AlignACE 3.0 10/20/99
AlignACE2 -i MG/MG_sum_all017_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944239123
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	MG249	44	RNA polymerase sigma-43 factor (rpoD)
#1	MG254	175	DNA ligase
#2	MG418	37	ribosomal protein L13 (rpL13)
#3	MG422	37	conserved hypothetical protein
#4	MG424	188	ribosomal protein S15 (rps15)

Motif 1
AATTTTAGCTTATATAACTT          	0	0	0
TGCGACTAGCATTATAATTTTAGCTTATAT	0	15	0
TATTTAGTATATTTTAACTTGC        	1	2	0
GCGTTGTTACTTTAATATTTAGTATATTTT	1	17	0
TCTGCTCCAAATTAAAACTTCTTTGTAAAA	1	110	1
AGTCAGGATTTTTCTTATTTATAGTA    	1	159	1
CGCATTCTATTTTAATATTA          	2	0	0
AAGATTAGCAATTAAAATTTGAAAGGTAC 	3	18	1
GTTAAATGGCTTTGTTAATTTGTTTAGATG	4	12	1
ATCGAGAGAATTTATTAATAAAAATAAAAA	4	64	1
CTCCTACTTACTTATTACTTATAATAAATA	4	97	0
AGTAGGAGAATTTATTACTTCTAACCTTGG	4	119	1
AATGAGCCGTTTTCTAATTTTGTTATAATT	4	150	1
ATTCAACGTGTTTATTAATTA         	4	177	1
          **********
MAP Score: 14.4285

Motif 2
ATATAAGCTAAAATTATAATGCTAGTCGCAT	0	15	1
        GCAAGTTAAAATATACTAAATAT	1	2	1
TATCTGCTCCAAATTAAAACTTCTTTGTAAA	1	108	1
        TAATATTAAAATAGAATGCGGTT	2	2	1
TAAAGATTAGCAATTAAAATTTGAAAGGTAC	3	16	1
ACATCTAAACAAATTAACAAAGCCATTTAAC	4	12	0
TCGAGAGAATTTATTAATAAAAATAAAAACT	4	65	1
AAAACTATATTTATTATAAGTAATAAGTAAG	4	90	1
TAAGTAGGAGAATTTATTACTTCTAACCTTG	4	117	1
AATTATAACAAAATTAGAAAACGGCTCATTG	4	149	0
          TAATTAATAAACACGTTGAAT	4	177	0
          ********* *
MAP Score: 3.10698