AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_mjan_reg_100.orf -o00300_mjan_100.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 MJ0206 95 conserved hypothetical protein #2 MJ0245 44 SSU ribosomal protein S17E #3 MJ0246 300 chorismate mutase/prephenate dehydratase (pheA) #4 MJ0422 65 dihydrodipicolinate reductase (dapB) #5 MJ0502 160 3-phosphoshikimate-1-carboxyvinyltransferase (aroA) #6 MJ0503 84 2-isopropylmalate synthase (leuA) #7 MJ0539 267 tRNA synthetase, putative #8 MJ0571 300 aspartate kinase (lysC) #9 MJ1097 108 diaminopimelate decarboxylase (lysA) #10 MJ1119 113 diaminopimelate epimerase (dapF) #11 MJ1195 135 2-isopropylmalate synthase (leuA) #12 MJ1391_MJ1392 474 MJ1391: putative aminotransferase, MJ1392: 2-isopropylmalate synthase (leuA) #13 MJ1530 178 ribosomal protein S18 alanine acetyltransferase #14 MJ1600 77 conserved hypothetical protein Motif number 1 TAAAGGTATATAATATTTATAATCATATATAT 1 52 0 TAATTTATAA 0.731253 -44 TAAATATTATATACCTTTAAATAATTTTATGA 1 65 1 ATATTTAAAT 0.798215 -31 TTATTTTTCTATTAATTTTTAA 2 1 0 ATTTTTTTAA 0.692493 -44 TCACCTTCTTATCCTTTTTTATTATTTTTCTA 2 22 0 ATCTTTTTAT 0.796208 -23 GGTTTTATAAATACCTTTTTATGTCAAACTTT 3 86 1 ATATTTTTAT 0.911454 -215 AAATTACTATTTACTTTTTTATTATAAATATA 3 129 0 TTATTTTTAT 0.895037 -172 AGGATTATAAAAACATTTTTATACTTCTTCTA 3 168 1 AAATTTTTAT 0.943197 -133 ATTGTCCATCTTTTGTTTTTATACATAAACAA 3 211 1 TTTTTTTTAT 0.85405 -90 AATATGGCGGATAACTTTATATATTTTATTTA 3 250 1 ATATTTATAT 0.864516 -51 TATATTTTATTTAAGTTTTTATAATAACATTC 3 269 1 TTATTTTTAT 0.895036 -32 ATATTGCATCAACTATTTATAAATA 4 51 1 AACTTTATAA 0.554903 -15 TGAGAAAAATTAACATTTATAAATTAAGTAAG 5 12 0 TAATTTATAA 0.731254 -149 ATCAACAGAGTATAATTTAAATGTGATATATT 5 123 0 TATTTTAAAT 0.783902 -38 CACCACTAATTTTTTAATCAACAGAGTA 5 143 0 TAATTTTAAT 0.895037 -18 TTACCTGTATAAATTTTTTTATTATTTTTTAA 6 53 0 AAATTTTTAT 0.943197 -32 GTCAATCATCAAAAGTTTTTATAGTTATATAA 7 83 0 AAATTTTTAT 0.943197 -185 ATTTGGATTTTTTGATTTTTATATTTTAAATA 7 202 1 TTTTTTTTAT 0.854049 -66 TTATTGTCTATATTATTTAAAATATAAAAATC 7 215 0 TATTTTAAAA 0.536508 -53 AAAGAAGTTTAATTATTTTTATTCTTTATACT 8 69 0 AATTTTTTAT 0.91932 -232 GCTTTTCCTAAATAGTTTTAATCAAATTTAAA 8 109 1 AATTTTTAAT 0.875989 -192 GAATATAATGTTCTATTTTTAAATTTGATTAA 8 126 0 TTCTTTTTAA 0.508059 -175 TCTTTTTATTAACCTTTTATATTTTTAGTTCA 8 171 0 AACTTTATAT 0.796208 -130 CCAATAAAGAAAAATTTTAAATATACATGGTC 8 225 1 AAATTTAAAT 0.864519 -76 TACACCAAAAATTATTTTATAATTGATAAGAT 8 275 0 ATTTTTATAA 0.582866 -26 CCAATTCTTTATATGATAAAATAA 9 95 0 AATTTTATAT 0.875989 -14 CTTTCCTTAGTTAGTTTTTAATCACATTTGCA 10 27 0 TTATTTTAAT 0.840919 -87 TCTGATTAGGTAAAATTTTTATAACATCCCAT 11 77 1 TAATTTTTAT 0.932227 -59 AATCCCACCAAAACTTTTTAATTTTCTGTTAT 11 114 0 AAATTTTAAT 0.911454 -22 ATTTCATTAAATTATTTTTTATGAGGGATTGT 12 12 0 ATTTTTTTAT 0.875987 -463 ATTTCCCACATAAATTTTAAATATACAATATC 12 97 0 TAATTTAAAT 0.840919 -378 ATCTTAATTTATAAATTTAAATTTAAAGATGT 12 156 0 ATATTTAAAT 0.797912 -319 CGCAGGAATAAAATCTTTAAAAGAAATCTTAA 12 181 0 AAATTTAAAA 0.67064 -294 ATAATCTTTATAAAATTTTTATTATTTTTGAA 12 234 1 TAATTTTTAT 0.932227 -241 AACAATAGCGAAATTTTTATATTTGTTAAAAT 12 315 1 AAATTTATAT 0.911454 -160 TAAGGTATTTTTTAATTTTAATAACTTTTGCA 12 373 0 TTTTTTTAAT 0.783844 -102 ACTACCCATATATTCTTTTAAAATGCTCCGCA 12 424 1 TATTTTTAAA 0.651233 -51 TAGTATTTCAAAATGTTTTAAAAGACTCTATA 13 53 1 AAATTTTAAA 0.766607 -126 TATTATTTTAAATTCTTTTTATAGAGTCTTTT 13 72 0 AATTTTTTAT 0.919321 -107 ATTTATTAAATTCTATTTTAATTTTAGTATTA 13 99 0 TTCTTTTAAT 0.667373 -80 AAAGCCTTTGAATAATTTTAATCAATGAATGT 13 137 0 AATTTTTAAT 0.875988 -42 TCTCACAGAATAATATTTTTATATATAAAGGA 14 13 1 TAATTTTTAT 0.932227 -65 GTAGTTAAATTATCCTTTATATATAAAAATAT 14 25 0 TATTTTATAT 0.85405 -53 *** ******* Masking position 6 Map Score: 53.4993 Number of sites scoring better than the average of aligned sites = 2955 Number in coding regions = 1875 Number in noncoding regions = 1080 Number of orfs with sites within 600 bp upstream = 657 Fraction of orfs with sites within 600 bp upstream = 0.105525 Motif number 2 TTATTTAAAGGTATATAATATTTATAATCATATATA 1 53 0 GTTATAATTA 0.580234 -43 TTATATACCTTTAAATAATTTTATGAGGGATATTA 1 71 1 TTAATATTTA 0.961864 -25 TTTATTATTTTTCTATTAATTTTTAA 2 1 0 TTTATATTTA 0.961947 -44 TTATAAAAACTTAAATAAAATATATAAAGTTATCCG 3 257 0 TTAATAATAA 0.79798 -44 AAAAATTAACATTTATAAATTAAGTAAGT 5 4 0 ATTATATTAA 0.527814 -157 AACAACCTTAATATATCACATTTAAATTATACTCTG 5 114 1 ATTATAATTA 0.754214 -47 GTATAAATTTTTTTATTATTTTTTAATCAAAATATC 6 43 0 TTTATATTTA 0.947254 -42 CCTTTTGAGCTTCTATAAGTTTATTATATAACTATA 7 60 1 TTTATATTTA 0.962103 -208 AATGATATAAATAACTTAGTTTTAGACAAAAAAGCT 7 123 0 ATACTATTTA 0.398688 -145 ACTAAGTTATTTATATCATTTTGGTAGTTAATATTT 7 139 1 TTTATATTTA 0.962121 -129 GTAGTTAATATTTTAACAAATTATTATGTAACCTAA 7 162 1 TTTAAAATTA 0.593016 -106 GAAATTTGGATTTTTTGATTTTTATATTTTAAATAA 7 199 1 TTTTTATTTA 0.567972 -69 TTTTTATATTTTAAATAATATAGACAATAAAATAGA 7 217 1 TTAATAATAA 0.79798 -51 CTTAAAGAAGTTTAATTATTTTTATTCTTTATACTA 8 68 0 TTAATATTTT 0.558423 -233 CCTAAATAGTTTTAATCAAATTTAAAAATAGAACAT 8 115 1 TTAATAATTA 0.943164 -186 GTTATTTTTATTTTATCATATAAAGAATTGG 9 88 1 TTTATAATAA 0.79798 -21 TTAGTTAGTTTTTAATCACATTTGCAAAGAACTATT 10 17 0 TTAATAATTA 0.943169 -97 ATGAACTTTAATCTATCATTTTGAAAGGTTAAGTTA 11 23 1 ATTATATTTA 0.824453 -113 TAAAAAATAATTTAATGAAATTTAAATACTCATAAT 12 23 1 TTAATAATTA 0.943164 -452 TTTATAAAATTTTTATTATTTTTGAAAGATACTATA 12 240 1 TTTATATTTA 0.947254 -235 AATGCGAGTATTTTATGACTTTCGTATAGTATCTTT 12 264 0 TTTATATTTA 0.962122 -211 CGCTATTGTTTTGTATTAAATCTTTAATGCGAGTAT 12 289 0 TTTATAATCA 0.590886 -186 TTTGTTAAAATTTACTTACATTAAAACAAGTAGTTT 12 336 1 TTACTAATTA 0.700861 -139 ATTTTTTAATTTTAATAACTTTTGCAAAAACTACTT 12 363 0 TTAATATTTA 0.962119 -112 ATAGAGTCTTTTAAAACATTTTGAAATACTAAGGAC 13 48 0 TTAAAATTTA 0.689818 -131 TAGTATTATTTTAAATTCTTTTTATAGAGTCTTTTA 13 71 0 TTAATCTTTA 0.643484 -108 TAAAATAGAATTTAATAAATTACACAACATTCATTG 13 111 1 TTAATATTAA 0.858066 -68 AGTAAAGCCTTTGAATAATTTTAATCAATGAATGTT 13 136 0 TTAATATTTC 0.652092 -43 ** *** * *** * Masking position 11 Map Score: 31.5244 Number of sites scoring better than the average of aligned sites = 582 Number in coding regions = 404 Number in noncoding regions = 178 Number of orfs with sites within 600 bp upstream = 184 Fraction of orfs with sites within 600 bp upstream = 0.0295535 Motif number 3 ATATCACCAATATTTTAGGTAGTTGCCAAA 3 13 1 TATTTTAGGT 0.697759 -288 CTCAGAAAAGTATATTTATTTTGGCAACTA 3 32 0 TATATTTATT 0.748892 -269 AAATAGGTTTTATATTTATTCCCTCAGAAA 3 54 0 TATATTTATT 0.748892 -247 ACTTCTTCTATATTTTTAGGTATTGTCCAT 3 190 1 TATTTTTAGG 0.694465 -111 TCCGCCATATTATTTGTATTGTTTATGTAT 3 231 0 TATTTGTATT 0.61851 -70 TTCATATTGATATTTTGATTAAAAAATAAT 6 35 1 TATTTTGATT 0.645564 -50 CCTGTATAAATTTTTTTATTATTTTTTAAT 6 52 0 TTTTTTTATT 0.561715 -33 AAATGTTATCTATTTTTGATGATTGA 7 7 0 TATTTTTGAT 0.865503 -261 GTTATTTATATCATTTTGGTAGTTAATATT 7 144 1 TCATTTTGGT 0.468543 -124 TTGATTTTTATATTTTAAATAATATAGACA 7 213 1 TATTTTAAAT 0.614144 -55 TTTCCCTCAAAATTTTTGTTTCTTCTATTT 7 246 0 AATTTTTGTT 0.749247 -22 TTTTTTCAAATATTTTTAGTATAAAGAATA 8 52 1 TATTTTTAGT 0.968554 -249 GAAGTTTAATTATTTTTATTCTTTATACTA 8 68 0 TATTTTTATT 0.957992 -233 TAACCTTTTATATTTTTAGTTCATAAGCTA 8 164 0 TATTTTTAGT 0.968554 -137 TATTGGAGCATCTTTTTATTAACCTTTTAT 8 183 0 TCTTTTTATT 0.86993 -118 ATTATAAAATAATTTTTGGTGTAAGTT 8 284 1 AATTTTTGGT 0.801412 -17 TCCCGGGCGTTATTTTTATTTTATCATATA 9 80 1 TATTTTTATT 0.957992 -29 TACAAATAACTATTTTTGGTGTGAAAAT 10 96 1 TATTTTTGGT 0.944307 -18 TCCCACCAAAACTTTTTAATTTTCTGTTAT 11 114 0 ACTTTTTAAT 0.449331 -22 TATATTACCAACTTTTTAGTCCAGAACTAT 12 127 0 ACTTTTTAGT 0.682532 -348 ATCTTTATAAAATTTTTATTATTTTTGAAA 12 237 1 AATTTTTATT 0.844416 -238 GCGAAATTTTTATATTTGTTAAAATTTACT 12 322 1 TATATTTGTT 0.62147 -153 AGGTATTTTTTAATTTTAATAACTTTTGCA 12 373 0 TAATTTTAAT 0.674532 -102 ACCAAATTGGCATTTTTAGTTTTTGCGGAG 12 449 0 CATTTTTAGT 0.728295 -26 ATTTTAGTATTATTTTAAATTCTTTTTATA 13 81 0 TATTTTAAAT 0.614144 -98 AATTCTATTTTAATTTTAGTATTATTTTAA 13 93 0 TAATTTTAGT 0.845218 -86 AGCCTTTGAATAATTTTAATCAATGAATGT 13 137 0 TAATTTTAAT 0.674532 -42 CACAGAATAATATTTTTATATATAAAGGAT 14 16 1 TATTTTTATA 0.531721 -62 ********** Masking position 5 Map Score: 21.9001 Number of sites scoring better than the average of aligned sites = 1055 Number in coding regions = 705 Number in noncoding regions = 350 Number of orfs with sites within 600 bp upstream = 290 Fraction of orfs with sites within 600 bp upstream = 0.0465789 Motif number 4 ATATATCACCAATATTTTAGGT 3 2 1 TATATCACAA 0.962276 -299 AGTATTATACTTTATCAACAGCATT 4 5 0 TTTATCACAG 0.934469 -61 CACTAATTTTTTAATCAACAGAGTATAATTT 5 137 0 TTAATCACAG 0.880884 -24 TCAATCATCAAAAATAGATAA 7 1 1 TCAATCACAA 0.898954 -267 TGAATTATAGTCAATCATCAAAAGTTTTTAT 7 93 0 TCAATCACAA 0.898954 -175 TGGTAGTTAATATTTTAACAAATTATTATGT 7 160 1 TATTTTACAA 0.557844 -108 AAAGTTCATTTAATTCATCAA 11 1 0 TAATTCACAA 0.747692 -135 CCTAATCAGATATATCATTAAAACGCTATAA 11 56 0 TATATCATAA 0.779836 -80 ATGATTCAATTTTATCATCAGATTCATTATG 12 53 0 TTTATCACAG 0.934462 -422 TTTAAAGATGTATATTACCAACTTTTTAGTC 12 136 0 TATATTACAA 0.849193 -339 CCCCATTAACTTTATTAATAATCTTTATAAA 12 217 1 TTTATTATAA 0.438451 -258 TTTATCACCAAATTGGCATTT 12 464 0 TTTATCACAA 0.962265 -11 ******* *** Masking position 7 Map Score: 6.97189 Number of sites scoring better than the average of aligned sites = 642 Number in coding regions = 572 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 TAATATCCCTCATAAAATTATTTAAA 1 80 0 TTCCCCAAAA 0.979484 -16 TTTTATATTTATTCCCTCAGAAAAGTATATTTA 3 44 0 ATCCCCAAAA 0.986784 -257 AATTTCCCTCAAAATTTTTGTTTCT 7 253 0 TTCCCCAAAT 0.906979 -15 ATAACTCCTAACTCCCCAATAAAGAAAAATTTT 8 210 1 ATCCCAAAAA 0.842793 -91 TGATAAGATTAACCACACAAAATTTTAGACCAT 8 251 0 ACCACCAAAT 0.690491 -50 AACTTACACCAAAAATTATTTTAT 8 287 0 ATTACCCAAA 0.48721 -14 AGGGGATTTGAACCCCTGAAAAAACTGGCTCCG 9 48 0 ACCCCGAAAA 0.853684 -61 ATTTTCACACCAAAAATAGTTATTT 10 99 0 TTCACCCAAA 0.827534 -15 TTTTTATAACATCCCATCATAAATAACAGAAAA 11 92 1 ACCCACAAAA 0.783253 -44 AATCCCACCAAAACTTTTTAATT 11 123 0 ATCCCCCAAA 0.974173 -13 AACAATCCCTCATAAAAAATAATTTA 12 4 1 ATCCCCAAAA 0.986793 -471 TCCAGAACTATTTCCCACATAAATTTTAAATAT 12 105 0 TTCCCCAAAA 0.979483 -370 TCTTTTAAAATGCTCCGCAAAAACTAAAAATGC 12 437 1 TCTCCCAAAA 0.816029 -38 * **** ** *** Masking position 11 Map Score: 13.1295 Number of sites scoring better than the average of aligned sites = 178 Number in coding regions = 139 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 6 CTGTAGTGTTTTTTATACAGATGTATAGGAA 1 20 1 TTTTATACAA 0.867296 -76 GGTATATAATATTTATAATCATATATATCTT 1 49 0 ATTTATAATA 0.731607 -47 CTCAAATAGGTTTTATATTTATTCCCTCAGA 3 56 0 TTTTATATTA 0.772438 -245 CTATTTGAGGTTTTATAAATACCTTTTTATG 3 78 1 TTTTATAAAA 0.939693 -223 CTATTTACTTTTTTATTATAAATATAATCTG 3 124 0 TTTTATTATA 0.731368 -177 ATAAAAATGTTTTTATAATCCTAATGGATAA 3 159 0 TTTTATAATC 0.865949 -142 ATAAAAACATTTTTATACTTCTTCTATATTT 3 174 1 TTTTATACTC 0.730286 -127 CATCTTTTGTTTTTATACATAAACAATACAA 3 217 1 TTTTATACAA 0.867296 -84 TTATTTAAGTTTTTATAATAACATTCTGGGG 3 275 1 TTTTATAATA 0.959911 -26 TATTTATAAATAGTTGATGCAA 4 54 0 ATTTATAAAA 0.639437 -12 ATATTAAGGTTGTTATAATTACACAGTTAAT 5 97 0 TGTTATAATA 0.800741 -64 CACCACTAATTTTTTAATCAACAGAGTATA 5 141 0 TTTTTTAATA 0.731567 -20 TTTTTTATTATTTTTTAATCAAAATATCAAT 6 40 0 TTTTTTAATA 0.731567 -45 CATCAAAAGTTTTTATAGTTATATAATAAAC 7 78 0 TTTTATAGTA 0.740464 -190 TATTTTTATTCTTTATACTAAAAATATTTGA 8 57 0 CTTTATACTA 0.489881 -244 TGGAGCATCTTTTTATTAACCTTTTATATTT 8 179 0 TTTTATTAAC 0.323393 -122 CCAAAAATTATTTTATAATTGATAAGATTAA 8 272 0 TTTTATAATG 0.706726 -29 TTGTAAAACATTTTGTAATAAAGAAAGGCAT 10 60 0 TTTTGTAATA 0.696132 -54 TTACAAAATGTTTTACAAAGAGCTACAAATA 10 73 1 TTTTACAAAA 0.575703 -41 TATGATGGGATGTTATAAAAATTTTACCTAA 11 82 0 TGTTATAAAA 0.721321 -54 GATGATTCAATTTTATCATCAGATTCATTAT 12 54 0 TTTTATCATA 0.69615 -421 ATAATAAAAATTTTATAAAGATTATTAATAA 12 228 0 TTTTATAAAA 0.939693 -247 AGAATAATATTTTTATATATAAAGGATAATT 14 19 1 TTTTATATAA 0.688316 -59 ********* * Masking position 4 Map Score: 17.1318 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 385 Number in noncoding regions = 151 Number of orfs with sites within 600 bp upstream = 150 Fraction of orfs with sites within 600 bp upstream = 0.0240925 Motif number 7 TTAAAAATTAATAGAAAAATA 2 2 1 TAAAAATTAA 0.693063 -43 AATCCTAATGGATAAATTACTATTTACTTT 3 144 0 GATAAATTAC 0.775979 -157 AATGCTGTTGATAAAGTATAATACTTAGC 4 10 1 GATAAAGTAT 0.580168 -56 AATTAACATTTATAAATTAAGTAAGT 5 7 0 TATAAATTAA 0.874587 -154 TCTCTAATGAGAAAAATTAACATTTATAAA 5 21 0 GAAAAATTAA 0.867262 -140 ATTTAAATGTGATATATTAAGGTTGTTATA 5 111 0 GATATATTAA 0.633226 -50 ATATATCACATTTAAATTATACTCTGTTGA 5 124 1 TTTAAATTAT 0.585459 -37 ATAATAATTTGTTAAAATATTAACTACCAA 7 159 0 GTTAAAATAT 0.504023 -109 TGAAAACTAAGAAAAATTATATTTCACTAT 8 23 1 GAAAAATTAT 0.754156 -278 TCTTATCAATTATAAAATAATTTTTGGTGT 8 276 1 TATAAAATAA 0.634269 -25 TTCTTTATATGATAAAATAAAAATAACGCC 9 85 0 GATAAAATAA 0.833828 -24 TTGATGAATTAAATGAACTTTA 11 3 1 GATGAATTAA 0.706054 -133 CTTTCAAAATGATAGATTAAAGTTCATTTA 11 20 0 GATAGATTAA 0.719013 -116 AATTTAAATTTATAAATTAAGATTTCTTTT 12 165 1 TATAAATTAA 0.874587 -310 GCAAAAGTTATTAAAATTAAAAAATACCTT 12 374 1 TTAAAATTAA 0.492703 -101 CTCTATGGTAGTTAAATTATCCTTTATATA 14 34 0 GTTAAATTAT 0.803396 -44 CTACCATAGAGTTAAATTAATGTAAGGGGA 14 53 1 GTTAAATTAA 0.896943 -25 ********** Masking position 6 Map Score: 10.6154 Number of sites scoring better than the average of aligned sites = 711 Number in coding regions = 599 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 129 Fraction of orfs with sites within 600 bp upstream = 0.0207196 Motif number 8 TTTTATTATTTTTCTATTAATTTTTAA 2 8 0 TTTCTATTAA 0.923555 -37 TTGTCCATCTTTTGTTTTTATACATAAACA 3 212 1 TTTGTTTTTA 0.648147 -89 CATAATTTCATTTGTATTAACTGTGTAATT 5 82 1 TTTGTATTAA 0.946927 -79 ATTCAGCTTTTTTGTCTAAAACTAAGTTAT 7 119 1 TTTGTCTAAA 0.604266 -149 TAGGAAAAGCTTTCTCTTAAAGAAGTTTAA 8 89 0 TTTCTCTTAA 0.890539 -212 TTGGAGCATCTTTTTATTAACCTTTTATAT 8 181 0 TTTTTATTAA 0.698336 -120 TGTAAAACATTTTGTAATAAAGAAAGGCAT 10 60 0 TTTGTAATAA 0.693974 -54 TAAATTAAGATTTCTTTTAAAGATTTTATT 12 177 1 TTTCTTTTAA 0.907521 -298 TCGCTATTGTTTTGTATTAAATCTTTAATG 12 296 0 TTTGTATTAA 0.946927 -179 GCAAAAACTACTTGTTTTAATGTAAGTAAA 12 346 0 CTTGTTTTAA 0.751458 -129 CTACCCATATATTCTTTTAAAATGCTCCGC 12 425 1 ATTCTTTTAA 0.579981 -50 ********** Masking position 10 Map Score: 4.70237 Number of sites scoring better than the average of aligned sites = 289 Number in coding regions = 248 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 AATAATTTTATGAGGGATATTA 1 84 1 TGAGGGATAT 0.967207 -12 TATACTTTTCTGAGGGAATAAATATAAAAC 3 48 1 TGAGGGAATA 0.921092 -253 ACAAAAATTTTGAGGGAAATT 7 257 1 TGAGGGAAAT 0.976885 -11 TTATTTTTTATGAGGGATTGTT 12 3 0 TGAGGGATTG 0.923512 -472 TTAAAATTTATGTGGGAAATAGTTCTGGAC 12 109 1 TGTGGGAAAT 0.927774 -366 ********** Masking position 7 Map Score: 0.858775 Number of sites scoring better than the average of aligned sites = 79 Number in coding regions = 65 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 10 ********** No masking Map Score: -3.82739e-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 11 ********** No masking Map Score: -3.82739e-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: -3.82739e-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