AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions039_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944242002
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	yjaX	164	similar to 3-oxoacyl- acyl-carrier protein synthase
#1	yjaY	22	similar to 3-oxoacyl- acyl-carrier protein synthase
#2	yjaZ	75	yjaZ
#3	appD	191	oligopeptide ABC transporter (ATP-binding protein)
#4	appA	87	oligopeptide ABC transporter (oligopeptide-binding protein)
#5	ykeA	168	alternate gene name: yzcA; similar to pyrroline-5-carboxylate reductase
#6	dppA	128	dipeptide ABC transporter
#7	dinG	125	ATP-dependent helicase
#8	panB	245	ketopantoate hydroxymethyltransferase
#9	ypjH	31	alternate gene name: jojH; similar to lipopolysaccharide biosynthesis-related protein
#10	ypjD	300	alternate gene name: jojD
#11	yvyE	216	alternate gene name: yvhK; similar to hypothetical proteins

Motif 1
    GTGATCGCCTCCTCTTTTAATCCTAT	2	59	0
   TAGATATTCCCCCTCTTGAAATGTTCG	4	70	0
     AACGCTCCTCCTTTTTTACTAAATT	6	113	0
GCTCCCCTTTCCCCCCTCTTGTTGTCAAAC	3	167	0
        ACGCCTCCTTTCCATATACCAT	0	2	1
   AAGAAAAGCCCCCTTTATCGGGGGTTT	7	7	1
TAGTGTGCATACCCCCTCTCAAAGCTGTGC	4	18	0
AAACCTCCTATCATCCTCTTACATGTTAGC	10	274	0
    GTTTTCTCCTCCTCATGTTTAGAGGA	8	229	0
CATCACACAAAACCCCTTTTCCTTCCATTA	10	168	1
   TAGGGAAGACTCCTTTATATCTTAAAT	0	147	0
GATAAAAAAAGAATCCTCTTTCAAGGAT  	6	8	0
ATTGCATTTTTCCTCTTTTTTTAATATAAT	6	67	1
TGTGTGCACCTCACCTTTTT          	1	0	0
          **********
MAP Score: 15.7785

Motif 2
CATAATTTAGTAAAAAAGGAGGAGCGTT  	6	110	1
     ATCCTTGAAAGAGGATTCTTTTTTT	6	5	1
TGCATAGGATTAAAAGAGGAGGCGATCAC 	2	56	1
CATTCAGTGATAAAAAAAGAATCCTCTTTC	6	16	0
CAAATTATATTAAAAAAAGAGGAAAAATGC	6	70	0
TTATAGTGGATGAAAAAGAAAACAGCAAAC	10	211	1
TGCCTTGATCCAAAAAAGGACTGGGACAGA	8	108	1
TATTGCCATGTGAAAAAAAATAGGATAGAA	0	70	1
CTCAAAATCTTAAAAGAAAACCCCCGATAA	7	24	0
AATAGACATGTGAAAATAGAGAAACGGAGT	5	17	0
TTAGCTAACATGTAAGAGGATGATAGGAGG	10	271	1
AACTGTGGGATAAAAATGAAAAGATTATGG	5	87	1
AACCTATCAATATAAATAGACATGTGAAAA	5	31	0
          **********
MAP Score: 13.8581

Motif 3
         ACGCCTCCTTTCCATATACCAT	0	1	1
CTTGTGTGCACCTCACCTTTTT         	1	1	0
     GTGATCGCCTCCTCTTTTAATCCTAT	2	59	0
TCCCCTTTCCCCCCTCTTGTTGTCAAACGTT	3	164	0
    TGTTGCCCGCACAGCTTTGAGAGGGGG	4	6	1
GTACCGTTTTCCGCACTTTTTCACAATTTCC	5	116	0
      AACGCTCCTCCTTTTTTACTAAATT	6	113	0
AACGGTTTTGCCGCTCCATTTCCGTACAAAA	7	59	1
CGCCTGCGAACTGCACCTATTATTAAAATAG	8	59	1
  GTTTTCTCCTCCTCATGTTTAGAGGAGAT	8	226	0
GAAAAAATTGCCGCTCCGATTAAAATAAAAA	10	109	1
          ******** **
MAP Score: 12.6141

Motif 4
TATTACATTTATCCTAAAAAATTCTTGATTTTGCAAAAT	3	40	1
TGAGTTTATCATAAACAAAAACTGTGGGATAAAAATGAA	5	68	1
ATTATGGGAAATTGTGAAAAAGTGCGGAAAACGGTACAC	5	110	1
TCATTCAGTGATAAAAAAAGAATCCTCTTTCAAGGAT  	6	8	0
AATGCAATATAACTGGGAAAAATCTCAATCATTCAGTGA	6	36	0
TATATTAAAAAAAGAGGAAAAATGCAATATAACTGGGAA	6	56	0
CAATTCTTGCATACGACAAAAGTGTAACACGTTTTGTAC	7	82	0
CCTTTTTTGGATCAAGGCAGACTGCTGCAATGTCTATCT	8	88	0
GGAAAAGGGCATAAAGCAAAAGTGTAATACCTGTAAAAC	10	23	1
GAACCAAGCCAAATGAAAAAATTGCCGCTCCGATTAAAA	10	95	1
GCTCCGATTAAAATAAAAAATATGTTTTTTAATCTAATT	10	121	1
ATGAAAAAGAAAACAGCAAACGTGCTTAAACATTTGTCA	10	220	1
ATGTCGAATTATAATGAAAGAATGCGTATATTCTAGAAA	11	72	1
AAGAGTAGATAGTATATAAAAATGTTTTTTTCTAGAATA	11	100	0
TACGCACAAAAATTCTAAAGACTGTACGAATTTGTATAG	11	152	1
CCTCCTGCTAAGCATAAAAGACTGCCTATACAAATTCGT	11	177	0
          * *    **** ***   *
MAP Score: 9.28067

Motif 5
CTATCAGTTCATCTTACTCATAGAGTATGGTATA	0	24	0
TTTTGTGTGCATAGGATTAAAAGAGGAGGCGATC	2	49	1
TTGCAAAATGATTGTAATAATATACAACTATAAA	3	70	1
ACTTGAGTTTATCATAAACAAAAACTGTGGGATA	5	65	1
CAATCATTCAGTGATAAAAAAAGAATCCTCTTTC	6	16	0
ATTCTAACAAATTATATTAAAAAAAGAGGAAAAA	6	73	0
GAATATTCATAATTTAGTAAAAAAGGAGGAGCGT	6	103	1
TACTCTCAAAATCTTAAAAGAAAACCCCCGATAA	7	24	0
CGAACTGCACCTATTATTAAAATAGATAGACATT	8	65	1
AAAATTGCCGCTCCGATTAAAATAAAAAATATGT	10	112	1
GCTTGGAGAAATTAGATTAAAAAACATATTTTTT	10	135	0
AATTACATTTATAATAAAAATATATGACAACGCC	11	26	0
ATTATGTCGAATTATAATGAAAGAATGCGTATAT	11	69	1
GAATGCGTATATTCTAGAAAAAAACATTTTTATA	11	91	1
TAAAGAGTAGATAGTATATAAAAATGTTTTTTTC	11	107	0
TCTACTCTTTATGATACCAAAATACGCACAAAAA	11	130	1
          **  ** ***** *
MAP Score: 8.9765

Motif 6
         AAAAAGGTGAGGTGCACACAAG    	1	1	1
GCATAGGATTAAAAGAGGAGGCGATCAC       	2	57	1
ACGTTTGACAACAAGAGGGGGGAAAGGGGAGCTAG	3	165	1
AACGAACATTTCAAGAGGGGGAATATCTA      	4	68	1
TTTATCATAAACAAAAACTGTGGGATAAAAATGAA	5	72	1
GGAAATTGTGAAAAAGTGCGGAAAACGGTACACTT	5	116	1
CCTTTCATATACAATATGAAGTGTACCGTTTTCCG	5	134	0
AAATTATATTAAAAAAAGAGGAAAAATGCAATATA	6	64	0
ATAATTTAGTAAAAAAGGAGGAGCGTT        	6	111	1
CCATTTCCGTACAAAACGTGTTACACTTTTGTCGT	7	74	1
GCCTTGATCCAAAAAAGGACTGGGACAGAGGGATG	8	109	1
ACCTTCCGTTACAACGAGAAGGATTCTTCACTTTC	8	161	0
TCATCTCCTCTAAACATGAGGAGGAGAAAAC    	8	224	1
TTGGTTCATTTCAATATGCAGAACAATCTGGCTGA	10	67	0
TTATGATACCAAAATACGCACAAAAATTCTAAAGA	11	138	1
          **** * * ** * *
MAP Score: 8.35778

Motif 7
ACCTGATTGATCTTCTAAATTTAAGATATAAAGGAGTCTTCCC	0	129	1
TTTGTTAGAATATTCATAATTTAGTAAAAAAGGAGGAGCGTT 	6	96	1
CCCCTCTTGTTGTCAAACGTTTTCAAGAGAAAGCAATCCCTTT	3	142	0
ATATTGCATTTTTCCTCTTTTTTTAATATAATTTGTTAGAATA	6	65	1
GGGGGTTTTCTTTTAAGATTTTGAGAGTAAAACGGTTTTGCCG	7	29	1
TCCACTATAATATAAACGCTATCTAATGGAAGGAAAAGGGGTT	10	178	0
TCAGCCAGATTGTTCTGCATATTGAAATGAACCAAGCCAAATG	10	67	1
AATTCAATATTATTTATTATTTCTGAATAAAGGGATTGCTTTC	3	114	1
ACGACAAAAGTGTAACACGTTTTGTACGGAAATGGAGCGGCAA	7	66	0
TTATATACTATCTACTCTTTATGATACCAAAATACGCACAAAA	11	120	1
CTTGAAAGAGGATTCTTTTTTTATCACTGAATGATTGAGATTT	6	13	1
TCATTAATAATATTACATTTATCCTAAAAAATTCTTGATTTTG	3	30	1
TAACGGAAGGTTTTTTGGCTTGCAGAAGAAAACGGCAGATCAT	8	185	1
          * * *    ***   *   ** *
MAP Score: 6.9407

Motif 8
TTCTATCCTATTTTTTTTCACATGGCAATATATTCGTCTAAACTA	0	55	0
CACAACCTGATTGATCTTCTAAATTTAAGATATAAAGGAGTCTTC	0	125	1
TAGCCGGTTTTTTTTGTGTGCATAGGATTAAAAGAGGAGGCGATC	2	38	1
TAAAAAATTCTTGATTTTGCAAAATGATTGTAATAATATACAACT	3	54	1
AAAGCAATCCCTTTATTCAGAAATAATAAATAATATTGAATTATC	3	111	0
AAGGGATTGCTTTCTCTTGAAAACGTTTGACAACAAGAGGGGGGA	3	143	1
TTCTAACAAATTATATTAAAAAAAGAGGAAAAATGCAATATAACT	6	61	0
AACGCTCCTCCTTTTTTACTAAATTATGAATATTCTAACAAATTA	6	93	0
CAAAACCGTTTTACTCTCAAAATCTTAAAAGAAAACCCCCGATAA	7	24	0
CGAACTGCACCTATTATTAAAATAGATAGACATTGCAGCAGTCTG	8	65	1
    GAGGGGCTGATGTGGAAAAGGGCATAAAGCAAAAGTGTAAT	10	6	1
TTAGATAGCGTTTATATTATAGTGGATGAAAAAGAAAACAGCAAA	10	195	1
TGCAGATCAATTACATTTATAATAAAAATATATGACAACGCCGTG	11	23	0
ATAAATGTAATTGATCTGCAAATTATGTCGAATTATAATGAAAGA	11	48	1
TGTGCGTATTTTGGTATCATAAAGAGTAGATAGTATATAAAAATG	11	115	0
          **  * *   ***      * *  *
MAP Score: 4.61239

Motif 9
      ACGCCTCCTTTCCATATACCATACTCT	0	4	1
AACCTGATTGATCTTCTAAATTTAAGATATAAA	0	128	1
 TAGGGAAGACTCCTTTATATCTTAAATTTAGA	0	142	0
  CTTGTGTGCACCTCACCTTTTT         	1	1	0
TGATCGCCTCCTCTTTTAATCCTATGCACACAA	2	51	0
TCCCCTTTCCCCCCTCTTGTTGTCAAACGTTTT	3	162	0
ATTTCCCATAATCTTTTCATTTTTATCCCACAG	5	89	0
GAAAACGGTACACTTCATATTGTATATGAAAGG	5	136	1
TATTGCATTTTTCCTCTTTTTTTAATATAATTT	6	66	1
      AACGCTCCTCCTTTTTTACTAAATTAT	6	111	0
 TAAAATGGACACCTCAATTCTTGCATACGACA	7	103	0
ACGAGAAGGATTCTTCACTTTCTAAAGTTCGGC	8	150	0
AAGTGAAGAATCCTTCTCGTTGTAACGGAAGGT	8	163	1
GGCAGATCATCTCCTCTAAACATGAGGAGGAGA	8	218	1
TTGCTTTATGCCCTTTTCCACATCAGCCCCTC 	10	9	0
AGCACGTTTGCTGTTTTCTTTTTCATCCACTAT	10	213	0
TGAACGAAACCTCCTATCATCCTCTTACATGTT	10	277	0
TTTATATACTATCTACTCTTTATGATACCAAAA	11	119	1
          *******  ** *
MAP Score: 1.76962

Motif 10
       GTGATCGCCTCCTCTTTTAATCCTATG	2	58	0
GAATAAAGGGATTGCTTTCTCTTGAAAACGTTTG	3	138	1
CTAGCTCCCCTTTCCCCCCTCTTGTTGTCAAACG	3	166	0
      TAGATATTCCCCCTCTTGAAATGTTCGT	4	69	0
      CATGTTCACTCCGTTTCTCTATTTTCAC	5	4	1
GCAAAACCGTTTTACTCTCAAAATCTTAAAAGAA	7	36	0
TTGATTTTGGTATACTTCCATTGGGCAGTATCGC	8	28	1
AGAAGGATTCTTCACTTTCTAAAGTTCGGCGAGT	8	146	0
TGAAGAATCCTTCTCGTTGTAACGGAAGGTTTTT	8	166	1
       GTTTTCTCCTCCTCATGTTTAGAGGAG	8	228	0
CAAAACCCCTTTTCCTTCCATTAGATAGCGTTTA	10	175	1
GCTGTTTTCTTTTTCATCCACTATAATATAAACG	10	203	0
       AATTTCCCTCCGTCACGGCGTTGTCAT	11	3	1
          *** * **** * *
MAP Score: 0.846915