AlignACE version 2.2 July 7, 1998 alignACE -a/home/amcguire/genomes/ORF_ctra.txt -z/home/amcguire/genomes/ctra.fna -iglpR_ctra_opreg_100.orf -g0.413 -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 = 0.413 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 uhpC 300 Hexosphosphate Transport #2 CT565 90 hypothetical protein #3 CT569 61 predicted OMP [leader (16) peptide] #4 CT573 127 hypothetical protein #5 CT646 100 hypothetical protein Motif number 1 TCTCTATTATTTCTTTTATTTGACACACCT 1 12 1 TTCTTTTATT 0.832346 -289 TATGCATTTGTATTTTTCTTAAGCTTCTAG 1 251 1 TATTTTTCTT 0.946784 -50 ATGGTTTTTTATGTTTATATTTAAA 2 6 1 TTTTTATGTT 0.918578 -85 CCATACCTGATTTTTTTCTTTTTATTAAAT 2 68 0 TTTTTTTCTT 0.992153 -23 ATTGTTTTCTTTTTTTTGTTTTCTTCACAG 3 25 0 TTTTTTTGTT 0.990655 -37 TAAAAGCCGATTTTTTTGTTTTTTAACAAA 4 18 1 TTTTTTTGTT 0.990655 -110 AGAAAAGCCGTTTTTTTGTTAAAAAACAAA 4 32 0 TTTTTTTGTT 0.990655 -96 ACGGCTTTTCTTATTTTCTTTTGTAAAAAT 4 51 1 TTATTTTCTT 0.936082 -77 AAAAATTGATTTTTTTTCTCAAATCAGTTA 4 75 1 TTTTTTTCTC 0.95225 -53 TTATACAATTCTTTTTTGTTTCTCTGTTGT 4 107 1 CTTTTTTGTT 0.971008 -21 TTATAATTAATGTTTTTCTTGAAAAAGATG 5 25 1 TGTTTTTCTT 0.98605 -76 TTGAAAAAGATGTTTTTATTTTTTAAAATG 5 43 1 TGTTTTTATT 0.941751 -58 TTAGCGTTTTTCTTTATCTTTTTA 5 87 0 CGTTTTTCTT 0.95714 -14 ********** Masking position 5 Map Score: 29.2105 Number of sites scoring better than the average of aligned sites = 129 Number in coding regions = 129 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 AGCAAACGTATTGTCTTCTAAAAGCTATTAAGC 1 103 1 TTTCTTTAAA 0.981416 -198 TTCTAAGACCTCGTTTTTTGCTATCAGTCTAGG 1 199 0 TCTTTTTCTA 0.868871 -102 TATATTTAAATTATCTTTTGATAATTGTTTAGT 2 26 1 TTTCTTTATA 0.922194 -65 CTGATTTTTTTCTTTTTATTAAATTAATCTCGT 2 59 0 TCTTTTTAAA 0.972934 -32 TTTCTTTTTTTTGTTTTCTTCACAGTTTCCCTC 3 17 0 TTTTTTTCAC 0.900806 -45 AGAAAAGCCGTTTTTTTGTTAAAAAACAAAAAA 4 29 0 TTTTTTTAAA 0.984686 -99 TTTTCTTATTTTCTTTTGTAAAAATTGATTTTT 4 56 1 TTTTTTTAAA 0.984685 -72 AAAAATTGATTTTTTTTCTCAAATCAGTTACTT 4 75 1 TTTTTTTAAA 0.984686 -53 CTCAAATCAGTTACTTTATACAATTCTTTTTTG 4 92 1 TTCTTTTCAA 0.900755 -36 AAAAATAAAAACATCTTTTTCAAGAAAAACATT 5 33 0 ACTCTTTCAA 0.73808 -68 AAAGATGTTTTTATTTTTTAAAATGAGCGCTCT 5 48 1 TTTTTTTAAA 0.984685 -53 GCGTTTTTCTTTATCTTTTTAAAATGAAGAGCG 5 75 0 TTTCTTTAAA 0.981447 -26 ** **** * *** Masking position 7 Map Score: 21.0568 Number of sites scoring better than the average of aligned sites = 179 Number in coding regions = 179 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 CTTTTAGAAGACAATACGTTTGCTGTGTAAA 1 96 0 ACAATAGTTT 0.860116 -205 ATTGTCTTCTAAAAGCTATTAAGCTAAATGA 1 112 1 AAAAGCATTA 0.919154 -189 TAAAAAGAAAAAAATCAGGTATGGCTT 2 74 1 AAAATCGGTA 0.92968 -17 AAAAAAGAAAACAATCCATTACGTTAGTGGA 3 40 1 ACAATCATTA 0.872871 -22 AAAAAACAAAAAAATCGGCTTTTATATGAAA 4 11 0 AAAATCGCTT 0.950868 -117 AGAAAATAAGAAAAGCCGTTTTTTTGTTAAA 4 39 0 AAAAGCGTTT 0.976026 -89 TTTGAGAAAAAAAATCAATTTTTACAAAAGA 4 67 0 AAAATCATTT 0.957363 -61 TTTTTTTTCTCAAATCAGTTACTTTATACAA 4 84 1 CAAATCGTTA 0.921874 -44 TTAAAAAACTCTGTTTATAATTAATG 5 6 1 AAACTCGTTT 0.929767 -95 TTTTTCTTGAAAAAGATGTTTTTATTTTTTA 5 37 1 AAAAGAGTTT 0.910291 -64 ****** **** Masking position 3 Map Score: 9.08438 Number of sites scoring better than the average of aligned sites = 192 Number in coding regions = 192 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 CACACCTTACTCTCCGCTTATCCATCCACAATA 1 35 1 TCCCTTATCC 0.974742 -266 CGCTTATCCATCCACAATACGCCGCATCCTCAC 1 49 1 TCCATACGCC 0.98921 -252 CGCCGCATCCTCACCCCTACTCCCTCTCTTTAC 1 68 1 TCCCTACTCC 0.995469 -233 TGTAGTAATGTCGTCAATACTCCTTTCATTTAG 1 135 0 TCCATACTCC 0.99511 -166 TGACGACATTACTACAATTGTCCAATATGATGC 1 152 1 ACCATTGTCC 0.941535 -149 ** * ******* Masking position 8 Map Score: 0.909019 Number of sites scoring better than the average of aligned sites = 23 Number in coding regions = 23 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 TAATAGCTTTTAGAAGACAATACGTTTGCT 1 103 0 TAGAAGACAA 0.92881 -198 AACGAGGTCTTAGAAGCTGATACTTTCGTC 1 217 1 TAGAAGCTGA 0.989173 -84 GTGTTTGCTCTAGAAGCTTAAGAAAAATAC 1 260 0 TAGAAGCTTA 0.970868 -41 TTTCATATAAAAGCCGATTTTTTTGTT 4 8 1 TAAAAGCCGA 0.972654 -120 ********** Masking position 5 Map Score: 0.793368 Number of sites scoring better than the average of aligned sites = 48 Number in coding regions = 47 Number in noncoding regions = 1 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: -1.78814e-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 7 ********** No masking Map Score: -1.78814e-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 8 ********** No masking Map Score: -1.78814e-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