AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00640_ctra_reg_100.orf -o00640_ctra_100.ace -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -g0.41 -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 = 0.41 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 araD 83 Ribulose-P Epimerase #2 accA 132 AcCoA Carboxylase/Transferase Alpha #3 accD 71 AcCoA Carboxylase/Transferase Beta #4 sodM 131 Superoxide Dismutase (Mn) #5 sucC 69 Succinyl-CoA Synthetase, Beta Motif number 1 TCTTTTTAAGAGAAATTAAAATTGTTTGCG 2 13 1 AGAAATTAAA 0.833088 -120 CAAAGGTCATTATAATCAAATAGTTGGTTT 2 48 1 TATAATCAAA 0.949768 -85 AATAATCAAAAACAACCAAAAACCAACTAT 2 67 0 AACAACCAAA 0.93422 -66 TAATACAAACAATAATCAAAAACAACCAAA 2 77 0 AATAATCAAA 0.98578 -56 TTAACCAATCAATAATAAAA 3 1 0 AATAATAAAA 0.977649 -71 TAAAAAAAATTACAATAAAATTATTGCTCA 3 28 1 TACAATAAAA 0.92266 -44 CCTCTAGATTATCAATAAAATATTCACTGT 4 42 0 ATCAATAAAA 0.884951 -90 TGAGTAATCAAAGTTGATTGAA 5 3 1 AGTAATCAAA 0.971366 -67 AAGTAAAAAGAATAATAAAAGATAAGGAGG 5 31 1 AATAATAAAA 0.977649 -39 GATAAGGAGGAAAAATTAAAGGGTTATTT 5 51 1 AAAAATTAAA 0.910788 -19 ********** Masking position 5 Map Score: 15.217 Number of sites scoring better than the average of aligned sites = 153 Number in coding regions = 153 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 2 TGTACACTCTCCTTCTTATCGTAGAGGG 1 9 1 CTCCTTCTTA 0.981316 -75 TTTCTTTTTAAGAGAAATTA 2 1 1 TTTCTTTTTA 0.967765 -132 ATTAAAATAACTCTTTTTTATAAGAAGGGA 2 103 1 CTCTTTTTTA 0.954272 -30 CGTAGCACGCTCCCTTCTTATAAAAAAGAG 2 113 0 TCCCTTCTTA 0.936715 -20 TTTTATTGTAATTTTTTTTAACCAATCAAT 3 18 0 ATTTTTTTTA 0.883129 -54 AAAACCATCCTCTTTACAAAAAATTG 3 56 0 ATCCTCTTTA 0.966479 -16 GATAGTAACCTTATTTTTTAGGATGGCT 4 114 1 TTATTTTTTA 0.795673 -18 ATCTTTTATTATTCTTTTTACTTCAATCAA 5 24 0 ATTCTTTTTA 0.958431 -46 CCTTTAATTTTTCCTCCTTATCTTTTATTA 5 43 0 TTCCTCCTTA 0.968717 -27 ********** Masking position 5 Map Score: 10.8043 Number of sites scoring better than the average of aligned sites = 287 Number in coding regions = 287 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 3 GAAATTAAAATTGTTTGCGTGAAACAAAGGTCAT 2 24 1 TTGTTGTAAA 0.994757 -109 TAGTTGGTTTTTGGTTGTTTTTGATTATTGTTTG 2 68 1 TTGTTGTTGA 0.945506 -65 TTTTTGATTATTGTTTGTATTAAAATAACTCTTT 2 85 1 TTGTTGTAAA 0.994784 -48 TTTTATTATTGATTGGTTAAAAAAAATTACAA 3 9 1 TTGTTGTAAA 0.994826 -63 TCTATCTAGCTAGCCTGTAGAAAATAGAGAAGGT 4 74 1 TAGCTGGAAA 0.934824 -58 GTAATCAAAGTTGATTGAAGTAAAAAGAATAATA 5 14 1 TTGTTGGAAA 0.993492 -56 *** *** * *** Masking position 6 Map Score: 7.03393 Number of sites scoring better than the average of aligned sites = 21 Number in coding regions = 21 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 4 TCTTGTGGTCAAAAATTTTAACCCTCTACG 1 30 0 AAAAATTTTA 0.923387 -54 GTTTCACGCAAACAATTTTAATTTCTCTTA 2 19 0 AACAATTTTA 0.965398 -114 ACCAAAAACCAACTATTTGATTATAATGAC 2 53 0 AACTATTTGA 0.912927 -80 TATAAAAAAGAGTTATTTTAATACAAACAA 2 95 0 AGTTATTTTA 0.760742 -38 TGATTGGTTAAAAAAAATTACAATAAAATT 3 20 1 AAAAAAATTA 0.700652 -52 AAAATTGAGCAATAATTTTATTGTAATTTT 3 33 0 AATAATTTTA 0.948508 -39 TCCTCTTTACAAAAAATTGAGCAATAATTT 3 45 0 AAAAAATTGA 0.881277 -27 TCTTGACAGTGAATATTTTATTGATAATCT 4 37 1 GAATATTTTA 0.847255 -95 ********** Masking position 5 Map Score: 4.8558 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 154 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 5 TCAAAAATTTTAACCCTCTACGATAAGAAG 1 22 0 TAACCCTCTA 0.993899 -62 TGTATTAAAATAACTCTTTTTTATAAGAAG 2 100 1 TAACTCTTTT 0.914043 -33 TAGCTAGATAGATCCCTCTAGATTATCAAT 4 56 0 GATCCCTCTA 0.974601 -76 AAATAACCCTTTAATTTTTCCTC 5 57 0 TAACCCTTTA 0.989798 -13 ********** Masking position 7 Map Score: 1.96229 Number of sites scoring better than the average of aligned sites = 16 Number in coding regions = 16 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 6 ********** No masking Map Score: 6.06393e-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: 6.06393e-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: 6.06393e-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