AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i197_replication1_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 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 HI0568 95 transcription accessory protein (tex) #6 HI0993 191 chromosomal replication initiator protein (dnaA) #7 HI0994 27 transferrin-binding protein 1 precursor (tbp1) #8 HI0995 97 transferrin-binding protein 2 precursor (tbp2) #9 HI1264 300 DNA gyrase, subunit A (gyrA) Motif number 1 CCCAAGTATAAATGAGCGAGAAACGTTG 2 8 1 ATAATGGAGA 0.95466 -21 TAAATCGGGAAAATCTGTGAGAAACAGAAGATCT 3 98 1 AAATTGGAAA 0.891757 -203 GATCATAGCCTAAACTGCGCAAGAGATCTTCTGT 3 121 0 TAAATGGAGA 0.951419 -180 TGCACTAAAAAATTGGAAAAAATAACAAGTT 4 8 1 AAAATTGAAA 0.854248 -143 AAACGATAAAAAAAGGGCGAATAATTTCGCCCCA 4 43 0 AAAAGGGTAA 0.867275 -108 TTTGTAAATAAAAATTGGGCGAGATTATAGCAAA 4 112 0 AAAATGGAGA 0.991825 -39 TTATTTACAAAAGAATGAGATAAATT 4 135 1 AAGATGGAAA 0.924302 -16 TTATTATAAAAAAACGAAGATAGAATACTGGTTT 5 60 0 AAAAGAGAGA 0.835859 -36 ATTAAAATGCGCCAGATAGATTAAAT 6 3 1 TAAATGGAGA 0.951419 -189 TAGAACAGAAAAAAATGCGCCAGTATTGTATAGA 6 45 0 AAAATGGAGT 0.951419 -147 AGATTTTACAATAAATGCGTGAAAAGATCTTCTA 6 115 0 ATAATGGAAA 0.943536 -77 TGTAATAGAGAAAAGTGCGGTAAAAATTGTCGGA 6 148 0 AAAATGGAAA 0.989721 -44 ATTCAATTCCACAAAGGTGGAAAAGAAGGGAACC 9 41 0 ACAAGGGAAA 0.845969 -260 TCGCCAAAGAAAAAGTAAGTAAAAAGAAAGGCGA 9 168 0 AAAATAGAAA 0.911777 -133 ATTATAGCATAAAATTGTGGATATGTGGTTTTTG 9 244 0 AAAATGGTAT 0.729545 -57 TTTTTGATCAAAAATTGTGGCGGATTATAGCATA 9 267 0 AAAATGGGGA 0.946517 -34 **** ** * *** Masking position 9 Map Score: 19.8704 Number of sites scoring better than the average of aligned sites = 619 Number in coding regions = 458 Number in noncoding regions = 161 Number of orfs with sites within 600 bp upstream = 181 Fraction of orfs with sites within 600 bp upstream = 0.0290716 Motif number 2 ATTGGGCGAGATTATAGCAAAAAATCGCCGTTTTGGC 4 96 0 ATTTAAAATG 0.954204 -55 ATCTCGCCCAATTTTTATTTACAAAAGAATGAGATAA 4 121 1 ATTTTAAAAG 0.977011 -30 GTCGTACTTCTTTATTATAAAAAAACGAAGATAGAAT 5 68 0 TTTTTAAAAG 0.938021 -28 ACTTAAGCAGATTATAGAACAGAAAAAAATGCGCCAG 6 56 0 ATTTAAAAAA 0.890612 -136 CCTTATTGTTTTTGTAATAGAGAAAAGTGCGGTAAAA 6 157 0 TTTTAAAAAG 0.954197 -35 ATAAGTTGACATTATTACAAAAAAAAAATGATAATGC 8 36 1 ATTTTAAAAA 0.855229 -62 AGAATTATATTCTTATACAAAATTGATAATTGTTC 8 73 0 ATTTTAAATG 0.938024 -25 CGCACTTTAAATCGGATAAAGGACAAATTGGG 9 6 1 TTTAAAAAAG 0.881059 -295 TTTCCTACAAATTCAATTCCACAAAGGTGGAAAAGAA 9 48 0 ATTAAAAAAG 0.954204 -253 CGTTAAGGAAATTCAATGGAACAAAGGAAACAAGGAA 9 123 1 ATTAAAAAAG 0.954204 -178 ATTGTGGCGGATTATAGCATAAAATTGTGGATATGTG 9 251 0 ATTTAAAATG 0.954204 -50 ATCCGCCACAATTTTTGATCAAAAAAGGAATACCA 9 276 1 ATTTTAAAAG 0.976399 -25 *** ** * *** * Masking position 11 Map Score: 14.2828 Number of sites scoring better than the average of aligned sites = 89 Number in coding regions = 56 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 36 Fraction of orfs with sites within 600 bp upstream = 0.0057822 Motif number 3 GTTATTTTTTCCAATTTTTTAGTGCA 4 7 0 CCAATTTTTT 0.79555 -144 AAATTATTCGCCCTTTTTTTATCGTTTTCC 4 50 1 CCCTTTTTTT 0.967968 -101 TATAATCTCGCCCAATTTTTATTTACAAAA 4 117 1 CCCAATTTTT 0.74075 -34 AATTTATCTCATTCTTTTGTAAATAAAA 4 133 0 TCATTCTTTT 0.90904 -18 AATTCAAAAAACTTTCTTTTATTTTTATT 5 10 0 ACTTTCTTTT 0.874601 -86 TATTCTATCTTCGTTTTTTTATAATAAAGA 5 67 1 TCGTTTTTTT 0.707738 -29 CAATACTGGCGCATTTTTTTCTGTTCTATA 6 51 1 GCATTTTTTT 0.759221 -141 GTTCGCATTATCATTTTTTTTTTGTAATAA 8 47 0 TCATTTTTTT 0.843151 -51 AAATTGGGTTCCCTTCTTTTCCACCTTTGT 9 35 1 CCCTTCTTTT 0.982511 -266 AGAAAGGCGACCCTACTTTTCCTTGTTTCC 9 148 0 CCCTACTTTT 0.962974 -153 AGTAGGGTCGCCTTTCTTTTTACTTACTTT 9 161 1 CCTTTCTTTT 0.972542 -140 CTTTCTTTTTACTTACTTTTTCTTTGGCGA 9 172 1 ACTTACTTTT 0.763527 -129 CCTGATGGCGCCTTACTTTTTCTTTGCTTC 9 200 0 CCTTACTTTT 0.942519 -101 ********** Masking position 7 Map Score: 15.44 Number of sites scoring better than the average of aligned sites = 324 Number in coding regions = 222 Number in noncoding regions = 102 Number of orfs with sites within 600 bp upstream = 115 Fraction of orfs with sites within 600 bp upstream = 0.0184709 Motif number 4 ATCCAATGCCTGATATACTCGTTTGTCTTG 1 34 0 TGATATACTC 0.883595 -113 GCGCAGTTTAGGCTATGATCCGCGGTCCCG 3 135 1 GGCTATGATC 0.975997 -166 GGCGATTTTTTGCTATAATCTCGCCCAATT 4 104 1 TGCTATAATC 0.983379 -47 TTTTTTTCTGTTCTATAATCTGCTTAAGTG 6 64 1 TTCTATAATC 0.901535 -128 TGCCGGACCTGGCTACGCTCAAACAGACGA 9 88 0 GGCTACGCTC 0.92499 -213 CACAATTTTATGCTATAATCCGCCACAATT 9 259 1 TGCTATAATC 0.983379 -42 ********** Masking position 5 Map Score: 3.4523 Number of sites scoring better than the average of aligned sites = 31 Number in coding regions = 20 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 5 CGCTAAGTGTAAACGATCCTGCCGCGAGGC 3 47 0 AAACGATCCT 0.978446 -254 TAAACTGCGCAAGAGATCTTCTGTTTCTCA 3 115 0 AAGAGATCTT 0.906002 -186 ACGTACGTCGAAAAGACCCTGCTTGAGGGT 3 221 0 AAAAGACCCT 0.97202 -80 TAAATGCGTGAAAAGATCTTCTAAAAAATC 6 108 0 AAAAGATCTT 0.933783 -84 AAAAGGATCCTTATTGTTTTT 6 181 0 AAAGGATCCT 0.960906 -11 GTAAAAAGAAAGGCGACCCTACTTTTCCTT 9 154 0 AGGCGACCCT 0.918714 -147 ********** Masking position 6 Map Score: 2.73941 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 6 AACTTGTTATTTTTTCCAATTTTTTAGTGC 4 12 0 TTTTTCCAAT 0.737521 -139 TTTTTTTATCGTTTTCCTTTCCCGAAAAGC 4 63 1 GTTTTCCTTT 0.974073 -88 AAAATCCAAGTTTGACCTTTCACTTAAGCA 6 84 0 TTTGACCTTT 0.812955 -108 TTTTAGTATTCCATTATTTGGTTGT 7 13 0 GTATTCCATT 0.876697 -15 GGGAACCCAATTTGTCCTTTATCCGATTTA 9 18 0 TTTGTCCTTT 0.954411 -283 TACTTTTCCTTGTTTCCTTTGTTCCATTGA 9 135 0 TGTTTCCTTT 0.905419 -166 TGGTATTCCTTTTTTGATCAAA 9 289 0 GTATTCCTTT 0.942343 -12 ********** Masking position 10 Map Score: 2.22853 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 121 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 39 Fraction of orfs with sites within 600 bp upstream = 0.00626405 Motif number 7 GTATAGGTTTACCTCAAACTGCGCGGCTGTG 1 75 1 ACCTCAAACG 0.926467 -72 CGCGGATCATAGCCTAAACTGCGCAAGAGAT 3 128 0 AGCCTAAACG 0.821823 -173 TTGAGGGTGACGCACGAACCGCTGTCTGCGG 3 198 0 CGCACGAACG 0.938978 -103 TCGTGCGTCACCCTCAAGCAGGGTCTTTTCG 3 212 1 CCCTCAAGCG 0.969017 -89 GGCGGACTCCACTCGAACAAAAGTCGATAA 3 281 0 CACTCGAACA 0.799257 -20 CGAAAAGCATCGCCAAAACGGCGATTTTTTG 4 85 1 CGCCAAAACG 0.959051 -66 TGAGCCATCCCGCTAAAACCAGTATTCTATC 5 45 1 CGCTAAAACA 0.890654 -51 TTTGACCTTTCACTTAAGCAGATTATAGAAC 6 73 0 CACTTAAGCG 0.846513 -119 GACCTGGCTACGCTCAAACAGACGAAAATTT 9 82 0 CGCTCAAACG 0.993448 -219 ********* * Masking position 7 Map Score: 3.58844 Number of sites scoring better than the average of aligned sites = 1194 Number in coding regions = 1123 Number in noncoding regions = 71 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 8 ATTCACATCCAATGCCTGATATACTCGTTT 1 40 0 AATGCCTGAT 0.842527 -107 CCCTCTACTGTATCCCGGATTCAAAGGTCG 1 116 0 TATCCCGGAT 0.892392 -31 GGGCACGATTTACGCCGCATATTGGAAAAT 3 17 0 TACGCCGCAT 0.926409 -284 TTCTCACAGATTTTCCCGATTTATCCACAG 3 91 0 TTTTCCCGAT 0.839957 -210 TCCCGATCGTTTTGCAGGATCTTGACTCGG 3 160 1 TTTGCAGGAT 0.858193 -141 TCTGCGGTTATATGCCCGAGTCAAGATCCT 3 175 0 TATGCCCGAG 0.910171 -126 GGCGAATAATTTCGCCCCATAACTTGTTAT 4 32 0 TTCGCCCCAT 0.92191 -119 CTTAACGGAAATTGCCGGACCTGGCTACGC 9 100 0 ATTGCCGGAC 0.83822 -201 ATATCAGGATTTCGCCTGATGGCGCCTTAC 9 214 0 TTCGCCTGAT 0.945066 -87 ********** Masking position 9 Map Score: 1.66835 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 ********** No masking Map Score: -3.48633e-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 10 ********** No masking Map Score: -3.48633e-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: -3.48633e-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