AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions030_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241667
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yhdD	152	similar to cell wall-binding protein
#1	yocA	193	similar to transposon-related protein
#2	yojL	300	similar to cell wall-binding protein
#3	yubE	160	similar to N-acetylmuramoyl-L-alanine amidase
#4	ywtD	140	similar to murein hydrolase

Motif 1
AAAAAGGGCATAAAAAAAGAAGGAATCTTAAT   	0	7	0
TTTGCCTTTTTATAAAAATAGCCAAATTATCTTAA	0	53	0
ATGTGCCGATATAAAAAAGAAACAGCAAATGCAAA	0	100	1
TTATGTCATAATAAAAAAGGTCATACTGCTCCAAA	1	150	1
GAGAATTGATTAGAAAAATAGACAAGAAAGGAGGA	2	10	1
CCTTAGACTTTCGAAAAACATATCGTGCTTATGTA	2	101	1
GCGCCAAATGTTTGAAAAGGGTTTAACTTGCTGAA	2	189	1
GTATTTTGTTTCCAAAAATGGCACACAACTGTTTT	2	235	0
ACTGTTTTTTTGCAAAAACAGCTAGTATTTTGTTT	2	259	0
GGGATAAAGTTGGGAAAAGATTGCAAAATAAAAAC	3	44	0
CCCTAAAGAATTGAAAAATATTAGAAGTGCAAGTA	3	76	1
         TTCAAAAAAGAGAGTGTCTGATGAGA	4	1	1
ATGCTGGGCAAATAAAAAGAGAGTGTCTCATCAGA	4	26	0
ATATTCATTCTGTAAAAATATTAAAAAGTCTCTTA	4	59	1
TCTTAACATATTCAAAAAAATACCGATGTTAAAAC	4	89	1
ATGTTAAAACTGCAAAAAGAGGAGGAGATAATAAA	4	114	1
          *  ********   *
MAP Score: 19.7031

Motif 2
AAGGGGGAAAAAGGGCATAAAAAAAGAAGGAATCTT	0	13	0
AAAAAGGCAAAACGATGAGACAAATGTGCCGATATA	0	77	1
CCGATATAAAAAAGAAACAGCAAATGCAAAATCATT	0	105	1
ATGCAAAATCATTGGGGGAAAAAGGAGAACTAAG  	0	128	1
TGCTCCAAACATTGAGGGTGAAACACA         	1	176	1
      GAGAATTGATTAGAAAAATAGACAAGAAAG	2	4	1
AATAGACAAGAAAGGAGGAGAAACTGCTTCGTTCAT	2	26	1
GAACTATTTAAGCGAGGGTAAAAATGATGGTTTTCT	2	66	0
TTAAAGGTCGAACGATGCTGAAAATGCTGCGCCAAA	2	161	1
TTGCTGAAAAATTGACGATAAAACAGTTGTGTGCCA	2	216	1
AAAGTTGGGAAAAGATTGCAAAATAAAAACCTTTTC	3	38	0
CTTTATCCCTAAAGAATTGAAAAATATTAGAAGTGC	3	70	1
TCAAAAAAATACCGATGTTAAAACTGCAAAAAGAGG	4	100	1
AAAACTGCAAAAAGAGGAGGAGATAATAAAA     	4	119	1
          *  ** *  **** **
MAP Score: 13.9276

Motif 3
AATAAGGGGGAAAAAGGGCATAAAAAAAGAAGG	0	19	0
CCTTTTTATAAAAATAGCCAAATTATCTTAACA	0	51	0
GCTATTTTTATAAAAAGGCAAAACGATGAGACA	0	66	1
AAAAAGAAACAGCAAATGCAAAATCATTGGGGG	0	113	1
TTATAAGATAAAACTATGAATAAAGAAAGGTGA	1	15	0
AATAGACAAGAAAGGAGGAGAAACTGCTTCGTT	2	26	1
GAACTATTTAAGCGAGGGTAAAAATGATGGTTT	2	69	0
ATAGTTCCTTAGACTTTCGAAAAACATATCGTG	2	95	1
AAACATATCGTGCTTATGTAAAATGTTAGATGT	2	116	1
TTAAAGGTCGAACGATGCTGAAAATGCTGCGCC	2	161	1
ATGCTGCGCCAAATGTTTGAAAAGGGTTTAACT	2	184	1
GAAAAGGGTTTAACTTGCTGAAAAATTGACGAT	2	202	1
          AAACATGGTAAAAACCTTTTCAT	3	0	1
AAAGTTGGGAAAAGATTGCAAAATAAAAACCTT	3	41	0
CTTTATCCCTAAAGAATTGAAAAATATTAGAAG	3	70	1
GAAGTGCAAGTAAAATTCTAAAAGGTAGATTCT	3	99	1
ATTAAAAGATTACGAATGTAAAAGAATCTACCT	3	121	0
TCATTCTGTAAAAATATTAAAAAGTCTCTTAAC	4	63	1
AAAGTCTCTTAACATATTCAAAAAAATACCGAT	4	83	1
ATACCGATGTTAAAACTGCAAAAAGAGGAGGAG	4	108	1
          *** * ** ****
MAP Score: 13.06

Motif 4
     ATTAAGATTCCTTCTTTTTTTATGCCC	0	5	1
CTTCTTTTTTTATGCCCTTTTTCCCCCTTATT	0	20	1
GTCTCATCGTTTTGCCTTTTTATAAAAATAGC	0	66	0
       ATGTATCACCTTTCTTTATTCATAG	1	3	1
AGCCTGCTTGTATTCCATTTCAATCTCATAGT	1	70	1
CTTGGTCTGATATACCCTCTTATGTCATAATA	1	131	1
TTTGGAGCAGTATGACCTTTTTTATTATGACA	1	153	0
AAGCAGTTTCTCCTCCTTTCTTGTCTATTTTT	2	23	0
AACCATCATTTTTACCCTCGCTTAAATAGTTC	2	70	1
CAAATAAACATCTAACATTTTACATAAGCACG	2	124	0
AAAACAGTTGTGTGCCATTTTTGGAAACAAAA	2	235	1
       TCATTCAACCTCCTAAACTGTTTTT	2	285	0
TGAAAAGGTTTTTACCATGTTT          	3	0	0
AGGTTTTTATTTTGCAATCTTTTCCCAACTTT	3	42	1
TTCTAATATTTTTCAATTCTTTAGGGATAAAG	3	70	0
AGGTAGATTCTTTTACATTCGTAATCTTTTAA	3	121	1
TGTCTGATGAGACACTCTCTTTTTATTTGCCC	4	24	1
TAAGAGACTTTTTAATATTTTTACAGAATGAA	4	62	0
          * * ********
MAP Score: 2.21867

Motif 5
   ATTAAGATTCCTTCTTTTTTTATGCCC	0	7	1
TTCTTTTTTTATGCCCTTTTTCCCCCTTAT	0	21	1
TAAGATAATTTGGCTATTTTTATAAAAAGG	0	54	1
TCTCATCGTTTTGCCTTTTTATAAAAATAG	0	67	0
GCATTTGCTGTTTCTTTTTTATATCGGCAC	0	102	0
   CTTAGTTCTCCTTTTTCCCCCAATGAT	0	135	0
GCAGTTTCTCCTCCTTTCTTGTCTATTTTT	2	23	0
GGAGGAGAAACTGCTTCGTTCATCAATAGA	2	39	1
AACAGTTGTGTGCCATTTTTGGAAACAAAA	2	237	1
ACCTCCTAAACTGTTTTTTTGCAAAAACAG	2	273	0
ATCAGACACTCTCTTTTTTGAA        	4	2	0
TGATGAGACACTCTCTTTTTATTTGCCCAG	4	28	1
GTTTTAACATCGGTATTTTTTTGAATATGT	4	94	0
TTATTATCTCCTCCTCTTTTTGCAGTTTTA	4	118	0
          **********
MAP Score: 0.0107224