AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i00520_aful_reg_100.orf -o00520_aful_100.ace -a/home/amcguire/genomes/ORF_aful.txt -z/home/amcguire/genomes/aful.fna -g0.49 -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 = 0.49 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 AF0242 50 glucose-1-phosphate thymidylyltransferase (graD-1) #2 AF0325 300 glucose-1-phosphate thymidylyltransferase (graD-2) #3 AF0361 59 UDP-glucose 4-epimerase (galE-1) #4 AF1142 221 glucose-1-phosphate cytidylyltransferase (rfbF) #5 AF2013 275 coenzyme F390 synthetase (ftsA-3) #6 AF2014 63 sugar transporter, putative Motif number 1 CTTCTGTGATAGTGTCTCTGCAGGCTAATTCT 2 17 0 AGGTTCTGCA 0.972232 -284 TTGTCCCTGCCGGCTCTCTGCACAGAATAGAG 2 132 1 CGCTTCTGCA 0.946787 -169 TGCAGATTGGAGATTATCTGGAGGAGGATGAC 2 198 1 AGTTTCTGGA 0.992894 -103 GTTGTTATATACTTTTTCTGCACAGGTCAGCG 3 18 0 ACTTTCTGCA 0.969434 -42 CCTCTGGCAAAGATTCTCTCGAAAACAGGTGT 4 96 0 AGTTTCTCGA 0.981957 -126 TGTTTATCGGAGGTTTTCCCGACCTCTGGCAA 4 118 0 AGTTTCCCGA 0.959019 -104 TCAACCTGTCAGCTTTTCTGGAACTGCAGCTC 5 15 1 AGTTTCTGGA 0.992894 -261 TGCAGCTCAGACAGTATCTGGCAGTATTAAAA 5 39 1 ACGTTCTGGC 0.899814 -237 TATTAAAAAACGGTTTTCCCGCCAGTTCAATG 5 63 1 CGTTTCCCGC 0.893611 -213 GCTTTTAAAGCCTTTTGCTGCAAACGCATTCG 5 192 1 CCTTGCTGCA 0.848156 -84 CAAACGCATTCGTTTTTCAGGATGGTGAAGTA 5 212 1 CGTTTCAGGA 0.953703 -64 ** ** ****** Masking position 5 Map Score: 11.1015 Number of sites scoring better than the average of aligned sites = 473 Number in coding regions = 440 Number in noncoding regions = 33 Number of orfs with sites within 600 bp upstream = 28 Fraction of orfs with sites within 600 bp upstream = 0.00449727 Motif number 2 GTGAACGGTACTGCAAGGATTGTTGTTGATGGGAA 2 65 1 CTGCAGGAGG 0.993717 -236 GAAAGAGATACTGCTGAGGAAGAGAGAGAGCACTT 2 97 1 CTGCTAGGGA 0.675406 -204 TGCAGAGAGCCGGCAGGGACAAAAGTGCTCTCTCT 2 119 0 CGGCAGGAAG 0.969696 -182 TGCCGGCTCTCTGCACAGAATAGAGAACCCCGGAA 2 139 1 CTGCAAGAAG 0.975564 -162 TATACTTTTTCTGCACAGGTCAGCGAGGTGAT 3 8 0 CTGCAAGGAG 0.97431 -52 ATTTCTCCAGCTGCAATGACCGCTGCTGCCCCCAA 4 21 1 CTGCATGAGG 0.987127 -201 CTGCCAGATACTGTCTGAGCTGCAGTTCCAGAAAA 5 28 0 CTGTCGAGGG 0.729871 -248 CATCATTGAACTGGCGGGAAAACCGTTTTTTAATA 5 63 0 CTGGCGGAAG 0.919491 -213 GTGATCCTCTCGGCTTTGGGAGCCGGTGACCCGAG 5 116 0 CGGCTTGGGG 0.912637 -160 TACGGCCCCTCTGTAATGATTAAAGGCAGTGGCTT 5 161 1 CTGTATGAAG 0.932729 -115 GTGTATCTTTCTGTCATGAGGGAGGCAGGATTTAA 5 245 0 CTGTCTGAGG 0.958535 -31 ***** *** * * Masking position 1 Map Score: 8.20717 Number of sites scoring better than the average of aligned sites = 1035 Number in coding regions = 982 Number in noncoding regions = 53 Number of orfs with sites within 600 bp upstream = 38 Fraction of orfs with sites within 600 bp upstream = 0.00610344 Motif number 3 GACACTATCACAGAAGCGAGCACTGGATTG 2 33 1 CAGAAGCGAG 0.967822 -268 TACTGCTGAGGAAGAGAGAGAGCACTTTTG 2 105 1 GAAGAGAGAG 0.866979 -196 GCTCTCTGCACAGAATAGAGAACCCCGGAA 2 144 1 CAGAATAGAG 0.945864 -157 TCAATTATCTCAAGAGGGATTTTTCCGGGG 2 166 0 CAAGAGGGAT 0.827069 -135 AATTGAGGTGCAGATTGGAGATTATCTGGA 2 190 1 CAGATTGGAG 0.968285 -111 ATGACATAGAAAGGTTCGAGGACGATTTTG 2 225 1 AAGGTTCGAG 0.771223 -76 GATTTTGGGAGAGGTTAGAGTTAAAACCGA 2 248 1 GAGGTTAGAG 0.894933 -53 TGATTTAAATCAAATGGGAGTATCTGCTGA 4 157 0 CAAATGGGAG 0.941027 -65 ATTCGTTTTTCAGGATGGTGAAGTATTTAA 5 219 1 CAGGATGGTG 0.936356 -57 ATCTTTCTGTCATGAGGGAGGCAGGATTTA 5 246 0 CATGAGGGAG 0.955879 -30 ********** Masking position 2 Map Score: 6.58619 Number of sites scoring better than the average of aligned sites = 1768 Number in coding regions = 1685 Number in noncoding regions = 83 Number of orfs with sites within 600 bp upstream = 57 Fraction of orfs with sites within 600 bp upstream = 0.00915516 Motif number 4 TTTGTTCAAAAAGAATAAAAAGCTTTTGAGGGA 1 19 0 AAATAAAAGC 0.960221 -32 CCTTATGGGTAATTTTAAATAACTCTCCTTTTA 4 190 1 AATTAAATAC 0.703798 -32 GAAAAATGTTAAAAGGAGAGTTATTTA 4 205 0 AATTAAAAGA 0.818551 -17 AGTATCTGGCAGTATTAAAAAACGGTTTTCCCG 5 51 1 AGTTAAAAAC 0.959848 -225 GCCCCTCTGTAATGATTAAAGGCAGTGGCTTTT 5 165 1 AAATTAAAGC 0.926806 -111 TTGCAGCAAAAGGCTTTAAAAGCCACTGCCTTT 5 182 0 AGTTTAAAGC 0.974544 -94 TGAGGGAGGCAGGATTTAAATACTTCACCATCC 5 231 0 AGTTTAAAAC 0.926142 -45 GCAAATAAATATGCATAAAATGCACACT 6 6 0 ATATAAAAGC 0.88005 -58 GGAAATTTAAAGAATTAAAAAGCTAAAAATTTT 6 41 0 AGTTAAAAGC 0.986478 -23 ** ****** ** Masking position 6 Map Score: 5.78615 Number of sites scoring better than the average of aligned sites = 131 Number in coding regions = 97 Number in noncoding regions = 34 Number of orfs with sites within 600 bp upstream = 43 Fraction of orfs with sites within 600 bp upstream = 0.00690652 Motif number 5 ATCACAGAAGCGAGCACTGGATTGTCGTGA 2 39 1 CGAGCACTGG 0.84245 -262 CGTCGGATTGGGGGCAGCAGCGGTCATTGC 4 33 0 GGGGCAGCAG 0.996301 -189 TAAACAAGTTCTGTCAGCAGATACTCCCAT 4 144 1 CTGTCAGCAG 0.877347 -78 GTTCAATGATGGGGCCGCCGAGATTTGAAC 5 87 1 GGGGCCGCCG 0.987859 -189 ATTTGAACTCGGGTCACCGGCTCCCAAAGC 5 109 1 GGGTCACCGG 0.988024 -167 AAAGCCGAGAGGATCACCAGGCTACCCTAC 5 134 1 GGATCACCAG 0.964477 -142 TCATTACAGAGGGGCCGTAGGGTAGCCTGG 5 150 0 GGGGCCGTAG 0.980222 -126 ********** Masking position 5 Map Score: 4.78002 Number of sites scoring better than the average of aligned sites = 352 Number in coding regions = 315 Number in noncoding regions = 37 Number of orfs with sites within 600 bp upstream = 29 Fraction of orfs with sites within 600 bp upstream = 0.00465789 Motif number 6 ATTTTGACTCCCTCAAAAGCTTTTTATTCT 1 10 1 CCCTCAAAAC 0.982756 -41 GAATAGAGAACCCCGGAAAAATCCCTCTTGA 2 156 1 CCCCGGAAAA 0.886645 -145 ACTCTAACCTCTCCCAAAATCGTCCTCGAAC 2 238 0 CTCCCAAAAC 0.989845 -63 GGCAAAGATTCTCTCGAAAACAGGTGTTTCG 4 92 0 CTCTCGAAAC 0.969473 -130 TCGGGAAAACCTCCGATAAACAAGTTCTGTC 4 128 1 CTCCGATAAC 0.939048 -94 GGGTCACCGGCTCCCAAAGCCGAGAGGATCA 5 119 1 CTCCCAAAGC 0.967734 -157 TACTTCACCATCCTGAAAAACGAATGCGTTT 5 213 0 TCCTGAAAAC 0.849126 -63 ********* * Masking position 8 Map Score: 3.17802 Number of sites scoring better than the average of aligned sites = 502 Number in coding regions = 460 Number in noncoding regions = 42 Number of orfs with sites within 600 bp upstream = 48 Fraction of orfs with sites within 600 bp upstream = 0.0077096 Motif number 7 TCAGCAGTATCTCTTTCCCATCAACAACAA 2 84 0 CTCTTTCCCA 0.992785 -217 AGTGCTCTCTCTCTTCCTCAGCAGTATCTC 2 101 0 CTCTTCCTCA 0.922348 -200 TTTAACTCTAACCTCTCCCAAAATCGTCCT 2 243 0 ACCTCTCCCA 0.96278 -58 TCATTTTAAAATCTTTCCCA 3 50 1 ATCTTTCCCA 0.992216 -10 TTTCGAGAGAATCTTTGCCAGAGGTCGGGA 4 104 1 ATCTTTGCCA 0.973119 -118 ********** Masking position 4 Map Score: 2.94609 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 97 Number in noncoding regions = 10 Number of orfs with sites within 600 bp upstream = 12 Fraction of orfs with sites within 600 bp upstream = 0.0019274 Motif number 8 TCCTTGCAGTACCGTTCACGACAATCCAGTG 2 53 0 ACCTTCACGA 0.937841 -248 TTTCTATGTCATCCTCCTCCAGATAATCTCC 2 206 0 ATCTCCTCCA 0.986922 -95 CTCTCCCAAAATCGTCCTCGAACCTTTCTAT 2 230 0 ATCTCCTCGA 0.981063 -71 GCCCCAGTATATTTCTCCAGCTGCAATGA 4 9 1 ATATTCTCCA 0.968775 -213 CAGGATTTAAATACTTCACCATCCTGAAAAA 5 224 0 ATATTCACCA 0.955855 -52 *** ******* Masking position 5 Map Score: 0.121698 Number of sites scoring better than the average of aligned sites = 107 Number in coding regions = 99 Number in noncoding regions = 8 Number of orfs with sites within 600 bp upstream = 9 Fraction of orfs with sites within 600 bp upstream = 0.00144555 Motif number 9 ********** No masking Map Score: -1.13444e-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: -1.13444e-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 11 ********** No masking Map Score: -1.13444e-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