AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00340_ecoli_reg_100.orf -o00340_ecoli_100.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 surA 52 survival protein #2 imp 254 organic solvent tolerance #3 lpxC 100 UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis #4 hlpA 121 histone-like protein, located in outer membrane or nucleoid #5 pepD 260 aminoacyl-histidine dipeptidase (peptidase D) #6 mhpA 76 3-(3-hydroxyphenyl)propionate hydroxylase #7 ybdL 108 putative aminotransferase #8 lnt 24 apolipoprotein N-acyltransferase, copper homeostasis protein, inner membrane #9 ybeX 89 putative transport protein #10 ybeZ 113 putative ATP-binding protein in pho regulon #11 potF 300 periplasmic putrescine-binding protein; permease protein #12 ybjO 59 orf, hypothetical protein #13 ybjF 40 putative enzyme #14 htrB 224 heat shock protein #15 aldH 274 aldehyde dehydrogenase, prefers NADP over NAD #16 tynA 247 copper amine oxidase (tyramine oxidase) #17 ydcH 72 orf, hypothetical protein #18 rimL 62 acetylation of N-terminal serine of 30S ribosomal subunit protein L7; acetyl transferase #19 malX 174 PTS system, maltose and glucose-specific II ABC #20 cstC 300 acetylornithine delta-aminotransferase #21 msbB 119 suppressor of htrB, heat shock protein #22 hisG 145 ATP phosphoribosyltransferase #23 wcaA 34 putative regulator #24 BIME92 24 BIME #25 wza 300 putative polysaccharide export protein #26 xapA 248 xanthosine phosphorylase #27 hisS 110 histidine tRNA synthetase #28 ygcA 56 putative enzyme #29 pepP 25 proline aminopeptidase P II #30 ygfB 161 orf, hypothetical protein #31 agaZ 248 putative tagatose 6-phosphate kinase 2 #32 yhbL 220 sigma cross-reacting protein 27A (SCRP-27A) #33 yhdT 108 orf, hypothetical protein #34 yigN 140 putative alpha helix chain #35 ubiE 94 2-octaprenyl-6-methoxy-1,4-benzoquinone --> 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone Motif number 1 CACGTAATCCGCAGTGCGGTTAATTGAAATGGA 1 24 1 GCAGTGCTAA 0.899067 -29 CAATTGTGGGACATCGCCTATAATTTGCATTAT 2 90 1 ACATCGCTAA 0.912594 -165 TCAGGGAGAGGCAGTGCGTAAAAAGACGCGGAC 5 119 0 GCAGTGCAAA 0.918993 -142 CGCGCACAGTACAGCGCAACTTATTTTGTTAAA 6 20 0 ACAGCGCTTA 0.599119 -57 GTTGCGCTGTACTGTGCGCGCAACGACATTTTG 6 33 1 ACTGTGCCAA 0.494202 -44 AAAGGCGCAAGCATTGCAATAAAGATGGGGATA 10 54 0 GCATTGCAAA 0.850082 -60 CTATATAAAAGCATCGCAAGAATAACTTTAGCC 11 147 0 GCATCGCAAT 0.720729 -154 CTTTTCTTACACCGCGCCGATAAAAAATATGCA 11 208 1 ACCGCGCTAA 0.959625 -93 GGGCGAAATTGCCGCGCTTGTAAATAACAAATA 14 117 0 GCCGCGCTAA 0.971884 -108 ATCTACATTTACAGCGCAAACATTACTTATTAT 20 239 1 ACAGCGCCAT 0.664967 -62 GGCGCAACTTGCCCCGCACCAAATAAAAAAAGC 21 48 0 GCCCCGCAAA 0.837165 -72 CTTCCAGCACACATCGCCTGAAAGA 22 3 0 ACATCGCAAA 0.930057 -143 ACCGTTATCAACCGCGCAATAAAAAAGCCCCCG 22 95 0 ACCGCGCAAA 0.968021 -51 ATGCACATTTACCTTGCAGTTAATTGAATAAAA 25 219 0 ACCTTGCTAA 0.776949 -82 GTGCATGGCGACATTGCTATTAATAGTGCACAG 25 246 1 ACATTGCTAA 0.753775 -55 AGCCGGGACAACCTCGCTATAAAAAGGCGTTAG 26 199 1 ACCTCGCAAA 0.938005 -50 AAAGACGAAGGCAGCGCAGTCAATCAGCAGGAA 30 17 0 GCAGCGCCAA 0.955811 -145 GGAAATCTTGGCTGCGCCGTAAATTATTATGAT 32 53 1 GCTGCGCAAA 0.896576 -168 TTTGCGTAGCGCCTCGCAGGAAATGCCTTTCCA 34 56 1 GCCTCGCAAA 0.95653 -85 ******* *** Masking position 7 Map Score: 19.6795 Number of sites scoring better than the average of aligned sites = 1205 Number in coding regions = 1125 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 2 GTGCGCGCAACGACATTTTGTCCGAGTCGTG 6 46 1 CGACTTTTGT 0.861568 -31 TGATTAACGACGGCGTTTTGATTAACTAACA 9 50 1 CGGCTTTTGA 0.978979 -40 CCGTTCCGGTGGGCCTTGTTTTTTCTCTCTT 10 23 1 GGGCTTGTTT 0.857775 -91 GCGACATGCGCGGCATTATGTAGCCAGGTTG 12 27 0 CGGCTTATGT 0.925661 -33 GCGCATGTCGCGGCATTGTTTTC 12 47 1 CGGCTTGTTT 0.96199 -13 GCCAGCCAGGCGGCTTTTTTAACAACTGCAT 18 24 1 CGGCTTTTTA 0.971992 -39 CAGTCAGTACCGGCTTTTTTTATTTGGTGCG 21 36 1 CGGCTTTTTT 0.983294 -84 CACCTTCCGGGGGCTTTTTTATTGCGCGGTT 22 88 1 GGGCTTTTTA 0.892125 -58 CCGGAAAATCCGGCCTTTTGACGCTTTAGCA 33 14 0 CGGCTTTTGA 0.978979 -95 CCGGATTTTCCGGCCTTTTTTATTACTGGGG 33 32 1 CGGCTTTTTT 0.983294 -77 CCGACGCGTTCGGCCTTTTGTATTTTTGCGT 34 32 1 CGGCTTTTGT 0.987498 -109 **** ****** Masking position 6 Map Score: 16.9442 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 217 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 53 Fraction of orfs with sites within 600 bp upstream = 0.00851269 Motif number 3 CTTTTACCGTTTTCCGGCTGCGGTCAATTGT 2 66 1 TTTCCGGCGC 0.946769 -189 TGTGCTAAACTGGCCCGCCGAATGTATAGTA 3 43 1 TGGCCCGCGA 0.821211 -58 GTTCTTTGCGTGGCCCGGCGATCTTATATTG 4 62 0 TGGCCCGGGA 0.893305 -60 CTTTATCCCGCGTCAGGGAGAGGCAGTGCGT 5 133 0 CGTCAGGGGA 0.895702 -128 CGAGCAGTGCTGGCCGGGAGAAAGTTCTCTT 11 180 1 TGGCCGGGGA 0.961258 -121 TGTGTATAGATTGCCGGGCGCATTGCGCTTA 15 33 0 TTGCCGGGGC 0.9777 -242 AACGGGCATACGGCCCGGGGATCTCTGCGCC 15 204 1 CGGCCCGGGA 0.898349 -71 AGTTTGTGAACGTCAGGGCGCAGAGATCCCC 15 220 0 CGTCAGGGGC 0.967243 -55 AAAAGCCGCCTGGCTGGCGGCTTAGGAAAGT 18 11 0 TGGCTGGCGC 0.800647 -52 TAAATGTAGATTGCAGGGTTCGTGCCAGCCA 20 219 0 TTGCAGGGTC 0.74013 -82 GGAAGGTGATCTTCCGGGGGCTTTCTCATGC 22 65 0 CTTCCGGGGC 0.971597 -81 GGAAGATCACCTTCCGGGGGCTTTTTTATTG 22 81 1 CTTCCGGGGC 0.971597 -65 CAGACTGGTCTTTCAGGCATCCAGACACGCT 25 127 0 TTTCAGGCTC 0.535147 -174 ATAGCGAGGTTGTCCCGGCTCTTACCAATAC 26 188 0 TGTCCCGGTC 0.790908 -61 CAGCACTGTTTTTCAGGCCGCACGCAGTTAA 32 100 1 TTTCAGGCGC 0.882143 -121 TAAGTTGTTGCGTCAGGAGGCGTT 34 127 1 CGTCAGGAGC 0.699394 -14 ******** ** Masking position 7 Map Score: 15.0898 Number of sites scoring better than the average of aligned sites = 2020 Number in coding regions = 1812 Number in noncoding regions = 208 Number of orfs with sites within 600 bp upstream = 145 Fraction of orfs with sites within 600 bp upstream = 0.0232894 Motif number 4 ATCAGGGCTATCTCCCACAATATAAAGGTGCTTT 2 36 1 TCCCCACAAA 0.978975 -219 TTATAGGCGATGTCCCACAATTGACCGCAGCCGG 2 79 0 TGCCCACAAA 0.918443 -176 TGACCGTTTGTCACGCGCAACGTTACCGATGATG 2 213 1 TCCGCGCAAT 0.837848 -42 ATCTCTATAATCTCGCGCAACCTATTTTCCCCTC 5 54 0 TCCGCGCAAA 0.984694 -207 TACCACTTTATCCCGCGTCAGGGAGAGGCAGTGC 5 135 0 TCCGCGTCAA 0.800319 -126 TCCTTGTCGATCACCCGCAAAACAGTATTGCAGG 5 229 0 TCCCCGCAAA 0.990646 -32 TCGCATTTTTTCGCCCGCAACCAAAATTTGTGGC 14 158 0 TCCCCGCAAA 0.990646 -67 CGTTTTATCTTCTCGCGCAATTTACTGAATCCAG 19 126 1 TCCGCGCAAA 0.984694 -49 TTCTTTTTATTCACCCACATCGCAAACGTATTCA 20 101 1 TCCCCACATA 0.882581 -200 CGGCGCAACTTGCCCCGCACCAAATAAAAAAAGC 21 48 0 TGCCCGCACA 0.776543 -72 AACCGTTATCAACCGCGCAATAAAAAAGCCCCCG 22 95 0 AACGCGCAAA 0.475286 -51 AATACACTTTTCTCACGCATTCAATAGCGATTCG 26 159 0 TCCACGCATA 0.573926 -90 TGACCTTAATTGTCCCATAACGGAACTCC 28 6 0 TGCCCATAAA 0.750411 -51 GGGTTGTCGATCCCCAGTAATAAAAAAGGCCGGA 33 40 0 TCCCAGTAAA 0.583714 -69 GGGATCGACAACCCCCATAAGGTACAATCCCCGC 33 60 1 ACCCCATAAA 0.74197 -49 CCCGCTTTCTTCACCCATCAGGGACAAAAA 33 89 1 TCCCCATCAA 0.74368 -20 GCAACAACTTACCCGCACAAAATAGAATTGTGCT 34 104 0 ACCGCACAAA 0.86742 -37 ** ******* * Masking position 4 Map Score: 12.2515 Number of sites scoring better than the average of aligned sites = 528 Number in coding regions = 467 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 5 ACTGACGCTATTCGGACAGGATTAACACTA 2 155 1 TTCGGACAGG 0.830652 -100 TGTTGTCAACACAAGACAGGCTTGCGAGAT 5 180 0 ACAAGACAGG 0.583114 -81 CAAGAATAACTTTAGCCAGGGTTTGAGACT 11 134 0 TTTAGCCAGG 0.949698 -167 AGCGAGCAGTGCTGGCCGGGAGAAAGTTCT 11 178 1 GCTGGCCGGG 0.634924 -123 CGCGGCATTATGTAGCCAGGTTGGCAAATT 12 20 0 TGTAGCCAGG 0.86743 -40 AATTTGTGGCTGAAGACTGGGCGAAATTGC 14 138 0 TGAAGACTGG 0.498749 -87 TTTTTGTTCTGTAAGCCGGGTAAGCGCAAT 15 13 1 GTAAGCCGGG 0.913489 -262 CTGTGGGCGGTTTAGTCAGGTTCACATTAT 16 185 0 TTTAGTCAGG 0.64923 -63 ATTTTCGTTTTTCAGACGGGATATTAAATC 17 44 0 TTCAGACGGG 0.959797 -29 TTCCTAAGCCGCCAGCCAGGCGGCTTTTTT 18 14 1 GCCAGCCAGG 0.916356 -49 TTGATAACGGTTCAGACAGGTTTAAAGAGG 22 117 1 TTCAGACAGG 0.951559 -29 AAACCAGCTCATAAGCCGGGAGAACAACCT 23 15 1 ATAAGCCGGG 0.824144 -20 GACAGAATAATTCAGACTGGTCTTTCAGGC 25 140 0 TTCAGACTGG 0.845215 -161 CGCACCCCGGTCTAGCCGGGG 32 2 0 TCTAGCCGGG 0.938306 -219 CGCGTCGGCCTTCAGACAGGAGAAGAGAA 34 10 0 TTCAGACAGG 0.951559 -131 TTGGGAGTAGTTAAGCCGGGTAGAAATCTA 35 15 1 TTAAGCCGGG 0.958238 -80 ********** Masking position 5 Map Score: 12.481 Number of sites scoring better than the average of aligned sites = 962 Number in coding regions = 902 Number in noncoding regions = 60 Number of orfs with sites within 600 bp upstream = 75 Fraction of orfs with sites within 600 bp upstream = 0.0120463 Motif number 6 CTCCCACAATATAAAGGTGCTTTTACCGTT 2 47 1 ATAAAGGTGC 0.79335 -208 TAAGCCGTAGATAAACAGGCTGGGACACTT 5 14 0 ATAAACAGGC 0.930558 -247 AAGATATGCAATAAACGTGCATATTTTTTA 11 228 0 ATAAACGTGC 0.911437 -73 GTCGCCAGAAATAAACGGGCATACGGCCCG 15 191 1 ATAAACGGGC 0.969137 -84 ACTTAGTGAAATAAAAGGGCAACTATTCGC 16 31 0 ATAAAAGGGC 0.974404 -217 CCAGCCAGTGATAAAAGTGCATAAACGGCG 20 196 0 ATAAAAGTGC 0.925798 -105 CAACCGCGCAATAAAAAAGCCCCCGGAAGG 22 90 0 ATAAAAAAGC 0.678176 -56 CAACCTCGCTATAAAAAGGCGTTAGATTCC 26 207 1 ATAAAAAGGC 0.942016 -42 CTGGTGGACCAGAAAAGGGCTTGTCTCTTC 30 95 0 AGAAAAGGGC 0.888134 -67 CATTTGCTTAATAGAAAGGCGTTAATAGGC 31 50 0 ATAGAAAGGC 0.772111 -199 ********** Masking position 5 Map Score: 8.66694 Number of sites scoring better than the average of aligned sites = 99 Number in coding regions = 67 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 TTTCCATTTCAATTAACCGCACTGCGGATTA 1 28 0 AATTAACCGA 0.775824 -25 GATGTCCCACAATTGACCGCAGCCGGAAAAC 2 74 0 AATTGACCGA 0.952425 -181 GAATTGACTGGAATTTGGGTTT 3 2 1 AATTGACTGA 0.972834 -99 CAATACATACAATTGCCCGAATAGGTTGAAA 14 192 1 AATTGCCCGA 0.863477 -33 ATGCAAAGGGGATTGCCTGCACCTGCCAGGT 16 146 0 GATTGCCTGA 0.876327 -102 CAACTGCATGGATTGACTGGAGATAAG 18 46 1 GATTGACTGA 0.957317 -17 CTTCTCGCGCAATTTACTGAATCCAGATTGT 19 134 1 AATTTACTGA 0.898687 -41 TCATTGACGAAATTTACTGGAAATTACTGCG 20 21 0 AATTTACTGA 0.898687 -280 AATAACGAATTATTTACTGTAGAGGTCGCT 20 281 1 TATTTACTGA 0.711464 -20 ATCCGCAGGCTATTGACAGAATAATTCAGAC 25 153 0 TATTGACAGA 0.583451 -148 ATTTTTATTCAATTAACTGCAAGGTAAATGT 25 217 1 AATTAACTGA 0.860928 -84 CCTTCCTGCTGATTGACTGCGCTGCCTTCGT 30 15 1 GATTGACTGG 0.779616 -147 CCTTTCGCAATTGACTGAAACACATTAAT 32 202 0 AATTGACTGA 0.972834 -19 ********* * Masking position 2 Map Score: 11.6379 Number of sites scoring better than the average of aligned sites = 94 Number in coding regions = 77 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 8 GATAAACAGGCTGGGACACTTCAC 5 3 0 CTGGACACTC 0.960359 -258 AGGCATTTGACTGGCAGACGTCCCCGCCGTTG 9 17 1 CTGGAGACTC 0.976511 -73 AGTTGTCACACTGAAAGATATGCAATAAACGT 11 240 0 CTGAAGATTG 0.841362 -61 CTGCATATATCTGATAGACGTGAAACAGGAGT 15 249 1 CTGAAGACTG 0.971771 -26 GTATGAAAAGCTGGCACACCTGCCAAACAACC 16 117 1 CTGGACACTG 0.979098 -131 GCGATGTGTGCTGGAAGACATTCAGATCTTCC 22 19 1 CTGGAGACTT 0.948589 -127 TCATGCACCACTGGAAGATCTGAATGTCTTCC 22 31 0 CTGGAGATTG 0.925523 -115 GTCTGGATGCCTGAAAGACCAGTCTGAATTAT 25 132 1 CTGAAGACAG 0.895138 -169 ACTTTGGGCCCTGGTGGACCAGAAAAGGGCTT 30 103 0 CTGGGGACAG 0.635864 -59 TCGCAATTGACTGAAACACATTAATTTTTTTA 32 195 0 CTGAACACTT 0.821066 -26 GACGCCCAATCTGTTACACTTCTGGAACAATT 35 52 1 CTGTACACTC 0.758596 -43 **** **** ** Masking position 8 Map Score: 7.17419 Number of sites scoring better than the average of aligned sites = 344 Number in coding regions = 327 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 ATATTCCCCAAATCGACACACGGATATC 2 9 1 CAAATCGACA 0.883799 -246 GTGATAAAGCCAAATCGACACAAGAGAAGT 11 50 0 CAAATCGACA 0.883799 -251 ATCCCGTCTGAAAAACGAAAATCCTCGCTT 17 52 1 AAAAACGAAA 0.948444 -21 AAAAAGAATAAAAAACGCAATGTTATGCAG 20 79 0 AAAAACGCAA 0.830112 -222 GTGGTTTGCTAAAAACGACATATTGTTAAT 26 57 1 AAAAACGACA 0.938173 -192 AAACAAAAAACGTAAGGAGAGTGTT 29 6 1 AAAAACGTAA 0.767267 -20 CGTTAATAGGCAAAACGAAATGAAACGAAA 31 31 0 CAAAACGAAA 0.966865 -218 GAGATAAAAATAAAACGAAAGATAATGGTT 31 160 0 TAAAACGAAA 0.84829 -89 TCAACTGAAACAAAACGAAAGATTAATATC 31 204 1 CAAAACGAAA 0.966865 -45 ********** Masking position 4 Map Score: 5.83644 Number of sites scoring better than the average of aligned sites = 84 Number in coding regions = 61 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 10 ATCCTGTCCGAATAGCGTCAGTGGTGTTAGG 2 146 0 AATGCGTCAG 0.881014 -109 CGTATTATCTCGCCAAATTACCTATC 3 85 0 TATTCGCCAA 0.849099 -16 TACTGGTTTTTAGTGCGCCAGATCTCTATAA 5 78 0 TAGGCGCCAG 0.823645 -183 TTCTCAAACATATCTCGCAAGCCTGTCTTGT 5 169 1 TATTCGCAAG 0.674143 -92 TTCAACACGCAACTTCGTCAGGTACAATAAA 7 87 1 AACTCGTCAG 0.866672 -22 GTATATAAAGAATGTCGCCAGAAATAAACGG 15 178 1 AATTCGCCAG 0.94059 -97 TATTAACCTCGTCAGATGTTGTGTT 16 233 0 AACTCGTCAG 0.866672 -15 GGATTCAGTAAATTGCGCGAGAAGATAAAAC 19 127 0 AATGCGCGAG 0.713079 -48 TACTGGAAATTACTGCGCCATTCTGAC 20 7 0 TACGCGCCAT 0.91203 -294 ATTTCCAGTAAATTTCGTCAATGATCACAAT 20 28 1 AATTCGTCAA 0.675774 -273 AATCTACATTTACAGCGCAAACATTACTTAT 20 238 1 TACGCGCAAA 0.680075 -63 AACCGTTATCAACCGCGCAATAAAAAAGCCC 22 98 0 AACGCGCAAT 0.687253 -48 TATTAATAGCAATGTCGCCATGCACATTTAC 25 240 0 AATTCGCCAT 0.853303 -61 CAAAGGAATTAATATCGCCAATACAGTTTTT 26 88 1 AATTCGCCAA 0.877546 -161 TTTCAGTTGATACTGCGTCATGGTGAGATAA 31 183 0 TACGCGTCAT 0.750953 -66 GGTGCGCGAATACTGCGCCAACACCAGGGAA 32 26 1 TACGCGCCAA 0.927394 -195 *** ******* Masking position 2 Map Score: 11.0039 Number of sites scoring better than the average of aligned sites = 2241 Number in coding regions = 2156 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 92 Fraction of orfs with sites within 600 bp upstream = 0.0147767 Motif number 11 TCGCCCCTGATGATGTGAAGGTCAATGT 13 23 1 TGATGGAAGG 0.989507 -18 GGTTCCTGCGAGATGGGAAAGTAAAAATCCG 14 18 1 AGATGGAAAG 0.794463 -207 TTATCAGTACTGATGCAAAGGGGATTGCCTG 16 158 0 TGATGAAAGG 0.955691 -90 ATGCAGTCGTTGATGAGAAAGGGTTATTACG 25 33 0 TGATGGAAAG 0.955691 -268 GACATATTGTTAATGCAAAGGAATTAATATC 26 73 1 TAATGAAAGG 0.706624 -176 TAACGTGATGGGAAGCGCCTCGCTTC 27 6 1 TGATGGAAGC 0.947723 -105 ATAGCTACCCTGATGAGAAGAGACAAGCCCT 30 79 1 TGATGGAAGA 0.924424 -83 AACAATTTTTTGATGAGCAGGCATTGAG 35 77 1 TGATGGCAGG 0.961608 -18 ***** ***** Masking position 3 Map Score: 3.53259 Number of sites scoring better than the average of aligned sites = 164 Number in coding regions = 146 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 12 TTGATCGCCTAAAGTCATCGCTACACTACCACTA 4 31 0 ATCACGCTAC 0.787147 -91 GACTGGGCGAAATTGCCGCGCTTGTAAATAACAA 14 120 0 AGCCCGCTTG 0.866072 -105 CTGAAAAACGAAAATCCTCGCTTT 17 59 1 ATCCCGCTTT 0.969358 -14 ATTTCCAGTTAGCCTCCGCCGTTTATGCACTTTT 20 180 1 ATCCCCGTTT 0.708323 -121 GTGCGGGGCAAGTTGCGCCGCTACACTATCACCA 21 62 1 AGCGCGCTAC 0.761786 -58 AAAAGGCGTTAGATTCCACCCTACAGAAAAAGGA 26 220 1 ATCCCCCTAC 0.939179 -29 ACGTGATGGGAAGCGCCTCGCTTCCCGTGTATGA 27 13 1 AGCCCGCTTC 0.97113 -98 ATAAAAATGAACCCTCAACGCTTCCCTCAATGTT 27 68 0 ATCACGCTTC 0.912293 -43 GGGTAGCTATAGTGTCGCCCCTTCGCAGACCATG 30 55 0 ATCGCCCTTC 0.920722 -107 CATATCATGAATATTCCTCCCTTTGACGACGA 30 140 1 ATCCCCCTTT 0.958045 -22 AAAAGGCCGGAAAATCCGGCCTTTTGACGCTTTA 33 17 0 ATCCGCCTTT 0.707727 -92 CCCATAAGGTACAATCCCCGCTTTCTTCACCCAT 33 73 1 ATCCCGCTTT 0.969358 -36 * *** ****** Masking position 1 Map Score: 4.97624 Number of sites scoring better than the average of aligned sites = 320 Number in coding regions = 278 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 45 Fraction of orfs with sites within 600 bp upstream = 0.00722775 Motif number 13 GGCGCACTAAAAACCAGTATTTCACATGAGT 5 90 1 AAACCGTATT 0.897307 -171 GATCACCCGCAAAACAGTATTGCAGGTCACA 5 224 0 AAAACGTATT 0.904577 -37 CTCGGATTAAAAAACGGTATTTAACAAATTT 11 99 0 AAAACGTATT 0.904577 -202 AATAGGTTGAAAAACAGGATTGAT 14 211 1 AAAACGGATT 0.897307 -14 ATCCACGGTAAAAACTGTATTGGCGATATTA 26 97 0 AAAACGTATT 0.904577 -152 AATGCGTGAGAAAAGTGTATTGGTAAGAGCC 26 172 1 AAAAGGTATT 0.879325 -77 ***** ***** Masking position 3 Map Score: 2.55218 Number of sites scoring better than the average of aligned sites = 32 Number in coding regions = 24 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 14 CGCTACACTACCACTACATTCCTTTGTGGA 4 17 0 CCACTACATT 0.907176 -105 CCTAAAGTCATCGCTACACTACCACTACAT 4 28 0 TCGCTACACT 0.825224 -94 AGCGACCTCTACAGTAAATAATTCG 20 286 0 CCTCTACAGT 0.954135 -15 GCAAGTTGCGCCGCTACACTATCACCAGAT 21 69 1 CCGCTACACT 0.976896 -51 TTTTTAGCTACCAATACACTGATTTAGTTT 25 85 0 CCAATACACT 0.952235 -216 ATTAATATCGCCAATACAGTTTTTACCGTG 26 95 1 CCAATACAGT 0.938186 -154 CCGGCTCTTACCAATACACTTTTCTCACGC 26 175 0 CCAATACACT 0.952235 -74 TTTCCTCTCCAGTTCAGATTACT 31 236 0 CCTCTCCAGT 0.846801 -13 ********** Masking position 8 Map Score: 2.71441 Number of sites scoring better than the average of aligned sites = 37 Number in coding regions = 25 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 Motif number 15 AGTCCGCGTCTTTTTACGCACTGCCTCTCC 5 118 1 TTTTTACGCA 0.778533 -143 ATTTAACAAATTTTTATGCATATTTGCTCT 11 82 0 TTTTTATGCA 0.929748 -219 GGCGACATTCTTTATATACACTTCATCCTT 15 167 0 TTTATATACA 0.715643 -108 TTTTTTATTCTTTTTATTCACCCACATCGC 20 94 1 TTTTTATTCA 0.865012 -207 ACGTATTCACTTTATATGCACTTTAAATGC 20 126 1 TTTATATGCA 0.929676 -175 TTATATGCACTTTAAATGCATATGGTTTGG 20 137 1 TTTAAATGCA 0.703424 -164 GCCAGTTAAATTTTTATTCAATTAACTGCA 25 208 1 TTTTTATTCA 0.865012 -93 AGGGTTCATTTTTATATTCAGAAAGAGAAT 27 87 1 TTTATATTCA 0.864944 -24 ********** Masking position 6 Map Score: 2.41359 Number of sites scoring better than the average of aligned sites = 46 Number in coding regions = 20 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 32 Fraction of orfs with sites within 600 bp upstream = 0.00513974