AlignACE 3.0 10/20/99
AlignACE2 -i RP/RP_fusions004_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944236863
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	RP179	24	DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT (sucB)
#1	RP180	300	2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (sucA)
#2	RP460	146	DIHYDROLIPOAMIDE DEHYDROGENASE PRECURSOR  (pdhD)
#3	RP530	125	DIHYDROLIPOAMIDE ACETYLTRANSFERASE COMPONENT (pdhC)
#4	RP805	249	DIHYDROLIPOAMIDE DEHYDROGENASE  (pdhD)

Motif 1
  AGAAACACAAAAATATAAAAGATGATATA	1	8	1
TTAAAAACTAAAAAATATAAAACAACGATAC	4	22	0
ATTGCAGTTAAGAAATATAAAACATTTAGCT	4	65	1
CAAAAAAAATAATAACATAAATCTCAATAAA	3	102	1
AAATAGAACCAATAAAATAAAAATAAA    	4	232	1
ACATTTGCACAAAAAAATAAACAATACAAAC	1	273	1
GAGTGTCAACAATGACATAAAAGATCTCAGA	1	205	0
CCTTTACTGAAAAAATATATAGAATTTAGTA	4	111	0
GAATAGCAGACAGGATATAAAAGTGAGCTAT	1	241	1
TGCGTGACTTCAGGATATAAACCTTATAATA	3	50	0
CGTTTTTAGGAGTAAAATAAATT        	0	11	1
TTATTTAGATAATGATTTAAATTACTAAAAT	1	49	0
ACAATACTACAATATTATAAACA        	2	2	0
AATATAAAACAACGATACAAATTTTTCAAA 	4	9	0
CCTTTTTTGGAATAATTTATACCTTAAAATA	4	206	1
TAAAAGATCTCAGAATATAACCTATAAATAT	1	188	0
          ** ********
MAP Score: 25.2366

Motif 2
        AGAAACACAAAAATATAAAAGATGATATA	1	2	1
TCATTATCTAAATAATAATTTGAGAAATTTCGGTTCG	1	65	1
AAAAGTGAGCTATTACATTTGCACAAAAAAATAAACA	1	259	1
TTTGCACAAAAAAATAAACAATACAAACAACAAT   	1	276	1
GGCATTACAATACTACAATATTATAAACA        	2	2	0
GTTGTGTGACTACGATATTTTAAAAAAGATTATTATA	2	40	1
CTTATGCAAAAAAAATAATAACATAAATCTCAATAAA	3	96	1
CTAAAAAATATAAAACAACGATACAAATTTTTCAAA 	4	9	0
ACATACTAGTACTTAAAAACTAAAAAATATAAAACAA	4	28	0
TAAAGGTTAAAATCAAGTGTTGATAAAGTTCTTTAAA	4	136	1
TTTTAAGGTATAAATTATTCCAAAAAAGGTGAAATCT	4	198	0
TTTATACCTTAAAATAGAACCAATAAAATAAAAATAA	4	221	1
          *** * **    * ***
MAP Score: 6.16458

Motif 3
 AATTTATTTTACTCCTAAAAACGG       	0	3	0
        AGAAACACAAAAATATAAAAGATG	1	2	1
TAATGATTTAAATTACTAAAATCACCCCTTAA	1	39	0
AATTCAGCCGATTTACTAAAAAGTGCTAGTGA	1	108	1
TCTCAGAATATAACCTATAAATATTTCTCTTC	1	180	0
GAGTGTCAACAATGACATAAAAGATCTCAGAA	1	204	0
GCTATTACATTTGCACAAAAAAATAAACAATA	1	267	1
CACAAAAAAATAAACAATACAAACAACAAT  	1	280	1
GTGACTACGATATTTTAAAAAAGATTATTATA	2	45	1
CTACGGTATCTAATCTTTATAATAATCTTTTT	2	62	0
CTTCAGGATATAAACCTTATAATACTAGAACA	3	42	0
CGTGAAGGCTTATGCAAAAAAAATAATAACAT	3	88	1
CAAAAAAAATAATAACATAAATCTCAATAAAT	3	102	1
TTAAAAACTAAAAAATATAAAACAACGATACA	4	21	0
CAATACATACTAGTACTTAAAAACTAAAAAAT	4	37	0
AGGTATAAATTATTCCAAAAAAGGTGAAATCT	4	198	0
TGGAATAATTTATACCTTAAAATAGAACCAAT	4	213	1
CCTTAAAATAGAACCAATAAAATAAAAATAAA	4	227	1
          **  ********
MAP Score: 4.26407