AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i197_replication1_bsub_reg_300.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 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) Motif number 1 ACCTTTCCTCTTTATCCACAAAGTGTGGAT 1 83 1 TTTATCCACA 0.981485 -218 CAATCCACAACTTATCCACACTTTGTGGAT 1 96 0 CTTATCCACA 0.992014 -205 CTGTGTGAAATCAATCCACAACTTATCCAC 1 107 0 TCAATCCACA 0.7046 -194 TGTGGACAACCTTCTACACAAGCTGTGTGA 1 129 0 CTTCTACACA 0.89296 -172 TGTGTAGAAGGTTGTCCACAAGTTGTGAAA 1 139 1 GTTGTCCACA 0.981365 -162 AGATAAATAGCTTTTCGACAAATTTCACAA 1 161 0 CTTTTCGACA 0.816986 -140 TATATTATATGTTTTCAACATTTAATGTGT 1 193 1 GTTTTCAACA 0.67092 -108 GCGCTTACCATTCGTACACATTAAATGTTG 1 208 0 TTCGTACACA 0.734723 -93 CTTCCGAAAAGTTATTCACACTTTCCCCGA 2 27 0 GTTATTCACA 0.928337 -162 CTTTTCGGAAGTCATACACAGTCTGTCCAC 2 46 1 GTCATACACA 0.875245 -143 TCATACACAGTCTGTCCACATGTGGATAGG 2 57 1 TCTGTCCACA 0.933447 -132 GGAAACACAGCCTATCCACATGTGGACAGA 2 67 0 CCTATCCACA 0.981316 -122 TGTTTCCTGTCTTTTTCACAACTTATCCAC 2 90 1 CTTTTTCACA 0.884029 -99 TTTTTCACAACTTATCCACAAATCCACAGG 2 101 1 CTTATCCACA 0.992014 -88 TAAACTTATGATTATACACATTAAATTGCT 5 98 0 ATTATACACA 0.822428 -113 ********** Masking position 8 Map Score: 21.2791 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 386 Number in noncoding regions = 87 Number of orfs with sites within 600 bp upstream = 71 Fraction of orfs with sites within 600 bp upstream = 0.0114038 Motif number 2 CCAAAATAAACGAGAGCTTGCAATGGTTGT 1 16 0 CGAGAGCTTG 0.846084 -285 TGGATAAAGAGGAAAGGTAGGATTAGTAAT 1 71 0 GGAAAGGTAG 0.926792 -230 CACAAAGTGTGGATAAGTTGTGGATTGATT 1 99 1 GGATAAGTTG 0.98379 -202 TGAAATTTGTCGAAAAGCTATTTATCTACT 1 164 1 CGAAAAGCTA 0.906714 -137 GTATGACTTCCGAAAAGTTATTCACACTTT 2 33 0 CGAAAAGTTA 0.921776 -156 GTCCACATGTGGATAGGCTGTGTTTCCTGT 2 70 1 GGATAGGCTG 0.976354 -119 GTGGATTTGTGGATAAGTTGTGAAAAAGAC 2 98 0 GGATAAGTTG 0.98379 -91 GATACCGAATAGAAAAGCTGCCGACGGGTC 3 28 0 AGAAAAGCTG 0.925505 -103 TTAGGGAAAGGGAAAACTTGTCGGAGCAGA 3 56 0 GGAAAACTTG 0.967379 -75 ********** Masking position 5 Map Score: 8.28818 Number of sites scoring better than the average of aligned sites = 712 Number in coding regions = 644 Number in noncoding regions = 68 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 3 ACTTATCCACACTTTGTGGATAAAGAGGAAAGGTAGGA 1 79 0 ACTTAAAGAG 0.81257 -222 TGTTTTCAACATTTAATGTGTACGAATGGTAAGCGCCA 1 202 1 ATTTGACAAG 0.812532 -99 TGCTCTTTTTTTGTGTTCTATAACAGAGAAAGACGCCA 1 242 1 TTTTAAAAGG 0.970702 -59 ACGTCCCTCCTTTTCTTAGAAAATGGCGTCTTTCTCTG 1 265 0 TTTTAAAGGG 0.938962 -36 TAATATCTAATTGTACTAAAAAAAAACGAATTAGGGAA 3 78 0 TTTTAAAAAG 0.970608 -53 CGTTTTTTTAATGTGCTGGAAGATAAGGGAGAGTAATA 4 28 0 ATTTAGAAAG 0.909769 -113 TATCACGAATATATCGTTTAGAAAAGTGTAGGTGAATG 4 105 1 ATTTAAAAGG 0.981251 -36 AAAGCCTTATTTCTTATTGGAAATAAGGCTTTTTATGA 5 11 0 TTTTGAAAAG 0.934196 -200 GCTGCATCTGATCTTGTTCAGAAAAAAGCCTTATTTCT 5 35 0 ATTTAAAAAG 0.975556 -176 AAGTTTATTGATATAATGGAGAATAGTGAAATCGTATT 5 121 1 ATTTAAAAGG 0.981266 -90 ** * * * ** ** * Masking position 7 Map Score: 6.5309 Number of sites scoring better than the average of aligned sites = 277 Number in coding regions = 189 Number in noncoding regions = 88 Number of orfs with sites within 600 bp upstream = 96 Fraction of orfs with sites within 600 bp upstream = 0.0154192 Motif number 4 TTGCAAGCTCTCGTTTATTTTGGTATTATA 1 23 1 TCGTTTATTT 0.846037 -278 TTTCCCTAATTCGTTTTTTTTTAGTACAAT 3 77 1 TCGTTTTTTT 0.957033 -54 TAAATTGCGCACGTTTTTTTAATGTGCTGG 4 47 0 ACGTTTTTTT 0.976503 -94 ATTGGAAATAAGGCTTTTTATGA 5 4 0 AGGCTTTTTA 0.948628 -207 ATAAGAAATAAGGCTTTTTTCTGAACAAGA 5 32 1 AGGCTTTTTT 0.971794 -179 TACTTCAGGGAGGTTTTTTA 5 201 1 AGGTTTTTTA 0.957033 -10 ********** Masking position 5 Map Score: 3.97667 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 5 ACACAAATATAATACCAAAATAAACGAGAGC 1 29 0 AATACAAAAT 0.9237 -272 CAAGAGTTAAAACACAAATATAATACCAAAA 1 40 0 AACACAATAT 0.9829 -261 TCTGTTATAGAACACAAAAAAAGAGCAAATG 1 238 0 AACACAAAAA 0.838479 -63 ATTTTTTATAAATATATATATTAATACATTA 2 150 1 AATATTATAT 0.610948 -39 TCTTTCAAATATCACTAATATCTAATTGTAC 3 100 0 ATCACAATAT 0.961544 -31 GAAATTTTTTATCACGAATATATCGTTTAGA 4 96 1 ATCACAATAT 0.961544 -45 CGATGCCTGCAATACCTATATATTCTAGCAA 5 72 1 AATACTATAT 0.923703 -139 ***** ***** Masking position 4 Map Score: 2.14855 Number of sites scoring better than the average of aligned sites = 220 Number in coding regions = 179 Number in noncoding regions = 41 Number of orfs with sites within 600 bp upstream = 34 Fraction of orfs with sites within 600 bp upstream = 0.00546097 Motif number 6 TTGAAAACATATAATATAGTAGATAAATAGCT 1 179 0 ATAAATAGAG 0.904845 -122 ATAGAACACAAAAAAAGAGCAAATGGCGCTTA 1 231 0 AAAAAGAGAA 0.970932 -70 TTTGTGTTCTATAACAGAGAAAGACGCCATTT 1 251 1 ATAAAGAGAA 0.958866 -50 TAAGTTGTGAAAAAGACAGGAAACACAGCCTA 2 83 0 AAAAACAGAA 0.904638 -106 ATATATTTATAAAAAATAGTAGAAGTAATAGT 2 135 0 AAAAATAGAG 0.931644 -54 TATATCGTTTAGAAAAGTGTAGGTGAATGACG 4 114 1 AGAAAGTGAG 0.949855 -27 GATATAATGGAGAATAGTGAAATCGTATTGAA 5 130 1 AGAAAGTGAA 0.940069 -81 **** **** ** Masking position 6 Map Score: 2.10669 Number of sites scoring better than the average of aligned sites = 263 Number in coding regions = 191 Number in noncoding regions = 72 Number of orfs with sites within 600 bp upstream = 81 Fraction of orfs with sites within 600 bp upstream = 0.01301 Motif number 7 CTATAACAGAGAAAGACGCCATTTTCTAAG 1 259 1 GAAAGACGCC 0.976921 -42 AAAAAGACAGGAAACACAGCCTATCCACAT 2 76 0 GAAACACAGC 0.921968 -113 AGTGATATTTGAAAGAGGTCGATATA 3 115 1 GAAAGAGGTC 0.939451 -16 TTTCTTATTGGAAATAAGGCTTTTTATGA 5 10 0 GAAATAAGGC 0.979336 -201 TTTCCAATAAGAAATAAGGCTTTTTTCTGA 5 26 1 GAAATAAGGC 0.979336 -185 ********** Masking position 6 Map Score: 0.789813 Number of sites scoring better than the average of aligned sites = 222 Number in coding regions = 203 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 8 GTGGATAAAGAGGAAAGGTAGGATTAGTAAT 1 71 0 AGGAAAGGTG 0.927414 -230 ACAAAAAAAGAGCAAATGGCGCTTACCATTC 1 225 0 AGCAAATGGG 0.976954 -76 TCCTTTTCTTAGAAAATGGCGTCTTTCTCTG 1 265 0 AGAAAATGGG 0.989487 -36 CCATTTTCTAAGAAAAGGAGGGACGTGCCGG 1 277 1 AGAAAAGGAG 0.965943 -24 ATGTGCTGGAAGATAAGGGAGAGTAATATAT 4 25 0 AGATAAGGGG 0.987551 -116 AAGTTTATTGATATAATGGAGAATAGTGAAA 5 121 1 ATATAATGGG 0.886424 -90 ********* * Masking position 6 Map Score: 2.94298 Number of sites scoring better than the average of aligned sites = 271 Number in coding regions = 214 Number in noncoding regions = 57 Number of orfs with sites within 600 bp upstream = 67 Fraction of orfs with sites within 600 bp upstream = 0.0107613 Motif number 9 TTTATAAATATATATATTAATACATTATCC 2 154 1 TATATATTAA 0.847208 -35 TTAGTACAATTAGATATTAGTGATATTTGA 3 97 1 TAGATATTAG 0.872133 -34 GGGAGAGTAATATATATTCTGAACCGTGA 4 10 0 TATATATTCT 0.956616 -131 TTTTCTAAACGATATATTCGTGATAAAAAA 4 100 0 GATATATTCG 0.938907 -41 CTGCAATACCTATATATTCTAGCAATTTAA 5 78 1 TATATATTCT 0.956616 -133 ********** Masking position 5 Map Score: 0.00338527 Number of sites scoring better than the average of aligned sites = 64 Number in coding regions = 44 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 25 Fraction of orfs with sites within 600 bp upstream = 0.00401542 Motif number 10 ********** No masking Map Score: 2.34722e-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: 2.34722e-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: 2.34722e-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