AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i056_Branched_Chain_Aminoacid_biosynthesis__mjan_reg_300.orf -o056_mjan_300.ace -a/home/amcguire/genomes/ORF_mjan.txt -z/home/amcguire/genomes/mjan.fna -g0.31 -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 = 0.31 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 Motif number 1 TACGAAAAACTATGAAAATTTTCTTTTAATC 1 31 0 TATGAAAATT 0.846062 -270 TAAATTTAGTTATGAAAAATTGAACACCCTC 1 69 1 TATGAAAATT 0.846062 -232 TGTCATATCCTATCAAAAATATGCAAATCAA 1 195 1 TATCAAAATA 0.869281 -106 AAAATATGCAAATCAAAAATTTCAGGTATCA 1 210 1 AATCAAAATT 0.90754 -91 GAACTCACCATATAATAATTATGATACCTGA 1 231 0 TATAATAATA 0.656733 -70 TAAATCTTACTATAAAAAGGATTG 1 287 1 TATAAAAAGA 0.838783 -14 AAAGACTAAAAATAAAAAATAGAATTAAAGA 2 17 0 AATAAAAATA 0.892856 -167 AAGATTAGTAATTAAATATTAAATACCAACA 2 48 1 ATTAAATATA 0.631101 -136 AAAAGTTTGATATAAAAAAGTGTTGGTATTT 2 68 0 TATAAAAAGT 0.925305 -116 TTTGAAGAACTTTAAAAAGTTTGATATAAAA 2 82 0 TTTAAAAATT 0.941788 -102 AAATCCTTAGTATAAAAATTTTTATATATGA 2 117 1 TATAAAAATT 0.969703 -67 ATTTCAATTTTATCATTACTTTACCCTTAAC 2 147 1 TATCATTATT 0.477865 -37 GTGAAGGGTATATAAATAGTTTTTTGTTATT 3 49 0 TATAAATATT 0.928567 -55 GATGATGAGCAATAAAAAGCTGACTTAATAT 4 23 0 AATAAAAACT 0.847172 -278 ATCTTTCATGAATAATAATTTAGGATGATGA 4 89 0 AATAATAATT 0.738486 -212 TAAAAAAGTTTATAAAAAATCTTTCATGAAT 4 107 0 TATAAAAATC 0.679511 -194 GTGTAAGTGATATAAAAAAGTTTATAAAAAA 4 119 0 TATAAAAAGT 0.925305 -182 GTATAGTGCCTTTCAAAACTTATTGAGATAA 4 157 1 TTTCAAAATT 0.888933 -144 TTCAAAGTTTAATAATAAGTTTATTAATTTT 4 224 1 AATAATAATT 0.738486 -77 ATATAGTGCCTTTCAAAATTAATAAACTTAT 4 238 0 TTTCAAAATA 0.770717 -63 TAACTTAACCTTTCAAAATGATAGATTAAAG 5 28 0 TTTCAAAAGA 0.565405 -108 GATGGGATGTTATAAAAATTTTACCTAATCA 5 79 0 TATAAAAATT 0.969703 -57 ATAACAGAAAATTAAAAAGTTTTGGTGGGAT 5 114 1 ATTAAAAATT 0.909334 -22 AAAAAGATATATTAAATATTTTTGCTTTGTT 6 59 1 ATTAAATATT 0.802891 -45 AATTCTGGAATTTCAAAAGTTAAAGTTATCG 7 45 0 TTTCAAAATT 0.888933 -182 TATTGTTTAATATGAAAATCTAAATATAAGA 8 25 0 TATGAAAACT 0.605599 -99 AAAGTAAGTGAATAAATAAGTTTTGTTTTCT 8 57 0 AATAAATAGT 0.757216 -67 TTATAACTAAAATAAAAAGTAAGTGAATAAA 8 72 0 AATAAAAATA 0.892857 -52 CATTAATCATATTCAAAAGGTGAAATA 8 107 1 ATTCAAAAGT 0.657568 -17 TAGTTTTAAATATAAAAATTTGTATATTTAA 9 27 0 TATAAAAATT 0.969703 -158 CATTCAACTATATAAAAATTTCTACTGTATT 9 92 0 TATAAAAATT 0.969703 -93 ATGGATACCTAATAAATACTTTAAAATTATT 9 120 1 AATAAATATT 0.889605 -65 AAATTATTTCTATAAATAGTTTAAAGTATTA 9 143 1 TATAAATATT 0.928567 -42 AGTTTAAAGTATTAAAAATTTTATTATGGCA 9 160 1 ATTAAAAATT 0.909334 -25 TTATCCTAAAATTAAATAGTATGGTGAAATT 10 12 0 ATTAAATATA 0.631101 -194 TAACATAGAATTTAAATACCATTAGAACACA 10 117 0 TTTAAATACA 0.435344 -89 AAATCGATACTATAAAAACCATATAATAATA 10 146 0 TATAAAAACA 0.78972 -60 ATTAATAAACTTTAATTAATTTTGAAGACAG 11 93 0 TTTAATTATT 0.483245 -143 AAAGTTTATTAATAAATATTTGACAATAAAT 11 111 1 AATAAATATT 0.889605 -125 AATATTTGACAATAAATATTTAAATGCCTTC 11 125 1 AATAAATATT 0.889605 -111 ATATAGTGTCTTTCAAAAACATTTTGAAGTA 11 184 0 TTTCAAAACA 0.484298 -52 AAAGACACTATATAAAAAAGTTTTTGGTGCT 11 202 1 TATAAAAAGT 0.925305 -34 ******** ** Masking position 5 Map Score: 52.9102 Number of sites scoring better than the average of aligned sites = 2623 Number in coding regions = 1744 Number in noncoding regions = 879 Number of orfs with sites within 600 bp upstream = 622 Fraction of orfs with sites within 600 bp upstream = 0.0999036 Motif number 2 GAAACCAAAAATTAAGTTAAGATTA 1 2 1 AAAAAAATAA 0.802189 -299 TTTAACAACTTTACGAAAAACTATGAAAATTTTC 1 39 0 TTAAAAATAT 0.795502 -262 TCAATTTTTCATAACTAAATTTAACAACTTTACG 1 58 0 ATATAAATAA 0.849484 -243 ATTAATTAACAAAAGAAAAATTAAGCCTTGTCAT 1 167 1 AAAAAAATAA 0.802189 -134 ATGCAAATCAAAAATTTCAGGTATCATAATTATT 1 215 1 AAATTCATAT 0.289903 -86 AATTGAAATCATATATAAAAATTTTTATACTAAG 2 122 0 ATATAAATTT 0.836033 -62 TAAAAAATAATAACAAAAAACTATTTATATACCC 3 41 1 TAAAAAATAT 0.773462 -63 AGTGTAAGTGATATAAAAAAGTTTATAAAAAATC 4 117 0 ATAAAAATTT 0.821937 -184 ACTTATTGAGATAATAAAAGGTATTAATGAACGC 4 174 1 ATAAAAATAT 0.925152 -127 GCCTTTCAAAATTAATAAACTTATTATTAAACTT 4 228 0 ATTTAAATAT 0.418959 -73 AAGGCACTATATATCTACAGTTATTCTTATAAAG 4 257 1 ATATACATAT 0.753053 -44 TATCATTTTGAAAGGTTAAGTTATAGCGTTTTAA 5 36 1 AAATTAATAT 0.49603 -100 ATATATCTGATTAGGTAAAATTTTTATAACATCC 5 72 1 TTATAAATTT 0.647179 -64 AAATAACAGAAAATTAAAAAGTTTTGGTGGGATT 5 112 1 AAAAAAATTT 0.802138 -24 CAATTAAATTTTAGATAAAGATAATTATAAAAGA 6 26 1 TTATAAATAA 0.651163 -78 GATAATTATAAAAGAAAAAGATATATTAAATATT 6 45 1 AAAAAAATAT 0.915787 -59 TGGAATTTCAAAAGTTAAAGTTATCGTCTGTGTA 7 37 0 AAATAAATAT 0.923839 -190 TTTAATATGAAAATCTAAATATAAGAAAATAGAA 8 17 0 AAATAAATAA 0.837713 -107 AACAATACAGAAAACAAAACTTATTTATTCACTT 8 49 1 AAAAAAATAT 0.915787 -75 GATTATAACTAAAATAAAAAGTAAGTGAATAAAT 8 71 0 AAAAAAATAA 0.802189 -53 AAAAATTTGTATATTTAAATATATAGGTGAAAAT 9 11 0 ATATAAATAT 0.915045 -174 ACAAATTTTTATATTTAAAACTAATATAAAATTT 9 35 1 ATATAAATAA 0.849484 -150 TATTGCTTAAAAATTTAAAATTTTATATTAGTTT 9 52 0 AAATAAATTT 0.832566 -133 TTTATAGAAATAATTTTAAAGTATTTATTAGGTA 9 125 0 TAATTAATAT 0.352106 -60 ATTTCTATAAATAGTTTAAAGTATTAAAAATTTT 9 148 1 ATATTAATAT 0.46235 -37 CAATTGCCATAATAAAATTTTTAATACTTTAA 9 163 0 ATAAAAATTT 0.821937 -22 ATATCGTTTATAACCAACATTTATGTTTTAAATT 10 64 1 TAAAACATAT 0.394237 -142 TACCGTATTAATACTTAAAAATATCTTTAAACTA 11 57 1 ATATAAATAT 0.915045 -179 GTCTTCAAAATTAATTAAAGTTTATTAATAAATA 11 95 1 TTATAAATTA 0.4113 -141 GAAAGACACTATATAAAAAAGTTTTTGGTGCTGT 11 201 1 ATAAAAATTT 0.821937 -35 *** **** *** Masking position 9 Map Score: 34.3449 Number of sites scoring better than the average of aligned sites = 1825 Number in coding regions = 1237 Number in noncoding regions = 588 Number of orfs with sites within 600 bp upstream = 428 Fraction of orfs with sites within 600 bp upstream = 0.068744 Motif number 3 ATTTTCTTTTAATCTTAACTTAATTTTTGGTTTC 1 10 0 AATTTTAATT 0.509318 -291 GTGTTCAATTTTTCATAACTAAATTTAACAACTTT 1 61 0 TTTATTAATT 0.886081 -240 AGGCTTAATTTTTCTTTTGTTAATTAATTGGCATC 1 160 0 TTTTTTAATT 0.974572 -141 TTTCTTTCTTTAATTCTATTTTTTA 2 1 1 TTTTTTAATT 0.974572 -183 AAAATTTTTATATATGATTTCAATTTTATCATTAC 2 131 1 TATTGTAATT 0.776444 -53 TATAAATAGTTTTTTGTTATTATTTTTTATGGACA 3 35 0 TTTTGTATTT 0.578871 -69 TTTTATAAACTTTTTTATATCACTTACACTCTAAA 4 121 1 TTTTTTACTT 0.893578 -180 ATTAATACCTTTTATTATCTCAATAAGTTTTGAAA 4 167 0 TTTTTTAATA 0.732771 -134 CTTCATATTATCCCTCAATTAAATTTTAGA 6 6 1 TATATTAATT 0.61218 -98 ATATTTTTGCTTTGTTTAATCAATTTATAAGGGTG 6 74 1 TTTTTTAATT 0.974572 -30 TTTTATTTTTTGGTGGTAATTATGGCTACAC 7 7 1 TTTTGGAATT 0.845232 -220 TTGAATTTATTTTTATCAATAAATTCTGGAATTTC 7 62 0 TTTATTAATT 0.88608 -165 CCAAGATTTTTTTCTTGATGAAATTTTCAAGCTCC 7 100 0 TTTTTGAATT 0.924417 -127 CTGAATTTGAATTTTTTTCTAAATTCTTCACATTC 7 190 0 ATTTTTAATT 0.836453 -37 ATAAATAAGTTTTGTTTTCTGTATTGTTTAATATG 8 42 0 TTTTTTTATT 0.836459 -82 ACAAAACTTATTTATTCACTTACTTTTTATTTTAG 8 62 1 TTTTTTACTT 0.893578 -62 TATTAAAAATTTTATTATGGCAATTG 9 169 1 TTTTTGAATT 0.924417 -16 ATAACCAACATTTATGTTTTAAATTTATTTCACTA 10 73 1 TTTTGTAATT 0.944794 -133 ATACGGTATATTTATTGTTTCTATTTCTATTAAAC 11 30 0 TTTTTTTATT 0.836459 -206 *** ** * **** Masking position 3 Map Score: 22.3483 Number of sites scoring better than the average of aligned sites = 515 Number in coding regions = 392 Number in noncoding regions = 123 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 4 GGACATAATAAATGTCTTTCGATAGAGGGT 1 94 0 AATGTCTTTC 0.94904 -207 CTAAAAGTATAGTGCCTTTCAAAACTTATT 4 151 1 AGTGCCTTTC 0.988015 -150 TTAAACTTTGAACGCCTTCCTTTAGGAGGC 4 206 0 AACGCCTTCC 0.982293 -95 GTAGATATATAGTGCCTTTCAAAATTAATA 4 245 0 AGTGCCTTTC 0.988015 -56 TAAATATTTAAATGCCTTCCTTTGGAAGGT 11 137 1 AATGCCTTCC 0.988015 -99 GTAGCTTATGAACACCTTCCAAAGGAAGGC 11 150 0 AACACCTTCC 0.877984 -86 TTTTTTATATAGTGTCTTTCAAAAACATTT 11 191 0 AGTGTCTTTC 0.957427 -45 ********** Masking position 1 Map Score: 9.13038 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 5 TTAGTTATGAAAAATTGAACACCCTCTATC 1 74 1 AAAATTGAAC 0.827664 -227 TAAAAATAATAAAATAGATATTTAGTAGAA 1 259 0 AAAATAGATA 0.607406 -42 CTAAAAATAAAAAATAGAATTAAAGAAAGA 2 13 0 AAAATAGAAT 0.924558 -171 AAGTAATGATAAAATTGAAATCATATATAA 2 138 0 AAAATTGAAA 0.958383 -46 TAAATAACAGAAAATTAAAAAGTTTTGGTG 5 111 1 AAAATTAAAA 0.820942 -25 ATCTTTATCTAAAATTTAATTGAGGGATAA 6 18 0 AAAATTTAAT 0.684404 -86 AGATGTTGAAAAAATTGAAAAAGAATGTGA 7 168 1 AAAATTGAAA 0.958383 -59 AATTTAGAAAAAAATTCAAATTCAGAAATT 7 200 1 AAAATTCAAA 0.728948 -27 TTCAAATTCAGAAATTGAATTTT 7 214 1 GAAATTGAAT 0.795806 -13 TAAATATAAGAAAATAGAAATAACA 8 6 0 AAAATAGAAA 0.947594 -118 GATTATAACTAAAATAAAAAGTAAGTGAAT 8 75 0 AAAATAAAAA 0.782602 -49 ATATTGCTTAAAAATTTAAAATTTTATATT 9 57 0 AAAATTTAAA 0.761885 -128 GCATTATCCTAAAATTAAATAGTATGGTGA 10 16 0 AAAATTAAAT 0.756537 -190 ATATAATAATAACATAGAATTTAAATACCA 10 127 0 AACATAGAAT 0.608484 -79 CGAAAACCTTAAAATAGTATT 10 195 1 AAAATAGTAT 0.511863 -11 ACGTTTAATAGAAATAGAAACAATAAATAT 11 28 1 GAAATAGAAA 0.818674 -208 ********** Masking position 5 Map Score: 15.3688 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 342 Number in noncoding regions = 98 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 6 TAATTATTATATGGTGAGTTCTACTAAATA 1 241 1 ATGGTGAGTT 0.932069 -60 GGGTAAAGTAATGATAAAATTGAAATCATA 2 143 0 ATGATAAAAT 0.629439 -41 GACTAATTAAATGGTGAGATT 4 290 1 ATGGTGAGAT 0.980142 -11 TTGATGAATTAAATGAACTT 5 1 1 TTGATGAATT 0.709911 -135 TCTGTTATTTATGATGGGATGTTATAAAAA 5 92 0 ATGATGGGAT 0.900569 -44 TTAAAAAGTTTTGGTGGGATT 5 125 1 TTGGTGGGAT 0.90575 -11 GATTTTTTTCTTGATGAAATTTTCAAGCTC 7 101 0 TTGATGAAAT 0.897997 -126 TCATATTCAAAAGGTGAAATA 8 113 1 AAGGTGAAAT 0.865057 -11 ATTAAATAGTATGGTGAAATTT 10 3 0 ATGGTGAAAT 0.978522 -203 CAACTAAATTATAGTGAAATAAATTTAAAA 10 89 0 ATAGTGAAAT 0.799211 -117 ********** Masking position 5 Map Score: 6.33704 Number of sites scoring better than the average of aligned sites = 246 Number in coding regions = 193 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 7 AAGTTAAGATTAAAAGAAAATTTTCATAGT 1 24 1 TAAAAGAAAA 0.965475 -277 AATTAATTAACAAAAGAAAAATTAAGCCTT 1 166 1 CAAAAGAAAA 0.853629 -135 TAAAAAATAATAACAAAAAACTATTTATAT 3 41 1 TAACAAAAAA 0.573151 -63 ACTTACACTCTAAAAGTATAGTGCCTTTCA 4 142 1 TAAAAGTATA 0.64042 -159 AATTAGTCTTTATAAGAATAACTGTAGATA 4 268 0 TATAAGAATA 0.85134 -33 CCATCATAAATAACAGAAAATTAAAAAGTT 5 105 1 TAACAGAAAA 0.923221 -31 AAGATAATTATAAAAGAAAAAGATATATTA 6 43 1 TAAAAGAAAA 0.965475 -61 AAAATCTAAATATAAGAAAATAGAAATAAC 8 12 0 TATAAGAAAA 0.926802 -112 AGATTATAACTAAAATAAAAAGTAAGTGAA 8 76 0 TAAAATAAAA 0.846306 -48 ATAAAAACCATATAATAATAACATAGAATT 10 136 0 TATAATAATA 0.527213 -70 ********** Masking position 5 Map Score: 6.20172 Number of sites scoring better than the average of aligned sites = 461 Number in coding regions = 416 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 8 TTTGCAAATATTCTAAAGATAAAGGACATAATAA 1 113 0 TTAAAGTAAG 0.903377 -188 TGATAGGATATGACAAGGCTTAATTTTTCTTTTG 1 176 0 TGAAGGTAAT 0.883758 -125 AAAATTTTTATACTAAGGATTTAGCATTTGAAGA 2 105 0 TAAAGGTTAG 0.792131 -79 CACCAAAAAATGTTAAGGGTAAAGTAATGATAAA 2 155 0 TGAAGGTAAG 0.949971 -29 AAATACTTTTTGTGAAGGGTATATAAATAGTTTT 3 57 0 TGAAGGTTAT 0.921648 -47 CAAAAAGTATTTGGAAAGGTTAGGAGTTGATTAA 3 79 1 TTAAAGTAGG 0.685738 -25 TCAATAAGTTTTGAAAGGCACTATACTTTTAGAG 4 149 0 TTAAGGATAT 0.651042 -152 TTTATTAATTTTGAAAGGCACTATATATCTACAG 4 243 1 TTAAGGATAT 0.651042 -58 AATCTATCATTTTGAAAGGTTAAGTTATAGCGTT 5 32 1 TTAAAGTAAG 0.903377 -104 AGTTATAGCGTTTTAATGATATATCTGATTAGGT 5 54 1 TTAATGTTAT 0.509306 -82 TAACAGAAAATTAAAAAGTTTTGGTGGGATT 5 115 1 TTAAAGTTGG 0.771484 -21 TTTAATCAATTTATAAGGGTGTAGTT 6 88 1 TTAAGGTTAG 0.970502 -16 ATTCTGGAATTTCAAAAGTTAAAGTTATCGTCTG 7 41 0 TTAAAGTAAG 0.903377 -186 CAGAATTTATTGATAAAAATAAATTCAAAAAGGA 7 69 1 TGAAAATAAT 0.237553 -158 TATAAACTTATGGAAAAGGTGTAGATGTTGAAAA 7 146 1 TGAAAGTTAG 0.928147 -81 TGAAAAAGAATGTGAAGAATTTAGAAAAAAATTC 7 183 1 TGAAGATTAG 0.732499 -44 TAGAAATAATTTTAAAGTATTTATTAGGTATCCA 9 121 0 TTAAGTTTAT 0.410475 -64 AATACTATTTTAAGGTTTTCGGTTTAATTTG 10 185 0 TTAAGGTTCG 0.806663 -21 ** **** * *** Masking position 1 Map Score: 12.5197 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 580 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 9 AAAAATATGCAAATCAAAAATTTCAGGTAT 1 209 1 AAATCAAAAA 0.514256 -92 ATTGAAATCATATATAAAAATTTTTATACT 2 125 0 TATATAAAAA 0.716869 -59 TCACAAAAAGTATTTGGAAAGGTTAGGAGT 3 76 1 TATTTGGAAA 0.550178 -28 TAAGTTTATTAATTTTGAAAGGCACTATAT 4 239 1 AATTTTGAAA 0.718462 -62 TTTATCAATAAATTCTGGAATTTCAAAAGT 7 56 0 AATTCTGGAA 0.339633 -171 GATAAAAATAAATTCAAAAAGGAGCTTGAA 7 80 1 AATTCAAAAA 0.914935 -147 ATGTTGAAAAAATTGAAAAAGAATGTGAAG 7 170 1 AATTGAAAAA 0.674046 -57 GAATGTGAAGAATTTAGAAAAAAATTCAAA 7 190 1 AATTTAGAAA 0.925894 -37 AAAAAATTCAAATTCAGAAATTGAATTTT 7 208 1 AATTCAGAAA 0.945242 -19 CATATTAAACAATACAGAAAACAAAACTTA 8 42 1 AATACAGAAA 0.907797 -82 ATTAGTTTTAAATATAAAAATTTGTATATT 9 30 0 AATATAAAAA 0.816196 -155 TCCATTCAACTATATAAAAATTTCTACTGT 9 95 0 TATATAAAAA 0.716869 -90 TTTAATTTGATATTCAGAAATCGATACTAT 10 164 0 TATTCAGAAA 0.907786 -42 TGAAAGACACTATATAAAAAAGTTTTTGGT 11 200 1 TATATAAAAA 0.716869 -36 ********** Masking position 2 Map Score: 5.49297 Number of sites scoring better than the average of aligned sites = 632 Number in coding regions = 497 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 10 ACTTTTTAAAGTTCTTCAAATGCTAAATCC 2 93 1 GTTCTTCAAA 0.828039 -91 GTTAATCAACTCCTAACCTT 3 94 0 GTTAATCAAC 0.799598 -10 GAAAGGTTCATCATATTAAGTCAGC 4 6 1 GTTCATCATA 0.973212 -295 GCTTTTTATTGCTCATCATCGAGGAATTAA 4 34 1 GCTCATCATC 0.954176 -267 CCCCCGTAAGGTTCATCATCCTAAATTATT 4 77 1 GTTCATCATC 0.980871 -224 CTTCATCATAGACAGCACCA 11 226 0 CTTCATCATA 0.893079 -10 ********** Masking position 6 Map Score: 1.1175 Number of sites scoring better than the average of aligned sites = 103 Number in coding regions = 90 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 13 Fraction of orfs with sites within 600 bp upstream = 0.00208802 Motif number 11 ********** No masking Map Score: -5.39059e-12 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 12 ********** No masking Map Score: -5.39059e-12 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 13 ********** No masking Map Score: -5.39059e-12 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