AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_operons038_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944238674
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CPn0148	171	S/T Protein Kinase
#1	polA	23	DNA Polymerase I
#2	sohB	123	Protease
#3	uvrD	102	DNA Helicase

Motif 1
AGTATTTTAACTGTAGGTTTTTCCTTCCGTTGTT	0	34	1
TCTAGTTATTCTTGAGGTTCTTTTAAAACAACGG	0	60	0
TCAAGAATAACTAGAGGTTCTTGTTTGTTTATTG	0	79	1
GTTTATTGCAATCTTCGTTTTTGCTATCTATAGT	0	105	1
GATAGAAAAACTCTGTGTTATTCTCGGTGAGCAT	2	13	1
TAATTTTCATCTTTAAGCTTTTCTGCTCATCCCT	2	57	1
    AACGACCTATAAATTCTAGTAAATTCTAAA	2	103	0
   AAATCACCTTTCTATAATTGTGATGAAAGTA	3	7	1
AGTATACTCGCTTTTTATTTTAGCTCGACAGAGA	3	37	1
          ** *  *** ****
MAP Score: 8.33987

Motif 2
          ATTTTTTATCTAACCTACTA	0	0	1
TAACTGTAGGTTTTTCCTTCCGTTGTTTTA	0	41	1
CTTGTTTGTTTATTGCAATCTTCGTTTTTG	0	98	1
CAATCTTCGTTTTTGCTATCTATAGTTAAC	0	113	1
TAACACAGAGTTTTTCTATCAAC       	2	3	0
AGAATTTTATAATTTTCATCTTTAAGCTTT	2	48	1
TGCTCATCCCTTATTTTATCCATTTTAGAA	2	80	1
AAAGCGAGTATACTTTCATCACAATTATAG	3	21	0
TACTCGCTTTTTATTTTAGCTCGACAGAGA	3	41	1
AATAAGTCCTAATTTTTAGCTTTACACCTC	3	82	0
          **********
MAP Score: 7.89071

Motif 3
         ATTTTTTATCTAACCTACTAA	0	1	1
ACTAAGTTAGTATTTTAACTGTAGGTTTTT	0	26	1
CCTCTAGTTATTCTTGAGGTTCTTTTAAAA	0	66	0
CCTCAAGAATAACTAGAGGTTCTTGTTTGT	0	77	1
CGTTTTTGCTATCTATAGTTAACTTATATA	0	120	1
TGCCTTATATTTATATAAGTTAACTATAGA	0	131	0
AGCATGAGAATTTTATAATTTTCATCTTTA	2	42	1
ATTTTATCCATTTTAGAATTTACTAGAATT	2	92	1
TTTTAGAATTTACTAGAATTTATAGGTCGT	2	102	1
 AAATCACCTTTCTATAATTGTGATGAAAG	3	9	1
ACTCGCTTTTTATTTTAGCTCGACAGAGAT	3	42	1
ATAAGTCCTAATTTTTAGCTTTACACCTCG	3	81	0
          **********
MAP Score: 6.88135

Motif 4
          ATTTTTTATCTAACCTACTAA	0	0	1
CTAAGTTAGTATTTTAACTGTAGGTTTTTCC	0	27	1
TTTAACTGTAGGTTTTTCCTTCCGTTGTTTT	0	39	1
TGCAATCTTCGTTTTTGCTATCTATAGTTAA	0	111	1
ATATTTATATAAGTTAACTATAGATAGCAAA	0	124	0
AAATGGTGGAGAGTTAGCTCT          	0	160	1
AATAACACAGAGTTTTTCTATCAAC      	2	4	0
GAGCATGAGAATTTTATAATTTTCATCTTTA	2	41	1
CTCATCCCTTATTTTATCCATTTTAGAATTT	2	82	1
AAGTATACTCGCTTTTTATTTTAGCTCGACA	3	36	1
TAAGTCCTAATTTTTAGCTTTACACCTCGAG	3	79	0
          ********* *
MAP Score: 0.521776