AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i054_Arginine_Biosynthesis_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 argC 206 N-acetylglutamate gamma-semialdehyde dehydrogenase #2 carA 70 carbamoyl-phosphate transferase-arginine (subunit A) #3 argG 169 argininosuccinate synthase Motif number 1 GTCAGCCTGTTTTTTTATGCGGCTGAAATG 1 15 1 TTTTTTATGC 0.984402 -192 CCGCATCAACGTTTTTGTGCTGGAGTCGTG 1 50 1 GTTTTTGTGC 0.934249 -157 GTCGTGCTGATTTTTTTTGAGCGGAATTCC 1 74 1 TTTTTTTTGA 0.765413 -133 TATATTTAATATTTTTATTCATTTATAAAT 1 117 0 ATTTTTATTC 0.986988 -90 GATTGAATTAATTTTTATTCATGTTATAAT 1 148 1 ATTTTTATTC 0.986988 -59 ATAAAAATGAATTTTTATGCCTTTATATCG 2 19 0 ATTTTTATGC 0.991757 -52 ATAAAAATTCATTTTTATAATTAATTATTC 2 31 1 ATTTTTATAA 0.955361 -40 AAGTTTCATAGTATTTATTCAT 3 3 0 GTATTTATTC 0.845077 -167 AGGTGAAGTTTTTTTTATAAAAGGCTTGAA 3 45 1 TTTTTTATAA 0.918189 -125 TACAAAATGTATTTTTATTAAATATAATTT 3 106 1 ATTTTTATTA 0.965361 -64 AATATAATTTATTTTTATACAAAATAGAAA 3 126 1 ATTTTTATAC 0.983122 -44 ********** Masking position 5 Map Score: 21.925 Number of sites scoring better than the average of aligned sites = 594 Number in coding regions = 444 Number in noncoding regions = 150 Number of orfs with sites within 600 bp upstream = 163 Fraction of orfs with sites within 600 bp upstream = 0.0261805 Motif number 2 TTTAATATTTTTATTCATTTATAAATTTTC 1 113 0 TTATTCATTT 0.744395 -94 ATGAATAAAAATATTAAATATACGATTGAA 1 125 1 ATATTAAATA 0.701769 -82 ACATGAATAAAAATTAATTCAATCGTATAT 1 142 0 AAATTAATTC 0.602514 -65 GGTCTTTGTGAAATTATTTAACATTATAAC 1 170 0 AAATTATTTA 0.684845 -37 AAAGGCATAAAAATTCATTTTTATAATTAA 2 25 1 AAATTCATTT 0.613267 -46 TTCATTTTTATAATTAATTATTCATCAAGA 2 38 1 TAATTAATTA 0.497714 -33 TATTTAATAAAAATACATTTTGTATGTATA 3 100 0 AAATACATTT 0.847661 -70 TTTTGTATAAAAATAAATTATATTTAATAA 3 120 0 AAATAAATTA 0.679708 -50 ********** Masking position 3 Map Score: 4.33122 Number of sites scoring better than the average of aligned sites = 599 Number in coding regions = 453 Number in noncoding regions = 146 Number of orfs with sites within 600 bp upstream = 151 Fraction of orfs with sites within 600 bp upstream = 0.0242531 Motif number 3 AAATCAGCACGACTCCAGCACAAAAACGTT 1 57 0 GACTCCAGCA 0.895887 -150 CCGCTCAAAAAAAATCAGCACGACTCCAGC 1 68 0 AAAATCAGCA 0.919987 -139 TGTTCAATGGGAATTCCGCTCAAAAAAAAT 1 83 0 GAATTCCGCT 0.957136 -124 AACAAGTTCACCCTCTTGGTCTT 1 194 0 AAGTTCACCC 0.944765 -13 AATACTATGAAACTTCACCTGAAATTTAGG 3 18 1 AACTTCACCT 0.990236 -152 TTATAAAAAAAACTTCACCTAAATTTCAGG 3 35 0 AACTTCACCT 0.990236 -135 GATAAAAATCCCCTCTCAACCGTG 3 156 0 AAAATCCCCT 0.949903 -14 ********** Masking position 2 Map Score: 4.09521 Number of sites scoring better than the average of aligned sites = 518 Number in coding regions = 421 Number in noncoding regions = 97 Number of orfs with sites within 600 bp upstream = 94 Fraction of orfs with sites within 600 bp upstream = 0.015098 Motif number 4 GTTAAATAATTTCACAAAGACCAAGAGGGT 1 178 1 TTCACAAAGA 0.974172 -29 TAATTAATTATTCATCAAGAGGTGGGCTGT 2 48 1 TTCATCAAGA 0.974172 -23 ACTATGAAACTTCACCTGAAATTTAGGTGA 3 21 1 TTCACCTGAA 0.891531 -149 TAAAAAAAACTTCACCTAAATTTCAGGTGA 3 32 0 TTCACCTAAA 0.965618 -138 TTTCAAGCCTTTTATAAAAAAAACTTCACC 3 46 0 TTTATAAAAA 0.753777 -124 TAAATTATATTTAATAAAAATACATTTTGT 3 107 0 TTAATAAAAA 0.841272 -63 ********** Masking position 4 Map Score: 2.03833 Number of sites scoring better than the average of aligned sites = 750 Number in coding regions = 635 Number in noncoding regions = 115 Number of orfs with sites within 600 bp upstream = 133 Fraction of orfs with sites within 600 bp upstream = 0.021362 Motif number 5 CGCATAAAAAAACAGGCTGACCGCG 1 6 0 AACAGGCTGA 0.966349 -201 CTGTTTTTTTATGCGGCTGAAATGCGGCAC 1 21 1 ATGCGGCTGA 0.983049 -186 CTCCAGCACAAAAACGTTGATGCGGTGCCG 1 45 0 AAAACGTTGA 0.911857 -162 AATATTAAATATACGATTGAATTAATTTTT 1 134 1 ATACGATTGA 0.885044 -73 CACAAAGACCAAGAGGGTGAACTTGTT 1 190 1 AAGAGGGTGA 0.966348 -17 CAAAATAGAAACACGGTTGAGAGGGGATTT 3 145 1 ACACGGTTGA 0.976343 -25 ********** Masking position 8 Map Score: 1.90478 Number of sites scoring better than the average of aligned sites = 1080 Number in coding regions = 987 Number in noncoding regions = 93 Number of orfs with sites within 600 bp upstream = 74 Fraction of orfs with sites within 600 bp upstream = 0.0118856 Motif number 6 ********** No masking Map Score: -8.6443e-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: -8.6443e-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: -8.6443e-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