AlignACE 3.0 10/20/99
AlignACE2 -i CY/CY_fusions010_100.orf 
Parameter values:
 expect =      	10
 gcback =      	0.38
 minpass =     	200
 seed =        	944246422
 numcols =     	10
 undersample = 	1
 oversample = 	1

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

Motif 1
ACCCAAAAGTACAGTTAACCCCCAGAATCCGGAAA	0	25	1
GAACGACGGCACAAAAATCCCCCTAAAATCCTAGC	0	74	0
GGATTTTTGTGCCGTCGTTCCCCCGAGGTTAAAAG	0	89	1
TGCATTAACTGGCGATCGCCCCCAATATGGATCCC	1	127	1
ATATGGGGCAGGCGGTAGTCCCCAGGGATCCATAT	1	151	0
TCACAGTCGAGCCAGACTACCCCTGGAGGTAAACT	3	110	1
TAATCTTTATGGCTCCAGCCCCGGAGTTTACCTCC	3	134	0
TCTAGATCATACCACGCCCCCACTGTCCGGCAGGG	3	200	1
GGTGAACAGAGGAGACTTTCCCCTGTTACAGTGTC	3	233	1
TTCTGACATCACTGCCATCCCCCCAAGACCATTAA	4	11	1
         AGCCGTTATCCCCGATTGTCCAATGT	4	96	0
      ATTAGCAGATTCGCCCCTGTCGTCTGTTC	5	31	0
          ****    ***** *
MAP Score: 19.3605

Motif 2
CAACCTTTCCGGATTCTGGGGGTTAACTGTAC	0	33	0
TAAAATCCTAGCAAAGTTGGGCAACCTTTCCG	0	54	0
AACTTTGCTAGGATTTTAGGGGGATTTTTGTG	0	68	1
TCAAAGGCAGTCAAATTAGGGCAAAAGCTAAA	1	12	1
CCCCAGGGATCCATATTGGGGGCGATCGCCAG	1	135	0
TCTATCTAAGGCAATCTAAGGCAATCTAAGGC	1	185	1
ATTCGGACCCGGATTTTTGGTCAATAAACCTG	2	11	1
TGGGCAATAATCACAGTCGAGCCAGACTACCC	3	100	1
TCACCCTGCCGGACAGTGGGGGCGTGGTATGA	3	206	0
ACCGAGTATGGCAAAATGGGGCTTAATTCGAT	4	45	1
CCACCACATTGGACAATCGGGGATAACGGCT 	4	91	1
CAGGACAATTTGACATTAGTGGAACAGACGAC	5	10	1
          ***** * ****
MAP Score: 18.539

Motif 3
GATTTTTGTGCCGTCGTTCCCCCGAGGTTAAAAGGTTA	0	90	1
     ATTAGCAGATTCGCCCCTGTCGTCTGTTCCACT	5	27	0
CACAGTCGAGCCAGACTACCCCTGGAGGTAAACTCCGG	3	111	1
CCGTAAAAGACCTCTGCACCGCCGACGGGTCTGGATTA	3	62	1
TCTGACATCACTGCCATCCCCCCAAGACCATTAACCGA	4	12	1
TGCATTAACTGGCGATCGCCCCCAATATGGATCCCTGG	1	127	1
GTGAACAGAGGAGACTTTCCCCTGTTACAGTGTCAGTG	3	234	1
AACGACGGCACAAAAATCCCCCTAAAATCCTAGCAAAG	0	70	0
GTTCTAGATCATACCACGCCCCCACTGTCCGGCAGGGT	3	198	1
GGAAAGTCTCCTCTGTTCACCCTGCCGGACAGTGGGGG	3	216	0
CTAATCTTTATGGCTCCAGCCCCGGAGTTTACCTCCAG	3	132	0
TAGGGCAAAAGCTAAACACCGTTGGCGCATTTCAGAAT	1	28	1
      GGCTCACCACCTGCACCGATGCCAAAAAGTTG	3	278	0
          *     * ******  **
MAP Score: 9.73265

Motif 4
ATGTTAATTCGACCACCACATTGGACAATCGGGGATAACGGCT  	4	79	1
AACTGGCGATCGCCCCCAATATGGATCCCTGGGGACTACCGCCTG	1	133	1
CCTCTGCACCGCCGACGGGTCTGGATTATGGGCAATAATCACAGT	3	72	1
AAGTTGTTTTGTCACTGACACTGTAACAGGGGAAAGTCTCCTCTG	3	239	0
CATTTTGCCATACTCGGTTAATGGTCTTGGGGGGATGGCAGTGAT	4	18	0
TATGGCTCCAGCCCCGGAGTTTACCTCCAGGGGTAGTCTGGCTCG	3	117	0
TAGATCATACCACGCCCCCACTGTCCGGCAGGGTGAACAGAGGAG	3	202	1
          GGCTCACCACCTGCACCGATGCCAAAAAGTTGTTT	3	275	0
         AGTCAAAGGCAGTCAAATTAGGGCAAAAGCTAAACA	1	1	1
AGCAAAGTTGGGCAACCTTTCCGGATTCTGGGGGTTAACTGTACT	0	32	0
GGGACTACCGCCTGCCCCATATCTATCTAAGGCAATCTAAGGCAA	1	164	1
          * * * *    **       *** *
MAP Score: 8.73097

Motif 5
CTGGCGATCGCCCCCAATATGGATCCCTGGGGACTACCG	1	135	1
CACTGCCATCCCCCCAAGACCATTAACCGAGTATGGCAA	4	20	1
GTACAGTTAACCCCCAGAATCCGGAAAGGTTGCCCAACT	0	33	1
GATCATACCACGCCCCCACTGTCCGGCAGGGTGAACAGA	3	204	1
CTGTGATTATTGCCCATAATCCAGACCCGTCGGCGGTGC	3	77	0
GACTACCGCCTGCCCCATATCTATCTAAGGCAATCTAAG	1	166	1
GAGGAGACTTTCCCCTGTTACAGTGTCAGTGACAAAACA	3	241	1
GGGATTTTTGTGCCGTCGTTCCCCCGAGGTTAAAAGGTT	0	88	1
TGGGAACGTTCCTCCCTAGTGTAGCGAGGAAAAGACTTG	1	90	1
AAAAGCTAAACACCGTTGGCGCATTTCAGAATACCACGG	1	34	1
ATGGCTCCAGCCCCGGAGTTTACCTCCAGGGGTAGTCTG	3	122	0
 AGCCGTTATCCCCGATTGTCCAATGTGGTGGTCGAATT	4	84	0
          *****    **  *  * *
MAP Score: 7.18276

Motif 6
GTACAGTTAACCCCCAGAATCCGGAAAGGTTGCCCAACTTTG	0	33	1
TGTGCCGTCGTTCCCCCGAGGTTAAAAGGTTAA         	0	96	1
TGGGAACGTTCCTCCCTAGTGTAGCGAGGAAAAGACTTGCAT	1	90	1
TGGCGATCGCCCCCAATATGGATCCCTGGGGACTACCGCCTG	1	136	1
AAGACCTCTGCACCGCCGACGGGTCTGGATTATGGGCAATAA	3	68	1
TCATACCACGCCCCCACTGTCCGGCAGGGTGAACAGAGGAGA	3	206	1
GTTGTTTTGTCACTGACACTGTAACAGGGGAAAGTCTCCTCT	3	240	0
ACTGCCATCCCCCCAAGACCATTAACCGAGTATGGCAAAATG	4	21	1
TTAATTCGACCACCACATTGGACAATCGGGGATAACGGCT  	4	82	1
          **** *    *   *  **  *
MAP Score: 3.50158

Motif 7
ACCTCGGGGGAACGACGGCACAAAAATCCC	0	88	0
         AGTCAAAGGCAGTCAAATTAG	1	1	1
CCATATTGGGGGCGATCGCCAGTTAATGCA	1	127	0
GATCCCTGGGGACTACCGCCTGCCCCATAT	1	156	1
CCCCATATCTATCTAAGGCAATCTAAGGCA	1	178	1
ATCTAAGGCAATCTAAGGCAATCTAAGGCA	1	188	1
ATCTAAGGCAATCTAAGGCA          	1	198	1
CAATAAACCTGGATATGGGAACGG      	2	32	1
GACGGGTCTGGATTATGGGCAATAATCACA	3	85	1
ATGGTCTTGGGGGGATGGCAGTGATGTCAG	4	13	0
ACCATTAACCGAGTATGGCAAAATGGGGCT	4	38	1
GGACAATCGGGGATAACGGCT         	4	101	1
          **********
MAP Score: 2.1809

Motif 8
TTAACCCCCAGAATCCGGAAAGGTTGCCCAACTTTG	0	39	1
ATTTTAGGGGGATTTTTGTGCCGTCGTTCCCCCGAG	0	80	1
GCAAAAGCTAAACACCGTTGGCGCATTTCAGAATAC	1	32	1
TGCCTTAGATAGATATGGGGCAGGCGGTAGTCCCCA	1	162	0
ATCCGTAAAAGACCTCTGCACCGCCGACGGGTCTGG	3	60	1
CCTGGAGGTAAACTCCGGGGCTGGAGCCATAAAGAT	3	131	1
CACCCTGCCGGACAGTGGGGGCGTGGTATGATCTAG	3	201	0
GTCCGGCAGGGTGAACAGAGGAGACTTTCCCCTGTT	3	224	1
TTTTGTCACTGACACTGTAACAGGGGAAAGTCTCCT	3	242	0
ACAACTTTTTGGCATCGGTGCAGGTGGTGAGCC   	3	277	1
ATGGTCTTGGGGGGATGGCAGTGATGTCAGAAA   	4	7	0
TAGTGGAACAGACGACAGGGGCGAATCTGCTAAT  	5	26	1
          ***  *** ** *  *
MAP Score: 2.12763

Motif 9
TTAACCCCCAGAATCCGGAAAGGTTGCCCAAC	0	39	1
CCTCCCTAGTGTAGCGAGGAAAAGACTTGCAT	1	100	1
TAGTCCCCAGGGATCCATATTGGGGGCGATCG	1	139	0
GAGACTGCATCATTCGATACAATCAAGGCGAT	3	19	0
CTCTAAAATTGTATCCGTAAAAGACCTCTGCA	3	48	1
TAATCACAGTCGAGCCAGACTACCCCTGGAGG	3	107	1
CTCCGGGGCTGGAGCCATAAAGATTAGGAATT	3	143	1
CTCTGTTCACCCTGCCGGACAGTGGGGGCGTG	3	212	0
CAACTTTTTGGCATCGGTGCAGGTGGTGAGCC	3	278	1
GGGCTTAATTCGATCGATGTTAATTCGACCAC	4	63	1
CCACATTGGACAATCGGGGATAACGGCT    	4	94	1
          * ******* **
MAP Score: 1.55711

Motif 10
GGATTTTTGTGCCGTCGTTCCCCCGAGGTTAAAAGGTTAA     	0	89	1
      AGTCAAAGGCAGTCAAATTAGGGCAAAAGCTAAACACCG	1	4	1
AATACATGGGAACGTTCCTCCCTAGTGTAGCGAGGAAAAGACTTG	1	84	1
AAGACCTCTGCACCGCCGACGGGTCTGGATTATGGGCAATAATCA	3	68	1
CACAGTCGAGCCAGACTACCCCTGGAGGTAAACTCCGGGGCTGGA	3	111	1
CATACCACGCCCCCACTGTCCGGCAGGGTGAACAGAGGAGACTTT	3	207	1
TCCCCCCAAGACCATTAACCGAGTATGGCAAAATGGGGCTTAATT	4	28	1
ATTCGACCACCACATTGGACAATCGGGGATAACGGCT        	4	85	1
      CAGGACAATTTGACATTAGTGGAACAGACGACAGGGGCG	5	4	1
          ***  *   *      **  **  *
MAP Score: 0.392412