AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icpxR_ecoli_bsub_300.orf -g0.5 -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 = 0.5 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 dgt 83 deoxyguanosine triphosphate triphosphohydrolase #2 htrA 129 periplasmic serine protease Do; heat shock protein HtrA #3 tig 300 trigger factor; a molecular chaperone involved in cell division #4 clpP 245 ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5 #5 clpX 125 ATP-dependent specificity component of clpP serine protease, chaperone #6 lon 187 DNA-binding, ATP-dependent protease La; heat shock K-protein #7 hupB 208 DNA-binding protein HU-beta, NS1 (HU-1) #8 ybaU 191 putative protease maturation protein #9 cydD 122 ATP-binding component of cytochrome-related transport, Zn sensitive #10 trxB 300 thioredoxin reductase #11 motA 126 proton conductor component of motor; no effect on switching #12 flhD 300 regulator of flagellar biosynthesis, acting on class 2 operons; transcriptional initiation factor #13 ygjQ 76 orf, hypothetical protein #14 ygjR 60 orf, hypothetical protein #15 ygjT 283 putative transport protein #16 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #17 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #18 ftsY 149 cell division membrane protein #19 yihD 69 orf, hypothetical protein #20 yihE 77 orf, hypothetical protein #21 cpxR_b3913 146 cpxR: transcriptional regulator in 2-component system, b3913: orf, hypothetical protein #22 yjdA 300 putative vimentin #23 yjcZ 29 orf, hypothetical protein #24 proP 263 low-affinity transport system; proline permease II #25 spoIIE 300 serine phosphatase #26 yabS 84 similar to hypothetical proteins #27 yabT 88 yabT #28 yacA 103 similar to cell-cycle protein #29 ftsH 97 cell-division protein and general stress protein (class III heat-shock) #30 yacB 194 similar to hypothetical proteins #31 yacC 85 similar to hypothetical proteins #32 yacD 46 similar to protein secretion PrsA homolog #33 ybcO 300 ybcO #34 ybcP 66 ybcP #35 ybcQ 43 similar to hypothetical proteins #36 ybdB 64 similar to ABC transporter (permease) #37 ybdD 46 ybdD #38 ybdE 105 similar to hypothetical proteins #39 yczA 300 yczA #40 ycbL 96 similar to two-component response regulator [YcbM] #41 yclJ 212 similar to two-component response regulator [YclK] #42 yerE 264 similar to hypothetical proteins #43 yerF 61 similar to ATP-dependent DNA helicase #44 yerG 23 similar to DNA ligase #45 yerI 161 yerI #46 htrA 168 serine protease Do (heat-shock protein) #47 ykoG 300 similar to two-component response regulator [YkoH] #48 motA 300 motility protein A #49 flgB 300 flagellar basal-body rod protein #50 fliF 45 flagellar basal-body M-ring protein #51 fliH 117 flagellar assembly protein #52 fliK 160 fliK #53 flgE 21 flagellar hook protein #54 fliL 251 flagellar protein #55 fliM 33 flagellar motor switch protein #56 cheY 25 two-component response regulator #57 flhA 32 flagella-associated protein #58 cheW 21 cheW #59 resD 80 two-component response regulator #60 resC 135 essential protein similar to cytochrome c biogenesis protein #61 resA 131 essential protein similar to cytochrome c biogenesis protein #62 ypuL 91 similar to hypothetical proteins #63 dacB 122 D-alanyl-D-alanine carboxypeptidase (penicillin-binding protein 5*) #64 ypuI 54 similar to hypothetical proteins from B. subtilis #65 ypuG 280 similar to hypothetical proteins #66 ppiB 253 peptidyl-prolyl isomerase #67 yrkP 267 similar to two-component response regulator [YrkQ] #68 phoP 211 two-component response regulator #69 citH 43 malate dehydrogenase #70 citC 163 isocitrate dehydrogenase #71 citZ 300 citrate synthase II #72 yvqA 277 similar to two-component response regulator [YvqB] #73 yvrI 300 yvrI #74 cydA 300 cytochrome bd ubiquinol oxidase (subunit I) #75 yyxA 68 alternate gene name: yycK; similar to serine protease Do #76 yycJ 21 yycJ #77 yycF 300 similar to two-component response regulator [YycG] Motif number 1 AATTGCTGTGTTCTTCAGATTCGTTTTATAGCCT 2 75 0 TTCTTCTTCT 0.756305 -55 TACAGCAGGTTTTTTCAATTTTATCCAGGAGACG 4 219 1 TTTTTCTTTT 0.897586 -27 TCTTCTCTTCCTCTTTATAATTTATATC 7 191 0 CTCTTCTTTT 0.78311 -18 TGGTGTCGCCTTCTTTACTTTTGTTACTGATTTG 9 16 0 TTCTTTTTTT 0.756527 -107 AAGAATACTGTTTTTTTTCTTCCTCGAATGTTTT 10 11 1 TTTTTTTTCT 0.812885 -290 GTCATACTCTTTTTTTACGTCTGTAAATTCCCTA 10 238 1 TTTTTTTCTT 0.834825 -63 TCACTTGCTTTTTTTCTGCTCTGTTTGTTAAGGA 16 241 1 TTTTTCTCTT 0.877667 -30 AGAAAATAATCTTTTTGCCTCTATTTATTATTTA 22 60 1 CTTTTTTCTT 0.805348 -241 CAGAAGCCGATTTTTTTCATTTTTAGACAACATT 25 135 1 TTTTTTTTTT 0.860611 -166 AGGACGGGGGTTTTTTGTGTTTCTTAAAGGAGGT 39 216 1 TTTTTTTTTT 0.860611 -85 TACGTGTGTGTTTTTTGATTTTGTAAAGGTTAGG 40 54 1 TTTTTTTTTT 0.860611 -43 AGATTAACGGCTTTTTCCGTTTTTCCGCGCTATG 42 189 1 CTTTTTTTTT 0.834825 -76 TTCCCATAATCTTTTCATTTTTATCCCACAGTTT 46 69 1 CTTTTCTTTT 0.877667 -100 GAATTTCTGTTTTTTCTCCTTTCTTTTCGGCATT 49 68 0 TTTTTCTTTT 0.897586 -233 GAAAGTTTTCTTTTTTCCTTTTGTGGAGAAATAG 51 31 0 TTTTTTTTTT 0.860611 -87 CTCCTGGCTACTTTTCATGTTTTTAGCGGCAGAA 52 45 0 CTTTTCTTTT 0.877667 -116 CCAGAACAGCTTCTTCATCTTCTTTTACTACAAA 54 161 0 TTCTTCTTCT 0.756305 -91 GCTGTTTTTTCTCTCCTTTTAAATCGAA 57 15 0 TTTTTTTCCT 0.780521 -18 TTGGCCTGCCCTTTTTATCTTTATTCCCGCGTAT 60 108 0 CTTTTTTTTT 0.834825 -28 ACAAACAAGCTTTTTCAAATTCCTATGCCAAATC 62 28 0 TTTTTCTTCT 0.860467 -64 CCGGGCGTTCTTTTTTCCTTTTATCCCTTCTATG 65 44 0 TTTTTTTTTT 0.860611 -237 AAACCTGAATCTCTTTATCTCCGTCTAACCTAAC 66 92 0 CTCTTTTCCT 0.594332 -162 GTCTCTCTTCTCCTTTATGGCTAGTTTT 69 26 0 CTCTTCTTTT 0.78311 -18 TATAATTTTTTTTTTCCATTCTGTGATTTCCCCG 71 39 0 TTTTTCTCTT 0.877667 -262 TTCCTCGCTCTTTTTCTCTTCCTTTCTTCCCTTA 72 138 1 TTTTTCTCCT 0.834659 -140 TTCACATATTCTTTTCATTTTTATCCCACAATGT 72 188 0 CTTTTCTTTT 0.877667 -90 GGCTCTTCACATCCTTTCAACGTCAT 72 262 0 CTCTTCTCCT 0.67529 -16 TAGTTTACTTTTTTTTGCTTTCCTTCATTTAATT 73 262 1 TTTTTTTTCT 0.812885 -39 TTGAGCAATATTTTTTTCGTCTATTTTGTGAATT 74 202 1 TTTTTTTCTT 0.834825 -99 TAAACCTTTATTTTTTTTATCTTTTGACCTTAAA 77 174 1 TTTTTTTCTT 0.834825 -127 ****** *** * Masking position 5 Map Score: 27.1605 Number of sites scoring better than the average of aligned sites = 357 Number in coding regions = 250 Number in noncoding regions = 107 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 2 GTATAGCGGCACAGTTGCGCCTCTGGCA 5 5 0 ACAGTCCCCT 0.718685 -121 TAAAGGGGAGATAAAATCCCCCCTTTTTGGTTAA 6 33 0 ATAAACCCCT 0.912586 -155 CTTGAACTTCGTCACATCCCCACTGGGGACAACG 8 12 0 GTCAACCCCT 0.808247 -180 AGGCACATCAGTAGATGCGCCCTTGAACTTCGTC 8 33 0 GTAGTCCCTT 0.653478 -159 ATTATTGAAAATCGCAGCCCCCCTCCGTTGTATG 12 60 1 ATCGACCCCT 0.861521 -241 GCTGCAATAAGCAGAACCACCTTTTTGGTTTAAT 12 177 0 GCAGACCCTT 0.647231 -124 GACCGGCAATGAAGTTACTCCCCTTTGCAGGTAA 15 81 0 GAAGTCCCCT 0.645347 -203 AGGATAATATACAAAATCCCCCTTACTTCGACAA 33 201 1 ACAAACCCTT 0.819631 -100 ATAAAATCCCCCTTAAGAGAAAAT 34 53 0 ATAAACCCTT 0.891099 -14 AAAAGAGCCCCTCTCCTCGTTTTA 37 33 0 AAAAACCCCT 0.887564 -14 TCCTTCAGGAATAGTTGCTCCGTTTGCGGCTGAA 38 27 1 ATAGTCCCTT 0.782404 -79 GCAGGTGTGAACCGATCCTCCCCTGATGCCGAAT 39 23 1 ACCGTCCCCT 0.663544 -278 ATTTTTATTGATAAGACCGCCTCTGGGGCGCGTC 41 31 1 ATAAACCCCT 0.912586 -182 GCTTTTTTATATAATAGCACCATTTTAAACAGAA 41 167 0 ATAAACCCTT 0.891099 -46 TGAAAAAAGAATCAAAACACCTTTTTCAGTGAAT 42 151 1 ATCAACCCTT 0.863326 -114 TTCCAGCATCAACATACCTCCCCTTGATTTGTGT 45 95 0 AACAACCCCT 0.859057 -67 AAGCGCACAAAAAAATACACCATTCGGTCAACCT 47 75 1 AAAATCCCTT 0.77937 -226 TATCTCAGCCAAAACAGCACCCCTAGTGCTTTCC 47 176 1 AAAAACCCCT 0.887584 -125 GAGGCGAGTAATCGCTTCTCCGCTGTTTTATGAT 54 21 1 ATCGTCCCCT 0.780278 -231 GCCAAATCTAAAAAAAACGCCGTTT 62 2 0 AAAAACCCTT 0.860889 -90 ATCAATACTCCTTTCCCATTTATC 67 1 1 ATCATCCCTT 0.782875 -267 AGGACATTCCGACAATTCGCCTTTTACATCATTT 68 98 0 GACATCCCTT 0.587839 -114 TGATTTCCCCGAAAAAACGCCTTTATTTGCGGGT 71 16 0 GAAAACCCTT 0.763967 -285 ATATAACATCTCCTTTTCAATAAATT 71 285 0 ATAAACCCTT 0.891099 -16 GATCCATAGGAAAATACCTCCCTTCTTTTTCTGC 73 149 1 AAAAACCCTT 0.860889 -152 **** * * ** ** Masking position 14 Map Score: 20.2634 Number of sites scoring better than the average of aligned sites = 279 Number in coding regions = 230 Number in noncoding regions = 49 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 3 AGATTTTATGAAAAACGGCCTGCGGGCCGT 3 11 1 AAAAACGGCC 0.964937 -290 CCAGACAAAACAAAACGGCCCGCAGGCCGT 3 25 0 CAAAACGGCC 0.72458 -276 TTCATGACAAAAAAAAGCCCACCACCTGGC 4 55 0 AAAAAAGCCC 0.772895 -191 ATAAAATTGAAAAAACCTGCTGTACCGATT 4 213 0 AAAAACCTGC 0.628392 -33 AAGGGGAGATAAAATCCCCCCTTTTTGGTT 6 35 0 AAAATCCCCC 0.904335 -153 TAAATGATGAATAAACGCCCCTGTTAATGA 10 106 0 ATAAACGCCC 0.663094 -195 TTACACATAAAAAAACGGCCAACGTCGGAA 15 255 0 AAAAACGGCC 0.964937 -29 AAAATCACCTAAAATCGCCCGCTCGCGGCA 16 51 0 AAAATCGCCC 0.883691 -220 TTCTTTCTAAAAAAACTGCCGGCTGACGCT 30 17 1 AAAAACTGCC 0.872071 -178 ATTTACATAAAAAAACTGCCAGCGTCAGCC 30 37 0 AAAAACTGCC 0.872071 -158 TTCTCAAATTAAAAACCCGCTAAAGAGC 32 9 0 AAAAACCCGC 0.924074 -38 GATAATATACAAAATCCCCCTTACTTCGAC 33 203 1 AAAATCCCCC 0.904335 -98 ATAAAATCCCCCTTAAGAGAAA 34 55 0 AAAATCCCCC 0.904335 -12 AAGAAACACAAAAAACCCCCGTCCTATGCA 39 211 0 AAAAACCCCC 0.974337 -90 AGAAATAAACAAAAACGGGCTCTCCAAAAT 48 162 0 AAAAACGGGC 0.898188 -139 CCAAATCTAAAAAAAACGCCGTTT 62 5 0 AAAAAACGCC 0.792478 -87 AAAAGGAAAAAAGAACGCCCGGCCTCTAGT 65 56 1 AAGAACGCCC 0.744709 -225 TCATTGCCGGAAAAACTGGCTACCCTATAG 65 235 0 AAAAACTGGC 0.686054 -46 AATAAAAACCTCCCAGTATGTAA 70 151 0 AAAAACCTCC 0.840638 -13 CAAAAACCCGCAAATAAAGGC 71 2 1 AAAAACCCGC 0.924074 -299 GATTTCCCCGAAAAAACGCCTTTATTTGCG 71 19 0 AAAAAACGCC 0.792478 -282 ********** Masking position 4 Map Score: 21.0069 Number of sites scoring better than the average of aligned sites = 456 Number in coding regions = 323 Number in noncoding regions = 133 Number of orfs with sites within 600 bp upstream = 124 Fraction of orfs with sites within 600 bp upstream = 0.0199165 Motif number 4 CGTTGTCCCCAGTGGGGATGTGACGAAGTTC 8 12 1 AGGGGGATGT 0.483666 -180 TGCGAAAACATTCGAGGAAGAAAAAAAACAG 10 18 0 TTGAGGAAGA 0.743447 -283 TGGTCAACAGTGGAAGGATGATGTC 11 112 1 TGAAGGATGA 0.691905 -15 CCTTAACGAAAGGGGGGAGGTCGATTTTAGG 13 47 0 AGGGGGAGGT 0.849138 -30 CAAAATTTGCTTTAAGGAAGAATTTTCT 22 283 1 TTAAGGAAGA 0.682095 -18 ACCTGCTCATTGTGAGGAGGACATT 28 89 1 TGGAGGAGGA 0.947985 -15 GTGCTTACTGTGGGAGGAGGTAAGGA 29 82 1 TGGAGGAGGT 0.960156 -16 ATGCAAAAATTGAGAGGAGGTTTACTT 33 284 1 TGGAGGAGGT 0.960156 -17 TTTGTGTTTCTTAAAGGAGGTGACGGCCAAT 39 229 1 TTAAGGAGGT 0.885305 -72 CAGATGAGTTAGAAAGGAGGATATCAA 39 284 1 AGAAGGAGGA 0.865645 -17 GTGTAAAGGATGAAGGGAAGTAGCGCT 48 7 0 TGAGGGAAGT 0.762359 -294 TTTACACTTTTTTAAGGAGGGATGGAACATG 48 31 1 TTAAGGAGGG 0.549029 -270 TCATGAAATATTCAAGGAAGAGGCATAGAAG 48 194 0 TTAAGGAAGA 0.682095 -107 CCATTCGAGGAGGTGTCTCAC 58 4 1 TTGAGGAGGT 0.912472 -18 TAAAAGCACATTAAAGGAGGAAGCACC 65 7 0 TTAAGGAGGA 0.853752 -274 GCTTGTGAAATTGAAGGAGGTCAAACTGCT 66 10 0 TTAAGGAGGT 0.885305 -244 AGAGAAAAAGAGCGAGGAAGATGTAGGATGA 72 126 0 AGGAGGAAGA 0.761808 -152 GGTTAAGGGAAGAAAGGAAGAGAAAAAGAGC 72 144 0 AGAAGGAAGA 0.703093 -134 ATAATGACGTTGAAAGGATGTGAAGAGCC 72 259 1 TGAAGGATGT 0.748073 -19 TCAGGTTTTTATAGAGGAAGTCGTAAAACAG 73 120 0 ATGAGGAAGT 0.646575 -181 CTGCAGAAAAAGAAGGGAGGTATTTTCCTAT 73 154 0 AGAGGGAGGT 0.806482 -147 CGCACTCCGGTGAGGGGAGGTTTCAATAAAG 77 64 1 TGGGGGAGGT 0.921804 -237 ** ******** Masking position 8 Map Score: 16.3184 Number of sites scoring better than the average of aligned sites = 108 Number in coding regions = 77 Number in noncoding regions = 31 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 5 GAGGAAAAATTAAAGGGGAGATAAAATCCC 6 47 0 TAAAGGGGAG 0.84761 -141 GAAATTAAACTAAGAGAGAGCTCT 6 174 1 TAAGAGAGAG 0.619301 -14 TCGAAGATGAAAAAGGCGTGCTACATTGAC 14 27 1 AAAAGGCGTG 0.697618 -34 TAAAAGCGTGTTATACTCTT 17 1 1 TAAAAGCGTG 0.297983 -244 CAAACATGCGTCAGGGGGTGTAAAACAACG 21 68 1 TCAGGGGGTG 0.545452 -79 CGACGGCCGCAAAAGGGGAGCGGGAATTGC 24 193 0 AAAAGGGGAG 0.891768 -71 ATGGTTACATAAAAAGGGAGGCTGAGAG 42 9 0 AAAAAGGGAG 0.691892 -256 TTTTTCATAAAAAAAGAGAGCATATGGCAG 42 128 0 AAAAAGAGAG 0.7322 -137 GAAACACAAATCAAGGGGAGGTATGTTGAT 45 92 1 TCAAGGGGAG 0.796976 -70 CAGGCTTATATCAGGGCGAGAAATGTAGTT 49 111 1 TCAGGGCGAG 0.736371 -190 TTCAGCCTGCAAAAGGTGAGAATGATCAAT 51 81 0 AAAAGGTGAG 0.560373 -37 CGAAACACAAGGAGAGAGATAGATT 56 7 1 ACAAGGAGAG 0.876239 -19 TTTTCGATTTAAAAGGAGAGAAAAAACAGC 57 13 1 AAAAGGAGAG 0.909353 -20 GCGAAAAGGGAGTGATGTCATGGC 60 5 1 AAAGGGAGTG 0.754095 -131 TCTCCCTGAAAAAGGGAGAGTAAACG 63 7 0 AAAGGGAGAG 0.898392 -116 TCTCCCTTTTTCAGGGAGAGTTTTTTTATG 63 18 1 TCAGGGAGAG 0.808154 -105 AATAGCCGCGACAAGGAGAGACAGGCTATA 66 183 1 ACAAGGAGAG 0.876239 -71 TAAAAAGAGAGAAAGGCTTGC 68 2 1 AAAAAGAGAG 0.7322 -210 GAATAACCGTTAAAGGAGTGTAAGAAC 72 8 0 TAAAGGAGTG 0.701384 -270 AGGAAGAGAAAAAGAGCGAGGAAGATGTAG 72 131 0 AAAGAGCGAG 0.615069 -147 ********** Masking position 3 Map Score: 13.9114 Number of sites scoring better than the average of aligned sites = 213 Number in coding regions = 139 Number in noncoding regions = 74 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 6 AAAATTGCTGTGTTCTTCAGATTCGTTTTATAGCCTG 2 74 0 TTTCTGATTT 0.511169 -56 TTTTGTGATCTGTTTAAATGTTTTATTGCAATCGGTT 16 77 1 TTTTAGTTTT 0.507102 -194 ATTTAGAATCTCTTCACTTGCTTTTTTTCTGCTCTGT 16 228 1 TTTCAGCTTT 0.88011 -43 GTGCGTAATTTATTCACAAGCTTGCATTGAACTTGTG 17 107 1 TTTCAGCTTT 0.88011 -138 TCAATCGATATCTTCTGGCGCTTCAGTGGTAGCAACA 17 208 0 TTTCTGCTTT 0.951885 -37 AAGATTATTTTCTTTTTGCGTTTCCTTTCAAATGAAA 22 36 0 TTTTTGTTTT 0.734929 -265 TATCATTTCTTTTTTATGGCTTCAGTCAAAAAGGCG 36 10 1 TTTTTGCTTT 0.954044 -55 ATCCTCCGGTTGTTTTGATGCTTTTTTATATAATAGC 41 183 0 TTTTTGCTTT 0.954044 -30 CTGAAAAAGGTGTTTTGATTCTTTTTTCATAAAAAAA 42 143 0 TTTTTTCTTT 0.507275 -122 ACCAAATCCTTTTTTACTAGCTTGTCTATGGTTAATA 48 267 0 TTTTAGCTTT 0.885101 -34 GAAATTCTGCTATTTTCAGGCTTATATCAGGGCGAGA 49 95 1 TTTTTGCTTT 0.954044 -206 TCAGGGAGAGTTTTTTTATGTTTGCTTCCAGAAATAT 63 28 1 TTTTTGTTTT 0.734929 -95 AGCAAAGGCTTTTTCTCCCGCTTCTGCGCTCCGAGCA 65 109 1 TTTCTGCTTC 0.677192 -172 ACATAACAAATTTTTATAAGCTTATTTAAGTTTAAGC 71 119 0 TTTTAGCTTT 0.885101 -182 AAACATATTCTATTTTGGTGCTTTGCTTTTCTCCTCA 72 87 0 TTTTTGCTTT 0.954044 -191 TCCTCGCTCTTTTTCTCTTCCTTTCTTCCCTTAACCA 72 139 1 TTTCTCCTTT 0.727971 -139 TAGTAGTTTACTTTTTTTTGCTTTCCTTCATTTAATT 73 259 1 CTTTTGCTTT 0.687631 -42 GATTTTTGTCTATTTTGTTGCTTATTTATGTCGGC 74 9 0 TTTTTGCTTT 0.954044 -292 CATGTGTTTTTTTTCTAAACCTTTATTTTTTTTATCT 77 159 1 TTTCTCCTTT 0.727971 -142 * **** **** * Masking position 12 Map Score: 10.2871 Number of sites scoring better than the average of aligned sites = 147 Number in coding regions = 123 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 7 GGCGTTGAATGTGGGGGAAACATCCCCATATA 6 84 1 GGGGGAAACA 0.852869 -104 TCTGCGTCTTGTGGGCTGACAATTGCCCCCGT 8 90 1 GGGGTGACAA 0.624156 -102 GAAAACATTCGAGGAAGAAAAAAAACAGTATT 10 14 0 GGGAGAAAAA 0.707163 -287 ACATGCGTCAGGGGGTGTAAAACAACGTAAAG 21 71 1 GGGGGTAAAA 0.901357 -76 TTAAACACTGGTAGGGTAAAAAGGTCATTAAC 24 69 1 GAGGTAAAAA 0.706405 -195 TCTTTGCTTGGAGGGGTTGAAAGTGTTAGGAT 28 40 1 GGGGTTGAAA 0.684781 -64 CTCTTGGTAACGGGGAGAGAAACCCGGCATCG 39 92 0 CGGGGAGAAA 0.828452 -209 TTTTGTATAGGCGGGTGAACAAATT 43 47 1 GGGGGAACAA 0.919124 -15 AACAAAAACTGTGGGATAAAAATGAAAAGATT 46 76 0 GGGGTAAAAA 0.943913 -93 AGGCTTATATCAGGGCGAGAAATGTAGTTCTA 49 112 1 CGGGGAGAAA 0.828452 -189 CAAGGATATTGAGGGTGAAAAAAACTGAAATG 49 266 1 GGGGGAAAAA 0.979877 -35 CAGAAGGAAAGCAGGGGGAAAAC 59 68 1 GAGGGGAAAA 0.746414 -13 GAGCGCAGAAGCGGGAGAAAAAGCCTTTGCTT 65 108 0 GGGGGAAAAA 0.979877 -173 TTTTCTTTTTGGGGGAGAGAAATACTTGCATC 71 206 1 GGGGGAGAAA 0.971011 -95 AACAAACATTGTGGGATAAAAATGAAAAGAAT 72 183 1 GGGGTAAAAA 0.943913 -95 TGGTTATATTGTGGGTTAGAAACTCCTAGAAT 75 20 0 GGGGTAGAAA 0.920488 -49 AAGTCATTCGGCAGGAGGAAAATCAAAATG 77 281 1 GAGGGGAAAA 0.746414 -20 * *** ****** Masking position 12 Map Score: 14.2604 Number of sites scoring better than the average of aligned sites = 317 Number in coding regions = 273 Number in noncoding regions = 44 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 8 GACTCATAAAAGTGATGCCGCTATAATGCCG 3 139 1 AGTGTGCCGC 0.883875 -162 GAATTTAGCGCGTTATGCTGCGTAAA 4 6 0 CGTTTGCTGC 0.816912 -240 CTTGAAATATGGTGATGCCGTACCCATAACA 4 148 1 GGTGTGCCGT 0.814577 -98 CCGCTTACAGCGTTGTGCCGCCCTGGATAAG 5 38 0 CGTTTGCCGC 0.976508 -88 CTTCTTTGTTCTTTGTGCCGCACACGACGAC 5 93 0 CTTTTGCCGC 0.816912 -33 AAACCAAAAAGGTGGTTCTGCTTATTGCAGC 12 180 1 GGTGTTCTGC 0.647852 -121 CACCGCACCCCGTGATGTCGCCGGGAAGCCC 12 248 0 CGTGTGTCGC 0.768533 -53 ATTTTTATGCGGTTTCACCGCACCCCGTGAT 12 263 0 GGTTCACCGC 0.765222 -38 TGGCATAGCGGGATATGCCGCGAGCGGGCGA 16 36 1 GGATTGCCGC 0.834294 -235 CGATGATTTTGGTGGCGCCGCTTACAAGCTT 20 11 0 GGTGCGCCGC 0.954219 -67 GATTCGAACCCGTGTTACCGCCGTGAAAGGG 25 69 0 CGTGTACCGC 0.928335 -232 TGTTAATAAAGGTGGTACCGCGAGACCCTCG 39 175 1 GGTGTACCGC 0.944871 -126 CGGCTTTTTCCGTTTTTCCGCGCTATGTGAA 42 196 1 CGTTTTCCGC 0.901731 -69 ATCAAAGCGCGTTTCTTCCGCGCTTTATCTC 47 151 1 GTTTTTCCGC 0.565823 -150 ACCGACGACGGGTTCTGCCGCTAAAAACATG 52 33 1 GGTTTGCCGC 0.982142 -128 **** ****** Masking position 10 Map Score: 9.85874 Number of sites scoring better than the average of aligned sites = 963 Number in coding regions = 916 Number in noncoding regions = 47 Number of orfs with sites within 600 bp upstream = 44 Fraction of orfs with sites within 600 bp upstream = 0.00706714 Motif number 9 AATACGCTTCCCCGTAAGCGCATGGTAAACTATG 1 42 0 CCGTCGCATG 0.975495 -42 CGCACAAAGGCCCGTCACCGCCAGGTGGTGGGCT 4 36 1 CCGTCGCCAG 0.989393 -210 ATAAAGGCGACCCATAGTCGCATGGTGTCGCCTT 9 38 0 CCATCGCATG 0.961483 -85 GCCCCAATCGCGCGTTAACGCCTGACGACTGAAC 11 69 1 CCGTCGCCTG 0.989393 -58 TAACTTAATTCACATCACCGCCTGCAAGTATGTG 18 37 0 CCATCGCCTG 0.983192 -113 TACAATCAAACCAGTTGACGCCTGAATTGGGCAG 24 100 0 CAGTCGCCTG 0.890706 -164 GCAGAGTTGGCCCATTTCCGCAAACGCCAGAAAA 24 230 0 CCATCGCAAA 0.685624 -34 TTCATATATTCCCATCTTCGCCAGAAGAAATTTG 26 26 0 CCATCGCCAG 0.983192 -59 TCTGAGAATCCTCGTATTCTCCAGGAGGAATGAA 26 60 1 CCGTCTCCAG 0.890706 -25 AGAGGCTAACCTCATTGACGCAAGCCAGCCTCCA 70 19 0 CCATCGCAAG 0.961483 -145 * *** ****** Masking position 5 Map Score: 8.31707 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 154 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 AAAAACAGGGCTGGCAGGCTAATTCGGGCT 7 35 1 CTGGCAGGCT 0.666327 -174 CAAAAAAAGGCTGGCAAGCCCGAATTAGCC 7 51 0 CTGGCAAGCC 0.930193 -158 CCCCTTAATAAGGGCAAGCCCGATCCGCCA 7 96 0 AGGGCAAGCC 0.930193 -113 TTGTAAGGGGATGGCTGGCCTGATATAACT 7 128 1 ATGGCTGGCC 0.787636 -81 GTGATGTCGCCGGGAAGCCCCGGTAAAAAA 12 238 0 CGGGAAGCCC 0.934755 -63 ATCCGGTCACCGGGCAACCCGAAAGGAATA 15 144 1 CGGGCAACCC 0.968163 -140 AATTAGGTAAAGGGATGGCCTTGTTCTTGA 16 193 1 AGGGATGGCC 0.714333 -78 CCCGTTTGAACGGGCAGCCCTTTACACTGA 54 63 1 CGGGCAGCCC 0.983004 -189 AAAGATAAAAAGGGCAGGCCAAACCG 60 120 1 AGGGCAGGCC 0.962041 -16 GCCGGAAAAACTGGCTACCCTATAGTATAA 65 230 0 CTGGCTACCC 0.81652 -51 GCAATCAGCGCGGGAAACCCCAAATTGCCG 73 88 1 CGGGAAACCC 0.882802 -213 ********** Masking position 9 Map Score: 7.50111 Number of sites scoring better than the average of aligned sites = 437 Number in coding regions = 413 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 11 TCTCCTGGATAAAATTGAAAAAACCTGCTGT 4 220 0 AAAATTGAAA 0.598336 -26 ATCAGTAACAAAAGTAAAGAAGGCGACACCA 9 19 1 AAAGTAAAAA 0.330515 -104 TGTAAAAAGTAAAGTAGAGAAACTATTCAAA 30 160 1 AAAGTAGAAA 0.697356 -35 TAACCCTTTAAAAATAGAAAAGCTGACAAGC 33 136 0 AAAATAGAAA 0.921921 -165 TAGACATGTGAAAATAGAGAAACGGAGTGAA 46 144 1 AAAATAGAAA 0.921921 -25 TTTTTTTGGTAAAATAAAAAACTGCATATCC 47 16 1 AAAATAAAAA 0.716698 -285 TTATGATGTTAAAATAAAAAATTGTATACGG 47 208 0 AAAATAAAAA 0.716698 -93 CGGGCTCTCCAAAATTGAAAAGCCCGGGGGT 48 146 0 AAAATTGAAA 0.598336 -155 ACCTAGTTGCAAAATAGATAATTGTGAGGAC 49 161 1 AAAATAGAAA 0.921921 -140 CCACAAAAGGAAAAAAGAAAACTTTCTATAC 51 39 1 AAAAAAGAAA 0.705558 -79 TTTGAAAATTAAAATAAAGAAAGTAGGCATA 66 230 1 AAAATAAAAA 0.716698 -24 TAAAAAGAGAGAAAGGCTTGCTT 68 3 1 AAAAGAGAAA 0.584302 -209 AAGATGACATAAAATAGAGAAATAGGATGTC 68 164 1 AAAATAGAAA 0.921921 -48 GCAAAGCACCAAAATAGAATATGTTTGATCA 72 98 1 AAAATAGATA 0.457929 -180 AATAAGCAACAAAATAGACAAAAATCCGTCA 74 20 1 AAAATAGAAA 0.921921 -281 AGTAATTCACAAAATAGACGAAAAAAATATT 74 208 0 AAAATAGAGA 0.555962 -93 AACTTTTTTTAAAAAAGATAACTTTATTGAA 77 85 0 AAAAAAGAAA 0.705558 -216 GACCAGCATGACAATAGATAAACAACTGGCG 77 116 1 ACAATAGAAA 0.555962 -185 GTCAAAAGATAAAAAAAATAAAGGTTTAGAA 77 171 0 AAAAAAAAAA 0.339239 -130 TTAAACCGTTATAATAGACAAGGACCCATTC 77 203 1 ATAATAGAAA 0.457929 -98 ******** ** Masking position 8 Map Score: 12.1174 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 42 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 12 CCTCCCCCCTTTCGTTAAGGATAACGACC 13 58 1 TTGTTAGGAA 0.926249 -19 TTCTGCTCTGTTTGTTAAGGAAATCTC 16 254 1 TTGTTAGGAA 0.92623 -17 ACACATGGATTTCGTTTAGGACTCATTGATGTA 24 20 0 TTGTTAGGAT 0.552793 -244 TGCCTTGATATTCGTTTATGAAAAGAATTTCCG 25 170 0 TTGTTATGAA 0.949851 -131 AGGGCTGGAATTGATTTATGAAAGAAACCGCGT 31 39 1 TTATTATGAA 0.576098 -47 TTTGTAAAGGTTAGGTGAGGAGATGCAGCGCAT 40 73 1 TTGGTAGGAA 0.646899 -24 CAATCTATTTCTAGTTGATGAAATAAAAACTAA 41 114 1 CTGTTATGAA 0.734252 -99 ATATGCTCTCTTTTTTTATGAAAAAAGAATCAA 42 133 1 TTTTTATGAA 0.705574 -132 TTGTACGGATTTGGTTTATGATAGAACGTATGT 43 15 1 TTGTTATGAA 0.949851 -47 TCCCACAGTTTTTGTTTATGATAAACTCAAGTC 46 92 1 TTGTTATGAA 0.949851 -77 ACATTGTGAATTTGTTCATGAAATATTCAAGGA 48 207 0 TTGTTATGAA 0.949832 -94 TAGATGATTCTTGTTTAATGATA 51 1 0 TTTTTATGAA 0.705576 -117 TCCCACAATGTTTGTTTATGATATGGTTAAGGG 72 166 0 TTGTTATGAA 0.949851 -112 ATTAGTTCTATTAGTTGATCAAACTTCTTTTCG 73 34 1 TTGTTATCAA 0.630821 -267 ** *** **** * Masking position 8 Map Score: 8.57301 Number of sites scoring better than the average of aligned sites = 28 Number in coding regions = 23 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 CGAACAATAAATTTTTACCTTTTGCAGAAACTT 2 28 1 ATTTACTTTT 0.574082 -102 ATTTCATCTCTATGTCACATTTTGTGCGTAATT 17 84 1 TATTACTTTT 0.658862 -161 TATTTTTATCTTTCTGACGTTTTAAACGTATCA 22 138 1 TTTTACTTTT 0.909912 -163 AATTGGGCAGTTAATGACCTTTTTACCCTACCA 24 77 0 TTATACTTTT 0.406602 -187 CAGAAGCCGATTTTTTTCATTTTTAGACAACAT 25 135 1 TTTTTCTTTT 0.72745 -166 ATGGACCGTCTTTTTGACGTTTTGTTTATAGAA 33 39 1 TTTTACTTTT 0.909912 -262 CCTCCCTTTTTATGTAACCATTTCCACAGTAGA 42 18 1 TATTACATTT 0.514735 -247 CCTCCATTCGTTTGTTACCATTTAAACATTATA 42 232 0 TTTTACATTT 0.847263 -33 TAATGATTGTTTTCACACGATTTCCAGCATCAA 45 117 0 TTTAACATTT 0.411708 -45 TTTTCCGCACTTTTTCACAATTTCCCATAATCT 46 48 1 TTTTACATTT 0.847263 -121 TTTCGGCATTTTTGAAACTTTTTGAAGAAAAAT 49 45 0 TTTAACTTTT 0.560296 -256 CGTATTGATCATTCTCACCTTTTGCAGGCTGAA 51 78 1 ATTTACTTTT 0.574082 -40 TTACTACAAACTTCTTACCATTTGACAGAGTAA 54 138 0 CTTTACATTT 0.383554 -114 GCTGTTTTTTCTCTCCTTTTAAATCGAAAA 57 13 0 TTTTTCTTTT 0.72745 -20 GTTCTCAAACTTTCTCACGATTTGATAAAATGA 59 29 1 TTTTACATTT 0.847263 -52 TCATTTCACATTTCTTACTTTTTGAAGGTTATG 61 61 0 TTTTACTTTT 0.909912 -71 CCTCAAGTATTATCTTACTTTTTTCAACCTTAA 62 61 0 TATTACTTTT 0.658862 -31 TCGCCACAAATTTGTCACATTTTCTAAAAAAAA 67 125 0 TTTTACTTTT 0.909912 -143 TAAGCAAGCCTTTCTCTCTTTTTA 68 2 0 TTTTTCTTTT 0.72745 -210 ATGTGACGGATTTTTGTCTATTTTGTTGCTTAT 74 21 0 TTTTTCATTT 0.594464 -280 *** * ** **** Masking position 11 Map Score: 11.6134 Number of sites scoring better than the average of aligned sites = 61 Number in coding regions = 34 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 14 ATTCGTTTTATAGCCTGAAGTTCCGAACTA 2 61 0 TAGCCTGAAG 0.696953 -69 TTTTCAATTTTATCCAGGAGACGGAA 4 230 1 TATCCAGGAG 0.695194 -16 TACCACTGAAGCGCCAGAAGATATCGATTG 17 214 1 GCGCCAGAAG 0.926513 -31 ATTCCCATCTTCGCCAGAAGAAATTTGATT 26 23 0 TCGCCAGAAG 0.96702 -62 ATCCTCGTATTCTCCAGGAGGAATGAAT 26 67 1 TCTCCAGGAG 0.889909 -18 TGCTCCGTTTGCGGCTGAAGAGGCATTAGG 38 42 1 GCGGCTGAAG 0.70347 -64 GAGTCCTGTATCGGCAGGAGCACACATTTT 42 86 0 TCGGCAGGAG 0.969374 -179 GATTTGTGTTTCGGCAGAAGTGAAAATATT 45 74 0 TCGGCAGAAG 0.952034 -88 ACATGAAAAGTAGCCAGGAGTTTTCAAAAC 52 59 1 TAGCCAGGAG 0.929546 -102 ATGAAGTCATTCGGCAGGAGGAAAATCAAA 77 278 1 TCGGCAGGAG 0.969374 -23 ********** Masking position 9 Map Score: 6.18551 Number of sites scoring better than the average of aligned sites = 327 Number in coding regions = 307 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 15 TGCCCGGGAATTGTGAAAAAATACGCGACAGC 3 90 1 TTGTGAAAAT 0.9436 -211 TATGACGATTTTGTTAACAATTTGTGCAATCG 10 212 0 TTGTTAAAAT 0.593776 -89 CAATGCAAGCTTGTGAATAAATTACGCACAAA 17 104 0 TTGTGAAAAT 0.9436 -141 GTGTTTAAATTTGTGATCAACTTCACACATGG 24 45 0 TTGTGATAAT 0.659614 -219 AGCGGCTCATTTGTAAACAAATCGATACCAGA 30 102 0 TTGTAAAAAT 0.720475 -93 TTATGGGAAATTGTGAAAAAGTGCGGAAAACG 46 46 0 TTGTGAAAAT 0.9436 -123 TTTAGGGACATTGTGAATTTGTTCATGAAATA 48 215 0 TTGTGAATTT 0.584658 -86 TTTTTTCCTTTTGTGGAGAAATAGATGATTCT 51 23 0 TTGTGGAAAT 0.741744 -95 AAATGAATCGTTGTAAAGTACTTAATATGAAC 74 92 1 TTGTAAATAT 0.651847 -209 TTTGACACATTTGTGAAATATTGAGCAATATT 74 182 1 TTGTGAATAT 0.923972 -119 TTCGTCTATTTTGTGAATTACTGATCAAAGTC 74 217 1 TTGTGAATAT 0.923972 -84 TCGGTTCTATTTGTGAAGTAGTGAGCAAATTA 74 249 1 TTGTGAATAT 0.923972 -52 ******* ** * Masking position 4 Map Score: 3.66048 Number of sites scoring better than the average of aligned sites = 36 Number in coding regions = 22 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295