AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_mpneu.txt -z/home/amcguire/genomes/mpneu.fna -iargR_mpneu_opreg_300.orf -g0.400 -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 = 0.4 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 argI 247 ornithine carbamoyl transferase; similar to Swiss-Prot Accession Number P04391, from E. coli #2 arcA 300 arginine deiminase; similar to Swiss-Prot Accession Number P23793, from M. capricolum #3 1674278 300 MG116 homolog, from M. genitalium Motif number 1 GTAGCCTTGACTCTGCTTTAAACTTTACTACT 1 60 1 CTCTGCTAAA 0.957093 -188 TAAACTTTACTACTGCTCAAATTAACTATTTA 1 78 1 TACTGCCAAT 0.969209 -170 AACATTGTTTTACTGTTCCAAAAAGATTCTAC 1 183 1 TACTGTCAAA 0.951522 -65 GGCAGTTCGATTCTGCCCGAGACCACCATAAA 2 87 1 TTCTGCCAGA 0.966284 -214 ACAGCTGTTGTACTGCCTTAAATAAAGGTGGT 2 167 0 TACTGCTAAA 0.987259 -134 AGGCTAAGCTTACTGCTTTAATTGTTACACGT 2 266 0 TACTGCTAAT 0.960766 -35 AACATTGAGTTTTTGCATTAAACCTAACGCCA 3 47 0 TTTTGCTAAA 0.963797 -254 CAGCTGGTAGTTTTGTTTCAAAGTCATAAGCC 3 174 0 TTTTGTTAAA 0.859735 -127 TTGCAAGATTTTTTGCACAAAAAGCTGGCGCA 3 221 0 TTTTGCCAAA 0.522115 -80 ****** * *** Masking position 4 Map Score: 9.27061 Number of sites scoring better than the average of aligned sites = 105 Number in coding regions = 87 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 2 ACTTAAAAGGTCGTAGCCTTGACTCTGCTT 1 48 1 TCGTAGCCTT 0.9347 -200 CAGAACCGTCCCTTAGCGGGGAAGAACATT 1 159 1 CCTTAGCGGG 0.900556 -89 AAGATTCTACCCGTACCCGTTGTGCCTTTG 1 205 1 CCGTACCCGT 0.975791 -43 GAAGTGGCTGCCTTTGACTTGGGT 1 234 1 CCTTTGACTT 0.818082 -14 AGCTACAAGACCGTGGCGGTTCCAACGGGA 2 21 0 CCGTGGCGGT 0.94717 -280 GTTCTTCAGACCGTTGCTCTACCGACTGAG 2 49 0 CCGTTGCTCT 0.800232 -252 AACTTTCTTACCTTACCTTTAAAACTAAGG 2 118 1 CCTTACCTTT 0.892988 -183 CAATAAAAAACCTTACCCTTAGTTTTAAAG 2 134 0 CCTTACCCTT 0.976947 -167 AATCAAGTTCACTTTGCCTTTTTTTCTTGG 2 224 1 ACTTTGCCTT 0.848373 -77 AAAGCAGTAAGCTTAGCCTTATTACATGTA 2 279 1 GCTTAGCCTT 0.940507 -22 GTTGATATTGCCGTGGCCTGCAGTGGGGTA 3 76 1 CCGTGGCCTG 0.969422 -225 ********** Masking position 4 Map Score: 8.60989 Number of sites scoring better than the average of aligned sites = 230 Number in coding regions = 201 Number in noncoding regions = 29 Number of orfs with sites within 600 bp upstream = 24 Fraction of orfs with sites within 600 bp upstream = 0.0038548 Motif number 3 ATTTATGCCAATTAACTTAAAAGGTCGTAG 1 34 1 ATTAACTTAA 0.82704 -214 TGACTCTGCTTTAAACTTTACTACTGCTCA 1 67 1 TTAAACTTTA 0.927303 -181 TACCTTACCTTTAAAACTAAGGGTAAGGTT 2 126 1 TTAAAACTAA 0.887653 -175 AGTTTTTGCATTAAACCTAACGCCATTTCA 3 42 0 TTAAACCTAA 0.982238 -259 ACCTAAGAAATTTCACTTAAAATGTGTTCA 3 258 0 TTTCACTTAA 0.876253 -43 TTAAACCTTATTTAACCTAAGAAATTTCAC 3 272 0 TTTAACCTAA 0.97934 -29 CTTGTTCTCTTAAACCTTATTTAACCTAA 3 282 0 TTAAACCTTA 0.964153 -19 ********** Masking position 5 Map Score: 5.92001 Number of sites scoring better than the average of aligned sites = 134 Number in coding regions = 112 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 19 Fraction of orfs with sites within 600 bp upstream = 0.00305172 Motif number 4 GACCGTTGCTCTACCGACTGAGCTACAAGA 2 41 0 CTACCGACTG 0.956008 -260 TTAAGGCAGTACAACAGCTGTAAATTAGTT 2 178 1 ACAACAGCTG 0.912214 -123 GAAAAACAAGCTACCAACTGCTTGGTTTTC 3 124 0 CTACCAACTG 0.983793 -177 TGAAACAAAACTACCAGCTGGCTCTAGAAA 3 186 1 CTACCAGCTG 0.993853 -115 ATTTTTTGCACAAAAAGCTGGCGCAATTCG 3 216 0 CAAAAAGCTG 0.925083 -85 AAAAATCTTGCAAACAGTTGAACACATTTT 3 240 1 CAAACAGTTG 0.914513 -61 ********** Masking position 3 Map Score: 3.12499 Number of sites scoring better than the average of aligned sites = 117 Number in coding regions = 106 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 5 Fraction of orfs with sites within 600 bp upstream = 0.000803084 Motif number 5 CAGTAGTAAAGTTTAAAGCAGAGTCAAGGCTACG 1 59 0 GTTAAAGGAT 0.807927 -189 CTCGCCATTGATTTAAAACGCAGTAAATACCAAG 1 116 1 ATTAAAACAT 0.762751 -132 TAAATACCAAGTTGCACATCCAGAACCGTCCCTT 1 139 1 GTTCACACAA 0.968766 -109 TTGTTTTACTGTTCCAAAAAGATTCTACCCGTAC 1 187 1 GTTCAAAGAT 0.967213 -61 AAAGGCAGCCACTTCAAAGGCACAACGGGTACGG 1 215 0 ACTCAAACAA 0.795024 -33 GACCGTGGCGGTTCCAACGGGAATCAAACCCG 2 9 0 GTTCAACGAT 0.900723 -292 AGTGAACTTGATTGCAAAAAGAATTGGGCAACTA 2 203 0 ATTCAAAGAT 0.926387 -98 TGCTTTAATTGTTACACGTCCACACAAAAGCCCA 2 251 0 GTTCACGCAA 0.962397 -50 ACCTAACGCCATTTCACGAACACAATAACGCGAT 3 24 0 ATTCACGCAA 0.916125 -277 TGGTAGTTTTGTTTCAAAGTCATAAGCCTTGTTG 3 168 0 GTTCAAACAA 0.977569 -133 *** **** ** * Masking position 6 Map Score: 4.00971 Number of sites scoring better than the average of aligned sites = 149 Number in coding regions = 131 Number in noncoding regions = 18 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 6 CCAAGTTGCACATCCAGAACCGTCCCTTAGCG 1 145 1 CATCAGACCG 0.974225 -103 GTTCCAACGGGAATCAAACCCG 2 1 0 GAACAACCCG 0.857542 -300 TACCGACTGAGCTACAAGACCGTGGCGGTTCC 2 28 0 GCTCAAACCG 0.989348 -273 AGAGCAACGGTCTGAAGAACCGTGTGTCGGCA 2 59 1 TCTAAGACCG 0.890691 -242 ACAATAACGCGATACAGCACCGTGGT 3 5 0 GATCAGACCG 0.99397 -296 GTTTTCCAATGCATCAGGACCCGCTACCCCAC 3 98 0 GCACAGACCC 0.966072 -203 CTACCAGCTGGCTCTAGAAACGAATTGCGCCA 3 196 1 GCTTAGAACG 0.872319 -105 *** *** **** Masking position 6 Map Score: 1.20258 Number of sites scoring better than the average of aligned sites = 65 Number in coding regions = 56 Number in noncoding regions = 9 Number of orfs with sites within 600 bp upstream = 7 Fraction of orfs with sites within 600 bp upstream = 0.00112432 Motif number 7 GGATGTGCAACTTGGTATTTACTGCGTTTT 1 130 0 CTTGGTATTT 0.958877 -118 GCCTTTTTTTCTTGGGCTTTTGTGTGGACG 2 239 1 CTTGGGCTTT 0.966274 -62 CTACCAACTGCTTGGTTTTCCAATGCATCA 3 114 0 CTTGGTTTTC 0.977967 -187 CAGTTGGTAGCTTGTTTTTCTGTGTGATTG 3 134 1 CTTGTTTTTC 0.95169 -167 CTTGTTCTCTTAAACCTTAT 3 291 0 CTTGTTCTCT 0.927092 -10 ********** Masking position 3 Map Score: 0.92257 Number of sites scoring better than the average of aligned sites = 78 Number in coding regions = 67 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 8 TTTTTCTTTATTTACTTATACAAA 1 5 1 TCTTTATTTA 0.885986 -243 TTGACCTCGCCATTGATTTAAAACGCAGTA 1 111 1 CATTGATTTA 0.951051 -137 CGGGGAAGAACATTGTTTTACTGTTCCAAA 1 175 1 CATTGTTTTA 0.931317 -73 TTGCTTACCACCTTTATTTAAGGCAGTACA 2 161 1 CCTTTATTTA 0.975935 -140 GTTCACTTTGCCTTTTTTTCTTGGGCTTTT 2 230 1 CCTTTTTTTC 0.92727 -71 ********** Masking position 4 Map Score: 0.332606 Number of sites scoring better than the average of aligned sites = 92 Number in coding regions = 68 Number in noncoding regions = 24 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 9 ********** No masking Map Score: -3.30951e-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 10 ********** No masking Map Score: -3.30951e-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 11 ********** No masking Map Score: -3.30951e-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