AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i197_replication1_ecoli_hinf_reg_100.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 gyrA 146 DNA gyrase, subunit A, type II topoisomerase #2 gyrB 28 DNA gyrase subunit B, type II topoisomerase, ATPase activity #3 dnaA 300 DNA biosynthesis; initiation of chromosome replication; can be transcription regulator #4 HI0567 150 DNA gyrase, subunit B (gyrB) #5 HI0993 191 chromosomal replication initiator protein (dnaA) #6 HI1264 300 DNA gyrase, subunit A (gyrA) Motif number 1 CAACGTTTCTCGCTCATTTATACTTGGG 2 8 0 TCTCCATTAT 0.95761 -21 AGATCTTCTGTTTCTCACAGATTTTCCCGATTTA 3 98 0 TTTCCAATTT 0.90697 -203 ACAGAAGATCTCTTGCGCAGTTTAGGCTATGATC 3 121 1 TCTCCATTTA 0.95761 -180 AACTTGTTATTTTTTCCAATTTTTTAGTGCA 4 8 0 TTTCAATTTT 0.867098 -143 GGGCGAAATTATTCGCCCTTTTTTTATCGTTTTC 4 45 1 ATTCCTTTTT 0.740477 -106 TTTGCTATAATCTCGCCCAATTTTTATTTACAAA 4 112 1 TCTCCATTTT 0.991762 -39 AATTTATCTCATTCTTTTGTAAATAA 4 135 0 TTTCCATCTT 0.935273 -16 ATTTAATCTATCTGGCGCATTTTAAT 5 3 0 TCTCCATTTA 0.95761 -189 TCTATACAATACTGGCGCATTTTTTTCTGTTCTA 5 45 1 ACTCCATTTT 0.9724 -147 TAGAAGATCTTTTCACGCATTTATTGTAAAATCT 5 115 1 TTTCCATTAT 0.948948 -77 TCCGACAATTTTTACCGCACTTTTCTCTATTACA 5 148 1 TTTCCATTTT 0.990005 -44 TCGCCTTTCTTTTTACTTACTTTTTCTTTGGCGA 6 168 1 TTTCTATTTT 0.867098 -133 CAAAAACCACATATCCACAATTTTATGCTATAAT 6 244 1 ATACCATTTT 0.755202 -57 TATGCTATAATCCGCCACAATTTTTGATCAAAAA 6 267 1 TCCCCATTTT 0.949969 -34 *** * ** **** Masking position 6 Map Score: 20.5413 Number of sites scoring better than the average of aligned sites = 348 Number in coding regions = 252 Number in noncoding regions = 96 Number of orfs with sites within 600 bp upstream = 114 Fraction of orfs with sites within 600 bp upstream = 0.0183103 Motif number 2 CATTGGATGTGAATAAAGCGTATAGGTTTACCTC 1 56 1 GATAAAGCAA 0.989331 -91 CGGGACCGCGGATCATAGCCTAAACTGCGCAAGA 3 131 0 GACATAGCAA 0.981312 -170 AGTCGATAATGACTAAGGCTGAAACATTCATGAT 3 256 0 GATAAGGCAA 0.960983 -45 AATTGGGCGAGATTATAGCAAAAAATCGCCGTTT 4 100 0 GATATAGCAA 0.989331 -51 CACTTAAGCAGATTATAGAACAGAAAAAAATGCG 5 60 0 GATATAGAAA 0.934834 -132 ACTTTAAATCGGATAAAGGACAAATTGGGTTCCC 6 14 1 GGTAAAGGAA 0.912226 -287 AAATTCAATGGAACAAAGGAAACAAGGAAAAGTA 6 131 1 GACAAAGGAA 0.956817 -170 AATTGTGGCGGATTATAGCATAAAATTGTGGATA 6 255 0 GATATAGCAA 0.989331 -46 ** ****** * * Masking position 5 Map Score: 8.58753 Number of sites scoring better than the average of aligned sites = 58 Number in coding regions = 53 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 AATTATTCGCCCTTTTTTTATCGTTTTCCTTT 4 51 1 CCTTTTTATC 0.965372 -100 ATAATCTCGCCCAATTTTTATTTACAAAAGAA 4 118 1 CCATTTTATT 0.672092 -33 ACAATACTGGCGCATTTTTTTCTGTTCTATAA 5 50 1 CGATTTTTTC 0.765018 -142 TCTAAAAAATCCAAGTTTGACCTTTCACTTAA 5 87 0 CCATTTGACC 0.951734 -105 AAAATCTCCGACAATTTTTACCGCACTTTTCT 5 142 1 ACATTTTACC 0.712697 -50 AAGAAGGGAACCCAATTTGTCCTTTATCCGAT 6 21 0 CCATTTGTCC 0.95907 -280 AAATTGGGTTCCCTTCTTTTCCACCTTTGTGG 6 35 1 CCTCTTTTCC 0.976513 -266 AGAAAGGCGACCCTACTTTTCCTTGTTTCCTT 6 146 0 CCTCTTTTCC 0.976513 -155 AGTAGGGTCGCCTTTCTTTTTACTTACTTTTT 6 161 1 CCTCTTTTTA 0.730223 -140 CCTGATGGCGCCTTACTTTTTCTTTGCTTCGC 6 198 0 CCTCTTTTTC 0.968732 -103 TGGTATTCCTTTTTTGATCAAAAATTGTG 6 282 0 CCTTTTGATC 0.945831 -19 ** * ******* Masking position 7 Map Score: 9.23295 Number of sites scoring better than the average of aligned sites = 890 Number in coding regions = 772 Number in noncoding regions = 118 Number of orfs with sites within 600 bp upstream = 131 Fraction of orfs with sites within 600 bp upstream = 0.0210408 Motif number 4 CGCTAAGTGTAAACGATCCTGCCGCGAGGC 3 47 0 AAACGATCCT 0.984945 -254 TAAACTGCGCAAGAGATCTTCTGTTTCTCA 3 115 0 AAGAGATCTT 0.921449 -186 ACGTACGTCGAAAAGACCCTGCTTGAGGGT 3 221 0 AAAAGACCCT 0.980347 -80 TAAATGCGTGAAAAGATCTTCTAAAAAATC 5 108 0 AAAAGATCTT 0.952754 -84 AAAAGGATCCTTATTGTTTTT 5 181 0 AAAGGATCCT 0.972445 -11 GTAAAAAGAAAGGCGACCCTACTTTTCCTT 6 154 0 AGGCGACCCT 0.94164 -147 ********** Masking position 6 Map Score: 3.74498 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 71 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 5 ACTTCTACTCCGTAATTGGCAAGACAAACGAG 1 15 1 CGATTGGCAA 0.932773 -132 ATCCCGGATTCAAAGGTCGCAAATTATAACAC 1 103 0 CAAGTCGCAA 0.987462 -44 CAGGACTTTCCAGAACTCGCTAAGTGTAAACG 3 62 0 CAACTCGCTA 0.969337 -239 TGATTGTTGACGTACGTCGAAAAGACCCTGCT 3 228 0 CGAGTCGAAA 0.978745 -73 TCCACTCGAACAAAAGTCGATAATGACTAAGG 3 272 0 CAAGTCGATA 0.96698 -29 TTCAATTCCACAAAGGTGGAAAAGAAGGGAAC 6 42 0 CAAGTGGAAA 0.966701 -259 CGGAAATTGCCGGACCTGGCTACGCTCAAACA 6 93 0 CGACTGGCTA 0.966738 -208 ** * ******* Masking position 4 Map Score: 4.47587 Number of sites scoring better than the average of aligned sites = 139 Number in coding regions = 126 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 6 CGTATAGGTTTACCTCAAACTGCGCGGCTGTG 1 74 1 TACCCAAACG 0.974652 -73 CCGCGGATCATAGCCTAAACTGCGCAAGAGAT 3 128 0 TAGCTAAACG 0.932258 -173 TCGGGCATATAACCGCAGACAGCGGTTCGTGC 3 186 1 AACCCAGACG 0.910821 -115 CTTGAGGGTGACGCACGAACCGCTGTCTGCGG 3 198 0 ACGCCGAACG 0.971686 -103 TTCGTGCGTCACCCTCAAGCAGGGTCTTTTCG 3 211 1 ACCCCAAGCG 0.982358 -90 CCGAAAAGCATCGCCAAAACGGCGATTTTTTG 4 84 1 TCGCAAAACG 0.952349 -67 GTTTGACCTTTCACTTAAGCAGATTATAGAAC 5 73 0 TCACTAAGCG 0.792716 -119 GGACCTGGCTACGCTCAAACAGACGAAAATTT 6 82 0 ACGCCAAACG 0.992313 -219 **** ***** * Masking position 4 Map Score: 3.74646 Number of sites scoring better than the average of aligned sites = 641 Number in coding regions = 604 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 7 CATTAAATTTTCCAATATGCGGC 3 4 1 TAAATTTTCC 0.780976 -297 AAAGGGCGAATAATTTCGCCCCATAACTTG 4 36 0 TAATTTCGCC 0.953012 -115 GATTATAGCAAAAAATCGCCGTTTTGGCGA 4 94 0 AAAAATCGCC 0.965423 -57 TTTTTTGCTATAATCTCGCCCAATTTTTAT 4 109 1 TAATCTCGCC 0.88118 -42 ATTAAAATGCGCCAGATAGATTA 5 4 1 AAAATGCGCC 0.936674 -188 AGAACAGAAAAAAATGCGCCAGTATTGTAT 5 48 0 AAAATGCGCC 0.936674 -144 GCATTTATTGTAAAATCTCCGACAATTTTT 5 131 1 TAAAATCTCC 0.911157 -61 TCAAACAGACGAAAATTTCCTACAAATTCA 6 70 0 GAAAATTTCC 0.75707 -231 TTTCCTTAACGGAAATTGCCGGACCTGGCT 6 104 0 GGAAATTGCC 0.807313 -197 TTTGATATCAGGATTTCGCCTGATGGCGCC 6 218 0 GGATTTCGCC 0.913274 -83 ********** Masking position 3 Map Score: 6.92313 Number of sites scoring better than the average of aligned sites = 2009 Number in coding regions = 1870 Number in noncoding regions = 139 Number of orfs with sites within 600 bp upstream = 144 Fraction of orfs with sites within 600 bp upstream = 0.0231288 Motif number 8 AAACGAGTATATCAGGCATTGGATGTGAAT 1 40 1 ATCAGGCATT 0.868883 -107 CGACCTTTGAATCCGGGATACAGTAGAGGG 1 116 1 ATCCGGGATA 0.911281 -31 ATTTTCCAATATGCGGCGTAAATCGTGCCC 3 17 1 ATGCGGCGTA 0.93973 -284 CTGTGGATAAATCGGGAAAATCTGTGAGAA 3 91 1 ATCGGGAAAA 0.866675 -210 CCGAGTCAAGATCCTGCAAAACGATCGGGA 3 160 0 ATCCTGCAAA 0.882293 -141 AGGATCTTGACTCGGGCATATAACCGCAGA 3 175 1 CTCGGGCATA 0.926197 -126 ATAACAAGTTATGGGGCGAAATTATTCGCC 4 32 1 ATGGGGCGAA 0.935983 -119 GCGTAGCCAGGTCCGGCAATTTCCGTTAAG 6 100 1 GTCCGGCAAT 0.86518 -201 GTAAGGCGCCATCAGGCGAAATCCTGATAT 6 214 1 ATCAGGCGAA 0.95517 -87 ********** Masking position 2 Map Score: 3.1771 Number of sites scoring better than the average of aligned sites = 2264 Number in coding regions = 1598 Number in noncoding regions = 666 Number of orfs with sites within 600 bp upstream = 242 Fraction of orfs with sites within 600 bp upstream = 0.0388693 Motif number 9 ACAGTAGAGGGATAGCGGTTAG 1 135 1 GATAGCGGTT 0.982033 -12 AAACGATCGGGACCGCGGATCATAGCCTAA 3 142 0 GACCGCGGAT 0.921503 -159 TATAACCGCAGACAGCGGTTCGTGCGTCAC 3 193 1 GACAGCGGTT 0.949393 -108 ********** Masking position 2 Map Score: 0.530129 Number of sites scoring better than the average of aligned sites = 24 Number in coding regions = 22 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 10 ********** No masking Map Score: 8.19556e-13 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: 8.19556e-13 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: 8.19556e-13 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