AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00310_tpal_reg_100.orf -o00310_tpal_100.ace -a/home/amcguire/genomes/ORF_tpal.txt -z/home/amcguire/genomes/tpal.fna -g0.53 -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 = 0.53 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 TP0251 153 DNA-binding protein II #2 TP0329 117 serine hydroxymethyltransferase (glyA) #3 TP0417 26 apolipoprotein N-acyltransferase (cutE) #4 TP0997 33 protease IV (sppA) #5 TP0998 71 sodium/proton-dependent alanine transporter Motif number 1 CCGGGCAGCGGTGTCAAGTCGCT 1 4 0 GTGTCAAGTC 0.893192 -150 GAGCCACAGCCTTTCTAGCGAAAACACCTT 1 35 0 CTTTCTAGCG 0.891197 -119 TAGAAAGGCTGTGGCTCGCCAGAAGTCCCG 1 48 1 GTGGCTCGCC 0.994245 -106 TTCACCCGAGGTGGTGCGCGTTTGAGGCGG 1 108 1 GTGGTGCGCG 0.970735 -46 GTTTGAGGCGGCTGTTTGCCCGCGTGTGTT 1 127 1 GCTGTTTGCC 0.941587 -27 GCCCGCGTGTGTTTCTTGTC 1 144 1 GTTTCTTGTC 0.920489 -10 TGCCCGATACCCGTCGTGCGTAACAGGGGA 2 19 0 CCGTCGTGCG 0.951687 -99 TATCGGGCATGCGGCGCGCGGCGTTTTGTC 2 40 1 GCGGCGCGCG 0.988307 -78 GCGGCGCGCGGCGTTTTGTCCATTCTTTGC 2 50 1 GCGTTTTGTC 0.871571 -68 TGTTCGCTCTGTTTCTAGCGCAAAGAATGG 2 69 0 GTTTCTAGCG 0.959345 -49 CACCTCATGTGTGTTATGCCTCGT 4 5 0 GTGTTATGCC 0.951462 -29 AATCTGTTAGCTTGCACGCCCTGCAGGCTA 5 29 1 CTTGCACGCC 0.934378 -43 ********** Masking position 8 Map Score: 15.3861 Number of sites scoring better than the average of aligned sites = 2354 Number in coding regions = 2148 Number in noncoding regions = 206 Number of orfs with sites within 600 bp upstream = 139 Fraction of orfs with sites within 600 bp upstream = 0.0223257 Motif number 2 GCGAAAACACCTTTCCGGGCAGCGGTGTCAAGTCG 1 13 0 CTCGGGAGGG 0.986332 -141 AAGGCTGTGGCTCGCCAGAAGTCCCGAATGTGTAG 1 52 1 CCCAGAGTCC 0.918884 -102 GTGTTCTCTTCACCCGAGGTGGTGCGCGTTTGAGG 1 100 1 CCGAGGGGGC 0.995368 -54 AGGTGGTGCGCGTTTGAGGCGGCTGTTTGCCCGCG 1 116 1 CTGAGGGGTG 0.952075 -38 ACCCGTCGTGCGTAACAGGGGAACATACCA 2 6 0 CTCAGGGACA 0.923016 -112 CCCTGTTACGCACGACGGGTATCGGGCATGCGGCG 2 21 1 CCCGGGATGG 0.974797 -97 GTTTTTCTCTCCTCAGGTAGGCAGAATATTGTT 2 95 0 CCCAGGAGCA 0.986058 -23 AAATGCTTTTCTGGCAGGGGAAAGTT 3 6 1 CTCTGGAGGG 0.963479 -21 AGGCATAACACACATGAGGTGGAGGTTACA 4 14 1 CCGAGGGGGG 0.997606 -20 AGCTTGCACGCCCTGCAGGCTACCGACCCCGACAG 5 37 1 CCCAGGTACG 0.948736 -35 GGCTACCGACCCCGACAGAAGGAGCCGA 5 54 1 CCCAGAGGGC 0.98837 -18 * * **** ** ** Masking position 1 Map Score: 14.7955 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 972 Number in noncoding regions = 108 Number of orfs with sites within 600 bp upstream = 85 Fraction of orfs with sites within 600 bp upstream = 0.0136524 Motif number 3 CGACTTGACACCGCTGCCCGGAAAGGTGTT 1 13 1 CCGCTGCCCG 0.995458 -141 TTCTGGCGAGCCACAGCCTTTCTAGCGAAA 1 42 0 CCACAGCCTT 0.898595 -112 CCTCAAACGCGCACCACCTCGGGTGAAGAG 1 105 0 GCACCACCTC 0.962125 -49 CGCGGGCAAACAGCCGCCTCAAACGCGCAC 1 121 0 CAGCCGCCTC 0.967353 -33 CGCCGCATGCCCGATACCCGTCGTGCGTAA 2 26 0 CCGATACCCG 0.910254 -92 AAAACGCCGCGCGCCGCATGCCCGATACCC 2 37 0 GCGCCGCATG 0.965371 -81 AACTTTCCCCTGCCAGAAAAGCATTT 3 11 0 CCCCTGCCAG 0.960356 -16 TGTAACCTCCACCTCATGTGTGTTA 4 19 0 CCTCCACCTC 0.975982 -15 ********** Masking position 7 Map Score: 5.78131 Number of sites scoring better than the average of aligned sites = 1283 Number in coding regions = 1162 Number in noncoding regions = 121 Number of orfs with sites within 600 bp upstream = 91 Fraction of orfs with sites within 600 bp upstream = 0.0146161 Motif number 4 TCCCGAATGTGTAGACTGTACAACGGTGTG 1 73 1 GTAGACTGTA 0.97253 -81 TGTAACCTCCACCTCATGTGT 4 23 0 GTAACCTCCA 0.981299 -11 AGTTAATCTGTTAGCTTGCACGCCCTGCAG 5 25 1 TTAGCTTGCA 0.97253 -47 GTCGGGGTCGGTAGCCTGCAGGGCGTGCAA 5 40 0 GTAGCCTGCA 0.998214 -32 ********** Masking position 7 Map Score: 2.23849 Number of sites scoring better than the average of aligned sites = 110 Number in coding regions = 100 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 10 Fraction of orfs with sites within 600 bp upstream = 0.00160617 Motif number 5 GCCTTTCTAGCGAAAACACCTTTCCGGGCA 1 27 0 CGAAAACACC 0.948469 -127 GACTTCTGGCGAGCCACAGCCTTTCTAGCG 1 45 0 GAGCCACAGC 0.895136 -109 TCGGGTGAAGAGAACACACCGTTGTACAGT 1 87 0 AGAACACACC 0.989663 -67 AACACACGCGGGCAAACAGCCGCCTCAAAC 1 127 0 GGCAAACAGC 0.938203 -27 GACAAGAAACACACGCGGGCAAACA 1 139 0 GAAACACACG 0.970299 -15 GCGTAACAGGGGAACATACCA 2 2 0 GGAACATACC 0.978412 -116 CTTTGCGCTAGAAACAGAGCGAACAATATT 2 74 1 GAAACAGAGC 0.952561 -44 ACGAGGCATAACACACATGAGGTGGAG 4 8 1 ATAACACACA 0.704119 -26 ********** Masking position 6 Map Score: 3.60044 Number of sites scoring better than the average of aligned sites = 648 Number in coding regions = 583 Number in noncoding regions = 65 Number of orfs with sites within 600 bp upstream = 69 Fraction of orfs with sites within 600 bp upstream = 0.0110826 Motif number 6 ********** No masking Map Score: 2.44017e-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: 2.44017e-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: 2.44017e-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