AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i179_ecoli_bsub_300.orf -o179_ecoli_bsub_300.ace -a/home/amcguire/alignace/lib/ORF_ecoli.txt -z/skink1/amcguire/genomes/ecoli.fna -g0.47 -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 = 0.47 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 folC 69 dihydrofolate:folylpolyglutamate synthetase; dihydrofolate synthetase #2 accD 155 acetylCoA carboxylase, carboxytransferase component, beta subunit #3 dedA 82 orf, hypothetical protein #4 usg 65 putative PTS system enzyme II A component #5 pdxB 98 erythronate-4-phosphate dehyrogenase #6 holC 52 DNA polymerase III, chi subunit #7 BIME233 22 BIME #8 pepA 266 aminopeptidase A/I #9 folC 59 folyl-polyglutamate synthetase #10 valS 300 valyl-tRNA synthetase Motif number 1 GCAGAGCCAGTGGCCCTGCCCTTATCAGTTA 1 9 0 TGGCGCCCTT 0.990905 -61 GCAGGGCCACTGGCTCTGCCCTTTTGCTATTCT 1 23 1 TGGCGCCCTT 0.99081 -47 AAAGTAACTCCGCGGTTCGACCACTTT 2 5 1 TAACGCGGTT 0.855992 -151 GCTGTAACATTGGCAGGGAGCTTTGCTATTTCT 4 30 1 TGGCGAGCTT 0.958946 -36 CAAGTATGCCTGGCCGCGAGATTATGGCACACT 5 38 1 TGGCGAGATT 0.854675 -61 TTGCGTCAGGCAAGGCTGTTAT 7 8 1 AGGCGCTGTT 0.965174 -15 TGTTCTGACGTGCCAATGCCGTAATAACGTTAA 8 144 1 TGCCGCCGTA 0.948221 -123 TTCTATCTGTAGCCACCGCCGTTGTCTTTAAGA 8 228 1 AGCCGCCGTT 0.988752 -39 TGAAAAGCCGGGGCGGTTTCTAGAGAAA 9 6 1 AGCCGCGGTT 0.985713 -54 CTCTTTTATAAGACAAGGCGGTTTCTCTAGAAA 9 27 0 AGACGCGGTT 0.979945 -33 **** ****** Masking position 12 Map Score: 12.1971 Number of sites scoring better than the average of aligned sites = 1122 Number in coding regions = 1079 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 2 TATCCAAAGTTTCGGGCTGTTATGTTTTAA 2 40 1 TTCGGGCTGT 0.97528 -116 ATGTGCAACATTCATGGTCTGTTGGGGGCA 2 69 1 TTCATGGTCT 0.969676 -87 CTCGGAACATTTCAGGCTGTAGCCAACGTA 3 22 1 TTCAGGCTGT 0.992261 -61 CTCGTCATCTTTCAGGCTGTAACTACGTTG 3 45 0 TTCAGGCTGT 0.992261 -38 TCTCTTCTTCATGCTCTCTGCTGTAAC 4 8 1 TTCATGCTCT 0.992881 -58 ACTCAATCAGTTCATGCACTTATAACGGAT 10 178 0 TTCATGCACT 0.983785 -123 ACCACCTTTTTTCATGAACTCAATCAGTTC 10 195 0 TTCATGAACT 0.903715 -106 ********** Masking position 2 Map Score: 10.7134 Number of sites scoring better than the average of aligned sites = 127 Number in coding regions = 115 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 3 AAAAGGGCAGAGCCAGTGGCCCTGCCCTTA 1 18 0 AGCCAGTGGC 0.951709 -52 GGAACATTTCAGGCTGTAGCCAACGTAGTT 3 25 1 AGGCTGTAGC 0.970085 -58 GTCATCTTTCAGGCTGTAACTACGTTGGCT 3 42 0 AGGCTGTAAC 0.739115 -41 GACGAGTACAAGGCATAGGCAAAT 3 69 1 AGGCATAGGC 0.886415 -14 CGTAAAAACTCGTCTTTTGCAGGATTTTAG 8 23 1 CGTCTTTTGC 0.744669 -244 AACGTTATTACGGCATTGGCACGTCAGAAC 8 145 0 CGGCATTGGC 0.967121 -122 TAACTCATGTCCGCTGTTGCGATGACTTCG 8 185 0 CCGCTGTTGC 0.890602 -82 TTAAAGACAACGGCGGTGGCTACAGATAGA 8 229 0 CGGCGGTGGC 0.993024 -38 TTATAAGACAAGGCGGTTTCTCTAGAAACC 9 25 0 AGGCGGTTTC 0.911737 -35 AGTACAAAAAAGGCGCATGCAGAGAGAGAA 10 50 1 AGGCGCATGC 0.849392 -251 CAGAGAGAGAAGCCGTTTGCTGAAAGGCTT 10 69 1 AGCCGTTTGC 0.930997 -232 ********** Masking position 4 Map Score: 8.25797 Number of sites scoring better than the average of aligned sites = 3639 Number in coding regions = 3474 Number in noncoding regions = 165 Number of orfs with sites within 600 bp upstream = 158 Fraction of orfs with sites within 600 bp upstream = 0.0253774 Motif number 4 TCTGAACCTGGTTCGATGCCAGTTTTATCT 2 122 0 GTTCGATGCC 0.920618 -34 AGCCTGAAATGTTCCGAGCATTATTCTCG 3 10 0 GTTCCGAGCA 0.809973 -73 TCTTCTTCATGCTCTCTGCTGTAACATTGG 4 13 1 GCTCTCTGCT 0.948952 -53 AAATAGCAAAGCTCCCTGCCAATGTTACAG 4 31 0 GCTCCCTGCC 0.993155 -35 TGTGCCATAATCTCGCGGCCAGGCATACTT 5 39 0 TCTCGCGGCC 0.941961 -60 TACTCTTCCCGTTCTAAGCAGGTGTATTTA 10 24 0 GTTCTAAGCA 0.807672 -277 AAACGGCTTCTCTCTCTGCATGCGCCTTTT 10 57 0 TCTCTCTGCA 0.902431 -244 AAGAAATTATGCTCCCGGGCGACCTTCCAA 10 113 0 GCTCCCGGGC 0.944389 -188 CTCTTTTTTCGTTCTCAGCCATTTTTAAAC 10 265 1 GTTCTCAGCC 0.979154 -36 ********** Masking position 3 Map Score: 4.95945 Number of sites scoring better than the average of aligned sites = 1351 Number in coding regions = 1268 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 72 Fraction of orfs with sites within 600 bp upstream = 0.0115644 Motif number 5 CCTATGCCTTGTACTCGTCATCTTTCAGGCT 3 57 0 GTACTCGTCT 0.979834 -26 CCTTATACCTGAAATCTTCGCAAGTATGCCT 5 18 1 GAAATCTTCC 0.946887 -81 ACGCCCGTAAAAACTCGTCTTTTGCAGGATT 8 18 1 AAACTCGTCT 0.909993 -249 TTGAGTCGTCGAAATCGTCGCTAAGATAATT 8 85 1 GAAATCGTCC 0.945871 -182 CGCCTTTTTTGTACTCTTCCCGTTCTAAGCA 10 34 0 GTACTCTTCC 0.979834 -267 CCGAATTTCTCTACTCTTCTTTCAAGAAATT 10 135 0 CTACTCTTCT 0.90503 -166 TACCGCGAAAGAGCTTTTCGTCCTTTTACAG 10 224 1 GAGCTTTTCT 0.834123 -77 AACGAAAAAAGAGCTCTTCATCCCTGTAAAA 10 247 0 GAGCTCTTCT 0.978274 -54 ********* * Masking position 5 Map Score: 4.78877 Number of sites scoring better than the average of aligned sites = 308 Number in coding regions = 288 Number in noncoding regions = 20 Number of orfs with sites within 600 bp upstream = 23 Fraction of orfs with sites within 600 bp upstream = 0.00369419 Motif number 6 CGCGGTTCGACCACTTTTTTATCCAAAGTTT 2 21 1 CCATTTTTTA 0.904612 -135 ACGCATAATGCCATTTTTGCCCCCAACAGAC 2 85 0 CCATTTTGCC 0.962639 -71 TGGTTCGATGCCAGTTTTATCTTTGGGGACG 2 113 0 CCATTTTATC 0.946433 -43 AAGCTCCCTGCCAATGTTACAGCAGAGAGCA 4 22 0 CCATGTTACA 0.909154 -44 CGTAAAAACTCGTCTTTTGCAGGATTTTAGC 8 23 1 CGTTTTTGCA 0.824385 -244 TGATAATCCCCTCTTTTATAAGACAAGGCG 9 40 0 CCTTTTTATA 0.951099 -20 TCTGCATGCGCCTTTTTTGTACTCTTCCCGT 10 42 0 CCTTTTTGTA 0.959162 -259 TCGTTCTCAGCCATTTTTAAACATGCTGGAG 10 273 1 CCATTTTAAA 0.904612 -28 *** ******* Masking position 5 Map Score: 2.84978 Number of sites scoring better than the average of aligned sites = 486 Number in coding regions = 402 Number in noncoding regions = 84 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 7 TGGTCGAACCGCGGAGTTACTTT 2 4 0 GCGGAGTTAC 0.985722 -152 GCTGTAGCCAACGTAGTTACAGCCTGAAAG 3 37 1 ACGTAGTTAC 0.965971 -46 TATACCTGATGCGTATTTAAATCCACCACA 6 20 1 GCGTATTTAA 0.963364 -33 GTTTTTACGGGCGTATTTAAA 8 2 0 GCGTATTTAA 0.963364 -265 ATTATACTCAACGGATTCACCTCTCAGATT 8 113 1 ACGGATTCAC 0.927454 -154 ********** Masking position 5 Map Score: 1.4533 Number of sites scoring better than the average of aligned sites = 120 Number in coding regions = 109 Number in noncoding regions = 11 Number of orfs with sites within 600 bp upstream = 14 Fraction of orfs with sites within 600 bp upstream = 0.00224863 Motif number 8 ********** No masking Map Score: -1.56076e-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 9 ********** No masking Map Score: -1.56076e-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 10 ********** No masking Map Score: -1.56076e-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