AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -icpxR6_ecoli_hinf_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 ppiA 270 peptidyl-prolyl cis-trans isomerase A (rotamase A) #10 yihD 69 orf, hypothetical protein #11 yihE 77 orf, hypothetical protein #12 cpxR_b3913 146 cpxR: transcriptional regulator in 2-component system, b3913: orf, hypothetical protein #13 HI0079 102 peptidyl-prolyl cis-trans isomerase B (ppiB) #14 HI0837 53 response regulator (cpxR) #15 HI0839 116 conserved hypothetical protein #16 HI0845 86 conserved hypothetical protein #17 HI0997 300 H. influenzae predicted coding region HI0997 #18 HI0998 180 ribosomal protein L34 (rpL34) #19 HI1002 130 thiophene and furan oxidation protein (thdF) #20 HI1004 272 peptidyl-prolyl cis-trans isomerse, putative #21 HI1259 193 periplasmic serine protease Motif number 1 ACGGCCTGCGGGCCGTTTTGTTTTGTCTGGATTT 3 25 1 GGCTTTTTTT 0.976569 -276 ACAATTCCCGGGCAATTTTCGTCTGAATGCTGGG 3 70 0 GGCTTTGTCT 0.873271 -231 CGTGCGAAAAGCCTCTTTCGGTGTTAGCGTAACA 4 98 1 GCCTTTGTGT 0.895309 -148 GGATTTTATCTCCCCTTTAATTTTTCCTCTATTC 6 48 1 TCCTTTTTTT 0.952642 -140 GGGCTTGCCAGCCTTTTTTTGTCTCGCTAAGTTA 7 60 1 GCCTTTGTCT 0.925689 -149 CTACTGATGTGCCTTTTTTATTTGTATTCGGTGA 8 53 1 GCCTTTTTTG 0.89969 -139 ATCCCGCTATGCCATTTTATTTTTGAACGCAGGC 9 16 0 GCCTTTTTTT 0.986901 -255 CGATATCGCCTCTTTTATTGTGGGATTGACC 10 8 1 GCCTTTTTGT 0.956274 -62 GCTATAAAAGTGCGGTTTGTTTTTATTTCATTTT 13 23 0 TGCTTTTTTT 0.917542 -80 GGTATCATAAGCCAAATTTTTTTTATTTTTAACA 15 13 0 GCCATTTTTT 0.873375 -104 TTTATTTCATTGCTATTTCCTTTTTAATCGTAAA 16 51 0 TGCTTTTTTT 0.917542 -36 TGCTATTTCCTTTTTATTTCATTG 16 73 0 TGCTTTTTTT 0.917542 -14 ATTGAATTTTGGCAGCTTCATTTTCATAGTTAAA 17 14 0 GGCCTTTTTT 0.912334 -287 CCTACCCCCTGCCCACTTTCTTTTTCCCAAGCGG 17 219 0 GCCCTTTTTT 0.949529 -82 TCTGCCCATGGCCATTTTTTTTCTACTGATAAAG 17 258 0 GCCTTTTTCT 0.969564 -43 ACCAAATATTGCCGCTTTTGATTTAAATTTTGCC 20 36 0 GCCTTTATTT 0.881172 -237 TTTGTACTGCTCCGATTTCCTTTTAAACAAGATA 21 89 1 TCCTTTTTTT 0.952642 -105 *** *** **** Masking position 7 Map Score: 23.1102 Number of sites scoring better than the average of aligned sites = 328 Number in coding regions = 240 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 2 CGAACAATAAATTTTTACCTTTTGCAGAAACT 2 28 1 ATTTTACTTT 0.770539 -102 TGTCGCGTATTTTTTCACAATTCCCGGGCAAT 3 88 0 TTTTTACATT 0.948785 -213 TACAGCAGGTTTTTTCAATTTTATCCAGGAGA 4 219 1 TTTTTAATTT 0.914175 -27 AAGCCAAATTTTTTTTATTTTTAACATT 15 7 0 TTTTTATTTT 0.850944 -110 CATTTGCCTATTTTTTACGATTAAAAAGGAAA 16 38 1 TTTTTACATT 0.948785 -49 TTTTTTAACTATGAAAATGAAGC 17 2 1 TTTTTACATG 0.854073 -299 CTGTACGTAATTTTTCAAATTGAATTTTGGCA 17 34 0 TTTTTAATTG 0.770914 -267 AGTGCATATATTTTTTAATATTCGTTTGAAGT 18 59 1 TTTTTAAATT 0.871898 -122 TTTGAAGTTTTTTTTAAAAATTTCCGTTTCTT 18 83 1 TTTTTAAATT 0.871898 -98 TGAGGATGGAGTTTTCACTTTTTAAGATGCTA 20 108 1 GTTTTACTTT 0.832693 -165 AAGATGCTAATTTTTTACGTTTAGATTATAAT 20 131 1 TTTTTACTTT 0.966658 -142 TTTTTGACCTTTTTATTGACTA 21 1 1 TTTTTACTTT 0.966658 -193 ATTGAACATTTTTTTTATTTTTTTGTCTTACA 21 138 1 TTTTTATTTT 0.850944 -56 ***** ** *** Masking position 7 Map Score: 11.4092 Number of sites scoring better than the average of aligned sites = 100 Number in coding regions = 54 Number in noncoding regions = 46 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 3 AATGCTGGGCAAAAAGCGCAAAATCCAGACAAAA 3 45 0 AAGCGCAAAT 0.96703 -256 AAAATACGCGACAGCGCGCAATAACCGTTCTCGA 3 107 1 ACGCGCAATA 0.834981 -194 TAACGCGCTAAATTCGCACAAAGGCCCGTCACCG 4 22 1 AAGCACAAAG 0.700667 -224 TCATCTGATTACCTGGCGGAAATTAAACTAAGAG 6 156 1 ACGCGGAAAT 0.95132 -32 TGACCTCGCGCAAAATGCACTAATAA 7 3 1 ACGCGCAAAT 0.946422 -206 GTCAGCCCACAAGACGCAGAAAGTCACCGAATAC 8 76 0 AAGCAGAAAT 0.93405 -116 TCCTTAACAAACAGAGCAGAAAAAAAGCAAGTGA 9 241 0 ACGCAGAAAA 0.781602 -30 GTGCGGTTATAATTTGCGGCAAATTTTTCAAAG 15 94 1 AAGCGGCAAT 0.81102 -23 TTTAACACTAAATCAGCGGAATCAATGGATATGG 17 109 1 AAGCGGAATA 0.905084 -192 ACGCTCCAAAAAGTGGCACAAAAATTGGTAGTTG 17 183 1 AAGCACAAAA 0.838652 -118 TTCGTCAAATAAGAAACGGAAATTTTTAAAAAAA 18 91 0 AAACGGAAAT 0.783199 -90 GGCAAAAAGAAAGGCACGGAATGTGCTTTCTTTA 19 20 1 AAACGGAATT 0.710014 -111 CTATCTCTACAAAATGCAGAATATATTAAGATCA 19 59 0 AAGCAGAATT 0.905652 -72 GTTAATTGAAAAAATGCACAATTTAACAAACTCA 20 200 1 AAGCACAATT 0.889438 -73 TTTATGTTCTAATACGCGCAATTTTCTAGTCAAT 21 25 0 AAGCGCAATT 0.940414 -169 ** ******* * Masking position 11 Map Score: 12.1463 Number of sites scoring better than the average of aligned sites = 669 Number in coding regions = 599 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 4 ACTCATAAAAGTGATGCCGCTATAATGCCG 3 140 1 GTGATGCCGC 0.97809 -161 AATTTAGCGCGTTATGCTGCGTAAA 4 6 0 GTTATGCTGC 0.846013 -240 TTGAAATATGGTGATGCCGTACCCATAACA 4 149 1 GTGATGCCGT 0.885584 -97 TAGCGGCACAGTTGCGCCTCTGGCA 5 6 0 GTTGCGCCTC 0.900516 -120 CGCTTACAGCGTTGTGCCGCCCTGGATAAG 5 38 0 GTTGTGCCGC 0.993188 -88 TTCTTTGTTCTTTGTGCCGCACACGACGAC 5 93 0 TTTGTGCCGC 0.962225 -33 CGCATCTACTGATGTGCCTTTTTTATTTGT 8 48 1 GATGTGCCTT 0.582338 -144 GGCATAGCGGGATATGCCGCGAGCGGGCGA 9 37 1 GATATGCCGC 0.945887 -234 GATGATTTTGGTGGCGCCGCTTACAAGCTT 11 11 0 GTGGCGCCGC 0.845089 -67 ACTACCAATTTTTGTGCCACTTTTTGGAGC 17 185 0 TTTGTGCCAC 0.739862 -116 ********** Masking position 7 Map Score: 9.44263 Number of sites scoring better than the average of aligned sites = 1033 Number in coding regions = 970 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 5 CAATTAGTTAACCAAAAAGGGGGGATTTTA 6 26 1 ACCAAAAAGG 0.527341 -162 AAAATGCACTAATAAAAACAGGGCTGGCAG 7 22 1 AATAAAAACA 0.743551 -187 ACTTAGCGAGACAAAAAAAGGCTGGCAAGC 7 62 0 ACAAAAAAAG 0.420541 -147 ACCGAATACAAATAAAAAAGGCACATCAGT 8 55 0 AATAAAAAAG 0.94488 -137 TGCGTTCAAAAATAAAATGGCATAGCGGGA 9 19 1 AATAAAATGG 0.691661 -252 TTGATCACGGAATAAAAAGTGATCGTCAGG 9 140 1 AATAAAAAGT 0.673747 -131 TCAATCCCACAATAAAAGAGGCGATATCG 10 10 0 AATAAAAGAG 0.645107 -60 CGTAAAATGAAATAAAAACAAACCGCACTT 13 20 1 AATAAAAACA 0.743551 -83 GTGTGGTGAAAATAAAAAGA 14 1 0 AATAAAAAGA 0.867286 -53 AATGTTAAAAATAAAAAAAATTTGGCTTA 15 10 1 AATAAAAAAA 0.863022 -107 CTTTTTCAGCAAGAAAAAAGAAATTATTTA 15 65 0 AAGAAAAAAG 0.645107 -52 ATTTTTTACGATTAAAAAGGAAATAGCAAT 16 47 1 ATTAAAAAGG 0.741616 -40 ATAGCAATGAAATAAAAAGGAAATAGCA 16 69 1 AATAAAAAGG 0.946753 -18 AGTTTTACTAAAAAAATGATCTGCCC 17 285 0 ACTAAAAAAA 0.788507 -16 TCAAACGAATATTAAAAAATATATGCACTT 18 58 0 ATTAAAAAAT 0.243224 -123 ATTAAGAGTGAATAAAATAGAGCGCAATTC 18 142 0 AATAAAATAG 0.683812 -39 ATTAAGATCAAATAATAAAGAAAGCACATT 19 39 0 AATAATAAAG 0.525093 -92 CCCTGTTTCTACTAAAAAAACTCTATCTCT 19 85 0 ACTAAAAAAA 0.788507 -46 CAACTAAAAACGATACAGCAAT 20 261 0 ACTAAAAACG 0.823574 -12 TTTTCTAGTCAATAAAAAGGTCAAAAA 21 8 0 AATAAAAAGG 0.946753 -186 AAGACAAAAAAATAAAAAAAATGTTCAATA 21 137 0 AATAAAAAAA 0.863022 -57 ********** Masking position 5 Map Score: 15.9473 Number of sites scoring better than the average of aligned sites = 369 Number in coding regions = 215 Number in noncoding regions = 154 Number of orfs with sites within 600 bp upstream = 161 Fraction of orfs with sites within 600 bp upstream = 0.0258593 Motif number 6 TCTGAAGAACACAGCAATTTTGCGTTATCT 2 90 1 ACAGCAATTT 0.831241 -40 TATAATTTATATCGCACTTGAATCCTTCAA 7 174 0 ATCGCACTTG 0.920899 -35 ATAAAAACAAACCGCACTTTTATAGCACTT 13 31 1 ACCGCACTTT 0.989494 -72 CCGCACTTTTATAGCACTTTTACCTCGATT 13 42 1 ATAGCACTTT 0.914859 -61 GCAAATTATAACCGCACTTTTTCAGCAAGA 15 81 0 ACCGCACTTT 0.989494 -36 CCAAAAAATGACCGCACTTTACGCTTC 20 8 0 ACCGCACTTT 0.989494 -265 ********** Masking position 6 Map Score: 6.38879 Number of sites scoring better than the average of aligned sites = 42 Number in coding regions = 33 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 7 ACGCTTCCCCGTAAGCGCATGGTAAACTATGC 1 41 0 GTAACGATGG 0.984694 -43 TGTACCGATTGTAACCTTATGGACGGATTATC 4 191 0 GTAACTATGG 0.956025 -55 TTAACTAATTGTATGGGAATGGTTAA 6 5 0 GTATGGATGG 0.96812 -183 AAGGGGTGTTGTAAGGGGATGGCTGGCCTGAT 7 120 1 GTAAGGATGG 0.991942 -89 GTAAAATTAGGTAAAGGGATGGCCTTGTTCTT 9 189 1 GTAAGGATGG 0.991942 -82 GTAAAACAACGTAAAGTCATGGATTAGCGACG 12 87 1 GTAAGTATGG 0.976523 -60 **** ** **** Masking position 9 Map Score: 6.36076 Number of sites scoring better than the average of aligned sites = 33 Number in coding regions = 27 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 8 Fraction of orfs with sites within 600 bp upstream = 0.00128493 Motif number 8 TTTACCATGCGCTTACGGGGAAGCGTATTT 1 47 1 GCTTACGGGG 0.932173 -37 ATGAAAAACGGCCTGCGGGCCGTTTTGTTT 3 18 1 GCCTGCGGGC 0.686964 -283 GGATGATTCTGGTAACAGGGAATGTGATTG 3 191 1 GGTAACAGGG 0.745512 -110 AACAACCTGTGCTTGCGGGGTAAGAGTTGA 3 251 1 GCTTGCGGGG 0.975929 -50 ACCACCTGGCGGTGACGGGCCTTTGTGCGA 4 35 0 GGTGACGGGC 0.943235 -211 GTCACCGCCAGGTGGTGGGCTTTTTTTTGT 4 49 1 GGTGGTGGGC 0.78707 -197 TAAAAACAGGGCTGGCAGGCTAATTCGGGC 7 34 1 GCTGGCAGGC 0.939515 -175 ACAAAAAAAGGCTGGCAAGCCCGAATTAGC 7 52 0 GCTGGCAAGC 0.759786 -157 GGGATATGCCGCGAGCGGGCGATTTTAGGT 9 45 1 GCGAGCGGGC 0.945235 -226 AGACAGACACGTTAGCAGGGTCAATCCCAC 10 30 0 GTTAGCAGGG 0.801224 -40 TGGTGGCGCCGCTTACAAGCTT 11 3 0 GCTTACAAGC 0.506181 -75 GAAAAAGAAAGTGGGCAGGGGGTAGGGTAT 17 227 1 GTGGGCAGGG 0.798301 -74 ********** Masking position 9 Map Score: 7.24575 Number of sites scoring better than the average of aligned sites = 2609 Number in coding regions = 2475 Number in noncoding regions = 134 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 9 TCCCTGTTACCAGAATCATCCCGAAAGCAT 3 182 0 CAGAATCATC 0.705935 -119 TGTTACCTCAAAAAATCACAGTGCTCGGTC 3 279 0 AAAAATCACA 0.596825 -22 AAACAGATCACAAAATCACCTAAAATCGCC 9 62 0 CAAAATCACC 0.948339 -209 ATTCCGTGATCAAAATCACCTCTTAAAATG 9 123 0 CAAAATCACC 0.948339 -148 TCACGGAATAAAAAGTGATCGTCAGGTTAC 9 144 1 AAAAGTGATC 0.689035 -127 GCGGCGCCACCAAAATCATCGTGAAATGAT 11 21 1 CAAAATCATC 0.920071 -57 TCAGTAGAAAAAAAATGGCCATGGGCAGAT 17 263 1 AAAAATGGCC 0.798337 -38 GTTTTACTAAAAAAATGATCTGCCCATGGC 17 280 0 AAAAATGATC 0.913978 -21 AATTTTGCCAAAAAATGACCGCACTTTACG 20 15 0 AAAAATGACC 0.94427 -258 AAAAAATAAAAAAAATGTTCAATAAGAGGA 21 131 0 AAAAATGTTC 0.626156 -63 ********** Masking position 6 Map Score: 3.12804 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 276 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 54 Fraction of orfs with sites within 600 bp upstream = 0.00867331 Motif number 10 AAAGCCCACCACCTGGCGGTGACGGGCCTT 4 42 0 ACCTGGCGGT 0.96863 -204 TCATCTGATTACCTGGCGGAAATTAAACTA 6 156 1 ACCTGGCGGA 0.983663 -32 TGACCTCGCGCAAAATGCACTA 7 3 1 ACCTCGCGCA 0.97872 -206 ATGACTGTGTACCTCACGCAACGTATCGAT 8 149 0 ACCTCACGCA 0.967007 -43 AATATATGTAACCTGACGATCACTTTTTAT 9 151 0 ACCTGACGAT 0.883249 -120 GTTTTACACCCCCTGACGCATGTTTGCAGC 12 64 0 CCCTGACGCA 0.953502 -83 ********** Masking position 4 Map Score: 2.27935 Number of sites scoring better than the average of aligned sites = 349 Number in coding regions = 334 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 11 GCGGGCCGTTTTGTTTTGTCTGGATTTTGC 3 32 1 TTGTTTTGTC 0.851538 -269 TGGATTTTGCGCTTTTTGCCCAGCATTCAG 3 52 1 GCTTTTTGCC 0.926325 -249 GTGGTGGGCTTTTTTTTGTCATGAATTTTG 4 60 1 TTTTTTTGTC 0.911188 -186 GCCGCTTACAGCGTTGTGCCGCCCTGGATA 5 40 0 GCGTTGTGCC 0.814897 -86 TCTTCTTTGTTCTTTGTGCCGCACACGACG 5 95 0 TCTTTGTGCC 0.957845 -31 CTTGCCAGCCTTTTTTTGTCTCGCTAAGTT 7 63 1 TTTTTTTGTC 0.911188 -146 GCTCCCAAAATCTTTCTGTCGCGATTCAAC 12 13 1 TCTTTCTGTC 0.793249 -134 TTTGTTTTCCCTCTAAAAAAT 13 92 0 TTGTTTTCCC 0.731423 -11 CAACTACCAATTTTTGTGCCACTTTTTGGA 17 187 0 TTTTTGTGCC 0.934195 -114 CTGCCCACTTTCTTTTTCCCAAGCGGTCCA 17 215 0 TCTTTTTCCC 0.886323 -86 TCCGTGCCTTTCTTTTTGCCTGTTCGTGA 19 10 0 TCTTTTTGCC 0.973175 -121 ATTTTTTTTATTTTTTTGTCTTACAGACCA 21 145 1 TTTTTTTGTC 0.911188 -49 ********** Masking position 5 Map Score: 12.6805 Number of sites scoring better than the average of aligned sites = 574 Number in coding regions = 484 Number in noncoding regions = 90 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 12 CACTGTGATTTTTTGAGGTAACAAG 3 286 1 TTTTGAGGTA 0.957831 -15 CCCTTAATTTTTTAGAGGGAAAACAAA 13 86 1 TTTAGAGGGA 0.972326 -17 GTAACCTAACTTTTGAGGTATCTCTAACTT 18 23 1 TTTTGAGGTA 0.957831 -158 TTTTAATTTAGAGGGATAAGGCTTAT 19 115 0 TTTAGAGGGA 0.972326 -16 ********** Masking position 6 Map Score: 0.866966 Number of sites scoring better than the average of aligned sites = 4 Number in coding regions = 4 Number in noncoding regions = 0 Number of orfs with sites within 600 bp upstream = 0 Fraction of orfs with sites within 600 bp upstream = 0 Motif number 13 GGGAATTGTGAAAAAATACGCGACAGCGCG 3 95 1 AAAAAATACG 0.897381 -206 TTCAGATACGTAAAATTAGGTAAAGGGATG 9 180 1 TAAAATTAGG 0.736117 -91 ATCATCCGGAAAACATTACGAATGACGAAG 11 55 0 AAACATTACG 0.805238 -23 CCTCCGAGGCAGAAATTACGTCATCAGACG 12 117 0 AGAAATTACG 0.820735 -30 TTTCCCTCTAAAAAATTAAGGGTTGTATTA 13 78 0 AAAAATTAAG 0.772541 -25 TAAAAATAAAAAAAATTTGGCTTATGATAC 15 16 1 AAAAATTTGG 0.736116 -101 TTTTAATCGTAAAAAATAGGCAAATGATAC 16 34 0 AAAAAATAGG 0.897381 -53 ATTCAATTTGAAAAATTACGTACAGAGGTA 17 41 1 AAAAATTACG 0.956435 -260 GAGATACCTCAAAAGTTAGGTTACAACTTT 18 17 0 AAAAGTTAGG 0.805238 -164 AATTCTAGTCATAAAATACGCGTTCGTCAA 18 117 0 ATAAAATACG 0.551665 -64 TCTAAACGTAAAAAATTAGCATCTTAAAAA 20 126 0 AAAAATTAGC 0.719406 -147 ********** Masking position 3 Map Score: 2.3772 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 84 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 14 CTTCAAATCGGGCTTATCGCGAGTAAATCT 1 11 0 GGCTTATCGC 0.974368 -73 ACAGGTTGTTGGCTTCGCGGAACCGGGATG 3 231 0 GGCTTCGCGG 0.951147 -70 GCGGTGACGGGCCTTTGTGCGAATTTAGCG 4 27 0 GCCTTTGTGC 0.811507 -219 CACCGAAAGAGGCTTTTCGCACGGTTCCAT 4 91 0 GGCTTTTCGC 0.974413 -155 GTCACAATAGGCCTTTGCGCGCATCGATAC 8 127 1 GCCTTTGCGC 0.970751 -65 AAAATAAAATGGCATAGCGGGATATGCCGC 9 27 1 GGCATAGCGG 0.873268 -244 AGAGGGATAAGGCTTATCCCTGTTTCTACT 19 102 0 GGCTTATCCC 0.879732 -29 ********** Masking position 5 Map Score: 1.23896 Number of sites scoring better than the average of aligned sites = 651 Number in coding regions = 615 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 15 GTATTTCAGTCTCGATTAACAGATAAC 2 113 0 CAGTCCGATT 0.9481 -17 TTATTGCGCGCTGTCGCGTATTTTTTCACAA 3 100 0 CTGTCCGTAT 0.927267 -201 AAAAAACCTGCTGTACCGATTGTAACCTTAT 4 203 0 CTGTACGATT 0.963867 -43 CAAAATCTTTCTGTCGCGATTCAACGATAGA 12 18 1 CTGTCCGATT 0.983634 -129 GGTTTGATTGCTGTATCGTTTTTAGTTG 20 255 1 CTGTACGTTT 0.949022 -18 ***** ***** Masking position 4 Map Score: 0.0650045 Number of sites scoring better than the average of aligned sites = 14 Number in coding regions = 10 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701