 9 126 0 ATATTTAAGA 0.817484 -59 TATTTCTATAAATAGTTTAAAGTATTAAAAATTT 9 147 1 AAATTTAAGA 0.872694 -38 TTATAGTGAAATAAATTTAAAACATAAATGTTGG 10 77 0 ATATTTAAAA 0.940924 -129 AATTAAACCGAAAACCTTAAAATAGTATT 10 187 1 AAACTTAAAA 0.86201 -19 ATACCGTATTAATACTTAAAAATATCTTTAAACT 11 56 1 AAATTAAAAA 0.852982 -180 ATAAACTTTAATTAATTTTGAAGACAGTATAGTT 11 86 0 ATATTTGAAA 0.916818 -150 GTCTTTCAAAAACATTTTGAAGTAACCAGTAGCT 11 174 0 AAATTTAAGA 0.872694 -62 AAAAATTGTGAACATTATAAAATAGGAGTACAAT 12 45 0 AAATATAAAA 0.681556 -171 ATATAATACTAAGATTTTCGAAAAAAATTGTGAA 12 67 0 AAATTTGAAA 0.944037 -149 AAATCTTAGTATTATATAGAAAAATTTTCTAAAA 12 84 1 ATAATAAAAA 0.497768 -132 TAAGATCTTAAAAATTTTAGAAAATTTTTCTATA 12 98 0 AAATTTGAAA 0.944037 -118 CTAGGTATATAAAATTTTCGAGAAATATCTTGGA 12 148 0 AAATTTGAGA 0.825898 -68 ** * *** *** * Masking position 4 Map Score: 26.3107 Number of sites scoring better than the average of aligned sites = 1759 Number in coding regions = 1346 Number in noncoding regions = 413 Number of orfs with sites within 600 bp upstream = 327 Fraction of orfs with sites within 600 bp upstream = 0.0525217 Motif number 4 TTTCATAGTTTTTCGTAAAGTTGTTAAATTTA 1 45 1 TTTGTAAAGT 0.565364 -256 TTAAATTTAGTTATGAAAAATTGAACACCCTC 1 68 1 TTAGAAAAAT 0.556362 -233 GAACACCCTCTATCGAAAGACATTTATTATGT 1 90 1 TATGAAAGAA 0.860162 -211 ATTTGCATATTTTTGATAGGATATGACAAGGC 1 191 0 TTTGATAGGT 0.690575 -110 CAATCCTTTTTATAGTAAGATTTAAAAATAAT 1 279 0 TATGTAAGAT 0.465595 -22 AAAATAGAATTAAAGAAAGAAA 2 1 0 TAAGAAAGAA 0.465595 -183 ACAAAAAGTATTTGGAAAGGTTAGGAGTTGAT 3 78 1 TTTGAAAGGT 0.936676 -26 TCTCAATAAGTTTTGAAAGGCACTATACTTTT 4 153 0 TTTGAAAGGA 0.936676 -148 AGTTTATTAATTTTGAAAGGCACTATATATCT 4 241 1 TTTGAAAGGA 0.936676 -60 TAATCTATCATTTTGAAAGGTTAAGTTATAGC 5 31 1 TTTGAAAGGT 0.936676 -105 TCAATTAAATTTTAGATAAAGATAATTATAAA 6 25 1 TTTGATAAAA 0.571918 -79 TCTATAAACTTATGGAAAAGGTGTAGATGTTG 7 144 1 TATGAAAAGT 0.798456 -83 AAGGTGTAGATGTTGAAAAAATTGAAAAAGAA 7 161 1 TGTGAAAAAT 0.582739 -66 ATGTGAAGAATTTAGAAAAAAATTCAAATTCA 7 192 1 TTTGAAAAAA 0.898524 -35 TTCAAAATGTTTTTGAAAGACACTATATAAAA 11 187 1 TTTGAAAGAA 0.934468 -49 ATACTAAGATTTTCGAAAAAAATTGTGAACAT 12 64 0 TTTGAAAAAA 0.898476 -152 CTTAGTATTATATAGAAAAATTTTCTAAAATT 12 88 1 TATGAAAAAT 0.79251 -128 TATATAAAATTTTCGAGAAATATCTTGGATTA 12 145 0 TTTGAGAAAA 0.52895 -71 *** ****** * Masking position 1 Map Score: 14.856 Number of sites scoring better than the average of aligned sites = 480 Number in coding regions = 366 Number in noncoding regions = 114 Number of orfs with sites within 600 bp upstream = 98 Fraction of orfs with sites within 600 bp upstream = 0.0157404 Motif number 5 AAAATTAAGTTAAGATTAAAAGAAAATTTTCATAGTT 1 18 1 TAATAAAAAT 0.471503 -283 ATGCCAATTAATTAACAAAAGAAAAATTAAGCCTTGT 1 161 1 ATAAAAAAAT 0.934132 -140 GTCATATCCTATCAAAAATATGCAAATCAAAAATTTC 1 196 1 ATAAATAAAT 0.532509 -105 AAGATTTAAAAATAATAAAATAGATATTTAGTAGAAC 1 258 0 AAAAAAAATT 0.776558 -43 TAAAGACTAAAAATAAAAAATAGAATTAAAGAAAGAA 2 12 0 AAAAAAAAAT 0.952996 -172 AGGGTAAAGTAATGATAAAATTGAAATCATATATAAA 2 137 0 AAAAAAAAAT 0.952997 -47 GTCCATAAAAAATAATAACAAAAAACTATTTATATAC 3 36 1 AAAAACAAAT 0.913244 -68 ACATCCCATCATAAATAACAGAAAATTAAAAAGTTTT 5 100 1 ATAAACAAAT 0.880426 -36 AGATAAAGATAATTATAAAAGAAAAAGATATATTAAA 6 38 1 AAAAAAAAAG 0.648789 -66 TCCAGAATTTATTGATAAAAATAAATTCAAAAAGGAG 7 67 1 ATAAAAAAAT 0.934132 -160 GTGAAGAATTTAGAAAAAAATTCAAATTCAGAAATTG 7 194 1 TAAAAAAAAT 0.88693 -33 AAAATCTAAATATAAGAAAATAGAAATAACA 8 5 0 TAAAAAAAAT 0.88693 -119 ATATTAAACAATACAGAAAACAAAACTTATTTATTCA 8 43 1 ATAAAAAAAT 0.934132 -81 AGATTATAACTAAAATAAAAAGTAAGTGAATAAATAA 8 69 0 TAAAAAAAAT 0.88693 -55 AGTGAAATAAATTTAAAACATAAATGTTGGTTATAAA 10 70 0 ATAAACAATT 0.557938 -136 AAAACCATATAATAATAACATAGAATTTAAATACCAT 10 126 0 AAAAACAAAT 0.913244 -80 CAGAAATCGATACTATAAAAACCATATAATAATAACA 10 143 0 TAAAAAAATT 0.573484 -63 CGTTTAATAGAAATAGAAACAATAAATATACCGTATT 11 29 1 AAAAAACAAT 0.781036 -207 TCAAATATTTATTAATAAACTTTAATTAATTTTGAAG 11 97 0 ATAAAACAAT 0.713877 -139 CAAGAGATTTATGGACAAAAGTAAAGTGTA 12 4 0 ATAAAAAAAT 0.934132 -212 AGCAGATTTAAAAAACTAAATCAAACTTTCAATC 13 8 0 AAATAAAAAT 0.697523 -231 CATTGATACCTTGGATAACACCGAAGTTAGGGCCCAT 13 107 0 TTAAACAAAT 0.740166 -132 ** * **** ** * Masking position 8 Map Score: 27.0495 Number of sites scoring better than the average of aligned sites = 677 Number in coding regions = 489 Number in noncoding regions = 188 Number of orfs with sites within 600 bp upstream = 156 Fraction of orfs with sites within 600 bp upstream = 0.0250562 Motif number 6 TTATTATGTCCTTTATCTTTAGAATATTTGCAAA 1 113 1 CTTATCTTTA 0.846955 -188 TCTTCAAATGCTAAATCCTTAGTATAAAAATTTT 2 105 1 CTAATCCTTA 0.830093 -79 TTTATCATTACTTTACCCTTAACATTTTTTGGTG 2 155 1 CTTACCCTTA 0.980248 -29 AAAACTATTTATATACCCTTCACAAAAAGTATTT 3 57 1 ATAACCCTTA 0.815025 -47 TTAATCAACTCCTAACCTTTCCAAATACTTTTTG 3 79 0 CCTACCTTTA 0.947737 -25 AACGCTATAACTTAACCTTTCAAAATGATAGATT 5 32 0 CTTACCTTTA 0.972915 -104 AATCCCACCAAAACTTTTTAATTTTCTGTTA 5 115 0 CCAAACTTTA 0.640951 -21 AACTACACCCTTATAAATTGATTAAA 6 88 0 CTAACCCTTA 0.96943 -16 CAGACGATAACTTTAACTTTTGAAATTCCAGAAT 7 41 1 CTTAACTTTA 0.846955 -186 TTTTCAACATCTACACCTTTTCCATAAGTTTATA 7 146 0 CTAACCTTTA 0.958252 -81 TATTTCACCTTTTGAATATGATTAAT 8 108 0 TTTACCTTTA 0.738928 -16 ACGTCAATGGACTTACCCTTCTCATTGATACCTT 13 132 0 ACTACCCTTA 0.776836 -107 CTGGTTTTTACTTACCCCTTATTATTTACCTCAA 13 193 1 CTTCCCCTTA 0.88672 -46 *** ****** * Masking position 14 Map Score: 11.7234 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 105 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 7 GGACATAATAAATGTCTTTCGATAGAGGGT 1 94 0 AATGTCTTTC 0.928208 -207 CTAAAAGTATAGTGCCTTTCAAAACTTATT 4 151 1 AGTGCCTTTC 0.982828 -150 TTAAACTTTGAACGCCTTCCTTTAGGAGGC 4 206 0 AACGCCTTCC 0.974692 -95 GTAGATATATAGTGCCTTTCAAAATTAATA 4 245 0 AGTGCCTTTC 0.982828 -56 TAAATATTTAAATGCCTTCCTTTGGAAGGT 11 137 1 AATGCCTTCC 0.982828 -99 GTAGCTTATGAACACCTTCCAAAGGAAGGC 11 150 0 AACACCTTCC 0.833209 -86 TTTTTTATATAGTGTCTTTCAAAAACATTT 11 191 0 AGTGTCTTTC 0.939806 -45 ********** Masking position 1 Map Score: 7.74599 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 28 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 TTATGTCCTTTATCTTTAGAATATTTGCAA 1 116 1 TATCTTTAGA 0.920095 -185 TCTATTTTATTATTTTTAAATCTTACTATA 1 271 1 TATTTTTAAA 0.898214 -30 AAAGGCACTATACTTTTAGAGTGTAAGTGA 4 140 0 TACTTTTAGA 0.757374 -161 TTAATAAACTTATTATTAAACTTTGAACGC 4 221 0 TATTATTAAA 0.75825 -80 TAATCAGATATATCATTAAAACGCTATAAC 5 55 0 TATCATTAAA 0.832616 -81 TCTATTTTCTTATATTTAGATTTTCATATT 8 18 1 TATATTTAGA 0.878866 -106 TTTTCACCTATATATTTAAATATACAAATT 9 12 1 TATATTTAAA 0.898149 -173 TACAAATTTTTATATTTAAAACTAATATAA 9 34 1 TATATTTAAA 0.898149 -151 TTTATAGAAATAATTTTAAAGTATTTATTA 9 129 0 TAATTTTAAA 0.710403 -56 TATAGTGAAATAAATTTAAAACATAAATGT 10 80 0 TAAATTTAAA 0.710402 -126 AGAATTTAAATACCATTAGAACACAACTAA 10 112 0 TACCATTAGA 0.637724 -94 TACTTAAAAATATCTTTAAACTATACTGTC 11 68 1 TATCTTTAAA 0.93332 -168 ********** Masking position 8 Map Score: 8.85789 Number of sites scoring better than the average of aligned sites = 464 Number in coding regions = 340 Number in noncoding regions = 124 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 9 TATTTAGTAGAACTCACCATATAATAATTA 1 241 0 AACTCACCAT 0.921404 -60 AATCTCACCATTTAATTAGTC 4 290 0 ATCTCACCAT 0.973752 -11 AAGTTCATTTAATTCATCAA 5 1 0 AATTCATCAA 0.610212 -135 TTTTTATAACATCCCATCATAAATAACAGA 5 92 1 ATCCCATCAT 0.855975 -44 AATCCCACCAAAACTTTTTAA 5 125 0 ATCCCACCAA 0.904874 -11 GAGCTTGAAAATTTCATCAAGAAAAAAATC 7 101 1 ATTTCATCAA 0.832046 -126 TATTTCACCTTTTGAATATGA 8 113 0 ATTTCACCTT 0.819578 -11 AAATTTCACCATACTATTTAAT 10 3 1 ATTTCACCAT 0.966461 -203 TTTTAAATTTATTTCACTATAATTTAGTTG 10 89 1 ATTTCACTAT 0.738558 -117 ********** Masking position 6 Map Score: 4.4954 Number of sites scoring better than the average of aligned sites = 174 Number in coding regions = 134 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 10 TTATTATGTCCTTTATCTTTAGAATATTTG 1 113 1 CTTTATCTTT 0.795339 -188 TCTTCAAATGCTAAATCCTTAGTATAAAAA 2 105 1 CTAAATCCTT 0.651359 -79 TTTATCATTACTTTACCCTTAACATTTTTT 2 155 1 CTTTACCCTT 0.95035 -29 AAAACTATTTATATACCCTTCACAAAAAGT 3 57 1 ATATACCCTT 0.746254 -47 TTAATCAACTCCTAACCTTTCCAAATACTT 3 83 0 CCTAACCTTT 0.85549 -21 TTGAAAGGCACTATACTTTTAGAGTGTAAG 4 143 0 CTATACTTTT 0.586188 -158 TAAACTTATTATTAAACTTTGAACGCCTTC 4 217 0 ATTAAACTTT 0.390042 -84 AACGCTATAACTTAACCTTTCAAAATGATA 5 36 0 CTTAACCTTT 0.942117 -100 AATCCCACCAAAACTTTTTAATTTTCT 5 119 0 CCAAAACTTT 0.432129 -17 AAAATATTTAATATATCTTTTTCTTTTATA 6 51 0 ATATATCTTT 0.373862 -53 AACTACACCCTTATAAATTGAT 6 92 0 CTACACCCTT 0.894737 -12 CAGACGATAACTTTAACTTTTGAAATTCCA 7 41 1 CTTTAACTTT 0.795339 -186 TTTTCAACATCTACACCTTTTCCATAAGTT 7 150 0 CTACACCTTT 0.904933 -77 TATTTCACCTTTTGAATATGAT 8 112 0 TTTCACCTTT 0.469291 -12 TACACTTTACTTTTGTCCATAAAT 12 5 1 CTTTACTTTT 0.666433 -211 ACGTCAATGGACTTACCCTTCTCATTGATA 13 136 0 ACTTACCCTT 0.60138 -103 CTGGTTTTTACTTACCCCTTATTATTTACC 13 193 1 CTTACCCCTT 0.633725 -46 ********** Masking position 9 Map Score: 5.43032 Number of sites scoring better than the average of aligned sites = 1014 Number in coding regions = 926 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 11 CAATAAGTTTTGAAAGGCACTATACTTTTA 4 152 0 TGAAAGGCAC 0.980353 -149 AAGGTATTAATGAACGCCTCCTAAAGGAAG 4 191 1 TGAACGCCTC 0.976773 -110 TATTAAACTTTGAACGCCTTCCTTTAGGAG 4 208 0 TGAACGCCTT 0.866768 -93 TTATTAATTTTGAAAGGCACTATATATCTA 4 244 1 TGAAAGGCAC 0.980353 -57 AAAATGTTTTTGAAAGACACTATATAAAAA 11 190 1 TGAAAGACAC 0.948171 -46 AGGGCCCATGTGAAAGCCGCACTGAAGGCT 13 86 0 TGAAAGCCGC 0.977083 -153 ********** Masking position 4 Map Score: 3.50896 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 9 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 12 TTAATTAATTGGCATCTAAATTATTGGTTTTTGC 1 142 0 GGATAAATTT 0.98372 -159 AAAAATTTCAGGTATCATAATTATTATATGGTGA 1 224 1 GGATTAATTT 0.937484 -77 CTAAATCCTTAGTATAAAAATTTTTATATATGAT 2 115 1 AGATAAATTT 0.825603 -69 TTTTGTGAAGGGTATATAAATAGTTTTTTGTTAT 3 50 0 GGATAAATAT 0.960018 -54 TCATCATCGAGGAATTAAAATAATCTCTCAGCCC 4 46 1 GGATAAATAT 0.957697 -255 ATGATGGGATGTTATAAAAATTTTACCTAATCAG 5 78 0 GTATAAATTT 0.826497 -58 AAAAAATCTTGGGAGAGAAATTCTATAAACTTAT 7 123 1 GGAGAAATTT 0.919271 -104 GTGTTCTAATGGTATTTAAATTCTATGTTATTAT 10 118 1 GGATAAATTT 0.937419 -88 GTATTAATACGGTATATTTATTGTTTCTATTTCT 11 37 0 GGATTTATTT 0.655843 -199 TCCAAAGGAAGGCATTTAAATATTTATTGTCAAA 11 129 0 GGATAAATAT 0.960049 -107 CTTGAACCTAGGTATATAAAATTTTCGAGAAATA 12 155 0 GGATAAAATT 0.884831 -61 ** ** ***** * Masking position 10 Map Score: 12.5034 Number of sites scoring better than the average of aligned sites = 83 Number in coding regions = 44 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 13 CAAACTTTTTAAAGTTCTTCAAATGCTAAA 2 90 1 AAAGTTCTTC 0.886608 -94 GAAAGGTTCATCATATTAAGTC 4 3 1 AAGGTTCATC 0.977164 -298 CAGCCCCCGTAAGGTTCATCATCCTAAATT 4 74 1 AAGGTTCATC 0.977164 -227 ATGATAGATTAAAGTTCATTTAATTCATCA 5 12 0 AAAGTTCATT 0.870949 -124 AGGAGCTTGAAAATTTCATCAAGAAAAAAA 7 99 1 AAATTTCATC 0.829796 -128 TTTATATACCTAGGTTCAAGATGGAGGTGT 12 169 1 TAGGTTCAAG 0.542258 -47 CTCCTAGAGCAAAGTTCATGCTATATACTT 13 49 0 AAAGTTCATG 0.948509 -190 CCAATCTAAGAAAGTTCAACGTCAATGGAC 13 154 0 AAAGTTCAAC 0.941116 -85 ********** Masking position 2 Map Score: 4.99688 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 36 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 14 TAATCTTAACTTAATTTTTGGTTTC 1 5 0 TTAATTTTGG 0.899998 -296 AATTGGCATCTAAATTATTGGTTTTTGCAAA 1 139 0 TAAATTATGG 0.807647 -162 TTTCTTTTGTTAATTAATTGGCATCTAAATT 1 154 0 TAATTAATGG 0.860083 -147 GGTATCATAATTATTATATGGTGAGTTCTAC 1 234 1 TTATTATTGG 0.929459 -67 TTATAAAGACTAATTAAATGGTGAGATT 4 283 1 TAATTAATGG 0.860082 -18 CAAAACTTTTTAATTTTCTGTTATTTATGAT 5 107 0 TAATTTTTGT 0.44018 -29 TTTTATTTTTTGGTGGTAATTAT 7 3 1 TTATTTTTGG 0.929459 -224 ACCATACTATTTAATTTTAGGATAATGCTCT 10 18 1 TTAATTTAGG 0.714429 -188 TTCTATGTTATTATTATATGGTTTTTATAGT 10 138 1 TTATTATTGG 0.929459 -68 CTATTAAACGTTAATAAGAGGGATAAAA 11 8 0 TTAATAAAGG 0.630834 -228 ******* *** Masking position 5 Map Score: 2.95965 Number of sites scoring better than the average of aligned sites = 330 Number in coding regions = 261 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 66 Fraction of orfs with sites within 600 bp upstream = 0.0106007 Motif number 15 AGGACATAATAAATGTCTTTCGATAGAGGG 1 95 0 AAATGTCTTT 0.779179 -206 GAGTTCTACTAAATATCTATTTTATTATTT 1 256 1 AAATATCTAT 0.898576 -45 TCCTTAGTATAAAAATTTTTATATATGATT 2 120 1 AAAAATTTTT 0.431085 -64 AAAGTTTATAAAAAATCTTTCATGAATAAT 4 104 0 AAAAATCTTT 0.764711 -197 TTTCTTTTATAATTATCTTTATCTAAAATT 6 32 0 AATTATCTTT 0.689126 -72 AAAATATTTAATATATCTTTTTCTTTTATA 6 51 0 ATATATCTTT 0.677717 -53 AAGATATATTAAATATTTTTGCTTTGTTTA 6 62 1 AAATATTTTT 0.652575 -42 TCATCAAGAAAAAAATCTTGGGAGAGAAAT 7 114 1 AAAAATCTTG 0.795388 -113 TTGTATATTTAAATATATAGGTGAAAAT 9 9 0 AAATATATAG 0.30495 -176 TGTAATTGCTAAATATCGTTTATAACCAAC 10 52 1 AAATATCGTT 0.766454 -154 TAATACTTAAAAATATCTTTAAACTATACT 11 65 1 AAATATCTTT 0.918313 -171 ATTTATTGTCAAATATTTATTAATAAACTT 11 112 0 AAATATTTAT 0.676037 -124 GAAGGCATTTAAATATTTATTGTCAAATAT 11 126 0 AAATATTTAT 0.676037 -110 TTTTGTCCATAAATCTCTTGCTCTATTGTA 12 21 1 AAATCTCTTG 0.681746 -195 AATTTTCGAGAAATATCTTGGATTATCGAA 12 140 0 AAATATCTTG 0.935336 -76 ********** Masking position 1 Map Score: 10.773 Number of sites scoring better than the average of aligned sites = 835 Number in coding regions = 688 Number in noncoding regions = 147 Number of orfs with sites within 600 bp upstream = 140 Fraction of orfs with sites within 600 bp upstream = 0.0224863