AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icpxR9_ecoli_bsub_100.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 htrA 129 periplasmic serine protease Do; heat shock protein HtrA #2 ybaU 191 putative protease maturation protein #3 motA 126 proton conductor component of motor; no effect on switching #4 ygjT 283 putative transport protein #5 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #6 yihD 69 orf, hypothetical protein #7 yihE 77 orf, hypothetical protein #8 cpxR_b3913 146 cpxR: transcriptional regulator in 2-component system, b3913: orf, hypothetical protein #9 yacB 194 similar to hypothetical proteins #10 yacC 85 similar to hypothetical proteins #11 yacD 46 similar to protein secretion PrsA homolog #12 ybdE 105 similar to hypothetical proteins #13 yczA 300 yczA #14 ycbL 96 similar to two-component response regulator [YcbM] #15 yclJ 212 similar to two-component response regulator [YclK] #16 yerI 161 yerI #17 htrA 168 serine protease Do (heat-shock protein) #18 ykoG 300 similar to two-component response regulator [YkoH] #19 motA 300 motility protein A #20 fliL 251 flagellar protein #21 fliM 33 flagellar motor switch protein #22 cheY 25 two-component response regulator #23 flhA 32 flagella-associated protein #24 cheW 21 cheW #25 resD 80 two-component response regulator #26 resC 135 essential protein similar to cytochrome c biogenesis protein #27 ppiB 253 peptidyl-prolyl isomerase #28 yrkP 267 similar to two-component response regulator [YrkQ] #29 phoP 211 two-component response regulator #30 yvqA 277 similar to two-component response regulator [YvqB] #31 yvrI 300 yvrI #32 yyxA 68 alternate gene name: yycK; similar to serine protease Do #33 yycJ 21 yycJ #34 yycF 300 similar to two-component response regulator [YycG] Motif number 1 TTGCCAAAGTAAAACAGTGTAAAAGGTATGTA 4 11 1 AAAAAGGTAA 0.929564 -273 CAGGGGGTGTAAAACAACGTAAAGTCATGGAT 8 79 1 AAAAAAGTAA 0.900739 -68 TGTAAAAAGTAAAGTAGAGAAACTATTCAAAA 9 160 1 AAAGAGGAAA 0.934633 -35 TATCAAATCTATAGCAATGAAAGG 16 148 1 ATAGAAGAAA 0.734585 -14 AAACTGTGGGATAAAAATGAAAAGATTATGGG 17 71 0 ATAAAAGAAA 0.84347 -98 TAGACATGTGAAAATAGAGAAACGGAGTGAAC 17 144 1 AAAAAGGAAA 0.965323 -25 AATCATTTTGTAAACAACGAAATCATTTTTTT 18 250 1 TAAAAAGAAA 0.718657 -51 ATCCCTCCTTAAAAAAGTGTAAAGGATGAAGG 19 22 0 AAAAAGGTAA 0.929564 -279 TTTCGATTTAAAAGGAGAGAAAAAACAGC 23 14 1 AAAGAGGAAA 0.934633 -19 CGATTTGATAAAATGAAAGTAACAGAAGGAAA 25 46 1 AAATAAGTAA 0.611637 -35 TTACTAAAAAATAAAAATGAAACCTGAATCTC 27 113 0 ATAAAAGAAA 0.84347 -141 TTTGAAAATTAAAATAAAGAAAGTAGGCATAC 27 230 1 AAAAAAGAAA 0.950351 -24 TAAAAAGAGAGAAAGGCTTGCTTA 29 3 1 AAAAAGGAAA 0.965323 -209 TCATTTATAGTAAAAAGAGAAAGGCTGTATTA 29 33 0 TAAAAGGAAA 0.787908 -179 AAGATGACATAAAATAGAGAAATAGGATGTCG 29 164 1 AAAAAGGAAA 0.965323 -48 AATAACCGTTAAAGGAGTGTAAGAAC 30 5 0 AAAGAGGTAA 0.87144 -273 ACATTGTGGGATAAAAATGAAAAGAATATGTG 30 188 1 ATAAAAGAAA 0.84347 -90 GAAGGAAAGCAAAAAAAAGTAAACTACTACTT 31 256 0 AAAAAAGTAA 0.900739 -45 CTACTAAATTAAATGAAGGAAAGCAAAAAAAA 31 270 0 AAATAAGAAA 0.768628 -31 **** ** **** Masking position 6 Map Score: 22.9866 Number of sites scoring better than the average of aligned sites = 162 Number in coding regions = 111 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 2 TGACGACTGAACATCCTGTCATGGTCAACA 3 91 1 ACATCCTGTC 0.838349 -36 GACATCATCCTTCCACTGTTGACC 3 113 0 TCATCCTTCC 0.9011 -14 ACCTGCTTTCAGCCCCTTTT 11 37 0 ACCTGCTTTC 0.901196 -10 ACGAGCATGAACATCCTTCAGGAATAGTTG 12 14 1 ACATCCTTCA 0.683982 -92 ATTGGCCGTCACCTCCTTTAAGAAACACAA 13 230 0 ACCTCCTTTA 0.852954 -71 TTGATATCCTCCTTTCTAACTCATCT 13 285 0 TCCTCCTTTC 0.960659 -16 ATTTGACCATCCTCTCCCGTCCCTAT 18 285 0 CCATCCTCTC 0.849759 -16 AGCGCTACTTCCCTTCATCCTTTACA 19 7 1 ACTTCCCTTC 0.773576 -294 TAAACATGTTCCATCCCTCCTTAAAAAAGT 19 36 0 CCATCCCTCC 0.882954 -265 TACTCGCCTCCCCTCCCTCC 20 1 0 CCCTCCCTCC 0.943097 -251 GTTTTCCCCCTGCTTTCCTTCTGTTAC 25 64 0 CCCTGCTTTC 0.87227 -17 AGCAGTTTGACCTCCTTCAATTTCACAAG 27 10 1 ACCTCCTTCA 0.826245 -244 CTTGCTTAATACAGCCTTTCTCTTTTTACT 29 27 1 ACAGCCTTTC 0.814142 -185 TGTCGGAATGTCCTGCTTTCGCTAAAATAA 29 118 1 TCCTGCTTTC 0.810688 -94 GCTCTTTTTCTCTTCCTTTCTTCCCTTAAC 30 144 1 TCTTCCTTTC 0.755473 -134 GGCTCTTCACATCCTTTCAACGTCATTA 30 260 0 ACATCCTTTC 0.95947 -18 ATAGGAAAATACCTCCCTTCTTTTTCTGCA 31 154 1 ACCTCCCTTC 0.964289 -147 ACCGCCTCCCTACTAAATTA 31 291 0 ACCGCCTCCC 0.715721 -10 ATTCCATCCTTTCCAAGAACGTT 32 56 0 CCATCCTTTC 0.946593 -13 CTTTATTGAAACCTCCCCTCACCGGAGTGC 34 65 0 ACCTCCCCTC 0.896017 -236 ATTTTGATTTTCCTCCTGCCGAATGACTTC 34 280 0 TCCTCCTGCC 0.814314 -21 ********** Masking position 6 Map Score: 22.1507 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 258 Number in noncoding regions = 75 Number of orfs with sites within 600 bp upstream = 86 Fraction of orfs with sites within 600 bp upstream = 0.013813 Motif number 3 GATTGGGGCAAAAAAAAGCAGCGGTACGTCGT 3 46 0 AAAAAAGCGC 0.897021 -81 TTACGATGTGTGAAAAAACACATCCGGTCACC 4 123 1 TAAAAAACCA 0.841318 -161 AGGTCTATGCATAAAAAGCAGCGGCTGGACGT 4 222 1 AAAAAAGCGC 0.897021 -62 TCCTTACACATAAAAAAACGGCCAACGTCGGA 4 256 0 TAAAAAACGC 0.967752 -28 GCTTTCTTTCTAAAAAAACTGCCGGCTGACGC 9 14 1 TAAAAAACGC 0.967752 -181 ATCATTTACATAAAAAAACTGCCAGCGTCAGC 9 38 0 TAAAAAACGC 0.967752 -157 TTTTCTCAAATTAAAAACCCGCTAAAGAGC 11 9 0 TAAAAACCGC 0.897021 -38 TTTAAGAAACACAAAAAACCCCCGTCCTATGC 13 212 0 AAAAAAACCC 0.947997 -89 TTTTTATAAAACACACACGTTTTTC 14 4 1 TATAAAACCA 0.461168 -93 CTTTACAAAATCAAAAAACACACACGTAATTA 14 50 0 TAAAAAACCA 0.841318 -47 TTTTGGTAAAATAAAAAACTGCATATCCTAAG 18 19 1 AAAAAAACGC 0.967752 -282 TAAGCGCACAAAAAAATACACCATTCGGTCAA 18 74 1 AAAAATACCC 0.609347 -227 GTTACTTTAATCATAAAACAGCGGAGAAGCGA 20 32 0 TATAAAACGC 0.828894 -220 TTAAAAGGAGAGAAAAAACAGC 23 21 1 AAAAAAACGC 0.967752 -12 GACTTCCTCTATAAAAACCTGATCCATAGGAA 31 129 1 AAAAAACCGA 0.71699 -172 AAAGGTTTAGAAAAAAAACACATGTTTCACCT 34 151 0 AAAAAAACCA 0.841318 -150 * ******* ** Masking position 6 Map Score: 16.3578 Number of sites scoring better than the average of aligned sites = 419 Number in coding regions = 290 Number in noncoding regions = 129 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 4 CCTGCTTTCAGCCCCTTTTCTCAAATTAAAAA 11 24 0 GCCCTTTCTC 0.929781 -23 TATGCGCTGCATCTCCTCACCTAACCTTTA 14 77 0 GCTCTCTCAC 0.622147 -20 ACCGTTTTCCGCACTTTTTCACAATTTCCCAT 17 44 1 GCCTTTTCAC 0.90882 -125 CGGTCAACCTGCACTTCCCCACGCTGGTATTA 18 99 1 GCCTTCCCAC 0.940566 -202 CGTTTCTTCCGCGCTTTATCTCAGCCAAAACA 18 160 1 GCCTTTTCTC 0.959747 -141 AAGCGATTACTCGCCTCCCCTCCCTCC 20 6 0 TCCCTCCCTC 0.888629 -246 AGGCGAGTAATCGCTTCTCCGCTGTTTTATGA 20 22 1 TCCTTCCCGC 0.832759 -230 GGTTTGGCCTGCCCTTTTTATCTTTATTCCCG 26 113 0 GCCTTTTATC 0.78574 -23 GAAACCTGAATCTCTTTATCTCCGTCTAACCT 27 95 0 TCCTTTTCTC 0.900489 -159 ATAGCCTGTCTCTCCTTGTCGCGGCTATTATA 27 180 0 TCCCTTTCGC 0.635259 -74 CCGACAATTCGCCTTTTACATCATTTTTAAAA 29 92 0 GCTTTTCATC 0.521725 -120 TTGGTGCTTTGCTTTTCTCCTCATTATTGGGA 30 78 0 GCTTTCCCTC 0.899363 -200 CATCTTCCTCGCTCTTTTTCTCTTCCTTTCTT 30 134 1 GCCTTTTCTC 0.959747 -144 GGCTCTTCACATCCTTTCAACGT 30 265 0 GCCTTCCATC 0.853427 -13 TTACGTTTTATCGGTTTTCCTCACTTACATAC 31 189 0 TCGTTTCCTC 0.54804 -112 TATATAACATTCGTTTCATCACTTATGGCCCA 34 240 0 TCTTTCTCAC 0.52947 -61 ** **** **** Masking position 6 Map Score: 9.11633 Number of sites scoring better than the average of aligned sites = 769 Number in coding regions = 683 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 5 TAACAACACTCCGCTGTAGATGACTGTGTACC 2 166 0 CCGCTGTGAG 0.863516 -26 CGCGCGTTAACGCCTGACGACTGAACATCCTG 3 77 1 CGCCTGAGAT 0.912127 -50 AAACGGCCAACGTCGGAAGACGTCCAGCCGCT 4 241 0 CGTCGGAGAG 0.83494 -43 TGTTTTACACCCCCTGACGCATGTTTGCAGCC 8 63 0 CCCCTGAGCT 0.943227 -84 GGATTAGCGACGTCTGATGACGTAATTTCTGC 8 107 1 CGTCTGAGAG 0.951267 -40 TGTTTAAATACCTCCGAGGCAGAAATTACGTC 8 125 0 CCTCCGAGCG 0.940377 -22 AAAAAACTGCCGGCTGACGCTGGCAGTTTTTT 9 26 1 CGGCTGAGCG 0.982255 -169 GCTCCGTTTGCGGCTGAAGAGGCATTAGGAAA 12 43 1 CGGCTGAGAG 0.961026 -63 AACCGATCCTCCCCTGATGCCGAATGGGCTTC 13 32 1 CCCCTGAGCG 0.985124 -269 AGGGGACGCGCCCCAGAGGCGGTCTTATCAAT 15 37 0 CCCCAGAGCG 0.922629 -176 GCGTATGGCCCCGCCGAAGATTGGGACAGCGA 26 82 0 CCGCCGAGAT 0.85818 -54 ******* ** * Masking position 4 Map Score: 7.46159 Number of sites scoring better than the average of aligned sites = 652 Number in coding regions = 609 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 6 TGGTCTGTTACATACCTTTTACACTGTTTTACT 4 18 0 CTATTTTACA 0.836648 -266 TTGGCTCAGCTGCGGCTTTTACAATCATCCAAT 9 69 1 TCGTTTTACA 0.622562 -126 GTTTCTCTACTTTACTTTTTACAAACATTCTAC 9 150 0 TTATTTTACA 0.526044 -45 CCGCGAGACCCTCGTCCTTTGCATAGGACGGGG 13 192 1 CCGCTTTGCA 0.743701 -109 TTATAAAACACACACGTTTTTCAATTACAATAA 14 14 1 CCATTTTTCA 0.949683 -83 CATCTCCTCACCTAACCTTTACAAAATCAAAAA 14 65 0 CTACTTTACA 0.880257 -32 ATAGATTGTTCATATTTTTTTCATACCTTTGGA 15 89 0 CTATTTTTCA 0.867075 -124 CGACTCAGTCCTTTCATATACAATAT 17 4 1 CCACCTTTCA 0.763303 -165 CACAATTTCCCATAATCTTTTCATTTTTATCCC 17 63 1 CTACTTTTCA 0.903499 -106 AAACAACGAAATCATTTTTTTCATATAGGGACG 18 261 1 ACATTTTTCA 0.554196 -40 GCTACTTCCCTTCATCCTTTACACTTTTTTAAG 19 14 1 TCACTTTACA 0.821725 -287 TCAGTAGACCCCCGGGCTTTTCAATTTTGGAGA 19 139 1 CCGCTTTTCA 0.932948 -162 CATTGTAAGGCTCAAGTTTTTCAGATCCGCACT 28 47 0 CCATTTTTCA 0.949683 -221 TGATGCTCGCCACAAATTTGTCACATTTTCTAA 28 131 0 CCATTTGTCA 0.692003 -137 ATTCCGACAATTCGCCTTTTACATCATTTTTAA 29 94 0 TCGTTTTACA 0.622562 -118 CATAATTTCACATATTCTTTTCATTTTTATCCC 30 195 0 CTACTTTTCA 0.903499 -83 TAGACAAGGACCCATTCTTTACATGGGCCATAA 34 217 1 CCACTTTACA 0.955097 -84 * ** ******* Masking position 9 Map Score: 8.66772 Number of sites scoring better than the average of aligned sites = 353 Number in coding regions = 294 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 7 GCGTTGTCCCCAGTGGGGATGT 2 3 1 GTTGTCCCCA 0.929771 -189 CATTCGTAATGTTTTCCGGATGATGGG 7 61 1 GTTTTCCGGA 0.947225 -17 GAAGTGTACCGTTTTCCGCACTTTTTCACA 17 37 1 GTTTTCCGCA 0.972089 -132 AGTTTTCACCAAATCCTTTTT 19 290 0 GTTTTCACCA 0.847445 -11 CAGATTGAATGTTTTCCGGATACTACAATT 20 110 1 GTTTTCCGGA 0.947225 -142 GTTTTCCCCCTGCTTTCCTT 25 71 0 GTTTTCCCCC 0.979053 -10 CGGGAGATTCGTTTTCCCCCGAAAGGTGTG 27 149 1 GTTTTCCCCC 0.979053 -105 GGCAATTTGGGGTTTCCCGCGCTGATTGCA 31 87 0 GGTTTCCCGC 0.849118 -214 CGTTTTATCGGTTTTCCTCACTTACATACA 31 188 0 GTTTTCCTCA 0.897604 -113 ********** Masking position 5 Map Score: 8.14132 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 161 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 8 ACATCCGGTCACCGGGCAACCCGAAAGGAATA 4 142 1 ACCGGCACCC 0.969739 -142 CACATAAAAAAACGGCCAACGTCGGAAGACGT 4 250 0 AACGCCACGT 0.968469 -34 TACATAAAAAAACTGCCAGCGTCAGCCGGCAG 9 32 0 AACGCCACGT 0.968469 -163 ATCGGTTCACACCTGCCACCGACTCTCT 13 7 0 ACCGCCACGA 0.961696 -294 GGGGAGAGAAACCCGGCATCGCCTACTATCCG 13 81 0 ACCGGCACGC 0.987002 -220 CTATGCCACCACCAGCCATCGTACATTGGCCG 13 252 0 ACCGCCACGT 0.98448 -49 AACCCGTTTGAACGGGCAGCCCTTTACACTGA 20 61 1 AACGGCACCC 0.939453 -191 *** **** *** Masking position 8 Map Score: 4.40304 Number of sites scoring better than the average of aligned sites = 212 Number in coding regions = 205 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 GCTGCTTTTTTTTGCCCCAATCGCGCGTTAA 3 56 1 TTGCCCCAAT 0.449018 -71 CGGGTTGCCCGGTGACCGGATGTGTTTTTTC 4 134 0 GTGACCGGAT 0.983546 -150 CATTCGTAATGTTTTCCGGATGATGGG 7 61 1 GTTTCCGGAT 0.711682 -17 AAAAGCCGCAGCTGAGCCAATCATTTACATA 9 58 0 GTGAGCCAAT 0.73622 -137 CGGTGGCAGGTGTGAACCGATCCTCCCCTGA 13 18 1 TTGAACCGAT 0.643895 -283 GAATTGCTTTGCTGAACGGATAGTAGGCGAT 13 65 1 GTGAACGGAT 0.929557 -236 GGAAGTGCAGGTTGACCGAATGGTGTATTTT 18 86 0 GTGACCGAAT 0.939381 -215 TTTGATCCCTTATGACCCGATCTGGATAATA 18 126 0 TTGACCCGAT 0.891197 -175 TATCGGTTTTGGTGCCCGGAACTTTAGGGAC 19 238 0 GTGCCCGGAA 0.811505 -63 CAGATTGAATGTTTTCCGGATACTACAATTA 20 110 1 GTTTCCGGAT 0.711682 -142 TCATGGCAGAGCTGAGCGGAAATTTTCTTTA 26 28 1 GTGAGCGGAA 0.727752 -108 GTATTTAATCGCTGTCCCAATCTTCGGCGGG 26 74 1 GTGTCCCAAT 0.806353 -62 TTATAATGACGTTGAAAGGATGTGAAGAGCC 30 257 1 GTGAAAGGAT 0.44545 -21 CAATGTATCTGCTGACCCGATTCGAAAAGAA 31 58 0 GTGACCCGAT 0.978345 -243 * ********* Masking position 10 Map Score: 5.24098 Number of sites scoring better than the average of aligned sites = 812 Number in coding regions = 752 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 10 TGAAGTTACTCCCCTTTGCAGGTAACAAAG 4 76 0 CCCCTTTGCA 0.620439 -208 ACAAGGCCATCCCTTTACCTAATTTTACGT 5 187 0 CCCTTTACCT 0.631997 -84 CTGCTTTCAGCCCCTTTTCTCAAATTAAAA 11 25 0 CCCCTTTTCT 0.601092 -22 TACCGCGAGACCCTCGTCCTTTGCATAGGA 13 190 1 CCCTCGTCCT 0.953761 -111 ACACAAAAAACCCCCGTCCTATGCAAAGGA 13 206 0 CCCCCGTCCT 0.970676 -95 TAGAAAACCCTTGTGCCATATTGGCAC 16 8 1 CCCTTGTGCC 0.918412 -154 AACATAAAAACCCTTGTGCCAATATGGCAC 16 23 0 CCCTTGTGCC 0.918412 -139 AAAATATTTTCCCTTTTCCTGTTAATTGTA 16 52 0 CCCTTTTCCT 0.893712 -110 AAAACAGCACCCCTAGTGCTTTCCGTATAC 18 186 1 CCCTAGTGCT 0.828894 -115 TGACCATCCTCTCCCGTCCCTATATGAAAA 18 278 0 CTCCCGTCCC 0.863036 -23 TTTCAGTAGACCCCCGGGCTTTTCAATTTT 19 137 1 CCCCCGGGCT 0.830285 -164 TCCGGTTCCTCTATTCCTTGATCCATTG 20 234 0 CTCTATTCCT 0.40787 -18 GAAAACGAATCTCCCGAGCTTTACTAAAAA 27 135 0 CTCCCGAGCT 0.601419 -119 ATCAATACTCCTTTCCCATTTATCACG 28 8 1 CTCCTTTCCC 0.719781 -260 ********** Masking position 3 Map Score: 4.23472 Number of sites scoring better than the average of aligned sites = 370 Number in coding regions = 311 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 11 AGGATTATCATTTCACGATGATTTTGGTGG 7 27 0 TTTCACGATG 0.75367 -51 ACGCGGTTTCTTTCATAAATCAATTCCAGC 10 42 0 TTTCATAAAT 0.713953 -44 AGGTTTTGCGTTTCACAATTGTTAGTTTTT 15 138 0 TTTCACAATT 0.910488 -75 TTCCGCACTTTTTCACAATTTCCCATAATC 17 50 1 TTTCACAATT 0.910488 -119 TCTCAAACTTTCTCACGATTTGATAAAATG 25 31 1 TCTCACGATT 0.753673 -50 GAACTGTATTTTTCATGATTCAGGTCCTCA 27 61 0 TTTCATGATT 0.910352 -193 GAGCATCAGCTTTCATAAATTGGTAAGATT 28 156 1 TTTCATAAAT 0.713953 -112 TCTTAACATGTTTCATGATTTTATTTTAGC 29 138 0 TTTCATGATT 0.910352 -74 GGCAGGCAATTTTCATAATTTCACATATTC 30 211 0 TTTCATAATT 0.887646 -67 ********** Masking position 5 Map Score: 3.66971 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 50 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 12 GCAACATTCCAGCAGCGGTAACGACGTACC 3 26 1 AGCAGCGGTA 0.971535 -101 GGCAAAAAAAAGCAGCGGTACGTCGTTACC 3 42 0 AGCAGCGGTA 0.971535 -85 ATGCATAAAAAGCAGCGGCTGGACGTCTTC 4 228 1 AGCAGCGGCT 0.806314 -56 TGATTGGCTCAGCTGCGGCTTTTACAATCA 9 66 1 AGCTGCGGCT 0.791162 -129 ACCATACACGATCAGCGGCTCATTTGTAAA 9 117 0 ATCAGCGGCT 0.939585 -78 ********** Masking position 1 Map Score: 2.91125 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 159 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 13 AACAGTGGAAGGATGATGTC 3 117 1 GGATGATGTC 0.652666 -10 CAACCCGAAAGGAATACGCAGACGTATTCC 4 158 1 GGAATACGCA 0.874261 -126 CAACAAAAAAGGAATACGTCTGCGTATTCC 4 168 0 GGAATACGTC 0.874268 -116 GGCCAACGTCGGAAGACGTCCAGCCGCTGC 4 239 0 GGAAGACGTC 0.945941 -45 TAGCGACGTCTGATGACGTAATTTCTGCCT 8 111 1 TGATGACGTA 0.610873 -36 CGTTTGCGGCTGAAGAGGCATTAGGAAAGC 12 47 1 TGAAGAGGCA 0.666312 -59 ATATCCTAAGGGAATATGCAGTCATAGATC 18 41 1 GGAATATGCA 0.784992 -260 TTATATACAGTGAATATGTATTTCTACTAT 19 63 1 TGAATATGTA 0.616247 -238 AAATATTCAAGGAAGAGGCATAGAAGGGAG 19 190 0 GGAAGAGGCA 0.860934 -111 GTACATGCGATGAATATGTAACGATAAATG 30 37 0 TGAATATGTA 0.616247 -241 AAAAGAGCGAGGAAGATGTAGGATGATCAA 30 122 0 GGAAGATGTA 0.926085 -156 TTTTTATAGAGGAAGTCGTAAAACAGATCG 31 116 0 GGAAGTCGTA 0.71719 -185 GGTTCAAAGAAGAAGACGTCATTGATAAAG 34 33 1 AGAAGACGTC 0.631736 -268 ********** Masking position 3 Map Score: 3.26048 Number of sites scoring better than the average of aligned sites = 498 Number in coding regions = 466 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 14 AACAAACAGAGCAGAAAAAAAGCAAGTGAAG 5 239 0 GAGAAAAAAA 0.577824 -32 ATTTCTAGTTGATGAAATAAAAACTAACAAT 15 120 1 GTGAAATAAA 0.956956 -93 CTGTTTTTTTGGTAAAATAAAAAACTGCATA 18 13 1 GTAAAATAAA 0.921191 -288 TGCTGTTTTGGCTGAGATAAAGCGCGGAAGA 18 164 0 GTGAGATAAA 0.822582 -137 CTATTATGATGTTAAAATAAAAAATTGTATA 18 211 0 GTAAAATAAA 0.921191 -90 GGCATAGAAGGGAGAAATAAACAAAAACGGG 19 173 0 GAGAAATAAA 0.846536 -128 CTCACGATTTGATAAAATGAAAGTAACAGAA 25 42 1 GTAAAATGAA 0.817723 -39 TCCTGCTTTCGCTAAAATAAAATCATGAAAC 29 128 1 GTAAAATAAA 0.921191 -84 AACATGTTAAGATGACATAAAATAGAGAAAT 29 156 1 GTGACATAAA 0.822582 -56 AAGGTCAAAAGATAAAAAAAATAAAGGTTTA 34 174 0 GTAAAAAAAA 0.743606 -127 ATGTTATATAGATGAAATGAAGTCATTCGGC 34 262 1 GTGAAATGAA 0.895096 -39 * ********* Masking position 5 Map Score: 5.39914 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 95 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974 Motif number 15 CTTTCTGCGTCTTGTGGGCTGACAATTGCC 2 87 1 CTTGTGGGCT 0.917601 -105 CGCCTCTTTTATTGTGGGATTGACCCTGCT 6 17 1 ATTGTGGGAT 0.976821 -53 ATAAACAAAAACTGTGGGATAAAAATGAAA 17 81 0 ACTGTGGGAT 0.949962 -88 ATAAACAAACATTGTGGGATAAAAATGAAA 30 180 1 ATTGTGGGAT 0.976821 -98 ATATGGTTATATTGTGGGTTAGAAACTCCT 32 25 0 ATTGTGGGTT 0.943436 -44 ********** Masking position 5 Map Score: 1.1735 Number of sites scoring better than the average of aligned sites = 18 Number in coding regions = 14 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467