AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions005_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944254924
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0112	300	855aa long hypothetical replication factor C subunit
#1	PH0452	30	1127aa long hypothetical ATP-dependent protease La

Motif 1
GCTTACCTCTCAAAGGTTCTGGAATTCATATATA	0	24	1
GTCGCCGGTAGTAGGGCCAAGGAAAAGCTAATAC	0	75	1
ACGCTTTCTGCGAAGGATTTGGAAACCTTCGAGA	0	132	1
CTTCGAGATACTAAGGCCATGGAAGAGGTTCTAT	0	158	1
ATTTAGAAAGCTGTGGTTGTGGTATTAAGCCTTA	0	273	0
          * * ** * *****
MAP Score: 7.1788

Motif 2
ATTATATATGAATTCCAGAACCTTTGAGAGGT	0	28	0
ATTCATATATAATCCCAATAGACTGAACGTCG	0	47	1
AGGAAAAGCTAATACTAATAGCATCAAAGAAT	0	94	1
AAAGTAGGAAATTTACAAAAGCTGATTACATA	0	214	1
AGTAAGGCTTAATACCACAACCACAGCTTTCT	0	271	1
          *** *** ****
MAP Score: 2.37024

Motif 3
AGTAGGGCCAAGGAAAAGCTAATACTAATA	0	84	1
CTATATAAAAATGAGAAGGGAAGGAGAAAG	0	188	1
TGAGAAGGGAAGGAGAAAGTAGGAAATTTA	0	199	1
CTGATTACATATTAGAAGTGTTTAGGTGGG	0	235	1
        GTAGGTGAAGTTTATAAAACTG	1	2	1
          **********
MAP Score: 0.936551