AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00300_mjan_reg_300.orf -o00300_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 Purged sequences: MJ1118 24 conserved hypothetical protein 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 MJ0541 89 conserved hypothetical protein #9 MJ0542 127 phosphoenolpyruvate synthase #10 MJ0543 132 ubiquinol-cytochrome C reductase complex, subunitVI requiring protein #11 MJ0544 103 dolichyl-phosphate mannose synthase #12 MJ0547 165 cell division inhibitor minD #13 MJ0548 111 conserved hypothetical protein #14 MJ0571 300 aspartate kinase (lysC) #15 MJ1097 108 diaminopimelate decarboxylase (lysA) #16 MJ1098 227 RNA maturase isolog #17 MJ1099 205 conserved hypothetical protein #18 MJ1117 136 conserved hypothetical protein #19 MJ1119 113 diaminopimelate epimerase (dapF) #20 MJ1195 135 2-isopropylmalate synthase (leuA) #21 MJ1196 85 asoB protein #22 MJ1391_MJ1392 474 MJ1391: putative aminotransferase, MJ1392: 2-isopropylmalate synthase (leuA) #23 MJ1530 178 ribosomal protein S18 alanine acetyltransferase #24 MJ1600 77 conserved hypothetical protein Motif number 1 TATATATGATTATAAATATTATATACCTTT 1 53 1 TATAAATATT 0.828292 -43 ATTATATACCTTTAAATAATTTTATGAGGG 1 70 1 TTTAAATAAT 0.712243 -26 TTAAAAATTAATAGAAAAATA 2 2 1 TAAAAATTAA 0.874382 -43 ACTTTTTTATTATAAATATAATCTGCTGTC 3 119 0 TATAAATATA 0.8063 -182 ATTAGGATTATAAAAACATTTTTATACTTC 3 165 1 TAAAAACATT 0.848744 -136 GGACAATACCTAAAAATATAGAAGAAGTAT 3 188 0 TAAAAATATA 0.921354 -113 TGTTTATGTATAAAAACAAAAGATGGACAA 3 212 0 TAAAAACAAA 0.756092 -89 AAATAAAATATATAAAGTTATCCGCCATAT 3 251 0 TATAAAGTTA 0.615181 -50 AATGTTATTATAAAAACTTAAATAAAATAT 3 270 0 TAAAAACTTA 0.818286 -31 AATTAACATTTATAAATTAAGTAAGT 5 7 0 TATAAATTAA 0.712147 -154 ATATATCACATTTAAATTATACTCTGTTGA 5 124 1 TTTAAATTAT 0.696996 -37 TTATTACCTGTATAAATTTTTTTATTATTT 6 58 0 TATAAATTTT 0.817619 -27 TATATAACTATAAAAACTTTTGATGATTGA 7 84 1 TAAAAACTTT 0.839096 -184 TAATAATTTGTTAAAATATTAACTACCAAA 7 158 0 TTAAAATATT 0.915955 -110 TCTATATTATTTAAAATATAAAAATCAAAA 7 211 0 TTAAAATATA 0.903876 -57 AAAACAAAACTTAAAAGTTAAAGGTAA 8 8 0 TTAAAAGTTA 0.783163 -82 AAAATAGTCATAAAAACAAAACTTAAAAGT 8 20 0 TAAAAACAAA 0.756092 -70 TTTGGAATTGTTAAAATATATAATGATAAA 8 47 0 TTAAAATATA 0.903876 -43 ATGATAATATTATAAATAAAATAGTAGAGT 9 56 0 TATAAATAAA 0.727062 -72 TTAAAATAAATTTAAATATTTGAATGATAA 9 79 0 TTTAAATATT 0.794617 -49 AGCTTTTATTTTAAAATAAATTTAAATATT 9 89 0 TTAAAATAAA 0.85751 -39 AACAGTAAGCTTTAAATATTAAGTTAAAAA 10 17 1 TTTAAATATT 0.794617 -116 AATATTAAGTTAAAAATATTAGCATCACAA 10 31 1 TAAAAATATT 0.931452 -102 TAACAAAATTTTAAAATTTTATGGTAATAA 11 47 0 TTAAAATTTT 0.91014 -57 AAAATTTTGTTAAAAATTTACTAGCATCCA 11 65 1 TAAAAATTTA 0.915676 -39 AAATAGGTAATATAAAGATTTTAGA 12 151 1 TATAAAGATT 0.665777 -15 TTCTTTATACTAAAAATATTTGAAAAAATA 14 50 0 TAAAAATATT 0.931452 -251 GTATAAAGAATAAAAATAATTAAACTTCTT 14 70 1 TAAAAATAAT 0.896834 -231 TTAAATTTGATTAAAACTATTTAGGAAAAG 14 110 0 TTAAAACTAT 0.727951 -191 GCTTATGAACTAAAAATATAAAAGGTTAAT 14 166 1 TAAAAATATA 0.921354 -135 CCATGTATATTTAAAATTTTTCTTTATTGG 14 225 0 TTAAAATTTT 0.91014 -76 TATTTTATCATATAAAGAATTGG 15 96 1 TATAAAGAAT 0.560321 -13 AAAACAAAATTAAAAATTATAAAAAT 16 7 0 TAAAAATTAT 0.889854 -221 CCTAACATTATAAAAAGAAAACAAAATTAA 16 24 0 TAAAAAGAAA 0.756092 -204 TTCAAAAGTATTAAAATTAATAAGGAACAC 17 105 0 TTAAAATTAA 0.848225 -101 ACTTAATGTTTTAAAATTTTAATGTCTTTC 17 132 0 TTAAAATTTT 0.91014 -74 ACAATATATATAAAAACTTAATGTTTTAAA 17 147 0 TAAAAACTTA 0.818286 -59 ATTTTTAAATATACCTTATTTTT 18 4 1 TTTAAATATA 0.769569 -133 GATATTTAAATTAAAATTTTGCAAATATTT 18 68 0 TTAAAATTTT 0.91014 -69 CAAATGTGATTAAAAACTAACTAAGGAAAG 19 29 1 TAAAAACTAA 0.742328 -85 TGGGATGTTATAAAAATTTTACCTAATCAG 20 78 0 TAAAAATTTT 0.926622 -58 AACAGAAAATTAAAAAGTTTTGGTGGGATT 20 116 1 TAAAAAGTTT 0.839096 -20 TATTGTATATTTAAAATTTATGTGGGAAAT 22 99 1 TTAAAATTTA 0.897193 -376 AATCTTAATTTATAAATTTAAATTTAAAGA 22 159 0 TATAAATTTA 0.794411 -316 AATAAAATCTTTAAAAGAAATCTTAATTTA 22 177 0 TTAAAAGAAA 0.713161 -298 TCAAAAATAATAAAAATTTTATAAAGATTA 22 235 0 TAAAAATTTT 0.926622 -240 TTTATATTTGTTAAAATTTACTTACATTAA 22 330 1 TTAAAATTTA 0.897193 -145 GCAAAAGTTATTAAAATTAAAAAATACCTT 22 374 1 TTAAAATTAA 0.848225 -101 GCGGAGCATTTTAAAAGAATATATGGGTAG 22 425 0 TTAAAAGAAT 0.742215 -50 ATAGAGTCTTTTAAAACATTTTGAAATACT 23 54 0 TTAAAACATT 0.8182 -125 AAAGACTCTATAAAAAGAATTTAAAATAAT 23 73 1 TAAAAAGAAT 0.782127 -106 TAAAAAGAATTTAAAATAATACTAAAATTA 23 83 1 TTAAAATAAT 0.874565 -96 CATTCATTGATTAAAATTATTCAAAGGCTT 23 138 1 TTAAAATTAT 0.866304 -41 CCTTTATATATAAAAATATTATTCTGTGAG 24 14 0 TAAAAATATT 0.931452 -64 ********** Masking position 5 Map Score: 68.489 Number of sites scoring better than the average of aligned sites = 2086 Number in coding regions = 1309 Number in noncoding regions = 777 Number of orfs with sites within 600 bp upstream = 539 Fraction of orfs with sites within 600 bp upstream = 0.0865724 Motif number 2 TCTTATCCTTTTTTATTATTTTTCTATTAATTT 2 15 0 TTTTATTTTT 0.95026 -30 CTCAAATAGGTTTTATATTTATTCCCTCAGAAA 3 54 0 TTTTATATTT 0.869526 -247 CTATTTACTTTTTTATTATAAATATAATCTGCT 3 122 0 TTTTATTTAT 0.840335 -179 ATAAAAACATTTTTATACTTCTTCTATATTTTT 3 174 1 TTTTATATTT 0.869548 -127 ACTTTATATATTTTATTTAAGTTTTTATAATAA 3 263 1 TTTTATTATT 0.856229 -38 GTAGGCTAAGTATTATACTTTATCAACAGCATT 4 11 0 TATTATATAT 0.21957 -55 GTATAAATTTTTTTATTATTTTTTAATCAAAAT 6 46 0 TTTTATTTTT 0.95026 -39 TTTTTGATTTTTATATTTTAAATAATATAGACA 7 210 1 TTATATTTAT 0.782714 -58 GTTTCTTCTATTTTATTGTCTATATTATTTAAA 7 226 0 TTTTATTTAT 0.840851 -42 TGAAACTTTTTTTAATTTTTTATAACATTTTCA 9 14 1 TTTAATTTAT 0.767442 -114 ATTTTATTTATAATATTATCATTCAAATATTTA 9 64 1 TAATATTTTT 0.665778 -64 ATTCAAATATTTAAATTTATTTTAAAATAAAAG 9 84 1 TTAAATTATT 0.717328 -44 ATATAGGGGATTATATATAGCTTTTATTTTAAA 9 104 0 TTATATAATT 0.586126 -24 CCATAAAATTTTAAAATTTTGTTAAAAATTTAC 11 53 1 TTAAAATTTT 0.554454 -51 AGCATCCAATTTATATTGTGATTACCT 11 87 1 TTATATTTTT 0.928782 -17 ATCGTTAATCTTATATATTAGTTATTAAATAGT 13 46 0 TTATATATTT 0.819709 -66 TAGTTAGTATTATTATTATCGTTAATCTTATAT 13 63 0 TATTATTTTT 0.744931 -49 AATAGTGAAATATAATTTTTCTTAGTTTTCATC 14 21 0 TATAATTTTT 0.645947 -280 CTTAAAGAAGTTTAATTATTTTTATTCTTTATA 14 71 0 TTTAATTTTT 0.922708 -230 ATGTTCTATTTTTAAATTTGATTAAAACTATTT 14 118 0 TTTAAATTTT 0.645948 -183 AAATAGAACATTATATTCTCTTTTTAGCTTATG 14 140 1 TTATATTTTT 0.928782 -161 TGGAGCATCTTTTTATTAACCTTTTATATTTTT 14 177 0 TTTTATTATT 0.856229 -124 CATGTATATTTAAAATTTTTCTTTATTGGGGAG 14 221 0 TAAAATTTTT 0.554453 -80 CCAAAAATTATTTTATAATTGATAAGATTAACC 14 270 0 TTTTATATAT 0.648121 -31 TTTTATAATTTTTAATTTTGTTTTCTTTTTATA 16 13 1 TTTAATTTTT 0.922745 -215 GTTAGGGAAATTTTATTAAGTATGATTGAGTAT 16 48 1 TTTTATTAAT 0.622029 -180 ATTTTTGTTCTTTTATACTTCTTTTCTATTGAT 16 79 0 TTTTATATTT 0.869548 -149 CCCATTCTTTTTTTATTCTTCTTATATGGATGC 16 188 0 TTTTATTTTT 0.950298 -40 TGTTTTAAAATTTTAATGTCTTTCAAAAGTATT 17 123 0 TTTTAATTTT 0.744931 -83 AAGTTTTTATATATATTGTCATTAATCATTTTT 17 158 1 ATATATTTTT 0.399356 -48 ATTTTTAAATATACCTTATTTTTTAAT 18 5 1 TTAAATAATT 0.469411 -132 ATTAAGATATTTAAATTAAAATTTTGCAAATAT 18 70 0 TTAAATTATT 0.717327 -67 GATTAAATCAATTTATTATAAATAACCTTAGAG 18 106 1 ATTTATTTAT 0.199232 -31 CTTAGTTAGTTTTTAATCACATTTGCAAAGAAC 19 21 0 TTTTAATATT 0.476355 -93 TTAAATTTTAGATAAAGATAATT 21 1 1 TTAAATTTAT 0.692429 -85 CTTTTTCTTTTATAATTATCTTTATCTAAAATT 21 14 0 TATAATTTTT 0.645946 -72 AGCAAAAATATTTAATATATCTTTTTCTTTTAT 21 34 0 TTTAATAATT 0.564657 -52 AACTACACCCTTATAAATTGATTAAACAAAGCA 21 63 0 TTATAAATTT 0.409848 -23 TTAAATTTCATTAAATTATTTTTTATGAGGGAT 22 15 0 TTAAATTTTT 0.890639 -460 ATATACATCTTTAAATTTAAATTTATAAATTAA 22 152 1 TTAAATTATT 0.717328 -323 ATAATAAAAATTTTATAAAGATTATTAATAAAG 22 226 0 TTTTATAATT 0.674929 -249 TTTATAAAATTTTTATTATTTTTGAAAGATACT 22 240 1 TTTTATTTTT 0.95026 -235 ATAGCGAAATTTTTATATTTGTTAAAATTTACT 22 319 1 TTTTATATTT 0.869548 -156 GTAAGGTATTTTTTAATTTTAATAACTTTTGCA 22 373 0 TTTTAATTAT 0.44658 -102 TAGTATTATTTTAAATTCTTTTTATAGAGTCTT 23 74 0 TTAAATTTTT 0.890674 -105 GTGTAATTTATTAAATTCTATTTTAATTTTAGT 23 103 0 TTAAATTTTT 0.890674 -76 TCTATGGTAGTTAAATTATCCTTTATATATAAA 24 30 0 TTAAATTTTT 0.890675 -48 ******* * ** Masking position 5 Map Score: 55.0118 Number of sites scoring better than the average of aligned sites = 2410 Number in coding regions = 1658 Number in noncoding regions = 752 Number of orfs with sites within 600 bp upstream = 504 Fraction of orfs with sites within 600 bp upstream = 0.0809509 Motif number 3 CAGAAAAGTATATTTATTTTGGCAACTACCT 3 29 0 TATTTATTTG 0.690595 -272 AAATGTTATCTATTTTTGATGATTGA 7 6 0 TATTTTTGTG 0.972348 -262 TAACTATAAAAACTTTTGATGATTGACTATA 7 88 1 AACTTTTGTG 0.818582 -180 TTTCCCTCAAAATTTTTGTTTCTTCTATTTT 7 245 0 AATTTTTGTT 0.782257 -23 AAATCTTCACTATTTTTGGTGATACA 8 74 1 TATTTTTGTG 0.972348 -16 CAATATATAAAATTTATTGTGATGCTAATAT 10 46 0 AATTTATTTG 0.662552 -87 ATCATCACCTATTTTGGCTGTTTCGTTTTA 10 113 0 TATTTTGGTG 0.904213 -20 CATGGTCTAAAATTTTGTGTGGTTAATCTTA 14 250 1 AATTTTGTTG 0.662194 -51 ATTATAAAATAATTTTTGGTGTAAGTT 14 284 1 AATTTTTGTG 0.968683 -17 ATTAATAAGCAATTTTTGTTCTTTTATACTT 16 92 0 AATTTTTGTC 0.751218 -136 TACAAATAACTATTTTTGGTGTGAAAAT 19 96 1 TATTTTTGTG 0.972348 -18 AATTTTCTGTTATTTATGATGGGATGTTATA 20 96 0 TATTTATGTG 0.904351 -40 GAAAATTAAAAAGTTTTGGTGGGATT 20 120 1 AAGTTTTGTG 0.818582 -16 ATATATTAAATATTTTTGCTTTGTTTAATCA 21 47 1 TATTTTTGTT 0.803305 -39 TTCATTAAATTATTTTTTATGAGGGATTGTT 22 11 0 TATTTTTTTG 0.892484 -464 ******** ** Masking position 2 Map Score: 13.9446 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 169 Number in noncoding regions = 55 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 TATTTGAGGTTTTATAAATACCTTTTTATGTCAAAC 3 79 1 TTTATAATTT 0.950476 -222 ATCCATTAGGATTATAAAAACATTTTTATACTTCTT 3 161 1 ATTATAATTT 0.563733 -140 TATTTAAGTTTTTATAATAACATTCTGGGGTTACA 3 276 1 TTTATAATTT 0.950476 -25 TATTTATAAATAGTTGATGCAATATAAA 4 48 0 TTTATAATGT 0.916233 -18 CTGTATAAATTTTTTTATTATTTTTTAATCAAAATA 6 45 0 TTTTTAATTT 0.849254 -40 TTTTTATAGTTATATAATAAACTTATAGAAGCTCAA 7 64 0 TATATAATTT 0.799821 -204 TGGTAGTTAATATTTTAACAAATTATTATGTAACCT 7 160 1 TATTTAATTT 0.53977 -108 AAGTTTTGTTTTTATGACTATTTTATCATTATATAT 8 26 1 TTTATAATTT 0.950476 -64 CTTTTTTTAATTTTTTATAACATTTTCACTTGTAAT 9 19 1 TTTTTAATTT 0.849254 -109 CTCTACTATTTTATTTATAATATTATCATTCAAATA 9 57 1 TTATTAATTT 0.488606 -71 TGCTAGTAAATTTTTAACAAAATTTTAAAATTTTAT 11 55 0 TTTTTAATTT 0.849254 -49 AGAAAAATTATATTTCACTATTTTTTCAAATATTTT 14 32 1 TATTTAATTT 0.53977 -269 ATATAAAAGGTTAATAAAAAGATGCTCCAATAACTC 14 181 1 TTAATAATGT 0.649737 -120 TCTACGCCTATTAATAAGCAATTTTTGTTCTTTTAT 16 96 0 TTAATAATTT 0.764978 -132 TAATACCTCAATTATTACAAAATGTTTTGATTATTA 17 40 0 ATTATAATGT 0.424101 -166 AATTGAGGTATTAATGAACGCCTTCTATAAGAAGAC 17 63 1 TTAATAGTTT 0.605734 -143 TTTGCAAATATTTAGCATAAAATGTTAAGTTGTGTT 18 45 0 TTTAGAATGT 0.698276 -92 TGATTTAATCTTTATTAAGATATTTAAATTAAAATT 18 80 0 TTTATAATTA 0.782601 -57 TCTAAGGTTATTTATAATAAATTGATTTAATCTTTA 18 102 0 TTTATAATGT 0.916233 -35 CCTTAGTTAGTTTTTAATCACATTTGCAAAGAACTA 19 19 0 TTTTTAATTG 0.508778 -95 TATGCCTTTCTTTATTACAAAATGTTTTACAAAGAG 19 59 1 TTTATAATGT 0.916233 -55 TTTTCTGTTATTTATGATGGGATGTTATAAAAATTT 20 89 0 TTTATAGTGT 0.837736 -47 ATCTTTTTCTTTTATAATTATCTTTATCTAAAATTT 21 13 0 TTTATAATTA 0.782602 -73 GTTTAATCAATTTATAAGGGTGTAGTT 21 69 1 TTTATAGTAT 0.310848 -17 TAAATTATTTTTTATGAGGGATTGTT 22 1 0 TTTATAGTGT 0.837736 -474 ATGATTCAATTTTATCATCAGATTCATTATGAGTAT 22 48 0 TTTATAATTA 0.782602 -427 TTTAAAGATGTATATTACCAACTTTTTAGTCCAGAA 22 131 0 TATATAATTT 0.799821 -344 CCCCATTAACTTTATTAATAATCTTTATAAAATTTT 22 217 1 TTTATAACTT 0.513459 -258 AATGCCTTCCTTTAGTAAGGTATTTTTTAATTTTAA 22 384 0 TTTAGAGTTT 0.657153 -91 TTTATCACCAAATTGGCATTTTTAGT 22 459 0 TTTATAATTG 0.779176 -16 AAACACCCCCTTTATGAAAGCGTTCAAAATTCA 23 8 0 TTTATAGTTA 0.629516 -171 TGGTCCTTAGTATTTCAAAATGTTTTAAAAGACTCT 23 46 1 TATTTAATTT 0.53977 -133 CTATTTTAATTTTAGTATTATTTTAAATTCTTTTTA 23 83 0 TTTAGAATTA 0.432358 -96 TTGAATAATTTTAATCAATGAATGTTGTGTAATTTA 23 126 0 TTAATAGTGT 0.466832 -53 TCACTTAACCTTTAGTAAAGCCTTTGAATAATTTTA 23 149 0 TTTAGAGTTG 0.260569 -30 TTATCCTTTATATATAAAAATATTATTCTGTGAGAC 24 12 0 TATATAATTT 0.79982 -66 ***** * * ** * Masking position 7 Map Score: 34.906 Number of sites scoring better than the average of aligned sites = 1371 Number in coding regions = 1043 Number in noncoding regions = 328 Number of orfs with sites within 600 bp upstream = 307 Fraction of orfs with sites within 600 bp upstream = 0.0493093 Motif number 5 AATTAATAGAAAAATAATAAAAAAGGATAA 2 16 1 AAAATAATAA 0.695186 -29 AAAATAATAAAAAAGGATAAGAAGGTGAG 2 26 1 AAAAGGATAA 0.860317 -19 TTTATAATCCTAATGGATAAATTACTATTT 3 149 0 TAATGGATAA 0.702287 -152 ATGCTGTTGATAAAGTATAATACTTAGCCT 4 12 1 TAAAGTATAA 0.575092 -54 ACTTAATTTATAAATGTTAATTTTTCTCAT 5 15 1 TAAATGTTAA 0.897085 -146 TTTTGATTAAAAAATAATAAAAAAATTTAT 6 47 1 AAAATAATAA 0.695186 -38 ATAATTTGTTAAAATATTAACTACCAAAAT 7 156 0 AAAATATTAA 0.695182 -112 AAACAAAACTTAAAAGTTAAAGGTAA 8 7 0 TAAAAGTTAA 0.427236 -83 TGAAGATTTGGAATTGTTAAAATATATAAT 8 53 0 GAATTGTTAA 0.441364 -37 TTTAAATATTTGAATGATAATATTATAAAT 9 69 0 TGAATGATAA 0.400746 -59 CAGTAAGCTTTAAATATTAAGTTAAAAATA 10 19 1 TAAATATTAA 0.777659 -114 ATTTTTAGTATAAAGAATAAAAATAATTAA 14 63 1 TAAAGAATAA 0.79196 -238 CTAAAAATATAAAAGGTTAATAAAAAGATG 14 175 1 AAAAGGTTAA 0.860317 -126 AATTATTTTATAATTGATAAGATTAACCAC 14 268 0 TAATTGATAA 0.684764 -33 CCAATTCTTTATATGATAAAATAAAAATA 15 90 0 TATATGATAA 0.310919 -19 AATAGGCGTAGAAATGATAAAGCCCGGGTC 16 120 1 GAAATGATAA 0.760233 -108 AAAAGTATTAAAATTAATAAGGAACACTTG 17 102 0 AAATTAATAA 0.362367 -104 TTGATTTCAAAAATGATTAATGACAATATA 17 169 0 AAATGATTAA 0.381625 -37 TATTTAGCATAAAATGTTAAGTTGTGTTAG 18 43 0 AAAATGTTAA 0.850112 -94 AATATCTTAATAAAGATTAAATCAATTTAT 18 92 1 TAAAGATTAA 0.79195 -45 CTATCATTTTGAAAGGTTAAGTTATAGCGT 20 35 1 GAAAGGTTAA 0.774938 -101 ATTTCCCACATAAATTTTAAATATACAATA 22 99 0 TAAATTTTAA 0.554807 -376 GTATCTTTCAAAAATAATAAAAATTTTATA 22 242 0 AAAATAATAA 0.695186 -233 TTAATGTAAGTAAATTTTAACAAATATAAA 22 330 0 TAAATTTTAA 0.554807 -145 AAGGCTTTACTAAAGGTTAAGTGAGAAC 23 161 1 TAAAGGTTAA 0.90446 -18 TTTTTATATATAAAGGATAATTTAACTACC 24 28 1 TAAAGGATAA 0.90446 -50 ********** Masking position 8 Map Score: 17.4488 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 577 Number in noncoding regions = 173 Number of orfs with sites within 600 bp upstream = 171 Fraction of orfs with sites within 600 bp upstream = 0.0274655 Motif number 6 ATACTTCTTCTATATTTTTAGGTATTGTCCA 3 188 1 TATATTTTAG 0.787107 -113 CTTCTATACCAATAACCTTAGAAAATGTTAT 7 28 0 AATAACTTAG 0.807236 -240 CTATTTTATTTATAATATTATCATTCAAATA 9 62 1 TATAATTTAT 0.458897 -66 ATATTAAGTTAAAAATATTAGCATCACAATA 10 32 1 AAAAATTTAG 0.569447 -101 CATTTGCTTATTGAACTTTAGGACTATG 12 8 0 TTGAACTTAG 0.455062 -158 TACTCTTCGGTTTAATATTAGGACACGCTTA 12 88 0 TTTAATTTAG 0.932356 -78 TTAACTTAACTATAACTTTAGTGTTGTAAAT 12 124 1 TATAACTTAG 0.890944 -42 CCCTTAGACTAATAATATTAGTTAGTATTAT 13 83 0 AATAATTTAG 0.897602 -29 TATTTTTTCAAATATTTTTAGTATAAAGAAT 14 50 1 AATATTTTAG 0.654595 -251 ATTAACCTTTTATATTTTTAGTTCATAAGCT 14 165 0 TATATTTTAG 0.787107 -136 GTTTTCTTTTTATAATGTTAGGGAAATTTTA 16 32 1 TATAATTTAG 0.944754 -196 TACCTTATTTTTTAATATTAGCTAACACAAC 18 22 1 TTTAATTTAG 0.932356 -115 ATTTATTATAAATAACCTTAGAGGTTTTAAA 18 116 1 AATAACTTAG 0.807236 -21 TTAAATTTTAGATAAAGATAA 21 1 1 TTAAATTTAG 0.675254 -85 AACTACTTGTTTTAATGTAAGTAAATTTTAA 22 340 0 TTTAATTAAG 0.661267 -135 TAAGGTATTTTTTAATTTTAATAACTTTTGC 22 374 0 TTTAATTTAA 0.405893 -101 TAAATTCTATTTTAATTTTAGTATTATTTTA 23 94 0 TTTAATTTAG 0.93235 -85 ATAGAGTTAAATTAATGTAAGGGGAGACAG 24 58 1 ATTAATTAAG 0.500167 -20 ****** **** Masking position 8 Map Score: 12.0451 Number of sites scoring better than the average of aligned sites = 332 Number in coding regions = 280 Number in noncoding regions = 52 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 7 AAGTATATTTATTTTGGCAACTACCTAAAA 3 25 0 ATTTTGGCAA 0.50771 -276 TTTATGTCAAACTTTTGACAGCAGATTATA 3 103 1 ACTTTTGACA 0.525799 -198 TTTGATTTTTATATTTTAAATAATATAGAC 7 212 1 ATATTTTAAA 0.571054 -56 ATAAATTTAAATATTTGAATGATAATATTA 9 74 0 ATATTTGAAT 0.629427 -54 TATACTAAAAATATTTGAAAAAATAGTGAA 14 45 0 ATATTTGAAA 0.94886 -256 TAGACCATGTATATTTAAAATTTTTCTTTA 14 229 0 ATATTTAAAA 0.770842 -72 TAATTTTAATACTTTTGAAAGACATTAAAA 17 116 1 ACTTTTGAAA 0.883737 -90 GTCATTAATCATTTTTGAAATCAATATCAT 17 175 1 ATTTTTGAAA 0.926337 -31 AAAATAAGGTATATTTAAAAAT 18 3 0 ATATTTAAAA 0.770842 -134 TTTATGCTAAATATTTGCAAAATTTTAATT 18 60 1 ATATTTGCAA 0.918134 -77 GTTTTTAATCACATTTGCAAAGAACTATTG 19 16 0 ACATTTGCAA 0.871447 -98 CATCTCAAAGATATTTGATATTGTATATTT 22 81 1 ATATTTGATA 0.646161 -394 TTGATATTGTATATTTAAAATTTATGTGGG 22 95 1 ATATTTAAAA 0.770842 -380 AATTTTTATTATTTTTGAAAGATACTATAC 22 247 1 ATTTTTGAAA 0.926337 -228 AATTTTAATAACTTTTGCAAAAACTACTTG 22 362 0 ACTTTTGCAA 0.821253 -113 ********** Masking position 1 Map Score: 9.09384 Number of sites scoring better than the average of aligned sites = 247 Number in coding regions = 196 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 47 Fraction of orfs with sites within 600 bp upstream = 0.00754899 Motif number 8 ATACTTAGCCTACATCATTTATATTGCATCA 4 31 1 TAATCATTTA 0.893747 -35 CTAAGTTATTTATATCATTTTGGTAGTTAAT 7 140 1 TAATCATTTT 0.933274 -128 TTATGACTATTTTATCATTATATATTTTAAC 8 37 1 TTATCATTAT 0.790036 -53 TTTAATTTTTTATAACATTTTCACTTGTAAT 9 24 1 TAAACATTTT 0.867894 -104 TCAAAAACATTACATCATTAATTAATTGAAT 12 54 0 TAATCATTAA 0.894992 -112 AATTTAAAAATAGAACATTATATTCTCTTTT 14 133 1 TAAACATTAT 0.867902 -168 ATTAAAATTTTAAAACATTAAGTTTTTATAT 17 139 1 TAAACATTAA 0.793424 -67 TATATTGTCATTAATCATTTTTGAAATCAAT 17 169 1 TTATCATTTT 0.788541 -37 ATAAATTGATTTAATCTTTATTAAGATATTT 18 91 0 TTATCTTTAT 0.568358 -46 TAGCTCTTTGTAAAACATTTTGTAATAAAGA 19 67 0 TAAACATTTT 0.867325 -47 TGAACTTTAATCTATCATTTTGAAAGGTTAA 20 24 1 TCATCATTTT 0.688204 -112 CCTAATCAGATATATCATTAAAACGCTATAA 20 56 0 TAATCATTAA 0.894992 -80 AAATATTTAATATATCTTTTTCTTTTATAAT 21 31 0 TAATCTTTTT 0.830486 -55 GTTGGTAATATACATCTTTAAATTTAAATTT 22 145 1 TAATCTTTAA 0.749742 -330 TGTTTTGTATTAAATCTTTAATGCGAGTATT 22 288 0 TAATCTTTAA 0.74068 -187 TAGAGTCTTTTAAAACATTTTGAAATACTAA 23 52 0 TAAACATTTT 0.867325 -127 ** ******** Masking position 4 Map Score: 13.7205 Number of sites scoring better than the average of aligned sites = 177 Number in coding regions = 138 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 41 Fraction of orfs with sites within 600 bp upstream = 0.00658529 Motif number 9 TTCTTATCCTTTTTTATTATTTTTCTATTAAT 2 17 0 TTTTTATTTT 0.925131 -28 TGTATAAATTTTTTTATTATTTTTTAATCAAA 6 48 0 TTTTTATTTT 0.925131 -37 ATGTTATCTATTTTTGATGATTGA 7 3 0 TTTTTGATTT 0.8539 -265 AAATTTGGATTTTTTGATTTTTATATTTTAAA 7 200 1 TTTTTGATTT 0.8539 -68 TCCCTCAAAATTTTTGTTTCTTCTATTTTATT 7 242 0 TTTTTGTTTT 0.959187 -26 TATGAAACTTTTTTTAATTTTTTATAACATTT 9 12 1 TTTTTAATTT 0.754476 -116 CCAATTCCTATTTTTCTACTTTTTCTTATTAC 11 22 1 TTTTTCTATT 0.627711 -82 TAAATAGTAATATTTGTTAGTTTGAAAATAAA 13 22 0 TATTTGTTTT 0.66788 -90 TGAAATATAATTTTTCTTAGTTTTCATCCTCT 14 17 0 TTTTTCTTTT 0.951703 -284 AGTTTAATTATTTTTATTCTTTATACTAAAAA 14 64 0 TTTTTATTTT 0.925131 -237 ATATTTAAAATTTTTCTTTATTGGGGAGTTAG 14 217 0 TTTTTCTTTT 0.951703 -84 TAATAAGCAATTTTTGTTCTTTTATACTTCTT 16 89 0 TTTTTGTTTT 0.959187 -139 ACTTTTTAATTTTCTGTTATTTATGATGGGAT 20 102 0 TTTCTGTTTT 0.748774 -34 TTAATATATCTTTTTCTTTTATAATTATCTTT 21 24 0 TTTTTCTTAT 0.627711 -62 TATTAAATATTTTTGCTTTGTTTAATCAATTT 21 50 1 TTTTGCTTTT 0.714203 -36 CTTTATAAAATTTTTATTATTTTTGAAAGATA 22 239 1 TTTTTATTTT 0.925131 -236 ******** ** Masking position 3 Map Score: 17.2929 Number of sites scoring better than the average of aligned sites = 549 Number in coding regions = 390 Number in noncoding regions = 159 Number of orfs with sites within 600 bp upstream = 142 Fraction of orfs with sites within 600 bp upstream = 0.0228076 Motif number 10 ATATATCACCAATATTTTAGGT 3 2 1 TTATCACCAA 0.944797 -299 ACATCATTTATATTGCATCAACTATTTATAA 4 42 1 TTTGCATCAA 0.701409 -24 CACCACTAATTTTTTAATCAACAGAGTATAA 5 140 0 TTTTAATCAA 0.766755 -21 TTTTTATTATTTTTTAATCAAAATATCAATA 6 39 0 TTTTAATCAA 0.766755 -46 TCAATCATCAAAAATAGATAA 7 1 1 TAATCATCAA 0.882097 -267 TGAATTATAGTCAATCATCAAAAGTTTTTAT 7 93 0 TAATCATCAA 0.882097 -175 TGTATCACCAAAAATAGTGAA 8 79 0 TTATCACCAA 0.944797 -11 AAAGTTCATTTAATTCATCAA 20 1 0 TATTCATCAA 0.827035 -135 CCTAATCAGATATATCATTAAAACGCTATAA 20 56 0 TTATCATTAA 0.605519 -80 ATTTTTGCTTTGTTTAATCAATTTATAAGGG 21 58 1 TTTTAATCAA 0.766778 -28 ATGATTCAATTTTATCATCAGATTCATTATG 22 53 0 TTATCATCAG 0.786148 -422 TTTAAAGATGTATATTACCAACTTTTTAGTC 22 136 0 TTATTACCAA 0.599243 -339 TTTATCACCAAATTGGCATTT 22 464 0 TTATCACCAA 0.944789 -11 * ********* Masking position 7 Map Score: 7.73705 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 368 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 11 TAATATCCCTCATAAAATTATTTAAA 1 80 0 TCCCTCAAAA 0.978167 -16 TTATATTTATTCCCTCAGAAAAGTATATTTA 3 44 0 TCCCTCAAAA 0.978162 -257 AATTTCCCTCAAAATTTTTGTTTCT 7 253 0 TCCCTCAAAT 0.889242 -15 AACTTACACCAAAAATTATTTTAT 14 287 0 TTACACCAAA 0.528661 -14 ATTTTCACACCAAAAATAGTTATTT 19 99 0 TCACACCAAA 0.909454 -15 AATCCCACCAAAACTTTTTAATT 20 123 0 TCCCACCAAA 0.977735 -13 AACAATCCCTCATAAAAAATAATTTA 22 6 1 TCCCTCAAAA 0.978167 -469 CAGAACTATTTCCCACATAAATTTTAAATAT 22 105 0 TCCCACAAAA 0.978167 -370 ******* *** Masking position 9 Map Score: 7.92218 Number of sites scoring better than the average of aligned sites = 51 Number in coding regions = 34 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 AATTTTTTTATTATTTTTTAATCAAAATAT 6 44 0 TTATTTTTTA 0.735455 -41 TATATAGCTTTTATTTTAAAATAAATTTAA 9 94 0 TTATTTTAAA 0.742575 -34 CACATAGTCCTTCTCTTTATCTATAAAACG 10 90 1 TTCTCTTTAT 0.667446 -43 TAGGACACGCTTATCTTCAAAAACATTACA 12 71 0 TTATCTTCAA 0.513173 -95 TCTCCCCCGTTTATTTTCAAACTAACAAAT 13 13 1 TTATTTTCAA 0.64371 -99 AGAAGTTTAATTATTTTTATTCTTTATACT 14 69 0 TTATTTTTAT 0.698739 -232 AGGAAAAGCTTTCTCTTAAAGAAGTTTAAT 14 88 0 TTCTCTTAAA 0.713971 -213 GAACATTATATTCTCTTTTTAGCTTATGAA 14 145 1 TTCTCTTTTT 0.566304 -156 ACACCAAAAATTATTTTATAATTGATAAGA 14 276 0 TTATTTTATA 0.652382 -25 CTCCCGGGCGTTATTTTTATTTTATCATAT 15 79 1 TTATTTTTAT 0.698739 -30 TAATTTTGTTTTCTTTTTATAATGTTAGGG 16 25 1 TTCTTTTTAT 0.774772 -203 TCTTTTATACTTCTTTTCTATTGATACTCA 16 74 0 TTCTTTTCTA 0.635478 -154 GCAATTTTTGTTCTTTTATACTTCTTTTCT 16 85 0 TTCTTTTATA 0.735689 -143 GAATAACCCATTCTTTTTTTATTCTTCTTA 16 197 0 TTCTTTTTTT 0.691168 -31 GTTTTGATTATTATCTTTAATGATTATAGC 17 23 0 TTATCTTTAA 0.713725 -183 TAAATATACCTTATTTTTTAATATTAGCTA 18 16 1 TTATTTTTTA 0.735455 -121 TCTTTTATAATTATCTTTATCTAAAATTTA 21 12 0 TTATCTTTAT 0.575053 -74 ATATATCTTTTTCTTTTATAATTATCTTTA 21 23 0 TTCTTTTATA 0.735689 -63 TTTCATTAAATTATTTTTTATGAGGGATTG 22 13 0 TTATTTTTTA 0.735455 -462 AAATTAAGATTTCTTTTAAAGATTTTATTC 22 178 1 TTCTTTTAAA 0.810544 -297 TACCCATATATTCTTTTAAAATGCTCCGCA 22 426 1 TTCTTTTAAA 0.810544 -49 TTATTTTAAATTCTTTTTATAGAGTCTTTT 23 72 0 TTCTTTTTAT 0.774772 -107 AATTTTAGTATTATTTTAAATTCTTTTTAT 23 82 0 TTATTTTAAA 0.742575 -97 ********** Masking position 6 Map Score: 25.519 Number of sites scoring better than the average of aligned sites = 1269 Number in coding regions = 984 Number in noncoding regions = 285 Number of orfs with sites within 600 bp upstream = 238 Fraction of orfs with sites within 600 bp upstream = 0.0382268 Motif number 13 CCTGGCTAGGCGACCCGGGCT 15 2 0 CGACCCGGGC 0.996636 -107 GTTCAAATCCCCTCCCGGGCGTTATTTTTA 15 68 1 CCTCCCGGGC 0.989153 -41 TCTGGCTAGGCGACCCGGGCTTTATCATTT 16 131 0 CGACCCGGGC 0.996636 -97 ********** Masking position 5 Map Score: 1.37581 Number of sites scoring better than the average of aligned sites = 2 Number in coding regions = 0 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 TATAATATTATCATTCAAATATTTAAATTT 9 72 1 TCATTCAAAT 0.599533 -56 ATTTCACTATTTTTTCAAATATTTTTAGTA 14 43 1 TTTTTCAAAT 0.831071 -258 AATTTTAATGTCTTTCAAAAGTATTAAAAT 17 118 0 TCTTTCAAAA 0.949479 -88 TAAATTAAAATTTTGCAAATATTTAGCATA 18 62 0 TTTTGCAAAT 0.663405 -75 ACCAATAGTTCTTTGCAAATGTGATTAAAA 19 14 1 CTTTGCAAAT 0.543202 -100 TATAACTTAACCTTTCAAAATGATAGATTA 20 31 0 CCTTTCAAAA 0.884543 -105 TCGTATAGTATCTTTCAAAAATAATAAAAA 22 249 0 TCTTTCAAAA 0.949479 -226 AACAAGTAGTTTTTGCAAAAGTTATTAAAA 22 360 1 TTTTGCAAAA 0.487566 -115 ACCCATATATTCTTTTAAAATGCTCCGCAA 22 427 1 TCTTTTAAAA 0.754687 -48 TGGTCCTTAGTATTTCAAAATGTTTTAAAA 23 46 1 TATTTCAAAA 0.719442 -133 TTTTATAGAGTCTTTTAAAACATTTTGAAA 23 58 0 TCTTTTAAAA 0.754687 -121 ********** Masking position 7 Map Score: 3.57122 Number of sites scoring better than the average of aligned sites = 445 Number in coding regions = 323 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 15 TTACCTGTATAAATTTTTTTATTATTTTTTA 6 54 0 AAATTTTTTA 0.831695 -31 CAAAAAATCCAAATTTCTTTAGGTTACATAA 7 185 0 AAATTTCTTA 0.955762 -83 TAAAATTTTAAAATTTTGTTAAAAATTTACT 11 56 1 AAATTTTTTA 0.831695 -48 AAGAAAAATTATATTTCACTATTTTTTCAAA 14 31 1 ATATTTCCTA 0.683994 -270 AAAAATAATTAAACTTCTTTAAGAGAAAGCT 14 81 1 AAACTTCTTA 0.818369 -220 TTCTATTTTTAAATTTGATTAAAACTATTTA 14 117 0 AAATTTGTTA 0.805954 -184 ATACTTAATAAAATTTCCCTAACATTATAAA 16 40 0 AAATTTCCTA 0.93896 -188 ATGAGTATTTAAATTTCATTAAATTATTTTT 22 25 0 AAATTTCTTA 0.95576 -450 ACAAATATAAAAATTTCGCTATTGTTTTGTA 22 310 0 AAATTTCCTA 0.93896 -165 ATATTTGTTAAAATTTACTTACATTAAAACA 22 333 1 AAATTTATTA 0.737005 -142 ******* *** Masking position 6 Map Score: 6.86873 Number of sites scoring better than the average of aligned sites = 75 Number in coding regions = 55 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925