AlignACE 3.0 10/20/99
AlignACE2 -i PA/PA_fusions014_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944248727
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PAB3055	115	hypothetical protein
#1	PAB1655	62	PAB1655
#2	mgtE-like	133	PAB0883
#3	PAB1305	61	PAB1305

Motif 1
TTTTGAGGAACCCCTTAAAAAACATGGGCGA	3	20	1
   GCTCTCACCACATACAAAGGGGGTATTT	0	7	1
TACATGGAGACCACTTAAAAACCTTTTCCTG	2	54	1
   GACCTATCCCCATACAAGGAAAAGCCAT	1	7	1
GACGGTTATTCTCCTTAATAAATTTTAATGT	2	96	0
  TCTCTCACCTCCGTTCTAAGAATCAAAAT	2	8	1
  CCAACTCCCCACCTTATATTTCGCCCATG	3	42	0
TATAAATTACCGACCTTAAATACCCCCTTTG	0	24	0
GGTTCATCAACTAGCTTAAAAGTCTTGGGCC	0	72	0
          **** ******
MAP Score: 10.3796

Motif 2
ATCAACTAGCTTAAAAGTCTTGGGCCGATCT	0	67	0
TTAAGCTAGTTGATGAACCATACTTAAGGAG	0	84	1
CCCCATACAAGGAAAAGCCATTTATATCAAA	1	17	1
GCCATTTATATCAAAAACCTTTTTCCTTTGG	1	33	1
TGGAGACCACTTAAAAACCTTTTCCTGCATT	2	58	1
TTATTCTCCTTAATAAATTTTAATGTTTTCC	2	91	0
AACCGTCGGGTGAGAAGTCATGG        	2	120	1
AAGGGGTTCCTCAAAAACTATCAAAT     	3	5	0
GAGGAACCCCTTAAAAAACATGGGCGAAATA	3	24	1
          * *********
MAP Score: 9.19727

Motif 3
   GCTCTCACCACATACAAAGGGGGTATTTAAGGT	0	7	1
AGTTGATGAACCATACTTAAGGAGGGGTATAAAA  	0	91	1
   GACCTATCCCCATACAAGGAAAAGCCATTTATA	1	7	1
       CGTCAACACCAAAGGAAAAAGGTTTTTGA	1	43	0
ATTTTGATTCTTAGAACGGAGGTGAGAGA       	2	3	0
TTCTAAGAATCAAAATGAAAGCTAAAACCACTACAT	2	23	1
TTAATGTTTTCCAGAATGCAGGAAAAGGTTTTTAAG	2	67	0
AAAACATGGGCGAAATATAAGGTGGGGAGTTGG   	3	38	1
          * * *   **** ***
MAP Score: 7.59828

Motif 4
    GCTCTCACCACATACAAAGGGGGTATTT	0	6	1
AGATCGGCCCAAGACTTTTAAGCTAGTTGATG	0	67	1
TAGTTGATGAACCATACTTAAGGAGGGGTATA	0	90	1
    GACCTATCCCCATACAAGGAAAAGCCAT	1	6	1
ATACAAGGAAAAGCCATTTATATCAAAAACCT	1	21	1
CTACATGGAGACCACTTAAAAACCTTTTCCTG	2	53	1
TGCATTCTGGAAAACATTAAAATTTATTAAGG	2	83	1
GTTTTTGAGGAACCCCTTAAAAAACATGGGCG	3	18	1
          ***** ** ***
MAP Score: 1.00883