AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i057_Chorismate_Biosynthes_ecoli_hinf_reg_300.orf -a/home/amcguire/genomes/ORF_ecoli.txt -z/home/amcguire/genomes/ecoli.fna -g0.46 -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 = 0.46 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 aroL 182 shikimate kinase II #2 ycaP 120 orf, hypothetical protein #3 serC 198 3-phosphoserine aminotransferase #4 aroA 70 5-enolpyruvylshikimate-3-phosphate synthetase #5 b1689 300 orf, hypothetical protein #6 b1690 99 putative transport system permease protein #7 b1691 220 putative amino acid/amine transport protein #8 aroD 30 3-dehydroquinate dehydratase #9 aroC 34 chorismate synthase #10 yrdD 62 putative DNA topoisomerase #11 smf_2 53 orf, fragment 2 #12 smf_1 129 orf, fragment 1 #13 aroB 56 3-dehydroquinate synthase #14 aroK 199 shikimate kinase I #15 yrfD 68 orf, hypothetical protein #16 HI0195.1 26 conserved hypothetical transmembrane protein (aefA) #17 HI0205 292 H. influenzae predicted coding region HI0205 #18 HI0206 22 5'-nucleotidase, putative #19 HI0207 284 shikimic acid kinase I (aroK) #20 HI0604 300 adenylate cyclase (cyaA) #21 HI0605 73 glycerol-3-phosphate dehydrogenase (NAD+) (gpsA) #22 HI0658 160 ABC transporter, ATP-binding protein #23 HI0660 269 H. influenzae predicted coding region HI0660 #24 HI0661 300 hemoglobin-binding protein #25 HI0967 25 H. influenzae predicted coding region HI0967 #26 HI0970 57 3-dehydroquinase (aroQ) #27 HI1587 300 DNA-binding protein H-NS (hns) #28 HI1588 69 formyltetrahydrofolate deformylase (purU) Motif number 1 TGTAATTTATTATTTACACTTCATTCTTGAATATTTATTGGTATAGTAA 1 12 1 TATATTTATT 0.755236 -171 TCCGACGGTTTACATAATTACTATACTGAAGATGATTTTCCCTGGGTAC 7 139 0 TATAATTTTT 0.960365 -82 TTTTTGTCTATATATACAGAGAAAAAAGTAAGCTATATTCTCAAATCAC 17 61 0 TATAAATATT 0.755229 -232 GAATACAACCTACTTTATGCATACAAAACTTGCAATTTTGCTTGAAAAG 17 126 0 TATAAATTTT 0.925331 -167 GTATTCCTTTTAATTATCATTCACAATTTATTTTGTTTTACGATATAAT 17 169 1 TATAATTTTT 0.96041 -124 AATAGCGCGTTAAATACGCGCTATTTTTAGCCTATTTTTCAATT 19 6 0 TATATTTTTT 0.925262 -279 AAAAATGGGGTAGATTATCGCAATAAATCACCCTATTTTTCAACCTCTA 19 150 0 TATAAATTTT 0.92533 -135 TTTTACGCAGTTTATTTTCATTAGAAATGATCGAATTTTATTTCACTTT 19 224 1 TTTAAATTTT 0.903589 -61 ATTCCTTAATAAGTGATATTGAGTAAGGTATTTTATAATACTTT 20 6 1 TTTATATTTT 0.827218 -295 CGTAAATAGCTTAATTCTGCCGATATAAAAATCTATATTTTCTATTATT 20 87 0 TTTAAATATT 0.700024 -214 GTCATTTTGATTGTTGATAGGTAAAATTTATAGTATTTTTCGAAAAATT 20 177 1 TTTAATTTTT 0.948313 -124 CTGTGGTTGATAGGTTACCGAAAGATATCTATACTTATTTCCTCTTTTA 21 18 1 TATAAATATT 0.755236 -56 TAAATAGTTTTTATTGCGTCTTATTATACGTGGCTTTTTTGACTAGAAA 22 42 1 TTTATTTTTT 0.90359 -119 ACATAGGTCTTAATTTGAGGCTATTTTGCAATATTTTTTCTTTTCTCGG 22 116 0 TATATTTTTT 0.92533 -45 ACCTATCTAAAATCAAAAGTGCGGTAAATTTTTACCGCACTT 23 4 1 TATAATTTTT 0.960401 -266 CAAGCACGTTTAAATACAGCAAATAATGAGAATAGTTTTTATTTCTTGA 24 205 1 TATAATTTTT 0.960374 -96 TTTTAATCCTTTTTGTGTGGCACATTATACTGGTTTTTTCGATTTTTG 26 20 0 TTTAATTTTT 0.948313 -38 TTTATTTGATTTCGGCAACTATTCCTTTCTTTTTTCTTCTTCGT 27 6 1 TTTATTTTTT 0.90359 -295 TTATTTTCTTTATATTTTTATTAAAGTTTATAAAATTTTTATAAAATCT 27 143 0 TATAATTTTT 0.959784 -158 TACAATAAATTTTATTTTCTCTATTATTAAATAAATTTTCCCACATTTA 27 240 1 TTTATTTTTT 0.903573 -61 TTTTTCTATTTGAAACTAGAACCTATTTTATGGGTTCTA 28 1 1 TTTAATTTTT 0.948313 -69 ** * * * * **** Masking position 5 Map Score: 25.3465 Number of sites scoring better than the average of aligned sites = 111 Number in coding regions = 60 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 65 Fraction of orfs with sites within 600 bp upstream = 0.0104401 Motif number 2 AGCGAAGCGGAAAAATGTTAAAAAAAAGCCCATCG 5 185 0 AAAATAAAAA 0.838216 -116 TCTACTTAGCAAAGGTGCTTTAAAAAGTGAAGCGA 6 71 0 AAAGTTAAAA 0.939754 -29 GATTAGCGTAAAAAAGACAGCAAAATGCCGCCTGA 14 149 0 AAAAGCAAAA 0.722205 -51 CTATACGCGTAAATTTGACCTAAAACAGCTGGATG 17 224 0 AAATTTAAAA 0.859101 -69 TAGCTTGATAAAATATCAGTTAAATGAGGTTTATA 17 267 1 AAAATTAAAT 0.925215 -26 AATTGAAAAATAGGCTAAAAATAGCGCGTA 19 6 1 AAAATTAAAA 0.9542 -279 CAGAAGATAGAAAGATCTCCCAAAAAATGGGGTAG 19 186 0 AAAATCAAAA 0.890673 -99 TAATTAAATTAAAAGTGAAATAAAATTCGATCATT 19 249 0 AAAGTTAAAA 0.939754 -36 CAATTTTTCGAAAAATACTATAAATTTTACCTATC 20 192 0 AAAATTAAAT 0.925215 -109 AAATGCAAAAAAATGTGACATAAATCACAATTTTT 20 219 0 AAAGTTAAAT 0.90256 -82 CGAGAAAAGAAAAAATATTGCAAAATAGCCTCAAA 22 117 1 AAAATCAAAA 0.890673 -44 ATCTAAAATCAAAAGTGCGGTAAATTTTTACCGCA 23 15 1 AAAGTTAAAT 0.902561 -255 TTTCTTAAGAAAAAGTGCGGTAAAAATTTACCGCA 23 30 0 AAAGTTAAAA 0.939754 -240 ATTGGCTTTGAAAGAGAGAGTAAAAGATAGATCCT 23 64 0 AAAAGTAAAA 0.869253 -206 TCTAGATCGCAAAAATAGCGAAAATAGCTTGATTT 23 134 0 AAAATAAAAT 0.754701 -136 GTGTAATCATAAATAGAAACTAAAAATTTGGCGAG 23 190 0 AAAAGTAAAA 0.869253 -80 TAAAGTTTATAAAATTTTTATAAAATCTGTTGGCA 27 136 0 AAATTTAAAA 0.859101 -165 ACTTTAATAAAAATATAAAGAAAATAAACACAAAA 27 165 1 AAAATAAAAT 0.754701 -136 AGAGAAAATAAAATTTATTGTAAATATCTATTATT 27 227 0 AAATTTAAAT 0.783584 -74 *** ** ***** Masking position 12 Map Score: 18.3289 Number of sites scoring better than the average of aligned sites = 148 Number in coding regions = 72 Number in noncoding regions = 76 Number of orfs with sites within 600 bp upstream = 102 Fraction of orfs with sites within 600 bp upstream = 0.0163829 Motif number 3 TACAATTTCGATTGTAAAGAAAAAATTCCACTTAA 1 83 0 ATTGAGAAAA 0.666991 -100 GTTGACTATGCTTTTAGCGGATAAACCACGTTAAG 2 87 1 CTTTAGAAAA 0.950476 -34 GGATAAACCACGTTAAGAGCATAAAA 2 105 1 CGTTAGAAAA 0.926796 -16 AAAAATGTGGCTTGCATCACACAAAAGAATCTCTC 3 43 0 CTTGAAAAAA 0.8491 -156 TGAGTAAAACCGTTGAGGGCAAAAATGTGGCTTGC 3 63 0 CGTTAGAAAA 0.926796 -136 ACGACAATTCCTTTCTGTGGAAAAA 6 1 0 CTTTTGAAAA 0.862038 -99 GGGGATTTGTCTAGAATAGAAGAAATAATCTTTCT 12 38 0 CTAGAGAAAA 0.861518 -92 AGATGAAACACGTTCAGCGTAAAAACATTACCGCT 14 22 0 CGTTAGAAAA 0.926796 -178 TCACCGGGTAAGATTAGCGTAAAAAAGACAGCAAA 14 160 0 AGATAGAAAA 0.613745 -40 TTTTCTCTGTATATATAGACAAAAAGCCTGCGAAT 17 85 1 ATATTAAAAA 0.306924 -208 TGCAATTTTGCTTGAAAAGTATAAAATTCGCAGGC 17 110 0 CTTGAGAAAA 0.908795 -183 ATACAACCTACTTTATGCATACAAAACTTGCAATT 17 138 0 CTTTTAAAAA 0.779175 -155 TTCACTTTTAATTTAATTAGATAAAGAACA 19 265 1 ATTTAAAAAA 0.685401 -20 TAATACTTTGCGTTGATAAGAAAAATATCAAGCTA 20 46 1 CGTTAAAAAA 0.877292 -255 CTTATTTCCTCTTTTACTAGATAAATTGTAGAT 21 51 1 CTTTAAAAAA 0.915525 -23 TAGACTGTTCCGAGAAAAGAAAAAATATTGCAAAA 22 107 1 CGAGAGAAAA 0.804071 -54 AAGATAGATCCTTTCTTAAGAAAAAGTGCGGTAAA 23 41 0 CTTTTAAAAA 0.779175 -229 ACATATTATAGGAGAAAGTATTCTCTC 24 284 0 ATATAGAAAA 0.706636 -17 TTGTAAATATCTATTATTAAATAAATGGTCGAAAC 27 210 0 CTATAAAAAA 0.871243 -91 TTTATTTTCTCTATTATTAAATAAATTTTCCCACA 27 250 1 CTATAAAAAA 0.871243 -51 ATGTTGTGTGCTATGTTTAGATAAAAAAATAGAAC 28 44 0 CTATTAAAAA 0.687791 -26 **** * * * *** Masking position 11 Map Score: 20.7343 Number of sites scoring better than the average of aligned sites = 326 Number in coding regions = 223 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 4 TTATTGTTGTAACAACGACAATTCCTTTCTG 6 19 0 AACAACGAAA 0.811873 -81 GTAAACACGCAAACACAACAATAACGGAGCC 9 11 1 AAACACAAAA 0.85838 -24 ACCTAGGACTAATAACAAAAATAGCGCGTTA 19 43 0 AATAACAAAA 0.774068 -242 TCCCTACCAGAACAACAAAAATTGGCGAACA 20 274 0 AACAACAAAA 0.885314 -27 TTTTGACTAGAAAATCGATAAAATCGGAATA 22 78 1 AAAATCGAAA 0.892981 -83 ACCTATCTAAAATCAAAAGTGCGGTAAAT 23 9 1 AAAATCAAAG 0.719279 -261 TTACACATCAAAAATCAATAACTTATTGGTT 23 219 1 AAAATCAAAA 0.937208 -51 TACAATTACTAATATCAACAATCAACGGCTC 24 161 1 AATATCAAAA 0.825069 -140 ATTTTTGATCAAAATCAAGAAATAAAAACTA 24 237 0 AAAATCAAAA 0.937208 -64 TCGACCACCAAAAATCGAAAAAACCAGTATA 26 12 1 AAAATCGAAA 0.892981 -46 TAAAGAAAATAAACACAAAAAAATATATCTG 27 180 1 AAACACAAAA 0.85838 -121 AATAAACCTCAATAAATAACATTAA 27 286 0 AACCTCAAAA 0.855929 -15 ******** ** Masking position 8 Map Score: 7.62438 Number of sites scoring better than the average of aligned sites = 262 Number in coding regions = 201 Number in noncoding regions = 61 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 5 GTTAAAAAAAAGCCCATCGTGGGAGATGGG 5 174 0 AGCCCATCGT 0.944661 -127 GGTGGGCTGAAGCCCACCCTACATTAAGTA 24 89 0 AGCCCACCCT 0.993936 -212 GGTGGGCTTCAGCCCACCAAAATATCTTAC 24 101 1 AGCCCACCAA 0.969892 -200 GGTGGGCTTCAGCCCACCATCAAACAATCG 24 130 0 AGCCCACCAT 0.990653 -171 GGTGGGCTGAAGCCCACCCTACAATTACTA 24 142 1 AGCCCACCCT 0.993936 -159 ********** Masking position 6 Map Score: 5.69504 Number of sites scoring better than the average of aligned sites = 15 Number in coding regions = 15 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 6 ATGTGTGTCACTGAATGATAAAACCGATAGCC 3 103 1 CTAATGTAAA 0.931931 -96 CTACTATTAGCTCACGGTTATAAATCAACATA 5 82 1 CTACGGTATA 0.902049 -219 TATCAGCCTGCTGACGGCTTGAAGAGAGTCAC 5 262 0 CTACGGTTGA 0.778019 -39 CATGCAAGATCTTACGGATAAATAACTCTTTC 7 30 1 CTACGGTAAA 0.966824 -191 AGCGAAGGGCCTCACTGGTTAATAAAACAAGG 11 22 1 CTACTGTTAA 0.924126 -32 AAAATGCCGCCTGAATGATAAATCATCATCAT 14 131 0 CTAATGTAAA 0.931931 -69 TCTGACGGGTATATCAATGCGTC 15 56 0 CTACGGTATA 0.902049 -13 TTTCCCTAATCTAAATGGTAAA 16 1 0 CTAATGTAAA 0.931925 -26 AACCTTCCTCTAAATGTTTAATTACTAAAAG 17 10 1 CTAATGTTAA 0.861096 -283 TTTATACTCCCTAAGTGGTAAATTGTTCGCCA 20 251 1 CTAGTGTAAA 0.860477 -50 ** **** **** Masking position 4 Map Score: 5.92564 Number of sites scoring better than the average of aligned sites = 90 Number in coding regions = 70 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 7 CAATGCGGCGAAAGCCGGTGTCATGAGAAT 1 140 0 AAAGCCGGTG 0.965998 -43 TCACCGCCGCCATGCCGATGAACTGTTGAC 2 63 1 CATGCCGATG 0.948605 -58 TTATTAGCAAAAAGCCGATGTTTTTACTG 3 10 0 AAAGCCGATG 0.984391 -189 CGCAATGAGTAAAACCGTTGAGGGCAAAAA 3 73 0 AAAACCGTTG 0.814273 -126 TCTCTCTTTCAAAGCCAATGTTCAAACATC 23 80 1 AAAGCCAATG 0.891069 -190 ATTTTGCACAAATGCCGATGTTTGAACATT 23 96 0 AATGCCGATG 0.964832 -174 TCCTATAATGCGAGCCGTTGATTGTTGATA 24 173 0 CGAGCCGTTG 0.874976 -128 ********** Masking position 9 Map Score: 3.20751 Number of sites scoring better than the average of aligned sites = 392 Number in coding regions = 370 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 8 GATAAAACCCGTATTATTGCGCGCTTTCCGTAC 2 18 0 GTTATTGCCG 0.665858 -103 TAAAAACATCGGCTTTTTGCTAATAATCCGAGA 3 14 1 GTTTTTGCAA 0.650945 -185 TGCCGAAATTTTGCTTAATCCCCACAG 4 5 1 GATTTTGCTA 0.96194 -66 TAGGCATACGGACTTTTTGCGTCGATCAGATTC 5 52 0 GTTTTTGCTC 0.777635 -249 GTTTTTGATCGCGATTTTCCTTAGTTAGCGCAG 7 61 0 GATTTTCCTA 0.650068 -160 TATGTTTCCAGGAATATTGCATGTCATAGTTTG 7 93 0 GATATTGCTG 0.871754 -128 GACGCGCGCAGGTATTTAGCATACAAGGAGTAC 14 61 1 GATTTAGCTA 0.78164 -139 AAAATTCGCAGGCTTTTTGTCTATATATACAGA 17 90 0 GTTTTTGTTA 0.702913 -203 TACAAAACTTGCAATTTTGCTTGAAAAGTATAA 17 121 0 GATTTTGCTG 0.957571 -172 GCGTATAGCGGTATTTTAGCTTGATAAAATATC 17 251 1 GTTTTAGCTG 0.720389 -42 TCCTTAATAAGTGATATTGAGTAAGGTATTTTA 20 13 1 GATATTGATA 0.622585 -288 TGGATAGCTTGATATTTTTCTTATCAACGCAAA 20 52 0 GATTTTTCTA 0.556228 -249 ATAGTACCTAGTTTTATTGCGTAAATAGCTTAA 20 122 0 GTTATTGCTA 0.859857 -179 AGGTAAAAAAGTCATTTTGATTGTTGATAGGTA 20 167 1 GATTTTGATG 0.830243 -134 ATTATACGTGGCTTTTTTGACTAGAAAATCGAT 22 64 1 GTTTTTGATA 0.815311 -97 GATTTTCAAGGAGATTTTGCACAAATGCCGATG 23 106 0 GATTTTGCCA 0.901889 -164 TACTAAAAGTGTATTTTTGATCAAAATCAAGAA 24 247 0 GTTTTTGACA 0.616214 -54 AAAATCTGTTGGCATTTTGTTTGTTTTACGGTA 27 117 0 GATTTTGTTG 0.723854 -184 * ******* ** Masking position 7 Map Score: 10.4144 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 599 Number in noncoding regions = 113 Number of orfs with sites within 600 bp upstream = 116 Fraction of orfs with sites within 600 bp upstream = 0.0186315 Motif number 9 GATAAAACCGATAGCCACAGGAATAATGTA 3 119 1 ATAGCCACAG 0.882054 -80 ATTTTGCTTAATCCCCACAGCCAGCCTGTG 4 18 1 ATCCCCACAG 0.985997 -53 CAGAAATAAAAACCCCACAGGCTGGCTGTG 4 33 0 AACCCCACAG 0.945568 -38 AAGCATGGAAATCCCCTGAGTGAAACAACG 5 123 1 ATCCCCTGAG 0.945568 -178 AAATCTCCAGAGATGTGTTCAG 12 3 1 ATCTCCAGAG 0.946566 -127 CCGGTGATTTATCGCCAGAGCG 14 188 1 ATCGCCAGAG 0.979731 -12 ********** Masking position 9 Map Score: 2.53808 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 64 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 10 GCAACATTATTGGAAAGAGTGAGGGGCGAGG 5 221 0 TGAAAGAGTG 0.889708 -80 AATTGAAAAATAGGCTAAAAATA 19 3 1 TGAAAAATAG 0.958946 -282 CCTATAGAGGTTGAAAAATAGGGTGATTTAT 19 146 1 TGAAAAATAG 0.958946 -139 ATAGTATTTTTCGAAAAATTGTGATTTATGT 20 206 1 TGAAAAATTG 0.932305 -95 ACAATTTATCTAGTAAAAGAGGAAATAAGTA 21 49 0 TGTAAAAGAG 0.754526 -25 AGAAAAAATATTGCAAAATAGCCTCAAATTA 22 124 1 TGCAAAATAG 0.829681 -37 ATCCTTTCTTAAGAAAAAGTGCGGTAAAAAT 23 38 0 AGAAAAAGTG 0.620711 -232 AACATTGGCTTTGAAAGAGAGAGTAAAAGAT 23 71 0 TGAAAGAGAG 0.931889 -199 GCGATCTAGATCGAAAGATTGAAATGACTAT 23 159 1 TGAAAGATTG 0.896113 -111 TTGAAATAAGTAGATAAATAGGATAAATT 23 251 1 TGATAAATAG 0.74798 -19 TATGTTTAGATAAAAAAATAGAACCCATAAA 28 37 0 TAAAAAATAG 0.647947 -33 * ********* Masking position 6 Map Score: 4.67749 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 104 Number in noncoding regions = 15 Number of orfs with sites within 600 bp upstream = 18 Fraction of orfs with sites within 600 bp upstream = 0.0028911 Motif number 11 GCCTGTGGGGTTTTTATTTCTGTTGTAGAG 4 41 1 TTTTTATTTC 0.922242 -30 GAATATAGCTTACTTTTTTCTCTGTATATA 17 70 1 TACTTTTTTC 0.788939 -223 AAATGATCGAATTTTATTTCACTTTTAATT 19 248 1 ATTTTATTTC 0.601118 -37 AAAATATAGATTTTTATATCGGCAGAATTA 20 95 1 TTTTTATATC 0.767277 -206 AAGATATCTATACTTATTTCCTCTTTTACT 21 39 1 TACTTATTTC 0.863756 -35 TTATAAATAGTTTTTATTGCGTCTTATTAT 22 39 1 TTTTTATTGC 0.690744 -122 GCAATATTTTTTCTTTTCTCGGAACAGTCT 22 108 0 TTCTTTTCTC 0.686777 -53 CCTATTTATCTACTTATTTCAATAACCAAT 23 243 0 TACTTATTTC 0.863756 -27 ATGAGAATAGTTTTTATTTCTTGATTTTGA 24 230 1 TTTTTATTTC 0.922242 -71 AACTATTCCTTTCTTTTTTCTTCTTCGTTA 27 27 1 TTCTTTTTTC 0.903702 -274 ATGGGTTCTATTTTTTTATCTAAACATAGC 28 40 1 TTTTTTTATC 0.660314 -30 ********** Masking position 5 Map Score: 3.59404 Number of sites scoring better than the average of aligned sites = 122 Number in coding regions = 71 Number in noncoding regions = 51 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 12 AAATCAATATGTTGATTTATAACCGTGAGC 5 91 0 GTTGATTTAT 0.942025 -210 AAATCAACATATTGATTTATAAGCATGGAA 5 103 1 ATTGATTTAT 0.756902 -198 GTTCCATGATGATGATTTATCATTCAGGCG 14 126 1 GATGATTTAT 0.902103 -74 AATCTTACCCGGTGATTTATCGCCAGAGCG 14 180 1 GGTGATTTAT 0.973412 -20 TGAAAAATAGGGTGATTTATTGCGATAATC 19 157 1 GGTGATTTAT 0.973412 -128 TTCGAAAAATTGTGATTTATGTCACATTTT 20 215 1 TGTGATTTAT 0.875243 -86 ********** Masking position 5 Map Score: 3.04416 Number of sites scoring better than the average of aligned sites = 49 Number in coding regions = 39 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 13 TGAGGGGCGAGGTAGCGAAGCGGAAAAATG 5 203 0 GGTAGCGAAG 0.988611 -98 CAATACGTACGGTAACGAAATTATCTTTCA 7 191 1 GGTAACGAAA 0.880713 -30 GGAATCCGGGAAGCGAAGGGCCTCACTG 11 9 1 GGAAGCGAAG 0.971717 -45 ATGGAACGCAGGCAGCGAAGAGCACCAACT 14 103 0 GGCAGCGAAG 0.98074 -97 TTTCAGAGTGGATAACGAAGAAGAAAAAAG 27 39 0 GATAACGAAG 0.880713 -262 ********** Masking position 4 Map Score: 0.934503 Number of sites scoring better than the average of aligned sites = 66 Number in coding regions = 62 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 14 ATTGGTATAGTAAGGGGTGTATTGAGATTTTCA 1 48 1 TAGGGTTATT 0.924444 -135 CGCGCAATAATACGGGTTTTATCTCAAAGGCGC 2 28 1 TAGGGTTATC 0.973912 -93 TTCCTGTGGCTATCGGTTTTATCATTCAGTGAC 3 109 0 TACGGTTATC 0.978832 -90 ATACGTACGGTAACGAAATTATCTTTCAGCAAG 7 193 1 TACGAATATC 0.704936 -28 TCTGACGGGTATATCAATGCGTCTG 15 54 0 TGCGGTTATC 0.924711 -15 TCAACCTCTATAGGGAATTTATTTTCCACGAGA 19 127 0 TAGGATTATT 0.800397 -158 CAAGTCAATATAACGGGTATATC 22 1 0 TACGGTTATC 0.978832 -160 GAACAGTCTATTCCGATTTTATCGATTTTCTAG 22 84 0 TTCGATTATC 0.730888 -77 GAACCTATTTTATGGGTTCTATTTTTTTATCTA 28 29 1 TAGGGTTATT 0.924443 -41 ** *** * **** Masking position 10 Map Score: 2.96283 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 114 Number in noncoding regions = 6 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 15 ACGGTTTTACTCATTGCGATGTGTGTCACT 3 85 1 TCATTGCGAT 0.950829 -114 GCCTTAGCAATCTTTGCGATTGGTCAGTGA 12 88 0 TCTTTGCGAT 0.965167 -42 ATAGGGTGATTTATTGCGATAATCTACCCC 19 163 1 TTATTGCGAT 0.947126 -122 ATTTTCGCTATTTTTGCGATCTAGATCGAA 23 144 1 TTTTTGCGAT 0.962501 -126 ATTATACTGGTTTTTTCGATTTTTGGTGGT 26 15 0 TTTTTTCGAT 0.831038 -43 ********** Masking position 5 Map Score: 1.54573 Number of sites scoring better than the average of aligned sites = 86 Number in coding regions = 73 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987