AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i078_Lipopolysaccharide_Biosynthesis_3_bbur_reg_100.orf -o078_borburg_100.ace -a/home/amcguire/genomes/ORF_borburg.txt -z/home/amcguire/genomes/borburg.fna -g0.28 -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 = 0.28 maxlen = 30 weight = 0.8 exclude = 1 Input sequences: #1 RBB00314 240 3615 #2 RBB00313 90 3615 #3 RBB00312 91 3615 #4 RBB00307 45 3615 Motif number 1 TTGTTTAAAATAATTTTTGATTCTTCAATTAAGT 1 11 0 TTTTTATTCT 0.957213 -230 TGATAAATTATTTGGTTCAATTGTTTAAAATAAT 1 31 0 TGGTTATTGT 0.929891 -210 TAGGTTGTTTTTTTGTTGTATTTTTGATAAATTA 1 55 0 TTGTTATTTT 0.989001 -186 CAAGTAAATATCTTGTTAAATTGTAGGTTGTTTT 1 78 0 TTGTTATTGT 0.988248 -163 GATTGTTTAATTGTATTTAATACTATATGATGCA 1 110 0 TTATTATACT 0.877785 -131 AGTAGTAAGCTACTGTTTGATTGTTTAATTGTAT 1 128 0 TTGTTATTGT 0.988248 -113 AAGATTTTGTGGATTTTGTATTTTTATTTTTTAT 1 179 0 GTTTTATTTT 0.962387 -62 TCCTTATATATTCTATTACATTTTATCTTAATAA 1 211 0 TTATTATTTT 0.978618 -30 GTTATTAATGCTATTTTGAATATTAAAATAAGCT 2 16 1 CTTTTATATT 0.753956 -75 GCTTTTCTAGGTTTATTCAATATTGTTTTTTGCA 2 47 1 GTATTATATT 0.891475 -44 ATTCAATATTGTTTTTTGCATTGTGGTATAAAAA 2 61 1 GTTTTATTGT 0.959885 -30 TATACCATGTTAGTGTTTAATTTGTAGCTTGGCA 3 38 1 TTGTTATTTG 0.934135 -54 TGGGCTTGCTTTGTATTGAATTTTAAAGAGGAAT 4 16 1 TTATTATTTT 0.978618 -30 * **** ***** Masking position 10 Map Score: 19.013 Number of sites scoring better than the average of aligned sites = 1062 Number in coding regions = 692 Number in noncoding regions = 370 Number of orfs with sites within 600 bp upstream = 70 Fraction of orfs with sites within 600 bp upstream = 0.0112432 Motif number 2 TTGAAGAATCAAAAATTATTTTAAACAATT 1 17 1 AAAAATTATT 0.724881 -224 AAAAATTATTTTAAACAATTGAACCAAATA 1 27 1 TTAAACAATT 0.769554 -214 TGTATTTTTGATAAATTATTTGGTTCAATT 1 43 0 ATAAATTATT 0.774961 -198 CTACAATTTAACAAGATATTTACTTGCATC 1 86 1 ACAAGATATT 0.592435 -155 TACTTGCATCATATAGTATTAAATACAATT 1 106 1 ATATAGTATT 0.672495 -135 ATATAGTATTAAATACAATTAAACAATCAA 1 116 1 AAATACAATT 0.920349 -125 CTATATATCTATAAAAAATAAAAATACAAA 1 169 1 ATAAAAAATA 0.650126 -72 TTTTATCTTAATAAGATTTTGTGGATTTTG 1 195 0 ATAAGATTTT 0.506288 -46 GCCTCCTTATATATTCTATTACATTTTATC 1 218 0 ATATTCTATT 0.813338 -23 AGTGAGTTATTAATGCTATTTTGAATATTA 2 11 1 TAATGCTATT 0.682233 -80 GAATATTAAAATAAGCTTTTCTAGGTTTAT 2 33 1 ATAAGCTTTT 0.761746 -58 CCACAATGCAAAAAACAATATTGAATAAAC 2 57 0 AAAAACAATA 0.848408 -34 GCATTGTGGTATAAAAAATTGAT 2 78 1 ATAAAAAATT 0.851577 -13 TATAGCATATAAATGCAATTGTCAATAATA 3 12 0 AAATGCAATT 0.899137 -80 AATTGCATTTATATGCTATACCATGTTAGT 3 22 1 ATATGCTATA 0.86054 -70 CTCCTCCATTAAAAACAATTTTATGCTGCC 3 68 0 AAAAACAATT 0.940339 -24 TTCCTCTTTAAAATTCAATACAAAGCAAGC 4 19 0 AAATTCAATA 0.496815 -27 ********** Masking position 3 Map Score: 13.0494 Number of sites scoring better than the average of aligned sites = 2358 Number in coding regions = 1601 Number in noncoding regions = 757 Number of orfs with sites within 600 bp upstream = 141 Fraction of orfs with sites within 600 bp upstream = 0.022647 Motif number 3 TGTAGGTTGTTTTTTTGTTGTATTTTTGAT 1 61 0 TTTTTTGTTG 0.952973 -180 TCTTGTTAAATTGTAGGTTGTTTTTTTGTT 1 72 0 TTGTAGGTTG 0.984967 -169 GATTTTGTATTTTTATTTTTTATAGATATA 1 172 0 TTTTATTTTT 0.83613 -69 TTCTATTACATTTTATCTTAATAAGATTTT 1 205 0 TTTTATCTTA 0.817379 -36 AAATAAGCTTTTCTAGGTTTATTCAATATT 2 41 1 TTCTAGGTTT 0.86958 -50 TTATTCAATATTGTTTTTTGCATTGTGGTA 2 59 1 TTGTTTTTTG 0.892111 -32 AGTGTTTAATTTGTAGCTTGGCAGCATAAA 3 49 1 TTGTAGCTTG 0.971628 -43 TTAAAAACAATTTTATGCTGCCAAGCTACA 3 60 0 TTTTATGCTG 0.936315 -32 ********** Masking position 4 Map Score: 4.63696 Number of sites scoring better than the average of aligned sites = 424 Number in coding regions = 293 Number in noncoding regions = 131 Number of orfs with sites within 600 bp upstream = 27 Fraction of orfs with sites within 600 bp upstream = 0.00433665 Motif number 4 ********** No masking Map Score: 2.79544e-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 5 ********** No masking Map Score: 2.79544e-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 6 ********** No masking Map Score: 2.79544e-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