AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -irpoH_ecoli_opreg_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 dnaK 300 chaperone Hsp70; DNA biosynthesis; autoregulated heat shock proteins #2 dnaJ 88 chaperone with DnaK; heat shock protein #3 clpP 245 ATP-dependent proteolytic subunit of clpA-clpP serine protease, heat shock protein F21.5 #4 clpX 125 ATP-dependent specificity component of clpP serine protease, chaperone #5 lon 187 DNA-binding, ATP-dependent protease La; heat shock K-protein #6 htpG 109 chaperone Hsp90, heat shock protein C 62.5 #7 gapA 300 glyceraldehyde-3-phosphate dehydrogenase A #8 clpB 129 heat shock protein #9 grpE 122 phage lambda replication; host DNA synthesis; heat shock protein; protein repair #10 rpsU 237 30S ribosomal subunit protein S21 #11 dnaG 110 DNA biosynthesis; DNA primase #12 rpoD 194 RNA polymerase, sigma(70) factor; regulation of proteins induced at high temperatures #13 hflB 99 degrades sigma32, integral membrane peptidase, cell division protein #14 ftsJ 125 cell division protein #15 ibpA 230 heat shock protein #16 hslV 92 heat shock protein hslVU, proteasome-related peptidase subunit #17 ftsN 91 essential cell division protein #18 cytR 155 regulator for deo operon, udp, cdd, tsx, nupC, and nupG #19 mopB 275 GroES, 10 Kd chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity #20 mopA 43 GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein Motif number 1 ACCACGTCATCAAGGGGGAGATGCAAAAATTTT 1 142 0 CAAGGGGAGG 0.993492 -159 GAGTCTGTAATAGGGGCGAAACGTCTGGTTTCA 1 238 0 TAGGGGGAAG 0.906383 -63 ATTATACTGACACGGGCGAAGGGGAATTTCCTC 2 29 1 CACGGGGAAG 0.970503 -60 TAGATGAATGCACGGGCGGAGAGGAAATTCCCC 2 49 0 CACGGGGGAG 0.927879 -40 ATGCCATTCTCAGGCGCAAGCCGCTTACAGCGT 4 56 0 CAGGCGAAGG 0.776356 -70 GAGGAAAAATTAAAGGGGAGATAAAATCCCCCC 5 44 0 TAAAGGGAGA 0.665113 -144 GCAAACGAGAGCAGGATCACCTGC 6 2 1 CAAACGGAGG 0.938502 -108 AGAATAATTTCAAGCGAGAGCAGGTGATCCTGC 6 21 0 CAAGCGGAGG 0.981298 -89 GAGATGGGGACAAGGGAGAATAATTTCAAGCGA 6 37 0 CAAGGGGAAA 0.965048 -73 GTCTCAAGCCCAAAGGAAGAGTGAGGCGAGTCA 7 151 1 CAAAGGAGAG 0.518594 -150 AGGCTTTCTCCAGGGGCGAACAAAGTTTTACAT 10 63 0 CAGGGGGAAA 0.948208 -175 GGGACTTTTATAAGGGTGAGGAGTATACACGAG 10 94 0 TAAGGGGAGG 0.959149 -144 CCGAATTAATCAAAGGTGAGAGGCAC 10 222 1 CAAAGGGAGG 0.977973 -16 CCTGACGTGCCAGGCGAGGAGTGAGT 18 140 1 CAGGCGGGAG 0.894301 -16 TTCGCCCCTTCAAGGGGGAAAAAGAAAAAAAAT 19 158 0 CAAGGGGAAA 0.965048 -118 CGGACTTTCTCAAAGGAGAGTTATCA 19 260 1 CAAAGGGAGA 0.928124 -16 ****** *** * Masking position 2 Map Score: 21.1131 Number of sites scoring better than the average of aligned sites = 647 Number in coding regions = 559 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 95 Fraction of orfs with sites within 600 bp upstream = 0.0152586 Motif number 2 CGTGGTTTACGACCCCATTTAGTAGTCAAC 1 169 1 GACCCCATTT 0.976523 -132 GAGATAAAATCCCCCCTTTTTGGTTAACTA 5 30 0 CCCCCCTTTT 0.903612 -158 GACTGTGCTTCACGCCATCTATTAACATGT 5 123 0 CACGCCATCT 0.852704 -65 ATTCTCCCTTGTCCCCATCTCTCCCACATC 6 49 1 GTCCCCATCT 0.930526 -61 TGGGGTCGGCGCCCCGAATTTTAAAGGGCA 7 117 0 GCCCCGAATT 0.867471 -184 TCGGGGCGCCGACCCCATGTGGTCTCAAGC 7 130 1 GACCCCATGT 0.963034 -171 ATTGAGGGATGACCTCATTTAATCTCCAGT 8 81 1 GACCTCATTT 0.687361 -49 AGGCCCCGATTTTTAGCAATTC 11 99 0 GCCCCGATTT 0.975932 -12 TTGGGCGATTGACCCGATGTCCTTCAGCCG 12 140 0 GACCCGATGT 0.940566 -55 GCGGTAGAATGACCCGTTTTCAATCCCAAC 14 27 0 GACCCGTTTT 0.862704 -99 GGGTCATTCTACCGCCATCTCCCATATATC 14 42 1 ACCGCCATCT 0.717062 -84 CCTCAAAATCCCCCCCATCTATAATTGCAT 16 14 1 CCCCCCATCT 0.974628 -79 ATTGCATTATGCCCCGTACTTTTGTACGGG 16 37 1 GCCCCGTACT 0.623877 -56 CGTTCGTCAGCCCGCCATGTTACTTAAGCG 17 51 0 CCCGCCATGT 0.850973 -41 TCAGGGTTTTCACCCGATTTTGTGCTGATC 19 125 1 CACCCGATTT 0.934509 -151 GCGAAGCCTCATCCCCATTTCTCTGGTCAC 19 186 1 ATCCCCATTT 0.669419 -90 ********** Masking position 10 Map Score: 15.3827 Number of sites scoring better than the average of aligned sites = 440 Number in coding regions = 372 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 3 CTGCCATATCGCGAAATTTCTGCGCAAAAG 1 107 1 GCGAAATTTC 0.679535 -194 CACGGGCGAAGGGGAATTTCCTCTCCGCCC 2 39 1 GGGGAATTTC 0.932426 -50 CCTGGCGGTGACGGGCCTTTGTGCGAATTT 3 31 0 ACGGGCCTTT 0.793581 -215 CCGCCAGGTGGTGGGCTTTTTTTTGTCATG 3 53 1 GTGGGCTTTT 0.894021 -193 AACCAAAAAGGGGGGATTTTATCTCCCCTT 5 35 1 GGGGGATTTT 0.972661 -153 GATCCGGTACGCGTGATTTTCTTTTCACAT 8 27 1 GCGTGATTTT 0.756129 -103 CTTTTTTGAAAGGGACTTTTATAAGGGTGA 10 108 0 AGGGACTTTT 0.836362 -130 GTAAAGCACCGCGGCCTTTTTTGAAAGGGA 10 123 0 GCGGCCTTTT 0.925942 -115 TCAAAATGGTGCGGAATTTTACTGCAATTG 10 163 0 GCGGAATTTT 0.95695 -75 TGCGGCTGTCGGGGGCTTCCCGATCGCTCT 12 31 0 GGGGGCTTCC 0.878701 -164 CCGGGAGATTTCAGACGAAAGT 13 3 1 GGGAGATTTC 0.772412 -97 AGCCTTATCAGCGGACTTTTTTTTGCAGTT 15 82 0 GCGGACTTTT 0.975981 -149 TTATAGATGGGGGGGATTTTGAGGGTT 16 8 0 GGGGGATTTT 0.972661 -85 TACTTAAGCGGCGGGCCTTTGACCAGTCAC 17 31 0 GCGGGCCTTT 0.958507 -61 CATAACAGATACGGACTTTCTCAAAGGAGA 19 249 1 ACGGACTTTC 0.847426 -27 ********** Masking position 8 Map Score: 13.9902 Number of sites scoring better than the average of aligned sites = 1004 Number in coding regions = 809 Number in noncoding regions = 195 Number of orfs with sites within 600 bp upstream = 167 Fraction of orfs with sites within 600 bp upstream = 0.026823 Motif number 4 CGGCACAGTTGCGCCTCTGGCA 4 2 0 GCGCCTCTGC 0.939443 -124 TTACAGCGTTGTGCCGCCCTGGATAAGTATA 4 34 0 GTGCCGCCCG 0.980534 -92 TTTGTTCTTTGTGCCGCACACGACGACGCAA 4 89 0 GTGCCGCACC 0.990235 -37 TGACACGACTGTGCTTCACGCCATCTATTAA 5 128 0 GTGCTTCACC 0.839609 -60 AAAATTCGGGGCGCCGACCCCATGTGGTCTC 7 125 1 GCGCCGACCC 0.935956 -176 CGCGACTGACTCGCCTCACTCTTCCTTTGGG 7 159 0 TCGCCTCACC 0.758294 -142 TTAATTCGGTTTGCCGCTGGCATCAACGCCA 10 200 0 TTGCCGCTGC 0.97119 -38 GTGCCTCTCACCTTTGATTAA 10 227 0 GTGCCTCTCC 0.978068 -11 AACGGCTTAAGTGCCGAAGAGCGATCGGGAA 12 14 1 GTGCCGAAGG 0.890981 -181 CTGCCTCTCAGTGCGGCTGTCGGGGGCTTCC 12 41 0 GTGCGGCTGC 0.938218 -154 ACTTATATATTTGCCGCTGCCTCTCAGTGCG 12 57 0 TTGCCGCTGC 0.97119 -138 TTAACGTTTCGTGCTGCCCCCTCAGTCTATG 15 39 1 GTGCTGCCCC 0.960611 -192 GCTAAAAATGTTGCCGATGTGAAGTAAACAT 18 97 1 TTGCCGATGG 0.782295 -59 ACCCGATTTTGTGCTGATCAGAATTTTTTTT 19 136 1 GTGCTGATCG 0.785004 -140 ********* * Masking position 4 Map Score: 13.9581 Number of sites scoring better than the average of aligned sites = 2289 Number in coding regions = 2203 Number in noncoding regions = 86 Number of orfs with sites within 600 bp upstream = 84 Fraction of orfs with sites within 600 bp upstream = 0.0134918 Motif number 5 CTTTGTGCGAATTTAGCGCGTTATGCTGCGTAA 3 12 0 ATTTACCGTA 0.777671 -234 CGAAAGAGGCTTTTCGCACGGTTCCATGCAAAA 3 85 0 TTTTCCCGTT 0.954877 -161 TATGGGGATGTTTCCCCCACATTCAACGCCGAG 5 81 0 TTTCCCACTT 0.642675 -107 CTTAGTTTAATTTCCGCCAGGTAATCAGATGAC 5 155 0 TTTCCCAGTA 0.811682 -33 AAAATGTGATTTTCATCACGATTTAGGTGCAGC 7 75 0 TTTCACCGTT 0.969073 -226 ATATTCCACCAGCTATTTGTTAGTG 7 286 0 ATTCCCAGTA 0.68943 -15 TTTTTTTCGCATTCATCTCGCTAACTTCGCTTA 9 87 0 ATTCACCGTA 0.892609 -36 GAATTTCTCCGCGTTTTTTTCGCATT 9 107 0 TTTCTCCGTT 0.848836 -16 GACTTGTTTTACCTCGCTTTATTACCGCG 10 7 1 TTTTACCGTT 0.92951 -231 TTGCAGTAAAATTCCGCACCATTTTGAAATAAG 10 166 1 ATTCCCCCTT 0.847702 -72 CTGACGCTGTTTTTAACACAGTTGTAATAAGAG 13 59 1 TTTTACCATT 0.724159 -41 AAAATTCAATATTCATCACACTTTTCATGAAAA 18 37 1 ATTCACCATT 0.762637 -119 TCTGTAACCGTTTTCACGCGCTATCTGCTAAAA 18 71 1 TTTTCCCGTA 0.915959 -85 TCACCTCACATTTCATCGCAATTTCTTCATCGC 19 91 0 TTTCACCATT 0.861847 -185 TGAATCAGGGTTTTCACCCGATTTTGTGCTGAT 19 121 1 TTTTCCCGTT 0.954877 -155 ***** * ** ** Masking position 3 Map Score: 11.4281 Number of sites scoring better than the average of aligned sites = 706 Number in coding regions = 630 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 100 Fraction of orfs with sites within 600 bp upstream = 0.0160617 Motif number 6 TCCCCCTTGATGACGTGGTTTACGACCCCATTTA 1 156 1 TGCGTGTTCG 0.784921 -145 AGACTCACAACCACATGATGACCGAATATATAGT 1 265 1 CCCATATACG 0.973406 -36 ATGGCATTTGCGTCGTCGTGTGCGGCACAAAGAA 4 82 1 CGCGTGTTCG 0.926987 -44 GGGATGTTTCCCCCACATTCAACGCCGAGAATAG 5 76 0 CCCACTTACG 0.751756 -112 GTGATGAAAATCACATTTTTATCGTAATTGCCCT 7 89 1 TCCATTTACG 0.846601 -212 TGAAACTGATCCCCATAATAAGCGAAGTTAGCGA 9 69 1 CCCATATACG 0.973406 -54 GAATTTCTCCGCGTTTTTTTCGCATTCATCTC 9 101 0 CCCGTTTTCG 0.951542 -22 TTGTTTTACCTCGCTTTATTACCGCGCAGTGTAG 10 14 1 TCCTTATACG 0.685952 -224 ATAAGTACGCCCTCGTAATTATCGTTGGCGGTAA 12 82 1 CCCGTATACG 0.983217 -113 TCAGGCGCGTCCTCATCGGCTACGATGTAAAAAT 15 134 0 CCCATGGTCG 0.888954 -97 TCGATCCGCCTCGCATCGTGAGCGGT 18 3 0 TCCATGTACG 0.919345 -153 ATTTCTTCATCGCCGTCATAAGCGAATCTGATTG 19 70 0 CGCGTATACG 0.948292 -206 AGCCGGGAAACCACGTAAGCTCCGGCGTCACCCA 19 217 1 CCCGTAGTCG 0.922036 -59 ** *** ** * ** Masking position 4 Map Score: 10.5314 Number of sites scoring better than the average of aligned sites = 649 Number in coding regions = 596 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 7 ACGTGGTTTACGACCCCATTTAGTAGTCAA 1 168 1 CGACCCCATT 0.959401 -133 GTCAGTATAATTACCCGTTTATAGGGCGA 2 10 0 TTACCCGTTT 0.782801 -79 TTCGGGGCGCCGACCCCATGTGGTCTCAAG 7 129 1 CGACCCCATG 0.9439 -172 TCGCAATGATTGACACGATTCCGCTTGACG 7 216 1 TGACACGATT 0.876442 -85 TCAAGGTTATTGACCAGATTAATGTGAAAA 8 48 0 TGACCAGATT 0.888386 -82 AATTGAGGGATGACCTCATTTAATCTCCAG 8 80 1 TGACCTCATT 0.84345 -50 GTTGGGCGATTGACCCGATGTCCTTCAGCC 12 141 0 TGACCCGATG 0.982995 -54 GGCGGTAGAATGACCCGTTTTCAATCCCAA 14 28 0 TGACCCGTTT 0.973519 -98 GAGCTGACCCCTTGGTTACGAATA 16 79 0 TGACCCCTTG 0.946576 -14 ATCAGGGTTTTCACCCGATTTTGTGCTGAT 19 124 1 TCACCCGATT 0.921856 -152 ********** Masking position 3 Map Score: 8.93733 Number of sites scoring better than the average of aligned sites = 221 Number in coding regions = 208 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 8 AAGCCCACCACCTGGCGGTGACGGGCCTTTG 3 40 0 CTGGCGGTGA 0.97826 -206 TTCCTCTATTCTCGGCGTTGAATGTGGGGGA 5 71 1 CCGGCGTTGA 0.891298 -117 CATGTTAATAGATGGCGTGAAGCACAGTCGT 5 124 1 GTGGCGTGAA 0.950794 -64 CATCTGATTACCTGGCGGAAATTAAACTAAG 5 157 1 CTGGCGGAAA 0.762519 -31 AATTTTGCCAGTTGGTGTTAATGTTTTGTTA 7 16 0 GTGGTGTTAA 0.826176 -285 TTTGAAATAAGCTGGCGTTGATGCCAGCGGC 10 188 1 GTGGCGTTGA 0.98554 -50 TCTCAGTGCGGCTGTCGGGGGCTTCCCGATC 12 36 0 GTGTCGGGGG 0.765085 -159 CGTAATTATCGTTGGCGGTAAACAACCGTTG 12 95 1 GTGGCGGTAA 0.983243 -100 ATTTCATGAGGTTGGTGTTGGGCGATTGACC 12 156 0 GTGGTGTTGG 0.854444 -39 ATATATGGGAGATGGCGGTAGAATGACCCGT 14 40 0 GTGGCGGTAG 0.970418 -86 TGCAATTATAGATGGGGGGGATTTTGAGGGT 16 12 0 GTGGGGGGGA 0.913146 -81 ATTCGCTTATGACGGCGATGAAGAAATTGCG 19 77 1 GCGGCGATGA 0.853535 -199 * ********* Masking position 7 Map Score: 7.64842 Number of sites scoring better than the average of aligned sites = 3335 Number in coding regions = 3239 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 108 Fraction of orfs with sites within 600 bp upstream = 0.0173466 Motif number 9 GATATGGCAGGACAAGACGTAAAATTGACAGCAATT 1 81 0 GGAGTAAAAT 0.981728 -220 CGTCATCAAGGGGGAGATGCAAAAATTTTTTGTGCT 1 135 0 GGAGCAAAAT 0.968178 -166 CTTTTCGCACGGTTCCATGCAAAATTCATGACAAAA 3 73 0 GCAGCAAAAT 0.902602 -173 TCAACGCCGAGAATAGAGGAAAAATTAAAGGGGAGA 5 56 0 GGAGAAAAAT 0.917726 -132 GTGAATAAAAGGTTGCCTGTAAAATTACAAAAACCT 7 253 0 GCCGTAAAAT 0.888882 -48 GGACCAATGCGGGTTGATGTAAAACTTTGTTCGCCC 10 47 1 GGAGTAAAAT 0.981728 -191 AAAGCAGCAGCAATTGCAGTAAAATTCCGCACCATT 10 153 1 CGCGTAAAAT 0.792358 -85 GTCCTCATCGGCTACGATGTAAAAATGGGTCTGGAA 15 124 0 GGAGTAAAAT 0.981728 -107 AAATGTTGCCGATGTGAAGTAAACATGGATGTAGTA 18 102 1 GGAGTAAACT 0.926218 -54 * ** ****** * Masking position 11 Map Score: 5.19442 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 58 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 10 CACGTCATCAAGGGGGAGATGCAAAAATTT 1 143 0 AGGGGGAGAT 0.910413 -158 GAGTCTGTAATAGGGGCGAAACGTCTGGTT 1 241 0 TAGGGGCGAA 0.662874 -60 GTTAACCAAAAAGGGGGGATTTTATCTCCC 5 32 1 AAGGGGGGAT 0.799163 -156 GGAAAAATTAAAGGGGAGATAAAATCCCCC 5 45 0 AAGGGGAGAT 0.912033 -143 ACGTCAGTATATGGGGATGTTTCCCCCACA 5 93 0 ATGGGGATGT 0.788653 -95 TGTGGGAGAGATGGGGACAAGGGAGAATAA 6 47 0 ATGGGGACAA 0.829055 -63 TTCGCTTATTATGGGGATCAGTTTCAGGGT 9 65 0 ATGGGGATCA 0.691853 -58 AGGCTTTCTCCAGGGGCGAACAAAGTTTTA 10 66 0 CAGGGGCGAA 0.744522 -172 GACTTTTATAAGGGTGAGGAGTATACACGA 10 95 0 AGGGTGAGGA 0.722495 -143 TTATTTCAAAATGGTGCGGAATTTTACTGC 10 168 0 ATGGTGCGGA 0.728634 -70 TAACTTTCCCATGGGGATAACTCATCGTAA 14 105 0 ATGGGGATAA 0.915009 -21 GCAATTATAGATGGGGGGGATTTTGAGGGT 16 12 0 ATGGGGGGGA 0.92895 -81 CGCCCCTTCAAGGGGGAAAAAGAAAAAAAA 19 159 0 AGGGGGAAAA 0.699685 -117 TTCCCCCTTGAAGGGGCGAAGCCTCATCCC 19 171 1 AAGGGGCGAA 0.95233 -105 GACCAGAGAAATGGGGATGAGGCTTCGCCC 19 184 0 ATGGGGATGA 0.90734 -92 ********** Masking position 6 Map Score: 9.43342 Number of sites scoring better than the average of aligned sites = 536 Number in coding regions = 436 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 106 Fraction of orfs with sites within 600 bp upstream = 0.0170254 Motif number 11 TTTACGCAGCATAACGCGCTAA 3 3 1 TACGCAGCAT 0.880253 -243 CACAACGCTGTAAGCGGCTTGCGCCTGAGA 4 52 1 TAAGCGGCTT 0.907014 -74 GCCTAAGCATTACGCGACTGACTCGCCTCA 7 172 0 TACGCGACTG 0.901207 -129 ACAAAAACCTTACGCAGCGTCAAGCGGAAT 7 233 0 TACGCAGCGT 0.919163 -68 CCGAAAGGAATGCGCGGCTTATTTTCGTTT 11 67 1 TGCGCGGCTT 0.922622 -44 CGTAAAAATTTACGCAATTGGTTACGATGA 14 84 1 TACGCAATTG 0.551841 -42 CGTACAAAAGTACGGGGCATAATGCAATTA 16 35 0 TACGGGGCAT 0.842522 -58 CGTACTTTTGTACGGGGTTTGTACTCTGTA 16 51 1 TACGGGGTTT 0.861501 -42 CCATGTTACTTAAGCGGCGGGCCTTTGACC 17 37 0 TAAGCGGCGG 0.816816 -55 ATCGAAAATCTACGCAGTTGCCCAAAATTT 19 33 0 TACGCAGTTG 0.888799 -243 CGCCGGAGCTTACGTGGTTTCCCGGCTGGT 19 214 0 TACGTGGTTT 0.695167 -62 ********** Masking position 1 Map Score: 3.55176 Number of sites scoring better than the average of aligned sites = 1523 Number in coding regions = 1440 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 105 Fraction of orfs with sites within 600 bp upstream = 0.0168648 Motif number 12 CCCATTTAGTAGTCAACCGCAGTGAGTGAG 1 182 1 AGTCAACCGC 0.870213 -119 CATTCTCAGGCGCAAGCCGCTTACAGCGTT 4 55 0 CGCAAGCCGC 0.921085 -71 GAGTGAGGCGAGTCAGTCGCGTAATGCTTA 7 169 1 AGTCAGTCGC 0.746345 -132 CCTTACGCAGCGTCAAGCGGAATCGTGTCA 7 226 0 CGTCAAGCGG 0.887806 -75 CAAAGTTTTACATCAACCCGCATTGGTCCT 10 46 0 CATCAACCCG 0.621095 -192 CATAAACGAAAATAAGCCGCGCATTCCTTT 11 70 0 AATAAGCCGC 0.711267 -41 CTCTTCGGCACTTAAGCCGTTAAA 12 5 0 CTTAAGCCGT 0.684888 -190 GGGAAGCCCCCGACAGCCGCACTGAGAGGC 12 40 1 CGACAGCCGC 0.955544 -155 ACCCGATGTCCTTCAGCCGTTAACGCTGAA 12 129 0 CTTCAGCCGT 0.916087 -66 CCAGAACACCCATCAGGCGCGTCCTCATCG 15 150 0 CATCAGGCGC 0.9557 -81 TTTATTCGTTCGTCAGCCCGCCATGTTACT 17 57 0 CGTCAGCCCG 0.957283 -35 TCGCCTGGCACGTCAGGCGTACTACATCCA 18 127 0 CGTCAGGCGT 0.950604 -29 TTTCTCTGGTCACCAGCCGGGAAACCACGT 19 203 1 CACCAGCCGG 0.935816 -73 ********** Masking position 5 Map Score: 6.48765 Number of sites scoring better than the average of aligned sites = 3008 Number in coding regions = 2876 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 123 Fraction of orfs with sites within 600 bp upstream = 0.0197559 Motif number 13 TTTATTACAATTTTTTGATGAATGCCTTGG 1 25 1 TTTTTTGATG 0.678068 -276 TTTTTTGTGCTTTTGCGCAGAAATTTCGCG 1 116 0 TTTTGCGCAG 0.875403 -185 AGCACAAAAAATTTTTGCATCTCCCCCTTG 1 135 1 ATTTTTGCAT 0.488548 -166 CCAATTTCATTTTTTTGCAGACTCACTCAC 1 203 0 TTTTTTGCAG 0.966918 -98 TCTCCGCGTTTTTTTCGCATTCATCTCGCT 9 98 0 TTTTTCGCAT 0.780028 -25 CACCGCGGCCTTTTTTGAAAGGGACTTTTA 10 117 0 TTTTTTGAAA 0.444332 -121 AGGCCCCGATTTTTAGCAATTCATAAACG 11 92 0 TTTTTAGCAA 0.615359 -19 CGTATTTTTTGCTTACGTTGGGAT 14 5 1 TTTTTTGCTT 0.810509 -121 CACTTTAACGTTTCGTGCTGCCCCCTCAGT 15 35 1 TTTCGTGCTG 0.592645 -196 CAGCGGACTTTTTTTTGCAGTTTATGGTCT 15 74 0 TTTTTTGCAG 0.966918 -157 ATCGGCAACATTTTTAGCAGATAGCGCGTG 18 85 0 TTTTTAGCAG 0.890409 -71 TTTCACCCGATTTTGTGCTGATCAGAATTT 19 132 1 TTTTGTGCTG 0.894457 -144 ********** Masking position 3 Map Score: 5.03492 Number of sites scoring better than the average of aligned sites = 683 Number in coding regions = 583 Number in noncoding regions = 100 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 14 TTGTAATAAAAAGAAAAGATTACG 1 4 0 AAAAAAGATT 0.93197 -297 TTAGCGTAACAACAAAAGATTGTTATGCTTG 3 121 1 AAAAAAGATT 0.931964 -125 ACAAAGAACAAAGAAGAGGTTTTGACCC 4 108 1 AAAAGAGGTT 0.946974 -18 GATTCTAACAAAACATTAACACCAACT 7 7 1 AAAAAACATT 0.758514 -294 TTTGTTAGTGAATAAAAGGTTGCCTGTAAAA 7 265 0 AAAAAAGGTT 0.955633 -36 ACACAGTTGTAATAAGAGGTTAATCCCTTGA 13 74 1 AAAAGAGGTT 0.94697 -26 ** ******** Masking position 5 Map Score: 1.32333 Number of sites scoring better than the average of aligned sites = 47 Number in coding regions = 30 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 15 TTTTTGCAGACTCACTCACTGCGGTTGACTAC 1 190 0 CCACTACTGC 0.919132 -111 CGCAGCATAACGCGCTAAATTCGCACAAAGGC 3 15 1 CCGCTAATTC 0.956686 -231 TCGCATTCATCTCGCTAACTTCGCTTATTATG 9 82 0 CCGCTACTTC 0.988733 -41 GAATTTCTCCGCGTTTTTTTCGCATTCATCT 9 102 0 CCGTTTTTTC 0.748157 -21 GGCATCAACGCCAGCTTATTTCAAAATGGTGC 10 181 0 CAGCTATTTC 0.890289 -57 AGACGGTATCCACACTTATTTCATGAGGTTGG 12 172 0 CCACTATTTC 0.94325 -23 GTCTTACATTCTCGCTGATTTCAGGAGCTATT 15 205 1 CCGCTATTTC 0.986426 -26 ACCGTTTTCACGCGCTATCTGCTAAAAATGTT 18 77 1 CCGCTTCTGC 0.947894 -79 * **** ***** Masking position 6 Map Score: 4.35058 Number of sites scoring better than the average of aligned sites = 269 Number in coding regions = 248 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