AlignACE 3.0 10/20/99
AlignACE2 -i WIT_ctrl_PID012_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	943390988
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	potF	300	periplasmic putrescine-binding protein; permease protein
#1	potA	249	ATP-binding component of spermidine/putrescine transport

Motif 1
  ATTATCTGCTGTTTTTAACCTTTTCTTA	0	8	1
TGTTTTTAACCTTTTCTTAAAGATTATTTC	0	19	1
TGTTAAATACCGTTTTTTAATCCGAGCTAT	0	103	1
AGAAAGTTCTCTTTTCTTACACCGCGCCGA	0	197	1
AAAATATGCACGTTTATTGCATATCTTTCA	0	230	1
AACTTTTGTTCGTTTGTTAACGAACTTTCA	0	267	1
GTCACCCTCACTTTTTGTGACAACATTATT	1	13	1
CAATATTTGTCTTTTCTTGCTTCTTAATAA	1	38	0
          **********
MAP Score: 8.72241

Motif 2
AGGGTTTGAGACTATAGCTCGGATTAAAAAAC	0	114	0
CGCAAGAATAACTTTAGCCAGGGTTTGAGACT	0	133	0
AGAAAAGAGAACTTTCTCCCGGCCAGCACTGC	0	182	0
AAACGTGCATATTTTTTATCGGCGCGGTGTAA	0	213	0
CAGTGTGACAACTTTTGTTCGTTTGTTAACGA	0	258	1
GCGTCAGGTCACTTTTACCCCTGCAAGCGGGA	1	67	1
          *****  *****
MAP Score: 2.00575

Motif 3
TTATCTGCTGTTTTTAACCTTTTCTTAAAGATTATTTCA	0	11	1
TATGTGATAAAGCCAAATCGACACAAGAGAAGTGAAATA	0	43	0
TAAATACCGTTTTTTAATCCGAGCTATAGTCTCAAACCC	0	106	1
CGAGCTATAGTCTCAAACCCTGGCTAAAGTTATTCTTGC	0	125	1
CTGCTCGCTATATAAAAGCATCGCAAGAATAACTTTAGC	0	147	0
AGTTCTCTTTTCTTACACCGCGCCGATAAAAAATATGCA	0	201	1
AAGTTGTCACACTGAAAGATATGCAATAAACGTGCATAT	0	233	0
CTGAAAGTTCGTTAACAAACGAACAAAAGTTGTCACACT	0	259	0
AGCGGGAATATTTATCAGCATTACCTTAATGAATATAAA	1	92	1
          * * *** *    * * **
MAP Score: 1.55252

Motif 4
  ATTATCTGCTGTTTTTAACCTTTTCTTAAAGATTAT	0	8	1
TTCTTAAAGATTATTTCACTTCTCTTGTGTCGATTTGG	0	32	1
ATTTAACAAATTTTTATGCATATTTGCTCTATGTGATA	0	73	0
GCATAAAAATTTGTTAAATACCGTTTTTTAATCCGAGC	0	92	1
GCTAAAGTTATTCTTGCGATGCTTTTATATAGCGAGCA	0	147	1
ATATGCACGTTTATTGCATATCTTTCAGTGTGACAACT	0	233	1
TTTTGTTCGTTTGTTAACGAACTTTCAGAAGGAAAGAG	0	270	1
          ** **    * ****  *
MAP Score: 1.51655

Motif 5
GCAAGAATAACTTTAGCCAGGGTTTGAGACTATAGC	0	128	0
CATATCTTTCAGTGTGACAACTTTTGTTCGTTTGTT	0	249	1
TAAGAAGCAAGAAAAGACAAATATTGCGTCAGGTCA	1	42	1
TGAATATAAAGCTAAGCCAGTAATTCACAACAAAGA	1	121	1
CAAACCGCTTGAATCGCCAATCTTTGTTGTGAATTA	1	141	0
ACCCCGCATCGGTAAGCCATCCGTTGCGTTTAC   	1	226	1
          * * *****    ***
MAP Score: 1.41121