AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00910_mjan_reg_300.orf -o00910_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 MJ0020 300 asparaginase (ansA) #2 MJ0685 68 nitrogenase reductase (nifH2) #3 MJ0823 300 CODH nickel-insertion accessory protein CooC (cooC) #4 MJ0878 300 M. jannaschii predicted coding region MJ0878 #5 MJ0879 149 nitrogenase iron protein (nifH) #6 MJ1054 300 UDP-glucose dehydrogenase, putative #7 MJ1116 136 asparagine synthetase (asnB) #8 MJ1345 300 O-linked GlnNAc transferase #9 MJ1346 87 glutamine synthetase (glnA) #10 MJ1351 300 glutamate synthase (gltB) #11 MJ1352 300 NH(3)-dependent NAD+ synthetase (nadE) Motif number 1 GTTCCTTAATATATTTAAATTGCATTCAAC 1 13 1 ATATTTAAAT 0.577779 -288 AAGCTACTTAATATATTTATGGCGGATGAT 1 108 1 ATATATTTAT 0.752956 -193 TTTATTTTGCAAATATTAATTTATATATTT 1 190 1 AAATATTAAT 0.77418 -111 ATTAATTTATATATTTAAATATAAAAATTT 1 204 1 ATATTTAAAT 0.577779 -97 GCTATCATATAAATTTTTATATTTAAATAT 1 214 0 AAATTTTTAT 0.93978 -87 TATCTTTTTATAATTTTTATACCCTAATCT 1 244 1 TAATTTTTAT 0.857606 -57 TAAAAGGAATTATTATTAATTAATAATACT 2 32 1 TATTATTAAT 0.520578 -37 TGAATGAAAAATTTTATTATATCTTTGTTA 3 98 1 ATTTTATTAT 0.707419 -203 TACAAAATTTAATTTATAATATCGCTCTAT 3 128 1 AATTTATAAT 0.729998 -173 AACTTTTTTTATTTTTTAATAGAGCGATAT 3 146 0 ATTTTTTAAT 0.88578 -155 TGTTTGCAACTTTTTTAAATGGATAAAAAT 3 181 1 TTTTTTAAAT 0.356243 -120 ATATCAAAATTAATTTTTATCCATTTAAAA 3 193 0 TAATTTTTAT 0.857606 -108 AAACCCCCACATATTTTTATAAGTTTCTAC 3 236 0 ATATTTTTAT 0.919539 -65 AAAAATTTCTAATTCATTATAAACCCCCAC 3 256 0 AATTCATTAT 0.451967 -45 GCTAATTCTTTATTTTTTATAGAAATGGTT 4 15 1 TATTTTTTAT 0.831732 -286 AATGTAATATATTTTTTAATATGGCTTGGA 4 198 1 ATTTTTTAAT 0.88578 -103 AATTATTCAGTAATCTTTATTTTTGGCATG 4 244 0 TAATCTTTAT 0.601217 -57 GAAACAAGTGTTATTTTTATTTTGTTATTT 5 11 0 TTATTTTTAT 0.817261 -139 AAACTGCTAATATTATTAATGTATTATTTA 5 80 0 TATTATTAAT 0.520578 -70 TTATTCACCAAAATTTTTATTATAAAATAT 5 128 0 AAATTTTTAT 0.93978 -22 GAATTTATTATCACAAGATTA 6 2 1 AATTTATTAT 0.767128 -299 TAATTGTATAATATTATTATATTTCTCTTA 6 255 0 ATATTATTAT 0.745683 -46 AATATTATACAATTATTAATAAATAAACTC 6 270 1 AATTATTAAT 0.73779 -31 AGATTAAATCAATTTATTATAAATAACCTT 7 23 0 AATTTATTAT 0.767128 -114 TTTAATTTAAATATCTTAATAAAGATTAAA 7 45 0 ATATCTTAAT 0.704221 -92 AATATTTGCAAAATTTTAATTTAAATATCT 7 59 0 AAATTTTAAT 0.92758 -78 AATATACCTTATTTTTTAATATTAGCTAAC 7 110 0 ATTTTTTAAT 0.88578 -27 ATTTTTAAATATACCTTATT 7 127 0 ATTTTTAAAT 0.543452 -10 TTATCCCAATATTTGTTTATTTTGCATTTC 8 12 0 ATTTGTTTAT 0.554463 -289 TTTTATAATTAAATTTTTATATTTATAATT 8 59 1 AAATTTTTAT 0.93978 -242 ATACGCTATAATATAATTATAAATATAAAA 8 73 0 ATATAATTAT 0.436897 -228 ACAGATAGAAAAATTTATATTTTACACTAA 8 195 1 AAATTTATAT 0.7408 -106 TACACTAAAATAATTTTAATAAATAATATC 8 217 1 TAATTTTAAT 0.831732 -84 GAATTTCGTTAAATTATTATTACTATGATA 8 243 0 AAATTATTAT 0.800545 -58 ATTTTTATATTTTAATTTAAATTGAA 9 7 1 ATATTTTAAT 0.904038 -81 ACCGTAAATTATATATATATGGAAGTAGGA 9 40 1 ATATATATAT 0.297299 -48 CCTCAAGGTTTAATCTTTATGAATGGAGAT 10 47 1 TAATCTTTAT 0.601217 -254 CTCATGTTTTTATTTTTAATCTTTTAATCT 10 270 0 TATTTTTAAT 0.802242 -31 CACCATTCTCAATTTTTAATGATTTGGCAT 11 45 0 AATTTTTAAT 0.913136 -256 TAATTTATAGAATTGTTTATATAATAGGAA 11 269 1 AATTGTTTAT 0.626304 -32 ********** Masking position 4 Map Score: 35.3661 Number of sites scoring better than the average of aligned sites = 2939 Number in coding regions = 1964 Number in noncoding regions = 975 Number of orfs with sites within 600 bp upstream = 630 Fraction of orfs with sites within 600 bp upstream = 0.101189 Motif number 2 GTTGAATGCAATTTAAATATATTAAGGAACTT 1 11 0 ATTTAAATAT 0.588934 -290 TGAGGTAAGTATATATACTTAAAGCTACTTAA 1 87 1 ATATAATTAA 0.635318 -214 TCATATAAATTTTTATATTTAAATATATAAAT 1 208 0 TTTTAATTAA 0.927449 -93 TAGAGCGATATTATAAATTAAATTTTGTATAA 3 125 0 TTATAATAAA 0.672862 -176 CCTTAAGATTTTTTAAAGAAAAAATTTCTAAT 3 273 0 TTTTAAAAAA 0.78568 -28 ATTCTTTATTTTTTATAGAAATGGTTCCTAAT 4 19 1 TTTTAAAAAT 0.619368 -282 CTTAAAAGATTTTTAACCTTATCAATAATCCT 4 90 0 TTTTACTTAT 0.732643 -211 TTTTTATTTCTTTTATAATTAAAAAGTTATTA 5 42 1 TTTTAATTAA 0.935504 -108 CTATATAATATTTTATAATAAAAATTTTGGTG 5 121 1 TTTTAATAAA 0.923413 -29 GTAATGCTATATTTACAATTAATTGTTGGAGG 6 167 1 ATTTAATTAA 0.910435 -134 TATAATAATATTATACAATTATTAATAAATAA 6 264 1 TTATAATTAT 0.543255 -37 CTCTAAGGTTATTTATAATAAATTGATTTAAT 7 19 1 ATTTAATAAA 0.89458 -118 TTATTAAGATATTTAAATTAAAATTTTGCAAA 7 53 1 ATTTAATAAA 0.893217 -84 TTTTGCAAATATTTAGCATAAAATGTTAAGTT 7 76 1 ATTTACTAAA 0.77066 -61 ATTTATGGACTTTTATAATTAAATTTTTATAT 8 49 1 TTTTAATTAA 0.935504 -252 ATAATTAAATTTTTATATTTATAATTATATTA 8 63 1 TTTTAATTAT 0.868671 -238 ACATTAGTTTATTTAAAGTTAATAAGATTGGG 8 125 0 ATTTAATTAA 0.910432 -176 AAAATTTATATTTTACACTAAAATAATTTTAA 8 204 1 TTTTAATAAA 0.924067 -97 AGTAATAATAATTTAACGAAATTCGTAAAATA 8 249 1 ATTTACAAAT 0.32954 -52 GGTTTTAGCAATATGCGATTTTAA 8 287 0 TTTTACATAT 0.455597 -14 GGTATATTCAATTTAAATTAAAATATAAAAAT 9 11 0 ATTTAATAAA 0.893217 -77 TTCCTCATGTTTTTATTTTTAATCTTTTAATC 10 271 0 TTTTATTTAA 0.519226 -30 ***** * **** Masking position 4 Map Score: 21.2385 Number of sites scoring better than the average of aligned sites = 995 Number in coding regions = 689 Number in noncoding regions = 306 Number of orfs with sites within 600 bp upstream = 271 Fraction of orfs with sites within 600 bp upstream = 0.0435271 Motif number 3 TAAATATATAAATTAATATTTGCAAAATAAAAAGTGGC 1 183 0 ATTAAAAAAT 0.663365 -118 TCTATTAAAAAATAAAAAAAGTTACAAATGTTTGCAAC 3 153 1 ATAAAAAAAA 0.772763 -148 TAATAACGTAATTAAATAGTAAATGAGTGTGTTATTAT 4 126 0 ATAAAATAGT 0.869943 -175 AATAAAGATTACTGAATAATTTATAAAACTTCTTTTAA 4 253 1 ATGAAATAAA 0.715698 -48 TTATAAAAGAAATAAAAAAGAAACAAGTGTTATTTTTA 5 22 0 ATAAAACAGT 0.789206 -128 TTCTTTTATAATTAAAAAGTTATTAAATCATTAAATAA 5 49 1 ATAAAATAAT 0.543795 -101 TTATTAAATCATTAAATAATACATTAATAATATTAGCA 5 68 1 ATAAAATAAT 0.942619 -82 ATATAGTGTTAATAAATAAACTGCTAATATTATTAATG 5 89 0 ATAAAACAAT 0.911442 -61 TTATCACAAGATTAAAGAGGTTTTAAATAGATTTCCAA 6 18 1 ATAAAATAAT 0.543795 -283 TTGTTAGTTGAGTAAAAAGCTCCATAATGTTCTACAAT 6 77 1 ATAAAAAAAT 0.912942 -224 TAAATATCTTAATAAAGATTAAATCAATTTATTATAAA 7 30 0 ATAAAATAAT 0.948434 -107 AAGATATTTAAATTAAAATTTTGCAAATATTTAGCATA 7 58 1 ATTAAACAAT 0.65888 -79 AAATAATTTTAATAAATAATATCATAGTAATAATAATT 8 224 1 ATAAAAAAGT 0.792516 -77 TTTAATTTAAATTGAATATACCGTAAATTATATATATA 9 21 1 ATGAAATAAT 0.879744 -67 AGACCTTGGAAATAAACAAAGATTAAAAGATTAAAAAT 10 251 1 ATAAAATAAA 0.856351 -50 GATTTATTTCAATAAATGGTTCATTAAT 11 1 0 ATAAAGTAAT 0.681889 -300 AGCAAGAATAACTGAAGACATTAAAAAAGGAGTTGTAT 11 118 1 ATGAAAAAAA 0.589797 -183 * **** * * *** Masking position 6 Map Score: 14.5243 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 259 Number in noncoding regions = 111 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 4 CTAATTCATTATAAACCCCCACATATTTTT 3 248 0 ATAAACCCCC 0.937167 -53 ATATATTACATTATTACCTCTTACTCATAT 4 180 0 TTATTACCTC 0.763322 -121 TGAATAATTTATAAAACTTCTTTTAATAAG 4 265 1 ATAAAACTTC 0.667296 -36 AATAAAACCTCCTTACCTTAT 4 290 0 ATAAAACCTC 0.953399 -11 GGAAATCTATTTAAAACCTCTTTAATCTTG 6 24 0 TTAAAACCTC 0.975001 -277 TTAAATCCCCTGAGTTTATT 6 291 0 TTAAATCCCC 0.912468 -10 TTTAAAACCTCTAAGGTTATT 7 2 1 TTAAAACCTC 0.975001 -135 CATAAAACAATTAATACCCCAATCTTATTA 8 108 1 TTAATACCCC 0.963423 -193 ATATGCGATTTTAATCCCCCTATTTTACGA 8 271 0 TTAATCCCCC 0.937167 -30 ********** Masking position 3 Map Score: 7.87863 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 183 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 TGACGCCACTTTTTATTTTGCAAATATTAA 1 179 1 TTTTATTTTG 0.888746 -122 TCATATAAATTTTTATATTTAAATATATAA 1 210 0 TTTTATATTT 0.65918 -91 TTGTAACTTTTTTTATTTTTTAATAGAGCG 3 150 0 TTTTATTTTT 0.899457 -151 TCAGCTAATTCTTTATTTTTTATAGAAATG 4 12 1 CTTTATTTTT 0.864306 -289 ATTCAGTAATCTTTATTTTTGGCATGTATA 4 240 0 CTTTATTTTT 0.864306 -61 CAAGTGTTATTTTTATTTTGTTATTT 5 7 0 TTTTATTTTG 0.888746 -143 AATAACACTTGTTTCTTTTTTATTTCTTTT 5 26 1 GTTTCTTTTT 0.647173 -124 AATATTAGCAGTTTATTTATTAACACTATA 5 96 1 GTTTATTTAT 0.893418 -54 TGGAGGAGTAGTTTATTTTGGAGTTTATTT 6 193 1 GTTTATTTTG 0.935909 -108 TTATTTTGGAGTTTATTTAGCTGTAATTTT 6 205 1 GTTTATTTAG 0.882149 -96 AATCCCCTGAGTTTATTTATTAATAATTGT 6 278 0 GTTTATTTAT 0.893418 -23 AAACCTCTAAGGTTATTTATAATAAATTGA 7 15 1 GGTTATTTAT 0.484595 -122 TTGATTTAATCTTTATTAAGATATTTAAAT 7 41 1 CTTTATTAAG 0.180614 -96 CCCAATATTTGTTTATTTTGCATTTCC 8 8 0 GTTTATTTTG 0.935909 -293 ATAATTAAATTTTTATATTTATAATTATAT 8 63 1 TTTTATATTT 0.65918 -238 TTCCACATTAGTTTATTTAAAGTTAATAAG 8 131 0 GTTTATTTAA 0.492621 -170 ATTTTTATATTTTAATTTAAAT 9 3 1 TTTTATATTT 0.65918 -85 TTCCTCATGTTTTTATTTTTAATCTTTTAA 10 273 0 TTTTATTTTT 0.899457 -28 ********** Masking position 6 Map Score: 19.8215 Number of sites scoring better than the average of aligned sites = 788 Number in coding regions = 555 Number in noncoding regions = 233 Number of orfs with sites within 600 bp upstream = 187 Fraction of orfs with sites within 600 bp upstream = 0.0300353 Motif number 6 TTTATTTTGCAAATATTAATTTATATATTTAAATA 1 190 1 AATTATTATA 0.769817 -111 AGAGATTGTTATAGATTAGGGTATAAAAATTATAA 1 251 0 AATTAGTATA 0.968903 -50 TTAATTAATAATACTTTTCGTGGTGGCATAAA 2 47 1 AATTTGGGTG 0.354287 -22 ACTACTATATAAATCTTACGATATGAAACGGTTAT 3 51 1 AATTAGTATG 0.962392 -250 TTTGTTATACAAAATTTAATTTATAATATCGCTCT 3 121 1 AATTATTATA 0.769817 -180 AGTTTCTACTAAATATTTGGATATATCAAAATTAA 3 210 0 AATTTGTATA 0.843931 -91 TTTCTTTAAAAAATCTTAAGGGATAAA 3 284 1 AATTAGGATA 0.893211 -17 AAATGGTTCCTAATTTTATGCTATAGATTGAAGAA 4 37 1 TATTAGTATA 0.740411 -264 AACGAAAATTATAAGTAATGCTATATTTACAATTA 6 153 1 AATAAGTATA 0.740411 -148 ATTTAGCATAAAATGTTAAGTTGTGTTAGCTAATA 7 86 1 AATTAGTGTG 0.92173 -51 AGCTAATATTAAAAAATAAGGTATATTTAAAAAT 7 113 1 AAATAGTATA 0.843931 -24 TTGTTTTATGACATTATACGCTATAATATAATTAT 8 83 0 AAATAGTATA 0.843931 -218 CCATATATATATAATTTACGGTATATTCAATTTAA 9 27 0 AATTAGTATA 0.968903 -61 GTATTGGTTAATACGTTAGGATTTGCCTCAACGAA 11 170 0 AATTAGTTTG 0.747731 -131 GTAAAATTCCAGAGCTTAAGGTGTGTGCTGTAAAG 11 222 1 AATTAGTGTG 0.92173 -79 * * *** * **** Masking position 3 Map Score: 10.9894 Number of sites scoring better than the average of aligned sites = 249 Number in coding regions = 187 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 7 GTATATATACTTACCTCAATAGGACTTCGCA 1 74 0 TTACCTCAAA 0.747612 -227 TATTTCCATATTATTTCCACATTAGTTTATT 8 144 0 TTATTTCCAA 0.966786 -157 ATATTTTCTTTTATTTCCATATTATTTCCAC 8 155 0 TTATTTCCAA 0.966786 -146 AGTAAGTTTCCTACTTCCATATATATATAAT 9 47 0 CTACTTCCAA 0.883423 -41 AGTAGGAAACTTACTTCCAGAATTATTCAAT 9 63 1 TTACTTCCAA 0.966137 -25 GATATGATATTTATTTCAAGTGAAGAATCTG 10 152 1 TTATTTCAAT 0.702571 -149 TAATCTTTGTTTATTTCCAAGGTCTTGCTAT 10 245 0 TTATTTCCAG 0.899563 -56 TCATCTGGATTTATTTCAATAAATGGTTCAT 11 15 0 TTATTTCAAA 0.919211 -286 ********* * Masking position 3 Map Score: 3.46308 Number of sites scoring better than the average of aligned sites = 57 Number in coding regions = 47 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 AAACTTTCCTTTAAAGATTTTATTCCTGCG 1 48 1 TTAAAGATTT 0.936147 -253 AAACTGATTCTTAGAGATTGTTATAGATTA 1 268 0 TTAGAGATTG 0.91876 -33 TTATAATGAATTAGAAATTTTTTCTTTAAA 3 264 1 TTAGAAATTT 0.733036 -37 AAGTATTTTGTTAGTGATTTCTTCAATCTA 4 60 0 TTAGTGATTT 0.915606 -241 TTATGAAACTTAAAAGATTTTTAACCTTAT 4 100 0 TAAAAGATTT 0.673513 -201 AATGTATTATTTAATGATTTAATAACTTTT 5 63 0 TTAATGATTT 0.909206 -87 AGTTTATTTATTAATAATTGTATAATATTA 6 269 0 TTAATAATTG 0.552084 -32 ATAAATAACCTTAGAGGTTTTAAA 7 5 0 TTAGAGGTTT 0.768116 -132 TTCTCAATTTTTAATGATTTGGCATCATCT 11 40 0 TTAATGATTT 0.909206 -261 GGTGTGTGCTGTAAAGATTGAACGAATTTA 11 241 1 GTAAAGATTG 0.685231 -60 ********** Masking position 3 Map Score: 3.69809 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 300 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 CTTTTAGTGTTTATAAATGGTGATGTC 2 4 0 TTAAAGGGAT 0.976928 -65 CTTCTTTTAATAAGGTAAGGAGGTTTTATT 4 281 1 TAATAGGGGT 0.890369 -20 TATTAATAAATAAACTCAGGGGATTTAA 6 283 1 TAATCGGGAT 0.875164 -18 ACGAAATTCGTAAAATAGGGGGATTAAAATCGCA 8 264 1 TAATAGGGAT 0.963496 -37 GGTTTAATCTTTATGAATGGAGATATTGAGAAAG 10 53 1 TTAAAGGGAT 0.976928 -248 TCATTAAAAATTGAGAATGGTGATTTAGTTAAGG 11 53 1 TTGAAGGGAT 0.918344 -248 GAATGGTGATTTAGTTAAGGTGATTTCAAGGAGA 11 67 1 TTATAGGGAT 0.976928 -234 ACTGAAGACATTAAAAAAGGAGTTGTATTTATGC 11 128 1 TTAAAGGGTT 0.897861 -173 *** ** ** *** Masking position 1 Map Score: 3.03555 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 71 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 AATAGTTTCTGAATGAAAAATTTTATTATATC 3 89 1 GAATGAAAAT 0.862362 -212 TTATGCTATAGATTGAAGAAATCACTAACAAA 4 52 1 GATTGAAAAT 0.975457 -249 ATTATTTAATGATTTAATAACTTTTTAATTAT 5 56 0 GATTTAAAAT 0.860113 -94 ATTATCACAAGATTAAAGAGGTTTTAAATAGA 6 17 1 GATTAAAAGT 0.784011 -284 TCTTAATAAAGATTAAATCAATTTATTATAAA 7 30 0 GATTAAACAT 0.827001 -107 AGTATTCACAGATAGAAAAATTTATATTTTAC 8 188 1 GATAGAAAAT 0.862362 -113 TTTGATTGAATAATTCTGGAAGTAA 9 73 0 GATTGAAAAT 0.975446 -15 AATAAACAAAGATTAAAAGATTAAAAATAAAA 10 261 1 GATTAAAGAT 0.897933 -40 GTGCTGTAAAGATTGAACGAATTTAATTTATA 11 246 1 GATTGAAGAT 0.957458 -55 ******* ** * Masking position 6 Map Score: 4.2015 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 77 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 11 TAGCTGCTGAGCTATGATGATTGATGGGCGAA 1 146 1 GTATGAGATT 0.922725 -155 ATTTAATTACGTTATTATGATTACTTACTACG 4 147 1 GTATTAGATT 0.902673 -154 ATATGGCTTGGATAATAAGATTTATATACATG 4 216 1 GTAATAGATT 0.967028 -85 CTTTTAATAAGGTAAGGAGGTTTTATT 4 284 1 GTAAGGGGTT 0.81187 -17 TAAATAAACTGCTAATATTATTAATGTATTAT 5 83 0 GTAATATATT 0.766163 -67 TTTATTTAAAGTTAATAAGATTGGGGTATTAA 8 118 0 GTAATAGATT 0.967051 -183 ATAGAATTAAGTTAAGACCATTAATTGCAGCT 10 111 1 GTAAGACATT 0.862145 -190 TGGTGATTTAGTTAAGGTGATTTCAAGGAGAG 11 70 1 GTAAGGGATT 0.94864 -231 TAGGAAATATGATTCCTATTATAT 11 287 0 GAAATAGATT 0.82228 -14 * ***** **** Masking position 4 Map Score: 3.634 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 75 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 12 AACAATCTCTAAGAATCAGTTTTTAAGGTG 1 276 1 AAGAATCAGT 0.925022 -25 ATAAAAAATAAAGAATTAGCTGAT 4 5 0 AAGAATTAGC 0.925022 -296 ATTTCAAGTGAAGAATCTGCTATAAGAAGA 10 164 1 AAGAATCTGC 0.980008 -137 CTGCTATAAGAAGAATCTGCCCTGACTTAG 10 180 1 AAGAATCTGC 0.980008 -121 ********** Masking position 5 Map Score: 0.226385 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 8 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 ATTTAAATATATTAAGGAACTT 1 2 0 ATTAAGAACT 0.949495 -299 CCATAAATATATTAAGTAGCTTTAAGTATAT 1 99 0 ATTAAGAGCT 0.939708 -202 AAAATTTTTCATTCAGAAACTATTGTTATAA 3 82 0 ATTCAGAACT 0.939705 -219 TGAGTGTGTTATTATGAAACTTAAAAGATTT 4 110 0 ATTATGAACT 0.949492 -191 ATTGTAGAACATTATGGAGCTTTTTACTCAA 6 84 0 ATTATGAGCT 0.939708 -217 TGATTGAATAATTCTGGAAGTAAGTTTCCTA 9 65 0 ATTCTGAAGT 0.781357 -23 ****** **** Masking position 8 Map Score: 0.445449 Number of sites scoring better than the average of aligned sites = 87 Number in coding regions = 72 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 14 ********** No masking Map Score: -1.49681e-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 15 TAAAAATTTATATGATAGCTATCTTTTTATAATTTT 1 225 1 TAATCTTTTT 0.553961 -76 TGAAAAATTTTATTATATCTTTGTTATACAAAATTT 3 102 1 TAATCTTTTA 0.910321 -199 ATTTAATTTATAATATCGCTCTATTAAAAAATAAAA 3 134 1 TAATCTTTTA 0.945347 -167 ATATATTTTTTAATATGGCTTGGATAATAAGATTTA 4 204 1 TAATCTGATA 0.809485 -97 CTTGTTTCTTTTTTATTTCTTTTATAATTAAAAAGT 5 33 1 TTATCTTATA 0.759122 -117 AAACTGCTAATATTATTAATGTATTATTTAATGATT 5 74 0 TAATATTTTA 0.673409 -76 TGTATAATATTATTATATTTCTCTTACATCGATAAC 6 245 0 TAATTTTTTA 0.751097 -56 TATTTTACACTAAAATAATTTTAATAAATAATATCA 8 212 1 TAATTTTATA 0.725481 -89 TTCGTTAAATTATTATTACTATGATATTATTTATTA 8 233 0 TAATCTTATA 0.883923 -68 TGCCTGACGCTGGAATGCCTGTTATAGCAAGACCTT 10 222 1 TGATCTTATA 0.823681 -79 ATGGCATAAATACAACTCCTTTTTTAATGTCTTCAG 11 129 0 TAACCTTTTA 0.80982 -172 TAGGAAATATGATTCCTATTATATAAACAATTC 11 278 0 TAATCTTATA 0.949154 -23 ** ** ** * *** Masking position 5 Map Score: 5.92354 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 69 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