AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i128_bsub_mtub_300.orf -o128_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 ytsC 101 similar to ABC transporter (ATP-binding protein) #2 ytsA 96 similar to two-component response regulator [YtsB] #3 ytrD 29 similar to cytochrome c oxidase subunit #4 ytrA 300 similar to transcriptional regulator (GntR family) #5 yusC 300 similar to ABC transporter (ATP-binding protein) Motif number 1 ATACGGCGAACAAAAAAGAAAAGCATGTGA 1 19 0 CAAAAAAGAA 0.918082 -83 TAATCTCATTATAAAAAGGAATGCCGGGCT 1 58 0 ATAAAAAGGA 0.983908 -44 AGATTATCCAATATAAAGGAGACTGCGTAA 1 82 1 ATATAAAGGA 0.956021 -20 ATACACTTGATAAAAAAGGAAAAAGTGCGG 2 69 1 TAAAAAAGGA 0.943142 -28 GTTTTTTTGTAAAAAAAGGATTGACTTTGT 4 12 1 AAAAAAAGGA 0.991589 -289 TAATGTCAATATATAAATGATTTTATATTA 4 98 0 ATATAAATGA 0.827547 -203 TATGAAACATAAAAAACGAAACAAACGTAA 4 139 1 AAAAAACGAA 0.910074 -162 CAAGAACAAGAAAAAAAGAACAAGCGATCA 4 195 0 AAAAAAAGAA 0.966889 -106 TTTTGAATGGCAAAAAAGTATAATTGATCA 4 235 1 CAAAAAAGTA 0.816025 -66 CCTTTTATAGATAAAAATGATCAATTATAC 4 252 0 ATAAAAATGA 0.931021 -49 AATGTCAATAAAATAAATGATGTCAACTT 5 10 0 AAATAAATGA 0.90246 -291 CTTTTGCAGAAAAAACCGGAAGATTTCTTA 5 255 1 AAAAACCGGA 0.875214 -46 ********** Masking position 5 Map Score: 16.2001 Number of sites scoring better than the average of aligned sites = 2045 Number in coding regions = 1479 Number in noncoding regions = 566 Number of orfs with sites within 600 bp upstream = 568 Fraction of orfs with sites within 600 bp upstream = 0.0912303 Motif number 2 ACGGCGAACAAAAAAGAAAAGCATGTGACATT 1 15 0 AAAAGAAAGC 0.53682 -87 CGTATCGAAGGAAAAGCCCGGCATTCCTTTTT 1 44 1 GAAAGCCGGC 0.993943 -58 TGCGAACGAGCCGGCTGAGACAGCC 2 4 1 GACGACCGGC 0.75803 -93 ATGCGCTATAGAAAAAGCCGGCTGTCTCAGCC 2 23 0 GAAAACCGGC 0.977033 -74 ATAAAAAAGGAAAAAGTGCGGTGAGTCGA 2 78 1 AAAAGGCGGT 0.868617 -19 CGTTTTTTTGTAAAAAAAGGATTGACTTTGT 4 10 1 GTAAAAAGGA 0.619834 -291 ATATATTGACATTAAGGGAGGCAGTTATGAAA 4 114 1 ATAAGGAGGC 0.934084 -187 TCTTAATGTAGAATAGCACGGCGAATGATTAA 5 39 0 GATAGACGGC 0.916408 -262 TATTTCTCTTATCAAGAGAGGTGGAGGGAAGT 5 94 1 ATAAGGAGGT 0.757765 -207 GAAGTGCCCTATGAAGCCCGGCAACCATCAAC 5 121 1 ATAAGCCGGC 0.977841 -180 CTGCACACTTGAGCAGAAAGGCTTATATAAAA 5 213 0 GACAGAAGGC 0.964465 -88 CTGCTCAAGTGTGCAGAAAGGCTTTTCTTTTG 5 229 1 GTCAGAAGGC 0.953723 -72 TTCTTTTGCAGAAAAAACCGGAAGATTTCTTA 5 253 1 GAAAACCGGA 0.867617 -48 TTAGAATAGTGTTAAGGCAGGTGATTGCT 5 282 1 GTAAGCAGGT 0.944875 -19 ** *** ***** Masking position 11 Map Score: 13.5831 Number of sites scoring better than the average of aligned sites = 2399 Number in coding regions = 2167 Number in noncoding regions = 232 Number of orfs with sites within 600 bp upstream = 196 Fraction of orfs with sites within 600 bp upstream = 0.0314809 Motif number 3 CGAAAATGTCACATGCTTTT 1 1 1 CGAAAATGTC 0.838732 -101 GCCGTATCGAAGGAAAAGCCCGGCATTCCT 1 42 1 AGGAAAAGCC 0.979181 -60 TGCGAACGAGCCGGCTGAGACA 2 3 1 CGAACGAGCC 0.95136 -94 CATGCGCTATAGAAAAAGCCGGCTGTCTCA 2 26 0 AGAAAAAGCC 0.984627 -71 TGATAAAAAAGGAAAAAGTGCGGTGAGTCG 2 76 1 GGAAAAAGTG 0.769944 -21 TAGGTTTGGAGGGAAGTGAG 3 20 1 GGGAAGTGAG 0.535529 -10 CGAAACAAACGTAACGTGCCAATGCTGATT 4 155 1 GTAACGTGCC 0.694562 -146 CAAGAAAAAAAGAACAAGCGATCACAGATG 4 189 0 AGAACAAGCG 0.910091 -112 AATTTCCGGACGAAAAAGACTATATATTTC 5 70 1 CGAAAAAGAC 0.890582 -231 GAGAGGTGGAGGGAAGTGCCCTATGAAGCC 5 109 1 GGGAAGTGCC 0.959483 -192 AAAGGCTTATATAAAATGCCTTTCTCTCAT 5 199 0 ATAAAATGCC 0.850446 -102 TTTTCTGCAAAAGAAAAGCCTTTCTGCACA 5 238 0 AAGAAAAGCC 0.787499 -63 TTTCTTTTGCAGAAAAAACCGGAAGATTTC 5 252 1 AGAAAAAACC 0.808384 -49 ********** Masking position 4 Map Score: 10.3422 Number of sites scoring better than the average of aligned sites = 3419 Number in coding regions = 3040 Number in noncoding regions = 379 Number of orfs with sites within 600 bp upstream = 322 Fraction of orfs with sites within 600 bp upstream = 0.0517186 Motif number 4 TGCTGGCGTTTTGCTATACACTTGATAAAAAAGGAAAA 2 54 1 TGCTACACTA 0.971498 -43 GAAGTAATACACTATAGACACTAATATAAAATCATTTA 4 77 1 ATATACACTA 0.96461 -224 AAATCATTTATATATTGACATTAAGGGAGGCAGTTATG 4 105 1 TTATACATTA 0.943961 -196 CATCATTTATTTTATTGACATTTAATCATTCGCCGTGC 5 18 1 TTATACATTA 0.944725 -283 AAGCCCGGCAACCATCAACACTGTTGAAATGGTGCCAA 5 134 1 ACATACACTA 0.957622 -167 AAGAAAAGCCTTTCTGCACACTTGAGCAGAAAGGCTTA 5 220 0 TTCTACACTA 0.986956 -81 AGCAATCACCTGCCTTAACACTATTCTAAGAAATCTTC 5 273 0 TCCTACACTA 0.984293 -28 * *** ***** * Masking position 10 Map Score: 1.94803 Number of sites scoring better than the average of aligned sites = 50 Number in coding regions = 29 Number in noncoding regions = 21 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 ACAGATGCCGCAATCAGCATTGGCACGTTA 4 166 0 CAATCAGCAT 0.90277 -135 CATTCAAAACCGATCATCACAAGAACAAGA 4 214 0 CGATCATCAC 0.933992 -87 ACTTTTTTGCCATTCAAAACCGATCATCAC 4 224 0 CATTCAAAAC 0.716944 -77 ACTTTCTATACGATCTGAACCTTTTATAGA 4 271 0 CGATCTGAAC 0.928778 -30 AGCCCGGCAACCATCAACACTGTTGAAATG 5 135 1 CCATCAACAC 0.902985 -166 TCACACGAAGCGTTCAGCTTTGAAAGATGA 5 173 1 CGTTCAGCTT 0.884507 -128 TTATATAAGCCTTTCTGCTCAAGTGTGCAG 5 215 1 CTTTCTGCTC 0.902568 -86 AAAGAAAAGCCTTTCTGCACACTTGAGCAG 5 229 0 CTTTCTGCAC 0.961984 -72 ********** Masking position 4 Map Score: 1.7048 Number of sites scoring better than the average of aligned sites = 1702 Number in coding regions = 1590 Number in noncoding regions = 112 Number of orfs with sites within 600 bp upstream = 101 Fraction of orfs with sites within 600 bp upstream = 0.0162223 Motif number 6 ********** No masking Map Score: -1.62471e-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 7 ********** No masking Map Score: -1.62471e-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 8 ********** No masking Map Score: -1.62471e-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