AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_mgen_reg_300.orf -o03010_mgen_300.ace -a/home/amcguire/genomes/ORF_mgen.txt -z/home/amcguire/genomes/mgen.fna -g0.32 -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 = 0.32 maxlen = 30 weight = 0.8 exclude = 1 Purged sequences: MG087 28 ribosomal protein S12 (rpS12) MG466 25 ribosomal protein L34 (rpL34) MG362 22 ribosomal protein L7/L12 (rpl7) MG311 22 ribosomal protein S4 Input sequences: #1 MG069 300 PTS system, glucose-specific IIABC component (ptsG) #2 MG070 110 ribosomal protein S2 (rpS2) #3 MG077 233 oligopeptide ABC transporter, permease protein (oppB) #4 MG081 55 ribosomal protein L11 (rpl11) #5 MG090 51 ribosomal protein S6 (rpS6) #6 MG140 300 conserved hypothetical protein #7 MG142 258 translation initiation factor 2 (infB) #8 MG144 24 conserved hypothetical protein #9 MG148 38 conserved hypothetical protein #10 MG149 75 lipoprotein, putative #11 MG149.1 90 conserved hypothetical protein #12 MG150 89 ribosomal protein S10 (rpS10) #13 MG194 300 phenylalanyl-tRNA synthetase, subunit alpha (pheS) #14 MG196 58 translation initiation factor 3 (infC) #15 MG227 300 thymidylate synthase (thyA) #16 MG232 92 ribosomal protein L21 (rpL21) #17 MG255 175 conserved hypothetical protein #18 MG255.1 196 conserved hypothetical protein #19 MG256 166 conserved hypothetical protein #20 MG257 45 ribosomal protein L31 (rpL31) #21 MG312 59 cytadherence accessory protein (hmw1) #22 MG313 44 conserved hypothetical protein #23 MG314 23 conserved hypothetical protein #24 MG316 40 conserved hypothetical protein #25 MG319 103 conserved hypothetical protein #26 MG320 43 conserved hypothetical protein #27 MG321 300 lipoprotein, putative #28 MG328 38 conserved hypothetical protein #29 MG332 300 conserved hypothetical protein #30 MG361 119 ribosomal protein L10 (rpl10) #31 MG363.1 63 ribosomal protein S20 (rpsT) #32 MG418 37 ribosomal protein L13 (rpL13) #33 MG422 37 conserved hypothetical protein #34 MG424_MG425 188 MG424: ribosomal protein S15 (rps15), MG425: ATP-dependent RNA helicase (deaD) #35 MG426 22 ribosomal protein L28 (rpL28) #36 MG446 300 ribosomal protein S16 (rps16) #37 MG468.1 62 ABC transporter, ATP-binding protein #38 MG469 300 chromosomal replication initiator protein (dnaA) Motif number 1 GTCCAATTAGAACTAATAAAATTCCAAAAA 1 46 0 AACTAATAAA 0.77597 -255 GTTATAAACAAGCTAAAAACCACAAAACCA 2 49 0 AGCTAAAAAC 0.920754 -62 AAAAAAATGATACTAATAACGATTACTAG 3 10 0 TACTAATAAC 0.717057 -224 TACTAAATAGAAATAAAAAAAGAACCTGTT 3 213 0 AAATAAAAAA 0.804283 -21 GCCATTGAATAGTTAAAAACCTGATTTATT 6 158 1 AGTTAAAAAC 0.929492 -143 TGCAACTAATAACAAGACTTTGT 7 4 1 AACTAATAAC 0.863857 -255 AATGTTTTCTTGTTAATAAACAAAGTCTTG 7 23 0 TGTTAATAAA 0.717679 -236 AAAAACACTCAAATAATAACCCCTGCCCTT 7 124 0 AAATAATAAC 0.869424 -135 GTTTAAAGCTAGATAAAAAACACCTCAAAG 7 155 1 AGATAAAAAA 0.869375 -104 TTCTAAATTAAGTTAATAACTATCTTTTTT 11 13 0 AGTTAATAAC 0.921009 -78 TTTCTCAATTAAATAAAAAAACAGTGTAAG 11 63 0 AAATAAAAAA 0.804283 -28 TTGGTGTATCAACTAAAAACTAAAGCGTTA 12 27 0 AACTAAAAAC 0.877663 -63 TTCACTAGTTAGTTAATAAATTGACTACGG 12 60 0 AGTTAATAAA 0.864218 -30 AAATCGCTTTTAATAAAAAATTACACGCTT 13 94 0 TAATAAAAAA 0.621399 -207 CCAATTCTTCTGATAATAAAGTCACTCAAG 15 135 1 TGATAATAAA 0.701589 -166 TTAAAATGTTTATTAAAAAAACAAAATAAA 15 238 1 TATTAAAAAA 0.639592 -63 GGCCAATTTATGATAAAAACTTAGTTAAAT 19 43 1 TGATAAAAAC 0.829632 -124 CCCTAAAACTAGATAAAAACCTAGCAATTT 19 69 0 AGATAAAAAC 0.924199 -98 AAAATAAATCTATTAATAAAACAGC 24 26 1 TATTAATAAA 0.610833 -15 AAGTTAGCAAAACTAAAAACATGGTGCACC 27 92 0 AACTAAAAAC 0.877663 -209 AGTGAGCAATTGATAAAAACATTAGTTTTT 27 148 1 TGATAAAAAC 0.829632 -153 ATTTACCCTTAGTTAAAAACTAAAAGTAGT 27 215 0 AGTTAAAAAC 0.929492 -86 AGTAAAAAAGAGTTAAAAAACAGCAATTTA 27 240 0 AGTTAAAAAA 0.877992 -61 ATGTCTTTGTAGCTAATAAAACCTTTCAAG 29 12 1 AGCTAATAAA 0.848707 -289 TTCTTTACAAAGATAAAAACAAGCAAGAGG 29 225 1 AGATAAAAAC 0.924199 -76 TATTGCAAGTAAATAATAACATAACTTGAT 30 15 0 AAATAATAAC 0.869424 -105 ACTTTATTAAAGTTAAAAACTCGTTATTTT 30 54 0 AGTTAAAAAC 0.929492 -66 CTCTAAAACTAATTAATAACCTAA 31 50 1 AATTAATAAC 0.878038 -14 TTTTTATTTTTATTAATAAATTCTCTCGAT 34 65 0 TATTAATAAA 0.610833 -124 TTATTAATAAAAATAAAAACTATATTTATT 34 76 1 AAATAAAAAC 0.882742 -113 TAATTAATAAACACGTTGAAT 34 178 0 AATTAATAAA 0.797155 -11 TTATTCGTCTAGTTAATAAATTTAATCATC 36 177 0 AGTTAATAAA 0.864218 -124 ********** Masking position 5 Map Score: 40.8584 Number of sites scoring better than the average of aligned sites = 520 Number in coding regions = 443 Number in noncoding regions = 77 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 2 GATGAAAAAGAAACAACAAATTAGTTTTATTTTTGCT 1 190 1 AAAATTAGTT 0.696999 -111 AACCTGAAAAAAACAGGTTCTTTTTTTATTTCTATTT 3 202 1 AAATTTTTTT 0.912206 -32 CTCATTGAGTAAAGTTATATTTTTATTAAGTAT 5 7 0 AAAATTTTTT 0.853528 -45 GGTGTTAGTCAAACCTTTTCCTTTGTTGTTCCTTATT 6 15 1 AAATCTTTTT 0.775333 -286 TGAATAGTTAAAAACCTGATTTATTTTTATAGAAACA 6 163 1 AAAATTATTT 0.842831 -138 TAAGCAATCTAAAGGGATTAATATATTAGTATGAGTG 6 238 0 AAATATATTT 0.725508 -63 AATTTATTTGAAAGCGTATCTTTTATTAATGAATGTG 13 26 1 AAATTTTTTT 0.9239 -275 AAACACAGCAAAAGCGTGTAATTTTTTATTAAAAGCG 13 83 1 AAATATTTTT 0.74078 -218 TTTTTTTGTCAAAAAGCTTTTTTTGTGCAATTTAGTA 13 178 0 AAATTTTTTG 0.739062 -123 GCAATTACAAAAAATAACTATTTTTTTGTCAAAAAGC 13 198 0 AAATTTTTTT 0.516515 -103 ACATTGTATAAAACCGCTTTTTATTTTGTTTTTTTAA 15 250 0 AAATTTATTT 0.918208 -51 TAAATAAGAAAAATCCTGACTTAGTTGATACCAATCA 17 16 1 AAAATTAGTG 0.446199 -160 AAGAAAATCAAAAGAAATTATTTGATTTTTTAGCGTT 18 37 1 AAATTTTGTT 0.885016 -160 AAAGTTTCAAAACAGTTTTTTAGATTGAAGCTTGAA 22 19 0 AAATTTAGTT 0.877844 -26 AAACTAGAATAAAACTACTTTTAGTTTTTAACTAAGG 27 202 1 AAATTTAGTT 0.876505 -99 TTTCATAAATAAATCGGTTAATTGATTGCTGATTAGT 27 267 0 AAATATTGTT 0.646764 -34 TTAGTAATTTAAAGGGCTTGTTTGGTTTTGCAGGTGT 29 150 1 AAATTTTGTT 0.886084 -151 TTAAAGTTAAAAACTCGTTATTTTCTTTGGTTTTATT 30 41 0 AAATTTTTTT 0.923765 -79 TTTAGATACAAAACCGCATTCTATTTTAATATTA 32 8 0 AAATCTATTT 0.761425 -30 TTTATTAATAAAAATAAAAACTATATTTATTATAAGT 34 75 1 AAAACTATTT 0.544125 -114 TATATCTAACAAAGTCTTAATTATTTTCTGTTGTTTA 36 66 0 AAAATTATTT 0.843055 -235 TTTTTTAGATAAATAAGTTCTTATCTTTATATCTAAC 36 93 0 AAATTTATTT 0.917909 -208 TGTCATCTGCAAACTCATTATTTTTTTAGATAAATAA 36 114 0 AAATTTTTTT 0.887983 -187 ACCAAAAAAAGAGAGATATTTTCAAGAGGAAC 38 6 1 AAAAATATTT 0.500464 -295 TTGTTGTTGAAAATTTTGATTTTTTTGCTGTAAGAAA 38 68 0 AAAATTTTTG 0.576215 -233 *** * **** ** Masking position 12 Map Score: 24.9426 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 279 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 3 ACTACTAAATTTTATTAACCAAACAGCTTAGGAA 1 271 0 TTTTTAAAAC 0.799856 -30 TTCTTGATTATTTTATAAAAAAATGATACTAATA 3 22 0 TTTATAAAAT 0.935557 -212 TTGTTGTTCCTTATTCAATGAATCATACAAATAC 6 37 1 TTATCAAAAC 0.473726 -264 TAAAACTTCCCTTTATAATCAAATATCGCC 6 281 1 CTTATAAAAT 0.507903 -20 TCTTGTAAAATTAGACAACCAACTTGAAATTGAT 7 75 1 TTAACAAAAT 0.765805 -184 TCTAAACTTTTTGCAACTAATTAATTAGTTAA 9 9 1 TTTGCAAAAT 0.650985 -30 TATTAGTTAACTAATTAATTAGTTGC 9 23 0 TTATTAAAAT 0.78318 -16 TATTTTGAATTTTTCTAAATAAGCTAACAAATTA 10 15 0 TTTCTAAAAC 0.605338 -61 CCCAATATTTTCTCAATTAAATAAAAAAACAG 11 69 0 TTTTCAAAAT 0.829348 -22 CCGTAGTCAATTTATTAACTAACTAGTGAACTAG 12 60 1 TTTTTAAAAT 0.898252 -30 CTAAATCGCTTTTAATAAAAAATTACACGCTTTT 13 92 0 TTTATAAAAT 0.935557 -209 AAAAAAGCTTTTTGACAAAAAAATAGTTATTTTT 13 192 1 TTTACAAAAT 0.888789 -109 AATTGCTTAATTTAATAACAAACTAAACTATTAT 13 229 1 TTTATAAAAT 0.935557 -72 TGTATTAAGTTTTACTAACAAAATAGTTGGTAAC 14 34 0 TTTCTAAAAT 0.772118 -25 TGTTAAAATGTTTATTAAAAAAACAAAATAAAAA 15 236 1 TTTTTAAAAC 0.799856 -65 CCAATCAGGATTTTACAAAGAAGTTTTAATTTGG 17 46 1 TTTACAAAAT 0.888789 -130 TTAACTAAGTTTTTATCATAAATTGGCCTTCCCT 19 37 0 TTTATCAAAT 0.663486 -130 AAGCGATAAGTTTTATAATCAAGCTTGACTAAAC 21 15 1 TTTATAAAAC 0.867934 -45 TTTGATAAGTAATTTTAGAGAGG 23 10 0 TTTATAAAAT 0.935557 -14 AGCAAATGGTTTATGTAATTAATTAAATTAACTA 25 28 0 TTAGTAAAAT 0.580945 -76 TTAACTTTATTTAGTTAAGCAAATGGTTTATGTA 25 45 0 TTATTAAAAT 0.78318 -59 TGCTCACTTTTTAAACAAGAAAATGCTTAATACA 27 122 0 TTAACAAAAT 0.765805 -179 TGTGTTCTTTCATAAATAAATCGGTTAATTG 27 280 0 TTTATAAAAT 0.935557 -21 TGTTGGAATATTAGATAAATAAGTATATTATC 28 9 0 TTAATAAAAT 0.855908 -30 AGTTTTTATTTTTATTAATAAATTCTCTCGATAT 34 63 0 TTTTTAAAAT 0.898252 -126 ACAACTATTTCATCATTAATTCTGAAAACAA 36 8 1 TTTATCAAAT 0.663486 -293 CATTATTTTTTTAGATAAATAAGTTCTTATCTTT 36 102 0 TTAATAAAAT 0.855908 -199 CAATGATTTTTTTCTTAATAAAGCGGCTAATTAT 36 262 0 TTTTTAAAAC 0.799856 -39 *** **** ** * Masking position 8 Map Score: 32.9544 Number of sites scoring better than the average of aligned sites = 214 Number in coding regions = 172 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 4 TTTTAAAGCTCAAAATAAAAATCCTAGTCCAA 1 70 0 CAAAATAAAT 0.965284 -231 TATTGCAAGCAAAAATAAAACTAATTTGTTGT 1 202 0 AAAAATAAAT 0.883424 -99 ATACTTAATAAAAATATAACTTTACTCAATG 5 10 1 AAAAATTAAT 0.666949 -42 ATTAGACAACCAACTTGAAATTGATCTTAATC 7 84 1 CAACTTAAAT 0.60559 -175 CTTATTTAGAAAAATTCAAAATAAGCAAATTA 10 26 1 AAAATTAAAT 0.806275 -50 TCAAAATAAGCAAATTATAATTAGGTGTCTTT 10 41 1 CAAATTTAAT 0.801404 -35 ATTAAAAAAACAAAATAAAAAGCGGTTTTATA 15 249 1 CAAAATAAAG 0.767978 -52 GTAATTCTAACAAATTCTAACTGCTTTAATAG 16 11 0 CAAATTTAAT 0.801404 -82 TTATCTGCTCCAAATTAAAACTTCTTTGTAAA 17 57 0 CAAATTAAAT 0.93854 -119 CATAACGCTAAAAAATCAAATAATTTCTTTTG 18 45 0 AAAAATAAAA 0.605976 -152 TTAAAAAGTTCAAAATAAATCTATTAATAAAA 24 15 1 CAAAATAATT 0.653534 -26 TGTATTAGTCAAAAATAAAACTACTCTGTGAA 25 81 0 AAAAATAAAT 0.883424 -23 TTTATATTGACAAATTAAAATTTAACAAGTCA 26 15 1 CAAATTAAAT 0.93854 -29 CATTAGATTGCAAAATCAAAAACTAATGTTTT 27 163 0 CAAAATAAAA 0.849461 -138 GTACCTTTCAAATTTTAATTGCTAATCTTT 33 18 0 CAAATTTAAT 0.801404 -20 TGAATTATAACAAAATTAGAAAACGGCTCATT 34 151 0 CAAAATAGAA 0.524076 -38 AGATGACATGCAAAATGAAAATCGGGCCTTAT 36 143 1 CAAAATAAAT 0.965284 -158 AATCATTGGTCAAAATAAGATTG 36 288 1 CAAAATAGAT 0.844383 -13 CAAAATTAAAATTTTCTAATAG 37 1 1 CAAAATAAAT 0.965284 -62 CTTACAGCAAAAAAATCAAAATTTTCAACAAC 38 71 1 AAAAATAAAT 0.883424 -230 ****** *** * Masking position 6 Map Score: 18.3459 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 128 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 ATTTTTTTATAAAATAATCAAGAACATCAGCAC 3 32 1 AAATATCAAA 0.757728 -202 AGAAAAATTCAAAATAAGCAAATTATAATTAGG 10 33 1 AAATAGCAAT 0.971011 -43 AATGAATGTGGAACTAAGCAACTATTATTTAAA 13 53 1 GAATAGCAAT 0.819645 -248 ACTATTATTTAAACACAGCAAAAGCGTGTAATT 13 73 1 AAAAAGCAAA 0.88872 -228 GTTTGTTATTAAATTAAGCAATTACAAAAAATA 13 219 0 AAATAGCAAT 0.97101 -82 AACTAGATAAAAACCTAGCAATTTAACTAAGTT 19 60 0 AAACAGCAAT 0.927826 -107 TGACAAATTAAAATTTAACAAGTCAAATTGTC 26 22 1 AAATAACAAT 0.706172 -22 TGCTTAATACAAAGTTAGCAAAACTAAAAACAT 27 100 0 AAATAGCAAA 0.945209 -201 TCTTGTTTAAAAAGTGAGCAATTGATAAAAACA 27 136 1 AAATAGCAAT 0.971011 -165 AAAAGAGTTAAAAAACAGCAATTTACCCTTAGT 27 232 0 AAAAAGCAAT 0.939417 -69 TACAAAGATAAAAACAAGCAAGAGGTAGTTGAT 29 230 1 AAACAGCAAA 0.868783 -71 CTTTGTGTGCAAACAGATCAACTACCTCTTGCT 29 246 0 AAAAATCAAT 0.73762 -55 GTACCTTAAAGATTAGCAATTAAAATTTGAA 33 9 1 AAGTAGCAAT 0.819645 -29 TTCTTACAGCAAAAAAATCAAAATTTTCAACAA 38 69 1 AAAAATCAAA 0.591486 -232 AGTATGACAAAAAGTTAGAAATTACTCCAAAGC 38 218 1 AAATAGAAAT 0.654606 -83 *** * ***** * Masking position 7 Map Score: 11.986 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 126 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 TAAAATTCCAAAAACAACTAAAAGAGCATA 1 30 0 AAAACAACTA 0.758008 -271 AAGCAAAAATAAAACTAATTTGTTGTTTCT 1 198 0 AAAACTAATT 0.475424 -103 TTTAAAACTACTAAATTTTATTA 1 288 0 AAAACTACTA 0.822699 -13 TCAATAAAACTCGATAATAACTAAA 2 6 1 AAAACTCGAT 0.533925 -105 AAACAAGCTAAAAACCACAAAACCAAGGTT 2 44 0 AAAACCACAA 0.467885 -67 ATTATGCAGTAAAACTGCAATAATATTGTT 2 76 0 AAAACTGCAA 0.63048 -35 GAACCTGAAAAAAACAGGTTCTTTTTTTAT 3 201 1 AAAACAGGTT 0.718236 -33 TGGAACCATTAAAACTGCTTATCCAGTGAA 6 80 1 AAAACTGCTT 0.881689 -221 AGCTAGATAAAAAACACCTCAAAGCTGTAG 7 161 1 AAAACACCTC 0.459546 -98 CTGTAGTTGAAAAACACCTTAAGGTTAGTT 7 185 1 AAAACACCTT 0.773002 -74 TACATTGTATAAAACCGCTTTTTATTTTGT 15 258 0 AAAACCGCTT 0.759087 -43 AGATAGTTTTAAAACAAGTAATTCTAACAA 16 30 0 AAAACAAGTA 0.613474 -63 GCTCCAAATTAAAACTTCTTTGTAAAATCC 17 53 0 AAAACTTCTT 0.491518 -123 TACACCCCCTAAAACTAGATAAAAACCTAG 19 75 0 AAAACTAGAT 0.673503 -92 AGTCAAAAATAAAACTACTCTGTGAATTTT 25 77 0 AAAACTACTC 0.694012 -27 AAACTAGAATAAAACTACTTTTAGTTTTTA 27 202 1 AAAACTACTT 0.900828 -99 AAAGAGTTAAAAAACAGCAATTTACCCTTA 27 234 0 AAAACAGCAA 0.535272 -67 TTGTGACGCTAAAACAACTACCTTAAGATT 29 83 0 AAAACAACTA 0.758008 -218 ATTAAAGTTAAAAACTCGTTATTTTCTTTG 30 49 0 AAAACTCGTT 0.718785 -71 AATATACTCTAAAACTAATTAATAACCTAA 31 44 1 AAAACTAATT 0.475424 -20 ATTTAGATACAAAACCGCATTCTATTTTAA 32 16 0 AAAACCGCAT 0.58544 -22 ATTAATTCTGAAAACAAGTTTAACGCCTTA 36 25 1 AAAACAAGTT 0.756513 -276 AACGCCAAGAAAAACTAGATACAGGTGTAC 38 169 1 AAAACTAGAT 0.673503 -132 ********** Masking position 4 Map Score: 13.2866 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 340 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 TAGCATTAAAAAAACTATTGCAAGCAAAAATAAA 1 215 0 AAAACTTTAG 0.636529 -86 TTTAAAATTTTCCAAAAATGTGGGAGC 4 4 1 AAAATTTCAA 0.893587 -52 AAAAACTTTTTGGAAAAACTCATTG 5 37 0 AAAACTTTAA 0.893587 -15 TACTTGTTTTAAAACTATCTTAATCCCTAATATA 16 40 1 AAAACTTCAT 0.861853 -53 ATTCCTGTTTAAAACTGTTATCAATTACAAAGTG 18 135 0 AAAACTTTAA 0.893587 -62 TTCAATCTAAAAAACTGTTTTGAAACTTT 22 26 1 AAAACTTTAA 0.893587 -19 CATCAATTAAAACACTCTCAAAATGTGTAACACC 29 182 0 AACACTTCAT 0.741666 -119 TGATGACACTAAAATTCTTTACAAAGATAAAAAC 29 211 1 AAAATTTTAA 0.839555 -90 GTAAGATTAAAAATTATTAGCAACTTGGTCAAC 29 278 0 AAAATTTTAA 0.839555 -23 ATACCCTGAGAACACTATTAGAAAATTTTAATTT 37 13 0 AACACTTTAA 0.794424 -50 CAAGAGGAACAAAATTTTCAATATCATAATAATG 38 33 1 AAAATTTCAT 0.795396 -268 CAAAAAAATCAAAATTTTCAACAACAATTCACAC 38 78 1 AAAATTTCAA 0.893587 -223 AATGATAGTTAAAATTCTCGAAATTGGGATATTA 38 254 0 AAAATTTCAT 0.795396 -47 ATTCTTCTATAACATTGTCAAGAATGATAGTTAA 38 276 0 AACATTTCAA 0.794424 -25 ****** ** ** Masking position 4 Map Score: 8.46707 Number of sites scoring better than the average of aligned sites = 104 Number in coding regions = 94 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GTTCCTAGAGGGAGTTGATGAAAAAGAAAC 1 174 1 GGAGTTGATG 0.848748 -127 CGTTGATCAAGGAATTGATCGCTACTTGGG 6 124 0 GGAATTGATC 0.975248 -177 CAACCAACTTGAAATTGATCTTAATCAAAA 7 90 1 GAAATTGATC 0.90012 -169 GCAGATAACGGGAATCGAACCCGCATCTTA 17 81 1 GGAATCGAAC 0.939877 -95 TGATTTTCTTGAAATTGATCAAGGTTAGGT 18 17 0 GAAATTGATC 0.90012 -180 CTTCCCTAGAGGAGTTGAACCTCTATTTAC 19 14 0 GGAGTTGAAC 0.969085 -153 GGGGGTGGAAGGAATCGAACCCACACAGAC 19 136 0 GGAATCGAAC 0.939877 -31 GCACCCGAAGGGACTTGAACCCCCACTTCT 27 67 0 GGACTTGAAC 0.921221 -234 CAAGCAAGAGGTAGTTGATCTGTTTGCACA 29 244 1 GTAGTTGATC 0.833594 -57 ********** Masking position 5 Map Score: 5.19396 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 27 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 9 TTTTATTTTGAGCTTTAAAAATTTCACTTAA 1 82 1 ACTTTAAAAA 0.827757 -219 TGGAAGTCAAATCATTAGTAATTTGACCTTT 1 123 0 ACATTAGTAA 0.88495 -178 ACCTATTCCTAGCATTAAAAAAACTATTGCA 1 227 0 ACATTAAAAA 0.766494 -74 ATTTTTAGTAAAGAAAGACAC 10 65 0 ATTTTAGTAA 0.66064 -11 TAGCGTTATGAGCATTAGTAATTGGTACTGA 18 67 1 ACATTAGTAA 0.88495 -130 TTAACTATAGAGCTTTAGAAAGCT 25 4 0 ACTTTAGAAA 0.918442 -100 CCTTAGAAGCACCTTTAGTAACATATTTGTC 29 41 0 ACTTTAGTAA 0.918442 -260 ACGAGTTTTTAACTTTAATAAAGTTATCGAG 30 60 1 ACTTTAATAA 0.827757 -60 GATAAAATAGAACTTTAAAAAGTTATAATTA 36 238 1 ACTTTAAAAA 0.827757 -63 CCCTGAGAACACTATTAGAAAATTTTAATTT 37 13 0 ATATTAGAAA 0.570759 -50 * ********* Masking position 6 Map Score: 4.48335 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 58 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 ATAGGTGGACTTGTTTCCCTTCCTAAGCTGTTTGGTTA 1 252 1 TTGTTTTAGC 0.946377 -49 ATAAAACCTTGGTTTTGTGGTTTTTAGCTTGTTTATAA 2 40 1 GGTTTTTAGC 0.484875 -71 CTGGTTACTTTTGTTTCAGGTAACCAGTACCATTTCCA 3 154 1 TTGTTTTAGT 0.83805 -80 AAGAACCTGTTTTTTTCAGGTTCTCAGTTTTTTGGAAA 3 186 0 TTTTTTTAGT 0.872119 -48 AAGCTTCATCTTTTTTCACTGGATAAGCAGTTTTAATG 6 86 0 TTTTTTGAGC 0.759364 -215 TATTATTTGAGTGTTTTTGGTTTAAAGCTAGATAAAAA 7 136 1 GTGTTTTAGC 0.857136 -123 TAACCTTAAGGTGTTTTTCAACTACAGCTTTGAGGTGT 7 174 0 GTGTTTAAGC 0.643756 -85 TCAAAAAGCTTTTTTTGTGCAATTTAGTAGATGGGAAC 13 169 0 TTTTTTAAGT 0.672564 -132 TACTTAATGATTTTTTGATCTATATAGCACAATTAATA 13 266 1 TTTTTTTAGC 0.958778 -35 TATTGTTACCTTGTTTGCGATACCCTGCTCCTGTTCAG 15 44 0 TTGTTTTTGC 0.571851 -257 TAGGTGGTTGTTTTTTTGGCTGGGGAGCCACCACCTTG 15 161 0 TTTTTTTAGC 0.958778 -140 CTAAGTCAGGATTTTTCTTATTTATAGTA 17 2 0 ATTTTTTAGT 0.3685 -174 AATTATTTGATTTTTTAGCGTTATGAGCATTAGTAATT 18 52 1 TTTTTTTAGC 0.958778 -145 GTTTTTTAACTCTTTTTTACTAATCAGCAATCAATTAA 27 249 1 TCTTTTTAGC 0.734664 -52 TTTAAAGGGCTTGTTTGGTTTTGCAGGTGTTACACATT 29 157 1 TTGTTTTGGT 0.36726 -144 AAGTCTTAATTATTTTCTGTTGTTTAGCATATTATTTT 36 54 0 TATTTTTAGC 0.651342 -247 AACTCATTATTTTTTTAGATAAATAAGTTCTTATCTTT 36 102 0 TTTTTTAAGT 0.672564 -199 TGACCAATGATTTTTTTCTTAATAAAGCGGCTAATTAT 36 262 0 TTTTTTAAGC 0.875082 -39 AAATTTTGATTTTTTTGCTGTAAGAAACCATTATTATG 38 57 0 TTTTTTTAAC 0.50657 -244 ****** * *** Masking position 6 Map Score: 7.2878 Number of sites scoring better than the average of aligned sites = 202 Number in coding regions = 174 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 TACTAAATTTTATTAACCAAACAGCTTAGG 1 273 0 TATTAACCAA 0.606684 -28 AAAGGAAAAGGTTTGACTAACACCCCCT 6 9 0 GTTTGACTAA 0.554933 -292 AAAAGTTCTCTTTTAACAAAATGTTTTCTT 7 42 0 TTTTAACAAA 0.904576 -217 GTAGTCAATTTATTAACTAACTAGTGAACT 12 62 1 TATTAACTAA 0.65042 -28 AAAAAAAGCTTTTTGACAAAAAAATAGTTA 13 191 1 TTTTGACAAA 0.922748 -110 TTGCTTAATTTAATAACAAACTAAACTATT 13 231 1 TAATAACAAA 0.565698 -70 TATTAAGTTTTACTAACAAAATAGTTGGTA 14 36 0 TACTAACAAA 0.58439 -23 AAACAAGTAATTCTAACAAATTCTAACTGC 16 19 0 TTCTAACAAA 0.749682 -74 CTTATTTTTTGACAAAGACCAATAAA 20 30 0 TTTTGACAAA 0.922748 -16 ATTTTGAACTTTTTAACAAA 24 1 0 TTTTAACAAA 0.904576 -40 GTAGTTTTATTTTTGACTAATACAA 25 89 1 TTTTGACTAA 0.833151 -15 TTTTTTTATATTGACAAATTAAAATTTA 26 9 1 TATTGACAAA 0.84867 -35 TACTTTTAGTTTTTAACTAAGGGTAAATTG 27 217 1 TTTTAACTAA 0.798505 -84 ACACGTTGAATTATAACAAAATTAGAAAAC 34 159 0 TTATAACAAA 0.735053 -30 CAATCTTATTTTGACCAATGATTTTTTT 36 283 0 TTTTGACCAA 0.805439 -18 AAGTCAAAGAGTATGACAAAAAGTTAGAAA 38 209 1 GTATGACAAA 0.466067 -92 ********** Masking position 6 Map Score: 12.2693 Number of sites scoring better than the average of aligned sites = 159 Number in coding regions = 133 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 12 TCAATAAAACTCGATAATAACTAAA 2 5 1 TAAAACTGAT 0.840207 -106 ATGATTACAATAAAGCAGGATTTATAATCCA 3 107 0 TAAAGCAGAT 0.96817 -127 CTTCTAAATCTAAAGCATGATTACAATAAAG 3 123 0 TAAAGCAGAT 0.96817 -111 GTTTTTGGTTTAAAGCTAGATAAAAAACACC 7 148 1 TAAAGCTGAT 0.96817 -111 ATTTTTAGTAAAGAAAGACACCTAATTAT 10 57 0 TAAAGAAGAC 0.523029 -19 TGGAGTTTGGTAAAGCAGGATAGGTGGTTGT 15 188 0 TAAAGCAGAT 0.96817 -113 CTACACCCCCTAAAACTAGATAAAAACCTAG 19 75 0 TAAAACTGAT 0.840207 -92 GCCAGTTTAGTCAAGCTTGATTATAAAACTT 21 22 0 TCAAGCTGAT 0.92897 -38 AGCTTTCTAAAGCTCTATAGTTAATTTA 25 8 1 TAAAGCTTAT 0.726582 -96 TATAACATTGTCAAGAATGATAGTTAAAATT 38 272 0 TCAAGAAGAT 0.693336 -29 ******* *** Masking position 4 Map Score: 6.23863 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 26 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 13 GCATATGTTGTTTGCATGCAACAT 1 4 0 TTTGATGCAA 0.907923 -297 TAGTTTTATTTTTGCTTGCAATAGTTTTTTT 1 211 1 TTTGTTGCAA 0.975591 -90 TAAATTTATGTTTGGTTTCAAATGAAGTTGG 3 79 1 TTTGTTTCAA 0.816961 -155 CAAAAAGCTTTTTTTGTGCAATTTAGTAGAT 13 175 0 TTTTGTGCAA 0.777215 -126 TGCAATCACATTAGATTGCAAAATCAAAAAC 27 172 0 TTAGTTGCAA 0.877485 -129 TGCAATCTAATGTGATTGCAAACTAGAATAA 27 183 1 TGTGTTGCAA 0.913912 -118 CTTGGTCAACTTTGTGTGCAAACAGATCAAC 29 257 0 TTTGGTGCAA 0.964152 -44 TATGTTATTATTTACTTGCAATAAAACCAAA 30 22 1 TTTATTGCAA 0.838302 -98 **** ****** Masking position 10 Map Score: 1.35924 Number of sites scoring better than the average of aligned sites = 26 Number in coding regions = 21 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 14 AACTAATAAAATTCCAAAAACAACTAAAAG 1 36 0 ATTCCAAAAA 0.68162 -265 ACCAGTACCATTTCCAAAAAACTGAGAACC 3 176 1 TTTCCAAAAA 0.938174 -58 TTTAAAATTTTCCAAAAATGTGGGAGCT 4 9 1 TTTCCAAAAA 0.938174 -47 TCAATGAGTTTTTCCAAAAAGTTTTT 5 36 1 TTTCCAAAAA 0.938174 -16 AAAGATACGCTTTCAAATAAATTAGGTTGG 13 19 0 TTTCAAATAA 0.663975 -282 AATTAAGCAATTACAAAAAATAACTATTTT 13 211 0 TTACAAAAAA 0.663975 -90 CCTTGATCAATTTCAAGAAAATCAAAAGAA 18 23 1 TTTCAAGAAA 0.850419 -174 TATTGGTCTTTGTCAAAAAATAAG 20 32 1 TGTCAAAAAA 0.745418 -14 AAAGTTTCAAAACAGTTTTTTAGA 22 31 0 TTTCAAAACA 0.857897 -14 TAATAAAACCTTTCAAGACAAATATGTTAC 29 25 1 TTTCAAGACA 0.720616 -276 ********** Masking position 6 Map Score: 2.85324 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 117 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 TACTGCATAATGTAAAATTACACAGC 2 95 1 TGTAAAATTA 0.804247 -16 AAACTCATTGAGTAAAGTTATATTTTTATT 5 17 0 AGTAAAGTTA 0.905902 -35 TTTTACGTCTTGTAAAATTAGACAACCAAC 7 68 1 TGTAAAATTA 0.804247 -191 CAGCTTGAAGTAAAATTAATCCTA 8 9 1 AGTAAAATTA 0.804247 -16 TCGCTTTTAATAAAAAATTACACGCTTTTG 13 91 0 TAAAAAATTA 0.544954 -210 AGATGTCAGGTGAAAAGTTAGGTATAAACA 15 16 0 TGAAAAGTTA 0.868001 -285 CAAGAAAAGTTATTTATGCCAG 21 48 0 AGAAAAGTTA 0.868001 -12 TGCTTAACTAAATAAAGTTAAAATTCACAG 25 58 1 AATAAAGTTA 0.804247 -46 TTTTAACTTTAATAAAGTTATCGAGGATTT 30 66 1 AATAAAGTTA 0.804247 -54 AATAGAACTTTAAAAAGTTATAATTAGCCG 36 243 1 TAAAAAGTTA 0.737274 -58 ********** Masking position 5 Map Score: 3.85855 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 38 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084