AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i175_biotin_biosynthesis1_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 bioA_bioB 86 bioA: 7,8-diaminopelargonic acid synthetase, bioB: biotin synthesis, sulfur insertion? #2 HI1019 300 thiamin ABC transporter, periplasmic-binding protein (tbpA) #3 HI1022 112 biotin synthetase (bioB) #4 HI1556 59 2-hydroxyacid dehydrogenase #5 HI1560 22 H. influenzae predicted coding region HI1560 #6 HI1561 106 peptide chain release factor 1 (prfA) #7 HI1562 252 H. influenzae predicted coding region HI1562 #8 HI1563 32 conserved hypothetical protein #9 HI1564 32 H. influenzae predicted coding region HI1564 #10 HI1564.1 284 H. influenzae predicted coding region HI1564.1 Motif number 1 ACCGAATTAACAACAAAAAACACGTTTTGG 1 20 0 CAACAAAAAA 0.879985 -67 ACATTTTCTGAAAAAATAAAGGGGCTGACG 2 82 0 AAAAAATAAA 0.916868 -219 GCTTTTTAAAAAGAAATAAACTTTCTACAT 2 108 0 AAGAAATAAA 0.939648 -193 GATTAAAAGGCAGCAATAATGACGAAAAGG 2 263 0 CAGCAATAAT 0.880864 -38 TATATGGTAGAAACAATCAATTCAACGTTA 3 26 0 AAACAATCAA 0.852399 -87 TGGGTAAATCACAAATAAAGCGTCTGAGA 6 10 1 CACAAATAAA 0.895363 -97 GACAGCGAAAAGGAAATTAAGAATCTCAGA 6 33 0 AGGAAATTAA 0.515376 -74 TGTAAGTCACCGAAAATAAAATCGGCGTAT 6 86 0 CGAAAATAAA 0.822837 -21 CCTGATCTTCAAGAAAAAATTGAAGCAATT 7 221 1 AAGAAAAAAT 0.538357 -32 GAAAAAATTGAAGCAATTAAAGAAGAATTG 7 233 1 AAGCAATTAA 0.83831 -20 AGTCCTATAAAAAAAATAATAATAATTCTC 10 73 1 AAAAAATAAT 0.718398 -212 TATTTTCTCACAACAATAAAGATTGATTTT 10 125 1 CAACAATAAA 0.957705 -160 TGATTTTTATCAAAAATCAATCTTTATTGT 10 137 0 CAAAAATCAA 0.901555 -148 GATAAAAATCAAGAAATAAAAACTATTCTT 10 156 1 AAGAAATAAA 0.939648 -129 GGTTTAAATACAGAAAATAATAAGAATAGT 10 177 0 CAGAAAATAA 0.72695 -108 AACTACTAATCAACAATCAACGGCTCGCAT 10 222 0 CAACAATCAA 0.912436 -63 GGCTTTAGCCCACCAAAAAACAATCGAGAG 10 260 1 CACCAAAAAA 0.759197 -25 ********** Masking position 5 Map Score: 16.0936 Number of sites scoring better than the average of aligned sites = 1240 Number in coding regions = 976 Number in noncoding regions = 264 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 2 ACCACGCTTTTTATACTTTCTTAATTGATGAA 3 62 0 TTATACTCTT 0.946573 -51 CGTGGTGTTTTTAACCGCACTTTCAAAGGAAA 3 88 1 TTAACCCCTT 0.986163 -25 GCGGTCAAAATTAACCGCACTTTTGATGAAAT 4 11 0 TTAACCCCTT 0.986163 -49 GCGGTTAATTTTGACCGCACTTTGTATATAAA 4 25 1 TTGACCCCTT 0.985887 -35 ATACTGGGTGTTGTACTCTCTTTACAGAGAGT 7 109 1 TTGTACCCTT 0.977986 -144 TTATGCTTTGTTGTACTCTCTGTAAAGAGAGT 7 123 0 TTGTACCCTG 0.921875 -130 CAATTTTAGATTAAACGTGCTTGCCTATTCCG 10 32 0 TTAAACTCTT 0.966012 -253 TTTTCTGTATTTAAACCTGCTTGTTTCCTATA 10 190 1 TTAAACTCTT 0.966012 -95 ****** * *** Masking position 2 Map Score: 9.88584 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 41 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 17 Fraction of orfs with sites within 600 bp upstream = 0.00273049 Motif number 3 GGTTAAAAACACCACGCTTTTTATACTTTC 3 74 0 ACCACGCTTT 0.97872 -39 GGTGTTTTTAACCGCACTTTCAAAGGAAAA 3 91 1 ACCGCACTTT 0.996725 -22 GTCAAAATTAACCGCACTTTTGATGAAAT 4 10 0 ACCGCACTTT 0.996725 -50 GTTAATTTTGACCGCACTTTGTATATAAAA 4 28 1 ACCGCACTTT 0.996725 -32 ********** Masking position 8 Map Score: 7.7683 Number of sites scoring better than the average of aligned sites = 6 Number in coding regions = 4 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 3 Fraction of orfs with sites within 600 bp upstream = 0.00048185 Motif number 4 AAAAGATTTAGGTTTACAAGTCTACACCGA 1 45 0 GGTTTACAAG 0.981373 -42 TTTTCAATTTGGTTTACAAGTCGATT 1 71 1 GGTTTACAAG 0.981373 -16 GGCTGACGTAGATTAGCAAGTGCACTAGTC 2 60 0 GATTAGCAAG 0.981374 -241 TGGCAACTAGGATTAGCAAGCATATTGTCG 7 156 1 GATTAGCAAG 0.981374 -97 AAAACAGCCTGATCTTCAAGAAAAAATTGA 7 214 1 GATCTTCAAG 0.958742 -39 TAAATTTGAAGATTTTCAAGTAACTACT 9 15 1 GATTTTCAAG 0.984509 -18 ********** Masking position 3 Map Score: 7.0248 Number of sites scoring better than the average of aligned sites = 43 Number in coding regions = 36 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 CTTGTAAACCAAATTGAAAAGATTTAGGTT 1 61 0 AAATTGAAAA 0.843021 -26 AACTCATTGTAAATTAAAGAAATCTATACA 2 15 0 AAATTAAAGA 0.859493 -286 CTAGTCTATAAAAATGAAGATAACTCATTG 2 36 0 AAAATGAAGA 0.978004 -265 ATTTTTTCAGAAAATGTAGAAAGTTTATTT 2 95 1 AAAATGTAGA 0.875144 -206 TATACTTTCTTAATTGATGAATTAGTGTAT 3 53 0 TAATTGATGA 0.731816 -60 CTTCAAGAAAAAATTGAAGCAATTAAAGAA 7 227 1 AAATTGAAGC 0.92753 -26 AGCTTAAATTTGAAGATTTTCAAGTA 9 7 1 AATTTGAAGA 0.945386 -26 TCAAACATATTATATGAAGAAAGGTATTTT 10 101 1 TATATGAAGA 0.816177 -184 ATTTTTGATAAAAATCAAGAAATAAAAACT 10 150 1 AAAATCAAGA 0.880368 -135 ********** Masking position 5 Map Score: 5.09397 Number of sites scoring better than the average of aligned sites = 442 Number in coding regions = 372 Number in noncoding regions = 70 Number of orfs with sites within 600 bp upstream = 79 Fraction of orfs with sites within 600 bp upstream = 0.0126887 Motif number 6 GACGAAAAGGAGATAAGGTTATATTCCTAGTTTCC 2 238 0 AGATAGGATT 0.739902 -63 TTTTAATCATAAATAAGGATGTAATA 2 285 1 AAATAGGAAT 0.899055 -16 AAGAAAGTATAAAAAGCGTGGTGTTTTTAACCGCA 3 72 1 AAAAACGGTT 0.783577 -41 CTTTGTATATAAAAAAGGAGCAATTA 4 44 1 AAAAAGGATT 0.981928 -16 AATTTTCCCTAAAATCGGCTAGAATACGCCGATTT 6 63 1 AAAATGGAAT 0.888264 -44 TTAAGACTGAAAAAAGTGAGCAATTTTGATCACTT 7 18 0 AAAAATGATT 0.946834 -235 TGAAATGATTAAAAATTGAACTATTTAATTAGGAG 7 66 0 AAAAATGATT 0.946829 -187 AAACACACTAAAACAAGGCGACAATATGCTTGCTA 7 169 0 AAACAGGAAT 0.882157 -84 ATCTTCAAGAAAAAATTGAAGCAATTAAAGAAGAA 7 225 1 AAAAATGAAT 0.913049 -28 TCGACTCCTAAAAAACCGCAAGATTATA 8 4 0 AAAAACGATT 0.950516 -29 CGTTTAATCTAAAATTGGTCATATTTAGTCCTATA 10 47 1 AAAATGGATT 0.930949 -238 ***** ** *** Masking position 3 Map Score: 8.11218 Number of sites scoring better than the average of aligned sites = 273 Number in coding regions = 195 Number in noncoding regions = 78 Number of orfs with sites within 600 bp upstream = 87 Fraction of orfs with sites within 600 bp upstream = 0.0139737 Motif number 7 GCTTCTCCAAAACGTGTTTTTTGTTGTTAA 1 14 1 AACGTGTTTT 0.76948 -73 CTAGTTGCCAATTATGCTTTGTTGTACTCT 7 136 0 ATTATGCTTT 0.841723 -117 ACAAGGCGACAATATGCTTGCTAATCCTAG 7 162 0 AATATGCTTG 0.978171 -91 TGCCTATTCCGTTATGCTTGGGCTAACGGC 10 13 0 GTTATGCTTG 0.857112 -272 TTTTAGATTAAACGTGCTTGCCTATTCCGT 10 31 0 AACGTGCTTG 0.978195 -254 TTCTTCATATAATATGTTTGAGAATTATTA 10 92 0 AATATGTTTG 0.924383 -193 TCTGTATTTAAACCTGCTTGTTTCCTATAA 10 193 1 AACCTGCTTG 0.960596 -92 ********** Masking position 5 Map Score: 2.35089 Number of sites scoring better than the average of aligned sites = 163 Number in coding regions = 150 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 8 AAAAATAAAGGGGCTGACGTAGATTAGCAAG 2 70 0 GGGCTGACGA 0.983075 -231 GGGAATTGGAGGGCTTAAGACTGAAAAAAGT 7 36 0 GGGCTTAAGC 0.990064 -217 CGTTATGCTTGGGCTAACGGCAA 10 3 0 GGGCTAACGC 0.996314 -282 GTTTTTTGGTGGGCTAAAGCCCACCCTACAA 10 250 0 GGGCTAAAGC 0.993149 -35 ********* * Masking position 5 Map Score: 2.33692 Number of sites scoring better than the average of aligned sites = 35 Number in coding regions = 33 Number in noncoding regions = 2 Number of orfs with sites within 600 bp upstream = 1 Fraction of orfs with sites within 600 bp upstream = 0.000160617 Motif number 9 CTAGAAAGCCTAGTCGGGGTGCAATACGCT 2 167 1 TAGTCGGGGT 0.920619 -134 ACACCCAGTATACTGGGTGTGAAATGATTA 7 90 0 TACTGGGTGT 0.983788 -163 ACACCCAGTATACTGGGTGTTGTACTCTCT 7 100 1 TACTGGGTGT 0.983788 -153 CTGGGTGTTGTACTCTCTTTACAGAGAGTA 7 112 1 TACTCTCTTT 0.872056 -141 TGCTTTGTTGTACTCTCTGTAAAGAGAGTA 7 122 0 TACTCTCTGT 0.952766 -131 CGCCTTGTTTTAGTGTGTTTTTGATTTGCC 7 184 1 TAGTGTGTTT 0.872056 -69 ********** Masking position 4 Map Score: 0.882409 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 96 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 10 ********** No masking Map Score: 1.21035e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 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 11 ********** No masking Map Score: 1.21035e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 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 12 ********** No masking Map Score: 1.21035e-12 Number of sites scoring better than the average of aligned sites = 0 Number in coding regions = 0 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