AlignACE version 2.2 July 7, 1998 /home/amcguire/bin/alignACE -i060_Diaminopimelate_Pathway_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 asd 125 aspartate-semialdehyde dehydrogenase #2 dapG 91 aspartokinase I (alpha and beta subunits) #3 dapA 30 dihydrodipicolinate synthase #4 ypjD 300 alternate gene name: jojD #5 lysC 175 aspartokinase II alpha subunit (aa 1->408) and beta subunit (aa 246->408) Motif number 1 AAAAAATTCGGTCATCACCCGCATATTCTATGGT 1 36 1 GCATCACCCT 0.994732 -90 ACTCCTTCCGCCAATCAGCTTCATTGAATTGATT 1 95 0 CAATCACTCT 0.860428 -31 AGAGTAAGGCGCTATCAGCCTGCTCTCTTCTGTT 2 41 1 GTATCACCGT 0.969383 -51 TTTATTCACCTCATCATGATTCAATCACAT 3 11 0 CCCTCACAGT 0.959989 -20 TGCCCTTTTCCACATCAGCCCCTC 4 1 0 CCATCACCCC 0.994285 -300 CTGTAAAACCGCCCTCAGCCAGATTGTTCTGCAT 4 54 1 GCCTCACCGT 0.991286 -247 AACGAAACCTCCTATCATCCTCTTACATGTTAGC 4 275 0 CTATCACCCT 0.988209 -26 AGCGCTCTTTCTCCTCACCCGCACGAACCAAAAT 5 135 1 CCCTCACCCC 0.99417 -41 * ***** ** * * Masking position 7 Map Score: 9.36568 Number of sites scoring better than the average of aligned sites = 248 Number in coding regions = 209 Number in noncoding regions = 39 Number of orfs with sites within 600 bp upstream = 26 Fraction of orfs with sites within 600 bp upstream = 0.00417604 Motif number 2 GATAGCGCCTTACTCTCTTCTATTCGTCTTTAGA 2 23 0 TCTCTCTTTT 0.994105 -69 GCTATCAGCCTGCTCTCTTCTGTTACGTCCGAAT 2 51 1 TCTCTCTTTT 0.994105 -41 TTACAGGTATTACACTTTTGCTTTATGCCCTTTT 4 26 0 TCACTTTTTT 0.944297 -275 TAAGCACGTTTGCTGTTTTCTTTTTCATCCACTA 4 215 0 TCTGTTTTTT 0.940113 -86 CCTCCTATCATCCTCTTACATGTTAGCTAATTCA 4 268 0 TCTCTTACTT 0.950729 -33 ATGAGAGGAATACTCTCATTGCTTATCAATTAAT 5 80 0 TCTCTCATTT 0.992338 -96 ATGAGAGTATTCCTCTCATTGCTTTTTTTATTGT 5 95 1 TCTCTCATTT 0.992338 -81 * ******* ** Masking position 6 Map Score: 8.38999 Number of sites scoring better than the average of aligned sites = 158 Number in coding regions = 115 Number in noncoding regions = 43 Number of orfs with sites within 600 bp upstream = 52 Fraction of orfs with sites within 600 bp upstream = 0.00835207 Motif number 3 ATGACCGAATTTTTTAGTTTGGGAAAGATTT 1 20 0 TTTTTATTTG 0.908191 -106 ATGATTTTACGTTTTATTTTACCATAGAATA 1 59 0 GTTTTATTTA 0.908191 -67 TGTTTTCACTCCAAATTATTCGG 2 79 0 TTTTCATCCA 0.934991 -13 CATTTGGCTTGGTTCATTTCAATATGCAGAA 4 80 0 GGTTCATTCA 0.761399 -221 GAGCGGCAATTTTTTCATTTGGCTTGGTTCA 4 95 0 TTTTTCTTTG 0.902451 -206 AAAAACATATTTTTTATTTTAATCGGAGCGG 4 120 0 TTTTTATTTA 0.940455 -181 AAAAATATGTTTTTTAATCTAATTTCTCCAA 4 137 1 TTTTTATCTA 0.944787 -164 ACAAAACCCCTTTTCCTTCCATTAGATAGCG 4 175 1 TTTTCCTCCA 0.930798 -126 TGCTGTTTTCTTTTTCATCCACTATAATATA 4 208 0 TTTTTCTCCA 0.955507 -93 GATGATAGGAGGTTTCGTTCA 4 290 1 GGTTTCTTCA 0.826534 -11 CTCATTGCTTTTTTTATTGTGGACAAAGCGC 5 109 1 TTTTTATGTG 0.752709 -67 ****** **** Masking position 4 Map Score: 7.55406 Number of sites scoring better than the average of aligned sites = 1159 Number in coding regions = 930 Number in noncoding regions = 229 Number of orfs with sites within 600 bp upstream = 257 Fraction of orfs with sites within 600 bp upstream = 0.0412785 Motif number 4 CCCAAACTAAAAAATTCGGTCATCACCCGCA 1 28 1 AAAATTCGTC 0.845553 -98 CTGTAAAACTCCTTCCGCCAATCAG 1 111 0 AAAACTCCTC 0.978144 -15 TCGTCTTTAGAAAATTCTCTCTT 2 3 0 AAAATTCTTC 0.937373 -89 AGAAGAGAGTAAGGCGCTATCAGCCTGCTCT 2 36 1 AAGGCGCTTC 0.939253 -56 AATACCTGTAAAACCGCCCTCAGCCAGATTG 4 49 1 AAACCGCCTC 0.972407 -252 AGCATCACACAAAACCCCTTTTCCTTCCATT 4 167 1 AAAACCCCTT 0.830363 -134 CACTATAATATAAACGCTATCTAATGGAAGG 4 189 0 TAAACGCTTC 0.948517 -112 GCCCTCCAAGAAAATGATTTCTTGACAGCCT 5 20 0 AAAATGATTC 0.784778 -156 TATTGTGGACAAAGCGCTCTTTCTCCTCACC 5 123 1 AAAGCGCTTT 0.927938 -53 ******** ** Masking position 2 Map Score: 2.81148 Number of sites scoring better than the average of aligned sites = 1499 Number in coding regions = 1249 Number in noncoding regions = 250 Number of orfs with sites within 600 bp upstream = 218 Fraction of orfs with sites within 600 bp upstream = 0.0350145 Motif number 5 ********** No masking Map Score: -1.51813e-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 6 ********** No masking Map Score: -1.51813e-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 7 ********** No masking Map Score: -1.51813e-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