AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions023_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944241370
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yjbQ	234	similar to Na+/H+ antiporter
#1	tenA	248	transcriptional regulator
#2	ywdC	42	alternate gene name: ipa-53r
#3	thiD	148	phosphomethylpyrimidine kinase
#4	ywbI	105	alternate gene name: ipa-24d; similar to transcriptional regulator (LysR family)

Motif 1
ATAAGGTCTTAATCCTGTTTAGAAAATGATTCT	0	97	0
GTTTTTTAAAAATGAGGTTTTGTTCTCTGAGTG	0	171	1
CTGACTTAAAAAGGAGGTTCTGATT        	0	219	1
ATCTTGACCAAATAAGGATTCGTGTTAATATAG	1	10	1
TCGTGTTAATATAGAGGTGCAGAACAATTCAAT	1	29	1
CTCATAACTTGAACAGGTTCAGACCTGCGTAGG	1	128	1
CCTGCGTAGGGAAGTGGAGCGGTATTTGTGTTA	1	151	1
CCCGCAAGGAAAAGTGGTTTGGAATTGGCATAG	1	189	0
TCCTTGCGGGAAAGTGGTTTTTTTATTTTCAGA	1	212	1
AGAAAACTAGGTAGGGGTTTTGAGATG      	3	4	0
TGACAATCTCAACGGGCTTTCGTAAAATGCTAC	3	40	0
          ** * ***** **
MAP Score: 8.92839

Motif 2
ACAATCGGTAAGGAGGAGACCGC        	0	2	0
TTTTCTAAACAGGATTAAGACCTTATCACTT	0	104	1
GATTTTAACAAGGGTGATGATGAAAAATAAA	0	133	0
TTTTTAAGTCAGGGTTATGCTAGTTCTCACT	0	200	0
GTTAATATAGAGGTGCAGAACAATTCAATAT	1	33	1
TAACTTGAACAGGTTCAGACCTGCGTAGGGA	1	132	1
GGAAAGAGTGAGGAGGAAGCT          	2	0	0
AACATGATGGAGGTTCAAGAC          	3	137	1
GTCTATAGAAAGGGTGAAGCGC         	4	93	1
          *** *******
MAP Score: 6.95691

Motif 3
      GCGGTCTCCTCCTTACCGATTGTT	0	4	1
TTGTGATGACTCACAACACTTTGCTTCATA	0	42	0
AGTGATAAGGTCTTAATCCTGTTTAGAAAA	0	104	0
AGGATTAAGACCTTATCACTTTATTTTTCA	0	114	1
TTATTTTTCATCATCACCCTTGTTAAAATC	0	134	1
GTGAGAACTAGCATAACCCTGACTTAAAAA	0	201	1
CACACTTTTATCTCAGCCCTTATGAAGGAC	1	87	0
ACTTTTAGACCCTCATAACTTGAACAGGTT	1	117	1
AAATACCGCTCCACTTCCCTACGCAGGTCT	1	148	0
     AGCTTCCTCCTCACTCTTTCCTTCC	2	5	1
        GCGCTTCACCCTTTCTATAGAC	4	93	0
          **********
MAP Score: 6.7994

Motif 4
CAATCGGTAAGGAGGAGACCGC         	0	1	0
TATTTATTATGAAGCAAAGTGTTGTGAGTCA	0	35	1
TCAGACCTGCGTAGGGAAGTGGAGCGGTATT	1	146	1
ACTTTTCCTTGCGGGAAAGTGGTTTTTTTAT	1	207	1
TTTATTTTCAGAGGGGGAATGATTT      	1	233	1
CTCTTTTCAGGAAGGAAAGAGTGAGGAGGAA	2	13	0
TTCCTGAAAAGAGCGAAACAG          	2	31	1
          * *********
MAP Score: 3.70384

Motif 5
CTCCTTACCGATTGTTTTATTTATTATGAAGC	0	18	1
GAGTCATCACAAGCTTTTATGTGCAAATTATA	0	60	1
TTAAGACCTTATCACTTTATTTTTCATCATCA	0	118	1
CCTTGTTAAAATCGCGTTATGTTTTTTAAAAA	0	151	1
TTTTTTAAAAATGAGGTTTTGTTCTCTGAGTG	0	172	1
ATATTAACACGAATCCTTATTTGGTCAAGAT 	1	9	0
TGGAGCGGTATTTGTGTTATTTTACTATGCCA	1	165	1
CGGGAAAGTGGTTTTTTTATTTTCAGAGGGGG	1	218	1
CCCCTACCTAGTTTTCTTATGTAGCATTTTAC	3	20	1
TTGAACCTCCATCATGTTTTGTCTTTCATTAT	3	123	0
TACCTATAGAGAGACCTTATGTACAATAAGTA	4	28	0
GAATAAGAAGTATTCCTTTTGTCTATAGAAAG	4	73	1
          **  ********
MAP Score: 3.23646