AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icpxR_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 cydD 122 ATP-binding component of cytochrome-related transport, Zn sensitive #4 motA 126 proton conductor component of motor; no effect on switching #5 ygjT 283 putative transport protein #6 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #7 rpoH 244 RNA polymerase, sigma(32) factor; regulation of proteins induced at high temperatures #8 yihD 69 orf, hypothetical protein #9 yihE 77 orf, hypothetical protein #10 cpxR_b3913 146 cpxR: transcriptional regulator in 2-component system, b3913: orf, hypothetical protein #11 proP 263 low-affinity transport system; proline permease II #12 yacB 194 similar to hypothetical proteins #13 yacC 85 similar to hypothetical proteins #14 yacD 46 similar to protein secretion PrsA homolog #15 ybdE 105 similar to hypothetical proteins #16 yczA 300 yczA #17 ycbL 96 similar to two-component response regulator [YcbM] #18 yclJ 212 similar to two-component response regulator [YclK] #19 yerI 161 yerI #20 htrA 168 serine protease Do (heat-shock protein) #21 ykoG 300 similar to two-component response regulator [YkoH] #22 motA 300 motility protein A #23 fliL 251 flagellar protein #24 fliM 33 flagellar motor switch protein #25 cheY 25 two-component response regulator #26 flhA 32 flagella-associated protein #27 cheW 21 cheW #28 resD 80 two-component response regulator #29 resC 135 essential protein similar to cytochrome c biogenesis protein #30 ppiB 253 peptidyl-prolyl isomerase #31 yrkP 267 similar to two-component response regulator [YrkQ] #32 phoP 211 two-component response regulator #33 yvqA 277 similar to two-component response regulator [YvqB] #34 yvrI 300 yvrI #35 cydA 300 cytochrome bd ubiquinol oxidase (subunit I) #36 yyxA 68 alternate gene name: yycK; similar to serine protease Do #37 yycJ 21 yycJ #38 yycF 300 similar to two-component response regulator [YycG] Motif number 1 TCGCCTTTATTTTTTCCCCGTTGTAACATTGCTC 3 62 1 TTTTTCCTGT 0.698803 -61 TGTTACATACCTTTTACACTGTTTTACTTTGGCA 5 12 0 CTTTTCCTTT 0.807765 -272 CGGATGTGTTTTTTCACACATCGTAATGACGATC 5 115 0 TTTTCCCCGT 0.808085 -169 ACTTGCTTTTTTTCTGCTCTGTTTGTTAAGGAAA 6 243 1 TTTCTCCTTT 0.886209 -28 CTTCCCGGTATTTCATCTCTATGTCACATTTTGT 7 75 1 TTTCACCTGT 0.617392 -170 CATCCTGCAATTCCCGCTCCCCTTTTGCGGCCGT 11 187 1 TTCCCCCCTT 0.910444 -77 AGCTTTCCTCGCAGAGTTGGCCCATTT 11 247 0 TTTCCCCAGT 0.470232 -17 CCTCTATCACCACTTTTGAATAGTT 12 180 0 CTCTACCCTT 0.557133 -15 TCCTATACACTTCCTACGCGGTTTCTTTCATAAA 13 53 0 TTCCTCCTTT 0.848522 -33 ACCTGCTTTCAGCCCCTTTTCTCAAATTAA 14 27 0 TTTCACCTTT 0.816242 -20 ATAATGATTGTTTTCACACGATTTCCAGCATCAA 19 117 0 TTTTCCCTTT 0.940766 -45 AGTGTACCGTTTTCCGCACTTTTTCACAATTTCC 20 39 1 TTTCCCCTTT 0.950902 -130 CTTTTCATTTTTATCCCACAGTTTTTGTTTATGA 20 79 1 TTATCCCTTT 0.837945 -90 CAAAGCGCGTTTCTTCCGCGCTTTATCTCAGCCA 21 153 1 TTCTTCCTTT 0.821225 -148 TATAAACATGTTCCATCCCTCCTTAAAAAAGTGT 22 34 0 TTCCACCCTT 0.699847 -267 CGAGTAATCGCTTCTCCGCTGTTTTATGATTAAA 23 25 1 CTTCTCCTTT 0.836709 -227 AATCTATCTCTCTCCTTGTGTTTCG 25 9 0 CTATCCCCTT 0.712873 -17 GCTGTTTTTTCTCTCCTTTTAAATCGAAAA 26 13 0 TTTTCCCTTT 0.940766 -20 AGTTCTCAAACTTTCTCACGATTTGATAAAATGA 28 28 1 CTTTCCCTTT 0.91266 -53 GTTTTCCCCCTGCTTTCCTTCTGTT 28 66 0 TTTTCCCCTT 0.920577 -15 GTCGCGGCTATTATACCACACCTTTCGGGGGAAA 30 161 0 TTATACCCTT 0.463947 -93 TTAAGCAAGCCTTTCTCTCTTTTTA 32 2 0 CTTTCCCTTT 0.91266 -210 CCCCGACATCCTATTTCTCTATTTTATGTCATCT 32 165 0 CTATTCCTTT 0.577707 -47 GTTCTTACACTCCTTTAACGGTTAT 33 2 1 TTCTTCCCTT 0.770243 -276 CATCCTACATCTTCCTCGCTCTTTTTCTCTTCCT 33 127 1 CTTCCCCTTT 0.927233 -151 CTTTTCATTTTTATCCCACAATGTTTGTTTATGA 33 178 0 TTATCCCTGT 0.652584 -100 AATTTGGGGTTTCCCGCGCTGATTGCAATGTATC 34 80 0 TTCCCCCATT 0.637343 -221 GCTTTCTCCTCCATTTCCGGTTAAAA 35 285 0 TTTCTCCTTT 0.886209 -16 ***** * * *** Masking position 2 Map Score: 26.176 Number of sites scoring better than the average of aligned sites = 639 Number in coding regions = 485 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 2 ACGACGTACCGCTGCTTTTTTTTGCCCCAATCG 4 46 1 GCGTTTTTTT 0.972916 -81 ACGTCCAGCCGCTGCTTTTTATGCATAGACCTC 5 221 0 GCGTTTTTTG 0.973407 -63 TCCGACGTTGGCCGTTTTTTTATGTGTAAGGAA 5 256 1 GCGTTTTTAT 0.972916 -28 CGGCCGTCGCGCTGATTTTTCTGGCGTTTGCGG 11 214 1 GCGTTTTTTG 0.973407 -50 GCGTCAGCCGGCAGTTTTTTTAGAAAGAAAGCG 12 13 0 GCGTTTTTAG 0.973407 -182 GCTGACGCTGGCAGTTTTTTTATGTAAATGATT 12 38 1 GCGTTTTTAT 0.972916 -157 GCTCTTTAGCGGGTTTTTAATTTGAGAAAAG 14 9 1 GCGTTTTTAT 0.972916 -38 GCATAGGACGGGGGTTTTTTGTGTTTCTTAAAG 16 212 1 GGGTTTTTTG 0.781342 -89 CGGTTGTTTTGATGCTTTTTTATATAATAGCAC 18 181 0 GAGTTTTTAT 0.702913 -32 CTTAGGATATGCAGTTTTTTATTTTACCAAAAA 21 18 0 GCGTTTTTTT 0.972916 -283 ATTTTGGAGAGCCCGTTTTTGTTTATTTCTCCC 22 162 1 GCCTTTTTTT 0.764199 -139 TCGCTTCTCCGCTGTTTTATGATTAAAGTAACC 23 32 1 GCGTTTATAT 0.792648 -220 GCTGTTTTTTCTCTCCTTTTAAA 26 20 0 GCGTTTTTTC 0.893537 -13 GCTGGATAGTGCTGCTTTGTGAGGACCTGAATC 30 42 1 GCGTTTGTAG 0.852363 -212 ** * ***** ** Masking position 7 Map Score: 16.1981 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 141 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 GAACAATAAATTTTTACCTTTTGCAGAAACTT 1 29 1 TTTTTACTTT 0.650476 -101 TTACATACCTTTTACACTGTTTTACTTTGGCA 5 12 0 TTTACACTTT 0.838317 -272 TTAGAATCTCTTCACTTGCTTTTTTTCTGCTC 6 230 1 TTCACTTTTT 0.838192 -41 AAATAGATTGTTCATATTTTTTTCATACCTTT 18 92 0 TTCATATTTT 0.726639 -121 AATGATTGTTTTCACACGATTTCCAGCATCAA 19 117 0 TTCACACTTT 0.909109 -45 TTTCCGCACTTTTTCACAATTTCCCATAATCT 20 49 1 TTTTCACTTT 0.838317 -120 CATGTTCACTCCGTTTCTCTATTTTC 20 153 0 TTCACTCTTT 0.874942 -16 CCCTTCATCCTTTACACTTTTTTAAGGAGGGA 22 21 1 TTTACACTTT 0.838317 -280 TACTACAAACTTCTTACCATTTGACAGAGTAA 23 138 0 TTCTTACTTT 0.78214 -114 GCTGTTTTTTCTCTCCTTTTAAATCGAAAA 26 13 0 TTCTCTCTTT 0.874942 -20 TTCTCAAACTTTCTCACGATTTGATAAAATGA 28 30 1 TTCTCACTTT 0.909109 -51 TCAGGTTTCATTTTTATTTTTTAGTAAAGCTC 30 118 1 TTTTTATTTT 0.579467 -136 AAGCAAGCCTTTCTCTCTTTTTA 32 2 0 TTCTCTCTTT 0.874942 -210 CATAAACGTCTTTATTTCTTTTAAAAATGATG 32 74 1 TTTATTTTTT 0.490791 -138 CAATTCGCCTTTTACATCATTTTTAAAAGAAA 32 88 0 TTTACATTTT 0.793346 -124 CTCGCTCTTTTTCTCTTCCTTTCTTCCCTTAA 33 141 1 TTCTCTTTTT 0.838192 -137 ATTTCACATATTCTTTTCATTTTTATCCCACA 33 192 0 TTCTTTTTTT 0.650267 -86 CGGCAGGCAATTTTCATAATTTCACATATTCT 33 210 0 TTTTCATTTT 0.793346 -68 GGCTCTTCACATCCTTTCAACGTCATT 33 261 0 TTCACATTTT 0.881035 -17 AAAGTAGTAGTTTACTTTTTTTTGCTTTCCTT 34 255 1 TTTACTTTTT 0.728651 -46 TTTGCTTTCCTTCATTTAATTTAGTAGGGAGG 34 275 1 TTCATTTTTT 0.650267 -26 ACCTTTATTTTTTTTATCTTTTGACCTTAAAC 38 177 1 TTTTTATTTT 0.579467 -124 ******* *** Masking position 10 Map Score: 19.0486 Number of sites scoring better than the average of aligned sites = 333 Number in coding regions = 262 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 4 AAGTCACCGAATACAAATAAAAAAGGCACATCAGTA 2 54 0 AAAAAAAAGG 0.910486 -138 CAAATCAGTAACAAAAGTAAAGAAGGCGACACCATG 3 16 1 AAAAGAGAGG 0.888294 -107 TTGAATCGCGACAGAAAGATTTTGGGAGCAA 10 6 0 AAAAAATGGG 0.673308 -141 TTGATTTATGAAAGAAACCGCGTAGGAAGTGTATAG 13 49 1 AAAAACGAGG 0.888294 -37 ACTTCTGCCGAAACACAAATCAAGGGGAGGTATGTT 19 83 1 AAACAAAGGG 0.675954 -79 AGTTTATCATAAACAAAAACTGTGGGATAAAAATGA 20 83 0 AAAAAAGGGG 0.963177 -86 GTTTTGGCTGAGATAAAGCGCGGAAGAAACGCGCTT 21 155 0 AAAAACGAAG 0.442406 -146 TAGAAGGGAGAAATAAACAAAAACGGGCTCTCCAAA 22 164 0 AAAAAAACGG 0.657003 -137 AATGAAAGTAACAGAAGGAAAGCAGGGGGAAAAC 28 57 1 AAAAGAGAGG 0.888294 -24 GACAGCGATTAAATACACAAGAAAGGCCGCATAAAG 29 54 0 AAACAAAAGG 0.717495 -82 GCGGGAATAAAGATAAAAAGGGCAGGCCAAACCG 29 112 1 AAAAAAGAGG 0.969556 -24 TTGAAAATTAAAATAAAGAAAGTAGGCATACAA 30 231 1 AAAAAAGAGG 0.969556 -23 GAAGAAAGGAAGAGAAAAAGAGCGAGGAAGATGTAG 33 131 0 AAAAAAGGAG 0.722976 -147 ACCATATCATAAACAAACATTGTGGGATAAAAATGA 33 172 1 AAAAAAGGGG 0.963177 -106 ACATGACTGCAGAAAAAGAAGGGAGGTATTTTCCTA 34 155 0 AAAAAAGAGG 0.969556 -146 AGGTCAAAAGATAAAAAAAATAAAGGTTTAGAAAAA 38 168 0 AAAAAAAAGG 0.910486 -133 * * *** * * *** Masking position 5 Map Score: 13.8675 Number of sites scoring better than the average of aligned sites = 85 Number in coding regions = 57 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 5 ATAATTCTGATAACTCACCTGCTAAGCGTG 3 101 1 TAACTCACCT 0.655114 -22 GGCAATGAAGTTACTCCCCTTTGCAGGTAA 5 81 0 TTACTCCCCT 0.855999 -203 TATTTAGAATCTCTTCACTTGCTTTTTTTC 6 227 1 CTCTTCACTT 0.432304 -44 GTGTGAACCGATCCTCCCCTGATGCCGAAT 16 27 1 ATCCTCCCCT 0.91979 -274 TGCGCTGCATCTCCTCACCTAACCTTTACA 17 75 0 CTCCTCACCT 0.915776 -22 AGCATCAACATACCTCCCCTTGATTTGTGT 19 95 0 TACCTCCCCT 0.974914 -67 AGCGCTACTTCCCTTCATCCTTTAC 22 6 1 TACTTCCCTT 0.731313 -295 TTTTTGTTTATTTCTCCCTTCTATGCCTCT 22 177 1 TTTCTCCCTT 0.586544 -124 AGCGATTACTCGCCTCCCCTCCCTCC 23 7 0 CGCCTCCCCT 0.857888 -245 TTTCCTCACCTCCGTATTCTG 24 23 0 TTCCTCACCT 0.955631 -11 GCGGCTATTATACCACACCTTTCGGGGGAA 30 162 0 TACCACACCT 0.599547 -92 TTCTCTTCCTTTCTTCCCTTAACCATATCA 33 151 1 TTCTTCCCTT 0.781874 -127 CATAGGAAAATACCTCCCTTCTTTTTCTGC 34 153 1 TACCTCCCTT 0.942378 -148 TTTATCGGTTTTCCTCACTTACATACATGA 34 185 0 TTCCTCACTT 0.900636 -116 ACTTTATTGAAACCTCCCCTCACCGGAGTG 38 66 0 AACCTCCCCT 0.896986 -235 ********** Masking position 10 Map Score: 10.5879 Number of sites scoring better than the average of aligned sites = 194 Number in coding regions = 143 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 6 TCCCCAGTGGGGATGTGACGAAGTTCAAGG 2 17 1 GGATGTGACG 0.897898 -175 ACGATCGACCGGCAATGAAGTTACTCCCCT 5 91 0 GGCAATGAAG 0.724974 -193 TGGCATAGCGGGATATGCCGCGAGCGGGCG 6 36 1 GGATATGCCG 0.921573 -235 ACGGATAGTAGGCGATGCCGGGTTTCTCTC 16 80 1 GGCGATGCCG 0.92276 -221 GTTTCTTAAAGGAGGTGACGGCCAATGTAC 16 234 1 GGAGGTGACG 0.951048 -67 GGTTAGGTGAGGAGATGCAGCGCATA 17 81 1 GGAGATGCAG 0.972493 -16 TATTCCCTTAGGATATGCAGTTTTTTATTT 21 27 0 GGATATGCAG 0.941186 -274 TATCCTAAGGGAATATGCAGTCATAGATCG 21 42 1 GAATATGCAG 0.650182 -259 ACCAGCGTGGGGAAGTGCAGGTTGACCGAA 21 97 0 GGAAGTGCAG 0.86361 -204 TGTAGTAAAAGAAGATGAAGAAGCTGTTCT 23 163 1 GAAGATGAAG 0.771617 -89 GACAGAATACGGAGGTGAGGAAA 24 21 1 GGAGGTGAGG 0.846575 -13 TAGGTTAGACGGAGATAAAGAGATTCAGGT 30 94 1 GGAGATAAAG 0.771617 -160 GACGTTGAAAGGATGTGAAGAGCC 33 264 1 GGATGTGAAG 0.922936 -14 ATAAACAACTGGCGATAAAGGTGAAACATG 38 133 1 GGCGATAAAG 0.60858 -168 ********** Masking position 6 Map Score: 9.44539 Number of sites scoring better than the average of aligned sites = 846 Number in coding regions = 801 Number in noncoding regions = 45 Number of orfs with sites within 600 bp upstream = 46 Fraction of orfs with sites within 600 bp upstream = 0.00738837 Motif number 7 AATGAAGTTACTCCCCTTTGCAGGTAACAA 5 78 0 CTCCCCTTTG 0.796087 -206 AGAACAAGGCCATCCCTTTACCTAATTTTA 6 190 0 CATCCCTTTA 0.494205 -81 CGTTGTTTTACACCCCCTGACGCATGTTTG 10 68 0 CACCCCCTGA 0.839961 -79 GCAATTCCCGCTCCCCTTTTGCGGCCGTCG 11 193 1 CTCCCCTTTT 0.961169 -71 CCTCTATCACCACTTTTGAATAGTTTC 12 178 0 CACCACTTTT 0.611425 -17 AAATCAATTCCAGCCCTTTTAGGGTTAAGA 13 26 0 CAGCCCTTTT 0.908655 -60 ACCTGCTTTCAGCCCCTTTTCTCAAATTA 14 28 0 CAGCCCCTTT 0.836314 -19 CCGGGTTTCTCTCCCCGTTACCAAGAGAGG 16 97 1 CTCCCCGTTA 0.773045 -204 CATTGGCCGTCACCTCCTTTAAGAAACACA 16 231 0 CACCTCCTTT 0.44696 -70 ATCAACATACCTCCCCTTGATTTGTGTTTC 19 92 0 CTCCCCTTGA 0.882464 -70 CATGTTCACTCCGTTTCTCTATTTTC 20 153 0 CACTCCGTTT 0.726158 -16 GCCAAAACAGCACCCCTAGTGCTTTCCGTA 21 183 1 CACCCCTAGT 0.587843 -118 TTTGAACGGGCAGCCCTTTACACTGAATGC 23 67 1 CAGCCCTTTA 0.836038 -185 AATCTATCTCTCTCCTTGTGTTTCG 25 7 0 CTCTCCTTGT 0.811131 -19 GCTGTTTTTTCTCTCCTTTTAAATCGAAAA 26 13 0 CTCTCCTTTT 0.8789 -20 GCCATGACATCACTCCCTTTTCGC 29 5 0 CACTCCCTTT 0.835348 -131 CGGTTTGGCCTGCCCTTTTTATCTTTATT 29 117 0 CTGCCCTTTT 0.879647 -19 TATAGCCTGTCTCTCCTTGTCGCGGCTATT 30 183 0 CTCTCCTTGT 0.811131 -71 GTTCTTACACTCCTTTAACGGTTATTC 33 8 1 CACTCCTTTA 0.835072 -270 ********** Masking position 6 Map Score: 14.3669 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 210 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 8 TTTGTGCGTAATTTATTCACAAGCTTGCATTG 7 104 1 ATTTTCACAA 0.954921 -141 CCATGTGTGAAGTTGATCACAAATTTAAACAC 11 45 1 ATTATCACAA 0.769552 -219 TCTGGTATCGATTTGTTTACAAATGAGCCGCT 12 102 1 ATTTTTACAA 0.806624 -93 CGTTTTCCGCACTTTTTCACAATTTCCCATAA 20 46 1 ATTTTCACAA 0.954921 -123 TATTTCATGAACAAATTCACAATGTCCCTAAA 22 215 1 AAATTCACAA 0.804465 -86 GTTCATATTAAGTACTTTACAACGATTCATTT 35 92 0 ATATTTACAA 0.83711 -209 AATATTGCTCAATATTTCACAAATGTGTCAAA 35 182 0 ATATTCACAA 0.963097 -119 GACTTTGATCAGTAATTCACAAAATAGACGAA 35 217 0 ATATTCACAA 0.963097 -84 TAATTTGCTCACTACTTCACAAATAGAACCGA 35 249 0 ATATTCACAA 0.963097 -52 * ** ******* Masking position 7 Map Score: 5.1551 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 Motif number 9 GACCATTGACTGGCTGAATGGTCTGTCATAC 5 46 1 TGGCTGAAGG 0.819966 -238 AAAAATAAAATGGCATAGCGGGATATGCCGC 6 26 1 TGGCATAGGG 0.898739 -245 TCTTAAGCTCTGGCACAGTTGTTGCTACCAC 7 189 1 TGGCACAGTG 0.972059 -56 AGCTTTCCTCGCAGAGTTGGCCCATTTCC 11 245 0 TCGCAGAGTG 0.787221 -19 TGTAAATGATTGGCTCAGCTGCGGCTTTTAC 12 60 1 TGGCTCAGTG 0.886283 -135 TGGCTGGTGGTGGCATAGCAGATGAGTTAGA 16 266 1 TGGCATAGAG 0.629733 -35 TGTGCCAATATGGCACAAGGGTTTTCTA 19 8 0 TGGCACAAGG 0.953112 -154 TGTGCCATATTGGCACAAGGGTTTTTATGTT 19 22 1 TGGCACAAGG 0.953112 -140 ATTTGTGTTTCGGCAGAAGTGAAAATATTTT 19 72 0 CGGCAGAATG 0.788647 -90 AGTGATGTCATGGCAGAGCTGAGCGGAAATT 29 21 1 TGGCAGAGTG 0.972059 -115 TCCTCATTATTGGGACAATTGAACTTGTACA 33 62 0 TGGGACAATG 0.698025 -216 ATAGAACTAATGACAGAACTGAAAGATCATG 34 14 0 TGACAGAATG 0.609315 -287 ******** ** Masking position 7 Map Score: 5.44153 Number of sites scoring better than the average of aligned sites = 507 Number in coding regions = 483 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 10 ATCAGTAACAAAAGTAAAGAAGGCGACACCA 3 19 1 AAAGTAAAAA 0.526882 -104 TGTAAAAAGTAAAGTAGAGAAACTATTCAAA 12 160 1 AAAGTAGAAA 0.847093 -35 ACTGTGGGATAAAAATGAAAAGATTATGGGA 20 70 0 AAAAATGAAA 0.527895 -99 TAGACATGTGAAAATAGAGAAACGGAGTGAA 20 144 1 AAAATAGAAA 0.933455 -25 TTTTTTTGGTAAAATAAAAAACTGCATATCC 21 16 1 AAAATAAAAA 0.738207 -285 TTATGATGTTAAAATAAAAAATTGTATACGG 21 208 0 AAAATAAAAA 0.738207 -93 TTTTAACATCATAATAGATGATAAGAATCAT 21 225 1 ATAATAGAGA 0.425873 -76 CGGGCTCTCCAAAATTGAAAAGCCCGGGGGT 22 146 0 AAAATTGAAA 0.71718 -155 GTTTGTAGTAAAAGAAGATGAAGAAGCTGTT 23 160 1 AAAGAAGAGA 0.505907 -92 TTTGAAAATTAAAATAAAGAAAGTAGGCATA 30 230 1 AAAATAAAAA 0.738207 -24 TAAAAAGAGAGAAAGGCTTGCTT 32 3 1 AAAAGAGAAA 0.655558 -209 AAGATGACATAAAATAGAGAAATAGGATGTC 32 164 1 AAAATAGAAA 0.933455 -48 GCAAAGCACCAAAATAGAATATGTTTGATCA 33 98 1 AAAATAGATA 0.529781 -180 ATTGTGGGATAAAAATGAAAAGAATATGTGA 33 190 1 AAAAATGAAA 0.527895 -88 AATAAGCAACAAAATAGACAAAAATCCGTCA 35 20 1 AAAATAGAAA 0.933455 -281 AGTAATTCACAAAATAGACGAAAAAAATATT 35 208 0 AAAATAGAGA 0.854643 -93 CGGCCGGTTCAAAGAAGAAGACGTCATTGAT 38 28 1 AAAGAAGAGA 0.505907 -273 AACTTTTTTTAAAAAAGATAACTTTATTGAA 38 85 0 AAAAAAGAAA 0.860829 -216 GACCAGCATGACAATAGATAAACAACTGGCG 38 116 1 ACAATAGAAA 0.597984 -185 GTCAAAAGATAAAAAAAATAAAGGTTTAGAA 38 171 0 AAAAAAAAAA 0.554247 -130 TTAAACCGTTATAATAGACAAGGACCCATTC 38 203 1 ATAATAGAAA 0.638952 -98 ******** ** Masking position 8 Map Score: 13.0908 Number of sites scoring better than the average of aligned sites = 225 Number in coding regions = 146 Number in noncoding regions = 79 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 11 GCGTTAACGCCTGACGACTGAACATCCTGTC 4 80 1 CTGACGCTGA 0.971908 -47 TGACGCATGTTTGCAGCCTGAATCGTAAACT 10 50 0 TTGCAGCTGA 0.741658 -97 TTTACACCCCCTGACGCATGTTTGCAGCCTG 10 61 0 CTGACGATGT 0.93149 -86 ATCAAACCAGTTGACGCCTGAATTGGGCAGT 11 99 0 TTGACGCTGA 0.887807 -165 TCTAAAAAAACTGCCGGCTGACGCTGGCAGT 12 22 1 CTGCCGCTGA 0.982103 -173 GCAACTATTCCTGAAGGATGTTCATGCTCGT 15 14 0 CTGAAGATGT 0.756682 -92 TGAAAATTGCCTGCCGTATGTTAAAACTAGT 33 226 1 CTGCCGATGT 0.955686 -52 GATTTTCCTCCTGCCGAATGACTTCATTTCA 38 274 0 CTGCCGATGA 0.971908 -27 ****** **** Masking position 9 Map Score: 3.76309 Number of sites scoring better than the average of aligned sites = 251 Number in coding regions = 237 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 12 GGTACGTCGTTACCGCTGCTGGAATGTTGC 4 26 0 TACCGCTGCT 0.893239 -101 GGTAACGACGTACCGCTGCTTTTTTTTGCC 4 42 1 TACCGCTGCT 0.893239 -85 TCGGAAGACGTCCAGCCGCTGCTTTTTATG 5 231 0 TCCAGCCGCT 0.900641 -53 CTGGGGCGCGTCCCCTTGCTGATAAATTAA 18 53 1 TCCCCTTGCT 0.960989 -160 TCAACATACCTCCCCTTGATTTGTGTTTCG 19 91 0 TCCCCTTGAT 0.682762 -71 AACCTGCACTTCCCCACGCTGGTATTATCC 21 104 1 TCCCCACGCT 0.890253 -197 GACCATCCTCTCCCGTCCCTATATGAAAAA 21 277 0 TCCCGTCCCT 0.877098 -24 ATTACTCGCCTCCCCTCCCTCC 23 3 0 TCCCCTCCCT 0.877098 -249 GTTTTCCCCCTGCTTTCCTTCTGT 28 67 0 TCCCCCTGCT 0.979757 -14 AGCAGCACTATCCAGCTGCTTGTGAAATTG 30 28 0 TCCAGCTGCT 0.893236 -226 ********** Masking position 1 Map Score: 5.93201 Number of sites scoring better than the average of aligned sites = 377 Number in coding regions = 356 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 13 CGGGCAACCCGAAAGGAATACGCAGACGTA 5 154 1 GAAAGGAATA 0.721306 -130 AAAAGGGGCTGAAAGCAGGT 14 37 1 GAAAGCAGGT 0.605875 -10 CCGTTACCAAGAGAGGAGTATCGAAACATA 16 111 1 GAGAGGAGTA 0.818512 -190 AGATGAGTTAGAAAGGAGGATATCAA 16 285 1 GAAAGGAGGA 0.95954 -16 TATTGTATATGAAAGGACTGAGTCG 20 6 0 GAAAGGACTG 0.829512 -163 ATTGTATACGGAAAGCACTAGGGGTGCTGT 21 189 0 GAAAGCACTA 0.622093 -112 ATAGGGACGGGAGAGGATGGTCAAAT 21 285 1 GAGAGGATGG 0.543809 -16 GTAACAGAAGGAAAGCAGGGGGAAAAC 28 64 1 GAAAGCAGGG 0.922189 -17 GTTTTCCCCCGAAAGGTGTGGTATAATAGC 30 159 1 GAAAGGTGTG 0.651459 -95 TGATAAATGGGAAAGGAGTATTGAT 31 6 0 GAAAGGAGTA 0.94382 -262 TTATTTTAGCGAAAGCAGGACATTCCGACA 32 118 0 GAAAGCAGGA 0.906991 -94 GAATAACCGTTAAAGGAGTGTAAGAAC 33 8 0 TAAAGGAGTG 0.53602 -270 GTTAAGGGAAGAAAGGAAGAGAAAAAGAGC 33 144 0 GAAAGGAAGA 0.785115 -134 ACACTAGGCGGAAAGTAGTAGTTTACTTTT 34 244 1 GAAAGTAGTA 0.569654 -57 AACGTTCTTGGAAAGGATGGAAT 36 56 1 GAAAGGATGG 0.816191 -13 ********** Masking position 4 Map Score: 7.9478 Number of sites scoring better than the average of aligned sites = 219 Number in coding regions = 160 Number in noncoding regions = 59 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 14 TTTTATTCCGTGATCAAAATCACCTCTTAAAATGCAA 6 120 0 TAAAATACCT 0.792948 -151 TGGAATTGATTTATGAAAGAAACCGCGTAGGAAGTGT 13 44 1 TAAAAAACCG 0.775568 -42 TTTTTATAAAACACACACGTTTTTCAATTA 17 4 1 TAAAAAACAT 0.917805 -93 CTTTACAAAATCAAAAAACACACACGTAATTACACTT 17 45 0 TAAAAAACAT 0.917805 -52 GGCGGTCTTATCAATAAAAATACCTATACGGAGGAAC 18 15 0 TAAAAAACCT 0.916235 -198 GTTTTTTATTTTACCAAAAAAACAGGA 21 1 0 TAAAAAACAA 0.765694 -300 ATTAAGCGCACAAAAAAATACACCATTCGGTCAACCT 21 72 1 CAAAAAACCT 0.810508 -229 GAATATTTCATGAACAAATTCACAATGTCCCTAAAGT 22 212 1 TAAAATACAG 0.5526 -89 CGCTGTTTTATGATTAAAGTAACCCGTTTGAACGGGC 23 41 1 TAAAATACCT 0.792948 -211 CGCAGCTTTCTACCGAAAAATACAAATATTTGCAATG 23 202 1 TCAAAAACAT 0.586106 -50 ATTGGGACAGCGATTAAATACACAAGAAAGGCCGCAT 29 58 0 CAAAAAACAA 0.560997 -78 AGGACCTGAATCATGAAAAATACAGTTCCGTTAGGTT 30 63 1 TAAAAAACAT 0.917805 -191 CATAAATAAGCAACAAAATAGACAAAAATCCGTCACA 35 16 1 CAAAAAACAA 0.560997 -285 TGTGAAGTAGTGAGCAAATTAACAGTTTTAACCGGAA 35 260 1 TAAAATACAT 0.796315 -41 TCAACTTTTTTTAAAAAAGATAACTTTATTGAAACCT 38 81 0 TAAAAAAACT 0.366353 -220 AAATAAAGGTTTAGAAAAAAAACACATGTTTCACCTT 38 150 0 TAAAAAACAT 0.917805 -151 * * *** * *** * Masking position 8 Map Score: 5.86132 Number of sites scoring better than the average of aligned sites = 183 Number in coding regions = 129 Number in noncoding regions = 54 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 15 CGGGTTGCCCGGTGACCGGATGTGTTTTTTC 5 134 0 GTGACCGGAT 0.979118 -150 CATTCGTAATGTTTTCCGGATGATGGG 9 61 1 GTTTCCGGAT 0.785878 -17 AAAAGCCGCAGCTGAGCCAATCATTTACATA 12 58 0 GTGAGCCAAT 0.686485 -137 CGGTGGCAGGTGTGAACCGATCCTCCCCTGA 16 18 1 TTGAACCGAT 0.614806 -283 GAATTGCTTTGCTGAACGGATAGTAGGCGAT 16 65 1 GTGAACGGAT 0.902276 -236 GGAAGTGCAGGTTGACCGAATGGTGTATTTT 21 86 0 GTGACCGAAT 0.929725 -215 TTTGATCCCTTATGACCCGATCTGGATAATA 21 126 0 TTGACCCGAT 0.890177 -175 CAGATTGAATGTTTTCCGGATACTACAATTA 23 110 1 GTTTCCGGAT 0.785878 -142 GTATTTAATCGCTGTCCCAATCTTCGGCGGG 29 74 1 GTGTCCCAAT 0.856949 -62 CAATGTATCTGCTGACCCGATTCGAAAAGAA 34 58 0 GTGACCCGAT 0.979118 -243 * ********* Masking position 3 Map Score: 3.32979 Number of sites scoring better than the average of aligned sites = 393 Number in coding regions = 361 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789