AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i131_Transmembrane_Transport_5_bsub_reg_100.orf -aORF_bsub.txt -zbsub.fna -g0.435 -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 = 0.435 maxlen = 30 weight = 0.8 exclude = 0 Input sequences: #1 yfiL 143 similar to ABC transporter (ATP-binding protein) #2 yvfT 132 similar to two-component sensor histidine kinase [YvfU] #3 yvfR 283 similar to ABC transporter (ATP-binding protein) Motif number 1 CATAGGGCATGAAAAAAAGGCCTGTAAAAG 1 48 0 GAAAAAAAGG 0.980478 -96 CATTGTAGAAGAAAGAAAGGCGTGCGGCAT 1 94 0 GAAAGAAAGG 0.994414 -50 GGCAATGGATCAAAAAAAGGAGTGAGACGA 1 123 1 CAAAAAAAGG 0.938643 -21 GTATACACCAGAAAGATATAAGGGAAAAAC 2 52 0 GAAAGATATA 0.888816 -81 CTTTCAGCCGGAAAGTAATATAAAGTTCAA 3 20 1 GAAAGTAATA 0.888817 -264 CGAGTGTTATGATAGAAATATTGAACTTTA 3 40 0 GATAGAAATA 0.962582 -244 CTGTGACATTCATAGAAAGATACACTCTTC 3 78 0 CATAGAAAGA 0.939005 -206 ACAGCAGTTTAAAAGAAAGAGGACATGGGA 3 104 1 AAAAGAAAGA 0.925732 -180 GGACATGGGAGATAGAAAAGATGGATGAAT 3 124 1 GATAGAAAAG 0.925756 -160 ACCGGGGTGAGAAAAAAATGACATTTGTCA 3 184 1 GAAAAAAATG 0.962354 -100 ********** Masking position 4 Map Score: 13.8547 Number of sites scoring better than the average of aligned sites = 1347 Number in coding regions = 1086 Number in noncoding regions = 261 Number of orfs with sites within 600 bp upstream = 284 Fraction of orfs with sites within 600 bp upstream = 0.0456152 Motif number 2 AAAGGCCTGTAAAAGGCCTTTTCAGAGAAG 1 33 0 AAAAGGCCTT 0.983752 -111 GGGCATGAAAAAAAGGCCTGTAAAAGGCCT 1 44 0 AAAAGGCCTG 0.991664 -100 GTAGAAGAAAGAAAGGCGTGCGGCATGTAG 1 90 0 GAAAGGCGTG 0.921436 -54 ATGGATCAAAAAAAGGAGTGAGACGAC 1 127 1 AAAAGGAGTG 0.962335 -17 TACATGAAAAAGGCAATATCTATTTTC 2 8 1 AAAAGGCAAT 0.926929 -125 GTTTAAAAGAAAGAGGACATGGGAGATAGA 3 110 1 AAGAGGACAT 0.92044 -174 GATGAATTGGAAGATGCAGGAGGAGGATTG 3 147 1 AAGATGCAGG 0.81168 -137 GGGTGAGAAAAAAATGACATTTGTCACTCC 3 188 1 AAAATGACAT 0.885806 -96 CATTGATTGTAAAATGACGGAGAAGACGAT 3 242 0 AAAATGACGG 0.9427 -42 ********** Masking position 4 Map Score: 8.25548 Number of sites scoring better than the average of aligned sites = 1785 Number in coding regions = 1507 Number in noncoding regions = 278 Number of orfs with sites within 600 bp upstream = 262 Fraction of orfs with sites within 600 bp upstream = 0.0420816 Motif number 3 ATCAAAAAAAGGAGTGAGACGAC 1 131 1 GGAGTGAGAC 0.992101 -13 AAAAGAATCAGGGGTCAAACAGGGGATCGG 2 106 1 GGGGTCAAAC 0.967178 -27 CCTAGACACCGGGGTGAGAAAAAAATGACA 3 177 1 GGGGTGAGAA 0.994564 -107 TCATGATGATGGAGTGACAAATGTCATTTT 3 198 0 GGAGTGACAA 0.987835 -86 ATGTTAGTATGGGGTGTCATGATGATGGAG 3 214 0 GGGGTGTCAT 0.969264 -70 ********** Masking position 5 Map Score: 4.53516 Number of sites scoring better than the average of aligned sites = 68 Number in coding regions = 32 Number in noncoding regions = 36 Number of orfs with sites within 600 bp upstream = 35 Fraction of orfs with sites within 600 bp upstream = 0.00562159 Motif number 4 TTTATTAAAAGAATCAGGGGTCAAACAGGG 2 100 1 GAATCAGGGG 0.99373 -33 AATCAGGGGTCAAACAGGGGATCGGATATG 2 111 1 CAAACAGGGG 0.990893 -22 TGAATTGGAAGATGCAGGAGGAGGATTGCC 3 149 1 GATGCAGGAG 0.959016 -135 GGATTGCCTAGACACCGGGGTGAGAAAAAA 3 171 1 GACACCGGGG 0.976679 -113 TCAATGTAAACGATCAGGAGGTGCTCAT 3 266 1 CGATCAGGAG 0.956053 -18 ********** Masking position 5 Map Score: 2.04738 Number of sites scoring better than the average of aligned sites = 189 Number in coding regions = 149 Number in noncoding regions = 40 Number of orfs with sites within 600 bp upstream = 31 Fraction of orfs with sites within 600 bp upstream = 0.00497912 Motif number 5 GCCCTATGTTCTATCTGCCGCTACATGCCG 1 70 1 CTATCTGCCG 0.996062 -74 CTATCTGCCGCTACATGCCGCACGCCTTTC 1 80 1 CTACATGCCG 0.968775 -64 TCCCTTATATCTTTCTGGTGTATACGATTA 2 57 1 CTTTCTGGTG 0.899727 -76 TGGTGTATACGATTATGCCGTTCCTCTCTT 2 72 1 GATTATGCCG 0.828622 -61 GATTGGCTCCTTTCAGCCGGAAAGTAATA 3 10 1 CTTTCAGCCG 0.984229 -274 TCCATCTTTTCTATCTCCCATGTCCTCTTT 3 119 0 CTATCTCCCA 0.899729 -165 ********** Masking position 6 Map Score: 1.25133 Number of sites scoring better than the average of aligned sites = 1344 Number in coding regions = 1264 Number in noncoding regions = 80 Number of orfs with sites within 600 bp upstream = 77 Fraction of orfs with sites within 600 bp upstream = 0.0123675 Motif number 6 TTTTCAGAGAAGCGTATATGCAAAACGTCA 1 15 0 AGCGTATATG 0.970392 -129 GAACGGCATAATCGTATACACCAGAAAGAT 2 65 0 ATCGTATACA 0.982418 -68 CAAACAGGGGATCGGATATGGT 2 121 1 ATCGGATATG 0.970393 -12 GCACCTCCTGATCGTTTACATTGATTGTAA 3 260 0 ATCGTTTACA 0.956736 -24 ********** Masking position 7 Map Score: 0.202697 Number of sites scoring better than the average of aligned sites = 74 Number in coding regions = 62 Number in noncoding regions = 12 Number of orfs with sites within 600 bp upstream = 2 Fraction of orfs with sites within 600 bp upstream = 0.000321234 Motif number 7 ********** No masking Map Score: 1.81432e-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: 1.81432e-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 9 ********** No masking Map Score: 1.81432e-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