AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i243_ecoli_bsub_100.orf -o243_ecoli_bsub_100.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 yhdG 300 putative dehydrogenase #2 fis 25 site-specific DNA inversion stimulation factor; DNA-binding protein; a trans activator for transcription #3 pabB 166 para-aminobenzoate synthase (subunit A) #4 yacF 23 similar to transcriptional regulator (nitrogen regulation protein) Motif number 1 CACAAAAGGCACGTAAATTTGCCGATTATT 1 29 1 ACGTAAATTT 0.940175 -272 CCGATTATTTACGCAAATTTGCGTGCCAAA 1 50 1 ACGCAAATTT 0.992944 -251 TTCTTTATGAATGAAAATTTTGGCACGCAA 1 68 0 ATGAAAATTT 0.886611 -233 TTGAGTAAGTTCTCAATTTTTCTTTATGAA 1 87 0 TCTCAATTTT 0.852338 -214 TTGAGAACTTACTCAAATTTCTTTGAGTGT 1 101 1 ACTCAAATTT 0.983622 -200 GAAAATAGTGACTAAAATTTACACTCAAAG 1 121 0 ACTAAAATTT 0.922035 -180 TTATCGCACCACGCTCATTTTAAATGCAAT 1 175 1 ACGCTCATTT 0.906363 -126 CTCATTTTAAATGCAATTCTTTGATCCATC 1 188 1 ATGCAATTCT 0.849769 -113 GGCGTATATTACGCATTTTTTGCACGAGAT 1 247 0 ACGCATTTTT 0.945135 -54 TGGAAGAGAAATTCACTTTTTTCACTAACA 3 94 1 ATTCACTTTT 0.849801 -73 ********** Masking position 8 Map Score: 11.2874 Number of sites scoring better than the average of aligned sites = 829 Number in coding regions = 683 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 179 Fraction of orfs with sites within 600 bp upstream = 0.0287504 Motif number 2 GTGCCAAAATTTTCATTCATAAAGAAAAATT 1 72 1 TTTCATCATA 0.954717 -229 TGACTAAAATTTACACTCAAAGAAATTTGAG 1 112 0 TTACATCAAA 0.978441 -189 GATCAAAGAATTGCATTTAAAATGAGCGTGG 1 183 0 TTGCATTAAA 0.971223 -118 ATACGCCGCCTTGCAGTCACAGTATGGTCAT 1 270 1 TTGCATCACA 0.989924 -31 AATTCACTTTTTTCACTAACAACATTGCTTT 3 103 1 TTTCATAACA 0.937538 -64 CAACATTGCTTTACAATTAAAAACAAGTAAA 3 122 1 TTACATTAAA 0.958883 -45 ***** ***** Masking position 5 Map Score: 4.95665 Number of sites scoring better than the average of aligned sites = 73 Number in coding regions = 51 Number in noncoding regions = 22 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 3 GCGAAGTGCGAGCAAGCTCACAAAA 1 6 1 GTGCGAGCAA 0.92183 -295 ATCGGCAAATTTACGTGCCTTTTGTGAGCT 1 25 0 TTACGTGCCT 0.979349 -276 TTACGCAAATTTGCGTGCCAAAATTTTCAT 1 58 1 TTGCGTGCCA 0.964173 -243 TGGCCTTTCATCTCGTGCAAAAAATGCGTA 1 238 1 TCTCGTGCAA 0.978952 -63 TTTTTTTATATTTCGTGCATCAAATATGCC 3 41 1 TTTCGTGCAT 0.98613 -126 ********** Masking position 5 Map Score: 3.68452 Number of sites scoring better than the average of aligned sites = 154 Number in coding regions = 137 Number in noncoding regions = 17 Number of orfs with sites within 600 bp upstream = 22 Fraction of orfs with sites within 600 bp upstream = 0.00353357 Motif number 4 TAAATTTGCCGATTATTTACGCAAATTTGCGTGC 1 42 1 GATATTACAA 0.855536 -259 AAGAAAAATTGAGAACTTACTCAAATTTCTTTGA 1 93 1 GAGATTACAA 0.981493 -208 TCATATTAGAAAATAGTGACTAAAATTTACACTC 1 125 0 AAAATGACAA 0.901933 -176 TGATTTTTATGAGTAATTATCGCACCACGCTCAT 1 159 1 GAGATTATCA 0.892538 -142 ATCCATCTCAGAGGATTGGTCAAAGTTTGGCCTT 1 211 1 GAGATGGTAA 0.956285 -90 GAGTTAAGAAATGACCATACTGTGACTGC 1 282 0 AAGATGACTA 0.967898 -19 ACAGAAATAAAGAGCTGACAGAACT 2 10 1 AAGGTGACAA 0.9506 -16 TTTAATTGTAAAGCAATGTTGTTAGTGAAAAAAG 3 109 0 AAGATGTTTA 0.733343 -58 AAAGAAAATAGAGGAATGATACAA 3 153 1 GAGATGATAA 0.988004 -14 *** * **** ** Masking position 7 Map Score: 3.00859 Number of sites scoring better than the average of aligned sites = 490 Number in coding regions = 428 Number in noncoding regions = 62 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 5 AAAAAGCCAAAACTCCCGGTTCGCCGGGA 3 10 1 AAACTCCCGG 0.998237 -157 AAATATAAAAAAACTCCCGGCGAACCGGGA 3 24 0 AAACTCCCGG 0.998237 -143 ********** Masking position 5 Map Score: 1.72086 Number of sites scoring better than the average of aligned sites = 9 Number in coding regions = 6 Number in noncoding regions = 3 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 6 TTGGTCAAAGTTTGGCCTTTCATCTCGTGC 1 226 1 TTTGGCCTTT 0.967007 -75 AACCGGGAGTTTTGGCTTTTT 3 2 0 TTTGGCTTTT 0.96448 -165 AAAAAGTGAATTTCTCTTCCAAGAATAACA 3 85 0 TTTCTCTTCC 0.977115 -82 ATTCCTCTATTTTCTTTTTTACTTGTTTTT 3 140 0 TTTCTTTTTT 0.875325 -27 TTTTTCTCCTCCTTTCATTTGT 4 12 0 TTTCTCCTCC 0.978764 -12 ********** Masking position 3 Map Score: 0.157071 Number of sites scoring better than the average of aligned sites = 610 Number in coding regions = 546 Number in noncoding regions = 64 Number of orfs with sites within 600 bp upstream = 83 Fraction of orfs with sites within 600 bp upstream = 0.0133312 Motif number 7 ********** No masking Map Score: 2.72438e-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: 2.72438e-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 9 ********** No masking Map Score: 2.72438e-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