AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i006_mjan_pyro_300.orf -o006_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 RMJ14456 184 M_jannaschii_chromosome #2 RMJ00407 205 M_jannaschii_chromosome #3 RMJ01820 25 M_jannaschii_chromosome #4 RMJ02054 97 M_jannaschii_chromosome #5 RMJ04312 88 M_jannaschii_chromosome #6 RMJ00776 21 M_jannaschii_chromosome #7 RMJ00835 128 M_jannaschii_chromosome #8 RMJ09510 85 M_jannaschii_chromosome #9 RMJ09945 140 M_jannaschii_chromosome #10 RMJ06351 220 M_jannaschii_chromosome #11 RMJ07785 131 M_jannaschii_chromosome #12 RMJ15852 162 M_jannaschii_chromosome #13 RMJ09311 240 M_jannaschii_chromosome #14 RMJ09076 45 M_jannaschii_chromosome #15 RMJ08813 224 M_jannaschii_chromosome #16 RMJ02718 147 M_jannaschii_chromosome #17 RMJ10497 83 M_jannaschii_chromosome #18 RPH01395 71 Pyrococcus_OT3 #19 RPH01070 300 Pyrococcus_OT3 Motif number 1 ATGTTTTCTTAATTTTTAATTTACCATTAA 1 103 1 AATTTTTAAT 0.961777 -82 TATGATATTAAATTTTTAATGGTAAATTAA 1 118 0 AATTTTTAAT 0.961777 -67 TATGTTATTTATTTTATTATCCACAATAAA 2 158 1 ATTTTATTAT 0.841695 -48 AAAATCTTAAAATTTATTGTGGATAATAAA 2 170 0 AATTTATTGT 0.895287 -36 CAAAGTTATTATTTATAAAATCTTAAAAT 2 187 0 TATTTATAAA 0.83463 -19 TCCCTCCAAAAATTTTTAATT 3 2 0 AATTTTTAAT 0.961777 -24 TCAAACTTTTTATTTTTTGTTGTAAATATT 4 14 1 TATTTTTTGT 0.844867 -84 TTGTTGTAAATATTTATAATTTATAGAACA 4 30 1 TATTTATAAT 0.92795 -68 TATTTGTTTAATTTTTTTATCTATATTGGT 7 45 1 ATTTTTTTAT 0.855729 -84 TATTCAATACATTTTTTAATCTTTGGAAAA 7 76 1 ATTTTTTAAT 0.880751 -53 CATATTAAGCTATTTTTTATTACAT 7 114 1 TATTTTTTAT 0.920243 -15 TTTTCTCTTTTATTTATTATGTATAAATTT 9 32 1 TATTTATTAT 0.91184 -109 ATTATGTATAAATTTATAAAAATAAATATA 9 47 1 AATTTATAAA 0.898361 -94 ATGTGTTTGGAATTTTTAGTTTGATATTAG 10 151 1 AATTTTTAGT 0.922342 -70 TATTAGGTTATATTTTTAGTTTTTTGCTCC 10 175 1 TATTTTTAGT 0.871494 -46 TTTGCTCCCCAATTTTTTATCTGCTGTTTT 10 197 1 AATTTTTTAT 0.952845 -24 TTTTAATTTTTTATTTTTTATGAA 12 5 1 AATTTTTTAT 0.952845 -158 ACAATTTTAGTATTTATAATTTGTCATTAA 12 49 0 TATTTATAAT 0.92795 -114 CTTTAGTGCTAATTTTTTGTAGATTTTATT 12 90 0 AATTTTTTGT 0.905104 -73 TAAGTAATTTAATTTTTTAAAGTTATATAA 13 47 0 AATTTTTTAA 0.887871 -194 TTAAATTACTTATTTATAATATTTTAGCTG 13 65 1 TATTTATAAT 0.92795 -176 CTATCTTTACAATTTTTAATTTTGGCTATG 13 134 0 AATTTTTAAT 0.961777 -107 AGCATAAGAATTTTTATAAAGTTCTACGGT 13 185 1 TTTTTATAAA 0.596953 -56 ACTATGAGGAAATTTTTAATATTTTTAATA 13 218 1 AATTTTTAAT 0.961777 -23 TATACGTAAATTTTTATAAAAAGGATGAAT 14 12 0 TTTTTATAAA 0.596953 -34 AAAACGGTTTAATTTTTTAAATTTCTATAG 15 41 0 AATTTTTTAA 0.887871 -184 GCATAAAAGATATTTATAAAAAACGGTTTA 15 60 0 TATTTATAAA 0.83463 -165 AAATTAATAAAATTTATTGATAAAGATTTG 15 159 0 AATTTATTGA 0.770138 -66 AAAACACTATAATTTTTAGTTAAGATTAAA 15 192 1 AATTTTTAGT 0.922342 -33 CTATTGCAGTATTTTATAATATTTGCATGG 16 73 0 ATTTTATAAT 0.868366 -75 ATTATTCCAATTTTTTATTAGAGTTTTA 16 130 0 AATTTTTTAT 0.952845 -18 TAAAAACTTAAATTTATTAAATACTT 17 7 0 AATTTATTAA 0.876516 -77 AAGTTTTTAGTTTTTATTATTTTATTTTTA 17 28 1 TTTTTATTAT 0.752231 -56 TTTATTATTTTATTTTTAGTTTTTAATAGA 17 40 1 TATTTTTAGT 0.871494 -44 TTAATAGAAAATTTTATAATTCAGGTGATA 17 62 1 ATTTTATAAT 0.868366 -22 CTATAGCTCAAATTTATTAACAATTACGCT 19 154 1 AATTTATTAA 0.876516 -147 ********** Masking position 5 Map Score: 60.5755 Number of sites scoring better than the average of aligned sites = 1243 Number in coding regions = 806 Number in noncoding regions = 437 Number of orfs with sites within 600 bp upstream = 369 Fraction of orfs with sites within 600 bp upstream = 0.0592676 Motif number 2 GTTTTCTTAATTTTTAATTTACCATTAAAAA 1 105 1 TTTTTATTTA 0.730436 -80 AGAATTAGTATTTAAAACTTTTGGTTGGGTG 1 156 1 TTTAAACTTT 0.761681 -29 TTTAGGCATCTAAATACCTTTTTAATATAAA 2 72 1 TAAATACTTT 0.733484 -134 AACCATATGTTATTTATTTTATTATCCACAA 2 153 1 TATTTATTTA 0.534709 -53 AATTAAAAATTTTTGGAGGGATA 3 3 1 TTAAAATTTT 0.478075 -23 GCTTCAAACTTTTTATTTTTTGTTGTAAAT 4 10 1 TTTTTATTTT 0.923995 -88 GTTGTAAATATTTATAATTTATAGAACATCT 4 32 1 TTTATATTTA 0.753916 -66 GTTGTTATTGTTATTATCTTTAAAACCTTAA 4 64 1 TTATTACTTT 0.85162 -34 CTATTATTAACATATACCTTTTATCATTCAT 7 13 0 CATATACTTT 0.452779 -116 TCAATACATTTTTTAATCTTTGGAAAAGTTG 7 79 1 TTTTAACTTT 0.738684 -50 CAATCACATATATATACTTTTTTAAAGATAG 8 18 0 TATATATTTT 0.853575 -68 AATATCAACCCTTATAATTTTCAATCACATA 8 39 0 CTTATATTTT 0.603188 -47 AAATAGTTTATATTTATTTTTATAAATTTAT 9 54 0 TATTTATTTT 0.837554 -87 AATATAAAATTTTTTGGGGATAA 10 3 1 TATAAATTTT 0.513642 -218 TTAGGTTATATTTTTAGTTTTTTGCTCCCCA 10 177 1 TTTTTATTTT 0.923995 -44 TTTTAATTTTTTATTTTTTATGAAATTT 12 8 1 TTTTTATTTT 0.923995 -155 CACCGTAATATTAATAACTTATAATAACTAC 12 119 0 TTAATACTTA 0.591232 -44 ATTGGACTATTTTTATTTTTGTAAAATTTT 13 10 1 TTTTTATTTT 0.923995 -231 TTTTGTAAAATTTTTACCTTTTATATAACTT 13 27 1 TTTTTACTTT 0.939771 -214 TTTTACCTTTTATATAACTTTAAAAAATTAA 13 38 1 TATATACTTT 0.882101 -203 ATCTTTACAATTTTTAATTTTGGCTATGGAA 13 131 0 TTTTTATTTT 0.923995 -110 TTATATAAATTTTCTATCTTTACAATTTTTA 13 146 0 TTTCTACTTT 0.784556 -95 GAGGAAATTTTTAATATTTTTAATATTT 13 223 1 TTAATATTTT 0.834875 -18 TTTTTAACTTTTGTCTATTTT 15 1 1 TTTTTACTTT 0.939771 -224 CCGTTTTTTATAAATATCTTTTATGCAGTTA 15 64 1 TAAATACTTT 0.733484 -161 AAGGAGTTCATTAATACCTTAGTTATTTAAG 15 114 0 TTAATACTTA 0.591233 -111 TCAATAAATTTTATTAATTTTGAAAAACACT 15 169 1 TTATTATTTT 0.817247 -56 TTTATATAATTTTGTGGGATGTC 16 3 1 TATATATTTT 0.853574 -145 TAAATTTAAGTTTTTAGTTTTTATTATTTTA 17 21 1 TTTTTATTTT 0.923995 -63 TATTATTTTATTTTTAGTTTTTAATAGAAAA 17 42 1 TTTTTATTTT 0.923995 -42 TCACCTGAATTATAAAATTTTCTATTAAAAA 17 59 0 TATAAATTTT 0.513642 -25 CGAATACCCATTTATAGCTTAAATTTGCGGA 19 107 0 TTTATACTTA 0.797247 -194 TCTTAAGTTTTTTCTACCTTTCTTTTTTGGT 19 246 0 TTTCTACTTT 0.784556 -55 TAAGAACCTTTTAATAACTTTCTAACTTTGG 19 272 1 TTAATACTTT 0.866475 -29 ****** **** Masking position 6 Map Score: 51.1988 Number of sites scoring better than the average of aligned sites = 1608 Number in coding regions = 1086 Number in noncoding regions = 522 Number of orfs with sites within 600 bp upstream = 411 Fraction of orfs with sites within 600 bp upstream = 0.0660135 Motif number 3 AACTCACCTTTTAGTATGAATTTTGATAGTATT 1 15 1 TTGTAGATTT 0.668221 -170 ATACACACTATGATTACGATTTTTTGATAATAA 1 63 0 TGTTAGTTTT 0.860846 -122 TGGTATTATGATATTAAATTTTTAATGGTAAAT 1 121 0 ATTTAATTTT 0.769207 -64 TAAATACTAATTCTTATGGTATTATGATATTAA 1 137 0 TTTTAGTATT 0.932336 -48 TCCACAATAAATTTTAAGATTTTATAAATAATA 2 177 1 ATTTAGTTTT 0.892752 -29 AATCTCACCATTATTAAGGTTTTAAAGATAATA 4 75 0 TTTTAGTTTT 0.970957 -23 AGTTGATTACATATTAAGCTATTTTTTATTACA 7 105 1 ATTTAGTATT 0.774307 -24 TTTATATTTATTTTTATAAATTTATACATAATA 9 46 0 TTTTAAATTT 0.813361 -95 TTTTGGGAGGTTATTATATTATTTTTTGCAAGT 9 99 1 TTTTAATATT 0.846552 -42 GGGATAACAATGTTTAAGGAATTTAAAGCACTG 10 27 1 TGTTAGAATT 0.453579 -194 TTAGGTTATATTTTTAGTTTTTTGCTCCCCAAT 10 177 1 TTTTATTTTT 0.858379 -44 AATTTTTTATTTTTTATGAAATTTATCATGATT 12 15 1 TTTTAGAATT 0.817716 -148 TATTACTACATTATTACAATTTTAGTATTTATA 12 61 0 TTTTAATTTT 0.930486 -102 TATTTTTATTTTTGTAAAATTTTTACCTTTTAT 13 18 1 TTGTAATTTT 0.712388 -223 TTTATAAAAATTCTTATGCTTGTCATGCTTATA 13 172 0 TTTTAGTTGT 0.761677 -69 TATGAGGAAATTTTTAATATTTTTAATATTT 13 220 1 TTTTATTTTT 0.858379 -21 CTTTTGTCTATTTTTATGGATTTCTATAGAAAT 15 18 1 TTTTAGATTT 0.915855 -207 CTATTGCAGTATTTTATAATATTTGCATGGTTA 16 70 0 ATTTAATATT 0.578707 -78 TTCCAATTTTTTATTAGAGTTTTATTCATCTCC 16 121 0 TTTTAATTTT 0.930486 -27 AAGTTTTTAGTTTTTATTATTTTATTTTTAGTT 17 28 1 TTTTATTTTT 0.858379 -56 TATTAAAAGGTTCTTAAGTTTTTTCTACCTTTC 19 255 0 TTTTAGTTTT 0.970957 -46 ** *** * **** Masking position 5 Map Score: 24.828 Number of sites scoring better than the average of aligned sites = 843 Number in coding regions = 589 Number in noncoding regions = 254 Number of orfs with sites within 600 bp upstream = 237 Fraction of orfs with sites within 600 bp upstream = 0.0380662 Motif number 4 TAGAATTAGCTTCTTATTATTATCAAAAAATCGTAATC 1 47 1 TTTTTCAAAA 0.920892 -138 AACATATGGTTTATGTTATTTAACAAAATTAATGAATG 2 126 0 TTTTTCAAAA 0.916308 -80 CACAATAAATTTTAAGATTTTATAAATAATAACTTTG 2 179 1 TTATTAAATA 0.854953 -27 CAACCAGATGTTCTATAAATTATAAATATTTACAACAA 4 30 0 TTATTAAATA 0.85491 -68 AATCTCACCATTATTAAGGTTTTAAAGATAATAACAAT 4 70 0 TTATTAAAGA 0.644566 -28 AGCTATTTGTTTAATTTTTTTATCTATATTGGTTTATT 7 42 1 TTTTTCTATA 0.357251 -87 TTCAATACATTTTTTAATCTTTGGAAAAGTTGATTACA 7 78 1 TTATTGAAAA 0.667562 -51 TTTTTTGCTATCTTTAAAAAAGTATATATAT 8 4 1 TTATTAAAAA 0.94747 -82 ACTCCCACCTTTTGACATCTTATAAATATCAACCCTTA 8 56 0 TTATTAAATA 0.854953 -30 TTATTTATTATGTATAAATTTATAAAAATAAATATAAA 9 41 1 TGATTAAAAA 0.621448 -100 AATATCCCCCTTAATCTACTTGCAAAAAATAATATAAT 9 111 0 TTTTTAAAAA 0.939424 -30 TCTACATAGATTGGAATCCTTGTAAAAAATGACAACAG 10 57 0 TTTTTAAAAA 0.939456 -164 ATAAAAATAGTTGGCAATGTTTTCAAAATCAAAATCTT 10 94 0 TTATTCAAAA 0.932996 -127 TTATGCATTATCATGAACCTTTAATAAAGGTTCATCAA 11 35 1 TCATTATAAA 0.451056 -97 ATTGGACTATTTTTATTTTTGTAAAATTTTTACCTTT 13 10 1 TTTTTAAAAT 0.445407 -231 TTTTTACCTTTTATATAACTTTAAAAAATTAAATTACT 13 37 1 TTATTAAAAA 0.947287 -204 ATTTTCACAATTTGTATTATTATCAATAATTTCCATAG 13 101 1 TTTTTCAATA 0.796481 -140 ATTCTTATGCTTGTCATGCTTATATAAATTTTCTATCT 13 158 0 TTTTTATAAA 0.687828 -83 AATTCATCCTTTTTATAAAAATTTACGTATA 14 4 1 TCTTTAAAAA 0.832715 -42 TTATGGATTTCTATAGAAATTTAAAAAATTAAACCGTT 15 31 1 CTATTAAAAA 0.580369 -194 ACCTTAGTTATTTAAGAAGTTTGAAAAACACTATATAA 15 92 0 TTATTAAAAA 0.946962 -133 TTGGAAGGCGTTCAAATCTTTATCAATAAATTTTATTA 15 147 1 TTTTTCAATA 0.796509 -78 TAACTAAAAATTATAGTGTTTTTCAAAATTAATAAAAT 15 176 0 TTTTTCAAAA 0.922947 -49 TTTATTCATCTCCTCAACATTTGAAAAAGGTCTATTGC 16 96 0 TCATTAAAAA 0.852626 -52 ACAGTATCACTCCATATTTTTCCCAAAAGTAACGTAGA 19 208 1 TCTTTCAAAA 0.793504 -93 TAGAAAAAACTTAAGAACCTTTTAATAACTTTCTAACT 19 261 1 TTATTAATAA 0.482825 -40 ** * ** ***** Masking position 10 Map Score: 30.1666 Number of sites scoring better than the average of aligned sites = 723 Number in coding regions = 534 Number in noncoding regions = 189 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 5 AGATTCACCTCAATATTATAGAACTT 2 4 1 TTCACCTATT 0.963448 -202 GAAATCACCTAAATATGGATATTAAT 5 73 0 ATCACCTATT 0.988153 -16 ATAATTTTCAATCACATATATATACTTTTTTAA 8 24 0 ATCACATATT 0.891033 -62 ATAATATCCCCCTTAATCTACTTGCAAAA 9 122 0 TCCCCCTATT 0.862972 -19 TTTTCATAACACCACCGTAATATTAATAACTTA 12 129 0 ACCACCGATT 0.904997 -34 AAATATCACCTATATATACGTAAATTT 14 29 0 ATCACCTATT 0.988153 -17 GTTATCCCCTACATTTAATCTTAACT 15 209 0 ATCCCCTATT 0.97606 -16 AATATCACCTGAATTATAAAATTTTC 17 68 0 ATCACCTATA 0.929323 -16 GTCAGATCACCTAATTTTAGAATTACAG 18 6 1 ATCACCTTTT 0.929323 -66 ******* ** * Masking position 11 Map Score: 7.08935 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 27 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 6 TTTGTTAAATAACATAAACCATATGTTATT 2 137 1 AACATAAACC 0.725038 -69 AGATAATAACAATAACAACCAGATGTTCTA 4 53 0 AATAACAACC 0.84635 -45 ACATCTTATAAATATCAACCCTTATAATTT 8 50 0 AATATCAACC 0.960914 -36 TATAAAAATAAATATAAACTATTTTAGTTA 9 61 1 AATATAAACT 0.929855 -80 AACCTCCCAAAATTTAAACTTAACTAAAAT 9 81 0 AATTTAAACT 0.605218 -60 ATAATATCCCCCTTAATCTACT 9 129 0 AATATCCCCC 0.776386 -12 AATATAAAATTTTTTGGGGA 10 1 1 AATATAAAAT 0.648163 -220 AATATAACCTAATATCAAACTAAAAATTCC 10 159 0 AATATCAAAC 0.773542 -62 AAAAACTAAAAATATAACCTAATATCAAAC 10 169 0 AATATAACCT 0.916025 -52 AAATATCACCTATATATACGT 14 35 0 AATATCACCT 0.945827 -11 AAAATAAAATAATAAAAACTAAAAACTTAA 17 26 0 AATAAAAACT 0.748169 -58 AATATCACCTGAATTATAAA 17 74 0 AATATCACCT 0.945827 -10 ********** Masking position 2 Map Score: 7.75926 Number of sites scoring better than the average of aligned sites = 407 Number in coding regions = 338 Number in noncoding regions = 69 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 7 AATTCATACTAAAAGGTGAGTTAAAC 1 7 0 AAAAGGTGAG 0.96883 -178 AAAACCTTAATAATGGTGAGATT 4 85 1 TAATGGTGAG 0.845677 -13 AATATCCATATTTAGGTGATTTC 5 76 1 TTTAGGTGAT 0.763795 -13 TTTATTATAAAAGGTGAGAGG 6 9 1 AAAAGGTGAG 0.96883 -13 TAATCTTTGGAAAAGTTGATTACATATTAA 7 92 1 AAAAGTTGAT 0.817483 -37 AAAAAGTATATATATGTGATTGAAAATTAT 8 27 1 TATATGTGAT 0.667247 -59 ATAAGATGTCAAAAGGTGGGAGTAG 8 71 1 AAAAGGTGGG 0.830577 -15 ATAAAATGTGATTTTCATAACA 12 151 0 AAAATGTGAT 0.817483 -12 TTTACGTATATATAGGTGATATTT 14 32 1 TATAGGTGAT 0.909683 -14 GACCTTTTTCAAATGTTGAGGAGATGAATA 16 102 1 AAATGTTGAG 0.558281 -46 AATTTTATAATTCAGGTGATATT 17 71 1 TTCAGGTGAT 0.592933 -13 TAATTCTAAAATTAGGTGATCTGAC 18 6 0 ATTAGGTGAT 0.789293 -66 TAATTGTTAATAAATTTGAGCTATAGCCTG 19 150 0 TAAATTTGAG 0.515374 -151 ********** Masking position 7 Map Score: 5.50094 Number of sites scoring better than the average of aligned sites = 342 Number in coding regions = 247 Number in noncoding regions = 95 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 8 AAGAAAACATTATAGAAATACACACTATGAT 1 82 0 TATAGAAATC 0.958079 -103 ACCTCAATATTATAGAACTTTCGCAGGAATA 2 17 1 TATAGAACTT 0.939591 -189 AATGAATTAATATAGAACTTCGCAGTTTTTA 2 99 0 TATAGAACTC 0.973295 -107 ATTTATAATTTATAGAACATCTGGTTGTTAT 4 41 1 TATAGAACAC 0.836824 -57 TTTTACCTTTTATATAACTTTAAAAAATTAA 13 38 1 TATATAACTT 0.858752 -203 TTGTCATGCTTATATAAATTTTCTATCTTTA 13 155 0 TATATAAATT 0.792206 -86 CGTAGAACTTTATAAAAATTCTTATGCTTGT 13 182 0 TATAAAAATC 0.861776 -59 TCATCCTTTTTATAAAAATTTACGTATATAT 14 14 1 TATAAAAATT 0.726825 -32 TTTAAATTTCTATAGAAATCCATAAAAATAG 15 25 0 TATAGAAATC 0.958079 -200 TGAAAAACACTATATAACTGCATAAAAGATA 15 78 0 TATATAACTC 0.934411 -147 ********* * Masking position 6 Map Score: 9.51044 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 59 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 9 AAAAATTAAGAAAACATTATAGAAATACAC 1 90 0 AAAACATTAT 0.916698 -95 TATTATTTATAAAATCTTAAAATTTATTGT 2 180 0 AAAATCTTAA 0.768675 -26 TATTATCTTTAAAACCTTAATAATGGTGAG 4 75 1 AAAACCTTAA 0.731634 -23 TGTATTGAATAAACCAATATAGATAAAAAA 7 57 0 AAACCAATAT 0.314757 -72 CTACTTGCAAAAAATAATATAATAACCTCC 9 104 0 AAAATAATAT 0.824389 -37 TTATCCCCAAAAAATTTTATATT 10 4 0 AAAATTTTAT 0.811685 -217 TTTCAAAATCAAAATCTTCTACATAGATTG 10 82 0 AAAATCTTCT 0.553016 -139 TTATCCAGCTAAAATATTATAAATAAGTAA 13 70 0 AAAATATTAT 0.926955 -171 ACAAATTGTGAAAATATTATCCAGCTAAAA 13 86 0 AAAATATTAT 0.926955 -155 AACTTTATAAAAATTCTTATGCTTGTCATG 13 178 0 AAATTCTTAT 0.469801 -63 AAATATTAAAAATATTAAAAATTTCCTC 13 223 0 AAAATATTAA 0.801758 -18 AGAAGTTTGAAAAACACTATATAACTGCAT 15 86 0 AAAACACTAT 0.761842 -139 TTAATTTTGAAAAACACTATAATTTTTAGT 15 182 1 AAAACACTAT 0.761842 -43 GACATCCCACAAAATTATATAAA 16 4 0 AAAATTATAT 0.601579 -144 TTTAACCATGCAAATATTATAAAATACTGC 16 68 1 CAAATATTAT 0.601017 -80 AACTAAAAATAAAATAATAAAAACTAAAAA 17 31 0 AAAATAATAA 0.586181 -53 TTTTTAATAGAAAATTTTATAATTCAGGTG 17 59 1 AAAATTTTAT 0.811685 -25 GTTTAATATAAAAACCTTATTTGAAACTTT 18 38 1 AAAACCTTAT 0.900511 -34 ********** Masking position 8 Map Score: 13.0692 Number of sites scoring better than the average of aligned sites = 798 Number in coding regions = 596 Number in noncoding regions = 202 Number of orfs with sites within 600 bp upstream = 200 Fraction of orfs with sites within 600 bp upstream = 0.0321234 Motif number 10 CTTTCGCAGGAATAAATGATTTATTGAATAATGAT 2 34 1 AATATATTAT 0.497336 -172 TAACAAAATTAATGAATGAATTAATATAGAACTTC 2 109 0 AATATATTAT 0.915529 -97 TTAGGACTGAAAGTCCTAACTTAATAGACGGGTGG 5 39 0 AAGCTATTAT 0.741547 -50 AAAAAATCACTCCATTACTTTTGTAGCTA 11 113 0 AATATCTTAT 0.952587 -19 TTGTAGATTTTATTACTACATTATTACAATTTTAG 12 69 0 TATATCTTAT 0.73894 -94 AATAACTTATAATAACTACTTTAGTGCTAATTTTT 12 103 0 AATATCTTAT 0.94226 -60 AAATATTATAAATAAGTAATTTAATTTTTTAAAGT 13 54 0 AATATATTAT 0.729661 -187 CCTTCCAAAGAAGGAGTTCATTAATACCTTAGTTA 15 120 0 AAGATCTTAT 0.956405 -105 AAGTATTTAATAAATTTAAGTTTTT 17 1 1 AAGATATAAT 0.658366 -83 TATGCCTTGTAAGCACTACCTTAGGCATCTCTGTT 19 32 0 AAGATCTTAG 0.820671 -269 *** * * * *** * Masking position 7 Map Score: 2.80597 Number of sites scoring better than the average of aligned sites = 160 Number in coding regions = 121 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 11 TAAATACCTTTTTAATATAAAAACTGCGAAGT 2 82 1 TTAATAAAAA 0.939388 -124 TTTATTATAAAAGGTGAGAGG 6 1 1 TTATTAAAAA 0.92274 -21 AAATGAATGATAAAAGGTATATGTT 7 4 1 TAATGAAAAA 0.741547 -125 ATGTAATAAAAAATAGCTTAATA 7 116 0 TTAATAAAAA 0.951851 -13 ACATAATAAATAAAAGAGAAAAAAAGAATGGG 9 22 0 TAAAGAAAAA 0.797973 -119 TCATGATAAATTTCATAAAAAATAAAAAATTA 12 14 0 TTCATAAAAA 0.765786 -149 TTGTGGGATGTCTATGAGAAAAATTTACCTCA 16 22 1 TTATGAAAAA 0.889747 -126 TAACCATGCAAATATTATAAAATACTGCAATA 16 70 1 ATATTAAAAA 0.625744 -78 TGAATAAAACTCTAATAAAAAATTGGAATAAT 16 126 1 TTAATAAAAA 0.951851 -22 ATTTTTAGTTTTTAATAGAAAATTTTATAATT 17 51 1 TTAATAAAAA 0.951537 -33 AATATCACCTGAATTATAAAATTTTCTATTA 17 63 0 TAATTAAAAA 0.83692 -21 AGAATTACAGTTTAATATAAAAACCTTATTTG 18 29 1 TTAATAAAAA 0.939388 -43 * ***** **** Masking position 7 Map Score: 13.0898 Number of sites scoring better than the average of aligned sites = 242 Number in coding regions = 171 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 78 Fraction of orfs with sites within 600 bp upstream = 0.0125281 Motif number 12 TATTTAAAACTTTTGGTTGGGTGAATGTATG 1 164 1 TTTTGTGGGT 0.895548 -21 AATCTTAAAATTTATTGTGGATAATAAAATAA 2 166 0 TTTATTGGAT 0.828201 -40 AATTAAAAATTTTTGGAGGGATATA 3 11 1 TTTTGGGGAT 0.977052 -15 TTGCAAGTAGATTAAGGGGGATATTAT 9 124 1 ATTAGGGGAT 0.807985 -17 AATATAAAATTTTTTGGGGATAACAATGTTT 10 10 1 TTTTTGGGAT 0.947836 -211 TATCTGATTATTTTAATTGGATATGTGTTTGG 10 129 1 TTTTATGGAT 0.855185 -92 TGTTTGGAATTTTTAGTTTGATATTAGGTTAT 10 154 1 TTTTGTTGAT 0.7991 -67 TTAGTGCTAATTTTTTGTAGATTTTATTACTA 12 86 0 TTTTTTAGAT 0.629282 -77 ATTTATAATATTTTAGCTGGATAATATTTTCA 13 76 1 TTTTGTGGAT 0.978507 -165 ACTTTTGTCTATTTTTATGGATTTCTATAGAA 15 17 1 ATTTTTGGAT 0.885569 -208 TTTATATAATTTTGTGGGATGTCTATGAGA 16 9 1 ATTTGGGGAT 0.944318 -139 **** * ***** Masking position 3 Map Score: 7.38891 Number of sites scoring better than the average of aligned sites = 216 Number in coding regions = 174 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 13 ATTTATTTTATTATCCACAATAAATTTTAA 2 164 1 TTATCCACAA 0.972683 -42 TTTTATAAATTTATACATAATAAATAAAAG 9 38 0 TTATACATAA 0.811149 -103 TTAAACATTGTTATCCCCAAAAAATTTTAT 10 14 0 TTATCCCCAA 0.961327 -207 ATTTGTATTATTATCAATAATTTCCATAGC 13 110 1 TTATCAATAA 0.811149 -131 GTTCAAATCTTTATCAATAAATTTTATTAA 15 156 1 TTATCAATAA 0.811149 -69 GTTATCCCCTACATTTAATCT 15 214 0 TTATCCCCTA 0.837831 -11 AGGCATAACTTTATACACAAACTCTGATAT 19 60 1 TTATACACAA 0.908893 -241 ********** Masking position 3 Map Score: 2.18778 Number of sites scoring better than the average of aligned sites = 186 Number in coding regions = 167 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 14 ********** No masking Map Score: -5.58897e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 15 ********** No masking Map Score: -5.58897e-13 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0