AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_fusions002_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248526
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	APE0919	300	254aa long hypothetical high-affinity branched-chain amino acid transport ATP-binding protein
#1	APE0921	131	237aa long hypothetical high-affinity branched-chain amino acid transport ATP-binding protein
#2	APE1548	145	338aa long hypothetical nodulation ATP-binding protein I
#3	APE2522	168	265aa long hypothetical high-affinity branched-chain amino acid transport permease protein

Motif 1
          CCGAGGAGGGCGGAGTCTCGACA	0	0	1
CCCCGGGTCATCTCCGCGGGCGGCTGGGTTCGC	0	182	1
GTTCTGGAGAGCTACCTGGGTGGGTAGCC    	1	112	1
AGATCAGCTAGCCGGGGGGGTTGCCAGCCTTAG	0	104	0
TCGAAGGGATACACCTCGGGCTGTACGTTATAA	2	97	0
CCGCGGAGATGACCCGGGGGCGTTTAAAAATAG	0	168	0
         CGCTACGAGGGCATAGGCTCCTCC	3	154	0
TTCCTCAGGTCCCGCTAAGGCTGGCAACCCCCC	0	90	1
TTTAAAAATAGCATAGAGGGAGGGAAAAAGGGG	0	146	0
GTAGAGATTGGAAGCTGAGGCTGTAACGTCAGC	3	99	1
TTGTTCAGCACCTCGTCGGGCTTGCCCGACGCT	1	72	0
TATTATCGCGGCTATCAGGGTTGTCGAGACTCC	0	21	0
TCGTGATTCCCACTCTGGGGTAGAGGCTGCGTG	0	275	1
GGACCTGAGGAAGAAGTAGGCGGCAGCAGCTAT	0	69	0
AGCTCTCCAGAACTACGGGGTTGTTCAGCACCT	1	92	0
          **  ** ******
MAP Score: 13.4623

Motif 2
TTAAACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGTTC	0	174	1
CTATCACCTCGAAGGGATACACCTCGGGCTGTACGTTAT	2	99	0
TGAGCATGGGCAAGGTTATAGCGTCGGGCAAGCCCGACG	1	53	1
CTACGGGGTTGTTCAGCACCTCGTCGGGCTTGCCCGACG	1	74	0
AGCTATAGTCGATGGGTTACTCATCGGAGGAGCCTATGC	3	129	1
AGTATGTAGACCGGGTTTACGCTATGAGCATGGGCAAGG	1	29	1
GTCCCGCTAAGGCTGGCAACCCCCCCGGCTAGCTGATCT	0	98	1
AGTAGTTAATCGTGATTCCCACTCTGGGGTAGAGGCTGC	0	266	1
CACCCAGGTAGCTCTCCAGAACTACGGGGTTGTTCAGCA	1	95	0
          *  **    * *  *****
MAP Score: 11.4086

Motif 3
CGAGACTCCGCCCTCCTCGG          	0	0	0
AAGGCTGGCAACCCCCCCGGCTAGCTGATC	0	106	1
CTATTTTTAAACGCCCCCGGGTCATCTCCG	0	168	1
GCGAACCCAGCCGCCCGCGGAGATGACCCG	0	185	0
     GGCTACCCACCCAGGTAGCTCTCCA	1	116	0
TTATAACGTACAGCCCGAGGTGTATCCCTT	2	97	1
          **********
MAP Score: 10.7952

Motif 4
CCGCCTACTTCTTCCTCAGGTCCCGCTAAGGCTGGCAACCCCCCCG	0	79	1
AGGCTGGCAACCCCCCCGGCTAGCTGATCTGTCTTCAATCCCCTTT	0	107	1
ATTTTTAAACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGTTCGCC	0	170	1
AGTTAATCGTGATTCCCACTCTGGGGTAGAGGCTGCGTGTA     	0	269	1
GGGTTGTTCAGCACCTCGTCGGGCTTGCCCGACGCTATAACCTTGC	1	62	0
AGGTGCTGAACAACCCCGTAGTTCTGGAGAGCTACCTGGGTGGGTA	1	92	1
TCGTAAGCCTGCTCCAGTGTTAACTATTCTGTCTCCAAGAGAATGT	2	19	1
AATGTACATTGAACCCCAGATACGGGTCTAGCCAGCTTTATAACGT	2	60	1
GAGGGCATAGGCTCCTCCGATGAGTAACCCATCGACTATAGCTGAC	3	126	0
          *  ** * *    **     * *  *
MAP Score: 9.50181

Motif 5
ACTTCTTCCTCAGGTCCCGCTAAGGCTGGCAACCCCCCCGGCTAGCTG	0	85	1
GGCAACCCCCCCGGCTAGCTGATCTGTCTTCAATCCCCTTTTTCCCTC	0	112	1
CTATTTTTAAACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGTTCGCC	0	168	1
TAGCGTAAACCCGGTCTACATACTCCTTCACAAGCCCTATCCT     	1	5	0
CGGGGTTGTTCAGCACCTCGTCGGGCTTGCCCGACGCTATAACCTTGC	1	62	0
ACTCGTAAGCCTGCTCCAGTGTTAACTATTCTGTCTCCAAGAGAATGT	2	17	1
TGGCTAGACCCGTATCTGGGGTTCAATGTACATTCTCTTGGAGACAGA	2	46	0
CCGCCTATATCAGTGCTAGGCCTTATTAGTCATTCCCACATTTGTTTT	3	10	1
GCTGACGTTACAGCCTCAGCTTCCAATCTCTACACACCATTAACCCAC	3	84	0
ACGAGGGCATAGGCTCCTCCGATGAGTAACCCATCGACTATAGCTGAC	3	126	0
          * *  ** *       *   *   * **
MAP Score: 8.78042

Motif 6
CCCGCTAAGGCTGGCAACCCCCCCGGCTAGCTGATCT	0	100	1
TAAACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGTT	0	175	1
AGTAGTTAATCGTGATTCCCACTCTGGGGTAGAGGCT	0	266	1
GTATGTAGACCGGGTTTACGCTATGAGCATGGGCAAG	1	30	1
GTTATAGCGTCGGGCAAGCCCGACGAGGTGCTGAACA	1	67	1
CCCCGTAGTTCTGGAGAGCTACCTGGGTGGGTAGCC 	1	105	1
          ****    * *  ****
MAP Score: 4.46675

Motif 7
          CCGAGGAGGGCGGAGTCTCGACAA	0	0	1
TAATAGTCATCGTAATAGCTGCTGCCGCCTACTT	0	55	1
AGACAGATCAGCTAGCCGGGGGGGTTGCCAGCCT	0	107	0
TTTAAAAATAGCATAGAGGGAGGGAAAAAGGGGA	0	145	0
TAGAGGCGAACCCAGCCGCCCGCGGAGATGACCC	0	186	0
TCCCACTCTGGGGTAGAGGCTGCGTGTA      	0	282	1
         AGGATAGGGCTTGTGAAGGAGTATG	1	1	1
CCGGGTTTACGCTATGAGCATGGGCAAGGTTATA	1	39	1
GCATGGGCAAGGTTATAGCGTCGGGCAAGCCCGA	1	56	1
ATAGCGTCGGGCAAGCCCGACGAGGTGCTGAACA	1	70	1
CAGCTTTATAACGTACAGCCCGAGGTGTATCCCT	2	92	1
CACTATACAACTCTAGAGGATCGGGGAAAAACAA	3	51	0
CTATAGCTGACGTTACAGCCTCAGCTTCCAATCT	3	103	0
GGTTACTCATCGGAGGAGCCTATGCCCTCGTAGC	3	143	1
          ** ******  * *
MAP Score: 2.54123

Motif 8
         CCGAGGAGGGCGGAGTCTCGACAACCCTGATAGCCG	0	1	1
ACTTCTTCCTCAGGTCCCGCTAAGGCTGGCAACCCCCCCGGCTAG	0	85	1
TAAGGCTGGCAACCCCCCCGGCTAGCTGATCTGTCTTCAATCCCC	0	105	1
CTATTTTTAAACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGTTC	0	168	1
CGGGGTTGTTCAGCACCTCGTCGGGCTTGCCCGACGCTATAACCT	1	65	0
ACTCGTAAGCCTGCTCCAGTGTTAACTATTCTGTCTCCAAGAGAA	2	17	1
AGCTTTATAACGTACAGCCCGAGGTGTATCCCTTCGAGGTGATAG	2	93	1
    CCGCCTATATCAGTGCTAGGCCTTATTAGTCATTCCCACAT	3	6	1
TCGATGGGTTACTCATCGGAGGAGCCTATGCCCTCGTAGCG    	3	137	1
          *    ** * *  * **   *   *
MAP Score: 2.15065

Motif 9
          CCGAGGAGGGCGGAGTCTCG	0	0	1
ATAGCTGCTGCCGCCTACTTCTTCCTCAGG	0	69	1
ATCAGCTAGCCGGGGGGGTTGCCAGCCTTA	0	105	0
GGAGATGACCCGGGGGCGTTTAAAAATAGC	0	167	0
ACCCAGCCGCCCGCGGAGATGACCCGGGGG	0	181	0
TCTCCGCGGGCGGCTGGGTTCGCCTCTATT	0	192	1
TTCAGCACCTCGTCGGGCTTGCCCGACGCT	1	72	0
TCCAGAACTACGGGGTTGTTCAGCACCTCG	1	90	0
GGAGAGCTACCTGGGTGGGTAGCC      	1	117	1
AAGGGATACACCTCGGGCTGTACGTTATAA	2	97	0
          **********
MAP Score: 1.60455

Motif 10
GGAGGGCGGAGTCTCGACAACCCTGATAGCCGCGATAAT	0	14	1
AACCCTGATAGCCGCGATAATAATAATAGTCATCGTAAT	0	32	1
GTAGGCGGCAGCAGCTATTACGATGACTATTATTATTAT	0	48	0
TCTTCCTCAGGTCCCGCTAAGGCTGGCAACCCCCCCGGC	0	88	1
AGACCGGGTTTACGCTATGAGCATGGGCAAGGTTATAGC	1	36	1
GGGCTTGCCCGACGCTATAACCTTGCCCATGCTCATAGC	1	49	0
TAACTATTCTGTCTCCAAGAGAATGTACATTGAACCCCA	2	39	1
CCTCGGGCTGTACGTTATAAAGCTGGCTAGACCCGTATC	2	78	0
GAATTAAAGTGAAGCTATCACCTCGAAGGGATACACCTC	2	113	0
          * *** ** *   **   *
MAP Score: 1.55515

Motif 11
          CCGAGGAGGGCGGAGTCTCG	0	0	1
GATCAGCTAGCCGGGGGGGTTGCCAGCCTT	0	106	0
CGGAGATGACCCGGGGGCGTTTAAAAATAG	0	168	0
ACCCAGCCGCCCGCGGAGATGACCCGGGGG	0	181	0
ATCTCCGCGGGCGGCTGGGTTCGCCTCTAT	0	191	1
GCCTCTACCCCAGAGTGGGAATCACGATTA	0	272	0
TTGTTCAGCACCTCGTCGGGCTTGCCCGAC	1	75	0
TGCTGAACAACCCCGTAGTTCTGGAGAGCT	1	95	1
GGCTACCCACCCAGGTAGCTCTCCAGAACT	1	111	0
GAAGCTATCACCTCGAAGGGATACACCTCG	2	112	0
ATGGGTTACTCATCGGAGGAGCCTATGCCC	3	140	1
GAGCCTATGCCCTCGTAGCG          	3	158	1
          **********
MAP Score: 0.965488

Motif 12
TAATAGTCATCGTAATAGCTGCTGCCGCCTACTT	0	55	1
CGCTAAGGCTGGCAACCCCCCCGGCTAGCTGATC	0	102	1
AACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGT	0	177	1
CCCACTCTGGGGTAGAGGCTGCGTGTA       	0	283	1
GCATGGGCAAGGTTATAGCGTCGGGCAAGCCCGA	1	56	1
CCCAGATACGGGTCTAGCCAGCTTTATAACGTAC	2	74	1
TCACCTCGAAGGGATACACCTCGGGCTGTACGTT	2	101	0
ATCCCTTCGAGGTGATAGCTTCACTTTAATTCTG	2	120	1
TATAGTCGATGGGTTACTCATCGGAGGAGCCTAT	3	132	1
          ***  ** * ****
MAP Score: 0.306577

Motif 13
GCCTACTTCTTCCTCAGGTCCCGCTAAGGCTGGCAACCCCCC	0	81	1
GGGATTGAAGACAGATCAGCTAGCCGGGGGGGTTGCCAGCCT	0	107	0
CTCTATGCTATTTTTAAACGCCCCCGGGTCATCTCCGCGGGC	0	161	1
CCCCGGGTCATCTCCGCGGGCGGCTGGGTTCGCCTCTATTGT	0	182	1
TAATCGTGATTCCCACTCTGGGGTAGAGGCTGCGTGTA    	0	272	1
TAGACCGGGTTTACGCTATGAGCATGGGCAAGGTTATAGCGT	1	35	1
GGTTATAGCGTCGGGCAAGCCCGACGAGGTGCTGAACAACCC	1	66	1
ACCCCGTAGTTCTGGAGAGCTACCTGGGTGGGTAGCC     	1	104	1
TAGCCAGCTTTATAACGTACAGCCCGAGGTGTATCCCTTCGA	2	88	1
ACATTTGTTTTTCCCCGATCCTCTAGAGTTGTATAGTGTGGG	3	47	1
TAATGGTGTGTAGAGATTGGAAGCTGAGGCTGTAACGTCAGC	3	90	1
GGCTGTAACGTCAGCTATAGTCGATGGGTTACTCATCGGAGG	3	117	1
          **       *  ** ****  *
MAP Score: 0.275285