AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240781
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	ybaN	300	alternate gene name: ybxG; similar to polysaccharide deacetylase
#1	ydaJ	202	ydaJ
#2	yfjS	100	similar to polysaccharide deacetylase
#3	yjeA	178	similar to endo-1,4-beta-xylanase
#4	ylxY	117	alternate gene name: ymxI; similar to deacetylase
#5	xynA	300	endo-1,4-beta-xylanase
#6	yveR	24	similar to spore coat polysaccharide biosynthesis
#7	yveM	258	similar to capsular polysaccharide biosynthesis
#8	bglS	295	endo-beta-1,3-1,4 glucanase

Motif 1
TTATGCCAATAAAAAAACCGCGGCGGGCAC	2	16	0
TTTCATCATAAAAAAAACCGAATTTC    	3	6	0
         TAAAAAAACCTGTGCCTATCG	1	1	1
GCTTCAAAATAAAGAAGCCGGGTCTCCCAG	4	29	0
CTACAATGTTACAAAAACATTTCTAAATAG	3	101	1
ATAAAAGAAAAAAAATGCAGATTGCTAGCT	1	89	0
TAAAATAAGAAAAAATGCAGAAGGAGCGCT	2	76	1
TTTTGGAGAGACGAAAACCGCCGCAGCTAA	7	186	1
CAAAAAGGGAAAAAAAAGCTAGCAATCTGC	1	73	1
TTTGAACATTAAGAAAACAGGACCTAAGTC	1	47	0
TCTGAAAAAAATAAAAACCTAAATTACCAT	8	142	0
TGATCCTGCGAAAAAAGGATCAGGATATGG	5	88	1
CTAAGTCCAATAAAAAACCTGTGCGATAGG	1	24	0
TAATTCAATTACAAATACCTAGAAACACAT	5	137	0
TTGAAGCTTTTCAAAAGCAGGCGGGTTCTA	4	52	1
AATGGCTACGAAAGAAGGAGTTTTTG    	3	162	1
  ATGAAAACATAAAAGGAGCCTGGGAGAC	4	8	1
TGAAATTCCTTAAAAAGGATTGACATGAAC	3	31	1
          **********
MAP Score: 12.1356

Motif 2
ATAAGATGTAAAACAAGAATGATGGACAAGATAA	0	263	1
ATAAAAGAAAAAAAATGCAGATTGCTAGCTTTTT	1	85	0
TAAAATAAGAAAAAATGCAGAAGGAGCGCTGGCC	2	76	1
AATGGCTACGAAAGAAGGAGTTTTTG        	3	162	1
  ATGAAAACATAAAAGGAGCCTGGGAGACCCGG	4	8	1
AAAGCTTCAAAATAAAGAAGCCGGGTCTCCCAGG	4	28	0
TTGAAGCTTTTCAAAAGCAGGCGGGTTCTACCTT	4	52	1
CACCTCACATTATGAAGGAGAAGGACAAGGTAGA	4	78	0
TCTGAATTAGAAACAAGAATTGTGATCCTGCGAA	5	66	1
TGATCCTGCGAAAAAAGGATCAGGATATGGTGGA	5	88	1
TGAGCAAATATTAAAAGTATTTGTAATTCAATTA	5	156	0
AGCTAAACCGATAAAAGAATTAGGGGGGAAAAGG	7	210	1
ATGTTCCCTTTTAAAAGAATCATGTAAGATCAAC	8	236	1
          * ***** **  **
MAP Score: 10.5736

Motif 3
TGCTCATAAGATGTAAAACAAGAATGATGGACAA	0	258	1
TTTTTGAACATTAAGAAAACAGGACCTAAGTCCA	1	45	0
CAAAGTACATTTACTATAAAAGAAAAAAAATGCA	1	100	0
AAGTCTCTATCTGTAAAATAAGAAAAAATGCAGA	2	63	1
TATGATGAAATTCCTTAAAAAGGATTGACATGAA	3	26	1
ATCGAAATGGCTACGAAAGAAGGAGTTTTTG   	3	157	1
TTTGAAAAGCTTCAAAATAAAGAAGCCGGGTCTC	4	33	0
TTTTGAAGCTTTTCAAAAGCAGGCGGGTTCTACC	4	50	1
CATTGAACCATTTCAAATAAAGGAGATATAC   	5	7	0
CTCCATCTGAATTAGAAACAAGAATTGTGATCCT	5	61	1
AATTGTGATCCTGCGAAAAAAGGATCAGGATATG	5	83	1
AGCTTTGGCGTTAGTAATTAAGAATGTTTTAAAT	5	226	1
AGGATTGTTACTGATAAAGCAGGCAAAACCTAAA	8	74	1
          **   *** *****
MAP Score: 10.3117

Motif 4
AGTCAACAACTTTTTTCAAAGTATTTAATGA	0	100	1
TGCATTTTTTTTCTTTTATAGTAAATGTACT	1	100	1
CCCGCCGCGGTTTTTTTATTGGCATAAAGCA	2	19	1
GCATTTTTTCTTATTTTACAGATAGAGACTT	2	63	0
CAAAAACTCCTTCTTTCGTAGCCATTTCGAT	3	157	0
CCCGGCTTCTTTATTTTGAAGCTTTTCAAAA	4	37	1
ATCCTGATCCTTTTTTCGCAGGATCACAATT	5	83	0
          TTTTTGTAAAGGTGATGTCTC	7	0	1
GCTGCTGCCGATTTTTTGGAGAGACGAAAAC	7	173	1
TCCCCCCTAATTCTTTTATCGGTTTAGCTGC	7	208	0
AGGTTTTTATTTTTTTCAGAGGGAAGATGAT	8	152	1
TCTTACATGATTCTTTTAAAAGGGAACATCG	8	234	0
          ******** **
MAP Score: 9.76219

Motif 5
TGAAGCTTTTAGTTGATGTCAGCTGTTTATCAGC	0	128	1
          TGATGATGCCTCCTTATCTTGTCC	0	286	0
TATTGGACTTAGGTCCTGTTTTCTTAATGTTCAA	1	42	1
GAGATTTAGAAGTTCATGTCAATCCTTTTTAAGG	3	38	0
 TTTTTGTAAAGGTGATGTCTCCTGACCTGTATC	7	9	1
TTGCTGCCTTAGATGCTGGTCGTCGCTGGCGGGG	7	79	1
TTGTCGGTTTAGCTGCTGCCGATTTTTTGGAGAG	7	162	1
TCTCTGTCTGTGCTGATGGTAATTTAGGTTTTTA	8	127	1
TTCAGAGGGAAGATGATGATAGTTACAGGATTCA	8	166	1
          ** ***** *  **
MAP Score: 6.77244

Motif 6
    AACAGGTACGTTTTGTCTTGTTTAGTTTTCAAAG	0	6	1
TTTATTACTATAACATTTAGCTTCTTTTAAGTCAACAA	0	71	1
TGCAGATTGCTAGCTTTTTTTTCCCTTTTTGAACATTA	1	66	0
AGCTAGCAATCTGCATTTTTTTTCTTTTATAGTAAATG	1	89	1
GCGCTCCTTCTGCATTTTTTCTTATTTTACAGATAGAG	2	67	0
      GAAATTCGGTTTTTTTTATGATGAAATTCCTT	3	4	1
AACATTGTAGTAACATTTATTTCACATTTGTAATACTA	3	73	0
GTCTCCCAGGCTCCTTTTATGTTTTCAT          	4	0	0
 TGAGAGCGCTGACATTTGTGTTTCCTTGTGTTCACTT	8	9	1
TTTCCTTGTGTTCACTTTTTCTTACATTCACATATGAA	8	30	1
TGATGGTAATTTAGGTTTTTATTTTTTTCAGAGGGAAG	8	140	1
          *    *** * ** * **
MAP Score: 6.14323

Motif 7
TACTGCCGCTTAACGAAGCAGCTTTATTACT	0	49	1
TTTTGAACATTAAGAAAACAGGACCTAAGTC	1	47	0
TATAAAAGAAAAAAAATGCAGATTGCTAGCT	1	89	0
TTTCTTATTTTACAGATAGAGACTTTGTTTT	2	57	0
GTAAAATAAGAAAAAATGCAGAAGGAGCGCT	2	75	1
ATACAGTTCCAACTGATGAAGAGTAAATCGA	3	131	1
TCGAAATGGCTACGAAAGAAGGAGTTTTTG 	3	158	1
AAAAGCTTCAAAATAAAGAAGCCGGGTCTCC	4	32	0
TTTGAAGCTTTTCAAAAGCAGGCGGGTTCTA	4	51	1
TCACCTCACATTATGAAGGAGAAGGACAAGG	4	82	0
GAACCATTTCAAATAAAGGAGATATAC    	5	6	0
TTGTTTCTAATTCAGATGGAGTAATATCTGC	5	51	0
CGTGGTATTATACTGAAGGGGACGATCAAAA	5	196	1
TCCTGACCTGTATCAATGGAGGCACTCGGCT	7	29	1
GTAGGATTGTTACTGATAAAGCAGGCAAAAC	8	72	1
          *** *******
MAP Score: 5.36739

Motif 8
TTGTTGACTTAAAAGAAGCTAAATGTTATAGT	0	77	0
          TAAAAAAACCTGTGCCTATCGC	1	0	1
TCAAAAAGGGAAAAAAAAGCTAGCAATCTGCA	1	72	1
CTATAAAAGAAAAAAAATGCAGATTGCTAGCT	1	89	0
TATGCCAATAAAAAAACCGCGGCGGGCACGCG	2	13	0
TGTAAAATAAGAAAAAATGCAGAAGGAGCGCT	2	74	1
ATTTCATCATAAAAAAAACCGAATTTC     	3	5	0
ATGAAAACATAAAAGGAGCCTGGGAGACCCGG	4	10	1
AGCTTCAAAATAAAGAAGCCGGGTCTCCCAGG	4	28	0
GAAGCTTTTCAAAAGCAGGCGGGTTCTACCTT	4	54	1
CGTCTCTCCAAAAAATCGGCAGCAGCTAAACC	7	167	0
          ******* ** *
MAP Score: 3.07719

Motif 9
GTTATAGTAATAAAGCTGCTTCGTTAAGCGGCAG	0	51	0
TTGTTGACTTAAAAGAAGCTAAATGTTATAGTAA	0	75	0
ATACTTTGAAAAAAGTTGTTGACTTAAAAGAAGC	0	90	0
TATAAAAGAAAAAAAATGCAGATTGCTAGCTTTT	1	86	0
ATGCCAATAAAAAAACCGCGGCGGGCACGCGGTT	2	10	0
TTTATTGGCATAAAGCAACAGTATAAAACAAAGT	2	33	1
GTAAAATAAGAAAAAATGCAGAAGGAGCGCTGGC	2	75	1
ATTTCATCATAAAAAAAACCGAATTTC       	3	3	0
AAATTCCTTAAAAAGGATTGACATGAACTTCTAA	3	33	1
ATGAAAACATAAAAGGAGCCTGGGAGACCCGGCT	4	10	1
AGCTTCAAAATAAAGAAGCCGGGTCTCCCAGGCT	4	26	0
GAAGCTTTTCAAAAGCAGGCGGGTTCTACCTTGT	4	54	1
ATCCTGCGAAAAAAGGATCAGGATATGGTGGAAG	5	90	1
GGGGACGATCAAAAGCTTTGGCGTTAGTAATTAA	5	213	1
TGTGGGCAGCTGAAGTTGCTGCCTTAGATGCTGG	7	64	1
CTAAACCGATAAAAGAATTAGGGGGGAAAAGGTT	7	212	1
          ***** *** *  *
MAP Score: 2.29201

Motif 10
    AACAGGTACGTTTTGTCTTGTTTAGTTTTCA	0	6	1
GCCTATCGCACAGGTTTTTTATTGGACTTAGGTCC	1	23	1
GATTGCTAGCTTTTTTTTCCCTTTTTGAACATTAA	1	65	0
TAGCAATCTGCATTTTTTTTCTTTTATAGTAAATG	1	92	1
GCGCTCCTTCTGCATTTTTTCTTATTTTACAGATA	2	70	0
GTCTCCCAGGCTCCTTTTATGTTTTCAT       	4	3	0
CTGGGAGACCCGGCTTCTTTATTTTGAAGCTTTTC	4	29	1
CAAAAGCAGGCGGGTTCTACCTTGTCCTTCTCCTT	4	63	1
AGCGCTGACATTTGTGTTTCCTTGTGTTCACTTTT	8	14	1
ATTATTTTGACCGATGTTCCCTTTTAAAAGAATCA	8	223	1
          *   **** **** *
MAP Score: 1.72548

Motif 11
TCTTGTTTAGTTTTCAAAGATCATTACTGC	0	25	1
TCAACAACTTTTTTCAAAGTATTTAATGAA	0	102	1
ATTTTGAAGCTTTTCAAAAGCAGGCGGGTT	4	49	1
ATTAAGAATGTTTTAAATGTATACGAGTGC	5	242	1
GTTTTTATTTTTTTCAGAGGGAAGATGATG	8	154	1
TACATGATTCTTTTAAAAGGGAACATCGGT	8	232	0
          **********
MAP Score: 0.276833