AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_fusions005_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236959
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CPn0408	300	CT102 hypothetical protein
#1	CPn0409	60	CT260 hypothetical protein
#2	dnaQ_2	24	DNA Polymerase III Epsilon Chain
#3	uhpC	243	Hexosphosphate Transport
#4	mutS	300	DNA Mismatch Repair

Motif 1
TGCATCCACCGACAGACTGCTGTCGTTTTGTCTATGAA	0	11	1
CAGACTCCTTTATACCCTTCTAGGGTGTGCTCGTTCCA	0	69	0
AGCATCGACTAAAACTATACTTCATTATTACTTGTATG	0	212	1
GAAATACTCCAAGTTGTTCCTAGAGCCTGCATCATTGC	1	28	0
          AATTTCCTTCTACTTCCTCTATCT    	2	6	0
GAGCAGTAAAAATACGCTGTTTTAGTATTTCTTATTTA	3	60	1
AACCAAGAAAAACACTCTACTAATGCATCTTTACTCTC	3	107	1
AACCTGAAACGATTCCCTCCTTGTTTTTTCATCCTTGA	3	147	1
AAATGCGAAGAAAAGCCTACTTTACCATATCAAGGATG	3	176	0
GGCTCGTTCGAAAACTCTACTTTCTTGTATAGTCAAAG	4	170	1
GTATTGAGCTAATTGATTACTGCTTTATTACCGTGGCT	4	222	0
          ** ** ** **    * *
MAP Score: 6.68845

Motif 2
GACAGCAGTCTGTCGGTGGATGCAA     	0	5	0
GCTGTCGTTTTGTCTATGAAAGACAAGAGC	0	29	1
AAGAGCTTGGGCTCTGTGGAACGAGCACAC	0	53	1
GGTATAAAGGAGTCTGTGAATTACCCAAAT	0	91	1
ATCTAGGGGAGCTCTCTAGACGGTACTTGC	0	122	1
CCCGCGATCATCTCTATAAAATTATAGTGG	0	272	0
AATGATGCAGGCTCTAGGAACAACTTGGAG	1	30	1
TCGCATTTCATCTCAGTGAAAAAGATTTTA	3	206	1
ACTGAGGCTGTCTCTCAGGAATTTTAGAGG	4	142	1
          **********
MAP Score: 1.957

Motif 3
TTACCCAAATCATCTAGGGGAGCTCTCTAGA	0	111	1
TATCCAACTACATACAAGTAATAATGAAGTA	0	229	0
GACCCGCGATCATCTCTATAAAATTATAGTG	0	273	0
CCTACTTTACCATATCAAGGATGAAAAAACA	3	168	0
CTTCGCATTTCATCTCAGTGAAAAAGATTTT	3	204	1
CTATTTACAGCATCCCAGGGAAGGATTTACT	4	12	1
TTATTGTTTTCATATCCATTAGGATTCAAAT	4	260	0
          ****** ****
MAP Score: 1.79463

Motif 4
GCTGTCGTTTTGTCTATGAAAGACAAGAGCT	0	29	1
CGGTTTAATCTGTACTTGGAAATCATTGTAC	0	169	1
TATTTTTAATTAAATAAGAAATACTAAAACA	3	77	0
TAATTAAAAATAACCAAGAAAAACACTCTAC	3	96	1
AAAAAGATTTTACACATGGAAATTGAAAG  	3	224	1
CTACCGAGAATTGCCTTGGAATTAATATCCC	4	41	1
TTGCTTTGACTATACAAGAAAGTAGAGTTTT	4	180	0
TGAATCCTAATGGATATGAAAACAATAACGT	4	263	1
          ** ********
MAP Score: 1.76311

Motif 5
ATAGTACAATGATTTCCAAGTACAGATTAA	0	173	0
     CTTTCAATTTCCATGTGTAAAATCT	3	228	0
          AATTTCCTTCTACTTCCTCT	2	14	0
TACTTGCAGGAATATACATGATTACGGTTT	0	145	1
TCCCACTCTAGATTTACAACTGAGGCTGTC	4	124	1
CCCAGGGAAGGATTTACTACCGAGAATTGC	4	25	1
TACTACCGAGAATTGCCTTGGAATTAATAT	4	39	1
TTTAATTAAAAATAACCAAGAAAAACACTC	3	94	1
GGTTGCTTTGACTATACAAGAAAGTAGAGT	4	183	0
ATCGACTAAAACTATACTTCATTATTACTT	0	215	1
          **********
MAP Score: 1.20105

Motif 6
ATCTTTACTCTCGCAACCTGAAACGATTCC	3	133	1
CTGAAACGATTCCCTCCTTGTTTTTTCATC	3	150	1
CGGTAGTAAATCCTTCCCTGGGATGCTGTA	4	17	0
GGAATTAATATCCCATCCTGTTTATCTTTT	4	58	1
CATTCTTAACTCCCACTCTAGATTTACAAC	4	114	1
          **********
MAP Score: 0.665238