AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i03010_ecoli_reg_300.orf -o03010_ecoli_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.51 -x5 -e 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 = 0.51 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 rpsT 102 30S ribosomal subunit protein S20 #2 rpsB 300 30S ribosomal subunit protein S2 #3 ycaP 120 orf, hypothetical protein #4 serC 198 3-phosphoserine aminotransferase #5 aroA 70 5-enolpyruvylshikimate-3-phosphate synthetase #6 ycaL 144 putative heat shock protein #7 cmk 172 cytidylate kinase #8 rpsA 110 30S ribosomal subunit protein S1 #9 yceD 159 orf, hypothetical protein #10 rpmF 51 50S ribosomal subunit protein L32 #11 rpsV 101 30S ribosomal subunit protein S22 #12 b1481 281 orf, hypothetical protein #13 rplT 52 50S ribosomal subunit protein L20, and regulator #14 rpmI 96 50S ribosomal subunit protein A #15 thrS 300 threonine tRNA synthetase #16 yejH 148 putative ATP-dependent helicase #17 rplY 124 50S ribosomal subunit protein L25 #18 rplS 41 50S ribosomal subunit protein L19 #19 trmD 30 tRNA methyltransferase; tRNA (guanine-7-)-methyltransferase #20 rpsP 248 30S ribosomal subunit protein S16 #21 ffh 91 GTP-binding export factor binds to signal sequence, GTP and RNA #22 rpsU 237 30S ribosomal subunit protein S21 #23 rpsO 148 30S ribosomal subunit protein S15 #24 rbfA 74 ribosome-binding factor A #25 infB 24 protein chain initiation factor IF-2 #26 nusA 27 transcription pausing; L factor #27 yhbC 200 orf, hypothetical protein #28 metY 300 tRNA #29 rplU 258 50S ribosomal subunit protein L21 #30 rplM 218 50S ribosomal subunit protein L13 #31 yhcM 187 orf, hypothetical protein #32 rplQ 40 50S ribosomal subunit protein L17 #33 rpoA 25 RNA polymerase, alpha subunit #34 rpsD 33 30S ribosomal subunit protein S4 #35 rpsM 146 30S ribosomal subunit protein S13 #36 rpmJ 31 50S ribosomal subunit protein L36 #37 rpsH 33 30S ribosomal subunit protein S8, and regulator #38 rplN 164 50S ribosomal subunit protein L14 #39 rplC 32 50S ribosomal subunit protein L3 #40 rpsJ 237 30S ribosomal subunit protein S10 #41 yheD 179 putative export protein A for general secretion pathway (GSP) #42 rpsG 96 30S ribosomal subunit protein S7, initiates assembly #43 rpsL 125 30S ribosomal subunit protein S12 #44 yheO 154 orf, hypothetical protein #45 fkpA 220 FKBP-type peptidyl-prolyl cis-trans isomerase (rotamase) #46 rpmB 216 50S ribosomal subunit protein L28 #47 radC 93 DNA repair protein #48 rpmH 300 50S ribosomal subunit protein L34 #49 rpmE 202 50S ribosomal subunit protein L31 #50 glyT 116 tRNA #51 tufB 114 protein chain elongation factor EF-Tu (duplicate of tufA) #52 secE 229 preprotein translocase #53 rplK 157 50S ribosomal subunit protein L11 #54 rplJ 300 50S ribosomal subunit protein L10 #55 rplL 66 50S ribosomal subunit protein L7/L12 #56 rpsF 300 30S ribosomal subunit protein S6 #57 rplI 41 50S ribosomal subunit protein L9 Motif number 1 GATTTGTGCAAATAAGCGCCGTTA 1 4 0 AATAACGCCG 0.879227 -99 TTTGTGGTATAAAGCGCGCCGGACTTCCGAT 2 130 1 AAAGCCGCCG 0.876723 -171 AAGGTCCGAAAAAAAACGCCGACAATGTGCC 6 58 0 AAAAACGCCG 0.968341 -87 TATTCCGAATAAAATCCGGCGAAAATATTAC 12 80 1 AAAATCGGCG 0.860713 -202 TTGCGTATGCAAAAGCGGGCGAGATTCTATA 17 44 0 AAAAGGGGCG 0.950517 -81 GATAAACGGTAAAAGACGGCGCT 19 18 1 AAAAGCGGCG 0.975675 -13 CTCTGCTGTAAAAGGCCGTCGGCGGTGCAGC 20 111 0 AAAGGCGTCG 0.64434 -138 AGTCCCTTTCAAAAAAGGCCGCGGTGCTTTA 22 121 1 AAAAAGGCCG 0.936094 -117 ATATAGAATGAAAGGACGCCGATCTCTAATT 23 112 0 AAAGGCGCCG 0.939753 -37 AATTAATTTTAAAAAGGGGCTAACAGCCCCT 24 33 1 AAAAAGGGCT 0.811371 -42 TCTCCTGACAAAAAAGGGGCTGTTAGCCCCT 24 47 0 AAAAAGGGCT 0.811371 -28 GGATGAGGTGAAAAGCCCGCG 26 17 1 AAAAGCCGCG 0.874177 -11 GTCAGATAACAAAAAACCCCGATAAATCGGG 27 137 0 AAAAACCCCG 0.84122 -64 CAAGACATAAAAAAAGGGCCTAAAGCCCAGT 27 177 0 AAAAAGGCCT 0.787015 -24 ATCGGGGCGAAAAGCCCGGCTTTTGCG 29 7 0 AAAGCCGGCT 0.676208 -252 AAATATTCACAATAGGGCGCGAATATTACGC 29 188 0 AATAGGCGCG 0.441935 -71 ATAAAACTCCGCTTCCGCGCACA 29 246 0 AAAACCCGCT 0.444162 -13 ACAAATCACAAAAAGGGGTCGATCTTTGACC 30 19 1 AAAAGGGTCG 0.65713 -200 CGGTTGACGAAAAAAAGGCCGTTCTACACTA 31 124 0 AAAAAGGCCG 0.936094 -64 TCTCAATACGAATAAACGGCTCAGAAATGAG 38 23 1 AATAACGGCT 0.681305 -142 GGGTAGAAAAAATAAACGGCTCATTTCTGAG 38 42 0 AATAACGGCT 0.681305 -123 GCATCGCCCTAAAATTCGGCGTCCTCATATT 43 47 1 AAAATCGGCG 0.860713 -79 GCATTAAGAACCGCCGCCTGACCAGG 44 6 1 AAGAACGCCG 0.726917 -149 CCTGTAATAAAAAAACCGCCGCCTGGTCAGG 44 27 0 AAAAACGCCG 0.968341 -128 TCTTTTGTCGAATGGTCGCCGCGGATTCTAC 45 19 1 AATGGCGCCG 0.787802 -202 TCCAGGATTGAAAACTGGCCGTCGATTTAAC 47 36 1 AAAACGGCCG 0.882677 -58 CCAGCGATCAAAAAAGCGGCGATTTAATCGT 53 12 1 AAAAACGGCG 0.972682 -146 GGAACGTGTTAAAGGTCGGCTGAAAAATGAC 56 218 0 AAAGGCGGCT 0.820805 -83 ***** ***** Masking position 2 Map Score: 31.4664 Number of sites scoring better than the average of aligned sites = 1349 Number in coding regions = 1179 Number in noncoding regions = 170 Number of orfs with sites within 600 bp upstream = 160 Fraction of orfs with sites within 600 bp upstream = 0.0256987 Motif number 2 AACCCGTATTATTGCGCGCTTTCCGTACGACTA 3 13 0 ATGCGCGCTC 0.946776 -108 ATGGGGATTTATTGCGCAATTATAGCGGGCTGG 7 41 0 ATGCGCAAAT 0.550138 -132 CGGCGCGTATAATGCGCGCGGTTATGTTAACGG 7 126 1 ATGCGCGCTT 0.976784 -47 AGGGCGCGCATATTAACTTTGTA 9 147 0 AGGCGCGCAT 0.980949 -13 CGCTCCGGTGACTGCGCGCACTCCGGCACCAAA 20 75 1 ATGCGCGCTC 0.946776 -174 TTGGTCCTACACTGCGCGGTAATAAAGCGAGGT 22 21 0 ATGCGCGGAT 0.936174 -217 TTATTTCAAAATGGTGCGGAATTTTACTGCAAT 22 165 0 AGGTGCGGTT 0.792923 -73 GCACTTGTCAAAGGCGTGCGTTTTGCGTAATAT 29 164 1 AGGCGTGCTT 0.914759 -95 TATTCACAATAGGGCGCGAATATTACGCAAAAC 29 183 0 AGGCGCGAAT 0.964378 -76 ACCGTGAACAACGGCGCACCGATTATTCAAGGA 31 151 1 AGGCGCACAT 0.846791 -37 CCCCATATCGAGGGCGCGGCATTATAACACCGC 38 84 0 AGGCGCGGTT 0.985436 -81 AAGTATGTATAATGCGCGGGCTTGTCGTAGTTG 40 58 1 ATGCGCGGTT 0.966075 -180 ATTTCGTACGAAGGCGCGAAATCATACAGAAAT 49 93 0 AGGCGCGATC 0.956942 -110 ATCGTTGCACAAGGCGTGAGATTGGAATACAAT 53 38 1 AGGCGTGATT 0.849448 -120 ATAAAAACAAAAGGCGCGAAATTGTATTCCAAT 53 58 0 AGGCGCGATT 0.981331 -100 * ******* ** Masking position 1 Map Score: 17.4987 Number of sites scoring better than the average of aligned sites = 668 Number in coding regions = 618 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 3 CTCTTAACGTGGTTTATCCGCTAAAAGCATA 3 93 0 GGTTTACCGC 0.644618 -28 CTATGCGCTTCGTTTTGCAGGTTGATGTTTG 9 17 1 CGTTTTCAGG 0.947147 -143 GTTCTTTAAGCGTTTTGCTGGTGTACTCACT 15 43 1 CGTTTTCTGG 0.849917 -258 GTTATTAGACCGCTATACTGGGCAGACAACA 16 66 0 CGCTATCTGG 0.72023 -83 CGTCTTTTACCGTTTATCCGGTGGT 19 5 0 CGTTTACCGG 0.854393 -26 TTGATTAATTCGGTTTGCCGCTGGCATCAAC 22 204 0 CGGTTTCCGC 0.850514 -34 ATTTACGCGACGTTAAGCGGCAGTATTCTAC 23 44 0 CGTTAACGGC 0.586776 -105 CGCCTCGTTTTCCAGGTTTGTTGGAG 34 6 1 CGTTTTCAGG 0.947147 -28 CCTGAAAACGGGCTTTTCAGCATGGAACGTA 35 102 1 GGCTTTCAGC 0.910124 -45 GCGGAGGTTCCGCTTTCCAGCACTAATTATA 44 63 0 CGCTTTCAGC 0.976674 -92 CGCCTCGTCAGGCTTTACAGCCCGGTCATCG 46 147 0 GGCTTTCAGC 0.910124 -70 CTTTGCGAGGCGCTTTCCAGGATTGAAAACT 47 21 1 CGCTTTCAGG 0.970378 -73 TTATTTACCGCGCTTTTCCGCACCTTTTCGC 48 139 0 CGCTTTCCGC 0.975098 -162 ACGATAAGTTCGCTTACCGGCTCGAATAAAG 50 40 1 CGCTTACGGC 0.912571 -77 TATAAAAAATCGTTTTACGGGCAAGGCCATA 53 88 0 CGTTTTCGGG 0.927322 -70 TTCTATCCGTCGCTATTCAGCTTGTGACGGC 54 60 0 CGCTATCAGC 0.912378 -241 ****** **** Masking position 4 Map Score: 14.1937 Number of sites scoring better than the average of aligned sites = 1005 Number in coding regions = 873 Number in noncoding regions = 132 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 4 GTCAACAGTTCATCGGCATGGCGGCGGTGATAGCG 3 58 0 CTCGGCCGGC 0.824718 -63 TTGGTGCTCCCCGTTGGATCGGGGATAAACCGT 10 9 1 CCCGTTCGGG 0.939515 -43 TTAGTGTTAACATCGCTCAACCGGGTGGAAGGTGA 15 130 1 CTCGCTCGGG 0.977584 -171 AATGCCCGACCTCCGTTTTTACAGGCAAAATCACA 16 14 0 CCCGTTCAGG 0.932015 -135 TGTAAAAGGCCGTCGGCGGTGCAGCCAGTTTGGTG 20 101 0 CTCGGCCAGC 0.805263 -148 TAACAAAAAACCCCGATAAATCGGGGCTTTATATA 27 127 0 CCCGATCGGG 0.871386 -74 GGAAATACTCCGTTGTTAATTCAGGATTGTCCAAA 42 72 0 CTTGTTCAGG 0.81702 -25 CATTAAGAACCGCCGCCTGACCAGGCGGCGGTTTT 44 12 1 CCCGCCCAGG 0.977234 -143 CCTTCGGGATCTTTGTCTGTTCGGGACTTGAGCAC 46 26 1 CTTGTCCGGG 0.864895 -191 GACTTGAGCACATCGCTGAGTCAGCGTATACTACG 46 50 1 CTCGCTCAGC 0.924657 -167 TTTAAGGCCGCGTCGCTCTTCCAGCCCTAACGCCA 49 165 0 CTCGCTCAGC 0.924658 -38 CAAAGAAAATCACTGATGAGCCAGGTTCTGGTACG 52 77 0 CCTGATCAGG 0.633946 -153 TTGTCATAATCATTGCTGAGACAGGCTCTGTTGAG 52 109 1 CTTGCTCAGG 0.918272 -121 ATTTGGTTTGCCTCGCGATCGCGGGGTGAAAATGT 52 177 1 CTCGCGCGGG 0.901645 -53 TTCGTTGGAGCCTGGCCTATCCAGGCCTCCGTCGA 54 99 1 CTGGCCCAGG 0.605373 -202 AGCGTTCTGTCACCGTCTACGCAGGGGATTAAGTT 54 156 0 CCCGTCCAGG 0.945276 -145 TTAACACGTTCCTTGCCTCCCCGGGATTCGGCTGA 56 237 1 CTTGCCCGGG 0.939435 -64 * ***** **** Masking position 5 Map Score: 16.6667 Number of sites scoring better than the average of aligned sites = 1145 Number in coding regions = 1020 Number in noncoding regions = 125 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 GGCATGGAGCCAGGTGGACGTTAAATATAAAC 8 76 1 CAGGTGGAGT 0.975563 -35 CTTCGTTTTGCAGGTTGATGTTTGTTATCAGC 9 24 1 CAGGTTGAGT 0.970457 -136 AAGATTAGTCCTGGTTGATGATTTTTATATTT 12 228 0 CTGGTTGAGT 0.937004 -54 ATCGCTCAACCGGGTGGAAGGTGAGAGGTTAA 15 141 1 CGGGTGGAGT 0.973914 -160 AGGACCAATGCGGGTTGATGTAAAACTTTGTT 22 46 1 CGGGTTGAGA 0.812121 -192 AAATTAATTTCAGGTGGAAGGGCTGTTCACG 24 10 0 CAGGTGGAGG 0.967013 -65 TAGTCTGGATGAGGTGAAAAGCCCGC 26 5 1 CTGGATGAGG 0.730455 -23 CCGGATCACAGGTTAAGGTTTTACTGAGAA 32 9 1 CAGGTTAAGT 0.666618 -32 GCCGCCTGGTCAGGCGGCGGTTCTTAATGC 44 9 0 CAGGCGGCGT 0.866279 -146 GCCGCCTGACCAGGCGGCGGTTTTTTTATTAC 44 23 1 CAGGCGGCGT 0.866279 -132 GAGGATTATACGGGCTGATGGGTAAAGCGCAA 48 55 0 CGGGCTGAGG 0.926529 -246 CATGGCGCGCCGGGTGGAGGATTATACGGGCT 48 71 0 CGGGTGGAGT 0.973914 -230 AATTTCAAGTCAGGATGATGCT 49 1 0 CAGGATGAGT 0.890715 -202 GGCATGTTGCCTGGTTGATGTGGTGATATCAC 51 63 1 CTGGTTGAGG 0.916121 -52 ******** * * Masking position 1 Map Score: 12.8991 Number of sites scoring better than the average of aligned sites = 420 Number in coding regions = 402 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 6 ATCGGCACATATTCCGGGGTGCCCTTTGGGG 2 223 1 ATTCCGGGGG 0.93595 -78 AACTGATAACATCACGGTGCGTCTGAAAGGT 15 12 0 ATCACGGTGG 0.944503 -289 GTAAACTGATATCTCGGGGGC 18 1 0 ATCTCGGGGC 0.902899 -41 TGACGAGCACATCCCGGTGCCAAAATGGCAA 20 25 0 ATCCCGGTGC 0.912451 -224 CCGACTGCATATCGCGTAGTGTAGAACGGCC 31 108 1 ATCGCGTAGG 0.77509 -80 TACTTTTAACATCGCGTGGTGTCTGGCGTTA 49 142 1 ATCGCGTGGG 0.968614 -61 GGGCTACGCCATCGCGTGGCCGAAAT 50 6 0 ATCGCGTGGC 0.923197 -111 TTGCCTCGCGATCGCGGGGTGAAAATGTTTG 52 184 1 ATCGCGGGGG 0.992037 -46 GATTTTTTATATCACGGGGAGCCTCTCAGAG 53 108 1 ATCACGGGGG 0.983409 -50 GAGCGTCTTAATTACGGTGAGCAGAAACAAG 54 214 0 ATTACGGTGG 0.72392 -87 GGTCAGCCGAATCCCGGGGAGGCAAGGAACG 56 243 0 ATCCCGGGGG 0.988556 -58 ********* * Masking position 1 Map Score: 10.6092 Number of sites scoring better than the average of aligned sites = 144 Number in coding regions = 126 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 7 AGGGCATATTCCTCGGCCTTTGAATTGTCC 1 56 1 CCTCGGCCTT 0.721041 -47 GGCGCTATCACCGCCGCCATGCCGATGAAC 3 56 1 CCGCCGCCAT 0.964346 -65 TGCTATTAACCCGCGGTCAATCGATTGCGA 4 159 0 CCGCGGTCAA 0.725762 -40 GTTAACATAACCGCGCGCATTATACGCGCC 7 127 0 CCGCGCGCAT 0.829305 -46 TTTAACATACCCGCTGTCATTCCATTGCAA 8 35 0 CCGCTGTCAT 0.85066 -76 AGCGCCGTCTTTTACCGTTTA 19 20 0 GCGCCGTCTT 0.729103 -11 TTGTAAAGCACCGCGGCCTTTTTTGAAAGG 22 125 0 CCGCGGCCTT 0.98321 -113 ATTCGGTTTGCCGCTGGCATCAACGCCAGC 22 198 0 CCGCTGGCAT 0.868387 -40 ACTACGAAGGCCGAAGTCTTCACAGTATAT 27 35 0 CCGAAGTCTT 0.544266 -166 GACGTAAAATCTGCAGGCATTATAGTGATC 28 207 0 CTGCAGGCAT 0.555293 -94 GCATAATCAGCCGCAGGCATGGAGCCTGAA 31 45 0 CCGCAGGCAT 0.938142 -143 TATGTATAATGCGCGGGCTTGTCGTAGTTG 40 61 1 GCGCGGGCTT 0.859038 -177 GCATTAAGAACCGCCGCCTGACCAGGCGGC 44 11 1 CCGCCGCCTG 0.867766 -144 AATAAAAAAACCGCCGCCTGGTCAGGCGGC 44 23 0 CCGCCGCCTG 0.867766 -132 AGCACTCATTTCGCGGTCATCGAAACTAAT 45 70 1 TCGCGGTCAT 0.635257 -151 ACGATGGACACCGAAGCCATGGGTGATTAA 48 218 0 CCGAAGCCAT 0.633787 -83 GCAAACTGATCCGCACTCTTCTACGGCAAT 49 51 0 CCGCACTCTT 0.648791 -152 TGGAAGAGCGACGCGGCCTTAAACCGAGGT 49 177 1 ACGCGGCCTT 0.755813 -26 TGCGAAACTCCTGCGGTCTTCGACGGAGGC 54 123 0 CTGCGGTCTT 0.750315 -178 ********** Masking position 8 Map Score: 10.4442 Number of sites scoring better than the average of aligned sites = 1448 Number in coding regions = 1395 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 63 Fraction of orfs with sites within 600 bp upstream = 0.0101189 Motif number 8 AAAGAAGGCTAAAAGGGCATATTCCTCGGCC 1 43 1 AAAAGGGCAA 0.955197 -60 TTACCGACCCCAAAGGGCACCCCGGAATATG 2 230 0 CAAAGGGCAC 0.957029 -71 GAATTATTGGCAAAAGGCAACCACAGGCTGC 9 93 1 CAAAAGGCAC 0.918935 -67 AGAGTCAAAGAAAAAGGCAGCCTGTGGTTGC 9 109 0 AAAAAGGCAC 0.967252 -51 TCCCGGTGCCAAAATGGCAAACAAGCCAGGC 20 14 0 AAAATGGCAA 0.853286 -235 GTCCCTTTCAAAAAAGGCCGCGGTGCTTTAC 22 122 1 AAAAAGGCCC 0.918935 -116 AAGACATAAAAAAAGGGCCTAAAGCCCAGTT 27 176 0 AAAAGGGCCA 0.891098 -25 CTTACTGTGAACAAAGGCAACTTAGGGTTTA 29 41 1 ACAAAGGCAC 0.847611 -218 TTGTACTGAAAAAATGGCACAGATAAACGTT 29 92 1 AAAATGGCAA 0.853286 -167 AATGCGCACTAAAAGGGCATCATTTGATGCC 52 31 1 AAAAGGGCAC 0.983059 -199 AAAGCGTGCAAAAAGGGCATCAAATGATGCC 52 46 0 AAAAGGGCAC 0.983059 -184 ********* * Masking position 4 Map Score: 10.1436 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 123 Number in noncoding regions = 35 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 9 CTATGCTTGATCGGCAACCTAATTTAGGGG 11 15 1 TCGGCAACCT 0.9614 -87 CGGGATGTGCTCGTCATCCTCACGTACTGC 20 40 1 TCGTCATCCT 0.735543 -209 GAATTAGAGATCGGCGTCCTTTCATTCTAT 23 111 1 TCGGCGTCCT 0.9747 -38 GTAGCCAAATTCGGCTAACTGAGGTTCAGA 40 104 0 TCGGCTAACT 0.838434 -134 TTAGCCGAATTTGGCTACCTAACAATGCTC 40 116 1 TTGGCTACCT 0.914009 -122 GCCCTAAAATTCGGCGTCCTCATATTGTGT 43 52 1 TCGGCGTCCT 0.9747 -74 ATCCTGGAACTCGGCTACCTGATTTTCATT 50 97 0 TCGGCTACCT 0.978935 -20 TGTGACGGCGTTGGCTTCCTTCATTCGCAC 54 39 0 TTGGCTTCCT 0.914009 -262 ********** Masking position 1 Map Score: 6.04178 Number of sites scoring better than the average of aligned sites = 116 Number in coding regions = 106 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 10 CCCCACAGCCAGCCTGTGGGGTTTTTATTT 5 30 1 AGCCTGTGGG 0.951882 -41 ATCATTGTCATCTTTCGGGCTGGTCTTCT 7 10 1 ATCTTTCGGG 0.872238 -163 AGAAAAAGGCAGCCTGTGGTTGCCTTTTGC 9 102 0 AGCCTGTGGT 0.773744 -58 TGTTGCTCTCCTGTGGGCTTAAAAAGG 12 8 1 CTCCTGTGGG 0.887021 -274 TTGATACAATATCTTTTGGGTTATATATTC 12 149 0 ATCTTTTGGG 0.744473 -133 CTGTCTGTGGAGCCTTCGGGCTTCACAGGC 14 26 1 AGCCTTCGGG 0.977162 -71 ATTTGAAAAAATCCTTCTGGAAAGTGCTCC 27 68 1 ATCCTTCTGG 0.775297 -133 TAAAGTAAACAGCCTTCGGG 40 1 0 AGCCTTCGGG 0.977162 -237 GCTATGCGCGATCCTTCGGGATCTTTGTCT 46 14 1 ATCCTTCGGG 0.975304 -203 TCTTGCGAAACTCCTGCGGTCTTCGACGGA 54 126 0 CTCCTGCGGT 0.760786 -175 ********** Masking position 5 Map Score: 5.83258 Number of sites scoring better than the average of aligned sites = 270 Number in coding regions = 234 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 11 CAAAACTGGTTTTTGCACACAACGTTAACGATTTG 7 85 1 TTTGCAAACT 0.965003 -88 AAAATATTACTTCTGCACTTAAATTAAATTCCCAC 12 101 1 TTCGCAAAAT 0.901622 -181 GGCTAGATGGTTTCGCAATGAACTGTTAATAAACA 15 219 1 TTTGCAAACG 0.81305 -82 AACTCATTTATTTTGCATAAAAATTCAGTGAGA 28 9 0 TTTGCAAAAT 0.925822 -292 CATTCACATGATTAGCAATAAACGTTGACAAAATG 28 165 1 ATTGCAAACT 0.761551 -136 TTTCTTTCTCCAACAAACCTGGAAAACGAG 34 14 0 TTCCCAAACT 0.798493 -20 CTCAACCCAACTTTGCAAGAAAAATATGCGAAAAA 35 12 0 CTTGCAAAAT 0.681794 -135 AAACGGGCTTTTCAGCATGGAACGTACATATTAAA 35 107 1 TTCGCAAACT 0.952935 -40 TTCCGCACCTTTTCGCAGGGAAAATGTACGACCTC 48 120 0 TTTGCAAAAT 0.925822 -181 CTGATTTTCATTCTGCACTGAATATCGAGAGAAGC 50 74 0 TTCGCAAATT 0.693346 -43 ACCGCAGGAGTTTCGCAAGAAACTTAATCCCCTGC 54 136 1 TTTGCAAACT 0.965003 -165 CTCCTGGATGTTTGCCAGAGAAAATCTCTGGAACT 54 268 0 TTTCCAAAAT 0.709529 -33 AAATCTCCCCTTTCGCAATTAACCTCTAACACGCT 56 134 0 TTTGCAAACT 0.965003 -167 *** *** *** * Masking position 7 Map Score: 6.72582 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 35 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 12 GGACCTTACTCCTCAATTACGGTT 10 38 0 ACCTCTCCTC 0.277052 -14 TTTAACTCCTCAATCCTGTAGCTAGTTT 11 84 0 TCCCATCCTG 0.757582 -18 TGTTGCTCTCCTGTGGGCTTAAA 12 2 1 GTTCCTCCTG 0.68332 -280 ATGTGCTCTCCTGTATCTATATT 13 40 0 TGTCCTCCTG 0.963137 -13 AATTTAATCTCTTATCCTGGGTAAACTGA 18 23 0 TCTTATCCTG 0.791752 -19 ACGTACTGCGTGTACGCTCCGGTGACTGCGCG 20 61 1 TGTCCTCCGG 0.843587 -188 TGTAAAACTTTGTTCGCCCCTGGAGAAAGCCT 22 64 1 TGTCCCCCTG 0.724297 -174 GAAAGCCTCGTGTATACTCCTCACCCTTATAA 22 88 1 TGTTCTCCTC 0.819892 -150 GCTGTTCCTTCCTGCTACAGTTTA 25 11 0 TGTCTTCCTG 0.596509 -14 TGAATACTTTTGCCTTCTCCTGCTCTCCCTTA 28 109 0 TGCTCTCCTG 0.848127 -192 CCCCGACTTCTCTATAATCCTGCGACCCCACG 30 48 1 TCTTATCCTG 0.791752 -171 CTGTCTTTACTCCCGTGATTCAATT 37 19 0 TCTTCTCCCG 0.65027 -15 GGGGTGAGATGCCCCGATCCTGGAGATATGG 45 200 1 GCCCATCCTG 0.59887 -21 CGACGGCCAGTTTTCAATCCTGGAAAGCGCCT 47 28 0 TTTCATCCTG 0.508821 -66 TTGTAATAATTGTACACTCCGGAGTCAATTCT 48 176 0 TGTCCTCCGG 0.843587 -125 CTTCTTTTCTCCTCCCTGTTTTTT 51 3 1 TCTTCTCCTC 0.849937 -112 CACATAGTTAGCTATGCTCCTGGC 54 3 0 GCTTCTCCTG 0.887883 -298 TCTGGAACTCACTTCACTCCTCCAAACGGAGA 54 245 0 ACTCCTCCTC 0.641959 -56 TAGCTTTGCTCCTGGATGTTTGCC 54 287 0 GCTTCTCCTG 0.887883 -14 TGTGCTCTCCTCTGTGATGATC 56 1 1 TGTCCTCCTC 0.899266 -300 *** * ****** Masking position 9 Map Score: 10.0571 Number of sites scoring better than the average of aligned sites = 439 Number in coding regions = 351 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 107 Fraction of orfs with sites within 600 bp upstream = 0.017186 Motif number 13 GGCTGGTCTTCTGCCAGCCCGCTATAATTG 7 28 1 CTGCCAGCCC 0.978265 -145 CAAAGTTAATATGCGCGCCCT 9 149 1 ATGCGCGCCC 0.98166 -11 TTTCGGGTCAATGCCCGACCTCCGTTTTTA 16 28 0 ATGCCCGACC 0.815244 -121 GCTCCGGTGACTGCGCGCACTCCGGCACCA 20 76 1 CTGCGCGCAC 0.938982 -173 TTTGCGTAATATTCGCGCCCTATTGTGAAT 29 185 1 ATTCGCGCCC 0.916453 -74 CTCTATAATCCTGCGACCCCACGTTACAAG 30 57 1 CTGCGACCCC 0.890122 -162 CGAATAGCCTATGCCAGCACACAAAAAGTT 30 103 0 ATGCCAGCAC 0.919699 -116 CTATGACAGGATGCGAGCACCACAAAGGAG 47 74 1 ATGCGAGCAC 0.933428 -20 CCGCGTCGCTCTTCCAGCCCTAACGCCAGA 49 163 0 CTTCCAGCCC 0.898615 -40 ********** Masking position 2 Map Score: 5.47637 Number of sites scoring better than the average of aligned sites = 301 Number in coding regions = 278 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 14 TGACACACATCGCAATGAGTAAAACCGTTGAGGG 4 79 0 CGCAGGTAAA 0.971688 -120 TGTCTCTCGCCTGGGGTGGAAACGGTTGGCC 21 71 0 CGCTGGTGAA 0.981807 -21 GATAACAGGTCGCTACGAGTAGAATACTGCCGCT 23 26 1 CGCAGGTGAA 0.971131 -123 GTGTACGTTACGCAAAGTGTTAAACAATTTACGC 23 67 0 CGCAGGTAAA 0.971688 -82 AAATTCTACTCGTTTTGGGTAAAAAATGCAAATA 28 264 0 CGTTGGTAAA 0.926433 -37 CAAAGGCGTGCGTTTTGCGTAATATTCGCGCCCT 29 172 1 CGTTGGTATA 0.692945 -87 GACTGCATATCGCGTAGTGTAGAACGGCCTTTTT 31 110 1 CGCTGGTGAA 0.981807 -78 CCTTTTAGTGCGCATTGCGTCAAATGTTATCGGC 52 13 0 CGCTGGTAAA 0.982161 -217 *** * * ** *** Masking position 14 Map Score: 4.92879 Number of sites scoring better than the average of aligned sites = 56 Number in coding regions = 47 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 15 GGGGTACTGCAAATTCGGTCGC 8 2 0 AAATTGGTCG 0.960139 -109 CTAAACCCCTAAATTAGGTTGCCGATCAAGC 11 19 0 AAATTGGTTG 0.728981 -83 AACAAATGCTAAATTGGTTCGCAATCAGGTA 15 188 0 AAATTGTTCG 0.924584 -113 GTTGATGTAAAACTTTGTTCGCCCCTGGAGA 22 59 1 AACTTGTTCG 0.697773 -179 GACATACAAAAGATTGGCTGGCTAATCTAGC 35 50 0 AGATTGCTGG 0.808327 -97 TGAGACCCGAAAATCAGGTCGTTAAAAATCC 38 115 0 AAATCGGTCG 0.819366 -50 CTAATAAAATAGATTGGGTGGGTTGTATATT 41 21 1 AGATTGGTGG 0.909043 -159 GTCTGTATGTAGATTTGTTCGACAACGCTTT 45 140 1 AGATTGTTCG 0.919778 -81 TCCAAAAATCAAATTAGCTCGAGCTTCGTAT 46 188 0 AAATTGCTCG 0.910425 -29 TCCTGACTTGAAATTCGGTGGGTTAGTATAC 49 18 1 AAATTGGTGG 0.914433 -185 CGGATAGAAAAGATTTGTTCGTTGGAGCCTG 54 82 1 AGATTGTTCG 0.919778 -219 ***** ***** Masking position 1 Map Score: 4.79948 Number of sites scoring better than the average of aligned sites = 60 Number in coding regions = 48 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925