AlignACE 3.0 10/20/99
AlignACE2 -i AP/AP_fusions002_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248510
 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
CGTCGGGCTTGCCCGACGCTATAACCTTGC	1	62	0
GAACCCAGCCGCCCGCGGAGATGACCCGGG	0	183	0
CGTCGGGCAAGCCCGACGAGGTGCTGAACA	1	74	1
ATAACGTACAGCCCGAGGTGTATCCCTTCG	2	99	1
AGACAGATCAGCTAGCCGGGGGGGTTGCCA	0	111	0
CGACAACCCTGATAGCCGCGATAATAATAA	0	28	1
TATAAAGCTGGCTAGACCCGTATCTGGGGT	2	72	0
GCCTAGCACTGATATAGGCGG         	3	1	0
CCCACTCTGGGGTAGAGGCTGCGTGTA   	0	283	1
TCGAGACTCCGCCCTCCTCGG         	0	1	0
TGTAACGTCAGCTATAGTCGATGGGTTACT	3	120	1
 CGCTACGAGGGCATAGGCTCCTCCGATGA	3	149	0
ATTTTTAAACGCCCCCGGGTCATCTCCGCG	0	170	1
CAAAAATAACAATAGAGGCGAACCCAGCCG	0	202	0
AGAAGTAGGCGGCAGCAGCTATTACGATGA	0	61	0
          **********
MAP Score: 10.7868

Motif 2
GGCGGAGTCTCGACAACCCTGATAGCCGCGATAA	0	18	1
ACCTGAGGAAGAAGTAGGCGGCAGCAGCTATTAC	0	66	0
GCTAGCCGGGGGGGTTGCCAGCCTTAGCGGGACC	0	97	0
GAAGACAGATCAGCTAGCCGGGGGGGTTGCCAGC	0	109	0
AACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGT	0	177	1
TAACAATAGAGGCGAACCCAGCCGCCCGCGGAGA	0	192	0
ATGCTCATAGCGTAAACCCGGTCTACATACTCCT	1	26	0
GCACCTCGTCGGGCTTGCCCGACGCTATAACCTT	1	64	0
ACGAGGTGCTGAACAACCCCGTAGTTCTGGAGAG	1	89	1
TAGTTCTGGAGAGCTACCTGGGTGGGTAGCC   	1	110	1
CCCAGATACGGGTCTAGCCAGCTTTATAACGTAC	2	74	1
AGCTTTATAACGTACAGCCCGAGGTGTATCCCTT	2	93	1
          ** ****** *  *
MAP Score: 10.7689

Motif 3
GCCTTAGCGGGACCTGAGGAAGAAGTAGGCGGCAGCAGCTATT	0	68	0
GTCCCGCTAAGGCTGGCAACCCCCCCGGCTAGCTGATCTGTCT	0	98	1
CCAGCCGCCCGCGGAGATGACCCGGGGGCGTTTAAAAATAGCA	0	166	0
  TACACGCAGCCTCTACCCCAGAGTGGGAATCACGATTAACT	0	269	0
CTACGGGGTTGTTCAGCACCTCGTCGGGCTTGCCCGACGCTAT	1	70	0
CCGTAGTTCTGGAGAGCTACCTGGGTGGGTAGCC         	1	107	1
CTTGGAGACAGAATAGTTAACACTGGAGCAGGCTTACGAGTAT	2	15	0
TTATAAAGCTGGCTAGACCCGTATCTGGGGTTCAATGTACATT	2	60	0
CTATCACCTCGAAGGGATACACCTCGGGCTGTACGTTATAAAG	2	95	0
GTGGGTTAATGGTGTGTAGAGATTGGAAGCTGAGGCTGTAACG	3	84	1
AGCTATAGTCGATGGGTTACTCATCGGAGGAGCCTATGCCCTC	3	129	1
          *    *   *    *****  **
MAP Score: 10.4689

Motif 4
TAATAATAGTCATCGTAATAGCTGCTGCCGCCTACTTCTTCCTCA	0	52	1
GTCCCGCTAAGGCTGGCAACCCCCCCGGCTAGCTGATCTGTCTTC	0	98	1
TTAAACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGTTCGCCTCT	0	174	1
TGAGCATGGGCAAGGTTATAGCGTCGGGCAAGCCCGACGAGGTGC	1	53	1
CTACGGGGTTGTTCAGCACCTCGTCGGGCTTGCCCGACGCTATAA	1	68	0
 GGCTACCCACCCAGGTAGCTCTCCAGAACTACGGGGTTGTTCAG	1	97	0
AAGCCTGCTCCAGTGTTAACTATTCTGTCTCCAAGAGAATGTACA	2	23	1
CTATCACCTCGAAGGGATACACCTCGGGCTGTACGTTATAAAGCT	2	93	0
AGCTATAGTCGATGGGTTACTCATCGGAGGAGCCTATGCCCTCGT	3	129	1
          *   ** * * *  * * *     *
MAP Score: 9.22985

Motif 5
AGGGCGGAGTCTCGACAACCCTGATAGCCGCGATAATAATA	0	16	1
CCCGCTAAGGCTGGCAACCCCCCCGGCTAGCTGATCTGTCT	0	100	1
TAAACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGTTCGCC	0	175	1
GTATGTAGACCGGGTTTACGCTATGAGCATGGGCAAGGTTA	1	30	1
GTTATAGCGTCGGGCAAGCCCGACGAGGTGCTGAACAACCC	1	67	1
CCCCGTAGTTCTGGAGAGCTACCTGGGTGGGTAGCC     	1	105	1
CAGCTTTATAACGTACAGCCCGAGGTGTATCCCTTCGAGGT	2	92	1
CTGAGGCTGTAACGTCAGCTATAGTCGATGGGTTACTCATC	3	113	1
          * **  * * *   * *  **
MAP Score: 6.60664

Motif 6
GGGCGGAGTCTCGACAACCCTGATAGCCGCG	0	17	1
CCCGCTAAGGCTGGCAACCCCCCCGGCTAGC	0	100	1
AGCTGATCTGTCTTCAATCCCCTTTTTCCCT	0	128	1
TAGTAGTTAATCGTGATTCCCACTCTGGGGT	0	265	1
TACATACTCCTTCACAAGCCCTATCCT    	1	6	0
GTTATAGCGTCGGGCAAGCCCGACGAGGTGC	1	67	1
GACGAGGTGCTGAACAACCCCGTAGTTCTGG	1	88	1
AGAGAATGTACATTGAACCCCAGATACGGGT	2	56	1
TAGGCCTTATTAGTCATTCCCACATTTGTTT	3	26	1
          * *********
MAP Score: 5.83673

Motif 7
CGAGGAGGGCGGAGTCTCGACAACCCTGATAGCCGCGA	0	11	1
AATAGTCATCGTAATAGCTGCTGCCGCCTACTTCTTCC	0	56	1
TTCTTCCTCAGGTCCCGCTAAGGCTGGCAACCCCCCCG	0	87	1
GGGGATTGAAGACAGATCAGCTAGCCGGGGGGGTTGCC	0	112	0
ACGCCCCCGGGTCATCTCCGCGGGCGGCTGGGTTCGCC	0	178	1
TGTAGACCGGGTTTACGCTATGAGCATGGGCAAGGTTA	1	33	1
CATGGGCAAGGTTATAGCGTCGGGCAAGCCCGACGAGG	1	57	1
AAGCCCGACGAGGTGCTGAACAACCCCGTAGTTCTGGA	1	82	1
       CCAAGATACTCGTAAGCCTGCTCCAGTGTTA	2	3	1
ATTGAACCCCAGATACGGGTCTAGCCAGCTTTATAACG	2	67	1
CACCTCGAAGGGATACACCTCGGGCTGTACGTTATAAA	2	96	0
ACAGAATTAAAGTGAAGCTATCACCTCGAAGGGATACA	2	117	0
TATAGCTGACGTTACAGCCTCAGCTTCCAATCTCTACA	3	98	0
GTTACTCATCGGAGGAGCCTATGCCCTCGTAGCG    	3	144	1
          **   ***  * ***  *
MAP Score: 4.58542