AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -icpxR6_bsub_opreg_100.orf -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yacB 194 similar to hypothetical proteins #2 yacC 85 similar to hypothetical proteins #3 yacD 46 similar to protein secretion PrsA homolog #4 ybdE 105 similar to hypothetical proteins #5 yczA 300 yczA #6 ycbL 96 similar to two-component response regulator [YcbM] #7 yclJ 212 similar to two-component response regulator [YclK] #8 yerI 161 yerI #9 htrA 168 serine protease Do (heat-shock protein) #10 ykoG 300 similar to two-component response regulator [YkoH] #11 resD 80 two-component response regulator #12 resC 135 essential protein similar to cytochrome c biogenesis protein #13 ppiB 253 peptidyl-prolyl isomerase #14 yrkP 267 similar to two-component response regulator [YrkQ] #15 phoP 211 two-component response regulator #16 yvqA 277 similar to two-component response regulator [YvqB] #17 yvrI 300 yvrI #18 yyxA 68 alternate gene name: yycK; similar to serine protease Do #19 yycJ 21 yycJ #20 yycF 300 similar to two-component response regulator [YycG] Motif number 1 CGTGTGTGTTTTTTGATTTTGTAAAGGTTA 6 56 1 TTTTGATTTT 0.859061 -41 CAATTGTTAGTTTTTATTTCATCAACTAGA 7 123 0 TTTTTATTTC 0.877703 -90 GGCACAAGGGTTTTTATGTTACAATTAACA 8 33 1 TTTTTATGTT 0.682499 -129 GTGAAAATATTTTCCCTTTTCCTGTTAATT 8 55 0 TTTCCCTTTT 0.621882 -107 TCCCATAATCTTTTCATTTTTATCCCACAG 9 70 1 TTTTCATTTT 0.859061 -99 TCACTCCGTTTCTCTATTTTCACATGTCTA 9 144 0 TCTCTATTTT 0.873429 -25 GATATGCAGTTTTTTATTTTACCAAAAAAA 10 16 0 TTTTTATTTT 0.952989 -285 CGTATACAATTTTTTATTTTAACATCATAA 10 209 1 TTTTTATTTT 0.952989 -92 TGGCCTGCCCTTTTTATCTTTATTCCCGCG 12 111 0 TTTTTATCTT 0.883297 -25 AACCTGAATCTCTTTATCTCCGTCTAACCT 13 95 0 TCTTTATCTC 0.609891 -159 TCAGGTTTCATTTTTATTTTTTAGTAAAGC 13 118 1 TTTTTATTTT 0.952989 -136 ATGCCTACTTTCTTTATTTTAATTTTCAAA 13 230 0 TCTTTATTTT 0.922042 -24 AGCAAGCCTTTCTCTCTTTTTA 15 3 0 TCTCTCTTTT 0.761416 -209 TAATACAGCCTTTCTCTTTTTACTATAAAT 15 33 1 TTTCTCTTTT 0.845438 -179 ATCATAAACGTCTTTATTTCTTTTAAAAAT 15 72 1 TCTTTATTTC 0.807221 -140 ATGTTTCATGATTTTATTTTAGCGAAAGCA 15 131 0 ATTTTATTTT 0.687251 -81 ACATCCTATTTCTCTATTTTATGTCATCTT 15 164 0 TCTCTATTTT 0.873429 -48 GATCAAACATATTCTATTTTGGTGCTTTGC 16 98 0 ATTCTATTTT 0.561806 -180 TTCCTCGCTCTTTTTCTCTTCCTTTCTTCC 16 138 1 TTTTTCTCTT 0.777795 -140 TCACATATTCTTTTCATTTTTATCCCACAA 16 191 0 TTTTCATTTT 0.859061 -87 GTTTACTTTTTTTTGCTTTCCTTCATTTAA 17 264 1 TTTTGCTTTC 0.499493 -37 ACCTTTATTTTTTTTATCTTTTGACCTTAA 20 177 1 TTTTTATCTT 0.883297 -124 CATTTTGATTTTCCTCCTGCCG 20 289 0 TTTTGATTTT 0.859061 -12 ********** Masking position 7 Map Score: 22.8504 Number of sites scoring better than the average of aligned sites = 1258 Number in coding regions = 912 Number in noncoding regions = 346 Number of orfs with sites within 600 bp upstream = 344 Fraction of orfs with sites within 600 bp upstream = 0.0552522 Motif number 2 ACCTGCTTTCAGCCCCTTTTC 3 36 0 CCTGCTTTCA 0.932158 -11 ACACCTGCCACCGACTCTCT 5 1 0 CCGACTCTCT 0.577757 -300 ATGTTTCGATACTCCTCTCTTGGTAACGGG 5 110 0 ACTCCTCTCT 0.890032 -191 TTGGCCGTCACCTCCTTTAAGAAACACAAA 5 229 0 CCTCCTTTAA 0.777432 -72 TTGATATCCTCCTTTCTAACTCATCTG 5 284 0 CCTCCTTTCT 0.986576 -17 CGACTCAGTCCTTTCATATACAATAT 9 7 1 AGTCCTTTCA 0.780378 -162 CAGCACCCCTAGTGCTTTCCGTATACAATT 10 190 1 AGTGCTTTCC 0.610707 -111 ATTTGACCATCCTCTCCCGTCCCTATA 10 284 0 CATCCTCTCC 0.880164 -17 GTTTTCCCCCTGCTTTCCTTCTGTTACT 11 63 0 CCTGCTTTCC 0.956506 -18 TTTCTTTATGCGGCCTTTCTTGTGTATTTA 12 51 1 CGGCCTTTCT 0.869048 -85 TTGTATGCCTACTTTCTTTATTTTAAT 13 237 0 CCTACTTTCT 0.907541 -17 ATCAATACTCCTTTCCCATTTATCAC 14 7 1 ACTCCTTTCC 0.959209 -261 TGTATTAAGCAAGCCTTTCTCTCTTTTTA 15 10 0 AAGCCTTTCT 0.666334 -202 TTGCTTAATACAGCCTTTCTCTTTTTACTA 15 28 1 CAGCCTTTCT 0.87131 -184 GTCGGAATGTCCTGCTTTCGCTAAAATAAA 15 119 1 CCTGCTTTCG 0.808715 -93 GTTCTTACACTCCTTTAACGGTTATTCA 16 9 1 ACTCCTTTAA 0.507455 -269 CTCTTTTTCTCTTCCTTTCTTCCCTTAACC 16 145 1 CTTCCTTTCT 0.81731 -133 GGCTCTTCACATCCTTTCAACGTCATTAT 16 259 0 CATCCTTTCA 0.924759 -19 TAGGAAAATACCTCCCTTCTTTTTCTGCAG 17 155 1 CCTCCCTTCT 0.928212 -146 AAAGTAAACTACTACTTTCCGCCTAGTGTC 17 243 0 ACTACTTTCC 0.75849 -58 ATTCCATCCTTTCCAAGAACGTTA 18 55 0 CATCCTTTCC 0.951625 -14 TTTATTGAAACCTCCCCTCACCGGAGTGCG 20 64 0 CCTCCCCTCA 0.765916 -237 ********** Masking position 8 Map Score: 21.2742 Number of sites scoring better than the average of aligned sites = 997 Number in coding regions = 621 Number in noncoding regions = 376 Number of orfs with sites within 600 bp upstream = 427 Fraction of orfs with sites within 600 bp upstream = 0.0685834 Motif number 3 GCTTTCTTTCTAAAAAAACTGCCGGCTGACG 1 14 1 TAAAAAAATG 0.901944 -181 ATCATTTACATAAAAAAACTGCCAGCGTCAG 1 39 0 TAAAAAAATG 0.901944 -156 GTAGAATGTTTGTAAAAAGTAAAGTAGAGAA 1 150 1 TGTAAAAATA 0.7022 -45 TTATTGTAATTGAAAAACGTGTGTGTTTTAT 6 16 0 TGAAAAACTG 0.911499 -81 TCCAAAGGTATGAAAAAAATATGAACAATCT 7 89 1 TGAAAAAATA 0.926284 -124 ATATTGTATATGAAAGGACTGAGTCG 9 6 0 TGAAAGGATG 0.835802 -163 GGGATAAAAATGAAAAGATTATGGGAAATTG 9 65 0 TGAAAAGATA 0.919543 -104 CGTCCCTATATGAAAAAAATGATTTCGTTGT 10 263 0 TGAAAAAATG 0.972589 -38 AGTGCGGATCTGAAAAACTTGAGCCTTACAA 14 47 1 TGAAAAACTG 0.911499 -221 TCACATTTTCTAAAAAAAATGATGACTCTTC 14 113 0 TAAAAAAATG 0.901944 -155 GGGATAAAAATGAAAAGAATATGTGAAATTA 16 195 1 TGAAAAGATA 0.919543 -83 GGTCAAAAGATAAAAAAAATAAAGGTTTAGA 20 172 0 TAAAAAAATA 0.765117 -129 TTATGGCCCATGTAAAGAATGGGTCCTTGTC 20 219 0 TGTAAAGATG 0.858278 -82 CCATAAGTGATGAAACGAATGTTATATAGAT 20 244 1 TGAAACGATG 0.835802 -57 ******** ** Masking position 5 Map Score: 13.0355 Number of sites scoring better than the average of aligned sites = 673 Number in coding regions = 570 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 4 TTGATATCCTCCTTTCTAACTCATCTG 5 284 0 TCCTCCTTCT 0.864382 -17 TCTGGGGCGCGTCCCCTTGCTGATAAATTAA 7 52 1 GTCCCCTGCT 0.890337 -161 AAGTGTACCGTTTTCCGCACTTTTTCACAAT 9 38 1 TTTTCCCACT 0.903556 -131 CAACCTGCACTTCCCCACGCTGGTATTATCC 10 103 1 TTCCCCCGCT 0.978049 -198 AAAGCGCGTTTCTTCCGCGCTTTATCTCAGC 10 154 1 TCTTCCCGCT 0.981531 -147 GTTTTCCCCCTGCTTTCCTTCTGT 11 67 0 TTCCCCTGCT 0.95906 -14 GGAAAACGAATCTCCCGAGCTTTACTAAAAA 13 135 0 TCTCCCAGCT 0.888707 -119 TCATCCTACATCTTCCTCGCTCTTTTTCTCT 16 126 1 TCTTCCCGCT 0.981531 -152 GCTCTTTTTCTCTTCCTTTCTTCCCTTAACC 16 144 1 TCTTCCTTCT 0.846204 -134 CAATTTGGGGTTTCCCGCGCTGATTGCAATG 17 84 0 TTTCCCCGCT 0.97466 -217 GTTTTATCGGTTTTCCTCACTTACATACATG 17 186 0 TTTTCCCACT 0.903556 -115 ACCGCCTCCCTACTAAATTAAATG 17 287 0 GCCTCCTACT 0.759914 -14 ****** **** Masking position 11 Map Score: 10.739 Number of sites scoring better than the average of aligned sites = 292 Number in coding regions = 254 Number in noncoding regions = 38 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 5 ACGCGGTTTCTTTCATAAATCAATTCCAGC 2 42 0 TTTCATAAAT 0.876886 -44 AGGTTTTGCGTTTCACAATTGTTAGTTTTT 7 138 0 TTTCACAATT 0.918129 -75 TTCCGCACTTTTTCACAATTTCCCATAATC 9 50 1 TTTCACAATT 0.918129 -119 TCTCAAACTTTCTCACGATTTGATAAAATG 11 31 1 TCTCACGATT 0.839336 -50 GAACTGTATTTTTCATGATTCAGGTCCTCA 13 61 0 TTTCATGATT 0.944337 -193 AATGATGACTCTTCATAAATTGTTAAGATT 14 97 0 CTTCATAAAT 0.753972 -171 GAGCATCAGCTTTCATAAATTGGTAAGATT 14 156 1 TTTCATAAAT 0.876886 -112 GTCTCTCTCACCTCATGATTCTTGTTGTTA 14 248 0 CCTCATGATT 0.759299 -20 TCTTAACATGTTTCATGATTTTATTTTAGC 15 138 0 TTTCATGATT 0.944337 -74 GGCAGGCAATTTTCATAATTTCACATATTC 16 211 0 TTTCATAATT 0.940295 -67 ********** Masking position 5 Map Score: 7.71764 Number of sites scoring better than the average of aligned sites = 185 Number in coding regions = 156 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 6 GTTTCTCTACTTTACTTTTTACAAACATTC 1 153 0 TTTACTTTTT 0.829419 -42 ACGGGGGTTTTTTGTGTTTCTTAAAGGAGG 5 219 1 TTTGTGTTTC 0.904611 -82 TTGAAAAACGTGTGTGTTTTATAAAAA 6 8 0 TGTGTGTTTT 0.904611 -89 TGTAATTACGTGTGTGTTTTTTGATTTTGT 6 48 1 TGTGTGTTTT 0.904611 -49 AACAGAAGGTTTTGCGTTTCACAATTGTTA 7 144 0 TTTGCGTTTC 0.89611 -69 CTCCCCTTGATTTGTGTTTCGGCAGAAGTG 8 82 0 TTTGTGTTTC 0.904611 -80 GACCGAATGGTGTATTTTTTTGTGCGCTTA 10 74 0 TGTATTTTTT 0.829419 -227 CTAACGGAACTGTATTTTTCATGATTCAGG 13 67 0 TGTATTTTTC 0.815584 -187 AGGTTTCATTTTTATTTTTTAGTAAAGCTC 13 120 1 TTTATTTTTT 0.842417 -134 ATTTTGGTGCTTTGCTTTTCTCCTCATTAT 16 83 0 TTTGCTTTTC 0.876501 -195 TTTGCAGCAGTTTACGTTTTATCGGTTTTC 17 202 0 TTTACGTTTT 0.855269 -99 AAAGTAGTAGTTTACTTTTTTTTGCTTTCC 17 255 1 TTTACTTTTT 0.829419 -46 AGGTGAAACATGTGTTTTTTTTCTAAACCT 20 151 1 TGTGTTTTTT 0.886403 -150 TTTCTAAACCTTTATTTTTTTTATCTTTTG 20 170 1 TTTATTTTTT 0.842417 -131 ********** Masking position 7 Map Score: 14.0395 Number of sites scoring better than the average of aligned sites = 885 Number in coding regions = 732 Number in noncoding regions = 153 Number of orfs with sites within 600 bp upstream = 135 Fraction of orfs with sites within 600 bp upstream = 0.0216833 Motif number 7 CAATCAGCTTTCCTAATGCCTCTTCAGCCG 4 53 0 TCCTAATGCC 0.863377 -53 ACCGATCCTCCCCTGATGCCGAATGGGCTT 5 33 1 CCCTGATGCC 0.980253 -268 TAGAAAACCCTTGTGCCATATTGGCAC 8 8 1 CCCTTGTGCC 0.989491 -154 AACATAAAAACCCTTGTGCCAATATGGCAC 8 23 0 CCCTTGTGCC 0.989491 -139 AAAATATTTTCACTTCTGCCGAAACACAAA 8 72 1 CACTTCTGCC 0.902251 -90 GCGCTTTGATCCCTTATGACCCGATCTGGA 10 131 0 CCCTTATGAC 0.854442 -170 AAAACAGCACCCCTAGTGCTTTCCGTATAC 10 186 1 CCCTAGTGCT 0.831851 -115 GGAGAACCGGCCCTGCGGCCGGTTCAAAGA 20 13 1 CCCTGCGGCC 0.948018 -288 ATTTTGATTTTCCTCCTGCCGAATGACTTC 20 280 0 TCCTCCTGCC 0.893071 -21 ********** Masking position 4 Map Score: 6.7445 Number of sites scoring better than the average of aligned sites = 136 Number in coding regions = 105 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 GAAACCGCGTAGGAAGTGTATAGGAGGTTTA 2 62 1 AGGAGTGTAT 0.792383 -24 GGAAGTGTATAGGAGGTTTAGTA 2 73 1 AGGAGTTTAG 0.861679 -13 CTATTCCTGAAGGATGTTCATGCTCGTATT 4 10 0 AGGAGTTCAT 0.824769 -96 AACGGATAGTAGGCGATGCCGGGTTTCTCTC 5 79 1 AGGCATGCCG 0.859421 -222 TGTTTCTTAAAGGAGGTGACGGCCAATGTAC 5 233 1 AGGAGTGACG 0.940191 -68 AGGTTAGGTGAGGAGATGCAGCGCATA 6 80 1 AGGAATGCAG 0.976299 -17 ATATTCCCTTAGGATATGCAGTTTTTTATTT 10 27 0 AGGAATGCAG 0.976299 -274 TACCAGCGTGGGGAAGTGCAGGTTGACCGAA 10 97 0 GGGAGTGCAG 0.952674 -204 TAGCGAAAGCAGGACATTCCGACAATTCGCC 15 111 0 AGGAATTCCG 0.8921 -101 TGACGTTGAAAGGATGTGAAGAGCC 16 263 1 AGGAGTGAAG 0.956669 -15 **** ****** Masking position 7 Map Score: 6.33337 Number of sites scoring better than the average of aligned sites = 421 Number in coding regions = 358 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577 Motif number 9 GCGATGCCGGGTTTCTCTCCCCGTTACCAAG 5 91 1 GTTTTCTCCC 0.858889 -210 GAAGTGTACCGTTTTCCGCACTTTTTCACAA 9 37 1 GTTTCCGCAC 0.968671 -132 ATCTTTTCATTTTTATCCCACAGTTTTTGTT 9 77 1 TTTTTCCCAC 0.813521 -92 CAAAGCGCGTTTCTTCCGCGCTTTATCTCAG 10 153 1 TTCTCCGCGC 0.856144 -148 GTCTCTCTCACCTCATGATTC 14 257 0 GTCTTCTCAC 0.933706 -11 ATCATCCTACATCTTCCTCGCTCTTTTTCTC 16 125 1 ATCTCCTCGC 0.706143 -153 TTCTTTTCATTTTTATCCCACAATGTTTGTT 16 183 0 TTTTTCCCAC 0.813521 -95 GCAATTTGGGGTTTCCCGCGCTGATTGCAAT 17 85 0 GTTTCCGCGC 0.96227 -216 CGTTTTATCGGTTTTCCTCACTTACATACAT 17 187 0 GTTTCCTCAC 0.969273 -114 GTTTGTCTCACTCCATTATTT 19 11 0 GTTTTCTCAC 0.951878 -11 **** ****** Masking position 4 Map Score: 4.77535 Number of sites scoring better than the average of aligned sites = 187 Number in coding regions = 157 Number in noncoding regions = 30 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 10 AAGCCGCAGCTGAGCCAATCATTTACATAAAA 1 55 0 TGAGCCAATT 0.938464 -140 TGTTTACAAATGAGCCGCTGATCGTGTATGGT 1 115 1 TGAGCCGCTT 0.81725 -80 GTGGCAGGTGTGAACCGATCCTCCCCTGATGC 5 20 1 TGAACCGATT 0.885512 -281 ATTGCTTTGCTGAACGGATAGTAGGCGATGCC 5 67 1 TGAACGGATT 0.830548 -234 TAAAAACCCTTGTGCCAATATGGCACAAGGGT 8 17 0 TGTGCCAATG 0.838301 -145 AAGTGCAGGTTGACCGAATGGTGTATTTTTTT 10 83 0 TGACCGAATT 0.920169 -218 TGATCCCTTATGACCCGATCTGGATAATACCA 10 123 0 TGACCCGATG 0.961287 -178 ATGGCAGAGCTGAGCGGAAATTTTCTTTATGC 12 30 1 TGAGCGGAAT 0.656598 -106 ATTTAATCGCTGTCCCAATCTTCGGCGGGGCC 12 76 1 TGTCCCAATT 0.89385 -60 GGCAATGTGTAGTGCGGATCTGAAAAACTTGA 14 37 1 AGTGCGGATG 0.555056 -231 ATAAATATAAAGACCGAATCTTAACAATTTAT 14 81 1 AGACCGAATT 0.701868 -187 CAAGTTCAATTGTCCCAATAATGAGGAGAAAA 16 66 1 TGTCCCAATT 0.89385 -212 ATGTATCTGCTGACCCGATTCGAAAAGAAGTT 17 55 0 TGACCCGATG 0.961287 -246 ********* * Masking position 5 Map Score: 5.18221 Number of sites scoring better than the average of aligned sites = 453 Number in coding regions = 427 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 11 AGCTTTCCTAATGCCTCTTCAGCCGCAAACGGAGC 4 43 0 ACCTTCAGCG 0.988977 -63 AGGAAAGCTGATTGCTTTTCAGCTGAAAGATAAGG 4 69 1 AGCTTCAGCG 0.992407 -37 TCCGTTCAGCAAAGCAATTCAGAAGCCCATTCGGC 5 50 0 AGCATCAGAG 0.880976 -251 ACCTTTATTAACAGCTATACAGCCGTTCACTCTAA 5 153 0 AGCTTCAGCG 0.992407 -148 ATCAATAAAAATACCTATACGGAGGAACATAA 7 8 0 ACCTTCGGAG 0.882784 -205 CTCACAAAGCAGCACTATCCAGCTGCTTGTGAAAT 13 30 0 AACTTCAGCG 0.983052 -224 TGTCTTCCAAAATACTTTGCAGCAGTTTACGTTTT 17 212 0 AACTTCAGCG 0.983052 -89 * *** * **** * Masking position 1 Map Score: 4.2699 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 55 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 TGATTGTAAAAGCCGCAGCTGAGCCAATCATTT 1 63 0 ACGCAGTGAG 0.859598 -132 CAAATTAAAAACCCGCTAAAGAGC 3 2 0 ACGCTAAGAG 0.912381 -45 TTGCTCCGTTTGCGGCTGAAGAGGCATTAGGAA 4 41 1 TCGCTGAGAG 0.982368 -65 CTCCTTATCTTTCAGCTGAAAAGCAATCAGCTT 4 73 0 TCGCTGAAAG 0.938268 -33 ACTTAGAGTGAACGGCTGTATAGCTGTTAATAA 5 151 1 ACGCTGATAG 0.96664 -150 TGATTTGTGTTTCGGCAGAAGTGAAAATATTTT 8 72 0 TCGCAGAGTG 0.78513 -90 CAATTTCACAAGCAGCTGGATAGTGCTGCTTTG 13 28 1 ACGCTGATAG 0.96664 -226 ATAAAACGTAAACTGCTGCAAAGTATTTTGGAA 17 210 1 ACGCTGAAAG 0.966498 -91 TCTTCTTTGAACCGGCCGCAGGGCCGGTTCTCC 20 13 0 ACGCCGAGGG 0.896656 -288 * * **** **** Masking position 6 Map Score: 3.89781 Number of sites scoring better than the average of aligned sites = 288 Number in coding regions = 266 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 TTGAATAGTTTCTCTACTTTACTTTTTACAA 1 159 0 TCTCTACTTA 0.732731 -36 CCTCTATCACCACTTTTGAATAGTTTC 1 178 0 TCACCACTTT 0.852481 -17 ACCTGCTTTCAGCCCCTTTTCTCAAATTA 3 28 0 TCAGCCCTTT 0.737076 -19 GCCGGGTTTCTCTCCCCGTTACCAAGAGAGG 5 96 1 TCTCCCCTTA 0.945067 -205 ACATTGGCCGTCACCTCCTTTAAGAAACACA 5 231 0 TCACCTCTTT 0.92999 -70 CATGTTCACTCCGTTTCTCTATTTTC 9 153 0 TCACTCCTTT 0.968569 -16 TGCCATGACATCACTCCCTTTTCGC 12 5 0 TCACTCCTTT 0.968569 -131 TTATAGCCTGTCTCTCCTTGTCGCGGCTATT 13 183 0 TCTCTCCTGT 0.862668 -71 GTCTCTCTCACCTCATGATTCTTGTTGT 14 250 0 TCACCTCTGA 0.70734 -18 AGCAAGCCTTTCTCTCTTTTTA 15 2 0 TCTCTCTTTT 0.569702 -210 GTTCTTACACTCCTTTAACGGTTATTC 16 7 1 ACACTCCTTA 0.656589 -271 GCTTTGCTTTTCTCCTCATTATTGGGACAAT 16 74 0 TCTCCTCTTA 0.872391 -204 TCGCTCTTTTTCTCTTCCTTTCTTCCCTTAA 16 142 1 TCTCTTCTTT 0.902896 -136 GGAAAATACCTCCCTTCTTTTTCTGCAGTCA 17 157 1 TCCCTTCTTT 0.741003 -144 GTTTGTCTCACTCCATTATTT 19 4 0 TCACTCCTTA 0.954308 -18 ******* *** Masking position 9 Map Score: 12.5552 Number of sites scoring better than the average of aligned sites = 684 Number in coding regions = 445 Number in noncoding regions = 239 Number of orfs with sites within 600 bp upstream = 268 Fraction of orfs with sites within 600 bp upstream = 0.0430453 Motif number 14 CTTAACCCTAAAAGGGCTGGAATTGATTTA 2 27 1 AAAGGGCTGG 0.925893 -59 CCATTCGGCATCAGGGGAGGATCGGTTCAC 5 29 0 TCAGGGGAGG 0.930259 -272 TTGATTTTGTAAAGGTTAGGTGAGGAGATG 6 68 1 AAAGGTTAGG 0.741063 -29 AATTTATCAGCAAGGGGACGCGCCCCAGAG 7 51 0 CAAGGGGACG 0.917342 -162 AAACACAAATCAAGGGGAGGTATGTTGATG 8 93 1 CAAGGGGAGG 0.985306 -69 ATAAAGATAAAAAGGGCAGGCCAAACCG 12 118 1 AAAGGGCAGG 0.971534 -18 TTTTCCCCCGAAAGGTGTGGTATAATAGCC 13 160 1 AAAGGTGTGG 0.871341 -94 CGCACTCCGGTGAGGGGAGGTTTCAATAAA 20 64 1 TGAGGGGAGG 0.930259 -237 ********** Masking position 3 Map Score: 2.6103 Number of sites scoring better than the average of aligned sites = 161 Number in coding regions = 104 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 56 Fraction of orfs with sites within 600 bp upstream = 0.00899454 Motif number 15 CAGCCGGCAGTTTTTTTAGAAAGAAAGCGAA 1 8 0 TTTTAGAAGA 0.765152 -187 TGGTATCGATTTGTTTACAAATGAGCCGCTGATC 1 104 1 TTTTCAAAGA 0.946246 -91 GAGACCCTCGTCCTTTGCATAGGACGGGGGTTTT 5 196 1 TTTTCATAGA 0.578879 -105 TTGATAATGATTGTTTTCACACGATTTCCAGCAT 8 120 0 TTTTCACAGA 0.875466 -42 ATGATTTCGTTGTTTACAAAATGATTCTTATCAT 10 242 0 TTTAAAAAGA 0.696978 -59 GAGAACTGTGTCGCTTTCAAAGGA 11 1 0 TCTTCAAAGA 0.663242 -80 TTCTTTATTTTAATTTTCAAAGGAGATTATGTAT 13 217 0 TTTTCAAAGA 0.785441 -37 CGTCTTTATTTCTTTTAAAAATGATGTAAAAGGC 15 80 1 TTTTAAAAGA 0.625945 -132 CTGGTCAACTTTTTTTAAAAAAGATAACTTTATT 20 88 0 TTTTAAAAGA 0.916533 -213 * *** **** ** Masking position 5 Map Score: 2.49448 Number of sites scoring better than the average of aligned sites = 175 Number in coding regions = 131 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096