AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i111_bsub_mtub_100.orf -o111_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 yknW 109 yknW #2 ytrD 29 similar to cytochrome c oxidase subunit #3 ytrA 300 similar to transcriptional regulator (GntR family) #4 Rv0986 300 hypothetical protein Rv0986 Motif number 1 AAAGAACAAGCGATCACAGATGCCGCAATCAGCATT 3 175 0 CGTCACGGGC 0.997494 -126 GTGTTCCACTCGCGGACTGCCGGCCG 4 1 0 CGGGACGGCG 0.983458 -300 ATGGCAACGGCGATCCCAGCGTCGTGGCCATTGACA 4 59 0 CGTCCCGTTG 0.966546 -242 CTGGGATCGCCGTTGCCATGGGGAGCTGACGCTGCC 4 76 1 CGTGCCTGGC 0.974888 -225 GGGGAGCTGACGCTGCCGGGATCCGGTGCTGTTGTT 4 95 1 CGTGCCGTGG 0.99341 -206 TGCTGTTGTTTGTTGACGGGATGCCCTTGACTTCGC 4 121 1 TGTGACGTCC 0.845962 -180 CCCTTGACTTCGCTGACCGTGGTGTGCGCGTAACCG 4 144 1 CGTGACGGTG 0.992047 -157 TCCGTCGCCGCGTTCCCGACCGGCCGGTTACGCGCA 4 168 0 CGTCCCAGCG 0.952064 -133 GTCGGGAACGCGGCGACGGATGGCGCGGTGGCCAGG 4 184 1 CGCGACGGGC 0.990095 -117 GATGTCATCTCGATCACTGTCCTGGCCACCGCGCCA 4 204 0 CGTCACGCGC 0.985189 -97 TAGCCCGGATCGCTCACAGCTGAAGGCGTTGTTGGC 4 242 0 CGTCACGGGG 0.991785 -59 ** **** * * ** Masking position 7 Map Score: 15.8808 Number of sites scoring better than the average of aligned sites = 511 Number in coding regions = 485 Number in noncoding regions = 26 Number of orfs with sites within 600 bp upstream = 16 Fraction of orfs with sites within 600 bp upstream = 0.00256987 Motif number 2 ACCTTCAATATTGAAGGCTTTTCATA 1 5 0 TTGAAGTTTT 0.97339 -105 GCCTTCAATATTGAAGGTTTTTGGAAATTTAT 1 19 1 TTGAAGTTTT 0.973389 -91 TTAGAAAAACATGAAACTTTTTGATATCCTTC 1 50 1 ATGAACTTTT 0.837518 -60 CCCGTACTATTTGTTAGATATTCTCAAGGAGG 1 81 1 TTGTTGTATT 0.900756 -29 ATGTCAATATATAAATGATTTTATATTAGTGT 3 94 0 ATAAAGTTTT 0.691625 -207 CACGTTACGTTTGTTTCGTTTTTTATGTTTCA 3 141 0 TTGTTCTTTT 0.928273 -160 CTGTGATCGCTTGTTCTTTTTTTCTTGTTCTT 3 192 1 TTGTTTTTTT 0.893239 -109 TGTTCTTGTGATGATCGGTTTTGAATGGCAAA 3 217 1 ATGATGTTTT 0.945395 -84 AAATGATCAATTATACTTTTTTGCCATTCAAA 3 236 0 TTATATTTTT 0.520313 -65 AAAAGTATAATTGATCATTTTTATCTATAAAA 3 248 1 TTGATATTTT 0.849358 -53 GTAGGTCCTTTGTTGGATATTTCGGCGGTAG 4 280 0 TTGTTGTATT 0.900756 -21 ***** * **** Masking position 9 Map Score: 9.31977 Number of sites scoring better than the average of aligned sites = 1463 Number in coding regions = 1228 Number in noncoding regions = 235 Number of orfs with sites within 600 bp upstream = 245 Fraction of orfs with sites within 600 bp upstream = 0.0393511 Motif number 3 TTTTATGTTTCATAACTGCCTCCCTTAATGTC 3 121 0 CATAACCCTC 0.907022 -180 ATGCCGCAATCAGCATTGGCACGTTACGTTTG 3 160 0 CAGCATGCAC 0.922392 -141 CAAAACCGATCATCACAAGAACAAGAAAAAAA 3 208 0 CATCACGAAC 0.983071 -93 TGGCCATTGACACCACCTGGTCTAGTTTTTCT 4 39 0 CACCACGGTC 0.985189 -262 CGGATCCCGGCAGCGTCAGCTCCCCATGGCAA 4 88 0 CAGCGTGCTC 0.907841 -213 CAACAAACAACAGCACCGGATCCCGGCAGCGT 4 104 0 CAGCACGATC 0.989981 -197 AAGTCAAGGGCATCCCGTCAACAAACAACAGC 4 122 0 CATCCCCAAC 0.957003 -179 CGGTTACGCGCACACCACGGTCAGCGAAGTCA 4 148 0 CACACCGGTC 0.871166 -153 CTGTCCTGGCCACCGCGCCATCCGTCGCCGCG 4 192 0 CACCGCCATC 0.974974 -109 ATCGAGATGACATCACGCCAACAACGCCTTCA 4 226 1 CATCACCAAC 0.97519 -75 ****** **** Masking position 2 Map Score: 8.10086 Number of sites scoring better than the average of aligned sites = 963 Number in coding regions = 901 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 4 AATTTATTAGAAAAACATGAAACTTTTTGA 1 44 1 AAAAACATGA 0.955042 -66 ACAAGAAAAAAAGAACAAGCGATCACAGAT 3 190 0 AAGAACAAGC 0.97988 -111 CGATCATCACAAGAACAAGAAAAAAAGAAC 3 204 0 AAGAACAAGA 0.988099 -97 GAACACCTAGAAAAACTAGACCAGGTGGTG 4 31 1 AAAAACTAGA 0.955042 -270 ********** Masking position 5 Map Score: 1.61207 Number of sites scoring better than the average of aligned sites = 157 Number in coding regions = 141 Number in noncoding regions = 16 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 5 TTAGGTTTGGAGGGAAGTGAG 2 19 1 AGGGAAGTGA 0.994336 -11 AAGTGTACTAATTGAAGTAATACACTATAG 3 64 1 ATTGAAGTAA 0.845543 -237 TATAGAAAGTAGGGAAGTAA 3 291 1 AGGGAAGTAA 0.991267 -10 CACCACGGTCAGCGAAGTCAAGGGCATCCC 4 138 0 AGCGAAGTCA 0.972669 -163 CGCGGTGGCCAGGACAGTGATCGAGATGAC 4 207 1 AGGACAGTGA 0.938102 -94 ********** Masking position 6 Map Score: 1.62156 Number of sites scoring better than the average of aligned sites = 76 Number in coding regions = 52 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 6 ********** No masking Map Score: 9.40348e-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: 9.40348e-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: 9.40348e-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