AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/alignace/lib/ORF_bsub.txt -z/skink1/amcguire/genomes/bsub.fna -iflhCD_bsub_opreg_300.orf -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 flgB 300 flagellar basal-body rod protein #2 fliF 45 flagellar basal-body M-ring protein #3 fliH 117 flagellar assembly protein #4 fliK 160 fliK #5 flgE 21 flagellar hook protein #6 fliL 251 flagellar protein #7 fliM 33 flagellar motor switch protein #8 cheY 25 two-component response regulator #9 flhA 32 flagella-associated protein #10 cheW 21 cheW #11 sigD 22 RNA polymerase sigma-28 factor (sigma-D) Motif number 1 GAATTTCTGTTTTTTCTCCTTTCTTTTCGGC 1 71 0 TTTTTCCCTT 0.985806 -230 TAGAACTACATTTCTCGCCCTGATATAAGCC 1 113 0 TTTCTCCCCT 0.99064 -188 CATTTCAGTTTTTTTCACCCTCAATATCCTT 1 267 0 TTTTTCCCCT 0.967598 -34 CGTATTGATCATTCTCACCTTTTGCAGGCTG 3 78 1 ATTCTCCCTT 0.971937 -40 AATTAGGAGTTCCCTTTCCTTGTTCTGAAAG 4 119 0 TCCCTTCCTT 0.884085 -42 GGAGAAGCGATTACTCGCCTCCCCTCCCTCC 6 11 0 TTACTCCCTC 0.95647 -241 CCAGAACAGCTTCTTCATCTTCTTTTACTAC 6 164 0 TTCTTCTCTT 0.833469 -88 TTTCCTCACCTCCGTATTCTGT 7 22 0 TTCCTCCCTC 0.988675 -12 AATCTATCTCTCTCCTTGTGTTTCG 8 9 0 TCTCTCCCTT 0.99064 -17 GCTGTTTTTTCTCTCCTTTTAAATCGAA 9 15 0 TTTCTCCCTT 0.995954 -18 ****** **** Masking position 5 Map Score: 16.3208 Number of sites scoring better than the average of aligned sites = 450 Number in coding regions = 347 Number in noncoding regions = 103 Number of orfs with sites within 600 bp upstream = 125 Fraction of orfs with sites within 600 bp upstream = 0.0200771 Motif number 2 GCAAAATTTATTAAAATTATTACATAGAAAGACT 1 4 0 TTTTTAGAAG 0.985139 -297 TTTAATAAATTTTGCATTTTTCTTCAAAAAGTTTCAAAAAT 1 30 1 TTTTTAAAAG 0.989951 -271 ATCTAGGACTTTATACCTAGTTGCAAAATAGATAATTGTGA 1 147 1 TTCTTAAAAG 0.985138 -154 AGTTTTCTTTTTTCCTTTTGTGGAGAAATAGATGATTCTTG 3 21 0 TTTTTAAAAG 0.989848 -97 GTTCAAACGGGTTACTTTAATCATAAAACAGCGGAGAAGCG 6 33 0 GTTTTAAAAG 0.968057 -219 CCGGAAAACATTCAATCTGTTCAATAAATAGCGCATTCAGT 6 88 0 TTCTTAAAAG 0.985138 -164 ATTGCAAATATTTGTATTTTTCGGTAGAAAGCTGCGATCTT 6 197 0 TTTTTAGAAG 0.985139 -55 ** ** * *** ** Masking position 16 Map Score: 6.46202 Number of sites scoring better than the average of aligned sites = 82 Number in coding regions = 56 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 3 CAGGCTGAAGAGAACCCGGAGCGCTT 3 102 1 AGAACCCGGA 0.993743 -16 AGGAACTTTCAGAACAAGGAAAGGGAACTC 4 114 1 AGAACAAGGA 0.959709 -47 GCTGATCTTCAGAATTAGGAGTTCCCTTTC 4 132 0 AGAATTAGGA 0.925997 -29 GAGTAATTGTAGTATCCGGAAAACATTCAA 6 114 0 AGTATCCGGA 0.978127 -138 CAAGGAATAGAGGAACCGGA 6 242 1 AGGAACCGGA 0.963278 -10 ATAATTTGACAGAATACGGAGGTGAGGAAA 7 14 1 AGAATACGGA 0.984917 -20 ********** Masking position 4 Map Score: 5.84016 Number of sites scoring better than the average of aligned sites = 166 Number in coding regions = 143 Number in noncoding regions = 23 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 4 TTAATAAATTTTGCATTTTTCTTCAAAAAG 1 31 1 TTGCATTTTT 0.957907 -270 AATAGCAGAATTTCTGTTTTTTCTCCTTTC 1 79 0 TTTCTGTTTT 0.922705 -222 ATTCTGCTATTTTCAGGCTTATATCAGGGC 1 98 1 TTTCAGGCTT 0.872535 -203 CTTACCTCCATTTCAGTTTTTTTCACCCTC 1 276 0 TTTCAGTTTT 0.957907 -25 GAAATAGATGATTCTTGTTTAATGATA 3 8 0 ATTCTTGTTT 0.746014 -110 TATAGAAAGTTTTCTTTTTTCCTTTTGTGG 3 39 0 TTTCTTTTTT 0.935369 -79 CCTGGCTACTTTTCATGTTTTTAGCGGCAG 4 47 0 TTTCATGTTT 0.972617 -114 ATTGAACAGATTGAATGTTTTCCGGATACT 6 104 1 TTGAATGTTT 0.7659 -148 TTGCAAATATTTGTATTTTTCGGTAGAAAG 6 207 0 TTGTATTTTT 0.717613 -45 ********** Masking position 2 Map Score: 5.73224 Number of sites scoring better than the average of aligned sites = 1242 Number in coding regions = 997 Number in noncoding regions = 245 Number of orfs with sites within 600 bp upstream = 255 Fraction of orfs with sites within 600 bp upstream = 0.0409573 Motif number 5 TCAAAAATGCCGAAAAGAAAGGAGAAAAAACA 1 63 1 CGAAGAAAGG 0.941133 -238 TCATCTATTTCTCCACAAAAGGAAAAAAGAAA 3 27 1 CTCCAAAAGG 0.988448 -91 AGAAAACTTTCTATACAAGAGGTGCGTATTGA 3 54 1 CTACAAGAGG 0.956134 -64 CGTCGTCGGTCTCGACGAAAGGTCCGGCTAAT 4 11 0 CTCCGAAAGG 0.990415 -150 CGAAACACAAGGAGAGAGATAG 8 1 1 CGACACAAGG 0.963413 -25 ATTTTTCGATTTAAAAGGAGAGAAAAAA 9 7 1 CGATAAAAGG 0.929482 -26 GTGAGACACCTCCTCGAATGG 10 1 0 CTCCGAATGG 0.953129 -21 *** ******* Masking position 11 Map Score: 3.71219 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 117 Number in noncoding regions = 14 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 6 GTTCTAACAATCTAGGACTTTATACCTAGTTGCAAAA 1 138 1 TCTCTTATCT 0.988549 -163 TACACGAACTTCATAGACTTTATGCCTGTTATTTCTT 1 199 1 TCACTTATCT 0.974064 -102 TGTCGAGAATTGTAAAACTATATGCTTATTGTAAGAA 1 231 0 TGTCTAATCT 0.955773 -70 TCAGTTTTTTTCACCCTCAATATCCTTGTCGAGAATT 1 257 0 TCACAAATCT 0.910333 -44 GACGACGGGTTCTGCCGCTAAAAACATGAAAAGTAGC 4 36 1 TCTCTAAACT 0.979961 -125 TTCTTCATCTTCTTTTACTACAAACTTCTTACCATTT 6 148 0 TCTCTAAACT 0.979961 -104 TCCGGTTCCTCTATTCCTTGATCCATTGCAAATATT 6 226 0 TCTCTTATCT 0.988549 -26 *** *** ** * * Masking position 12 Map Score: 4.60398 Number of sites scoring better than the average of aligned sites = 123 Number in coding regions = 104 Number in noncoding regions = 19 Number of orfs with sites within 600 bp upstream = 15 Fraction of orfs with sites within 600 bp upstream = 0.00240925 Motif number 7 AGAAATGTAGTTCTAACAATCTAGGACTTT 1 129 1 TTCTAACAAT 0.914527 -172 TAAAAAAATGTCCTCACAATTATCTATTTT 1 171 0 TCCTCACAAT 0.936831 -130 TGCCTGTTATTTCTTACAATAAGCATATAG 1 221 1 TTCTTACAAT 0.96433 -80 ATTCCACTCTTTCTCTAAATCGTCAGACCC 2 12 0 TTCTCTAAAT 0.795365 -34 GTATTGATCATTCTCACCTTTTGCAGGCTG 3 79 1 TTCTCACCTT 0.952462 -39 GTTCTGAAAGTTCCTTCAATCCAGCCTCAG 4 99 0 TTCCTTCAAT 0.817387 -62 TACTACAAACTTCTTACCATTTGACAGAGT 6 140 0 TTCTTACCAT 0.963635 -112 GCTGTTTTTTCTCTCCTTTTAAATCGAA 9 15 0 TTCTCTCCTT 0.925867 -18 ********** Masking position 1 Map Score: 5.71209 Number of sites scoring better than the average of aligned sites = 401 Number in coding regions = 307 Number in noncoding regions = 94 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 8 TCGCCCTGATATAAGCCTGAAAATAGCAGA 1 100 0 ATAAGCCTGA 0.920237 -201 CAGGCTGAAGAGAACCCGGAGCGCTT 3 102 1 AGAACCCGGA 0.896238 -16 ATTAGCCGGACCTTTCGTCG 4 1 1 ATTAGCCGGA 0.986583 -160 AAACATGAAAAGTAGCCAGGAGTTTTCAAA 4 57 1 AGTAGCCAGG 0.948361 -104 AGCCTCAGACATAAGCCAGTTTTGAAAACT 4 77 0 ATAAGCCAGT 0.887387 -84 GAGTAATTGTAGTATCCGGAAAACATTCAA 6 114 0 AGTATCCGGA 0.903373 -138 ACTTCTTACCATTTGACAGAGTAATTGTAG 6 132 0 ATTTGACAGA 0.836033 -120 AGCATAATTTGACAGAATACGGAGGT 7 7 1 ATTTGACAGA 0.836033 -27 ********** Masking position 1 Map Score: 2.55431 Number of sites scoring better than the average of aligned sites = 743 Number in coding regions = 679 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 9 TCTCTAAATCGTCAGACCCC 2 1 0 GTCAGACCCC 0.994977 -45 GTTAACCCCCGGTCATTCCA 2 36 0 GTTAACCCCC 0.972297 -10 TGTTTTTAGCGGCAGAACCCGTCGTCGGTC 4 32 0 GGCAGAACCC 0.943851 -129 GTGAGACACCTCCTCGAATG 10 12 0 GTGAGACACC 0.952811 -10 TGTTATCCCCCTAATACCTTA 11 12 0 GTTATCCCCC 0.971495 -11 ********** Masking position 4 Map Score: 0.532642 Number of sites scoring better than the average of aligned sites = 53 Number in coding regions = 40 Number in noncoding regions = 13 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 10 ********** No masking Map Score: 2.54618e-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: 2.54618e-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: 2.54618e-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