AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_fusions006_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236973
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	glnP	48	ABC Amino Acid Transporter Permease
#1	argR	83	Arginine Repressor
#2	dppF_1	300	Dipeptide Transporter ATPase
#3	CPn0541	300	Solute binding protein
#4	CPn0692	300	ABC Transporter

Motif 1
ACATCTATTCAACCCTCTTTTTGTTTATAT	2	141	1
GTTCGTCTTGAAAATGCTTTCGATGAAATC	2	66	1
GGATTTTTAGAAAATTCTTTCTCTTTTCTT	4	142	1
TCATCTTATCAAACTGCTTTTGTC      	3	286	1
CCCGTCGCGCAAAACTCTTGAATTTATCGT	4	270	0
TGGCTTAAGGAGCACGCTTGGAAAGCGTGT	3	83	0
CGTTAACGCACACACGCTTTCCAAGCGTGC	3	72	1
TCGTCTTTCAAGCCTTCTTTGTTATACTGA	4	193	1
ACGAATCTTCAAGATTCTTTGTATTCTATT	2	247	1
AAGAGCAGTAAACTTGCTTGCAGAAATATA	2	195	1
TTCAATTGAAAACACTATTTCCCTAGTTTA	4	17	0
TTAGAAGACAAAAATTTTTTATTTCCCTAG	4	48	1
TCTTACTATGAGAATTTTTTCCTAAGATCA	3	201	1
          **********
MAP Score: 6.6353

Motif 2
ATAAAAGGCAACGTTTTCTTTTCTTGGTTTTTT 	1	9	0
GCAGCTATTTATTTTTTGTGATGTATCGTCACCA	2	28	1
AGTAGATCAAATGTTGTGTCGTTTGAAATAGAAC	2	105	1
TTCTGCAAGCAAGTTTACTGCTCTTAAAATTTTG	2	186	0
AATCTTCAAGATTCTTTGTATTCTATTTTATATT	2	250	1
GGAAATAAAAAATTTTTGTCTTCTAATTTCAATT	4	40	0
TTTTTAGAAAATTCTTTCTCTTTTCTTCTGGGCT	4	145	1
CTGAAAAAATAATCTGTGTGCTATCTTAGCTTTG	4	219	1
          * *******  * *
MAP Score: 4.81625

Motif 3
CTCTTATGCATATTTATTTATAATGAAATCAT	0	20	0
CGTTTTCTTTTCTTGGTTTTTT          	1	0	0
AAATCGCAGCTATTTATTTTTTGTGATGTATC	2	23	1
TTCGATGAAATCTTGTTGTATAGTAGATCAAA	2	84	1
TATTCAACCCTCTTTTTGTTTATATTAGATAG	2	146	1
TCTTCAAGATTCTTTGTATTCTATTTTATATT	2	252	1
GCCACGCCTCTCCTTTTATTTATGAATATAAA	2	276	0
CTTAGGATATTCGTTCTTTATTAAAATTATGC	3	237	1
AAATAAAAAATTTTTGTCTTCTAATTTCAATT	4	40	0
TTTAGAAAATTCTTTCTCTTTTCTTCTGGGCT	4	147	1
          ***** * ****
MAP Score: 4.21969

Motif 4
GTTTGATAACAAAATTTTAAGAGCAGTAAA	2	177	1
ACGAATCTTCAAGATTCTTTGTATTCTATT	2	247	1
  TACAATTAAAGATTTTATGAAATTGAGG	3	8	1
TCTTACTATGAGAATTTTTTCCTAAGATCA	3	201	1
TTAGAAGACAAAAATTTTTTATTTCCCTAG	4	48	1
CAAGGGAGTTAGGATTTTTAGAAAATTCTT	4	131	1
GGATTTTTAGAAAATTCTTTCTCTTTTCTT	4	142	1
          **********
MAP Score: 3.57868

Motif 5
GAAGTTCGTCTTGAAAATGCTTTCGATGAAATC	2	63	1
TGAAATCTTGTTGTATAGTAGATCAAATGTTGT	2	89	1
CAGAAATATATAGTATTATAGTTTAATGGTTAA	2	215	1
ACAAAGAATCTTGAAGATTCGTTAACCATTAAA	2	236	0
TCAAGATTCTTTGTATTCTATTTTATATTCATA	2	255	1
GTCTTTTTGCCTGGAAAATCTATAAATATGGAG	3	124	0
CACCGCTTCTTAGGATATTCGTTCTTTATTAAA	3	229	1
TATGCCCCAATAGAATAATAGATCATCTTATCA	3	264	1
CTAATTTCAATTGAAAACACTATTTCCCTAGTT	4	19	0
TTAGGATTTTTAGAAAATTCTTTCTCTTTTCTT	4	139	1
          *** * * *****
MAP Score: 2.87373

Motif 6
AGGCAACGTTTTCTTTTCTTGGTTTTTT          	1	0	0
TCTGTTTAAAATCGCAGCTATTTATTTTTTGTGATGTA	2	15	1
CGAAAGCATTTTCAAGACGAACTTCTTGGTGACGATAC	2	50	0
TGAAAATGCTTTCGATGAAATCTTGTTGTATAGTAGAT	2	74	1
TAGAACTTACATCTATTCAACCCTCTTTTTGTTTATAT	2	133	1
ATCTTCAAGATTCTTTGTATTCTATTTTATATTCATAA	2	251	1
CACACACGCTTTCCAAGCGTGCTCCTTAAGCCACTCGG	3	80	1
TTAAGATATGTTCTCGGCAAGTCTTTTTGCCTGGAAAA	3	139	0
CCGAGAACATATCTTAACCTTTCCATTTTTATCAACAT	3	160	1
ATAATAGATCATCTTATCAAACTGCTTTTGTC      	3	278	1
AGGTTCGTCTTTCAAGCCTTCTTTGTTATACTGAAAAA	4	189	1
          ***    * * **  ***
MAP Score: 2.49722

Motif 7
   AAAAAACCAAGAAAAGAAAACGTTGCC	1	7	1
GTCCCCCATACTATAAAAGGCAACGTTTTC	1	25	0
TCAATATGAGCAAGTAAAAGTTACATGGGG	1	58	1
ACATCACAAAAAATAAATAGCTGCGATTTT	2	22	0
TATCTAATATAAACAAAAAGAGGGTTGAAT	2	147	0
TATGAATATAAAATAGAATACAAAGAATCT	2	258	0
TTATATTCATAAATAAAAGGAGAGGCGTGG	2	277	1
        TACAATTAAAGATTTTATGAAA	3	2	1
ATGTTGATAAAAATGGAAAGGTTAAGATAT	3	168	0
AATTATGCCCCAATAGAATAATAGATCATC	3	261	1
CTTCTAATTTCAATTGAAAACACTATTTCC	4	25	0
CATTCTAGGGAAATAAAAAATTTTTGTCTT	4	52	0
GCCCAGAAGAAAAGAGAAAGAATTTTCTAA	4	148	0
          **********
MAP Score: 1.99941

Motif 8
GACTTCTCAATATGAGCAAGTAAAAGTTACATGG	1	52	1
TCACCAAGAAGTTCGTCTTGAAAATGCTTTCGAT	2	56	1
ATACTATATATTTCTGCAAGCAAGTTTACTGCTC	2	197	0
TCGGCAAGTCTTTTTGCCTGGAAAATCTATAAAT	3	130	0
CCCTAGAATGGCTTTGCATGTAAGCGCCTTAGTG	4	72	1
GAGATCACACCATCAGCATGGAATACACTAAGGC	4	97	0
TCTCTTTTCTTCTGGGCTTGAAAGGGGTAGGTTC	4	161	1
AAAGGGGTAGGTTCGTCTTTCAAGCCTTCTTTGT	4	181	1
ATCTTAGCTTTGTCCTCGTGTAATTTAATACGAT	4	241	1
          * ** ** ** ***
MAP Score: 1.70441