AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -icpxR9_bsub_opreg_300.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 spoIIE 300 serine phosphatase #2 yabS 84 similar to hypothetical proteins #3 yabT 88 yabT #4 yacA 103 similar to cell-cycle protein #5 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #6 yacB 194 similar to hypothetical proteins #7 yacC 85 similar to hypothetical proteins #8 yacD 46 similar to protein secretion PrsA homolog #9 ybcO 300 ybcO #10 ybcP 66 ybcP #11 ybcQ 43 similar to hypothetical proteins #12 ybdB 64 similar to ABC transporter (permease) #13 ybdD 46 ybdD #14 ybdE 105 similar to hypothetical proteins #15 yczA 300 yczA #16 ycbL 96 similar to two-component response regulator [YcbM] #17 yclJ 212 similar to two-component response regulator [YclK] #18 yerE 264 similar to hypothetical proteins #19 yerF 61 similar to ATP-dependent DNA helicase #20 yerG 23 similar to DNA ligase #21 yerI 161 yerI #22 htrA 168 serine protease Do (heat-shock protein) #23 ykoG 300 similar to two-component response regulator [YkoH] #24 motA 300 motility protein A #25 flgB 300 flagellar basal-body rod protein #26 fliF 45 flagellar basal-body M-ring protein #27 fliH 117 flagellar assembly protein #28 fliK 160 fliK #29 flgE 21 flagellar hook protein #30 fliL 251 flagellar protein #31 fliM 33 flagellar motor switch protein #32 cheY 25 two-component response regulator #33 flhA 32 flagella-associated protein #34 cheW 21 cheW #35 resD 80 two-component response regulator #36 resC 135 essential protein similar to cytochrome c biogenesis protein #37 resA 131 essential protein similar to cytochrome c biogenesis protein #38 ypuL 91 similar to hypothetical proteins #39 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #40 ypuI 54 similar to hypothetical proteins from B. subtilis #41 ypuG 280 similar to hypothetical proteins #42 ppiB 253 peptidyl-prolyl isomerase #43 yrkP 267 similar to two-component response regulator [YrkQ] #44 phoP 211 two-component response regulator #45 citH 43 malate dehydrogenase #46 citC 163 isocitrate dehydrogenase #47 citZ 300 citrate synthase II #48 yvqA 277 similar to two-component response regulator [YvqB] #49 yvrI 300 yvrI #50 yyxA 68 alternate gene name: yycK; similar to serine protease Do #51 yycJ 21 yycJ #52 yycF 300 similar to two-component response regulator [YycG] Motif number 1 GAAGCCGATTTTTTTCATTTTTAGACAACATT 1 137 1 TTTTTCTTTT 0.941769 -164 TTTTGAATAGTTTCTCTACTTTACTTTTTACA 6 160 0 TTTCTCCTTT 0.89957 -35 CTCACCCCTAATTTTCCACTTATGTTTTGAAT 9 81 0 ATTTTCCTTA 0.372588 -220 AGCTTGTCAGCTTTTCTATTTTTAAAGGGTTA 9 135 1 CTTTTCTTTT 0.859916 -166 TACGTGTGTGTTTTTTGATTTTGTAAAGGTTA 16 54 1 TTTTTTTTTT 0.873019 -43 GATTAACGGCTTTTTCCGTTTTTCCGCGCTAT 18 190 1 TTTTTCTTTT 0.941769 -75 AAGTGAAAATATTTTCCCTTTTCCTGTTAATT 21 55 0 ATTTTCTTTT 0.793786 -107 TTCCCATAATCTTTTCATTTTTATCCCACAGT 22 69 1 CTTTTCTTTT 0.859916 -100 GTTCACTCCGTTTCTCTATTTTCACATGTCTA 22 144 0 TTTCTCTTTT 0.932998 -25 GGATATGCAGTTTTTTATTTTACCAAAAAAAC 23 15 0 TTTTTTTTTA 0.622485 -286 CCGTATACAATTTTTTATTTTAACATCATAAT 23 208 1 TTTTTTTTTA 0.622485 -93 GACCCCCGGGCTTTTCAATTTTGGAGAGCCCG 24 145 1 CTTTTCTTTT 0.859916 -156 GAATTTCTGTTTTTTCTCCTTTCTTTTCGGCA 25 70 0 TTTTTCCTTT 0.912306 -231 TGTCCTCACAATTATCTATTTTGCAACTAGGT 25 161 0 ATTATCTTTT 0.397528 -140 GAAAGTTTTCTTTTTTCCTTTTGTGGAGAAAT 27 33 0 TTTTTTTTTT 0.873019 -85 CGTATTGATCATTCTCACCTTTTGCAGGCTGA 27 78 1 ATTCTCCTTT 0.680705 -40 ATTTTTCGATTTAAAAGGAGAGA 33 2 1 TTTTTCTTTA 0.795032 -31 GCTGTTTTTTCTCTCCTTTTAAATCGAAA 33 14 0 TTTCTCCTTT 0.89957 -19 TTGGCCTGCCCTTTTTATCTTTATTCCCGCGT 36 110 0 CTTTTTCTTT 0.626669 -26 TCATTTCACATTTCTTACTTTTTGAAGGTTAT 37 62 0 TTTCTTTTTT 0.855481 -70 CCGGGCGTTCTTTTTTCCTTTTATCCCTTCTA 41 46 0 TTTTTTTTTT 0.873019 -235 TTCAGGTTTCATTTTTATTTTTTAGTAAAGCT 42 117 1 ATTTTTTTTT 0.62069 -137 GTATGCCTACTTTCTTTATTTTAATTTTCAAA 42 230 0 TTTCTTTTTT 0.855481 -24 TAAGCAAGCCTTTCTCTCTTTTTA 44 3 0 TTTCTCTTTT 0.932998 -209 TAATACAGCCTTTCTCTTTTTACTATAAATGA 44 33 1 TTTCTCTTTA 0.769566 -179 CATAAACGTCTTTATTTCTTTTAAAAATGATG 44 74 1 TTTATTTTTT 0.54097 -138 CGACATCCTATTTCTCTATTTTATGTCATCTT 44 164 0 TTTCTCTTTT 0.932998 -48 TTTCTCTTCCTTTCTTCCCTTAACCATATCAT 48 150 1 TTTCTTCTTA 0.477321 -128 TTCACATATTCTTTTCATTTTTATCCCACAAT 48 190 0 CTTTTCTTTT 0.859916 -88 CAGTTTACGTTTTATCGGTTTTCCTCACTTAC 49 193 0 TTTATCTTTT 0.734908 -108 GTAGTTTACTTTTTTTTGCTTTCCTTCATTTA 49 261 1 TTTTTTCTTT 0.815583 -40 AACCTTTATTTTTTTTATCTTTTGACCTTAAA 52 176 1 TTTTTTCTTT 0.815583 -125 ****** **** Masking position 5 Map Score: 32.7904 Number of sites scoring better than the average of aligned sites = 1732 Number in coding regions = 1331 Number in noncoding regions = 401 Number of orfs with sites within 600 bp upstream = 367 Fraction of orfs with sites within 600 bp upstream = 0.0589464 Motif number 2 AATGTCCTCCTCACAATGAGCAGG 4 90 0 TCCTCCTCAC 0.588458 -14 TCCTTACCTCCTCCCACAGTAAGCA 5 83 0 ACCTCCTCCC 0.910138 -15 ACCTGCTTTCAGCCCCTTTT 8 37 0 ACCTGCTTTC 0.831942 -10 AAGTAAACCTCCTCTCAATTTTTGCA 9 285 0 ACCTCCTCTC 0.957216 -16 ACGAGCATGAACATCCTTCAGGAATAGTTG 14 14 1 ACATCCTTCA 0.330922 -92 TATGTTTCGATACTCCTCTCTTGGTAACGG 15 111 0 TACTCCTCTC 0.671298 -190 ATTGGCCGTCACCTCCTTTAAGAAACACAA 15 230 0 ACCTCCTTTA 0.871432 -71 TTGATATCCTCCTTTCTAACTCATCT 15 285 0 TCCTCCTTTC 0.977894 -16 GTCATACGTTCCTCCATTCGTTTGTTACC 18 246 0 TCCTCCATTC 0.722025 -19 CTGCTTCTTCCTTTCCTCTTCAA 20 9 0 TCTTCCTTTC 0.852675 -15 ATTTGACCATCCTCTCCCGTCCCTAT 23 285 0 CCATCCTCTC 0.76306 -16 AGCGCTACTTCCCTTCATCCTTTACA 24 7 1 ACTTCCCTTC 0.706504 -294 TAAACATGTTCCATCCCTCCTTAAAAAAGT 24 36 0 CCATCCCTCC 0.545217 -265 TTTTGTTTATTTCTCCCTTCTATGCCTCTT 24 178 1 TTCTCCCTTC 0.539603 -123 TTTCTGTTTTTTCTCCTTTCTTTTCGGCAT 25 69 0 TTCTCCTTTC 0.721376 -232 TACTCGCCTCCCCTCCCTCC 30 1 0 CCCTCCCTCC 0.881478 -251 GTTTTCCCCCTGCTTTCCTTCTGTTAC 35 64 0 CCCTGCTTTC 0.815515 -17 GGTGCTTCCTCCTTTAATGTGCTTTT 41 7 1 TCCTCCTTTA 0.880629 -274 AGCAGTTTGACCTCCTTCAATTTCACAAG 42 10 1 ACCTCCTTCA 0.754198 -244 ATCAATACTCCTTTCCCATTTATCA 43 6 1 TACTCCTTTC 0.78768 -262 TGTCGGAATGTCCTGCTTTCGCTAAAATAA 44 118 1 TCCTGCTTTC 0.843457 -94 GTTCTTACACTCCTTTAACGGTTATTC 48 8 1 CACTCCTTTA 0.336693 -270 GCTCTTTTTCTCTTCCTTTCTTCCCTTAAC 48 144 1 TCTTCCTTTC 0.852675 -134 GGCTCTTCACATCCTTTCAACGTCATTA 48 260 0 ACATCCTTTC 0.867573 -18 CTGTTTTACGACTTCCTCTATAAAAACCTG 49 120 1 ACTTCCTCTA 0.328042 -181 ATAGGAAAATACCTCCCTTCTTTTTCTGCA 49 154 1 ACCTCCCTTC 0.948449 -147 ATTCCATCCTTTCCAAGAACGTT 50 56 0 CCATCCTTTC 0.854017 -13 CTTTATTGAAACCTCCCCTCACCGGAGTGC 52 65 0 ACCTCCCCTC 0.910138 -236 ATTTTGATTTTCCTCCTGCCGAATGACTTC 52 280 0 TCCTCCTGCC 0.645956 -21 ********** Masking position 4 Map Score: 23.6881 Number of sites scoring better than the average of aligned sites = 772 Number in coding regions = 425 Number in noncoding regions = 347 Number of orfs with sites within 600 bp upstream = 374 Fraction of orfs with sites within 600 bp upstream = 0.0600707 Motif number 3 TCAAGCGGTTAAGACACCGCCCTTTCACGGCGGT 1 50 1 AAGAACCCTT 0.839431 -251 AGGATAATATACAAAATCCCCCTTACTTCGACAA 9 201 1 ACAAACCCTT 0.860185 -100 ATAAAATCCCCCTTAAGAGAAAAT 10 53 0 ATAAACCCTT 0.952369 -14 GACCTTGACTTACAAAACGCCTTTTTGACTGAAG 12 30 0 TACAACCCTT 0.596523 -35 AAAAGAGCCCCTCTCCTCGTTTTA 13 33 0 AAAAACCCCT 0.957981 -14 TAAGAAACACAAAAAACCCCCGTCCTATGCAAAG 15 208 0 AAAAACCCTC 0.800789 -93 ATTTTTATTGATAAGACCGCCTCTGGGGCGCGTC 17 31 1 ATAAACCCCT 0.927117 -182 GCTTTTTTATATAATAGCACCATTTTAAACAGAA 17 167 0 ATAAACCCTT 0.952369 -46 TGAAAAAAGAATCAAAACACCTTTTTCAGTGAAT 18 151 1 ATCAACCCTT 0.911266 -114 TTCCAGCATCAACATACCTCCCCTTGATTTGTGT 21 95 0 AACAACCCCT 0.921327 -67 AAGCGCACAAAAAAATACACCATTCGGTCAACCT 23 75 1 AAAATCCCTT 0.835413 -226 TATCTCAGCCAAAACAGCACCCCTAGTGCTTTCC 23 176 1 AAAAACCCCT 0.957984 -125 GCTGTTCTGGAAAAGATCGCAGCTTTCTACCGAA 30 185 1 AAAAACCACT 0.515728 -67 GCCAAATCTAAAAAAAACGCCGTTT 38 2 0 AAAAACCCTT 0.972854 -90 ATCAATACTCCTTTCCCATTTATC 43 1 1 ATCATCCCTT 0.592586 -267 TGATTTCCCCGAAAAAACGCCTTTATTTGCGGGT 47 16 0 GAAAACCCTT 0.810112 -285 ATATAACATCTCCTTTTCAATAAATT 47 285 0 ATAAACCCTT 0.952369 -16 GATCCATAGGAAAATACCTCCCTTCTTTTTCTGC 49 149 1 AAAAACCCTT 0.972854 -152 **** * * ** ** Masking position 4 Map Score: 19.2907 Number of sites scoring better than the average of aligned sites = 167 Number in coding regions = 113 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 64 Fraction of orfs with sites within 600 bp upstream = 0.0102795 Motif number 4 TGCCTTGATATTCGTTTATGAAAAGAATTTCCG 1 170 0 TTTTATGAAA 0.926638 -131 ACGCTGGCAGTTTTTTTATGTAAATGATTGGCT 6 42 1 TTTTATGTAA 0.670374 -153 AGGGCTGGAATTGATTTATGAAAGAAACCGCGT 7 39 1 TTTTATGAAA 0.92687 -47 TCTATTTATACTAATTAATGTAATTTTTAGGAT 9 173 1 CTTTATGTAA 0.667269 -128 TGGCCGTCACCTCCTTTAAGAAACACAAAAAAC 15 225 0 CTTTAAGAAA 0.666712 -76 CAATCTATTTCTAGTTGATGAAATAAAAACTAA 17 114 1 CTTTATGAAA 0.925465 -99 ATATGCTCTCTTTTTTTATGAAAAAAGAATCAA 18 133 1 TTTTATGAAA 0.924892 -132 TTGTACGGATTTGGTTTATGATAGAACGTATGT 19 15 1 TTTTATGATA 0.816186 -47 TCCCACAGTTTTTGTTTATGATAAACTCAAGTC 22 92 1 TTTTATGATA 0.815964 -77 ACATTGTGAATTTGTTCATGAAATATTCAAGGA 24 207 0 TTTTATGAAA 0.914546 -94 ATTTTTGAAACTTTTTGAAGAAAAATGCAAAAT 25 38 0 CTTTAAGAAA 0.666949 -263 TAGATGATTCTTGTTTAATGATA 27 1 0 TTTTATGATA 0.81619 -117 TTGTGAGGACCTGAATCATGAAAAATACAGTTC 42 58 1 CTATATGAAA 0.51527 -196 GTAAATCTTACCAATTTATGAAAGCTGATGCTC 43 156 0 CCTTATGAAA 0.611729 -112 TCCCACAATGTTTGTTTATGATATGGTTAAGGG 48 166 0 TTTTATGATA 0.815964 -112 ATTAGTTCTATTAGTTGATCAAACTTCTTTTCG 49 34 1 TTTTATCAAA 0.497288 -267 ** ** ****** Masking position 6 Map Score: 10.9131 Number of sites scoring better than the average of aligned sites = 231 Number in coding regions = 172 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 73 Fraction of orfs with sites within 600 bp upstream = 0.011725 Motif number 5 ATCCTAACACTTTCAACCCCTCCAAGCAAAGA 4 40 0 TTTCAACCCC 0.801217 -64 CGATGCCGGGTTTCTCTCCCCGTTACCAAGAG 15 92 1 TTTCTCCCCG 0.971123 -209 AATTTGTTCACCCGCCTATACAAAA 19 47 0 TTGTTCCCCC 0.923759 -15 AATCTTTTCATTTTTATCCCACAGTTTTTGTT 22 76 1 TTTTTACCCC 0.959412 -93 TAGAACTACATTTCTCGCCCTGATATAAGCCT 25 112 0 TTTCTCCCCG 0.971123 -189 CATTTCAGTTTTTTTCACCCTCAATATCCTTG 25 266 0 TTTTTCCCCC 0.984695 -35 GTTTTCCCCCTGCTTTCCTTCT 35 69 0 GTTTTCCCCG 0.825152 -12 AAGCAAAGGCTTTTTCTCCCGCTTCTGCGCTC 41 108 1 TTTTTCCCCC 0.984695 -173 GATGCAAGTATTTCTCTCCCCCAAAAAGAAAA 47 206 0 TTTCTCCCCC 0.988551 -95 ATTCTTTTCATTTTTATCCCACAATGTTTGTT 48 183 0 TTTTTACCCC 0.959412 -95 ATTCTAGGAGTTTCTAACCCACAATATAACCA 50 20 1 TTTCTACCCC 0.969439 -49 ****** *** * Masking position 2 Map Score: 13.9193 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 50 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 6 CGTATTCTCCAGGAGGAATGAAT 2 72 1 AGGAGGAATG 0.666061 -13 TTACTGTGGGAGGAGGTAAGGA 5 86 1 AGGAGGTAAG 0.507319 -12 TTGTTTTAAAACGAGGAGAGGGGCTCTTTT 13 27 1 ACGAGGAGAG 0.94354 -20 TCTCTTGGTAACGGGGAGAGAAACCCGGCA 15 95 0 ACGGGGAGAG 0.949562 -206 TTGAAGAGGAAAGGAAGAAGCAG 20 4 1 AAGAGGAAAG 0.836075 -20 GTTACAATTAACAGGAAAAGGGAAAATATT 21 50 1 ACAGGAAAAG 0.498408 -112 AACTTTCAGAACAAGGAAAGGGAACTCCTA 28 117 1 ACAAGGAAAG 0.865003 -44 CGAAACACAAGGAGAGAGATAGATT 32 7 1 ACAAGGAGAG 0.904792 -19 TTTTCGATTTAAAAGGAGAGAAAAAACAGC 33 13 1 AAAAGGAGAG 0.811378 -20 TGAAAGTAACAGAAGGAAAGCAGGGGGAAA 35 59 1 AGAAGGAAAG 0.908861 -22 GAAGGAAAGCAGGGGGAAAAC 35 70 1 AGGGGGAAAA 0.568959 -11 GCGAAAAGGGAGTGATGTCATGGC 36 5 1 AAAGGGAGTG 0.355322 -131 GATCTGCAATAGGGGGAAGGGGGCA 37 117 1 AGGGGGAAGG 0.653809 -15 TCTCCCTGAAAAAGGGAGAGTAAACG 39 7 0 AAAGGGAGAG 0.828941 -116 TCTCCCTTTTTCAGGGAGAGTTTTTTTATG 39 18 1 TCAGGGAGAG 0.63567 -105 AATAGCCGCGACAAGGAGAGACAGGCTATA 42 183 1 ACAAGGAGAG 0.904792 -71 CTAGCCATAAAGGAGAAGAGAGAC 45 30 1 AGGAGAAGAG 0.781673 -14 ATTTTCTTTTTGGGGGAGAGAAATACTTGC 47 205 1 TGGGGGAGAG 0.826845 -96 CCCAATAATGAGGAGAAAAGCAAAGCACCA 48 79 1 AGGAGAAAAG 0.707089 -199 TTAAGGGAAGAAAGGAAGAGAAAAAGAGCG 48 143 0 AAAGGAAGAG 0.400145 -135 GGAAGACACTAGGCGGAAAGTAGTAGTTTA 49 239 1 AGGCGGAAAG 0.718953 -62 CTAAATTAAATGAAGGAAAGCAAAAAAAAG 49 269 0 TGAAGGAAAG 0.61908 -32 GTCATTCGGCAGGAGGAAAATCAAAATG 52 283 1 AGGAGGAAAA 0.539532 -18 ********** Masking position 5 Map Score: 14.8267 Number of sites scoring better than the average of aligned sites = 703 Number in coding regions = 504 Number in noncoding regions = 199 Number of orfs with sites within 600 bp upstream = 210 Fraction of orfs with sites within 600 bp upstream = 0.0337295 Motif number 7 ATAGACTCTATGCAAAAATTGAGAGGAGGTT 9 275 1 TGCAAAATTG 0.585367 -26 TTATTGTAATTGAAAAACGTGTGTGTTTTAT 16 16 0 TGAAAAAGTG 0.972466 -81 AACCTTCTGTTTAAAATGGTGCTATTATATA 17 163 1 TTAAAATGTG 0.631652 -50 AGGAATCTGGTGAAAAATGTGTGCTCCTGCC 18 73 1 TGAAAAAGTG 0.972466 -192 CGTTATTCACTGAAAAAGGTGTTTTGATTCT 18 158 0 TGAAAAAGTG 0.972466 -107 ATGTTGATGCTGGAAATCGTGTGAAAACAAT 21 114 1 TGGAAATGTG 0.717084 -48 AATAGACATGTGAAAATAGAGAAACGGAGTG 22 142 1 TGAAAATGAG 0.592362 -27 CGTCCCTATATGAAAAAAATGATTTCGTTGT 23 263 0 TGAAAAAATG 0.717047 -38 CCATCCCTCCTTAAAAAAGTGTAAAGGATGA 24 25 0 TTAAAAAGTG 0.804 -276 CTCTTCAGCCTGCAAAAGGTGAGAATGATCA 27 83 0 TGCAAAAGTG 0.91775 -35 TTGTTAAGGTTGAAAAAAGTAAGATAATACT 38 58 1 TGAAAAAGTA 0.68253 -34 GAGTGATACTTGAAAATGGTGAGATG 41 265 1 TGAAAATGTG 0.936566 -16 AGTGCGGATCTGAAAAACTTGAGCCTTACAA 43 47 1 TGAAAAATTG 0.817139 -221 GCGATAAAGGTGAAACATGTGTTTTTTTTCT 52 144 1 TGAAACAGTG 0.837452 -157 ******* *** Masking position 5 Map Score: 10.3126 Number of sites scoring better than the average of aligned sites = 323 Number in coding regions = 258 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 8 TTGCGTAAACAGCTTGGTAAAGGGGCCAATG 3 63 1 AGCTGGTAAA 0.621683 -26 AAATTCACATAGCGCGGAAAAACGGAAAAAG 18 199 0 AGCGGGAAAA 0.974704 -66 ATTGTGAAAAAGTGCGGAAAACGGTACACTT 22 38 0 AGTGGGAAAA 0.855828 -131 GGATAATACCAGCGTGGGGAAGTGCAGGTTG 23 103 0 AGCGGGGGAA 0.959322 -198 GCTGAGATAAAGCGCGGAAGAAACGCGCTTT 23 154 0 AGCGGGAAGA 0.960212 -147 ACAGAAGGAAAGCAGGGGGAAAAC 35 67 1 AGCAGGGGAA 0.698063 -14 GGAGCGCAGAAGCGGGAGAAAAAGCCTTTGC 41 110 0 AGCGGAGAAA 0.828813 -171 TTTTTAGTAAAGCTCGGGAGATTCGTTTTCC 42 135 1 AGCTGGGAGA 0.869332 -119 AGAGAAAAAGAGCGAGGAAGATGTAGGATGA 48 126 0 AGCGGGAAGA 0.960212 -152 CATTGCAATCAGCGCGGGAAACCCCAAATTG 49 84 1 AGCGGGGAAA 0.983986 -217 CATGTATGTAAGTGAGGAAAACCGATAAAAC 49 186 1 AGTGGGAAAA 0.855828 -115 **** ****** Masking position 1 Map Score: 8.33219 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 93 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 9 ATTTCCGGAATGTTGTCTAAAAATGAAAAAAAT 1 144 0 TGTTTCAAAA 0.904068 -157 ACAGATAGGATTTTGTCAAAAGAAGGTAACAAT 1 227 0 TTTTTCAAAA 0.79061 -74 AGCCGGCAGTTTTTTTAGAAAGAAAGCGAA 6 8 0 TTTTTAAAAA 0.891198 -187 CGGTCCATTATGTTATAAAAATTCTGATGCCTA 9 14 0 TGTTTAAAAT 0.670486 -287 AATATTTTCTTGTTCTATAAACAAAACGTCAAA 9 51 0 TGTTTAAAAA 0.951678 -250 GTAGAGTAATTGTTTTAAAACGAGGAGAGGGGC 13 18 1 TGTTTAAACA 0.750784 -29 AAAACGTGTGTGTTTTATAAAAA 16 1 0 TGTTTAAAAA 0.916767 -96 AAAATGGTGCTATTATATAAAAAAGCATCAAAA 17 175 1 TATTTAAAAA 0.66902 -38 TTTTGAAACTTTTTGAAGAAAAATGCAAAATTT 25 36 0 TTTTAAAAAA 0.606496 -265 ACATTCAATCTGTTCAATAAATAGCGCATTCAG 30 89 0 TGTTAAAAAA 0.794895 -163 ATTTGTCACATTTTCTAAAAAAAATGATGACTC 43 116 0 TTTTTAAAAA 0.887188 -152 AAAAATAAAATGTTTTCTAAATATGAATTACAT 46 124 1 TGTTTCAAAA 0.895664 -40 CCTTTAAGAGTGTTGTAAAAACATGAGGCTTAC 47 249 0 TGTTTAAAAA 0.942442 -52 TAAAGTTATCTTTTTTAAAAAAAGTTGACCAGC 52 90 1 TTTTTAAAAA 0.755642 -211 **** ** *** * Masking position 9 Map Score: 7.32058 Number of sites scoring better than the average of aligned sites = 200 Number in coding regions = 108 Number in noncoding regions = 92 Number of orfs with sites within 600 bp upstream = 99 Fraction of orfs with sites within 600 bp upstream = 0.0159011 Motif number 10 AATTCACATAGCGCGGAAAAACGGAAAAAG 18 199 0 GCGCGGAAAA 0.978944 -66 TTGTGAAAAAGTGCGGAAAACGGTACACTT 22 38 0 GTGCGGAAAA 0.938413 -131 CTGAGATAAAGCGCGGAAGAAACGCGCTTT 23 154 0 GCGCGGAAGA 0.974586 -147 TTTTAGTAAAGCTCGGGAGATTCGTTTTCC 42 136 1 GCTCGGGAGA 0.810869 -118 GCAAGGAAAAAGCCTAAAAC 45 1 1 GCAAGGAAAA 0.754262 -43 TAAATTGAATGTTAGGAAAAATCATTTTAT 46 82 1 GTTAGGAAAA 0.639491 -82 GAGAAAAAGAGCGAGGAAGATGTAGGATGA 48 126 0 GCGAGGAAGA 0.951263 -152 ATTGCAATCAGCGCGGGAAACCCCAAATTG 49 85 1 GCGCGGGAAA 0.957851 -216 ATGTATGTAAGTGAGGAAAACCGATAAAAC 49 187 1 GTGAGGAAAA 0.885785 -114 ********** Masking position 8 Map Score: 5.95427 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 117 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 11 TTCTTTCTAAAAAAACTGCCGGCTGACGCT 6 17 1 AAAAACTGCC 0.853384 -178 ATTTACATAAAAAAACTGCCAGCGTCAGCC 6 37 0 AAAAACTGCC 0.853384 -158 TCCTCTCGAGAAAAACAGGAGCTCACCCCT 9 104 0 AAAAACAGGA 0.931795 -197 ATTTTACCAAAAAAACAGGA 23 1 0 AAAAACAGGA 0.931795 -300 TGGTAAAATAAAAAACTGCATATCCTAAGG 23 22 1 AAAAACTGCA 0.83648 -279 TTATCTCAGCCAAAACAGCACCCCTAGTGC 23 175 1 CAAAACAGCA 0.650419 -126 AGAAATAAACAAAAACGGGCTCTCCAAAAT 24 162 0 AAAAACGGGC 0.784106 -139 AGAAAGGAGAAAAAACAGAAATTCTGCTAT 25 78 1 AAAAACAGAA 0.633502 -223 TATTGTAAGAAATAACAGGCATAAAGTCTA 25 212 0 AATAACAGGC 0.570829 -89 TGAGGGTGAAAAAAACTGAAATGGAGGTAA 25 275 1 AAAAACTGAA 0.633502 -26 TTCTGCCGCTAAAAACATGAAAAGTAGCCA 28 45 1 AAAAACATGA 0.661381 -116 CAGGAGTTTTCAAAACTGGCTTATGTCTGA 28 73 1 CAAAACTGGC 0.84971 -88 CAAACTCCTTCAAAACAGGATATGAAATAG 41 175 1 CAAAACAGGA 0.832465 -106 TCATTGCCGGAAAAACTGGCTACCCTATAG 41 235 0 AAAAACTGGC 0.939557 -46 TGCGGATCTGAAAAACTTGAGCCTTACAAT 43 49 1 AAAAACTTGA 0.661381 -219 AGAGTGTTGTAAAAACATGAGGCTTACTTA 47 246 0 AAAAACATGA 0.661381 -55 ACAATAGATAAACAACTGGCGATAAAGGTG 52 126 1 AACAACTGGC 0.663451 -175 ********** Masking position 5 Map Score: 12.0535 Number of sites scoring better than the average of aligned sites = 724 Number in coding regions = 596 Number in noncoding regions = 128 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 12 AATATGGTAGCGGCGGAGGGGATC 1 4 0 CGGCGAGGGG 0.968119 -297 GCTCCGTTTGCGGCTGAAGAGGCATTAGGAA 14 43 1 CGGCGAAGAG 0.966299 -63 GAAGCCCATTCGGCATCAGGGGAGGATCGGT 15 33 0 CGGCTCAGGG 0.87487 -268 TGTGCCAATATGGCACAAGGGTTTTCTA 21 8 0 TGGCCAAGGG 0.923658 -154 TGTGCCATATTGGCACAAGGGTTTTTATGTT 21 22 1 TGGCCAAGGG 0.923658 -140 ATTTGTGTTTCGGCAGAAGTGAAAATATTTT 21 72 0 CGGCGAAGTG 0.942064 -90 AAAAGTGTAAAGGATGAAGGGAAGTAGCGCT 24 11 0 AGGAGAAGGG 0.848023 -290 CACCTTTTGCAGGCTGAAGAGAACCCGGAGC 27 93 1 AGGCGAAGAG 0.918086 -25 GATCTGCAATAGGGGGAAGGGGGCA 37 117 1 AGGGGAAGGG 0.892127 -15 TTCTTTGAACCGGCCGCAGGGCCGGTTCTCC 52 13 0 CGGCGCAGGG 0.984279 -288 **** ****** Masking position 3 Map Score: 5.99284 Number of sites scoring better than the average of aligned sites = 201 Number in coding regions = 160 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 13 GAATCCCGTACGGGTCATCCTAACAAATCG 1 95 1 CGGGTCATCC 0.536205 -206 CCTAACAAATCGGTTTCTCTTGCAGAAGCC 1 113 1 CGGTTTCTCT 0.957024 -188 TGAAAAAAATCGGCTTCTGCAAGAGAAACC 1 124 0 CGGCTTCTGC 0.923041 -177 AAATCTTCGACGGTTTCTGCCTTGATATTC 1 190 0 CGGTTTCTGC 0.954916 -111 ACTTCCTACGCGGTTTCTTTCATAAATCAA 7 49 0 CGGTTTCTTT 0.685844 -37 AGGCGATGCCGGGTTTCTCTCCCCGTTACC 15 89 1 GGGTTTCTCT 0.684933 -212 CATGTTCACTCCGTTTCTCTATTTTCACAT 22 149 0 CCGTTTCTCT 0.874551 -20 TAAACAAAAACGGGCTCTCCAAAATTGAAA 24 157 0 CGGGCTCTCC 0.897572 -144 AAGCGCTCCGGGTTCTCTTCAGCCTGCA 27 100 0 CGGGTTCTCT 0.967621 -18 AGACCGACGACGGGTTCTGCCGCTAAAAAC 28 31 1 CGGGTTCTGC 0.966014 -130 TCCGGTTCCTCTATTCCTTGAT 30 240 0 CGGTTCCTCT 0.875551 -12 GCTTTTTCTCCCGCTTCTGCGCTCCGAGCA 41 116 1 CCGCTTCTGC 0.789683 -165 GGCCGCAGGGCCGGTTCTCCCT 52 3 0 CCGGTTCTCC 0.945631 -298 ********** Masking position 8 Map Score: 8.6063 Number of sites scoring better than the average of aligned sites = 359 Number in coding regions = 323 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 33 Fraction of orfs with sites within 600 bp upstream = 0.00530035 Motif number 14 TCCAAGCAAAGAAGAAGCATAGGCTCTGCA 4 22 0 GAAGAAGCAT 0.954943 -82 GTTTGCGGCTGAAGAGGCATTAGGAAAGCT 14 48 1 GAAGAGGCAT 0.951971 -58 AAGAGGAAAGGAAGAAGCAG 20 14 1 GAAGAAGCAG 0.799651 -10 TAATAGATGATAAGAATCATTTTGTAAACA 23 236 1 TAAGAATCAT 0.638155 -65 AATATTCAAGGAAGAGGCATAGAAGGGAGA 24 189 0 GAAGAGGCAT 0.951971 -112 TTATTTCTTACAATAAGCATATAGTTTTAC 25 227 1 CAATAAGCAT 0.619126 -74 TATCATTAAACAAGAATCATCTATTTCTCC 27 11 1 CAAGAATCAT 0.875109 -107 AACAATTTATGAAGAGTCATCATTTTTTTT 43 103 1 GAAGAGTCAT 0.936588 -165 GAAATAACAACAAGAATCATGAGGTGAGAG 43 244 1 CAAGAATCAT 0.875109 -24 TGAATGTTAGGAAAAATCATTTTATTTTCT 46 87 1 GAAAAATCAT 0.607578 -77 GAAACTCCTAGAATAGTCATGAT 50 4 0 GAATAGTCAT 0.718568 -65 ********** Masking position 5 Map Score: 4.77464 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 130 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 15 CGTCCTATGCAAAGGACGAGGGTCTCGCGGTA 15 190 0 AAGACGAGGG 0.954845 -111 CGTCCTTTGCATAGGACGGGGGTTTTTTGTGT 15 204 1 AAGACGGGGG 0.986832 -97 TTGTATACGGAAAGCACTAGGGGTGCTGTTTT 23 186 0 AAGACTAGGG 0.856455 -115 CCAAAATTGAAAAGCCCGGGGGTCTACTGAAA 24 137 0 AAGCCGGGGG 0.984081 -164 GAAAGAGTGGAATGACCGGGGGTTAAC 26 29 1 ATGCCGGGGG 0.945006 -17 AAAGGCTCAGAGCACTGGCGGATCACGGTA 37 9 1 AAGACTGGCG 0.928557 -123 AAGAAGCACTAGAGGCCGGGCGTTCTTTTTTC 41 61 0 AAGCCGGGCG 0.974356 -220 ATGAAATAGTATTGGACGAGAGCTTTTTGGTG 41 196 1 ATGACGAGAG 0.615904 -85 ATTTTTTAGTAAAGCTCGGGAGATTCGTTTTC 42 133 1 AAGTCGGGAG 0.80932 -121 GACAATAGATAAACAACTGGCGATAAAGGTGA 52 125 1 AACACTGGCG 0.627281 -176 * ** ******* Masking position 1 Map Score: 2.99208 Number of sites scoring better than the average of aligned sites = 106 Number in coding regions = 90 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925