AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_sum_all070_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944250602
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH890	145	conserved protein
#1	MTH891	59	conserved protein
#2	MTH892	21	ATP-dependent protease LA related protein
#3	MTH893	60	integrase-recombinase protein
#4	MTH894	179	conserved protein
#5	MTH895	51	conserved protein
#6	MTH898	22	conserved protein
#7	MTH1795	72	transcriptional regulator

Motif 1
AATGATATAGTATTATGATAACATAGATATTTA	0	32	1
ATCTACAACATGTCATGTTAACAGGTTCAACCT	5	13	1
CAAATTGAAGTGTGATGATAACAGCAT      	1	4	0
CATAATACTATATCATTTTAACAGATTCATGGA	0	16	0
CTGACCTGAATTTTATTGAAATAAATGAAAAAT	4	17	0
          * * *** *****
MAP Score: 4.32823

Motif 2
ATCATAATACTATATCATTTTAACAGATTCAT	0	19	0
ATAACATAGATATTTAAATATAGCCCAGAAAC	0	49	1
GATTATTTTATATATCAGTATCGTCATATAAG	0	89	1
ATTTTTCATTTATTTCAATAAAATTCAGGTCA	4	17	1
ATTGCCAGTATATATAACTTTCCATGGTTCGA	4	118	0
AATTTACCTTTATATCCATAAATTTGAATATA	4	153	1
TCCATCCGAATATTTCACCAGAGTCTCTGCGT	7	15	1
          ******* ** *
MAP Score: 3.20055

Motif 3
CTCCATGAATCTGTTAAAATGATATAGTATTATGAT	0	15	1
TATGATAACATAGATATTTAAATATAGCCCAGAAAC	0	45	1
AAACACACCTCTGATTATTTTATATATCAGTATCGT	0	77	1
ATATCAGTATCGTCATATAAGATATAGATATTATCA	0	100	1
ATTTATTTTTCATTTATTTCAATAAAATTCAGGTCA	4	13	1
CATCGAACCATGGAAAGTTATATATACTGGCAATCC	4	116	1
CCTTTATATCCATAAATTTGAATATATTGA      	4	159	1
TTATTATCTACGGTTCCATCTATAAAGTATTTC   	7	49	1
          * * *  **  *****
MAP Score: 2.38825

Motif 4
ACCAGTCATTCCTCAAAAGGAGGGTTTAC         	1	40	1
          AATTAACAGAAGGCATCAAAA       	2	0	1
TCATCGAACTCATCTGATGCAGTTCTCA          	3	0	0
TCGATGAGTGCATGATCCGCAAGGTTTAAGTGGATATT	3	31	1
TTAAGCCCGCCCTTGAAGGAAGAATTCAGGCAATCTTC	4	56	0
TATAACTTTCCATGGTTCGATGAAGTCACTGACCTTCT	4	100	0
       CAGCACCCTAAGGAGGTATGAT         	6	3	1
ACTCTGGTGAAATATTCGGATGGATTAAA         	7	1	0
          ***   * * ***  * *
MAP Score: 2.03268

Motif 5
     ATGCTGTTATCATCACACTTCAATTTGATAA	1	5	1
ACTTCAATTTGATAACCAGTCATTCCTCAAAAGGAG	1	26	1
   TGAGAACTGCATCAGATGAGTTCGATGAGTGCA	3	7	1
ATTTTTCATTTATTTCAATAAAATTCAGGTCAGGAG	4	17	1
TGGAAAGTTATATATACTGGCAATCCCAATTTACCT	4	126	1
AATTTACCTTTATATCCATAAATTTGAATATATTGA	4	153	1
TGTTAACAGGTTCAACCTGGAATTTGAGGTGAA   	5	28	1
     TTTAATCCATCCGAATATTTCACCAGAGTCT	7	5	1
          * *****    * ***
MAP Score: 0.758139