AlignACE 3.0 10/20/99
AlignACE2 -i BS/BS_fusions011_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944240863
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	mobA	136	molybdopterin-guanine dinucleotide biosynthesis protein A
#1	moeB	50	molybdopterin biosynthesis protein
#2	yknU	223	similar to ABC transporter (ATP-binding protein)
#3	yknW	109	yknW
#4	ytsC	101	similar to ABC transporter (ATP-binding protein)
#5	ytsA	96	similar to two-component response regulator [YtsB]
#6	ytrD	29	similar to cytochrome c oxidase subunit
#7	ytrA	300	similar to transcriptional regulator (GntR family)
#8	yvrM	32	similar to hypothetical proteins
#9	yvrN	104	alternate gene name: yziB; similar to hypothetical proteins from B. subtilis
#10	yvrP	170	similar to hypothetical proteins from B. subtilis
#11	fhuB	97	ferrichrome ABC transporter (permease)
#12	opuBA	274	choline ABC transporter (ATP-binding protein)

Motif 1
GTTTTTTTGTAAAAAAAGGATTGACTTTGT	7	11	1
AAGATAGATGAAAAAGAGAATCATTATCAT	11	30	1
CAAGAACAAGAAAAAAAGAACAAGCGATCA	7	194	0
ATACACTTGATAAAAAAGGAAAAAGTGCGG	5	68	1
TAATCTCATTATAAAAAGGAATGCCGGGCT	4	57	0
CATAGTTTACAGAAAGAGGAGATCGTT   	10	153	1
TGAAATACAGAAAAACCGGACGGCTGAAAT	2	22	0
TATGAAACATAAAAAACGAAACAAACGTAA	7	138	1
AAAATGCTGTCAAAAGAGAATTTGGCAGGA	12	60	1
ATACGGCGAACAAAAAAGAAAAGCATGTGA	4	18	0
GACGTCGCCAAAAAAGCTGACAGAACCGTT	9	56	1
TGTCTGTTTATTAAAGAGGAATAGCTGTTC	0	56	0
AATTTATTAGAAAAACATGAAACTTTTTGA	3	43	1
CCGTCATTTCAATAAAAGGATTGCAAGTCT	10	77	1
CCTTTTATAGATAAAAATGATCAATTATAC	7	251	0
TAAGATGACATAAAAGATAAGGAGAACAGG	1	26	1
    CGGGGCAATAACATGATAAGATGACA	1	6	1
          **********
MAP Score: 14.5506

Motif 2
TCAACGCTACTGCTTGTCTGTTTATTAAAGAGG	0	67	0
AGTAGCGTTGAGCCTTTGCTTTTGCTATGCTTT	0	89	1
ACGGCTGAAATGCCGTCCGGTTT          	2	0	0
ACGGCATTTCAGCCGTCCGGTTTTTCTGTATTT	2	17	1
CTCCATAATTAGACTGAAATTTTGAAAAATAAT	2	141	1
   TATGAAAAGCCTTCAATATTGAAGGTTTTT	3	7	1
AAATGTCACATGCTTTTCTTTTTTGTTCGCCGT	4	13	1
TAAAAAGGAATGCCGGGCTTTTCCTTCGATACG	4	43	0
CGGCTGTCTCAGCCGGCTCGTTCGCA       	5	3	0
CGGCTGAGACAGCCGGCTTTTTCTATAGCGCAT	5	21	1
CTATAGCGCATGCTGGCGTTTTGCTATACACTT	5	43	1
      GAAATGCCTTAGGTTTGGAGGGAAGTG	6	4	1
ATAATGGTCTTGCCTTCCCGATGCAGT      	9	4	0
TTTTTATCAGAGACGGAGAGTTGGTATTAG   	9	84	1
CCCGGCTTCAAACCGGGATTTTT          	10	0	0
CCCGGTTTGAAGCCGGGATTTTTTTTATTCGGC	10	16	1
          ******   ****
MAP Score: 14.439

Motif 3
    AAACCGGACGGCATTTCAGCCGTCCGG	2	6	1
ATTTCAGCCGTCCGGTTTTTCTGTATTTCAT	2	22	1
CTTCAATATTGAAGGCTTTTCATA       	3	3	0
AAAAAGGAATGCCGGGCTTTTCCTTCGATAC	4	44	0
GGCTGAGACAGCCGGCTTTTTCTATAGCGCA	5	22	1
TATAGCGCATGCTGGCGTTTTGCTATACACT	5	44	1
CCTCCAAACCTAAGGCATTTC          	6	0	0
AAACGGTTCTGTCAGCTTTTTTGGCGACGTC	9	56	0
CCGGCTTCAAACCGGGATTTTT         	10	1	0
CCGGTTTGAAGCCGGGATTTTTTTTATTCGG	10	17	1
TCTATTTGATTCCGTCATTTCAATAAAAGGA	10	66	1
TAAAAGGATTGCAAGTCTTTTTGAATTAATA	10	89	1
ATTCTCTTTTGACAGCATTTTCGCCGTATCA	12	50	0
          ****** ****
MAP Score: 14.2649

Motif 4
GAACCATCTCCCTCATGATGTTAACACTACA	0	12	1
TTGAGCCTTTGCTTTTGCTATGCTTTTAACG	0	96	1
TCAGCCGTCCGGTTTTTCTGTATTTCATTGG	2	25	1
AAACATGAAACTTTTTGATATCCTTCCCGTA	3	55	1
GCCCGGCATTCCTTTTTATAATGAGATTATC	4	58	1
GAGACAGCCGGCTTTTTCTATAGCGCATGCT	5	26	1
CGCATGCTGGCGTTTTGCTATACACTTGATA	5	49	1
GCACTTTTTCCTTTTTTATCAAGTGTATAGC	5	65	0
          CGTTTTTTTGTAAAAAAAGGA	7	0	1
CGTTTGTTTCGTTTTTTATGTTTCATAACTG	7	134	0
TATAATTGATCATTTTTATCTATAAAAGGTT	7	252	1
AAGGCAAGACCATTATTATGATAACCCACGA	9	21	1
CTGACAGAACCGTTTTTATCAGAGACGGAGA	9	72	1
  AACGATCTCCTCTTTCTGTAAACTATGTA	10	151	0
 ATCTCATACCTTCTTTCTAAAAGATAGATG	11	9	1
TAATGATTCTCTTTTTCATCTATCTTTTAGA	11	25	0
AAAAGAGAATCATTATCATCTGTGATTATAC	11	41	1
ATTTTATAAACTTTATTCTATAATGGGAAGC	12	184	1
          * *********
MAP Score: 11.1644

Motif 5
CGGCTGAAATGCCGTCCGGTTT         	2	1	0
CGGCATTTCAGCCGTCCGGTTTTTCTGTATT	2	18	1
CTTTTTGATATCCTTCCCGTACTATTTGTTA	3	65	1
TTTTTTGTTCGCCGTATCGAAGGAAAAGCCC	4	31	1
GGCTGTCTCAGCCGGCTCGTTCGCA      	5	4	0
TATAGAAAAAGCCGGCTGTCTCAGCCGGCTC	5	17	0
TAATGGTCTTGCCTTCCCGATGCAGT     	9	5	0
CTTTTTTGGCGACGTCCGGGTCGTGGGTTAT	9	41	0
ATACCAACTCTCCGTCTCTGATAAAAACGGT	9	80	0
CAGCATTTTCGCCGTATCAAAAATGTGGTAT	12	38	0
          ********* *
MAP Score: 7.83229

Motif 6
CACTACAATATGCAAATACTGAACAGCTATTCCTC	0	36	1
GCTATACACTTGATAAAAAAGGAAAAAGTGCGGTG	5	65	1
  CGTTTTTTTGTAAAAAAAGGATTGACTTTGTGA	7	8	1
AAGTATTTATTGTATTAAGTGTACTAATTGAAGTA	7	47	1
TTTATATTAGTGTCTATAGTGTATTACTTCAATTA	7	71	0
CGGTTTTGAATGGCAAAAAAGTATAATTGATCATT	7	231	1
CGGAATCAAATAGAAAAATTGTATTTTCAAAGCCG	10	45	0
TTACATAGTTTACAGAAAGAGGAGATCGTT     	10	150	1
GCGAAAATGCTGTCAAAAGAGAATTTGGCAGGAAA	12	57	1
ATAAATAATATGAACAAATTGTAAACTTTTTATTT	12	153	1
AAATTTAAACTGAACAAATTGAATAAACTTAATTT	12	235	1
          ** * *** ** * *
MAP Score: 6.75571

Motif 7
TTTCAGCCGTCCGGTTTTTCTGTATTTCATTGGC	2	23	1
CTCAGCATACAATGATTTTCTGTAAGCGTTTATT	2	72	1
GAAAATGTCACATGCTTTTCTTTTTTGTTCGCCG	4	11	1
AAAAGCCCGGCATTCCTTTTTATAATGAGATTAT	4	54	1
CTGAGACAGCCGGCTTTTTCTATAGCGCATGCTG	5	24	1
CGACTCACCGCACTTTTTCCTTTTTTATCAAGTG	5	71	0
CTCACAAAGTCAATCCTTTTTTTACAAAAAAACG	7	10	0
TCAATATATAAATGATTTTATATTAGTGTCTATA	7	88	0
GTGATCGCTTGTTCTTTTTTTCTTGTTCTTGTGA	7	193	1
AGTATAATTGATCATTTTTATCTATAAAAGGTTC	7	250	1
    TTACTTCCCTACTTTCTATACGATCTGAAC	7	280	0
GGTTTGAAGCCGGGATTTTTTTTATTCGGCTTTG	10	19	1
CTTTGAAAATACAATTTTTCTATTTGATTCCGTC	10	48	1
AAAAGGATTGCAAGTCTTTTTGAATTAATAGATA	10	90	1
    AACGATCTCCTCTTTCTGTAAACTATGTAA	10	150	0
     ATCTCATACCTTCTTTCTAAAAGATAGAT	11	5	1
CACAGATGATAATGATTCTCTTTTTCATCTATCT	11	31	0
TGTCAATATACCACATTTTTGATACGGCGAAAAT	12	31	1
CAATTTCCTGCCAAATTCTCTTTTGACAGCATTT	12	61	0
AACAAATTGTAAACTTTTTATTTTATAAACTTTA	12	165	1
          *   ******* **
MAP Score: 2.35364

Motif 8
GCAAATACTGAACAGCTATTCCTCTTTAATAAAC	0	47	1
    AAACCGGACGGCATTTCAGCCGTCCGGTTT	2	6	1
ATGATTTTCTGTAAGCGTTTATTCTACATATGTT	2	83	1
GGCTGAGACAGCCGGCTTTTTCTATAGCGCATGC	5	22	1
AGATGCCGCAATCAGCATTGGCACGTTACGTTTG	7	159	0
ATTCTCTTTTGACAGCATTTTCGCCGTATCAAAA	12	47	0
ATGCGGGTAAATCAGCGTTTACACATACTTTATA	12	122	1
          * **** *** * *
MAP Score: 1.09159