AlignACE 3.0 10/20/99
AlignACE2 -i CP/CP_fusions006_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236990
 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
GGCAACGTTTTCTTTTCTTGGTTTTTT         	1	1	0
AAGAAGTTCGTCTTGAAAATGCTTTCGATGAAATCT	2	61	1
TATTCAACCCTCTTTTTGTTTATATTAGATAGTTTG	2	146	1
AGTTTACTGCTCTTAAAATTTTGTTATCAAACTATC	2	173	0
ATACAAAGAATCTTGAAGATTCGTTAACCATTAAAC	2	235	0
TCTTCAAGATTCTTTGTATTCTATTTTATATTCATA	2	252	1
CGAGAACATATCTTAACCTTTCCATTTTTATCAACA	3	161	1
GATCACCGCTTCTTAGGATATTCGTTCTTTATTAAA	3	226	1
TAATAGATCATCTTATCAAACTGCTTTTGTC     	3	279	1
AAAATTTTTGTCTTCTAATTTCAATTGAAAACACTA	4	30	0
TTTAGAAAATTCTTTCTCTTTTCTTCTGGGCTTGAA	4	147	1
CTGTGTGCTATCTTAGCTTTGTCCTCGTGTAATTTA	4	232	1
CGCGCAAAACTCTTGAATTTATCGTATTAAATTACA	4	259	0
          ****    ****  **
MAP Score: 6.63905

Motif 2
    TTGCATAAATATGATTTCATTATAAATA	0	6	1
AGTTCGTCTTGAAAATGCTTTCGATGAAATCT	2	65	1
ATCTACTATACAACAAGATTTCATCGAAAGCA	2	80	0
ATATAAACAAAAAGAGGGTTGAATAGATGTAA	2	139	0
TAAGAGCAGTAAACTTGCTTGCAGAAATATAT	2	194	1
AATAGAATACAAAGAATCTTGAAGATTCGTTA	2	245	0
GCGTTAACGCACACACGCTTTCCAAGCGTGCT	3	71	1
TTTTCCAGGCAAAAAGACTTGCCGAGAACATA	3	139	1
TTTCAATTGAAAACACTATTTCCCTAGTTTAT	4	16	0
AGGATTTTTAGAAAATTCTTTCTCTTTTCTTC	4	141	1
CAGTATAACAAAGAAGGCTTGAAAGACGAACC	4	190	0
TCCCGTCGCGCAAAACTCTTGAATTTATCGTA	4	269	0
          *** * ******
MAP Score: 5.02232

Motif 3
CTATAAAAGGCAACGTTTTCTTTTCTTGGTTTTTT      	1	4	0
TTTAAAATCGCAGCTATTTATTTTTTGTGATGTATCGTCAC	2	19	1
ATAGTAGATCAAATGTTGTGTCGTTTGAAATAGAACTTACA	2	103	1
TACATCTATTCAACCCTCTTTTTGTTTATATTAGATAGTTT	2	140	1
AACGAATCTTCAAGATTCTTTGTATTCTATTTTATATTCAT	2	246	1
AGGGAAATAAAAAATTTTTGTCTTCTAATTTCAATTGAAAA	4	35	0
GATTTTTAGAAAATTCTTTCTCTTTTCTTCTGGGCTTGAAA	4	143	1
TATACTGAAAAAATAATCTGTGTGCTATCTTAGCTTTGTCC	4	215	1
          ***   * * * * **    *
MAP Score: 4.44473

Motif 4
    TTGCATAAATATGATTTCATTATAAATAAATATGCATAAG	0	6	1
AGTTCGTCTTGAAAATGCTTTCGATGAAATCTTGTTGTATAGTA	2	65	1
ATAGTAGATCAAATGTTGTGTCGTTTGAAATAGAACTTACATCT	2	103	1
TAAGAGCAGTAAACTTGCTTGCAGAAATATATAGTATTATAGTT	2	194	1
TGTTCTCGGCAAGTCTTTTTGCCTGGAAAATCTATAAATATGGA	3	125	0
GTCTTACTATGAGAATTTTTTCCTAAGATCACCGCTTCTTAGGA	3	200	1
AAACTAGGGAAATAGTGTTTTCAATTGAAATTAGAAGACAAAAA	4	18	1
AGGGAAATAAAAAATTTTTGTCTTCTAATTTCAATTGAAAACAC	4	32	0
AGGATTTTTAGAAAATTCTTTCTCTTTTCTTCTGGGCTTGAAAG	4	141	1
ATAGCACACAGATTATTTTTTCAGTATAACAAAGAAGGCTTGAA	4	199	0
          **   ** ****     *     *
MAP Score: 4.35036

Motif 5
TTACTTGCTCATATTGAGAAGTCCCCCATAC	1	44	0
TATATTAGATAGTTTGATAACAAAATTTTAA	2	166	1
TGATAACAAAATTTTAAGAGCAGTAAACTTG	2	180	1
ATTCTATTTTATATTCATAAATAAAAGGAGA	2	269	1
CCGTATCCTCAATTTCATAAAATCTTTAATT	3	13	0
ACATCTCTCCATATTTATAGATTTTCCAGGC	3	118	1
TAACCTTTCCATTTTTATCAACATCCGTCTT	3	174	1
TTGGGGCATAATTTTAATAAAGAACGAATAT	3	243	0
 GACAAAAGCAGTTTGATAAGATGATCTATT	3	280	0
GGGAGTTAGGATTTTTAGAAAATTCTTTCTC	4	134	1
          ***** *****
MAP Score: 3.91482

Motif 6
   TTGCATAAATATGATTTCATTATAAATAAATATGC	0	7	1
ACTATAAAAGGCAACGTTTTCTTTTCTTGGTTTTTT  	1	8	0
GTTCGTCTTGAAAATGCTTTCGATGAAATCTTGTTGTA	2	66	1
GCTTTCGATGAAATCTTGTTGTATAGTAGATCAAATGT	2	81	1
ACGAATCTTCAAGATTCTTTGTATTCTATTTTATATTC	2	247	1
TGTTCTCGGCAAGTCTTTTTGCCTGGAAAATCTATAAA	3	131	0
GTCTTACTATGAGAATTTTTTCCTAAGATCACCGCTTC	3	200	1
CGCTTCTTAGGATATTCGTTCTTTATTAAAATTATGCC	3	232	1
TTCAATTGAAAACACTATTTCCCTAGTTTATTGCTGT 	4	9	0
TAGGGAAATAAAAAATTTTTGTCTTCTAATTTCAATTG	4	39	0
TATTTCCCTAGAATGGCTTTGCATGTAAGCGCCTTAGT	4	67	1
GGATTTTTAGAAAATTCTTTCTCTTTTCTTCTGGGCTT	4	142	1
TAGCACACAGATTATTTTTTCAGTATAACAAAGAAGGC	4	204	0
          ** * * ****  *   *
MAP Score: 2.92685

Motif 7
  ATGCGTCTGTTTAAAATCGCAGCTATTTA	2	8	1
AAGAAGTTCGTCTTGAAAATGCTTTCGATGA	2	61	1
ATGTTGTGTCGTTTGAAATAGAACTTACATC	2	115	1
ATTAAAGATTTTATGAAATTGAGGATACGGA	3	14	1
TAAGGAGCACGCTTGGAAAGCGTGTGTGCGT	3	77	0
GAATGGCTTTGCATGTAAGCGCCTTAGTGTA	4	77	1
CACACCATCAGCATGGAATACACTAAGGCGC	4	95	0
TTTCTTCTGGGCTTGAAAGGGGTAGGTTCGT	4	166	1
AACAAAGAAGGCTTGAAAGACGAACCTACCC	4	185	0
          ********* *
MAP Score: 2.86543

Motif 8
TAAAAGGAGAGGCGTGGCTT          	2	290	1
GGATACGGAGAGAGTGGGATTCGAACCCAC	3	36	1
GTTAACGCGTACCGTGGGTTCGAATCCCAC	3	49	0
GAGAGATGTCCGAGTGGCTTAAGGAGCACG	3	97	0
TTATTTCCCTAGAATGGCTTTGCATGTAAG	4	66	1
TCACACCATCAGCATGGAATACACTAAGGC	4	97	0
          **********
MAP Score: 0.972034