AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i150_ATP_synthase_1_mtub_reg_100.orf -a/home/amcguire/alignace/lib/ORF_mtub.txt -z/skink1/amcguire/genomes/mtub.fna -g0.66 -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 = 0.66 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 Rv1303 256 hypothetical protein Rv1303 #2 atpE 48 atpE #3 atpF 30 atpF #4 atpA 44 atpA #5 atpD 39 atpD Motif number 1 TCGTAGTTCTCGGCTCCGGG 1 1 0 CGGCTCCGGG 0.969855 -256 GACACCACTACTACTCCTTGTCGTAGTTCT 1 21 0 CTACTCCTTG 0.975333 -236 GTAGTGGTGTCTACCTTGTGGTACGGTGCG 1 40 1 CTACCTTGTG 0.959646 -217 CCCGCGAGGTCTCCTTCGGGGTTCTAGCCG 1 68 0 CTCCTTCGGG 0.99186 -189 CGCGGGTTGCCGGCCCCCGGCCCATCGGAT 1 92 1 CGGCCCCCGG 0.918544 -165 CAAGGGGTAGCTCCCTATGTCGGTCGTGAA 1 141 0 CTCCCTATGT 0.691363 -116 ACATAGGGAGCTACCCCTTGGGTGATTCCG 1 151 1 CTACCCCTTG 0.988198 -106 ATCCTCCTTGATGGCTCTGGTAGCCGTTAC 2 23 0 ATGGCTCTGG 0.821304 -26 TTCCTTATCCTCCTTGATGGCTCTGG 2 33 0 ATCCTCCTTG 0.765801 -16 TGCTACCTATTGCAACCATTTG 3 19 0 CTACCTATTG 0.927491 -12 TTTGTGCTGACTAGTTCGGGT 4 2 0 CTAGTTCGGG 0.979899 -43 TTTCGTCTTCCTACTTCGGTTTGTGCTGAC 4 21 0 CTACTTCGGT 0.952105 -24 TGGGGCTAACCTAGCTTGGGC 5 2 0 CTAGCTTGGG 0.93488 -38 ATCTTCTTCGCTTCCTCGTGGGGCTAACCT 5 20 0 CTTCCTCGTG 0.968427 -20 ********** Masking position 2 Map Score: 18.9301 Number of sites scoring better than the average of aligned sites = 8471 Number in coding regions = 7714 Number in noncoding regions = 757 Number of orfs with sites within 600 bp upstream = 557 Fraction of orfs with sites within 600 bp upstream = 0.0894635 Motif number 2 ACCTTGTGGTACGGTGCGGCTAGAACCCCG 1 52 1 ACGGTGCGGC 0.985464 -205 GGGCCGGCAACCCGCGAGGTCTCCTTCGGG 1 78 0 CCCGCGAGGT 0.910947 -179 GGATACGCATCCGATGGGCCGGGGGCCGGC 1 100 0 CCGATGGGCC 0.983802 -157 CGGTCGTGAATCGGCGCGACCGGATACGCA 1 121 0 TCGGCGCGAC 0.986555 -136 ACCGGAATCACCCAAGGGGTAGCTCCCTAT 1 153 0 CCCAAGGGGT 0.908056 -104 TTGGGTGATTCCGGTGCGACGACTGCGATA 1 168 1 CCGGTGCGAC 0.996491 -89 TGCGATACGCTCGGCGGGCCACCGATCAGT 1 191 1 TCGGCGGGCC 0.988393 -66 GCGGAAACCACCCGATCGACTGATCGGTGG 1 209 0 CCCGATCGAC 0.921952 -48 TCTTCGCTTCCTCGTGGGGCTAACCTAGCT 5 16 0 CTCGTGGGGC 0.978903 -24 ********** Masking position 8 Map Score: 11.3174 Number of sites scoring better than the average of aligned sites = 15362 Number in coding regions = 14199 Number in noncoding regions = 1163 Number of orfs with sites within 600 bp upstream = 797 Fraction of orfs with sites within 600 bp upstream = 0.128012 Motif number 3 TGGGCCGGGGGCCGGCAACCCGCGAGGTCT 1 86 0 GCCGGCAACC 0.992072 -171 AATCGGCGCGACCGGATACGCATCCGATGG 1 113 0 ACCGGATACG 0.971112 -144 CAGTCGTCGCACCGGAATCACCCAAGGGGT 1 163 0 ACCGGAATCA 0.957773 -94 GGGCTGATGGAGCGGAAACCACCCGATCGA 1 220 0 AGCGGAAACC 0.994355 -37 GGTAGCCGTTACCAGCATCCGGTA 2 5 0 ACCAGCATCC 0.979714 -44 GGATGCTGGTAACGGCTACCAGAGCCATCA 2 15 1 AACGGCTACC 0.971367 -34 CGAACTAGTCAGCACAAACCGAAGTAGGAA 4 14 1 AGCACAAACC 0.902325 -31 ********** Masking position 3 Map Score: 7.94162 Number of sites scoring better than the average of aligned sites = 3572 Number in coding regions = 3315 Number in noncoding regions = 257 Number of orfs with sites within 600 bp upstream = 231 Fraction of orfs with sites within 600 bp upstream = 0.0371025 Motif number 4 CACTACTACTCCTTGTCGTAGTTCTCGGCT 1 16 0 CCTTGTCGTA 0.940104 -241 GTGGTGTCTACCTTGTGGTACGGTGCGGCT 1 43 1 CCTTGTGGTA 0.9879 -214 CGCGAGGTCTCCTTCGGGGTTCTAGCCGCA 1 66 0 CCTTCGGGGT 0.990871 -191 CCGAAGGAGACCTCGCGGGTTGCCGGCCCC 1 79 1 CCTCGCGGGT 0.977573 -178 GGGAGCTACCCCTTGGGTGATTCCGGTGCG 1 156 1 CCTTGGGTGA 0.986339 -101 TCGTCTTCCTACTTCGGTTTGTGCTGACTA 4 19 0 ACTTCGGTTT 0.65715 -26 TTCTTCGCTTCCTCGTGGGGCTAACCTAGC 5 17 0 CCTCGTGGGG 0.983022 -23 ********** Masking position 3 Map Score: 5.95444 Number of sites scoring better than the average of aligned sites = 1522 Number in coding regions = 1364 Number in noncoding regions = 158 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 5 GCCGCACCGTACCACAAGGTAGACACCACT 1 42 0 ACCACAAGGT 0.402804 -215 GCGGGTTGCCGGCCCCCGGCCCATCGGATG 1 93 1 GGCCCCCGGC 0.972086 -164 CGACCGGATACGCATCCGATGGGCCGGGGG 1 105 0 CGCATCCGAT 0.981124 -152 CGTGAATCGGCGCGACCGGATACGCATCCG 1 117 0 CGCGACCGGA 0.899572 -140 CCCAAGGGGTAGCTCCCTATGTCGGTCGTG 1 143 0 AGCTCCCTAT 0.792363 -114 TCGCAGTCGTCGCACCGGAATCACCCAAGG 1 166 0 CGCACCGGAA 0.920286 -91 ACGCTCGGCGGGCCACCGATCAGTCGATCG 1 197 1 GGCCACCGAT 0.960016 -60 TGGAGCGGAAACCACCCGATCGACTGATCG 1 213 0 ACCACCCGAT 0.979573 -44 AGCCGTTACCAGCATCCGGTA 2 2 0 AGCATCCGGT 0.982179 -47 ********** Masking position 3 Map Score: 3.4852 Number of sites scoring better than the average of aligned sites = 11891 Number in coding regions = 10963 Number in noncoding regions = 928 Number of orfs with sites within 600 bp upstream = 666 Fraction of orfs with sites within 600 bp upstream = 0.106971 Motif number 6 ********** No masking Map Score: -6.86222e-14 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: -6.86222e-14 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: -6.86222e-14 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