AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -icpxR_tpal_opreg_300.orf -g0.528 -x5 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 = 0.528 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 TP0363 300 chemotaxis histidine kinase (cheA) #2 TP0438 29 conserved hypothetical protein #3 TP0439 86 purine-binding chemotaxis protein (cheW-2) #4 TP0726 57 flagellar protein (flbD) #5 TP0727 70 flagellar hook protein (flgE) #6 TP0728 75 flagellar hook assembly scaffolding protein (flgD) #7 TP0773 300 periplasmic serine protease DO (htrA-1) #8 TP0841 300 periplasmic serine protease DO (htrA-2) #9 TP0949 275 membrane protein #10 TP0951 119 ribosomal protein L34 (rpmH) #11 TP0952 81 lipase, putative #12 TP0953 86 pheromone shutdown protein (traB) #13 TP0954 71 conserved hypothetical protein #14 TP0955 95 T. pallidum predicted coding region TP0955 #15 TP1016 72 basic membrane protein (tpn39b) #16 TP1017 171 alanyl-tRNA synthetase (alaS) Motif number 1 GGCTGGCGTGTCCGCCAATCGATAC 1 5 1 GGCGTGCCGC 0.967148 -296 ACCCAAGACGACCGCGCGTGGGTAGAAAGCT 1 34 1 ACCGCGGTGG 0.976852 -267 TGGGTAGAAAGCTGCGAGAGGGTCTGGTTTT 1 52 1 GCTGCGGAGG 0.970901 -249 CTCCTTGTATGCCGCGGGACTGGTCCTACTC 1 126 0 GCCGCGGACT 0.870991 -175 GACAAACGTACCTGCGCGCGGGCCATGGCGG 1 184 1 CCTGCGGCGG 0.949726 -117 GTCAAGGGATGCAGCGGGTGGCGGGGTCTTT 1 239 1 GCAGCGGTGG 0.971995 -62 TGCTCTGCAAGGTGCGTGAGCGAACGGAGTG 3 11 1 GGTGCGGAGC 0.968432 -76 GCTGCAGTCAAGCGCGTGTCCTGCACTCCGT 3 34 0 AGCGCGGTCC 0.843171 -53 ATAGGCGCGCCGGTTTTGCCTACC 6 4 1 GGCGCGCGGT 0.914662 -72 TGCCTTCACCGGCGTGGGAGTTCAAGTC 7 8 0 GGCGTGGAGT 0.960142 -293 GCTAGCTTCAGGTGCTAGTGCCTTCACCGGC 7 26 0 GGTGCTGTGC 0.85786 -275 ACCTGAAGCTAGCGTGTCTGCCAATTCCACC 7 44 1 AGCGTGCTGC 0.881822 -257 CACGCGCAGCGCCGCGGGCAGCGTGTATTGG 7 188 0 GCCGCGGCAG 0.886461 -113 TGCCCGCGGCGCTGCGCGTGGCGCCGTGGGC 7 199 1 GCTGCGGTGG 0.990789 -102 GCCCTTTTAAGGCGTGGGTCGATGGTTCGAA 7 254 1 GGCGTGGTCG 0.945615 -47 AAGTGTGCGCGGTGTGCTGATA 8 2 1 AGTGTGGCGG 0.853883 -299 CATGCAGGGAGCAGTTTGTGCACGGTAGGCA 8 36 1 GCAGTTGTGC 0.491787 -265 CCCCTCTTCACCTGTGCCCGCCACGTACACT 8 74 0 CCTGTGCCGC 0.769608 -227 TTTAACCCGGGCTGTGTCGGTAGGGGTTTGG 8 137 1 GCTGTGCGGT 0.692741 -164 CCTCCACGTCCCTGCGCGTACCCAAACCCCT 8 158 0 CCTGCGGTAC 0.552787 -143 AACGAGCAACGCCGCTGCTGTAAAAAAACTG 8 244 0 GCCGCTCTGT 0.786706 -57 ATCAGCGGCTGCTGTGCGTGTTGTGTGATCG 9 54 1 GCTGTGGTGT 0.970557 -222 TGTGTGATCGCGCGCGTCTGTTCTCTGAATT 9 75 1 CGCGCGCTGT 0.942078 -201 GCAGGAATAGGCCGTGAGTGTGCGTCGCTTG 9 118 1 GCCGTGGTGT 0.987263 -158 TGCCTATGAGAGCGTGCGAGTACATGG 9 259 1 AGCGTGGAGT 0.800709 -17 CTCGGGAGGAGCCGCGTCAGCACCT 10 5 0 GCCGCGCAGC 0.965259 -115 GCTCCGTTTGCCCGTGACTGCTCCATCACTT 11 42 0 CCCGTGCTGC 0.916596 -40 ACGGGCAAACGGAGCGGGCGTGTAAGCGGCG 11 58 1 GGAGCGGCGT 0.934143 -24 CTTGGGCGCCACCGTGTGTGGGAGGGACAGT 12 16 1 ACCGTGGTGG 0.954325 -71 CAGTCGGCAAGGTGCGACTGGTTGATGGCGT 12 43 1 GGTGCGCTGG 0.976268 -44 ACTGGTTGATGGCGTGAGTCTCGGGTAAAGG 12 59 1 GGCGTGGTCT 0.914981 -28 AATTCAGCGACGCGCGGGTGTCGGCAGCGTG 13 34 1 CGCGCGGTGT 0.976637 -38 GCGGGTGTCGGCAGCGTGCGGTACAGGGGGT 13 47 1 GCAGCGGCGG 0.95819 -25 GAGCAGTTTCTGTGCGAGTGGAGACGCCAGC 14 45 0 TGTGCGGTGG 0.78833 -51 TAGTTTCTCCGGCGTGTGTGCTGGTGACTGA 15 27 1 GGCGTGGTGC 0.99138 -46 AGAGGCTAGAGGTGTGTGCGAATTCTGTCAA 16 55 1 GGTGTGGCGA 0.697703 -117 ****** **** Masking position 4 Map Score: 58.1459 Number of sites scoring better than the average of aligned sites = 4112 Number in coding regions = 3756 Number in noncoding regions = 356 Number of orfs with sites within 600 bp upstream = 202 Fraction of orfs with sites within 600 bp upstream = 0.0324446 Motif number 2 ACTCCTCTACCGAGCGGTGGGGGTCTACGTTT 1 98 0 CGAGGGTGGG 0.978794 -203 GGAGTAACCACCGAGGGCGAGAAACCGACCTG 1 153 1 CCGAGGCGGA 0.896001 -148 AGGGATGCAGCGGGTGGCGGGGTCTTTTGGAC 1 243 1 CGGGGGCGGG 0.988631 -58 GGTGCGTGAGCGAACGGAGTGCAGGACACGCG 3 21 1 CGAAGGAGGC 0.71877 -66 TGACTGCAGCTGAGAGGAGGGATTGTACGAAG 3 55 1 TGAGGGAGGA 0.877559 -32 TCTTAAGCGGCAGGTGGCGTGATGGGGATGAG 4 34 1 CAGGGGCGGA 0.92995 -24 TGAAAAAAGAGGAGGGCCGGGGC 6 63 1 GGAGGCCGGG 0.758607 -13 GCTAGTGCCTTCACCGGCGTGGGAGTTCAAGT 7 12 0 TCACGGCGGG 0.810527 -289 AGAAAACCCTTCCATGGTGGGAAATATAGTTT 7 84 1 TCCAGGTGGA 0.665404 -217 GGCACGGGATGCAAAGGCGGCGTACTTGACAA 7 146 1 GCAAGGCGCG 0.872851 -155 ATACACGCTGCCCGCGGCGCTGCGCGTGGCGC 7 191 1 CCCGGGCGTG 0.940169 -110 CGCGGCGCTGCGCGTGGCGCCGTGGGCTATTA 7 203 1 CGCGGGCGCG 0.987622 -98 CCATCATGGCTCAGAGGTGGGATTG 7 286 1 TCAGGGTGGA 0.877558 -15 AAGTGTGCGCGGTGTGCTGATAGTACA 8 6 1 TGCGGGTGGC 0.818638 -295 CGTGTAAGTGTACGTGGCGGGCACAGGTGAAG 8 68 1 TACGGGCGGC 0.862745 -233 TACGCGCAGGGACGTGGAGGGACTCATGAACA 8 169 1 GACGGGAGGA 0.757435 -132 TTTTTTTACAGCAGCGGCGTTGCTCGTTTTTA 8 247 1 GCAGGGCGTG 0.845881 -54 CGCGGCTCCTCCCGAGGAGCCGGTTCCCCCTA 10 20 1 CCCGGGAGCG 0.956038 -100 ACCAAAGGTACCGGAGGCGTCAAGATCCCCTC 10 55 0 CCGGGGCGCA 0.93602 -65 CAGTCACGGGCAAACGGAGCGGGCGTGTAAGC 11 53 1 CAAAGGAGGG 0.811848 -29 AGCGGGCGTGTAAGCGGCGGCG 11 70 1 TAAGGGCGCG 0.912137 -12 GTCCCTCCCACACACGGTGGCGCCCAAGACGG 12 12 0 CACAGGTGCG 0.670308 -75 AGGGACAGTCGGCAAGGTGCGACTGGTTGATG 12 38 1 GGCAGGTGGA 0.669585 -49 TTTTCCATGCTCAGGGGCGAGGCAGTGCTCAG 14 14 1 TCAGGGCGGG 0.984939 -82 AGTTTCTGTGCGAGTGGAGACGCCAGCTGAGC 14 40 0 CGAGGGAGCG 0.950754 -56 AACTGTCTTGCGAGAGGCTAGAGGTGTGTGCG 16 43 1 CGAGGGCTGA 0.684612 -129 **** **** ** Masking position 6 Map Score: 30.0785 Number of sites scoring better than the average of aligned sites = 1844 Number in coding regions = 1630 Number in noncoding regions = 214 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 3 TTTCTACCCACGCGCGGTCGTCTTGGGTATCGATTGG 1 25 0 CGCGGTGTGG 0.965793 -276 TGGGTAGAAAGCTGCGAGAGGGTCTGGTTTTGATAAA 1 52 1 GCTGGGGGGG 0.84117 -249 ACCCCCACCGCTCGGTAGAGGAGTAGGACCAGTCCCG 1 106 1 CTCGTGGGGG 0.991198 -195 AACGTACCTGCGCGCGGGCCATGGCGGAGTCTATTCT 1 188 1 CGCGGGCAGG 0.930819 -113 TGCTCTGCAAGGTGCGTGAGCGAACGGAGTGCAGGAC 3 11 1 GGTGGGGCGG 0.852275 -76 CGGCAGGTGGCGTGATGGGGATGAGGG 4 41 1 CGTGTGGAGG 0.918686 -17 TGCCTTCACCGGCGTGGGAGTTCAAGTC 7 2 0 GGCGGGGTGT 0.848731 -299 GTTTTCTTGCCTCGATGGTGGAATTGGCAGACACGCT 7 54 0 CTCGTGGGGG 0.991201 -247 CCCGCGGCGCTGCGCGTGGCGCCGTGGGCTATTAGCT 7 201 1 TGCGGGCGGG 0.796863 -100 CGGTAGGCAGCGTGTAAGTGTACGTGGCGGGCACAGG 8 58 1 CGTGAGGTGG 0.918686 -243 CCCGGGCTGTGTCGGTAGGGGTTTGGGTACGCGCAGG 8 142 1 GTCGTGGGGG 0.97868 -159 TATTGTTTACCTCGTTTGTGTGTGGGGTACATGCGGT 8 201 1 CTCGTGGTGG 0.982889 -100 TTTGGTCCTCTTGGTTTCCGTTGTGGAAGACAGCTT 9 10 1 CTTGTTCGGG 0.448465 -266 GTGAGTGTGCGTCGCTTGTGTGCATGGGTATTTAGTG 9 131 1 GTCGTGGTGG 0.95903 -145 GGGGAAAGAGCGCGCTGGTAAAAACGGATCAGCGCGA 9 177 0 CGCGTGAAGG 0.800215 -99 TGCCTATGAGAGCGTGCGAGTACATGG 9 259 1 AGCGGGGTGG 0.952637 -17 GAACCGGCTCCTCGGGAGGAGCCGCGTCAGCACCT 10 9 0 CTCGGGAGGT 0.631328 -111 AAGATCCCCTCTTGTAGGGGGAACCGGCTCCTCGGGA 10 29 0 CTTGAGGGGG 0.926464 -91 AGTGGACCCTCGTGTTCTTAGCAGGGGGAGGAGAAAT 10 91 1 CGTGTTAGGG 0.476244 -29 GGGCAAACGGAGCGGGCGTGTAAGCGGCGGCG 11 60 1 AGCGGGGTGG 0.952637 -22 AATTCAGCGACGCGCGGGTGTCGGCAGCGTGCGGTAC 13 34 1 CGCGGGGTAG 0.932289 -38 ACAGAAACTGCTCGTACGCGGCTATGGTAGCGTCCAG 14 63 1 CTCGAGGGGG 0.975639 -33 TGGTGACTGAGTCGCGGTTGTTACGGGGAGTTCTC 15 48 1 GTCGGTGTGG 0.867421 -25 GCGAAACTGTCTTGCGAGAGGCTAGAGGTGTGTGCGA 16 39 1 CTTGGGGGAG 0.828398 -133 **** * * ** ** Masking position 4 Map Score: 36.1505 Number of sites scoring better than the average of aligned sites = 1327 Number in coding regions = 1192 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 93 Fraction of orfs with sites within 600 bp upstream = 0.0149374 Motif number 4 CTGACAAACGTACCTGCGCGCGGGCCATGG 1 182 1 TACCTGCGCG 0.562004 -119 CAATCCCTCCTCTCAGCTGCAGTCAAGCGC 3 50 0 TCTCAGCTGC 0.958605 -37 CAATACACGCTGCCCGCGGCGCTGCGCGTG 7 189 1 TGCCCGCGGC 0.83587 -112 TGGGCTATTAGCTCAGCTGGTAGAGCAACG 7 225 1 GCTCAGCTGG 0.88466 -76 AAGTGTGCGCGGTGTGCTGATAGTACATGC 8 11 1 GGTGTGCTGA 0.497017 -290 ACCATATCGCTGTGTGCTGCTTTTAACCCG 8 116 1 TGTGTGCTGC 0.958335 -185 TCCCTCCACGTCCCTGCGCGTACCCAAACC 8 161 0 TCCCTGCGCG 0.799121 -140 TTACCTCGTTTGTGTGTGGGGTACATGCGG 8 207 1 TGTGTGTGGG 0.439335 -94 TGCTCGTTTTTATCTGCTGCTCTGGTCATC 8 267 1 TATCTGCTGC 0.926353 -34 GCTTGCGGCGTATCAGCGGCTGCTGTGCGT 9 43 1 TATCAGCGGC 0.86813 -233 GCCGTTATTATCCGAGTTGCTCGCAGTATG 9 231 1 TCCGAGTTGC 0.517384 -45 TGACGGTAAGGACGTGCTGCAGCACGTGTA 11 12 1 GACGTGCTGC 0.833027 -70 CGTTTGCCCGTGACTGCTCCATCACTTTAC 11 39 0 TGACTGCTCC 0.517844 -43 GGAGCGGGCGTGTAAGCGGCGGCG 11 68 1 TGTAAGCGGC 0.573442 -14 TCTTTTCCATGCTCAGGGGCGAGGCAGTGC 14 12 1 GCTCAGGGGC 0.499268 -84 GCGAGGCAGTGCTCAGCTGGCGTCTCCACT 14 30 1 GCTCAGCTGG 0.88466 -66 CTTGCCCTGCTGCGTATAGTTTC 15 4 1 GCCCTGCTGC 0.963123 -69 TTCTCCGGCGTGTGTGCTGGTGACTGAGTC 15 31 1 TGTGTGCTGG 0.915215 -42 GTGTGTGCTCCTTATATTTTT 16 2 1 TGTGTGCTCC 0.856174 -170 TATCGCCTTTTCCCTGCTGCGGTCAACATC 16 143 0 TCCCTGCTGC 0.973787 -29 ********** Masking position 6 Map Score: 13.6307 Number of sites scoring better than the average of aligned sites = 1715 Number in coding regions = 1583 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 109 Fraction of orfs with sites within 600 bp upstream = 0.0175072 Motif number 5 AGTGTCAAGGGATGCAGCGGGTGGCGGGGTC 1 236 1 GATGCAGGGG 0.904604 -65 ACCAAAGGCTGAGAATGCGGGAAGATT 1 284 1 GAGAATGGGG 0.782735 -17 GTGGCGTGATGGGGATGAGGG 4 47 1 GGGGATGGGG 0.940749 -11 CTACAGGGTAGGCAAAACCGGCGCGCCTAT 6 10 0 GGCAAAACGG 0.914912 -66 GGGCACGGGATGCAAAGGCGGCGTACTTGAC 7 145 1 TGCAAAGCGG 0.652911 -156 CGCTGCCCGCGGCGCTGCGCGTGGCGCCGTG 7 196 1 GGCGCTGGCG 0.856702 -105 CGCTGCGCGTGGCGCCGTGGGCTATTAGCTC 7 208 1 GGCGCCGGGG 0.895914 -93 GGCGGGCACAGGTGAAGAGGGGATAAACTCG 8 83 1 GGTGAAGGGG 0.972595 -218 AACCCCTACCGACACAGCCCGGGTTAAAAGC 8 134 0 GACACAGCCG 0.773551 -167 TTGTGTGTGGGGTACATGCGGTATGCCGCAG 8 216 1 GGTACATCGG 0.766725 -85 AGAGCGCGCTGGTAAAAACGGATCAGCGCGA 9 177 0 GGTAAAACGG 0.902745 -99 AAAAGATGAGGGGAAAGAGCGCGCTGGTAAA 9 192 0 GGGAAAGGCG 0.949961 -84 GAGCAACTCGGATAATAACGGCACGAAGGCA 9 222 0 GATAATACGG 0.358789 -54 CCCTCTTGTAGGGGGAACCGGCTCCTCGGGA 10 29 0 GGGGGAACGG 0.686934 -91 CGGTACCTTTGGTACAGAGTGGACCCTCGTG 10 74 1 GGTACAGGTG 0.790767 -46 GTGTGTGGGAGGGACAGTCGGCAAGGTGCGA 12 29 1 GGGACAGCGG 0.985692 -58 GGCAGCGTGCGGTACAGGGGGTCGGT 13 56 1 GGTACAGGGG 0.984149 -16 GACCGCAGCAGGGAAAAGGCGATAATACCCT 16 149 1 GGGAAAAGCG 0.835219 -23 ******* *** Masking position 11 Map Score: 14.545 Number of sites scoring better than the average of aligned sites = 1066 Number in coding regions = 944 Number in noncoding regions = 122 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 6 TGCCGCGGGACTGGTCCTACTCCTCTACCGA 1 117 0 CTGTCCTACT 0.868581 -184 CCCTCATCCCCATCACGCCACCT 4 45 0 CTCTCCCCAT 0.852097 -13 GTTGTGTACGCTGACCCCCCTACAGGGTAGG 6 29 0 CTGCCCCCCT 0.993828 -47 GCCCCGGCCCTCCTCTTTTTTCAC 6 62 0 CCGCCCTCCT 0.95608 -14 TACCAGCGCGCTCTTTCCCCTCATCTTTTGC 9 194 1 CTCTTCCCCT 0.919352 -82 GGTGCTGACGCGGCTCCTCCCGAGGAGCCGG 10 12 1 CGGTCCTCCC 0.963408 -108 CCCGAGGAGCCGGTTCCCCCTACAAGAGGGG 10 30 1 CGGTCCCCCT 0.986422 -90 CGATTTCTCCTCCCCCTGCTAAGAACA 10 103 0 CTCTCCCCCT 0.985062 -17 ACCTTGCCGACTGTCCCTCCCACACACGGTG 12 25 0 CTGCCCTCCC 0.983152 -62 CAGCTGAGCACTGCCTCGCCCCTGAGCATGG 14 18 0 CTGCTCGCCC 0.819638 -78 *** ******* Masking position 7 Map Score: 10.2318 Number of sites scoring better than the average of aligned sites = 224 Number in coding regions = 185 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 7 CGCCACCCGCTGCATCCCTTGACACTTCCAT 1 231 0 TGCATCCCTG 0.992662 -70 GCGCCGGTTTTGCCTACCCTGTAGGGGGGTC 6 17 1 TGCCTACCTG 0.981918 -59 ACGCCGCCTTTGCATCCCGTGCCCTGAAAGC 7 138 0 TGCATCCCTG 0.992662 -163 ACTTACACGCTGCCTACCGTGCACAAACTGC 8 46 0 TGCCTACCTG 0.981918 -255 ACGCGCAGAACTTGGATGACCAGA 8 287 0 CGCAGAACTG 0.820878 -14 GCCGTGAGTGTGCGTCGCTTGTGTGCATGGG 9 128 1 TGCGTCGCTG 0.945381 -148 AAGGACGTGCTGCAGCACGTGTAAAGTGATG 11 19 1 TGCAGCACTG 0.968514 -63 ******** ** Masking position 10 Map Score: 4.89739 Number of sites scoring better than the average of aligned sites = 77 Number in coding regions = 68 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 8 GGCTGGCGTGTCCGCCAATCGATACCCA 1 9 1 TGTCCGCCAA 0.985955 -292 GTCAAGCGCGTGTCCTGCACTCCGTTCGCT 3 29 0 TGTCCTGCAC 0.968048 -58 ATGCTCTGTGTCCTCCTCATGTGACTCA 5 53 0 TGTCCTCCTC 0.970237 -18 GAAGCTAGCGTGTCTGCCAATTCCACCATC 7 48 1 TGTCTGCCAA 0.959552 -253 TCTTCACCTGTGCCCGCCACGTACACTTAC 8 71 0 TGCCCGCCAC 0.987008 -230 CGCCGCAAGCTGTCTTCCACAACGGAAACC 9 23 0 TGTCTTCCAC 0.978094 -253 ********** Masking position 1 Map Score: 5.03396 Number of sites scoring better than the average of aligned sites = 63 Number in coding regions = 56 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 9 GGCTGGCGTGTCCGCCAATCGAT 1 4 1 TGGCGTGTCC 0.889956 -297 CGCGGGACTGGTCCTACTCCTCTACCGAGC 1 115 0 GTCCTACTCC 0.716007 -186 TTTTGGACGTTGCCTTGACCAAAGGCTGAG 1 267 1 TGCCTTGACC 0.933099 -34 CAGGTGCTAGTGCCTTCACCGGCGTGGGAG 7 19 0 TGCCTTCACC 0.963939 -282 CTAGCGTGTCTGCCAATTCCACCATCGAGG 7 52 1 TGCCAATTCC 0.941829 -249 CTTGACAAAATGCCAATTCCAATACACGCT 7 170 1 TGCCAATTCC 0.941829 -131 GCACACTCACGGCCTATTCCTGCCTTTCAG 9 111 0 GGCCTATTCC 0.947638 -165 TACCGCACGCTGCCGACACCCGCGCGTCGC 13 40 0 TGCCGACACC 0.963239 -32 AGTGCTCAGCTGGCGTCTCCACTCGCACAG 14 37 1 TGGCGTCTCC 0.939298 -59 AGGGTATTATCGCCTTTTCCCTGCTGCGGT 16 150 0 CGCCTTTTCC 0.908138 -22 ********** Masking position 4 Map Score: 5.94948 Number of sites scoring better than the average of aligned sites = 267 Number in coding regions = 239 Number in noncoding regions = 28 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 GATAAAAGTGGATCCAAACGTAGACCCCCA 1 83 1 GATCCAAACG 0.815284 -218 CAGAGCAGCAGATAAAAACGAGCAACGCCG 8 261 0 GATAAAAACG 0.805271 -40 AGAGCGCGCTGGTAAAAACGGATCAGCGCG 9 178 0 GGTAAAAACG 0.868318 -98 GAGCAACTCGGATAATAACGGCACGAAGGC 9 223 0 GATAATAACG 0.869008 -53 AGGTGCTGACGCGGCTCCTCC 10 2 1 GGTGCTGACG 0.83629 -118 TACAAGAGGGGATCTTGACGCCTCCGGTAC 10 50 1 GATCTTGACG 0.93152 -70 GTGACGGTAAGGACGTGCTGCAGCA 11 6 1 GGTAAGGACG 0.918835 -76 ATCGGTCTGGACGCTACCATAGC 14 83 0 GGTCTGGACG 0.93234 -13 TTCTGTCAAGGATCTTGTCGCAAGGTTGCT 16 77 1 GATCTTGTCG 0.791062 -95 GGAGGGTATTATCGCCTTTTCCCT 16 158 0 GGTATTATCG 0.746247 -14 ********** Masking position 3 Map Score: 2.50216 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 164 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 11 AAGTGTCAAGGGATGCAGCGGGTGGCGGGG 1 235 1 GGATGCAGCG 0.781206 -66 GCTCCTTGCAGGTAACTGCGCCG 2 4 1 CCTTGCAGGT 0.755169 -26 CGCTCACGCACCTTGCAGAGCA 3 3 0 CCTTGCAGAG 0.917368 -84 ACGCTGACCCCCCTACAGGGTAGGCAAAAC 6 23 0 CCCTACAGGG 0.568239 -53 GATTAGAGCAGCTTTCAGGGCACGGGATGC 7 128 1 GCTTTCAGGG 0.91136 -173 TGCTGATAGTACATGCAGGGAGCAGTTTGT 8 25 1 ACATGCAGGG 0.749544 -276 GTGGAAGACAGCTTGCGGCGTATCAGCGGC 9 33 1 GCTTGCGGCG 0.945268 -243 CCTATTCCTGCCTTTCAGCGGTAAATTCAG 9 99 0 CCTTTCAGCG 0.957117 -177 CTTGCCCTGCTGCGTATAGTTTCT 15 5 1 CCCTGCTGCG 0.762713 -68 ATCGCCTTTTCCCTGCTGCGGTCAACATCT 16 142 0 CCCTGCTGCG 0.762713 -30 ********** Masking position 4 Map Score: 7.47351 Number of sites scoring better than the average of aligned sites = 430 Number in coding regions = 397 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 12 TTACTCCTTGTATGCCGCGGGACTGGTCCT 1 130 0 TATGCCGCGG 0.938241 -171 GGACACGCGCTTGACTGCAGCTGAGAGGAG 3 44 1 TTGACTGCAG 0.876804 -43 GTACATGCGGTATGCCGCAGTTTTTTTACA 8 227 1 TATGCCGCAG 0.976497 -74 CCGCAGTTTTTTTACAGCAGCGGCGTTGCT 8 241 1 TTTACAGCAG 0.938035 -60 GTTCTCTGAATTTACCGCTGAAAGGCAGGA 9 94 1 TTTACCGCTG 0.91703 -182 GGAGAAACTATACGCAGCAGGGCAAG 15 7 0 TACGCAGCAG 0.863471 -66 GGGTCAGATGTTGACCGCAGCAGGGAAAAG 16 137 1 TTGACCGCAG 0.973782 -35 ********** Masking position 1 Map Score: 2.72878 Number of sites scoring better than the average of aligned sites = 121 Number in coding regions = 113 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 13 GGATCCAAACGTAGACCCCCACCGCTCGGT 1 92 1 GTAGACCCCC 0.896317 -209 TCAGCCGAGAATAGACTCCGCCATGGCCCG 1 202 0 ATAGACTCCG 0.897866 -99 GCAACGTCCAAAAGACCCCGCCACCCGCTG 1 250 0 AAAGACCCCG 0.985016 -51 AAGGTAAAAGAAAGACGCCGAGAATTCAGC 13 12 1 AAAGACGCCG 0.980411 -60 CTGTGCGAGTGGAGACGCCAGCTGAGCACT 14 37 0 GGAGACGCCA 0.872917 -59 AGTCACCAGCACACACGCCGGAGAAACTAT 15 26 0 ACACACGCCG 0.912176 -47 GAGAACTCCCCGTAACAACCGC 15 61 0 GAACTCCCCG 0.892996 -12 GGTTGCTCAGAGAGTCCCCGTTTCTTTTTC 16 100 1 AGAGTCCCCG 0.962934 -72 ********** Masking position 3 Map Score: 2.02816 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 94 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 14 CACGCGCGGTCGTCTTGGGTATCGATTGGC 1 24 0 CGTCTTGGGT 0.911362 -277 CAAGACGACCGCGCGTGGGTAGAAAGCTGC 1 37 1 GCGCGTGGGT 0.917496 -264 CTCTACCGAGCGGTGGGGGTCTACGTTTGG 1 96 0 CGGTGGGGGT 0.897404 -205 ACCTGCGCGCGGGCCATGGCGGAGTCTATT 1 193 1 GGGCCATGGC 0.794501 -108 AAAAAGAGGAGGGCCGGGGC 6 66 1 GGGCCGGGGC 0.83267 -10 GTGCCTTCACCGGCGTGGGAGTTCAAGTC 7 10 0 CGGCGTGGGA 0.922165 -291 GGTTTTCTTGCCTCGATGGTGGAATTGGCA 7 62 0 CCTCGATGGT 0.562711 -239 CTGCGCGTGGCGCCGTGGGCTATTAGCTCA 7 210 1 CGCCGTGGGC 0.906658 -91 CGCCTTAAAAGGGCGTTGCTCTACCAGCTG 7 238 0 GGGCGTTGCT 0.830207 -63 TTAAGGCGTGGGTCGATGGTTCGAATCCAT 7 260 1 GGTCGATGGT 0.884339 -41 GTGTCGGTAGGGGTTTGGGTACGCGCAGGG 8 150 1 GGGTTTGGGT 0.855066 -151 TTTACAGCAGCGGCGTTGCTCGTTTTTATC 8 251 1 CGGCGTTGCT 0.858827 -50 GCCGTCTTGGGCGCCACCGTGT 12 3 1 CGTCTTGGGC 0.901781 -84 AGGTGCGACTGGTTGATGGCGTGAGTCTCG 12 52 1 GGTTGATGGC 0.627511 -35 AGCGACGCGCGGGTGTCGGCAGCGTGCGGT 13 39 1 GGGTGTCGGC 0.679009 -33 TGCTCGTACGCGGCTATGGTAGCGTCCAGA 14 71 1 CGGCTATGGT 0.888956 -25 ATAGTTTCTCCGGCGTGTGTGCTGGTGACT 15 26 1 CGGCGTGTGT 0.826918 -47 TTCTTTTTCCCGTTTAGGGTCAGATGTTGA 16 121 1 CGTTTAGGGT 0.608255 -51 ********** Masking position 8 Map Score: 12.9611 Number of sites scoring better than the average of aligned sites = 1016 Number in coding regions = 899 Number in noncoding regions = 117 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 15 ********** No masking Map Score: 4.90518e-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