AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_fusions004_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236924
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	CPn0276	263	CT191 hypothetical protein
#1	CPn0277	146	hypothetical protein
#2	dppF_1	300	Dipeptide Transporter ATPase
#3	gyrB_2	300	DNA Gyrase Subunit B

Motif 1
CGAAGAGGAATTCTTATGATAAAAATCCCT	0	63	0
TTCCTCTTCGTCTTATTGACTTTTTTCGTT	0	83	1
TATAAGAAGTTTCTTTTGATGCAGCATGTT	0	121	1
TCTCTGTTTTTCTTTATGATCAGTTTTTAA	0	164	0
TAAATCTGTGTTTTTGTGATATGCGCTGTG	0	225	1
ACTTGTGCGCTCTTTTTGATCTTATTTCCT	1	26	1
GATCGAAATATTTTATTGAAGGAAATAAGA	1	45	0
ACCCGAAATATTTTATTGAAGGAAAAGAAG	1	79	1
GGGGGTAGATTCTTTATGAGAACTTCTTTT	1	101	0
AGCTATTTATTTTTTGTGATGTATCGTCAC	2	30	1
AAGACGAACTTCTTGGTGACGATACATCAC	2	45	0
TTCGATGAAATCTTGTTGTATAGTAGATCA	2	84	1
TATTCAACCCTCTTTTTGTTTATATTAGAT	2	146	1
ATACAAAGAATCTTGAAGATTCGTTAACCA	2	241	0
CCTCTCCTTTTATTTATGAATATAAAATAG	2	272	0
TTTTGTTGAATTTTTAAGAAGAGCGGATAG	3	272	0
  GTGTGATATTTTGTTGAATTTTTAAGAA	3	282	0
          **********
MAP Score: 13.8789

Motif 2
AAAAGTCAATAAGACGAAGAGGAATTCTTA	0	77	0
ACTGATCATAAAGAAAAACAGAGAAAAGAC	0	170	1
ATCCTACCTGAAGAATAACACAGCGCATAT	0	243	0
TATTTTATTGAAGGAAAAGAAGTTCTCATA	1	87	1
ATCTAATATAAACAAAAAGAGGGTTGAATA	2	146	0
TATAAAATAGAATACAAAGAATCTTGAAGA	2	252	0
TATATTCATAAATAAAAGGAGAGGCGTGGC	2	278	1
TTCCTAATCAAGGAAGAACAAAACACGGGA	3	17	0
TTCCTTGATTAGGAAAAAGAGGTTCGGGTA	3	32	1
TCTGTCCTTAAATGATAAGACTTTAGCGGA	3	98	1
ATACATTCCCAAGACTAAGATCCATAAGTT	3	165	1
ATTTTGCGCCAAGAAAAGGGACAAGCTCAA	3	219	0
ATAGATAAGCAATCAAAAGATTGTCCTATC	3	247	1
TTGAATTTTTAAGAAGAGCGGATAGGACAA	3	267	0
          **********
MAP Score: 10.7706

Motif 3
CTCGTCTTTTCTCTGTTTTTCTTTATGATC	0	173	0
ACATAAAGGTCTCTCAATTTGATAAATCTG	0	203	1
TTTGATAAATCTGTGTTTTTGTGATATGCG	0	220	1
TGTACTTGTGCGCTCTTTTTGATCTTATTT	1	23	1
AATCTACCCCCCCTAATTTTCTACGGTGTA	1	120	1
ATCTATTCAACCCTCTTTTTGTTTATATTA	2	143	1
 AAGCCACGCCTCTCCTTTTATTTATGAAT	2	281	0
TCTTACCCGAACCTCTTTTTCCTAATCAAG	3	35	0
TTGAGCTTGTCCCTTTTCTTGGCGCAAAAT	3	219	1
TTGTCCTATCCGCTCTTCTTAAAAATTCAA	3	267	1
          **********
MAP Score: 9.20051

Motif 4
TGTACTTGTGCGCTCTTTTTGATCTTATTT	1	23	1
TAAAATATTTCGATCTTTTACCCGAAATAT	1	60	1
ATTCTTTATGAGAACTTCTTTTCCTTCAAT	1	93	0
ATTTTCAAGACGAACTTCTTGGTGACGATA	2	51	0
TACATCTATTCAACCCTCTTTTTGTTTATA	2	140	1
GCATCTTACCCGAACCTCTTTTTCCTAATC	3	38	0
TTGTCCTATCCGCTCTTCTTAAAAATTCAA	3	267	1
          **********
MAP Score: 4.6924