AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions010_300.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246440
 numcols =     	10
 undersample = 	1
 oversample = 	1

Input sequences:
#0	pyrC	119	dihydroorotase
#1	amt1	241	ammonium transporter
#2	pyrB	208	aspartate carbamoyltransferase
#3	carB	46	carbamoyl-phosphate synthase, pyrimidine-specific, large chain
#4	pyrR	300	pyrimidine operon regulatory protein PyrR
#5	argF	112	ornithine carbamoyltransferase chain f
#6	purE	100	phosphoribosylaminoimidazole carboxylase
#7	carA	50	carbamoyl-phosphate synthetase subunit A

Motif 1
TGCATTAACTGGCGATCGCCCCCAATATGGATC	2	127	1
GGATTTTTGTGCCGTCGTTCCCCCGAGGTTAAA	0	89	1
ATATGGGGCAGGCGGTAGTCCCCAGGGATCCAT	2	153	0
      ATTAGCAGATTCGCCCCTGTCGTCTGT	7	33	0
GGTGAACAGAGGAGACTTTCCCCTGTTACAGTG	4	233	1
         AGCCGTTATCCCCGATTGTCCAAT	5	98	0
ACCCAAAAGTACAGTTAACCCCCAGAATCCGGA	0	25	1
TTCTGACATCACTGCCATCCCCCCAAGACCATT	5	11	1
CTCCAGCCCCGGAGTTTACCTCCAGGGGTAGTC	4	124	0
TTGCAGAAGAGGATTCATTCCCCTCTTTTTCAG	1	36	1
TCATCAGAGTACTGCTTTTCCCGGGCCGGCAAA	1	112	1
ATACGCTATTAGCGGTTAGCCTCAGTTTAAAGT	6	44	1
AACTTTTGTTACTGTTTGTCCACAATTTGCCGG	1	137	0
GGCAATAATCACAGTCGAGCCAGACTACCCCTG	4	102	1
          **** *  *****
MAP Score: 20.0438

Motif 2
GTACAGTTAACCCCCAGAATCCGGAAAGGTTG	0	33	1
CGGAAAGGTTGCCCAACTTTGCTAGGATTTTA	0	54	1
CACAAAAATCCCCCTAAAATCCTAGCAAAGTT	0	68	0
CTTCCTCGTTCCACTAGATTGGAGCCCAAATA	1	80	1
CTAGATTGGAGCCCAAATATCATCAGAGTACT	1	93	1
TACTGTTTGTCCACAATTTGCCGGCCCGGGAA	1	129	0
TTTAGCTTTTGCCCTAATTTGACTGCCTTTGA	2	12	0
CTGGCGATCGCCCCCAATATGGATCCCTGGGG	2	135	1
GCCTTAGATTGCCTTAGATTGCCTTAGATAGA	2	185	0
CAGGTTTATTGACCAAAAATCCGGGTCCGAAT	3	11	0
TCATACCACGCCCCCACTGTCCGGCAGGGTGA	4	206	1
ATCGAATTAAGCCCCATTTTGCCATACTCGGT	5	45	0
 AGCCGTTATCCCCGATTGTCCAATGTGGTGG	5	91	0
GTCGTCTGTTCCACTAATGTCAAATTGTCCTG	7	10	0
          **** * *****
MAP Score: 19.0965

Motif 3
CCCAAAAGTACAGTTAACCCCCAGAATCCGGAAAGGTTG	0	26	1
CCCTCTTTTTCAGTGTACCGTGCACTTCCTCGTTCCACT	1	56	1
CATCAGAGTACTGCTTTTCCCGGGCCGGCAAATTGTGGA	1	113	1
TCACTGCCAACTTTTGTTACTGTTTGTCCACAATTTGCC	1	139	0
GTGAACAATTCATTCCCTCCTAAGATGCCATCTTGAGAA	1	174	1
TACATGGGAACGTTCCTCCCTAGTGTAGCGAGGAAAAGA	2	86	1
ATGGGGCAGGCGGTAGTCCCCAGGGATCCATATTGGGGG	2	145	0
GCAATAATCACAGTCGAGCCAGACTACCCCTGGAGGTAA	4	103	1
AAAGTCTCCTCTGTTCACCCTGCCGGACAGTGGGGGCGT	4	213	0
TCTGACATCACTGCCATCCCCCCAAGACCATTAACCGAG	5	12	1
ACATCGATCGAATTAAGCCCCATTTTGCCATACTCGGTT	5	44	0
        AGCCGTTATCCCCGATTGTCCAATGTGGTGG	5	91	0
          * **   *****     **
MAP Score: 11.9952

Motif 4
CAAAAGTACAGTTAACCCCCAGAATCCGGA	0	28	1
TTTGTGCCGTCGTTCCCCCGAGGTTAAAAG	0	94	1
GAAGAGGATTCATTCCCCTCTTTTTCAGTG	1	41	1
GTGAACAATTCATTCCCTCCTAAGATGCCA	1	174	1
TACATGGGAACGTTCCTCCCTAGTGTAGCG	2	86	1
CATTAACTGGCGATCGCCCCCAATATGGAT	2	129	1
CAGCCCCGGAGTTTACCTCCAGGGGTAGTC	4	124	0
ACAGAGGAGACTTTCCCCTGTTACAGTGTC	4	238	1
GACATCACTGCCATCCCCCCAAGACCATTA	5	15	1
       AGCCGTTATCCCCGATTGTCCAA	5	99	0
CGCTATTAGCGGTTAGCCTCAGTTTAAAGT	6	47	1
   ATTAGCAGATTCGCCCCTGTCGTCTGT	7	33	0
          **********
MAP Score: 11.8849

Motif 5
GTACAGTTAACCCCCAGAATCCGGAAAGGTTGCCCAACTTTGC	0	33	1
GGGGATTTTTGTGCCGTCGTTCCCCCGAGGTTAAAAGGTTAA 	0	87	1
TGATATTTGGGCTCCAATCTAGTGGAACGAGGAAGTGCACGGT	1	72	0
AGTACTGCTTTTCCCGGGCCGGCAAATTGTGGACAAACAGTAA	1	119	1
ACATGGGAACGTTCCTCCCTAGTGTAGCGAGGAAAAGACTTGC	2	87	1
CTGGCGATCGCCCCCAATATGGATCCCTGGGGACTACCGCCTG	2	135	1
       AATGCTCCAATCGCCTTGATTGTATCGAATGATGCA	4	3	1
AAAGACCTCTGCACCGCCGACGGGTCTGGATTATGGGCAATAA	4	67	1
ATCATACCACGCCCCCACTGTCCGGCAGGGTGAACAGAGGAGA	4	205	1
CACTGCCATCCCCCCAAGACCATTAACCGAGTATGGCAAAATG	5	20	1
GTTAATTCGACCACCACATTGGACAATCGGGGATAACGGCT  	5	81	1
          ** **      *   *  * ***
MAP Score: 9.12286

Motif 6
CCCTCTTTTTCAGTGTACCGTGCACTTCCTCGTT	1	56	1
TGTCCACAATTTGCCGGCCCGGGAAAAGCAGTAC	1	120	0
CTTGCATTAACTGGCGATCGCCCCCAATATGGAT	2	125	1
AGATATGGGGCAGGCGGTAGTCCCCAGGGATCCA	2	154	0
TAATCCAGACCCGTCGGCGGTGCAGAGGTCTTTT	4	66	0
GAGGTAAACTCCGGGGCTGGAGCCATAAAGATTA	4	135	1
TTCACCCTGCCGGACAGTGGGGGCGTGGTATGAT	4	205	0
AAACAACTTTTTGGCATCGGTGCAGGTGGTGAGC	4	275	1
       TTTCTGACATCACTGCCATCCCCCCAA	5	3	1
ACCACCACATTGGACAATCGGGGATAACGGCT  	5	90	1
 CAGGACAATTTGACATTAGTGGAACAGACGACA	7	9	1
ATTAGTGGAACAGACGACAGGGGCGAATCTGCTA	7	24	1
          * * ** *** ***
MAP Score: 8.53519

Motif 7
TGTACTTTTGGGTTGAGCCAATCAGCGC     	0	5	0
AATCCTAGCAAAGTTGGGCAACCTTTCCGGATT	0	50	0
         AGTCAAAGGCAGTCAAATTAGGGC	2	1	1
AAGGCAGTCAAATTAGGGCAAAAGCTAAACACC	2	15	1
CCTTAGATAGATATGGGGCAGGCGGTAGTCCCC	2	163	0
CCCCATATCTATCTAAGGCAATCTAAGGCAATC	2	178	1
ATCTAAGGCAATCTAAGGCAATCTAAGGCA   	2	188	1
TGATTGTATCGAATGATGCAGTCTCTAAAATTG	4	26	1
ACGGGTCTGGATTATGGGCAATAATCACAGTCG	4	86	1
TTCGACCACCACATTGGACAATCGGGGATAACG	5	86	1
TTTGACTTTAAACTGAGGCTAACCGCTAATAGC	6	48	0
          *  ******** *
MAP Score: 5.67194

Motif 8
CTTTTGGGTTGAGCCAATCAGCGC       	0	3	0
ACTGAAAAAGAGGGGAATGAATCCTCTTCTG	1	39	0
CTAGTGGAACGAGGAAGTGCACGGTACACTG	1	66	0
GGCATCTTAGGAGGGAATGAATTGTTCACTG	1	172	0
     AGTCAAAGGCAGTCAAATTAGGGCAA	2	5	1
ATTAGGGCAAAAGCTAAACACCGTTGGCGCA	2	26	1
CTAGTGTAGCGAGGAAAAGACTTGCATTAAC	2	105	1
ATATCTATCTAAGGCAATCTAAGGCAATCTA	2	182	1
AAGGCAATCTAAGGCAATCTAAGGCA     	2	192	1
TGTATCGAATGATGCAGTCTCTAAAATTGTA	4	30	1
AATCACAGTCGAGCCAGACTACCCCTGGAGG	4	108	1
ACTACCCCTGGAGGTAAACTCCGGGGCTGGA	4	125	1
ACACTGTAACAGGGGAAAGTCTCCTCTGTTC	4	236	0
CAGACGACAGGGGCGAATCTGCTAAT     	7	34	1
          **** ******
MAP Score: 4.53399

Motif 9
AGTTGGGCAACCTTTCCGGATTCTGGGGGTTAACTGTAC	0	33	0
TTTGCTAGGATTTTAGGGGGATTTTTGTGCCGTCGTTCC	0	71	1
GTGCCGTCGTTCCCCCGAGGTTAAAAGGTTAA       	0	97	1
CCTTAGATTGCCTTAGATAGATATGGGGCAGGCGGTAGT	2	167	0
       GATTCGGACCCGGATTTTTGGTCAATAAACCT	3	3	1
   CCGTTCCCATATCCAGGTTTATTGACCAAAAATCCG	3	20	0
ATCATTCGATACAATCAAGGCGATTGGAGCATT      	4	4	0
TAATCCAGACCCGTCGGCGGTGCAGAGGTCTTTTACGGA	4	61	0
CTTTATGGCTCCAGCCCCGGAGTTTACCTCCAGGGGTAG	4	126	0
GCCCCCACTGTCCGGCAGGGTGAACAGAGGAGACTTTCC	4	215	1
CTTTTTGGCATCGGTGCAGGTGGTGAGCC          	4	281	1
CCCCATTTTGCCATACTCGGTTAATGGTCTTGGGGGGAT	5	27	0
ACCACATTGGACAATCGGGGATAACGGCT          	5	93	1
AATTGAGATGACGAAGATGGAGGTTTGACTTTAAACTGA	6	65	0
          **   *  **** *  * *
MAP Score: 0.92837