AlignACE 3.0 10/20/99
AlignACE2 -i PH/PH_fusions011_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944255016
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	PH0209	300	131aa long hypothetical protein
#1	PH0437	263	367aa long hypothetical protein
#2	PH0438	58	339aa long hypothetical adenylosuccinate synthetase
#3	PH0439	31	255aa long hypothetical competence-damage protein
#4	PH0702	46	364aa long hypothetical translation initiation factor eIF-2 beta chain
#5	PH1136	86	131aa long hypothetical protein

Motif 1
AAATTTGCTACTAATACTTTTAAATTTACT	0	43	1
AGGAAAGGTTCTAATACTTGCACTACCAGG	0	205	1
GTAAGGAACTCCAACCCTTTCTCCTGGTAG	0	227	0
AACTCTTCACCTAATATTTTGAGGAGATCC	1	40	0
CATAATACTCCTCATACTTTTCGATTGGAG	1	90	0
CCTTAAAATGCTTACCCTTTTGACAGGG  	2	8	0
TACCCCTTTACTTACCCTTTGGTAAGGAGT	2	38	1
CCCTCTTTCCCTTAAACTTTTCT       	4	3	0
CAAGCAGAGGCTTATACTTACTCAAGTATC	5	15	1
          **********
MAP Score: 11.2753

Motif 2
AAATTTGCTACTAATACTTTTAAATTTACT	0	43	1
ATTTAGTTCACCATTCCCTAACTATGAACT	0	73	0
ATTTCATCAACTTTTCCAATGTACTTGCCC	0	151	0
AGTATTAGAACCTTTCCTTCGCCCTCCTTG	0	193	0
GTAAGGAACTCCAACCCTTTCTCCTGGTAG	0	227	0
ACTCCTCATACTTTTCGATTGGAGTCTCCT	1	84	0
GCTTCTCTAGCCTTCACATAATACTCCTCA	1	106	0
CTCTCAATAGCCATTCTATTCATTGCAGGG	1	196	0
CCTTAAAATGCTTACCCTTTTGACAGGG  	2	8	0
TTAAGGTACCCCTTTACTTACCCTTTGGTA	2	32	1
CTTTAAATTTCCTATCCCTATTTTTCTTTT	3	10	1
TCTCTACCCTCTTTCCCTTAAACTTTTCT 	4	9	0
CAAGCAGAGGCTTATACTTACTCAAGTATC	5	15	1
AGGAAAGAACCCTTTATATAGCAAAAAATC	5	53	1
AGCAAAAAATCTTTTCCATTCACG      	5	72	1
          **********
MAP Score: 9.85976

Motif 3
GTTCATAGTTAGGGAATGGTGAACTAAATGGTTATGGA	0	74	1
TCAAAGATGTACGGGAAGCTGATATATAACACCAGGGG	0	116	1
TATAACACCAGGGGCAAGTACATTGGAAAAGTTGATGA	0	140	1
TTCTCCTGGTAGTGCAAGTATTAGAACCTTTCCTTCGC	0	201	0
TCAAAATATTAGGTGAAGAGTTTGAGAAGAGAATTAAG	1	48	1
AGAGAAGCGGAGTGGAAGCGCCTAAGAAGCTTTACGAC	1	128	1
CCCTGTCAAAAGGGTAAGCATTTTAAGGTACCCCTTTA	2	10	1
TCCTTACCAAAGGGTAAGTAAAGGGGTACCTTAAAATG	2	28	0
AAAGAAAAATAGGGATAGGAAATTTAAAG         	3	1	0
GAAAAGTTTAAGGGAAAGAGGGTAGAGATCTAAATAGG	4	11	1
          **** ***    *  * *
MAP Score: 9.15958

Motif 4
ATGAACTAGTAAATTTAAAAGTATTAGTAGCAAATTTTT	0	41	0
TGGTGAACTAAATGGTTATGGAATTATCAAAGATGTACG	0	90	1
AGTACATTGGAAAAGTTGATGAAATTGTAATTGACATCA	0	156	1
AGGGCGAAGGAAAGGTTCTAATACTTGCACTACCAGGAG	0	198	1
TTCCTTACGAAAAAGTTACAGCAGTTGGAGATATAATTT	0	249	1
ACTCCAATCGAAAAGTATGAGGAGTATTATGTGAAGGCT	1	89	1
   CCCTGTCAAAAGGGTAAGCATTTTAAGGTACCCCTT	2	7	1
CAAAAGAAAAATAGGGATAGGAAATTTAAAG        	3	2	0
          *** **    * * * * *
MAP Score: 7.60535

Motif 5
GATATATAACACCAGGGGCAAGTACATTGGAAAA	0	136	1
ATTGACATCAAGGAGGGCGAAGGAAAGGTTCTAA	0	185	1
TAAGGAGACTCCAATCGAAAAGTATGAGGAGTAT	1	82	1
ATGAAGATACCGTACTGGGAAGCACTAAATCCCT	1	166	1
    CCCTGTCAAAAGGGTAAGCATTTTAAGGTA	2	6	1
  ACTCCTTACCAAAGGGTAAGTAAAGGGGTACC	2	36	0
AAGTATCATCCCCATAGGAAAGAACCCTTTATAT	5	38	1
          ** * *** *** *
MAP Score: 6.81732

Motif 6
GGGCTATTTAAGGAGCCTTGCTTATAAAAAT	0	16	1
GAAAGGGTTGGAGTTCCTTACGAAAAAGTTA	0	236	1
GATAAGAAGAGAAATCTCTACCAGGGATCTC	1	16	1
ATCTCTACCAGGGATCTCCTCAAAATATTAG	1	29	1
GGAGTCTCCTTAATTCTCTTCTCAAACTCTT	1	63	0
GAAGCGCCTAAGAAGCTTTACGACATGAAGA	1	142	1
TGCAGGGATTTAGTGCTTCCCAGTACGGTAT	1	172	0
TGGGAAGCACTAAATCCCTGCAATGAATAGA	1	181	1
TCCACCTATTTAGATCTCTACCCTCTTTCCC	4	22	0
GCTATATAAAGGGTTCTTTCCTATGGGGATG	5	44	0
TATATAGCAAAAAATCTTTTCCATTCACG  	5	67	1
          ********* *
MAP Score: 6.51875

Motif 7
       ACAAAGGGGCTATTTAAGGAGCCTTGCTT	0	3	1
CATAGTTAGGGAATGGTGAACTAAATGGTTATGGAA	0	77	1
TTGACATCAAGGAGGGCGAAGGAAAGGTTCTAATAC	0	186	1
AAGTTACAGCAGTTGGAGATATAATTTTAGTCCAAG	0	261	1
TGAAGAGTTTGAGAAGAGAATTAAGGAGACTCCAAT	1	61	1
GCAATGAATAGAATGGCTATTGAGAGCAAACCTTAT	1	200	1
CTGTCAAAAGGGTAAGCATTTTAAGGTACCCCTTTA	2	12	1
 ACTCCTTACCAAAGGGTAAGTAAAGGGGTACCTTA	2	33	0
GAAAAATAGGGATAGGAAATTTAAAG          	3	0	0
AAGGGAAAGAGGGTAGAGATCTAAATAGGTGGAACT	4	20	1
          **  **  ** *** *
MAP Score: 5.51003