AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i197_bsub_mtub_300.orf -o197_bsub_mtub_300.ace -a/home/amcguire/genomes/ORF_bsub.txt -z/home/amcguire/genomes/bsub.fna -g0.55 -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 = 0.55 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 dnaA 300 alternate gene name: dnaH, dnaJ, dnaK #2 dnaN 188 DNA polymerase III (beta subunit) #3 yaaA 130 similar to hypothetical proteins #4 gyrB 140 DNA gyrase (subunit B) #5 gyrA 210 DNA gyrase (subunit A) #6 dnaN 300 dnaN #7 gyrB 125 gyrB #8 gyrA 34 gyrA Motif number 1 ATCCACACTTTGTGGATAAAGAGGAAAGGTA 1 82 0 TGTGGATAAG 0.938192 -219 ATCCACAAAGTGTGGATAAGTTGTGGATTGA 1 96 1 TGTGGATAAT 0.982803 -205 GTGGATAAGTTGTGGATTGATTTCACACAGC 1 107 1 TGTGGATTGT 0.945155 -194 TTTCACAACTTGTGGACAACCTTCTACACAA 1 138 0 TGTGGACAAC 0.986264 -163 CAACATTTAATGTGTACGAATGGTAAGCGCC 1 208 1 TGTGTACGAT 0.798863 -93 TCGGGGAAAGTGTGAATAACTTTTCGGAAGT 2 27 1 TGTGAATAAT 0.818279 -162 GTGGACAGACTGTGTATGACTTCCGAAAAGT 2 45 0 TGTGTATGAT 0.813667 -144 CCTATCCACATGTGGACAGACTGTGTATGAC 2 56 0 TGTGGACAGC 0.988672 -133 TCTGTCCACATGTGGATAGGCTGTGTTTCCT 2 67 1 TGTGGATAGC 0.989686 -122 CCTGTGGATTTGTGGATAAGTTGTGAAAAAG 2 100 0 TGTGGATAAT 0.982803 -89 AGCAATTTAATGTGTATAATCATAAGTTTAT 5 98 1 TGTGTATAAC 0.940189 -113 GTGTGCAGTTTGGGGACAGTCTG 6 3 0 TGGGGACAGC 0.975708 -298 AAGACAGCGCTGGGGATCGTTCGCTGGATAC 6 78 1 TGGGGATCGT 0.869549 -223 CCCGCTAGCGTGGGGACTGCCAACGACGAAT 6 236 0 TGGGGACTGC 0.908807 -65 ********* * Masking position 6 Map Score: 20.5085 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 236 Number in noncoding regions = 27 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 2 CTTCCGGCACGTCCCTCCTTTTCTTAGA 1 283 0 CCGCCGCCCC 0.988994 -18 TACACTGCTGCCGACCCGTCGGCAGCTTTTCTATT 3 16 1 CCGCCGCGAG 0.997301 -115 GACCTCTGACCCACCGCGACGAGCCAGTTATGCGG 6 112 0 CCACCGCGCC 0.989311 -189 GACGCGTGACCCGCCACGACGGCCGCAACAGCAGT 6 195 0 CCGCCGCGCG 0.998366 -106 TCGTCGTTGGCAGTCCCCACGCTAGCGGGGCGCTA 6 238 1 CAGCCCCGAG 0.907068 -63 ACGATGAGTTCGATCCCGTGGCTAGCGCCCCGCTA 6 260 0 CGACCGGGAG 0.917919 -41 CAAGGCGCTCCGGTCCCGGCCTGAGAGCCTCGAGG 7 30 1 CGGCCGCCAG 0.976914 -96 TCTTCCTGGTGCGTCCCGACGTCCGGCATACGGAT 7 74 0 GCGCCGCGCG 0.994462 -52 AGAAAGATGTCCGACGCACGGCGCGGTTAG 7 106 1 CCGCCAGGCG 0.973417 -20 CGCAACCCTGCGTTCGATTGCAAACG 8 2 1 GCACCTCGCG 0.890795 -33 *** * ** ** ** Masking position 7 Map Score: 13.7779 Number of sites scoring better than the average of aligned sites = 207 Number in coding regions = 198 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 3 ACAAAAAAAGAGCAAATGGCGCTTACCATTC 1 225 0 AGCAAAGGCG 0.98653 -76 TCCTTTTCTTAGAAAATGGCGTCTTTCTCTG 1 265 0 AGAAAAGGCG 0.973937 -36 CCATTTTCTAAGAAAAGGAGGGACGTGCCGG 1 277 1 AGAAAAGAGG 0.932433 -24 GGATAAGTTGTGAAAAAGACAGGAAACACAG 2 87 0 TGAAAAGACA 0.782855 -102 TCTTTCCAAGAACAAACGACGAAGAAATCTC 6 51 0 AACAAAGACG 0.89719 -250 CAACGACGAATGCCCATGACGCGTGACCCGC 6 216 0 TGCCCAGACG 0.945008 -85 GCGTGGGGACTGCCAACGACGAATGCCCATG 6 229 0 TGCCAAGACG 0.972454 -72 CGATCGGCCCAGAACAAGGCGCTCCGGTCCC 7 16 1 AGAACAGGCG 0.948098 -110 TGCGTTCGATTGCAAACGAGGAATAG 8 19 1 TGCAAAGAGG 0.956535 -16 ****** **** Masking position 6 Map Score: 7.86779 Number of sites scoring better than the average of aligned sites = 617 Number in coding regions = 578 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 40 Fraction of orfs with sites within 600 bp upstream = 0.00642467 Motif number 4 CTTAGAAAATGGCGTCTTTCTCTGTTATAG 1 259 0 GGCGTCTTTC 0.981952 -42 ATGTGGATAGGCTGTGTTTCCTGTCTTTTT 2 76 1 GCTGTGTTTC 0.936878 -113 TATATCGACCTCTTTCAAATATCACT 3 115 0 GACCTCTTTC 0.960221 -16 TCATAAAAAGCCTTATTTCCAATAAGAAA 5 10 1 GCCTTATTTC 0.96635 -201 TCAGAAAAAAGCCTTATTTCTTATTGGAAA 5 26 0 GCCTTATTTC 0.96635 -185 GATCCCCAGCGCTGTCTTTCCAAGAACAAA 6 66 0 GCTGTCTTTC 0.981224 -235 CCGTGCGTCGGACATCTTTCTTCCTGGTGC 7 97 0 GACATCTTTC 0.941832 -29 ********** Masking position 5 Map Score: 4.99086 Number of sites scoring better than the average of aligned sites = 366 Number in coding regions = 337 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 5 ACCATTCGTACACATTAAATGTTGAAAACA 1 202 0 CACATTAAAT 0.985312 -99 TATCTTCCAGCACATTAAAAAAACGTGCGC 4 41 1 CACATTAAAA 0.963702 -100 TATGATTATACACATTAAATTGCTAGAATA 5 92 0 CACATTAAAT 0.985312 -119 CCTGAAGTATCACATGAAATATGTGGGAGT 5 180 0 CACATGAAAT 0.975217 -31 ********** Masking position 5 Map Score: 3.86803 Number of sites scoring better than the average of aligned sites = 12 Number in coding regions = 7 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 6 GTCCCTCCTTTTCTTAGAAAATGGCGTCTT 1 271 0 TTCTTAGAAA 0.979031 -30 TTGAAATAGATTCTTAGAAATTTTTTATCA 4 80 1 TTCTTAGAAA 0.979031 -61 GCCTTATTTCTTATTGGAAATAAGGCTTTT 5 16 0 TTATTGGAAA 0.949398 -195 TCGTCGTTTGTTCTTGGAAAGACAGCGCTG 6 60 1 TTCTTGGAAA 0.986727 -241 ********** Masking position 5 Map Score: 3.24166 Number of sites scoring better than the average of aligned sites = 52 Number in coding regions = 43 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 7 CAGGACCGGGGATCAATCGGGGAAA 2 4 1 GACCGGATCA 0.934572 -185 GTTCATCATTGACCTCTGACCCACCGCGACGA 6 125 0 GACCCGACCC 0.984286 -176 GAATGCCCATGACGCGTGACCCGCCACGACGG 6 208 0 GACGGGACCC 0.990673 -93 GACTGCCAACGACGAATGCCCATGACGCGTGA 6 221 0 GACGAGCCCA 0.879202 -80 TCGATCCCGTGGCTAGCGCCCCGCTAGCGTGG 6 254 0 GGCTGGCCCC 0.945037 -47 CTCAGGCCGGGACCGGAGCGCCTTGTTCTGGG 7 23 0 GACCGGCGCC 0.994143 -103 CTCCGGTCCCGGCCTGAGAGCCTCGAGGACGA 7 37 1 GGCCGGAGCC 0.988437 -89 **** * ***** Masking position 8 Map Score: 3.6628 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 75 Number in noncoding regions = 7 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 8 AACTTATCCACACTTTGTGGATAAAGAGGA 1 88 0 CACTTTGTGG 0.914192 -213 AAAGTGTGGATAAGTTGTGGATTGATTTCA 1 102 1 TAAGTTGTGG 0.892449 -199 ACAAATTTCACAACTTGTGGACAACCTTCT 1 144 0 CAACTTGTGG 0.976286 -157 ACAAGTTGTGAAATTTGTCGAAAAGCTATT 1 156 1 AAATTTGTCG 0.92271 -145 CACAGTCTGTCCACATGTGGATAGGCTGTG 2 62 1 CCACATGTGG 0.490174 -127 GGGAAAGGGAAAACTTGTCGGAGCAGATAC 3 53 0 AAACTTGTCG 0.949394 -78 GTATCACATGAAATATGTGGGAGTAGATTG 5 174 0 AAATATGTGG 0.876598 -37 GATGAACTTTCAAGTTGACGTGAGAAGCTC 6 150 1 CAAGTTGACG 0.826688 -151 ********** Masking position 6 Map Score: 2.54023 Number of sites scoring better than the average of aligned sites = 143 Number in coding regions = 125 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 9 CCATTGCAAGCTCTCGTTTATTTTGGTATTA 1 20 1 CTCTCGTTAT 0.974976 -281 AATGGCGTCTTTCTCTGTTATAGAACACAAA 1 251 0 TTCTCTTTAT 0.960554 -50 ATATATATTACTCTCCCTTATCTTCCAGCAC 4 23 1 CTCTCCTTAT 0.990516 -118 GATTTCACTATTCTCCATTATATCAATAAAC 5 123 0 TTCTCCTTAT 0.98977 -88 TGGGAGTAGATTGTCCATTATGACCTTCAAT 5 156 0 TTGTCCTTAT 0.964885 -55 ****** **** Masking position 4 Map Score: 2.1266 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 32 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 10 GTTGTCCACAAGTTGTGAAATTTGTCGAAA 1 149 1 AGTTGTGAAA 0.957808 -152 TTTGTGGATAAGTTGTGAAAAAGACAGGAA 2 93 0 AGTTGTGAAA 0.957808 -96 AAAAAAACGAATTAGGGAAAGGGAAAACTT 3 67 0 ATTAGGGAAA 0.916789 -64 ACAATTAGATATTAGTGATATTTGAAAGAG 3 102 1 ATTAGTGATA 0.94169 -29 TAAACGATATATTCGTGATAAAAAATTTCT 4 95 0 ATTCGTGATA 0.904492 -46 TATAATGGAGAATAGTGAAATCGTATTGAA 5 132 1 AATAGTGAAA 0.922633 -79 ********** Masking position 3 Map Score: 1.86099 Number of sites scoring better than the average of aligned sites = 119 Number in coding regions = 94 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 11 TCCGATACACTGCTGCCGACCCGTCGGCAG 3 10 1 CTGTGCCGAC 0.993544 -121 CCGAATAGAAAAGCTGCCGACGGGTCGGCAG 3 23 0 AAGTGCCGAC 0.938768 -108 CTTGTCGGAGCAGATACCGAATAGAAAAGCT 3 39 0 CAGTACCGAA 0.860698 -92 TGAACAAGATCAGATGCAGCGATGCCTGCAA 5 53 1 CAGTGCAGCG 0.934622 -158 CCCTCTAATACTGTTACCGAGATTTCTTCGT 6 33 1 CTGTACCGAG 0.956416 -268 TGTTCGACTGCTGTTGCGGCCGTCGTGGCGG 6 189 1 CTGTGCGGCC 0.989811 -112 ATCTTTCTTCCTGGTGCGTCCCGACGTCCGG 7 83 0 CTGTGCGTCC 0.926472 -43 *** ******* Masking position 5 Map Score: 1.35625 Number of sites scoring better than the average of aligned sites = 783 Number in coding regions = 749 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 12 TATAATACCAAAATAAACGAGAGCTTGCAA 1 23 0 AAATAAACGA 0.76692 -278 ATTGTACTAAAAAAAAACGAATTAGGGAAA 3 77 0 AAAAAAACGA 0.930252 -54 CCAGCACATTAAAAAAACGTGCGCAATTTA 4 47 1 AAAAAAACGT 0.961367 -94 TCATAAAAAGCCTTATTTCCAAT 5 4 1 TAAAAAGCCT 0.917062 -207 TCTTGTTCAGAAAAAAGCCTTATTTCTTAT 5 32 0 AAAAAAGCCT 0.953769 -179 TAAAAAACCTCCCTGAAGTA 5 201 0 TAAAAAACCT 0.930252 -10 ********** Masking position 5 Map Score: 1.65493 Number of sites scoring better than the average of aligned sites = 354 Number in coding regions = 235 Number in noncoding regions = 119 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 13 TACTAATCCTACCTTTCCTCTTTATCCACA 1 73 1 ACCTTTCCTC 0.915608 -228 AAGTTATTCACACTTTCCCCGATTGATCCC 2 19 0 CACTTTCCCC 0.990083 -170 GACAAGTTTTCCCTTTCCCTAATTCGTTTT 3 64 1 CCCTTTCCCT 0.977327 -67 CAGACTGTCCCCAAACTGCACA 6 3 1 GACTGTCCCC 0.94375 -298 TGCGCCCTTTCACCTCACGATGAG 6 287 0 CCCTTTCACC 0.977327 -14 ********** Masking position 6 Map Score: 1.14207 Number of sites scoring better than the average of aligned sites = 124 Number in coding regions = 99 Number in noncoding regions = 25 Number of orfs with sites within 600 bp upstream = 30 Fraction of orfs with sites within 600 bp upstream = 0.0048185 Motif number 14 ********** No masking Map Score: 2.79487e-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 15 ********** No masking Map Score: 2.79487e-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