AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i131_bsub_mtub_100.orf -o131_bsub_mtub_100.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 yfiL 143 similar to ABC transporter (ATP-binding protein) #2 yvfT 132 similar to two-component sensor histidine kinase [YvfU] #3 yvfR 283 similar to ABC transporter (ATP-binding protein) #4 Rv1458c 102 hypothetical protein Rv1458c #5 Rv1686c 71 hypothetical protein Rv1686c #6 Rv1687c 58 hypothetical protein Rv1687c Motif number 1 ATGCCCTATGTTCTATCTGCCGCTACATGCCGCACG 1 68 1 TCTATCCGAC 0.705894 -76 GCCGCTACATGCCGCACGCCTTTCTTTCTTCTACAA 1 86 1 GCGCACCTTT 0.960848 -58 GTCGTCTCACTCCTTTTTTTGATCCATTG 1 125 0 GCTCACCTTT 0.930678 -19 TTAATAAAGAGAGGAACGGCATAATCGTATACACCA 2 72 0 GGGAACCTTC 0.929536 -61 ACCATATCCGATCCCCTGTTTGACCCCTGATT 2 111 0 TCGATCCGTG 0.823902 -22 CATCCATCTTTTCTATCTCCCATGTCCTCTTTCTTT 3 115 0 TCTATCCATC 0.833998 -169 TGTCATTTTTTTCTCACCCCGGTGTCTAGGCAATCC 3 171 0 TCTCACCGTC 0.989398 -113 AAAATGACATTTGTCACTCCATCATCATGACACCCC 3 198 1 TGTCACCTTC 0.964966 -86 TGACACCCCATACTAACATCGTCTTCTCCGTCATTT 3 225 1 TCTAACCTTC 0.978236 -59 ATGAGCACCTCCTGATCGTTTACATTG 3 267 0 TAGCACCTTC 0.970194 -17 TCCTCATCGCTTCGCTCTGCATCGTCGTCGGCGCGG 4 12 0 TCGCTCCTTC 0.995592 -91 GTTCACGAGCGCCGCTCCTCCTCATCGCTTCGCTCT 4 30 0 GCGCTCCTTC 0.994649 -73 TCCTCATCGCTTCGCTCTGCATCGTCGTCGGCGCGG 4 65 0 TCGCTCCTTC 0.995592 -38 GAGCGCCGCTCCTCCTCATCGCTTCGCTCT 4 83 0 GCGCTCCTTC 0.994649 -20 AGCTTGCCGCTGATCACCGCAGTGTCGCG 5 53 1 TATCACCGTC 0.921919 -19 * ***** * * ** Masking position 7 Map Score: 27.557 Number of sites scoring better than the average of aligned sites = 741 Number in coding regions = 656 Number in noncoding regions = 85 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 2 TTTTTGATCCATTGCCATTGTAGAAGAAAGAAAG 1 105 0 ATGCCATGGA 0.872189 -39 GCCGCGCCGACGACGATGCAGAGCGA 4 3 1 CGGCCGCGGA 0.998365 -100 CGATGCAGAGCGAAGCGATGAGGAGGAGCGGCGC 4 24 1 CGAGCGTGGA 0.990946 -79 GATGAGGAGGAGCGGCGCTCGTGAACCGCGCCGA 4 40 1 AGGGCGTCGA 0.963596 -63 GCTCGTGAACCGCGCCGACGACGATGCAGAGCGA 4 56 1 CGGCCGCGGA 0.998365 -47 CGATGCAGAGCGAAGCGATGAGGAGGAGCGGCGC 4 77 1 CGAGCGTGGA 0.990946 -26 CCGGAGAATCCGCGCCGTAGTGGCCGTGTAGTTC 5 18 0 CGGCCGAGGC 0.981245 -54 TCTCCGGCAGCTTGCCGCTGATCACCGCAGTGTC 5 45 1 CTGCCGTGCA 0.984776 -27 GGGTTTGTCAAGGGCCGGTGCACAATCGTCTCTG 6 11 0 AGGCCGTGCA 0.990789 -48 ** **** ** ** Masking position 6 Map Score: 12.9585 Number of sites scoring better than the average of aligned sites = 433 Number in coding regions = 424 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 6 Fraction of orfs with sites within 600 bp upstream = 0.000963701 Motif number 3 AAAAAAGGCCTGTAAAAGGCCTTTTCAGAG 1 36 0 TGTAAAAGGC 0.927078 -108 ATAGGGCATGAAAAAAAGGCCTGTAAAAGG 1 47 0 AAAAAAAGGC 0.983491 -97 ATTGTAGAAGAAAGAAAGGCGTGCGGCATG 1 93 0 AAAGAAAGGC 0.966798 -51 GCAATGGATCAAAAAAAGGAGTGAGACGAC 1 124 1 AAAAAAAGGA 0.978845 -20 TACATGAAAAAGGCAATATCTATT 2 5 1 TGAAAAAGGC 0.975747 -128 TTCTTTTAATAAAGAGAGGAACGGCATAAT 2 83 0 AAAGAGAGGA 0.917051 -50 GCAGTTTAAAAGAAAGAGGACATGGGAGAT 3 107 1 AGAAAGAGGA 0.966798 -177 CCGGGGTGAGAAAAAAATGACATTTGTCAC 3 185 1 AAAAAAATGA 0.901102 -99 TTACATTGATTGTAAAATGACGGAGAAGAC 3 245 0 TGTAAAATGA 0.660383 -39 ********** Masking position 5 Map Score: 10.4274 Number of sites scoring better than the average of aligned sites = 1735 Number in coding regions = 1402 Number in noncoding regions = 333 Number of orfs with sites within 600 bp upstream = 344 Fraction of orfs with sites within 600 bp upstream = 0.0552522 Motif number 4 TTCAGAGAAGCGTATATGCAAAACGTCATA 1 13 0 CGTATATGCA 0.960805 -131 CTGGTGTATACGATTATGCCGTTCCTCTCT 2 71 1 CGATTATGCC 0.973354 -62 TGGATGAATTGGAAGATGCAGGAGGAGGAT 3 145 1 GGAAGATGCA 0.972966 -139 GCCGCGCCGACGACGATGCAGAGCGAAGCG 4 11 1 CGACGATGCA 0.995918 -92 ACCGCGCCGACGACGATGCAGAGCGAAGCG 4 64 1 CGACGATGCA 0.995918 -39 CAGAGACGATTGTGCACCGGCCCTTG 6 7 1 CGATTGTGCA 0.973467 -52 ********** Masking position 7 Map Score: 7.29806 Number of sites scoring better than the average of aligned sites = 88 Number in coding regions = 83 Number in noncoding regions = 5 Number of orfs with sites within 600 bp upstream = 4 Fraction of orfs with sites within 600 bp upstream = 0.000642467 Motif number 5 TTTCCCTTATATCTTTCTGGTGTATACGATTA 2 55 1 ACTTCTGGTG 0.857999 -78 ACTTTATATTACTTTCCGGCTGAAAGGAGCCA 3 14 0 ATTCCGGCTG 0.99294 -270 CACTCTTCAAACCATCCGAGTGTTATGATAGA 3 54 0 ACTCCGAGTG 0.966769 -230 TGTCTAGGCAATCCTCCTCCTGCATCTTCCAA 3 153 0 ACTCCTCCTG 0.98088 -131 TACGGCGCGGATTCTCCGGCAGCTTGCCGCTG 5 33 1 ATTCCGGCAG 0.986907 -39 GTGATGAATATCCGCCAGTCGTGCGGGT 6 41 0 ATTCCGCCAG 0.981042 -18 * * ******** Masking position 5 Map Score: 2.1633 Number of sites scoring better than the average of aligned sites = 534 Number in coding regions = 502 Number in noncoding regions = 32 Number of orfs with sites within 600 bp upstream = 37 Fraction of orfs with sites within 600 bp upstream = 0.00594282 Motif number 6 ********** No masking Map Score: -2.67574e-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 7 ********** No masking Map Score: -2.67574e-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 8 ********** No masking Map Score: -2.67574e-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