AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i230_bsub_mtub_300.orf -o230_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 clpC 276 clpC #2 lsr2 103 lsr2 #3 Rv3603c 184 hypothetical protein Rv3603c #4 ftsH 66 ftsH Motif number 1 TTTGGCTACCGGCGCCCAGGCGAAAGCCTGG 1 13 1 GGCGCCCGGC 0.910309 -264 GCAAAGTACCGGCGCCCAGGCTTTCGCCTGG 1 28 0 GGCGCCCGGC 0.910309 -249 AGCGGCCATCGGTTCGCCGCCAGCGAACGCG 1 59 0 GGTTCGCGCC 0.936014 -218 CGTTTCCGGCGCCGAGCGGCCATCGGTTCGC 1 73 0 GCCGAGCGCC 0.833597 -204 TCTGTTCAACGGCGACTTGGGGCGCTGCGCC 1 138 1 GGCGACTGGG 0.943308 -139 GGTCGGTTCCGGGGCGCAGCGCCCCAAGTCG 1 150 0 GGGGCGCGCG 0.964205 -127 GCGCCCCGGAACCGACCAGGCACCGCAAGGT 1 164 1 ACCGACCGGC 0.891676 -113 GTAATGGTCGGCCTGCCAGGGTTCCTAACCT 1 191 0 GCCTGCCGGG 0.880563 -86 GGTCGACACCGCGTACCTGCCGTCCACTGTA 1 219 0 GCGTACCGCC 0.972264 -58 CGGTGGCTACCTGCTCTCCCTCACC 1 262 0 GGCTACCGCT 0.947509 -15 ATGGCAGATTGGTGACCGGGGAGTCTATCCG 2 51 1 GGTGACCGGG 0.995981 -53 TGGCTTACCCTCGCGTTTCTTCC 2 91 0 GCTTACCTCG 0.804395 -13 TTGTGCCAGGGTGTACCCGCCCGATTGCCGC 3 20 1 GTGTACCGCC 0.837927 -165 CAACAGTGTCGGTTGCCGGCGGCAATCGGGC 3 38 0 GGTTGCCGCG 0.980151 -147 CCAAATCAGCAGTGCCCCGGGTGGGTCTTGA 3 78 1 AGTGCCCGGG 0.952392 -107 CTACAGTCTTGGTGACCGTCCGGTACCCGGG 3 121 1 GGTGACCTCC 0.959246 -64 GTGACCGTCCGGTACCCGGGCATGGGACTGG 3 132 1 GGTACCCGGC 0.977295 -53 GAGCGGTAACCTGGACTTTCCAGCT 4 5 1 GGTAACCGGA 0.793693 -62 CATCGGCCGTGCCGGCCAGGTCCTTCCCGAT 4 42 0 GCCGGCCGGT 0.647559 -25 ******* *** Masking position 7 Map Score: 39.0174 Number of sites scoring better than the average of aligned sites = 1664 Number in coding regions = 1548 Number in noncoding regions = 116 Number of orfs with sites within 600 bp upstream = 80 Fraction of orfs with sites within 600 bp upstream = 0.0128493 Motif number 2 CTTTCGCCTGGGCGCCGGTAGCCAAATG 1 9 0 GGCGCCGGTA 0.997485 -268 CGAAAGCCTGGGCGCCGGTACTTTGCCGCG 1 33 1 GGCGCCGGTA 0.997485 -244 ATGGCCGCTCGGCGCCGGAAACGCTTGGGT 1 81 1 GGCGCCGGAA 0.997085 -196 TGGGGCGCTGCGCCCCGGAACCGACCAGGC 1 155 1 CGCCCCGGAA 0.98148 -122 GAACCGACCAGGCACCGCAAGGTTAGGAAC 1 172 1 GGCACCGCAA 0.98945 -105 TACGGATAGACTCCCCGGTCACCAATCTGC 2 54 0 CTCCCCGGTC 0.878809 -50 GGAGTCTATCCGTACTGCACAGGAAGAAAC 2 70 1 CGTACTGCAC 0.717247 -34 CGGCGCCGCTTGTGCCAGGGT 3 2 1 GGCGCCGCTT 0.969552 -183 CGGCGGCAATCGGGCGGGTACACCCTGGCA 3 23 0 CGGGCGGGTA 0.836575 -162 CCGCCCGATTGCCGCCGGCAACCGACACTG 3 36 1 GCCGCCGGCA 0.94981 -149 ACCCACCCGGGGCACTGCTGATTTGGTCAC 3 74 0 GGCACTGCTG 0.821503 -111 CCCATGCCCGGGTACCGGACGGTCACCAAG 3 128 0 GGTACCGGAC 0.981795 -57 ACCCGGGCATGGGACTGGAACGAACCAAGA 3 145 1 GGGACTGGAA 0.888338 -40 GAAAGTCCAGGTTACCGCTC 4 1 0 GTTACCGCTC 0.787066 -66 GATCATCGGCCGTGCCGGCCAGGTCCTTCC 4 46 0 CGTGCCGGCC 0.966574 -21 ********** Masking position 5 Map Score: 24.6789 Number of sites scoring better than the average of aligned sites = 1760 Number in coding regions = 1671 Number in noncoding regions = 89 Number of orfs with sites within 600 bp upstream = 68 Fraction of orfs with sites within 600 bp upstream = 0.0109219 Motif number 3 GCGCCGAGCGGCCATCGGTTCGCCGCCAGC 1 66 0 GCCATCGGTT 0.944849 -211 ACCCTGGCAGGCCGACCATTACAGTGGACG 1 200 1 GCCGACCATT 0.971641 -77 CCGCGTACCTGCCGTCCACTGTAATGGTCG 1 212 0 GCCGTCCACT 0.993887 -65 GGTACGCGGTGTCGACCGCTGTATCCGATG 1 233 1 GTCGACCGCT 0.976399 -44 AGTGTCGGTTGCCGGCGGCAATCGGGCGGG 3 35 0 GCCGGCGGCA 0.954013 -150 CACCAAGACTGTAGTCGATTTGCACGTCAA 3 105 0 GTAGTCGATT 0.605011 -80 AGTCTTGGTGACCGTCCGGTACCCGGGCAT 3 125 1 ACCGTCCGGT 0.845122 -60 AACCTGTGAGGCCGTCTGCT 3 175 1 GCCGTCTGCT 0.9876 -10 ********** Masking position 6 Map Score: 6.57031 Number of sites scoring better than the average of aligned sites = 1414 Number in coding regions = 1351 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 55 Fraction of orfs with sites within 600 bp upstream = 0.00883392 Motif number 4 CCAGGCTTTCGCCTGGGCGCCGGTAGCCAA 1 14 0 GCCTGGGCGC 0.989593 -263 CCAGGCGAAAGCCTGGGCGCCGGTACTTTG 1 28 1 GCCTGGGCGC 0.989593 -249 CGCCGGAAACGCTTGGGTGGTTTTCTCGTT 1 93 1 GCTTGGGTGG 0.956687 -184 TGGTCGGCCTGCCAGGGTTCCTAACCTTGC 1 188 0 GCCAGGGTTC 0.936717 -89 ACCGCTGTATCCGATGGTGAGGGAGAGCAG 1 247 1 CCGATGGTGA 0.913255 -30 ACTGTGGGTGTTGTGTCTGGA 2 2 1 CTGTGGGTGT 0.939075 -102 AGGAAGAAACGCGAGGGTAAGCCA 2 90 1 GCGAGGGTAA 0.864352 -14 CGCCGCTTGTGCCAGGGTGTACCCGCCCGA 3 14 1 GCCAGGGTGT 0.990804 -171 GCAACCGACACTGTTGGTGTAGTGACCAAA 3 53 1 CTGTTGGTGT 0.792446 -132 ATCAGCAGTGCCCCGGGTGGGTCTTGACGT 3 82 1 CCCCGGGTGG 0.968277 -103 ATCGACTACAGTCTTGGTGACCGTCCGGTA 3 116 1 GTCTTGGTGA 0.906358 -69 ********** Masking position 6 Map Score: 13.4516 Number of sites scoring better than the average of aligned sites = 580 Number in coding regions = 517 Number in noncoding regions = 63 Number of orfs with sites within 600 bp upstream = 49 Fraction of orfs with sites within 600 bp upstream = 0.00787022 Motif number 5 CGCTCGGCGCCGGAAACGCTTGGGTGGTTT 1 86 1 CGGAAACGCT 0.961805 -191 CGCTGCGCCCCGGAACCGACCAGGCACCGC 1 160 1 CGGAACCGAC 0.976321 -117 CCCTCACCATCGGATACAGCGGTCGACACC 1 240 0 CGGATACAGC 0.906516 -37 CTGTGCAGTACGGATAGACTCCCCGGTCAC 2 62 0 CGGATAGACT 0.911624 -42 GGCAATCGGGCGGGTACACCCTGGCACAAG 3 19 0 CGGGTACACC 0.959894 -166 GGCATGGGACTGGAACGAACCAAGAAACCT 3 150 1 TGGAACGAAC 0.863766 -35 TACACGCAGCTGGAAAGTCCAGGTTACCGC 4 13 0 TGGAAAGTCC 0.856671 -54 CTGCGTGTATCGGGAAGGACCTGGCCGGCA 4 34 1 CGGGAAGGAC 0.97227 -33 AGGACCTGGCCGGCACGGCCGATGATCG 4 49 1 CGGCACGGCC 0.97573 -18 ********** Masking position 3 Map Score: 7.11513 Number of sites scoring better than the average of aligned sites = 1561 Number in coding regions = 1416 Number in noncoding regions = 145 Number of orfs with sites within 600 bp upstream = 82 Fraction of orfs with sites within 600 bp upstream = 0.0131706 Motif number 6 ********** No masking Map Score: 2.65333e-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: 2.65333e-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: 2.65333e-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