AlignACE 3.0 10/20/99
AlignACE2 -i TH/TH_operons024_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944245133
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MTH42	171	DNA-dependent RNA polymerase, subunit K 
#1	MTH43	51	enolase
#2	MTH44	27	ribosomal protein Sa (E.coli S2)
#3	MTH47	21	conserved protein
#4	MTH48	73	conserved protein
#5	MTH684	42	conserved protein
#6	MTH686	65	proteasome, alpha subunit
#7	MTH689	74	conserved protein
#8	MTH690	170	ribosomal protein L15
#9	MTH1202	236	proteasome, beta subunit
#10	MTH1203	69	cleavage and polyadenylation specificity factor

Motif 1
CTTTTCAACTGGAACGGGGATGGTCAGCAC	0	63	1
GAAAAACATTAAAATAGAGGTTCTTGGATT	0	141	0
TCTAGACTGAAAAATAGTGGTTTATTAGAG	1	11	0
TAGCCTTCAAAAAACAGGGAGGCATAAC  	5	24	1
         AAGAACAGGGGCCTCCGAAAC	7	1	1
AGGGGCCTCCGAAACAGGGGTAAAGGGGCT	7	16	1
AAAAAAAGTTAAGACGGGGGGCTTTATCTT	7	54	0
GTATCCCTGAAAAATAGCGGTTTAGGTGCT	8	106	0
AAAGCCGAACAGAATAGAGGTGTAA     	8	155	1
GTACCAATATATAACAGGAGGTCCTTATTA	9	97	0
ACTGCAATTAAAAATAGGAGAAAAA     	10	5	0
TCACTTCTAAAAAACAGGGAATATCAGTAA	10	45	0
          **********
MAP Score: 19.0735

Motif 2
CTTGGATTCGATTTGATGGGACCGCCGAGA	0	119	0
TATTTTAATGTTTTTCTTGGAGGCAT    	0	155	1
TAAACCACTATTTTTCAGTCTAGAGTTTAT	1	17	1
CTATAAATTCCTTTGAATGTTGATTGATAA	4	22	0
TGATGGAAAATTTTTAAGGGCGTTAAAAT 	4	54	1
CCTCCCTGTTTTTTGAAGGCTAAAAGGAGA	5	16	0
GACAGTAAACTTTTTAAGTGATCACACCAG	8	69	1
TAAACCGCTATTTTTCAGGGATACGTTCCC	8	112	1
TGGTACAGAACTTTTATGTCCATGGGGACA	9	121	1
GGGGACAGCCCTTTGCAGGGTTAAATGAAA	9	144	1
TCCCATTGTGTTTTTATGGTATATAAAGGG	9	175	0
TTTTCTCCTATTTTTAATTGCAGTAAACAC	10	11	1
TTCCCTGTTTTTTAGAAGTGATCTT     	10	54	1
          **********
MAP Score: 10.3537

Motif 3
CCGGAACGCTGGAGACCCGAGTTCAAATCTCG	0	92	1
TTCAAATCTCGGCGGTCCCATCAAATCGAATC	0	113	1
CCCCTGTTTCGGAGGCCCCTGTTCTT      	7	4	0
AAATGTCAGTGAAGGTCCGTTTAATGGAAAAA	8	24	0
TTTAATGACCGGATAACCGTTCTTCAACCCCT	9	28	1
CAACCCCTCAGGAAGCCCCATCTATTATAAAA	9	52	1
ATATATAACAGGAGGTCCTTATTAAACTTTGC	9	89	0
ATGTCCATGGGGACAGCCCTTTGCAGGGTTAA	9	136	1
CAGGGTTAAATGAAAACCCTTTATATACCATA	9	159	1
          *** * ******
MAP Score: 8.20986

Motif 4
TAATAAACTCTAGACTGAAAAATAGTGGTTT	1	18	0
CCTTTGAATGTTGATTGATAATCGTGAATGT	4	12	0
AATTTATAGGGTGATGGAAAATTTTTAAGGG	4	43	1
TCCCTGTTTTTTGAAGGCTAAAAGGAGAGGA	5	13	0
CCTCTCTTTATTGATGGATAATTTATGTAAT	6	36	0
GAAGGTCCGTTTAATGGAAAAATCAAAGGTG	8	15	0
AGTAAACTTTTTAAGTGATCACACCAGATGT	8	72	1
CTTTGCAGGGTTAAATGAAAACCCTTTATAT	9	154	1
          **** ******
MAP Score: 5.77127

Motif 5
AATCCAAGAACCTCTATTTTAATGTTTTTCTTGGA	0	141	1
CTCTAATAAACCACTATTTTTCAGTCTAGAGTTTA	1	11	1
GTTATGCCTCCCTGTTTTTTGAAGGCTAAAAGGAG	5	17	0
AGCACCTAAACCGCTATTTTTCAGGGATACGTTCC	8	106	1
ATAAGGACCTCCTGTTATATATTGGTACAGAACTT	9	99	1
GGATCCAGGACTGGTTTTTTATTATTTTTATTAGA	9	202	1
ACTGATATTCCCTGTTTTTTAGAAGTGATCTT   	10	47	1
          ** ** ****   **
MAP Score: 5.08369

Motif 6
GTCCGGAAACTTCTTCAATGGCTGGGAGGAT	0	33	0
TTTTAATGTTTTTCTTGGAGGCAT       	0	157	1
AAAATAGTGGTTTATTAGAGT          	1	0	0
TGCCTCCCTGTTTTTTGAAGGCTAAAAGGAG	5	17	0
CTAACCTCTCTTTATTGATGGATAATTTATG	6	40	0
CCTTTACCCCTGTTTCGGAGGCCCCTGTTCT	7	11	0
TCACTGACATTTCATTGATGTGACTGACAGT	8	44	1
TTTTATTATTTTTATTAGAGGTGTATCT   	9	218	1
TCTCCTATTTTTAATTGCAGTAAACACCTGT	10	14	1
ATATTCCCTGTTTTTTAGAAGTGATCTT   	10	51	1
          *** *******
MAP Score: 3.20126

Motif 7
CGAGATTTGAACTCGGGTCTCCAGCGTTCCGG	0	92	0
AAAAACATTAAAATAGAGGTTCTTGGATTCGA	0	138	0
      AAGAACAGGGGCCTCCGAAACAGGGG	7	4	1
AAAAGTTAAGACGGGGGGCTTTATCTTACCTT	7	49	0
TTTTTCCATTAAACGGACCTTCACTGACATTT	8	24	1
TTTTTATAATAGATGGGGCTTCCTGAGGGGTT	9	53	0
GCAAAGTTTAATAAGGACCTCCTGTTATATAT	9	89	1
CCATAAAAACACAATGGGATCCAGGACTGGTT	9	186	1
          * * ********
MAP Score: 2.06759