AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions048_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242342
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	gcaD	192	UDP-N-acetylglucosamine pyrophosphorylase
#1	ybbP	160	alternate gene name: ybbQ; similar to hypothetical proteins
#2	yfnH	235	similar to glucose-1-phosphate cytidylyltransferase
#3	spsI	24	alternate gene name: ipa-71d
#4	spsA	300	alternate gene name: ipa-63d

Motif 1
TAAATATCTTCTGATTTCAAGGAGACTTCA	0	128	0
AGAGGGCTGGCACATTTCACTTGCTAAATC	1	46	1
CCCATTATACCACATTTCGATTTAGCAAGT	1	64	0
CGATTTCAATCCGGTTTCAAAATCTACTGT	2	131	0
GATAATTTGTCCGATTTCAATCCGGTTTCA	2	142	0
GAAGATGTACCAGGTTTCGAACTCAATATT	2	195	1
GCGGACCGATCAGATTTCGCTCTGGGCAGC	4	154	1
          **********
MAP Score: 9.75555

Motif 2
AGCAAGGACTGCTGAAAGGGCTGACATAAGC	0	23	1
TTTTTCTATGGATAAAAGGGATATTGGAGGC	0	165	1
CTCTCAGCCCGCAAAAAAAGAGCAAAGCGGC	1	19	0
TTTTTTGCGGGCTGAGAGGGCTGGCACATTT	1	32	1
          GATGAAAAAGAGCCTTGAGCG	2	0	1
CAAAAAAAGAGCCTTGAGCGAAGGCAATGCG	2	33	0
CAACCAACTTGAAAAAATAGATTCCATTTGG	2	70	1
CAGCCTTGGTGACCAAATGGAATCTATTTTT	2	82	0
CTACTGTAATGATATGAGAGAAAGCCAGCCT	2	107	0
TCGGGGAAATGCCTTGATAGATTGTGAAGAT	2	170	1
AGCCTCATAAGGTGAAAGAGATAAAAATCGC	4	95	0
CTTGGATTATGCTGAAAAAGAACAGCGGACC	4	130	1
AACAGCGGCTGCCCAGAGCGAAATCTGATCG	4	160	0
          *** *******
MAP Score: 9.4323

Motif 3
TAACCAAAAAGCAAGGACTGCTGAAAGGGC	0	14	1
AAGGACTGCTGAAAGGGCTGACATAAGCCT	0	26	1
TTTGCGGGCTGAGAGGGCTGGCACATTTCA	1	35	1
CACAAAATACGAAATGACTGAAATCTTGGA	1	130	1
TTGAGCGGGCGCATTGCCTTCGCTCAAGGC	2	24	1
AATTATCGGGGAAATGCCTTGATAGATTGT	2	165	1
TGAACGCTCCGCGATGACTCACCTCCGATG	4	43	1
          **********
MAP Score: 5.21503

Motif 4
TAACCAAAAAGCAAGGACTGCTGAAAGGGC	0	14	1
AAGGACTGCTGAAAGGGCTGACATAAGCCT	0	26	1
TTTGCGGGCTGAGAGGGCTGGCACATTTCA	1	35	1
CACAAAATACGAAATGACTGAAATCTTGGA	1	130	1
AAAGAGCCTTGAGCGGGCGCATTGCCTTCG	2	16	1
AAAGAGCCTTGAGCGAAGGCAATGCGCCCG	2	29	0
GTAATGATATGAGAGAAAGCCAGCCTTGGT	2	103	0
AATATTCATAGAGATGAGGGGTAGAG    	2	219	1
TGAACGCTCCGCGATGACTCACCTCCGATG	4	43	1
CGGCTGCCCAGAGCGAAATCTGATCGGTCC	4	156	0
          **********
MAP Score: 4.84594

Motif 5
AAAAAGCAAGGACTGCTGAAAGGGCTGACATAAGCCTTTTGC	0	19	1
CTCTTTTTTTGCGGGCTGAGAGGGCTGGCACATTTCACTTGC	1	28	1
TAAATCGAAATGTGGTATAATGGGCTCGCTATGTAAAGTACA	1	70	1
CGAAGGCAATGCGCCCGCTCAAGGCTCTTTTTCATC      	2	4	0
CGGGCGCATTGCCTTCGCTCAAGGCTCTTTTTTTGGTTATAC	2	29	1
ATAGATTCCATTTGGTCACCAAGGCTGGCTTTCTCTCATATC	2	86	1
TTTTATCTCTTTCACCTTATGAGGCTGATGCTTGGATTATGC	4	100	1
GGACCGATCAGATTTCGCTCTGGGCAGCCGCTGTTTTTCAGA	4	156	1
          *    *     ****** *  *
MAP Score: 4.56694

Motif 6
GACATAAGCCTTTTGCCGGCGGTCCTTTTTTA	0	45	1
ATAAAAGGGATATTGGAGGCCAATAA      	0	176	1
TTTGCTCTTTTTTTGCGGGCTGAGAGGGCTGG	1	24	1
ATGACTGAAATCTTGGAGGACGAGGAA     	1	143	1
AGAAAGCCAGCCTTGGTGACCAAATGGAATCT	2	88	0
GTTCTGGATGTATAGGTGAACGCTCCGCGATG	4	27	1
CAGATTTCGCTCTGGGCAGCCGCTGTTTTTCA	4	164	1
          * **** *****
MAP Score: 0.458883