AlignACE 3.0 10/20/99
AlignACE2 -i CT/CT_profile006_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944243496
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	flhA	181	Flagellar Secretion Protein
#1	yscU	256	YopS Translocation Protein U
#2	yscL	275	Yop Translocation L
#3	uvrD	80	DNA Helicase

Motif 1
ACTAATCTTTTCTTTTTCCTTCTGGAGTCC	0	11	0
TTCCTTAGCTCCTACTTTTTTAAATCGGAG	0	117	0
  TTACAGTATCTTTCTCTTGTCTAGTATA	0	163	0
AAGTTGTACAGCTTTTTCTTAAGGCTAACA	1	18	1
GCTAACACAGCCTTTTTATTATTAAGGAAA	1	41	1
CTTTAGAATTTCTTTTTCCTTAATAATAAA	1	55	0
CACTAATCTTGCTTTTTCTTTAGAATTTCT	1	72	0
GAGAACGGAATATTTTTTTTAAAGAGCGTT	1	112	0
CTAAAGAACCCCTTACTCTTTGTTTATAAA	1	141	1
GCATCTGCCACCTTCTTTCTTGAGAAAAAC	1	179	1
ATTTGGTGCTTCTTTTTTTTGTATATATGG	2	42	0
TAGCATTGTAGATTTTTTCTCCGATGGCTA	2	71	1
ACAAGGATCGCATTCTTTTTTACACAGAGA	2	141	0
          **********
MAP Score: 15.158

Motif 2
AATCCCTCTACTCCGATTCTTAACTAATCTTTTCT	0	28	0
GGATTCGAACCCCCGACCTATTGCTCCCAAAGCAA	0	58	1
ATAAGGAATACTTCGCAAGTTACCGTATATAAATG	1	208	0
TAGATTTTTTCTCCGATGGCTATGTTAAAAACGAG	2	79	1
TTTTCCTGACCCTCGATCGCTCTCGTTTTTAACAT	2	100	0
GTCAGGAAAACCTCGATCTCTGTGTAAAAAAGAAT	2	125	1
AGGCAGGGAACCTCGCTCCTTTGCTCGTTACTTTA	2	213	0
GAGCGAGGTTCCCTGCCTGTTGGCTTTGCCAAAGG	2	230	1
GTATATGCATTCTCGAAAATTTTCTTCGAACCCGA	3	36	1
          *******   *  **
MAP Score: 6.20374

Motif 3
TTTAAATCGGAGTATAGCGCAGCCTGGTTAG	0	98	0
TAAGGAAGTTAGCATATTGCCTATATACTAG	0	140	1
AAATGGGATGAGCATCTGCCACCTTCTTTCT	1	168	1
ATAGCGCTTAAGCAACTGGCCATCT      	1	241	1
AAAAAGAAGCACCAAATAGCATTGTAGATTT	2	55	1
GGCTATCCCTAGTAAATGACATGCCTCATCG	2	173	1
TTGGGAATAAAGTAACGAGCAAAGGAGCGAG	2	206	1
          ******* ***
MAP Score: 1.09959