AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00780_hinf_reg_300.orf -o00780_hinf_300.ace -a/home/amcguire/genomes/ORF_hinf.txt -z/home/amcguire/genomes/hinf.fna -g0.38 -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 = 0.38 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 HI0151 109 hflK protein (hflK) #2 HI0152 300 H. influenzae predicted coding region HI0152 #3 HI0415 300 hydroxyethylthiazole kinase #4 HI0419 168 protease, putative #5 HI0587 99 peptidase E (pepE) #6 HI1019 300 thiamin ABC transporter, periplasmic-binding protein (tbpA) #7 HI1022 112 biotin synthetase (bioB) #8 HI1445 102 dethiobiotin synthase (bioD-1) #9 HI1447 137 GTP cyclohydrolase I (folE) #10 HI1541 97 protease IV (sppA) #11 HI1556 59 2-hydroxyacid dehydrogenase #12 HI1560 22 H. influenzae predicted coding region HI1560 #13 HI1561 106 peptide chain release factor 1 (prfA) #14 HI1562 252 H. influenzae predicted coding region HI1562 #15 HI1563 32 conserved hypothetical protein #16 HI1564 32 H. influenzae predicted coding region HI1564 #17 HI1564.1 284 H. influenzae predicted coding region HI1564.1 #18 HI1682 197 protease, putative (sohB) Motif number 1 TATTATTTTAACCACAGTTTTATGGTGCCA 2 156 1 ACCACAGTTT 0.956592 -145 TAAGAATTTAACCGCACTTTCCTTTACAAG 4 67 1 ACCGCACTTT 0.998282 -102 GGTTAAAAACACCACGCTTTTTATACTTTC 7 74 0 ACCACGCTTT 0.972498 -39 GGTGTTTTTAACCGCACTTTCAAAGGAAAA 7 91 1 ACCGCACTTT 0.998282 -22 TTTAAAATCCACCGCACTTTTTAAAGGAGA 8 78 1 ACCGCACTTT 0.998282 -25 GCTATAATCCACCGCACTTTTACTTATAAG 10 21 0 ACCGCACTTT 0.998282 -77 GTCAAAATTAACCGCACTTTTGATGAAAT 11 10 0 ACCGCACTTT 0.998282 -50 GTTAATTTTGACCGCACTTTGTATATAAAA 11 28 1 ACCGCACTTT 0.998282 -32 ********** Masking position 1 Map Score: 26.4818 Number of sites scoring better than the average of aligned sites = 1115 Number in coding regions = 700 Number in noncoding regions = 415 Number of orfs with sites within 600 bp upstream = 285 Fraction of orfs with sites within 600 bp upstream = 0.0457758 Motif number 2 ATACAAGGCTTTTTAGGCAATAAAAAATCCTTGATTT 1 30 0 TTTTAAAAAA 0.97449 -80 TTTACGCTTCTTTTCAAGAAAAAACAAGCGGTCAAAT 3 54 0 TTTTAAAAAA 0.978044 -247 CAATTATAATTTTTCGTTGAAAATTAACCTTTTCTAA 5 52 1 TTTTAAATAA 0.942502 -48 GTATAGATTTCTTTAATTTACAATGAGTTATCTTCAT 6 16 1 CTTTAAATAG 0.813716 -285 ACTTTCTACATTTTCTGAAAAAATAAAGGGGCTGACG 6 82 0 TTTTAAATAA 0.941522 -219 TGCCAACGGCTTTTTAAAAAGAAATAAACTTTCTACA 6 109 0 TTTTAAAAAA 0.977834 -192 TTATTGCTGCCTTTTAATCATAAATAAGGATGTAATA 6 274 1 CTTTAAAAAA 0.944604 -27 TTTTCACTTTTTTTATCTTATAAATAGACAAA 8 6 0 TTTTAAAAAG 0.958567 -97 TAAAGGAATTTTTTATTTAATAATTTGAGATAACGCA 8 45 0 TTTTAAATTG 0.665026 -58 CCACCGCACTTTTTAAAGGAGAAAAAA 8 86 1 TTTTAAAAAA 0.977834 -17 AATAGTCTTTCCTAAAAAAATAATCGGCTATTC 9 115 0 CTTTAAAAAA 0.952138 -23 AATTGCTCCTTTTTTATATACAAAGTGCGGTCAAAAT 11 32 0 TTTTAAAATG 0.842529 -28 GATCAGGCTGTTTTGGCAAATCAAAAACACACTAAAA 14 191 0 TTTTACAAAA 0.930888 -62 ATTGGTCATATTTAGTCCTATAAAAAAAATAATAATA 17 60 1 TTTAAAAAAA 0.852409 -225 AAGAAAGGTATTTTCTCACAACAATAAAGATTGATTT 17 117 1 TTTTACAAAA 0.934114 -168 TAAAGATTGATTTTTGATAAAAATCAAGAAATAAAAA 17 141 1 TTTTAAATAA 0.915937 -144 AACAAGCAGGTTTAAATACAGAAAATAATAAGAATAG 17 178 0 TTTAAAAATA 0.546815 -107 GTAGGGTGGGCTTTAGCCCACCAAAAAACAATCGAGA 17 252 1 CTTTACAAAA 0.862053 -33 TAATTTAAAATTTTTTGTTATAAATAGCACAAACAAT 18 88 1 TTTTAAAAAG 0.777066 -110 **** * *** ** Masking position 3 Map Score: 25.1823 Number of sites scoring better than the average of aligned sites = 314 Number in coding regions = 179 Number in noncoding regions = 135 Number of orfs with sites within 600 bp upstream = 121 Fraction of orfs with sites within 600 bp upstream = 0.0194346 Motif number 3 AGCGGTCAAATTCTTCTCATTATTTGCAAAATG 3 13 1 TTTTCATTAT 0.934618 -288 CGGTCAAATTTTTCCCTCATTTTGCAAATAATG 3 30 0 TTCTCATTTT 0.916935 -271 CACGATTTTATCCTGTTTATTTTCCCAATTTTC 3 203 1 TCTTTATTTT 0.760366 -98 ATTTTCCCAATTTTCTACATTTTATTACACCTG 3 221 1 TTTACATTTT 0.881628 -80 TAGCGGGCATTTTTGTTTATTTTATATTCAACA 3 272 1 TTTTTATTTT 0.952646 -29 TTACAATGAGTTATCTTCATTTTTATAGACTAG 6 33 1 TTTTCATTTT 0.985913 -268 CCTTATCTCCTTTTCGTCATTATTGCTGCCTTT 6 255 1 TTTTCATTAT 0.934618 -46 AAATTTGCAATTTTTCTCATTTTACCATCCTAT 9 70 1 TTTTCATTTT 0.985913 -68 AAGTGAGCAATTTTGATCACTTTCTGCCA 14 7 0 TTTTCACTTT 0.916935 -246 ATAGTTCAATTTTTAATCATTTCACACCCAGTA 14 77 1 TTTTCATTTC 0.916935 -176 TGTTTGAGAATTATTATTATTTTTTTTATAGGA 17 75 0 TTTTTATTTT 0.952646 -210 ATAAAAACTATTCTTATTATTTTCTGTATTTAA 17 171 1 TTTTTATTTT 0.952646 -114 TTCTTACTTTTTATTTTCATTTTGGCTAATTTG 18 54 0 TTTTCATTTT 0.985913 -144 ** * ******* Masking position 9 Map Score: 16.954 Number of sites scoring better than the average of aligned sites = 69 Number in coding regions = 50 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 20 Fraction of orfs with sites within 600 bp upstream = 0.00321234 Motif number 4 AGGCAATAAAAAATCCTTGATTTTATATAAGGAT 1 19 0 AACTTATTTT 0.803515 -91 TATTGCCTAAAAAGCCTTGTATTTTCATAGACGT 1 45 1 AACTTTATTT 0.810653 -65 TTTTATATTAAAAGGATTTAGTTTGTGTGTAAAT 2 251 0 AAGTTAGTTT 0.943582 -50 TAAGCGGTCAAATTCTTCTCATTAT 3 2 1 AAGTCAATTC 0.891991 -299 AAGAAAAAACAAGCGGTCAAATTTTTCCCTCATT 3 42 0 AAGTCAATTT 0.974158 -259 CGTCAGTGCTAACTGTTTCAGGTTCACGGGTATC 3 131 0 AAGTTAGGTT 0.785594 -170 TTAACCGCTTAATAGGTTGTATTTAATTCCTCAA 4 14 0 AAGTTTATTT 0.935481 -155 ACAACCTATTAAGCGGTTAAATTTTATATAAAAT 4 28 1 AAGTTAATTT 0.973222 -141 TTACGCTTAGAAAAGGTTAATTTTCAACGAAAAA 5 61 0 AAGTTATTTT 0.932657 -39 CGTCAGTATTAACTGTTTCAGGTTCACGGGTATG 6 202 0 AAGTTAGGTT 0.785594 -99 TAATTGCTCCTTTTTTATATACAAA 11 45 0 AAGTCTTTTT 0.851435 -15 TTTCAGTCTTAAGCCCTCCAATTCCCTCCTAATT 14 41 1 AACTCAATTC 0.709181 -212 CTCCTAATTAAATAGTTCAATTTTTAATCATTTC 14 66 1 AAGTCATTTT 0.934919 -187 ATTCTTCTTTAATTGCTTCAATTTTTTCTTGAAG 14 227 0 AAGTTAATTT 0.973222 -26 AGTTACTTGAAAATCTTCAAATTTAAGCT 16 6 0 AACTCAATTT 0.917562 -27 TTTAATCTAAAATTGGTCATATTTAGTCCTATAA 17 49 1 AAGTCTATTT 0.937652 -236 AAATAATAAGAATAGTTTTTATTTCTTGATTTTT 17 159 0 AAGTTTATTT 0.935481 -126 GTTGATATTTAATGGATTAAATTTTCACGACACT 18 164 0 AAGTTAATTT 0.973222 -34 ** * ** ***** Masking position 7 Map Score: 21.8605 Number of sites scoring better than the average of aligned sites = 281 Number in coding regions = 215 Number in noncoding regions = 66 Number of orfs with sites within 600 bp upstream = 62 Fraction of orfs with sites within 600 bp upstream = 0.00995824 Motif number 5 ATTATTTTAACCACAGTTTTATGGTGCCAG 2 157 1 CCACAGTTTT 0.911616 -144 AAGAATTTAACCGCACTTTCCTTTACAAGC 4 68 1 CCGCACTTTC 0.994575 -101 GTTAAAAACACCACGCTTTTTATACTTTCT 7 73 0 CCACGCTTTT 0.943028 -40 GTGTTTTTAACCGCACTTTCAAAGGAAAAA 7 92 1 CCGCACTTTC 0.994575 -21 TTAAAATCCACCGCACTTTTTAAAGGAGAA 8 79 1 CCGCACTTTT 0.996343 -24 CTATAATCCACCGCACTTTTACTTATAAGG 10 20 0 CCGCACTTTT 0.996343 -78 TCAAAATTAACCGCACTTTTGATGAAAT 11 9 0 CCGCACTTTT 0.996343 -51 TTAATTTTGACCGCACTTTGTATATAAAAA 11 29 1 CCGCACTTTG 0.990062 -31 ********** Masking position 7 Map Score: 19.302 Number of sites scoring better than the average of aligned sites = 1040 Number in coding regions = 687 Number in noncoding regions = 353 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 6 AAAAAATCCTTATATAAAATCAAGGATTTTT 1 14 1 TATATAAATC 0.302531 -96 CTTTTTAGGCAATAAAAAATCCTTGATTTTA 1 28 0 AATAAAAATC 0.853409 -82 ATTTGGAATGAAGAAATACGCATAAGTTGCA 2 65 0 AAGAAAACGC 0.554126 -236 AAATCCTTTTAATATAAAAGCACCTTTGAAT 2 266 1 AATATAAAGC 0.695731 -35 AAAATAAAAGCACCATTCAAA 2 290 0 AAAATAAAGC 0.857148 -11 TCTTTTCAAGAAAAAACAAGCGGTCAAATTT 3 52 0 AAAAAAAAGC 0.935726 -249 TGTTTTTTCTTGAAAAGAAGCGTAAACTTCT 3 65 1 TGAAAAAAGC 0.427953 -236 GAAAATAAACAGGATAAAATCGTGATAGAGA 3 196 0 AGGATAAATC 0.615121 -105 GACGAATATCAAAAAATAAACCGTATCAGGA 5 18 0 AAAAAAAAAC 0.741385 -82 GCTTTTTAAAAAGAAATAAACTTTCTACATT 6 107 0 AAGAAAAAAC 0.719095 -194 GTGTATATGGTAGAAACAATCAATTCAACGT 7 28 0 TAGAAAAATC 0.711492 -85 CAAATTATTAAATAAAAAATTCCTTTAAAAT 8 55 1 AATAAAAATT 0.311828 -48 GTCTTTCCTAAAAAAATAATCGGCTATTCTA 9 113 0 AAAAAAAATC 0.938563 -25 CTTTGTATATAAAAAAGGAGCAATTA 11 44 1 AAAAAAGAGC 0.581895 -16 TAAGTCACCGAAAATAAAATCGGCGTATTCT 13 83 0 AAAATAAATC 0.862946 -24 CCTGATCTTCAAGAAAAAATTGAAGCAATTA 14 221 1 AAGAAAAATT 0.514987 -32 AGTCCTATAAAAAAAATAATAATAATTCTCA 17 73 1 AAAAAAAATA 0.402743 -212 GATTTTTATCAAAAATCAATCTTTATTGTTG 17 135 0 AAAAATAATC 0.646335 -150 CTCGCATTATAGGAAACAAGCAGGTTTAAAT 17 198 0 AGGAAAAAGC 0.787026 -87 TTAGCCCACCAAAAAACAATCGAGAGATATT 17 264 1 AAAAAAAATC 0.938563 -21 CAGTGTCGTGAAAATTTAATCCATTAAATAT 18 163 1 AAAATTAATC 0.42962 -35 ****** **** Masking position 4 Map Score: 10.5856 Number of sites scoring better than the average of aligned sites = 609 Number in coding regions = 430 Number in noncoding regions = 179 Number of orfs with sites within 600 bp upstream = 155 Fraction of orfs with sites within 600 bp upstream = 0.0248956 Motif number 7 ACCTGTTGGTATTGGTTTAGGTATTC 2 6 1 TTGGTTTGGT 0.550375 -295 TGCGCCAATCTTAGTTGGTTTAATGCCTGCA 2 38 1 TTAGTGGTTT 0.905611 -263 GGTGCCAGGTTTAATTGGGGTTGTTGTTGCT 2 179 1 TTAATGGGGT 0.868164 -122 TGTTGCTTGCTTGGTCGGTGTTTCTGTGGCG 2 203 1 TTGGTGGTGT 0.959843 -98 TTAAAAGGATTTAGTTTGTGTGTAAATTAGC 2 247 0 TTAGTTGTGT 0.939123 -54 CTTTCGACTTTTAGTCGGGGTGCCGAAAGGC 3 94 1 TTAGTGGGGT 0.988176 -207 CTGTGAGCAATTAGCAGGTGTAATAAAATGT 3 237 0 TTAGCGGTGT 0.92851 -64 AGGTAAATCGTTAGGTGGGGTATTGTAGAGA 4 107 0 TTAGGGGGGT 0.945739 -62 ACTAGAAAGCCTAGTCGGGGTGCAATACGCT 6 166 1 CTAGTGGGGT 0.940259 -135 TCGCCTTGTTTTAGTGTGTTTTTGATTTGCC 14 183 1 TTAGTTGTTT 0.703845 -70 TGATTGTTGATTAGTAGTTGTAGGGTGGGCT 17 233 1 TTAGTGTTGT 0.905611 -52 ***** ***** Masking position 2 Map Score: 9.04857 Number of sites scoring better than the average of aligned sites = 96 Number in coding regions = 84 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 8 AGCTAAACTCTTAACAATTTTTTGACAA 1 92 1 TTACAATTTT 0.920792 -18 TATTTCTTCATTCCAAATTATCCGTCAGATA 2 78 1 TTCAAATTAT 0.719363 -223 AAAATAATATTTACCAATTTTTGTTGTACCC 2 134 0 TTCCAATTTT 0.97258 -167 CCTGTTTATTTTCCCAATTTTCTACATTTTA 3 214 1 TTCCAATTTT 0.97258 -87 TAAAAAGCCGTTGGCAATCTTAGTAAATTTT 6 130 1 TTGCAATCTT 0.86367 -171 ATAGAATAGCTGACAAATTTTATCAAATAAG 9 19 0 TGCAAATTTT 0.864789 -119 TTCATTCAAATTTGCAATTTTTCTCATTTTA 9 63 1 TTGCAATTTT 0.948131 -75 CTGAAAAAAGTGAGCAATTTTGATCACTTTC 14 16 0 TGGCAATTTT 0.910866 -237 CTAATCCTAGTTGCCAATTATGCTTTGTTGT 14 141 0 TTCCAATTAT 0.888234 -112 AGTAGTTACTTGAAAATCTTCAAATTTAAG 16 13 0 TTAAAATCTT 0.56512 -20 GGACTAAATATGACCAATTTTAGATTAAACG 17 47 0 TGCCAATTTT 0.951991 -238 TAAGAATTAATTTAAAATTTTTTGTTATAAA 18 81 1 TTAAAATTTT 0.789453 -117 ** ******** Masking position 6 Map Score: 10.9844 Number of sites scoring better than the average of aligned sites = 284 Number in coding regions = 234 Number in noncoding regions = 50 Number of orfs with sites within 600 bp upstream = 50 Fraction of orfs with sites within 600 bp upstream = 0.00803084 Motif number 9 GGGAAAATAAACAGGATAAAATCGTGATAGA 3 198 0 ACAGGAAAAA 0.861896 -103 GAAATCAGACAAAAGAGAATATT 4 156 1 AAAAGAAATA 0.82031 -13 CGGCTTTTTAAAAAGAAATAAACTTTCTACA 6 109 0 AAAAGAATAA 0.690821 -192 ATAATGACGAAAAGGAGATAAGGTTATATTC 6 247 0 AAAGGAATAA 0.928187 -54 ATCAATTAAGAAAGTATAAAAAGCGTGGTGT 7 65 1 AAAGTAAAAA 0.722876 -48 CCGCACTTTCAAAGGAAAAAC 7 102 1 AAAGGAAAAC 0.861896 -11 CGCACTTTTTAAAGGAGAAAAAA 8 90 1 AAAGGAAAAA 0.973229 -13 TAGGATGGTAAAATGAGAAAAATTGCAAATT 9 71 0 AAATGAAAAA 0.862724 -67 CTATTCTAGCAAAGGATAATAGGATGGTAAA 9 90 0 AAAGGAAATA 0.963514 -48 TTTTACTTATAAGGGATAATAAA 10 3 0 AAGGGAAATA 0.81928 -95 TTGACAGCGAAAAGGAAATTAAGAATCTCAG 13 34 0 AAAGGAATTA 0.903743 -73 AAATTAGCCAAAATGAAAATAAAAAGTAAGA 18 55 1 AAATGAAATA 0.82031 -143 ****** **** Masking position 6 Map Score: 9.86532 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 91 Number in noncoding regions = 58 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 10 GTTGCAATATCTGACGGATAATTTGGAATG 2 86 0 CTGACGGATA 0.936046 -215 ACAGTTAGCACTGACGTAGGAAACTAATAT 3 149 1 CTGACGTAGG 0.991402 -152 AATAAAGGGGCTGACGTAGATTAGCAAGTG 6 68 0 CTGACGTAGA 0.989918 -233 ACAGTTAATACTGACGTAGGAAACTAGGAA 6 220 1 CTGACGTAGG 0.991402 -81 ********** Masking position 4 Map Score: 2.18574 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 1 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 11 GGTTCACGGGTATCATCTCAGCCTTTCGGCA 3 114 0 TATATCTCAG 0.916481 -187 TTCTCTTTTGTCTGATTTCAGGTCAGGGACT 4 144 0 TCTATTTCAG 0.968491 -25 TCAGCCCCTTTATTTTTTCAGAAAATGTAGA 6 84 1 TATTTTTCAG 0.950928 -217 GGTTCACGGGTATGATCTCAGCGTATTGCAC 6 185 0 TATATCTCAG 0.916481 -116 AATAGCCGATTATTTTTTTAGGAAAGACTAT 9 116 1 TATTTTTTAG 0.683941 -22 GATAGGGACATCTGATTTCAG 12 12 1 TCTATTTCAG 0.968491 -11 AAAATTGCTCACTTTTTTCAGTCTTAAGCCC 14 26 1 ACTTTTTCAG 0.846349 -227 GGTGTTGTACTCTCTTTACAGAGAGTACAAC 14 115 1 TCTTTTACAG 0.846349 -138 *** ******* Masking position 10 Map Score: 2.68158 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 33 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 11 Fraction of orfs with sites within 600 bp upstream = 0.00176678 Motif number 12 TTGATTTTATATAAGGATTTTTTTGA 1 7 0 ATAAGGATTT 0.935265 -103 TTATATAAAATCAAGGATTTTTTATTGCCT 1 23 1 TCAAGGATTT 0.640419 -87 CTATGAAAATACAAGGCTTTTTAGGCAATA 1 45 0 ACAAGGCTTT 0.968859 -65 CTTTTATATTAAAAGGATTTAGTTTGTGTG 2 256 0 AAAAGGATTT 0.721373 -45 ACCTTTCTCTATCACGATTTTATCCTGTTT 3 191 1 ATCACGATTT 0.68855 -110 TTGCACCCCGACTAGGCTTTCTAGTGTATT 6 161 0 ACTAGGCTTT 0.933725 -140 TTAATCATAAATAAGGATGTAATA 6 287 1 ATAAGGATGT 0.820286 -14 GGTTAAAAACACCACGCTTTTTATACTTTC 7 74 0 ACCACGCTTT 0.82642 -39 ATTTTATCAAATAAGGATTTTCT 9 4 0 ATAAGGATTT 0.935265 -134 ATTTGAATGAATTAGGCTTTAGATATAGAA 9 44 0 ATTAGGCTTT 0.924025 -94 ATAGTTTTTGACAAGGCTTTGTGATACGCT 10 51 1 ACAAGGCTTT 0.968859 -47 CTAGTTGCCAATTATGCTTTGTTGTACTCT 14 136 0 ATTATGCTTT 0.489354 -117 TTTCTTGAAGATCAGGCTGTTTTGGCAAAT 14 207 0 ATCAGGCTGT 0.857993 -46 ********** Masking position 4 Map Score: 12.329 Number of sites scoring better than the average of aligned sites = 197 Number in coding regions = 171 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 21 Fraction of orfs with sites within 600 bp upstream = 0.00337295 Motif number 13 TACCAATTTTTGTTGTACCCGTTACGTCAA 2 124 0 TGTTGTACCC 0.986636 -177 GCTTTATTTGTGATTTACCCA 13 2 0 TGATTTACCC 0.88033 -105 GTATACTGGGTGTTGTACTCTCTTTACAGA 14 107 1 TGTTGTACTC 0.979485 -146 AATTATGCTTTGTTGTACTCTCTGTAAAGA 14 127 0 TGTTGTACTC 0.979485 -126 ********** Masking position 6 Map Score: 0.903441 Number of sites scoring better than the average of aligned sites = 5 Number in coding regions = 2 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 14 CCGCCACAGAAACACCGACCAAGCAAGCAA 2 205 0 AACACCGACC 0.919796 -96 AGCCTTTCGGCACCCCGACTAAAAGTCGAA 3 96 0 CACCCCGACT 0.984107 -205 CAGCGTATTGCACCCCGACTAGGCTTTCTA 6 168 0 CACCCCGACT 0.984107 -133 TTAATCATTTCACACCCAGTATACTGGGTG 14 89 1 CACACCCAGT 0.964329 -164 AAGAGAGTACAACACCCAGTATACTGGGTG 14 101 0 AACACCCAGT 0.923068 -152 ********** Masking position 8 Map Score: 0.0998451 Number of sites scoring better than the average of aligned sites = 13 Number in coding regions = 9 Number in noncoding regions = 4 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 15 AATCCTTATATAAAATCAAGGATTTTTTAT 1 18 1 TAAAATCAAG 0.762145 -92 TCTTTTCAAGAAAAAACAAGCGGTCAAATT 3 53 0 AAAAAACAAG 0.762145 -248 ACGAATATCAAAAAATAAACCGTATCAGGA 5 18 0 AAAAATAAAC 0.731024 -82 ACTAGTCTATAAAAATGAAGATAACTCATT 6 37 0 AAAAATGAAG 0.820744 -264 CATTTTCTGAAAAAATAAAGGGGCTGACGT 6 81 0 AAAAATAAAG 0.910425 -220 ATATGGTAGAAACAATCAATTCAACGTTAT 7 25 0 AACAATCAAT 0.797334 -88 TGGGTAAATCACAAATAAAGCGTCTGAGAT 13 11 1 ACAAATAAAG 0.635677 -96 ATTTTCTCACAACAATAAAGATTGATTTTT 17 126 1 AACAATAAAG 0.893178 -159 GATTTTTATCAAAAATCAATCTTTATTGTT 17 136 0 AAAAATCAAT 0.827058 -149 GATTTTTGATAAAAATCAAGAAATAAAAAC 17 149 1 AAAAATCAAG 0.965113 -136 ACTACTAATCAACAATCAACGGCTCGCATT 17 221 0 AACAATCAAC 0.858867 -64 CCCACCAAAAAACAATCGAGAGATATT 17 268 1 AACAATCGAG 0.796205 -17 ********** Masking position 5 Map Score: 8.19782 Number of sites scoring better than the average of aligned sites = 278 Number in coding regions = 207 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 58 Fraction of orfs with sites within 600 bp upstream = 0.00931577