AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_sum_all062_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250428
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH496	122	endonuclease III homolog
#1	MTH641	223	conserved protein
#2	MTH746_MTH747	96	MTH746: endonuclease III related protein (probably non-iron-sulfur homolog), MTH747: conserved protein
#3	MTH765	66	GTP-binding protein Rab related protein
#4	MTH766	29	5-enolpyruvylshikimate 3-phosphate synthase
#5	MTH767	83	valyl-tRNA synthetase

Motif 1
TGGTATGAATATCAAGCAGCAGATCCTTTTCAGA	0	12	0
    TATTTCAGCCAGCAGAATTCCATAGTCATC	0	102	0
TGGTAATGGTACCCTGCAGAAACCAGAATTAATA	1	24	1
TAAAATTTATATCCATCACAATTTAATATTAATT	1	50	0
ACAATCAGTAAACCAGCAATACCCCGATGATATA	2	36	0
TAAAAAGCAGCACAATCAGTAAACCAGCAATACC	2	47	0
     AAAAACACCTGCAGATACCTCCAGATGGA	4	10	0
          * ******* *  *
MAP Score: 4.49668

Motif 2
TGCGAATGGGGAAAAAAGAATTTAAGGAAATTTCC	0	51	1
TCCCTGGCGCGAAAGAAGAGATGACTATGGAATTC	0	83	1
GTACCCTGCAGAAACCAGAATTAATATTAAATTGT	1	32	1
TTTATTACCTGAAATGAGTGTACATCATCTTAAAT	1	118	1
TACATCATCTTAAATTAGTAAATGTTCAGCTAAGA	1	138	1
GCACAATCAGTAAACCAGCAATACCCCGATGATAT	2	37	0
    AATATATAAAATAGGGTTAACCCATATTCAA	3	6	1
CCTTGTAGGAGAAATAAGGGGAAGCAAGTTCTCAT	5	23	0
          ****  ** * * **
MAP Score: 3.73594

Motif 3
       AATATATAAAATAGGGTTAACCCATATTCAAATGTT	3	3	1
GGTATTCACCATATGAGAACTTGCTTCCCCTTATTTCTCCTAC	5	11	1
TGTACAGAAGATATGCACCTATGAAAACGCCCAGTTAAATCCA	1	186	1
CTTTTAATTAATATATCATCGGGGTATTGCTGGTTTACTGATT	2	25	1
TCACAATTTAATATTAATTCTGGTTTCTGCAGGGTACCATTAC	1	26	0
CTGCTGCTTGATATTCATACCAGAATCTGCGAATGGGGAAAAA	0	24	1
CCCAATCTTTATAAAGATGTTTGAATACTCTAACCTTGTAGGA	5	48	0
         AAAAACACCTGCAGATACCTCCAGATGGA     	4	5	0
TGCTGTGATAATAACCATTCGATTTATTACCTGAAATGAGTGT	1	96	1
          ****        * ** * *  *
MAP Score: 3.06888

Motif 4
CTGGCGCGAAAGAAGAGATGACTATGGAATT	0	86	1
TATTTCAGCCAGCAGAATTCCATAGTCATCT	0	101	0
CCCTGCAGAAACCAGAATTAATATTAAATTG	1	35	1
TCGATTTATTACCTGAAATGAGTGTACATCA	1	114	1
TACTAATTTAAGATGATGTACACTCATTTCA	1	127	0
AGATTATTATACATGATGTACAGAAGATATG	1	170	1
CATGATGTACAGAAGATATGCACCTATGAAA	1	181	1
CAATCAGTAAACCAGCAATACCCCGATGATA	2	38	0
CTAACCTTGTAGGAGAAATAAGGGGAAGCAA	5	31	0
          ******* ***
MAP Score: 1.49642